From 30df5835a1f377c4bd7e3533df5e2870cab3d5ed Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 4 Jun 2015 12:09:28 +0200 Subject: [PATCH] update_readme.py and so one --- scripts/compilation/create_ninja_build.py | 23 ++-- scripts/module/update_README.py | 108 ++++++--------- src/CAS_SD/README.rst | 53 +++++++- src/CID_SC2_selected/README.rst | 19 ++- src/CIS/README.rst | 24 +++- src/CISD_SC2_selected/README.rst | 53 +++++++- src/DDCI_selected/README.rst | 36 ++++- src/FCIdump/README.rst | 6 +- src/Full_CI/README.rst | 143 +++++++++++++++++++- src/MP2/README.rst | 23 +++- src/MRCC/README.rst | 158 ++++++++++++++-------- src/Molden/README.rst | 10 +- src/Pseudo/README.rst | 67 +++++++-- src/QmcChem/README.rst | 18 ++- 14 files changed, 564 insertions(+), 177 deletions(-) diff --git a/scripts/compilation/create_ninja_build.py b/scripts/compilation/create_ninja_build.py index f77f36f6..9b8bea7c 100755 --- a/scripts/compilation/create_ninja_build.py +++ b/scripts/compilation/create_ninja_build.py @@ -484,13 +484,14 @@ def get_program(path_module): return [] -def get_dict_binaries(mode): +def get_dict_binaries(mode="production"): """ Return a dict [module] = list_binaries - If a the production mode is enable only header module will produce binaries + If a the production mode is enable only header module + who will produce all binaries Example : The module Full_CI can produce the binary SCF - so you dont need to use at all the module Hartree-Fock + so you dont need to compile at all the module Hartree-Fock """ d_binaries = defaultdict(list) @@ -653,7 +654,6 @@ if __name__ == "__main__": d_irp = get_file_dependency(d_genealogy_path) d_binaries_production = get_dict_binaries(mode="production") - d_binaries_development = get_dict_binaries(mode="development") # ~#~#~#~#~#~#~#~#~#~#~#~#~ # # M o d u l e _ t o _ i r p # @@ -663,15 +663,7 @@ if __name__ == "__main__": l_module_to_irp = d_binaries_production.keys() elif arguments["--development"]: - l_module_to_irp = d_binaries_development.keys() - - l_all_module = d_genealogy_path.keys() - - for module in l_all_module: - # ~#~#~#~#~#~#~#~ # - # d o t _ t r e e # - # ~#~#~#~#~#~#~#~ # - l_string += ninja_dot_tree_build(module) + l_module_to_irp = d_genealogy_path.keys() for module_to_compile in l_module_to_irp: @@ -689,6 +681,11 @@ if __name__ == "__main__": l_string += ninja_irpf90_make_build(module_to_compile, l_children, d_irp) + # ~#~#~#~#~#~#~#~ # + # d o t _ t r e e # + # ~#~#~#~#~#~#~#~ # + l_string += ninja_dot_tree_build(module_to_compile) + # ~#~#~#~#~#~#~ # # b i n a r y # # ~#~#~#~#~#~#~ # diff --git a/scripts/module/update_README.py b/scripts/module/update_README.py index ee9f9ca6..7f4624b3 100755 --- a/scripts/module/update_README.py +++ b/scripts/module/update_README.py @@ -12,10 +12,11 @@ URL = "http://github.com/LCPQ/quantum_package/tree/master/src/" import os import subprocess +from collections import namedtuple header = """ .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. """ @@ -43,18 +44,19 @@ def fetch_splitted_data(): 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.""" - file = open('NEEDED_CHILDREN_MODULES', 'r') - modules = file.read() - file.close() + with open('NEEDED_CHILDREN_MODULES', 'r') as f: + modules = f.read() header_image = ".. image:: tree_dependency.png\n\n" - if modules.strip() != "": - modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()] + 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' @@ -70,71 +72,50 @@ def update_needed(data): return data +def extract_doc(item): + """Extracts the documentation contained in IRPF90_man file""" + + with open("IRPF90_man/%s.l" % (item), '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 - try: - file = open('tags', 'r') - except: - return - tags = file.readlines() - file.close() - def extract_doc(item): - """Extracts the documentation contained in IRPF90_man file""" - file = open("IRPF90_man/%s.l" % (item), 'r') - lines = file.readlines() - file.close() - result = [] - inside = False - for line in lines: - if not inside: - inside = line.startswith(".SH Description") - else: - if line.startswith(".SH"): - break - result.append(" " + line.strip()) + with open('tags', 'r') as f: + l_info = [IRP_info(*i.split()) for i in f.readlines() + if "/" not in i.split()[1]] - if result == []: - result = [" Undocumented"] - return "\n".join(result) + '\n' + l_line = [] + module_name = os.path.basename(os.getcwd()) - items = [] - dirname = os.path.basename(os.getcwd()) - command = "git ls-tree --full-tree --name-only HEAD:src/%s" - command = command % (dirname) - try: - if dirname != 'src': - p = subprocess.Popen(command.split(), stdout=subprocess.PIPE) - tracked_files = p.stdout.read() - else: - tracked_files = "" - tracked_files = tracked_files.splitlines() - except: - tracked_files = [] - for filename in tracked_files: - if filename.endswith('.irp.f'): - # Search for providers, subroutines and functions in each file using - # the tags file - search = "\t" + filename + "\t" - tmp = filter(lambda line: search in line, tags) + for irp in l_info: + url = os.path.join(URL, module_name, irp.file) + doc = extract_doc(irp.name) - # Search for the documentation in the IRPF90_man directory - for item in tmp: - item, _, line = item.strip().split('\t') - doc = extract_doc(item) - items.append((item, filename, doc, line)) + l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc, + ""] - dirname = os.path.basename(os.getcwd()) - # Write the documentation in the README - template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n" - - documentation = Doc_key + header - url = URL - for item, filename, doc, line in items: - documentation += template % locals() - documentation += '\n\n' + documentation = Doc_key + header + "\n".join(l_line) has_doc = False for i in range(len(data)): @@ -153,8 +134,6 @@ def git_add(): git add README.rst throw an error if git is not precent""" - import subprocess - try: # pipe output to /dev/null for silence null = open("/dev/null", "w") @@ -167,6 +146,7 @@ def git_add(): def main(): data = fetch_splitted_data() + data = update_documentation(data) data = update_needed(data) output = ''.join(data) diff --git a/src/CAS_SD/README.rst b/src/CAS_SD/README.rst index 3c21586d..f0fbbd17 100644 --- a/src/CAS_SD/README.rst +++ b/src/CAS_SD/README.rst @@ -11,18 +11,67 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `full_ci `_ Undocumented +`h_apply_cas_sd `_ + 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_cas_sd_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_cas_sd_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_cas_sd_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_cas_sd_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_cas_sd_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_cas_sd_selected `_ + 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_cas_sd_selected_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_cas_sd_selected_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/CID_SC2_selected/README.rst b/src/CID_SC2_selected/README.rst index 1bbb52b1..49ad9aac 100644 --- a/src/CID_SC2_selected/README.rst +++ b/src/CID_SC2_selected/README.rst @@ -6,18 +6,33 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `cisd_sc2_selected `_ Undocumented +`h_apply_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_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_pt2_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/CIS/README.rst b/src/CIS/README.rst index 65f86baa..5d8437e6 100644 --- a/src/CIS/README.rst +++ b/src/CIS/README.rst @@ -11,21 +11,37 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `cis `_ Undocumented + +`h_apply_cis `_ + 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_cis_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_cis_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + `super_ci `_ Undocumented - - Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/CISD_SC2_selected/README.rst b/src/CISD_SC2_selected/README.rst index 9e91a55f..307063a6 100644 --- a/src/CISD_SC2_selected/README.rst +++ b/src/CISD_SC2_selected/README.rst @@ -6,18 +6,67 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `cisd_sc2_selected `_ Undocumented +`h_apply_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_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_pt2_en_sc2 `_ + 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_en_sc2_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_en_sc2_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_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_sc2_selected `_ + 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_sc2_selected_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_sc2_selected_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/DDCI_selected/README.rst b/src/DDCI_selected/README.rst index e1ec90f4..471ebd21 100644 --- a/src/DDCI_selected/README.rst +++ b/src/DDCI_selected/README.rst @@ -6,18 +6,50 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `full_ci `_ Undocumented +`h_apply_ddci_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_ddci_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_ddci_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_ddci_selection `_ + 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_ddci_selection_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_ddci_selection_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/FCIdump/README.rst b/src/FCIdump/README.rst index 68d3a7d8..f867eb70 100644 --- a/src/FCIdump/README.rst +++ b/src/FCIdump/README.rst @@ -8,18 +8,16 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `fcidump `_ Undocumented - - Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/Full_CI/README.rst b/src/Full_CI/README.rst index bb2b75e4..396fbcd6 100644 --- a/src/Full_CI/README.rst +++ b/src/Full_CI/README.rst @@ -8,21 +8,156 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. 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 ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/MP2/README.rst b/src/MP2/README.rst index 4c871b37..248c4815 100644 --- a/src/MP2/README.rst +++ b/src/MP2/README.rst @@ -6,18 +6,33 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. + +`h_apply_mp2 `_ + 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_mp2_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_mp2_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + `mp2 `_ Undocumented - - Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/MRCC/README.rst b/src/MRCC/README.rst index 2b649954..608b8f86 100644 --- a/src/MRCC/README.rst +++ b/src/MRCC/README.rst @@ -6,7 +6,7 @@ Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png @@ -18,7 +18,23 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. + +`ci_eigenvectors_dressed `_ + Eigenvectors/values of the CI matrix + + +`ci_eigenvectors_s2_dressed `_ + Eigenvectors/values of the CI matrix + + +`ci_electronic_energy_dressed `_ + Eigenvectors/values of the CI matrix + + +`ci_energy_dressed `_ + N_states lowest eigenvalues of the dressed CI matrix + `davidson_diag_hjj_mrcc `_ Davidson diagonalization with specific diagonal elements of the H matrix @@ -40,6 +56,7 @@ Documentation .br Initial guess vectors are not necessarily orthonormal + `davidson_diag_mrcc `_ Davidson diagonalization. .br @@ -58,6 +75,66 @@ Documentation .br Initial guess vectors are not necessarily orthonormal + +`delta_ij `_ + Dressing matrix in N_det basis + + +`delta_ij_non_cas `_ + Dressing matrix in SD basis + + +`diagonalize_ci_dressed `_ + Replace the coefficients of the CI states by the coefficients of the + eigenstates of the CI matrix + + +`dressing_type `_ + [ Simple | MRCC ] + + +`find_triples_and_quadruples `_ + Undocumented + + +`h_apply_mrcc `_ + 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_mrcc_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_mrcc_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_mrcc_simple `_ + 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_mrcc_simple_diexc `_ + Generate all double excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_apply_mrcc_simple_monoexc `_ + Generate all single excitations of key_in using the bit masks of holes and + particles. + Assume N_int is already provided. + + +`h_matrix_dressed `_ + Dressed H with Delta_ij + + `h_u_0_mrcc `_ Computes v_0 = H|u_0> .br @@ -65,60 +142,35 @@ Documentation .br H_jj : array of -`mrcc `_ - Undocumented - -`run `_ - Undocumented - -`run_mrcc `_ - Undocumented - -`run_mrcc_test `_ - Undocumented - -`find_triples_and_quadruples `_ - Undocumented - -`mrcc_dress `_ - Undocumented - -`mrcc_dress_simple `_ - Undocumented - -`psi_cas_lock `_ - Locks on CAS determinants to fill delta_ij - -`ci_eigenvectors_dressed `_ - Eigenvectors/values of the CI matrix - -`ci_eigenvectors_s2_dressed `_ - Eigenvectors/values of the CI matrix - -`ci_electronic_energy_dressed `_ - Eigenvectors/values of the CI matrix - -`ci_energy_dressed `_ - N_states lowest eigenvalues of the dressed CI matrix - -`delta_ij `_ - Dressing matrix in N_det basis - -`delta_ij_non_cas `_ - Dressing matrix in SD basis - -`diagonalize_ci_dressed `_ - Replace the coefficients of the CI states by the coefficients of the - eigenstates of the CI matrix - -`dressing_type `_ - [ Simple | MRCC ] - -`h_matrix_dressed `_ - Dressed H with Delta_ij `lambda_mrcc `_ cm/ +`mrcc `_ + Undocumented + + +`mrcc_dress `_ + Undocumented + + +`mrcc_dress_simple `_ + Undocumented + + +`psi_cas_lock `_ + Locks on CAS determinants to fill delta_ij + + +`run `_ + Undocumented + + +`run_mrcc `_ + Undocumented + + +`run_mrcc_test `_ + Undocumented diff --git a/src/Molden/README.rst b/src/Molden/README.rst index 05fb8b4a..c97e6319 100644 --- a/src/Molden/README.rst +++ b/src/Molden/README.rst @@ -6,30 +6,32 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `print_mos `_ Undocumented + `write_ao_basis `_ Undocumented + `write_geometry `_ Undocumented + `write_intro_gamess `_ Undocumented + `write_mo_basis `_ Undocumented - - Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png diff --git a/src/Pseudo/README.rst b/src/Pseudo/README.rst index 45a589d4..f52f15a7 100644 --- a/src/Pseudo/README.rst +++ b/src/Pseudo/README.rst @@ -2,25 +2,66 @@ Pseudo Module ============= -Documentation -============= - -.. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. - - - Needed Modules ============== .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. -.. image:: tree_dependancy.png +.. image:: tree_dependency.png -<<<<<<< HEAD -======= -* `Ezfio_files `_ ->>>>>>> LCPQ-master * `Nuclei `_ +Documentation +============= + +.. Do not edit this section. It was auto-generated from the +.. NEEDED_MODULES_CHILDREN file 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/QmcChem/README.rst b/src/QmcChem/README.rst index 562703cd..9a390cfd 100644 --- a/src/QmcChem/README.rst +++ b/src/QmcChem/README.rst @@ -6,7 +6,7 @@ Documentation ============= .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. `ao_pseudo_grid `_ Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C @@ -14,40 +14,46 @@ Documentation + `aux_pseudo_integral `_ Pseudo-potential + `aux_pseudo_integral_local `_ Local pseudo-potential + `aux_pseudo_integral_non_local `_ Local pseudo-potential + `mo_pseudo_grid `_ Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \phi_i^{A} (r-r_A) d\Omega_C .br -`test_pseudo_grid_ao `_ - Undocumented `pseudo_matrix `_ Pseudo-potential expressed in the basis of ao products -`write_pseudopotential `_ - Write the pseudo_potential into the EZFIO file `save_for_qmc `_ Undocumented +`test_pseudo_grid_ao `_ + Undocumented + + +`write_pseudopotential `_ + Write the pseudo_potential into the EZFIO file Needed Modules ============== .. Do not edit this section. It was auto-generated from the -.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script. +.. by the `update_README.py` script. .. image:: tree_dependency.png