src/integrators/NgammaT.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/NgammaT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {
  NgammaT::NgammaT(SimInfo* info) : NPT(info) {
    Globals* simParams = info_->getSimParams();
    if (!simParams->haveSurfaceTension()) {
      sprintf(painCave.errMsg,
              "If you use the NgammaT integrator, you must set a surface tension.\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    } else {
      surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
    }

  }
  void NgammaT::evolveEtaA() {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    RealType hz = hmat(2, 2);
    RealType Axy = hmat(0,0) * hmat(1, 1);
    RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
    RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
    eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2);
    eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2);
    eta(2,2) = 0.0;
    oldEta = eta;  
  }

  void NgammaT::evolveEtaB() {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    RealType hz = hmat(2, 2);
    RealType Axy = hmat(0,0) * hmat(1, 1);
    prevEta = eta;
    RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
    RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
    eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2);
    eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2);
    eta(2,2) = 0.0;
  }

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

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

  void NgammaT::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 NgammaT::scaleSimBox(){
    Mat3x3d scaleMat;

    scaleMat(0, 0) = exp(dt*eta(0, 0));
    scaleMat(1, 1) = exp(dt*eta(1, 1));    
    scaleMat(2, 2) = exp(dt*eta(2, 2));
    Mat3x3d hmat = currentSnapshot_->getHmat();
    hmat = hmat *scaleMat;
    currentSnapshot_->setHmat(hmat);

  }

  bool NgammaT::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 NgammaT::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 totalEnergy = thermo.getTotalE();

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

    RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;

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

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

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

    RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
      barostat_kinetic + barostat_potential - surfaceTension * area/ PhysicalConstants::energyConvert;

    return conservedQuantity;

  }

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

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

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

}


Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	7077 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	gezelter	1032	/*
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	gezelter	1032	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	1032	* 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	gezelter	1032	*/
41
42			#include "brains/SimInfo.hpp"
43			#include "brains/Thermo.hpp"
44			#include "integrators/IntegratorCreator.hpp"
45			#include "integrators/NgammaT.hpp"
46			#include "primitives/Molecule.hpp"
47	gezelter	1390	#include "utils/PhysicalConstants.hpp"
48	gezelter	1032	#include "utils/simError.h"
49
50	gezelter	1390	namespace OpenMD {
51	gezelter	1032	NgammaT::NgammaT(SimInfo* info) : NPT(info) {
52			Globals* simParams = info_->getSimParams();
53			if (!simParams->haveSurfaceTension()) {
54			sprintf(painCave.errMsg,
55			"If you use the NgammaT integrator, you must set a surface tension.\n");
56	gezelter	1390	painCave.severity = OPENMD_ERROR;
57	gezelter	1032	painCave.isFatal = 1;
58			simError();
59			} else {
60	gezelter	1390	surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
61	gezelter	1032	}
62
63			}
64			void NgammaT::evolveEtaA() {
65			Mat3x3d hmat = currentSnapshot_->getHmat();
66			RealType hz = hmat(2, 2);
67			RealType Axy = hmat(0,0) * hmat(1, 1);
68	gezelter	1390	RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
69			RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
70	gezelter	1032	eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2);
71			eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2);
72			eta(2,2) = 0.0;
73			oldEta = eta;
74			}
75
76			void NgammaT::evolveEtaB() {
77			Mat3x3d hmat = currentSnapshot_->getHmat();
78			RealType hz = hmat(2, 2);
79			RealType Axy = hmat(0,0) * hmat(1, 1);
80			prevEta = eta;
81	gezelter	1390	RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
82			RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
83	gezelter	1032	eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2);
84			eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2);
85			eta(2,2) = 0.0;
86			}
87
88			void NgammaT::calcVelScale(){
89
90			for (int i = 0; i < 3; i++ ) {
91			for (int j = 0; j < 3; j++ ) {
92			vScale(i, j) = eta(i, j);
93
94			if (i == j) {
95			vScale(i, j) += chi;
96			}
97			}
98			}
99			}
100
101			void NgammaT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
102			sc = vScale * vel;
103			}
104
105			void NgammaT::getVelScaleB(Vector3d& sc, int index ) {
106			sc = vScale * oldVel[index];
107			}
108
109			void NgammaT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
110
111			/*@todo /
112			Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
113			sc = eta * rj;
114			}
115
116			void NgammaT::scaleSimBox(){
117			Mat3x3d scaleMat;
118
119			scaleMat(0, 0) = exp(dt*eta(0, 0));
120			scaleMat(1, 1) = exp(dt*eta(1, 1));
121			scaleMat(2, 2) = exp(dt*eta(2, 2));
122			Mat3x3d hmat = currentSnapshot_->getHmat();
123			hmat = hmat *scaleMat;
124			currentSnapshot_->setHmat(hmat);
125
126			}
127
128			bool NgammaT::etaConverged() {
129			int i;
130			RealType diffEta, sumEta;
131
132			sumEta = 0;
133			for(i = 0; i < 3; i++) {
134			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
135			}
136
137			diffEta = sqrt( sumEta / 3.0 );
138
139			return ( diffEta <= etaTolerance );
140			}
141
142			RealType NgammaT::calcConservedQuantity(){
143
144			chi= currentSnapshot_->getChi();
145			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
146			loadEta();
147
148			// We need NkBT a lot, so just set it here: This is the RAW number
149			// of integrableObjects, so no subtraction or addition of constraints or
150			// orientational degrees of freedom:
151	gezelter	1390	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
152	gezelter	1032
153			// fkBT is used because the thermostat operates on more degrees of freedom
154			// than the barostat (when there are particles with orientational degrees
155			// of freedom).
156	gezelter	1390	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
157	gezelter	1032
158
159			RealType totalEnergy = thermo.getTotalE();
160
161	gezelter	1390	RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
162	gezelter	1032
163	gezelter	1390	RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
164	gezelter	1032
165			SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
166			RealType trEta = tmp.trace();
167
168	gezelter	1390	RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
169	gezelter	1032
170	gezelter	1390	RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
171	gezelter	1032
172			Mat3x3d hmat = currentSnapshot_->getHmat();
173			RealType hz = hmat(2, 2);
174			RealType area = hmat(0,0) * hmat(1, 1);
175
176			RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
177	gezelter	1390	barostat_kinetic + barostat_potential - surfaceTension * area/ PhysicalConstants::energyConvert;
178	gezelter	1032
179			return conservedQuantity;
180
181			}
182
183			void NgammaT::loadEta() {
184			eta= currentSnapshot_->getEta();
185
186			//if (!eta.isDiagonal()) {
187			// sprintf( painCave.errMsg,
188			// "NgammaT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
189			// painCave.isFatal = 1;
190			// simError();
191			//}
192			}
193
194			void NgammaT::saveEta() {
195			currentSnapshot_->setEta(eta);
196			}
197
198			}
199
200