def __init__(self, molecule, **kwargs):
self.molecule = qtk.toMolecule(molecule)
if 'temperature' not in kwargs:
kwargs['temperatur'] = 298
if 'temperature_tolerance' not in kwargs:
kwargs['temperature_tolerance'] = 50
if 'md_sample_period' not in kwargs:
kwargs['md_sample_period'] = 50
self.setting = kwargs
def __init__(self, molecule, **kwargs):
self.molecule = qtk.toMolecule(molecule)
if 'temperature' not in kwargs:
kwargs['temperatur'] = 298
if 'temperature_tolerance' not in kwargs:
kwargs['temperature_tolerance'] = 50
if 'md_sample_period' not in kwargs:
kwargs['md_sample_period'] = 50
self.setting = kwargs
def ESP(self, coord=None, **kwargs):
"""
method for electron density
Note: CUBE file is assumed to be orthorohmbic
"""
data = self.data
grid = self.grid
if 'molecule' not in kwargs:
mol = self.molecule
else:
try:
mol = copy.deepcopy(qtk.toMolecule(kwargs['molecule']))
except:
qtk.exit("error when loading molecule:%s" % \
str(kwargs['molecule']))
N = mol.N
Q = self.integrate()
Z_sum = sum(mol.Z)
ne_diff = abs(Q - Z_sum)
ve_diff = abs(Q - mol.getValenceElectrons())
if min(ne_diff, ve_diff) > 1E-2:
qtk.warning("charge not conserved... ESP is wrong!")
qtk.warning("charge integrate to %.2f, " % Q + \
"while nuclear charge adds to %.2f" % Z_sum)
if ve_diff < ne_diff:
Z = [qtk.n2ve(qtk.Z2n(z)) for z in mol.Z]
Z = np.array(Z).reshape(N, 1)
else:
Z = mol.Z.reshape(N, 1)
structure = np.hstack([Z, mol.R * 1.889725989])
if coord is not None:
x, y, z = np.array(coord) * 1.889725989
V = ESP_c.esp_point(grid, structure, data, x, y, z)
return V
else:
qtk.warning("known issue: unidentifed memory leak")
out = copy.deepcopy(self)
out.molecule = mol
out.data = np.nan_to_num(
ESP_cube_c.esp_cube(grid, structure, data)
)
return out
def ESP(self, coord=None, **kwargs):
"""
method for electron density
Note: CUBE file is assumed to be orthorohmbic
"""
data = self.data
grid = self.grid
if 'molecule' not in kwargs:
mol = self.molecule
else:
try:
mol = copy.deepcopy(qtk.toMolecule(kwargs['molecule']))
except:
qtk.exit("error when loading molecule:%s" % \
str(kwargs['molecule']))
N = mol.N
Q = self.integrate()
Z_sum = sum(mol.Z)
ne_diff = abs(Q - Z_sum)
ve_diff = abs(Q - mol.getValenceElectrons())
if min(ne_diff, ve_diff) > 1E-2:
qtk.warning("charge not conserved... ESP is wrong!")
qtk.warning("charge integrate to %.2f, " % Q + \
"while nuclear charge adds to %.2f" % Z_sum)
if ve_diff < ne_diff:
Z = [qtk.n2ve(qtk.Z2n(z)) for z in mol.Z]
Z = np.array(Z).reshape(N, 1)
else:
Z = mol.Z.reshape(N, 1)
structure = np.hstack([Z, mol.R * 1.889725989])
if coord is not None:
x, y, z = np.array(coord) * 1.889725989
V = ESP_c.esp_point(grid, structure, data, x, y, z)
return V
else:
qtk.warning("known issue: unidentifed memory leak")
out = copy.deepcopy(self)
out.molecule = mol
out.data = np.nan_to_num(ESP_cube_c.esp_cube(
grid, structure, data))
return out
def __init__(self, xyz_file, parameter_file, **kwargs):
self.structure = qtk.toMolecule(xyz_file)
# mutation related variables
self.mutation_list = []
self.mutation_target = []
self.mutation_size = 0
# stretching related variables
self.stretching_list = []
self.stretching_direction = []
self.stretching_range = []
# rotation related variables
self.rotation_list = []
self.rotation_center = []
self.rotation_axis = []
self.rotation_range = []
# replacing realted variables
# not yet implemented
# constraint variables #
self.constraint = False
self.forbiden_bonds = []
self.ztotal = 0
self.vtotal = 0
self.element_count = {}
# setup all parameters
self.read_param(parameter_file)
self.coor = flatten([
['m' for _ in flatten(self.mutation_list)],
['s' for _ in flatten(self.stretching_list)],
['r' for _ in flatten(self.rotation_list)],
])
MList = self.mutation_list
_flatten = [item for sublist in MList for item in sublist]
vlen = np.vectorize(len)
try:
lenList = vlen(MList)
except TypeError:
lenList = [len(MList[0]) for i in range(len(MList))]
if not qtk.setting.quiet:
report_itr = False
if self.mutation_list:
report_itr += True
qtk.report('', "===== CCS REPORT =====", color=None)
qtk.report("generating molecule", xyz_file)
qtk.report("ccs parameter file", parameter_file)
qtk.report("mutation indices", self.mutation_list)
qtk.report("target atomic numbers", self.mutation_target)
qtk.report("length of mutation vector", len(_flatten), "<=>",
lenList)
#print ""
if self.stretching_list:
qtk.report("stretching indices", self.stretching_list)
qtk.report("stretching range", self.stretching_range)
qtk.report("stretching direction indices",
self.stretching_direction)
#print ""
if self.rotation_list:
qtk.report("rotation indices", self.rotation_list)
qtk.report("rotation center", self.rotation_center)
qtk.report("rotation axis", self.rotation_axis)
qtk.report("rotation range", self.rotation_range)
#print ""
qtk.status("ccs coordinate", self.coor)
qtk.report('', "========= END ========", color=None)
