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) += thermostat.first;
        }
      }
    }
  }

  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 = snap->getHmat();
    hmat = hmat *scaleMat;
    snap->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(){

    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 conservedQuantity;
    RealType totalEnergy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    RealType barostat_kinetic;
    RealType barostat_potential;
    RealType trEta;

    totalEnergy = thermo.getTotalEnergy();

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

    thermostat_potential = fkBT* thermostat.second / 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= snap->getBarostat();

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

}

Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 9 months ago) by gezelter
File size:	5931 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	#include "utils/PhysicalConstants.hpp"
49	#include "utils/simError.h"
50
51	namespace OpenMD {
52
53	void NPAT::evolveEtaA() {
54
55	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
56	oldEta = eta;
57	}
58
59	void NPAT::evolveEtaB() {
60
61	prevEta = eta;
62	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
63	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
64	}
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) += thermostat.first;
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	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
91	sc = eta * rj;
92	}
93
94	void NPAT::scaleSimBox(){
95	Mat3x3d scaleMat;
96
97	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	}
104	}
105
106	scaleMat(2, 2) = exp(dt*eta(2, 2));
107	Mat3x3d hmat = snap->getHmat();
108	hmat = hmat *scaleMat;
109	snap->setHmat(hmat);
110	}
111
112	bool NPAT::etaConverged() {
113	int i;
114	RealType diffEta, sumEta;
115
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	RealType NPAT::calcConservedQuantity(){
127
128	thermostat = snap->getThermostat();
129	loadEta();
130
131	// We need NkBT a lot, so just set it here: This is the RAW number
132	// of integrableObjects, so no subtraction or addition of constraints or
133	// orientational degrees of freedom:
134	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
135
136	// fkBT is used because the thermostat operates on more degrees of freedom
137	// than the barostat (when there are particles with orientational degrees
138	// of freedom).
139	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
140
141	RealType conservedQuantity;
142	RealType totalEnergy;
143	RealType thermostat_kinetic;
144	RealType thermostat_potential;
145	RealType barostat_kinetic;
146	RealType barostat_potential;
147	RealType trEta;
148
149	totalEnergy = thermo.getTotalEnergy();
150
151	thermostat_kinetic = fkBT * tt2 * thermostat.first *
152	thermostat.first /(2.0 * PhysicalConstants::energyConvert);
153
154	thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
155
156	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
157	trEta = tmp.trace();
158
159	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
160
161	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
162
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= snap->getBarostat();
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	snap->setBarostat(eta);
183	}
184
185	}
186