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Commit 51b7f9e2 authored by Robert McGibbon's avatar Robert McGibbon
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plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ 51b7f9e2
...@@ -81,15 +81,15 @@ public: ...@@ -81,15 +81,15 @@ public:
/** /**
* Get the force field parameters for a stretch-bend term. * Get the force field parameters for a stretch-bend term.
* *
* @param index the index of the stretch-bend for which to get parameters * @param index the index of the stretch-bend for which to get parameters
* @param particle1 the index of the first particle connected by the stretch-bend * @param[out] particle1 the index of the first particle connected by the stretch-bend
* @param particle2 the index of the second particle connected by the stretch-bend * @param[out] particle2 the index of the second particle connected by the stretch-bend
* @param particle3 the index of the third particle connected by the stretch-bend * @param[out] particle3 the index of the third particle connected by the stretch-bend
* @param lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm * @param[out] lengthAB the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
* @param lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm * @param[out] lengthCB the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
* @param angle the equilibrium angle in radians * @param[out] angle the equilibrium angle in radians
* @param k1 the force constant of the product of bond ab and angle a-b-c * @param[out] k1 the force constant of the product of bond ab and angle a-b-c
* @param k2 the force constant of the product of bond bc and angle a-b-c * @param[out] k2 the force constant of the product of bond bc and angle a-b-c
*/ */
void getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3, double& lengthAB, void getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3, double& lengthAB,
double& lengthCB, double& angle, double& k1, double& k2) const; double& lengthCB, double& angle, double& k1, double& k2) const;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h
View file @ 51b7f9e2
...@@ -89,14 +89,14 @@ public: ...@@ -89,14 +89,14 @@ public:
/** /**
* Get the force field parameters for a torsion-torsion term. * Get the force field parameters for a torsion-torsion term.
* *
* @param index the index of the torsion-torsion for which to get parameters * @param index the index of the torsion-torsion for which to get parameters
* @param particle1 the index of the first particle connected by the torsion-torsion * @param[out] particle1 the index of the first particle connected by the torsion-torsion
* @param particle2 the index of the second particle connected by the torsion-torsion * @param[out] particle2 the index of the second particle connected by the torsion-torsion
* @param particle3 the index of the third particle connected by the torsion-torsion * @param[out] particle3 the index of the third particle connected by the torsion-torsion
* @param particle4 the index of the fourth particle connected by the torsion-torsion * @param[out] particle4 the index of the fourth particle connected by the torsion-torsion
* @param particle5 the index of the fifth particle connected by the torsion-torsion * @param[out] particle5 the index of the fifth particle connected by the torsion-torsion
* @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check * @param[out] chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
* @param gridIndex the grid index * @param[out] gridIndex the grid index
*/ */
void getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const; void getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const;
...@@ -117,7 +117,7 @@ public: ...@@ -117,7 +117,7 @@ public:
/** /**
* Get the torsion-torsion grid at the specified index * Get the torsion-torsion grid at the specified index
* *
* @param gridIndex the grid index * @param index the grid index
* @return grid return grid reference * @return grid return grid reference
*/ */
const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid(int index) const; const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid(int index) const;
...@@ -172,7 +172,7 @@ public: ...@@ -172,7 +172,7 @@ public:
} }
TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) : TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) :
particle1(particle1), particle2(particle2), particle3(particle3), particle1(particle1), particle2(particle2), particle3(particle3),
particle4(particle4), particle5(particle5), gridIndex(gridIndex), chiralCheckAtomIndex(chiralCheckAtomIndex) { particle4(particle4), particle5(particle5), chiralCheckAtomIndex(chiralCheckAtomIndex), gridIndex(gridIndex) {
} }
}; };
......
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ 51b7f9e2
#ifndef OPENMM_AMOEBA_VDW_FORCE_H_ #ifndef OPENMM_AMOEBA_VDW_FORCE_H_
#define OPENMM_AMOEBA_VDW_FORCE_H_ #define OPENMM_AMOEBA_VDW_FORCE_H_
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMAmoeba *
* -------------------------------------------------------------------------- * * -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from * * This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of * * Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. * * Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman * * Authors: Mark Friedrichs, Peter Eastman *
* Contributors: * * Contributors: *
* * * *
* Permission is hereby granted, free of charge, to any person obtaining a * * Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), * * copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation * * to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, * * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the * * 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: * * Software is furnished to do so, subject to the following conditions: *
* * * *
* The above copyright notice and this permission notice shall be included in * * The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. * * all copies or substantial portions of the Software. *
* * * *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * * 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 * * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/Force.h" #include "openmm/Force.h"
#include "internal/windowsExportAmoeba.h" #include "internal/windowsExportAmoeba.h"
#include <vector> #include <vector>
namespace OpenMM { namespace OpenMM {
/** /**
* This class implements a buffered 14-7 potential used to model van der Waals forces. * This class implements a buffered 14-7 potential used to model van der Waals forces.
* *
* To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. After * To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. After
* a particle has been added, you can modify its force field parameters by calling setParticleParameters(). * a particle has been added, you can modify its force field parameters by calling setParticleParameters().
* This will have no effect on Contexts that already exist unless you call updateParametersInContext(). * This will have no effect on Contexts that already exist unless you call updateParametersInContext().
* *
* A unique feature of this class is that the interaction site for a particle does not need to be * A unique feature of this class is that the interaction site for a particle does not need to be
* exactly at the particle's location. Instead, it can be placed a fraction of the distance from that * exactly at the particle's location. Instead, it can be placed a fraction of the distance from that
* particle to another one. This is typically done for hydrogens to place the interaction site slightly * particle to another one. This is typically done for hydrogens to place the interaction site slightly
* closer to the parent atom. The fraction is known as the "reduction factor", since it reduces the distance * closer to the parent atom. The fraction is known as the "reduction factor", since it reduces the distance
* from the parent atom to the interaction site. * from the parent atom to the interaction site.
*/ */
class OPENMM_EXPORT_AMOEBA AmoebaVdwForce : public Force { class OPENMM_EXPORT_AMOEBA AmoebaVdwForce : public Force {
public: public:
/** /**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces. * This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/ */
enum NonbondedMethod { enum NonbondedMethod {
/** /**
* No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly. * No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default. * This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/ */
NoCutoff = 0, NoCutoff = 0,
/** /**
* Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of * Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
* each other particle. Interactions beyond the cutoff distance are ignored. * each other particle. Interactions beyond the cutoff distance are ignored.
*/ */
CutoffPeriodic = 1, CutoffPeriodic = 1,
}; };
/** /**
* Create an Amoeba VdwForce. * Create an Amoeba VdwForce.
*/ */
AmoebaVdwForce(); AmoebaVdwForce();
/** /**
* Get the number of particles * Get the number of particles
*/ */
int getNumParticles() const { int getNumParticles() const {
return parameters.size(); return parameters.size();
} }
/** /**
* Set the force field parameters for a vdw particle. * Set the force field parameters for a vdw particle.
* *
* @param particleIndex the particle index * @param particleIndex the particle index
* @param parentIndex the index of the parent particle * @param parentIndex the index of the parent particle
* @param sigma vdw sigma * @param sigma vdw sigma
* @param epsilon vdw epsilon * @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle * @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed * at which the interaction site should be placed
*/ */
void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor); void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);
/** /**
* Get the force field parameters for a vdw particle. * Get the force field parameters for a vdw particle.
* *
* @param particleIndex the particle index * @param particleIndex the particle index
* @param parentIndex the index of the parent particle * @param[out] parentIndex the index of the parent particle
* @param sigma vdw sigma * @param[out] sigma vdw sigma
* @param epsilon vdw epsilon * @param[out] epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle * @param[out] reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed * at which the interaction site should be placed
*/ */
void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const; void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
/** /**
* Add the force field parameters for a vdw particle. * Add the force field parameters for a vdw particle.
* *
* @param parentIndex the index of the parent particle * @param parentIndex the index of the parent particle
* @param sigma vdw sigma * @param sigma vdw sigma
* @param epsilon vdw epsilon * @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle * @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed * at which the interaction site should be placed
* @return index of added particle * @return index of added particle
*/ */
int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor); int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);
/** /**
* Set sigma combining rule * Set sigma combining rule
* *
* @param sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN' * @param sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/ */
void setSigmaCombiningRule(const std::string& sigmaCombiningRule); void setSigmaCombiningRule(const std::string& sigmaCombiningRule);
/** /**
* Get sigma combining rule * Get sigma combining rule
* *
* @return sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN' * @return sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/ */
const std::string& getSigmaCombiningRule(void) const; const std::string& getSigmaCombiningRule(void) const;
/** /**
* Set epsilon combining rule * Set epsilon combining rule
* *
* @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG' * @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/ */
void setEpsilonCombiningRule(const std::string& epsilonCombiningRule); void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
/** /**
* Get epsilon combining rule * Get epsilon combining rule
* *
* @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG' * @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/ */
const std::string& getEpsilonCombiningRule(void) const; const std::string& getEpsilonCombiningRule(void) const;
/** /**
* Get whether to add a contribution to the energy that approximately represents the effect of VdW * Get whether to add a contribution to the energy that approximately represents the effect of VdW
* interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only * interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only
* applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding * applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding
* this contribution can improve the quality of results. * this contribution can improve the quality of results.
*/ */
bool getUseDispersionCorrection() const { bool getUseDispersionCorrection() const {
return useDispersionCorrection; return useDispersionCorrection;
} }
/** /**
* Set whether to add a contribution to the energy that approximately represents the effect of VdW * Set whether to add a contribution to the energy that approximately represents the effect of VdW
* interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only * interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only
* applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding * applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding
* this contribution can improve the quality of results. * this contribution can improve the quality of results.
*/ */
void setUseDispersionCorrection(bool useCorrection) { void setUseDispersionCorrection(bool useCorrection) {
useDispersionCorrection = useCorrection; useDispersionCorrection = useCorrection;
} }
/** /**
* Set exclusions for specified particle * Set exclusions for specified particle
* *
* @param particleIndex particle index * @param particleIndex particle index
* @param exclusions vector of exclusions * @param exclusions vector of exclusions
*/ */
void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions); void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions);
/** /**
* Get exclusions for specified particle * Get exclusions for specified particle
* *
* @param particleIndex particle index * @param particleIndex particle index
* @param exclusions vector of exclusions * @param[out] exclusions vector of exclusions
*/ */
void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const; void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
/** /**
* Set the cutoff distance. * Set the cutoff distance.
*/ */
void setCutoff(double cutoff); void setCutoff(double cutoff);
/** /**
* Get the cutoff distance. * Get the cutoff distance.
*/ */
double getCutoff() const; double getCutoff() const;
/** /**
* Get the method used for handling long range nonbonded interactions. * Get the method used for handling long range nonbonded interactions.
*/ */
NonbondedMethod getNonbondedMethod() const; NonbondedMethod getNonbondedMethod() const;
/** /**
* Set the method used for handling long range nonbonded interactions. * Set the method used for handling long range nonbonded interactions.
