def load(self):
"Rewrite load method"
PosCar.load(self)
with open(self.filename, 'r') as f:
for i in range(self.totline):
f.readline()
#get dimension of 3d array
grid = f.readline().strip(whitespace)
empty = not grid # empty row
while empty:
grid = f.readline().strip(whitespace)
empty = not grid
x, y, z = line2list(grid, dtype=int)
#read electron localization function data
elf_data = []
for line in f:
datalist = line2list(line)
elf_data.extend(datalist)
#########################################
# #
# !!! Notice !!! #
# NGX is the length of the **0th** axis #
# NGY is the length of the **1st** axis #
# NGZ is the length of the **2nd** axis #
# #
#########################################
#reshape to 3d array
elf_data = np.array(elf_data).reshape((x, y, z), order='F')
#set attrs
self.grid = x, y, z
self.elf_data = elf_data
return
def load(self):
"Rewrite load method"
PosCar.load(self)
with open(self.filename, 'r') as f:
for i in range(self.totline):
f.readline()
#get dimension of 3d array
grid = f.readline().strip(whitespace)
empty = not grid # empty row
while empty:
grid = f.readline().strip(whitespace)
empty = not grid
x, y, z = line2list(grid, dtype=int)
#read electron localization function data
elf_data = []
for line in f:
datalist = line2list(line)
elf_data.extend(datalist)
#########################################
# #
# !!! Notice !!! #
# NGX is the length of the **0th** axis #
# NGY is the length of the **1st** axis #
# NGZ is the length of the **2nd** axis #
# #
#########################################
#reshape to 3d array
elf_data = np.array(elf_data).reshape((x, y, z), order='F')
#set attrs
self.grid = x, y, z
self.elf_data = elf_data
return
def test_get_poscar_content(self):
" Make sure we can get the correct poscar content. "
poscar = PosCar(self.filename)
ref_content = """Created by VASPy\n 1.000000000\n 7.29321435 -4.21073927 0.00000000\n 0.00000000 8.42147853 0.00000000\n -0.00000000 0.00000000 16.87610843\n Pt\n 36\nSelective Dynamics\nDirect\n 0.244666665792 0.223999996980 0.135815443038 F F F \n 0.022444443570 0.112888885869 0.271630886077 T T T \n 0.133555554681 0.001777774758 0.000000000000 F F F \n 0.133555554681 0.001777774758 0.407446329115 T T T \n 0.577999999126 0.223999996980 0.135815443038 F F F \n 0.355777776904 0.112888885869 0.271630886077 T T T \n 0.466888888015 0.001777774758 0.000000000000 F F F \n 0.466888888015 0.001777774758 0.407446329115 T T T \n 0.911333332459 0.223999996980 0.135815443038 F F F \n 0.689111110237 0.112888885869 0.271630886077 T T T \n 0.800222221348 0.001777774758 0.000000000000 F F F \n 0.800222221348 0.001777774758 0.407446329115 T T T \n 0.244666665792 0.557333330313 0.135815443038 F F F \n 0.022444443570 0.446222219202 0.271630886077 T T T \n 0.133555554681 0.335111108091 0.000000000000 F F F \n 0.133555554681 0.335111108091 0.407446329115 T T T \n 0.577999999126 0.557333330313 0.135815443038 F F F \n 0.355777776904 0.446222219202 0.271630886077 T T T \n 0.466888888015 0.335111108091 0.000000000000 F F F \n 0.466888888015 0.335111108091 0.407446329115 T T T \n 0.911333332459 0.557333330313 0.135815443038 F F F \n 0.689111110237 0.446222219202 0.271630886077 T T T \n 0.800222221348 0.335111108091 0.000000000000 F F F \n 0.800222221348 0.335111108091 0.407446329115 T T T \n 0.244666665792 0.890666663647 0.135815443038 F F F \n 0.022444443570 0.779555552536 0.271630886077 T T T \n 0.133555554681 0.668444441424 0.000000000000 F F F \n 0.133555554681 0.668444441424 0.407446329115 T T T \n 0.577999999126 0.890666663647 0.135815443038 F F F \n 0.355777776904 0.779555552536 0.271630886077 T T T \n 0.466888888015 0.668444441424 0.000000000000 F F F \n 0.466888888015 0.668444441424 0.407446329115 T T T \n 0.911333332459 0.890666663647 0.135815443038 F F F \n 0.689111110237 0.779555552536 0.271630886077 T T T \n 0.800222221348 0.668444441424 0.000000000000 F F F \n 0.800222221348 0.668444441424 0.407446329115 T T T \n"""
ret_content = poscar.get_poscar_content()
self.assertEqual(ref_content, ret_content)
import numpy as np
from vaspy.atomco import XyzFile, PosCar
from vaspy.functions import str2list
class ContinueError(Exception):
pass
if len(sys.argv) != 2:
print 'Usage: %s *.xyz' % sys.argv[0]
exit(1)
filename = sys.argv[1]
a = XyzFile(filename=filename)
b = PosCar(filename='POSCAR')
#create new dir
if not os.path.exists('./continue'):
os.mkdir('./continue')
if os.path.isfile('./fort.188'):
fail = os.system("cp INCAR POTCAR KPOINTS fort.188 vasp.script ./continue")
else:
fail = os.system("cp INCAR POTCAR KPOINTS vasp.script ./continue")
if not fail:
#new fort.188
#change distance of 2 atoms
with open('./continue/fort.188', 'r') as f:
content_list = f.readlines()
m, n, distance = str2list(content_list[5]) # atom number and distance
x = a.data[int(m)-1, :] # atom coordinates
from vaspy.matstudio import XsdFile
from vaspy.functions import str2list
_logger = logging.getLogger("vaspy.script")
# Set arguments parser.
parser = argparse.ArgumentParser()
parser.add_argument("--xsd",
help="create MaterStudio .xsd file",
action="store_true")
args = parser.parse_args()
outcar = OutCar()
poses, forces = outcar.forces(-1)
poscar = PosCar()
tfs = poscar.tf
incar = InCar()
#print(incar.paras)
EDIFFG = incar.get_pvalue('EDIFFG')
#EDIFFG = 0.05
bad_ids = []
max_idx = [-1, -1, -1]
max_force = [0., 0., 0.]
for i, (pos, force, tf) in enumerate(zip(poses, forces, tfs)):
for j, (c, f) in enumerate(zip(tf, force)):
if c == 'T':
if np.fabs(f) >= max_force[j]:
max_idx[j] = i
from vaspy.atomco import XyzFile, PosCar
from vaspy.functions import str2list
class ContinueError(Exception):
pass
if len(sys.argv) != 2:
print 'Usage: %s *.xyz' % sys.argv[0]
exit(1)
filename = sys.argv[1]
a = XyzFile(filename=filename)
b = PosCar(filename='POSCAR')
#create new dir
if not os.path.exists('./continue'):
os.mkdir('./continue')
if os.path.isfile('./fort.188'):
fail = os.system("cp INCAR POTCAR KPOINTS fort.188 vasp.script ./continue")
else:
fail = os.system("cp INCAR POTCAR KPOINTS vasp.script ./continue")
if not fail:
#new fort.188
#change distance of 2 atoms
with open('./continue/fort.188', 'r') as f:
content_list = f.readlines()
m, n, distance = str2list(content_list[5]) # atom number and distance
x = a.data[int(m) - 1, :] # atom coordinates