Skip to content

GitLab

Commit e1a378b7 authored by peastman's avatar peastman
Browse files

Began implementing CustomManyParticleForce

parent d20e4edd
Hide whitespace changes
Inline Side-by-side
Showing with 1907 additions and 10 deletions
olla/include/openmm/kernels.h
View file @ e1a378b7
......@@ -44,6 +44,7 @@
#include "openmm/CustomHbondForce.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/CustomManyParticleForce.h"
#include "openmm/CustomTorsionForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
......@@ -826,6 +827,46 @@ public:
virtual void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) = 0;
};
/**
* This kernel is invoked by CustomManyParticleForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcCustomManyParticleForceKernel : public KernelImpl {
public:
enum NonbondedMethod {
NoCutoff = 0,
CutoffNonPeriodic = 1,
CutoffPeriodic = 2
};
static std::string Name() {
return "CalcCustomManyParticleForce";
}
CalcCustomManyParticleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomManyParticleForce this kernel will be used for
*/
virtual void initialize(const System& system, const CustomManyParticleForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomManyParticleForce to copy the parameters from
*/
virtual void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force) = 0;
};
/**
* This kernel is invoked by VerletIntegrator to take one time step.
*/
......
openmmapi/include/openmm/CustomManyParticleForce.h 0 → 100644
View file @ e1a378b7
#ifndef OPENMM_CUSTOMTHREEBODYFORCE_H_
#define OPENMM_CUSTOMTHREEBODYFORCE_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "Force.h"
#include "TabulatedFunction.h"
#include "internal/windowsExport.h"
#include <set>
#include <vector>
namespace OpenMM {
/**
* This class supports a wide variety of nonbonded N-particle interactions, where N is user specified. The
* interaction energy is determined by an arbitrary, user specified algebraic expression that is evaluated for
* every possible set of N particles in the system. It may depend on the positions of the individual particles,
* the distances between pairs of particles, the angles formed by sets of three particles, and the dihedral
* angles formed by sets of four particles.
*
* Be aware that the cost of evaluating an N-particle interaction increases very rapidly with N. Values larger
* than N=3 are rarely used.
*
* We refer to a set of particles for which the energy is being evaluated as p1, p2, p3, etc. The energy expression
* may depend on the following variables and functions:
*
* <ul>
* <li>x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the particle positions. For example, x1
* is the x coordinate of particle p1, and y3 is the y coordinate of particle p3.</li>
* <li>distance(p1, p2): the distance between particles p1 and p2 (where "p1" and "p2" may be replaced by the names
* of whichever particles you want to calculate the distance between).</li>
* <li>angle(p1, p2, p3): the angle formed by the three specified particles.</li>
* <li>dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles.</li>
* <li>arbitrary global and per-particle parameters that you define.</li>
* </ul>
*
* To use this class, create a CustomManyParticleForce object, passing an algebraic expression to the constructor
* that defines the interaction energy of each set of particles. 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().
*
* Next, call addParticle() once for each particle in the System to set the values of its per-particle parameters.
* 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().
*
* Multi-particle interactions can be very expensive to evaluate, so they are usually used with a cutoff distance. If two particles
* are further apart than the cutoff, <i>all</i> sets that include those two particles will be omitted.
*
* CustomManyParticleForce also lets you specify "exclusions", particular pairs of particles whose interactions should be
* omitted from force and energy calculations. This is most often used for particles that are bonded to each other.
* If you specify a pair of particles as an exclusion, <i>all</i> sets that include those two particles will be omitted.
*
* As an example, the following code creates a CustomManyParticleForce that implements an Axilrod-Teller potential. This
* is an interaction between three particles that depends on all three distances and angles formed by the particles.
*
* <tt>CustomManyParticleForce* force = new CustomManyParticleForce(3,
* "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
* "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
* "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
* </tt>
*
* This force depends on one parameter, C. The following code defines it as a global parameter:
*
* <tt><pre>
* force->addGlobalParameter("C", 1.0);
* </pre></tt>
*
* The expression <i>must</i> be symmetric with respect to the particles. It typically will only be evaluated once for
* each set of particles, and no guarantee is made about which particle will be identified as "particle 1". In the above
* example, the energy only depends on the products cos(theta1)*cos(theta2)*cos(theta3) and r12*r13*r23, both of which are
* unchanged if the labels p1, p2, and p3 are permuted. If that were not true, the results would be undefined, because
* permuting the labels would change the energy.
*
* In some cases this requirement is overly restrictive. When some particles are fundamentally different from others,
* the expression may be inherently non-symmetric. An example would be a water model that involves three particles,
* two of which <i>must</i> be hydrogen and one of which <i>must</i> be oxygen. Cases like this can be implemented
* using particle types.
*
* A particle type is an integer that you specify when you call addParticle(). (If you omit the argument, it defaults
* to 0.) For the water model, you could specify 0 for all oxygen atoms and 1 for all hydrogen atoms. You can then
* call setTypeFilter() to specify the list of allowed types for each of the N particles involved in an interaction:
*
* <tt><pre>
* set&lt;int&gt; oxygenTypes, hydrogenTypes;
* oxygenTypes.insert(0);
* hydrogenTypes.insert(1);
* force->setTypeFilter(0, oxygenTypes);
* force->setTypeFilter(1, hydrogenTypes);
* force->setTypeFilter(2, hydrogenTypes);
* </pre></tt>
*
* This specifies that of the three particles in an interaction, p1 must be oxygen while p2 and p3 must be hydrogen.
* The energy expression will only be evaluated for triplets of particles that satisfy those requirements. It will
* still only be evaluated once for each triplet, so it must still be symmetric with respect to p2 and p3.
*
* 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.
* The names of per-particle parameters have the suffix "1", "2", etc. appended to them to indicate the values for the multiple interacting particles.
* For example, if you define a per-particle parameter called "charge", then the variable "charge2" is the charge of particle p2.
* As seen above, the expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
*
* 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.