*/ */
void setNonbondedMethod(NonbondedMethod method); void setNonbondedMethod(NonbondedMethod method);
/** /**
* Update the per-particle parameters in a Context to match those stored in this Force object. This method provides * 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. * 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() * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context. * to copy them over to the Context.
* *
* The only information this method updates is the values of per-particle parameters. All other aspects of the Force * The only information this method updates is the values of per-particle parameters. All other aspects of the Force
* (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. * (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context.
*/ */
void updateParametersInContext(Context& context); void updateParametersInContext(Context& context);
/** /**
* Returns whether or not this force makes use of periodic boundary * Returns whether or not this force makes use of periodic boundary
* conditions. * conditions.
* *
* @returns true if nonbondedMethod uses PBC and false otherwise * @returns true if nonbondedMethod uses PBC and false otherwise
*/ */
bool usesPeriodicBoundaryConditions() const { bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == AmoebaVdwForce::CutoffPeriodic; return nonbondedMethod == AmoebaVdwForce::CutoffPeriodic;
} }
protected: protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
class VdwInfo; class VdwInfo;
NonbondedMethod nonbondedMethod; NonbondedMethod nonbondedMethod;
double cutoff; double cutoff;
bool useDispersionCorrection; bool useDispersionCorrection;
std::string sigmaCombiningRule; std::string sigmaCombiningRule;
std::string epsilonCombiningRule; std::string epsilonCombiningRule;
std::vector< std::vector<int> > exclusions; std::vector< std::vector<int> > exclusions;
std::vector<VdwInfo> parameters; std::vector<VdwInfo> parameters;
std::vector< std::vector< std::vector<double> > > sigEpsTable; std::vector< std::vector< std::vector<double> > > sigEpsTable;
}; };
/** /**
* This is an internal class used to record information about a particle. * This is an internal class used to record information about a particle.
* @private * @private
*/ */
class AmoebaVdwForce::VdwInfo { class AmoebaVdwForce::VdwInfo {
public: public:
int parentIndex; int parentIndex;
double reductionFactor, sigma, epsilon, cutoff; double reductionFactor, sigma, epsilon, cutoff;
VdwInfo() { VdwInfo() {
parentIndex = -1; parentIndex = -1;
reductionFactor = 0.0; reductionFactor = 0.0;
sigma = 1.0; sigma = 1.0;
epsilon = 0.0; epsilon = 0.0;
} }
VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) : VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
parentIndex(parentIndex), sigma(sigma), epsilon(epsilon), reductionFactor(reductionFactor) { parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon) {
} }
}; };
} // namespace OpenMM } // namespace OpenMM
#endif /*OPENMM_AMOEBA_VDW_FORCE_H_*/ #endif /*OPENMM_AMOEBA_VDW_FORCE_H_*/
plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h
View file @ 51b7f9e2
...@@ -75,9 +75,9 @@ public: ...@@ -75,9 +75,9 @@ public:
/** /**
* Get the force field parameters for a WCA dispersion particle. * Get the force field parameters for a WCA dispersion particle.
* *
* @param particleIndex the particle index * @param particleIndex the particle index
* @param radius radius * @param[out] radius radius
* @param epsilon epsilon * @param[out] epsilon epsilon
*/ */
void getParticleParameters(int particleIndex, double& radius, double& epsilon) const; void getParticleParameters(int particleIndex, double& radius, double& epsilon) const;
......
plugins/drude/openmmapi/include/openmm/DrudeForce.h
View file @ 51b7f9e2
...@@ -44,7 +44,7 @@ namespace OpenMM { ...@@ -44,7 +44,7 @@ namespace OpenMM {
* it applies: an anisotropic harmonic force connecting each Drude particle to its parent particle; and * it applies: an anisotropic harmonic force connecting each Drude particle to its parent particle; and
* a screened Coulomb interaction between specific pairs of dipoles. The latter is typically used between * a screened Coulomb interaction between specific pairs of dipoles. The latter is typically used between
* closely bonded particles whose Coulomb interaction would otherwise be fully excluded. * closely bonded particles whose Coulomb interaction would otherwise be fully excluded.
* *
* To use this class, create a DrudeForce object, then call addParticle() once for each Drude particle in the * To use this class, create a DrudeForce object, then call addParticle() once for each Drude particle in the
* System to define its parameters. After a particle has been added, you can modify its force field parameters * System to define its parameters. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you * by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you
...@@ -91,19 +91,19 @@ public: ...@@ -91,19 +91,19 @@ public:
/** /**
* Get the parameters for a Drude particle. * Get the parameters for a Drude particle.
* *
* @param index the index of the Drude particle for which to get parameters * @param index the index of the Drude particle for which to get parameters
* @param particle the index within the System of the Drude particle * @param[out] particle the index within the System of the Drude particle
* @param particle1 the index within the System of the particle to which the Drude particle is attached * @param[out] particle1 the index within the System of the particle to which the Drude particle is attached
* @param particle2 the index within the System of the second particle used for defining anisotropic polarizability. * @param[out] particle2 the index within the System of the second particle used for defining anisotropic polarizability.
* This may be set to -1, in which case aniso12 will be ignored. * This may be set to -1, in which case aniso12 will be ignored.
* @param particle3 the index within the System of the third particle used for defining anisotropic polarizability. * @param[out] particle3 the index within the System of the third particle used for defining anisotropic polarizability.
* This may be set to -1, in which case aniso34 will be ignored. * This may be set to -1, in which case aniso34 will be ignored.
* @param particle4 the index within the System of the fourth particle used for defining anisotropic polarizability. * @param[out] particle4 the index within the System of the fourth particle used for defining anisotropic polarizability.
* This may be set to -1, in which case aniso34 will be ignored. * This may be set to -1, in which case aniso34 will be ignored.
* @param charge The charge on the Drude particle * @param[out] charge The charge on the Drude particle
* @param polarizability The isotropic polarizability * @param[out] polarizability The isotropic polarizability
* @param aniso12 The scale factor for the polarizability along the direction defined by particle1 and particle2 * @param[out] aniso12 The scale factor for the polarizability along the direction defined by particle1 and particle2
* @param aniso34 The scale factor for the polarizability along the direction defined by particle3 and particle4 * @param[out] aniso34 The scale factor for the polarizability along the direction defined by particle3 and particle4
*/ */
void getParticleParameters(int index, int& particle, int& particle1, int& particle2, int& particle3, int& particle4, double& charge, double& polarizability, double& aniso12, double& aniso34) const; void getParticleParameters(int index, int& particle, int& particle1, int& particle2, int& particle3, int& particle4, double& charge, double& polarizability, double& aniso12, double& aniso34) const;
/** /**
...@@ -135,16 +135,16 @@ public: ...@@ -135,16 +135,16 @@ public:
int addScreenedPair(int particle1, int particle2, double thole); int addScreenedPair(int particle1, int particle2, double thole);
/** /**
* Get the force field parameters for screened pair. * Get the force field parameters for screened pair.
* *
* @param index the index of the pair for which to get parameters * @param index the index of the pair for which to get parameters
* @param particle1 the index within this Force of the first particle involved in the interaction * @param[out] particle1 the index within this Force of the first particle involved in the interaction
* @param particle2 the index within this Force of the second particle involved in the interaction * @param[out] particle2 the index within this Force of the second particle involved in the interaction
* @param thole the Thole screening factor * @param[out] thole the Thole screening factor
*/ */
void getScreenedPairParameters(int index, int& particle1, int& particle2, double& thole) const; void getScreenedPairParameters(int index, int& particle1, int& particle2, double& thole) const;
/** /**
* Set the force field parameters for screened pair. * Set the force field parameters for screened pair.
* *
* @param index the index of the pair for which to get parameters * @param index the index of the pair for which to get parameters
* @param particle1 the index within this Force of the first particle involved in the interaction * @param particle1 the index within this Force of the first particle involved in the interaction
* @param particle2 the index within this Force of the second particle involved in the interaction * @param particle2 the index within this Force of the second particle involved in the interaction
...@@ -156,7 +156,7 @@ public: ...@@ -156,7 +156,7 @@ public:
* provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setParticleParameters() and setScreenedPairParameters() to modify this object's parameters, then call * Simply call setParticleParameters() and setScreenedPairParameters() to modify this object's parameters, then call
* updateParametersInContext() to copy them over to the Context. * updateParametersInContext() to copy them over to the Context.
* *
* This method has several limitations. It can be used to modify the numeric parameters associated with a particle or * This method has several limitations. It can be used to modify the numeric parameters associated with a particle or
* screened pair (polarizability, thole, etc.), but not the identities of the particles they involve. It also cannot * screened pair (polarizability, thole, etc.), but not the identities of the particles they involve. It also cannot
* be used to add new particles or screenedPairs, only to change the parameters of existing ones. * be used to add new particles or screenedPairs, only to change the parameters of existing ones.
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 51b7f9e2
...@@ -128,21 +128,15 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int ...@@ -128,21 +128,15 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
center *= 1.0/molecules[i].size(); center *= 1.0/molecules[i].size();
// Find the displacement to move it into the first periodic box. // Find the displacement to move it into the first periodic box.
Vec3 diff;
int xcell = (int) floor(center[0]/periodicBoxSize[0][0]); diff -= periodicBoxSize[0]*static_cast<int>(center[0]/periodicBoxSize[0][0]);
int ycell = (int) floor(center[1]/periodicBoxSize[1][1]); diff -= periodicBoxSize[1]*static_cast<int>(center[1]/periodicBoxSize[1][1]);
int zcell = (int) floor(center[2]/periodicBoxSize[2][2]); diff -= periodicBoxSize[2]*static_cast<int>(center[2]/periodicBoxSize[2][2]);
double dx = xcell*periodicBoxSize[0][0];
double dy = ycell*periodicBoxSize[1][1];
double dz = zcell*periodicBoxSize[2][2];
// Translate all the particles in the molecule. // Translate all the particles in the molecule.
for (int j = 0; j < (int) molecules[i].size(); j++) { for (int j = 0; j < (int) molecules[i].size(); j++) {
Vec3& pos = positions[molecules[i][j]]; Vec3& pos = positions[molecules[i][j]];
pos[0] -= dx; pos -= diff;
pos[1] -= dy;
pos[2] -= dz;
} }
} }
...@@ -170,7 +164,7 @@ double RPMDIntegrator::computeKineticEnergy() { ...@@ -170,7 +164,7 @@ double RPMDIntegrator::computeKineticEnergy() {
void RPMDIntegrator::step(int steps) { void RPMDIntegrator::step(int steps) {
if (context == NULL) if (context == NULL)
throw OpenMMException("This Integrator is not bound to a context!"); throw OpenMMException("This Integrator is not bound to a context!");
if (!hasSetPosition) { if (!hasSetPosition) {
// Initialize the positions from the context. // Initialize the positions from the context.
......
serialization/include/openmm/serialization/CompoundIntegratorProxy.h 0 → 100644
View file @ 51b7f9e2
#ifndef OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
#define OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
#include "openmm/serialization/XmlSerializer.h"
namespace OpenMM {
class CompoundIntegratorProxy : public SerializationProxy {
public:
CompoundIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_COMPOUND_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
serialization/include/openmm/serialization/SerializationNode.h
View file @ 51b7f9e2
...@@ -105,7 +105,7 @@ public: ...@@ -105,7 +105,7 @@ public:
/** /**
* Determine whether this node has a property with a particular node. * Determine whether this node has a property with a particular node.
