LCPQ/quantum_package
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Code Issues Releases Wiki Activity

Merge pull request #23 from LCPQ/master

Browse Source 
Merge with scemama
This commit is contained in:
Thomas Applencourt 2015-07-02 09:22:03 +02:00
commit 46fe6fcc92
11 changed files with 102 additions and 84 deletions
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2
config/ifort.cfg
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@ -31,7 +31,7 @@ OPENMP : 1 ; Append OpenMP flags
# -ftz : Flushes denormal results to zero
#
[OPT]
FCFLAGS : -xHost -O2 -ip -opt-prefetch -ftz
FCFLAGS : -xHost -O2 -ip -opt-prefetch -ftz -g
# Profiling flags
#################

10
configure vendored
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@ -429,8 +429,9 @@ def create_ninja_and_rc(l_installed):
if os.path.isdir(path):
l_python.append(path)
l_rc = [
'export QP_ROOT={0}'.format(QP_ROOT),
l_rc = [ 'export QP_ROOT={0}'.format(QP_ROOT) ] + \
[ i.replace(QP_ROOT,"${QP_ROOT}") for i in
[
'export QP_EZFIO={0}'.format(find_path('ezfio', l_installed)),
'export IRPF90={0}'.format(find_path("irpf90", l_installed)),
'export NINJA={0}'.format(find_path("ninja", l_installed)),
@ -438,10 +439,11 @@ def create_ninja_and_rc(l_installed):
'export PYTHONPATH="${QP_PYTHON}":"${PYTHONPATH}"',
'export PATH="${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml:"${PATH}"',
'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', ""
'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', "",
'source ${QP_ROOT}/install/EZFIO/Bash/ezfio.sh', "",
'source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true',
""
]
] ]
path = join(QP_ROOT, "quantum_package.rc")
with open(path, "w+") as f:

3
plugins/CAS_SD/.gitignore vendored
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@ -1,4 +1,4 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
@ -6,7 +6,6 @@ tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f

7
plugins/Full_CI/.gitignore vendored
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@ -1,4 +1,4 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
@ -6,7 +6,6 @@ tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
@ -28,6 +27,6 @@ Nuclei
Hartree_Fock
Properties
target_pt2
full_ci
full_ci_no_skip
var_pt2_ratio
full_ci_no_skip
full_ci

3
plugins/MRCC/.gitignore vendored
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@ -1,4 +1,4 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
@ -6,7 +6,6 @@ tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f

3
plugins/MRCC/mrcc.irp.f
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@ -59,6 +59,9 @@ subroutine run_mrcc
call diagonalize_ci_dressed
E_new = sum(ci_energy_dressed)
delta_E = dabs(E_new - E_old)
if (iteration > 20) then
exit
endif
enddo
call write_double(6,ci_energy_dressed(1),"Final MRCC energy")
call ezfio_set_mrcc_energy(ci_energy_dressed(1))

36
plugins/Perturbation/README.rst
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@ -85,92 +85,92 @@ Documentation
Undocumented
`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
`perturb_buffer_by_mono_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
`perturb_buffer_by_mono_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L686>`_
`perturb_buffer_by_mono_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L791>`_
`perturb_buffer_by_mono_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L581>`_
`perturb_buffer_by_mono_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L476>`_
`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L371>`_
`perturb_buffer_by_mono_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L161>`_
Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L266>`_
`perturb_buffer_by_mono_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L56>`_
`perturb_buffer_by_mono_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L896>`_
Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
`perturb_buffer_delta_rho_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
`perturb_buffer_dipole_moment_z <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L635>`_
`perturb_buffer_epstein_nesbet <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L740>`_
`perturb_buffer_epstein_nesbet_2x2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L530>`_
`perturb_buffer_epstein_nesbet_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L425>`_
`perturb_buffer_epstein_nesbet_sc2_no_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L320>`_
`perturb_buffer_epstein_nesbet_sc2_projected <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L110>`_
Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L215>`_
`perturb_buffer_h_core <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply
routine.
`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L5>`_
`perturb_buffer_moller_plesset <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/perturbation.irp.f_shell_13#L845>`_
Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply
routine.

37
plugins/QmcChem/.gitignore vendored
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@ -1,26 +1,23 @@
#
# Do not modify this file. Add your ignored files to the gitignore
# (without the dot at the beginning) file.
#
# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90.make
tags
Makefile.depend
irpf90_entities
build.ninja
tags
irpf90.make
Makefile
Makefile.depend
.ninja_log
.ninja_deps
Pseudo
Integrals_Monoelec
Bitmask
Integrals_Bielec
AOs
MOs
Determinants
Electrons
DensityFit
Utils
Nuclei
ezfio_interface.irp.f
Ezfio_files
save_for_qmcchem
Determinants
Integrals_Monoelec
MO_Basis
Utils
Pseudo
Bitmask
AO_Basis
Electrons
Nuclei
Integrals_Bielec
save_for_qmcchem

2
plugins/QmcChem/NEEDED_CHILDREN_MODULES
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@ -1 +1 @@
Determinants DensityFit
Determinants

23
plugins/QmcChem/README.rst
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@ -8,41 +8,25 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script.
`ao_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L225>`_
`ao_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L2>`_
Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C
.br
<img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
`aux_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L1>`_
Pseudo-potential
`aux_pseudo_integral_local <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L15>`_
Local pseudo-potential
`aux_pseudo_integral_non_local <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L121>`_
Local pseudo-potential
`mo_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L276>`_
`mo_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L56>`_
Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \phi_i^{A} (r-r_A) d\Omega_C
.br
<img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
`pseudo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pseudo.irp.f#L12>`_
Pseudo-potential expressed in the basis of ao products
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/save_for_qmcchem.irp.f#L1>`_
Undocumented
`test_pseudo_grid_ao <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L321>`_
`test_pseudo_grid_ao <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L105>`_
Undocumented
@ -58,5 +42,4 @@ Needed Modules
.. image:: tree_dependency.png
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `DensityFit <http://github.com/LCPQ/quantum_package/tree/master/src/DensityFit>`_

60
src/Ezfio_files/README.rst
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@ -38,51 +38,87 @@ Documentation
Output file for Bitmask
`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
Output file for CAS_SD
`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
Initial CPU and wall times when printing in the output files
`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
Output file for Determinants
`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
Output file for Electrons
`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
Output file for Ezfio_files
`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
Output file for Full_CI
`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
Output file for Generators_CAS
`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
Output file for Generators_full
`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
Output file for Hartree_Fock
`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
Output file for Integrals_Bielec
`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
Output file for Integrals_Monoelec
`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
Output file for MO_Basis
`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
Output file for MOGuess
`output_molden <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
Output file for Molden
`output_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
Output file for MRCC
`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
Output file for Nuclei
`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
Output file for Perturbation
`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
Output file for Properties
`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
Output file for Pseudo
`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
Output file for QmcChem
`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
Output file for Selectors_full
`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
Output file for Utils