diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index a35dbe2c..6e694ffa 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -155,7 +155,7 @@ def create_png(l_module): # Save path = '{0}.png'.format("_".join(l_module)) - print "png saved in {0}".format(path) + # print "png saved in {0}".format(path) graph.write_png(path) if __name__ == '__main__': diff --git a/scripts/module/pydot.py b/scripts/module/pydot.py index c788c137..c4a84bb6 100644 --- a/scripts/module/pydot.py +++ b/scripts/module/pydot.py @@ -31,7 +31,8 @@ import sys try: import dot_parser except Exception as e: - print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible." + pass + # print >> sys.stderr, "Couldn't import dot_parser, loading of dot files will not be possible." GRAPH_ATTRIBUTES = set(['Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor', diff --git a/scripts/run_Makefile_common.sh b/scripts/run_Makefile_common.sh index 859cc8d0..8673611e 100755 --- a/scripts/run_Makefile_common.sh +++ b/scripts/run_Makefile_common.sh @@ -66,3 +66,6 @@ ${QPACKAGE_ROOT}/scripts/module/create_Makefile_depend.sh # Update EZFIO interface ${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py + +# Create png +${QPACKAGE_ROOT}/scripts/module/module_handler.py create_png \ No newline at end of file diff --git a/scripts/update_README.py b/scripts/update_README.py index 177d57a4..49077a01 100755 --- a/scripts/update_README.py +++ b/scripts/update_README.py @@ -2,7 +2,7 @@ """Updates the README.rst file as the include directive is disabled on GitHub.""" __date__ = "Thu Apr 3 23:06:18 CEST 2014" -__author__ = "Anthony Scemama " +__author__ = "Anthony Scemama & TApplencourt" README = "README.rst" @@ -21,12 +21,6 @@ header = """ """ -try: - # subprocess.check_output("git status".split()) - has_git = True -except OSError: - has_git = False - def fetch_splitted_data(): """Read the README.rst file and split it in strings: diff --git a/src/AOs/AOs.png b/src/AOs/AOs.png new file mode 100644 index 00000000..41a281a5 Binary files /dev/null and b/src/AOs/AOs.png differ diff --git a/src/AOs/NEEDED_CHILDREN_MODULES b/src/AOs/NEEDED_CHILDREN_MODULES index 2c80725f..ac848c17 100644 --- a/src/AOs/NEEDED_CHILDREN_MODULES +++ b/src/AOs/NEEDED_CHILDREN_MODULES @@ -1 +1 @@ -Nuclei +Nuclei Utils diff --git a/src/AOs/README.rst b/src/AOs/README.rst index 3b1675ba..7a8a83ee 100644 --- a/src/AOs/README.rst +++ b/src/AOs/README.rst @@ -40,6 +40,7 @@ Needed Modules .. NEEDED_MODULES file. * `Nuclei `_ +* `Utils `_ Documentation ============= diff --git a/src/Bielec_integrals/Bielec_integrals.png b/src/Bielec_integrals/Bielec_integrals.png new file mode 100644 index 00000000..c7b29381 Binary files /dev/null and b/src/Bielec_integrals/Bielec_integrals.png differ diff --git a/src/Bitmask/Bitmask.png b/src/Bitmask/Bitmask.png new file mode 100644 index 00000000..0eb69ca7 Binary files /dev/null and b/src/Bitmask/Bitmask.png differ diff --git a/src/CAS_SD/CAS_SD.png b/src/CAS_SD/CAS_SD.png index d7d4c3d2..13d92380 100644 Binary files a/src/CAS_SD/CAS_SD.png and b/src/CAS_SD/CAS_SD.png differ diff --git a/src/CID/CID.png b/src/CID/CID.png new file mode 100644 index 00000000..5e1c8ae0 Binary files /dev/null and b/src/CID/CID.png differ diff --git a/src/CID_SC2_selected/CID_SC2_selected.png