From 795f1076a66d6f5cc92d16d5c6c8c4acb81170c3 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Thu, 19 Mar 2020 12:22:45 +0100
Subject: [PATCH] Added metainfo python code.
---
gaussianparser/metainfo/__init__.py | 13 +
gaussianparser/metainfo/gaussian.py | 1632 +++++++++++++++++++++
gaussianparser/parser_gaussian.py | 2 +-
parser/parser-gaussian/parser_gaussian.py | 114 +-
4 files changed, 1703 insertions(+), 58 deletions(-)
create mode 100644 gaussianparser/metainfo/__init__.py
create mode 100644 gaussianparser/metainfo/gaussian.py
diff --git a/gaussianparser/metainfo/__init__.py b/gaussianparser/metainfo/__init__.py
new file mode 100644
index 0000000..9491b9a
--- /dev/null
+++ b/gaussianparser/metainfo/__init__.py
@@ -0,0 +1,13 @@
+import sys
+from nomad.metainfo import Environment
+from nomad.metainfo.legacy import LegacyMetainfoEnvironment
+import gaussianparser.metainfo.gaussian
+import nomad.datamodel.metainfo.common
+import nomad.datamodel.metainfo.public
+import nomad.datamodel.metainfo.general
+
+m_env = LegacyMetainfoEnvironment()
+m_env.m_add_sub_section(Environment.packages, sys.modules['gaussianparser.metainfo.gaussian'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package) # type: ignore
diff --git a/gaussianparser/metainfo/gaussian.py b/gaussianparser/metainfo/gaussian.py
new file mode 100644
index 0000000..bcb5f51
--- /dev/null
+++ b/gaussianparser/metainfo/gaussian.py
@@ -0,0 +1,1632 @@
+import numpy as np # pylint: disable=unused-import
+import typing # pylint: disable=unused-import
+from nomad.metainfo import ( # pylint: disable=unused-import
+ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
+ Reference
+)
+from nomad.metainfo.legacy import LegacyDefinition
+
+from nomad.datamodel.metainfo import public
+
+m_package = Package(
+ name='gaussian_nomadmetainfo_json',
+ description='None',
+ a_legacy=LegacyDefinition(name='gaussian.nomadmetainfo.json'))
+
+
+class x_gaussian_configuration_core(MCategory):
+ '''
+ Properties defining the current configuration.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='x_gaussian_configuration_core'))
+
+
+class x_gaussian_atom_forces_type(MCategory):
+ '''
+ Some forces on the atoms (i.e. minus derivatives of some energy with respect to the
+ atom position).
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_forces_type'))
+
+
+class x_gaussian_scf_info(MCategory):
+ '''
+ Information on the self-consistent field (SCF) procedure.
+ '''
+
+ m_def = Category(
+ a_legacy=LegacyDefinition(name='x_gaussian_scf_info'))
+
+
+class x_gaussian_section_geometry(MSection):
+ '''
+ section that contains Cartesian coordinates of the system for a given geometry
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_geometry'))
+
+ x_gaussian_atomic_number = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ atomic number for atoms
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atomic_number'))
+
+ x_gaussian_atom_x_coord = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='meter',
+ description='''
+ x coordinate for the atoms
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_x_coord'))
+
+ x_gaussian_atom_y_coord = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='meter',
+ description='''
+ y coordinate for the atoms
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_y_coord'))
+
+ x_gaussian_atom_z_coord = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='meter',
+ description='''
+ z coordinate for the atoms
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_z_coord'))
+
+
+class x_gaussian_section_hybrid_coeffs(MSection):
+ '''
+ section that contains coefficients for the hybrid DFT functionals
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_hybrid_coeffs'))
+
+ hybrid_xc_coeff1 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Coefficient for Hartree-Fock exchange in hybrid DFT functionals
+ ''',
+ a_legacy=LegacyDefinition(name='hybrid_xc_coeff1'))
+
+ hybrid_xc_coeff2 = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Coefficients for Slater exchange, non-local exchange, local correlation, and non-
+ local correlation, respectively, in hybrid DFT functionals
+ ''',
+ a_legacy=LegacyDefinition(name='hybrid_xc_coeff2'))
+
+ x_gaussian_hybrid_xc_hfx = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Hartree-Fock exchange
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_hybrid_xc_hfx'))
+
+ x_gaussian_hybrid_xc_slater = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Slater exchange
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_hybrid_xc_slater'))
+
+ x_gaussian_hybrid_xc_nonlocalex = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Slater exchange
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_hybrid_xc_nonlocalex'))
+
+ x_gaussian_hybrid_xc_localcorr = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Slater exchange
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_hybrid_xc_localcorr'))
+
+ x_gaussian_hybrid_xc_nonlocalcorr = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Slater exchange
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_hybrid_xc_nonlocalcorr'))
+
+
+class x_gaussian_section_total_scf_one_geometry(MSection):
+ '''
+ Check for SCF convergence and writes the total energy value to backend
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_total_scf_one_geometry'))
+
+
+class x_gaussian_section_times(MSection):
+ '''
+ section that contains the execution times of the run
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_times'))
+
+ x_gaussian_program_termination_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_program_termination_date'))
+
+ x_gaussian_program_cpu_time = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_program_cpu_time'))
+
+
+class x_gaussian_section_atom_forces(MSection):
+ '''
+ section that contains Cartesian coordinates of the system for a given geometry
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_atom_forces'))
+
+ x_gaussian_atom_x_force = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_x_force'))
+
+ x_gaussian_atom_y_force = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_y_force'))
+
+ x_gaussian_atom_z_force = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='newton',
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_z_force'))
+
+
+class x_gaussian_section_molecular_multipoles(MSection):
+ '''
+ Section describing multipoles (charges, dipoles,...).
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_molecular_multipoles'))
+
+ charge = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the total charge of the system (in electronic units).
+ ''',
+ a_legacy=LegacyDefinition(name='charge'))
+
+ dipole_moment_x = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the x component of the dipole moment (Debye).
+ ''',
+ a_legacy=LegacyDefinition(name='dipole_moment_x'))
+
+ dipole_moment_y = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the y component of the dipole moment (Debye).
+ ''',
+ a_legacy=LegacyDefinition(name='dipole_moment_y'))
+
+ dipole_moment_z = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the z component of the dipole moment (Debye).
+ ''',
+ a_legacy=LegacyDefinition(name='dipole_moment_z'))
+
+ quadrupole_moment_xx = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xx component of the quadrupole moment (Debye-Ang).
+ ''',
+ a_legacy=LegacyDefinition(name='quadrupole_moment_xx'))
+
+ quadrupole_moment_yy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yy component of the quadrupole moment (Debye-Ang).
+ ''',
+ a_legacy=LegacyDefinition(name='quadrupole_moment_yy'))
+
+ quadrupole_moment_zz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the zz component of the quadrupole moment (Debye-Ang).
+ ''',
+ a_legacy=LegacyDefinition(name='quadrupole_moment_zz'))
+
+ quadrupole_moment_xy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xy component of the quadrupole moment (Debye-Ang).
+ ''',
+ a_legacy=LegacyDefinition(name='quadrupole_moment_xy'))
+
+ quadrupole_moment_xz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xz component of the quadrupole moment (Debye-Ang).
+ ''',
+ a_legacy=LegacyDefinition(name='quadrupole_moment_xz'))
+
+ quadrupole_moment_yz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yz component of the quadrupole moment (Debye-Ang).
+ ''',
+ a_legacy=LegacyDefinition(name='quadrupole_moment_yz'))
+
+ octapole_moment_xxx = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxx component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_xxx'))
+
+ octapole_moment_yyy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyy component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_yyy'))
+
+ octapole_moment_zzz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the zzz component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_zzz'))
+
+ octapole_moment_xyy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xyy component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_xyy'))
+
+ octapole_moment_xxy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxy component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_xxy'))
+
+ octapole_moment_xxz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxz component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_xxz'))
+
+ octapole_moment_xzz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xzz component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_xzz'))
+
+ octapole_moment_yzz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yzz component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_yzz'))
+
+ octapole_moment_yyz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyz component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_yyz'))
+
+ octapole_moment_xyz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xyz component of the octapole moment (Debye-Ang**2).
+ ''',
+ a_legacy=LegacyDefinition(name='octapole_moment_xyz'))
+
+ hexadecapole_moment_xxxx = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxxx component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_xxxx'))
+
+ hexadecapole_moment_yyyy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyyy component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_yyyy'))
+
+ hexadecapole_moment_zzzz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the zzzz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_zzzz'))
+
+ hexadecapole_moment_xxxy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxxy component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_xxxy'))
+
+ hexadecapole_moment_xxxz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxxz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_xxxz'))
+
+ hexadecapole_moment_yyyx = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyyx component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_yyyx'))
+
+ hexadecapole_moment_yyyz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyyz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_yyyz'))
+
+ hexadecapole_moment_zzzx = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the zzzx component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_zzzx'))
+
+ hexadecapole_moment_zzzy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the zzzy component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_zzzy'))
+
+ hexadecapole_moment_xxyy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxyy component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_xxyy'))
+
+ hexadecapole_moment_xxzz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxzz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_xxzz'))
+
+ hexadecapole_moment_yyzz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyzz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_yyzz'))
+
+ hexadecapole_moment_xxyz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the xxyz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_xxyz'))
+
+ hexadecapole_moment_yyxz = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the yyxz component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_yyxz'))
+
+ hexadecapole_moment_zzxy = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Value of the zzxy component of the hexadecapole moment (Debye-Ang**3).
+ ''',
+ a_legacy=LegacyDefinition(name='hexadecapole_moment_zzxy'))
+
+ x_gaussian_molecular_multipole_lm = Quantity(
+ type=np.dtype(np.int32),
+ shape=['x_gaussian_number_of_lm_molecular_multipoles', 2],
+ description='''
+ Tuples of $l$ and $m$ values for which the molecular multipoles (including the
+ electric charge, dipole, etc.) are given. The meaning of the integer number $l$ is
+ monopole/charge for $l=0$, dipole for $l=1$, quadrupole for $l=2$, etc. The
+ meaning of the integer numbers $m$ is specified by molecular_multipole_m_kind.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_molecular_multipole_lm'))
+
+ x_gaussian_molecular_multipole_m_kind = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String describing what the integer numbers $m$ in molecular_multipole_lm mean.
+ Allowed values (for atomic multipoles) are listed in the [m\\_kind wiki
+ page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_molecular_multipole_m_kind'))
+
+ x_gaussian_molecular_multipole_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['x_gaussian_number_of_lm_molecular_multipoles'],
+ description='''
+ Value of the multipoles (including the monopole/charge for $l$ = 0, the dipole for
+ $l$ = 1, etc.).
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_molecular_multipole_values'))
+
+ x_gaussian_number_of_lm_molecular_multipoles = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of $l,m$ combinations for which molecular multipoles are given.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_number_of_lm_molecular_multipoles'))
+
+
+class x_gaussian_section_geometry_optimization_info(MSection):
+ '''
+ Specifies whether a geometry optimization is converged.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_geometry_optimization_info'))
+
+ x_gaussian_geometry_optimization_converged = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Specifies whether a geometry optimization is converged.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_geometry_optimization_converged'))
+
+
+class x_gaussian_section_frequencies(MSection):
+ '''
+ section for the values of the frequencies, reduced masses and normal mode vectors
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_frequencies'))
+
+ x_gaussian_frequency_values = Quantity(
+ type=str,
+ shape=['number_of_frequency_rows'],
+ description='''
+ values of frequencies, in cm-1
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_frequency_values'))
+
+ x_gaussian_frequencies = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_frequencies'],
+ description='''
+ values of frequencies, in cm-1
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_frequencies'))
+
+ x_gaussian_reduced_masses = Quantity(
+ type=str,
+ shape=['number_of_reduced_masses_rows'],
+ description='''
+ values of normal mode reduced masses
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_reduced_masses'))
+
+ x_gaussian_red_masses = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_frequencies'],
+ description='''
+ values of normal mode reduced masses
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_red_masses'))
+
+ x_gaussian_normal_modes = Quantity(
+ type=str,
+ shape=['number_of_normal_modes_rows'],
+ description='''
+ normal mode vectors
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_normal_modes'))
+
+ x_gaussian_normal_mode_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_frequencies', 'number_of_atoms', 3],
+ description='''
+ normal mode vectors
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_normal_mode_values'))
+
+
+class x_gaussian_section_thermochem(MSection):
+ '''
+ section for thermochemical quantities
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_thermochem'))
+
+ x_gaussian_temperature = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of temperature for thermochemical values
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_temperature'))
+
+ x_gaussian_pressure = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of pressure for thermochemical values
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_pressure'))
+
+ x_gaussian_moment_of_inertia_X = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ X component of moment of inertia
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_moment_of_inertia_X'))
+
+ x_gaussian_moment_of_inertia_Y = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Y component of moment of inertia
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_moment_of_inertia_Y'))
+
+ x_gaussian_moment_of_inertia_Z = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Z component of moment of inertia
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_moment_of_inertia_Z'))
+
+ x_gaussian_moments = Quantity(
+ type=np.dtype(np.float64),
+ shape=[3],
+ description='''
+ Values of moments of inertia
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_moments'))
+
+ x_gaussian_zero_point_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of zero-point energy
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_zero_point_energy'))
+
+ x_gaussian_thermal_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of thermal correction to total energy
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_thermal_correction_energy'))
+
+ x_gaussian_thermal_correction_enthalpy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of thermal correction to enthalpy
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_thermal_correction_enthalpy'))
+
+ x_gaussian_thermal_correction_free_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Value of thermal correction to Gibbs free energy
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_thermal_correction_free_energy'))
+
+
+class x_gaussian_section_force_constant_matrix(MSection):
+ '''
+ section for force constant matrix in Cartesians. Units are mdyne.Angstrom
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_force_constant_matrix'))
+
+ x_gaussian_force_constants = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Force constant matrix elements
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_force_constants'))
+
+ x_gaussian_force_constant_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_degrees_of_freedom', 'number_of_degrees_of_freedom'],
+ description='''
+ Force constant matrix element values
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_force_constant_values'))
+
+
+class x_gaussian_section_orbital_symmetries(MSection):
+ '''
+ section for the symmetry of the MOs
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_orbital_symmetries'))
+
+ x_gaussian_alpha_occ_symmetry_values = Quantity(
+ type=str,
+ shape=['number_of_alpha_occ_rows'],
+ description='''
+ symmetry of the alpha occupied MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_occ_symmetry_values'))
+
+ x_gaussian_alpha_vir_symmetry_values = Quantity(
+ type=str,
+ shape=['number_of_alpha_vir_rows'],
+ description='''
+ symmetry of the alpha virtual MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_vir_symmetry_values'))
+
+ x_gaussian_beta_occ_symmetry_values = Quantity(
+ type=str,
+ shape=['number_of_beta_occ_rows'],
+ description='''
+ symmetry of the beta occupied MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_occ_symmetry_values'))
+
+ x_gaussian_beta_vir_symmetry_values = Quantity(
+ type=str,
+ shape=['number_of_beta_vir_rows'],
+ description='''
+ symmetry of the beta virtual MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_vir_symmetry_values'))
+
+ x_gaussian_alpha_symmetries = Quantity(
+ type=str,
+ shape=['number_of_alpha_mos'],
+ description='''
+ symmetry of the alpha MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_symmetries'))
+
+ x_gaussian_beta_symmetries = Quantity(
+ type=str,
+ shape=['number_of_beta_mos'],
+ description='''
+ symmetry of the beta MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_symmetries'))
+
+
+class x_gaussian_section_symmetry(MSection):
+ '''
+ section for the symmetry of the electronic state
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_symmetry'))
+
+ x_gaussian_elstate_symmetry = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ symmetry group of the electronic state
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_elstate_symmetry'))
+
+
+class x_gaussian_section_elstruc_method(MSection):
+ '''
+ Section containing electronic structure method.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_elstruc_method'))
+
+ x_gaussian_electronic_structure_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Name of electronic structure method.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_electronic_structure_method'))
+
+
+class x_gaussian_section_energy_components(MSection):
+ '''
+ Section containing total energy components
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_energy_components'))
+
+
+class x_gaussian_section_moller_plesset(MSection):
+ '''
+ Perturbative Moller-Plesset energies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_moller_plesset'))
+
+ x_gaussian_mp2_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and MP2 energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_mp2_correction_energy'))
+
+ x_gaussian_mp3_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and MP3 energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_mp3_correction_energy'))
+
+ x_gaussian_mp4dq_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and MP4(DQ) energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_mp4dq_correction_energy'))
+
+ x_gaussian_mp4sdq_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and MP4(SDQ) energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_mp4sdq_correction_energy'))
+
+ x_gaussian_mp4sdtq_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and MP4(SDTQ) energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_mp4sdtq_correction_energy'))
+
+ x_gaussian_mp5_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and MP5 energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_mp5_correction_energy'))
+
+
+class x_gaussian_section_coupled_cluster(MSection):
+ '''
+ Coupled cluster energies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_coupled_cluster'))
+
+ x_gaussian_ccsd_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and CCSD energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_ccsd_correction_energy'))
+
+
+class x_gaussian_section_quadratic_ci(MSection):
+ '''
+ Quadratic CI energies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_quadratic_ci'))
+
+ x_gaussian_qcisd_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and QCISD energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_qcisd_correction_energy'))
+
+ x_gaussian_qcisdtq_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and QCISD(TQ) energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_qcisdtq_correction_energy'))
+
+
+class x_gaussian_section_ci(MSection):
+ '''
+ CI energies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_ci'))
+
+ x_gaussian_ci_correction_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Difference between SCF and CI energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_ci_correction_energy'))
+
+
+class x_gaussian_section_semiempirical(MSection):
+ '''
+ semiempirical convergence cycles and energies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_semiempirical'))
+
+ x_gaussian_semiempirical_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ semiempirical energies.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_semiempirical_energy'))
+
+ x_gaussian_semiempirical_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ semiempirical method.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_semiempirical_method'))
+
+
+class x_gaussian_section_molmech(MSection):
+ '''
+ molecular mechanics method and energies.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_molmech'))
+
+ x_gaussian_molmech_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ molecular mechanics method.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_molmech_method'))
+
+
+class x_gaussian_section_models(MSection):
+ '''
+ composite model chemistries.
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_models'))
+
+
+class x_gaussian_section_excited_initial(MSection):
+ '''
+ Excited state energies and properties
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_excited_initial'))
+
+
+class x_gaussian_section_excited(MSection):
+ '''
+ CI singles, TDDFT/TDHF, ZINDO or EOMCCSD excited state energies and properties
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_excited'))
+
+ x_gaussian_excited_state_number = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ CIS, TDDFT/TDHF, ZINDO or EOMCCSD excited state number
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_excited_state_number'))
+
+ x_gaussian_excited_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ CIS, TDDFT/TDHF, ZINDO or EOMCCSD excited state energy
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_excited_energy'))
+
+ x_gaussian_excited_oscstrength = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ CIS, TDDFT/TDHF, ZINDO or EOMCCSD excited state oscillator strength
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_excited_oscstrength'))
+
+ x_gaussian_excited_spin_squared = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ CIS, TDDFT/TDHF, ZINDO or EOMCCSD excited state spin squared value
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_excited_spin_squared'))
+
+ x_gaussian_excited_transition = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ CIS, TDDFT/TDHF, ZINDO or EOMCCSD excited state MOs involved in transitions and
+ their coefficients
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_excited_transition'))
+
+
+class x_gaussian_section_casscf(MSection):
+ '''
+ CASSCF energies and properties
+ '''
+
+ m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gaussian_section_casscf'))
+
+ x_gaussian_casscf_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ CASSCF energy
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_casscf_energy'))
+
+ x_gaussian_casscf_determinant = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ CASSCF determinant number
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_casscf_determinant'))
+
+ x_gaussian_casscf_coefficient = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ CASSCF determinant coefficient
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_casscf_coefficient'))
+
+
+class section_system(public.section_system):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
+
+ x_gaussian_number_of_atoms = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ number of atoms of the system
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_number_of_atoms'))
+
+ x_gaussian_atomic_masses = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ atomic masses for atoms
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_atomic_masses'))
+
+ x_gaussian_total_charge = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Total charge of the system.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_total_charge'))
+
+ x_gaussian_spin_target_multiplicity = Quantity(
+ type=np.dtype(np.int32),
+ shape=[],
+ description='''
+ Target (user-imposed) value of the spin multiplicity $M=2S+1$, where $S$ is the
+ total spin. It is an integer value. This value is not necessarly the value
+ obtained at the end of the calculation. See spin_S2 for the converged value of the
+ spin moment.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_spin_target_multiplicity'))
+
+ x_gaussian_geometry_lattice_vector_x = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ x component of lattice vector
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_geometry_lattice_vector_x'))
+
+ x_gaussian_geometry_lattice_vector_y = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ y component of lattice vector
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_geometry_lattice_vector_y'))
+
+ x_gaussian_geometry_lattice_vector_z = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ z component of lattice vector
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_geometry_lattice_vector_z'))
+
+ x_gaussian_masses = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms'],
+ description='''
+ values of atomic masses
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_masses'))
+
+
+class section_single_configuration_calculation(public.section_single_configuration_calculation):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_single_configuration_calculation'))
+
+ x_gaussian_atom_forces = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='newton',
+ description='''
+ Forces acting on the atoms, calculated as minus gradient of energy_total.
+ ''',
+ categories=[x_gaussian_atom_forces_type],
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_forces'))
+
+ x_gaussian_energy_total_scf_converged = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ SCF total energy converged for a given geometry.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_energy_total_scf_converged'))
+
+ x_gaussian_number_of_scf_iterations = Quantity(
+ type=int,
+ shape=[],
+ description='''
+ Number of performed self-consistent field (SCF) iterations at DFT level.
+ ''',
+ categories=[x_gaussian_scf_info],
+ a_legacy=LegacyDefinition(name='x_gaussian_number_of_scf_iterations'))
+
+ x_gaussian_section_hybrid_coeffs = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_hybrid_coeffs'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_hybrid_coeffs'))
+
+ x_gaussian_section_total_scf_one_geometry = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_total_scf_one_geometry'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_total_scf_one_geometry'))
+
+ x_gaussian_section_atom_forces = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_atom_forces'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_atom_forces'))
+
+ x_gaussian_section_molecular_multipoles = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_molecular_multipoles'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_molecular_multipoles'))
+
+ x_gaussian_section_energy_components = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_energy_components'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_energy_components'))
+
+ x_gaussian_section_moller_plesset = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_moller_plesset'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_moller_plesset'))
+
+ x_gaussian_section_coupled_cluster = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_coupled_cluster'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_coupled_cluster'))
+
+ x_gaussian_section_quadratic_ci = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_quadratic_ci'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_quadratic_ci'))
+
+ x_gaussian_section_ci = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_ci'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_ci'))
+
+ x_gaussian_section_semiempirical = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_semiempirical'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_semiempirical'))
+
+ x_gaussian_section_molmech = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_molmech'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_molmech'))
+
+ x_gaussian_section_models = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_models'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_models'))
+
+ x_gaussian_section_excited_initial = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_excited_initial'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_excited_initial'))
+
+ x_gaussian_section_excited = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_excited'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_excited'))
+
+ x_gaussian_section_casscf = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_casscf'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_casscf'))
+
+
+class section_run(public.section_run):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
+
+ x_gaussian_chk_file = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ binary file with detailed output information
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_chk_file'))
+
+ x_gaussian_memory = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ total memory for the run
+ ''',
+ categories=[public.settings_run],
+ a_legacy=LegacyDefinition(name='x_gaussian_memory'))
+
+ x_gaussian_number_of_processors = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ number of processors used
+ ''',
+ categories=[public.settings_run, public.parallelization_info, public.accessory_info],
+ a_legacy=LegacyDefinition(name='x_gaussian_number_of_processors'))
+
+ x_gaussian_program_execution_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_program_execution_date'))
+
+ x_gaussian_program_release_date = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_program_release_date'))
+
+ x_gaussian_program_implementation = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ -
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_program_implementation'))
+
+ x_gaussian_atom_positions = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_atoms', 3],
+ unit='meter',
+ description='''
+ Positions of all the atoms, in Cartesian coordinates. This metadata defines a
+ configuration and is therefore required.
+ ''',
+ categories=[x_gaussian_configuration_core],
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_positions'))
+
+ x_gaussian_atom_labels = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Labels of the atoms. These strings identify the atom kind and conventionally start
+ with the symbol of the atomic species, possibly followed by a number. The same
+ atomic species can be labelled with more than one atom_labels in order to
+ distinguish, e.g., atoms of the same species assigned to different atom-centered
+ basis sets or pseudopotentials, or simply atoms in different locations in the
+ structure (e.g., bulk and surface). These labels can also be used for *particles*
+ that do not correspond to physical atoms (e.g., ghost atoms in some codes using
+ atom-centered basis sets). This metadata defines a configuration and is therefore
+ required.
+ ''',
+ categories=[x_gaussian_configuration_core],
+ a_legacy=LegacyDefinition(name='x_gaussian_atom_labels'))
+
+ x_gaussian_section_geometry = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_geometry'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_geometry'))
+
+ x_gaussian_section_times = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_times'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_times'))
+
+ x_gaussian_section_geometry_optimization_info = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_geometry_optimization_info'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_geometry_optimization_info'))
+
+ x_gaussian_section_frequencies = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_frequencies'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_frequencies'))
+
+ x_gaussian_section_thermochem = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_thermochem'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_thermochem'))
+
+ x_gaussian_section_force_constant_matrix = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_force_constant_matrix'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_force_constant_matrix'))
+
+ x_gaussian_section_orbital_symmetries = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_orbital_symmetries'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_orbital_symmetries'))
+
+ x_gaussian_section_symmetry = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_symmetry'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_symmetry'))
+
+
+class section_scf_iteration(public.section_scf_iteration):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_scf_iteration'))
+
+ x_gaussian_energy_total_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total energy calculated with a given method during the self-consistent field (SCF)
+ iterations.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_energy_total_scf_iteration'))
+
+ x_gaussian_delta_energy_total_scf_iteration = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total energy increment calculated with a given method during the self-consistent
+ field (SCF) iterations.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_delta_energy_total_scf_iteration'))
+
+ x_gaussian_single_configuration_calculation_converged = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Determines whether a single configuration calculation is converged.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_single_configuration_calculation_converged'))
+
+ x_gaussian_spin_S2 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Real value of spin squared.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_spin_S2'))
+
+ x_gaussian_after_annihilation_spin_S2 = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='''
+ Real value of spin squared resulting from the annihilation of the first spin
+ contaminant.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_after_annihilation_spin_S2'))
+
+ x_gaussian_energy_scf = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the SCF total energy, either HF or DFT.
+ ''',
+ categories=[public.energy_value, public.energy_total_potential, public.energy_component],
+ a_legacy=LegacyDefinition(name='x_gaussian_energy_scf'))
+
+ x_gaussian_perturbation_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Value of the perturbation energy for double hybrids
+ ''',
+ categories=[public.energy_value, public.energy_total_potential, public.energy_component],
+ a_legacy=LegacyDefinition(name='x_gaussian_perturbation_energy'))
+
+ x_gaussian_hf_detect = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ Determine if the SCF method is one of RHF, UHF, or ROHF
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_hf_detect'))
+
+ x_gaussian_energy_electrostatic = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Total electrostatic energy (nuclei + electrons), defined consistently with
+ calculation_method.
+ ''',
+ categories=[public.energy_value, public.energy_component],
+ a_legacy=LegacyDefinition(name='x_gaussian_energy_electrostatic'))
+
+ x_gaussian_energy_error = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Error in the total energy. Defined consistently with XC_method.
+ ''',
+ categories=[public.error_estimate_contribution, public.energy_value],
+ a_legacy=LegacyDefinition(name='x_gaussian_energy_error'))
+
+ x_gaussian_electronic_kinetic_energy = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ unit='joule',
+ description='''
+ Self-consistent electronic kinetic energy as defined in XC_method.
+ ''',
+ categories=[public.energy_value, public.energy_component],
+ a_legacy=LegacyDefinition(name='x_gaussian_electronic_kinetic_energy'))
+
+
+class section_eigenvalues(public.section_eigenvalues):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_eigenvalues'))
+
+ x_gaussian_alpha_occ_eigenvalues_values = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ values of eigenenergies for occupied alpha MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_occ_eigenvalues_values'))
+
+ x_gaussian_alpha_vir_eigenvalues_values = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ values of eigenenergies for virtual alpha MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_vir_eigenvalues_values'))
+
+ x_gaussian_beta_occ_eigenvalues_values = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ values of eigenenergies for occupied beta MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_occ_eigenvalues_values'))
+
+ x_gaussian_beta_vir_eigenvalues_values = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ values of eigenenergies for virtual beta MOs
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_vir_eigenvalues_values'))
+
+ x_gaussian_alpha_eigenvalues = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_alpha_mos'],
+ description='''
+ values of eigenenergies, alpha occ
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_eigenvalues'))
+
+ x_gaussian_beta_eigenvalues = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_beta_mos'],
+ description='''
+ values of eigenenergies, beta occ
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_eigenvalues'))
+
+ x_gaussian_alpha_occupations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_alpha_mos'],
+ description='''
+ values of eigenenergies, alpha occ
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_alpha_occupations'))
+
+ x_gaussian_beta_occupations = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_beta_mos'],
+ description='''
+ values of eigenenergies, beta occ
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_beta_occupations'))
+
+ x_gaussian_eigenvalues_occupation = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ description='''
+ Occupation of the eigenstates whose (energy) eigenvalues are given in
+ eigenvalues_values.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_eigenvalues_occupation'))
+
+ x_gaussian_eigenvalues_values = Quantity(
+ type=np.dtype(np.float64),
+ shape=['number_of_spin_channels', 'number_of_eigenvalues_kpoints', 'number_of_eigenvalues'],
+ unit='joule',
+ description='''
+ Values of the (electronic-energy) eigenvalues. Their occupations are given in
+ eigenvalues_occupation.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_eigenvalues_values'))
+
+
+class section_method(public.section_method):
+
+ m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
+
+ x_gaussian_settings = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ electronic structure method, basis set, etc.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_settings'))
+
+ x_gaussian_settings_corrected = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ electronic structure method, basis set, etc.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_settings_corrected'))
+
+ x_gaussian_method = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String identifying in an unique way the electronic structure method used for the
+ final wavefunctions.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_method'))
+
+ x_gaussian_xc = Quantity(
+ type=str,
+ shape=[],
+ description='''
+ String identifying in an unique way the XC method used for the final
+ wavefunctions.
+ ''',
+ a_legacy=LegacyDefinition(name='x_gaussian_xc'))
+
+ x_gaussian_section_elstruc_method = SubSection(
+ sub_section=SectionProxy('x_gaussian_section_elstruc_method'),
+ repeats=True,
+ a_legacy=LegacyDefinition(name='x_gaussian_section_elstruc_method'))
+
+
+m_package.__init_metainfo__()
diff --git a/gaussianparser/parser_gaussian.py b/gaussianparser/parser_gaussian.py
index bb5c8cc..16c8393 100644
--- a/gaussianparser/parser_gaussian.py
+++ b/gaussianparser/parser_gaussian.py
@@ -826,7 +826,7 @@ class GaussianParserContext(object):
for k in range(i+1,dim):
cartforceconst[i,k] = cartforceconst[k,i]
- cartforceconst = convert_unit(cartforceconst, "forceAu / bohr", "J / (meter**2)")
+ cartforceconst = convert_unit(cartforceconst, "hartree / (bohr ** 2)", "J / (meter**2)")
backend.addArrayValues("x_gaussian_force_constant_values", cartforceconst)
diff --git a/parser/parser-gaussian/parser_gaussian.py b/parser/parser-gaussian/parser_gaussian.py
index c2fc4c3..5d236fd 100644
--- a/parser/parser-gaussian/parser_gaussian.py
+++ b/parser/parser-gaussian/parser_gaussian.py
@@ -1,11 +1,11 @@
# Copyright 2015-2018 Rosendo Valero, Fawzi Mohamed, Ankit Kariryaa
-#
+#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
-#
+#
# http://www.apache.org/licenses/LICENSE-2.0
-#
+#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -37,7 +37,7 @@ logger = logging.getLogger("nomad.GaussianParser")
mainFileDescription = SM(
name = 'root',
weak = True,
- forwardMatch = True,
+ forwardMatch = True,
startReStr = "",
subMatchers = [
SM(name = 'newRun',
@@ -220,7 +220,7 @@ mainFileDescription = SM(
]
)
]
- ),
+ ),
SM(name = 'CASSCFStates',
sections = ['x_gaussian_section_casscf'],
startReStr = r"\s*EIGENVALUES AND\s*",
@@ -247,7 +247,7 @@ mainFileDescription = SM(
startReStr = r"\s+Population analysis",
subFlags = SM.SubFlags.Sequenced,
subMatchers = [
- SM(r"\s*Orbital symmetries"),
+ SM(r"\s*Orbital symmetries"),
SM(r"\s*Alpha Orbitals"),
SM(r"\s*Occupied\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\))?"),
SM(r"\s+(?P<x_gaussian_alpha_occ_symmetry_values>\((.+)\)?)", repeats = True),
@@ -274,7 +274,7 @@ mainFileDescription = SM(
forwardMatch = True,
subFlags = SM.SubFlags.Sequenced,
subMatchers = [
- SM(r"\s*Alpha occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
+ SM(r"\s*Alpha occ. eigenvalues --\s+(?P<x_gaussian_alpha_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*Alpha virt. eigenvalues --\s+(?P<x_gaussian_alpha_vir_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*Beta occ. eigenvalues --\s+(?P<x_gaussian_beta_occ_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
SM(r"\s*Beta virt. eigenvalues --\s+(?P<x_gaussian_beta_vir_eigenvalues_values>-?[^\s.-]+\s+|(\-?\d*\.\d*)\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?\s+(\-?\d*\.\d*)?)", repeats = True),
@@ -297,10 +297,10 @@ mainFileDescription = SM(
forwardMatch = False,
subMatchers = [
SM(r"\s*Charge=(?P<charge>\s*[-0-9.]+)"),
- SM(r"\s*Dipole moment "),
+ SM(r"\s*Dipole moment "),
SM(r"\s+\w+=\s+(?P<dipole_moment_x>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_y>[-+0-9EeDd.]+)\s+\w+=\s+(?P<dipole_moment_z>[-+0-9EeDd.]+)"),
- SM(r"\s*Quadrupole moment"),
- SM(r"\s+\w+=\s+(?P<quadrupole_moment_xx>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_zz>[0-9-.]+)"),
+ SM(r"\s*Quadrupole moment"),
+ SM(r"\s+\w+=\s+(?P<quadrupole_moment_xx>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_zz>[0-9-.]+)"),
SM(r"\s+\w+=\s+(?P<quadrupole_moment_xy>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_xz>[0-9-.]+)\s+\w+=\s+(?P<quadrupole_moment_yz>[0-9-.]+)"),
SM(r"\s*Traceless Quadrupole moment"),
SM(r"\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+\s+\w+=\s+[0-9-.]+"),
@@ -315,7 +315,7 @@ mainFileDescription = SM(
SM(r"\s+\w+=\s+(?P<hexadecapole_moment_zzzy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxyy>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_xxzz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyzz>[-+0-9EeDd.]+)"),
SM(r"\s+\w+=\s+(?P<hexadecapole_moment_xxyz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_yyxz>[-+0-9EeDd.]+)\s+\w+=\s+(?P<hexadecapole_moment_zzxy>[-+0-9EeDd.]+)")
]
- ),
+ ),
SM (name = 'Frequencies',
sections = ['x_gaussian_section_frequencies'],
startReStr = r"\s*Frequencies --\s+(?:(?:[-]?[0-9]+\.\d*)\s*(?:[-]?[-0-9]+\.\d*)?\s*(?:[-]?[-0-9]+\.\d*)?)",
@@ -347,9 +347,9 @@ mainFileDescription = SM(
SM(r"\s*Zero-point correction=\s*(?P<x_gaussian_zero_point_energy__hartree>[0-9.]+)"),
SM(r"\s*Thermal correction to Energy=\s*(?P<x_gaussian_thermal_correction_energy__hartree>[0-9.]+)"),
SM(r"\s*Thermal correction to Enthalpy=\s*(?P<x_gaussian_thermal_correction_enthalpy__hartree>[0-9.]+)"),
- SM(r"\s*Thermal correction to Gibbs Free Energy=\s*(?P<x_gaussian_thermal_correction_free_energy__hartree>[0-9.]+)"),
+ SM(r"\s*Thermal correction to Gibbs Free Energy=\s*(?P<x_gaussian_thermal_correction_free_energy__hartree>[0-9.]+)"),
]
- ),
+ ),
SM(name = 'Forceconstantmatrix',
sections = ['x_gaussian_section_force_constant_matrix'],
startReStr = r"\s*Force constants in Cartesian coordinates",
@@ -632,12 +632,12 @@ class GaussianParserContext(object):
symmetry = [str(f) for f in symoccalpha[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("'E","E").replace("G'","G").replace("\"A'\"","A'").split()]
sym1 = []
- sym1 = np.append(sym1, symmetry)
+ sym1 = np.append(sym1, symmetry)
symmetry = [str(f) for f in symviralpha[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("\"A'\"","A'").replace("'E","E").replace("G'","G").split()]
sym2 = []
sym2 = np.append(sym2, symmetry)
symmetrycon = np.concatenate((sym1, sym2), axis=0)
- backend.addArrayValues("x_gaussian_alpha_symmetries", symmetrycon)
+ backend.addArrayValues("x_gaussian_alpha_symmetries", symmetrycon)
if(section["x_gaussian_beta_occ_symmetry_values"]):
symmetry = [str(f) for f in symoccbeta[1:].replace(",","").replace("(","").replace(")","").replace("]","").replace("'A","A").replace("\\'","'").replace("A''","A'").replace("\"A'\"","A'").replace("'E","E").replace("G'","G").split()]
@@ -677,7 +677,7 @@ class GaussianParserContext(object):
quadyz = section["quadrupole_moment_yz"]
quadzz = section["quadrupole_moment_zz"]
quad = str([quadxx, quadxy, quadyy, quadxz, quadyz, quadzz])
- quadrupoles = [float(f) for f in quad[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").split()]
+ quadrupoles = [float(f) for f in quad[1:].replace("-."," -0.").replace("'."," 0.").replace("'","").replace("[","").replace("]","").replace(",","").split()]
quadrupoles = convert_unit(quadrupoles, "debye * angstrom", "coulomb * meter**2")
if(section["octapole_moment_xxx"]):
@@ -719,7 +719,7 @@ class GaussianParserContext(object):
if(section["quadrupole_moment_xx"]):
multipoles = np.hstack((charge, dipoles, quadrupoles, octapoles, hexadecapoles))
else:
- multipoles = np.hstack((charge, dipoles))
+ multipoles = np.hstack((charge, dipoles))
x_gaussian_molecular_multipole_values = np.resize(multipoles, (x_gaussian_number_of_lm_molecular_multipoles))
@@ -746,12 +746,12 @@ class GaussianParserContext(object):
disps = [float(s) for s in vibdisps[1:].replace("'","").replace(",","").replace("]","").replace("one","").replace("\\n","").replace(" ."," 0.").replace(" -."," -0.").split()]
dispsnew = np.zeros(len(disps), dtype = float)
-# Reorder disps
+# Reorder disps
if len(vibfreqs) % 3 == 0:
k = 0
for p in range(0,len(vibfreqs) // 3):
- M = int(len(disps)/len(vibfreqs)) * (p+1)
+ M = int(len(disps)/len(vibfreqs)) * (p+1)
for m in range(3):
for n in range(M - int(len(disps) / len(vibfreqs)),M,3):
for l in range(3):
@@ -782,9 +782,9 @@ class GaussianParserContext(object):
forceconst = str(section["x_gaussian_force_constants"])
numbers = [float(s) for s in forceconst[1:].replace("'","").replace(",","").replace("]","").replace("\\n","").replace("D","E").replace(" ."," 0.").replace(" -."," -0.").split()]
length = len(numbers)
- dim = int(((1 + 8 * length)**0.5 - 1) / 2)
+ dim = int(((1 + 8 * length)**0.5 - 1) / 2)
cartforceconst = np.zeros([dim, dim])
- forcecnstvalues = np.append(forcecnstvalues, numbers)
+ forcecnstvalues = np.append(forcecnstvalues, numbers)
if dim > 6:
l = 0
for i in range(0,5):
@@ -795,7 +795,7 @@ class GaussianParserContext(object):
for k in range(0,5):
l = l + 1
cartforceconst[i,k] = forcecnstvalues[l-1]
- for i in range(5,dim-2):
+ for i in range(5,dim-2):
for k in range(5,i+1):
l = l + 1
cartforceconst[i,k] = forcecnstvalues[l-1]
@@ -821,14 +821,14 @@ class GaussianParserContext(object):
for k in range(i,dim):
l = l + 1
cartforceconst[i,k] = forcecnstvalues[l-1]
-
+
for i in range(0,dim):
for k in range(i+1,dim):
cartforceconst[i,k] = cartforceconst[k,i]
- cartforceconst = convert_unit(cartforceconst, "forceAu / bohr", "J / (meter**2)")
+ cartforceconst = convert_unit(cartforceconst, "hartree / (bohr ** 2)", "J / (meter**2)")
- backend.addArrayValues("x_gaussian_force_constant_values", cartforceconst)
+ backend.addArrayValues("x_gaussian_force_constant_values", cartforceconst)
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
@@ -844,7 +844,7 @@ class GaussianParserContext(object):
'XA': [{'name': 'X_ALPHA'}],
'VWN': [{'name': 'LDA_C_VWN'}],
'VWN3': [{'name': 'LDA_C_VWN_3'}],
- 'LSDA': [{'name': 'LDA_X'}, {'name': 'LDA_C_VWN'}],
+ 'LSDA': [{'name': 'LDA_X'}, {'name': 'LDA_C_VWN'}],
'B': [{'name': 'GGA_X_B88'}],
'BLYP': [{'name': 'GGA_C_LYP'}, {'name': 'GGA_X_B88'}],
'PBEPBE': [{'name': 'GGA_C_PBE'}, {'name': 'GGA_X_PBE'}],
@@ -877,9 +877,9 @@ class GaussianParserContext(object):
'V5LYP': [{'name': 'GGA_C_V5LYP'}],
'THCTH': [{'name': 'MGGA_XC_TAU_HCTH'}],
'TPSSTPSS': [{'name': 'MGGA_C_TPSS'}, {'name': 'MGGA_X_TPSS'}],
- 'B3LYP': [{'name': 'HYB_GGA_XC_B3LYP'}],
+ 'B3LYP': [{'name': 'HYB_GGA_XC_B3LYP'}],
'B3PW91': [{'name': 'HYB_GGA_XC_B3PW91'}],
- 'B3P86': [{'name': 'HYB_GGA_XC_B3P86'}],
+ 'B3P86': [{'name': 'HYB_GGA_XC_B3P86'}],
'B1B95': [{'name': 'HYB_GGA_XC_B1B95'}],
'MPW1PW91': [{'name': 'HYB_GGA_XC_MPW1PW91'}],
'MPW1LYP': [{'name': 'HYB_GGA_XC_MPW1LYP'}],
@@ -888,7 +888,7 @@ class GaussianParserContext(object):
'B98': [{'name': 'HYB_GGA_XC_B98'}],
'B971': [{'name': 'HYB_GGA_XC_B971'}],
'B972': [{'name': 'HYB_GGA_XC_B972'}],
- 'O3LYP': [{'name': 'HYB_GGA_XC_O3LYP'}],
+ 'O3LYP': [{'name': 'HYB_GGA_XC_O3LYP'}],
'TPSSH': [{'name': 'HYB_GGA_XC_TPSSh'}],
'BMK': [{'name': 'HYB_MGGA_XC_BMK'}],
'X3LYP': [{'name': 'HYB_GGA_XC_X3LYP'}],
@@ -925,7 +925,7 @@ class GaussianParserContext(object):
'MPW2PLYP': [{'name': 'MPW2PLYP'}],
'B2PLYPD': [{'name': 'B2PLYPD'}],
'MPW2PLYPD': [{'name': 'MPW2PLYPD'}],
- 'B97D3': [{'name': 'B97D3'}],
+ 'B97D3': [{'name': 'B97D3'}],
'B2PLYPD3': [{'name': 'B2PLYPD3'}],
'MPW2PLYPD3': [{'name': 'MPW2PLYPD3'}],
'LC-': [{'name': 'LONG-RANGE CORRECTED'}],
@@ -1017,7 +1017,7 @@ class GaussianParserContext(object):
'SV': [{'name': 'SV'}],
'SVP': [{'name': 'SVP'}],
'TZV': [{'name': 'TZV'}],
- 'TZVP': [{'name': 'TZVP'}],
+ 'TZVP': [{'name': 'TZVP'}],
'DEF2SV': [{'name': 'Def2SV'}],
'DEF2SVP': [{'name': 'Def2SVP'}],
'DEF2SVPP': [{'name': 'Def2SVPP'}],
@@ -1031,12 +1031,12 @@ class GaussianParserContext(object):
'MIDIX': [{'name': 'MidiX'}],
'EPR-II': [{'name': 'EPR-II'}],
'EPR-III': [{'name': 'EPR-III'}],
- 'UGBS': [{'name': 'UGBS'}],
+ 'UGBS': [{'name': 'UGBS'}],
'MTSMALL': [{'name': 'MTSmall'}],
'DGDZVP': [{'name': 'DGDZVP'}],
'DGDZVP2': [{'name': 'DGDZVP2'}],
'DGTZVP': [{'name': 'DGTZVP'}],
- 'CBSB3': [{'name': 'CBSB3'}],
+ 'CBSB3': [{'name': 'CBSB3'}],
'CBSB7': [{'name': 'CBSB7'}],
'SHC': [{'name': 'SHC'}],
'SEC': [{'name': 'SHC'}],
@@ -1046,7 +1046,7 @@ class GaussianParserContext(object):
'LANL1': [{'name': 'LANL1'}],
'LANL2': [{'name': 'LANL2'}],
'SDD': [{'name': 'SDD'}],
- 'OLDSDD': [{'name': 'OldSDD'}],
+ 'OLDSDD': [{'name': 'OldSDD'}],
'SDDALL': [{'name': 'SDDAll'}],
'GEN': [{'name': 'General'}],
'GENECP': [{'name': 'General ECP'}],
@@ -1070,7 +1070,7 @@ class GaussianParserContext(object):
methodWrite = False
basissetWrite = False
methodreal = None
- basissetreal = None
+ basissetreal = None
methodprefix = None
exc = None
corr = None
@@ -1088,7 +1088,7 @@ class GaussianParserContext(object):
method1 = settings.replace("['#p ","").replace("['#P ","").replace("['#","")
method1 = method1.upper()
- if 'ONIOM' not in method1:
+ if 'ONIOM' not in method1:
if settings.find("/") >= 0:
method1 = settings.split('/')[0].replace("['#p ","").replace("['#P ","").replace("['#","")
method1 = method1.upper()
@@ -1096,7 +1096,7 @@ class GaussianParserContext(object):
method2 = str(x)
if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF' and method2 != 'UFF':
if (method2[0] == 'R' and method2[0:2] != 'RO') or method2[0] == 'U':
- methodprefix = method2[0]
+ methodprefix = method2[0]
method2 = method2[1:]
elif method2[0:2] == 'RO':
methodprefix = method2[0:2]
@@ -1130,7 +1130,7 @@ class GaussianParserContext(object):
if method2 in xcDict.keys():
xc = method2
xcWrite= True
- methodWrite = True
+ methodWrite = True
method = 'DFT'
if method2 in methodDict.keys():
method = method2
@@ -1152,7 +1152,7 @@ class GaussianParserContext(object):
methodWrite = True
methodreal = method2
rest = settings.split('/')[1].replace("'","").replace("]","")
- rest = rest.upper()
