Merge branch 'dev-stable' of https://github.com/QuantumPackage/qp2 into dev-stable

bin/python

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+exec python3 $@
+

bin/qpsh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
-export QP_ROOT=$(dirname "$(readlink -f "$0")")/..
+REALPATH=$( cd "$(dirname "$0")" ; pwd -P )
+export QP_ROOT=${REALPATH}/..
 
 bash --init-file <(cat << EOF
     [[ -f /etc/bashrc ]] && source /etc/bashrc 

bin/zcat

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# On Darwin: try gzcat if available, otherwise use Python
+
+if [[ $(uname -s) = Darwin ]] ; then
+   which gzcat &> /dev/null
+   if [[ $? -eq 0 ]] ; then 
+      exec gzcat $@
+   else
+
+      exec python3 << EOF
+import sys
+import gzip
+with gzip.open("$1", "rt") as f:
+    print(f.read())
+EOF
+   fi
+else
+   command=$(which -a zcat | grep -v 'qp2/bin/' | head -1)
+   exec $command $@
+fi
+

config/gfortran.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
 LAPACK_LIB   : -lblas -llapack
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

config/gfortran_armpl.cfg

@@ -13,7 +13,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
 LAPACK_LIB   : -larmpl_lp64_mp
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

config/gfortran_avx.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -ffree-line-length-none -I . -mavx -g -fPIC
+FC           : gfortran -ffree-line-length-none -I . -mavx -g -fPIC -std=legacy
 LAPACK_LIB   : -llapack -lblas
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED

config/gfortran_debug.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -std=legacy
 LAPACK_LIB   : -lblas -llapack
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

config/gfortran_macos.cfg

@@ -0,0 +1,62 @@
+# Common flags
+##############
+#
+# -ffree-line-length-none : Needed for IRPF90 which produces long lines
+# -lblas -llapack         : Link with libblas and liblapack libraries provided by the system
+# -I .                    : Include the curent directory (Mandatory)
+#
+# --ninja                 : Allow the utilisation of ninja. (Mandatory)
+# --align=32              : Align all provided arrays on a 32-byte boundary
+#
+#
+[COMMON]
+FC           : gfortran -ffree-line-length-none -I . -g -fPIC -std=legacy
+LAPACK_LIB   : -llapack -lblas
+IRPF90       : irpf90
+IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED -DMACOS
+
+# 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
+####################
+#
+# -Ofast                  : Disregard strict standards compliance. Enables all -O3 optimizations.
+#                           It also enables optimizations that are not valid
+#                           for all standard-compliant programs.  It turns on
+#                           -ffast-math and the Fortran-specific
+#                           -fno-protect-parens and -fstack-arrays.
+[OPT]
+FCFLAGS : -Ofast -march=native
+
+# Profiling flags
+#################
+#
+[PROFILE]
+FC      : -p -g
+FCFLAGS : -Ofast
+
+# Debugging flags
+#################
+#
+# -fcheck=all  : Checks uninitialized variables,  array subscripts, etc...
+# -g           : Extra debugging information
+#
+[DEBUG]
+FCFLAGS : -fcheck=all -g
+
+# OpenMP flags
+#################
+#
+[OPENMP]
+FC           : -fopenmp
+IRPF90_FLAGS : --openmp
+

config/gfortran_mpi.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : mpif90 -ffree-line-length-none -I . -g -fPIC
+FC           : mpif90 -ffree-line-length-none -I . -g -fPIC -std=legacy
 LAPACK_LIB   :  -lblas -llapack
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED

config/gfortran_openblas.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
 LAPACK_LIB   : -lopenblas
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

configure

@@ -19,7 +19,11 @@ git submodule init
 git submodule update
 
 # Update ARM or x86 dependencies
-ARCHITECTURE=$(uname -m)
+SYSTEM=$(uname -s)
+if [[ $SYSTEM = "Linux" ]] ; then
+  SYSTEM=""
+fi
+ARCHITECTURE=$(uname -m)$SYSTEM
 cd ${QP_ROOT}/external/qp2-dependencies
 git checkout master
 git pull
@@ -211,6 +215,7 @@ EOF
             execute << EOF
               cd "\${QP_ROOT}"/external
               wget https://github.com/TREX-CoE/trexio/releases/download/v${VERSION}/trexio-${VERSION}.tar.gz
+              rm -rf trexio-${VERSION}
               tar -zxf trexio-${VERSION}.tar.gz && rm trexio-${VERSION}.tar.gz
               cd trexio-${VERSION}
               ./configure --prefix=\${QP_ROOT} --without-hdf5 CFLAGS='-g'
@@ -224,6 +229,7 @@ EOF
             execute << EOF
               cd "\${QP_ROOT}"/external
               wget https://github.com/TREX-CoE/trexio/releases/download/v${VERSION}/trexio-${VERSION}.tar.gz
+              rm -rf trexio-${VERSION}
               tar -zxf trexio-${VERSION}.tar.gz && rm trexio-${VERSION}.tar.gz
               cd trexio-${VERSION}
               ./configure --prefix=\${QP_ROOT} CFLAGS="-g"
@@ -235,11 +241,24 @@ EOF
             execute << EOF
               cd "\${QP_ROOT}"/external
               wget https://github.com/TREX-CoE/qmckl/releases/download/v${VERSION}/qmckl-${VERSION}.tar.gz
+              rm -rf qmckl-${VERSION}
               tar -zxf qmckl-${VERSION}.tar.gz && rm qmckl-${VERSION}.tar.gz
               cd qmckl-${VERSION}
               ./configure --prefix=\${QP_ROOT} --enable-hpc --disable-doc CFLAGS='-g'
               make && make -j 4 check && make install
 EOF
+    elif [[ ${PACKAGE} = qmckl-intel ]] ; then
+
+            VERSION=0.5.4
+            execute << EOF
+              cd "\${QP_ROOT}"/external
+              wget https://github.com/TREX-CoE/qmckl/releases/download/v${VERSION}/qmckl-${VERSION}.tar.gz
+              rm -rf qmckl-${VERSION}
+              tar -zxf qmckl-${VERSION}.tar.gz && rm qmckl-${VERSION}.tar.gz
+              cd qmckl-${VERSION}
+              ./configure --prefix=\${QP_ROOT} --enable-hpc --disable-doc --with-icc --with-ifort CFLAGS='-g'
+              make && make -j 4 check && make install
+EOF
  
