def outcar2poscar(outcar,outposcar,wantconfig):
basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcar,wantconfig)
poscarIO.write(outposcar,basis,atoms,atypes,head)
def outcar2poscar(outcar, outposcar, wantconfig):
basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
outcar, wantconfig)
poscarIO.write(outposcar, basis, atoms, atypes, head)
#unit is femto, but in 10E-10*10E-15 seconds to account for angstroms in distance
timestep = outcarIO.timestep(outcarFile) * 10E-1
#Error check requested configuration
if configRequest == -1:
configRequest = nSteps - 1
if configRequest > nSteps:
print "%d configurations available" % nSteps
exit(0)
if configRequest < 5:
print "Need more than 5 steps for backwards - finite difference method."
exit(0)
#Gather poscar information for last set of atoms
basis, atypes, atoms, head, poscar = outcarIO.outcar2poscar(
outcarFile, configRequest)
#Convert from fractional units to cartesian
def u2a(u):
a = list()
a.append(u[0] * basis[0][0] + u[0] * basis[1][0] + u[0] * basis[2][0])
a.append(u[0] * basis[0][1] + u[1] * basis[1][1] + u[1] * basis[2][1])
a.append(u[0] * basis[0][2] + u[2] * basis[1][2] + u[2] * basis[2][2])
return a
stepb0 = map(u2a, atoms)
stepb1 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 1)[2])
stepb2 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 2)[2])
stepb3 = map(u2a, outcarIO.outcar2poscar(outcarFile, configRequest - 3)[2])
#unit is femto, but in 10E-10*10E-15 seconds to account for angstroms in distance
timestep = outcarIO.timestep(outcarFile) * 10E-1
#Error check requested configuration
if configRequest == -1:
configRequest = nSteps-1
if configRequest > nSteps:
print "%d configurations available"%nSteps
exit(0)
if configRequest < 5:
print "Need more than 5 steps for backwards - finite difference method."
exit(0)
#Gather poscar information for last set of atoms
basis,atypes,atoms,head,poscar = outcarIO.outcar2poscar(outcarFile,configRequest)
#Convert from fractional units to cartesian
def u2a(u):
a=list()
a.append(u[0]*basis[0][0]+u[0]*basis[1][0]+u[0]*basis[2][0])
a.append(u[0]*basis[0][1]+u[1]*basis[1][1]+u[1]*basis[2][1])
a.append(u[0]*basis[0][2]+u[2]*basis[1][2]+u[2]*basis[2][2])
return a
stepb0 = map(u2a,atoms)
stepb1 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-1)[2])
stepb2 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-2)[2])
stepb3 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-3)[2])
stepb4 = map(u2a,outcarIO.outcar2poscar(outcarFile,configRequest-4)[2])
