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Commit 65ee8fd7 authored by Peter Eastman's avatar Peter Eastman
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Renamed BAOABLangevinIntegrator to LangevinMiddleIntegrator

parent ba9f6b0a
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Showing with 86 additions and 69 deletions
platforms/cpu/src/CpuKernelFactory.cpp
View file @ 65ee8fd7
......@@ -61,7 +61,7 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform&
return new CpuCalcGayBerneForceKernel(name, platform, data);
if (name == IntegrateLangevinStepKernel::Name())
return new CpuIntegrateLangevinStepKernel(name, platform, data);
if (name == IntegrateBAOABStepKernel::Name())
return new CpuIntegrateBAOABStepKernel(name, platform, data);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new CpuIntegrateLangevinMiddleStepKernel(name, platform, data);
throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str());
}
platforms/cpu/src/CpuKernels.cpp
View file @ 65ee8fd7
......@@ -1353,12 +1353,12 @@ double CpuIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context
return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
}
CpuIntegrateBAOABStepKernel::~CpuIntegrateBAOABStepKernel() {
CpuIntegrateLangevinMiddleStepKernel::~CpuIntegrateLangevinMiddleStepKernel() {
if (dynamics)
delete dynamics;
}
void CpuIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLangevinIntegrator& integrator) {
void CpuIntegrateLangevinMiddleStepKernel::initialize(const System& system, const LangevinMiddleIntegrator& integrator) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
......@@ -1366,7 +1366,7 @@ void CpuIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLa
data.random.initialize(integrator.getRandomNumberSeed(), data.threads.getNumThreads());
}
void CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
void CpuIntegrateLangevinMiddleStepKernel::execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -1377,7 +1377,7 @@ void CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLange
if (dynamics)
delete dynamics;
dynamics = new CpuBAOABDynamics(context.getSystem().getNumParticles(), stepSize, friction, temperature, data.threads, data.random);
dynamics = new CpuLangevinMiddleDynamics(context.getSystem().getNumParticles(), stepSize, friction, temperature, data.threads, data.random);
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature;
prevFriction = friction;
......@@ -1389,6 +1389,6 @@ void CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLange
refData->stepCount++;
}
double CpuIntegrateBAOABStepKernel::computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
double CpuIntegrateLangevinMiddleStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
return computeShiftedKineticEnergy(context, masses, 0.0);
}
platforms/cpu/src/CpuBAOABDynamics.cpp → platforms/cpu/src/CpuLangevinMiddleDynamics.cpp
View file @ 65ee8fd7
......@@ -23,19 +23,19 @@
*/
#include "SimTKOpenMMUtilities.h"
#include "CpuBAOABDynamics.h"
#include "CpuLangevinMiddleDynamics.h"
using namespace OpenMM;
using namespace std;
CpuBAOABDynamics::CpuBAOABDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, ThreadPool& threads, CpuRandom& random) :
ReferenceBAOABDynamics(numberOfAtoms, deltaT, friction, temperature), threads(threads), random(random) {
CpuLangevinMiddleDynamics::CpuLangevinMiddleDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, ThreadPool& threads, CpuRandom& random) :
ReferenceLangevinMiddleDynamics(numberOfAtoms, deltaT, friction, temperature), threads(threads), random(random) {
}
CpuBAOABDynamics::~CpuBAOABDynamics() {
CpuLangevinMiddleDynamics::~CpuLangevinMiddleDynamics() {
}
void CpuBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses) {
void CpuLangevinMiddleDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses) {
// Record the parameters for the threads.
this->numberOfAtoms = numberOfAtoms;
......@@ -49,7 +49,7 @@ void CpuBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities,
threads.waitForThreads();
}
void CpuBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
void CpuLangevinMiddleDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
vector<double>& inverseMasses, vector<Vec3>& xPrime) {
// Record the parameters for the threads.
