def rename_canonical_dirs():
"""
Rename canonical dirs just below top level directory.
"""
canonical_dirs = glob.glob('{}*'.format(or_x))
canonical_dirs = filter(os.path.isdir, canonical_dirs)
for canonical_dir in canonical_dirs:
#update top level canonical dir name to new convention
with open(canonical_dir + '/gb.json') as f:
gb_json = json.load(f)
old_canonical_name = gb_json['gbid']
new_canonical_name = canonical_name_from_gb_json(gb_json)
print canonical_name_from_gb_json(gb_json)
shutil.move(canonical_dir, new_canonical_name)
with pushd(new_canonical_name) as ctx1:
shutil.move(old_canonical_name + '.png',
new_canonical_name + '.png')
shutil.move(old_canonical_name + '.xyz',
new_canonical_name + '.xyz')
shutil.move('csl_' + old_canonical_name + '.svg',
'csl_' + new_canonical_name + '.svg')
with open('gb.json') as f:
gb_json = json.load(f)
old_gbid = gb_json['gbid']
gb_json['old_gbid'] = old_gbid
gb_json['gbid'] = new_canonical_name
def gen_forceconstants(species,
index,
cart,
displacement=0.1,
hour=5,
np=48,
template_dir='templates'):
"""
generate directory and POSCAR perturbation
Args:
species(str): Name of perturbed atom.
"""
target_dir = "{spec}_{index}_{cart}_disp".format(spec=species,
index=index,
cart=cart[1])
dir_util.copy_tree(template_dir, target_dir)
with pushd(target_dir) as ctx0:
#Fix the pbs string
with open('vasp.sh', 'r') as f:
pbs_str = f.read()
pbs_str = pbs_str.format(hour=hour,
index=index,
np=np,
species=species)
with open('vasp.sh', 'w') as f:
print >> f, pbs_str
ats = vasp.read_vasp('POSCAR')
print "before pert", ats[index].position[:]
ats[index].position[cart[0]] += displacement
print "after pert", ats[index].position[:]
vasp.write_vasp("POSCAR", ats)
def gen_multiple_images():
at_images = io.read("restart_images.xyz", index=":")
print "{} images in file".format(len(at_images))
for image_num, atoms in enumerate(at_images):
#Create separate directory for each image along path
try:
os.mkdir("image_{}".format(image_num))
except OSError:
print "dir {} already exists".format(image_num)
with pushd("image_{}".format(image_num)) as ctx1:
shutil.copy("../ctrl.dat", "./ctrl.dat")
atoms_to_site(atoms)
def pull_forces(species, index, cart):
"""
pull forces from OUTCAR and save to file.
"""
target_dir = "{spec}_{index}_{cart}_disp".format(spec=species,
index=index,
cart=cart)
with pushd(target_dir) as ctx0:
print os.getcwd()
ats = vasp.read_vasp_out()
forces = ats.get_forces()
np.save("col_vec", forces)
ats.write("{}.xyz".format(target_dir))
np.savetxt(prefix + "_fit.txt", np.array([Sfit, Efit]))
np.savetxt(prefix + "_lines.txt", np.vstack(lines))
fig.savefig(prefix + "_barrier.eps")
if __name__ == '__main__':
prefix = sys.argv[1]
job_dirs = glob.glob("{prefix}*".format(prefix=prefix))
job_dirs = filter(os.path.isdir, job_dirs)
func = lambda x: int(x.split("_")[1])
job_dirs.sort(key=func)
images = []
print "Removing old neb path"
if os.path.isfile("neb_path.xyz"):
os.remove("neb_path.xyz")
for job in job_dirs:
print "pulling ", job
with pushd(job) as ctx0:
try:
ats = io.read('OUTCAR', index='-1')
ats.arrays['forces'] = ats.get_forces()
except StopIteration:
print "Could not pull OUTCAR for:", job
else:
images.append(ats)
for image in images:
write_xyz("neb_path.xyz", image, append=True)
calc_neb_barriers(prefix, images)
sub_file)
if __name__ == '__main__':
#or_axes = ['001', '110', '111']
#1
#ENTER ORIENTATION AXIS LEVEL AND RENAME CANONICAL DIRS.
#for or_x in or_axes:
# with pushd(or_x) as ctx0:
# rename_canonical_dirs()
#2
#Correct SubGrainBoundary Directories:
or_axes = ['0_0_1', '1_1_0', '1_1_1']
pot_dirs = ['POTBH', 'EAM_Dud', 'EAM_Men', 'EAM_Mish', 'EAM_Ack']
for or_x in or_axes:
with pushd(or_x) as ctx0:
canonical_dirs = glob.glob('{}*'.format(or_x))
canonical_dirs = filter(os.path.isdir, canonical_dirs)
for canonical_dir in canonical_dirs:
with pushd(canonical_dir) as ctx1:
print canonical_dir
with open('gb.json', 'r') as f:
gb_dict = json.load(f)
#use old canonical name:
#old_gbid = gb_dict['old_gbid']
old_gbid = gb_dict['gbid']
new_canonical_name = canonical_name_from_gb_json(gb_dict)
for pot in pot_dirs:
if os.path.isdir(pot):
with pushd(pot) as ctx2:
recursive_rename('./',