From b0aad99429b2dd23f4740a0b5aae5321280bf6ac Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 31 Oct 2017 15:41:55 -0500 Subject: [PATCH 01/54] Should fix #215 --- configure | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/configure b/configure index cd76e907..4cd15fbb 100755 --- a/configure +++ b/configure @@ -486,11 +486,15 @@ def create_ninja_and_rc(l_installed): 'export QP_PYTHON={0}'.format(":".join(l_python)), "", 'export IRPF90={0}'.format(path_irpf90.replace(QP_ROOT,"${QP_ROOT}")), 'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")), - 'export PYTHONPATH="${QP_EZFIO}/Python":"${QP_PYTHON}":"${PYTHONPATH}"', - 'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"', - 'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${QP_ROOT}"/lib64:"${LD_LIBRARY_PATH}"', - 'export LIBRARY_PATH="${QP_ROOT}"/lib:"${QP_ROOT}"/lib64:"${LIBRARY_PATH}"', - 'export C_INCLUDE_PATH="${C_INCLUDE_PATH}":"${QP_ROOT}"/include', + 'qp_append_export () {', + ' #Append path $2:${!1}. Add the semicolon only if ${!1} is defined' + ' echo ${2}${!1:+:${!1}}' + '}', + 'export PYTHONPATH=$(qp_append_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PYTHON}")', + 'export PATH=$(qp_append_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)', + 'export LD_LIBRARY_PATH=$(qp_append_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)', + 'export LIBRARY_PATH=$(qp_append_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)', + 'export C_INCLUDE_PATH=$(qp_append_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)' '', 'source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh', '', From 06e4868d3dac8f0526fc3d882896ca6bf60b8156 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 31 Oct 2017 15:49:59 -0500 Subject: [PATCH 02/54] Fix path You should never modify the repo directly... --- configure | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/configure b/configure index 4cd15fbb..70fd677f 100755 --- a/configure +++ b/configure @@ -487,8 +487,8 @@ def create_ninja_and_rc(l_installed): 'export IRPF90={0}'.format(path_irpf90.replace(QP_ROOT,"${QP_ROOT}")), 'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")), 'qp_append_export () {', - ' #Append path $2:${!1}. Add the semicolon only if ${!1} is defined' - ' echo ${2}${!1:+:${!1}}' + ' #Append path $2:${!1}. Add the semicolon only if ${!1} is defined', + ' echo ${2}${!1:+:${!1}}', '}', 'export PYTHONPATH=$(qp_append_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PYTHON}")', 'export PATH=$(qp_append_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)', From 803d079b50dd88e7d7b65926edc16ecc61092ff6 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 1 Dec 2017 13:28:40 +0100 Subject: [PATCH 03/54] Minor changes in slater rules --- src/Determinants/slater_rules.irp.f | 34 ++++++++++++++--------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/src/Determinants/slater_rules.irp.f b/src/Determinants/slater_rules.irp.f index f3dd1441..75baf269 100644 --- a/src/Determinants/slater_rules.irp.f +++ b/src/Determinants/slater_rules.irp.f @@ -20,7 +20,7 @@ subroutine get_excitation_degree(key1,key2,degree,Nint) case (1) xorvec(1) = xor( key1(1), key2(1)) xorvec(2) = xor( key1(2), key2(2)) - degree = sum(popcnt(xorvec(1:2))) + degree = popcnt(xorvec(1))+popcnt(xorvec(2)) case (2) xorvec(1) = xor( key1(1), key2(1)) @@ -1396,7 +1396,7 @@ subroutine get_excitation_degree_vector_mono_or_exchange(key1,key2,degree,Nint,s popcnt(xor( key1(1,2,i), key2(1,2))) key_tmp(1,1) = xor(key1(1,1,i),key2(1,1)) key_tmp(1,2) = xor(key1(1,2,i),key2(1,2)) - if(popcnt(key_tmp(1,1)) .gt.3 .or. popcnt(key_tmp(1,2)) .gt.3 )cycle !! no double excitations of same spin + if(popcnt(key_tmp(1,1)) .ge.3 .or. popcnt(key_tmp(1,2)) .ge.3 )cycle !! no double excitations of same spin if (d > 4)cycle if (d ==4)then if(popcnt(xor(key_tmp(1,1),key_tmp(1,2))) == 0)then @@ -1457,10 +1457,10 @@ subroutine get_excitation_degree_vector_double_alpha_beta(key1,key2,degree,Nint, key_tmp(1,2) = xor(key1(1,2,i),key2(1,2)) degree_alpha = popcnt(key_tmp(1,1)) degree_beta = popcnt(key_tmp(1,2)) - if(degree_alpha .gt.3 .or. degree_beta .gt.3 )cycle !! no double excitations of same spin - degree(l) = ishft(d,-1) - idx(l) = i - l = l+1 + if(degree_alpha .ge.3 .or. degree_beta .ge.3 )cycle !! no double excitations of same spin + degree(l) = ishft(d,-1) + idx(l) = i + l = l+1 enddo else if (Nint==2) then @@ -1477,9 +1477,9 @@ subroutine get_excitation_degree_vector_double_alpha_beta(key1,key2,degree,Nint, key_tmp(2,2) = xor(key1(2,2,i),key2(2,2)) degree_alpha = popcnt(key_tmp(1,1)) + popcnt(key_tmp(2,1)) degree_beta = popcnt(key_tmp(1,2)) + popcnt(key_tmp(2,2)) - if(degree_alpha .gt.3 .or. degree_beta .gt.3 )cycle !! no double excitations of same spin - degree(l) = ishft(d,-1) - idx(l) = i + if(degree_alpha .ge.3 .or. degree_beta .ge.3 )cycle !! no double excitations of same spin + degree(l) = ishft(d,-1) + idx(l) = i l = l+1 enddo @@ -1502,10 +1502,10 @@ subroutine get_excitation_degree_vector_double_alpha_beta(key1,key2,degree,Nint, key_tmp(3,2) = xor(key1(3,2,i),key2(3,2)) degree_alpha = popcnt(key_tmp(1,1)) + popcnt(key_tmp(2,1)) + popcnt(key_tmp(3,1)) degree_beta = popcnt(key_tmp(1,2)) + popcnt(key_tmp(2,2)) + popcnt(key_tmp(3,2)) - if(degree_alpha .gt.3 .or. degree_beta .gt.3 )cycle !! no double excitations of same spin - degree(l) = ishft(d,-1) - idx(l) = i - l = l+1 + if(degree_alpha .ge.3 .or. degree_beta .ge.3 )cycle !! no double excitations of same spin + degree(l) = ishft(d,-1) + idx(l) = i + l = l+1 enddo else @@ -1524,10 +1524,10 @@ subroutine get_excitation_degree_vector_double_alpha_beta(key1,key2,degree,Nint, degree_alpha += popcnt(key_tmp(m,1)) degree_beta += popcnt(key_tmp(m,2)) enddo - if(degree_alpha .gt.3 .or. degree_beta .gt.3 )cycle !! no double excitations of same spin - degree(l) = ishft(d,-1) - idx(l) = i - l = l+1 + if(degree_alpha .ge.3 .or. degree_beta .ge.3 )cycle !! no double excitations of same spin + degree(l) = ishft(d,-1) + idx(l) = i + l = l+1 enddo endif From d98805b3e5ec8d70fbe549f377077bf0b5fa06ac Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 5 Dec 2017 18:54:10 +0100 Subject: [PATCH 04/54] Added ZMQ 4idx --- config/ifort.cfg | 2 +- plugins/CAS_SD_ZMQ/run_selection_slave.irp.f | 2 +- plugins/Full_CI_ZMQ/fci_zmq.irp.f | 2 + plugins/Full_CI_ZMQ/run_pt2_slave.irp.f | 2 +- plugins/Full_CI_ZMQ/run_selection_slave.irp.f | 2 +- plugins/mrcepa0/dressing_slave.irp.f | 2 +- plugins/mrcepa0/run_mrcc_slave.irp.f | 2 +- src/Davidson/davidson_parallel.irp.f | 2 +- src/Determinants/H_apply_zmq.template.f | 2 +- src/FourIdx/four_index_block.irp.f | 4 - ...lave.irp.f.todo => four_index_slave.irp.f} | 36 +- src/FourIdx/four_index_zmq.irp.f | 361 ++++++++++++++++++ src/FourIdx/four_index_zmq.irp.f.todo | 273 ------------- .../ao_bielec_integrals_in_map_slave.irp.f | 2 +- src/Integrals_Bielec/mo_bi_integrals.irp.f | 7 +- src/ZMQ/utils.irp.f | 4 +- 16 files changed, 404 insertions(+), 301 deletions(-) rename src/FourIdx/{four_index_slave.irp.f.todo => four_index_slave.irp.f} (89%) create mode 100644 src/FourIdx/four_index_zmq.irp.f delete mode 100644 src/FourIdx/four_index_zmq.irp.f.todo diff --git a/config/ifort.cfg b/config/ifort.cfg index 77761c85..b94d0cd4 100644 --- a/config/ifort.cfg +++ b/config/ifort.cfg @@ -9,7 +9,7 @@ FC : ifort LAPACK_LIB : -mkl=parallel IRPF90 : irpf90 -IRPF90_FLAGS : --ninja --align=32 -DZMQ_PUSH +IRPF90_FLAGS : --ninja --align=32 # Global options ################ diff --git a/plugins/CAS_SD_ZMQ/run_selection_slave.irp.f b/plugins/CAS_SD_ZMQ/run_selection_slave.irp.f index 3e0d3e07..2a59437e 100644 --- a/plugins/CAS_SD_ZMQ/run_selection_slave.irp.f +++ b/plugins/CAS_SD_ZMQ/run_selection_slave.irp.f @@ -88,7 +88,7 @@ subroutine run_selection_slave(thread,iproc,energy) end do integer, external :: disconnect_from_taskserver - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif diff --git a/plugins/Full_CI_ZMQ/fci_zmq.irp.f b/plugins/Full_CI_ZMQ/fci_zmq.irp.f index b669a938..7cb54841 100644 --- a/plugins/Full_CI_ZMQ/fci_zmq.irp.f +++ b/plugins/Full_CI_ZMQ/fci_zmq.irp.f @@ -112,6 +112,8 @@ program fci_zmq write(*,fmt) '# Excit. (eV)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1))*27.211396641308d0, & dsqrt(error(k)*error(k)+error(1)*error(1))*27.211396641308d0, k=1,N_states_p) endif + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) print *, '' print *, 'N_det = ', N_det diff --git a/plugins/Full_CI_ZMQ/run_pt2_slave.irp.f b/plugins/Full_CI_ZMQ/run_pt2_slave.irp.f index 949eef3c..03b62937 100644 --- a/plugins/Full_CI_ZMQ/run_pt2_slave.irp.f +++ b/plugins/Full_CI_ZMQ/run_pt2_slave.irp.f @@ -73,7 +73,7 @@ subroutine run_pt2_slave(thread,iproc,energy) end do integer, external :: disconnect_from_taskserver - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif diff --git a/plugins/Full_CI_ZMQ/run_selection_slave.irp.f b/plugins/Full_CI_ZMQ/run_selection_slave.irp.f index fc89ff14..464f0a9f 100644 --- a/plugins/Full_CI_ZMQ/run_selection_slave.irp.f +++ b/plugins/Full_CI_ZMQ/run_selection_slave.irp.f @@ -93,7 +93,7 @@ subroutine run_selection_slave(thread,iproc,energy) integer, external :: disconnect_from_taskserver - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif diff --git a/plugins/mrcepa0/dressing_slave.irp.f b/plugins/mrcepa0/dressing_slave.irp.f index b897ff0f..115d1749 100644 --- a/plugins/mrcepa0/dressing_slave.irp.f +++ b/plugins/mrcepa0/dressing_slave.irp.f @@ -208,7 +208,7 @@ subroutine mrsc2_dressing_slave(thread,iproc) deallocate(delta) - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) diff --git a/plugins/mrcepa0/run_mrcc_slave.irp.f b/plugins/mrcepa0/run_mrcc_slave.irp.f index 31c2507b..3b3cfe44 100644 --- a/plugins/mrcepa0/run_mrcc_slave.irp.f +++ b/plugins/mrcepa0/run_mrcc_slave.irp.f @@ -130,7 +130,7 @@ subroutine run_mrcc_slave(thread,iproc,energy) if(done) exit ctask = ctask + 1 end do - call disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) + call disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) call end_zmq_push_socket(zmq_socket_push,thread) ! call delete_selection_buffer(buf) diff --git a/src/Davidson/davidson_parallel.irp.f b/src/Davidson/davidson_parallel.irp.f index cae13fbc..ce6d670a 100644 --- a/src/Davidson/davidson_parallel.irp.f +++ b/src/Davidson/davidson_parallel.irp.f @@ -45,7 +45,7 @@ subroutine davidson_run_slave(thread,iproc) call davidson_slave_work(zmq_to_qp_run_socket, zmq_socket_push, N_states_diag, N_det, worker_id) integer, external :: disconnect_from_taskserver - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif diff --git a/src/Determinants/H_apply_zmq.template.f b/src/Determinants/H_apply_zmq.template.f index bcc30726..7bc5795f 100644 --- a/src/Determinants/H_apply_zmq.template.f +++ b/src/Determinants/H_apply_zmq.template.f @@ -213,7 +213,7 @@ subroutine $subroutine_slave(thread, iproc) integer, external :: disconnect_from_taskserver - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif call end_zmq_push_socket(zmq_socket_push,thread) diff --git a/src/FourIdx/four_index_block.irp.f b/src/FourIdx/four_index_block.irp.f index 8666bdee..95710381 100644 --- a/src/FourIdx/four_index_block.irp.f +++ b/src/FourIdx/four_index_block.irp.f @@ -261,10 +261,6 @@ subroutine four_index_transform_block(map_a,map_c,matrix_B,LDB, & enddo - - - - !$OMP CRITICAL call map_update(map_c, key, value, idx,1.d-15) !$OMP END CRITICAL diff --git a/src/FourIdx/four_index_slave.irp.f.todo b/src/FourIdx/four_index_slave.irp.f similarity index 89% rename from src/FourIdx/four_index_slave.irp.f.todo rename to src/FourIdx/four_index_slave.irp.f index 47124823..f396b436 100644 --- a/src/FourIdx/four_index_slave.irp.f.todo +++ b/src/FourIdx/four_index_slave.irp.f @@ -1,4 +1,4 @@ -subroutine four_index_transform_slave(map_a,map_c,matrix_B,LDB, & +subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & i_start, j_start, k_start, l_start, & i_end , j_end , k_end , l_end , & a_start, b_start, c_start, d_start, & @@ -13,7 +13,6 @@ subroutine four_index_transform_slave(map_a,map_c,matrix_B,LDB, & ! Loops run over *_start->*_end END_DOC type(map_type), intent(in) :: map_a - type(map_type), intent(inout) :: map_c integer, intent(in) :: LDB double precision, intent(in) :: matrix_B(LDB,*) integer, intent(in) :: i_start, j_start, k_start, l_start @@ -66,7 +65,14 @@ subroutine four_index_transform_slave(map_a,map_c,matrix_B,LDB, & integer*8 :: new_size new_size = max(1024_8, 5_8 * map_a % n_elements ) - allocate(a_array_ik(new_size), a_array_j(new_size), a_array_value(new_size)) + integer*8 :: tempspace + integer :: npass, l_block + + tempspace = (new_size * 16_8) / (1024_8 * 1024_8) + npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 2048_8),4) ! 2 GiB of scratch space + l_block = (l_end-l_start+1)/npass + + allocate(a_array_ik(new_size/npass), a_array_j(new_size/npass), a_array_value(new_size/npass)) allocate(l_pointer(l_start:l_end+1), value((i_max*k_max)) ) @@ -127,18 +133,18 @@ subroutine four_index_transform_slave(map_a,map_c,matrix_B,LDB, & !open(unit=10,file='OUTPUT',form='FORMATTED') ! END INPUT DATA - !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & !$OMP a_start,a_end,b_start,b_end,c_start,c_end,d_start,d_end,& !$OMP i_start,i_end,j_start,j_end,k_start,k_end,l_start,l_end,& !$OMP i_min,i_max,j_min,j_max,k_min,k_max,l_min,l_max, & - !$OMP map_c,matrix_B,l_pointer) & + !$OMP matrix_B,l_pointer,thread,task_id) & !$OMP PRIVATE(key,value,T,U,V,i,j,k,l,idx,ik,ll, & - !$OMP a,b,c,d,tmp,T2d,V2d,ii) + !$OMP a,b,c,d,p,q,tmp,T2d,V2d,ii,zmq_socket_push) allocate( key(i_max*j_max*k_max), value(i_max*j_max*k_max) ) allocate( U(a_start:a_end, c_start:c_end, b_start:b_end) ) integer(ZMQ_PTR) :: zmq_socket_push + integer(ZMQ_PTR), external :: new_zmq_push_socket zmq_socket_push = new_zmq_push_socket(thread) @@ -232,22 +238,27 @@ subroutine four_index_transform_slave(map_a,map_c,matrix_B,LDB, & enddo idx = 0_8 + + integer :: p, q do b=b_start,d + q = b+ishft(d*d-d,-1) do c=c_start,c_end + p = a_start+ishft(c*c-c,-1) do a=a_start,min(b,c) if (dabs(U(a,c,b)) < 1.d-15) then cycle endif + if ((a==b).and.(p>q)) cycle + p = p+1 idx = idx+1_8 call bielec_integrals_index(a,b,c,d,key(idx)) +!print *, int(key(idx),4), int(a,2),int(b,2),int(c,2),int(d,2), p, q value(idx) = U(a,c,b) enddo enddo enddo - !$OMP CRITICAL - call four_idx_push_results(zmq_socket_push, key, value, idx, task_id) - !$OMP END CRITICAL + call four_idx_push_results(zmq_socket_push, key, value, idx, -task_id) !WRITE OUTPUT ! OMP CRITICAL @@ -268,10 +279,13 @@ subroutine four_index_transform_slave(map_a,map_c,matrix_B,LDB, & enddo !$OMP END DO - call end_zmq_push_socket(zmq_socket_push,thread) deallocate(key,value,V,T) + !$OMP BARRIER + !$OMP MASTER + call four_idx_push_results(zmq_socket_push, 0_8, 0.d0, 0, task_id) + !$OMP END MASTER + call end_zmq_push_socket(zmq_socket_push) !$OMP END PARALLEL - call map_merge(map_c) deallocate(l_pointer) deallocate(a_array_ik,a_array_j,a_array_value) diff --git a/src/FourIdx/four_index_zmq.irp.f b/src/FourIdx/four_index_zmq.irp.f new file mode 100644 index 00000000..72c478b7 --- /dev/null +++ b/src/FourIdx/four_index_zmq.irp.f @@ -0,0 +1,361 @@ +subroutine four_index_transform_zmq(map_a,map_c,matrix_B,LDB, & + i_start, j_start, k_start, l_start, & + i_end , j_end , k_end , l_end , & + a_start, b_start, c_start, d_start, & + a_end , b_end , c_end , d_end ) + implicit none + use f77_zmq + use map_module + BEGIN_DOC +! Performs a four-index transformation of map_a(N^4) into map_c(M^4) using b(NxM) +! C_{abcd} = \sum_{ijkl} A_{ijkl}.B_{ia}.B_{jb}.B_{kc}.B_{ld} +! Loops run over *_start->*_end + END_DOC + type(map_type), intent(in) :: map_a + type(map_type), intent(inout) :: map_c + integer, intent(in) :: LDB + double precision, intent(in) :: matrix_B(LDB,*) + integer, intent(in) :: i_start, j_start, k_start, l_start + integer, intent(in) :: i_end , j_end , k_end , l_end + integer, intent(in) :: a_start, b_start, c_start, d_start + integer, intent(in) :: a_end , b_end , c_end , d_end + + double precision, allocatable :: T(:,:), U(:,:,:), V(:,:) + double precision, allocatable :: T2d(:,:), V2d(:,:) + integer :: i_max, j_max, k_max, l_max + integer :: i_min, j_min, k_min, l_min + integer :: i, j, k, l, ik, ll + integer :: l_start_block, l_end_block, l_block + integer :: a, b, c, d + double precision, external :: get_ao_bielec_integral + integer*8 :: ii + integer(key_kind) :: idx + real(integral_kind) :: tmp + integer(key_kind), allocatable :: key(:) + real(integral_kind), allocatable :: value(:) + integer*8, allocatable :: l_pointer(:) + + ASSERT (k_start == i_start) + ASSERT (l_start == j_start) + ASSERT (a_start == c_start) + ASSERT (b_start == d_start) + + i_min = min(i_start,a_start) + i_max = max(i_end ,a_end ) + j_min = min(j_start,b_start) + j_max = max(j_end ,b_end ) + k_min = min(k_start,c_start) + k_max = max(k_end ,c_end ) + l_min = min(l_start,d_start) + l_max = max(l_end ,d_end ) + + ASSERT (0 < i_max) + ASSERT (0 < j_max) + ASSERT (0 < k_max) + ASSERT (0 < l_max) + ASSERT (LDB >= i_max) + ASSERT (LDB >= j_max) + ASSERT (LDB >= k_max) + ASSERT (LDB >= l_max) + + + integer(ZMQ_PTR) :: zmq_to_qp_run_socket + integer(ZMQ_PTR) :: zmq_socket_pull + call new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'four_idx') + + integer*8 :: new_size + new_size = max(1024_8, 5_8 * map_a % n_elements ) + + integer :: npass + integer*8 :: tempspace + + tempspace = (new_size * 16_8) / (1024_8 * 1024_8) + npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 2048_8),4) ! 2 GiB of scratch space + l_block = (l_end-l_start+1)/npass + + ! Create tasks + ! ============ + + character(len=256) :: task + + integer, external :: add_task_to_taskserver + + do l_start_block = l_start, l_end, l_block + l_end_block = min(l_end, l_start_block+l_block-1) + write(task,'(16(I10,X))') & + i_start, j_start, k_start, l_start_block, & + i_end , j_end , k_end , l_end_block , & + a_start, b_start, c_start, d_start, & + a_end , b_end , c_end , d_end + if (add_task_to_taskserver(zmq_to_qp_run_socket,trim(task)) == -1) then + stop 'Unable to add task to server' + endif + enddo + + integer, external :: zmq_set_running + if (zmq_set_running(zmq_to_qp_run_socket) == -1) then + print *, irp_here, ': Failed in zmq_set_running' + endif + + + PROVIDE nproc + + call omp_set_nested(.True.) + integer :: ithread + !$OMP PARALLEL NUM_THREADS(2) PRIVATE(ithread) + ithread = omp_get_thread_num() + if (ithread==0) then + call four_idx_collector(zmq_socket_pull,map_c) + else + call four_index_transform_slave_inproc(ithread) + endif + !$OMP END PARALLEL + + call end_parallel_job(zmq_to_qp_run_socket, zmq_socket_pull, 'four_idx') + + +end + + +subroutine four_index_transform_slave_tcp(i) + implicit none + integer, intent(in) :: i + BEGIN_DOC +! Computes a buffer of integrals. i is the ID of the current thread. + END_DOC + call four_index_transform_slave(0,i) +end + + +subroutine four_index_transform_slave_inproc(i) + implicit none + integer, intent(in) :: i + BEGIN_DOC +! Computes a buffer of integrals. i is the ID of the current thread. + END_DOC + call four_index_transform_slave(1,i) +end + + + +subroutine four_index_transform_slave(thread,worker_id) + use f77_zmq + implicit none + + integer(ZMQ_PTR) :: zmq_to_qp_run_socket + integer,intent(in) :: worker_id, thread + integer :: task_id + character*(512) :: msg + + integer :: i_start, j_start, k_start, l_start_block + integer :: i_end , j_end , k_end , l_end_block + integer :: a_start, b_start, c_start, d_start + integer :: a_end , b_end , c_end , d_end + + integer, external :: get_task_from_taskserver + integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket + + zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() + + integer, external :: connect_to_taskserver + if (connect_to_taskserver(zmq_to_qp_run_socket,worker_id,thread) == -1) then + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) + return + endif + + do + if (get_task_from_taskserver(zmq_to_qp_run_socket,worker_id, task_id, msg) == -1) then + exit + endif + if(task_id == 0) exit + read (msg,*) & + i_start, j_start, k_start, l_start_block, & + i_end , j_end , k_end , l_end_block , & + a_start, b_start, c_start, d_start, & + a_end , b_end , c_end , d_end + + call four_index_transform_slave_work(ao_integrals_map, & + mo_coef, size(mo_coef,1), & + i_start, j_start, k_start, l_start_block, & + i_end , j_end , k_end , l_end_block , & + a_start, b_start, c_start, d_start, & + a_end , b_end , c_end , d_end, & + task_id, thread) + + integer, external :: task_done_to_taskserver + if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id) == -1) then + print *, irp_here, ': Unable to send task_done' + stop + endif + + enddo + integer, external :: disconnect_from_taskserver + if (disconnect_from_taskserver(zmq_to_qp_run_socket,thread) == -1) then + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) + return + endif + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) + +end + + +BEGIN_PROVIDER [ integer, nthreads_four_idx ] + implicit none + BEGIN_DOC + ! Number of threads for 4-index transformation + END_DOC + nthreads_four_idx = nproc + character*(32) :: env + call getenv('NTHREADS_FOUR_IDX',env) + if (trim(env) /= '') then + read(env,*) nthreads_four_idx + endif + call write_int(6,nthreads_four_idx,'Number of threads for 4-index transformation') +END_PROVIDER + + + +subroutine four_idx_collector(zmq_socket_pull,map_c) + use f77_zmq + use map_module + implicit none + type(map_type), intent(inout) :: map_c + integer(ZMQ_PTR), intent(in) :: zmq_socket_pull + + integer :: more + integer, external :: zmq_delete_task + integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket + integer(ZMQ_PTR) :: zmq_to_qp_run_socket + integer :: task_id + + + zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() + + more = 1 + do while (more == 1) + call four_idx_pull_results(zmq_socket_pull, map_c, task_id) + if (task_id > 0) then + if (zmq_delete_task(zmq_to_qp_run_socket,zmq_socket_pull,task_id,more) == -1) then + stop 'Unable to delete task' + endif + endif + enddo + + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) + +end + + +subroutine four_idx_pull_results(zmq_socket_pull, map_c, task_id) + use f77_zmq + use map_module + implicit none + type(map_type), intent(inout) :: map_c + integer(ZMQ_PTR), intent(inout) :: zmq_socket_pull + + integer, intent(out) :: task_id + + integer :: rc, sze + integer*8 :: rc8 + + + rc = f77_zmq_recv( zmq_socket_pull, task_id, 4, 0) + if(rc /= 4) stop 'four_idx_pull_results failed to pull task_id' + + if (task_id > 0) then + IRP_IF ZMQ_PUSH + IRP_ELSE + rc = f77_zmq_send( zmq_socket_pull, 'ok', 2, 0) + if (rc /= 2) then + print *, irp_here, ' : f77_zmq_send (zmq_socket_pull,...' + stop 'error' + endif + IRP_ENDIF + call map_merge(map_c) + return + endif + + rc = f77_zmq_recv( zmq_socket_pull, sze, 4, 0) + if(rc /= 4) stop 'four_idx_pull_results failed to pull sze' + + integer(key_kind), allocatable :: key(:) + real(integral_kind), allocatable :: value(:) + + allocate(key(sze), value(sze)) + + rc8 = f77_zmq_recv8( zmq_socket_pull, key, int(key_kind*sze,8), 0) + if(rc8 /= key_kind*sze) stop 'four_idx_pull_results failed to pull key' + + rc8 = f77_zmq_recv8( zmq_socket_pull, value, int(integral_kind*sze,8), 0) + if(rc8 /= integral_kind*sze) stop 'four_idx_pull_results failed to pull value' + + call map_update(map_c, key, value, sze, mo_integrals_threshold) + +! Activate if zmq_socket_pull is a REP + IRP_IF ZMQ_PUSH + IRP_ELSE + rc = f77_zmq_send( zmq_socket_pull, 'ok', 2, 0) + if (rc /= 2) then + print *, irp_here, ' : f77_zmq_send (zmq_socket_pull,...' + stop 'error' + endif + IRP_ENDIF + + deallocate(key, value) +end + + + +subroutine four_idx_push_results(zmq_socket_push, key, value, sze, task_id) + use f77_zmq + use map_module + implicit none + integer, intent(in) :: sze + integer(key_kind), intent(in) :: key(sze) + real(integral_kind), intent(in) :: value(sze) + integer(ZMQ_PTR), intent(in) :: zmq_socket_push + integer, intent(in) :: task_id + + integer :: rc + integer*8 :: rc8 + + + if (task_id > 0) then + rc = f77_zmq_send( zmq_socket_push, task_id, 4, 0) + if(rc /= 4) stop 'four_idx_push_results failed to push task_id' + else + rc = f77_zmq_send( zmq_socket_push, task_id, 4, ZMQ_SNDMORE) + if(rc /= 4) stop 'four_idx_push_results failed to push task_id' + + rc = f77_zmq_send( zmq_socket_push, sze, 4, ZMQ_SNDMORE) + if(rc /= 4) stop 'four_idx_push_results failed to push sze' + + rc8 = f77_zmq_send8( zmq_socket_push, key, int(key_kind*sze,8), ZMQ_SNDMORE) + if(rc8 /= key_kind*sze) then + print *, sze, key_kind, rc8 + stop 'four_idx_push_results failed to push key' + endif + + rc8 = f77_zmq_send8( zmq_socket_push, value, int(integral_kind*sze,8), 0) + if(rc8 /= integral_kind*sze) then + print *, sze, integral_kind, rc8 + stop 'four_idx_push_results failed to push value' + endif + endif + + +! Activate if zmq_socket_push is a REP +IRP_IF ZMQ_PUSH +IRP_ELSE + character*(2) :: reply + rc = f77_zmq_recv( zmq_socket_push, reply, 2, 0) + if (reply(1:2) /= 'ok') then + print *, reply(1:rc) + print *, irp_here, ' : f77_zmq_send (zmq_socket_push,...' + stop 'error' + endif +IRP_ENDIF + +end + + diff --git a/src/FourIdx/four_index_zmq.irp.f.todo b/src/FourIdx/four_index_zmq.irp.f.todo deleted file mode 100644 index b2f639a7..00000000 --- a/src/FourIdx/four_index_zmq.irp.f.todo +++ /dev/null @@ -1,273 +0,0 @@ -subroutine four_index_transform_zmq(map_a,map_c,matrix_B,LDB, & - i_start, j_start, k_start, l_start, & - i_end , j_end , k_end , l_end , & - a_start, b_start, c_start, d_start, & - a_end , b_end , c_end , d_end ) - implicit none - use f77_zmq - use map_module - BEGIN_DOC -! Performs a four-index transformation of map_a(N^4) into map_c(M^4) using b(NxM) -! C_{abcd} = \sum_{ijkl} A_{ijkl}.B_{ia}.B_{jb}.B_{kc}.B_{ld} -! Loops run over *_start->*_end - END_DOC - type(map_type), intent(in) :: map_a - type(map_type), intent(inout) :: map_c - integer, intent(in) :: LDB - double precision, intent(in) :: matrix_B(LDB,*) - integer, intent(in) :: i_start, j_start, k_start, l_start - integer, intent(in) :: i_end , j_end , k_end , l_end - integer, intent(in) :: a_start, b_start, c_start, d_start - integer, intent(in) :: a_end , b_end , c_end , d_end - - double precision, allocatable :: T(:,:), U(:,:,:), V(:,:) - double precision, allocatable :: T2d(:,:), V2d(:,:) - integer :: i_max, j_max, k_max, l_max - integer :: i_min, j_min, k_min, l_min - integer :: i, j, k, l, ik, ll - integer :: l_start_block, l_end_block, l_block - integer :: a, b, c, d - double precision, external :: get_ao_bielec_integral - integer*8 :: ii - integer(key_kind) :: idx - real(integral_kind) :: tmp - integer(key_kind), allocatable :: key(:) - real(integral_kind), allocatable :: value(:) - integer*8, allocatable :: l_pointer(:) - - ASSERT (k_start == i_start) - ASSERT (l_start == j_start) - ASSERT (a_start == c_start) - ASSERT (b_start == d_start) - - i_min = min(i_start,a_start) - i_max = max(i_end ,a_end ) - j_min = min(j_start,b_start) - j_max = max(j_end ,b_end ) - k_min = min(k_start,c_start) - k_max = max(k_end ,c_end ) - l_min = min(l_start,d_start) - l_max = max(l_end ,d_end ) - - ASSERT (0 < i_max) - ASSERT (0 < j_max) - ASSERT (0 < k_max) - ASSERT (0 < l_max) - ASSERT (LDB >= i_max) - ASSERT (LDB >= j_max) - ASSERT (LDB >= k_max) - ASSERT (LDB >= l_max) - - - integer(ZMQ_PTR) :: zmq_to_qp_run_socket - call new_parallel_job(zmq_to_qp_run_socket,'four_idx') - - integer*8 :: new_size - new_size = max(1024_8, 5_8 * map_a % n_elements ) - - integer :: npass - integer*8 :: tempspace - - tempspace = (new_size * 14_8) / (1024_8 * 1024_8) - npass = min(l_end-l_start,1 + tempspace / 2048) ! 2 GiB of scratch space - l_block = (l_end-l_start)/npass - - ! Create tasks - ! ============ - - character(len=64), allocatable :: task - - do l_start_block = l_start, l_end, l_block - l_end_block = min(l_end, l_start_block+l_block-1) - write(task,'I10,X,I10') l_start_block, l_end_block - call add_task_to_taskserver(zmq_to_qp_run_socket,trim(task)) - enddo - - call zmq_set_running(zmq_to_qp_run_socket) - - PROVIDE nproc - - call omp_set_nested(.True.) - integer :: ithread - !$OMP PARALLEL NUM_THREADS(2) PRIVATE(ithread) - ithread = omp_get_thread_num() - if (ithread==0) then - call four_idx_collector(zmq_to_qp_run_socket,map_c) - else - !TODO : Put strings of map_a and matrix_b on server and broadcast - call four_index_transform_slave_inproc(map_a,map_c,matrix_B,LDB, & - i_start, j_start, k_start, l_start_block, & - i_end , j_end , k_end , l_end_block , & - a_start, b_start, c_start, d_start, & - a_end , b_end , c_end , d_end, 1 ) - endif - !$OMP END PARALLEL - - call end_parallel_job(zmq_to_qp_run_socket, 'four_idx') - - -end - - -subroutine four_idx_slave_work(zmq_to_qp_run_socket, worker_id) - use f77_zmq - implicit none - - integer(ZMQ_PTR),intent(in) :: zmq_to_qp_run_socket - integer,intent(in) :: worker_id - integer :: task_id - character*(512) :: msg - - integer :: i_start, j_start, k_start, l_start_block - integer :: i_end , j_end , k_end , l_end_block - integer :: a_start, b_start, c_start, d_start - integer :: a_end , b_end , c_end , d_end - - !TODO : get map_a and matrix_B from server - do - call get_task_from_taskserver(zmq_to_qp_run_socket,worker_id, task_id, msg) - if(task_id == 0) exit - read (msg,*) LDB, & - i_start, j_start, k_start, l_start_block, & - i_end , j_end , k_end , l_end_block , & - a_start, b_start, c_start, d_start, & - a_end , b_end , c_end , d_end - - call four_index_transform_slave(map_a,map_c,matrix_B,LDB, & - i_start, j_start, k_start, l_start_block, & - i_end , j_end , k_end , l_end_block , & - a_start, b_start, c_start, d_start, & - a_end , b_end , c_end , d_end, zmq_to_qp_run_socket, & - task_id) - call task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id) - - enddo -end - - -BEGIN_PROVIDER [ integer, nthreads_four_idx ] - implicit none - BEGIN_DOC - ! Number of threads for 4-index transformation - END_DOC - nthreads_four_idx = nproc - character*(32) :: env - call getenv('NTHREADS_FOUR_IDX',env) - if (trim(env) /= '') then - read(env,*) nthreads_four_idx - endif - call write_int(6,nthreads_davidson,'Number of threads for 4-index transformation') -END_PROVIDER - - - -subroutine four_idx_collector(zmq_to_qp_run_socket,map_c) - use f77_zmq - use map_module - implicit none - type(map_type), intent(inout) :: map_c - - integer :: more - integer(ZMQ_PTR), external :: new_zmq_pull_socket - integer(ZMQ_PTR) :: zmq_socket_pull - - - more = 1 - zmq_socket_pull = new_zmq_pull_socket() - - do while (more == 1) - call four_idx_pull_results(zmq_socket_pull, map_c, task_id) - call zmq_delete_task(zmq_to_qp_run_socket,zmq_socket_pull,task_id,more) - enddo - - call end_zmq_pull_socket(zmq_socket_pull) - -end - - -subroutine four_idx_pull_results(zmq_socket_pull, map_c, task_id) - use f77_zmq - use map_module - implicit none - type(map_type), intent(inout) :: map_c - integer(ZMQ_PTR), intent(inout) :: zmq_socket_pull - - integer, intent(out) :: task_id - - integer :: rc, sze - integer*8 :: rc8 - - - rc = f77_zmq_recv( zmq_socket_pull, task_id, 4, 0) - if(rc /= 4) stop "four_idx_pull_results failed to pull task_id" - - rc = f77_zmq_recv( zmq_socket_pull, sze, 4, 0) - if(rc /= 4) stop "four_idx_pull_results failed to pull sze" - - integer(key_kind), allocatable :: key(:) - real(integral_kind), allocatable :: value(:) - - allocate(key(sze), value(sze)) - - rc8 = f77_zmq_recv8( zmq_socket_pull, key, key_kind*sze, 0) - if(rc8 /= key_kind*sze) stop "four_idx_pull_results failed to pull key" - - rc8 = f77_zmq_recv8( zmq_socket_pull, value, integral_kind*sze, 0) - if(rc8 /= integral_kind*sze) stop "four_idx_pull_results failed to pull value" - -! Activate if zmq_socket_pull is a REP -IRP_IF ZMQ_PUSH -IRP_ELSE - rc = f77_zmq_send( zmq_socket_pull, 0, 4, 0) - if (rc /= 4) then - print *, irp_here, ' : f77_zmq_send (zmq_socket_pull,...' - stop 'error' - endif -IRP_ENDIF - - call map_update(map_c, key, value, sze, 1.d-15) ! TODO : threshold - - deallocate(key, value) -end - - - -subroutine four_idx_push_results(zmq_socket_push, key, value, sze, task_id) - use f77_zmq - use map_module - implicit none - integer, intent(in) :: sze - integer(key_kind), intent(in) :: key(sze) - real(integral_kind), intent(in) :: value(sze) - integer(ZMQ_PTR), intent(in) :: zmq_socket_push - integer, intent(in) :: task_id - - integer :: rc, sze - integer*8 :: rc8 - - - rc = f77_zmq_send( zmq_socket_push, task_id, 4, ZMQ_SNDMORE) - if(rc /= 4) stop "four_idx_push_results failed to push task_id" - - rc = f77_zmq_send( zmq_socket_push, sze, 4, ZMQ_SNDMORE) - if(rc /= 4) stop "four_idx_push_results failed to push sze" - - rc8 = f77_zmq_send8( zmq_socket_push, key, key_kind*sze, ZMQ_SNDMORE) - if(rc8 /= key_kind*sze) stop "four_idx_push_results failed to push key" - - rc8 = f77_zmq_send8( zmq_socket_push, value, integral_kind*sze, 0) - if(rc8 /= integral_kind*sze) stop "four_idx_push_results failed to push value" - -! Activate if zmq_socket_push is a REP -IRP_IF ZMQ_PUSH -IRP_ELSE - rc = f77_zmq_send( zmq_socket_push, 0, 4, 0) - if (rc /= 4) then - print *, irp_here, ' : f77_zmq_send (zmq_socket_push,...' - stop 'error' - endif -IRP_ENDIF - -end - - diff --git a/src/Integrals_Bielec/ao_bielec_integrals_in_map_slave.irp.f b/src/Integrals_Bielec/ao_bielec_integrals_in_map_slave.irp.f index 153993bc..4b915963 100644 --- a/src/Integrals_Bielec/ao_bielec_integrals_in_map_slave.irp.f +++ b/src/Integrals_Bielec/ao_bielec_integrals_in_map_slave.irp.f @@ -126,7 +126,7 @@ subroutine ao_bielec_integrals_in_map_slave(thread,iproc) enddo integer, external :: disconnect_from_taskserver - if (disconnect_from_taskserver(zmq_to_qp_run_socket,zmq_socket_push,worker_id) == -1) then + if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) == -1) then continue endif deallocate( buffer_i, buffer_value ) diff --git a/src/Integrals_Bielec/mo_bi_integrals.irp.f b/src/Integrals_Bielec/mo_bi_integrals.irp.f index 2b05965f..4459342a 100644 --- a/src/Integrals_Bielec/mo_bi_integrals.irp.f +++ b/src/Integrals_Bielec/mo_bi_integrals.irp.f @@ -119,11 +119,16 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ] else ! call add_integrals_to_map(full_ijkl_bitmask_4) - call four_index_transform_block(ao_integrals_map,mo_integrals_map, & + call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & mo_coef, size(mo_coef,1), & 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) ! +! call four_index_transform_block(ao_integrals_map,mo_integrals_map, & +! mo_coef, size(mo_coef,1), & +! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & +! 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) +! ! call four_index_transform(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & diff --git a/src/ZMQ/utils.irp.f b/src/ZMQ/utils.irp.f index 5309fa4e..86c13432 100644 --- a/src/ZMQ/utils.irp.f +++ b/src/ZMQ/utils.irp.f @@ -691,15 +691,13 @@ integer function connect_to_taskserver(zmq_to_qp_run_socket,worker_id,thread) connect_to_taskserver = -1 end -integer function disconnect_from_taskserver(zmq_to_qp_run_socket, & - zmq_socket_push, worker_id) +integer function disconnect_from_taskserver(zmq_to_qp_run_socket, worker_id) use f77_zmq implicit none BEGIN_DOC ! Disconnect from the task server END_DOC integer(ZMQ_PTR), intent(in) :: zmq_to_qp_run_socket - integer(ZMQ_PTR), intent(in) :: zmq_socket_push integer, intent(in) :: worker_id integer :: rc, sze From 146e75b89a719b3a3996d6312af1d8081f4d48cd Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 5 Dec 2017 19:10:53 +0100 Subject: [PATCH 05/54] More tasks in AO-MO transformation --- src/FourIdx/four_index_slave.irp.f | 2 +- src/FourIdx/four_index_zmq.irp.f | 2 +- src/Integrals_Bielec/mo_bi_integrals.irp.f | 5 +++++ 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index f396b436..06604760 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -69,7 +69,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & integer :: npass, l_block tempspace = (new_size * 16_8) / (1024_8 * 1024_8) - npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 2048_8),4) ! 2 GiB of scratch space + npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 1024_8),4) ! 1 GiB of scratch space l_block = (l_end-l_start+1)/npass allocate(a_array_ik(new_size/npass), a_array_j(new_size/npass), a_array_value(new_size/npass)) diff --git a/src/FourIdx/four_index_zmq.irp.f b/src/FourIdx/four_index_zmq.irp.f index 72c478b7..1726a778 100644 --- a/src/FourIdx/four_index_zmq.irp.f +++ b/src/FourIdx/four_index_zmq.irp.f @@ -70,7 +70,7 @@ subroutine four_index_transform_zmq(map_a,map_c,matrix_B,LDB, & integer*8 :: tempspace tempspace = (new_size * 16_8) / (1024_8 * 1024_8) - npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 2048_8),4) ! 2 GiB of scratch space + npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 1024_8),4) ! 1 GiB of scratch space l_block = (l_end-l_start+1)/npass ! Create tasks diff --git a/src/Integrals_Bielec/mo_bi_integrals.irp.f b/src/Integrals_Bielec/mo_bi_integrals.irp.f index 4459342a..3fa01292 100644 --- a/src/Integrals_Bielec/mo_bi_integrals.irp.f +++ b/src/Integrals_Bielec/mo_bi_integrals.irp.f @@ -38,6 +38,11 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ] else PROVIDE ao_bielec_integrals_in_map endif + + print *, '' + print *, 'AO -> MO integrals transformation' + print *, '---------------------------------' + print *, '' if(no_vvvv_integrals)then integer :: i,j,k,l From f7d715ba6cd5f0afcd87252fe0164ed092c10791 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 6 Dec 2017 19:22:52 +0100 Subject: [PATCH 06/54] CIS doesn't read wf --- plugins/CIS/cis.irp.f | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/plugins/CIS/cis.irp.f b/plugins/CIS/cis.irp.f index c14deaa2..a9341a10 100644 --- a/plugins/CIS/cis.irp.f +++ b/plugins/CIS/cis.irp.f @@ -1,4 +1,11 @@ program cis + implicit none + read_wf = .False. + SOFT_TOUCH read_wf + call run +end + +subroutine run implicit none integer :: i From 97297f68a832ee5bd63044d16b56d2e6734bde15 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 7 Dec 2017 10:02:59 +0100 Subject: [PATCH 07/54] FCI with NOS --- plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f | 246 ++++++++++++++++++++++++++ src/Determinants/determinants.irp.f | 2 + 2 files changed, 248 insertions(+) create mode 100644 plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f diff --git a/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f b/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f new file mode 100644 index 00000000..c29f9640 --- /dev/null +++ b/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f @@ -0,0 +1,246 @@ +program fci_zmq + implicit none + integer :: i,j,k + double precision, allocatable :: pt2(:) + integer :: degree + integer :: n_det_before, to_select + double precision :: threshold_davidson_in + + allocate (pt2(N_states)) + + double precision :: hf_energy_ref + logical :: has + double precision :: relative_error, absolute_error + integer :: N_states_p + character*(512) :: fmt + + relative_error=PT2_relative_error + absolute_error=PT2_absolute_error + + pt2 = -huge(1.e0) + threshold_davidson_in = threshold_davidson + threshold_davidson = threshold_davidson_in * 100.d0 + SOFT_TOUCH threshold_davidson + + call diagonalize_CI + call save_wavefunction + + call ezfio_has_hartree_fock_energy(has) + if (has) then + call ezfio_get_hartree_fock_energy(hf_energy_ref) + else + hf_energy_ref = ref_bitmask_energy + endif + + if (N_det > N_det_max) then + psi_det = psi_det_sorted + psi_coef = psi_coef_sorted + N_det = N_det_max + soft_touch N_det psi_det psi_coef + call diagonalize_CI + call save_wavefunction + N_states_p = min(N_det,N_states) + endif + + n_det_before = 0 + + character*(8) :: pt2_string + double precision :: correlation_energy_ratio + double precision :: threshold_selectors_save, threshold_generators_save + threshold_selectors_save = threshold_selectors + threshold_generators_save = threshold_generators + double precision :: error(N_states) + + correlation_energy_ratio = 0.d0 + + if (.True.) then ! Avoid pre-calculation of CI_energy + do while ( & + (N_det < N_det_max) .and. & + (maxval(abs(pt2(1:N_states))) > pt2_max) .and. & + (correlation_energy_ratio <= correlation_energy_ratio_max) & + ) + write(*,'(A)') '--------------------------------------------------------------------------------' + + + if (do_pt2) then + pt2_string = ' ' + pt2 = 0.d0 + threshold_selectors = 1.d0 + threshold_generators = 1d0 + SOFT_TOUCH threshold_selectors threshold_generators + call ZMQ_pt2(CI_energy, pt2,relative_error,absolute_error,error) ! Stochastic PT2 + threshold_selectors = threshold_selectors_save + threshold_generators = threshold_generators_save + SOFT_TOUCH threshold_selectors threshold_generators + else + pt2_string = '(approx)' + endif + + + correlation_energy_ratio = (CI_energy(1) - hf_energy_ref) / & + (CI_energy(1) + pt2(1) - hf_energy_ref) + correlation_energy_ratio = min(1.d0,correlation_energy_ratio) + + N_states_p = min(N_det,N_states) + + print *, '' + print '(A,I12)', 'Summary at N_det = ', N_det + print '(A)', '-----------------------------------' + print *, '' + call write_double(6,correlation_energy_ratio, 'Correlation ratio') + print *, '' + + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) + write(fmt,*) '(12X,', N_states_p, '(6X,A7,1X,I6,10X))' + write(*,fmt) ('State',k, k=1,N_states_p) + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) + write(fmt,*) '(A12,', N_states_p, '(1X,F14.8,15X))' + write(*,fmt) '# E ', CI_energy(1:N_states_p) + if (N_states_p > 1) then + write(*,fmt) '# Excit. (au)', CI_energy(1:N_states_p)-CI_energy(1) + write(*,fmt) '# Excit. (eV)', (CI_energy(1:N_states_p)-CI_energy(1))*27.211396641308d0 + endif + write(fmt,*) '(A12,', 2*N_states_p, '(1X,F14.8))' + write(*,fmt) '# PT2'//pt2_string, (pt2(k), error(k), k=1,N_states_p) + write(*,'(A)') '#' + write(*,fmt) '# E+PT2 ', (CI_energy(k)+pt2(k),error(k), k=1,N_states_p) + if (N_states_p > 1) then + write(*,fmt) '# Excit. (au)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1)), & + dsqrt(error(k)*error(k)+error(1)*error(1)), k=1,N_states_p) + write(*,fmt) '# Excit. (eV)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1))*27.211396641308d0, & + dsqrt(error(k)*error(k)+error(1)*error(1))*27.211396641308d0, k=1,N_states_p) + endif + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) + print *, '' + + print *, 'N_det = ', N_det + print *, 'N_states = ', N_states + print*, 'correlation_ratio = ', correlation_energy_ratio + + do k=1, N_states_p + print*,'State ',k + print *, 'PT2 = ', pt2(k) + print *, 'E = ', CI_energy(k) + print *, 'E+PT2'//pt2_string//' = ', CI_energy(k)+pt2(k), ' +/- ', error(k) + enddo + + print *, '-----' + if(N_states.gt.1)then + print *, 'Variational Energy difference (au | eV)' + do i=2, N_states_p + print*,'Delta E = ', (CI_energy(i) - CI_energy(1)), & + (CI_energy(i) - CI_energy(1)) * 27.211396641308d0 + enddo + print *, '-----' + print*, 'Variational + perturbative Energy difference (au | eV)' + do i=2, N_states_p + print*,'Delta E = ', (CI_energy(i)+ pt2(i) - (CI_energy(1) + pt2(1))), & + (CI_energy(i)+ pt2(i) - (CI_energy(1) + pt2(1))) * 27.211396641308d0 + enddo + endif + call ezfio_set_full_ci_zmq_energy_pt2(CI_energy(1)+pt2(1)) + call dump_fci_iterations_value(N_det,CI_energy,pt2) + + n_det_before = N_det + if (s2_eig) then + to_select = N_det/2+1 + to_select = max(N_det/2+1, to_select) + to_select = min(to_select, N_det_max-n_det_before) + else + to_select = N_det + to_select = max(N_det, to_select) + to_select = min(to_select, N_det_max-n_det_before) + endif + call save_natural_mos + call map_deinit(mo_integrals_map) + FREE mo_integrals_map + PROVIDE mo_integrals_map + call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & + mo_coef, size(mo_coef,1), & + 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & + 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) + + call ZMQ_selection(to_select, pt2) + + PROVIDE psi_coef + PROVIDE psi_det + PROVIDE psi_det_sorted + + if (N_det >= N_det_max) then + threshold_davidson = threshold_davidson_in + end if + call diagonalize_CI + call save_wavefunction + call ezfio_set_full_ci_zmq_energy(CI_energy(1)) + enddo + endif + + if (N_det < N_det_max) then + threshold_davidson = threshold_davidson_in + call diagonalize_CI + call save_wavefunction + call ezfio_set_full_ci_zmq_energy(CI_energy(1)) + call ezfio_set_full_ci_zmq_energy_pt2(CI_energy(1)+pt2(1)) + endif + + if (do_pt2) then + pt2 = 0.d0 + threshold_selectors = 1.d0 + threshold_generators = 1d0 + SOFT_TOUCH threshold_selectors threshold_generators + call ZMQ_pt2(CI_energy, pt2,relative_error,absolute_error,error) ! Stochastic PT2 + threshold_selectors = threshold_selectors_save + threshold_generators = threshold_generators_save + SOFT_TOUCH threshold_selectors threshold_generators + call ezfio_set_full_ci_zmq_energy(CI_energy(1)) + call ezfio_set_full_ci_zmq_energy_pt2(CI_energy(1)+pt2(1)) + endif + print *, 'N_det = ', N_det + print *, 'N_states = ', N_states + print*, 'correlation_ratio = ', correlation_energy_ratio + + + call dump_fci_iterations_value(N_det,CI_energy,pt2) + + print *, '' + print '(A,I12)', 'Summary at N_det = ', N_det + print '(A)', '-----------------------------------' + print *, '' + call write_double(6,correlation_energy_ratio, 'Correlation ratio') + print *, '' + + + N_states_p = min(N_det,N_states) + print *, '' + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) + write(fmt,*) '(12X,', N_states_p, '(6X,A7,1X,I6,10X))' + write(*,fmt) ('State',k, k=1,N_states_p) + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) + write(fmt,*) '(A12,', N_states_p, '(1X,F14.8,15X))' + write(*,fmt) '# E ', CI_energy(1:N_states_p) + if (N_states_p > 1) then + write(*,fmt) '# Excit. (au)', CI_energy(1:N_states_p)-CI_energy(1) + write(*,fmt) '# Excit. (eV)', (CI_energy(1:N_states_p)-CI_energy(1))*27.211396641308d0 + endif + write(fmt,*) '(A12,', 2*N_states_p, '(1X,F14.8))' + write(*,fmt) '# PT2'//pt2_string, (pt2(k), error(k), k=1,N_states_p) + write(*,'(A)') '#' + write(*,fmt) '# E+PT2 ', (CI_energy(k)+pt2(k),error(k), k=1,N_states_p) + if (N_states_p > 1) then + write(*,fmt) '# Excit. (au)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1)), & + dsqrt(error(k)*error(k)+error(1)*error(1)), k=1,N_states_p) + write(*,fmt) '# Excit. (eV)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1))*27.211396641308d0, & + dsqrt(error(k)*error(k)+error(1)*error(1))*27.211396641308d0, k=1,N_states_p) + endif + write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' + write(*,fmt) + print *, '' + + + +end diff --git a/src/Determinants/determinants.irp.f b/src/Determinants/determinants.irp.f index 99b0beef..d161edd6 100644 --- a/src/Determinants/determinants.irp.f +++ b/src/Determinants/determinants.irp.f @@ -517,6 +517,7 @@ subroutine save_wavefunction_general(ndet,nstates,psidet,dim_psicoef,psicoef) call ezfio_set_determinants_mo_label(mo_label) allocate (psi_det_save(N_int,2,ndet)) + !$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(i,j,k) SHARED(psi_det_save,psidet,ndet,N_int) do i=1,ndet do j=1,2 do k=1,N_int @@ -524,6 +525,7 @@ subroutine save_wavefunction_general(ndet,nstates,psidet,dim_psicoef,psicoef) enddo enddo enddo + !$OMP END PARALLEL DO call ezfio_set_determinants_psi_det(psi_det_save) deallocate (psi_det_save) From 4f0a90bf6a39cde9e86ae6010fd8e3b5d21ec1a7 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 7 Dec 2017 10:25:36 +0100 Subject: [PATCH 08/54] Fixed EZFIO --- plugins/Full_CI_ZMQ/EZFIO.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/plugins/Full_CI_ZMQ/EZFIO.cfg b/plugins/Full_CI_ZMQ/EZFIO.cfg index a0b71e6b..e73c08fb 100644 --- a/plugins/Full_CI_ZMQ/EZFIO.cfg +++ b/plugins/Full_CI_ZMQ/EZFIO.cfg @@ -29,10 +29,10 @@ size: (full_ci_zmq.n_iter) interface: ezfio doc: The energy without a pt2 correction for n_det type: double precision -size: (full_ci_zmq.n_iter,determinants.n_states) +size: (determinants.n_states,full_ci_zmq.n_iter) [pt2_iter] interface: ezfio doc: The pt2 correction for n_det type: double precision -size: (full_ci_zmq.n_iter,determinants.n_states) +size: (determinants.n_states,full_ci_zmq.n_iter) From 2b1d6bc9fcc3f469630b5652b0f8ef4f8700bbef Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 09:45:18 +0100 Subject: [PATCH 09/54] Cleaning --- plugins/Full_CI_ZMQ/pt2_stoch_routines.irp.f | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/plugins/Full_CI_ZMQ/pt2_stoch_routines.irp.f b/plugins/Full_CI_ZMQ/pt2_stoch_routines.irp.f index 906b14d2..5848cec0 100644 --- a/plugins/Full_CI_ZMQ/pt2_stoch_routines.irp.f +++ b/plugins/Full_CI_ZMQ/pt2_stoch_routines.irp.f @@ -141,10 +141,7 @@ subroutine ZMQ_pt2(E, pt2,relative_error, absolute_error, error) deallocate(pt2_detail, comb, computed, tbc) enddo - pt2_stoch_istate = 1 - w(:) = 1.d0/N_states - call update_psi_average_norm_contrib(w) - SOFT_TOUCH psi_average_norm_contrib + FREE psi_average_norm_contrib pt2_stoch_istate endif do k=N_det+1,N_states pt2(k) = 0.d0 From 2472e63bd514b354fd85d856cde815c53f58e007 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 10:48:09 +0100 Subject: [PATCH 10/54] Removed parallelism in old selection --- plugins/MP2/NEEDED_CHILDREN_MODULES | 2 +- plugins/MP2/mp2.irp.f | 2 +- scripts/generate_h_apply.py | 79 +++++++---------------- src/Determinants/H_apply.template.f | 34 ---------- src/Determinants/H_apply_nozmq.template.f | 69 +------------------- src/Determinants/H_apply_zmq.template.f | 10 +-- 6 files changed, 32 insertions(+), 164 deletions(-) diff --git a/plugins/MP2/NEEDED_CHILDREN_MODULES b/plugins/MP2/NEEDED_CHILDREN_MODULES index d26e4dee..bdf4b736 100644 --- a/plugins/MP2/NEEDED_CHILDREN_MODULES +++ b/plugins/MP2/NEEDED_CHILDREN_MODULES @@ -1 +1 @@ -Perturbation Selectors_full SingleRefMethod +Perturbation Selectors_full SingleRefMethod ZMQ diff --git a/plugins/MP2/mp2.irp.f b/plugins/MP2/mp2.irp.f index d4721c71..2ea5fd14 100644 --- a/plugins/MP2/mp2.irp.f +++ b/plugins/MP2/mp2.irp.f @@ -9,7 +9,7 @@ subroutine run double precision, allocatable :: pt2(:), norm_pert(:) double precision :: H_pert_diag, E_old integer :: N_st, iter - PROVIDE Fock_matrix_diag_mo + PROVIDE Fock_matrix_diag_mo H_apply_buffer_allocated N_st = N_states allocate (pt2(N_st), norm_pert(N_st)) E_old = HF_energy diff --git a/scripts/generate_h_apply.py b/scripts/generate_h_apply.py index a7e95e06..da1aac5a 100755 --- a/scripts/generate_h_apply.py +++ b/scripts/generate_h_apply.py @@ -8,7 +8,6 @@ copy_buffer declarations decls_main deinit_thread -skip init_main filter_integrals filter2p @@ -56,7 +55,6 @@ parameters params_main printout_always printout_now -skip subroutine """.split() @@ -82,25 +80,24 @@ class H_apply(object): self.energy = "CI_electronic_energy" self.perturbation = None self.do_double_exc = do_double_exc - #s["omp_parallel"] = """!$OMP PARALLEL DEFAULT(NONE) & - s["omp_parallel"] = """ PROVIDE elec_num_tab - !$OMP PARALLEL DEFAULT(SHARED) & - !$OMP PRIVATE(i,j,k,l,keys_out,hole,particle, & - !$OMP occ_particle,occ_hole,j_a,k_a,other_spin, & - !$OMP hole_save,ispin,jj,l_a,ib_jb_pairs,array_pairs, & - !$OMP accu,i_a,hole_tmp,particle_tmp,occ_particle_tmp, & - !$OMP occ_hole_tmp,key_idx,i_b,j_b,key,N_elec_in_key_part_1,& - !$OMP N_elec_in_key_hole_1,N_elec_in_key_part_2, & - !$OMP N_elec_in_key_hole_2,ia_ja_pairs,key_union_hole_part) & - !$OMP SHARED(key_in,N_int,elec_num_tab,mo_tot_num, & - !$OMP hole_1, particl_1, hole_2, particl_2, & - !$OMP elec_alpha_num,i_generator) FIRSTPRIVATE(iproc)""" - s["omp_end_parallel"] = "!$OMP END PARALLEL" - s["omp_master"] = "!$OMP MASTER" - s["omp_end_master"] = "!$OMP END MASTER" - s["omp_barrier"] = "!$OMP BARRIER" - s["omp_do"] = "!$OMP DO SCHEDULE (static,1)" - s["omp_enddo"] = "!$OMP ENDDO NOWAIT" +# s["omp_parallel"] = """ PROVIDE elec_num_tab +# !$OMP PARALLEL DEFAULT(SHARED) & +# !$OMP PRIVATE(i,j,k,l,keys_out,hole,particle, & +# !$OMP occ_particle,occ_hole,j_a,k_a,other_spin, & +# !$OMP hole_save,ispin,jj,l_a,ib_jb_pairs,array_pairs, & +# !$OMP accu,i_a,hole_tmp,particle_tmp,occ_particle_tmp, & +# !$OMP occ_hole_tmp,key_idx,i_b,j_b,key,N_elec_in_key_part_1,& +# !$OMP N_elec_in_key_hole_1,N_elec_in_key_part_2, & +# !$OMP N_elec_in_key_hole_2,ia_ja_pairs,key_union_hole_part) & +# !$OMP SHARED(key_in,N_int,elec_num_tab,mo_tot_num, & +# !$OMP hole_1, particl_1, hole_2, particl_2, & +# !$OMP elec_alpha_num,i_generator) FIRSTPRIVATE(iproc)""" +# s["omp_end_parallel"] = "!$OMP END PARALLEL" +# s["omp_master"] = "!$OMP MASTER" +# s["omp_end_master"] = "!$OMP END MASTER" +# s["omp_barrier"] = "!$OMP BARRIER" +# s["omp_do"] = "!$OMP DO SCHEDULE (static,1)" +# s["omp_enddo"] = "!$OMP ENDDO" d = { True : '.True.', False : '.False.'} s["do_mono_excitations"] = d[do_mono_exc] @@ -289,11 +286,6 @@ class H_apply(object): """ - def unset_skip(self): - self["skip"] = """ - """ - - def set_filter_2h_2p(self): self["filter2h2p_double"] = """ if (is_a_two_holes_two_particles(key)) cycle @@ -400,9 +392,9 @@ class H_apply(object): pt2_old(k) = pt2(k) enddo """ - self.data["omp_parallel"] += """& - !$OMP SHARED(N_st) PRIVATE(e_2_pert_buffer,coef_pert_buffer) & - !$OMP PRIVATE(sum_e_2_pert, sum_norm_pert, sum_H_pert_diag)""" +# self.data["omp_parallel"] += """& +# !$OMP SHARED(N_st) PRIVATE(e_2_pert_buffer,coef_pert_buffer) & +# !$OMP PRIVATE(sum_e_2_pert, sum_norm_pert, sum_H_pert_diag)""" def set_selection_pt2(self,pert): if self.selection_pt2 is not None: @@ -434,22 +426,8 @@ class H_apply(object): call fill_H_apply_buffer_selection(key_idx,keys_out,e_2_pert_buffer, & coef_pert_buffer,N_st,N_int,iproc,select_max_out) """ - self.data["omp_parallel"] += """& - !$OMP REDUCTION (max:select_max_out)""" - self.data["skip"] = """ - if (i_generator < size_select_max) then - if (select_max(i_generator) < selection_criterion_min*selection_criterion_factor) then - ! OMP CRITICAL - do k=1,N_st - norm_psi(k) = norm_psi(k) + psi_coef_generators(i_generator,k)*psi_coef_generators(i_generator,k) - pt2_old(k) = 0.d0 - enddo - ! OMP END CRITICAL - cycle - endif - select_max(i_generator) = 0.d0 - endif - """ +# self.data["omp_parallel"] += """& +# !$OMP REDUCTION (max:select_max_out)""" def unset_openmp(self): @@ -498,15 +476,4 @@ class H_apply_zmq(H_apply): def set_selection_pt2(self,pert): H_apply.set_selection_pt2(self,pert) - self.data["skip"] = """ - if (i_generator < size_select_max) then - if (select_max(i_generator) < selection_criterion_min*selection_criterion_factor) then - do k=1,N_st - pt2(k) = select_max(i_generator) - enddo - cycle - endif - select_max(i_generator) = 0.d0 - endif - """ diff --git a/src/Determinants/H_apply.template.f b/src/Determinants/H_apply.template.f index 5f59fe84..81d0d465 100644 --- a/src/Determinants/H_apply.template.f +++ b/src/Determinants/H_apply.template.f @@ -14,14 +14,6 @@ subroutine $subroutine_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl $declarations -! print *, "bbbbbbbbbbbbbbb" -! call debug_det(key_in, N_int) -! call debug_det(hole_1, N_int) -! call debug_det(hole_2, N_int) -! call debug_det(particl_1, N_int) -! call debug_det(particl_2, N_int) -! print *, "eeeeeeeeeeeeeeee" - highest = 0 do k=1,N_int*bit_kind_size status(k,1) = 0 @@ -43,32 +35,6 @@ subroutine $subroutine_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl end do end do -! ! GEL D'ELECTRONS -! ! nt = 0 -! do i=1,i_generator-1 -! if(key_in(1,1) == key_prev(1,1,i)) then -! tmp = xor(key_in(1,2), key_prev(1,2,i)) -! if(popcnt(tmp) == 2) then -! ns = 1+trailz(iand(tmp, key_in(1,2))) -! ! if(status(ns, 2) /= 0) then -! ! nt += 1 -! ! end if -! status(ns, 2) = 0 -! end if -! else if(key_in(1,2) == key_prev(1,2,i)) then -! tmp = xor(key_in(1,1), key_prev(1,1,i)) -! if(popcnt(tmp) == 2) then -! ns = 1+trailz(iand(tmp, key_in(1,1))) -! ! if(status(ns, 1) /= 0) then -! ! nt += 1 -! ! end if -! status(ns, 1) = 0 -! end if -! end if -! end do -! ! print *, "nt", nt, i_generator - - do sp=1,2 do p1=1,highest if(status(p1, sp) == 0) then diff --git a/src/Determinants/H_apply_nozmq.template.f b/src/Determinants/H_apply_nozmq.template.f index 0c319fe3..a8ea9b76 100644 --- a/src/Determinants/H_apply_nozmq.template.f +++ b/src/Determinants/H_apply_nozmq.template.f @@ -9,7 +9,7 @@ subroutine $subroutine($params_main) $decls_main - integer :: i_generator, nmax + integer :: i_generator double precision :: wall_0, wall_1 integer(bit_kind), allocatable :: mask(:,:,:) integer :: ispin, k @@ -20,15 +20,11 @@ subroutine $subroutine($params_main) PROVIDE H_apply_buffer_allocated mo_bielec_integrals_in_map psi_det_generators psi_coef_generators - nmax = mod( N_det_generators,nproc ) - call wall_time(wall_0) iproc = 0 allocate( mask(N_int,2,6), fock_diag_tmp(2,mo_tot_num+1) ) - do i_generator=1,nmax - - $skip + do i_generator=1,N_det_generators ! Compute diagonal of the Fock matrix call build_fock_tmp(fock_diag_tmp,psi_det_generators(1,1,i_generator),N_int) @@ -78,67 +74,6 @@ subroutine $subroutine($params_main) deallocate( mask, fock_diag_tmp ) - !$OMP PARALLEL DEFAULT(SHARED) & - !$OMP PRIVATE(i_generator,wall_1,wall_0,ispin,k,mask,iproc,fock_diag_tmp) - call wall_time(wall_0) - !$ iproc = omp_get_thread_num() - allocate( mask(N_int,2,6), fock_diag_tmp(2,mo_tot_num+1) ) - !$OMP DO SCHEDULE(dynamic,1) - do i_generator=nmax+1,N_det_generators - $skip - - ! Compute diagonal of the Fock matrix - call build_fock_tmp(fock_diag_tmp,psi_det_generators(1,1,i_generator),N_int) - - ! Create bit masks for holes and particles - do ispin=1,2 - do k=1,N_int - mask(k,ispin,s_hole) = & - iand(generators_bitmask(k,ispin,s_hole,i_bitmask_gen), & - psi_det_generators(k,ispin,i_generator) ) - mask(k,ispin,s_part) = & - iand(generators_bitmask(k,ispin,s_part,i_bitmask_gen), & - not(psi_det_generators(k,ispin,i_generator)) ) - mask(k,ispin,d_hole1) = & - iand(generators_bitmask(k,ispin,d_hole1,i_bitmask_gen), & - psi_det_generators(k,ispin,i_generator) ) - mask(k,ispin,d_part1) = & - iand(generators_bitmask(k,ispin,d_part1,i_bitmask_gen), & - not(psi_det_generators(k,ispin,i_generator)) ) - mask(k,ispin,d_hole2) = & - iand(generators_bitmask(k,ispin,d_hole2,i_bitmask_gen), & - psi_det_generators(k,ispin,i_generator) ) - mask(k,ispin,d_part2) = & - iand(generators_bitmask(k,ispin,d_part2,i_bitmask_gen), & - not (psi_det_generators(k,ispin,i_generator)) ) - enddo - enddo - - if($do_double_excitations)then - call $subroutine_diexc(psi_det_generators(1,1,i_generator), & - psi_det_generators(1,1,1), & - mask(1,1,d_hole1), mask(1,1,d_part1), & - mask(1,1,d_hole2), mask(1,1,d_part2), & - fock_diag_tmp, i_generator, iproc $params_post) - endif - if($do_mono_excitations)then - call $subroutine_monoexc(psi_det_generators(1,1,i_generator), & - mask(1,1,s_hole ), mask(1,1,s_part ), & - fock_diag_tmp, i_generator, iproc $params_post) - endif - !$OMP CRITICAL - call wall_time(wall_1) - $printout_always - if (wall_1 - wall_0 > 2.d0) then - $printout_now - wall_0 = wall_1 - endif - !$OMP END CRITICAL - enddo - !$OMP END DO - deallocate( mask, fock_diag_tmp ) - !$OMP END PARALLEL - $copy_buffer $generate_psi_guess diff --git a/src/Determinants/H_apply_zmq.template.f b/src/Determinants/H_apply_zmq.template.f index 7bc5795f..57499e2a 100644 --- a/src/Determinants/H_apply_zmq.template.f +++ b/src/Determinants/H_apply_zmq.template.f @@ -22,8 +22,8 @@ subroutine $subroutine($params_main) $initialization PROVIDE H_apply_buffer_allocated mo_bielec_integrals_in_map psi_det_generators psi_coef_generators - integer(ZMQ_PTR), external :: new_zmq_pair_socket, zmq_socket_pull - integer(ZMQ_PTR) :: zmq_socket_pair + integer(ZMQ_PTR), external :: new_zmq_pair_socket + integer(ZMQ_PTR) :: zmq_socket_pair, zmq_socket_pull integer(ZMQ_PTR) :: zmq_to_qp_run_socket double precision, allocatable :: pt2_generators(:,:), norm_pert_generators(:,:) @@ -41,10 +41,10 @@ subroutine $subroutine($params_main) if (zmq_put_psi(zmq_to_qp_run_socket,1) == -1) then stop 'Unable to put psi on ZMQ server' endif - if (zmq_put_N_det_generators(zmq_to_qp_run_socket, worker_id) == -1) then + if (zmq_put_N_det_generators(zmq_to_qp_run_socket, 1) == -1) then stop 'Unable to put N_det_generators on ZMQ server' endif - if (zmq_put_N_det_selectors(zmq_to_qp_run_socket, worker_id) == -1) then + if (zmq_put_N_det_selectors(zmq_to_qp_run_socket, 1) == -1) then stop 'Unable to put N_det_selectors on ZMQ server' endif if (zmq_put_dvector(zmq_to_qp_run_socket,1,'energy',energy,size(energy)) == -1) then @@ -67,7 +67,7 @@ subroutine $subroutine($params_main) PROVIDE nproc N_states !$OMP PARALLEL DEFAULT(NONE) & !$OMP PRIVATE(i) & - !$OMP SHARED(zmq_socket_pair,N_states, pt2_generators, norm_pert_generators, H_pert_diag_generators, n, task_id, i_generator) & + !$OMP SHARED(zmq_socket_pair,N_states, pt2_generators, norm_pert_generators, H_pert_diag_generators, n, task_id, i_generator,zmq_socket_pull) & !$OMP num_threads(nproc+1) i = omp_get_thread_num() if (i == 0) then From f2da24ae4c2445d3e99a458edc22eb7f80c9c911 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 11:49:58 +0100 Subject: [PATCH 11/54] Fixed psi_coef I/O bug --- src/Determinants/determinants.irp.f | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/src/Determinants/determinants.irp.f b/src/Determinants/determinants.irp.f index d161edd6..3722dff3 100644 --- a/src/Determinants/determinants.irp.f +++ b/src/Determinants/determinants.irp.f @@ -177,14 +177,15 @@ BEGIN_PROVIDER [ double precision, psi_coef, (psi_det_size,N_states) ] integer :: i,k, N_int2 logical :: exists + double precision, allocatable :: psi_coef_read(:,:) character*(64) :: label - + PROVIDE read_wf N_det mo_label ezfio_filename psi_coef = 0.d0 do i=1,min(N_states,psi_det_size) psi_coef(i,i) = 1.d0 enddo - + if (mpi_master) then if (read_wf) then call ezfio_has_determinants_psi_coef(exists) @@ -195,12 +196,21 @@ BEGIN_PROVIDER [ double precision, psi_coef, (psi_det_size,N_states) ] exists = (label == mo_label) endif endif - if (exists) then - call ezfio_get_determinants_psi_coef(psi_coef) - endif + endif + + if (exists) then + + allocate (psi_coef_read(N_det,N_states)) + call ezfio_get_determinants_psi_coef(psi_coef_read) + do k=1,N_states + do i=1,N_det + psi_coef(i,k) = psi_coef_read(i,k) + enddo + enddo + deallocate(psi_coef_read) + print *, 'Read psi_coef' endif - print *, 'Read psi_coef' endif IRP_IF MPI include 'mpif.h' From ad58d8c55d67eb5326227d80d0d16e5687672ca9 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 14:12:39 +0100 Subject: [PATCH 12/54] Removed ezfio_interface file --- plugins/mrcepa0/ezfio_interface.irp.f | 80 --------------------------- 1 file changed, 80 deletions(-) delete mode 100644 plugins/mrcepa0/ezfio_interface.irp.f diff --git a/plugins/mrcepa0/ezfio_interface.irp.f b/plugins/mrcepa0/ezfio_interface.irp.f deleted file mode 100644 index 3627abe6..00000000 --- a/plugins/mrcepa0/ezfio_interface.irp.f +++ /dev/null @@ -1,80 +0,0 @@ -! DO NOT MODIFY BY HAND -! Created by $QP_ROOT/scripts/ezfio_interface/ei_handler.py -! from file /home/garniron/quantum_package/src/mrcepa0/EZFIO.cfg - - -BEGIN_PROVIDER [ logical, perturbative_triples ] - implicit none - BEGIN_DOC -! Compute perturbative contribution of the Triples - END_DOC - - logical :: has - PROVIDE ezfio_filename - - call ezfio_has_mrcepa0_perturbative_triples(has) - if (has) then - call ezfio_get_mrcepa0_perturbative_triples(perturbative_triples) - else - print *, 'mrcepa0/perturbative_triples not found in EZFIO file' - stop 1 - endif - -END_PROVIDER - -BEGIN_PROVIDER [ double precision, thresh_dressed_ci ] - implicit none - BEGIN_DOC -! Threshold on the convergence of the dressed CI energy - END_DOC - - logical :: has - PROVIDE ezfio_filename - - call ezfio_has_mrcepa0_thresh_dressed_ci(has) - if (has) then - call ezfio_get_mrcepa0_thresh_dressed_ci(thresh_dressed_ci) - else - print *, 'mrcepa0/thresh_dressed_ci not found in EZFIO file' - stop 1 - endif - -END_PROVIDER - -BEGIN_PROVIDER [ integer, n_it_max_dressed_ci ] - implicit none - BEGIN_DOC -! Maximum number of dressed CI iterations - END_DOC - - logical :: has - PROVIDE ezfio_filename - - call ezfio_has_mrcepa0_n_it_max_dressed_ci(has) - if (has) then - call ezfio_get_mrcepa0_n_it_max_dressed_ci(n_it_max_dressed_ci) - else - print *, 'mrcepa0/n_it_max_dressed_ci not found in EZFIO file' - stop 1 - endif - -END_PROVIDER - -BEGIN_PROVIDER [ integer, lambda_type ] - implicit none - BEGIN_DOC -! lambda type - END_DOC - - logical :: has - PROVIDE ezfio_filename - - call ezfio_has_mrcepa0_lambda_type(has) - if (has) then - call ezfio_get_mrcepa0_lambda_type(lambda_type) - else - print *, 'mrcepa0/lambda_type not found in EZFIO file' - stop 1 - endif - -END_PROVIDER From f93cfb8a6f86e1e81cef088f2f45028ac910c233 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 16:17:54 +0100 Subject: [PATCH 13/54] Revert 4idx --- plugins/Properties/print_hcc.irp.f | 13 ++++++++++++- src/Integrals_Bielec/mo_bi_integrals.irp.f | 14 +++++++------- 2 files changed, 19 insertions(+), 8 deletions(-) diff --git a/plugins/Properties/print_hcc.irp.f b/plugins/Properties/print_hcc.irp.f index 45bca5e6..7f74f996 100644 --- a/plugins/Properties/print_hcc.irp.f +++ b/plugins/Properties/print_hcc.irp.f @@ -2,5 +2,16 @@ program print_hcc_main implicit none read_wf = .True. touch read_wf - call print_hcc +! call print_hcc + call routine end + + +subroutine routine + implicit none + integer :: i + do i = 1, mo_tot_num + write(*,'(1000(F16.10,X))')one_body_dm_mo_beta(i,:,1) + enddo +end + diff --git a/src/Integrals_Bielec/mo_bi_integrals.irp.f b/src/Integrals_Bielec/mo_bi_integrals.irp.f index 3fa01292..d7b0fa5b 100644 --- a/src/Integrals_Bielec/mo_bi_integrals.irp.f +++ b/src/Integrals_Bielec/mo_bi_integrals.irp.f @@ -124,16 +124,16 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ] else ! call add_integrals_to_map(full_ijkl_bitmask_4) - call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & - mo_coef, size(mo_coef,1), & - 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & - 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) -! -! call four_index_transform_block(ao_integrals_map,mo_integrals_map, & +! call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & ! 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) -! + + call four_index_transform_block(ao_integrals_map,mo_integrals_map, & + mo_coef, size(mo_coef,1), & + 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & + 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) + ! call four_index_transform(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & From 660e87bb30e25c249b8d41de0f4d5b74ff40b592 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 17:02:26 +0100 Subject: [PATCH 14/54] Fixed one-body DM --- src/Determinants/density_matrix.irp.f | 87 ++++++++++++++++++--------- 1 file changed, 60 insertions(+), 27 deletions(-) diff --git a/src/Determinants/density_matrix.irp.f b/src/Determinants/density_matrix.irp.f index b948182d..86c7fcd4 100644 --- a/src/Determinants/density_matrix.irp.f +++ b/src/Determinants/density_matrix.irp.f @@ -99,7 +99,7 @@ END_PROVIDER ! Alpha and beta one-body density matrix for each state END_DOC - integer :: j,k,l,m + integer :: j,k,l,m,k_a,k_b integer :: occ(N_int*bit_kind_size,2) double precision :: ck, cl, ckl double precision :: phase @@ -114,7 +114,7 @@ END_PROVIDER one_body_dm_mo_alpha = 0.d0 one_body_dm_mo_beta = 0.d0 !$OMP PARALLEL DEFAULT(NONE) & - !$OMP PRIVATE(j,k,l,m,occ,ck, cl, ckl,phase,h1,h2,p1,p2,s1,s2, degree,exc, & + !$OMP PRIVATE(j,k,k_a,k_b,l,m,occ,ck, cl, ckl,phase,h1,h2,p1,p2,s1,s2, degree,exc, & !$OMP tmp_a, tmp_b, n_occ, krow, kcol, lrow, lcol, tmp_det, tmp_det2)& !$OMP SHARED(psi_det,psi_coef,N_int,N_states,elec_alpha_num,& !$OMP elec_beta_num,one_body_dm_mo_alpha,one_body_dm_mo_beta,N_det,& @@ -124,28 +124,31 @@ END_PROVIDER !$OMP psi_bilinear_matrix_values, psi_bilinear_matrix_transp_values) allocate(tmp_a(mo_tot_num,mo_tot_num,N_states), tmp_b(mo_tot_num,mo_tot_num,N_states) ) tmp_a = 0.d0 - tmp_b = 0.d0 - !$OMP DO SCHEDULE(guided) - do k=1,N_det - krow = psi_bilinear_matrix_rows(k) - kcol = psi_bilinear_matrix_columns(k) - tmp_det(:,1) = psi_det_alpha_unique(:,krow) - tmp_det(:,2) = psi_det_beta_unique (:,kcol) + !$OMP DO SCHEDULE(dynamic,64) + do k_a=1,N_det + krow = psi_bilinear_matrix_rows(k_a) + ASSERT (krow <= N_det_alpha_unique) + + kcol = psi_bilinear_matrix_columns(k_a) + ASSERT (kcol <= N_det_beta_unique) + + tmp_det(1:N_int,1) = psi_det_alpha_unique(1:N_int,krow) + tmp_det(1:N_int,2) = psi_det_beta_unique (1:N_int,kcol) + + ! Diagonal part + ! ------------- + call bitstring_to_list_ab(tmp_det, occ, n_occ, N_int) do m=1,N_states - ck = psi_bilinear_matrix_values(k,m)*psi_bilinear_matrix_values(k,m) + ck = psi_bilinear_matrix_values(k_a,m)*psi_bilinear_matrix_values(k_a,m) do l=1,elec_alpha_num j = occ(l,1) tmp_a(j,j,m) += ck enddo - do l=1,elec_beta_num - j = occ(l,2) - tmp_b(j,j,m) += ck - enddo enddo - if (k == N_det) cycle - l = k+1 + if (k_a == N_det) cycle + l = k_a+1 lrow = psi_bilinear_matrix_rows(l) lcol = psi_bilinear_matrix_columns(l) ! Fix beta determinant, loop over alphas @@ -157,7 +160,7 @@ END_PROVIDER call get_mono_excitation_spin(tmp_det(1,1),tmp_det2,exc,phase,N_int) call decode_exc_spin(exc,h1,p1,h2,p2) do m=1,N_states - ckl = psi_bilinear_matrix_values(k,m)*psi_bilinear_matrix_values(l,m) * phase + ckl = psi_bilinear_matrix_values(k_a,m)*psi_bilinear_matrix_values(l,m) * phase tmp_a(h1,p1,m) += ckl tmp_a(p1,h1,m) += ckl enddo @@ -168,20 +171,52 @@ END_PROVIDER lcol = psi_bilinear_matrix_columns(l) enddo - l = psi_bilinear_matrix_order_reverse(k) - if (l == N_det) cycle - l = l+1 - ! Fix alpha determinant, loop over betas + enddo + !$OMP END DO NOWAIT + + !$OMP CRITICAL + one_body_dm_mo_alpha(:,:,:) = one_body_dm_mo_alpha(:,:,:) + tmp_a(:,:,:) + !$OMP END CRITICAL + deallocate(tmp_a) + + tmp_b = 0.d0 + !$OMP DO SCHEDULE(dynamic,64) + do k_b=1,N_det + krow = psi_bilinear_matrix_transp_rows(k_b) + ASSERT (krow <= N_det_alpha_unique) + + kcol = psi_bilinear_matrix_transp_columns(k_b) + ASSERT (kcol <= N_det_beta_unique) + + tmp_det(1:N_int,1) = psi_det_alpha_unique(1:N_int,krow) + tmp_det(1:N_int,2) = psi_det_beta_unique (1:N_int,kcol) + + ! Diagonal part + ! ------------- + + call bitstring_to_list_ab(tmp_det, occ, n_occ, N_int) + do m=1,N_states + ck = psi_bilinear_matrix_transp_values(k_b,m)*psi_bilinear_matrix_transp_values(k_b,m) + do l=1,elec_beta_num + j = occ(l,2) + tmp_b(j,j,m) += ck + enddo + enddo + + if (k_b == N_det) cycle + l = k_b+1 lrow = psi_bilinear_matrix_transp_rows(l) lcol = psi_bilinear_matrix_transp_columns(l) + ! Fix beta determinant, loop over alphas do while ( lrow == krow ) - tmp_det2(:) = psi_det_beta_unique (:, lcol) + tmp_det2(:) = psi_det_beta_unique(:, lcol) call get_excitation_degree_spin(tmp_det(1,2),tmp_det2,degree,N_int) if (degree == 1) then + exc = 0 call get_mono_excitation_spin(tmp_det(1,2),tmp_det2,exc,phase,N_int) call decode_exc_spin(exc,h1,p1,h2,p2) do m=1,N_states - ckl = psi_bilinear_matrix_values(k,m)*psi_bilinear_matrix_transp_values(l,m) * phase + ckl = psi_bilinear_matrix_transp_values(k_b,m)*psi_bilinear_matrix_transp_values(l,m) * phase tmp_b(h1,p1,m) += ckl tmp_b(p1,h1,m) += ckl enddo @@ -195,12 +230,10 @@ END_PROVIDER enddo !$OMP END DO NOWAIT !$OMP CRITICAL - one_body_dm_mo_alpha(:,:,:) = one_body_dm_mo_alpha(:,:,:) + tmp_a(:,:,:) - !$OMP END CRITICAL - !$OMP CRITICAL one_body_dm_mo_beta(:,:,:) = one_body_dm_mo_beta(:,:,:) + tmp_b(:,:,:) !$OMP END CRITICAL - deallocate(tmp_a,tmp_b) + + deallocate(tmp_b) !$OMP END PARALLEL END_PROVIDER From 61d1a2b551f6436f45420379e32e850f712c32b0 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 8 Dec 2017 17:07:28 +0100 Subject: [PATCH 15/54] Fixed old FCI: --- plugins/Full_CI/H_apply.irp.f | 4 ---- 1 file changed, 4 deletions(-) diff --git a/plugins/Full_CI/H_apply.irp.f b/plugins/Full_CI/H_apply.irp.f index 4f63e29e..a37e2165 100644 --- a/plugins/Full_CI/H_apply.irp.f +++ b/plugins/Full_CI/H_apply.irp.f @@ -5,24 +5,20 @@ from generate_h_apply import * s = H_apply("FCI") s.set_selection_pt2("epstein_nesbet_2x2") #s.set_selection_pt2("qdpt") -s.unset_skip() print s s = H_apply("FCI_PT2") s.set_perturbation("epstein_nesbet_2x2") #s.set_perturbation("qdpt") -s.unset_skip() s.unset_openmp() print s s = H_apply("FCI_no_selection") s.set_selection_pt2("dummy") -s.unset_skip() print s s = H_apply("FCI_mono") s.set_selection_pt2("epstein_nesbet_2x2") -s.unset_skip() s.unset_double_excitations() s.unset_openmp() print s From 60ecb0006fa8a54dbea1a54eadbd559b450a8964 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 12 Dec 2017 15:28:27 +0100 Subject: [PATCH 16/54] Fixed memory leak in 4idx --- plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f | 2 +- plugins/mrcepa0/dressing_slave.irp.f | 2 +- src/FourIdx/four_index_slave.irp.f | 5 ++--- src/FourIdx/four_index_zmq.irp.f | 2 -- src/Integrals_Bielec/mo_bi_integrals.irp.f | 2 +- 5 files changed, 5 insertions(+), 8 deletions(-) diff --git a/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f b/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f index c29f9640..01405ef8 100644 --- a/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f +++ b/plugins/Full_CI_ZMQ/fci_zmq_nos.irp.f @@ -158,7 +158,7 @@ program fci_zmq call map_deinit(mo_integrals_map) FREE mo_integrals_map PROVIDE mo_integrals_map - call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & + call four_index_transform_block(ao_integrals_map,mo_integrals_map, & mo_coef, size(mo_coef,1), & 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) diff --git a/plugins/mrcepa0/dressing_slave.irp.f b/plugins/mrcepa0/dressing_slave.irp.f index 115d1749..972db860 100644 --- a/plugins/mrcepa0/dressing_slave.irp.f +++ b/plugins/mrcepa0/dressing_slave.irp.f @@ -59,7 +59,6 @@ subroutine mrsc2_dressing_slave(thread,iproc) integer, external :: connect_to_taskserver, disconnect_from_taskserver !double precision, external :: get_dij - integer, external :: add_task_to_taskserver zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() if (connect_to_taskserver(zmq_to_qp_run_socket,worker_id,thread) == -1) then @@ -514,6 +513,7 @@ end logical, external :: is_in_wavefunction, isInCassd, detEq character*(512) :: task integer(ZMQ_PTR) :: zmq_to_qp_run_socket, zmq_socket_pull + integer, external :: add_task_to_taskserver integer :: KKsize = 1000000 diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index 06604760..029c444d 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -279,7 +279,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & enddo !$OMP END DO - deallocate(key,value,V,T) + deallocate(key,value,V,T,U,T2d,V2d) !$OMP BARRIER !$OMP MASTER call four_idx_push_results(zmq_socket_push, 0_8, 0.d0, 0, task_id) @@ -287,7 +287,6 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & call end_zmq_push_socket(zmq_socket_push) !$OMP END PARALLEL - deallocate(l_pointer) - deallocate(a_array_ik,a_array_j,a_array_value) + deallocate(l_pointer,a_array_ik,a_array_j,a_array_value) end diff --git a/src/FourIdx/four_index_zmq.irp.f b/src/FourIdx/four_index_zmq.irp.f index 1726a778..4e0673b1 100644 --- a/src/FourIdx/four_index_zmq.irp.f +++ b/src/FourIdx/four_index_zmq.irp.f @@ -20,8 +20,6 @@ subroutine four_index_transform_zmq(map_a,map_c,matrix_B,LDB, & integer, intent(in) :: a_start, b_start, c_start, d_start integer, intent(in) :: a_end , b_end , c_end , d_end - double precision, allocatable :: T(:,:), U(:,:,:), V(:,:) - double precision, allocatable :: T2d(:,:), V2d(:,:) integer :: i_max, j_max, k_max, l_max integer :: i_min, j_min, k_min, l_min integer :: i, j, k, l, ik, ll diff --git a/src/Integrals_Bielec/mo_bi_integrals.irp.f b/src/Integrals_Bielec/mo_bi_integrals.irp.f index 3fa01292..479b373d 100644 --- a/src/Integrals_Bielec/mo_bi_integrals.irp.f +++ b/src/Integrals_Bielec/mo_bi_integrals.irp.f @@ -133,7 +133,7 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ] ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & ! 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) -! + ! call four_index_transform(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & From a6ed2457b427922189bef10f1daf774753aa71bf Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 12 Dec 2017 16:26:48 +0100 Subject: [PATCH 17/54] Nested parallelism in 4idx --- plugins/Hartree_Fock/Fock_matrix.irp.f | 2 +- src/FourIdx/four_index_slave.irp.f | 52 ++++++++++---------------- 2 files changed, 20 insertions(+), 34 deletions(-) diff --git a/plugins/Hartree_Fock/Fock_matrix.irp.f b/plugins/Hartree_Fock/Fock_matrix.irp.f index 0764c83f..7f473f7a 100644 --- a/plugins/Hartree_Fock/Fock_matrix.irp.f +++ b/plugins/Hartree_Fock/Fock_matrix.irp.f @@ -219,7 +219,7 @@ END_PROVIDER ao_bi_elec_integral_alpha_tmp = 0.d0 ao_bi_elec_integral_beta_tmp = 0.d0 - !$OMP DO SCHEDULE(dynamic) + !$OMP DO SCHEDULE(dynamic,64) !DIR$ NOVECTOR do i8=0_8,ao_integrals_map%map_size n_elements = n_elements_max diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index 029c444d..67150787 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -133,6 +133,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & !open(unit=10,file='OUTPUT',form='FORMATTED') ! END INPUT DATA + call omp_set_nested(.true.) !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & !$OMP a_start,a_end,b_start,b_end,c_start,c_end,d_start,d_end,& !$OMP i_start,i_end,j_start,j_end,k_start,k_end,l_start,l_end,& @@ -140,8 +141,6 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & !$OMP matrix_B,l_pointer,thread,task_id) & !$OMP PRIVATE(key,value,T,U,V,i,j,k,l,idx,ik,ll, & !$OMP a,b,c,d,p,q,tmp,T2d,V2d,ii,zmq_socket_push) - allocate( key(i_max*j_max*k_max), value(i_max*j_max*k_max) ) - allocate( U(a_start:a_end, c_start:c_end, b_start:b_end) ) integer(ZMQ_PTR) :: zmq_socket_push integer(ZMQ_PTR), external :: new_zmq_push_socket @@ -149,13 +148,10 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & - allocate( T2d((i_end-i_start+1)*(k_end-k_start+2)/2, j_start:j_end), & - V2d((i_end-i_start+1)*(k_end-k_start+2)/2, b_start:b_end), & - V(i_start:i_end, k_start:k_end), & - T(k_start:k_end, a_start:a_end)) + allocate( U(a_start:a_end, c_start:c_end, b_start:b_end) ) - !$OMP DO SCHEDULE(dynamic) + !$OMP DO SCHEDULE(dynamic,1) do d=d_start,d_end U = 0.d0 do l=l_start,l_end @@ -163,6 +159,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & cycle endif + allocate( T2d((i_end-i_start+1)*(k_end-k_start+2)/2, j_start:j_end) ) ii=l_pointer(l) do j=j_start,j_end !DIR$ VECTOR NONTEMPORAL @@ -174,13 +171,21 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & enddo enddo + allocate (V2d((i_end-i_start+1)*(k_end-k_start+2)/2, b_start:b_end)) call DGEMM('N','N', ishft( (i_end-i_start+1)*(i_end-i_start+2), -1),& (d-b_start+1), & (j_end-j_start+1), 1.d0, & T2d(1,j_start), size(T2d,1), & matrix_B(j_start,b_start), size(matrix_B,1),0.d0, & V2d(1,b_start), size(V2d,1) ) + deallocate(T2d) + !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & + !$OMP a_start,b_start,b_end,c_start,c_end,i_start,k_start,k_end, & + !$OMP matrix_B,U,l,d,V2d,i_end,a_end) & + !$OMP PRIVATE(T,V,i,k,ik) + allocate( V(i_start:i_end, k_start:k_end), T(k_start:k_end, a_start:a_end)) + !$OMP DO SCHEDULE(static,1) do b=b_start,d ik = 0 do k=k_start,k_end @@ -190,42 +195,18 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & enddo enddo -! T = 0.d0 -! do a=a_start,b -! do k=k_start,k_end -! do i=i_start,k -! T(k,a) = T(k,a) + V(i,k)*matrix_B(i,a) -! enddo -! do i=k+1,i_end -! T(k,a) = T(k,a) + V(k,i)*matrix_B(i,a) -! enddo -! enddo -! enddo call DSYMM('L','U', (k_end-k_start+1), (b-a_start+1), & 1.d0, & V(i_start,k_start), size(V,1), & matrix_B(i_start,a_start), size(matrix_B,1),0.d0, & T(k_start,a_start), size(T,1) ) -! do c=c_start,b -! do a=a_start,c -! do k=k_start,k_end -! U(a,c,b) = U(a,c,b) + T(k,a)*matrix_B(k,c)*matrix_B(l,d) -! enddo -! enddo -! enddo call DGEMM('T','N', (b-a_start+1), (b-c_start+1), & (k_end-k_start+1), matrix_B(l, d), & T(k_start,a_start), size(T,1), & matrix_B(k_start,c_start), size(matrix_B,1), 1.d0, & U(a_start,c_start,b), size(U,1) ) -! do c=b+1,c_end -! do a=a_start,b -! do k=k_start,k_end -! U(a,c,b) = U(a,c,b) + T(k,a)*matrix_B(k,c)*matrix_B(l,d) -! enddo -! enddo -! enddo + if (b < b_end) then call DGEMM('T','N', (b-a_start+1), (c_end-b), & (k_end-k_start+1), matrix_B(l, d), & @@ -234,11 +215,15 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & U(a_start,b+1,b), size(U,1) ) endif enddo + deallocate(T,V) + !$OMP END PARALLEL + deallocate(V2d) enddo idx = 0_8 + allocate( key(i_max*j_max*k_max), value(i_max*j_max*k_max) ) integer :: p, q do b=b_start,d q = b+ishft(d*d-d,-1) @@ -259,6 +244,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & enddo call four_idx_push_results(zmq_socket_push, key, value, idx, -task_id) + deallocate(key,value) !WRITE OUTPUT ! OMP CRITICAL @@ -279,7 +265,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & enddo !$OMP END DO - deallocate(key,value,V,T,U,T2d,V2d) + deallocate(U) !$OMP BARRIER !$OMP MASTER call four_idx_push_results(zmq_socket_push, 0_8, 0.d0, 0, task_id) From 2ede44f48386ef343220795834e484b9cd2ae08e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 12 Dec 2017 16:56:14 +0100 Subject: [PATCH 18/54] Genius amazing parallelism --- src/FourIdx/four_index_slave.irp.f | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index 67150787..7a69cd58 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -69,7 +69,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & integer :: npass, l_block tempspace = (new_size * 16_8) / (1024_8 * 1024_8) - npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 1024_8),4) ! 1 GiB of scratch space + npass = int(min(1_8+int(l_end-l_start,8),1_8 + tempspace / 1024_8),4) ! 1 GiB of scratch space l_block = (l_end-l_start+1)/npass allocate(a_array_ik(new_size/npass), a_array_j(new_size/npass), a_array_value(new_size/npass)) @@ -133,12 +133,15 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & !open(unit=10,file='OUTPUT',form='FORMATTED') ! END INPUT DATA + PROVIDE nproc + integer :: n_running_threads + n_running_threads = 0 call omp_set_nested(.true.) !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & !$OMP a_start,a_end,b_start,b_end,c_start,c_end,d_start,d_end,& !$OMP i_start,i_end,j_start,j_end,k_start,k_end,l_start,l_end,& !$OMP i_min,i_max,j_min,j_max,k_min,k_max,l_min,l_max, & - !$OMP matrix_B,l_pointer,thread,task_id) & + !$OMP matrix_B,l_pointer,thread,task_id,n_running_threads,nproc) & !$OMP PRIVATE(key,value,T,U,V,i,j,k,l,idx,ik,ll, & !$OMP a,b,c,d,p,q,tmp,T2d,V2d,ii,zmq_socket_push) @@ -150,6 +153,8 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & allocate( U(a_start:a_end, c_start:c_end, b_start:b_end) ) + !$OMP ATOMIC + n_running_threads = n_running_threads+1 !$OMP DO SCHEDULE(dynamic,1) do d=d_start,d_end @@ -183,7 +188,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & !$OMP a_start,b_start,b_end,c_start,c_end,i_start,k_start,k_end, & !$OMP matrix_B,U,l,d,V2d,i_end,a_end) & - !$OMP PRIVATE(T,V,i,k,ik) + !$OMP PRIVATE(T,V,i,k,ik) NUM_THREADS(nproc-n_running_threads+1) allocate( V(i_start:i_end, k_start:k_end), T(k_start:k_end, a_start:a_end)) !$OMP DO SCHEDULE(static,1) do b=b_start,d @@ -266,6 +271,10 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & enddo !$OMP END DO deallocate(U) + + !$OMP ATOMIC + n_running_threads = n_running_threads-1 + !$OMP BARRIER !