def test_construction_from_content(self):
" Make sure we can construct xyz file object from content string."
content = """ 19\nSTEP = 208\nH 1.2205526 1.2669640 7.889939\nC 0.6099598 2.3301233 8.089289\nO 0.4463443 2.7548679 9.193083\nNi 0.3159743 0.0807476 0.1953107\nNi 0.3159743 2.5693302 0.1953107\nNi 2.4711501 -1.1635438 0.1953107\nNi 2.4711501 1.3250389 0.1953107\nNi 1.0343662 1.3250389 2.22723\nNi 1.0343662 3.8136215 2.22723\nNi 3.1895420 0.0807476 2.22723\nNi 3.1895420 2.5693302 2.22723\nNi 1.7497810 0.0876549 4.241213\nNi 3.9059343 -1.1526532 4.244936\nNi 1.7448029 2.5773365 4.245788\nNi 3.8955944 1.3376415 4.262553\nNi 2.4322196 1.3387538 6.300457\nNi 0.2766297 2.6108661 6.334991\nNi 0.2884736 0.0896520 6.252682\nNi 2.4521349 -1.1427412 6.231869\n"""
xyz = XyzFile(content=content)
ret_content = xyz.get_xyz_content()
self.assertEqual(ret_content, content)
def test_construction_from_content(self):
" Make sure we can construct xyz file object from content string."
content = """ 19\nSTEP = 208\nH 1.2205526 1.2669640 7.889939\nC 0.6099598 2.3301233 8.089289\nO 0.4463443 2.7548679 9.193083\nNi 0.3159743 0.0807476 0.1953107\nNi 0.3159743 2.5693302 0.1953107\nNi 2.4711501 -1.1635438 0.1953107\nNi 2.4711501 1.3250389 0.1953107\nNi 1.0343662 1.3250389 2.22723\nNi 1.0343662 3.8136215 2.22723\nNi 3.1895420 0.0807476 2.22723\nNi 3.1895420 2.5693302 2.22723\nNi 1.7497810 0.0876549 4.241213\nNi 3.9059343 -1.1526532 4.244936\nNi 1.7448029 2.5773365 4.245788\nNi 3.8955944 1.3376415 4.262553\nNi 2.4322196 1.3387538 6.300457\nNi 0.2766297 2.6108661 6.334991\nNi 0.2884736 0.0896520 6.252682\nNi 2.4521349 -1.1427412 6.231869\n"""
xyz = XyzFile(content=content)
ret_content = xyz.get_xyz_content()
self.assertEqual(ret_content, content)
def test_construction_from_content(self):
" Make sure we can construct xyz file object from content string."
content = """ 19\nSTEP = 208\nH 1.22055264 1.26696399 7.88993886\nC 0.6099598 2.33012325 8.08928947\nO 0.44634426 2.75486791 9.19308296\nNi 0.3159743 0.08074755 0.19531066\nNi 0.3159743 2.5693302 0.19531066\nNi 2.47115009 -1.16354378 0.19531066\nNi 2.47115009 1.32503887 0.19531066\nNi 1.03436623 1.32503887 2.22722988\nNi 1.03436623 3.81362152 2.22722988\nNi 3.18954202 0.08074755 2.22722988\nNi 3.18954202 2.56933019 2.22722988\nNi 1.749781 0.08765486 4.24121319\nNi 3.90593433 -1.15265324 4.24493562\nNi 1.74480294 2.57733648 4.24578757\nNi 3.89559445 1.33764149 4.26255328\nNi 2.43221958 1.33875376 6.3004568\nNi 0.27662972 2.61086614 6.33499111\nNi 0.28847357 0.08965201 6.25268207\nNi 2.45213494 -1.14274124 6.23186924\n"""
xyz = XyzFile(content=content)
ret_content = xyz.get_xyz_content()
self.assertEqual(ret_content, content)
def test_construction_from_content(self):
" Make sure we can construct xyz file object from content string."
