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Commit ccef261b authored by Sebastian Alarcon Villaseca's avatar Sebastian Alarcon Villaseca
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add files and corrections to parser

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with 44 additions and 64 deletions
parser/parser-orca/orca_parser.py
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......@@ -59,51 +59,31 @@ class OrcaContext(object):
backend.addArrayValue("geometry_optimization_converged", pos)
backend.addValue("atom_labels", value["x_orca_atom_labels_geo_opt"])
def onClose_x_orca_XC_functional(self, backend, gIndex, value):
x = value["x_orca_dft_method"]
backend.addValue("XC_functional_name", x)
def onClose_x_total_energy(self, backend, gIndex, value):
x = value["x_orca_total_energy"]
backend.addValue("energy_total", x)
def onClose_x_exchange_energy(self, backend, gIndex, value):
x = value["x_orca_exchange_energy"]
backend.addValue("energy_X", x)
def onClose_x_correlation_energy(self, backend, gIndex, value):
x = value["x_orca_correlation_energy"]
backend.addValue("energy_C", x)
def onClose_x_xc_energy(self, backend, gIndex, value):
x = value["x_orca_exchange_correlation_energy"]
backend.addValue("energy_XC", x)
def onClose_x_orca_orbital_energies(self, backend, gIndex, value):
x = value["x_orca_orbital_nb"]
y = value["x_orca_orbital_occupation_nb"]
z = value["x_orca_orbital_energy"]
orbitals = np.zeros((len(x),3), dtype=float)
orbitals[:,0] = x
orbitals[:,1] = y
orbitals[:,2] = z
backend.addArrayValue("eigenvalues_occupation", orbitals)
def onClose_x_orca_basis_set_info(self, backend, gIndex, value):
x = value["x_orca_atom_labels"]
y = value["x_orca_basis_set"]
z = value["x_orca_basis_set_contracted"]
basisSet = np.zeros((len(x),3), dtype=float)
basisSet[:,0] = x
basisSet[:,1] = y
basisSet[:,2] = z
backend.addArrayValue("program_basis_set_type", 'Gaussian' + basisSet)
def onClose_x_orca_program_name(self, backend, gIndex, value):
x = 'ORCA'
y = value["x_orca_program_version"]
z = value["x_orca_program_compilation_date"]
backend.addValue("program_name", x + y + z)
# def onClose_x_orca_orbital_energies(self, backend, gIndex, value):
# x = value["x_orca_orbital_nb"]
# y = value["x_orca_orbital_occupation_nb"]
# z = value["x_orca_orbital_energy"]
# orbitals = np.zeros((len(x),3), dtype=float)
# orbitals[:,0] = x
# orbitals[:,1] = y
# orbitals[:,2] = z
# backend.addArrayValue("eigenvalues_occupation", orbitals)
#
# def onClose_x_orca_basis_set_info(self, backend, gIndex, value):
# x = value["x_orca_atom_labels"]
# y = value["x_orca_basis_set"]
# z = value["x_orca_basis_set_contracted"]
# basisSet = np.zeros((len(x),3), dtype=float)
# basisSet[:,0] = x
# basisSet[:,1] = y
# basisSet[:,2] = z
# backend.addArrayValue("program_basis_set_type", 'Gaussian' + basisSet)
#
# def onClose_x_orca_program_name(self, backend, gIndex, value):
# x = 'ORCA'
# y = value["x_orca_program_version"]
# z = value["x_orca_program_compilation_date"]
# backend.addValue("program_name", x + y + z)
##########################################################
############ [2] MAIN PARSER STARTS HERE ############
......@@ -160,14 +140,14 @@ def buildSinglePointMatcher():
# Get basis set information:
SM(name = 'Basis set information',
startReStr = r"BASIS SET INFORMATION\s*",
sections = ["x_orca_basis_set_info"],
sections = ["section_basis_set"],
subMatchers = [
# Atom labels and basis set:
SM(r"\s*Group\s+[0-9]+\s+Type\s+(?P<x_orca_atom_labels>[a-zA-Z]+)\s+:\s+(?P<x_orca_basis_set>[0-9a-z]+)\s+contracted\s+to\s+(?P<x_orca_basis_set_contracted>[0-9a-z]+)\s+pattern\s+\{[0-9/]+\}", repeats = True),
# Auxiliary basis set information:
SM(name = 'Auxiliary basis set information',
startReStr = r"AUXILIARY BASIS SET INFORMATION\s*",
sections = ["x_orca_auxiliary_basis_set_info"],
sections = ["section_basis_set"],
subMatchers = [
SM(r"\s*Group\s+[0-9]+\s+Type\s+(?P<x_orca_atom_labels>[a-zA-Z]+)\s+:\s+(?P<x_orca_auxiliary_basis_set>[0-9a-z]+)\s+contracted\s+to\s+(?P<x_orca_auxiliary_basis_set_contracted>[0-9a-z]+)\s+pattern\s+\{[0-9/]+\}", repeats = True)
]
......@@ -177,7 +157,7 @@ def buildSinglePointMatcher():
# Basis set statistics and startup info:
SM(name = 'Basis set statistics and startup info',
startReStr = r"\s*BASIS SET STATISTICS AND STARTUP INFO\s*",
sections = ["x_orca_basis_set_statistics_and_startup_info"],
sections = ["section_basis_set"],
subMatchers = [
# Gaussian basis set:
SM(name = 'Gaussian basis set',
......@@ -210,7 +190,7 @@ def buildSinglePointMatcher():
# SCF Settings:
SM(name = 'Orca SCF settings',
startReStr = r"\s*ORCA SCF\s*",
sections = ["x_orca_scf_settings"],
sections = ["section_method"],
subMatchers = [
SM(r"\s+Density Functional\s+Method\s+\.\.\.\s+(?P<x_orca_dft_method>[a-zA-Z()]+)"),
SM(r"\s+Exchange Functional\s+Exchange\s+\.\.\.\s+(?P<x_orca_exchange_functional>[a-zA-Z0-9]+)"),
......@@ -259,7 +239,7 @@ def buildSinglePointMatcher():
# *****************************************************
SM(name = 'Final step after convergence',
startReStr = r"Setting up the final grid:",
sections = ["x_orca_final_run_after_convergence"],
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]+)"),
......@@ -280,13 +260,13 @@ def buildSinglePointMatcher():
# Final SCF total Energy:
SM(name = 'Total Energy',
startReStr = r"\s*TOTAL SCF ENERGY\s*",
sections = ["x_orca_total_energy"],
sections = ["section_scf_iteration"],
subMatchers = [
SM(r"\s*Total Energy\s+:\s+(?P<x_orca_total_energy__hartree>[-+0-9.eEdD]+)"),
# Energy Components:
SM(name = 'Energy Components',
startReStr = r"\s*Components:\s*",
sections = ["x_orca_energy_componets"],
sections = ["section_scf_iteration"],
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]+)"),
......@@ -314,7 +294,7 @@ def buildSinglePointMatcher():
# Orbitals Energies:
SM(name = 'Orbital Energies',
startReStr = r"\s*ORBITAL ENERGIES\s*",
sections = ["x_orca_orbital_energies"],
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)
]
......@@ -322,7 +302,7 @@ def buildSinglePointMatcher():
# Mulliken population analysis:
SM(name = 'Mulliken population analysis',
startReStr = r"\s*\* MULLIKEN POPULATION ANALYSIS \*\s*",
sections = ["x_orca_mulliken_analysis"],
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]+)"),
......@@ -333,7 +313,7 @@ def buildSinglePointMatcher():
# Time table:
SM(name = 'timings',
startReStr = r"\s*TIMINGS\s*",
sections = ["x_orca_timings"],
sections = ["section_scf_iteration"],
subMatchers = [
SM(r"\s*Total SCF time:\s+(?P<x_orca_total_days_time>[0-9]+) days (?P<x_orca_total_hours_time>[0-9]+) hours (?P<x_orca_total_mins_time>[0-9]+) min (?P<x_orca_total_secs_time>[0-9]+) sec"),
SM(r"\s*Total time\s*\.\.\.\.\s*(?P<x_orca_final_time>[0-9.]+) sec"),
......@@ -362,7 +342,7 @@ def buildSinglePointMatcher():
#
SM(name = 'Geometry optimization',
startReStr = r"\s*\* Geometry Optimization Run \*\s*",
sections = ["x_orca_geometry_optimization"],
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]+)"),
......@@ -388,7 +368,7 @@ def buildSinglePointMatcher():
#
SM(name = 'Final step after geometry convergence',
startReStr = r"Setting up the final grid:",
sections = ["x_orca_final_run_after_convergence"],
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]+)"),
......@@ -409,13 +389,13 @@ def buildSinglePointMatcher():
# Final SCF total Energy:
SM(name = 'Final total Energy',
startReStr = r"\s*TOTAL SCF ENERGY\s*",
sections = ["x_orca_total_energy"],
sections = ["section_single_configuration_calculation"],
subMatchers = [
SM(r"\s*Total Energy\s+:\s+(?P<x_orca_total_energy__hartree>[-+0-9.eEdD]+)"),
# Energy Components:
SM(name = 'Final energy Components',
startReStr = r"\s*Components:\s*",
sections = ["x_orca_energy_componets"],
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]+)"),
......@@ -443,7 +423,7 @@ def buildSinglePointMatcher():
# Orbitals Energies:
SM(name = 'Orbital Energies',
startReStr = r"\s*ORBITAL ENERGIES\s*",
sections = ["x_orca_orbital_energies"],
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)
]
......@@ -451,7 +431,7 @@ def buildSinglePointMatcher():
# Mulliken population analysis:
SM(name = 'Mulliken population analysis',
startReStr = r"\s*\* MULLIKEN POPULATION ANALYSIS \*\s*",
sections = ["x_orca_mulliken_analysis"],
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]+)"),
......@@ -466,11 +446,11 @@ def buildSinglePointMatcher():
# MP2 Calculation (post-proc):
SM(name = 'mp2',
startReStr = r"\s*ORCA MP2 CALCULATION\s*",
sections = ["x_orca_mp2"],
sections = ["section_method"],
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*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")
]
......@@ -478,7 +458,7 @@ def buildSinglePointMatcher():
# Driven CI (post-proc):
SM(name = 'CI',
startReStr = r"\s*ORCA-MATRIX DRIVEN CI\s*",
sections = ["x_orca_driven_CI"],
sections = ["section_method"],
subMatchers = [
SM(r"\s*Correlation treatment\s*\.\.\.\s*(?P<x_orca_wave_function_correlation_treatment>[a-zA-Z0-9.]+)"),
SM(r"\s*Single excitations\s*\.\.\.\s*(?P<x_orca_single_excitations_on_off>[a-zA-Z]+)"),
......
......
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