src/integrators/NPT.cpp

#include <math.h>

#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/NPT.hpp"
#include "utils/simError.h"


// Basic isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533.
//
//           and
//
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

namespace oopse {

NPT::NPT(SimInfo* info) :
    VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(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();
    }

    if (!globals->haveTargetPressure()) {
        sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
                                     "   without a targetPressure!\n");

        painCave.isFatal = 1;
        simError();
    } else {
        targetPressure = globals->getTargetPressure();
    }
    
    if (!globals->haveTauBarostat()) {
        sprintf(painCave.errMsg,
                "If you use the NPT integrator, you must set tauBarostat.\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
    } else {
        tauBarostat = globals->getTauBarostat();
    }
    
    tt2 = tauThermostat * tauThermostat;
    tb2 = tauBarostat * tauBarostat;

    update();
}

NPT::~NPT() {
}

void NPT::update() {
    oldPos.resize(info_->getNIntegrableObjects());
    oldVel.resize(info_->getNIntegrableObjects());
    oldJi.resize(info_->getNIntegrableObjects());
    // We need NkBT a lot, so just set it here: This is the RAW number
    // of integrableObjects, so no subtraction or addition of constraints or
    // orientational degrees of freedom:
    NkBT = info_->getNGlobalIntegrableObjects()*kB *targetTemp;

    // fkBT is used because the thermostat operates on more degrees of freedom
    // than the barostat (when there are particles with orientational degrees
    // of freedom).  
    fkBT = info_->getNdf()*kB *targetTemp;    
}

void NPT::moveA() {
    typename SimInfo::MoleculeIterator i;
    typename Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d Tb, ji;
    double mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d sc;
    Vector3d COM;
    int index;
    
    instaTemp = tStats->getTemperature();
    tStats->getPressureTensor(press);
    instaPress = p_convert * (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
    instaVol = tStats->getVolume();

    tStats->getCOM(COM);

    //evolve velocity half step

    calcVelScale();

    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();
            frc = integrableObject->getFrc();

            mass = integrableObject->getMass();

            getVelScaleA(sc, vel);

            // velocity half step  (use chi from previous step here):
            //vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]);
            vel += dt2*eConvert/mass* frc - dt2*sc;
            integrableObject->setVel(vel);

            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] * eConvert - ji[j]*chi);
                ji += dt2*eConvert * Tb - dt2*chi* ji;
                
                this->rotationPropagation(integrableObject, ji);

                integrableObject->setJ(ji);
            }
            
        }
    }
    // evolve chi and eta  half step

    evolveChiA();
    evolveEtaA();

    //calculate the integral of chidt
    integralOfChidt += dt2 * chi;
    
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {
            oldPos[index++] = integrableObject->getPos();            
        }
    }
    
    //the first estimation of r(t+dt) is equal to  r(t)

    for(int k = 0; k < maxIterNum_; k++) {
        index = 0;
        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();

                this->getPosScale(pos, COM, index, sc);

                pos = oldPos[index] + dt * (vel + sc);
                integrableObject->setPos(pos);     

                ++index;
           }
        }

        //constraintAlgorithm->doConstrainA();
    }

    // Scale the box after all the positions have been moved:

    this->scaleSimBox();
}

void NPT::moveB(void) {
    typename SimInfo::MoleculeIterator i;
    typename Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    int index;
    Vector3d Tb;
    Vector3d ji;
    Vector3d sc;
    Vector3d vel;
    Vector3d frc;
    double mass;

    //save velocity and angular momentum
    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[3 * i + j] = integrableObject->getJ();
            ++index;
        }
    }

    // do the iteration:
    instaVol = tStats->getVolume();

    for(int k = 0; k < maxIterNum_; k++) {
        instaTemp = tStats->getTemperature();
        instaPress = tStats->getPressure();

        // evolve chi another half step using the temperature at t + dt/2
        this->evolveChiB();
        this->evolveEtaB();
        this->calcVelScale();

        index = 0;
        for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
            for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
                   integrableObject = mol->nextIntegrableObject(j)) {            
                integrableObject->getFrc(frc);
                vel = integrableObject->getVel();

                mass = integrableObject->getMass();

                getVelScaleB(sc, i);

                // velocity half step
                //vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * eConvert - sc[j]);
                vel = oldVel[index] + dt2*eConvert/mass* frc - dt2*sc;
                integrableObject->setVel(vel);

                if (integrableObject->isDirectional()) {
                    // get and convert the torque to body frame
                    Tb = integrableObject->getTrq();
                    integrableObject->lab2Body(Tb);

