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 (19 years, 6 months ago) by tim
File size:	7186 byte(s)
Log Message:	create a register module to register force fields, integrators and minimizers
#	Content
1	#include "integrators/NVT.hpp"
2	#include "primitives/Molecule.hpp"
3	#include "utils/simError.h"
4	#include "utils/OOPSEConstant.hpp"
5
6	namespace oopse {
7
8	NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6) {
9
10	Globals* simParams = info_->getSimParams();
11
12	if (simParams->getUseInitXSstate()) {
13	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
14	currSnapshot->setChi(0.0);
15	currSnapshot->setIntegralOfChiDt(0.0);
16	}
17
18	if (!simParams->haveTargetTemp()) {
19	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	targetTemp_ = simParams->getTargetTemp();
25	}
26
27	// We must set tauThermostat_.
28
29	if (!simParams->haveTauThermostat()) {
30	sprintf(painCave.errMsg, "If you use the constant temperature\n"
31	"\tintegrator, you must set tauThermostat_.\n");
32
33	painCave.severity = OOPSE_ERROR;
34	painCave.isFatal = 1;
35	simError();
36	} else {
37	tauThermostat_ = simParams->getTauThermostat();
38	}
39
40	update();
41	}
42
43	void NVT::doUpdate() {
44	oldVel_.resize(info_->getNIntegrableObjects());
45	oldJi_.resize(info_->getNIntegrableObjects());
46	}
47	void NVT::moveA() {
48	SimInfo::MoleculeIterator i;
49	Molecule::IntegrableObjectIterator j;
50	Molecule* mol;
51	StuntDouble* integrableObject;
52	Vector3d Tb;
53	Vector3d ji;
54	double mass;
55	Vector3d vel;
56	Vector3d pos;
57	Vector3d frc;
58
59	double chi = currentSnapshot_->getChi();
60	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
61
62	// We need the temperature at time = t for the chi update below:
63
64	double instTemp = thermo.getTemperature();
65
66	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
70	vel = integrableObject->getVel();
71	pos = integrableObject->getPos();
72	frc = integrableObject->getFrc();
73
74	mass = integrableObject->getMass();
75
76	// velocity half step (use chi from previous step here):
77	//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
78	vel += dt2 OOPSEConstant::energyConvert/massfrc - dt2chivel;
79
80	// position whole step
81	//pos[j] += dt * vel[j];
82	pos += dt * vel;
83
84	integrableObject->setVel(vel);
85	integrableObject->setPos(pos);
86
87	if (integrableObject->isDirectional()) {
88
89	//convert the torque to body frame
90	Tb = integrableObject->lab2Body(integrableObject->getTrq());
91
92	// get the angular momentum, and propagate a half step
93
94	ji = integrableObject->getJ();
95
96	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
97	ji += dt2OOPSEConstant::energyConvertTb - dt2chi ji;
98	rotAlgo->rotate(integrableObject, ji, dt);
99
100	integrableObject->setJ(ji);
101	}
102	}
103
104	}
105
106	rattle->constraintA();
107
108	// Finally, evolve chi a half step (just like a velocity) using
109	// temperature at time t, not time t+dt/2
110
111
112	chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
113	integralOfChidt += chi * dt2;
114
115	currentSnapshot_->setChi(chi);
116	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
117	}
118
119	void NVT::moveB() {
120	SimInfo::MoleculeIterator i;
121	Molecule::IntegrableObjectIterator j;
122	Molecule* mol;
123	StuntDouble* integrableObject;
124
125	Vector3d Tb;
126	Vector3d ji;
127	Vector3d vel;
128	Vector3d frc;
129	double mass;
130	double instTemp;
131	int index;
132	// Set things up for the iteration:
133
134	double chi = currentSnapshot_->getChi();
135	double oldChi = chi;
136	double prevChi;
137	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
138
139	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
146	++index;
147	}
148
149	}
150
151	// do the iteration:
152
153	for(int k = 0; k < maxIterNum_; k++) {
154	index = 0;
155	instTemp = thermo.getTemperature();
156
157	// evolve chi another half step using the temperature at t + dt/2
158
159	prevChi = chi;
160	chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
161
162	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
166	frc = integrableObject->getFrc();
167	vel = integrableObject->getVel();
168
169	mass = integrableObject->getMass();
170
171	// velocity half step
172	//for(j = 0; j < 3; j++)
173	// 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
176	integrableObject->setVel(vel);
177
178	if (integrableObject->isDirectional()) {
179
180	// get and convert the torque to body frame
181
182	Tb = integrableObject->lab2Body(integrableObject->getTrq());
183
184	//for(j = 0; j < 3; j++)
185	// ji[j] = oldJi_[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3i+j]chi);
186	ji = oldJi_[index] + dt2OOPSEConstant::energyConvertTb - dt2chi oldJi_[index];
187
188	integrableObject->setJ(ji);
189	}
190
191
192	++index;
193	}
194	}
195
196
197	rattle->constraintB();
198
199	if (fabs(prevChi - chi) <= chiTolerance_)
200	break;
201
202	}
203
204	integralOfChidt += dt2 * chi;
205
206	currentSnapshot_->setChi(chi);
207	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
208	}
209
210
211	double NVT::calcConservedQuantity() {
212
213	double chi = currentSnapshot_->getChi();
214	double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
215	double conservedQuantity;
216	double fkBT;
217	double Energy;
218	double thermostat_kinetic;
219	double thermostat_potential;
220
221	fkBT = info_->getNdf() OOPSEConstant::kB targetTemp_;
222
223	Energy = thermo.getTotalE();
224
225	thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert);
226
227	thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert;
228
229	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
230
231	return conservedQuantity;
232	}
233
234
235	}//end namespace oopse