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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 600 by gezelter, Mon Jul 14 22:38:13 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 851 by mmeineke, Wed Nov 5 19:18:17 2003 UTC

# Line 1 | Line 1
1 + #include <stdlib.h>
2 + #include <math.h>
3 + #include <string.h>
4 +
5   #include "Atom.hpp"
6   #include "SRI.hpp"
7   #include "AbstractClasses.hpp"
# Line 6 | Line 10
10   #include "Thermo.hpp"
11   #include "ReadWrite.hpp"
12   #include "Integrator.hpp"
13 < #include "simError.h"
13 > #include "simError.h"
14  
15 + #ifdef IS_MPI
16 + #include "mpiSimulation.hpp"
17 + #endif
18  
19   // Basic non-isotropic thermostating and barostating via the Melchionna
20   // modification of the Hoover algorithm:
21   //
22   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
23 < //       Molec. Phys., 78, 533.
23 > //       Molec. Phys., 78, 533.
24   //
25   //           and
26 < //
26 > //
27   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
28  
29   NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
30 <  Integrator( theInfo, the_ff )
30 >  NPT( theInfo, the_ff )
31   {
32 +  GenericData* data;
33 +  double *etaArray;
34 +  int i,j;
35 +
36 +  for(i = 0; i < 3; i++){
37 +    for (j = 0; j < 3; j++){
38 +
39 +      eta[i][j] = 0.0;
40 +      oldEta[i][j] = 0.0;
41 +    }
42 +  }
43 +
44 +  // retrieve eta array from simInfo if it exists
45 +  data = info->getProperty(ETAVALUE_ID);
46 +  if(data != NULL){
47 +    
48 +    int test = data->getDarray(etaArray);
49 +    
50 +    if( test == 9 ){
51 +      
52 +      for(i = 0; i < 3; i++){
53 +        for (j = 0; j < 3; j++){
54 +          eta[i][j] = etaArray[3*i+j];
55 +          oldEta[i][j] = eta[i][j];
56 +        }
57 +      }    
58 +      delete[] etaArray;
59 +    }
60 +    else
61 +      std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test
62 +                << ").\n"
63 +                << "            Simulation wil proceed with eta = 0;\n";
64 +  }
65 + }
66 +
67 + NPTf::~NPTf() {
68 +
69 +  // empty for now
70 + }
71 +
72 + void NPTf::resetIntegrator() {
73 +
74    int i, j;
26 –  chi = 0.0;
75  
76 <  for(i = 0; i < 3; i++)
77 <    for (j = 0; j < 3; j++)
76 >  for(i = 0; i < 3; i++)
77 >    for (j = 0; j < 3; j++)
78        eta[i][j] = 0.0;
79  
80 <  have_tau_thermostat = 0;
33 <  have_tau_barostat = 0;
34 <  have_target_temp = 0;
35 <  have_target_pressure = 0;
80 >  NPT::resetIntegrator();
81   }
82  
83 < void NPTf::moveA() {
39 <  
40 <  int i, j, k;
41 <  DirectionalAtom* dAtom;
42 <  double Tb[3], ji[3];
43 <  double A[3][3], I[3][3];
44 <  double angle, mass;
45 <  double vel[3], pos[3], frc[3];
83 > void NPTf::evolveEtaA() {
84  
85 <  double rj[3];
48 <  double instaTemp, instaPress, instaVol;
49 <  double tt2, tb2;
50 <  double sc[3];
51 <  double eta2ij;
52 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
85 >  int i, j;
86  
87 <  tt2 = tauThermostat * tauThermostat;
88 <  tb2 = tauBarostat * tauBarostat;
87 >  for(i = 0; i < 3; i ++){
88 >    for(j = 0; j < 3; j++){
89 >      if( i == j)
90 >        eta[i][j] += dt2 *  instaVol *
91 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
92 >      else
93 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
94 >    }
95 >  }
96  
97 <  instaTemp = tStats->getTemperature();
98 <  tStats->getPressureTensor(press);
99 <  instaVol = tStats->getVolume();
100 <  
61 <  // first evolve chi a half step
62 <  
63 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
97 >  for(i = 0; i < 3; i++)
98 >    for (j = 0; j < 3; j++)
99 >      oldEta[i][j] = eta[i][j];
100 > }
101  
102 + void NPTf::evolveEtaB() {
103 +
104 +  int i,j;
105 +
106 +  for(i = 0; i < 3; i++)
107 +    for (j = 0; j < 3; j++)
108 +      prevEta[i][j] = eta[i][j];
109 +
110 +  for(i = 0; i < 3; i ++){
111 +    for(j = 0; j < 3; j++){
112 +      if( i == j) {
113 +        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
114 +          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
115 +      } else {
116 +        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
117 +      }
118 +    }
119 +  }
120 + }
121 +
122 + void NPTf::getVelScaleA(double sc[3], double vel[3]) {
123 +  int i,j;
124 +  double vScale[3][3];
125 +
126    for (i = 0; i < 3; i++ ) {
127      for (j = 0; j < 3; j++ ) {
128 <      if (i == j) {
68 <        
69 <        eta[i][j] += dt2 * instaVol *
70 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
71 <        
72 <        vScale[i][j] = eta[i][j] + chi;
73 <        
74 <      } else {
75 <        
76 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
128 >      vScale[i][j] = eta[i][j];
129  
130 <        vScale[i][j] = eta[i][j];
131 <        
130 >      if (i == j) {
131 >        vScale[i][j] += chi;
132        }
133      }
134    }
135  
136 <  for( i=0; i<nAtoms; i++ ){
136 >  info->matVecMul3( vScale, vel, sc );
137 > }
138  
139 <    atoms[i]->getVel( vel );
140 <    atoms[i]->getPos( pos );
141 <    atoms[i]->getFrc( frc );
139 > void NPTf::getVelScaleB(double sc[3], int index ){
140 >  int i,j;
141 >  double myVel[3];
142 >  double vScale[3][3];
143  
144 <    mass = atoms[i]->getMass();
145 <    
146 <    // velocity half step
147 <        
148 <    info->matVecMul3( vScale, vel, sc );
149 <    
150 <    for (j = 0; j < 3; j++) {
151 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
152 <      rj[j] = pos[j];
144 > //   std::cerr << "velScaleB chi = " << chi << "\n";
145 >
146 >  for (i = 0; i < 3; i++ ) {
147 >    for (j = 0; j < 3; j++ ) {
148 >      vScale[i][j] = eta[i][j];
149 >
150 >      if (i == j) {
151 >        vScale[i][j] += chi;
152 >      }
153      }
154 +  }
155  
156 <    atoms[i]->setVel( vel );
156 >  for (j = 0; j < 3; j++)
157 >    myVel[j] = oldVel[3*index + j];
158  
159 <    // position whole step    
159 > //   std::cerr << "velScaleB = \n"
160 > //          << "[ " << vScale[0][0] << " , " << vScale[0][1] << " , " << vScale[0][2] << "]\n"
161 > //          << "[ " << vScale[1][0] << " , " << vScale[1][1] << " , " << vScale[1][2] << "]\n"
162 > //          << "[ " << vScale[2][0] << " , " << vScale[2][1] << " , " << vScale[2][2] << "]\n\n";
163  
105 –    info->wrapVector(rj);
164  
165 <    info->matVecMul3( eta, rj, sc );
165 > //  std::cerr << "myVel " << index << " in => "
166 > //          << myVel[0] << ", " << myVel[1] << ", " << myVel[2] << "\n";
167  
168 <    for (j = 0; j < 3; j++ )
110 <      pos[j] += dt * (vel[j] + sc[j]);
111 <  
112 <    if( atoms[i]->isDirectional() ){
168 >  info->matVecMul3( vScale, myVel, sc );
169  
170 <      dAtom = (DirectionalAtom *)atoms[i];
171 <          
172 <      // get and convert the torque to body frame
117 <      
118 <      dAtom->getTrq( Tb );
119 <      dAtom->lab2Body( Tb );
120 <      
121 <      // get the angular momentum, and propagate a half step
170 > //  std::cerr << "sc " << index << " out => "
171 > //          << sc[0] << ", " << sc[1] << ", " << sc[2] << "\n";
172 > }
173  
174 <      dAtom->getJ( ji );
174 > void NPTf::getPosScale(double pos[3], double COM[3],
175 >                                               int index, double sc[3]){
176 >  int j;
177 >  double rj[3];
178  
179 <      for (j=0; j < 3; j++)
180 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
127 <      
128 <      // use the angular velocities to propagate the rotation matrix a
129 <      // full time step
179 >  for(j=0; j<3; j++)
180 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
181  
182 <      dAtom->getA(A);
183 <      dAtom->getI(I);
133 <    
134 <      // rotate about the x-axis      
135 <      angle = dt2 * ji[0] / I[0][0];
136 <      this->rotate( 1, 2, angle, ji, A );
182 >  info->matVecMul3( eta, rj, sc );
183 > }
184  
185 <      // rotate about the y-axis
186 <      angle = dt2 * ji[1] / I[1][1];
187 <      this->rotate( 2, 0, angle, ji, A );
188 <      
189 <      // rotate about the z-axis
190 <      angle = dt * ji[2] / I[2][2];
191 <      this->rotate( 0, 1, angle, ji, A);
192 <      
193 <      // rotate about the y-axis
194 <      angle = dt2 * ji[1] / I[1][1];
148 <      this->rotate( 2, 0, angle, ji, A );
149 <      
150 <       // rotate about the x-axis
151 <      angle = dt2 * ji[0] / I[0][0];
152 <      this->rotate( 1, 2, angle, ji, A );
153 <      
154 <      dAtom->setJ( ji );
155 <      dAtom->setA( A  );    
