def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hs:o:n:b:e:t:", ["help", "structure=", "output=", "nparal=",
"binary=", "energy_tol=", "target_forces="])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
workdir = '.'
structure_file = 'POSCAR'
output_file = 'pcm_results.json'
nparal = 2
energy_tol = 1E-3
target_forces = 1E-3
binary = 'vasp'
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-s", "--structure"):
structure_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-e", "--energy_tol"):
energy_tol = get_float(arg)
elif opt in ("-t", "--target_forces"):
target_forces = get_float(arg)
elif opt in ("-s", "--structure"):
structure_file = arg
structure = pychemia.structure_from_file(structure_file)
if structure is None:
print(" ERROR: Invalid structure, no structure could be obtained from '%s'" % structure_file)
sys.exit(2)
if structure_file == 'POSCAR':
os.rename('POSCAR', 'POSCAR_original')
print("\n PyChemia VASP Relaxator")
print(" =======================\n")
print(" VASP binary : ", binary)
print(" Energy tolerance : ", energy_tol)
print(" Target forces : ", target_forces)
print(" MPI number of procs : ", nparal)
print(" Structure :\n")
print(structure)
wf = open(output_file, 'w')
data = {'input': {'binary': binary,
'energy_tol': energy_tol,
'target_forces': target_forces,
'nparal': nparal,
'structure': structure.to_dict}}
json.dump(data, wf)
wf.close()
# First Round (Relaxing the original structure)
print('\nFirst Round')
print('===========')
cleaner()
print('\nConvergence of Cut-off Energy')
print('-----------------------------\n')
ce = ConvergenceCutOffEnergy(structure, energy_tolerance=energy_tol)
if os.path.isfile('convergence_encut.json'):
print('A previous convergence study was found, loading...')
ce.load()
if not ce.is_converge:
ce.run(nparal)
ce.save()
ce.plot()
encut = ce.best_encut
data['output'] = {'1R_ENCUT': encut}
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
print('\nConvergence of K-Point Grid')
print('---------------------------\n')
ck = ConvergenceKPointGrid(structure, encut=encut, energy_tolerance=energy_tol)
if os.path.isfile('convergence_kpoints.json'):
print('A previous convergence study was found, loading...')
ce.load()
if not ce.is_converge:
ce.run(nparal)
ce.save()
ce.plot()
kp = ck.best_kpoints
data['output'] = {'1R_KPOINTS': list(kp.grid)}
print(data)
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
os.rename('convergence_encut.json', 'convergence_encut_phase1.json')
os.rename('convergence_encut.pdf', 'convergence_encut_phase1.pdf')
os.rename('convergence_kpoints.json', 'convergence_kpoints_phase1.json')
os.rename('convergence_kpoints.pdf', 'convergence_kpoints_phase1.pdf')
cleaner()
print('\nIonic Relaxation')
print('----------------\n')
vr = IonRelaxation(structure=structure, encut=encut, kp_grid=kp.grid, workdir=workdir,
target_forces=10 * target_forces)
vr.run(nparal)
structure = vr.get_final_geometry()
structure.save_json(workdir + os.sep + 'structure_phase1.json')
data['output'] = {'1R_structure': structure.to_dict}
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
# Second Round (Symetrize structure and redo convergences)
st = symmetrize(structure)
print('\nSecond Round')
print('============')
cleaner()
print('\nConvergence of K-Point Grid')
print('---------------------------\n')
ck = ConvergenceKPointGrid(st, encut=encut, energy_tolerance=energy_tol, recover=True)
ck.run(nparal)
ck.save()
ck.plot()
kp = ck.best_kpoints
data['output'] = {'2R_KPOINTS': list(kp.grid)}
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
print('\nConvergence of Cut-off Energy')
print('-----------------------------\n')
ce = ConvergenceCutOffEnergy(st, energy_tolerance=energy_tol, kpoints=kp)
ce.run(nparal)
