DualAMDIntegrator¶
- class openmm.amd.DualAMDIntegrator(dt, group, alphaTotal, ETotal, alphaGroup, EGroup)¶
DualAMDIntegrator implements a dual boost aMD integration algorithm.
This is similar to AMDIntegrator, but two different boosts are applied to the potential: one based on the total energy, and one based on the energy of a single force group (typically representing torsions).
For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
- __init__(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
Methods
__init__(dt, group, alphaTotal, ETotal, …)Create a DualAMDIntegrator.
addComputeGlobal(self, variable, expression)Add a step to the integration algorithm that computes a global value.
addComputePerDof(self, variable, expression)Add a step to the integration algorithm that computes a per-DOF value.
addComputeSum(self, variable, expression)Add a step to the integration algorithm that computes a sum over degrees of freedom.
addConstrainPositions(self)Add a step to the integration algorithm that updates particle positions so all constraints are satisfied.
addConstrainVelocities(self)Add a step to the integration algorithm that updates particle velocities so the net velocity along all constraints is 0.
addGlobalVariable(self, name, initialValue)Define a new global variable.
addPerDofVariable(self, name, initialValue)Define a new per-DOF variable.
addTabulatedFunction(self, name, function)Add a tabulated function that may appear in expressions.
addUpdateContextState(self)Add a step to the integration algorithm that allows Forces to update the context state.
beginIfBlock(self, condition)Add a step which begins a new “if” block.
beginWhileBlock(self, condition)Add a step which begins a new “while” block.
endBlock(self)Add a step which marks the end of the most recently begun “if” or “while” block.
Get the value of alpha for the boosted force group.
Get the value of alpha for the total energy.
getComputationStep(self, index)Get the details of a computation step that has been added to the integration algorithm.
getConstraintTolerance(self)Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
Get the energy threshold E for the boosted force group.
Get the energy threshold E for the total energy.
getEffectiveEnergy(totalEnergy, groupEnergy)Given the actual potential energy of the system, return the value of the effective potential.
getGlobalVariable(self, index)Get the current value of a global variable.
getGlobalVariableByName(self, name)Get the current value of a global variable, specified by name.
getGlobalVariableName(self, index)Get the name of a global variable.
Get which force groups to use for integration.
Get the expression to use for computing the kinetic energy.
getNumComputations(self)Get the number of computation steps that have been added.
getNumGlobalVariables(self)Get the number of global variables that have been defined.
getNumPerDofVariables(self)Get the number of per-DOF variables that have been defined.
getNumTabulatedFunctions(self)Get the number of tabulated functions that have been defined.
getPerDofVariableByName(self, name)Get the value of a per-DOF variable, specified by name.
getPerDofVariableName(self, index)Get the name of a per-DOF variable.
getRandomNumberSeed(self)Get the random number seed.
getStepSize(self)Get the size of each time step, in picoseconds.
getTabulatedFunction(-> TabulatedFunction)Get a reference to a tabulated function that may appear in expressions.
getTabulatedFunctionName(self, index)Get the name of a tabulated function that may appear in expressions.
setAlphaGroup(alpha)Set the value of alpha for the boosted force group.
setAlphaTotal(alpha)Set the value of alpha for the total energy.
setConstraintTolerance(self, tol)Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
setEGroup(E)Set the energy threshold E for the boosted force group.
setETotal(E)Set the energy threshold E for the total energy.
setGlobalVariable(self, index, value)Set the value of a global variable.
setGlobalVariableByName(self, name, value)Set the value of a global variable, specified by name.
setIntegrationForceGroups(groups)Set which force groups to use for integration.
setKineticEnergyExpression(self, expression)Set the expression to use for computing the kinetic energy.
setPerDofVariable(self, index, values)Set the value of a per-DOF variable.
setPerDofVariableByName(self, name, values)Set the value of a per-DOF variable, specified by name.
setRandomNumberSeed(self, seed)Set the random number seed.
setStepSize(self, size)Set the size of each time step, in picoseconds.
step(self, steps)Advance a simulation through time by taking a series of time steps.
Attributes
BlockEndComputeGlobalComputePerDofComputeSumConstrainPositionsConstrainVelocitiesIfBlockStartUpdateContextStateWhileBlockStartThe membership flag
- getAlphaTotal()¶
Get the value of alpha for the total energy.
- setAlphaTotal(alpha)¶
Set the value of alpha for the total energy.
- getETotal()¶
Get the energy threshold E for the total energy.
- setETotal(E)¶
Set the energy threshold E for the total energy.
