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Unverified Commit cf1d38d8 authored by Andy Simmonett's avatar Andy Simmonett
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Remove system from NHC constructor

parent cca3e11a
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Showing with 203 additions and 118 deletions
openmmapi/include/openmm/NoseHooverIntegrator.h
View file @ cf1d38d8
......@@ -41,7 +41,6 @@
namespace OpenMM {
class System;
/**
* This is an Integrator which simulates a System using one or more Nose Hoover chain
* thermostats, using the velocity Verlet propagation algorithm.
......@@ -60,8 +59,6 @@ public:
* Create a NoseHooverIntegrator.
*
* @param stepSize the step size with which to integrate the system (in picoseconds)
* @param system the system to be thermostated. Note: this must be setup, i.e. all
* particles should have been added, before calling this function.
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the interaction with the heat bath (in 1/ps).
* @param chainLength the number of beads in the Nose-Hoover chain.
......@@ -69,7 +66,7 @@ public:
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
explicit NoseHooverIntegrator(double stepSize, System &system, double temperature, int collisionFrequnency,
explicit NoseHooverIntegrator(double stepSize, double temperature, int collisionFrequnency,
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
virtual ~NoseHooverIntegrator();
......@@ -82,8 +79,6 @@ public:
/**
* Add a simple Nose-Hoover Chain thermostat to control the temperature of the full system
*
* @param system the system to be thermostated. Note: this must be setup, i.e. all
* particles should have been added, before calling this function.
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the interaction with the heat bath (in 1/ps).
* @param chainLength the number of beads in the Nose-Hoover chain.
......@@ -91,7 +86,7 @@ public:
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
int addThermostat(System& system, double temperature, double collisionFrequency,
int addThermostat(double temperature, double collisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki);
/**
* Add a Nose-Hoover Chain thermostat to control the temperature of a collection of atoms and/or pairs of
......@@ -100,8 +95,6 @@ public:
* connected atoms may be provided; in this case both the center of mass absolute motion of each pair is
* controlled as well as their motion relative to each other, which is independently thermostated.
*
* @param system the system to be thermostated. Note: this must be setup, i.e. all
* particles should have been added, before calling this function.
* @param thermostatedParticles list of particle ids to be thermostated.
* @param thermostatedPairs a list of pairs of connected atoms whose absolute center of mass motion
* and motion relative to one another will be independently thermostated.
......@@ -116,7 +109,7 @@ public:
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
int addSubsystemThermostat(System& system, const std::vector<int>& thermostatedParticles,
int addSubsystemThermostat(const std::vector<int>& thermostatedParticles,
const std::vector< std::pair< int, int> >& thermostatedPairs,
double temperature, double relativeTemperature,
double collisionFrequency, double relativeCollisionFrequency,
......@@ -221,6 +214,10 @@ protected:
* It will also get called again if the application calls reinitialize() on the Context.
*/
void initialize(ContextImpl& context);
/**
* Goes through the list of requested thermostat data and creates the thermostat chains.
*/
void createThermostats(const System& system);
/**
* This will be called by the Context when it is destroyed to let the Integrator do any necessary
* cleanup. It will also get called again if the application calls reinitialize() on the Context.
......@@ -235,6 +232,25 @@ protected:
*/
virtual double computeKineticEnergy();
struct ThermostatData {
std::vector<int> thermostatedParticles;
std::vector< std::pair< int, int> > thermostatedPairs;
double temperature;
double relativeTemperature;
double collisionFrequency;
double relativeCollisionFrequency;
int chainLength;
int numMTS;
int numYoshidaSuzuki;
ThermostatData(const std::vector<int>&particles, const std::vector<std::pair<int, int>> &pairs, double temp,
double relTemp, double freq, double relFreq, int length, int MTS, int YS) :
thermostatedParticles(particles), thermostatedPairs(pairs), temperature(temp),
relativeTemperature(relTemp), collisionFrequency(freq), relativeCollisionFrequency(relFreq),
chainLength(length), numMTS(MTS), numYoshidaSuzuki(YS) {}
};
std::vector<ThermostatData> thermostatData;
std::vector<NoseHooverChain> noseHooverChains;
bool forcesAreValid;
Kernel vvKernel, nhcKernel;
......