ce.save()
ce.plot()
encut = ce.best_encut
data['output'] = {'2R_ENCUT': encut}
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
os.rename('convergence_encut.json', 'convergence_encut_phase2.json')
os.rename('convergence_encut.pdf', 'convergence_encut_phase2.pdf')
os.rename('convergence_kpoints.json', 'convergence_kpoints_phase2.json')
os.rename('convergence_kpoints.pdf', 'convergence_kpoints_phase2.pdf')
cleaner()
print('\nIonic Relaxation')
print('----------------\n')
vr = IonRelaxation(structure=st, workdir='.', encut=encut, kp_grid=kp.grid, target_forces=target_forces)
vr.run(nparal)
structure = vr.get_final_geometry()
structure.save_json(workdir + os.sep + 'structure_phase2.json')
data['output'] = {'2R_structure': structure.to_dict}
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hi:p:", ["help", "ip=", "port="])
except getopt.GetoptError:
print('Wrong parsing of options')
usage(argv[0])
sys.exit(2)
# Default Values
port = None
ip = None
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-p", "--port"):
port = get_int(arg)
elif opt in ("-i", "--ip"):
ip = arg
if ip is None:
ip = socket.gethostbyname(socket.gethostname())
print('PyChemia Client connecting to server on : ', ip)
workdir = None
entry_id = None
while True:
if port is not None:
try:
workdir, entry_id = inquirer(ip, port)
except TimedOutExc as e:
print("INQUIRER took too long: %s", e.message)
else:
lt = time.localtime()
random.seed(lt.tm_yday * 24 + lt.tm_hour)
rndport = random.randint(10000, 20000)
print('PyChemia Client using port : ', rndport)
try:
workdir, entry_id = inquirer(ip, rndport)
except TimedOutExc as e:
print("Error({0}): {1}".format(e, e.message))
print('We got the workdir: ', workdir)
print('The entry_id is : ', entry_id)
if workdir is not None and entry_id is not None:
if entry_id == '':
print('No entries to execute, taking a nap')
time.sleep(15)
else:
break
else:
'Inquierer failed to get data, retry...'
executor(workdir)
if port is not None:
finisher(entry_id, ip, port)
else:
lt = time.localtime()
random.seed(lt.tm_yday * 24 + lt.tm_hour)
rndport = random.randint(10000, 20000)
print('PyChemia Client using port : ', rndport)
try:
finisher(entry_id, ip, rndport)
except TimedOutExc as e:
print("Error({0}): {1}".format(e, e.message))
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hs:o:n:b:e:", ["help", "structure=", "output=", "nparal=",
"binary=", "energy_tol="])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
structure_file = 'POSCAR'
output_file = 'static_calculation.json'
nparal = 2
energy_tol = 1E-3
binary = 'vasp'
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-s", "--structure"):
structure_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-e", "--energy_tol"):
energy_tol = get_float(arg)
elif opt in ("-s", "--structure"):
structure_file = get_int(arg)
structure = pychemia.structure_from_file(structure_file)
if structure is None:
print(" ERROR: Invalid structure, no structure could be obtained from '%s'" % structure_file)
sys.exit(2)
if structure_file == 'POSCAR':
os.rename('POSCAR', 'POSCAR_original')
print("\n PyChemia VASP Static")
print(" =======================\n")
print(" Executable : ", binary)
print(" Energy tolerance : ", energy_tol)
print(" MPI number of procs : ", nparal)
print(" Structure :\n")
print(structure)
data = {}
cleaner()
print('\nConvergence of Cut-off Energy')
print('-----------------------------\n')
ce = ConvergenceCutOffEnergy(structure, energy_tolerance=energy_tol, binary=binary)
ce.run(nparal)
ce.save()
ce.plot()
encut = ce.best_encut
cvg = json.load(open('task.json'))
data['Convergece Cut-off'] = cvg
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
print('\nConvergence of K-Point Grid')
print('---------------------------\n')
