mirror of
https://github.com/LCPQ/quantum_package
synced 2024-12-22 20:35:19 +01:00
Thomas Applencourt
commit
447b3b3523
29
.travis.yml
29
.travis.yml
@ -1,17 +1,28 @@
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sudo: true
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#
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#cache:
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# directories:
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# - $HOME/.opam/
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#sudo: true
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#before_script:
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# - sudo apt-get update -q
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# - sudo apt-get install gfortran liblapack-dev gcc
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# - sudo apt-get install graphviz
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sudo: false
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addons:
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apt:
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packages:
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- gfortran
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- gcc
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- liblapack-dev
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- graphviz
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cache:
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directories:
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- $HOME/.opam/
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language: python
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python:
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- "2.6"
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before_script:
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- sudo apt-get update -q
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- sudo apt-get install gfortran liblapack-dev gcc
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- sudo apt-get install graphviz
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script:
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- ./configure --production ./config/gfortran.cfg
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@ -29,7 +29,17 @@ Documentation
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Alpha Fock matrix in AO basis set
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`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
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`big <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/test.irp.f#L1>`_
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Produce `Huckel` MO orbital
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output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
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Produce `Hartree_Fock` MO orbital
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output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
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output: hartree_fock.energy
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input: mo_basis.mo_coef
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Run SCF calculation
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`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
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Create an MO guess if no MOs are present in the EZFIO directory
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@ -139,12 +149,15 @@ Documentation
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Maximum number of SCF iterations
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`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
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`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L38>`_
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Run SCF calculation
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`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
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Undocumented
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`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L1>`_
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Produce `Hartree_Fock` MO orbital
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output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
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output: hartree_fock.energy
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optional: mo_basis.mo_coef
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`thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_
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@ -1,5 +1,10 @@
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program scf
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BEGIN_DOC
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! Produce `Hartree_Fock` MO orbital
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! output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
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! output: hartree_fock.energy
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! optional: mo_basis.mo_coef
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END_DOC
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call create_guess
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call orthonormalize_mos
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call run
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@ -12,15 +12,17 @@ subroutine huckel_guess
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TOUCH mo_coef
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label = "Guess"
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call mo_as_eigvectors_of_mo_matrix(mo_mono_elec_integral, &
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size(mo_mono_elec_integral,1),size(mo_mono_elec_integral,2),label)
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size(mo_mono_elec_integral,1), &
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size(mo_mono_elec_integral,2),label)
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TOUCH mo_coef
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c = 0.5d0 * 1.75d0
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do j=1,ao_num
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do i=1,ao_num
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if (i/=j) then
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if (i.ne.j) then
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Fock_matrix_ao(i,j) = c*ao_overlap(i,j)*(ao_mono_elec_integral(i,i) + &
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ao_mono_elec_integral(j,j))
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ao_mono_elec_integral(j,j))
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else
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Fock_matrix_ao(i,j) = Fock_matrix_alpha_ao(i,j)
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endif
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@ -8,7 +8,7 @@ Documentation
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This program performs a localization of the active orbitals
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of a CASSCF wavefunction, reading the orbitals from a RASORB
