ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/branches/new-templateless/OOPSE/libmdtools/NPTf.cpp
(Generate patch)

Comparing:
trunk/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 852 by mmeineke, Thu Nov 6 18:20:47 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
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 7 | 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 < template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
30 <  T( theInfo, the_ff )
29 > NPTf::NPTf ( SimInfo *theInfo, ForceFields* 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;
27 –  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;
34 <  have_tau_barostat = 0;
35 <  have_target_temp = 0;
36 <  have_target_pressure = 0;
80 >  NPT::resetIntegrator();
81   }
82  
83 < template<typename T> void NPTf<T>::moveA() {
40 <  
41 <  int i, j, k;
42 <  DirectionalAtom* dAtom;
43 <  double Tb[3], ji[3];
44 <  double A[3][3], I[3][3];
45 <  double angle, mass;
46 <  double vel[3], pos[3], frc[3];
83 > void NPTf::evolveEtaA() {
84  
85 <  double rj[3];
49 <  double instaTemp, instaPress, instaVol;
50 <  double tt2, tb2;
51 <  double sc[3];
52 <  double eta2ij;
53 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
54 <  double bigScale, smallScale, offDiagMax;
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 <  
63 <  // first evolve chi a half step
64 <  
65 <  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) {
70 <        
71 <        eta[i][j] += dt2 * instaVol *
72 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
73 <        
74 <        vScale[i][j] = eta[i][j] + chi;
75 <        
76 <      } else {
77 <        
78 <        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 >  info->matVecMul3( vScale, myVel, sc );
160 > }
161  
162 <    info->wrapVector(rj);
162 > void NPTf::getPosScale(double pos[3], double COM[3],
163 >                       int index, double sc[3]){
164 >  int j;
165 >  double rj[3];
166  
167 <    info->matVecMul3( eta, rj, sc );
167 >  for(j=0; j<3; j++)
168 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
169  
170 <    for (j = 0; j < 3; j++ )
171 <      pos[j] += dt * (vel[j] + sc[j]);
170 >  info->matVecMul3( eta, rj, sc );
171 > }
172  
173 <    atoms[i]->setPos( pos );
115 <  
116 <    if( atoms[i]->isDirectional() ){
173 > void NPTf::scaleSimBox( void ){
174  
175 <      dAtom = (DirectionalAtom *)atoms[i];
176 <          
177 <      // get and convert the torque to body frame
178 <      
179 <      dAtom->getTrq( Tb );
123 <      dAtom->lab2Body( Tb );
124 <      
125 <      // get the angular momentum, and propagate a half step
175 >  int i,j,k;
176 >  double scaleMat[3][3];
177 >  double eta2ij;
178 >  double bigScale, smallScale, offDiagMax;
179 >  double hm[3][3], hmnew[3][3];
180  
127 –      dAtom->getJ( ji );
181  
129 –      for (j=0; j < 3; j++)
130 –        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
131 –      
132 –      // use the angular velocities to propagate the rotation matrix a
133 –      // full time step
182  
183 <      dAtom->getA(A);
136 <      dAtom->getI(I);
137 <    
138 <      // rotate about the x-axis      
139 <      angle = dt2 * ji[0] / I[0][0];
140 <      this->rotate( 1, 2, angle, ji, A );
183 >  // Scale the box after all the positions have been moved:
184  
142 –      // rotate about the y-axis
143 –      angle = dt2 * ji[1] / I[1][1];
144 –      this->rotate( 2, 0, angle, ji, A );
145 –      
146 –      // rotate about the z-axis
147 –      angle = dt * ji[2] / I[2][2];
148 –      this->rotate( 0, 1, angle, ji, A);
149 –      
150 –      // rotate about the y-axis
151 –      angle = dt2 * ji[1] / I[1][1];
152 –      this->rotate( 2, 0, angle, ji, A );
153 –      
154 –       // rotate about the x-axis
155 –      angle = dt2 * ji[0] / I[0][0];
156 –      this->rotate( 1, 2, angle, ji, A );
157 –      
158 –      dAtom->setJ( ji );
159 –      dAtom->setA( A  );    
160 –    }                    
161 –  }
162 –  
163 –  // Scale the box after all the positions have been moved:
164 –  
185    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
186    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
187 <  
187 >
188    bigScale = 1.0;
189    smallScale = 1.0;
190    offDiagMax = 0.0;
191 <  
191 >
192    for(i=0; i<3; i++){
193      for(j=0; j<3; j++){
194 <      
194 >
195        // Calculate the matrix Product of the eta array (we only need
196        // the ij element right now):
197 <      
197 >
198        eta2ij = 0.0;
199        for(k=0; k<3; k++){
200          eta2ij += eta[i][k] * eta[k][j];
201        }
202 <      
202 >
203        scaleMat[i][j] = 0.0;
204        // identity matrix (see above):
205        if (i == j) scaleMat[i][j] = 1.0;
# Line 187 | Line 207 | template<typename T> void NPTf<T>::moveA() {
207        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
208  
209        if (i != j)
210 <        if (fabs(scaleMat[i][j]) > offDiagMax)
210 >        if (fabs(scaleMat[i][j]) > offDiagMax)
211            offDiagMax = fabs(scaleMat[i][j]);
192 –      
212      }
213  
214      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
215      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
216    }
217 <  
218 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
217 >
218 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
219      sprintf( painCave.errMsg,
220 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
220 >             "NPTf error: Attempting a 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 208 | Line 227 | template<typename T> void NPTf<T>::moveA() {
227               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
228      painCave.isFatal = 1;
229      simError();
230 <  } else if (offDiagMax > 0.1) {
230 >  } else if (offDiagMax > 0.01) {
231      sprintf( painCave.errMsg,
232 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
232 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 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"
# Line 225 | Line 244 | template<typename T> void NPTf<T>::moveA() {
244      info->matMul3(hm, scaleMat, hmnew);
245      info->setBoxM(hmnew);
246    }
228 –  
247   }
248  
249 < template<typename T> void NPTf<T>::moveB( void ){
249 > bool NPTf::etaConverged() {
250 >  int i;
251 >  double diffEta, sumEta;
252  
253 <  int i, j;
254 <  DirectionalAtom* dAtom;
255 <  double Tb[3], ji[3];
236 <  double vel[3], frc[3];
237 <  double mass;
253 >  sumEta = 0;
254 >  for(i = 0; i < 3; i++)
255 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
256  
257 <  double instaTemp, instaPress, instaVol;
240 <  double tt2, tb2;
241 <  double sc[3];
242 <  double press[3][3], vScale[3][3];
243 <  
244 <  tt2 = tauThermostat * tauThermostat;
245 <  tb2 = tauBarostat * tauBarostat;
257 >  diffEta = sqrt( sumEta / 3.0 );
258  
259 <  instaTemp = tStats->getTemperature();
260 <  tStats->getPressureTensor(press);
249 <  instaVol = tStats->getVolume();
250 <  
251 <  // first evolve chi a half step
252 <  
253 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
254 <  
255 <  for (i = 0; i < 3; i++ ) {
256 <    for (j = 0; j < 3; j++ ) {
257 <      if (i == j) {
259 >  return ( diffEta <= etaTolerance );
260 > }
261  
262 <        eta[i][j] += dt2 * instaVol *
260 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
262 > double NPTf::getConservedQuantity(void){
263  
264 <        vScale[i][j] = eta[i][j] + chi;
265 <        
266 <      } else {
267 <        
268 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
264 >  double conservedQuantity;
265 >  double totalEnergy;
266 >  double thermostat_kinetic;
267 >  double thermostat_potential;
