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, 9 months ago) by tim
File size:	7413 byte(s)
Log Message:	NVT get built
#	User	Rev	Content
1	tim	1821	#include "integrators/NVT.hpp"
2			#include "primitives/Molecule.hpp"
3			#include "utils/simError.h"
4			#include "utils/OOPSEConstant.hpp"
5	tim	1765	namespace oopse {
6	tim	1762
7	tim	1774	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
8	tim	1762
9	tim	1774	Globals* globals = info_->getGlobals();
10	tim	1762
11	tim	1774	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	tim	1762
26	tim	1774	// We must set tauThermostat_.
27	tim	1762
28	tim	1774	if (!globals->haveTauThermostat()) {
29			sprintf(painCave.errMsg, "If you use the constant temperature\n"
30			"\tintegrator, you must set tauThermostat_.\n");
31	tim	1762
32	tim	1774	painCave.severity = OOPSE_ERROR;
33			painCave.isFatal = 1;
34			simError();
35			} else {
36			tauThermostat_ = globals->getTauThermostat();
37	tim	1762	}
38
39	tim	1774	update();
40	tim	1762	}
41
42	tim	1774	void NVT::update() {
43			oldVel_.resize(info_->getNIntegrableObjects());
44			oldJi_.resize(info_->getNIntegrableObjects());
45			}
46	tim	1765	void NVT::moveA() {
47	tim	1821	SimInfo::MoleculeIterator i;
48			Molecule::IntegrableObjectIterator j;
49	tim	1765	Molecule* mol;
50			StuntDouble* integrableObject;
51	tim	1762	Vector3d Tb;
52			Vector3d ji;
53			double mass;
54			Vector3d vel;
55			Vector3d pos;
56			Vector3d frc;
57
58	tim	1821	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
59			double chi = currSnapshot->getChi();
60			double integralOfChidt = currSnapshot->getIntegralOfChiDt();
61
62	tim	1762	// We need the temperature at time = t for the chi update below:
63
64	tim	1821	double instTemp = thermo.getTemperature();
65	tim	1762
66	tim	1765	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	tim	1762
70	tim	1765	vel = integrableObject->getVel();
71			pos = integrableObject->getPos();
72			frc = integrableObject->getFrc();
73	tim	1762
74	tim	1765	mass = integrableObject->getMass();
75	tim	1762
76	tim	1765	// velocity half step (use chi from previous step here):
77	tim	1821	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
78			vel = dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
79	tim	1765
80			// position whole step
81			//pos[j] += dt * vel[j];
82	tim	1774	pos += dt * vel;
83	tim	1762
84	tim	1765	integrableObject->setVel(vel);
85			integrableObject->setPos(pos);
86	tim	1762
87	tim	1765	if (integrableObject->isDirectional()) {
88	tim	1762
89			// get and convert the torque to body frame
90
91	tim	1765	Tb = integrableObject->getTrq();
92			integrableObject->lab2Body(Tb);
93	tim	1762
94			// get the angular momentum, and propagate a half step
95
96	tim	1765	ji = integrableObject->getJ();
97	tim	1762
98	tim	1821	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
99			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
100			rotAlgo->rotate(integrableObject, ji, dt);
101	tim	1762
102	tim	1765	integrableObject->setJ(ji);
103	tim	1762	}
104			}
105
106	tim	1765	}
107
108	tim	1774	//constraintAlgorithm->doConstrainA();
109	tim	1762
110			// Finally, evolve chi a half step (just like a velocity) using
111			// temperature at time t, not time t+dt/2
112
113	tim	1765
114	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
115			integralOfChidt += chi * dt2;
116	tim	1762
117	tim	1765	currSnapshot->setChi(chi);
118			currSnapshot->setIntegralOfChiDt(integralOfChidt);
119	tim	1762	}
120
121	tim	1765	void NVT::moveB() {
122	tim	1821	SimInfo::MoleculeIterator i;
123			Molecule::IntegrableObjectIterator j;
124	tim	1765	Molecule* mol;
125			StuntDouble* integrableObject;
126
127			Vector3d Tb;
128			Vector3d ji;
129			Vector3d vel;
130			Vector3d frc;
131	tim	1762	double mass;
132			double instTemp;
133	tim	1765	int index;
134	tim	1762	// Set things up for the iteration:
135
136	tim	1765	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
137			double chi = currSnapshot->getChi();
138	tim	1821	double oldChi = chi;
139			double prevChi;
140	tim	1765	double integralOfChidt = currSnapshot->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	1762	}
149	tim	1765	++index;
150	tim	1762	}
151
152			// do the iteration:
153
154	tim	1765	for(int k = 0; k < maxIterNum_; k++) {
155			index = 0;
156	tim	1821	instTemp = thermo.getTemperature();
157	tim	1762
158			// evolve chi another half step using the temperature at t + dt/2
159
160			prevChi = chi;
161	tim	1774	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
162	tim	1762
163	tim	1765	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	tim	1762
167	tim	1765	frc = integrableObject->getFrc();
168			vel = integrableObject->getVel();
169	tim	1762
170	tim	1765	mass = integrableObject->getMass();
171	tim	1762
172	tim	1765	// velocity half step
173			//for(j = 0; j < 3; j++)
174	tim	1821	// 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	tim	1765
177			integrableObject->setVel(vel);
178	tim	1762
179	tim	1765	if (integrableObject->isDirectional()) {
180	tim	1762
181	tim	1765	// get and convert the torque to body frame
182	tim	1762
183	tim	1765	Tb = integrableObject->getTrq();
184			integrableObject->lab2Body(Tb);
185	tim	1762
186	tim	1765	//for(j = 0; j < 3; j++)
187	tim	1821	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
188			ji += dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
189	tim	1762
190	tim	1765	integrableObject->setJ(ji);
191			}
192	tim	1762	}
193			}
194	tim	1765
195	tim	1762
196	tim	1774	//constraintAlgorithm->doConstrainB();
197	tim	1762
198	tim	1821	if (fabs(prevChi - chi) <= chiTolerance_)
199	tim	1762	break;
200	tim	1765
201			++index;
202	tim	1762	}
203
204	tim	1774	integralOfChidt += dt2 * chi;
205	tim	1762
206	tim	1765	currSnapshot->setChi(chi);
207			currSnapshot->setIntegralOfChiDt(integralOfChidt);
208	tim	1762	}
209
210
211	tim	1774	double NVT::calcConservedQuantity() {
212	tim	1821	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
213			double chi = currSnapshot->getChi();
214			double integralOfChidt = currSnapshot->getIntegralOfChiDt();
215	tim	1762	double conservedQuantity;
216			double fkBT;
217			double Energy;
218			double thermostat_kinetic;
219			double thermostat_potential;
220	tim	1821
221			fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
222	tim	1762
223	tim	1821	Energy = thermo.getTotalE();
224	tim	1762
225	tim	1821	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
226	tim	1762
227	tim	1821	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
228	tim	1762
229			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
230
231			return conservedQuantity;
232			}
233
234
235	tim	1765	}//end namespace oopse