def prepare(infname='POSCAR', dlt1max=0.01, dlt2max=0.06):
#...original system
nsys0 = NAPSystem(fname=infname)
#orig_atoms = read(infname,format='vasp')
orig_atoms = nsys0.to_ase_atoms()
#...get deformations
fmats = get_deformations(dlt1max, dlt2max)
#...deform original system and save to _prefix_##/POSCAR
for i, fmat in enumerate(fmats):
atoms = orig_atoms.copy()
#nsys = copy.deepcopy(nsys0)
dname = _prefix + "{0:02d}".format(i)
os.system('mkdir -p {}'.format(dname))
print(dname)
cell0 = atoms.get_cell()
emat = 0.5 * (np.dot(fmat.T, fmat) - np.identity(3)) + np.identity(3)
cell = np.dot(emat, cell0)
#print(i,emat,cell)
# cell = np.dot(cell0,fmat.T)
atoms.set_cell(cell, scale_atoms=True)
atoms.write(dname + '/POSCAR',
format='vasp',
vasp5=True,
direct=True,
sort=False)
print('prepare done')
print('')
print('After performing VASP or pmd calculations in these directories, ' +
'run the following command:')
print(' $ python elasticity.py analyze str.ref')
print('or')
print(' $ python elasticity.py analyze strs.pmd')
print('')
def read_results(self, relax=False):
"""
Only erg.pmd and frc.pmd are to be read.
"""
outfname = 'out.' + self.label
ergfname = 'erg.' + self.label
frcfname = 'frc.' + self.label
strfname = 'strs.' + self.label
if not os.path.exists(outfname):
raise RuntimeError(outfname + ' does not exists.')
if not os.path.exists(ergfname):
raise RuntimeError(ergfname + ' does not exists.')
if not os.path.exists(frcfname):
raise RuntimeError(frcfname + ' does not exists.')
if not os.path.exists(strfname):
print('Warning: ' + strfname + ' does not exists.')
self.results = {k: None for k in self.implemented_properties}
fout = open(outfname, 'r')
lines = fout.readlines()
if CALC_END_MARK not in lines[-1]:
raise RuntimeError(self.label + ' seems to stop somewhere..')
if relax:
relax_converged = False
num_step_relax = -1
for line in lines:
if 'Damped MD converged with' in line:
relax_converged = True
num_step_relax = int(line.split()[4])
break
if not relax_converged:
print('')
print('** Warning: pmd relaxation does not' +\
' seem to be converged**')
print('')
self.results['num_step_relax'] = num_step_relax
fout.close()
with open(ergfname, 'r') as f:
erg = float(f.readline().split()[0])
self.results['energy'] = erg
with open(frcfname, 'r') as f:
num = int(f.readline().split()[0])
frcs = np.zeros((num, 3))
for i in range(num):
data = [float(x) for x in f.readline().split()]
frcs[i, 0:3] = data[0:3]
self.results['forces'] = frcs
if os.path.exists(strfname):
try:
with open(strfname, 'r') as f:
strs = np.array([float(x) for x in f.readline().split()])
self.results['stress'] = strs
except:
self.results['srress'] = None
if relax:
posfile = 'pmdfin'
nsys = NAPSystem(fname=posfile, specorder=self.specorder)
#tmpatoms = read_pmd(fname=posfile,specorder=self.specorder)
tmpatoms = nsys.to_ase_atoms()
self.results['relaxed_scaled_positions'] \
= tmpatoms.get_scaled_positions()
self.results['relaxed_cell'] = tmpatoms.get_cell()