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]  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/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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5975 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	536	*/
42
43			#include "brains/SimInfo.hpp"
44			#include "brains/Thermo.hpp"
45			#include "integrators/IntegratorCreator.hpp"
46			#include "integrators/NPAT.hpp"
47			#include "primitives/Molecule.hpp"
48	gezelter	1390	#include "utils/PhysicalConstants.hpp"
49	tim	536	#include "utils/simError.h"
50
51	gezelter	1390	namespace OpenMD {
52	tim	536
53			void NPAT::evolveEtaA() {
54
55	gezelter	1390	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
56	tim	536	oldEta = eta;
57			}
58
59			void NPAT::evolveEtaB() {
60
61			prevEta = eta;
62			eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
63	gezelter	1390	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
64	tim	536	}
65
66			void NPAT::calcVelScale(){
67
68			for (int i = 0; i < 3; i++ ) {
69			for (int j = 0; j < 3; j++ ) {
70			vScale(i, j) = eta(i, j);
71
72			if (i == j) {
73			vScale(i, j) += chi;
74			}
75			}
76			}
77			}
78
79			void NPAT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
80			sc = vScale * vel;
81			}
82
83			void NPAT::getVelScaleB(Vector3d& sc, int index ) {
84			sc = vScale * oldVel[index];
85			}
86
87			void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
88
89			/*@todo /
90	tim	963	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
91	tim	536	sc = eta * rj;
92			}
93
94			void NPAT::scaleSimBox(){
95			Mat3x3d scaleMat;
96
97	tim	538	for(int i=0; i<3; i++){
98			for(int j=0; j<3; j++){
99			scaleMat(i, j) = 0.0;
100			if(i==j) {
101			scaleMat(i, j) = 1.0;
102			}
103	tim	536	}
104			}
105	tim	538
106			scaleMat(2, 2) = exp(dt*eta(2, 2));
107			Mat3x3d hmat = currentSnapshot_->getHmat();
108			hmat = hmat *scaleMat;
109			currentSnapshot_->setHmat(hmat);
110	tim	536	}
111
112			bool NPAT::etaConverged() {
113			int i;
114	tim	963	RealType diffEta, sumEta;
115	tim	536
116			sumEta = 0;
117			for(i = 0; i < 3; i++) {
118			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
119			}
120
121			diffEta = sqrt( sumEta / 3.0 );
122
123			return ( diffEta <= etaTolerance );
124			}
125
126	tim	963	RealType NPAT::calcConservedQuantity(){
127	tim	536
128			chi= currentSnapshot_->getChi();
129			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
130			loadEta();
131
132			// We need NkBT a lot, so just set it here: This is the RAW number
133			// of integrableObjects, so no subtraction or addition of constraints or
134			// orientational degrees of freedom:
135	gezelter	1390	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
136	tim	536
137			// fkBT is used because the thermostat operates on more degrees of freedom
138			// than the barostat (when there are particles with orientational degrees
139			// of freedom).
140	gezelter	1390	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
141	tim	536
142	tim	963	RealType conservedQuantity;
143			RealType totalEnergy;
144			RealType thermostat_kinetic;
145			RealType thermostat_potential;
146			RealType barostat_kinetic;
147			RealType barostat_potential;
148			RealType trEta;
149	tim	536
150			totalEnergy = thermo.getTotalE();
151
152	gezelter	1390	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
153	tim	536
154	gezelter	1390	thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
155	tim	536
156	tim	963	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
157	tim	536	trEta = tmp.trace();
158
159	gezelter	1390	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
160	tim	536
161	gezelter	1390	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
162	tim	536
163			conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
164			barostat_kinetic + barostat_potential;
165
166			return conservedQuantity;
167
168			}
169
170			void NPAT::loadEta() {
171			eta= currentSnapshot_->getEta();
172
173			//if (!eta.isDiagonal()) {
174			// sprintf( painCave.errMsg,
175			// "NPAT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
176			// painCave.isFatal = 1;
177			// simError();
178			//}
179			}
180
181			void NPAT::saveEta() {
182			currentSnapshot_->setEta(eta);
183			}
184
185			}
186