                    //ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
                    ji = oldJi[index] + dt2*eConvert*Tb - dt2*chi*oldJi[index];
                    integrableObject->setJ(ji);
                }

                ++index;
            }
        }
        
        //constraintAlgorithm->doConstrainB();

        if (this->chiConverged() && this->etaConverged())
            break;
    }

    //calculate integral of chidt
    integralOfChidt += dt2 * chi;
}

void NPT::evolveChiA() {
    chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
    oldChi = chi;
}

void NPT::evolveChiB() {
    prevChi = chi;
    chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
}

bool NPT::chiConverged() {
    return (fabs(prevChi - chi) <= chiTolerance);
}

}
Revision:	1774
Committed:	Tue Nov 23 23:12:23 2004 UTC (21 years, 6 months ago) by tim
File size:	8969 byte(s)
Log Message:	refactory NPT integrator
#	User	Rev	Content
1	tim	1774	#include <math.h>
2
3			#include "brains/SimInfo.hpp"
4			#include "brains/Thermo.hpp"
5			#include "integrators/NPT.hpp"
6			#include "utils/simError.h"
7
8
9			// Basic isotropic thermostating and barostating via the Melchionna
10			// modification of the Hoover algorithm:
11			//
12			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
13			// Molec. Phys., 78, 533.
14			//
15			// and
16			//
17			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
18
19			namespace oopse {
20
21			NPT::NPT(SimInfo* info) :
22			VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6) {
23
24			Globals* globals = info_->getGlobals();
25
26			if (globals->getUseInitXSstate()) {
27			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
28			currSnapshot->setChi(0.0);
29			currSnapshot->setIntegralOfChiDt(0.0);
30			}
31
32			if (!globals->haveTargetTemp()) {
33			sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
34			painCave.isFatal = 1;
35			painCave.severity = OOPSE_ERROR;
36			simError();
37			} else {
38			targetTemp = globals->getTargetTemp();
39			}
40
41			// We must set tauThermostat
42			if (!globals->haveTauThermostat()) {
43			sprintf(painCave.errMsg, "If you use the constant temperature\n"
44			"\tintegrator, you must set tauThermostat_.\n");
45
46			painCave.severity = OOPSE_ERROR;
47			painCave.isFatal = 1;
48			simError();
49			} else {
50			tauThermostat = globals->getTauThermostat();
51			}
52
53			if (!globals->haveTargetPressure()) {
54			sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
55			" without a targetPressure!\n");
56
57			painCave.isFatal = 1;
58			simError();
59			} else {
60			targetPressure = globals->getTargetPressure();
61			}
62
63			if (!globals->haveTauBarostat()) {
64			sprintf(painCave.errMsg,
65			"If you use the NPT integrator, you must set tauBarostat.\n");
66			painCave.severity = OOPSE_ERROR;
67			painCave.isFatal = 1;
68			simError();
69			} else {
70			tauBarostat = globals->getTauBarostat();
71			}
72
73			tt2 = tauThermostat * tauThermostat;
74			tb2 = tauBarostat * tauBarostat;
75
76			update();
77			}
78
79			NPT::~NPT() {
80			}
81
82			void NPT::update() {
83			oldPos.resize(info_->getNIntegrableObjects());
84			oldVel.resize(info_->getNIntegrableObjects());
85			oldJi.resize(info_->getNIntegrableObjects());
86			// We need NkBT a lot, so just set it here: This is the RAW number
87			// of integrableObjects, so no subtraction or addition of constraints or
88			// orientational degrees of freedom:
89			NkBT = info_->getNGlobalIntegrableObjects()kB targetTemp;
90
91			// fkBT is used because the thermostat operates on more degrees of freedom
92			// than the barostat (when there are particles with orientational degrees
93			// of freedom).
94			fkBT = info_->getNdf()kB targetTemp;
95			}
96
97			void NPT::moveA() {
98			typename SimInfo::MoleculeIterator i;
99			typename Molecule::IntegrableObjectIterator j;
100			Molecule* mol;
101			StuntDouble* integrableObject;
102			Vector3d Tb, ji;
103			double mass;
104			Vector3d vel;
105			Vector3d pos;
106			Vector3d frc;
107			Vector3d sc;
108			Vector3d COM;
109			int index;
110
111			instaTemp = tStats->getTemperature();
112			tStats->getPressureTensor(press);
113			instaPress = p_convert * (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
114			instaVol = tStats->getVolume();
115
116			tStats->getCOM(COM);
117
118			//evolve velocity half step
119
120			calcVelScale();
121
122			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
123			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
124			integrableObject = mol->nextIntegrableObject(j)) {
125
126			vel = integrableObject->getVel();
