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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 577 by gezelter, Wed Jul 9 01:41:11 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 6 | Line 7
7   #include "Thermo.hpp"
8   #include "ReadWrite.hpp"
9   #include "Integrator.hpp"
10 < #include "simError.h"
10 > #include "simError.h"
11  
12 + #ifdef IS_MPI
13 + #include "mpiSimulation.hpp"
14 + #endif
15  
16 < // Basic isotropic thermostating and barostating via the Melchionna
16 > // Basic non-isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
18   //
19   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
20 < //       Molec. Phys., 78, 533.
20 > //       Molec. Phys., 78, 533.
21   //
22   //           and
23 < //
23 > //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26 < NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27 <  Integrator( theInfo, the_ff )
26 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
28   {
29 <  int i;
30 <  chi = 0.0;
31 <  for(i = 0; i < 9; i++) eta[i] = 0.0;
32 <  have_tau_thermostat = 0;
29 <  have_tau_barostat = 0;
30 <  have_target_temp = 0;
31 <  have_target_pressure = 0;
32 < }
29 >  GenericData* data;
30 >  DoubleArrayData * etaValue;
31 >  vector<double> etaArray;
32 >  int i,j;
33  
34 < void NPTf::moveA() {
35 <  
36 <  int i,j,k;
37 <  int atomIndex, aMatIndex;
38 <  DirectionalAtom* dAtom;
39 <  double Tb[3];
40 <  double ji[3];
41 <  double rj[3];
42 <  double instaTemp, instaPress, instaVol;
43 <  double tt2, tb2;
44 <  double angle;
45 <  double press[9];
46 <  const double p_convert = 1.63882576e8;
34 >  for(i = 0; i < 3; i++){
35 >    for (j = 0; j < 3; j++){
36  
37 <  tt2 = tauThermostat * tauThermostat;
38 <  tb2 = tauBarostat * tauBarostat;
37 >      eta[i][j] = 0.0;
38 >      oldEta[i][j] = 0.0;
39 >    }
40 >  }
41  
51  instaTemp = tStats->getTemperature();
52  tStats->getPressureTensor(press);
42  
43 <  for (i=0; i < 9; i++) press[i] *= p_convert;
43 >  if( theInfo->useInitXSstate ){
44 >    // retrieve eta array from simInfo if it exists
45 >    data = info->getProperty(ETAVALUE_ID);
46 >    if(data){
47 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
48 >      
49 >      if(etaValue){
50 >        etaArray = etaValue->getData();
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 >      }
59 >    }
60 >  }
61  
62 <  instaVol = tStats->getVolume();
57 <  
58 <  // first evolve chi a half step
59 <  
60 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
61 <  
62 <  eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2);
63 <  eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2);
64 <  eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2);
65 <  eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2);
66 <  eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2);
67 <  eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2);
68 <  eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2);
69 <  eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2);
70 <  eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2);
71 <  
72 <  for( i=0; i<nAtoms; i++ ){
73 <    atomIndex = i * 3;
74 <    aMatIndex = i * 9;
75 <    
76 <    // velocity half step
77 <    
78 <    vx = vel[atomIndex];
79 <    vy = vel[atomIndex+1];
80 <    vz = vel[atomIndex+2];
81 <    
82 <    scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz;
83 <    scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz;
84 <    scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz;
85 <    
86 <    vx += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - scx);
87 <    vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy);
88 <    vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz);
62 > }
63  
64 <    vel[atomIndex] = vx;
91 <    vel[atomIndex+1] = vy;
92 <    vel[atomIndex+2] = vz;
64 > template<typename T> NPTf<T>::~NPTf() {
65  
66 <    // position whole step    
66 >  // empty for now
67 > }
68  
69 <    rj[0] = pos[atomIndex];
97 <    rj[1] = pos[atomIndex+1];
98 <    rj[2] = pos[atomIndex+2];
69 > template<typename T> void NPTf<T>::resetIntegrator() {
70  
71 <    info->wrapVector(rj);
71 >  int i, j;
72  
73 <    scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2];
74 <    scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2];
75 <    scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2];
73 >  for(i = 0; i < 3; i++)
