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Comparing trunk/OOPSE/libmdtools/ExtendedSystem.cpp (file contents):
Revision 468 by gezelter, Mon Apr 7 16:56:38 2003 UTC vs.
Revision 488 by gezelter, Thu Apr 10 16:35:31 2003 UTC

# Line 4 | Line 4
4   #include "SimInfo.hpp"
5   #include "Thermo.hpp"
6   #include "ExtendedSystem.hpp"
7 + #include "simError.h"
8  
9   ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
10  
11    // get what information we need from the SimInfo object
12    
13    entry_plug = the_entry_plug;
13 –  nAtoms = entry_plug->n_atoms;
14 –  atoms = entry_plug->atoms;
15 –  nMols = entry_plug->n_mol;
16 –  molecules = entry_plug->molecules;
17 –  nOriented = entry_plug->n_oriented;
18 –  ndf = entry_plug->ndf;
14    zeta = 0.0;
15    epsilonDot = 0.0;
16 +  epsilonDotX = 0.0;
17 +  epsilonDotY = 0.0;
18 +  epsilonDotZ = 0.0;  
19 +  have_tau_thermostat = 0;
20 +  have_tau_barostat = 0;
21 +  have_target_temp = 0;
22 +  have_target_pressure = 0;
23 +  have_qmass = 0;
24  
25   }
26  
# Line 33 | Line 36 | void ExtendedSystem::NoseHooverNVT( double dt, double
36                                          // amu*Ang^2*fs^-2/K
37    DirectionalAtom* dAtom;    
38  
39 <  ke_temp = ke * e_convert;
37 <  NkBT = (double)ndf * kB * targetTemp;
39 >  if (this->NVTready()) {
40  
41 <  // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
40 <  // qmass is set in the parameter file
41 <
42 <  zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
43 <  zetaScale = zeta * dt;
44 <
45 <  // perform thermostat scaling on linear velocities and angular momentum
46 <  for(i = 0; i < nAtoms; i++){
41 >    atoms = entry_plug->atoms;
42      
43 <    vx = atoms[i]->get_vx();
44 <    vy = atoms[i]->get_vy();
50 <    vz = atoms[i]->get_vz();
43 >    ke_temp = ke * e_convert;
44 >    NkBT = (double)entry_plug->ndf * kB * targetTemp;
45      
46 <    atoms[i]->set_vx(vx * (1.0 - zetaScale));
47 <    atoms[i]->set_vy(vy * (1.0 - zetaScale));
54 <    atoms[i]->set_vz(vz * (1.0 - zetaScale));
55 <  }
56 <  if( nOriented ){
46 >    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
47 >    // qmass is set in the parameter file
48      
49 <    for( i=0; i < nAtoms; i++ ){
49 >    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
50 >    
51 >    zetaScale = zeta * dt;
52 >    
53 >    //std::cerr << "zetaScale = " << zetaScale << "\n";
54 >    
55 >    // perform thermostat scaling on linear velocities and angular momentum
56 >    for(i = 0; i < entry_plug->n_atoms; i++){
57        
58 <      if( atoms[i]->isDirectional() ){
59 <        
60 <        dAtom = (DirectionalAtom *)atoms[i];
58 >      vx = atoms[i]->get_vx();
59 >      vy = atoms[i]->get_vy();
60 >      vz = atoms[i]->get_vz();
61 >      
62 >      atoms[i]->set_vx(vx * (1.0 - zetaScale));
63 >      atoms[i]->set_vy(vy * (1.0 - zetaScale));
64 >      atoms[i]->set_vz(vz * (1.0 - zetaScale));
65 >    }
66 >    if( entry_plug->n_oriented ){
67 >      
68 >      for( i=0; i < entry_plug->n_atoms; i++ ){
69          
70 <        jx = dAtom->getJx();
71 <        jy = dAtom->getJy();
72 <        jz = dAtom->getJz();
73 <        
74 <        dAtom->setJx(jx * (1.0 - zetaScale));
75 <        dAtom->setJy(jy * (1.0 - zetaScale));
76 <        dAtom->setJz(jz * (1.0 - zetaScale));
77 <      }
78 <    }  
70 >        if( atoms[i]->isDirectional() ){
71 >          
72 >          dAtom = (DirectionalAtom *)atoms[i];
73 >          
74 >          jx = dAtom->getJx();
75 >          jy = dAtom->getJy();
76 >          jz = dAtom->getJz();
77 >          
78 >          dAtom->setJx(jx * (1.0 - zetaScale));
79 >          dAtom->setJy(jy * (1.0 - zetaScale));
80 >          dAtom->setJz(jz * (1.0 - zetaScale));
81 >        }
82 >      }
83 >    }
84    }
85   }
86  
87  
88   void ExtendedSystem::NoseHooverAndersonNPT( double dt,
89                                              double ke,
90 <                                            double p_int ) {
90 >                                            double p_tensor[9] ) {
91  
92    // Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
93    // Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