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file of molcas.
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id1=max number of MO in a given symmetry.
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id1=max is the number of MO in a given symmetry.
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Needed Modules
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==============
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@ -19,11 +19,14 @@ try:
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from read_compilation_cfg import get_compilation_option
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from docopt import docopt
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except ImportError:
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f = os.path.realpath(os.path.join(os.path.dirname(__file__),"..","..","quantum_package.rc"))
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f = os.path.realpath(os.path.join(os.path.dirname(__file__),
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"..",
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"..",
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"quantum_package.rc"))
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print """
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Error:
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source %s
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"""%f
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""" % f
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sys.exit(1)
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# __
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@ -311,8 +314,11 @@ def ninja_symlink_build(path_module, l_symlink):
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if not l_symlink:
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return []
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l_string = ["build l_symlink_{0} : phony {1}".format(
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path_module.rel, " ".join([s.destination for s in l_symlink])), ""]
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l_folder = [s.destination for s in l_symlink]
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l_string = ["build l_symlink_{0} : phony {1}".format(path_module.rel,
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" ".join(l_folder)),
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""]
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for symlink in l_symlink:
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l_string += ["build {0}: build_symlink {1}".format(symlink.destination,
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@ -334,20 +340,22 @@ def ninja_gitignore_rule():
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" description = Create gitignore for $module_rel", ""]
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def ninja_gitignore_build(path_module, d_binaries):
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def ninja_gitignore_build(path_module, d_binaries, l_symlink):
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"""
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"""
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path_gitignore = join(path_module.abs, ".gitignore")
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l_b = [i.abs for i in d_binaries[path_module]]
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l_sym = [i.destination for i in l_symlink]
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l_string = ["build {0}: build_gitignore {1} || l_symlink_{2}".format(path_gitignore,
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" ".join(l_b),
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path_module.rel),
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" module_rel = {0}".format(path_module.rel),
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""]
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root = "build {0}: build_gitignore {1}".format(path_gitignore,
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" ".join(l_b))
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if l_symlink:
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l_string = ["{0} || l_symlink_{1}".format(root, path_module.rel)]
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else:
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l_string = ["{0}".format(root)]
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l_string.extend((" module_rel = {0}".format(path_module.rel), ""))
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return l_string
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@ -909,7 +917,8 @@ if __name__ == "__main__":
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l_string += ninja_binaries_build(module_to_compile, l_children,
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d_binaries)
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l_string += ninja_gitignore_build(module_to_compile, d_binaries)
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l_string += ninja_gitignore_build(module_to_compile, d_binaries,
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l_symlink)
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with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
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f.write(header)
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@ -86,6 +86,7 @@ from os.path import isdir, join, exists
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from qp_path import QP_ROOT, QP_SRC, QP_OCAML, QP_EZFIO
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Type = namedtuple('Type', 'fancy ocaml fortran')
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Module = namedtuple('Module', 'path lower')
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def is_bool(str_):
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@ -789,8 +790,6 @@ if __name__ == "__main__":
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l_module_with_ezfio = []
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Module = namedtuple('Module', 'path lower')
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for f in l_module:
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path = join(QP_SRC, f, "EZFIO.cfg")
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if exists(path):
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@ -174,8 +174,16 @@ class ModuleHandler():
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def create_png(self, l_module):
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"""Create the png of the dependency tree for a l_module"""
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path = '{0}.png'.format("tree_dependency")
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# Init
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import pydot
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try:
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import pydot
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except:
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with open(path, 'a'):
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os.utime(path, None)
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return
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all_ready_done = []
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def draw_module_edge(module, l_children):
