Commit a4020466 authored by Peter Eastman's avatar Peter Eastman
Browse files

Renamed OpenMMContext to Context

parent 95b8dbd6
......@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/HarmonicBondForceImpl.h"
#include "openmm/kernels.h"
......@@ -44,16 +44,16 @@ HarmonicBondForceImpl::HarmonicBondForceImpl(HarmonicBondForce& owner) : owner(o
HarmonicBondForceImpl::~HarmonicBondForceImpl() {
}
void HarmonicBondForceImpl::initialize(OpenMMContextImpl& context) {
void HarmonicBondForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcHarmonicBondForceKernel::Name(), context);
dynamic_cast<CalcHarmonicBondForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void HarmonicBondForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
void HarmonicBondForceImpl::calcForces(ContextImpl& context, Stream& forces) {
dynamic_cast<CalcHarmonicBondForceKernel&>(kernel.getImpl()).executeForces(context);
}
double HarmonicBondForceImpl::calcEnergy(OpenMMContextImpl& context) {
double HarmonicBondForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcHarmonicBondForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
......
......@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/LangevinIntegrator.h"
#include "openmm/OpenMMContext.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include <ctime>
#include <string>
......@@ -48,7 +48,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
setRandomNumberSeed((int) time(NULL));
}
void LangevinIntegrator::initialize(OpenMMContextImpl& contextRef) {
void LangevinIntegrator::initialize(ContextImpl& contextRef) {
context = &contextRef;
kernel = context->getPlatform().createKernel(IntegrateLangevinStepKernel::Name(), contextRef);
dynamic_cast<IntegrateLangevinStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
......
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/OpenMMException.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/kernels.h"
#include <sstream>
......@@ -47,7 +47,7 @@ NonbondedForceImpl::NonbondedForceImpl(NonbondedForce& owner) : owner(owner) {
NonbondedForceImpl::~NonbondedForceImpl() {
}
void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
void NonbondedForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcNonbondedForceKernel::Name(), context);
// Check for errors in the specification of exceptions.
......@@ -86,11 +86,11 @@ void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void NonbondedForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
void NonbondedForceImpl::calcForces(ContextImpl& context, Stream& forces) {
dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).executeForces(context);
}
double NonbondedForceImpl::calcEnergy(OpenMMContextImpl& context) {
double NonbondedForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
......
......@@ -29,51 +29,51 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/OpenMMContext.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"
using namespace OpenMM;
using namespace std;
OpenMMContext::OpenMMContext(System& system, Integrator& integrator) {
impl = new OpenMMContextImpl(*this, system, integrator, 0);
Context::Context(System& system, Integrator& integrator) {
impl = new ContextImpl(*this, system, integrator, 0);
}
OpenMMContext::OpenMMContext(System& system, Integrator& integrator, Platform& platform) {
impl = new OpenMMContextImpl(*this, system, integrator, &platform);
Context::Context(System& system, Integrator& integrator, Platform& platform) {
impl = new ContextImpl(*this, system, integrator, &platform);
}
OpenMMContext::~OpenMMContext() {
Context::~Context() {
delete impl;
}
const System& OpenMMContext::getSystem() const {
const System& Context::getSystem() const {
return impl->getSystem();
}
System& OpenMMContext::getSystem() {
System& Context::getSystem() {
return impl->getSystem();
}
const Integrator& OpenMMContext::getIntegrator() const {
const Integrator& Context::getIntegrator() const {
return impl->getIntegrator();
}
Integrator& OpenMMContext::getIntegrator() {
Integrator& Context::getIntegrator() {
return impl->getIntegrator();
}
const Platform& OpenMMContext::getPlatform() const {
const Platform& Context::getPlatform() const {
return impl->getPlatform();
}
Platform& OpenMMContext::getPlatform() {
Platform& Context::getPlatform() {
return impl->getPlatform();
}
State OpenMMContext::getState(int types) const {
State Context::getState(int types) const {
State state(impl->getTime(), impl->getSystem().getNumParticles(), State::DataType(types));
if (types&State::Energy)
state.setEnergy(impl->calcKineticEnergy(), impl->calcPotentialEnergy());
......@@ -92,34 +92,34 @@ State OpenMMContext::getState(int types) const {
return state;
}
void OpenMMContext::setTime(double time) {
void Context::setTime(double time) {
impl->setTime(time);
}
void OpenMMContext::setPositions(const vector<Vec3>& positions) {
void Context::setPositions(const vector<Vec3>& positions) {
if ((int) positions.size() != impl->getSystem().getNumParticles())
throw OpenMMException("Called setPositions() on an OpenMMContext with the wrong number of positions");
throw OpenMMException("Called setPositions() on a Context with the wrong number of positions");
impl->getPositions().loadFromArray(&positions[0]);
}
void OpenMMContext::setVelocities(const vector<Vec3>& velocities) {
void Context::setVelocities(const vector<Vec3>& velocities) {
if ((int) velocities.size() != impl->getSystem().getNumParticles())
