src/integrators/NVT.cpp

#inlcude "integrators/NVT.hpp"

namespace oopse {

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

    Globals* globals = info_->getGlobals();

    if (globals->getUseInitXSstate()) {
        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
        currSnapshot->setChi(0.0);
        currSnapshot->setIntegralOfChiDt(0.0);
    }
    
    if (!globals->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_ = globals->getTargetTemp();
    }

    // We must set tauThermostat_.

    if (!globals->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_ = globals->getTauThermostat();
    }

    update();
}

NVT::~NVT() {
}

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

    double instTemp;

    // We need the temperature at time = t for the chi update below:

    instTemp = tStats->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 ) * eConvert - vel[j]*chi);
        vel = dt2 *eConvert/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] * eConvert - ji[j]*chi);
            ji += dt2*eConvert*Tb - dt2*ch *ji;
            this->rotationPropagation(integrableObject, ji);

            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

    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    double chi = currSnapshot->getChi();
    double integralOfChidt = currSnapshot->getIntegralOfChiDt();
    
    chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
    integralOfChidt += chi * dt2;

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

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

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

    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 = tStats->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 ) * eConvert - oldVel_[3*i + j]*chi);
                vel = oldVel_ + dt2/mass*eConvert * 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] * eConvert - oldJi_[3*i+j]*chi);
                    ji += dt2*eConvert*Tb - dt2*ch *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() {
    double conservedQuantity;
    double fkBT;
    double Energy;
    double thermostat_kinetic;
    double thermostat_potential;

    fkBT = info_->getNdf() *kB *targetTemp_;

    Energy = tStats->getTotalE();

    thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * eConvert);

    thermostat_potential = fkBT * integralOfChidt / eConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

    return conservedQuantity;
}


}//end namespace oopse
Revision:	1774
Committed:	Tue Nov 23 23:12:23 2004 UTC (19 years, 9 months ago) by tim
File size:	6973 byte(s)
Log Message:	refactory NPT integrator
#	User	Rev	Content
1	tim	1765	#inlcude "integrators/NVT.hpp"
2	tim	1762
3	tim	1765	namespace oopse {
4	tim	1762
5	tim	1774	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
6	tim	1762
7	tim	1774	Globals* globals = info_->getGlobals();
8	tim	1762
9	tim	1774	if (globals->getUseInitXSstate()) {
10			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
11			currSnapshot->setChi(0.0);
12			currSnapshot->setIntegralOfChiDt(0.0);
13			}
14
15			if (!globals->haveTargetTemp()) {
16			sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
17			painCave.isFatal = 1;
18			painCave.severity = OOPSE_ERROR;
19			simError();
20			} else {
21			targetTemp_ = globals->getTargetTemp();
22			}
23	tim	1762
24	tim	1774	// We must set tauThermostat_.
25	tim	1762
26	tim	1774	if (!globals->haveTauThermostat()) {
27			sprintf(painCave.errMsg, "If you use the constant temperature\n"
28			"\tintegrator, you must set tauThermostat_.\n");
29	tim	1762
30	tim	1774	painCave.severity = OOPSE_ERROR;
31			painCave.isFatal = 1;
32			simError();
33			} else {
34			tauThermostat_ = globals->getTauThermostat();
35	tim	1762	}
36
37	tim	1774	update();
38	tim	1762	}
39
40	tim	1765	NVT::~NVT() {
41	tim	1762	}
42
43	tim	1774	void NVT::update() {
44			oldVel_.resize(info_->getNIntegrableObjects());
45			oldJi_.resize(info_->getNIntegrableObjects());
46			}
47	tim	1765	void NVT::moveA() {
48			typename SimInfo::MoleculeIterator i;
49			typename Molecule::IntegrableObjectIterator j;
50			Molecule* mol;
51			StuntDouble* integrableObject;
52	tim	1762	Vector3d Tb;
53			Vector3d ji;
54			double mass;
55			Vector3d vel;
56			Vector3d pos;
57			Vector3d frc;
58
59			double instTemp;
60
61			// We need the temperature at time = t for the chi update below:
62
63			instTemp = tStats->getTemperature();
64
65	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
66			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
67			integrableObject = mol->nextIntegrableObject(j)) {
68	tim	1762
69	tim	1765	vel = integrableObject->getVel();
70			pos = integrableObject->getPos();
71			frc = integrableObject->getFrc();
72	tim	1762
73	tim	1765	mass = integrableObject->getMass();
74	tim	1762
75	tim	1765	// velocity half step (use chi from previous step here):
76	tim	1774	//vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
77			vel = dt2 eConvert/massfrc - dt2chivel;
78	tim	1765
79			// position whole step
80			//pos[j] += dt * vel[j];
81	tim	1774	pos += dt * vel;
82	tim	1762
83	tim	1765	integrableObject->setVel(vel);
84			integrableObject->setPos(pos);
85	tim	1762
86	tim	1765	if (integrableObject->isDirectional()) {
87	tim	1762
88			// get and convert the torque to body frame
89
90	tim	1765	Tb = integrableObject->getTrq();
91			integrableObject->lab2Body(Tb);
92	tim	1762
93			// get the angular momentum, and propagate a half step
94
95	tim	1765	ji = integrableObject->getJ();
96	tim	1762
97	tim	1774	//ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
98			ji += dt2eConvertTb - dt2ch ji;
99	tim	1765	this->rotationPropagation(integrableObject, ji);
100	tim	1762
101	tim	1765	integrableObject->setJ(ji);
102	tim	1762	}
103			}
104
105	tim	1765	}
106
107	tim	1774	//constraintAlgorithm->doConstrainA();
108	tim	1762
109			// Finally, evolve chi a half step (just like a velocity) using
110			// temperature at time t, not time t+dt/2
111
112	tim	1765	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113			double chi = currSnapshot->getChi();
114			double integralOfChidt = currSnapshot->getIntegralOfChiDt();
115
116	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
117			integralOfChidt += chi * dt2;
118	tim	1762
119	tim	1765	currSnapshot->setChi(chi);
120			currSnapshot->setIntegralOfChiDt(integralOfChidt);
121	tim	1762	}
122
123	tim	1765	void NVT::moveB() {
124			typename SimInfo::MoleculeIterator i;
125			typename Molecule::IntegrableObjectIterator j;
126			Molecule* mol;
127			StuntDouble* integrableObject;
128
129			Vector3d Tb;
130			Vector3d ji;
131			Vector3d vel;
132			Vector3d frc;
133	tim	1762	double mass;
134			double instTemp;
135			double oldChi, prevChi;
136	tim	1765	int index;
137	tim	1762	// Set things up for the iteration:
138
139	tim	1765	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
140			double chi = currSnapshot->getChi();
141			double integralOfChidt = currSnapshot->getIntegralOfChiDt();
142	tim	1762	oldChi = chi;
143
144	tim	1765	index = 0;
145			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
146			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
147			integrableObject = mol->nextIntegrableObject(j)) {
148			oldVel_[index] = integrableObject->getVel();
149			oldJi_[index] = integrableObject->getJ();
150	tim	1762	}
151	tim	1765	++index;
152	tim	1762	}
153
154			// do the iteration:
155
156	tim	1765	for(int k = 0; k < maxIterNum_; k++) {
157			index = 0;
158	tim	1762	instTemp = tStats->getTemperature();
159
160			// evolve chi another half step using the temperature at t + dt/2
161
162			prevChi = chi;
163	tim	1774	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
164	tim	1762
165	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
166			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
167			integrableObject = mol->nextIntegrableObject(j)) {
168	tim	1762
169	tim	1765	frc = integrableObject->getFrc();
170			vel = integrableObject->getVel();
171	tim	1762
172	tim	1765	mass = integrableObject->getMass();
173	tim	1762
174	tim	1765	// velocity half step
175			//for(j = 0; j < 3; j++)
176	tim	1774	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel_[3i + j]chi);
177			vel = oldVel_ + dt2/masseConvert frc - dt2chioldVel_[index];
178	tim	1765
179			integrableObject->setVel(vel);
180	tim	1762
181	tim	1765	if (integrableObject->isDirectional()) {
182	tim	1762
183	tim	1765	// get and convert the torque to body frame
184	tim	1762
185	tim	1765	Tb = integrableObject->getTrq();
186			integrableObject->lab2Body(Tb);
187	tim	1762
188	tim	1765	//for(j = 0; j < 3; j++)
189	tim	1774	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * eConvert - oldJi_[3i+j]chi);
190			ji += dt2eConvertTb - dt2ch oldJi_[index];
191	tim	1762
192	tim	1765	integrableObject->setJ(ji);
193			}
194	tim	1762	}
195			}
196	tim	1765
197	tim	1762
198	tim	1774	//constraintAlgorithm->doConstrainB();
199	tim	1762
200			if (fabs(prevChi - chi) <= chiTolerance)
201			break;
202	tim	1765
203			++index;
204	tim	1762	}
205
206	tim	1774	integralOfChidt += dt2 * chi;
207	tim	1762
208	tim	1765	currSnapshot->setChi(chi);
209			currSnapshot->setIntegralOfChiDt(integralOfChidt);
210	tim	1762	}
211
212
213	tim	1774	double NVT::calcConservedQuantity() {
214	tim	1762	double conservedQuantity;
215			double fkBT;
216			double Energy;
217			double thermostat_kinetic;
218			double thermostat_potential;
219
220	tim	1765	fkBT = info_->getNdf() kB targetTemp_;
221	tim	1762
222			Energy = tStats->getTotalE();
223
224	tim	1765	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * eConvert);
225	tim	1762
226			thermostat_potential = fkBT * integralOfChidt / eConvert;
227
228			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
229
230			return conservedQuantity;
231			}
232
233
234	tim	1765	}//end namespace oopse