diff --git a/ocaml/.gitignore b/ocaml/.gitignore index 1b2a9841..235419de 100644 --- a/ocaml/.gitignore +++ b/ocaml/.gitignore @@ -39,11 +39,11 @@ qp_run qp_set_ddci qp_set_mo_class Input_determinants.ml -Input_integrals_bielec.ml -Input_pseudo.ml -Input_perturbation.ml Input_properties.ml Input_hartree_fock.ml +Input_integrals_bielec.ml +Input_perturbation.ml +Input_pseudo.ml qp_edit.ml qp_edit qp_edit.native diff --git a/plugins/CISD/README.rst b/plugins/CISD/README.rst index a17ce64e..79123d2a 100644 --- a/plugins/CISD/README.rst +++ b/plugins/CISD/README.rst @@ -59,6 +59,10 @@ Documentation .. by the `update_README.py` script. +`cisd `_ + Undocumented + + `h_apply_cisd `_ 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. diff --git a/plugins/CISD/tree_dependency.png b/plugins/CISD/tree_dependency.png index fcf48831..fbe8169d 100644 Binary files a/plugins/CISD/tree_dependency.png and b/plugins/CISD/tree_dependency.png differ diff --git a/plugins/Full_CI/tree_dependency.png b/plugins/Full_CI/tree_dependency.png index caedb2e0..0dca9e35 100644 Binary files a/plugins/Full_CI/tree_dependency.png and b/plugins/Full_CI/tree_dependency.png differ diff --git a/plugins/Generators_full/tree_dependency.png b/plugins/Generators_full/tree_dependency.png index 94ad6358..ec074255 100644 Binary files a/plugins/Generators_full/tree_dependency.png and b/plugins/Generators_full/tree_dependency.png differ diff --git a/plugins/Hartree_Fock/damping_SCF.irp.f b/plugins/Hartree_Fock/damping_SCF.irp.f index d55bc8b8..d7d9c2bf 100644 --- a/plugins/Hartree_Fock/damping_SCF.irp.f +++ b/plugins/Hartree_Fock/damping_SCF.irp.f @@ -30,9 +30,12 @@ subroutine damping_SCF call write_time(output_hartree_fock) - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), '====','================','================','================', '====' - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), ' N ', 'Energy ', 'Energy diff ', 'Density diff ', 'Save' - write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), '====','================','================','================', '====' + write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), & + '====','================','================','================', '====' + write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), & + ' N ', 'Energy ', 'Energy diff ', 'Density diff ', 'Save' + write(output_hartree_fock,'(A4,X,A16, X, A16, X, A16, X, A4 )'), & + '====','================','================','================', '====' E = HF_energy + 1.d0 E_min = HF_energy diff --git a/plugins/Hartree_Fock/tree_dependency.png b/plugins/Hartree_Fock/tree_dependency.png index cb1d9738..410232bd 100644 Binary files a/plugins/Hartree_Fock/tree_dependency.png and b/plugins/Hartree_Fock/tree_dependency.png differ diff --git a/plugins/MRCC_Utils/tree_dependency.png b/plugins/MRCC_Utils/tree_dependency.png index 500e5d43..cd3d2f4b 100644 Binary files a/plugins/MRCC_Utils/tree_dependency.png and b/plugins/MRCC_Utils/tree_dependency.png differ diff --git a/plugins/Perturbation/README.rst b/plugins/Perturbation/README.rst index 088bf2de..507e843c 100644 --- a/plugins/Perturbation/README.rst +++ b/plugins/Perturbation/README.rst @@ -107,92 +107,92 @@ Documentation 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. diff --git a/plugins/Perturbation/tree_dependency.png b/plugins/Perturbation/tree_dependency.png index dac64544..4b13b985 100644 Binary files a/plugins/Perturbation/tree_dependency.png and b/plugins/Perturbation/tree_dependency.png differ diff --git a/plugins/Properties/tree_dependency.png b/plugins/Properties/tree_dependency.png index 1ba8d487..6a6c00ca 100644 Binary files a/plugins/Properties/tree_dependency.png and b/plugins/Properties/tree_dependency.png differ diff --git a/plugins/Psiref_CAS/tree_dependency.png b/plugins/Psiref_CAS/tree_dependency.png index 1a922bdc..8c7c26e6 100644 Binary files a/plugins/Psiref_CAS/tree_dependency.png and b/plugins/Psiref_CAS/tree_dependency.png differ diff --git a/plugins/Psiref_Utils/tree_dependency.png b/plugins/Psiref_Utils/tree_dependency.png index 20482ad2..a2c21ac9 100644 Binary files a/plugins/Psiref_Utils/tree_dependency.png and b/plugins/Psiref_Utils/tree_dependency.png differ diff --git a/plugins/Selectors_full/tree_dependency.png b/plugins/Selectors_full/tree_dependency.png index f49b2e9a..53d48336 100644 Binary files a/plugins/Selectors_full/tree_dependency.png and b/plugins/Selectors_full/tree_dependency.png differ diff --git a/plugins/SingleRefMethod/tree_dependency.png b/plugins/SingleRefMethod/tree_dependency.png index 2b7f777f..aea802f4 100644 Binary files a/plugins/SingleRefMethod/tree_dependency.png and b/plugins/SingleRefMethod/tree_dependency.png differ diff --git a/scripts/module/qp_install_module.py b/scripts/module/qp_install_module.py index 99674e14..2dddfcb7 100755 --- a/scripts/module/qp_install_module.py +++ b/scripts/module/qp_install_module.py @@ -2,7 +2,7 @@ # -*- coding: utf-8 -*- """ Usage: - qp_install_module.py create -n [...] + qp_install_module.py create -n [...] qp_install_module.py download -n [...] qp_install_module.py install ... qp_install_module.py list (--installed | --available-local) @@ -10,7 +10,7 @@ Usage: Options: - list: List all the module available + list: List all the modules available create: Create a new module """ @@ -25,8 +25,8 @@ try: 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" - print "(`source .quantum_package.rc`)" + print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" + print "(`source ${QP_ROOT}/quantum_package.rc`)" print sys.exit(1) @@ -39,7 +39,7 @@ def save_new_module(path, l_child): try: os.makedirs(path) except OSError: - print "The module ({0}) already exist...".format(path) + print "The module ({0}) already exists...".format(path) sys.exit(1) with open(os.path.join(path, "NEEDED_CHILDREN_MODULES"), "w") as f: @@ -78,39 +78,41 @@ if __name__ == '__main__': elif arguments["create"]: m_instance = ModuleHandler([QP_SRC]) - l_children = arguments[""] + l_children = arguments[""] name = arguments[""][0] path = os.path.join(QP_PLUGINS, name) - print "You will create the module:" - print path + print "Created module:" + print path, '\n' for children in l_children: if children not in m_instance.dict_descendant: - print "This module ({0}) is not a valide module.".format(children) - print "Run `list` flag for the list of module available" - print "Maybe you need to install some module first" + print "This module ({0}) is not a valid module.".format(children) + print "Run `list` for the list of available modules." + print "Maybe you need to install some other module first." print "Aborting..." sys.exit(1) - print "You ask for this submodule:" - print l_children + print "Needed module:" + print l_children, '\n' - print "You can use all the routine in this module" - print l_children + m_instance.l_descendant_unique(l_children) + print "This corresponds to using the following modules:" + print l_children + m_instance.l_descendant_unique(l_children), '\n' - print "This can be reduce to:" + print "Which is reduced to:" l_child_reduce = m_instance.l_reduce_tree(l_children) - print l_child_reduce + print l_child_reduce, '\n' + print "Installation", save_new_module(path, l_child_reduce) print " [ OK ]" - 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" + print "Your module is created in the `plugins` directory." + print "You need to create some `.irp.f` to be able to install it." +# print "` {0} install {1} `".format(os.path.basename(__file__), name) + print "" elif arguments["download"]: pass @@ -203,4 +205,5 @@ if __name__ == '__main__': try: os.unlink(os.path.join(QP_SRC, module)) except OSError: - print "%s is a core module which can not be renmoved" % module + print "%s is a core module which can't be removed" % module + diff --git a/src/AO_Basis/tree_dependency.png b/src/AO_Basis/tree_dependency.png index acaeb7af..5d3366ea 100644 Binary files a/src/AO_Basis/tree_dependency.png and b/src/AO_Basis/tree_dependency.png differ diff --git a/src/Bitmask/tree_dependency.png b/src/Bitmask/tree_dependency.png index 24ce3397..2308df3d 100644 Binary files a/src/Bitmask/tree_dependency.png and b/src/Bitmask/tree_dependency.png differ diff --git a/src/Determinants/tree_dependency.png b/src/Determinants/tree_dependency.png index f9eb10c3..53c75ffc 100644 Binary files a/src/Determinants/tree_dependency.png and b/src/Determinants/tree_dependency.png differ diff --git