 
     elif [[ ${PACKAGE} = gmp ]] ; then
@@ -260,6 +279,7 @@ EOF
               cd "\${QP_ROOT}"/external
               tar --gunzip --extract --file qp2-dependencies/zeromq-4.2.5.tar.gz
               cd zeromq-*
+              [[ "${SYSTEM}" = "Darwin" ]] && ./autogen.sh
               ./configure --prefix="\$QP_ROOT" --without-libsodium --enable-libunwind=no
               make -j 8
               make install
@@ -378,13 +398,13 @@ fi
 
 TREXIO=$(find_lib -ltrexio)
 if [[ ${TREXIO} = $(not_found) ]] ; then
-        error "TREXIO (trexio,trexio-nohdf5) is not installed. If you don't have HDF5, use trexio-nohdf5"
+        error "TREXIO (trexio | trexio-nohdf5) is not installed. If you don't have HDF5, use trexio-nohdf5"
         fail
 fi
 
 QMCKL=$(find_lib -lqmckl)
 if [[ ${QMCKL} = $(not_found) ]] ; then
-        error "QMCkl (qmckl) is not installed."
+        error "QMCkl (qmckl | qmckl-intel) is not installed."
         fail
 fi
 

external/irpf90

@@ -1 +1 @@
-Subproject commit 0007f72f677fe7d61c5e1ed461882cb239517102
+Subproject commit 4ab1b175fc7ed0d96c1912f13dc53579b24157a6

scripts/module/create_executables_list.sh

@@ -11,7 +11,11 @@ fi
 
 cd ${QP_ROOT}/data
 rm -f executables
+if [[ "$(uname -s)" = "Darwin" ]] ; then
+EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -perm +111 -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort ) 
+else
 EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -executable -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort ) 
+fi
 
 for EXE in $EXES
 do

scripts/module/module_handler.py

@@ -115,9 +115,7 @@ def get_l_module_descendant(d_child, l_module):
             except KeyError:
                 print("Error: ", file=sys.stderr)
                 print("`{0}` is not a submodule".format(module), file=sys.stderr)
-                print("Check the typo (spelling, case, '/', etc.) ", file=sys.stderr)
-#                pass
-                sys.exit(1)
+                raise
 
     return list(set(l))
 

src/ao_one_e_ints/kin_ao_ints.irp.f

@@ -52,7 +52,7 @@
     !$OMP DEFAULT(NONE) &
     !$OMP PRIVATE(A_center,B_center,power_A,power_B,&
     !$OMP  overlap_y, overlap_z, overlap, &
-    !$OMP  alpha, beta,i,j,c,d_a_2,d_2,deriv_tmp, &
+    !$OMP  alpha, beta, n, l, i,j,c,d_a_2,d_2,deriv_tmp, &
     !$OMP  overlap_x0,overlap_y0,overlap_z0) &
     !$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
     !$OMP  ao_deriv2_x,ao_deriv2_y,ao_deriv2_z,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &

src/ao_tc_eff_map/NEED

@@ -1,4 +1,4 @@
-ao_two_e_erf_ints
+ao_two_e_ints
 mo_one_e_ints
 ao_many_one_e_ints
 dft_utils_in_r

src/ao_two_e_erf_ints/EZFIO.cfg

@@ -1,13 +0,0 @@
-[io_ao_two_e_integrals_erf]
-type: Disk_access
-doc: Read/Write |AO| integrals with the long range interaction from/to disk [ Write | Read | None ]
-interface: ezfio,provider,ocaml
-default: None
-
-[mu_erf]
-type: double precision
-doc: cutting of the interaction in the range separated model
-interface: ezfio,provider,ocaml
-default: 0.5
-ezfio_name: mu_erf
-

