Commit f566fa36 authored by Berk Onat's avatar Berk Onat
Browse files

Added meta info for NAMD parser

parent 374107c0
......@@ -23,6 +23,10 @@
"relativePath": "lammps.nomadmetainfo.json"
}, {
"relativePath": "amber.nomadmetainfo.json"
}, {
"relativePath": "gromacs.nomadmetainfo.json"
}, {
"relativePath": "namd.nomadmetainfo.json"
}, {
"relativePath": "castep.nomadmetainfo.json"
}, {
......
{
"type": "nomad_meta_info_1_0",
"description": "meta info used by the NAMD parser, all names are expected to start with x_namd_",
"dependencies": [ {
"relativePath": "common.nomadmetainfo.json"
}, {
"relativePath": "meta_types.nomadmetainfo.json"
}],
"metaInfos": [ {
"description": "PBC image flag index.",
"dtypeStr": "i",
"name": "x_namd_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_namd_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_namd_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_namd_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_namd_lattice_angles",
"repeats": true,
"shape": [
3
],
"superNames": [
"section_system",
"configuration_core"
]
}, {
"description": "MD barostat target pressure.",
"dtypeStr": "f",
"name": "x_namd_barostat_target_pressure",
"shape": [],
"units": "Pa",
"superNames": [
"settings_barostat"
]
}, {
"description": "MD barostat relaxation time.",
"dtypeStr": "f",
"name": "x_namd_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_namd_barostat_type",
"shape": [],
"superNames": [
"settings_barostat"
]
}, {
"description": "MD integration time step.",
"dtypeStr": "f",
"name": "x_namd_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_namd_integrator_type",
"shape": [],
"superNames": [
"settings_integrator"
]
}, {
"description": "Periodic boundary condition type in the sampling (non-PBC or PBC).",
"dtypeStr": "C",
"name": "x_namd_periodicity_type",
"shape": [],
"superNames": [
"settings_integrator"
]
}, {
"description": "Atom name of an atom in topology definition.",
"name": "x_namd_atom_name",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Atom type of an atom in topology definition.",
"name": "x_namd_atom_type",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Atom type of an atom in topology definition.",
"name": "x_namd_atom_element",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Element symbol of an atom type.",
"dtypeStr": "C",
"name": "x_namd_atom_type_element",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "van der Waals radius of an atom type.",
"dtypeStr": "f",
"name": "x_namd_atom_type_radius",
"shape": [],
"superNames": [
"section_atom_type"
]
}, {
"description": "Reference to the atom type of each interaction atoms.",
"dtypeStr": "r",
"name": "x_namd_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_namd_atom_to_atom_type_ref",
"referencedSections": [
"section_atom_type",
"x_namd_section_atom_to_atom_type_ref"
],
"shape": ["number_of_atoms_per_type"],
"superNames": [
"section_topology",
"x_namd_section_atom_to_atom_type_ref"
]
}, {
"description": "Langevin thermostat damping factor.",
"dtypeStr": "f",
"name": "x_namd_langevin_gamma",
"shape": [],
"units": "s",
"superNames": [
"settings_thermostat"
]
}, {
"description": "Reference to the atom type of each molecule interaction atoms.",
"dtypeStr": "r",
"name": "x_namd_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_namd_number_of_defined_molecule_pair_interactions",
"shape": [],
"superNames": [
"section_molecule_interaction"
]
}, {
"description": "Number of defined pair interactions (L-J pairs).",
"dtypeStr": "i",
"name": "x_namd_number_of_defined_pair_interactions",
"shape": [],
"superNames": [
"section_interaction"
]
}, {
"description": "Number of requested MD integration time steps.",
"dtypeStr": "f",
"name": "x_namd_number_of_steps_requested",
"shape": [],
"superNames": [
"settings_integrator"
]
}, {
"description": "Reference to the atom type for pair interactions.",
"dtypeStr": "r",
"name": "x_namd_pair_interaction_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [
"x_namd_number_of_defined_pair_interactions",
"number_of_atoms_per_interaction"
],
"superNames": [
"section_interaction"
]
}, {
"description": "Pair interactions parameters.",
"dtypeStr": "f",
"name": "x_namd_pair_interaction_parameters",
"shape": [
"x_namd_number_of_defined_pair_interactions",
2
],
"superNames": [
"section_interaction"
]
}, {
"description": "Molecule pair interactions parameters.",
"dtypeStr": "f",