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@ -190,16 +198,7 @@ class ModuleHandler():
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draw_module_edge(children, d_ref[children])
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all_ready_done.append(module)
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path = '{0}.png'.format("tree_dependency")
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# Init
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try:
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graph = pydot.Dot(graph_type='digraph')
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except:
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with open(path, 'a'):
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os.utime(path, None)
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return
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graph = pydot.Dot(graph_type='digraph')
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d_ref = self.dict_child
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# Create all the edge
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@ -16,6 +16,7 @@ Options:
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import sys
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import os
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import subprocess
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try:
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from docopt import docopt
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@ -152,6 +153,11 @@ if __name__ == '__main__':
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except OSError:
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print "Your src directory is broken. Please remove %s" % des
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raise
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try:
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import subprocess
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subprocess.check_call(["qp_create_ninja.py", "update"])
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except:
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raise
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print "Done"
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print "You can now compile as usual"
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@ -164,24 +170,29 @@ if __name__ == '__main__':
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l_name = arguments["<name>"]
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l_failed = [name for name in l_name if name not in d_local]
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if l_failed:
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print "Modules not installed:"
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for name in sorted(l_failed):
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print "* %s" % name
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sys.exit(1)
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if arguments["--and_ancestor"]:
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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]]
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print "You will remove all of:"
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print l_name_to_remove
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else:
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if arguments["--and_ancestor"]:
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l_name_to_remove = l_name
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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]]
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print "You will remove all of:"
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print l_name_to_remove
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for module in l_name_to_remove:
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else:
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l_name_to_remove = l_name
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try:
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subprocess.check_call(["module_handler.py", "clean", module])
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except:
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raise
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def unlink(x):
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try:
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os.unlink(os.path.join(QP_SRC, x))
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except OSError:
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print "%s is a core module which can not be renmoved" % x
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map(unlink, l_name_to_remove)
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try:
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os.unlink(os.path.join(QP_SRC, module))
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except OSError:
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print "%s is a core module which can not be renmoved" % x
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@ -26,130 +26,157 @@ import re
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import subprocess
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import tempfile
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import copy
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import sys
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import dot_parser
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try:
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import dot_parser
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except Exception as e:
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pass
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# print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible."
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GRAPH_ATTRIBUTES = set(['Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor',
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'center', 'charset', 'clusterrank', 'colorscheme', 'comment', 'compound',
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'concentrate', 'defaultdist', 'dim', 'dimen', 'diredgeconstraints',
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'dpi', 'epsilon', 'esep', 'fontcolor', 'fontname', 'fontnames',
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'fontpath', 'fontsize', 'id', 'label', 'labeljust', 'labelloc',
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'landscape', 'layers', 'layersep', 'layout', 'levels', 'levelsgap',
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'lheight', 'lp', 'lwidth', 'margin', 'maxiter', 'mclimit', 'mindist',
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'mode', 'model', 'mosek', 'nodesep', 'nojustify', 'normalize', 'nslimit',
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'nslimit1', 'ordering', 'orientation', 'outputorder', 'overlap',
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'overlap_scaling', 'pack', 'packmode', 'pad', 'page', 'pagedir',
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'quadtree', 'quantum', 'rankdir', 'ranksep', 'ratio', 'remincross',
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'repulsiveforce', 'resolution', 'root', 'rotate', 'searchsize', 'sep',
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'showboxes', 'size', 'smoothing', 'sortv', 'splines', 'start',
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'stylesheet', 'target', 'truecolor', 'viewport', 'voro_margin',
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GRAPH_ATTRIBUTES = set(['Damping',
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'K',
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'URL',
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'aspect',
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'bb',
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'bgcolor',
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'center',
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'charset',
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'clusterrank',
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'colorscheme',
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'comment',
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'compound',
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'concentrate',
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'defaultdist',
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'dim',
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'dimen',
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'diredgeconstraints',
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'dpi',
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'epsilon',
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'esep',
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'fontcolor',
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'fontname',
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'fontnames',
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'fontpath',
|
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'fontsize',
|
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'id',
|
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'label',
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'labeljust',
|
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'labelloc',
|
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'landscape',
|
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'layers',
|
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'layersep',
|
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'layout',
|
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'levels',
|
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'levelsgap',
|
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'lheight',
|
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'lp',
|
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'lwidth',
|
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'margin',
|
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'maxiter',
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'mclimit',
|
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'mindist',
|
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'mode',
|
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'model',
|
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'mosek',
|
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'nodesep',
|
||||
'nojustify',
|
||||
'normalize',
|
||||
'nslimit',
|
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'nslimit1',
|
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'ordering',
|
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'orientation',
|
||||
'outputorder',
|
||||
'overlap',
|
||||
'overlap_scaling',
|
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'pack',
|
||||
'packmode',
|
||||
'pad',
|
||||
'page',
|
||||
'pagedir',
|
||||
'quadtree',
|
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'quantum',
|
||||
'rankdir',
|
||||
'ranksep',
|
||||
'ratio',
|
||||
'remincross',
|
||||
'repulsiveforce',
|
||||
'resolution',
|
||||
'root',
|
||||
'rotate',
|
||||
'searchsize',
|
||||
'sep',
|
||||
'showboxes',
|
||||
'size',
|
||||
'smoothing',
|
||||
'sortv',
|
||||
'splines',
|
||||
'start',
|
||||
'stylesheet',
|
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'target',
|
||||
'truecolor',
|
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'viewport',
|
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'voro_margin',
|
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# for subgraphs
|
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'rank'])
|
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|
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EDGE_ATTRIBUTES = set(
|
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['URL', 'arrowhead', 'arrowsize', 'arrowtail', 'color', 'colorscheme',
|
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'comment', 'constraint', 'decorate', 'dir', 'edgeURL', 'edgehref',
|
||||
'edgetarget', 'edgetooltip', 'fontcolor', 'fontname', 'fontsize',
|
||||
'headURL', 'headclip', 'headhref', 'headlabel', 'headport', 'headtarget',
|
||||
'headtooltip', 'href', 'id', 'label', 'labelURL', 'labelangle',
|
||||
'labeldistance', 'labelfloat', 'labelfontcolor', 'labelfontname',
|
||||
'labelfontsize', 'labelhref', 'labeltarget', 'labeltooltip', 'layer',
|
||||
'len', 'lhead', 'lp', 'ltail', 'minlen', 'nojustify', 'penwidth', 'pos',
|
||||
'samehead', 'sametail', 'showboxes', 'style', 'tailURL', 'tailclip',
|
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'tailhref', 'taillabel', 'tailport', 'tailtarget', 'tailtooltip',
|
||||
'target', 'tooltip', 'weight', 'rank'])
|
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|
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EDGE_ATTRIBUTES = set(['URL',
|
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'arrowhead',
|
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'arrowsize',
|
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'arrowtail',
|
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NODE_ATTRIBUTES = set(['URL',
|
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'color',
|
||||
'colorscheme',
|
||||
'comment',
|
||||
'constraint',
|
||||
'decorate',
|
||||
'dir',
|
||||
'edgeURL',
|
||||
'edgehref',
|
||||
'edgetarget',
|
||||
'edgetooltip',
|
||||
'distortion',
|
||||
'fillcolor',
|
||||
'fixedsize',
|
||||
'fontcolor',
|
||||
'fontname',
|
||||
'fontsize',
|
||||
'headURL',
|
||||
'headclip',
|
||||
'headhref',
|
||||
'headlabel',
|
||||
'headport',
|
||||
'headtarget',
|
||||
'headtooltip',
|
||||
'href',
|
||||
'group',
|
||||
'height',
|
||||
'id',
|
||||
'image',
|
||||
'imagescale',
|
||||
'label',
|
||||
'labelURL',
|
||||
'labelangle',
|
||||
'labeldistance',
|
||||
'labelfloat',
|
||||
'labelfontcolor',
|
||||
'labelfontname',
|
||||
'labelfontsize',
|
||||
'labelhref',
|
||||
'labeltarget',
|
||||
'labeltooltip',
|
||||
'labelloc',
|
||||
'layer',
|
||||
'len',
|
||||
'lhead',
|
||||
'lp',
|
||||
'ltail',
|
||||
'minlen',
|
||||
'margin',
|
||||
'nojustify',
|
||||
'orientation',
|
||||
'penwidth',
|
||||
'peripheries',
|
||||
'pin',
|
||||
'pos',
|
||||
'samehead',
|
||||
'sametail',
|
||||
'rects',
|
||||
'regular',
|
||||
'root',
|
||||
'samplepoints',
|
||||
'shape',
|
||||
'shapefile',
|
||||
'showboxes',
|
||||
'sides',
|
||||
'skew',
|
||||
'sortv',
|
||||
'style',
|
||||
'tailURL',
|
||||
'tailclip',
|
||||
'tailhref',
|
||||
'taillabel',
|
||||
'tailport',
|
||||
'tailtarget',
|
||||
'tailtooltip',
|
||||
'target',
|
||||
'tooltip',