* *
* @param the name of the property to check for * @param name the name of the property to check for
*/ */
bool hasProperty(const std::string& name) const; bool hasProperty(const std::string& name) const;
/** /**
......
serialization/src/CompoundIntegratorProxy.cpp 0 → 100644
View file @ 51b7f9e2
/* -------------------------------------------------------------------------- *
* 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) 2015 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/serialization/CompoundIntegratorProxy.h"
#include <OpenMM.h>
using namespace std;
using namespace OpenMM;
CompoundIntegratorProxy::CompoundIntegratorProxy() : SerializationProxy("CompoundIntegrator") {
}
void CompoundIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const CompoundIntegrator& integrator = *reinterpret_cast<const CompoundIntegrator*>(object);
node.setIntProperty("currentIntegrator", integrator.getCurrentIntegrator());
for (int i = 0; i < integrator.getNumIntegrators(); i++)
node.createChildNode("Integrator", &integrator.getIntegrator(i));
}
void* CompoundIntegratorProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
CompoundIntegrator *integrator = new CompoundIntegrator();
for (int i = 0; i < node.getChildren().size(); i++)
integrator->addIntegrator(node.getChildren()[i].decodeObject<Integrator>());
integrator->setCurrentIntegrator(node.getIntProperty("currentIntegrator"));
return integrator;
}
\ No newline at end of file
serialization/src/SerializationProxyRegistration.cpp
View file @ 51b7f9e2
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. * * Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -33,6 +33,7 @@ ...@@ -33,6 +33,7 @@
#include "openmm/BrownianIntegrator.h" #include "openmm/BrownianIntegrator.h"
#include "openmm/CMAPTorsionForce.h" #include "openmm/CMAPTorsionForce.h"
#include "openmm/CMMotionRemover.h" #include "openmm/CMMotionRemover.h"
#include "openmm/CompoundIntegrator.h"
#include "openmm/CustomAngleForce.h" #include "openmm/CustomAngleForce.h"
#include "openmm/CustomBondForce.h" #include "openmm/CustomBondForce.h"
#include "openmm/CustomCompoundBondForce.h" #include "openmm/CustomCompoundBondForce.h"
...@@ -65,6 +66,7 @@ ...@@ -65,6 +66,7 @@
#include "openmm/serialization/AndersenThermostatProxy.h" #include "openmm/serialization/AndersenThermostatProxy.h"
#include "openmm/serialization/CMAPTorsionForceProxy.h" #include "openmm/serialization/CMAPTorsionForceProxy.h"
#include "openmm/serialization/CMMotionRemoverProxy.h" #include "openmm/serialization/CMMotionRemoverProxy.h"
#include "openmm/serialization/CompoundIntegratorProxy.h"
#include "openmm/serialization/CustomAngleForceProxy.h" #include "openmm/serialization/CustomAngleForceProxy.h"
#include "openmm/serialization/CustomBondForceProxy.h" #include "openmm/serialization/CustomBondForceProxy.h"
#include "openmm/serialization/CustomCompoundBondForceProxy.h" #include "openmm/serialization/CustomCompoundBondForceProxy.h"
...@@ -112,6 +114,7 @@ extern "C" void registerSerializationProxies() { ...@@ -112,6 +114,7 @@ extern "C" void registerSerializationProxies() {
SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy()); SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy()); SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy()); SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());
SerializationProxy::registerProxy(typeid(CompoundIntegrator), new CompoundIntegratorProxy());
SerializationProxy::registerProxy(typeid(Continuous1DFunction), new Continuous1DFunctionProxy()); SerializationProxy::registerProxy(typeid(Continuous1DFunction), new Continuous1DFunctionProxy());
SerializationProxy::registerProxy(typeid(Continuous2DFunction), new Continuous2DFunctionProxy()); SerializationProxy::registerProxy(typeid(Continuous2DFunction), new Continuous2DFunctionProxy());
SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy()); SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());
......
serialization/tests/TestSerializeIntegrator.cpp
View file @ 51b7f9e2
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2010 Stanford University and the Authors. * * Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman, Yutong Zhao * * Authors: Peter Eastman, Yutong Zhao *
* Contributors: * * Contributors: *
* * * *
...@@ -32,6 +32,7 @@ ...@@ -32,6 +32,7 @@
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
#include "openmm/BrownianIntegrator.h" #include "openmm/BrownianIntegrator.h"
#include "openmm/CompoundIntegrator.h"
#include "openmm/CustomIntegrator.h" #include "openmm/CustomIntegrator.h"
#include "openmm/LangevinIntegrator.h" #include "openmm/LangevinIntegrator.h"
#include "openmm/VariableLangevinIntegrator.h" #include "openmm/VariableLangevinIntegrator.h"
...@@ -185,6 +186,29 @@ void testSerializeCustomIntegrator() { ...@@ -185,6 +186,29 @@ void testSerializeCustomIntegrator() {
delete intg2; delete intg2;
} }
void testSerializeCompoundIntegrator() {
CompoundIntegrator integ;
integ.addIntegrator(new LangevinIntegrator(372.4, 1.234, 0.0018));
integ.addIntegrator(new VerletIntegrator(0.002));
integ.setCurrentIntegrator(1);
stringstream ss;
XmlSerializer::serialize<Integrator>(&integ, "CompoundIntegrator", ss);
CompoundIntegrator *integ2 = dynamic_cast<CompoundIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
ASSERT_EQUAL(integ.getCurrentIntegrator(), integ2->getCurrentIntegrator());
LangevinIntegrator& langevin1 = dynamic_cast<LangevinIntegrator&>(integ.getIntegrator(0));
LangevinIntegrator& langevin2 = dynamic_cast<LangevinIntegrator&>(integ2->getIntegrator(0));
ASSERT_EQUAL(langevin1.getConstraintTolerance(), langevin2.getConstraintTolerance());
ASSERT_EQUAL(langevin1.getStepSize(), langevin2.getStepSize());
ASSERT_EQUAL(langevin1.getTemperature(), langevin2.getTemperature());
ASSERT_EQUAL(langevin1.getFriction(), langevin2.getFriction());
ASSERT_EQUAL(langevin1.getRandomNumberSeed(), langevin2.getRandomNumberSeed());
VerletIntegrator& verlet1 = dynamic_cast<VerletIntegrator&>(integ.getIntegrator(1));
VerletIntegrator& verlet2 = dynamic_cast<VerletIntegrator&>(integ2->getIntegrator(1));
ASSERT_EQUAL(verlet1.getConstraintTolerance(), verlet2.getConstraintTolerance());
ASSERT_EQUAL(verlet1.getStepSize(), verlet2.getStepSize());
delete integ2;
}
int main() { int main() {
try { try {
testSerializeBrownianIntegrator(); testSerializeBrownianIntegrator();
...@@ -193,6 +217,7 @@ int main() { ...@@ -193,6 +217,7 @@ int main() {
testSerializeVariableLangevinIntegrator(); testSerializeVariableLangevinIntegrator();
testSerializeVariableVerletIntegrator(); testSerializeVariableVerletIntegrator();
testSerializeLangevinIntegrator(); testSerializeLangevinIntegrator();
testSerializeCompoundIntegrator();
} }
catch(const exception& e) { catch(const exception& e) {
return 1; return 1;
......
tests/TestCompoundIntegrator.h 0 → 100644
View file @ 51b7f9e2
/* -------------------------------------------------------------------------- *
* 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) 2015 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/internal/AssertionUtilities.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CompoundIntegrator.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testChangingIntegrator() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.5, 1);
system.addForce(bonds);
CompoundIntegrator integrator;
integrator.addIntegrator(new VerletIntegrator(0.01));
integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.011));
integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.012));
Context context(system, integrator, platform);
ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
for (int iteration = 0; iteration < 2; ++iteration) {
context.setPositions(positions);
// First integrate with the Verlet integrator and compare it to the analytical solution.
const double freq = 1.0;
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 100; ++i) {
state = context.getState(State::Positions | State::Velocities | State::Energy);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
double expectedSpeed = -0.5*freq*std::sin(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1);
}
ASSERT_EQUAL_TOL(100*0.01, context.getState(0).getTime(), 1e-5);
// Switch to the Langevin integrator and make sure that it heats up.
integrator.setCurrentIntegrator(1);
integrator.step(100);
double ke = 0.0;
for (int i = 0; i < 1000; ++i) {
integrator.step(10);
state = context.getState(State::Energy);
ke += state.getKineticEnergy();
}
double expectedKE = 0.5*2*3*BOLTZ*300.0;
ASSERT_USUALLY_EQUAL_TOL(expectedKE, ke/1000, 0.1);
ASSERT_EQUAL_TOL(100*0.01+10100*0.011, context.getState(0).getTime(), 1e-5);
// Now reinitialize the context and repeat all of these tests to make sure that works correctly.
context.reinitialize();
integrator.setCurrentIntegrator(0);
}
}
void testChangingParameters() {
System system;
system.addParticle(1.0);
CompoundIntegrator integrator;
integrator.addIntegrator(new VerletIntegrator(0.01));
integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.02));
integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.03));
// Try getting and setting the step size for different component integrators.
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
ASSERT_EQUAL_TOL(0.01*(i+1), integrator.getStepSize(), 1e-7);
}
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
integrator.setStepSize(0.02*(i+1));
ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
}
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
}
// Try getting and setting the constraint tolerance for different component integrators.
