The parameters group

The initial H5MD proposed a simple and flexible schema for the storage of general "parameter" information within the parameters group, with the following structure:

parameters
 +-- <user_attribute1>
 \-- <user_data1>
 \-- <user_group1>
 |    \-- <user_data2>
 |    \-- ...
 \-- ...

In contrast, the H5MD-NOMAD schema calls for very specific structures to be used when storing parameter information. While the previous groups have attempted to stay away from enforcing NOMAD-specific data structures on the user, instead opting for more intuitive and generally-convenient structures, the parameters group utilizes already-existing metadata and structures within NOMAD to efficiently import simulation parameters in a way that is searchable and comparable to simulations performed by other users.

In this way, the H5MD-NOMAD parameters group has the following structure:

parameters
 \-- <parameter_subgroup_1>
 |    \-- ...
 \-- <parameter_subgroup_2>
 |    \-- ...
 \-- ...

The subgroups force_calculations and workflow are supported. The following pages describe the detailed data structures for these subgroups, using the NOMAD MetaInfo definitions for each underlying Quantity. Please note that:

1. Quantities with type=MEnum() are restricted to the provided allowed values.

2. The unit given in the MetaInfo definition does not have to be used within the H5MD-NOMAD file, however, the dimensionality of the unit should match.

Force calculations

The force_calculations group contains the parameters for force calculations according to the force field during a molecular dynamics run.

The following json template illustrates the structure of the force_calculations group, with example values for clarity:

{
    "vdw_cutoff": {"value": 1.2, "unit": "nm"},
    "coulomb_type": "particle_mesh_ewald",
    "coulomb_cutoff": {"value": 1.2, "unit": "nm"},
    "neighbor_searching": {
        "neighbor_update_frequency": 1,
        "neighbor_update_cutoff": {"value": 1.2, "unit": "nm"}
        }
    }

In the following, we provide the NOMAD definitions for each of these quantities:

• vdw_cutoff :

  Quantity(
          type=np.float64,
          shape=[],
          unit='m',
          description='''
          Cutoff for calculating VDW forces.
          ''')
  

• coulomb_type :

  Quantity(
      type=MEnum('cutoff', 'ewald', 'multilevel_summation', 'particle_mesh_ewald',
              'particle_particle_particle_mesh', 'reaction_field'),
      shape=[],
      description='''
      Method used for calculating long-ranged Coulomb forces.
  
      Allowed values are:
  
      | Barostat Name          | Description                               |
  
      | ---------------------- | ----------------------------------------- |
  
      | `""`                   | No thermostat               |
  
      | `"Cutoff"`          | Simple cutoff scheme. |
  
      | `"Ewald"` | Standard Ewald summation as described in any solid-state physics text. |
  
      | `"Multi-Level Summation"` |  D. Hardy, J.E. Stone, and K. Schulten,
      [Parallel. Comput. **35**, 164](https://doi.org/10.1016/j.parco.2008.12.005)|
  
      | `"Particle-Mesh-Ewald"`        | T. Darden, D. York, and L. Pedersen,
      [J. Chem. Phys. **98**, 10089 (1993)](https://doi.org/10.1063/1.464397) |
  
      | `"Particle-Particle Particle-Mesh"` | See e.g. Hockney and Eastwood, Computer Simulation Using Particles,
      Adam Hilger, NY (1989). |
  
      | `"Reaction-Field"` | J.A. Barker and R.O. Watts,
      [Mol. Phys. **26**, 789 (1973)](https://doi.org/10.1080/00268977300102101)|
      ''')
  

• coulomb_cutoff :

  Quantity(
      type=np.float64,
      shape=[],
      unit='m',
      description='''
      Cutoff for calculating short-ranged Coulomb forces.
      ''')
  

• neighbor_searching : Section containing the parameters for neighbor searching/lists during a molecular dynamics run.

• neighbor_update_frequency :

  Quantity(
      type=int,
      shape=[],
      description='''
      Number of timesteps between updating the neighbor list.
      ''')
  

• neighbor_update_cutoff :

  Quantity(
      type=np.float64,
      shape=[],
      unit='m',
      description='''
      The distance cutoff for determining the neighbor list.
      ''')
  

The molecular dynamics workflow

The workflow group contains the parameters for any type of workflow. Here we describe the specific case of the well-defined molecular_dynamics workflow. Custom workflows are described in detail HERE.