127			frc = integrableObject->getFrc();
128
129			mass = integrableObject->getMass();
130
131			getVelScaleA(sc, vel);
132
133			// velocity half step (use chi from previous step here):
134			//vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]);
135			vel += dt2eConvert/mass frc - dt2*sc;
136			integrableObject->setVel(vel);
137
138			if (integrableObject->isDirectional()) {
139
140			// get and convert the torque to body frame
141
142			Tb = integrableObject->getTrq();
143			integrableObject->lab2Body(Tb);
144
145			// get the angular momentum, and propagate a half step
146
147			ji = integrableObject->getJ();
148
149			//ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
150			ji += dt2eConvert Tb - dt2chi ji;
151
152			this->rotationPropagation(integrableObject, ji);
153
154			integrableObject->setJ(ji);
155			}
156
157			}
158			}
159			// evolve chi and eta half step
160
161			evolveChiA();
162			evolveEtaA();
163
164			//calculate the integral of chidt
165			integralOfChidt += dt2 * chi;
166
167			index = 0;
168			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
169			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
170			integrableObject = mol->nextIntegrableObject(j)) {
171			oldPos[index++] = integrableObject->getPos();
172			}
173			}
174
175			//the first estimation of r(t+dt) is equal to r(t)
176
177			for(int k = 0; k < maxIterNum_; k++) {
178			index = 0;
179			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
180			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
181			integrableObject = mol->nextIntegrableObject(j)) {
182
183			vel = integrableObject->getVel();
184			pos = integrableObject->getPos();
185
186			this->getPosScale(pos, COM, index, sc);
187
188			pos = oldPos[index] + dt * (vel + sc);
189			integrableObject->setPos(pos);
190
191			++index;
192			}
193			}
194
195			//constraintAlgorithm->doConstrainA();
196			}
197
198			// Scale the box after all the positions have been moved:
199
200			this->scaleSimBox();
201			}
202
203			void NPT::moveB(void) {
204			typename SimInfo::MoleculeIterator i;
205			typename Molecule::IntegrableObjectIterator j;
206			Molecule* mol;
207			StuntDouble* integrableObject;
208			int index;
209			Vector3d Tb;
210			Vector3d ji;
211			Vector3d sc;
212			Vector3d vel;
213			Vector3d frc;
214			double mass;
215
216			//save velocity and angular momentum
217			index = 0;
218			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
219			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
220			integrableObject = mol->nextIntegrableObject(j)) {
221
222			oldVel[index] = integrableObject->getVel();
223			oldJi[3 * i + j] = integrableObject->getJ();
224			++index;
225			}
226			}
227
228			// do the iteration:
229			instaVol = tStats->getVolume();
230
231			for(int k = 0; k < maxIterNum_; k++) {
232			instaTemp = tStats->getTemperature();
233			instaPress = tStats->getPressure();
234
235			// evolve chi another half step using the temperature at t + dt/2
236			this->evolveChiB();
237			this->evolveEtaB();
238			this->calcVelScale();
239
240			index = 0;
241			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
242			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
243			integrableObject = mol->nextIntegrableObject(j)) {
244			integrableObject->getFrc(frc);
245			vel = integrableObject->getVel();
246
247			mass = integrableObject->getMass();
248
249			getVelScaleB(sc, i);
250
251			// velocity half step
252			//vel[j] = oldVel[3 * i + j] + dt2 ((frc[j] / mass) eConvert - sc[j]);
253			vel = oldVel[index] + dt2eConvert/mass frc - dt2*sc;
254			integrableObject->setVel(vel);
255
256			if (integrableObject->isDirectional()) {
257			// get and convert the torque to body frame
258			Tb = integrableObject->getTrq();
259			integrableObject->lab2Body(Tb);
260
261			//ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
262			ji = oldJi[index] + dt2eConvertTb - dt2chioldJi[index];
263			integrableObject->setJ(ji);
264			}
265
266			++index;
267			}
268			}
269
270			//constraintAlgorithm->doConstrainB();
271
272			if (this->chiConverged() && this->etaConverged())
273			break;
274			}
275
276			//calculate integral of chidt
277			integralOfChidt += dt2 * chi;
278			}
279
280			void NPT::evolveChiA() {
281			chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
282			oldChi = chi;
283			}
284
285			void NPT::evolveChiB() {
286			prevChi = chi;
287			chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
288			}
289
290			bool NPT::chiConverged() {
291			return (fabs(prevChi - chi) <= chiTolerance);
292			}
293
294			}