def __init__(self, system, alpha, gcut=0.35):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
gcut
The cutoff in reciprocal space.
'''
ForcePart.__init__(self, 'ewald_reci', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell.')
if system.charges is None:
raise ValueError('The system does not have charges.')
if system.dipoles is None:
raise ValueError('The system does not have dipoles.')
self.system = system
self.alpha = alpha
self.gcut = gcut
self.update_gmax()
self.work = np.empty(system.natom*2)
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' gcut: %s' % log.invlength(self.gcut))
log.hline()
def __init__(self, system, alpha, gcut=0.35):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
gcut
The cutoff in reciprocal space.
'''
ForcePart.__init__(self, 'ewald_reci', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell.')
if system.charges is None:
raise ValueError('The system does not have charges.')
if system.dipoles is None:
raise ValueError('The system does not have dipoles.')
self.system = system
self.alpha = alpha
self.gcut = gcut
self.update_gmax()
self.work = np.empty(system.natom * 2)
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' gcut: %s' % log.invlength(self.gcut))
log.hline()
def __init__(self,
system,
alpha,
gcut=0.35,
dielectric=1.0,
exclude_frame=False,
n_frame=0):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
**Optional arguments:**
gcut
The cutoff in reciprocal space.
dielectric
The scalar relative permittivity of the system.
exclude_frame
A boolean to exclude framework-framework interactions
(exclude_frame=True) for efficiency sake in MC simulations.
n_frame
Number of framework atoms. This parameter is used to exclude
framework-framework neighbors when exclude_frame=True.
'''
ForcePart.__init__(self, 'ewald_reci', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell.')
if system.charges is None:
raise ValueError('The system does not have charges.')
self.system = system
self.alpha = alpha
self.gcut = gcut
self.dielectric = dielectric
self.update_gmax()
self.work = np.empty(system.natom * 2)
if exclude_frame == True and n_frame < 0:
raise ValueError(
'The number of framework atoms to exclude must be positive.')
elif exclude_frame == False:
n_frame = 0
self.n_frame = n_frame
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' gcut: %s' % log.invlength(self.gcut))
log(' relative permittivity: %5.3f' % self.dielectric)
log.hline()
def __init__(self, system, alpha, gcut=0.35, dielectric=1.0, exclude_frame=False, n_frame=0):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
**Optional arguments:**
gcut
The cutoff in reciprocal space.
dielectric
The scalar relative permittivity of the system.
exclude_frame
A boolean to exclude framework-framework interactions
(exclude_frame=True) for efficiency sake in MC simulations.
n_frame
Number of framework atoms. This parameter is used to exclude
framework-framework neighbors when exclude_frame=True.
'''
ForcePart.__init__(self, 'ewald_reci', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell.')
if system.charges is None:
raise ValueError('The system does not have charges.')
self.system = system
self.alpha = alpha
self.gcut = gcut
self.dielectric = dielectric
self.update_gmax()
self.work = np.empty(system.natom*2)
if exclude_frame == True and n_frame < 0:
raise ValueError('The number of framework atoms to exclude must be positive.')
elif exclude_frame == False:
n_frame = 0
self.n_frame = n_frame
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' gcut: %s' % log.invlength(self.gcut))
log(' relative permittivity: %5.3f' % self.dielectric)
log.hline()
def __init__(self, system, alpha, dielectric=1.0):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
**Optional arguments:**
dielectric
The scalar relative permittivity of the system.
'''
ForcePart.__init__(self, 'ewald_neut', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell')
if system.charges is None:
raise ValueError('The system does not have charges.')
self.system = system
self.alpha = alpha
self.dielectric = dielectric
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' relative permittivity: %5.3f' % self.dielectric)
log.hline()
def __init__(self, system, alpha, scalings):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
scalings
A ``Scalings`` object. This object contains all the information
about the energy scaling of pairwise contributions that are
involved in covalent interactions. See
:class:`yaff.pes.scalings.Scalings` for more details.
'''
ForcePart.__init__(self, 'ewald_cor', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell')
if system.charges is None:
raise ValueError('The system does not have charges.')
self.system = system
self.alpha = alpha
self.scalings = scalings
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' scalings: %5.3f %5.3f %5.3f' % (scalings.scale1, scalings.scale2, scalings.scale3))
log.hline()
def __init__(self, system, alpha, dielectric=1.0):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
**Optional arguments:**
dielectric
The scalar relative permittivity of the system.
'''
ForcePart.__init__(self, 'ewald_neut', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell')
if system.charges is None:
raise ValueError('The system does not have charges.')
self.system = system
self.alpha = alpha
self.dielectric = dielectric
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' %
log.invlength(self.alpha))
log(' relative permittivity: %5.3f' % self.dielectric)
log.hline()
def __init__(self, system, alpha, scalings):
'''
**Arguments:**
system
The system to which this interaction applies.
alpha
The alpha parameter in the Ewald summation method.
scalings
A ``Scalings`` object. This object contains all the information
about the energy scaling of pairwise contributions that are
involved in covalent interactions. See
:class:`yaff.pes.scalings.Scalings` for more details.
'''
ForcePart.__init__(self, 'ewald_cor', system)
if not system.cell.nvec == 3:
raise TypeError('The system must have a 3D periodic cell')
if system.charges is None:
raise ValueError('The system does not have charges.')
self.system = system
self.alpha = alpha
self.scalings = scalings
if log.do_medium:
with log.section('FPINIT'):
log('Force part: %s' % self.name)
log.hline()
log(' alpha: %s' % log.invlength(self.alpha))
log(' scalings: %5.3f %5.3f %5.3f' %
(scalings.scale1, scalings.scale2, scalings.scale3))
log.hline()