From a7c1a04840f5222e4f65ddb8b7b753840265f555 Mon Sep 17 00:00:00 2001 From: Emmanuel Giner LCT Date: Thu, 16 May 2019 12:18:43 +0200 Subject: [PATCH 01/36] added get integral ao with two index only --- src/ao_two_e_ints/map_integrals.irp.f | 47 +++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/src/ao_two_e_ints/map_integrals.irp.f b/src/ao_two_e_ints/map_integrals.irp.f index 304fec49..01b923e5 100644 --- a/src/ao_two_e_ints/map_integrals.irp.f +++ b/src/ao_two_e_ints/map_integrals.irp.f @@ -279,6 +279,53 @@ subroutine get_ao_two_e_integrals_non_zero(j,k,l,sze,out_val,out_val_index,non_z end +subroutine get_ao_two_e_integrals_non_zero_jl(j,l,thresh,sze_max,sze,out_val,out_val_index,non_zero_int) + use map_module + implicit none + BEGIN_DOC + ! Gets multiple AO bi-electronic integral from the AO map . + ! All non-zero i are retrieved for j,k,l fixed. + END_DOC + double precision, intent(in) :: thresh + integer, intent(in) :: j,l, sze,sze_max + real(integral_kind), intent(out) :: out_val(sze_max) + integer, intent(out) :: out_val_index(2,sze_max),non_zero_int + + integer :: i,k + integer(key_kind) :: hash + double precision :: tmp + + PROVIDE ao_two_e_integrals_in_map + non_zero_int = 0 + if (ao_overlap_abs(j,l) < thresh) then + out_val = 0.d0 + return + endif + + non_zero_int = 0 + do k = 1, sze + do i = 1, sze + integer, external :: ao_l4 + double precision, external :: ao_two_e_integral + !DIR$ FORCEINLINE + if (ao_two_e_integral_schwartz(i,k)*ao_two_e_integral_schwartz(j,l) < thresh) then + cycle + endif + call two_e_integrals_index(i,j,k,l,hash) + call map_get(ao_integrals_map, hash,tmp) + if (dabs(tmp) < thresh ) cycle + non_zero_int = non_zero_int+1 + out_val_index(1,non_zero_int) = i + out_val_index(2,non_zero_int) = k + out_val(non_zero_int) = tmp + enddo + enddo + +end + + + + function get_ao_map_size() implicit none integer (map_size_kind) :: get_ao_map_size From 35cdb13bd4f4faf0cf8e42d72e45ae6d96fc9e38 Mon Sep 17 00:00:00 2001 From: Emmanuel Giner LCT Date: Mon, 20 May 2019 08:54:39 +0200 Subject: [PATCH 02/36] added some stuffs for getting the bielec integrals --- src/ao_two_e_ints/map_integrals.irp.f | 46 ++++++++++++++++ src/becke_numerical_grid/EZFIO.cfg | 6 +++ .../grid_becke_per_atom.irp.f | 53 +++++++++++++++++++ .../grid_becke_vector.irp.f | 12 ++--- src/dft_utils_in_r/ao_in_r.irp.f | 23 ++++++++ 5 files changed, 134 insertions(+), 6 deletions(-) create mode 100644 src/becke_numerical_grid/grid_becke_per_atom.irp.f diff --git a/src/ao_two_e_ints/map_integrals.irp.f b/src/ao_two_e_ints/map_integrals.irp.f index 01b923e5..c6b01b07 100644 --- a/src/ao_two_e_ints/map_integrals.irp.f +++ b/src/ao_two_e_ints/map_integrals.irp.f @@ -324,6 +324,52 @@ subroutine get_ao_two_e_integrals_non_zero_jl(j,l,thresh,sze_max,sze,out_val,out end +subroutine get_ao_two_e_integrals_non_zero_jl_from_list(j,l,thresh,list,n_list,sze_max,out_val,out_val_index,non_zero_int) + use map_module + implicit none + BEGIN_DOC + ! Gets multiple AO bi-electronic integral from the AO map . + ! All non-zero i are retrieved for j,k,l fixed. + END_DOC + double precision, intent(in) :: thresh + integer, intent(in) :: j,l, n_list,list(2,sze_max),sze_max + real(integral_kind), intent(out) :: out_val(sze_max) + integer, intent(out) :: out_val_index(2,sze_max),non_zero_int + + integer :: i,k + integer(key_kind) :: hash + double precision :: tmp + + PROVIDE ao_two_e_integrals_in_map + non_zero_int = 0 + if (ao_overlap_abs(j,l) < thresh) then + out_val = 0.d0 + return + endif + + non_zero_int = 0 + integer :: kk + do kk = 1, n_list + k = list(1,kk) + i = list(2,kk) + integer, external :: ao_l4 + double precision, external :: ao_two_e_integral + !DIR$ FORCEINLINE + if (ao_two_e_integral_schwartz(i,k)*ao_two_e_integral_schwartz(j,l) < thresh) then + cycle + endif + call two_e_integrals_index(i,j,k,l,hash) + call map_get(ao_integrals_map, hash,tmp) + if (dabs(tmp) < thresh ) cycle + non_zero_int = non_zero_int+1 + out_val_index(1,non_zero_int) = i + out_val_index(2,non_zero_int) = k + out_val(non_zero_int) = tmp + enddo + +end + + function get_ao_map_size() diff --git a/src/becke_numerical_grid/EZFIO.cfg b/src/becke_numerical_grid/EZFIO.cfg index ed89428c..ca2100a1 100644 --- a/src/becke_numerical_grid/EZFIO.cfg +++ b/src/becke_numerical_grid/EZFIO.cfg @@ -8,3 +8,9 @@ default: 2 type: integer doc: Total number of grid points interface: ezfio + +[thresh_grid] +type: double precision +doc: threshold on the weight of a given grid point +interface: ezfio,provider,ocaml +default: 1.e-20 diff --git a/src/becke_numerical_grid/grid_becke_per_atom.irp.f b/src/becke_numerical_grid/grid_becke_per_atom.irp.f new file mode 100644 index 00000000..6026350b --- /dev/null +++ b/src/becke_numerical_grid/grid_becke_per_atom.irp.f @@ -0,0 +1,53 @@ + + + BEGIN_PROVIDER [integer, n_pts_per_atom, (nucl_num)] +&BEGIN_PROVIDER [integer, n_pts_max_per_atom] + BEGIN_DOC + ! Number of points which are non zero + END_DOC + integer :: i,j,k,l + n_pts_per_atom = 0 + do j = 1, nucl_num + do i = 1, n_points_radial_grid -1 + do k = 1, n_points_integration_angular + if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then + cycle + endif + n_pts_per_atom(j) += 1 + enddo + enddo + enddo + n_pts_max_per_atom = maxval(n_pts_per_atom) +END_PROVIDER + + BEGIN_PROVIDER [double precision, final_grid_points_per_atom, (3,n_pts_max_per_atom,nucl_num)] +&BEGIN_PROVIDER [double precision, final_weight_at_r_vector_per_atom, (n_pts_max_per_atom,nucl_num) ] +&BEGIN_PROVIDER [integer, index_final_points_per_atom, (3,n_pts_max_per_atom,nucl_num) ] +&BEGIN_PROVIDER [integer, index_final_points_per_atom_reverse, (n_points_integration_angular,n_points_radial_grid,nucl_num) ] + implicit none + integer :: i,j,k,l,i_count(nucl_num) + double precision :: r(3) + i_count = 0 + do j = 1, nucl_num + do i = 1, n_points_radial_grid -1 + do k = 1, n_points_integration_angular + if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then + cycle + endif + i_count(j) += 1 + final_grid_points_per_atom(1,i_count(j),j) = grid_points_per_atom(1,k,i,j) + final_grid_points_per_atom(2,i_count(j),j) = grid_points_per_atom(2,k,i,j) + final_grid_points_per_atom(3,i_count(j),j) = grid_points_per_atom(3,k,i,j) + final_weight_at_r_vector_per_atom(i_count(j),j) = final_weight_at_r(k,i,j) + index_final_points_per_atom(1,i_count(j),j) = k + index_final_points_per_atom(2,i_count(j),j) = i + index_final_points_per_atom(3,i_count(j),j) = j + index_final_points_per_atom_reverse(k,i,j) = i_count(j) + enddo + enddo + enddo + + + + +END_PROVIDER diff --git a/src/becke_numerical_grid/grid_becke_vector.irp.f b/src/becke_numerical_grid/grid_becke_vector.irp.f index a595cd0b..9856bcbd 100644 --- a/src/becke_numerical_grid/grid_becke_vector.irp.f +++ b/src/becke_numerical_grid/grid_becke_vector.irp.f @@ -8,9 +8,9 @@ BEGIN_PROVIDER [integer, n_points_final_grid] do j = 1, nucl_num do i = 1, n_points_radial_grid -1 do k = 1, n_points_integration_angular -! if(dabs(final_weight_at_r(k,i,j)) < 1.d-30)then -! cycle -! endif + if(dabs(final_weight_at_r(k,i,j)) < tresh_grid)then + cycle + endif n_points_final_grid += 1 enddo enddo @@ -39,9 +39,9 @@ END_PROVIDER do j = 1, nucl_num do i = 1, n_points_radial_grid -1 do k = 1, n_points_integration_angular - !if(dabs(final_weight_at_r(k,i,j)) < 1.d-30)then - ! cycle - !endif + if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then + cycle + endif i_count += 1 final_grid_points(1,i_count) = grid_points_per_atom(1,k,i,j) final_grid_points(2,i_count) = grid_points_per_atom(2,k,i,j) diff --git a/src/dft_utils_in_r/ao_in_r.irp.f b/src/dft_utils_in_r/ao_in_r.irp.f index 17892832..767f329c 100644 --- a/src/dft_utils_in_r/ao_in_r.irp.f +++ b/src/dft_utils_in_r/ao_in_r.irp.f @@ -121,3 +121,26 @@ enddo END_PROVIDER + + BEGIN_PROVIDER[double precision, aos_in_r_array_per_atom, (ao_num,n_pts_max_per_atom,nucl_num)] +&BEGIN_PROVIDER[double precision, aos_in_r_array_per_atom_transp, (n_pts_max_per_atom,ao_num,nucl_num)] + implicit none + BEGIN_DOC + ! aos_in_r_array_per_atom(i,j,k) = value of the ith ao on the jth grid point attached on the kth atom + END_DOC + integer :: i,j,k + double precision :: aos_array(ao_num), r(3) + do k = 1, nucl_num + do i = 1, n_pts_per_atom(k) + r(1) = final_grid_points_per_atom(1,i,k) + r(2) = final_grid_points_per_atom(2,i,k) + r(3) = final_grid_points_per_atom(3,i,k) + call give_all_aos_at_r(r,aos_array) + do j = 1, ao_num + aos_in_r_array_per_atom(j,i,k) = aos_array(j) + aos_in_r_array_per_atom_transp(i,j,k) = aos_array(j) + enddo + enddo + enddo + END_PROVIDER + From 5e732b0f616cc8f7e820963ac14f9d3a9edc060d Mon Sep 17 00:00:00 2001 From: Pierre Loos Date: Thu, 23 May 2019 16:06:37 +0200 Subject: [PATCH 03/36] modified stuffs --- src/ao_two_e_ints/map_integrals.irp.f | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ao_two_e_ints/map_integrals.irp.f b/src/ao_two_e_ints/map_integrals.irp.f index c6b01b07..9e729cd4 100644 --- a/src/ao_two_e_ints/map_integrals.irp.f +++ b/src/ao_two_e_ints/map_integrals.irp.f @@ -328,11 +328,12 @@ subroutine get_ao_two_e_integrals_non_zero_jl_from_list(j,l,thresh,list,n_list,s use map_module implicit none BEGIN_DOC - ! Gets multiple AO bi-electronic integral from the AO map . + ! Gets multiple AO two-electron integrals from the AO map . ! All non-zero i are retrieved for j,k,l fixed. END_DOC double precision, intent(in) :: thresh - integer, intent(in) :: j,l, n_list,list(2,sze_max),sze_max + integer, intent(in) :: sze_max + integer, intent(in) :: j,l, n_list,list(2,sze_max) real(integral_kind), intent(out) :: out_val(sze_max) integer, intent(out) :: out_val_index(2,sze_max),non_zero_int From 6584a0c707207d288ae290c01c13a8694a91f108 Mon Sep 17 00:00:00 2001 From: Barthelemy Pradines LCT Date: Mon, 27 May 2019 15:17:10 +0200 Subject: [PATCH 04/36] added missing dependency inao_two_e_erf_ints/two_e_integrals_erf.irp.f --- src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f b/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f index 4433690f..97debfab 100644 --- a/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f +++ b/src/ao_two_e_erf_ints/two_e_integrals_erf.irp.f @@ -15,6 +15,8 @@ double precision function ao_two_e_integral_erf(i,j,k,l) double precision :: Q_new(0:max_dim,3),Q_center(3),fact_q,qq integer :: iorder_p(3), iorder_q(3) double precision :: ao_two_e_integral_schwartz_accel_erf + + provide mu_erf if (ao_prim_num(i) * ao_prim_num(j) * ao_prim_num(k) * ao_prim_num(l) > 1024 ) then ao_two_e_integral_erf = ao_two_e_integral_schwartz_accel_erf(i,j,k,l) From e98f745dba38d42acb253ca12257b440303c774d Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 15 May 2019 16:37:43 +0200 Subject: [PATCH 05/36] Removed install and uninstall from create_executables_list.sh --- scripts/module/create_executables_list.sh | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/scripts/module/create_executables_list.sh b/scripts/module/create_executables_list.sh index 8299a505..67e1aba2 100755 --- a/scripts/module/create_executables_list.sh +++ b/scripts/module/create_executables_list.sh @@ -15,5 +15,10 @@ EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -executable -type f | grep -e " for EXE in $EXES do - printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QP_ROOT}|\$QP_ROOT|g" >> executables + case "$(basename $EXE)" in + install) continue;; + uninstall) continue;; + *) + printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QP_ROOT}|\$QP_ROOT|g" >> executables ;; + esac done From a4e328d40dd09aad622c777306fae8e3965b2f11 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 24 May 2019 19:25:46 +0200 Subject: [PATCH 06/36] Added EPYC config file --- config/ifort_epyc.cfg | 63 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 config/ifort_epyc.cfg diff --git a/config/ifort_epyc.cfg b/config/ifort_epyc.cfg new file mode 100644 index 00000000..1b2427de --- /dev/null +++ b/config/ifort_epyc.cfg @@ -0,0 +1,63 @@ +# Common flags +############## +# +# -mkl=[parallel|sequential] : Use the MKL library +# --ninja : Allow the utilisation of ninja. It is mandatory ! +# --align=32 : Align all provided arrays on a 32-byte boundary +# +[COMMON] +FC : ifort -fpic +LAPACK_LIB : -mkl=parallel +IRPF90 : irpf90 +IRPF90_FLAGS : --ninja --align=32 + +# Global options +################ +# +# 1 : Activate +# 0 : Deactivate +# +[OPTION] +MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below +CACHE : 0 ; Enable cache_compile.py +OPENMP : 1 ; Append OpenMP flags + +# Optimization flags +#################### +# +# -xHost : Compile a binary optimized for the current architecture +# -O2 : O3 not better than O2. +# -ip : Inter-procedural optimizations +# -ftz : Flushes denormal results to zero +# +[OPT] +FC : -traceback +FCFLAGS : -march=core-avx2 -O2 -ip -ftz -g + +# Profiling flags +################# +# +[PROFILE] +FC : -p -g +FCFLAGS : -march=core-avx2 -O2 -ip -ftz + +# Debugging flags +################# +# +# -traceback : Activate backtrace on runtime +# -fpe0 : All floating point exaceptions +# -C : Checks uninitialized variables, array subscripts, etc... +# -g : Extra debugging information +# -xSSE2 : Valgrind needs a very simple x86 executable +# +[DEBUG] +FC : -g -traceback +FCFLAGS : -xSSE2 -C -fpe0 -implicitnone + +# OpenMP flags +################# +# +[OPENMP] +FC : -qopenmp +IRPF90_FLAGS : --openmp + From f133cb1e9fd5c9bd1957c8d6c65fdeb3a9b54190 Mon Sep 17 00:00:00 2001 From: Anouar Benali Date: Fri, 24 May 2019 16:19:34 -0500 Subject: [PATCH 07/36] NCSU ECP and Basis set (#41) * Adding Basis Sets and ECP from NCSU. When available He core ECP are chosen instead of large core. This applies to Na Mg Al Si P S Cl and Ar * ECP from ncsu * Update Readme file with description of Basis Set --- data/basis/00_README.rst | 12 + data/basis/aug-cc-pv5z_ecp_ncsu | 3535 +++++++++++++++++++++++++++++++ data/basis/aug-cc-pvdz_ecp_ncsu | 1777 ++++++++++++++++ data/basis/aug-cc-pvqz_ecp_ncsu | 2910 +++++++++++++++++++++++++ data/basis/aug-cc-pvtz_ecp_ncsu | 2325 ++++++++++++++++++++ data/basis/cc-pv5z_ecp_ncsu | 3512 ++++++++++++++++++++++++++++++ data/basis/cc-pvdz_ecp_ncsu | 1772 ++++++++++++++++ data/basis/cc-pvqz_ecp_ncsu | 2888 +++++++++++++++++++++++++ data/basis/cc-pvtz_ecp_ncsu | 2308 ++++++++++++++++++++ data/pseudo/ncsu | 346 +-- 10 files changed, 21252 insertions(+), 133 deletions(-) create mode 100644 data/basis/aug-cc-pv5z_ecp_ncsu create mode 100644 data/basis/aug-cc-pvdz_ecp_ncsu create mode 100644 data/basis/aug-cc-pvqz_ecp_ncsu create mode 100644 data/basis/aug-cc-pvtz_ecp_ncsu create mode 100644 data/basis/cc-pv5z_ecp_ncsu create mode 100644 data/basis/cc-pvdz_ecp_ncsu create mode 100644 data/basis/cc-pvqz_ecp_ncsu create mode 100644 data/basis/cc-pvtz_ecp_ncsu diff --git a/data/basis/00_README.rst b/data/basis/00_README.rst index 02b23f20..9d3510c3 100644 --- a/data/basis/00_README.rst +++ b/data/basis/00_README.rst @@ -263,4 +263,16 @@ vtz_mclean-chandler 'McLean/Chandler VTZ' VTZ Vale vtzp_binning-curtiss 'Binning/Curtiss VTZP' VTZP Valence Triple Zeta + Polarization wachters+f 'Wachters+f' VDZP Valence Double Zeta + Polarization on All Atoms +aug-cc-pvdz_ecp_ncsu 'aug-cc-pvdz ecp ncsu' augmented cc-pvDz basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +aug-cc-pvtz_ecp_ncsu 'aug-cc-pvtz ecp ncsu' augmented cc-pvTz basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +aug-cc-pvqz_ecp_ncsu 'aug-cc-pvqz ecp ncsu' augmented cc-pvQz basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +aug-cc-pv5z_ecp_ncsu 'aug-cc-pv5z ecp ncsu' augmented cc-pv5z basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +cc-pvdz_ecp_ncsu 'cc-pvdz ecp ncsu' cc-pvDz basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +cc-pvtz_ecp_ncsu 'cc-pvtz ecp ncsu' cc-pvTz basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +cc-pvqz_ecp_ncsu 'cc-pvqz ecp ncsu' cc-pvQz basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ +cc-pv5z_ecp_ncsu 'cc-pv5z ecp ncsu' cc-pv5z basis set designed for the NCSU ECP found in https://pseudopotentiallibrary.org/ + + + + # ; vim::nowrap diff --git a/data/basis/aug-cc-pv5z_ecp_ncsu b/data/basis/aug-cc-pv5z_ecp_ncsu new file mode 100644 index 00000000..1fd4b7d9 --- /dev/null +++ b/data/basis/aug-cc-pv5z_ecp_ncsu @@ -0,0 +1,3535 @@ +HYDROGEN +S 8 + 1 23.843185 0.00411490 + 2 10.212443 0.01046440 + 3 4.374164 0.02801110 + 4 1.873529 0.07588620 + 5 0.802465 0.18210620 + 6 0.343709 0.34852140 + 7 0.147217 0.37823130 + 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12 0.068195 -0.59782200 + 13 0.031465 -0.25611700 +S 13 + 1 114.485022 0.00070400 + 2 61.996430 0.01284100 + 3 40.117132 -0.08591000 + 4 20.119649 0.11798200 + 5 10.171676 0.63016400 + 6 5.601641 -0.60034400 + 7 2.864122 -1.24906000 + 8 1.592779 -0.32949800 + 9 0.826525 2.59246900 + 10 0.263975 -1.00448100 + 11 0.145302 -1.37951400 + 12 0.068195 1.04684200 + 13 0.031465 0.32467600 +S 1 + 1 0.031465 1.00000000 +P 13 + 1 158.770986 -0.00015300 + 2 75.802876 0.00189300 + 3 44.547824 0.01046100 + 4 31.445269 -0.04514100 + 5 13.080125 -0.08420100 + 6 7.788616 0.10497300 + 7 4.195040 0.30771400 + 8 2.362276 0.36856300 + 9 1.302584 0.28633600 + 10 0.660704 0.09515600 + 11 0.249042 0.00585100 + 12 0.091781 -0.00003400 + 13 0.048931 0.00025200 +P 13 + 1 158.770986 0.00005300 + 2 75.802876 -0.00057100 + 3 44.547824 -0.00107300 + 4 31.445269 0.00746300 + 5 13.080125 0.01867600 + 6 7.788616 -0.02809000 + 7 4.195040 -0.05443800 + 8 2.362276 -0.09374400 + 9 1.302584 -0.05416900 + 10 0.660704 -0.00797200 + 11 0.249042 0.35619800 + 12 0.091781 0.41239900 + 13 0.048931 0.36132100 +P 13 + 1 158.770986 -0.00017000 + 2 75.802876 0.00060400 + 3 44.547824 -0.01998700 + 4 31.445269 0.06115300 + 5 13.080125 0.06731700 + 6 7.788616 -0.13921100 + 7 4.195040 -0.52704100 + 8 2.362276 -0.17619400 + 9 1.302584 0.03712900 + 10 0.660704 1.07932200 + 11 0.249042 -0.05014900 + 12 0.091781 -0.68897100 + 13 0.048931 0.03733100 +P 13 + 1 158.770986 -0.00078100 + 2 75.802876 0.00785500 + 3 44.547824 -0.00867100 + 4 31.445269 -0.04055300 + 5 13.080125 -0.20006200 + 6 7.788616 0.52859900 + 7 4.195040 0.52855200 + 8 2.362276 0.24357600 + 9 1.302584 -1.80718200 + 10 0.660704 0.62949600 + 11 0.249042 1.13761300 + 12 0.091781 -1.06715000 + 13 0.048931 0.02219000 +P 1 + 1 0.048931 1.00000000 +D 11 + 1 270.014061 -0.00001600 + 2 100.161579 0.00069600 + 3 43.530609 0.01353600 + 4 21.262419 0.06935000 + 5 10.577821 0.14955900 + 6 5.343620 0.23958800 + 7 2.704857 0.28674400 + 8 1.353018 0.27145900 + 9 0.660873 0.20242600 + 10 0.309149 0.10330700 + 11 0.133879 0.02321100 +D 11 + 1 270.014061 0.00001300 + 2 100.161579 -0.00088900 + 3 43.530609 -0.01864000 + 4 21.262419 -0.09464600 + 5 10.577821 -0.21565900 + 6 5.343620 -0.32246900 + 7 2.704857 -0.19752900 + 8 1.353018 0.16444800 + 9 0.660873 0.41001700 + 10 0.309149 0.32783800 + 11 0.133879 0.10574900 +D 11 + 1 270.014061 0.00000700 + 2 100.161579 0.00086800 + 3 43.530609 0.02163100 + 4 21.262419 0.10774800 + 5 10.577821 0.27899700 + 6 5.343620 0.31454300 + 7 2.704857 -0.24192600 + 8 1.353018 -0.60241500 + 9 0.660873 -0.11801300 + 10 0.309149 0.54548200 + 11 0.133879 0.36382900 +D 1 + 1 0.133879 1.00000000 +F 1 + 1 1.520399 1.00000000 +F 1 + 1 6.000349 1.00000000 +G 1 + 1 4.099533 1.00000000 + diff --git a/data/pseudo/ncsu b/data/pseudo/ncsu index ee17ba13..ab54ffa9 100644 --- a/data/pseudo/ncsu +++ b/data/pseudo/ncsu @@ -1,56 +1,46 @@ H GEN 0 1 3 --10.851924053 2 21.7769665504 -1.0 1 21.2435950826 -21.2435950826 3 21.2435950826 +1.00000000000000 1 21.24359508259891 +21.24359508259891 3 21.24359508259891 +-10.85192405303825 2 21.77696655044365 1 -0.0 2 1.0 +0.00000000000000 2 1.000000000000000 -C GEN 2 1 +B GEN 2 1 3 -4.0 1 14.43502 -57.74008 3 8.39889 --25.81955 2 7.38188 + 3.00000 1 31.49298 + 94.47895 3 22.56509 +-9.74800 2 8.64669 1 -52.13345 2 7.76079 + 20.74800 2 4.06246 -Cl GEN 10 2 +C GEN 2 1 3 -7.0 1 22.71655173 -159.01586213 3 78.57185685 --15.6531065 2 7.47352436 -2 -6.50888648 2 17.23708573 -46.763467 2 4.31148447 -2 -2.9946477 2 11.38275704 -28.0170341 2 3.83218762 + 4.00000 1 14.43502 +57.74008 3 8.39889 +-25.81955 2 7.38188 +1 +52.13345 2 7.76079 -Co GEN 10 2 -4 -17.0 1 24.7400138129 -420.580234819 3 23.5426031368 --194.630579018 2 24.0406241364 --2.94301943013 2 10.237411369 +N GEN 2 1 +6 + 3.25000 1 12.91881 + 1.75000 1 9.22825 + 41.98612 3 12.96581 + 16.14945 3 8.05477 + -26.09522 2 12.54876 + -10.32626 2 7.53360 2 -270.86974114 2 23.0205711168 -54.1910212498 2 10.9219568474 -2 -200.63032558 2 25.3244045243 -38.9480947892 2 10.6533915029 + 34.77692 2 9.41609 + 15.20330 2 8.16694 -Cr GEN 10 2 -4 -14.0 1 18.2809107439 -255.932750414 3 17.0980065531 --132.018263171 2 16.7226727605 --0.773887613451 2 5.02865105891 -2 -219.481462096 2 16.9007876081 -28.079331766 2 7.33662150761 -2 -139.983968717 2 17.3197451654 -19.5483578632 2 6.92409757503 +O GEN 2 1 +3 + 6.000000 1 12.30997 + 73.85984 3 14.76962 + -47.87600 2 13.71419 +1 + 85.86406 2 13.65512 F GEN 2 1 3 @@ -60,124 +50,214 @@ F GEN 2 1 1 51.3934743997 2 11.3903478843 -Fe GEN 10 2 -4 -16.0 1 23.2209171361 -371.534674178 3 23.5471467972 --181.226034452 2 23.4725634461 --2.3730523614 2 9.85238815041 -2 -277.500325475 2 22.2106269743 -46.2049558527 2 9.51515800919 -2 -194.998750566 2 24.5700087185 -31.6794513291 2 8.86648776669 - -Mn GEN 10 2 -4 -15.0 1 21.9061889166 -328.592833748 3 21.3460106503 --162.049880237 2 21.2709151562 --1.85679609726 2 7.90771171833 -2 -244.669998154 2 18.9263045646 -33.5399867643 2 8.31114792811 -2 -162.350195446 2 20.162449313 -24.1593874179 2 7.79269955633 - -Ni GEN 10 2 -4 -18.0 1 37.839331506 -681.107967108 3 23.875701156 --173.162219465 2 19.8803935987 -0.34274858261 2 3.56565870195 -2 -91.6513902571 2 13.545098213 -331.659352198 2 27.7907700999 -2 -7.5147228016 2 6.46792786898 -265.586894944 2 23.6921476759 - -O GEN 2 1 +Na GEN 10 2 3 -6.0 1 12.30997 -73.85984 3 14.76962 --47.876 2 13.71419 -1 -85.86406 2 13.65512 + 1.000000 1 4.311678 + 4.311678 3 1.925689 + -2.083137 2 1.549498 +2 + 6.234064 2 5.377666 + 9.075931 2 1.408414 +2 + 3.232724 2 1.379949 + 2.494079 2 0.862453 + +Mg GEN 10 2 +3 + 2.000000 1 6.048538 + 12.097075 3 2.796989 +-17.108313 2 2.547408 +2 + 6.428631 2 5.936017 + 14.195491 2 1.592891 +2 + 3.315069 2 1.583969 + 4.403025 2 1.077297 + +Al GEN 2 1 +3 + 11.000000 1 11.062056 + 121.682619 3 12.369778 + -82.624567 2 11.965444 +2 + 25.157259 2 81.815564 + 113.067525 2 24.522883 + +Si GEN 10 2 +3 + 4.000000 1 5.168316 + 20.673264 3 8.861690 + -14.818174 2 3.933474 +2 + 14.832760 2 9.447023 + 26.349664 2 2.553812 +2 + 7.621400 2 3.660001 + 10.331583 2 1.903653 + +P GEN 2 1 +3 + 13.000000 1 15.073300 + 195.952906 3 18.113176 + -117.611086 2 17.371539 +2 + 25.197230 2 101.982019 + 189.426261 2 37.485881 S GEN 2 1 3 - 14.00000000 1 17.46806994 - 244.55297916 3 16.40396851 - -128.37752591 2 16.71429998 + 14.000000 1 17.977612 + 251.686565 3 20.435964 + -135.538891 2 19.796579 2 - 30.00006536 2 54.87912854 - 125.50010056 2 31.32968867 + 25.243283 2 111.936344 + 227.060768 2 43.941844 + +Cl GEN 2 1 +3 + 15.000000 1 22.196266 + 332.943994 3 26.145117 + -161.999982 2 25.015118 +2 + 26.837357 2 124.640433 + 277.296696 2 52.205433 + +Ar GEN 2 1 +3 + 16.000000 1 23.431337 + 374.901386 3 26.735872 + -178.039517 2 26.003325 +2 + 25.069215 2 135.620522 + 332.151842 2 60.471053 Sc GEN 10 2 4 -11.0 1 16.0484863686 -176.533350054 3 14.07764439 --83.673420518 2 11.993486653 -0.331064789149 2 3.75115298216 + 11.00000000 1 16.02394388 + 176.26338271 3 14.08647403 + -83.68149599 2 11.93985121 + 0.43282764 2 3.69440111 2 -153.959870288 2 11.4712713921 -14.9643185607 2 5.00756742752 + 153.96530175 2 11.49466541 + 14.93675657 2 5.01031394 2 -97.2094454291 2 11.4449481137 -10.8162163087 2 4.78509457131 + 97.21725690 2 11.45126730 + 10.81704018 2 4.76798446 Ti GEN 10 2 4 -12.0 1 18.4136620219 -220.963944263 3 15.9229241432 --94.2902582468 2 13.6500062314 -0.0979114248227 2 5.0955521057 + 12.00000000 1 18.41366202 + 220.96394426 3 15.92292414 + -94.29025824 2 13.65000623 + 0.09791142 2 5.09555210 2 -173.946572359 2 12.7058061392 -18.8376833381 2 6.11178551988 + 173.94657235 2 12.70580613 + 18.83768333 2 6.11178551 2 -111.45672882 2 12.6409192965 -11.1770268269 2 5.35437415684 + 111.45672882 2 12.64091929 + 11.17702682 2 5.35437415 V GEN 10 2 4 -13.0 1 20.3216891426 -264.181958854 3 19.5969804012 --115.292932083 2 17.3314734817 --0.662887260057 2 5.12320657929 + 13.00000000 1 20.32168914 + 264.18195885 3 19.59698040 + -115.29293208 2 17.33147348 + -0.66288726 2 5.12320657 2 -195.567138911 2 15.1250215054 -22.8864283476 2 6.2989891447 + 195.56713891 2 15.12502150 + 22.88642834 2 6.29898914 2 -126.421195008 2 15.9385511327 -16.0359712766 2 5.74006266866 + 126.42119500 2 15.93855113 + 16.03597127 2 5.74006266 -Zn GEN 10 2 +Cr GEN 10 2 4 -20.0 1 35.8079761618 -716.159523235 3 34.536460837 --204.683933235 2 28.6283017827 -0.760266144617 2 7.9623968256 + 14.00000000 1 18.28091074 + 255.93275041 3 17.09800655 + -132.01826317 2 16.72267276 + -0.77388761 2 5.02865105 2 -95.8764043739 2 14.6349869153 -431.708043027 2 35.0214135667 + 219.48146209 2 16.90078760 + 28.07933176 2 7.33662150 2 -74.0127004894 2 14.5742930415 -313.577705639 2 42.2297923499 + 139.98396871 2 17.31974516 + 19.54835786 2 6.92409757 + +Mn GEN 10 2 +4 + 15.00000000 1 21.91937433 + 328.79061500 3 21.35527127 + -162.05172805 2 21.27162653 + -1.82694272 2 7.93913962 +2 + 244.66870492 2 18.92044965 + 33.54162717 2 8.32764757 +2 + 162.35033685 2 20.17347020 + 24.17956695 2 7.80047874 + +Fe GEN 10 2 +4 + 16.00000000 1 23.22091713 + 371.53467417 3 23.54714679 + -181.22603445 2 23.47256344 + -2.37305236 2 9.85238815 +2 + 277.50032547 2 22.21062697 + 46.20495585 2 9.51515800 +2 + 194.99875056 2 24.57000871 + 31.67945132 2 8.86648776 + +Co GEN 10 2 +4 + 17.00000000 1 25.00124115 + 425.02109971 3 22.83490096 + -195.48211282 2 23.47468155 + -2.81572866 2 10.33794825 +2 + 271.77708486 2 23.41427030 + 54.26461121 2 10.76931694 +2 + 201.53430745 2 25.47446316 + 38.99231927 2 10.68404901 + +Ni GEN 10 2 +4 + 18.000 1 2.82630001015327e+01 + 508.7340018275886 3 2.69360254587070e+01 + -2.20099999296390e+02 2 2.70860075292970e+01 + -2.13493270999809e+00 2 1.22130001295874e+01 +2 + 3.21240002430625e+02 2 2.64320193944270e+01 + 6.03470084610628e+01 2 1.17489696842121e+01 +2 + 2.36539998999428e+02 2 2.94929998193907e+01 + 4.43969887908906e+01 2 1.15569831458722e+01 Cu GEN 10 2 4 -19.0 1 31.5381126304 -599.224139977 3 31.0692553147 --244.689154841 2 30.5903586806 --1.2934952584 2 14.0514106386 + 19.00000000 1 31.53811263 + 599.22413997 3 31.06925531 +-244.68915484 2 30.59035868 + -1.29349525 2 14.05141063 2 -66.2756081341 2 12.7723591969 -370.71371825 2 29.355622426 + 370.71371824 2 29.35562242 + 66.27560813 2 12.77235919 2 -49.7626505709 2 12.5247148487 -271.662810283 2 33.5169454376 + 271.66281028 2 33.51694543 + 49.76265057 2 12.52471484 + +Zn GEN 10 2 +4 + 20.00000000 1 35.80797616 + 716.15952323 3 34.53646083 + -204.68393323 2 28.62830178 + 0.76026614 2 7.96239682 +2 + 431.70804302 2 35.02141356 + 95.87640437 2 14.63498691 +2 + 313.57770563 2 42.22979234 + 74.01270048 2 14.57429304 From 3d70b0f9c2e9f72fa9fc88fe19219b7a3b3281c5 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 27 May 2019 10:46:01 +0200 Subject: [PATCH 08/36] Deterministic PT2 for < 1000 dets --- bin/qp_tunnel | 71 ++++++++++++++++++++++++++++++ src/cipsi/pt2_stoch_routines.irp.f | 2 +- src/determinants/EZFIO.cfg | 2 +- 3 files changed, 73 insertions(+), 2 deletions(-) create mode 100755 bin/qp_tunnel diff --git a/bin/qp_tunnel b/bin/qp_tunnel new file mode 100755 index 00000000..554c28ae --- /dev/null +++ b/bin/qp_tunnel @@ -0,0 +1,71 @@ +#!/usr/bin/env python2 + + +""" +Creates an ssh tunnel for using slaves on another network. +Launch a server on the front-end node of the cluster on which the master +process runs. Then start a client ont the front-end node of the distant +cluster. + +Usage: + qp_tunnel server EZFIO_DIR + qp_tunnel client
EZFIO_DIR + +Options: + -h --help + +""" + +import os +import sys +import zmq + +try: + import qp_path +except ImportError: + print "source .quantum_package.rc" + raise + +from docopt import docopt +from ezfio import ezfio + + +def get_address(filename): + with open(os.path.join(filename,'work','qp_run_address'),'r') as f: + a = f.readlines()[0].strip() + return a + + +def set_address(filename,address): + with open(os.path.join(filename,'work','qp_run_address'),'r') as f: + backup = f.readlines() + + with open(os.path.join(filename,'work','qp_run_address'),'w') as f: + f.write('\n'.join([address]+backup)) + + +def main_server(arguments,filename): + destination = get_address(filename) + print destination + + +def main_client(arguments,filename): + destination = arguments["
"] + print destination + + +def main(arguments): + """Main function""" + + print arguments + filename = arguments["EZFIO_DIR"] + + if arguments["server"]: + return main_server(arguments, filename) + if arguments["client"]: + return main_client(arguments, filename) + + +if __name__ == '__main__': + ARGUMENTS = docopt(__doc__) + main(ARGUMENTS) diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index a8f34e03..0e143a9c 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -135,7 +135,7 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in) PROVIDE psi_occ_pattern_hii det_to_occ_pattern endif - if (N_det < max(10,N_states)) then + if (N_det < max(1000,N_states)) then pt2=0.d0 variance=0.d0 norm=0.d0 diff --git a/src/determinants/EZFIO.cfg b/src/determinants/EZFIO.cfg index 0b289e99..b8fc7406 100644 --- a/src/determinants/EZFIO.cfg +++ b/src/determinants/EZFIO.cfg @@ -38,7 +38,7 @@ default: 1 type: Threshold doc: Thresholds on generators (fraction of the square of the norm) interface: ezfio,provider,ocaml -default: 0.99 +default: 0.999 [n_int] interface: ezfio From b86a5ba963fc200203c5e519f9403a6b4779e210 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 27 May 2019 11:02:52 +0200 Subject: [PATCH 09/36] research.bib --- docs/source/research.bib | 63 ++++++++++++++++++++++++++++++++++------ 1 file changed, 54 insertions(+), 9 deletions(-) diff --git a/docs/source/research.bib b/docs/source/research.bib index 348c5a15..df7d1b54 100644 --- a/docs/source/research.bib +++ b/docs/source/research.bib @@ -1,14 +1,62 @@ %%% ARXIV TO BE UPDATED %%% -@misc{BibEntry2019Feb, - title = {{Quantum Package 2.0: An Open-Source Determinant-Driven Suite of -Programs}}, +@article{Dash2019May, + author = {Dash, Monika and Feldt, Jonas and Moroni, Saverio and Scemama, Anthony and Filippi, Claudia}, + title = {{Excited states with selected CI-QMC: chemically accurate excitation energies and geometries}}, journal = {arXiv}, year = {2019}, - month = {Feb}, - note = {[Online; accessed 7. Mar. 2019]}, - url = {https://arxiv.org/abs/1902.08154.pdf} + month = {May}, + eprint = {1905.06737}, + url = {https://arxiv.org/abs/1905.06737} } +@article{Burton2019May, + author = {Burton, Hugh G. A. and Thom, Alex J. W.}, + title = {{A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction}}, + journal = {arXiv}, + year = {2019}, + month = {May}, + eprint = {1905.02626}, + url = {https://arxiv.org/abs/1905.02626} +} + + + +%%%% PUBLISHED PAPERS +@article{Loos_2019, + doi = {10.1021/acs.jpclett.9b01176}, + url = {https://doi.org/10.1021%2Facs.jpclett.9b01176}, + year = 2019, + month = {may}, + publisher = {American Chemical Society ({ACS})}, + author = {Pierre-Francois Loos and Bartélémy Pradines and Anthony Scemama and Julien Toulouse and Emmanuel Giner}, + title = {A Density-Based Basis-Set Correction For Wave Function Theory}, + journal = {The Journal of Physical Chemistry Letters} +} + +@article{Garniron_2019, + doi = {10.1021/acs.jctc.9b00176}, + url = {https://doi.org/10.1021%2Facs.jctc.9b00176}, + year = 2019, + month = {may}, + publisher = {American Chemical Society ({ACS})}, + author = {Yann Garniron and Thomas Applencourt and Kevin Gasperich and Anouar Benali and Anthony Ferte and Julien Paquier and Bartélémy Pradines and Roland Assaraf and Peter Reinhardt and Julien Toulouse and Pierrette Barbaresco and Nicolas Renon and Gregoire David and Jean-Paul Malrieu and Mickael Veril and Michel Caffarel and Pierre-Francois Loos and Emmanuel Giner and Anthony Scemama}, + title = {Quantum Package 2.0: An Open-Source Determinant-Driven Suite of Programs}, + journal = {Journal of Chemical Theory and Computation} +} + +@article{Scemama_2019, + doi = {10.1016/j.rechem.2019.100002}, + url = {https://doi.org/10.1016%2Fj.rechem.2019.100002}, + year = 2019, + month = {may}, + publisher = {Elsevier {BV}}, + pages = {100002}, + author = {Anthony Scemama and Michel Caffarel and Anouar Benali and Denis Jacquemin and Pierre-Fran{\c{c}}ois Loos}, + title = {Influence of pseudopotentials on excitation energies from selected configuration interaction and diffusion Monte Carlo}, + journal = {Results in Chemistry} +} + + @article{Applencourt2018Dec, author = {Applencourt, Thomas and Gasperich, Kevin and Scemama, Anthony}, title = {{Spin adaptation with determinant-based selected configuration interaction}}, @@ -19,9 +67,6 @@ Programs}}, url = {https://arxiv.org/abs/1812.06902} } - -%%%% PUBLISHED PAPERS - @article{Loos2019Mar, author = {Loos, Pierre-Fran\c{c}ois and Boggio-Pasqua, Martial and Scemama, Anthony and Caffarel, Michel and Jacquemin, Denis}, title = {{Reference Energies for Double Excitations}}, From f74e57ddef09f57cd2b364f882a7ebc569864056 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 27 May 2019 12:07:09 +0200 Subject: [PATCH 10/36] Fixing travis --- src/fci/40.fci.bats | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fci/40.fci.bats b/src/fci/40.fci.bats index 7083f9fe..fe62f699 100644 --- a/src/fci/40.fci.bats +++ b/src/fci/40.fci.bats @@ -59,7 +59,7 @@ function run_stoch() { @test "H2O2" { # 12.9214s qp set_file h2o2.ezfio qp set_mo_class --core="[1-2]" --act="[3-24]" --del="[25-38]" - run -151.004888189874 4.e-5 + run -151.004680718982 4.e-5 } @test "HBO" { # 13.3144s From 926378c1bcea0f03362897f53adf63bd3405e1a0 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 27 May 2019 18:11:21 +0200 Subject: [PATCH 11/36] Fixed tests --- src/fci/40.fci.bats | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/fci/40.fci.bats b/src/fci/40.fci.bats index fe62f699..d3809ff3 100644 --- a/src/fci/40.fci.bats +++ b/src/fci/40.fci.bats @@ -53,13 +53,13 @@ function run_stoch() { @test "HCO" { # 12.2868s qp set_file hco.ezfio - run -113.296794171915 2.e-05 + run -113.296794173622 2.e-05 } @test "H2O2" { # 12.9214s qp set_file h2o2.ezfio qp set_mo_class --core="[1-2]" --act="[3-24]" --del="[25-38]" - run -151.004680718982 4.e-5 + run -151.00477 1.e-4 } @test "HBO" { # 13.3144s @@ -83,7 +83,7 @@ function run_stoch() { @test "SO" { # 13.4952s [[ -n $TRAVIS ]] && skip qp set_file so.ezfio - run -26.0144622194831 1.e-5 + run -26.0124797722154 1.e-5 } @test "H2S" { # 13.6745s @@ -120,13 +120,13 @@ function run_stoch() { [[ -n $TRAVIS ]] && skip qp set_file ch4.ezfio qp set_mo_class --core="[1]" --act="[2-30]" --del="[31-59]" - run -40.2409858175829 2.e-5 + run -40.2409059687324 2.e-5 } @test "ClF" { # 16.8864s [[ -n $TRAVIS ]] && skip qp set_file clf.ezfio - run -559.170116079903 1.e-5 + run -559.170406471496 1.e-5 } @test "SO2" { # 17.5645s @@ -140,14 +140,14 @@ function run_stoch() { [[ -n $TRAVIS ]] && skip qp set_file c2h2.ezfio qp set_mo_class --act="[1-30]" --del="[31-36]" - run -12.3678973551285 2.e-5 + run -12.3670840202635 2.e-5 } @test "N2" { # 18.0198s [[ -n $TRAVIS ]] && skip qp set_file n2.ezfio qp set_mo_class --core="[1,2]" --act="[3-40]" --del="[41-60]" - run -109.291310557766 1.e-4 + run -109.291600196629 1.e-4 } @test "N2H4" { # 18.5006s @@ -161,7 +161,7 @@ function run_stoch() { [[ -n $TRAVIS ]] && skip qp set_file co2.ezfio qp set_mo_class --core="[1,2]" --act="[3-30]" --del="[31-42]" - run -187.969556614801 1.e-5 + run -187.969676381867 1.e-5 } @@ -176,6 +176,6 @@ function run_stoch() { [[ -n $TRAVIS ]] && skip qp set_file hcn.ezfio qp set_mo_class --core="[1,2]" --act="[3-40]" --del="[41-55]" - run -93.0794109423741 2.e-5 + run -93.0799328685679 2.e-5 } From 7bc6c7e709b05880a9bebe2073a02fde38856989 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 27 May 2019 19:03:58 +0200 Subject: [PATCH 12/36] Fixed tests --- src/fci/40.fci.bats | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fci/40.fci.bats b/src/fci/40.fci.bats index d3809ff3..f3b7db2c 100644 --- a/src/fci/40.fci.bats +++ b/src/fci/40.fci.bats @@ -48,12 +48,12 @@ function run_stoch() { @test "DHNO" { # 11.4721s qp set_file dhno.ezfio qp set_mo_class --core="[1-7]" --act="[8-64]" - run -130.458875747063 1.e-5 + run -130.459020029816 1.e-5 } @test "HCO" { # 12.2868s qp set_file hco.ezfio - run -113.296794173622 2.e-05 + run -113.297494345682 2.e-05 } @test "H2O2" { # 12.9214s From 714d53363e13155cc0f284eb0e34b2592b29e39e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 28 May 2019 10:23:50 +0200 Subject: [PATCH 13/36] Update documentation and qp_set_frozne_core --- bin/qp_plugins | 29 +- bin/qp_set_frozen_core | 94 +++--- docs/source/modules/ao_two_e_ints.rst | 22 +- docs/source/modules/aux_quantities.rst | 10 + docs/source/modules/becke_numerical_grid.rst | 7 + docs/source/modules/bitmask.rst | 127 ++++++- docs/source/modules/cipsi.rst | 40 ++- docs/source/modules/cis.rst | 222 ++++++++++++- docs/source/modules/cisd.rst | 222 ++++++++++++- docs/source/modules/density_for_dft.rst | 150 +++++++++ docs/source/modules/determinants.rst | 48 ++- docs/source/modules/dft_utils_in_r.rst | 233 +++++++++++++ docs/source/modules/dft_utils_one_e.rst | 314 ------------------ docs/source/modules/ezfio_files.rst | 16 + docs/source/modules/hartree_fock.rst | 1 + docs/source/modules/mo_basis.rst | 8 +- docs/source/modules/mpi.rst | 4 + docs/source/modules/nuclei.rst | 4 +- docs/source/modules/scf_utils.rst | 2 +- docs/source/modules/tools.rst | 6 + docs/source/modules/utils.rst | 1 + .../programmers_guide/index_providers.rst | 45 ++- docs/source/programs/fci.rst | 5 + docs/source/programs/save_one_e_dm.rst | 8 +- docs/source/users_guide/qp_plugins.rst | 4 + .../source/users_guide/qp_set_frozen_core.rst | 35 +- man/cis.1 | 2 +- man/cisd.1 | 2 +- man/configure.1 | 2 +- man/diagonalize_h.1 | 2 +- man/excited_states.1 | 2 +- man/fci.1 | 20 +- man/fcidump.1 | 2 +- man/four_idx_transform.1 | 2 +- man/interfaces.1 | 2 +- man/ks_scf.1 | 2 +- man/molden.1 | 2 +- man/natural_orbitals.1 | 2 +- man/plugins.1 | 2 +- man/print_ci_vectors.1 | 87 +++++ man/print_e_conv.1 | 2 +- man/print_wf.1 | 2 +- man/printing.1 | 2 +- man/pt2.1 | 2 +- man/qp_convert_output_to_ezfio.1 | 2 +- man/qp_create_ezfio.1 | 235 +++++++++++++ man/qp_edit.1 | 2 +- man/qp_export_as_tgz.1 | 2 +- man/qp_plugins.1 | 7 +- man/qp_reset.1 | 2 +- man/qp_run.1 | 2 +- man/qp_set_frozen_core.1 | 201 ++++++++++- man/qp_set_mo_class.1 | 2 +- man/qp_stop.1 | 2 +- man/qp_update.1 | 2 +- man/qpsh.1 | 2 +- man/rs_ks_scf.1 | 2 +- man/save_natorb.1 | 2 +- man/save_one_e_dm.1 | 10 +- man/save_ortho_mos.1 | 2 +- man/scf.1 | 2 +- man/write_integrals_erf.1 | 2 +- src/generators_cas/extract_cas.irp.f | 23 ++ 63 files changed, 1834 insertions(+), 466 deletions(-) create mode 100644 man/print_ci_vectors.1 create mode 100644 man/qp_create_ezfio.1 create mode 100644 src/generators_cas/extract_cas.irp.f diff --git a/bin/qp_plugins b/bin/qp_plugins index dc14b8ea..b32f907f 100755 --- a/bin/qp_plugins +++ b/bin/qp_plugins @@ -6,6 +6,7 @@ Usage: qp_plugins download [-n ] qp_plugins install ... qp_plugins uninstall + qp_plugins update [-r ] qp_plugins create -n [-r ] [...] Options: @@ -23,6 +24,8 @@ Options: uninstall Uninstall a plugin + update Update the repository + create -n --name= Create a new plugin named -r --repository= Name of the repository in which to create the plugin @@ -89,16 +92,19 @@ def save_new_module(path, l_child): end """) +def get_repositories(): + l_result = [f for f in os.listdir(QP_PLUGINS) \ + if f not in [".gitignore", "local"] ] + return sorted(l_result) + + def main(arguments): """Main function""" arguments[""] = [os.path.normpath(name) for name in arguments[""]] if arguments["list"]: if arguments["--repositories"]: - l_result = [f for f in os.listdir(QP_PLUGINS) \ - if f not in [".gitignore", "local"] ] - - for repo in sorted(l_result): + for repo in get_repositories(): print repo else: @@ -138,6 +144,7 @@ def main(arguments): for module in sorted(l_result): print "%-30s %-30s"%(module, repo_of_plugin[module]) + if arguments["create"]: m_instance = ModuleHandler([QP_SRC]) @@ -306,6 +313,20 @@ def main(arguments): print "%s is a core module which can't be removed" % module + elif arguments["update"]: + + if arguments["--repository"]: + l_repositories = [ arguments["--repository"] ] + else: + l_repositories = get_repositories() + + for repo in l_repositories: + print "Updating ", repo + os.chdir(os.path.join(QP_PLUGINS,repo)) + git_cmd=["git", "pull"] + subprocess.check_call(git_cmd) + + if __name__ == '__main__': ARG = docopt(__doc__) main(ARG) diff --git a/bin/qp_set_frozen_core b/bin/qp_set_frozen_core index 3a7795cd..25b450dd 100755 --- a/bin/qp_set_frozen_core +++ b/bin/qp_set_frozen_core @@ -6,18 +6,39 @@ Automatically finds n, the number of core electrons. Calls qp_set_mo_class setting all MOs as Active, except the n/2 first ones which are set as Core. If pseudo-potentials are used, all the MOs are set as Active. -For elements on the right of the periodic table, qp_set_frozen_core will work -as expected. But for elements on the left, a small core will be chosen. For -example, a Carbon atom will have 2 core electrons, but a Lithium atom will have -zero. - - Usage: - qp_set_frozen_core [-q|--query] [-l|--large] EZFIO_DIR + qp_set_frozen_core [-q|--query] [(-l|-s|--large|--small)] EZFIO_DIR Options: -q --query Prints in the standard output the number of frozen MOs - -l --large Use a large core + -l --large Use a small core + -s --small Use a large core + + +Default numbers of frozen electrons: + + ========== ========= ======= ======= + Range Default Small Large + ========== ========= ======= ======= + H -> He 0 0 0 + Li -> Be 0 0 2 + B -> Ne 2 2 2 + Na -> Mg 2 2 10 + Al -> Ar 10 2 10 + K -> Ca 10 10 18 + Sc -> Zn 10 10 18 + Ga -> Kr 18 10 18 + Rb -> Sr 18 18 36 + Y -> Cd 18 18 36 + In -> Xe 36 18 36 + Cs -> Ba 36 36 54 + La -> Hg 36 36 54 + Tl -> Rn 54 36 54 + Fr -> Ra 54 54 86 + Ac -> Cn 54 54 86 + Nh -> Og 86 54 86 + ========== ========= ======= ======= + """ @@ -47,47 +68,36 @@ def main(arguments): except: do_pseudo = False - large = 0 - small = 1 - - size = small - if arguments["--large"]: - size = large if not do_pseudo: - if size == large: + if arguments["--large"]: for charge in ezfio.nuclei_nucl_charge: - if charge <= 2: - pass - elif charge <= 10: - n_frozen += 1 - elif charge <= 18: - n_frozen += 5 - elif charge <= 36: - n_frozen += 9 - elif charge <= 54: - n_frozen += 18 - elif charge <= 86: - n_frozen += 27 - elif charge <= 118: - n_frozen += 43 + if charge <= 2: pass + elif charge <= 10: n_frozen += 1 + elif charge <= 18: n_frozen += 5 + elif charge <= 36: n_frozen += 9 + elif charge <= 54: n_frozen += 18 + elif charge <= 86: n_frozen += 27 + elif charge <= 118: n_frozen += 43 - if size == small: + elif arguments["--small"]: + if charge <= 4: pass + elif charge <= 18: n_frozen += 1 + elif charge <= 36: n_frozen += 5 + elif charge <= 54: n_frozen += 9 + elif charge <= 86: n_frozen += 18 + elif charge <= 118: n_frozen += 27 + else: # default for charge in ezfio.nuclei_nucl_charge: - if charge < 5: - pass - elif charge < 13: - n_frozen += 1 - elif charge < 31: - n_frozen += 5 - elif charge < 49: - n_frozen += 9 - elif charge < 81: - n_frozen += 18 - elif charge < 113: - n_frozen += 27 + if charge <= 4: pass + elif charge <= 12: n_frozen += 1 + elif charge <= 30: n_frozen += 5 + elif charge <= 48: n_frozen += 9 + elif charge <= 80: n_frozen += 18 + elif charge <= 112: n_frozen += 27 + mo_num = ezfio.mo_basis_mo_num diff --git a/docs/source/modules/ao_two_e_ints.rst b/docs/source/modules/ao_two_e_ints.rst index 3c833a90..64a942f4 100644 --- a/docs/source/modules/ao_two_e_ints.rst +++ b/docs/source/modules/ao_two_e_ints.rst @@ -953,6 +953,7 @@ Subroutines / functions Gets multiple AO bi-electronic integral from the AO map . All i are retrieved for j,k,l fixed. + physicist convention : Needs: @@ -1224,6 +1225,8 @@ Subroutines / functions subroutine two_e_integrals_index(i,j,k,l,i1) + Gives a unique index for i,j,k,l using permtuation symmetry. + i <-> k, j <-> l, and (i,k) <-> (j,l) Called by: @@ -1255,7 +1258,7 @@ Subroutines / functions * :c:data:`mo_integrals_erf_cache` * :c:data:`mo_integrals_erf_map` * :c:data:`mo_integrals_map` - * :c:func:`two_e_integrals_index_reverse` + * :c:func:`test` .. c:function:: two_e_integrals_index_reverse: @@ -1268,6 +1271,15 @@ Subroutines / functions subroutine two_e_integrals_index_reverse(i,j,k,l,i1) + Computes the 4 indices $i,j,k,l$ from a unique index $i_1$. + For 2 indices $i,j$ and $i \le j$, we have + $p = i(i-1)/2 + j$. + The key point is that because $j < i$, + $i(i-1)/2 < p \le i(i+1)/2$. So $i$ can be found by solving + $i^2 - i - 2p=0$. One obtains $i=1 + \sqrt{1+8p}/2$ + and $j = p - i(i-1)/2$. + This rule is applied 3 times. First for the symmetry of the + pairs (i,k) and (j,l), and then for the symmetry within each pair. Called by: @@ -1275,11 +1287,5 @@ Subroutines / functions :columns: 3 * :c:data:`ao_two_e_integral_alpha` - - Calls: - - .. hlist:: - :columns: 3 - - * :c:func:`two_e_integrals_index` + * :c:func:`test` diff --git a/docs/source/modules/aux_quantities.rst b/docs/source/modules/aux_quantities.rst index e71dc325..c305c1fa 100644 --- a/docs/source/modules/aux_quantities.rst +++ b/docs/source/modules/aux_quantities.rst @@ -51,3 +51,13 @@ EZFIO parameters Beta one body density matrix on the |MO| basis computed with the wave function + +.. option:: data_one_e_dm_alpha_ao + + Alpha one body density matrix on the |AO| basis computed with the wave function + + +.. option:: data_one_e_dm_beta_ao + + Beta one body density matrix on the |AO| basis computed with the wave function + diff --git a/docs/source/modules/becke_numerical_grid.rst b/docs/source/modules/becke_numerical_grid.rst index 7868a547..d0ea3351 100644 --- a/docs/source/modules/becke_numerical_grid.rst +++ b/docs/source/modules/becke_numerical_grid.rst @@ -241,6 +241,7 @@ Providers * :c:data:`mos_in_r_array` * :c:data:`one_e_dm_alpha_at_r` * :c:data:`one_e_dm_and_grad_alpha_in_r` + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` .. c:var:: final_weight_at_r @@ -339,6 +340,7 @@ Providers * :c:data:`mos_in_r_array` * :c:data:`one_e_dm_alpha_at_r` * :c:data:`one_e_dm_and_grad_alpha_in_r` + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` .. c:var:: grid_points_per_atom @@ -468,6 +470,7 @@ Providers * :c:data:`mos_in_r_array` * :c:data:`one_e_dm_alpha_at_r` * :c:data:`one_e_dm_and_grad_alpha_in_r` + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` .. c:var:: index_final_points_reverse @@ -532,6 +535,7 @@ Providers * :c:data:`mos_in_r_array` * :c:data:`one_e_dm_alpha_at_r` * :c:data:`one_e_dm_and_grad_alpha_in_r` + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` .. c:var:: m_knowles @@ -608,6 +612,7 @@ Providers * :c:data:`mos_lapl_in_r_array` * :c:data:`one_e_dm_alpha_at_r` * :c:data:`one_e_dm_and_grad_alpha_in_r` + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` * :c:data:`pot_grad_x_alpha_ao_pbe` * :c:data:`pot_grad_xc_alpha_ao_pbe` * :c:data:`pot_scal_x_alpha_ao_pbe` @@ -749,6 +754,7 @@ Providers * :c:data:`grid_points_per_atom` * :c:data:`n_points_radial_grid` + * :c:data:`nucl_charge` * :c:data:`nucl_coord_transp` * :c:data:`nucl_dist_inv` * :c:data:`nucl_num` @@ -818,6 +824,7 @@ Subroutines / functions * :c:data:`nucl_dist_inv` * :c:data:`slater_bragg_type_inter_distance_ua` * :c:data:`nucl_coord_transp` + * :c:data:`nucl_charge` * :c:data:`nucl_num` diff --git a/docs/source/modules/bitmask.rst b/docs/source/modules/bitmask.rst index 3e7f9077..f07d5dd9 100644 --- a/docs/source/modules/bitmask.rst +++ b/docs/source/modules/bitmask.rst @@ -108,10 +108,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -150,8 +152,6 @@ Providers * :c:data:`closed_shell_ref_bitmask` * :c:data:`psi_cas` * :c:data:`reunion_of_bitmask` - * :c:data:`reunion_of_cas_inact_bitmask` - * :c:data:`reunion_of_core_inact_act_bitmask` .. c:var:: closed_shell_ref_bitmask @@ -246,10 +246,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -374,10 +376,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -814,10 +818,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -943,10 +949,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1021,10 +1029,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1099,10 +1109,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1110,12 +1122,12 @@ Providers .. c:var:: list_core_inact_act - File : :file:`bitmask/bitmasks.irp.f` + File : :file:`bitmask/core_inact_act_virt.irp.f` .. code:: fortran integer, allocatable :: list_core_inact_act (n_core_inact_act_orb) - integer, allocatable :: list_core_inact_act_reverse (mo_num) + integer, allocatable :: list_core_inact_act_reverse (n_core_inact_act_orb) @@ -1125,7 +1137,8 @@ Providers :columns: 3 * :c:data:`list_inact` - * :c:data:`mo_num` + * :c:data:`n_core_inact_act_orb` + * :c:data:`n_core_orb` * :c:data:`n_int` * :c:data:`reunion_of_core_inact_act_bitmask` @@ -1134,12 +1147,12 @@ Providers .. c:var:: list_core_inact_act_reverse - File : :file:`bitmask/bitmasks.irp.f` + File : :file:`bitmask/core_inact_act_virt.irp.f` .. code:: fortran integer, allocatable :: list_core_inact_act (n_core_inact_act_orb) - integer, allocatable :: list_core_inact_act_reverse (mo_num) + integer, allocatable :: list_core_inact_act_reverse (n_core_inact_act_orb) @@ -1149,7 +1162,8 @@ Providers :columns: 3 * :c:data:`list_inact` - * :c:data:`mo_num` + * :c:data:`n_core_inact_act_orb` + * :c:data:`n_core_orb` * :c:data:`n_int` * :c:data:`reunion_of_core_inact_act_bitmask` @@ -1225,10 +1239,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1303,10 +1319,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1381,10 +1399,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1459,14 +1479,38 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` +.. c:var:: list_inact_act + + + File : :file:`bitmask/core_inact_act_virt.irp.f` + + .. code:: fortran + + integer, allocatable :: list_inact_act (n_inact_act_orb) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`list_inact` + * :c:data:`n_core_orb` + * :c:data:`n_inact_act_orb` + + + .. c:var:: list_inact_reverse @@ -1537,10 +1581,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1615,10 +1661,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1693,10 +1741,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` @@ -1772,9 +1822,13 @@ Providers * :c:data:`dim_list_core_orb` * :c:data:`eigenvectors_fock_matrix_mo` * :c:data:`fock_matrix_mo` + * :c:data:`list_core_inact_act` * :c:data:`list_inact` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_vv_from_ao` + * :c:data:`n_core_inact_act_orb` * :c:data:`n_core_orb_allocate` + * :c:data:`n_inact_act_orb` * :c:data:`n_inact_orb_allocate` * :c:data:`n_virt_orb_allocate` * :c:data:`pt2_f` @@ -1813,31 +1867,26 @@ Providers .. c:var:: n_core_inact_act_orb - File : :file:`bitmask/bitmasks.irp.f` + File : :file:`bitmask/core_inact_act_virt.irp.f` .. code:: fortran - integer(bit_kind), allocatable :: reunion_of_core_inact_act_bitmask (N_int,2) integer :: n_core_inact_act_orb - Reunion of the core, inactive and active bitmasks Needs: .. hlist:: :columns: 3 - * :c:data:`cas_bitmask` - * :c:data:`n_int` - * :c:data:`reunion_of_core_inact_bitmask` + * :c:data:`n_core_orb` Needed by: .. hlist:: :columns: 3 - * :c:data:`core_inact_act_bitmask_4` * :c:data:`list_core_inact_act` @@ -1919,9 +1968,13 @@ Providers * :c:data:`dim_list_core_orb` * :c:data:`eigenvectors_fock_matrix_mo` * :c:data:`fock_matrix_mo` + * :c:data:`list_core_inact_act` * :c:data:`list_inact` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_vv_from_ao` + * :c:data:`n_core_inact_act_orb` * :c:data:`n_core_orb_allocate` + * :c:data:`n_inact_act_orb` * :c:data:`n_inact_orb_allocate` * :c:data:`n_virt_orb_allocate` * :c:data:`pt2_f` @@ -2004,9 +2057,13 @@ Providers * :c:data:`dim_list_core_orb` * :c:data:`eigenvectors_fock_matrix_mo` * :c:data:`fock_matrix_mo` + * :c:data:`list_core_inact_act` * :c:data:`list_inact` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_vv_from_ao` + * :c:data:`n_core_inact_act_orb` * :c:data:`n_core_orb_allocate` + * :c:data:`n_inact_act_orb` * :c:data:`n_inact_orb_allocate` * :c:data:`n_virt_orb_allocate` * :c:data:`pt2_f` @@ -2072,6 +2129,32 @@ Providers * :c:data:`generators_bitmask_restart` +.. c:var:: n_inact_act_orb + + + File : :file:`bitmask/core_inact_act_virt.irp.f` + + .. code:: fortran + + integer :: n_inact_act_orb + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_core_orb` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`list_inact_act` + + .. c:var:: n_inact_orb @@ -2129,9 +2212,13 @@ Providers * :c:data:`dim_list_core_orb` * :c:data:`eigenvectors_fock_matrix_mo` * :c:data:`fock_matrix_mo` + * :c:data:`list_core_inact_act` * :c:data:`list_inact` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_vv_from_ao` + * :c:data:`n_core_inact_act_orb` * :c:data:`n_core_orb_allocate` + * :c:data:`n_inact_act_orb` * :c:data:`n_inact_orb_allocate` * :c:data:`n_virt_orb_allocate` * :c:data:`pt2_f` @@ -2309,9 +2396,13 @@ Providers * :c:data:`dim_list_core_orb` * :c:data:`eigenvectors_fock_matrix_mo` * :c:data:`fock_matrix_mo` + * :c:data:`list_core_inact_act` * :c:data:`list_inact` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_vv_from_ao` + * :c:data:`n_core_inact_act_orb` * :c:data:`n_core_orb_allocate` + * :c:data:`n_inact_act_orb` * :c:data:`n_inact_orb_allocate` * :c:data:`n_virt_orb_allocate` * :c:data:`pt2_f` @@ -2412,7 +2503,6 @@ Providers .. hlist:: :columns: 3 - * :c:data:`cas_bitmask` * :c:data:`list_inact` * :c:data:`n_int` @@ -2426,7 +2516,6 @@ Providers .. code:: fortran integer(bit_kind), allocatable :: reunion_of_core_inact_act_bitmask (N_int,2) - integer :: n_core_inact_act_orb Reunion of the core, inactive and active bitmasks @@ -2436,7 +2525,7 @@ Providers .. hlist:: :columns: 3 - * :c:data:`cas_bitmask` + * :c:data:`list_inact` * :c:data:`n_int` * :c:data:`reunion_of_core_inact_bitmask` @@ -2570,10 +2659,12 @@ Providers * :c:data:`fock_matrix_mo` * :c:data:`inact_virt_bitmask` * :c:data:`list_core_inact_act` + * :c:data:`list_inact_act` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`mo_two_e_integrals_vv_from_ao` * :c:data:`reunion_of_bitmask` * :c:data:`reunion_of_cas_inact_bitmask` + * :c:data:`reunion_of_core_inact_act_bitmask` * :c:data:`reunion_of_core_inact_bitmask` * :c:data:`virt_bitmask_4` diff --git a/docs/source/modules/cipsi.rst b/docs/source/modules/cipsi.rst index af9f600d..a03b2e3c 100644 --- a/docs/source/modules/cipsi.rst +++ b/docs/source/modules/cipsi.rst @@ -344,6 +344,34 @@ Providers +.. c:var:: pt2_match_weight + + + File : :file:`cipsi/selection.irp.f` + + .. code:: fortran + + double precision, allocatable :: pt2_match_weight (N_states) + + + Weights adjusted along the selection to make the PT2 contributions + of each state coincide. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_states` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`selection_weight` + + .. c:var:: pt2_mindetinfirstteeth @@ -698,6 +726,7 @@ Providers * :c:data:`c0_weight` * :c:data:`n_states` + * :c:data:`pt2_match_weight` @@ -854,6 +883,8 @@ Subroutines / functions * :c:data:`psi_det_hii` * :c:data:`do_only_1h1p` * :c:data:`h0_type` + * :c:data:`thresh_sym` + * :c:data:`pseudo_sym` * :c:data:`psi_det_generators` Called by: @@ -1584,6 +1615,7 @@ Subroutines / functions * :c:data:`psi_energy` * :c:data:`psi_occ_pattern` * :c:data:`psi_energy` + * :c:data:`pt2_match_weight` * :c:data:`pt2_stoch_istate` * :c:data:`state_average_weight` * :c:data:`threshold_generators` @@ -1805,6 +1837,7 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:func:`fci` * :c:func:`pt2` Calls: @@ -1991,6 +2024,7 @@ Subroutines / functions * :c:data:`psi_energy` * :c:data:`psi_occ_pattern` * :c:data:`psi_energy` + * :c:data:`pt2_match_weight` * :c:data:`pt2_stoch_istate` * :c:data:`state_average_weight` * :c:data:`threshold_generators` @@ -2344,6 +2378,7 @@ Subroutines / functions * :c:data:`state_average_weight` * :c:data:`n_det` * :c:data:`s2_eig` + * :c:data:`pt2_match_weight` * :c:data:`pt2_j` * :c:data:`mo_two_e_integrals_in_map` * :c:data:`psi_bilinear_matrix_transp_values` @@ -2415,6 +2450,7 @@ Subroutines / functions * :c:data:`psi_det` * :c:data:`psi_det_size` * :c:data:`psi_det_sorted_bit` + * :c:data:`pt2_match_weight` * :c:data:`pt2_stoch_istate` * :c:data:`state_average_weight` @@ -2441,6 +2477,7 @@ Subroutines / functions * :c:data:`n_det` * :c:data:`psi_bilinear_matrix_columns_loc` * :c:data:`n_det_selectors` + * :c:data:`psi_bilinear_matrix_transp_values` * :c:data:`psi_det_alpha_unique` * :c:data:`psi_bilinear_matrix_transp_values` * :c:data:`state_average_weight` @@ -2456,7 +2493,7 @@ Subroutines / functions * :c:data:`n_states` * :c:data:`pt2_f` * :c:data:`n_det_generators` - * :c:data:`psi_bilinear_matrix_transp_values` + * :c:data:`pt2_match_weight` * :c:data:`n_int` Called by: @@ -2496,4 +2533,5 @@ Subroutines / functions * :c:data:`psi_det` * :c:data:`psi_det_size` * :c:data:`psi_det_sorted_bit` + * :c:data:`pt2_match_weight` diff --git a/docs/source/modules/cis.rst b/docs/source/modules/cis.rst index 7943d7ce..151e3bda 100644 --- a/docs/source/modules/cis.rst +++ b/docs/source/modules/cis.rst @@ -72,7 +72,7 @@ Subroutines / functions .. c:function:: h_apply_cis: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_13` .. code:: fortran @@ -134,7 +134,7 @@ Subroutines / functions .. c:function:: h_apply_cis_diexc: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_13` .. code:: fortran @@ -169,7 +169,7 @@ Subroutines / functions .. c:function:: h_apply_cis_diexcorg: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_13` .. code:: fortran @@ -208,7 +208,7 @@ Subroutines / functions .. c:function:: h_apply_cis_diexcp: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_13` .. code:: fortran @@ -243,7 +243,7 @@ Subroutines / functions .. c:function:: h_apply_cis_monoexc: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_13` .. code:: fortran @@ -278,3 +278,215 @@ Subroutines / functions * :c:func:`bitstring_to_list_ab` * :c:func:`fill_h_apply_buffer_no_selection` + +.. c:function:: h_apply_cis_sym: + + + File : :file:`h_apply.irp.f_shell_13` + + .. code:: fortran + + subroutine H_apply_cis_sym() + + + Calls H_apply on the |HF| determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`psi_coef` + * :c:data:`n_states` + * :c:data:`generators_bitmask` + * :c:data:`mo_num` + * :c:data:`mo_two_e_integrals_in_map` + * :c:data:`h_apply_buffer_allocated` + * :c:data:`n_det` + * :c:data:`s2_eig` + * :c:data:`n_det_generators` + * :c:data:`i_bitmask_gen` + * :c:data:`n_int` + * :c:data:`psi_det` + * :c:data:`psi_det_generators` + * :c:data:`psi_det_generators` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`build_fock_tmp` + * :c:func:`copy_h_apply_buffer_to_wf` + * :c:func:`dsort` + * :c:func:`h_apply_cis_sym_diexc` + * :c:func:`h_apply_cis_sym_monoexc` + * :c:func:`make_s2_eigenfunction` + * :c:func:`wall_time` + + Touches: + + .. hlist:: + :columns: 3 + + * :c:data:`n_det` + * :c:data:`psi_occ_pattern` + * :c:data:`c0_weight` + * :c:data:`psi_coef` + * :c:data:`psi_det_sorted_bit` + * :c:data:`psi_det` + * :c:data:`psi_det_size` + * :c:data:`psi_det_sorted_bit` + * :c:data:`psi_occ_pattern` + + +.. c:function:: h_apply_cis_sym_diexc: + + + File : :file:`h_apply.irp.f_shell_13` + + .. code:: fortran + + subroutine H_apply_cis_sym_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in ) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`n_det` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cis_sym` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cis_sym_diexcp` + + +.. c:function:: h_apply_cis_sym_diexcorg: + + + File : :file:`h_apply.irp.f_shell_13` + + .. code:: fortran + + subroutine H_apply_cis_sym_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in ) + + + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`elec_alpha_num` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cis_sym_diexcp` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`bitstring_to_list_ab` + * :c:func:`connected_to_hf` + * :c:func:`fill_h_apply_buffer_no_selection` + + +.. c:function:: h_apply_cis_sym_diexcp: + + + File : :file:`h_apply.irp.f_shell_13` + + .. code:: fortran + + subroutine H_apply_cis_sym_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2, fock_diag_tmp, i_generator, iproc_in ) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`n_det` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cis_sym_diexc` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cis_sym_diexcorg` + + +.. c:function:: h_apply_cis_sym_monoexc: + + + File : :file:`h_apply.irp.f_shell_13` + + .. code:: fortran + + subroutine H_apply_cis_sym_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generator,iproc_in ) + + + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`elec_alpha_num` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cis_sym` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`bitstring_to_list_ab` + * :c:func:`connected_to_hf` + * :c:func:`fill_h_apply_buffer_no_selection` + diff --git a/docs/source/modules/cisd.rst b/docs/source/modules/cisd.rst index 7816de30..94c6408f 100644 --- a/docs/source/modules/cisd.rst +++ b/docs/source/modules/cisd.rst @@ -65,7 +65,7 @@ Subroutines / functions .. c:function:: h_apply_cisd: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_12` .. code:: fortran @@ -127,7 +127,7 @@ Subroutines / functions .. c:function:: h_apply_cisd_diexc: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_12` .. code:: fortran @@ -162,7 +162,7 @@ Subroutines / functions .. c:function:: h_apply_cisd_diexcorg: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_12` .. code:: fortran @@ -201,7 +201,7 @@ Subroutines / functions .. c:function:: h_apply_cisd_diexcp: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_12` .. code:: fortran @@ -236,7 +236,7 @@ Subroutines / functions .. c:function:: h_apply_cisd_monoexc: - File : :file:`h_apply.irp.f_shell_8` + File : :file:`h_apply.irp.f_shell_12` .. code:: fortran @@ -271,3 +271,215 @@ Subroutines / functions * :c:func:`bitstring_to_list_ab` * :c:func:`fill_h_apply_buffer_no_selection` + +.. c:function:: h_apply_cisd_sym: + + + File : :file:`h_apply.irp.f_shell_12` + + .. code:: fortran + + subroutine H_apply_cisd_sym() + + + Calls H_apply on the |HF| determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`psi_coef` + * :c:data:`n_states` + * :c:data:`generators_bitmask` + * :c:data:`mo_num` + * :c:data:`mo_two_e_integrals_in_map` + * :c:data:`h_apply_buffer_allocated` + * :c:data:`n_det` + * :c:data:`s2_eig` + * :c:data:`n_det_generators` + * :c:data:`i_bitmask_gen` + * :c:data:`n_int` + * :c:data:`psi_det` + * :c:data:`psi_det_generators` + * :c:data:`psi_det_generators` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`build_fock_tmp` + * :c:func:`copy_h_apply_buffer_to_wf` + * :c:func:`dsort` + * :c:func:`h_apply_cisd_sym_diexc` + * :c:func:`h_apply_cisd_sym_monoexc` + * :c:func:`make_s2_eigenfunction` + * :c:func:`wall_time` + + Touches: + + .. hlist:: + :columns: 3 + + * :c:data:`n_det` + * :c:data:`psi_occ_pattern` + * :c:data:`c0_weight` + * :c:data:`psi_coef` + * :c:data:`psi_det_sorted_bit` + * :c:data:`psi_det` + * :c:data:`psi_det_size` + * :c:data:`psi_det_sorted_bit` + * :c:data:`psi_occ_pattern` + + +.. c:function:: h_apply_cisd_sym_diexc: + + + File : :file:`h_apply.irp.f_shell_12` + + .. code:: fortran + + subroutine H_apply_cisd_sym_diexc(key_in, key_prev, hole_1,particl_1, hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in ) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`n_det` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cisd_sym` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cisd_sym_diexcp` + + +.. c:function:: h_apply_cisd_sym_diexcorg: + + + File : :file:`h_apply.irp.f_shell_12` + + .. code:: fortran + + subroutine H_apply_cisd_sym_diexcOrg(key_in,key_mask,hole_1,particl_1,hole_2, particl_2, fock_diag_tmp, i_generator, iproc_in ) + + + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`elec_alpha_num` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cisd_sym_diexcp` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`bitstring_to_list_ab` + * :c:func:`connected_to_hf` + * :c:func:`fill_h_apply_buffer_no_selection` + + +.. c:function:: h_apply_cisd_sym_diexcp: + + + File : :file:`h_apply.irp.f_shell_12` + + .. code:: fortran + + subroutine H_apply_cisd_sym_diexcP(key_in, fs1, fh1, particl_1, fs2, fh2, particl_2, fock_diag_tmp, i_generator, iproc_in ) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`n_det` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cisd_sym_diexc` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cisd_sym_diexcorg` + + +.. c:function:: h_apply_cisd_sym_monoexc: + + + File : :file:`h_apply.irp.f_shell_12` + + .. code:: fortran + + subroutine H_apply_cisd_sym_monoexc(key_in, hole_1,particl_1,fock_diag_tmp,i_generator,iproc_in ) + + + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`n_int` + * :c:data:`elec_alpha_num` + * :c:data:`mo_num` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:func:`h_apply_cisd_sym` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`bitstring_to_list_ab` + * :c:func:`connected_to_hf` + * :c:func:`fill_h_apply_buffer_no_selection` + diff --git a/docs/source/modules/density_for_dft.rst b/docs/source/modules/density_for_dft.rst index fb48eb83..bf293eba 100644 --- a/docs/source/modules/density_for_dft.rst +++ b/docs/source/modules/density_for_dft.rst @@ -44,6 +44,12 @@ EZFIO parameters Default: full_density +.. option:: normalize_dm + + if .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb + + Default: True + Providers --------- @@ -131,6 +137,9 @@ Providers :columns: 3 * :c:data:`ao_num` + * :c:data:`data_one_e_dm_alpha_ao` + * :c:data:`data_one_e_dm_beta_ao` + * :c:data:`density_for_dft` * :c:data:`mo_coef` * :c:data:`mo_num` * :c:data:`n_states` @@ -147,6 +156,39 @@ Providers * :c:data:`one_e_dm_and_grad_alpha_in_r` +.. c:var:: one_e_dm_alpha_ao_for_dft_no_core + + + File : :file:`density_for_dft/density_for_dft.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_alpha_ao_for_dft_no_core (ao_num,ao_num,N_states) + double precision, allocatable :: one_e_dm_beta_ao_for_dft_no_core (ao_num,ao_num,N_states) + + + one body density matrix on the AO basis based on one_e_dm_mo_alpha_for_dft_no_core + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`mo_coef` + * :c:data:`mo_num` + * :c:data:`n_states` + * :c:data:`one_e_dm_mo_alpha_for_dft_no_core` + * :c:data:`one_e_dm_mo_beta_for_dft_no_core` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` + + .. c:var:: one_e_dm_average_mo_for_dft @@ -195,6 +237,9 @@ Providers :columns: 3 * :c:data:`ao_num` + * :c:data:`data_one_e_dm_alpha_ao` + * :c:data:`data_one_e_dm_beta_ao` + * :c:data:`density_for_dft` * :c:data:`mo_coef` * :c:data:`mo_num` * :c:data:`n_states` @@ -211,6 +256,39 @@ Providers * :c:data:`one_e_dm_and_grad_alpha_in_r` +.. c:var:: one_e_dm_beta_ao_for_dft_no_core + + + File : :file:`density_for_dft/density_for_dft.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_alpha_ao_for_dft_no_core (ao_num,ao_num,N_states) + double precision, allocatable :: one_e_dm_beta_ao_for_dft_no_core (ao_num,ao_num,N_states) + + + one body density matrix on the AO basis based on one_e_dm_mo_alpha_for_dft_no_core + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`mo_coef` + * :c:data:`mo_num` + * :c:data:`n_states` + * :c:data:`one_e_dm_mo_alpha_for_dft_no_core` + * :c:data:`one_e_dm_mo_beta_for_dft_no_core` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` + + .. c:var:: one_e_dm_mo_alpha_for_dft @@ -228,14 +306,18 @@ Providers .. hlist:: :columns: 3 + * :c:data:`ao_num` * :c:data:`damping_for_rs_dft` * :c:data:`data_one_e_dm_alpha_mo` * :c:data:`density_for_dft` + * :c:data:`elec_alpha_num` + * :c:data:`list_inact` * :c:data:`mo_coef` * :c:data:`mo_num` * :c:data:`n_core_orb` * :c:data:`n_states` * :c:data:`no_core_density` + * :c:data:`normalize_dm` * :c:data:`one_body_dm_mo_alpha_one_det` * :c:data:`one_e_dm_mo_alpha` * :c:data:`one_e_dm_mo_alpha_average` @@ -246,12 +328,44 @@ Providers :columns: 3 * :c:data:`one_e_dm_alpha_ao_for_dft` + * :c:data:`one_e_dm_mo_alpha_for_dft_no_core` * :c:data:`one_e_dm_mo_for_dft` * :c:data:`psi_dft_energy_kinetic` * :c:data:`trace_v_xc` * :c:data:`trace_v_xc_new` +.. c:var:: one_e_dm_mo_alpha_for_dft_no_core + + + File : :file:`density_for_dft/density_for_dft.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_mo_alpha_for_dft_no_core (mo_num,mo_num,N_states) + + + density matrix for alpha electrons in the MO basis without the core orbitals + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`list_inact` + * :c:data:`mo_num` + * :c:data:`n_core_orb` + * :c:data:`n_states` + * :c:data:`one_e_dm_mo_alpha_for_dft` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` + + .. c:var:: one_e_dm_mo_beta_for_dft @@ -269,14 +383,18 @@ Providers .. hlist:: :columns: 3 + * :c:data:`ao_num` * :c:data:`damping_for_rs_dft` * :c:data:`data_one_e_dm_beta_mo` * :c:data:`density_for_dft` + * :c:data:`elec_beta_num` + * :c:data:`list_inact` * :c:data:`mo_coef` * :c:data:`mo_num` * :c:data:`n_core_orb` * :c:data:`n_states` * :c:data:`no_core_density` + * :c:data:`normalize_dm` * :c:data:`one_body_dm_mo_alpha_one_det` * :c:data:`one_e_dm_mo_alpha` * :c:data:`one_e_dm_mo_alpha_average` @@ -287,12 +405,44 @@ Providers :columns: 3 * :c:data:`one_e_dm_alpha_ao_for_dft` + * :c:data:`one_e_dm_mo_beta_for_dft_no_core` * :c:data:`one_e_dm_mo_for_dft` * :c:data:`psi_dft_energy_kinetic` * :c:data:`trace_v_xc` * :c:data:`trace_v_xc_new` +.. c:var:: one_e_dm_mo_beta_for_dft_no_core + + + File : :file:`density_for_dft/density_for_dft.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_mo_beta_for_dft_no_core (mo_num,mo_num,N_states) + + + density matrix for beta electrons in the MO basis without the core orbitals + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`list_inact` + * :c:data:`mo_num` + * :c:data:`n_core_orb` + * :c:data:`n_states` + * :c:data:`one_e_dm_mo_beta_for_dft` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` + + .. c:var:: one_e_dm_mo_for_dft diff --git a/docs/source/modules/determinants.rst b/docs/source/modules/determinants.rst index 0f2b7348..9b0fab33 100644 --- a/docs/source/modules/determinants.rst +++ b/docs/source/modules/determinants.rst @@ -71,7 +71,7 @@ EZFIO parameters Thresholds on generators (fraction of the square of the norm) - Default: 0.99 + Default: 0.999 .. option:: n_int @@ -119,6 +119,18 @@ EZFIO parameters Weight of the states in state-average calculations. +.. option:: thresh_sym + + Thresholds to check if a determinant is connected with HF + + Default: 1.e-15 + +.. option:: pseudo_sym + + If |true|, discard any Slater determinants with an interaction smaller than thresh_sym with HF. + + Default: False + Providers --------- @@ -3971,6 +3983,37 @@ Subroutines / functions * :c:func:`debug_det` +.. c:function:: connected_to_hf: + + + File : :file:`determinants/slater_rules.irp.f` + + .. code:: fortran + + subroutine connected_to_hf(key_i,yes_no) + + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`thresh_sym` + * :c:data:`ref_bitmask` + * :c:data:`mo_one_e_integrals` + * :c:data:`n_int` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`get_excitation_degree` + * :c:func:`get_single_excitation` + * :c:func:`i_h_j` + + .. c:function:: connected_to_ref: @@ -5367,6 +5410,7 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:func:`connected_to_hf` * :c:data:`degree_max_generators` * :c:func:`diag_h_mat_elem_fock` * :c:func:`example_determinants` @@ -5699,6 +5743,7 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:func:`connected_to_hf` * :c:func:`diag_h_mat_elem_fock` * :c:func:`get_excitation` * :c:func:`i_h_j` @@ -5866,6 +5911,7 @@ Subroutines / functions :columns: 3 * :c:data:`coef_hf_selector` + * :c:func:`connected_to_hf` * :c:func:`example_determinants` * :c:func:`get_d0` * :c:func:`get_d1` diff --git a/docs/source/modules/dft_utils_in_r.rst b/docs/source/modules/dft_utils_in_r.rst index a5164ee5..0cfa30d6 100644 --- a/docs/source/modules/dft_utils_in_r.rst +++ b/docs/source/modules/dft_utils_in_r.rst @@ -344,6 +344,94 @@ Providers * :c:data:`mos_lapl_in_r_array` +.. c:var:: elec_alpha_num_grid_becke + + + File : :file:`dft_utils_in_r/dm_in_r.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_alpha_at_r (n_points_final_grid,N_states) + double precision, allocatable :: one_e_dm_beta_at_r (n_points_final_grid,N_states) + double precision, allocatable :: elec_beta_num_grid_becke (N_states) + double precision, allocatable :: elec_alpha_num_grid_becke (N_states) + + + one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate) + one_e_dm_beta_at_r(i,istate) = n_beta(r_i,istate) + where r_i is the ith point of the grid and istate is the state number + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`final_grid_points` + * :c:data:`n_points_final_grid` + * :c:data:`n_states` + * :c:data:`one_e_dm_alpha_ao_for_dft` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`aos_sr_vc_alpha_lda_w` + * :c:data:`aos_sr_vxc_alpha_lda_w` + * :c:data:`aos_vc_alpha_lda_w` + * :c:data:`aos_vxc_alpha_lda_w` + * :c:data:`energy_c_lda` + * :c:data:`energy_c_sr_lda` + * :c:data:`energy_sr_x_lda` + * :c:data:`energy_x_lda` + * :c:data:`energy_x_sr_lda` + + +.. c:var:: elec_beta_num_grid_becke + + + File : :file:`dft_utils_in_r/dm_in_r.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_alpha_at_r (n_points_final_grid,N_states) + double precision, allocatable :: one_e_dm_beta_at_r (n_points_final_grid,N_states) + double precision, allocatable :: elec_beta_num_grid_becke (N_states) + double precision, allocatable :: elec_alpha_num_grid_becke (N_states) + + + one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate) + one_e_dm_beta_at_r(i,istate) = n_beta(r_i,istate) + where r_i is the ith point of the grid and istate is the state number + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`final_grid_points` + * :c:data:`n_points_final_grid` + * :c:data:`n_states` + * :c:data:`one_e_dm_alpha_ao_for_dft` + + Needed by: + + .. hlist:: + :columns: 3 + + * :c:data:`aos_sr_vc_alpha_lda_w` + * :c:data:`aos_sr_vxc_alpha_lda_w` + * :c:data:`aos_vc_alpha_lda_w` + * :c:data:`aos_vxc_alpha_lda_w` + * :c:data:`energy_c_lda` + * :c:data:`energy_c_sr_lda` + * :c:data:`energy_sr_x_lda` + * :c:data:`energy_x_lda` + * :c:data:`energy_x_sr_lda` + + .. c:var:: mos_grad_in_r_array @@ -467,6 +555,8 @@ Providers double precision, allocatable :: one_e_dm_alpha_at_r (n_points_final_grid,N_states) double precision, allocatable :: one_e_dm_beta_at_r (n_points_final_grid,N_states) + double precision, allocatable :: elec_beta_num_grid_becke (N_states) + double precision, allocatable :: elec_alpha_num_grid_becke (N_states) one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate) @@ -628,6 +718,8 @@ Providers double precision, allocatable :: one_e_dm_alpha_at_r (n_points_final_grid,N_states) double precision, allocatable :: one_e_dm_beta_at_r (n_points_final_grid,N_states) + double precision, allocatable :: elec_beta_num_grid_becke (N_states) + double precision, allocatable :: elec_alpha_num_grid_becke (N_states) one_e_dm_alpha_at_r(i,istate) = n_alpha(r_i,istate) @@ -688,6 +780,66 @@ Providers +.. c:var:: one_e_dm_no_core_and_grad_alpha_in_r + + + File : :file:`dft_utils_in_r/dm_in_r.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_no_core_and_grad_alpha_in_r (4,n_points_final_grid,N_states) + double precision, allocatable :: one_e_dm_no_core_and_grad_beta_in_r (4,n_points_final_grid,N_states) + + + one_e_dm_no_core_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate) without core orbitals + one_e_dm_no_core_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate) without core orbitals + one_e_dm_no_core_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate) without core orbitals + one_e_dm_no_core_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate) without core orbitals + where r_i is the ith point of the grid and istate is the state number + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`final_grid_points` + * :c:data:`n_points_final_grid` + * :c:data:`n_states` + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` + + + +.. c:var:: one_e_dm_no_core_and_grad_beta_in_r + + + File : :file:`dft_utils_in_r/dm_in_r.irp.f` + + .. code:: fortran + + double precision, allocatable :: one_e_dm_no_core_and_grad_alpha_in_r (4,n_points_final_grid,N_states) + double precision, allocatable :: one_e_dm_no_core_and_grad_beta_in_r (4,n_points_final_grid,N_states) + + + one_e_dm_no_core_and_grad_alpha_in_r(1,i,i_state) = d\dx n_alpha(r_i,istate) without core orbitals + one_e_dm_no_core_and_grad_alpha_in_r(2,i,i_state) = d\dy n_alpha(r_i,istate) without core orbitals + one_e_dm_no_core_and_grad_alpha_in_r(3,i,i_state) = d\dz n_alpha(r_i,istate) without core orbitals + one_e_dm_no_core_and_grad_alpha_in_r(4,i,i_state) = n_alpha(r_i,istate) without core orbitals + where r_i is the ith point of the grid and istate is the state number + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`final_grid_points` + * :c:data:`n_points_final_grid` + * :c:data:`n_states` + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` + + + .. c:var:: one_e_grad_2_dm_alpha_at_r @@ -784,6 +936,55 @@ Providers Subroutines / functions ----------------------- +.. c:function:: dens_grad_a_b_no_core_and_aos_grad_aos_at_r: + + + File : :file:`dft_utils_in_r/dm_in_r.irp.f` + + .. code:: fortran + + subroutine dens_grad_a_b_no_core_and_aos_grad_aos_at_r(r,dm_a,dm_b, grad_dm_a, grad_dm_b, aos_array, grad_aos_array) + + + input: + + * r(1) ==> r(1) = x, r(2) = y, r(3) = z + + output: + + * dm_a = alpha density evaluated at r without the core orbitals + * dm_b = beta density evaluated at r without the core orbitals + * aos_array(i) = ao(i) evaluated at r without the core orbitals + * grad_dm_a(1) = X gradient of the alpha density evaluated in r without the core orbitals + * grad_dm_a(1) = X gradient of the beta density evaluated in r without the core orbitals + * grad_aos_array(1) = X gradient of the aos(i) evaluated at r + + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` + * :c:data:`n_states` + + Called by: + + .. hlist:: + :columns: 3 + + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`dsymv` + * :c:func:`give_all_aos_and_grad_at_r` + + .. c:function:: density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r: @@ -905,3 +1106,35 @@ Subroutines / functions * :c:func:`dgemv` * :c:func:`give_all_aos_at_r` + +.. c:function:: dm_dft_alpha_beta_no_core_at_r: + + + File : :file:`dft_utils_in_r/dm_in_r.irp.f` + + .. code:: fortran + + subroutine dm_dft_alpha_beta_no_core_at_r(r,dm_a,dm_b) + + + input: r(1) ==> r(1) = x, r(2) = y, r(3) = z + output : dm_a = alpha density evaluated at r(3) without the core orbitals + output : dm_b = beta density evaluated at r(3) without the core orbitals + + Needs: + + .. hlist:: + :columns: 3 + + * :c:data:`ao_num` + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` + * :c:data:`n_states` + + Calls: + + .. hlist:: + :columns: 3 + + * :c:func:`dgemv` + * :c:func:`give_all_aos_at_r` + diff --git a/docs/source/modules/dft_utils_one_e.rst b/docs/source/modules/dft_utils_one_e.rst index 1e78a3f4..05a75570 100644 --- a/docs/source/modules/dft_utils_one_e.rst +++ b/docs/source/modules/dft_utils_one_e.rst @@ -387,320 +387,6 @@ Providers * :c:data:`energy_x_sr_pbe` -.. c:var:: potential_sr_c_alpha_ao_lda - - - File : :file:`dft_utils_one_e/sr_pot_ao_lda.