*/
class OPENMM_EXPORT CustomManyParticleForce : public Force {
public:
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
/**
* No cutoff is applied to nonbonded interactions. The full set of interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/
NoCutoff = 0,
/**
* Interactions are ignored if any two particles are further apart than the cutoff distance.
*/
CutoffNonPeriodic = 1,
/**
* Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
* each other particle. Interactions are ignored if any two particles are further apart than the cutoff distance.
*/
CutoffPeriodic = 2,
};
/**
* Create a CustomManyParticleForce.
*
* @param particlesPerSet the number of particles in each set for which the energy is evaluated
* @param energy an algebraic expression giving the interaction energy of each triplet as a function
* of particle positions, inter-particle distances, angles, and any global and per-particle parameters
*/
explicit CustomManyParticleForce(int particlesPerSet, const std::string& energy);
~CustomManyParticleForce();
/**
* Get the number of particles in each set for which the energy is evaluated
*/
int getNumParticlesPerSet() const {
return particlesPerSet;
}
/**
* Get the number of particles for which force field parameters have been defined.
*/
int getNumParticles() const {
return particles.size();
}
/**
* Get the number of particle pairs whose interactions should be excluded.
*/
int getNumExclusions() const {
return exclusions.size();
}
/**
* Get the number of per-particle parameters that the interaction depends on.
*/
int getNumPerParticleParameters() const {
return particleParameters.size();
}
/**
* Get the number of global parameters that the interaction depends on.
*/
int getNumGlobalParameters() const {
return globalParameters.size();
}
/**
* Get the number of tabulated functions that have been defined.
*/
int getNumTabulatedFunctions() const {
return functions.size();
}
/**
* Get the algebraic expression that gives the interaction energy of each bond
*/
const std::string& getEnergyFunction() const;
/**
* Set the algebraic expression that gives the interaction energy of each bond
*/
void setEnergyFunction(const std::string& energy);
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* Add a new per-particle parameter that the interaction may depend on.
*
* @param name the name of the parameter
* @return the index of the parameter that was added
*/
int addPerParticleParameter(const std::string& name);
/**
* Get the name of a per-particle parameter.
*
* @param index the index of the parameter for which to get the name
* @return the parameter name
*/
const std::string& getPerParticleParameterName(int index) const;
/**
* Set the name of a per-particle parameter.
*
* @param index the index of the parameter for which to set the name
* @param name the name of the parameter
*/
void setPerParticleParameterName(int index, const std::string& name);
/**
* Add a new global parameter that the interaction may depend on.
*
* @param name the name of the parameter
* @param defaultValue the default value of the parameter
* @return the index of the parameter that was added
*/
int addGlobalParameter(const std::string& name, double defaultValue);
/**
* Get the name of a global parameter.
*
* @param index the index of the parameter for which to get the name
* @return the parameter name
*/
const std::string& getGlobalParameterName(int index) const;
/**
* Set the name of a global parameter.
*
* @param index the index of the parameter for which to set the name
* @param name the name of the parameter
*/
void setGlobalParameterName(int index, const std::string& name);
/**
* Get the default value of a global parameter.
*
* @param index the index of the parameter for which to get the default value
* @return the parameter default value
*/
double getGlobalParameterDefaultValue(int index) const;
/**
* Set the default value of a global parameter.
*
* @param index the index of the parameter for which to set the default value
* @param name the default value of the parameter
*/
void setGlobalParameterDefaultValue(int index, double defaultValue);
/**
* 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.
*
* @param parameters the list of parameters for the new particle
* @param type the type of the new particle
* @return the index of the particle that was added
*/
int addParticle(const std::vector<double>& parameters, int type=0);
/**
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param parameters the list of parameters for the specified particle
* @param type the type of the specified particle
*/
void getParticleParameters(int index, std::vector<double>& parameters, int& type) const;
/**
* Set the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to set parameters
* @param parameters the list of parameters for the specified particle
* @param type the type of the specified particle
*/
void setParticleParameters(int index, const std::vector<double>& parameters, int type);
/**
* Add a particle pair to the list of interactions that should be excluded.
*
* In many cases, you can use createExclusionsFromBonds() rather than adding each exclusion explicitly.
*
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
* @return the index of the exclusion that was added
*/
int addExclusion(int particle1, int particle2);
/**
* Get the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to get particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
*/
void getExclusionParticles(int index, int& particle1, int& particle2) const;
/**
* Set the particles in a pair whose interaction should be excluded.
*
* @param index the index of the exclusion for which to set particle indices
* @param particle1 the index of the first particle in the pair
* @param particle2 the index of the second particle in the pair
*/
void setExclusionParticles(int index, int particle1, int particle2);
/**
* Identify exclusions based on the molecular topology. Particles which are separated by up to a specified number of
* bonds are added as exclusions.
*
* @param bonds the set of bonds based on which to construct exclusions. Each element specifies the indices of
* two particles that are bonded to each other.
* @param bondCutoff pairs of particles that are separated by this many bonds or fewer are added to the list of exclusions
*/
void createExclusionsFromBonds(const std::vector<std::pair<int, int> >& bonds, int bondCutoff);
/**
* Get the allowed particle types for one of the particles involved in the interaction.
* If this an empty set (the default), no filter is applied and all interactions are evaluated
* regardless of the type of the specified particle.
*
* @param index the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
* @param types the allowed types for the specified particle
*/
void getTypeFilter(int index, std::set<int>& types) const;
/**
* Set the allowed particle types for one of the particles involved in the interaction.
* If this an empty set (the default), no filter is applied and all interactions are evaluated
* regardless of the type of the specified particle.
*
* @param index the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
* @param types the allowed types for the specified particle
*/
void setTypeFilter(int index, const std::set<int>& types);
/**
* Add a tabulated function that may appear in the energy expression.
*
* @param name the name of the function as it appears in expressions
* @param function 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.
* @return the index of the function that was added
*/
int addTabulatedFunction(const std::string& name, TabulatedFunction* function);
/**
* Get a const reference to a tabulated function that may appear in the energy expression.
*
* @param index the index of the function to get
* @return the TabulatedFunction object defining the function
*/
const TabulatedFunction& getTabulatedFunction(int index) const;
/**
* Get a reference to a tabulated function that may appear in the energy expression.
