def __init__(self, symbol, filename=None, index=None, txt=None):
if filename is None or filename == '-':
formula, index = get_system(symbol)
filename = restart_filename % formula
calc = Calculator(filename, txt=txt)
atoms = calc.get_atoms()
symbols = atoms.get_chemical_symbols()
if index is None:
index = symbols.index(symbol)
else:
if not symbols[index] == symbol:
raise ValueError(('Atom (%s) at specified index (%d) not of '+
'requested type (%s)') % (symbols[index],
index, symbol))
self.calc = calc
self.filename = filename
self.atoms = atoms
self.symbol = symbol
self.symbols = symbols
self.index = index
self.cell = atoms.get_cell().diagonal() # cubic cell
#self.center = atoms.positions[index]
self.spos_ac = atoms.positions / self.cell
self.gpts = calc.wfs.gd.N_c
if calc.kpt_u[0].psit_nG is None:
raise RuntimeError('No wave functions found in .gpw file')
def __init__(self, symbol, filename=None, index=None, txt=None):
if filename is None or filename == '-':
formula, index = get_system(symbol)
filename = restart_filename % formula
calc = Calculator(filename, txt=txt)
atoms = calc.get_atoms()
symbols = atoms.get_chemical_symbols()
if index is None:
index = symbols.index(symbol)
else:
if not symbols[index] == symbol:
raise ValueError(
('Atom (%s) at specified index (%d) not of ' +
'requested type (%s)') % (symbols[index], index, symbol))
self.calc = calc
self.filename = filename
self.atoms = atoms
self.symbol = symbol
self.symbols = symbols
self.index = index
self.cell = atoms.get_cell().diagonal() # cubic cell
#self.center = atoms.positions[index]
self.spos_ac = atoms.positions / self.cell
self.gpts = calc.wfs.gd.N_c
if calc.kpt_u[0].psit_nG is None:
raise RuntimeError('No wave functions found in .gpw file')
txt=file_prefix + '.txt',
tolerance=1e-10)
fcc.set_calculator(calc)
#fcc[0].set_magnetic_moment(magmom)
e = fcc.get_potential_energy()
calc.write(file_prefix + '.gpw')
del calc, fcc
for nhosts in nhostsread:
file_prefix = 'Fe_%d_%1.1f_par%d' % (nkpt, magmom, nhosts)
print '------ restart calculation ', file_prefix, rank * 111111111
calc = Calculator(file_prefix + '.gpw',
txt=file_prefix + '_restart.txt',
tolerance=1e-10)
atoms = calc.get_atoms()
atoms.positions[0] = (0, 0, -0.0001)
erg = atoms.get_potential_energy()
result = 'ok'
equal(e, erg, 1e-4)
niter = calc.niter
tests.append((test, result, niter, nhosts))
del calc, atoms
for test in tests:
print "%s ---- %10s --- %d ---- %d " % (test[0], test[1], test[2], test[3])
nhosts = 8
txt=file_prefix+'.txt',
tolerance = 1e-10)
fcc.set_calculator(calc)
#fcc[0].set_magnetic_moment(magmom)
e = fcc.get_potential_energy()
calc.write(file_prefix+'.gpw')
del calc,fcc
for nhosts in nhostsread:
file_prefix = 'Fe_%d_%1.1f_par%d'%(nkpt,magmom,nhosts)
print '------ restart calculation ',file_prefix, rank*111111111
calc = Calculator(file_prefix+'.gpw',
txt=file_prefix+'_restart.txt',
tolerance = 1e-10)
atoms = calc.get_atoms()
atoms.positions[0] = (0, 0, -0.0001)
erg = atoms.get_potential_energy()
result = 'ok'
equal(e,erg,1e-4)
niter = calc.niter
tests.append((test,result,niter,nhosts))
del calc,atoms
for test in tests:
print "%s ---- %10s --- %d ---- %d "%(test[0],test[1],test[2],test[3])