$OMP MASTER call four_idx_push_results(zmq_socket_push, 0_8, 0.d0, 0, task_id) From 31b3b7dd797f0c5f399b4e028da65404fc5e4fab Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 12 Dec 2017 22:56:09 +0100 Subject: [PATCH 19/54] Fixed 4 idx --- src/FourIdx/four_index_slave.irp.f | 22 +++------------------- 1 file changed, 3 insertions(+), 19 deletions(-) diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index 7a69cd58..28859c9a 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -185,9 +185,10 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & V2d(1,b_start), size(V2d,1) ) deallocate(T2d) + !$OMP FLUSH(n_running_threads) !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & !$OMP a_start,b_start,b_end,c_start,c_end,i_start,k_start,k_end, & - !$OMP matrix_B,U,l,d,V2d,i_end,a_end) & + !$OMP matrix_B,U,l,d,V2d,i_end,a_end,n_running_threads) & !$OMP PRIVATE(T,V,i,k,ik) NUM_THREADS(nproc-n_running_threads+1) allocate( V(i_start:i_end, k_start:k_end), T(k_start:k_end, a_start:a_end)) !$OMP DO SCHEDULE(static,1) @@ -251,25 +252,8 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & call four_idx_push_results(zmq_socket_push, key, value, idx, -task_id) deallocate(key,value) -!WRITE OUTPUT -! OMP CRITICAL -!print *, d -!do b=b_start,d -! do c=c_start,c_end -! do a=a_start,min(b,c) -! if (dabs(U(a,c,b)) < 1.d-15) then -! cycle -! endif -! write(10,*) d,c,b,a,U(a,c,b) -! enddo -! enddo -!enddo -! OMP END CRITICAL -!END WRITE OUTPUT - - enddo - !$OMP END DO + !$OMP END DO NOWAIT deallocate(U) !$OMP ATOMIC From af229e702829fe8da7de631e4d830e83d6316e35 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 14 Dec 2017 14:01:30 +0100 Subject: [PATCH 20/54] Load balancing in 4idx --- src/FourIdx/four_index_slave.irp.f | 46 +++++++++++------------------- src/FourIdx/four_index_zmq.irp.f | 26 +++++++---------- 2 files changed, 28 insertions(+), 44 deletions(-) diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index 28859c9a..bc967528 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -2,7 +2,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & i_start, j_start, k_start, l_start, & i_end , j_end , k_end , l_end , & a_start, b_start, c_start, d_start, & - a_end , b_end , c_end , d_end, task_id, thread ) + a_end , b_end , c_end , d_end, task_id, worker_id, thread ) implicit none use f77_zmq use map_module @@ -19,7 +19,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & integer, intent(in) :: i_end , j_end , k_end , l_end integer, intent(in) :: a_start, b_start, c_start, d_start integer, intent(in) :: a_end , b_end , c_end , d_end - integer, intent(in) :: task_id, thread + integer, intent(in) :: task_id, thread, worker_id double precision, allocatable :: T(:,:), U(:,:,:), V(:,:) double precision, allocatable :: T2d(:,:), V2d(:,:) @@ -63,13 +63,13 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & double precision, allocatable :: a_array_value(:) integer*8 :: new_size - new_size = max(1024_8, 5_8 * map_a % n_elements ) + new_size = max(2048_8, 5_8 * map_a % n_elements ) integer*8 :: tempspace integer :: npass, l_block - tempspace = (new_size * 16_8) / (1024_8 * 1024_8) - npass = int(min(1_8+int(l_end-l_start,8),1_8 + tempspace / 1024_8),4) ! 1 GiB of scratch space + tempspace = (new_size * 16_8) / (2048_8 * 2048_8) + npass = int(min(1_8+int(l_end-l_start,8),1_8 + tempspace / 2048_8),4) ! 2 GiB of scratch space l_block = (l_end-l_start+1)/npass allocate(a_array_ik(new_size/npass), a_array_j(new_size/npass), a_array_value(new_size/npass)) @@ -133,17 +133,13 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & !open(unit=10,file='OUTPUT',form='FORMATTED') ! END INPUT DATA - PROVIDE nproc - integer :: n_running_threads - n_running_threads = 0 - call omp_set_nested(.true.) !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & !$OMP a_start,a_end,b_start,b_end,c_start,c_end,d_start,d_end,& !$OMP i_start,i_end,j_start,j_end,k_start,k_end,l_start,l_end,& !$OMP i_min,i_max,j_min,j_max,k_min,k_max,l_min,l_max, & - !$OMP matrix_B,l_pointer,thread,task_id,n_running_threads,nproc) & - !$OMP PRIVATE(key,value,T,U,V,i,j,k,l,idx,ik,ll, & - !$OMP a,b,c,d,p,q,tmp,T2d,V2d,ii,zmq_socket_push) + !$OMP matrix_B,l_pointer,thread,task_id,worker_id) & + !$OMP PRIVATE(key,value,T,U,V,i,j,k,l,idx,ik,ll,zmq_to_qp_run_socket, & + !$OMP a,b,c,d,p,q,tmp,T2d,V2d,ii,zmq_socket_push) integer(ZMQ_PTR) :: zmq_socket_push integer(ZMQ_PTR), external :: new_zmq_push_socket @@ -153,9 +149,6 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & allocate( U(a_start:a_end, c_start:c_end, b_start:b_end) ) - !$OMP ATOMIC - n_running_threads = n_running_threads+1 - !$OMP DO SCHEDULE(dynamic,1) do d=d_start,d_end U = 0.d0 @@ -185,13 +178,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & V2d(1,b_start), size(V2d,1) ) deallocate(T2d) - !$OMP FLUSH(n_running_threads) - !$OMP PARALLEL DEFAULT(NONE) SHARED(a_array_ik,a_array_j,a_array_value, & - !$OMP a_start,b_start,b_end,c_start,c_end,i_start,k_start,k_end, & - !$OMP matrix_B,U,l,d,V2d,i_end,a_end,n_running_threads) & - !$OMP PRIVATE(T,V,i,k,ik) NUM_THREADS(nproc-n_running_threads+1) allocate( V(i_start:i_end, k_start:k_end), T(k_start:k_end, a_start:a_end)) - !$OMP DO SCHEDULE(static,1) do b=b_start,d ik = 0 do k=k_start,k_end @@ -221,10 +208,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & U(a_start,b+1,b), size(U,1) ) endif enddo - deallocate(T,V) - !$OMP END PARALLEL - - deallocate(V2d) + deallocate(T,V,V2d) enddo idx = 0_8 @@ -253,19 +237,23 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & deallocate(key,value) enddo - !$OMP END DO NOWAIT deallocate(U) - !$OMP ATOMIC - n_running_threads = n_running_threads-1 - !$OMP BARRIER !$OMP MASTER + integer(ZMQ_PTR) :: zmq_to_qp_run_socket + integer(ZMQ_PTR), external :: task_done_to_taskserver, new_zmq_to_qp_run_socket + zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() + if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id) == -1) then + stop 'Unable to send task done' + endif call four_idx_push_results(zmq_socket_push, 0_8, 0.d0, 0, task_id) + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) !$OMP END MASTER call end_zmq_push_socket(zmq_socket_push) !$OMP END PARALLEL + deallocate(l_pointer,a_array_ik,a_array_j,a_array_value) end diff --git a/src/FourIdx/four_index_zmq.irp.f b/src/FourIdx/four_index_zmq.irp.f index 4e0673b1..5fffe999 100644 --- a/src/FourIdx/four_index_zmq.irp.f +++ b/src/FourIdx/four_index_zmq.irp.f @@ -62,13 +62,13 @@ subroutine four_index_transform_zmq(map_a,map_c,matrix_B,LDB, & call new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'four_idx') integer*8 :: new_size - new_size = max(1024_8, 5_8 * map_a % n_elements ) + new_size = max(2048_8, 5_8 * map_a % n_elements ) integer :: npass integer*8 :: tempspace - tempspace = (new_size * 16_8) / (1024_8 * 1024_8) - npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 1024_8),4) ! 1 GiB of scratch space + tempspace = (new_size * 16_8) / (2048_8 * 2048_8) + npass = int(min(int(l_end-l_start,8),1_8 + tempspace / 2048_8),4) ! 2 GiB of scratch space l_block = (l_end-l_start+1)/npass ! Create tasks @@ -98,9 +98,11 @@ subroutine four_index_transform_zmq(map_a,map_c,matrix_B,LDB, & PROVIDE nproc + integer :: ithread, sqnproc + sqnproc = int(sqrt(float(nproc))+0.5) call omp_set_nested(.True.) - integer :: ithread - !$OMP PARALLEL NUM_THREADS(2) PRIVATE(ithread) + call omp_set_dynamic(.True.) + !$OMP PARALLEL NUM_THREADS(1+max(1,sqnproc)) PRIVATE(ithread) ithread = omp_get_thread_num() if (ithread==0) then call four_idx_collector(zmq_socket_pull,map_c) @@ -178,19 +180,13 @@ subroutine four_index_transform_slave(thread,worker_id) i_end , j_end , k_end , l_end_block , & a_start, b_start, c_start, d_start, & a_end , b_end , c_end , d_end, & - task_id, thread) + task_id, worker_id, thread) - integer, external :: task_done_to_taskserver - if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id) == -1) then - print *, irp_here, ': Unable to send task_done' - stop - endif enddo integer, external :: disconnect_from_taskserver if (disconnect_from_taskserver(zmq_to_qp_run_socket,thread) == -1) then - call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) - return + continue endif call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) @@ -287,8 +283,6 @@ subroutine four_idx_pull_results(zmq_socket_pull, map_c, task_id) rc8 = f77_zmq_recv8( zmq_socket_pull, value, int(integral_kind*sze,8), 0) if(rc8 /= integral_kind*sze) stop 'four_idx_pull_results failed to pull value' - call map_update(map_c, key, value, sze, mo_integrals_threshold) - ! Activate if zmq_socket_pull is a REP IRP_IF ZMQ_PUSH IRP_ELSE @@ -299,6 +293,8 @@ subroutine four_idx_pull_results(zmq_socket_pull, map_c, task_id) endif IRP_ENDIF + call map_update(map_c, key, value, sze, mo_integrals_threshold) + deallocate(key, value) end From 816e70a683ea6550c33d1d942080b79b82009fcf Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 14 Dec 2017 19:03:51 +0100 Subject: [PATCH 21/54] Added symmetry detection --- plugins/Symmetry/NEEDED_CHILDREN_MODULES | 1 + plugins/Symmetry/README.rst | 12 + plugins/Symmetry/Symmetry.main.irp.f | 30 +++ plugins/Symmetry/aos.irp.f | 113 ++++++++ plugins/Symmetry/find_sym.irp.f | 318 +++++++++++++++++++++++ src/Nuclei/inertia.irp.f | 32 +++ src/Nuclei/nuclei.irp.f | 149 ++++++++++- 7 files changed, 652 insertions(+), 3 deletions(-) create mode 100644 plugins/Symmetry/NEEDED_CHILDREN_MODULES create mode 100644 plugins/Symmetry/README.rst create mode 100644 plugins/Symmetry/Symmetry.main.irp.f create mode 100644 plugins/Symmetry/aos.irp.f create mode 100644 plugins/Symmetry/find_sym.irp.f create mode 100644 src/Nuclei/inertia.irp.f diff --git a/plugins/Symmetry/NEEDED_CHILDREN_MODULES b/plugins/Symmetry/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..7ea84ba4 --- /dev/null +++ b/plugins/Symmetry/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bitmask Nuclei Determinants diff --git a/plugins/Symmetry/README.rst b/plugins/Symmetry/README.rst new file mode 100644 index 00000000..ba643f88 --- /dev/null +++ b/plugins/Symmetry/README.rst @@ -0,0 +1,12 @@ +======== +Symmetry +======== + +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f new file mode 100644 index 00000000..d8d2f350 --- /dev/null +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -0,0 +1,30 @@ +program Symmetry + implicit none + BEGIN_DOC +! TODO + END_DOC + integer :: n_sym_points, i, j + double precision, allocatable :: tmp(:,:), sym_points(:,:) + character*8 :: sym + n_sym_points = 3 + + print *, 'Molecule is linear:', molecule_is_linear + print *, 'Has center of inversion:', molecule_has_center_of_inversion + print *, 'Symmetry rotation axis:', sym_rotation_axis(:) + call find_symmetry(sym) + print *, 'Group:'//sym + return + allocate(tmp(n_sym_points,n_det), sym_points(3,n_sym_points)) + + call generate_sym_coord(n_sym_points,sym_points) + call compute_sym_det_values(sym_points,n_sym_points,tmp) + do i=1,mo_tot_num + print *, i, real(tmp(1:3,i)) + enddo + sym_points(1,:) = -sym_points(1,:) + call compute_sym_det_values(sym_points,n_sym_points,tmp) + do i=1,n_det + print *, i, real(tmp(1:3,i)) + enddo + +end diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f new file mode 100644 index 00000000..97b7aa62 --- /dev/null +++ b/plugins/Symmetry/aos.irp.f @@ -0,0 +1,113 @@ +BEGIN_PROVIDER [ double precision, sym_box, (3,2) ] + implicit none + BEGIN_DOC + ! Opposite points of the box containing the molecule + END_DOC + integer :: i,xyz + sym_box(:,:) = 0.d0 + do xyz=1,3 + do i=1,nucl_num + sym_box(xyz,1) = min(sym_box(xyz,1), nucl_coord(i,xyz)) + sym_box(xyz,2) = max(sym_box(xyz,2), nucl_coord(i,xyz)) + enddo + enddo + sym_box(:,1) = sym_box(:,1) - 2.d0 + sym_box(:,2) = sym_box(:,2) + 2.d0 +END_PROVIDER + +subroutine generate_sym_coord(n_sym_points,result) + implicit none + integer, intent(in) :: n_sym_points + double precision, intent(out) :: result(3,n_sym_points) + BEGIN_DOC + ! xyz coordinates of points to check the symmetry, drawn uniformly in the molecular box. + END_DOC + integer :: i, xyz + + call random_number(result) + do xyz=1,3 + result(xyz,:) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) + enddo + +end + + +subroutine compute_sym_ao_values(sym_points, n_sym_points, result) + implicit none + BEGIN_DOC + ! Values of the AO symmetry functions + END_DOC + integer, intent(in) :: n_sym_points + double precision, intent(in) :: sym_points(3,n_sym_points) + double precision, intent(out) :: result(n_sym_points, ao_num) + integer :: i, j + double precision :: x, y, z + result (:,:) = 0.d0 + do j=1,ao_num + do i=1,n_sym_points + x = sym_points(1,i) - nucl_coord_transp(1,ao_nucl(j)) + y = sym_points(2,i) - nucl_coord_transp(2,ao_nucl(j)) + z = sym_points(3,i) - nucl_coord_transp(3,ao_nucl(j)) + x = x**ao_power(j,1) + y = y**ao_power(j,2) + z = z**ao_power(j,3) + result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) + enddo + enddo + +end + +subroutine compute_sym_mo_values(sym_points, n_sym_points, result) + implicit none + BEGIN_DOC + ! Values of the MO symmetry functions + END_DOC + integer, intent(in) :: n_sym_points + double precision, intent(in) :: sym_points(3,n_sym_points) + double precision, intent(out) :: result(n_sym_points, mo_tot_num) + + double precision, allocatable :: tmp(:,:) + allocate(tmp(n_sym_points,ao_num)) + call compute_sym_ao_values(sym_points,n_sym_points,tmp) + call dgemm('N','N',n_sym_points,mo_tot_num,ao_num, & + 1.d0, tmp,size(tmp,1), mo_coef, size(mo_coef,1), & + 0.d0, result,size(result,1)) + deallocate(tmp) +end + + +subroutine compute_sym_det_values(sym_points, n_sym_points, result) + use bitmasks + implicit none + BEGIN_DOC + ! Values of the determinant symmetry functions + END_DOC + integer, intent(in) :: n_sym_points + double precision, intent(in) :: sym_points(3,n_sym_points) + double precision, intent(out) :: result(n_sym_points, N_det) + + integer :: list(N_int*bit_kind_size,2) + integer :: n_elements(2) + + integer :: i, j, imo + + double precision, allocatable :: tmp(:,:) + + allocate(tmp(n_sym_points,mo_tot_num)) + call compute_sym_mo_values(sym_points, n_sym_points, tmp) + + result = 1.d0 + do i=1,N_det + call bitstring_to_list_ab(psi_det(1,1,i), list, n_elements, N_int) + do j=1,n_elements(1) + imo = list(j,1) + result(:,i) *= tmp(:,imo) + enddo + do j=1,n_elements(2) + imo = list(j,2) + result(:,i) *= tmp(:,imo) + enddo + enddo + + deallocate(tmp) +end diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f new file mode 100644 index 00000000..4a100805 --- /dev/null +++ b/plugins/Symmetry/find_sym.irp.f @@ -0,0 +1,318 @@ +BEGIN_PROVIDER [ logical, molecule_is_linear ] + implicit none + BEGIN_DOC + ! True if the molecule is linear + END_DOC + molecule_is_linear = (minval(inertia_tensor_eigenvalues) < 1.d-5) +END_PROVIDER + +BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] + implicit none + BEGIN_DOC + ! If true, there is a center of inversion in the WF + END_DOC + molecule_has_center_of_inversion = .True. + integer :: i,j,k + double precision :: point(3) + logical :: found + double precision, external :: u_dot_u + do i=1,nucl_num + found = .False. + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + if (u_dot_u(point,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_center_of_inversion = .False. + exit + endif + enddo + +END_PROVIDER + + +BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] + implicit none + BEGIN_DOC + ! Order of the rotation axis + END_DOC + include 'constants.include.F' + + integer :: i,j,k + double precision :: point(3), point2(3) + logical :: found + double precision, external :: u_dot_u + integer :: iorder, iaxis + double precision :: theta, sin_t, cos_t + do iaxis=1,3 + do iorder=12,2,-1 + sym_rotation_axis(iaxis) = iorder + theta = 2.d0*pi/dble(iorder) + sin_t = dsin(theta) + cos_t = dcos(theta) + do i=1,nucl_num + found = .False. + if (iaxis==1) then + point(1) = nucl_coord_transp(1,i) + point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t + else if (iaxis==2) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(2) = nucl_coord_transp(2,i) + point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t + endif + if (iaxis==3) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t + point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t + point(3) = nucl_coord_transp(3,i) + endif + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point2(:) = nucl_coord_transp(:,j) - point(:) + if (u_dot_u(point2,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + sym_rotation_axis(iaxis) = 1 + exit + endif + enddo + if (sym_rotation_axis(iaxis) /= 1) then + exit + endif + enddo + enddo + +END_PROVIDER + + BEGIN_PROVIDER [ integer, molecule_principal_axis ] +&BEGIN_PROVIDER [ integer, molecule_secondary_axis ] +&BEGIN_PROVIDER [ integer, molecule_ternary_axis ] + implicit none + BEGIN_DOC +! Which axis is the Z axis + END_DOC + molecule_principal_axis = maxloc(sym_rotation_axis,1) + if (molecule_principal_axis == 1) then + if (sym_rotation_axis(2) >= sym_rotation_axis(3)) then + molecule_secondary_axis = 2 + molecule_ternary_axis = 3 + else + molecule_secondary_axis = 3 + molecule_ternary_axis = 2 + endif + else if (molecule_principal_axis == 2) then + if (sym_rotation_axis(1) >= sym_rotation_axis(3)) then + molecule_secondary_axis = 1 + molecule_ternary_axis = 3 + else + molecule_secondary_axis = 3 + molecule_ternary_axis = 1 + endif + else if (molecule_principal_axis == 3) then + if (sym_rotation_axis(1) >= sym_rotation_axis(2)) then + molecule_secondary_axis = 1 + molecule_ternary_axis = 2 + else + molecule_secondary_axis = 2 + molecule_ternary_axis = 1 + endif + endif +END_PROVIDER + +BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] + implicit none + BEGIN_DOC +! If true, the molecule has a C2 rotation perpendicular to the main axis + END_DOC + if (molecule_principal_axis == 1) then + molecule_has_secondary_c2_rotation = (sym_rotation_axis(2)==2) .or. (sym_rotation_axis(3)==2) + else if (molecule_principal_axis == 2) then + molecule_has_secondary_c2_rotation = (sym_rotation_axis(1)==2) .or. (sym_rotation_axis(3)==2) + else if (molecule_principal_axis == 3) then + molecule_has_secondary_c2_rotation = (sym_rotation_axis(1)==2) .or. (sym_rotation_axis(2)==2) + endif +END_PROVIDER + + +BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] + implicit none + BEGIN_DOC + ! Order of the rotation axis + END_DOC + include 'constants.include.F' + + integer :: i,j,k + double precision :: point(3), point2(3) + logical :: found + double precision, external :: u_dot_u + integer :: iorder, iaxis + double precision :: theta, sin_t, cos_t + iaxis=molecule_principal_axis + iorder = 2*sym_rotation_axis(iaxis) + molecule_has_improper_rotation = .True. + theta = 2.d0*pi/dble(iorder) + sin_t = dsin(theta) + cos_t = dcos(theta) + do i=1,nucl_num + found = .False. + if (iaxis==1) then + point(1) = -nucl_coord_transp(1,i) + point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t + else if (iaxis==2) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t + point(2) = -nucl_coord_transp(2,i) + point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t + endif + if (iaxis==3) then + point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t + point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t + point(3) = -nucl_coord_transp(3,i) + endif + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point2(:) = nucl_coord_transp(:,j) - point(:) + if (u_dot_u(point2,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_improper_rotation = .False. + exit + endif + enddo + +END_PROVIDER + +BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] + implicit none + BEGIN_DOC + ! If true, there is a center of inversion in the WF + END_DOC + molecule_has_center_of_inversion = .True. + integer :: i,j,k + double precision :: point(3) + logical :: found + double precision, external :: u_dot_u + do i=1,nucl_num + found = .False. + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + if (u_dot_u(point,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_center_of_inversion = .False. + exit + endif + enddo + +END_PROVIDER + + +BEGIN_PROVIDER [ logical, molecule_has_sigma_plane, (3) ] + implicit none + BEGIN_DOC + ! If true, there is a symmetry plane perpendicular to the main axis + END_DOC + integer :: i,j,k + double precision :: point(3), point2(3) + logical :: found + double precision, external :: u_dot_u + integer :: iaxis + do iaxis=1,3 + molecule_has_sigma_plane(iaxis) = .True. + do i=1,nucl_num + found = .False. + point(:) = nucl_coord_transp(:,i) + point(iaxis) = -point(iaxis) + do j=1,nucl_num + if (nucl_charge(i) /= nucl_charge(j)) cycle + point2(:) = nucl_coord_transp(:,j) - point(:) + if (u_dot_u(point2,3) < 1.d-5) then + found = .True. + exit + endif + enddo + if (.not.found) then + molecule_has_sigma_plane(iaxis) = .False. + exit + endif + enddo + enddo + +END_PROVIDER + +subroutine find_symmetry(result) + implicit none + BEGIN_DOC +! Finds the point group of the molecule + END_DOC + character*16 :: result + character*2, save :: i_to_a(24) = (/ '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',& + '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24' /) + result = 'C1' + if (molecule_is_linear) then + if (molecule_has_center_of_inversion) then + result = 'D*h' + else + result = 'C*v' + endif + else + if (maxval(sym_rotation_axis) == 1) then + if (molecule_has_sigma_plane(1).or.molecule_has_sigma_plane(2).or.& + molecule_has_sigma_plane(3) ) then + result = 'Cs' + else + if (molecule_has_center_of_inversion) then + result = 'Ci' + endif + endif + else + if (molecule_has_secondary_c2_rotation) then + if (molecule_has_sigma_plane(molecule_principal_axis)) then + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + else + if (molecule_has_sigma_plane(molecule_secondary_axis)) then + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + else + if (molecule_has_sigma_plane(molecule_ternary_axis)) then + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + else + result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + endif + endif + endif + else + if (molecule_has_sigma_plane(molecule_principal_axis)) then + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + else + if (molecule_has_sigma_plane(molecule_secondary_axis)) then + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + else + if (molecule_has_sigma_plane(molecule_ternary_axis)) then + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + else + if (molecule_has_improper_rotation) then + result = 'S'//trim(i_to_a(2*sym_rotation_axis(molecule_principal_axis))) + else + result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + endif + endif + endif + endif + endif + endif + endif +end diff --git a/src/Nuclei/inertia.irp.f b/src/Nuclei/inertia.irp.f new file mode 100644 index 00000000..c4517cde --- /dev/null +++ b/src/Nuclei/inertia.irp.f @@ -0,0 +1,32 @@ +BEGIN_PROVIDER [ double precision, inertia_tensor, (3,3) ] + implicit none + BEGIN_DOC + ! Inertia tensor + END_DOC + integer :: i,j,k + inertia_tensor = 0.d0 + do k=1,nucl_num + inertia_tensor(1,1) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) + inertia_tensor(2,2) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) + inertia_tensor(3,3) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2) + inertia_tensor(1,2) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) ) + inertia_tensor(1,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + inertia_tensor(2,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + enddo + inertia_tensor(2,1) = inertia_tensor(1,2) + inertia_tensor(3,1) = inertia_tensor(1,3) + inertia_tensor(3,2) = inertia_tensor(2,3) +END_PROVIDER + + BEGIN_PROVIDER [ double precision, inertia_tensor_eigenvectors, (3,3) ] +&BEGIN_PROVIDER [ double precision, inertia_tensor_eigenvalues , (3) ] + implicit none + BEGIN_DOC + ! Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation. + END_DOC + integer :: k + call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,inertia_tensor,3,3) + print *, 'Rotational constants (GHZ):' + print *, (1805.65468542d0/inertia_tensor_eigenvalues(k), k=3,1,-1) +END_PROVIDER + diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 307a9610..43609506 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -1,4 +1,4 @@ -BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] +BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] implicit none BEGIN_DOC @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] if (mpi_master) then double precision, allocatable :: buffer(:,:) - nucl_coord = 0.d0 + nucl_coord_input = 0.d0 allocate (buffer(nucl_num,3)) buffer = 0.d0 logical :: has @@ -22,7 +22,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] do i=1,3 do j=1,nucl_num - nucl_coord(j,i) = buffer(j,i) + nucl_coord_input(j,i) = buffer(j,i) enddo enddo deallocate(buffer) @@ -31,6 +31,65 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 + call write_time(output_Nuclei) + write(output_Nuclei,'(A)') '' + write(output_Nuclei,'(A)') 'Input Nuclear Coordinates (Angstroms)' + write(output_Nuclei,'(A)') '=====================================' + write(output_Nuclei,'(A)') '' + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,*) & + ' Atom Charge X Y Z ' + write(output_Nuclei,ft) & + '================','============','============','============','============' + do i=1,nucl_num + write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & + nucl_coord_input(i,1)*a0, & + nucl_coord_input(i,2)*a0, & + nucl_coord_input(i,3)*a0 + enddo + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,'(A)') '' + + endif + + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nucl_coord_input, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nucl_coord_input with MPI' + endif + IRP_ENDIF + +END_PROVIDER + +BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] + implicit none + + BEGIN_DOC + ! Nuclear coordinates in standard orientation + END_DOC + + if (mpi_master) then + integer :: i + do i=1,nucl_num + nucl_coord(i,1) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) + nucl_coord(i,2) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) + nucl_coord(i,3) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) + enddo + + character*(64), parameter :: f = '(A16, 4(1X,F12.6))' + character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' + double precision, parameter :: a0= 0.529177249d0 + call write_time(output_Nuclei) write(output_Nuclei,'(A)') '' write(output_Nuclei,'(A)') 'Nuclear Coordinates (Angstroms)' @@ -285,3 +344,87 @@ BEGIN_PROVIDER [ character*(128), element_name, (78)] element_name(78) = 'Pt' END_PROVIDER + +BEGIN_PROVIDER [ double precision, mass, (0:110) ] + implicit none + BEGIN_DOC + ! Atomic masses + END_DOC + + mass( 0 ) = 0. + mass( 1 ) = 1.0079 + mass( 2 ) = 4.00260 + mass( 3 ) = 6.941 + mass( 4 ) = 9.01218 + mass( 5 ) = 10.81 + mass( 6 ) = 12.011 + mass( 7 ) = 14.0067 + mass( 8 ) = 15.9994 + mass( 9 ) = 18.998403 + mass( 10 ) = 20.179 + mass( 11 ) = 22.98977 + mass( 12 ) = 24.305 + mass( 13 ) = 26.98154 + mass( 14 ) = 28.0855 + mass( 15 ) = 30.97376 + mass( 16 ) = 32.06 + mass( 17 ) = 35.453 + mass( 18 ) = 39.948 + mass( 19 ) = 39.0983 + mass( 20 ) = 40.08 + mass( 21 ) = 44.9559 + mass( 22 ) = 47.90 + mass( 23 ) = 50.9415 + mass( 24 ) = 51.996 + mass( 25 ) = 54.9380 + mass( 26 ) = 55.9332 + mass( 27 ) = 58.9332 + mass( 28 ) = 58.70 + mass( 29 ) = 63.546 + mass( 30 ) = 65.38 + mass( 31 ) = 69.72 + mass( 32 ) = 72.59 + mass( 33 ) = 74.9216 + mass( 34 ) = 78.96 + mass( 35 ) = 79.904 + mass( 36 ) = 83.80 + mass( 37 ) = 85.4678 + mass( 38 ) = 87.62 + mass( 39 ) = 88.90584 + mass( 40 ) = 91.224 + mass( 41 ) = 92.90637 + mass( 42 ) = 95.95 + mass( 43 ) = 98. + mass( 44 ) = 101.07 + mass( 45 ) = 102.90550 + mass( 46 ) = 106.42 + mass( 47 ) = 107.8682 + mass( 48 ) = 112.414 + mass( 49 ) = 114.818 + mass( 50 ) = 118.710 + mass( 51 ) = 121.760 + mass( 52 ) = 127.60 + mass( 53 ) = 126.90447 + mass( 54 ) = 131.293 + mass( 78 ) = 195.084 +END_PROVIDER + +BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] + implicit none + BEGIN_DOC + ! Center of mass of the molecule + END_DOC + integer :: i,j + double precision :: s + center_of_mass(:) = 0.d0 + s = 0.d0 + do i=1,nucl_num + do j=1,3 + center_of_mass(j) += nucl_coord_input(i,j)* mass(int(nucl_charge(i))) + enddo + s += mass(int(nucl_charge(i))) + enddo + s = 1.d0/s + center_of_mass(:) = center_of_mass(:)*s +END_PROVIDER + From 407abf5d77cebd8448c7805232e683537f147ab9 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 15 Dec 2017 19:24:18 +0100 Subject: [PATCH 22/54] Added character tables --- data/Symmetry/C1 | 10 + data/Symmetry/C10 | 20 ++ data/Symmetry/C10h | 32 ++++ data/Symmetry/C10v | 24 +++ data/Symmetry/C11 | 20 ++ data/Symmetry/C11h | 32 ++++ data/Symmetry/C11v | 22 +++ data/Symmetry/C12 | 22 +++ data/Symmetry/C12h | 36 ++++ data/Symmetry/C12v | 26 +++ data/Symmetry/C13 | 22 +++ data/Symmetry/C13h | 36 ++++ data/Symmetry/C13v | 24 +++ data/Symmetry/C14 | 24 +++ data/Symmetry/C14h | 40 ++++ data/Symmetry/C14v | 28 +++ data/Symmetry/C15 | 24 +++ data/Symmetry/C15h | 40 ++++ data/Symmetry/C15v | 26 +++ data/Symmetry/C16 | 26 +++ data/Symmetry/C16h | 44 +++++ data/Symmetry/C16v | 30 +++ data/Symmetry/C17 | 26 +++ data/Symmetry/C17h | 44 +++++ data/Symmetry/C17v | 28 +++ data/Symmetry/C18 | 28 +++ data/Symmetry/C18h | 48 +++++ data/Symmetry/C18v | 32 ++++ data/Symmetry/C19 | 28 +++ data/Symmetry/C19h | 48 +++++ data/Symmetry/C19v | 30 +++ data/Symmetry/C1h | 12 ++ data/Symmetry/C1v | 12 ++ data/Symmetry/C2 | 12 ++ data/Symmetry/C20 | 30 +++ data/Symmetry/C20h | 52 +++++ data/Symmetry/C20v | 34 ++++ data/Symmetry/C21 | 30 +++ data/Symmetry/C21h | 52 +++++ data/Symmetry/C21v | 32 ++++ data/Symmetry/C22 | 32 ++++ data/Symmetry/C22h | 56 ++++++ data/Symmetry/C22v | 36 ++++ data/Symmetry/C23 | 32 ++++ data/Symmetry/C23h | 56 ++++++ data/Symmetry/C23v | 34 ++++ data/Symmetry/C24 | 34 ++++ data/Symmetry/C24h | 60 ++++++ data/Symmetry/C24v | 38 ++++ data/Symmetry/C25 | 34 ++++ data/Symmetry/C25h | 60 ++++++ data/Symmetry/C25v | 36 ++++ data/Symmetry/C26 | 36 ++++ data/Symmetry/C26h | 64 +++++++ data/Symmetry/C26v | 40 ++++ data/Symmetry/C27 | 36 ++++ data/Symmetry/C27h | 64 +++++++ data/Symmetry/C27v | 38 ++++ data/Symmetry/C28 | 38 ++++ data/Symmetry/C28h | 68 +++++++ data/Symmetry/C28v | 42 ++++ data/Symmetry/C29 | 38 ++++ data/Symmetry/C29h | 68 +++++++ data/Symmetry/C29v | 40 ++++ data/Symmetry/C2h | 16 ++ data/Symmetry/C2v | 16 ++ data/Symmetry/C3 | 12 ++ data/Symmetry/C30 | 40 ++++ data/Symmetry/C30h | 72 +++++++ data/Symmetry/C30v | 44 +++++ data/Symmetry/C31 | 40 ++++ data/Symmetry/C31h | 72 +++++++ data/Symmetry/C31v | 42 ++++ data/Symmetry/C32 | 42 ++++ data/Symmetry/C32h | 76 ++++++++ data/Symmetry/C32v | 46 +++++ data/Symmetry/C3h | 16 ++ data/Symmetry/C3v | 14 ++ data/Symmetry/C4 | 14 ++ data/Symmetry/C4h | 20 ++ data/Symmetry/C4v | 18 ++ data/Symmetry/C5 | 14 ++ data/Symmetry/C5h | 20 ++ data/Symmetry/C5v | 16 ++ data/Symmetry/C6 | 16 ++ data/Symmetry/C6h | 24 +++ data/Symmetry/C6v | 20 ++ data/Symmetry/C7 | 16 ++ data/Symmetry/C7h | 24 +++ data/Symmetry/C7v | 18 ++ data/Symmetry/C8 | 18 ++ data/Symmetry/C8h | 28 +++ data/Symmetry/C8v | 22 +++ data/Symmetry/C9 | 18 ++ data/Symmetry/C9h | 28 +++ data/Symmetry/C9v | 20 ++ data/Symmetry/Ci | 12 ++ data/Symmetry/Cinfv | 42 ++++ data/Symmetry/Cs | 12 ++ data/Symmetry/D1 | 12 ++ data/Symmetry/D10 | 24 +++ data/Symmetry/D10d | 34 ++++ data/Symmetry/D10h | 40 ++++ data/Symmetry/D11 | 22 +++ data/Symmetry/D11d | 36 ++++ data/Symmetry/D11h | 36 ++++ data/Symmetry/D12 | 26 +++ data/Symmetry/D12d | 38 ++++ data/Symmetry/D12h | 44 +++++ data/Symmetry/D13 | 24 +++ data/Symmetry/D13d | 40 ++++ data/Symmetry/D13h | 40 ++++ data/Symmetry/D14 | 28 +++ data/Symmetry/D14d | 42 ++++ data/Symmetry/D14h | 48 +++++ data/Symmetry/D15 | 26 +++ data/Symmetry/D15d | 44 +++++ data/Symmetry/D15h | 44 +++++ data/Symmetry/D16 | 30 +++ data/Symmetry/D16d | 46 +++++ data/Symmetry/D16h | 52 +++++ data/Symmetry/D17 | 28 +++ data/Symmetry/D17d | 48 +++++ data/Symmetry/D17h | 48 +++++ data/Symmetry/D18 | 32 ++++ data/Symmetry/D18d | 50 +++++ data/Symmetry/D18h | 56 ++++++ data/Symmetry/D19 | 30 +++ data/Symmetry/D19d | 52 +++++ data/Symmetry/D19h | 52 +++++ data/Symmetry/D1d | 16 ++ data/Symmetry/D1h | 16 ++ data/Symmetry/D2 | 16 ++ data/Symmetry/D20 | 34 ++++ data/Symmetry/D20d | 54 ++++++ data/Symmetry/D20h | 60 ++++++ data/Symmetry/D21 | 32 ++++ data/Symmetry/D21d | 56 ++++++ data/Symmetry/D21h | 56 ++++++ data/Symmetry/D22 | 36 ++++ data/Symmetry/D22d | 58 ++++++ data/Symmetry/D22h | 64 +++++++ data/Symmetry/D23 | 34 ++++ data/Symmetry/D23d | 60 ++++++ data/Symmetry/D23h | 60 ++++++ data/Symmetry/D24 | 38 ++++ data/Symmetry/D24d | 62 ++++++ data/Symmetry/D24h | 68 +++++++ data/Symmetry/D25 | 36 ++++ data/Symmetry/D25d | 64 +++++++ data/Symmetry/D25h | 64 +++++++ data/Symmetry/D26 | 40 ++++ data/Symmetry/D26d | 66 +++++++ data/Symmetry/D26h | 72 +++++++ data/Symmetry/D27 | 38 ++++ data/Symmetry/D27d | 68 +++++++ data/Symmetry/D27h | 68 +++++++ data/Symmetry/D28 | 42 ++++ data/Symmetry/D28d | 70 +++++++ data/Symmetry/D28h | 76 ++++++++ data/Symmetry/D29 | 40 ++++ data/Symmetry/D29d | 72 +++++++ data/Symmetry/D29h | 72 +++++++ data/Symmetry/D2d | 18 ++ data/Symmetry/D2h | 24 +++ data/Symmetry/D3 | 14 ++ data/Symmetry/D30 | 44 +++++ data/Symmetry/D30d | 74 +++++++ data/Symmetry/D30h | 80 ++++++++ data/Symmetry/D31 | 42 ++++ data/Symmetry/D31d | 76 ++++++++ data/Symmetry/D31h | 76 ++++++++ data/Symmetry/D32 | 46 +++++ data/Symmetry/D32d | 78 ++++++++ data/Symmetry/D32h | 84 ++++++++ data/Symmetry/D3d | 20 ++ data/Symmetry/D3h | 20 ++ data/Symmetry/D4 | 18 ++ data/Symmetry/D4d | 22 +++ data/Symmetry/D4h | 28 +++ data/Symmetry/D5 | 16 ++ data/Symmetry/D5d | 24 +++ data/Symmetry/D5h | 24 +++ data/Symmetry/D6 | 20 ++ data/Symmetry/D6d | 26 +++ data/Symmetry/D6h | 32 ++++ data/Symmetry/D7 | 18 ++ data/Symmetry/D7d | 28 +++ data/Symmetry/D7h | 28 +++ data/Symmetry/D8 | 22 +++ data/Symmetry/D8d | 30 +++ data/Symmetry/D8h | 36 ++++ data/Symmetry/D9 | 20 ++ data/Symmetry/D9d | 32 ++++ data/Symmetry/D9h | 32 ++++ data/Symmetry/Dinfh | 84 ++++++++ data/Symmetry/I | 18 ++ data/Symmetry/Ih | 28 +++ data/Symmetry/O | 18 ++ data/Symmetry/Oh | 28 +++ data/Symmetry/S12 | 22 +++ data/Symmetry/S16 | 26 +++ data/Symmetry/S20 | 30 +++ data/Symmetry/S24 | 34 ++++ data/Symmetry/S28 | 38 ++++ data/Symmetry/S32 | 42 ++++ data/Symmetry/S4 | 14 ++ data/Symmetry/S8 | 18 ++ data/Symmetry/T | 14 ++ data/Symmetry/Td | 18 ++ data/Symmetry/Th | 20 ++ plugins/Symmetry/Symmetry.main.irp.f | 27 +-- plugins/Symmetry/aos.irp.f | 10 +- plugins/Symmetry/find_sym.irp.f | 276 +++++++++++++++++++++------ plugins/Symmetry/sym_operation.irp.f | 77 ++++++++ scripts/utility/get_groups.py | 72 +++++++ 216 files changed, 8098 insertions(+), 82 deletions(-) create mode 100644 data/Symmetry/C1 create mode 100644 data/Symmetry/C10 create mode 100644 data/Symmetry/C10h create mode 100644 data/Symmetry/C10v create mode 100644 data/Symmetry/C11 create mode 100644 data/Symmetry/C11h create mode 100644 data/Symmetry/C11v create mode 100644 data/Symmetry/C12 create mode 100644 data/Symmetry/C12h create mode 100644 data/Symmetry/C12v create mode 100644 data/Symmetry/C13 create mode 100644 data/Symmetry/C13h create mode 100644 data/Symmetry/C13v create mode 100644 data/Symmetry/C14 create mode 100644 data/Symmetry/C14h create mode 100644 data/Symmetry/C14v create mode 100644 data/Symmetry/C15 create mode 100644 data/Symmetry/C15h create mode 100644 data/Symmetry/C15v create mode 100644 data/Symmetry/C16 create mode 100644 data/Symmetry/C16h create mode 100644 data/Symmetry/C16v create mode 100644 data/Symmetry/C17 create mode 100644 data/Symmetry/C17h create mode 100644 data/Symmetry/C17v create mode 100644 data/Symmetry/C18 create mode 100644 data/Symmetry/C18h create mode 100644 data/Symmetry/C18v create mode 100644 data/Symmetry/C19 create mode 100644 data/Symmetry/C19h create mode 100644 data/Symmetry/C19v create mode 100644 data/Symmetry/C1h create mode 100644 data/Symmetry/C1v create mode 100644 data/Symmetry/C2 create mode 100644 data/Symmetry/C20 create mode 100644 data/Symmetry/C20h create mode 100644 data/Symmetry/C20v create mode 100644 data/Symmetry/C21 create mode 100644 data/Symmetry/C21h create mode 100644 data/Symmetry/C21v create mode 100644 data/Symmetry/C22 create mode 100644 data/Symmetry/C22h create mode 100644 data/Symmetry/C22v create mode 100644 data/Symmetry/C23 create mode 100644 data/Symmetry/C23h create mode 100644 data/Symmetry/C23v create mode 100644 data/Symmetry/C24 create mode 100644 data/Symmetry/C24h create mode 100644 data/Symmetry/C24v create mode 100644 data/Symmetry/C25 create mode 100644 data/Symmetry/C25h create mode 100644 data/Symmetry/C25v create mode 100644 data/Symmetry/C26 create mode 100644 data/Symmetry/C26h create mode 100644 data/Symmetry/C26v create mode 100644 data/Symmetry/C27 create mode 100644 data/Symmetry/C27h create mode 100644 data/Symmetry/C27v 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data/Symmetry/D13h create mode 100644 data/Symmetry/D14 create mode 100644 data/Symmetry/D14d create mode 100644 data/Symmetry/D14h create mode 100644 data/Symmetry/D15 create mode 100644 data/Symmetry/D15d create mode 100644 data/Symmetry/D15h create mode 100644 data/Symmetry/D16 create mode 100644 data/Symmetry/D16d create mode 100644 data/Symmetry/D16h create mode 100644 data/Symmetry/D17 create mode 100644 data/Symmetry/D17d create mode 100644 data/Symmetry/D17h create mode 100644 data/Symmetry/D18 create mode 100644 data/Symmetry/D18d create mode 100644 data/Symmetry/D18h create mode 100644 data/Symmetry/D19 create mode 100644 data/Symmetry/D19d create mode 100644 data/Symmetry/D19h create mode 100644 data/Symmetry/D1d create mode 100644 data/Symmetry/D1h create mode 100644 data/Symmetry/D2 create mode 100644 data/Symmetry/D20 create mode 100644 data/Symmetry/D20d create mode 100644 data/Symmetry/D20h create mode 100644 data/Symmetry/D21 create mode 100644 data/Symmetry/D21d create mode 100644 data/Symmetry/D21h create mode 100644 data/Symmetry/D22 create mode 100644 data/Symmetry/D22d create mode 100644 data/Symmetry/D22h create mode 100644 data/Symmetry/D23 create mode 100644 data/Symmetry/D23d create mode 100644 data/Symmetry/D23h create mode 100644 data/Symmetry/D24 create mode 100644 data/Symmetry/D24d create mode 100644 data/Symmetry/D24h create mode 100644 data/Symmetry/D25 create mode 100644 data/Symmetry/D25d create mode 100644 data/Symmetry/D25h create mode 100644 data/Symmetry/D26 create mode 100644 data/Symmetry/D26d create mode 100644 data/Symmetry/D26h create mode 100644 data/Symmetry/D27 create mode 100644 data/Symmetry/D27d create mode 100644 data/Symmetry/D27h create mode 100644 data/Symmetry/D28 create mode 100644 data/Symmetry/D28d create mode 100644 data/Symmetry/D28h create mode 100644 data/Symmetry/D29 create mode 100644 data/Symmetry/D29d create mode 100644 data/Symmetry/D29h create mode 100644 data/Symmetry/D2d create mode 100644 data/Symmetry/D2h create mode 100644 data/Symmetry/D3 create mode 100644 data/Symmetry/D30 create mode 100644 data/Symmetry/D30d create mode 100644 data/Symmetry/D30h create mode 100644 data/Symmetry/D31 create mode 100644 data/Symmetry/D31d create mode 100644 data/Symmetry/D31h create mode 100644 data/Symmetry/D32 create mode 100644 data/Symmetry/D32d create mode 100644 data/Symmetry/D32h create mode 100644 data/Symmetry/D3d create mode 100644 data/Symmetry/D3h create mode 100644 data/Symmetry/D4 create mode 100644 data/Symmetry/D4d create mode 100644 data/Symmetry/D4h create mode 100644 data/Symmetry/D5 create mode 100644 data/Symmetry/D5d create mode 100644 data/Symmetry/D5h create mode 100644 data/Symmetry/D6 create mode 100644 data/Symmetry/D6d create mode 100644 data/Symmetry/D6h create mode 100644 data/Symmetry/D7 create mode 100644 data/Symmetry/D7d create mode 100644 data/Symmetry/D7h create mode 100644 data/Symmetry/D8 create mode 100644 data/Symmetry/D8d create mode 100644 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1 A E + +Table + 1 + 1 1.00000 + diff --git a/data/Symmetry/C10 b/data/Symmetry/C10 new file mode 100644 index 00000000..2fc79009 --- /dev/null +++ b/data/Symmetry/C10 @@ -0,0 +1,20 @@ +Group C10 +n 6 + + Irred Operation + 1 A E + 2 B C10 + 3 E1 C5 + 4 E2 C10^3 + 5 E3 C5^2 + 6 E4 C2 + +Table + 1 2 3 4 5 6 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 + 3 2.00000 1.61800 0.61800 -0.61800 -1.61800 -2.00000 + 4 2.00000 0.61800 -1.61800 -1.61800 0.61800 2.00000 + 5 2.00000 -0.61800 -1.61800 1.61800 0.61800 -2.00000 + 6 2.00000 -1.61800 0.61800 0.61800 -1.61800 2.00000 + diff --git a/data/Symmetry/C10h b/data/Symmetry/C10h new file mode 100644 index 00000000..ca22cc4a --- /dev/null +++ b/data/Symmetry/C10h @@ -0,0 +1,32 @@ +Group C10h +n 12 + + Irred Operation + 1 Ag E + 2 Bg C10 + 3 E1g C5 + 4 E2g C10^3 + 5 E3g C5^2 + 6 E4g C2 + 7 Au i + 8 Bu S10 + 9 E1u S5 + 10 E2u S10^3 + 11 E3u S5^2 + 12 E4u sh + +Table + 1 2 3 4 5 6 7 8 9 10 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b/data/Symmetry/C7v new file mode 100644 index 00000000..95478ae3 --- /dev/null +++ b/data/Symmetry/C7v @@ -0,0 +1,18 @@ +Group C7v +n 5 + + Irred Operation + 1 A1 E + 2 A2 C7 + 3 E1 C7^2 + 4 E2 C7^3 + 5 E3 sv + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 1.00000 1.00000 1.00000 -1.00000 + 3 2.00000 1.24690 -0.44500 -1.80190 0.00000 + 4 2.00000 -0.44500 -1.80190 1.24690 0.00000 + 5 2.00000 -1.80190 1.24690 -0.44500 0.00000 + diff --git a/data/Symmetry/C8 b/data/Symmetry/C8 new file mode 100644 index 00000000..b93bf8fd --- /dev/null +++ b/data/Symmetry/C8 @@ -0,0 +1,18 @@ +Group C8 +n 5 + + Irred Operation + 1 A E + 2 B C8 + 3 E1 C4 + 4 E2 C8^3 + 5 E3 C2 + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 + 3 2.00000 1.41420 0.00000 -1.41420 -2.00000 + 4 2.00000 0.00000 -2.00000 0.00000 2.00000 + 5 2.00000 -1.41420 0.00000 1.41420 -2.00000 + diff --git a/data/Symmetry/C8h b/data/Symmetry/C8h new file mode 100644 index 00000000..afd739be --- /dev/null +++ b/data/Symmetry/C8h @@ -0,0 +1,28 @@ +Group C8h +n 10 + + Irred Operation + 1 Ag E + 2 Bg C8 + 3 E1g C4 + 4 E2g C8^3 + 5 E3g C2 + 6 Au i + 7 Bu S8 + 8 E1u S4 + 9 E2u S8^3 + 10 E3u sh + +Table + 1 2 3 4 5 6 7 8 9 10 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 + 3 2.00000 1.41420 0.00000 -1.41420 -2.00000 2.00000 -1.41420 0.00000 1.41420 -2.00000 + 4 2.00000 0.00000 -2.00000 0.00000 2.00000 2.00000 0.00000 -2.00000 0.00000 2.00000 + 5 2.00000 -1.41420 0.00000 1.41420 -2.00000 2.00000 1.41420 0.00000 -1.41420 -2.00000 + 6 1.00000 1.00000 1.00000 1.00000 1.00000 -1.00000 -1.00000 -1.00000 -1.00000 -1.00000 + 7 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 1.00000 -1.00000 + 8 2.00000 1.41420 0.00000 -1.41420 -2.00000 -2.00000 1.41420 0.00000 -1.41420 2.00000 + 9 2.00000 0.00000 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b/data/Symmetry/C9 @@ -0,0 +1,18 @@ +Group C9 +n 5 + + Irred Operation + 1 A E + 2 E1 C9 + 3 E2 C9^2 + 4 E3 C3 + 5 E4 C9^4 + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 2.00000 1.53200 0.34730 -1.00000 -1.87930 + 3 2.00000 0.34730 -1.87930 -1.00000 1.53200 + 4 2.00000 -1.00000 -1.00000 2.00000 -1.00000 + 5 2.00000 -1.87930 1.53200 -1.00000 0.34730 + diff --git a/data/Symmetry/C9h b/data/Symmetry/C9h new file mode 100644 index 00000000..fb34a5d5 --- /dev/null +++ b/data/Symmetry/C9h @@ -0,0 +1,28 @@ +Group C9h +n 10 + + Irred Operation + 1 A' E + 2 A" C9 + 3 E1' C9^2 + 4 E1" C3 + 5 E2' C9^4 + 6 E2" sh + 7 E3' S9 + 8 E3" S3 + 9 E4' S9^5 + 10 E4" S9^7 + +Table + 1 2 3 4 5 6 7 8 9 10 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 1.00000 1.00000 1.00000 1.00000 -1.00000 -1.00000 -1.00000 -1.00000 -1.00000 + 3 2.00000 1.53200 0.34730 -1.00000 -1.87930 2.00000 1.53200 -1.00000 -1.87930 0.34730 + 4 2.00000 1.53200 0.34730 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2.00000 -1.84776 1.41421 -0.76537 0.00000 0.76537 -1.41421 1.84776 -2.00000 1.84776 -1.41421 0.76537 0.00000 -0.76537 1.41421 -1.84776 2.00000 + 17 2.00000 -1.96157 1.84776 -1.66294 1.41421 -1.11114 0.76537 -0.39018 0.00000 0.39018 -0.76537 1.11114 -1.41421 1.66294 -1.84776 1.96157 -2.00000 + diff --git a/data/Symmetry/S4 b/data/Symmetry/S4 new file mode 100644 index 00000000..faabefbf --- /dev/null +++ b/data/Symmetry/S4 @@ -0,0 +1,14 @@ +Group S4 +n 3 + + Irred Operation + 1 A E + 2 B S4 + 3 E C2 + +Table + 1 2 3 + 1 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 + 3 2.00000 0.00000 -2.00000 + diff --git a/data/Symmetry/S8 b/data/Symmetry/S8 new file mode 100644 index 00000000..a7a0a0e0 --- /dev/null +++ b/data/Symmetry/S8 @@ -0,0 +1,18 @@ +Group S8 +n 5 + + Irred Operation + 1 A E + 2 B S8 + 3 E1 C4 + 4 E2 S8^3 + 5 E3 C2 + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 -1.00000 1.00000 -1.00000 1.00000 + 3 2.00000 1.41420 0.00000 -1.41420 -2.00000 + 4 2.00000 0.00000 -2.00000 0.00000 2.00000 + 5 2.00000 -1.41420 0.00000 1.41420 -2.00000 + diff --git a/data/Symmetry/T b/data/Symmetry/T new file mode 100644 index 00000000..660b5106 --- /dev/null +++ b/data/Symmetry/T @@ -0,0 +1,14 @@ +Group T +n 3 + + Irred Operation + 1 A E + 2 E C3 + 3 T C2 + +Table + 1 2 3 + 1 1.00000 1.00000 1.00000 + 2 2.00000 -1.00000 2.00000 + 3 3.00000 0.00000 -1.00000 + diff --git a/data/Symmetry/Td b/data/Symmetry/Td new file mode 100644 index 00000000..bb0dbb12 --- /dev/null +++ b/data/Symmetry/Td @@ -0,0 +1,18 @@ +Group Td +n 5 + + Irred Operation + 1 A1 E + 2 A2 C3 + 3 E C2 + 4 T1 S4 + 5 T2 sd + +Table + 1 2 3 4 5 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 1.00000 1.00000 1.00000 -1.00000 -1.00000 + 3 2.00000 -1.00000 2.00000 0.00000 0.00000 + 4 3.00000 0.00000 -1.00000 1.00000 -1.00000 + 5 3.00000 0.00000 -1.00000 -1.00000 1.00000 + diff --git a/data/Symmetry/Th b/data/Symmetry/Th new file mode 100644 index 00000000..06232415 --- /dev/null +++ b/data/Symmetry/Th @@ -0,0 +1,20 @@ +Group Th +n 6 + + Irred Operation + 1 Ag E + 2 Eg C3 + 3 Tg C2 + 4 Au i + 5 Eu S6 + 6 Tu sh + +Table + 1 2 3 4 5 6 + 1 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 + 2 2.00000 -1.00000 2.00000 2.00000 -1.00000 2.00000 + 3 3.00000 0.00000 -1.00000 3.00000 0.00000 -1.00000 + 4 1.00000 1.00000 1.00000 -1.00000 -1.00000 -1.00000 + 5 2.00000 -1.00000 2.00000 -2.00000 1.00000 -2.00000 + 6 3.00000 0.00000 -1.00000 -3.00000 0.00000 1.00000 + diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f index d8d2f350..78bf126e 100644 --- a/plugins/Symmetry/Symmetry.main.irp.f +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -3,28 +3,19 @@ program Symmetry BEGIN_DOC ! TODO END_DOC - integer :: n_sym_points, i, j - double precision, allocatable :: tmp(:,:), sym_points(:,:) + integer :: i, j character*8 :: sym - n_sym_points = 3 print *, 'Molecule is linear:', molecule_is_linear print *, 'Has center of inversion:', molecule_has_center_of_inversion + print *, 'Has S2n improper rotation:', molecule_has_improper_rotation print *, 'Symmetry rotation axis:', sym_rotation_axis(:) - call find_symmetry(sym) - print *, 'Group:'//sym - return - allocate(tmp(n_sym_points,n_det), sym_points(3,n_sym_points)) - - call generate_sym_coord(n_sym_points,sym_points) - call compute_sym_det_values(sym_points,n_sym_points,tmp) - do i=1,mo_tot_num - print *, i, real(tmp(1:3,i)) + print *, 'Group:'//point_group + print *, 'Symmetry irreps', sym_irrep(1:n_irrep) + print *, 'Symmetry operations', sym_operation(1:n_irrep) + print *, 'Character table' + do i=1,n_irrep + print *, character_table(i,:) enddo - sym_points(1,:) = -sym_points(1,:) - call compute_sym_det_values(sym_points,n_sym_points,tmp) - do i=1,n_det - print *, i, real(tmp(1:3,i)) - enddo - + PROVIDE mo_sym end diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index 97b7aa62..e4352948 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -51,7 +51,15 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) x = x**ao_power(j,1) y = y**ao_power(j,2) z = z**ao_power(j,3) - result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) +! result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) + result(i,j) = x*y*z + if (result(i,j) > 0.d0) then + result(i,j) = 1.d0 + else if (result(i,j) < 0.d0) then + result(i,j) = -1.d0 + else + result(i,j) = 0.d0 + endif enddo enddo diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 4a100805..c23146c5 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -47,29 +47,12 @@ BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] logical :: found double precision, external :: u_dot_u integer :: iorder, iaxis - double precision :: theta, sin_t, cos_t do iaxis=1,3 do iorder=12,2,-1 sym_rotation_axis(iaxis) = iorder - theta = 2.d0*pi/dble(iorder) - sin_t = dsin(theta) - cos_t = dcos(theta) do i=1,nucl_num found = .False. - if (iaxis==1) then - point(1) = nucl_coord_transp(1,i) - point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t - else if (iaxis==2) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(2) = nucl_coord_transp(2,i) - point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t - endif - if (iaxis==3) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t - point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t - point(3) = nucl_coord_transp(3,i) - endif + call sym_apply_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle point2(:) = nucl_coord_transp(:,j) - point(:) @@ -94,6 +77,7 @@ END_PROVIDER BEGIN_PROVIDER [ integer, molecule_principal_axis ] &BEGIN_PROVIDER [ integer, molecule_secondary_axis ] &BEGIN_PROVIDER [ integer, molecule_ternary_axis ] +&BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] implicit none BEGIN_DOC ! Which axis is the Z axis @@ -124,13 +108,7 @@ END_PROVIDER molecule_ternary_axis = 1 endif endif -END_PROVIDER -BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] - implicit none - BEGIN_DOC -! If true, the molecule has a C2 rotation perpendicular to the main axis - END_DOC if (molecule_principal_axis == 1) then molecule_has_secondary_c2_rotation = (sym_rotation_axis(2)==2) .or. (sym_rotation_axis(3)==2) else if (molecule_principal_axis == 2) then @@ -138,9 +116,21 @@ BEGIN_PROVIDER [ logical, molecule_has_secondary_c2_rotation ] else if (molecule_principal_axis == 3) then molecule_has_secondary_c2_rotation = (sym_rotation_axis(1)==2) .or. (sym_rotation_axis(2)==2) endif + + if (molecule_has_secondary_c2_rotation) then + integer :: swap + if ( (sym_rotation_axis(molecule_secondary_axis) /= 2).and. & + (sym_rotation_axis(molecule_ternary_axis) == 2) ) then + swap = molecule_secondary_axis + molecule_secondary_axis = molecule_ternary_axis + molecule_ternary_axis = swap + endif + endif + END_PROVIDER + BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] implicit none BEGIN_DOC @@ -153,29 +143,12 @@ BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] logical :: found double precision, external :: u_dot_u integer :: iorder, iaxis - double precision :: theta, sin_t, cos_t iaxis=molecule_principal_axis iorder = 2*sym_rotation_axis(iaxis) molecule_has_improper_rotation = .True. - theta = 2.d0*pi/dble(iorder) - sin_t = dsin(theta) - cos_t = dcos(theta) do i=1,nucl_num found = .False. - if (iaxis==1) then - point(1) = -nucl_coord_transp(1,i) - point(2) = nucl_coord_transp(2,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(3) = nucl_coord_transp(2,i)*sin_t + nucl_coord_transp(3,i)*cos_t - else if (iaxis==2) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(3,i)*sin_t - point(2) = -nucl_coord_transp(2,i) - point(3) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(3,i)*cos_t - endif - if (iaxis==3) then - point(1) = nucl_coord_transp(1,i)*cos_t - nucl_coord_transp(2,i)*sin_t - point(2) = nucl_coord_transp(1,i)*sin_t + nucl_coord_transp(2,i)*cos_t - point(3) = -nucl_coord_transp(3,i) - endif + call sym_apply_improper_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle point2(:) = nucl_coord_transp(:,j) - point(:) @@ -254,60 +227,68 @@ BEGIN_PROVIDER [ logical, molecule_has_sigma_plane, (3) ] END_PROVIDER -subroutine find_symmetry(result) - implicit none - BEGIN_DOC -! Finds the point group of the molecule - END_DOC - character*16 :: result +BEGIN_PROVIDER [ character*16, point_group ] + implicit none + BEGIN_DOC +! Point group of the molecule + END_DOC + character*2, save :: i_to_a(24) = (/ '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',& '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24' /) - result = 'C1' + point_group = 'C1' if (molecule_is_linear) then if (molecule_has_center_of_inversion) then - result = 'D*h' + point_group = 'Dinfh' else - result = 'C*v' + point_group = 'Cinfv' endif else if (maxval(sym_rotation_axis) == 1) then if (molecule_has_sigma_plane(1).or.molecule_has_sigma_plane(2).or.& molecule_has_sigma_plane(3) ) then - result = 'Cs' + point_group = 'Cs' else if (molecule_has_center_of_inversion) then - result = 'Ci' + point_group = 'Ci' endif endif else if (molecule_has_secondary_c2_rotation) then if (molecule_has_sigma_plane(molecule_principal_axis)) then - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' else if (molecule_has_sigma_plane(molecule_secondary_axis)) then - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' else if (molecule_has_sigma_plane(molecule_ternary_axis)) then - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'d' else - result = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + if ( (sym_rotation_axis(1) == 2).and. & + (sym_rotation_axis(2) == 2).and. & + (sym_rotation_axis(3) == 2).and. & + (inertia_tensor_eigenvalues(1) == inertia_tensor_eigenvalues(2)).and. & + (inertia_tensor_eigenvalues(1) == inertia_tensor_eigenvalues(3)) ) then + point_group = 'Td' + else + point_group = 'D'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + endif endif endif endif else if (molecule_has_sigma_plane(molecule_principal_axis)) then - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'h' else if (molecule_has_sigma_plane(molecule_secondary_axis)) then - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' else if (molecule_has_sigma_plane(molecule_ternary_axis)) then - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis)))//'v' else if (molecule_has_improper_rotation) then - result = 'S'//trim(i_to_a(2*sym_rotation_axis(molecule_principal_axis))) + point_group = 'S'//trim(i_to_a(2*sym_rotation_axis(molecule_principal_axis))) else - result = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) + point_group = 'C'//trim(i_to_a(sym_rotation_axis(molecule_principal_axis))) endif endif endif @@ -315,4 +296,173 @@ subroutine find_symmetry(result) endif endif endif -end +END_PROVIDER + + +BEGIN_PROVIDER [ character*8, mo_symmetry ] + implicit none + BEGIN_DOC + ! Symmetry of the MOs + END_DOC + integer :: i,j +END_PROVIDER + + +BEGIN_PROVIDER [ integer, n_irrep ] + implicit none + BEGIN_DOC + ! Number of Irreducible representations + END_DOC + integer :: iunit, n, i + character*(256) :: qproot, buffer + integer, external :: getUnitAndOpen + call getenv('QP_ROOT',qproot) + iunit = getUnitAndOpen(trim(qproot)//'/data/Symmetry/'//trim(point_group),'r') + read(iunit,*) ! 1st line + read(iunit,*) buffer, n_irrep + close(iunit) +END_PROVIDER + + BEGIN_PROVIDER [ character*8, sym_irrep, (n_irrep) ] +&BEGIN_PROVIDER [ character*8, sym_operation, (n_irrep) ] +&BEGIN_PROVIDER [ double precision, character_table, (n_irrep,n_irrep) ] + implicit none + BEGIN_DOC + ! Irreducible representation labels, labels of symmetry operations and + ! Character table : columns are sym operations and lines are Irreps + END_DOC + integer :: iunit, n, i + character*(256) :: qproot, buffer + integer, external :: getUnitAndOpen + call getenv('QP_ROOT',qproot) + iunit = getUnitAndOpen(trim(qproot)//'/data/Symmetry/'//trim(point_group),'r') + buffer = '' + read(iunit,*) ! 1st line + read(iunit,*) buffer, n + read(iunit,*) ! empty line + read(iunit,*) ! Irred Operation + do i=1,n + read(iunit,*) buffer, sym_irrep(i), sym_operation(i) + enddo + read(iunit,*) ! empty line + read(iunit,*) ! Table + read(iunit,*) ! 1 2 3 ... + do i=1,n + read(iunit,*) buffer, character_table(i,1:n) + enddo + close(iunit) +END_PROVIDER + + +BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] + implicit none + BEGIN_DOC + ! Symmetry operations applied on MOs + END_DOC + + double precision, allocatable :: sym_points(:,:), ref_points(:,:) + double precision, allocatable :: val(:,:,:) + integer :: iangle, n_sym_points + double precision :: angle + integer :: iop, imo, ipoint, l, i + double precision :: sym_operations_on_mos(n_irrep) + logical :: possible_irrep(n_irrep,mo_tot_num) + + n_sym_points = 10000 + allocate(val(n_sym_points,mo_tot_num,2), sym_points(3,n_sym_points), ref_points(3,n_sym_points)) + + call generate_sym_coord(n_sym_points,ref_points) + call compute_sym_mo_values(ref_points,n_sym_points,val(1,1,2)) + + do iop=1,n_irrep + if (sym_operation(iop) == 'E') then + cycle + endif + possible_irrep = .True. + + if (sym_operation(iop) == 'i') then + do ipoint=1,n_sym_points + call sym_apply_inversion(ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'sh') then + do ipoint=1,n_sym_points + call sym_apply_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 's') then + do ipoint=1,n_sym_points + call sym_apply_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'sv') then + do ipoint=1,n_sym_points + call sym_apply_reflexion(molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'sd') then + do ipoint=1,n_sym_points + call sym_apply_diagonal_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'C2''') then + do ipoint=1,n_sym_points + call sym_apply_rotation(angle,molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop) == 'C2"') then + do ipoint=1,n_sym_points + call sym_apply_rotation(angle,molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else + do l=2,len(sym_operation(iop)) + if (sym_operation(iop)(l:l) == '^') exit + enddo + read(sym_operation(iop)(2:l-1), *) iangle + l=1 + read(sym_operation(iop)(l+1:), *, err=10, end=10) l + 10 continue + angle = dble(iangle)/(dble(l)) + if (sym_operation(iop)(1:1) == 'C') then + do ipoint=1,n_sym_points + call sym_apply_rotation(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + else if (sym_operation(iop)(1:1) == 'S') then + do ipoint=1,n_sym_points + call sym_apply_improper_rotation(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + enddo + endif + endif + + call compute_sym_mo_values(sym_points,n_sym_points,val(1,1,1)) + + print *, sym_operation(iop) + do imo=1,mo_tot_num + sym_operations_on_mos(imo) = 0.d0 + do ipoint=1,n_sym_points + double precision :: x + x = val(ipoint,imo,1)/val(ipoint,imo,2) + if (dabs(x) > 1.d0) then + x = 1.d0/x + endif + sym_operations_on_mos(imo) += x + enddo + sym_operations_on_mos(imo) *= 1.d0/n_sym_points + if (dabs(sym_operations_on_mos(imo)-1.d0) < 1.d-2) then + sym_operations_on_mos(imo)=1.d0 + else if (dabs(sym_operations_on_mos(imo)+1.d0) < 1.d-2) then + sym_operations_on_mos(imo)=-1.d0 + endif + do i=1,n_irrep + if (character_table(i,iop) /= sym_operations_on_mos(imo)) then + possible_irrep(i,imo) = .False. + endif + enddo + enddo + enddo + do imo=1,mo_tot_num + print *, imo + do i=1,n_irrep + if (possible_irrep(i,imo)) then + print *, sym_irrep(i) + endif + enddo + print *, '' + enddo + +END_PROVIDER + diff --git a/plugins/Symmetry/sym_operation.irp.f b/plugins/Symmetry/sym_operation.irp.f new file mode 100644 index 00000000..93e580e2 --- /dev/null +++ b/plugins/Symmetry/sym_operation.irp.f @@ -0,0 +1,77 @@ +subroutine sym_apply_inversion(point_in, point_out) + implicit none + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + point_out(:) = -point_in(:) +end + +subroutine sym_apply_reflexion(iaxis,point_in,point_out) + implicit none + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + point_out(:) = point_in(:) + point_out(iaxis) = -point_in(iaxis) + +end + +subroutine sym_apply_diagonal_reflexion(iaxis,point_in,point_out) + implicit none + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + if (iaxis == 1) then + point_out(1) = point_in(1) + point_out(2) = point_in(3) + point_out(3) = point_in(2) + else if (iaxis == 2) then + point_out(1) = point_in(3) + point_out(2) = point_in(2) + point_out(3) = point_in(1) + else if (iaxis == 3) then + point_out(1) = point_in(2) + point_out(2) = point_in(1) + point_out(3) = point_in(3) + endif + +end + +subroutine sym_apply_rotation(angle,iaxis,point_in,point_out) + implicit none + double precision, intent(in) :: angle + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + double precision :: theta, sin_t, cos_t + double precision, parameter :: pi = dacos(-1.d0) + theta = 2.d0*pi/angle + sin_t = dsin(theta) + cos_t = dcos(theta) + if (iaxis==1) then + point_out(1) = point_in(1) + point_out(2) = point_in(2)*cos_t - point_in(3)*sin_t + point_out(3) = point_in(2)*sin_t + point_in(3)*cos_t + else if (iaxis==2) then + point_out(1) = point_in(1)*cos_t - point_in(3)*sin_t + point_out(2) = point_in(2) + point_out(3) = point_in(1)*sin_t + point_in(3)*cos_t + endif + if (iaxis==3) then + point_out(1) = point_in(1)*cos_t - point_in(2)*sin_t + point_out(2) = point_in(1)*sin_t + point_in(2)*cos_t + point_out(3) = point_in(3) + endif +end + +subroutine sym_apply_improper_rotation(angle,iaxis,point_in,point_out) + implicit none + double precision, intent(in) :: angle + integer, intent(in) :: iaxis + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + double precision :: point_tmp(3) + call sym_apply_rotation(angle,iaxis,point_in,point_tmp) + call sym_apply_reflexion(iaxis,point_tmp,point_out) +end + + diff --git a/scripts/utility/get_groups.py b/scripts/utility/get_groups.py new file mode 100755 index 00000000..e8a24d84 --- /dev/null +++ b/scripts/utility/get_groups.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import urllib +import sys +from bs4 import BeautifulSoup + +address="http://gernot-katzers-spice-pages.com/character_tables/%s.html?fmt=simple" + +def clean_up(text): + soup = BeautifulSoup(text, "lxml") + pre = soup.pre + group = pre.b.get_text() + sop = {} + irred = {} + irred_count = 0 + sop_count = 0 + for span in pre.find_all('span'): + cls = span.get('class') + if cls == ['sop']: + a = span.decode_contents() + if a not in sop: + sop[a] = sop_count + sop_count += 1 + elif cls == ['irred']: + a = span.decode_contents() + if a not in irred: + irred[a] = irred_count + irred_count += 1 + table = [ [] for j in sop ] + data = pre.get_text().splitlines() + def f(x): + y = x.split() + if len(y) == 0: + return False + else: + return y[0] in irred + data = filter(f,data)[:len(irred)] + for line in data: + s = line.replace('*','').split() + l = irred[s[0]] + data[l] = map(float,s[1:len(irred)+1]) + + d = {} + e = {} + for k in irred: + d[irred[k]] = k + for k in sop: + e[sop[k]] = k + n = len(irred) + print "Group\t", group, "\nn\t", n + print "\n \tIrred \tOperation" + for i in range(n): + print "%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)) + + print "\nTable\n ", + for j in range(n): + print "%8s "%(str(j+1).center(8)), + for i in range(n): + print "\n%4d "%(i+1), + for j in range(n): + print "%8.5f "%(data[i][j]), + print "\n" + +def main(): + for group in sys.argv[1:]: + f = urllib.urlopen(address%(group)) + html = f.read().split('\n',1)[1] + text = clean_up(html) + +if __name__ == "__main__": + main() From 87e00d415ba512d3fe0502092f7fe486799938de Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 09:34:06 +0100 Subject: [PATCH 23/54] mrcc_zmq updated for recent changes (#57) --- plugins/mrcepa0/dressing.irp.f | 4 +-- plugins/mrcepa0/dressing_slave.irp.f | 2 +- plugins/mrcepa0/mrcc_stoch_routines.irp.f | 33 +++++++++-------------- 3 files changed, 15 insertions(+), 24 deletions(-) diff --git a/plugins/mrcepa0/dressing.irp.f b/plugins/mrcepa0/dressing.irp.f index 620605ff..5dfa8556 100644 --- a/plugins/mrcepa0/dressing.irp.f +++ b/plugins/mrcepa0/dressing.irp.f @@ -925,7 +925,6 @@ end E_CI_before = mrcc_E0_denominator(1) + nuclear_repulsion threshold_selectors = 1.d0 threshold_generators = 1d0 - !errr = errr / 2d0 if(errr /= 0d0) then errr = errr / 2d0 ! (-mrcc_E0_denominator(1) + mrcc_previous_E(1)) / 1d1 else @@ -934,7 +933,7 @@ end relative_error = errr print *, "RELATIVE ERROR", relative_error call ZMQ_mrcc(E_CI_before, mrcc, delta_ij_mrcc_zmq, delta_ij_s2_mrcc_zmq, abs(relative_error)) - !errr = + mrcc_previous_E(:) = mrcc_E0_denominator(:) do i=N_det_non_ref,1,-1 delta_ii_mrcc_zmq(:,1) -= delta_ij_mrcc_zmq(:, i, 1) / psi_ref_coef(1,1) * psi_non_ref_coef(i, 1) @@ -950,7 +949,6 @@ END_PROVIDER use bitmasks implicit none integer :: i, j, i_state - !mrmode : 1=mrcepa0, 2=mrsc2 add, 3=mrcc if(mrmode == 4) then do i = 1, N_det_ref diff --git a/plugins/mrcepa0/dressing_slave.irp.f b/plugins/mrcepa0/dressing_slave.irp.f index 115d1749..7d1ddd8d 100644 --- a/plugins/mrcepa0/dressing_slave.irp.f +++ b/plugins/mrcepa0/dressing_slave.irp.f @@ -516,7 +516,7 @@ end integer(ZMQ_PTR) :: zmq_to_qp_run_socket, zmq_socket_pull integer :: KKsize = 1000000 - + integer, external :: add_task_to_taskserver call new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'mrsc2') diff --git a/plugins/mrcepa0/mrcc_stoch_routines.irp.f b/plugins/mrcepa0/mrcc_stoch_routines.irp.f index 1ad9b8da..a6c893b4 100644 --- a/plugins/mrcepa0/mrcc_stoch_routines.irp.f +++ b/plugins/mrcepa0/mrcc_stoch_routines.irp.f @@ -5,7 +5,7 @@ END_PROVIDER subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) - use dress_types + !use dress_types use f77_zmq implicit none @@ -24,14 +24,14 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) double precision, external :: omp_get_wtime double precision :: time - double precision :: w(N_states) - + double precision :: w!(N_states) + integer, external :: add_task_to_taskserver provide nproc fragment_first fragment_count mo_bielec_integrals_in_map mo_mono_elec_integral mrcc_weight psi_selectors - w(:) = 0.d0 - w(mrcc_stoch_istate) = 1.d0 + w = 0.d0 + w = 1.d0 call update_psi_average_norm_contrib(w) @@ -48,7 +48,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) integer, external :: zmq_put_N_det_generators integer, external :: zmq_put_N_det_selectors integer, external :: zmq_put_dvector - + integer, external :: zmq_set_running if (zmq_put_psi(zmq_to_qp_run_socket,1) == -1) then stop 'Unable to put psi on ZMQ server' endif @@ -98,7 +98,6 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) stop 'Unable to add task to task server' endif endif - if (zmq_set_running(zmq_to_qp_run_socket) == -1) then print *, irp_here, ': Failed in zmq_set_running' endif @@ -107,7 +106,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) !$OMP PRIVATE(i) i = omp_get_thread_num() if (i==0) then - call mrcc_collector(zmq_socket_pull,E(mrcc_stoch_istate), relative_error, delta, delta_s2, mrcc) + call mrcc_collector(zmq_socket_pull,E, relative_error, delta, delta_s2, mrcc) else call mrcc_slave_inproc(i) @@ -152,7 +151,7 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m integer(ZMQ_PTR) :: zmq_to_qp_run_socket integer(ZMQ_PTR), external :: new_zmq_pull_socket - integer(ZMQ_PTR) :: zmq_socket_pull + !integer(ZMQ_PTR) :: zmq_socket_pull integer :: more integer :: i, j, k, i_state, N, ntask @@ -167,6 +166,8 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m logical, allocatable :: actually_computed(:) integer :: total_computed + delta = 0d0 + delta_s2 = 0d0 allocate(delta_det(N_states, N_det_non_ref, 0:comb_teeth+1, 2)) allocate(cp(N_states, N_det_non_ref, N_cp, 2), mrcc_detail(N_states, N_det_generators)) allocate(delta_loc(N_states, N_det_non_ref, 2)) @@ -191,7 +192,7 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m actually_computed = .false. zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() - zmq_socket_pull = new_zmq_pull_socket() + !zmq_socket_pull = new_zmq_pull_socket() allocate(task_id(N_det_generators), ind(1)) more = 1 if (time0 < 0.d0) then @@ -225,7 +226,7 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m toothMwen = tooth_of_det(ind(i)) fracted = (toothMwen /= 0) if(fracted) fracted = (ind(i) == first_det_of_teeth(toothMwen)) - + if(fracted) then delta_det(:,:,toothMwen-1, 1) += delta_loc(:,:,1) * (1d0-fractage(toothMwen)) delta_det(:,:,toothMwen-1, 2) += delta_loc(:,:,2) * (1d0-fractage(toothMwen)) @@ -262,7 +263,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m do i=2,N_det_generators if(.not. actually_computed(mrcc_jobs(i))) then - print *, "first not comp", i cur_cp = done_cp_at(i-1) exit end if @@ -303,7 +303,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m print *, irp_here, ': Error in sending abort signal (2)' endif endif - else if (cur_cp > old_cur_cp) then old_cur_cp = cur_cp @@ -316,7 +315,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m end do pullLoop if(total_computed == N_det_generators) then - print *, "TOTALLY COMPUTED" delta = 0d0 delta_s2 = 0d0 do i=comb_teeth+1,0,-1 @@ -325,22 +323,17 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m end do else - delta = cp(:,:,cur_cp,1) delta_s2 = cp(:,:,cur_cp,2) - do i=cp_first_tooth(cur_cp)-1,0,-1 delta += delta_det(:,:,i,1) delta_s2 += delta_det(:,:,i,2) end do end if - mrcc(1) = E - call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) - - call end_zmq_pull_socket(zmq_socket_pull) + !call end_zmq_pull_socket(zmq_socket_pull) end subroutine From 0cf6d6c682fbc7286acfdcdce53a123f853613ab Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 09:35:14 +0100 Subject: [PATCH 24/54] Merge LCPQ (#58) * Should fix #215 * Fix path You should never modify the repo directly... --- configure | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/configure b/configure index baeae947..c32420a0 100755 --- a/configure +++ b/configure @@ -480,11 +480,15 @@ def create_ninja_and_rc(l_installed): 'export QP_PYTHON={0}'.format(":".join(l_python)), "", 'export IRPF90={0}'.format(path_irpf90.replace(QP_ROOT,"${QP_ROOT}")), 'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")), - 'export PYTHONPATH="${QP_EZFIO}/Python":"${QP_PYTHON}":"${PYTHONPATH}"', - 'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"', - 'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${QP_ROOT}"/lib64:"${LD_LIBRARY_PATH}"', - 'export LIBRARY_PATH="${QP_ROOT}"/lib:"${QP_ROOT}"/lib64:"${LIBRARY_PATH}"', - 'export C_INCLUDE_PATH="${C_INCLUDE_PATH}":"${QP_ROOT}"/include', + 'qp_append_export () {', + ' #Append path $2:${!1}. Add the semicolon only if ${!1} is defined', + ' echo ${2}${!1:+:${!1}}', + '}', + 'export PYTHONPATH=$(qp_append_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PYTHON}")', + 'export PATH=$(qp_append_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)', + 'export LD_LIBRARY_PATH=$(qp_append_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)', + 'export LIBRARY_PATH=$(qp_append_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)', + 'export C_INCLUDE_PATH=$(qp_append_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)' '', 'source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh', '', From c83dc311b1c8a6793a1723eed7d55f07cbcf19df Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 10:19:23 +0100 Subject: [PATCH 25/54] Fix compiling with gfortran --- src/FourIdx/four_index_slave.irp.f | 2 +- src/FourIdx/four_index_zmq.irp.f | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index bc967528..5f82901a 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -101,7 +101,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & tmp=value(ik) if (tmp /= 0.d0) then a_array_ik(ii) = ik - a_array_j(ii) = j + a_array_j(ii) = int(iand(j,32767),2) ! Warning: integer*2 a_array_value(ii) = tmp ii=ii+1_8 endif diff --git a/src/FourIdx/four_index_zmq.irp.f b/src/FourIdx/four_index_zmq.irp.f index 5fffe999..2a0c56ce 100644 --- a/src/FourIdx/four_index_zmq.irp.f +++ b/src/FourIdx/four_index_zmq.irp.f @@ -245,7 +245,7 @@ subroutine four_idx_pull_results(zmq_socket_pull, map_c, task_id) use map_module implicit none type(map_type), intent(inout) :: map_c - integer(ZMQ_PTR), intent(inout) :: zmq_socket_pull + integer(ZMQ_PTR), intent(in) :: zmq_socket_pull integer, intent(out) :: task_id From a8254ef73c76eef3cdf64ce5298c90db2ca6075f Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 11:05:12 +0100 Subject: [PATCH 26/54] Removed ZMQ_PUSH --- config/travis.cfg | 2 +- src/Determinants/EZFIO.cfg | 9 ++++++++- src/Determinants/density_matrix.irp.f | 13 +++++++++++-- src/Determinants/determinants.irp.f | 2 +- src/FourIdx/four_index_slave.irp.f | 2 +- src/ZMQ/utils.irp.f | 2 +- 6 files changed, 23 insertions(+), 7 deletions(-) diff --git a/config/travis.cfg b/config/travis.cfg index 42180e43..b0144119 100644 --- a/config/travis.cfg +++ b/config/travis.cfg @@ -13,7 +13,7 @@ FC : gfortran -ffree-line-length-none -I . -g LAPACK_LIB : -llapack -lrefblas -ltmglib IRPF90 : irpf90 -IRPF90_FLAGS : --ninja --align=32 --assert -DZMQ_PUSH +IRPF90_FLAGS : --ninja --align=32 --assert # Global options ################ diff --git a/src/Determinants/EZFIO.cfg b/src/Determinants/EZFIO.cfg index f4c5d866..dc7dddfb 100644 --- a/src/Determinants/EZFIO.cfg +++ b/src/Determinants/EZFIO.cfg @@ -115,7 +115,14 @@ default: False [n_det_max_stored] type: Det_number_max -doc: Maximum number of determinants for which the full H matrix is stored. Be careful, the memory requested scales as 10*n_det_max_stored**2. For instance, 90000 determinants represent a matrix of size 60 Gb. +doc: Maximum number of determinants for which the full h matrix is stored. be careful, the memory requested scales as 10*n_det_max_stored**2. for instance, 90000 determinants represent a matrix of size 60 Gb. interface: ezfio,provider,ocaml default: 90000 +[state_average_weight] +type: Strictly_positive_float +doc: Weight of the states in state-average calculations. +interface: ezfio,provider,ocaml +default: 1. +size: (determinants.n_states) + diff --git a/src/Determinants/density_matrix.irp.f b/src/Determinants/density_matrix.irp.f index 86c7fcd4..eef347e7 100644 --- a/src/Determinants/density_matrix.irp.f +++ b/src/Determinants/density_matrix.irp.f @@ -121,7 +121,8 @@ END_PROVIDER !$OMP mo_tot_num,psi_bilinear_matrix_rows,psi_bilinear_matrix_columns, & !$OMP psi_bilinear_matrix_transp_rows, psi_bilinear_matrix_transp_columns, & !$OMP psi_bilinear_matrix_order_reverse, psi_det_alpha_unique, psi_det_beta_unique, & - !$OMP psi_bilinear_matrix_values, psi_bilinear_matrix_transp_values) + !$OMP psi_bilinear_matrix_values, psi_bilinear_matrix_transp_values, & + !$OMP N_det_alpha_unique,N_det_beta_unique,irp_here) allocate(tmp_a(mo_tot_num,mo_tot_num,N_states), tmp_b(mo_tot_num,mo_tot_num,N_states) ) tmp_a = 0.d0 !$OMP DO SCHEDULE(dynamic,64) @@ -365,7 +366,15 @@ BEGIN_PROVIDER [ double precision, state_average_weight, (N_states) ] BEGIN_DOC ! Weights in the state-average calculation of the density matrix END_DOC - state_average_weight = 1.d0/dble(N_states) + logical :: exists + + state_average_weight = 0.d0 + call ezfio_has_state_average_weight(exists) + if (exists) then + call ezfio_get_state_average_weight(state_average_weight) + endif + state_average_weight = state_average_weight+1.d-31 + state_average_weight = state_average_weight/(sum(state_average_weight)) END_PROVIDER diff --git a/src/Determinants/determinants.irp.f b/src/Determinants/determinants.irp.f index 3722dff3..876eb124 100644 --- a/src/Determinants/determinants.irp.f +++ b/src/Determinants/determinants.irp.f @@ -177,7 +177,6 @@ BEGIN_PROVIDER [ double precision, psi_coef, (psi_det_size,N_states) ] integer :: i,k, N_int2 logical :: exists - double precision, allocatable :: psi_coef_read(:,:) character*(64) :: label PROVIDE read_wf N_det mo_label ezfio_filename @@ -200,6 +199,7 @@ BEGIN_PROVIDER [ double precision, psi_coef, (psi_det_size,N_states) ] if (exists) then + double precision, allocatable :: psi_coef_read(:,:) allocate (psi_coef_read(N_det,N_states)) call ezfio_get_determinants_psi_coef(psi_coef_read) do k=1,N_states diff --git a/src/FourIdx/four_index_slave.irp.f b/src/FourIdx/four_index_slave.irp.f index 5f82901a..ca07062f 100644 --- a/src/FourIdx/four_index_slave.irp.f +++ b/src/FourIdx/four_index_slave.irp.f @@ -101,7 +101,7 @@ subroutine four_index_transform_slave_work(map_a,matrix_B,LDB, & tmp=value(ik) if (tmp /= 0.d0) then a_array_ik(ii) = ik - a_array_j(ii) = int(iand(j,32767),2) ! Warning: integer*2 + a_array_j(ii) = int(j,2) ! Warning: integer*2 a_array_value(ii) = tmp ii=ii+1_8 endif diff --git a/src/ZMQ/utils.irp.f b/src/ZMQ/utils.irp.f index 86c13432..570cf30f 100644 --- a/src/ZMQ/utils.irp.f +++ b/src/ZMQ/utils.irp.f @@ -701,7 +701,7 @@ integer function disconnect_from_taskserver(zmq_to_qp_run_socket, worker_id) integer, intent(in) :: worker_id integer :: rc, sze - character*(64) :: message, reply, state + character*(512) :: message, reply, state disconnect_from_taskserver = 0 From 9196d3064e15b5f3f8db0d2fd58258d9238b8e41 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 11:26:38 +0100 Subject: [PATCH 27/54] Removed ZMQ in 4idx (temporary) --- src/Determinants/density_matrix.irp.f | 2 +- src/Integrals_Bielec/mo_bi_integrals.irp.f | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/Determinants/density_matrix.irp.f b/src/Determinants/density_matrix.irp.f index eef347e7..409f8420 100644 --- a/src/Determinants/density_matrix.irp.f +++ b/src/Determinants/density_matrix.irp.f @@ -368,7 +368,7 @@ BEGIN_PROVIDER [ double precision, state_average_weight, (N_states) ] END_DOC logical :: exists - state_average_weight = 0.d0 + state_average_weight = 1.d0 call ezfio_has_state_average_weight(exists) if (exists) then call ezfio_get_state_average_weight(state_average_weight) diff --git a/src/Integrals_Bielec/mo_bi_integrals.irp.f b/src/Integrals_Bielec/mo_bi_integrals.irp.f index 65594810..c39dba36 100644 --- a/src/Integrals_Bielec/mo_bi_integrals.irp.f +++ b/src/Integrals_Bielec/mo_bi_integrals.irp.f @@ -124,16 +124,16 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ] else ! call add_integrals_to_map(full_ijkl_bitmask_4) - call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & - mo_coef, size(mo_coef,1), & - 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & - 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) - -! call four_index_transform_block(ao_integrals_map,mo_integrals_map, & +! call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & ! 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) - +! + call four_index_transform_block(ao_integrals_map,mo_integrals_map, & + mo_coef, size(mo_coef,1), & + 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & + 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) +! ! call four_index_transform(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & From 87b0257dbeaee77311411cabad0e8888a9af712d Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 11:50:10 +0100 Subject: [PATCH 28/54] Fixed EZFIO --- src/Determinants/EZFIO.