src/ao_two_e_erf_ints/NEED

@@ -1 +0,0 @@
-ao_two_e_ints

src/ao_two_e_erf_ints/README.rst

@@ -1,19 +0,0 @@
-======================
-ao_two_e_erf_ints
-======================
-
-Here, all two-electron integrals (:math:`erf(\mu r_{12})/r_{12}`) are computed.
-As they have 4 indices and many are zero, they are stored in a map, as defined
-in :file:`utils/map_module.f90`.
-
-The main parameter of this module is :option:`ao_two_e_erf_ints mu_erf` which is the range-separation parameter.
-
-To fetch an |AO| integral, use the
-`get_ao_two_e_integral_erf(i,j,k,l,ao_integrals_erf_map)` function.
-
-
-The conventions are:
-* For |AO| integrals : (ij|kl) = (11|22) = <ik|jl> = <12|12>
-
-
-

src/ao_two_e_ints/EZFIO.cfg

@@ -35,3 +35,15 @@ type: logical
 doc: Perform Cholesky decomposition of AO integrals
 interface: ezfio,provider,ocaml
 default: False
+
+[io_ao_two_e_integrals_erf]
+type: Disk_access
+doc: Read/Write |AO| erf integrals from/to disk [ Write | Read | None ] 
+interface: ezfio,provider,ocaml
+default: None
+
+[use_only_lr]
+type: logical
+doc: If true, use only the long range part of the two-electron integrals instead of 1/r12
+interface: ezfio, provider, ocaml
+default: False

src/ao_two_e_ints/NEED

@@ -1,3 +1,4 @@
+hamiltonian
 ao_one_e_ints
 pseudo
 bitmask

src/ao_two_e_ints/providers_ao_erf.irp.f

@@ -90,7 +90,7 @@ BEGIN_PROVIDER [ logical, ao_two_e_integrals_erf_in_map ]
   if (write_ao_two_e_integrals_erf) then
     call ezfio_set_work_empty(.False.)
     call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints_erf',ao_integrals_erf_map)
-    call ezfio_set_ao_two_e_erf_ints_io_ao_two_e_integrals_erf("Read")
+    call ezfio_set_ao_two_e_ints_io_ao_two_e_integrals_erf('Read')
   endif
 
 END_PROVIDER

src/ao_two_e_ints/routines_save_integrals_erf.irp.f

@@ -4,7 +4,7 @@ subroutine save_erf_two_e_integrals_ao
  PROVIDE ao_two_e_integrals_erf_in_map
  call ezfio_set_work_empty(.False.)
  call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints_erf',ao_integrals_erf_map)
- call ezfio_set_ao_two_e_erf_ints_io_ao_two_e_integrals_erf('Read')
+ call ezfio_set_ao_two_e_ints_io_ao_two_e_integrals_erf('Read')
 end
 
 subroutine save_erf_two_e_ints_ao_into_ints_ao

src/ao_two_e_ints/two_e_integrals.irp.f

@@ -21,9 +21,9 @@ double precision function ao_two_e_integral(i, j, k, l)
   double precision               :: P_new(0:max_dim,3),P_center(3),fact_p,pp
   double precision               :: Q_new(0:max_dim,3),Q_center(3),fact_q,qq
 
-  double precision               :: ao_two_e_integral_schwartz_accel
-
-  double precision               :: ao_two_e_integral_cosgtos
+  double precision, external     :: ao_two_e_integral_erf
+  double precision, external     :: ao_two_e_integral_cosgtos
+  double precision, external     :: ao_two_e_integral_schwartz_accel
 
 
   if(use_cosgtos) then
@@ -31,13 +31,15 @@ double precision function ao_two_e_integral(i, j, k, l)
 
     ao_two_e_integral = ao_two_e_integral_cosgtos(i, j, k, l)
 
-  else
+  else if (use_only_lr) then
 
-    if (ao_prim_num(i) * ao_prim_num(j) * ao_prim_num(k) * ao_prim_num(l) > 1024 ) then
+    ao_two_e_integral = ao_two_e_integral_erf(i, j, k, l)
+
+  else if (ao_prim_num(i) * ao_prim_num(j) * ao_prim_num(k) * ao_prim_num(l) > 1024 ) then
 
        ao_two_e_integral = ao_two_e_integral_schwartz_accel(i,j,k,l)
 
-    else
+  else
 
       dim1 = n_pt_max_integrals
 
@@ -117,8 +119,6 @@ double precision function ao_two_e_integral(i, j, k, l)
           enddo   ! q
         enddo    ! p
 