openmmapi/src/NoseHooverIntegrator.cpp
View file @ cf1d38d8
......@@ -52,11 +52,11 @@ NoseHooverIntegrator::NoseHooverIntegrator(double stepSize):
setStepSize(stepSize);
setConstraintTolerance(1e-5);
}
NoseHooverIntegrator::NoseHooverIntegrator(double stepSize, System &system, double temperature, int collisionFrequnency,
NoseHooverIntegrator::NoseHooverIntegrator(double stepSize, double temperature, int collisionFrequnency,
int chainLength, int numMTS, int numYoshidaSuzuki) : forcesAreValid(false) {
setStepSize(stepSize);
setConstraintTolerance(1e-5);
addThermostat(system, temperature, collisionFrequnency, chainLength, numMTS, numYoshidaSuzuki);
addThermostat(temperature, collisionFrequnency, chainLength, numMTS, numYoshidaSuzuki);
}
NoseHooverIntegrator::~NoseHooverIntegrator() {}
......@@ -65,48 +65,53 @@ std::pair<double, double> NoseHooverIntegrator::propagateChain(std::pair<double,
return nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, noseHooverChains.at(chainID), kineticEnergy, getStepSize());
}
int NoseHooverIntegrator::addThermostat(System& system, double temperature, double collisionFrequency,
int NoseHooverIntegrator::addThermostat(double temperature, double collisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki) {
std::vector<int> thermostatedParticles;
for(int particle = 0; particle < system.getNumParticles(); ++particle) {
double mass = system.getParticleMass(particle);
if ( (mass > 0) && (mass < 0.8) ){
std::cout << "Warning: Found particles with mass between 0.0 and 0.8 dalton. Did you mean to make a DrudeVelocityVerletIntegrator instead? "
"The thermostat you are about to use will not treat these particles as Drude particles!" << std::endl;
}
if(system.getParticleMass(particle) > 0) {
thermostatedParticles.push_back(particle);
}
}
return addSubsystemThermostat(system, thermostatedParticles, std::vector<std::pair<int, int>>(), temperature, temperature,
return addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature, temperature,
collisionFrequency, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
}
int NoseHooverIntegrator::addSubsystemThermostat(System& system, const std::vector<int>& thermostatedParticles,
int NoseHooverIntegrator::addSubsystemThermostat(const std::vector<int>& thermostatedParticles,
const std::vector< std::pair< int, int> > &thermostatedPairs,
double temperature, double relativeTemperature,
double collisionFrequency, double relativeCollisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki) {
if (context) {
throw OpenMMException("Nose-Hoover chains cannot be added after binding this integrator to a context.");
}
auto data = ThermostatData(thermostatedParticles, thermostatedPairs, temperature,
relativeTemperature, collisionFrequency,
relativeCollisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
thermostatData.push_back(data);
return thermostatData.size() - 1;
}
void NoseHooverIntegrator::createThermostats(const System &system) {
for (const auto &thermostat : thermostatData) {
// figure out the number of DOFs
int nDOF = 3*(thermostatedParticles.size() + thermostatedPairs.size());
int nDOF = 3*(thermostat.thermostatedParticles.size() + thermostat.thermostatedPairs.size());
for (int constraintNum = 0; constraintNum < system.getNumConstraints(); constraintNum++) {
int particle1, particle2;
double distance;
system.getConstraintParameters(constraintNum, particle1, particle2, distance);
bool particle1_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(), thermostatedParticles.end(), particle1)
!= thermostatedParticles.end())) ||
(std::find_if(thermostatedPairs.begin(), thermostatedPairs.end(),
[&particle1](const std::pair<int, int>& pair){ return pair.first == particle1 || pair.second == particle1;})
!= thermostatedPairs.end());
bool particle2_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(), thermostatedParticles.end(), particle2)
!= thermostatedParticles.end())) ||
(std::find_if(thermostatedPairs.begin(), thermostatedPairs.end(),
[&particle2](const std::pair<int, int>& pair){ return pair.first == particle2 || pair.second == particle2;})
!= thermostatedPairs.end());
bool particle1_in_thermostatedParticles = ((std::find(thermostat.thermostatedParticles.begin(),
thermostat.thermostatedParticles.end(), particle1)
!= thermostat.thermostatedParticles.end())) ||
(std::find_if(thermostat.thermostatedPairs.begin(),
thermostat.thermostatedPairs.end(),
[&particle1](const std::pair<int, int>& pair){
return pair.first == particle1 || pair.second == particle1;})
!= thermostat.thermostatedPairs.end());
bool particle2_in_thermostatedParticles = ((std::find(thermostat.thermostatedParticles.begin(),
thermostat.thermostatedParticles.end(), particle2)
!= thermostat.thermostatedParticles.end())) ||
(std::find_if(thermostat.thermostatedPairs.begin(),
thermostat.thermostatedPairs.end(),
[&particle2](const std::pair<int, int>& pair){
return pair.first == particle2 || pair.second == particle2;})
!= thermostat.thermostatedPairs.end());
