def incorporate_structure(self,structure):
s = structure.copy()
s.change_units('A')
s.recenter()
elem = []
for e in s.elem:
ne = len(e)
if ne>1:
if ne==2 and not e[1].isalpha():
e = e[0]
elif ne>2:
e = e[0:2]
#end if
#end if
if is_element(e):
elem.append(ptable.elements[e].atomic_number)
else:
elem.append(0)
#end if
#end for
self.filetype = 'xsf'
self.periodicity = 'crystal' # assumed
self.primvec = s.axes
self.elem = array(elem,dtype=int)
self.pos = s.pos
def test_is_element():
from periodic_table import is_element
elements = '''
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
'''.split()
for e in elements:
assert (is_element(e))
is_elem, symbol = is_element(e, symbol=True)
assert (is_elem)
assert (symbol == e)
#end for
valid = '''
C
C1
C2
C12
C123
C_1
C_2
C_12
C_123
C_a
C_abc
'''.split()
for e in valid:
assert (is_element(e))
is_elem, symbol = is_element(e, symbol=True)
assert (is_elem)
assert (symbol == 'C')
#end for
valid = '''
Co
Co1
Co2
Co12
Co123
Co_1
Co_2
Co_12
Co_123
Co_a
Co_abc
'''.split()
for e in valid:
assert (is_element(e))
is_elem, symbol = is_element(e, symbol=True)
assert (is_elem)
assert (symbol == 'Co')
def __init__(self,filepath=None):
self.element = None
self.element_label = None
self.filename = None
self.location = None
if filepath!=None:
self.filename = os.path.basename(filepath)
self.location = os.path.abspath(filepath)
elem_label = self.filename.split('.')[0]
is_elem,symbol = is_element(elem_label,symbol=True)
if not is_elem:
self.error('cannot determine element for basis file: {0}\nbasis file names must be prefixed by an atomic symbol or label\n(e.g. Si, Si1, etc)'.format(filepath))
#end if
self.element = symbol
self.element_label = elem_label
def __init__(self,filepath=None):
self.element = None
self.element_label = None
self.filename = None
self.location = None
if filepath!=None:
self.filename = os.path.basename(filepath)
self.location = os.path.abspath(filepath)
elem_label = self.filename.split('.')[0]
is_elem,symbol = is_element(elem_label,symbol=True)
if not is_elem:
self.error('cannot determine element for basis file: {0}\nbasis file names must be prefixed by an atomic symbol or label\n(e.g. Si, Si1, etc)'.format(filepath))
#end if
self.element = symbol
self.element_label = elem_label
def write_text(self):
text = ''
if self.description is None:
text += 'System cell and coordinates\n'
else:
text += self.description+'\n'
#end if
text += ' {0}\n'.format(self.scale)
for a in self.axes:
text += ' {0:20.14f} {1:20.14f} {2:20.14f}\n'.format(*a)
#end for
if self.elem is not None:
for e in self.elem:
iselem,symbol = is_element(e,symbol=True)
if not iselem:
self.error('{0} is not an element'.format(e))
#end if
text += symbol+' '
#end for
text += '\n'
#end if
for ec in self.elem_count:
text += ' {0}'.format(ec)
#end for
text += '\n'
if self.dynamic!=None:
text += 'selective dynamics\n'
#end if
text += self.coord+'\n'
if self.dynamic is None:
for p in self.pos:
text += ' {0:20.14f} {1:20.14f} {2:20.14f}\n'.format(*p)
#end for
else:
bm = self.bool_map
for i in xrange(len(self.pos)):
p = self.pos[i]
d = self.dynamic[i]
text += ' {0:20.14f} {1:20.14f} {2:20.14f} {3} {4} {5}\n'.format(p[0],p[1],p[2],bm[d[0]],bm[d[1]],bm[d[2]])
#end for
#end if
if self.vel!=None:
text += self.vel_coord+'\n'
for v in self.vel:
text += ' {0:20.14f} {1:20.14f} {2:20.14f}\n'.format(*v)
#end for
#end if
return text
def validity_checks(self):
msgs = []
if self.description is None:
msgs.append('description is missing')
elif not isinstance(self.description,str):
msgs.append('description must be text')
#end if
if self.scale is None:
msgs.append('scale is missing')
elif not isinstance(self.scale,(float,int)):
msgs.append('scale must be a real number')
elif self.scale<0:
msgs.append('scale must be greater than zero')
#end if
if self.axes is None:
msgs.append('axes is missing')
elif not isinstance(self.axes,ndarray):
msgs.append('axes must be an array')
elif self.axes.shape!=(3,3):
msgs.append('axes must be a 3x3 array, shape provided is {0}'.format(self.axes.shape))
elif not isinstance(self.axes[0,0],float):
msgs.append('axes must be an array of real numbers')
#end if
natoms = -1
if self.elem_count is None:
msgs.append('elem_count is missing')
