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Merge pull request #50 from scemama/master

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merge
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Emmanuel Giner 2019-01-08 19:16:34 +01:00 committed by GitHub
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9 changed files with 57 additions and 27 deletions
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11
TODO
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@ -42,3 +42,14 @@
# EZFIO sans fork
Refaire les benchmarks
# Commande qp avec completion dans le shell
* qp set => ezfio set
* qp get => ezfio get
* qp run => qp_run
* qp srun => qp_run
* qp mpirun => qp_run
* qp edit => qp_edit
* qp set_mo_class => qp_set_mo_class
* qp set_frozen_core => qp_set_frozen_core

20
docs/source/users_guide/qp_export_as_tgz.rst
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@ -4,6 +4,22 @@ qp_export_as_tgz
.. program:: qp_export_as_tgz
.. TODO
In some HPC facilities, the access to the internet is limited for security reasons.
In such an environment, the installation of |QP| is sometimes very painful because
the OCaml compiler and the libraries can't be installed by a non-root user.
This command creates a self-contained binary distribution in the form of a `tar.gz` file
that can be copied on another machine.
Usage
-----
.. code:: bash
qp_export_as_tgz
.. note::
There can be conflicts due to the version of Glibc. The machine on which |QP| is
compiled should be the oldest one.
.. include:: /work.rst

6
quantum_package.rc.default
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@ -25,6 +25,11 @@ export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib:"$
export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)
function qp() {
ezfio $@
}
# EZFIO completion
if [[ $SHELL == "/bin/bash" ]] ; then
if [[ -f ${QP_EZFIO}/Bash/ezfio.sh ]]; then
source ${QP_EZFIO}/Bash/ezfio.sh
@ -33,6 +38,7 @@ if [[ $SHELL == "/bin/bash" ]] ; then
fi
fi
#### END Don't modify

4
scripts/qp_export_as_tgz
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@ -176,10 +176,10 @@ sed "s!^export QP_ROOT=.*\$!export QP_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}")
echo "Creating the archive"
# --------------------
tar --gzip --compress --file "${QPACKAGE_STATIC}".tar.gz quantum_package_static && rm --recursive --force -- "${QPACKAGE_STATIC}"
tar --create --gzip --file "${QPACKAGE_STATIC}".tar.gz quantum_package_static && rm --recursive --force -- "${QPACKAGE_STATIC}"
if [[ $? -ne 0 ]] ;
then
echo 'tar --gzip --compress --file "${QPACKAGE_STATIC}".tar.gz "${QPACKAGE_STATIC}" && rm --recursive --force -- "${QPACKAGE_STATIC}"'
echo 'tar --create --gzip --file "${QPACKAGE_STATIC}".tar.gz "${QPACKAGE_STATIC}" && rm --recursive --force -- "${QPACKAGE_STATIC}"'
exit 1
fi

4
scripts/qp_mpirun
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@ -49,7 +49,7 @@ fi
# Check if the integrals can be read
source ${QP_ROOT}/external/ezfio/Bash/ezfio.sh
ezfio set_file $INPUT
RW=$(ezfio get integrals_bielec disk_access_mo_integrals)
RW=$(ezfio set mo_two_e_ints io_mo_two_e_integrals)
if [[ $RW != Read ]]
then
echo "
@ -60,7 +60,7 @@ Two-electron integrals were not saved to disk in a previous run.
If the 4-index transformation takes time, you may consider
killing this job and running
qp_run Four_idx_transform $INPUT
qp_run four_idx_transform $INPUT
as a single-node job before re-submitting the current job.

4
scripts/qp_srun
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@ -49,7 +49,7 @@ fi
# Check if the integrals can be read
source ${QP_ROOT}/external/ezfio/Bash/ezfio.sh
ezfio set_file $INPUT
RW=$(ezfio get integrals_bielec disk_access_mo_integrals)
RW=$(ezfio get mo_two_e_ints io_mo_two_e_integrals)
if [[ $RW != Read ]]
then
echo "
@ -60,7 +60,7 @@ Two-electron integrals were not saved to disk in a previous run.
If the 4-index transformation takes time, you may consider
killing this job and running
qp_run Four_idx_transform $INPUT
qp_run four_idx_transform $INPUT
as a single-node job before re-submitting the current job.