if ((system.getParticleMass(particle1) > 0) && (system.getParticleMass(particle2) > 0)){
if ((particle1_in_thermostatedParticles && !particle2_in_thermostatedParticles) ||
(!particle1_in_thermostatedParticles && particle2_in_thermostatedParticles)){
......@@ -118,16 +123,34 @@ int NoseHooverIntegrator::addSubsystemThermostat(System& system, const std::vect
}
}
}
// remove 3 degrees of freedom from thermostats that act on absolute motions
int numForces = system.getNumForces();
if (thermostatedPairs.size() == 0){ // remove 3 degrees of freedom from thermostats that act on absolute motions
if (thermostat.thermostatedPairs.size() == 0){
for (int forceNum = 0; forceNum < numForces; ++forceNum) {
if (dynamic_cast<CMMotionRemover*>(&system.getForce(forceNum))) nDOF -= 3;
if (dynamic_cast<const CMMotionRemover*>(&system.getForce(forceNum))) nDOF -= 3;
}
}
// create and add new chain
int chainID = noseHooverChains.size();
auto chain = NoseHooverChain(thermostat.temperature, thermostat.relativeTemperature,
thermostat.collisionFrequency, thermostat.relativeCollisionFrequency,
nDOF, thermostat.chainLength, thermostat.numMTS,
thermostat.numYoshidaSuzuki, chainID,
thermostat.thermostatedParticles, thermostat.thermostatedPairs);
noseHooverChains.push_back(chain);
}
for (int chain1 = 0; chain1 < noseHooverChains.size(); ++chain1){
const auto& nhc = noseHooverChains[chain1];
// make sure that thermostats do not overlap
for (auto &other_nhc: noseHooverChains) {
for (auto &particle: thermostatedParticles){
for (int chain2 = 0; chain2 < chain1; ++chain2){
const auto& other_nhc = noseHooverChains[chain2];
for (auto &particle: nhc.getThermostatedAtoms()){
bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
particle) != other_nhc.getThermostatedAtoms().end()) ||
......@@ -140,14 +163,35 @@ int NoseHooverIntegrator::addSubsystemThermostat(System& system, const std::vect
"but particles can only be thermostated by one thermostat.");
}
}
for (auto &pair: nhc.getThermostatedPairs()){
bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
pair.first) != other_nhc.getThermostatedAtoms().end()) ||
(std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
pair.second) != other_nhc.getThermostatedAtoms().end()) ||
(std::find_if(other_nhc.getThermostatedPairs().begin(),
other_nhc.getThermostatedPairs().end(),
[&pair](const std::pair<int, int>& other_pair){
return pair.first == other_pair.first || pair.first == other_pair.second ||
pair.second == other_pair.first || pair.second == other_pair.second;})
!= other_nhc.getThermostatedPairs().end());
if (isParticleInOtherChain){
throw OpenMMException("Found pair " + std::to_string(pair.first) + "," +
std::to_string(pair.second) + " in a different NoseHooverChain, "
"but particles can only be thermostated by one thermostat.");
}
}
}
// create and add new chain
int chainID = noseHooverChains.size();
auto nhc = NoseHooverChain(temperature, relativeTemperature, collisionFrequency, relativeCollisionFrequency,
nDOF, chainLength, numMTS, numYoshidaSuzuki, chainID, thermostatedParticles, thermostatedPairs);
noseHooverChains.push_back(nhc);
return chainID;
// make sure that massless particles are not thermostated
for(auto particle: nhc.getThermostatedAtoms()){
double mass = system.getParticleMass(particle);
if (mass < 1e-8) {
throw OpenMMException("Found a particle with no mass (" + std::to_string(particle) + ") in a thermostat. Massless particles cannot be thermostated.");
}
}
}
}
double NoseHooverIntegrator::getTemperature(int chainID) const {
......@@ -247,6 +291,7 @@ double NoseHooverIntegrator::computeHeatBathEnergy() {
void NoseHooverIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
context = &contextRef;
owner = &contextRef.getOwner();
vvKernel = context->getPlatform().createKernel(IntegrateVelocityVerletStepKernel::Name(), contextRef);
......@@ -254,6 +299,26 @@ void NoseHooverIntegrator::initialize(ContextImpl& contextRef) {
nhcKernel = context->getPlatform().createKernel(NoseHooverChainKernel::Name(), contextRef);
nhcKernel.getAs<NoseHooverChainKernel>().initialize();
forcesAreValid = false;
// check for drude particles and build the Nose-Hoover Chains
const System& system = context->getSystem();
for (auto& thermostat: thermostatData){
// if there are no thermostated particles or pairs in the lists this is a regular thermostat for the whole (non-Drude) system
if ( (thermostat.thermostatedParticles.size() == 0) && (thermostat.thermostatedPairs.size() == 0) ){
for(int particle = 0; particle < system.getNumParticles(); ++particle) {
double mass = system.getParticleMass(particle);
if ( (mass > 0) && (mass < 0.8) ){
std::cout << "Warning: Found particles with mass between 0.0 and 0.8 dalton. Did you mean to make a DrudeVelocityVerletIntegrator instead? "
"The thermostat you are about to use will not treat these particles as Drude particles!" << std::endl;
}
if(system.getParticleMass(particle) > 0) {
thermostat.thermostatedParticles.push_back(particle);
}
}
}
}
createThermostats(system);
}
void NoseHooverIntegrator::cleanup() {
......
