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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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 = 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) += dt2 *  instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
    oldEta = eta;  
  }

  void NPrT::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) = 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) += 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)/(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 = currentSnapshot_->getHmat();
    hmat = hmat *scaleMat;
    currentSnapshot_->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(){

    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 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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	7229 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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/NPrT.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	NPrT::NPrT(SimInfo* info) : NPT(info) {
52			Globals* simParams = info_->getSimParams();
53	tim	538	if (!simParams->haveSurfaceTension()) {
54	tim	536	sprintf(painCave.errMsg,
55			"If you use the NPT integrator, you must set tauBarostat.\n");
56	gezelter	1390	painCave.severity = OPENMD_ERROR;
57	tim	536	painCave.isFatal = 1;
58			simError();
59			} else {
60	gezelter	1390	surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
61	tim	536	}
62
63			}
64			void NPrT::evolveEtaA() {
65	tim	537	Mat3x3d hmat = currentSnapshot_->getHmat();
66	tim	963	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	tim	540	eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2);
71			eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2);
72	gezelter	1390	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
73	tim	536	oldEta = eta;
74			}
75
76			void NPrT::evolveEtaB() {
77	tim	537	Mat3x3d hmat = currentSnapshot_->getHmat();
78	tim	963	RealType hz = hmat(2, 2);
79			RealType Axy = hmat(0,0) * hmat(1, 1);
80	tim	536	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	tim	540	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	tim	536	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
86	gezelter	1390	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
87	tim	536	}
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	tim	963	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
114	tim	536	sc = eta * rj;
115			}
116
117			void NPrT::scaleSimBox(){
118			Mat3x3d scaleMat;
119
120	tim	539	scaleMat(0, 0) = exp(dt*eta(0, 0));
121			scaleMat(1, 1) = exp(dt*eta(1, 1));
122			scaleMat(2, 2) = exp(dt*eta(2, 2));
123			Mat3x3d hmat = currentSnapshot_->getHmat();
124			hmat = hmat *scaleMat;
125			currentSnapshot_->setHmat(hmat);
126	tim	536
127			}
128
129			bool NPrT::etaConverged() {
130			int i;
131	tim	963	RealType diffEta, sumEta;
132	tim	536
133			sumEta = 0;
134			for(i = 0; i < 3; i++) {
135			sumEta += pow(prevEta(i, i) - eta(i, i), 2);
136			}
137
138			diffEta = sqrt( sumEta / 3.0 );
139
140			return ( diffEta <= etaTolerance );
141			}
142
143	tim	963	RealType NPrT::calcConservedQuantity(){
144	tim	536
145			chi= currentSnapshot_->getChi();
146			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
147			loadEta();
148
149			// We need NkBT a lot, so just set it here: This is the RAW number
150			// of integrableObjects, so no subtraction or addition of constraints or
151			// orientational degrees of freedom:
152	gezelter	1390	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
153	tim	536
154			// fkBT is used because the thermostat operates on more degrees of freedom
155			// than the barostat (when there are particles with orientational degrees
156			// of freedom).
157	gezelter	1390	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
158	tim	536
159
160	tim	963	RealType totalEnergy = thermo.getTotalE();
161	tim	536
162	gezelter	1390	RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
163	tim	536
164	gezelter	1390	RealType thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
165	tim	536
166	tim	963	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
167			RealType trEta = tmp.trace();
168	tim	536
169	gezelter	1390	RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
170	tim	536
171	gezelter	1390	RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
172	tim	536
173	tim	538	Mat3x3d hmat = currentSnapshot_->getHmat();
174	tim	963	RealType hz = hmat(2, 2);
175			RealType area = hmat(0,0) * hmat(1, 1);
176	tim	536
177	tim	963	RealType conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
178	gezelter	1390	barostat_kinetic + barostat_potential - surfaceTension * area/ PhysicalConstants::energyConvert;
179	tim	538
180	tim	536	return conservedQuantity;
181
182			}
183
184			void NPrT::loadEta() {
185			eta= currentSnapshot_->getEta();
186
187			//if (!eta.isDiagonal()) {
188			// sprintf( painCave.errMsg,
189			// "NPrT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
190			// painCave.isFatal = 1;
191			// simError();
192			//}
193			}
194
195			void NPrT::saveEta() {
196			currentSnapshot_->setEta(eta);
197			}
198
199			}
200
201