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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 590 by mmeineke, Thu Jul 10 22:15:53 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 <  int atomIndex, aMatIndex;
42 <  DirectionalAtom* dAtom;
43 <  double Tb[3];
44 <  double ji[3];
45 <  double ri[3], vi[3], sc[3];
46 <  double instaTemp, instaVol;
47 <  double tt2, tb2, eta2ij;
48 <  double angle;
49 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
83 > void NPTf::evolveEtaA() {
84  
85 <  tt2 = tauThermostat * tauThermostat;
52 <  tb2 = tauBarostat * tauBarostat;
85 >  int i, j;
86  
87 <  instaTemp = tStats->getTemperature();
88 <  tStats->getPressureTensor(press);
89 <  instaVol = tStats->getVolume();
90 <  
91 <  // first evolve chi a half step
92 <  
93 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
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 +  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 +      vScale[i][j] = eta[i][j];
129 +
130        if (i == j) {
131 +        vScale[i][j] += chi;
132 +      }
133 +    }
134 +  }
135  
136 <        eta[i][j] += dt2 * instaVol *
137 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
136 >  info->matVecMul3( vScale, vel, sc );
137 > }
138  
139 <        vScale[i][j] = eta[i][j] + chi;
140 <        
141 <      } else {
142 <        
73 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
139 > void NPTf::getVelScaleB(double sc[3], int index ){
140 >  int i,j;
141 >  double myVel[3];
142 >  double vScale[3][3];
143  
144 <        vScale[i][j] = eta[i][j];
145 <        
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 <  for( i=0; i<nAtoms; i++ ){
157 <    atomIndex = i * 3;
83 <    aMatIndex = i * 9;
84 <    
85 <    // velocity half step
86 <    
87 <    vi[0] = vel[atomIndex];
88 <    vi[1] = vel[atomIndex+1];
89 <    vi[2] = vel[atomIndex+2];
90 <    
91 <    info->matVecMul3( vScale, vi, sc );
92 <    
93 <    vi[0] += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - sc[0]);
94 <    vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]);
95 <    vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]);
156 >  for (j = 0; j < 3; j++)
157 >    myVel[j] = oldVel[3*index + j];
158  
159 <    vel[atomIndex]   = vi[0];
160 <    vel[atomIndex+1] = vi[1];
161 <    vel[atomIndex+2] = vi[2];
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  
101 –    // position whole step    
164  
165 <    ri[0] = pos[atomIndex];
166 <    ri[1] = pos[atomIndex+1];
105 <    ri[2] = pos[atomIndex+2];
165 > //  std::cerr << "myVel " << index << " in => "
166 > //          << myVel[0] << ", " << myVel[1] << ", " << myVel[2] << "\n";
167  
168 <    info->wrapVector(ri);
168 >  info->matVecMul3( vScale, myVel, sc );
169  
170 <    info->matVecMul3( eta, ri, sc );
170 > //  std::cerr << "sc " << index << " out => "
171 > //          << sc[0] << ", " << sc[1] << ", " << sc[2] << "\n";
172 > }
173  
174 <    pos[atomIndex]   += dt * (vel[atomIndex] + sc[0]);
175 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]);
176 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]);
177 <  
115 <    if( atoms[i]->isDirectional() ){
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 <      dAtom = (DirectionalAtom *)atoms[i];
180 <          
119 <      // get and convert the torque to body frame
120 <      
121 <      Tb[0] = dAtom->getTx();
122 <      Tb[1] = dAtom->getTy();
123 <      Tb[2] = dAtom->getTz();
124 <      
125 <      dAtom->lab2Body( Tb );
126 <      
127 <      // get the angular momentum, and propagate a half step
179 >  for(j=0; j<3; j++)
180 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
181  
182 <      ji[0] = dAtom->getJx();
183 <      ji[1] = dAtom->getJy();
131 <      ji[2] = dAtom->getJz();
132 <      
133 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
134 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
135 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
136 <      
137 <      // use the angular velocities to propagate the rotation matrix a
138 <      // full time step
139 <      
140 <      // rotate about the x-axis      
141 <      angle = dt2 * ji[0] / dAtom->getIxx();
142 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
143 <      
144 <      // rotate about the y-axis
145 <      angle = dt2 * ji[1] / dAtom->getIyy();
146 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
147 <      
148 <      // rotate about the z-axis
149 <      angle = dt * ji[2] / dAtom->getIzz();
150 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
151 <      
152 <      // rotate about the y-axis
153 <      angle = dt2 * ji[1] / dAtom->getIyy();
154 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
155 <      
156 <       // rotate about the x-axis
157 <      angle = dt2 * ji[0] / dAtom->getIxx();
158 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
159 <      
160 <      dAtom->setJx( ji[0] );
161 <      dAtom->setJy( ji[1] );
162 <      dAtom->setJz( ji[2] );
163 <    }
164 <    
165 <  }
182 >  info->matVecMul3( eta, rj, sc );
183 > }
184  
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  
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 +  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++){
# Line 180 | Line 211 | void NPTf::moveA() {
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  
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 ){
262 <  int i,j, k;
263 <  int atomIndex;
202 <  DirectionalAtom* dAtom;
203 <  double Tb[3];
204 <  double ji[3];
205 <  double vi[3], sc[3];
206 <  double instaTemp, instaVol;
207 <  double tt2, tb2;
208 <  double press[3][3], vScale[3][3];
209 <  
210 <  tt2 = tauThermostat * tauThermostat;
211 <  tb2 = tauBarostat * tauBarostat;
261 > bool NPTf::etaConverged() {
262 >  int i;
263 >  double diffEta, sumEta;
264  
265 <  instaTemp = tStats->getTemperature();
266 <  tStats->getPressureTensor(press);
267 <  instaVol = tStats->getVolume();
216 <  
217 <  // first evolve chi a half step
218 <  
219 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
220 <  
221 <  for (i = 0; i < 3; i++ ) {
222 <    for (j = 0; j < 3; j++ ) {
223 <      if (i == j) {
265 >  sumEta = 0;
266 >  for(i = 0; i < 3; i++)
267 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
268  
269 <        eta[i][j] += dt2 * instaVol *
226 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
269 >  diffEta = sqrt( sumEta / 3.0 );
270  
271 <        vScale[i][j] = eta[i][j] + chi;
272 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
271 >  return ( diffEta <= etaTolerance );
272 > }
273  
274 <        vScale[i][j] = eta[i][j];
235 <        
236 <      }
237 <    }
238 <  }
274 > double NPTf::getConservedQuantity(void){
275  
276 <  for( i=0; i<nAtoms; i++ ){
277 <    atomIndex = i * 3;
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 <    // velocity half step
244 <    
245 <    vi[0] = vel[atomIndex];
246 <    vi[1] = vel[atomIndex+1];
247 <    vi[2] = vel[atomIndex+2];
248 <    
249 <    info->matVecMul3( vScale, vi, sc );
250 <    
251 <    vi[0] += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - sc[0]);
252 <    vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]);
253 <    vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]);
285 >  totalEnergy = tStats->getTotalE();
286  
287 <    vel[atomIndex]   = vi[0];
288 <    vel[atomIndex+1] = vi[1];
257 <    vel[atomIndex+2] = vi[2];
258 <    
259 <    if( atoms[i]->isDirectional() ){
260 <      
261 <      dAtom = (DirectionalAtom *)atoms[i];
262 <      
263 <      // get and convert the torque to body frame
264 <      
265 <      Tb[0] = dAtom->getTx();
266 <      Tb[1] = dAtom->getTy();
267 <      Tb[2] = dAtom->getTz();
268 <      
269 <      dAtom->lab2Body( Tb );
270 <      
271 <      // get the angular momentum, and complete the angular momentum
272 <      // half step
273 <      
274 <      ji[0] = dAtom->getJx();
275 <      ji[1] = dAtom->getJy();
276 <      ji[2] = dAtom->getJz();
277 <      
278 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
279 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
280 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
281 <      
282 <      dAtom->setJx( ji[0] );
283 <      dAtom->setJy( ji[1] );
284 <      dAtom->setJz( ji[2] );
285 <    }
286 <  }
287 < }
287 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
288 >    (2.0 * eConvert);
289  
290 < int NPTf::readyCheck() {
290 <
291 <  // First check to see if we have a target temperature.
292 <  // Not having one is fatal.
293 <  
294 <  if (!have_target_temp) {
295 <    sprintf( painCave.errMsg,
296 <             "NPTf error: You can't use the NPTf integrator\n"
297 <             "   without a targetTemp!\n"
298 <             );
299 <    painCave.isFatal = 1;
300 <    simError();
301 <    return -1;
302 <  }
290 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
291  
292 <  if (!have_target_pressure) {
293 <    sprintf( painCave.errMsg,
294 <             "NPTf error: You can't use the NPTf integrator\n"
307 <             "   without a targetPressure!\n"
308 <             );
309 <    painCave.isFatal = 1;
310 <    simError();
311 <    return -1;
312 <  }
313 <  
314 <  // We must set tauThermostat.
315 <  
316 <  if (!have_tau_thermostat) {
317 <    sprintf( painCave.errMsg,
318 <             "NPTf error: If you use the NPTf\n"
319 <             "   integrator, you must set tauThermostat.\n");
320 <    painCave.isFatal = 1;
321 <    simError();
322 <    return -1;
323 <  }    
292 >  info->transposeMat3(eta, a);
293 >  info->matMul3(a, eta, b);
294 >  trEta = info->matTrace3(b);
295  
296 <  // We must set tauBarostat.
297 <  
327 <  if (!have_tau_barostat) {
328 <    sprintf( painCave.errMsg,
329 <             "NPTf error: If you use the NPTf\n"
330 <             "   integrator, you must set tauBarostat.\n");
331 <    painCave.isFatal = 1;
332 <    simError();
333 <    return -1;
334 <  }    
296 >  barostat_kinetic = NkBT * tb2 * trEta /
297 >    (2.0 * eConvert);
298  
299 <  // We need NkBT a lot, so just set it here:
299 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
300 >    eConvert;
301  
302 <  NkBT = (double)info->ndf * kB * targetTemp;
302 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
303 >    barostat_kinetic + barostat_potential;
304  
305 <  return 1;
305 > //   cout.width(8);
306 > //   cout.precision(8);
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 >  return conservedQuantity;
313 >
314   }
315 +
316 + char* NPTf::getAdditionalParameters(void){
317 +
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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