plugins/drude/openmmapi/include/openmm/DrudeNoseHooverIntegrator.h
View file @ cf1d38d8
......@@ -55,8 +55,6 @@ public:
* Create a DrudeNoseHooverIntegrator.
*
* @param stepSize the step size with which to integrator the system (in picoseconds)
* @param system the system to be thermostated. Note: this must be setup, i.e. all
* particles should have been added, before calling this function.
* @param temperature the target temperature for the system.
* @param drudeTemperature the target temperature for the Drude particles, relative to their parent atom.
* @param collisionFrequency the frequency of the system's interaction with the heat bath (in 1/ps).
......@@ -66,7 +64,7 @@ public:
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
DrudeNoseHooverIntegrator(double stepSize, System &system, double temperature, double drudeTemperature,
DrudeNoseHooverIntegrator(double stepSize, double temperature, double drudeTemperature,
double collisionFrequency, double drudeCollisionFrequency,
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
......
plugins/drude/openmmapi/src/DrudeNoseHooverIntegrator.cpp
View file @ cf1d38d8
......@@ -46,49 +46,36 @@ using namespace OpenMM;
using std::string;
using std::vector;
DrudeNoseHooverIntegrator::DrudeNoseHooverIntegrator(double stepSize, System &system, double temperature, double drudeTemperature,
DrudeNoseHooverIntegrator::DrudeNoseHooverIntegrator(double stepSize, double temperature, double drudeTemperature,
double collisionFrequency, double drudeCollisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki) :
NoseHooverIntegrator(stepSize) {
const DrudeForce* drudeForce = NULL;
for (int i = 0; i < system.getNumForces(); i++)
if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
if (drudeForce == NULL)
drudeForce = dynamic_cast<const DrudeForce*>(&system.getForce(i));
else
throw OpenMMException("The System contains multiple DrudeForces");
}
if (drudeForce == NULL)
throw OpenMMException("The System does not contain a DrudeForce");
std::set<int> realParticlesSet;
vector<int> realParticles, drudeParticles, drudeParents;
vector<std::pair<int, int>> drudePairs;
for (int i = 0; i < system.getNumParticles(); i++) {
if (system.getParticleMass(i) > 0.0) realParticlesSet.insert(i);
}
for (int i = 0; i < drudeForce->getNumParticles(); i++) {
int p, p1, p2, p3, p4;
double charge, polarizability, aniso12, aniso34;
drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
realParticlesSet.erase(p);
realParticlesSet.erase(p1);
drudePairs.push_back({p,p1});
}
for(const auto &p : realParticlesSet) realParticles.push_back(p);
addSubsystemThermostat(system, realParticles, drudePairs, temperature, drudeTemperature, collisionFrequency,
drudeCollisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
drudeTemperature, collisionFrequency, drudeCollisionFrequency,
chainLength, numMTS, numYoshidaSuzuki);
}
DrudeNoseHooverIntegrator::~DrudeNoseHooverIntegrator() { }
void DrudeNoseHooverIntegrator::initialize(ContextImpl& contextRef) {
NoseHooverIntegrator::initialize(contextRef);
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
context = &contextRef;
owner = &contextRef.getOwner();
vvKernel = context->getPlatform().createKernel(IntegrateVelocityVerletStepKernel::Name(), contextRef);
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().initialize(contextRef.getSystem(), *this);
nhcKernel = context->getPlatform().createKernel(NoseHooverChainKernel::Name(), contextRef);
nhcKernel.getAs<NoseHooverChainKernel>().initialize();
forcesAreValid = false;
// check for drude particles and build the Nose-Hoover Chains
const System& system = context->getSystem();
const DrudeForce* drudeForce = NULL;
const System& system = contextRef.getSystem();
bool hasCMMotionRemover = false;
for (int i = 0; i < system.getNumForces(); i++){
if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
