def run_vasp(override=[], suffix=''):
'''
execute vasp with given override and suffix
:param override:
:param suffix:
:return:
'''
from Classes_Pymatgen import Incar
from Classes_Custodian import StandardJob
from custodian.custodian import Custodian
import os
# Determine wheter to use Gamma optimized vasp
incar = Incar.from_file('INCAR')
if 'AUTO_GAMMA' in incar and incar['AUTO_GAMMA']:
vasp = os.environ['VASP_GAMMA']
else:
vasp = os.environ['VASP_KPTS']
handlers = []
vaspjob = [StandardJob(['mpirun', '-np', os.environ['VASP_PROCS'], vasp], 'vasp.log', auto_npar=False, backup=False,
settings_override=override, suffix=suffix, final=False)]
c = Custodian(handlers, vaspjob, max_errors=10)
c.run()
def run_vasp(override=[], suffix='', walltime=None, buffer_time=None):
"""
execute vasp with given override and suffix
:param override:
:param suffix:
:return:
"""
from Classes_Pymatgen import Incar
from Classes_Custodian import StandardJob
from custodian.custodian import Custodian
import os
# Determine wheter to use Gamma optimized vasp
incar = Incar.from_file('INCAR')
if 'AUTO_GAMMA' in incar and incar['AUTO_GAMMA']:
vasp = os.environ['VASP_GAMMA']
else:
vasp = os.environ['VASP_KPTS']
handlers = []
if walltime:
handlers += [
WalltimeHandler(
wall_time=walltime,
buffer_time=buffer_time,
electronic_step_stop=True,
)
]
if os.environ['VASP_MPI'] == 'srun':
vaspjob = [
StandardJob(['srun', vasp],
'vasp.log',
auto_npar=False,
backup=False,
settings_override=override,
suffix=suffix,
final=False)
]
else:
vaspjob = [
StandardJob(['mpirun', '-np', os.environ['VASP_PROCS'], vasp],
'vasp.log',
auto_npar=False,
backup=False,
settings_override=override,
suffix=suffix,
final=False)
]
c = Custodian(handlers, vaspjob, max_errors=10)
c.run()
def neb2dim(neb_dir, dimer_dir, ts_i=None):
if not ts_i:
neb_dir = os.path.abspath(neb_dir)
dimer_dir = os.path.abspath(dimer_dir)
try:
energies = NEBAnalysis.from_dir(neb_dir).energies
except:
if input('Failed, do: rm ' + neb_dir + '*/*.xyz and try again? (y)') == 'y':
os.system('rm ' + neb_dir + '/*/*.xyz')
energies = NEBAnalysis.from_dir(neb_dir).energies
else:
raise Exception('Could not read NEB dir')
ts_i = list(energies).index(energies.max())
print('Copying TS directory {}'.format(str(ts_i).zfill(2)))
if not os.path.exists(dimer_dir):
os.makedirs(dimer_dir)
for f in os.listdir(os.path.join(neb_dir, str(ts_i).zfill(2))):
shutil.copy(os.path.join(neb_dir, str(ts_i).zfill(2), f), dimer_dir)
for f in ['INCAR', 'KPOINTS', 'POTCAR']:
shutil.copy(os.path.join(neb_dir, f), dimer_dir)
print('Modifying INCAR')
incar = Incar.from_file(os.path.join(dimer_dir, 'INCAR'))
incar['ICHAIN'] = 2
incar['EDIFF'] = 1e-7
incar['NSW'] = 5000
if 'neb' in incar['SYSTEM']:
incar['SYSTEM'] = incar['SYSTEM'].replace('neb', 'dim')
else:
incar['SYSTEM'] = incar['SYSTEM'] + ' dim'
for neb_setting in ['IMAGES', 'LCLIMB']:
if neb_setting in incar:
del incar[neb_setting]
incar.write_file(os.path.join(dimer_dir, 'INCAR'))
print('Making MODECAR')
mode1 = os.path.join(neb_dir, str(ts_i - 1).zfill(2))
mode2 = os.path.join(neb_dir, str(ts_i + 1).zfill(2))
cwd = os.path.abspath('.')