156 <    }                    
157 <  }
158 <  
185 > void NPTf::scaleSimBox( void ){
186 >
187 >  int i,j,k;
188 >  double scaleMat[3][3];
189 >  double eta2ij;
190 >  double bigScale, smallScale, offDiagMax;
191 >  double hm[3][3], hmnew[3][3];
192 >
193 >
194 >
195    // Scale the box after all the positions have been moved:
196 <  
196 >
197    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
198    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
199 <  
200 <  
199 >
200 >  bigScale = 1.0;
201 >  smallScale = 1.0;
202 >  offDiagMax = 0.0;
203 >
204    for(i=0; i<3; i++){
205      for(j=0; j<3; j++){
206 <      
206 >
207        // Calculate the matrix Product of the eta array (we only need
208        // the ij element right now):
209 <      
209 >
210        eta2ij = 0.0;
211        for(k=0; k<3; k++){
212          eta2ij += eta[i][k] * eta[k][j];
213        }
214 <      
214 >
215        scaleMat[i][j] = 0.0;
216        // identity matrix (see above):
217        if (i == j) scaleMat[i][j] = 1.0;
218        // Taylor expansion for the exponential truncated at second order:
219        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
220 <      
220 >
221 >      if (i != j)
222 >        if (fabs(scaleMat[i][j]) > offDiagMax)
223 >          offDiagMax = fabs(scaleMat[i][j]);
224      }
225 +
226 +    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
227 +    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
228    }
229 <  
230 <  info->getBoxM(hm);
231 <  info->matMul3(hm, scaleMat, hmnew);
232 <  info->setBoxM(hmnew);
233 <  
229 >
230 >  if ((bigScale > 1.1) || (smallScale < 0.9)) {
231 >    sprintf( painCave.errMsg,
232 >             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
233 >             " Check your tauBarostat, as it is probably too small!\n\n"
234 >             " scaleMat = [%lf\t%lf\t%lf]\n"
235 >             "            [%lf\t%lf\t%lf]\n"
236 >             "            [%lf\t%lf\t%lf]\n",
237 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
238 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
239 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
240 >    painCave.isFatal = 1;
241 >    simError();
242 >  } else if (offDiagMax > 0.1) {
243 >    sprintf( painCave.errMsg,
244 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
245 >             " Check your tauBarostat, as it is probably too small!\n\n"
246 >             " scaleMat = [%lf\t%lf\t%lf]\n"
247 >             "            [%lf\t%lf\t%lf]\n"
248 >             "            [%lf\t%lf\t%lf]\n",
249 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
250 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
251 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
252 >    painCave.isFatal = 1;
253 >    simError();
254 >  } else {
255 >    info->getBoxM(hm);
256 >    info->matMul3(hm, scaleMat, hmnew);
257 >    info->setBoxM(hmnew);
258 >  }
259   }
260  
261 < void NPTf::moveB( void ){
261 > bool NPTf::etaConverged() {
262 >  int i;
263 >  double diffEta, sumEta;
264  
265 <  int i, j;
266 <  DirectionalAtom* dAtom;
267 <  double Tb[3], ji[3];
196 <  double vel[3], frc[3];
197 <  double mass;
265 >  sumEta = 0;
266 >  for(i = 0; i < 3; i++)
267 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
268  
269 <  double instaTemp, instaPress, instaVol;
200 <  double tt2, tb2;
201 <  double sc[3];
202 <  double press[3][3], vScale[3][3];
203 <  
204 <  tt2 = tauThermostat * tauThermostat;
205 <  tb2 = tauBarostat * tauBarostat;
269 >  diffEta = sqrt( sumEta / 3.0 );
270  
271 <  instaTemp = tStats->getTemperature();
272 <  tStats->getPressureTensor(press);
209 <  instaVol = tStats->getVolume();
210 <  
211 <  // first evolve chi a half step
212 <  
213 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
214 <  
215 <  for (i = 0; i < 3; i++ ) {
216 <    for (j = 0; j < 3; j++ ) {
217 <      if (i == j) {
271 >  return ( diffEta <= etaTolerance );
272 > }
273  
274 <        eta[i][j] += dt2 * instaVol *
220 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
274 > double NPTf::getConservedQuantity(void){
275  
276 <        vScale[i][j] = eta[i][j] + chi;
277 <        
278 <      } else {
279 <        
