Build using CMake in a separate directory (out of source build). That keeps the source tree clean and allows separating multiple builds. For a basic build, just do:
$ mkdir build
$ cd build
$ cmake .. [options]
$ make
Use make VERBOSE=1 to see the actual compilation commands.
| Option | Description |
|---|---|
-DENABLE_OPENMP=ON |
Enable OpenMP support (on by default) |
Installation is currently not supported, just run the binary from the build directory.
Possible input options: (have to be given in lower case (I know, I know) then ' = ' and then input value (see also tests directory))
option valid keywords
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task surface_distribution - calculates instantaneous surface (string)
structure XYZ coordinate input (needed with actual atom names) (string)
trajectory either XYZ, or XTC file, if XYZ, each snapshot should be the same number of bytes as every other one
xdrread activate XTC reading (integer, 0 - off, everything else - on)
batch batch processing mode (three integers: start stop iteration, 0-based)
pbc only orthogonal cells, expects three reals (x,y,z), default unit Bohr, if prepended by ANG or NM, angstrom or nano-meters can be given
periodic activate periodicity (integer, 0 - off, everything else - on)
resolution expects real, giving grid spacing (only in Bohr!!!)
refmask give atoms of one solute of which the distance to the surface will be calculated
mask atoms used for surface construction
atoms 1 6 8
indices 0 1 2 34
or similar
output string: silent, normal, debug
surfxyz turn on output of 2D surface as XYZ file (integer, 0 - off, 1 - two files, surface up and down without atoms, 2 - two files, surface up and down, with atoms)