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OpenMM
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OpenMM
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This class implements complex, multiple stage nonbonded interactions between particles. More...
Inheritance diagram for CustomGBForce:Public Member Functions | |
| def | getNumParticles |
| getNumParticles(CustomGBForce self) -> int | |
| def | getNumExclusions |
| getNumExclusions(CustomGBForce self) -> int | |
| def | getNumPerParticleParameters |
| getNumPerParticleParameters(CustomGBForce self) -> int | |
| def | getNumGlobalParameters |
| getNumGlobalParameters(CustomGBForce self) -> int | |
| def | getNumFunctions |
| getNumFunctions(CustomGBForce self) -> int | |
| def | getNumComputedValues |
| getNumComputedValues(CustomGBForce self) -> int | |
| def | getNumEnergyTerms |
| getNumEnergyTerms(CustomGBForce self) -> int | |
| def | getNonbondedMethod |
| getNonbondedMethod(CustomGBForce self) -> OpenMM::CustomGBForce::NonbondedMethod | |
| def | setNonbondedMethod |
| setNonbondedMethod(CustomGBForce self, OpenMM::CustomGBForce::NonbondedMethod method) | |
| def | getCutoffDistance |
| getCutoffDistance(CustomGBForce self) -> double | |
| def | setCutoffDistance |
| setCutoffDistance(CustomGBForce self, double distance) | |
| def | addPerParticleParameter |
| addPerParticleParameter(CustomGBForce self, std::string const & name) -> int | |
| def | getPerParticleParameterName |
| getPerParticleParameterName(CustomGBForce self, int index) -> std::string const & | |
| def | setPerParticleParameterName |
| setPerParticleParameterName(CustomGBForce self, int index, std::string const & name) | |
| def | addGlobalParameter |
| addGlobalParameter(CustomGBForce self, std::string const & name, double defaultValue) -> int | |
| def | getGlobalParameterName |
| getGlobalParameterName(CustomGBForce self, int index) -> std::string const & | |
| def | setGlobalParameterName |
| setGlobalParameterName(CustomGBForce self, int index, std::string const & name) | |
| def | getGlobalParameterDefaultValue |
| getGlobalParameterDefaultValue(CustomGBForce self, int index) -> double | |
| def | setGlobalParameterDefaultValue |
| setGlobalParameterDefaultValue(CustomGBForce self, int index, double defaultValue) | |
| def | addParticle |
| addParticle(CustomGBForce self, vectord parameters) -> int | |
| def | getParticleParameters |
| getParticleParameters(CustomGBForce self, int index) | |
| def | setParticleParameters |
| setParticleParameters(CustomGBForce self, int index, vectord parameters) | |
| def | addComputedValue |
| addComputedValue(CustomGBForce self, std::string const & name, std::string const & expression, OpenMM::CustomGBForce::ComputationType type) -> int | |
| def | getComputedValueParameters |
| getComputedValueParameters(CustomGBForce self, int index) | |
| def | setComputedValueParameters |
| setComputedValueParameters(CustomGBForce self, int index, std::string const & name, std::string const & expression, OpenMM::CustomGBForce::ComputationType type) | |
| def | addEnergyTerm |
| addEnergyTerm(CustomGBForce self, std::string const & expression, OpenMM::CustomGBForce::ComputationType type) -> int | |
| def | getEnergyTermParameters |
| getEnergyTermParameters(CustomGBForce self, int index) | |
| def | setEnergyTermParameters |
| setEnergyTermParameters(CustomGBForce self, int index, std::string const & expression, OpenMM::CustomGBForce::ComputationType type) | |
| def | addExclusion |
| addExclusion(CustomGBForce self, int particle1, int particle2) -> int | |
| def | getExclusionParticles |
| getExclusionParticles(CustomGBForce self, int index) | |
| def | setExclusionParticles |
| setExclusionParticles(CustomGBForce self, int index, int particle1, int particle2) | |
| def | addFunction |
| addFunction(CustomGBForce self, std::string const & name, vectord values, double min, double max) -> int | |
| def | getFunctionParameters |
| getFunctionParameters(CustomGBForce self, int index) | |
| def | setFunctionParameters |
| setFunctionParameters(CustomGBForce self, int index, std::string const & name, vectord values, double min, double max) | |
| def | updateParametersInContext |
| updateParametersInContext(CustomGBForce self, Context context) | |
| def | __init__ |
| init(OpenMM::CustomGBForce self) -> CustomGBForce init(OpenMM::CustomGBForce self, CustomGBForce other) -> CustomGBForce | |
| def | __del__ |
| del(OpenMM::CustomGBForce self) | |
| Public Member Functions inherited from Force | |
| def | __init__ |
| def | __del__ |
| del(OpenMM::Force self) | |
| def | getForceGroup |
| getForceGroup(Force self) -> int | |
| def | setForceGroup |
| setForceGroup(Force self, int group) | |
| def | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
Static Public Attributes | |
| NoCutoff _openmm.CustomGBForce_NoCutoff | |
| CutoffNonPeriodic _openmm.CustomGBForce_CutoffNonPeriodic | |
| CutoffPeriodic _openmm.CustomGBForce_CutoffPeriodic | |
| SingleParticle _openmm.CustomGBForce_SingleParticle | |
| ParticlePair _openmm.CustomGBForce_ParticlePair | |
| ParticlePairNoExclusions _openmm.CustomGBForce_ParticlePairNoExclusions | |
This class implements complex, multiple stage nonbonded interactions between particles.
