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. 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/NPTxyz.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.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 OpenMD {

    
  RealType NPTxyz::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 NPTxyz::scaleSimBox(){

    int i,j,k;
    Mat3x3d scaleMat;
    RealType eta2ij, scaleFactor;
    RealType 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 = snap->getHmat();
      hmat = hmat *scaleMat;
      snap->setHmat(hmat);
    }
  }

  void NPTxyz::loadEta() {
    eta= snap->getBarostat();
  }

}
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	5952 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	tim	3	#include "brains/SimInfo.hpp"
44			#include "brains/Thermo.hpp"
45	gezelter	246	#include "integrators/IntegratorCreator.hpp"
46			#include "integrators/NPTxyz.hpp"
47			#include "primitives/Molecule.hpp"
48	gezelter	1390	#include "utils/PhysicalConstants.hpp"
49	tim	3	#include "utils/simError.h"
50	gezelter	2
51			// Basic non-isotropic thermostating and barostating via the Melchionna
52			// modification of the Hoover algorithm:
53			//
54			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
55			// Molec. Phys., 78, 533.
56			//
57			// and
58			//
59			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
60
61	gezelter	1390	namespace OpenMD {
62	gezelter	2
63	gezelter	246
64	tim	963	RealType NPTxyz::calcConservedQuantity(){
65	gezelter	1764	thermostat = snap->getThermostat();
66	gezelter	1629	loadEta();
67
68	gezelter	246	// We need NkBT a lot, so just set it here: This is the RAW number
69			// of integrableObjects, so no subtraction or addition of constraints or
70			// orientational degrees of freedom:
71	gezelter	1390	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
72	gezelter	2
73	gezelter	246	// fkBT is used because the thermostat operates on more degrees of freedom
74			// than the barostat (when there are particles with orientational degrees
75			// of freedom).
76	gezelter	1390	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
77	gezelter	2
78	tim	963	RealType conservedQuantity;
79			RealType totalEnergy;
80			RealType thermostat_kinetic;
81			RealType thermostat_potential;
82			RealType barostat_kinetic;
83			RealType barostat_potential;
84			RealType trEta;
85	gezelter	2
86	gezelter	1764	totalEnergy = thermo.getTotalEnergy();
87	gezelter	2
88	gezelter	1764	thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first
89			/ (2.0 * PhysicalConstants::energyConvert);
90	gezelter	2
91	gezelter	1764	thermostat_potential = fkBT* thermostat.second
92			/ PhysicalConstants::energyConvert;
93	gezelter	2
94	tim	963	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
95	gezelter	246	trEta = tmp.trace();
96	gezelter	2
97	gezelter	1390	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
98	gezelter	2
99	gezelter	1390	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
100	gezelter	2
101	gezelter	246	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
102	gezelter	507	barostat_kinetic + barostat_potential;
103	gezelter	2
104
105	gezelter	246	return conservedQuantity;
106	gezelter	2
107	gezelter	507	}
108	gezelter	2
109	gezelter	246
110	gezelter	507	void NPTxyz::scaleSimBox(){
111	gezelter	2
112	gezelter	246	int i,j,k;
113			Mat3x3d scaleMat;
114	tim	963	RealType eta2ij, scaleFactor;
115			RealType bigScale, smallScale, offDiagMax;
116	gezelter	246	Mat3x3d hm;
117			Mat3x3d hmnew;
118	gezelter	2
119
120
121	gezelter	507	// Scale the box after all the positions have been moved:
122	gezelter	2
123	gezelter	507	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
124			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
125	gezelter	2
126	gezelter	246	bigScale = 1.0;
127			smallScale = 1.0;
128			offDiagMax = 0.0;
129	gezelter	2
130	gezelter	246	for(i=0; i<3; i++){
131	gezelter	507	for(j=0; j<3; j++){
132			scaleMat(i, j) = 0.0;
133			if(i==j) {
134			scaleMat(i, j) = 1.0;
135			}
136			}
137	gezelter	2	}
138
139	gezelter	246	for(i=0;i<3;i++){
140	gezelter	2
141	gezelter	507	// calculate the scaleFactors
142	gezelter	2
143	gezelter	507	scaleFactor = exp(dt*eta(i, i));
144	gezelter	2
145	gezelter	507	scaleMat(i, i) = scaleFactor;
146	gezelter	2
147	gezelter	507	if (scaleMat(i, i) > bigScale) {
148			bigScale = scaleMat(i, i);
149			}
150	gezelter	246
151	gezelter	507	if (scaleMat(i, i) < smallScale) {
152			smallScale = scaleMat(i, i);
153			}
154	gezelter	246	}
155	gezelter	2
156	gezelter	246	if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
157	gezelter	507	sprintf( painCave.errMsg,
158			"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
159			" Check your tauBarostat, as it is probably too small!\n\n"
160			" scaleMat = [%lf\t%lf\t%lf]\n"
161			" [%lf\t%lf\t%lf]\n"
162			" [%lf\t%lf\t%lf]\n",
163			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
164			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
165			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2));
166			painCave.isFatal = 1;
167			simError();
168	gezelter	246	} else {
169	gezelter	2
170	gezelter	1764	Mat3x3d hmat = snap->getHmat();
171	gezelter	507	hmat = hmat *scaleMat;
172	gezelter	1764	snap->setHmat(hmat);
173	gezelter	246	}
174	gezelter	507	}
175	gezelter	2
176	gezelter	507	void NPTxyz::loadEta() {
177	gezelter	1764	eta= snap->getBarostat();
178	gezelter	507	}
179	gezelter	2
180			}