def process_coeff(self, coeff):
v0 = coeff['v0']
eps = coeff['eps']
scaledr_cut = coeff['scaledr_cut']
kappa = coeff['kappa']
return _hoomd.make_scalar4(v0, eps, scaledr_cut, kappa)
def process_coeff(self, coeff):
A = coeff['A'];
i = coeff['i'];
w = coeff['w'];
p = coeff['p'];
return _hoomd.make_scalar4(_hoomd.int_as_scalar(i), A, w, _hoomd.int_as_scalar(p));
def process_coeff(self, coeff):
A = coeff['A']
sigma = coeff['sigma']
x = coeff['x']
y = coeff['y']
return _hoomd.make_scalar4(x, y, A, sigma)
def process_coeff(self, coeff):
D0 = coeff['D0']
alpha = coeff['alpha']
r0 = coeff['r0']
return _md.make_wall_morse_params(
_hoomd.make_scalar4(D0, alpha, r0, 0.0),
coeff['r_cut'] * coeff['r_cut'], coeff['r_extrap'])
def process_coeff(self, coeff):
A = coeff['A']
i = coeff['i']
w = coeff['w']
p = coeff['p']
return _hoomd.make_scalar4(_hoomd.int_as_scalar(i), A, w,
_hoomd.int_as_scalar(p))
def process_coeff(self, coeff):
epsilon = float(coeff['epsilon']);
sigma = float(coeff['sigma']);
n = float(coeff['n']);
m = float(coeff['m']);
mie1 = epsilon * math.pow(sigma, n) * (n/(n-m)) * math.pow(n/m,m/(n-m));
mie2 = epsilon * math.pow(sigma, m) * (n/(n-m)) * math.pow(n/m,m/(n-m));
mie3 = n
mie4 = m
return _md.make_wall_mie_params(_hoomd.make_scalar4(mie1, mie2, mie3, mie4), coeff['r_cut']*coeff['r_cut'], coeff['r_extrap']);
def process_coeff(self, coeff):
epsilon = float(coeff['epsilon']);
sigma = float(coeff['sigma']);
n = float(coeff['n']);
m = float(coeff['m']);
mie1 = epsilon * math.pow(sigma, n) * (n/(n-m)) * math.pow(n/m,m/(n-m));
mie2 = epsilon * math.pow(sigma, m) * (n/(n-m)) * math.pow(n/m,m/(n-m));
mie3 = n
mie4 = m
return _md.make_wall_mie_params(_hoomd.make_scalar4(mie1, mie2, mie3, mie4), coeff['r_cut']*coeff['r_cut'], coeff['r_extrap']);
def process_coeff(self, coeff):
epsilon = coeff['epsilon']
sigma = coeff['sigma']
style = coeff['style']
if style == 'slv-slv':
style = 0
elif style == 'coll-slv':
style = 1
elif style == 'coll-coll':
style = 2
else:
hoomd.context.msg.error('Unknown interaction style\n')
raise RuntimeError('Unknown interaction style')
return _hoomd.make_scalar4(epsilon, sigma**3, sigma**6, _hoomd.int_as_scalar(style))
def set_orientation(self, i, ref_orient):
R""" Set the reference orientation for a particular particle.
Args:
i (int): Index of the particle
ref_orient (array_like): Reference orientation for the particle
Examples::
field = azplugins.restrain.position(group=hoomd.group.all(), k=1.0)
director = [1., 0., 0., 0.]
field.set_reference_orientation(0,director)
"""
hoomd.util.print_status_line()
try:
xyzw = _hoomd.make_scalar4(ref_orient[0],ref_orient[1],ref_orient[2],ref_orient[3])
except:
hoomd.context.msg.error('restrain.orientation.set_orientation: ref_orient must be a 4-item iterable composed of scalars\n')
raise ValueError('ref_orient must be a 4-item iterable composed of scalars')
self.cpp_force.setOrientation(i,xyzw)
def process_coeff(self, coeff):
k = coeff['k']
r0 = coeff['r0']
epsilon = coeff['epsilon']
sigma = coeff['sigma']
lj1 = 4.0 * epsilon * math.pow(sigma, 12.0)
lj2 = 4.0 * epsilon * math.pow(sigma, 6.0)
if epsilon==0:
hoomd.context.msg.error("azplugins.bond.fene(): epsilon must be non-zero.\n")
raise ValueError('epsilon must be non-zero')
if sigma==0:
hoomd.context.msg.error("azplugins.bond.fene(): sigma must be non-zero.\n")
raise ValueError('sigma must be non-zero')
if k==0:
hoomd.context.msg.error("azplugins.bond.fene(): k must be non-zero.\n")
raise ValueError('k must be non-zero')
if r0==0:
hoomd.context.msg.error("azplugins.bond.fene(): r0 must be non-zero.\n")
raise ValueError('r0 must be non-zero')
return _hoomd.make_scalar4(k, r0, lj1, lj2)
def set_position(self, i, ref_pos):
R""" Set the reference position for a particular particle.
Args:
i (int): Index of the particle
ref_pos (array_like): Reference position for the particle
Examples::
springs = azplugins.restrain.position(group=hoomd.group.all(), k=1.0)
lattice = [1., 2., 3.]
springs.set_reference_position(0,lattice)
"""
hoomd.util.print_status_line()
try:
xyz = _hoomd.make_scalar4(ref_pos[0],ref_pos[1],ref_pos[2],0.0)
except:
hoomd.context.msg.error('restrain.orientation.set_positions: ref_pos must be a 3-item iterable composed of scalars\n')
raise ValueError('ref_pos must be a 3-item iterable composed of scalars')
self.cpp_force.setPosition(i,xyz)
def set_param(self,
type_name,
types,
positions,
orientations=None,
charges=None,
diameters=None):
R""" Set constituent particle types and coordinates for a rigid body.
Args:
type_name (str): The type of the central particle
types (list): List of types of constituent particles
positions (list): List of relative positions of constituent particles
orientations (list): List of orientations of constituent particles (**optional**)
charge (list): List of charges of constituent particles (**optional**)
diameters (list): List of diameters of constituent particles (**optional**)
.. caution::
The constituent particle type must be exist.
If it does not exist, it can be created on the fly using
``system.particles.types.add('A_const')`` (see :py:mod:`hoomd.data`).
Example::
rigid = constrain.rigd()
rigid.set_param('A', types = ['A_const', 'A_const'], positions = [(0,0,1),(0,0,-1)])
rigid.set_param('B', types = ['B_const', 'B_const'], positions = [(0,0,.5),(0,0,-.5)])
"""
# get a list of types from the particle data
ntypes = hoomd.context.current.system_definition.getParticleData(
).getNTypes()
type_list = []
for i in range(0, ntypes):
type_list.append(hoomd.context.current.system_definition.
getParticleData().getNameByType(i))
if type_name not in type_list:
hoomd.context.msg.error('Type '
'{}'
' not found.\n'.format(type_name))
raise RuntimeError(
'Error setting up parameters for constrain.rigid()')
type_id = type_list.index(type_name)
if not isinstance(types, list):
hoomd.context.msg.error('Expecting list of particle types.\n')
raise RuntimeError(
'Error setting up parameters for constrain.rigid()')
type_vec = _hoomd.std_vector_uint()
for t in types:
if t not in type_list:
hoomd.context.msg.error('Type ' '{}' ' not found.\n'.format(t))
raise RuntimeError(
'Error setting up parameters for constrain.rigid()')
constituent_type_id = type_list.index(t)
type_vec.append(constituent_type_id)
pos_vec = _hoomd.std_vector_scalar3()
positions_list = list(positions)
for p in positions_list:
p = tuple(p)
if len(p) != 3:
hoomd.context.msg.error(
'Particle position is not a coordinate triple.\n')
raise RuntimeError(
'Error setting up parameters for constrain.rigid()')
pos_vec.append(_hoomd.make_scalar3(p[0], p[1], p[2]))
orientation_vec = _hoomd.std_vector_scalar4()
if orientations is not None:
orientations_list = list(orientations)
for o in orientations_list:
o = tuple(o)
if len(o) != 4:
hoomd.context.msg.error(
'Particle orientation is not a 4-tuple.\n')
raise RuntimeError(
'Error setting up parameters for constrain.rigid()')
orientation_vec.append(
_hoomd.make_scalar4(o[0], o[1], o[2], o[3]))
else:
for p in positions:
orientation_vec.append(_hoomd.make_scalar4(1, 0, 0, 0))
charge_vec = _hoomd.std_vector_scalar()
if charges is not None:
charges_list = list(charges)
for c in charges_list:
charge_vec.append(float(c))
else:
for p in positions:
charge_vec.append(0.0)
diameter_vec = _hoomd.std_vector_scalar()
if diameters is not None:
diameters_list = list(diameters)
for d in diameters_list:
diameter_vec.append(float(d))
else:
for p in positions:
diameter_vec.append(1.0)
# set parameters in C++ force
self.cpp_force.setParam(type_id, type_vec, pos_vec, orientation_vec,
charge_vec, diameter_vec)
def process_coeff(self, coeff):
k = coeff['k'];
r0 = coeff['r0'];
lj1 = 4.0 * coeff['epsilon'] * math.pow(coeff['sigma'], 12.0);
lj2 = 4.0 * coeff['epsilon'] * math.pow(coeff['sigma'], 6.0);
return _hoomd.make_scalar4(k, r0, lj1, lj2);
def set_param(self,type_name, types, positions, orientations=None, charges=None, diameters=None):
R""" Set constituent particle types and coordinates for a rigid body.