-      endif
-
     endif
 
   endif

src/basis_correction/51.basis_c.bats

@@ -10,8 +10,8 @@ function run() {
   qp set perturbation do_pt2 False
   qp set determinants n_det_max 8000
   qp set determinants n_states  1
-  qp set davidson threshold_davidson 1.e-10
-  qp set davidson n_states_diag 8
+  qp set davidson_keywords threshold_davidson 1.e-10
+  qp set davidson_keywords n_states_diag 8
   qp run fci 
   energy1="$(ezfio get fci energy | tr '[]' ' ' | cut -d ',' -f 1)"
   eq $energy1 $1 $thresh

src/casscf_cipsi/50.casscf.bats

@@ -9,8 +9,8 @@ function run_stoch() {
   test_exe casscf || skip
   qp set perturbation do_pt2 True
   qp set determinants n_det_max $3
-  qp set davidson threshold_davidson 1.e-10
-  qp set davidson n_states_diag 4
+  qp set davidson_keywords threshold_davidson 1.e-10
+  qp set davidson_keywords n_states_diag 4
   qp run casscf | tee casscf.out 
   energy1="$(ezfio get casscf energy_pt2 | tr '[]' ' ' | cut -d ',' -f 1)"
   eq $energy1 $1 $thresh

src/cis/20.cis.bats

@@ -9,7 +9,7 @@ function run() {
   qp set_file $1
   qp edit --check
   qp set determinants n_states  3
-  qp set davidson threshold_davidson 1.e-12
+  qp set davidson_keywords threshold_davidson 1.e-12
   qp set mo_two_e_ints io_mo_two_e_integrals Write
   qp set_frozen_core 
   qp run cis 
@@ -59,7 +59,7 @@ function run() {
 
 @test "ClO" { # 1.65582s 2.06465s
   [[ -n $TRAVIS ]] && skip
-  run clo.ezfio -534.263560525680 -534.256601571199 -534.062020844428
+  run clo.ezfio -534.2635737789097 -534.2566081298855 -534.0620070783308
 }
 
 @test "SO" { # 1.9667s 2.91234s
@@ -69,7 +69,7 @@ function run() {
 
 @test "OH" { # 2.201s 2.65573s
   [[ -n $TRAVIS ]] && skip
-  run oh.ezfio -75.4314648243896 -75.4254639668256 -75.2707675632313
+  run oh.ezfio -75.4314822573358 -75.4254733392003 -75.2707586997333
 }
 
 @test "H2O2" { # 2.27079s 3.07875s
@@ -109,7 +109,7 @@ function run() {
 
 @test "DHNO" { # 6.42976s 12.9899s
   [[ -n $TRAVIS ]] && skip
-  run dhno.ezfio -130.4472288472718 -130.3571808164850 -130.2196257046987
+  run dhno.ezfio -130.447238897118 -130.357186843611 -130.219626716369
 }
 
 @test "CH4" { # 6.4969s 10.9157s
@@ -129,7 +129,7 @@ function run() {
 
 @test "[Cu(NH3)4]2+" { # 29.7711s  3.45478m
   [[ -n ${TRAVIS} ]] && skip
-  run  cu_nh3_4_2plus.ezfio -1862.97958885180 -1862.92457657404 -1862.91134959451
+  run  cu_nh3_4_2plus.ezfio -1862.97958844302 -1862.92454785007 -1862.91130869967
 
 }
 

src/cisd/30.cisd.bats

@@ -8,10 +8,9 @@ function run() {
   test_exe cisd || skip
   qp edit --check
   qp set determinants n_states  2
-  qp set davidson threshold_davidson 1.e-12
-  qp set davidson n_states_diag 24
-  qp run cis
-  qp run cisd 
+  qp set davidson_keywords threshold_davidson 1.e-12
+  qp set davidson_keywords n_states_diag 24
+  qp run cisd
   energy1="$(qp get cisd energy | tr '[]' ' ' | cut -d ',' -f 1)"
   energy2="$(qp get cisd energy | tr '[]' ' ' | cut -d ',' -f 2)"
   eq $energy1 $1 $thresh
@@ -19,7 +18,7 @@ function run() {
 }
 
 
-@test "B-B" { # 
+@test "B-B" { #
   qp set_file b2_stretched.ezfio
   qp set_frozen_core
   run  -49.120607088648597 -49.055152453388231
@@ -34,7 +33,7 @@ function run() {
 @test "HBO" { # 4.42968s  19.6099s
   qp set_file hbo.ezfio
   qp set_frozen_core
-  run -100.2019254455993 -99.79484127741013 
+  run -100.2019254455993 -99.79484127741013
 }
 
 @test "HCO" { # 6.6077s 28.6801s
@@ -46,7 +45,7 @@ function run() {
 @test "H2O" { # 7.0651s 30.6642s
   qp set_file h2o.ezfio
   qp set_frozen_core
-  run -76.22975602077072 -75.80609108747208 
+  run -76.22975602077072 -75.80609108747208
 }
 
 
@@ -78,7 +77,7 @@ function run() {
   [[ -n $TRAVIS ]] && skip
   qp set_file oh.ezfio
   qp set_frozen_core
-  run -75.6087472926588 -75.5370393736601
+  run -75.6088105201621  -75.5370802925698
 }
 
 @test "CH4" { # 19.821s 1.38648m
@@ -105,8 +104,9 @@ function run() {
 @test "DHNO" { # 24.7077s 1.46487m
   [[ -n $TRAVIS ]] && skip
   qp set_file dhno.ezfio
-  qp set_mo_class --core="[1-7]" --act="[8-64]" 
-  run -130.458814562403 -130.356308303681
+  qp set_mo_class --core="[1-7]" --act="[8-64]"
+  run -130.4659881027444 -130.2692384198501
+#  run -130.458814562403 -130.356308303681
 }
 
