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Domain-Specific Naming Conventions for Molecular Dynamics Simulation Codes

openPMD extension name: MD

VERSION: 0.0.2 (September 19th, 2019)

Introduction

This extension is specifically designed for the molecular dynamics simulation codes.

The current version of this extension is suitable to allow the output of arbitrary simulation codes to be post-processed and compared with common tools and frameworks. Future versions will define a common set of required records and further attributes.

The example data structure can be found HERE.

Root Group

Additional Attributes for the Root group

The following additional attributes are defined in this extension. The individual requirement is given in scope.

  • forceField
    • type: 1-dimensional array of N (string) elements, where N is the number of force fields (interatomic potentials) implemented in the simulation.
    • scope: optional
    • description: the methods implemented in the simulation to describe the force fields (interatomic potentials). See Interatomic Potentials Repository.
    • example values:
      • eam/alloy
      • lj/cut 3.0
      • ...
  • forceFieldParameters
    • type: 1-dimensional array of N (string) elements, where N is the number of force fields (interatomic potentials) implemented in the simulation.
    • scope: optional
    • description: the parameters specification for the forceField methods. See Interatomic Potentials Repository.
    • example values:
      • pair_coeff * * 1 1
      • pair_coeff 1 1 Cu_mishin1.eam.alloy Cu
      • ...

Observable Records

observables is an optional group that contains physical observables that are derived from the system state, i.e., thermodynamic information (e.g. temperature, energy, pressure).

Naming conventions

The naming conventions conforming the naming conventions for Scalar, Vector and Tensor Records in openPMD base standard.

  • scalar record
    • type: (any type)
    • data set: recordName unique name in group basePath + observables
    • examples:
      • /data/observables/temperature
      • /data/observables/pressure

Attributes for each observable record

The attributes of unit system for records should be included as defined in openPMD base standard .

Particle Records

Additional attributes for each position record

The following attributes are defined in this extension. The individual requirement is given in scope.

  • coordinate
    • type: (string)
    • scope: required
    • description: the representation of the stored position coordinates
    • available values:
      • absolute the unscaled coordinates
      • fractional the coordinates that are scaled in the range of [0,1] relative to the length of each box edge; in this coordinate system, the unitSI of each position component should be 1.0

Additional Sub-Group for each Particle Species

box is an optional sub-group for each particle species to contain the information of the simulation box.

Attributes for Sub-Group box

The following attributes are defined in this extension. If the box sub-group exists, the following attributes within it are required. The individual requirement is given in scope.

  • dimension

    • type: (uint32)
    • scope: required, if box sub-group exists
    • description: the spacial dimension D of the simulation box.
    • example values:
      • 2 2D simulation box
      • 3 3D simulation box
      • ...

  • boundary

    • type: array of (string) containing D elements, where D is the value of dimension.
    • scope: required, if box sub-group exists
    • description: the boundary condition of the box along each dimension. The allowed values in boundary are either periodic or none.
    • example values:
      • ["periodic","periodic","periodic"] periodic in all the three dimensions
      • ["none","periodic","periodic"] periodic in only y and z dimensions

Records for Sub-Group box

The following records are defined in this extension. If the box sub-group exists, the following records within it are required. The individual requirement is given in scope.

  • edge
    • type: DxD array of (floatX), where D is the value of dimension.
    • scope: required, if box sub-group exists
    • description: the edge vector of the simulation box in each dimension.
    • example values:
      • [[1.,0.,0.],[0.,1.,0.],[0.,0.,1.]] 3D cubic simulation box, Ax = (1.,0.,0.), Ay = (0.,1.,0.), Az = (0.,0.,1.)
      • [[3.46,0.,0.],[1.73,2.997,0.],[0.,0.,10.]] 3D triclinic simulation box, Ax = (3.46,0.,0.), Ay = (1.73,2.997,0.), Az = (0.,0.,10.)
      • [[1.,0.],[1.,1.]] 2D rectangle simulation box, Ax = (1.,0.), Ay = (0.,1.)
  • limit
    • type: Dx2 array of (floatX), where D is the value of dimension.
    • scope: required, if box sub-group exists
    • description: the starting and the ending of each edge vector.
    • example values:
      • [[0.,300.],[0.,150.],[0.,180.]] A 3D box example: xlo = 0, xhi = 300, ylo = 0, yhi = 150, zlo = 0, zhi = 180
      • [[0.,300.],[15.,280.]] A 2D box example: xlo = 0, xhi = 300, ylo = 15, yhi = 280
  • unitSI
    • type: (float64)
    • scope: required, if box sub-group exists
    • description: unit-conversion factor to convert simulation unit to SI units
    • example: 1.0e-10