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 {

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:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 6 months ago) by tim
File size:	7231 byte(s)
Log Message:	constraints in progress
#	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	1774	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
10	tim	1762
11	tim	1841	Globals* simParams = info_->getSimParams();
12	tim	1762
13	tim	1841	if (simParams->getUseInitXSstate()) {
14	tim	1774	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
15			currSnapshot->setChi(0.0);
16			currSnapshot->setIntegralOfChiDt(0.0);
17			}
18
19	tim	1841	if (!simParams->haveTargetTemp()) {
20	tim	1774	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n");
21			painCave.isFatal = 1;
22			painCave.severity = OOPSE_ERROR;
23			simError();
24			} else {
25	tim	1841	targetTemp_ = simParams->getTargetTemp();
26	tim	1774	}
27	tim	1762
28	tim	1774	// We must set tauThermostat_.
29	tim	1762
30	tim	1841	if (!simParams->haveTauThermostat()) {
31	tim	1774	sprintf(painCave.errMsg, "If you use the constant temperature\n"
32			"\tintegrator, you must set tauThermostat_.\n");
33	tim	1762
34	tim	1774	painCave.severity = OOPSE_ERROR;
35			painCave.isFatal = 1;
36			simError();
37			} else {
38	tim	1841	tauThermostat_ = simParams->getTauThermostat();
39	tim	1762	}
40
41	tim	1774	update();
42	tim	1762	}
43
44	tim	1867	void NVT::doUpdate() {
45	tim	1774	oldVel_.resize(info_->getNIntegrableObjects());
46			oldJi_.resize(info_->getNIntegrableObjects());
47			}
48	tim	1765	void NVT::moveA() {
49	tim	1821	SimInfo::MoleculeIterator i;
50			Molecule::IntegrableObjectIterator j;
51	tim	1765	Molecule* mol;
52			StuntDouble* integrableObject;
53	tim	1762	Vector3d Tb;
54			Vector3d ji;
55			double mass;
56			Vector3d vel;
57			Vector3d pos;
58			Vector3d frc;
59
60	tim	1867	double chi = currentSnapshot_->getChi();
61			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
62	tim	1821
63	tim	1762	// We need the temperature at time = t for the chi update below:
64
65	tim	1821	double instTemp = thermo.getTemperature();
66	tim	1762
67	tim	1765	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
68			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
69			integrableObject = mol->nextIntegrableObject(j)) {
70	tim	1762
71	tim	1765	vel = integrableObject->getVel();
72			pos = integrableObject->getPos();
73			frc = integrableObject->getFrc();
74	tim	1762
75	tim	1765	mass = integrableObject->getMass();
76	tim	1762
77	tim	1765	// velocity half step (use chi from previous step here):
78	tim	1821	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
79	tim	1852	vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
80	tim	1765
81			// position whole step
82			//pos[j] += dt * vel[j];
83	tim	1774	pos += dt * vel;
84	tim	1762
85	tim	1765	integrableObject->setVel(vel);
86			integrableObject->setPos(pos);
87	tim	1762
88	tim	1765	if (integrableObject->isDirectional()) {
89	tim	1762
90	tim	1871	//convert the torque to body frame
91			Tb = integrableObject->lab2Body(integrableObject->getTrq());
92	tim	1762
93			// get the angular momentum, and propagate a half step
94
95	tim	1765	ji = integrableObject->getJ();
96	tim	1762
97	tim	1821	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
98			ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
99			rotAlgo->rotate(integrableObject, ji, dt);
100	tim	1762
101	tim	1765	integrableObject->setJ(ji);
102	tim	1762	}
103			}
104
105	tim	1765	}
106
107	tim	1901	rattle->constraintA();
108	tim	1762
109			// Finally, evolve chi a half step (just like a velocity) using
110			// temperature at time t, not time t+dt/2
111
112	tim	1765
113	tim	1774	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
114			integralOfChidt += chi * dt2;
115	tim	1762
116	tim	1867	currentSnapshot_->setChi(chi);
117			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
118	tim	1762	}
119
120	tim	1765	void NVT::moveB() {
121	tim	1821	SimInfo::MoleculeIterator i;
122			Molecule::IntegrableObjectIterator j;
123	tim	1765	Molecule* mol;
124			StuntDouble* integrableObject;
125
126			Vector3d Tb;
127			Vector3d ji;
128			Vector3d vel;
129			Vector3d frc;
130	tim	1762	double mass;
131			double instTemp;
132	tim	1765	int index;
133	tim	1762	// Set things up for the iteration:
134
135	tim	1867	double chi = currentSnapshot_->getChi();
136	tim	1821	double oldChi = chi;
137			double prevChi;
138	tim	1867	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
139	tim	1762
140	tim	1765	index = 0;
141			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
142			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
143			integrableObject = mol->nextIntegrableObject(j)) {
144			oldVel_[index] = integrableObject->getVel();
145			oldJi_[index] = integrableObject->getJ();
146	tim	1868
147			++index;
148	tim	1762	}
149	tim	1868
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	1871	Tb = integrableObject->lab2Body(integrableObject->getTrq());
184	tim	1762
185	tim	1765	//for(j = 0; j < 3; j++)
186	tim	1821	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
187	tim	1868	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
188	tim	1762
189	tim	1765	integrableObject->setJ(ji);
190			}
191	tim	1852
192
193			++index;
194	tim	1762	}
195			}
196	tim	1765
197	tim	1762
198	tim	1901	rattle->constraintB();
199	tim	1762
200	tim	1821	if (fabs(prevChi - chi) <= chiTolerance_)
201	tim	1762	break;
202	tim	1765
203	tim	1762	}
204
205	tim	1774	integralOfChidt += dt2 * chi;
206	tim	1762
207	tim	1867	currentSnapshot_->setChi(chi);
208			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
209	tim	1762	}
210
211
212	tim	1774	double NVT::calcConservedQuantity() {
213	tim	1867
214			double chi = currentSnapshot_->getChi();
215			double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
216	tim	1762	double conservedQuantity;
217			double fkBT;
218			double Energy;
219			double thermostat_kinetic;
220			double thermostat_potential;
221	tim	1821
222			fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
223	tim	1762
224	tim	1821	Energy = thermo.getTotalE();
225	tim	1762
226	tim	1821	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
227	tim	1762
228	tim	1821	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
229	tim	1762
230			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
231
232			return conservedQuantity;
233			}
234
235
236	tim	1765	}//end namespace oopse