src/integrators/NPAT.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 "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "integrators/NPAT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {
  
  void NPAT::evolveEtaA() {

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

  void NPAT::evolveEtaB() {

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

  void NPAT::calcVelScale(){

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

        if (i == j) {
          vScale(i, j) += chi;
        }
      }
    }
  }

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

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

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

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

  void NPAT::scaleSimBox(){

    int i;
    int j;
    int k;
    Mat3x3d scaleMat;
    double eta2ij;
    double bigScale, smallScale, offDiagMax;
    Mat3x3d hm;
    Mat3x3d hmnew;


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

    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)

    bigScale = 1.0;
    smallScale = 1.0;
    offDiagMax = 0.0;

    for(i=0; i<3; i++){
      for(j=0; j<3; j++){

        // Calculate the matrix Product of the eta array (we only need
        // the ij element right now):

        eta2ij = 0.0;
        for(k=0; k<3; k++){
          eta2ij += eta(i, k) * eta(k, j);
        }

        scaleMat(i, j) = 0.0;
        // identity matrix (see above):
        if (i == j) scaleMat(i, j) = 1.0;
        // Taylor expansion for the exponential truncated at second order:
        scaleMat(i, j) += dt*eta(i, j)  + 0.5*dt*dt*eta2ij;
      

        if (i != j)
          if (fabs(scaleMat(i, j)) > offDiagMax)
            offDiagMax = fabs(scaleMat(i, j));
      }

      if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
      if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
    }

    if ((bigScale > 1.01) || (smallScale < 0.99)) {
      sprintf( painCave.errMsg,
               "NPAT error: Attempting a Box scaling of more than 1 percent.\n"
               " Check your tauBarostat, as it is probably too small!\n\n"
               " scaleMat = [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n"
               "      eta = [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n",
               scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
               scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
               scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
               eta(0, 0),eta(0, 1),eta(0, 2),
               eta(1, 0),eta(1, 1),eta(1, 2),
               eta(2, 0),eta(2, 1),eta(2, 2));
      painCave.isFatal = 1;
      simError();
    } else if (offDiagMax > 0.01) {
      sprintf( painCave.errMsg,
               "NPAT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
               " Check your tauBarostat, as it is probably too small!\n\n"
               " scaleMat = [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n"
               "      eta = [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n"
               "            [%lf\t%lf\t%lf]\n",
               scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
               scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
               scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
               eta(0, 0),eta(0, 1),eta(0, 2),
               eta(1, 0),eta(1, 1),eta(1, 2),
               eta(2, 0),eta(2, 1),eta(2, 2));
      painCave.isFatal = 1;
      simError();
    } else {

      Mat3x3d hmat = currentSnapshot_->getHmat();
      hmat = hmat *scaleMat;
      currentSnapshot_->setHmat(hmat);
        
    }
  }

  bool NPAT::etaConverged() {
    int i;
    double 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 );
  }

  double NPAT::calcConservedQuantity(){

    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    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()*OOPSEConstant::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()*OOPSEConstant::kB *targetTemp;    
    
    double conservedQuantity;
    double totalEnergy;
    double thermostat_kinetic;
    double thermostat_potential;
    double barostat_kinetic;
    double barostat_potential;
    double trEta;

    totalEnergy = thermo.getTotalE();

    thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);

    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;

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

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

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

    return conservedQuantity;

  }

  void NPAT::loadEta() {
    eta= currentSnapshot_->getEta();

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

  void NPAT::saveEta() {
    currentSnapshot_->setEta(eta);
  }

}

Revision:	2233
Committed:	Thu May 19 04:28:26 2005 UTC (19 years, 1 month ago) by tim
File size:	8313 byte(s)
Log Message:	adding NPAT and NPrT integrators
#	User	Rev	Content
1	tim	2233	/*
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			#include "brains/SimInfo.hpp"
43			#include "brains/Thermo.hpp"
44			#include "integrators/IntegratorCreator.hpp"
45			#include "integrators/NPAT.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/OOPSEConstant.hpp"
48			#include "utils/simError.h"
49
50			namespace oopse {
51
52			void NPAT::evolveEtaA() {
53
54			eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
55			oldEta = eta;
56			}
57
58			void NPAT::evolveEtaB() {
59
60			prevEta = eta;
61			eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
62			(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
63			}
64
65			void NPAT::calcVelScale(){
66
67			for (int i = 0; i < 3; i++ ) {
68			for (int j = 0; j < 3; j++ ) {
69			vScale(i, j) = eta(i, j);
70
71			if (i == j) {
72			vScale(i, j) += chi;
73			}
74			}
75			}
76			}
77
78			void NPAT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
79			sc = vScale * vel;
80			}
81
82			void NPAT::getVelScaleB(Vector3d& sc, int index ) {
83			sc = vScale * oldVel[index];
84			}
85
86			void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
87
88			/*@todo /
89			Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
90			sc = eta * rj;
91			}
92
93			void NPAT::scaleSimBox(){
94
95			int i;
96			int j;
97			int k;
98			Mat3x3d scaleMat;
99			double eta2ij;
100			double bigScale, smallScale, offDiagMax;
101			Mat3x3d hm;
102			Mat3x3d hmnew;
103
104
105
106			// Scale the box after all the positions have been moved:
107
108			// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
109			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
110
111			bigScale = 1.0;
112			smallScale = 1.0;
113			offDiagMax = 0.0;
114
115			for(i=0; i<3; i++){
116			for(j=0; j<3; j++){
117
118			// Calculate the matrix Product of the eta array (we only need
119			// the ij element right now):
120
121			eta2ij = 0.0;
122			for(k=0; k<3; k++){
123			eta2ij += eta(i, k) * eta(k, j);
124			}
125
126			scaleMat(i, j) = 0.0;
127			// identity matrix (see above):
128			if (i == j) scaleMat(i, j) = 1.0;
129			// Taylor expansion for the exponential truncated at second order:
130			scaleMat(i, j) += dteta(i, j) + 0.5dtdteta2ij;
131
132
133			if (i != j)
134			if (fabs(scaleMat(i, j)) > offDiagMax)
135			offDiagMax = fabs(scaleMat(i, j));
136			}
137
138			if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
139			if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
140			}
141
142			if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
143			sprintf( painCave.errMsg,
144			"NPAT error: Attempting a Box scaling of more than 1 percent.\n"
145			" Check your tauBarostat, as it is probably too small!\n\n"
146			" scaleMat = [%lf\t%lf\t%lf]\n"
147			" [%lf\t%lf\t%lf]\n"
148			" [%lf\t%lf\t%lf]\n"
149			" eta = [%lf\t%lf\t%lf]\n"
150			" [%lf\t%lf\t%lf]\n"
151			" [%lf\t%lf\t%lf]\n",
152			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
153			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
154			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
155			eta(0, 0),eta(0, 1),eta(0, 2),
156			eta(1, 0),eta(1, 1),eta(1, 2),
157			eta(2, 0),eta(2, 1),eta(2, 2));
158			painCave.isFatal = 1;
159			simError();
160			} else if (offDiagMax > 0.01) {
161			sprintf( painCave.errMsg,
162			"NPAT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
163			" Check your tauBarostat, as it is probably too small!\n\n"
164			" scaleMat = [%lf\t%lf\t%lf]\n"
165			" [%lf\t%lf\t%lf]\n"
166			" [%lf\t%lf\t%lf]\n"
167			" eta = [%lf\t%lf\t%lf]\n"
168			" [%lf\t%lf\t%lf]\n"
169			" [%lf\t%lf\t%lf]\n",
170			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
171			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
172			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
173			eta(0, 0),eta(0, 1),eta(0, 2),
174			eta(1, 0),eta(1, 1),eta(1, 2),
175			eta(2, 0),eta(2, 1),eta(2, 2));
176			painCave.isFatal = 1;
177			simError();
178			} else {
179
180			Mat3x3d hmat = currentSnapshot_->getHmat();
181			hmat = hmat *scaleMat;
182			currentSnapshot_->setHmat(hmat);
183
184			}
185			}
186
187			bool NPAT::etaConverged() {
188			int i;
189			double diffEta, sumEta;
190
191			sumEta = 0;
192			for(i = 0; i < 3; i++) {
193			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
194			}
195
196			diffEta = sqrt( sumEta / 3.0 );
197
198			return ( diffEta <= etaTolerance );
199			}
200
201			double NPAT::calcConservedQuantity(){
202
203			chi= currentSnapshot_->getChi();
204			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
205			loadEta();
206
207			// We need NkBT a lot, so just set it here: This is the RAW number
208			// of integrableObjects, so no subtraction or addition of constraints or
209			// orientational degrees of freedom:
210			NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
211
212			// fkBT is used because the thermostat operates on more degrees of freedom
213			// than the barostat (when there are particles with orientational degrees
214			// of freedom).
215			fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
216
217			double conservedQuantity;
218			double totalEnergy;
219			double thermostat_kinetic;
220			double thermostat_potential;
221			double barostat_kinetic;
222			double barostat_potential;
223			double trEta;
224
225			totalEnergy = thermo.getTotalE();
226
227			thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
228
229			thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
230
231			SquareMatrix<double, 3> tmp = eta.transpose() * eta;
232			trEta = tmp.trace();
233
234			barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
235
236			barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
237
238			conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
239			barostat_kinetic + barostat_potential;
240
241			return conservedQuantity;
242
243			}
244
245			void NPAT::loadEta() {
246			eta= currentSnapshot_->getEta();
247
248			//if (!eta.isDiagonal()) {
249			// sprintf( painCave.errMsg,
250			// "NPAT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
251			// painCave.isFatal = 1;
252			// simError();
253			//}
254			}
255
256			void NPAT::saveEta() {
257			currentSnapshot_->setEta(eta);
258			}
259
260			}
261