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Commit 855ece90 authored by leeping's avatar leeping
Browse files

Merge branch 'master' of https://github.com/SimTk/openmm

parents 471bea82 a42c55ad
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Showing with 541 additions and 379 deletions
platforms/cuda/tests/TestCudaVariableVerletIntegrator.cpp
View file @ 855ece90
......@@ -211,6 +211,37 @@ void testConstrainedClusters() {
ASSERT(context.getState(State::Positions).getTime() > 0.1);
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
VariableVerletIntegrator integrator(0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testArgonBox() {
const int gridSize = 8;
const double mass = 40.0; // Ar atomic mass
......@@ -274,6 +305,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testConstraints();
testConstrainedClusters();
testConstrainedMasslessParticles();
testArgonBox();
}
catch(const exception& e) {
......
platforms/cuda/tests/TestCudaVerletIntegrator.cpp
View file @ 855ece90
......@@ -203,6 +203,37 @@ void testConstrainedClusters() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
VerletIntegrator integrator(0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -210,6 +241,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testConstraints();
testConstrainedClusters();
testConstrainedMasslessParticles();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ 855ece90
......@@ -141,15 +141,21 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
// Record the set of constraints and how many constraints each atom is involved in.
int numConstraints = system.getNumConstraints();
vector<int> atom1(numConstraints);
vector<int> atom2(numConstraints);
vector<double> distance(numConstraints);
vector<int> atom1;
vector<int> atom2;
vector<double> distance;
vector<int> constraintCount(context.getNumAtoms(), 0);
for (int i = 0; i < numConstraints; i++) {
system.getConstraintParameters(i, atom1[i], atom2[i], distance[i]);
constraintCount[atom1[i]]++;
constraintCount[atom2[i]]++;
for (int i = 0; i < system.getNumConstraints(); i++) {
int p1, p2;
double d;
system.getConstraintParameters(i, p1, p2, d);
if (system.getParticleMass(p1) != 0 || system.getParticleMass(p2) != 0) {
atom1.push_back(p1);
atom2.push_back(p2);
distance.push_back(d);
constraintCount[p1]++;
constraintCount[p2]++;
}
}
// Identify clusters of three atoms that can be treated with SETTLE. First, for every
......
platforms/opencl/tests/TestOpenCLBrownianIntegrator.cpp
View file @ 855ece90
......@@ -172,6 +172,37 @@ void testConstraints() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
BrownianIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
......@@ -237,6 +268,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
}
catch(const exception& e) {
......
platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
View file @ 855ece90
......@@ -233,6 +233,43 @@ void testVelocityConstraints() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
CustomIntegrator integrator(0.002);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addConstrainPositions();
integrator.addComputePerDof("v", "(x-oldx)/dt");
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities | State::Positions);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
/**
* Test an integrator with an AndersenThermostat to see if updateContextState()
* is being handled correctly.
......@@ -724,6 +761,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testConstraints();
testVelocityConstraints();
testConstrainedMasslessParticles();
testWithThermostat();
testMonteCarlo();
testSum();
......
platforms/opencl/tests/TestOpenCLLangevinIntegrator.cpp
View file @ 855ece90
......@@ -177,6 +177,37 @@ void testConstraints() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
LangevinIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
......@@ -241,6 +272,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
}
catch(const exception& e) {
......
platforms/opencl/tests/TestOpenCLVariableLangevinIntegrator.cpp
View file @ 855ece90
......@@ -172,6 +172,37 @@ void testConstraints() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
VariableLangevinIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
......@@ -295,6 +326,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
testArgonBox();
}
......
platforms/opencl/tests/TestOpenCLVariableVerletIntegrator.cpp
View file @ 855ece90
......@@ -210,6 +210,38 @@ void testConstrainedClusters() {
ASSERT(context.getState(State::Positions).getTime() > 0.1);
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
VariableVerletIntegrator integrator(0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testArgonBox() {
const int gridSize = 8;
const double mass = 40.0; // Ar atomic mass
......@@ -273,6 +305,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testConstraints();
testConstrainedClusters();
testConstrainedMasslessParticles();
testArgonBox();
}
catch(const exception& e) {
......
