src/integrators/NPTsz.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/NPTsz.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {

  /**
   * There is no known conserved quantity for the NPTsz integrator,
   * but we still compute the equivalent quantity from a fully
   * flexible constant pressure integrator.
   */   
  RealType NPTsz::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 NPTsz::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;
        }
      }
    }

    // scale x & y together:
    scaleFactor = 0.5 * (exp(dt*eta(0,0)) + exp(dt*eta(1,1) ) );
    scaleMat(0,0) = scaleFactor;
    scaleMat(1,1) = scaleFactor;

    bigScale = scaleFactor;
    smallScale = scaleFactor;

    // scale z separately
    scaleFactor = exp(dt * eta(2,2));
    scaleMat(2,2) = scaleFactor;
    if (scaleFactor > bigScale) bigScale = scaleFactor;
    if (scaleFactor < smallScale) smallScale = scaleFactor;

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

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

  void NPTsz::loadEta() {
    eta= currentSnapshot_->getEta();
  }
}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	6131 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1629	/*
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	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	1629	*/
42
43			#include "brains/SimInfo.hpp"
44			#include "brains/Thermo.hpp"
45			#include "integrators/IntegratorCreator.hpp"
46			#include "integrators/NPTsz.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "utils/PhysicalConstants.hpp"
49			#include "utils/simError.h"
50
51			namespace OpenMD {
52
53			/**
54			* There is no known conserved quantity for the NPTsz integrator,
55			* but we still compute the equivalent quantity from a fully
56			* flexible constant pressure integrator.
57			*/
58			RealType NPTsz::calcConservedQuantity(){
59
60			chi= currentSnapshot_->getChi();
61			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
62			loadEta();
63
64			// We need NkBT a lot, so just set it here: This is the RAW number
65			// of integrableObjects, so no subtraction or addition of
66			// constraints or orientational degrees of freedom:
67			NkBT = info_->getNGlobalIntegrableObjects() *
68			PhysicalConstants::kB * targetTemp;
69
70			// fkBT is used because the thermostat operates on more degrees of
71			// freedom than the barostat (when there are particles with
72			// orientational degrees of freedom).
73			fkBT = info_->getNdf() * PhysicalConstants::kB * targetTemp;
74
75			RealType conservedQuantity;
76			RealType totalEnergy;
77			RealType thermostat_kinetic;
78			RealType thermostat_potential;
79			RealType barostat_kinetic;
80			RealType barostat_potential;
81			RealType trEta;
82
83			totalEnergy = thermo.getTotalE();
84
85			thermostat_kinetic = fkBT * tt2 * chi * chi /
86			(2.0 * PhysicalConstants::energyConvert);
87
88			thermostat_potential = fkBT* integralOfChidt /
89			PhysicalConstants::energyConvert;
90
91			SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
92			trEta = tmp.trace();
93
94			barostat_kinetic = NkBT * tb2 * trEta /
95			(2.0 * PhysicalConstants::energyConvert);
96
97			barostat_potential = (targetPressure * thermo.getVolume() /
98			PhysicalConstants::pressureConvert) /
99			PhysicalConstants::energyConvert;
100
101			conservedQuantity = totalEnergy + thermostat_kinetic +
102			thermostat_potential + barostat_kinetic + barostat_potential;
103
104			return conservedQuantity;
105			}
106
107
108			void NPTsz::scaleSimBox(){
109
110			int i,j,k;
111			Mat3x3d scaleMat;
112			RealType eta2ij, scaleFactor;
113			RealType bigScale, smallScale, offDiagMax;
114			Mat3x3d hm;
115			Mat3x3d hmnew;
116
117			// Scale the box after all the positions have been moved:
118
119			// Use a taylor expansion for eta products:
120			// Hmat = Hmat . exp(dt * etaMat)
121			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
122
123			bigScale = 1.0;
124			smallScale = 1.0;
125			offDiagMax = 0.0;
126
127			for(i=0; i<3; i++){
128			for(j=0; j<3; j++){
129			scaleMat(i, j) = 0.0;
130			if(i==j) {
131			scaleMat(i, j) = 1.0;
132			}
133			}
134			}
135
136			// scale x & y together:
137			scaleFactor = 0.5 * (exp(dteta(0,0)) + exp(dteta(1,1) ) );
138			scaleMat(0,0) = scaleFactor;
139			scaleMat(1,1) = scaleFactor;
140
141			bigScale = scaleFactor;
142			smallScale = scaleFactor;
143
144			// scale z separately
145			scaleFactor = exp(dt * eta(2,2));
146			scaleMat(2,2) = scaleFactor;
147			if (scaleFactor > bigScale) bigScale = scaleFactor;
148			if (scaleFactor < smallScale) smallScale = scaleFactor;
149
150			if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
151			sprintf( painCave.errMsg,
152			"NPTsz: Attempting a Box scaling of more than 10 percent.\n"
153			"\tCheck your tauBarostat, as it is probably too small!\n\n"
154			"\tscaleMat = [%lf\t%lf\t%lf]\n"
155			"\t [%lf\t%lf\t%lf]\n"
156			"\t [%lf\t%lf\t%lf]\n",
157			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
158			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
159			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2));
160			painCave.severity = OPENMD_ERROR;
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 NPTsz::loadEta() {
172			eta= currentSnapshot_->getEta();
173			}
174			}