Skip to content

GitLab

Commit 51b8c4e2 authored by Alarcon Villaseca, Sebastian (sebas81)'s avatar Alarcon Villaseca, Sebastian (sebas81)
Browse files

split single_conf_calculation by method, avoid repetitions

parent 1b769cf9
Hide whitespace changes
Inline Side-by-side
parser/parser-orca/orca_parser.py
View file @ 51b8c4e2
......@@ -118,7 +118,10 @@ def build_OrcaMainFileSimpleMatcher():
SM(r"\s*Program Version\s*(?P<x_orca_program_version>[0-9a-zA-Z_.]*)"),
SM(r" *\(\$Date\: *(?P<x_orca_program_compilation_date>[0-9/]+) at (?P<x_orca_program_compilation_time>[0-9:]+)")
]),
buildSinglePointMatcher()
buildSinglePointMatcher(),
buildGeoOptMatcher(),
buildMp2Matcher(),
buildCIMatcher()
])
def buildSinglePointMatcher():
......@@ -128,12 +131,16 @@ def buildSinglePointMatcher():
#
return SM(name = 'SinglePointCalculation',
startReStr = r"\s*\* Single Point Calculation \*\s",
sections = ["section_system", "section_single_configuration_calculation"],
subMatchers = [
sections = ["section_single_configuration_calculation"],
subMatchers = buildSinglePointSubMatchers()
)
def buildSinglePointSubMatchers():
return [
# Get atomic positions:
SM(name = 'Atomic Coordinates',
startReStr = r"CARTESIAN COORDINATES \(ANGSTROEM\)\s*",
sections = ["x_orca_atom_positions", "section_basis_set"],
sections = ["section_system", "x_orca_atom_positions"],
subMatchers = [
SM(r"\s+(?P<x_orca_atom_labels>[a-zA-Z]+)\s+(?P<x_orca_atom_positions_x>[-+0-9.]+)\s+(?P<x_orca_atom_positions_y>[-+0-9.]+)\s+(?P<x_orca_atom_positions_z>[-+0-9.]+)", repeats = True)
]
......@@ -192,6 +199,9 @@ def buildSinglePointMatcher():
SM(name = 'Orca SCF settings',
startReStr = r"\s*ORCA SCF\s*",
sections = ["section_method"],
fixedStartValues = {
"electronic_structure_method": "DFT"
},
subMatchers = [
# A - For HF methods:
SM(r"\s+Ab initio Hamiltonian\s+Method\s+\.\.\.\s+(?P<x_orca_hf_method>[-+0-9a-zA-Z()]+)"),
......@@ -235,7 +245,7 @@ def buildSinglePointMatcher():
startReStr = r"\s*SCF ITERATIONS\s*",
sections = ["section_scf_iteration"],
subMatchers = [
SM(r"\s*(?P<x_orca_iteration_nb>[0-9]+)\s+(?P<x_orca_scf_total_energy__hartree>[-+0-9.eEdD]+)", repeats = True),
SM(r"\s*(?P<x_orca_iteration_nb>[0-9]+)\s+(?P<energy_total_scf_iteration__hartree>[-+0-9.eEdD]+)", repeats = True),
]
),
# *****************************************************
......@@ -265,7 +275,7 @@ def buildSinglePointMatcher():
# Final SCF total Energy:
SM(name = 'Total Energy',
startReStr = r"\s*TOTAL SCF ENERGY\s*",
sections = ["section_single_configuration_calculation"],
sections = [],
subMatchers = [
SM(r"\s*Total Energy\s+:\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)"),
# Energy Components:
......@@ -340,24 +350,31 @@ def buildSinglePointMatcher():
SM(r"\s*DIIS solution\s*\.\.\.\.\s*(?P<x_orca_diis_solution>[0-9.]+) sec"),
SM(r"\s*Grid generation\s*\.\.\.\.\s*(?P<x_orca_grid_generation>[0-9.]+) sec")
]
),
)]
def buildGeoOptMatcher():
#
# c) SimpleMatcher for geometry optimization:
# *******************************************
#
SM(name = 'Geometry optimization',
return SM(name = 'Geometry optimization',
startReStr = r"\s*\* Geometry Optimization Run \*\s*",
sections = ["section_sampling_method"],
subMatchers = [
# Geometry optimization settings:
SM("Update method\s*(?P<x_orca_update_method>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_update_method_name>[a-zA-Z]+)"),
SM("Choice of coordinates\s*(?P<x_orca_coords_choice>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_coords_choice_name>[a-zA-Z ]+)"),