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_c_alpha_ao_lda (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_beta_ao_lda (ao_num,ao_num,N_states) - - - short range correlation alpha/beta potentials with LDA functional on the |AO| basis - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`aos_in_r_array` - * :c:data:`aos_sr_vc_alpha_lda_w` - * :c:data:`n_points_final_grid` - * :c:data:`n_states` - - - -.. c:var:: potential_sr_c_alpha_ao_pbe - - - File : :file:`dft_utils_one_e/sr_pot_ao_pbe.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_x_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_x_beta_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_beta_ao_pbe (ao_num,ao_num,N_states) - - - exchange / correlation potential for alpha / beta electrons with the Perdew-Burke-Ernzerhof GGA functional - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`n_states` - * :c:data:`pot_sr_grad_x_alpha_ao_pbe` - * :c:data:`pot_sr_scal_x_alpha_ao_pbe` - - - -.. c:var:: potential_sr_c_beta_ao_lda - - - File : :file:`dft_utils_one_e/sr_pot_ao_lda.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_c_alpha_ao_lda (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_beta_ao_lda (ao_num,ao_num,N_states) - - - short range correlation alpha/beta potentials with LDA functional on the |AO| basis - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`aos_in_r_array` - * :c:data:`aos_sr_vc_alpha_lda_w` - * :c:data:`n_points_final_grid` - * :c:data:`n_states` - - - -.. c:var:: potential_sr_c_beta_ao_pbe - - - File : :file:`dft_utils_one_e/sr_pot_ao_pbe.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_x_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_x_beta_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_beta_ao_pbe (ao_num,ao_num,N_states) - - - exchange / correlation potential for alpha / beta electrons with the Perdew-Burke-Ernzerhof GGA functional - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`n_states` - * :c:data:`pot_sr_grad_x_alpha_ao_pbe` - * :c:data:`pot_sr_scal_x_alpha_ao_pbe` - - - -.. c:var:: potential_sr_x_alpha_ao_lda - - - File : :file:`dft_utils_one_e/sr_pot_ao_lda.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_x_alpha_ao_lda (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_x_beta_ao_lda (ao_num,ao_num,N_states) - - - short range exchange alpha/beta potentials with LDA functional on the |AO| basis - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`aos_in_r_array` - * :c:data:`aos_sr_vc_alpha_lda_w` - * :c:data:`n_points_final_grid` - * :c:data:`n_states` - - - -.. c:var:: potential_sr_x_alpha_ao_pbe - - - File : :file:`dft_utils_one_e/sr_pot_ao_pbe.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_x_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_x_beta_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_beta_ao_pbe (ao_num,ao_num,N_states) - - - exchange / correlation potential for alpha / beta electrons with the Perdew-Burke-Ernzerhof GGA functional - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`n_states` - * :c:data:`pot_sr_grad_x_alpha_ao_pbe` - * :c:data:`pot_sr_scal_x_alpha_ao_pbe` - - - -.. c:var:: potential_sr_x_beta_ao_lda - - - File : :file:`dft_utils_one_e/sr_pot_ao_lda.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_x_alpha_ao_lda (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_x_beta_ao_lda (ao_num,ao_num,N_states) - - - short range exchange alpha/beta potentials with LDA functional on the |AO| basis - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`aos_in_r_array` - * :c:data:`aos_sr_vc_alpha_lda_w` - * :c:data:`n_points_final_grid` - * :c:data:`n_states` - - - -.. c:var:: potential_sr_x_beta_ao_pbe - - - File : :file:`dft_utils_one_e/sr_pot_ao_pbe.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_x_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_x_beta_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_c_beta_ao_pbe (ao_num,ao_num,N_states) - - - exchange / correlation potential for alpha / beta electrons with the Perdew-Burke-Ernzerhof GGA functional - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`n_states` - * :c:data:`pot_sr_grad_x_alpha_ao_pbe` - * :c:data:`pot_sr_scal_x_alpha_ao_pbe` - - - -.. c:var:: potential_sr_xc_alpha_ao_lda - - - File : :file:`dft_utils_one_e/sr_pot_ao_lda_smashed.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_xc_alpha_ao_lda (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_xc_beta_ao_lda (ao_num,ao_num,N_states) - - - short range exchange/correlation alpha/beta potentials with LDA functional on the AO basis - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`aos_in_r_array` - * :c:data:`aos_sr_vxc_alpha_lda_w` - * :c:data:`n_points_final_grid` - * :c:data:`n_states` - - - -.. c:var:: potential_sr_xc_alpha_ao_pbe - - - File : :file:`dft_utils_one_e/sr_pot_ao_pbe_smashed.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_xc_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_xc_beta_ao_pbe (ao_num,ao_num,N_states) - - - exchange / correlation potential for alpha / beta electrons with the Perdew-Burke-Ernzerhof GGA functional - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`n_states` - * :c:data:`pot_sr_grad_xc_alpha_ao_pbe` - * :c:data:`pot_sr_scal_xc_alpha_ao_pbe` - - - -.. c:var:: potential_sr_xc_beta_ao_lda - - - File : :file:`dft_utils_one_e/sr_pot_ao_lda_smashed.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_xc_alpha_ao_lda (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_xc_beta_ao_lda (ao_num,ao_num,N_states) - - - short range exchange/correlation alpha/beta potentials with LDA functional on the AO basis - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`aos_in_r_array` - * :c:data:`aos_sr_vxc_alpha_lda_w` - * :c:data:`n_points_final_grid` - * :c:data:`n_states` - - - -.. c:var:: potential_sr_xc_beta_ao_pbe - - - File : :file:`dft_utils_one_e/sr_pot_ao_pbe_smashed.irp.f` - - .. code:: fortran - - double precision, allocatable :: potential_sr_xc_alpha_ao_pbe (ao_num,ao_num,N_states) - double precision, allocatable :: potential_sr_xc_beta_ao_pbe (ao_num,ao_num,N_states) - - - exchange / correlation potential for alpha / beta electrons with the Perdew-Burke-Ernzerhof GGA functional - - Needs: - - .. hlist:: - :columns: 3 - - * :c:data:`ao_num` - * :c:data:`n_states` - * :c:data:`pot_sr_grad_xc_alpha_ao_pbe` - * :c:data:`pot_sr_scal_xc_alpha_ao_pbe` - - - .. c:var:: psi_dft_energy_h_core diff --git a/docs/source/modules/ezfio_files.rst b/docs/source/modules/ezfio_files.rst index f9cb0ade..22329d4f 100644 --- a/docs/source/modules/ezfio_files.rst +++ b/docs/source/modules/ezfio_files.rst @@ -58,7 +58,9 @@ Providers * :c:data:`correlation_energy_ratio_max` * :c:data:`data_energy_proj` * :c:data:`data_energy_var` + * :c:data:`data_one_e_dm_alpha_ao` * :c:data:`data_one_e_dm_alpha_mo` + * :c:data:`data_one_e_dm_beta_ao` * :c:data:`data_one_e_dm_beta_mo` * :c:data:`davidson_sze_max` * :c:data:`disk_access_nuclear_repulsion` @@ -131,6 +133,7 @@ Providers * :c:data:`pseudo_lmax` * :c:data:`pseudo_n_k` * :c:data:`pseudo_n_kl` + * :c:data:`pseudo_sym` * :c:data:`pseudo_v_k` * :c:data:`pseudo_v_kl` * :c:data:`psi_coef` @@ -146,6 +149,7 @@ Providers * :c:data:`state_following` * :c:data:`target_energy` * :c:data:`thresh_scf` + * :c:data:`thresh_sym` * :c:data:`threshold_davidson` * :c:data:`threshold_diis` * :c:data:`threshold_generators` @@ -219,7 +223,9 @@ Providers * :c:data:`correlation_energy_ratio_max` * :c:data:`data_energy_proj` * :c:data:`data_energy_var` + * :c:data:`data_one_e_dm_alpha_ao` * :c:data:`data_one_e_dm_alpha_mo` + * :c:data:`data_one_e_dm_beta_ao` * :c:data:`data_one_e_dm_beta_mo` * :c:data:`davidson_sze_max` * :c:data:`disk_access_nuclear_repulsion` @@ -281,6 +287,7 @@ Providers * :c:data:`pseudo_lmax` * :c:data:`pseudo_n_k` * :c:data:`pseudo_n_kl` + * :c:data:`pseudo_sym` * :c:data:`pseudo_v_k` * :c:data:`pseudo_v_kl` * :c:data:`pt2_iterations` @@ -292,6 +299,7 @@ Providers * :c:data:`state_following` * :c:data:`target_energy` * :c:data:`thresh_scf` + * :c:data:`thresh_sym` * :c:data:`threshold_davidson` * :c:data:`threshold_diis` * :c:data:`threshold_generators` @@ -330,7 +338,9 @@ Providers * :c:data:`correlation_energy_ratio_max` * :c:data:`data_energy_proj` * :c:data:`data_energy_var` + * :c:data:`data_one_e_dm_alpha_ao` * :c:data:`data_one_e_dm_alpha_mo` + * :c:data:`data_one_e_dm_beta_ao` * :c:data:`data_one_e_dm_beta_mo` * :c:data:`davidson_sze_max` * :c:data:`disk_access_nuclear_repulsion` @@ -392,6 +402,7 @@ Providers * :c:data:`pseudo_lmax` * :c:data:`pseudo_n_k` * :c:data:`pseudo_n_kl` + * :c:data:`pseudo_sym` * :c:data:`pseudo_v_k` * :c:data:`pseudo_v_kl` * :c:data:`pt2_iterations` @@ -403,6 +414,7 @@ Providers * :c:data:`state_following` * :c:data:`target_energy` * :c:data:`thresh_scf` + * :c:data:`thresh_sym` * :c:data:`threshold_davidson` * :c:data:`threshold_diis` * :c:data:`threshold_generators` @@ -673,7 +685,9 @@ Subroutines / functions * :c:func:`damping_scf` * :c:data:`data_energy_proj` * :c:data:`data_energy_var` + * :c:data:`data_one_e_dm_alpha_ao` * :c:data:`data_one_e_dm_alpha_mo` + * :c:data:`data_one_e_dm_beta_ao` * :c:data:`data_one_e_dm_beta_mo` * :c:func:`davidson_diag_hjj_sjj` * :c:data:`davidson_sze_max` @@ -740,6 +754,7 @@ Subroutines / functions * :c:data:`pseudo_lmax` * :c:data:`pseudo_n_k` * :c:data:`pseudo_n_kl` + * :c:data:`pseudo_sym` * :c:data:`pseudo_v_k` * :c:data:`pseudo_v_kl` * :c:data:`pt2_iterations` @@ -752,6 +767,7 @@ Subroutines / functions * :c:data:`state_following` * :c:data:`target_energy` * :c:data:`thresh_scf` + * :c:data:`thresh_sym` * :c:data:`threshold_davidson` * :c:data:`threshold_diis` * :c:data:`threshold_generators` diff --git a/docs/source/modules/hartree_fock.rst b/docs/source/modules/hartree_fock.rst index 90857d0b..415c8973 100644 --- a/docs/source/modules/hartree_fock.rst +++ b/docs/source/modules/hartree_fock.rst @@ -51,6 +51,7 @@ Programs -------- * :ref:`scf` + * :ref:`test` Providers --------- diff --git a/docs/source/modules/mo_basis.rst b/docs/source/modules/mo_basis.rst index aae2e481..1c6e3c66 100644 --- a/docs/source/modules/mo_basis.rst +++ b/docs/source/modules/mo_basis.rst @@ -80,9 +80,9 @@ Providers Molecular orbital coefficients on |AO| basis set - mo_coef(i,j) = coefficient of the i-th |AO| on the jth mo + mo_coef(i,j) = coefficient of the i-th |AO| on the jth |MO| - mo_label : Label characterizing the MOS (local, canonical, natural, etc) + mo_label : Label characterizing the |MOs| (local, canonical, natural, etc) Needs: @@ -286,7 +286,6 @@ Providers * :c:data:`fps_spf_matrix_mo` * :c:data:`full_ijkl_bitmask` * :c:data:`int_erf_3_index` - * :c:data:`list_core_inact_act` * :c:data:`list_inact` * :c:data:`mo_class` * :c:data:`mo_coef` @@ -762,8 +761,11 @@ Subroutines / functions * :c:func:`hcore_guess` * :c:func:`huckel_guess` * :c:func:`roothaan_hall_scf` + * :c:func:`rotate_mos` * :c:func:`save_natural_mos` * :c:func:`save_ortho_mos` + * :c:func:`sort_by_fock_energies` + * :c:func:`swap_mos` Calls: diff --git a/docs/source/modules/mpi.rst b/docs/source/modules/mpi.rst index 5dde771a..3711b26c 100644 --- a/docs/source/modules/mpi.rst +++ b/docs/source/modules/mpi.rst @@ -74,7 +74,9 @@ Providers * :c:data:`correlation_energy_ratio_max` * :c:data:`data_energy_proj` * :c:data:`data_energy_var` + * :c:data:`data_one_e_dm_alpha_ao` * :c:data:`data_one_e_dm_alpha_mo` + * :c:data:`data_one_e_dm_beta_ao` * :c:data:`data_one_e_dm_beta_mo` * :c:data:`davidson_sze_max` * :c:data:`disk_access_nuclear_repulsion` @@ -152,6 +154,7 @@ Providers * :c:data:`pseudo_lmax` * :c:data:`pseudo_n_k` * :c:data:`pseudo_n_kl` + * :c:data:`pseudo_sym` * :c:data:`pseudo_v_k` * :c:data:`pseudo_v_kl` * :c:data:`psi_cas` @@ -174,6 +177,7 @@ Providers * :c:data:`state_following` * :c:data:`target_energy` * :c:data:`thresh_scf` + * :c:data:`thresh_sym` * :c:data:`threshold_davidson` * :c:data:`threshold_diis` * :c:data:`threshold_generators` diff --git a/docs/source/modules/nuclei.rst b/docs/source/modules/nuclei.rst index 0bd4b325..04ff1f5b 100644 --- a/docs/source/modules/nuclei.rst +++ b/docs/source/modules/nuclei.rst @@ -526,7 +526,7 @@ Providers .. code:: fortran - double precision, allocatable :: slater_bragg_radii (100) + double precision, allocatable :: slater_bragg_radii (0:100) atomic radii in Angstrom defined in table I of JCP 41, 3199 (1964) Slater @@ -604,7 +604,7 @@ Providers .. code:: fortran - double precision, allocatable :: slater_bragg_radii_ua (100) + double precision, allocatable :: slater_bragg_radii_ua (0:100) diff --git a/docs/source/modules/scf_utils.rst b/docs/source/modules/scf_utils.rst index 4bf431b9..d32daf5f 100644 --- a/docs/source/modules/scf_utils.rst +++ b/docs/source/modules/scf_utils.rst @@ -165,7 +165,7 @@ Providers double precision, allocatable :: eigenvectors_fock_matrix_mo (ao_num,mo_num) - Eigenvectors of the Fock matrix in the MO basis obtained with level shift. + Eigenvectors of the Fock matrix in the |MO| basis obtained with level shift. Needs: diff --git a/docs/source/modules/tools.rst b/docs/source/modules/tools.rst index d8e2aa46..2ad351c7 100644 --- a/docs/source/modules/tools.rst +++ b/docs/source/modules/tools.rst @@ -22,9 +22,12 @@ Programs * :ref:`print_ci_vectors` * :ref:`print_e_conv` * :ref:`print_wf` + * :ref:`rotate_mos` * :ref:`save_natorb` * :ref:`save_one_e_dm` * :ref:`save_ortho_mos` + * :ref:`sort_by_fock_energies` + * :ref:`swap_mos` * :ref:`write_integrals_erf` Subroutines / functions @@ -115,6 +118,7 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:data:`one_e_dm_ao_alpha` * :c:data:`one_e_dm_mo_alpha` Called by: @@ -129,6 +133,8 @@ Subroutines / functions .. hlist:: :columns: 3 + * :c:func:`ezfio_set_aux_quantities_data_one_e_dm_alpha_ao` * :c:func:`ezfio_set_aux_quantities_data_one_e_dm_alpha_mo` + * :c:func:`ezfio_set_aux_quantities_data_one_e_dm_beta_ao` * :c:func:`ezfio_set_aux_quantities_data_one_e_dm_beta_mo` diff --git a/docs/source/modules/utils.rst b/docs/source/modules/utils.rst index f11ee43e..d7d078ca 100644 --- a/docs/source/modules/utils.rst +++ b/docs/source/modules/utils.rst @@ -997,6 +997,7 @@ Subroutines / functions * :c:func:`make_selection_buffer_s2` * :c:data:`psi_det_sorted` * :c:func:`reorder_core_orb` + * :c:func:`sort_by_fock_energies` * :c:func:`sort_selection_buffer` Calls: diff --git a/docs/source/programmers_guide/index_providers.rst b/docs/source/programmers_guide/index_providers.rst index 179d90c4..a491f509 100644 --- a/docs/source/programmers_guide/index_providers.rst +++ b/docs/source/programmers_guide/index_providers.rst @@ -168,7 +168,9 @@ Index of Providers * :c:data:`damping_for_rs_dft` * :c:data:`data_energy_proj` * :c:data:`data_energy_var` + * :c:data:`data_one_e_dm_alpha_ao` * :c:data:`data_one_e_dm_alpha_mo` + * :c:data:`data_one_e_dm_beta_ao` * :c:data:`data_one_e_dm_beta_mo` * :c:data:`davidson_criterion` * :c:data:`davidson_sze_max` @@ -214,7 +216,9 @@ Index of Providers * :c:data:`eigenvectors_fock_matrix_ao` * :c:data:`eigenvectors_fock_matrix_mo` * :c:data:`elec_alpha_num` + * :c:data:`elec_alpha_num_grid_becke` * :c:data:`elec_beta_num` + * :c:data:`elec_beta_num_grid_becke` * :c:data:`elec_num` * :c:data:`elec_num_tab` * :c:data:`element_mass` @@ -351,6 +355,7 @@ Index of Providers * :c:data:`list_del` * :c:data:`list_del_reverse` * :c:data:`list_inact` + * :c:data:`list_inact_act` * :c:data:`list_inact_reverse` * :c:data:`list_virt` * :c:data:`list_virt_reverse` @@ -441,6 +446,7 @@ Index of Providers * :c:data:`n_double_selectors` * :c:data:`n_generators_bitmask` * :c:data:`n_generators_bitmask_restart` + * :c:data:`n_inact_act_orb` * :c:data:`n_inact_orb` * :c:data:`n_inact_orb_allocate` * :c:data:`n_int` @@ -463,6 +469,7 @@ Index of Providers * :c:data:`no_ivvv_integrals` * :c:data:`no_vvv_integrals` * :c:data:`no_vvvv_integrals` + * :c:data:`normalize_dm` * :c:data:`nproc` * :c:data:`nthreads_davidson` * :c:data:`nthreads_pt2` @@ -487,6 +494,7 @@ Index of Providers * :c:data:`one_body_dm_mo_alpha_one_det` * :c:data:`one_body_dm_mo_beta_one_det` * :c:data:`one_e_dm_alpha_ao_for_dft` + * :c:data:`one_e_dm_alpha_ao_for_dft_no_core` * :c:data:`one_e_dm_alpha_at_r` * :c:data:`one_e_dm_alpha_in_r` * :c:data:`one_e_dm_and_grad_alpha_in_r` @@ -495,6 +503,7 @@ Index of Providers * :c:data:`one_e_dm_ao_beta` * :c:data:`one_e_dm_average_mo_for_dft` * :c:data:`one_e_dm_beta_ao_for_dft` + * :c:data:`one_e_dm_beta_ao_for_dft_no_core` * :c:data:`one_e_dm_beta_at_r` * :c:data:`one_e_dm_beta_in_r` * :c:data:`one_e_dm_dagger_mo_spin_index` @@ -502,12 +511,16 @@ Index of Providers * :c:data:`one_e_dm_mo_alpha` * :c:data:`one_e_dm_mo_alpha_average` * :c:data:`one_e_dm_mo_alpha_for_dft` + * :c:data:`one_e_dm_mo_alpha_for_dft_no_core` * :c:data:`one_e_dm_mo_beta` * :c:data:`one_e_dm_mo_beta_average` * :c:data:`one_e_dm_mo_beta_for_dft` + * :c:data:`one_e_dm_mo_beta_for_dft_no_core` * :c:data:`one_e_dm_mo_diff` * :c:data:`one_e_dm_mo_for_dft` * :c:data:`one_e_dm_mo_spin_index` + * :c:data:`one_e_dm_no_core_and_grad_alpha_in_r` + * :c:data:`one_e_dm_no_core_and_grad_beta_in_r` * :c:data:`one_e_energy` * :c:data:`one_e_grad_2_dm_alpha_at_r` * :c:data:`one_e_grad_2_dm_beta_at_r` @@ -556,18 +569,6 @@ Index of Providers * :c:data:`potential_c_beta_ao_sr_lda` * :c:data:`potential_c_beta_ao_sr_pbe` * :c:data:`potential_c_beta_mo` - * :c:data:`potential_sr_c_alpha_ao_lda` - * :c:data:`potential_sr_c_alpha_ao_pbe` - * :c:data:`potential_sr_c_beta_ao_lda` - * :c:data:`potential_sr_c_beta_ao_pbe` - * :c:data:`potential_sr_x_alpha_ao_lda` - * :c:data:`potential_sr_x_alpha_ao_pbe` - * :c:data:`potential_sr_x_beta_ao_lda` - * :c:data:`potential_sr_x_beta_ao_pbe` - * :c:data:`potential_sr_xc_alpha_ao_lda` - * :c:data:`potential_sr_xc_alpha_ao_pbe` - * :c:data:`potential_sr_xc_beta_ao_lda` - * :c:data:`potential_sr_xc_beta_ao_pbe` * :c:data:`potential_x_alpha_ao` * :c:data:`potential_x_alpha_ao_lda` * :c:data:`potential_x_alpha_ao_none` @@ -609,6 +610,7 @@ Index of Providers * :c:data:`pseudo_n_k_transp` * :c:data:`pseudo_n_kl` * :c:data:`pseudo_n_kl_transp` + * :c:data:`pseudo_sym` * :c:data:`pseudo_v_k` * :c:data:`pseudo_v_k_transp` * :c:data:`pseudo_v_kl` @@ -679,6 +681,7 @@ Index of Providers * :c:data:`pt2_f` * :c:data:`pt2_iterations` * :c:data:`pt2_j` + * :c:data:`pt2_match_weight` * :c:data:`pt2_max` * :c:data:`pt2_mindetinfirstteeth` * :c:data:`pt2_n_0` @@ -773,6 +776,7 @@ Index of Providers * :c:data:`target_energy` * :c:data:`theta_angular_integration_lebedev` * :c:data:`thresh_scf` + * :c:data:`thresh_sym` * :c:data:`threshold_davidson` * :c:data:`threshold_diis` * :c:data:`threshold_diis_nonzero` @@ -891,6 +895,7 @@ Index of Subroutines/Functions * :c:func:`compute_ao_two_e_integrals` * :c:func:`compute_ao_two_e_integrals_erf` * :c:func:`connect_to_taskserver` + * :c:func:`connected_to_hf` * :c:func:`connected_to_ref` * :c:func:`connected_to_ref_by_single` * :c:func:`copy_h_apply_buffer_to_wf` @@ -925,6 +930,7 @@ Index of Subroutines/Functions * :c:func:`decode_exc` * :c:func:`decode_exc_spin` * :c:func:`delete_selection_buffer` + * :c:func:`dens_grad_a_b_no_core_and_aos_grad_aos_at_r` * :c:func:`density_and_grad_alpha_beta_and_all_aos_and_grad_aos_at_r` * :c:func:`derivative_knowles_function` * :c:func:`det_inf` @@ -942,6 +948,7 @@ Index of Subroutines/Functions * :c:func:`disconnect_from_taskserver_state` * :c:func:`dm_dft_alpha_beta_and_all_aos_at_r` * :c:func:`dm_dft_alpha_beta_at_r` + * :c:func:`dm_dft_alpha_beta_no_core_at_r` * :c:func:`do_single_excitation` * :c:func:`dpol` * :c:func:`dpold` @@ -1093,11 +1100,21 @@ Index of Subroutines/Functions * :c:func:`h_apply_cis_diexcorg` * :c:func:`h_apply_cis_diexcp` * :c:func:`h_apply_cis_monoexc` + * :c:func:`h_apply_cis_sym` + * :c:func:`h_apply_cis_sym_diexc` + * :c:func:`h_apply_cis_sym_diexcorg` + * :c:func:`h_apply_cis_sym_diexcp` + * :c:func:`h_apply_cis_sym_monoexc` * :c:func:`h_apply_cisd` * :c:func:`h_apply_cisd_diexc` * :c:func:`h_apply_cisd_diexcorg` * :c:func:`h_apply_cisd_diexcp` * :c:func:`h_apply_cisd_monoexc` + * :c:func:`h_apply_cisd_sym` + * :c:func:`h_apply_cisd_sym_diexc` + * :c:func:`h_apply_cisd_sym_diexcorg` + * :c:func:`h_apply_cisd_sym_diexcp` + * :c:func:`h_apply_cisd_sym_monoexc` * :c:func:`h_s2_u_0_nstates_openmp` * :c:func:`h_s2_u_0_nstates_openmp_work` * :c:func:`h_s2_u_0_nstates_openmp_work_1` @@ -1321,6 +1338,7 @@ Index of Subroutines/Functions * :c:func:`rinteg` * :c:func:`rintgauss` * :c:func:`roothaan_hall_scf` + * :c:func:`rotate_mos` * :c:func:`routine` * :c:func:`routine_e_conv` * :c:func:`routine_example_psi_det` @@ -1369,6 +1387,7 @@ Index of Subroutines/Functions * :c:func:`set_order_big` * :c:func:`single_excitation_wee` * :c:func:`sort` + * :c:func:`sort_by_fock_energies` * :c:func:`sort_dets_ab` * :c:func:`sort_dets_ab_v` * :c:func:`sort_dets_ba_v` @@ -1384,10 +1403,12 @@ Index of Subroutines/Functions * :c:func:`spot_isinwf` * :c:func:`step_function_becke` * :c:func:`svd` + * :c:func:`swap_mos` * :c:func:`switch_qp_run_to_master` * :c:func:`tamiser` * :c:func:`task_done_to_taskserver` * :c:func:`tasks_done_to_taskserver` + * :c:func:`test` * :c:func:`testteethbuilding` * :c:func:`total_memory` * :c:func:`two_e_integrals_index` diff --git a/docs/source/programs/fci.rst b/docs/source/programs/fci.rst index c5717b1a..e037c974 100644 --- a/docs/source/programs/fci.rst +++ b/docs/source/programs/fci.rst @@ -60,6 +60,7 @@ fci :columns: 3 * :c:func:`run_cipsi` + * :c:func:`run_slave_cipsi` * :c:func:`run_stochastic_cipsi` Touches: @@ -75,6 +76,7 @@ fci * :c:data:`n_iter` * :c:data:`psi_occ_pattern` * :c:data:`c0_weight` + * :c:data:`distributed_davidson` * :c:data:`psi_coef` * :c:data:`psi_det_sorted_bit` * :c:data:`psi_det` @@ -83,6 +85,9 @@ fci * :c:data:`psi_energy` * :c:data:`psi_occ_pattern` * :c:data:`psi_energy` + * :c:data:`pt2_e0_denominator` + * :c:data:`pt2_match_weight` * :c:data:`pt2_stoch_istate` + * :c:data:`read_wf` * :c:data:`state_average_weight` * :c:data:`threshold_generators` diff --git a/docs/source/programs/save_one_e_dm.rst b/docs/source/programs/save_one_e_dm.rst index 5758aad6..a47a0af8 100644 --- a/docs/source/programs/save_one_e_dm.rst +++ b/docs/source/programs/save_one_e_dm.rst @@ -9,15 +9,15 @@ save_one_e_dm - Program that computes the one body density on the |MO| basis + Program that computes the one body density on the |MO| and |AO| basis for $\alpha$ and $\beta$ electrons from the wave function stored in the |EZFIO| directory, and then saves it into the :ref:`module_aux_quantities`. Then, the global variable :option:`aux_quantities data_one_e_dm_alpha_mo` - and :option:`aux_quantities data_one_e_dm_beta_mo` will automatically - read this density in the next calculation. This can be used to perform - damping on the density in |RSDFT| calculations (see + and :option:`aux_quantities data_one_e_dm_beta_mo` (and the corresponding for |AO|) + will automatically ! read this density in the next calculation. + This can be used to perform damping on the density in |RSDFT| calculations (see :ref:`module_density_for_dft`). Needs: diff --git a/docs/source/users_guide/qp_plugins.rst b/docs/source/users_guide/qp_plugins.rst index 18a41ba8..bea6fd9f 100644 --- a/docs/source/users_guide/qp_plugins.rst +++ b/docs/source/users_guide/qp_plugins.rst @@ -53,6 +53,10 @@ Usage Uninstall the plugin ``plugin_name``. +.. option:: update + + Update the repositories of the plugins. Should be followed by a re-compilation. + .. option:: -n, --name= Create a new plugin named ``plugin_name`` (in local repository by default). diff --git a/docs/source/users_guide/qp_set_frozen_core.rst b/docs/source/users_guide/qp_set_frozen_core.rst index 09231c32..d404ff59 100644 --- a/docs/source/users_guide/qp_set_frozen_core.rst +++ b/docs/source/users_guide/qp_set_frozen_core.rst @@ -11,6 +11,29 @@ Automatically finds *n*, the number of core electrons. Calls :math:`n/2` first ones which are set as ``Core``. If pseudo-potentials are used, all the |MOs| are set as ``Active``. + +========== ========= ======= ======= + Range Default Small Large +========== ========= ======= ======= + H -> He 0 0 0 + Li -> Be 0 0 2 + B -> Ne 2 2 2 + Na -> Mg 2 2 10 + Al -> Ar 10 2 10 + K -> Ca 10 10 18 + Sc -> Zn 10 10 18 + Ga -> Kr 18 10 18 + Rb -> Sr 18 18 36 + Y -> Cd 18 18 36 + In -> Xe 36 18 36 + Cs -> Ba 36 36 54 + La -> Hg 36 36 54 + Tl -> Rn 54 36 54 + Fr -> Ra 54 54 86 + Ac -> Cn 54 54 86 + Nh -> Og 86 54 86 +========== ========= ======= ======= + For elements on the right of the periodic table, `qp_set_frozen_core` will work as expected. But for elements on the left, a small core will be chosen. For example, a Carbon atom will have 2 core electrons, but a @@ -21,11 +44,19 @@ Usage .. code:: bash - qp_set_frozen_core [-q] EZFIO_DIR + qp_set_frozen_core [-q|--query] [(-l|-s|--large|--small) EZFIO_DIR -.. option:: -q +.. option:: -q, --query Prints in the standard output the number of core electrons. +.. option:: -s, --small + + Use a small core. + +.. option:: -l, --large + + Use a large core. + diff --git a/man/cis.1 b/man/cis.1 index 5bfa5045..d533b377 100644 --- a/man/cis.1 +++ b/man/cis.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "CIS" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "CIS" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME cis \- | Quantum Package > . diff --git a/man/cisd.1 b/man/cisd.1 index e123534f..33d6212e 100644 --- a/man/cisd.1 +++ b/man/cisd.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "CISD" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "CISD" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME cisd \- | Quantum Package > . diff --git a/man/configure.1 b/man/configure.1 index 97b74e0d..c3ec2bd8 100644 --- a/man/configure.1 +++ b/man/configure.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "CONFIGURE" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "CONFIGURE" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME configure \- | Quantum Package > . diff --git a/man/diagonalize_h.1 b/man/diagonalize_h.1 index ba943f6c..3f4a3a30 100644 --- a/man/diagonalize_h.1 +++ b/man/diagonalize_h.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "DIAGONALIZE_H" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "DIAGONALIZE_H" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME diagonalize_h \- | Quantum Package > . diff --git a/man/excited_states.1 b/man/excited_states.1 index f140561f..37d343d2 100644 --- a/man/excited_states.1 +++ b/man/excited_states.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "EXCITED_STATES" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "EXCITED_STATES" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME excited_states \- | Quantum Package > . diff --git a/man/fci.1 b/man/fci.1 index 389f6453..5312866e 100644 --- a/man/fci.1 +++ b/man/fci.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "FCI" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "FCI" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME fci \- | Quantum Package > . @@ -98,9 +98,11 @@ Calls: .UNINDENT .INDENT 2.0 .IP \(bu 2 -\fBrun_stochastic_cipsi()\fP +\fBrun_slave_cipsi()\fP .UNINDENT .INDENT 2.0 +.IP \(bu 2 +\fBrun_stochastic_cipsi()\fP .UNINDENT .UNINDENT .sp @@ -121,10 +123,12 @@ Touches: \fBn_iter\fP .IP \(bu 2 \fBpsi_occ_pattern\fP +.IP \(bu 2 +\fBc0_weight\fP .UNINDENT .INDENT 2.0 .IP \(bu 2 -\fBc0_weight\fP +\fBdistributed_davidson\fP .IP \(bu 2 \fBpsi_coef\fP .IP \(bu 2 @@ -135,17 +139,23 @@ Touches: \fBpsi_det_size\fP .IP \(bu 2 \fBpsi_det_sorted_bit\fP +.IP \(bu 2 +\fBpsi_energy\fP +.IP \(bu 2 +\fBpsi_occ_pattern\fP .UNINDENT .INDENT 2.0 .IP \(bu 2 \fBpsi_energy\fP .IP \(bu 2 -\fBpsi_occ_pattern\fP +\fBpt2_e0_denominator\fP .IP \(bu 2 -\fBpsi_energy\fP +\fBpt2_match_weight\fP .IP \(bu 2 \fBpt2_stoch_istate\fP .IP \(bu 2 +\fBread_wf\fP +.IP \(bu 2 \fBstate_average_weight\fP .IP \(bu 2 \fBthreshold_generators\fP diff --git a/man/fcidump.1 b/man/fcidump.1 index 93d87ddd..e3ad0d11 100644 --- a/man/fcidump.1 +++ b/man/fcidump.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "FCIDUMP" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "FCIDUMP" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME fcidump \- | Quantum Package > . diff --git a/man/four_idx_transform.1 b/man/four_idx_transform.1 index a909c524..9188fe72 100644 --- a/man/four_idx_transform.1 +++ b/man/four_idx_transform.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "FOUR_IDX_TRANSFORM" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "FOUR_IDX_TRANSFORM" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME four_idx_transform \- | Quantum Package > . diff --git a/man/interfaces.1 b/man/interfaces.1 index c3f6625c..9cd6a115 100644 --- a/man/interfaces.1 +++ b/man/interfaces.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "INTERFACES" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "INTERFACES" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME interfaces \- | Quantum Package > . diff --git a/man/ks_scf.1 b/man/ks_scf.1 index 1b2651ca..b57a3342 100644 --- a/man/ks_scf.1 +++ b/man/ks_scf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "KS_SCF" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "KS_SCF" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME ks_scf \- | Quantum Package > . diff --git a/man/molden.1 b/man/molden.1 index 5cc2824e..d92a75e3 100644 --- a/man/molden.1 +++ b/man/molden.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "MOLDEN" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "MOLDEN" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME molden \- | Quantum Package > . diff --git a/man/natural_orbitals.1 b/man/natural_orbitals.1 index 56185c52..5aa70b42 100644 --- a/man/natural_orbitals.1 +++ b/man/natural_orbitals.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "NATURAL_ORBITALS" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "NATURAL_ORBITALS" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME natural_orbitals \- | Quantum Package > . diff --git a/man/plugins.1 b/man/plugins.1 index d1c319a2..4a680ec6 100644 --- a/man/plugins.1 +++ b/man/plugins.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PLUGINS" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "PLUGINS" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME plugins \- | Quantum Package > . diff --git a/man/print_ci_vectors.1 b/man/print_ci_vectors.1 new file mode 100644 index 00000000..3905e63e --- /dev/null +++ b/man/print_ci_vectors.1 @@ -0,0 +1,87 @@ +.\" Man page generated from reStructuredText. +. +.TH "PRINT_CI_VECTORS" "1" "May 28, 2019" "2.0" "Quantum Package" +.SH NAME +print_ci_vectors \- | Quantum Package > +. +.nr rst2man-indent-level 0 +. +.de1 rstReportMargin +\\$1 \\n[an-margin] +level \\n[rst2man-indent-level] +level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] +- +\\n[rst2man-indent0] +\\n[rst2man-indent1] +\\n[rst2man-indent2] +.. +.de1 INDENT +.\" .rstReportMargin pre: +. RS \\$1 +. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] +. nr rst2man-indent-level +1 +.\" .rstReportMargin post: +.. +.de UNINDENT +. RE +.\" indent \\n[an-margin] +.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] +.nr rst2man-indent-level -1 +.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] +.in \\n[rst2man-indent\\n[rst2man-indent-level]]u +.. +.INDENT 0.0 +.INDENT 3.5 +Print the ground state wave function stored in the \fI\%EZFIO\fP directory +in the intermediate normalization. +.sp +It also prints a lot of information regarding the excitation +operators from the reference determinant ! and a first\-order +perturbative analysis of the wave function. +.sp +If the wave function strongly deviates from the first\-order analysis, +something funny is going on :) +.sp +Needs: +.INDENT 0.0 +.INDENT 2.0 +.IP \(bu 2 +\fBread_wf\fP +.UNINDENT +.INDENT 2.0 +.UNINDENT +.INDENT 2.0 +.UNINDENT +.UNINDENT +.sp +Calls: +.INDENT 0.0 +.INDENT 2.0 +.IP \(bu 2 +\fBroutine()\fP +.UNINDENT +.INDENT 2.0 +.UNINDENT +.INDENT 2.0 +.UNINDENT +.UNINDENT +.sp +Touches: +.INDENT 0.0 +.INDENT 2.0 +.IP \(bu 2 +\fBread_wf\fP +.UNINDENT +.INDENT 2.0 +.UNINDENT +.INDENT 2.0 +.UNINDENT +.UNINDENT +.UNINDENT +.UNINDENT +.SH AUTHOR +A. Scemama, E. Giner +.SH COPYRIGHT +2019, A. Scemama, E. Giner +.\" Generated by docutils manpage writer. +. diff --git a/man/print_e_conv.1 b/man/print_e_conv.1 index fb65e355..4fc03a3d 100644 --- a/man/print_e_conv.1 +++ b/man/print_e_conv.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PRINT_E_CONV" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "PRINT_E_CONV" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME print_e_conv \- | Quantum Package > . diff --git a/man/print_wf.1 b/man/print_wf.1 index bc2fa570..a1ae9233 100644 --- a/man/print_wf.1 +++ b/man/print_wf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PRINT_WF" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "PRINT_WF" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME print_wf \- | Quantum Package > . diff --git a/man/printing.1 b/man/printing.1 index 4fd17a27..7b0e2514 100644 --- a/man/printing.1 +++ b/man/printing.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PRINTING" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "PRINTING" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME printing \- | Quantum Package > . diff --git a/man/pt2.1 b/man/pt2.1 index e54469fe..de04c26d 100644 --- a/man/pt2.1 +++ b/man/pt2.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "PT2" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "PT2" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME pt2 \- | Quantum Package > . diff --git a/man/qp_convert_output_to_ezfio.1 b/man/qp_convert_output_to_ezfio.1 index d5f6f147..7378da9f 100644 --- a/man/qp_convert_output_to_ezfio.1 +++ b/man/qp_convert_output_to_ezfio.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_CONVERT_OUTPUT_TO_EZFIO" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_convert_output_to_ezfio \- | Quantum Package > . diff --git a/man/qp_create_ezfio.1 b/man/qp_create_ezfio.1 new file mode 100644 index 00000000..0fe7ffaf --- /dev/null +++ b/man/qp_create_ezfio.1 @@ -0,0 +1,235 @@ +.\" Man page generated from reStructuredText. +. +.TH "QP_CREATE_EZFIO" "1" "May 28, 2019" "2.0" "Quantum Package" +.SH NAME +qp_create_ezfio \- | Quantum Package > +. +.nr rst2man-indent-level 0 +. +.de1 rstReportMargin +\\$1 \\n[an-margin] +level \\n[rst2man-indent-level] +level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] +- +\\n[rst2man-indent0] +\\n[rst2man-indent1] +\\n[rst2man-indent2] +.. +.de1 INDENT +.\" .rstReportMargin pre: +. RS \\$1 +. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] +. nr rst2man-indent-level +1 +.\" .rstReportMargin post: +.. +.de UNINDENT +. RE +.\" indent \\n[an-margin] +.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] +.nr rst2man-indent-level -1 +.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] +.in \\n[rst2man-indent\\n[rst2man-indent-level]]u +.. +.sp +This command creates an \fI\%EZFIO\fP directory from a standard \fIxyz\fP file or +from a \fIz\-matrix\fP file in Gaussian format. +.SH USAGE +.INDENT 0.0 +.INDENT 3.5 +.sp +.nf +.ft C +qp_create_ezfio [\-a] \-b [\-c ] [\-d ] + [\-h] [\-m ] [\-o EZFIO_DIR] [\-p ] [\-x] [\-\-] FILE +.ft P +.fi +.UNINDENT +.UNINDENT +.INDENT 0.0 +.TP +.B \-a, \-\-au +If present, input geometry is in atomic units. +.UNINDENT +.INDENT 0.0 +.TP +.B \-b, \-\-basis= +Name of basis set. The basis set is defined as a single string if +all the atoms are taken from the same basis set, otherwise specific +elements can be defined as follows: +.INDENT 7.0 +.INDENT 3.5 +.sp +.nf +.ft C +\-b "cc\-pcvdz | H:cc\-pvdz | C:6\-31g" +\-b "cc\-pvtz | 1,H:sto\-3g | 3,H:6\-31g" +.ft P +.fi +.UNINDENT +.UNINDENT +.sp +By default, the basis set is obtained from the local database of the. +\fIQuantum Package\fP This option is mandatory . +.sp +If \fB\fP is set to \fBshow\fP, the list of all available basis +sets is displayed. +.UNINDENT +.INDENT 0.0 +.TP +.B \-c, \-\-charge= +Total charge of the molecule. Default is 0. +.UNINDENT +.INDENT 0.0 +.TP +.B \-d, \-\-dummy= +Add dummy atoms (X) between atoms when the distance between two atoms +is less than x \etimes \esum R_\emathrm{cov}, the covalent radii +of the atoms. The default is x=0, so no dummy atom is added. +.UNINDENT +.INDENT 0.0 +.TP +.B \-h, \-\-help +Print the help text and exit +.UNINDENT +.INDENT 0.0 +.TP +.B \-m, \-\-multiplicity= +Spin multiplicity 2S+1 of the molecule. Default is 1. +.UNINDENT +.INDENT 0.0 +.TP +.B \-o, \-\-output=EZFIO_DIR +Name of the created \fI\%EZFIO\fP directory. +.UNINDENT +.INDENT 0.0 +.TP +.B \-p , \-\-pseudo= +Name of the pseudo\-potential. Follows the same conventions as the basis set. +.UNINDENT +.INDENT 0.0 +.TP +.B \-x, \-\-cart +Compute AOs in the Cartesian basis set (6d, 10f, …) +.UNINDENT +.SH USING CUSTOM ATOMIC BASIS SETS +.sp +If a file with the same name as the basis set exists, this file will +be read. For example, if the file containing the basis set is named +\fBcustom.basis\fP, and the \fIxyz\fP geometry is in \fBmolecule.xyz\fP, the +following should be used: +.INDENT 0.0 +.INDENT 3.5 +.sp +.nf +.ft C +qp_create_ezfio \-b custom.basis molecule.xyz +.ft P +.fi +.UNINDENT +.UNINDENT +.sp +Basis set files should be given in \fI\%GAMESS\fP format, where the full +names of the atoms are given, and the basis sets for each element are +separated by a blank line. Here is an example +.INDENT 0.0 +.INDENT 3.5 +.sp +.nf +.ft C +HYDROGEN +S 3 +1 13.0100000 0.0196850 +2 1.9620000 0.1379770 +3 0.4446000 0.4781480 +S 1 +1 0.1220000 1.0000000 +P 1 +1 0.7270000 1.0000000 + +BORON +S 8 +1 4570.0000000 0.0006960 +2 685.9000000 0.0053530 +3 156.5000000 0.0271340 +4 44.4700000 0.1013800 +5 14.4800000 0.2720550 +6 5.1310000 0.4484030 +7 1.8980000 0.2901230 +8 0.3329000 0.0143220 +S 8 +1 4570.0000000 \-0.0001390 +2 685.9000000 \-0.0010970 +3 156.5000000 \-0.0054440 +4 44.4700000 \-0.0219160 +5 14.4800000 \-0.0597510 +6 5.1310000 \-0.1387320 +7 1.8980000 \-0.1314820 +8 0.3329000 0.5395260 +S 1 +1 0.1043000 1.0000000 +P 3 +1 6.0010000 0.0354810 +2 1.2410000 0.1980720 +3 0.3364000 0.5052300 +P 1 +1 0.0953800 1.0000000 +D 1 +1 0.3430000 1.0000000 +.ft P +.fi +.UNINDENT +.UNINDENT +.SH USING CUSTOM PSEUDO-POTENTIALS +.sp +As for the basis set, if a file with the same name as the +pseudo\-potential exists, this file will be read. For example, if the +file containing the custom pseudo\-potential is named \fBcustom.pseudo\fP, +the basis set is named \fBcustom.basis\fP, and the \fIxyz\fP geometry is in +\fBmolecule.xyz\fP, the following command should be used +.INDENT 0.0 +.INDENT 3.5 +.sp +.nf +.ft C +qp_create_ezfio \-b custom.basis \-p custom.pseudo molecule.xyz +.ft P +.fi +.UNINDENT +.UNINDENT +.sp +Pseudo\-potential files should be given in a format very close to +\fI\%GAMESS\fP format. The first line should be formatted as \fB%s GEN %d %d\fP +where the first string is the chemical symbol, the first integer is +the number of core electrons to be removed and the second integer is +LMAX+1 as in \fI\%GAMESS\fP format. The pseudo\-potential for each element are +separated by a blank line. Here is an example +.INDENT 0.0 +.INDENT 3.5 +.sp +.nf +.ft C +Ne GEN 2 1 +3 +8.00000000 1 10.74945199 +85.99561593 3 10.19801460 +\-56.79004456 2 10.18694048 +1 +55.11144535 2 12.85042963 + +F GEN 2 1 +3 +7.00000000 1 11.39210685 +79.74474797 3 10.74911370 +\-49.45159098 2 10.45120693 +1 +50.25646328 2 11.30345826 +.ft P +.fi +.UNINDENT +.UNINDENT +.SH AUTHOR +A. Scemama, E. Giner +.SH COPYRIGHT +2019, A. Scemama, E. Giner +.\" Generated by docutils manpage writer. +. diff --git a/man/qp_edit.1 b/man/qp_edit.1 index 94b8cb7a..20167ac3 100644 --- a/man/qp_edit.1 +++ b/man/qp_edit.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_EDIT" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_EDIT" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_edit \- | Quantum Package > . diff --git a/man/qp_export_as_tgz.1 b/man/qp_export_as_tgz.1 index f5d93a01..d0b5a58b 100644 --- a/man/qp_export_as_tgz.1 +++ b/man/qp_export_as_tgz.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_EXPORT_AS_TGZ" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_EXPORT_AS_TGZ" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_export_as_tgz \- | Quantum Package > . diff --git a/man/qp_plugins.1 b/man/qp_plugins.1 index 890f7254..cf1f94a9 100644 --- a/man/qp_plugins.1 +++ b/man/qp_plugins.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_PLUGINS" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_PLUGINS" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_plugins \- | Quantum Package > . @@ -93,6 +93,11 @@ Uninstall the plugin \fBplugin_name\fP\&. .UNINDENT .INDENT 0.0 .TP +.B update +Update the repositories of the plugins. Should be followed by a re\-compilation. +.UNINDENT +.INDENT 0.0 +.TP .B \-n, \-\-name= Create a new plugin named \fBplugin_name\fP (in local repository by default). .UNINDENT diff --git a/man/qp_reset.1 b/man/qp_reset.1 index c9481bda..bfa38f6f 100644 --- a/man/qp_reset.1 +++ b/man/qp_reset.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_RESET" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_RESET" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_reset \- | Quantum Package > . diff --git a/man/qp_run.1 b/man/qp_run.1 index 583bce63..7f1f106e 100644 --- a/man/qp_run.1 +++ b/man/qp_run.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_RUN" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_RUN" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_run \- | Quantum Package > . diff --git a/man/qp_set_frozen_core.1 b/man/qp_set_frozen_core.1 index 2e8ab3f4..9f40b0b2 100644 --- a/man/qp_set_frozen_core.1 +++ b/man/qp_set_frozen_core.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_SET_FROZEN_CORE" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_SET_FROZEN_CORE" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_set_frozen_core \- | Quantum Package > . @@ -35,6 +35,191 @@ Automatically finds \fIn\fP, the number of core electrons. Calls qp_set_mo_class setting all MOs as \fBActive\fP, except the n/2 first ones which are set as \fBCore\fP\&. If pseudo\-potentials are used, all the MOs are set as \fBActive\fP\&. +.TS +center; +|l|l|l|l|. +_ +T{ +Range +T} T{ +Default +T} T{ +Small +T} T{ +Large +T} +_ +T{ +H \-> He +T} T{ +0 +T} T{ +0 +T} T{ +0 +T} +_ +T{ +Li \-> Be +T} T{ +0 +T} T{ +0 +T} T{ +2 +T} +_ +T{ +B \-> Ne +T} T{ +2 +T} T{ +2 +T} T{ +2 +T} +_ +T{ +Na \-> Mg +T} T{ +2 +T} T{ +2 +T} T{ +10 +T} +_ +T{ +Al \-> Ar +T} T{ +10 +T} T{ +2 +T} T{ +10 +T} +_ +T{ +K \-> Ca +T} T{ +10 +T} T{ +10 +T} T{ +18 +T} +_ +T{ +Sc \-> Zn +T} T{ +10 +T} T{ +10 +T} T{ +18 +T} +_ +T{ +Ga \-> Kr +T} T{ +18 +T} T{ +10 +T} T{ +18 +T} +_ +T{ +Rb \-> Sr +T} T{ +18 +T} T{ +18 +T} T{ +36 +T} +_ +T{ +Y \-> Cd +T} T{ +18 +T} T{ +18 +T} T{ +36 +T} +_ +T{ +In \-> Xe +T} T{ +36 +T} T{ +18 +T} T{ +36 +T} +_ +T{ +Cs \-> Ba +T} T{ +36 +T} T{ +36 +T} T{ +54 +T} +_ +T{ +La \-> Hg +T} T{ +36 +T} T{ +36 +T} T{ +54 +T} +_ +T{ +Tl \-> Rn +T} T{ +54 +T} T{ +36 +T} T{ +54 +T} +_ +T{ +Fr \-> Ra +T} T{ +54 +T} T{ +54 +T} T{ +86 +T} +_ +T{ +Ac \-> Cn +T} T{ +54 +T} T{ +54 +T} T{ +86 +T} +_ +T{ +Nh \-> Og +T} T{ +86 +T} T{ +54 +T} T{ +86 +T} +_ +.TE .sp For elements on the right of the periodic table, \fIqp_set_frozen_core\fP will work as expected. But for elements on the left, a small core will @@ -46,16 +231,26 @@ Lithium atom will have zero. .sp .nf .ft C -qp_set_frozen_core [\-q] EZFIO_DIR +qp_set_frozen_core [\-q|\-\-query] [(\-l|\-s|\-\-large|\-\-small) EZFIO_DIR .ft P .fi .UNINDENT .UNINDENT .INDENT 0.0 .TP -.B \-q +.B \-q, \-\-query Prints in the standard output the number of core electrons. .UNINDENT +.INDENT 0.0 +.TP +.B \-s, \-\-small +Use a small core. +.UNINDENT +.INDENT 0.0 +.TP +.B \-l, \-\-large +Use a large core. +.UNINDENT .SH AUTHOR A. Scemama, E. Giner .SH COPYRIGHT diff --git a/man/qp_set_mo_class.1 b/man/qp_set_mo_class.1 index 3dc3cb76..7cc5b84d 100644 --- a/man/qp_set_mo_class.1 +++ b/man/qp_set_mo_class.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_SET_MO_CLASS" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_SET_MO_CLASS" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_set_mo_class \- | Quantum Package > . diff --git a/man/qp_stop.1 b/man/qp_stop.1 index f183cd2a..6ee8be22 100644 --- a/man/qp_stop.1 +++ b/man/qp_stop.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_STOP" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_STOP" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_stop \- | Quantum Package > . diff --git a/man/qp_update.1 b/man/qp_update.1 index 2270b0d0..89808d41 100644 --- a/man/qp_update.1 +++ b/man/qp_update.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QP_UPDATE" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QP_UPDATE" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qp_update \- | Quantum Package > . diff --git a/man/qpsh.1 b/man/qpsh.1 index 6ece5c35..b8f777e8 100644 --- a/man/qpsh.1 +++ b/man/qpsh.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "QPSH" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "QPSH" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME qpsh \- | Quantum Package > . diff --git a/man/rs_ks_scf.1 b/man/rs_ks_scf.1 index 2c54c2ef..d09e993a 100644 --- a/man/rs_ks_scf.1 +++ b/man/rs_ks_scf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "RS_KS_SCF" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "RS_KS_SCF" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME rs_ks_scf \- | Quantum Package > . diff --git a/man/save_natorb.1 b/man/save_natorb.1 index 3f14b228..930bc613 100644 --- a/man/save_natorb.1 +++ b/man/save_natorb.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SAVE_NATORB" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "SAVE_NATORB" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME save_natorb \- | Quantum Package > . diff --git a/man/save_one_e_dm.1 b/man/save_one_e_dm.1 index f49acb7a..cd8b665d 100644 --- a/man/save_one_e_dm.1 +++ b/man/save_one_e_dm.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SAVE_ONE_E_DM" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "SAVE_ONE_E_DM" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME save_one_e_dm \- | Quantum Package > . @@ -32,15 +32,15 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] .. .INDENT 0.0 .INDENT 3.5 -Program that computes the one body density on the MO basis +Program that computes the one body density on the MO and AO basis for $alpha$ and $beta$ electrons from the wave function stored in the \fI\%EZFIO\fP directory, and then saves it into the module_aux_quantities\&. .sp Then, the global variable \fBaux_quantities data_one_e_dm_alpha_mo\fP -and \fBaux_quantities data_one_e_dm_beta_mo\fP will automatically -read this density in the next calculation. This can be used to perform -damping on the density in RSDFT calculations (see +and \fBaux_quantities data_one_e_dm_beta_mo\fP (and the corresponding for AO) +will automatically ! read this density in the next calculation. +This can be used to perform damping on the density in RSDFT calculations (see module_density_for_dft). .sp Needs: diff --git a/man/save_ortho_mos.1 b/man/save_ortho_mos.1 index 0874c79a..1f168802 100644 --- a/man/save_ortho_mos.1 +++ b/man/save_ortho_mos.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SAVE_ORTHO_MOS" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "SAVE_ORTHO_MOS" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME save_ortho_mos \- | Quantum Package > . diff --git a/man/scf.1 b/man/scf.1 index 1817bebc..4274f341 100644 --- a/man/scf.1 +++ b/man/scf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "SCF" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "SCF" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME scf \- | Quantum Package > . diff --git a/man/write_integrals_erf.1 b/man/write_integrals_erf.1 index e863c478..26f7b984 100644 --- a/man/write_integrals_erf.1 +++ b/man/write_integrals_erf.1 @@ -1,6 +1,6 @@ .\" Man page generated from reStructuredText. . -.TH "WRITE_INTEGRALS_ERF" "1" "Mar 07, 2019" "2.0" "Quantum Package" +.TH "WRITE_INTEGRALS_ERF" "1" "May 28, 2019" "2.0" "Quantum Package" .SH NAME write_integrals_erf \- | Quantum Package > . diff --git a/src/generators_cas/extract_cas.irp.f b/src/generators_cas/extract_cas.irp.f new file mode 100644 index 00000000..9cdaf27f --- /dev/null +++ b/src/generators_cas/extract_cas.irp.f @@ -0,0 +1,23 @@ +subroutine extract_cas + implicit none + BEGIN_DOC + ! Replaces the total wave function by the normalized projection on the CAS. + END_DOC + + integer :: i,j,k + do k=1,N_states + do j=1,N_det_generators + psi_coef(j,k) = psi_coef_generators(j,k) + enddo + enddo + + do j=1,N_det_generators + do k=1,N_int + psi_det(k,1,j) = psi_det_generators(k,1,j) + psi_det(k,2,j) = psi_det_generators(k,2,j) + enddo + enddo + N_det = N_det_generators + + SOFT_TOUCH N_det psi_det psi_coef +end From d50cca6f8825501a680848770d0c5f55600e655b Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 28 May 2019 11:42:36 +0200 Subject: [PATCH 14/36] Updated atomic data --- ocaml/Element.ml | 1043 +++++++++++++++++++++++++++++++++------------ ocaml/Element.mli | 13 +- 2 files changed, 786 insertions(+), 270 deletions(-) diff --git a/ocaml/Element.ml b/ocaml/Element.ml index bd080f00..f0d4455d 100644 --- a/ocaml/Element.ml +++ b/ocaml/Element.ml @@ -3,74 +3,142 @@ open Qptypes exception ElementError of string -type t = -|X +type t = X + |H |He |Li|Be |B |C |N |O |F |Ne |Na|Mg |Al|Si|P |S |Cl|Ar |K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr |Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe - |Pt +|Cs|Ba|La|Hf|Ta|W |Re|Os|Ir|Pt|Au|Hg|Tl|Pb|Bi|Po|At|Rn +|Fr|Ra|Ac|Rf|Db|Sg|Bh|Hs|Mt|Ds|Rg|Cn|Nh|Fl|Mc|Lv|Ts|Og + + |Ce|Pr|Nd|Pm|Sm|Eu|Gd|Tb|Dy|Ho|Er|Tm|Yb|Lu + |Th|Pa|U |Np|Pu|Am|Cm|Bk|Cf|Es|Fm|Md|No|Lr + [@@deriving sexp] let of_string x = match (String.capitalize_ascii (String.lowercase_ascii x)) with -| "X" | "Dummy" -> X -| "H" | "Hydrogen" -> H -| "He" | "Helium" -> He -| "Li" | "Lithium" -> Li -| "Be" | "Beryllium" -> Be -| "B" | "Boron" -> B -| "C" | "Carbon" -> C -| "N" | "Nitrogen" -> N -| "O" | "Oxygen" -> O -| "F" | "Fluorine" -> F -| "Ne" | "Neon" -> Ne -| "Na" | "Sodium" -> Na -| "Mg" | "Magnesium" -> Mg -| "Al" | "Aluminum" -> Al -| "Si" | "Silicon" -> Si -| "P" | "Phosphorus" -> P -| "S" | "Sulfur" -> S -| "Cl" | "Chlorine" -> Cl -| "Ar" | "Argon" -> Ar -| "K" | "Potassium" -> K -| "Ca" | "Calcium" -> Ca -| "Sc" | "Scandium" -> Sc -| "Ti" | "Titanium" -> Ti -| "V" | "Vanadium" -> V -| "Cr" | "Chromium" -> Cr -| "Mn" | "Manganese" -> Mn -| "Fe" | "Iron" -> Fe -| "Co" | "Cobalt" -> Co -| "Ni" | "Nickel" -> Ni -| "Cu" | "Copper" -> Cu -| "Zn" | "Zinc" -> Zn -| "Ga" | "Gallium" -> Ga -| "Ge" | "Germanium" -> Ge -| "As" | "Arsenic" -> As -| "Se" | "Selenium" -> Se -| "Br" | "Bromine" -> Br -| "Kr" | "Krypton" -> Kr -| "Rb" | "Rubidium" -> Rb -| "Sr" | "Strontium" -> Sr -| "Y" | "Yttrium" -> Y -| "Zr" | "Zirconium" -> Zr -| "Nb" | "Niobium" -> Nb -| "Mo" | "Molybdenum" -> Mo -| "Tc" | "Technetium" -> Tc -| "Ru" | "Ruthenium" -> Ru -| "Rh" | "Rhodium" -> Rh -| "Pd" | "Palladium" -> Pd -| "Ag" | "Silver" -> Ag -| "Cd" | "Cadmium" -> Cd -| "In" | "Indium" -> In -| "Sn" | "Tin" -> Sn -| "Sb" | "Antimony" -> Sb -| "Te" | "Tellurium" -> Te -| "I" | "Iodine" -> I -| "Xe" | "Xenon" -> Xe -| "Pt" | "Platinum" -> Pt +| "X" | "Dummy" -> X +| "H" | "Hydrogen" -> H +| "He" | "Helium" -> He +| "Li" | "Lithium" -> Li +| "Be" | "Beryllium" -> Be +| "B" | "Boron" -> B +| "C" | "Carbon" -> C +| "N" | "Nitrogen" -> N +| "O" | "Oxygen" -> O +| "F" | "Fluorine" -> F +| "Ne" | "Neon" -> Ne +| "Na" | "Sodium" -> Na +| "Mg" | "Magnesium" -> Mg +| "Al" | "Aluminum" -> Al +| "Si" | "Silicon" -> Si +| "P" | "Phosphorus" -> P +| "S" | "Sulfur" -> S +| "Cl" | "Chlorine" -> Cl +| "Ar" | "Argon" -> Ar +| "K" | "Potassium" -> K +| "Ca" | "Calcium" -> Ca +| "Sc" | "Scandium" -> Sc +| "Ti" | "Titanium" -> Ti +| "V" | "Vanadium" -> V +| "Cr" | "Chromium" -> Cr +| "Mn" | "Manganese" -> Mn +| "Fe" | "Iron" -> Fe +| "Co" | "Cobalt" -> Co +| "Ni" | "Nickel" -> Ni +| "Cu" | "Copper" -> Cu +| "Zn" | "Zinc" -> Zn +| "Ga" | "Gallium" -> Ga +| "Ge" | "Germanium" -> Ge +| "As" | "Arsenic" -> As +| "Se" | "Selenium" -> Se +| "Br" | "Bromine" -> Br +| "Kr" | "Krypton" -> Kr +| "Rb" | "Rubidium" -> Rb +| "Sr" | "Strontium" -> Sr +| "Y" | "Yttrium" -> Y +| "Zr" | "Zirconium" -> Zr +| "Nb" | "Niobium" -> Nb +| "Mo" | "Molybdenum" -> Mo +| "Tc" | "Technetium" -> Tc +| "Ru" | "Ruthenium" -> Ru +| "Rh" | "Rhodium" -> Rh +| "Pd" | "Palladium" -> Pd +| "Ag" | "Silver" -> Ag +| "Cd" | "Cadmium" -> Cd +| "In" | "Indium" -> In +| "Sn" | "Tin" -> Sn +| "Sb" | "Antimony" -> Sb +| "Te" | "Tellurium" -> Te +| "I" | "Iodine" -> I +| "Xe" | "Xenon" -> Xe +| "Cs" | "Cesium" -> Cs +| "Ba" | "Barium" -> Ba +| "La" | "Lanthanum" -> La +| "Ce" | "Cerium" -> Ce +| "Pr" | "Praseodymium" -> Pr +| "Nd" | "Neodymium" -> Nd +| "Pm" | "Promethium" -> Pm +| "Sm" | "Samarium" -> Sm +| "Eu" | "Europium" -> Eu +| "Gd" | "Gadolinium" -> Gd +| "Tb" | "Terbium" -> Tb +| "Dy" | "Dysprosium" -> Dy +| "Ho" | "Holmium" -> Ho +| "Er" | "Erbium" -> Er +| "Tm" | "Thulium" -> Tm +| "Yb" | "Ytterbium" -> Yb +| "Lu" | "Lutetium" -> Lu +| "Hf" | "Hafnium" -> Hf +| "Ta" | "Tantalum" -> Ta +| "W" | "Tungsten" -> W +| "Re" | "Rhenium" -> Re +| "Os" | "Osmium" -> Os +| "Ir" | "Iridium" -> Ir +| "Pt" | "Platinum" -> Pt +| "Au" | "Gold" -> Au +| "Hg" | "Mercury" -> Hg +| "Tl" | "Thallium" -> Tl +| "Pb" | "Lead" -> Pb +| "Bi" | "Bismuth" -> Bi +| "Po" | "Polonium" -> Po +| "At" | "Astatine" -> At +| "Rn" | "Radon" -> Rn +| "Fr" | "Francium" -> Fr +| "Ra" | "Radium" -> Ra +| "Ac" | "Actinium" -> Ac +| "Th" | "Thorium" -> Th +| "Pa" | "Protactinium" -> Pa +| "U" | "Uranium" -> U +| "Np" | "Neptunium" -> Np +| "Pu" | "Plutonium" -> Pu +| "Am" | "Americium" -> Am +| "Cm" | "Curium" -> Cm +| "Bk" | "Berkelium" -> Bk +| "Cf" | "Californium" -> Cf +| "Es" | "Einsteinium" -> Es +| "Fm" | "Fermium" -> Fm +| "Md" | "Mendelevium" -> Md +| "No" | "Nobelium" -> No +| "Lr" | "Lawrencium" -> Lr +| "Rf" | "Rutherfordium"-> Rf +| "Db" | "Dubnium" -> Db +| "Sg" | "Seaborgium" -> Sg +| "Bh" | "Bohrium" -> Bh +| "Hs" | "Hassium" -> Hs +| "Mt" | "Meitnerium" -> Mt +| "Ds" | "Darmstadtium" -> Ds +| "Rg" | "Roentgenium" -> Rg +| "Cn" | "Copernicium" -> Cn +| "Nh" | "Nihonium" -> Nh +| "Fl" | "Flerovium" -> Fl +| "Mc" | "Moscovium" -> Mc +| "Lv" | "Livermorium" -> Lv +| "Ts" | "Tennessine" -> Ts +| "Og" | "Oganesson" -> Og | x -> raise (ElementError ("Element "^x^" unknown")) @@ -130,7 +198,70 @@ let to_string = function | Te -> "Te" | I -> "I" | Xe -> "Xe" +| Cs -> "Cs" +| Ba -> "Ba" +| La -> "La" +| Hf -> "Hf" +| Ta -> "Ta" +| W -> "W" +| Re -> "Re" +| Os -> "Os" +| Ir -> "Ir" | Pt -> "Pt" +| Au -> "Au" +| Hg -> "Hg" +| Tl -> "Tl" +| Pb -> "Pb" +| Bi -> "Bi" +| Po -> "Po" +| At -> "At" +| Rn -> "Rn" +| Fr -> "Fr" +| Ra -> "Ra" +| Ac -> "Ac" +| Rf -> "Rf" +| Db -> "Db" +| Sg -> "Sg" +| Bh -> "Bh" +| Hs -> "Hs" +| Mt -> "Mt" +| Ds -> "Ds" +| Rg -> "Rg" +| Cn -> "Cn" +| Nh -> "Nh" +| Fl -> "Fl" +| Mc -> "Mc" +| Lv -> "Lv" +| Ts -> "Ts" +| Og -> "Og" +| Ce -> "Ce" +| Pr -> "Pr" +| Nd -> "Nd" +| Pm -> "Pm" +| Sm -> "Sm" +| Eu -> "Eu" +| Gd -> "Gd" +| Tb -> "Tb" +| Dy -> "Dy" +| Ho -> "Ho" +| Er -> "Er" +| Tm -> "Tm" +| Yb -> "Yb" +| Lu -> "Lu" +| Th -> "Th" +| Pa -> "Pa" +| U -> "U" +| Np -> "Np" +| Pu -> "Pu" +| Am -> "Am" +| Cm -> "Cm" +| Bk -> "Bk" +| Cf -> "Cf" +| Es -> "Es" +| Fm -> "Fm" +| Md -> "Md" +| No -> "No" +| Lr -> "Lr" let to_long_string = function @@ -171,26 +302,88 @@ let to_long_string = function | Se -> "Selenium" | Br -> "Bromine" | Kr -> "Krypton" -| Rb -> "Rubidium" -| Sr -> "Strontium" -| Y -> "Yttrium" -| Zr -> "Zirconium" -| Nb -> "Niobium" -| Mo -> "Molybdenum" -| Tc -> "Technetium" -| Ru -> "Ruthenium" -| Rh -> "Rhodium" -| Pd -> "Palladium" -| Ag -> "Silver" -| Cd -> "Cadmium" -| In -> "Indium" -| Sn -> "Tin" -| Sb -> "Antimony" -| Te -> "Tellurium" -| I -> "Iodine" -| Xe -> "Xenon" -| Pt -> "Platinum" - +| Rb -> "Rubidium" +| Sr -> "Strontium" +| Y -> "Yttrium" +| Zr -> "Zirconium" +| Nb -> "Niobium" +| Mo -> "Molybdenum" +| Tc -> "Technetium" +| Ru -> "Ruthenium" +| Rh -> "Rhodium" +| Pd -> "Palladium" +| Ag -> "Silver" +| Cd -> "Cadmium" +| In -> "Indium" +| Sn -> "Tin" +| Sb -> "Antimony" +| Te -> "Tellurium" +| I -> "Iodine" +| Xe -> "Xenon" +| Cs -> "Cesium" +| Ba -> "Barium" +| La -> "Lanthanum" +| Ce -> "Cerium" +| Pr -> "Praseodymium" +| Nd -> "Neodymium" +| Pm -> "Promethium" +| Sm -> "Samarium" +| Eu -> "Europium" +| Gd -> "Gadolinium" +| Tb -> "Terbium" +| Dy -> "Dysprosium" +| Ho -> "Holmium" +| Er -> "Erbium" +| Tm -> "Thulium" +| Yb -> "Ytterbium" +| Lu -> "Lutetium" +| Hf -> "Hafnium" +| Ta -> "Tantalum" +| W -> "Tungsten" +| Re -> "Rhenium" +| Os -> "Osmium" +| Ir -> "Iridium" +| Pt -> "Platinum" +| Au -> "Gold" +| Hg -> "Mercury" +| Tl -> "Thallium" +| Pb -> "Lead" +| Bi -> "Bismuth" +| Po -> "Polonium" +| At -> "Astatine" +| Rn -> "Radon" +| Fr -> "Francium" +| Ra -> "Radium" +| Ac -> "Actinium" +| Th -> "Thorium" +| Pa -> "Protactinium" +| U -> "Uranium" +| Np -> "Neptunium" +| Pu -> "Plutonium" +| Am -> "Americium" +| Cm -> "Curium" +| Bk -> "Berkelium" +| Cf -> "Californium" +| Es -> "Einsteinium" +| Fm -> "Fermium" +| Md -> "Mendelevium" +| No -> "Nobelium" +| Lr -> "Lawrencium" +| Rf -> "Rutherfordium" +| Db -> "Dubnium" +| Sg -> "Seaborgium" +| Bh -> "Bohrium" +| Hs -> "Hassium" +| Mt -> "Meitnerium" +| Ds -> "Darmstadtium" +| Rg -> "Roentgenium" +| Cn -> "Copernicium" +| Nh -> "Nihonium" +| Fl -> "Flerovium" +| Mc -> "Moscovium" +| Lv -> "Livermorium" +| Ts -> "Tennessine" +| Og -> "Oganesson" let to_charge c = let result = match c with @@ -249,109 +442,235 @@ let to_charge c = | 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 + | Nh -> 113 + | Fl -> 114 + | Mc -> 115 + | Lv -> 116 + | Ts -> 117 + | Og -> 118 in Charge.of_int result let of_charge c = match (Charge.to_int c) with -| 0 -> X -| 1 -> H -| 2 -> He -| 3 -> Li -| 4 -> Be -| 5 -> B -| 6 -> C -| 7 -> N -| 8 -> O -| 9 -> F -| 10 -> Ne -| 11 -> Na -| 12 -> Mg -| 13 -> Al -| 14 -> Si -| 15 -> P -| 16 -> S -| 17 -> Cl -| 18 -> Ar -| 19 -> K -| 20 -> Ca -| 21 -> Sc -| 22 -> Ti -| 23 -> V -| 24 -> Cr -| 25 -> Mn -| 26 -> Fe -| 27 -> Co -| 28 -> Ni -| 29 -> Cu -| 30 -> Zn -| 31 -> Ga -| 32 -> Ge -| 33 -> As -| 34 -> Se -| 35 -> Br -| 36 -> Kr -| 37 -> Rb -| 38 -> Sr -| 39 -> Y -| 40 -> Zr -| 41 -> Nb -| 42 -> Mo -| 43 -> Tc -| 44 -> Ru -| 45 -> Rh -| 46 -> Pd -| 47 -> Ag -| 48 -> Cd -| 49 -> In -| 50 -> Sn -| 51 -> Sb -| 52 -> Te -| 53 -> I -| 54 -> Xe -| 78 -> Pt +| 0 -> X +| 1 -> H +| 2 -> He +| 3 -> Li +| 4 -> Be +| 5 -> B +| 6 -> C +| 7 -> N +| 8 -> O +| 9 -> F +| 10 -> Ne +| 11 -> Na +| 12 -> Mg +| 13 -> Al +| 14 -> Si +| 15 -> P +| 16 -> S +| 17 -> Cl +| 18 -> Ar +| 19 -> K +| 20 -> Ca +| 21 -> Sc +| 22 -> Ti +| 23 -> V +| 24 -> Cr +| 25 -> Mn +| 26 -> Fe +| 27 -> Co +| 28 -> Ni +| 29 -> Cu +| 30 -> Zn +| 31 -> Ga +| 32 -> Ge +| 33 -> As +| 34 -> Se +| 35 -> Br +| 36 -> Kr +| 37 -> Rb +| 38 -> Sr +| 39 -> Y +| 40 -> Zr +| 41 -> Nb +| 42 -> Mo +| 43 -> Tc +| 44 -> Ru +| 45 -> Rh +| 46 -> Pd +| 47 -> Ag +| 48 -> Cd +| 49 -> In +| 50 -> Sn +| 51 -> Sb +| 52 -> Te +| 53 -> I +| 54 -> Xe +| 55 -> Cs +| 56 -> Ba +| 57 -> La +| 58 -> Ce +| 59 -> Pr +| 60 -> Nd +| 61 -> Pm +| 62 -> Sm +| 63 -> Eu +| 64 -> Gd +| 65 -> Tb +| 66 -> Dy +| 67 -> Ho +| 68 -> Er +| 69 -> Tm +| 70 -> Yb +| 71 -> Lu +| 72 -> Hf +| 73 -> Ta +| 74 -> W +| 75 -> Re +| 76 -> Os +| 77 -> Ir +| 78 -> Pt +| 79 -> Au +| 80 -> Hg +| 81 -> Tl +| 82 -> Pb +| 83 -> Bi +| 84 -> Po +| 85 -> At +| 86 -> Rn +| 87 -> Fr +| 88 -> Ra +| 89 -> Ac +| 90 -> Th +| 91 -> Pa +| 92 -> U +| 93 -> Np +| 94 -> Pu +| 95 -> Am +| 96 -> Cm +| 97 -> Bk +| 98 -> Cf +| 99 -> Es +| 100 -> Fm +| 101 -> Md +| 102 -> No +| 103 -> Lr +| 104 -> Rf +| 105 -> Db +| 106 -> Sg +| 107 -> Bh +| 108 -> Hs +| 109 -> Mt +| 110 -> Ds +| 111 -> Rg +| 112 -> Cn +| 113 -> Nh +| 114 -> Fl +| 115 -> Mc +| 116 -> Lv +| 117 -> Ts +| 118 -> Og | x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown")) let covalent_radius x = let result = function | X -> 0. - | H -> 0.37 - | He -> 0.70 - | Li -> 1.23 - | Be -> 0.89 - | B -> 0.90 - | C -> 0.85 - | N -> 0.74 - | O -> 0.74 - | F -> 0.72 - | Ne -> 0.70 - | Na -> 1.00 - | Mg -> 1.36 - | Al -> 1.25 - | Si -> 1.17 - | P -> 1.10 - | S -> 1.10 - | Cl -> 0.99 - | Ar -> 0.70 + | H -> 0.31 + | He -> 0.28 + | Li -> 1.28 + | Be -> 0.96 + | B -> 0.85 + | C -> 0.76 + | N -> 0.71 + | O -> 0.66 + | F -> 0.57 + | Ne -> 0.58 + | Na -> 1.66 + | Mg -> 1.41 + | Al -> 1.21 + | Si -> 1.11 + | P -> 1.07 + | S -> 1.05 + | Cl -> 1.02 + | Ar -> 1.06 | K -> 2.03 - | Ca -> 1.74 - | Sc -> 1.44 - | Ti -> 1.32 - | V -> 1.22 - | Cr -> 0.00 - | Mn -> 1.16 - | Fe -> 0.00 - | Co -> 1.15 - | Ni -> 1.17 - | Cu -> 1.25 - | Zn -> 1.25 - | Ga -> 1.20 - | Ge -> 1.21 - | As -> 1.16 - | Se -> 0.70 - | Br -> 1.24 - | Kr -> 1.91 + | Ca -> 1.76 + | Sc -> 1.70 + | Ti -> 1.60 + | V -> 1.53 + | Cr -> 1.39 + | Mn -> 1.39 + | Fe -> 1.32 + | Co -> 1.26 + | Ni -> 1.24 + | Cu -> 1.32 + | Zn -> 1.22 + | Ga -> 1.22 + | Ge -> 1.20 + | As -> 1.19 + | Se -> 1.20 + | Br -> 1.20 + | Kr -> 1.16 | Rb -> 2.20 | Sr -> 1.95 | Y -> 1.90 @@ -370,112 +689,241 @@ let covalent_radius x = | Te -> 1.38 | I -> 1.39 | Xe -> 1.40 - | Pt -> 1.30 + | Cs -> 2.44 + | Ba -> 2.15 + | La -> 2.07 + | Ce -> 2.04 + | Pr -> 2.03 + | Nd -> 2.01 + | Pm -> 1.99 + | Sm -> 1.98 + | Eu -> 1.98 + | Gd -> 1.96 + | Tb -> 1.94 + | Dy -> 1.92 + | Ho -> 1.92 + | Er -> 1.89 + | Tm -> 1.90 + | Yb -> 1.87 + | Lu -> 1.87 + | Hf -> 1.75 + | Ta -> 1.70 + | W -> 1.62 + | Re -> 1.51 + | Os -> 1.44 + | Ir -> 1.41 + | Pt -> 1.36 + | Au -> 1.36 + | Hg -> 1.32 + | Tl -> 1.45 + | Pb -> 1.46 + | Bi -> 1.48 + | Po -> 1.40 + | At -> 1.50 + | Rn -> 1.50 + | Fr -> 2.60 + | Ra -> 2.21 + | Ac -> 2.15 + | Th -> 2.06 + | Pa -> 2.00 + | U -> 1.96 + | Np -> 1.90 + | Pu -> 1.87 + | Am -> 1.80 + | Cm -> 1.69 + | Bk -> raise (ElementError "Covalent radius not defined for Bk") + | Cf -> raise (ElementError "Covalent radius not defined for Cf") + | Es -> raise (ElementError "Covalent radius not defined for Es") + | Fm -> raise (ElementError "Covalent radius not defined for Fm") + | Md -> raise (ElementError "Covalent radius not defined for Md") + | No -> raise (ElementError "Covalent radius not defined for No") + | Lr -> raise (ElementError "Covalent radius not defined for Lr") + | Rf -> raise (ElementError "Covalent radius not defined for Rf") + | Db -> raise (ElementError "Covalent radius not defined for Db") + | Sg -> raise (ElementError "Covalent radius not defined for Sg") + | Bh -> raise (ElementError "Covalent radius not defined for Bh") + | Hs -> raise (ElementError "Covalent radius not defined for Hs") + | Mt -> raise (ElementError "Covalent radius not defined for Mt") + | Ds -> raise (ElementError "Covalent radius not defined for Ds") + | Rg -> raise (ElementError "Covalent radius not defined for Rg") + | Cn -> raise (ElementError "Covalent radius not defined for Cn") + | Nh -> raise (ElementError "Covalent radius not defined for Nh") + | Fl -> raise (ElementError "Covalent radius not defined for Fl") + | Mc -> raise (ElementError "Covalent radius not defined for Mc") + | Lv -> raise (ElementError "Covalent radius not defined for Lv") + | Ts -> raise (ElementError "Covalent radius not defined for Ts") + | Og -> raise (ElementError "Covalent radius not defined for Og") in Units.angstrom_to_bohr *. (result x) |> Positive_float.of_float + let vdw_radius x = let result = function - | X -> 0. - | H -> 1.20 - | He -> 1.70 - | Li -> 1.70 - | Be -> 1.70 - | B -> 1.70 - | C -> 1.70 - | N -> 1.55 - | O -> 1.52 - | F -> 1.47 - | Ne -> 1.70 - | Na -> 1.70 - | Mg -> 1.70 - | Al -> 1.94 - | Si -> 2.10 - | P -> 1.80 - | S -> 1.80 - | Cl -> 1.75 - | Ar -> 1.70 - | K -> 1.70 - | Ca -> 1.70 - | Sc -> 1.70 - | Ti -> 1.70 - | V -> 1.98 - | Cr -> 1.94 - | Mn -> 1.93 - | Fe -> 1.93 - | Co -> 1.92 - | Ni -> 1.70 - | Cu -> 1.70 - | Zn -> 1.70 - | Ga -> 2.02 - | Ge -> 1.70 - | As -> 1.96 - | Se -> 1.70 - | Br -> 2.10 - | Kr -> 1.70 - | Rb -> 3.03 - | Sr -> 2.49 - | Y -> 0. - | Zr -> 0. - | Nb -> 0. - | Mo -> 0. - | Tc -> 0. - | Ru -> 0. - | Rh -> 0. - | Pd -> 1.63 - | Ag -> 1.72 - | Cd -> 1.58 - | In -> 1.93 - | Sn -> 2.17 - | Sb -> 2.06 - | Te -> 2.06 - | I -> 1.98 - | Xe -> 2.16 - | Pt -> 1.75 + | X -> Some 0. + | H -> Some 1.20 + | He -> Some 1.40 + | Li -> Some 1.82 + | Be -> None + | B -> None + | C -> Some 1.70 + | N -> Some 1.55 + | O -> Some 1.52 + | F -> Some 1.47 + | Ne -> Some 1.54 + | Na -> Some 2.27 + | Mg -> Some 1.73 + | Al -> Some 1.94 + | Si -> Some 2.10 + | P -> Some 1.80 + | S -> Some 1.80 + | Cl -> Some 1.75 + | Ar -> Some 1.88 + | K -> Some 2.75 + | Ca -> None + | Sc -> None + | Ti -> None + | V -> Some 1.98 + | Cr -> Some 1.94 + | Mn -> Some 1.93 + | Fe -> Some 1.93 + | Co -> Some 1.92 + | Ni -> Some 1.63 + | Cu -> Some 1.40 + | Zn -> Some 1.39 + | Ga -> Some 1.87 + | Ge -> None + | As -> Some 1.85 + | Se -> Some 1.90 + | Br -> Some 1.85 + | Kr -> Some 2.02 + | Rb -> Some 3.03 + | Sr -> Some 2.49 + | Y -> None + | Zr -> None + | Nb -> None + | Mo -> None + | Tc -> None + | Ru -> None + | Rh -> None + | Pd -> Some 1.63 + | Ag -> Some 1.72 + | Cd -> Some 1.58 + | In -> Some 1.93 + | Sn -> Some 2.17 + | Sb -> Some 2.06 + | Te -> Some 2.06 + | I -> Some 1.98 + | Xe -> Some 2.16 + | Cs -> None + | Ba -> None + | La -> None + | Ce -> None + | Pr -> None + | Nd -> None + | Pm -> None + | Sm -> None + | Eu -> None + | Gd -> None + | Tb -> None + | Dy -> None + | Ho -> None + | Er -> None + | Tm -> None + | Yb -> None + | Lu -> None + | Hf -> None + | Ta -> None + | W -> None + | Re -> None + | Os -> None + | Ir -> None + | Pt -> Some 1.75 + | Au -> Some 1.66 + | Hg -> Some 1.55 + | Tl -> Some 1.96 + | Pb -> Some 2.02 + | Bi -> None + | Po -> None + | At -> None + | Rn -> None + | Fr -> None + | Ra -> None + | Ac -> None + | Th -> None + | Pa -> None + | U -> Some 1.86 + | Np -> None + | Pu -> None + | Am -> None + | Cm -> None + | Bk -> None + | Cf -> None + | Es -> None + | Fm -> None + | Md -> None + | No -> None + | Lr -> None + | Rf -> None + | Db -> None + | Sg -> None + | Bh -> None + | Hs -> None + | Mt -> None + | Ds -> None + | Rg -> None + | Cn -> None + | Nh -> None + | Fl -> None + | Mc -> None + | Lv -> None + | Ts -> None + | Og -> None in - Units.angstrom_to_bohr *. (result x) - |> Positive_float.of_float + match result x with + | Some y -> Some (Positive_float.of_float @@ Units.angstrom_to_bohr *. y ) + | None -> None + let mass x = let result = function - | X -> 0. - | H -> 1.0079 - | He -> 4.00260 - | Li -> 6.941 - | Be -> 9.01218 - | B -> 10.81 - | C -> 12.011 - | N -> 14.0067 - | O -> 15.9994 - | F -> 18.998403 - | Ne -> 20.179 - | Na -> 22.98977 - | Mg -> 24.305 - | Al -> 26.98154 - | Si -> 28.0855 - | P -> 30.97376 - | S -> 32.06 - | Cl -> 35.453 - | Ar -> 39.948 - | K -> 39.0983 - | Ca -> 40.08 - | Sc -> 44.9559 - | Ti -> 47.90 - | V -> 50.9415 - | Cr -> 51.996 - | Mn -> 54.9380 - | Fe -> 55.9332 - | Co -> 58.9332 - | Ni -> 58.70 - | Cu -> 63.546 - | Zn -> 65.38 - | Ga -> 69.72 - | Ge -> 72.59 - | As -> 74.9216 - | Se -> 78.96 - | Br -> 79.904 - | Kr -> 83.80 + | X -> 0. + | H -> 1.0079 + | He -> 4.002602 + | Li -> 6.941 + | Be -> 9.0121831 + | B -> 10.81 + | C -> 12.011 + | N -> 14.0067 + | O -> 15.9994 + | F -> 18.998403163 + | Ne -> 20.1797 + | Na -> 22.98976928 + | Mg -> 24.305 + | Al -> 26.9815385 + | Si -> 28.0855 + | P -> 30.973761998 + | S -> 32.06 + | Cl -> 35.453 + | Ar -> 39.948 + | K -> 39.0983 + | Ca -> 40.078 + | Sc -> 44.955908 + | Ti -> 47.867 + | V -> 50.9415 + | Cr -> 51.9961 + | Mn -> 54.938044 + | Fe -> 55.845 + | Co -> 58.933194 + | Ni -> 58.6934 + | Cu -> 63.546 + | Zn -> 65.38 + | Ga -> 69.723 + | Ge -> 72.630 + | As -> 74.921595 + | Se -> 78.971 + | Br -> 79.904 + | Kr -> 83.798 | Rb -> 85.4678 | Sr -> 87.62 | Y -> 88.90584 @@ -494,7 +942,70 @@ let mass x = | Te -> 127.60 | I -> 126.90447 | Xe -> 131.293 + | Cs -> 132.90545196 + | Ba -> 137.327 + | La -> 138.90547 + | Ce -> 140.116 + | Pr -> 140.90766 + | Nd -> 144.242 + | Pm -> 145. + | Sm -> 150.36 + | Eu -> 151.964 + | Gd -> 157.25 + | Tb -> 158.92535 + | Dy -> 162.500 + | Ho -> 164.93033 + | Er -> 167.259 + | Tm -> 168.93422 + | Yb -> 173.045 + | Lu -> 174.9668 + | Hf -> 178.49 + | Ta -> 180.94788 + | W -> 183.84 + | Re -> 186.207 + | Os -> 190.23 + | Ir -> 192.217 | Pt -> 195.084 + | Au -> 196.966569 + | Hg -> 200.592 + | Tl -> 204.38 + | Pb -> 207.2 + | Bi -> 208.98040 + | Po -> 209. + | At -> 210. + | Rn -> 222. + | Fr -> 223. + | Ra -> 226. + | Ac -> 227. + | Th -> 232.0377 + | Pa -> 231.03588 + | U -> 238.02891 + | Np -> 237. + | Pu -> 244. + | Am -> 243. + | Cm -> 247. + | Bk -> 247. + | Cf -> 251. + | Es -> 252. + | Fm -> 257. + | Md -> 258. + | No -> 259. + | Lr -> 262. + | Rf -> 267. + | Db -> 270. + | Sg -> 269. + | Bh -> 270. + | Hs -> 270. + | Mt -> 278. + | Ds -> 281. + | Rg -> 281. + | Cn -> 285. + | Nh -> 286. + | Fl -> 289. + | Mc -> 289. + | Lv -> 293. + | Ts -> 293. + | Og -> 294. in result x |> Positive_float.of_float diff --git a/ocaml/Element.mli b/ocaml/Element.mli index fc6c679f..cd0f6bff 100644 --- a/ocaml/Element.mli +++ b/ocaml/Element.mli @@ -1,13 +1,18 @@ exception ElementError of string -type t = -|X +type t = X + |H |He |Li|Be |B |C |N |O |F |Ne |Na|Mg |Al|Si|P |S |Cl|Ar |K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr |Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe - |Pt +|Cs|Ba|La|Hf|Ta|W |Re|Os|Ir|Pt|Au|Hg|Tl|Pb|Bi|Po|At|Rn +|Fr|Ra|Ac|Rf|Db|Sg|Bh|Hs|Mt|Ds|Rg|Cn|Nh|Fl|Mc|Lv|Ts|Og + + |Ce|Pr|Nd|Pm|Sm|Eu|Gd|Tb|Dy|Ho|Er|Tm|Yb|Lu + |Th|Pa|U |Np|Pu|Am|Cm|Bk|Cf|Es|Fm|Md|No|Lr + [@@deriving sexp] (** String conversion functions *) @@ -19,5 +24,5 @@ val to_long_string : t -> string val to_charge : t -> Charge.t val of_charge : Charge.t -> t val covalent_radius : t -> Qptypes.Positive_float.t -val vdw_radius : t -> Qptypes.Positive_float.t +val vdw_radius : t -> Qptypes.Positive_float.t option val mass : t -> Qptypes.Positive_float.t From 982855eeb5103277850ee1b17e77e8cf9f164e0e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 28 May 2019 15:39:07 +0200 Subject: [PATCH 15/36] AVX work with AMD --- config/ifort_avx.cfg | 2 +- config/ifort_avx_mpi.cfg | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/ifort_avx.cfg b/config/ifort_avx.cfg index d3fcd1f0..7a13348c 100644 --- a/config/ifort_avx.cfg +++ b/config/ifort_avx.cfg @@ -32,7 +32,7 @@ OPENMP : 1 ; Append OpenMP flags # [OPT] FC : -traceback -FCFLAGS : -xAVX -O2 -ip -ftz -g +FCFLAGS : -march=corei7-avx -O2 -ip -ftz -g # Profiling flags ################# diff --git a/config/ifort_avx_mpi.cfg b/config/ifort_avx_mpi.cfg index a6784058..550dbf91 100644 --- a/config/ifort_avx_mpi.cfg +++ b/config/ifort_avx_mpi.cfg @@ -31,14 +31,14 @@ OPENMP : 1 ; Append OpenMP flags # -ftz : Flushes denormal results to zero # [OPT] -FCFLAGS : -xAVX -O2 -ip -ftz -g -traceback +FCFLAGS : -march=corei7-avx -O2 -ip -ftz -g -traceback # Profiling flags ################# # [PROFILE] FC : -p -g -FCFLAGS : -xSSE4.2 -O2 -ip -ftz +FCFLAGS : -march=corei7 -O2 -ip -ftz # Debugging flags From 96c17686b447cca1dd0a5e97446fc76a6e87280f Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 28 May 2019 18:49:21 +0200 Subject: [PATCH 16/36] fixed bugs with dummy atom and becke grid --- src/becke_numerical_grid/atomic_number.irp.f | 9 +++++++++ src/becke_numerical_grid/grid_becke.irp.f | 6 +++--- src/becke_numerical_grid/grid_becke_vector.irp.f | 3 ++- src/becke_numerical_grid/step_function_becke.irp.f | 5 ----- src/nuclei/atomic_radii.irp.f | 4 ++-- 5 files changed, 16 insertions(+), 11 deletions(-) create mode 100644 src/becke_numerical_grid/atomic_number.irp.f diff --git a/src/becke_numerical_grid/atomic_number.irp.f b/src/becke_numerical_grid/atomic_number.irp.f new file mode 100644 index 00000000..eea1fad7 --- /dev/null +++ b/src/becke_numerical_grid/atomic_number.irp.f @@ -0,0 +1,9 @@ +BEGIN_PROVIDER [ integer, grid_atomic_number, (nucl_num) ] + implicit none + BEGIN_DOC + ! Atomic number used to adjust the grid + END_DOC + grid_atomic_number(:) = max(1,int(nucl_charge(:))) + +END_PROVIDER + diff --git a/src/becke_numerical_grid/grid_becke.irp.f b/src/becke_numerical_grid/grid_becke.irp.f index 38d4053f..e72f6460 100644 --- a/src/becke_numerical_grid/grid_becke.irp.f +++ b/src/becke_numerical_grid/grid_becke.irp.f @@ -146,7 +146,7 @@ BEGIN_PROVIDER [double precision, grid_points_per_atom, (3,n_points_integration_ x = grid_points_radial(j) ! value of the radial coordinate for the integration - r = knowles_function(alpha_knowles(int(nucl_charge(i))),m_knowles,x) + r = knowles_function(alpha_knowles(grid_atomic_number(i)),m_knowles,x) ! explicit values of the grid points centered around each atom do k = 1, n_points_integration_angular @@ -232,8 +232,8 @@ BEGIN_PROVIDER [double precision, final_weight_at_r, (n_points_integration_angul do i = 1, n_points_radial_grid -1 !for each radial grid attached to the "jth" atom x = grid_points_radial(i) ! x value for the mapping of the [0, +\infty] to [0,1] do k = 1, n_points_integration_angular ! for each angular point attached to the "jth" atom - contrib_integration = derivative_knowles_function(alpha_knowles(int(nucl_charge(j))),m_knowles,x)& - *knowles_function(alpha_knowles(int(nucl_charge(j))),m_knowles,x)**2 + contrib_integration = derivative_knowles_function(alpha_knowles(grid_atomic_number(j)),m_knowles,x)& + *knowles_function(alpha_knowles(grid_atomic_number(j)),m_knowles,x)**2 final_weight_at_r(k,i,j) = weights_angular_points(k) * weight_at_r(k,i,j) * contrib_integration * dr_radial_integral if(isnan(final_weight_at_r(k,i,j)))then print*,'isnan(final_weight_at_r(k,i,j))' diff --git a/src/becke_numerical_grid/grid_becke_vector.irp.f b/src/becke_numerical_grid/grid_becke_vector.irp.f index 9856bcbd..3c2a6b91 100644 --- a/src/becke_numerical_grid/grid_becke_vector.irp.f +++ b/src/becke_numerical_grid/grid_becke_vector.irp.f @@ -1,5 +1,6 @@ BEGIN_PROVIDER [integer, n_points_final_grid] + implicit none BEGIN_DOC ! Number of points which are non zero END_DOC @@ -8,7 +9,7 @@ BEGIN_PROVIDER [integer, n_points_final_grid] do j = 1, nucl_num do i = 1, n_points_radial_grid -1 do k = 1, n_points_integration_angular - if(dabs(final_weight_at_r(k,i,j)) < tresh_grid)then + if(dabs(final_weight_at_r(k,i,j)) < thresh_grid)then cycle endif n_points_final_grid += 1 diff --git a/src/becke_numerical_grid/step_function_becke.irp.f b/src/becke_numerical_grid/step_function_becke.irp.f index b6335c3d..2905c6c0 100644 --- a/src/becke_numerical_grid/step_function_becke.irp.f +++ b/src/becke_numerical_grid/step_function_becke.irp.f @@ -31,10 +31,6 @@ double precision function cell_function_becke(r,atom_number) double precision :: mu_ij,nu_ij double precision :: distance_i,distance_j,step_function_becke integer :: j - if(int(nucl_charge(atom_number))==0)then - cell_function_becke = 0.d0 - return - endif distance_i = (r(1) - nucl_coord_transp(1,atom_number) ) * (r(1) - nucl_coord_transp(1,atom_number)) distance_i += (r(2) - nucl_coord_transp(2,atom_number) ) * (r(2) - nucl_coord_transp(2,atom_number)) distance_i += (r(3) - nucl_coord_transp(3,atom_number) ) * (r(3) - nucl_coord_transp(3,atom_number)) @@ -42,7 +38,6 @@ double precision function cell_function_becke(r,atom_number) cell_function_becke = 1.d0 do j = 1, nucl_num if(j==atom_number)cycle - if(int(nucl_charge(j))==0)cycle distance_j = (r(1) - nucl_coord_transp(1,j) ) * (r(1) - nucl_coord_transp(1,j)) distance_j+= (r(2) - nucl_coord_transp(2,j) ) * (r(2) - nucl_coord_transp(2,j)) distance_j+= (r(3) - nucl_coord_transp(3,j) ) * (r(3) - nucl_coord_transp(3,j)) diff --git a/src/nuclei/atomic_radii.irp.f b/src/nuclei/atomic_radii.irp.f index 82487b9d..439b5cec 100644 --- a/src/nuclei/atomic_radii.irp.f +++ b/src/nuclei/atomic_radii.irp.f @@ -66,7 +66,7 @@ BEGIN_PROVIDER [double precision, slater_bragg_radii_per_atom, (nucl_num)] implicit none integer :: i do i = 1, nucl_num - slater_bragg_radii_per_atom(i) = slater_bragg_radii(int(nucl_charge(i))) + slater_bragg_radii_per_atom(i) = slater_bragg_radii(max(1,int(nucl_charge(i)))) enddo END_PROVIDER @@ -74,7 +74,7 @@ BEGIN_PROVIDER [double precision, slater_bragg_radii_per_atom_ua, (nucl_num)] implicit none integer :: i do i = 1, nucl_num - slater_bragg_radii_per_atom_ua(i) = slater_bragg_radii_ua(int(nucl_charge(i))) + slater_bragg_radii_per_atom_ua(i) = slater_bragg_radii_ua(max(1,int(nucl_charge(i)))) enddo END_PROVIDER From fedc20dc3113930f046e71423a00440aae9259f0 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 11:14:42 +0200 Subject: [PATCH 17/36] rPT2 matching instead of pt2 matching --- src/cipsi/cipsi.irp.f | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cipsi/cipsi.irp.f b/src/cipsi/cipsi.irp.f index f0cab384..d5cf4085 100644 --- a/src/cipsi/cipsi.irp.f +++ b/src/cipsi/cipsi.irp.f @@ -65,7 +65,7 @@ subroutine run_cipsi do while ( & (N_det < N_det_max) .and. & - (maxval(abs(pt2(1:N_states))) > pt2_max) .and. & + (maxval(abs(rpt2(1:N_states))) > pt2_max) .and. & (correlation_energy_ratio <= correlation_energy_ratio_max) & ) write(*,'(A)') '--------------------------------------------------------------------------------' From e53e7585f925c98e7c80fc5e059aa021a5bcf6ce Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 11:15:43 +0200 Subject: [PATCH 18/36] Fixed rPT2 small bug --- src/cipsi/cipsi.irp.f | 6 +++--- src/cipsi/stochastic_cipsi.irp.f | 4 ++-- src/fci/pt2.irp.f | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/cipsi/cipsi.irp.f b/src/cipsi/cipsi.irp.f index d5cf4085..ef3dd8ee 100644 --- a/src/cipsi/cipsi.irp.f +++ b/src/cipsi/cipsi.irp.f @@ -92,7 +92,7 @@ subroutine run_cipsi call print_summary(psi_energy_with_nucl_rep(1:N_states),pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) do k=1,N_states - rpt2(:) = pt2(:)/(1.d0 + norm(k)) + rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo call save_energy(psi_energy_with_nucl_rep, rpt2) @@ -137,7 +137,7 @@ subroutine run_cipsi norm,0) ! Stochastic PT2 SOFT_TOUCH threshold_generators do k=1,N_states - rpt2(:) = pt2(:)/(1.d0 + norm(k)) + rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo call save_energy(psi_energy_with_nucl_rep, pt2) endif @@ -148,7 +148,7 @@ subroutine run_cipsi do k=1,N_states - rpt2(:) = pt2(:)/(1.d0 + norm(k)) + rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo call save_energy(psi_energy_with_nucl_rep, rpt2) diff --git a/src/cipsi/stochastic_cipsi.irp.f b/src/cipsi/stochastic_cipsi.irp.f index 157479d9..a598f080 100644 --- a/src/cipsi/stochastic_cipsi.irp.f +++ b/src/cipsi/stochastic_cipsi.irp.f @@ -88,7 +88,7 @@ subroutine run_stochastic_cipsi call print_summary(psi_energy_with_nucl_rep,pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) do k=1,N_states - rpt2(:) = pt2(:)/(1.d0 + norm(k)) + rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo call save_energy(psi_energy_with_nucl_rep, rpt2) @@ -128,7 +128,7 @@ subroutine run_stochastic_cipsi norm,0) ! Stochastic PT2 do k=1,N_states - rpt2(:) = pt2(:)/(1.d0 + norm(k)) + rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo call save_energy(psi_energy_with_nucl_rep, rpt2) diff --git a/src/fci/pt2.irp.f b/src/fci/pt2.irp.f index 45860fb5..6135864f 100644 --- a/src/fci/pt2.irp.f +++ b/src/fci/pt2.irp.f @@ -46,7 +46,7 @@ subroutine run call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, & norm,0) ! Stochastic PT2 do k=1,N_states - rpt2(:) = pt2(:)/(1.d0 + norm(k)) + rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo call print_summary(psi_energy_with_nucl_rep(1:N_states),pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) From ce0a5f4e700b354b634395949baa1c8d3ab2745b Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 11:16:20 +0200 Subject: [PATCH 19/36] Added selection factor --- src/cipsi/cipsi.irp.f | 3 +-- src/cipsi/stochastic_cipsi.irp.f | 2 +- src/determinants/EZFIO.cfg | 5 +++++ 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/src/cipsi/cipsi.irp.f b/src/cipsi/cipsi.irp.f index ef3dd8ee..b07ab22f 100644 --- a/src/cipsi/cipsi.irp.f +++ b/src/cipsi/cipsi.irp.f @@ -103,9 +103,8 @@ subroutine run_cipsi if (qp_stop()) exit n_det_before = N_det - to_select = N_det + to_select = N_det*int(sqrt(dble(N_states)))*selection_factor to_select = max(N_states_diag, to_select) -! to_select = min(to_select, N_det_max-n_det_before) call ZMQ_selection(to_select, pt2, variance, norm) PROVIDE psi_coef diff --git a/src/cipsi/stochastic_cipsi.irp.f b/src/cipsi/stochastic_cipsi.irp.f index a598f080..98e842e5 100644 --- a/src/cipsi/stochastic_cipsi.irp.f +++ b/src/cipsi/stochastic_cipsi.irp.f @@ -70,7 +70,7 @@ subroutine run_stochastic_cipsi write(*,'(A)') '--------------------------------------------------------------------------------' - to_select = N_det*int(sqrt(dble(N_states))) + to_select = N_det*int(sqrt(dble(N_states)))*selection_factor to_select = max(N_states_diag, to_select) pt2 = 0.d0 diff --git a/src/determinants/EZFIO.cfg b/src/determinants/EZFIO.cfg index b8fc7406..fdda9be2 100644 --- a/src/determinants/EZFIO.cfg +++ b/src/determinants/EZFIO.cfg @@ -89,6 +89,11 @@ doc: Weight of the states in state-average calculations. interface: ezfio size: (determinants.n_states) +[selection_factor] +type: double precision +doc: f such that the number of determinants to add is f * N_det * sqrt(N_states) +interface: ezfio,provider,ocaml +default: 1. [thresh_sym] type: Threshold From 4a72ca6b12034d1528d19bbedea614c149b292a1 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 11:16:47 +0200 Subject: [PATCH 20/36] Added switch for multiple selection weights, including variance --- src/cipsi/pt2_stoch_routines.irp.f | 8 +--- src/cipsi/selection.irp.f | 63 ++++++++++++++++++++++++++- src/determinants/EZFIO.cfg | 8 +++- src/determinants/density_matrix.irp.f | 4 +- 4 files changed, 72 insertions(+), 11 deletions(-) diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index 0e143a9c..994b98f3 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -333,13 +333,7 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in) pt2(k) = 0.d0 enddo - ! Adjust PT2 weights for next selection - double precision :: pt2_avg - pt2_avg = sum(pt2) / dble(N_states) - do k=1,N_states - pt2_match_weight(k) *= (pt2(k)/pt2_avg)**2 - enddo - SOFT_TOUCH pt2_match_weight + call update_pt2_and_variance_weights(pt2, variance, norm) end subroutine diff --git a/src/cipsi/selection.irp.f b/src/cipsi/selection.irp.f index eedcd67f..ba2caa1b 100644 --- a/src/cipsi/selection.irp.f +++ b/src/cipsi/selection.irp.f @@ -9,12 +9,73 @@ BEGIN_PROVIDER [ double precision, pt2_match_weight, (N_states) ] pt2_match_weight = 1.d0 END_PROVIDER +BEGIN_PROVIDER [ double precision, variance_match_weight, (N_states) ] + implicit none + BEGIN_DOC + ! Weights adjusted along the selection to make the variances + ! of each state coincide. + END_DOC + variance_match_weight = 1.d0 +END_PROVIDER + +subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_states) + implicit none + BEGIN_DOC +! Updates the rPT2- and Variance- matching weights. + END_DOC + integer, intent(in) :: N_st + double precision, intent(in) :: pt2(N_st) + double precision, intent(in) :: variance(N_st) + double precision, intent(in) :: norm(N_st) + + double precision :: avg, rpt2(N_st) + integer :: k + + do k=1,N_st + rpt2(k) = pt2(k)/(1.d0 + norm(k)) + enddo + + avg = sum(rpt2(1:N_st)) / dble(N_st) + do k=1,N_states + pt2_match_weight(k) *= (rpt2(k)/avg)**2 + enddo + + avg = sum(variance(1:N_st)) / dble(N_st) + do k=1,N_states + variance_match_weight(k) *= (variance(k)/avg)**2 + enddo + + SOFT_TOUCH pt2_match_weight variance_match_weight +end + + BEGIN_PROVIDER [ double precision, selection_weight, (N_states) ] implicit none BEGIN_DOC ! Weights used in the selection criterion END_DOC - selection_weight(1:N_states) = c0_weight(1:N_states) * pt2_match_weight(1:N_states) + select (weight_selection) + + case (0) + selection_weight(1:N_states) = weight_one_e_dm(1:N_states) + + case (1) + selection_weight(1:N_states) = c0_weight(1:N_states) + + case (2) + selection_weight(1:N_states) = c0_weight(1:N_states) * pt2_match_weight(1:N_states) + + case (3) + selection_weight(1:N_states) = c0_weight(1:N_states) * variance_match_weight(1:N_states) + + case (4) + selection_weight(1:N_states) = c0_weight(1:N_states) * variance_match_weight(1:N_states) * pt2_match_weight(1:N_states) + + case (5) + selection_weight(1:N_states) = c0_weight(1:N_states) * variance_match_weight(1:N_states) + + end select + END_PROVIDER diff --git a/src/determinants/EZFIO.cfg b/src/determinants/EZFIO.cfg index fdda9be2..95128969 100644 --- a/src/determinants/EZFIO.cfg +++ b/src/determinants/EZFIO.cfg @@ -28,12 +28,18 @@ doc: Force the wave function to be an eigenfunction of |S^2| interface: ezfio,provider,ocaml default: True -[used_weight] +[weight_one_e_dm] type: integer doc: Weight used in the calculation of the one-electron density matrix. 0: 1./(c_0^2), 1: 1/N_states, 2: input state-average weight, 3: 1/(Norm_L3(Psi)) interface: ezfio,provider,ocaml default: 1 +[weight_selection] +type: integer +doc: Weight used in the selection. 0: input state-average weight, 1: 1./(c_0^2), 2: rPT2 matching, 3: variance matching, 4: variance and rPT2 matching, 5: variance minimization and matching +interface: ezfio,provider,ocaml +default: 2 + [threshold_generators] type: Threshold doc: Thresholds on generators (fraction of the square of the norm) diff --git a/src/determinants/density_matrix.irp.f b/src/determinants/density_matrix.irp.f index a9630977..e4f76bca 100644 --- a/src/determinants/density_matrix.irp.f +++ b/src/determinants/density_matrix.irp.f @@ -305,9 +305,9 @@ BEGIN_PROVIDER [ double precision, state_average_weight, (N_states) ] logical :: exists state_average_weight(:) = 1.d0 - if (used_weight == 0) then + if (weight_one_e_dm == 0) then state_average_weight(:) = c0_weight(:) - else if (used_weight == 1) then + else if (weight_one_e_dm == 1) then state_average_weight(:) = 1./N_states else call ezfio_has_determinants_state_average_weight(exists) From 6455b281ffc4a866f2f22232e2961105316a5c64 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 11:42:55 +0200 Subject: [PATCH 21/36] Compiles --- src/cipsi/pt2_stoch_routines.irp.f | 2 +- src/cipsi/selection.irp.f | 24 +++++++++++++----------- src/cipsi/zmq_selection.irp.f | 14 ++++++-------- 3 files changed, 20 insertions(+), 20 deletions(-) diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index 994b98f3..d101c6e0 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -333,7 +333,7 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in) pt2(k) = 0.d0 enddo - call update_pt2_and_variance_weights(pt2, variance, norm) + call update_pt2_and_variance_weights(pt2, variance, norm, N_states) end subroutine diff --git a/src/cipsi/selection.irp.f b/src/cipsi/selection.irp.f index ba2caa1b..4b527874 100644 --- a/src/cipsi/selection.irp.f +++ b/src/cipsi/selection.irp.f @@ -6,7 +6,7 @@ BEGIN_PROVIDER [ double precision, pt2_match_weight, (N_states) ] ! Weights adjusted along the selection to make the PT2 contributions ! of each state coincide. END_DOC - pt2_match_weight = 1.d0 + pt2_match_weight(:) = 1.d0 END_PROVIDER BEGIN_PROVIDER [ double precision, variance_match_weight, (N_states) ] @@ -15,10 +15,10 @@ BEGIN_PROVIDER [ double precision, variance_match_weight, (N_states) ] ! Weights adjusted along the selection to make the variances ! of each state coincide. END_DOC - variance_match_weight = 1.d0 + variance_match_weight(:) = 1.d0 END_PROVIDER -subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_states) +subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) implicit none BEGIN_DOC ! Updates the rPT2- and Variance- matching weights. @@ -36,12 +36,12 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_states) enddo avg = sum(rpt2(1:N_st)) / dble(N_st) - do k=1,N_states + do k=1,N_st pt2_match_weight(k) *= (rpt2(k)/avg)**2 enddo avg = sum(variance(1:N_st)) / dble(N_st) - do k=1,N_states + do k=1,N_st variance_match_weight(k) *= (variance(k)/avg)**2 enddo @@ -54,10 +54,10 @@ BEGIN_PROVIDER [ double precision, selection_weight, (N_states) ] BEGIN_DOC ! Weights used in the selection criterion END_DOC - select (weight_selection) + select case (weight_selection) case (0) - selection_weight(1:N_states) = weight_one_e_dm(1:N_states) + selection_weight(1:N_states) = state_average_weight(1:N_states) case (1) selection_weight(1:N_states) = c0_weight(1:N_states) @@ -682,11 +682,13 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d variance(istate) = variance(istate) + alpha_h_psi * alpha_h_psi norm(istate) = norm(istate) + coef * coef -! if (h0_type == "Variance") then -! sum_e_pert = sum_e_pert - alpha_h_psi * alpha_h_psi * selection_weight(istate) -! else + if (weight_selection /= 5) then + ! Energy selection sum_e_pert = sum_e_pert + e_pert * selection_weight(istate) -! endif + else + ! Variance selection + sum_e_pert = sum_e_pert - alpha_h_psi * alpha_h_psi * selection_weight(istate) + endif end do if(pseudo_sym)then if(dabs(mat(1, p1, p2)).lt.thresh_sym)then diff --git a/src/cipsi/zmq_selection.irp.f b/src/cipsi/zmq_selection.irp.f index c7c11eec..b9bd1d02 100644 --- a/src/cipsi/zmq_selection.irp.f +++ b/src/cipsi/zmq_selection.irp.f @@ -85,7 +85,11 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm) endif integer :: nproc_target - nproc_target = nproc + if (N_det < 3*nproc) then + nproc_target = N_det/3 + else + nproc_target = nproc + endif double precision :: mem mem = 8.d0 * N_det * (N_int * 2.d0 * 3.d0 + 3.d0 + 5.d0) / (1024.d0**3) call write_double(6,mem,'Estimated memory/thread (Gb)') @@ -131,13 +135,7 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm) norm(k) = norm(k) * f(k) enddo - ! Adjust PT2 weights for next selection - double precision :: pt2_avg - pt2_avg = sum(pt2) / dble(N_states) - do k=1,N_states - pt2_match_weight(k) *= (pt2(k)/pt2_avg)**2 - enddo - SOFT_TOUCH pt2_match_weight + call update_pt2_and_variance_weights(pt2, variance, norm, N_states) end subroutine From bd9816d6e307783958a7c3fad2b17be8a3d942cb Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 18:10:56 +0200 Subject: [PATCH 22/36] Fixed ZMQ stalling because of pseudo_sym --- src/cipsi/pt2_stoch_routines.irp.f | 4 ++-- src/cipsi/run_selection_slave.irp.f | 4 ++-- src/cipsi/slave_cipsi.irp.f | 2 +- src/cipsi/zmq_selection.irp.f | 10 +++++----- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index d101c6e0..7cb834d9 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -129,13 +129,13 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in) PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns PROVIDE psi_bilinear_matrix_transp_order psi_selectors_coef_transp psi_det_sorted - PROVIDE psi_det_hii N_generators_bitmask + PROVIDE psi_det_hii N_generators_bitmask selection_weight pseudo_sym if (h0_type == 'SOP') then PROVIDE psi_occ_pattern_hii det_to_occ_pattern endif - if (N_det < max(1000,N_states)) then + if (N_det < max(4,N_states)) then pt2=0.d0 variance=0.d0 norm=0.d0 diff --git a/src/cipsi/run_selection_slave.irp.f b/src/cipsi/run_selection_slave.irp.f index 480ef12b..ee97eb20 100644 --- a/src/cipsi/run_selection_slave.irp.f +++ b/src/cipsi/run_selection_slave.irp.f @@ -25,8 +25,8 @@ subroutine run_selection_slave(thread,iproc,energy) 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 PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns - PROVIDE psi_bilinear_matrix_transp_order N_int pt2_F - PROVIDE psi_selectors_coef_transp psi_det_sorted + PROVIDE psi_bilinear_matrix_transp_order N_int pt2_F pseudo_sym + PROVIDE psi_selectors_coef_transp psi_det_sorted weight_selection zmq_to_qp_run_socket = new_zmq_to_qp_run_socket() diff --git a/src/cipsi/slave_cipsi.irp.f b/src/cipsi/slave_cipsi.irp.f index 58b53f94..8668db01 100644 --- a/src/cipsi/slave_cipsi.irp.f +++ b/src/cipsi/slave_cipsi.irp.f @@ -17,7 +17,7 @@ subroutine provide_everything PROVIDE H_apply_buffer_allocated mo_two_e_integrals_in_map psi_det_generators psi_coef_generators psi_det_sorted_bit psi_selectors n_det_generators n_states generators_bitmask zmq_context N_states_diag PROVIDE pt2_e0_denominator mo_num N_int ci_energy mpi_master zmq_state zmq_context PROVIDE psi_det psi_coef threshold_generators state_average_weight - PROVIDE N_det_selectors pt2_stoch_istate N_det + PROVIDE N_det_selectors pt2_stoch_istate N_det selection_weight pseudo_sym end subroutine run_slave_main diff --git a/src/cipsi/zmq_selection.irp.f b/src/cipsi/zmq_selection.irp.f index b9bd1d02..816221e2 100644 --- a/src/cipsi/zmq_selection.irp.f +++ b/src/cipsi/zmq_selection.irp.f @@ -21,7 +21,7 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm) 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 PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns - PROVIDE psi_bilinear_matrix_transp_order + PROVIDE psi_bilinear_matrix_transp_order selection_weight pseudo_sym call new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'selection') @@ -86,7 +86,7 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm) integer :: nproc_target if (N_det < 3*nproc) then - nproc_target = N_det/3 + nproc_target = N_det/4 else nproc_target = nproc endif @@ -157,9 +157,9 @@ subroutine selection_collector(zmq_socket_pull, b, N, pt2, variance, norm) integer(ZMQ_PTR), intent(in) :: zmq_socket_pull type(selection_buffer), intent(inout) :: b integer, intent(in) :: N - double precision, intent(inout) :: pt2(N_states) - double precision, intent(inout) :: variance(N_states) - double precision, intent(inout) :: norm(N_states) + double precision, intent(out) :: pt2(N_states) + double precision, intent(out) :: variance(N_states) + double precision, intent(out) :: norm(N_states) double precision :: pt2_mwen(N_states) double precision :: variance_mwen(N_states) double precision :: norm_mwen(N_states) From f514ba0acd32394039ba3b041c70c222e549989e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 18:11:50 +0200 Subject: [PATCH 23/36] Fixed bug in deterministic variance --- src/cipsi/run_selection_slave.irp.f | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/cipsi/run_selection_slave.irp.f b/src/cipsi/run_selection_slave.irp.f index ee97eb20..c1542445 100644 --- a/src/cipsi/run_selection_slave.irp.f +++ b/src/cipsi/run_selection_slave.irp.f @@ -230,6 +230,8 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det endif else pt2(:) = 0.d0 + variance(:) = 0.d0 + norm(:) = 0.d0 endif rc = f77_zmq_recv( zmq_socket_pull, ntask, 4, 0) From 04ca07a5403fb5a31aaf4426a21ebdd0bacdb881 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 4 Jun 2019 18:12:55 +0200 Subject: [PATCH 24/36] Modified weighted selection for exp --- src/cipsi/selection.irp.f | 16 +++++++++++++--- src/cipsi/zmq_selection.irp.f | 1 + 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/src/cipsi/selection.irp.f b/src/cipsi/selection.irp.f index 4b527874..88b05554 100644 --- a/src/cipsi/selection.irp.f +++ b/src/cipsi/selection.irp.f @@ -28,22 +28,32 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) double precision, intent(in) :: variance(N_st) double precision, intent(in) :: norm(N_st) - double precision :: avg, rpt2(N_st) + double precision :: avg, rpt2(N_st), element, dt, x integer :: k + dt = 2.d0 * selection_factor + do k=1,N_st rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo avg = sum(rpt2(1:N_st)) / dble(N_st) do k=1,N_st - pt2_match_weight(k) *= (rpt2(k)/avg)**2 + element = exp(dt*(rpt2(k)/avg -1.d0)) + element = max(0.8d0, element) + element = min(1.2d0 , element) + pt2_match_weight(k) *= element enddo avg = sum(variance(1:N_st)) / dble(N_st) do k=1,N_st - variance_match_weight(k) *= (variance(k)/avg)**2 + element = exp(dt*(variance(k)/avg -1.d0)) + element = max(0.8d0, element) + element = min(1.2d0 , element) + variance_match_weight(k) *= element enddo + print *, "rPT2-weights:", real(pt2_match_weight(:),4) + print *, "Variance-weights:", real(variance_match_weight(:),4) SOFT_TOUCH pt2_match_weight variance_match_weight end diff --git a/src/cipsi/zmq_selection.irp.f b/src/cipsi/zmq_selection.irp.f index 816221e2..9562bbe0 100644 --- a/src/cipsi/zmq_selection.irp.f +++ b/src/cipsi/zmq_selection.irp.f @@ -23,6 +23,7 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm) PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns PROVIDE psi_bilinear_matrix_transp_order selection_weight pseudo_sym + call new_parallel_job(zmq_to_qp_run_socket,zmq_socket_pull,'selection') integer, external :: zmq_put_psi From 453cfa0b65e982a2c9f6bb627bf9d859f06f3358 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 15:07:36 +0200 Subject: [PATCH 25/36] Improved weights --- src/cipsi/selection.irp.f | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/cipsi/selection.irp.f b/src/cipsi/selection.irp.f index 88b05554..0237e064 100644 --- a/src/cipsi/selection.irp.f +++ b/src/cipsi/selection.irp.f @@ -31,7 +31,7 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) double precision :: avg, rpt2(N_st), element, dt, x integer :: k - dt = 2.d0 * selection_factor + dt = n_iter * selection_factor do k=1,N_st rpt2(k) = pt2(k)/(1.d0 + norm(k)) @@ -40,7 +40,6 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) avg = sum(rpt2(1:N_st)) / dble(N_st) do k=1,N_st element = exp(dt*(rpt2(k)/avg -1.d0)) - element = max(0.8d0, element) element = min(1.2d0 , element) pt2_match_weight(k) *= element enddo @@ -48,12 +47,9 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) avg = sum(variance(1:N_st)) / dble(N_st) do k=1,N_st element = exp(dt*(variance(k)/avg -1.d0)) - element = max(0.8d0, element) element = min(1.2d0 , element) variance_match_weight(k) *= element enddo - print *, "rPT2-weights:", real(pt2_match_weight(:),4) - print *, "Variance-weights:", real(variance_match_weight(:),4) SOFT_TOUCH pt2_match_weight variance_match_weight end @@ -67,21 +63,27 @@ BEGIN_PROVIDER [ double precision, selection_weight, (N_states) ] select case (weight_selection) case (0) + print *, 'Using input weights in selection' selection_weight(1:N_states) = state_average_weight(1:N_states) case (1) + print *, 'Using 1/c_max^2 weight in selection' selection_weight(1:N_states) = c0_weight(1:N_states) case (2) + print *, 'Using pt2-matching weight in selection' selection_weight(1:N_states) = c0_weight(1:N_states) * pt2_match_weight(1:N_states) case (3) + print *, 'Using variance-matching weight in selection' selection_weight(1:N_states) = c0_weight(1:N_states) * variance_match_weight(1:N_states) case (4) + print *, 'Using variance- and pt2-matching weights in selection' selection_weight(1:N_states) = c0_weight(1:N_states) * variance_match_weight(1:N_states) * pt2_match_weight(1:N_states) case (5) + print *, 'Using variance-matching weight in selection' selection_weight(1:N_states) = c0_weight(1:N_states) * variance_match_weight(1:N_states) end select From 7c285bddf3d839e155076f8135dc3176ad1e4e5d Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 15:38:05 +0200 Subject: [PATCH 26/36] Printing of components of energy: --- src/determinants/utils.irp.f | 53 ++++++++++++++++++++++++++++++ src/iterations/print_summary.irp.f | 9 +++-- 2 files changed, 59 insertions(+), 3 deletions(-) diff --git a/src/determinants/utils.irp.f b/src/determinants/utils.irp.f index 20d9e1e5..7e6ad39c 100644 --- a/src/determinants/utils.irp.f +++ b/src/determinants/utils.irp.f @@ -43,4 +43,57 @@ BEGIN_PROVIDER [ double precision, S2_matrix_all_dets,(N_det,N_det) ] !$OMP END PARALLEL DO END_PROVIDER +subroutine print_energy_components() + implicit none + BEGIN_DOC +! Prints the different components of the energy. + END_DOC + integer, save :: ifirst = 0 + double precision :: Vee, Ven, Vnn, Vecp, T, f + integer :: i,j,k + Vnn = nuclear_repulsion + + print *, 'Energy components' + print *, '=================' + print *, '' + do k=1,N_states + + Ven = 0.d0 + Vecp = 0.d0 + T = 0.d0 + + do j=1,mo_num + do i=1,mo_num + f = one_e_dm_mo_alpha(i,j,k) + one_e_dm_mo_beta(i,j,k) + Ven = Ven + f * mo_integrals_n_e(i,j) + Vecp = Vecp + f * mo_pseudo_integrals(i,j) + T = T + f * mo_kinetic_integrals(i,j) + enddo + enddo + Vee = psi_energy(k) - Ven - Vecp - T + + if (ifirst == 0) then + ifirst = 1 + print *, 'Vnn : Nucleus-Nucleus potential energy' + print *, 'Ven : Electron-Nucleus potential energy' + print *, 'Vee : Electron-Electron potential energy' + print *, 'Vecp : Potential energy of the pseudo-potentials' + print *, 'T : Electronic kinetic energy' + print *, '' + endif + + print *, 'State ', k + print *, '---------' + print *, '' + print *, 'Vnn = ', Vnn + print *, 'Ven = ', Ven + print *, 'Vee = ', Vee + print *, 'Vecp = ', Vecp + print *, 'T = ', T + print *, '' + enddo + + print *, '' + +end diff --git a/src/iterations/print_summary.irp.f b/src/iterations/print_summary.irp.f index a8037982..ad87bc8e 100644 --- a/src/iterations/print_summary.irp.f +++ b/src/iterations/print_summary.irp.f @@ -31,18 +31,19 @@ subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_,n_ write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))' write(*,fmt) - write(fmt,*) '(12X,', N_states_p, '(6X,A7,1X,I6,10X))' + write(fmt,*) '(13X,', 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,*) '(A13,', N_states_p, '(1X,F14.8,15X))' write(*,fmt) '# E ', e_(1:N_states_p) if (N_states_p > 1) then write(*,fmt) '# Excit. (au)', e_(1:N_states_p)-e_(1) write(*,fmt) '# Excit. (eV)', (e_(1:N_states_p)-e_(1))*27.211396641308d0 endif write(fmt,*) '(A13,', 2*N_states_p, '(1X,F14.8))' - write(*,fmt) '# PT2'//pt2_string, (pt2_(k), error_(k), k=1,N_states_p) + write(*,fmt) '# PT2 '//pt2_string, (pt2_(k), error_(k), k=1,N_states_p) + write(*,fmt) '# rPT2'//pt2_string, (pt2_(k)*f(k), error_(k)*f(k), k=1,N_states_p) write(*,'(A)') '#' write(*,fmt) '# E+PT2 ', (e_(k)+pt2_(k),error_(k), k=1,N_states_p) write(*,fmt) '# E+rPT2 ', (e_(k)+pt2_(k)*f(k),error_(k)*f(k), k=1,N_states_p) @@ -97,5 +98,7 @@ subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_,n_ enddo endif + call print_energy_components() + end subroutine From b71579ab4383d441f3251a3b46bc9aba59faf27a Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 16:12:04 +0200 Subject: [PATCH 27/36] Moved print_e_components --- ocaml/Input_determinants_by_hand.ml | 3 -- src/davidson/print_e_components.irp.f | 54 +++++++++++++++++++++++++++ src/determinants/utils.irp.f | 54 --------------------------- 3 files changed, 54 insertions(+), 57 deletions(-) create mode 100644 src/davidson/print_e_components.irp.f diff --git a/ocaml/Input_determinants_by_hand.ml b/ocaml/Input_determinants_by_hand.ml index ab6fb2ca..e4c6ff2a 100644 --- a/ocaml/Input_determinants_by_hand.ml +++ b/ocaml/Input_determinants_by_hand.ml @@ -81,9 +81,6 @@ end = struct ;; let write_n_det n = - let n_det_old = - Ezfio.get_determinants_n_det () - in Det_number.to_int n |> Ezfio.set_determinants_n_det ;; diff --git a/src/davidson/print_e_components.irp.f b/src/davidson/print_e_components.irp.f new file mode 100644 index 00000000..ddf83474 --- /dev/null +++ b/src/davidson/print_e_components.irp.f @@ -0,0 +1,54 @@ +subroutine print_energy_components() + implicit none + BEGIN_DOC +! Prints the different components of the energy. + END_DOC + integer, save :: ifirst = 0 + double precision :: Vee, Ven, Vnn, Vecp, T, f + integer :: i,j,k + + Vnn = nuclear_repulsion + + print *, 'Energy components' + print *, '=================' + print *, '' + do k=1,N_states + + Ven = 0.d0 + Vecp = 0.d0 + T = 0.d0 + + do j=1,mo_num + do i=1,mo_num + f = one_e_dm_mo_alpha(i,j,k) + one_e_dm_mo_beta(i,j,k) + Ven = Ven + f * mo_integrals_n_e(i,j) + Vecp = Vecp + f * mo_pseudo_integrals(i,j) + T = T + f * mo_kinetic_integrals(i,j) + enddo + enddo + Vee = psi_energy(k) - Ven - Vecp - T + + if (ifirst == 0) then + ifirst = 1 + print *, 'Vnn : Nucleus-Nucleus potential energy' + print *, 'Ven : Electron-Nucleus potential energy' + print *, 'Vee : Electron-Electron potential energy' + print *, 'Vecp : Potential energy of the pseudo-potentials' + print *, 'T : Electronic kinetic energy' + print *, '' + endif + + print *, 'State ', k + print *, '---------' + print *, '' + print *, 'Vnn = ', Vnn + print *, 'Ven = ', Ven + print *, 'Vee = ', Vee + print *, 'Vecp = ', Vecp + print *, 'T = ', T + print *, '' + enddo + + print *, '' + +end diff --git a/src/determinants/utils.irp.f b/src/determinants/utils.irp.f index 7e6ad39c..3aec16f9 100644 --- a/src/determinants/utils.irp.f +++ b/src/determinants/utils.irp.f @@ -43,57 +43,3 @@ BEGIN_PROVIDER [ double precision, S2_matrix_all_dets,(N_det,N_det) ] !