......@@ -65,7 +65,7 @@ void CpuBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordina
threads.waitForThreads();
}
void CpuBAOABDynamics::updatePart3(ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
void CpuLangevinMiddleDynamics::updatePart3(ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
vector<double>& inverseMasses, vector<Vec3>& xPrime) {
// Record the parameters for the threads.
......@@ -81,7 +81,7 @@ void CpuBAOABDynamics::updatePart3(ContextImpl& context, int numberOfAtoms, vect
threads.waitForThreads();
}
void CpuBAOABDynamics::threadUpdate1(int threadIndex) {
void CpuLangevinMiddleDynamics::threadUpdate1(int threadIndex) {
int start = threadIndex*numberOfAtoms/threads.getNumThreads();
int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
......@@ -90,7 +90,7 @@ void CpuBAOABDynamics::threadUpdate1(int threadIndex) {
velocities[i] += (getDeltaT()*inverseMasses[i])*forces[i];
}
void CpuBAOABDynamics::threadUpdate2(int threadIndex) {
void CpuLangevinMiddleDynamics::threadUpdate2(int threadIndex) {
const double halfdt = 0.5*getDeltaT();
const double kT = BOLTZ*getTemperature();
const double friction = getFriction();
......@@ -110,7 +110,7 @@ void CpuBAOABDynamics::threadUpdate2(int threadIndex) {
}
}
void CpuBAOABDynamics::threadUpdate3(int threadIndex) {
void CpuLangevinMiddleDynamics::threadUpdate3(int threadIndex) {
int start = threadIndex*numberOfAtoms/threads.getNumThreads();
int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
......
platforms/cpu/src/CpuPlatform.cpp
View file @ 65ee8fd7
......@@ -74,7 +74,7 @@ CpuPlatform::CpuPlatform() {
registerKernelFactory(CalcCustomGBForceKernel::Name(), factory);
registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
platformProperties.push_back(CpuThreads());
platformProperties.push_back(CpuDeterministicForces());
int threads = getNumProcessors();
......
platforms/cpu/tests/TestCpuBAOABLangevinIntegrator.cpp → platforms/cpu/tests/TestCpuLangevinMiddleIntegrator.cpp
View file @ 65ee8fd7
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "CpuTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
platforms/cuda/src/CudaKernelFactory.cpp
View file @ 65ee8fd7
......@@ -121,8 +121,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
return new CommonIntegrateVerletStepKernel(name, platform, cu);
if (name == IntegrateLangevinStepKernel::Name())
return new CommonIntegrateLangevinStepKernel(name, platform, cu);
if (name == IntegrateBAOABStepKernel::Name())
return new CommonIntegrateBAOABStepKernel(name, platform, cu);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new CommonIntegrateLangevinMiddleStepKernel(name, platform, cu);
if (name == IntegrateBrownianStepKernel::Name())
return new CommonIntegrateBrownianStepKernel(name, platform, cu);
if (name == IntegrateVariableVerletStepKernel::Name())
......
platforms/cuda/src/CudaPlatform.cpp
View file @ 65ee8fd7
......@@ -98,7 +98,7 @@ CudaPlatform::CudaPlatform() {
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
......
platforms/cuda/tests/TestCudaBAOABLangevinIntegrator.cpp → platforms/cuda/tests/TestCudaLangevinMiddleIntegrator.cpp
View file @ 65ee8fd7
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "CudaTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
platforms/opencl/src/OpenCLKernelFactory.cpp
View file @ 65ee8fd7
......@@ -119,8 +119,8 @@ KernelImpl* OpenCLKernelFactory::createKernelImpl(std::string name, const Platfo
return new CommonIntegrateVerletStepKernel(name, platform, cl);
if (name == IntegrateLangevinStepKernel::Name())
return new CommonIntegrateLangevinStepKernel(name, platform, cl);
if (name == IntegrateBAOABStepKernel::Name())
return new CommonIntegrateBAOABStepKernel(name, platform, cl);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new CommonIntegrateLangevinMiddleStepKernel(name, platform, cl);
if (name == IntegrateBrownianStepKernel::Name())
return new CommonIntegrateBrownianStepKernel(name, platform, cl);
if (name == IntegrateVariableVerletStepKernel::Name())
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ 65ee8fd7
......@@ -89,7 +89,7 @@ OpenCLPlatform::OpenCLPlatform() {
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
......
