def __init__(self, dt, group, alphaGroup, EGroup):
"""Create a AMDForceGroupIntegrator.
Parameters:
- dt (time) The integration time step to use
- group (int) The force group to apply the boost to
- alphaGroup (energy) The alpha parameter to use for the boosted force group
- EGroup (energy) The energy cutoff to use for the boosted force group
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaGroup", alphaGroup)
self.addGlobalVariable("EGroup", EGroup)
self.addGlobalVariable("groupEnergy", 0)
self.addPerDofVariable("oldx", 0)
self.addPerDofVariable("fg", 0)
self.addUpdateContextState()
self.addComputeGlobal("groupEnergy", "energy" + str(group))
self.addComputePerDof("fg", "f" + str(group))
self.addComputePerDof(
"v",
"v+dt*fprime/m; fprime=fother + fg*((1-modify) + modify*(alphaGroup/(alphaGroup+EGroup-groupEnergy))^2); fother=f-fg; modify=step(EGroup-groupEnergy)"
)
self.addComputePerDof("oldx", "x")
self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt")
def __init__(self, dt, group, alphaGroup, EGroup):
"""Create a AMDForceGroupIntegrator.
Parameters
----------
dt : time
The integration time step to use
group : int
The force group to apply the boost to
alphaGroup : energy
The alpha parameter to use for the boosted force group
EGroup : energy
The energy cutoff to use for the boosted force group
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaGroup", alphaGroup)
self.addGlobalVariable("EGroup", EGroup)
self.addGlobalVariable("groupEnergy", 0)
self.addPerDofVariable("oldx", 0)
self.addPerDofVariable("fg", 0)
self.addUpdateContextState();
self.addComputeGlobal("groupEnergy", "energy"+str(group))
self.addComputePerDof("fg", "f"+str(group))
self.addComputePerDof("v", "v+dt*fprime/m; fprime=fother + fg*((1-modify) + modify*(alphaGroup/(alphaGroup+EGroup-groupEnergy))^2); fother=f-fg; modify=step(EGroup-groupEnergy)")
self.addComputePerDof("oldx", "x")
self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt")
def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup):
"""Create a DualAMDIntegrator.
Parameters:
- dt (time) The integration time step to use
- group (int) The force group to apply the second boost to
- alphaTotal (energy) The alpha parameter to use for the total energy
- ETotal (energy) The energy cutoff to use for the total energy
- alphaGroup (energy) The alpha parameter to use for the boosted force group
- EGroup (energy) The energy cutoff to use for the boosted force group
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaTotal", alphaTotal)
self.addGlobalVariable("ETotal", ETotal)
self.addGlobalVariable("alphaGroup", alphaGroup)
self.addGlobalVariable("EGroup", EGroup)
self.addGlobalVariable("groupEnergy", 0)
self.addPerDofVariable("oldx", 0)
self.addPerDofVariable("fg", 0)
self.addUpdateContextState()
self.addComputeGlobal("groupEnergy", "energy" + str(group))
self.addComputePerDof("fg", "f" + str(group))
self.addComputePerDof(
"v", """v+dt*fprime/m;
fprime=fprime1 + fprime2;
fprime2=fg*((1-modifyGroup) + modifyGroup*(alphaGroup/(alphaGroup+EGroup-groupEnergy))^2);
fprime1=fother*((1-modifyTotal) + modifyTotal*(alphaTotal/(alphaTotal+ETotal-energy))^2);
fother=f-fg;
modifyTotal=step(ETotal-energy); modifyGroup=step(EGroup-groupEnergy)"""
)
self.addComputePerDof("oldx", "x")
self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt")
def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup):
"""Create a DualAMDIntegrator.
Parameters:
- dt (time) The integration time step to use
- group (int) The force group to apply the second boost to
- alphaTotal (energy) The alpha parameter to use for the total energy
- ETotal (energy) The energy cutoff to use for the total energy
- alphaGroup (energy) The alpha parameter to use for the boosted force group
- EGroup (energy) The energy cutoff to use for the boosted force group
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaTotal", alphaTotal)
self.addGlobalVariable("ETotal", ETotal)
self.addGlobalVariable("alphaGroup", alphaGroup)
self.addGlobalVariable("EGroup", EGroup)
self.addGlobalVariable("groupEnergy", 0)
self.addPerDofVariable("oldx", 0)
self.addPerDofVariable("fg", 0)
self.addUpdateContextState();
self.addComputeGlobal("groupEnergy", "energy"+str(group))
self.addComputePerDof("fg", "f"+str(group))
self.addComputePerDof("v", """v+dt*fprime/m;
fprime=fprime1 + fprime2;
fprime2=fg*((1-modifyGroup) + modifyGroup*(alphaGroup/(alphaGroup+EGroup-groupEnergy))^2);
fprime1=fother*((1-modifyTotal) + modifyTotal*(alphaTotal/(alphaTotal+ETotal-energy))^2);
fother=f-fg;
modifyTotal=step(ETotal-energy); modifyGroup=step(EGroup-groupEnergy)""")
self.addComputePerDof("oldx", "x")
self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt")
def __init__(self, temperature, friction, dt, groups):
"""Create an MTSLangevinIntegrator.
Parameters
----------
temperature : temperature
the temperature of the heat bath
friction : 1/temperature
the friction coefficient which couples the system to the heat bath
dt : time
The largest (outermost) integration time step to use
groups : list
A list of tuples defining the force groups. The first element of
each tuple is the force group index, and the second element is the
number of times that force group should be evaluated in one time step.
"""
if len(groups) == 0:
raise ValueError("No force groups specified")
groups = sorted(groups, key=lambda x: x[1])
CustomIntegrator.__init__(self, dt)
self.temperature = temperature
self.friction = friction
import math
self.addGlobalVariable("a", math.exp(-friction*dt))
self.addGlobalVariable("b", math.sqrt(1-math.exp(-2*friction*dt)))
from simtk.unit import MOLAR_GAS_CONSTANT_R
self.addGlobalVariable('kT', MOLAR_GAS_CONSTANT_R*temperature)
self.addPerDofVariable("x1", 0)
self.addUpdateContextState();
self._createSubsteps(1, groups)
self.addConstrainVelocities();
def __init__(self, dt, alpha, E):
"""Create an AMDIntegrator.
Parameters
----------
dt : time
The integration time step to use
alpha : energy
The alpha parameter to use
E : energy
The energy cutoff to use
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alpha", alpha)
self.addGlobalVariable("E", E)
self.addPerDofVariable("oldx", 0)
self.addUpdateContextState()
self.addComputePerDof(
"v",
"v+dt*fprime/m; fprime=f*((1-modify) + modify*(alpha/(alpha+E-energy))^2); modify=step(E-energy)"
)
self.addComputePerDof("oldx", "x")
self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt")
def __init__(self, temperature, friction, dt, group, scaleFactor):
CustomIntegrator.__init__(self, dt)
#added:
self.addGlobalVariable("scaleFactor", scaleFactor)
#normal langevin:
self.addGlobalVariable("temperature", temperature);
self.addGlobalVariable("friction", friction);
self.addGlobalVariable("vscale", 0);
self.addGlobalVariable("fscale", 0);
self.addGlobalVariable("noisescale", 0);
self.addPerDofVariable("x0", 0);
#added:
self.addPerDofVariable("fg", 0)
#normal langevin:
self.addUpdateContextState();
self.addComputeGlobal("vscale", "exp(-dt*friction)");
self.addComputeGlobal("fscale", "(1-vscale)/friction");
self.addComputeGlobal("noisescale", "sqrt(kT*(1-vscale*vscale)); kT=0.00831451*temperature");
self.addComputePerDof("x0", "x");
#added:
self.addComputePerDof("fg", "f"+str(group))
#original:
#self.addComputePerDof("v", "vscale*v + fscale*f/m + noisescale*gaussian/sqrt(m)");
#new (same as AMDForceGroupIntegrator code but with a globalvariable scaling factor)
self.addComputePerDof("v", "vscale*v + fscale*fprime/m + noisescale*gaussian/sqrt(m); fprime=fother+fg*scaleFactor; fother=f-fg");
#normal langevin
self.addComputePerDof("x", "x+dt*v");
self.addConstrainPositions();
self.addComputePerDof("v", "(x-x0)/dt");
def __init__(self, dt, groups):
"""Create an MTSIntegrator.
Parameters:
- dt (time) The largest (outermost) integration time step to use
- groups (list) A list of tuples defining the force groups. The first element of each
tuple is the force group index, and the second element is the number of times that force
group should be evaluated in one time step.
"""
if len(groups) == 0:
raise ValueError("No force groups specified")
groups = sorted(groups, key=lambda x: x[1])
CustomIntegrator.__init__(self, dt)
self.addPerDofVariable("x1", 0)
self.addUpdateContextState()
self._createSubsteps(1, groups)
self.addConstrainVelocities()
def __init__(self, dt, groups):
"""Create an MTSIntegrator.
Parameters:
- dt (time) The largest (outermost) integration time step to use
- groups (list) A list of tuples defining the force groups. The first element of each
tuple is the force group index, and the second element is the number of times that force
group should be evaluated in one time step.
"""
if len(groups) == 0:
raise ValueError("No force groups specified")
groups = sorted(groups, key=lambda x: x[1])
CustomIntegrator.__init__(self, dt)
self.addPerDofVariable("x1", 0)
self.addUpdateContextState();
self._createSubsteps(1, groups)
self.addConstrainVelocities();
def __init__(self, dt, alpha, E):
"""Create an AMDIntegrator.
Parameters:
- dt (time) The integration time step to use
- alpha (energy) The alpha parameter to use
- E (energy) The energy cutoff to use
"""
CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alpha", alpha)
self.addGlobalVariable("E", E)
self.addPerDofVariable("oldx", 0)
self.addUpdateContextState();
self.addComputePerDof("v", "v+dt*fprime/m; fprime=f*((1-modify) + modify*(alpha/(alpha+E-energy))^2); modify=step(E-energy)")
self.addComputePerDof("oldx", "x")
self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt")
def VelocityVerletIntegrator(timestep):
# Velocity Verlet integrator with explicit velocities.
integrator = CustomIntegrator(timestep)
integrator.addPerDofVariable("x1", 0)
integrator.addPerDofVariable("x2", 0)
integrator.addUpdateContextState()
integrator.addComputePerDof("v", "v+0.5*dt*f/m")
integrator.addComputePerDof("x", "x+dt*v")
integrator.addComputePerDof("x1", "x")
integrator.addConstrainPositions()
integrator.addComputePerDof("x2", "x")
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x2-x1)/dt")
integrator.addConstrainVelocities()
return integrator
def VelocityVerletIntegrator(timestep):
# Velocity Verlet integrator with explicit velocities.
integrator = CustomIntegrator(timestep)
integrator.addPerDofVariable("x1", 0)
integrator.addPerDofVariable("x2", 0)
integrator.addUpdateContextState()
integrator.addComputePerDof("v", "v+0.5*dt*f/m")
integrator.addComputePerDof("x", "x+dt*v")
integrator.addComputePerDof("x1", "x")
integrator.addConstrainPositions()
integrator.addComputePerDof("x2", "x")
integrator.addComputePerDof("v", "v+0.5*dt*f/m+(x2-x1)/dt")
integrator.addConstrainVelocities()
return integrator