From e4d2eda17f029b48e0270061e0004231ab0313e0 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 21 Jul 2015 10:11:12 +0200 Subject: [PATCH 01/11] Add python --- configure | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure b/configure index 90f52769..e87badbb 100755 --- a/configure +++ b/configure @@ -451,7 +451,7 @@ def create_ninja_and_rc(l_installed): 'export IRPF90={0}'.format(path_irpf90), 'export NINJA={0}'.format(path_ninja), 'export QP_PYTHON={0}'.format(":".join(l_python)), "", - 'export PYTHONPATH="${QP_PYTHON}":"${PYTHONPATH}"', + 'export PYTHONPATH="${QP_EZFIO}":"${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}"', "", From 97df8d192254aa87c344d41e917aa56c8c527912 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 09:46:38 +0200 Subject: [PATCH 02/11] Fix graphiz --- scripts/module/module_handler.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index 9160a49d..99200994 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -180,13 +180,7 @@ class ModuleHandler(): basename = "tree_dependency" path = '{0}.png'.format(basename) - # Init - try: - from graphviz import Digraph - except: - with open(path, 'a'): - os.utime(path, None) - return + from graphviz import Digraph all_ready_done = [] @@ -209,7 +203,12 @@ class ModuleHandler(): graph.node(module, fontcolor="red") draw_module_edge(module, d_ref[module]) - graph.render(cleanup=True) + try: + graph.render(cleanup=True) + except: + with open(path, 'a'): + os.utime(path, None) + return if __name__ == '__main__': From a56df23d9a0e51a6058f9f115cee6c2302c626cf Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 09:48:47 +0200 Subject: [PATCH 03/11] Remove graphiz dependancy for testing purpose --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 0e78a8c6..af20008b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,7 @@ addons: - gfortran - gcc - liblapack-dev - - graphviz +# - graphviz cache: directories: From d36d9e317784d2da75e7799516dedf18c36b1ccd Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 10:03:14 +0200 Subject: [PATCH 04/11] Add beter instruction for readme --- .travis.yml | 2 +- scripts/module/module_handler.py | 2 ++ scripts/module/qp_install_module.py | 3 ++- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index af20008b..0e78a8c6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,7 @@ addons: - gfortran - gcc - liblapack-dev -# - graphviz + - graphviz cache: directories: diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index 99200994..b79e03b9 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -203,6 +203,8 @@ class ModuleHandler(): graph.node(module, fontcolor="red") draw_module_edge(module, d_ref[module]) + # Try to render the png + # If not just touch it try: graph.render(cleanup=True) except: diff --git a/scripts/module/qp_install_module.py b/scripts/module/qp_install_module.py index 1c9911a6..80d418a6 100755 --- a/scripts/module/qp_install_module.py +++ b/scripts/module/qp_install_module.py @@ -108,8 +108,9 @@ if __name__ == '__main__': save_new_module(path, l_child_reduce) print " [ OK ]" - print "If this was a plugins, you can install it normaly. Type:" + print "You can now install it normaly. Type:" print "` {0} install {1} `".format(os.path.basename(__file__), name) + print "And don't forgot to add this to the git if you want" elif arguments["download"]: pass From 5e98b8c2ae6d24b28624d333822f9a524987478d Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 10:23:17 +0200 Subject: [PATCH 05/11] Beter separation in development mode and production one --- scripts/compilation/qp_create_ninja.py | 51 +++++++++++++++++--------- 1 file changed, 33 insertions(+), 18 deletions(-) diff --git a/scripts/compilation/qp_create_ninja.py b/scripts/compilation/qp_create_ninja.py index f2b261ad..114a2b0e 100755 --- a/scripts/compilation/qp_create_ninja.py +++ b/scripts/compilation/qp_create_ninja.py @@ -666,20 +666,26 @@ def ninja_binaries_build(path_module, l_children, d_binaries): # s t r i n g # # ~#~#~#~#~#~ # - path_readme = os.path.join(path_module.abs, "README.rst") - path_png = os.path.join(path_module.abs, "tree_dependency.png") - l_string = ["build {0}: build_binaries {1} {2}".format(" ".join(l_abs_bin), EZFIO_LIB, ninja_module_path), " module_abs = {0}".format(path_module.abs), " module_rel = {0}".format(path_module.rel), ""] - l_string += ["build module_{0}: phony {1} {2} {3}".format(path_module.rel, - " ".join(l_abs_bin), - path_readme, - path_png - ), ""] + return l_string + + +def ninja_module_build(path_module, d_binaries): + + l_abs_bin = [binary.abs for binary in d_binaries[path_module]] + + path_readme = os.path.join(path_module.abs, "README.rst") + path_png = os.path.join(path_module.abs, "tree_dependency.png") + + l_string = ["build module_{0}: phony {1} {2} {3}".format(path_module.rel, + " ".join(l_abs_bin), + path_readme, + path_png), ""] return l_string @@ -732,17 +738,19 @@ def create_build_ninja_module(path_module): ""] l_string += ["rule make_local_binaries", - " command = ninja -f {0} module_{1}".format( - ROOT_BUILD_NINJA, path_module.rel), " pool = console", + " command = ninja -f {0} module_{1}".format(ROOT_BUILD_NINJA, path_module.rel), + " pool = console", " description = Compile only {0}".format(path_module.rel), ""] l_string += ["rule make_all_binaries", " command = ninja -f {0}".format(ROOT_BUILD_NINJA), - " pool = console", " description = Compiling all modules", + " pool = console", + " description = Compiling all modules", ""] - l_string += ["rule make_clean", " command = module_handler.py clean {0}".format(path_module.rel), + l_string += ["rule make_clean", + " command = module_handler.py clean {0}".format(path_module.rel), " description = Cleaning module {0}".format(path_module.rel), ""] @@ -766,7 +774,7 @@ def create_build_ninja_global(): " command = {0} update".format(__file__), ""] - l_string += ["rule make_all_binaries", + l_string += ["rule make_all", " command = ninja -f {0}".format(ROOT_BUILD_NINJA), " pool = console", " description = Compiling all modules", ""] @@ -777,7 +785,7 @@ def create_build_ninja_global(): l_string += ["build dummy_target: update_build_ninja_root", "", - "build all: make_all_binaries dummy_target", + "build all: make_all dummy_target", "default all", "", "build clean: make_clean dummy_target", @@ -938,11 +946,18 @@ if __name__ == "__main__": l_string += ninja_irpf90_make_build(module_to_compile, l_children, d_irp) - l_string += ninja_binaries_build(module_to_compile, l_children, - d_binaries) + if arguments["--development"]: + l_string += ninja_binaries_build(module_to_compile, l_children, + d_binaries) - l_string += ninja_gitignore_build(module_to_compile, d_binaries, - l_symlink) + elif arguments["--production"]: + l_string += ninja_binaries_build(module_to_compile, l_children, + d_binaries) + + l_string += ninja_module_build(module_to_compile, d_binaries) + + l_string += ninja_gitignore_build(module_to_compile, d_binaries, + l_symlink) # ~#~#~#~#~ # # S a v e s # From b97e337f4bedb1a5189b38f18ead91f7d2ba4535 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 16:45:45 +0200 Subject: [PATCH 06/11] Refortorisation of update_readme --- plugins/Full_CI/.gitignore | 1 - plugins/Full_CI/README.rst | 26 ++-- plugins/Generators_full/README.rst | 24 +-- plugins/Hartree_Fock/README.rst | 4 +- plugins/Perturbation/README.rst | 24 +-- plugins/Properties/README.rst | 22 +-- plugins/Selectors_full/README.rst | 24 +-- scripts/compilation/qp_create_ninja.py | 28 ++-- scripts/module/module_handler.py | 2 - scripts/module/qp_update_readme.py | 196 +++++++++++++++++++++++++ scripts/module/update_README.py | 188 ------------------------ src/AO_Basis/README.rst | 4 +- src/Bitmask/README.rst | 4 +- src/Determinants/README.rst | 4 +- src/Electrons/README.rst | 4 +- src/Integrals_Bielec/README.rst | 4 +- src/Integrals_Monoelec/README.rst | 4 +- src/MOGuess/README.rst | 4 +- src/MO_Basis/README.rst | 4 +- src/Nuclei/README.rst | 4 +- src/Pseudo/README.rst | 4 +- src/Utils/README.rst | 3 +- 22 files changed, 291 insertions(+), 291 deletions(-) create mode 100755 scripts/module/qp_update_readme.py delete mode 100755 scripts/module/update_README.py diff --git a/plugins/Full_CI/.gitignore b/plugins/Full_CI/.gitignore index 2d978fa6..a806bcbc 100644 --- a/plugins/Full_CI/.gitignore +++ b/plugins/Full_CI/.gitignore @@ -22,7 +22,6 @@ Properties Pseudo Selectors_full Utils -exc_degree ezfio_interface.irp.f full_ci full_ci_no_skip diff --git a/plugins/Full_CI/README.rst b/plugins/Full_CI/README.rst index d94675eb..853b82e3 100644 --- a/plugins/Full_CI/README.rst +++ b/plugins/Full_CI/README.rst @@ -4,10 +4,22 @@ Full_CI Module Performs a perturbatively selected Full-CI. +Needed Modules +============== + +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + +.. image:: tree_dependency.png + +* `Perturbation `_ +* `Selectors_full `_ +* `Generators_full `_ + Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `full_ci `_ @@ -153,15 +165,3 @@ Documentation `var_pt2_ratio_run `_ Undocumented -Needed Modules -============== - -.. Do not edit this section. It was auto-generated from the -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Perturbation `_ -* `Selectors_full `_ -* `Generators_full `_ - diff --git a/plugins/Generators_full/README.rst b/plugins/Generators_full/README.rst index dc6965e8..2a1d22df 100644 --- a/plugins/Generators_full/README.rst +++ b/plugins/Generators_full/README.rst @@ -5,10 +5,21 @@ Generators_full Module All the determinants of the wave function are generators. In this way, the Full CI space is explored. +Needed Modules +============== + +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + +.. image:: tree_dependency.png + +* `Determinants `_ +* `Hartree_Fock `_ + Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `degree_max_generators `_ @@ -37,14 +48,3 @@ Documentation `size_select_max `_ Size of the select_max array -Needed Modules -============== - -.. Do not edit this section. It was auto-generated from the -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Determinants `_ -* `Hartree_Fock `_ - diff --git a/plugins/Hartree_Fock/README.rst b/plugins/Hartree_Fock/README.rst index 28b3aec1..2fdb630a 100644 --- a/plugins/Hartree_Fock/README.rst +++ b/plugins/Hartree_Fock/README.rst @@ -7,7 +7,7 @@ From the 140 molecules of the G2 set, only LiO, ONa don't converge well. Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -18,7 +18,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_bi_elec_integral_alpha `_ diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index 9162e94b..7e468907 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -67,10 +67,21 @@ Assumptions pt2_.... +Needed Modules +============== + +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + +.. image:: tree_dependency.png + +* `Properties `_ +* `Hartree_Fock `_ + Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `do_pt2_end `_ @@ -350,14 +361,3 @@ Documentation The selection process stops when the energy ratio variational/(variational+PT2) is equal to var_pt2_ratio -Needed Modules -============== - -.. Do not edit this section. It was auto-generated from the -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Properties `_ -* `Hartree_Fock `_ - diff --git a/plugins/Properties/README.rst b/plugins/Properties/README.rst index 5e5ab1cc..ffe67574 100644 --- a/plugins/Properties/README.rst +++ b/plugins/Properties/README.rst @@ -2,10 +2,20 @@ Properties Module ================= +Needed Modules +============== + +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + +.. image:: tree_dependency.png + +* `Determinants `_ + Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_integrated_delta_rho_all_points `_ @@ -142,13 +152,3 @@ Documentation `z_one_point `_ z point on which the integrated delta rho is calculated -Needed Modules -============== - -.. Do not edit this section. It was auto-generated from the -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Determinants `_ - diff --git a/plugins/Selectors_full/README.rst b/plugins/Selectors_full/README.rst index 33cbaf16..7d5cd0e8 100644 --- a/plugins/Selectors_full/README.rst +++ b/plugins/Selectors_full/README.rst @@ -2,10 +2,21 @@ Selectors_full Module ===================== +Needed Modules +============== + +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + +.. image:: tree_dependency.png + +* `Determinants `_ +* `Hartree_Fock `_ + Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `coef_hf_selector `_ @@ -175,14 +186,3 @@ Documentation `psi_selectors_size `_ Undocumented -Needed Modules -============== - -.. Do not edit this section. It was auto-generated from the -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Determinants `_ -* `Hartree_Fock `_ - diff --git a/scripts/compilation/qp_create_ninja.py b/scripts/compilation/qp_create_ninja.py index 114a2b0e..0ff96f7e 100755 --- a/scripts/compilation/qp_create_ninja.py +++ b/scripts/compilation/qp_create_ninja.py @@ -23,12 +23,11 @@ except ImportError: "..", "..", "quantum_package.rc")) - print """ -Error: - source %s -""" % f + + print "\n".join(["", "Error:", "source %s" % f, ""]) sys.exit(1) + # __ # /__ | _ |_ _. | _. ._ o _. |_ | _ _ # \_| | (_) |_) (_| | \/ (_| | | (_| |_) | (/_ _> @@ -516,7 +515,7 @@ def ninja_readme_rule(): For not dealted the readme when ninja -t clean and the generator option """ l_string = ["rule build_readme", - " command = cd $module_abs ; update_README.py $module_root", + " command = qp_update_readme.py $module_abs --root_module $module_root", " description = update_README $module_rel", " generator = 1", ""] @@ -552,7 +551,8 @@ def ninja_readme_build(path_module, d_irp, dict_root_path): # / def get_binaries(path_module): """ - Return the list of binaries (Path= namedtuple('Path', ['abs', 'rel']) for a module + Return the list of binaries + (Path= namedtuple('Path', ['abs', 'rel']) for a module """ import subprocess @@ -729,7 +729,7 @@ def ninja_dot_tree_build(path_module, l_module): # |\/| _ _| | _ # | | (_) (_| |_| | (/_ # -def create_build_ninja_module(path_module): +def save_subninja_file(path_module): l_string = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)), ""] @@ -929,9 +929,6 @@ if __name__ == "__main__": for module_to_compile in l_module: - if arguments["--development"]: - create_build_ninja_module(module_to_compile) - # ~#~#~#~#~#~#~#~ # # S y m l i n k # # ~#~#~#~#~#~#~#~ # @@ -946,19 +943,18 @@ if __name__ == "__main__": l_string += ninja_irpf90_make_build(module_to_compile, l_children, d_irp) - if arguments["--development"]: - l_string += ninja_binaries_build(module_to_compile, l_children, - d_binaries) + l_string += ninja_binaries_build(module_to_compile, l_children, + d_binaries) - elif arguments["--production"]: - l_string += ninja_binaries_build(module_to_compile, l_children, - d_binaries) + if arguments["--development"]: l_string += ninja_module_build(module_to_compile, d_binaries) l_string += ninja_gitignore_build(module_to_compile, d_binaries, l_symlink) + save_subninja_file(module_to_compile) + # ~#~#~#~#~ # # S a v e s # # ~#~#~#~#~ # diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index b79e03b9..08a0b297 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -30,7 +30,6 @@ except ImportError: raise -# Canot cache for namedtuple are not hashable def is_module(path_module): return os.path.isfile(os.path.join(QP_SRC, path_module, "NEEDED_CHILDREN_MODULES")) @@ -290,4 +289,3 @@ if __name__ == '__main__': l_text = l_dir + l_file + l_symlink + l_exe l_text.sort() f.write("\n".join(l_text)) - diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py new file mode 100755 index 00000000..682b4d60 --- /dev/null +++ b/scripts/module/qp_update_readme.py @@ -0,0 +1,196 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +Updates the README.rst of a module +Usage: + qp_update_readme.py [...] [--root_module=] + +Options: + path_readme: All the absolute path you want to update. + By default is the cwd + --root_module: Is the path of the root module who containt the tags file. + By default is the cwd +""" + +import sys + +try: + from docopt import docopt +except: + print "Please check if you have sourced the .quantum_package.rc" + print "(`source .quantum_package.rc`)" + print sys.exit(1) + +import os +from collections import namedtuple +from collections import defaultdict + + +def header_format(str_): + return "{0}\n{1}\n".format(str_, "=" * len(str_)) + + +D_KEY = {"needed_module": header_format("Needed Modules"), + "documentation": header_format("Documentation")} + + +URL = "http://github.com/LCPQ/quantum_package/tree/master/src" + +HEADER = "\n".join([".. Do not edit this section It was auto-generated", + ".. by the `update_README.py` script."]) + +# d[Path] ={humain, needed_module, documentation} +d_readme = defaultdict(dict) + + +def fetch_splitted_data(l_module_readme): + """Read the README.rst file and split it in strings: + * The documentation + * The needed modules + The result is given as a list of strings + """ + + sentinel = "@@$%&@@" + + for path_readme in l_module_readme: + with open(os.path.join(path_readme, "README.rst"), 'r') as f: + data = f.read() + + # Place sentinels + + for v in D_KEY.values(): + data = data.replace(v, sentinel + v) + + # Now Split data using the sentinels + d_readme[path_readme] = {"human": data.split(sentinel)[0]} + + +def update_needed(d_readme): + """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it. + Create the links to the GitHub pages.""" + + header_image = ".. image:: tree_dependency.png" + + for path in d_readme: + + with open(os.path.join(path, 'NEEDED_CHILDREN_MODULES'), 'r') as f: + modules = f.read() + + if modules.strip(): + l_module = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name)) + for name in modules.split()] + + l_module_section = [D_KEY["needed_module"], + HEADER, '', + header_image, '', + '\n'.join(l_module), '', ''] + else: + l_module_section = "" + + d_readme[path]["needed_module"] = "\n".join(l_module_section) + + +def extract_doc(item): + """Extracts the documentation contained in IRPF90_man file""" + + path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item)) + with open(path, 'r') as f: + l_line = f.readlines() + + result = [] + inside = False + for line in l_line: + if not inside: + inside = line.startswith(".SH Description") + else: + if line.startswith(".SH"): + break + result.append(" {0}".format(line.strip())) + + if not result: + result = [" Undocumented"] + + return "\n".join(result) + "\n" + + +def update_documentation(ROOT_module, d_readme): + """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation""" + + IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"]) + + # If the file does not exist, don't do anything + path = os.path.join(ROOT_module, "tags") + + with open(path, 'r') as f: + dump = f.readlines() + + d_info = defaultdict(list) + + for i in dump: + # i = + # output_cpu_time_0 Ezfio_files/output.irp.f 2 + provider, irp_file_raw, ligne = i.split() + + for path in d_readme: + + if ROOT_module == path and "/" not in irp_file_raw: + d_info[path].append(IRP_info(os.path.basename(path), + irp_file_raw, + provider, + ligne)) + + elif "/" in irp_file_raw and os.path.dirname(irp_file_raw) in path: + + module, irp_file = os.path.split(irp_file_raw) + d_info[path].append(IRP_info(module, irp_file, provider, ligne)) + + for path in d_readme: + + l_doc = [] + + for irp in d_info[path]: + url = os.path.join(URL, os.path.basename(path), irp.file) + doc = extract_doc(irp.provider) + + l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line), + doc, + ""] + + l_doc_section = [D_KEY["documentation"], + HEADER, '', + "\n".join(l_doc)] + + d_readme[path]["documentation"] = "\n".join(l_doc_section) + +if __name__ == '__main__': + arguments = docopt(__doc__) + + if arguments["--root_module"]: + ROOT_module = os.path.realpath(arguments["--root_module"]) + else: + ROOT_module = os.getcwd() + + if not arguments[""]: + l_module_readme = [os.path.join(os.getcwd())] + else: + l_module_readme = arguments[""] + + try: + fetch_splitted_data(l_module_readme) + except IOError: + print l_module_readme, "is not a module and/or", + print "have not a `README.rst` file inside" + print "Abort..." + sys.exit(1) + + update_needed(d_readme) + update_documentation(ROOT_module, d_readme) + + for path, d in d_readme.iteritems(): + + with open(os.path.join(path, "README.rst"), 'w') as f: + for k in ["human", + "needed_module", + "documentation"]: + + f.write(d[k]) diff --git a/scripts/module/update_README.py b/scripts/module/update_README.py deleted file mode 100755 index 8cc102c3..00000000 --- a/scripts/module/update_README.py +++ /dev/null @@ -1,188 +0,0 @@ -#!/usr/bin/env python -"""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 & TApplencourt " - -README = "README.rst" -Assum_key = "Assumptions\n===========\n" -Needed_key = "Needed Modules\n==============\n" -Doc_key = "Documentation\n=============\n" -Sentinel = "@@$%&@@" -URL = "http://github.com/LCPQ/quantum_package/tree/master/src/" - -import os -import subprocess -from collections import namedtuple -import sys - -""" -NEED to call in a module -First arg can be the root parent -""" -try: - ROOT_module = os.path.realpath(sys.argv[1]) -except: - ROOT_module = os.getcwd() - -if ROOT_module != os.getcwd(): - change = True -else: - change = False - -MODULE_NAME = os.path.basename(os.getcwd()) - - -header = """ -.. Do not edit this section. It was auto-generated from the -.. by the `update_README.py` script. - -""" - - -def fetch_splitted_data(): - """Read the README.rst file and split it in strings: - * The documentation - * The needed modules - The result is given as a list of strings - """ - - with open(README, 'r') as f: - data = f.read() - - # Place sentinels - data = data.replace(Doc_key, Sentinel + Doc_key) - data = data.replace(Needed_key, Sentinel + Needed_key) - - # Now Split data using the sentinels - result = data.split(Sentinel) - - return result - - -def update_needed(data): - """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it. - Create the links to the GitHub pages.""" - - with open('NEEDED_CHILDREN_MODULES', 'r') as f: - modules = f.read() - - header_image = ".. image:: tree_dependency.png\n\n" - - if modules.strip(): - modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name)) - for name in modules.split()] - modules = "\n".join(modules) - modules = Needed_key + header + header_image + modules + '\n\n' - - has_modules = False - for i in range(len(data)): - if data[i].startswith(Needed_key): - has_modules = True - data[i] = modules - - if not has_modules: - data.append(modules) - - return data - - -def extract_doc(item): - """Extracts the documentation contained in IRPF90_man file""" - - path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item)) - with open(path, 'r') as f: - l_line = f.readlines() - - result = [] - inside = False - for line in l_line: - if not inside: - inside = line.startswith(".SH Description") - else: - if line.startswith(".SH"): - break - result.append(" {0}".format(line.strip())) - - if not result: - result = [" Undocumented"] - - return "\n".join(result) + '\n' - - -def update_documentation(data): - """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation""" - - IRP_info = namedtuple('IRP_info', ["name", "file", "line"]) - - # If the file does not exist, don't do anything - - path = os.path.join(ROOT_module, "tags") - - with open(path, 'r') as f: - dump = f.readlines() - - l_info = [] - for i in dump: - name, f, ligne = i.split() - - if not change and "/" not in i: - l_info.append(IRP_info(name, f, ligne)) - elif change and MODULE_NAME in i: - l_info.append(IRP_info(name, f.split("/")[-1], ligne)) - - l_line = [] - - for irp in l_info: - url = os.path.join(URL, MODULE_NAME, irp.file) - doc = extract_doc(irp.name) - - l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc, - ""] - - documentation = Doc_key + header + "\n".join(l_line) - - has_doc = False - for i in range(len(data)): - if data[i].startswith(Doc_key): - has_doc = True - data[i] = documentation - - if not has_doc: - data.append(documentation) - - return data - - -def git_add(): - """Executes: - git add README.rst - throw an error if git is not precent""" - - try: - # pipe output to /dev/null for silence - null = open("/dev/null", "w") - subprocess.Popen("git add README.rst", stdout=null, stderr=null) - null.close() - - except OSError: - raise - - -def main(): - data = fetch_splitted_data() - - data = update_documentation(data) - data = update_needed(data) - output = ''.join(data) - - with open(README, 'w') as f: - f.write(output) - - try: - git_add() - except OSError: - pass - - -if __name__ == '__main__': - main() diff --git a/src/AO_Basis/README.rst b/src/AO_Basis/README.rst index 4a1aa1ef..b174f41c 100644 --- a/src/AO_Basis/README.rst +++ b/src/AO_Basis/README.rst @@ -33,7 +33,7 @@ Assumptions Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -43,7 +43,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_coef `_ diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index f8d44248..d42457be 100644 --- a/src/Bitmask/README.rst +++ b/src/Bitmask/README.rst @@ -37,7 +37,7 @@ Assumptions Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -47,7 +47,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `bitstring_to_hexa `_ diff --git a/src/Determinants/README.rst b/src/Determinants/README.rst index 823cdd39..f3eb596f 100644 --- a/src/Determinants/README.rst +++ b/src/Determinants/README.rst @@ -29,7 +29,7 @@ Assumptions Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -40,7 +40,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `a_operator `_ diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index 5c785e4e..a087908d 100644 --- a/src/Electrons/README.rst +++ b/src/Electrons/README.rst @@ -21,7 +21,7 @@ Assumptions Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -31,7 +31,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `elec_alpha_num `_ diff --git a/src/Integrals_Bielec/README.rst b/src/Integrals_Bielec/README.rst index eed456c4..1fa66a1b 100644 --- a/src/Integrals_Bielec/README.rst +++ b/src/Integrals_Bielec/README.rst @@ -13,7 +13,7 @@ MO integral, use ``get_mo_bielec_integral(i,j,k,l,mo_integrals_map)`` or Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -24,7 +24,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `add_integrals_to_map `_ diff --git a/src/Integrals_Monoelec/README.rst b/src/Integrals_Monoelec/README.rst index 98ec1331..ed7af931 100644 --- a/src/Integrals_Monoelec/README.rst +++ b/src/Integrals_Monoelec/README.rst @@ -1,7 +1,7 @@ Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -12,7 +12,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_deriv2_x `_ diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index d10b1ef5..643e8945 100644 --- a/src/MOGuess/README.rst +++ b/src/MOGuess/README.rst @@ -5,7 +5,7 @@ MOGuess Module Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -15,7 +15,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_ortho_lowdin_coef `_ diff --git a/src/MO_Basis/README.rst b/src/MO_Basis/README.rst index 5cbe0165..ee83de36 100644 --- a/src/MO_Basis/README.rst +++ b/src/MO_Basis/README.rst @@ -33,7 +33,7 @@ ASSUMPTONS Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -44,7 +44,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `ao_to_mo `_ diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index 9f0b15d9..13058a7f 100644 --- a/src/Nuclei/README.rst +++ b/src/Nuclei/README.rst @@ -9,7 +9,7 @@ The coordinates are expressed in atomic units. Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -20,7 +20,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `element_name `_ diff --git a/src/Pseudo/README.rst b/src/Pseudo/README.rst index 84a555da..d6890929 100644 --- a/src/Pseudo/README.rst +++ b/src/Pseudo/README.rst @@ -5,7 +5,7 @@ Pseudo Module Needed Modules ============== -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. .. image:: tree_dependency.png @@ -15,7 +15,7 @@ Needed Modules Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `do_pseudo `_ diff --git a/src/Utils/README.rst b/src/Utils/README.rst index 104705a4..8ca88b1a 100644 --- a/src/Utils/README.rst +++ b/src/Utils/README.rst @@ -7,7 +7,7 @@ Contains general purpose utilities. Documentation ============= -.. Do not edit this section. It was auto-generated from the +.. Do not edit this section It was auto-generated .. by the `update_README.py` script. `a_coef `_ @@ -634,4 +634,3 @@ Documentation `write_git_log `_ Write the last git commit in file iunit. - From 3d702eff52dfdda43651687741d5a5fcb9a79ee8 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 16:47:29 +0200 Subject: [PATCH 07/11] Remove global variable --- scripts/module/qp_update_readme.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py index 682b4d60..df880bd9 100755 --- a/scripts/module/qp_update_readme.py +++ b/scripts/module/qp_update_readme.py @@ -90,10 +90,10 @@ def update_needed(d_readme): d_readme[path]["needed_module"] = "\n".join(l_module_section) -def extract_doc(item): +def extract_doc(root_module, provider): """Extracts the documentation contained in IRPF90_man file""" - path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item)) + path = os.path.join(root_module, "IRPF90_man/%s.l" % (provider)) with open(path, 'r') as f: l_line = f.readlines() @@ -113,13 +113,13 @@ def extract_doc(item): return "\n".join(result) + "\n" -def update_documentation(ROOT_module, d_readme): +def update_documentation(root_module, d_readme): """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation""" IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"]) # If the file does not exist, don't do anything - path = os.path.join(ROOT_module, "tags") + path = os.path.join(root_module, "tags") with open(path, 'r') as f: dump = f.readlines() @@ -133,7 +133,7 @@ def update_documentation(ROOT_module, d_readme): for path in d_readme: - if ROOT_module == path and "/" not in irp_file_raw: + if root_module == path and "/" not in irp_file_raw: d_info[path].append(IRP_info(os.path.basename(path), irp_file_raw, provider, @@ -150,7 +150,7 @@ def update_documentation(ROOT_module, d_readme): for irp in d_info[path]: url = os.path.join(URL, os.path.basename(path), irp.file) - doc = extract_doc(irp.provider) + doc = extract_doc(root_module, irp.provider) l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line), doc, @@ -166,9 +166,9 @@ if __name__ == '__main__': arguments = docopt(__doc__) if arguments["--root_module"]: - ROOT_module = os.path.realpath(arguments["--root_module"]) + root_module = os.path.realpath(arguments["--root_module"]) else: - ROOT_module = os.getcwd() + root_module = os.getcwd() if not arguments[""]: l_module_readme = [os.path.join(os.getcwd())] @@ -184,7 +184,7 @@ if __name__ == '__main__': sys.exit(1) update_needed(d_readme) - update_documentation(ROOT_module, d_readme) + update_documentation(root_module, d_readme) for path, d in d_readme.iteritems(): From 97c0dcf40bb6300a00078765785aeb7c276f0487 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 17:02:00 +0200 Subject: [PATCH 08/11] Fix qp_install_module --- plugins/Full_CI/README.rst | 161 +++++ plugins/Generators_full/README.rst | 43 ++ plugins/Hartree_Fock/README.rst | 149 +++++ plugins/Perturbation/README.rst | 294 +++++++++ plugins/Properties/README.rst | 150 +++++ plugins/Selectors_full/README.rst | 184 ++++++ scripts/module/qp_install_module.py | 6 +- scripts/module/qp_update_readme.py | 16 +- src/AO_Basis/README.rst | 148 +++++ src/Bitmask/README.rst | 134 +++++ src/Determinants/README.rst | 887 ++++++++++++++++++++++++++++ src/Electrons/README.rst | 31 + src/Integrals_Bielec/README.rst | 292 +++++++++ src/Integrals_Monoelec/README.rst | 278 +++++++++ src/MOGuess/README.rst | 39 ++ src/MO_Basis/README.rst | 102 ++++ src/Nuclei/README.rst | 82 +++ src/Pseudo/README.rst | 63 ++ src/Utils/README.rst | 630 ++++++++++++++++++++ 19 files changed, 3676 insertions(+), 13 deletions(-) diff --git a/plugins/Full_CI/README.rst b/plugins/Full_CI/README.rst index 853b82e3..8debefdb 100644 --- a/plugins/Full_CI/README.rst +++ b/plugins/Full_CI/README.rst @@ -165,3 +165,164 @@ Documentation `var_pt2_ratio_run `_ Undocumented +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Perturbation `_ +* `Selectors_full `_ +* `Generators_full `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`full_ci `_ + Undocumented + + +`h_apply_fci `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_fci_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_mono `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_fci_mono_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_mono_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_no_skip `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_fci_no_skip_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_no_skip_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_pt2 `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_fci_pt2_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_fci_pt2_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_pt2_mono_delta_rho `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_pt2_mono_delta_rho_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_pt2_mono_delta_rho_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_pt2_mono_di_delta_rho `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_pt2_mono_di_delta_rho_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_pt2_mono_di_delta_rho_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_select_mono_delta_rho `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_select_mono_delta_rho_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_select_mono_delta_rho_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_select_mono_di_delta_rho `_ + Calls H_apply on the HF determinant and selects all connected single and double + excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. + + +`h_apply_select_mono_di_delta_rho_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_select_mono_di_delta_rho_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`var_pt2_ratio_run `_ + Undocumented + diff --git a/plugins/Generators_full/README.rst b/plugins/Generators_full/README.rst index 2a1d22df..6c5890c0 100644 --- a/plugins/Generators_full/README.rst +++ b/plugins/Generators_full/README.rst @@ -48,3 +48,46 @@ Documentation `size_select_max `_ Size of the select_max array +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Determinants `_ +* `Hartree_Fock `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`degree_max_generators `_ + Max degree of excitation (respect to HF) of the generators + + +`n_det_generators `_ + For Single reference wave functions, the number of generators is 1 : the + Hartree-Fock determinant + + +`psi_coef_generators `_ + For Single reference wave functions, the generator is the + Hartree-Fock determinant + + +`psi_det_generators `_ + For Single reference wave functions, the generator is the + Hartree-Fock determinant + + +`select_max `_ + Memo to skip useless selectors + + +`size_select_max `_ + Size of the select_max array + diff --git a/plugins/Hartree_Fock/README.rst b/plugins/Hartree_Fock/README.rst index 2fdb630a..18c0b3ec 100644 --- a/plugins/Hartree_Fock/README.rst +++ b/plugins/Hartree_Fock/README.rst @@ -153,3 +153,152 @@ Documentation `thresh_scf `_ Threshold on the convergence of the Hartree Fock energy +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Integrals_Bielec `_ +* `MOGuess `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ao_bi_elec_integral_alpha `_ + Alpha Fock matrix in AO basis set + + +`ao_bi_elec_integral_beta `_ + Alpha Fock matrix in AO basis set + + +`create_guess `_ + Create an MO guess if no MOs are present in the EZFIO directory + + +`damping_scf `_ + Undocumented + + +`diagonal_fock_matrix_mo `_ + Diagonal Fock matrix in the MO basis + + +`diagonal_fock_matrix_mo_sum `_ + diagonal element of the fock matrix calculated as the sum over all the interactions + with all the electrons in the RHF determinant + diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij + + +`eigenvectors_fock_matrix_mo `_ + Diagonal Fock matrix in the MO basis + + +`fock_matrix_alpha_ao `_ + Alpha Fock matrix in AO basis set + + +`fock_matrix_alpha_mo `_ + Fock matrix on the MO basis + + +`fock_matrix_ao `_ + Fock matrix in AO basis set + + +`fock_matrix_beta_ao `_ + Alpha Fock matrix in AO basis set + + +`fock_matrix_beta_mo `_ + Fock matrix on the MO basis + + +`fock_matrix_diag_mo `_ + Fock matrix on the MO basis. + For open shells, the ROHF Fock Matrix is + .br + | F-K | F + K/2 | F | + |---------------------------------| + | F + K/2 | F | F - K/2 | + |---------------------------------| + | F | F - K/2 | F + K | + .br + F = 1/2 (Fa + Fb) + .br + K = Fb - Fa + .br + + +`fock_matrix_mo `_ + Fock matrix on the MO basis. + For open shells, the ROHF Fock Matrix is + .br + | F-K | F + K/2 | F | + |---------------------------------| + | F + K/2 | F | F - K/2 | + |---------------------------------| + | F | F - K/2 | F + K | + .br + F = 1/2 (Fa + Fb) + .br + K = Fb - Fa + .br + + +`fock_mo_to_ao `_ + Undocumented + + +`guess `_ + Undocumented + + +`hf_density_matrix_ao `_ + S^-1 Density matrix in the AO basis S^-1 + + +`hf_density_matrix_ao_alpha `_ + S^-1 x Alpha density matrix in the AO basis x S^-1 + + +`hf_density_matrix_ao_beta `_ + S^-1 Beta density matrix in the AO basis x S^-1 + + +`hf_energy `_ + Hartree-Fock energy + + +`huckel_guess `_ + Build the MOs using the extended Huckel model + + +`mo_guess_type `_ + Initial MO guess. Can be [ Huckel | HCore ] + + +`n_it_scf_max `_ + Maximum number of SCF iterations + + +`run `_ + Run SCF calculation + + +`scf `_ + 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 `_ + Threshold on the convergence of the Hartree Fock energy + diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index 7e468907..a23b8fe9 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -361,3 +361,297 @@ Documentation The selection process stops when the energy ratio variational/(variational+PT2) is equal to var_pt2_ratio +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Properties `_ +* `Hartree_Fock `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`do_pt2_end `_ + If true, compute the PT2 at the end of the selection + + +`fill_h_apply_buffer_selection `_ + Fill the H_apply buffer with determiants for the selection + + +`max_exc_pert `_ + Undocumented + + +`perturb_buffer_by_mono_delta_rho_one_point `_ + Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_dipole_moment_z `_ + Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_epstein_nesbet `_ + Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_epstein_nesbet_2x2 `_ + Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_epstein_nesbet_sc2 `_ + 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 `_ + 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 `_ + Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_h_core `_ + Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_by_mono_moller_plesset `_ + Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_delta_rho_one_point `_ + Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_dipole_moment_z `_ + Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet `_ + Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_2x2 `_ + Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_sc2 `_ + Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_sc2_no_projected `_ + Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_epstein_nesbet_sc2_projected `_ + Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_h_core `_ + Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply + routine. + + +`perturb_buffer_moller_plesset `_ + Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply + routine. + + +`pt2_delta_rho_one_point `_ + compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant + .br + for the various n_st states, at various level of theory. + .br + c_pert(i) = /( - ) + .br + e_2_pert(i) = c_pert(i) * + .br + H_pert_diag(i) = c_pert(i)^2 * + .br + To get the contribution of the first order : + .br + = sum(over i) e_2_pert(i) + .br + To get the contribution of the diagonal elements of the second order : + .br + [ + + sum(over i) H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2] + .br + + +`pt2_dipole_moment_z `_ + compute the perturbatibe contribution to the dipole moment of one determinant + .br + for the various n_st states, at various level of theory. + .br + c_pert(i) = /( - ) + .br + e_2_pert(i) = c_pert(i) * + .br + H_pert_diag(i) = c_pert(i)^2 * + .br + To get the contribution of the first order : + .br + = sum(over i) e_2_pert(i) + .br + To get the contribution of the diagonal elements of the second order : + .br + [ + + sum(over i) H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2] + .br + + +`pt2_epstein_nesbet `_ + compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution + .br + for the various N_st states. + .br + c_pert(i) = /( E(i) - ) + .br + e_2_pert(i) = ^2/( E(i) - ) + .br + + +`pt2_epstein_nesbet_2x2 `_ + compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution + .br + for the various N_st states. + .br + e_2_pert(i) = 0.5 * (( - E(i) ) - sqrt( ( - E(i)) ^2 + 4 ^2 ) + .br + c_pert(i) = e_2_pert(i)/ + .br + + +`pt2_epstein_nesbet_sc2 `_ + compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution + .br + for the various N_st states, but with the CISD_SC2 energies and coefficients + .br + c_pert(i) = /( E(i) - ) + .br + e_2_pert(i) = ^2/( E(i) - ) + .br + + +`pt2_epstein_nesbet_sc2_no_projected `_ + compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution + .br + for the various N_st states, + .br + but with the correction in the denominator + .br + comming from the interaction of that determinant with all the others determinants + .br + that can be repeated by repeating all the double excitations + .br + : you repeat all the correlation energy already taken into account in CI_electronic_energy(1) + .br + that could be repeated to this determinant. + .br + In addition, for the perturbative energetic contribution you have the standard second order + .br + e_2_pert = ^2/(Delta_E) + .br + and also the purely projected contribution + .br + H_pert_diag = c_pert + + +`pt2_epstein_nesbet_sc2_projected `_ + compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution + .br + for the various N_st states, + .br + but with the correction in the denominator + .br + comming from the interaction of that determinant with all the others determinants + .br + that can be repeated by repeating all the double excitations + .br + : you repeat all the correlation energy already taken into account in CI_electronic_energy(1) + .br + that could be repeated to this determinant. + .br + In addition, for the perturbative energetic contribution you have the standard second order + .br + e_2_pert = ^2/(Delta_E) + .br + and also the purely projected contribution + .br + H_pert_diag = c_pert + + +`pt2_h_core `_ + compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution + .br + for the various N_st states. + .br + c_pert(i) = /( E(i) - ) + .br + e_2_pert(i) = ^2/( E(i) - ) + .br + + +`pt2_max `_ + The selection process stops when the largest PT2 (for all the state) is lower + than pt2_max in absolute value + + +`pt2_moller_plesset `_ + compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution + .br + for the various n_st states. + .br + c_pert(i) = /(difference of orbital energies) + .br + e_2_pert(i) = ^2/(difference of orbital energies) + .br + + +`remove_small_contributions `_ + Remove determinants with small contributions. N_states is assumed to be + provided. + + +`repeat_all_e_corr `_ + Undocumented + + +`selection_criterion `_ + Threshold to select determinants. Set by selection routines. + + +`selection_criterion_factor `_ + Threshold to select determinants. Set by selection routines. + + +`selection_criterion_min `_ + Threshold to select determinants. Set by selection routines. + + +`var_pt2_ratio `_ + The selection process stops when the energy ratio variational/(variational+PT2) + is equal to var_pt2_ratio + diff --git a/plugins/Properties/README.rst b/plugins/Properties/README.rst index ffe67574..7af3f5c7 100644 --- a/plugins/Properties/README.rst +++ b/plugins/Properties/README.rst @@ -152,3 +152,153 @@ Documentation `z_one_point `_ z point on which the integrated delta rho is calculated +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Determinants `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ao_integrated_delta_rho_all_points `_ + array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis + for all the z points that are given (N_z_pts) + + +`ao_integrated_delta_rho_one_point `_ + array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis + for one specific z point + + +`average_position `_ + average_position(1) = + average_position(2) = + average_position(3) = + + +`average_spread `_ + average_spread(1) = + average_spread(2) = + average_spread(3) = + + +`delta_z `_ + Undocumented + + +`diag_o1_mat_elem `_ + Computes + + +`diag_o1_mat_elem_alpha_beta `_ + Computes + + +`filter_connected_mono `_ + Filters out the determinants that are not connected through PURE + .br + MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i) + .br + returns the array idx which contains the index of the + .br + determinants in the array key1 that interact + .br + via some PURE MONO EXCITATIONS OPERATORS + .br + idx(0) is the number of determinants that interact with key1 + + +`get_average `_ + computes the average value of a pure MONO ELECTRONIC OPERATOR + whom integrals on the MO basis are stored in "array" + and with the density is stored in "density" + + +`i_o1_j `_ + Returns where i and j are determinants + and O1 is a ONE BODY OPERATOR + array is the array of the mono electronic operator + on the MO basis + + +`i_o1_j_alpha_beta `_ + Returns where i and j are determinants + and O1 is a ONE BODY OPERATOR + array is the array of the mono electronic operator + on the MO basis + + +`i_o1_psi `_ + for the various Nstates + and O1 is a ONE BODY OPERATOR + array is the array of the mono electronic operator + on the MO basis + + +`i_o1_psi_alpha_beta `_ + for the various Nstates + and O1 is a ONE BODY OPERATOR + array is the array of the mono electronic operator + on the MO basis + + +`i_unit_integrated_delta_rho `_ + fortran unit for the writing of the integrated delta_rho + + +`integrated_delta_rho_all_points `_ + .br + integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points + chosen + .br + + +`integrated_delta_rho_one_point `_ + .br + integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta) + on the MO basis + .br + + +`mo_integrated_delta_rho_one_point `_ + .br + array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point + on the MO basis + .br + + +`n_z_pts `_ + Undocumented + + +`test_average_value `_ + Undocumented + + +`test_average_value_alpha_beta `_ + Undocumented + + +`test_dm `_ + Undocumented + + +`z_max `_ + Undocumented + + +`z_min `_ + Undocumented + + +`z_one_point `_ + z point on which the integrated delta rho is calculated + diff --git a/plugins/Selectors_full/README.rst b/plugins/Selectors_full/README.rst index 7d5cd0e8..1fe14576 100644 --- a/plugins/Selectors_full/README.rst +++ b/plugins/Selectors_full/README.rst @@ -186,3 +186,187 @@ Documentation `psi_selectors_size `_ Undocumented +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Determinants `_ +* `Hartree_Fock `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`coef_hf_selector `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`delta_e_per_selector `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`double_index_selectors `_ + degree of excitation respect to Hartree Fock for the wave function + .br + for the all the selectors determinants + .br + double_index_selectors = list of the index of the double excitations + .br + n_double_selectors = number of double excitations in the selectors determinants + + +`e_corr_double_only `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`e_corr_per_selectors `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`e_corr_second_order `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`exc_degree_per_selectors `_ + degree of excitation respect to Hartree Fock for the wave function + .br + for the all the selectors determinants + .br + double_index_selectors = list of the index of the double excitations + .br + n_double_selectors = number of double excitations in the selectors determinants + + +`i_h_hf_per_selectors `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`inv_selectors_coef_hf `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`inv_selectors_coef_hf_squared `_ + energy of correlation per determinant respect to the Hartree Fock determinant + .br + for the all the double excitations in the selectors determinants + .br + E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation + .br + E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation + .br + coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants + + +`n_det_selectors `_ + For Single reference wave functions, the number of selectors is 1 : the + Hartree-Fock determinant + + +`n_double_selectors `_ + degree of excitation respect to Hartree Fock for the wave function + .br + for the all the selectors determinants + .br + double_index_selectors = list of the index of the double excitations + .br + n_double_selectors = number of double excitations in the selectors determinants + + +`psi_selectors `_ + Determinants on which we apply for perturbation. + + +`psi_selectors_ab `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`psi_selectors_coef `_ + Determinants on which we apply for perturbation. + + +`psi_selectors_coef_ab `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`psi_selectors_diag_h_mat `_ + Diagonal elements of the H matrix for each selectors + + +`psi_selectors_next_ab `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`psi_selectors_size `_ + Undocumented + diff --git a/scripts/module/qp_install_module.py b/scripts/module/qp_install_module.py index 80d418a6..99674e14 100755 --- a/scripts/module/qp_install_module.py +++ b/scripts/module/qp_install_module.py @@ -22,7 +22,7 @@ try: from docopt import docopt from module_handler import ModuleHandler, get_dict_child from module_handler import get_l_module_descendant - from update_README import Doc_key, Needed_key + from qp_update_readme import D_KEY from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT except ImportError: print "Please check if you have sourced the .quantum_package.rc" @@ -56,8 +56,8 @@ def save_new_module(path, l_child): with open(os.path.join(path, "README.rst"), "w") as f: f.write(header + "\n") - f.write(Doc_key + "\n") - f.write(Needed_key + "\n") + f.write(D_KEY["needed_module"]) + f.write(D_KEY["documentation"]) if __name__ == '__main__': diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py index df880bd9..4c681d82 100755 --- a/scripts/module/qp_update_readme.py +++ b/scripts/module/qp_update_readme.py @@ -25,20 +25,18 @@ import os from collections import namedtuple from collections import defaultdict - def header_format(str_): - return "{0}\n{1}\n".format(str_, "=" * len(str_)) + warning = "\n".join([".. Do not edit this section It was auto-generated", + ".. by the `update_README.py` script."]) + + return "{0}\n{1}\n{2}\n".format(str_, "=" * len(str_), warning) D_KEY = {"needed_module": header_format("Needed Modules"), "documentation": header_format("Documentation")} - URL = "http://github.com/LCPQ/quantum_package/tree/master/src" -HEADER = "\n".join([".. Do not edit this section It was auto-generated", - ".. by the `update_README.py` script."]) - # d[Path] ={humain, needed_module, documentation} d_readme = defaultdict(dict) @@ -80,8 +78,7 @@ def update_needed(d_readme): l_module = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name)) for name in modules.split()] - l_module_section = [D_KEY["needed_module"], - HEADER, '', + l_module_section = [D_KEY["needed_module"], '', header_image, '', '\n'.join(l_module), '', ''] else: @@ -156,8 +153,7 @@ def update_documentation(root_module, d_readme): doc, ""] - l_doc_section = [D_KEY["documentation"], - HEADER, '', + l_doc_section = [D_KEY["documentation"], '', "\n".join(l_doc)] d_readme[path]["documentation"] = "\n".join(l_doc_section) diff --git a/src/AO_Basis/README.rst b/src/AO_Basis/README.rst index b174f41c..6a8d0add 100644 --- a/src/AO_Basis/README.rst +++ b/src/AO_Basis/README.rst @@ -178,3 +178,151 @@ Documentation Per convention, for P,D,F and G AOs, we take the index of the AO with the the corresponding power in the "X" axis +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Nuclei `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ao_coef `_ + AO Coefficients, read from input. Those should not be used directly, as the MOs are expressed on the basis of **normalized** AOs. + + +`ao_coef_normalized `_ + Coefficients including the AO normalization + + +`ao_coef_normalized_ordered `_ + Sorted primitives to accelerate 4 index MO transformation + + +`ao_coef_normalized_ordered_transp `_ + Transposed ao_coef_normalized_ordered + + +`ao_expo `_ + expo for each primitive of each ao_basis + + +`ao_expo_ordered `_ + Sorted primitives to accelerate 4 index MO transformation + + +`ao_expo_ordered_transp `_ + Transposed ao_expo_ordered + + +`ao_l `_ + ao_l = l value of the AO: a+b+c in x^a y^b z^c + + +`ao_l_char `_ + ao_l = l value of the AO: a+b+c in x^a y^b z^c + + +`ao_l_char_space `_ + Undocumented + + +`ao_md5 `_ + MD5 key characteristic of the AO basis + + +`ao_nucl `_ + Index of the nuclei on which the ao is centered + + +`ao_num `_ + number of ao + + +`ao_num_align `_ + Number of atomic orbitals align + + +`ao_overlap `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_overlap_abs `_ + Overlap between absolute value of atomic basis functions: + :math:`\int |\chi_i(r)| |\chi_j(r)| dr)` + + +`ao_overlap_x `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_overlap_y `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_overlap_z `_ + Overlap between atomic basis functions: + :math:`\int \chi_i(r) \chi_j(r) dr)` + + +`ao_power `_ + power for each dimension for each ao_basis + + +`ao_prim_num `_ + Number of primitives per atomic orbital + + +`ao_prim_num_max `_ + Undocumented + + +`ao_prim_num_max_align `_ + Number of primitives per atomic orbital aligned + + +`l_to_charater `_ + character corresponding to the "L" value of an AO orbital + + +`n_aos_max `_ + Number of AOs per atom + + +`n_pt_max_i_x `_ + Undocumented + + +`n_pt_max_integrals `_ + Undocumented + + +`nucl_aos `_ + List of AOs attached on each atom + + +`nucl_list_shell_aos `_ + Index of the shell type Aos and of the corresponding Aos + Per convention, for P,D,F and G AOs, we take the index + of the AO with the the corresponding power in the "X" axis + + +`nucl_n_aos `_ + Number of AOs per atom + + +`nucl_num_shell_aos `_ + Index of the shell type Aos and of the corresponding Aos + Per convention, for P,D,F and G AOs, we take the index + of the AO with the the corresponding power in the "X" axis + diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index d42457be..bf041e66 100644 --- a/src/Bitmask/README.rst +++ b/src/Bitmask/README.rst @@ -168,3 +168,137 @@ Documentation `virt_bitmask `_ Bitmasks for the inactive orbitals that are excited in post CAS method +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `MO_Basis `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`bitstring_to_hexa `_ + Transform a bit string to a string in hexadecimal format for printing + + +`bitstring_to_list `_ + Gives the inidices(+1) of the bits set to 1 in the bit string + + +`bitstring_to_str `_ + Transform a bit string to a string for printing + + +`cas_bitmask `_ + Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference) + + +`cis_ijkl_bitmask `_ + Bitmask to include all possible single excitations from Hartree-Fock + + +`debug_det `_ + Subroutine to print the content of a determinant in '+-' notation and + hexadecimal representation. + + +`debug_spindet `_ + Subroutine to print the content of a determinant in '+-' notation and + hexadecimal representation. + + +`full_ijkl_bitmask `_ + Bitmask to include all possible MOs + + +`generators_bitmask `_ + Bitmasks for generator determinants. + (N_int, alpha/beta, hole/particle, generator). + .br + 3rd index is : + .br + * 1 : hole for single exc + .br + * 2 : particle for single exc + .br + * 3 : hole for 1st exc of double + .br + * 4 : particle for 1st exc of double + .br + * 5 : hole for 2nd exc of double + .br + * 6 : particle for 2nd exc of double + .br + + +`hf_bitmask `_ + Hartree Fock bit mask + + +`i_bitmask_gen `_ + Current bitmask for the generators + + +`inact_bitmask `_ + Bitmasks for the inactive orbitals that are excited in post CAS method + + +`is_a_two_holes_two_particles `_ + Undocumented + + +`list_to_bitstring `_ + Returns the physical string "string(N_int,2)" from the array of + occupations "list(N_int*bit_kind_size,2) + + +`n_cas_bitmask `_ + Number of bitmasks for CAS + + +`n_generators_bitmask `_ + Number of bitmasks for generators + + +`n_int `_ + Number of 64-bit integers needed to represent determinants as binary strings + + +`number_of_holes `_ + Undocumented + + +`number_of_holes_verbose `_ + Undocumented + + +`number_of_particles `_ + Undocumented + + +`number_of_particles_verbose `_ + Undocumented + + +`print_det `_ + Subroutine to print the content of a determinant using the '+-' notation + + +`print_spindet `_ + Subroutine to print the content of a determinant using the '+-' notation + + +`ref_bitmask `_ + Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask + + +`virt_bitmask `_ + Bitmasks for the inactive orbitals that are excited in post CAS method + diff --git a/src/Determinants/README.rst b/src/Determinants/README.rst index f3eb596f..ac97074c 100644 --- a/src/Determinants/README.rst +++ b/src/Determinants/README.rst @@ -913,3 +913,890 @@ Documentation `write_spindeterminants `_ Undocumented +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Integrals_Monoelec `_ +* `Integrals_Bielec `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`a_operator `_ + Needed for diag_H_mat_elem + + +`abs_psi_coef_max `_ + Max and min values of the coefficients + + +`abs_psi_coef_min `_ + Max and min values of the coefficients + + +`ac_operator `_ + Needed for diag_H_mat_elem + + +`apply_mono `_ + Undocumented + + +`bi_elec_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`ci_eigenvectors `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2 `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy_mono `_ + Eigenvectors/values of the CI matrix + + +`ci_energy `_ + N_states lowest eigenvalues of the CI matrix + + +`ci_sc2_eigenvectors `_ + Eigenvectors/values of the CI matrix + + +`ci_sc2_electronic_energy `_ + Eigenvectors/values of the CI matrix + + +`ci_sc2_energy `_ + N_states_diag lowest eigenvalues of the CI matrix + + +`cisd `_ + Undocumented + + +`cisd_sc2 `_ + CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not) + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + Initial guess vectors are not necessarily orthonormal + + +`connected_to_ref `_ + Undocumented + + +`connected_to_ref_by_mono `_ + Undocumented + + +`copy_h_apply_buffer_to_wf `_ + Copies the H_apply buffer to psi_coef. + After calling this subroutine, N_det, psi_det and psi_coef need to be touched + + +`create_wf_of_psi_svd_matrix `_ + Matrix of wf coefficients. Outer product of alpha and beta determinants + + +`davidson_converged `_ + True if the Davidson algorithm is converged + + +`davidson_criterion `_ + Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] + + +`davidson_diag `_ + Davidson diagonalization. + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + iunit : Unit number for the I/O + .br + Initial guess vectors are not necessarily orthonormal + + +`davidson_diag_hjj `_ + Davidson diagonalization with specific diagonal elements of the H matrix + .br + H_jj : specific diagonal H matrix elements to diagonalize de Davidson + .br + dets_in : bitmasks corresponding to determinants + .br + u_in : guess coefficients on the various states. Overwritten + on exit + .br + dim_in : leftmost dimension of u_in + .br + sze : Number of determinants + .br + N_st : Number of eigenstates + .br + iunit : Unit for the I/O + .br + Initial guess vectors are not necessarily orthonormal + + +`davidson_iter_max `_ + Max number of Davidson iterations + + +`davidson_sze_max `_ + Max number of Davidson sizes + + +`davidson_threshold `_ + Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] + + +`decode_exc `_ + Decodes the exc arrays returned by get_excitation. + h1,h2 : Holes + p1,p2 : Particles + s1,s2 : Spins (1:alpha, 2:beta) + degree : Degree of excitation + + +`det_coef `_ + det_coef + + +`det_connections `_ + Build connection proxy between determinants + + +`det_num `_ + det_num + + +`det_occ `_ + det_occ + + +`det_search_key `_ + Return an integer*8 corresponding to a determinant index for searching + + +`det_svd `_ + Computes the SVD of the Alpha x Beta determinant coefficient matrix + + +`det_to_occ_pattern `_ + Transform a determinant to an occupation pattern + + +`diag_algorithm `_ + Diagonalization algorithm (Davidson or Lapack) + + +`diag_h_mat_elem `_ + Computes + + +`diagonalize_ci `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix + + +`diagonalize_ci_mono `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix + + +`diagonalize_ci_sc2 `_ + Replace the coefficients of the CI states_diag by the coefficients of the + eigenstates of the CI matrix + + +`do_mono_excitation `_ + Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin + on key_in + ispin = 1 == alpha + ispin = 2 == beta + i_ok = 1 == the excitation is possible + i_ok = -1 == the excitation is not possible + + +`double_exc_bitmask `_ + double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1 + double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1 + double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2 + double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2 + for a given couple of hole/particle excitations i. + + +`expected_s2 `_ + Expected value of S2 : S*(S+1) + + +`fill_h_apply_buffer_no_selection `_ + Fill the H_apply buffer with determiants for CISD + + +`filter_3_highest_electrons `_ + Returns a determinant with only the 3 highest electrons + + +`filter_connected `_ + Filters out the determinants that are not connected by H + .br + returns the array idx which contains the index of the + .br + determinants in the array key1 that interact + .br + via the H operator with key2. + .br + idx(0) is the number of determinants that interact with key1 + + +`filter_connected_davidson `_ + Filters out the determinants that are not connected by H + returns the array idx which contains the index of the + determinants in the array key1 that interact + via the H operator with key2. + .br + idx(0) is the number of determinants that interact with key1 + key1 should come from psi_det_sorted_ab. + + +`filter_connected_i_h_psi0 `_ + returns the array idx which contains the index of the + .br + determinants in the array key1 that interact + .br + via the H operator with key2. + .br + idx(0) is the number of determinants that interact with key1 + + +`filter_connected_i_h_psi0_sc2 `_ + standard filter_connected_i_H_psi but returns in addition + .br + the array of the index of the non connected determinants to key1 + .br + in order to know what double excitation can be repeated on key1 + .br + idx_repeat(0) is the number of determinants that can be used + .br + to repeat the excitations + + +`filter_connected_sorted_ab `_ + Filters out the determinants that are not connected by H + returns the array idx which contains the index of the + determinants in the array key1 that interact + via the H operator with key2. + idx(0) is the number of determinants that interact with key1 + .br + Determinants are taken from the psi_det_sorted_ab array + + +`generate_all_alpha_beta_det_products `_ + Create a wave function from all possible alpha x beta determinants + + +`get_double_excitation `_ + Returns the two excitation operators between two doubly excited determinants and the phase + + +`get_excitation `_ + Returns the excitation operators between two determinants and the phase + + +`get_excitation_degree `_ + Returns the excitation degree between two determinants + + +`get_excitation_degree_vector `_ + Applies get_excitation_degree to an array of determinants + + +`get_index_in_psi_det_alpha_unique `_ + Returns the index of the determinant in the ``psi_det_alpha_unique`` array + + +`get_index_in_psi_det_beta_unique `_ + Returns the index of the determinant in the ``psi_det_beta_unique`` array + + +`get_index_in_psi_det_sorted_bit `_ + Returns the index of the determinant in the ``psi_det_sorted_bit`` array + + +`get_mono_excitation `_ + Returns the excitation operator between two singly excited determinants and the phase + + +`get_occ_from_key `_ + Returns a list of occupation numbers from a bitstring + + +`get_s2 `_ + Returns + + +`get_s2_u0 `_ + Undocumented + + +`get_s2_u0_old `_ + Undocumented + + +`h_apply_buffer_allocated `_ + Buffer of determinants/coefficients/perturbative energy for H_apply. + Uninitialized. Filled by H_apply subroutines. + + +`h_apply_buffer_lock `_ + Buffer of determinants/coefficients/perturbative energy for H_apply. + Uninitialized. Filled by H_apply subroutines. + + +`h_matrix_all_dets `_ + H matrix on the basis of the slater determinants defined by psi_det + + +`h_matrix_cas `_ + Undocumented + + +`h_u_0 `_ + Computes v_0 = H|u_0> + .br + n : number of determinants + .br + H_jj : array of + + +`i_h_j `_ + Returns where i and j are determinants + + +`i_h_j_verbose `_ + Returns where i and j are determinants + + +`i_h_psi `_ + for the various Nstates + + +`i_h_psi_sc2 `_ + for the various Nstate + .br + returns in addition + .br + the array of the index of the non connected determinants to key1 + .br + in order to know what double excitation can be repeated on key1 + .br + idx_repeat(0) is the number of determinants that can be used + .br + to repeat the excitations + + +`i_h_psi_sc2_verbose `_ + for the various Nstate + .br + returns in addition + .br + the array of the index of the non connected determinants to key1 + .br + in order to know what double excitation can be repeated on key1 + .br + idx_repeat(0) is the number of determinants that can be used + .br + to repeat the excitations + + +`i_h_psi_sec_ord `_ + for the various Nstates + + +`idx_cas `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`idx_non_cas `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`int_of_3_highest_electrons `_ + Returns an integer*8 as : + .br + |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->| + .br + |0<--- i1 ---><--- i2 ---><--- i3 --->| + .br + It encodes the value of the indices of the 3 highest MOs + in descending order + .br + + +`is_in_wavefunction `_ + True if the determinant ``det`` is in the wave function + + +`kinetic_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`make_s2_eigenfunction `_ + Undocumented + + +`max_degree_exc `_ + Maximum degree of excitation in the wf + + +`mono_elec_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`n_con_int `_ + Number of integers to represent the connections between determinants + + +`n_det `_ + Number of determinants in the wave function + + +`n_det_alpha_unique `_ + Unique alpha determinants + + +`n_det_beta_unique `_ + Unique beta determinants + + +`n_det_cas `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`n_det_max `_ + Max number of determinants in the wave function + + +`n_det_max_jacobi `_ + Maximum number of determinants diagonalized by Jacobi + + +`n_det_max_property `_ + Max number of determinants in the wave function when you select for a given property + + +`n_det_non_cas `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`n_double_exc_bitmasks `_ + Number of double excitation bitmasks + + +`n_occ_pattern `_ + array of the occ_pattern present in the wf + psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation + psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation + + +`n_single_exc_bitmasks `_ + Number of single excitation bitmasks + + +`n_states `_ + Number of states to consider + + +`n_states_diag `_ + Number of states to consider for the diagonalization + + +`nucl_elec_ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`occ_pattern_search_key `_ + Return an integer*8 corresponding to a determinant index for searching + + +`occ_pattern_to_dets `_ + Generate all possible determinants for a give occ_pattern + + +`occ_pattern_to_dets_size `_ + Number of possible determinants for a given occ_pattern + + +`one_body_dm_mo `_ + One-body density matrix + + +`one_body_dm_mo_alpha `_ + Alpha and beta one-body density matrix for each state + + +`one_body_dm_mo_beta `_ + Alpha and beta one-body density matrix for each state + + +`one_body_single_double_dm_mo_alpha `_ + Alpha and beta one-body density matrix for each state + + +`one_body_single_double_dm_mo_beta `_ + Alpha and beta one-body density matrix for each state + + +`one_body_spin_density_mo `_ + rho(alpha) - rho(beta) + + +`only_single_double_dm `_ + If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements + + +`pouet `_ + Undocumented + + +`psi_average_norm_contrib `_ + Contribution of determinants to the state-averaged density + + +`psi_average_norm_contrib_sorted `_ + Wave function sorted by determinants contribution to the norm (state-averaged) + + +`psi_cas `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`psi_cas_coef `_ + CAS wave function, defined from the application of the CAS bitmask on the + determinants. idx_cas gives the indice of the CAS determinant in psi_det. + + +`psi_cas_coef_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_cas_energy `_ + Undocumented + + +`psi_cas_energy_diagonalized `_ + Undocumented + + +`psi_cas_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_coef `_ + The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file + is empty + + +`psi_coef_cas_diagonalized `_ + Undocumented + + +`psi_coef_max `_ + Max and min values of the coefficients + + +`psi_coef_min `_ + Max and min values of the coefficients + + +`psi_coef_sorted `_ + Wave function sorted by determinants contribution to the norm (state-averaged) + + +`psi_coef_sorted_ab `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`psi_coef_sorted_bit `_ + Determinants on which we apply for perturbation. + They are sorted by determinants interpreted as integers. Useful + to accelerate the search of a random determinant in the wave + function. + + +`psi_det `_ + The wave function determinants. Initialized with Hartree-Fock if the EZFIO file + is empty + + +`psi_det_alpha `_ + List of alpha determinants of psi_det + + +`psi_det_alpha_unique `_ + Unique alpha determinants + + +`psi_det_beta `_ + List of beta determinants of psi_det + + +`psi_det_beta_unique `_ + Unique beta determinants + + +`psi_det_size `_ + Size of the psi_det/psi_coef arrays + + +`psi_det_sorted `_ + Wave function sorted by determinants contribution to the norm (state-averaged) + + +`psi_det_sorted_ab `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`psi_det_sorted_bit `_ + Determinants on which we apply for perturbation. + They are sorted by determinants interpreted as integers. Useful + to accelerate the search of a random determinant in the wave + function. + + +`psi_det_sorted_next_ab `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`psi_non_cas `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`psi_non_cas_coef `_ + Set of determinants which are not part of the CAS, defined from the application + of the CAS bitmask on the determinants. + idx_non_cas gives the indice of the determinant in psi_det. + + +`psi_non_cas_coef_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_non_cas_sorted_bit `_ + CAS determinants sorted to accelerate the search of a random determinant in the wave + function. + + +`psi_occ_pattern `_ + array of the occ_pattern present in the wf + psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation + psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation + + +`psi_svd_alpha `_ + SVD wave function + + +`psi_svd_beta `_ + SVD wave function + + +`psi_svd_coefs `_ + SVD wave function + + +`psi_svd_matrix `_ + Matrix of wf coefficients. Outer product of alpha and beta determinants + + +`psi_svd_matrix_columns `_ + Matrix of wf coefficients. Outer product of alpha and beta determinants + + +`psi_svd_matrix_rows `_ + Matrix of wf coefficients. Outer product of alpha and beta determinants + + +`psi_svd_matrix_values `_ + Matrix of wf coefficients. Outer product of alpha and beta determinants + + +`put_gess `_ + Undocumented + + +`read_dets `_ + Reads the determinants from the EZFIO file + + +`read_wf `_ + If true, read the wave function from the EZFIO file + + +`rec_occ_pattern_to_dets `_ + Undocumented + + +`ref_bitmask_energy `_ + Energy of the reference bitmask used in Slater rules + + +`remove_duplicates_in_psi_det `_ + Removes duplicate determinants in the wave function. + + +`resize_h_apply_buffer `_ + Resizes the H_apply buffer of proc iproc. The buffer lock should + be set before calling this function. + + +`routine `_ + Undocumented + + +`s2_eig `_ + Force the wave function to be an eigenfunction of S^2 + + +`s2_values `_ + array of the averaged values of the S^2 operator on the various states + + +`s_z `_ + z component of the Spin + + +`s_z2_sz `_ + z component of the Spin + + +`save_natorb `_ + Undocumented + + +`save_natural_mos `_ + Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis + + +`save_wavefunction `_ + Save the wave function into the EZFIO file + + +`save_wavefunction_general `_ + Save the wave function into the EZFIO file + + +`save_wavefunction_unsorted `_ + Save the wave function into the EZFIO file + + +`set_natural_mos `_ + Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis + + +`single_exc_bitmask `_ + single_exc_bitmask(:,1,i) is the bitmask for holes + single_exc_bitmask(:,2,i) is the bitmask for particles + for a given couple of hole/particle excitations i. + + +`sort_dets_by_3_highest_electrons `_ + Determinants on which we apply . + They are sorted by the 3 highest electrons in the alpha part, + then by the 3 highest electrons in the beta part to accelerate + the research of connected determinants. + + +`sort_dets_by_det_search_key `_ + Determinants are sorted are sorted according to their det_search_key. + Useful to accelerate the search of a random determinant in the wave + function. + + +`spin_det_search_key `_ + Return an integer*8 corresponding to a determinant index for searching + + +`state_average_weight `_ + Weights in the state-average calculation of the density matrix + + +`threshold_convergence_sc2 `_ + convergence of the correlation energy of SC2 iterations + + +`threshold_generators `_ + Thresholds on generators (fraction of the norm) + + +`threshold_selectors `_ + Thresholds on selectors (fraction of the norm) + + +`write_spindeterminants `_ + Undocumented + diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index a087908d..2bc9f70d 100644 --- a/src/Electrons/README.rst +++ b/src/Electrons/README.rst @@ -49,3 +49,34 @@ Documentation `elec_num_tab `_ Numbers of alpha ("up") , beta ("down") and total electrons +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Ezfio_files `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`elec_alpha_num `_ + Numbers of electrons alpha ("up") + + +`elec_beta_num `_ + Numbers of electrons beta ("down") + + +`elec_num `_ + Numbers of alpha ("up") , beta ("down") and total electrons + + +`elec_num_tab `_ + Numbers of alpha ("up") , beta ("down") and total electrons + diff --git a/src/Integrals_Bielec/README.rst b/src/Integrals_Bielec/README.rst index 1fa66a1b..054a6720 100644 --- a/src/Integrals_Bielec/README.rst +++ b/src/Integrals_Bielec/README.rst @@ -302,3 +302,295 @@ Documentation `write_mo_integrals `_ One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Pseudo `_ +* `Bitmask `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`add_integrals_to_map `_ + Adds integrals to tha MO map according to some bitmask + + +`ao_bielec_integral `_ + integral of the AO basis or (ij|kl) + i(r1) j(r1) 1/r12 k(r2) l(r2) + + +`ao_bielec_integral_schwartz `_ + Needed to compute Schwartz inequalities + + +`ao_bielec_integral_schwartz_accel `_ + integral of the AO basis or (ij|kl) + i(r1) j(r1) 1/r12 k(r2) l(r2) + + +`ao_bielec_integrals_in_map `_ + Map of Atomic integrals + i(r1) j(r2) 1/r12 k(r1) l(r2) + + +`ao_integrals_map `_ + AO integrals + + +`ao_integrals_threshold `_ + If || < ao_integrals_threshold then is zero + + +`ao_l4 `_ + Computes the product of l values of i,j,k,and l + + +`bielec_integrals_index `_ + Undocumented + + +`bielec_integrals_index_reverse `_ + Undocumented + + +`clear_ao_map `_ + Frees the memory of the AO map + + +`clear_mo_map `_ + Frees the memory of the MO map + + +`compute_ao_bielec_integrals `_ + Compute AO 1/r12 integrals for all i and fixed j,k,l + + +`disk_access_ao_integrals `_ + Read/Write AO integrals from/to disk [ Write | Read | None ] + + +`disk_access_mo_integrals `_ + Read/Write MO integrals from/to disk [ Write | Read | None ] + + +`do_direct_integrals `_ + Compute integrals on the fly + + +`dump_ao_integrals `_ + Save to disk the $ao integrals + + +`dump_mo_integrals `_ + Save to disk the $ao integrals + + +`eri `_ + ATOMIC PRIMTIVE bielectronic integral between the 4 primitives :: + primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2) + primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2) + primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2) + primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2) + + +`gauleg `_ + Gauss-Legendre + + +`gauleg_t2 `_ + t_w(i,1,k) = w(i) + t_w(i,2,k) = t(i) + + +`gauleg_w `_ + t_w(i,1,k) = w(i) + t_w(i,2,k) = t(i) + + +`general_primitive_integral `_ + Computes the integral where p,q,r,s are Gaussian primitives + + +`get_ao_bielec_integral `_ + Gets one AO bi-electronic integral from the AO map + + +`get_ao_bielec_integrals `_ + Gets multiple AO bi-electronic integral from the AO map . + All i are retrieved for j,k,l fixed. + + +`get_ao_bielec_integrals_non_zero `_ + Gets multiple AO bi-electronic integral from the AO map . + All non-zero i are retrieved for j,k,l fixed. + + +`get_ao_map_size `_ + Returns the number of elements in the AO map + + +`get_mo_bielec_integral `_ + Returns one integral in the MO basis + + +`get_mo_bielec_integrals `_ + Returns multiple integrals in the MO basis, all + i for j,k,l fixed. + + +`get_mo_bielec_integrals_existing_ik `_ + Returns multiple integrals in the MO basis, all + i(1)j(1) 1/r12 k(2)l(2) + i for j,k,l fixed. + + +`get_mo_map_size `_ + Return the number of elements in the MO map + + +`give_polynom_mult_center_x `_ + subroutine that returns the explicit polynom in term of the "t" + variable of the following polynomw : + I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q) + + +`i_x1_new `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult_a1 `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult_a2 `_ + recursive function involved in the bielectronic integral + + +`i_x1_pol_mult_recurs `_ + recursive function involved in the bielectronic integral + + +`i_x2_new `_ + recursive function involved in the bielectronic integral + + +`i_x2_pol_mult `_ + recursive function involved in the bielectronic integral + + +`insert_into_ao_integrals_map `_ + Create new entry into AO map + + +`insert_into_mo_integrals_map `_ + Create new entry into MO map, or accumulate in an existing entry + + +`integrale_new `_ + calculate the integral of the polynom :: + I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) + between ( 0 ; 1) + + +`load_ao_integrals `_ + Read from disk the $ao integrals + + +`load_mo_integrals `_ + Read from disk the $ao integrals + + +`mo_bielec_integral `_ + Returns one integral in the MO basis + + +`mo_bielec_integral_jj `_ + mo_bielec_integral_jj(i,j) = J_ij + mo_bielec_integral_jj_exchange(i,j) = K_ij + mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij + + +`mo_bielec_integral_jj_anti `_ + mo_bielec_integral_jj(i,j) = J_ij + mo_bielec_integral_jj_exchange(i,j) = K_ij + mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij + + +`mo_bielec_integral_jj_anti_from_ao `_ + mo_bielec_integral_jj_from_ao(i,j) = J_ij + mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij + mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij + + +`mo_bielec_integral_jj_exchange `_ + mo_bielec_integral_jj(i,j) = J_ij + mo_bielec_integral_jj_exchange(i,j) = K_ij + mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij + + +`mo_bielec_integral_jj_exchange_from_ao `_ + mo_bielec_integral_jj_from_ao(i,j) = J_ij + mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij + mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij + + +`mo_bielec_integral_jj_from_ao `_ + mo_bielec_integral_jj_from_ao(i,j) = J_ij + mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij + mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij + + +`mo_bielec_integrals_in_map `_ + If True, the map of MO bielectronic integrals is provided + + +`mo_bielec_integrals_index `_ + Computes an unique index for i,j,k,l integrals + + +`mo_integrals_map `_ + MO integrals + + +`mo_integrals_threshold `_ + If || < ao_integrals_threshold then is zero + + +`n_pt_max_integrals_16 `_ + Aligned n_pt_max_integrals + + +`n_pt_sup `_ + Returns the upper boundary of the degree of the polynomial involved in the + bielctronic integral : + Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z) + + +`read_ao_integrals `_ + One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + + +`read_mo_integrals `_ + One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + + +`write_ao_integrals `_ + One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + + +`write_mo_integrals `_ + One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals + diff --git a/src/Integrals_Monoelec/README.rst b/src/Integrals_Monoelec/README.rst index ed7af931..dbdd753b 100644 --- a/src/Integrals_Monoelec/README.rst +++ b/src/Integrals_Monoelec/README.rst @@ -276,3 +276,281 @@ Documentation `wallis `_ Undocumented +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `MO_Basis `_ +* `Pseudo `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ao_deriv2_x `_ + second derivatives matrix elements in the ao basis + .. math:: + .br + {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle + + +`ao_deriv2_y `_ + second derivatives matrix elements in the ao basis + .. math:: + .br + {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle + + +`ao_deriv2_z `_ + second derivatives matrix elements in the ao basis + .. math:: + .br + {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle + + +`ao_deriv_1_x `_ + array of the integrals of AO_i * d/dx AO_j + array of the integrals of AO_i * d/dy AO_j + array of the integrals of AO_i * d/dz AO_j + + +`ao_deriv_1_y `_ + array of the integrals of AO_i * d/dx AO_j + array of the integrals of AO_i * d/dy AO_j + array of the integrals of AO_i * d/dz AO_j + + +`ao_deriv_1_z `_ + array of the integrals of AO_i * d/dx AO_j + array of the integrals of AO_i * d/dy AO_j + array of the integrals of AO_i * d/dz AO_j + + +`ao_dipole_x `_ + array of the integrals of AO_i * x AO_j + array of the integrals of AO_i * y AO_j + array of the integrals of AO_i * z AO_j + + +`ao_dipole_y `_ + array of the integrals of AO_i * x AO_j + array of the integrals of AO_i * y AO_j + array of the integrals of AO_i * z AO_j + + +`ao_dipole_z `_ + array of the integrals of AO_i * x AO_j + array of the integrals of AO_i * y AO_j + array of the integrals of AO_i * z AO_j + + +`ao_kinetic_integral `_ + array of the priminitve basis kinetic integrals + \langle \chi_i |\hat{T}| \chi_j \rangle + + +`ao_mono_elec_integral `_ + array of the mono electronic hamiltonian on the AOs basis + : sum of the kinetic and nuclear electronic potential + + +`ao_nucl_elec_integral `_ + interaction nuclear electron + + +`ao_nucl_elec_integral_per_atom `_ + ao_nucl_elec_integral_per_atom(i,j,k) = - + where Rk is the geometry of the kth atom + + +`ao_pseudo_integral `_ + Pseudo-potential + + +`ao_pseudo_integral_local `_ + Local pseudo-potential + + +`ao_pseudo_integral_non_local `_ + Local pseudo-potential + + +`ao_spread_x `_ + array of the integrals of AO_i * x^2 AO_j + array of the integrals of AO_i * y^2 AO_j + array of the integrals of AO_i * z^2 AO_j + + +`ao_spread_y `_ + array of the integrals of AO_i * x^2 AO_j + array of the integrals of AO_i * y^2 AO_j + array of the integrals of AO_i * z^2 AO_j + + +`ao_spread_z `_ + array of the integrals of AO_i * x^2 AO_j + array of the integrals of AO_i * y^2 AO_j + array of the integrals of AO_i * z^2 AO_j + + +`check_ortho `_ + Undocumented + + +`do_print `_ + Undocumented + + +`give_polynom_mult_center_mono_elec `_ + Undocumented + + +`i_x1_pol_mult_mono_elec `_ + Undocumented + + +`i_x2_pol_mult_mono_elec `_ + Undocumented + + +`int_gaus_pol `_ + Undocumented + + +`mo_deriv_1_x `_ + array of the integrals of MO_i * d/dx MO_j + array of the integrals of MO_i * d/dy MO_j + array of the integrals of MO_i * d/dz MO_j + + +`mo_deriv_1_y `_ + array of the integrals of MO_i * d/dx MO_j + array of the integrals of MO_i * d/dy MO_j + array of the integrals of MO_i * d/dz MO_j + + +`mo_deriv_1_z `_ + array of the integrals of MO_i * d/dx MO_j + array of the integrals of MO_i * d/dy MO_j + array of the integrals of MO_i * d/dz MO_j + + +`mo_dipole_x `_ + array of the integrals of MO_i * x MO_j + array of the integrals of MO_i * y MO_j + array of the integrals of MO_i * z MO_j + + +`mo_dipole_y `_ + array of the integrals of MO_i * x MO_j + array of the integrals of MO_i * y MO_j + array of the integrals of MO_i * z MO_j + + +`mo_dipole_z `_ + array of the integrals of MO_i * x MO_j + array of the integrals of MO_i * y MO_j + array of the integrals of MO_i * z MO_j + + +`mo_kinetic_integral `_ + Undocumented + + +`mo_mono_elec_integral `_ + array of the mono electronic hamiltonian on the MOs basis + : sum of the kinetic and nuclear electronic potential + + +`mo_nucl_elec_integral `_ + interaction nuclear electron on the MO basis + + +`mo_nucl_elec_integral_per_atom `_ + 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 + + +`mo_spread_x `_ + array of the integrals of MO_i * x^2 MO_j + array of the integrals of MO_i * y^2 MO_j + array of the integrals of MO_i * z^2 MO_j + + +`mo_spread_y `_ + array of the integrals of MO_i * x^2 MO_j + array of the integrals of MO_i * y^2 MO_j + array of the integrals of MO_i * z^2 MO_j + + +`mo_spread_z `_ + array of the integrals of MO_i * x^2 MO_j + array of the integrals of MO_i * y^2 MO_j + array of the integrals of MO_i * z^2 MO_j + + +`nai_pol_mult `_ + Undocumented + + +`orthonormalize_mos `_ + Undocumented + + +`overlap_bourrin_deriv_x `_ + Undocumented + + +`overlap_bourrin_dipole `_ + Undocumented + + +`overlap_bourrin_spread `_ + Undocumented + + +`overlap_bourrin_x `_ + Undocumented + + +`overlap_bourrin_x_abs `_ + Undocumented + + +`power `_ + Undocumented + + +`save_ortho_mos `_ + Undocumented + + +`v_e_n `_ + Undocumented + + +`v_phi `_ + Undocumented + + +`v_r `_ + Undocumented + + +`v_theta `_ + Undocumented + + +`wallis `_ + Undocumented + diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index 643e8945..a2d58aec 100644 --- a/src/MOGuess/README.rst +++ b/src/MOGuess/README.rst @@ -41,3 +41,42 @@ Documentation `hcore_guess `_ Produce `H_core` MO orbital +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Integrals_Monoelec `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ao_ortho_lowdin_coef `_ + matrix of the coefficients of the mos generated by the + orthonormalization by the S^{-1/2} canonical transformation of the aos + ao_ortho_lowdin_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_lowdin orbital + + +`ao_ortho_lowdin_nucl_elec_integral `_ + Undocumented + + +`ao_ortho_lowdin_overlap `_ + overlap matrix of the ao_ortho_lowdin + supposed to be the Identity + + +`h_core_guess `_ + 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 `_ + Produce `H_core` MO orbital + diff --git a/src/MO_Basis/README.rst b/src/MO_Basis/README.rst index ee83de36..361ef96f 100644 --- a/src/MO_Basis/README.rst +++ b/src/MO_Basis/README.rst @@ -132,3 +132,105 @@ Documentation `save_mos `_ Undocumented +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `AO_Basis `_ +* `Electrons `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`ao_to_mo `_ + Transform A from the AO basis to the MO basis + + +`cholesky_mo `_ + Cholesky decomposition of AO Density matrix to + generate MOs + + +`mix_mo_jk `_ + subroutine that rotates the jth MO with the kth MO + to give two new MO's that are + '+' = 1/sqrt(2) (|j> + |k>) + '-' = 1/sqrt(2) (|j> - |k>) + by convention, the '+' MO is in the lower index (min(j,k)) + by convention, the '-' MO is in the greater index (max(j,k)) + + +`mo_as_eigvectors_of_mo_matrix `_ + Undocumented + + +`mo_as_eigvectors_of_mo_matrix_sort_by_observable `_ + Undocumented + + +`mo_coef `_ + Molecular orbital coefficients on AO basis set + mo_coef(i,j) = coefficient of the ith ao on the jth mo + mo_label : Label characterizing the MOS (local, canonical, natural, etc) + + +`mo_coef_transp `_ + Molecular orbital coefficients on AO basis set + + +`mo_density_matrix `_ + Density matrix in MO basis + + +`mo_density_matrix_virtual `_ + Density matrix in MO basis (virtual MOs) + + +`mo_label `_ + Molecular orbital coefficients on AO basis set + mo_coef(i,j) = coefficient of the ith ao on the jth mo + mo_label : Label characterizing the MOS (local, canonical, natural, etc) + + +`mo_occ `_ + MO occupation numbers + + +`mo_overlap `_ + Undocumented + + +`mo_sort_by_observable `_ + Undocumented + + +`mo_to_ao `_ + Transform A from the MO basis to the AO basis + + +`mo_to_ao_no_overlap `_ + Transform A from the MO basis to the S^-1 AO basis + + +`mo_tot_num `_ + Total number of molecular orbitals and the size of the keys corresponding + + +`mo_tot_num_align `_ + Aligned variable for dimensioning of arrays + + +`s_mo_coef `_ + Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix. + + +`save_mos `_ + Undocumented + diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index 13058a7f..032c9963 100644 --- a/src/Nuclei/README.rst +++ b/src/Nuclei/README.rst @@ -88,3 +88,85 @@ Documentation `positive_charge_barycentre `_ Centroid of the positive charges +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Ezfio_files `_ +* `Utils `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`element_name `_ + Array of the name of element, sorted by nuclear charge (integer) + + +`nucl_charge `_ + Nuclear charges + + +`nucl_coord `_ + Nuclear coordinates in the format (:, {x,y,z}) + + +`nucl_coord_transp `_ + Transposed array of nucl_coord + + +`nucl_dist `_ + nucl_dist : Nucleus-nucleus distances + nucl_dist_2 : Nucleus-nucleus distances squared + nucl_dist_vec : Nucleus-nucleus distances vectors + + +`nucl_dist_2 `_ + nucl_dist : Nucleus-nucleus distances + nucl_dist_2 : Nucleus-nucleus distances squared + nucl_dist_vec : Nucleus-nucleus distances vectors + + +`nucl_dist_vec_x `_ + nucl_dist : Nucleus-nucleus distances + nucl_dist_2 : Nucleus-nucleus distances squared + nucl_dist_vec : Nucleus-nucleus distances vectors + + +`nucl_dist_vec_y `_ + nucl_dist : Nucleus-nucleus distances + nucl_dist_2 : Nucleus-nucleus distances squared + nucl_dist_vec : Nucleus-nucleus distances vectors + + +`nucl_dist_vec_z `_ + nucl_dist : Nucleus-nucleus distances + nucl_dist_2 : Nucleus-nucleus distances squared + nucl_dist_vec : Nucleus-nucleus distances vectors + + +`nucl_label `_ + Nuclear labels + + +`nucl_num `_ + Number of nuclei + + +`nucl_num_aligned `_ + Number of nuclei algined + + +`nuclear_repulsion `_ + Nuclear repulsion energy + + +`positive_charge_barycentre `_ + Centroid of the positive charges + diff --git a/src/Pseudo/README.rst b/src/Pseudo/README.rst index d6890929..60023235 100644 --- a/src/Pseudo/README.rst +++ b/src/Pseudo/README.rst @@ -65,3 +65,66 @@ Documentation `pseudo_v_kl `_ test +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +.. image:: tree_dependency.png + +* `Nuclei `_ + +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`do_pseudo `_ + Using pseudo potential integral of not + + +`pseudo_dz_k `_ + test + + +`pseudo_dz_kl `_ + test + + +`pseudo_grid_rmax `_ + R_maxof the QMC grid + + +`pseudo_grid_size `_ + Nb of points of the QMC grid + + +`pseudo_klocmax `_ + test + + +`pseudo_kmax `_ + test + + +`pseudo_lmax `_ + test + + +`pseudo_n_k `_ + test + + +`pseudo_n_kl `_ + test + + +`pseudo_v_k `_ + test + + +`pseudo_v_kl `_ + test + diff --git a/src/Utils/README.rst b/src/Utils/README.rst index 8ca88b1a..5c271c93 100644 --- a/src/Utils/README.rst +++ b/src/Utils/README.rst @@ -634,3 +634,633 @@ Documentation `write_git_log `_ Write the last git commit in file iunit. +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. + + +`a_coef `_ + Undocumented + + +`abort_all `_ + If True, all the calculation is aborted + + +`abort_here `_ + If True, all the calculation is aborted + + +`add_poly `_ + Add two polynomials + D(t) =! D(t) +( B(t)+C(t)) + + +`add_poly_multiply `_ + Add a polynomial multiplied by a constant + D(t) =! D(t) +( cst * B(t)) + + +`align_double `_ + Compute 1st dimension such that it is aligned for vectorization. + + +`apply_rotation `_ + Apply the rotation found by find_rotation + + +`approx_dble `_ + Undocumented + + +`b_coef `_ + Undocumented + + +`binom `_ + Binomial coefficients + + +`binom_func `_ + .. math :: + .br + \frac{i!}{j!(i-j)!} + .br + + +`binom_transp `_ + Binomial coefficients + + +`catch_signal `_ + What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted. + + +`dble_fact `_ + Undocumented + + +`dble_fact_even `_ + n!! + + +`dble_fact_odd `_ + n!! + + +`dble_logfact `_ + n!! + + +`ddfact2 `_ + Undocumented + + +`dset_order `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + + +`dset_order_big `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`dsort `_ + Sort array x(isize). + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`erf0 `_ + Undocumented + + +`f_integral `_ + function that calculates the following integral + \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx + + +`fact `_ + n! + + +`fact_inv `_ + 1/n! + + +`find_rotation `_ + Find A.C = B + + +`gammln `_ + Undocumented + + +`gammp `_ + Undocumented + + +`gaussian_product `_ + Gaussian product in 1D. + e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2} + + +`gaussian_product_x `_ + Gaussian product in 1D. + e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2} + + +`gcf `_ + Undocumented + + +`get_pseudo_inverse `_ + Find C = A^-1 + + +`give_explicit_poly_and_gaussian `_ + Transforms the product of + (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) + into + fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 ) + * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 ) + * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 ) + + +`give_explicit_poly_and_gaussian_double `_ + Transforms the product of + (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) + exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama + .br + into + fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 ) + * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 ) + * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 ) + + +`give_explicit_poly_and_gaussian_x `_ + Transform the product of + (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) + into + fact_k (x-x_P)^iorder(1) (y-y_P)^iorder(2) (z-z_P)^iorder(3) exp(-p(r-P)^2) + + +`gser `_ + Undocumented + + +`heap_dsort `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`heap_dsort_big `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`heap_i2sort `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`heap_i2sort_big `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`heap_i8sort `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`heap_i8sort_big `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`heap_isort `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`heap_isort_big `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`heap_sort `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`heap_sort_big `_ + Sort array x(isize) using the heap sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`hermite `_ + Hermite polynomial + + +`i2radix_sort `_ + Sort integer array x(isize) using the radix sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + iradix should be -1 in input. + + +`i2set_order `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + + +`i2set_order_big `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`i2sort `_ + Sort array x(isize). + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`i8radix_sort `_ + Sort integer array x(isize) using the radix sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + iradix should be -1 in input. + + +`i8radix_sort_big `_ + Sort integer array x(isize) using the radix sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + iradix should be -1 in input. + + +`i8set_order `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + + +`i8set_order_big `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`i8sort `_ + Sort array x(isize). + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`insertion_dsort `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`insertion_dsort_big `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`insertion_i2sort `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`insertion_i2sort_big `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`insertion_i8sort `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`insertion_i8sort_big `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`insertion_isort `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`insertion_isort_big `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`insertion_sort `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`insertion_sort_big `_ + Sort array x(isize) using the insertion sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`inv_int `_ + 1/i + + +`iradix_sort `_ + Sort integer array x(isize) using the radix sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + iradix should be -1 in input. + + +`iradix_sort_big `_ + Sort integer array x(isize) using the radix sort algorithm. + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + iradix should be -1 in input. + + +`iset_order `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + + +`iset_order_big `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`isort `_ + Sort array x(isize). + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`lapack_diag `_ + Diagonalize matrix H + .br + H is untouched between input and ouptut + .br + eigevalues(i) = ith lowest eigenvalue of the H matrix + .br + eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector + .br + + +`lapack_diag_s2 `_ + Diagonalize matrix H + .br + H is untouched between input and ouptut + .br + eigevalues(i) = ith lowest eigenvalue of the H matrix + .br + eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector + .br + + +`lapack_diagd `_ + Diagonalize matrix H + .br + H is untouched between input and ouptut + .br + eigevalues(i) = ith lowest eigenvalue of the H matrix + .br + eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector + .br + + +`lapack_partial_diag `_ + Diagonalize matrix H + .br + H is untouched between input and ouptut + .br + eigevalues(i) = ith lowest eigenvalue of the H matrix + .br + eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector + .br + + +`logfact `_ + n! + + +`multiply_poly `_ + Multiply two polynomials + D(t) =! D(t) +( B(t)*C(t)) + + +`normalize `_ + Normalizes vector u + u is expected to be aligned in memory. + + +`nproc `_ + Number of current OpenMP threads + + +`ortho_lowdin `_ + Compute C_new=C_old.S^-1/2 canonical orthogonalization. + .br + overlap : overlap matrix + .br + LDA : leftmost dimension of overlap array + .br + N : Overlap matrix is NxN (array is (LDA,N) ) + .br + C : Coefficients of the vectors to orthogonalize. On exit, + orthogonal vectors + .br + LDC : leftmost dimension of C + .br + m : Coefficients matrix is MxN, ( array is (LDC,N) ) + .br + + +`overlap_a_b_c `_ + Undocumented + + +`overlap_gaussian_x `_ + .. math:: + .br + \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx + .br + + +`overlap_gaussian_xyz `_ + .. math:: + .br + S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2) (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\ + S = S_x S_y S_z + .br + + +`overlap_x_abs `_ + .. math :: + .br + \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx + .br + + +`progress_active `_ + Current status for displaying progress bars. Global variable. + + +`progress_bar `_ + Current status for displaying progress bars. Global variable. + + +`progress_timeout `_ + Current status for displaying progress bars. Global variable. + + +`progress_title `_ + Current status for displaying progress bars. Global variable. + + +`progress_value `_ + Current status for displaying progress bars. Global variable. + + +`recentered_poly2 `_ + Recenter two polynomials + + +`rint `_ + .. math:: + .br + \int_0^1 dx \exp(-p x^2) x^n + .br + + +`rint1 `_ + Standard version of rint + + +`rint_large_n `_ + Version of rint for large values of n + + +`rint_sum `_ + Needed for the calculation of two-electron integrals. + + +`rinteg `_ + Undocumented + + +`rintgauss `_ + Undocumented + + +`run_progress `_ + Display a progress bar with documentation of what is happening + + +`sabpartial `_ + Undocumented + + +`set_order `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + + +`set_order_big `_ + array A has already been sorted, and iorder has contains the new order of + elements of A. This subroutine changes the order of x to match the new order of A. + This is a version for very large arrays where the indices need + to be in integer*8 format + + +`set_zero_extra_diag `_ + Undocumented + + +`sort `_ + Sort array x(isize). + iorder in input should be (1,2,3,...,isize), and in output + contains the new order of the elements. + + +`start_progress `_ + Starts the progress bar + + +`stop_progress `_ + Stop the progress bar + + +`trap_signals `_ + What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine. + + +`u_dot_u `_ + Compute + + +`u_dot_v `_ + Compute + + +`wall_time `_ + The equivalent of cpu_time, but for the wall time. + + +`write_git_log `_ + Write the last git commit in file iunit. + From 1c35435ea6517dab553c128fd7a4fdcc91032f35 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 17:18:45 +0200 Subject: [PATCH 09/11] Fixing doc in double --- plugins/Full_CI/README.rst | 160 ------ plugins/Generators_full/README.rst | 32 -- plugins/Hartree_Fock/README.rst | 138 ----- plugins/Perturbation/README.rst | 283 ---------- plugins/Properties/README.rst | 140 ----- plugins/Selectors_full/README.rst | 173 ------ scripts/module/qp_update_readme.py | 14 +- src/AO_Basis/README.rst | 138 ----- src/Bitmask/README.rst | 124 ---- src/Determinants/README.rst | 876 ----------------------------- src/Electrons/README.rst | 21 - src/Integrals_Bielec/README.rst | 281 --------- src/Integrals_Monoelec/README.rst | 267 --------- src/MOGuess/README.rst | 29 - src/MO_Basis/README.rst | 91 --- src/Nuclei/README.rst | 71 --- src/Pseudo/README.rst | 53 -- src/Utils/README.rst | 630 --------------------- 18 files changed, 7 insertions(+), 3514 deletions(-) diff --git a/plugins/Full_CI/README.rst b/plugins/Full_CI/README.rst index 8debefdb..913fd972 100644 --- a/plugins/Full_CI/README.rst +++ b/plugins/Full_CI/README.rst @@ -4,166 +4,6 @@ Full_CI Module Performs a perturbatively selected Full-CI. -Needed Modules -============== - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -.. image:: tree_dependency.png - -* `Perturbation `_ -* `Selectors_full `_ -* `Generators_full `_ - -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`full_ci `_ - Undocumented - - -`h_apply_fci `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_fci_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_mono `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_fci_mono_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_mono_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_no_skip `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_fci_no_skip_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_no_skip_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_pt2 `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_fci_pt2_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_fci_pt2_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_delta_rho `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_pt2_mono_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_di_delta_rho `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_pt2_mono_di_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_pt2_mono_di_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_delta_rho `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_select_mono_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_di_delta_rho `_ - Calls H_apply on the HF determinant and selects all connected single and double - excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. - - -`h_apply_select_mono_di_delta_rho_diexc `_ - Generate all double excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`h_apply_select_mono_di_delta_rho_monoexc `_ - Generate all single excitations of key_in using the bit masks of holes and - particles. - Assume N_int is already provided. - - -`var_pt2_ratio_run `_ - Undocumented Needed Modules ============== diff --git a/plugins/Generators_full/README.rst b/plugins/Generators_full/README.rst index 6c5890c0..12acdabb 100644 --- a/plugins/Generators_full/README.rst +++ b/plugins/Generators_full/README.rst @@ -16,38 +16,6 @@ Needed Modules * `Determinants `_ * `Hartree_Fock `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`degree_max_generators `_ - Max degree of excitation (respect to HF) of the generators - - -`n_det_generators `_ - For Single reference wave functions, the number of generators is 1 : the - Hartree-Fock determinant - - -`psi_coef_generators `_ - For Single reference wave functions, the generator is the - Hartree-Fock determinant - - -`psi_det_generators `_ - For Single reference wave functions, the generator is the - Hartree-Fock determinant - - -`select_max `_ - Memo to skip useless selectors - - -`size_select_max `_ - Size of the select_max array - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/plugins/Hartree_Fock/README.rst b/plugins/Hartree_Fock/README.rst index 18c0b3ec..a1da75e1 100644 --- a/plugins/Hartree_Fock/README.rst +++ b/plugins/Hartree_Fock/README.rst @@ -15,144 +15,6 @@ Needed Modules * `Integrals_Bielec `_ * `MOGuess `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_bi_elec_integral_alpha `_ - Alpha Fock matrix in AO basis set - - -`ao_bi_elec_integral_beta `_ - Alpha Fock matrix in AO basis set - - -`create_guess `_ - Create an MO guess if no MOs are present in the EZFIO directory - - -`damping_scf `_ - Undocumented - - -`diagonal_fock_matrix_mo `_ - Diagonal Fock matrix in the MO basis - - -`diagonal_fock_matrix_mo_sum `_ - diagonal element of the fock matrix calculated as the sum over all the interactions - with all the electrons in the RHF determinant - diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij - - -`eigenvectors_fock_matrix_mo `_ - Diagonal Fock matrix in the MO basis - - -`fock_matrix_alpha_ao `_ - Alpha Fock matrix in AO basis set - - -`fock_matrix_alpha_mo `_ - Fock matrix on the MO basis - - -`fock_matrix_ao `_ - Fock matrix in AO basis set - - -`fock_matrix_beta_ao `_ - Alpha Fock matrix in AO basis set - - -`fock_matrix_beta_mo `_ - Fock matrix on the MO basis - - -`fock_matrix_diag_mo `_ - Fock matrix on the MO basis. - For open shells, the ROHF Fock Matrix is - .br - | F-K | F + K/2 | F | - |---------------------------------| - | F + K/2 | F | F - K/2 | - |---------------------------------| - | F | F - K/2 | F + K | - .br - F = 1/2 (Fa + Fb) - .br - K = Fb - Fa - .br - - -`fock_matrix_mo `_ - Fock matrix on the MO basis. - For open shells, the ROHF Fock Matrix is - .br - | F-K | F + K/2 | F | - |---------------------------------| - | F + K/2 | F | F - K/2 | - |---------------------------------| - | F | F - K/2 | F + K | - .br - F = 1/2 (Fa + Fb) - .br - K = Fb - Fa - .br - - -`fock_mo_to_ao `_ - Undocumented - - -`guess `_ - Undocumented - - -`hf_density_matrix_ao `_ - S^-1 Density matrix in the AO basis S^-1 - - -`hf_density_matrix_ao_alpha `_ - S^-1 x Alpha density matrix in the AO basis x S^-1 - - -`hf_density_matrix_ao_beta `_ - S^-1 Beta density matrix in the AO basis x S^-1 - - -`hf_energy `_ - Hartree-Fock energy - - -`huckel_guess `_ - Build the MOs using the extended Huckel model - - -`mo_guess_type `_ - Initial MO guess. Can be [ Huckel | HCore ] - - -`n_it_scf_max `_ - Maximum number of SCF iterations - - -`run `_ - Run SCF calculation - - -`scf `_ - 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 `_ - Threshold on the convergence of the Hartree Fock energy - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index a23b8fe9..e9aafe82 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -78,289 +78,6 @@ Needed Modules * `Properties `_ * `Hartree_Fock `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`do_pt2_end `_ - If true, compute the PT2 at the end of the selection - - -`fill_h_apply_buffer_selection `_ - Fill the H_apply buffer with determiants for the selection - - -`max_exc_pert `_ - Undocumented - - -`perturb_buffer_by_mono_delta_rho_one_point `_ - Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_by_mono_dipole_moment_z `_ - Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_by_mono_epstein_nesbet `_ - Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_by_mono_epstein_nesbet_2x2 `_ - Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_by_mono_epstein_nesbet_sc2 `_ - 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 `_ - 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 `_ - Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_by_mono_h_core `_ - Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_by_mono_moller_plesset `_ - Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_delta_rho_one_point `_ - Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_dipole_moment_z `_ - Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_epstein_nesbet `_ - Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_epstein_nesbet_2x2 `_ - Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_epstein_nesbet_sc2 `_ - Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_epstein_nesbet_sc2_no_projected `_ - Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_epstein_nesbet_sc2_projected `_ - Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_h_core `_ - Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply - routine. - - -`perturb_buffer_moller_plesset `_ - Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply - routine. - - -`pt2_delta_rho_one_point `_ - compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant - .br - for the various n_st states, at various level of theory. - .br - c_pert(i) = /( - ) - .br - e_2_pert(i) = c_pert(i) * - .br - H_pert_diag(i) = c_pert(i)^2 * - .br - To get the contribution of the first order : - .br - = sum(over i) e_2_pert(i) - .br - To get the contribution of the diagonal elements of the second order : - .br - [ + + sum(over i) H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2] - .br - - -`pt2_dipole_moment_z `_ - compute the perturbatibe contribution to the dipole moment of one determinant - .br - for the various n_st states, at various level of theory. - .br - c_pert(i) = /( - ) - .br - e_2_pert(i) = c_pert(i) * - .br - H_pert_diag(i) = c_pert(i)^2 * - .br - To get the contribution of the first order : - .br - = sum(over i) e_2_pert(i) - .br - To get the contribution of the diagonal elements of the second order : - .br - [ + + sum(over i) H_pert_diag(i) ] / [1. + sum(over i) c_pert(i) **2] - .br - - -`pt2_epstein_nesbet `_ - compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution - .br - for the various N_st states. - .br - c_pert(i) = /( E(i) - ) - .br - e_2_pert(i) = ^2/( E(i) - ) - .br - - -`pt2_epstein_nesbet_2x2 `_ - compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution - .br - for the various N_st states. - .br - e_2_pert(i) = 0.5 * (( - E(i) ) - sqrt( ( - E(i)) ^2 + 4 ^2 ) - .br - c_pert(i) = e_2_pert(i)/ - .br - - -`pt2_epstein_nesbet_sc2 `_ - compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution - .br - for the various N_st states, but with the CISD_SC2 energies and coefficients - .br - c_pert(i) = /( E(i) - ) - .br - e_2_pert(i) = ^2/( E(i) - ) - .br - - -`pt2_epstein_nesbet_sc2_no_projected `_ - compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution - .br - for the various N_st states, - .br - but with the correction in the denominator - .br - comming from the interaction of that determinant with all the others determinants - .br - that can be repeated by repeating all the double excitations - .br - : you repeat all the correlation energy already taken into account in CI_electronic_energy(1) - .br - that could be repeated to this determinant. - .br - In addition, for the perturbative energetic contribution you have the standard second order - .br - e_2_pert = ^2/(Delta_E) - .br - and also the purely projected contribution - .br - H_pert_diag = c_pert - - -`pt2_epstein_nesbet_sc2_projected `_ - compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution - .br - for the various N_st states, - .br - but with the correction in the denominator - .br - comming from the interaction of that determinant with all the others determinants - .br - that can be repeated by repeating all the double excitations - .br - : you repeat all the correlation energy already taken into account in CI_electronic_energy(1) - .br - that could be repeated to this determinant. - .br - In addition, for the perturbative energetic contribution you have the standard second order - .br - e_2_pert = ^2/(Delta_E) - .br - and also the purely projected contribution - .br - H_pert_diag = c_pert - - -`pt2_h_core `_ - compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution - .br - for the various N_st states. - .br - c_pert(i) = /( E(i) - ) - .br - e_2_pert(i) = ^2/( E(i) - ) - .br - - -`pt2_max `_ - The selection process stops when the largest PT2 (for all the state) is lower - than pt2_max in absolute value - - -`pt2_moller_plesset `_ - compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution - .br - for the various n_st states. - .br - c_pert(i) = /(difference of orbital energies) - .br - e_2_pert(i) = ^2/(difference of orbital energies) - .br - - -`remove_small_contributions `_ - Remove determinants with small contributions. N_states is assumed to be - provided. - - -`repeat_all_e_corr `_ - Undocumented - - -`selection_criterion `_ - Threshold to select determinants. Set by selection routines. - - -`selection_criterion_factor `_ - Threshold to select determinants. Set by selection routines. - - -`selection_criterion_min `_ - Threshold to select determinants. Set by selection routines. - - -`var_pt2_ratio `_ - The selection process stops when the energy ratio variational/(variational+PT2) - is equal to var_pt2_ratio - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/plugins/Properties/README.rst b/plugins/Properties/README.rst index 7af3f5c7..0be70c6c 100644 --- a/plugins/Properties/README.rst +++ b/plugins/Properties/README.rst @@ -12,146 +12,6 @@ Needed Modules * `Determinants `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_integrated_delta_rho_all_points `_ - array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis - for all the z points that are given (N_z_pts) - - -`ao_integrated_delta_rho_one_point `_ - array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis - for one specific z point - - -`average_position `_ - average_position(1) = - average_position(2) = - average_position(3) = - - -`average_spread `_ - average_spread(1) = - average_spread(2) = - average_spread(3) = - - -`delta_z `_ - Undocumented - - -`diag_o1_mat_elem `_ - Computes - - -`diag_o1_mat_elem_alpha_beta `_ - Computes - - -`filter_connected_mono `_ - Filters out the determinants that are not connected through PURE - .br - MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i) - .br - returns the array idx which contains the index of the - .br - determinants in the array key1 that interact - .br - via some PURE MONO EXCITATIONS OPERATORS - .br - idx(0) is the number of determinants that interact with key1 - - -`get_average `_ - computes the average value of a pure MONO ELECTRONIC OPERATOR - whom integrals on the MO basis are stored in "array" - and with the density is stored in "density" - - -`i_o1_j `_ - Returns where i and j are determinants - and O1 is a ONE BODY OPERATOR - array is the array of the mono electronic operator - on the MO basis - - -`i_o1_j_alpha_beta `_ - Returns where i and j are determinants - and O1 is a ONE BODY OPERATOR - array is the array of the mono electronic operator - on the MO basis - - -`i_o1_psi `_ - for the various Nstates - and O1 is a ONE BODY OPERATOR - array is the array of the mono electronic operator - on the MO basis - - -`i_o1_psi_alpha_beta `_ - for the various Nstates - and O1 is a ONE BODY OPERATOR - array is the array of the mono electronic operator - on the MO basis - - -`i_unit_integrated_delta_rho `_ - fortran unit for the writing of the integrated delta_rho - - -`integrated_delta_rho_all_points `_ - .br - integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points - chosen - .br - - -`integrated_delta_rho_one_point `_ - .br - integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta) - on the MO basis - .br - - -`mo_integrated_delta_rho_one_point `_ - .br - array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point - on the MO basis - .br - - -`n_z_pts `_ - Undocumented - - -`test_average_value `_ - Undocumented - - -`test_average_value_alpha_beta `_ - Undocumented - - -`test_dm `_ - Undocumented - - -`z_max `_ - Undocumented - - -`z_min `_ - Undocumented - - -`z_one_point `_ - z point on which the integrated delta rho is calculated - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/plugins/Selectors_full/README.rst b/plugins/Selectors_full/README.rst index 1fe14576..e90ee6c2 100644 --- a/plugins/Selectors_full/README.rst +++ b/plugins/Selectors_full/README.rst @@ -13,179 +13,6 @@ Needed Modules * `Determinants `_ * `Hartree_Fock `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`coef_hf_selector `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`delta_e_per_selector `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`double_index_selectors `_ - degree of excitation respect to Hartree Fock for the wave function - .br - for the all the selectors determinants - .br - double_index_selectors = list of the index of the double excitations - .br - n_double_selectors = number of double excitations in the selectors determinants - - -`e_corr_double_only `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`e_corr_per_selectors `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`e_corr_second_order `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`exc_degree_per_selectors `_ - degree of excitation respect to Hartree Fock for the wave function - .br - for the all the selectors determinants - .br - double_index_selectors = list of the index of the double excitations - .br - n_double_selectors = number of double excitations in the selectors determinants - - -`i_h_hf_per_selectors `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`inv_selectors_coef_hf `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`inv_selectors_coef_hf_squared `_ - energy of correlation per determinant respect to the Hartree Fock determinant - .br - for the all the double excitations in the selectors determinants - .br - E_corr_per_selectors(i) = * c(D_i)/c(HF) if |D_i> is a double excitation - .br - E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation - .br - coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants - - -`n_det_selectors `_ - For Single reference wave functions, the number of selectors is 1 : the - Hartree-Fock determinant - - -`n_double_selectors `_ - degree of excitation respect to Hartree Fock for the wave function - .br - for the all the selectors determinants - .br - double_index_selectors = list of the index of the double excitations - .br - n_double_selectors = number of double excitations in the selectors determinants - - -`psi_selectors `_ - Determinants on which we apply for perturbation. - - -`psi_selectors_ab `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`psi_selectors_coef `_ - Determinants on which we apply for perturbation. - - -`psi_selectors_coef_ab `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`psi_selectors_diag_h_mat `_ - Diagonal elements of the H matrix for each selectors - - -`psi_selectors_next_ab `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`psi_selectors_size `_ - Undocumented - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py index 4c681d82..eef1b699 100755 --- a/scripts/module/qp_update_readme.py +++ b/scripts/module/qp_update_readme.py @@ -37,11 +37,8 @@ D_KEY = {"needed_module": header_format("Needed Modules"), URL = "http://github.com/LCPQ/quantum_package/tree/master/src" -# d[Path] ={humain, needed_module, documentation} -d_readme = defaultdict(dict) - -def fetch_splitted_data(l_module_readme): +def fetch_splitted_data(d_readme, l_module_readme): """Read the README.rst file and split it in strings: * The documentation * The needed modules @@ -110,7 +107,7 @@ def extract_doc(root_module, provider): return "\n".join(result) + "\n" -def update_documentation(root_module, d_readme): +def update_documentation(d_readmen, root_module): """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation""" IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"]) @@ -171,8 +168,11 @@ if __name__ == '__main__': else: l_module_readme = arguments[""] + # d[Path] ={humain, needed_module, documentation} + d_readme = defaultdict(dict) + try: - fetch_splitted_data(l_module_readme) + fetch_splitted_data(d_readme, l_module_readme) except IOError: print l_module_readme, "is not a module and/or", print "have not a `README.rst` file inside" @@ -180,7 +180,7 @@ if __name__ == '__main__': sys.exit(1) update_needed(d_readme) - update_documentation(root_module, d_readme) + update_documentation(d_readme, root_module) for path, d in d_readme.iteritems(): diff --git a/src/AO_Basis/README.rst b/src/AO_Basis/README.rst index 6a8d0add..e0a487fe 100644 --- a/src/AO_Basis/README.rst +++ b/src/AO_Basis/README.rst @@ -40,144 +40,6 @@ Needed Modules * `Nuclei `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_coef `_ - AO Coefficients, read from input. Those should not be used directly, as the MOs are expressed on the basis of **normalized** AOs. - - -`ao_coef_normalized `_ - Coefficients including the AO normalization - - -`ao_coef_normalized_ordered `_ - Sorted primitives to accelerate 4 index