def GSM_Setup():
file_loc = os.environ['GSM_DIR']
jinja_vars = Helpers.load_variables(os.path.join(file_loc, 'VARS.jinja2'))
if len(sys.argv) == 2:
jinja_vars['IMAGES'] = sys.argv[1]
start = 'start'
final = 'final'
elif len(sys.argv) == 3:
start = sys.argv[1]
final = sys.argv[2]
elif len(sys.argv) == 4:
start = sys.argv[1]
final = sys.argv[2]
jinja_vars['IMAGES'] = sys.argv[3]
start_pos = os.path.join(start, 'CONTCAR') if os.path.exists(os.path.join(start, 'CONTCAR')) else os.path.join(start, 'POSCAR')
final_pos = os.path.join(final, 'CONTCAR') if os.path.exists(os.path.join(final, 'CONTCAR')) else os.path.join(final, 'POSCAR')
shutil.copy(os.path.join(file_loc, 'gfstringq.exe'), 'gfstringq.exe')
shutil.copy(os.path.join(file_loc, 'status'), 'status')
shutil.copy(start_pos, 'start')
shutil.copy(final_pos, 'final')
shutil.copy(os.path.join(start, 'INCAR'), 'INCAR')
shutil.copy(os.path.join(start, 'KPOINTS'), 'KPOINTS')
shutil.copy(os.path.join(start, 'POTCAR'), 'POTCAR')
env = jinja2.Environment(loader=jinja2.FileSystemLoader(file_loc))
with open('grad.py', 'w') as f:
template = env.get_template('grad.jinja2.py')
f.write(template.render(jinja_vars))
with open('inpfileq', 'w') as f:
template = env.get_template('inpfileq.jinja2')
f.write(template.render(jinja_vars))
os.chmod('grad.py', 0o755)
start = ase.io.read(start_pos)
final = ase.io.read(final_pos)
if not os.path.exists('scratch'):
os.makedirs('scratch')
ase.io.write('scratch/initial0000.xyz',[start,final])
def GSM_Setup(start, final=None, new_gsm_dir='.', images=None, center=[0.5,0.5,0.5], f_center=None,
copy_wavefunction=False, tolerance=None, poscar_override=[], name=None, is_neb=True,
fix_positions=True):
# Initializing Variables to be called later in function
file_loc = os.environ['GSM_DIR']
jinja_vars = Helpers.load_variables(os.path.join(file_loc, 'VARS.jinja2'))
if f_center == None:
f_center = center
if images == None:
if final or is_neb: #is GSM
images = 9
jinja_vars["SM_TYPE"] = 'GSM'
print('Setting up GSM run')
else: # is SSM
images = 40
jinja_vars["SM_TYPE"] = 'SSM'
print('Setting up SSM run, make sure to create ISOMERS File at scratch/ISOMERS0000')
else:
if final or is_neb: #is GSM
jinja_vars["SM_TYPE"] = 'GSM'
print('Setting up GSM run')
else: # is SSM
jinja_vars["SM_TYPE"] = 'SSM'
print('Setting up SSM run, make sure to create ISOMERS File at scratch/ISOMERS0000')
jinja_vars["IMAGES"] = images
# Finding the Starting Structure
if is_neb:
start_file = os.path.join(start, '00', 'POSCAR')
start_folder = os.path.join(start)
elif os.path.isfile(start):
start_file = start
start_folder = os.path.dirname(start)
else:
start_file = os.path.join(start, 'CONTCAR') if os.path.exists(os.path.join(start, 'CONTCAR')) else os.path.join(start, 'POSCAR')
start_folder = start
# Copying and Updating Files into the directory
if not os.path.exists(new_gsm_dir):
os.makedirs(new_gsm_dir)
env = jinja2.Environment(loader=jinja2.FileSystemLoader(file_loc))