2
src/cipsi/pt2_stoch_routines.irp.f
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@ -257,8 +257,6 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
call make_selection_buffer_s2(b)
endif
call fill_H_apply_buffer_no_selection(b%cur,b%det,N_int,0)
call copy_H_apply_buffer_to_wf()
call save_wavefunction
endif
call delete_selection_buffer(b)

19
src/cipsi/stochastic_cipsi.irp.f
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@ -5,7 +5,7 @@ subroutine run_stochastic_cipsi
END_DOC
integer :: i,j,k
double precision, allocatable :: pt2(:), variance(:), norm(:), rpt2(:)
integer :: N_det_before, N_occ_pattern_before, to_select
integer :: to_select
double precision :: rss
double precision, external :: memory_of_double
@ -52,9 +52,6 @@ subroutine run_stochastic_cipsi
call save_wavefunction
endif
N_det_before = 0
N_occ_pattern_before = 0
double precision :: correlation_energy_ratio
double precision :: error(N_states)
@ -68,8 +65,6 @@ subroutine run_stochastic_cipsi
write(*,'(A)') '--------------------------------------------------------------------------------'
N_det_before = N_det
N_occ_pattern_before = N_occ_pattern
to_select = N_det
to_select = max(N_states_diag, to_select)
@ -77,7 +72,7 @@ subroutine run_stochastic_cipsi
variance = 0.d0
norm = 0.d0
call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, &
norm, to_select) ! Stochastic PT2
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)
@ -85,16 +80,20 @@ subroutine run_stochastic_cipsi
call save_energy(psi_energy_with_nucl_rep, pt2)
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_before,N_occ_pattern_before)
call print_summary(psi_energy_with_nucl_rep,pt2,error,variance,norm,N_det,N_occ_pattern,N_states)
do k=1,N_states
rpt2(:) = pt2(:)/(1.d0 + norm(k))
enddo
call save_iterations(psi_energy_with_nucl_rep(1:N_states),rpt2,N_det_before)
call save_iterations(psi_energy_with_nucl_rep(1:N_states),rpt2,N_det)
call print_extrapolated_energy()
N_iter += 1
! Add selected determinants
call copy_H_apply_buffer_to_wf()
call save_wavefunction
PROVIDE psi_coef
PROVIDE psi_det
PROVIDE psi_det_sorted
@ -123,7 +122,7 @@ subroutine run_stochastic_cipsi
rpt2(:) = pt2(:)/(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)
call print_summary(psi_energy_with_nucl_rep(1:N_states),pt2,error,variance,norm,N_det,N_occ_pattern,N_states)
call save_iterations(psi_energy_with_nucl_rep(1:N_states),rpt2,N_det)
call print_extrapolated_energy()

14
src/iterations/print_summary.irp.f
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@ -1,16 +1,16 @@
subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_)
subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_,n_st)
implicit none
BEGIN_DOC
! Print the extrapolated energy in the output
END_DOC
double precision, intent(in) :: e_(N_states), pt2_(N_states), variance_(N_states), norm_(N_states), error_(N_states)
integer, intent(in) :: n_det_, n_occ_pattern_
integer, intent(in) :: n_det_, n_occ_pattern_, n_st
double precision, intent(in) :: e_(n_st), pt2_(n_st), variance_(n_st), norm_(n_st), error_(n_st)
integer :: i, k
integer :: N_states_p
character*(9) :: pt2_string
character*(512) :: fmt
double precision :: f(N_states)
double precision :: f(n_st)
if (do_pt2) then
pt2_string = ' '
@ -18,7 +18,7 @@ subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_)
pt2_string = '(approx)'
endif
N_states_p = min(N_det_,N_states)
N_states_p = min(N_det_,n_st)
do i=1,N_states_p
f(i) = 1.d0/(1.d0+norm_(i))
@ -57,7 +57,7 @@ subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_)
print *, ''
print *, 'N_det = ', N_det_
print *, 'N_states = ', N_states
print *, 'N_states = ', n_st
if (s2_eig) then
print *, 'N_sop = ', N_occ_pattern_
endif
@ -76,7 +76,7 @@ subroutine print_summary(e_,pt2_,error_,variance_,norm_,n_det_,n_occ_pattern_)
enddo
print *, '-----'
if(N_states.gt.1)then
if(n_st.gt.1)then
print *, 'Variational Energy difference (au | eV)'
do i=2, N_states_p
print*,'Delta E = ', (e_(i) - e_(1)), &