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Determinants/EZFIO.cfg b/src/Determinants/EZFIO.cfg index dc7dddfb..d5bc89dc 100644 --- a/src/Determinants/EZFIO.cfg +++ b/src/Determinants/EZFIO.cfg @@ -120,9 +120,9 @@ interface: ezfio,provider,ocaml default: 90000 [state_average_weight] -type: Strictly_positive_float +type: double precision doc: Weight of the states in state-average calculations. -interface: ezfio,provider,ocaml +interface: ezfio,provider default: 1. size: (determinants.n_states) From 864a2955e13af9440bb00627e2b95aa4a5342964 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 14:07:17 +0100 Subject: [PATCH 29/54] capitalize_ascii --- ocaml/Element.ml | 2 +- ocaml/qptypes_generator.ml | 6 +++--- src/Determinants/EZFIO.cfg | 2 +- src/Determinants/density_matrix.irp.f | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/ocaml/Element.ml b/ocaml/Element.ml index fd08b8da..827e7e41 100644 --- a/ocaml/Element.ml +++ b/ocaml/Element.ml @@ -14,7 +14,7 @@ type t = [@@deriving sexp] let of_string x = - match (String.capitalize (String.lowercase x)) with + match (String.capitalize_ascii (String.lowercase x)) with | "X" | "Dummy" -> X | "H" | "Hydrogen" -> H | "He" | "Helium" -> He diff --git a/ocaml/qptypes_generator.ml b/ocaml/qptypes_generator.ml index 600debf4..ba633a60 100644 --- a/ocaml/qptypes_generator.ml +++ b/ocaml/qptypes_generator.ml @@ -249,7 +249,7 @@ let parse_input input= in let typ = String_ext.strip typ and name = String_ext.strip name in - let typ_cap = String.capitalize typ in + let typ_cap = String.capitalize_ascii typ in let newstring = Printf.sprintf template name typ typ typ params_val typ typ typ typ params ( String_ext.strip text ) typ_cap in @@ -320,8 +320,8 @@ let parse_input_ezfio input= | _ -> assert false in Printf.sprintf ezfio_template - name typ typ typ typ typ typ typ typ (String.capitalize typ) - ezfio_func ezfio_func max min typ typ max msg min name (String.capitalize typ) + name typ typ typ typ typ typ typ typ (String.capitalize_ascii typ) + ezfio_func ezfio_func max min typ typ max msg min name (String.capitalize_ascii typ) end | _ -> failwith "Error in input_ezfio" in diff --git a/src/Determinants/EZFIO.cfg b/src/Determinants/EZFIO.cfg index d5bc89dc..9bf08b14 100644 --- a/src/Determinants/EZFIO.cfg +++ b/src/Determinants/EZFIO.cfg @@ -122,7 +122,7 @@ default: 90000 [state_average_weight] type: double precision doc: Weight of the states in state-average calculations. -interface: ezfio,provider +interface: ezfio default: 1. size: (determinants.n_states) diff --git a/src/Determinants/density_matrix.irp.f b/src/Determinants/density_matrix.irp.f index 409f8420..be28183b 100644 --- a/src/Determinants/density_matrix.irp.f +++ b/src/Determinants/density_matrix.irp.f @@ -369,9 +369,9 @@ BEGIN_PROVIDER [ double precision, state_average_weight, (N_states) ] logical :: exists state_average_weight = 1.d0 - call ezfio_has_state_average_weight(exists) + call ezfio_has_determinants_state_average_weight(exists) if (exists) then - call ezfio_get_state_average_weight(state_average_weight) + call ezfio_get_determinants_state_average_weight(state_average_weight) endif state_average_weight = state_average_weight+1.d-31 state_average_weight = state_average_weight/(sum(state_average_weight)) From e837d7d2ad0c821790e67ae4f4c3a0a66add0e9b Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 14:31:45 +0100 Subject: [PATCH 30/54] Compiles --- ocaml/Element.ml | 2 +- plugins/All_singles/H_apply.irp.f | 5 ----- plugins/Symmetry/find_sym.irp.f | 5 +++-- src/Determinants/EZFIO.cfg | 1 - 4 files changed, 4 insertions(+), 9 deletions(-) diff --git a/ocaml/Element.ml b/ocaml/Element.ml index 827e7e41..fd08b8da 100644 --- a/ocaml/Element.ml +++ b/ocaml/Element.ml @@ -14,7 +14,7 @@ type t = [@@deriving sexp] let of_string x = - match (String.capitalize_ascii (String.lowercase x)) with + match (String.capitalize (String.lowercase x)) with | "X" | "Dummy" -> X | "H" | "Hydrogen" -> H | "He" | "Helium" -> He diff --git a/plugins/All_singles/H_apply.irp.f b/plugins/All_singles/H_apply.irp.f index b30fb6d5..04eb1804 100644 --- a/plugins/All_singles/H_apply.irp.f +++ b/plugins/All_singles/H_apply.irp.f @@ -4,21 +4,18 @@ from generate_h_apply import * s = H_apply("just_1h_1p") s.set_selection_pt2("epstein_nesbet_2x2") -s.unset_skip() s.filter_only_1h1p() print s s = H_apply("just_2p") s.set_selection_pt2("epstein_nesbet_2x2") -s.unset_skip() s.filter_only_2p() print s s = H_apply("just_1p") s.set_selection_pt2("epstein_nesbet_2x2") -s.unset_skip() s.filter_only_1p() print s @@ -26,14 +23,12 @@ print s s = H_apply("just_1h_1p_singles",do_double_exc=False) s.set_selection_pt2("epstein_nesbet_2x2") -s.unset_skip() s.filter_only_1h1p() print s s = H_apply("just_mono",do_double_exc=False) s.set_selection_pt2("epstein_nesbet_2x2") -s.unset_skip() print s END_SHELL diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index c23146c5..80e2fccd 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -233,8 +233,9 @@ BEGIN_PROVIDER [ character*16, point_group ] ! Point group of the molecule END_DOC - character*2, save :: i_to_a(24) = (/ '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',& - '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24' /) + character*2, save :: i_to_a(24) = (/ ' 1', ' 2', ' 3', ' 4', ' 5', ' 6', ' 7', ' 8', ' 9', & + '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', & + '21', '22', '23', '24' /) point_group = 'C1' if (molecule_is_linear) then if (molecule_has_center_of_inversion) then diff --git a/src/Determinants/EZFIO.cfg b/src/Determinants/EZFIO.cfg index 9bf08b14..c86f831d 100644 --- a/src/Determinants/EZFIO.cfg +++ b/src/Determinants/EZFIO.cfg @@ -123,6 +123,5 @@ default: 90000 type: double precision doc: Weight of the states in state-average calculations. interface: ezfio -default: 1. size: (determinants.n_states) From 7bb866e8adb4aca3af45dda8a36b016c17698c8c Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 18:05:06 +0100 Subject: [PATCH 31/54] Forgot file --- plugins/mrcepa0/dress_types.f90 | 10 ++++++++ plugins/mrcepa0/mrcc_stoch_routines.irp.f | 14 ++++++++---- src/Determinants/determinants.irp.f | 28 +++++++++++------------ 3 files changed, 34 insertions(+), 18 deletions(-) create mode 100644 plugins/mrcepa0/dress_types.f90 diff --git a/plugins/mrcepa0/dress_types.f90 b/plugins/mrcepa0/dress_types.f90 new file mode 100644 index 00000000..7b1a3c70 --- /dev/null +++ b/plugins/mrcepa0/dress_types.f90 @@ -0,0 +1,10 @@ +module dress_types + type dress_buffer + double precision, pointer :: buf(:,:,:), buf0(:,:), coef(:) + double precision :: N + integer, pointer :: det_to_buf(:), buf_to_det(:) + integer :: free_under, pos, N_slot + logical :: full + endtype +end module + diff --git a/plugins/mrcepa0/mrcc_stoch_routines.irp.f b/plugins/mrcepa0/mrcc_stoch_routines.irp.f index 1ad9b8da..78940d5e 100644 --- a/plugins/mrcepa0/mrcc_stoch_routines.irp.f +++ b/plugins/mrcepa0/mrcc_stoch_routines.irp.f @@ -4,6 +4,14 @@ BEGIN_PROVIDER [ integer, fragment_first ] END_PROVIDER +BEGIN_PROVIDER [ integer, mrcc_stoch_istate ] + implicit none + BEGIN_DOC + ! State considered + END_DOC + mrcc_stoch_istate = 1 +END_PROVIDER + subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) use dress_types use f77_zmq @@ -14,7 +22,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) integer(ZMQ_PTR) :: zmq_to_qp_run_socket, zmq_socket_pull integer, external :: omp_get_thread_num - double precision, intent(in) :: relative_error, E + double precision, intent(in) :: relative_error, E(N_states) double precision, intent(out) :: mrcc(N_states) double precision, intent(out) :: delta(N_states, N_det_non_ref) double precision, intent(out) :: delta_s2(N_states, N_det_non_ref) @@ -67,6 +75,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) ! end do integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket + integer, external :: add_task_to_taskserver, zmq_set_running integer :: ipos ipos=1 do i=1,N_mrcc_jobs @@ -152,7 +161,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m integer(ZMQ_PTR) :: zmq_to_qp_run_socket integer(ZMQ_PTR), external :: new_zmq_pull_socket - integer(ZMQ_PTR) :: zmq_socket_pull integer :: more integer :: i, j, k, i_state, N, ntask @@ -191,7 +199,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m actually_computed = .false. zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() - zmq_socket_pull = new_zmq_pull_socket() allocate(task_id(N_det_generators), ind(1)) more = 1 if (time0 < 0.d0) then @@ -340,7 +347,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) - call end_zmq_pull_socket(zmq_socket_pull) end subroutine diff --git a/src/Determinants/determinants.irp.f b/src/Determinants/determinants.irp.f index 876eb124..40c4524a 100644 --- a/src/Determinants/determinants.irp.f +++ b/src/Determinants/determinants.irp.f @@ -195,27 +195,27 @@ BEGIN_PROVIDER [ double precision, psi_coef, (psi_det_size,N_states) ] exists = (label == mo_label) endif endif - endif - if (exists) then - - double precision, allocatable :: psi_coef_read(:,:) - allocate (psi_coef_read(N_det,N_states)) - call ezfio_get_determinants_psi_coef(psi_coef_read) - do k=1,N_states - do i=1,N_det - psi_coef(i,k) = psi_coef_read(i,k) + if (exists) then + + double precision, allocatable :: psi_coef_read(:,:) + allocate (psi_coef_read(N_det,N_states)) + print *, 'Read psi_coef', N_det, N_states + call ezfio_get_determinants_psi_coef(psi_coef_read) + do k=1,N_states + do i=1,N_det + psi_coef(i,k) = psi_coef_read(i,k) + enddo enddo - enddo - deallocate(psi_coef_read) - print *, 'Read psi_coef' - + deallocate(psi_coef_read) + + endif endif endif IRP_IF MPI include 'mpif.h' integer :: ierr - call MPI_BCAST( psi_coef, N_states*psi_det_size, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + call MPI_BCAST( psi_coef, size(psi_coef), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) if (ierr /= MPI_SUCCESS) then stop 'Unable to read psi_coef with MPI' endif From 333b4b1b07bbe7e204dacbf0fb4e0187bd5e6943 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 18 Dec 2017 18:40:49 +0100 Subject: [PATCH 32/54] Fixed MRCEPA --- plugins/mrcepa0/dressing_slave.irp.f | 1 - plugins/mrcepa0/mrcc_stoch_routines.irp.f | 25 +++++++++++++++-------- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/plugins/mrcepa0/dressing_slave.irp.f b/plugins/mrcepa0/dressing_slave.irp.f index 2f7ed195..fa486101 100644 --- a/plugins/mrcepa0/dressing_slave.irp.f +++ b/plugins/mrcepa0/dressing_slave.irp.f @@ -513,7 +513,6 @@ end logical, external :: is_in_wavefunction, isInCassd, detEq character*(512) :: task integer(ZMQ_PTR) :: zmq_to_qp_run_socket, zmq_socket_pull - integer, external :: add_task_to_taskserver integer :: KKsize = 1000000 integer, external :: add_task_to_taskserver diff --git a/plugins/mrcepa0/mrcc_stoch_routines.irp.f b/plugins/mrcepa0/mrcc_stoch_routines.irp.f index d9b93172..78940d5e 100644 --- a/plugins/mrcepa0/mrcc_stoch_routines.irp.f +++ b/plugins/mrcepa0/mrcc_stoch_routines.irp.f @@ -13,7 +13,7 @@ BEGIN_PROVIDER [ integer, mrcc_stoch_istate ] END_PROVIDER subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) - !use dress_types + use dress_types use f77_zmq implicit none @@ -32,14 +32,14 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) double precision, external :: omp_get_wtime double precision :: time - double precision :: w!(N_states) - integer, external :: add_task_to_taskserver + double precision :: w(N_states) + provide nproc fragment_first fragment_count mo_bielec_integrals_in_map mo_mono_elec_integral mrcc_weight psi_selectors - w = 0.d0 - w = 1.d0 + w(:) = 0.d0 + w(mrcc_stoch_istate) = 1.d0 call update_psi_average_norm_contrib(w) @@ -56,7 +56,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) integer, external :: zmq_put_N_det_generators integer, external :: zmq_put_N_det_selectors integer, external :: zmq_put_dvector - integer, external :: zmq_set_running + if (zmq_put_psi(zmq_to_qp_run_socket,1) == -1) then stop 'Unable to put psi on ZMQ server' endif @@ -107,6 +107,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) stop 'Unable to add task to task server' endif endif + if (zmq_set_running(zmq_to_qp_run_socket) == -1) then print *, irp_here, ': Failed in zmq_set_running' endif @@ -115,7 +116,7 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) !$OMP PRIVATE(i) i = omp_get_thread_num() if (i==0) then - call mrcc_collector(zmq_socket_pull,E, relative_error, delta, delta_s2, mrcc) + call mrcc_collector(zmq_socket_pull,E(mrcc_stoch_istate), relative_error, delta, delta_s2, mrcc) else call mrcc_slave_inproc(i) @@ -174,8 +175,6 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m logical, allocatable :: actually_computed(:) integer :: total_computed - delta = 0d0 - delta_s2 = 0d0 allocate(delta_det(N_states, N_det_non_ref, 0:comb_teeth+1, 2)) allocate(cp(N_states, N_det_non_ref, N_cp, 2), mrcc_detail(N_states, N_det_generators)) allocate(delta_loc(N_states, N_det_non_ref, 2)) @@ -270,6 +269,7 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m do i=2,N_det_generators if(.not. actually_computed(mrcc_jobs(i))) then + print *, "first not comp", i cur_cp = done_cp_at(i-1) exit end if @@ -310,6 +310,7 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m print *, irp_here, ': Error in sending abort signal (2)' endif endif + else if (cur_cp > old_cur_cp) then old_cur_cp = cur_cp @@ -322,6 +323,7 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m end do pullLoop if(total_computed == N_det_generators) then + print *, "TOTALLY COMPUTED" delta = 0d0 delta_s2 = 0d0 do i=comb_teeth+1,0,-1 @@ -330,16 +332,21 @@ subroutine mrcc_collector(zmq_socket_pull, E, relative_error, delta, delta_s2, m end do else + delta = cp(:,:,cur_cp,1) delta_s2 = cp(:,:,cur_cp,2) + do i=cp_first_tooth(cur_cp)-1,0,-1 delta += delta_det(:,:,i,1) delta_s2 += delta_det(:,:,i,2) end do end if + mrcc(1) = E + call end_zmq_to_qp_run_socket(zmq_to_qp_run_socket) + end subroutine From 28afcc8c59a2271e164cceaf1c8c1ebfbca26db9 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 09:59:46 +0100 Subject: [PATCH 33/54] Fixes #211 --- data/list_element.txt | 174 ++++++++++------------------- ocaml/Element.ml | 1 + ocaml/Makefile | 5 +- ocaml/element_create_db.ml | 27 +++++ plugins/QMC/save_for_qmcchem.irp.f | 1 - scripts/pseudo/elts_num_ele.py | 134 +++------------------- src/Nuclei/inertia.irp.f | 14 +-- src/Nuclei/nuclei.irp.f | 168 ++++------------------------ 8 files changed, 132 insertions(+), 392 deletions(-) create mode 100644 ocaml/element_create_db.ml diff --git a/data/list_element.txt b/data/list_element.txt index b2d081c1..2a9733e6 100644 --- a/data/list_element.txt +++ b/data/list_element.txt @@ -1,118 +1,56 @@ -1 H Hydrogen -2 He Helium -3 Li Lithium -4 Be Beryllium -5 B Boron -6 C Carbon -7 N Nitrogen -8 O Oxygen -9 F Fluorine -10 Ne Neon -11 Na Sodium -12 Mg Magnesium -13 Al Aluminum -14 Si Silicon -15 P Phosphorus -16 S Sulfur -17 Cl Chlorine -18 Ar Argon -19 K Potassium -20 Ca Calcium -21 Sc Scandium -22 Ti Titanium -23 V Vanadium -24 Cr Chromium -25 Mn Manganese -26 Fe Iron -27 Co Cobalt -28 Ni Nickel -29 Cu Copper -30 Zn Zinc -31 Ga Gallium -32 Ge Germanium -33 As Arsenic -34 Se Selenium -35 Br Bromine -36 Kr Krypton -37 Rb Rubidium -38 Sr Strontium -39 Y Yttrium -40 Zr Zirconium -41 Nb Niobium -42 Mo Molybdenum -43 Tc Technetium -44 Ru Ruthenium -45 Rh Rhodium -46 Pd Palladium -47 Ag Silver -48 Cd Cadmium -49 In Indium -50 Sn Tin -51 Sb Antimony -52 Te Tellurium -53 I Iodine -54 Xe Xenon -55 Cs Cesium -56 Ba Barium -57 La Lanthanum -58 Ce Cerium -59 Pr Praseodymium -60 Nd Neodymium -61 Pm Promethium -62 Sm Samarium -63 Eu Europium -64 Gd Gadolinium -65 Tb Terbium -66 Dy Dysprosium -67 Ho Holmium -68 Er Erbium -69 Tm Thulium -70 Yb Ytterbium -71 Lu Lutetium -72 Hf Hafnium -73 Ta Tantalum -74 W Tungsten -75 Re Rhenium -76 Os Osmium -77 Ir Iridium -78 Pt Platinum -79 Au Gold -80 Hg Mercury -81 Tl Thallium -82 Pb Lead -83 Bi Bismuth -84 Po Polonium -85 At Astatine -86 Rn Radon -87 Fr Francium -88 Ra Radium -89 Ac Actinium -90 Th Thorium -91 Pa Protactinium -92 U Uranium -93 Np Neptunium -94 Pu Plutonium -95 Am Americium -96 Cm Curium -97 Bk Berkelium -98 Cf Californium -99 Es Einsteinium -100 Fm Fermium -101 Md Mendelevium -102 No Nobelium -103 Lr Lawrencium -104 Rf Rutherfordium -105 Db Dubnium -106 Sg Seaborgium -107 Bh Bohrium -108 Hs Hassium -109 Mt Meitnerium -110 Ds Darmstadtium -111 Rg Roentgenium -112 Cn Copernicium -113 Uut Ununtrium -114 Fl Flerovium -115 Uup Ununpentium -116 Lv Livermorium -117 Uus Ununseptium -118 Uuo Ununoctium \ No newline at end of file + 0 X Dummy 0.000000 + 1 H Hydrogen 1.007900 + 2 He Helium 4.002600 + 3 Li Lithium 6.941000 + 4 Be Beryllium 9.012180 + 5 B Boron 10.810000 + 6 C Carbon 12.011000 + 7 N Nitrogen 14.006700 + 8 O Oxygen 15.999400 + 9 F Fluorine 18.998403 + 10 Ne Neon 20.179000 + 11 Na Sodium 22.989770 + 12 Mg Magnesium 24.305000 + 13 Al Aluminum 26.981540 + 14 Si Silicon 28.085500 + 15 P Phosphorus 30.973760 + 16 S Sulfur 32.060000 + 17 Cl Chlorine 35.453000 + 18 Ar Argon 39.948000 + 19 K Potassium 39.098300 + 20 Ca Calcium 40.080000 + 21 Sc Scandium 44.955900 + 22 Ti Titanium 47.900000 + 23 V Vanadium 50.941500 + 24 Cr Chromium 51.996000 + 25 Mn Manganese 54.938000 + 26 Fe Iron 55.933200 + 27 Co Cobalt 58.933200 + 28 Ni Nickel 58.700000 + 29 Cu Copper 63.546000 + 30 Zn Zinc 65.380000 + 31 Ga Gallium 69.720000 + 32 Ge Germanium 72.590000 + 33 As Arsenic 74.921600 + 34 Se Selenium 78.960000 + 35 Br Bromine 79.904000 + 36 Kr Krypton 83.800000 + 37 Rb Rubidium 85.467800 + 38 Sr Strontium 87.620000 + 39 Y Yttrium 88.905840 + 40 Zr Zirconium 91.224000 + 41 Nb Niobium 92.906370 + 42 Mo Molybdenum 95.950000 + 43 Tc Technetium 98.000000 + 44 Ru Ruthenium 101.070000 + 45 Rh Rhodium 102.905500 + 46 Pd Palladium 106.420000 + 47 Ag Silver 107.868200 + 48 Cd Cadmium 112.414000 + 49 In Indium 114.818000 + 50 Sn Tin 118.710000 + 51 Sb Antimony 121.760000 + 52 Te Tellurium 127.600000 + 53 I Iodine 126.904470 + 54 Xe Xenon 131.293000 + 78 Pt Platinum 195.084000 diff --git a/ocaml/Element.ml b/ocaml/Element.ml index fd08b8da..d3b68d52 100644 --- a/ocaml/Element.ml +++ b/ocaml/Element.ml @@ -499,3 +499,4 @@ let mass x = result x |> Positive_float.of_float + diff --git a/ocaml/Makefile b/ocaml/Makefile index 3534c614..b666187f 100644 --- a/ocaml/Makefile +++ b/ocaml/Makefile @@ -17,7 +17,7 @@ MLLFILES=$(wildcard *.mll) MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml Input_auto_generated.ml qp_edit.ml MLIFILES=$(wildcard *.mli) git ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml)) -ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native +ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native element_create_db.byte .PHONY: executables default remake_executables @@ -37,8 +37,9 @@ tests: $(ALL_TESTS) executables: $(QP_ROOT)/data/executables -$(QP_ROOT)/data/executables: remake_executables +$(QP_ROOT)/data/executables: remake_executables element_create_db.byte Qptypes.ml $(QP_ROOT)/scripts/module/create_executables_list.sh + $(QP_ROOT)/ocaml/element_create_db.byte external_libs: opam install cryptokit core diff --git a/ocaml/element_create_db.ml b/ocaml/element_create_db.ml new file mode 100644 index 00000000..03fbf3cd --- /dev/null +++ b/ocaml/element_create_db.ml @@ -0,0 +1,27 @@ +open Core +open Qptypes +open Element + +let () = + let indices = + Array.init 78 (fun i -> i) + in + Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt") + ~f:(fun out_channel -> + Array.init 110 ~f:(fun i -> + let element = + try + Some (of_charge (Charge.of_int i)) + with + | _ -> None + in + match element with + | None -> "" + | Some x -> Printf.sprintf "%3d %3s %s %f\n" + i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x ) + ) + |> Array.to_list + |> String.concat ~sep:"" + |> Out_channel.output_string out_channel + ) + diff --git a/plugins/QMC/save_for_qmcchem.irp.f b/plugins/QMC/save_for_qmcchem.irp.f index 771bf618..e9fa60c4 100644 --- a/plugins/QMC/save_for_qmcchem.irp.f +++ b/plugins/QMC/save_for_qmcchem.irp.f @@ -1,7 +1,6 @@ program save_for_qmc integer :: iunit - integer, external :: get_unit_and_open logical :: exists double precision :: e_ref diff --git a/scripts/pseudo/elts_num_ele.py b/scripts/pseudo/elts_num_ele.py index 8f31f4f7..f0aa3179 100644 --- a/scripts/pseudo/elts_num_ele.py +++ b/scripts/pseudo/elts_num_ele.py @@ -1,119 +1,15 @@ -name_to_elec = {"X": 0, - "H": 1, - "He": 2, - "Li": 3, - "Be": 4, - "B": 5, - "C": 6, - "N": 7, - "O": 8, - "F": 9, - "Ne": 10, - "Na": 11, - "Mg": 12, - "Al": 13, - "Si": 14, - "P": 15, - "S": 16, - "Cl": 17, - "Ar": 18, - "K": 19, - "Ca": 20, - "Sc": 21, - "Ti": 22, - "V": 23, - "Cr": 24, - "Mn": 25, - "Fe": 26, - "Co": 27, - "Ni": 28, - "Cu": 29, - "Zn": 30, - "Ga": 31, - "Ge": 32, - "As": 33, - "Se": 34, - "Br": 35, - "Kr": 36, - "Rb": 37, - "Sr": 38, - "Y": 39, - "Zr": 40, - "Nb": 41, - "Mo": 42, - "Tc": 43, - "Ru": 44, - "Rh": 45, - "Pd": 46, - "Ag": 47, - "Cd": 48, - "In": 49, - "Sn": 50, - "Sb": 51, - "Te": 52, - "I": 53, - "Xe": 54, - "Cs": 55, - "Ba": 56, - "La": 57, - "Ce": 58, - "Pr": 59, - "Nd": 60, - "Pm": 61, - "Sm": 62, - "Eu": 63, - "Gd": 64, - "Tb": 65, - "Dy": 66, - "Ho": 67, - "Er": 68, - "Tm": 69, - "Yb": 70, - "Lu": 71, - "Hf": 72, - "Ta": 73, - "W": 74, - "Re": 75, - "Os": 76, - "Ir": 77, - "Pt": 78, - "Au": 79, - "Hg": 80, - "Tl": 81, - "Pb": 82, - "Bi": 83, - "Po": 84, - "At": 85, - "Rn": 86, - "Fr": 87, - "Ra": 88, - "Ac": 89, - "Th": 90, - "Pa": 91, - "U": 92, - "Np": 93, - "Pu": 94, - "Am": 95, - "Cm": 96, - "Bk": 97, - "Cf": 98, - "Es": 99, - "Fm": 100, - "Md": 101, - "No": 102, - "Lr": 103, - "Rf": 104, - "Db": 105, - "Sg": 106, - "Bh": 107, - "Hs": 108, - "Mt": 109, - "Ds": 110, - "Rg": 111, - "Cn": 112, - "Uut": 113, - "Fl": 114, - "Uup": 115, - "Lv": 116, - "Uus": 117, - "Uuo": 118} +#!/usr/bin/env python + +import os + +QP_ROOT=os.environ["QP_ROOT"] + +name_to_elec = {} +with open(QP_ROOT+"/data/list_element.txt","r") as f: + data = f.readlines() + for line in data: + b = line.split() + name_to_elec[b[1]] = int(b[0]) + +if __name__ == '__main__': + print name_to_elec diff --git a/src/Nuclei/inertia.irp.f b/src/Nuclei/inertia.irp.f index c4517cde..97e32711 100644 --- a/src/Nuclei/inertia.irp.f +++ b/src/Nuclei/inertia.irp.f @@ -6,12 +6,12 @@ BEGIN_PROVIDER [ double precision, inertia_tensor, (3,3) ] integer :: i,j,k inertia_tensor = 0.d0 do k=1,nucl_num - inertia_tensor(1,1) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) - inertia_tensor(2,2) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) - inertia_tensor(3,3) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2) - inertia_tensor(1,2) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) ) - inertia_tensor(1,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) - inertia_tensor(2,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + inertia_tensor(1,1) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) + inertia_tensor(2,2) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) + inertia_tensor(3,3) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2) + inertia_tensor(1,2) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) ) + inertia_tensor(1,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + inertia_tensor(2,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) enddo inertia_tensor(2,1) = inertia_tensor(1,2) inertia_tensor(3,1) = inertia_tensor(1,3) @@ -27,6 +27,6 @@ END_PROVIDER integer :: k call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,inertia_tensor,3,3) print *, 'Rotational constants (GHZ):' - print *, (1805.65468542d0/inertia_tensor_eigenvalues(k), k=3,1,-1) + print *, (1805.65468542d0/(inertia_tensor_eigenvalues(k)+1.d-32), k=3,1,-1) END_PROVIDER diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 43609506..df5fcd00 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -260,155 +260,33 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] endif END_PROVIDER -BEGIN_PROVIDER [ character*(128), element_name, (78)] + BEGIN_PROVIDER [ character*(4), element_name, (0:128)] +&BEGIN_PROVIDER [ double precision, element_mass, (0:128) ] BEGIN_DOC ! Array of the name of element, sorted by nuclear charge (integer) END_DOC - element_name(1) = 'H' - element_name(2) = 'He' - element_name(3) = 'Li' - element_name(4) = 'Be' - element_name(5) = 'B' - element_name(6) = 'C' - element_name(7) = 'N' - element_name(8) = 'O' - element_name(9) = 'F' - element_name(10) = 'Ne' - element_name(11) = 'Na' - element_name(12) = 'Mg' - element_name(13) = 'Al' - element_name(14) = 'Si' - element_name(15) = 'P' - element_name(16) = 'S' - element_name(17) = 'Cl' - element_name(18) = 'Ar' - element_name(19) = 'K' - element_name(20) = 'Ca' - element_name(21) = 'Sc' - element_name(22) = 'Ti' - element_name(23) = 'V' - element_name(24) = 'Cr' - element_name(25) = 'Mn' - element_name(26) = 'Fe' - element_name(27) = 'Co' - element_name(28) = 'Ni' - element_name(29) = 'Cu' - element_name(30) = 'Zn' - element_name(31) = 'Ga' - element_name(32) = 'Ge' - element_name(33) = 'As' - element_name(34) = 'Se' - element_name(35) = 'Br' - element_name(36) = 'Kr' - element_name(37) = 'Rb' - element_name(38) = 'Sr' - element_name(39) = 'Y' - element_name(40) = 'Zr' - element_name(41) = 'Nb' - element_name(42) = 'Mo' - element_name(43) = 'Tc' - element_name(44) = 'Ru' - element_name(45) = 'Rh' - element_name(46) = 'Pd' - element_name(47) = 'Ag' - element_name(48) = 'Cd' - element_name(49) = 'In' - element_name(50) = 'Sn' - element_name(51) = 'Sb' - element_name(52) = 'Te' - element_name(53) = 'I' - element_name(54) = 'Xe' - element_name(55) = 'Cs' - element_name(56) = 'Ba' - element_name(57) = 'La' - element_name(58) = 'Ce' - element_name(59) = 'Pr' - element_name(60) = 'Nd' - element_name(61) = 'Pm' - element_name(62) = 'Sm' - element_name(63) = 'Eu' - element_name(64) = 'Gd' - element_name(65) = 'Tb' - element_name(66) = 'Dy' - element_name(67) = 'Ho' - element_name(68) = 'Er' - element_name(69) = 'Tm' - element_name(70) = 'Yb' - element_name(71) = 'Lu' - element_name(72) = 'Hf' - element_name(73) = 'Ta' - element_name(74) = 'W' - element_name(75) = 'Re' - element_name(76) = 'Os' - element_name(77) = 'Ir' - element_name(78) = 'Pt' + integer :: iunit + integer, external :: getUnitAndOpen + character*(128) :: filename + call getenv('QP_ROOT',filename) + filename = trim(filename)//'/data/list_element.txt' + iunit = getUnitAndOpen(filename,'r') + element_mass(:) = 0.d0 + do i=0,128 + write(element_name(i),'(I4)') i + enddo + character*(80) :: buffer, dummy + do + read(iunit,'(A80)',end=10) buffer + read(buffer,*) i ! First read i + read(buffer,*) i, element_name(i), dummy, element_mass(i) + print *, i, element_name(i), element_mass(i) + enddo + 10 continue + close(10) END_PROVIDER -BEGIN_PROVIDER [ double precision, mass, (0:110) ] - implicit none - BEGIN_DOC - ! Atomic masses - END_DOC - - mass( 0 ) = 0. - mass( 1 ) = 1.0079 - mass( 2 ) = 4.00260 - mass( 3 ) = 6.941 - mass( 4 ) = 9.01218 - mass( 5 ) = 10.81 - mass( 6 ) = 12.011 - mass( 7 ) = 14.0067 - mass( 8 ) = 15.9994 - mass( 9 ) = 18.998403 - mass( 10 ) = 20.179 - mass( 11 ) = 22.98977 - mass( 12 ) = 24.305 - mass( 13 ) = 26.98154 - mass( 14 ) = 28.0855 - mass( 15 ) = 30.97376 - mass( 16 ) = 32.06 - mass( 17 ) = 35.453 - mass( 18 ) = 39.948 - mass( 19 ) = 39.0983 - mass( 20 ) = 40.08 - mass( 21 ) = 44.9559 - mass( 22 ) = 47.90 - mass( 23 ) = 50.9415 - mass( 24 ) = 51.996 - mass( 25 ) = 54.9380 - mass( 26 ) = 55.9332 - mass( 27 ) = 58.9332 - mass( 28 ) = 58.70 - mass( 29 ) = 63.546 - mass( 30 ) = 65.38 - mass( 31 ) = 69.72 - mass( 32 ) = 72.59 - mass( 33 ) = 74.9216 - mass( 34 ) = 78.96 - mass( 35 ) = 79.904 - mass( 36 ) = 83.80 - mass( 37 ) = 85.4678 - mass( 38 ) = 87.62 - mass( 39 ) = 88.90584 - mass( 40 ) = 91.224 - mass( 41 ) = 92.90637 - mass( 42 ) = 95.95 - mass( 43 ) = 98. - mass( 44 ) = 101.07 - mass( 45 ) = 102.90550 - mass( 46 ) = 106.42 - mass( 47 ) = 107.8682 - mass( 48 ) = 112.414 - mass( 49 ) = 114.818 - mass( 50 ) = 118.710 - mass( 51 ) = 121.760 - mass( 52 ) = 127.60 - mass( 53 ) = 126.90447 - mass( 54 ) = 131.293 - mass( 78 ) = 195.084 -END_PROVIDER - BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] implicit none BEGIN_DOC @@ -420,9 +298,9 @@ BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] s = 0.d0 do i=1,nucl_num do j=1,3 - center_of_mass(j) += nucl_coord_input(i,j)* mass(int(nucl_charge(i))) + center_of_mass(j) += nucl_coord_input(i,j)* element_mass(int(nucl_charge(i))) enddo - s += mass(int(nucl_charge(i))) + s += element_mass(int(nucl_charge(i))) enddo s = 1.d0/s center_of_mass(:) = center_of_mass(:)*s From ac37a499d32732f79e76a8a5f7ac8fafece12dbf Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 10:07:13 +0100 Subject: [PATCH 34/54] Removed debug print --- src/Nuclei/nuclei.irp.f | 1 - 1 file changed, 1 deletion(-) diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index df5fcd00..0d14ae7e 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -280,7 +280,6 @@ END_PROVIDER read(iunit,'(A80)',end=10) buffer read(buffer,*) i ! First read i read(buffer,*) i, element_name(i), dummy, element_mass(i) - print *, i, element_name(i), element_mass(i) enddo 10 continue close(10) From 17e0518410142a3621854b45d70863359a1662eb Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 11:49:48 +0100 Subject: [PATCH 35/54] Revert input coordinates --- plugins/Symmetry/Symmetry.main.irp.f | 14 +- plugins/Symmetry/aos.irp.f | 38 +++-- plugins/Symmetry/find_sym.irp.f | 21 +-- plugins/Symmetry/nuclei.irp.f | 92 +++++++++++ src/Nuclei/inertia.irp.f | 12 +- src/Nuclei/nuclei.irp.f | 223 ++++++++++++--------------- 6 files changed, 235 insertions(+), 165 deletions(-) create mode 100644 plugins/Symmetry/nuclei.irp.f diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f index 78bf126e..1d438af5 100644 --- a/plugins/Symmetry/Symmetry.main.irp.f +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -6,13 +6,13 @@ program Symmetry integer :: i, j character*8 :: sym - print *, 'Molecule is linear:', molecule_is_linear - print *, 'Has center of inversion:', molecule_has_center_of_inversion - print *, 'Has S2n improper rotation:', molecule_has_improper_rotation - print *, 'Symmetry rotation axis:', sym_rotation_axis(:) - print *, 'Group:'//point_group - print *, 'Symmetry irreps', sym_irrep(1:n_irrep) - print *, 'Symmetry operations', sym_operation(1:n_irrep) + print *, 'Molecule is linear: ', molecule_is_linear + print *, 'Has center of inversion: ', molecule_has_center_of_inversion + print *, 'Has S2n improper rotation: ', molecule_has_improper_rotation + print *, 'Symmetry rotation axis: ', sym_rotation_axis(:) + print *, 'Group: '//point_group + print *, 'Symmetry irreps : ', sym_irrep(1:n_irrep) + print *, 'Symmetry operations : ', sym_operation(1:n_irrep) print *, 'Character table' do i=1,n_irrep print *, character_table(i,:) diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index e4352948..e0aade1e 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -7,8 +7,8 @@ BEGIN_PROVIDER [ double precision, sym_box, (3,2) ] sym_box(:,:) = 0.d0 do xyz=1,3 do i=1,nucl_num - sym_box(xyz,1) = min(sym_box(xyz,1), nucl_coord(i,xyz)) - sym_box(xyz,2) = max(sym_box(xyz,2), nucl_coord(i,xyz)) + sym_box(xyz,1) = min(sym_box(xyz,1), nucl_coord_sym(i,xyz)) + sym_box(xyz,2) = max(sym_box(xyz,2), nucl_coord_sym(i,xyz)) enddo enddo sym_box(:,1) = sym_box(:,1) - 2.d0 @@ -42,24 +42,28 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) double precision, intent(out) :: result(n_sym_points, ao_num) integer :: i, j double precision :: x, y, z + double precision :: x2, y2, z2 result (:,:) = 0.d0 do j=1,ao_num do i=1,n_sym_points - x = sym_points(1,i) - nucl_coord_transp(1,ao_nucl(j)) - y = sym_points(2,i) - nucl_coord_transp(2,ao_nucl(j)) - z = sym_points(3,i) - nucl_coord_transp(3,ao_nucl(j)) - x = x**ao_power(j,1) - y = y**ao_power(j,2) - z = z**ao_power(j,3) -! result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) - result(i,j) = x*y*z - if (result(i,j) > 0.d0) then - result(i,j) = 1.d0 - else if (result(i,j) < 0.d0) then - result(i,j) = -1.d0 - else - result(i,j) = 0.d0 - endif + x = sym_points(1,i) - nucl_coord_sym_transp(1,ao_nucl(j)) + y = sym_points(2,i) - nucl_coord_sym_transp(2,ao_nucl(j)) + z = sym_points(3,i) - nucl_coord_sym_transp(3,ao_nucl(j)) + x2 = x*sym_molecule_rotation_inv(1,1) + y*sym_molecule_rotation_inv(2,1) + z*sym_molecule_rotation_inv(3,1) + y2 = x*sym_molecule_rotation_inv(1,2) + y*sym_molecule_rotation_inv(2,2) + z*sym_molecule_rotation_inv(3,2) + z2 = x*sym_molecule_rotation_inv(1,3) + y*sym_molecule_rotation_inv(2,3) + z*sym_molecule_rotation_inv(3,3) + x = x2**ao_power(j,1) + y = y2**ao_power(j,2) + z = z2**ao_power(j,3) + result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) +! result(i,j) = x*y*z +! if (result(i,j) > 0.d0) then +! result(i,j) = 1.d0 +! else if (result(i,j) < 0.d0) then +! result(i,j) = -1.d0 +! else +! result(i,j) = 0.d0 +! endif enddo enddo diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 80e2fccd..95bb4e6c 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -20,7 +20,7 @@ BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] found = .False. do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + point(:) = nucl_coord_sym_transp(:,i) + nucl_coord_sym_transp(:,j) if (u_dot_u(point,3) < 1.d-5) then found = .True. exit @@ -52,10 +52,10 @@ BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] sym_rotation_axis(iaxis) = iorder do i=1,nucl_num found = .False. - call sym_apply_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) + call sym_apply_rotation(dble(iorder),iaxis,nucl_coord_sym_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point2(:) = nucl_coord_transp(:,j) - point(:) + point2(:) = nucl_coord_sym_transp(:,j) - point(:) if (u_dot_u(point2,3) < 1.d-5) then found = .True. exit @@ -148,10 +148,10 @@ BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] molecule_has_improper_rotation = .True. do i=1,nucl_num found = .False. - call sym_apply_improper_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) + call sym_apply_improper_rotation(dble(iorder),iaxis,nucl_coord_sym_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point2(:) = nucl_coord_transp(:,j) - point(:) + point2(:) = nucl_coord_sym_transp(:,j) - point(:) if (u_dot_u(point2,3) < 1.d-5) then found = .True. exit @@ -179,7 +179,7 @@ BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] found = .False. do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + point(:) = nucl_coord_sym_transp(:,i) + nucl_coord_sym_transp(:,j) if (u_dot_u(point,3) < 1.d-5) then found = .True. exit @@ -208,11 +208,11 @@ BEGIN_PROVIDER [ logical, molecule_has_sigma_plane, (3) ] molecule_has_sigma_plane(iaxis) = .True. do i=1,nucl_num found = .False. - point(:) = nucl_coord_transp(:,i) + point(:) = nucl_coord_sym_transp(:,i) point(iaxis) = -point(iaxis) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point2(:) = nucl_coord_transp(:,j) - point(:) + point2(:) = nucl_coord_sym_transp(:,j) - point(:) if (u_dot_u(point2,3) < 1.d-5) then found = .True. exit @@ -233,7 +233,7 @@ BEGIN_PROVIDER [ character*16, point_group ] ! Point group of the molecule END_DOC - character*2, save :: i_to_a(24) = (/ ' 1', ' 2', ' 3', ' 4', ' 5', ' 6', ' 7', ' 8', ' 9', & + character*2, save :: i_to_a(24) = (/ '1 ', '2 ', '3 ', '4 ', '5 ', '6 ', '7 ', '8 ', '9 ', & '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', & '21', '22', '23', '24' /) point_group = 'C1' @@ -366,7 +366,7 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] integer :: iangle, n_sym_points double precision :: angle integer :: iop, imo, ipoint, l, i - double precision :: sym_operations_on_mos(n_irrep) + double precision :: sym_operations_on_mos(mo_tot_num) logical :: possible_irrep(n_irrep,mo_tot_num) n_sym_points = 10000 @@ -443,6 +443,7 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] sym_operations_on_mos(imo) += x enddo sym_operations_on_mos(imo) *= 1.d0/n_sym_points + print *, iop, imo, sym_operations_on_mos(imo) if (dabs(sym_operations_on_mos(imo)-1.d0) < 1.d-2) then sym_operations_on_mos(imo)=1.d0 else if (dabs(sym_operations_on_mos(imo)+1.d0) < 1.d-2) then diff --git a/plugins/Symmetry/nuclei.irp.f b/plugins/Symmetry/nuclei.irp.f new file mode 100644 index 00000000..caa4781e --- /dev/null +++ b/plugins/Symmetry/nuclei.irp.f @@ -0,0 +1,92 @@ + +BEGIN_PROVIDER [ double precision, nucl_coord_sym, (nucl_num,3) ] + implicit none + + BEGIN_DOC + ! Nuclear coordinates in standard orientation + END_DOC + + if (mpi_master) then + integer :: i + do i=1,nucl_num + nucl_coord_sym(i,1) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & + (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & + (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) + nucl_coord_sym(i,2) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & + (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & + (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) + nucl_coord_sym(i,3) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & + (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & + (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) + enddo + + character*(64), parameter :: f = '(A16, 4(1X,F12.6))' + character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' + double precision, parameter :: a0= 0.529177249d0 + + call write_time(output_Nuclei) + write(output_Nuclei,'(A)') '' + write(output_Nuclei,'(A)') 'Nuclear Coordinates in standard orientation (Angstroms)' + write(output_Nuclei,'(A)') '=======================================================' + write(output_Nuclei,'(A)') '' + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,*) & + ' Atom Charge X Y Z ' + write(output_Nuclei,ft) & + '================','============','============','============','============' + do i=1,nucl_num + write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & + nucl_coord_sym(i,1)*a0, & + nucl_coord_sym(i,2)*a0, & + nucl_coord_sym(i,3)*a0 + enddo + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,'(A)') '' + + endif + + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nucl_coord_sym, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nucl_coord_sym with MPI' + endif + IRP_ENDIF + +END_PROVIDER + + +BEGIN_PROVIDER [ double precision, nucl_coord_sym_transp, (3,nucl_num) ] + implicit none + BEGIN_DOC + ! Transposed array of nucl_coord + END_DOC + integer :: i, k + nucl_coord_sym_transp = 0.d0 + + do i=1,nucl_num + nucl_coord_sym_transp(1,i) = nucl_coord_sym(i,1) + nucl_coord_sym_transp(2,i) = nucl_coord_sym(i,2) + nucl_coord_sym_transp(3,i) = nucl_coord_sym(i,3) + enddo +END_PROVIDER + +BEGIN_PROVIDER [ double precision, sym_molecule_rotation, (3,3) ] + implicit none + BEGIN_DOC + ! Rotation of the molecule to go from input orientation to standard orientation + END_DOC + call find_rotation(nucl_coord, size(nucl_coord,1), nucl_coord_sym, 3, sym_molecule_rotation, 3) +END_PROVIDER + +BEGIN_PROVIDER [ double precision, sym_molecule_rotation_inv, (3,3) ] + implicit none + BEGIN_DOC + ! Rotation of the molecule to go from standard orientation to input orientation + END_DOC + call find_rotation(nucl_coord_sym, size(nucl_coord_sym,1), nucl_coord, 3, sym_molecule_rotation_inv, 3) +END_PROVIDER + diff --git a/src/Nuclei/inertia.irp.f b/src/Nuclei/inertia.irp.f index 97e32711..d2cb7cf8 100644 --- a/src/Nuclei/inertia.irp.f +++ b/src/Nuclei/inertia.irp.f @@ -6,12 +6,12 @@ BEGIN_PROVIDER [ double precision, inertia_tensor, (3,3) ] integer :: i,j,k inertia_tensor = 0.d0 do k=1,nucl_num - inertia_tensor(1,1) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) - inertia_tensor(2,2) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) - inertia_tensor(3,3) += element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2) - inertia_tensor(1,2) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) ) - inertia_tensor(1,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) - inertia_tensor(2,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + inertia_tensor(1,1) += element_mass(int(nucl_charge(k))) * ((nucl_coord(k,2)-center_of_mass(2))**2 + (nucl_coord(k,3)-center_of_mass(3))**2) + inertia_tensor(2,2) += element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1))**2 + (nucl_coord(k,3)-center_of_mass(3))**2) + inertia_tensor(3,3) += element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1))**2 + (nucl_coord(k,2)-center_of_mass(2))**2) + inertia_tensor(1,2) -= element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1)) * (nucl_coord(k,2)-center_of_mass(2)) ) + inertia_tensor(1,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1)) * (nucl_coord(k,3)-center_of_mass(3)) ) + inertia_tensor(2,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord(k,2)-center_of_mass(2)) * (nucl_coord(k,3)-center_of_mass(3)) ) enddo inertia_tensor(2,1) = inertia_tensor(1,2) inertia_tensor(3,1) = inertia_tensor(1,3) diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 0d14ae7e..7e4de39f 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -1,4 +1,4 @@ -BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] +BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] implicit none BEGIN_DOC @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] if (mpi_master) then double precision, allocatable :: buffer(:,:) - nucl_coord_input = 0.d0 + nucl_coord = 0.d0 allocate (buffer(nucl_num,3)) buffer = 0.d0 logical :: has @@ -22,7 +22,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] do i=1,3 do j=1,nucl_num - nucl_coord_input(j,i) = buffer(j,i) + nucl_coord(j,i) = buffer(j,i) enddo enddo deallocate(buffer) @@ -31,65 +31,6 @@ BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 - call write_time(output_Nuclei) - write(output_Nuclei,'(A)') '' - write(output_Nuclei,'(A)') 'Input Nuclear Coordinates (Angstroms)' - write(output_Nuclei,'(A)') '=====================================' - write(output_Nuclei,'(A)') '' - write(output_Nuclei,ft) & - '================','============','============','============','============' - write(output_Nuclei,*) & - ' Atom Charge X Y Z ' - write(output_Nuclei,ft) & - '================','============','============','============','============' - do i=1,nucl_num - write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & - nucl_coord_input(i,1)*a0, & - nucl_coord_input(i,2)*a0, & - nucl_coord_input(i,3)*a0 - enddo - write(output_Nuclei,ft) & - '================','============','============','============','============' - write(output_Nuclei,'(A)') '' - - endif - - IRP_IF MPI - include 'mpif.h' - integer :: ierr - call MPI_BCAST( nucl_coord_input, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read nucl_coord_input with MPI' - endif - IRP_ENDIF - -END_PROVIDER - -BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] - implicit none - - BEGIN_DOC - ! Nuclear coordinates in standard orientation - END_DOC - - if (mpi_master) then - integer :: i - do i=1,nucl_num - nucl_coord(i,1) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) - nucl_coord(i,2) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) - nucl_coord(i,3) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) - enddo - - character*(64), parameter :: f = '(A16, 4(1X,F12.6))' - character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' - double precision, parameter :: a0= 0.529177249d0 - call write_time(output_Nuclei) write(output_Nuclei,'(A)') '' write(output_Nuclei,'(A)') 'Nuclear Coordinates (Angstroms)' @@ -205,35 +146,36 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] END_DOC PROVIDE mpi_master nucl_coord nucl_charge nucl_num - if (disk_access_nuclear_repulsion.EQ.'Read') then - logical :: has - - if (mpi_master) then - call ezfio_has_nuclei_nuclear_repulsion(has) - if (has) then - call ezfio_get_nuclei_nuclear_repulsion(nuclear_repulsion) - else - print *, 'nuclei/nuclear_repulsion not found in EZFIO file' - stop 1 + if (mpi_master) then + if (disk_access_nuclear_repulsion.EQ.'Read') then + logical :: has + + if (mpi_master) then + call ezfio_has_nuclei_nuclear_repulsion(has) + if (has) then + call ezfio_get_nuclei_nuclear_repulsion(nuclear_repulsion) + else + print *, 'nuclei/nuclear_repulsion not found in EZFIO file' + stop 1 + endif + print*, 'Read nuclear_repulsion' endif - print*, 'Read nuclear_repulsion' - endif - IRP_IF MPI - include 'mpif.h' - integer :: ierr - call MPI_BCAST( nuclear_repulsion, 1, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read nuclear_repulsion with MPI' - endif - IRP_ENDIF - - - else - - integer :: k,l - double precision :: Z12, r2, x(3) - nuclear_repulsion = 0.d0 - do l = 1, nucl_num + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nuclear_repulsion, 1, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nuclear_repulsion with MPI' + endif + IRP_ENDIF + + + else + + integer :: k,l + double precision :: Z12, r2, x(3) + nuclear_repulsion = 0.d0 + do l = 1, nucl_num do k = 1, nucl_num if(k == l) then cycle @@ -245,45 +187,76 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] r2 = x(1)*x(1) + x(2)*x(2) + x(3)*x(3) nuclear_repulsion += Z12/dsqrt(r2) enddo - enddo - nuclear_repulsion *= 0.5d0 - end if - - call write_time(output_Nuclei) - call write_double(output_Nuclei,nuclear_repulsion, & - 'Nuclear repulsion energy') - - if (disk_access_nuclear_repulsion.EQ.'Write') then - if (mpi_master) then - call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion) + enddo + nuclear_repulsion *= 0.5d0 + end if + + call write_time(output_Nuclei) + call write_double(output_Nuclei,nuclear_repulsion, & + 'Nuclear repulsion energy') + + if (disk_access_nuclear_repulsion.EQ.'Write') then + if (mpi_master) then + call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion) + endif endif - endif + + endif + + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( element_name, size(element_name)*4, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read element_name with MPI' + endif + call MPI_BCAST( element_mass, size(element_mass), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read element_name with MPI' + endif + IRP_ENDIF + END_PROVIDER - BEGIN_PROVIDER [ character*(4), element_name, (0:128)] + BEGIN_PROVIDER [ character*(4), element_name, (0:128)] &BEGIN_PROVIDER [ double precision, element_mass, (0:128) ] - BEGIN_DOC - ! Array of the name of element, sorted by nuclear charge (integer) - END_DOC - integer :: iunit - integer, external :: getUnitAndOpen - character*(128) :: filename - call getenv('QP_ROOT',filename) - filename = trim(filename)//'/data/list_element.txt' - iunit = getUnitAndOpen(filename,'r') - element_mass(:) = 0.d0 - do i=0,128 - write(element_name(i),'(I4)') i - enddo - character*(80) :: buffer, dummy - do - read(iunit,'(A80)',end=10) buffer - read(buffer,*) i ! First read i - read(buffer,*) i, element_name(i), dummy, element_mass(i) - enddo - 10 continue - close(10) + BEGIN_DOC + ! Array of the name of element, sorted by nuclear charge (integer) + END_DOC + integer :: iunit + integer, external :: getUnitAndOpen + character*(128) :: filename + if (mpi_master) then + call getenv('QP_ROOT',filename) + filename = trim(filename)//'/data/list_element.txt' + iunit = getUnitAndOpen(filename,'r') + element_mass(:) = 0.d0 + do i=0,128 + write(element_name(i),'(I4)') i + enddo + character*(80) :: buffer, dummy + do + read(iunit,'(A80)',end=10) buffer + read(buffer,*) i ! First read i + read(buffer,*) i, element_name(i), dummy, element_mass(i) + enddo + 10 continue + close(10) + endif + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( element_name, size(element_name)*4, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read element_name with MPI' + endif + call MPI_BCAST( element_mass, size(element_mass), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read element_name with MPI' + endif + IRP_ENDIF + END_PROVIDER BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] @@ -297,7 +270,7 @@ BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] s = 0.d0 do i=1,nucl_num do j=1,3 - center_of_mass(j) += nucl_coord_input(i,j)* element_mass(int(nucl_charge(i))) + center_of_mass(j) += nucl_coord(i,j)* element_mass(int(nucl_charge(i))) enddo s += element_mass(int(nucl_charge(i))) enddo From d031148512c5b4d848896ce67273df7f680b0515 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 11:54:20 +0100 Subject: [PATCH 36/54] Fix MPI --- src/Nuclei/nuclei.irp.f | 119 ++++++++++++++++++---------------------- 1 file changed, 52 insertions(+), 67 deletions(-) diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 7e4de39f..910e9167 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -146,76 +146,61 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] END_DOC PROVIDE mpi_master nucl_coord nucl_charge nucl_num - if (mpi_master) then - if (disk_access_nuclear_repulsion.EQ.'Read') then - logical :: has - - if (mpi_master) then - call ezfio_has_nuclei_nuclear_repulsion(has) - if (has) then - call ezfio_get_nuclei_nuclear_repulsion(nuclear_repulsion) - else - print *, 'nuclei/nuclear_repulsion not found in EZFIO file' - stop 1 - endif - print*, 'Read nuclear_repulsion' - endif - IRP_IF MPI - include 'mpif.h' - integer :: ierr - call MPI_BCAST( nuclear_repulsion, 1, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read nuclear_repulsion with MPI' - endif - IRP_ENDIF - - - else - - integer :: k,l - double precision :: Z12, r2, x(3) - nuclear_repulsion = 0.d0 - do l = 1, nucl_num - do k = 1, nucl_num - if(k == l) then - cycle - endif - Z12 = nucl_charge(k)*nucl_charge(l) - x(1) = nucl_coord(k,1) - nucl_coord(l,1) - x(2) = nucl_coord(k,2) - nucl_coord(l,2) - x(3) = nucl_coord(k,3) - nucl_coord(l,3) - r2 = x(1)*x(1) + x(2)*x(2) + x(3)*x(3) - nuclear_repulsion += Z12/dsqrt(r2) - enddo - enddo - nuclear_repulsion *= 0.5d0 - end if + if (disk_access_nuclear_repulsion.EQ.'Read') then + logical :: has - call write_time(output_Nuclei) - call write_double(output_Nuclei,nuclear_repulsion, & - 'Nuclear repulsion energy') - - if (disk_access_nuclear_repulsion.EQ.'Write') then - if (mpi_master) then - call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion) + if (mpi_master) then + call ezfio_has_nuclei_nuclear_repulsion(has) + if (has) then + call ezfio_get_nuclei_nuclear_repulsion(nuclear_repulsion) + else + print *, 'nuclei/nuclear_repulsion not found in EZFIO file' + stop 1 endif + print*, 'Read nuclear_repulsion' endif - - endif - - IRP_IF MPI - include 'mpif.h' - integer :: ierr - call MPI_BCAST( element_name, size(element_name)*4, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read element_name with MPI' - endif - call MPI_BCAST( element_mass, size(element_mass), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read element_name with MPI' - endif - IRP_ENDIF - + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nuclear_repulsion, 1, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nuclear_repulsion with MPI' + endif + IRP_ENDIF + + + else + + integer :: k,l + double precision :: Z12, r2, x(3) + nuclear_repulsion = 0.d0 + do l = 1, nucl_num + do k = 1, nucl_num + if(k == l) then + cycle + endif + Z12 = nucl_charge(k)*nucl_charge(l) + x(1) = nucl_coord(k,1) - nucl_coord(l,1) + x(2) = nucl_coord(k,2) - nucl_coord(l,2) + x(3) = nucl_coord(k,3) - nucl_coord(l,3) + r2 = x(1)*x(1) + x(2)*x(2) + x(3)*x(3) + nuclear_repulsion += Z12/dsqrt(r2) + enddo + enddo + nuclear_repulsion *= 0.5d0 + end if + + call write_time(output_Nuclei) + call write_double(output_Nuclei,nuclear_repulsion, & + 'Nuclear repulsion energy') + + if (disk_access_nuclear_repulsion.EQ.'Write') then + if (mpi_master) then + call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion) + endif + endif + + END_PROVIDER BEGIN_PROVIDER [ character*(4), element_name, (0:128)] From 7ebc2ac89620a8cad0254b02673e92790d3a8d70 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 13:48:21 +0100 Subject: [PATCH 37/54] Fixed last merge (#217) * Fixes #211 * Removed debug print * Revert input coordinates * Fix MPI --- data/list_element.txt | 174 +++++----------- ocaml/Element.ml | 1 + ocaml/Makefile | 5 +- ocaml/element_create_db.ml | 27 +++ plugins/QMC/save_for_qmcchem.irp.f | 1 - plugins/Symmetry/Symmetry.main.irp.f | 14 +- plugins/Symmetry/aos.irp.f | 38 ++-- plugins/Symmetry/find_sym.irp.f | 21 +- plugins/Symmetry/nuclei.irp.f | 92 +++++++++ scripts/pseudo/elts_num_ele.py | 134 ++---------- src/Nuclei/inertia.irp.f | 14 +- src/Nuclei/nuclei.irp.f | 299 ++++++--------------------- 12 files changed, 307 insertions(+), 513 deletions(-) create mode 100644 ocaml/element_create_db.ml create mode 100644 plugins/Symmetry/nuclei.irp.f diff --git a/data/list_element.txt b/data/list_element.txt index b2d081c1..2a9733e6 100644 --- a/data/list_element.txt +++ b/data/list_element.txt @@ -1,118 +1,56 @@ -1 H Hydrogen -2 He Helium -3 Li Lithium -4 Be Beryllium -5 B Boron -6 C Carbon -7 N Nitrogen -8 O Oxygen -9 F Fluorine -10 Ne Neon -11 Na Sodium -12 Mg Magnesium -13 Al Aluminum -14 Si Silicon -15 P Phosphorus -16 S Sulfur -17 Cl Chlorine -18 Ar Argon -19 K Potassium -20 Ca Calcium -21 Sc Scandium -22 Ti Titanium -23 V Vanadium -24 Cr Chromium -25 Mn Manganese -26 Fe Iron -27 Co Cobalt -28 Ni Nickel -29 Cu Copper -30 Zn Zinc -31 Ga Gallium -32 Ge Germanium -33 As Arsenic -34 Se Selenium -35 Br Bromine -36 Kr Krypton -37 Rb Rubidium -38 Sr Strontium -39 Y Yttrium -40 Zr Zirconium -41 Nb Niobium -42 Mo Molybdenum -43 Tc Technetium -44 Ru Ruthenium -45 Rh Rhodium -46 Pd Palladium -47 Ag Silver -48 Cd Cadmium -49 In Indium -50 Sn Tin -51 Sb Antimony -52 Te Tellurium -53 I Iodine -54 Xe Xenon -55 Cs Cesium -56 Ba Barium -57 La Lanthanum -58 Ce Cerium -59 Pr Praseodymium -60 Nd Neodymium -61 Pm Promethium -62 Sm Samarium -63 Eu Europium -64 Gd Gadolinium -65 Tb Terbium -66 Dy Dysprosium -67 Ho Holmium -68 Er Erbium -69 Tm Thulium -70 Yb Ytterbium -71 Lu Lutetium -72 Hf Hafnium -73 Ta Tantalum -74 W Tungsten -75 Re Rhenium -76 Os Osmium -77 Ir Iridium -78 Pt Platinum -79 Au Gold -80 Hg Mercury -81 Tl Thallium -82 Pb Lead -83 Bi Bismuth -84 Po Polonium -85 At Astatine -86 Rn Radon -87 Fr Francium -88 Ra Radium -89 Ac Actinium -90 Th Thorium -91 Pa Protactinium -92 U Uranium -93 Np Neptunium -94 Pu Plutonium -95 Am Americium -96 Cm Curium -97 Bk Berkelium -98 Cf Californium -99 Es Einsteinium -100 Fm Fermium -101 Md Mendelevium -102 No Nobelium -103 Lr Lawrencium -104 Rf Rutherfordium -105 Db Dubnium -106 Sg Seaborgium -107 Bh Bohrium -108 Hs Hassium -109 Mt Meitnerium -110 Ds Darmstadtium -111 Rg Roentgenium -112 Cn Copernicium -113 Uut Ununtrium -114 Fl Flerovium -115 Uup Ununpentium -116 Lv Livermorium -117 Uus Ununseptium -118 Uuo Ununoctium \ No newline at end of file + 0 X Dummy 0.000000 + 1 H Hydrogen 1.007900 + 2 He Helium 4.002600 + 3 Li Lithium 6.941000 + 4 Be Beryllium 9.012180 + 5 B Boron 10.810000 + 6 C Carbon 12.011000 + 7 N Nitrogen 14.006700 + 8 O Oxygen 15.999400 + 9 F Fluorine 18.998403 + 10 Ne Neon 20.179000 + 11 Na Sodium 22.989770 + 12 Mg Magnesium 24.305000 + 13 Al Aluminum 26.981540 + 14 Si Silicon 28.085500 + 15 P Phosphorus 30.973760 + 16 S Sulfur 32.060000 + 17 Cl Chlorine 35.453000 + 18 Ar Argon 39.948000 + 19 K Potassium 39.098300 + 20 Ca Calcium 40.080000 + 21 Sc Scandium 44.955900 + 22 Ti Titanium 47.900000 + 23 V Vanadium 50.941500 + 24 Cr Chromium 51.996000 + 25 Mn Manganese 54.938000 + 26 Fe Iron 55.933200 + 27 Co Cobalt 58.933200 + 28 Ni Nickel 58.700000 + 29 Cu Copper 63.546000 + 30 Zn Zinc 65.380000 + 31 Ga Gallium 69.720000 + 32 Ge Germanium 72.590000 + 33 As Arsenic 74.921600 + 34 Se Selenium 78.960000 + 35 Br Bromine 79.904000 + 36 Kr Krypton 83.800000 + 37 Rb Rubidium 85.467800 + 38 Sr Strontium 87.620000 + 39 Y Yttrium 88.905840 + 40 Zr Zirconium 91.224000 + 41 Nb Niobium 92.906370 + 42 Mo Molybdenum 95.950000 + 43 Tc Technetium 98.000000 + 44 Ru Ruthenium 101.070000 + 45 Rh Rhodium 102.905500 + 46 Pd Palladium 106.420000 + 47 Ag Silver 107.868200 + 48 Cd Cadmium 112.414000 + 49 In Indium 114.818000 + 50 Sn Tin 118.710000 + 51 Sb Antimony 121.760000 + 52 Te Tellurium 127.600000 + 53 I Iodine 126.904470 + 54 Xe Xenon 131.293000 + 78 Pt Platinum 195.084000 diff --git a/ocaml/Element.ml b/ocaml/Element.ml index fd08b8da..d3b68d52 100644 --- a/ocaml/Element.ml +++ b/ocaml/Element.ml @@ -499,3 +499,4 @@ let mass x = result x |> Positive_float.of_float + diff --git a/ocaml/Makefile b/ocaml/Makefile index 3534c614..b666187f 100644 --- a/ocaml/Makefile +++ b/ocaml/Makefile @@ -17,7 +17,7 @@ MLLFILES=$(wildcard *.mll) MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml Input_auto_generated.ml qp_edit.ml MLIFILES=$(wildcard *.mli) git ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml)) -ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native +ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qp_edit.native element_create_db.byte .PHONY: executables default remake_executables @@ -37,8 +37,9 @@ tests: $(ALL_TESTS) executables: $(QP_ROOT)/data/executables -$(QP_ROOT)/data/executables: remake_executables +$(QP_ROOT)/data/executables: remake_executables element_create_db.byte Qptypes.ml $(QP_ROOT)/scripts/module/create_executables_list.sh + $(QP_ROOT)/ocaml/element_create_db.byte external_libs: opam install cryptokit core diff --git a/ocaml/element_create_db.ml b/ocaml/element_create_db.ml new file mode 100644 index 00000000..03fbf3cd --- /dev/null +++ b/ocaml/element_create_db.ml @@ -0,0 +1,27 @@ +open Core +open Qptypes +open Element + +let () = + let indices = + Array.init 78 (fun i -> i) + in + Out_channel.with_file (Qpackage.root ^ "/data/list_element.txt") + ~f:(fun out_channel -> + Array.init 110 ~f:(fun i -> + let element = + try + Some (of_charge (Charge.of_int i)) + with + | _ -> None + in + match element with + | None -> "" + | Some x -> Printf.sprintf "%3d %3s %s %f\n" + i (to_string x) (to_long_string x) (Positive_float.to_float @@ mass x ) + ) + |> Array.to_list + |> String.concat ~sep:"" + |> Out_channel.output_string out_channel + ) + diff --git a/plugins/QMC/save_for_qmcchem.irp.f b/plugins/QMC/save_for_qmcchem.irp.f index 771bf618..e9fa60c4 100644 --- a/plugins/QMC/save_for_qmcchem.irp.f +++ b/plugins/QMC/save_for_qmcchem.irp.f @@ -1,7 +1,6 @@ program save_for_qmc integer :: iunit - integer, external :: get_unit_and_open logical :: exists double precision :: e_ref diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f index 78bf126e..1d438af5 100644 --- a/plugins/Symmetry/Symmetry.main.irp.f +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -6,13 +6,13 @@ program Symmetry integer :: i, j character*8 :: sym - print *, 'Molecule is linear:', molecule_is_linear - print *, 'Has center of inversion:', molecule_has_center_of_inversion - print *, 'Has S2n improper rotation:', molecule_has_improper_rotation - print *, 'Symmetry rotation axis:', sym_rotation_axis(:) - print *, 'Group:'//point_group - print *, 'Symmetry irreps', sym_irrep(1:n_irrep) - print *, 'Symmetry operations', sym_operation(1:n_irrep) + print *, 'Molecule is linear: ', molecule_is_linear + print *, 'Has center of inversion: ', molecule_has_center_of_inversion + print *, 'Has S2n improper rotation: ', molecule_has_improper_rotation + print *, 'Symmetry rotation axis: ', sym_rotation_axis(:) + print *, 'Group: '//point_group + print *, 'Symmetry irreps : ', sym_irrep(1:n_irrep) + print *, 'Symmetry operations : ', sym_operation(1:n_irrep) print *, 'Character table' do i=1,n_irrep print *, character_table(i,:) diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index e4352948..e0aade1e 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -7,8 +7,8 @@ BEGIN_PROVIDER [ double precision, sym_box, (3,2) ] sym_box(:,:) = 0.d0 do xyz=1,3 do i=1,nucl_num - sym_box(xyz,1) = min(sym_box(xyz,1), nucl_coord(i,xyz)) - sym_box(xyz,2) = max(sym_box(xyz,2), nucl_coord(i,xyz)) + sym_box(xyz,1) = min(sym_box(xyz,1), nucl_coord_sym(i,xyz)) + sym_box(xyz,2) = max(sym_box(xyz,2), nucl_coord_sym(i,xyz)) enddo enddo sym_box(:,1) = sym_box(:,1) - 2.d0 @@ -42,24 +42,28 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) double precision, intent(out) :: result(n_sym_points, ao_num) integer :: i, j double precision :: x, y, z + double precision :: x2, y2, z2 result (:,:) = 0.d0 do j=1,ao_num do i=1,n_sym_points - x = sym_points(1,i) - nucl_coord_transp(1,ao_nucl(j)) - y = sym_points(2,i) - nucl_coord_transp(2,ao_nucl(j)) - z = sym_points(3,i) - nucl_coord_transp(3,ao_nucl(j)) - x = x**ao_power(j,1) - y = y**ao_power(j,2) - z = z**ao_power(j,3) -! result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) - result(i,j) = x*y*z - if (result(i,j) > 0.d0) then - result(i,j) = 1.d0 - else if (result(i,j) < 0.d0) then - result(i,j) = -1.d0 - else - result(i,j) = 0.d0 - endif + x = sym_points(1,i) - nucl_coord_sym_transp(1,ao_nucl(j)) + y = sym_points(2,i) - nucl_coord_sym_transp(2,ao_nucl(j)) + z = sym_points(3,i) - nucl_coord_sym_transp(3,ao_nucl(j)) + x2 = x*sym_molecule_rotation_inv(1,1) + y*sym_molecule_rotation_inv(2,1) + z*sym_molecule_rotation_inv(3,1) + y2 = x*sym_molecule_rotation_inv(1,2) + y*sym_molecule_rotation_inv(2,2) + z*sym_molecule_rotation_inv(3,2) + z2 = x*sym_molecule_rotation_inv(1,3) + y*sym_molecule_rotation_inv(2,3) + z*sym_molecule_rotation_inv(3,3) + x = x2**ao_power(j,1) + y = y2**ao_power(j,2) + z = z2**ao_power(j,3) + result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) +! result(i,j) = x*y*z +! if (result(i,j) > 0.d0) then +! result(i,j) = 1.d0 +! else if (result(i,j) < 0.d0) then +! result(i,j) = -1.d0 +! else +! result(i,j) = 0.d0 +! endif enddo enddo diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 80e2fccd..95bb4e6c 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -20,7 +20,7 @@ BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] found = .False. do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + point(:) = nucl_coord_sym_transp(:,i) + nucl_coord_sym_transp(:,j) if (u_dot_u(point,3) < 1.d-5) then found = .True. exit @@ -52,10 +52,10 @@ BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] sym_rotation_axis(iaxis) = iorder do i=1,nucl_num found = .False. - call sym_apply_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) + call sym_apply_rotation(dble(iorder),iaxis,nucl_coord_sym_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point2(:) = nucl_coord_transp(:,j) - point(:) + point2(:) = nucl_coord_sym_transp(:,j) - point(:) if (u_dot_u(point2,3) < 1.d-5) then found = .True. exit @@ -148,10 +148,10 @@ BEGIN_PROVIDER [ logical, molecule_has_improper_rotation ] molecule_has_improper_rotation = .True. do i=1,nucl_num found = .False. - call sym_apply_improper_rotation(dble(iorder),iaxis,nucl_coord_transp(1,i),point) + call sym_apply_improper_rotation(dble(iorder),iaxis,nucl_coord_sym_transp(1,i),point) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point2(:) = nucl_coord_transp(:,j) - point(:) + point2(:) = nucl_coord_sym_transp(:,j) - point(:) if (u_dot_u(point2,3) < 1.d-5) then found = .True. exit @@ -179,7 +179,7 @@ BEGIN_PROVIDER [ logical, molecule_has_center_of_inversion ] found = .False. do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point(:) = nucl_coord_transp(:,i) + nucl_coord_transp(:,j) + point(:) = nucl_coord_sym_transp(:,i) + nucl_coord_sym_transp(:,j) if (u_dot_u(point,3) < 1.d-5) then found = .True. exit @@ -208,11 +208,11 @@ BEGIN_PROVIDER [ logical, molecule_has_sigma_plane, (3) ] molecule_has_sigma_plane(iaxis) = .True. do i=1,nucl_num found = .False. - point(:) = nucl_coord_transp(:,i) + point(:) = nucl_coord_sym_transp(:,i) point(iaxis) = -point(iaxis) do j=1,nucl_num if (nucl_charge(i) /= nucl_charge(j)) cycle - point2(:) = nucl_coord_transp(:,j) - point(:) + point2(:) = nucl_coord_sym_transp(:,j) - point(:) if (u_dot_u(point2,3) < 1.d-5) then found = .True. exit @@ -233,7 +233,7 @@ BEGIN_PROVIDER [ character*16, point_group ] ! Point group of the molecule END_DOC - character*2, save :: i_to_a(24) = (/ ' 1', ' 2', ' 3', ' 4', ' 5', ' 6', ' 7', ' 8', ' 9', & + character*2, save :: i_to_a(24) = (/ '1 ', '2 ', '3 ', '4 ', '5 ', '6 ', '7 ', '8 ', '9 ', & '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', & '21', '22', '23', '24' /) point_group = 'C1' @@ -366,7 +366,7 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] integer :: iangle, n_sym_points double precision :: angle integer :: iop, imo, ipoint, l, i - double precision :: sym_operations_on_mos(n_irrep) + double precision :: sym_operations_on_mos(mo_tot_num) logical :: possible_irrep(n_irrep,mo_tot_num) n_sym_points = 10000 @@ -443,6 +443,7 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] sym_operations_on_mos(imo) += x enddo sym_operations_on_mos(imo) *= 1.d0/n_sym_points + print *, iop, imo, sym_operations_on_mos(imo) if (dabs(sym_operations_on_mos(imo)-1.d0) < 1.d-2) then sym_operations_on_mos(imo)=1.d0 else if (dabs(sym_operations_on_mos(imo)+1.d0) < 1.d-2) then diff --git a/plugins/Symmetry/nuclei.irp.f b/plugins/Symmetry/nuclei.irp.f new file mode 100644 index 00000000..caa4781e --- /dev/null +++ b/plugins/Symmetry/nuclei.irp.f @@ -0,0 +1,92 @@ + +BEGIN_PROVIDER [ double precision, nucl_coord_sym, (nucl_num,3) ] + implicit none + + BEGIN_DOC + ! Nuclear coordinates in standard orientation + END_DOC + + if (mpi_master) then + integer :: i + do i=1,nucl_num + nucl_coord_sym(i,1) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & + (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & + (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) + nucl_coord_sym(i,2) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & + (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & + (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) + nucl_coord_sym(i,3) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & + (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & + (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) + enddo + + character*(64), parameter :: f = '(A16, 4(1X,F12.6))' + character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' + double precision, parameter :: a0= 0.529177249d0 + + call write_time(output_Nuclei) + write(output_Nuclei,'(A)') '' + write(output_Nuclei,'(A)') 'Nuclear Coordinates in standard orientation (Angstroms)' + write(output_Nuclei,'(A)') '=======================================================' + write(output_Nuclei,'(A)') '' + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,*) & + ' Atom Charge X Y Z ' + write(output_Nuclei,ft) & + '================','============','============','============','============' + do i=1,nucl_num + write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & + nucl_coord_sym(i,1)*a0, & + nucl_coord_sym(i,2)*a0, & + nucl_coord_sym(i,3)*a0 + enddo + write(output_Nuclei,ft) & + '================','============','============','============','============' + write(output_Nuclei,'(A)') '' + + endif + + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nucl_coord_sym, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nucl_coord_sym with MPI' + endif + IRP_ENDIF + +END_PROVIDER + + +BEGIN_PROVIDER [ double precision, nucl_coord_sym_transp, (3,nucl_num) ] + implicit none + BEGIN_DOC + ! Transposed array of nucl_coord + END_DOC + integer :: i, k + nucl_coord_sym_transp = 0.d0 + + do i=1,nucl_num + nucl_coord_sym_transp(1,i) = nucl_coord_sym(i,1) + nucl_coord_sym_transp(2,i) = nucl_coord_sym(i,2) + nucl_coord_sym_transp(3,i) = nucl_coord_sym(i,3) + enddo +END_PROVIDER + +BEGIN_PROVIDER [ double precision, sym_molecule_rotation, (3,3) ] + implicit none + BEGIN_DOC + ! Rotation of the molecule to go from input orientation to standard orientation + END_DOC + call find_rotation(nucl_coord, size(nucl_coord,1), nucl_coord_sym, 3, sym_molecule_rotation, 3) +END_PROVIDER + +BEGIN_PROVIDER [ double precision, sym_molecule_rotation_inv, (3,3) ] + implicit none + BEGIN_DOC + ! Rotation of the molecule to go from standard orientation to input orientation + END_DOC + call find_rotation(nucl_coord_sym, size(nucl_coord_sym,1), nucl_coord, 3, sym_molecule_rotation_inv, 3) +END_PROVIDER + diff --git a/scripts/pseudo/elts_num_ele.py b/scripts/pseudo/elts_num_ele.py index 8f31f4f7..f0aa3179 100644 --- a/scripts/pseudo/elts_num_ele.py +++ b/scripts/pseudo/elts_num_ele.py @@ -1,119 +1,15 @@ -name_to_elec = {"X": 0, - "H": 1, - "He": 2, - "Li": 3, - "Be": 4, - "B": 5, - "C": 6, - "N": 7, - "O": 8, - "F": 9, - "Ne": 10, - "Na": 11, - "Mg": 12, - "Al": 13, - "Si": 14, - "P": 15, - "S": 16, - "Cl": 17, - "Ar": 18, - "K": 19, - "Ca": 20, - "Sc": 21, - "Ti": 22, - "V": 23, - "Cr": 24, - "Mn": 25, - "Fe": 26, - "Co": 27, - "Ni": 28, - "Cu": 29, - "Zn": 30, - "Ga": 31, - "Ge": 32, - "As": 33, - "Se": 34, - "Br": 35, - "Kr": 36, - "Rb": 37, - "Sr": 38, - "Y": 39, - "Zr": 40, - "Nb": 41, - "Mo": 42, - "Tc": 43, - "Ru": 44, - "Rh": 45, - "Pd": 46, - "Ag": 47, - "Cd": 48, - "In": 49, - "Sn": 50, - "Sb": 51, - "Te": 52, - "I": 53, - "Xe": 54, - "Cs": 55, - "Ba": 56, - "La": 57, - "Ce": 58, - "Pr": 59, - "Nd": 60, - "Pm": 61, - "Sm": 62, - "Eu": 63, - "Gd": 64, - "Tb": 65, - "Dy": 66, - "Ho": 67, - "Er": 68, - "Tm": 69, - "Yb": 70, - "Lu": 71, - "Hf": 72, - "Ta": 73, - "W": 74, - "Re": 75, - "Os": 76, - "Ir": 77, - "Pt": 78, - "Au": 79, - "Hg": 80, - "Tl": 81, - "Pb": 82, - "Bi": 83, - "Po": 84, - "At": 85, - "Rn": 86, - "Fr": 87, - "Ra": 88, - "Ac": 89, - "Th": 90, - "Pa": 91, - "U": 92, - "Np": 93, - "Pu": 94, - "Am": 95, - "Cm": 96, - "Bk": 97, - "Cf": 98, - "Es": 99, - "Fm": 100, - "Md": 101, - "No": 102, - "Lr": 103, - "Rf": 104, - "Db": 105, - "Sg": 106, - "Bh": 107, - "Hs": 108, - "Mt": 109, - "Ds": 110, - "Rg": 111, - "Cn": 112, - "Uut": 113, - "Fl": 114, - "Uup": 115, - "Lv": 116, - "Uus": 117, - "Uuo": 118} +#!/usr/bin/env python + +import os + +QP_ROOT=os.environ["QP_ROOT"] + +name_to_elec = {} +with open(QP_ROOT+"/data/list_element.txt","r") as f: + data = f.readlines() + for line in data: + b = line.split() + name_to_elec[b[1]] = int(b[0]) + +if __name__ == '__main__': + print name_to_elec diff --git a/src/Nuclei/inertia.irp.f b/src/Nuclei/inertia.irp.f index c4517cde..d2cb7cf8 100644 --- a/src/Nuclei/inertia.irp.f +++ b/src/Nuclei/inertia.irp.f @@ -6,12 +6,12 @@ BEGIN_PROVIDER [ double precision, inertia_tensor, (3,3) ] integer :: i,j,k inertia_tensor = 0.d0 do k=1,nucl_num - inertia_tensor(1,1) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) - inertia_tensor(2,2) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,3)-center_of_mass(3))**2) - inertia_tensor(3,3) += mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1))**2 + (nucl_coord_input(k,2)-center_of_mass(2))**2) - inertia_tensor(1,2) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,2)-center_of_mass(2)) ) - inertia_tensor(1,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,1)-center_of_mass(1)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) - inertia_tensor(2,3) -= mass(int(nucl_charge(k))) * ((nucl_coord_input(k,2)-center_of_mass(2)) * (nucl_coord_input(k,3)-center_of_mass(3)) ) + inertia_tensor(1,1) += element_mass(int(nucl_charge(k))) * ((nucl_coord(k,2)-center_of_mass(2))**2 + (nucl_coord(k,3)-center_of_mass(3))**2) + inertia_tensor(2,2) += element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1))**2 + (nucl_coord(k,3)-center_of_mass(3))**2) + inertia_tensor(3,3) += element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1))**2 + (nucl_coord(k,2)-center_of_mass(2))**2) + inertia_tensor(1,2) -= element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1)) * (nucl_coord(k,2)-center_of_mass(2)) ) + inertia_tensor(1,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord(k,1)-center_of_mass(1)) * (nucl_coord(k,3)-center_of_mass(3)) ) + inertia_tensor(2,3) -= element_mass(int(nucl_charge(k))) * ((nucl_coord(k,2)-center_of_mass(2)) * (nucl_coord(k,3)-center_of_mass(3)) ) enddo inertia_tensor(2,1) = inertia_tensor(1,2) inertia_tensor(3,1) = inertia_tensor(1,3) @@ -27,6 +27,6 @@ END_PROVIDER integer :: k call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,inertia_tensor,3,3) print *, 'Rotational constants (GHZ):' - print *, (1805.65468542d0/inertia_tensor_eigenvalues(k), k=3,1,-1) + print *, (1805.65468542d0/(inertia_tensor_eigenvalues(k)+1.d-32), k=3,1,-1) END_PROVIDER diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 43609506..910e9167 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -1,4 +1,4 @@ -BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] +BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] implicit none BEGIN_DOC @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] if (mpi_master) then double precision, allocatable :: buffer(:,:) - nucl_coord_input = 0.d0 + nucl_coord = 0.d0 allocate (buffer(nucl_num,3)) buffer = 0.d0 logical :: has @@ -22,7 +22,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] do i=1,3 do j=1,nucl_num - nucl_coord_input(j,i) = buffer(j,i) + nucl_coord(j,i) = buffer(j,i) enddo enddo deallocate(buffer) @@ -31,65 +31,6 @@ BEGIN_PROVIDER [ double precision, nucl_coord_input, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 - call write_time(output_Nuclei) - write(output_Nuclei,'(A)') '' - write(output_Nuclei,'(A)') 'Input Nuclear Coordinates (Angstroms)' - write(output_Nuclei,'(A)') '=====================================' - write(output_Nuclei,'(A)') '' - write(output_Nuclei,ft) & - '================','============','============','============','============' - write(output_Nuclei,*) & - ' Atom Charge X Y Z ' - write(output_Nuclei,ft) & - '================','============','============','============','============' - do i=1,nucl_num - write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & - nucl_coord_input(i,1)*a0, & - nucl_coord_input(i,2)*a0, & - nucl_coord_input(i,3)*a0 - enddo - write(output_Nuclei,ft) & - '================','============','============','============','============' - write(output_Nuclei,'(A)') '' - - endif - - IRP_IF MPI - include 'mpif.h' - integer :: ierr - call MPI_BCAST( nucl_coord_input, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read nucl_coord_input with MPI' - endif - IRP_ENDIF - -END_PROVIDER - -BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] - implicit none - - BEGIN_DOC - ! Nuclear coordinates in standard orientation - END_DOC - - if (mpi_master) then - integer :: i - do i=1,nucl_num - nucl_coord(i,1) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) - nucl_coord(i,2) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) - nucl_coord(i,3) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) - enddo - - character*(64), parameter :: f = '(A16, 4(1X,F12.6))' - character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' - double precision, parameter :: a0= 0.529177249d0 - call write_time(output_Nuclei) write(output_Nuclei,'(A)') '' write(output_Nuclei,'(A)') 'Nuclear Coordinates (Angstroms)' @@ -207,7 +148,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] PROVIDE mpi_master nucl_coord nucl_charge nucl_num if (disk_access_nuclear_repulsion.EQ.'Read') then logical :: has - + if (mpi_master) then call ezfio_has_nuclei_nuclear_repulsion(has) if (has) then @@ -229,184 +170,78 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] else - - integer :: k,l - double precision :: Z12, r2, x(3) - nuclear_repulsion = 0.d0 - do l = 1, nucl_num - do k = 1, nucl_num - if(k == l) then - cycle - endif - Z12 = nucl_charge(k)*nucl_charge(l) - x(1) = nucl_coord(k,1) - nucl_coord(l,1) - x(2) = nucl_coord(k,2) - nucl_coord(l,2) - x(3) = nucl_coord(k,3) - nucl_coord(l,3) - r2 = x(1)*x(1) + x(2)*x(2) + x(3)*x(3) - nuclear_repulsion += Z12/dsqrt(r2) - enddo - enddo - nuclear_repulsion *= 0.5d0 + + integer :: k,l + double precision :: Z12, r2, x(3) + nuclear_repulsion = 0.d0 + do l = 1, nucl_num + do k = 1, nucl_num + if(k == l) then + cycle + endif + Z12 = nucl_charge(k)*nucl_charge(l) + x(1) = nucl_coord(k,1) - nucl_coord(l,1) + x(2) = nucl_coord(k,2) - nucl_coord(l,2) + x(3) = nucl_coord(k,3) - nucl_coord(l,3) + r2 = x(1)*x(1) + x(2)*x(2) + x(3)*x(3) + nuclear_repulsion += Z12/dsqrt(r2) + enddo + enddo + nuclear_repulsion *= 0.5d0 end if - + call write_time(output_Nuclei) call write_double(output_Nuclei,nuclear_repulsion, & 'Nuclear repulsion energy') - + if (disk_access_nuclear_repulsion.EQ.'Write') then if (mpi_master) then - call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion) + call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion) endif endif + + END_PROVIDER -BEGIN_PROVIDER [ character*(128), element_name, (78)] - BEGIN_DOC - ! Array of the name of element, sorted by nuclear charge (integer) - END_DOC - element_name(1) = 'H' - element_name(2) = 'He' - element_name(3) = 'Li' - element_name(4) = 'Be' - element_name(5) = 'B' - element_name(6) = 'C' - element_name(7) = 'N' - element_name(8) = 'O' - element_name(9) = 'F' - element_name(10) = 'Ne' - element_name(11) = 'Na' - element_name(12) = 'Mg' - element_name(13) = 'Al' - element_name(14) = 'Si' - element_name(15) = 'P' - element_name(16) = 'S' - element_name(17) = 'Cl' - element_name(18) = 'Ar' - element_name(19) = 'K' - element_name(20) = 'Ca' - element_name(21) = 'Sc' - element_name(22) = 'Ti' - element_name(23) = 'V' - element_name(24) = 'Cr' - element_name(25) = 'Mn' - element_name(26) = 'Fe' - element_name(27) = 'Co' - element_name(28) = 'Ni' - element_name(29) = 'Cu' - element_name(30) = 'Zn' - element_name(31) = 'Ga' - element_name(32) = 'Ge' - element_name(33) = 'As' - element_name(34) = 'Se' - element_name(35) = 'Br' - element_name(36) = 'Kr' - element_name(37) = 'Rb' - element_name(38) = 'Sr' - element_name(39) = 'Y' - element_name(40) = 'Zr' - element_name(41) = 'Nb' - element_name(42) = 'Mo' - element_name(43) = 'Tc' - element_name(44) = 'Ru' - element_name(45) = 'Rh' - element_name(46) = 'Pd' - element_name(47) = 'Ag' - element_name(48) = 'Cd' - element_name(49) = 'In' - element_name(50) = 'Sn' - element_name(51) = 'Sb' - element_name(52) = 'Te' - element_name(53) = 'I' - element_name(54) = 'Xe' - element_name(55) = 'Cs' - element_name(56) = 'Ba' - element_name(57) = 'La' - element_name(58) = 'Ce' - element_name(59) = 'Pr' - element_name(60) = 'Nd' - element_name(61) = 'Pm' - element_name(62) = 'Sm' - element_name(63) = 'Eu' - element_name(64) = 'Gd' - element_name(65) = 'Tb' - element_name(66) = 'Dy' - element_name(67) = 'Ho' - element_name(68) = 'Er' - element_name(69) = 'Tm' - element_name(70) = 'Yb' - element_name(71) = 'Lu' - element_name(72) = 'Hf' - element_name(73) = 'Ta' - element_name(74) = 'W' - element_name(75) = 'Re' - element_name(76) = 'Os' - element_name(77) = 'Ir' - element_name(78) = 'Pt' + BEGIN_PROVIDER [ character*(4), element_name, (0:128)] +&BEGIN_PROVIDER [ double precision, element_mass, (0:128) ] + BEGIN_DOC + ! Array of the name of element, sorted by nuclear charge (integer) + END_DOC + integer :: iunit + integer, external :: getUnitAndOpen + character*(128) :: filename + if (mpi_master) then + call getenv('QP_ROOT',filename) + filename = trim(filename)//'/data/list_element.txt' + iunit = getUnitAndOpen(filename,'r') + element_mass(:) = 0.d0 + do i=0,128 + write(element_name(i),'(I4)') i + enddo + character*(80) :: buffer, dummy + do + read(iunit,'(A80)',end=10) buffer + read(buffer,*) i ! First read i + read(buffer,*) i, element_name(i), dummy, element_mass(i) + enddo + 10 continue + close(10) + endif -END_PROVIDER - -BEGIN_PROVIDER [ double precision, mass, (0:110) ] - implicit none - BEGIN_DOC - ! Atomic masses - END_DOC - - mass( 0 ) = 0. - mass( 1 ) = 1.0079 - mass( 2 ) = 4.00260 - mass( 3 ) = 6.941 - mass( 4 ) = 9.01218 - mass( 5 ) = 10.81 - mass( 6 ) = 12.011 - mass( 7 ) = 14.0067 - mass( 8 ) = 15.9994 - mass( 9 ) = 18.998403 - mass( 10 ) = 20.179 - mass( 11 ) = 22.98977 - mass( 12 ) = 24.305 - mass( 13 ) = 26.98154 - mass( 14 ) = 28.0855 - mass( 15 ) = 30.97376 - mass( 16 ) = 32.06 - mass( 17 ) = 35.453 - mass( 18 ) = 39.948 - mass( 19 ) = 39.0983 - mass( 20 ) = 40.08 - mass( 21 ) = 44.9559 - mass( 22 ) = 47.90 - mass( 23 ) = 50.9415 - mass( 24 ) = 51.996 - mass( 25 ) = 54.9380 - mass( 26 ) = 55.9332 - mass( 27 ) = 58.9332 - mass( 28 ) = 58.70 - mass( 29 ) = 63.546 - mass( 30 ) = 65.38 - mass( 31 ) = 69.72 - mass( 32 ) = 72.59 - mass( 33 ) = 74.9216 - mass( 34 ) = 78.96 - mass( 35 ) = 79.904 - mass( 36 ) = 83.80 - mass( 37 ) = 85.4678 - mass( 38 ) = 87.62 - mass( 39 ) = 88.90584 - mass( 40 ) = 91.224 - mass( 41 ) = 92.90637 - mass( 42 ) = 95.95 - mass( 43 ) = 98. - mass( 44 ) = 101.07 - mass( 45 ) = 102.90550 - mass( 46 ) = 106.42 - mass( 47 ) = 107.8682 - mass( 48 ) = 112.414 - mass( 49 ) = 114.818 - mass( 50 ) = 118.710 - mass( 51 ) = 121.760 - mass( 52 ) = 127.60 - mass( 53 ) = 126.90447 - mass( 54 ) = 131.293 - mass( 78 ) = 195.084 + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( element_name, size(element_name)*4, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read element_name with MPI' + endif + call MPI_BCAST( element_mass, size(element_mass), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read element_name with MPI' + endif + IRP_ENDIF + END_PROVIDER BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] @@ -420,9 +255,9 @@ BEGIN_PROVIDER [ double precision, center_of_mass, (3) ] s = 0.d0 do i=1,nucl_num do j=1,3 - center_of_mass(j) += nucl_coord_input(i,j)* mass(int(nucl_charge(i))) + center_of_mass(j) += nucl_coord(i,j)* element_mass(int(nucl_charge(i))) enddo - s += mass(int(nucl_charge(i))) + s += element_mass(int(nucl_charge(i))) enddo s = 1.d0/s center_of_mass(:) = center_of_mass(:)*s From f838765834cb456fcf34735b2cb8495cd72d944e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 18:26:24 +0100 Subject: [PATCH 38/54] Multi-state modification for qmcpack --- plugins/QMC/README.rst | 8 ++++++++ plugins/QMC/qp_convert_qmcpack_to_ezfio.py | 5 ++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/plugins/QMC/README.rst b/plugins/QMC/README.rst index 7e942878..129ca95e 100644 --- a/plugins/QMC/README.rst +++ b/plugins/QMC/README.rst @@ -2,6 +2,14 @@ QmcChem Module ============== +For multi-state calculations, to extract state 2 use: + +`` +QP_STATE=2 qp_run save_for_qmcpack x.ezfio +`` +(state 1 is the ground state). + + Documentation ============= diff --git a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py index 8e8cea7b..acf48708 100755 --- a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py +++ b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py @@ -345,7 +345,10 @@ print "mo_num", mo_num print "det_num", n_det print "" -state = 0 +if "QP_STATE" in os.environ: + state = int(os.environ["QP_STATE"])-1 +else: + state = 0 psi_coef = psi_coef[state] encode = 8*bit_kind From c4a2b1f9a0e5819c5451beb0ca9faf73d1e9524f Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 18:28:53 +0100 Subject: [PATCH 39/54] Removed useless file --- data/list_element.txt | 56 -------------------------------- plugins/Symmetry/aos.irp.f | 57 +++++++++++++++++++++------------ plugins/Symmetry/find_sym.irp.f | 25 +++++++++------ 3 files changed, 52 insertions(+), 86 deletions(-) delete mode 100644 data/list_element.txt diff --git a/data/list_element.txt b/data/list_element.txt deleted file mode 100644 index 2a9733e6..00000000 --- a/data/list_element.txt +++ /dev/null @@ -1,56 +0,0 @@ - 0 X Dummy 0.000000 - 1 H Hydrogen 1.007900 - 2 He Helium 4.002600 - 3 Li Lithium 6.941000 - 4 Be Beryllium 9.012180 - 5 B Boron 10.810000 - 6 C Carbon 12.011000 - 7 N Nitrogen 14.006700 - 8 O Oxygen 15.999400 - 9 F Fluorine 18.998403 - 10 Ne Neon 20.179000 - 11 Na Sodium 22.989770 - 12 Mg Magnesium 24.305000 - 13 Al Aluminum 26.981540 - 14 Si Silicon 28.085500 - 15 P Phosphorus 30.973760 - 16 S Sulfur 32.060000 - 17 Cl Chlorine 35.453000 - 18 Ar Argon 39.948000 - 19 K Potassium 39.098300 - 20 Ca Calcium 40.080000 - 21 Sc Scandium 44.955900 - 22 Ti Titanium 47.900000 - 23 V Vanadium 50.941500 - 24 Cr Chromium 51.996000 - 25 Mn Manganese 54.938000 - 26 Fe Iron 55.933200 - 27 Co Cobalt 58.933200 - 28 Ni Nickel 58.700000 - 29 Cu Copper 63.546000 - 30 Zn Zinc 65.380000 - 31 Ga Gallium 69.720000 - 32 Ge Germanium 72.590000 - 33 As Arsenic 74.921600 - 34 Se Selenium 78.960000 - 35 Br Bromine 79.904000 - 36 Kr Krypton 83.800000 - 37 Rb Rubidium 85.467800 - 38 Sr Strontium 87.620000 - 39 Y Yttrium 88.905840 - 40 Zr Zirconium 91.224000 - 41 Nb Niobium 92.906370 - 42 Mo Molybdenum 95.950000 - 43 Tc Technetium 98.000000 - 44 Ru Ruthenium 101.070000 - 45 Rh Rhodium 102.905500 - 46 Pd Palladium 106.420000 - 47 Ag Silver 107.868200 - 48 Cd Cadmium 112.414000 - 49 In Indium 114.818000 - 50 Sn Tin 118.710000 - 51 Sb Antimony 121.760000 - 52 Te Tellurium 127.600000 - 53 I Iodine 126.904470 - 54 Xe Xenon 131.293000 - 78 Pt Platinum 195.084000 diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index e0aade1e..a20c1a08 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -24,9 +24,13 @@ subroutine generate_sym_coord(n_sym_points,result) END_DOC integer :: i, xyz - call random_number(result) + do i=1,n_sym_points + call random_number(result(1,i)) + call random_number(result(2,i)) + call random_number(result(3,i)) + enddo do xyz=1,3 - result(xyz,:) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) + result(xyz,1:n_sym_points) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) enddo end @@ -43,27 +47,35 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) integer :: i, j double precision :: x, y, z double precision :: x2, y2, z2 + integer :: k result (:,:) = 0.d0 +print *, sym_molecule_rotation_inv +print *, '' +print *, sym_molecule_rotation +stop do j=1,ao_num do i=1,n_sym_points - x = sym_points(1,i) - nucl_coord_sym_transp(1,ao_nucl(j)) - y = sym_points(2,i) - nucl_coord_sym_transp(2,ao_nucl(j)) - z = sym_points(3,i) - nucl_coord_sym_transp(3,ao_nucl(j)) - x2 = x*sym_molecule_rotation_inv(1,1) + y*sym_molecule_rotation_inv(2,1) + z*sym_molecule_rotation_inv(3,1) - y2 = x*sym_molecule_rotation_inv(1,2) + y*sym_molecule_rotation_inv(2,2) + z*sym_molecule_rotation_inv(3,2) - z2 = x*sym_molecule_rotation_inv(1,3) + y*sym_molecule_rotation_inv(2,3) + z*sym_molecule_rotation_inv(3,3) - x = x2**ao_power(j,1) - y = y2**ao_power(j,2) - z = z2**ao_power(j,3) - result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) -! result(i,j) = x*y*z -! if (result(i,j) > 0.d0) then -! result(i,j) = 1.d0 -! else if (result(i,j) < 0.d0) then -! result(i,j) = -1.d0 -! else -! result(i,j) = 0.d0 -! endif + x2 = sym_points(1,i) + y2 = sym_points(2,i) + z2 = sym_points(3,i) + x = x2*sym_molecule_rotation_inv(1,1) + y2*sym_molecule_rotation_inv(2,1) + z2*sym_molecule_rotation_inv(3,1) + y = x2*sym_molecule_rotation_inv(1,2) + y2*sym_molecule_rotation_inv(2,2) + z2*sym_molecule_rotation_inv(3,2) + z = x2*sym_molecule_rotation_inv(1,3) + y2*sym_molecule_rotation_inv(2,3) + z2*sym_molecule_rotation_inv(3,3) + x = x - nucl_coord_transp(1,ao_nucl(j)) + y = y - nucl_coord_transp(2,ao_nucl(j)) + z = z - nucl_coord_transp(3,ao_nucl(j)) + x2 = x*x + y*y + z*z + result(i,j) = 0.d0 + do k=1,ao_prim_num(j) + result(i,j) += ao_coef_normalized_ordered_transp(k,j)*exp(-ao_expo_ordered_transp(k,j)*x2) + enddo +print *, real(x), ao_power(j,1), real(y), ao_power(j,2), real(z), ao_power(j,3) + x = x**ao_power(j,1) + y = y**ao_power(j,2) + z = z**ao_power(j,3) +print *, result(i,j) + result(i,j) = x*y*z*result(i,j) + print *, result(i,j) enddo enddo @@ -81,6 +93,11 @@ subroutine compute_sym_mo_values(sym_points, n_sym_points, result) double precision, allocatable :: tmp(:,:) allocate(tmp(n_sym_points,ao_num)) call compute_sym_ao_values(sym_points,n_sym_points,tmp) +integer :: i +do i=1,ao_num + print *, tmp(:,i) +enddo +stop call dgemm('N','N',n_sym_points,mo_tot_num,ao_num, & 1.d0, tmp,size(tmp,1), mo_coef, size(mo_coef,1), & 0.d0, result,size(result,1)) diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 95bb4e6c..c7e2ba37 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -369,7 +369,7 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] double precision :: sym_operations_on_mos(mo_tot_num) logical :: possible_irrep(n_irrep,mo_tot_num) - n_sym_points = 10000 + n_sym_points = 10 