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. 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, 234107 (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/NPrT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {
  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 = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    } else {
      surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
    }

  }
  void NPrT::evolveEtaA() {
    Mat3x3d hmat = snap->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) += dt2 *  instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
    oldEta = eta;  
  }

  void NPrT::evolveEtaB() {
    Mat3x3d hmat = snap->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) = oldEta(2, 2) + dt2 *  instaVol *
            (press(2, 2) - targetPressure/PhysicalConstants::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) += thermostat.first;
        }
      }
    }
  }

  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)/(RealType)2.0 -COM;
    sc = eta * rj;
  }

  void NPrT::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 = snap->getHmat();
    hmat = hmat *scaleMat;
    snap->setHmat(hmat);

  }

  bool NPrT::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 NPrT::calcConservedQuantity(){
    thermostat = snap->getThermostat();
    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.getTotalEnergy();

    RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /(2.0 * PhysicalConstants::energyConvert);

    RealType thermostat_potential = fkBT* thermostat.second / 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 = snap->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 NPrT::loadEta() {
    eta= snap->getBarostat();

    //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() {
    snap->setBarostat(eta);
  }

}


Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	7208 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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/NPrT.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	NPrT::NPrT(SimInfo* info) : NPT(info) {
53			Globals* simParams = info_->getSimParams();
54	tim	538	if (!simParams->haveSurfaceTension()) {
55	tim	536	sprintf(painCave.errMsg,
56			"If you use the NPT integrator, you must set tauBarostat.\n");
57	gezelter	1390	painCave.severity = OPENMD_ERROR;
58	tim	536	painCave.isFatal = 1;
59			simError();
60			} else {
61	gezelter	1390	surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
62	tim	536	}
63
64			}
65			void NPrT::evolveEtaA() {
66	gezelter	1764	Mat3x3d hmat = snap->getHmat();
67	tim	963	RealType hz = hmat(2, 2);
68			RealType Axy = hmat(0,0) * hmat(1, 1);
69	gezelter	1390	RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
70			RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
71	tim	540	eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2);
72			eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2);
73	gezelter	1390	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
74	tim	536	oldEta = eta;
75			}
76
77			void NPrT::evolveEtaB() {
78	gezelter	1764	Mat3x3d hmat = snap->getHmat();
79	tim	963	RealType hz = hmat(2, 2);
80			RealType Axy = hmat(0,0) * hmat(1, 1);
81	tim	536	prevEta = eta;
82	gezelter	1390	RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
83			RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
84	tim	540	eta(0,0) = oldEta(0, 0) - dt2 * Axy * (sx -surfaceTension) / (NkBT*tb2);
85			eta(1,1) = oldEta(1, 1) - dt2 * Axy * (sy -surfaceTension) / (NkBT*tb2);
86	tim	536	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
87	gezelter	1390	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
88	tim	536	}
89
90			void NPrT::calcVelScale(){
91
92			for (int i = 0; i < 3; i++ ) {
93			for (int j = 0; j < 3; j++ ) {
94			vScale(i, j) = eta(i, j);
95
96			if (i == j) {
97	gezelter	1764	vScale(i, j) += thermostat.first;
98	tim	536	}
99			}
100			}
101			}
102
103			void NPrT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
104			sc = vScale * vel;
105			}
106
107			void NPrT::getVelScaleB(Vector3d& sc, int index ) {
108			sc = vScale * oldVel[index];
109			}
110
111			void NPrT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
112
113			/*@todo /
114	tim	963	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
115	tim	536	sc = eta * rj;
116			}
117
118			void NPrT::scaleSimBox(){
119			Mat3x3d scaleMat;
120
121	tim	539	scaleMat(0, 0) = exp(dt*eta(0, 0));
122			scaleMat(1, 1) = exp(dt*eta(1, 1));
123			scaleMat(2, 2) = exp(dt*eta(2, 2));
124	gezelter	1764	Mat3x3d hmat = snap->getHmat();
125	tim	539	hmat = hmat *scaleMat;
126	gezelter	1764	snap->setHmat(hmat);
127	tim	536
128			}
129
130			bool NPrT::etaConverged() {
131			int i;
132	tim	963	RealType diffEta, sumEta;
133	tim	536
134			sumEta = 0;
135			for(i = 0; i < 3; i++) {
136			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
137			}
138
139			diffEta = sqrt( sumEta / 3.0 );
140
141			return ( diffEta <= etaTolerance );
142			}
143
144	tim	963	RealType NPrT::calcConservedQuantity(){
145	gezelter	1764	thermostat = snap->getThermostat();
146	tim	536	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	tim	536
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	tim	536
158
159	gezelter	1764	RealType totalEnergy = thermo.getTotalEnergy();
160	tim	536
161	gezelter	1764	RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /(2.0 * PhysicalConstants::energyConvert);
162	tim	536
163	gezelter	1764	RealType thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
164	tim	536
165	tim	963	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
166			RealType trEta = tmp.trace();
167	tim	536
168	gezelter	1390	RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
169	tim	536
170	gezelter	1390	RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
171	tim	536
172	gezelter	1764	Mat3x3d hmat = snap->getHmat();
173	tim	963	RealType hz = hmat(2, 2);
174			RealType area = hmat(0,0) * hmat(1, 1);
175	tim	536
176	tim	963	RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
177	gezelter	1390	barostat_kinetic + barostat_potential - surfaceTension * area/ PhysicalConstants::energyConvert;
178	tim	538
179	tim	536	return conservedQuantity;
180
181			}
182
183			void NPrT::loadEta() {
184	gezelter	1764	eta= snap->getBarostat();
185	tim	536
186			//if (!eta.isDiagonal()) {
187			// sprintf( painCave.errMsg,
188			// "NPrT 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 NPrT::saveEta() {
195	gezelter	1764	snap->setBarostat(eta);
196	tim	536	}
197
198			}
199
200