......@@ -107,8 +94,27 @@ void DrudeNoseHooverIntegrator::initialize(ContextImpl& contextRef) {
std::cout << "Warning: Did not find a center-of-mass motion remover in the system. "
"This is problematic when using Drude." << std::endl;
}
context = &contextRef;
owner = &contextRef.getOwner();
for (auto& thermostat: thermostatData){
if ( (thermostat.thermostatedParticles.size() == 0) && (thermostat.thermostatedPairs.size() == 0) ){
std::set<int> realParticlesSet;
vector<int> realParticles, drudeParticles, drudeParents;
vector<std::pair<int, int>> drudePairs;
for (int i = 0; i < system.getNumParticles(); i++) {
if (system.getParticleMass(i) > 0.0) realParticlesSet.insert(i);
}
for (int i = 0; i < drudeForce->getNumParticles(); i++) {
int p, p1, p2, p3, p4;
double charge, polarizability, aniso12, aniso34;
drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
realParticlesSet.erase(p);
realParticlesSet.erase(p1);
thermostat.thermostatedPairs.push_back({p,p1});
}
for(const auto &p : realParticlesSet) thermostat.thermostatedParticles.push_back(p);
}
}
createThermostats(system);
}
double DrudeNoseHooverIntegrator::computeDrudeKineticEnergy() {
......
plugins/drude/tests/TestDrudeNoseHoover.h
View file @ cf1d38d8
......@@ -120,7 +120,7 @@ void testWaterBox(Platform& platform){
double frequency = 100.0;
double frequencyDrude = 80.0;
int randomSeed = 100;
DrudeNoseHooverIntegrator integ(0.0005, system, temperature, temperatureDrude,
DrudeNoseHooverIntegrator integ(0.0005, temperature, temperatureDrude,
frequency, frequencyDrude, chainLength, numMTS, numYS);;
Context context(system, integ, platform);
context.setPositions(positions);
......
tests/TestNoseHooverThermostat.h
View file @ cf1d38d8
......@@ -66,7 +66,7 @@ void testHarmonicOscillator() {
harmonic_restraint->addParticle(0);
system.addForce(harmonic_restraint);
NoseHooverIntegrator integrator(0.001);
integrator.addThermostat(system, temperature, frequency, chain_length, mts, ys);
integrator.addThermostat(temperature, frequency, chain_length, mts, ys);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
......@@ -162,10 +162,10 @@ void testDimerBox(bool constrain=true) {
int numMTS = 3;
int numYS = 3;
int chainLength = 5;
auto integrator = simpleConstruct ? NoseHooverIntegrator(0.001, system, temperature, collisionFrequency, chainLength, numMTS, numYS)
auto integrator = simpleConstruct ? NoseHooverIntegrator(0.001, temperature, collisionFrequency, chainLength, numMTS, numYS)
: NoseHooverIntegrator(0.001);
if (!simpleConstruct)
integrator.addThermostat(system, temperature, collisionFrequency, chainLength, numMTS, numYS);
integrator.addThermostat(temperature, collisionFrequency, chainLength, numMTS, numYS);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(temperature);
......@@ -225,9 +225,9 @@ void testCheckpoints() {
double kineticEnergy = 1e6;
double temperature=300, collisionFrequency=1, chainLength=3, numMTS=3, numYS=3;
chainLength = 10;
integrator.addSubsystemThermostat(system, std::vector<int>(), std::vector<std::pair<int,int>>{{0,1}}, temperature, temperature, collisionFrequency, collisionFrequency,
integrator.addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int,int>>{{0,1}}, temperature, temperature, collisionFrequency, collisionFrequency,
chainLength, numMTS, numYS);
newIntegrator.addSubsystemThermostat(system, std::vector<int>(), std::vector<std::pair<int,int>>{{0,1}}, temperature, temperature, collisionFrequency, collisionFrequency,
newIntegrator.addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int,int>>{{0,1}}, temperature, temperature, collisionFrequency, collisionFrequency,
chainLength, numMTS, numYS);
Context context(system, integrator, platform);
Context newContext(system, newIntegrator, platform);
......
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