268 >  double barostat_kinetic;
269 >  double barostat_potential;
270 >  double trEta;
271 >  double a[3][3], b[3][3];
272  
273 <        vScale[i][j] = eta[i][j];
269 <        
270 <      }
271 <    }
272 <  }
273 >  totalEnergy = tStats->getTotalE();
274  
275 <  for( i=0; i<nAtoms; i++ ){
275 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
276 >    (2.0 * eConvert);
277  
278 <    atoms[i]->getVel( vel );
277 <    atoms[i]->getFrc( frc );
278 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
279  
280 <    mass = atoms[i]->getMass();
281 <    
282 <    // velocity half step
282 <        
283 <    info->matVecMul3( vScale, vel, sc );
284 <    
285 <    for (j = 0; j < 3; j++) {
286 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
287 <    }
280 >  info->transposeMat3(eta, a);
281 >  info->matMul3(a, eta, b);
282 >  trEta = info->matTrace3(b);
283  
284 <    atoms[i]->setVel( vel );
285 <    
291 <    if( atoms[i]->isDirectional() ){
284 >  barostat_kinetic = NkBT * tb2 * trEta /
285 >    (2.0 * eConvert);
286  
287 <      dAtom = (DirectionalAtom *)atoms[i];
288 <          
295 <      // get and convert the torque to body frame
296 <      
297 <      dAtom->getTrq( Tb );
298 <      dAtom->lab2Body( Tb );
299 <      
300 <      // get the angular momentum, and propagate a half step
301 <      
302 <      dAtom->getJ( ji );
303 <      
304 <      for (j=0; j < 3; j++)
305 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
306 <      
307 <      dAtom->setJ( ji );
287 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
288 >    eConvert;
289  
290 <    }                    
291 <  }
311 < }
290 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
291 >    barostat_kinetic + barostat_potential;
292  
293 < template<typename T> int NPTf<T>::readyCheck() {
314 <
315 <  // First check to see if we have a target temperature.
316 <  // Not having one is fatal.
317 <  
318 <  if (!have_target_temp) {
319 <    sprintf( painCave.errMsg,
320 <             "NPTf error: You can't use the NPTf integrator\n"
321 <             "   without a targetTemp!\n"
322 <             );
323 <    painCave.isFatal = 1;
324 <    simError();
325 <    return -1;
326 <  }
293 >  return conservedQuantity;
294  
295 <  if (!have_target_pressure) {
329 <    sprintf( painCave.errMsg,
330 <             "NPTf error: You can't use the NPTf integrator\n"
331 <             "   without a targetPressure!\n"
332 <             );
333 <    painCave.isFatal = 1;
334 <    simError();
335 <    return -1;
336 <  }
337 <  
338 <  // We must set tauThermostat.
339 <  
340 <  if (!have_tau_thermostat) {
341 <    sprintf( painCave.errMsg,
342 <             "NPTf error: If you use the NPTf\n"
343 <             "   integrator, you must set tauThermostat.\n");
344 <    painCave.isFatal = 1;
345 <    simError();
346 <    return -1;
347 <  }    
295 > }
296  
297 <  // We must set tauBarostat.
350 <  
351 <  if (!have_tau_barostat) {
352 <    sprintf( painCave.errMsg,
353 <             "NPTf error: If you use the NPTf\n"
354 <             "   integrator, you must set tauBarostat.\n");
355 <    painCave.isFatal = 1;
356 <    simError();
357 <    return -1;
358 <  }    
297 > char* NPTf::getAdditionalParameters(void){
298  
299 <  // We need NkBT a lot, so just set it here:
299 >  sprintf(addParamBuffer,
300 >          "\t%G\t%G;"
301 >          "\t%G\t%G\t%G;"
302 >          "\t%G\t%G\t%G;"
303 >          "\t%G\t%G\t%G;",
304 >          chi, integralOfChidt,
305 >          eta[0][0], eta[0][1], eta[0][2],
306 >          eta[1][0], eta[1][1], eta[1][2],
307 >          eta[2][0], eta[2][1], eta[2][2]
308 >          );
309  
310 <  NkBT = (double)info->ndf * kB * targetTemp;
363 <
364 <  return 1;
310 >  return addParamBuffer;
311   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines