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:

   # Comments
   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 have been shown in bold and include

Comments

Any number of comment lines, each line starting with the "#" symbol

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 shown in bold and defined as:

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