Topology - matthew-hennefarth/CPET GitHub Wiki

We can use the topology keyword to specify a region to sample the electric field topology according to this paper. This has been studied in chemical systems, see the following references^1,2.

The simple command is as

topology 10 box 1 1 1

The first option after the topology keyword specifies the number of points to sample. After this, the remaining commands are there to specify the volume in which to sample in. In this case we sample in a box of side lengths 2x2x2. The default step size for following path lines is 0.001. Smaller values indicate more accurate path lines, but also much longer computational times. It will save the data to topology_sample_#index.top with #index being the frame number in the coordinate file.

As above, the key is topology the following options are available.

%topology
    volume box 1 1 1 # Required, volume to sample in
    stepSize 0.001 #Step size to use for following path lines, default is 0.001
    samples 10 # Required, number of samples to perform
    sampleOutput topology_sample # Output file prefix to use for saving the sampled data
end

Note that only the volume and samples options are required. If sampleOutput is not set, then the sample data will not be saved.