def load_cif(sample, filename, reset_muon=True, reset_sym=True):
"""
Loads the structural information from a Cif file.
:param muesr.core.sample.Sample sample: the sample object.
:param str filename: the cif file path (path + filename).
:param bool reset_muon: if true the muon positions is reinitialized.
:param bool reset_sym: if true the symmetry is reinitialized. ALWAYS TRUE
:returns: True if succesfull, false otherwise
:rtype: bool
"""
filename = str(filename)
f = open(os.path.expanduser(filename),'r')
#nprint ("Problems with file name...file not found!", 'warn')
#return False
#print(read_cif(f,0))
atoms, sym = read_cif(f,0) # selectd index 0
f.close()
if atoms:
sample._reset(cell=True,sym=True,magdefs=True,muon=reset_muon)
sample.cell = atoms
sample.sym = sym
return True
else:
nprint ("Atoms not loaded!", 'warn')
return False
def muon_set_frac(sample, arg = None):
"""
Set muon position in lattice coordinates.
returns: None
"""
if sample._check_lattice():
try:
if arg is None:
pos=ninput('Muon position (frac coord): ', parse_vector)
else:
if isinstance(arg, np.ndarray) and ( arg.shape == (3,)):
pos = arg
else:
pos = parse_vector(arg,3)
except EOFError:
nprint("Ok.")
return False
except TypeError:
nprint("Cannot parse position.",'warn')
return False
if (not isinstance(arg, np.ndarray)):
pos = np.array(pos)
sample.add_muon(pos)
return True
else:
#nprintmsg('NS')
return False
def ninput_mt(message, parser = None, emessage = 'Parser could not parse your input or invalid input.'):
"""
Nice input multiple trials function
"""
while True:
try:
ui = ninput(message)
if parser:
ui = parser(ui)
return ui
except ValueError: # tries again if parser fails
nprint(emessage,'warn')
def ninput_mt(message,
parser=None,
emessage='Parser could not parse your input or invalid input.'):
"""
Nice input multiple trials function
"""
while True:
try:
ui = ninput(message)
if parser:
ui = parser(ui)
return ui
except ValueError: # tries again if parser fails
nprint(emessage, 'warn')
def ninput(message,parser = None):
"""
Nice input function
"""
try:
choice = ""
if sys.version_info >= (3,0):
choice = input('\t ' + message )
else:
choice = raw_input('\t ' + message )
#readline.remove_history_item(readline.get_current_history_length()-1)
if parser:
choice = parser(choice)
return choice
except KeyboardInterrupt:
nprint ("Use crtl+D to stop input!\n",'warn')
pass
def ninput(message, parser=None):
"""
Nice input function
"""
try:
choice = ""
if sys.version_info >= (3, 0):
choice = input('\t ' + message)
else:
choice = raw_input('\t ' + message)
#readline.remove_history_item(readline.get_current_history_length()-1)
if parser:
choice = parser(choice)
return choice
except KeyboardInterrupt:
nprint("Use crtl+D to stop input!\n", 'warn')
pass
def mago_set_k(sample, kvalue=None, mm=None):
"""
Set propagation with respect to the conventional reciprocal cell
kavalue : propagation vector (either string or tuple or list), if None, input is prompetd
mm : Magnetic Model to be used. If None the current magnetic model is used
returns: None
"""
if mm is None:
smm = sample.mm
else:
smm = mm
if sample._check_lattice():
if not kvalue is None:
if isinstance(kvalue, np.ndarray) and ( kvalue.shape == (3,)):
smm.k = kvalue
return True
else:
raise TypeError("Invalid type for kvalue. Must be 3D vector defined as numpy array.")
else:
try:
if kvalue is None:
kval=ninput('Propagation vector (w.r.t. conv. rec. cell): ', parse_vector)
else:
kval = parse_vector(kvalue,3)
except EOFError:
nprint("Ok.")
return False
except TypeError:
nprint("Cannot parse position.",'warn')
return
smm.k=np.array(kval,dtype=np.float)
return True
def mago_set_k(sample, kvalue=None, mm=None):
"""
Set propagation with respect to the conventional reciprocal cell
kavalue : propagation vector (either string or tuple or list), if None, input is prompetd
mm : Magnetic Model to be used. If None the current magnetic model is used
returns: None
"""
if mm is None:
smm = sample.mm
else:
smm = mm
if sample._check_lattice():
if not kvalue is None:
if isinstance(kvalue, np.ndarray) and (kvalue.shape == (3, )):
smm.k = kvalue
return True
else:
raise TypeError(
"Invalid type for kvalue. Must be 3D vector defined as numpy array."
)
else:
try:
if kvalue is None:
kval = ninput(
'Propagation vector (w.r.t. conv. rec. cell): ',
parse_vector)
else:
kval = parse_vector(kvalue, 3)
except EOFError:
nprint("Ok.")
return False
except TypeError:
nprint("Cannot parse position.", 'warn')
return
smm.k = np.array(kval, dtype=np.float)
return True
import sys
from muesr.core.nprint import nprint
try:
import readline
except:
nprint ("readline not present, using standard python input functions.\n",'warn')
def ninput(message,parser = None):
"""
Nice input function
"""
try:
choice = ""
if sys.version_info >= (3,0):
choice = input('\t ' + message )
else:
choice = raw_input('\t ' + message )
#readline.remove_history_item(readline.get_current_history_length()-1)
if parser:
choice = parser(choice)
return choice
except KeyboardInterrupt:
nprint ("Use crtl+D to stop input!\n",'warn')
pass
def ninput_mt(message, parser = None, emessage = 'Parser could not parse your input or invalid input.'):
"""
Nice input multiple trials function
"""
def read_xsf(fileobj, index=-1, read_data=False):
if not hasattr(fileobj, 'read'):
fileobj = open(fileobj, 'r')
readline = fileobj.readline
while True:
line = readline().strip()
if line != '':
if line[0] != '#':
break
if 'INFO' in line:
while True:
line = readline().strip()
if line != '':
if line[0] != '#':
if 'END_INFO' in line:
break
line = readline().strip()
if 'ANIMSTEPS' in line:
nimages = int(line.split()[1])
line = readline().strip()
else:
nimages = 1
if 'CRYSTAL' in line:
pbc = True
elif 'SLAB' in line:
pbc = (True, True, False)
elif 'POLYMER' in line:
pbc = (True, False, False)
elif 'DIM-GROUP' in line:
line = readline().strip()
if int(line.split(' ')[0]) == 3:
pbc = True
else:
nprint("WARNING: I'm missing something in your XCrysDen file.",
'warn')
pbc = False
else:
nprint("WARNING: I'm missing something in your XCrysDen file.", 'warn')
pbc = False
images = []
for n in range(nimages):
cell = None
if pbc:
while True:
line = readline().strip()
if line != '':
if line[0] != '#':
break
assert 'PRIMVEC' in line
cell = []
for i in range(3):
cell.append([float(x) for x in readline().split()])
else:
nprint(
"This program cannot work without PBC...create a fake cell.",
'warn')
return None
while not 'PRIMCOORD' in readline().strip():
continue
natoms = int(readline().split()[0])
symbols = []
numbers = []
positions = []
for a in range(natoms):
line = readline().split()
try:
numbers.append(int(line[0]))
except:
atm_name = re.sub("\d", "", str(line[0]))
symbols.append(atm_name)
positions.append([float(x) for x in line[1:]])
positions = np.array(positions)
if len(positions[0]) == 3:
forces = None
else:
positions = positions[:, :3]
forces = positions[:, 3:]
if len(symbols) != 0:
image = Atoms(symbols, positions, cell=cell, pbc=pbc)
elif len(numbers) != 0:
image = Atoms(numbers=numbers,
positions=positions,
cell=cell,
pbc=pbc)
images.append(image)
if read_data:
data = read_xsf_data(fileobj)
#line = readline()
#assert 'BEGIN_BLOCK_DATAGRID_3D' in line
#line = readline()
#assert 'BEGIN_DATAGRID_3D' in line
#
#shape = [int(x) for x in readline().split()]
#start = [float(x) for x in readline().split()]
#
#for i in range(3):
# readline()
#
#n_data = shape[0]*shape[1]*shape[2]
#data = np.array([float(readline())
# for s in range(n_data)]).reshape(shape[::-1])
#data = np.swapaxes(data, 0, 2)
#
fileobj.close()
return images[index], data
fileobj.close()
return images[index]
import warnings
from muesr.core.spg import spacegroup_from_data
from muesr.core.parsers import *
#from muesr.core.symmetry import Symmetry
from muesr.core.nprint import nprint, nprintmsg
have_spg = True
try:
import spglib as spg
except ImportError:
try:
from pyspglib import spglib as spg
except ImportError:
nprint("Spg Library not loaded", "warn")
have_spg = False
def symsearch(sample, precision=1e-4):
"""
Identifies symmetry operations of the unit cell using spglib and
update the sample definition.
