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mirror of https://github.com/LCPQ/quantum_package synced 2024-06-25 22:52:15 +02:00

Merge branch 'LCPQ-master'

Conflicts:
	scripts/module/module_handler.py
This commit is contained in:
Anthony Scemama 2017-04-20 19:20:09 +02:00
commit 9e32c9250e
44 changed files with 22 additions and 988 deletions

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@ -35,7 +35,7 @@ OPENMP : 1 ; Append OpenMP flags
# -ffast-math and the Fortran-specific
# -fno-protect-parens and -fstack-arrays.
[OPT]
FCFLAGS : -Ofast -march=native
FCFLAGS : -Ofast
# Profiling flags
#################

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@ -1,34 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Davidson
Determinants
Electrons
Ezfio_files
Generators_CAS
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
Utils
ZMQ
cas_s
cas_s_selected
cas_sd
cas_sd_selected
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,28 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Selectors_full
SingleRefMethod
Utils
cid
cid_lapack
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,31 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
CID
CID_selected
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
SingleRefMethod
Utils
cid_sc2_selection
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,30 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
CID
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
SingleRefMethod
Utils
cid_selection
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,28 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Selectors_full
SingleRefMethod
Utils
cis
ezfio_interface.irp.f
irpf90.make
irpf90_entities
super_ci
tags

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@ -1,29 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Selectors_full
SingleRefMethod
Utils
ZMQ
cisd
cisd_lapack
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,31 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
CISD
CISD_selected
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
SingleRefMethod
Utils
cisd_sc2_selection
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,31 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
CISD
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
SingleRefMethod
Utils
ZMQ
cisd_selection
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,23 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Utils
ezfio_interface.irp.f
irpf90.make
irpf90_entities
save_for_casino
tags

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@ -1,29 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
Generators_CAS
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
Utils
ddci
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

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@ -1,13 +0,0 @@
#
# Do not modify this file. Add your ignored files to the gitignore
# (without the dot at the beginning) file.
#
IRPF90_temp
IRPF90_man
irpf90.make
tags
Makefile.depend
irpf90_entities
build.ninja
.ninja_log
.ninja_deps

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@ -1,24 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Utils
ZMQ
ezfio_interface.irp.f
fcidump
irpf90.make
irpf90_entities
tags

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@ -1,34 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Davidson
Determinants
Electrons
Ezfio_files
Generators_full
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
Utils
ZMQ
ezfio_interface.irp.f
full_ci
full_ci_no_skip
irpf90.make
irpf90_entities
tags
target_pt2
var_pt2_ratio

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@ -1,23 +0,0 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
Ezfio_files
Determinants
Integrals_Monoelec
MO_Basis
Utils
Pseudo
Bitmask
AO_Basis
Electrons
Nuclei
Integrals_Bielec

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@ -1,25 +0,0 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
Ezfio_files
Determinants
Integrals_Monoelec
MO_Basis
Utils
Pseudo
Bitmask
AO_Basis
Electrons
MOGuess
Nuclei
Hartree_Fock
Integrals_Bielec

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@ -1,13 +0,0 @@
#
# Do not modify this file. Add your ignored files to the gitignore
# (without the dot at the beginning) file.
#
IRPF90_temp
IRPF90_man
irpf90.make
tags
Makefile.depend
irpf90_entities
build.ninja
.ninja_log
.ninja_deps

View File

@ -1,25 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Electrons
Ezfio_files
Huckel_guess
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
SCF
Utils
ZMQ
ezfio_interface.irp.f
irpf90.make
irpf90_entities
tags

View File

@ -1,31 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
SingleRefMethod
Utils
ZMQ
ezfio_interface.irp.f
irpf90.make
irpf90_entities
mp2
mp2_wf
tags

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@ -1,33 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Davidson
Determinants
Electrons
Ezfio_files
Generators_full
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Psiref_CAS
Psiref_Utils
Selectors_full
Utils
ZMQ
ezfio_interface.irp.f
irpf90.make
irpf90_entities
mrcc_dummy
tags

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@ -1,18 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
MO_Basis
Makefile
Makefile.depend
Nuclei
Utils
ezfio_interface.irp.f
irpf90.make
irpf90_entities
print_mo
tags

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@ -1,26 +0,0 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
Ezfio_files
Determinants
Integrals_Monoelec
MO_Basis
Utils
Pseudo
Properties
Bitmask
AO_Basis
Electrons
MOGuess
Nuclei
Hartree_Fock
Integrals_Bielec

View File

@ -1,25 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Utils
ZMQ
ezfio_interface.irp.f
irpf90.make
irpf90_entities
print_hcc
print_mulliken
tags

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@ -1,26 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Davidson
Determinants
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Psiref_Utils
Utils
ZMQ
ezfio_interface.irp.f
irpf90.make
irpf90_entities
overwrite_with_cas
tags

View File

@ -1,29 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
Generators_full
Hartree_Fock
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MOGuess
MO_Basis
Makefile
Makefile.depend
Nuclei
Perturbation
Properties
Pseudo
Selectors_full
Utils
ezfio_interface.irp.f
irpf90.make
irpf90_entities
mrcc_general
tags

View File

@ -1,25 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Bitmask
Determinants
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
Integrals_Bielec
Integrals_Monoelec
MO_Basis
Makefile
Makefile.depend
Nuclei
Pseudo
Utils
ZMQ
ezfio_interface.irp.f
irpf90.make
irpf90_entities
save_for_qmcchem
tags
target_pt2_qmc

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@ -1,25 +0,0 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
Ezfio_files
Determinants
Integrals_Monoelec
MO_Basis
Utils
Pseudo
Bitmask
AO_Basis
Electrons
MOGuess
Nuclei
Hartree_Fock
Integrals_Bielec

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@ -1,13 +0,0 @@
#
# Do not modify this file. Add your ignored files to the gitignore
# (without the dot at the beginning) file.
#
IRPF90_temp
IRPF90_man
irpf90.make
tags
Makefile.depend
irpf90_entities
build.ninja
.ninja_log
.ninja_deps

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@ -1,19 +0,0 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
Ezfio_files
MO_Basis
Utils
Bitmask
AO_Basis
Electrons
Nuclei

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@ -1,18 +0,0 @@
# Automatically created by $QP_ROOT/scripts/module/module_handler.py
.ninja_deps
.ninja_log
AO_Basis
Electrons
Ezfio_files
IRPF90_man
IRPF90_temp
MO_Basis
Makefile
Makefile.depend
Nuclei
Utils
ezfio_interface.irp.f
irpf90.make
irpf90_entities
loc_cele
tags