*
* @param index the index of the function to get
* @return the TabulatedFunction object defining the function
*/
TabulatedFunction& getTabulatedFunction(int index);
/**
* Get the name of a tabulated function that may appear in the energy expression.
*
* @param index the index of the function to get
* @return the name of the function as it appears in expressions
*/
const std::string& getTabulatedFunctionName(int index) const;
/**
* 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 (the energy function, nonbonded method, cutoff distance, etc.) 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.
*/
void updateParametersInContext(Context& context);
protected:
ForceImpl* createImpl() const;
private:
class ParticleInfo;
class ParticleParameterInfo;
class GlobalParameterInfo;
class ExclusionInfo;
class FunctionInfo;
int particlesPerSet;
NonbondedMethod nonbondedMethod;
double cutoffDistance;
std::string energyExpression;
std::vector<ParticleParameterInfo> particleParameters;
std::vector<GlobalParameterInfo> globalParameters;
std::vector<ParticleInfo> particles;
std::vector<ExclusionInfo> exclusions;
std::vector<FunctionInfo> functions;
std::vector<std::set<int> > typeFilters;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class CustomManyParticleForce::ParticleInfo {
public:
std::vector<double> parameters;
int type;
ParticleInfo() {
}
ParticleInfo(const std::vector<double>& parameters, int type) : parameters(parameters), type(type) {
}
};
/**
* This is an internal class used to record information about a per-particle parameter.
* @private
*/
class CustomManyParticleForce::ParticleParameterInfo {
public:
std::string name;
ParticleParameterInfo() {
}
ParticleParameterInfo(const std::string& name) : name(name) {
}
};
/**
* This is an internal class used to record information about a global parameter.
* @private
*/
class CustomManyParticleForce::GlobalParameterInfo {
public:
std::string name;
double defaultValue;
GlobalParameterInfo() {
}
GlobalParameterInfo(const std::string& name, double defaultValue) : name(name), defaultValue(defaultValue) {
}
};
/**
* This is an internal class used to record information about an exclusion.
* @private
*/
class CustomManyParticleForce::ExclusionInfo {
public:
int particle1, particle2;
ExclusionInfo() {
particle1 = particle2 = -1;
}
ExclusionInfo(int particle1, int particle2) :
particle1(particle1), particle2(particle2) {
}
};
/**
* This is an internal class used to record information about a tabulated function.
* @private
*/
class CustomManyParticleForce::FunctionInfo {
public:
std::string name;
TabulatedFunction* function;
FunctionInfo() {
}
FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
}
};
} // namespace OpenMM
#endif /*OPENMM_CUSTOMTHREEBODYFORCE_H_*/
openmmapi/include/openmm/internal/CustomManyParticleForceImpl.h 0 → 100644
View file @ e1a378b7
#ifndef OPENMM_CUSTOMMANYPARTICLEFORCEIMPL_H_
#define OPENMM_CUSTOMMANYPARTICLEFORCEIMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ForceImpl.h"
#include "openmm/CustomManyParticleForce.h"
#include "openmm/Kernel.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionTreeNode.h"
#include "lepton/ParsedExpression.h"
#include <utility>
#include <map>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of CustomManyParticleForce.
*/
class OPENMM_EXPORT CustomManyParticleForceImpl : public ForceImpl {
public:
CustomManyParticleForceImpl(const CustomManyParticleForce& owner);
~CustomManyParticleForceImpl();
void initialize(ContextImpl& context);
const CustomManyParticleForce& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
std::map<std::string, double> getDefaultParameters();
std::vector<std::string> getKernelNames();
void updateParametersInContext(ContextImpl& context);
/**
* This is a utility routine that parses the energy expression, identifies the angles and dihedrals
* in it, and replaces them with variables.
*
* @param force the CustomManyParticleForce to process
* @param functions definitions of custom function that may appear in the expression
* @param distances on exit, this will contain an entry for each distance used in the expression. The key is the name
* of the corresponding variable, and the value is the list of particle indices.
* @param angles on exit, this will contain an entry for each angle used in the expression. The key is the name
* of the corresponding variable, and the value is the list of particle indices.
* @param dihedrals on exit, this will contain an entry for each dihedral used in the expression. The key is the name
* of the corresponding variable, and the value is the list of particle indices.