ck = ConvergenceKPointGrid(structure, encut=encut, energy_tolerance=energy_tol, binary=binary)
ck.run(nparal)
ck.save()
ck.plot()
kp = ck.best_kpoints
cvg = json.load(open('task.json'))
data['Convergece KPoints'] = cvg
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
job = StaticCalculation(structure, encut=encut, kpoints=kp, binary=binary)
job.run(nparal)
job.save()
cvg = json.load(open('task.json'))
data['Static'] = cvg
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hs:o:i:f:d:n:b:e:x:t:", ["help", "structure=", "output=", "ini_factor=",
"fin_factor=", "delta_factor", "nparal=",
"binary=", "energy_tol=", "expansion=",
"target_forces"])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
structure_file = 'POSCAR'
delta_factor = 0.01
ini_factor = 0.01
fin_factor = 0.1
output_file = 'IdealStrength.json'
nparal = 2
energy_tol = 1E-3
target_forces = 1E-3
binary = 'vasp'
expansion = 111
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-s", "--structure"):
structure_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-i", "--ini_factor"):
ini_factor = get_float(arg)
elif opt in ("-f", "--fin_factor"):
fin_factor = get_float(arg)
elif opt in ("-d", "--delta_factor"):
delta_factor = get_float(arg)
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-e", "--energy_tol"):
energy_tol = get_float(arg)
elif opt in ("-t", "--target_forces"):
target_forces = get_float(arg)
elif opt in ("-x", "--expansion"):
expansion = get_int(arg)
elif opt in ("-s", "--structure"):
structure_file = get_int(arg)
expansion = [int(expansion / 100), int(expansion / 10) % 10, expansion % 10]
if len(expansion) == 0:
print(" ERROR: ini_factor, fin_factor and delta_factor are not creating a finite range of values")
sys.exit(2)
structure = pychemia.structure_from_file(structure_file)
if structure is None:
print(" ERROR: Invalid structure, no structure could be obtained from '%s'" % structure_file)
sys.exit(2)
if structure_file == 'POSCAR':
os.rename('POSCAR', 'POSCAR_original')
print("\n PyChemia Ideal Strenght")
print(" =======================\n")
print(" Scaling factors : ", str(np.arange(ini_factor, fin_factor + 0.9 * delta_factor, delta_factor)))
print(" Executable : ", binary)
print(" Energy tolerance : ", energy_tol)
print(" Target forces : ", target_forces)
print(" Expansion directions: ", str(expansion))
print(" MPI number of procs : ", nparal)
print(" Structure :\n")
print(structure)
cleaner()
print('\nConvergence of Cut-off Energy')
print('-----------------------------\n')
ce = ConvergenceCutOffEnergy(structure, energy_tolerance=energy_tol, binary=binary)
if os.path.isfile('convergence_encut.json'):
print('A previous convergence study was found, loading...')
ce.load()
if not ce.is_converge:
ce.run(nparal)
ce.save()
ce.plot()
encut = ce.best_encut
print('ENCUT: ', encut)
cleaner()
print('\nConvergence of K-Point Grid')
print('---------------------------\n')
ck = ConvergenceKPointGrid(structure, workdir='.', binary=binary, encut=encut,
energy_tolerance=energy_tol, recover=True)
if os.path.isfile('convergence_kpoints.json'):
print('A previous convergence study was found, loading...')
ck.load()
if not ck.is_converge:
ck.run(nparal)
ck.save()
ck.plot()
kp = ck.best_kpoints
kp_density = kp.get_density_of_kpoints(structure.lattice)
print('KPOINT GRID', kp.grid)
strenght = IdealStrength(structure, ini_factor, fin_factor, delta_factor, kp, kp_density, expansion, encut,
nparal, binary, target_forces, output_file)
strenght.run(nparal)
strenght.save()
cleaner()
def main(argv):
try:
opts, args = getopt.getopt(
argv[1:], "hi:o:n:b:p:",
["help", "input=", "output=", "nparal=", "binary=", 'pseudo='])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
workdir = '.'
