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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 780 by mmeineke, Mon Sep 22 21:23:25 2003 UTC vs.
Revision 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2 >
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 7 | Line 8
8   #include "Thermo.hpp"
9   #include "ReadWrite.hpp"
10   #include "Integrator.hpp"
11 < #include "simError.h"
11 > #include "simError.h"
12  
13   #ifdef IS_MPI
14   #include "mpiSimulation.hpp"
# Line 17 | Line 18
18   // modification of the Hoover algorithm:
19   //
20   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
21 < //       Molec. Phys., 78, 533.
21 > //       Molec. Phys., 78, 533.
22   //
23   //           and
24 < //
24 > //
25   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
26  
27   template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
28    T( theInfo, the_ff )
29   {
30 <  
30 >  GenericData* data;
31 >  DoubleArrayData * etaValue;
32 >  vector<double> etaArray;
33    int i,j;
34 <  
34 >
35    for(i = 0; i < 3; i++){
36      for (j = 0; j < 3; j++){
37 <      
37 >
38        eta[i][j] = 0.0;
39        oldEta[i][j] = 0.0;
40      }
41    }
42 +
43 +
44 +  if( theInfo->useInitXSstate ){
45 +    // retrieve eta array from simInfo if it exists
46 +    data = info->getProperty(ETAVALUE_ID);
47 +    if(data){
48 +      etaValue = dynamic_cast<DoubleArrayData*>(data);
49 +      
50 +      if(etaValue){
51 +        etaArray = etaValue->getData();
52 +        
53 +        for(i = 0; i < 3; i++){
54 +          for (j = 0; j < 3; j++){
55 +            eta[i][j] = etaArray[3*i+j];
56 +            oldEta[i][j] = eta[i][j];
57 +          }
58 +        }
59 +      }
60 +    }
61 +  }
62 +
63   }
64  
65   template<typename T> NPTf<T>::~NPTf() {
# Line 44 | Line 68 | template<typename T> void NPTf<T>::resetIntegrator() {
68   }
69  
70   template<typename T> void NPTf<T>::resetIntegrator() {
71 <  
71 >
72    int i, j;
73 <  
73 >
74    for(i = 0; i < 3; i++)
75      for (j = 0; j < 3; j++)
76        eta[i][j] = 0.0;
77 <  
77 >
78    T::resetIntegrator();
79   }
80  
81   template<typename T> void NPTf<T>::evolveEtaA() {
82 <  
82 >
83    int i, j;
84 <  
84 >
85    for(i = 0; i < 3; i ++){
86      for(j = 0; j < 3; j++){
87        if( i == j)
88 <        eta[i][j] += dt2 *  instaVol *
88 >        eta[i][j] += dt2 *  instaVol *
89            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
90        else
91          eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
92      }
93    }
94 <  
94 >
95    for(i = 0; i < 3; i++)
96      for (j = 0; j < 3; j++)
97        oldEta[i][j] = eta[i][j];
98   }
99  
100   template<typename T> void NPTf<T>::evolveEtaB() {
101 <  
101 >
102    int i,j;
103  
104    for(i = 0; i < 3; i++)
# Line 84 | Line 108 | template<typename T> void NPTf<T>::evolveEtaB() {
108    for(i = 0; i < 3; i ++){
109      for(j = 0; j < 3; j++){
110        if( i == j) {
111 <        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
111 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
112            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
113        } else {
114          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
# Line 93 | Line 117 | template<typename T> void NPTf<T>::getVelScaleA(double
117    }
118   }
119  
120 < template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
120 > template<typename T> void NPTf<T>::calcVelScale(void){
121    int i,j;
98 –  double vScale[3][3];
122  
123    for (i = 0; i < 3; i++ ) {
124      for (j = 0; j < 3; j++ ) {
125        vScale[i][j] = eta[i][j];
126 <      
126 >
127        if (i == j) {
128 <        vScale[i][j] += chi;          
129 <      }              
128 >        vScale[i][j] += chi;
129 >      }
130      }
131    }
132 <  
132 > }
133 >
134 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
135 >
136    info->matVecMul3( vScale, vel, sc );
137   }
138  
139   template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
140 <  int i,j;
140 >  int j;
141    double myVel[3];
142    double vScale[3][3];
143  
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 –  
144    for (j = 0; j < 3; j++)
145      myVel[j] = oldVel[3*index + j];
146  
147    info->matVecMul3( vScale, myVel, sc );
148   }
149  
150 < template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
150 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
151                                                 int index, double sc[3]){
152    int j;
153    double rj[3];
# Line 149 | Line 165 | template<typename T> void NPTf<T>::scaleSimBox( void )
165    double eta2ij;
166    double bigScale, smallScale, offDiagMax;
167    double hm[3][3], hmnew[3][3];
152 –  
168  
169  
170 +
171    // Scale the box after all the positions have been moved:
172 <  
172 >
173    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
174    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
175 <  
175 >
176    bigScale = 1.0;
177    smallScale = 1.0;
178    offDiagMax = 0.0;
179 <  
179 >
180    for(i=0; i<3; i++){
181      for(j=0; j<3; j++){
182 <      
182 >
183        // Calculate the matrix Product of the eta array (we only need
184        // the ij element right now):
185 <      
185 >
186        eta2ij = 0.0;
187        for(k=0; k<3; k++){
188          eta2ij += eta[i][k] * eta[k][j];
189        }
190 <      
190 >
191        scaleMat[i][j] = 0.0;
192        // identity matrix (see above):
193        if (i == j) scaleMat[i][j] = 1.0;
# Line 179 | Line 195 | template<typename T> void NPTf<T>::scaleSimBox( void )
195        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
196  
197        if (i != j)
198 <        if (fabs(scaleMat[i][j]) > offDiagMax)
198 >        if (fabs(scaleMat[i][j]) > offDiagMax)
199            offDiagMax = fabs(scaleMat[i][j]);
200      }
201  
202      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
203      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
204    }
205 <  
206 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
205 >
206 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
207      sprintf( painCave.errMsg,
208 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
208 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
209               " Check your tauBarostat, as it is probably too small!\n\n"
210               " scaleMat = [%lf\t%lf\t%lf]\n"
211               "            [%lf\t%lf\t%lf]\n"
# Line 199 | Line 215 | template<typename T> void NPTf<T>::scaleSimBox( void )
215               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
216      painCave.isFatal = 1;
217      simError();
218 <  } else if (offDiagMax > 0.1) {
218 >  } else if (offDiagMax > 0.01) {
219      sprintf( painCave.errMsg,
220 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
220 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
221               " Check your tauBarostat, as it is probably too small!\n\n"
222               " scaleMat = [%lf\t%lf\t%lf]\n"
223               "            [%lf\t%lf\t%lf]\n"
# Line 224 | Line 240 | template<typename T> bool NPTf<T>::etaConverged() {
240  
241    sumEta = 0;
242    for(i = 0; i < 3; i++)
243 <    sumEta += pow(prevEta[i][i] - eta[i][i], 2);    
244 <  
243 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
244 >
245    diffEta = sqrt( sumEta / 3.0 );
246 <  
246 >
247    return ( diffEta <= etaTolerance );
248   }
249  
250   template<typename T> double NPTf<T>::getConservedQuantity(void){
251 <  
251 >
252    double conservedQuantity;
253 <  double Energy;
253 >  double totalEnergy;
254    double thermostat_kinetic;
255    double thermostat_potential;
256    double barostat_kinetic;
# Line 242 | Line 258 | template<typename T> double NPTf<T>::getConservedQuant
258    double trEta;
259    double a[3][3], b[3][3];
260  
261 <  Energy = tStats->getTotalE();
261 >  totalEnergy = tStats->getTotalE();
262  
263 <  thermostat_kinetic = fkBT* tt2 * chi * chi /
263 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
264      (2.0 * eConvert);
265  
266    thermostat_potential = fkBT* integralOfChidt / eConvert;
# Line 253 | Line 269 | template<typename T> double NPTf<T>::getConservedQuant
269    info->matMul3(a, eta, b);
270    trEta = info->matTrace3(b);
271  
272 <  barostat_kinetic = NkBT * tb2 * trEta /
272 >  barostat_kinetic = NkBT * tb2 * trEta /
273      (2.0 * eConvert);
274 <  
275 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
274 >
275 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
276      eConvert;
277  
278 <  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
278 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
279      barostat_kinetic + barostat_potential;
264 –  
265 – //   cout.width(8);
266 – //   cout.precision(8);
280  
281 < //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
269 < //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
270 < //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
281 >  return conservedQuantity;
282  
272 –  return conservedQuantity;
273 –  
283   }
284 +
285 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
286 +  string parameters;
287 +  const int BUFFERSIZE = 2000; // size of the read buffer
288 +  char buffer[BUFFERSIZE];
289 +
290 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
291 +  parameters += buffer;
292 +
293 +  for(int i = 0; i < 3; i++){
294 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
295 +    parameters += buffer;
296 +  }
297 +
298 +  return parameters;
299 +
300 + }

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