 @test "H3COH" { # 24.7248s 1.85043m
@@ -120,7 +120,7 @@ function run() {
   [[ -n $TRAVIS ]] && skip
   qp set_file cu_nh3_4_2plus.ezfio
   qp set_mo_class --core="[1-24]" --act="[25-45]" --del="[46-87]"
-  run -1862.98689579931  -1862.6883044626563
+  run -1862.98310702274  -1862.88506319755
 
 }
 
@@ -135,14 +135,14 @@ function run() {
   [[ -n $TRAVIS ]] && skip
   qp set_file c2h2.ezfio
   qp set_mo_class --act="[1-30]" --del="[31-36]"
-  run -12.3566731164213 -11.9495394759914 
+  run -12.3566731164213 -11.9495394759914
 }
 
 @test "ClO" { # 37.6949s
   [[ -n $TRAVIS ]] && skip
   qp set_file clo.ezfio
   qp set_frozen_core
-  run -534.5404021326773 -534.3818725793897 
+  run -534.540464615019  -534.381904487587
 }
 
 @test "F2" { # 45.2078s
@@ -155,7 +155,7 @@ function run() {
 @test "SO2" { # 47.6922s
   [[ -n $TRAVIS ]] && skip
   qp set_file so2.ezfio
-  qp set_mo_class --core="[1-8]" --act="[9-87]" 
+  qp set_mo_class --core="[1-8]" --act="[9-87]"
   run -41.5746738710350 -41.3800467740750
 }
 
@@ -177,7 +177,7 @@ function run() {
   [[ -n $TRAVIS ]] && skip
   qp set_file n2.ezfio
   qp set_mo_class --core="[1,2]" --act="[3-40]" --del="[41-60]"
-  run -109.275693633982 -108.757794570948 
+  run -109.275693633982 -108.757794570948
 }
 
 @test "HCN" { # 133.8696s

src/dft_one_e/NEED

@@ -4,6 +4,4 @@ mo_one_e_ints
 mo_two_e_ints
 ao_one_e_ints
 ao_two_e_ints
-mo_two_e_erf_ints
-ao_two_e_erf_ints
 mu_of_r

src/dft_one_e/mu_erf_dft.irp.f

@@ -3,7 +3,7 @@ BEGIN_PROVIDER [double precision, mu_erf_dft]
  BEGIN_DOC
 ! range separation parameter used in RS-DFT. 
 ! 
-! It is set to mu_erf in order to be consistent with the module "ao_two_e_erf_ints"
+! It is set to mu_erf in order to be consistent with the module "hamiltonian"
  END_DOC
  mu_erf_dft = mu_erf
 

src/dummy/NEED

@@ -1,6 +1,5 @@
 ao_basis
 ao_one_e_ints
-ao_two_e_erf_ints
 ao_two_e_ints
 aux_quantities
 becke_numerical_grid
@@ -24,13 +23,13 @@ functionals
 generators_cas
 generators_full
 hartree_fock
+hamiltonian
 iterations
 kohn_sham
 kohn_sham_rs
 mo_basis
 mo_guess
 mo_one_e_ints
-mo_two_e_erf_ints
 mo_two_e_ints
 mpi
 nuclei

src/ezfio_files/00.create.bats

@@ -53,7 +53,6 @@ function run {
 
 
 @test "B-B" {
-  qp set_file b2_stretched.ezfio
   run b2_stretched.zmt 1 0 6-31g
 }
 

src/ezfio_files/ezfio.irp.f

@@ -33,6 +33,8 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
 
   call ezfio_set_file(ezfio_filename)
 
+IRP_IF MACOS
+IRP_ELSE
   ! Adjust out-of-memory killer flag such that the current process will be
   ! killed first by the OOM killer, allowing compute nodes to survive
   integer :: getpid
@@ -40,6 +42,7 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
   write(pidc,*) getpid()
   write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
   call system(command)
+IRP_ENDIF
 
   PROVIDE file_lock
 

src/hamiltonian/EZFIO.cfg

@@ -0,0 +1,8 @@
+[mu_erf]
+type: double precision
+doc: cutting of the interaction in the range separated model
+interface: ezfio,provider,ocaml
+default: 0.5
+ezfio_name: mu_erf
+
+

src/hamiltonian/README.rst

@@ -0,0 +1,5 @@
+===========
+hamiltonian
+===========
+
+Parameters of the Hamiltonian.

