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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "integrators/NgammaT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {
  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 = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    } else {
      surfaceTension= simParams->getSurfaceTension()* OOPSEConstant::surfaceTensionConvert * OOPSEConstant::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/OOPSEConstant::pressureConvert);
    RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::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/OOPSEConstant::pressureConvert);
    RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::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()*OOPSEConstant::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()*OOPSEConstant::kB *targetTemp;    
    

    RealType totalEnergy = thermo.getTotalE();

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

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

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

    RealType barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::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/ OOPSEConstant::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:	3516
Committed:	Wed Jul 22 15:00:21 2009 UTC (15 years, 9 months ago) by gezelter
File size:	6974 byte(s)
Log Message:	units for thermalConductivity, spelling error fixed
#	Content
1	/*
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	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
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	#include "utils/OOPSEConstant.hpp"
48	#include "utils/simError.h"
49
50	namespace oopse {
51	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	painCave.severity = OOPSE_ERROR;
57	painCave.isFatal = 1;
58	simError();
59	} else {
60	surfaceTension= simParams->getSurfaceTension()* OOPSEConstant::surfaceTensionConvert * OOPSEConstant::energyConvert;
61	}
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	RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
69	RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
70	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	RealType sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
82	RealType sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
83	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	NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
152
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	fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
157
158
159	RealType totalEnergy = thermo.getTotalE();
160
161	RealType thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
162
163	RealType thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
164
165	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
166	RealType trEta = tmp.trace();
167
168	RealType barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
169
170	RealType barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
171
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	barostat_kinetic + barostat_potential - surfaceTension * area/ OOPSEConstant::energyConvert;
178
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