Prim

Description

The primitive crystal structure and allowed degrees of freedom (DoF) (the “prim”) specifies lattice vectors, crystal basis sites, occupation DoF, continuous site DoF, and continuous global DoF.

Project files

This format is used for prim.json files.

A user-generated prim.json file is used to initialize a CASM project. When the project is initialized, CASM writes a standardized prim.json file to <root>/.casm/prim.json, where <root> is the CASM project root directory.

For subsequent project actions, CASM will read the prim from <root>/.casm/prim.json, not the user-generated file used to initialize the project. It is not recommended to modify the CASM-generated prim.json file because that may cause inconsistencies in the project.

JSON Attributes List

BasicStructure attributes:

Name Description Format
basis Basis site descriptions array of Site
coordinate_mode Basis site coordinate type string
description Project description string
dofs Continuous global DoF dict of DoF
lattice_vectors Lattice vectors 2d array of number
species Fixed atom properties and molecule definitions dict of Molecule
title Project title string

Site attributes:

Name Description Format
coordinate Site coordinate array of number
occupants Site allowed occupants array of string
dofs Continuous site DoF dict of DoF

DoF attributes:

Name Description Format
axis_names User-specified axis names array of string
basis User-specified DoF basis 2d array of number

Molecule attributes:

Name Description Format
atoms List of atoms that comprise a molecule array of Atom Component
properties Fixed molecular properties dict of Species Property
name Chemical name string

Atom Component attributes:

Name Description Format
name Atom name string
coordinate Atom coordinate, relative to site location array of number
properties Fixed atomic properties dict of Species Property

Species Property attributes:

Name Description Format
value Species attribute value array of number

JSON Attributes Description

BasicStructure JSON object

  • basis: array of Site (required, shape=(n_sublattice,))

    An array of Site objects that specifies the coordinate, allowed occupants, and allowed continuous site DoF for each sublattice of the crystal. The size of the basis array defines the number of sublattices in the crystal (n_sublattice). Elsewhere, the variables sublattice_index or b (in the “integral site coordinate” convention), are used to indicate a particular sublattice.

  • coordinate_mode: string (required)

    Coordinate mode for basis sites. One of:

    • “Fractional” or “Direct”,
    • “Cartesian”
  • description: string (optional)

    An extended description for the project. Included by convention in most example prim.json files, this attribute is not read by CASM.

  • dofs: dict (optional, default={})

    A dictionary specifying the types of continuous global DoF and their basis. For more details on the allowed global DoF types and specifiying the standard or user-specified basis, see DoF.

    Example: Strain DoF, using the Hencky strain metric, with standard basis:

    "dofs": {
      "Hstrain" : {}
    }
    

    Example: Strain DoF, using the Hencky strain metric, with user-specified basis:

    "dofs": {
      "Hstrain" : {
        "axis_names": ["e_1", "e_2", "e_3"],
        "basis" : [
          [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
          [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
          [0.0, 0.0, 1.0, 0.0, 0.0, 0.0]
        ]
      }
    }
    
  • lattice_vectors: 2d array of number, shape=(3,3) (required)

    Lattice vectors (as row vectors), in Angstroms.

    Example:

    "lattice_vectors": [
      [ 4.0, 0.0, 0.0], // lattice vector 1
      [ 0.0, 4.0, 0.0], // lattice vector 2
      [ 0.0, 0.0, 4.0], // lattice vector 3
    ]
    
  • species: dict (optional, default={})

    A dictionary used to define fixed properties of any species listed as an allowed occupant in "basis/<sublattice_index>/occupants" that is not a single isotropic atom. Allows for specifying fixed properties of an atom, such as magnetic spin, or selective dynamics flags, defining molecules, and specifying allowed molecular orientations and fixed molecular properties. See “Molecule JSON object” format.

    Example: Specifying selective dynamics by species type

    "species" : {
      "H": {
        "properties": {
          "selectivedynamics": {
            "value": [1, 1, 1]
          }
        }
      },
      "Zr": {
        "properties": {
          "selectivedynamics": {
            "value": [0, 0, 0]
          }
        }
      }
    }
    
  • title: string (required)

    A title for the project. Must consist of alphanumeric characters and underscores only. The first character may not be a number.

Site JSON object

Used to specify the coordinate, allowed occupants, and allowed continuous site DoF for a sublattice in the prim.