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
ASSERT_EQUAL_TOL(1e-5, integrator.getConstraintTolerance(), 1e-7);
}
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
integrator.setConstraintTolerance(1e-4*(i+1));
ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
}
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
}
}
void testDifferentStepSizes() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.5, 1);
system.addForce(bonds);
CompoundIntegrator integrator;
integrator.addIntegrator(new VerletIntegrator(0.005));
integrator.addIntegrator(new VerletIntegrator(0.01));
Context context(system, integrator, platform);
ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// Integrate with the first Verlet integrator and compare it to the analytical solution.
const double freq = 1.0;
double expectedTime = 0;
for (int i = 0; i < 100; ++i) {
State state = context.getState(State::Positions);
double time = state.getTime();
ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
integrator.step(1);
expectedTime += 0.005;
}
// Now switch to the second Verlet integrator which has a different step size.
integrator.setCurrentIntegrator(1);
for (int i = 0; i < 100; ++i) {
State state = context.getState(State::Positions);
double time = state.getTime();
ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
integrator.step(1);
expectedTime += 0.01;
}
// Finally, switch back to the first one again.
integrator.setCurrentIntegrator(0);
for (int i = 0; i < 100; ++i) {
State state = context.getState(State::Positions);
double time = state.getTime();
ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
integrator.step(1);
expectedTime += 0.005;
}
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testChangingIntegrator();
testChangingParameters();
testDifferentStepSizes();
runPlatformTests();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
tests/TestEnforcePeriodicBox.cpp 0 → 100644
View file @ 51b7f9e2
/* -------------------------------------------------------------------------- *
* 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) 2010-2015 Stanford University and the Authors. *
* Authors: Robert McGibbon *
* 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/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
using namespace OpenMM;
using namespace std;
void testTruncatedOctahedron() {
const int numMolecules = 5;
const int numParticles = numMolecules*2;
const float cutoff = 2.0;
Vec3 a(6.7929, 0, 0);
Vec3 b(-2.264163559406279, 6.404455775962287, 0);
Vec3 c(-2.264163559406279, -3.2019384603140684, 5.54658849047036);
System system;
system.setDefaultPeriodicBoxVectors(a, b, c);
NonbondedForce* force = new NonbondedForce();
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
force->setCutoffDistance(cutoff);
force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
force->addParticle(-1, 0.2, 0.2);
force->addParticle(1, 0.2, 0.2);
positions[2*i] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[2*i+1] = positions[2*i] + Vec3(1.0, 0.0, 0.0);
system.addConstraint(2*i, 2*i+1, 1.0);
}
system.addForce(force);
VerletIntegrator integrator(0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
context.setPositions(positions);
State initialState = context.getState(State::Positions | State::Energy, true);
double initialEnergy = initialState.getPotentialEnergy();
context.setState(initialState);
State finalState = context.getState(State::Positions | State::Energy, true);
double finalEnergy = finalState.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, finalEnergy, 1e-4);
}
int main(int argc, char* argv[]) {
try {
testTruncatedOctahedron();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
wrappers/python/simtk/openmm/amd.py
View file @ 51b7f9e2
...@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors. ...@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
Authors: Peter Eastman, Steffen Lindert Authors: Peter Eastman, Steffen Lindert
Contributors: Contributors:
Permission is hereby granted, free of charge, to any person obtaining a Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"), copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense, the rights to use, copy, modify, merge, publish, distribute, sublicense,
...@@ -37,22 +37,26 @@ from simtk.unit import kilojoules_per_mole, is_quantity ...@@ -37,22 +37,26 @@ from simtk.unit import kilojoules_per_mole, is_quantity
class AMDIntegrator(CustomIntegrator): class AMDIntegrator(CustomIntegrator):
"""AMDIntegrator implements the aMD integration algorithm. """AMDIntegrator implements the aMD integration algorithm.
The system is integrated based on a modified potential. Whenever the energy V(r) is less than a The system is integrated based on a modified potential. Whenever the energy V(r) is less than a
cutoff value E, the following effective potential is used: cutoff value E, the following effective potential is used:
V*(r) = V(r) + (E-V(r))^2 / (alpha+E-V(r)) V*(r) = V(r) + (E-V(r))^2 / (alpha+E-V(r))
For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007). For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
""" """
def __init__(self, dt, alpha, E): def __init__(self, dt, alpha, E):
"""Create an AMDIntegrator. """Create an AMDIntegrator.
Parameters: Parameters
- dt (time) The integration time step to use ----------
- alpha (energy) The alpha parameter to use dt : time
- E (energy) The energy cutoff to use The integration time step to use
alpha : energy
The alpha parameter to use
E : energy
The energy cutoff to use
""" """
CustomIntegrator.__init__(self, dt) CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alpha", alpha) self.addGlobalVariable("alpha", alpha)
...@@ -64,23 +68,23 @@ class AMDIntegrator(CustomIntegrator): ...@@ -64,23 +68,23 @@ class AMDIntegrator(CustomIntegrator):
self.addComputePerDof("x", "x+dt*v") self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions() self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt") self.addComputePerDof("v", "(x-oldx)/dt")
def getAlpha(self): def getAlpha(self):
"""Get the value of alpha for the integrator.""" """Get the value of alpha for the integrator."""
return self.getGlobalVariable(0)*kilojoules_per_mole return self.getGlobalVariable(0)*kilojoules_per_mole
def setAlpha(self, alpha): def setAlpha(self, alpha):
"""Set the value of alpha for the integrator.""" """Set the value of alpha for the integrator."""
self.setGlobalVariable(0, alpha) self.setGlobalVariable(0, alpha)
def getE(self): def getE(self):
"""Get the energy threshold E for the integrator.""" """Get the energy threshold E for the integrator."""
return self.getGlobalVariable(1)*kilojoules_per_mole return self.getGlobalVariable(1)*kilojoules_per_mole
def setE(self, E): def setE(self, E):
"""Set the energy threshold E for the integrator.""" """Set the energy threshold E for the integrator."""
self.setGlobalVariable(1, E) self.setGlobalVariable(1, E)
def getEffectiveEnergy(self, energy): def getEffectiveEnergy(self, energy):
"""Given the actual potential energy of the system, return the value of the effective potential.""" """Given the actual potential energy of the system, return the value of the effective potential."""
alpha = self.getAlpha() alpha = self.getAlpha()
...@@ -94,21 +98,26 @@ class AMDIntegrator(CustomIntegrator): ...@@ -94,21 +98,26 @@ class AMDIntegrator(CustomIntegrator):
class AMDForceGroupIntegrator(CustomIntegrator): class AMDForceGroupIntegrator(CustomIntegrator):
"""AMDForceGroupIntegrator implements a single boost aMD integration algorithm. """AMDForceGroupIntegrator implements a single boost aMD integration algorithm.
This is similar to AMDIntegrator, but is applied based on the energy of a single force group This is similar to AMDIntegrator, but is applied based on the energy of a single force group
(typically representing torsions). (typically representing torsions).
For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007). For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
""" """
def __init__(self, dt, group, alphaGroup, EGroup): def __init__(self, dt, group, alphaGroup, EGroup):
"""Create a AMDForceGroupIntegrator. """Create a AMDForceGroupIntegrator.
Parameters: Parameters
- dt (time) The integration time step to use ----------
- group (int) The force group to apply the boost to dt : time
- alphaGroup (energy) The alpha parameter to use for the boosted force group The integration time step to use
- EGroup (energy) The energy cutoff to use for the boosted force group group : int
The force group to apply the boost to
alphaGroup : energy
The alpha parameter to use for the boosted force group
EGroup : energy
The energy cutoff to use for the boosted force group
""" """
CustomIntegrator.__init__(self, dt) CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaGroup", alphaGroup) self.addGlobalVariable("alphaGroup", alphaGroup)
...@@ -124,29 +133,35 @@ class AMDForceGroupIntegrator(CustomIntegrator): ...@@ -124,29 +133,35 @@ class AMDForceGroupIntegrator(CustomIntegrator):
self.addComputePerDof("x", "x+dt*v") self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions() self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt") self.addComputePerDof("v", "(x-oldx)/dt")
def getAlphaGroup(self): def getAlphaGroup(self):
"""Get the value of alpha for the boosted force group.""" """Get the value of alpha for the boosted force group."""
return self.getGlobalVariable(0)*kilojoules_per_mole return self.getGlobalVariable(0)*kilojoules_per_mole
def setAlphaGroup(self, alpha): def setAlphaGroup(self, alpha):
"""Set the value of alpha for the boosted force group.""" """Set the value of alpha for the boosted force group."""
self.setGlobalVariable(0, alpha) self.setGlobalVariable(0, alpha)
def getEGroup(self): def getEGroup(self):
"""Get the energy threshold E for the boosted force group.""" """Get the energy threshold E for the boosted force group."""
return self.getGlobalVariable(1)*kilojoules_per_mole return self.getGlobalVariable(1)*kilojoules_per_mole
def setEGroup(self, E): def setEGroup(self, E):
"""Set the energy threshold E for the boosted force group.""" """Set the energy threshold E for the boosted force group."""
self.setGlobalVariable(1, E) self.setGlobalVariable(1, E)
def getEffectiveEnergy(self, groupEnergy): def getEffectiveEnergy(self, groupEnergy):
"""Given the actual group energy of the system, return the value of the effective potential. """Given the actual group energy of the system, return the value of the effective potential.
Parameters: Parameters
- groupEnergy (energy): the actual potential energy of the boosted force group ----------
Returns: the value of the effective potential groupEnergy : energy
the actual potential energy of the boosted force group
Returns
-------
energy
the value of the effective potential
""" """
alphaGroup = self.getAlphaGroup() alphaGroup = self.getAlphaGroup()
EGroup = self.getEGroup() EGroup = self.getEGroup()
...@@ -161,24 +176,31 @@ class AMDForceGroupIntegrator(CustomIntegrator): ...@@ -161,24 +176,31 @@ class AMDForceGroupIntegrator(CustomIntegrator):
class DualAMDIntegrator(CustomIntegrator): class DualAMDIntegrator(CustomIntegrator):
"""DualAMDIntegrator implements a dual boost aMD integration algorithm. """DualAMDIntegrator implements a dual boost aMD integration algorithm.
This is similar to AMDIntegrator, but two different boosts are applied to the potential: This is similar to AMDIntegrator, but two different boosts are applied to the potential:
one based on the total energy, and one based on the energy of a single force group one based on the total energy, and one based on the energy of a single force group
(typically representing torsions). (typically representing torsions).
For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007). For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
""" """
def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup): def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup):
"""Create a DualAMDIntegrator. """Create a DualAMDIntegrator.
Parameters: Parameters
- dt (time) The integration time step to use ----------
- group (int) The force group to apply the second boost to dt : time
- alphaTotal (energy) The alpha parameter to use for the total energy The integration time step to use
- ETotal (energy) The energy cutoff to use for the total energy group : int
- alphaGroup (energy) The alpha parameter to use for the boosted force group The force group to apply the second boost to
- EGroup (energy) The energy cutoff to use for the boosted force group alphaTotal : energy
The alpha parameter to use for the total energy
ETotal : energy
The energy cutoff to use for the total energy
alphaGroup : energy
The alpha parameter to use for the boosted force group
EGroup : energy
The energy cutoff to use for the boosted force group
""" """
CustomIntegrator.__init__(self, dt) CustomIntegrator.__init__(self, dt)
self.addGlobalVariable("alphaTotal", alphaTotal) self.addGlobalVariable("alphaTotal", alphaTotal)
...@@ -201,46 +223,53 @@ class DualAMDIntegrator(CustomIntegrator): ...@@ -201,46 +223,53 @@ class DualAMDIntegrator(CustomIntegrator):
self.addComputePerDof("x", "x+dt*v") self.addComputePerDof("x", "x+dt*v")
self.addConstrainPositions() self.addConstrainPositions()
self.addComputePerDof("v", "(x-oldx)/dt") self.addComputePerDof("v", "(x-oldx)/dt")
def getAlphaTotal(self): def getAlphaTotal(self):
"""Get the value of alpha for the total energy.""" """Get the value of alpha for the total energy."""
return self.getGlobalVariable(0)*kilojoules_per_mole return self.getGlobalVariable(0)*kilojoules_per_mole
def setAlphaTotal(self, alpha): def setAlphaTotal(self, alpha):
"""Set the value of alpha for the total energy.""" """Set the value of alpha for the total energy."""
self.setGlobalVariable(0, alpha) self.setGlobalVariable(0, alpha)
def getETotal(self): def getETotal(self):
"""Get the energy threshold E for the total energy.""" """Get the energy threshold E for the total energy."""
