src/integrators/NPrT.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/NPrT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {
  NPrT::NPrT(SimInfo* info) : NPT(info) {
    Globals* simParams = info_->getSimParams();
    if (!simParams->haveSurfaceTension()) {
      sprintf(painCave.errMsg,
              "If you use the NPT integrator, you must set tauBarostat.\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    } else {
      surfaceTension= simParams->getSurfaceTension();
    }

  }
  void NPrT::evolveEtaA() {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    double hz = hmat(2, 2);
    double Axy = hmat(0,0) * hmat(1, 1);
    double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
    double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
    eta(0,0) -= Axy * (sx - surfaceTension) / (NkBT*tb2);
    eta(1,1) -= Axy * (sy - surfaceTension) / (NkBT*tb2);
    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
    oldEta = eta;  
  }

  void NPrT::evolveEtaB() {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    double hz = hmat(2, 2);
    double Axy = hmat(0,0) * hmat(1, 1);
    prevEta = eta;
    double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
    double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
    eta(0,0) = oldEta(0, 0) - Axy * (sx -surfaceTension) / (NkBT*tb2);
    eta(1,1) = oldEta(1, 1) - Axy * (sy -surfaceTension) / (NkBT*tb2);
    eta(2,2) = oldEta(2, 2) + dt2 *  instaVol *
            (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
  }

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

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

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

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

  void NPrT::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,
               "NPrT 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,
               "NPrT 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 NPrT::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 NPrT::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 totalEnergy = thermo.getTotalE();

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

    double thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;

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

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

    Mat3x3d hmat = currentSnapshot_->getHmat();
    double hz = hmat(2, 2);
    double area = hmat(0,0) * hmat(1, 1);

    double conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
      barostat_kinetic + barostat_potential - surfaceTension * area;

    return conservedQuantity;

