PSF - read and write psf format¶
PSF file format given at http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/node24.html
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espressopp.tools.
psfwrite
(filename, system, maxdist=None, molsize=4, typenames=None)¶ Writes !NATOM and !NBOND sections of a psf format file
Parameters: - filename (string) – output file name
- system (espressopp System object) – espressopp system
- maxdist (float) – if this is specified, only bonds in which the pair of particles are separated by a distance < maxdist are written to the !NBOND section
- molsize (int) – if molsize>0, the molecule count is increased every molsize particles
- typenames (dict, key=int, value=string) – dictionary used for mapping from espressopp’s integer particle types to the particle type strings written in a psf file
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espressopp.tools.
psfread
(filename)¶ Reads !NATOM section of a psf format file
Parameters: filename (string) – input file name Returns: pid,segname,resindex,resname,atomname,atomtype,mass,charge (lists of type int,str,int,str,str,str,float,float)