allocate(val(n_sym_points,mo_tot_num,2), sym_points(3,n_sym_points), ref_points(3,n_sym_points)) call generate_sym_coord(n_sym_points,ref_points) @@ -402,10 +402,12 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] call sym_apply_diagonal_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo else if (sym_operation(iop) == 'C2''') then + angle = 2.d0 do ipoint=1,n_sym_points call sym_apply_rotation(angle,molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo else if (sym_operation(iop) == 'C2"') then + angle = 2.d0 do ipoint=1,n_sym_points call sym_apply_rotation(angle,molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo @@ -414,9 +416,12 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] if (sym_operation(iop)(l:l) == '^') exit enddo read(sym_operation(iop)(2:l-1), *) iangle - l=1 - read(sym_operation(iop)(l+1:), *, err=10, end=10) l - 10 continue + if (l == len(sym_operation(iop))+1) then + l=1 + else + read(sym_operation(iop)(l+1:), *, err=10, end=10) l + 10 continue + endif angle = dble(iangle)/(dble(l)) if (sym_operation(iop)(1:1) == 'C') then do ipoint=1,n_sym_points @@ -432,23 +437,23 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] call compute_sym_mo_values(sym_points,n_sym_points,val(1,1,1)) print *, sym_operation(iop) + double precision :: icount do imo=1,mo_tot_num sym_operations_on_mos(imo) = 0.d0 + icount = 0 do ipoint=1,n_sym_points double precision :: x + if (dabs(val(ipoint,imo,1)) < 1.d-5) cycle + icount += 1.d0 x = val(ipoint,imo,1)/val(ipoint,imo,2) if (dabs(x) > 1.d0) then x = 1.d0/x endif sym_operations_on_mos(imo) += x enddo - sym_operations_on_mos(imo) *= 1.d0/n_sym_points + sym_operations_on_mos(imo) *= 1.d0/icount print *, iop, imo, sym_operations_on_mos(imo) - if (dabs(sym_operations_on_mos(imo)-1.d0) < 1.d-2) then - sym_operations_on_mos(imo)=1.d0 - else if (dabs(sym_operations_on_mos(imo)+1.d0) < 1.d-2) then - sym_operations_on_mos(imo)=-1.d0 - endif + print *, val(:,imo,1) do i=1,n_irrep if (character_table(i,iop) /= sym_operations_on_mos(imo)) then possible_irrep(i,imo) = .False. From e70bf2800ebc291f7b894fd014fe165b3dc301cd Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 18:33:34 +0100 Subject: [PATCH 40/54] Multi-state in qmcpack (#218) * Fixes #211 * Removed debug print * Revert input coordinates * Fix MPI * Multi-state modification for qmcpack * Removed useless file --- data/list_element.txt | 56 --------------------- plugins/QMC/README.rst | 8 +++ plugins/QMC/qp_convert_qmcpack_to_ezfio.py | 5 +- plugins/Symmetry/aos.irp.f | 58 ++++++++++++++-------- plugins/Symmetry/find_sym.irp.f | 25 ++++++---- 5 files changed, 65 insertions(+), 87 deletions(-) delete mode 100644 data/list_element.txt diff --git a/data/list_element.txt b/data/list_element.txt deleted file mode 100644 index 2a9733e6..00000000 --- a/data/list_element.txt +++ /dev/null @@ -1,56 +0,0 @@ - 0 X Dummy 0.000000 - 1 H Hydrogen 1.007900 - 2 He Helium 4.002600 - 3 Li Lithium 6.941000 - 4 Be Beryllium 9.012180 - 5 B Boron 10.810000 - 6 C Carbon 12.011000 - 7 N Nitrogen 14.006700 - 8 O Oxygen 15.999400 - 9 F Fluorine 18.998403 - 10 Ne Neon 20.179000 - 11 Na Sodium 22.989770 - 12 Mg Magnesium 24.305000 - 13 Al Aluminum 26.981540 - 14 Si Silicon 28.085500 - 15 P Phosphorus 30.973760 - 16 S Sulfur 32.060000 - 17 Cl Chlorine 35.453000 - 18 Ar Argon 39.948000 - 19 K Potassium 39.098300 - 20 Ca Calcium 40.080000 - 21 Sc Scandium 44.955900 - 22 Ti Titanium 47.900000 - 23 V Vanadium 50.941500 - 24 Cr Chromium 51.996000 - 25 Mn Manganese 54.938000 - 26 Fe Iron 55.933200 - 27 Co Cobalt 58.933200 - 28 Ni Nickel 58.700000 - 29 Cu Copper 63.546000 - 30 Zn Zinc 65.380000 - 31 Ga Gallium 69.720000 - 32 Ge Germanium 72.590000 - 33 As Arsenic 74.921600 - 34 Se Selenium 78.960000 - 35 Br Bromine 79.904000 - 36 Kr Krypton 83.800000 - 37 Rb Rubidium 85.467800 - 38 Sr Strontium 87.620000 - 39 Y Yttrium 88.905840 - 40 Zr Zirconium 91.224000 - 41 Nb Niobium 92.906370 - 42 Mo Molybdenum 95.950000 - 43 Tc Technetium 98.000000 - 44 Ru Ruthenium 101.070000 - 45 Rh Rhodium 102.905500 - 46 Pd Palladium 106.420000 - 47 Ag Silver 107.868200 - 48 Cd Cadmium 112.414000 - 49 In Indium 114.818000 - 50 Sn Tin 118.710000 - 51 Sb Antimony 121.760000 - 52 Te Tellurium 127.600000 - 53 I Iodine 126.904470 - 54 Xe Xenon 131.293000 - 78 Pt Platinum 195.084000 diff --git a/plugins/QMC/README.rst b/plugins/QMC/README.rst index 7e942878..129ca95e 100644 --- a/plugins/QMC/README.rst +++ b/plugins/QMC/README.rst @@ -2,6 +2,14 @@ QmcChem Module ============== +For multi-state calculations, to extract state 2 use: + +`` +QP_STATE=2 qp_run save_for_qmcpack x.ezfio +`` +(state 1 is the ground state). + + Documentation ============= diff --git a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py index 8e8cea7b..acf48708 100755 --- a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py +++ b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py @@ -345,7 +345,10 @@ print "mo_num", mo_num print "det_num", n_det print "" -state = 0 +if "QP_STATE" in os.environ: + state = int(os.environ["QP_STATE"])-1 +else: + state = 0 psi_coef = psi_coef[state] encode = 8*bit_kind diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index e0aade1e..5515e1b7 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -24,9 +24,13 @@ subroutine generate_sym_coord(n_sym_points,result) END_DOC integer :: i, xyz - call random_number(result) + do i=1,n_sym_points + call random_number(result(1,i)) + call random_number(result(2,i)) + call random_number(result(3,i)) + enddo do xyz=1,3 - result(xyz,:) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) + result(xyz,1:n_sym_points) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) enddo end @@ -43,27 +47,36 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) integer :: i, j double precision :: x, y, z double precision :: x2, y2, z2 + integer :: k + result (:,:) = 0.d0 +print *, sym_molecule_rotation_inv +print *, '' +print *, sym_molecule_rotation +stop do j=1,ao_num do i=1,n_sym_points - x = sym_points(1,i) - nucl_coord_sym_transp(1,ao_nucl(j)) - y = sym_points(2,i) - nucl_coord_sym_transp(2,ao_nucl(j)) - z = sym_points(3,i) - nucl_coord_sym_transp(3,ao_nucl(j)) - x2 = x*sym_molecule_rotation_inv(1,1) + y*sym_molecule_rotation_inv(2,1) + z*sym_molecule_rotation_inv(3,1) - y2 = x*sym_molecule_rotation_inv(1,2) + y*sym_molecule_rotation_inv(2,2) + z*sym_molecule_rotation_inv(3,2) - z2 = x*sym_molecule_rotation_inv(1,3) + y*sym_molecule_rotation_inv(2,3) + z*sym_molecule_rotation_inv(3,3) - x = x2**ao_power(j,1) - y = y2**ao_power(j,2) - z = z2**ao_power(j,3) - result(i,j) = x*y*z*exp(-(x*x+y*y+z*z)) -! result(i,j) = x*y*z -! if (result(i,j) > 0.d0) then -! result(i,j) = 1.d0 -! else if (result(i,j) < 0.d0) then -! result(i,j) = -1.d0 -! else -! result(i,j) = 0.d0 -! endif + x2 = sym_points(1,i) + y2 = sym_points(2,i) + z2 = sym_points(3,i) + x = x2*sym_molecule_rotation_inv(1,1) + y2*sym_molecule_rotation_inv(2,1) + z2*sym_molecule_rotation_inv(3,1) + y = x2*sym_molecule_rotation_inv(1,2) + y2*sym_molecule_rotation_inv(2,2) + z2*sym_molecule_rotation_inv(3,2) + z = x2*sym_molecule_rotation_inv(1,3) + y2*sym_molecule_rotation_inv(2,3) + z2*sym_molecule_rotation_inv(3,3) + x = x - nucl_coord_transp(1,ao_nucl(j)) + y = y - nucl_coord_transp(2,ao_nucl(j)) + z = z - nucl_coord_transp(3,ao_nucl(j)) + x2 = x*x + y*y + z*z + result(i,j) = 0.d0 + do k=1,ao_prim_num(j) + result(i,j) += ao_coef_normalized_ordered_transp(k,j)*exp(-ao_expo_ordered_transp(k,j)*x2) + enddo +print *, real(x), ao_power(j,1), real(y), ao_power(j,2), real(z), ao_power(j,3) + x = x**ao_power(j,1) + y = y**ao_power(j,2) + z = z**ao_power(j,3) +print *, result(i,j) + result(i,j) = x*y*z*result(i,j) + print *, result(i,j) enddo enddo @@ -81,6 +94,11 @@ subroutine compute_sym_mo_values(sym_points, n_sym_points, result) double precision, allocatable :: tmp(:,:) allocate(tmp(n_sym_points,ao_num)) call compute_sym_ao_values(sym_points,n_sym_points,tmp) +integer :: i +do i=1,ao_num + print *, tmp(:,i) +enddo +stop call dgemm('N','N',n_sym_points,mo_tot_num,ao_num, & 1.d0, tmp,size(tmp,1), mo_coef, size(mo_coef,1), & 0.d0, result,size(result,1)) diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 95bb4e6c..c7e2ba37 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -369,7 +369,7 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] double precision :: sym_operations_on_mos(mo_tot_num) logical :: possible_irrep(n_irrep,mo_tot_num) - n_sym_points = 10000 + n_sym_points = 10 allocate(val(n_sym_points,mo_tot_num,2), sym_points(3,n_sym_points), ref_points(3,n_sym_points)) call generate_sym_coord(n_sym_points,ref_points) @@ -402,10 +402,12 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] call sym_apply_diagonal_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo else if (sym_operation(iop) == 'C2''') then + angle = 2.d0 do ipoint=1,n_sym_points call sym_apply_rotation(angle,molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo else if (sym_operation(iop) == 'C2"') then + angle = 2.d0 do ipoint=1,n_sym_points call sym_apply_rotation(angle,molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo @@ -414,9 +416,12 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] if (sym_operation(iop)(l:l) == '^') exit enddo read(sym_operation(iop)(2:l-1), *) iangle - l=1 - read(sym_operation(iop)(l+1:), *, err=10, end=10) l - 10 continue + if (l == len(sym_operation(iop))+1) then + l=1 + else + read(sym_operation(iop)(l+1:), *, err=10, end=10) l + 10 continue + endif angle = dble(iangle)/(dble(l)) if (sym_operation(iop)(1:1) == 'C') then do ipoint=1,n_sym_points @@ -432,23 +437,23 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] call compute_sym_mo_values(sym_points,n_sym_points,val(1,1,1)) print *, sym_operation(iop) + double precision :: icount do imo=1,mo_tot_num sym_operations_on_mos(imo) = 0.d0 + icount = 0 do ipoint=1,n_sym_points double precision :: x + if (dabs(val(ipoint,imo,1)) < 1.d-5) cycle + icount += 1.d0 x = val(ipoint,imo,1)/val(ipoint,imo,2) if (dabs(x) > 1.d0) then x = 1.d0/x endif sym_operations_on_mos(imo) += x enddo - sym_operations_on_mos(imo) *= 1.d0/n_sym_points + sym_operations_on_mos(imo) *= 1.d0/icount print *, iop, imo, sym_operations_on_mos(imo) - if (dabs(sym_operations_on_mos(imo)-1.d0) < 1.d-2) then - sym_operations_on_mos(imo)=1.d0 - else if (dabs(sym_operations_on_mos(imo)+1.d0) < 1.d-2) then - sym_operations_on_mos(imo)=-1.d0 - endif + print *, val(:,imo,1) do i=1,n_irrep if (character_table(i,iop) /= sym_operations_on_mos(imo)) then possible_irrep(i,imo) = .False. From e8df53857ae14ade933a698a1a5779feb3ffceae Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 22:19:29 +0100 Subject: [PATCH 41/54] Fixed QMCPack pseudo bug --- plugins/QMC/qp_convert_qmcpack_to_ezfio.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py index acf48708..94f0c347 100755 --- a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py +++ b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py @@ -26,7 +26,7 @@ if do_pseudo: l_element_raw = data_raw.split("\n") l_element = [element_raw.split() for element_raw in l_element_raw] - d_z = dict((abr, z) for (z, abr, ele) in l_element) + d_z = dict((abr, z) for (z, abr, ele, _) in filter(lambda x: x != [], l_element) ) else: print "do_pseudo False" From 279c225f3b8d47049afc07c74e3a2f90818716d7 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Dec 2017 23:14:03 +0100 Subject: [PATCH 42/54] Fix broken QMCPack pseudo (#219) * Fixes #211 * Removed debug print * Revert input coordinates * Fix MPI * Multi-state modification for qmcpack * Removed useless file * Fixed QMCPack pseudo bug --- plugins/QMC/qp_convert_qmcpack_to_ezfio.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py index acf48708..94f0c347 100755 --- a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py +++ b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py @@ -26,7 +26,7 @@ if do_pseudo: l_element_raw = data_raw.split("\n") l_element = [element_raw.split() for element_raw in l_element_raw] - d_z = dict((abr, z) for (z, abr, ele) in l_element) + d_z = dict((abr, z) for (z, abr, ele, _) in filter(lambda x: x != [], l_element) ) else: print "do_pseudo False" From 4a04e769c5ac2ea4bd0f99b6b84838574e75fc91 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 20 Dec 2017 18:02:55 +0100 Subject: [PATCH 43/54] pin old core library --- install/scripts/install_ocaml.sh | 2 +- plugins/Symmetry/Symmetry.main.irp.f | 2 +- plugins/Symmetry/aos.irp.f | 28 +++------- plugins/Symmetry/find_sym.irp.f | 27 ++++++---- plugins/Symmetry/nuclei.irp.f | 78 +++++++++++++++++++--------- plugins/Symmetry/sym_operation.irp.f | 25 ++++----- src/Nuclei/inertia.irp.f | 5 +- 7 files changed, 91 insertions(+), 76 deletions(-) diff --git a/install/scripts/install_ocaml.sh b/install/scripts/install_ocaml.sh index 88d38845..f322bd0b 100755 --- a/install/scripts/install_ocaml.sh +++ b/install/scripts/install_ocaml.sh @@ -5,7 +5,7 @@ QP_ROOT=$PWD cd - # Normal installation -PACKAGES="core cryptokit.1.10 ocamlfind sexplib ZMQ ppx_sexp_conv ppx_deriving" +PACKAGES="core.v0.9.1 cryptokit.1.10 ocamlfind sexplib.v0.9.1 ZMQ ppx_sexp_conv ppx_deriving" # Needed for ZeroMQ export C_INCLUDE_PATH="${QP_ROOT}"/include:"${C_INCLUDE_PATH}" diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f index 1d438af5..9540295f 100644 --- a/plugins/Symmetry/Symmetry.main.irp.f +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -15,7 +15,7 @@ program Symmetry print *, 'Symmetry operations : ', sym_operation(1:n_irrep) print *, 'Character table' do i=1,n_irrep - print *, character_table(i,:) + print *, i, real(character_table(i,:)) enddo PROVIDE mo_sym end diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index 5515e1b7..1ed567bc 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -45,38 +45,27 @@ subroutine compute_sym_ao_values(sym_points, n_sym_points, result) double precision, intent(in) :: sym_points(3,n_sym_points) double precision, intent(out) :: result(n_sym_points, ao_num) integer :: i, j + double precision :: point(3) double precision :: x, y, z double precision :: x2, y2, z2 integer :: k - + result (:,:) = 0.d0 -print *, sym_molecule_rotation_inv -print *, '' -print *, sym_molecule_rotation -stop do j=1,ao_num do i=1,n_sym_points - x2 = sym_points(1,i) - y2 = sym_points(2,i) - z2 = sym_points(3,i) - x = x2*sym_molecule_rotation_inv(1,1) + y2*sym_molecule_rotation_inv(2,1) + z2*sym_molecule_rotation_inv(3,1) - y = x2*sym_molecule_rotation_inv(1,2) + y2*sym_molecule_rotation_inv(2,2) + z2*sym_molecule_rotation_inv(3,2) - z = x2*sym_molecule_rotation_inv(1,3) + y2*sym_molecule_rotation_inv(2,3) + z2*sym_molecule_rotation_inv(3,3) - x = x - nucl_coord_transp(1,ao_nucl(j)) - y = y - nucl_coord_transp(2,ao_nucl(j)) - z = z - nucl_coord_transp(3,ao_nucl(j)) + call point_to_input_orientation(sym_points(:,i), point) + x = point(1) - nucl_coord_transp(1,ao_nucl(j)) + y = point(2) - nucl_coord_transp(2,ao_nucl(j)) + z = point(3) - nucl_coord_transp(3,ao_nucl(j)) x2 = x*x + y*y + z*z result(i,j) = 0.d0 do k=1,ao_prim_num(j) result(i,j) += ao_coef_normalized_ordered_transp(k,j)*exp(-ao_expo_ordered_transp(k,j)*x2) enddo -print *, real(x), ao_power(j,1), real(y), ao_power(j,2), real(z), ao_power(j,3) x = x**ao_power(j,1) y = y**ao_power(j,2) z = z**ao_power(j,3) -print *, result(i,j) result(i,j) = x*y*z*result(i,j) - print *, result(i,j) enddo enddo @@ -94,11 +83,6 @@ subroutine compute_sym_mo_values(sym_points, n_sym_points, result) double precision, allocatable :: tmp(:,:) allocate(tmp(n_sym_points,ao_num)) call compute_sym_ao_values(sym_points,n_sym_points,tmp) -integer :: i -do i=1,ao_num - print *, tmp(:,i) -enddo -stop call dgemm('N','N',n_sym_points,mo_tot_num,ao_num, & 1.d0, tmp,size(tmp,1), mo_coef, size(mo_coef,1), & 0.d0, result,size(result,1)) diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index c7e2ba37..38c0a6b7 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -84,7 +84,7 @@ END_PROVIDER END_DOC molecule_principal_axis = maxloc(sym_rotation_axis,1) if (molecule_principal_axis == 1) then - if (sym_rotation_axis(2) >= sym_rotation_axis(3)) then + if (sym_rotation_axis(2) > sym_rotation_axis(3)) then molecule_secondary_axis = 2 molecule_ternary_axis = 3 else @@ -92,7 +92,7 @@ END_PROVIDER molecule_ternary_axis = 2 endif else if (molecule_principal_axis == 2) then - if (sym_rotation_axis(1) >= sym_rotation_axis(3)) then + if (sym_rotation_axis(1) > sym_rotation_axis(3)) then molecule_secondary_axis = 1 molecule_ternary_axis = 3 else @@ -100,7 +100,7 @@ END_PROVIDER molecule_ternary_axis = 1 endif else if (molecule_principal_axis == 3) then - if (sym_rotation_axis(1) >= sym_rotation_axis(2)) then + if (sym_rotation_axis(1) > sym_rotation_axis(2)) then molecule_secondary_axis = 1 molecule_ternary_axis = 2 else @@ -375,11 +375,11 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] call generate_sym_coord(n_sym_points,ref_points) call compute_sym_mo_values(ref_points,n_sym_points,val(1,1,2)) + possible_irrep = .True. do iop=1,n_irrep if (sym_operation(iop) == 'E') then cycle endif - possible_irrep = .True. if (sym_operation(iop) == 'i') then do ipoint=1,n_sym_points @@ -395,11 +395,12 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] enddo else if (sym_operation(iop) == 'sv') then do ipoint=1,n_sym_points - call sym_apply_reflexion(molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + call sym_apply_reflexion(molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo else if (sym_operation(iop) == 'sd') then + angle = dble(maxval(sym_rotation_axis)) do ipoint=1,n_sym_points - call sym_apply_diagonal_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) + call sym_apply_diagonal_reflexion(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) enddo else if (sym_operation(iop) == 'C2''') then angle = 2.d0 @@ -452,17 +453,23 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] sym_operations_on_mos(imo) += x enddo sym_operations_on_mos(imo) *= 1.d0/icount - print *, iop, imo, sym_operations_on_mos(imo) - print *, val(:,imo,1) + if (dabs(sym_operations_on_mos(imo) - 1.d0) < 1.d-2) then + sym_operations_on_mos(imo) = 1.d0 + else if (dabs(sym_operations_on_mos(imo) + 1.d0) < 1.d-2) then + sym_operations_on_mos(imo) = -1.d0 + else if (dabs(sym_operations_on_mos(imo)) < 1.d-2) then + sym_operations_on_mos(imo) = 0.d0 + endif + print *, imo, sym_operations_on_mos(imo) do i=1,n_irrep - if (character_table(i,iop) /= sym_operations_on_mos(imo)) then + if (dabs(character_table(i,iop) - sym_operations_on_mos(imo)) > 1.d-2) then possible_irrep(i,imo) = .False. endif enddo enddo enddo do imo=1,mo_tot_num - print *, imo + print *, 'MO ', imo do i=1,n_irrep if (possible_irrep(i,imo)) then print *, sym_irrep(i) diff --git a/plugins/Symmetry/nuclei.irp.f b/plugins/Symmetry/nuclei.irp.f index caa4781e..d680393d 100644 --- a/plugins/Symmetry/nuclei.irp.f +++ b/plugins/Symmetry/nuclei.irp.f @@ -1,3 +1,56 @@ +subroutine point_to_standard_orientation(point_in,point_out) + implicit none + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + BEGIN_DOC + ! Returns the coordinates of a point in the standard orientation + END_DOC + double precision :: point_tmp(3) + + point_tmp(1) = point_in(1) - center_of_mass(1) + point_tmp(2) = point_in(2) - center_of_mass(2) + point_tmp(3) = point_in(3) - center_of_mass(3) + + point_out(1) = point_tmp(1)*inertia_tensor_eigenvectors(1,1) + & + point_tmp(2)*inertia_tensor_eigenvectors(2,1) + & + point_tmp(3)*inertia_tensor_eigenvectors(3,1) + + point_out(2) = point_tmp(1)*inertia_tensor_eigenvectors(1,2) + & + point_tmp(2)*inertia_tensor_eigenvectors(2,2) + & + point_tmp(3)*inertia_tensor_eigenvectors(3,2) + + point_out(3) = point_tmp(1)*inertia_tensor_eigenvectors(1,3) + & + point_tmp(2)*inertia_tensor_eigenvectors(2,3) + & + point_tmp(3)*inertia_tensor_eigenvectors(3,3) + +end + +subroutine point_to_input_orientation(point_in,point_out) + implicit none + double precision, intent(in) :: point_in(3) + double precision, intent(out) :: point_out(3) + BEGIN_DOC + ! Returns the coordinates of a point in the input orientation + END_DOC + double precision :: point_tmp(3) + + point_tmp(1) = point_in(1)*inertia_tensor_eigenvectors(1,1) + & + point_in(2)*inertia_tensor_eigenvectors(1,2) + & + point_in(3)*inertia_tensor_eigenvectors(1,3) + + point_tmp(2) = point_in(1)*inertia_tensor_eigenvectors(2,1) + & + point_in(2)*inertia_tensor_eigenvectors(2,2) + & + point_in(3)*inertia_tensor_eigenvectors(2,3) + + point_tmp(3) = point_in(1)*inertia_tensor_eigenvectors(3,1) + & + point_in(2)*inertia_tensor_eigenvectors(3,2) + & + point_in(3)*inertia_tensor_eigenvectors(3,3) + + point_out(1) = point_tmp(1) + center_of_mass(1) + point_out(2) = point_tmp(2) + center_of_mass(2) + point_out(3) = point_tmp(3) + center_of_mass(3) + +end BEGIN_PROVIDER [ double precision, nucl_coord_sym, (nucl_num,3) ] implicit none @@ -9,15 +62,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord_sym, (nucl_num,3) ] if (mpi_master) then integer :: i do i=1,nucl_num - nucl_coord_sym(i,1) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & - (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & - (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) - nucl_coord_sym(i,2) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & - (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & - (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) - nucl_coord_sym(i,3) = (nucl_coord(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & - (nucl_coord(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & - (nucl_coord(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) + call point_to_standard_orientation(nucl_coord(i,:), nucl_coord_sym(i,:)) enddo character*(64), parameter :: f = '(A16, 4(1X,F12.6))' @@ -74,19 +119,4 @@ BEGIN_PROVIDER [ double precision, nucl_coord_sym_transp, (3,nucl_num) ] enddo END_PROVIDER -BEGIN_PROVIDER [ double precision, sym_molecule_rotation, (3,3) ] - implicit none - BEGIN_DOC - ! Rotation of the molecule to go from input orientation to standard orientation - END_DOC - call find_rotation(nucl_coord, size(nucl_coord,1), nucl_coord_sym, 3, sym_molecule_rotation, 3) -END_PROVIDER - -BEGIN_PROVIDER [ double precision, sym_molecule_rotation_inv, (3,3) ] - implicit none - BEGIN_DOC - ! Rotation of the molecule to go from standard orientation to input orientation - END_DOC - call find_rotation(nucl_coord_sym, size(nucl_coord_sym,1), nucl_coord, 3, sym_molecule_rotation_inv, 3) -END_PROVIDER diff --git a/plugins/Symmetry/sym_operation.irp.f b/plugins/Symmetry/sym_operation.irp.f index 93e580e2..cfc86621 100644 --- a/plugins/Symmetry/sym_operation.irp.f +++ b/plugins/Symmetry/sym_operation.irp.f @@ -15,25 +15,18 @@ subroutine sym_apply_reflexion(iaxis,point_in,point_out) end -subroutine sym_apply_diagonal_reflexion(iaxis,point_in,point_out) +subroutine sym_apply_diagonal_reflexion(angle,iaxis,point_in,point_out) implicit none integer, intent(in) :: iaxis - double precision, intent(in) :: point_in(3) + double precision, intent(in) :: point_in(3), angle double precision, intent(out) :: point_out(3) - if (iaxis == 1) then - point_out(1) = point_in(1) - point_out(2) = point_in(3) - point_out(3) = point_in(2) - else if (iaxis == 2) then - point_out(1) = point_in(3) - point_out(2) = point_in(2) - point_out(3) = point_in(1) - else if (iaxis == 3) then - point_out(1) = point_in(2) - point_out(2) = point_in(1) - point_out(3) = point_in(3) - endif - + double precision :: point_tmp1(3), point_tmp2(3) + integer :: iaxis2 + iaxis2 = mod(iaxis,3)+1 + iaxis2 = mod(iaxis2,3)+1 + call sym_apply_rotation(-angle,iaxis,point_in,point_tmp1) + call sym_apply_reflexion(iaxis2,point_tmp1,point_tmp2) + call sym_apply_rotation(angle,iaxis,point_tmp2,point_out) end subroutine sym_apply_rotation(angle,iaxis,point_in,point_out) diff --git a/src/Nuclei/inertia.irp.f b/src/Nuclei/inertia.irp.f index d2cb7cf8..c79fa243 100644 --- a/src/Nuclei/inertia.irp.f +++ b/src/Nuclei/inertia.irp.f @@ -25,8 +25,9 @@ END_PROVIDER ! Eigenvectors/eigenvalues of the inertia_tensor. Used to find normal orientation. END_DOC integer :: k - call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,inertia_tensor,3,3) + call lapack_diagd(inertia_tensor_eigenvalues,inertia_tensor_eigenvectors,-inertia_tensor,3,3) + inertia_tensor_eigenvalues = -inertia_tensor_eigenvalues print *, 'Rotational constants (GHZ):' - print *, (1805.65468542d0/(inertia_tensor_eigenvalues(k)+1.d-32), k=3,1,-1) + print *, (1805.65468542d0/(inertia_tensor_eigenvalues(k)+1.d-32), k=1,3) END_PROVIDER From 49d85cf27c291ea39e61b49a407bbf2cd100cb22 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 21 Dec 2017 22:59:27 +0100 Subject: [PATCH 45/54] State-average weights and Zsh fix --- configure | 16 +++++------ ocaml/Input_determinants_by_hand.ml | 43 ++++++++++++++++++++++++++++- 2 files changed, 50 insertions(+), 9 deletions(-) diff --git a/configure b/configure index c32420a0..9b59b209 100755 --- a/configure +++ b/configure @@ -480,24 +480,24 @@ def create_ninja_and_rc(l_installed): 'export QP_PYTHON={0}'.format(":".join(l_python)), "", 'export IRPF90={0}'.format(path_irpf90.replace(QP_ROOT,"${QP_ROOT}")), 'export NINJA={0}'.format(path_ninja.replace(QP_ROOT,"${QP_ROOT}")), - 'qp_append_export () {', - ' #Append path $2:${!1}. Add the semicolon only if ${!1} is defined', - ' echo ${2}${!1:+:${!1}}', + 'function qp_append_export () {', + ' #Append path $2:${!1}. Add the semicolon only if ${!1} is defined', + ' eval "value_1=\"\${$1}\""', + ' echo ${2}${value_1:+:${value_1}}', '}', 'export PYTHONPATH=$(qp_append_export "PYTHONPATH" "${QP_EZFIO}/Python":"${QP_PYTHON}")', 'export PATH=$(qp_append_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml)', 'export LD_LIBRARY_PATH=$(qp_append_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)', 'export LIBRARY_PATH=$(qp_append_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)', - 'export C_INCLUDE_PATH=$(qp_append_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)' + 'export C_INCLUDE_PATH=$(qp_append_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)', '', - 'source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh', + 'if [[ $SHELL == "bash" ]] ; then', + ' source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh', + 'fi', '', '# Choose the correct network interface', '# export QP_NIC=ib0', '# export QP_NIC=eth0', - '', - '# Choose how to start MPI processes', - '# export QP_MPIRUN="mpirun"', '' ] diff --git a/ocaml/Input_determinants_by_hand.ml b/ocaml/Input_determinants_by_hand.ml index 48887ca0..90174e18 100644 --- a/ocaml/Input_determinants_by_hand.ml +++ b/ocaml/Input_determinants_by_hand.ml @@ -11,6 +11,7 @@ module Determinants_by_hand : sig expected_s2 : Positive_float.t; psi_coef : Det_coef.t array; psi_det : Determinant.t array; + state_average_weight : Positive_float.t array; } [@@deriving sexp] val read : unit -> t val read_maybe : unit -> t option @@ -30,6 +31,7 @@ end = struct expected_s2 : Positive_float.t; psi_coef : Det_coef.t array; psi_det : Determinant.t array; + state_average_weight : Positive_float.t array; } [@@deriving sexp] ;; @@ -82,7 +84,6 @@ end = struct |> Ezfio.set_determinants_n_det ;; - let read_n_states () = if not (Ezfio.has_determinants_n_states ()) then Ezfio.set_determinants_n_states 1 @@ -96,6 +97,36 @@ end = struct |> Ezfio.set_determinants_n_states ;; + let write_state_average_weight data = + let n_states = + read_n_states () + |> States_number.to_int + in + let data = + Array.map ~f:Positive_float.to_float data + |> Array.to_list + in + Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_states |] ~data + |> Ezfio.set_determinants_state_average_weight + ;; + + let read_state_average_weight () = + if not (Ezfio.has_determinants_state_average_weight ()) then + begin + let n_states = + read_n_states () + |> States_number.to_int + in + let data = + Array.init n_states (fun _ -> 1./.(float_of_int n_states)) + |> Array.map ~f:Positive_float.of_float + in + write_state_average_weight data; + end; + Ezfio.get_determinants_state_average_weight () + |> Ezfio.flattened_ezfio + |> Array.map ~f:Positive_float.of_float + ;; let read_expected_s2 () = if not (Ezfio.has_determinants_expected_s2 ()) then @@ -205,6 +236,7 @@ end = struct psi_coef = read_psi_coef () ; psi_det = read_psi_det () ; n_states = read_n_states () ; + state_average_weight = read_state_average_weight () ; } else failwith "No molecular orbitals, so no determinants" @@ -228,6 +260,7 @@ end = struct psi_coef ; psi_det ; n_states ; + state_average_weight ; } = write_n_int n_int ; write_bit_kind bit_kind; @@ -236,6 +269,7 @@ end = struct write_expected_s2 expected_s2; write_psi_coef ~n_det:n_det ~n_states:n_states psi_coef ; write_psi_det ~n_int:n_int ~n_det:n_det psi_det; + write_state_average_weight state_average_weight; ;; @@ -288,12 +322,17 @@ Number of determinants :: n_det = %s +State average weights :: + + state_average_weight = (%s) + Determinants :: %s " (b.expected_s2 |> Positive_float.to_string) (b.n_det |> Det_number.to_string) + (b.state_average_weight |> Array.to_list |> List.map ~f:Positive_float.to_string |> String.concat ~sep:"\t") det_text |> Rst_string.of_string ;; @@ -307,6 +346,7 @@ bit_kind = %s n_det = %s n_states = %s expected_s2 = %s +state_average_weight = %s psi_coef = %s psi_det = %s " @@ -315,6 +355,7 @@ psi_det = %s (b.n_det |> Det_number.to_string) (b.n_states |> States_number.to_string) (b.expected_s2 |> Positive_float.to_string) + (b.state_average_weight |> Array.to_list |> List.map ~f:Positive_float.to_string |> String.concat ~sep:",") (b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string |> String.concat ~sep:", ") (b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string From ee8d6db3c1fc62af3eaeae77b263de41522ed888 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 29 Dec 2017 16:06:35 +0100 Subject: [PATCH 46/54] Correct end of line in basis file --- ocaml/Gto.ml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ocaml/Gto.ml b/ocaml/Gto.ml index ab265202..a46be191 100644 --- a/ocaml/Gto.ml +++ b/ocaml/Gto.ml @@ -36,7 +36,10 @@ let of_prim_coef_list pc = let read_one in_channel = (* Fetch number of lines to read on first line *) - let buffer = input_line in_channel in + let buffer = + try input_line in_channel with + | End_of_file -> raise End_Of_Basis + in if ( (String_ext.strip buffer) = "" ) then raise End_Of_Basis; let sym_str = String.sub buffer 0 2 in From 792288600d8028e75fbb0a904138d3cd379cd8bb Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 5 Jan 2018 15:31:08 +0100 Subject: [PATCH 47/54] Minor changes --- ocaml/Zmatrix.ml | 11 ----------- src/Nuclei/nuclei.irp.f | 10 +++++----- 2 files changed, 5 insertions(+), 16 deletions(-) diff --git a/ocaml/Zmatrix.ml b/ocaml/Zmatrix.ml index 0aae3441..b963479f 100644 --- a/ocaml/Zmatrix.ml +++ b/ocaml/Zmatrix.ml @@ -196,17 +196,6 @@ let rotation_matrix axis angle = (2. *. (b *. d -. a *. c), 2. *. (c *. d +. a *. b), a *. a +. d *. d -. b *. b -. c *. c)] -(* - [(a *. a +. b *. b -. c *. c -. d *. d, - 2. *. (b *. c +. a *. d), - 2. *. (b *. d -. a *. c)); - (2. *. (b *. c -. a *. d), - a *. a +. c *. c -.b *. b -. d *. d, - 2. *. (c *. d +. a *. b)); - (2. *. (b *. d +. a *. c), - 2. *. (c *. d -. a *. b), - a *. a +. d *. d -. b *. b -. c *. c)] -*) diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 910e9167..c78228a8 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -203,8 +203,8 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] END_PROVIDER - BEGIN_PROVIDER [ character*(4), element_name, (0:128)] -&BEGIN_PROVIDER [ double precision, element_mass, (0:128) ] + BEGIN_PROVIDER [ character*(4), element_name, (0:127)] +&BEGIN_PROVIDER [ double precision, element_mass, (0:127) ] BEGIN_DOC ! Array of the name of element, sorted by nuclear charge (integer) END_DOC @@ -216,7 +216,7 @@ END_PROVIDER filename = trim(filename)//'/data/list_element.txt' iunit = getUnitAndOpen(filename,'r') element_mass(:) = 0.d0 - do i=0,128 + do i=0,127 write(element_name(i),'(I4)') i enddo character*(80) :: buffer, dummy @@ -232,11 +232,11 @@ END_PROVIDER IRP_IF MPI include 'mpif.h' integer :: ierr - call MPI_BCAST( element_name, size(element_name)*4, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr) + call MPI_BCAST( element_name, 128*4, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr) if (ierr /= MPI_SUCCESS) then stop 'Unable to read element_name with MPI' endif - call MPI_BCAST( element_mass, size(element_mass), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + call MPI_BCAST( element_mass, 128, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) if (ierr /= MPI_SUCCESS) then stop 'Unable to read element_name with MPI' endif From ddc2dd44e9e8895aa2d12840660afcefd4db4bfc Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 5 Jan 2018 15:32:32 +0100 Subject: [PATCH 48/54] Switched back to old 4-idx --- src/Integrals_Bielec/mo_bi_integrals.irp.f | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/Integrals_Bielec/mo_bi_integrals.irp.f b/src/Integrals_Bielec/mo_bi_integrals.irp.f index c39dba36..9d884456 100644 --- a/src/Integrals_Bielec/mo_bi_integrals.irp.f +++ b/src/Integrals_Bielec/mo_bi_integrals.irp.f @@ -122,17 +122,17 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ] endif else -! call add_integrals_to_map(full_ijkl_bitmask_4) + call add_integrals_to_map(full_ijkl_bitmask_4) ! call four_index_transform_zmq(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & ! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & ! 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) ! - call four_index_transform_block(ao_integrals_map,mo_integrals_map, & - mo_coef, size(mo_coef,1), & - 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & - 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) +! call four_index_transform_block(ao_integrals_map,mo_integrals_map, & +! mo_coef, size(mo_coef,1), & +! 1, 1, 1, 1, ao_num, ao_num, ao_num, ao_num, & +! 1, 1, 1, 1, mo_num, mo_num, mo_num, mo_num) ! ! call four_index_transform(ao_integrals_map,mo_integrals_map, & ! mo_coef, size(mo_coef,1), & From b88a0eac78e3a644143b2bd2958bea6984e2918b Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 5 Jan 2018 14:12:27 +0000 Subject: [PATCH 49/54] Removed output variables --- plugins/CIS/super_ci.irp.f | 14 ++-- plugins/Generators_full/generators.irp.f | 4 +- plugins/Hartree_Fock/Roothaan_Hall_SCF.irp.f | 18 ++-- plugins/Hartree_Fock/damping_SCF.irp.f | 18 ++-- plugins/MRPT_Utils/mrpt_utils.irp.f | 6 +- plugins/Perturbation/selection.irp.f | 2 +- plugins/Selectors_Utils/zmq.irp.f | 1 + plugins/Selectors_full/selectors.irp.f | 4 +- scripts/ezfio_interface/ei_handler.py | 3 +- scripts/generate_h_apply.py | 10 +-- src/Bitmask/bitmasks.irp.f | 2 +- src/Davidson/diagonalize_CI.irp.f | 10 +-- src/Determinants/H_apply.irp.f | 2 +- src/Determinants/determinants.irp.f | 10 +-- src/Determinants/psi_cas.irp.f | 2 +- src/Determinants/zmq.irp.f | 3 + src/Ezfio_files/output.irp.f | 30 ------- src/MO_Basis/utils.irp.f | 72 ++++++++-------- src/Nuclei/nuclei.irp.f | 86 ++++++++++++++++++-- src/ZMQ/put_get.irp.f | 1 + 20 files changed, 174 insertions(+), 124 deletions(-) diff --git a/plugins/CIS/super_ci.irp.f b/plugins/CIS/super_ci.irp.f index 630b9599..979a48a4 100644 --- a/plugins/CIS/super_ci.irp.f +++ b/plugins/CIS/super_ci.irp.f @@ -12,12 +12,12 @@ subroutine super_CI integer :: k character :: save_char - call write_time(output_hartree_fock) - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16 )') & + call write_time(6) + write(6,'(A4,X,A16, X, A16, X, A16 )') & '====','================','================','================' - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16 )') & + write(6,'(A4,X,A16, X, A16, X, A16 )') & ' N ', 'Energy ', 'Energy diff ', 'Save ' - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16 )') & + write(6,'(A4,X,A16, X, A16, X, A16 )') & '====','================','================','================' E = HF_energy + 1.d0 @@ -39,7 +39,7 @@ subroutine super_CI save_char = ' ' endif E_min = min(E,E_min) - write(output_hartree_fock,'(I4,X,F16.10, X, F16.10, X, A8 )') & + write(6,'(I4,X,F16.10, X, F16.10, X, A8 )') & k, E, delta_E, save_char if ( (delta_E < 0.d0).and.(dabs(delta_E) < thresh_scf) ) then exit @@ -55,8 +55,8 @@ subroutine super_CI TOUCH mo_coef enddo - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16 )') & + write(6,'(A4,X,A16, X, A16, X, A16 )') & '====','================','================','================' - call write_time(output_hartree_fock) + call write_time(6) end diff --git a/plugins/Generators_full/generators.irp.f b/plugins/Generators_full/generators.irp.f index eea5821b..a04065cf 100644 --- a/plugins/Generators_full/generators.irp.f +++ b/plugins/Generators_full/generators.irp.f @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] END_DOC integer :: i double precision :: norm - call write_time(output_determinants) + call write_time(6) norm = 0.d0 N_det_generators = N_det do i=1,N_det @@ -19,7 +19,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] endif enddo N_det_generators = max(N_det_generators,1) - call write_int(output_determinants,N_det_generators,'Number of generators') + call write_int(6,N_det_generators,'Number of generators') END_PROVIDER BEGIN_PROVIDER [ integer(bit_kind), psi_det_generators, (N_int,2,psi_det_size) ] diff --git a/plugins/Hartree_Fock/Roothaan_Hall_SCF.irp.f b/plugins/Hartree_Fock/Roothaan_Hall_SCF.irp.f index 241721ae..860cc825 100644 --- a/plugins/Hartree_Fock/Roothaan_Hall_SCF.irp.f +++ b/plugins/Hartree_Fock/Roothaan_Hall_SCF.irp.f @@ -20,13 +20,13 @@ END_DOC error_matrix_DIIS(ao_num,ao_num,max_dim_DIIS) & ) - call write_time(output_hartree_fock) + call write_time(6) - write(output_hartree_fock,'(A4, 1X, A16, 1X, A16, 1X, A16)') & + write(6,'(A4, 1X, A16, 1X, A16, 1X, A16)') & '====','================','================','================' - write(output_hartree_fock,'(A4, 1X, A16, 1X, A16, 1X, A16)') & + write(6,'(A4, 1X, A16, 1X, A16, 1X, A16)') & ' N ', 'Energy ', 'Energy diff ', 'DIIS error ' - write(output_hartree_fock,'(A4, 1X, A16, 1X, A16, 1X, A16)') & + write(6,'(A4, 1X, A16, 1X, A16, 1X, A16)') & '====','================','================','================' ! Initialize energies and density matrices @@ -115,7 +115,7 @@ END_DOC ! Print results at the end of each iteration - write(output_hartree_fock,'(I4, 1X, F16.10, 1X, F16.10, 1X, F16.10, 1X, I3)') & + write(6,'(I4, 1X, F16.10, 1X, F16.10, 1X, F16.10, 1X, I3)') & iteration_SCF, energy_SCF, Delta_energy_SCF, max_error_DIIS, dim_DIIS if (Delta_energy_SCF < 0.d0) then @@ -128,18 +128,18 @@ END_DOC ! End of Main SCF loop ! - write(output_hartree_fock,'(A4, 1X, A16, 1X, A16, 1X, A16)') & + write(6,'(A4, 1X, A16, 1X, A16, 1X, A16)') & '====','================','================','================' - write(output_hartree_fock,*) + write(6,*) if(.not.no_oa_or_av_opt)then call mo_as_eigvectors_of_mo_matrix(Fock_matrix_mo,size(Fock_matrix_mo,1),size(Fock_matrix_mo,2),mo_label,1,.true.) endif - call write_double(output_hartree_fock, Energy_SCF, 'Hartree-Fock energy') + call write_double(6, Energy_SCF, 'Hartree-Fock energy') call ezfio_set_hartree_fock_energy(Energy_SCF) - call write_time(output_hartree_fock) + call write_time(6) end diff --git a/plugins/Hartree_Fock/damping_SCF.irp.f b/plugins/Hartree_Fock/damping_SCF.irp.f index 20a8abd7..f97fbf82 100644 --- a/plugins/Hartree_Fock/damping_SCF.irp.f +++ b/plugins/Hartree_Fock/damping_SCF.irp.f @@ -28,13 +28,13 @@ subroutine damping_SCF enddo - call write_time(output_hartree_fock) + call write_time(6) - write(output_hartree_fock,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') & + write(6,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') & '====','================','================','================', '====' - write(output_hartree_fock,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') & + write(6,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') & ' N ', 'Energy ', 'Energy diff ', 'Density diff ', 'Save' - write(output_hartree_fock,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') & + write(6,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') & '====','================','================','================', '====' E = HF_energy + 1.d0 @@ -58,7 +58,7 @@ subroutine damping_SCF save_char = ' ' endif - write(output_hartree_fock,'(I4,1X,F16.10, 1X, F16.10, 1X, F16.10, 3X, A )') & + write(6,'(I4,1X,F16.10, 1X, F16.10, 1X, F16.10, 3X, A )') & k, E, delta_E, delta_D, save_char D_alpha = HF_density_matrix_ao_alpha @@ -115,17 +115,17 @@ subroutine damping_SCF TOUCH mo_coef enddo - write(output_hartree_fock,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') '====','================','================','================', '====' - write(output_hartree_fock,*) + write(6,'(A4,1X,A16, 1X, A16, 1X, A16, 1X, A4 )') '====','================','================','================', '====' + write(6,*) if(.not.no_oa_or_av_opt)then call mo_as_eigvectors_of_mo_matrix(Fock_matrix_mo,size(Fock_matrix_mo,1),size(Fock_matrix_mo,2),mo_label,1,.true.) endif - call write_double(output_hartree_fock, E_min, 'Hartree-Fock energy') + call write_double(6, E_min, 'Hartree-Fock energy') call ezfio_set_hartree_fock_energy(E_min) - call write_time(output_hartree_fock) + call write_time(6) deallocate(D_alpha,D_beta,F_new,D_new_alpha,D_new_beta,delta_alpha,delta_beta) end diff --git a/plugins/MRPT_Utils/mrpt_utils.irp.f b/plugins/MRPT_Utils/mrpt_utils.irp.f index 34d26127..e186116d 100644 --- a/plugins/MRPT_Utils/mrpt_utils.irp.f +++ b/plugins/MRPT_Utils/mrpt_utils.irp.f @@ -354,12 +354,12 @@ BEGIN_PROVIDER [ double precision, CI_dressed_pt2_new_energy, (N_states) ] integer :: j character*(8) :: st - call write_time(output_determinants) + call write_time(6) do j=1,N_states CI_dressed_pt2_new_energy(j) = CI_electronic_dressed_pt2_new_energy(j) + nuclear_repulsion write(st,'(I4)') j - call write_double(output_determinants,CI_dressed_pt2_new_energy(j),'Energy of state '//trim(st)) - call write_double(output_determinants,CI_dressed_pt2_new_eigenvectors_s2(j),'S^2 of state '//trim(st)) + call write_double(6,CI_dressed_pt2_new_energy(j),'Energy of state '//trim(st)) + call write_double(6,CI_dressed_pt2_new_eigenvectors_s2(j),'S^2 of state '//trim(st)) enddo END_PROVIDER diff --git a/plugins/Perturbation/selection.irp.f b/plugins/Perturbation/selection.irp.f index a9a5b3bb..6ec5062b 100644 --- a/plugins/Perturbation/selection.irp.f +++ b/plugins/Perturbation/selection.irp.f @@ -125,7 +125,7 @@ subroutine remove_small_contributions if (N_removed > 0) then N_det = N_det - N_removed SOFT_TOUCH N_det psi_det psi_coef - call write_int(output_determinants,N_removed, 'Removed determinants') + call write_int(6,N_removed, 'Removed determinants') endif end diff --git a/plugins/Selectors_Utils/zmq.irp.f b/plugins/Selectors_Utils/zmq.irp.f index 5f40cd4f..b32436aa 100644 --- a/plugins/Selectors_Utils/zmq.irp.f +++ b/plugins/Selectors_Utils/zmq.irp.f @@ -45,6 +45,7 @@ integer function zmq_get_$X(zmq_to_qp_run_socket, worker_id) integer :: rc character*(256) :: msg + PROVIDE zmq_state zmq_get_$X = 0 if (mpi_master) then diff --git a/plugins/Selectors_full/selectors.irp.f b/plugins/Selectors_full/selectors.irp.f index 42e3c87b..3d58bdcc 100644 --- a/plugins/Selectors_full/selectors.irp.f +++ b/plugins/Selectors_full/selectors.irp.f @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ integer, N_det_selectors] END_DOC integer :: i double precision :: norm, norm_max - call write_time(output_determinants) + call write_time(6) N_det_selectors = N_det if (threshold_generators < 1.d0) then norm = 0.d0 @@ -21,7 +21,7 @@ BEGIN_PROVIDER [ integer, N_det_selectors] enddo N_det_selectors = max(N_det_selectors,N_det_generators) endif - call write_int(output_determinants,N_det_selectors,'Number of selectors') + call write_int(6,N_det_selectors,'Number of selectors') END_PROVIDER BEGIN_PROVIDER [ integer(bit_kind), psi_selectors, (N_int,2,psi_selectors_size) ] diff --git a/scripts/ezfio_interface/ei_handler.py b/scripts/ezfio_interface/ei_handler.py index ee44a1e1..8d154fc2 100755 --- a/scripts/ezfio_interface/ei_handler.py +++ b/scripts/ezfio_interface/ei_handler.py @@ -329,7 +329,8 @@ def create_ezfio_provider(dict_ezfio_cfg): ez_p.set_doc(dict_info['doc']) ez_p.set_ezfio_dir(dict_info['ezfio_dir']) ez_p.set_ezfio_name(dict_info['ezfio_name']) - ez_p.set_output("output_%s" % dict_info['module'].lower) + ez_p.set_output("6") +# ez_p.set_output("output_%s" % dict_info['module'].lower) # (nuclei.nucl_num,pseudo.klocmax) => (nucl_num,klocmax) ez_p.set_size(re.sub(r'\w+\.', "", dict_info['size'])) diff --git a/scripts/generate_h_apply.py b/scripts/generate_h_apply.py index da1aac5a..3b5d96c2 100755 --- a/scripts/generate_h_apply.py +++ b/scripts/generate_h_apply.py @@ -142,7 +142,7 @@ class H_apply(object): endif SOFT_TOUCH psi_det psi_coef N_det """ - s["printout_now"] = """write(output_determinants,*) & + s["printout_now"] = """write(6,*) & 100.