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root/group/branches/new-templateless/OOPSE/libmdtools/NPTf.cpp
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Comparing:
trunk/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <math.h>
3 >
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 )
28 > NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29 >  NPT( theInfo, the_ff )
30   {
31 <  
31 >  GenericData* data;
32 >  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 +  // retrieve eta array from simInfo if it exists
44 +  data = info->getProperty(ETAVALUE_ID);
45 +  if(data != NULL){
46 +    
47 +    int test = data->getDarray(etaArray);
48 +    
49 +    if( test == 9 ){
50 +      
51 +      for(i = 0; i < 3; i++){
52 +        for (j = 0; j < 3; j++){
53 +          eta[i][j] = etaArray[3*i+j];
54 +          oldEta[i][j] = eta[i][j];
55 +        }
56 +      }    
57 +      delete[] etaArray;
58 +    }
59 +    else
60 +      std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test
61 +                << ").\n"
62 +                << "            Simulation wil proceed with eta = 0;\n";
63 +  }
64   }
65  
66 < template<typename T> NPTf<T>::~NPTf() {
66 > NPTf::~NPTf() {
67  
68    // empty for now
69   }
70  
71 < template<typename T> void NPTf<T>::resetIntegrator() {
72 <  
71 > void NPTf::resetIntegrator() {
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 <  
79 <  T::resetIntegrator();
78 >
79 >  NPT::resetIntegrator();
80   }
81  
82 < template<typename T> void NPTf<T>::evolveEtaA() {
83 <  
82 > void NPTf::evolveEtaA() {
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 <  
101 > void NPTf::evolveEtaB() {
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>::evolveEtaB() {
118    }
119   }
120  
121 < template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
121 > void NPTf::getVelScaleA(double sc[3], double vel[3]) {
122    int i,j;
123    double vScale[3][3];
124  
125    for (i = 0; i < 3; i++ ) {
126      for (j = 0; j < 3; j++ ) {
127        vScale[i][j] = eta[i][j];
128 <      
128 >
129        if (i == j) {
130 <        vScale[i][j] += chi;          
131 <      }              
130 >        vScale[i][j] += chi;
131 >      }
132      }
133    }
134 <  
134 >
135    info->matVecMul3( vScale, vel, sc );
136   }
137  
138 < template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
138 > void NPTf::getVelScaleB(double sc[3], int index ){
139    int i,j;
140    double myVel[3];
141    double vScale[3][3];
# Line 118 | Line 143 | template<typename T> void NPTf<T>::getVelScaleB(double
143    for (i = 0; i < 3; i++ ) {
144      for (j = 0; j < 3; j++ ) {
145        vScale[i][j] = eta[i][j];
146 <      
146 >
147        if (i == j) {
148 <        vScale[i][j] += chi;          
149 <      }              
148 >        vScale[i][j] += chi;
149 >      }
150      }
151    }
152 <  
152 >
153    for (j = 0; j < 3; j++)
154      myVel[j] = oldVel[3*index + j];
155  
156    info->matVecMul3( vScale, myVel, sc );
157   }
158  
159 < template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
159 > void NPTf::getPosScale(double pos[3], double COM[3],
160                                                 int index, double sc[3]){
161    int j;
162    double rj[3];
# Line 142 | Line 167 | template<typename T> void NPTf<T>::getPosScale(double
167    info->matVecMul3( eta, rj, sc );
168   }
169  
170 < template<typename T> void NPTf<T>::scaleSimBox( void ){
170 > void NPTf::scaleSimBox( void ){
171  
172    int i,j,k;
173    double scaleMat[3][3];
174    double eta2ij;
175    double bigScale, smallScale, offDiagMax;
176    double hm[3][3], hmnew[3][3];
152 –  
177  
178  
179 +
180    // Scale the box after all the positions have been moved:
181 <  
181 >
182    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
183    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
184 <  
184 >
185    bigScale = 1.0;
186    smallScale = 1.0;
187    offDiagMax = 0.0;
188 <  
188 >
189    for(i=0; i<3; i++){
190      for(j=0; j<3; j++){
191 <      
191 >
192        // Calculate the matrix Product of the eta array (we only need
193        // the ij element right now):
194 <      
194 >
195        eta2ij = 0.0;
196        for(k=0; k<3; k++){
197          eta2ij += eta[i][k] * eta[k][j];
198        }
199 <      
199 >
200        scaleMat[i][j] = 0.0;
201        // identity matrix (see above):
202        if (i == j) scaleMat[i][j] = 1.0;
# Line 179 | Line 204 | template<typename T> void NPTf<T>::scaleSimBox( void )
204        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
205  
206        if (i != j)
207 <        if (fabs(scaleMat[i][j]) > offDiagMax)
207 >        if (fabs(scaleMat[i][j]) > offDiagMax)
208            offDiagMax = fabs(scaleMat[i][j]);
209      }
210  
211      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
212      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
213    }
214 <  
214 >
215    if ((bigScale > 1.1) || (smallScale < 0.9)) {
216      sprintf( painCave.errMsg,
217               "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
# Line 218 | Line 243 | template<typename T> void NPTf<T>::scaleSimBox( void )
243    }
244   }
245  
246 < template<typename T> bool NPTf<T>::etaConverged() {
246 > bool NPTf::etaConverged() {
247    int i;
248    double diffEta, sumEta;
249  
250    sumEta = 0;
251    for(i = 0; i < 3; i++)
252 <    sumEta += pow(prevEta[i][i] - eta[i][i], 2);    
253 <  
252 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
253 >
254    diffEta = sqrt( sumEta / 3.0 );
255 <  
255 >
256    return ( diffEta <= etaTolerance );
257   }
258  
259 < template<typename T> double NPTf<T>::getConservedQuantity(void){
260 <  
259 > double NPTf::getConservedQuantity(void){
260 >
261    double conservedQuantity;
262    double totalEnergy;
263    double thermostat_kinetic;
# Line 244 | Line 269 | template<typename T> double NPTf<T>::getConservedQuant
269  
270    totalEnergy = tStats->getTotalE();
271  
272 <  thermostat_kinetic = fkBT * tt2 * chi * chi /
272 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
273      (2.0 * eConvert);
274  
275    thermostat_potential = fkBT* integralOfChidt / eConvert;
# Line 253 | Line 278 | template<typename T> double NPTf<T>::getConservedQuant
278    info->matMul3(a, eta, b);
279    trEta = info->matTrace3(b);
280  
281 <  barostat_kinetic = NkBT * tb2 * trEta /
281 >  barostat_kinetic = NkBT * tb2 * trEta /
282      (2.0 * eConvert);
283 <  
284 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283 >
284 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
285      eConvert;
286  
287    conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
288      barostat_kinetic + barostat_potential;
289 <  
289 >
290   //   cout.width(8);
291   //   cout.precision(8);
292  
293 < //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
294 < //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
293 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
294 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
295   //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
296  
297 <  return conservedQuantity;
298 <  
297 >  return conservedQuantity;
298 >
299   }
300 +
301 + string NPTf::getAdditionalParameters(void){
302 +  string parameters;
303 +  const int BUFFERSIZE = 2000; // size of the read buffer
304 +  char buffer[BUFFERSIZE];
305 +
306 +  sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt);
307 +  parameters += buffer;
308 +
309 +  for(int i = 0; i < 3; i++){
310 +    sprintf(buffer,"\t%lf\t%lf\t%lf;", eta[3*i], eta[3*i+1], eta[3*i+2]);
311 +    parameters += buffer;
312 +  }
313 +
314 +  return parameters;
315 +
316 + }

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