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 (19 years, 7 months ago) by tim
File size:	8969 byte(s)
Log Message:	refactory NPT integrator
#	Content
1	#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	}