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OpenMM
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OpenMM
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This class implements an "external" force on particles. More...
Inheritance diagram for CustomExternalForce:Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | getNumPerParticleParameters |
| getNumPerParticleParameters(self) -> int | |
| def | getNumGlobalParameters |
| getNumGlobalParameters(self) -> int | |
| def | getEnergyFunction |
| getEnergyFunction(self) -> std::string const & | |
| def | setEnergyFunction |
| Set the algebraic expression that gives the potential energy of each particle. | |
| def | addPerParticleParameter |
| addPerParticleParameter(self, name) -> int | |
| def | getPerParticleParameterName |
| getPerParticleParameterName(self, index) -> std::string const & | |
| def | setPerParticleParameterName |
| Set the name of a per-particle parameter. | |
| def | addGlobalParameter |
| addGlobalParameter(self, name, defaultValue) -> int | |
| def | getGlobalParameterName |
| getGlobalParameterName(self, index) -> std::string const & | |
| def | setGlobalParameterName |
| Set the name of a global parameter. | |
| def | getGlobalParameterDefaultValue |
| getGlobalParameterDefaultValue(self, index) -> double | |
| def | setGlobalParameterDefaultValue |
| Set the default value of a global parameter. | |
| def | addParticle |
| addParticle(self, particle, parameters) -> int addParticle(self, particle) -> int | |
| def | getParticleParameters |
| Get the force field parameters for a force field term. | |
| def | setParticleParameters |
| Set the force field parameters for a force field term. | |
| def | updateParametersInContext |
| Update the per-particle parameters in a Context to match those stored in this Force object. | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(self) -> bool | |
| def | __init__ |
| __init__(self, energy) -> CustomExternalForce __init__(self, other) -> CustomExternalForce | |
Public Attributes | |
| this | |
This class implements an "external" force on particles.
The force may be applied to any subset of the particles in the System. The force on each particle is specified by an arbitrary algebraic expression, which may depend on the current position of the particle as well as on arbitrary global and per-particle parameters.
To use this class, create a CustomExternalForce object, passing an algebraic expression to the constructor that defines the potential energy of each affected particle. The expression may depend on the particle's x, y, and z coordinates, as well as on any parameters you choose. Then call addPerParticleParameter() to define per-particle parameters, and addGlobalParameter() to define global parameters. The values of per-particle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter(). Finally, call addParticle() once for each particle that should be affected by the force. After a particle has been added, you can modify its parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
As an example, the following code creates a CustomExternalForce that attracts each particle to a target position (x0, y0, z0) via a harmonic potential:
CustomExternalForce* force = new CustomExternalForce("k*((x-x0)^2+(y-y0)^2+(z-z0)^2)");
This force depends on four parameters: the spring constant k and equilibrium coordinates x0, y0, and z0. The following code defines these parameters:
force->addGlobalParameter("k", 100.0);
force->addPerParticleParameter("x0");
force->addPerParticleParameter("y0");
force->addPerParticleParameter("z0");
Special care is needed in systems that use periodic boundary conditions. In that case, each particle really represents an infinite set of particles repeating through space. The variables x, y, and z contain the coordinates of one of those periodic copies, but there is no guarantee about which. It might even change from one time step to the next. You can handle this situation by using the function periodicdistance(x1, y1, z1, x2, y2, z2), which returns the minimum distance between periodic copies of the points (x1, y1, z1) and (x2, y2, z2). For example, the force given above would be rewritten as
CustomExternalForce* force = new CustomExternalForce("k*periodicdistance(x, y, z, x0, y0, z0)^2");
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.
| def __init__ | ( | self, | |
| args | |||
| ) |
__init__(self, energy) -> CustomExternalForce __init__(self, other) -> CustomExternalForce
Create a CustomExternalForce.
| energy | (string) an algebraic expression giving the potential energy of each particle as a function of its x, y, and z coordinates |
| def addGlobalParameter | ( | self, | |
| name, | |||
| defaultValue | |||
| ) |
addGlobalParameter(self, name, defaultValue) -> int
Add a new global parameter that the force may depend on.
| name | (string) the name of the parameter |
| defaultValue | (double) the default value of the parameter |
| def addParticle | ( | self, | |
| args | |||
| ) |
addParticle(self, particle, parameters) -> int addParticle(self, particle) -> int
Add a particle term to the force field.
| particle | (int) the index of the particle this term is applied to |
| parameters | (vector< double >) the list of parameters for the new force term |
| def addPerParticleParameter | ( | self, | |
| name | |||
| ) |
addPerParticleParameter(self, name) -> int
Add a new per-particle parameter that the force may depend on.
| name | (string) the name of the parameter |
| def getEnergyFunction | ( | self | ) |
getEnergyFunction(self) -> std::string const &
Get the algebraic expression that gives the potential energy of each particle
| def getGlobalParameterDefaultValue | ( | self, | |
| index | |||
| ) |
getGlobalParameterDefaultValue(self, index) -> double
Get the default value of a global parameter.
| index | (int) the index of the parameter for which to get the default value |
| def getGlobalParameterName | ( | self, | |
| index | |||
| ) |
getGlobalParameterName(self, index) -> std::string const &
Get the name of a global parameter.
| index | (int) the index of the parameter for which to get the name |
| def getNumGlobalParameters | ( | self | ) |
getNumGlobalParameters(self) -> int
Get the number of global parameters that the force depends on.
| def getNumParticles | ( | self | ) |
getNumParticles(self) -> int
Get the number of particles for which force field parameters have been defined.
| def getNumPerParticleParameters | ( | self | ) |
getNumPerParticleParameters(self) -> int
Get the number of per-particle parameters that the force depends on
| def getParticleParameters | ( | self, | |
| index | |||
| ) |
Get the force field parameters for a force field term.
| index | (int) the index of the particle term for which to get parameters |
| def getPerParticleParameterName | ( | self, | |
| index | |||
| ) |
getPerParticleParameterName(self, index) -> std::string const &
Get the name of a per-particle parameter.
| index | (int) the index of the parameter for which to get the name |
| def setEnergyFunction | ( | self, | |
| energy | |||
| ) |
Set the algebraic expression that gives the potential energy of each particle.
| def setGlobalParameterDefaultValue | ( | self, | |
| index, | |||
| defaultValue | |||
| ) |
Set the default value of a global parameter.
| index | (int) the index of the parameter for which to set the default value |
| defaultValue | (double) the default value of the parameter |
| def setGlobalParameterName | ( | self, | |
| index, | |||
| name | |||
| ) |
Set the name of a global parameter.
| index | (int) the index of the parameter for which to set the name |
| name | (string) the name of the parameter |
| def setParticleParameters | ( | self, | |
| args | |||
| ) |
Set the force field parameters for a force field term.
| index | (int) the index of the particle term for which to set parameters |
| particle | (int) the index of the particle this term is applied to |
| parameters | (vector< double >) the list of parameters for the force field term |
| def setPerParticleParameterName | ( | self, | |
| index, | |||
| name | |||
| ) |
Set the name of a per-particle parameter.
| index | (int) the index of the parameter for which to set the name |
| name | (string) the name of the parameter |
| def updateParametersInContext | ( | self, | |
| context | |||
| ) |
Update the per-particle 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 setParticleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.
This method has several limitations. The only information it updates is the values of per-particle parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
| def usesPeriodicBoundaryConditions | ( | self | ) |
usesPeriodicBoundaryConditions(self) -> bool
Returns whether or not this force makes use of periodic boundary conditions.
Reimplemented from Force.
1.7.6.1