# shutil.copy(os.path.join(file_loc, 'gfstringq.exe'), os.path.join(new_gsm_dir, 'gfstringq.exe'))
shutil.copy(os.path.join(file_loc, 'status'), os.path.join(new_gsm_dir, 'status'))
shutil.copy(start_file, os.path.join(new_gsm_dir, 'POSCAR.start'))
if not os.path.exists(os.path.join(new_gsm_dir, 'scratch')):
os.makedirs(os.path.join(new_gsm_dir, 'scratch'))
start = ase.io.read(start_file, format='vasp')
start.wrap(center)
initial = [start]
if final:
if os.path.isfile(final):
final_file = final
final_folder = os.path.dirname(final)
else:
final_file = os.path.join(final, 'CONTCAR') if os.path.exists(os.path.join(final, 'CONTCAR')) else os.path.join(final, 'POSCAR')
final_folder = final
final = ase.io.read(final_file, format='vasp')
final.wrap(f_center)
if poscar_override: # If structure needs realigning
atoms = []
# Format the poscar override into pairs
for i in range(int(len(poscar_override) / 2)):
atoms.append((poscar_override[i * 2], poscar_override[i * 2 + 1]))
(s1, s2) = reorganize_structures(Structure.from_file(start_file), Structure.from_file(final_file), atoms=atoms, autosort_tol=tolerance) # pymatgen.core.Structure
# Reset the start and final file
start_file = tempfile.NamedTemporaryFile(delete=False).name
final_file = tempfile.NamedTemporaryFile(delete=False).name
s1.to('POSCAR', start_file)
s2.to('POSCAR', final_file)
start = ase.io.read(start_file, format='vasp')
final = ase.io.read(final_file, format='vasp')
start.wrap(center)
final.wrap(f_center)
shutil.copy(start_file, os.path.join(new_gsm_dir, 'POSCAR.start'))
initial = [start, final]
else:
initial.append(final)
try:
shutil.copy(os.path.join(start_folder, 'KPOINTS'), os.path.join(new_gsm_dir, 'KPOINTS'))
except:
print('Copying KPOINTS failed, make sure to add an appropriate KPOINTS to the directory')
try:
potcar = Potcar()
for symbol in Poscar.from_file(os.path.join(new_gsm_dir, 'POSCAR.start'), check_for_POTCAR=False).site_symbols:
for potcar_single in Potcar.from_file(os.path.join(start_folder, 'POTCAR')): # pymatgen.io.vasp.PotcarSingle
if symbol == potcar_single.element:
potcar.append(potcar_single)
break
potcar.write_file(os.path.join(new_gsm_dir, 'POTCAR'))
except:
print('Copying POTCAR failed, make sure to add an appropriate POTCAR to the directory')
try:
incar = Incar.from_file(os.path.join(start_folder, 'INCAR'))
incar['NSW']=0
if final and 'NUPDOWN' in incar:
incar_final = Incar.from_file(os.path.join(final_folder, 'INCAR'))
incar['AUTO_NUPDOWN'] = 'r {} {}'.format(incar['NUPDOWN'], incar_final['NUPDOWN'])
incar['AUTO_NUPDOWN_ITERS'] = 20
if name:
incar['SYSTEM'] = name
if is_neb:
images = incar['IMAGES']
for tag in ['IMAGES', 'LCLIMB']:
if tag in incar:
del incar[tag]
final_folder = os.path.join(start_folder, str(images+1).zfill(2))
final_file = os.path.join(final_folder, 'POSCAR')
final = ase.io.read(final_file, format='vasp')
initial.append(final)
start_folder = os.path.join(start_folder, '00')
incar.write_file(os.path.join(new_gsm_dir, 'INCAR'))
except:
print('Copying INCAR failed, make sure to add an appropriate INCAR to the directory')
currdir = os.path.abspath('.')