* @return a Parsed expression for the energy
*/
static Lepton::ParsedExpression prepareExpression(const CustomManyParticleForce& force, const std::map<std::string, Lepton::CustomFunction*>& functions, std::map<std::string, std::vector<int> >& distances,
std::map<std::string, std::vector<int> >& angles, std::map<std::string, std::vector<int> >& dihedrals);
private:
class FunctionPlaceholder;
static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
std::map<std::string, std::vector<int> >& dihedrals);
const CustomManyParticleForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_CUSTOMMANYPARTICLEFORCEIMPL_H_*/
openmmapi/src/CustomManyParticleForce.cpp 0 → 100644
View file @ e1a378b7
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/CustomManyParticleForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include <cmath>
#include <map>
#include <set>
#include <sstream>
#include <utility>
using namespace OpenMM;
using namespace std;
CustomManyParticleForce::CustomManyParticleForce(int particlesPerSet, const string& energy) :
particlesPerSet(particlesPerSet), energyExpression(energy), typeFilters(particlesPerSet) {
}
CustomManyParticleForce::~CustomManyParticleForce() {
for (int i = 0; i < (int) functions.size(); i++)
delete functions[i].function;
}
const string& CustomManyParticleForce::getEnergyFunction() const {
return energyExpression;
}
void CustomManyParticleForce::setEnergyFunction(const string& energy) {
energyExpression = energy;
}
CustomManyParticleForce::NonbondedMethod CustomManyParticleForce::getNonbondedMethod() const {
return nonbondedMethod;
}
void CustomManyParticleForce::setNonbondedMethod(NonbondedMethod method) {
nonbondedMethod = method;
}
double CustomManyParticleForce::getCutoffDistance() const {
return cutoffDistance;
}
void CustomManyParticleForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
int CustomManyParticleForce::addPerParticleParameter(const string& name) {
particleParameters.push_back(ParticleParameterInfo(name));
return particleParameters.size()-1;
}
const string& CustomManyParticleForce::getPerParticleParameterName(int index) const {
ASSERT_VALID_INDEX(index, particleParameters);
return particleParameters[index].name;
}
void CustomManyParticleForce::setPerParticleParameterName(int index, const string& name) {
ASSERT_VALID_INDEX(index, particleParameters);
particleParameters[index].name = name;
}
int CustomManyParticleForce::addGlobalParameter(const string& name, double defaultValue) {
globalParameters.push_back(GlobalParameterInfo(name, defaultValue));
return globalParameters.size()-1;
}
const string& CustomManyParticleForce::getGlobalParameterName(int index) const {
ASSERT_VALID_INDEX(index, globalParameters);
return globalParameters[index].name;
}
void CustomManyParticleForce::setGlobalParameterName(int index, const string& name) {
ASSERT_VALID_INDEX(index, globalParameters);
globalParameters[index].name = name;
}
double CustomManyParticleForce::getGlobalParameterDefaultValue(int index) const {
ASSERT_VALID_INDEX(index, globalParameters);
return globalParameters[index].defaultValue;
}
void CustomManyParticleForce::setGlobalParameterDefaultValue(int index, double defaultValue) {
ASSERT_VALID_INDEX(index, globalParameters);
globalParameters[index].defaultValue = defaultValue;
}
int CustomManyParticleForce::addParticle(const vector<double>& parameters, int type) {
particles.push_back(ParticleInfo(parameters, type));
return particles.size()-1;
}
void CustomManyParticleForce::getParticleParameters(int index, vector<double>& parameters, int& type) const {
ASSERT_VALID_INDEX(index, particles);
parameters = particles[index].parameters;
type = particles[index].type;
}
void CustomManyParticleForce::setParticleParameters(int index, const vector<double>& parameters, int type) {
ASSERT_VALID_INDEX(index, particles);
particles[index].parameters = parameters;
particles[index].type = type;
}
int CustomManyParticleForce::addExclusion(int particle1, int particle2) {
exclusions.push_back(ExclusionInfo(particle1, particle2));
return exclusions.size()-1;
}
void CustomManyParticleForce::getExclusionParticles(int index, int& particle1, int& particle2) const {
ASSERT_VALID_INDEX(index, exclusions);
particle1 = exclusions[index].particle1;
particle2 = exclusions[index].particle2;
}
void CustomManyParticleForce::setExclusionParticles(int index, int particle1, int particle2) {
ASSERT_VALID_INDEX(index, exclusions);
exclusions[index].particle1 = particle1;
exclusions[index].particle2 = particle2;
}
void CustomManyParticleForce::createExclusionsFromBonds(const vector<pair<int, int> >& bonds, int bondCutoff) {
if (bondCutoff < 1)
return;
vector<set<int> > exclusions(particles.size());
vector<set<int> > bonded12(exclusions.size());
for (int i = 0; i < (int) bonds.size(); ++i) {
int p1 = bonds[i].first;
int p2 = bonds[i].second;
exclusions[p1].insert(p2);
exclusions[p2].insert(p1);
bonded12[p1].insert(p2);
bonded12[p2].insert(p1);
}
for (int level = 0; level < bondCutoff-1; level++) {
vector<set<int> > currentExclusions = exclusions;
for (int i = 0; i < (int) particles.size(); i++) {
for (set<int>::const_iterator iter = currentExclusions[i].begin(); iter != currentExclusions[i].end(); ++iter)
exclusions[*iter].insert(bonded12[i].begin(), bonded12[i].end());
}
}
for (int i = 0; i < (int) exclusions.size(); ++i)
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
if (*iter < i)
addExclusion(*iter, i);
}
void CustomManyParticleForce::getTypeFilter(int index, set<int>& types) const {
if (index < 0 || index >= particlesPerSet)
throw OpenMMException("CustomManyParticleForce: index to getTypeFilter out of range");
types = typeFilters[index];
}
void CustomManyParticleForce::setTypeFilter(int index, const set<int>& types) {
if (index < 0 || index >= particlesPerSet)
throw OpenMMException("CustomManyParticleForce: index to setTypeFilter out of range");
typeFilters[index] = types;
}
int CustomManyParticleForce::addTabulatedFunction(const string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomManyParticleForce::getTabulatedFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomManyParticleForce::getTabulatedFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomManyParticleForce::getTabulatedFunctionName(int index) const {
ASSERT_VALID_INDEX(index, functions);
return functions[index].name;
}
ForceImpl* CustomManyParticleForce::createImpl() const {
return new CustomManyParticleForceImpl(*this);
}
void CustomManyParticleForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomManyParticleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
openmmapi/src/CustomManyParticleForceImpl.cpp 0 → 100644
View file @ e1a378b7
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "openmm/kernels.h"
#include "lepton/Operation.h"
#include "lepton/Parser.h"
#include <sstream>
using namespace OpenMM;
using Lepton::CustomFunction;
using Lepton::ExpressionTreeNode;
using Lepton::Operation;
using Lepton::ParsedExpression;
using std::map;
using std::pair;
using std::vector;
using std::set;
using std::string;
using std::stringstream;
/**
* This class serves as a placeholder for angles and dihedrals in expressions.
