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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 6 | Line 8
8   #include "Thermo.hpp"
9   #include "ReadWrite.hpp"
10   #include "Integrator.hpp"
11 < #include "simError.h"
11 > #include "simError.h"
12  
13 + #ifdef IS_MPI
14 + #include "mpiSimulation.hpp"
15 + #endif
16  
17   // Basic non-isotropic thermostating and barostating via the Melchionna
18   // modification of the Hoover algorithm:
19   //
20   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
21 < //       Molec. Phys., 78, 533.
21 > //       Molec. Phys., 78, 533.
22   //
23   //           and
24 < //
24 > //
25   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
26  
27 < NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
28 <  Integrator( theInfo, the_ff )
27 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
28 >  T( theInfo, the_ff )
29   {
30 <  int i;
31 <  chi = 0.0;
32 <  for(i = 0; i < 9; i++) eta[i] = 0.0;
33 <  have_tau_thermostat = 0;
34 <  have_tau_barostat = 0;
35 <  have_target_temp = 0;
36 <  have_target_pressure = 0;
30 >  GenericData* data;
31 >  DoubleArrayData * etaValue;
32 >  vector<double> etaArray;
33 >  int i,j;
34 >
35 >  for(i = 0; i < 3; i++){
36 >    for (j = 0; j < 3; j++){
37 >
38 >      eta[i][j] = 0.0;
39 >      oldEta[i][j] = 0.0;
40 >    }
41 >  }
42 >
43 >
44 >  if( theInfo->useInitXSstate ){
45 >    // retrieve eta array from simInfo if it exists
46 >    data = info->getProperty(ETAVALUE_ID);
47 >    if(data){
48 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
49 >      
50 >      if(etaValue){
51 >        etaArray = etaValue->getData();
52 >        
53 >        for(i = 0; i < 3; i++){
54 >          for (j = 0; j < 3; j++){
55 >            eta[i][j] = etaArray[3*i+j];
56 >            oldEta[i][j] = eta[i][j];
57 >          }
58 >        }
59 >      }
60 >    }
61 >  }
62 >
63   }
64  
65 < 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 ident[3][3], eta1[3][3], eta2[3][3], hmnew[3][3];
43 <  double hm[9];
44 <  double vx, vy, vz;
45 <  double scx, scy, scz;
46 <  double instaTemp, instaPress, instaVol;
47 <  double tt2, tb2;
48 <  double angle;
49 <  double press[9];
65 > template<typename T> NPTf<T>::~NPTf() {
66  
67 <  tt2 = tauThermostat * tauThermostat;
68 <  tb2 = tauBarostat * tauBarostat;
67 >  // empty for now
68 > }
69  
70 <  instaTemp = tStats->getTemperature();
55 <  tStats->getPressureTensor(press);
56 <  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/p_convert) /
63 <    (NkBT*tb2);
64 <  eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2);
65 <  eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2);
66 <  eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2);
67 <  eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) /
68 <    (NkBT*tb2);
69 <  eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2);
70 <  eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2);
71 <  eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2);
72 <  eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) /
73 <    (NkBT*tb2);
74 <  
75 <  for( i=0; i<nAtoms; i++ ){
76 <    atomIndex = i * 3;
77 <    aMatIndex = i * 9;
78 <    
79 <    // velocity half step
80 <    
81 <    vx = vel[atomIndex];
82 <    vy = vel[atomIndex+1];
83 <    vz = vel[atomIndex+2];
84 <    
85 <    scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz;
86 <    scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz;
87 <    scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz;
88 <    
89 <    vx += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - scx);
90 <    vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy);
91 <    vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz);
70 > template<typename T> void NPTf<T>::resetIntegrator() {
71  
72 <    vel[atomIndex] = vx;
94 <    vel[atomIndex+1] = vy;
95 <    vel[atomIndex+2] = vz;
72 >  int i, j;
73  
74 <    // position whole step    
74 >  for(i = 0; i < 3; i++)
75 >    for (j = 0; j < 3; j++)
76 >      eta[i][j] = 0.0;
77  
78 <    rj[0] = pos[atomIndex];
79 <    rj[1] = pos[atomIndex+1];
101 <    rj[2] = pos[atomIndex+2];
78 >  T::resetIntegrator();
79 > }
80  
81 <    info->wrapVector(rj);
81 > template<typename T> void NPTf<T>::evolveEtaA() {
82  
83 <    scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2];
106 <    scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2];
107 <    scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2];
83 >  int i, j;
84  
