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nomad-lab
nomad-meta-info
Commits
5e6e9864
Commit
5e6e9864
authored
Mar 13, 2018
by
Berk Onat
Browse files
CHARMMing meta info for CHARMM parser
parent
a6830c42
Changes
2
Pipelines
1
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."
,