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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 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3 + #include "MatVec3.h"
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "AbstractClasses.hpp"
# Line 6 | Line 9
9   #include "Thermo.hpp"
10   #include "ReadWrite.hpp"
11   #include "Integrator.hpp"
12 < #include "simError.h"
12 > #include "simError.h"
13  
14 + #ifdef IS_MPI
15 + #include "mpiSimulation.hpp"
16 + #endif
17  
18   // Basic non-isotropic thermostating and barostating via the Melchionna
19   // modification of the Hoover algorithm:
20   //
21   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22 < //       Molec. Phys., 78, 533.
22 > //       Molec. Phys., 78, 533.
23   //
24   //           and
25 < //
25 > //
26   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27  
28 < NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29 <  Integrator( theInfo, the_ff )
28 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29 >  T( theInfo, the_ff )
30   {
31 <  int i;
32 <  chi = 0.0;
33 <  for(i = 0; i < 9; i++) eta[i] = 0.0;
34 <  have_tau_thermostat = 0;
35 <  have_tau_barostat = 0;
36 <  have_target_temp = 0;
37 <  have_target_pressure = 0;
31 >  GenericData* data;
32 >  DoubleArrayData * etaValue;
33 >  vector<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 >
45 >  if( theInfo->useInitXSstate ){
46 >    // retrieve eta array from simInfo if it exists
47 >    data = info->getProperty(ETAVALUE_ID);
48 >    if(data){
49 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
50 >      
51 >      if(etaValue){
52 >        etaArray = etaValue->getData();
53 >        
54 >        for(i = 0; i < 3; i++){
55 >          for (j = 0; j < 3; j++){
56 >            eta[i][j] = etaArray[3*i+j];
57 >            oldEta[i][j] = eta[i][j];
58 >          }
59 >        }
60 >      }
61 >    }
62 >  }
63 >
64   }
65  
66 < 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];
66 > template<typename T> NPTf<T>::~NPTf() {
67  
68 <  tt2 = tauThermostat * tauThermostat;
69 <  tb2 = tauBarostat * tauBarostat;
68 >  // empty for now
69 > }
70  
71 <  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);
71 > template<typename T> void NPTf<T>::resetIntegrator() {
72  
73 <    vel[atomIndex] = vx;
94 <    vel[atomIndex+1] = vy;
95 <    vel[atomIndex+2] = vz;
73 >  int i, j;
74  
75 <    // position whole step    
75 >  for(i = 0; i < 3; i++)
76 >    for (j = 0; j < 3; j++)
77 >      eta[i][j] = 0.0;
78  
79 <    rj[0] = pos[atomIndex];
80 <    rj[1] = pos[atomIndex+1];
101 <    rj[2] = pos[atomIndex+2];
79 >  T::resetIntegrator();
80 > }
81  
82 <    info->wrapVector(rj);
82 > template<typename T> void NPTf<T>::evolveEtaA() {
83  
84 <    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];
84 >  int i, j;
85  
86 <    pos[atomIndex] += dt * (vel[atomIndex] + scx);
87 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy);
88 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz);
89 <  
90 <    if( atoms[i]->isDirectional() ){
86 >  for(i = 0; i < 3; i ++){
87 >    for(j = 0; j < 3; j++){
88 >      if( i == j)
89 >        eta[i][j] += dt2 *  instaVol *
90 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91 >      else
92 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
93 >    }
94 >  }
95  
96 <      dAtom = (DirectionalAtom *)atoms[i];
97 <          
98 <      // get and convert the torque to body frame
99 <      
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
96 >  for(i = 0; i < 3; i++)
97 >    for (j = 0; j < 3; j++)
98 >      oldEta[i][j] = eta[i][j];
99 > }
100  
101 <      ji[0] = dAtom->getJx();
102 <      ji[1] = dAtom->getJy();
103 <      ji[2] = dAtom->getJz();
104 <      
105 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
106 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
107 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
108 <      
109 <      // use the angular velocities to propagate the rotation matrix a
110 <      // full time step
111 <      
112 <      // rotate about the x-axis      
113 <      angle = dt2 * ji[0] / dAtom->getIxx();
114 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
115 <      
116 <      // 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] );
101 > template<typename T> void NPTf<T>::evolveEtaB() {
102 >
103 >  int i,j;
104 >
105 >  for(i = 0; i < 3; i++)
106 >    for (j = 0; j < 3; j++)
107 >      prevEta[i][j] = eta[i][j];
108 >
109 >  for(i = 0; i < 3; i ++){
110 >    for(j = 0; j < 3; j++){
111 >      if( i == j) {
112 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
113 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114 >      } else {
115 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
116 >      }
117      }
162 –    
118    }
119 + }
120  
121 + template<typename T> void NPTf<T>::calcVelScale(void){
122 +  int i,j;
123 +
124 +  for (i = 0; i < 3; i++ ) {
125 +    for (j = 0; j < 3; j++ ) {
126 +      vScale[i][j] = eta[i][j];
127 +
128 +      if (i == j) {
129 +        vScale[i][j] += chi;
130 +      }
131 +    }
132 +  }
133 + }
134 +
135 + template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
136 +
137 +  matVecMul3( vScale, vel, sc );
138 + }
139 +
140 + template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
141 +  int j;
142 +  double myVel[3];
143 +  double vScale[3][3];
144 +
145 +  for (j = 0; j < 3; j++)
146 +    myVel[j] = oldVel[3*index + j];
147 +
148 +  matVecMul3( vScale, myVel, sc );
149 + }
150 +
151 + template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
152 +                                               int index, double sc[3]){
153 +  int j;
154 +  double rj[3];
155 +
156 +  for(j=0; j<3; j++)
157 +    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
158 +
159 +  matVecMul3( eta, rj, sc );
160 + }
161 +
162 + template<typename T> void NPTf<T>::scaleSimBox( void ){
163 +
164 +  int i,j,k;
165 +  double scaleMat[3][3];
166 +  double eta2ij;
167 +  double bigScale, smallScale, offDiagMax;
168 +  double hm[3][3], hmnew[3][3];
169 +
170 +
171 +
172    // Scale the box after all the positions have been moved:
173  
174    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
175    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
176  
177 +  bigScale = 1.0;
178 +  smallScale = 1.0;
179 +  offDiagMax = 0.0;
180  
181    for(i=0; i<3; i++){
182      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 –  }
183  
184 <  
185 <  info->getBoxM(hm);
186 <
187 <  for(i=0; i<3; i++){
187 <    for(j=0; j<3; j++){      
188 <      hmnew[i][j] = 0.0;
184 >      // Calculate the matrix Product of the eta array (we only need
185 >      // the ij element right now):
186 >
187 >      eta2ij = 0.0;
188        for(k=0; k<3; k++){
189 <        // 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]);
189 >        eta2ij += eta[i][k] * eta[k][j];
190        }
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 –  }
191  
192 <  info->setBoxM(hm);
193 <  
194 < }
192 >      scaleMat[i][j] = 0.0;
193 >      // identity matrix (see above):
194 >      if (i == j) scaleMat[i][j] = 1.0;
195 >      // Taylor expansion for the exponential truncated at second order:
196 >      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
197  
198 < void NPTf::moveB( void ){
199 <  int i,j,k;
200 <  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] );
198 >      if (i != j)
199 >        if (fabs(scaleMat[i][j]) > offDiagMax)
200 >          offDiagMax = fabs(scaleMat[i][j]);
201      }
294 –  }
295 – }
202  
203 < int NPTf::readyCheck() {
204 <
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;
203 >    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
204 >    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
205    }
206  
207 <  if (!have_target_pressure) {
207 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
208      sprintf( painCave.errMsg,
209 <             "NPTf error: You can't use the NPTf integrator\n"
210 <             "   without a targetPressure!\n"
211 <             );
209 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
210 >             " Check your tauBarostat, as it is probably too small!\n\n"
211 >             " scaleMat = [%lf\t%lf\t%lf]\n"
212 >             "            [%lf\t%lf\t%lf]\n"
213 >             "            [%lf\t%lf\t%lf]\n",
214 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
215 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
216 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
217      painCave.isFatal = 1;
218      simError();
219 <    return -1;
320 <  }
321 <  
322 <  // We must set tauThermostat.
323 <  
324 <  if (!have_tau_thermostat) {
219 >  } else if (offDiagMax > 0.01) {
220      sprintf( painCave.errMsg,
221 <             "NPTf error: If you use the NPTf\n"
222 <             "   integrator, you must set tauThermostat.\n");
221 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
222 >             " Check your tauBarostat, as it is probably too small!\n\n"
223 >             " scaleMat = [%lf\t%lf\t%lf]\n"
224 >             "            [%lf\t%lf\t%lf]\n"
225 >             "            [%lf\t%lf\t%lf]\n",
226 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
227 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
228 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
229      painCave.isFatal = 1;
230      simError();
231 <    return -1;
232 <  }    
231 >  } else {
232 >    info->getBoxM(hm);
233 >    matMul3(hm, scaleMat, hmnew);
234 >    info->setBoxM(hmnew);
235 >  }
236 > }
237  
238 <  // We must set tauBarostat.
239 <  
240 <  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 <  }    
238 > template<typename T> bool NPTf<T>::etaConverged() {
239 >  int i;
240 >  double diffEta, sumEta;
241  
242 <  // We need NkBT a lot, so just set it here:
242 >  sumEta = 0;
243 >  for(i = 0; i < 3; i++)
244 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
245  
246 <  NkBT = (double)info->ndf * kB * targetTemp;
246 >  diffEta = sqrt( sumEta / 3.0 );
247  
248 <  return 1;
248 >  return ( diffEta <= etaTolerance );
249   }
250 +
251 + template<typename T> double NPTf<T>::getConservedQuantity(void){
252 +
253 +  double conservedQuantity;
254 +  double totalEnergy;
255 +  double thermostat_kinetic;
256 +  double thermostat_potential;
257 +  double barostat_kinetic;
258 +  double barostat_potential;
259 +  double trEta;
260 +  double a[3][3], b[3][3];
261 +
262 +  totalEnergy = tStats->getTotalE();
263 +
264 +  thermostat_kinetic = fkBT * tt2 * chi * chi /
265 +    (2.0 * eConvert);
266 +
267 +  thermostat_potential = fkBT* integralOfChidt / eConvert;
268 +
269 +  transposeMat3(eta, a);
270 +  matMul3(a, eta, b);
271 +  trEta = matTrace3(b);
272 +
273 +  barostat_kinetic = NkBT * tb2 * trEta /
274 +    (2.0 * eConvert);
275 +
276 +  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
277 +    eConvert;
278 +
279 +  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
280 +    barostat_kinetic + barostat_potential;
281 +
282 +  return conservedQuantity;
283 +
284 + }
285 +
286 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
287 +  string parameters;
288 +  const int BUFFERSIZE = 2000; // size of the read buffer
289 +  char buffer[BUFFERSIZE];
290 +
291 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
292 +  parameters += buffer;
293 +
294 +  for(int i = 0; i < 3; i++){
295 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
296 +    parameters += buffer;
297 +  }
298 +
299 +  return parameters;
300 +
301 + }

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