b/src/CID_SC2_selected/CID_SC2_selected.png new file mode 100644 index 00000000..5dcdedb7 Binary files /dev/null and b/src/CID_SC2_selected/CID_SC2_selected.png differ diff --git a/src/CID_selected/CID_selected.png b/src/CID_selected/CID_selected.png new file mode 100644 index 00000000..4851f85f Binary files /dev/null and b/src/CID_selected/CID_selected.png differ diff --git a/src/CIS/CIS.png b/src/CIS/CIS.png new file mode 100644 index 00000000..42ed2dd4 Binary files /dev/null and b/src/CIS/CIS.png differ diff --git a/src/CISD/CISD.png b/src/CISD/CISD.png new file mode 100644 index 00000000..1fb8e088 Binary files /dev/null and b/src/CISD/CISD.png differ diff --git a/src/CISD_SC2_selected/CISD_SC2_selected.png b/src/CISD_SC2_selected/CISD_SC2_selected.png index 85fa072a..e87a40d6 100644 Binary files a/src/CISD_SC2_selected/CISD_SC2_selected.png and b/src/CISD_SC2_selected/CISD_SC2_selected.png differ diff --git a/src/CISD_selected/CISD_selected.png b/src/CISD_selected/CISD_selected.png new file mode 100644 index 00000000..b5ce7870 Binary files /dev/null and b/src/CISD_selected/CISD_selected.png differ diff --git a/src/DDCI_selected/DDCI_selected.png b/src/DDCI_selected/DDCI_selected.png new file mode 100644 index 00000000..b3160ebc Binary files /dev/null and b/src/DDCI_selected/DDCI_selected.png differ diff --git a/src/Determinants/Determinants.png b/src/Determinants/Determinants.png new file mode 100644 index 00000000..29ed2c99 Binary files /dev/null and b/src/Determinants/Determinants.png differ diff --git a/src/Electrons/Electrons.png b/src/Electrons/Electrons.png new file mode 100644 index 00000000..8c7bb855 Binary files /dev/null and b/src/Electrons/Electrons.png differ diff --git a/src/Ezfio_files/Ezfio_files.png b/src/Ezfio_files/Ezfio_files.png new file mode 100644 index 00000000..4b0b9fd0 Binary files /dev/null and b/src/Ezfio_files/Ezfio_files.png differ diff --git a/src/Ezfio_files/README.rst b/src/Ezfio_files/README.rst index e0ef23da..4a4ce480 100644 --- a/src/Ezfio_files/README.rst +++ b/src/Ezfio_files/README.rst @@ -28,6 +28,24 @@ Documentation 'x' : READ/WRITE, FORMATTED .br +`output_cpu_time_0 `_ + Initial CPU and wall times when printing in the output files + +`output_wall_time_0 `_ + Initial CPU and wall times when printing in the output files + +`write_bool `_ + Write an logical value in output + +`write_double `_ + Write a double precision value in output + +`write_int `_ + Write an integer value in output + +`write_time `_ + Write a time stamp in the output for chronological reconstruction + diff --git a/src/FCIdump/FCIdump.png b/src/FCIdump/FCIdump.png new file mode 100644 index 00000000..f81d2d4f Binary files /dev/null and b/src/FCIdump/FCIdump.png differ diff --git a/src/FCIdump/README.rst b/src/FCIdump/README.rst index faf69203..8a467b16 100644 --- a/src/FCIdump/README.rst +++ b/src/FCIdump/README.rst @@ -10,6 +10,9 @@ Documentation .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. +`fcidump `_ + Undocumented + Needed Modules diff --git a/src/Full_CI/Full_CI.png b/src/Full_CI/Full_CI.png index c4603535..d3f1cbfb 100644 Binary files a/src/Full_CI/Full_CI.png and b/src/Full_CI/Full_CI.png differ diff --git a/src/Generators_CAS/Generators_CAS.png b/src/Generators_CAS/Generators_CAS.png new file mode 100644 index 00000000..c7ba13a2 Binary files /dev/null and b/src/Generators_CAS/Generators_CAS.png differ diff --git a/src/Generators_full/Generators_full.png b/src/Generators_full/Generators_full.png new file mode 100644 index 00000000..ee54b2d8 Binary files /dev/null and b/src/Generators_full/Generators_full.png differ diff --git a/src/Hartree_Fock/Hartree_Fock.png b/src/Hartree_Fock/Hartree_Fock.png new file mode 100644 index 00000000..51a6fc7b Binary files /dev/null and b/src/Hartree_Fock/Hartree_Fock.png differ diff --git a/src/MOGuess/MOGuess.png b/src/MOGuess/MOGuess.png new file mode 100644 index 00000000..96786bd2 Binary files /dev/null and b/src/MOGuess/MOGuess.png differ diff --git a/src/MOs/MOs.png b/src/MOs/MOs.png new file mode 100644 index 00000000..276be274 Binary files /dev/null and b/src/MOs/MOs.png differ diff --git a/src/MP2/MP2.png b/src/MP2/MP2.png new file mode 100644 index 00000000..ec81a4e6 Binary files /dev/null and b/src/MP2/MP2.png differ diff --git a/src/MRCC/MRCC.png b/src/MRCC/MRCC.png index e5570c7c..c9afd049 100644 Binary files a/src/MRCC/MRCC.png and b/src/MRCC/MRCC.png differ diff --git a/src/Molden/Hartree_Fock.png b/src/Molden/Hartree_Fock.png new file mode 100644 index 00000000..1f4747db Binary files /dev/null and b/src/Molden/Hartree_Fock.png differ diff --git a/src/Molden/Molden.png b/src/Molden/Molden.png index b993bb3a..fd419b86 100644 Binary files a/src/Molden/Molden.png and b/src/Molden/Molden.png differ diff --git a/src/MonoInts/MonoInts.png b/src/MonoInts/MonoInts.png new file mode 100644 index 00000000..123f3008 Binary files /dev/null and b/src/MonoInts/MonoInts.png differ diff --git a/src/MonoInts/NEEDED_CHILDREN_MODULES b/src/MonoInts/NEEDED_CHILDREN_MODULES index 62dc97d3..31cf3c24 100644 --- a/src/MonoInts/NEEDED_CHILDREN_MODULES +++ b/src/MonoInts/NEEDED_CHILDREN_MODULES @@ -1 +1 @@ -MOs Pseudo Utils +MOs Pseudo diff --git a/src/MonoInts/README.rst b/src/MonoInts/README.rst index c5c8d2af..2f5d4e07 100644 --- a/src/MonoInts/README.rst +++ b/src/MonoInts/README.rst @@ -6,7 +6,6 @@ Needed Modules * `MOs `_ * `Pseudo `_ -* `Utils `_ Documentation ============= @@ -115,6 +114,9 @@ Documentation mo_nucl_elec_integral_per_atom(i,j,k) = - where Rk is the geometry of the kth atom +`mo_pseudo_integral `_ + interaction nuclear electron on the MO basis + `save_ortho_mos `_ Undocumented diff --git a/src/Nuclei/Nuclei.png b/src/Nuclei/Nuclei.png new file mode 100644 index 00000000..91922cea Binary files /dev/null and b/src/Nuclei/Nuclei.png differ diff --git a/src/Pseudo/Pseudo.png b/src/Pseudo/Pseudo.png new file mode 100644 index 00000000..ce0dbd5b Binary files /dev/null and b/src/Pseudo/Pseudo.png differ diff --git a/src/Pseudo_integrals/Molden.png b/src/Pseudo_integrals/Molden.png new file mode 100644 index 00000000..c087d6f9 Binary files /dev/null and b/src/Pseudo_integrals/Molden.png differ diff --git a/src/Selectors_full/Selectors_full.png b/src/Selectors_full/Selectors_full.png new file mode 100644 index 00000000..e8d35ba8 Binary files /dev/null and b/src/Selectors_full/Selectors_full.png differ diff --git a/src/Utils/Utils.png b/src/Utils/Utils.png new file mode 100644 index 00000000..68f0c2ca Binary files /dev/null and b/src/Utils/Utils.png differ