diff --git a/meta_info/nomad_meta_info/all.nomadmetainfo.json b/meta_info/nomad_meta_info/all.nomadmetainfo.json index c5cfdd42f021fe1c38225cef1dff6330811c8121..32222d68950e4cc86f34ce93124b053f6b58a627 100644 --- a/meta_info/nomad_meta_info/all.nomadmetainfo.json +++ b/meta_info/nomad_meta_info/all.nomadmetainfo.json @@ -27,6 +27,8 @@ "relativePath": "gromacs.nomadmetainfo.json" }, { "relativePath": "namd.nomadmetainfo.json" + }, { + "relativePath": "charmm.nomadmetainfo.json" }, { "relativePath": "castep.nomadmetainfo.json" }, { diff --git a/meta_info/nomad_meta_info/charmm.nomadmetainfo.json b/meta_info/nomad_meta_info/charmm.nomadmetainfo.json new file mode 100644 index 0000000000000000000000000000000000000000..c9757df008abaf27b5983afa582ae4791225b5f3 --- /dev/null +++ b/meta_info/nomad_meta_info/charmm.nomadmetainfo.json @@ -0,0 +1,2673 @@ +{ + "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", + 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"name": "x_charmm_inout_control_langevin_oscillation_period", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_langevin_decay_time", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_langevin_piston_temperature", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_pressure_control", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_particle_mesh_ewald", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_pme_tolerance", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_pme_ewald_coefficient", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_pme_interpolation_order", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_pme_grid_dimensions", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_pme_maximum_grid_spacing", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_minimization", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_verlet_integrator", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_random_number_seed", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_structure_file", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_parameter_file", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_number_of_parameters", + "dtypeStr": "i", + "shape": [], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "description": "charmm running environment and control parameters.", + "name": "x_charmm_inout_control_parameters", + "dtypeStr": "C", + "shape": [ + "x_charmm_inout_control_number_of_parameters" + ], + "superNames": [ + "section_run", + "x_charmm_section_control_parameters" + ] + }, { + "name": "x_charmm_section_atom_to_atom_type_ref", + "kindStr": "type_section", + "description": "Section to store atom label to atom type definition list", + "repeats": true, + "shape": [], + "superNames": [ + "section_topology" + ] + }, { + "description": "Parameters of mdin belonging to x_charmm_section_control_parameters.", + "kindStr": "type_abstract_document_content", + "name": "x_charmm_mdin_control_parameters", + "repeats": true, + "superNames": [ + "x_charmm_section_control_parameters" + ] + }, { + "description":"finline in mdin", + "name": "x_charmm_mdin_finline", + "superNames": [ + "section_system", + "section_run" + ], + "dtypeStr": "C", + "shape": [] + }, { + "name": "x_charmm_input_units_store", + "description": "It determines the units of all quantities specified in the input script and data file, as well as quantities output to the screen, log file, and dump files.", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_data_bond_types_store", + "description": "store temporarly", + "superNames": ["section_topology"], + "dtypeStr": "i", + "shape": [] + }, + { + "name": "x_charmm_data_bond_count_store", + "description": "store temporarly", + "superNames": ["section_topology"], + "dtypeStr": "i", + "shape": [] + }, + { + "name": "x_charmm_data_angle_count_store", + "description": "store temporarly", + "superNames": ["section_topology"], + "dtypeStr": "i", + "shape": [] + }, + { + "name": "x_charmm_data_atom_types_store", + "description": "store temporarly", + "superNames": ["section_topology"], + "dtypeStr": "i", + "shape": [] + }, + { + "name": "x_charmm_data_dihedral_count_store", + "description": "store temporarly", + "superNames": ["section_topology"], + "dtypeStr": "i", + "shape": [] + }, + { + "name": "x_charmm_data_angles_store", + "description": "store temporarly", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_data_angle_list_store", + "description": "tmp", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_data_bond_list_store", + "description": "tmp", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_data_dihedral_list_store", + "description": "tmp", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_data_dihedral_coeff_list_store", + "description": "tmp", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_masses_store", + "description": "tmp", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_data_topo_list_store", + "description": "tmp", + "superNames": ["section_topology"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_traj_timestep_store", + "description": "tmp", + "superNames": ["section_system"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_traj_number_of_atoms_store", + "description": "tmp", + "superNames": ["section_system"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_traj_box_bound_store", + "description": "tmp", + "superNames": ["section_system"], + "dtypeStr": "C", + "shape": [] + }, { + "name": "x_charmm_traj_box_bounds_store", + "description": "tmp", + "superNames": ["section_system"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_traj_variables_store", + "description": "tmp", + "superNames": ["section_system"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_traj_atoms_store", + "description": "tmp", + "superNames": ["section_system"], + "dtypeStr": "C", + "shape": [] + }, + { + "name": "x_charmm_program_working_path", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_program_execution_host", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_program_execution_path", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_program_module", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_program_execution_date", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_program_execution_time", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_mdin_header", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, + { + "name": "x_charmm_mdin_wt", + "description": "tmp", + "dtypeStr": "C", + "shape": [], + "superNames": [ + "section_run" + ] + }, { + "description": "Gives the number of volumes in this sequence of frames, see x_charmm_frame_sequence_volume.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_volumes_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of densities in this sequence of frames, see x_charmm_frame_sequence_density.