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* 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);
        }
    }

    }
    
    rattle->constraintA();

    // 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;
            }
        }
    

        rattle->constraintB();

        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:	1913
Committed:	Mon Jan 10 22:04:20 2005 UTC (21 years, 5 months ago) by tim
File size:	7186 byte(s)
Log Message:	create a register module to register force fields, integrators and minimizers
#	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	1837
6	tim	1765	namespace oopse {
7	tim	1762
8	tim	1774	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
9	tim	1762
10	tim	1841	Globals* simParams = info_->getSimParams();
11	tim	1762
12	tim	1841	if (simParams->getUseInitXSstate()) {
13	tim	1774	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
14			currSnapshot->setChi(0.0);
15			currSnapshot->setIntegralOfChiDt(0.0);
16			}
17
18	tim	1841	if (!simParams->haveTargetTemp()) {
19	tim	1774	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
20			painCave.isFatal = 1;
21			painCave.severity = OOPSE_ERROR;
22			simError();
23			} else {
24	tim	1841	targetTemp_ = simParams->getTargetTemp();
25	tim	1774	}
26	tim	1762
27	tim	1774	// We must set tauThermostat_.
28	tim	1762
29	tim	1841	if (!simParams->haveTauThermostat()) {
30	tim	1774	sprintf(painCave.errMsg, "If you use the constant temperature\n"
31			"\tintegrator, you must set tauThermostat_.\n");
32	tim	1762
33	tim	1774	painCave.severity = OOPSE_ERROR;
34			painCave.isFatal = 1;
35			simError();
36			} else {
37	tim	1841	tauThermostat_ = simParams->getTauThermostat();
38	tim	1762	}
39
40	tim	1774	update();
41	tim	1762	}
42
43	tim	1867	void NVT::doUpdate() {
44	tim	1774	oldVel_.resize(info_->getNIntegrableObjects());
45			oldJi_.resize(info_->getNIntegrableObjects());
46			}
47	tim	1765	void NVT::moveA() {
48	tim	1821	SimInfo::MoleculeIterator i;
49			Molecule::IntegrableObjectIterator j;
50	tim	1765	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	tim	1867	double chi = currentSnapshot_->getChi();
60			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
61	tim	1821
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	tim	1852	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	tim	1871	//convert the torque to body frame
90			Tb = integrableObject->lab2Body(integrableObject->getTrq());
91	tim	1762
92			// get the angular momentum, and propagate a half step
93
94	tim	1765	ji = integrableObject->getJ();
95	tim	1762
96	tim	1821	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
97			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
98			rotAlgo->rotate(integrableObject, ji, dt);
99	tim	1762
100	tim	1765	integrableObject->setJ(ji);
101	tim	1762	}
102			}
103
104	tim	1765	}
105
106	tim	1901	rattle->constraintA();
107	tim	1762
108			// Finally, evolve chi a half step (just like a velocity) using
109			// temperature at time t, not time t+dt/2
110
111	tim	1765
112	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
113			integralOfChidt += chi * dt2;
114	tim	1762
115	tim	1867	currentSnapshot_->setChi(chi);
116			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
117	tim	1762	}
118
119	tim	1765	void NVT::moveB() {
120	tim	1821	SimInfo::MoleculeIterator i;
121			Molecule::IntegrableObjectIterator j;
122	tim	1765	Molecule* mol;
123			StuntDouble* integrableObject;
124
125			Vector3d Tb;
126			Vector3d ji;
127			Vector3d vel;
128			Vector3d frc;
129	tim	1762	double mass;
130			double instTemp;
131	tim	1765	int index;
132	tim	1762	// Set things up for the iteration:
133
134	tim	1867	double chi = currentSnapshot_->getChi();
135	tim	1821	double oldChi = chi;
136			double prevChi;
137	tim	1867	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
138	tim	1762
139	tim	1765	index = 0;
140			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
141			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
142			integrableObject = mol->nextIntegrableObject(j)) {
143			oldVel_[index] = integrableObject->getVel();
144			oldJi_[index] = integrableObject->getJ();
145	tim	1868
146			++index;
147	tim	1762	}
148	tim	1868
149	tim	1762	}
150
151			// do the iteration:
152
153	tim	1765	for(int k = 0; k < maxIterNum_; k++) {
154			index = 0;
155	tim	1821	instTemp = thermo.getTemperature();
156	tim	1762
157			// evolve chi another half step using the temperature at t + dt/2
158
159			prevChi = chi;
160	tim	1774	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
161	tim	1762
162	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
163			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
164			integrableObject = mol->nextIntegrableObject(j)) {
165	tim	1762
166	tim	1765	frc = integrableObject->getFrc();
167			vel = integrableObject->getVel();
168	tim	1762
169	tim	1765	mass = integrableObject->getMass();
170	tim	1762
171	tim	1765	// velocity half step
172			//for(j = 0; j < 3; j++)
173	tim	1821	// vel[j] = oldVel_[3i+j] + dt2 ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3i + j]chi);
174			vel = oldVel_[index] + dt2/massOOPSEConstant::energyConvert frc - dt2chioldVel_[index];
175	tim	1765
176			integrableObject->setVel(vel);
177	tim	1762
178	tim	1765	if (integrableObject->isDirectional()) {
179	tim	1762
180	tim	1765	// get and convert the torque to body frame
181	tim	1762
182	tim	1871	Tb = integrableObject->lab2Body(integrableObject->getTrq());
183	tim	1762
184	tim	1765	//for(j = 0; j < 3; j++)
185	tim	1821	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
186	tim	1868	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
187	tim	1762
188	tim	1765	integrableObject->setJ(ji);
189			}
190	tim	1852
191
192			++index;
193	tim	1762	}
194			}
195	tim	1765
196	tim	1762
197	tim	1901	rattle->constraintB();
198	tim	1762
199	tim	1821	if (fabs(prevChi - chi) <= chiTolerance_)
200	tim	1762	break;
201	tim	1765
202	tim	1762	}
203
204	tim	1774	integralOfChidt += dt2 * chi;
205	tim	1762
206	tim	1867	currentSnapshot_->setChi(chi);
207			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
208	tim	1762	}
209
210
211	tim	1774	double NVT::calcConservedQuantity() {
212	tim	1867
213			double chi = currentSnapshot_->getChi();
214			double integralOfChidt = currentSnapshot_->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