  • coordinate: array of number, shape=(3,) (required)

    Coordinate of the basis site with units as specified by the coordinate_mode parameter. The default tolerance for checking symmetry is 1e-5, so basis site coordinates should include 6 significant digits or more.

  • occupants: array of string (optional, default=["UNKNOWN"])

    A list of the possible occupant species that may reside at each site. The names are case sensitive, and "Va" is reserved for vacancies. If not specified, an "UNKNOWN" occupant species is created.

  • dofs: dict (optional, default={}):

    A dictionary specifying the types of continuous site DoF allowed on this site and their basis. For more details on the allowed site DoF types and specifiying the standard or user-specified basis, see DoF.

    Example: Atomic displacement, using standard basis

    "dofs": {
      "disp" : {}
    }
    

    Example: Atomic displacement DoF, with user-specified basis:

    "dofs": {
      "disp": {
        "axis_names": ["d1", "d2"],
        "basis": [
          [0.70710678, 0.70710678, 0.],
          [-0.70710678, 0.70710678, 0.]
        ]
      }
    }
    

Degrees of freedom (DoF) JSON object

Degrees of freedom (DoF) are continuous-valued vectors having a standard basis that is related to the fixed reference frame of the crystal. CASM supports both site DoF, which are associated with a particular prim basis site, and global DoF, which are associated with the infinite crystal. Standard DoF types are implemented in CASM and a traits system allows developers to extend CASM to include additional types of DoF.

DoF List

Standard DoF types included in CASM:

Name Description Type Standard basis Axis names (if different)
"disp"[1] Atomic displacement Site $[d_x, d_y, d_z]$  
"Cmagspin" Collinear magnetic spin Site $[m]$  
"Cunitmagspin" Collinear magnetic spin, constrained to unit length Site $[m]$  
"NCmagspin" Non-collinear magnetic spin, without spin-orbit coupling Site $[s_x, s_y, s_z]$  
"NCunitmagspin" Non-collinear magnetic spin, without spin-orbit coupling, constrained to unit length Site $[s_x, s_y, s_z]$  
"SOmagspin" Non-collinear magnetic spin, with spin-orbit coupling Site $[s_x, s_y, s_z]$  
"SOunitmagspin" Non-collinear magnetic spin, with spin-orbit coupling, constrained to unit length Site $[s_x, s_y, s_z]$  
"EAstrain"[1][2] Euler-Almansi strain metric, $\frac{1}{2}(I-(F F^{T})^{-1})$ Global $[E_{xx}, E_{yy}, E_{zz}, \sqrt(2)E_{yz}, \sqrt(2)E_{xz}, \sqrt(2)E_{xy}]$ $[e_1, e_2, e_3, e_4, e_5, e_6]$
"GLstrain"[1][2] Green-Lagrange strain metric, $\frac{1}{2}(C-I)$ Global $[E_{xx}, E_{yy}, E_{zz}, \sqrt(2)E_{yz}, \sqrt(2)E_{xz}, \sqrt(2)E_{xy}]$ $[e_1, e_2, e_3, e_4, e_5, e_6]$
"Hstrain"[1][2] Hencky strain metric, $\frac{1}{2}ln(C)$ Global $[E_{xx}, E_{yy}, E_{zz}, \sqrt(2)E_{yz}, \sqrt(2)E_{xz}, \sqrt(2)E_{xy}]$ $[e_1, e_2, e_3, e_4, e_5, e_6]$

Notes:

  1. When both displacements and strain are applied, displacements are applied first and then the displaced coordinates and lattice vectors are strained.
  2. The strain metrics, $E$, are defined in terms of the deformation gradient tensor, $F$, and Green’s deformation tensor, $C$. The deformation gradient tensor relates the strained and unstrained lattices through $L^{strained} = F * L^{ideal}$, where $L$ is a column-vector matrix of the lattice vectors. The deformation matrix tensor can be decomposed, via $F = R * U$, into a rotation tensor, $R$, and stretch tensor, $U$. Green’s deformation tensor, $C = F^{T}*F$, excludes rigid rotations.
User-specified DoF basis

In many cases, the standard basis is the appropriate choice, but CASM also allows for a user-specified basis in terms of the standard basis. A user-specified basis may fully span the standard basis or only a subspace. Within a "dofs" dict, each DoF is given by the key/object pair "<dofname>" : {...} where <dofname> is the name specifier of a particular DoF type and the associated object specifies non-default options.