It is designed primarily for implementing Generalized Born implicit solvation models, although it is not strictly limited to that purpose. The interaction is specified as a series of computations, each defined by an arbitrary algebraic expression. It also allows tabulated functions to be defined and used with the computations. It optionally supports periodic boundary conditions and cutoffs for long range interactions.
The computation consists of calculating some number of per-particle computed values, followed by one or more energy terms. A computed value is a scalar value that is computed for each particle in the system. It may depend on an arbitrary set of global and per-particle parameters, and well as on other computed values that have been calculated before it. Once all computed values have been calculated, the energy terms and their derivatives are evaluated to determine the system energy and particle forces. The energy terms may depend on global parameters, per-particle parameters, and per-particle computed values.
When specifying a computed value or energy term, you provide an algebraic expression to evaluate and a computation type describing how the expression is to be evaluated. There are two main types of computations:
Single Particle: The expression is evaluated once for each particle in the System. In the case of a computed value, this means the value for a particle depends only on other properties of that particle (its position, parameters, and other computed values). In the case of an energy term, it means each particle makes an independent contribution to the System energy.
Particle Pairs: The expression is evaluated for every pair of particles in the system. In the case of a computed value, the value for a particular particle is calculated by pairing it with every other particle in the system, evaluating the expression for each pair, and summing them. For an energy term, each particle pair makes an independent contribution to the System energy. (Note that energy terms are assumed to be symmetric with respect to the two interacting particles, and therefore are evaluated only once per pair. In contrast, expressions for computed values need not be symmetric and therefore are calculated twice for each pair: once when calculating the value for the first particle, and again when calculating the value for the second particle.)
Be aware that, although this class is extremely general in the computations it can define, particular Platforms may only support more restricted types of computations. In particular, all currently existing Platforms require that the first computed value must be a particle pair computation, and all computed values after the first must be single particle computations. This is sufficient for most Generalized Born models, but might not permit some other types of calculations to be implemented.
This is a complicated class to use, and an example may help to clarify it. The following code implements the OBC variant of the GB/SA solvation model, using the ACE approximation to estimate surface area:
CustomGBForce* custom = new CustomGBForce();
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
"U=r+sr2;"
"C=2*(1/or1-1/L)*step(sr2-r-or1);"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B",
CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePair);
It begins by defining three per-particle parameters (charge, atomic radius, and scale factor) and two global parameters (the dielectric constants for the solute and solvent). It then defines a computed value "I" of type ParticlePair. The expression for evaluating it is a complicated function of the distance between each pair of particles (r), their atomic radii (radius1 and radius2), and their scale factors (scale1 and scale2). Very roughly speaking, it is a measure of the distance between each particle and other nearby particles.
Next a computation is defined for the Born Radius (B). It is computed independently for each particle, and is a function of that particle's atomic radius and the intermediate value I defined above.
Finally, two energy terms are defined. The first one is computed for each particle and represents the surface area term, as well as the self interaction part of the polarization energy. The second term is calculated for each pair of particles, and represents the screening of electrostatic interactions by the solvent.
After defining the force as shown above, you should then call addParticle() once for each particle in the System to set the values of its per-particle parameters (q, radius, and scale). The number of particles for which you set parameters must be exactly equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. 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().
CustomGBForce also lets you specify "exclusions", particular pairs of particles whose interactions should be omitted from calculations. This is most often used for particles that are bonded to each other. Even if you specify exclusions, however, you can use the computation type ParticlePairNoExclusions to indicate that exclusions should not be applied to a particular piece of the computation.
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, step, delta. 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. In expressions for particle pair calculations, the names of per-particle parameters and computed values have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles. As seen in the above example, an expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
In addition, you can call addFunction() to define a new function based on tabulated values. You specify a vector of values, and a natural spline is created from them. That function can then appear in expressions.