  }

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

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

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

}


Revision:	2235
Committed:	Thu May 19 21:31:23 2005 UTC (19 years, 1 month ago) by tim
File size:	9542 byte(s)
Log Message:	NPAT is working
#	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/NPrT.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/OOPSEConstant.hpp"
48			#include "utils/simError.h"
49
50			namespace oopse {
51			NPrT::NPrT(SimInfo* info) : NPT(info) {
52			Globals* simParams = info_->getSimParams();
53	tim	2235	if (!simParams->haveSurfaceTension()) {
54	tim	2233	sprintf(painCave.errMsg,
55			"If you use the NPT integrator, you must set tauBarostat.\n");
56			painCave.severity = OOPSE_ERROR;
57			painCave.isFatal = 1;
58			simError();
59			} else {
60	tim	2235	surfaceTension= simParams->getSurfaceTension();
61	tim	2233	}
62
63			}
64			void NPrT::evolveEtaA() {
65	tim	2234	Mat3x3d hmat = currentSnapshot_->getHmat();
66			double hz = hmat(2, 2);
67			double Axy = hmat(0,0) * hmat(1, 1);
68	tim	2233	double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
69			double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
70	tim	2235	eta(0,0) -= Axy * (sx - surfaceTension) / (NkBT*tb2);
71			eta(1,1) -= Axy * (sy - surfaceTension) / (NkBT*tb2);
72	tim	2233	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
73			oldEta = eta;
74			}
75
76			void NPrT::evolveEtaB() {
77	tim	2234	Mat3x3d hmat = currentSnapshot_->getHmat();
78			double hz = hmat(2, 2);
79			double Axy = hmat(0,0) * hmat(1, 1);
80	tim	2233	prevEta = eta;
81			double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
82			double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
83	tim	2235	eta(0,0) = oldEta(0, 0) - Axy * (sx -surfaceTension) / (NkBT*tb2);
84			eta(1,1) = oldEta(1, 1) - Axy * (sy -surfaceTension) / (NkBT*tb2);
85	tim	2233	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
86			(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
87			}
88
89			void NPrT::calcVelScale(){
90
91			for (int i = 0; i < 3; i++ ) {
92			for (int j = 0; j < 3; j++ ) {
93			vScale(i, j) = eta(i, j);
94
95			if (i == j) {
96			vScale(i, j) += chi;
97			}
98			}
99			}
100			}
101
102			void NPrT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
103			sc = vScale * vel;
104			}
105
106			void NPrT::getVelScaleB(Vector3d& sc, int index ) {
107			sc = vScale * oldVel[index];
108			}
109
110			void NPrT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
111
112			/*@todo /
113			Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
114			sc = eta * rj;
115			}
116
117			void NPrT::scaleSimBox(){
118
119			int i;
120			int j;
121			int k;
122			Mat3x3d scaleMat;
123			double eta2ij;
124			double bigScale, smallScale, offDiagMax;
125			Mat3x3d hm;
126			Mat3x3d hmnew;
127
128
129
130			// Scale the box after all the positions have been moved:
131
132			// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
133			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
134
135			bigScale = 1.0;
136			smallScale = 1.0;
137			offDiagMax = 0.0;
138
139			for(i=0; i<3; i++){
140			for(j=0; j<3; j++){
141
142			// Calculate the matrix Product of the eta array (we only need
143			// the ij element right now):
144
145			eta2ij = 0.0;
146			for(k=0; k<3; k++){
147			eta2ij += eta(i, k) * eta(k, j);
148			}
149
150			scaleMat(i, j) = 0.0;
151			// identity matrix (see above):
152			if (i == j) scaleMat(i, j) = 1.0;
153			// Taylor expansion for the exponential truncated at second order:
154			scaleMat(i, j) += dteta(i, j) + 0.5dtdteta2ij;
155
156
157			if (i != j)
158			if (fabs(scaleMat(i, j)) > offDiagMax)
159			offDiagMax = fabs(scaleMat(i, j));
160			}
161
162			if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
163			if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
164			}
165
166			if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
167			sprintf( painCave.errMsg,
168			"NPrT error: Attempting a Box scaling of more than 1 percent.\n"
169			" Check your tauBarostat, as it is probably too small!\n\n"
170			" scaleMat = [%lf\t%lf\t%lf]\n"
171			" [%lf\t%lf\t%lf]\n"
172			" [%lf\t%lf\t%lf]\n"
173			" eta = [%lf\t%lf\t%lf]\n"
174			" [%lf\t%lf\t%lf]\n"
175			" [%lf\t%lf\t%lf]\n",
176			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
177			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
178			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
179			eta(0, 0),eta(0, 1),eta(0, 2),
180			eta(1, 0),eta(1, 1),eta(1, 2),
181			eta(2, 0),eta(2, 1),eta(2, 2));
182			painCave.isFatal = 1;
183			simError();
184			} else if (offDiagMax > 0.01) {
185			sprintf( painCave.errMsg,
186			"NPrT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
187			" Check your tauBarostat, as it is probably too small!\n\n"
188			" scaleMat = [%lf\t%lf\t%lf]\n"
189			" [%lf\t%lf\t%lf]\n"
190			" [%lf\t%lf\t%lf]\n"
191			" eta = [%lf\t%lf\t%lf]\n"
192			" [%lf\t%lf\t%lf]\n"
193			" [%lf\t%lf\t%lf]\n",
194			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
195			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
196			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
197			eta(0, 0),eta(0, 1),eta(0, 2),
198			eta(1, 0),eta(1, 1),eta(1, 2),
199			eta(2, 0),eta(2, 1),eta(2, 2));
200			painCave.isFatal = 1;
201			simError();
202			} else {
203
204			Mat3x3d hmat = currentSnapshot_->getHmat();
205			hmat = hmat *scaleMat;
206			currentSnapshot_->setHmat(hmat);
207
208			}
209			}
210
211			bool NPrT::etaConverged() {
212			int i;
213			double diffEta, sumEta;
214
215			sumEta = 0;
216			for(i = 0; i < 3; i++) {
217			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
218			}
219
220			diffEta = sqrt( sumEta / 3.0 );
221
222			return ( diffEta <= etaTolerance );
223			}
224
225			double NPrT::calcConservedQuantity(){
226
227			chi= currentSnapshot_->getChi();
228			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
229			loadEta();
230
231			// We need NkBT a lot, so just set it here: This is the RAW number
232			// of integrableObjects, so no subtraction or addition of constraints or
233			// orientational degrees of freedom:
234			NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
235
236			// fkBT is used because the thermostat operates on more degrees of freedom
237			// than the barostat (when there are particles with orientational degrees
238			// of freedom).
239			fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
240
241
242	tim	2235	double totalEnergy = thermo.getTotalE();
243	tim	2233
244	tim	2235	double thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
245	tim	2233
246	tim	2235	double thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
247	tim	2233
248			SquareMatrix<double, 3> tmp = eta.transpose() * eta;
249	tim	2235	double trEta = tmp.trace();
250	tim	2233
251	tim	2235	double barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
252	tim	2233
253	tim	2235	double barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
254	tim	2233
255	tim	2235	Mat3x3d hmat = currentSnapshot_->getHmat();
256			double hz = hmat(2, 2);
257			double area = hmat(0,0) * hmat(1, 1);
258	tim	2233
259	tim	2235	double conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
260			barostat_kinetic + barostat_potential - surfaceTension * area;
261
262	tim	2233	return conservedQuantity;
263
264			}
265
266			void NPrT::loadEta() {
267			eta= currentSnapshot_->getEta();
268
269			//if (!eta.isDiagonal()) {
270			// sprintf( painCave.errMsg,
271			// "NPrT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
272			// painCave.isFatal = 1;
273			// simError();
274			//}
275			}
276
277			void NPrT::saveEta() {
278			currentSnapshot_->setEta(eta);
279			}
280
281			}
282
283