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@ -3,7 +3,7 @@
convert output of gamess/GAU$$IAN to ezfio
Usage:
qp_convert_output_to_ezfio.py <file.out> [-o <ezfio_directory>]
qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
Option:
file.out is the file to check (like gamess.out)
@ -20,17 +20,18 @@ from functools import reduce
# Add to the path #
# ~#~#~#~#~#~#~#~ #
try:
QP_ROOT = os.environ["QP_ROOT"]
except:
print "Error: QP_ROOT environment variable not found."
sys.exit(1)
else:
sys.path = [ QP_ROOT + "/install/EZFIO/Python",
QP_ROOT + "/resultsFile",
QP_ROOT + "/scripts"] + sys.path
# ~#~#~#~#~#~ #
# I m p o r t #
# ~#~#~#~#~#~ #
@ -271,7 +272,7 @@ def write_ezfio(res, filename):
#
# INPUT
# {% for label,zcore, l_block in l_atom $}
# {% for lanel,zcore, l_block in l_atom $}
# #local l_block l=0}
# {label} GEN {zcore} {len(l_block)-1 #lmax_block}
# {% for l_param in l_block%}
@ -279,7 +280,6 @@ def write_ezfio(res, filename):
# {% for coef,n,zeta for l_param}
# {coef,n, zeta}
# OUTPUT
# Local are 1 array padded by max(n_max_block) when l == 0 (output:k_loc_max)
@ -309,16 +309,8 @@ def write_ezfio(res, filename):
array_l_max_block.append(l_max_block)
array_z_remove.append(z_remove)
x = [[coef_n_zeta.split() for coef_n_zeta in l.split('\n')] \
for l in array_party[1:] ]
x = []
for l in array_party[1:]:
y = []
for coef_n_zeta in l.split('\n'):
z = coef_n_zeta.split()
if z : y.append(z)
x.append(y)
matrix.append(x)
matrix.append([[coef_n_zeta.split()[1:] for coef_n_zeta in l.split('\n')] for l in array_party[1:]])
return (matrix, array_l_max_block, array_z_remove)
def get_local_stuff(matrix):
@ -327,6 +319,7 @@ def write_ezfio(res, filename):
k_loc_max = max(len(i) for i in matrix_local_unpad)
matrix_local = [ pad(ll, k_loc_max, [0., 2, 0.]) for ll in matrix_local_unpad]
m_coef = [[float(i[0]) for i in atom] for atom in matrix_local]
m_n = [[int(i[1]) - 2 for i in atom] for atom in matrix_local]
m_zeta = [[float(i[2]) for i in atom] for atom in matrix_local]
@ -350,42 +343,26 @@ def write_ezfio(res, filename):
return (l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc)
try:
pseudo_str = []
label = ezfio.get_nuclei_nucl_label()
for ecp in res.pseudo:
pseudo_str += [ "%(label)s GEN %(zcore)d %(lmax)d" % { "label": label[ ecp["atom"]-1 ],
"zcore": ecp["zcore"], "lmax": ecp["lmax"] } ]
lmax = ecp["lmax"]
for l in [lmax] + list(range(0,lmax)):
pseudo_str += [ "%d"%len(ecp[str(l)]) ]
for t in ecp[str(l)]:
pseudo_str += [ "%f %d %f"%t ]
pseudo_str += [""]
pseudo_str = "\n".join(pseudo_str)
pseudo_str = res_file.get_pseudo()
matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
array_z_remove = map(float,array_z_remove)
except:
ezfio.set_pseudo_do_pseudo(False)
else:
ezfio.set_pseudo_do_pseudo(True)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.set_pseudo_nucl_charge_remove(array_z_remove)
charge = ezfio.get_nuclei_nucl_charge()
charge = [ i - j for i, j in zip(charge, array_z_remove) ]
ezfio.set_nuclei_nucl_charge (charge)
ezfio.pseudo_charge_remove = array_z_remove
ezfio.nuclei_nucl_charge = [i - j for i, j in zip(ezfio.nuclei_nucl_charge, array_z_remove)]
import math
num_elec_diff = sum(array_z_remove)/2
nalpha = ezfio.get_electrons_elec_alpha_num() - num_elec_diff
nbeta = ezfio.get_electrons_elec_beta_num() - num_elec_diff
num_elec = sum(ezfio.nuclei_nucl_charge)
ezfio.set_electrons_elec_alpha_num(nalpha)
ezfio.set_electrons_elec_beta_num( nbeta )
ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
# Change all the array 'cause EZFIO
# v_kl (v, l) => v_kl(l,v)
@ -431,8 +408,8 @@ if __name__ == '__main__':
file_ = get_full_path(arguments['<file.out>'])
if arguments["-o"]:
ezfio_file = get_full_path(arguments["<ezfio_directory>"])
if arguments["--ezfio"]:
ezfio_file = get_full_path(arguments["--ezfio"])
else:
ezfio_file = "{0}.ezfio".format(file_)
@ -444,4 +421,3 @@ if __name__ == '__main__':
print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
write_ezfio(res_file, ezfio_file)
os.system("qp_run save_ortho_mos "+ezfio_file)

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@ -253,6 +253,9 @@ if __name__ == '__main__':
m.create_png(l_module)
except RuntimeError:
pass
except SyntaxError:
print "Warning: The graphviz API dropped support for python 2.6."
pass
if arguments["clean"] or arguments["create_git_ignore"]:
@ -298,6 +301,7 @@ if __name__ == '__main__':
# Don't update if we are not in the main repository
from is_master_repository import is_master_repository
if not is_master_repository:
print >> sys.stderr, 'Not in the master repo'
sys.exit(0)
path = os.path.join(module_abs, ".gitignore")

28
src/.gitignore vendored
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@ -1,28 +0,0 @@
CAS_SD
CID
CID_SC2_selected
CID_selected
CIS
CISD
CISD_SC2_selected
CISD_selected
DDCI_selected
DensityMatrix
FCIdump
Full_CI
Generators_CAS
Generators_full
Generators_restart
Hartree_Fock
Molden
MP2
MRCC
Perturbation
Properties
QmcChem
Selectors_full
Selectors_no_sorted
SingleRefMethod
Casino
loc_cele
Alavi

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@ -1,15 +0,0 @@
# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py
IRPF90_temp
IRPF90_man
irpf90_entities
tags
irpf90.make
Makefile
Makefile.depend
build.ninja
.ninja_log
.ninja_deps
ezfio_interface.irp.f
Nuclei
Ezfio_files
Utils

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