platforms/opencl/tests/TestOpenCLBAOABLangevinIntegrator.cpp → platforms/opencl/tests/TestOpenCLLangevinMiddleIntegrator.cpp
View file @ 65ee8fd7
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "OpenCLTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
platforms/reference/include/ReferenceKernels.h
View file @ 65ee8fd7
......@@ -45,7 +45,7 @@ namespace OpenMM {
class ReferenceObc;
class ReferenceAndersenThermostat;
class ReferenceBAOABDynamics;
class ReferenceLangevinMiddleDynamics;
class ReferenceCustomBondIxn;
class ReferenceCustomAngleIxn;
class ReferenceCustomTorsionIxn;
......@@ -1213,38 +1213,38 @@ private:
};
/**
* This kernel is invoked by BAOABLangevinIntegrator to take one time step.
* This kernel is invoked by LangevinMiddleIntegrator to take one time step.
*/
class ReferenceIntegrateBAOABStepKernel : public IntegrateBAOABStepKernel {
class ReferenceIntegrateLangevinMiddleStepKernel : public IntegrateLangevinMiddleStepKernel {
public:
ReferenceIntegrateBAOABStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBAOABStepKernel(name, platform),
ReferenceIntegrateLangevinMiddleStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinMiddleStepKernel(name, platform),
data(data), dynamics(0) {
}
~ReferenceIntegrateBAOABStepKernel();
~ReferenceIntegrateLangevinMiddleStepKernel();
/**
* Initialize the kernel, setting up the particle masses.
*
* @param system the System this kernel will be applied to
* @param integrator the BAOABLangevinIntegrator this kernel will be used for
* @param integrator the LangevinMiddleIntegrator this kernel will be used for
*/
void initialize(const System& system, const BAOABLangevinIntegrator& integrator);
void initialize(const System& system, const LangevinMiddleIntegrator& integrator);
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param integrator the LangevinMiddleIntegrator this kernel is being used for
*/
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
void execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator);
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param integrator the LangevinMiddleIntegrator this kernel is being used for
*/
double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
double computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator);
private:
ReferencePlatform::PlatformData& data;
ReferenceBAOABDynamics* dynamics;
ReferenceLangevinMiddleDynamics* dynamics;
std::vector<double> masses;
double prevTemp, prevFriction, prevStepSize;
};
......
