src/integrators/NVT.cpp

#include "integrators/NVT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/OOPSEConstant.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();
}

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:	1821
Committed:	Thu Dec 2 00:26:23 2004 UTC (19 years, 7 months ago) by tim
File size:	7413 byte(s)
Log Message:	NVT get built
#	Content
1	#include "integrators/NVT.hpp"
2	#include "primitives/Molecule.hpp"
3	#include "utils/simError.h"
4	#include "utils/OOPSEConstant.hpp"
5	namespace oopse {
6
7	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
8
9	Globals* globals = info_->getGlobals();
10
11	if (globals->getUseInitXSstate()) {
12	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
13	currSnapshot->setChi(0.0);
14	currSnapshot->setIntegralOfChiDt(0.0);
15	}
16
17	if (!globals->haveTargetTemp()) {
18	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
19	painCave.isFatal = 1;
20	painCave.severity = OOPSE_ERROR;
21	simError();
22	} else {
23	targetTemp_ = globals->getTargetTemp();
24	}
25
26	// We must set tauThermostat_.
27
28	if (!globals->haveTauThermostat()) {
29	sprintf(painCave.errMsg, "If you use the constant temperature\n"
30	"\tintegrator, you must set tauThermostat_.\n");
31
32	painCave.severity = OOPSE_ERROR;
33	painCave.isFatal = 1;
34	simError();
35	} else {
36	tauThermostat_ = globals->getTauThermostat();
37	}
38
39	update();
40	}
41
42	void NVT::update() {
43	oldVel_.resize(info_->getNIntegrableObjects());
44	oldJi_.resize(info_->getNIntegrableObjects());
45	}
46	void NVT::moveA() {
47	SimInfo::MoleculeIterator i;
48	Molecule::IntegrableObjectIterator j;
49	Molecule* mol;
50	StuntDouble* integrableObject;
51	Vector3d Tb;
52	Vector3d ji;
53	double mass;
54	Vector3d vel;
55	Vector3d pos;
56	Vector3d frc;
57
58	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
59	double chi = currSnapshot->getChi();
60	double integralOfChidt = currSnapshot->getIntegralOfChiDt();
61
62	// We need the temperature at time = t for the chi update below:
63
64	double instTemp = thermo.getTemperature();
65
66	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
67	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
68	integrableObject = mol->nextIntegrableObject(j)) {
69
70	vel = integrableObject->getVel();
71	pos = integrableObject->getPos();
72	frc = integrableObject->getFrc();
73
74	mass = integrableObject->getMass();
75
76	// velocity half step (use chi from previous step here):
77	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
78	vel = dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
79
80	// position whole step
81	//pos[j] += dt * vel[j];
82	pos += dt * vel;
83
84	integrableObject->setVel(vel);
85	integrableObject->setPos(pos);
86
87	if (integrableObject->isDirectional()) {
88
89	// get and convert the torque to body frame
90
91	Tb = integrableObject->getTrq();
92	integrableObject->lab2Body(Tb);
93
94	// get the angular momentum, and propagate a half step
95
96	ji = integrableObject->getJ();
97
98	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
99	ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
100	rotAlgo->rotate(integrableObject, ji, dt);
101
102	integrableObject->setJ(ji);
103	}
104	}
105
106	}
107
108	//constraintAlgorithm->doConstrainA();
109
110	// Finally, evolve chi a half step (just like a velocity) using
111	// temperature at time t, not time t+dt/2
112
113
114	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
115	integralOfChidt += chi * dt2;
116
117	currSnapshot->setChi(chi);
118	currSnapshot->setIntegralOfChiDt(integralOfChidt);
119	}
120
121	void NVT::moveB() {
122	SimInfo::MoleculeIterator i;
123	Molecule::IntegrableObjectIterator j;
124	Molecule* mol;
125	StuntDouble* integrableObject;
126
127	Vector3d Tb;
128	Vector3d ji;
129	Vector3d vel;
130	Vector3d frc;
131	double mass;
132	double instTemp;
133	int index;
134	// Set things up for the iteration:
135
136	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
137	double chi = currSnapshot->getChi();
138	double oldChi = chi;
139	double prevChi;
140	double integralOfChidt = currSnapshot->getIntegralOfChiDt();
141
142	index = 0;
143	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
144	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
145	integrableObject = mol->nextIntegrableObject(j)) {
146	oldVel_[index] = integrableObject->getVel();
147	oldJi_[index] = integrableObject->getJ();
148	}
149	++index;
150	}
151
152	// do the iteration:
153
154	for(int k = 0; k < maxIterNum_; k++) {
155	index = 0;
156	instTemp = thermo.getTemperature();
157
158	// evolve chi another half step using the temperature at t + dt/2
159
160	prevChi = chi;
161	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
162
163	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
164	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
165	integrableObject = mol->nextIntegrableObject(j)) {
166
167	frc = integrableObject->getFrc();
168	vel = integrableObject->getVel();
169
170	mass = integrableObject->getMass();
171
172	// velocity half step
173	//for(j = 0; j < 3; j++)
174	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3i + j]chi);
175	vel = oldVel_[index] + dt2/massOOPSEConstant::energyConvert frc - dt2chioldVel_[index];
176
177	integrableObject->setVel(vel);
178
179	if (integrableObject->isDirectional()) {
180
181	// get and convert the torque to body frame
182
183	Tb = integrableObject->getTrq();
184	integrableObject->lab2Body(Tb);
185
186	//for(j = 0; j < 3; j++)
187	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
188	ji += dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
189
190	integrableObject->setJ(ji);
191	}
192	}
193	}
194
195
196	//constraintAlgorithm->doConstrainB();
197
198	if (fabs(prevChi - chi) <= chiTolerance_)
199	break;
200
201	++index;
202	}
203
204	integralOfChidt += dt2 * chi;
205
206	currSnapshot->setChi(chi);
207	currSnapshot->setIntegralOfChiDt(integralOfChidt);
208	}
209
210
211	double NVT::calcConservedQuantity() {
212	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
213	double chi = currSnapshot->getChi();
214	double integralOfChidt = currSnapshot->getIntegralOfChiDt();
215	double conservedQuantity;
216	double fkBT;
217	double Energy;
218	double thermostat_kinetic;
219	double thermostat_potential;
220
221	fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
222
223	Energy = thermo.getTotalE();
224
225	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
226
227	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
228
229	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
230
231	return conservedQuantity;
232	}
233
234
235	}//end namespace oopse