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
#	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	1867	void NVT::doUpdate() {
47	tim	1774	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	1867	double chi = currentSnapshot_->getChi();
63			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
64	tim	1821
65	tim	1762	// We need the temperature at time = t for the chi update below:
66
67	tim	1821	double instTemp = thermo.getTemperature();
68	tim	1762
69	tim	1765	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	tim	1762
73	tim	1765	vel = integrableObject->getVel();
74			pos = integrableObject->getPos();
75			frc = integrableObject->getFrc();
76	tim	1762
77	tim	1765	mass = integrableObject->getMass();
78	tim	1762
79	tim	1765	// velocity half step (use chi from previous step here):
80	tim	1821	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
81	tim	1852	vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
82	tim	1765
83			// position whole step
84			//pos[j] += dt * vel[j];
85	tim	1774	pos += dt * vel;
86	tim	1762
87	tim	1765	integrableObject->setVel(vel);
88			integrableObject->setPos(pos);
89	tim	1762
90	tim	1765	if (integrableObject->isDirectional()) {
91	tim	1762
92	tim	1871	//convert the torque to body frame
93			Tb = integrableObject->lab2Body(integrableObject->getTrq());
94	tim	1762
95			// get the angular momentum, and propagate a half step
96
97	tim	1765	ji = integrableObject->getJ();
98	tim	1762
99	tim	1821	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
100			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
101			rotAlgo->rotate(integrableObject, ji, dt);
102	tim	1762
103	tim	1765	integrableObject->setJ(ji);
104	tim	1762	}
105			}
106
107	tim	1765	}
108
109	tim	1774	//constraintAlgorithm->doConstrainA();
110	tim	1762
111			// Finally, evolve chi a half step (just like a velocity) using
112			// temperature at time t, not time t+dt/2
113
114	tim	1765
115	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
116			integralOfChidt += chi * dt2;
117	tim	1762
118	tim	1867	currentSnapshot_->setChi(chi);
119			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
120	tim	1762	}
121
122	tim	1765	void NVT::moveB() {
123	tim	1821	SimInfo::MoleculeIterator i;
124			Molecule::IntegrableObjectIterator j;
125	tim	1765	Molecule* mol;
126			StuntDouble* integrableObject;
127
128			Vector3d Tb;
129			Vector3d ji;
130			Vector3d vel;
131			Vector3d frc;
132	tim	1762	double mass;
133			double instTemp;
134	tim	1765	int index;
135	tim	1762	// Set things up for the iteration:
136
137	tim	1867	double chi = currentSnapshot_->getChi();
138	tim	1821	double oldChi = chi;
139			double prevChi;
140	tim	1867	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
141	tim	1762
142	tim	1765	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	tim	1868
149			++index;
150	tim	1762	}
151	tim	1868
152	tim	1762	}
153
154			// do the iteration:
155
156	tim	1765	for(int k = 0; k < maxIterNum_; k++) {
157			index = 0;
158	tim	1821	instTemp = thermo.getTemperature();
159	tim	1762
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	1821	// 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	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	1871	Tb = integrableObject->lab2Body(integrableObject->getTrq());
186	tim	1762
187	tim	1765	//for(j = 0; j < 3; j++)
188	tim	1821	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
189	tim	1868	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
190	tim	1762
191	tim	1765	integrableObject->setJ(ji);
192			}
193	tim	1852
194
195			++index;
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	tim	1762	}
206
207	tim	1774	integralOfChidt += dt2 * chi;
208	tim	1762
209	tim	1867	currentSnapshot_->setChi(chi);
210			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
211	tim	1762	}
212
213
214	tim	1774	double NVT::calcConservedQuantity() {
215	tim	1867
216			double chi = currentSnapshot_->getChi();
217			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
218	tim	1762	double conservedQuantity;
219			double fkBT;
220			double Energy;
221			double thermostat_kinetic;
222			double thermostat_potential;
223	tim	1821
224			fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
225	tim	1762
226	tim	1821	Energy = thermo.getTotalE();
227	tim	1762
228	tim	1821	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
229	tim	1762
230	tim	1821	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
231	tim	1762
232			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
233
234			return conservedQuantity;
235			}
236
237
238	tim	1765	}//end namespace oopse