src/integrators/NPT.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <math.h>

#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/NPT.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.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), maxIterNum_(4) {

    Globals* simParams = info_->getSimParams();
    
    if (!simParams->getUseInitXSstate()) {
        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
        currSnapshot->setChi(0.0);
        currSnapshot->setIntegralOfChiDt(0.0);
        currSnapshot->setEta(Mat3x3d(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();
    }

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

        painCave.isFatal = 1;
        simError();
    } else {
        targetPressure = simParams->getTargetPressure();
    }
    
    if (!simParams->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 = simParams->getTauBarostat();
    }
    
    tt2 = tauThermostat * tauThermostat;
    tb2 = tauBarostat * tauBarostat;

    update();
}

NPT::~NPT() {
}

void NPT::doUpdate() {

    oldPos.resize(info_->getNIntegrableObjects());
    oldVel.resize(info_->getNIntegrableObjects());
    oldJi.resize(info_->getNIntegrableObjects());

}

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

    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    loadEta();
    
    instaTemp =thermo.getTemperature();
    press = thermo.getPressureTensor();
    instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
    instaVol =thermo.getVolume();

    Vector3d  COM = info_->getCom();

    //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) * OOPSEConstant::energyConvert - sc[j]);
            vel += dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc;
            integrableObject->setVel(vel);

            if (integrableObject->isDirectional()) {

                // get and 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);
            }
            
        }
    }
    // evolve chi and eta  half step

    chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
    
    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;
           }
        }

        rattle->constraintA();
    }

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

    this->scaleSimBox();

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);

    saveEta();
}

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


    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    double oldChi  = chi;
    double prevChi;

    loadEta();
    
    //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[index] = integrableObject->getJ();
            ++index;
        }
    }

    // do the iteration:
    instaVol =thermo.getVolume();

    for(int k = 0; k < maxIterNum_; k++) {
        instaTemp =thermo.getTemperature();
        instaPress =thermo.getPressure();

        // evolve chi another half step using the temperature at t + dt/2
        prevChi = chi;
        chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;

        //evolve eta
        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)) {            

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

                mass = integrableObject->getMass();

                getVelScaleB(sc, index);

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

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

                    //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) && this->etaConverged())
            break;
    }

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

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);    