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::CustomGBForce self) -> CustomGBForce init(OpenMM::CustomGBForce self, CustomGBForce other) -> CustomGBForce
Create a CustomGBForce.
| def __del__ | ( | self | ) |
del(OpenMM::CustomGBForce self)
| def addComputedValue | ( | self, | |
| args | |||
| ) |
addComputedValue(CustomGBForce self, std::string const & name, std::string const & expression, OpenMM::CustomGBForce::ComputationType type) -> int
Add a computed value to calculate for each particle.
| name | the name of the value |
| expression | an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with. |
| type | the method to use for computing this value |
| def addEnergyTerm | ( | self, | |
| args | |||
| ) |
addEnergyTerm(CustomGBForce self, std::string const & expression, OpenMM::CustomGBForce::ComputationType type) -> int
Add a term to the energy computation.
| expression | an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair. |
| type | the method to use for computing this value |
| def addExclusion | ( | self, | |
| args | |||
| ) |
addExclusion(CustomGBForce self, int particle1, int particle2) -> int
Add a particle pair to the list of interactions that should be excluded.
| particle1 | the index of the first particle in the pair |
| particle2 | the index of the second particle in the pair |
| def addFunction | ( | self, | |
| args | |||
| ) |
addFunction(CustomGBForce self, std::string const & name, vectord values, double min, double max) -> int
Add a tabulated function that may appear in the energy expression.
| name | the name of the function as it appears in expressions |
| values | the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max. |
| min | the value of the independent variable corresponding to the first element of values |
| max | the value of the independent variable corresponding to the last element of values |
| def addGlobalParameter | ( | self, | |
| args | |||
| ) |
addGlobalParameter(CustomGBForce self, std::string const & name, double defaultValue) -> int
Add a new global parameter that the interaction may depend on.
| name | the name of the parameter |
| defaultValue | the default value of the parameter |
| def addParticle | ( | self, | |
| args | |||
| ) |
addParticle(CustomGBForce self, vectord parameters) -> int
Add the nonbonded force parameters for a particle. This should be called once for each particle in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
| parameters | the list of parameters for the new particle |
| def addPerParticleParameter | ( | self, | |
| args | |||
| ) |
addPerParticleParameter(CustomGBForce self, std::string const & name) -> int
Add a new per-particle parameter that the interaction may depend on.
| name | the name of the parameter |
| def getComputedValueParameters | ( | self, | |
| args | |||
| ) |
getComputedValueParameters(CustomGBForce self, int index)
Get the properties of a computed value.
| index | the index of the computed value for which to get parameters |
| name | the name of the value |
| expression | an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with. |
| type | the method to use for computing this value |
| def getCutoffDistance | ( | self | ) |
getCutoffDistance(CustomGBForce self) -> double
Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
| def getEnergyTermParameters | ( | self, | |
| args | |||
| ) |
getEnergyTermParameters(CustomGBForce self, int index)
Get the properties of a term to the energy computation.
| index | the index of the term for which to get parameters |
| expression | an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair. |
| type | the method to use for computing this value |
| def getExclusionParticles | ( | self, | |
| args | |||
| ) |
getExclusionParticles(CustomGBForce self, int index)
Get the particles in a pair whose interaction should be excluded.
| index | the index of the exclusion for which to get particle indices |
| particle1 | the index of the first particle in the pair |
| particle2 | the index of the second particle in the pair |
| def getFunctionParameters | ( | self, | |
| args | |||
| ) |
getFunctionParameters(CustomGBForce self, int index)
Get the parameters for a tabulated function that may appear in the energy expression.
| index | the index of the function for which to get parameters |
| name | the name of the function as it appears in expressions |
| values | the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max. |
| min | the value of the independent variable corresponding to the first element of values |
| max | the value of the independent variable corresponding to the last element of values |
| def getGlobalParameterDefaultValue | ( | self, | |
| args | |||
| ) |
getGlobalParameterDefaultValue(CustomGBForce self, int index) -> double
Get the default value of a global parameter.
| index | the index of the parameter for which to get the default value |
| def getGlobalParameterName | ( | self, | |
| args | |||
| ) |
getGlobalParameterName(CustomGBForce self, int index) -> std::string const &
Get the name of a global parameter.
| index | the index of the parameter for which to get the name |
| def getNonbondedMethod | ( | self | ) |
getNonbondedMethod(CustomGBForce self) -> OpenMM::CustomGBForce::NonbondedMethod
Get the method used for handling long range nonbonded interactions.
| def getNumComputedValues | ( | self | ) |
getNumComputedValues(CustomGBForce self) -> int
Get the number of per-particle computed values the interaction depends on.