os.chdir(dimer_dir)
os.system('modemake.pl ' + mode1 + '/CONTCAR ' + mode2 + '/CONTCAR &> /dev/null')
os.chdir(cwd)
def write_run(run, run_folder, write_vasprun=False):
os.makedirs(run_folder, exist_ok=True)
incar = Incar.from_dict(run['incar'])
poscar = Poscar.from_dict(run['poscar'])
kpoints = Kpoints.from_dict(run['kpoints'])
energy = run['energy']
files = [
('INCAR', incar),
('KPOINTS', kpoints),
('POSCAR', poscar),
]
for filename, pymg_object in files:
pymg_object.write_file(os.path.join(run_folder, filename))
with open(os.path.join(run_folder, 'energy.txt'), 'w') as f:
f.write(str(energy))
if write_vasprun:
if not os.path.exists(os.path.join(run_folder, 'vasprun.xml')):
print(' Writing Vasprun')
get_file(fs, run['vasprun'], new_file=os.path.join(run_folder, 'vasprun.xml'))
def get_energy(i, structure: Structure, target=0.01):
"""
:param i: folder for structure to be placed in
:param structure: Structure
:param target: energy to converge to
:return: energy in eV
"""
cwd = os.path.abspath('.')
handlers = [VaspErrorHandler('vasp.log'), PositiveEnergyErrorHandler(), NonConvergingErrorHandler(nionic_steps=10, change_algo=True)]
settings = [
{'dict': 'INCAR',
'action': {'_set': {'NSW': 5000,
'IOPT': 0,
'IBRION': 3,
'EDIFFG': 1e-5,
'POTIM' : 0},
}}
]
folder = os.path.join(cwd, str(i).zfill(4))
if os.path.exists(folder):
Poscar(structure).write_file(os.path.join(folder, 'POSCAR'))
try:
vasprun_above = Vasprun(os.path.join(folder, 'above', 'vasprun.xml'))
vasprun_below = Vasprun(os.path.join(folder, 'below', 'vasprun.xml'))
if vasprun_above.converged and vasprun_below.converged:
# if vasprun_above.final_energy - vasprun_below.final_energy < target:
# for f in ['WAVECAR', 'CHGCAR', 'vasprun.xml', 'CONTCAR', 'POSCAR', 'INCAR', 'KPOINTS', 'POTCAR']
# shutil.copy(os.path.join(folder, 'above', f), f
with open(os.path.join(folder, 'energy.txt'), 'w') as f:
f.write(str(min(vasprun_above.final_energy, vasprun_below.final_energy)))
return min(vasprun_above.final_energy, vasprun_below.final_energy)
except:
try:
if os.path.exists(os.path.join(folder, 'energy.txt')):
with open(os.path.join(folder, 'energy.txt'), 'r') as f:
energy = float(f.read().split()[0])
return energy
else:
shutil.copy('INCAR', os.path.join(folder, 'INCAR'))
vasprun = Vasprun(os.path.join(folder, 'vasprun.xml'))
with open(os.path.join(folder, 'energy.txt'), 'w') as f:
f.write(str(vasprun.final_energy))
return vasprun.final_energy
except:
pass
else:
os.mkdir(folder)
above = None
below = None
for dir in [dir for dir in os.listdir(cwd) if os.path.isdir(os.path.join(cwd, dir))]:
try:
dir_i = int(dir)
if i == dir_i:
pass
if dir_i > i:
if above is None:
above = dir_i
elif dir_i - i < above - i:
above = dir_i
elif dir_i < i:
if below is None:
below = dir_i
elif dir_i - i < below - i:
below = dir_i
elif closest is None:
closest = dir
elif abs(i - int(closest)) >= abs(i - int(dir)):
closest = dir
except:
pass
same_wfxns = 0
for dir_i, dir in [(str(above).zfill(4), 'above'), (str(below).zfill(4), 'below')]:
try:
vasprun = Vasprun(os.path.join(folder, dir, 'vasprun.xml'))
if vasprun.converged:
pass
else:
raise Exception('Not Converged')
except:
os.makedirs(os.path.join(folder, dir), exist_ok=True)
if not os.path.exists(os.path.join(folder, dir, 'WAVECAR')):
try:
shutil.copy(os.path.join(dir_i, 'WAVECAR'), os.path.join(folder, dir, 'WAVECAR'))
shutil.copy(os.path.join(dir_i, 'CHGCAR'), os.path.join(folder, dir, 'CHGCAR'))
except:
if os.path.exists(os.path.join(dir_i, 'above', 'vasprun.xml')) and \
os.path.exists(os.path.join(dir_i, 'below', 'vasprun.xml')):
vasprun_above = Vasprun(os.path.join(dir_i, 'above', 'vasprun.xml'))
vasprun_below = Vasprun(os.path.join(dir_i, 'below', 'vasprun.xml'))
if vasprun_above.final_energy < vasprun_below.final_energy:
lowest_dir = 'above'
else:
lowest_dir = 'below'
shutil.copy(os.path.join(dir_i, lowest_dir, 'WAVECAR'), os.path.join(folder, dir, 'WAVECAR'))
shutil.copy(os.path.join(dir_i, lowest_dir, 'CHGCAR'), os.path.join(folder, dir, 'CHGCAR'))
if vasprun_above.final_energy - vasprun_below.final_energy < target:
same_wfxns += 1
if same_wfxns == 2:
logging.info('Wavefunctions are the same')
if os.path.exists(os.path.join(folder, dir, 'below')):
shutil.rmtree(os.path.join(folder, dir, 'below'))
shutil.copytree(os.path.join(folder, dir, 'above'), os.path.join(folder, dir, 'below'))
else:
shutil.copy('INCAR', os.path.join(folder, dir, 'INCAR'))
shutil.copy('KPOINTS', os.path.join(folder, dir, 'KPOINTS'))
shutil.copy('POTCAR', os.path.join(folder, dir, 'POTCAR'))
os.chdir(folder)
os.chdir(dir)
Poscar(structure).write_file('POSCAR')
incar = Incar.from_file('INCAR')
if 'AUTO_GAMMA' in incar and incar['AUTO_GAMMA']:
vasp = os.environ['VASP_GAMMA']
else:
vasp = os.environ['VASP_KPTS']
incar.write_file('INCAR')
if os.environ['VASP_MPI'] == 'srun':
j = StandardJob([os.environ['VASP_MPI'], vasp], 'vasp.log', auto_npar=False, final=True, settings_override=settings)
else:
j = StandardJob([os.environ['VASP_MPI'], '-np', os.environ['PBS_NP'], vasp], 'vasp.log', auto_npar=False, final=True, settings_override=settings)
c = Custodian(handlers, [j], max_errors=10)
c.run()
os.chdir(cwd)
return get_energy(i, structure)
# if (lb_e <= cutoff and ub_e >= cutoff) or (ub_e - lb_e > max_range and lb_e <= cutoff + max_range / 2 and ub_e >= cutoff - max_range / 2):
print('{} {}'.format(material,i))
material_folder = os.path.join(folder, material, str(i))
lb = ts['lb'][i - 1]
ubs = ts['ub'][i-1]
start = mat['start']
final = mat['finals'][i-1]
#Write LB
write_run(start, os.path.join(material_folder, 'start'), write_vasprun=True)
write_run(final, os.path.join(material_folder, 'final'), write_vasprun=True)
write_run(lb, os.path.join(material_folder, 'lb'), write_vasprun=True)
write_run(mat['base'], os.path.join(material_folder, 'base'), write_vasprun=True)
incar = Incar.from_dict(lb['incar'])
incar['IMAGES'] = 1
incar['SPRING'] = 0
incar['LCLIMB'] = False
incar['ISTART'] = 0
incar['ICHARG'] = 2
incar['IOPT'] = 1
incar['IBRION'] = 3
incar['POTIM'] = 0
incar['EDIFFG'] = -0.05
incar['EDIFF'] = 1e-5
incar['NELM'] = 100
incar['NSW'] = 5000
kpoints = Kpoints.from_dict(lb['kpoints'])
potcar = lb['potcar']
auto_npar=False,
backup=False,
settings_override=override,
suffix=suffix,
final=False)
]
c = Custodian(handlers, vaspjob, max_errors=10)
c.run()
try:
shutil.copy('POSCAR.real', 'POSCAR')
except:
pass
incar = Incar.from_file('INCAR')
# Check for NUPDOWNdd
if os.path.exists(
'nupdown_info'
) and 'AUTO_NUPDOWN' in incar: # Determine if full check must be done or if just using past NUPDOWN
with open('nupdown_info') as f:
lines = f.readlines()
nupdown_best = int(lines[0].strip()) # optimal NUPDOWN is first line
nupdown_iters = int(
lines[1].strip()) # number of iterations with best nupdown
if nupdown_iters < incar['AUTO_NUPDOWN_ITERS']:
nupdown_check = False
else:
nupdown_check = True
else:
nupdown_check = True
handlers = []
vaspjob = [StandardJob(['mpirun', '-np', os.environ['VASP_PROCS'], vasp], 'vasp.log', auto_npar=False, backup=False,
settings_override=override, suffix=suffix, final=False)]
c = Custodian(handlers, vaspjob, max_errors=10)
c.run()
shutil.copy('../../INCAR', 'INCAR')
shutil.copy('../../KPOINTS', 'KPOINTS')
shutil.copy('../../POTCAR', 'POTCAR')
try:
shutil.copy('POSCAR.real', 'POSCAR')
except:
pass
incar = Incar.from_file('INCAR')
# Check for NUPDOWN
if os.path.exists('nupdown_info'): # Determine if full check must be done or if just using past NUPDOWN
with open('nupdown_info') as f:
lines = f.readlines()
nupdown_best = int(lines[0].strip()) # optimal NUPDOWN is first line
nupdown_iters = int(lines[1].strip()) # number of iterations with best nupdown
if nupdown_iters < incar['AUTO_NUPDOWN_ITERS']:
nupdown_check = False
else:
nupdown_check = True
else:
nupdown_check = True
if 'AUTO_NUPDOWN' in incar and not nupdown_check: # have a guess of nupdown
override = [{"dict": "INCAR", "action": {"_set": {"NUPDOWN": nupdown_best}}}]
import numpy as np
import logging
import sys
FORMAT = '%(asctime)s %(message)s'
logging.basicConfig(format=FORMAT, level=logging.INFO, filename='run.log')
root = logging.getLogger()
root.setLevel(logging.DEBUG)
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
root.addHandler(ch)
iterate = None
i = Incar.from_file('INCAR')
atoms = read('POSCAR')# type: Atoms
if 'CONSATOM3' in i and 'CONTINUE_3PT' in i:
from Classes_ASE import LockedTo3AtomPlane
print('3 Atom Constraint cont.')
a = read('POSCAR')# type: Atoms
c = LockedTo3AtomPlane(i['DIFFATOM'], (i['CONSATOM1'], i['CONSATOM2'], i['CONSATOM3']), a.positions[i['DIFFATOM']])
elif 'CONSTYPE' in i and i['CONSTYPE'] == 'Bond':
if 'ITERATE' in i and i['ITERATE']:
from ase.constraints import FixInternals
print('Constraining Bonds to fixed length')
bond1 = atoms.get_distance(i['DIFFATOM'], i['CONSATOM1'], mic=True)
bond2 = atoms.get_distance(i['DIFFATOM'], i['CONSATOM2'], mic=True)
bonds = [
[ bond1, [ i['DIFFATOM'], i['CONSATOM1'] ] ],
[ bond2, [ i['DIFFATOM'], i['CONSATOM2'] ] ]
