CustomCVForce

class simtk.openmm.openmm.CustomCVForce(*args)

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 CustomCVForce 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, 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__(self, energy) → CustomCVForce

__init__(self, other) -> CustomCVForce

Create a CustomCVForce.

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

Methods

__init__((self, energy) -> CustomCVForce) __init__(self, other) -> CustomCVForce
addCollectiveVariable((self, name, ...) Add a collective variable that the force may depend on.
addEnergyParameterDerivative(self, name) Request that this Force compute the derivative of its energy with respect to a global parameter.
addGlobalParameter((self, name, ...) Add a new global parameter that the interaction may depend on.
addTabulatedFunction((self, name, ...) Add a tabulated function that may appear in the energy expression.
getCollectiveVariable((self, index) -> Force) getCollectiveVariable(self, index) -> Force
getCollectiveVariableName((self, ...) Get the name of a collective variable.
getCollectiveVariableValues(self, context) Get the current values of the collective variables in a Context.
getEnergyFunction((self) -> std::string const &) Get the algebraic expression that gives the energy of the system
getEnergyParameterDerivativeName((self, ...) Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getGlobalParameterDefaultValue((self, ...) Get the default value of a global parameter.
getGlobalParameterName((self, ...) Get the name of a global parameter.
getInnerContext((self, context) -> Context) Get the inner Context used for evaluating collective variables.
getNumCollectiveVariables((self) -> int) Get the number of collective variables that the interaction depends on.
getNumEnergyParameterDerivatives((self) -> int) Get the number of global parameters with respect to which the derivative of the energy should be computed.
getNumGlobalParameters((self) -> int) Get the number of global parameters that the interaction depends on.
getNumTabulatedFunctions((self) -> int) Get the number of tabulated functions that have been defined.
getTabulatedFunction((self, ...) getTabulatedFunction(self, index) -> TabulatedFunction
getTabulatedFunctionName((self, ...) Get the name of a tabulated function that may appear in the energy expression.
setEnergyFunction(self, energy) Set the algebraic expression that gives the energy of the system
setForceGroup(self, group) Set the force group this Force belongs to.
setGlobalParameterDefaultValue(self, index, ...) Set the default value of a global parameter.
setGlobalParameterName(self, index, name) Set the name of a global parameter.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
getNumCollectiveVariables(self) → int

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

getNumGlobalParameters(self) → int

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

getNumEnergyParameterDerivatives(self) → int

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

getNumTabulatedFunctions(self) → int

Get the number of tabulated functions that have been defined.

getEnergyFunction(self) → std::string const &

Get the algebraic expression that gives the energy of the system

setEnergyFunction(self, energy)

Set the algebraic expression that gives the energy of the system

addCollectiveVariable(self, name, variable) → int

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 CustomCVForce takes over ownership of it, and deletes the Force when the CustomCVForce itself is deleted.

Parameters:
  • name (string) – 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:

the index within the Force of the variable that was added

Return type:

int

getCollectiveVariableName(self, index) → std::string const &

Get the name of a collective variable.

Parameters:index (int) – the index of the collective variable for which to get the name
Returns:the variable name
Return type:string
getCollectiveVariable(self, index) → Force

getCollectiveVariable(self, index) -> Force

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:the Force object
Return type:Force
addGlobalParameter(self, name, defaultValue) → int

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 (string) – the name of the parameter
  • defaultValue (double) – the default value of the parameter
Returns:

the index of the parameter that was added

Return type:

int

getGlobalParameterName(self, index) → std::string const &

Get the name of a global parameter.

Parameters:index (int) – the index of the parameter for which to get the name
Returns:the parameter name
Return type:string
setGlobalParameterName(self, index, name)

Set the name of a global parameter.

Parameters:
  • index (int) – the index of the parameter for which to set the name
  • name (string) – the name of the parameter
getGlobalParameterDefaultValue(self, index) → double

Get the default value of a global parameter.

Parameters:index (int) – the index of the parameter for which to get the default value
Returns:the parameter default value
Return type:double
setGlobalParameterDefaultValue(self, 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
  • defaultValue (double) – the default value of the parameter
addEnergyParameterDerivative(self, 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 (string) – the name of the parameter
getEnergyParameterDerivativeName(self, index) → std::string const &

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:the parameter name
Return type:string
addTabulatedFunction(self, name, function) → int

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

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 Force takes over ownership of it, and deletes it when the Force itself is deleted.
Returns:

the index of the function that was added

Return type:

int

getTabulatedFunction(self, index) → TabulatedFunction

getTabulatedFunction(self, index) -> TabulatedFunction

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:the TabulatedFunction object defining the function
Return type:TabulatedFunction
getTabulatedFunctionName(self, index) → std::string const &

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:the name of the function as it appears in expressions
Return type:string
getCollectiveVariableValues(self, context)

Get the current values of the collective variables in a Context.

Parameters:context (Context) – the Context for which to get the values
Returns:values – the values of the collective variables are computed and stored into this
Return type:vector< double >
getInnerContext(self, context) → Context

Get the inner Context used for evaluating collective variables.

When you create a Context for a System that contains a CustomCVForce, 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 containing the CustomCVForce
Returns:the inner Context used to evaluate the collective variables
Return type:Context
usesPeriodicBoundaryConditions(self) → bool

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

Returns:true if force uses PBC and false otherwise
Return type:bool
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

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).