throw OpenMMException("Called setVelocities() on an OpenMMContext with the wrong number of velocities");
throw OpenMMException("Called setVelocities() on a Context with the wrong number of velocities");
impl->getVelocities().loadFromArray(&velocities[0]);
}
double OpenMMContext::getParameter(const string& name) {
double Context::getParameter(const string& name) {
return impl->getParameter(name);
}
void OpenMMContext::setParameter(const string& name, double value) {
void Context::setParameter(const string& name, double value) {
impl->setParameter(name, value);
}
void OpenMMContext::reinitialize() {
void Context::reinitialize() {
System& system = impl->getSystem();
Integrator& integrator = impl->getIntegrator();
Platform& platform = impl->getPlatform();
delete impl;
impl = new OpenMMContextImpl(*this, system, integrator, &platform);
impl = new ContextImpl(*this, system, integrator, &platform);
}
......@@ -35,7 +35,7 @@
#include "openmm/System.h"
#include "openmm/kernels.h"
#include "openmm/internal/ForceImpl.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include <map>
#include <vector>
......@@ -44,7 +44,7 @@ using std::map;
using std::vector;
using std::string;
OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integrator& integrator, Platform* platform) :
ContextImpl::ContextImpl(Context& owner, System& system, Integrator& integrator, Platform* platform) :
owner(owner), system(system),
integrator(integrator), platform(platform),
platformData(NULL)
......@@ -65,7 +65,7 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
if (platform == 0)
this->platform = platform = &Platform::findPlatform(kernelNames);
else if (!platform->supportsKernels(kernelNames))
throw OpenMMException("Specified a Platform for an OpenMMContext which does not support all required kernels");
throw OpenMMException("Specified a Platform for a Context which does not support all required kernels");
platform->contextCreated(*this);
initializeForcesKernel = platform->createKernel(InitializeForcesKernel::Name(), *this);
dynamic_cast<InitializeForcesKernel&>(initializeForcesKernel.getImpl()).initialize(system);
......@@ -83,58 +83,58 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
velocities.fillWithValue(&zero);
}
OpenMMContextImpl::~OpenMMContextImpl() {
ContextImpl::~ContextImpl() {
for (int i = 0; i < (int) forceImpls.size(); ++i)
delete forceImpls[i];
platform->contextDestroyed(*this);
}
double OpenMMContextImpl::getTime() const {
double ContextImpl::getTime() const {
return dynamic_cast<const UpdateTimeKernel&>(updateTimeKernel.getImpl()).getTime(*this);
}
void OpenMMContextImpl::setTime(double t) {
void ContextImpl::setTime(double t) {
dynamic_cast<UpdateTimeKernel&>(updateTimeKernel.getImpl()).setTime(*this, t);
}
double OpenMMContextImpl::getParameter(std::string name) {
double ContextImpl::getParameter(std::string name) {
if (parameters.find(name) == parameters.end())
throw OpenMMException("Called getParameter() with invalid parameter name");
return parameters[name];
}
void OpenMMContextImpl::setParameter(std::string name, double value) {
void ContextImpl::setParameter(std::string name, double value) {
if (parameters.find(name) == parameters.end())
throw OpenMMException("Called setParameter() with invalid parameter name");
parameters[name] = value;
}
void OpenMMContextImpl::calcForces() {
void ContextImpl::calcForces() {
dynamic_cast<InitializeForcesKernel&>(initializeForcesKernel.getImpl()).execute(*this);
for (int i = 0; i < (int) forceImpls.size(); ++i)
forceImpls[i]->calcForces(*this, forces);
}
double OpenMMContextImpl::calcKineticEnergy() {
double ContextImpl::calcKineticEnergy() {
return dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).execute(*this);
}
double OpenMMContextImpl::calcPotentialEnergy() {
double ContextImpl::calcPotentialEnergy() {
double energy = 0.0;
for (int i = 0; i < (int) forceImpls.size(); ++i)
energy += forceImpls[i]->calcEnergy(*this);
return energy;
}
void OpenMMContextImpl::updateContextState() {
void ContextImpl::updateContextState() {
for (int i = 0; i < (int) forceImpls.size(); ++i)
forceImpls[i]->updateContextState(*this);
}
void* OpenMMContextImpl::getPlatformData() {
void* ContextImpl::getPlatformData() {
return platformData;
}
void OpenMMContextImpl::setPlatformData(void* data) {
void ContextImpl::setPlatformData(void* data) {
platformData = data;
}
......@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/PeriodicTorsionForceImpl.h"
#include "openmm/kernels.h"
......@@ -44,16 +44,16 @@ PeriodicTorsionForceImpl::PeriodicTorsionForceImpl(PeriodicTorsionForce& owner)
PeriodicTorsionForceImpl::~PeriodicTorsionForceImpl() {
}
void PeriodicTorsionForceImpl::initialize(OpenMMContextImpl& context) {
void PeriodicTorsionForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcPeriodicTorsionForceKernel::Name(), context);
dynamic_cast<CalcPeriodicTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void PeriodicTorsionForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
void PeriodicTorsionForceImpl::calcForces(ContextImpl& context, Stream& forces) {
dynamic_cast<CalcPeriodicTorsionForceKernel&>(kernel.getImpl()).executeForces(context);
}
double PeriodicTorsionForceImpl::calcEnergy(OpenMMContextImpl& context) {
double PeriodicTorsionForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcPeriodicTorsionForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
......
