eofs = "path.EofS"
print "saving energies to", eofs
with open(eofs, "w") as fout:
for i in range(len(S)):
fout.write("%f %f\n" % (S[i], energies[i]))
xyzfile = "path.xyz"
print "saving path in xyz format to", xyzfile
with open(xyzfile, "w") as fout:
for m in mints:
printAtomsXYZ(fout, m.coords, line2=str(m.energy))
xyzfile = "path.smooth.xyz"
print "saving smoothed path in xyz format to", xyzfile
clist = [m.coords for m in mints]
smoothed = smoothPath(clist, mindist)
with open(xyzfile, "w") as fout:
for coords in smoothed:
printAtomsXYZ(fout, coords)
if False:
try:
import matplotlib.pyplot as plt
plt.plot(S, energies)
plt.show()
except:
print "problem plotting with pyplot, skipping"
pass
def smooth_path(self, path, **kwargs):
mindist = self.get_mindist()
return smoothPath(path, mindist, interpolator=self.aasystem.interpolate, **kwargs)
def smooth_path(self, path, **kwargs):
mindist = self.get_mindist()
return smoothPath(path, mindist, **kwargs)
def smooth_path(self, path, **kwargs):
mindist = self.get_mindist()
return smoothPath(path, mindist, **kwargs)