Commit d495dc67 authored by Berk Onat's avatar Berk Onat
Browse files

Adding missing meta data for Tinker Parser

parent 846d2b7e
{
"type": "nomad_meta_info_1_0",
"description": "meta info used by the Tinker parser, all names are expected to start with x_tinker_",
"description": "meta info used by the tinker parser, all names are expected to start with x_tinker_",
"dependencies": [ {
"relativePath": "common.nomadmetainfo.json"
}, {
......@@ -327,55 +327,55 @@
"section_run"
]
}, {
"description": "Program version date.",
"dtypeStr": "C",
"name": "x_tinker_output_created_by_user",
"description": "Program task no.",
"name": "x_tinker_parallel_task_nr",
"dtypeStr": "f",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program task no.",
"name": "x_tinker_parallel_task_nr",
"dtypeStr": "f",
"description": "Program Build OS/ARCH",
"name": "x_tinker_build_osarch",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Number of tasks in parallel program (MPI).",
"name": "x_tinker_number_of_tasks",
"dtypeStr": "f",
"description": "Output file creator",
"name": "x_tinker_output_created_by_user",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Number of nodes in parallel program (MPI).",
"name": "x_tinker_number_of_nodes",
"dtypeStr": "f",
"description": "Highest tinker warning level in the run.",
"name": "x_tinker_most_severe_warning_level",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Tinker program module (gmx) version.",
"name": "x_tinker_program_module_version",
"description": "Program Build date",
"name": "x_tinker_program_build_date",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Tinker program license.",
"name": "x_tinker_program_license",
"description": "Program citations",
"name": "x_tinker_program_citation",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Tinker program citations/copyright.",
"description": "Program copyright",
"name": "x_tinker_program_copyright",
"dtypeStr": "C",
"shape": [],
......@@ -383,24 +383,24 @@
"section_run"
]
}, {
"description": "Program OS arch.",
"name": "x_tinker_build_osarch",
"dtypeStr": "C",
"description": "Number of tasks in parallel program (MPI).",
"name": "x_tinker_number_of_tasks",
"dtypeStr": "f",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program warning levels.",
"name": "x_tinker_most_severe_warning_level",
"description": "tinker program module version.",
"name": "x_tinker_program_module_version",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Program built date.",
"name": "x_tinker_program_build_date",
"description": "tinker program license.",
"name": "x_tinker_program_license",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -438,11 +438,12 @@
"repeats": true,
"shape": [],
"superNames": [
"section_run"
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker input topology file.",
"name": "x_tinker_inout_file_topoltpr",
"description": "tinker input topology file.",
"name": "x_tinker_inout_file_structure",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -450,8 +451,8 @@
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker input trajectory file.",
"name": "x_tinker_inout_file_trajtrr",
"description": "tinker output trajectory file.",
"name": "x_tinker_inout_file_trajectory",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -459,8 +460,8 @@
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker input compressed trajectory file.",
"name": "x_tinker_inout_file_trajcompxtc",
"description": "tinker output trajectory file.",
"name": "x_tinker_inout_file_traj_coord",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -468,8 +469,8 @@
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker input coordinates and state file.",
"name": "x_tinker_inout_file_statecpt",
"description": "tinker output file for velocities in the trajectory.",
"name": "x_tinker_inout_file_traj_vel",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -477,8 +478,8 @@
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker output configuration file.",
"name": "x_tinker_inout_file_confoutgro",
"description": "tinker output file for forces in the trajectory.",
"name": "x_tinker_inout_file_traj_force",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -486,8 +487,8 @@
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker output energies file.",
"name": "x_tinker_inout_file_eneredr",
"description": "tinker output coordinates file.",
"name": "x_tinker_inout_file_output_coord",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -495,232 +496,88 @@
"x_tinker_section_input_output_files"
]
}, {
"description": "Parameters of mdin belonging to x_tinker_section_control_parameters.",
"kindStr": "type_abstract_document_content",
"name": "x_tinker_mdin_input_output_files",
"repeats": true,
"superNames": [
"x_tinker_section_input_output_files"
]
}, {
"name": "x_tinker_section_control_parameters",
"kindStr": "type_section",
"description": "Section to store the input and output control parameters",
"repeats": true,
"shape": [],
"superNames": [
"section_run"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_tinker_version",
"description": "tinker output velocities file.",