platforms/opencl/tests/TestOpenCLVerletIntegrator.cpp
View file @ 855ece90
......@@ -201,6 +201,37 @@ void testConstrainedClusters() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
VerletIntegrator integrator(0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -208,6 +239,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testConstraints();
testConstrainedClusters();
testConstrainedMasslessParticles();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/include/ReferenceCCMAAlgorithm.h
View file @ 855ece90
/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -34,151 +34,89 @@
class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {
protected:
protected:
int _maximumNumberOfIterations;
RealOpenMM _tolerance;
int _maximumNumberOfIterations;
RealOpenMM _tolerance;
int _numberOfConstraints;
std::vector<std::pair<int, int> > _atomIndices;
std::vector<RealOpenMM> _distance;
int _numberOfConstraints;
std::vector<std::pair<int, int> > _atomIndices;
std::vector<RealOpenMM> _distance;
std::vector<OpenMM::RealVec> _r_ij;
RealOpenMM* _d_ij2;
RealOpenMM* _distanceTolerance;
RealOpenMM* _reducedMasses;
bool _hasInitializedMasses;
std::vector<std::vector<std::pair<int, RealOpenMM> > > _matrix;
std::vector<OpenMM::RealVec> _r_ij;
RealOpenMM* _d_ij2;
RealOpenMM* _distanceTolerance;
RealOpenMM* _reducedMasses;
bool _hasInitializedMasses;
std::vector<std::vector<std::pair<int, RealOpenMM> > > _matrix;
private:
private:
int applyConstraints(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
void applyConstraints(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses, bool constrainingVelocities);
public:
class AngleInfo;
/**---------------------------------------------------------------------------------------
ReferenceCCMAAlgorithm constructor
@param numberOfAtoms number of atoms
@param numberOfConstraints number of constraints
@param atomIndices atom indices for contraints
@param distance distances for constraints
@param masses atom masses
@param angles angle force field terms
@param tolerance constraint tolerance
--------------------------------------------------------------------------------------- */
ReferenceCCMAAlgorithm( int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles, RealOpenMM tolerance );
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceCCMAAlgorithm( );
/**---------------------------------------------------------------------------------------
Get number of constraints
@return number of constraints
--------------------------------------------------------------------------------------- */
int getNumberOfConstraints( void ) const;
/**---------------------------------------------------------------------------------------
Get maximum number of iterations
@return maximum number of iterations
--------------------------------------------------------------------------------------- */
int getMaximumNumberOfIterations( void ) const;
/**---------------------------------------------------------------------------------------
Set maximum number of iterations
@param maximumNumberOfIterations new maximum number of iterations
--------------------------------------------------------------------------------------- */
void setMaximumNumberOfIterations( int maximumNumberOfIterations );
/**---------------------------------------------------------------------------------------
Get tolerance
@return tolerance
--------------------------------------------------------------------------------------- */
RealOpenMM getTolerance( void ) const;
/**---------------------------------------------------------------------------------------
Set tolerance
@param tolerance new tolerance
--------------------------------------------------------------------------------------- */
void setTolerance( RealOpenMM tolerance );
/**---------------------------------------------------------------------------------------
Apply CCMA algorithm
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomCoordinatesP atom coordinates prime
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int apply( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses );
/**---------------------------------------------------------------------------------------
Apply constraint algorithm to velocities.
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities atom velocities
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
public:
class AngleInfo;
/**
* Create a ReferenceCCMAAlgorithm object.
*
* @param numberOfAtoms the number of atoms in the system
* @param numberOfConstraints the number of constraints
* @param atomIndices atom indices for contraints
* @param distance distances for constraints
* @param masses atom masses
* @param angles angle force field terms
* @param tolerance constraint tolerance
*/
ReferenceCCMAAlgorithm( int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles, RealOpenMM tolerance );
~ReferenceCCMAAlgorithm( );
/**
* Get the number of constraints.
*/
int getNumberOfConstraints( void ) const;
/**
* Get the maximum number of iterations to perform.
*/
int getMaximumNumberOfIterations( void ) const;
/**
* Set the maximum number of iterations to perform.
*/
void setMaximumNumberOfIterations( int maximumNumberOfIterations );
/**
* Get the constraint tolerance.
*/
RealOpenMM getTolerance( void ) const;
/**
* Set the constraint tolerance.
*/
void setTolerance( RealOpenMM tolerance );
/**
* Apply the constraint algorithm.
*
* @param atomCoordinates the original atom coordinates
* @param atomCoordinatesP the new atom coordinates
* @param inverseMasses 1/mass
*/
void apply(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses);
/**
* Apply the constraint algorithm to velocities.
*
* @param atomCoordinates the atom coordinates
* @param atomCoordinatesP the velocities to modify
* @param inverseMasses 1/mass
*/
void applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
/**---------------------------------------------------------------------------------------
Report any violated constraints
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param message report
@return number of violated constraints
--------------------------------------------------------------------------------------- */
int reportCCMA( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::stringstream& message );
};
class ReferenceCCMAAlgorithm::AngleInfo
......
platforms/reference/include/ReferenceConstraint.h deleted 100644 → 0
View file @ 471bea82
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceConstraint_H__
#define __ReferenceConstraint_H__
// ---------------------------------------------------------------------------------------
class ReferenceConstraint {
private:
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
ReferenceConstraint( );
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceConstraint( );
};
class ReferenceShakeConstraint : public ReferenceConstraint {
private:
// force heavy atom into index 0
int _atomIndices[2];
RealOpenMM _inverseMasses[2];
RealOpenMM _constraintDistance;
public:
/**---------------------------------------------------------------------------------------
Constructor
@param atomIndex1 atom index 1
@param atomIndex2 atom index 2
@param distance distance constraint
@param inverseMass1 inverseMass of atom 1
@param inverseMass2 inverseMass of atom 2
--------------------------------------------------------------------------------------- */
ReferenceShakeConstraint( int atomIndex1, int atomIndex2, RealOpenMM distance,
RealOpenMM inverseMass1, RealOpenMM inverseMass2 );
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceShakeConstraint( );
/**---------------------------------------------------------------------------------------
Get constraint distance
@return distance
--------------------------------------------------------------------------------------- */
RealOpenMM getConstraintDistance( void );
/**---------------------------------------------------------------------------------------
Get inverse mass of heavy atom
@return inverse mass
--------------------------------------------------------------------------------------- */
RealOpenMM getHeavyAtomInverseMass( void );
/**---------------------------------------------------------------------------------------
Get inverse mass of light atom
@return inverse mass
--------------------------------------------------------------------------------------- */
RealOpenMM getLightAtomInverseMass( void );
/**---------------------------------------------------------------------------------------
Get index of heavy atom
@return index
--------------------------------------------------------------------------------------- */
int getHeavyAtomIndex( void );
/**---------------------------------------------------------------------------------------
Get index of light atom
@return index
--------------------------------------------------------------------------------------- */
int getLightAtomIndex( void );
};
// ---------------------------------------------------------------------------------------
#endif // __ReferenceShakeConstraint_H__
platforms/reference/include/ReferenceConstraintAlgorithm.h
View file @ 855ece90
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -36,54 +36,34 @@ public:
virtual ~ReferenceConstraintAlgorithm() {};
/**---------------------------------------------------------------------------------------
Get the constraint tolerance
--------------------------------------------------------------------------------------- */
/**
* Get the constraint tolerance.
*/
virtual RealOpenMM getTolerance() const = 0;
/**---------------------------------------------------------------------------------------
Set the constraint tolerance
--------------------------------------------------------------------------------------- */
/**
* Set the constraint tolerance.
*/
virtual void setTolerance(RealOpenMM tolerance) = 0;
/**---------------------------------------------------------------------------------------
Apply constraint algorithm
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomCoordinatesP atom coordinates prime
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
virtual int apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
/**
* Apply the constraint algorithm.
*
* @param atomCoordinates the original atom coordinates
* @param atomCoordinatesP the new atom coordinates
* @param inverseMasses 1/mass
*/
virtual void apply(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses) = 0;
/**---------------------------------------------------------------------------------------
Apply constraint algorithm to velocities.
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities atom velocities
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
virtual int applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
/**
* Apply the constraint algorithm to velocities.
*
* @param atomCoordinates the atom coordinates
* @param atomCoordinatesP the velocities to modify
* @param inverseMasses 1/mass
*/
virtual void applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses) = 0;
};
......
platforms/reference/include/ReferenceConstraints.h 0 → 100644
View file @ 855ece90
#ifndef OPENMM_REFERENCECONSTRAINTS_H_
#define OPENMM_REFERENCECONSTRAINTS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 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 "ReferenceConstraintAlgorithm.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceSETTLEAlgorithm.h"
#include "openmm/System.h"
namespace OpenMM {
/**
* This class uses multiple algorithms to apply constraints as efficiently as possible. It identifies clusters
* of three atoms that can be handled by SETTLE, and creates a ReferenceSETTLEAlgorithm object to handle them.
* It then creates a ReferenceCCMAAlgorithm object to handle any remaining constraints.
*/
class OPENMM_EXPORT ReferenceConstraints : public ReferenceConstraintAlgorithm {
public:
ReferenceConstraints(const System& system, RealOpenMM tolerance);
~ReferenceConstraints();
/**
* Get the constraint tolerance.
*/
RealOpenMM getTolerance() const;
/**
* Set the constraint tolerance.
*/
void setTolerance(RealOpenMM tolerance);
/**
* Apply the constraint algorithm.
*
* @param atomCoordinates the original atom coordinates
* @param atomCoordinatesP the new atom coordinates
* @param inverseMasses 1/mass
*/
void apply(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses);
/**
* Apply the constraint algorithm to velocities.
