Commit 0f78e215 authored by Adam Fekete's avatar Adam Fekete Committed by Mohamed, Fawzi Roberto (fawzi)
Browse files

rearranging the modifications

parent c464c884
......@@ -4806,31 +4806,43 @@
]
},
{
"description": "(deprecated) Reference to the method used for the calculation in section_single_configuration_calculation.",
"description": "(deprecated) Reference from each frame (a frame is one section_single_configuration_calculation) in this section_frame_sequence to the corresponding section_single_configuration_calculation. Each section_frame_sequence binds a collection of section_single_configuration_calculation, because they all belong to, e.g., a molecular dynamics trajectory, or geometry optimization. The full information for each frame is stored in section_single_configuration_calculation and this metadata establishes the link for each frame.",
"dtypeStr": "r",
"name": "single_configuration_to_calculation_method_ref",
"name": "frame_sequence_local_frames_ref",
"referencedSections": [
"section_method"
"section_single_configuration_calculation"
],
"shape": [
"number_of_frames_in_sequence"
],
"shape": [],
"superNames": [
"section_single_configuration_calculation"
"section_frame_sequence"
]
},
{
"description": "(deprecated) Reference from each frame (a frame is one section_single_configuration_calculation) in this section_frame_sequence to the corresponding section_single_configuration_calculation. Each section_frame_sequence binds a collection of section_single_configuration_calculation, because they all belong to, e.g., a molecular dynamics trajectory, or geometry optimization. The full information for each frame is stored in section_single_configuration_calculation and this metadata establishes the link for each frame.",
"description": "(deprecated) Reference from the present section_frame_sequence to the section_sampling_method, that defines the parameters used in this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation).",
"dtypeStr": "r",
"name": "frame_sequence_local_frames_ref",
"name": "frame_sequence_to_sampling_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"shape": [
"number_of_frames_in_sequence"
"section_sampling_method"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "(deprecated) Reference to the method used for the calculation in section_single_configuration_calculation.",
"dtypeStr": "r",
"name": "single_configuration_to_calculation_method_ref",
"referencedSections": [
"section_method"
],
"shape": [],
"superNames": [
"section_single_configuration_calculation"
]
},
{
"description": "(deprecated) Array containing the values of the 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_kinetic_energy_frames.",
"dtypeStr": "f",
......@@ -4902,18 +4914,6 @@
"section_system"
]
},
{
"description": "(deprecated) Reference from the present section_frame_sequence to the section_sampling_method, that defines the parameters used in this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation).",
"dtypeStr": "r",
"name": "frame_sequence_to_sampling_ref",
"referencedSections": [
"section_sampling_method"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "(deprecated) Section collecting some user-defined quantities evaluated along a sequence of frame.",
"kindStr": "type_section",
......@@ -4944,7 +4944,6 @@
]
},
{
"derived": true,
"description": "(deprecated) Average of frame_sequence_user_quantity and its standard deviation in this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation).",
"dtypeStr": "f",
"name": "frame_sequence_user_quantity_stats",
......@@ -4987,144 +4986,6 @@
"section_frame_sequence_user_quantity"
]
},
{
"description": "Type of continuation that has been performed from the previous sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation), upon restart.",
"dtypeStr": "C",
"name": "frame_sequence_continuation_kind",
"referencedSections": [
"section_frame_sequence"
],
"shape": [],
"superNames": [
"section_frame_sequence"
],
"values": {
"all": "Restart everything, including, e.g., thermostats, etc.",
"pos": "Position of atom and cell only",
"pos_vel": "Restart atom positions, cells and velocities"
}
},
{
"description": "If the energy, forces, and other quantities for the frames (a frame is one section_single_configuration_calculation) in section_frame_sequence are obtained by calling a different code than the code that drives the sequence (e.g., a wrapper that drives a molecular dynamics, Monte Carlo, geometry optimization and calls an electronic-structure code for energy and forces for each configuration), this metadata holds the reference to where the section_single_configuration_calculation for each frame are located. The format for this reference is described in the [frame_sequence_external_url wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/frame-sequence-external-url).",
"dtypeStr": "C",
"name": "frame_sequence_external_url",
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "Time along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). Time start is arbitrary, but when a sequence is a continuation of another time should be continued too.",
"dtypeStr": "f",
"name": "frame_sequence_time",
"shape": [
"number_of_frames_in_sequence"
],
"superNames": [
"section_frame_sequence"
],
"units": "s"
},
{
"description": "Contains a reference to the previous sequence. A sequence is a trajectory, which can have number_of_frames_in_sequence each representing one section_single_configuration_calculation section. If not given, a start from an initial configuration is assumed.",
"dtypeStr": "r",
"name": "previous_sequence_ref",
"referencedSections": [
"section_frame_sequence"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "Reference to the method used for the calculation in section_single_configuration_calculation.",
"dtypeStr": "r",
"name": "single_configuration_calculation_to_method_ref",
"referencedSections": [
"section_method"
],
"shape": [],
"superNames": [
"section_single_configuration_calculation"
]
},
{
"description": "Reference from the present section_frame_sequence to the section_sampling_method, that defines the parameters used in this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation).",
"dtypeStr": "r",
"name": "frame_sequence_to_sampling_method_ref",
"referencedSections": [
"section_sampling_method"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "Reference from each frame (a frame is one section_single_configuration_calculation) in this section_frame_sequence to the corresponding section_single_configuration_calculation. Each section_frame_sequence binds a collection of section_single_configuration_calculation, because they all belong to, e.g., a molecular dynamics trajectory, or geometry optimization. The full information for each frame is stored in section_single_configuration_calculation and this metadata establishes the link for each frame.",
"dtypeStr": "r",
"name": "frame_sequence_to_frames_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"shape": [
"number_of_frames_in_sequence"
],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "The values of the kinetic energy along this frame. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_kinetic_energy_frames.",
"dtypeStr": "f",
"name": "kinetic_energy",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "J"