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_densities_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of bond_energies in this sequence of frames, see x_charmm_frame_sequence_bond_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_bond_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of bond_energies in this sequence of frames, see x_charmm_frame_sequence_urey_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_urey_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of bond_energies in this sequence of frames, see x_charmm_frame_sequence_high_frequency_correction_total_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_high_frequency_correction_total_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of bond_energies in this sequence of frames, see x_charmm_frame_sequence_high_frequency_correction_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_high_frequency_correction_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of bond_energies in this sequence of frames, see x_charmm_frame_sequence_high_frequency_correction_kinetic_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_high_frequency_correction_kinetic_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of bond_energies in this sequence of frames, see x_charmm_frame_sequence_virial_kinetic_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_virial_kinetic_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of angle_energies in this sequence of frames, see x_charmm_frame_sequence_angle_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_angle_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of proper_dihedral_energies in this sequence of frames, see x_charmm_frame_sequence_proper_dihedral_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_proper_dihedral_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of improper_dihedral_energies in this sequence of frames, see x_charmm_frame_sequence_improper_dihedral_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_improper_dihedral_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of cmap_dihedral_energies in this sequence of frames, see x_charmm_frame_sequence_cmap_dihedral_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_cmap_dihedral_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of vdw_energies in this sequence of frames, see x_charmm_frame_sequence_vdw_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_vdw_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of boundary_energies in this sequence of frames, see x_charmm_frame_sequence_boundary_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_boundary_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of electrostatic_energies in this sequence of frames, see x_charmm_frame_sequence_electrostatic_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_electrostatic_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of total_energies in this sequence of frames, see x_charmm_frame_sequence_total_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_total_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of total_kinetic_energies in this sequence of frames, see x_charmm_frame_sequence_total_kinetic_energy_frames.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_total_kinetic_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Gives the number of misc_energies in this sequence of frames, see x_charmm_frame_sequence_misc_energy.", + "dtypeStr": "i", + "kindStr": "type_dimension", + "name": "x_charmm_number_of_misc_energies_in_sequence", + "shape": [], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_densities values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_density_frames", + "shape": [ + "x_charmm_number_of_densities_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the density along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_density_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_density", + "shape": [ + "x_charmm_number_of_densities_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_cmap_dihedral_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_cmap_dihedral_energy_frames", + "shape": [ + "x_charmm_number_of_cmap_dihedral_energy_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the cmap_dihedral_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_cmap_dihedral_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_cmap_dihedral_energy", + "shape": [ + "x_charmm_number_of_cmap_dihedral_energy_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_improper_dihedral_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_improper_dihedral_energy_frames", + "shape": [ + "x_charmm_number_of_improper_dihedral_energy_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the improper_dihedral_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_improper_dihedral_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_improper_dihedral_energy", + "shape": [ + "x_charmm_number_of_improper_dihedral_energy_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_proper_dihedral_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_proper_dihedral_energy_frames", + "shape": [ + "x_charmm_number_of_proper_dihedral_energy_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the proper_dihedral_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_proper_dihedral_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_proper_dihedral_energy", + "shape": [ + "x_charmm_number_of_proper_dihedral_energy_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_bond_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_bond_energy_frames", + "shape": [ + "x_charmm_number_of_bond_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_urey_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_urey_energy_frames", + "shape": [ + "x_charmm_number_of_urey_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_high_frequency_correction_total_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_high_frequency_correction_total_energy_frames", + "shape": [ + "x_charmm_number_of_high_frequency_correction_total_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_high_frequency_correction_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_high_frequency_correction_energy_frames", + "shape": [ + "x_charmm_number_of_high_frequency_correction_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_high_frequency_correction_kinetic_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_high_frequency_correction_kinetic_energy_frames", + "shape": [ + "x_charmm_number_of_high_frequency_correction_kinetic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_virial_kinetic_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_virial_kinetic_energy_frames", + "shape": [ + "x_charmm_number_of_virial_kinetic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the bond_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_bond_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_bond_energy", + "shape": [ + "x_charmm_number_of_bond_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the urey_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_urey_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_urey_energy", + "shape": [ + "x_charmm_number_of_urey_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the high_frequency_correction_total_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_high_frequency_correction_total_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_high_frequency_correction_total_energy", + "shape": [ + "x_charmm_number_of_high_frequency_correction_total_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the high_frequency_correction_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_high_frequency_correction_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_high_frequency_correction_energy", + "shape": [ + "x_charmm_number_of_high_frequency_correction_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the high_frequency_correction_kinetic_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_high_frequency_correction_kinetic_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_high_frequency_correction_kinetic_energy", + "shape": [ + "x_charmm_number_of_high_frequency_correction_kinetic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the virial_kinetic_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_virial_kinetic_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_virial_kinetic_energy", + "shape": [ + "x_charmm_number_of_virial_kinetic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_boundary values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_boundary_frames", + "shape": [ + "x_charmm_number_of_boundary_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the boundary along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_boundary_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_boundary", + "shape": [ + "x_charmm_number_of_boundary_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_angle_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_angle_energy_frames", + "shape": [ + "x_charmm_number_of_angle_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the angle_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_angle_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_angle_energy", + "shape": [ + "x_charmm_number_of_angle_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_vdw_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_vdw_energy_frames", + "shape": [ + "x_charmm_number_of_vdw_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the vdw_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_vdw_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_vdw_energy", + "shape": [ + "x_charmm_number_of_vdw_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_electrostatic_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_electrostatic_energy_frames", + "shape": [ + "x_charmm_number_of_electrostatic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the electrostatic_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_electrostatic_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_electrostatic_energy", + "shape": [ + "x_charmm_number_of_electrostatic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_total_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_total_energy_frames", + "shape": [ + "x_charmm_number_of_total_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the total_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_total_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_total_energy", + "shape": [ + "x_charmm_number_of_total_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_total_kinetic_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_total_kinetic_energy_frames", + "shape": [ + "x_charmm_number_of_total_kinetic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the total_kinetic_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_total_kinetic_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_total_kinetic_energy", + "shape": [ + "x_charmm_number_of_total_kinetic_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_misc_energy values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_misc_energy_frames", + "shape": [ + "x_charmm_number_of_misc_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the misc_energy along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_misc_energy_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_misc_energy", + "shape": [ + "x_charmm_number_of_misc_energies_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the strictly increasing indices of the frames the x_charmm_frame_sequence_volume values refers to. If not given it defaults to the trivial mapping 0,1,...", + "dtypeStr": "i", + "name": "x_charmm_frame_sequence_volume_frames", + "shape": [ + "x_charmm_number_of_volumes_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Array containing the values of the volume along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_volume_frames.", + "dtypeStr": "f", + "name": "x_charmm_frame_sequence_volume", + "shape": [ + "x_charmm_number_of_volumes_in_sequence" + ], + "superNames": [ + "section_frame_sequence" + ] + }, { + "description": "Parameters of mdin belonging to section method.", + "kindStr": "type_abstract_document_content", + "name": "x_charmm_mdin_method", + "superNames": [ + "section_run" + ] + }, { + "description": "section for gathering values for MD steps", + "kindStr": "type_section", + "name": "x_charmm_section_single_configuration_calculation", + "repeats": true, + "superNames": [ + "section_single_configuration_calculation" + ] + }, { + "description": "Parameters of mdout belonging to section_single_configuration_calculation.", + "kindStr": "type_abstract_document_content", + "name": "x_charmm_mdout_single_configuration_calculation", + "repeats": true, + "superNames": [ + "x_charmm_section_single_configuration_calculation" + ] + }, { + "description": "Parameters of mdin belonging to section method.", + "kindStr": "type_abstract_document_content", + "name": "x_charmm_mdout_method", + "superNames": [ + "section_run" + ] + }, { + "description": "Parameters of mdin belonging to settings run.", + "kindStr": "type_abstract_document_content", + "name": "x_charmm_mdout_run", + "superNames": [ + "settings_run" + ] + }, { + "description": "Parameters of mdin belonging to settings run.", + "kindStr": "type_abstract_document_content", + "name": "x_charmm_mdin_run", + "superNames": [ + "settings_run" + ] + } + ] +}