*
* @param atomCoordinates the atom coordinates
* @param atomCoordinatesP the velocities to modify
* @param inverseMasses 1/mass
*/
void applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
private:
RealOpenMM tolerance;
ReferenceCCMAAlgorithm* ccma;
ReferenceSETTLEAlgorithm* settle;
};
} // namespace OpenMM
#endif /*OPENMM_REFERENCECONSTRAINTS_H_*/
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 855ece90
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,17 +25,20 @@
#define __ReferenceCustomAngleIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomAngleIxn : public ReferenceBondIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyTheta;
double* forceTheta;
int numParameters;
public:
......@@ -45,7 +48,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ 855ece90
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -26,17 +26,20 @@
#define __ReferenceCustomBondIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomBondIxn : public ReferenceBondIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyR;
double* forceR;
int numParameters;
public:
......@@ -46,7 +49,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomExternalIxn.h
View file @ 855ece90
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -26,19 +26,26 @@
#define __ReferenceCustomExternalIxn_H__
#include "ReferenceCustomExternalIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomExternalIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpressionX;
Lepton::ExpressionProgram forceExpressionY;
Lepton::ExpressionProgram forceExpressionZ;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpressionX;
Lepton::CompiledExpression forceExpressionY;
Lepton::CompiledExpression forceExpressionZ;
std::vector<double*> energyParams;
std::vector<double*> forceXParams;
std::vector<double*> forceYParams;
std::vector<double*> forceZParams;
double *energyX, *energyY, *energyZ;
double *forceXX, *forceXY, *forceXZ;
double *forceYX, *forceYY, *forceYZ;
double *forceZX, *forceZY, *forceZZ;
int numParameters;
public:
......@@ -48,8 +55,8 @@ class ReferenceCustomExternalIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomExternalIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpressionX,
const Lepton::ExpressionProgram& forceExpressionY, const Lepton::ExpressionProgram& forceExpressionZ,
ReferenceCustomExternalIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpressionX,
const Lepton::CompiledExpression& forceExpressionY, const Lepton::CompiledExpression& forceExpressionZ,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomNonbondedIxn.h
View file @ 855ece90
/* Portions copyright (c) 2009 Stanford University and Simbios.
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -27,7 +27,7 @@
#include "ReferencePairIxn.h"
#include "ReferenceNeighborList.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
#include <map>
#include <set>
#include <utility>
......@@ -45,10 +45,13 @@ class ReferenceCustomNonbondedIxn {
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance, switchingDistance;
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<std::string> paramNames;
std::vector<std::string> particleParamNames;
std::vector<double*> energyParticleParams;
std::vector<double*> forceParticleParams;
double* energyR;
double* forceR;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
/**---------------------------------------------------------------------------------------
......@@ -65,9 +68,8 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
public:
......@@ -78,7 +80,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames);
/**---------------------------------------------------------------------------------------
......@@ -153,7 +155,7 @@ class ReferenceCustomNonbondedIxn {
void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ 855ece90
/* Portions copyright (c) 2010 Stanford University and Simbios.
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,17 +25,20 @@
#define __ReferenceCustomTorsionIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "lepton/CompiledExpression.h"
// ---------------------------------------------------------------------------------------
class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
private:
Lepton::ExpressionProgram energyExpression;
Lepton::ExpressionProgram forceExpression;
std::vector<std::string> paramNames;
std::map<std::string, double> globalParameters;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyTheta;
double* forceTheta;
int numParameters;
public:
......@@ -45,7 +48,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomTorsionIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceForce.h
View file @ 855ece90
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -25,6 +24,7 @@
#ifndef __ReferenceForce_H__
#define __ReferenceForce_H__
#include "lepton/CompiledExpression.h"
#include "openmm/internal/windowsExport.h"
// ---------------------------------------------------------------------------------------
......@@ -109,6 +109,18 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
RealOpenMM* deltaR );
/**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
* does not use the specified variable, return NULL.
*/
static double* getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name);
/**
* Set the value of a variable in a CompiledExpression, using the pointer that was returned by getVariablePointer().
*/
static void setVariable(double* pointer, double value);
};
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceKernels.h
View file @ 855ece90
......@@ -36,6 +36,7 @@
#include "openmm/kernels.h"
#include "SimTKOpenMMRealType.h"
#include "ReferenceNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "lepton/ExpressionProgram.h"
class CpuObc;
......@@ -316,7 +317,7 @@ private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
};
......@@ -392,7 +393,7 @@ private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
};
......@@ -534,7 +535,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
};
......@@ -621,7 +622,7 @@ private:
CustomNonbondedForce* forceCopy;
std::map<std::string, double> globalParamValues;
std::vector<std::set<int> > exclusions;
Lepton::ExpressionProgram energyExpression, forceExpression;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
NonbondedMethod nonbondedMethod;
......@@ -781,7 +782,7 @@ private:
int numParticles;
std::vector<int> particles;
RealOpenMM **particleParamArray;
Lepton::ExpressionProgram energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
std::vector<std::string> parameterNames, globalParameterNames;
};
......
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