$OMP END PARALLEL DO END_PROVIDER -subroutine print_energy_components() - implicit none - BEGIN_DOC -! Prints the different components of the energy. - END_DOC - integer, save :: ifirst = 0 - double precision :: Vee, Ven, Vnn, Vecp, T, f - integer :: i,j,k - - Vnn = nuclear_repulsion - - print *, 'Energy components' - print *, '=================' - print *, '' - do k=1,N_states - - Ven = 0.d0 - Vecp = 0.d0 - T = 0.d0 - - do j=1,mo_num - do i=1,mo_num - f = one_e_dm_mo_alpha(i,j,k) + one_e_dm_mo_beta(i,j,k) - Ven = Ven + f * mo_integrals_n_e(i,j) - Vecp = Vecp + f * mo_pseudo_integrals(i,j) - T = T + f * mo_kinetic_integrals(i,j) - enddo - enddo - Vee = psi_energy(k) - Ven - Vecp - T - - if (ifirst == 0) then - ifirst = 1 - print *, 'Vnn : Nucleus-Nucleus potential energy' - print *, 'Ven : Electron-Nucleus potential energy' - print *, 'Vee : Electron-Electron potential energy' - print *, 'Vecp : Potential energy of the pseudo-potentials' - print *, 'T : Electronic kinetic energy' - print *, '' - endif - - print *, 'State ', k - print *, '---------' - print *, '' - print *, 'Vnn = ', Vnn - print *, 'Ven = ', Ven - print *, 'Vee = ', Vee - print *, 'Vecp = ', Vecp - print *, 'T = ', T - print *, '' - enddo - - print *, '' - -end From 720a63aadfe9759792ea2500078c9ea04384b3e4 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 17:28:15 +0200 Subject: [PATCH 28/36] Bubblewrap and libcap install scripts --- INSTALL.rst | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++ configure | 40 +++++++++++++++++++++++++++++++++++++++- 2 files changed, 92 insertions(+), 1 deletion(-) diff --git a/INSTALL.rst b/INSTALL.rst index cc5b512a..baf7f051 100644 --- a/INSTALL.rst +++ b/INSTALL.rst @@ -45,6 +45,8 @@ Requirements - |ZeroMQ| : networking library - `GMP `_ : Gnu Multiple Precision Arithmetic Library - |OCaml| compiler with |OPAM| package manager +- `Bubblewrap `_ : Sandboxing tool required by Opam +- `libcap https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git`_ : POSIX capabilities required by Bubblewrap - |Ninja| : a parallel build system @@ -86,6 +88,8 @@ The following packages are supported by the :command:`configure` installer: * zeromq * f77zmq * gmp +* libcap +* bwrap * ocaml ( :math:`\approx` 10 minutes) * ezfio * docopt @@ -243,6 +247,55 @@ With Debian or Ubuntu, you can use sudo apt install libgmp-dev +libcap +------ + +Libcap is a library for getting and setting POSIX.1e draft 15 capabilities. + +* Download the latest version of libcap here: + ``_ + and move it in the :file:`${QP_ROOT}/external` directory + +* Extract the archive, go into the :file:`libcap-*/libcap` directory and run + the following command + +.. code:: bash + + prefix=$QP_ROOT make install + +With Debian or Ubuntu, you can use + +.. code:: bash + + sudo apt install libcap-dev + + +Bubblewrap +---------- + +Bubblewrap is an unprivileged sandboxing tool. + +* Download Bubblewrap here: + ``_ + and move it in the :file:`${QP_ROOT}/external` directory + +* Extract the archive, go into the :file:`bubblewrap-*` directory and run + the following commands + +.. code:: bash + + ./configure --prefix=$QP_ROOT && make -j 8 + make install-exec-am + + +With Debian or Ubuntu, you can use + +.. code:: bash + + sudo apt install bubblewrap + + + OCaml ----- diff --git a/configure b/configure index ffda5016..6600668a 100755 --- a/configure +++ b/configure @@ -175,7 +175,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then fi if [[ ${PACKAGES} = all ]] ; then - PACKAGES="zlib ninja irpf90 zeromq f77zmq gmp ocaml ezfio docopt resultsFile bats" + PACKAGES="bwrap libcap zlib ninja irpf90 zeromq f77zmq gmp ocaml ezfio docopt resultsFile bats" fi @@ -206,6 +206,32 @@ EOF make install EOF + elif [[ ${PACKAGE} = bwrap ]] ; then + + download \ + "https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz" \ + "${QP_ROOT}"/external/bwrap.tar.xz + execute << EOF + cd "\${QP_ROOT}"/external + tar --xz --extract --file bwrap.tar.xz + rm bwrap.tar.xz + cd bubblewrap* + ./configure --prefix=$QP_ROOT && make -j 8 + make install-exec-am +EOF + + elif [[ ${PACKAGE} = libcap ]] ; then + + download \ + "https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz" \ + "${QP_ROOT}"/external/libcap.tar.gz + execute << EOF + cd "\${QP_ROOT}"/external + tar --gunzip --extract --file libcap.tar.gz + rm libcap.tar.gz + cd libcap-*/libcap + prefix=$QP_ROOT make install +EOF elif [[ ${PACKAGE} = irpf90 ]] ; then @@ -399,6 +425,18 @@ if [[ ${ZLIB} = $(not_found) ]] ; then fail fi +BWRAP=$(find_exe bwrap) +if [[ ${BWRAP} = $(not_found) ]] ; then + error "Bubblewrap (bwrap) is not installed." + fail +fi + +LIBCAP=$(find_lib -lcap) +if [[ ${LIBCAP} = $(not_found) ]] ; then + error "Libcap (libcap) is not installed." + fail +fi + OPAM=$(find_exe opam) if [[ ${OPAM} = $(not_found) ]] ; then error "OPAM (ocaml) package manager is not installed." From 8a127a9bab8f63777bfcf0095f2d8329e27e24f4 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 17:34:36 +0200 Subject: [PATCH 29/36] added selection_weight to fci slave --- src/cipsi/pt2_stoch_routines.irp.f | 3 +++ src/cipsi/slave_cipsi.irp.f | 6 +++++- src/cipsi/zmq_selection.irp.f | 3 +++ 3 files changed, 11 insertions(+), 1 deletion(-) diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index 7cb834d9..9f891320 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -182,6 +182,9 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in) if (zmq_put_dvector(zmq_to_qp_run_socket,1,'state_average_weight',state_average_weight,N_states) == -1) then stop 'Unable to put state_average_weight on ZMQ server' endif + if (zmq_put_dvector(zmq_to_qp_run_socket,1,'selection_weight',selection_weight,N_states) == -1) then + stop 'Unable to put selection_weight on ZMQ server' + endif if (zmq_put_ivector(zmq_to_qp_run_socket,1,'pt2_stoch_istate',pt2_stoch_istate,1) == -1) then stop 'Unable to put pt2_stoch_istate on ZMQ server' endif diff --git a/src/cipsi/slave_cipsi.irp.f b/src/cipsi/slave_cipsi.irp.f index 8668db01..c9710c18 100644 --- a/src/cipsi/slave_cipsi.irp.f +++ b/src/cipsi/slave_cipsi.irp.f @@ -220,8 +220,12 @@ subroutine run_slave_main call mpi_print('zmq_get_dvector state_average_weight') IRP_ENDIF if (zmq_get_dvector(zmq_to_qp_run_socket,1,'state_average_weight',state_average_weight,N_states) == -1) cycle + IRP_IF MPI_DEBUG + call mpi_print('zmq_get_dvector selection_weight') + IRP_ENDIF + if (zmq_get_dvector(zmq_to_qp_run_socket,1,'selection_weight',selection_weight,N_states) == -1) cycle pt2_e0_denominator(1:N_states) = energy(1:N_states) - SOFT_TOUCH pt2_e0_denominator state_average_weight pt2_stoch_istate threshold_generators + SOFT_TOUCH pt2_e0_denominator state_average_weight pt2_stoch_istate threshold_generators selection_weight call wall_time(t1) call write_double(6,(t1-t0),'Broadcast time') diff --git a/src/cipsi/zmq_selection.irp.f b/src/cipsi/zmq_selection.irp.f index 9562bbe0..081d998f 100644 --- a/src/cipsi/zmq_selection.irp.f +++ b/src/cipsi/zmq_selection.irp.f @@ -46,6 +46,9 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm) if (zmq_put_dvector(zmq_to_qp_run_socket,1,'state_average_weight',state_average_weight,N_states) == -1) then stop 'Unable to put state_average_weight on ZMQ server' endif + if (zmq_put_dvector(zmq_to_qp_run_socket,1,'selection_weight',selection_weight,N_states) == -1) then + stop 'Unable to put selection_weight on ZMQ server' + endif if (zmq_put_dvector(zmq_to_qp_run_socket,1,'threshold_generators',threshold_generators,1) == -1) then stop 'Unable to put threshold_generators on ZMQ server' endif From f36629173d7e1ccf3d918bf7a4e2619feb381c4a Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 17:39:01 +0200 Subject: [PATCH 30/36] Updated configure --- configure | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/configure b/configure index 6600668a..b866efe2 100755 --- a/configure +++ b/configure @@ -206,6 +206,19 @@ EOF make install EOF + elif [[ ${PACKAGE} = libcap ]] ; then + + download \ + "https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz" \ + "${QP_ROOT}"/external/libcap.tar.gz + execute << EOF + cd "\${QP_ROOT}"/external + tar --gunzip --extract --file libcap.tar.gz + rm libcap.tar.gz + cd libcap-*/libcap + prefix=$QP_ROOT make install +EOF + elif [[ ${PACKAGE} = bwrap ]] ; then download \ @@ -220,19 +233,6 @@ EOF make install-exec-am EOF - elif [[ ${PACKAGE} = libcap ]] ; then - - download \ - "https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz" \ - "${QP_ROOT}"/external/libcap.tar.gz - execute << EOF - cd "\${QP_ROOT}"/external - tar --gunzip --extract --file libcap.tar.gz - rm libcap.tar.gz - cd libcap-*/libcap - prefix=$QP_ROOT make install -EOF - elif [[ ${PACKAGE} = irpf90 ]] ; then # When changing version of irpf90, don't forget to update etc/irpf90.rc From 9c028127a0e0ff7ac38c9ff440b497ddb5591a35 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 17:48:19 +0200 Subject: [PATCH 31/36] Updated configure --- configure | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/configure b/configure index b866efe2..c343c243 100755 --- a/configure +++ b/configure @@ -175,7 +175,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then fi if [[ ${PACKAGES} = all ]] ; then - PACKAGES="bwrap libcap zlib ninja irpf90 zeromq f77zmq gmp ocaml ezfio docopt resultsFile bats" + PACKAGES="zlib ninja irpf90 zeromq f77zmq gmp libcap bwrap ocaml ezfio docopt resultsFile bats" fi @@ -302,7 +302,7 @@ EOF rm ${QP_ROOT}/external/opam_installer.sh source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - ${QP_ROOT}/bin/opam init --disable-sandboxing --verbose --yes + ${QP_ROOT}/bin/opam init --verbose --yes eval $(${QP_ROOT}/bin/opam env) opam install -y ${OCAML_PACKAGES} || exit 1 @@ -316,7 +316,7 @@ EOF | sh \${QP_ROOT}/external/opam_installer.sh rm \${QP_ROOT}/external/opam_installer.sh source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true - \${QP_ROOT}/bin/opam init --disable-sandboxing --verbose --yes + \${QP_ROOT}/bin/opam init --verbose --yes eval \$(\${QP_ROOT}/bin/opam env) opam install -y \${OCAML_PACKAGES} || exit 1 EOF From 3c6b417ae7d4f6fb4f2f292cab52ee3e650dc35c Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 18:00:04 +0200 Subject: [PATCH 32/36] Type conversion --- src/cipsi/cipsi.irp.f | 2 +- src/cipsi/stochastic_cipsi.irp.f | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/cipsi/cipsi.irp.f b/src/cipsi/cipsi.irp.f index b07ab22f..a41fa911 100644 --- a/src/cipsi/cipsi.irp.f +++ b/src/cipsi/cipsi.irp.f @@ -103,7 +103,7 @@ subroutine run_cipsi if (qp_stop()) exit n_det_before = N_det - to_select = N_det*int(sqrt(dble(N_states)))*selection_factor + to_select = int(sqrt(dble(N_states)*dble(N_det))*selection_factor) to_select = max(N_states_diag, to_select) call ZMQ_selection(to_select, pt2, variance, norm) diff --git a/src/cipsi/stochastic_cipsi.irp.f b/src/cipsi/stochastic_cipsi.irp.f index 98e842e5..21b5f293 100644 --- a/src/cipsi/stochastic_cipsi.irp.f +++ b/src/cipsi/stochastic_cipsi.irp.f @@ -70,7 +70,7 @@ subroutine run_stochastic_cipsi write(*,'(A)') '--------------------------------------------------------------------------------' - to_select = N_det*int(sqrt(dble(N_states)))*selection_factor + to_select = int(sqrt(dble(N_states)*dble(N_det))*selection_factor) to_select = max(N_states_diag, to_select) pt2 = 0.d0 From c7ef5fc8c7911e4eb258c04a64c272a47b985861 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 5 Jun 2019 18:57:17 +0200 Subject: [PATCH 33/36] Fixed tests --- src/cipsi/cipsi.irp.f | 41 ++++++++++++++++---------------- src/cipsi/stochastic_cipsi.irp.f | 38 ++++++++++++++--------------- 2 files changed, 38 insertions(+), 41 deletions(-) diff --git a/src/cipsi/cipsi.irp.f b/src/cipsi/cipsi.irp.f index a41fa911..7e292d6e 100644 --- a/src/cipsi/cipsi.irp.f +++ b/src/cipsi/cipsi.irp.f @@ -5,7 +5,7 @@ subroutine run_cipsi ! stochastic PT2. END_DOC integer :: i,j,k - double precision, allocatable :: pt2(:), variance(:), norm(:), rpt2(:) + double precision, allocatable :: pt2(:), variance(:), norm(:), rpt2(:), zeros(:) integer :: n_det_before, to_select double precision :: rss @@ -13,7 +13,7 @@ subroutine run_cipsi rss = memory_of_double(N_states)*4.d0 call check_mem(rss,irp_here) - allocate (pt2(N_states), rpt2(N_states), norm(N_states), variance(N_states)) + allocate (pt2(N_states), zeros(N_states), rpt2(N_states), norm(N_states), variance(N_states)) double precision :: hf_energy_ref logical :: has @@ -23,10 +23,11 @@ subroutine run_cipsi relative_error=PT2_relative_error + zeros = 0.d0 pt2 = -huge(1.e0) rpt2 = -huge(1.e0) norm = 0.d0 - variance = 0.d0 + variance = huge(1.e0) if (s2_eig) then call make_s2_eigenfunction @@ -66,6 +67,7 @@ subroutine run_cipsi do while ( & (N_det < N_det_max) .and. & (maxval(abs(rpt2(1:N_states))) > pt2_max) .and. & + (maxval(variance(1:N_states)) > variance_max) .and. & (correlation_energy_ratio <= correlation_energy_ratio_max) & ) write(*,'(A)') '--------------------------------------------------------------------------------' @@ -83,17 +85,17 @@ subroutine run_cipsi SOFT_TOUCH threshold_generators endif + do k=1,N_states + rpt2(k) = pt2(k)/(1.d0 + norm(k)) + enddo correlation_energy_ratio = (psi_energy_with_nucl_rep(1) - hf_energy_ref) / & - (psi_energy_with_nucl_rep(1) + pt2(1) - hf_energy_ref) + (psi_energy_with_nucl_rep(1) + rpt2(1) - hf_energy_ref) correlation_energy_ratio = min(1.d0,correlation_energy_ratio) call write_double(6,correlation_energy_ratio, 'Correlation ratio') call print_summary(psi_energy_with_nucl_rep(1:N_states),pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) - do k=1,N_states - rpt2(k) = pt2(k)/(1.d0 + norm(k)) - enddo call save_energy(psi_energy_with_nucl_rep, rpt2) call save_iterations(psi_energy_with_nucl_rep(1:N_states),rpt2,N_det) @@ -103,7 +105,7 @@ subroutine run_cipsi if (qp_stop()) exit n_det_before = N_det - to_select = int(sqrt(dble(N_states)*dble(N_det))*selection_factor) + to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor) to_select = max(N_states_diag, to_select) call ZMQ_selection(to_select, pt2, variance, norm) @@ -113,32 +115,30 @@ subroutine run_cipsi call diagonalize_CI call save_wavefunction - rpt2(:) = 0.d0 - call save_energy(psi_energy_with_nucl_rep, rpt2) + call save_energy(psi_energy_with_nucl_rep, zeros) if (qp_stop()) exit +print *, (N_det < N_det_max) +print *, (maxval(abs(rpt2(1:N_states))) > pt2_max) +print *, (maxval(variance(1:N_states)) > variance_max) +print *, (correlation_energy_ratio <= correlation_energy_ratio_max) enddo if (.not.qp_stop()) then if (N_det < N_det_max) then call diagonalize_CI call save_wavefunction - rpt2(:) = 0.d0 - call save_energy(psi_energy_with_nucl_rep, rpt2) + call save_energy(psi_energy_with_nucl_rep, zeros) endif if (do_pt2) then - pt2 = 0.d0 - variance = 0.d0 - norm = 0.d0 + pt2(:) = 0.d0 + variance(:) = 0.d0 + norm(:) = 0.d0 threshold_generators = 1d0 SOFT_TOUCH threshold_generators call ZMQ_pt2(psi_energy_with_nucl_rep, pt2,relative_error,error,variance, & norm,0) ! Stochastic PT2 SOFT_TOUCH threshold_generators - do k=1,N_states - rpt2(k) = pt2(k)/(1.d0 + norm(k)) - enddo - call save_energy(psi_energy_with_nucl_rep, pt2) endif print *, 'N_det = ', N_det print *, 'N_sop = ', N_occ_pattern @@ -149,10 +149,9 @@ subroutine run_cipsi do k=1,N_states rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo - call save_energy(psi_energy_with_nucl_rep, rpt2) call print_summary(psi_energy_with_nucl_rep(1:N_states),pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) - call save_energy(psi_energy_with_nucl_rep, pt2) + call save_energy(psi_energy_with_nucl_rep, rpt2) call save_iterations(psi_energy_with_nucl_rep(1:N_states),rpt2,N_det) call print_extrapolated_energy() endif diff --git a/src/cipsi/stochastic_cipsi.irp.f b/src/cipsi/stochastic_cipsi.irp.f index 21b5f293..ae2b7519 100644 --- a/src/cipsi/stochastic_cipsi.irp.f +++ b/src/cipsi/stochastic_cipsi.irp.f @@ -4,7 +4,7 @@ subroutine run_stochastic_cipsi ! Selected Full Configuration Interaction with Stochastic selection and PT2. END_DOC integer :: i,j,k - double precision, allocatable :: pt2(:), variance(:), norm(:), rpt2(:) + double precision, allocatable :: pt2(:), variance(:), norm(:), rpt2(:), zeros(:) integer :: to_select logical, external :: qp_stop @@ -18,7 +18,7 @@ subroutine run_stochastic_cipsi rss = memory_of_double(N_states)*4.d0 call check_mem(rss,irp_here) - allocate (pt2(N_states), rpt2(N_states), norm(N_states), variance(N_states)) + allocate (pt2(N_states), zeros(N_states), rpt2(N_states), norm(N_states), variance(N_states)) double precision :: hf_energy_ref logical :: has @@ -26,6 +26,7 @@ subroutine run_stochastic_cipsi relative_error=PT2_relative_error + zeros = 0.d0 pt2 = -huge(1.e0) rpt2 = -huge(1.e0) norm = 0.d0 @@ -63,14 +64,14 @@ subroutine run_stochastic_cipsi do while ( & (N_det < N_det_max) .and. & - (maxval(abs(pt2(1:N_states))) > pt2_max) .and. & + (maxval(abs(rpt2(1:N_states))) > pt2_max) .and. & (maxval(abs(variance(1:N_states))) > variance_max) .and. & (correlation_energy_ratio <= correlation_energy_ratio_max) & ) write(*,'(A)') '--------------------------------------------------------------------------------' - to_select = int(sqrt(dble(N_states)*dble(N_det))*selection_factor) + to_select = int(sqrt(dble(N_states))*dble(N_det)*selection_factor) to_select = max(N_states_diag, to_select) pt2 = 0.d0 @@ -79,17 +80,17 @@ subroutine run_stochastic_cipsi call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, & norm, to_select) ! Stochastic PT2 and selection - correlation_energy_ratio = (psi_energy_with_nucl_rep(1) - hf_energy_ref) / & - (psi_energy_with_nucl_rep(1) + pt2(1) - hf_energy_ref) - correlation_energy_ratio = min(1.d0,correlation_energy_ratio) - - call save_energy(psi_energy_with_nucl_rep, rpt2) - call write_double(6,correlation_energy_ratio, 'Correlation ratio') - call print_summary(psi_energy_with_nucl_rep,pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) - do k=1,N_states rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo + + correlation_energy_ratio = (psi_energy_with_nucl_rep(1) - hf_energy_ref) / & + (psi_energy_with_nucl_rep(1) + rpt2(1) - hf_energy_ref) + correlation_energy_ratio = min(1.d0,correlation_energy_ratio) + + call write_double(6,correlation_energy_ratio, 'Correlation ratio') + call print_summary(psi_energy_with_nucl_rep,pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) + call save_energy(psi_energy_with_nucl_rep, rpt2) call save_iterations(psi_energy_with_nucl_rep(1:N_states),rpt2,N_det) @@ -108,8 +109,7 @@ subroutine run_stochastic_cipsi call diagonalize_CI call save_wavefunction - rpt2(:) = 0.d0 - call save_energy(psi_energy_with_nucl_rep, rpt2) + call save_energy(psi_energy_with_nucl_rep, zeros) if (qp_stop()) exit enddo @@ -117,20 +117,18 @@ subroutine run_stochastic_cipsi if (N_det < N_det_max) then call diagonalize_CI call save_wavefunction - rpt2(:) = 0.d0 - call save_energy(psi_energy_with_nucl_rep, rpt2) + call save_energy(psi_energy_with_nucl_rep, zeros) endif - pt2 = 0.d0 - variance = 0.d0 - norm = 0.d0 + pt2(:) = 0.d0 + variance(:) = 0.d0 + norm(:) = 0.d0 call ZMQ_pt2(psi_energy_with_nucl_rep, pt2,relative_error,error,variance, & norm,0) ! Stochastic PT2 do k=1,N_states rpt2(k) = pt2(k)/(1.d0 + norm(k)) enddo - call save_energy(psi_energy_with_nucl_rep, rpt2) call save_energy(psi_energy_with_nucl_rep, rpt2) call print_summary(psi_energy_with_nucl_rep(1:N_states),pt2,error,variance,norm,N_det,N_occ_pattern,N_states,psi_s2) From 4c5759fe6f8021a9a67a6c605a5b35578b7a25e7 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Sat, 8 Jun 2019 15:14:38 +0200 Subject: [PATCH 34/36] Modified README --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c94adb69..4f6d165c 100644 --- a/README.md +++ b/README.md @@ -3,10 +3,11 @@ *Quantum package 2.0: an open-source determinant-driven suite of programs*\ Y. Garniron, K. Gasperich, T. Applencourt, A. Benali, A. Ferté, J. Paquier, B. Pradines, R. Assaraf, P. Reinhardt, J. Toulouse, P. Barbaresco, N. Renon, G. David, J. P. Malrieu, M. Véril, M. Caffarel, P. F. Loos, E. Giner and A. Scemama\ +https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176\ https://arxiv.org/abs/1902.08154 -![QP](https://raw.githubusercontent.com/QuantumPackage/qp2/master/data/qp2.png) + # Getting started From c7dedf49ed20f274633d6d6fc111cb8aa1f1b2eb Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Sat, 8 Jun 2019 15:14:57 +0200 Subject: [PATCH 35/36] More efficient multi-state selection --- src/cipsi/selection.irp.f | 30 +++++++++++++++++++++++++----- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/src/cipsi/selection.irp.f b/src/cipsi/selection.irp.f index 0237e064..df31bc39 100644 --- a/src/cipsi/selection.irp.f +++ b/src/cipsi/selection.irp.f @@ -30,8 +30,22 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) double precision :: avg, rpt2(N_st), element, dt, x integer :: k + integer, save :: i_iter=0 + integer, parameter :: i_itermax = 3 + double precision, allocatable, save :: memo_variance(:,:), memo_pt2(:,:) - dt = n_iter * selection_factor + if (i_iter == 0) then + allocate(memo_variance(N_st,i_itermax), memo_pt2(N_st,i_itermax)) + memo_pt2(:,:) = 1.d0 + memo_variance(:,:) = 1.d0 + endif + + i_iter = i_iter+1 + if (i_iter > i_itermax) then + i_iter = 1 + endif + + dt = 4.d0 do k=1,N_st rpt2(k) = pt2(k)/(1.d0 + norm(k)) @@ -40,17 +54,23 @@ subroutine update_pt2_and_variance_weights(pt2, variance, norm, N_st) avg = sum(rpt2(1:N_st)) / dble(N_st) do k=1,N_st element = exp(dt*(rpt2(k)/avg -1.d0)) - element = min(1.2d0 , element) - pt2_match_weight(k) *= element + element = min(1.5d0 , element) + element = max(0.5d0 , element) + memo_pt2(k,i_iter) = element + pt2_match_weight(k) = product(memo_pt2(k,:)) enddo avg = sum(variance(1:N_st)) / dble(N_st) do k=1,N_st element = exp(dt*(variance(k)/avg -1.d0)) - element = min(1.2d0 , element) - variance_match_weight(k) *= element + element = min(1.5d0 , element) + element = max(0.5d0 , element) + memo_variance(k,i_iter) = element + variance_match_weight(k) = product(memo_variance(k,:)) enddo + print *, '# PT2 weight ', real(pt2_match_weight(:),4) + print *, '# var weight ', real(variance_match_weight(:),4) SOFT_TOUCH pt2_match_weight variance_match_weight end From cf4f9990bc769770b31d19383943b43f3d3280cd Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Sat, 8 Jun 2019 15:44:18 +0200 Subject: [PATCH 36/36] Updated citation.ccf --- CITATION.cff | 96 ++++++++++++++++++++++++++++++++++++++++++++-------- README.md | 4 +-- 2 files changed, 84 insertions(+), 16 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 9cd186d2..a391b8fa 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,32 +1,100 @@ # YAML 1.2 # Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/) cff-version: 1.0.3 -message: If you use this software, please cite it using these metadata. +message: "If you use this software, please cite it using these metadata." title: Quantum Package -doi: 10.5281/zenodo.825872 +doi: 10.1021/acs.jctc.9b00176 authors: -- given-names: Anthony - family-names: Scemama - affiliation: Laboratoire de Chimie et Physique Quantiques / CNRS - given-names: Yann family-names: Garniron - affiliation: Laboratoire de Chimie et Physique Quantiques / CNRS -- given-names: Michel - family-names: Caffarel - affiliation: Laboratoire de Chimie et Physique Quantiques / CNRS + affiliation: Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, Toulouse, France - given-names: Thomas family-names: Applencourt - affiliation: Argonne National Lab + affiliation: Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States - given-names: Kevin family-names: Gasperich - affiliation: Argonne National Lab + affiliation: Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States - given-names: Anouar family-names: Benali - affiliation: Argonne National Lab + affiliation: Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States +- given-names: Anthony + family-names: Ferté + affiliation: Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris, France +- given-names: Julien + family-names: Paquier + affiliation: Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris, France +- given-names: Barthélémy + family-names: Pradines + affiliation: Institut des Sciences du Calcul et des Données, Sorbonne Université, F-75005 Paris, France +- given-names: Roland + family-names: Assaraf + affiliation: Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris, France +- given-names: Peter + family-names: Reinhardt + affiliation: Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris, France +- given-names: Julien + family-names: Toulouse + affiliation: Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris, France +- given-names: Pierrette + family-names: Barbaresco + affiliation: CALMIP, Université de Toulouse, CNRS, INPT, INSA, UPS, UMS 3667, Toulouse, France +- given-names: Nicolas + family-names: Renon + affiliation: CALMIP, Université de Toulouse, CNRS, INPT, INSA, UPS, UMS 3667, Toulouse, France +- given-names: Grégoire + family-names: David + affiliation: Aix-Marseille Univ, CNRS, ICR, Marseille, France +- given-names: Jean-Paul + family-names: Malrieu + affiliation: Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, Toulouse, France +- given-names: Mickaël + family-names: Véril + affiliation: Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, Toulouse, France +- given-names: Michel + family-names: Caffarel + affiliation: Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, Toulouse, France +- given-names: Pierre-François + family-names: Loos + affiliation: Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, Toulouse, France - given-names: Emmanuel family-names: Giner - affiliation: Laboratoire de Chimie Theorique / CNRS + affiliation: Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris, France +- given-names: Anthony + family-names: Scemama + affiliation: Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, Toulouse, France +abstract: "Quantum chemistry is a discipline which relies heavily on very +expensive numerical computations. The scaling of correlated wave function +methods lies, in their standard implementation, between O(N^5) and O(exp(N)), +where N is proportional to the system size. Therefore, performing accurate +calculations on chemically meaningful systems requires (i) approximations that +can lower the computational scaling and (ii) efficient implementations that +take advantage of modern massively parallel architectures. Quantum Package is +an open-source programming environment for quantum chemistry specially designed +for wave function methods. Its main goal is the development of +determinant-driven selected configuration interaction (sCI) methods and +multireference second-order perturbation theory (PT2). The determinant-driven +framework allows the programmer to include any arbitrary set of determinants in +the reference space, hence providing greater methodological freedom. The sCI +method implemented in Quantum Package is based on the CIPSI (Configuration +Interaction using a Perturbative Selection made Iteratively) algorithm which +complements the variational sCI energy with a PT2 correction. Additional +external plugins have been recently added to perform calculations with +multireference coupled cluster theory and range-separated density-functional +theory. All the programs are developed with the IRPF90 code generator, which +simplifies collaborative work and the development of new features. Quantum +Package strives to allow easy implementation and experimentation of new +methods, while making parallel computation as simple and efficient as possible +on modern supercomputer architectures. Currently, the code enables, routinely, +to realize runs on roughly 2 000 CPU cores, with tens of millions of +determinants in the reference space. Moreover, we have been able to push up to +12 288 cores in order to test its parallel efficiency. In the present +manuscript, we also introduce some key new developments: (i) a renormalized +second-order perturbative correction for efficient extrapolation to the full CI +limit and (ii) a stochastic version of the CIPSI selection performed +simultaneously to the PT2 calculation at no extra cost." version: '2.0' -date-released: 2019-02-11 +url: https://quantumpackage.github.io/qp2/ +date-released: 2019-05-13 repository-code: https://github.com/QuantumPackage/qp2 +keywords: [ "computational chemistry", "configuration interaction", "cipsi", "perturbation theory" ] license: AGPL-3.0-or-later diff --git a/README.md b/README.md index 4f6d165c..3e85b4cc 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ # Quantum Package 2.0 -*Quantum package 2.0: an open-source determinant-driven suite of programs*\ +[*Quantum package 2.0: an open-source determinant-driven suite of programs*](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176)\ Y. Garniron, K. Gasperich, T. Applencourt, A. Benali, A. Ferté, J. Paquier, B. Pradines, R. Assaraf, P. Reinhardt, J. Toulouse, P. Barbaresco, N. Renon, G. David, J. P. Malrieu, M. Véril, M. Caffarel, P. F. Loos, E. Giner and A. Scemama\ -https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176\ +J. Chem. Theory Comput. (2019)\ https://arxiv.org/abs/1902.08154