74 >    for (j = 0; j < 3; j++)
75 >      eta[i][j] = 0.0;
76  
77 <    pos[atomIndex] += dt * (vel[atomIndex] + scx);
78 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy);
108 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz);
109 <  
110 <    if( atoms[i]->isDirectional() ){
77 >  T::resetIntegrator();
78 > }
79  
80 <      dAtom = (DirectionalAtom *)atoms[i];
113 <          
114 <      // get and convert the torque to body frame
115 <      
116 <      Tb[0] = dAtom->getTx();
117 <      Tb[1] = dAtom->getTy();
118 <      Tb[2] = dAtom->getTz();
119 <      
120 <      dAtom->lab2Body( Tb );
121 <      
122 <      // get the angular momentum, and propagate a half step
80 > template<typename T> void NPTf<T>::evolveEtaA() {
81  
82 <      ji[0] = dAtom->getJx();
83 <      ji[1] = dAtom->getJy();
84 <      ji[2] = dAtom->getJz();
85 <      
86 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
87 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
88 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
89 <      
90 <      // use the angular velocities to propagate the rotation matrix a
133 <      // full time step
134 <      
135 <      // rotate about the x-axis      
136 <      angle = dt2 * ji[0] / dAtom->getIxx();
137 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
138 <      
139 <      // rotate about the y-axis
140 <      angle = dt2 * ji[1] / dAtom->getIyy();
141 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
142 <      
143 <      // rotate about the z-axis
144 <      angle = dt * ji[2] / dAtom->getIzz();
145 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
146 <      
147 <      // rotate about the y-axis
148 <      angle = dt2 * ji[1] / dAtom->getIyy();
149 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
150 <      
151 <       // rotate about the x-axis
152 <      angle = dt2 * ji[0] / dAtom->getIxx();
153 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
154 <      
155 <      dAtom->setJx( ji[0] );
156 <      dAtom->setJy( ji[1] );
157 <      dAtom->setJz( ji[2] );
82 >  int i, j;
83 >
84 >  for(i = 0; i < 3; i ++){
85 >    for(j = 0; j < 3; j++){
86 >      if( i == j)
87 >        eta[i][j] += dt2 *  instaVol *
88 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89 >      else
90 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
91      }
159    
92    }
93  
94 <  // Scale the box after all the positions have been moved:
95 <  
94 >  for(i = 0; i < 3; i++)
95 >    for (j = 0; j < 3; j++)
96 >      oldEta[i][j] = eta[i][j];
97 > }
98  
99 + template<typename T> void NPTf<T>::evolveEtaB() {
100  
101 <  // Use a taylor expansion for eta products
167 <  
168 <  info->getBoxM(hm);
169 <  
101 >  int i,j;
102  
103 +  for(i = 0; i < 3; i++)
104 +    for (j = 0; j < 3; j++)
105 +      prevEta[i][j] = eta[i][j];
106  
107 +  for(i = 0; i < 3; i ++){
108 +    for(j = 0; j < 3; j++){
109 +      if( i == j) {
110 +        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
111 +          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
112 +      } else {
113 +        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
114 +      }
115 +    }
116 +  }
117 + }
118  
119 + template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
120 +  int i,j;
121 +  double vScale[3][3];
122  
123 +  for (i = 0; i < 3; i++ ) {
124 +    for (j = 0; j < 3; j++ ) {
125 +      vScale[i][j] = eta[i][j];
126  
127 <   info->scaleBox(exp(dt*eta));
127 >      if (i == j) {
128 >        vScale[i][j] += chi;
129 >      }
130 >    }
131 >  }
132  
133 <
133 >  info->matVecMul3( vScale, vel, sc );
134   }
135  
136 < void NPTi::moveB( void ){
137 <  int i,j,k;
138 <  int atomIndex;
139 <  DirectionalAtom* dAtom;
184 <  double Tb[3];
185 <  double ji[3];
186 <  double instaTemp, instaPress, instaVol;
187 <  double tt2, tb2;
188 <  
189 <  tt2 = tauThermostat * tauThermostat;
190 <  tb2 = tauBarostat * tauBarostat;
191 <
192 <  instaTemp = tStats->getTemperature();
193 <  instaPress = tStats->getPressure();
194 <  instaVol = tStats->getVolume();
136 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
137 >  int i,j;
138 >  double myVel[3];
139 >  double vScale[3][3];
140  
141 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
142 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
143 <  
144 <  for( i=0; i<nAtoms; i++ ){
145 <    atomIndex = i * 3;
146 <    
147 <    // velocity half step