:param sample: A sample object.
:param float precision: atoms are assumed equivalent if distances are
smaller than precision. In Angstrom.
:returns: True if successful, False otherwise.
:rtype: bool
def mago_set_FC(sample, fcs = None, atoms_types = None, mm=None, inputConvention='b-c'):
"""
Defines fourier components for the unit cell.
"""
sample._check_lattice()
if mm is None:
smm = sample.mm
else:
smm = mm
inputConvEnum = -1
if inputConvention.lower() in ['bohr-cartesian', 'b-c']:
nprint('Fourier components in Bohr magnetons and Cartesian coordinates.')
inputConvEnum = 0
elif inputConvention.lower() in ['bohr/angstrom-lattice', 'b/a-l']:
nprint('Fourier components in Bohr magnetons/Angstrom and lattice coordinates.')
inputConvEnum = 1
elif inputConvention.lower() in ['bohr-lattice','b-l']:
nprint('Fourier components in Bohr magnetons and lattice coordinates.')
inputConvEnum = 2
else:
nprint('Invalid Fourier Description method: ' + inputConvention.lower() ,'error.')
return False
if not fcs is None:
smm.fc_set(fcs, inputConvEnum)
return True
unit_cell = sample._cell
lattice = unit_cell.get_cell()
if atoms_types is None:
atoms_types=ninput('Which atom? (enter for all): ').split()
if atoms_types == []:
set_this_fc = lambda x: True
else:
atoms_types = [x.lower() for x in atoms_types] #lowercase
set_this_fc = lambda x: x.lower() in atoms_types
# Print where they are
print_cell(unit_cell,set_this_fc)
fcs = np.zeros([unit_cell.get_number_of_atoms(),3],dtype=np.complex)
gotEOS = False
for i, atom in enumerate(unit_cell):
try:
if set_this_fc(atom[0]): # check if we should set this fc
FCin = ninput_mt("FC for atom %i %s (3 real, [3 imag]): " % (i+1,atom[0]), parse_complex_vector)
fcs[i]=[FCin[j]+1.j*FCin[j+3] for j in range(3)]
else:
# 0 is always 0, no matter the input format! ;)
fcs[i]=([0.+0.j,0.+0.j,0.+0.j])
except EOFError:
gotEOS = True
break
if gotEOS:
nprint('Nothing set')
return False
else:
smm.fc_set(fcs, inputConvEnum)
return True
import warnings
from muesr.core.spg import spacegroup_from_data
from muesr.core.parsers import *
#from muesr.core.symmetry import Symmetry
from muesr.core.nprint import nprint, nprintmsg
have_spg = True
try:
import spglib as spg
except ImportError:
try:
from pyspglib import spglib as spg
except ImportError:
nprint("Spg Library not loaded", "warn")
have_spg = False
def symsearch(sample, precision=1e-4):
"""
Identifies symmetry operations of the unit cell using spglib and
update the sample definition.
:param sample: A sample object.
:param float precision: atoms are assumed equivalent if distances are
smaller than precision. In Angstrom.
:returns: True if successful, False otherwise.
