src/integrators/NPA.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "integrators/NPA.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {
  
  void NPA::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d Tb, ji;
    RealType mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d sc;
    int index;

    loadEta();
    
    instaTemp =thermo.getTemperature();
    press = thermo.getPressureTensor();
    instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + 
                                                      press(1, 1) + 
                                                      press(2, 2)) / 3.0;
    instaVol =thermo.getVolume();

    Vector3d  COM = thermo.getCom();

    //evolve velocity half step

    calcVelScale();

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
        
        vel = sd->getVel();
        frc = sd->getFrc();

        mass = sd->getMass();
        
        getVelScaleA(sc, vel);
        
        // velocity half step  (use chi from previous step here):
        
        vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc;
        sd->setVel(vel);
        
        if (sd->isDirectional()) {
          
          // get and convert the torque to body frame

          Tb = sd->lab2Body(sd->getTrq());
          
          // get the angular momentum, and propagate a half step
          
          ji = sd->getJ();
          
          ji += dt2*PhysicalConstants::energyConvert * Tb 
            - dt2*thermostat.first* ji;
          
          rotAlgo_->rotate(sd, ji, dt);
          
          sd->setJ(ji);
        }            
      }
    }
    // evolve eta a half step
    
    evolveEtaA();    
    flucQ_->moveA();

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      
      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

        oldPos[index++] = sd->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 (sd = mol->beginIntegrableObject(j); sd != NULL;
             sd = mol->nextIntegrableObject(j)) {
          
          vel = sd->getVel();
          pos = sd->getPos();
          
          this->getPosScale(pos, COM, index, sc);
          
          pos = oldPos[index] + dt * (vel + sc);
          sd->setPos(pos);     

          ++index;
        }
      }

      rattle_->constraintA();
    }

    // Scale the box after all the positions have been moved:
    
    this->scaleSimBox();
    
    saveEta();
  }

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

    loadEta();
    
    //save velocity and angular momentum
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      
      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {
        
        oldVel[index] = sd->getVel();

        if (sd->isDirectional())
          oldJi[index] = sd->getJ();
        
        ++index;
      }
    }
    
    instaVol = thermo.getVolume();
    instaTemp = thermo.getTemperature();
    instaPress = thermo.getPressure();
    
    //evolve eta
    this->evolveEtaB();
    this->calcVelScale();

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      
      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {            
        
        frc = sd->getFrc();
        mass = sd->getMass();

        getVelScaleB(sc, index);
        
        // velocity half step
        vel = oldVel[index] 
          + dt2*PhysicalConstants::energyConvert/mass* frc 
          - dt2*sc;
        
        sd->setVel(vel);
        
        if (sd->isDirectional()) {
          // get and convert the torque to body frame
          Tb = sd->lab2Body(sd->getTrq());
          
          ji = oldJi[index] 
            + dt2*PhysicalConstants::energyConvert*Tb 
            - dt2*thermostat.first*oldJi[index];
          
          sd->setJ(ji);
        }

        ++index;
      }
    }
        
    rattle_->constraintB();

    flucQ_->moveB();
    saveEta();
  }

  void NPA::evolveEtaA() {

    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
    oldEta = eta;  
  }

  void NPA::evolveEtaB() {

    prevEta = eta;
    eta(2,2) = oldEta(2, 2) + dt2 *  instaVol *
            (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
  }

  void NPA::calcVelScale(){

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0; j < 3; j++ ) {
        vScale(i, j) = eta(i, j);
      }
    }
  }

  void NPA::getVelScaleA(Vector3d& sc, const Vector3d& vel){
    sc = vScale * vel;
  }

  void NPA::getVelScaleB(Vector3d& sc, int index ) {
    sc = vScale * oldVel[index];
  }

  void NPA::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, 
                        Vector3d& sc) {

    Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
    sc = eta * rj;
  }

  void NPA::scaleSimBox(){
    Mat3x3d scaleMat;
    
    for(int i=0; i<3; i++){
      for(int j=0; j<3; j++){
        scaleMat(i, j) = 0.0;
        if(i==j) {
          scaleMat(i, j) = 1.0;
        }
      }
    }
    
    scaleMat(2, 2) = exp(dt*eta(2, 2));
    Mat3x3d hmat = snap->getHmat();
    hmat = hmat *scaleMat;
    snap->setHmat(hmat);
  }

  bool NPA::etaConverged() {
    int i;
    RealType diffEta, sumEta;

    sumEta = 0;
    for(i = 0; i < 3; i++) {
      sumEta += pow(prevEta(i, i) - eta(i, i), 2);
    }
    
    diffEta = sqrt( sumEta / 3.0 );

    return ( diffEta <= etaTolerance );
  }

  RealType NPA::calcConservedQuantity(){

    thermostat = snap->getThermostat();
    loadEta();
    
    // 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()*PhysicalConstants::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()*PhysicalConstants::kB *targetTemp;    
    
    RealType conservedQuantity;
    RealType totalEnergy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    RealType barostat_kinetic;
    RealType barostat_potential;
    RealType trEta;

    totalEnergy = thermo.getTotalEnergy();

    thermostat_kinetic = 0.0;
    thermostat_potential = 0.0;

    SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
    trEta = tmp.trace();
    
    barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);

    barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;

    conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
      barostat_kinetic + barostat_potential;

    return conservedQuantity;

  }

  void NPA::loadEta() {
    eta= snap->getBarostat();

    //if (!eta.isDiagonal()) {
    //    sprintf( painCave.errMsg,
    //             "NPA error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
    //    painCave.isFatal = 1;
    //    simError();
    //}
  }

  void NPA::saveEta() {
    snap->setBarostat(eta);
  }

}

Revision:	2011
Committed:	Wed Aug 6 19:27:37 2014 UTC (11 years, 2 months ago) by gezelter
File size:	10229 byte(s)
Log Message:	Added NPA integrator
#	User	Rev	Content
1	gezelter	2011	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "brains/SimInfo.hpp"
44			#include "brains/Thermo.hpp"
45			#include "integrators/IntegratorCreator.hpp"
46			#include "integrators/NPA.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "utils/PhysicalConstants.hpp"
49			#include "utils/simError.h"
50
51			namespace OpenMD {
52
53			void NPA::moveA() {
54			SimInfo::MoleculeIterator i;
55			Molecule::IntegrableObjectIterator j;
56			Molecule* mol;
57			StuntDouble* sd;
58			Vector3d Tb, ji;
59			RealType mass;
60			Vector3d vel;
61			Vector3d pos;
62			Vector3d frc;
63			Vector3d sc;
64			int index;
65
66			loadEta();
67
68			instaTemp =thermo.getTemperature();
69			press = thermo.getPressureTensor();
70			instaPress = PhysicalConstants::pressureConvert* (press(0, 0) +
71			press(1, 1) +
72			press(2, 2)) / 3.0;
73			instaVol =thermo.getVolume();
74
75			Vector3d COM = thermo.getCom();
76
77			//evolve velocity half step
78
79			calcVelScale();
80
81			for (mol = info_->beginMolecule(i); mol != NULL;
82			mol = info_->nextMolecule(i)) {
83
84			for (sd = mol->beginIntegrableObject(j); sd != NULL;
85			sd = mol->nextIntegrableObject(j)) {
86
87			vel = sd->getVel();
88			frc = sd->getFrc();
89
90			mass = sd->getMass();
91
92			getVelScaleA(sc, vel);
93
94			// velocity half step (use chi from previous step here):
95
96			vel += dt2PhysicalConstants::energyConvert/mass frc - dt2*sc;
97			sd->setVel(vel);
98
99			if (sd->isDirectional()) {
100
101			// get and convert the torque to body frame
102
103			Tb = sd->lab2Body(sd->getTrq());
104
105			// get the angular momentum, and propagate a half step
106
107			ji = sd->getJ();
108
109			ji += dt2PhysicalConstants::energyConvert Tb
110			- dt2thermostat.first ji;
111
112			rotAlgo_->rotate(sd, ji, dt);
113
114			sd->setJ(ji);
115			}
116			}
117			}
118			// evolve eta a half step
119
120			evolveEtaA();
121			flucQ_->moveA();
122
123			index = 0;
124			for (mol = info_->beginMolecule(i); mol != NULL;
125			mol = info_->nextMolecule(i)) {
126
127			for (sd = mol->beginIntegrableObject(j); sd != NULL;
128			sd = mol->nextIntegrableObject(j)) {
129
130			oldPos[index++] = sd->getPos();
131
132			}
133			}
134
135			//the first estimation of r(t+dt) is equal to r(t)
136
137			for(int k = 0; k < maxIterNum_; k++) {
138			index = 0;
139			for (mol = info_->beginMolecule(i); mol != NULL;
140			mol = info_->nextMolecule(i)) {
141
142			for (sd = mol->beginIntegrableObject(j); sd != NULL;
143			sd = mol->nextIntegrableObject(j)) {
144
145			vel = sd->getVel();
146			pos = sd->getPos();
147
148			this->getPosScale(pos, COM, index, sc);
149
150			pos = oldPos[index] + dt * (vel + sc);
151			sd->setPos(pos);
152
153			++index;
154			}
155			}
156
157			rattle_->constraintA();
158			}
159
160			// Scale the box after all the positions have been moved:
161
162			this->scaleSimBox();
163
164			saveEta();
165			}
166
167			void NPA::moveB(void) {
168			SimInfo::MoleculeIterator i;
169			Molecule::IntegrableObjectIterator j;
170			Molecule* mol;
171			StuntDouble* sd;
172			int index;
173			Vector3d Tb;
174			Vector3d ji;
175			Vector3d sc;
176			Vector3d vel;
177			Vector3d frc;
178			RealType mass;
179
180			loadEta();
181
182			//save velocity and angular momentum
183			index = 0;
184			for (mol = info_->beginMolecule(i); mol != NULL;
185			mol = info_->nextMolecule(i)) {
186