......@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/RBTorsionForceImpl.h"
#include "openmm/kernels.h"
......@@ -44,16 +44,16 @@ RBTorsionForceImpl::RBTorsionForceImpl(RBTorsionForce& owner) : owner(owner) {
RBTorsionForceImpl::~RBTorsionForceImpl() {
}
void RBTorsionForceImpl::initialize(OpenMMContextImpl& context) {
void RBTorsionForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcRBTorsionForceKernel::Name(), context);
dynamic_cast<CalcRBTorsionForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void RBTorsionForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
void RBTorsionForceImpl::calcForces(ContextImpl& context, Stream& forces) {
dynamic_cast<CalcRBTorsionForceKernel&>(kernel.getImpl()).executeForces(context);
}
double RBTorsionForceImpl::calcEnergy(OpenMMContextImpl& context) {
double RBTorsionForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcRBTorsionForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
......
......@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/VariableLangevinIntegrator.h"
#include "openmm/OpenMMContext.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include <limits>
#include <string>
......@@ -48,7 +48,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
setRandomNumberSeed((int) time(NULL));
}
void VariableLangevinIntegrator::initialize(OpenMMContextImpl& contextRef) {
void VariableLangevinIntegrator::initialize(ContextImpl& contextRef) {
context = &contextRef;
kernel = context->getPlatform().createKernel(IntegrateVariableLangevinStepKernel::Name(), contextRef);
dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
......
......@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/OpenMMContext.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include <limits>
#include <string>
......@@ -44,7 +44,7 @@ VariableVerletIntegrator::VariableVerletIntegrator(double errorTol) : errorTol(e
setConstraintTolerance(1e-4);
}
void VariableVerletIntegrator::initialize(OpenMMContextImpl& contextRef) {
void VariableVerletIntegrator::initialize(ContextImpl& contextRef) {
context = &contextRef;
kernel = context->getPlatform().createKernel(IntegrateVariableVerletStepKernel::Name(), contextRef);
dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
......
......@@ -30,8 +30,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/VerletIntegrator.h"
#include "openmm/OpenMMContext.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/kernels.h"
#include <string>
......@@ -44,7 +44,7 @@ VerletIntegrator::VerletIntegrator(double stepSize) {
setConstraintTolerance(1e-4);
}
void VerletIntegrator::initialize(OpenMMContextImpl& contextRef) {
void VerletIntegrator::initialize(ContextImpl& contextRef) {
context = &contextRef;
kernel = context->getPlatform().createKernel(IntegrateVerletStepKernel::Name(), contextRef);
dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
......
......@@ -44,7 +44,7 @@ class BrookKernelFactory : public KernelFactory {
public:
KernelImpl* createKernelImpl( std::string name, const Platform& platform, OpenMMContextImpl& context ) const;
KernelImpl* createKernelImpl( std::string name, const Platform& platform, ContextImpl& context ) const;
};
} // namespace OpenMM
......
......@@ -278,17 +278,17 @@ class OPENMM_EXPORT BrookPlatform : public Platform {
FILE* getLog( void ) const;
/**
* This is called whenever a new OpenMMContext is created. It gives the Platform a chance to initialize
* This is called whenever a new Context is created. It gives the Platform a chance to initialize
* the context and store platform-specific data in it.
*/
void contextCreated( OpenMMContextImpl& context ) const;
void contextCreated( ContextImpl& context ) const;
/**
* This is called whenever an OpenMMContext is deleted. It gives the Platform a chance to clean up
* This is called whenever a Context is deleted. It gives the Platform a chance to clean up
* any platform-specific data that was stored in it.
*/
void contextDestroyed( OpenMMContextImpl& context ) const;
void contextDestroyed( ContextImpl& context ) const;
/**
* Get minSuggestedThreads
......