    saveEta();
}

}
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (21 years, 4 months ago) by tim
File size:	11168 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	tim	1774	#include <math.h>
43
44			#include "brains/SimInfo.hpp"
45			#include "brains/Thermo.hpp"
46			#include "integrators/NPT.hpp"
47	tim	1822	#include "math/SquareMatrix3.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/OOPSEConstant.hpp"
50	tim	1774	#include "utils/simError.h"
51
52			// Basic isotropic thermostating and barostating via the Melchionna
53			// modification of the Hoover algorithm:
54			//
55			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
56			// Molec. Phys., 78, 533.
57			//
58			// and
59			//
60			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
61
62			namespace oopse {
63
64			NPT::NPT(SimInfo* info) :
65	tim	1883	VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) {
66	tim	1774
67	tim	1841	Globals* simParams = info_->getSimParams();
68	tim	1774
69	tim	1865	if (!simParams->getUseInitXSstate()) {
70	tim	1774	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
71			currSnapshot->setChi(0.0);
72			currSnapshot->setIntegralOfChiDt(0.0);
73	tim	1822	currSnapshot->setEta(Mat3x3d(0.0));
74	tim	1774	}
75
76	tim	1841	if (!simParams->haveTargetTemp()) {
77	tim	1774	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
78			painCave.isFatal = 1;
79			painCave.severity = OOPSE_ERROR;
80			simError();
81			} else {
82	tim	1841	targetTemp = simParams->getTargetTemp();
83	tim	1774	}
84
85			// We must set tauThermostat
86	tim	1841	if (!simParams->haveTauThermostat()) {
87	tim	1774	sprintf(painCave.errMsg, "If you use the constant temperature\n"
88			"\tintegrator, you must set tauThermostat_.\n");
89
90			painCave.severity = OOPSE_ERROR;
91			painCave.isFatal = 1;
92			simError();
93			} else {
94	tim	1841	tauThermostat = simParams->getTauThermostat();
95	tim	1774	}
96
97	tim	1841	if (!simParams->haveTargetPressure()) {
98	tim	1774	sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
99			" without a targetPressure!\n");
100
101			painCave.isFatal = 1;
102			simError();
103			} else {
104	tim	1841	targetPressure = simParams->getTargetPressure();
105	tim	1774	}
106
107	tim	1841	if (!simParams->haveTauBarostat()) {
108	tim	1774	sprintf(painCave.errMsg,
109			"If you use the NPT integrator, you must set tauBarostat.\n");
110			painCave.severity = OOPSE_ERROR;
111			painCave.isFatal = 1;
112			simError();
113			} else {
114	tim	1841	tauBarostat = simParams->getTauBarostat();
115	tim	1774	}
116
117			tt2 = tauThermostat * tauThermostat;
118			tb2 = tauBarostat * tauBarostat;
119
120			update();
121			}
122
123			NPT::~NPT() {
124			}
125
126	tim	1822	void NPT::doUpdate() {
127	tim	1867
128	tim	1774	oldPos.resize(info_->getNIntegrableObjects());
129			oldVel.resize(info_->getNIntegrableObjects());
130			oldJi.resize(info_->getNIntegrableObjects());
131
132			}
133
134			void NPT::moveA() {
135	tim	1822	SimInfo::MoleculeIterator i;
136			Molecule::IntegrableObjectIterator j;
137	tim	1774	Molecule* mol;
138			StuntDouble* integrableObject;
139			Vector3d Tb, ji;
140			double mass;
141			Vector3d vel;
142			Vector3d pos;
143			Vector3d frc;
144			Vector3d sc;
145			int index;
146	tim	1822
147	tim	1867	chi= currentSnapshot_->getChi();
148			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
149	tim	1822	loadEta();
150	tim	1774
151	tim	1822	instaTemp =thermo.getTemperature();
152			press = thermo.getPressureTensor();
153			instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
154			instaVol =thermo.getVolume();
155	tim	1774
156	tim	1822	Vector3d COM = info_->getCom();
157	tim	1774
158			//evolve velocity half step
159
160			calcVelScale();
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			vel = integrableObject->getVel();
167			frc = integrableObject->getFrc();
168
169			mass = integrableObject->getMass();
170
171			getVelScaleA(sc, vel);
172
173			// velocity half step (use chi from previous step here):
174	tim	1822	//vel[j] += dt2 * ((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]);
175			vel += dt2OOPSEConstant::energyConvert/mass frc - dt2*sc;
176	tim	1774	integrableObject->setVel(vel);
177
178			if (integrableObject->isDirectional()) {
179
180			// get and convert the torque to body frame
181
182	tim	1871	Tb = integrableObject->lab2Body(integrableObject->getTrq());
183	tim	1774
184			// get the angular momentum, and propagate a half step
185
186			ji = integrableObject->getJ();
187
188	tim	1822	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
189			ji += dt2OOPSEConstant::energyConvert Tb - dt2chi ji;
190	tim	1774
191	tim	1822	rotAlgo->rotate(integrableObject, ji, dt);
192	tim	1774
193			integrableObject->setJ(ji);
194			}
195
196			}
197			}
198			// evolve chi and eta half step
199
200	tim	1822	chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
201
202	tim	1774	evolveEtaA();
203
204			//calculate the integral of chidt
205			integralOfChidt += dt2 * chi;
206
207			index = 0;
208			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
209			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
210			integrableObject = mol->nextIntegrableObject(j)) {
211			oldPos[index++] = integrableObject->getPos();
212			}
213			}
214
215			//the first estimation of r(t+dt) is equal to r(t)
216
217			for(int k = 0; k < maxIterNum_; k++) {
218			index = 0;
219			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
220			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
221			integrableObject = mol->nextIntegrableObject(j)) {
222
223			vel = integrableObject->getVel();
224			pos = integrableObject->getPos();
225
226			this->getPosScale(pos, COM, index, sc);
227
228			pos = oldPos[index] + dt * (vel + sc);
229			integrableObject->setPos(pos);
230
231			++index;
232			}
233			}
234
235	tim	1901	rattle->constraintA();
236	tim	1774	}
237
238			// Scale the box after all the positions have been moved:
239
240			this->scaleSimBox();
241	tim	1822
242	tim	1867	currentSnapshot_->setChi(chi);
243			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
244	tim	1822
245			saveEta();
246	tim	1774	}
247
248			void NPT::moveB(void) {
249	tim	1822	SimInfo::MoleculeIterator i;
250			Molecule::IntegrableObjectIterator j;
251	tim	1774	Molecule* mol;
252			StuntDouble* integrableObject;
253			int index;
254			Vector3d Tb;
255			Vector3d ji;
256			Vector3d sc;
257			Vector3d vel;
258			Vector3d frc;
259			double mass;
260
261	tim	1822
262	tim	1867	chi= currentSnapshot_->getChi();
263			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
264	tim	1822	double oldChi = chi;
265			double prevChi;
266
267			loadEta();
268
269	tim	1774	//save velocity and angular momentum
270			index = 0;
271			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
272			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
273			integrableObject = mol->nextIntegrableObject(j)) {
274
275			oldVel[index] = integrableObject->getVel();
276	tim	1822	oldJi[index] = integrableObject->getJ();
277	tim	1774	++index;
278			}
279			}
280
281			// do the iteration:
282	tim	1822	instaVol =thermo.getVolume();
283	tim	1774
284			for(int k = 0; k < maxIterNum_; k++) {
285	tim	1822	instaTemp =thermo.getTemperature();
286			instaPress =thermo.getPressure();
287	tim	1774
288			// evolve chi another half step using the temperature at t + dt/2
289	tim	1822	prevChi = chi;
290			chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
291
292			//evolve eta
293	tim	1774	this->evolveEtaB();
294			this->calcVelScale();
295
296			index = 0;
297			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
298			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299			integrableObject = mol->nextIntegrableObject(j)) {
300	tim	1822
301			frc = integrableObject->getFrc();
302	tim	1774	vel = integrableObject->getVel();
303
304			mass = integrableObject->getMass();
305
306	tim	1822	getVelScaleB(sc, index);
307	tim	1774
308			// velocity half step
309	tim	1822	//vel[j] = oldVel[3 * i + j] + dt2 ((frc[j] / mass) OOPSEConstant::energyConvert - sc[j]);
310			vel = oldVel[index] + dt2OOPSEConstant::energyConvert/mass frc - dt2*sc;
311	tim	1774	integrableObject->setVel(vel);
312
313			if (integrableObject->isDirectional()) {
314			// get and convert the torque to body frame
315	tim	1871	Tb = integrableObject->lab2Body(integrableObject->getTrq());
316	tim	1774
317	tim	1822	//ji[j] = oldJi[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi[3i+j]chi);
318			ji = oldJi[index] + dt2OOPSEConstant::energyConvertTb - dt2chioldJi[index];
319	tim	1774	integrableObject->setJ(ji);
320			}
321
322			++index;
323			}
324			}
325
326	tim	1901	rattle->constraintB();
327	tim	1774
328	tim	1822	if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
329	tim	1774	break;
330			}
331
332			//calculate integral of chidt
333			integralOfChidt += dt2 * chi;
334
335	tim	1867	currentSnapshot_->setChi(chi);
336			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
337	tim	1774
338	tim	1822	saveEta();
339	tim	1774	}
340
341			}