def test_from_file_3(self):
"""
Test (pychemia.core.from_file) :
"""
filename = 'tests/data/abinit_05/structure.json'
st = pychemia.structure_from_file(filename)
self.assertEqual(st.nsites, 20)
def test_from_file_1(self):
"""
Test (pychemia.core.from_file) :
"""
filename = 'tests/data/vasp_07/POSCAR_new'
st = pychemia.structure_from_file(filename)
self.assertEqual(st.nsites, 44)
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:], "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:], "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: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()