def initial_run(xcart_voids, ):
"""1. Run initial calculation"""
if debug:
cl = CalculationVasp()
cl.read_poscar('1.POSCAR')
cl.end = cl.init
if xcart_voids: # read void coordinates
cl.end = cl.end.add_atoms(xcart_voids, 'void')
last_number = 0
else:
files_yes = glob.glob('*yes.pickle') #get list of calculated yes files
files_all = glob.glob('*.pickle') #get list of all calculated files
"""Find last yes pickle file"""
if files_yes:
yes_numbers = [int(file.split('-')[0]) for file in files_yes]
all_numbers = [int(file.split('-')[0]) for file in files_all]
last_yes_n = max(yes_numbers)
last_number = max(all_numbers)
last_yes_file = str(last_yes_n)+'-yes.pickle'
printlog('Last calculation file is ', last_yes_file, imp = 'y')
else:
last_number = 0
last_yes_file = None
"""Read last pickle file or run vasp """
if last_yes_file:
cl = CalculationVasp().deserialize(last_yes_file)
printlog('Successfully deserialized')
xcart_voids = cl.end.get_specific_elements([300], fmt = 'x') # extract voids form the last calculation
else:
cl = vasp_run(3, 'first run', vasprun_command = vasprun_command)
if xcart_voids: # read void coordinates
cl.end = cl.end.add_atoms(xcart_voids, 'void')
printlog('I found', len(xcart_voids), 'voids in config file. Added to structure.')
if check(cl) == 0:
cl.serialize('0-yes')
copyfile('OUTCAR', 'OUTCAR-0')
copyfile('OSZICAR', 'OSZICAR-0')
copyfile('CONTCAR', 'CONTCAR-0')
copyfile('OUTCAR', 'OUTCAR_last')
copyfile('CONTCAR', 'CONTCAR_last')
with open('ENERGIES', 'w') as f:
f.write('{:5d} {:.5f}\n'.format(0, cl.e0))
else:
printlog('Calculation is broken, no data was saved, exiting ...', imp = 'y')
sys.exit()
if debug2:
sys.exit()
return cl, last_number
last_yes_file = None
"""Read last pickle file or run vasp """
if last_yes_file:
cl = CalculationVasp().deserialize(last_yes_file)
printlog('Successfully deserialized')
if 0:
#to correct mistake on first step and add void to pickle
if 'xvoid' in params and len(
params['xvoid']) > 0: # read void coordinates
cl.end = cl.end.add_atoms(params['xvoid'], 'void')
printlog('I found', len(params['xvoid']),
'voids in config file. Added to structure.')
cl.serialize('0-yes')
else:
cl = vasp_run(3, 'first run')
if 'xvoid' in params and len(
params['xvoid']) > 0: # read void coordinates
cl.end = cl.end.add_atoms(params['xvoid'], 'void')
printlog('I found', len(params['xvoid']),
'voids in config file. Added to structure.')
cl.serialize('0-yes')
copyfile('OSZICAR', 'OSZICAR-0')
copyfile('CONTCAR', 'CONTCAR-0')
with open('ENERGIES', 'w') as f:
f.write('{:5d} {:.5f}\n'.format(0, cl.e0))
printlog('Energies before and after are {:3.3f} and {:3.3f}, dE = {:3.3f}'.format(E1, E2, E2 - E1), imp = 'y')
with open('ENERGIES', 'a') as f:
f.write('{:5d} {:.5f}\n'.format(i_mcstep, cl_new.e0))
if metropolis(E1, E2, temperature):
cl = cl_new
if xcart_voids:
#insert voids
cl_new.end = cl_new.end.add_atoms(xcart_voids, 'void') # here voids are inserted back
if not debug:
cl.serialize(str(i_mcstep)+'-yes')
copyfile('CONTCAR', 'CONTCAR_last')
copyfile('OUTCAR', 'OUTCAR_last')
if os.path.exists('LOCPOT'):
copyfile('LOCPOT', 'LOCPOT_last')
st = cl_new.end
printlog('The step was accepted', imp = 'y')
else:
printlog('The step was rejected', imp = 'y')
if not debug:
cl_new.serialize(str(i_mcstep)+'-no')