src/integrators/NPTi.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 "NPTi.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/NPT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {

  // Basic 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.

  NPTi::NPTi ( SimInfo *info) : NPT(info){

  }

  void NPTi::evolveEtaA() {
    eta += dt2 * ( instaVol * (instaPress - targetPressure) /
                   (PhysicalConstants::pressureConvert*NkBT*tb2));
    oldEta = eta;
  }

  void NPTi::evolveEtaB() {

    prevEta = eta;
    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
                           (PhysicalConstants::pressureConvert*NkBT*tb2));
  }

  void NPTi::calcVelScale() {
    vScale = thermostat.first + eta;
  }

  void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
    sc = vel * vScale;
  }

  void NPTi::getVelScaleB(Vector3d& sc, int index ){
    sc = oldVel[index] * vScale;    
  }


  void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
                         int index, Vector3d& sc){
    /**@todo*/
    sc  = (oldPos[index] + pos)/(RealType)2.0 -COM;
    sc *= eta;
  }

  void NPTi::scaleSimBox(){

    RealType scaleFactor;

    scaleFactor = exp(dt*eta);

    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
      sprintf( painCave.errMsg,
               "NPTi error: Attempting a Box scaling of more than 10 percent"
               " check your tauBarostat, as it is probably too small!\n"
               " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
               );
      painCave.isFatal = 1;
      simError();
    } else {
      Mat3x3d hmat = snap->getHmat();
      hmat *= scaleFactor;
      snap->setHmat(hmat);
    }

  }

  bool NPTi::etaConverged() {

    return ( fabs(prevEta - eta) <= etaTolerance );
  }

  RealType NPTi::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 Energy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    RealType barostat_kinetic;
    RealType barostat_potential;

    Energy =thermo.getTotalEnergy();

    thermostat_kinetic = fkBT* tt2 * thermostat.first * 
      thermostat.first / (2.0 * PhysicalConstants::energyConvert);

    thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;


    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert);

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

    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
      barostat_kinetic + barostat_potential;
    
    return conservedQuantity;
  }

  void NPTi::loadEta() {
    Mat3x3d etaMat = snap->getBarostat();
    eta = etaMat(0,0);
    //if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) {
    //    sprintf( painCave.errMsg,
    //             "NPTi error: the diagonal elements of  eta matrix are not the same or etaMat is not a diagonal matrix");
    //    painCave.isFatal = 1;
    //    simError();
    //}
  }

  void NPTi::saveEta() {
    Mat3x3d etaMat(0.0);
    etaMat(0, 0) = eta;
    etaMat(1, 1) = eta;
    etaMat(2, 2) = eta;
    snap->setBarostat(etaMat);
  }
}
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 9 months ago) by gezelter
File size:	6244 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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, 24107 (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 "NPTi.hpp"
44	#include "brains/SimInfo.hpp"
45	#include "brains/Thermo.hpp"
46	#include "integrators/NPT.hpp"
47	#include "primitives/Molecule.hpp"
48	#include "utils/PhysicalConstants.hpp"
49	#include "utils/simError.h"
50
51	namespace OpenMD {
52
53	// Basic isotropic thermostating and barostating via the Melchionna
54	// modification of the Hoover algorithm:
55	//
56	// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
57	// Molec. Phys., 78, 533.
58	//
59	// and
60	//
61	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
62
63	NPTi::NPTi ( SimInfo *info) : NPT(info){
64
65	}
66
67	void NPTi::evolveEtaA() {
68	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
69	(PhysicalConstants::pressureConvertNkBTtb2));
70	oldEta = eta;
71	}
72
73	void NPTi::evolveEtaB() {
74
75	prevEta = eta;
76	eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
77	(PhysicalConstants::pressureConvertNkBTtb2));
78	}
79
80	void NPTi::calcVelScale() {
81	vScale = thermostat.first + eta;
82	}
83
84	void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
85	sc = vel * vScale;
86	}
87
88	void NPTi::getVelScaleB(Vector3d& sc, int index ){
89	sc = oldVel[index] * vScale;
90	}
91
92
93	void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
94	int index, Vector3d& sc){
95	/*@todo/
96	sc = (oldPos[index] + pos)/(RealType)2.0 -COM;
97	sc *= eta;
98	}
99
100	void NPTi::scaleSimBox(){
101
102	RealType scaleFactor;
103
104	scaleFactor = exp(dt*eta);
105
106	if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
107	sprintf( painCave.errMsg,
108	"NPTi error: Attempting a Box scaling of more than 10 percent"
109	" check your tauBarostat, as it is probably too small!\n"
110	" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
111	);
112	painCave.isFatal = 1;
113	simError();
114	} else {
115	Mat3x3d hmat = snap->getHmat();
116	hmat *= scaleFactor;
117	snap->setHmat(hmat);
118	}
119
120	}
121
122	bool NPTi::etaConverged() {
123
124	return ( fabs(prevEta - eta) <= etaTolerance );
125	}
126
127	RealType NPTi::calcConservedQuantity(){
128
129	thermostat = snap->getThermostat();
130	loadEta();
131	// We need NkBT a lot, so just set it here: This is the RAW number
132	// of integrableObjects, so no subtraction or addition of constraints or
133	// orientational degrees of freedom:
134	NkBT = info_->getNGlobalIntegrableObjects()PhysicalConstants::kB targetTemp;
135
136	// fkBT is used because the thermostat operates on more degrees of freedom
137	// than the barostat (when there are particles with orientational degrees
138	// of freedom).
139	fkBT = info_->getNdf()PhysicalConstants::kB targetTemp;
140
141	RealType conservedQuantity;
142	RealType Energy;
143	RealType thermostat_kinetic;
144	RealType thermostat_potential;
145	RealType barostat_kinetic;
146	RealType barostat_potential;
147
148	Energy =thermo.getTotalEnergy();
149
150	thermostat_kinetic = fkBT* tt2 * thermostat.first *
151	thermostat.first / (2.0 * PhysicalConstants::energyConvert);
152
153	thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
154
155
156	barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert);
157
158	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /
159	PhysicalConstants::energyConvert;
160
161	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
162	barostat_kinetic + barostat_potential;
163
164	return conservedQuantity;
165	}
166
167	void NPTi::loadEta() {
168	Mat3x3d etaMat = snap->getBarostat();
169	eta = etaMat(0,0);
170	//if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon \|\| fabs(etaMat(1,1) - eta) >= OpenMD::epsilon \|\| !etaMat.isDiagonal()) {
171	// sprintf( painCave.errMsg,
172	// "NPTi error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
173	// painCave.isFatal = 1;
174	// simError();
175	//}
176	}
177
178	void NPTi::saveEta() {
179	Mat3x3d etaMat(0.0);
180	etaMat(0, 0) = eta;
181	etaMat(1, 1) = eta;
182	etaMat(2, 2) = eta;
183	snap->setBarostat(etaMat);
184	}
185	}