def write_input(datadict,
filename,
filetag=filetagtry,
endtag='end',
subdir=''):
endwithspace = endtag + '\n\n'
with open(subdir + filename, 'w') as f:
filepref = Mio.getFilePrefix(filename)
for key, val in sorted(datadict.items()):
if isinstance(val, np.ndarray):
f.write('{0}: \n'.format(key))
Mio.my_write_array(f, val)
f.write(endwithspace)
elif isinstance(val, dict):
dictfilename = key + '.' + filepref
f.write('{0}{1}: {2}\n\n'.format(filetag, key, dictfilename))
write_input(val, dictfilename, filetag, endtag, subdir)
elif isinstance(val, list):
f.write('{0}{1}: \n'.format(filetag, key))
for i, subdict in enumerate(val):
dictfilename = '{0}_{1}.{2}'.format(key, i, filepref)
f.write(dictfilename + '\n')
write_input(subdict, dictfilename, filetag, endtag, subdir)
f.write(endwithspace)
else:
f.write('{0}: {1}\n\n'.format(key, val))
def writeLammpsDump(datadict,filename,timestep):
xyarray = datadict['deformed_positions']
typesarray = datadict['types']
natoms = xyarray.shape[0]
with open(filename,'w') as f:
f.write('ITEM: TIMESTEP\n')
f.write('{0}\n'.format(timestep))
f.write('ITEM: NUMBER OF ATOMS\n')
f.write('{0}\n'.format(natoms))
f.write('ITEM: BOX BOUNDS ss ss pp\n') # may need to change this, if PBCS are implemented
boxbounds = getBoxBounds(xyarray)
Mio.my_write_array(f,boxbounds)
f.write('ITEM: ATOMS id type xs ys zs\n')
arrayout = getArrayOut(xyarray,typesarray,boxbounds)
Mio.my_write_array(f,arrayout,fmt=['{:d} ']*2+['{:f} ']*3)
def writeLammpsDump(datadict, filename, timestep):
xyarray = datadict['deformed_positions']
typesarray = datadict['types']
natoms = xyarray.shape[0]
with open(filename, 'w') as f:
f.write('ITEM: TIMESTEP\n')
f.write('{0}\n'.format(timestep))
f.write('ITEM: NUMBER OF ATOMS\n')
f.write('{0}\n'.format(natoms))
f.write('ITEM: BOX BOUNDS ss ss pp\n'
) # may need to change this, if PBCS are implemented
boxbounds = getBoxBounds(xyarray)
Mio.my_write_array(f, boxbounds)
f.write('ITEM: ATOMS id type xs ys zs\n')
arrayout = getArrayOut(xyarray, typesarray, boxbounds)
Mio.my_write_array(f, arrayout, fmt=['{:d} '] * 2 + ['{:f} '] * 3)
def write_input(datadict,filename,filetag=filetagtry,endtag='end',subdir=''):
endwithspace = endtag + '\n\n'
with open(subdir+filename,'w') as f:
filepref = Mio.getFilePrefix(filename)
for key, val in sorted(datadict.items()):
if isinstance(val,np.ndarray):
f.write('{0}: \n'.format(key))
Mio.my_write_array(f,val)
f.write(endwithspace)
elif isinstance(val,dict):
dictfilename = key + '.' + filepref
f.write('{0}{1}: {2}\n\n'.format(filetag,key,dictfilename))
write_input(val,dictfilename,filetag,endtag,subdir)
elif isinstance(val,list):
f.write('{0}{1}: \n'.format(filetag,key))
for i, subdict in enumerate(val):
dictfilename = '{0}_{1}.{2}'.format(key,i,filepref)
f.write(dictfilename + '\n')
write_input(subdict,dictfilename,filetag,endtag,subdir)
f.write(endwithspace)
else:
f.write('{0}: {1}\n\n'.format(key,val))