bridgeNO.translate([0.0, 0.0, dist])
Surf = contcar.copy()
Surf.extend(ontopNO)
Surf.extend(bridgeNO)
image.append(Surf)
dirname = "angle1-" + str(phi) + "-" + str(
theta) + "-angle2-" + str(phi2) + "-" + str(theta2)
os.makedirs(dirname, exist_ok=True)
dirs.append(dirname)
write(dirname + "/POSCAR",
Surf,
format='vasp',
vasp5=True,
direct=True,
sort=True)
for file_name in templete:
full_file_name = os.path.join('./template-RCCS', file_name)
if (os.path.isfile(full_file_name)):
target_file_name = os.path.join(dirname, file_name)
shutil.copy(full_file_name, target_file_name)
vaspfiles = os.listdir(dirs[0])
print(vaspfiles)
remote.sendDirsToRCCS(dirs=dirs, vaspfiles=vaspfiles)
lines=lines.replace(str(count),str(new))
with open(counter,"w") as f:
f.write(lines)
else:
count=1
shutil.copy(poscar, d+'/POSCAR.0')
shutil.copy(outcar, d+'/OUTCAR.0')
shutil.copy(xdatcar, d+'/XDATCAR.0')
shutil.copy(vaspdata,d+'/vasprun.xml.0')
shutil.copy(contcar, poscar)
with open(d+counter,"w") as f:
f.write(str(count))
'''
#resubmit job to RCCS
#prepare run.sh for RCCS
for d in dirs:
shutil.copy('./templete-RCCS/run.sh', d + '/run.sh')
#using lower energy 81~168 pattern
senddirs = []
for res in sorted_results[80:]:
senddirs.append(res['ID'])
print(senddirs)
vaspfiles = ['POTCAR', 'POSCAR', 'INCAR', 'vdw_kernel.bindat', 'run.sh']
remote.sendDirsToRCCS(senddirs, vaspfiles)
bridgeNO.translate([0.0, 0.0, dist])
Surf = contcar.copy()
Surf.extend(ontopNO)
Surf.extend(bridgeNO)
image.append(Surf)
dirname = "chain-flip"
os.makedirs(dirname, exist_ok=True)
dirs.append(dirname)
write(dirname + "/POSCAR",
Surf,
format='vasp',
vasp5=True,
direct=True,
sort=True)
for file_name in templete:
full_file_name = os.path.join('./templete-RCCS', file_name)
if (os.path.isfile(full_file_name)):
target_file_name = os.path.join(dirname, file_name)
shutil.copy(full_file_name, target_file_name)
vaspfiles = os.listdir(dirs[0])
print(vaspfiles)
workingdir = '/lustre/home/users/brx/NO-Au111-search/'
remote.sendDirsToRCCS(dirs=dirs, vaspfiles=vaspfiles, workingdir=workingdir)