src/integrators/NPTxyz.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/NPTxyz.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

// Basic non-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.

namespace oopse {

    
double NPTxyz::calcConservedQuantity(){

    // 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 totalEnergy;
    double thermostat_kinetic;
    double thermostat_potential;
    double barostat_kinetic;
    double barostat_potential;
    double trEta;

    totalEnergy = thermo.getTotalE();

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

    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;

    SquareMatrix<double, 3> tmp = eta.transpose() * eta;
    trEta = tmp.trace();

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

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

    conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
        barostat_kinetic + barostat_potential;


    return conservedQuantity;

}

    
void NPTxyz::scaleSimBox(){

    int i,j,k;
    Mat3x3d scaleMat;
    double eta2ij, scaleFactor;
    double bigScale, smallScale, offDiagMax;
    Mat3x3d hm;
    Mat3x3d hmnew;


  // Scale the box after all the positions have been moved:

  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)

    bigScale = 1.0;
    smallScale = 1.0;
    offDiagMax = 0.0;

    for(i=0; i<3; i++){
        for(j=0; j<3; j++){
            scaleMat(i, j) = 0.0;
            if(i==j) {
                scaleMat(i, j) = 1.0;
            }
        }
    }

    for(i=0;i<3;i++){

    // calculate the scaleFactors

        scaleFactor = exp(dt*eta(i, i));

        scaleMat(i, i) = scaleFactor;

        if (scaleMat(i, i) > bigScale) {
            bigScale = scaleMat(i, i);
        }
        
        if (scaleMat(i, i) < smallScale) {
            smallScale = scaleMat(i, i);
        }
    }

    if ((bigScale > 1.1) || (smallScale < 0.9)) {
        sprintf( painCave.errMsg,
            "NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
            " Check your tauBarostat, as it is probably too small!\n\n"
            " scaleMat = [%lf\t%lf\t%lf]\n"
            "            [%lf\t%lf\t%lf]\n"
            "            [%lf\t%lf\t%lf]\n",
        scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
        scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
        scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2));
        painCave.isFatal = 1;
        simError();
    } else {

        Mat3x3d hmat = currentSnapshot_->getHmat();
        hmat = hmat *scaleMat;
        currentSnapshot_->setHmat(hmat);
    }
}

void NPTxyz::loadEta() {
    eta= currentSnapshot_->getEta();
}

}
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	5817 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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/NPTxyz.hpp"
46	#include "primitives/Molecule.hpp"
47	#include "utils/OOPSEConstant.hpp"
48	#include "utils/simError.h"
49
50	// Basic non-isotropic thermostating and barostating via the Melchionna
51	// modification of the Hoover algorithm:
52	//
53	// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
54	// Molec. Phys., 78, 533.
55	//
56	// and
57	//
58	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
59
60	namespace oopse {
61
62
63	double NPTxyz::calcConservedQuantity(){
64
65	// We need NkBT a lot, so just set it here: This is the RAW number
66	// of integrableObjects, so no subtraction or addition of constraints or
67	// orientational degrees of freedom:
68	NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
69
70	// fkBT is used because the thermostat operates on more degrees of freedom
71	// than the barostat (when there are particles with orientational degrees
72	// of freedom).
73	fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
74
75	double conservedQuantity;
76	double totalEnergy;
77	double thermostat_kinetic;
78	double thermostat_potential;
79	double barostat_kinetic;
80	double barostat_potential;
81	double trEta;
82
83	totalEnergy = thermo.getTotalE();
84
85	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
86
87	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
88
89	SquareMatrix<double, 3> tmp = eta.transpose() * eta;
90	trEta = tmp.trace();
91
92	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
93
94	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
95
96	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
97	barostat_kinetic + barostat_potential;
98
99
100	return conservedQuantity;
101
102	}
103
104
105	void NPTxyz::scaleSimBox(){
106
107	int i,j,k;
108	Mat3x3d scaleMat;
109	double eta2ij, scaleFactor;
110	double bigScale, smallScale, offDiagMax;
111	Mat3x3d hm;
112	Mat3x3d hmnew;
113
114
115
116	// Scale the box after all the positions have been moved:
117
118	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
119	// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
120
121	bigScale = 1.0;
122	smallScale = 1.0;
123	offDiagMax = 0.0;
124
125	for(i=0; i<3; i++){
126	for(j=0; j<3; j++){
127	scaleMat(i, j) = 0.0;
128	if(i==j) {
129	scaleMat(i, j) = 1.0;
130	}
131	}
132	}
133
134	for(i=0;i<3;i++){
135
136	// calculate the scaleFactors
137
138	scaleFactor = exp(dt*eta(i, i));
139
140	scaleMat(i, i) = scaleFactor;
141
142	if (scaleMat(i, i) > bigScale) {
143	bigScale = scaleMat(i, i);
144	}
145
146	if (scaleMat(i, i) < smallScale) {
147	smallScale = scaleMat(i, i);
148	}
149	}
150
151	if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
152	sprintf( painCave.errMsg,
153	"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
154	" Check your tauBarostat, as it is probably too small!\n\n"
155	" scaleMat = [%lf\t%lf\t%lf]\n"
156	" [%lf\t%lf\t%lf]\n"
157	" [%lf\t%lf\t%lf]\n",
158	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
159	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
160	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2));
161	painCave.isFatal = 1;
162	simError();
163	} else {
164
165	Mat3x3d hmat = currentSnapshot_->getHmat();
166	hmat = hmat *scaleMat;
167	currentSnapshot_->setHmat(hmat);
168	}
169	}
170
171	void NPTxyz::loadEta() {
172	eta= currentSnapshot_->getEta();
173	}
174
175	}