*float(i_generator)/float(N_det_generators), '% in ', wall_1-wall_0, 's'""" self.data = s @@ -370,9 +370,9 @@ class H_apply(object): delta_pt2(k) = 0.d0 pt2_old(k) = 0.d0 enddo - write(output_determinants,'(A12, 1X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & + write(6,'(A12, 1X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & 'N_generators', 'Norm', 'Delta PT2', 'PT2', 'Est. PT2', 'secs' - write(output_determinants,'(A12, 1X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & + write(6,'(A12, 1X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') & '============', '========', '=========', '=========', '=========', & '=========' """ @@ -385,7 +385,7 @@ class H_apply(object): """ self.data["printout_now"] = """ do k=1,N_st - write(output_determinants,'(I10, 4(2X, F9.6), 2X, F8.1)') & + write(6,'(I10, 4(2X, F9.6), 2X, F8.1)') & i_generator, norm_psi(k), delta_pt2(k), pt2(k), & pt2(k)/(norm_psi(k)*norm_psi(k)), & wall_1-wall_0 @@ -416,7 +416,7 @@ class H_apply(object): SOFT_TOUCH psi_det psi_coef N_det selection_criterion_min = min(selection_criterion_min, maxval(select_max))*0.1d0 selection_criterion = selection_criterion_min - call write_double(output_determinants,selection_criterion,'Selection criterion') + call write_double(6,selection_criterion,'Selection criterion') """ self.data["keys_work"] = """ e_2_pert_buffer = 0.d0 diff --git a/src/Bitmask/bitmasks.irp.f b/src/Bitmask/bitmasks.irp.f index 5f3fc7f5..4eac3e0a 100644 --- a/src/Bitmask/bitmasks.irp.f +++ b/src/Bitmask/bitmasks.irp.f @@ -100,7 +100,7 @@ BEGIN_PROVIDER [ integer, N_generators_bitmask ] ! Number of bitmasks for generators END_DOC logical :: exists - PROVIDE ezfio_filename + PROVIDE ezfio_filename N_int if (mpi_master) then call ezfio_has_bitmasks_N_mask_gen(exists) diff --git a/src/Davidson/diagonalize_CI.irp.f b/src/Davidson/diagonalize_CI.irp.f index f01cfb28..c65d9763 100644 --- a/src/Davidson/diagonalize_CI.irp.f +++ b/src/Davidson/diagonalize_CI.irp.f @@ -7,14 +7,14 @@ BEGIN_PROVIDER [ double precision, CI_energy, (N_states_diag) ] integer :: j character*(8) :: st - call write_time(output_determinants) + call write_time(6) do j=1,min(N_det,N_states_diag) CI_energy(j) = CI_electronic_energy(j) + nuclear_repulsion enddo do j=1,min(N_det,N_states) write(st,'(I4)') j - call write_double(output_determinants,CI_energy(j),'Energy of state '//trim(st)) - call write_double(output_determinants,CI_eigenvectors_s2(j),'S^2 of state '//trim(st)) + call write_double(6,CI_energy(j),'Energy of state '//trim(st)) + call write_double(6,CI_eigenvectors_s2(j),'S^2 of state '//trim(st)) enddo END_PROVIDER @@ -58,14 +58,14 @@ END_PROVIDER ! call davidson_diag(psi_det,CI_eigenvectors,CI_electronic_energy, & ! size(CI_eigenvectors,1), & -! N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,output_determinants) +! N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,6) ! ! call u_0_S2_u_0(CI_eigenvectors_s2,CI_eigenvectors,N_det,psi_det,N_int,& ! min(N_det,N_states_diag),size(CI_eigenvectors,1)) call davidson_diag_HS2(psi_det,CI_eigenvectors, CI_eigenvectors_s2, & size(CI_eigenvectors,1),CI_electronic_energy, & - N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,output_determinants) + N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,6) else if (diag_algorithm == "Lapack") then diff --git a/src/Determinants/H_apply.irp.f b/src/Determinants/H_apply.irp.f index ef396f9c..e5197a21 100644 --- a/src/Determinants/H_apply.irp.f +++ b/src/Determinants/H_apply.irp.f @@ -265,7 +265,7 @@ subroutine remove_duplicates_in_psi_det(found_duplicates) endif enddo N_det = k - call write_bool(output_determinants,found_duplicates,'Found duplicate determinants') + call write_bool(6,found_duplicates,'Found duplicate determinants') SOFT_TOUCH N_det psi_det psi_coef endif deallocate (duplicate,bit_tmp) diff --git a/src/Determinants/determinants.irp.f b/src/Determinants/determinants.irp.f index 40c4524a..2ef5dfac 100644 --- a/src/Determinants/determinants.irp.f +++ b/src/Determinants/determinants.irp.f @@ -43,7 +43,7 @@ BEGIN_PROVIDER [ integer, N_det ] else N_det = 1 endif - call write_int(output_determinants,N_det,'Number of determinants') + call write_int(6,N_det,'Number of determinants') endif IRP_IF MPI include 'mpif.h' @@ -77,7 +77,7 @@ BEGIN_PROVIDER [ integer, psi_det_size ] BEGIN_DOC ! Size of the psi_det/psi_coef arrays END_DOC - PROVIDE ezfio_filename output_determinants + PROVIDE ezfio_filename logical :: exists if (mpi_master) then call ezfio_has_determinants_n_det(exists) @@ -87,7 +87,7 @@ BEGIN_PROVIDER [ integer, psi_det_size ] psi_det_size = 1 endif psi_det_size = max(psi_det_size,100000) - call write_int(output_determinants,psi_det_size,'Dimension of the psi arrays') + call write_int(6,psi_det_size,'Dimension of the psi arrays') endif IRP_IF MPI include 'mpif.h' @@ -562,7 +562,7 @@ subroutine save_wavefunction_general(ndet,nstates,psidet,dim_psicoef,psicoef) call ezfio_set_determinants_psi_coef(psi_coef_save) deallocate (psi_coef_save) - call write_int(output_determinants,ndet,'Saved determinants') + call write_int(6,ndet,'Saved determinants') endif end @@ -634,7 +634,7 @@ subroutine save_wavefunction_specified(ndet,nstates,psidet,psicoef,ndetsave,inde enddo call ezfio_set_determinants_psi_coef(psi_coef_save) - call write_int(output_determinants,ndet,'Saved determinants') + call write_int(6,ndet,'Saved determinants') deallocate (psi_coef_save) end diff --git a/src/Determinants/psi_cas.irp.f b/src/Determinants/psi_cas.irp.f index 968ced57..591843f7 100644 --- a/src/Determinants/psi_cas.irp.f +++ b/src/Determinants/psi_cas.irp.f @@ -41,7 +41,7 @@ use bitmasks enddo endif enddo - call write_int(output_determinants,N_det_cas, 'Number of determinants in the CAS') + call write_int(6,N_det_cas, 'Number of determinants in the CAS') END_PROVIDER diff --git a/src/Determinants/zmq.irp.f b/src/Determinants/zmq.irp.f index b0ef55d6..5e42cff5 100644 --- a/src/Determinants/zmq.irp.f +++ b/src/Determinants/zmq.irp.f @@ -87,6 +87,7 @@ integer function zmq_get_$X(zmq_to_qp_run_socket, worker_id) integer :: rc character*(256) :: msg + PROVIDE zmq_state zmq_get_$X = 0 if (mpi_master) then write(msg,'(A,1X,I8,1X,A200)') 'get_data '//trim(zmq_state), worker_id, '$X' @@ -272,6 +273,7 @@ integer function zmq_get_psi_det(zmq_to_qp_run_socket, worker_id) integer*8 :: rc8 character*(256) :: msg + PROVIDE zmq_state zmq_get_psi_det = 0 if (mpi_master) then write(msg,'(A,1X,I8,1X,A200)') 'get_data '//trim(zmq_state), worker_id, 'psi_det' @@ -319,6 +321,7 @@ integer function zmq_get_psi_coef(zmq_to_qp_run_socket, worker_id) integer*8 :: rc8 character*(256) :: msg + PROVIDE zmq_state psi_det_size zmq_get_psi_coef = 0 if (mpi_master) then write(msg,'(A,1X,I8,1X,A200)') 'get_data '//trim(zmq_state), worker_id, 'psi_coef' diff --git a/src/Ezfio_files/output.irp.f b/src/Ezfio_files/output.irp.f index 25f862bd..c8e50d48 100644 --- a/src/Ezfio_files/output.irp.f +++ b/src/Ezfio_files/output.irp.f @@ -8,36 +8,6 @@ call wall_time(output_wall_time_0) END_PROVIDER -BEGIN_SHELL [ /bin/bash ] - - for NAME in $(\ls -d ${QP_ROOT}/src/*/) - do - NAME=$(basename ${NAME}) - cat << EOF - BEGIN_PROVIDER [ integer, output_$NAME ] - implicit none - BEGIN_DOC - ! Output file for $NAME - END_DOC - PROVIDE output_wall_time_0 output_cpu_time_0 ezfio_filename -! integer :: getUnitAndOpen -! call ezfio_set_output_empty(.False.) -IRP_IF COARRAY - if (this_image() == 1) then - output_$NAME = 6 !getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a') - else - output_$NAME = getUnitAndOpen('/dev/null','w') - endif -IRP_ELSE - output_$NAME = 6 !getUnitAndOpen(trim(ezfio_filename)//'/output/'//'$NAME.rst','a') -IRP_ENDIF - write(output_$NAME,'(A)') & - '--------------------------------------------------------------------------------' - END_PROVIDER -EOF - done - -END_SHELL subroutine write_time(iunit) implicit none diff --git a/src/MO_Basis/utils.irp.f b/src/MO_Basis/utils.irp.f index 4806582b..212d2b6f 100644 --- a/src/MO_Basis/utils.irp.f +++ b/src/MO_Basis/utils.irp.f @@ -55,7 +55,7 @@ subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label,sign,output) double precision, allocatable :: mo_coef_new(:,:), R(:,:),eigvalues(:), A(:,:) !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: mo_coef_new, R - call write_time(output_mo_basis) + call write_time(6) if (m /= mo_tot_num) then print *, irp_here, ': Error : m/= mo_tot_num' stop 1 @@ -78,12 +78,12 @@ subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label,sign,output) call lapack_diag(eigvalues,R,A,n,m) if (output) then - write (output_mo_basis,'(A)') 'MOs are now **'//trim(label)//'**' - write (output_mo_basis,'(A)') '' - write (output_mo_basis,'(A)') 'Eigenvalues' - write (output_mo_basis,'(A)') '-----------' - write (output_mo_basis,'(A)') '' - write (output_mo_basis,'(A)') '======== ================' + write (6,'(A)') 'MOs are now **'//trim(label)//'**' + write (6,'(A)') '' + write (6,'(A)') 'Eigenvalues' + write (6,'(A)') '-----------' + write (6,'(A)') '' + write (6,'(A)') '======== ================' endif if (sign == -1) then do i=1,m @@ -92,15 +92,15 @@ subroutine mo_as_eigvectors_of_mo_matrix(matrix,n,m,label,sign,output) endif if (output) then do i=1,m - write (output_mo_basis,'(I8,1X,F16.10)') i,eigvalues(i) + write (6,'(I8,1X,F16.10)') i,eigvalues(i) enddo - write (output_mo_basis,'(A)') '======== ================' - write (output_mo_basis,'(A)') '' + write (6,'(A)') '======== ================' + write (6,'(A)') '' endif call dgemm('N','N',ao_num,m,m,1.d0,mo_coef_new,size(mo_coef_new,1),R,size(R,1),0.d0,mo_coef,size(mo_coef,1)) deallocate(A,mo_coef_new,R,eigvalues) - call write_time(output_mo_basis) + call write_time(6) mo_label = label end @@ -115,7 +115,7 @@ subroutine mo_as_svd_vectors_of_mo_matrix(matrix,lda,m,n,label) double precision, allocatable :: mo_coef_new(:,:), U(:,:),D(:), A(:,:), Vt(:,:), work(:) !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: mo_coef_new, U, Vt, A - call write_time(output_mo_basis) + call write_time(6) if (m /= mo_tot_num) then print *, irp_here, ': Error : m/= mo_tot_num' stop 1 @@ -132,22 +132,22 @@ subroutine mo_as_svd_vectors_of_mo_matrix(matrix,lda,m,n,label) call svd(A,lda,U,lda,D,Vt,lda,m,n) - write (output_mo_basis,'(A)') 'MOs are now **'//trim(label)//'**' - write (output_mo_basis,'(A)') '' - write (output_mo_basis,'(A)') 'Eigenvalues' - write (output_mo_basis,'(A)') '-----------' - write (output_mo_basis,'(A)') '' - write (output_mo_basis,'(A)') '======== ================' + write (6,'(A)') 'MOs are now **'//trim(label)//'**' + write (6,'(A)') '' + write (6,'(A)') 'Eigenvalues' + write (6,'(A)') '-----------' + write (6,'(A)') '' + write (6,'(A)') '======== ================' do i=1,m - write (output_mo_basis,'(I8,1X,F16.10)') i,D(i) + write (6,'(I8,1X,F16.10)') i,D(i) enddo - write (output_mo_basis,'(A)') '======== ================' - write (output_mo_basis,'(A)') '' + write (6,'(A)') '======== ================' + write (6,'(A)') '' call dgemm('N','N',ao_num,m,m,1.d0,mo_coef_new,size(mo_coef_new,1),U,size(U,1),0.d0,mo_coef,size(mo_coef,1)) deallocate(A,mo_coef_new,U,Vt,D) - call write_time(output_mo_basis) + call write_time(6) mo_label = label end @@ -162,7 +162,7 @@ subroutine mo_as_eigvectors_of_mo_matrix_sort_by_observable(matrix,observable,n, integer,allocatable :: iorder(:) !DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: mo_coef_new, R - call write_time(output_mo_basis) + call write_time(6) if (m /= mo_tot_num) then print *, irp_here, ': Error : m/= mo_tot_num' stop 1 @@ -213,21 +213,21 @@ subroutine mo_as_eigvectors_of_mo_matrix_sort_by_observable(matrix,observable,n, print*,'' enddo - write (output_mo_basis,'(A)') 'MOs are now **'//trim(label)//'**' - write (output_mo_basis,'(A)') '' - write (output_mo_basis,'(A)') 'Eigenvalues' - write (output_mo_basis,'(A)') '-----------' - write (output_mo_basis,'(A)') '' - write (output_mo_basis,'(A)') '======== ================' + write (6,'(A)') 'MOs are now **'//trim(label)//'**' + write (6,'(A)') '' + write (6,'(A)') 'Eigenvalues' + write (6,'(A)') '-----------' + write (6,'(A)') '' + write (6,'(A)') '======== ================' do i = 1, m - write (output_mo_basis,'(I8,1X,F16.10)') i,eigvalues(i) + write (6,'(I8,1X,F16.10)') i,eigvalues(i) enddo - write (output_mo_basis,'(A)') '======== ================' - write (output_mo_basis,'(A)') '' + write (6,'(A)') '======== ================' + write (6,'(A)') '' call dgemm('N','N',ao_num,m,m,1.d0,mo_coef_new,size(mo_coef_new,1),R,size(R,1),0.d0,mo_coef,size(mo_coef,1)) deallocate(mo_coef_new,R,eigvalues) - call write_time(output_mo_basis) + call write_time(6) mo_label = label SOFT_TOUCH mo_coef mo_label @@ -261,12 +261,12 @@ subroutine mo_sort_by_observable(observable,label) enddo enddo - write (output_mo_basis,'(A)') 'MOs are now **'//trim(label)//'**' - write (output_mo_basis,'(A)') '' + write (6,'(A)') 'MOs are now **'//trim(label)//'**' + write (6,'(A)') '' deallocate(mo_coef_new,value) -! call write_time(output_mo_basis) +! call write_time(6) mo_label = label SOFT_TOUCH mo_coef mo_label diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index c78228a8..c178458b 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] if (mpi_master) then double precision, allocatable :: buffer(:,:) - nucl_coord = 0.d0 + nucl_coord_input = 0.d0 allocate (buffer(nucl_num,3)) buffer = 0.d0 logical :: has @@ -31,26 +31,94 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 +<<<<<<< HEAD call write_time(output_Nuclei) write(output_Nuclei,'(A)') '' write(output_Nuclei,'(A)') 'Nuclear Coordinates (Angstroms)' write(output_Nuclei,'(A)') '===============================' write(output_Nuclei,'(A)') '' write(output_Nuclei,ft) & +======= + call write_time(6) + write(6,'(A)') '' + write(6,'(A)') 'Input Nuclear Coordinates (Angstroms)' + write(6,'(A)') '=====================================' + write(6,'(A)') '' + write(6,ft) & '================','============','============','============','============' - write(output_Nuclei,*) & + write(6,*) & ' Atom Charge X Y Z ' - write(output_Nuclei,ft) & + write(6,ft) & '================','============','============','============','============' do i=1,nucl_num - write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & + write(6,f) nucl_label(i), nucl_charge(i), & + nucl_coord_input(i,1)*a0, & + nucl_coord_input(i,2)*a0, & + nucl_coord_input(i,3)*a0 + enddo + write(6,ft) & + '================','============','============','============','============' + write(6,'(A)') '' + + endif + + IRP_IF MPI + include 'mpif.h' + integer :: ierr + call MPI_BCAST( nucl_coord_input, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) + if (ierr /= MPI_SUCCESS) then + stop 'Unable to read nucl_coord_input with MPI' + endif + IRP_ENDIF + +END_PROVIDER + +BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] + implicit none + + BEGIN_DOC + ! Nuclear coordinates in standard orientation + END_DOC + + if (mpi_master) then + integer :: i + do i=1,nucl_num + nucl_coord(i,1) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) + nucl_coord(i,2) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) + nucl_coord(i,3) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & + (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & + (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) + enddo + + character*(64), parameter :: f = '(A16, 4(1X,F12.6))' + character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' + double precision, parameter :: a0= 0.529177249d0 + + call write_time(6) + write(6,'(A)') '' + write(6,'(A)') 'Nuclear Coordinates (Angstroms)' + write(6,'(A)') '===============================' + write(6,'(A)') '' + write(6,ft) & +>>>>>>> 9bc0215d... Removed output variables + '================','============','============','============','============' + write(6,*) & + ' Atom Charge X Y Z ' + write(6,ft) & + '================','============','============','============','============' + do i=1,nucl_num + write(6,f) nucl_label(i), nucl_charge(i), & nucl_coord(i,1)*a0, & nucl_coord(i,2)*a0, & nucl_coord(i,3)*a0 enddo - write(output_Nuclei,ft) & + write(6,ft) & '================','============','============','============','============' - write(output_Nuclei,'(A)') '' + write(6,'(A)') '' endif @@ -189,9 +257,15 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] enddo nuclear_repulsion *= 0.5d0 end if +<<<<<<< HEAD call write_time(output_Nuclei) call write_double(output_Nuclei,nuclear_repulsion, & +======= + + call write_time(6) + call write_double(6,nuclear_repulsion, & +>>>>>>> 9bc0215d... Removed output variables 'Nuclear repulsion energy') if (disk_access_nuclear_repulsion.EQ.'Write') then diff --git a/src/ZMQ/put_get.irp.f b/src/ZMQ/put_get.irp.f index 4086b8ed..40d2e881 100644 --- a/src/ZMQ/put_get.irp.f +++ b/src/ZMQ/put_get.irp.f @@ -51,6 +51,7 @@ integer function zmq_get_dvector(zmq_to_qp_run_socket, worker_id, name, x, size_ integer*8 :: rc8 character*(256) :: msg + PROVIDE zmq_state ! Success zmq_get_dvector = 0 From 79f6285472c37f4b5aa00935ce5fd09141466a99 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 5 Jan 2018 14:39:19 +0000 Subject: [PATCH 50/54] Fixed nuclei.irp.f --- src/Nuclei/nuclei.irp.f | 77 +---------------------------------------- 1 file changed, 1 insertion(+), 76 deletions(-) diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index c178458b..4686418a 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -31,80 +31,12 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 -<<<<<<< HEAD - call write_time(output_Nuclei) - write(output_Nuclei,'(A)') '' - write(output_Nuclei,'(A)') 'Nuclear Coordinates (Angstroms)' - write(output_Nuclei,'(A)') '===============================' - write(output_Nuclei,'(A)') '' - write(output_Nuclei,ft) & -======= - call write_time(6) - write(6,'(A)') '' - write(6,'(A)') 'Input Nuclear Coordinates (Angstroms)' - write(6,'(A)') '=====================================' - write(6,'(A)') '' - write(6,ft) & - '================','============','============','============','============' - write(6,*) & - ' Atom Charge X Y Z ' - write(6,ft) & - '================','============','============','============','============' - do i=1,nucl_num - write(6,f) nucl_label(i), nucl_charge(i), & - nucl_coord_input(i,1)*a0, & - nucl_coord_input(i,2)*a0, & - nucl_coord_input(i,3)*a0 - enddo - write(6,ft) & - '================','============','============','============','============' - write(6,'(A)') '' - - endif - - IRP_IF MPI - include 'mpif.h' - integer :: ierr - call MPI_BCAST( nucl_coord_input, 3*nucl_num, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr) - if (ierr /= MPI_SUCCESS) then - stop 'Unable to read nucl_coord_input with MPI' - endif - IRP_ENDIF - -END_PROVIDER - -BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] - implicit none - - BEGIN_DOC - ! Nuclear coordinates in standard orientation - END_DOC - - if (mpi_master) then - integer :: i - do i=1,nucl_num - nucl_coord(i,1) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,1) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,1) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,1) - nucl_coord(i,2) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,2) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,2) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,2) - nucl_coord(i,3) = (nucl_coord_input(i,1) - center_of_mass(1))*inertia_tensor_eigenvectors(1,3) + & - (nucl_coord_input(i,2) - center_of_mass(2))*inertia_tensor_eigenvectors(2,3) + & - (nucl_coord_input(i,3) - center_of_mass(3))*inertia_tensor_eigenvectors(3,3) - enddo - - character*(64), parameter :: f = '(A16, 4(1X,F12.6))' - character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' - double precision, parameter :: a0= 0.529177249d0 - call write_time(6) write(6,'(A)') '' write(6,'(A)') 'Nuclear Coordinates (Angstroms)' write(6,'(A)') '===============================' write(6,'(A)') '' write(6,ft) & ->>>>>>> 9bc0215d... Removed output variables '================','============','============','============','============' write(6,*) & ' Atom Charge X Y Z ' @@ -257,16 +189,9 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ] enddo nuclear_repulsion *= 0.5d0 end if -<<<<<<< HEAD - - call write_time(output_Nuclei) - call write_double(output_Nuclei,nuclear_repulsion, & -======= call write_time(6) - call write_double(6,nuclear_repulsion, & ->>>>>>> 9bc0215d... Removed output variables - 'Nuclear repulsion energy') + call write_double(6,nuclear_repulsion,'Nuclear repulsion energy') if (disk_access_nuclear_repulsion.EQ.'Write') then if (mpi_master) then From a68f3bb909742c74a8fdf45c208b794e1fa26346 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 5 Jan 2018 18:15:34 +0100 Subject: [PATCH 51/54] Fixed travis --- plugins/Generators_CAS/generators.irp.f | 4 +- plugins/Generators_restart/generators.irp.f | 2 +- plugins/MRCC_Utils/mrcc_utils.irp.f | 8 +- plugins/Selectors_no_sorted/selectors.irp.f | 4 +- plugins/Symmetry/Symmetry.main.irp.f | 11 +- plugins/Symmetry/aos.irp.f | 20 ++-- plugins/Symmetry/find_sym.irp.f | 108 +------------------- plugins/Symmetry/nuclei.irp.f | 22 ++-- plugins/Symmetry/sym_operation.irp.f | 2 +- plugins/mrcepa0/dressing.irp.f | 13 +++ src/Nuclei/nuclei.irp.f | 2 +- 11 files changed, 57 insertions(+), 139 deletions(-) diff --git a/plugins/Generators_CAS/generators.irp.f b/plugins/Generators_CAS/generators.irp.f index 4e2fcd58..259af99d 100644 --- a/plugins/Generators_CAS/generators.irp.f +++ b/plugins/Generators_CAS/generators.irp.f @@ -7,7 +7,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] END_DOC integer :: i,k,l logical :: good - call write_time(output_determinants) + call write_time(6) N_det_generators = 0 do i=1,N_det do l=1,n_cas_bitmask @@ -28,7 +28,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] endif enddo N_det_generators = max(N_det_generators,1) - call write_int(output_determinants,N_det_generators,'Number of generators') + call write_int(6,N_det_generators,'Number of generators') END_PROVIDER BEGIN_PROVIDER [ integer(bit_kind), psi_det_generators, (N_int,2,psi_det_size) ] diff --git a/plugins/Generators_restart/generators.irp.f b/plugins/Generators_restart/generators.irp.f index 17854330..bcd8d0d2 100644 --- a/plugins/Generators_restart/generators.irp.f +++ b/plugins/Generators_restart/generators.irp.f @@ -14,7 +14,7 @@ BEGIN_PROVIDER [ integer, N_det_generators ] else print*,'PB in generators restart !!!' endif - call write_int(output_determinants,N_det_generators,'Number of generators') + call write_int(6,N_det_generators,'Number of generators') END_PROVIDER diff --git a/plugins/MRCC_Utils/mrcc_utils.irp.f b/plugins/MRCC_Utils/mrcc_utils.irp.f index 46b08de2..6609790b 100644 --- a/plugins/MRCC_Utils/mrcc_utils.irp.f +++ b/plugins/MRCC_Utils/mrcc_utils.irp.f @@ -211,7 +211,7 @@ END_PROVIDER call davidson_diag_mrcc_HS2(psi_det,eigenvectors, & size(eigenvectors,1), & eigenvalues,N_det,N_states,N_states_diag,N_int, & - output_determinants,mrcc_state) + 6,mrcc_state) CI_eigenvectors_dressed(1:N_det,mrcc_state) = eigenvectors(1:N_det,mrcc_state) CI_electronic_energy_dressed(mrcc_state) = eigenvalues(mrcc_state) enddo @@ -316,12 +316,12 @@ BEGIN_PROVIDER [ double precision, CI_energy_dressed, (N_states_diag) ] integer :: j character*(8) :: st - call write_time(output_determinants) + call write_time(6) do j=1,min(N_det,N_states) write(st,'(I4)') j CI_energy_dressed(j) = CI_electronic_energy_dressed(j) + nuclear_repulsion - call write_double(output_determinants,CI_energy_dressed(j),'Energy of state '//trim(st)) - call write_double(output_determinants,CI_eigenvectors_s2_dressed(j),'S^2 of state '//trim(st)) + call write_double(6,CI_energy_dressed(j),'Energy of state '//trim(st)) + call write_double(6,CI_eigenvectors_s2_dressed(j),'S^2 of state '//trim(st)) enddo END_PROVIDER diff --git a/plugins/Selectors_no_sorted/selectors.irp.f b/plugins/Selectors_no_sorted/selectors.irp.f index 3ac8218d..e81aa795 100644 --- a/plugins/Selectors_no_sorted/selectors.irp.f +++ b/plugins/Selectors_no_sorted/selectors.irp.f @@ -8,11 +8,11 @@ BEGIN_PROVIDER [ integer, N_det_selectors] END_DOC integer :: i double precision :: norm - call write_time(output_determinants) + call write_time(6) norm = 0.d0 N_det_selectors = N_det N_det_selectors = max(N_det_selectors,1) - call write_int(output_determinants,N_det_selectors,'Number of selectors') + call write_int(6,N_det_selectors,'Number of selectors') END_PROVIDER diff --git a/plugins/Symmetry/Symmetry.main.irp.f b/plugins/Symmetry/Symmetry.main.irp.f index 9540295f..ffce8082 100644 --- a/plugins/Symmetry/Symmetry.main.irp.f +++ b/plugins/Symmetry/Symmetry.main.irp.f @@ -3,9 +3,17 @@ program Symmetry BEGIN_DOC ! TODO END_DOC - integer :: i, j + integer :: i, j, k character*8 :: sym +do k=1,n_irrep + print *, sym_operation(k) + do i=1,mo_tot_num + print '(1000(F8.4,X))', mo_symm(i,:,k), sum(mo_symm(i,:,k)) + enddo + print *, '' +enddo + print *, 'Molecule is linear: ', molecule_is_linear print *, 'Has center of inversion: ', molecule_has_center_of_inversion print *, 'Has S2n improper rotation: ', molecule_has_improper_rotation @@ -17,5 +25,4 @@ program Symmetry do i=1,n_irrep print *, i, real(character_table(i,:)) enddo - PROVIDE mo_sym end diff --git a/plugins/Symmetry/aos.irp.f b/plugins/Symmetry/aos.irp.f index 1ed567bc..ed746a40 100644 --- a/plugins/Symmetry/aos.irp.f +++ b/plugins/Symmetry/aos.irp.f @@ -22,15 +22,19 @@ subroutine generate_sym_coord(n_sym_points,result) BEGIN_DOC ! xyz coordinates of points to check the symmetry, drawn uniformly in the molecular box. END_DOC - integer :: i, xyz + integer :: i, iop - do i=1,n_sym_points - call random_number(result(1,i)) - call random_number(result(2,i)) - call random_number(result(3,i)) - enddo - do xyz=1,3 - result(xyz,1:n_sym_points) = sym_box(xyz,1) + result(xyz,:) * (sym_box(xyz,2)-sym_box(xyz,1)) + double precision, external :: halton_ranf + do i=1,n_sym_points,n_irrep + result(1,i) = sym_box(1,1) + halton_ranf(1) * (sym_box(1,2)-sym_box(1,1)) + result(2,i) = sym_box(1,1) + halton_ranf(2) * (sym_box(2,2)-sym_box(2,1)) + result(3,i) = sym_box(1,1) + halton_ranf(3) * (sym_box(3,2)-sym_box(3,1)) + do iop=2,n_irrep + if (iop-1+i > n_sym_points) exit + call dgemm('N','N',3,1,3,1.d0,sym_transformation_matrices(1,1,iop), & + size(sym_transformation_matrices,1),& + result(1,i),size(result,1),0.d0,result(1,i+iop-1),size(result,1)) + enddo enddo end diff --git a/plugins/Symmetry/find_sym.irp.f b/plugins/Symmetry/find_sym.irp.f index 38c0a6b7..817638b4 100644 --- a/plugins/Symmetry/find_sym.irp.f +++ b/plugins/Symmetry/find_sym.irp.f @@ -47,6 +47,7 @@ BEGIN_PROVIDER [ integer, sym_rotation_axis, (3) ] logical :: found double precision, external :: u_dot_u integer :: iorder, iaxis + do iaxis=1,3 do iorder=12,2,-1 sym_rotation_axis(iaxis) = iorder @@ -300,14 +301,6 @@ BEGIN_PROVIDER [ character*16, point_group ] END_PROVIDER -BEGIN_PROVIDER [ character*8, mo_symmetry ] - implicit none - BEGIN_DOC - ! Symmetry of the MOs - END_DOC - integer :: i,j -END_PROVIDER - BEGIN_PROVIDER [ integer, n_irrep ] implicit none @@ -369,105 +362,6 @@ BEGIN_PROVIDER [ integer, mo_sym, (mo_tot_num) ] double precision :: sym_operations_on_mos(mo_tot_num) logical :: possible_irrep(n_irrep,mo_tot_num) - n_sym_points = 10 - allocate(val(n_sym_points,mo_tot_num,2), sym_points(3,n_sym_points), ref_points(3,n_sym_points)) - - call generate_sym_coord(n_sym_points,ref_points) - call compute_sym_mo_values(ref_points,n_sym_points,val(1,1,2)) - - possible_irrep = .True. - do iop=1,n_irrep - if (sym_operation(iop) == 'E') then - cycle - endif - - if (sym_operation(iop) == 'i') then - do ipoint=1,n_sym_points - call sym_apply_inversion(ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop) == 'sh') then - do ipoint=1,n_sym_points - call sym_apply_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop) == 's') then - do ipoint=1,n_sym_points - call sym_apply_reflexion(molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop) == 'sv') then - do ipoint=1,n_sym_points - call sym_apply_reflexion(molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop) == 'sd') then - angle = dble(maxval(sym_rotation_axis)) - do ipoint=1,n_sym_points - call sym_apply_diagonal_reflexion(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop) == 'C2''') then - angle = 2.d0 - do ipoint=1,n_sym_points - call sym_apply_rotation(angle,molecule_secondary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop) == 'C2"') then - angle = 2.d0 - do ipoint=1,n_sym_points - call sym_apply_rotation(angle,molecule_ternary_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else - do l=2,len(sym_operation(iop)) - if (sym_operation(iop)(l:l) == '^') exit - enddo - read(sym_operation(iop)(2:l-1), *) iangle - if (l == len(sym_operation(iop))+1) then - l=1 - else - read(sym_operation(iop)(l+1:), *, err=10, end=10) l - 10 continue - endif - angle = dble(iangle)/(dble(l)) - if (sym_operation(iop)(1:1) == 'C') then - do ipoint=1,n_sym_points - call sym_apply_rotation(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - else if (sym_operation(iop)(1:1) == 'S') then - do ipoint=1,n_sym_points - call sym_apply_improper_rotation(angle,molecule_principal_axis,ref_points(1,ipoint),sym_points(1,ipoint)) - enddo - endif - endif - - call compute_sym_mo_values(sym_points,n_sym_points,val(1,1,1)) - - print *, sym_operation(iop) - double precision :: icount - do imo=1,mo_tot_num - sym_operations_on_mos(imo) = 0.d0 - icount = 0 - do ipoint=1,n_sym_points - double precision :: x - if (dabs(val(ipoint,imo,1)) < 1.d-5) cycle - icount += 1.d0 - x = val(ipoint,imo,1)/val(ipoint,imo,2) - if (dabs(x) > 1.d0) then - x = 1.d0/x - endif - sym_operations_on_mos(imo) += x - enddo - sym_operations_on_mos(imo) *= 1.d0/icount - if (dabs(sym_operations_on_mos(imo) - 1.d0) < 1.d-2) then - sym_operations_on_mos(imo) = 1.d0 - else if (dabs(sym_operations_on_mos(imo) + 1.d0) < 1.d-2) then - sym_operations_on_mos(imo) = -1.d0 - else if (dabs(sym_operations_on_mos(imo)) < 1.d-2) then - sym_operations_on_mos(imo) = 0.d0 - endif - print *, imo, sym_operations_on_mos(imo) - do i=1,n_irrep - if (dabs(character_table(i,iop) - sym_operations_on_mos(imo)) > 1.d-2) then - possible_irrep(i,imo) = .False. - endif - enddo - enddo - enddo do imo=1,mo_tot_num print *, 'MO ', imo do i=1,n_irrep diff --git a/plugins/Symmetry/nuclei.irp.f b/plugins/Symmetry/nuclei.irp.f index d680393d..405b529a 100644 --- a/plugins/Symmetry/nuclei.irp.f +++ b/plugins/Symmetry/nuclei.irp.f @@ -69,26 +69,26 @@ BEGIN_PROVIDER [ double precision, nucl_coord_sym, (nucl_num,3) ] character*(64), parameter :: ft= '(A16, 4(1X,A12 ))' double precision, parameter :: a0= 0.529177249d0 - call write_time(output_Nuclei) - write(output_Nuclei,'(A)') '' - write(output_Nuclei,'(A)') 'Nuclear Coordinates in standard orientation (Angstroms)' - write(output_Nuclei,'(A)') '=======================================================' - write(output_Nuclei,'(A)') '' - write(output_Nuclei,ft) & + call write_time(6) + write(6,'(A)') '' + write(6,'(A)') 'Nuclear Coordinates in standard orientation (Angstroms)' + write(6,'(A)') '=======================================================' + write(6,'(A)') '' + write(6,ft) & '================','============','============','============','============' - write(output_Nuclei,*) & + write(6,*) & ' Atom Charge X Y Z ' - write(output_Nuclei,ft) & + write(6,ft) & '================','============','============','============','============' do i=1,nucl_num - write(output_Nuclei,f) nucl_label(i), nucl_charge(i), & + write(6,f) nucl_label(i), nucl_charge(i), & nucl_coord_sym(i,1)*a0, & nucl_coord_sym(i,2)*a0, & nucl_coord_sym(i,3)*a0 enddo - write(output_Nuclei,ft) & + write(6,ft) & '================','============','============','============','============' - write(output_Nuclei,'(A)') '' + write(6,'(A)') '' endif diff --git a/plugins/Symmetry/sym_operation.irp.f b/plugins/Symmetry/sym_operation.irp.f index cfc86621..ccf72ec3 100644 --- a/plugins/Symmetry/sym_operation.irp.f +++ b/plugins/Symmetry/sym_operation.irp.f @@ -23,7 +23,7 @@ subroutine sym_apply_diagonal_reflexion(angle,iaxis,point_in,point_out) double precision :: point_tmp1(3), point_tmp2(3) integer :: iaxis2 iaxis2 = mod(iaxis,3)+1 - iaxis2 = mod(iaxis2,3)+1 +! iaxis2 = mod(iaxis2,3)+1 call sym_apply_rotation(-angle,iaxis,point_in,point_tmp1) call sym_apply_reflexion(iaxis2,point_tmp1,point_tmp2) call sym_apply_rotation(angle,iaxis,point_tmp2,point_out) diff --git a/plugins/mrcepa0/dressing.irp.f b/plugins/mrcepa0/dressing.irp.f index 5dfa8556..727bdba7 100644 --- a/plugins/mrcepa0/dressing.irp.f +++ b/plugins/mrcepa0/dressing.irp.f @@ -963,6 +963,19 @@ END_PROVIDER enddo end do end do +! else if(mrmode == 10) then +! do i = 1, N_det_ref +! do i_state = 1, N_states +! delta_ii(i_state,i)= delta_ii_mrsc2(i_state,i) +! delta_ii_s2(i_state,i)= delta_ii_s2_mrsc2(i_state,i) +! enddo +! do j = 1, N_det_non_ref +! do i_state = 1, N_states +! delta_ij(i_state,j,i) = delta_ij_mrsc2(i_state,j,i) +! delta_ij_s2(i_state,j,i) = delta_ij_s2_mrsc2(i_state,j,i) +! enddo +! end do +! end do else if(mrmode == 5) then do i = 1, N_det_ref do i_state = 1, N_states diff --git a/src/Nuclei/nuclei.irp.f b/src/Nuclei/nuclei.irp.f index 4686418a..3528bf50 100644 --- a/src/Nuclei/nuclei.irp.f +++ b/src/Nuclei/nuclei.irp.f @@ -8,7 +8,7 @@ BEGIN_PROVIDER [ double precision, nucl_coord, (nucl_num,3) ] if (mpi_master) then double precision, allocatable :: buffer(:,:) - nucl_coord_input = 0.d0 + nucl_coord = 0.d0 allocate (buffer(nucl_num,3)) buffer = 0.d0 logical :: has From 41b774c064bd81e4fdaf146167865b930e7b7c0e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 8 Jan 2018 13:41:16 +0100 Subject: [PATCH 52/54] Distributed davidson may have a bug... --- src/Davidson/EZFIO.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Davidson/EZFIO.cfg b/src/Davidson/EZFIO.cfg index 9041325c..49a0f778 100644 --- a/src/Davidson/EZFIO.cfg +++ b/src/Davidson/EZFIO.cfg @@ -31,6 +31,6 @@ interface: ezfio,provider,ocaml [distributed_davidson] type: logical doc: If true, use the distributed algorithm -default: True +default: False interface: ezfio,provider,ocaml From 9d1ab2848dd829e2f3eb8e6aeddb840010e082a9 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 8 Jan 2018 18:26:51 +0100 Subject: [PATCH 53/54] Fixed linear-dep threshold --- src/MO_Basis/ao_ortho_canonical.irp.f | 2 +- src/Utils/LinearAlgebra.irp.f | 17 ++++++----------- 2 files changed, 7 insertions(+), 12 deletions(-) diff --git a/src/MO_Basis/ao_ortho_canonical.irp.f b/src/MO_Basis/ao_ortho_canonical.irp.f index b0400f67..5d01efb9 100644 --- a/src/MO_Basis/ao_ortho_canonical.irp.f +++ b/src/MO_Basis/ao_ortho_canonical.irp.f @@ -129,7 +129,7 @@ END_PROVIDER enddo ao_ortho_canonical_num = ao_cart_to_sphe_num - call ortho_canonical (ao_cart_to_sphe_overlap, size(ao_cart_to_sphe_overlap,1), & + call ortho_canonical(ao_cart_to_sphe_overlap, size(ao_cart_to_sphe_overlap,1), & ao_cart_to_sphe_num, S, size(S,1), ao_ortho_canonical_num) call dgemm('N','N', ao_num, ao_ortho_canonical_num, ao_cart_to_sphe_num, 1.d0, & diff --git a/src/Utils/LinearAlgebra.irp.f b/src/Utils/LinearAlgebra.irp.f index 6e1b9565..29d8784f 100644 --- a/src/Utils/LinearAlgebra.irp.f +++ b/src/Utils/LinearAlgebra.irp.f @@ -81,10 +81,11 @@ subroutine ortho_canonical(overlap,LDA,N,C,LDC,m) call svd(overlap,lda,U,ldc,D,Vt,lda,n,n) + D(:) = dsqrt(D(:)) m=n do i=1,n if ( D(i) >= 1.d-6 ) then - D(i) = 1.d0/dsqrt(D(i)) + D(i) = 1.d0/D(i) else m = i-1 print *, 'Removed Linear dependencies below:', 1.d0/D(m) @@ -101,25 +102,19 @@ subroutine ortho_canonical(overlap,LDA,N,C,LDC,m) endif enddo - - !$OMP PARALLEL DEFAULT(NONE) & - !$OMP SHARED(S,U,D,Vt,n,C,m) & - !$OMP PRIVATE(i,j) - - !$OMP DO do j=1,n do i=1,n S(i,j) = U(i,j)*D(j) enddo + enddo + + do j=1,n do i=1,n U(i,j) = C(i,j) enddo enddo - !$OMP END DO - !$OMP END PARALLEL - - call dgemm('N','N',n,m,n,1.d0,U,size(U,1),S,size(S,1),0.d0,C,size(C,1)) + call dgemm('N','N',n,n,n,1.d0,U,size(U,1),S,size(S,1),0.d0,C,size(C,1)) deallocate (U, Vt, D, S) end From 5166768d963dc0ca1fc4718fdbd9d4b0140172e4 Mon Sep 17 00:00:00 2001 From: Yann Garniron Date: Tue, 9 Jan 2018 13:29:34 +0100 Subject: [PATCH 54/54] merged stash --- plugins/dress_zmq/dress_slave.irp.f | 2 +- plugins/mrcepa0/mrcc_slave.irp.f | 15 +++++++++++++-- plugins/mrcepa0/mrcc_stoch_routines.irp.f | 1 - 3 files changed, 14 insertions(+), 4 deletions(-) diff --git a/plugins/dress_zmq/dress_slave.irp.f b/plugins/dress_zmq/dress_slave.irp.f index 560f536d..0b742003 100644 --- a/plugins/dress_zmq/dress_slave.irp.f +++ b/plugins/dress_zmq/dress_slave.irp.f @@ -1,4 +1,4 @@ -subroutine dress_slave() +subroutine dress_slave implicit none BEGIN_DOC ! Helper program to compute the dress in distributed mode. diff --git a/plugins/mrcepa0/mrcc_slave.irp.f b/plugins/mrcepa0/mrcc_slave.irp.f index 83295985..655536ff 100644 --- a/plugins/mrcepa0/mrcc_slave.irp.f +++ b/plugins/mrcepa0/mrcc_slave.irp.f @@ -25,7 +25,11 @@ subroutine run_wf double precision :: energy(N_states_diag) character*(64) :: states(1) integer :: rc, i - + + integer, external :: zmq_get_dvector, zmq_get_N_det_generators + integer, external :: zmq_get_psi, zmq_get_N_det_selectors + integer, external :: zmq_get_N_states_diag + call provide_everything zmq_context = f77_zmq_ctx_new () @@ -47,7 +51,14 @@ subroutine run_wf ! --------- print *, 'mrcc' - call zmq_get_psi(zmq_to_qp_run_socket,1,energy,N_states) + !call wall_time(t0) + if (zmq_get_psi(zmq_to_qp_run_socket,1) == -1) cycle + if (zmq_get_N_det_generators (zmq_to_qp_run_socket, 1) == -1) cycle + if (zmq_get_N_det_selectors(zmq_to_qp_run_socket, 1) == -1) cycle + if (zmq_get_dvector(zmq_to_qp_run_socket,1,'energy',energy,N_states) == -1) cycle + + !call wall_time(t1) + !call write_double(6,(t1-t0),'Broadcast time') PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order diff --git a/plugins/mrcepa0/mrcc_stoch_routines.irp.f b/plugins/mrcepa0/mrcc_stoch_routines.irp.f index d97308e1..7205837a 100644 --- a/plugins/mrcepa0/mrcc_stoch_routines.irp.f +++ b/plugins/mrcepa0/mrcc_stoch_routines.irp.f @@ -75,7 +75,6 @@ subroutine ZMQ_mrcc(E, mrcc, delta, delta_s2, relative_error) ! end do integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket - integer, external :: add_task_to_taskserver, zmq_set_running integer :: ipos ipos=1 do i=1,N_mrcc_jobs