elif not isinstance(self.elem_count,ndarray):
msgs.append('elem_count must be an array')
elif len(self.elem_count)==0:
msgs.append('elem_count array must contain at least one entry')
elif not isinstance(self.elem_count[0],int):
msgs.append('elem_count must be an array of integers')
else:
if (self.elem_count<1).sum()>0:
msgs.append('all elem_count entries must be greater than zero')
#end if
natoms = self.elem_count.sum()
#end if
if self.elem is not None: # presence depends on vasp version
if not isinstance(self.elem,ndarray):
msgs.append('elem must be an array')
elif isinstance(self.elem_count,ndarray) and len(self.elem)!=len(self.elem_count):
msgs.append('elem and elem_count arrays must be the same length')
elif not isinstance(self.elem[0],str):
msgs.append('elem must be an array of text')
else:
for e in self.elem:
iselem,symbol = is_element(e,symbol=True)
if not iselem:
msgs.append('elem entry "{0}" is not an element'.format(e))
#end if
#end for
#end for
#end if
if self.coord is None:
msgs.append('coord is missing')
elif not isinstance(self.coord,str):
msgs.append('coord must be text')
#end if
if self.pos is None:
msgs.append('pos is missing')
elif not isinstance(self.pos,ndarray):
msgs.append('pos must be an array')
elif natoms>0 and self.pos.shape!=(natoms,3):
msgs.append('pos must be a {0}x3 array, shape provided is {1}'.format(natoms),self.pos.shape)
elif natoms>0 and not isinstance(self.pos[0,0],float):
msgs.append('pos must be an array of real numbers')
#end if
if self.dynamic is not None: # dynamic is optional
if not isinstance(self.dynamic,ndarray):
msgs.append('dynamic must be an array')
elif natoms>0 and self.dynamic.shape!=(natoms,3):
msgs.append('dynamic must be a {0}x3 array, shape provided is {1}'.format(natoms),self.dynamic.shape)
elif natoms>0 and not isinstance(self.dynamic[0,0],bool):
msgs.append('dynamic must be an array of booleans (true/false)')
#end if
#end if
if self.vel_coord is not None: # velocities are optional
if not isinstance(self.vel_coord,str):
msgs.append('vel_coord must be text')
#end if
#end if
if self.vel is not None: # velocities are optional
if not isinstance(self.vel,ndarray):
msgs.append('vel must be an array')
elif natoms>0 and self.vel.shape!=(natoms,3):
msgs.append('vel must be a {0}x3 array, shape provided is {1}'.format(natoms),self.vel.shape)
elif natoms>0 and not isinstance(self.vel[0,0],float):
msgs.append('vel must be an array of real numbers')
#end if
#end if
return msgs
def generate_physical_system(**kwargs):
for var, val in ps_defaults.items():
if not var in kwargs:
kwargs[var] = val
#end if
#end for
type = kwargs['type']
if type == 'atom' or type == 'dimer' or type == 'trimer':
del kwargs['kshift']
del kwargs['tiling']
#if not 'units' in kwargs:
# kwargs['units'] = 'B'
##end if
tiling = None
else:
tiling = kwargs['tiling']
#end if
if 'structure' in kwargs:
s = kwargs['structure']
is_str = isinstance(s, str)
if is_str:
if os.path.exists(s):
if 'elem' in kwargs:
s = read_structure(s, elem=kwargs['elem'])
else:
s = read_structure(s)
#end if
if 'axes' in kwargs:
s.reset_axes(kwargs['axes'])
#end if
kwargs['structure'] = s
else:
slow = s.lower()
format = None
if '.' in slow:
format = slow.rsplit('.')[1]
elif 'poscar' in slow:
format = 'poscar'
#end if
is_path = '/' in s
is_file = format in set('xyz xsf poscar cif fhi-aims'.split())
if is_path or is_file:
PhysicalSystem.class_error(
'user provided structure file does not exist\nstructure file path: '
+ s, 'generate_physical_system')
#end if
#end if
#end if
#end if
generation_info = obj()
generation_info.transfer_from(deepcopy(kwargs))
net_charge = kwargs['net_charge']
net_spin = kwargs['net_spin']
tiled_spin = kwargs['tiled_spin']
extensive = kwargs['extensive']
del kwargs['net_spin']
del kwargs['net_charge']
del kwargs['tiled_spin']
del kwargs['extensive']
if 'particles' in kwargs:
particles = kwargs['particles']
del kwargs['particles']
else:
generation_info.particles = None
#end if
pretile = kwargs['pretile']
del kwargs['pretile']
valency = dict()
remove = []
for var in kwargs:
#if var in Matter.elements:
if is_element(var):
valency[var] = kwargs[var]
remove.append(var)
#end if
#end if
generation_info.valency = deepcopy(valency)
for var in remove:
del kwargs[var]
#end for
