ExtendedCustomCVForce

class ExtendedCustomCVForce(energy)

Bases: Force

This class supports energy functions that depend on collective variables. To use it, you define a set of collective variables (scalar valued functions that depend on the particle positions), and an algebraic expression for the energy as a function of the collective variables. The expression also may involve tabulated functions, and may depend on arbitrary global parameters.

Each collective variable is defined by a Force object. The Force’s potential energy is computed, and that becomes the value of the variable. This provides enormous flexibility in defining collective variables, especially by using custom forces. Anything that can be computed as a potential function can also be used as a collective variable.

To use this class, create a ExtendedCustomCVForce object, passing an algebraic expression to the constructor that defines the potential energy. Then call addCollectiveVariable() to define collective variables and addGlobalParameter() to define global parameters. The values of global parameters may be modified during a simulation by calling Context::setParameter().

This class also has the ability to compute derivatives of the potential energy with respect to global parameters. Call addEnergyParameterDerivative() to request that the derivative with respect to a particular parameter be computed. You can then query its value in a Context by calling getState() on it.

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. select(x,y,z) = z if x = 0, y otherwise.

In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by creating a TabulatedFunction object. That function can then appear in the expression.

__init__(energy)

Create a ExtendedCustomCVForce.

Parameters:

energy (str) – an algebraic expression giving the energy of the system as a function of the collective variables and global parameters

Methods

addCollectiveVariable(name, variable)	Add a collective variable that the force may depend on.
addEnergyParameterDerivative(name)	Request that this Force compute the derivative of its energy with respect to a global parameter.
addGlobalParameter(name, defaultValue)	Add a new global parameter that the interaction may depend on.
addTabulatedFunction(name, function)	Add a tabulated function that may appear in the energy expression.
getCollectiveVariable(*args)	Overload 1:
getCollectiveVariableName(index)	Get the name of a collective variable.
getCollectiveVariableValues(context)
getEnergyFunction()	Get the algebraic expression that gives the energy of the system
getEnergyParameterDerivativeName(index)	Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getForceGroup(self)	Get the force group this Force belongs to.
getGlobalParameterDefaultValue(index)	Get the default value of a global parameter.
getGlobalParameterName(index)	Get the name of a global parameter.
getInnerContext(context)	Get the inner Context used for evaluating collective variables.
getName(self)	Get the name of this Force.
getNumCollectiveVariables()	Get the number of collective variables that the interaction depends on.
getNumEnergyParameterDerivatives()	Get the number of global parameters with respect to which the derivative of the energy should be computed.
getNumGlobalParameters()	Get the number of global parameters that the interaction depends on.
getNumTabulatedFunctions()	Get the number of tabulated functions that have been defined.
getTabulatedFunction(*args)	Overload 1:
getTabulatedFunctionName(index)	Get the name of a tabulated function that may appear in the energy expression.
setEnergyFunction(energy)	Set the algebraic expression that gives the energy of the system
setForceGroup(self, group)	Set the force group this Force belongs to.
setGlobalParameterDefaultValue(index, ...)	Set the default value of a global parameter.
setGlobalParameterName(index, name)
setName(self, name)	Set the name of this Force.
updateParametersInContext(context)	Update the tabulated function parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions()	Returns whether or not this force makes use of periodic boundary conditions.

Attributes

thisown

The membership flag

addCollectiveVariable(name, variable)

Add a collective variable that the force may depend on. The collective variable is represented by a Force object, which should have been created on the heap with the “new” operator. The ExtendedCustomCVForce takes over ownership of it, and deletes the Force when the ExtendedCustomCVForce itself is deleted.

Parameters:

• name (str) – the name of the collective variable, as it will appear in the energy expression

• variable (Force) – the collective variable, represented by a Force object. The value of the variable is the energy computed by the Force.

Returns:

int – the index within the Force of the variable that was added

addEnergyParameterDerivative(name)

Request that this Force compute the derivative of its energy with respect to a global parameter. The parameter must have already been added with addGlobalParameter().

Parameters:

name (str) – the name of the parameter

addGlobalParameter(name, defaultValue)

Add a new global parameter that the interaction may depend on. The default value provided to this method is the initial value of the parameter in newly created Contexts. You can change the value at any time by calling setParameter() on the Context.