85 <    pos[atomIndex] += dt * (vel[atomIndex] + scx);
86 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy);
87 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz);
88 <  
89 <    if( atoms[i]->isDirectional() ){
85 >  for(i = 0; i < 3; i ++){
86 >    for(j = 0; j < 3; j++){
87 >      if( i == j)
88 >        eta[i][j] += dt2 *  instaVol *
89 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
90 >      else
91 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
92 >    }
93 >  }
94  
95 <      dAtom = (DirectionalAtom *)atoms[i];
96 <          
97 <      // get and convert the torque to body frame
98 <      
119 <      Tb[0] = dAtom->getTx();
120 <      Tb[1] = dAtom->getTy();
121 <      Tb[2] = dAtom->getTz();
122 <      
123 <      dAtom->lab2Body( Tb );
124 <      
125 <      // get the angular momentum, and propagate a half step
95 >  for(i = 0; i < 3; i++)
96 >    for (j = 0; j < 3; j++)
97 >      oldEta[i][j] = eta[i][j];
98 > }
99  
100 <      ji[0] = dAtom->getJx();
101 <      ji[1] = dAtom->getJy();
102 <      ji[2] = dAtom->getJz();
103 <      
104 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
105 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
106 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
107 <      
108 <      // use the angular velocities to propagate the rotation matrix a
109 <      // full time step
110 <      
111 <      // rotate about the x-axis      
112 <      angle = dt2 * ji[0] / dAtom->getIxx();
113 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
114 <      
115 <      // rotate about the y-axis
143 <      angle = dt2 * ji[1] / dAtom->getIyy();
144 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
145 <      
146 <      // rotate about the z-axis
147 <      angle = dt * ji[2] / dAtom->getIzz();
148 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
149 <      
150 <      // rotate about the y-axis
151 <      angle = dt2 * ji[1] / dAtom->getIyy();
152 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
153 <      
154 <       // rotate about the x-axis
155 <      angle = dt2 * ji[0] / dAtom->getIxx();
156 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
157 <      
158 <      dAtom->setJx( ji[0] );
159 <      dAtom->setJy( ji[1] );
160 <      dAtom->setJz( ji[2] );
100 > template<typename T> void NPTf<T>::evolveEtaB() {
101 >
102 >  int i,j;
103 >
104 >  for(i = 0; i < 3; i++)
105 >    for (j = 0; j < 3; j++)
106 >      prevEta[i][j] = eta[i][j];
107 >
108 >  for(i = 0; i < 3; i ++){
109 >    for(j = 0; j < 3; j++){
110 >      if( i == j) {
111 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
112 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
113 >      } else {
114 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
115 >      }
116      }
162 –    
117    }
118 + }
119  
120 + template<typename T> void NPTf<T>::calcVelScale(void){
121 +  int i,j;
122 +
123 +  for (i = 0; i < 3; i++ ) {
124 +    for (j = 0; j < 3; j++ ) {
125 +      vScale[i][j] = eta[i][j];
126 +
127 +      if (i == j) {
128 +        vScale[i][j] += chi;
129 +      }
130 +    }
131 +  }
132 + }
133 +
134 + template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
135 +
136 +  info->matVecMul3( vScale, vel, sc );
137 + }
138 +
139 + template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
140 +  int j;
141 +  double myVel[3];
142 +  double vScale[3][3];
143 +
144 +  for (j = 0; j < 3; j++)
145 +    myVel[j] = oldVel[3*index + j];
146 +
147 +  info->matVecMul3( vScale, myVel, sc );
148 + }
149 +
150 + template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
151 +                                               int index, double sc[3]){
152 +  int j;
153 +  double rj[3];
154 +
155 +  for(j=0; j<3; j++)
156 +    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
157 +
158 +  info->matVecMul3( eta, rj, sc );
159 + }
160 +
161 + template<typename T> void NPTf<T>::scaleSimBox( void ){
162 +
163 +  int i,j,k;
164 +  double scaleMat[3][3];
165 +  double eta2ij;
166 +  double bigScale, smallScale, offDiagMax;
167 +  double hm[3][3], hmnew[3][3];
168 +
169 +
170 +
171    // Scale the box after all the positions have been moved:
172  
173    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
174    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
175  
176 +  bigScale = 1.0;
177 +  smallScale = 1.0;
178 +  offDiagMax = 0.0;
179  
180    for(i=0; i<3; i++){
181      for(j=0; j<3; j++){
173 –      ident[i][j] = 0.0;
174 –      eta1[i][j] = eta[3*i+j];
175 –      eta2[i][j] = 0.0;
