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, 234107 (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;
    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;

    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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	6032 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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. 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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	thermostat = snap->getThermostat();
61	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	totalEnergy = thermo.getTotalEnergy();
83
84	thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /
85	(2.0 * PhysicalConstants::energyConvert);
86
87	thermostat_potential = fkBT* thermostat.second /
88	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	int i, j;
110	Mat3x3d scaleMat;
111	RealType scaleFactor;
112	RealType bigScale, smallScale;
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
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	// scale x & y together:
135	scaleFactor = 0.5 * (exp(dteta(0,0)) + exp(dteta(1,1) ) );
136	scaleMat(0,0) = scaleFactor;
137	scaleMat(1,1) = scaleFactor;
138
139	bigScale = scaleFactor;
140	smallScale = scaleFactor;
141
142	// scale z separately
143	scaleFactor = exp(dt * eta(2,2));
144	scaleMat(2,2) = scaleFactor;
145	if (scaleFactor > bigScale) bigScale = scaleFactor;
146	if (scaleFactor < smallScale) smallScale = scaleFactor;
147
148	if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
149	sprintf( painCave.errMsg,
150	"NPTsz: Attempting a Box scaling of more than 10 percent.\n"
151	"\tCheck your tauBarostat, as it is probably too small!\n\n"
152	"\tscaleMat = [%lf\t%lf\t%lf]\n"
153	"\t [%lf\t%lf\t%lf]\n"
154	"\t [%lf\t%lf\t%lf]\n",
155	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
156	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
157	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2));
158	painCave.severity = OPENMD_ERROR;
159	painCave.isFatal = 1;
160	simError();
161	} else {
162
163	Mat3x3d hmat = snap->getHmat();
164	hmat = hmat *scaleMat;
165	snap->setHmat(hmat);
166	}
167	}
168
169	void NPTsz::loadEta() {
170	eta= snap->getBarostat();
171	}
172	}