if pretile is None:
structure = generate_structure(**kwargs)
else:
for d in range(len(pretile)):
if tiling[d] % pretile[d] != 0:
PhysicalSystem.class_error(
'pretile does not divide evenly into tiling\n tiling provided: {0}\n pretile provided: {1}'
.format(tiling, pretile), 'generate_physical_system')
#end if
#end for
tiling = tuple(array(tiling) // array(pretile))
kwargs['tiling'] = pretile
pre = generate_structure(**kwargs)
pre.remove_folded_structure()
structure = pre.tile(tiling)
#end if
if tiling != None and tiling != (1, 1, 1) and structure.has_folded():
fps = PhysicalSystem(structure=structure.folded_structure,
net_charge=net_charge,
net_spin=net_spin,
**valency)
structure.remove_folded()
folded_structure = fps.structure
if extensive:
ncells = int(round(structure.volume() / folded_structure.volume()))
net_charge = ncells * net_charge
if not isinstance(net_spin, str):
net_spin = ncells * net_spin
#end if
#end if
if tiled_spin != None:
net_spin = tiled_spin
#end if
ps = PhysicalSystem(structure=structure,
net_charge=net_charge,
net_spin=net_spin,
**valency)
structure.set_folded(folded_structure)
ps.folded_system = fps
else:
ps = PhysicalSystem(structure=structure,
net_charge=net_charge,
net_spin=net_spin,
**valency)
#end if
ps.generation_info = generation_info
return ps
def is_element(self, name, symbol=False):
return is_element(name, symbol=symbol)
def is_element(self,name,symbol=False):
return is_element(name,symbol=symbol)
def generate_physical_system(**kwargs):
for var,val in ps_defaults.iteritems():
if not var in kwargs:
kwargs[var] = val
#end if
#end for
type = kwargs['type']
if type=='atom' or type=='dimer' or type=='trimer':
del kwargs['kshift']
del kwargs['tiling']
#if not 'units' in kwargs:
# kwargs['units'] = 'B'
##end if
tiling = None
else:
tiling = kwargs['tiling']
#end if
if 'structure' in kwargs:
s = kwargs['structure']
is_str = isinstance(s,str)
if is_str and os.path.exists(s):# and '.' in os.path.split(s)[1]:
if 'elem' in kwargs:
print 'system using elem'
kwargs['structure'] = read_structure(s,elem=kwargs['elem'])
else:
kwargs['structure'] = read_structure(s)
#end if
elif is_str and '/' in s:
PhysicalSystem.class_error('path provided for structure file does not exist: '+s,'generate_physical_system')
#end if
#end if
generation_info = obj()
generation_info.transfer_from(deepcopy(kwargs))
net_charge = kwargs['net_charge']
net_spin = kwargs['net_spin']
tiled_spin = kwargs['tiled_spin']
extensive = kwargs['extensive']
del kwargs['net_spin']
del kwargs['net_charge']
del kwargs['tiled_spin']
del kwargs['extensive']
if 'particles' in kwargs:
particles = kwargs['particles']
del kwargs['particles']
else:
generation_info.particles = None
#end if
pretile = kwargs['pretile']
del kwargs['pretile']
valency = dict()
remove = []
for var in kwargs:
#if var in Matter.elements:
if is_element(var):
valency[var] = kwargs[var]
remove.append(var)
#end if
#end if
generation_info.valency = deepcopy(valency)
for var in remove:
del kwargs[var]
#end for
if pretile is None:
structure = generate_structure(**kwargs)
else:
for d in range(len(pretile)):
if tiling[d]%pretile[d]!=0:
PhysicalSystem.class_error('pretile does not divide evenly into tiling\n tiling provided: {0}\n pretile provided: {1}'.format(tiling,pretile),'generate_physical_system')
#end if
#end for
tiling = tuple(array(tiling)/array(pretile))
kwargs['tiling'] = pretile
pre = generate_structure(**kwargs)
pre.remove_folded_structure()
structure = pre.tile(tiling)
#end if
if tiling!=None and tiling!=(1,1,1):
fps = PhysicalSystem(
structure = structure.folded_structure,
net_charge = net_charge,
net_spin = net_spin,
**valency
)
structure.remove_folded()
folded_structure = fps.structure
if extensive:
ncells = int(round(structure.volume()/folded_structure.volume()))
net_charge = ncells*net_charge
net_spin = ncells*net_spin
#end if
if tiled_spin!=None:
net_spin = tiled_spin
#end if
ps = PhysicalSystem(
structure = structure,
net_charge = net_charge,
net_spin = net_spin,
**valency
)
structure.set_folded(folded_structure)
ps.folded_system = fps
else:
ps = PhysicalSystem(
structure = structure,
net_charge = net_charge,
net_spin = net_spin,
**valency
)
#end if
ps.generation_info = generation_info
return ps