SM("Initial Hessian\s*(?P<x_orca_initial_hessian>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_initial_hessian_name>[a-zA-Z'\( \)]+)"),
SM("Energy Change\s*(?P<x_orca_energy_change_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_energy_change_tol_value__hartree>[-+0-9.eEdD]+) Eh"),
SM("Max\. Gradient\s*(?P<x_orca_max_gradient_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_max_gradient_tol_value__hartree_bohr_1>[-+0-9.eEdD]+) Eh/bohr"),
SM("RMS Gradient\s*(?P<x_orca_rms_gradient_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_rms_gradient_tol_value__hartree_bohr_1>[-+0-9.eEdD]+) Eh/bohr"),
SM("Max\. Displacement\s*(?P<x_orca_max_displacement_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_max_displacement_tol_value__bohr>[-+0-9.eEdD]+) bohr"),
SM("RMS Displacement\s*(?P<x_orca_rms_displacement_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_rms_displacement_tol_value__bohr>[-+0-9.eEdD]+) bohr"),
SM(r"Update method\s*(?P<x_orca_update_method>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_update_method_name>[a-zA-Z]+)"),
SM(r"Choice of coordinates\s*(?P<x_orca_coords_choice>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_coords_choice_name>[a-zA-Z ]+)"),
SM(r"Initial Hessian\s*(?P<x_orca_initial_hessian>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_initial_hessian_name>[a-zA-Z'\( \)]+)"),
SM(r"Energy Change\s*(?P<x_orca_energy_change_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_energy_change_tol_value__hartree>[-+0-9.eEdD]+) Eh"),
SM(r"Max\. Gradient\s*(?P<x_orca_max_gradient_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_max_gradient_tol_value__hartree_bohr_1>[-+0-9.eEdD]+) Eh/bohr"),
SM(r"RMS Gradient\s*(?P<x_orca_rms_gradient_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_rms_gradient_tol_value__hartree_bohr_1>[-+0-9.eEdD]+) Eh/bohr"),
SM(r"Max\. Displacement\s*(?P<x_orca_max_displacement_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_max_displacement_tol_value__bohr>[-+0-9.eEdD]+) bohr"),
SM(r"RMS Displacement\s*(?P<x_orca_rms_displacement_tol>[a-zA-Z]+)\s+\.\.\.\.\s+(?P<x_orca_rms_displacement_tol_value__bohr>[-+0-9.eEdD]+) bohr"),
SM(name="geoOptCycle",
startReStr=r"\s*\*\s*GEOMETRY OPTIMIZATION CYCLE\s*(?P<x_orca_geo_opt_cycle>[0-9]+)\s*\*\s*",
sections = ["section_single_configuration_calculation"],
subMatchers = buildSinglePointSubMatchers()
),
# Final geometry:
# CARTESIAN COORDINATES (ANGSTROEM)
SM(name = 'final geometry',
......@@ -366,106 +383,47 @@ def buildSinglePointMatcher():
subMatchers = [
SM(r"\s+(?P<x_orca_atom_labels_geo_opt>[a-zA-Z]+)\s+(?P<x_orca_atom_positions_x_geo_opt>[-+0-9.]+)\s+(?P<x_orca_atom_positions_y_geo_opt>[-+0-9.]+)\s+(?P<x_orca_atom_positions_z_geo_opt>[-+0-9.]+)", repeats = True)
]
)
]
),
),
# *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
#
SM(name = 'Final step after geometry convergence',
startReStr = r"Setting up the final grid:",
sections = ["section_scf_iteration"],
subMatchers = [
# Final DFT Grid generation:
SM(r"\s+General Integration Accuracy\s+IntAcc\s*\.\.\.\s+(?P<x_orca_gral_integ_accuracy_final>[-+0-9.eEdD]+)"),
SM(r"\s+Radial Grid Type\s+RadialGrid\s*\.\.\.\s+(?P<x_orca_radial_grid_type_final>[a-zA-Z-_]+)"),
SM(r"\s+Angular Grid \(max\. acc\.\)\s+AngularGrid\s*\.\.\.\s+(?P<x_orca_angular_grid_final>[a-zA-Z-+0-9.eEdD-_]+)"),
SM(r"\s+Angular grid pruning method\s+GridPruning\s*\.\.\.\s+(?P<x_orca_grid_pruning_method_final>[a-zA-Z-+0-9.eEdD-_]+)"),