280 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
276 >  double conservedQuantity;
277 >  double totalEnergy;
278 >  double thermostat_kinetic;
279 >  double thermostat_potential;
280 >  double barostat_kinetic;
281 >  double barostat_potential;
282 >  double trEta;
283 >  double a[3][3], b[3][3];
284  
285 <        vScale[i][j] = eta[i][j];
229 <        
230 <      }
231 <    }
232 <  }
285 >  totalEnergy = tStats->getTotalE();
286  
287 <  for( i=0; i<nAtoms; i++ ){
287 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
288 >    (2.0 * eConvert);
289  
290 <    atoms[i]->getVel( vel );
237 <    atoms[i]->getFrc( frc );
290 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
291  
292 <    mass = atoms[i]->getMass();
293 <    
294 <    // velocity half step
242 <        
243 <    info->matVecMul3( vScale, vel, sc );
244 <    
245 <    for (j = 0; j < 3; j++) {
246 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
247 <    }
292 >  info->transposeMat3(eta, a);
293 >  info->matMul3(a, eta, b);
294 >  trEta = info->matTrace3(b);
295  
296 <    atoms[i]->setVel( vel );
297 <    
251 <    if( atoms[i]->isDirectional() ){
296 >  barostat_kinetic = NkBT * tb2 * trEta /
297 >    (2.0 * eConvert);
298  
299 <      dAtom = (DirectionalAtom *)atoms[i];
300 <          
255 <      // get and convert the torque to body frame
256 <      
257 <      dAtom->getTrq( Tb );
258 <      dAtom->lab2Body( Tb );
259 <      
260 <      // get the angular momentum, and propagate a half step
261 <      
262 <      dAtom->getJ( ji );
263 <      
264 <      for (j=0; j < 3; j++)
265 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
266 <      
267 <      dAtom->setJ( ji );
299 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
300 >    eConvert;
301  
302 <    }                    
303 <  }
271 < }
302 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
303 >    barostat_kinetic + barostat_potential;
304  
305 < int NPTf::readyCheck() {
306 <
275 <  // First check to see if we have a target temperature.
276 <  // Not having one is fatal.
277 <  
278 <  if (!have_target_temp) {
279 <    sprintf( painCave.errMsg,
280 <             "NPTf error: You can't use the NPTf integrator\n"
281 <             "   without a targetTemp!\n"
282 <             );
283 <    painCave.isFatal = 1;
284 <    simError();
285 <    return -1;
286 <  }
305 > //   cout.width(8);
306 > //   cout.precision(8);
307  
308 <  if (!have_target_pressure) {
309 <    sprintf( painCave.errMsg,
310 <             "NPTf error: You can't use the NPTf integrator\n"
291 <             "   without a targetPressure!\n"
292 <             );
293 <    painCave.isFatal = 1;
294 <    simError();
295 <    return -1;
296 <  }
297 <  
298 <  // We must set tauThermostat.
299 <  
300 <  if (!have_tau_thermostat) {
301 <    sprintf( painCave.errMsg,
302 <             "NPTf error: If you use the NPTf\n"
303 <             "   integrator, you must set tauThermostat.\n");
304 <    painCave.isFatal = 1;
305 <    simError();
306 <    return -1;
307 <  }    
308 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
309 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
310 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
311  
312 <  // We must set tauBarostat.
310 <  
311 <  if (!have_tau_barostat) {
312 <    sprintf( painCave.errMsg,
313 <             "NPTf error: If you use the NPTf\n"
314 <             "   integrator, you must set tauBarostat.\n");
315 <    painCave.isFatal = 1;
316 <    simError();
317 <    return -1;
318 <  }    
312 >  return conservedQuantity;
313  
314 <  // We need NkBT a lot, so just set it here:
314 > }
315  
316 <  NkBT = (double)info->ndf * kB * targetTemp;
316 > char* NPTf::getAdditionalParameters(void){
317  
318 <  return 1;
318 >  sprintf(addParamBuffer,
319 >          "\t%G\t%G;"
320 >          "\t%G\t%G\t%G;"
321 >          "\t%G\t%G\t%G;"
322 >          "\t%G\t%G\t%G;",
323 >          chi, integralOfChidt,
324 >          eta[0][0], eta[0][1], eta[0][2],
325 >          eta[1][0], eta[1][1], eta[1][2],
326 >          eta[2][0], eta[2][1], eta[2][2]
327 >          );
328 >
329 >  return addParamBuffer;
330   }

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