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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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) += chi;
        }
      }
    }
  }

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

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

    totalEnergy = thermo.getTotalE();

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

    thermostat_potential = fkBT* integralOfChidt / 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= currentSnapshot_->getEta();

    //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() {
    currentSnapshot_->setEta(eta);
  }

}

Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	5909 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "brains/SimInfo.hpp"
43	#include "brains/Thermo.hpp"
44	#include "integrators/IntegratorCreator.hpp"
45	#include "integrators/NPAT.hpp"
46	#include "primitives/Molecule.hpp"
47	#include "utils/PhysicalConstants.hpp"
48	#include "utils/simError.h"
49
50	namespace OpenMD {
51
52	void NPAT::evolveEtaA() {
53
54	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
55	oldEta = eta;
56	}
57
58	void NPAT::evolveEtaB() {
59
60	prevEta = eta;
61	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
62	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
63	}
64
65	void NPAT::calcVelScale(){
66
67	for (int i = 0; i < 3; i++ ) {
68	for (int j = 0; j < 3; j++ ) {
69	vScale(i, j) = eta(i, j);
70
71	if (i == j) {
72	vScale(i, j) += chi;
73	}
74	}
75	}
76	}
77
78	void NPAT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
79	sc = vScale * vel;
80	}
81
82	void NPAT::getVelScaleB(Vector3d& sc, int index ) {
83	sc = vScale * oldVel[index];
84	}
85
86	void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
87
88	/*@todo /
89	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
90	sc = eta * rj;
91	}
92
93	void NPAT::scaleSimBox(){
94	Mat3x3d scaleMat;
95
96	for(int i=0; i<3; i++){
97	for(int j=0; j<3; j++){
98	scaleMat(i, j) = 0.0;
99	if(i==j) {
100	scaleMat(i, j) = 1.0;
101	}
102	}
103	}
104
105	scaleMat(2, 2) = exp(dt*eta(2, 2));
106	Mat3x3d hmat = currentSnapshot_->getHmat();
107	hmat = hmat *scaleMat;
108	currentSnapshot_->setHmat(hmat);
109	}
110
111	bool NPAT::etaConverged() {
112	int i;
113	RealType diffEta, sumEta;
114
115	sumEta = 0;
116	for(i = 0; i < 3; i++) {
117	sumEta += pow(prevEta(i, i) - eta(i, i), 2);
118	}
119
120	diffEta = sqrt( sumEta / 3.0 );
121
122	return ( diffEta <= etaTolerance );
123	}
124
125	RealType NPAT::calcConservedQuantity(){
126
127	chi= currentSnapshot_->getChi();
128	integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
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.getTotalE();
150
151	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
152
153	thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
154
155	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
156	trEta = tmp.trace();
157
158	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
159
160	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
161
162	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
163	barostat_kinetic + barostat_potential;
164
165	return conservedQuantity;
166
167	}
168
169	void NPAT::loadEta() {
170	eta= currentSnapshot_->getEta();
171
172	//if (!eta.isDiagonal()) {
173	// sprintf( painCave.errMsg,
174	// "NPAT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
175	// painCave.isFatal = 1;
176	// simError();
177	//}
178	}
179
180	void NPAT::saveEta() {
181	currentSnapshot_->setEta(eta);
182	}
183
184	}
185