return self.getGlobalVariable(1)*kilojoules_per_mole return self.getGlobalVariable(1)*kilojoules_per_mole
def setETotal(self, E): def setETotal(self, E):
"""Set the energy threshold E for the total energy.""" """Set the energy threshold E for the total energy."""
self.setGlobalVariable(1, E) self.setGlobalVariable(1, E)
def getAlphaGroup(self): def getAlphaGroup(self):
"""Get the value of alpha for the boosted force group.""" """Get the value of alpha for the boosted force group."""
return self.getGlobalVariable(2)*kilojoules_per_mole return self.getGlobalVariable(2)*kilojoules_per_mole
def setAlphaGroup(self, alpha): def setAlphaGroup(self, alpha):
"""Set the value of alpha for the boosted force group.""" """Set the value of alpha for the boosted force group."""
self.setGlobalVariable(2, alpha) self.setGlobalVariable(2, alpha)
def getEGroup(self): def getEGroup(self):
"""Get the energy threshold E for the boosted force group.""" """Get the energy threshold E for the boosted force group."""
return self.getGlobalVariable(3)*kilojoules_per_mole return self.getGlobalVariable(3)*kilojoules_per_mole
def setEGroup(self, E): def setEGroup(self, E):
"""Set the energy threshold E for the boosted force group.""" """Set the energy threshold E for the boosted force group."""
self.setGlobalVariable(3, E) self.setGlobalVariable(3, E)
def getEffectiveEnergy(self, totalEnergy, groupEnergy): def getEffectiveEnergy(self, totalEnergy, groupEnergy):
"""Given the actual potential energy of the system, return the value of the effective potential. """Given the actual potential energy of the system, return the value of the effective potential.
Parameters: Parameters
- totalEnergy (energy): the actual potential energy of the whole system ----------
- groupEnergy (energy): the actual potential energy of the boosted force group totalEnergy : energy
Returns: the value of the effective potential the actual potential energy of the whole system
groupEnergy : energy
the actual potential energy of the boosted force group
Returns
-------
energy
the value of the effective potential
""" """
alphaTotal = self.getAlphaTotal() alphaTotal = self.getAlphaTotal()
ETotal = self.getETotal() ETotal = self.getETotal()
......
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
View file @ 51b7f9e2
...@@ -60,12 +60,17 @@ class AmberInpcrdFile(object): ...@@ -60,12 +60,17 @@ class AmberInpcrdFile(object):
def __init__(self, file, loadVelocities=None, loadBoxVectors=None): def __init__(self, file, loadVelocities=None, loadBoxVectors=None):
"""Load an inpcrd file. """Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions. An inpcrd file contains atom positions and, optionally, velocities and
periodic box dimensions.
Parameters:
- file (string) the name of the file to load Parameters
- loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present ----------
- loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present file : str
The name of the file to load
loadVelocities : bool
Deprecated. Velocities are loaded automatically if present
loadBoxVectors : bool
Deprecated. Box vectors are loaded automatically if present
""" """
self.file = file self.file = file
if loadVelocities is not None or loadBoxVectors is not None: if loadVelocities is not None or loadBoxVectors is not None:
...@@ -84,8 +89,11 @@ class AmberInpcrdFile(object): ...@@ -84,8 +89,11 @@ class AmberInpcrdFile(object):
def getPositions(self, asNumpy=False): def getPositions(self, asNumpy=False):
"""Get the atomic positions. """Get the atomic positions.
Parameters: Parameters
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s ----------
asNumpy : bool=False
if true, the values are returned as a numpy array instead of a list
of Vec3s
""" """
if asNumpy: if asNumpy:
if self._numpyPositions is None: if self._numpyPositions is None:
...@@ -97,8 +105,10 @@ class AmberInpcrdFile(object): ...@@ -97,8 +105,10 @@ class AmberInpcrdFile(object):
def getVelocities(self, asNumpy=False): def getVelocities(self, asNumpy=False):
"""Get the atomic velocities. """Get the atomic velocities.
Parameters: Parameters
- asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s ----------
asNumpy : bool=False
if true, the vectors are returned as numpy arrays instead of Vec3s
""" """
if self.velocities is None: if self.velocities is None:
raise AttributeError('velocities not found in %s' % self.file) raise AttributeError('velocities not found in %s' % self.file)
...@@ -112,8 +122,11 @@ class AmberInpcrdFile(object): ...@@ -112,8 +122,11 @@ class AmberInpcrdFile(object):
def getBoxVectors(self, asNumpy=False): def getBoxVectors(self, asNumpy=False):
"""Get the periodic box vectors. """Get the periodic box vectors.
Parameters: Parameters
- asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s ----------
asNumpy : bool=False
if true, the values are returned as a numpy array instead of a list
of Vec3s
""" """
if self.boxVectors is None: if self.boxVectors is None:
raise AttributeError('Box information not found in %s' % self.file) raise AttributeError('Box information not found in %s' % self.file)
......
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ 51b7f9e2
...@@ -151,29 +151,52 @@ class AmberPrmtopFile(object): ...@@ -151,29 +151,52 @@ class AmberPrmtopFile(object):
implicitSolventKappa=None, temperature=298.15*unit.kelvin, implicitSolventKappa=None, temperature=298.15*unit.kelvin,
soluteDielectric=1.0, solventDielectric=78.5, soluteDielectric=1.0, solventDielectric=78.5,
removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005): removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005):
"""Construct an OpenMM System representing the topology described by this prmtop file. """Construct an OpenMM System representing the topology described by this
prmtop file.
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions. Allowed values are Parameters
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME. ----------
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions nonbondedMethod : object=NoCutoff
- constraints (object=None) Specifies which bonds angles should be implemented with constraints. The method to use for nonbonded interactions. Allowed values are
Allowed values are None, HBonds, AllBonds, or HAngles. NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument nonbondedCutoff : distance=1*nanometer
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2. The cutoff distance to use for nonbonded interactions
- implicitSolventSaltConc (float=0.0*unit.moles/unit.liter) The salt concentration for GB constraints : object=None
calculations (modelled as a debye screening parameter). It is converted to the debye length (kappa) Specifies which bonds angles should be implemented with constraints.
using the provided temperature and solventDielectric Allowed values are None, HBonds, AllBonds, or HAngles.
- temperature (float=300*kelvin) Temperature of the system. Only used to compute the Debye length from rigidWater : boolean=True
implicitSolventSoltConc If true, water molecules will be fully rigid regardless of the value
- implicitSolventKappa (float units of 1/length) If this value is set, implicitSolventSaltConc will be ignored. passed for the constraints argument
- soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model. implicitSolvent : object=None
- solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model. If not None, the implicit solvent model to use. Allowed values are
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System HCT, OBC1, OBC2, GBn, or GBn2.
- hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is implicitSolventSaltConc : float=0.0*unit.moles/unit.liter
subtracted from the heavy atom to keep their total mass the same. The salt concentration for GB calculations (modelled as a debye
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME. screening parameter). It is converted to the debye length (kappa)
Returns: the newly created System using the provided temperature and solventDielectric
temperature : float=300*kelvin
Temperature of the system. Only used to compute the Debye length
from implicitSolventSoltConc
implicitSolventKappa : float units of 1/length
If this value is set, implicitSolventSaltConc will be ignored.
soluteDielectric : float=1.0
The solute dielectric constant to use in the implicit solvent model.
solventDielectric : float=78.5
The solvent dielectric constant to use in the implicit solvent
model.
removeCMMotion : boolean=True
If true, a CMMotionRemover will be added to the System
hydrogenMass : mass=None
The mass to use for hydrogen atoms bound to heavy atoms. Any mass
added to a hydrogen is subtracted from the heavy atom to keep their
total mass the same.
ewaldErrorTolerance : float=0.0005
The error tolerance to use if nonbondedMethod is Ewald or PME.
Returns
-------
System
the newly created System
""" """
if self._prmtop.chamber: if self._prmtop.chamber:
raise ValueError("CHAMBER-style topology file detected. CHAMBER " raise ValueError("CHAMBER-style topology file detected. CHAMBER "
......
wrappers/python/simtk/openmm/app/charmmcrdfiles.py
View file @ 51b7f9e2
""" """
Provides a class for parsing CHARMM-style coordinate files, namely CHARMM .crd Provides a class for parsing CHARMM-style coordinate files, namely CHARMM .crd
(coordinate) files and CHARMM .rst (restart) file. Uses CharmmFile class in (coordinate) files and CHARMM .rst (restart) file. Uses CharmmFile class in
_charmmfile.py for reading files _charmmfile.py for reading files
This file is part of the OpenMM molecular simulation toolkit originating from This file is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of Biological Simbios, the NIH National Center for Physics-Based Simulation of Biological
...@@ -49,12 +49,17 @@ class CharmmCrdFile(object): ...@@ -49,12 +49,17 @@ class CharmmCrdFile(object):
Reads and parses a CHARMM coordinate file (.crd) into its components, Reads and parses a CHARMM coordinate file (.crd) into its components,
namely the coordinates, CHARMM atom types, resid, resname, etc. namely the coordinates, CHARMM atom types, resid, resname, etc.
Main attributes: Attributes
- natom (int) : Number of atoms in the system ----------
- resname (list) : Names of all residues natom : int
- positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...] Number of atoms in the system
resname : list
Example: Names of all residues
positions : list
All cartesian coordinates [x1, y1, z1, x2, ...]
Examples
--------
>>> chm = CharmmCrdFile('testfiles/1tnm.crd') >>> chm = CharmmCrdFile('testfiles/1tnm.crd')
>>> print '%d atoms; %d coords' % (chm.natom, len(chm.positions)) >>> print '%d atoms; %d coords' % (chm.natom, len(chm.positions))
1414 atoms; 1414 coords 1414 atoms; 1414 coords
...@@ -91,15 +96,15 @@ class CharmmCrdFile(object): ...@@ -91,15 +96,15 @@ class CharmmCrdFile(object):
intitle = False intitle = False
elif line.strip()[0] != '*': elif line.strip()[0] != '*':
intitle = False intitle = False
else: else:
intitle = True intitle = True
while len(line.strip()) == 0: # Skip whitespace while len(line.strip()) == 0: # Skip whitespace
line = crdfile.readline() line = crdfile.readline()
try: try:
self.natom = int(line.strip().split()[0]) self.natom = int(line.strip().split()[0])
for row in range(self.natom): for row in range(self.natom):
line = crdfile.readline().strip().split() line = crdfile.readline().strip().split()
self.atomno.append(int(line[0])) self.atomno.append(int(line[0]))
...@@ -131,14 +136,21 @@ class CharmmRstFile(object): ...@@ -131,14 +136,21 @@ class CharmmRstFile(object):
Reads and parses data, velocities and coordinates from a CHARMM restart Reads and parses data, velocities and coordinates from a CHARMM restart
file (.rst) of file name 'fname' into class attributes file (.rst) of file name 'fname' into class attributes
Main attributes: Attributes
- natom (int) : Number of atoms in the system ----------
- resname (list) : Names of all residues natom : int
- positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...] Number of atoms in the system
- positionsold (list) : Old cartesian coordinates resname : list
- velocities (list) : List of all cartesian velocities Names of all residues
positions : list
Example: All cartesian coordinates [x1, y1, z1, x2, ...]
positionsold : list
Old cartesian coordinates
velocities : list
List of all cartesian velocities
Examples
--------
>>> chm = CharmmRstFile('testfiles/sample-charmm.rst') >>> chm = CharmmRstFile('testfiles/sample-charmm.rst')
>>> print chm.header[0] >>> print chm.header[0]
REST 37 1 REST 37 1
...@@ -155,7 +167,7 @@ class CharmmRstFile(object): ...@@ -155,7 +167,7 @@ class CharmmRstFile(object):
self.positionsold = [] self.positionsold = []
self.positions = [] self.positions = []
self.velocities = [] self.velocities = []
self.ff_version = 0 self.ff_version = 0
self.natom = 0 self.natom = 0
self.npriv = 0 self.npriv = 0
...@@ -169,7 +181,7 @@ class CharmmRstFile(object): ...@@ -169,7 +181,7 @@ class CharmmRstFile(object):
def _parse(self, fname): def _parse(self, fname):
crdfile = open(fname, 'r') crdfile = open(fname, 'r')
readingHeader = True readingHeader = True
while readingHeader: while readingHeader:
line = crdfile.readline() line = crdfile.readline()
...@@ -177,7 +189,7 @@ class CharmmRstFile(object): ...@@ -177,7 +189,7 @@ class CharmmRstFile(object):
raise CharmmFileError('Premature end of file') raise CharmmFileError('Premature end of file')
line = line.strip() line = line.strip()
words = line.split() words = line.split()
if len(line) != 0: if len(line) != 0:
if words[0] == 'ENERGIES' or words[0] == '!ENERGIES': if words[0] == 'ENERGIES' or words[0] == '!ENERGIES':
readingHeader = False readingHeader = False
else: else:
...@@ -191,14 +203,14 @@ class CharmmRstFile(object): ...@@ -191,14 +203,14 @@ class CharmmRstFile(object):
if line[0][0:5] == 'NATOM' or line[0][0:6] == '!NATOM': if line[0][0:5] == 'NATOM' or line[0][0:6] == '!NATOM':
try: try:
line = self.header[row+1].strip().split() line = self.header[row+1].strip().split()
self.natom = int(line[0]) self.natom = int(line[0])
self.npriv = int(line[1]) # num. previous steps self.npriv = int(line[1]) # num. previous steps
self.nstep = int(line[2]) # num. steps in file self.nstep = int(line[2]) # num. steps in file
self.nsavc = int(line[3]) # coord save frequency self.nsavc = int(line[3]) # coord save frequency
self.nsavv = int(line[4]) # velocities " self.nsavv = int(line[4]) # velocities "
self.jhstrt = int(line[5]) # Num total steps? self.jhstrt = int(line[5]) # Num total steps?
break break
except (ValueError, IndexError) as e: except (ValueError, IndexError) as e:
raise CharmmFileError('Problem parsing CHARMM restart') raise CharmmFileError('Problem parsing CHARMM restart')
...@@ -244,7 +256,7 @@ class CharmmRstFile(object): ...@@ -244,7 +256,7 @@ class CharmmRstFile(object):
if len(line) < 3*CHARMMLEN: if len(line) < 3*CHARMMLEN:
raise CharmmFileError("Less than 3 coordinates present in " raise CharmmFileError("Less than 3 coordinates present in "
"coordinate row or positions may be " "coordinate row or positions may be "
"truncated.") "truncated.")
line = line.replace('D','E') # CHARMM uses 'D' for exponentials line = line.replace('D','E') # CHARMM uses 'D' for exponentials
......
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 51b7f9e2
...@@ -51,41 +51,43 @@ class CharmmParameterSet(object): ...@@ -51,41 +51,43 @@ class CharmmParameterSet(object):
the information found in the MASS section of the CHARMM topology file the information found in the MASS section of the CHARMM topology file
(TOP/RTF) and all of the information in the parameter files (PAR) (TOP/RTF) and all of the information in the parameter files (PAR)
Parameters: Parameters
- filenames : List of topology, parameter, and stream files to load into ----------
the parameter set. The following file type suffixes are recognized. filenames : List of topology, parameter, and stream files to load into the parameter set.
Unrecognized file types raise a TypeError The following file type suffixes are recognized. Unrecognized file types raise a TypeError
.rtf, .top -- Residue topology file * .rtf, .top -- Residue topology file
.par, .prm -- Parameter file * .par, .prm -- Parameter file
.str -- Stream file * .str -- Stream file
.inp -- If "par" is in the file name, it is a parameter file. If * .inp -- If "par" is in the file name, it is a parameter file. If
"top" is in the file name, it is a topology file. Otherwise, "top" is in the file name, it is a topology file. Otherwise,
raise TypeError raise TypeError
Attributes: Attributes
All type lists are dictionaries whose keys are tuples (with however ----------
many elements are needed to define that type of parameter). The types All type lists are dictionaries whose keys are tuples (with however
that can be in any order are SORTED. many elements are needed to define that type of parameter). The types
that can be in any order are SORTED.
- atom_types_str
- atom_types_int - atom_types_str
- atom_types_tuple - atom_types_int
- bond_types - atom_types_tuple
- angle_types - bond_types
- urey_bradley_types - angle_types
- dihedral_types - urey_bradley_types
- improper_types - dihedral_types
- cmap_types - improper_types
- nbfix_types - cmap_types
- nbfix_types
The dihedral types can be multiterm, so the values for each dict key is
actually a list of DihedralType instances. The atom_types are dicts that The dihedral types can be multiterm, so the values for each dict key is
match the name (str), number (int), or (name, number) tuple (tuple) to actually a list of DihedralType instances. The atom_types are dicts that
the atom type. The tuple is guaranteed to be the most robust, although match the name (str), number (int), or (name, number) tuple (tuple) to
when only the integer or string is available the other dictionaries are the atom type. The tuple is guaranteed to be the most robust, although
helpful when only the integer or string is available the other dictionaries are
helpful
Example:
Examples
--------
>>> params = CharmmParameterSet('charmm22.top', 'charmm22.par', 'file.str') >>> params = CharmmParameterSet('charmm22.top', 'charmm22.par', 'file.str')
""" """
...@@ -113,7 +115,7 @@ class CharmmParameterSet(object): ...@@ -113,7 +115,7 @@ class CharmmParameterSet(object):
self.cmap_types = dict() self.cmap_types = dict()
self.nbfix_types = dict() self.nbfix_types = dict()
self.parametersets = [] self.parametersets = []
# Load all of the files # Load all of the files
tops, pars, strs = [], [], [] tops, pars, strs = [], [], []
for arg in args: for arg in args:
...@@ -150,23 +152,30 @@ class CharmmParameterSet(object): ...@@ -150,23 +152,30 @@ class CharmmParameterSet(object):
Instantiates a CharmmParameterSet from a Topology file and a Parameter Instantiates a CharmmParameterSet from a Topology file and a Parameter
file (or just a Parameter file if it has all information) file (or just a Parameter file if it has all information)
Parameters: Parameters
- tfile (str) : Name of the Topology (RTF/TOP) file -----------
- pfile (str) : Name of the Parameter (PAR) file tfile : str
- sfiles (list of str) : List or tuple of stream (STR) file names. Name of the Topology (RTF/TOP) file
- permissive (bool) : Accept non-bonbded parameters for undefined pfile : str
atom types (default False) Name of the Parameter (PAR) file
sfiles : list of str
Returns: List or tuple of stream (STR) file names.
permissive : bool=False
Accept non-bonbded parameters for undefined atom types
Returns
-------
CharmmParameterSet
New CharmmParameterSet populated with the parameters found in the New CharmmParameterSet populated with the parameters found in the
provided files. provided files.
Notes: Notes
The RTF file is read first (if provided), followed by the PAR file, -----
followed by the list of stream files (in the order they are The RTF file is read first (if provided), followed by the PAR file,
provided). Parameters in each stream file will overwrite those that followed by the list of stream files (in the order they are
came before (or simply append to the existing set if they are provided). Parameters in each stream file will overwrite those that
different) came before (or simply append to the existing set if they are
different)
""" """
inst = cls() inst = cls()
if tfile is not None: if tfile is not None:
...@@ -183,21 +192,24 @@ class CharmmParameterSet(object): ...@@ -183,21 +192,24 @@ class CharmmParameterSet(object):
return inst return inst
def readParameterFile(self, pfile, permissive=False): def readParameterFile(self, pfile, permissive=False):
""" """Reads all of the parameters from a parameter file. Versions 36 and later
Reads all of the parameters from a parameter file. Versions 36 and of the CHARMM force field files have an ATOMS section defining all of
later of the CHARMM force field files have an ATOMS section defining the atom types. Older versions need to load this information from the
all of the atom types. Older versions need to load this information RTF/TOP files.
from the RTF/TOP files.
Parameters
Parameters: ----------
- pfile (str) : Name of the CHARMM PARameter file to read pfile : str
- permissive (bool) : Accept non-bonbded parameters for undefined Name of the CHARMM PARameter file to read
atom types (default False) permissive : bool
Accept non-bonbded parameters for undefined atom types (default:
Notes: The atom types must all be loaded by the end of this routine. False).
Either supply a PAR file with atom definitions in them or read in a
RTF/TOP file first. Failure to do so will result in a raised Notes
RuntimeError. -----
The atom types must all be loaded by the end of this routine. Either
supply a PAR file with atom definitions in them or read in a RTF/TOP
file first. Failure to do so will result in a raised RuntimeError.
""" """
conv = CharmmParameterSet._convert conv = CharmmParameterSet._convert
if isinstance(pfile, str): if isinstance(pfile, str):
...@@ -353,7 +365,7 @@ class CharmmParameterSet(object): ...@@ -353,7 +365,7 @@ class CharmmParameterSet(object):
if dtype.per == dihedral.per: if dtype.per == dihedral.per:
# Replace. Warn if they are different # Replace. Warn if they are different
if dtype != dihedral: if dtype != dihedral:
warnings.warn('Replacing dihedral %r with %r' % warnings.warn('Replacing dihedral %r with %r' %
(dtype, dihedral)) (dtype, dihedral))
self.dihedral_types[key] self.dihedral_types[key]
replaced = True replaced = True
...@@ -487,7 +499,7 @@ class CharmmParameterSet(object): ...@@ -487,7 +499,7 @@ class CharmmParameterSet(object):
ty = CmapType(current_cmap_res, current_cmap_data) ty = CmapType(current_cmap_res, current_cmap_data)
self.cmap_types[current_cmap] = ty self.cmap_types[current_cmap] = ty
# If in permissive mode create an atomtype for every type used in # If in permissive mode create an atomtype for every type used in
# the nonbonded parameters. This is a work-around for when all that's # the nonbonded parameters. This is a work-around for when all that's
# available is a CHARMM22 inp file, which has no ATOM/MASS fields # available is a CHARMM22 inp file, which has no ATOM/MASS fields
...@@ -499,7 +511,7 @@ class CharmmParameterSet(object): ...@@ -499,7 +511,7 @@ class CharmmParameterSet(object):
for key in nonbonded_types: for key in nonbonded_types:
if not key in self.atom_types_str: if not key in self.atom_types_str:
atype =AtomType(name=key, number=idx, mass= float('NaN'), atomic_number= 1 ) atype =AtomType(name=key, number=idx, mass= float('NaN'), atomic_number= 1 )
self.atom_types_str[key] = atype self.atom_types_str[key] = atype
self.atom_types_int[idx] = atype self.atom_types_int[idx] = atype
idx=idx+1 idx=idx+1
...@@ -518,14 +530,17 @@ class CharmmParameterSet(object): ...@@ -518,14 +530,17 @@ class CharmmParameterSet(object):
if own_handle: f.close() if own_handle: f.close()
def readTopologyFile(self, tfile): def readTopologyFile(self, tfile):
""" """Reads _only_ the atom type definitions from a topology file. This is
Reads _only_ the atom type definitions from a topology file. This is
unnecessary for versions 36 and later of the CHARMM force field. unnecessary for versions 36 and later of the CHARMM force field.