inpu_file = 'abinit.in'
output_file = 'pcm_results.json'
nparal = 2
binary = 'abinit'
pseudo = 'FHI_LDA'
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-i", "--input"):
inpu_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-p", "--pseudo"):
pseudo = arg
structure = pychemia.code.abinit.AbinitInput(inpu_file).get_structure()
if structure is None:
print(" ERROR: Invalid structure, no structure could be obtained")
sys.exit(2)
print("\n PyChemia ABINIT Job")
print(" =======================\n")
print(" MPI number of procs : ", nparal)
print(" ABINIT binary : ", binary)
print(" ABINIT input_file : ", inpu_file)
print(" ABINIT pseudo : ", pseudo)
print(" Structure :\n")
print(structure)
wf = open(output_file, 'w')
data = {
'input': {
'binary': binary,
'nparal': nparal,
'structure': structure.to_dict
},
'complete': False,
}
json.dump(data, wf, sort_keys=True)
wf.close()
cleaner()
aj = pychemia.code.abinit.AbinitJob()
aj.initialize(workdir=workdir,
input_file='abinit.in',
psp_kind=pseudo.split('_')[0],
psp_exchange=pseudo.split('_')[1])
aj.set_inputs()
if os.path.exists('abinit.out'):
os.remove('abinit.out')
aj.run(use_mpi=True, omp_max_threads=2, mpi_num_procs=nparal)
time.sleep(5)
ao = pychemia.code.abinit.AbinitOutput('abinit.out')
old_niter = 0
while aj.runner.returncode is None:
aj.runner.poll()
ao.reload()
energetics = ao.get_energetics()
if energetics is not None:
if len(energetics['iter']) > old_niter:
print(
"ITER %4d ETOT= %15.8f deltaE(h)= %9.2E residm= %9.2E nres2= %9.2E"
% (energetics['iter'][-1], energetics['etot'][-1],
energetics['deltaEh'][-1], energetics['residm'][-1],
energetics['nres2'][-1]))
old_niter = len(energetics['iter'])
time.sleep(60)
ao.reload()
energetics = ao.get_energetics()
occupation_matrix = ao.get_occupation_matrix()
output = {'energetics': energetics}
if occupation_matrix is not None:
output['occupation_matrix'] = occupation_matrix
if os.path.isfile('abinit-o_OUT.nc'):
nco = pychemia.code.abinit.netcdf2dict('abinit-o_OUT.nc')
output['variables'] = nco
data['output'] = output
data['complete'] = True
wf = open(output_file, 'w')
json.dump(data, wf, sort_keys=True)
wf.close()
cleaner()
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hs:o:n:b:e:", [
"help", "structure=", "output=", "nparal=", "binary=",
"energy_tol="
])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
structure_file = 'POSCAR'
output_file = 'static_calculation.json'
nparal = 2
energy_tol = 1E-3
binary = 'vasp'
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-s", "--structure"):
structure_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-e", "--energy_tol"):
energy_tol = get_float(arg)
elif opt in ("-s", "--structure"):
structure_file = get_int(arg)
structure = pychemia.structure_from_file(structure_file)
if structure is None:
print(
" ERROR: Invalid structure, no structure could be obtained from '%s'"
% structure_file)
sys.exit(2)
if structure_file == 'POSCAR':
os.rename('POSCAR', 'POSCAR_original')
print("\n PyChemia VASP Static")
print(" =======================\n")
print(" Executable : ", binary)
print(" Energy tolerance : ", energy_tol)
print(" MPI number of procs : ", nparal)
print(" Structure :\n")
print(structure)
data = {}
cleaner()
print('\nConvergence of Cut-off Energy')
print('-----------------------------\n')
ce = ConvergenceCutOffEnergy(structure,
energy_tolerance=energy_tol,
binary=binary)
ce.run(nparal)
ce.save()
ce.plot()
encut = ce.best_encut
cvg = json.load(open('task.json'))
data['Convergece Cut-off'] = cvg
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
print('\nConvergence of K-Point Grid')
print('---------------------------\n')
ck = ConvergenceKPointGrid(structure,
encut=encut,
energy_tolerance=energy_tol,
binary=binary)
ck.run(nparal)
ck.save()
ck.plot()
kp = ck.best_kpoints
cvg = json.load(open('task.json'))
data['Convergece KPoints'] = cvg
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
job = StaticCalculation(structure, encut=encut, kpoints=kp, binary=binary)
job.run(nparal)
job.save()
cvg = json.load(open('task.json'))