},
{
"description": "The value of the potential energy along this frame. This is equal to energy_total of the corresponding section_single_configuration_calculation and repeated here in a summary array for easier access. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_potential_energy_frames.",
"dtypeStr": "f",
"name": "potential_energy",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "J"
},
{
"description": "The values of the pressure (one third of the trace of the stress tensor) along this frame. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_pressure_frames.",
"dtypeStr": "f",
"name": "instant_pressure",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "Pa"
},
{
"description": "The values of the instantaneous temperature (a quantity, proportional to frame_sequence_kinetic_energy, whose ensemble average equals the thermodynamic temperature) along this frame. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_temperature_frames.",
"dtypeStr": "f",
"name": "instant_temperature",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "K"
},
{
"description": "The values of a quantity that should be conserved, along a sequence of frames (i.e., a trajectory). A frame is one section_single_configuration_calculation), for example the total energy in the NVE ensemble. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_conserved_quantity_frames.",
"dtypeStr": "f",
"name": "conserved_quantity",
"shape": [],
"superNames": [
"section_frame_sequence"
],
"units": "J"
},
{
"derived": true,
"description": "Average kinetic energy and its standard deviation over this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation).",
......@@ -5305,6 +5166,144 @@
"section_frame_sequence"
]
},
{
"description": "Time along this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation). Time start is arbitrary, but when a sequence is a continuation of another time should be continued too.",
"dtypeStr": "f",
"name": "frame_sequence_time",
"shape": [
"number_of_frames_in_sequence"
],
"superNames": [
"section_frame_sequence"
],
"units": "s"
},
{
"description": "Contains a reference to the previous sequence. A sequence is a trajectory, which can have number_of_frames_in_sequence each representing one section_single_configuration_calculation section. If not given, a start from an initial configuration is assumed.",
"dtypeStr": "r",
"name": "previous_sequence_ref",
"referencedSections": [
"section_frame_sequence"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "If the energy, forces, and other quantities for the frames (a frame is one section_single_configuration_calculation) in section_frame_sequence are obtained by calling a different code than the code that drives the sequence (e.g., a wrapper that drives a molecular dynamics, Monte Carlo, geometry optimization and calls an electronic-structure code for energy and forces for each configuration), this metadata holds the reference to where the section_single_configuration_calculation for each frame are located. The format for this reference is described in the [frame_sequence_external_url wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/frame-sequence-external-url).",
"dtypeStr": "C",
"name": "frame_sequence_external_url",
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "Type of continuation that has been performed from the previous sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation), upon restart.",
"dtypeStr": "C",
"name": "frame_sequence_continuation_kind",
"referencedSections": [
"section_frame_sequence"
],
"shape": [],
"superNames": [
"section_frame_sequence"
],
"values": {
"all": "Restart everything, including, e.g., thermostats, etc.",
"pos": "Position of atom and cell only",
"pos_vel": "Restart atom positions, cells and velocities"
}
},
{
"description": "Reference from each frame (a frame is one section_single_configuration_calculation) in this section_frame_sequence to the corresponding section_single_configuration_calculation. Each section_frame_sequence binds a collection of section_single_configuration_calculation, because they all belong to, e.g., a molecular dynamics trajectory, or geometry optimization. The full information for each frame is stored in section_single_configuration_calculation and this metadata establishes the link for each frame.",
"dtypeStr": "r",
"name": "frame_sequence_to_frames_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"shape": [
"number_of_frames_in_sequence"
],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "Reference from the present section_frame_sequence to the section_sampling_method, that defines the parameters used in this sequence of frames (i.e., a trajectory, a frame is one section_single_configuration_calculation).",
"dtypeStr": "r",
"name": "frame_sequence_to_sampling_method_ref",
"referencedSections": [
"section_sampling_method"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
},
{
"description": "Reference to the method used for the calculation in section_single_configuration_calculation.",
"dtypeStr": "r",
"name": "single_configuration_calculation_to_method_ref",
"referencedSections": [
"section_method"
],
"shape": [],
"superNames": [
"section_single_configuration_calculation"
]
},
{
"description": "The values of the kinetic energy along this frame. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_kinetic_energy_frames.",
"dtypeStr": "f",
"name": "kinetic_energy",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "J"
},
{
"description": "The value of the potential energy along this frame. This is equal to energy_total of the corresponding section_single_configuration_calculation and repeated here in a summary array for easier access. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_potential_energy_frames.",
"dtypeStr": "f",
"name": "potential_energy",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "J"
},
{
"description": "The values of the pressure (one third of the trace of the stress tensor) along this frame. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_pressure_frames.",
"dtypeStr": "f",
"name": "instant_pressure",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "Pa"
},
{
"description": "The values of the instantaneous temperature (a quantity, proportional to frame_sequence_kinetic_energy, whose ensemble average equals the thermodynamic temperature) along this frame. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_temperature_frames.",
"dtypeStr": "f",
"name": "instant_temperature",
"shape": [],
"superNames": [
"section_single_configuration_calculation"
],
"units": "K"
},
{
"description": "The values of a quantity that should be conserved, along a sequence of frames (i.e., a trajectory). A frame is one section_single_configuration_calculation), for example the total energy in the NVE ensemble. If not all frames have a value the indices of the frames that have a value are stored in frame_sequence_conserved_quantity_frames.",
"dtypeStr": "f",
"name": "conserved_quantity",
"shape": [],
"superNames": [
"section_frame_sequence"
],
"units": "J"
},
{
"description": "Section collecting some user-defined quantities evaluated along a sequence of frame.",
"kindStr": "type_section",
......
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