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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 852 by mmeineke, Thu Nov 6 18:20:47 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];
99 <    vel[atomIndex+2] = vi[2];
159 >  info->matVecMul3( vScale, myVel, sc );
160 > }
161  
162 <    // position whole step    
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 <    ri[0] = pos[atomIndex];
168 <    ri[1] = pos[atomIndex+1];
105 <    ri[2] = pos[atomIndex+2];
167 >  for(j=0; j<3; j++)
168 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
169  
170 <    info->wrapVector(ri);
170 >  info->matVecMul3( eta, rj, sc );
171 > }
172  
173 <    info->matVecMul3( eta, ri, sc );
173 > void NPTf::scaleSimBox( void ){
174  
175 <    pos[atomIndex]   += dt * (vel[atomIndex] + sc[0]);
176 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]);
177 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]);
178 <  
179 <    if( atoms[i]->isDirectional() ){
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  
117 –      dAtom = (DirectionalAtom *)atoms[i];
118 –          
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
181  
129 –      ji[0] = dAtom->getJx();
130 –      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  
183    // Scale the box after all the positions have been moved:
184  
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  
188 +  bigScale = 1.0;
189 +  smallScale = 1.0;
190 +  offDiagMax = 0.0;
191  
192    for(i=0; i<3; i++){
193      for(j=0; j<3; j++){
# Line 180 | Line 199 | void NPTf::moveA() {
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;
206        // Taylor expansion for the exponential truncated at second order:
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)
211 +          offDiagMax = fabs(scaleMat[i][j]);
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 <  info->getBoxM(hm);
219 <  info->matMul3(hm, scaleMat, hmnew);
220 <  info->setBoxM(hmnew);
221 <  
217 >
218 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
219 >    sprintf( painCave.errMsg,
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"
224 >             "            [%lf\t%lf\t%lf]\n",
225 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
226 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
227 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
228 >    painCave.isFatal = 1;
229 >    simError();
230 >  } else if (offDiagMax > 0.01) {
231 >    sprintf( painCave.errMsg,
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"
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 {
243 >    info->getBoxM(hm);
244 >    info->matMul3(hm, scaleMat, hmnew);
245 >    info->setBoxM(hmnew);
246 >  }
247   }
248  
249 < void NPTf::moveB( void ){
250 <  int i,j, k;
251 <  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;
249 > bool NPTf::etaConverged() {
250 >  int i;
251 >  double diffEta, sumEta;
252  
253 <  instaTemp = tStats->getTemperature();
254 <  tStats->getPressureTensor(press);
255 <  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) {
253 >  sumEta = 0;
254 >  for(i = 0; i < 3; i++)
255 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
256  
257 <        eta[i][j] += dt2 * instaVol *
226 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
257 >  diffEta = sqrt( sumEta / 3.0 );
258  
259 <        vScale[i][j] = eta[i][j] + chi;
260 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
259 >  return ( diffEta <= etaTolerance );
260 > }
261  
262 <        vScale[i][j] = eta[i][j];
235 <        
236 <      }
237 <    }
238 <  }
262 > double NPTf::getConservedQuantity(void){
263  
264 <  for( i=0; i<nAtoms; i++ ){
265 <    atomIndex = i * 3;
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 <    // 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]);
273 >  totalEnergy = tStats->getTotalE();
274  
275 <    vel[atomIndex]   = vi[0];
276 <    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 < }
275 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
276 >    (2.0 * eConvert);
277  
278 < 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 <  }
278 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
279  
280 <  if (!have_target_pressure) {
281 <    sprintf( painCave.errMsg,
282 <             "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 <  }    
280 >  info->transposeMat3(eta, a);
281 >  info->matMul3(a, eta, b);
282 >  trEta = info->matTrace3(b);
283  
284 <  // We must set tauBarostat.
285 <  
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 <  }    
284 >  barostat_kinetic = NkBT * tb2 * trEta /
285 >    (2.0 * eConvert);
286  
287 <  // We need NkBT a lot, so just set it here:
287 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
288 >    eConvert;
289  
290 <  NkBT = (double)info->ndf * kB * targetTemp;
290 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
291 >    barostat_kinetic + barostat_potential;
292  
293 <  return 1;
293 >  return conservedQuantity;
294 >
295   }
296 +
297 + char* NPTf::getAdditionalParameters(void){
298 +
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 +  return addParamBuffer;
311 + }

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