SM(r"\s+Weight generation scheme\s*WeightScheme\s*\.\.\.\s+(?P<x_orca_weight_gener_scheme_final>[a-zA-Z0-9]+)"),
SM(r"\s+Basis function cutoff\s+BFCut\s*\.\.\.\s+(?P<x_orca_basis_fn_cutoff_final>[-+0-9.eEdD]+)"),
SM(r"\s+Integration weight cutoff\s+WCut\s*\.\.\.\s+(?P<x_orca_integr_weight_cutoff_final>[-+0-9.eEdD]+)"),
SM(r"\s+# of grid points \(after initial pruning\)\s+WCut\s*\.\.\.\s+(?P<x_orca_nb_grid_pts_after_initial_pruning_final>[-+0-9.eEdD]+)"),
SM(r"\s+# of grid points \(after weights\+screening\)\s*\.\.\.\s+(?P<x_orca_nb_grid_pts_after_weights_screening_final>[-+0-9.eEdD]+)"),
SM(r"\s+Total number of grid points\s*\.\.\.\s+(?P<x_orca_total_nb_grid_pts_final>[-+0-9.eEdD]+)"),
SM(r"\s+Total number of batches\s*\.\.\.\s+(?P<x_orca_total_nb_batches_final>[-+0-9.eEdD]+)"),
SM(r"\s+Average number of points per batch\s*\.\.\.\s+(?P<x_orca_avg_nb_points_per_batch_final>[-+0-9.eEdD]+)"),
SM(r"\s+Average number of grid points per atom\s*\.\.\.\s+(?P<x_orca_avg_nb_grid_pts_per_atom_final>[-+0-9.eEdD]+)")
]
),
# Final SCF total Energy:
SM(name = 'Final total Energy',
startReStr = r"\s*TOTAL SCF ENERGY\s*",
sections = ["section_single_configuration_calculation"],
subMatchers = [
SM(r"\s*Total Energy\s+:\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)"),
# Energy Components:
SM(name = 'Final energy Components',
startReStr = r"\s*Components:\s*",
SM(name = 'Final step after geometry convergence',
startReStr = r"Setting up the final grid:",
sections = ["section_single_configuration_calculation"],
subMatchers = [
SM(r"\s*Nuclear Repulsion\s*:\s+(?P<x_orca_nuc_repulsion__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Electronic Energy\s*:\s+(?P<x_orca_elec_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*One Electron Energy:\s+(?P<x_orca_one_elec_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Two Electron Energy:\s+(?P<x_orca_two_elec_energy__hartree>[-+0-9.eEdD]+)"),
# Virial Components:
SM(r"\s*Potential Energy\s*:\s+(?P<x_orca_potential_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Kinetic Energy\s*:\s+(?P<x_orca_kinetc_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Virial Ratio\s*:\s+(?P<x_orca_virial_ratio>[-+0-9.eEdD]+)"),
# DFT Components:
SM(r"\s*N\(Alpha\)\s*:\s+(?P<x_orca_nb_elect_alpha_channel>[-+0-9.eEdD]+)"),
SM(r"\s*N\(Beta\)\s*:\s+(?P<x_orca_nb_elect_beta_channel>[-+0-9.eEdD]+)"),
SM(r"\s*N\(Total\)\s*:\s+(?P<x_orca_nb_elect_total>[-+0-9.eEdD]+)"),
SM(r"\s*E\(X\)\s*:\s+(?P<x_orca_exchange_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*E\(C\)\s*:\s+(?P<x_orca_correlation_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*E\(XC\)\s*:\s+(?P<x_orca_exchange_correlation_energy__hartree>[-+0-9.eEdD]+)")
]
),
# Final SCF convergence:
SM(r"\s*Last Energy change\s+\.\.\.\s+(?P<x_orca_last_energy_change__hartree>[-+0-9.eEdD]+)\s+Tolerance :\s*(?P<x_orca_last_energy_change_tolerance__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Last MAX-Density change\s+\.\.\.\s+(?P<x_orca_last_max_density_change__hartree>[-+0-9.eEdD]+)\s+Tolerance :\s*(?P<x_orca_last_max_density_tolerance__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Last RMS-Density change\s+\.\.\.\s+(?P<x_orca_last_rms_density_change__hartree>[-+0-9.eEdD]+)\s+Tolerance :\s*(?P<x_orca_last_rms_density_tolerance__hartree>[-+0-9.eEdD]+)")
]
),
# Orbitals Energies:
SM(name = 'Orbital Energies',
startReStr = r"\s*ORBITAL ENERGIES\s*",
sections = ["section_dos"],
subMatchers = [
SM(r"\s*(?P<x_orca_orbital_nb>[0-9]+)\s+(?P<x_orca_orbital_occupation_nb>[-+0-9]+)\s+(?P<x_orca_orbital_energy__hartree>[-+0-9.eEdD]+)", repeats = True)
]
),
# Mulliken population analysis:
SM(name = 'Mulliken population analysis',
startReStr = r"\s*\* MULLIKEN POPULATION ANALYSIS \*\s*",
sections = ["section_dos"],
subMatchers = [
SM(r"\s*(?P<x_orca_atom_nb>[0-9]+)\s+(?P<x_orca_atom_species>[a-zA-Z]+):\s+(?P<x_orca_mulliken_atom_charge>)", repeats = True),
SM(r"\s*Sum of atomic charges:\s*(?P<x_orca_mulliken_total_charge>[-+0-9.eEdD]+)"),
# Mulliken reduced orbital charges (mroc):
SM(r"\s*(?P<x_orca_atom_nb_mroc>[0-9]+)\s+(?P<x_orca_atom_species_mroc>[a-zA-Z]+)(?P<x_orca_atom_orbital_mroc>[-+0-9a-zA-Z]+)\s*:\s*(?P<x_orca_mulliken_partial_orbital_charge_mroc>[-+0-9.eEdD]+)", repeats = True)
]
),
subMatchers = buildSinglePointSubMatchers()
)
]
)
def buildMp2Matcher():
#
# d) Post-processing calculations:
# ********************************
#
# MP2 Calculation (post-proc):
SM(name = 'mp2',
return SM(name = 'mp2',
startReStr = r"\s*ORCA MP2 CALCULATION\s*",
sections = ["section_method"],
sections = ["section_method", "section_single_configuration_calculation"],
fixedStartValues = {
"electronic_structure_method": "MP2"
},
subMatchers = [
SM(r"\s*Dimension of the basis\s*\.\.\.\s*(?P<x_orca_mp2_basis_dimension>[0-9.]+)"),
SM(r"\s*Overall scaling of the MP2 energy\s*\.\.\.\s*(?P<x_orca_scaling_mp2_energy__hartree>[-+0-9.eEdD]+) Eh"),
SM(r"\s*Dimension of the aux-basis\s*\.\.\.\s*(?P<x_orca_mp2_aux_basis_dimension>[0-9.]+)"),
SM(r"\s*RI-MP2 CORRELATION ENERGY:\s*(?P<x_orca_mp2_corr_energy__hartree>[-+0-9.eEdD]+) Eh"),
SM(r"\s*MP2 TOTAL ENERGY:\s*(?P<x_orca_mp2_total_energy__hartree>[-+0-9.eEdD]+) Eh")
SM(r"\s*RI-MP2 CORRELATION ENERGY:\s*(?P<energy_method_current__hartree>[-+0-9.eEdD]+) Eh"),
SM(r"\s*MP2 TOTAL ENERGY:\s*(?P<energy_total__hartree>[-+0-9.eEdD]+) Eh")
]
),
)
def buildCIMatcher():
# Driven CI (post-proc):
SM(name = 'CI',
return SM(name = 'CI',
startReStr = r"\s*ORCA-MATRIX DRIVEN CI\s*",
sections = ["section_method"],
sections = ["section_method", "section_single_configuration_calculation"],
fixedStartValues = {
"electronic_structure_method": "CI"
},
subMatchers = [
SM(r"\s*Correlation treatment\s*\.\.\.\s*(?P<x_orca_wave_function_correlation_treatment>[a-zA-Z0-9.]+)"),
SM(r"\s*Correlation treatment\s*\.\.\.\s*(?P<electronic_structure_method>[()a-zA-Z0-9.]+)"),
SM(r"\s*Single excitations\s*\.\.\.\s*(?P<x_orca_single_excitations_on_off>[a-zA-Z]+)"),
SM(r"\s*Orbital optimization\s*\.\.\.\s*(?P<x_orca_orbital_opt_on_off>[a-zA-Z]+)"),
SM(r"\s*Calculation of Z vector\s*\.\.\.\s*(?P<x_orca_z_vector_calc_on_off>[a-zA-Z]+)"),
......@@ -514,7 +472,7 @@ def buildSinglePointMatcher():
SM(r"\s*beta -beta -beta\s*\.\.\.\s*(?P<x_orca_ccsdt_bbb_triples_contribution__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*Final correlation energy\s*\.\.\.\s*(?P<x_orca_ccsdt_final_corr_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*E\(CCSD\)\s*\.\.\.\s*(?P<x_orca_ccsd_final_energy__hartree>[-+0-9.eEdD]+)"),
SM(r"\s*E\(CCSD\(T\)\)\s*\.\.\.\s*(?P<x_orca_ccsd_t_final_energy__hartree>[-+0-9.eEdD]+)")
SM(r"\s*E\(CCSD\(T\)\)\s*\.\.\.\s*(?P<energy_total__hartree>[-+0-9.eEdD]+)")
]
)
# Here new stuff:
......@@ -527,8 +485,6 @@ def buildSinglePointMatcher():
# SM()
# ]
# ),
]
)
#
# c) SimpleMatcher for Calculation Including Atomic Optimizations:
# ****************************************************************
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment