Skip to content

GitLab

Commit 5e6e9864 authored by Berk Onat's avatar Berk Onat
Browse files

CHARMMing meta info for CHARMM parser

parent a6830c42
Hide whitespace changes
Inline Side-by-side
meta_info/nomad_meta_info/all.nomadmetainfo.json
View file @ 5e6e9864
......@@ -27,6 +27,8 @@
"relativePath": "gromacs.nomadmetainfo.json"
}, {
"relativePath": "namd.nomadmetainfo.json"
}, {
"relativePath": "charmm.nomadmetainfo.json"
}, {
"relativePath": "castep.nomadmetainfo.json"
}, {
......
meta_info/nomad_meta_info/charmm.nomadmetainfo.json 0 → 100644
View file @ 5e6e9864
{
"type": "nomad_meta_info_1_0",
"description": "meta info used by the charmm parser, all names are expected to start with x_charmm_",
"dependencies": [ {
"relativePath": "common.nomadmetainfo.json"
}, {
"relativePath": "meta_types.nomadmetainfo.json"
}],
"metaInfos": [ {
"description": "PBC image flag index.",
"dtypeStr": "i",
"name": "x_charmm_atom_positions_image_index",
"shape": [
"number_of_atoms",
3
],
"units": " ",
"superNames": [
"section_system"
]
}, {
"description": "Position of the atoms in a scaled format [0, 1].",
"dtypeStr": "f",
"name": "x_charmm_atom_positions_scaled",
"shape": [
"number_of_atoms",
3
],
"units": " ",
"superNames": [
"section_system"
]
}, {
"description": "Position of the atoms wrapped back to the periodic box.",
"dtypeStr": "f",
"name": "x_charmm_atom_positions_wrapped",
"shape": [
"number_of_atoms",
3
],
"units": "m",
"superNames": [
"section_system"
]
}, {
"description": "Lattice dimensions in a vector. Vector includes [a, b, c] lengths.",
"dtypeStr": "f",
"name": "x_charmm_lattice_lengths",
"repeats": true,
"shape": [
3
],
"superNames": [
"section_system",
"configuration_core"
]
}, {
"description": "Angles of lattice vectors. Vector includes [alpha, beta, gamma] in degrees.",
"dtypeStr": "f",
"name": "x_charmm_lattice_angles",
"repeats": true,
"shape": [
3
],
"superNames": [
"section_system",
"configuration_core"
]
}, {
"description": "MD barostat target pressure.",
"dtypeStr": "f",
"name": "x_charmm_barostat_target_pressure",
"shape": [],
"units": "Pa",
"superNames": [
"settings_barostat"
]
}, {
"description": "MD barostat relaxation time.",
"dtypeStr": "f",
"name": "x_charmm_barostat_tau",
"shape": [],
"units": "s",
"superNames": [
"settings_barostat"
]
}, {
"description": "MD barostat type, valid values are defined in the barostat_type wiki page.",
"dtypeStr": "C",
"name": "x_charmm_barostat_type",
"shape": [],
"superNames": [
"settings_barostat"
]
}, {
"description": "MD integration time step.",
"dtypeStr": "f",
"name": "x_charmm_integrator_dt",
"shape": [],
"units": "s",
"superNames": [
"settings_integrator"
]
}, {
"description": "MD integrator type, valid values are defined in the integrator_type wiki page.",
"dtypeStr": "C",
"name": "x_charmm_integrator_type",
"shape": [],
"superNames": [
"settings_integrator"
]
}, {
"description": "Periodic boundary condition type in the sampling (non-PBC or PBC).",
"dtypeStr": "C",
"name": "x_charmm_periodicity_type",
"shape": [],
"superNames": [
"settings_integrator"
]
}, {
"description": "Atom name of an atom in topology definition.",
"name": "x_charmm_atom_name",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Atom type of an atom in topology definition.",
"name": "x_charmm_atom_type",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Atom type of an atom in topology definition.",
"name": "x_charmm_atom_element",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Element symbol of an atom type.",
"dtypeStr": "C",
"name": "x_charmm_atom_type_element",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "van der Waals radius of an atom type.",
"dtypeStr": "f",
"name": "x_charmm_atom_type_radius",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Reference to the atom type of each interaction atoms.",
"dtypeStr": "r",
"name": "x_charmm_interaction_atom_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": ["number_of_atoms_per_interaction"],
"superNames": [
"section_interaction"
]
}, {
"description": "Number of atoms involved in this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_type",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Reference to the atoms of each atom type.",
"dtypeStr": "r",
"name": "x_charmm_atom_to_atom_type_ref",
"referencedSections": [
"section_atom_type",
"x_charmm_section_atom_to_atom_type_ref"
],
"shape": ["number_of_atoms_per_type"],
"superNames": [
"section_topology",
"x_charmm_section_atom_to_atom_type_ref"
]
}, {
"description": "Langevin thermostat damping factor.",
"dtypeStr": "f",
"name": "x_charmm_langevin_gamma",
"shape": [],
"units": "s",
"superNames": [
"settings_thermostat"
]
}, {
"description": "Reference to the atom type of each molecule interaction atoms.",
"dtypeStr": "r",
"name": "x_charmm_molecule_interaction_atom_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": ["number_of_atoms_per_interaction"],
"superNames": [
"section_molecule_interaction"
]
}, {
"description": "Number of defined pair interactions within a molecule (L-J pairs).",
"dtypeStr": "i",
"name": "x_charmm_number_of_defined_molecule_pair_interactions",
"shape": [],
"superNames": [
"section_molecule_interaction"
]
}, {
"description": "Number of defined pair interactions (L-J pairs).",
"dtypeStr": "i",
"name": "x_charmm_number_of_defined_pair_interactions",
"shape": [],
"superNames": [
"section_interaction"
]
}, {
"description": "Number of requested MD integration time steps.",
"dtypeStr": "f",
"name": "x_charmm_number_of_steps_requested",
"shape": [],
"superNames": [
"settings_integrator"
]
}, {
"description": "Reference to the atom type for pair interactions.",
"dtypeStr": "r",
"name": "x_charmm_pair_interaction_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [
"x_charmm_number_of_defined_pair_interactions",
"number_of_atoms_per_interaction"
],
"superNames": [
"section_interaction"
]
}, {
"description": "Pair interactions parameters.",
"dtypeStr": "f",
"name": "x_charmm_pair_interaction_parameters",
"shape": [
"x_charmm_number_of_defined_pair_interactions",
2
],
"superNames": [
"section_interaction"
]
}, {
"description": "Molecule pair interactions parameters.",
"dtypeStr": "f",
"name": "x_charmm_pair_molecule_interaction_parameters",
"shape": [
"number_of_defined_molecule_pair_interactions",
2
],
"superNames": [
"section_molecule_interaction"
]
}, {
"description": "Reference to the atom type for pair interactions within a molecule.",
"dtypeStr": "r",
"name": "x_charmm_pair_molecule_interaction_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [
"x_charmm_number_of_defined_pair_interactions",
"number_of_atoms_per_interaction"
],
"superNames": [
"section_molecule_interaction"
]
}, {
"description": "MD thermostat level (see wiki: single, multiple, regional).",
"dtypeStr": "C",
"name": "x_charmm_thermostat_level",
"shape": [],
"superNames": [
"settings_thermostat"
]
}, {
"description": "MD thermostat target temperature.",
"dtypeStr": "f",
"name": "x_charmm_thermostat_target_temperature",
"shape": [],
"units": "K",
"superNames": [
"settings_thermostat"
]
}, {
"description": "MD thermostat relaxation time.",
"dtypeStr": "f",
"name": "x_charmm_thermostat_tau",
"shape": [],
"units": "s",
"superNames": [
"settings_thermostat"
]
}, {
"description": "MD thermostat type, valid values are defined in the thermostat_type wiki page.",
"dtypeStr": "C",
"name": "x_charmm_thermostat_type",
"shape": [],
"superNames": [
"settings_thermostat"
]
}, {
"description": "Program version date.",
"dtypeStr": "C",
"name": "x_charmm_program_version_date",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program task no.",
"name": "x_charmm_parallel_task_nr",
"dtypeStr": "f",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program Build OS/ARCH",
"name": "x_charmm_build_osarch",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Output file creator",
"name": "x_charmm_output_created_by_user",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Highest charmm warning level in the run.",
"name": "x_charmm_most_severe_warning_level",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program Build date",
"name": "x_charmm_program_build_date",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program citations",
"name": "x_charmm_program_citation",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program copyright",
"name": "x_charmm_program_copyright",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Number of tasks in parallel program (MPI).",
"name": "x_charmm_number_of_tasks",
"dtypeStr": "f",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "charmm program module version.",
"name": "x_charmm_program_module_version",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "charmm program license.",
"name": "x_charmm_program_license",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description":"test",
"name": "x_charmm_xlo_xhi",
"superNames": [
"section_run"
],
"dtypeStr": "C",
"shape": []
}, {
"description":"Filename of data file",
"name": "x_charmm_data_file_store",
"superNames": [
"section_run"
],
"dtypeStr": "C",
"shape": []
}, {
"description":"dummy",
"name": "x_charmm_dummy",
"superNames": [
"section_system",
"section_run"
],
"dtypeStr": "C",
"shape": []
}, {
"name": "x_charmm_section_input_output_files",
"kindStr": "type_section",
"description": "Section to store input and output file names",
"repeats": true,
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_control_parameters"
]
}, {
"description": "charmm input topology file.",
"name": "x_charmm_inout_file_structure",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output trajectory file.",
"name": "x_charmm_inout_file_trajectory",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output trajectory file.",
"name": "x_charmm_inout_file_traj_coord",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output file for velocities in the trajectory.",
"name": "x_charmm_inout_file_traj_vel",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output file for forces in the trajectory.",
"name": "x_charmm_inout_file_traj_force",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output coordinates file.",
"name": "x_charmm_inout_file_output_coord",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output coordinates on log.",
"name": "x_charmm_inout_file_out_coor_str",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output velocities file.",
"name": "x_charmm_inout_file_output_vel",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm output forces file.",
"name": "x_charmm_inout_file_output_force",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm input coordinates file.",
"name": "x_charmm_inout_file_input_coord",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm input coordinate on log file.",
"name": "x_charmm_inout_file_in_coor_str",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm input velocities file.",
"name": "x_charmm_inout_file_input_vel",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm restart coordinates file.",
"name": "x_charmm_inout_file_restart_coord",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm restart velocities file.",
"name": "x_charmm_inout_file_restart_vel",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm RTF residue file.",
"name": "x_charmm_inout_file_rtf_file",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm PRM parameter file.",
"name": "x_charmm_inout_file_prm_file",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_charmm_section_input_output_files"
]
}, {
"description": "charmm CRD coordinates file.",
"name": "x_charmm_inout_file_cor_file",
"dtypeStr": "C",