  • axis_names: array of string, shape=(dim,) (required if basis present)

    Provides names for individual DoF when printing basis function formulas. If basis is present, then the size of axis_names must match the number of rows in basis. The default value is the standard basis, as defined by CASM for each DoF type.

  • basis: 2d array of number, shape=(dim, standard_dim) (optional, default is the standard basis)

    A row-vector matrix defining the user-specified “prim basis” for a site or global DoF in terms of the “standard basis”. The default value of basis is the “standard basis”, which is the identity matrix of shape (standard_dim, standard_dim).

Example: Atomic displacement DoF with user-specified basis:

"disp" : {
  "axis_names" : ["d1", "d2"],
  "basis" : [
    [0.70710678, 0.70710678, 0.0],
    [0.0,        0.0,        1.0]
  ]
}

Example: Strain DoF, using the Hencky strain metric, with user-specified basis:

"Hstrain" : {
  "axis_names": ["e_1", "e_2", "e_3"],
  "basis" : [
    [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
    [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
    [0.0, 0.0, 1.0, 0.0, 0.0, 0.0]
  ]
}

Molecule JSON object

Warning: Use of multi-atom molecular species should be considered an experimental development that is not supported by all CASM methods and not fully tested. Users should take extra care to check results.

Used to define species that are comprised of multiple atoms, off-centered atoms, or species with properties such as a magnetic spin or selective dynamics flags.

  • atoms: array of Atom Component (optional)

    Defines each atomic component of a multiple atom occupant. May be excluded for single-atom molecules.

  • properties: dict of Species Property (optional)

    Additonal fixed properties of the molecule as a whole, such as magnetic spin or selective dynamics flags. The name of each attribute must be a CASM-supported property type. The dimension of the value array must match the standard dimension of the property type.

    Example:

    "properties": {
      "selectivedynamics": {
        "value": [1, 1, 1]
      }
    }
    
  • name: string (optional)

    Chemical name of the species, used to override its name in the enclosing species dictionary. This name is used for chemical comparisons of molecules. Crystallographic and spatial comparisons are not dependent on molecule names.

Atom Component JSON object:

Warning: Use of multi-atom molecular species should be considered an experimental development that is not supported by all CASM methods and not fully tested. Users should take extra care to check results.

Used to define an atom that is a component of a molecule.

  • coordinate: size 3 array of number

    Position of the atom, relative to the basis site at which it is placed. Coordinate mode is same as rest of prim.json.

  • properties: dict of Species Property (optional)

    Additonal fixed properties of the atom, such as magnetic moment or selective dynamics flags. The name of each attribute must be a CASM-supported property type. The dimension of the value array must match the standard dimension of the property type.

    Example:

    "properties": {
      "selectivedynamics": {
        "value": [1, 1, 1]
      }
    }
    
  • name: string Name of atomic species.

Species Property JSON object:

Associates the discrete value of a vector property to an atom or moleule.

  • value: array of number

    The dimension of the value array must match the standard dimension of the CASM-supported property type whose name is the key for this object. See Example 6.

Examples

Example 1) FCC ternary alloy of elements A, B, and C

{
  "basis" : [
    {
      "coordinate" : [ 0.000000000000, 0.000000000000, 0.000000000000 ],
      "occupants" : [ "A", "B", "C" ]
    }
  ],
  "coordinate_mode" : "Fractional",
  "description" : "Face-centered Cubic (FCC, cF)",
  "lattice_vectors" : [
    [ 2.000000000000, 2.000000000000, 0.000000000000 ],
    [ 0.000000000000, 2.000000000000, 2.000000000000 ],
    [ 2.000000000000, 0.000000000000, 2.000000000000 ]
  ],
  "title" : "ABC"
}

Example 2) FCC binary alloy of elements A and B with Green-Lagrange strain DoF

{
  "basis" : [
    {
      "coordinate" : [ 0.000000000000, 0.000000000000, 0.000000000000 ],
      "occupants" : [ "A", "B" ]
    }
  ],
  "dofs" : {
    "GLstrain" : {},
  }
  "coordinate_mode" : "Fractional",
  "description" : "Face-centered Cubic (FCC, cF)",
  "lattice_vectors" : [
    [ 2.000000000000, 2.000000000000, 0.000000000000 ],
    [ 0.000000000000, 2.000000000000, 2.000000000000 ],
    [ 2.000000000000, 0.000000000000, 2.000000000000 ]
  ],
  "title" : "AB_with_GLstrain"
}