"name": "x_namd_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_namd_pair_molecule_interaction_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [
"x_namd_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_namd_thermostat_level",
"shape": [],
"superNames": [
"settings_thermostat"
]
}, {
"description": "MD thermostat target temperature.",
"dtypeStr": "f",
"name": "x_namd_thermostat_target_temperature",
"shape": [],
"units": "K",
"superNames": [
"settings_thermostat"
]
}, {
"description": "MD thermostat relaxation time.",
"dtypeStr": "f",
"name": "x_namd_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_namd_thermostat_type",
"shape": [],
"superNames": [
"settings_thermostat"
]
}, {
"description": "Program version date.",
"dtypeStr": "C",
"name": "x_namd_program_version_date",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program task no.",
"name": "x_namd_parallel_task_nr",
"dtypeStr": "f",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Number of tasks in parallel program (MPI).",
"name": "x_namd_number_of_tasks",
"dtypeStr": "f",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "NAMD program module (gmx) version.",
"name": "x_namd_program_module_version",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "NAMD program license.",
"name": "x_namd_program_license",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description":"test",
"name": "x_namd_xlo_xhi",
"superNames": [
"section_run"
],
"dtypeStr": "C",
"shape": []
}, {
"description":"Filename of data file",
"name": "x_namd_data_file_store",
"superNames": [
"section_run"
],
"dtypeStr": "C",
"shape": []
}, {
"description":"dummy",
"name": "x_namd_dummy",
"superNames": [
"section_system",
"section_run"
],
"dtypeStr": "C",
"shape": []
}, {
"name": "x_namd_section_input_output_files",
"kindStr": "type_section",
"description": "Section to store input and output file names",
"repeats": true,
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "NAMD input topology file.",
"name": "x_namd_inout_file_topoltpr",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_input_output_files"
]
}, {
"description": "NAMD input trajectory file.",
"name": "x_namd_inout_file_trajtrr",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_input_output_files"
]
}, {
"description": "NAMD input compressed trajectory file.",
"name": "x_namd_inout_file_trajcompxtc",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_input_output_files"
]
}, {
"description": "NAMD input coordinates and state file.",
"name": "x_namd_inout_file_statecpt",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_input_output_files"
]
}, {
"description": "NAMD output configuration file.",
"name": "x_namd_inout_file_confoutgro",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_input_output_files"
]
}, {
"description": "NAMD output energies file.",
"name": "x_namd_inout_file_eneredr",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_input_output_files"
]
}, {
"description": "Parameters of mdin belonging to x_namd_section_control_parameters.",
"kindStr": "type_abstract_document_content",
"name": "x_namd_mdin_input_output_files",
"repeats": true,
"superNames": [
"x_namd_section_input_output_files"
]
}, {
"name": "x_namd_section_control_parameters",
"kindStr": "type_section",
"description": "Section to store the input and output control parameters",
"repeats": true,
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_namd_version",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_precision",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_memory_model",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_mpi_library",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_openmp_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_gpu_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_opencl_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_invsqrt_routine",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_simd_instructions",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_fft_library",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_rdtscp_usage",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_cxx11_compilation",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_tng_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_namd_section_control_parameters"
]
}, {
"description": "NAMD running environment and control parameters.",
"name": "x_namd_inout_control_tracing_support",
"dtypeStr": "C",
"shape": [],
"superNames": [