176 –      for(k=0; k<3; k++){
177 –        eta2[i][j] += eta[3*i+k] * eta[3*k+j];
178 –      }
179 –    }
180 –    ident[i][i] = 1.0;
181 –  }
182  
183 <  
184 <  info->getBoxM(hm);
185 <
186 <  for(i=0; i<3; i++){
187 <    for(j=0; j<3; j++){      
188 <      hmnew[i][j] = 0.0;
183 >      // Calculate the matrix Product of the eta array (we only need
184 >      // the ij element right now):
185 >
186 >      eta2ij = 0.0;
187        for(k=0; k<3; k++){
188 <        // remember that hmat has transpose ordering for Fortran compat:
191 <        hmnew[i][j] += hm[3*k+i] * (ident[k][j]
192 <                                    + dt * eta1[k][j]
193 <                                    + 0.5 * dt * dt * eta2[k][j]);
188 >        eta2ij += eta[i][k] * eta[k][j];
189        }
195 –    }
196 –  }
197 –  
198 –  for (i = 0; i < 3; i++) {
199 –    for (j = 0; j < 3; j++) {
200 –      // remember that hmat has transpose ordering for Fortran compat:
201 –      hm[3*j + i] = hmnew[i][j];
202 –    }
203 –  }
190  
191 <  info->setBoxM(hm);
192 <  
193 < }
191 >      scaleMat[i][j] = 0.0;
192 >      // identity matrix (see above):
193 >      if (i == j) scaleMat[i][j] = 1.0;
194 >      // Taylor expansion for the exponential truncated at second order:
195 >      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
196  
197 < void NPTf::moveB( void ){
198 <  int i,j,k;
199 <  int atomIndex;
212 <  DirectionalAtom* dAtom;
213 <  double Tb[3];
214 <  double ji[3];
215 <  double press[9];
216 <  double instaTemp, instaVol;
217 <  double tt2, tb2;
218 <  double vx, vy, vz;
219 <  double scx, scy, scz;
220 <  const double p_convert = 1.63882576e8;
221 <  
222 <  tt2 = tauThermostat * tauThermostat;
223 <  tb2 = tauBarostat * tauBarostat;
224 <
225 <  instaTemp = tStats->getTemperature();
226 <  tStats->getPressureTensor(press);
227 <  instaVol = tStats->getVolume();
228 <  
229 <  // first evolve chi a half step
230 <  
231 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
232 <  
233 <  eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) /
234 <    (NkBT*tb2);
235 <  eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2);
236 <  eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2);
237 <  eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2);
238 <  eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) /
239 <    (NkBT*tb2);
240 <  eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2);
241 <  eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2);
242 <  eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2);
243 <  eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) /
244 <    (NkBT*tb2);
245 <
246 <  for( i=0; i<nAtoms; i++ ){
247 <    atomIndex = i * 3;
248 <
249 <    // velocity half step
250 <    
251 <    vx = vel[atomIndex];
252 <    vy = vel[atomIndex+1];
253 <    vz = vel[atomIndex+2];
254 <    
255 <    scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz;
256 <    scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz;
257 <    scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz;
258 <    
259 <    vx += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - scx);
260 <    vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy);
261 <    vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz);
262 <
263 <    vel[atomIndex] = vx;
264 <    vel[atomIndex+1] = vy;
265 <    vel[atomIndex+2] = vz;
266 <    
267 <    if( atoms[i]->isDirectional() ){
268 <      
269 <      dAtom = (DirectionalAtom *)atoms[i];
270 <      
271 <      // get and convert the torque to body frame
272 <      
273 <      Tb[0] = dAtom->getTx();
274 <      Tb[1] = dAtom->getTy();
275 <      Tb[2] = dAtom->getTz();
276 <      
277 <      dAtom->lab2Body( Tb );
278 <      
279 <      // get the angular momentum, and complete the angular momentum
280 <      // half step
281 <      
282 <      ji[0] = dAtom->getJx();
283 <      ji[1] = dAtom->getJy();
284 <      ji[2] = dAtom->getJz();
285 <      
286 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
287 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
288 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
289 <      
290 <      dAtom->setJx( ji[0] );
291 <      dAtom->setJy( ji[1] );
292 <      dAtom->setJz( ji[2] );
197 >      if (i != j)
198 >        if (fabs(scaleMat[i][j]) > offDiagMax)
199 >          offDiagMax = fabs(scaleMat[i][j]);
200      }
294 –  }
295 – }
201  
202 < int NPTf::readyCheck() {
203 <
299 <  // First check to see if we have a target temperature.
300 <  // Not having one is fatal.
301 <  
302 <  if (!have_target_temp) {
303 <    sprintf( painCave.errMsg,
304 <             "NPTf error: You can't use the NPTf integrator\n"
305 <             "   without a targetTemp!\n"
306 <             );
307 <    painCave.isFatal = 1;
308 <    simError();
309 <    return -1;
202 >    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
203 >    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
204    }
205  
206 <  if (!have_target_pressure) {
206 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
207      sprintf( painCave.errMsg,
208 <             "NPTf error: You can't use the NPTf integrator\n"
209 <             "   without a targetPressure!\n"
210 <             );
208 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
209 >             " Check your tauBarostat, as it is probably too small!\n\n"
210 >             " scaleMat = [%lf\t%lf\t%lf]\n"
211 >             "            [%lf\t%lf\t%lf]\n"
212 >             "            [%lf\t%lf\t%lf]\n",
213 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
214 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
215 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
216      painCave.isFatal = 1;
217      simError();
218 <    return -1;
320 <  }
321 <  
322 <  // We must set tauThermostat.
323 <  
324 <  if (!have_tau_thermostat) {
218 >  } else if (offDiagMax > 0.01) {
219      sprintf( painCave.errMsg,
220 <             "NPTf error: If you use the NPTf\n"
221 <             "   integrator, you must set tauThermostat.\n");
220 >             "NPTf error: Attempting an off-diagonal 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 <    return -1;
231 <  }    
230 >  } else {
231 >    info->getBoxM(hm);
232 >    info->matMul3(hm, scaleMat, hmnew);
233 >    info->setBoxM(hmnew);
234 >  }
235 > }
236  
237 <  // We must set tauBarostat.
238 <  
239 <  if (!have_tau_barostat) {
336 <    sprintf( painCave.errMsg,
337 <             "NPTf error: If you use the NPTf\n"
338 <             "   integrator, you must set tauBarostat.\n");
339 <    painCave.isFatal = 1;
340 <    simError();
341 <    return -1;
342 <  }    
237 > template<typename T> bool NPTf<T>::etaConverged() {
238 >  int i;
239 >  double diffEta, sumEta;
240  
241 <  // We need NkBT a lot, so just set it here:
241 >  sumEta = 0;
242 >  for(i = 0; i < 3; i++)
243 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
244  
245 <  NkBT = (double)info->ndf * kB * targetTemp;
245 >  diffEta = sqrt( sumEta / 3.0 );
246  
247 <  return 1;
247 >  return ( diffEta <= etaTolerance );
248   }
249 +
250 + template<typename T> double NPTf<T>::getConservedQuantity(void){
251 +
252 +  double conservedQuantity;
253 +  double totalEnergy;
254 +  double thermostat_kinetic;
255 +  double thermostat_potential;
256 +  double barostat_kinetic;
257 +  double barostat_potential;
258 +  double trEta;
259 +  double a[3][3], b[3][3];
260 +
261 +  totalEnergy = tStats->getTotalE();
262 +
263 +  thermostat_kinetic = fkBT * tt2 * chi * chi /
264 +    (2.0 * eConvert);
265 +
266 +  thermostat_potential = fkBT* integralOfChidt / eConvert;
267 +
268 +  info->transposeMat3(eta, a);
269 +  info->matMul3(a, eta, b);
270 +  trEta = info->matTrace3(b);
271 +
272 +  barostat_kinetic = NkBT * tb2 * trEta /
273 +    (2.0 * eConvert);
274 +
275 +  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
276 +    eConvert;
277 +
278 +  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
279 +    barostat_kinetic + barostat_potential;
280 +
281 +  return conservedQuantity;
282 +
283 + }
284 +
285 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
286 +  string parameters;
287 +  const int BUFFERSIZE = 2000; // size of the read buffer
288 +  char buffer[BUFFERSIZE];
289 +
290 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
291 +  parameters += buffer;
292 +
293 +  for(int i = 0; i < 3; i++){
294 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
295 +    parameters += buffer;
296 +  }
297 +
298 +  return parameters;
299 +
300 + }

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