*/
class CustomManyParticleForceImpl::FunctionPlaceholder : public CustomFunction {
public:
int numArguments;
FunctionPlaceholder(int numArguments) : numArguments(numArguments) {
}
int getNumArguments() const {
return numArguments;
}
double evaluate(const double* arguments) const {
return 0.0;
}
double evaluateDerivative(const double* arguments, const int* derivOrder) const {
return 0.0;
}
CustomFunction* clone() const {
return new FunctionPlaceholder(numArguments);
}
};
CustomManyParticleForceImpl::CustomManyParticleForceImpl(const CustomManyParticleForce& owner) : owner(owner) {
}
CustomManyParticleForceImpl::~CustomManyParticleForceImpl() {
}
void CustomManyParticleForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcCustomManyParticleForceKernel::Name(), context);
// Check for errors in the specification of parameters and exclusions.
const System& system = context.getSystem();
if (owner.getNumParticles() != system.getNumParticles())
throw OpenMMException("CustomManyParticleForce must have exactly as many particles as the System it belongs to.");
vector<set<int> > exclusions(owner.getNumParticles());
vector<double> parameters;
int type;
int numParameters = owner.getNumPerParticleParameters();
for (int i = 0; i < owner.getNumParticles(); i++) {
owner.getParticleParameters(i, parameters, type);
if (parameters.size() != numParameters) {
stringstream msg;
msg << "CustomManyParticleForce: Wrong number of parameters for particle ";
msg << i;
throw OpenMMException(msg.str());
}
}
for (int i = 0; i < owner.getNumExclusions(); i++) {
int particle1, particle2;
owner.getExclusionParticles(i, particle1, particle2);
if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
stringstream msg;
msg << "CustomManyParticleForce: Illegal particle index for an exclusion: ";
msg << particle1;
throw OpenMMException(msg.str());
}
if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
stringstream msg;
msg << "CustomManyParticleForce: Illegal particle index for an exclusion: ";
msg << particle2;
throw OpenMMException(msg.str());
}
if (exclusions[particle1].count(particle2) > 0 || exclusions[particle2].count(particle1) > 0) {
stringstream msg;
msg << "CustomManyParticleForce: Multiple exclusions are specified for particles ";
msg << particle1;
msg << " and ";
msg << particle2;
throw OpenMMException(msg.str());
}
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
}
if (owner.getNonbondedMethod() == CustomManyParticleForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("CustomManyParticleForce: The cutoff distance cannot be greater than half the periodic box size.");
}
kernel.getAs<CalcCustomManyParticleForceKernel>().initialize(context.getSystem(), owner);
}
double CustomManyParticleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
if ((groups&(1<<owner.getForceGroup())) != 0)
return kernel.getAs<CalcCustomManyParticleForceKernel>().execute(context, includeForces, includeEnergy);
return 0.0;
}
vector<string> CustomManyParticleForceImpl::getKernelNames() {
vector<string> names;
names.push_back(CalcCustomManyParticleForceKernel::Name());
return names;
}
map<string, double> CustomManyParticleForceImpl::getDefaultParameters() {
map<string, double> parameters;
for (int i = 0; i < owner.getNumGlobalParameters(); i++)
parameters[owner.getGlobalParameterName(i)] = owner.getGlobalParameterDefaultValue(i);
return parameters;
}
ParsedExpression CustomManyParticleForceImpl::prepareExpression(const CustomManyParticleForce& force, const map<string, CustomFunction*>& customFunctions, map<string, vector<int> >& distances,
map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
CustomManyParticleForceImpl::FunctionPlaceholder custom(1);
CustomManyParticleForceImpl::FunctionPlaceholder distance(2);
CustomManyParticleForceImpl::FunctionPlaceholder angle(3);
CustomManyParticleForceImpl::FunctionPlaceholder dihedral(4);
map<string, CustomFunction*> functions = customFunctions;
functions["distance"] = &distance;
functions["angle"] = &angle;
functions["dihedral"] = &dihedral;
ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
map<string, int> atoms;
for (int i = 0; i < force.getNumParticlesPerSet(); i++) {
stringstream name;
name << 'p' << (i+1);
atoms[name.str()] = i;
}
return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
}
ExpressionTreeNode CustomManyParticleForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
const Operation& op = node.getOperation();
if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
{
// This is not an angle or dihedral, so process its children.
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
return ExpressionTreeNode(op.clone(), children);
}
const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
// Identify the atoms this term is based on.
int numArgs = custom.getNumArguments();
vector<int> indices(numArgs);
for (int i = 0; i < numArgs; i++) {
map<string, int>::const_iterator iter = atoms.find(node.getChildren()[i].getOperation().getName());
if (iter == atoms.end())
throw OpenMMException("CustomManyParticleForce: Unknown particle '"+node.getChildren()[i].getOperation().getName()+"'");
indices[i] = iter->second;
}
// Select a name for the variable and add it to the appropriate map.
stringstream variable;
if (numArgs == 2)
variable << "distance";
else if (numArgs == 3)
variable << "angle";
else
variable << "dihedral";
for (int i = 0; i < numArgs; i++)
variable << indices[i];
string name = variable.str();
if (numArgs == 2)
distances[name] = indices;
else if (numArgs == 3)
angles[name] = indices;
else
dihedrals[name] = indices;
// Return a new node that represents it as a simple variable.
return ExpressionTreeNode(new Operation::Variable(name));
}
void CustomManyParticleForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcCustomManyParticleForceKernel>().copyParametersToContext(context, owner);
}
platforms/reference/include/ReferenceBondIxn.h
View file @ e1a378b7
......@@ -82,7 +82,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
RealOpenMM getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry ) const;
static RealOpenMM getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry );
/**---------------------------------------------------------------------------------------
......@@ -98,8 +98,8 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
RealOpenMM getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct, int hasREntry ) const;
static RealOpenMM getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct, int hasREntry );
/**---------------------------------------------------------------------------------------
......@@ -119,10 +119,10 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
RealOpenMM getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM** outputCrossProduct,
RealOpenMM* cosineOfAngle, RealOpenMM* signVector,
RealOpenMM* signOfAngle, int hasREntry ) const;
static RealOpenMM getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM** outputCrossProduct,
RealOpenMM* cosineOfAngle, RealOpenMM* signVector,
RealOpenMM* signOfAngle, int hasREntry );
};
......
