src/integrators/NVT.cpp

#include "integrators/IntegratorCreator.hpp"
#include "integrators/NVT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/OOPSEConstant.hpp"

namespace oopse {

static IntegratorBuilder<NVT>* NVTCreator = new IntegratorBuilder<NVT>("NVT");

NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {

    Globals* simParams = info_->getSimParams();

    if (simParams->getUseInitXSstate()) {
        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
        currSnapshot->setChi(0.0);
        currSnapshot->setIntegralOfChiDt(0.0);
    }
    
    if (!simParams->haveTargetTemp()) {
        sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
        painCave.isFatal = 1;
        painCave.severity = OOPSE_ERROR;
        simError();
    } else {
        targetTemp_ = simParams->getTargetTemp();
    }

    // We must set tauThermostat_.

    if (!simParams->haveTauThermostat()) {
        sprintf(painCave.errMsg, "If you use the constant temperature\n"
                                     "\tintegrator, you must set tauThermostat_.\n");

        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
    } else {
        tauThermostat_ = simParams->getTauThermostat();
    }

    update();
}

void NVT::update() {
    oldVel_.resize(info_->getNIntegrableObjects());
    oldJi_.resize(info_->getNIntegrableObjects());    
}
void NVT::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d Tb;
    Vector3d ji;
    double mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;

    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    double chi = currSnapshot->getChi();
    double integralOfChidt = currSnapshot->getIntegralOfChiDt();
    
    // We need the temperature at time = t for the chi update below:

    double instTemp = thermo.getTemperature();

    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {

        vel = integrableObject->getVel();
        pos = integrableObject->getPos();
        frc = integrableObject->getFrc();

        mass = integrableObject->getMass();

        // velocity half step  (use chi from previous step here):
        //vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
        vel = dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel;
        
        // position whole step
        //pos[j] += dt * vel[j];
        pos += dt * vel;

        integrableObject->setVel(vel);
        integrableObject->setPos(pos);

        if (integrableObject->isDirectional()) {

            // get and convert the torque to body frame

            Tb = integrableObject->getTrq();
            integrableObject->lab2Body(Tb);

            // get the angular momentum, and propagate a half step

            ji = integrableObject->getJ();

            //ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
            ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji;
            rotAlgo->rotate(integrableObject, ji, dt);

            integrableObject->setJ(ji);
        }
    }

    }
    
    //constraintAlgorithm->doConstrainA();

    // Finally, evolve chi a half step (just like a velocity) using
    // temperature at time t, not time t+dt/2

    
    chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
    integralOfChidt += chi * dt2;

    currSnapshot->setChi(chi);
    currSnapshot->setIntegralOfChiDt(integralOfChidt);
}

void NVT::moveB() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    
    Vector3d Tb;
    Vector3d ji;    
    Vector3d vel;
    Vector3d frc;
    double mass;
    double instTemp;
    int index;
    // Set things up for the iteration:

    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    double chi = currSnapshot->getChi();
    double oldChi = chi;
    double  prevChi;
    double integralOfChidt = currSnapshot->getIntegralOfChiDt();

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {
                oldVel_[index] = integrableObject->getVel();
                oldJi_[index] = integrableObject->getJ();                
        }
        ++index;               
    }

    // do the iteration:

    for(int k = 0; k < maxIterNum_; k++) {
        index = 0;
        instTemp = thermo.getTemperature();

        // evolve chi another half step using the temperature at t + dt/2

        prevChi = chi;
        chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);

        for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
            for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
                   integrableObject = mol->nextIntegrableObject(j)) {

                frc = integrableObject->getFrc();
                vel = integrableObject->getVel();

                mass = integrableObject->getMass();

                // velocity half step
                //for(j = 0; j < 3; j++)
                //    vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi);
                vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index];
            
                integrableObject->setVel(vel);

                if (integrableObject->isDirectional()) {

                    // get and convert the torque to body frame

                    Tb = integrableObject->getTrq();
                    integrableObject->lab2Body(Tb);

                    //for(j = 0; j < 3; j++)
                    //    ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi);
                    ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index];

                    integrableObject->setJ(ji);
                }
            }
        }
    

        //constraintAlgorithm->doConstrainB();

        if (fabs(prevChi - chi) <= chiTolerance_)
            break;

        ++index;
    }

    integralOfChidt += dt2 * chi;

    currSnapshot->setChi(chi);
    currSnapshot->setIntegralOfChiDt(integralOfChidt);
}


double NVT::calcConservedQuantity() {
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    double chi = currSnapshot->getChi();
    double integralOfChidt = currSnapshot->getIntegralOfChiDt();
    double conservedQuantity;
    double fkBT;
    double Energy;
    double thermostat_kinetic;
    double thermostat_potential;
    
    fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_;

    Energy = thermo.getTotalE();

    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);

    thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

    return conservedQuantity;
}


}//end namespace oopse
Revision:	1841
Committed:	Fri Dec 3 17:59:45 2004 UTC (19 years, 7 months ago) by tim
File size:	7553 byte(s)
Log Message:	begin to fix bugs
#	User	Rev	Content
1	tim	1837	#include "integrators/IntegratorCreator.hpp"
2	tim	1821	#include "integrators/NVT.hpp"
3			#include "primitives/Molecule.hpp"
4			#include "utils/simError.h"
5			#include "utils/OOPSEConstant.hpp"
6	tim	1837
7	tim	1765	namespace oopse {
8	tim	1762
9	tim	1837	static IntegratorBuilder<NVT>* NVTCreator = new IntegratorBuilder<NVT>("NVT");
10
11	tim	1774	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
12	tim	1762
13	tim	1841	Globals* simParams = info_->getSimParams();
14	tim	1762
15	tim	1841	if (simParams->getUseInitXSstate()) {
16	tim	1774	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
17			currSnapshot->setChi(0.0);
18			currSnapshot->setIntegralOfChiDt(0.0);
19			}
20
21	tim	1841	if (!simParams->haveTargetTemp()) {
22	tim	1774	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
23			painCave.isFatal = 1;
24			painCave.severity = OOPSE_ERROR;
25			simError();
26			} else {
27	tim	1841	targetTemp_ = simParams->getTargetTemp();
28	tim	1774	}
29	tim	1762
30	tim	1774	// We must set tauThermostat_.
31	tim	1762
32	tim	1841	if (!simParams->haveTauThermostat()) {
33	tim	1774	sprintf(painCave.errMsg, "If you use the constant temperature\n"
34			"\tintegrator, you must set tauThermostat_.\n");
35	tim	1762
36	tim	1774	painCave.severity = OOPSE_ERROR;
37			painCave.isFatal = 1;
38			simError();
39			} else {
40	tim	1841	tauThermostat_ = simParams->getTauThermostat();
41	tim	1762	}
42
43	tim	1774	update();
44	tim	1762	}
45
46	tim	1774	void NVT::update() {
47			oldVel_.resize(info_->getNIntegrableObjects());
48			oldJi_.resize(info_->getNIntegrableObjects());
49			}
50	tim	1765	void NVT::moveA() {
51	tim	1821	SimInfo::MoleculeIterator i;
52			Molecule::IntegrableObjectIterator j;
53	tim	1765	Molecule* mol;
54			StuntDouble* integrableObject;
55	tim	1762	Vector3d Tb;
56			Vector3d ji;
57			double mass;
58			Vector3d vel;
59			Vector3d pos;
60			Vector3d frc;
61
62	tim	1821	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
63			double chi = currSnapshot->getChi();
64			double integralOfChidt = currSnapshot->getIntegralOfChiDt();
65
66	tim	1762	// We need the temperature at time = t for the chi update below:
67
68	tim	1821	double instTemp = thermo.getTemperature();
69	tim	1762
70	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
71			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
72			integrableObject = mol->nextIntegrableObject(j)) {
73	tim	1762
74	tim	1765	vel = integrableObject->getVel();
75			pos = integrableObject->getPos();
76			frc = integrableObject->getFrc();
77	tim	1762
78	tim	1765	mass = integrableObject->getMass();
79	tim	1762
80	tim	1765	// velocity half step (use chi from previous step here):
81	tim	1821	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
82			vel = dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
83	tim	1765
84			// position whole step
85			//pos[j] += dt * vel[j];
86	tim	1774	pos += dt * vel;
87	tim	1762
88	tim	1765	integrableObject->setVel(vel);
89			integrableObject->setPos(pos);
90	tim	1762
91	tim	1765	if (integrableObject->isDirectional()) {
92	tim	1762
93			// get and convert the torque to body frame
94
95	tim	1765	Tb = integrableObject->getTrq();
96			integrableObject->lab2Body(Tb);
97	tim	1762
98			// get the angular momentum, and propagate a half step
99
100	tim	1765	ji = integrableObject->getJ();
101	tim	1762
102	tim	1821	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
103			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
104			rotAlgo->rotate(integrableObject, ji, dt);
105	tim	1762
106	tim	1765	integrableObject->setJ(ji);
107	tim	1762	}
108			}
109
110	tim	1765	}
111
112	tim	1774	//constraintAlgorithm->doConstrainA();
113	tim	1762
114			// Finally, evolve chi a half step (just like a velocity) using
115			// temperature at time t, not time t+dt/2
116
117	tim	1765
118	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
119			integralOfChidt += chi * dt2;
120	tim	1762
121	tim	1765	currSnapshot->setChi(chi);
122			currSnapshot->setIntegralOfChiDt(integralOfChidt);
123	tim	1762	}
124
125	tim	1765	void NVT::moveB() {
126	tim	1821	SimInfo::MoleculeIterator i;
127			Molecule::IntegrableObjectIterator j;
128	tim	1765	Molecule* mol;
129			StuntDouble* integrableObject;
130
131			Vector3d Tb;
132			Vector3d ji;
133			Vector3d vel;
134			Vector3d frc;
135	tim	1762	double mass;
136			double instTemp;
137	tim	1765	int index;
138	tim	1762	// Set things up for the iteration:
139
140	tim	1765	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
141			double chi = currSnapshot->getChi();
142	tim	1821	double oldChi = chi;
143			double prevChi;
144	tim	1765	double integralOfChidt = currSnapshot->getIntegralOfChiDt();
145	tim	1762
146	tim	1765	index = 0;
147			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
148			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
149			integrableObject = mol->nextIntegrableObject(j)) {
150			oldVel_[index] = integrableObject->getVel();
151			oldJi_[index] = integrableObject->getJ();
152	tim	1762	}
153	tim	1765	++index;
154	tim	1762	}
155
156			// do the iteration:
157
158	tim	1765	for(int k = 0; k < maxIterNum_; k++) {
159			index = 0;
160	tim	1821	instTemp = thermo.getTemperature();
161	tim	1762
162			// evolve chi another half step using the temperature at t + dt/2
163
164			prevChi = chi;
165	tim	1774	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
166	tim	1762
167	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
168			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
169			integrableObject = mol->nextIntegrableObject(j)) {
170	tim	1762
171	tim	1765	frc = integrableObject->getFrc();
172			vel = integrableObject->getVel();
173	tim	1762
174	tim	1765	mass = integrableObject->getMass();
175	tim	1762
176	tim	1765	// velocity half step
177			//for(j = 0; j < 3; j++)
178	tim	1821	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3i + j]chi);
179			vel = oldVel_[index] + dt2/massOOPSEConstant::energyConvert frc - dt2chioldVel_[index];
180	tim	1765
181			integrableObject->setVel(vel);
182	tim	1762
183	tim	1765	if (integrableObject->isDirectional()) {
184	tim	1762
185	tim	1765	// get and convert the torque to body frame
186	tim	1762
187	tim	1765	Tb = integrableObject->getTrq();
188			integrableObject->lab2Body(Tb);
189	tim	1762
190	tim	1765	//for(j = 0; j < 3; j++)
191	tim	1821	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
192			ji += dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
193	tim	1762
194	tim	1765	integrableObject->setJ(ji);
195			}
196	tim	1762	}
197			}
198	tim	1765
199	tim	1762
200	tim	1774	//constraintAlgorithm->doConstrainB();
201	tim	1762
202	tim	1821	if (fabs(prevChi - chi) <= chiTolerance_)
203	tim	1762	break;
204	tim	1765
205			++index;
206	tim	1762	}
207
208	tim	1774	integralOfChidt += dt2 * chi;
209	tim	1762
210	tim	1765	currSnapshot->setChi(chi);
211			currSnapshot->setIntegralOfChiDt(integralOfChidt);
212	tim	1762	}
213
214
215	tim	1774	double NVT::calcConservedQuantity() {
216	tim	1821	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
217			double chi = currSnapshot->getChi();
218			double integralOfChidt = currSnapshot->getIntegralOfChiDt();
219	tim	1762	double conservedQuantity;
220			double fkBT;
221			double Energy;
222			double thermostat_kinetic;
223			double thermostat_potential;
224	tim	1821
225			fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
226	tim	1762
227	tim	1821	Energy = thermo.getTotalE();
228	tim	1762
229	tim	1821	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
230	tim	1762
231	tim	1821	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
232	tim	1762
233			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
234
235			return conservedQuantity;
236			}
237
238
239	tim	1765	}//end namespace oopse