Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
nomad-lab
parser-orca
Commits
7fda44f1
Commit
7fda44f1
authored
Nov 15, 2016
by
Alarcon Villaseca, Sebastian (sebas81)
Browse files
Check sections and fix indentation errors
parent
51b8c4e2
Changes
1
Hide whitespace changes
Inline
Side-by-side
parser/parser-orca/orca_parser.py
View file @
7fda44f1
...
...
@@ -269,35 +269,35 @@ def buildSinglePointSubMatchers():
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
=
'Total Energy'
,
startReStr
=
r
"\s*TOTAL SCF ENERGY\s*"
,
sections
=
[],
subMatchers
=
[
SM
(
r
"\s*Total Energy\s+:\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)"
),
# Energy Components:
SM
(
name
=
'Energy Components'
,
startReStr
=
r
"\s*Components:\s*"
,
sections
=
[
"section_single_configuration_calculation"
],
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
=
'Total Energy'
,
startReStr
=
r
"\s*TOTAL SCF ENERGY\s*"
,
sections
=
[],
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]+)"
)
SM
(
r
"\s*Total Energy\s+:\s+(?P<energy_total__hartree>[-+0-9.eEdD]+)"
),
# Energy Components:
SM
(
name
=
'Energy Components'
,
startReStr
=
r
"\s*Components:\s*"
,
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:
...
...
@@ -306,29 +306,29 @@ def buildSinglePointSubMatchers():
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:
# Orbitals Energies
and Mulliken population analysis
:
SM
(
name
=
'Orbital Energies'
,
startReStr
=
r
"\s*ORBITAL ENERGIES\s*"
,
sections
=
[
"section_dos"
],
sections
=
[
"section_single_configuration_calculation"
,
"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
)
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
=
[],
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>[-+0-9.eEdD]+)"
,
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
)
]
)
]
),
# 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>[-+0-9.eEdD]+)"
,
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
)
]
),
# Time table:
SM
(
name
=
'timings'
,
startReStr
=
r
"\s*TIMINGS\s*"
,
sections
=
[
"section_scf_iteration"
],
sections
=
[
"section_single_configuration_calculation"
,
"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"
),
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment