| APBS 0.4.0 User Guide: Adaptive Poisson-Boltzmann Solver | ||
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We output most discretized scalar data (e.g., potential, accessibility, etc.) from APBS in the data format used by the OpenDX software package (http://www.opendx.org). The OpenDX data format is very flexible; the following sections describe the application of this format for APBS multigrid and finite element datasets.
This 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 times n
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-3,nz-3) u(0,ny-2,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
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Any number of comment lines, each line starting with the "#" symbol
The number of grid points in the x-, y-, and z-directions.
The coordinates of the grid lower corner.
The grid spacings in the x-, y-, and z-directions.
The total number of grid points; n = nx * ny * nz
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
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Number of vertices
Coordinates of vertex i
Number of simplices
IDs of vertices in simplex i
Data value associated with vertex i
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