187			for (sd = mol->beginIntegrableObject(j); sd != NULL;
188			sd = mol->nextIntegrableObject(j)) {
189
190			oldVel[index] = sd->getVel();
191
192			if (sd->isDirectional())
193			oldJi[index] = sd->getJ();
194
195			++index;
196			}
197			}
198
199			instaVol = thermo.getVolume();
200			instaTemp = thermo.getTemperature();
201			instaPress = thermo.getPressure();
202
203			//evolve eta
204			this->evolveEtaB();
205			this->calcVelScale();
206
207			index = 0;
208			for (mol = info_->beginMolecule(i); mol != NULL;
209			mol = info_->nextMolecule(i)) {
210
211			for (sd = mol->beginIntegrableObject(j); sd != NULL;
212			sd = mol->nextIntegrableObject(j)) {
213
214			frc = sd->getFrc();
215			mass = sd->getMass();
216
217			getVelScaleB(sc, index);
218
219			// velocity half step
220			vel = oldVel[index]
221			+ dt2PhysicalConstants::energyConvert/mass frc
222			- dt2*sc;
223
224			sd->setVel(vel);
225
226			if (sd->isDirectional()) {
227			// get and convert the torque to body frame
228			Tb = sd->lab2Body(sd->getTrq());
229
230			ji = oldJi[index]
231			+ dt2PhysicalConstants::energyConvertTb
232			- dt2thermostat.firstoldJi[index];
233
234			sd->setJ(ji);
235			}
236
237			++index;
238			}
239			}
240
241			rattle_->constraintB();
242
243			flucQ_->moveB();
244			saveEta();
245			}
246
247			void NPA::evolveEtaA() {
248
249			eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
250			oldEta = eta;
251			}
252
253			void NPA::evolveEtaB() {
254
255			prevEta = eta;
256			eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
257			(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
258			}
259
260			void NPA::calcVelScale(){
261
262			for (int i = 0; i < 3; i++ ) {
263			for (int j = 0; j < 3; j++ ) {
264			vScale(i, j) = eta(i, j);
265			}
266			}
267			}
268
269			void NPA::getVelScaleA(Vector3d& sc, const Vector3d& vel){
270			sc = vScale * vel;
271			}
272
273			void NPA::getVelScaleB(Vector3d& sc, int index ) {
274			sc = vScale * oldVel[index];
275			}
276
277			void NPA::getPosScale(const Vector3d& pos, const Vector3d& COM, int index,
278			Vector3d& sc) {
279
280			Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
281			sc = eta * rj;
282			}
283
284			void NPA::scaleSimBox(){
285			Mat3x3d scaleMat;
286
287			for(int i=0; i<3; i++){
288			for(int j=0; j<3; j++){
289			scaleMat(i, j) = 0.0;
290			if(i==j) {
291			scaleMat(i, j) = 1.0;
292			}
293			}
294			}
295
296			scaleMat(2, 2) = exp(dt*eta(2, 2));
297			Mat3x3d hmat = snap->getHmat();
298			hmat = hmat *scaleMat;
299			snap->setHmat(hmat);
300			}
301
302			bool NPA::etaConverged() {
303			int i;
304			RealType diffEta, sumEta;
305
306			sumEta = 0;
307			for(i = 0; i < 3; i++) {
308			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
309			}
310
311			diffEta = sqrt( sumEta / 3.0 );
312
313			return ( diffEta <= etaTolerance );
314			}
315
316			RealType NPA::calcConservedQuantity(){
317
318			thermostat = snap->getThermostat();
319			loadEta();
320
321			// We need NkBT a lot, so just set it here: This is the RAW number
322			// of integrableObjects, so no subtraction or addition of constraints or
323			// orientational degrees of freedom:
324			NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
325
326			// fkBT is used because the thermostat operates on more degrees of freedom
327			// than the barostat (when there are particles with orientational degrees
328			// of freedom).
329			fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
330
331			RealType conservedQuantity;
332			RealType totalEnergy;
333			RealType thermostat_kinetic;
334			RealType thermostat_potential;
335			RealType barostat_kinetic;
336			RealType barostat_potential;
337			RealType trEta;
338
339			totalEnergy = thermo.getTotalEnergy();
340
341			thermostat_kinetic = 0.0;
342			thermostat_potential = 0.0;
343
344			SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
345			trEta = tmp.trace();
346
347			barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
348
349			barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
350
351			conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
352			barostat_kinetic + barostat_potential;
353
354			return conservedQuantity;
355
356			}
357
358			void NPA::loadEta() {
359			eta= snap->getBarostat();
360
361			//if (!eta.isDiagonal()) {
362			// sprintf( painCave.errMsg,
363			// "NPA error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
364			// painCave.isFatal = 1;
365			// simError();
366			//}
367			}
368
369			void NPA::saveEta() {
370			snap->setBarostat(eta);
371			}
372
373			}
374