Parameters: Parameters
- tfile (str) : Name of the CHARMM TOPology file to read ----------
tfile : str
: Name of the CHARMM TOPology file to read
Note: The CHARMM TOPology file is also called a Residue Topology File Notes
-----
The CHARMM TOPology file is also called a Residue Topology File
""" """
conv = CharmmParameterSet._convert conv = CharmmParameterSet._convert
if isinstance(tfile, str): if isinstance(tfile, str):
...@@ -564,12 +579,13 @@ class CharmmParameterSet(object): ...@@ -564,12 +579,13 @@ class CharmmParameterSet(object):
if own_handle: f.close() if own_handle: f.close()
def readStreamFile(self, sfile): def readStreamFile(self, sfile):
""" """Reads RTF and PAR sections from a stream file and dispatches the
Reads RTF and PAR sections from a stream file and dispatches the
sections to readTopologyFile or readParameterFile sections to readTopologyFile or readParameterFile
Parameters: Parameters
- sfile (str or CharmmStreamFile) : Stream file to parse ----------
sfile : str or CharmmStreamFile
Stream file to parse
""" """
if isinstance(sfile, CharmmStreamFile): if isinstance(sfile, CharmmStreamFile):
f = sfile f = sfile
...@@ -594,14 +610,8 @@ class CharmmParameterSet(object): ...@@ -594,14 +610,8 @@ class CharmmParameterSet(object):
bond, angle, dihedral, improper, or cmap type will pair with EVERY key bond, angle, dihedral, improper, or cmap type will pair with EVERY key
in the type mapping dictionaries that points to the equivalent type in the type mapping dictionaries that points to the equivalent type
Returns: Example
- Returns the instance that is being condensed. -------
Notes:
The return value allows you to condense the types at construction
time.
Example:
>>> params = CharmmParameterSet('charmm.prm').condense() >>> params = CharmmParameterSet('charmm.prm').condense()
""" """
# First scan through all of the bond types # First scan through all of the bond types
...@@ -631,8 +641,10 @@ class CharmmParameterSet(object): ...@@ -631,8 +641,10 @@ class CharmmParameterSet(object):
""" """
Loops through the given dict and condenses all types. Loops through the given dict and condenses all types.
Parameter: Parameters
- typedict : Type dictionary to condense ----------
typedict
Type dictionary to condense
""" """
keylist = list(typedict.keys()) keylist = list(typedict.keys())
for i in range(len(keylist) - 1): for i in range(len(keylist) - 1):
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 51b7f9e2
...@@ -116,12 +116,8 @@ def _strip_optunit(thing, unit): ...@@ -116,12 +116,8 @@ def _strip_optunit(thing, unit):
_resre = re.compile(r'(\d+)([a-zA-Z]*)') _resre = re.compile(r'(\d+)([a-zA-Z]*)')
class CharmmPsfFile(object): class CharmmPsfFile(object):
""" """A chemical structure instantiated from CHARMM files.
A chemical structure instantiated from CHARMM files.
Example:
>>> cs = CharmmPsfFile("testfiles/test.psf")
This structure has numerous attributes that are lists of the elements of This structure has numerous attributes that are lists of the elements of
this structure, including atoms, bonds, torsions, etc. The attributes are this structure, including atoms, bonds, torsions, etc. The attributes are
- residue_list - residue_list
...@@ -138,13 +134,14 @@ class CharmmPsfFile(object): ...@@ -138,13 +134,14 @@ class CharmmPsfFile(object):
Additional attribute is available if a CharmmParameterSet is loaded into Additional attribute is available if a CharmmParameterSet is loaded into
this structure. this structure.
- urey_bradley_list - urey_bradley_list
The lengths of each of these lists gives the pointers (e.g., natom, nres, The lengths of each of these lists gives the pointers (e.g., natom, nres,
etc.) etc.)
Example: Examples
--------
>>> cs = CharmmPsfFile("testfiles/test.psf") >>> cs = CharmmPsfFile("testfiles/test.psf")
>>> len(cs.atom_list) >>> len(cs.atom_list)
33 33
...@@ -163,19 +160,21 @@ class CharmmPsfFile(object): ...@@ -163,19 +160,21 @@ class CharmmPsfFile(object):
CMAP_FORCE_GROUP = 5 CMAP_FORCE_GROUP = 5
NONBONDED_FORCE_GROUP = 6 NONBONDED_FORCE_GROUP = 6
GB_FORCE_GROUP = 6 GB_FORCE_GROUP = 6
@_catchindexerror @_catchindexerror
def __init__(self, psf_name): def __init__(self, psf_name):
""" """Opens and parses a PSF file, then instantiates a CharmmPsfFile
Opens and parses a PSF file, then instantiates a CharmmPsfFile
instance from the data. instance from the data.
Parameters: Parameters
psf_name (str) : Name of the PSF file (it must exist) ----------
psf_name : str
Exceptions Raised: Name of the PSF file (it must exist)
IOError : If file "psf_name" does not exist
CharmmPSFError: If any parsing errors are encountered Raises
------
IOError : If file "psf_name" does not exist
CharmmPSFError: If any parsing errors are encountered
""" """
conv = CharmmPsfFile._convert conv = CharmmPsfFile._convert
# Make sure the file exists # Make sure the file exists
...@@ -388,14 +387,17 @@ class CharmmPsfFile(object): ...@@ -388,14 +387,17 @@ class CharmmPsfFile(object):
@staticmethod @staticmethod
def _convert(string, type, message): def _convert(string, type, message):
""" """Converts a string to a specific type, making sure to raise
Converts a string to a specific type, making sure to raise
CharmmPSFError with the given message in the event of a failure. CharmmPSFError with the given message in the event of a failure.
Parameters: Parameters
- string (str) : Input string to process ----------
- type (type) : Type of data to convert to string : str
- message (str) : Error message to put in exception if failed Input string to process
type : type
Type of data to convert to
message : str
Error message to put in exception if failed
""" """
try: try:
return type(string) return type(string)
...@@ -405,23 +407,24 @@ class CharmmPsfFile(object): ...@@ -405,23 +407,24 @@ class CharmmPsfFile(object):
@staticmethod @staticmethod
def _parse_psf_section(psf): def _parse_psf_section(psf):
""" """This method parses a section of the PSF file
This method parses a section of the PSF file
Parameters
Parameters: ----------
- psf (CharmmFile) : Open file that is pointing to the first line psf : CharmmFile
of the section that is to be parsed Open file that is pointing to the first line of the section
that is to be parsed
Returns:
(title, pointers, data) Returns
--------
- title (str) : The label of the PSF section we are parsing str
- pointers (int/tuple of ints) : If one pointer is set, pointers is The label of the PSF section we are parsing
simply the integer that is value of that pointer. Otherwise int/tuple of ints
it is a tuple with every pointer value defined in the first If one pointer is set, pointers is simply the integer that is
line value of that pointer. Otherwise it is a tuple with every pointer
- data (list) : A list of all data in the parsed section converted value defined in the first line
to `dtype' list
A list of all data in the parsed section converted to `dtype'
""" """
conv = CharmmPsfFile._convert conv = CharmmPsfFile._convert
line = psf.readline() line = psf.readline()
...@@ -462,25 +465,25 @@ class CharmmPsfFile(object): ...@@ -462,25 +465,25 @@ class CharmmPsfFile(object):
return title, pointers, data return title, pointers, data
def loadParameters(self, parmset): def loadParameters(self, parmset):
""" """Loads parameters from a parameter set that was loaded via CHARMM RTF,
Loads parameters from a parameter set that was loaded via CHARMM RTF,
PAR, and STR files. PAR, and STR files.
Parameters: Parameters
- parmset (CharmmParameterSet) : List of all parameters ----------
parmset : CharmmParameterSet
Notes: List of all parameters
- If any parameters that are necessary cannot be found, a
MissingParameter exception is raised. Notes
-----
- If any dihedral or improper parameters cannot be found, I will try - If any parameters that are necessary cannot be found, a
inserting wildcards (at either end for dihedrals and as the two MissingParameter exception is raised.
central atoms in impropers) and see if that matches. Wild-cards - If any dihedral or improper parameters cannot be found, I will try
will apply ONLY if specific parameters cannot be found. inserting wildcards (at either end for dihedrals and as the two
central atoms in impropers) and see if that matches. Wild-cards
- This method will expand the dihedral_parameter_list attribute by will apply ONLY if specific parameters cannot be found.
adding a separate Dihedral object for each term for types that - This method will expand the dihedral_parameter_list attribute by
have a multi-term expansion adding a separate Dihedral object for each term for types that
have a multi-term expansion
""" """
# First load the atom types # First load the atom types
types_are_int = False types_are_int = False
...@@ -588,13 +591,22 @@ class CharmmPsfFile(object): ...@@ -588,13 +591,22 @@ class CharmmPsfFile(object):
def setBox(self, a, b, c, alpha=90.0*u.degrees, beta=90.0*u.degrees, def setBox(self, a, b, c, alpha=90.0*u.degrees, beta=90.0*u.degrees,
gamma=90.0*u.degrees): gamma=90.0*u.degrees):
""" """Sets the periodic box boundary conditions.
Sets the periodic box boundary conditions.
Parameters
Parameters: ----------
- a, b, c (floats) : Lengths of the periodic cell a : length
- alpha, beta, gamma (floats, optional) : Angles between the Lengths of the periodic cell
periodic cell vectors. b : length
Lengths of the periodic cell
c : length
Lengths of the periodic cell
alpha : floats, optional
Angles between the periodic cell vectors.
beta : floats, optional
Angles between the periodic cell vectors.
gamma : floats, optional
Angles between the periodic cell vectors.