- getAlphaGroup()¶
Get the value of alpha for the boosted force group.
- setAlphaGroup(alpha)¶
Set the value of alpha for the boosted force group.
- getEGroup()¶
Get the energy threshold E for the boosted force group.
- setEGroup(E)¶
Set the energy threshold E for the boosted force group.
- getEffectiveEnergy(totalEnergy, groupEnergy)¶
Given the actual potential energy of the system, return the value of the effective potential.
- Parameters
totalEnergy (energy) – the actual potential energy of the whole system
groupEnergy (energy) – the actual potential energy of the boosted force group
- Returns
the value of the effective potential
- Return type
energy
- addComputeGlobal(self, variable, expression) → int¶
Add a step to the integration algorithm that computes a global value.
- Parameters
variable (string) – the global variable to store the computed value into
expression (string) – a mathematical expression involving only global variables. In each integration step, its value is computed and stored into the specified variable.
- Returns
the index of the step that was added
- Return type
int
- addComputePerDof(self, variable, expression) → int¶
Add a step to the integration algorithm that computes a per-DOF value.
- Parameters
variable (string) – the per-DOF variable to store the computed value into
expression (string) – a mathematical expression involving both global and per-DOF variables. In each integration step, its value is computed for every degree of freedom and stored into the specified variable.
- Returns
the index of the step that was added
- Return type
int
- addComputeSum(self, variable, expression) → int¶
Add a step to the integration algorithm that computes a sum over degrees of freedom.
- Parameters
variable (string) – the global variable to store the computed value into
expression (string) – a mathematical expression involving both global and per-DOF variables. In each integration step, its value is computed for every degree of freedom. Those values are then added together, and the sum is stored in the specified variable.
- Returns
the index of the step that was added
- Return type
int
- addConstrainPositions(self) → int¶
Add a step to the integration algorithm that updates particle positions so all constraints are satisfied.
- Returns
the index of the step that was added
- Return type
int
- addConstrainVelocities(self) → int¶
Add a step to the integration algorithm that updates particle velocities so the net velocity along all constraints is 0.
- Returns
the index of the step that was added
- Return type
int
- addGlobalVariable(self, name, initialValue) → int¶
Define a new global variable.
- Parameters
name (string) – the name of the variable
initialValue (double) – the variable will initially be set to this value
- Returns
the index of the variable that was added
- Return type
int
- addPerDofVariable(self, name, initialValue) → int¶
Define a new per-DOF variable.
- Parameters
name (string) – the name of the variable
initialValue (double) – the variable will initially be set to this value for all degrees of freedom
- Returns
the index of the variable that was added
- Return type
int
- addTabulatedFunction(self, name, function) → int¶
Add a tabulated function that may appear in expressions.
- Parameters
name (string) – the name of the function as it appears in expressions
function (TabulatedFunction *) – a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the “new” operator. The integrator takes over ownership of it, and deletes it when the integrator itself is deleted.
- Returns
the index of the function that was added
- Return type
int
- addUpdateContextState(self) → int¶
Add a step to the integration algorithm that allows Forces to update the context state.
- Returns
the index of the step that was added
- Return type
int
- beginIfBlock(self, condition) → int¶
Add a step which begins a new “if” block.
- Parameters
condition (string) – a mathematical expression involving a comparison operator and global variables. All steps between this one and the end of the block are executed only if the condition is true.
- Returns
the index of the step that was added
- Return type
int
- beginWhileBlock(self, condition) → int¶
Add a step which begins a new “while” block.
- Parameters
condition (string) – a mathematical expression involving a comparison operator and global variables. All steps between this one and the end of the block are executed repeatedly as long as the condition remains true.
- Returns
the index of the step that was added
- Return type
int
- endBlock(self) → int¶
Add a step which marks the end of the most recently begun “if” or “while” block.
- Returns
the index of the step that was added
- Return type
int
- getComputationStep(self, index)¶
Get the details of a computation step that has been added to the integration algorithm.
- Parameters
index (int) – the index of the computation step to get
- Returns
type (ComputationType) – the type of computation this step performs
variable (string) – the variable into which this step stores its result. If this step does not store a result in a variable, this will be an empty string.
expression (string) – the expression this step evaluates. If this step does not evaluate an expression, this will be an empty string.
- getConstraintTolerance(self) → double¶
Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
- getGlobalVariable(self, index) → double¶
Get the current value of a global variable.
- Parameters
index (int) – the index of the variable to get
- Returns
the current value of the variable
- Return type
double
- getGlobalVariableByName(self, name) → double¶
Get the current value of a global variable, specified by name.