Parameters:

• name (str) – the name of the parameter

• default_value (float) – the default value of the parameter

Returns:

int – the index of the parameter that was added

addTabulatedFunction(name, function)

Add a tabulated function that may appear in the energy expression.

Parameters:

• name (str) – the name of the function

• function (TabulatedFunction) – a TabulatedFunction object defining the function

Returns:

int – the index of the function that was added

getCollectiveVariable(*args)

Overload 1:

Get a writable reference to the Force object that computes a collective variable.

Parameters:

index (int) – the index of the collective variable to get

Returns:

• Force – the Force object

• |

• *Overload 2 (***)

• Get a const reference to the Force object that computes a collective variable.

Parameters:

index (int) – the index of the collective variable to get

Returns:

const Force – the Force object

getCollectiveVariableName(index)

Get the name of a collective variable.

Parameters:

index (int) – the index of the collective variable for which to get the name

Returns:

str – the variable name

getEnergyFunction()

Get the algebraic expression that gives the energy of the system

getEnergyParameterDerivativeName(index)

Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.

Parameters:

index (int) – the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()

Returns:

str – the parameter name

getForceGroup(self) → int

Get the force group this Force belongs to.

getGlobalParameterDefaultValue(index)

Get the default value of a global parameter.

Parameters:

index (int) – the index of the parameter for which to get the default value

Returns:

float – the parameter default value

getGlobalParameterName(index)

Get the name of a global parameter.

Parameters:

index (int) – the index of the parameter for which to get the name

Returns:

str – the parameter name

getInnerContext(context)

Get the inner Context used for evaluating collective variables.

When you create a Context for a System that contains a ExtendedCustomCVForce, internally it creates a new System, adds the Forces that define the CVs to it, creates a new Context for that System, and uses it to evaluate the variables. In most cases you can ignore all of this. It is just an implementation detail. However, there are a few cases where you need to directly access that internal Context. For example, if you want to modify one of the Forces that defines a collective variable and call updateParametersInContext() on it, you need to pass that inner Context to it. This method returns a reference to it.

Parameters:

context (Context) – the Context

Returns:

Context – the inner Context used to evaluate the collective variables

getName(self) → std::string const &

Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.

getNumCollectiveVariables()

Get the number of collective variables that the interaction depends on.

getNumEnergyParameterDerivatives()

Get the number of global parameters with respect to which the derivative of the energy should be computed.

getNumGlobalParameters()

Get the number of global parameters that the interaction depends on.

getNumTabulatedFunctions()

Get the number of tabulated functions that have been defined.

getTabulatedFunction(*args)

Overload 1:

Get a const reference to a tabulated function that may appear in the energy expression.

Parameters:

index (int) – the index of the function to get

Returns:

• const TabulatedFunction – the TabulatedFunction object defining the function

• |

• *Overload 2 (***)

• Get a reference to a tabulated function that may appear in the energy expression.

Parameters:

index (int) – the index of the function to get

Returns:

TabulatedFunction – the TabulatedFunction object defining the function

getTabulatedFunctionName(index)

Get the name of a tabulated function that may appear in the energy expression.

Parameters:

index (int) – the index of the function to get

Returns:

str – the name of the function as it appears in expressions

setEnergyFunction(energy)

Set the algebraic expression that gives the energy of the system

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:

group (int) – the group index. Legal values are between 0 and 31 (inclusive).

setGlobalParameterDefaultValue(index, defaultValue)

Set the default value of a global parameter.

Parameters:

• index (int) – the index of the parameter for which to set the default value

• default_value (float) – the default value of the parameter

Returns:

float – the parameter default value

setName(self, name)

Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.

updateParametersInContext(context)

Update the tabulated function parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call getTabulatedFunction(index).setFunctionParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

This method is very limited. The only information it updates is the parameters of tabulated functions. All other aspects of the Force (the energy expression, the set of collective variables, etc.) are unaffected and can only be changed by reinitializing the Context.

usesPeriodicBoundaryConditions()

Returns whether or not this force makes use of periodic boundary conditions.

Returns:

bool – true if force uses PBC and false otherwise