:rtype: bool
"""
def read_xsf(fileobj, index=-1, read_data=False):
if not hasattr(fileobj, 'read'):
fileobj = open(fileobj,'r')
readline = fileobj.readline
while True:
line = readline().strip()
if line != '':
if line[0] != '#':
break
if 'INFO' in line:
while True:
line = readline().strip()
if line != '':
if line[0] != '#':
if 'END_INFO' in line:
break
line = readline().strip()
if 'ANIMSTEPS' in line:
nimages = int(line.split()[1])
line = readline().strip()
else:
nimages = 1
if 'CRYSTAL' in line:
pbc = True
elif 'SLAB' in line:
pbc = (True, True, False)
elif 'POLYMER' in line:
pbc = (True, False, False)
elif 'DIM-GROUP' in line:
line = readline().strip()
if int(line.split(' ')[0]) == 3:
pbc = True
else:
nprint ("WARNING: I'm missing something in your XCrysDen file.",'warn')
pbc = False
else:
nprint ("WARNING: I'm missing something in your XCrysDen file.",'warn')
pbc = False
images = []
for n in range(nimages):
cell = None
if pbc:
while True:
line = readline().strip()
if line != '':
if line[0] != '#':
break
assert 'PRIMVEC' in line
cell = []
for i in range(3):
cell.append([float(x) for x in readline().split()])
else:
nprint ("This program cannot work without PBC...create a fake cell.",'warn')
return None
while not 'PRIMCOORD' in readline().strip():
continue
natoms = int(readline().split()[0])
symbols = []
numbers = []
positions = []
for a in range(natoms):
line = readline().split()
try:
numbers.append(int(line[0]))
except:
atm_name = re.sub("\d","",str(line[0]))
symbols.append(atm_name)
positions.append([float(x) for x in line[1:]])
positions = np.array(positions)
if len(positions[0]) == 3:
forces = None
else:
positions = positions[:, :3]
forces = positions[:, 3:]
if len(symbols) != 0:
image = Atoms(symbols, positions, cell=cell, pbc=pbc)
elif len(numbers) != 0:
image = Atoms(numbers = numbers, positions = positions, cell=cell, pbc=pbc)
images.append(image)
if read_data:
data = read_xsf_data(fileobj)
#line = readline()
#assert 'BEGIN_BLOCK_DATAGRID_3D' in line
#line = readline()
#assert 'BEGIN_DATAGRID_3D' in line
#
#shape = [int(x) for x in readline().split()]
#start = [float(x) for x in readline().split()]
#
#for i in range(3):
# readline()
#
#n_data = shape[0]*shape[1]*shape[2]
#data = np.array([float(readline())
# for s in range(n_data)]).reshape(shape[::-1])
#data = np.swapaxes(data, 0, 2)
#
fileobj.close()
return images[index], data
fileobj.close()
return images[index]
def read_xsf_data(f):
found_data = False
def search_data_block(f):
while f.readline().find("BEGIN_BLOCK_DATAGRID_3D") == -1:
continue
return True
while search_data_block(f):
nprint ("Found data block:")
nprint("Desc" + f.readline())
nprint("type" + f.readline())
if ninput_mt("Use this? ", mybool):
found_data = True
break
if not found_data:
nprint ("No data found, exiting...", 'warn')
return None
grid = map(int, f.readline().split())
# Lattice vectors along lines
orig = np.array(map(float, f.readline().split()), dtype=object)
v1 = np.array(map(float, f.readline().split()), dtype=object)
v2 = np.array(map(float, f.readline().split()), dtype=object)
v3 = np.array(map(float, f.readline().split()), dtype=object)
v1n = v1/grid[0]
v2n = v2/grid[1]
v3n = v3/grid[2]
sdata = np.zeros(np.prod(grid))
data_buffer = []
nprint("Grid has " + str(np.prod(grid)) + " points.")
#grid_steps = [int(x/10) for x in grid]
#nprint("Setting steps throught grid to %i %i %i." % tuple(grid_steps) )
nprint ("Parsing data...")
for k in range(0, grid[2]):
for j in range(0,grid[1]):
for i in range(0, grid[0]):
if data_buffer == []:
data_buffer = [float(x) for x in f.readline().split()] # a random number of data may be on the line
sdata[i+grid[0]*j+grid[1]*grid[0]*k] = data_buffer[0]
data_buffer.pop(0) #empty the buffer
return [sdata, [grid, orig, [v1n,v2n,v3n]]]
def mago_set_FC(sample,
fcs=None,
atoms_types=None,
mm=None,
inputConvention='b-c'):
"""
Defines fourier components for the unit cell.