203 <    for( j=atomIndex; j<(atomIndex+3); j++ )
204 <    for( j=atomIndex; j<(atomIndex+3); j++ )
205 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
206 <                       - vel[j]*(chi+eta));
207 <    
208 <    if( atoms[i]->isDirectional() ){
209 <      
210 <      dAtom = (DirectionalAtom *)atoms[i];
211 <      
212 <      // get and convert the torque to body frame
213 <      
214 <      Tb[0] = dAtom->getTx();
215 <      Tb[1] = dAtom->getTy();
216 <      Tb[2] = dAtom->getTz();
217 <      
218 <      dAtom->lab2Body( Tb );
219 <      
220 <      // get the angular momentum, and complete the angular momentum
221 <      // half step
222 <      
223 <      ji[0] = dAtom->getJx();
224 <      ji[1] = dAtom->getJy();
225 <      ji[2] = dAtom->getJz();
226 <      
227 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
228 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
229 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
230 <      
231 <      dAtom->setJx( ji[0] );
232 <      dAtom->setJy( ji[1] );
233 <      dAtom->setJz( ji[2] );
141 >  for (i = 0; i < 3; i++ ) {
142 >    for (j = 0; j < 3; j++ ) {
143 >      vScale[i][j] = eta[i][j];
144 >
145 >      if (i == j) {
146 >        vScale[i][j] += chi;
147 >      }
148      }
149    }
150 +
151 +  for (j = 0; j < 3; j++)
152 +    myVel[j] = oldVel[3*index + j];
153 +
154 +  info->matVecMul3( vScale, myVel, sc );
155   }
156  
157 < int NPTi::readyCheck() {
158 <
159 <  // First check to see if we have a target temperature.
160 <  // Not having one is fatal.
161 <  
162 <  if (!have_target_temp) {
163 <    sprintf( painCave.errMsg,
164 <             "NPTi error: You can't use the NPTi integrator\n"
165 <             "   without a targetTemp!\n"
166 <             );
167 <    painCave.isFatal = 1;
168 <    simError();
169 <    return -1;
157 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
158 >                                               int index, double sc[3]){
159 >  int j;
160 >  double rj[3];
161 >
162 >  for(j=0; j<3; j++)
163 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164 >
165 >  info->matVecMul3( eta, rj, sc );
166 > }
167 >
168 > template<typename T> void NPTf<T>::scaleSimBox( void ){
169 >
170 >  int i,j,k;
171 >  double scaleMat[3][3];
172 >  double eta2ij;
173 >  double bigScale, smallScale, offDiagMax;
174 >  double hm[3][3], hmnew[3][3];
175 >
176 >
177 >
178 >  // Scale the box after all the positions have been moved:
179 >
180 >  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
181 >  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
182 >
183 >  bigScale = 1.0;
184 >  smallScale = 1.0;
185 >  offDiagMax = 0.0;
186 >
187 >  for(i=0; i<3; i++){
188 >    for(j=0; j<3; j++){
189 >
190 >      // Calculate the matrix Product of the eta array (we only need
191 >      // the ij element right now):
192 >
193 >      eta2ij = 0.0;
194 >      for(k=0; k<3; k++){
195 >        eta2ij += eta[i][k] * eta[k][j];
196 >      }
197 >
198 >      scaleMat[i][j] = 0.0;
199 >      // identity matrix (see above):
200 >      if (i == j) scaleMat[i][j] = 1.0;
201 >      // Taylor expansion for the exponential truncated at second order:
202 >      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
203 >
204 >      if (i != j)
205 >        if (fabs(scaleMat[i][j]) > offDiagMax)
206 >          offDiagMax = fabs(scaleMat[i][j]);
207 >    }
208 >
209 >    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
210 >    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
211    }
212  
213 <  if (!have_target_pressure) {
213 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
214      sprintf( painCave.errMsg,
215 <             "NPTi error: You can't use the NPTi integrator\n"
216 <             "   without a targetPressure!\n"
217 <             );
215 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
216 >             " Check your tauBarostat, as it is probably too small!\n\n"
217 >             " scaleMat = [%lf\t%lf\t%lf]\n"
218 >             "            [%lf\t%lf\t%lf]\n"
219 >             "            [%lf\t%lf\t%lf]\n",
220 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
221 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
222 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
223      painCave.isFatal = 1;
224      simError();
225 <    return -1;
261 <  }
262 <  
263 <  // We must set tauThermostat.
264 <  
265 <  if (!have_tau_thermostat) {
225 >  } else if (offDiagMax > 0.01) {
226      sprintf( painCave.errMsg,
227 <             "NPTi error: If you use the NPTi\n"
228 <             "   integrator, you must set tauThermostat.\n");
227 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
228 >             " Check your tauBarostat, as it is probably too small!\n\n"
229 >             " scaleMat = [%lf\t%lf\t%lf]\n"
230 >             "            [%lf\t%lf\t%lf]\n"
231 >             "            [%lf\t%lf\t%lf]\n",
232 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
233 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
234 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
235      painCave.isFatal = 1;
236      simError();
237 <    return -1;
238 <  }    
237 >  } else {
238 >    info->getBoxM(hm);
239 >    info->matMul3(hm, scaleMat, hmnew);
240 >    info->setBoxM(hmnew);
241 >  }
242 > }
243  
244 <  // We must set tauBarostat.
245 <  
246 <  if (!have_tau_barostat) {
277 <    sprintf( painCave.errMsg,
278 <             "NPTi error: If you use the NPTi\n"
279 <             "   integrator, you must set tauBarostat.\n");
280 <    painCave.isFatal = 1;
281 <    simError();
282 <    return -1;
283 <  }    
244 > template<typename T> bool NPTf<T>::etaConverged() {
245 >  int i;
246 >  double diffEta, sumEta;
247  
248 <  // We need NkBT a lot, so just set it here:
248 >  sumEta = 0;
249 >  for(i = 0; i < 3; i++)
250 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
251  
252 <  NkBT = (double)info->ndf * kB * targetTemp;
252 >  diffEta = sqrt( sumEta / 3.0 );
253  
254 <  return 1;
254 >  return ( diffEta <= etaTolerance );
255   }
256 +
257 + template<typename T> double NPTf<T>::getConservedQuantity(void){
258 +
259 +  double conservedQuantity;
260 +  double totalEnergy;
261 +  double thermostat_kinetic;
262 +  double thermostat_potential;
263 +  double barostat_kinetic;
264 +  double barostat_potential;
265 +  double trEta;
266 +  double a[3][3], b[3][3];
267 +
268 +  totalEnergy = tStats->getTotalE();
269 +
270 +  thermostat_kinetic = fkBT * tt2 * chi * chi /
271 +    (2.0 * eConvert);
272 +
273 +  thermostat_potential = fkBT* integralOfChidt / eConvert;
274 +
275 +  info->transposeMat3(eta, a);
276 +  info->matMul3(a, eta, b);
277 +  trEta = info->matTrace3(b);
278 +
279 +  barostat_kinetic = NkBT * tb2 * trEta /
280 +    (2.0 * eConvert);
281 +
282 +  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283 +    eConvert;
284 +
285 +  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
286 +    barostat_kinetic + barostat_potential;
287 +
288 +  return conservedQuantity;
289 +
290 + }
291 +
292 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
293 +  string parameters;
294 +  const int BUFFERSIZE = 2000; // size of the read buffer
295 +  char buffer[BUFFERSIZE];
296 +
297 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
298 +  parameters += buffer;
299 +
300 +  for(int i = 0; i < 3; i++){
301 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
302 +    parameters += buffer;
303 +  }
304 +
305 +  return parameters;
306 +
307 + }

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