The following json template illustrates the structure of the molecular_dynamics subsection of the workflow group, with example values for clarity:

{
    "molecular_dynamics": {
        "thermodynamic_ensemble": "NPT",
        "integrator_type": "langevin_leap_frog",
        "integration_timestep": {"value": 2e-15, "unit": "ps"},
        "n_steps": 20000000,
        "coordinate_save_frequency": 10000,
        "velocity_save_frequency": null,
        "force_save_frequency": null,
        "thermodynamics_save_frequency": null,
        "thermostat_parameters": {
            "thermostat_type": "langevin_leap_frog",
            "reference_temperature": {"value": 300.0, "unit": "kelvin"},
            "coupling_constant": {"value": 1.0, "unit": "ps"}},
        "barostat_parameters": {
            "barostat_type": "berendsen",
            "coupling_type": "isotropic",
            "reference_pressure": {"value": [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], "unit": "bar"},
            "coupling_constant": {"value": [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]},
            "compressibility": {"value": [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]}
            }
    }
}

In the following, we provide the NOMAD definitions for each of these quantities:

• thermodynamic_ensemble :

  Quantity(
      type=MEnum('NVE', 'NVT', 'NPT', 'NPH'),
      shape=[],
      description='''
      The type of thermodynamic ensemble that was simulated.
  
      Allowed values are:
  
      | Thermodynamic Ensemble          | Description                               |
  
      | ---------------------- | ----------------------------------------- |
  
      | `"NVE"`           | Constant number of particles, volume, and energy |
  
      | `"NVT"`           | Constant number of particles, volume, and temperature |
  
      | `"NPT"`           | Constant number of particles, pressure, and temperature |
  
      | `"NPH"`           | Constant number of particles, pressure, and enthalpy |
      ''')
  

• integrator_type : Quantity( type=MEnum( 'brownian', 'conjugant_gradient', 'langevin_goga', 'langevin_schneider', 'leap_frog', 'rRESPA_multitimescale', 'velocity_verlet' ), shape=[], description=''' Name of the integrator.

      Allowed values are:
  
      | Integrator Name          | Description                               |
  
      | ---------------------- | ----------------------------------------- |
  
      | `"langevin_goga"`           | N. Goga, A. J. Rzepiela, A. H. de Vries,
      S. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. **8**, 3637 (2012)]
      (https://doi.org/10.1021/ct3000876) |
  
      | `"langevin_schneider"`           | T. Schneider and E. Stoll,
      [Phys. Rev. B **17**, 1302](https://doi.org/10.1103/PhysRevB.17.1302) |
  
      | `"leap_frog"`          | R.W. Hockney, S.P. Goel, and J. Eastwood,
      [J. Comp. Phys. **14**, 148 (1974)](https://doi.org/10.1016/0021-9991(74)90010-2) |
  
      | `"velocity_verlet"` | W.C. Swope, H.C. Andersen, P.H. Berens, and K.R. Wilson,
      [J. Chem. Phys. **76**, 637 (1982)](https://doi.org/10.1063/1.442716) |
  
      | `"rRESPA_multitimescale"` | M. Tuckerman, B. J. Berne, and G. J. Martyna
      [J. Chem. Phys. **97**, 1990 (1992)](https://doi.org/10.1063/1.463137) |
      ''')
  

• integration_timestep : Quantity( type=np.float64, shape=[], unit='s', description=''' The timestep at which the numerical integration is performed. ''')

• n_steps : Quantity( type=int, shape=[], description=''' Number of timesteps performed. ''')

• coordinate_save_frequency : Quantity( type=int, shape=[], description=''' The number of timesteps between saving the coordinates. ''')

• velocity_save_frequency : Quantity( type=int, shape=[], description=''' The number of timesteps between saving the velocities. ''')

• force_save_frequency : Quantity( type=int, shape=[], description=''' The number of timesteps between saving the forces. ''')

• thermodynamics_save_frequency : Quantity( type=int, shape=[], description=''' The number of timesteps between saving the thermodynamic quantities. ''')

• thermostat_parameters : Section containing the parameters pertaining to the thermostat for a molecular dynamics run.

• thermostat_type :

  Quantity(
      type=MEnum('andersen', 'berendsen', 'brownian', 'langevin_goga', 'langevin_schneider', 'nose_hoover', 'velocity_rescaling',
              'velocity_rescaling_langevin'),
      shape=[],
      description='''
      The name of the thermostat used for temperature control. If skipped or an empty string is used, it
      means no thermostat was applied.
  
      Allowed values are:
  
      | Thermostat Name        | Description                               |
  
      | ---------------------- | ----------------------------------------- |
  
      | `""`                   | No thermostat               |
  
      | `"andersen"`           | H.C. Andersen, [J. Chem. Phys.
      **72**, 2384 (1980)](https://doi.org/10.1063/1.439486) |
  
      | `"berendsen"`          | H. J. C. Berendsen, J. P. M. Postma,
      W. F. van Gunsteren, A. DiNola, and J. R. Haak, [J. Chem. Phys.
      **81**, 3684 (1984)](https://doi.org/10.1063/1.448118) |
  
      | `"brownian"`           | Brownian Dynamics |
  
      | `"langevin_goga"`           | N. Goga, A. J. Rzepiela, A. H. de Vries,
      S. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. **8**, 3637 (2012)]
      (https://doi.org/10.1021/ct3000876) |
  
      | `"langevin_schneider"`           | T. Schneider and E. Stoll,
      [Phys. Rev. B **17**, 1302](https://doi.org/10.1103/PhysRevB.17.1302) |
  
      | `"nose_hoover"`        | S. Nosé, [Mol. Phys. **52**, 255 (1984)]
      (https://doi.org/10.1080/00268978400101201); W.G. Hoover, [Phys. Rev. A
      **31**, 1695 (1985) |
  
      | `"velocity_rescaling"` | G. Bussi, D. Donadio, and M. Parrinello,
      [J. Chem. Phys. **126**, 014101 (2007)](https://doi.org/10.1063/1.2408420) |
  
      | `"velocity_rescaling_langevin"` | G. Bussi and M. Parrinello,
      [Phys. Rev. E **75**, 056707 (2007)](https://doi.org/10.1103/PhysRevE.75.056707) |
      ''')
  