data['Static'] = cvg
wf = open(output_file, 'w')
json.dump(data, wf)
wf.close()
cleaner()
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hd:p:i:w:", ["help", "dbsettings_file=", "port=", "ip=", 'workdir='])
except getopt.GetoptError:
print('Error with options')
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
workdir = None
dbsettings_file = None
port = None
ip = None
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-w", "--workdir"):
workdir = arg
elif opt in ("-d", "--dbsettings_file"):
dbsettings_file = arg
elif opt in ("-p", "--port"):
port = get_int(arg)
elif opt in ("-i", "--ip"):
ip = arg
if workdir is None:
print('Missing workdir')
usage(argv[0])
sys.exit()
if not os.path.isdir(workdir):
os.mkdir(workdir)
print('dbsettings_file:', dbsettings_file)
if dbsettings_file is None or not os.path.exists(dbsettings_file):
print('Missing dbsettings')
usage(argv[0])
sys.exit()
else:
dbsettings = json.load(open(dbsettings_file))
if ip is None:
ip = socket.gethostbyname(socket.gethostname())
print('PyChemia Server binded to IP: ', ip)
pcq = get_database(dbsettings)
print('Connected with database, number of entries: ', pcq.db.pychemia_entries.count())
if port is not None:
print('Using port : %s' % port)
p = multiprocessing.Process(target=listener, args=(dbsettings, ip, port, workdir))
p.start()
else:
old_port = 0
p = None
while True:
lt = time.localtime()
random.seed(lt.tm_yday * 24 + lt.tm_hour)
port = random.randint(10000, 20000)
if port != old_port:
if p is not None and p.is_alive():
print('Terminating listener on port : %s' % old_port)
p.terminate()
print('Using port : %s' % port)
p = multiprocessing.Process(target=listener, args=(dbsettings, ip, port, workdir))
p.start()
old_port = port
time.sleep(300)
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hs:o:i:f:d:n:b:e:x:t:", [
"help", "structure=", "output=", "ini_factor=", "fin_factor=",
"delta_factor", "nparal=", "binary=", "energy_tol=", "expansion=",
"target_forces"
])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
structure_file = 'POSCAR'
delta_factor = 0.01
ini_factor = 0.01
fin_factor = 0.1
output_file = 'IdealStrength.json'
nparal = 2
energy_tol = 1E-3
target_forces = 1E-3
binary = 'vasp'
expansion = 111
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-s", "--structure"):
structure_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-i", "--ini_factor"):
ini_factor = get_float(arg)
elif opt in ("-f", "--fin_factor"):
fin_factor = get_float(arg)
elif opt in ("-d", "--delta_factor"):
delta_factor = get_float(arg)
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-e", "--energy_tol"):
energy_tol = get_float(arg)
elif opt in ("-t", "--target_forces"):
target_forces = get_float(arg)
elif opt in ("-x", "--expansion"):
expansion = get_int(arg)
elif opt in ("-s", "--structure"):
structure_file = get_int(arg)
expansion = [
int(expansion / 100),
int(expansion / 10) % 10, expansion % 10
]
if len(expansion) == 0:
print(
" ERROR: ini_factor, fin_factor and delta_factor are not creating a finite range of values"
)
sys.exit(2)
structure = pychemia.structure_from_file(structure_file)
if structure is None:
print(
" ERROR: Invalid structure, no structure could be obtained from '%s'"
% structure_file)
sys.exit(2)
if structure_file == 'POSCAR':
os.rename('POSCAR', 'POSCAR_original')
print("\n PyChemia Ideal Strenght")
print(" =======================\n")
print(
" Scaling factors : ",
str(
np.arange(ini_factor, fin_factor + 0.9 * delta_factor,
delta_factor)))
print(" Executable : ", binary)
print(" Energy tolerance : ", energy_tol)
print(" Target forces : ", target_forces)
print(" Expansion directions: ", str(expansion))
print(" MPI number of procs : ", nparal)
print(" Structure :\n")
print(structure)
cleaner()
print('\nConvergence of Cut-off Energy')
print('-----------------------------\n')
ce = ConvergenceCutOffEnergy(structure,
energy_tolerance=energy_tol,
binary=binary)
if os.path.isfile('convergence_encut.json'):
print('A previous convergence study was found, loading...')