"name": "x_tinker_inout_file_output_vel",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_precision",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_memory_model",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_mpi_library",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_openmp_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_gpu_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_opencl_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_invsqrt_routine",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_simd_instructions",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_fft_library",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_rdtscp_usage",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_cxx11_compilation",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_tng_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_tracing_support",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_built_on",
"description": "tinker output forces file.",
"name": "x_tinker_inout_file_output_force",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_built_by",
"dtypeStr": "C",
"shape": [],
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_build_osarch",
"description": "tinker input coordinates file.",
"name": "x_tinker_inout_file_input_coord",
"dtypeStr": "C",
"shape": [],
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_build_cpu_vendor",
"description": "tinker input velocities file.",
"name": "x_tinker_inout_file_input_vel",
"dtypeStr": "C",
"shape": [],
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_build_cpu_brand",
"description": "tinker restart coordinates file.",
"name": "x_tinker_inout_file_restart_coord",
"dtypeStr": "C",
"shape": [],
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_build_cpu_family",
"description": "tinker restart velocities file.",
"name": "x_tinker_inout_file_restart_vel",
"dtypeStr": "C",
"shape": [],
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_build_cpu_features",
"description": "tinker MD output log file.",
"name": "x_tinker_inout_file_output_log",
"dtypeStr": "C",
"shape": [],
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"x_tinker_section_input_output_files"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_c_compiler",
"dtypeStr": "C",
"shape": [],
"description": "Parameters of mdin belonging to x_tinker_section_control_parameters.",
"kindStr": "type_abstract_document_content",
"name": "x_tinker_mdin_input_output_files",
"repeats": true,
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_c_compiler_flags",
"dtypeStr": "C",
"shape": [],
"x_tinker_section_input_output_files"
]
}, {
"name": "x_tinker_section_control_parameters",
"kindStr": "type_section",
"description": "Section to store the input and output control parameters",
"repeats": true,
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
"section_run"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_cxx_compiler",
"description": "tinker running environment and control parameters.",
"name": "x_tinker_inout_control_number_of_steps",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -728,8 +585,8 @@
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_cxx_compiler_flags",
"description": "tinker running environment and control parameters.",
"name": "x_tinker_inout_control_steps_per_cycle",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -737,8 +594,8 @@
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_boost_version",
"description": "tinker running environment and control parameters.",
"name": "x_tinker_inout_control_initial_temperature",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -746,8 +603,8 @@
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_integrator",
"description": "tinker running environment and control parameters.",
"name": "x_tinker_inout_control_dielectric",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -755,8 +612,8 @@
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_tinit",
"description": "tinker running environment and control parameters.",
"name": "x_tinker_inout_control_minimization",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -764,8 +621,8 @@
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_dt",
"description": "tinker running environment and control parameters.",
"name": "x_tinker_inout_control_verlet_integrator",
"dtypeStr": "C",
"shape": [],
"superNames": [
......@@ -773,1268 +630,386 @@
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_nsteps",
"dtypeStr": "C",
"shape": [],
"description": "tinker running environment and control parameters.",
"name":"x_tinker_inout_control_topology_type",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_initstep",
"dtypeStr": "C",
"shape": [],
]
}, {
"description": "tinker running environment and control parameters.",
"name":"x_tinker_inout_control_resname",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_simulationpart",
"dtypeStr": "C",
"shape": [],
]
}, {
"description": "tinker running environment and control parameters.",
"name":"x_tinker_inout_control_number_of_atom_types",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_commmode",
"dtypeStr": "C",
"shape": [],
]
}, {
"description": "tinker running environment and control parameters.",
"name":"x_tinker_inout_control_number_of_atoms_solute",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_nstcomm",
"dtypeStr": "C",
"shape": [],
]
}, {
"description": "tinker running environment and control parameters.",
"name":"x_tinker_inout_control_lennard_jones_exceptions",
"dtypeStr": "C",
"shape": [],
"superNames": [
"section_run",
"x_tinker_section_control_parameters"
]
}, {
"description": "Tinker running environment and control parameters.",
"name": "x_tinker_inout_control_bdfric",
"dtypeStr": "C",
"shape": [],