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Comparing trunk/OOPSE-4/src/integrators/NPTi.cpp (file contents):
Revision 1625 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC

# Line 1 | Line 1
1 < #include <math.h>
2 < #include "primitives/Atom.hpp"
3 < #include "primitives/SRI.hpp"
4 < #include "primitives/AbstractClasses.hpp"
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. Acknowledgement of the program authors must be made in any
10 > *    publication of scientific results based in part on use of the
11 > *    program.  An acceptable form of acknowledgement is citation of
12 > *    the article in which the program was described (Matthew
13 > *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 > *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 > *    Parallel Simulation Engine for Molecular Dynamics,"
16 > *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 > *
18 > * 2. Redistributions of source code must retain the above copyright
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41 >
42 > #include "NPTi.hpp"
43   #include "brains/SimInfo.hpp"
6 – #include "UseTheForce/ForceFields.hpp"
44   #include "brains/Thermo.hpp"
45 < #include "io/ReadWrite.hpp"
46 < #include "integrators/Integrator.hpp"
45 > #include "integrators/NPT.hpp"
46 > #include "primitives/Molecule.hpp"
47 > #include "utils/OOPSEConstant.hpp"
48   #include "utils/simError.h"
49  
50 < #ifdef IS_MPI
13 < #include "brains/mpiSimulation.hpp"
14 < #endif
50 > namespace oopse {
51  
52   // Basic isotropic thermostating and barostating via the Melchionna
53   // modification of the Hoover algorithm:
# Line 23 | Line 59 | template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo,
59   //
60   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
61  
62 < template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 <  T( theInfo, the_ff )
28 < {
29 <  GenericData* data;
30 <  DoubleVectorGenericData * etaValue;
31 <  vector<double> etaArray;
62 > NPTi::NPTi ( SimInfo *info) : NPT(info){
63  
33 –  eta = 0.0;
34 –  oldEta = 0.0;
35 –
36 –  if( theInfo->useInitXSstate ){
37 –    // retrieve eta from simInfo if
38 –    data = info->getProperty(ETAVALUE_ID);
39 –    if(data){
40 –      etaValue = dynamic_cast<DoubleVectorGenericData*>(data);
41 –      
42 –      if(etaValue){
43 –        eta = (*etaValue)[0];
44 –        oldEta = eta;
45 –      }
46 –    }
47 –  }
64   }
65  
66 < template<typename T> NPTi<T>::~NPTi() {
67 <  //nothing for now
66 > void NPTi::evolveEtaA() {
67 >    eta += dt2 * ( instaVol * (instaPress - targetPressure) /
68 >         (OOPSEConstant::pressureConvert*NkBT*tb2));
69 >    oldEta = eta;
70   }
71  
72 < template<typename T> void NPTi<T>::resetIntegrator() {
55 <  eta = 0.0;
56 <  T::resetIntegrator();
57 < }
72 > void NPTi::evolveEtaB() {
73  
74 < template<typename T> void NPTi<T>::evolveEtaA() {
75 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
76 <                 (p_convert*NkBT*tb2));
62 <  oldEta = eta;
74 >    prevEta = eta;
75 >    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
76 >         (OOPSEConstant::pressureConvert*NkBT*tb2));
77   }
78  
79 < template<typename T> void NPTi<T>::evolveEtaB() {
80 <
67 <  prevEta = eta;
68 <  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
69 <                 (p_convert*NkBT*tb2));
79 > void NPTi::calcVelScale() {
80 >    vScale = chi + eta;
81   }
82  
83 < template<typename T> void NPTi<T>::calcVelScale(void) {
84 <  vScale = chi + eta;
83 > void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
84 >    sc = vel * vScale;
85   }
86  
87 < template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
88 <  int i;
78 <
79 <  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
87 > void NPTi::getVelScaleB(Vector3d& sc, int index ){
88 >    sc = oldVel[index] * vScale;    
89   }
90  
82 – template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
83 –  int i;
91  
92 <  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale;
92 > void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM,
93 >                           int index, Vector3d& sc){
94 >    /**@todo*/
95 >    sc  = (oldPos[index] + pos)/2.0 -COM;
96 >    sc *= eta;
97   }
98  
99 + void NPTi::scaleSimBox(){
100  
101 < template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
90 <                                               int index, double sc[3]){
91 <  int j;
101 >    double scaleFactor;
102  
103 <  for(j=0; j<3; j++)
94 <    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
103 >    scaleFactor = exp(dt*eta);
104  
105 <  for(j=0; j<3; j++)
106 <    sc[j] *= eta;
98 < }
99 <
100 < template<typename T> void NPTi<T>::scaleSimBox( void ){
101 <
102 <  double scaleFactor;
103 <
104 <  scaleFactor = exp(dt*eta);
105 <
106 <  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
107 <    sprintf( painCave.errMsg,
105 >    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
106 >        sprintf( painCave.errMsg,
107               "NPTi error: Attempting a Box scaling of more than 10 percent"
108               " check your tauBarostat, as it is probably too small!\n"
109               " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
110               );
111 <    painCave.isFatal = 1;
112 <    simError();
113 <  } else {
114 <    info->scaleBox(scaleFactor);
115 <  }
111 >        painCave.isFatal = 1;
112 >        simError();
113 >    } else {
114 >        Mat3x3d hmat = currentSnapshot_->getHmat();
115 >        hmat *= scaleFactor;
116 >        currentSnapshot_->setHmat(hmat);
117 >    }
118  
119   }
120  
121 < template<typename T> bool NPTi<T>::etaConverged() {
121 > bool NPTi::etaConverged() {
122  
123 <  return ( fabs(prevEta - eta) <= etaTolerance );
123 >    return ( fabs(prevEta - eta) <= etaTolerance );
124   }
125  
126 < template<typename T> double NPTi<T>::getConservedQuantity(void){
126 > double NPTi::calcConservedQuantity(){
127  
128 <  double conservedQuantity;
129 <  double Energy;
130 <  double thermostat_kinetic;
131 <  double thermostat_potential;
132 <  double barostat_kinetic;
133 <  double barostat_potential;
128 >    chi= currentSnapshot_->getChi();
129 >    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
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()*OOPSEConstant::kB *targetTemp;
135  
136 <  Energy = tStats->getTotalE();
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()*OOPSEConstant::kB *targetTemp;    
140 >    
141 >    double conservedQuantity;
142 >    double Energy;
143 >    double thermostat_kinetic;
144 >    double thermostat_potential;
145 >    double barostat_kinetic;
146 >    double barostat_potential;
147  
148 <  thermostat_kinetic = fkBT* tt2 * chi * chi /
137 <    (2.0 * eConvert);
148 >    Energy =thermo.getTotalE();
149  
150 <  thermostat_potential = fkBT* integralOfChidt / eConvert;
150 >    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
151  
152 +    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
153  
142 –  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
143 –    (2.0 * eConvert);
154  
155 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
146 <    eConvert;
155 >    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
156  
157 <  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
158 <    barostat_kinetic + barostat_potential;
157 >    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
158 >        OOPSEConstant::energyConvert;
159  
160 < //   cout.width(8);
161 < //   cout.precision(8);
160 >    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
161 >        barostat_kinetic + barostat_potential;
162 >    
163 >    return conservedQuantity;
164 > }
165  
166 < //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
167 < //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
168 < //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
169 <  return conservedQuantity;
166 > void NPTi::loadEta() {
167 >    Mat3x3d etaMat = currentSnapshot_->getEta();
168 >    eta = etaMat(0,0);
169 >    //if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) {
170 >    //    sprintf( painCave.errMsg,
171 >    //             "NPTi error: the diagonal elements of  eta matrix are not the same or etaMat is not a diagonal matrix");
172 >    //    painCave.isFatal = 1;
173 >    //    simError();
174 >    //}
175   }
176  
177 < template<typename T> string NPTi<T>::getAdditionalParameters(void){
178 <  string parameters;
179 <  const int BUFFERSIZE = 2000; // size of the read buffer
180 <  char buffer[BUFFERSIZE];
177 > void NPTi::saveEta() {
178 >    Mat3x3d etaMat(0.0);
179 >    etaMat(0, 0) = eta;
180 >    etaMat(1, 1) = eta;
181 >    etaMat(2, 2) = eta;
182 >    currentSnapshot_->setEta(etaMat);
183 > }
184  
165 –  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
166 –  parameters += buffer;
167 –
168 –  sprintf(buffer,"\t%G\t0\t0;", eta);
169 –  parameters += buffer;
170 –
171 –  sprintf(buffer,"\t0\t%G\t0;", eta);
172 –  parameters += buffer;
173 –
174 –  sprintf(buffer,"\t0\t0\t%G;", eta);
175 –  parameters += buffer;
176 –
177 –  return parameters;
178 –
185   }

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