def main(outname,pltname):
mol_info = read_output_as_dict(outname)
plt_info = read_plt(pltname)
name = mol_info['name']
scene = Scene(name)
#scene.set_camera((0,4,0.5),(0,0,0.5))
scene.set_camera((0,10,0))
atoms = mol_info['structure']
for i,j in get_bonds_from_distance(atoms):
atnoi,xyzi = atoms[i]
atnoj,xyzj = atoms[j]
scene.add(Cylinder(xyzi,xyzj,0.1))
for atno,xyz in atoms:
r,g,b = color[atno]
sphere = Sphere(xyz,rscale*radius[atno],(r/255.,g/255.,b/255.))
scene.add(sphere)
ptris = mcube_contour(plt_info,0.1)
ntris = mcube_contour(plt_info,-0.1)
# if desired, compute normals at each vertex
ptris = smooth_tris(ptris)
ntris = smooth_tris(ntris)
if ptris: scene.add(TriangleMesh(ptris,(1,0,0)))
if ntris: scene.add(TriangleMesh(ntris,(0,0,1)))
scene.write_pov()
scene.render()
scene.display()
return
def jagout_scanner(fname):
"""\
Scan a Jaguar output file and get the relevant information for kinetics calculations,
including:
- geometry
- frequencies
- rotational symmetry number
- spin multiplicity
- total energy
- zero point energy
"""
from Pistol.Jaguar import read_output_as_dict
props = read_output_as_dict(fname)
geo = props.get('structure')
if not geo:
raise Exception("Structure not obtained from Jaguar file")
freqs = props.get('freqs',[])
rotsym = props.get('rotsym',1)
emult = props.get('multiplicity',1)
energy = props.get('energy')
zpe = props.get('zpe',0)
#print "Properties obtained from Jaguar output"
#print "structure"
#for atno,(x,y,z) in geo:
# print "%d %10.4f %10.4f %10.4f" % (atno,x,y,z)
#print "multiplicity = ",emult
#print "frequencies = ",freqs
#print "zpe = ",zpe
#print "rotsym = ",rotsym
#print "energy = ",energy
return geo,freqs,rotsym,emult,energy,zpe
0.1 01/01/00 Original version
0.2 03/01/00 Fixed bug related to intensities and symmetries
0.3 12/04/00 Fixed bug related to reduced masses.
0.4 08/22/02 Cleaned code slightly
0.5 06/06/03 Fixed a bug related to the force constant line
in Jaguar v4.2
0.6 06/09/03 Put most of the functions into the appropriate parts of Pistol
Copyright (c) 2003 Richard P. Muller ([email protected]). All rights
reserved. See the LICENSE file for licensing details.
"""
# Things to do:
# Put the frequency stuff into the MOLF format in Pistol
import sys
for filename in sys.argv[1:]:
from Pistol.Jaguar import read_output_as_dict
from Pistol.MOLF import write
output = read_output_as_dict(filename)
mol = output['structure']
freqlist = output['freqs']
modes = output['modes']
fileout = filename.replace('.out','.molf')
write(fileout,mol,freqlist,modes)
