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. 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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "integrators/NPAT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {
  
  void NPAT::evolveEtaA() {

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

  void NPAT::evolveEtaB() {

    prevEta = eta;
    eta(2,2) = oldEta(2, 2) + dt2 *  instaVol *
            (press(2, 2) - targetPressure/PhysicalConstants::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)/(RealType)2.0 -COM;
    sc = eta * rj;
  }

  void NPAT::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 = currentSnapshot_->getHmat();
    hmat = hmat *scaleMat;
    currentSnapshot_->setHmat(hmat);
  }

  bool NPAT::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 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()*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.getTotalE();

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

    thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;

    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 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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/integrators/NPAT.cpp*
File size:	5909 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	tim	536	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	536	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	536	* 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	gezelter	1390	*
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, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	536	*/
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	gezelter	1390	#include "utils/PhysicalConstants.hpp"
48	tim	536	#include "utils/simError.h"
49
50	gezelter	1390	namespace OpenMD {
51	tim	536
52			void NPAT::evolveEtaA() {
53
54	gezelter	1390	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
55	tim	536	oldEta = eta;
56			}
57
58			void NPAT::evolveEtaB() {
59
60			prevEta = eta;
61			eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
62	gezelter	1390	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
63	tim	536	}
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	tim	963	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
90	tim	536	sc = eta * rj;
91			}
92
93			void NPAT::scaleSimBox(){
94			Mat3x3d scaleMat;
95
96	tim	538	for(int i=0; i<3; i++){
97			for(int j=0; j<3; j++){
98			scaleMat(i, j) = 0.0;
99			if(i==j) {
100			scaleMat(i, j) = 1.0;
101			}
102	tim	536	}
103			}
104	tim	538
105			scaleMat(2, 2) = exp(dt*eta(2, 2));
106			Mat3x3d hmat = currentSnapshot_->getHmat();
107			hmat = hmat *scaleMat;
108			currentSnapshot_->setHmat(hmat);
109	tim	536	}
110
111			bool NPAT::etaConverged() {
112			int i;
113	tim	963	RealType diffEta, sumEta;
114	tim	536
115			sumEta = 0;
116			for(i = 0; i < 3; i++) {
117			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
118			}
119
120			diffEta = sqrt( sumEta / 3.0 );
121
122			return ( diffEta <= etaTolerance );
123			}
124
125	tim	963	RealType NPAT::calcConservedQuantity(){
126	tim	536
127			chi= currentSnapshot_->getChi();
128			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
129			loadEta();
130
131			// We need NkBT a lot, so just set it here: This is the RAW number
132			// of integrableObjects, so no subtraction or addition of constraints or
133			// orientational degrees of freedom:
134	gezelter	1390	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
135	tim	536
136			// fkBT is used because the thermostat operates on more degrees of freedom
137			// than the barostat (when there are particles with orientational degrees
138			// of freedom).
139	gezelter	1390	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
140	tim	536
141	tim	963	RealType conservedQuantity;
142			RealType totalEnergy;
143			RealType thermostat_kinetic;
144			RealType thermostat_potential;
145			RealType barostat_kinetic;
146			RealType barostat_potential;
147			RealType trEta;
148	tim	536
149			totalEnergy = thermo.getTotalE();
150
151	gezelter	1390	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
152	tim	536
153	gezelter	1390	thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
154	tim	536
155	tim	963	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
156	tim	536	trEta = tmp.trace();
157
158	gezelter	1390	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
159	tim	536
160	gezelter	1390	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
161	tim	536
162			conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
163			barostat_kinetic + barostat_potential;
164
165			return conservedQuantity;
166
167			}
168
169			void NPAT::loadEta() {
170			eta= currentSnapshot_->getEta();
171
172			//if (!eta.isDiagonal()) {
173			// sprintf( painCave.errMsg,
174			// "NPAT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
175			// painCave.isFatal = 1;
176			// simError();
177			//}
178			}
179
180			void NPAT::saveEta() {
181			currentSnapshot_->setEta(eta);
182			}
183
184			}
185