Hello !
I created a snippet with Ovito Python package (Pro 3.10.0) for a rapid analysis of VASP AIMD trajectories. the use case here was a time averaging of the Radial Distribution Function from a sequence of XDATCAR files generated from VASP 5.4.4. .
When loading the trajectory it happens to read only the first frame of each XDATCAR file of the list.
Here is the code that I run with ovitos shell on Ubuntu 22.04
from ovito.pipeline import Pipeline
from ovito.io import import_file, export_file
from ovito.modifiers import CoordinationAnalysisModifier, TimeAveragingModifier
from ovito.modifiers import CombineDatasetsModifier
xdatcar_flles = ['./XDAT.Al90Fe10.1400K.9000.33', './XDAT.Al90Fe10.1400K.9000.34']
pipeline = import_file(xdatcar_files)
print('File import: ', xdatcar_files, 'Number of frames:', pipeline.source.num_frames)
rmax = 7.0
nbins = 150
dr = rmax/nbins
print("Partial RDFs, Number of MD frames:", pipeline.source.num_frames)
modifier = CoordinationAnalysisModifier(cutoff = rmax, number_of_bins = nbins, partial = True)
pipeline.modifiers.append(modifier) pipeline.modifiers.append(TimeAveragingModifier(operate_on='table:coordination-rdf'))
partial_rdf = pipeline.compute().tables['coordination-rdf[average]'].xy()
np.savetxt("rdf_ovito.dat", partial_rdf)
produces the following screen output
File import: ['./XDAT.Al90Fe10.1400K.9000.33', './XDAT.Al90Fe10.1400K.9000.34'] Number of frames: 2
Partial RDFs, Number of MD frames: 2
The RDF calculation works fine as far as Ican judge from the saved ascii file.
Maybe I missed something, but this seems to me a bug of reading XDATCAR files. The work around proposed by Alexander in a previous topic doesn’t work on my side.
Any help would be much appreciated, Thanks in advance.
All the best
Noel