def get_positions(self, coords='direct'):
if self.direct_coords == True and coords[0].lower() == 'c':
return oppvasp.direct_to_cartesian(self.positions, self.basis)
elif self.direct_coords == False and coords[0].lower() == 'd':
return oppvasp.cartesian_to_direct(self.positions, self.basis)
else:
return self.positions.copy()
def get_positions(self, coords = 'direct'):
if self.direct_coords == True and coords[0].lower() == 'c':
return oppvasp.direct_to_cartesian(self.positions, self.basis)
elif self.direct_coords == False and coords[0].lower() == 'd':
return oppvasp.cartesian_to_direct(self.positions, self.basis)
else:
return self.positions.copy()
def set_velocities(self, vel, coords):
if type(vel).__name__ == 'ndarray':
self._velocities = vel.copy()
elif type(vel).__name__ == 'list':
self._velocities = np.array(vel)
elif type(vel).__name__ == 'NoneType':
self._velocities = None
else:
print "Error: velocities must be a list or numpy array"
self._velocities = None
if self._velocities != None and coords[0] == 'c':
self._velocities = cartesian_to_direct(self._velocities, self._cell)
def set_velocities(self, vel, coords):
if type(vel).__name__ == 'ndarray':
self._velocities = vel.copy()
elif type(vel).__name__ == 'list':
self._velocities = np.array(vel)
elif type(vel).__name__ == 'NoneType':
self._velocities = None
else:
print "Error: velocities must be a list or numpy array"
self._velocities = None
if self._velocities != None and coords[0] == 'c':
self._velocities = cartesian_to_direct(self._velocities,
self._cell)
def set_positions(self, pos, coords):
"""
Define atom positions using a (n,3) numpy array as the first argument.
The function assumes cartesian coordinates by default, but
a second argument can be added to indicate if the coordinates
are direct ('d') or cartesian ('c').
"""
if type(pos).__name__ == 'ndarray':
self._positions = pos.copy()
elif type(pos).__name__ == 'list':
self._positions = np.array(pos)
else:
print "Error: positions must be a list or numpy array"
if coords[0].lower() == 'c':
self._positions = cartesian_to_direct(self._positions, self._cell)
def set_positions(self, pos, coords):
"""
Define atom positions using a (n,3) numpy array as the first argument.
The function assumes cartesian coordinates by default, but
a second argument can be added to indicate if the coordinates
are direct ('d') or cartesian ('c').
"""
if type(pos).__name__ == 'ndarray':
self._positions = pos.copy()
elif type(pos).__name__ == 'list':
self._positions = np.array(pos)
else:
print "Error: positions must be a list or numpy array"
if coords[0].lower() == 'c':
self._positions = cartesian_to_direct(self._positions, self._cell)
def set_forces(self, forces, coords):
"""
Parameters:
forces : (n,3) numpy array of forces on all atoms
coords : 'direct' or 'cartesian'
"""
if type(forces).__name__ == 'ndarray':
self._forces = forces.copy()
elif type(forces).__name__ == 'list':
self._forces = np.array(forces)
elif type(forces).__name__ == 'NoneType':
self._forces = None
else:
print "Error: forces must be a list or numpy array"
self._forces = None
if self._forces != None and coords[0] == 'c':
self._forces = cartesian_to_direct(self._forces, self._cell)
def set_forces(self, forces, coords):
"""
Parameters:
forces : (n,3) numpy array of forces on all atoms
coords : 'direct' or 'cartesian'
"""
if type(forces).__name__ == 'ndarray':
self._forces = forces.copy()
elif type(forces).__name__ == 'list':
self._forces = np.array(forces)
elif type(forces).__name__ == 'NoneType':
self._forces = None
else:
print "Error: forces must be a list or numpy array"
self._forces = None
if self._forces != None and coords[0] == 'c':
self._forces = cartesian_to_direct(self._forces, self._cell)
def unwrap_pbc(self, init_pos=None, silent=False):
"""
Unwraps periodic boundary conditions (PBCs).
Note that this procedure produces coordinates outside the unit cell.
An initial set of coordinates must be specified as a Structure object,
typically originating from a POSCAR file.
Example:
----------
>>> pp = PoscarParser('POSCAR')
>>> init_pos = pp.get_structure()
>>> vp = VasprunParser('vasprun.xml')
>>> fin_pos = vp.ionic_steps[-1].get_structure()
>>> fin_pos = fin_pos.unwrap_pbc(init_pos)
>>> print fin_pos - init_pos
"""
#if self.shape[0] != r0.shape[0]:
# print "ERROR: Mismatch between number of atoms in initial and final structure! Aborting"
# return
# Convert initial coordinates to final basis:
r0 = cartesian_to_direct(init_pos.get_positions('cart'), self._cell)
r = self.get_positions('direct')
n = r.shape[0]
dr = r - r0
c = np.abs(np.array((dr - 1, dr, dr + 1)))
diff = np.array([[np.argmin(c[:, i, j]) for j in range(3)]
for i in range(n)]) - 1 # (-1,0,1)
dr += diff
if not silent and np.max(dr) > 0.1:
print u"Warning: largest displacement of %.1f (direct units) is rather large..." % (
np.max(dr))
self.set_positions(r0 + dr, 'direct')
def unwrap_pbc(self, init_pos = None, silent = False):
"""
Unwraps periodic boundary conditions (PBCs).
Note that this procedure produces coordinates outside the unit cell.
An initial set of coordinates must be specified as a Structure object,
typically originating from a POSCAR file.
Example:
----------
>>> pp = PoscarParser('POSCAR')
>>> init_pos = pp.get_structure()
>>> vp = VasprunParser('vasprun.xml')
>>> fin_pos = vp.ionic_steps[-1].get_structure()
>>> fin_pos = fin_pos.unwrap_pbc(init_pos)
>>> print fin_pos - init_pos
"""
#if self.shape[0] != r0.shape[0]:
# print "ERROR: Mismatch between number of atoms in initial and final structure! Aborting"
# return
# Convert initial coordinates to final basis:
r0 = cartesian_to_direct(init_pos.get_positions('cart'), self._cell)
r = self.get_positions('direct')
n = r.shape[0]
dr = r-r0
c = np.abs(np.array((dr-1, dr, dr+1)))
diff = np.array([[np.argmin(c[:,i,j]) for j in range(3)] for i in range(n)]) - 1 # (-1,0,1)
dr += diff
if not silent and np.max(dr) > 0.1:
print u"Warning: largest displacement of %.1f (direct units) is rather large..." % (np.max(dr))
self.set_positions(r0+dr, 'direct')
