OpenDX scalar data format — APBS-PDB2PQR 1.6 documentation

# OpenDX scalar data format

We output most discretized scalar data (e.g., potential, accessibility, etc.) from APBS in the data format used by the OpenDX software package. The OpenDX data format is very flexible; the following sections describe the application of this format for APBS multigrid and finite element datasets.

The multigrid data format has the following form:

    object 1 class gridpositions counts nx ny nz
    origin xmin ymin zmin
    delta hx 0.0 0.0
    delta 0.0 hy 0.0
    delta 0.0 0.0 hz
    object 2 class gridconnections counts nx ny nz
    object 3 class array type double rank 0 items n data follows
    u(0,0,0) u(0,0,1) u(0,0,2)
    ...
    u(0,0,nz-3) u(0,0,nz-2) u(0,0,nz-1)
    u(0,1,0) u(0,1,1) u(0,1,2)
    ...
    u(0,1,nz-3) u(0,1,nz-2) u(0,1,nz-1)
    ...
    u(0,ny-1,nz-3) u(0,ny-1,nz-2) u(0,ny-1,nz-1)
    u(1,0,0) u(1,0,1) u(1,0,2)
    ...
    attribute "dep" string "positions"
    object "regular positions regular connections" class field
    component "positions" value 1
    component "connections" value 2
    component "data" value 3`

The variables in this format include:

`nx ny nz`
  The number of grid points in the x-, y-, and z-directions
`xmin ymin zmin`
  The coordinates of the grid lower corner
`hx hy hz`
  The grid spacings in the x-, y-, and z-directions.
`n`
  The total number of grid points; \(n = nx * ny * nz\)
`u(*,*,*)`
  The data values, ordered with the z-index increasing most quickly, followed by the y-index, and then the x-index.

For finite element solutions, the OpenDX format takes the following form:

    object 1 class array type float rank 1 shape 3 items N
    v1x v1y v1z
    v2x v2y v2z
    ...
    vNx vNy vNz
    object 2 class array type int rank 1 shape 4 items M
    s1a s1b s1c s1d
    s2a s2b s2c s2d
    ...
    sMa sMb sMc sMd
    attribute "element type" string "tetrahedra"
    object 3 class array type float rank 0 items N
    u1
    u2
    ...
    uN
    attribute "dep" string "positions"
    object "irregular positions irregular connections" class field
    component "positions" value 1
    component "connections" value 2
    component "data" value 3
    end

where the variables in this format are:

`N`
  Number of vertices
`vix viy viz`
  Coordinates of vertex i
`M`
  Number of simplices
`sia sib sic sid`
  IDs of vertices in simplex i
`ui`
  Data value associated with vertex i