src/hartree_fock/10.hf.bats

@@ -39,7 +39,7 @@ rm -rf $EZFIO
 qp create_ezfio -b def2-svp hcn.xyz -o $EZFIO
 qp run scf
 mv hcn_charges.xyz ${EZFIO}_point_charges.xyz
-python write_pt_charges.py ${EZFIO}
+python3 write_pt_charges.py ${EZFIO}
 qp set nuclei point_charges True
 qp run scf | tee ${EZFIO}.pt_charges.out
   energy="$(ezfio get hartree_fock energy)"

src/kohn_sham_rs/61.rsks.bats

@@ -13,7 +13,7 @@ function run() {
   qp set scf_utils thresh_scf 1.e-10
   qp set dft_keywords exchange_functional $functional
   qp set dft_keywords correlation_functional $functional
-  qp set ao_two_e_erf_ints mu_erf 0.5 
+  qp set hamiltonian mu_erf 0.5 
   qp set becke_numerical_grid grid_type_sgn 1 
   qp_reset --mos $1 
   qp run rs_ks_scf 

src/mo_two_e_erf_ints/EZFIO.cfg

@@ -1,6 +0,0 @@
-[io_mo_two_e_integrals_erf]
-type: Disk_access
-doc: Read/Write MO integrals with the long range interaction from/to disk [    Write | Read | None ]
-interface: ezfio,provider,ocaml
-default: None
-

src/mo_two_e_erf_ints/NEED

@@ -1,3 +0,0 @@
-ao_two_e_erf_ints
-mo_two_e_ints
-mo_basis

src/mo_two_e_erf_ints/README.rst

@@ -1,20 +0,0 @@
-======================
-mo_two_e_erf_ints
-======================
-
-Here, all two-electron integrals (:math:`erf({\mu}_{erf} * r_{12})/r_{12}`) are computed.
-As they have 4 indices and many are zero, they are stored in a map, as defined
-in :file:`Utils/map_module.f90`.
-
-The range separation parameter :math:`{\mu}_{erf}` is the variable :option:`ao_two_e_erf_ints mu_erf`.
-
-To fetch an |MO| integral, use
-`get_mo_two_e_integral_erf(i,j,k,l,mo_integrals_map_erf)`
-
-The conventions are:
-
-* For |MO| integrals : <ij|kl> = <12|12>
-
-Be aware that it might not be the same conventions for |MO| and |AO| integrals.
-
-

src/mo_two_e_ints/EZFIO.cfg

@@ -17,3 +17,10 @@ doc: If `True`, computes all integrals except for the integrals having 3 or 4 vi
 interface: ezfio,provider,ocaml
 default: false
 
+[io_mo_two_e_integrals_erf]
+type: Disk_access
+doc: Read/Write MO integrals with the long range interaction from/to disk [    Write | Read | None ]
+interface: ezfio,provider,ocaml
+default: None
+
+

src/mo_two_e_ints/mo_bi_integrals_erf.irp.f

@@ -9,25 +9,27 @@ subroutine mo_two_e_integrals_erf_index(i,j,k,l,i1)
   integer(key_kind)              :: p,q,r,s,i2
   p = min(i,k)
   r = max(i,k)
-  p = p+ishft(r*r-r,-1)
+  p = p+shiftr(r*r-r,1)
   q = min(j,l)
   s = max(j,l)
-  q = q+ishft(s*s-s,-1)
+  q = q+shiftr(s*s-s,1)
   i1 = min(p,q)
   i2 = max(p,q)
-  i1 = i1+ishft(i2*i2-i2,-1)
+  i1 = i1+shiftr(i2*i2-i2,1)
 end
 
 
 BEGIN_PROVIDER [ logical, mo_two_e_integrals_erf_in_map ]
   use map_module
   implicit none
-  integer(bit_kind)              :: mask_ijkl(N_int,4)
-  integer(bit_kind)              :: mask_ijk(N_int,3)
-
   BEGIN_DOC
   ! If True, the map of MO two-electron integrals is provided
   END_DOC
+  integer(bit_kind)              :: mask_ijkl(N_int,4)
+  integer(bit_kind)              :: mask_ijk(N_int,3)
+  double precision               :: cpu_1, cpu_2, wall_1, wall_2
+
+  PROVIDE mo_class
 
   real                           :: map_mb
 
@@ -55,7 +57,7 @@ BEGIN_PROVIDER [ logical, mo_two_e_integrals_erf_in_map ]
   if (write_mo_two_e_integrals_erf) then
     call ezfio_set_work_empty(.False.)
     call map_save_to_disk(trim(ezfio_filename)//'/work/mo_ints_erf',mo_integrals_erf_map)
-    call ezfio_set_mo_two_e_erf_ints_io_mo_two_e_integrals_erf("Read")
+    call ezfio_set_mo_two_e_ints_io_mo_two_e_integrals_erf("Read")
   endif
 
 END_PROVIDER

src/mo_two_e_ints/routines_save_integrals_erf.irp.f

@@ -4,7 +4,7 @@ subroutine save_erf_two_e_integrals_mo
  PROVIDE mo_two_e_integrals_erf_in_map
  call ezfio_set_work_empty(.False.)
  call map_save_to_disk(trim(ezfio_filename)//'/work/mo_ints_erf',mo_integrals_erf_map)
- call ezfio_set_mo_two_e_erf_ints_io_mo_two_e_integrals_erf('Read')
+ call ezfio_set_mo_two_e_ints_io_mo_two_e_integrals_erf('Read')
 end
 