"""
sample._check_lattice()
if mm is None:
smm = sample.mm
else:
smm = mm
inputConvEnum = -1
if inputConvention.lower() in ['bohr-cartesian', 'b-c']:
nprint(
'Fourier components in Bohr magnetons and Cartesian coordinates.')
inputConvEnum = 0
elif inputConvention.lower() in ['bohr/angstrom-lattice', 'b/a-l']:
nprint(
'Fourier components in Bohr magnetons/Angstrom and lattice coordinates.'
)
inputConvEnum = 1
elif inputConvention.lower() in ['bohr-lattice', 'b-l']:
nprint('Fourier components in Bohr magnetons and lattice coordinates.')
inputConvEnum = 2
else:
nprint(
'Invalid Fourier Description method: ' + inputConvention.lower(),
'error.')
return False
if not fcs is None:
smm.fc_set(fcs, inputConvEnum)
return True
unit_cell = sample._cell
lattice = unit_cell.get_cell()
if atoms_types is None:
atoms_types = ninput('Which atom? (enter for all): ').split()
if atoms_types == []:
set_this_fc = lambda x: True
else:
atoms_types = [x.lower() for x in atoms_types] #lowercase
set_this_fc = lambda x: x.lower() in atoms_types
# Print where they are
print_cell(unit_cell, set_this_fc)
fcs = np.zeros([unit_cell.get_number_of_atoms(), 3], dtype=np.complex)
gotEOS = False
for i, atom in enumerate(unit_cell):
try:
if set_this_fc(atom[0]): # check if we should set this fc
FCin = ninput_mt(
"FC for atom %i %s (3 real, [3 imag]): " %
(i + 1, atom[0]), parse_complex_vector)
fcs[i] = [FCin[j] + 1.j * FCin[j + 3] for j in range(3)]
else:
# 0 is always 0, no matter the input format! ;)
fcs[i] = ([0. + 0.j, 0. + 0.j, 0. + 0.j])
except EOFError:
gotEOS = True
break
if gotEOS:
nprint('Nothing set')
return False
else:
smm.fc_set(fcs, inputConvEnum)
return True
import sys
from muesr.core.nprint import nprint
try:
import readline
except:
nprint("readline not present, using standard python input functions.\n",
'warn')
def ninput(message, parser=None):
"""
Nice input function
"""
try:
choice = ""
if sys.version_info >= (3, 0):
choice = input('\t ' + message)
else:
choice = raw_input('\t ' + message)
#readline.remove_history_item(readline.get_current_history_length()-1)
if parser:
choice = parser(choice)
return choice
except KeyboardInterrupt:
nprint("Use crtl+D to stop input!\n", 'warn')
pass
def ninput_mt(message,
parser=None,
def read_xsf_data(f):
found_data = False
def search_data_block(f):
while f.readline().find("BEGIN_BLOCK_DATAGRID_3D") == -1:
continue
return True
while search_data_block(f):
nprint("Found data block:")
nprint("Desc" + f.readline())
nprint("type" + f.readline())
if ninput_mt("Use this? ", mybool):
found_data = True
break
if not found_data:
nprint("No data found, exiting...", 'warn')
return None
grid = map(int, f.readline().split())
# Lattice vectors along lines
orig = np.array(map(float, f.readline().split()), dtype=object)
v1 = np.array(map(float, f.readline().split()), dtype=object)
v2 = np.array(map(float, f.readline().split()), dtype=object)
v3 = np.array(map(float, f.readline().split()), dtype=object)
v1n = v1 / grid[0]
v2n = v2 / grid[1]
v3n = v3 / grid[2]
sdata = np.zeros(np.prod(grid))
data_buffer = []
nprint("Grid has " + str(np.prod(grid)) + " points.")
#grid_steps = [int(x/10) for x in grid]
#nprint("Setting steps throught grid to %i %i %i." % tuple(grid_steps) )
nprint("Parsing data...")
for k in range(0, grid[2]):
for j in range(0, grid[1]):
for i in range(0, grid[0]):
if data_buffer == []:
data_buffer = [
float(x) for x in f.readline().split()
] # a random number of data may be on the line
sdata[i + grid[0] * j + grid[1] * grid[0] * k] = data_buffer[0]
data_buffer.pop(0) #empty the buffer
return [sdata, [grid, orig, [v1n, v2n, v3n]]]