- Parameters
name (string) – the name of the variable to get
- Returns
the current value of the parameter
- Return type
double
- getGlobalVariableName(self, index) → std::string const &¶
Get the name of a global variable.
- Parameters
index (int) – the index of the variable to get
- Returns
the name of the variable
- Return type
string
- getIntegrationForceGroups(self) → int¶
Get which force groups to use for integration. By default, all force groups are included. This is interpreted as a set of bit flags: the forces from group i will be included if (groups&(1<<i)) != 0.
- getKineticEnergyExpression(self) → std::string const &¶
Get the expression to use for computing the kinetic energy. The expression is evaluated for every degree of freedom. Those values are then added together, and the sum is reported as the current kinetic energy.
- getNumComputations(self) → int¶
Get the number of computation steps that have been added.
- getNumGlobalVariables(self) → int¶
Get the number of global variables that have been defined.
- getNumPerDofVariables(self) → int¶
Get the number of per-DOF variables that have been defined.
- getNumTabulatedFunctions(self) → int¶
Get the number of tabulated functions that have been defined.
- getPerDofVariable(self, index)¶
- getPerDofVariable(self, index) → PyObject *
- getPerDofVariableByName(self, name)¶
Get the value of a per-DOF variable, specified by name.
- Parameters
name (string) – the name of the variable to get
- Returns
values – the values of the variable for all degrees of freedom are stored into this
- Return type
vector< Vec3 >
- getPerDofVariableName(self, index) → std::string const &¶
Get the name of a per-DOF variable.
- Parameters
index (int) – the index of the variable to get
- Returns
the name of the variable
- Return type
string
- getRandomNumberSeed(self) → int¶
Get the random number seed. See setRandomNumberSeed() for details.
- getStepSize(self) → double¶
Get the size of each time step, in picoseconds. If this integrator uses variable time steps, the size of the most recent step is returned.
- Returns
the step size, measured in ps
- Return type
double
- getTabulatedFunction(self, index) → TabulatedFunction¶
- getTabulatedFunction(self, index) → TabulatedFunction
Get a reference to a tabulated function that may appear in expressions.
- Parameters
index (int) – the index of the function to get
- Returns
the TabulatedFunction object defining the function
- Return type
- getTabulatedFunctionName(self, index) → std::string const &¶
Get the name of a tabulated function that may appear in expressions.
- Parameters
index (int) – the index of the function to get
- Returns
the name of the function as it appears in expressions
- Return type
string
- setConstraintTolerance(self, tol)¶
Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
- setGlobalVariable(self, index, value)¶
Set the value of a global variable.
- Parameters
index (int) – the index of the variable to set
value (double) – the new value of the variable
- setGlobalVariableByName(self, name, value)¶
Set the value of a global variable, specified by name.
- Parameters
name (string) – the name of the variable to set
value (double) – the new value of the variable
- setIntegrationForceGroups(groups)¶
Set which force groups to use for integration. By default, all force groups are included.
- Parameters
groups (set or int) – a set of indices for which force groups to include when integrating the equations of motion. Alternatively, the groups can be passed as a single unsigned integer interpreted as a bitmask, in which case group i will be included if (groups&(1<<i)) != 0.
- setKineticEnergyExpression(self, expression)¶
Set the expression to use for computing the kinetic energy. The expression is evaluated for every degree of freedom. Those values are then added together, and the sum is reported as the current kinetic energy.
- setPerDofVariable(self, index, values)¶
Set the value of a per-DOF variable.
- Parameters
index (int) – the index of the variable to set
values (vector< Vec3 >) – the new values of the variable for all degrees of freedom
- setPerDofVariableByName(self, name, values)¶
Set the value of a per-DOF variable, specified by name.
- Parameters
name (string) – the name of the variable to set
values (vector< Vec3 >) – the new values of the variable for all degrees of freedom
- setRandomNumberSeed(self, seed)¶
Set the random number seed. The precise meaning of this parameter is undefined, and is left up to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations are run with different random number seeds, the sequence of random numbers will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.
If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context is created from this Force. This is done to ensure that each Context receives unique random seeds without you needing to set them explicitly.
- setStepSize(self, size)¶
Set the size of each time step, in picoseconds. If this integrator uses variable time steps, the effect of calling this method is undefined, and it may simply be ignored.
- Parameters
size (double) – the step size, measured in ps
- step(self, steps)¶
Advance a simulation through time by taking a series of time steps.
- Parameters
steps (int) – the number of time steps to take
- property thisown¶
The membership flag
