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Convert British spelling to American

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This commit is contained in:
Eisuke Kawashima
2020-03-18 22:01:19 +09:00
parent 5109b7f1b1
commit ca1e1e2dff
40 changed files with 97 additions and 97 deletions
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48
tools/i-pi/ipi/engine/thermostats.py
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@ -31,11 +31,11 @@ Classes:
the entire system.
ThermoSVR: Holds the algorithms for a stochastic velocity rescaling
thermostat.
ThermoGLE: Holds the algorithms for a generalised langevin equation
ThermoGLE: Holds the algorithms for a generalized langevin equation
thermostat.
ThermoNMGLE: Holds the algorithms for a generalised langevin equation
ThermoNMGLE: Holds the algorithms for a generalized langevin equation
thermostat in the normal mode representation.
ThermoNMGLEG: Holds the algorithms for a generalised langevin equation
ThermoNMGLEG: Holds the algorithms for a generalized langevin equation
thermostat in the normal mode representation, with kinetic energy as
well as potential energy sampling optimization.
"""
@ -75,14 +75,14 @@ class Thermostat(dobject):
"""
def __init__(self, temp = 1.0, dt = 1.0, ethermo=0.0):
"""Initialises Thermostat.
"""Initializes Thermostat.
Args:
temp: The simulation temperature. Defaults to 1.0.
dt: The simulation time step. Defaults to 1.0.
ethermo: The initial heat energy transferred to the bath.
Defaults to 0.0. Will be non-zero if the thermostat is
initialised from a checkpoint file.
initialized from a checkpoint file.
"""
dset(self,"temp", depend_value(name='temp', value=temp))
@ -181,7 +181,7 @@ class ThermoLangevin(Thermostat):
return np.sqrt(Constants.kb*self.temp*(1 - self.T**2))
def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0):
"""Initialises ThermoLangevin.
"""Initializes ThermoLangevin.
Args:
temp: The simulation temperature. Defaults to 1.0.
@ -189,7 +189,7 @@ class ThermoLangevin(Thermostat):
tau: The thermostat damping timescale. Defaults to 1.0.
ethermo: The initial heat energy transferred to the bath.
Defaults to 0.0. Will be non-zero if the thermostat is
initialised from a checkpoint file.
initialized from a checkpoint file.
"""
super(ThermoLangevin,self).__init__(temp, dt, ethermo)
@ -241,14 +241,14 @@ class ThermoPILE_L(Thermostat):
"""
def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0, scale=1.0):
"""Initialises ThermoPILE_L.
"""Initializes ThermoPILE_L.
Args:
temp: The simulation temperature. Defaults to 1.0.
dt: The simulation time step. Defaults to 1.0.
tau: The centroid thermostat damping timescale. Defaults to 1.0.
ethermo: The initial conserved energy quantity. Defaults to 0.0. Will
be non-zero if the thermostat is initialised from a checkpoint file.
be non-zero if the thermostat is initialized from a checkpoint file.
scale: A float used to reduce the intensity of the PILE thermostat if
required.
@ -404,14 +404,14 @@ class ThermoSVR(Thermostat):
return Constants.kb*self.temp*0.5
def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0):
"""Initialises ThermoSVR.
"""Initializes ThermoSVR.
Args:
temp: The simulation temperature. Defaults to 1.0.
dt: The simulation time step. Defaults to 1.0.
tau: The thermostat damping timescale. Defaults to 1.0.
ethermo: The initial conserved energy quantity. Defaults to 0.0. Will
be non-zero if the thermostat is initialised from a checkpoint file.
be non-zero if the thermostat is initialized from a checkpoint file.
"""
super(ThermoSVR,self).__init__(temp,dt,ethermo)
@ -459,14 +459,14 @@ class ThermoPILE_G(ThermoPILE_L):
"""
def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0, scale = 1.0):
"""Initialises ThermoPILE_G.
"""Initializes ThermoPILE_G.
Args:
temp: The simulation temperature. Defaults to 1.0.
dt: The simulation time step. Defaults to 1.0.
tau: The centroid thermostat damping timescale. Defaults to 1.0.
ethermo: The initial conserved energy quantity. Defaults to 0.0. Will
be non-zero if the thermostat is initialised from a checkpoint file.
be non-zero if the thermostat is initialized from a checkpoint file.
scale: A float used to reduce the intensity of the PILE thermostat if
required.
"""
@ -556,7 +556,7 @@ class ThermoGLE(Thermostat):
return matrix_exp(-0.5*self.dt*self.A)
def get_S(self):
"""Calculates the matrix for the coloured noise."""
"""Calculates the matrix for the colored noise."""
SST = Constants.kb*(self.C - np.dot(self.T,np.dot(self.C,self.T.T)))
@ -570,7 +570,7 @@ class ThermoGLE(Thermostat):
return rC[:]
def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, ethermo=0.0):
"""Initialises ThermoGLE.
"""Initializes ThermoGLE.
Args:
temp: The simulation temperature. Defaults to 1.0.
@ -582,7 +582,7 @@ class ThermoGLE(Thermostat):
total number of degrees of freedom in the system.
ethermo: The initial heat energy transferred to the bath.
Defaults to 0.0. Will be non-zero if the thermostat is
initialised from a checkpoint file.
initialized from a checkpoint file.
"""
super(ThermoGLE,self).__init__(temp,dt,ethermo)
@ -643,15 +643,15 @@ class ThermoGLE(Thermostat):
# allocates, initializes or restarts an array of s's
if self.s.shape != (self.ns + 1, len(dget(self,"m"))):
if len(self.s) > 0:
warning("Mismatch in GLE s array size on restart, will reinitialise to free particle.", verbosity.low)
warning("Mismatch in GLE s array size on restart, will reinitialize to free particle.", verbosity.low)
self.s = np.zeros((self.ns + 1, len(dget(self,"m"))))
# Initializes the s vector in the free-particle limit
info(" GLE additional DOFs initialised to the free-particle limit.", verbosity.low)
info(" GLE additional DOFs initialized to the free-particle limit.", verbosity.low)
SC = stab_cholesky(self.C*Constants.kb)
self.s[:] = np.dot(SC, self.prng.gvec(self.s.shape))
else:
info("GLE additional DOFs initialised from input.", verbosity.medium)
info("GLE additional DOFs initialized from input.", verbosity.medium)
def step(self):
"""Updates the bound momentum vector with a GLE thermostat"""
@ -699,7 +699,7 @@ class ThermoNMGLE(Thermostat):
return rv[:]
def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, ethermo=0.0):
"""Initialises ThermoGLE.
"""Initializes ThermoGLE.
Args:
temp: The simulation temperature. Defaults to 1.0.
@ -711,7 +711,7 @@ class ThermoNMGLE(Thermostat):
total number of degrees of freedom in the system.
ethermo: The initial heat energy transferred to the bath.
Defaults to 0.0. Will be non-zero if the thermostat is
initialised from a checkpoint file.
initialized from a checkpoint file.
"""
super(ThermoNMGLE,self).__init__(temp,dt,ethermo)
@ -767,16 +767,16 @@ class ThermoNMGLE(Thermostat):
# allocates, initializes or restarts an array of s's
if self.s.shape != (self.nb, self.ns + 1, nm.natoms *3) :
if len(self.s) > 0:
warning("Mismatch in GLE s array size on restart, will reinitialise to free particle.", verbosity.low)
warning("Mismatch in GLE s array size on restart, will reinitialize to free particle.", verbosity.low)
self.s = np.zeros((self.nb, self.ns + 1, nm.natoms*3))
# Initializes the s vector in the free-particle limit
info(" GLE additional DOFs initialised to the free-particle limit.", verbosity.low)
info(" GLE additional DOFs initialized to the free-particle limit.", verbosity.low)
for b in range(self.nb):
SC = stab_cholesky(self.C[b]*Constants.kb)
self.s[b] = np.dot(SC, self.prng.gvec(self.s[b].shape))
else:
info("GLE additional DOFs initialised from input.", verbosity.medium)
info("GLE additional DOFs initialized from input.", verbosity.medium)
prev_ethermo = self.ethermo