def build_dsq_file(path):
done = 0
fail = 0
out = []
subfolders = [f.path for f in os.scandir(path) if f.is_dir()]
for folder in subfolders:
outcar = os.path.join(folder, 'OUTCAR')
flag = False
if os.path.exists(outcar):
try:
outcar_done = check_outcar_done(outcar)
except:
outcar_done = check_outcar_done_slow(outcar)
if outcar_done:
flag = True
if flag:
done += 1
else:
fail += 1
target_folder = cwd
failpath = os.path.join(target_folder, folder)
if fail < 1000:
out.append('cd ' + failpath + '; ' + 'mpirun vasp_std' + '\n')
else:
raise ValueError("job cannot exceed 1000!")
fw = open(os.path.join(path, 'out'), 'w')
fw.writelines(out)
fw.close()
return done, fail
def build_dsq_file(path):
done = 0
fail = 0
out = []
subfolders = [f.path for f in os.scandir(path) if f.is_dir()]
for folder in subfolders:
outcar = os.path.join(folder, 'OUTCAR')
flag = False
if os.path.exists(outcar):
try:
outcar_done = check_outcar_done(outcar)
except:
outcar_done = check_outcar_done_slow(outcar)
if outcar_done:
flag = True
if flag:
done += 1
else:
fail += 1
target_folder = cwd
failpath = os.path.join(target_folder, folder)
out.append('cd ' + failpath + '; ' +
'qsub {0}'.format(args.submissionscript) + '\n')
fw = open(os.path.join(path, 'out'), 'w')
fw.writelines(out)
fw.close()
return done, fail
def build_dsq_file(path):
done = 0
fail = 0
out = []
subfolders = [
f.path for f in os.scandir(path)
if f.is_dir() and not ('deepmd' in f.path)
] # remove deepmd folder
for folder in subfolders:
outcar = os.path.join(folder, 'OUTCAR')
flag = False
if os.path.exists(outcar):
try:
outcar_done = check_outcar_done(outcar)
except:
outcar_done = check_outcar_done_slow(outcar)
print("!!!!!ABNORMAL OUTCAR!!!!!", outcar)
if outcar_done:
flag = True
if flag:
done += 1
else:
fail += 1
# print("cwd : ",cwd)
# target_folder = cwd ## it works here cwd is cwd, but confused by the logic why it works??!
failpath = os.path.join(path, folder)
# if failpath != os.path.join(path,folder):
# print("They are different:", failpath, os.path.join(path,folder))
# raise ValueError()
# print("failpath is : ",failpath)
if fail < 1000:
out.append('cd ' + failpath + '; ' + 'mpirun vasp_std' + '\n')
else:
raise ValueError("job cannot exceed 1000!")
fw = open(os.path.join(path, 'out'), 'w')
fw.writelines(out)
fw.close()
return done, fail
def xdt2pos(path, sel_nsw, tot_ele, copybs=False):
"""
build POSCAR based on XDATCAR given in the path
copy INCAR, POTCAR, KPOINTS into the same folder
"""
XDATCAR = open(os.path.join(path, "XDATCAR"), 'r')
incar = os.path.join(path, 'INCAR')
path = os.path.join(path, 'recal')
for _ in range(7):
XDATCAR.readline()
assert len(sel_nsw) > 1 ## at least two iteration are selected
skp_nsw = []
for i in range(len(sel_nsw)):
if i == 0:
skp_nsw.append(sel_nsw[i] * (tot_ele + 1))
else:
skp_nsw.append((sel_nsw[i] - sel_nsw[i - 1] - 1) * (tot_ele + 1))
for i, diff_i in zip(sel_nsw, skp_nsw):
try:
os.mkdir(os.path.join(path, str(i + 1))) # return None
except:
print("Folder {0} already exists,skip making".format(i))
target_path = os.path.join(path, str(i + 1))
# print(target_path)
ls_target_path = os.listdir(target_path)
# skip some portion
for _ in range(diff_i):
XDATCAR.readline()
if 'OUTCAR' in ls_target_path and check_outcar_done(
os.path.join(target_path, 'OUTCAR')):
print('calculation done')
for _ in range(tot_ele + 1):
XDATCAR.readline()
elif 'INCAR' in ls_target_path and \
'POTCAR' in ls_target_path and \
'POSCAR' in ls_target_path and \
'KPOINTS' in ls_target_path:
for _ in range(tot_ele + 1):
XDATCAR.readline()
else:
coord = XDATCAR.readline() # Direct
# print(coord)
atomic_position = []
for j in range(tot_ele):
line_tmp = XDATCAR.readline()
atomic_position.append(line_tmp)
tobewriten = []
tobewriten.append(title + '\n')
tobewriten.append('{0}\n'.format(scaling_factor))
for j in range(3):
tobewriten.append(' {0:14.9f}{1:14.9f}{2:14.9f}\n'.format(
lattice[0][j], lattice[1][j], lattice[2][j]))
for j in range(len(list_ele)):
tobewriten.append(' %4s%s' % (list_ele[j], ' '))
tobewriten.append('\n')
for j in range(len(num_ele)):
tobewriten.append(' %4d%s' % (num_ele[j], ' '))
tobewriten.append('\n')
tobewriten.append('Direct\n')
for j in range(tot_ele):
tobewriten.append(atomic_position[j])
#begin to write POSCAR content to tmp file
fw = open(os.path.join(target_path, 'POSCAR'), 'w')
fw.writelines(tobewriten)
fw.close()
# os.rename('tmp',os.path.join(target_path,'POSCAR'))
target_incar = check_incar(incar)
copy(os.path.join(inputfile, target_incar), target_path)
os.rename(os.path.join(target_path, target_incar),
os.path.join(target_path, 'INCAR'))
copy(os.path.join(inputfile, 'KPOINTS'), target_path)
copy(os.path.join(inputfile, 'POTCAR'), target_path)
# if copybs:
# copy('bs.sh',target_path)
# copy('bs_job.sh',target_path)
XDATCAR.close()