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::doUpdate() {
    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;

    double chi = currentSnapshot_->getChi();
    double integralOfChidt = currentSnapshot_->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()) {

            //convert the torque to body frame
            Tb = integrableObject->lab2Body(integrableObject->getTrq());

            // 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;

    currentSnapshot_->setChi(chi);
    currentSnapshot_->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:

    double chi = currentSnapshot_->getChi();
    double oldChi = chi;
    double  prevChi;
    double integralOfChidt = currentSnapshot_->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->lab2Body(integrableObject->getTrq());

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

                    integrableObject->setJ(ji);
                }


                ++index;
            }
        }
    

        //constraintAlgorithm->doConstrainB();

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

    }

    integralOfChidt += dt2 * chi;

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


double NVT::calcConservedQuantity() {

    double chi = currentSnapshot_->getChi();
    double integralOfChidt = currentSnapshot_->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:	1871
Committed:	Thu Dec 9 16:22:42 2004 UTC (19 years, 6 months ago) by tim
File size:	7343 byte(s)
Log Message:	fix an interface inconsistency in lab2Bidy
#	Content
1	#include "integrators/IntegratorCreator.hpp"
2	#include "integrators/NVT.hpp"
3	#include "primitives/Molecule.hpp"
4	#include "utils/simError.h"
5	#include "utils/OOPSEConstant.hpp"
6
7	namespace oopse {
8
9	static IntegratorBuilder<NVT>* NVTCreator = new IntegratorBuilder<NVT>("NVT");
10
11	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
12
13	Globals* simParams = info_->getSimParams();
14
15	if (simParams->getUseInitXSstate()) {
16	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
17	currSnapshot->setChi(0.0);
18	currSnapshot->setIntegralOfChiDt(0.0);
19	}
20
21	if (!simParams->haveTargetTemp()) {
22	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	targetTemp_ = simParams->getTargetTemp();
28	}
29
30	// We must set tauThermostat_.
31
32	if (!simParams->haveTauThermostat()) {
33	sprintf(painCave.errMsg, "If you use the constant temperature\n"
34	"\tintegrator, you must set tauThermostat_.\n");
35
36	painCave.severity = OOPSE_ERROR;
37	painCave.isFatal = 1;
38	simError();
39	} else {
40	tauThermostat_ = simParams->getTauThermostat();
41	}
42
43	update();
44	}
45
46	void NVT::doUpdate() {
47	oldVel_.resize(info_->getNIntegrableObjects());
48	oldJi_.resize(info_->getNIntegrableObjects());
49	}
50	void NVT::moveA() {
51	SimInfo::MoleculeIterator i;
52	Molecule::IntegrableObjectIterator j;
53	Molecule* mol;
54	StuntDouble* integrableObject;
55	Vector3d Tb;
56	Vector3d ji;
57	double mass;
58	Vector3d vel;
59	Vector3d pos;
60	Vector3d frc;
61
62	double chi = currentSnapshot_->getChi();
63	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
64
65	// We need the temperature at time = t for the chi update below:
66
67	double instTemp = thermo.getTemperature();
68
69	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
70	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
71	integrableObject = mol->nextIntegrableObject(j)) {
72
73	vel = integrableObject->getVel();
74	pos = integrableObject->getPos();
75	frc = integrableObject->getFrc();
76
77	mass = integrableObject->getMass();
78
79	// velocity half step (use chi from previous step here):
80	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
81	vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
82
83	// position whole step
84	//pos[j] += dt * vel[j];
85	pos += dt * vel;
86
87	integrableObject->setVel(vel);
88	integrableObject->setPos(pos);
89
90	if (integrableObject->isDirectional()) {
91
92	//convert the torque to body frame
93	Tb = integrableObject->lab2Body(integrableObject->getTrq());
94
95	// get the angular momentum, and propagate a half step
96
97	ji = integrableObject->getJ();
98
99	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
100	ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
101	rotAlgo->rotate(integrableObject, ji, dt);
102
103	integrableObject->setJ(ji);
104	}
105	}
106
107	}
108
109	//constraintAlgorithm->doConstrainA();
110
111	// Finally, evolve chi a half step (just like a velocity) using
112	// temperature at time t, not time t+dt/2
113
114
115	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
116	integralOfChidt += chi * dt2;
117
118	currentSnapshot_->setChi(chi);
119	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
120	}
121
122	void NVT::moveB() {
123	SimInfo::MoleculeIterator i;
124	Molecule::IntegrableObjectIterator j;
125	Molecule* mol;
126	StuntDouble* integrableObject;
127
128	Vector3d Tb;
129	Vector3d ji;
130	Vector3d vel;
131	Vector3d frc;
132	double mass;
133	double instTemp;
134	int index;
135	// Set things up for the iteration:
136
137	double chi = currentSnapshot_->getChi();
138	double oldChi = chi;
139	double prevChi;
140	double integralOfChidt = currentSnapshot_->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	}
153
154	// do the iteration:
155
156	for(int k = 0; k < maxIterNum_; k++) {
157	index = 0;
158	instTemp = thermo.getTemperature();
159
160	// evolve chi another half step using the temperature at t + dt/2
161
162	prevChi = chi;
163	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
164
165	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
169	frc = integrableObject->getFrc();
170	vel = integrableObject->getVel();
171
172	mass = integrableObject->getMass();
173
174	// velocity half step
175	//for(j = 0; j < 3; j++)
176	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3i + j]chi);
177	vel = oldVel_[index] + dt2/massOOPSEConstant::energyConvert frc - dt2chioldVel_[index];
178
179	integrableObject->setVel(vel);
180
181	if (integrableObject->isDirectional()) {
182
183	// get and convert the torque to body frame
184
185	Tb = integrableObject->lab2Body(integrableObject->getTrq());
186
187	//for(j = 0; j < 3; j++)
188	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
189	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
190
191	integrableObject->setJ(ji);
192	}
193
194
195	++index;
196	}
197	}
198
199
200	//constraintAlgorithm->doConstrainB();
201
202	if (fabs(prevChi - chi) <= chiTolerance_)
203	break;
204
205	}
206
207	integralOfChidt += dt2 * chi;
208
209	currentSnapshot_->setChi(chi);
210	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
211	}
212
213
214	double NVT::calcConservedQuantity() {
215
216	double chi = currentSnapshot_->getChi();
217	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
218	double conservedQuantity;
219	double fkBT;
220	double Energy;
221	double thermostat_kinetic;
222	double thermostat_potential;
223
224	fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
225
226	Energy = thermo.getTotalE();
227
228	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
229
230	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
231
232	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
233
234	return conservedQuantity;
235	}
236
237
238	}//end namespace oopse