| def getNumEnergyTerms | ( | self | ) |
getNumEnergyTerms(CustomGBForce self) -> int
Get the number of terms in the energy computation.
| def getNumExclusions | ( | self | ) |
getNumExclusions(CustomGBForce self) -> int
Get the number of particle pairs whose interactions should be excluded.
| def getNumFunctions | ( | self | ) |
getNumFunctions(CustomGBForce self) -> int
Get the number of tabulated functions that have been defined.
| def getNumGlobalParameters | ( | self | ) |
getNumGlobalParameters(CustomGBForce self) -> int
Get the number of global parameters that the interaction depends on.
| def getNumParticles | ( | self | ) |
getNumParticles(CustomGBForce self) -> int
Get the number of particles for which force field parameters have been defined.
| def getNumPerParticleParameters | ( | self | ) |
getNumPerParticleParameters(CustomGBForce self) -> int
Get the number of per-particle parameters that the interaction depends on.
| def getParticleParameters | ( | self, | |
| args | |||
| ) |
getParticleParameters(CustomGBForce self, int index)
Get the nonbonded force parameters for a particle.
| index | the index of the particle for which to get parameters |
| parameters | the list of parameters for the specified particle |
| def getPerParticleParameterName | ( | self, | |
| args | |||
| ) |
getPerParticleParameterName(CustomGBForce self, int index) -> std::string const &
Get the name of a per-particle parameter.
| index | the index of the parameter for which to get the name |
| def setComputedValueParameters | ( | self, | |
| args | |||
| ) |
setComputedValueParameters(CustomGBForce self, int index, std::string const & name, std::string const & expression, OpenMM::CustomGBForce::ComputationType type)
Set the properties of a computed value.
| index | the index of the computed value for which to set parameters |
| name | the name of the value |
| expression | an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with. |
| type | the method to use for computing this value |
| def setCutoffDistance | ( | self, | |
| args | |||
| ) |
setCutoffDistance(CustomGBForce self, double distance)
Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
| distance | the cutoff distance, measured in nm |
| def setEnergyTermParameters | ( | self, | |
| args | |||
| ) |
setEnergyTermParameters(CustomGBForce self, int index, std::string const & expression, OpenMM::CustomGBForce::ComputationType type)
Set the properties of a term to the energy computation.
| index | the index of the term for which to set parameters |
| expression | an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair. |
| type | the method to use for computing this value |
| def setExclusionParticles | ( | self, | |
| args | |||
| ) |
setExclusionParticles(CustomGBForce self, int index, int particle1, int particle2)
Set the particles in a pair whose interaction should be excluded.
| index | the index of the exclusion for which to set particle indices |
| particle1 | the index of the first particle in the pair |
| particle2 | the index of the second particle in the pair |
| def setFunctionParameters | ( | self, | |
| args | |||
| ) |
setFunctionParameters(CustomGBForce self, int index, std::string const & name, vectord values, double min, double max)
Set the parameters for a tabulated function that may appear in algebraic expressions.
| index | the index of the function for which to set parameters |
| name | the name of the function as it appears in expressions |
| values | the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max. |
| min | the value of the independent variable corresponding to the first element of values |
| max | the value of the independent variable corresponding to the last element of values |
| def setGlobalParameterDefaultValue | ( | self, | |
| args | |||
| ) |
setGlobalParameterDefaultValue(CustomGBForce self, int index, double defaultValue)
Set the default value of a global parameter.
| index | the index of the parameter for which to set the default value |
| name | the default value of the parameter |
| def setGlobalParameterName | ( | self, | |
| args | |||
| ) |
setGlobalParameterName(CustomGBForce self, int index, std::string const & name)
Set the name of a global parameter.
| index | the index of the parameter for which to set the name |
| name | the name of the parameter |
| def setNonbondedMethod | ( | self, | |
| args | |||
| ) |
setNonbondedMethod(CustomGBForce self, OpenMM::CustomGBForce::NonbondedMethod method)
Set the method used for handling long range nonbonded interactions.
| def setParticleParameters | ( | self, | |
| args | |||
| ) |
setParticleParameters(CustomGBForce self, int index, vectord parameters)
Set the nonbonded force parameters for a particle.
| index | the index of the particle for which to set parameters |
| parameters | the list of parameters for the specified particle |
| def setPerParticleParameterName | ( | self, | |
| args | |||
| ) |
setPerParticleParameterName(CustomGBForce self, int index, std::string const & name)
Set the name of a per-particle parameter.
| index | the index of the parameter for which to set the name |
| name | the name of the parameter |
| def updateParametersInContext | ( | self, | |
| args | |||
| ) |
updateParametersInContext(CustomGBForce self, Context 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 updateParametersInState() 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.
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1.8.2