platforms/reference/include/ReferenceCustomManyParticleIxn.h 0 → 100644
View file @ e1a378b7
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceCustomManyParticleIxn_H__
#define __ReferenceCustomManyParticleIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/ParsedExpression.h"
#include <map>
#include <vector>
// ---------------------------------------------------------------------------------------
class ReferenceCustomManyParticleIxn {
private:
class ParticleTermInfo;
class DistanceTermInfo;
class AngleTermInfo;
class DihedralTermInfo;
int numParticlesPerSet, numPerParticleParameters;
bool useCutoff, usePeriodic;
RealOpenMM cutoffDistance;
RealOpenMM periodicBoxSize[3];
Lepton::ExpressionProgram energyExpression;
std::vector<std::vector<std::string> > particleParamNames;
std::vector<ParticleTermInfo> particleTerms;
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
void loopOverInteractions(std::vector<int>& particles, int loopIndex, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** particleParameters, std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
/**---------------------------------------------------------------------------------------
Calculate custom interaction for one set of particles
@param particles the indices of the particles
@param atomCoordinates atom coordinates
@param variables the values of variables that may appear in expressions
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateOneIxn(const std::vector<int>& particles, std::vector<OpenMM::RealVec>& atomCoordinates,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
void computeDelta(int atom1, int atom2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& atomCoordinates) const;
static RealOpenMM computeAngle(RealOpenMM* vec1, RealOpenMM* vec2);
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
ReferenceCustomManyParticleIxn(int numParticlesPerSet, const Lepton::ParsedExpression& energyExpression,
const std::vector<std::string>& particleParameterNames, const std::map<std::string, std::vector<int> >& distances,
const std::map<std::string, std::vector<int> >& angles, const std::map<std::string, std::vector<int> >& dihedrals);
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceCustomManyParticleIxn();
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
--------------------------------------------------------------------------------------- */
void setUseCutoff(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec& boxSize);
/**---------------------------------------------------------------------------------------
Calculate the interaction
@param atomCoordinates atom coordinates
@param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
@param globalParameters the values of global parameters
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** particleParameters,
const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
// ---------------------------------------------------------------------------------------
};
class ReferenceCustomManyParticleIxn::ParticleTermInfo {
public:
std::string name;
int atom, component;
Lepton::ExpressionProgram forceExpression;
ParticleTermInfo(const std::string& name, int atom, int component, const Lepton::ExpressionProgram& forceExpression) :
name(name), atom(atom), component(component), forceExpression(forceExpression) {
}
};
class ReferenceCustomManyParticleIxn::DistanceTermInfo {
public:
std::string name;
int p1, p2;
Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), forceExpression(forceExpression) {
}
};
class ReferenceCustomManyParticleIxn::AngleTermInfo {
public:
std::string name;
int p1, p2, p3;
Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), forceExpression(forceExpression) {
}
};
class ReferenceCustomManyParticleIxn::DihedralTermInfo {
public:
std::string name;
int p1, p2, p3, p4;
Lepton::ExpressionProgram forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM cross1[3];
mutable RealOpenMM cross2[3];
DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), p4(atoms[3]), forceExpression(forceExpression) {
}
};
#endif // __ReferenceCustomManyParticleIxn_H__
platforms/reference/include/ReferenceKernels.h
View file @ e1a378b7
......@@ -44,6 +44,7 @@ class CpuGBVI;
class ReferenceAndersenThermostat;
class ReferenceCustomCompoundBondIxn;
class ReferenceCustomHbondIxn;
class ReferenceCustomManyParticleIxn;
class ReferenceBrownianDynamics;
class ReferenceStochasticDynamics;
class ReferenceConstraintAlgorithm;
......@@ -861,6 +862,46 @@ private:
std::vector<std::string> globalParameterNames;
};
/**
* This kernel is invoked by CustomManyParticleForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcCustomManyParticleForceKernel : public CalcCustomManyParticleForceKernel {
public:
ReferenceCalcCustomManyParticleForceKernel(std::string name, const Platform& platform) : CalcCustomManyParticleForceKernel(name, platform), ixn(NULL) {
}
~ReferenceCalcCustomManyParticleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the CustomManyParticleForce this kernel will be used for
*/
void initialize(const System& system, const CustomManyParticleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomManyParticleForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force);
private:
int numParticles;
RealOpenMM cutoffDistance;
RealOpenMM **particleParamArray;
ReferenceCustomManyParticleIxn* ixn;
std::vector<std::string> globalParameterNames;
NonbondedMethod nonbondedMethod;
};
/**
* This kernel is invoked by VerletIntegrator to take one time step.
*/
......
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ e1a378b7
......@@ -80,6 +80,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceCalcCustomHbondForceKernel(name, platform);
if (name == CalcCustomCompoundBondForceKernel::Name())
return new ReferenceCalcCustomCompoundBondForceKernel(name, platform);
if (name == CalcCustomManyParticleForceKernel::Name())
return new ReferenceCalcCustomManyParticleForceKernel(name, platform);
if (name == IntegrateVerletStepKernel::Name())
return new ReferenceIntegrateVerletStepKernel(name, platform, data);
if (name == IntegrateLangevinStepKernel::Name())
......
platforms/reference/src/ReferenceKernels.cpp
View file @ e1a378b7
......@@ -47,6 +47,7 @@
#include "ReferenceCustomGBIxn.h"
#include "ReferenceCustomHbondIxn.h"
#include "ReferenceCustomNonbondedIxn.h"
#include "ReferenceCustomManyParticleIxn.h"
#include "ReferenceCustomTorsionIxn.h"
#include "ReferenceHarmonicBondIxn.h"
#include "ReferenceLJCoulomb14.h"
......@@ -67,6 +68,7 @@
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomCompoundBondForceImpl.h"
#include "openmm/internal/CustomHbondForceImpl.h"
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "openmm/internal/CustomNonbondedForceImpl.h"
#include "openmm/internal/CMAPTorsionForceImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
......@@ -1615,6 +1617,91 @@ void ReferenceCalcCustomCompoundBondForceKernel::copyParametersToContext(Context
}
}
ReferenceCalcCustomManyParticleForceKernel::~ReferenceCalcCustomManyParticleForceKernel() {
disposeRealArray(particleParamArray, numParticles);
if (ixn != NULL)
delete ixn;
}
void ReferenceCalcCustomManyParticleForceKernel::initialize(const System& system, const CustomManyParticleForce& force) {
// Build the arrays.
numParticles = system.getNumParticles();
int numParticleParameters = force.getNumPerParticleParameters();
particleParamArray = allocateRealArray(numParticles, numParticleParameters);
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
int type;
force.getParticleParameters(i, parameters, type);
for (int j = 0; j < numParticleParameters; j++)
particleParamArray[i][j] = parameters[j];
}
// Create custom functions for the tabulated functions.
map<string, Lepton::CustomFunction*> functions;
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
// Parse the expression and create the object used to calculate the interaction.
map<string, vector<int> > distances;
map<string, vector<int> > angles;
map<string, vector<int> > dihedrals;
Lepton::ParsedExpression energyExpression = CustomManyParticleForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
vector<string> particleParameterNames;
for (int i = 0; i < numParticleParameters; i++)
particleParameterNames.push_back(force.getPerParticleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
ixn = new ReferenceCustomManyParticleIxn(force.getNumParticlesPerSet(), energyExpression, particleParameterNames, distances, angles, dihedrals);
nonbondedMethod = CalcCustomManyParticleForceKernel::NonbondedMethod(force.getNonbondedMethod());
cutoffDistance = force.getCutoffDistance();
if (nonbondedMethod != NoCutoff)
ixn->setUseCutoff(cutoffDistance);
// Delete the custom functions.
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
}
double ReferenceCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealOpenMM energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
if (nonbondedMethod == CutoffPeriodic) {
RealVec& box = extractBoxSize(context);
double minAllowedSize = 2*cutoffDistance;
if (box[0] < minAllowedSize || box[1] < minAllowedSize || box[2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
ixn->setPeriodic(box);
}
ixn->calculateIxn(posData, particleParamArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
return energy;
}
void ReferenceCalcCustomManyParticleForceKernel::copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force) {
if (numParticles != force.getNumParticles())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the values.
int numParameters = force.getNumPerParticleParameters();
vector<double> params;
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
int type;
force.getParticleParameters(i, parameters, type);
for (int j = 0; j < numParameters; j++)
particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
}
ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
if (dynamics)
delete dynamics;
......
platforms/reference/src/ReferencePlatform.cpp
View file @ e1a378b7
......@@ -63,6 +63,7 @@ ReferencePlatform::ReferencePlatform() {
registerKernelFactory(CalcCustomExternalForceKernel::Name(), factory);
registerKernelFactory(CalcCustomHbondForceKernel::Name(), factory);
registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
......
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ e1a378b7
......@@ -105,7 +105,7 @@ ReferenceBondIxn::~ReferenceBondIxn( ){
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2,
int hasREntry = 0 ) const {
int hasREntry = 0 ) {
// ---------------------------------------------------------------------------------------
......@@ -187,7 +187,7 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenM
RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct = NULL,
int hasREntry = 0 ) const {
int hasREntry = 0 ) {
// ---------------------------------------------------------------------------------------
......@@ -249,7 +249,7 @@ RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM* v
RealOpenMM* cosineOfAngle = NULL,
RealOpenMM* signVector = NULL,
RealOpenMM* signOfAngle = NULL,
int hasREntry = 0 ) const {
int hasREntry = 0 ) {
// ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp 0 → 100644
View file @ e1a378b7
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <string.h>
#include <sstream>
#include <utility>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "ReferenceCustomManyParticleIxn.h"
using std::map;
using std::pair;
using std::string;
using std::stringstream;
using std::vector;
using OpenMM::RealVec;
ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(int numParticlesPerSet,
const Lepton::ParsedExpression& energyExpression, const vector<string>& particleParameterNames,
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
numParticlesPerSet(numParticlesPerSet), energyExpression(energyExpression.createProgram()), useCutoff(false), usePeriodic(false) {
particleParamNames.resize(numParticlesPerSet);
numPerParticleParameters = particleParameterNames.size();
for (int i = 0; i < numParticlesPerSet; i++) {
stringstream xname, yname, zname;
xname << 'x' << (i+1);
yname << 'y' << (i+1);
zname << 'z' << (i+1);
particleTerms.push_back(ReferenceCustomManyParticleIxn::ParticleTermInfo(xname.str(), i, 0, energyExpression.differentiate(xname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomManyParticleIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).optimize().createProgram()));
particleTerms.push_back(ReferenceCustomManyParticleIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).optimize().createProgram()));
for (int j = 0; j < numPerParticleParameters; j++) {
stringstream paramname;
paramname << particleParameterNames[j] << (i+1);
particleParamNames[i].push_back(paramname.str());
}
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomManyParticleIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomManyParticleIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomManyParticleIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
}
ReferenceCustomManyParticleIxn::~ReferenceCustomManyParticleIxn( ){
}
void ReferenceCustomManyParticleIxn::calculateIxn(vector<RealVec>& atomCoordinates, RealOpenMM** particleParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
map<string, double> variables = globalParameters;
vector<int> particles(numParticlesPerSet);
loopOverInteractions(particles, 0, atomCoordinates, particleParameters, variables, forces, totalEnergy);
}
void ReferenceCustomManyParticleIxn::setUseCutoff(RealOpenMM distance) {
useCutoff = true;
cutoffDistance = distance;
}
void ReferenceCustomManyParticleIxn::setPeriodic(RealVec& boxSize) {
assert(cutoff);
assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance);
assert(boxSize[2] >= 2.0*cutoffDistance);
usePeriodic = true;
periodicBoxSize[0] = boxSize[0];
periodicBoxSize[1] = boxSize[1];
periodicBoxSize[2] = boxSize[2];
}
void ReferenceCustomManyParticleIxn::loopOverInteractions(vector<int>& particles, int loopIndex, vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** particleParameters, map<string, double>& variables, vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const {
int numParticles = atomCoordinates.size();
int start = (loopIndex == 0 ? 0 : particles[loopIndex-1]+1);
for (int i = start; i < numParticles; i++) {
particles[loopIndex] = i;
for (int j = 0; j < numPerParticleParameters; j++)
variables[particleParamNames[loopIndex][j]] = particleParameters[i][j];
if (loopIndex == numParticlesPerSet-1)
calculateOneIxn(particles, atomCoordinates, variables, forces, totalEnergy);
else
loopOverInteractions(particles, loopIndex+1, atomCoordinates, particleParameters, variables, forces, totalEnergy);
}
}
void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particles, vector<RealVec>& atomCoordinates,
map<string, double>& variables, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
// Compute all of the variables the energy can depend on.