platforms/reference/include/ReferenceBAOABDynamics.h → platforms/reference/include/ReferenceLangevinMiddleDynamics.h
View file @ 65ee8fd7
......@@ -22,8 +22,8 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceBAOABDynamics_H__
#define __ReferenceBAOABDynamics_H__
#ifndef __ReferenceLangevinMiddleDynamics_H__
#define __ReferenceLangevinMiddleDynamics_H__
#include "ReferenceDynamics.h"
#include "openmm/internal/ContextImpl.h"
......@@ -31,7 +31,7 @@
namespace OpenMM {
class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
class OPENMM_EXPORT ReferenceLangevinMiddleDynamics : public ReferenceDynamics {
protected:
......@@ -52,7 +52,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceBAOABDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);
ReferenceLangevinMiddleDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);
/**---------------------------------------------------------------------------------------
......@@ -60,7 +60,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
~ReferenceBAOABDynamics();
~ReferenceLangevinMiddleDynamics();
/**---------------------------------------------------------------------------------------
......@@ -133,4 +133,4 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
} // namespace OpenMM
#endif // __ReferenceBAOABDynamics_H__
#endif // __ReferenceLangevinMiddleDynamics_H__
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ 65ee8fd7
......@@ -94,8 +94,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceNoseHooverChainKernel(name, platform);
if (name == IntegrateLangevinStepKernel::Name())
return new ReferenceIntegrateLangevinStepKernel(name, platform, data);
if (name == IntegrateBAOABStepKernel::Name())
return new ReferenceIntegrateBAOABStepKernel(name, platform, data);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new ReferenceIntegrateLangevinMiddleStepKernel(name, platform, data);
if (name == IntegrateBrownianStepKernel::Name())
return new ReferenceIntegrateBrownianStepKernel(name, platform, data);
if (name == IntegrateVariableLangevinStepKernel::Name())
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 65ee8fd7
......@@ -33,7 +33,6 @@
#include "ReferenceObc.h"
#include "ReferenceAndersenThermostat.h"
#include "ReferenceAngleBondIxn.h"
#include "ReferenceBAOABDynamics.h"
#include "ReferenceBondForce.h"
#include "ReferenceBrownianDynamics.h"
#include "ReferenceCCMAAlgorithm.h"
......@@ -53,6 +52,7 @@
#include "ReferenceCustomTorsionIxn.h"
#include "ReferenceGayBerneForce.h"
#include "ReferenceHarmonicBondIxn.h"
#include "ReferenceLangevinMiddleDynamics.h"
#include "ReferenceLJCoulomb14.h"
#include "ReferenceLJCoulombIxn.h"
#include "ReferenceMonteCarloBarostat.h"
......@@ -2225,12 +2225,12 @@ double ReferenceIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& c
return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
}
ReferenceIntegrateBAOABStepKernel::~ReferenceIntegrateBAOABStepKernel() {
ReferenceIntegrateLangevinMiddleStepKernel::~ReferenceIntegrateLangevinMiddleStepKernel() {
if (dynamics)
delete dynamics;
}
void ReferenceIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLangevinIntegrator& integrator) {
void ReferenceIntegrateLangevinMiddleStepKernel::initialize(const System& system, const LangevinMiddleIntegrator& integrator) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
......@@ -2238,7 +2238,7 @@ void ReferenceIntegrateBAOABStepKernel::initialize(const System& system, const B
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
void ReferenceIntegrateLangevinMiddleStepKernel::execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -2249,7 +2249,7 @@ void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOA
if (dynamics)
delete dynamics;
dynamics = new ReferenceBAOABDynamics(
dynamics = new ReferenceLangevinMiddleDynamics(
context.getSystem().getNumParticles(),
stepSize,
friction,
......@@ -2264,7 +2264,7 @@ void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOA
data.stepCount++;
}
double ReferenceIntegrateBAOABStepKernel::computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
double ReferenceIntegrateLangevinMiddleStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
return computeShiftedKineticEnergy(context, masses, 0.0);
}
......
platforms/reference/src/ReferencePlatform.cpp
View file @ 65ee8fd7
......@@ -69,7 +69,7 @@ ReferencePlatform::ReferencePlatform() {
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(NoseHooverChainKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
......
platforms/reference/src/SimTKReference/ReferenceBAOABDynamics.cpp → platforms/reference/src/SimTKReference/ReferenceLangevinMiddleDynamics.cpp
View file @ 65ee8fd7
......@@ -26,7 +26,7 @@
#include <sstream>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceBAOABDynamics.h"
#include "ReferenceLangevinMiddleDynamics.h"
#include "ReferencePlatform.h"
#include "ReferenceVirtualSites.h"
#include "openmm/OpenMMException.h"
......@@ -35,7 +35,7 @@
using std::vector;
using namespace OpenMM;
ReferenceBAOABDynamics::ReferenceBAOABDynamics(int numberOfAtoms,
ReferenceLangevinMiddleDynamics::ReferenceLangevinMiddleDynamics(int numberOfAtoms,
double deltaT, double friction,
double temperature) :
ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {
......@@ -44,20 +44,20 @@ ReferenceBAOABDynamics::ReferenceBAOABDynamics(int numberOfAtoms,
inverseMasses.resize(numberOfAtoms);
}
ReferenceBAOABDynamics::~ReferenceBAOABDynamics() {
ReferenceLangevinMiddleDynamics::~ReferenceLangevinMiddleDynamics() {
}
double ReferenceBAOABDynamics::getFriction() const {
double ReferenceLangevinMiddleDynamics::getFriction() const {
return friction;
}
void ReferenceBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses) {
void ReferenceLangevinMiddleDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses) {
for (int i = 0; i < numberOfAtoms; i++)
if (inverseMasses[i] != 0.0)
velocities[i] += (getDeltaT()*inverseMasses[i])*forces[i];
}
void ReferenceBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates,
void ReferenceLangevinMiddleDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
const double halfdt = 0.5*getDeltaT();
......@@ -79,7 +79,7 @@ void ReferenceBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCo
}
}
void ReferenceBAOABDynamics::updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates,
void ReferenceLangevinMiddleDynamics::updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& inverseMasses, vector<Vec3>& xPrime) {
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0) {
......@@ -89,7 +89,7 @@ void ReferenceBAOABDynamics::updatePart3(OpenMM::ContextImpl& context, int numbe
}
}
void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoordinates,
void ReferenceLangevinMiddleDynamics::update(ContextImpl& context, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& masses, double tolerance) {
int numberOfAtoms = context.getSystem().getNumParticles();
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
......
platforms/reference/tests/TestReferenceBAOABLangevinIntegrator.cpp → platforms/reference/tests/TestReferenceLangevinMiddleIntegrator.cpp
View file @ 65ee8fd7
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "ReferenceTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
serialization/include/openmm/serialization/BAOABLangevinIntegratorProxy.h → serialization/include/openmm/serialization/LangevinMiddleIntegratorProxy.h
View file @ 65ee8fd7
#ifndef OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
#define OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
#ifndef OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_
#define OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_
#include "openmm/serialization/XmlSerializer.h"
namespace OpenMM {
class BAOABLangevinIntegratorProxy : public SerializationProxy {
class LangevinMiddleIntegratorProxy : public SerializationProxy {
public:
BAOABLangevinIntegratorProxy();
LangevinMiddleIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
#endif /*OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
serialization/src/BAOABLangevinIntegratorProxy.cpp → serialization/src/LangevinMiddleIntegratorProxy.cpp
View file @ 65ee8fd7
......@@ -29,19 +29,19 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/BAOABLangevinIntegratorProxy.h"
#include "openmm/serialization/LangevinMiddleIntegratorProxy.h"
#include <OpenMM.h>
using namespace std;
using namespace OpenMM;
BAOABLangevinIntegratorProxy::BAOABLangevinIntegratorProxy() : SerializationProxy("BAOABLangevinIntegrator") {
LangevinMiddleIntegratorProxy::LangevinMiddleIntegratorProxy() : SerializationProxy("LangevinMiddleIntegrator") {
}
void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
void LangevinMiddleIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const BAOABLangevinIntegrator& integrator = *reinterpret_cast<const BAOABLangevinIntegrator*>(object);
const LangevinMiddleIntegrator& integrator = *reinterpret_cast<const LangevinMiddleIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("temperature", integrator.getTemperature());
......@@ -49,10 +49,10 @@ void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNo
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
}
void* BAOABLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
void* LangevinMiddleIntegratorProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
BAOABLangevinIntegrator *integrator = new BAOABLangevinIntegrator(node.getDoubleProperty("temperature"),
LangevinMiddleIntegrator *integrator = new LangevinMiddleIntegrator(node.getDoubleProperty("temperature"),
node.getDoubleProperty("friction"), node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
......
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