|
||||
'weight',
|
||||
'rank'])
|
||||
|
||||
|
||||
NODE_ATTRIBUTES = set(['URL', 'color', 'colorscheme', 'comment',
|
||||
'distortion', 'fillcolor', 'fixedsize', 'fontcolor', 'fontname',
|
||||
'fontsize', 'group', 'height', 'id', 'image', 'imagescale', 'label',
|
||||
'labelloc', 'layer', 'margin', 'nojustify', 'orientation', 'penwidth',
|
||||
'peripheries', 'pin', 'pos', 'rects', 'regular', 'root', 'samplepoints',
|
||||
'shape', 'shapefile', 'showboxes', 'sides', 'skew', 'sortv', 'style',
|
||||
'target', 'tooltip', 'vertices', 'width', 'z',
|
||||
'vertices',
|
||||
'width',
|
||||
'z',
|
||||
# The following are attributes dot2tex
|
||||
'texlbl', 'texmode'])
|
||||
'texlbl',
|
||||
'texmode'])
|
||||
|
||||
|
||||
CLUSTER_ATTRIBUTES = set(['K',
|
||||
'URL',
|
||||
'bgcolor',
|
||||
'color',
|
||||
'colorscheme',
|
||||
'fillcolor',
|
||||
'fontcolor',
|
||||
'fontname',
|
||||
'fontsize',
|
||||
'label',
|
||||
'labeljust',
|
||||
'labelloc',
|
||||
'lheight',
|
||||
'lp',
|
||||
'lwidth',
|
||||
'nojustify',
|
||||
'pencolor',
|
||||
'penwidth',
|
||||
'peripheries',
|
||||
'sortv',
|
||||
'style',
|
||||
'target',
|
||||
'tooltip'])
|
||||
CLUSTER_ATTRIBUTES = set(
|
||||
['K', 'URL', 'bgcolor', 'color', 'colorscheme', 'fillcolor', 'fontcolor',
|
||||
'fontname', 'fontsize', 'label', 'labeljust', 'labelloc', 'lheight', 'lp',
|
||||
'lwidth', 'nojustify', 'pencolor', 'penwidth', 'peripheries', 'sortv',
|
||||
'style', 'target', 'tooltip'])
|
||||
|
||||
|
||||
#
|
||||
@ -160,9 +187,9 @@ CLUSTER_ATTRIBUTES = set(['K',
|
||||
# This version freezes dictionaries used as values within dictionaries.
|
||||
#
|
||||
class frozendict(dict):
|
||||
|
||||
def _blocked_attribute(obj):
|
||||
raise AttributeError("A frozendict cannot be modified.")
|
||||
|
||||
_blocked_attribute = property(_blocked_attribute)
|
||||
|
||||
__delitem__ = __setitem__ = clear = _blocked_attribute
|
||||
@ -213,8 +240,7 @@ dot_keywords = ['graph', 'subgraph', 'digraph', 'node', 'edge', 'strict']
|
||||
|
||||
id_re_alpha_nums = re.compile('^[_a-zA-Z][a-zA-Z0-9_,]*$', re.UNICODE)
|
||||
id_re_alpha_nums_with_ports = re.compile(
|
||||
'^[_a-zA-Z][a-zA-Z0-9_,:\"]*[a-zA-Z0-9_,\"]+$',
|
||||
re.UNICODE)
|
||||
'^[_a-zA-Z][a-zA-Z0-9_,:\"]*[a-zA-Z0-9_,\"]+$', re.UNICODE)
|
||||
id_re_num = re.compile('^[0-9,]+$', re.UNICODE)
|
||||
id_re_with_port = re.compile('^([^:]*):([^:]*)$', re.UNICODE)
|
||||
id_re_dbl_quoted = re.compile('^\".*\"$', re.S | re.UNICODE)
|
||||
@ -245,11 +271,9 @@ def needs_quotes(s):
|
||||
return True
|
||||
|
||||
for test_re in [
|
||||
id_re_alpha_nums,
|
||||
id_re_num,
|
||||
id_re_dbl_quoted,
|
||||
id_re_html,
|
||||
id_re_alpha_nums_with_ports]:
|
||||
id_re_alpha_nums, id_re_num, id_re_dbl_quoted, id_re_html,
|
||||
id_re_alpha_nums_with_ports
|
||||
]:
|
||||
if test_re.match(s):
|
||||
return False
|
||||
|
||||
@ -274,9 +298,7 @@ def quote_if_necessary(s):
|
||||
return s
|
||||
|
||||
if needs_quotes(s):
|
||||
replace = {'"': r'\"',
|
||||
"\n": r'\n',
|
||||
"\r": r'\r'}
|
||||
replace = {'"': r'\"', "\n": r'\n', "\r": r'\r'}
|
||||
for (a, b) in replace.items():
|
||||
s = s.replace(a, b)
|
||||
|
||||
@ -374,8 +396,7 @@ def graph_from_adjacency_matrix(matrix, node_prefix=u'', directed=False):
|
||||
for e in r:
|
||||
if e:
|
||||
graph.add_edge(
|
||||
Edge(node_prefix + node_orig,
|
||||
node_prefix + node_dest))
|
||||
Edge(node_prefix + node_orig, node_prefix + node_dest))
|
||||
node_dest += 1
|
||||
node_orig += 1
|
||||
|
||||
@ -410,8 +431,7 @@ def graph_from_incidence_matrix(matrix, node_prefix='', directed=False):
|
||||
|
||||
if len(nodes) == 2:
|
||||
graph.add_edge(
|
||||
Edge(node_prefix + abs(nodes[0]),
|
||||
node_prefix + nodes[1]))
|
||||
Edge(node_prefix + abs(nodes[0]), node_prefix + nodes[1]))
|
||||
|
||||
if not directed:
|
||||
graph.set_simplify(True)
|
||||
@ -437,7 +457,8 @@ def __find_executables(path):
|
||||
'neato': '',
|
||||
'circo': '',
|
||||
'fdp': '',
|
||||
'sfdp': ''}
|
||||
'sfdp': ''
|
||||
}
|
||||
|
||||
was_quoted = False
|
||||
path = path.strip()
|
||||
@ -533,11 +554,7 @@ def find_graphviz():
|
||||
def RegOpenKeyEx(key, subkey, opt, sam):
|
||||
result = ctypes.c_uint(0)
|
||||
ctypes.windll.advapi32.RegOpenKeyExA(
|
||||
key,
|
||||
subkey,
|
||||
opt,
|
||||
sam,
|
||||
ctypes.byref(result))
|
||||
key, subkey, opt, sam, ctypes.byref(result))
|
||||
return result.value
|
||||
|
||||
def RegQueryValueEx(hkey, valuename):
|
||||
@ -546,11 +563,7 @@ def find_graphviz():
|
||||
data = ctypes.create_string_buffer(1024)
|
||||
|
||||
res = ctypes.windll.advapi32.RegQueryValueExA(
|
||||
hkey,
|
||||
valuename,
|
||||
0,
|
||||
ctypes.byref(data_type),
|
||||
data,
|
||||
hkey, valuename, 0, ctypes.byref(data_type), data,
|
||||
ctypes.byref(data_len))
|
||||
|
||||
return data.value
|
||||
@ -574,8 +587,8 @@ def find_graphviz():
|
||||
for potentialKey in potentialKeys:
|
||||
|
||||
try:
|
||||
hkey = RegOpenKeyEx(HKEY_LOCAL_MACHINE,
|
||||
potentialKey, 0, KEY_QUERY_VALUE)
|
||||
hkey = RegOpenKeyEx(HKEY_LOCAL_MACHINE, potentialKey, 0,
|
||||
KEY_QUERY_VALUE)
|
||||
|
||||
if hkey is not None:
|
||||
path = RegQueryValueEx(hkey, "InstallPath")
|
||||
@ -625,10 +638,7 @@ def find_graphviz():
|
||||
# information, but win32api may not be installed.
|
||||
|
||||
path = os.path.join(
|
||||
os.environ['PROGRAMFILES'],
|
||||
'ATT',
|
||||
'GraphViz',
|
||||
'bin')
|
||||
os.environ['PROGRAMFILES'], 'ATT', 'GraphViz', 'bin')
|
||||
|
||||
else:
|
||||
|
||||
@ -643,10 +653,8 @@ def find_graphviz():
|
||||
return progs
|
||||
|
||||
for path in (
|
||||
'/usr/bin', '/usr/local/bin',
|
||||
'/opt/local/bin',
|
||||
'/opt/bin', '/sw/bin', '/usr/share',
|
||||
'/Applications/Graphviz.app/Contents/MacOS/'):
|
||||
'/usr/bin', '/usr/local/bin', '/opt/local/bin', '/opt/bin', '/sw/bin',
|
||||
'/usr/share', '/Applications/Graphviz.app/Contents/MacOS/'):
|
||||
|
||||
progs = __find_executables(path)
|
||||
if progs is not None:
|
||||
@ -659,7 +667,6 @@ def find_graphviz():
|
||||
|
||||
|
||||
class Common:
|
||||
|
||||
"""Common information to several classes.
|
||||
|
||||
Should not be directly used, several classes are derived from
|
||||
@ -771,22 +778,17 @@ class Common:
|
||||
# Generate all the Setter methods.
|
||||
#
|
||||
self.__setattr__(
|
||||
'set_' +
|
||||
attr,
|
||||
lambda x,
|
||||
a=attr: self.obj_dict['attributes'].__setitem__(
|
||||
a,
|
||||
x))
|
||||
'set_' + attr,
|
||||
lambda x, a=attr: self.obj_dict['attributes'].__setitem__(
|
||||
a, x))
|
||||
|
||||
# Generate all the Getter methods.
|
||||
#
|
||||
self.__setattr__(
|
||||
'get_' + attr,
|
||||
lambda a=attr: self.__get_attribute__(a))
|
||||
'get_' + attr, lambda a=attr: self.__get_attribute__(a))
|
||||
|
||||
|
||||
class Error(Exception):
|
||||
|
||||
"""General error handling class.
|
||||
"""
|
||||
|
||||
@ -798,7 +800,6 @@ class Error(Exception):
|
||||
|
||||
|
||||
class InvocationException(Exception):
|
||||
|
||||
"""To indicate that a ploblem occurred while running any of the GraphViz executables.
|
||||
"""
|
||||
|
||||
@ -810,7 +811,6 @@ class InvocationException(Exception):
|
||||
|
||||
|
||||
class Node(object, Common):
|
||||
|
||||
"""A graph node.
|
||||
|
||||
This class represents a graph's node with all its attributes.
|
||||
@ -919,7 +919,6 @@ class Node(object, Common):
|
||||
|
||||
|
||||
class Edge(object, Common):
|
||||
|
||||
"""A graph edge.
|
||||
|
||||
This class represents a graph's edge with all its attributes.
|
||||
@ -1011,8 +1010,10 @@ class Edge(object, Common):
|
||||
# If the graph is undirected, the edge has neither
|
||||
# source nor destination.
|
||||
#
|
||||
if ((self.get_source() == edge.get_source() and self.get_destination() == edge.get_destination()) or (
|
||||
edge.get_source() == self.get_destination() and edge.get_destination() == self.get_source())):
|
||||
if ((self.get_source() == edge.get_source() and
|
||||
self.get_destination() == edge.get_destination()) or (
|
||||
edge.get_source() == self.get_destination() and
|
||||
edge.get_destination() == self.get_source())):
|
||||
return True
|
||||
|
||||
else:
|
||||
@ -1035,8 +1036,8 @@ class Edge(object, Common):
|
||||
node_port_idx = node_str.rfind(':')
|
||||
|
||||
if node_port_idx > 0 and node_str[0] == '"' and node_str[
|
||||
node_port_idx -
|
||||
1] == '"':
|
||||
node_port_idx - 1
|
||||
] == '"':
|
||||
|
||||
return node_str
|
||||
|
||||
@ -1068,8 +1069,8 @@ class Edge(object, Common):
|
||||
edge = [src]
|
||||
|
||||
if (self.get_parent_graph() and
|
||||
self.get_parent_graph().get_top_graph_type() and
|
||||
self.get_parent_graph().get_top_graph_type() == 'digraph'):
|
||||
self.get_parent_graph().get_top_graph_type() and
|
||||
self.get_parent_graph().get_top_graph_type() == 'digraph'):
|
||||
|
||||
edge.append('->')
|
||||
|
||||
@ -1101,7 +1102,6 @@ class Edge(object, Common):
|
||||
|
||||
|
||||
class Graph(object, Common):
|
||||
|
||||
"""Class representing a graph in Graphviz's dot language.
|
||||
|
||||
This class implements the methods to work on a representation
|
||||
@ -1138,14 +1138,13 @@ class Graph(object, Common):
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
graph_name='G',
|
||||
obj_dict=None,
|
||||
graph_type='digraph',
|
||||
strict=False,
|
||||
suppress_disconnected=False,
|
||||
simplify=False,
|
||||
**attrs):
|
||||
self,
|
||||
graph_name='G',
|
||||
obj_dict=None,
|
||||
graph_type='digraph',
|
||||
strict=False,
|
||||
suppress_disconnected=False,
|
||||
simplify=False, **attrs):
|
||||
|
||||
if obj_dict is not None:
|
||||
self.obj_dict = obj_dict
|
||||
@ -1158,8 +1157,8 @@ class Graph(object, Common):
|
||||
|
||||
if graph_type not in ['graph', 'digraph']:
|
||||
raise Error(
|
||||
'Invalid type "%s". Accepted graph types are: graph, digraph, subgraph' %
|
||||
graph_type)
|
||||
'Invalid type "%s". Accepted graph types are: graph, digraph, subgraph'
|
||||
% graph_type)
|
||||
|
||||
self.obj_dict['name'] = quote_if_necessary(graph_name)
|
||||
self.obj_dict['type'] = graph_type
|
||||
@ -1328,17 +1327,17 @@ class Graph(object, Common):
|
||||
if not node:
|
||||
|
||||
self.obj_dict['nodes'][
|
||||
graph_node.get_name()] = [
|
||||
graph_node.obj_dict]
|
||||
graph_node.get_name()
|
||||
] = [
|
||||
graph_node.obj_dict
|
||||
]
|
||||
|
||||
#self.node_dict[graph_node.get_name()] = graph_node.attributes
|
||||
graph_node.set_parent_graph(self.get_parent_graph())
|
||||
|
||||
else:
|
||||
|
||||
self.obj_dict['nodes'][
|
||||
graph_node.get_name()].append(
|
||||
graph_node.obj_dict)
|
||||
self.obj_dict['nodes'][graph_node.get_name()].append(graph_node.obj_dict)
|
||||
|
||||
graph_node.set_sequence(self.get_next_sequence_number())
|
||||
|
||||
@ -1474,7 +1473,8 @@ class Graph(object, Common):
|
||||
|
||||
if index is not None and index < len(
|
||||
self.obj_dict['edges'][
|
||||
(src, dst)]):
|
||||
(src, dst)
|
||||
]):
|
||||
del self.obj_dict['edges'][(src, dst)][index]
|
||||
return True
|
||||
else:
|
||||
@ -1504,7 +1504,8 @@ class Graph(object, Common):
|
||||
match = list()
|
||||
|
||||
if edge_points in self.obj_dict['edges'] or (
|
||||
self.get_top_graph_type() == 'graph' and edge_points_reverse in self.obj_dict['edges']):
|
||||
self.get_top_graph_type() == 'graph' and
|
||||
edge_points_reverse in self.obj_dict['edges']):
|
||||
|
||||
edges_obj_dict = self.obj_dict['edges'].get(
|
||||
edge_points,
|
||||
@ -1513,8 +1514,7 @@ class Graph(object, Common):
|
||||
for edge_obj_dict in edges_obj_dict:
|
||||
match.append(
|
||||
Edge(
|
||||
edge_points[0],
|
||||
edge_points[1],
|
||||
edge_points[0], edge_points[1],
|
||||
obj_dict=edge_obj_dict))
|
||||
|
||||
return match
|
||||
@ -1544,10 +1544,8 @@ class Graph(object, Common):
|
||||
"""
|
||||
|
||||
if not isinstance(
|
||||
sgraph,
|
||||
Subgraph) and not isinstance(
|
||||
sgraph,
|
||||
Cluster):
|
||||
sgraph, Subgraph) and not isinstance(
|
||||
sgraph, Cluster):
|
||||
raise TypeError(
|
||||
'add_subgraph() received a non subgraph class object:' +
|
||||
str(sgraph))
|
||||
@ -1638,14 +1636,14 @@ class Graph(object, Common):
|
||||
|
||||
if self.obj_dict['name'] == '':
|
||||
if 'show_keyword' in self.obj_dict and self.obj_dict[
|
||||
'show_keyword']:
|
||||
'show_keyword'
|
||||
]:
|
||||
graph.append('subgraph {\n')
|
||||
else:
|
||||
graph.append('{\n')
|
||||
else:
|
||||
graph.append(
|
||||
'%s %s {\n' %
|
||||
(self.obj_dict['type'], self.obj_dict['name']))
|
||||
'%s %s {\n' % (self.obj_dict['type'], self.obj_dict['name']))
|
||||
|
||||
for attr in self.obj_dict['attributes'].iterkeys():
|
||||
|
||||
@ -1692,7 +1690,7 @@ class Graph(object, Common):
|
||||
if self.obj_dict.get('suppress_disconnected', False):
|
||||
|
||||
if (node.get_name() not in edge_src_set and
|
||||
node.get_name() not in edge_dst_set):
|
||||
node.get_name() not in edge_dst_set):
|
||||
|
||||
continue
|
||||
|
||||
@ -1720,7 +1718,6 @@ class Graph(object, Common):
|
||||
|
||||
|
||||
class Subgraph(Graph):
|
||||
|
||||
"""Class representing a subgraph in Graphviz's dot language.
|
||||
|
||||
This class implements the methods to work on a representation
|
||||
@ -1752,20 +1749,18 @@ class Subgraph(Graph):
|
||||
# as a graph to all methods
|
||||
#
|
||||
def __init__(
|
||||
self,
|
||||
graph_name='',
|
||||
obj_dict=None,
|
||||
suppress_disconnected=False,
|
||||
simplify=False,
|
||||
**attrs):
|
||||
self,
|
||||
graph_name='',
|
||||
obj_dict=None,
|
||||
suppress_disconnected=False,
|
||||
simplify=False, **attrs):
|
||||
|
||||
Graph.__init__(
|
||||
self,
|
||||
graph_name=graph_name,
|
||||
obj_dict=obj_dict,
|
||||
suppress_disconnected=suppress_disconnected,
|
||||
simplify=simplify,
|
||||
**attrs)
|
||||
simplify=simplify, **attrs)
|
||||
|
||||
if obj_dict is None:
|
||||
|
||||
@ -1773,7 +1768,6 @@ class Subgraph(Graph):
|
||||
|
||||
|
||||
class Cluster(Graph):
|
||||
|
||||
"""Class representing a cluster in Graphviz's dot language.
|
||||
|
||||
This class implements the methods to work on a representation
|
||||
@ -1802,20 +1796,18 @@ class Cluster(Graph):
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
graph_name='subG',
|
||||
obj_dict=None,
|
||||
suppress_disconnected=False,
|
||||
simplify=False,
|
||||
**attrs):
|
||||
self,
|
||||
graph_name='subG',
|
||||
obj_dict=None,
|
||||
suppress_disconnected=False,
|
||||
simplify=False, **attrs):
|
||||
|
||||
Graph.__init__(
|
||||
self,
|
||||
graph_name=graph_name,
|
||||
obj_dict=obj_dict,
|
||||
suppress_disconnected=suppress_disconnected,
|
||||
simplify=simplify,
|
||||
**attrs)
|
||||
simplify=simplify, **attrs)
|
||||
|
||||
if obj_dict is None:
|
||||
|
||||
@ -1826,7 +1818,6 @@ class Cluster(Graph):
|
||||
|
||||
|
||||
class Dot(Graph):
|
||||
|
||||
"""A container for handling a dot language file.
|
||||
|
||||
This class implements methods to write and process
|
||||
@ -1842,42 +1833,12 @@ class Dot(Graph):
|
||||
self.progs = None
|
||||
|
||||
self.formats = [
|
||||
'canon',
|
||||
'cmap',
|
||||
'cmapx',
|
||||
'cmapx_np',
|
||||
'dia',
|
||||
'dot',
|
||||
'fig',
|
||||
'gd',
|
||||
'gd2',
|
||||
'gif',
|
||||
'hpgl',
|
||||
'imap',
|
||||
'imap_np',
|
||||
'ismap',
|
||||
'jpe',
|
||||
'jpeg',
|
||||
'jpg',
|
||||
'mif',
|
||||
'mp',
|
||||
'pcl',
|
||||
'pdf',
|
||||
'pic',
|
||||
'plain',
|
||||
'plain-ext',
|
||||
'png',
|
||||
'ps',
|
||||
'ps2',
|
||||
'svg',
|
||||
'svgz',
|
||||
'vml',
|
||||
'vmlz',
|
||||
'vrml',
|
||||
'vtx',
|
||||
'wbmp',
|
||||
'xdot',
|
||||
'xlib']
|
||||
'canon', 'cmap', 'cmapx', 'cmapx_np', 'dia', 'dot', 'fig', 'gd',
|
||||
'gd2', 'gif', 'hpgl', 'imap', 'imap_np', 'ismap', 'jpe', 'jpeg',
|
||||
'jpg', 'mif', 'mp', 'pcl', 'pdf', 'pic', 'plain', 'plain-ext',
|
||||
'png', 'ps', 'ps2', 'svg', 'svgz', 'vml', 'vmlz', 'vrml', 'vtx',
|
||||
'wbmp', 'xdot', 'xlib'
|
||||
]
|
||||
|
||||
self.prog = 'dot'
|
||||
|
||||
@ -1885,9 +1846,7 @@ class Dot(Graph):
|
||||
# of output in any of the supported formats.
|
||||
for frmt in self.formats:
|
||||
self.__setattr__(
|
||||
'create_' + frmt,
|
||||
lambda f=frmt,
|
||||
prog=self.prog: self.create(
|
||||
'create_' + frmt, lambda f=frmt, prog=self.prog: self.create(
|
||||
format=f,
|
||||
prog=prog))
|
||||
f = self.__dict__['create_' + frmt]
|
||||
@ -1896,9 +1855,7 @@ class Dot(Graph):
|
||||
for frmt in self.formats + ['raw']:
|
||||
self.__setattr__(
|
||||
'write_' + frmt,
|
||||
lambda path,
|
||||
f=frmt,
|
||||
prog=self.prog: self.write(
|
||||
lambda path, f=frmt, prog=self.prog: self.write(
|
||||
path,
|
||||
format=f,
|
||||
prog=prog))
|
||||
@ -2036,15 +1993,14 @@ class Dot(Graph):
|
||||
if self.progs is None:
|
||||
self.progs = find_graphviz()
|
||||
if self.progs is None:
|
||||
raise InvocationException(
|
||||
'GraphViz\'s executables not found')
|
||||
raise InvocationException('GraphViz\'s executables not found')
|
||||
|
||||
if prog not in self.progs:
|
||||
raise InvocationException(
|
||||
'GraphViz\'s executable "%s" not found' % prog)
|
||||
|
||||
if not os.path.exists(
|
||||
self.progs[prog]) or not os.path.isfile(
|
||||
self.progs[prog]) or not os.path.isfile(
|
||||
self.progs[prog]):
|
||||
raise InvocationException(
|
||||
'GraphViz\'s executable "%s" is not a file or doesn\'t exist' %
|
||||
@ -2076,7 +2032,8 @@ class Dot(Graph):
|
||||
p = subprocess.Popen(
|
||||
cmdline,
|
||||
cwd=tmp_dir,
|
||||
stderr=subprocess.PIPE, stdout=subprocess.PIPE)
|
||||
stderr=subprocess.PIPE,
|
||||
stdout=subprocess.PIPE)
|
||||
|
||||
stderr = p.stderr
|
||||
stdout = p.stdout
|
||||
@ -2109,7 +2066,8 @@ class Dot(Graph):
|
||||
if status != 0:
|
||||
raise InvocationException(
|
||||
'Program terminated with status: %d. stderr follows: %s' % (
|
||||
status, stderr_output))
|
||||
status, stderr_output
|
||||
))
|
||||
elif stderr_output:
|
||||
print stderr_output
|
||||
|
||||
|
||||
3
src/Ezfio_files/.gitignore
vendored
3
src/Ezfio_files/.gitignore
vendored
@ -9,4 +9,5 @@ Makefile.depend
|
||||
build.ninja
|
||||
.ninja_log
|
||||
.ninja_deps
|
||||
ezfio_interface.irp.f
|
||||
ezfio_interface.irp.f
|
||||
README.rst
|
||||
@ -4,7 +4,7 @@ Ezfio_files Module
|
||||
|
||||
This modules essentially contains the name of the EZFIO directory in the
|
||||
``ezfio_filename`` variable. This is read as the first argument of the
|
||||
command-line, or as the ``QPACKAGE_INPUT`` environment variable.
|
||||
command-line, or as the ``QP_INPUT`` environment variable.
|
||||
Documentation
|
||||
=============
|
||||
|
||||
|
||||
@ -1,11 +1,16 @@
|
||||
program H_CORE_guess
|
||||
BEGIN_DOC
|
||||
! 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
|
||||
END_DOC
|
||||
implicit none
|
||||
character*(64) :: label
|
||||
mo_coef = ao_ortho_lowdin_coef
|
||||
TOUCH mo_coef
|
||||
label = "Guess"
|
||||
call mo_as_eigvectors_of_mo_matrix(mo_mono_elec_integral, &
|
||||
size(mo_mono_elec_integral,1),size(mo_mono_elec_integral,2),label)
|
||||
size(mo_mono_elec_integral,1), &
|
||||
size(mo_mono_elec_integral,2),label)
|
||||
print *, 'save mos'
|
||||
call save_mos
|
||||
|
||||
|
||||
@ -34,5 +34,10 @@ Documentation
|
||||
|
||||
|
||||
`h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
|
||||
Undocumented
|
||||
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
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user