from sys import exit, argv
if '-h' in argv:
print 'usage: vef.py'
print ' prints the force and energy for each ionic step of a vasp run'
print
exit(0)
vtst_path = dirname(abspath(__file__))
filename = 'OUTCAR'
if not isfile(filename):
print 'No such file: %s' % filename
exit(1)
traj = aselite.read_vasp_out(filename)
if len(traj) == 0:
exit(0)
fe = open('fe.dat', 'w')
for i, atoms in enumerate(traj):
e = atoms.get_potential_energy()
if i == 0:
e0 = e
f = atoms.get_max_atom_force()
str = '%5i %20.8f %20.6f %20.6g ' % (i, f, e, e - e0)
print str
fe.write(str + '\n')
fe.close()
if i > 1:
from sys import exit, argv
if '-h' in argv:
print 'usage: vef.py'
print ' prints the force and energy for each ionic step of a vasp run'
print
exit(0)
vtst_path = dirname(abspath(__file__))
filename = 'OUTCAR'
if not isfile(filename):
print 'No such file: %s' % filename
exit(1)
traj = aselite.read_vasp_out(filename)
if len(traj) == 0:
exit(0)
fe = open('fe.dat', 'w')
for i, atoms in enumerate(traj):
e = atoms.get_potential_energy()
if i == 0:
e0 = e
f = atoms.get_max_atom_force()
str = '%5i %20.8f %20.6f %20.6g ' % (i,f,e,e-e0)
print str
fe.write(str+'\n')
fe.close()
if i > 1:
def dymmatrix(displacecars, outcars):
all_displacements = []
displacements = None
for displacecar in displacecars:
check_file(displacecar)
print('Reading %s' % displacecar)
d = numpy.loadtxt(displacecar).flatten()
all_displacements.extend(d)
if displacements == None:
displacements = d
else:
displacements += d
ndisp = numpy.count_nonzero(displacements)
#indices of the nonzero displacements
di = numpy.nonzero(all_displacements)[0] % ndisp
print('Number of displacements: %i' % ndisp)
traj = []
for outcar in outcars:
check_file(outcar)
print('Reading %s' % outcar)
images = aselite.read_vasp_out(outcar)
atoms = images[0]
traj += images[1:]
reference_force = atoms.get_forces().flatten()
masses = traj[0].get_masses()
displacement_masses = []
for mass in masses:
displacement_masses.extend([mass, mass, mass])
masses = numpy.array(displacement_masses)
if len(traj) != ndisp:
print('ERROR: number of displacements (%i) !=' % ndisp, end=' ')
print('number of calculations (%i)' % len(traj))
exit(1)
print('Building dynamical matrix')
dymmat = numpy.zeros((ndisp, ndisp))
hessian = numpy.zeros_like(dymmat)
for i in range(ndisp):
f1 = traj[i].get_forces().flatten()[di]
f0 = reference_force[di]
dymmat[i] = -(f1 - f0)
dymmat[i] /= displacements[di]
hessian[i] = dymmat[i]
for j in range(ndisp):
dymmat[i, j] /= numpy.sqrt(masses[di][i] * masses[di][j])
#symmetrize
dymmat = (dymmat + dymmat.transpose()) / 2.0
hessian = (hessian + hessian.transpose()) / 2.0
numpy.savetxt('freq.mat', dymmat, fmt='%16.8f')
print('Diagonalizing matrix')
omegas, ev = numpy.linalg.eigh(dymmat)
numpy.savetxt('eigs.dat', omegas, fmt='%25.15g')
f = open('freq.dat', 'w')
for omega in omegas:
imag = 0
if omega < 0:
imag = 1
freq = numpy.sqrt(numpy.abs(omega)) * 521.47
s = '%12.6f cm^{-1} ... %i ' % (freq, imag)
f.write(s + '\n')
print(s)
f.close()
numpy.savetxt('modes.dat', ev, fmt='%16.8f')
force_constants, ev = numpy.linalg.eigh(hessian)
numpy.savetxt('force_constants.dat', force_constants, fmt='%16.12f')
effective_masses = force_constants / omegas
numpy.savetxt('effective_masses.dat', effective_masses, fmt='%12.6f')
def dymmatrix(displacecars, outcars):
all_displacements = []
displacements = None
for displacecar in displacecars:
check_file(displacecar)
print 'Reading %s' % displacecar
d = numpy.loadtxt(displacecar)[:,:3].flatten()
all_displacements.extend(d)
if displacements == None:
displacements = d
else:
displacements += d
ndisp = numpy.count_nonzero(displacements)
#indices of the nonzero displacements
di = numpy.nonzero(all_displacements)[0] % ndisp
print 'Number of displacements: %i' % ndisp
traj = []
for outcar in outcars:
check_file(outcar)
print 'Reading %s' % outcar
images = aselite.read_vasp_out(outcar)
atoms = images[0]
traj += images[1:]
reference_force = atoms.get_forces().flatten()
masses = traj[0].get_masses()
displacement_masses = []
for mass in masses:
displacement_masses.extend([mass,mass,mass])
masses = numpy.array(displacement_masses)
if len(traj) != ndisp:
print 'ERROR: number of displacements (%i) !=' % ndisp,
print 'number of calculations (%i)' % len(traj)
exit(1)
print 'Building dynamical matrix'
dymmat = numpy.zeros((ndisp,ndisp))
hessian = numpy.zeros_like(dymmat)
for i in range(ndisp):
f1 = traj[i].get_forces().flatten()[di]
f0 = reference_force[di]
dymmat[i] = -(f1-f0)
dymmat[i] /= displacements[di]
hessian[i] = dymmat[i]
for j in range(ndisp):
dymmat[i,j] /= numpy.sqrt(masses[di][i]*masses[di][j])
#symmetrize
dymmat = (dymmat + dymmat.transpose()) / 2.0
hessian = (hessian + hessian.transpose()) / 2.0
numpy.savetxt('freq.mat', dymmat, fmt='%16.8f')
print 'Diagonalizing matrix'
omegas, ev = numpy.linalg.eigh(dymmat)
numpy.savetxt('eigs.dat', omegas, fmt='%25.15g')
f = open('freq.dat', 'w')
for omega in omegas:
imag = 0
if omega < 0:
imag = 1
freq = numpy.sqrt(numpy.abs(omega))*521.47
s = '%12.6f cm^{-1} ... %i ' % (freq, imag)
f.write(s+'\n')
print s
f.close()
numpy.savetxt('modes.dat', ev, fmt='%16.8f')
#
f = open('modes_sqrt_amu.dat', 'w')
masses_ = atoms.get_masses()
for i in range(len(atoms)*3):
evec = ev[:,i].tolist() # eigenvectors are in columns
for j in range(len(atoms)):
dx = evec[3*j]/numpy.sqrt(masses_[j])
dy = evec[3*j+1]/numpy.sqrt(masses_[j])
dz = evec[3*j+2]/numpy.sqrt(masses_[j])
f.write('%10.6f %10.6f %10.6f\n' % (dx, dy, dz))
f.write('\n')
f.close()
#
force_constants, ev = numpy.linalg.eigh(hessian)
numpy.savetxt('force_constants.dat', force_constants, fmt='%16.12f')
effective_masses = force_constants/omegas
numpy.savetxt('effective_masses.dat', effective_masses, fmt='%12.6f')