ce.load()
if not ce.is_converge:
ce.run(nparal)
ce.save()
ce.plot()
encut = ce.best_encut
print('ENCUT: ', encut)
cleaner()
print('\nConvergence of K-Point Grid')
print('---------------------------\n')
ck = ConvergenceKPointGrid(structure,
workdir='.',
binary=binary,
encut=encut,
energy_tolerance=energy_tol,
recover=True)
if os.path.isfile('convergence_kpoints.json'):
print('A previous convergence study was found, loading...')
ck.load()
if not ck.is_converge:
ck.run(nparal)
ck.save()
ck.plot()
kp = ck.best_kpoints
kp_density = kp.get_density_of_kpoints(structure.lattice)
print('KPOINT GRID', kp.grid)
strenght = IdealStrength(structure, ini_factor, fin_factor, delta_factor,
kp, kp_density, expansion, encut, nparal, binary,
target_forces, output_file)
strenght.run(nparal)
strenght.save()
cleaner()
def main(argv):
try:
opts, args = getopt.getopt(argv[1:], "hi:o:n:b:p:", ["help", "input=", "output=", "nparal=", "binary=",
'pseudo='])
except getopt.GetoptError:
usage(argv[0])
sys.exit(2)
if len(opts) == 0:
usage(argv[0])
sys.exit(2)
# Default Values
workdir = '.'
inpu_file = 'abinit.in'
output_file = 'pcm_results.json'
nparal = 2
binary = 'abinit'
pseudo = 'FHI_LDA'
for opt, arg in opts:
if opt in ("-h", "--help"):
usage(argv[0])
sys.exit()
elif opt in ("-i", "--input"):
inpu_file = arg
elif opt in ("-o", "--output"):
output_file = arg
elif opt in ("-n", "--nparal"):
nparal = get_int(arg)
elif opt in ("-b", "--binary"):
binary = arg
elif opt in ("-p", "--pseudo"):
pseudo = arg
structure = pychemia.code.abinit.AbinitInput(inpu_file).get_structure()
if structure is None:
print(" ERROR: Invalid structure, no structure could be obtained")
sys.exit(2)
print("\n PyChemia ABINIT Job")
print(" =======================\n")
print(" MPI number of procs : ", nparal)
print(" ABINIT binary : ", binary)
print(" ABINIT input_file : ", inpu_file)
print(" ABINIT pseudo : ", pseudo)
print(" Structure :\n")
print(structure)
wf = open(output_file, 'w')
data = {'input': {'binary': binary, 'nparal': nparal, 'structure': structure.to_dict}, 'complete': False, }
json.dump(data, wf, sort_keys=True)
wf.close()
cleaner()
aj = pychemia.code.abinit.AbinitJob()
aj.initialize(workdir=workdir, input_file='abinit.in',
psp_kind=pseudo.split('_')[0],
psp_exchange=pseudo.split('_')[1])
aj.set_inputs()
if os.path.exists('abinit.out'):
os.remove('abinit.out')
aj.run(use_mpi=True, omp_max_threads=2, mpi_num_procs=nparal)
time.sleep(5)
ao = pychemia.code.abinit.AbinitOutput('abinit.out')
old_niter = 0
while aj.runner.returncode is None:
aj.runner.poll()
ao.reload()
energetics = ao.get_energetics()
if energetics is not None:
if len(energetics['iter']) > old_niter:
print("ITER %4d ETOT= %15.8f deltaE(h)= %9.2E residm= %9.2E nres2= %9.2E" % (energetics['iter'][-1],
energetics['etot'][-1],
energetics['deltaEh'][-1],
energetics['residm'][-1],
energetics['nres2'][-1]))
old_niter = len(energetics['iter'])
time.sleep(60)
ao.reload()
energetics = ao.get_energetics()
occupation_matrix = ao.get_occupation_matrix()
output = {'energetics': energetics}
if occupation_matrix is not None:
output['occupation_matrix'] = occupation_matrix
if os.path.isfile('abinit-o_OUT.nc'):
nco = pychemia.code.abinit.netcdf2dict('abinit-o_OUT.nc')
output['variables'] = nco
data['output'] = output
data['complete'] = True
wf = open(output_file, 'w')
json.dump(data, wf, sort_keys=True)
wf.close()
cleaner()