 

src/mu_of_r/mu_of_r_conditions.irp.f

@@ -128,7 +128,7 @@
  BEGIN_PROVIDER [double precision, mu_average_prov, (N_states)]
  implicit none
  BEGIN_DOC
- ! average value of mu(r) weighted with the total one-e density and divised by the number of electrons 
+ ! average value of mu(r) weighted with the total one-e density and divided by the number of electrons 
  !
  ! !!!!!! WARNING !!!!!! if no_core_density == .True. then all contributions from the core orbitals 
  !

src/non_h_ints_mu/tc_integ_num.irp.f

@@ -47,7 +47,7 @@
   call total_memory(mem)
   mem      = max(1.d0, qp_max_mem - mem)
   n_double = mem * 1.d8
-  n_blocks = min(n_double / (n_points_extra_final_grid * 4), 1.d0*n_points_final_grid)
+  n_blocks = int(min(n_double / (n_points_extra_final_grid * 4.d0), 1.d0*n_points_final_grid))
   n_rest   = int(mod(n_points_final_grid, n_blocks))
   n_pass   = int((n_points_final_grid - n_rest) / n_blocks)
 

src/nuclei/write_pt_charges.py

@@ -52,7 +52,7 @@ fncharges.write(" "+str(n_charges)+'\n')
 fncharges.close()
 mv_in_ezfio(EZFIO,tmp)
 
-# Write the file containing the charges and set in EZFIO folder 
+# Write the file containing the charges and set in EZFIO folder
 tmp="pts_charge_z"
 fcharges = open(tmp,'w')
 fcharges.write(" 1\n")

src/tc_bi_ortho/save_tc_bi_ortho_nat.irp.f

@@ -15,7 +15,20 @@ program tc_natorb_bi_ortho
   PROVIDE tc_grid1_a tc_grid1_r
   my_n_pt_r_grid = tc_grid1_r
   my_n_pt_a_grid = tc_grid1_a
-  touch  my_grid_becke my_n_pt_r_grid my_n_pt_a_grid
+  touch my_grid_becke my_n_pt_r_grid my_n_pt_a_grid
+
+  if(j1b_type .ge. 100) then
+    my_extra_grid_becke  = .True.
+    PROVIDE tc_grid2_a tc_grid2_r
+    my_n_pt_r_extra_grid = tc_grid2_r
+    my_n_pt_a_extra_grid = tc_grid2_a
+    touch my_extra_grid_becke my_n_pt_r_extra_grid my_n_pt_a_extra_grid
+
+    call write_int(6, my_n_pt_r_extra_grid, 'radial  internal grid over')
+    call write_int(6, my_n_pt_a_extra_grid, 'angular internal grid over')
+  endif
+
+
 
   read_wf = .True.
   touch read_wf

src/tc_bi_ortho/tc_natorb.irp.f

@@ -29,6 +29,12 @@
     write(*, '(100(F16.10,X))') -dm_tmp(:,i)
   enddo
 
+  print *, ' Transition density matrix AO'
+  do i = 1, ao_num
+    write(*, '(100(F16.10,X))') tc_transition_matrix_ao(:,i,1,1)
+  enddo
+  stop
+
   thr_d   = 1.d-6
   thr_nd  = 1.d-6
   thr_deg = 1.d-3

src/tc_scf/11.tc_scf.bats

@@ -8,15 +8,15 @@ function run_Ne() {
   rm -rf Ne_tc_scf
   echo Ne > Ne.xyz
   qp create_ezfio -b cc-pcvdz Ne.xyz -o Ne_tc_scf
-  qp run scf 
+  qp run scf
 
-  qp set ao_two_e_erf_ints mu_erf 0.87
+  qp set hamiltonian mu_erf 0.87
   qp set tc_keywords j1b_type 3
-  qp set tc_keywords j1b_pen [1.5] 
-  qp set tc_keywords bi_ortho True 
+  qp set tc_keywords j1b_pen [1.5]
+  qp set tc_keywords bi_ortho True
   qp set tc_keywords test_cycle_tc True
 
-  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out 
+  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out
   eref=-128.552134
   energy="$(qp get tc_scf bitc_energy)"
   eq $energy $eref 1e-6
@@ -24,22 +24,22 @@ function run_Ne() {
 
 
 @test "Ne" {
- run_Ne 
+ run_Ne
 }
 
 function run_C() {
   rm -rf C_tc_scf
   echo C  > C.xyz
   qp create_ezfio -b cc-pcvdz C.xyz -o C_tc_scf -m 3
-  qp run scf 
+  qp run scf
 
-  qp set ao_two_e_erf_ints mu_erf 0.87
+  qp set hamiltonian mu_erf 0.87
   qp set tc_keywords j1b_type 3
-  qp set tc_keywords j1b_pen [1.5] 
-  qp set tc_keywords bi_ortho True 
+  qp set tc_keywords j1b_pen [1.5]
+  qp set tc_keywords bi_ortho True
   qp set tc_keywords test_cycle_tc True
 
-  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out 
+  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out
   eref=-37.691254356408791
   energy="$(qp get tc_scf bitc_energy)"
   eq $energy $eref 1e-6
@@ -47,7 +47,7 @@ function run_C() {
 