""" """
try: try:
# Since we are setting the box, delete the cached box lengths if we # Since we are setting the box, delete the cached box lengths if we
...@@ -620,7 +632,7 @@ class CharmmPsfFile(object): ...@@ -620,7 +632,7 @@ class CharmmPsfFile(object):
pass pass
# Cache the topology for easy returning later # Cache the topology for easy returning later
self._topology = topology = Topology() self._topology = topology = Topology()
last_chain = None last_chain = None
last_residue = None last_residue = None
# Add each chain (separate 'system's) and residue # Add each chain (separate 'system's) and residue
...@@ -752,52 +764,60 @@ class CharmmPsfFile(object): ...@@ -752,52 +764,60 @@ class CharmmPsfFile(object):
ewaldErrorTolerance=0.0005, ewaldErrorTolerance=0.0005,
flexibleConstraints=True, flexibleConstraints=True,
verbose=False): verbose=False):
""" """Construct an OpenMM System representing the topology described by the
Construct an OpenMM System representing the topology described by the
prmtop file. You MUST have loaded a parameter set into this PSF before prmtop file. You MUST have loaded a parameter set into this PSF before
calling createSystem. If not, AttributeError will be raised. ValueError calling createSystem. If not, AttributeError will be raised. ValueError
is raised for illegal input. is raised for illegal input.
Parameters: Parameters
- params (CharmmParameterSet) The parameter set to use to parametrize ----------
this molecule params : CharmmParameterSet
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded The parameter set to use to parametrize this molecule
interactions. Allowed values are NoCutoff, CutoffNonPeriodic, nonbondedMethod : object=NoCutoff
CutoffPeriodic, Ewald, or PME. The method to use for nonbonded interactions. Allowed values are
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
for nonbonded interactions. nonbondedCutoff : distance=1*nanometer
- switchDistance (distance=0*nanometer) The distance at which the The cutoff distance to use for nonbonded interactions.
switching function is active for nonbonded interactions. If the switchDistance : distance=0*nanometer
switchDistance evaluates to boolean False (if it is 0), no The distance at which the switching function is active for nonbonded
switching function will be used. Illegal values will raise a interactions. If the switchDistance evaluates to boolean False (if
ValueError it is 0), no switching function will be used. Illegal values will
- constraints (object=None) Specifies which bonds or angles should be raise a ValueError
implemented with constraints. Allowed values are None, HBonds, constraints : object=None
AllBonds, or HAngles. Specifies which bonds or angles should be implemented with
- rigidWater (boolean=True) If true, water molecules will be fully constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
rigid regardless of the value passed for the constraints argument rigidWater : boolean=True
- implicitSolvent (object=None) If not None, the implicit solvent If true, water molecules will be fully rigid regardless of the value
model to use. Allowed values are HCT, OBC1, OBC2, or GBn passed for the constraints argument
- implicitSolventKappa (float=None): Debye screening parameter to implicitSolvent : object=None
model salt concentrations in GB solvent. If not None, the implicit solvent model to use. Allowed values are
- implicitSolventSaltConc (float=0.0*u.moles/u.liter): Salt HCT, OBC1, OBC2, or GBn
concentration for GB simulations. Converted to Debye length implicitSolventKappa : float=None
`kappa' Debye screening parameter to model salt concentrations in GB
- temperature (float=298.15*u.kelvin): Temperature used in the salt solvent.
concentration-to-kappa conversion for GB salt concentration term implicitSolventSaltConc : float=0.0*u.moles/u.liter
- soluteDielectric (float=1.0) The solute dielectric constant to use Salt concentration for GB simulations. Converted to Debye length
in the implicit solvent model. `kappa'
- solventDielectric (float=78.5) The solvent dielectric constant to temperature : float=298.15*u.kelvin
use in the implicit solvent model. Temperature used in the salt concentration-to-kappa conversion for
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be GB salt concentration term
added to the System. soluteDielectric : float=1.0
- hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to The solute dielectric constant to use in the implicit solvent model.
heavy atoms. Any mass added to a hydrogen is subtracted from the solventDielectric : float=78.5
heavy atom to keep their total mass the same. The solvent dielectric constant to use in the implicit solvent
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if the model.
nonbonded method is Ewald or PME. removeCMMotion : boolean=True
- flexibleConstraints (bool=True) Are our constraints flexible or not? If true, a CMMotionRemover will be added to the System.
- verbose (bool=False) Optionally prints out a running progress report hydrogenMass : mass=None
The mass to use for hydrogen atoms bound to heavy atoms. Any mass
added to a hydrogen is subtracted from the heavy atom to keep their
total mass the same.
ewaldErrorTolerance : float=0.0005
The error tolerance to use if the nonbonded method is Ewald or PME.
flexibleConstraints : bool=True
Are our constraints flexible or not?
verbose : bool=False
Optionally prints out a running progress report
""" """
# Load the parameter set # Load the parameter set
self.loadParameters(params.condense()) self.loadParameters(params.condense())
...@@ -821,7 +841,7 @@ class CharmmPsfFile(object): ...@@ -821,7 +841,7 @@ class CharmmPsfFile(object):
raise ValueError('Illegal implicit solvent model choice.') raise ValueError('Illegal implicit solvent model choice.')
if not constraints in (None, ff.HAngles, ff.HBonds, ff.AllBonds): if not constraints in (None, ff.HAngles, ff.HBonds, ff.AllBonds):
raise ValueError('Illegal constraints choice') raise ValueError('Illegal constraints choice')
# Define conversion factors # Define conversion factors
length_conv = u.angstrom.conversion_factor_to(u.nanometer) length_conv = u.angstrom.conversion_factor_to(u.nanometer)
_chmfrc = u.kilocalorie_per_mole/(u.angstrom*u.angstrom) _chmfrc = u.kilocalorie_per_mole/(u.angstrom*u.angstrom)
...@@ -833,7 +853,7 @@ class CharmmPsfFile(object): ...@@ -833,7 +853,7 @@ class CharmmPsfFile(object):
dihe_frc_conv = u.kilocalorie_per_mole.conversion_factor_to( dihe_frc_conv = u.kilocalorie_per_mole.conversion_factor_to(
u.kilojoule_per_mole) u.kilojoule_per_mole)
ene_conv = dihe_frc_conv ene_conv = dihe_frc_conv
# Create the system and determine if any of our atoms have NBFIX (and # Create the system and determine if any of our atoms have NBFIX (and
# therefore requires a CustomNonbondedForce instead) # therefore requires a CustomNonbondedForce instead)
typenames = set() typenames = set()
...@@ -1358,7 +1378,7 @@ class CharmmPsfFile(object): ...@@ -1358,7 +1378,7 @@ class CharmmPsfFile(object):
def boxLengths(self, stuff): def boxLengths(self, stuff):
raise RuntimeError('Use setBox to set a box with lengths and angles ' raise RuntimeError('Use setBox to set a box with lengths and angles '
'or set the boxVectors attribute with box vectors') 'or set the boxVectors attribute with box vectors')
@property @property
def boxVectors(self): def boxVectors(self):
""" Return the box vectors """ """ Return the box vectors """
...@@ -1403,12 +1423,12 @@ def set_molecules(atom_list): ...@@ -1403,12 +1423,12 @@ def set_molecules(atom_list):
owner = [] owner = []
# The way I do this is via a recursive algorithm, in which # The way I do this is via a recursive algorithm, in which
# the "set_owner" method is called for each bonded partner an atom # the "set_owner" method is called for each bonded partner an atom
# has, which in turn calls set_owner for each of its partners and # has, which in turn calls set_owner for each of its partners and
# so on until everything has been assigned. # so on until everything has been assigned.
molecule_number = 1 # which molecule number we are on molecule_number = 1 # which molecule number we are on
for i in range(len(atom_list)): for i in range(len(atom_list)):
# If this atom has not yet been "owned", make it the next molecule # If this atom has not yet been "owned", make it the next molecule
# However, we only increment which molecule number we're on if # However, we only increment which molecule number we're on if
# we actually assigned a new molecule (obviously) # we actually assigned a new molecule (obviously)
if not atom_list[i].marked: if not atom_list[i].marked:
tmp = [i] tmp = [i]
...@@ -1429,7 +1449,7 @@ def _set_owner(atom_list, owner_array, atm, mol_id): ...@@ -1429,7 +1449,7 @@ def _set_owner(atom_list, owner_array, atm, mol_id):
owner_array.append(partner.idx) owner_array.append(partner.idx)
_set_owner(atom_list, owner_array, partner.idx, mol_id) _set_owner(atom_list, owner_array, partner.idx, mol_id)
elif partner.marked != mol_id: elif partner.marked != mol_id:
raise MoleculeError('Atom %d in multiple molecules' % raise MoleculeError('Atom %d in multiple molecules' %
partner.idx) partner.idx)
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......
wrappers/python/simtk/openmm/app/checkpointreporter.py
View file @ 51b7f9e2
...@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org. ...@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2014 Stanford University and the Authors. Portions copyright (c) 2014 Stanford University and the Authors.
Authors: Robert McGibbon Authors: Robert McGibbon
Contributors: Contributors:
Permission is hereby granted, free of charge, to any person obtaining a Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"), copy of this software and associated documentation files (the "Software"),
...@@ -71,10 +71,12 @@ class CheckpointReporter(object): ...@@ -71,10 +71,12 @@ class CheckpointReporter(object):
def __init__(self, file, reportInterval): def __init__(self, file, reportInterval):
"""Create a CheckpointReporter. """Create a CheckpointReporter.
Parameters: Parameters
- file (string or open file object) The file to write to. Any current ----------
contents will be overwritten. file : string or open file object
- reportInterval (int) The interval (in time steps) at which to write checkpoints The file to write to. Any current contents will be overwritten.
reportInterval : int
The interval (in time steps) at which to write checkpoints.
""" """
self._reportInterval = reportInterval self._reportInterval = reportInterval
...@@ -88,12 +90,18 @@ class CheckpointReporter(object): ...@@ -88,12 +90,18 @@ class CheckpointReporter(object):
def describeNextReport(self, simulation): def describeNextReport(self, simulation):
"""Get information about the next report this object will generate. """Get information about the next report this object will generate.
Parameters: Parameters
- simulation (Simulation) The Simulation to generate a report for ----------
simulation : Simulation
Returns: A five element tuple. The first element is the number of steps until the The Simulation to generate a report for
next report. The remaining elements specify whether that report will require
positions, velocities, forces, and energies respectively. Returns
-------
tuple
A five element tuple. The first element is the number of steps
until the next report. The remaining elements specify whether
that report will require positions, velocities, forces, and
energies respectively.
""" """
steps = self._reportInterval - simulation.currentStep%self._reportInterval steps = self._reportInterval - simulation.currentStep%self._reportInterval
return (steps, False, False, False, False) return (steps, False, False, False, False)
...@@ -101,9 +109,12 @@ class CheckpointReporter(object): ...@@ -101,9 +109,12 @@ class CheckpointReporter(object):
def report(self, simulation, state): def report(self, simulation, state):
"""Generate a report. """Generate a report.
Parameters: Parameters
- simulation (Simulation) The Simulation to generate a report for ----------
- state (State) The current state of the simulation simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
""" """
self._out.seek(0) self._out.seek(0)
chk = simulation.context.createCheckpoint() chk = simulation.context.createCheckpoint()
......
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