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]  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:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 9 months ago) by gezelter
File size:	7207 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/NPrT.hpp"
47	#include "primitives/Molecule.hpp"
48	#include "utils/PhysicalConstants.hpp"
49	#include "utils/simError.h"
50
51	namespace OpenMD {
52	NPrT::NPrT(SimInfo* info) : NPT(info) {
53	Globals* simParams = info_->getSimParams();
54	if (!simParams->haveSurfaceTension()) {
55	sprintf(painCave.errMsg,
56	"If you use the NPT integrator, you must set tauBarostat.\n");
57	painCave.severity = OPENMD_ERROR;
58	painCave.isFatal = 1;
59	simError();
60	} else {
61	surfaceTension= simParams->getSurfaceTension()* PhysicalConstants::surfaceTensionConvert * PhysicalConstants::energyConvert;
62	}
63
64	}
65	void NPrT::evolveEtaA() {
66	Mat3x3d hmat = snap->getHmat();
67	RealType hz = hmat(2, 2);
68	RealType Axy = hmat(0,0) * hmat(1, 1);
69	RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
70	RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
71	eta(0,0) -= dt2* Axy * (sx - surfaceTension) / (NkBT*tb2);
72	eta(1,1) -= dt2* Axy * (sy - surfaceTension) / (NkBT*tb2);
73	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
74	oldEta = eta;
75	}
76
77	void NPrT::evolveEtaB() {
78	Mat3x3d hmat = snap->getHmat();
79	RealType hz = hmat(2, 2);
80	RealType Axy = hmat(0,0) * hmat(1, 1);
81	prevEta = eta;
82	RealType sx = -hz * (press(0, 0) - targetPressure/PhysicalConstants::pressureConvert);
83	RealType sy = -hz * (press(1, 1) - targetPressure/PhysicalConstants::pressureConvert);
84	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	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
87	(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
88	}
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	vScale(i, j) += thermostat.first;
98	}
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	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
115	sc = eta * rj;
116	}
117
118	void NPrT::scaleSimBox(){
119	Mat3x3d scaleMat;
120
121	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	Mat3x3d hmat = snap->getHmat();
125	hmat = hmat *scaleMat;
126	snap->setHmat(hmat);
127
128	}
129
130	bool NPrT::etaConverged() {
131	int i;
132	RealType diffEta, sumEta;
133
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	RealType NPrT::calcConservedQuantity(){
145	thermostat = snap->getThermostat();
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()PhysicalConstants::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()PhysicalConstants::kB targetTemp;
157
158
159	RealType totalEnergy = thermo.getTotalEnergy();
160
161	RealType thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /(2.0 * PhysicalConstants::energyConvert);
162
163	RealType thermostat_potential = fkBT* thermostat.second / PhysicalConstants::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 * PhysicalConstants::energyConvert);
169
170	RealType barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
171
172	Mat3x3d hmat = snap->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/ PhysicalConstants::energyConvert;
178
179	return conservedQuantity;
180
181	}
182
183	void NPrT::loadEta() {
184	eta= snap->getBarostat();
185
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	snap->setBarostat(eta);
196	}
197
198	}
199
200