 
 @test "C" {
- run_C 
+ run_C
 }
 
 
@@ -55,15 +55,15 @@ function run_O() {
   rm -rf O_tc_scf
   echo O  > O.xyz
   qp create_ezfio -b cc-pcvdz O.xyz -o O_tc_scf -m 3
-  qp run scf 
+  qp run scf
 
-  qp set ao_two_e_erf_ints mu_erf 0.87
+  qp set hamiltonian mu_erf 0.87
   qp set tc_keywords j1b_type 3
-  qp set tc_keywords j1b_pen [1.5] 
-  qp set tc_keywords bi_ortho True 
+  qp set tc_keywords j1b_pen [1.5]
+  qp set tc_keywords bi_ortho True
   qp set tc_keywords test_cycle_tc True
 
-  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out 
+  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out
   eref=-74.814687229354590
   energy="$(qp get tc_scf bitc_energy)"
   eq $energy $eref 1e-6
@@ -71,7 +71,7 @@ function run_O() {
 
 
 @test "O" {
- run_O 
+ run_O
 }
 
 
@@ -79,16 +79,16 @@ function run_O() {
 function run_ch2() {
   rm -rf ch2_tc_scf
   cp ${QP_ROOT}/tests/input/ch2.xyz .
-  qp create_ezfio -b "C:cc-pcvdz|H:cc-pvdz" ch2.xyz -o ch2_tc_scf 
-  qp run scf 
+  qp create_ezfio -b "C:cc-pcvdz|H:cc-pvdz" ch2.xyz -o ch2_tc_scf
+  qp run scf
 
-  qp set ao_two_e_erf_ints mu_erf 0.87
+  qp set hamiltonian mu_erf 0.87
   qp set tc_keywords j1b_type 3
   qp set tc_keywords j1b_pen '[1.5,10000,10000]'
   qp set tc_keywords bi_ortho True
   qp set tc_keywords test_cycle_tc True
 
-  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out 
+  qp run tc_scf | tee ${EZFIO_FILE}.tc_scf.out
   eref=-38.903247818077737
   energy="$(qp get tc_scf bitc_energy)"
   eq $energy $eref 1e-6
@@ -96,6 +96,6 @@ function run_ch2() {
 
 
 @test "ch2" {
- run_ch2 
+ run_ch2
 }
 

src/tc_scf/fock_three_hermit.irp.f

@@ -95,7 +95,12 @@ BEGIN_PROVIDER [double precision, diag_three_elem_hf]
 
   if(.not. three_body_h_tc) then
 
-    diag_three_elem_hf = 0.d0
+   if(noL_standard) then
+      PROVIDE noL_0e
+      diag_three_elem_hf = noL_0e
+    else
+      diag_three_elem_hf = 0.d0
+    endif
 
   else
 

src/tc_scf/rh_tcscf_diis.irp.f

@@ -71,10 +71,7 @@ subroutine rh_tcscf_diis()
   etc_tot = TC_HF_energy
   etc_1e  = TC_HF_one_e_energy
   etc_2e  = TC_HF_two_e_energy
-  etc_3e  = 0.d0
-  if(three_body_h_tc) then
-    etc_3e = diag_three_elem_hf
-  endif
+  etc_3e  = diag_three_elem_hf
   !tc_grad = grad_non_hermit
   er_DIIS = maxval(abs(FQS_SQF_mo))
   e_delta = dabs(etc_tot - e_save)
@@ -202,10 +199,7 @@ subroutine rh_tcscf_diis()
     etc_tot = TC_HF_energy
     etc_1e  = TC_HF_one_e_energy
     etc_2e  = TC_HF_two_e_energy
-    etc_3e  = 0.d0
-    if(three_body_h_tc) then
-      etc_3e = diag_three_elem_hf
-    endif
+    etc_3e  = diag_three_elem_hf
     !tc_grad  = grad_non_hermit
     er_DIIS  = maxval(abs(FQS_SQF_mo))
     e_delta  = dabs(etc_tot - e_save)

src/tools/NEED

@@ -1,5 +1,4 @@
 fci
-mo_two_e_erf_ints
 aux_quantities
 hartree_fock
 two_body_rdm

src/utils/memory.irp.f

@@ -33,6 +33,8 @@ subroutine resident_memory(value)
   call usleep(10)
 
   value = 0.d0
+IRP_IF MACOS
+IRP_ELSE
   iunit = getUnitAndOpen('/proc/self/status','r')
   do
     read(iunit,*,err=10,end=20) key, value
@@ -43,6 +45,7 @@ subroutine resident_memory(value)
   end do
   20 continue
   close(iunit)
+IRP_ENDIF
   value = value / (1024.d0*1024.d0)
   call unlock_io()
 end function
@@ -58,6 +61,9 @@ subroutine total_memory(value)
   double precision, intent(out) :: value
 
   call lock_io()
+  value = 0.d0
+IRP_IF MACOS
+IRP_ELSE
   iunit = getUnitAndOpen('/proc/self/status','r')
   do
     read(iunit,*,err=10,end=20) key, value
@@ -68,6 +74,7 @@ subroutine total_memory(value)
   end do
   20 continue
   close(iunit)
+IRP_ENDIF
   value = value / (1024.d0*1024.d0)
   call unlock_io()
 end function