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Merge tag 'fix_new_module_tag_error' into develop

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Clean before unistall
This commit is contained in:
Thomas Applencourt 2015-07-15 11:01:16 +02:00
commit a427f27f3a
5 changed files with 62 additions and 27 deletions
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1
plugins/Hartree_Fock/.gitignore vendored
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@ -21,4 +21,5 @@ MOGuess
Nuclei
Utils
Huckel_guess
test
SCF

21
plugins/Hartree_Fock/README.rst
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@ -29,7 +29,17 @@ Documentation
Alpha Fock matrix in AO basis set
`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
`big <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/test.irp.f#L1>`_
Produce `Huckel` MO orbital
output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
Produce `Hartree_Fock` MO orbital
output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
output: hartree_fock.energy
input: mo_basis.mo_coef
Run SCF calculation
`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
Create an MO guess if no MOs are present in the EZFIO directory
@ -139,12 +149,15 @@ Documentation
Maximum number of SCF iterations
`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L38>`_
Run SCF calculation
`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
Undocumented
`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L1>`_
Produce `Hartree_Fock` MO orbital
output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
output: hartree_fock.energy
optional: mo_basis.mo_coef
`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_

28
scripts/compilation/qp_create_ninja.py
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@ -26,7 +26,7 @@ except ImportError:
print """
Error:
source %s
"""%f
""" % f
sys.exit(1)
header = r"""#
@ -313,8 +313,11 @@ def ninja_symlink_build(path_module, l_symlink):
if not l_symlink:
return []
l_string = ["build l_symlink_{0} : phony {1}".format(
path_module.rel, " ".join([s.destination for s in l_symlink])), ""]
l_folder = [s.destination for s in l_symlink]
l_string = ["build l_symlink_{0} : phony {1}".format(path_module.rel,
" ".join(l_folder)),
""]
for symlink in l_symlink:
l_string += ["build {0}: build_symlink {1}".format(symlink.destination,
@ -336,20 +339,22 @@ def ninja_gitignore_rule():
" description = Create gitignore for $module_rel", ""]
def ninja_gitignore_build(path_module, d_binaries):
def ninja_gitignore_build(path_module, d_binaries, l_symlink):
"""
"""
path_gitignore = join(path_module.abs, ".gitignore")
l_b = [i.abs for i in d_binaries[path_module]]
l_sym = [i.destination for i in l_symlink]
l_string = ["build {0}: build_gitignore {1} || l_symlink_{2}".format(path_gitignore,
" ".join(l_b),
path_module.rel),
" module_rel = {0}".format(path_module.rel),
""]
root = "build {0}: build_gitignore {1}".format(path_gitignore,
" ".join(l_b))
if l_symlink:
l_string = ["{0} || l_symlink_{1}".format(root, path_module.rel)]
else:
l_string = ["{0}".format(root)]
l_string.extend((" module_rel = {0}".format(path_module.rel), ""))
return l_string
@ -911,7 +916,8 @@ if __name__ == "__main__":
l_string += ninja_binaries_build(module_to_compile, l_children,
d_binaries)
l_string += ninja_gitignore_build(module_to_compile, d_binaries)
l_string += ninja_gitignore_build(module_to_compile, d_binaries,
l_symlink)
with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
f.write(header)

35
scripts/module/qp_install_module.py
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@ -16,6 +16,7 @@ Options:
import sys
import os
import subprocess
try:
from docopt import docopt
@ -152,6 +153,11 @@ if __name__ == '__main__':
except OSError:
print "Your src directory is broken. Please remove %s" % des
raise
try:
import subprocess
subprocess.check_call(["qp_create_ninja.py", "update"])
except:
raise
print "Done"
print "You can now compile as usual"
@ -164,24 +170,29 @@ if __name__ == '__main__':
l_name = arguments["<name>"]
l_failed = [name for name in l_name if name not in d_local]
if l_failed:
print "Modules not installed:"
for name in sorted(l_failed):
print "* %s" % name
sys.exit(1)
if arguments["--and_ancestor"]:
l_name_to_remove = l_name + [module for module in m_instance.l_module for name in l_name if name in d_descendant[module]]
print "You will remove all of:"
print l_name_to_remove
else:
if arguments["--and_ancestor"]:
l_name_to_remove = l_name
l_name_to_remove = l_name + [module for module in m_instance.l_module for name in l_name if name in d_descendant[module]]
print "You will remove all of:"
print l_name_to_remove
for module in l_name_to_remove:
else:
l_name_to_remove = l_name
try:
subprocess.check_call(["module_handler.py", "clean", module])
except:
raise
def unlink(x):
try:
os.unlink(os.path.join(QP_SRC, x))
except OSError:
print "%s is a core module which can not be renmoved" % x
map(unlink, l_name_to_remove)
try:
os.unlink(os.path.join(QP_SRC, module))
except OSError:
print "%s is a core module which can not be renmoved" % x

4
src/MOGuess/README.rst
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@ -37,3 +37,7 @@ Documentation
Produce `H_core` MO orbital
output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
`hcore_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/h_core_guess_routine.irp.f#L1>`_
Produce `H_core` MO orbital