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
variables[term.name] = atomCoordinates[term.atom][term.component];
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
computeDelta(particles[term.p1], particles[term.p2], term.delta, atomCoordinates);
variables[term.name] = term.delta[ReferenceForce::RIndex];
if (useCutoff && term.delta[ReferenceForce::RIndex] > cutoffDistance)
return;
}
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
computeDelta(particles[term.p1], particles[term.p2], term.delta1, atomCoordinates);
computeDelta(particles[term.p3], particles[term.p2], term.delta2, atomCoordinates);
variables[term.name] = computeAngle(term.delta1, term.delta2);
}
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
computeDelta(particles[term.p2], particles[term.p1], term.delta1, atomCoordinates);
computeDelta(particles[term.p2], particles[term.p3], term.delta2, atomCoordinates);
computeDelta(particles[term.p4], particles[term.p3], term.delta3, atomCoordinates);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
variables[term.name] = ReferenceBondIxn::getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1);
}
// Apply forces based on individual particle coordinates.
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
forces[particles[term.atom]][term.component] -= term.forceExpression.evaluate(variables);
}
// Apply forces based on distances.
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]));
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
forces[particles[term.p1]][i] -= force;
forces[particles[term.p2]][i] += force;
}
}
// Apply forces based on angles.
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-06)
lengthThetaCross = (RealOpenMM) 1.0e-06;
RealOpenMM termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, thetaCross, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(term.delta2, thetaCross, deltaCrossP[2]);
for (int i = 0; i < 3; i++) {
deltaCrossP[0][i] *= termA;
deltaCrossP[2][i] *= termC;
deltaCrossP[1][i] = -(deltaCrossP[0][i]+deltaCrossP[2][i]);
}
for (int i = 0; i < 3; i++) {
forces[particles[term.p1]][i] += deltaCrossP[0][i];
forces[particles[term.p2]][i] += deltaCrossP[1][i];
forces[particles[term.p3]][i] += deltaCrossP[2][i];
}
}
// Apply forces based on dihedrals.
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
RealOpenMM normBC = term.delta2[ReferenceForce::RIndex];
forceFactors[0] = (-dEdTheta*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
internalF[0][i] = forceFactors[0]*term.cross1[i];
internalF[3][i] = forceFactors[3]*term.cross2[i];
RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
internalF[1][i] = internalF[0][i] - s;
internalF[2][i] = internalF[3][i] + s;
}
for (int i = 0; i < 3; i++) {
forces[particles[term.p1]][i] += internalF[0][i];
forces[particles[term.p2]][i] -= internalF[1][i];
forces[particles[term.p3]][i] -= internalF[2][i];
forces[particles[term.p4]][i] += internalF[3][i];
}
}
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
}
void ReferenceCustomManyParticleIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom1], atomCoordinates[atom2], periodicBoxSize, delta);
else
ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
}
RealOpenMM ReferenceCustomManyParticleIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
RealOpenMM dot = DOT3(vec1, vec2);
RealOpenMM cosine = dot/SQRT((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
RealOpenMM angle;
if (cosine >= 1)
angle = 0;
else if (cosine <= -1)
angle = PI_M;
else
angle = ACOS(cosine);
return angle;
}
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp 0 → 100644
View file @ e1a378b7
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of CustomManyParticleForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/CustomManyParticleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
// Create a System and Context.
int numParticles = force->getNumParticles();
CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(force);
VerletIntegrator integrator(0.001);
ReferencePlatform platform;
Context context(system, integrator, platform);
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy);
double c = context.getParameter("C");
// See if the energy matches the expected value.
double expectedEnergy = 0;
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
double ctheta1 = d12.dot(d13)/(r12*r13);
double ctheta2 = -d12.dot(d23)/(r12*r23);
double ctheta3 = d13.dot(d23)/(r13*r23);
double rprod = r12*r13*r23;
expectedEnergy += c*(1+3*ctheta1*ctheta2*ctheta3)/(rprod*rprod*rprod);
}
ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
const vector<Vec3>& forces = state1.getForces();
double norm = 0.0;
for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm);
const double stepSize = 1e-3;
double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) {
Vec3 p = positions[i];
Vec3 f = forces[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
}
context.setPositions(positions2);
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
}
void testNoCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
}
void testCutoff() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
force->setCutoffDistance(1.55);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
int sets[7][3] = {{0,1,2}, {0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,2,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[7]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
}
void testPeriodic() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.05);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
double boxSize = 2.1;
int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, boxSize);
}
void testParameters() {
// Create a system.
int numParticles = 5;
System system;
CustomManyParticleForce* force = new CustomManyParticleForce(3, "C*scale1*scale2*scale3*(distance(p1,p2)+distance(p2,p3)+distance(p1,p3))");
force->addGlobalParameter("C", 2.0);
force->addPerParticleParameter("scale");
vector<double> params(1);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
params[0] = i+1;
force->addParticle(params);
positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
system.addParticle(1.0);
}
system.addForce(force);
VerletIntegrator integrator(0.001);
ReferencePlatform platform;
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the energy is correct.
State state1 = context.getState(State::Energy);
double expectedEnergy = 0;
for (int i = 0; i < numParticles; i++)
for (int j = i+1; j < numParticles; j++)
for (int k = j+1; k < numParticles; k++) {
Vec3 d12 = positions[j]-positions[i];
Vec3 d13 = positions[k]-positions[i];
Vec3 d23 = positions[k]-positions[j];
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
expectedEnergy += 2.0*(i+1)*(j+1)*(k+1)*(r12+r13+r23);
}
ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
}
int main() {
try {
testNoCutoff();
testCutoff();
testPeriodic();
testParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment