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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1   #include <math.h>
2 +
3 + #include "MatVec3.h"
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "AbstractClasses.hpp"
# Line 7 | Line 9
9   #include "Thermo.hpp"
10   #include "ReadWrite.hpp"
11   #include "Integrator.hpp"
12 < #include "simError.h"
12 > #include "simError.h"
13  
14   #ifdef IS_MPI
15   #include "mpiSimulation.hpp"
# Line 17 | Line 19
19   // modification of the Hoover algorithm:
20   //
21   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22 < //       Molec. Phys., 78, 533.
22 > //       Molec. Phys., 78, 533.
23   //
24   //           and
25 < //
25 > //
26   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27  
28   template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29    T( theInfo, the_ff )
30   {
31 <  
31 >  GenericData* data;
32 >  DoubleArrayData * etaValue;
33 >  vector<double> etaArray;
34    int i,j;
35 <  
35 >
36    for(i = 0; i < 3; i++){
37      for (j = 0; j < 3; j++){
38 <      
38 >
39        eta[i][j] = 0.0;
40        oldEta[i][j] = 0.0;
41      }
42    }
43 +
44 +
45 +  if( theInfo->useInitXSstate ){
46 +    // retrieve eta array from simInfo if it exists
47 +    data = info->getProperty(ETAVALUE_ID);
48 +    if(data){
49 +      etaValue = dynamic_cast<DoubleArrayData*>(data);
50 +      
51 +      if(etaValue){
52 +        etaArray = etaValue->getData();
53 +        
54 +        for(i = 0; i < 3; i++){
55 +          for (j = 0; j < 3; j++){
56 +            eta[i][j] = etaArray[3*i+j];
57 +            oldEta[i][j] = eta[i][j];
58 +          }
59 +        }
60 +      }
61 +    }
62 +  }
63 +
64   }
65  
66   template<typename T> NPTf<T>::~NPTf() {
# Line 44 | Line 69 | template<typename T> void NPTf<T>::resetIntegrator() {
69   }
70  
71   template<typename T> void NPTf<T>::resetIntegrator() {
72 <  
72 >
73    int i, j;
74 <  
74 >
75    for(i = 0; i < 3; i++)
76      for (j = 0; j < 3; j++)
77        eta[i][j] = 0.0;
78 <  
78 >
79    T::resetIntegrator();
80   }
81  
82   template<typename T> void NPTf<T>::evolveEtaA() {
83 <  
83 >
84    int i, j;
85 <  
85 >
86    for(i = 0; i < 3; i ++){
87      for(j = 0; j < 3; j++){
88        if( i == j)
89 <        eta[i][j] += dt2 *  instaVol *
89 >        eta[i][j] += dt2 *  instaVol *
90            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91        else
92          eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
93      }
94    }
95 <  
95 >
96    for(i = 0; i < 3; i++)
97      for (j = 0; j < 3; j++)
98        oldEta[i][j] = eta[i][j];
99   }
100  
101   template<typename T> void NPTf<T>::evolveEtaB() {
102 <  
102 >
103    int i,j;
104  
105    for(i = 0; i < 3; i++)
# Line 84 | Line 109 | template<typename T> void NPTf<T>::evolveEtaB() {
109    for(i = 0; i < 3; i ++){
110      for(j = 0; j < 3; j++){
111        if( i == j) {
112 <        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
112 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
113            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114        } else {
115          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
# Line 93 | Line 118 | template<typename T> void NPTf<T>::getVelScaleA(double
118    }
119   }
120  
121 < template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
121 > template<typename T> void NPTf<T>::calcVelScale(void){
122    int i,j;
98 –  double vScale[3][3];
123  
124    for (i = 0; i < 3; i++ ) {
125      for (j = 0; j < 3; j++ ) {
126        vScale[i][j] = eta[i][j];
127 <      
127 >
128        if (i == j) {
129 <        vScale[i][j] += chi;          
130 <      }              
129 >        vScale[i][j] += chi;
130 >      }
131      }
132    }
109 –  
110 –  info->matVecMul3( vScale, vel, sc );
133   }
134  
135 + template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
136 +
137 +  matVecMul3( vScale, vel, sc );
138 + }
139 +
140   template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
141 <  int i,j;
141 >  int j;
142    double myVel[3];
143    double vScale[3][3];
144  
118 –  for (i = 0; i < 3; i++ ) {
119 –    for (j = 0; j < 3; j++ ) {
120 –      vScale[i][j] = eta[i][j];
121 –      
122 –      if (i == j) {
123 –        vScale[i][j] += chi;          
124 –      }              
125 –    }
126 –  }
127 –  
145    for (j = 0; j < 3; j++)
146      myVel[j] = oldVel[3*index + j];
147  
148 <  info->matVecMul3( vScale, myVel, sc );
148 >  matVecMul3( vScale, myVel, sc );
149   }
150  
151 < template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
151 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
152                                                 int index, double sc[3]){
153    int j;
154    double rj[3];
# Line 139 | Line 156 | template<typename T> void NPTf<T>::getPosScale(double
156    for(j=0; j<3; j++)
157      rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
158  
159 <  info->matVecMul3( eta, rj, sc );
159 >  matVecMul3( eta, rj, sc );
160   }
161  
162   template<typename T> void NPTf<T>::scaleSimBox( void ){
# Line 149 | Line 166 | template<typename T> void NPTf<T>::scaleSimBox( void )
166    double eta2ij;
167    double bigScale, smallScale, offDiagMax;
168    double hm[3][3], hmnew[3][3];
152 –  
169  
170  
171 +
172    // Scale the box after all the positions have been moved:
173 <  
173 >
174    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
175    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
176 <  
176 >
177    bigScale = 1.0;
178    smallScale = 1.0;
179    offDiagMax = 0.0;
180 <  
180 >
181    for(i=0; i<3; i++){
182      for(j=0; j<3; j++){
183 <      
183 >
184        // Calculate the matrix Product of the eta array (we only need
185        // the ij element right now):
186 <      
186 >
187        eta2ij = 0.0;
188        for(k=0; k<3; k++){
189          eta2ij += eta[i][k] * eta[k][j];
190        }
191 <      
191 >
192        scaleMat[i][j] = 0.0;
193        // identity matrix (see above):
194        if (i == j) scaleMat[i][j] = 1.0;
# Line 179 | Line 196 | template<typename T> void NPTf<T>::scaleSimBox( void )
196        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
197  
198        if (i != j)
199 <        if (fabs(scaleMat[i][j]) > offDiagMax)
199 >        if (fabs(scaleMat[i][j]) > offDiagMax)
200            offDiagMax = fabs(scaleMat[i][j]);
201      }
202  
203      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
204      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
205    }
206 <  
207 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
206 >
207 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
208      sprintf( painCave.errMsg,
209 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
209 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
210               " Check your tauBarostat, as it is probably too small!\n\n"
211               " scaleMat = [%lf\t%lf\t%lf]\n"
212               "            [%lf\t%lf\t%lf]\n"
# Line 199 | Line 216 | template<typename T> void NPTf<T>::scaleSimBox( void )
216               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
217      painCave.isFatal = 1;
218      simError();
219 <  } else if (offDiagMax > 0.1) {
219 >  } else if (offDiagMax > 0.01) {
220      sprintf( painCave.errMsg,
221 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
221 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
222               " Check your tauBarostat, as it is probably too small!\n\n"
223               " scaleMat = [%lf\t%lf\t%lf]\n"
224               "            [%lf\t%lf\t%lf]\n"
# Line 213 | Line 230 | template<typename T> void NPTf<T>::scaleSimBox( void )
230      simError();
231    } else {
232      info->getBoxM(hm);
233 <    info->matMul3(hm, scaleMat, hmnew);
233 >    matMul3(hm, scaleMat, hmnew);
234      info->setBoxM(hmnew);
235    }
236   }
# Line 224 | Line 241 | template<typename T> bool NPTf<T>::etaConverged() {
241  
242    sumEta = 0;
243    for(i = 0; i < 3; i++)
244 <    sumEta += pow(prevEta[i][i] - eta[i][i], 2);    
245 <  
244 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
245 >
246    diffEta = sqrt( sumEta / 3.0 );
247 <  
247 >
248    return ( diffEta <= etaTolerance );
249   }
250  
251   template<typename T> double NPTf<T>::getConservedQuantity(void){
252 <  
252 >
253    double conservedQuantity;
254    double totalEnergy;
255    double thermostat_kinetic;
# Line 244 | Line 261 | template<typename T> double NPTf<T>::getConservedQuant
261  
262    totalEnergy = tStats->getTotalE();
263  
264 <  thermostat_kinetic = fkBT * tt2 * chi * chi /
264 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
265      (2.0 * eConvert);
266  
267    thermostat_potential = fkBT* integralOfChidt / eConvert;
268  
269 <  info->transposeMat3(eta, a);
270 <  info->matMul3(a, eta, b);
271 <  trEta = info->matTrace3(b);
269 >  transposeMat3(eta, a);
270 >  matMul3(a, eta, b);
271 >  trEta = matTrace3(b);
272  
273 <  barostat_kinetic = NkBT * tb2 * trEta /
273 >  barostat_kinetic = NkBT * tb2 * trEta /
274      (2.0 * eConvert);
275 <  
276 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
275 >
276 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
277      eConvert;
278  
279    conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
280      barostat_kinetic + barostat_potential;
264 –  
265 – //   cout.width(8);
266 – //   cout.precision(8);
281  
282 < //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
269 < //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
270 < //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
282 >  return conservedQuantity;
283  
272 –  return conservedQuantity;
273 –  
284   }
285 +
286 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
287 +  string parameters;
288 +  const int BUFFERSIZE = 2000; // size of the read buffer
289 +  char buffer[BUFFERSIZE];
290 +
291 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
292 +  parameters += buffer;
293 +
294 +  for(int i = 0; i < 3; i++){
295 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
296 +    parameters += buffer;
297 +  }
298 +
299 +  return parameters;
300 +
301 + }

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