Args:
type_name (str): The type of the central particle
types (list): List of types of constituent particles
positions (list): List of relative positions of constituent particles
orientations (list): List of orientations of constituent particles (**optional**)
charge (list): List of charges of constituent particles (**optional**)
diameters (list): List of diameters of constituent particles (**optional**)
.. caution::
The constituent particle type must be exist.
If it does not exist, it can be created on the fly using
``system.particles.types.add('A_const')`` (see :py:mod:`hoomd.data`).
Example::
rigid = constrain.rigd()
rigid.set_param('A', types = ['A_const', 'A_const'], positions = [(0,0,1),(0,0,-1)])
rigid.set_param('B', types = ['B_const', 'B_const'], positions = [(0,0,.5),(0,0,-.5)])
"""
# get a list of types from the particle data
ntypes = hoomd.context.current.system_definition.getParticleData().getNTypes();
type_list = [];
for i in range(0,ntypes):
type_list.append(hoomd.context.current.system_definition.getParticleData().getNameByType(i));
if type_name not in type_list:
hoomd.context.msg.error('Type ''{}'' not found.\n'.format(type_name))
raise RuntimeError('Error setting up parameters for constrain.rigid()')
type_id = type_list.index(type_name)
if not isinstance(types, list):
hoomd.context.msg.error('Expecting list of particle types.\n')
raise RuntimeError('Error setting up parameters for constrain.rigid()')
type_vec = _hoomd.std_vector_uint()
for t in types:
if t not in type_list:
hoomd.context.msg.error('Type ''{}'' not found.\n'.format(t))
raise RuntimeError('Error setting up parameters for constrain.rigid()')
constituent_type_id = type_list.index(t)
type_vec.append(constituent_type_id)
pos_vec = _hoomd.std_vector_scalar3()
positions_list = list(positions)
for p in positions_list:
p = tuple(p)
if len(p) != 3:
hoomd.context.msg.error('Particle position is not a coordinate triple.\n')
raise RuntimeError('Error setting up parameters for constrain.rigid()')
pos_vec.append(_hoomd.make_scalar3(p[0],p[1],p[2]))
orientation_vec = _hoomd.std_vector_scalar4()
if orientations is not None:
orientations_list = list(orientations)
for o in orientations_list:
o = tuple(o)
if len(o) != 4:
hoomd.context.msg.error('Particle orientation is not a 4-tuple.\n')
raise RuntimeError('Error setting up parameters for constrain.rigid()')
orientation_vec.append(_hoomd.make_scalar4(o[0], o[1], o[2], o[3]))
else:
for p in positions:
orientation_vec.append(_hoomd.make_scalar4(1,0,0,0))
charge_vec = _hoomd.std_vector_scalar()
if charges is not None:
charges_list = list(charges)
for c in charges_list:
charge_vec.append(float(c))
else:
for p in positions:
charge_vec.append(0.0)
diameter_vec = _hoomd.std_vector_scalar()
if diameters is not None:
diameters_list = list(diameters)
for d in diameters_list:
diameter_vec.append(float(d))
else:
for p in positions:
diameter_vec.append(1.0)
# set parameters in C++ force
self.cpp_force.setParam(type_id, type_vec, pos_vec, orientation_vec, charge_vec, diameter_vec)
def process_coeff(self, coeff):
D0 = coeff['D0'];
alpha = coeff['alpha'];
r0 = coeff['r0']
return _md.make_wall_morse_params(_hoomd.make_scalar4(D0, alpha, r0, 0.0), coeff['r_cut']*coeff['r_cut'], coeff['r_extrap']);