a/src/Electrons/tree_dependency.png b/src/Electrons/tree_dependency.png index b90a1f83..3f82c435 100644 Binary files a/src/Electrons/tree_dependency.png and b/src/Electrons/tree_dependency.png differ diff --git a/src/Ezfio_files/README.rst b/src/Ezfio_files/README.rst index b843770a..f361c168 100644 --- a/src/Ezfio_files/README.rst +++ b/src/Ezfio_files/README.rst @@ -203,119 +203,99 @@ Documentation Output file for Bitmask -`output_cas_sd `_ - Output file for CAS_SD - - -`output_cis `_ - Output file for CIS - - -`output_cisd `_ +`output_cisd `_ Output file for CISD -`output_cisd_selected `_ - Output file for CISD_selected - - `output_cpu_time_0 `_ Initial CPU and wall times when printing in the output files -`output_determinants `_ +`output_determinants `_ Output file for Determinants -`output_electrons `_ +`output_electrons `_ Output file for Electrons -`output_ezfio_files `_ +`output_ezfio_files `_ Output file for Ezfio_files -`output_fcidump `_ - Output file for FCIdump - - -`output_full_ci `_ +`output_full_ci `_ Output file for Full_CI -`output_generators_cas `_ - Output file for Generators_CAS - - -`output_generators_full `_ +`output_generators_full `_ Output file for Generators_full -`output_hartree_fock `_ +`output_hartree_fock `_ Output file for Hartree_Fock -`output_integrals_bielec `_ +`output_integrals_bielec `_ Output file for Integrals_Bielec -`output_integrals_monoelec `_ +`output_integrals_monoelec `_ Output file for Integrals_Monoelec -`output_mo_basis `_ +`output_mo_basis `_ Output file for MO_Basis -`output_moguess `_ +`output_moguess `_ Output file for MOGuess -`output_mrcc_cassd `_ +`output_mrcc_cassd `_ Output file for MRCC_CASSD -`output_mrcc_utils `_ +`output_mrcc_utils `_ Output file for MRCC_Utils -`output_nuclei `_ +`output_myhartreefock `_ + Output file for MyHartreeFock + + +`output_nuclei `_ Output file for Nuclei -`output_perturbation `_ +`output_perturbation `_ Output file for Perturbation -`output_properties `_ +`output_properties `_ Output file for Properties -`output_pseudo `_ +`output_pseudo `_ Output file for Pseudo -`output_psiref_cas `_ +`output_psiref_cas `_ Output file for Psiref_CAS -`output_psiref_utils `_ +`output_psiref_utils `_ Output file for Psiref_Utils -`output_qmcchem `_ - Output file for QmcChem - - -`output_selectors_full `_ +`output_selectors_full `_ Output file for Selectors_full -`output_singlerefmethod `_ +`output_singlerefmethod `_ Output file for SingleRefMethod -`output_utils `_ +`output_utils `_ Output file for Utils diff --git a/src/Ezfio_files/tree_dependency.png b/src/Ezfio_files/tree_dependency.png index 48f53991..6df8c015 100644 Binary files a/src/Ezfio_files/tree_dependency.png and b/src/Ezfio_files/tree_dependency.png differ diff --git a/src/Integrals_Bielec/tree_dependency.png b/src/Integrals_Bielec/tree_dependency.png index 4161fd0a..9c58a4ae 100644 Binary files a/src/Integrals_Bielec/tree_dependency.png and b/src/Integrals_Bielec/tree_dependency.png differ diff --git a/src/Integrals_Monoelec/tree_dependency.png b/src/Integrals_Monoelec/tree_dependency.png index f56c1e77..276dff5d 100644 Binary files a/src/Integrals_Monoelec/tree_dependency.png and b/src/Integrals_Monoelec/tree_dependency.png differ diff --git a/src/MOGuess/tree_dependency.png b/src/MOGuess/tree_dependency.png index f33b4bb3..13728161 100644 Binary files a/src/MOGuess/tree_dependency.png and b/src/MOGuess/tree_dependency.png differ diff --git a/src/MO_Basis/tree_dependency.png b/src/MO_Basis/tree_dependency.png index c8086369..4ce1ecce 100644 Binary files a/src/MO_Basis/tree_dependency.png and b/src/MO_Basis/tree_dependency.png differ diff --git a/src/Nuclei/tree_dependency.png b/src/Nuclei/tree_dependency.png index 72cfaeee..e3a17492 100644 Binary files a/src/Nuclei/tree_dependency.png and b/src/Nuclei/tree_dependency.png differ diff --git a/src/Pseudo/tree_dependency.png b/src/Pseudo/tree_dependency.png index 5a9af5ae..55656d8e 100644 Binary files a/src/Pseudo/tree_dependency.png and b/src/Pseudo/tree_dependency.png differ diff --git a/src/Utils/tree_dependency.png b/src/Utils/tree_dependency.png index 38b04785..5636a6e3 100644 Binary files a/src/Utils/tree_dependency.png and b/src/Utils/tree_dependency.png differ