openmmtools.integrators.GradientDescentMinimizationIntegrator¶

class
openmmtools.integrators.
GradientDescentMinimizationIntegrator
(initial_step_size=Quantity(value=0.01, unit=angstrom))[source]¶ Simple gradient descent minimizer implemented as an integrator.
Examples
Create a gradient descent minimization integrator.
>>> integrator = GradientDescentMinimizationIntegrator()
Methods
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 perDOF 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 perDOF 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. 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. 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. getKineticEnergyExpression
(self)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 perDOF variables that have been defined. getNumTabulatedFunctions
(self)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 perDOF variable, specified by name. getPerDofVariableName
(self, index)Get the name of a perDOF variable. getRandomNumberSeed
(self)Get the random number seed. getStepSize
(self)Get the size of each time step, in picoseconds. getTabulatedFunction
(self, index)getTabulatedFunction(self, index) > TabulatedFunction getTabulatedFunctionName
(self, index)Get the name of a tabulated function that may appear in expressions. 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. setGlobalVariableByName
(self, name, value)Set the value of a global variable, specified by name. setKineticEnergyExpression
(self, expression)Set the expression to use for computing the kinetic energy. setPerDofVariable
(self, index, values)Set the value of a perDOF variable. setPerDofVariableByName
(self, name, values)Set the value of a perDOF 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. 
__init__
(initial_step_size=Quantity(value=0.01, unit=angstrom))[source]¶ Construct a simple gradient descent minimization integrator.
Parameters:  initial_step_size : np.unit.Quantity compatible with nanometers, default: 0.01*unit.angstroms
The norm of the initial step size guess.
Notes
An adaptive step size is used.
Methods
__init__
([initial_step_size, unit])Construct a simple gradient descent minimization integrator. 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 perDOF 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 perDOF 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. 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. 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. getKineticEnergyExpression
(self)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 perDOF variables that have been defined. getNumTabulatedFunctions
(self)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 perDOF variable, specified by name. getPerDofVariableName
(self, index)Get the name of a perDOF variable. getRandomNumberSeed
(self)Get the random number seed. getStepSize
(self)Get the size of each time step, in picoseconds. getTabulatedFunction
(self, index)getTabulatedFunction(self, index) > TabulatedFunction getTabulatedFunctionName
(self, index)Get the name of a tabulated function that may appear in expressions. 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. setGlobalVariableByName
(self, name, value)Set the value of a global variable, specified by name. setKineticEnergyExpression
(self, expression)Set the expression to use for computing the kinetic energy. setPerDofVariable
(self, index, values)Set the value of a perDOF variable. setPerDofVariableByName
(self, name, values)Set the value of a perDOF 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
BlockEnd
ComputeGlobal
ComputePerDof
ComputeSum
ConstrainPositions
ConstrainVelocities
IfBlockStart
UpdateContextState
WhileBlockStart

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:  int
the index of the step that was added

addComputePerDof
(self, variable, expression) → int¶ Add a step to the integration algorithm that computes a perDOF value.
Parameters:  variable : string
the perDOF variable to store the computed value into
 expression : string
a mathematical expression involving both global and perDOF variables. In each integration step, its value is computed for every degree of freedom and stored into the specified variable.
Returns:  int
the index of the step that was added

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 perDOF 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:  int
the index of the step that was added

addConstrainPositions
(self) → int¶ Add a step to the integration algorithm that updates particle positions so all constraints are satisfied.
Returns:  int
the index of the step that was added

addConstrainVelocities
(self) → int¶ Add a step to the integration algorithm that updates particle velocities so the net velocity along all constraints is 0.
Returns:  int
the index of the step that was added

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:  int
the index of the variable that was added

addPerDofVariable
(self, name, initialValue) → int¶ Define a new perDOF 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:  int
the index of the variable that was added

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:  int
the index of the function that was added

addUpdateContextState
(self) → int¶ Add a step to the integration algorithm that allows Forces to update the context state.
Returns:  int
the index of the step that was added

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:  int
the index of the step that was added

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:  int
the index of the step that was added

endBlock
(self) → int¶ Add a step which marks the end of the most recently begun “if” or “while” block.
Returns:  int
the index of the step that was added

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:  double
the current value of the variable

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:  double
the current value of the parameter

getGlobalVariableName
(self, index) → std::string const &¶ Get the name of a global variable.
Parameters:  index : int
the index of the variable to get
Returns:  string
the name of the variable

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 perDOF 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 perDOF variable, specified by name.
Parameters:  name : string
the name of the variable to get
Returns:  values : vector< Vec3 >
the values of the variable for all degrees of freedom are stored into this

getPerDofVariableName
(self, index) → std::string const &¶ Get the name of a perDOF variable.
Parameters:  index : int
the index of the variable to get
Returns:  string
the name of the variable

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:  double
the step size, measured in ps

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:  TabulatedFunction
the TabulatedFunction object defining the function

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:  string
the name of the function as it appears in expressions

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

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 perDOF 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 perDOF 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 nondeterministic 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