• reference_temperature :

  Quantity(
      type=np.float64,
      shape=[],
      unit='kelvin',
      description='''
      The target temperature for the simulation.
      ''')
  

• coupling_constant :

  Quantity(
      type=np.float64,
      shape=[],
      unit='s',
      description='''
      The time constant for temperature coupling. Need to describe what this means for the various
      thermostat options...
      ''')
  

• effective_mass :

  Quantity(
      type=np.float64,
      shape=[],
      unit='kilogram',
      description='''
      The effective or fictitious mass of the temperature resevoir.
      ''')
  

• barostat_parameters : Section containing the parameters pertaining to the barostat for a molecular dynamics run.

• barostat_type :

  Quantity(
      type=MEnum('berendsen', 'martyna_tuckerman_tobias_klein', 'nose_hoover', 'parrinello_rahman', 'stochastic_cell_rescaling'),
      shape=[],
      description='''
      The name of the barostat used for temperature control. If skipped or an empty string is used, it
      means no barostat was applied.
  
      Allowed values are:
  
      | Barostat Name          | Description                               |
  
      | ---------------------- | ----------------------------------------- |
  
      | `""`                   | No thermostat               |
  
      | `"berendsen"`          | H. J. C. Berendsen, J. P. M. Postma,
      W. F. van Gunsteren, A. DiNola, and J. R. Haak, [J. Chem. Phys.
      **81**, 3684 (1984)](https://doi.org/10.1063/1.448118) |
  
      | `"martyna_tuckerman_tobias_klein"` | G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein,
      [Mol. Phys. **87**, 1117 (1996)](https://doi.org/10.1080/00268979600100761);
      M.E. Tuckerman, J. Alejandre, R. López-Rendón, A.L. Jochim, and G.J. Martyna,
      [J. Phys. A. **59**, 5629 (2006)](https://doi.org/10.1088/0305-4470/39/19/S18)|
  
      | `"nose_hoover"`        | S. Nosé, [Mol. Phys. **52**, 255 (1984)]
      (https://doi.org/10.1080/00268978400101201); W.G. Hoover, [Phys. Rev. A
      **31**, 1695 (1985) |
  
      | `"parrinello_rahman"`        | M. Parrinello and A. Rahman,
      [J. Appl. Phys. **52**, 7182 (1981)](https://doi.org/10.1063/1.328693);
      S. Nosé and M.L. Klein, [Mol. Phys. **50**, 1055 (1983) |
  
      | `"stochastic_cell_rescaling"` | M. Bernetti and G. Bussi,
      [J. Chem. Phys. **153**, 114107 (2020)](https://doi.org/10.1063/1.2408420) |
      ''')
  

• coupling_type :

  Quantity(
      type=MEnum('isotropic', 'semi_isotropic', 'anisotropic'),
      shape=[],
      description='''
      Describes the symmetry of pressure coupling. Specifics can be inferred from the `coupling constant`
  
      | Type          | Description                               |
  
      | ---------------------- | ----------------------------------------- |
  
      | `isotropic`          | Identical coupling in all directions. |
  
      | `semi_isotropic` | Identical coupling in 2 directions. |
  
      | `anisotropic`        | General case. |
      ''')
  

• reference_pressure :

  Quantity(
      type=np.float64,
      shape=[3, 3],
      unit='pascal',
      description='''
      The target pressure for the simulation, stored in a 3x3 matrix, indicating the values for individual directions
      along the diagonal, and coupling between directions on the off-diagonal.
      ''')
  

• coupling_constant :

  Quantity(
      type=np.float64,
      shape=[3, 3],
      unit='s',
      description='''
      The time constants for pressure coupling, stored in a 3x3 matrix, indicating the values for individual directions
      along the diagonal, and coupling between directions on the off-diagonal. 0 values along the off-diagonal
      indicate no-coupling between these directions.
      ''')
  

• compressibility :

  Quantity(
      type=np.float64,
      shape=[3, 3],
      unit='1 / pascal',
      description='''
      An estimate of the system's compressibility, used for box rescaling, stored in a 3x3 matrix indicating the values for individual directions
      along the diagonal, and coupling between directions on the off-diagonal. If None, it may indicate that these values
      are incorporated into the coupling_constant, or simply that the software used uses a fixed value that is not available in
      the input/output files.
      ''')