# Line 88 | Line 99 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
99    const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
100                                          // amu*Ang^2*fs^-2/K
101  
102 +  int i;
103    double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
104    double volume, p_mol;
105    double vx, vy, vz, jx, jy, jz;
106    DirectionalAtom* dAtom;
95 –  int i;
107  
108 <  p_ext = targetPressure * p_units;
109 <  p_mol = p_int * p_units;
108 >  if (this->NPTready()) {
109 >    atoms = entry_plug->atoms;
110 >    
111 >    p_ext = targetPressure * p_units;
112 >    p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0;
113 >  
114 >    entry_plug->getBox(oldBox);
115 >    volume = oldBox[0]*oldBox[1]*oldBox[2];
116 >    
117 >    ke_temp = ke * e_convert;
118 >    NkBT = (double)entry_plug->ndf * kB * targetTemp;
119 >    
120 >    // propagate the strain rate
121 >    
122 >    epsilonDot +=  dt * ((p_mol - p_ext) * volume /
123 >                         (tauBarostat*tauBarostat * kB * targetTemp) );
124 >    
125 >    // determine the change in cell volume
126 >    scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
127 >    //std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
128 >    
129 >    newBox[0] = oldBox[0] * scale;
130 >    newBox[1] = oldBox[1] * scale;
131 >    newBox[2] = oldBox[2] * scale;
132 >    volume = newBox[0]*newBox[1]*newBox[2];
133 >    
134 >    entry_plug->setBox(newBox);
135 >    
136 >    // perform affine transform to update positions with volume fluctuations
137 >    this->AffineTransform( oldBox, newBox );
138 >    
139 >    epsilonScale = epsilonDot * dt;
140 >    
141 >    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
142 >    // qmass is set in the parameter file
143 >    
144 >    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
145 >    zetaScale = zeta * dt;
146 >    
147 >    //std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
148 >    
149 >  // apply barostating and thermostating to velocities and angular momenta
150 >    for(i = 0; i < entry_plug->n_atoms; i++){
151 >      
152 >      vx = atoms[i]->get_vx();
153 >      vy = atoms[i]->get_vy();
154 >      vz = atoms[i]->get_vz();
155 >      
156 >      atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
157 >      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
158 >      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
159 >    }
160 >    if( entry_plug->n_oriented ){
161 >      
162 >      for( i=0; i < entry_plug->n_atoms; i++ ){
163 >        
164 >        if( atoms[i]->isDirectional() ){
165 >          
166 >          dAtom = (DirectionalAtom *)atoms[i];
167 >          
168 >          jx = dAtom->getJx();
169 >          jy = dAtom->getJy();
170 >          jz = dAtom->getJz();
171 >          
172 >          dAtom->setJx( jx * (1.0 - zetaScale));
173 >          dAtom->setJy( jy * (1.0 - zetaScale));
174 >          dAtom->setJz( jz * (1.0 - zetaScale));
175 >        }
176 >      }
177 >    }
178 >  }
179 > }
180  
100 –  entry_plug->getBox(oldBox);
181  
182 <  volume = oldBox[0]*oldBox[1]*oldBox[2];
182 > void ExtendedSystem::ConstantStress( double dt,
183 >                                     double ke,
184 >                                     double p_tensor[9] ) {
185  
186 <  ke_temp = ke * e_convert;
187 <  NkBT = (double)ndf * kB * targetTemp;
186 >  double oldBox[3];
187 >  double newBox[3];
188 >  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
189 >  const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
190 >  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
191 >                                        // amu*Ang^2*fs^-2/K
192  
193 <  // propogate the strain rate
193 >  int i;
194 >  double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
195 >  double pX_ext, pY_ext, pZ_ext;
196 >  double volume, p_mol;
197 >  double vx, vy, vz, jx, jy, jz;
198 >  DirectionalAtom* dAtom;
199  
200 <  epsilonDot +=  dt * ((p_mol - p_ext) * volume /
201 <                       (tauRelax*tauRelax * kB * targetTemp) );
200 >  if (this->NPTready()) {
201 >    atoms = entry_plug->atoms;
202 >    
203 >    p_ext = targetPressure * p_units;
204  
205 <  // determine the change in cell volume
206 <  scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
207 <
208 <  newBox[0] = oldBox[0] * scale;
209 <  newBox[1] = oldBox[1] * scale;
210 <  newBox[2] = oldBox[2] * scale;
211 <  volume = newBox[0]*newBox[1]*newBox[2];
212 <
213 <  entry_plug->setBox(newBox);
214 <
215 <  // perform affine transform to update positions with volume fluctuations
216 <  this->AffineTransform( oldBox, newBox );
217 <
218 <  epsilonScale = epsilonDot * dt;
205 >    pX_ext = p_ext / 3.0;
206 >    pY_ext = p_ext / 3.0;
207 >    pZ_ext = p_ext / 3.0;
208 >  
209 >    entry_plug->getBox(oldBox);
210 >    volume = oldBox[0]*oldBox[1]*oldBox[2];
211 >    
212 >    ke_temp = ke * e_convert;
213 >    NkBT = (double)entry_plug->ndf * kB * targetTemp;
214 >    
215 >    // propagate the strain rate
216 >    
217 >    epsilonDotX +=  dt * ((p_tensor[0] - pX_ext) * volume /
218 >                          (tauBarostat*tauBarostat * kB * targetTemp) );
219 >    epsilonDotY +=  dt * ((p_tensor[4] - pY_ext) * volume /
220 >                          (tauBarostat*tauBarostat * kB * targetTemp) );
221 >    epsilonDotZ +=  dt * ((p_tensor[8] - pZ_ext) * volume /
222 >                          (tauBarostat*tauBarostat * kB * targetTemp) );
223 >    
224 >    // determine the change in cell volume
225  
226 <  // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
227 <  // qmass is set in the parameter file
129 <
130 <  zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
131 <  zetaScale = zeta * dt;
132 <  
133 <  // apply barostating and thermostating to velocities and angular momenta
134 <  for(i = 0; i < nAtoms; i++){
226 >    //scale = pow( (1.0 + dt * 3.0 * (epsilonDot), (1.0 / 3.0));
227 >    //std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
228      
229 <    vx = atoms[i]->get_vx();
230 <    vy = atoms[i]->get_vy();
231 <    vz = atoms[i]->get_vz();
229 >    newBox[0] = oldBox[0] * scale;
230 >    newBox[1] = oldBox[1] * scale;
231 >    newBox[2] = oldBox[2] * scale;
232 >    volume = newBox[0]*newBox[1]*newBox[2];
233      
234 <    atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
141 <    atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
142 <    atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
143 <  }
144 <  if( nOriented ){
234 >    entry_plug->setBox(newBox);
235      
236 <    for( i=0; i < nAtoms; i++ ){
236 >    // perform affine transform to update positions with volume fluctuations
237 >    this->AffineTransform( oldBox, newBox );
238 >    
239 >    epsilonScale = epsilonDot * dt;
240 >    
241 >    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
242 >    // qmass is set in the parameter file
243 >    
244 >    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
245 >    zetaScale = zeta * dt;
246 >    
247 >    //std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
248 >    
249 >  // apply barostating and thermostating to velocities and angular momenta
250 >    for(i = 0; i < entry_plug->n_atoms; i++){
251        
252 <      if( atoms[i]->isDirectional() ){
253 <        
254 <        dAtom = (DirectionalAtom *)atoms[i];
252 >      vx = atoms[i]->get_vx();
253 >      vy = atoms[i]->get_vy();
254 >      vz = atoms[i]->get_vz();
255 >      
256 >      atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
257 >      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
258 >      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
259 >    }
260 >    if( entry_plug->n_oriented ){
261 >      
262 >      for( i=0; i < entry_plug->n_atoms; i++ ){
263          
264 <        jx = dAtom->getJx();
265 <        jy = dAtom->getJy();
266 <        jz = dAtom->getJz();
267 <        
268 <        dAtom->setJx( jx * (1.0 - zetaScale));
269 <        dAtom->setJy( jy * (1.0 - zetaScale));
270 <        dAtom->setJz( jz * (1.0 - zetaScale));
271 <      }
272 <    }  
264 >        if( atoms[i]->isDirectional() ){
265 >          
266 >          dAtom = (DirectionalAtom *)atoms[i];
267 >          
268 >          jx = dAtom->getJx();
269 >          jy = dAtom->getJy();
270 >          jz = dAtom->getJz();
271 >          
272 >          dAtom->setJx( jx * (1.0 - zetaScale));
273 >          dAtom->setJy( jy * (1.0 - zetaScale));
274 >          dAtom->setJz( jz * (1.0 - zetaScale));
275 >        }
276 >      }
277 >    }
278    }
279   }
280  
# Line 167 | Line 284 | void ExtendedSystem::AffineTransform( double oldBox[3]
284    double r[3];
285    double boxNum[3];
286    double percentScale[3];
287 +  double delta[3];
288    double rxi, ryi, rzi;
289 +
290 +  molecules = entry_plug->molecules;
291      
292    // first determine the scaling factor from the box size change
293    percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
294    percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
295    percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
296    
297 <  for (i=0; i < nMols; i++) {
297 >  for (i=0; i < entry_plug->n_mol; i++) {
298      
299      molecules[i].getCOM(r);
300 <    
300 >
301      // find the minimum image coordinates of the molecular centers of mass:    
302      
303      boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
# Line 198 | Line 318 | void ExtendedSystem::AffineTransform( double oldBox[3]
318      ryi += ryi*percentScale[1];
319      rzi += rzi*percentScale[2];
320  
321 <    r[0] = rxi + boxNum[0];
322 <    r[1] = ryi + boxNum[1];
323 <    r[2] = rzi + boxNum[2];
321 >    delta[0] = r[0] - (rxi + boxNum[0]);
322 >    delta[1] = r[1] - (ryi + boxNum[1]);
323 >    delta[2] = r[2] - (rzi + boxNum[2]);
324  
325 <    molecules[i].moveCOM(r);
325 >    molecules[i].moveCOM(delta);
326    }
327   }
328 +
329 + short int ExtendedSystem::NVTready() {
330 +  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
331 +  double NkBT;
332 +
333 +  if (!have_target_temp) {
334 +    sprintf( painCave.errMsg,
335 +             "ExtendedSystem error: You can't use NVT without a targetTemp!\n"
336 +             );
337 +    painCave.isFatal = 1;
338 +    simError();
339 +    return -1;
340 +  }
341 +    
342 +  if (!have_qmass) {
343 +    if (have_tau_thermostat) {
344 +
345 +      NkBT = (double)entry_plug->ndf * kB * targetTemp;
346 +      std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
347 +      this->setQmass(tauThermostat * NkBT);
348 +
349 +    } else {
350 +      sprintf( painCave.errMsg,
351 +               "ExtendedSystem error: If you use the constant temperature\n"
352 +               "    ensemble, you must set either tauThermostat or qMass.\n");
353 +      painCave.isFatal = 1;
354 +      simError();
355 +    }
356 +  }
357 +
358 +  return 1;
359 + }
360 +
361 + short int ExtendedSystem::NPTready() {
362 +  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
363 +  double NkBT;
364 +
365 +  if (!have_target_temp) {
366 +    sprintf( painCave.errMsg,
367 +             "ExtendedSystem error: You can't use NPT without a targetTemp!\n"
368 +             );
369 +    painCave.isFatal = 1;
370 +    simError();
371 +    return -1;
372 +  }
373 +
374 +  if (!have_target_pressure) {
375 +    sprintf( painCave.errMsg,
376 +             "ExtendedSystem error: You can't use NPT without a targetPressure!\n"
377 +             );
378 +    painCave.isFatal = 1;
379 +    simError();
380 +    return -1;
381 +  }
382 +    
383 +  if (!have_tau_barostat) {
384 +    sprintf( painCave.errMsg,
385 +             "ExtendedSystem error: If you use the NPT\n"
386 +             "    ensemble, you must set tauBarostat.\n");
387 +    painCave.isFatal = 1;
388 +    simError();
389 +  }
390 +
391 +  if (!have_qmass) {
392 +    if (have_tau_thermostat) {
393 +
394 +      NkBT = (double)entry_plug->ndf * kB * targetTemp;
395 +      std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
396 +      this->setQmass(tauThermostat * NkBT);
397 +
398 +    } else {
399 +      sprintf( painCave.errMsg,
400 +               "ExtendedSystem error: If you use the NPT\n"
401 +               "    ensemble, you must set either tauThermostat or qMass.\n");
402 +      painCave.isFatal = 1;
403 +      simError();
404 +    }  
405 +  }
406 +  return 1;
407 + }
408 +  

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