+ rest = rest.upper()
for x in rest.split():
if x in basissetDict.keys():
basisset = x
@@ -1206,7 +1206,7 @@ class GaussianParserContext(object):
if z in basissetDict.keys():
basisset = z
basissetWrite = True
- if (len(rest2.split('/')) == 2):
+ if (len(rest2.split('/')) == 2):
if(basisset is not None):
basissetreal = rest2.split('/')[1] + '/' + basisset
else:
@@ -1215,15 +1215,15 @@ class GaussianParserContext(object):
pass
else:
method1 = settings.split()
- for x in method1:
+ for x in method1:
method2 = str(x)
- method2 = method2.upper()
+ method2 = method2.upper()
if method2 != 'RHF' and method2 != 'UHF' and method2 != 'ROHF' and method2 != 'UFF':
if (method2[0] == 'R' and method2[0:2] != 'RO') or method2[0] == 'U':
- methodprefix = method2[0]
+ methodprefix = method2[0]
method2 = method2[1:]
elif method2[0:2] == 'RO':
- methodprefix = method2[0:2]
+ methodprefix = method2[0:2]
method2 = method2[2:]
if method2[0:2] == 'SV' or method2[0] == 'B' or method2[0] == 'O':
if method2[0] in xcDict.keys() and method2[1:] in xcDict.keys():
@@ -1250,12 +1250,12 @@ class GaussianParserContext(object):
exccorr = method2[3:]
if exccorr in xcDict.keys():
xc = 'LC-' + xcDict.get([exccorr][-1])
- if method2 in xcDict.keys():
+ if method2 in xcDict.keys():
xc = method2
xcWrite= True
method = 'DFT'
if method2 in methodDict.keys():
- method = method2
+ method = method2
methodWrite = True
methodreal = method2
else:
@@ -1300,7 +1300,7 @@ class GaussianParserContext(object):
# special options for ONIOM calculations
else:
- method = 'ONIOM'
+ method = 'ONIOM'
methodWrite = True
method1 = settings.split()
for x in method1:
@@ -1308,7 +1308,7 @@ class GaussianParserContext(object):
method2 = method2.upper()
if 'ONIOM' in method2:
methodreal = method2
-
+
# functionals where hybrid_xc_coeff are written
if xc is not None:
@@ -1415,7 +1415,7 @@ class GaussianParserContext(object):
unit_cell = []
for i in ['x', 'y', 'z']:
uci = str(section['x_gaussian_geometry_lattice_vector_' + i])
- uci = uci.split()
+ uci = uci.split()
for i in range(len(uci)):
uci[i] = str(uci[i]).replace("[","").replace("'","").replace("]","").replace("\"","").replace(",","")
if uci[i] is not None:
@@ -1460,11 +1460,11 @@ cachingLevelForMetaName = {
"x_gaussian_number_of_atoms": CachingLevel.ForwardAndCache,
"section_scf_iteration": CachingLevel.Forward,
"energy_total_scf_iteration": CachingLevel.ForwardAndCache,
- "x_gaussian_delta_energy_total_scf_iteration": CachingLevel.ForwardAndCache,
+ "x_gaussian_delta_energy_total_scf_iteration": CachingLevel.ForwardAndCache,
"energy_total": CachingLevel.ForwardAndCache,
"x_gaussian_energy_error": CachingLevel.ForwardAndCache,
"x_gaussian_electronic_kinetic_energy": CachingLevel.ForwardAndCache,
- "x_gaussian_energy_electrostatic": CachingLevel.ForwardAndCache,
+ "x_gaussian_energy_electrostatic": CachingLevel.ForwardAndCache,
"x_gaussian_section_frequencies": CachingLevel.Forward,
"x_gaussian_frequency_values": CachingLevel.Cache,
"x_gaussian_frequencies": CachingLevel.ForwardAndCache,
@@ -1472,25 +1472,25 @@ cachingLevelForMetaName = {
"x_gaussian_red_masses": CachingLevel.ForwardAndCache,
"x_gaussian_normal_modes": CachingLevel.Cache,
"x_gaussian_normal_mode_values": CachingLevel.ForwardAndCache,
- "x_gaussian_atomic_masses": CachingLevel.ForwardAndCache,
+ "x_gaussian_atomic_masses": CachingLevel.ForwardAndCache,
"x_gaussian_section_force_constant_matrix": CachingLevel.Forward,
"x_gaussian_force_constant_values": CachingLevel.ForwardAndCache,
"x_gaussian_force_constants": CachingLevel.Cache,
"section_eigenvalues": CachingLevel.Forward,
- "eigenvalues_values": CachingLevel.ForwardAndCache,
+ "eigenvalues_values": CachingLevel.ForwardAndCache,
"eigenvalues_occupation": CachingLevel.ForwardAndCache,
"x_gaussian_section_orbital_symmetries": CachingLevel.Forward,
"x_gaussian_alpha_occ_symmetry_values":CachingLevel.Cache,
"x_gaussian_alpha_vir_symmetry_values":CachingLevel.Cache,
"x_gaussian_beta_occ_symmetry_values":CachingLevel.Cache,
- "x_gaussian_beta_vir_symmetry_values":CachingLevel.Cache,
+ "x_gaussian_beta_vir_symmetry_values":CachingLevel.Cache,
"x_gaussian_alpha_symmetries": CachingLevel.ForwardAndCache,
"x_gaussian_beta_symmetries": CachingLevel.ForwardAndCache,
"x_gaussian_section_molecular_multipoles": CachingLevel.Forward,
"dipole_moment_x": CachingLevel.Cache,
"dipole_moment_y": CachingLevel.Cache,
"dipole_moment_z": CachingLevel.Cache,
- "quadrupole_moment_xx": CachingLevel.Cache,
+ "quadrupole_moment_xx": CachingLevel.Cache,
"quadrupole_moment_yy": CachingLevel.Cache,
"quadrupole_moment_zz": CachingLevel.Cache,
"quadrupole_moment_xy": CachingLevel.Cache,
@@ -1520,7 +1520,7 @@ cachingLevelForMetaName = {
"hexadecapole_moment_yyzz": CachingLevel.Cache,
"hexadecapole_moment_xxyz": CachingLevel.Cache,
"hexadecapole_moment_yyxz": CachingLevel.Cache,
- "hexadecapole_moment_zzxy": CachingLevel.Cache,
+ "hexadecapole_moment_zzxy": CachingLevel.Cache,
"x_gaussian_molecular_multipole_values": CachingLevel.ForwardAndCache,
"single_configuration_calculation_converged": CachingLevel.ForwardAndCache,
"x_gaussian_single_configuration_calculation_converged": CachingLevel.ForwardAndCache,
@@ -1531,7 +1531,7 @@ cachingLevelForMetaName = {
"section_method": CachingLevel.Forward,
"x_gaussian_section_elstruc_method": CachingLevel.Forward,
"x_gaussian_electronic_structure_method": CachingLevel.ForwardAndCache,
- "XC_functional_name": CachingLevel.ForwardAndCache,
+ "XC_functional_name": CachingLevel.ForwardAndCache,
"basis_set_atom_centered_short_name": CachingLevel.Forward,
"x_gaussian_settings": CachingLevel.Cache,
"x_gaussian_settings_corrected": CachingLevel.ForwardAndCache,
--
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