os.chdir(new_gsm_dir)
with open('grad.py', 'w') as f:
template = env.get_template('grad.jinja2.py')
f.write(template.render(jinja_vars))
with open('inpfileq', 'w') as f:
template = env.get_template('inpfileq.jinja2')
f.write(template.render(jinja_vars))
os.chmod('grad.py', 0o755)
os.chmod('status', 0o755)
poscar = Poscar.from_file('POSCAR.start', check_for_POTCAR=False)
if poscar.selective_dynamics:
sd = poscar.selective_dynamics
else:
sd = [(True, True, True)] * poscar.natoms
ase.io.write('scratch/initial0000.temp.xyz', initial, )
if fix_positions and final:
with open('scratch/initial0000.temp.xyz', 'r') as f:
lines = [ x.split() for x in f.readlines() ]
cell = start.get_cell()
sfp = final.get_scaled_positions() # Scaled Final Positions
# ssp = start.get_scaled_positions() # Scaled Final Positions
start_i = 2
final_i = 2*start_i + len(sfp)
for i, pos in enumerate(sfp):
start_coord = np.matrix([ np.float128(x) for x in lines[start_i + i][1:4] ])
final_coord = np.matrix([ np.float128(x) for x in lines[final_i + i][1:4] ])
final_coord_temp = final_coord
distance = np.linalg.norm(start_coord - final_coord)
for x in [-1, 0 , 1]:
for y in [-1, 0, 1]:
for z in [-1, 0, 1]:
final_coord_diff = np.matrix([x,y,z]) * cell
distance_temp = np.linalg.norm(start_coord - (final_coord+final_coord_diff))
if distance_temp < distance:
final_coord_temp = final_coord+final_coord_diff
distance = distance_temp
lines[final_i+i][1] = final_coord_temp[0,0]
lines[final_i+i][2] = final_coord_temp[0,1]
lines[final_i+i][3] = final_coord_temp[0,2]
with open('scratch/initial0000.temp.xyz', 'w') as f:
lines = [' '.join([ str(x) for x in line ]) for line in lines]
f.write( '\n'.join(lines) )
with open('scratch/initial0000.temp.xyz', 'r') as f:
# Convert True SD to frozen atoms
sd = list(map(lambda l : '\n' if (l[0] or l[1] or l[2]) else ' "X"\n', sd))
# Set up sd to be zipped (two buffer lines at top of each structure)
to_zip = (['\n', '\n'] + sd) * len(initial)
zipped = zip(f.readlines(), to_zip)
xyz = [ ' '.join(x.split()[0:4])+y for x, y in zipped ] # Remove atom number
with open('scratch/initial0000.xyz', 'w') as f:
f.writelines(xyz)
os.remove('scratch/initial0000.temp.xyz')
if copy_wavefunction:
if os.path.exists(os.path.join(start_folder, 'WAVECAR')):
print('Copying initial WAVECAR')
if not os.path.exists(os.path.join(new_gsm_dir, 'scratch/IMAGE.01')):
os.makedirs(os.path.join(new_gsm_dir, 'scratch/IMAGE.01'))
shutil.copy(os.path.join(start_folder, 'WAVECAR'),
os.path.join(new_gsm_dir, 'scratch/IMAGE.01/WAVECAR'))
if os.path.exists(os.path.join(start_folder, 'CHGCAR')):
print('Copying initial CHGCAR')
if not os.path.exists(os.path.join(new_gsm_dir, 'scratch/IMAGE.01')):
os.makedirs(os.path.join(new_gsm_dir, 'scratch/IMAGE.01'))
shutil.copy(os.path.join(start_folder, 'CHGCAR'),
os.path.join(new_gsm_dir, 'scratch/IMAGE.01/CHGCAR'))
if final: # is GSM
shutil.copy(final_file, os.path.join(new_gsm_dir, 'POSCAR.final'))
if os.path.exists(os.path.join(final_folder, 'WAVECAR')):
print('Copying final WAVECAR')
if not os.path.exists(os.path.join(new_gsm_dir, 'scratch/IMAGE.' + str(images).zfill(2))):
os.makedirs(os.path.join(new_gsm_dir, 'scratch/IMAGE.' + str(images).zfill(2)))
shutil.copy(os.path.join(final_folder, 'WAVECAR'),
os.path.join(new_gsm_dir, 'scratch/IMAGE.' + str(images).zfill(2) + '/WAVECAR'))
if os.path.exists(os.path.join(final_folder, 'CHGCAR')):
print('Copying final CHGCAR')
if not os.path.exists(os.path.join(new_gsm_dir, 'scratch/IMAGE.' + str(images).zfill(2))):
os.makedirs(os.path.join(new_gsm_dir, 'scratch/IMAGE.' + str(images).zfill(2)))
shutil.copy(os.path.join(final_folder, 'CHGCAR'),
os.path.join(new_gsm_dir, 'scratch/IMAGE.' + str(images).zfill(2) + '/CHGCAR'))
os.chdir(currdir)