Example 3) Zincblende GaAs with Hencky strain DoF along (x,x), (y,y), and (z,z) components

{
  "basis" : [
    {
      "coordinate" : [ 0.000000000000, 0.000000000000, 0.000000000000 ],
      "occupants" : [ "Ga" ]
    },
    {
      "coordinate" : [ 0.250000000000, 0.250000000000, 0.250000000000 ],
      "occupants" : [ "As" ]
    }
  ],
  "dofs" : {
    "Hstrain" : {
      "axis_names" : [ "Exx", "Eyy", "Ezz" ],
      "basis" : [[1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
                   [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
                   [0.0, 0.0, 1.0, 0.0, 0.0, 0.0]]
    },
  }
  "coordinate_mode" : "Fractional",
  "description" : "Zincblende GaAs with deviatoric strain",
  "lattice_vectors" : [
    [ 0.00000, 2.82663, 2.82663 ],
    [ 2.82663, 0.00000, 2.82663 ],
    [ 2.82663, 2.82663, 0.00000 ]
  ],
  "title" : "GaAs"
}

Example 4) BCC lithium with atomic displacement DoF

{
  "basis" : [
    {
      "coordinate" : [ 0.000000000000, 0.000000000000, 0.000000000000 ],
      "dofs" : {
        "disp" : {},
      }
      "occupants" : [ "Li" ]
    }
  ],
  "coordinate_mode" : "Fractional",
  "description" : "Body-centered Cubic (BCC, cI)",
  "lattice_vectors" : [
    [ -1.75445,  1.75445,  1.75445 ],
    [  1.75445, -1.75445,  1.75445 ],
    [  1.75445,  1.75445, -1.75445 ]
  ],
  "title" : "Li_with_displacement"
}

Example 5) HCP Zr with Va/O at octahedral interstitial positions

{
  "basis" : [
    {
      "coordinate" : [ 0.0, 0.0, 0.0 ],
      "occupants" : [ "Zr" ]
    },
    {
      "coordinate" : [ 0.666666, 0.333333, 0.5 ],
      "occupants" : [ "Zr" ]
    },
    {
      "coordinate" : [ 0.333333, 0.666666, 0.25 ],
      "occupants" : [ "Va", "O" ]
    },
    {
      "coordinate" : [ 0.333333, 0.666666, 0.75 ],
      "occupants" : [ "Va", "O" ]
    }
  ],
  "coordinate_mode" : "Fractional",
  "description" : "hcp Zr with oct (O) ",
  "lattice_vectors" : [
    [  3.233986860000, 0.000000000000, 0.000000000000 ],
    [ -1.616993430000, 2.800714770000, 0.000000000000 ],
    [ -0.000000000000, 0.000000000000, 5.168678340000 ]
  ],
  "title" : "ZrO"
}

Example 6) Cubic ZrH2, with Green-Lagrange strain and selectivedynamics

{
  "basis" : [
    {
      "coordinate" : [ 0.0000000, 0.0000000, 0.0000000 ],
      "occupant_dof" : [ "Zr" ],
      "dofs": {
        "disp": {}
      }
    },
    {
      "coordinate" : [ 0.2500000, 0.2500000, 0.2500000 ],
      "occupant_dof" : [ "H" ]
    },
    {
      "coordinate" : [ 0.7500000, 0.7500000, 0.7500000 ],
      "occupant_dof" : [ "H" ]
    }
  ],
  "species" : {
    "H": {
      "properties": {
        "selectivedynamics": {
          "value": [1, 1, 1]
        }
      }
    },
    "Zr": {
      "properties": {
        "selectivedynamics": {
          "value": [0, 0, 0]
        }
      }
    }
  },
  "dofs" : {
      "GLstrain" : {}
  },
  "coordinate_mode" : "Fractional",
  "description" : "Cubic ZrH_{2}",
  "lattice_vectors" : [
    [0.       , 2.4106965, 2.4106965],
    [2.4106965, 0.       , 2.4106965],
    [2.4106965, 2.4106965, 0.       ]
  ],
  "title" : "ZrH2"
}