src/integrators/NPTi.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 "NPTi.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/NPT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {

// Basic isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533.
//
//           and
//
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

NPTi::NPTi ( SimInfo *info) : NPT(info){

}

void NPTi::evolveEtaA() {
    eta += dt2 * ( instaVol * (instaPress - targetPressure) /
         (OOPSEConstant::pressureConvert*NkBT*tb2));
    oldEta = eta;
}

void NPTi::evolveEtaB() {

    prevEta = eta;
    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
         (OOPSEConstant::pressureConvert*NkBT*tb2));
}

void NPTi::calcVelScale() {
    vScale = chi + eta;
}

void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
    sc = vel * vScale;
}

void NPTi::getVelScaleB(Vector3d& sc, int index ){
    sc = oldVel[index] * vScale;    
}


void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
                           int index, Vector3d& sc){
    /**@todo*/
    sc  = (oldPos[index] + pos)/2.0 -COM;
    sc *= eta;
}

void NPTi::scaleSimBox(){

    double scaleFactor;

    scaleFactor = exp(dt*eta);

    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
        sprintf( painCave.errMsg,
             "NPTi error: Attempting a Box scaling of more than 10 percent"
             " check your tauBarostat, as it is probably too small!\n"
             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
             );
        painCave.isFatal = 1;
        simError();
    } else {
        Mat3x3d hmat = currentSnapshot_->getHmat();
        hmat *= scaleFactor;
        currentSnapshot_->setHmat(hmat);
    }

}

bool NPTi::etaConverged() {

    return ( fabs(prevEta - eta) <= etaTolerance );
}

double NPTi::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;    
    
    double conservedQuantity;
    double Energy;
    double thermostat_kinetic;
    double thermostat_potential;
    double barostat_kinetic;
    double barostat_potential;

    Energy =thermo.getTotalE();

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

    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;


    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);

    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
        OOPSEConstant::energyConvert;

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
        barostat_kinetic + barostat_potential;
    
    return conservedQuantity;
}

void NPTi::loadEta() {
    Mat3x3d etaMat = currentSnapshot_->getEta();
    eta = etaMat(0,0);
    //if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) {
    //    sprintf( painCave.errMsg,
    //             "NPTi error: the diagonal elements of  eta matrix are not the same or etaMat is not a diagonal matrix");
    //    painCave.isFatal = 1;
    //    simError();
    //}
}

void NPTi::saveEta() {
    Mat3x3d etaMat(0.0);
    etaMat(0, 0) = eta;
    etaMat(1, 1) = eta;
    etaMat(2, 2) = eta;
    currentSnapshot_->setEta(etaMat);
}

}
Revision:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
File size:	6114 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	246	/*
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 "NPTi.hpp"
43	tim	3	#include "brains/SimInfo.hpp"
44			#include "brains/Thermo.hpp"
45	gezelter	246	#include "integrators/NPT.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/OOPSEConstant.hpp"
48	tim	3	#include "utils/simError.h"
49	gezelter	2
50	gezelter	246	namespace oopse {
51	gezelter	2
52			// Basic isotropic thermostating and barostating via the Melchionna
53			// modification of the Hoover algorithm:
54			//
55			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
56			// Molec. Phys., 78, 533.
57			//
58			// and
59			//
60			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
61
62	gezelter	246	NPTi::NPTi ( SimInfo *info) : NPT(info){
63	gezelter	2
64			}
65
66	gezelter	246	void NPTi::evolveEtaA() {
67			eta += dt2 * ( instaVol * (instaPress - targetPressure) /
68			(OOPSEConstant::pressureConvertNkBTtb2));
69			oldEta = eta;
70	gezelter	2	}
71
72	gezelter	246	void NPTi::evolveEtaB() {
73	gezelter	2
74	gezelter	246	prevEta = eta;
75			eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
76			(OOPSEConstant::pressureConvertNkBTtb2));
77	gezelter	2	}
78
79	gezelter	246	void NPTi::calcVelScale() {
80			vScale = chi + eta;
81	gezelter	2	}
82
83	gezelter	246	void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
84			sc = vel * vScale;
85	gezelter	2	}
86
87	gezelter	246	void NPTi::getVelScaleB(Vector3d& sc, int index ){
88			sc = oldVel[index] * vScale;
89	gezelter	2	}
90
91
92	gezelter	246	void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
93			int index, Vector3d& sc){
94			/*@todo/
95			sc = (oldPos[index] + pos)/2.0 -COM;
96			sc *= eta;
97	gezelter	2	}
98
99	gezelter	246	void NPTi::scaleSimBox(){
100	gezelter	2
101	gezelter	246	double scaleFactor;
102	gezelter	2
103	gezelter	246	scaleFactor = exp(dt*eta);
104	gezelter	2
105	gezelter	246	if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
106			sprintf( painCave.errMsg,
107	gezelter	2	"NPTi error: Attempting a Box scaling of more than 10 percent"
108			" check your tauBarostat, as it is probably too small!\n"
109			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
110			);
111	gezelter	246	painCave.isFatal = 1;
112			simError();
113			} else {
114			Mat3x3d hmat = currentSnapshot_->getHmat();
115			hmat *= scaleFactor;
116			currentSnapshot_->setHmat(hmat);
117			}
118	gezelter	2
119			}
120
121	gezelter	246	bool NPTi::etaConverged() {
122	gezelter	2
123	gezelter	246	return ( fabs(prevEta - eta) <= etaTolerance );
124	gezelter	2	}
125
126	gezelter	246	double NPTi::calcConservedQuantity(){
127	gezelter	2
128	gezelter	246	chi= currentSnapshot_->getChi();
129			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
130			loadEta();
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()OOPSEConstant::kB targetTemp;
135	gezelter	2
136	gezelter	246	// 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()OOPSEConstant::kB targetTemp;
140
141			double conservedQuantity;
142			double Energy;
143			double thermostat_kinetic;
144			double thermostat_potential;
145			double barostat_kinetic;
146			double barostat_potential;
147	gezelter	2
148	gezelter	246	Energy =thermo.getTotalE();
149	gezelter	2
150	gezelter	246	thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
151	gezelter	2
152	gezelter	246	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
153	gezelter	2
154
155	gezelter	246	barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
156	gezelter	2
157	gezelter	246	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
158			OOPSEConstant::energyConvert;
159	gezelter	2
160	gezelter	246	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
161			barostat_kinetic + barostat_potential;
162
163			return conservedQuantity;
164			}
165	gezelter	2
166	gezelter	246	void NPTi::loadEta() {
167			Mat3x3d etaMat = currentSnapshot_->getEta();
168			eta = etaMat(0,0);
169			//if (fabs(etaMat(1,1) - eta) >= oopse::epsilon \|\| fabs(etaMat(1,1) - eta) >= oopse::epsilon \|\| !etaMat.isDiagonal()) {
170			// sprintf( painCave.errMsg,
171			// "NPTi error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
172			// painCave.isFatal = 1;
173			// simError();
174			//}
175	gezelter	2	}
176
177	gezelter	246	void NPTi::saveEta() {
178			Mat3x3d etaMat(0.0);
179			etaMat(0, 0) = eta;
180			etaMat(1, 1) = eta;
181			etaMat(2, 2) = eta;
182			currentSnapshot_->setEta(etaMat);
183			}
184	gezelter	2
185			}