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(){

    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 NPTsz::scaleSimBox(){

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

  void NPTsz::loadEta() {
    eta= snap->getBarostat();
  }
}
Revision:	1767
Committed:	Fri Jul 6 22:01:58 2012 UTC (12 years, 10 months ago) by gezelter
File size:	6065 byte(s)
Log Message:	Various fixes required to compile OpenMD with the MS Visual C++ compiler
#	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	gezelter	1764	thermostat = snap->getThermostat();
61	gezelter	1629	loadEta();
62
63			// We need NkBT a lot, so just set it here: This is the RAW number
64			// of integrableObjects, so no subtraction or addition of
65			// constraints or orientational degrees of freedom:
66			NkBT = info_->getNGlobalIntegrableObjects() *
67			PhysicalConstants::kB * targetTemp;
68
69			// fkBT is used because the thermostat operates on more degrees of
70			// freedom than the barostat (when there are particles with
71			// orientational degrees of freedom).
72			fkBT = info_->getNdf() * PhysicalConstants::kB * targetTemp;
73
74			RealType conservedQuantity;
75			RealType totalEnergy;
76			RealType thermostat_kinetic;
77			RealType thermostat_potential;
78			RealType barostat_kinetic;
79			RealType barostat_potential;
80			RealType trEta;
81
82	gezelter	1764	totalEnergy = thermo.getTotalEnergy();
83	gezelter	1629
84	gezelter	1764	thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /
85	gezelter	1629	(2.0 * PhysicalConstants::energyConvert);
86
87	gezelter	1764	thermostat_potential = fkBT* thermostat.second /
88	gezelter	1629	PhysicalConstants::energyConvert;
89
90			SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
91			trEta = tmp.trace();
92
93			barostat_kinetic = NkBT * tb2 * trEta /
94			(2.0 * PhysicalConstants::energyConvert);
95
96			barostat_potential = (targetPressure * thermo.getVolume() /
97			PhysicalConstants::pressureConvert) /
98			PhysicalConstants::energyConvert;
99
100			conservedQuantity = totalEnergy + thermostat_kinetic +
101			thermostat_potential + barostat_kinetic + barostat_potential;
102
103			return conservedQuantity;
104			}
105
106
107			void NPTsz::scaleSimBox(){
108
109	gezelter	1767	int i, j;
110	gezelter	1629	Mat3x3d scaleMat;
111	gezelter	1767	RealType scaleFactor;
112	gezelter	1629	RealType bigScale, smallScale, offDiagMax;
113			Mat3x3d hm;
114			Mat3x3d hmnew;
115
116			// Scale the box after all the positions have been moved:
117
118			// Use a taylor expansion for eta products:
119			// Hmat = Hmat . exp(dt * etaMat)
120			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
121
122			bigScale = 1.0;
123			smallScale = 1.0;
124			offDiagMax = 0.0;
125
126			for(i=0; i<3; i++){
127			for(j=0; j<3; j++){
128			scaleMat(i, j) = 0.0;
129			if(i==j) {
130			scaleMat(i, j) = 1.0;
131			}
132			}
133			}
134
135			// scale x & y together:
136			scaleFactor = 0.5 * (exp(dteta(0,0)) + exp(dteta(1,1) ) );
137			scaleMat(0,0) = scaleFactor;
138			scaleMat(1,1) = scaleFactor;
139
140			bigScale = scaleFactor;
141			smallScale = scaleFactor;
142
143			// scale z separately
144			scaleFactor = exp(dt * eta(2,2));
145			scaleMat(2,2) = scaleFactor;
146			if (scaleFactor > bigScale) bigScale = scaleFactor;
147			if (scaleFactor < smallScale) smallScale = scaleFactor;
148
149			if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
150			sprintf( painCave.errMsg,
151			"NPTsz: Attempting a Box scaling of more than 10 percent.\n"
152			"\tCheck your tauBarostat, as it is probably too small!\n\n"
153			"\tscaleMat = [%lf\t%lf\t%lf]\n"
154			"\t [%lf\t%lf\t%lf]\n"
155			"\t [%lf\t%lf\t%lf]\n",
156			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
157			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
158			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2));
159			painCave.severity = OPENMD_ERROR;
160			painCave.isFatal = 1;
161			simError();
162			} else {
163
164	gezelter	1764	Mat3x3d hmat = snap->getHmat();
165	gezelter	1629	hmat = hmat *scaleMat;
166	gezelter	1764	snap->setHmat(hmat);
167	gezelter	1629	}
168			}
169
170			void NPTsz::loadEta() {
171	gezelter	1764	eta= snap->getBarostat();
172	gezelter	1629	}
173			}