MO transformation - - -`ao_coef_normalized_ordered_transp `_ - Transposed ao_coef_normalized_ordered - - -`ao_expo `_ - expo for each primitive of each ao_basis - - -`ao_expo_ordered `_ - Sorted primitives to accelerate 4 index MO transformation - - -`ao_expo_ordered_transp `_ - Transposed ao_expo_ordered - - -`ao_l `_ - ao_l = l value of the AO: a+b+c in x^a y^b z^c - - -`ao_l_char `_ - ao_l = l value of the AO: a+b+c in x^a y^b z^c - - -`ao_l_char_space `_ - Undocumented - - -`ao_md5 `_ - MD5 key characteristic of the AO basis - - -`ao_nucl `_ - Index of the nuclei on which the ao is centered - - -`ao_num `_ - number of ao - - -`ao_num_align `_ - Number of atomic orbitals align - - -`ao_overlap `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - - -`ao_overlap_abs `_ - Overlap between absolute value of atomic basis functions: - :math:`\int |\chi_i(r)| |\chi_j(r)| dr)` - - -`ao_overlap_x `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - - -`ao_overlap_y `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - - -`ao_overlap_z `_ - Overlap between atomic basis functions: - :math:`\int \chi_i(r) \chi_j(r) dr)` - - -`ao_power `_ - power for each dimension for each ao_basis - - -`ao_prim_num `_ - Number of primitives per atomic orbital - - -`ao_prim_num_max `_ - Undocumented - - -`ao_prim_num_max_align `_ - Number of primitives per atomic orbital aligned - - -`l_to_charater `_ - character corresponding to the "L" value of an AO orbital - - -`n_aos_max `_ - Number of AOs per atom - - -`n_pt_max_i_x `_ - Undocumented - - -`n_pt_max_integrals `_ - Undocumented - - -`nucl_aos `_ - List of AOs attached on each atom - - -`nucl_list_shell_aos `_ - Index of the shell type Aos and of the corresponding Aos - Per convention, for P,D,F and G AOs, we take the index - of the AO with the the corresponding power in the "X" axis - - -`nucl_n_aos `_ - Number of AOs per atom - - -`nucl_num_shell_aos `_ - Index of the shell type Aos and of the corresponding Aos - Per convention, for P,D,F and G AOs, we take the index - of the AO with the the corresponding power in the "X" axis - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index bf041e66..6f3696b4 100644 --- a/src/Bitmask/README.rst +++ b/src/Bitmask/README.rst @@ -44,130 +44,6 @@ Needed Modules * `MO_Basis `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`bitstring_to_hexa `_ - Transform a bit string to a string in hexadecimal format for printing - - -`bitstring_to_list `_ - Gives the inidices(+1) of the bits set to 1 in the bit string - - -`bitstring_to_str `_ - Transform a bit string to a string for printing - - -`cas_bitmask `_ - Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference) - - -`cis_ijkl_bitmask `_ - Bitmask to include all possible single excitations from Hartree-Fock - - -`debug_det `_ - Subroutine to print the content of a determinant in '+-' notation and - hexadecimal representation. - - -`debug_spindet `_ - Subroutine to print the content of a determinant in '+-' notation and - hexadecimal representation. - - -`full_ijkl_bitmask `_ - Bitmask to include all possible MOs - - -`generators_bitmask `_ - Bitmasks for generator determinants. - (N_int, alpha/beta, hole/particle, generator). - .br - 3rd index is : - .br - * 1 : hole for single exc - .br - * 2 : particle for single exc - .br - * 3 : hole for 1st exc of double - .br - * 4 : particle for 1st exc of double - .br - * 5 : hole for 2nd exc of double - .br - * 6 : particle for 2nd exc of double - .br - - -`hf_bitmask `_ - Hartree Fock bit mask - - -`i_bitmask_gen `_ - Current bitmask for the generators - - -`inact_bitmask `_ - Bitmasks for the inactive orbitals that are excited in post CAS method - - -`is_a_two_holes_two_particles `_ - Undocumented - - -`list_to_bitstring `_ - Returns the physical string "string(N_int,2)" from the array of - occupations "list(N_int*bit_kind_size,2) - - -`n_cas_bitmask `_ - Number of bitmasks for CAS - - -`n_generators_bitmask `_ - Number of bitmasks for generators - - -`n_int `_ - Number of 64-bit integers needed to represent determinants as binary strings - - -`number_of_holes `_ - Undocumented - - -`number_of_holes_verbose `_ - Undocumented - - -`number_of_particles `_ - Undocumented - - -`number_of_particles_verbose `_ - Undocumented - - -`print_det `_ - Subroutine to print the content of a determinant using the '+-' notation - - -`print_spindet `_ - Subroutine to print the content of a determinant using the '+-' notation - - -`ref_bitmask `_ - Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask - - -`virt_bitmask `_ - Bitmasks for the inactive orbitals that are excited in post CAS method - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Determinants/README.rst b/src/Determinants/README.rst index ac97074c..1c114a19 100644 --- a/src/Determinants/README.rst +++ b/src/Determinants/README.rst @@ -37,882 +37,6 @@ Needed Modules * `Integrals_Monoelec `_ * `Integrals_Bielec `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`a_operator `_ - Needed for diag_H_mat_elem - - -`abs_psi_coef_max `_ - Max and min values of the coefficients - - -`abs_psi_coef_min `_ - Max and min values of the coefficients - - -`ac_operator `_ - Needed for diag_H_mat_elem - - -`apply_mono `_ - Undocumented - - -`bi_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - - -`ci_eigenvectors `_ - Eigenvectors/values of the CI matrix - - -`ci_eigenvectors_mono `_ - Eigenvectors/values of the CI matrix - - -`ci_eigenvectors_s2 `_ - Eigenvectors/values of the CI matrix - - -`ci_eigenvectors_s2_mono `_ - Eigenvectors/values of the CI matrix - - -`ci_electronic_energy `_ - Eigenvectors/values of the CI matrix - - -`ci_electronic_energy_mono `_ - Eigenvectors/values of the CI matrix - - -`ci_energy `_ - N_states lowest eigenvalues of the CI matrix - - -`ci_sc2_eigenvectors `_ - Eigenvectors/values of the CI matrix - - -`ci_sc2_electronic_energy `_ - Eigenvectors/values of the CI matrix - - -`ci_sc2_energy `_ - N_states_diag lowest eigenvalues of the CI matrix - - -`cisd `_ - Undocumented - - -`cisd_sc2 `_ - CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not) - .br - dets_in : bitmasks corresponding to determinants - .br - u_in : guess coefficients on the various states. Overwritten - on exit - .br - dim_in : leftmost dimension of u_in - .br - sze : Number of determinants - .br - N_st : Number of eigenstates - .br - Initial guess vectors are not necessarily orthonormal - - -`connected_to_ref `_ - Undocumented - - -`connected_to_ref_by_mono `_ - Undocumented - - -`copy_h_apply_buffer_to_wf `_ - Copies the H_apply buffer to psi_coef. - After calling this subroutine, N_det, psi_det and psi_coef need to be touched - - -`create_wf_of_psi_svd_matrix `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants - - -`davidson_converged `_ - True if the Davidson algorithm is converged - - -`davidson_criterion `_ - Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] - - -`davidson_diag `_ - Davidson diagonalization. - .br - dets_in : bitmasks corresponding to determinants - .br - u_in : guess coefficients on the various states. Overwritten - on exit - .br - dim_in : leftmost dimension of u_in - .br - sze : Number of determinants - .br - N_st : Number of eigenstates - .br - iunit : Unit number for the I/O - .br - Initial guess vectors are not necessarily orthonormal - - -`davidson_diag_hjj `_ - Davidson diagonalization with specific diagonal elements of the H matrix - .br - H_jj : specific diagonal H matrix elements to diagonalize de Davidson - .br - dets_in : bitmasks corresponding to determinants - .br - u_in : guess coefficients on the various states. Overwritten - on exit - .br - dim_in : leftmost dimension of u_in - .br - sze : Number of determinants - .br - N_st : Number of eigenstates - .br - iunit : Unit for the I/O - .br - Initial guess vectors are not necessarily orthonormal - - -`davidson_iter_max `_ - Max number of Davidson iterations - - -`davidson_sze_max `_ - Max number of Davidson sizes - - -`davidson_threshold `_ - Can be : [ energy | residual | both | wall_time | cpu_time | iterations ] - - -`decode_exc `_ - Decodes the exc arrays returned by get_excitation. - h1,h2 : Holes - p1,p2 : Particles - s1,s2 : Spins (1:alpha, 2:beta) - degree : Degree of excitation - - -`det_coef `_ - det_coef - - -`det_connections `_ - Build connection proxy between determinants - - -`det_num `_ - det_num - - -`det_occ `_ - det_occ - - -`det_search_key `_ - Return an integer*8 corresponding to a determinant index for searching - - -`det_svd `_ - Computes the SVD of the Alpha x Beta determinant coefficient matrix - - -`det_to_occ_pattern `_ - Transform a determinant to an occupation pattern - - -`diag_algorithm `_ - Diagonalization algorithm (Davidson or Lapack) - - -`diag_h_mat_elem `_ - Computes - - -`diagonalize_ci `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates of the CI matrix - - -`diagonalize_ci_mono `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates of the CI matrix - - -`diagonalize_ci_sc2 `_ - Replace the coefficients of the CI states_diag by the coefficients of the - eigenstates of the CI matrix - - -`do_mono_excitation `_ - Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin - on key_in - ispin = 1 == alpha - ispin = 2 == beta - i_ok = 1 == the excitation is possible - i_ok = -1 == the excitation is not possible - - -`double_exc_bitmask `_ - double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1 - double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1 - double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2 - double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2 - for a given couple of hole/particle excitations i. - - -`expected_s2 `_ - Expected value of S2 : S*(S+1) - - -`fill_h_apply_buffer_no_selection `_ - Fill the H_apply buffer with determiants for CISD - - -`filter_3_highest_electrons `_ - Returns a determinant with only the 3 highest electrons - - -`filter_connected `_ - Filters out the determinants that are not connected by H - .br - returns the array idx which contains the index of the - .br - determinants in the array key1 that interact - .br - via the H operator with key2. - .br - idx(0) is the number of determinants that interact with key1 - - -`filter_connected_davidson `_ - Filters out the determinants that are not connected by H - returns the array idx which contains the index of the - determinants in the array key1 that interact - via the H operator with key2. - .br - idx(0) is the number of determinants that interact with key1 - key1 should come from psi_det_sorted_ab. - - -`filter_connected_i_h_psi0 `_ - returns the array idx which contains the index of the - .br - determinants in the array key1 that interact - .br - via the H operator with key2. - .br - idx(0) is the number of determinants that interact with key1 - - -`filter_connected_i_h_psi0_sc2 `_ - standard filter_connected_i_H_psi but returns in addition - .br - the array of the index of the non connected determinants to key1 - .br - in order to know what double excitation can be repeated on key1 - .br - idx_repeat(0) is the number of determinants that can be used - .br - to repeat the excitations - - -`filter_connected_sorted_ab `_ - Filters out the determinants that are not connected by H - returns the array idx which contains the index of the - determinants in the array key1 that interact - via the H operator with key2. - idx(0) is the number of determinants that interact with key1 - .br - Determinants are taken from the psi_det_sorted_ab array - - -`generate_all_alpha_beta_det_products `_ - Create a wave function from all possible alpha x beta determinants - - -`get_double_excitation `_ - Returns the two excitation operators between two doubly excited determinants and the phase - - -`get_excitation `_ - Returns the excitation operators between two determinants and the phase - - -`get_excitation_degree `_ - Returns the excitation degree between two determinants - - -`get_excitation_degree_vector `_ - Applies get_excitation_degree to an array of determinants - - -`get_index_in_psi_det_alpha_unique `_ - Returns the index of the determinant in the ``psi_det_alpha_unique`` array - - -`get_index_in_psi_det_beta_unique `_ - Returns the index of the determinant in the ``psi_det_beta_unique`` array - - -`get_index_in_psi_det_sorted_bit `_ - Returns the index of the determinant in the ``psi_det_sorted_bit`` array - - -`get_mono_excitation `_ - Returns the excitation operator between two singly excited determinants and the phase - - -`get_occ_from_key `_ - Returns a list of occupation numbers from a bitstring - - -`get_s2 `_ - Returns - - -`get_s2_u0 `_ - Undocumented - - -`get_s2_u0_old `_ - Undocumented - - -`h_apply_buffer_allocated `_ - Buffer of determinants/coefficients/perturbative energy for H_apply. - Uninitialized. Filled by H_apply subroutines. - - -`h_apply_buffer_lock `_ - Buffer of determinants/coefficients/perturbative energy for H_apply. - Uninitialized. Filled by H_apply subroutines. - - -`h_matrix_all_dets `_ - H matrix on the basis of the slater determinants defined by psi_det - - -`h_matrix_cas `_ - Undocumented - - -`h_u_0 `_ - Computes v_0 = H|u_0> - .br - n : number of determinants - .br - H_jj : array of - - -`i_h_j `_ - Returns where i and j are determinants - - -`i_h_j_verbose `_ - Returns where i and j are determinants - - -`i_h_psi `_ - for the various Nstates - - -`i_h_psi_sc2 `_ - for the various Nstate - .br - returns in addition - .br - the array of the index of the non connected determinants to key1 - .br - in order to know what double excitation can be repeated on key1 - .br - idx_repeat(0) is the number of determinants that can be used - .br - to repeat the excitations - - -`i_h_psi_sc2_verbose `_ - for the various Nstate - .br - returns in addition - .br - the array of the index of the non connected determinants to key1 - .br - in order to know what double excitation can be repeated on key1 - .br - idx_repeat(0) is the number of determinants that can be used - .br - to repeat the excitations - - -`i_h_psi_sec_ord `_ - for the various Nstates - - -`idx_cas `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - - -`idx_non_cas `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - - -`int_of_3_highest_electrons `_ - Returns an integer*8 as : - .br - |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->| - .br - |0<--- i1 ---><--- i2 ---><--- i3 --->| - .br - It encodes the value of the indices of the 3 highest MOs - in descending order - .br - - -`is_in_wavefunction `_ - True if the determinant ``det`` is in the wave function - - -`kinetic_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - - -`make_s2_eigenfunction `_ - Undocumented - - -`max_degree_exc `_ - Maximum degree of excitation in the wf - - -`mono_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - - -`n_con_int `_ - Number of integers to represent the connections between determinants - - -`n_det `_ - Number of determinants in the wave function - - -`n_det_alpha_unique `_ - Unique alpha determinants - - -`n_det_beta_unique `_ - Unique beta determinants - - -`n_det_cas `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - - -`n_det_max `_ - Max number of determinants in the wave function - - -`n_det_max_jacobi `_ - Maximum number of determinants diagonalized by Jacobi - - -`n_det_max_property `_ - Max number of determinants in the wave function when you select for a given property - - -`n_det_non_cas `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - - -`n_double_exc_bitmasks `_ - Number of double excitation bitmasks - - -`n_occ_pattern `_ - array of the occ_pattern present in the wf - psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation - psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation - - -`n_single_exc_bitmasks `_ - Number of single excitation bitmasks - - -`n_states `_ - Number of states to consider - - -`n_states_diag `_ - Number of states to consider for the diagonalization - - -`nucl_elec_ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - - -`occ_pattern_search_key `_ - Return an integer*8 corresponding to a determinant index for searching - - -`occ_pattern_to_dets `_ - Generate all possible determinants for a give occ_pattern - - -`occ_pattern_to_dets_size `_ - Number of possible determinants for a given occ_pattern - - -`one_body_dm_mo `_ - One-body density matrix - - -`one_body_dm_mo_alpha `_ - Alpha and beta one-body density matrix for each state - - -`one_body_dm_mo_beta `_ - Alpha and beta one-body density matrix for each state - - -`one_body_single_double_dm_mo_alpha `_ - Alpha and beta one-body density matrix for each state - - -`one_body_single_double_dm_mo_beta `_ - Alpha and beta one-body density matrix for each state - - -`one_body_spin_density_mo `_ - rho(alpha) - rho(beta) - - -`only_single_double_dm `_ - If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements - - -`pouet `_ - Undocumented - - -`psi_average_norm_contrib `_ - Contribution of determinants to the state-averaged density - - -`psi_average_norm_contrib_sorted `_ - Wave function sorted by determinants contribution to the norm (state-averaged) - - -`psi_cas `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - - -`psi_cas_coef `_ - CAS wave function, defined from the application of the CAS bitmask on the - determinants. idx_cas gives the indice of the CAS determinant in psi_det. - - -`psi_cas_coef_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - - -`psi_cas_energy `_ - Undocumented - - -`psi_cas_energy_diagonalized `_ - Undocumented - - -`psi_cas_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - - -`psi_coef `_ - The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file - is empty - - -`psi_coef_cas_diagonalized `_ - Undocumented - - -`psi_coef_max `_ - Max and min values of the coefficients - - -`psi_coef_min `_ - Max and min values of the coefficients - - -`psi_coef_sorted `_ - Wave function sorted by determinants contribution to the norm (state-averaged) - - -`psi_coef_sorted_ab `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`psi_coef_sorted_bit `_ - Determinants on which we apply for perturbation. - They are sorted by determinants interpreted as integers. Useful - to accelerate the search of a random determinant in the wave - function. - - -`psi_det `_ - The wave function determinants. Initialized with Hartree-Fock if the EZFIO file - is empty - - -`psi_det_alpha `_ - List of alpha determinants of psi_det - - -`psi_det_alpha_unique `_ - Unique alpha determinants - - -`psi_det_beta `_ - List of beta determinants of psi_det - - -`psi_det_beta_unique `_ - Unique beta determinants - - -`psi_det_size `_ - Size of the psi_det/psi_coef arrays - - -`psi_det_sorted `_ - Wave function sorted by determinants contribution to the norm (state-averaged) - - -`psi_det_sorted_ab `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`psi_det_sorted_bit `_ - Determinants on which we apply for perturbation. - They are sorted by determinants interpreted as integers. Useful - to accelerate the search of a random determinant in the wave - function. - - -`psi_det_sorted_next_ab `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`psi_non_cas `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - - -`psi_non_cas_coef `_ - Set of determinants which are not part of the CAS, defined from the application - of the CAS bitmask on the determinants. - idx_non_cas gives the indice of the determinant in psi_det. - - -`psi_non_cas_coef_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - - -`psi_non_cas_sorted_bit `_ - CAS determinants sorted to accelerate the search of a random determinant in the wave - function. - - -`psi_occ_pattern `_ - array of the occ_pattern present in the wf - psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation - psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation - - -`psi_svd_alpha `_ - SVD wave function - - -`psi_svd_beta `_ - SVD wave function - - -`psi_svd_coefs `_ - SVD wave function - - -`psi_svd_matrix `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants - - -`psi_svd_matrix_columns `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants - - -`psi_svd_matrix_rows `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants - - -`psi_svd_matrix_values `_ - Matrix of wf coefficients. Outer product of alpha and beta determinants - - -`put_gess `_ - Undocumented - - -`read_dets `_ - Reads the determinants from the EZFIO file - - -`read_wf `_ - If true, read the wave function from the EZFIO file - - -`rec_occ_pattern_to_dets `_ - Undocumented - - -`ref_bitmask_energy `_ - Energy of the reference bitmask used in Slater rules - - -`remove_duplicates_in_psi_det `_ - Removes duplicate determinants in the wave function. - - -`resize_h_apply_buffer `_ - Resizes the H_apply buffer of proc iproc. The buffer lock should - be set before calling this function. - - -`routine `_ - Undocumented - - -`s2_eig `_ - Force the wave function to be an eigenfunction of S^2 - - -`s2_values `_ - array of the averaged values of the S^2 operator on the various states - - -`s_z `_ - z component of the Spin - - -`s_z2_sz `_ - z component of the Spin - - -`save_natorb `_ - Undocumented - - -`save_natural_mos `_ - Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis - - -`save_wavefunction `_ - Save the wave function into the EZFIO file - - -`save_wavefunction_general `_ - Save the wave function into the EZFIO file - - -`save_wavefunction_unsorted `_ - Save the wave function into the EZFIO file - - -`set_natural_mos `_ - Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis - - -`single_exc_bitmask `_ - single_exc_bitmask(:,1,i) is the bitmask for holes - single_exc_bitmask(:,2,i) is the bitmask for particles - for a given couple of hole/particle excitations i. - - -`sort_dets_by_3_highest_electrons `_ - Determinants on which we apply . - They are sorted by the 3 highest electrons in the alpha part, - then by the 3 highest electrons in the beta part to accelerate - the research of connected determinants. - - -`sort_dets_by_det_search_key `_ - Determinants are sorted are sorted according to their det_search_key. - Useful to accelerate the search of a random determinant in the wave - function. - - -`spin_det_search_key `_ - Return an integer*8 corresponding to a determinant index for searching - - -`state_average_weight `_ - Weights in the state-average calculation of the density matrix - - -`threshold_convergence_sc2 `_ - convergence of the correlation energy of SC2 iterations - - -`threshold_generators `_ - Thresholds on generators (fraction of the norm) - - -`threshold_selectors `_ - Thresholds on selectors (fraction of the norm) - - -`write_spindeterminants `_ - Undocumented - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index 2bc9f70d..d1c342b5 100644 --- a/src/Electrons/README.rst +++ b/src/Electrons/README.rst @@ -28,27 +28,6 @@ Needed Modules * `Ezfio_files `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`elec_alpha_num `_ - Numbers of electrons alpha ("up") - - -`elec_beta_num `_ - Numbers of electrons beta ("down") - - -`elec_num `_ - Numbers of alpha ("up") , beta ("down") and total electrons - - -`elec_num_tab `_ - Numbers of alpha ("up") , beta ("down") and total electrons - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Integrals_Bielec/README.rst b/src/Integrals_Bielec/README.rst index 054a6720..b71d9c0d 100644 --- a/src/Integrals_Bielec/README.rst +++ b/src/Integrals_Bielec/README.rst @@ -21,287 +21,6 @@ Needed Modules * `Pseudo `_ * `Bitmask `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`add_integrals_to_map `_ - Adds integrals to tha MO map according to some bitmask - - -`ao_bielec_integral `_ - integral of the AO basis or (ij|kl) - i(r1) j(r1) 1/r12 k(r2) l(r2) - - -`ao_bielec_integral_schwartz `_ - Needed to compute Schwartz inequalities - - -`ao_bielec_integral_schwartz_accel `_ - integral of the AO basis or (ij|kl) - i(r1) j(r1) 1/r12 k(r2) l(r2) - - -`ao_bielec_integrals_in_map `_ - Map of Atomic integrals - i(r1) j(r2) 1/r12 k(r1) l(r2) - - -`ao_integrals_map `_ - AO integrals - - -`ao_integrals_threshold `_ - If || < ao_integrals_threshold then is zero - - -`ao_l4 `_ - Computes the product of l values of i,j,k,and l - - -`bielec_integrals_index `_ - Undocumented - - -`bielec_integrals_index_reverse `_ - Undocumented - - -`clear_ao_map `_ - Frees the memory of the AO map - - -`clear_mo_map `_ - Frees the memory of the MO map - - -`compute_ao_bielec_integrals `_ - Compute AO 1/r12 integrals for all i and fixed j,k,l - - -`disk_access_ao_integrals `_ - Read/Write AO integrals from/to disk [ Write | Read | None ] - - -`disk_access_mo_integrals `_ - Read/Write MO integrals from/to disk [ Write | Read | None ] - - -`do_direct_integrals `_ - Compute integrals on the fly - - -`dump_ao_integrals `_ - Save to disk the $ao integrals - - -`dump_mo_integrals `_ - Save to disk the $ao integrals - - -`eri `_ - ATOMIC PRIMTIVE bielectronic integral between the 4 primitives :: - primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2) - primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2) - primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2) - primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2) - - -`gauleg `_ - Gauss-Legendre - - -`gauleg_t2 `_ - t_w(i,1,k) = w(i) - t_w(i,2,k) = t(i) - - -`gauleg_w `_ - t_w(i,1,k) = w(i) - t_w(i,2,k) = t(i) - - -`general_primitive_integral `_ - Computes the integral where p,q,r,s are Gaussian primitives - - -`get_ao_bielec_integral `_ - Gets one AO bi-electronic integral from the AO map - - -`get_ao_bielec_integrals `_ - Gets multiple AO bi-electronic integral from the AO map . - All i are retrieved for j,k,l fixed. - - -`get_ao_bielec_integrals_non_zero `_ - Gets multiple AO bi-electronic integral from the AO map . - All non-zero i are retrieved for j,k,l fixed. - - -`get_ao_map_size `_ - Returns the number of elements in the AO map - - -`get_mo_bielec_integral `_ - Returns one integral in the MO basis - - -`get_mo_bielec_integrals `_ - Returns multiple integrals in the MO basis, all - i for j,k,l fixed. - - -`get_mo_bielec_integrals_existing_ik `_ - Returns multiple integrals in the MO basis, all - i(1)j(1) 1/r12 k(2)l(2) - i for j,k,l fixed. - - -`get_mo_map_size `_ - Return the number of elements in the MO map - - -`give_polynom_mult_center_x `_ - subroutine that returns the explicit polynom in term of the "t" - variable of the following polynomw : - I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q) - - -`i_x1_new `_ - recursive function involved in the bielectronic integral - - -`i_x1_pol_mult `_ - recursive function involved in the bielectronic integral - - -`i_x1_pol_mult_a1 `_ - recursive function involved in the bielectronic integral - - -`i_x1_pol_mult_a2 `_ - recursive function involved in the bielectronic integral - - -`i_x1_pol_mult_recurs `_ - recursive function involved in the bielectronic integral - - -`i_x2_new `_ - recursive function involved in the bielectronic integral - - -`i_x2_pol_mult `_ - recursive function involved in the bielectronic integral - - -`insert_into_ao_integrals_map `_ - Create new entry into AO map - - -`insert_into_mo_integrals_map `_ - Create new entry into MO map, or accumulate in an existing entry - - -`integrale_new `_ - calculate the integral of the polynom :: - I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q) - between ( 0 ; 1) - - -`load_ao_integrals `_ - Read from disk the $ao integrals - - -`load_mo_integrals `_ - Read from disk the $ao integrals - - -`mo_bielec_integral `_ - Returns one integral in the MO basis - - -`mo_bielec_integral_jj `_ - mo_bielec_integral_jj(i,j) = J_ij - mo_bielec_integral_jj_exchange(i,j) = K_ij - mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij - - -`mo_bielec_integral_jj_anti `_ - mo_bielec_integral_jj(i,j) = J_ij - mo_bielec_integral_jj_exchange(i,j) = K_ij - mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij - - -`mo_bielec_integral_jj_anti_from_ao `_ - mo_bielec_integral_jj_from_ao(i,j) = J_ij - mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij - mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij - - -`mo_bielec_integral_jj_exchange `_ - mo_bielec_integral_jj(i,j) = J_ij - mo_bielec_integral_jj_exchange(i,j) = K_ij - mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij - - -`mo_bielec_integral_jj_exchange_from_ao `_ - mo_bielec_integral_jj_from_ao(i,j) = J_ij - mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij - mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij - - -`mo_bielec_integral_jj_from_ao `_ - mo_bielec_integral_jj_from_ao(i,j) = J_ij - mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij - mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij - - -`mo_bielec_integrals_in_map `_ - If True, the map of MO bielectronic integrals is provided - - -`mo_bielec_integrals_index `_ - Computes an unique index for i,j,k,l integrals - - -`mo_integrals_map `_ - MO integrals - - -`mo_integrals_threshold `_ - If || < ao_integrals_threshold then is zero - - -`n_pt_max_integrals_16 `_ - Aligned n_pt_max_integrals - - -`n_pt_sup `_ - Returns the upper boundary of the degree of the polynomial involved in the - bielctronic integral : - Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z) - - -`read_ao_integrals `_ - One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals - - -`read_mo_integrals `_ - One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals - - -`write_ao_integrals `_ - One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals - - -`write_mo_integrals `_ - One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Integrals_Monoelec/README.rst b/src/Integrals_Monoelec/README.rst index dbdd753b..13aceb0e 100644 --- a/src/Integrals_Monoelec/README.rst +++ b/src/Integrals_Monoelec/README.rst @@ -9,273 +9,6 @@ Needed Modules * `MO_Basis `_ * `Pseudo `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_deriv2_x `_ - second derivatives matrix elements in the ao basis - .. math:: - .br - {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle - - -`ao_deriv2_y `_ - second derivatives matrix elements in the ao basis - .. math:: - .br - {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle - - -`ao_deriv2_z `_ - second derivatives matrix elements in the ao basis - .. math:: - .br - {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle - - -`ao_deriv_1_x `_ - array of the integrals of AO_i * d/dx AO_j - array of the integrals of AO_i * d/dy AO_j - array of the integrals of AO_i * d/dz AO_j - - -`ao_deriv_1_y `_ - array of the integrals of AO_i * d/dx AO_j - array of the integrals of AO_i * d/dy AO_j - array of the integrals of AO_i * d/dz AO_j - - -`ao_deriv_1_z `_ - array of the integrals of AO_i * d/dx AO_j - array of the integrals of AO_i * d/dy AO_j - array of the integrals of AO_i * d/dz AO_j - - -`ao_dipole_x `_ - array of the integrals of AO_i * x AO_j - array of the integrals of AO_i * y AO_j - array of the integrals of AO_i * z AO_j - - -`ao_dipole_y `_ - array of the integrals of AO_i * x AO_j - array of the integrals of AO_i * y AO_j - array of the integrals of AO_i * z AO_j - - -`ao_dipole_z `_ - array of the integrals of AO_i * x AO_j - array of the integrals of AO_i * y AO_j - array of the integrals of AO_i * z AO_j - - -`ao_kinetic_integral `_ - array of the priminitve basis kinetic integrals - \langle \chi_i |\hat{T}| \chi_j \rangle - - -`ao_mono_elec_integral `_ - array of the mono electronic hamiltonian on the AOs basis - : sum of the kinetic and nuclear electronic potential - - -`ao_nucl_elec_integral `_ - interaction nuclear electron - - -`ao_nucl_elec_integral_per_atom `_ - ao_nucl_elec_integral_per_atom(i,j,k) = - - where Rk is the geometry of the kth atom - - -`ao_pseudo_integral `_ - Pseudo-potential - - -`ao_pseudo_integral_local `_ - Local pseudo-potential - - -`ao_pseudo_integral_non_local `_ - Local pseudo-potential - - -`ao_spread_x `_ - array of the integrals of AO_i * x^2 AO_j - array of the integrals of AO_i * y^2 AO_j - array of the integrals of AO_i * z^2 AO_j - - -`ao_spread_y `_ - array of the integrals of AO_i * x^2 AO_j - array of the integrals of AO_i * y^2 AO_j - array of the integrals of AO_i * z^2 AO_j - - -`ao_spread_z `_ - array of the integrals of AO_i * x^2 AO_j - array of the integrals of AO_i * y^2 AO_j - array of the integrals of AO_i * z^2 AO_j - - -`check_ortho `_ - Undocumented - - -`do_print `_ - Undocumented - - -`give_polynom_mult_center_mono_elec `_ - Undocumented - - -`i_x1_pol_mult_mono_elec `_ - Undocumented - - -`i_x2_pol_mult_mono_elec `_ - Undocumented - - -`int_gaus_pol `_ - Undocumented - - -`mo_deriv_1_x `_ - array of the integrals of MO_i * d/dx MO_j - array of the integrals of MO_i * d/dy MO_j - array of the integrals of MO_i * d/dz MO_j - - -`mo_deriv_1_y `_ - array of the integrals of MO_i * d/dx MO_j - array of the integrals of MO_i * d/dy MO_j - array of the integrals of MO_i * d/dz MO_j - - -`mo_deriv_1_z `_ - array of the integrals of MO_i * d/dx MO_j - array of the integrals of MO_i * d/dy MO_j - array of the integrals of MO_i * d/dz MO_j - - -`mo_dipole_x `_ - array of the integrals of MO_i * x MO_j - array of the integrals of MO_i * y MO_j - array of the integrals of MO_i * z MO_j - - -`mo_dipole_y `_ - array of the integrals of MO_i * x MO_j - array of the integrals of MO_i * y MO_j - array of the integrals of MO_i * z MO_j - - -`mo_dipole_z `_ - array of the integrals of MO_i * x MO_j - array of the integrals of MO_i * y MO_j - array of the integrals of MO_i * z MO_j - - -`mo_kinetic_integral `_ - Undocumented - - -`mo_mono_elec_integral `_ - array of the mono electronic hamiltonian on the MOs basis - : sum of the kinetic and nuclear electronic potential - - -`mo_nucl_elec_integral `_ - interaction nuclear electron on the MO basis - - -`mo_nucl_elec_integral_per_atom `_ - 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 - - -`mo_spread_x `_ - array of the integrals of MO_i * x^2 MO_j - array of the integrals of MO_i * y^2 MO_j - array of the integrals of MO_i * z^2 MO_j - - -`mo_spread_y `_ - array of the integrals of MO_i * x^2 MO_j - array of the integrals of MO_i * y^2 MO_j - array of the integrals of MO_i * z^2 MO_j - - -`mo_spread_z `_ - array of the integrals of MO_i * x^2 MO_j - array of the integrals of MO_i * y^2 MO_j - array of the integrals of MO_i * z^2 MO_j - - -`nai_pol_mult `_ - Undocumented - - -`orthonormalize_mos `_ - Undocumented - - -`overlap_bourrin_deriv_x `_ - Undocumented - - -`overlap_bourrin_dipole `_ - Undocumented - - -`overlap_bourrin_spread `_ - Undocumented - - -`overlap_bourrin_x `_ - Undocumented - - -`overlap_bourrin_x_abs `_ - Undocumented - - -`power `_ - Undocumented - - -`save_ortho_mos `_ - Undocumented - - -`v_e_n `_ - Undocumented - - -`v_phi `_ - Undocumented - - -`v_r `_ - Undocumented - - -`v_theta `_ - Undocumented - - -`wallis `_ - Undocumented - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index a2d58aec..86f352a9 100644 --- a/src/MOGuess/README.rst +++ b/src/MOGuess/README.rst @@ -12,35 +12,6 @@ Needed Modules * `Integrals_Monoelec `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_ortho_lowdin_coef `_ - matrix of the coefficients of the mos generated by the - orthonormalization by the S^{-1/2} canonical transformation of the aos - ao_ortho_lowdin_coef(i,j) = coefficient of the ith ao on the jth ao_ortho_lowdin orbital - - -`ao_ortho_lowdin_nucl_elec_integral `_ - Undocumented - - -`ao_ortho_lowdin_overlap `_ - overlap matrix of the ao_ortho_lowdin - supposed to be the Identity - - -`h_core_guess `_ - 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 `_ - Produce `H_core` MO orbital - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/MO_Basis/README.rst b/src/MO_Basis/README.rst index 361ef96f..87df08b1 100644 --- a/src/MO_Basis/README.rst +++ b/src/MO_Basis/README.rst @@ -41,97 +41,6 @@ Needed Modules * `AO_Basis `_ * `Electrons `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`ao_to_mo `_ - Transform A from the AO basis to the MO basis - - -`cholesky_mo `_ - Cholesky decomposition of AO Density matrix to - generate MOs - - -`mix_mo_jk `_ - subroutine that rotates the jth MO with the kth MO - to give two new MO's that are - '+' = 1/sqrt(2) (|j> + |k>) - '-' = 1/sqrt(2) (|j> - |k>) - by convention, the '+' MO is in the lower index (min(j,k)) - by convention, the '-' MO is in the greater index (max(j,k)) - - -`mo_as_eigvectors_of_mo_matrix `_ - Undocumented - - -`mo_as_eigvectors_of_mo_matrix_sort_by_observable `_ - Undocumented - - -`mo_coef `_ - Molecular orbital coefficients on AO basis set - mo_coef(i,j) = coefficient of the ith ao on the jth mo - mo_label : Label characterizing the MOS (local, canonical, natural, etc) - - -`mo_coef_transp `_ - Molecular orbital coefficients on AO basis set - - -`mo_density_matrix `_ - Density matrix in MO basis - - -`mo_density_matrix_virtual `_ - Density matrix in MO basis (virtual MOs) - - -`mo_label `_ - Molecular orbital coefficients on AO basis set - mo_coef(i,j) = coefficient of the ith ao on the jth mo - mo_label : Label characterizing the MOS (local, canonical, natural, etc) - - -`mo_occ `_ - MO occupation numbers - - -`mo_overlap `_ - Undocumented - - -`mo_sort_by_observable `_ - Undocumented - - -`mo_to_ao `_ - Transform A from the MO basis to the AO basis - - -`mo_to_ao_no_overlap `_ - Transform A from the MO basis to the S^-1 AO basis - - -`mo_tot_num `_ - Total number of molecular orbitals and the size of the keys corresponding - - -`mo_tot_num_align `_ - Aligned variable for dimensioning of arrays - - -`s_mo_coef `_ - Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix. - - -`save_mos `_ - Undocumented - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index 032c9963..bf7e6f52 100644 --- a/src/Nuclei/README.rst +++ b/src/Nuclei/README.rst @@ -17,77 +17,6 @@ Needed Modules * `Ezfio_files `_ * `Utils `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`element_name `_ - Array of the name of element, sorted by nuclear charge (integer) - - -`nucl_charge `_ - Nuclear charges - - -`nucl_coord `_ - Nuclear coordinates in the format (:, {x,y,z}) - - -`nucl_coord_transp `_ - Transposed array of nucl_coord - - -`nucl_dist `_ - nucl_dist : Nucleus-nucleus distances - nucl_dist_2 : Nucleus-nucleus distances squared - nucl_dist_vec : Nucleus-nucleus distances vectors - - -`nucl_dist_2 `_ - nucl_dist : Nucleus-nucleus distances - nucl_dist_2 : Nucleus-nucleus distances squared - nucl_dist_vec : Nucleus-nucleus distances vectors - - -`nucl_dist_vec_x `_ - nucl_dist : Nucleus-nucleus distances - nucl_dist_2 : Nucleus-nucleus distances squared - nucl_dist_vec : Nucleus-nucleus distances vectors - - -`nucl_dist_vec_y `_ - nucl_dist : Nucleus-nucleus distances - nucl_dist_2 : Nucleus-nucleus distances squared - nucl_dist_vec : Nucleus-nucleus distances vectors - - -`nucl_dist_vec_z `_ - nucl_dist : Nucleus-nucleus distances - nucl_dist_2 : Nucleus-nucleus distances squared - nucl_dist_vec : Nucleus-nucleus distances vectors - - -`nucl_label `_ - Nuclear labels - - -`nucl_num `_ - Number of nuclei - - -`nucl_num_aligned `_ - Number of nuclei algined - - -`nuclear_repulsion `_ - Nuclear repulsion energy - - -`positive_charge_barycentre `_ - Centroid of the positive charges - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Pseudo/README.rst b/src/Pseudo/README.rst index 60023235..062a9465 100644 --- a/src/Pseudo/README.rst +++ b/src/Pseudo/README.rst @@ -12,59 +12,6 @@ Needed Modules * `Nuclei `_ -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`do_pseudo `_ - Using pseudo potential integral of not - - -`pseudo_dz_k `_ - test - - -`pseudo_dz_kl `_ - test - - -`pseudo_grid_rmax `_ - R_maxof the QMC grid - - -`pseudo_grid_size `_ - Nb of points of the QMC grid - - -`pseudo_klocmax `_ - test - - -`pseudo_kmax `_ - test - - -`pseudo_lmax `_ - test - - -`pseudo_n_k `_ - test - - -`pseudo_n_kl `_ - test - - -`pseudo_v_k `_ - test - - -`pseudo_v_kl `_ - test - Needed Modules ============== .. Do not edit this section It was auto-generated diff --git a/src/Utils/README.rst b/src/Utils/README.rst index 5c271c93..e3c36e71 100644 --- a/src/Utils/README.rst +++ b/src/Utils/README.rst @@ -4,636 +4,6 @@ Utils Module Contains general purpose utilities. -Documentation -============= - -.. Do not edit this section It was auto-generated -.. by the `update_README.py` script. - -`a_coef `_ - Undocumented - - -`abort_all `_ - If True, all the calculation is aborted - - -`abort_here `_ - If True, all the calculation is aborted - - -`add_poly `_ - Add two polynomials - D(t) =! D(t) +( B(t)+C(t)) - - -`add_poly_multiply `_ - Add a polynomial multiplied by a constant - D(t) =! D(t) +( cst * B(t)) - - -`align_double `_ - Compute 1st dimension such that it is aligned for vectorization. - - -`apply_rotation `_ - Apply the rotation found by find_rotation - - -`approx_dble `_ - Undocumented - - -`b_coef `_ - Undocumented - - -`binom `_ - Binomial coefficients - - -`binom_func `_ - .. math :: - .br - \frac{i!}{j!(i-j)!} - .br - - -`binom_transp `_ - Binomial coefficients - - -`catch_signal `_ - What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted. - - -`dble_fact `_ - Undocumented - - -`dble_fact_even `_ - n!! - - -`dble_fact_odd `_ - n!! - - -`dble_logfact `_ - n!! - - -`ddfact2 `_ - Undocumented - - -`dset_order `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - - -`dset_order_big `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`dsort `_ - Sort array x(isize). - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`erf0 `_ - Undocumented - - -`f_integral `_ - function that calculates the following integral - \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx - - -`fact `_ - n! - - -`fact_inv `_ - 1/n! - - -`find_rotation `_ - Find A.C = B - - -`gammln `_ - Undocumented - - -`gammp `_ - Undocumented - - -`gaussian_product `_ - Gaussian product in 1D. - e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2} - - -`gaussian_product_x `_ - Gaussian product in 1D. - e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2} - - -`gcf `_ - Undocumented - - -`get_pseudo_inverse `_ - Find C = A^-1 - - -`give_explicit_poly_and_gaussian `_ - Transforms the product of - (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) - into - fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 ) - * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 ) - * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 ) - - -`give_explicit_poly_and_gaussian_double `_ - Transforms the product of - (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) - exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama - .br - into - fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 ) - * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 ) - * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 ) - - -`give_explicit_poly_and_gaussian_x `_ - Transform the product of - (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) - into - fact_k (x-x_P)^iorder(1) (y-y_P)^iorder(2) (z-z_P)^iorder(3) exp(-p(r-P)^2) - - -`gser `_ - Undocumented - - -`heap_dsort `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`heap_dsort_big `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`heap_i2sort `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`heap_i2sort_big `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`heap_i8sort `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`heap_i8sort_big `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`heap_isort `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`heap_isort_big `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`heap_sort `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`heap_sort_big `_ - Sort array x(isize) using the heap sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`hermite `_ - Hermite polynomial - - -`i2radix_sort `_ - Sort integer array x(isize) using the radix sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - iradix should be -1 in input. - - -`i2set_order `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - - -`i2set_order_big `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`i2sort `_ - Sort array x(isize). - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`i8radix_sort `_ - Sort integer array x(isize) using the radix sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - iradix should be -1 in input. - - -`i8radix_sort_big `_ - Sort integer array x(isize) using the radix sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - iradix should be -1 in input. - - -`i8set_order `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - - -`i8set_order_big `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`i8sort `_ - Sort array x(isize). - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`insertion_dsort `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`insertion_dsort_big `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`insertion_i2sort `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`insertion_i2sort_big `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`insertion_i8sort `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`insertion_i8sort_big `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`insertion_isort `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`insertion_isort_big `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`insertion_sort `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`insertion_sort_big `_ - Sort array x(isize) using the insertion sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`inv_int `_ - 1/i - - -`iradix_sort `_ - Sort integer array x(isize) using the radix sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - iradix should be -1 in input. - - -`iradix_sort_big `_ - Sort integer array x(isize) using the radix sort algorithm. - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - iradix should be -1 in input. - - -`iset_order `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - - -`iset_order_big `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`isort `_ - Sort array x(isize). - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`lapack_diag `_ - Diagonalize matrix H - .br - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector - .br - - -`lapack_diag_s2 `_ - Diagonalize matrix H - .br - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector - .br - - -`lapack_diagd `_ - Diagonalize matrix H - .br - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector - .br - - -`lapack_partial_diag `_ - Diagonalize matrix H - .br - H is untouched between input and ouptut - .br - eigevalues(i) = ith lowest eigenvalue of the H matrix - .br - eigvectors(i,j) = where i is the basis function and psi_j is the j th eigenvector - .br - - -`logfact `_ - n! - - -`multiply_poly `_ - Multiply two polynomials - D(t) =! D(t) +( B(t)*C(t)) - - -`normalize `_ - Normalizes vector u - u is expected to be aligned in memory. - - -`nproc `_ - Number of current OpenMP threads - - -`ortho_lowdin `_ - Compute C_new=C_old.S^-1/2 canonical orthogonalization. - .br - overlap : overlap matrix - .br - LDA : leftmost dimension of overlap array - .br - N : Overlap matrix is NxN (array is (LDA,N) ) - .br - C : Coefficients of the vectors to orthogonalize. On exit, - orthogonal vectors - .br - LDC : leftmost dimension of C - .br - m : Coefficients matrix is MxN, ( array is (LDC,N) ) - .br - - -`overlap_a_b_c `_ - Undocumented - - -`overlap_gaussian_x `_ - .. math:: - .br - \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx - .br - - -`overlap_gaussian_xyz `_ - .. math:: - .br - S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2) (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\ - S = S_x S_y S_z - .br - - -`overlap_x_abs `_ - .. math :: - .br - \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx - .br - - -`progress_active `_ - Current status for displaying progress bars. Global variable. - - -`progress_bar `_ - Current status for displaying progress bars. Global variable. - - -`progress_timeout `_ - Current status for displaying progress bars. Global variable. - - -`progress_title `_ - Current status for displaying progress bars. Global variable. - - -`progress_value `_ - Current status for displaying progress bars. Global variable. - - -`recentered_poly2 `_ - Recenter two polynomials - - -`rint `_ - .. math:: - .br - \int_0^1 dx \exp(-p x^2) x^n - .br - - -`rint1 `_ - Standard version of rint - - -`rint_large_n `_ - Version of rint for large values of n - - -`rint_sum `_ - Needed for the calculation of two-electron integrals. - - -`rinteg `_ - Undocumented - - -`rintgauss `_ - Undocumented - - -`run_progress `_ - Display a progress bar with documentation of what is happening - - -`sabpartial `_ - Undocumented - - -`set_order `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - - -`set_order_big `_ - array A has already been sorted, and iorder has contains the new order of - elements of A. This subroutine changes the order of x to match the new order of A. - This is a version for very large arrays where the indices need - to be in integer*8 format - - -`set_zero_extra_diag `_ - Undocumented - - -`sort `_ - Sort array x(isize). - iorder in input should be (1,2,3,...,isize), and in output - contains the new order of the elements. - - -`start_progress `_ - Starts the progress bar - - -`stop_progress `_ - Stop the progress bar - - -`trap_signals `_ - What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine. - - -`u_dot_u `_ - Compute - - -`u_dot_v `_ - Compute - - -`wall_time `_ - The equivalent of cpu_time, but for the wall time. - - -`write_git_log `_ - Write the last git commit in file iunit. - Documentation ============= .. Do not edit this section It was auto-generated From 006c28f4ee65798746ddd88f1d8fc9778acb3b7e Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Tue, 28 Jul 2015 17:31:54 +0200 Subject: [PATCH 10/11] Fix error in doc path --- plugins/Full_CI/README.rst | 58 +++++++++++----------- plugins/Generators_full/README.rst | 14 +++--- plugins/Hartree_Fock/README.rst | 52 ++++++++++---------- plugins/Perturbation/README.rst | 78 +++++++++++++++--------------- plugins/Properties/README.rst | 48 +++++++++--------- plugins/Selectors_full/README.rst | 40 +++++++-------- scripts/module/module_handler.py | 12 +++-- scripts/module/qp_update_readme.py | 19 ++++++-- 8 files changed, 169 insertions(+), 152 deletions(-) diff --git a/plugins/Full_CI/README.rst b/plugins/Full_CI/README.rst index 913fd972..1af26ae6 100644 --- a/plugins/Full_CI/README.rst +++ b/plugins/Full_CI/README.rst @@ -13,9 +13,9 @@ Needed Modules .. image:: tree_dependency.png -* `Perturbation `_ -* `Selectors_full `_ -* `Generators_full `_ +* `Perturbation `_ +* `Selectors_full `_ +* `Generators_full `_ Documentation ============= @@ -23,146 +23,146 @@ Documentation .. by the `update_README.py` script. -`full_ci `_ +`full_ci `_ Undocumented -`h_apply_fci `_ +`h_apply_fci `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_fci_diexc `_ +`h_apply_fci_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_mono `_ +`h_apply_fci_mono `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_fci_mono_diexc `_ +`h_apply_fci_mono_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_mono_monoexc `_ +`h_apply_fci_mono_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_monoexc `_ +`h_apply_fci_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_no_skip `_ +`h_apply_fci_no_skip `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_fci_no_skip_diexc `_ +`h_apply_fci_no_skip_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_no_skip_monoexc `_ +`h_apply_fci_no_skip_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_pt2 `_ +`h_apply_fci_pt2 `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_fci_pt2_diexc `_ +`h_apply_fci_pt2_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_fci_pt2_monoexc `_ +`h_apply_fci_pt2_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_pt2_mono_delta_rho `_ +`h_apply_pt2_mono_delta_rho `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_pt2_mono_delta_rho_diexc `_ +`h_apply_pt2_mono_delta_rho_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_pt2_mono_delta_rho_monoexc `_ +`h_apply_pt2_mono_delta_rho_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_pt2_mono_di_delta_rho `_ +`h_apply_pt2_mono_di_delta_rho `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_pt2_mono_di_delta_rho_diexc `_ +`h_apply_pt2_mono_di_delta_rho_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_pt2_mono_di_delta_rho_monoexc `_ +`h_apply_pt2_mono_di_delta_rho_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_select_mono_delta_rho `_ +`h_apply_select_mono_delta_rho `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_select_mono_delta_rho_diexc `_ +`h_apply_select_mono_delta_rho_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_select_mono_delta_rho_monoexc `_ +`h_apply_select_mono_delta_rho_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_select_mono_di_delta_rho `_ +`h_apply_select_mono_di_delta_rho `_ Calls H_apply on the HF determinant and selects all connected single and double excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script. -`h_apply_select_mono_di_delta_rho_diexc `_ +`h_apply_select_mono_di_delta_rho_diexc `_ Generate all double excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`h_apply_select_mono_di_delta_rho_monoexc `_ +`h_apply_select_mono_di_delta_rho_monoexc `_ Generate all single excitations of key_in using the bit masks of holes and particles. Assume N_int is already provided. -`var_pt2_ratio_run `_ +`var_pt2_ratio_run `_ Undocumented diff --git a/plugins/Generators_full/README.rst b/plugins/Generators_full/README.rst index 12acdabb..c30193a2 100644 --- a/plugins/Generators_full/README.rst +++ b/plugins/Generators_full/README.rst @@ -25,7 +25,7 @@ Needed Modules .. image:: tree_dependency.png * `Determinants `_ -* `Hartree_Fock `_ +* `Hartree_Fock `_ Documentation ============= @@ -33,29 +33,29 @@ Documentation .. by the `update_README.py` script. -`degree_max_generators `_ +`degree_max_generators `_ Max degree of excitation (respect to HF) of the generators -`n_det_generators `_ +`n_det_generators `_ For Single reference wave functions, the number of generators is 1 : the Hartree-Fock determinant -`psi_coef_generators `_ +`psi_coef_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`psi_det_generators `_ +`psi_det_generators `_ For Single reference wave functions, the generator is the Hartree-Fock determinant -`select_max `_ +`select_max `_ Memo to skip useless selectors -`size_select_max `_ +`size_select_max `_ Size of the select_max array diff --git a/plugins/Hartree_Fock/README.rst b/plugins/Hartree_Fock/README.rst index a1da75e1..345285ec 100644 --- a/plugins/Hartree_Fock/README.rst +++ b/plugins/Hartree_Fock/README.rst @@ -32,57 +32,57 @@ Documentation .. by the `update_README.py` script. -`ao_bi_elec_integral_alpha `_ +`ao_bi_elec_integral_alpha `_ Alpha Fock matrix in AO basis set -`ao_bi_elec_integral_beta `_ +`ao_bi_elec_integral_beta `_ Alpha Fock matrix in AO basis set -`create_guess `_ +`create_guess `_ Create an MO guess if no MOs are present in the EZFIO directory -`damping_scf `_ +`damping_scf `_ Undocumented -`diagonal_fock_matrix_mo `_ +`diagonal_fock_matrix_mo `_ Diagonal Fock matrix in the MO basis -`diagonal_fock_matrix_mo_sum `_ +`diagonal_fock_matrix_mo_sum `_ diagonal element of the fock matrix calculated as the sum over all the interactions with all the electrons in the RHF determinant diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij -`eigenvectors_fock_matrix_mo `_ +`eigenvectors_fock_matrix_mo `_ Diagonal Fock matrix in the MO basis -`fock_matrix_alpha_ao `_ +`fock_matrix_alpha_ao `_ Alpha Fock matrix in AO basis set -`fock_matrix_alpha_mo `_ +`fock_matrix_alpha_mo `_ Fock matrix on the MO basis -`fock_matrix_ao `_ +`fock_matrix_ao `_ Fock matrix in AO basis set -`fock_matrix_beta_ao `_ +`fock_matrix_beta_ao `_ Alpha Fock matrix in AO basis set -`fock_matrix_beta_mo `_ +`fock_matrix_beta_mo `_ Fock matrix on the MO basis -`fock_matrix_diag_mo `_ +`fock_matrix_diag_mo `_ Fock matrix on the MO basis. For open shells, the ROHF Fock Matrix is .br @@ -98,7 +98,7 @@ Documentation .br -`fock_matrix_mo `_ +`fock_matrix_mo `_ Fock matrix on the MO basis. For open shells, the ROHF Fock Matrix is .br @@ -114,53 +114,53 @@ Documentation .br -`fock_mo_to_ao `_ +`fock_mo_to_ao `_ Undocumented -`guess `_ +`guess `_ Undocumented -`hf_density_matrix_ao `_ +`hf_density_matrix_ao `_ S^-1 Density matrix in the AO basis S^-1 -`hf_density_matrix_ao_alpha `_ +`hf_density_matrix_ao_alpha `_ S^-1 x Alpha density matrix in the AO basis x S^-1 -`hf_density_matrix_ao_beta `_ +`hf_density_matrix_ao_beta `_ S^-1 Beta density matrix in the AO basis x S^-1 -`hf_energy `_ +`hf_energy `_ Hartree-Fock energy -`huckel_guess `_ +`huckel_guess `_ Build the MOs using the extended Huckel model -`mo_guess_type `_ +`mo_guess_type `_ Initial MO guess. Can be [ Huckel | HCore ] -`n_it_scf_max `_ +`n_it_scf_max `_ Maximum number of SCF iterations -`run `_ +`run `_ Run SCF calculation -`scf `_ +`scf `_ 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 `_ +`thresh_scf `_ Threshold on the convergence of the Hartree Fock energy diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index e9aafe82..3f77b2a2 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -86,8 +86,8 @@ Needed Modules .. image:: tree_dependency.png -* `Properties `_ -* `Hartree_Fock `_ +* `Properties `_ +* `Hartree_Fock `_ Documentation ============= @@ -95,109 +95,109 @@ Documentation .. by the `update_README.py` script. -`do_pt2_end `_ +`do_pt2_end `_ If true, compute the PT2 at the end of the selection -`fill_h_apply_buffer_selection `_ +`fill_h_apply_buffer_selection `_ Fill the H_apply buffer with determiants for the selection -`max_exc_pert `_ +`max_exc_pert `_ Undocumented -`perturb_buffer_by_mono_delta_rho_one_point `_ +`perturb_buffer_by_mono_delta_rho_one_point `_ Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_by_mono_dipole_moment_z `_ +`perturb_buffer_by_mono_dipole_moment_z `_ Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_by_mono_epstein_nesbet `_ +`perturb_buffer_by_mono_epstein_nesbet `_ Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_by_mono_epstein_nesbet_2x2 `_ +`perturb_buffer_by_mono_epstein_nesbet_2x2 `_ Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_by_mono_epstein_nesbet_sc2 `_ +`perturb_buffer_by_mono_epstein_nesbet_sc2 `_ 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 `_ +`perturb_buffer_by_mono_epstein_nesbet_sc2_no_projected `_ 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 `_ +`perturb_buffer_by_mono_epstein_nesbet_sc2_projected `_ Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_by_mono_h_core `_ +`perturb_buffer_by_mono_h_core `_ Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_by_mono_moller_plesset `_ +`perturb_buffer_by_mono_moller_plesset `_ Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_delta_rho_one_point `_ +`perturb_buffer_delta_rho_one_point `_ Applly pertubration ``delta_rho_one_point`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_dipole_moment_z `_ +`perturb_buffer_dipole_moment_z `_ Applly pertubration ``dipole_moment_z`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_epstein_nesbet `_ +`perturb_buffer_epstein_nesbet `_ Applly pertubration ``epstein_nesbet`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_epstein_nesbet_2x2 `_ +`perturb_buffer_epstein_nesbet_2x2 `_ Applly pertubration ``epstein_nesbet_2x2`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_epstein_nesbet_sc2 `_ +`perturb_buffer_epstein_nesbet_sc2 `_ Applly pertubration ``epstein_nesbet_sc2`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_epstein_nesbet_sc2_no_projected `_ +`perturb_buffer_epstein_nesbet_sc2_no_projected `_ Applly pertubration ``epstein_nesbet_sc2_no_projected`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_epstein_nesbet_sc2_projected `_ +`perturb_buffer_epstein_nesbet_sc2_projected `_ Applly pertubration ``epstein_nesbet_sc2_projected`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_h_core `_ +`perturb_buffer_h_core `_ Applly pertubration ``h_core`` to the buffer of determinants generated in the H_apply routine. -`perturb_buffer_moller_plesset `_ +`perturb_buffer_moller_plesset `_ Applly pertubration ``moller_plesset`` to the buffer of determinants generated in the H_apply routine. -`pt2_delta_rho_one_point `_ +`pt2_delta_rho_one_point `_ compute the perturbatibe contribution to the Integrated Spin density at z = z_one point of one determinant .br for the various n_st states, at various level of theory. @@ -218,7 +218,7 @@ Documentation .br -`pt2_dipole_moment_z `_ +`pt2_dipole_moment_z `_ compute the perturbatibe contribution to the dipole moment of one determinant .br for the various n_st states, at various level of theory. @@ -239,7 +239,7 @@ Documentation .br -`pt2_epstein_nesbet `_ +`pt2_epstein_nesbet `_ compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states. @@ -250,7 +250,7 @@ Documentation .br -`pt2_epstein_nesbet_2x2 `_ +`pt2_epstein_nesbet_2x2 `_ compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution .br for the various N_st states. @@ -261,7 +261,7 @@ Documentation .br -`pt2_epstein_nesbet_sc2 `_ +`pt2_epstein_nesbet_sc2 `_ compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states, but with the CISD_SC2 energies and coefficients @@ -272,7 +272,7 @@ Documentation .br -`pt2_epstein_nesbet_sc2_no_projected `_ +`pt2_epstein_nesbet_sc2_no_projected `_ compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states, @@ -296,7 +296,7 @@ Documentation H_pert_diag = c_pert -`pt2_epstein_nesbet_sc2_projected `_ +`pt2_epstein_nesbet_sc2_projected `_ compute the Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states, @@ -320,7 +320,7 @@ Documentation H_pert_diag = c_pert -`pt2_h_core `_ +`pt2_h_core `_ compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution .br for the various N_st states. @@ -331,12 +331,12 @@ Documentation .br -`pt2_max `_ +`pt2_max `_ The selection process stops when the largest PT2 (for all the state) is lower than pt2_max in absolute value -`pt2_moller_plesset `_ +`pt2_moller_plesset `_ compute the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution .br for the various n_st states. @@ -347,28 +347,28 @@ Documentation .br -`remove_small_contributions `_ +`remove_small_contributions `_ Remove determinants with small contributions. N_states is assumed to be provided. -`repeat_all_e_corr `_ +`repeat_all_e_corr `_ Undocumented -`selection_criterion `_ +`selection_criterion `_ Threshold to select determinants. Set by selection routines. -`selection_criterion_factor `_ +`selection_criterion_factor `_ Threshold to select determinants. Set by selection routines. -`selection_criterion_min `_ +`selection_criterion_min `_ Threshold to select determinants. Set by selection routines. -`var_pt2_ratio `_ +`var_pt2_ratio `_ The selection process stops when the energy ratio variational/(variational+PT2) is equal to var_pt2_ratio diff --git a/plugins/Properties/README.rst b/plugins/Properties/README.rst index 0be70c6c..cd92ba14 100644 --- a/plugins/Properties/README.rst +++ b/plugins/Properties/README.rst @@ -28,41 +28,41 @@ Documentation .. by the `update_README.py` script. -`ao_integrated_delta_rho_all_points `_ +`ao_integrated_delta_rho_all_points `_ array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis for all the z points that are given (N_z_pts) -`ao_integrated_delta_rho_one_point `_ +`ao_integrated_delta_rho_one_point `_ array of the overlap in x,y between the AO function and integrated between [z,z+dz] in the z axis for one specific z point -`average_position `_ +`average_position `_ average_position(1) = average_position(2) = average_position(3) = -`average_spread `_ +`average_spread `_ average_spread(1) = average_spread(2) = average_spread(3) = -`delta_z `_ +`delta_z `_ Undocumented -`diag_o1_mat_elem `_ +`diag_o1_mat_elem `_ Computes -`diag_o1_mat_elem_alpha_beta `_ +`diag_o1_mat_elem_alpha_beta `_ Computes -`filter_connected_mono `_ +`filter_connected_mono `_ Filters out the determinants that are not connected through PURE .br MONO EXCITATIONS OPERATORS (a^{\dagger}j a_i) @@ -76,89 +76,89 @@ Documentation idx(0) is the number of determinants that interact with key1 -`get_average `_ +`get_average `_ computes the average value of a pure MONO ELECTRONIC OPERATOR whom integrals on the MO basis are stored in "array" and with the density is stored in "density" -`i_o1_j `_ +`i_o1_j `_ Returns where i and j are determinants and O1 is a ONE BODY OPERATOR array is the array of the mono electronic operator on the MO basis -`i_o1_j_alpha_beta `_ +`i_o1_j_alpha_beta `_ Returns where i and j are determinants and O1 is a ONE BODY OPERATOR array is the array of the mono electronic operator on the MO basis -`i_o1_psi `_ +`i_o1_psi `_ for the various Nstates and O1 is a ONE BODY OPERATOR array is the array of the mono electronic operator on the MO basis -`i_o1_psi_alpha_beta `_ +`i_o1_psi_alpha_beta `_ for the various Nstates and O1 is a ONE BODY OPERATOR array is the array of the mono electronic operator on the MO basis -`i_unit_integrated_delta_rho `_ +`i_unit_integrated_delta_rho `_ fortran unit for the writing of the integrated delta_rho -`integrated_delta_rho_all_points `_ +`integrated_delta_rho_all_points `_ .br integrated_rho(alpha,z) - integrated_rho(beta,z) for all the z points chosen .br -`integrated_delta_rho_one_point `_ +`integrated_delta_rho_one_point `_ .br integral (x,y) and (z,z+delta_z) of rho(alpha) - rho(beta) on the MO basis .br -`mo_integrated_delta_rho_one_point `_ +`mo_integrated_delta_rho_one_point `_ .br array of the integrals needed of integrated_rho(alpha,z) - integrated_rho(beta,z) for z = z_one_point on the MO basis .br -`n_z_pts `_ +`n_z_pts `_ Undocumented -`test_average_value `_ +`test_average_value `_ Undocumented -`test_average_value_alpha_beta `_ +`test_average_value_alpha_beta `_ Undocumented -`test_dm `_ +`test_dm `_ Undocumented -`z_max `_ +`z_max `_ Undocumented -`z_min `_ +`z_min `_ Undocumented -`z_one_point `_ +`z_one_point `_ z point on which the integrated delta rho is calculated diff --git a/plugins/Selectors_full/README.rst b/plugins/Selectors_full/README.rst index e90ee6c2..795234b4 100644 --- a/plugins/Selectors_full/README.rst +++ b/plugins/Selectors_full/README.rst @@ -22,7 +22,7 @@ Needed Modules .. image:: tree_dependency.png * `Determinants `_ -* `Hartree_Fock `_ +* `Hartree_Fock `_ Documentation ============= @@ -30,7 +30,7 @@ Documentation .. by the `update_README.py` script. -`coef_hf_selector `_ +`coef_hf_selector `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -42,7 +42,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`delta_e_per_selector `_ +`delta_e_per_selector `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -54,7 +54,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`double_index_selectors `_ +`double_index_selectors `_ degree of excitation respect to Hartree Fock for the wave function .br for the all the selectors determinants @@ -64,7 +64,7 @@ Documentation n_double_selectors = number of double excitations in the selectors determinants -`e_corr_double_only `_ +`e_corr_double_only `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -76,7 +76,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`e_corr_per_selectors `_ +`e_corr_per_selectors `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -88,7 +88,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`e_corr_second_order `_ +`e_corr_second_order `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -100,7 +100,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`exc_degree_per_selectors `_ +`exc_degree_per_selectors `_ degree of excitation respect to Hartree Fock for the wave function .br for the all the selectors determinants @@ -110,7 +110,7 @@ Documentation n_double_selectors = number of double excitations in the selectors determinants -`i_h_hf_per_selectors `_ +`i_h_hf_per_selectors `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -122,7 +122,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`inv_selectors_coef_hf `_ +`inv_selectors_coef_hf `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -134,7 +134,7 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`inv_selectors_coef_hf_squared `_ +`inv_selectors_coef_hf_squared `_ energy of correlation per determinant respect to the Hartree Fock determinant .br for the all the double excitations in the selectors determinants @@ -146,12 +146,12 @@ Documentation coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants -`n_det_selectors `_ +`n_det_selectors `_ For Single reference wave functions, the number of selectors is 1 : the Hartree-Fock determinant -`n_double_selectors `_ +`n_double_selectors `_ degree of excitation respect to Hartree Fock for the wave function .br for the all the selectors determinants @@ -161,39 +161,39 @@ Documentation n_double_selectors = number of double excitations in the selectors determinants -`psi_selectors `_ +`psi_selectors `_ Determinants on which we apply for perturbation. -`psi_selectors_ab `_ +`psi_selectors_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_selectors_coef `_ +`psi_selectors_coef `_ Determinants on which we apply for perturbation. -`psi_selectors_coef_ab `_ +`psi_selectors_coef_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_selectors_diag_h_mat `_ +`psi_selectors_diag_h_mat `_ Diagonal elements of the H matrix for each selectors -`psi_selectors_next_ab `_ +`psi_selectors_next_ab `_ Determinants on which we apply . They are sorted by the 3 highest electrons in the alpha part, then by the 3 highest electrons in the beta part to accelerate the research of connected determinants. -`psi_selectors_size `_ +`psi_selectors_size `_ Undocumented diff --git a/scripts/module/module_handler.py b/scripts/module/module_handler.py index 08a0b297..1e3546df 100755 --- a/scripts/module/module_handler.py +++ b/scripts/module/module_handler.py @@ -23,15 +23,19 @@ import shutil try: from docopt import docopt - from qp_path import QP_SRC - from qp_path import QP_ROOT + from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS except ImportError: print "source .quantum_package.rc" raise -def is_module(path_module): - return os.path.isfile(os.path.join(QP_SRC, path_module, +def is_module(path_module_rel): + return os.path.isfile(os.path.join(QP_SRC, path_module_rel, + "NEEDED_CHILDREN_MODULES")) + + +def is_plugin(path_module_rel): + return os.path.isfile(os.path.join(QP_PLUGINS, path_module_rel, "NEEDED_CHILDREN_MODULES")) diff --git a/scripts/module/qp_update_readme.py b/scripts/module/qp_update_readme.py index eef1b699..9ff9603b 100755 --- a/scripts/module/qp_update_readme.py +++ b/scripts/module/qp_update_readme.py @@ -16,6 +16,7 @@ import sys try: from docopt import docopt + from module_handler import is_module, is_plugin except: print "Please check if you have sourced the .quantum_package.rc" print "(`source .quantum_package.rc`)" @@ -25,6 +26,7 @@ import os from collections import namedtuple from collections import defaultdict + def header_format(str_): warning = "\n".join([".. Do not edit this section It was auto-generated", @@ -35,7 +37,17 @@ def header_format(str_): D_KEY = {"needed_module": header_format("Needed Modules"), "documentation": header_format("Documentation")} -URL = "http://github.com/LCPQ/quantum_package/tree/master/src" + +def get_url(path_module_rel): + if is_plugin(path_module_rel): + url = "http://github.com/LCPQ/quantum_package/tree/master/plugins" + elif is_module(path_module_rel): + url = "http://github.com/LCPQ/quantum_package/tree/master/src" + else: + print "{0} Is not a valide module nor plugin".format(path_module_rel) + sys.exit(1) + + return os.path.join(url, path_module_rel) def fetch_splitted_data(d_readme, l_module_readme): @@ -72,7 +84,7 @@ def update_needed(d_readme): modules = f.read() if modules.strip(): - l_module = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name)) + l_module = ['* `{0} <{1}>`_'.format(name, get_url(name)) for name in modules.split()] l_module_section = [D_KEY["needed_module"], '', @@ -143,7 +155,8 @@ def update_documentation(d_readmen, root_module): l_doc = [] for irp in d_info[path]: - url = os.path.join(URL, os.path.basename(path), irp.file) + + url = os.path.join(get_url(os.path.basename(path)), irp.file) doc = extract_doc(root_module, irp.provider) l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line), From d071a9e395b639bb8d7dfa37e6d6c1612162c780 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 8 Sep 2015 16:41:26 +0200 Subject: [PATCH 11/11] Fixed ninja bug --- configure | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/configure b/configure index 12d2edef..fa207f6e 100755 --- a/configure +++ b/configure @@ -71,7 +71,7 @@ from collections import namedtuple Info = namedtuple("Info", ["url", "description", "default_path"]) -path_github = {"head": "http://github.com/", "tail": "archive/master.tar.gz"} +path_github = {"head": "http://github.com", "tail": "archive/master.tar.gz"} ocaml = Info( url='http://raw.github.com/ocaml/opam/master/shell/opam_installer.sh', @@ -180,6 +180,8 @@ def check_output(*popenargs, **kwargs): cmd = popenargs[0] error = subprocess.CalledProcessError(retcode, cmd) error.output = output +# print output +# print unused_err raise error return output @@ -224,7 +226,7 @@ def checking(d_dependency): return a - except subprocess.CalledProcessError: + except (OSError,subprocess.CalledProcessError): default_path = d_info[binary].default_path if os.path.exists(default_path): return default_path @@ -341,9 +343,9 @@ _|_ | | _> |_ (_| | | (_| |_ | (_) | | extension = splitext(url)[1] path_archive = "Downloads/{0}{1}".format("ninja", extension) - l_cmd = ["cd install &&", - "wget {0} -O {1} -o /dev/null &&".format(url, path_archive), - "./scripts/install_ninja.sh 2> /dev/null &&", "cd -"] + l_cmd = ["set -x ;", "cd install &&", + "wget {0} -O {1} &&".format(url, path_archive), + "./scripts/install_ninja.sh &&", "cd -"] try: check_output(" ".join(l_cmd), shell=True)