content = """ 19\nSTEP = 208\nH 1.22055264 1.26696399 7.88993886\nC 0.6099598 2.33012325 8.08928947\nO 0.44634426 2.75486791 9.19308296\nNi 0.3159743 0.08074755 0.19531066\nNi 0.3159743 2.5693302 0.19531066\nNi 2.47115009 -1.16354378 0.19531066\nNi 2.47115009 1.32503887 0.19531066\nNi 1.03436623 1.32503887 2.22722988\nNi 1.03436623 3.81362152 2.22722988\nNi 3.18954202 0.08074755 2.22722988\nNi 3.18954202 2.56933019 2.22722988\nNi 1.749781 0.08765486 4.24121319\nNi 3.90593433 -1.15265324 4.24493562\nNi 1.74480294 2.57733648 4.24578757\nNi 3.89559445 1.33764149 4.26255328\nNi 2.43221958 1.33875376 6.3004568\nNi 0.27662972 2.61086614 6.33499111\nNi 0.28847357 0.08965201 6.25268207\nNi 2.45213494 -1.14274124 6.23186924\n"""
xyz = XyzFile(content=content)
ret_content = xyz.get_xyz_content()
self.assertEqual(ret_content, content)
def test_get_poscar_content(self):
" Make sure we can get the correct poscar content. "
filename = path + "/ts.xyz"
xyz = XyzFile(filename=filename)
ref_content = """Created by VASPy\n 1.000000000\n 1.00000000 0.00000000 0.00000000\n 0.00000000 1.00000000 0.00000000\n 0.00000000 0.00000000 1.00000000\n H C O Ni\n 1 1 1 16\nSelective Dynamics\nDirect\n 1.220552640000 1.266963990000 7.889938860000 T T T \n 0.609959800000 2.330123250000 8.089289470000 T T T \n 0.446344260000 2.754867910000 9.193082960000 T T T \n 0.315974300000 0.080747550000 0.195310660000 T T T \n 0.315974300000 2.569330200000 0.195310660000 T T T \n 2.471150090000 -1.163543780000 0.195310660000 T T T \n 2.471150090000 1.325038870000 0.195310660000 T T T \n 1.034366230000 1.325038870000 2.227229880000 T T T \n 1.034366230000 3.813621520000 2.227229880000 T T T \n 3.189542020000 0.080747550000 2.227229880000 T T T \n 3.189542020000 2.569330190000 2.227229880000 T T T \n 1.749781000000 0.087654860000 4.241213190000 T T T \n 3.905934330000 -1.152653240000 4.244935620000 T T T \n 1.744802940000 2.577336480000 4.245787570000 T T T \n 3.895594450000 1.337641490000 4.262553280000 T T T \n 2.432219580000 1.338753760000 6.300456800000 T T T \n 0.276629720000 2.610866140000 6.334991110000 T T T \n 0.288473570000 0.089652010000 6.252682070000 T T T \n 2.452134940000 -1.142741240000 6.231869240000 T T T \n"""
ret_content = xyz.get_poscar_content()
self.assertEqual(ref_content, ret_content)
def test_get_poscar_content(self):
" Make sure we can get the correct poscar content. "
filename = path + "/ts.xyz"
xyz= XyzFile(filename=filename)
ref_content = """Created by VASPy\n 1.000000000\n 1.00000000 0.00000000 0.00000000\n 0.00000000 1.00000000 0.00000000\n 0.00000000 0.00000000 1.00000000\n H C O Ni\n 1 1 1 16\nSelective Dynamics\nDirect\n 1.220552640000 1.266963990000 7.889938860000 T T T \n 0.609959800000 2.330123250000 8.089289470000 T T T \n 0.446344260000 2.754867910000 9.193082960000 T T T \n 0.315974300000 0.080747550000 0.195310660000 T T T \n 0.315974300000 2.569330200000 0.195310660000 T T T \n 2.471150090000 -1.163543780000 0.195310660000 T T T \n 2.471150090000 1.325038870000 0.195310660000 T T T \n 1.034366230000 1.325038870000 2.227229880000 T T T \n 1.034366230000 3.813621520000 2.227229880000 T T T \n 3.189542020000 0.080747550000 2.227229880000 T T T \n 3.189542020000 2.569330190000 2.227229880000 T T T \n 1.749781000000 0.087654860000 4.241213190000 T T T \n 3.905934330000 -1.152653240000 4.244935620000 T T T \n 1.744802940000 2.577336480000 4.245787570000 T T T \n 3.895594450000 1.337641490000 4.262553280000 T T T \n 2.432219580000 1.338753760000 6.300456800000 T T T \n 0.276629720000 2.610866140000 6.334991110000 T T T \n 0.288473570000 0.089652010000 6.252682070000 T T T \n 2.452134940000 -1.142741240000 6.231869240000 T T T \n"""
ret_content = xyz.get_poscar_content()
self.assertEqual(ref_content, ret_content)
def __iter__(self):
""" Make MultiXyz object iterable.
"""
with open(self.filename, "r") as f:
content_list = []
for i, line in enumerate(f):
if (i + 1) % (self.natom + 2) == 0:
content_list.append(line)
yield XyzFile(content_list=content_list)
content_list = []
else:
content_list.append(line)
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
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
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