......@@ -77,7 +77,7 @@ class OPENMM_EXPORT BrookStreamFactory : public StreamFactory {
* @return StreamImpl
*/
StreamImpl* createStreamImpl( std::string name, int size, Stream::DataType type, const Platform& platform, OpenMMContextImpl& context ) const;
StreamImpl* createStreamImpl( std::string name, int size, Stream::DataType type, const Platform& platform, ContextImpl& context ) const;
/**
* Create StreamImpl
......
......@@ -31,7 +31,7 @@
#include "BrookStreamImpl.h"
#include "BrookCommon.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "BrookBondParameters.h"
namespace OpenMM {
......
......@@ -172,11 +172,11 @@ void BrookCalcGBSAOBCForceKernel::initialize( const System& system, const GBSAOB
/**
* Compute forces given particle coordinates
*
* @param context OpenMMContextImpl context
* @param context ContextImpl context
*
*/
void BrookCalcGBSAOBCForceKernel::executeForces( OpenMMContextImpl& context ){
void BrookCalcGBSAOBCForceKernel::executeForces( ContextImpl& context ){
// ---------------------------------------------------------------------------------------
......@@ -193,13 +193,13 @@ void BrookCalcGBSAOBCForceKernel::executeForces( OpenMMContextImpl& context ){
/**
* Execute the kernel to calculate the OBC energy
*
* @param context OpenMMContextImpl context
* @param context ContextImpl context
*
* @return energy
*
*/
double BrookCalcGBSAOBCForceKernel::executeEnergy( OpenMMContextImpl& context ){
double BrookCalcGBSAOBCForceKernel::executeEnergy( ContextImpl& context ){
// ---------------------------------------------------------------------------------------
......
......@@ -72,7 +72,7 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
*
*/
void executeForces( OpenMMContextImpl& context );
void executeForces( ContextImpl& context );
/**
* Execute the kernel to calculate the energy.
......@@ -84,7 +84,7 @@ class BrookCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
*
*/
double executeEnergy( OpenMMContextImpl& context );
double executeEnergy( ContextImpl& context );
/**
* Set log file reference
......
......@@ -171,11 +171,11 @@ void BrookCalcHarmonicAngleForceKernel::initialize( const System& system, const
/**
* Compute forces given particle coordinates
*
* @param context OpenMMContextImpl context
* @param context ContextImpl context
*
*/
void BrookCalcHarmonicAngleForceKernel::executeForces( OpenMMContextImpl& context ){
void BrookCalcHarmonicAngleForceKernel::executeForces( ContextImpl& context ){
// ---------------------------------------------------------------------------------------
......@@ -195,13 +195,13 @@ void BrookCalcHarmonicAngleForceKernel::executeForces( OpenMMContextImpl& contex
/**
* Execute the kernel to calculate the energy
*
* @param context OpenMMContextImpl context
* @param context ContextImpl context
*
* @return potential energy
*
*/
double BrookCalcHarmonicAngleForceKernel::executeEnergy( OpenMMContextImpl& context ){
double BrookCalcHarmonicAngleForceKernel::executeEnergy( ContextImpl& context ){
// ---------------------------------------------------------------------------------------
......
......@@ -72,7 +72,7 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
*
*/
void executeForces( OpenMMContextImpl& context );
void executeForces( ContextImpl& context );
/**
* Execute the kernel to calculate the energy.
......@@ -83,7 +83,7 @@ class BrookCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
*
*/
double executeEnergy( OpenMMContextImpl& context );
double executeEnergy( ContextImpl& context );
/**
* Set log file reference
......
......@@ -177,11 +177,11 @@ void BrookCalcHarmonicBondForceKernel::initialize( const System& system, const H
/**
* Compute forces given particle coordinates
*
* @param context OpenMMContextImpl context
* @param context ContextImpl context
*
*/
void BrookCalcHarmonicBondForceKernel::executeForces( OpenMMContextImpl& context ){
void BrookCalcHarmonicBondForceKernel::executeForces( ContextImpl& context ){
// ---------------------------------------------------------------------------------------
......@@ -201,13 +201,13 @@ void BrookCalcHarmonicBondForceKernel::executeForces( OpenMMContextImpl& context
/**
* Execute the kernel to calculate the energy
*
* @param context OpenMMContextImpl context
* @param context ContextImpl context
*
* @return potential energy
*
*/
double BrookCalcHarmonicBondForceKernel::executeEnergy( OpenMMContextImpl& context ){
double BrookCalcHarmonicBondForceKernel::executeEnergy( ContextImpl& context ){
// ---------------------------------------------------------------------------------------
......
......@@ -72,7 +72,7 @@ class BrookCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
*
*/
void executeForces( OpenMMContextImpl& context );
void executeForces( ContextImpl& context );
/**
* Execute the kernel to calculate the energy.
......@@ -83,7 +83,7 @@ class BrookCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
*
*/
double executeEnergy( OpenMMContextImpl& context );
double executeEnergy( ContextImpl& context );
/**
* Set log file reference
......
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