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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC

# Line 11 | Line 11 | Integrator::Integrator( SimInfo *theInfo, ForceFields*
11   #include "simError.h"
12  
13  
14 < Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){
15 <  
14 > template<typename T> Integrator<T>::Integrator(SimInfo* theInfo,
15 >                                               ForceFields* the_ff){
16    info = theInfo;
17    myFF = the_ff;
18    isFirst = 1;
# Line 21 | Line 21 | Integrator::Integrator( SimInfo *theInfo, ForceFields*
21    nMols = info->n_mol;
22  
23    // give a little love back to the SimInfo object
24 <  
25 <  if( info->the_integrator != NULL ) delete info->the_integrator;
24 >
25 >  if (info->the_integrator != NULL){
26 >    delete info->the_integrator;
27 >  }
28    info->the_integrator = this;
29  
30    nAtoms = info->n_atoms;
31  
32    // check for constraints
33 <  
34 <  constrainedA    = NULL;
35 <  constrainedB    = NULL;
33 >
34 >  constrainedA = NULL;
35 >  constrainedB = NULL;
36    constrainedDsqr = NULL;
37 <  moving          = NULL;
38 <  moved           = NULL;
39 <  oldPos          = NULL;
40 <  
37 >  moving = NULL;
38 >  moved = NULL;
39 >  oldPos = NULL;
40 >
41    nConstrained = 0;
42  
43    checkConstraints();
44   }
45  
46 < Integrator::~Integrator() {
47 <  
46 <  if( nConstrained ){
46 > template<typename T> Integrator<T>::~Integrator(){
47 >  if (nConstrained){
48      delete[] constrainedA;
49      delete[] constrainedB;
50      delete[] constrainedDsqr;
# Line 51 | Line 52 | Integrator::~Integrator() {
52      delete[] moved;
53      delete[] oldPos;
54    }
54 –  
55   }
56  
57 < void Integrator::checkConstraints( void ){
58 <
59 <
57 > template<typename T> void Integrator<T>::checkConstraints(void){
58    isConstrained = 0;
59  
60 <  Constraint *temp_con;
61 <  Constraint *dummy_plug;
60 >  Constraint* temp_con;
61 >  Constraint* dummy_plug;
62    temp_con = new Constraint[info->n_SRI];
63    nConstrained = 0;
64    int constrained = 0;
65 <  
65 >
66    SRI** theArray;
67 <  for(int i = 0; i < nMols; i++){
68 <    
69 <    theArray = (SRI**) molecules[i].getMyBonds();
72 <    for(int j=0; j<molecules[i].getNBonds(); j++){
73 <      
67 >  for (int i = 0; i < nMols; i++){
68 >    theArray = (SRI * *) molecules[i].getMyBonds();
69 >    for (int j = 0; j < molecules[i].getNBonds(); j++){
70        constrained = theArray[j]->is_constrained();
71 <      
72 <      if(constrained){
73 <        
74 <        dummy_plug = theArray[j]->get_constraint();
75 <        temp_con[nConstrained].set_a( dummy_plug->get_a() );
76 <        temp_con[nConstrained].set_b( dummy_plug->get_b() );
77 <        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
78 <        
79 <        nConstrained++;
84 <        constrained = 0;
71 >
72 >      if (constrained){
73 >        dummy_plug = theArray[j]->get_constraint();
74 >        temp_con[nConstrained].set_a(dummy_plug->get_a());
75 >        temp_con[nConstrained].set_b(dummy_plug->get_b());
76 >        temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
77 >
78 >        nConstrained++;
79 >        constrained = 0;
80        }
81      }
82  
83 <    theArray = (SRI**) molecules[i].getMyBends();
84 <    for(int j=0; j<molecules[i].getNBends(); j++){
90 <      
83 >    theArray = (SRI * *) molecules[i].getMyBends();
84 >    for (int j = 0; j < molecules[i].getNBends(); j++){
85        constrained = theArray[j]->is_constrained();
86 <      
87 <      if(constrained){
88 <        
89 <        dummy_plug = theArray[j]->get_constraint();
90 <        temp_con[nConstrained].set_a( dummy_plug->get_a() );
91 <        temp_con[nConstrained].set_b( dummy_plug->get_b() );
92 <        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
93 <        
94 <        nConstrained++;
101 <        constrained = 0;
86 >
87 >      if (constrained){
88 >        dummy_plug = theArray[j]->get_constraint();
89 >        temp_con[nConstrained].set_a(dummy_plug->get_a());
90 >        temp_con[nConstrained].set_b(dummy_plug->get_b());
91 >        temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
92 >
93 >        nConstrained++;
94 >        constrained = 0;
95        }
96      }
97  
98 <    theArray = (SRI**) molecules[i].getMyTorsions();
99 <    for(int j=0; j<molecules[i].getNTorsions(); j++){
107 <      
98 >    theArray = (SRI * *) molecules[i].getMyTorsions();
99 >    for (int j = 0; j < molecules[i].getNTorsions(); j++){
100        constrained = theArray[j]->is_constrained();
101 <      
102 <      if(constrained){
103 <        
104 <        dummy_plug = theArray[j]->get_constraint();
105 <        temp_con[nConstrained].set_a( dummy_plug->get_a() );
106 <        temp_con[nConstrained].set_b( dummy_plug->get_b() );
107 <        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
108 <        
109 <        nConstrained++;
118 <        constrained = 0;
101 >
102 >      if (constrained){
103 >        dummy_plug = theArray[j]->get_constraint();
104 >        temp_con[nConstrained].set_a(dummy_plug->get_a());
105 >        temp_con[nConstrained].set_b(dummy_plug->get_b());
106 >        temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
107 >
108 >        nConstrained++;
109 >        constrained = 0;
110        }
111      }
112    }
113  
114 <  if(nConstrained > 0){
124 <    
114 >  if (nConstrained > 0){
115      isConstrained = 1;
116  
117 <    if(constrainedA != NULL )    delete[] constrainedA;
118 <    if(constrainedB != NULL )    delete[] constrainedB;
119 <    if(constrainedDsqr != NULL ) delete[] constrainedDsqr;
117 >    if (constrainedA != NULL)
118 >      delete[] constrainedA;
119 >    if (constrainedB != NULL)
120 >      delete[] constrainedB;
121 >    if (constrainedDsqr != NULL)
122 >      delete[] constrainedDsqr;
123  
124 <    constrainedA =    new int[nConstrained];
125 <    constrainedB =    new int[nConstrained];
124 >    constrainedA = new int[nConstrained];
125 >    constrainedB = new int[nConstrained];
126      constrainedDsqr = new double[nConstrained];
127 <    
128 <    for( int i = 0; i < nConstrained; i++){
136 <      
127 >
128 >    for (int i = 0; i < nConstrained; i++){
129        constrainedA[i] = temp_con[i].get_a();
130        constrainedB[i] = temp_con[i].get_b();
131        constrainedDsqr[i] = temp_con[i].get_dsqr();
140 –
132      }
133  
134 <    
134 >
135      // save oldAtoms to check for lode balanceing later on.
136 <    
136 >
137      oldAtoms = nAtoms;
138 <    
138 >
139      moving = new int[nAtoms];
140 <    moved  = new int[nAtoms];
140 >    moved = new int[nAtoms];
141  
142 <    oldPos = new double[nAtoms*3];
142 >    oldPos = new double[nAtoms * 3];
143    }
144 <  
144 >
145    delete[] temp_con;
146   }
147  
148  
149 < void Integrator::integrate( void ){
159 <
149 > template<typename T> void Integrator<T>::integrate(void){
150    int i, j;                         // loop counters
151  
152 <  double runTime     = info->run_time;
153 <  double sampleTime  = info->sampleTime;
154 <  double statusTime  = info->statusTime;
152 >  double runTime = info->run_time;
153 >  double sampleTime = info->sampleTime;
154 >  double statusTime = info->statusTime;
155    double thermalTime = info->thermalTime;
156 +  double resetTime = info->resetTime;
157  
158 +
159    double currSample;
160    double currThermal;
161    double currStatus;
162 <  double currTime;
163 <
162 >  double currReset;
163 >  
164    int calcPot, calcStress;
165    int isError;
166  
167 +  tStats = new Thermo(info);
168 +  statOut = new StatWriter(info);
169 +  dumpOut = new DumpWriter(info);
170  
176 –
177 –  tStats   = new Thermo( info );
178 –  statOut  = new StatWriter( info );
179 –  dumpOut  = new DumpWriter( info );
180 –
171    atoms = info->atoms;
172    DirectionalAtom* dAtom;
173  
# Line 186 | Line 176 | void Integrator::integrate( void ){
176  
177    // initialize the forces before the first step
178  
179 <  myFF->doForces(1,1);
179 >  calcForce(1, 1);
180    
181 <  if( info->setTemp ){
182 <    
193 <    tStats->velocitize();
181 >  if (info->setTemp){
182 >    thermalize();
183    }
184 <  
196 <  dumpOut->writeDump( 0.0 );
197 <  statOut->writeStat( 0.0 );
198 <  
184 >
185    calcPot     = 0;
186    calcStress  = 0;
187 <  currSample  = sampleTime;
188 <  currThermal = thermalTime;
189 <  currStatus  = statusTime;
190 <  currTime    = 0.0;;
187 >  currSample  = sampleTime + info->getTime();
188 >  currThermal = thermalTime+ info->getTime();
189 >  currStatus  = statusTime + info->getTime();
190 >  currReset   = resetTime  + info->getTime();
191  
192 +  dumpOut->writeDump(info->getTime());
193 +  statOut->writeStat(info->getTime());
194  
195    readyCheck();
196  
197   #ifdef IS_MPI
198 <  strcpy( checkPointMsg,
211 <          "The integrator is ready to go." );
198 >  strcpy(checkPointMsg, "The integrator is ready to go.");
199    MPIcheckPoint();
200   #endif // is_mpi
201  
202 <
203 <  pos  = Atom::getPosArray();
217 <  vel  = Atom::getVelArray();
218 <  frc  = Atom::getFrcArray();
219 <  trq  = Atom::getTrqArray();
220 <  Amat = Atom::getAmatArray();
221 <
222 <  while( currTime < runTime ){
223 <
224 <    if( (currTime+dt) >= currStatus ){
202 >  while (info->getTime() < runTime){
203 >    if ((info->getTime() + dt) >= currStatus){
204        calcPot = 1;
205        calcStress = 1;
206      }
207  
208 <    integrateStep( calcPot, calcStress );
230 <      
231 <    currTime += dt;
208 >    integrateStep(calcPot, calcStress);
209  
210 <    if( info->setTemp ){
211 <      if( currTime >= currThermal ){
212 <        tStats->velocitize();
213 <        currThermal += thermalTime;
210 >    info->incrTime(dt);
211 >
212 >    if (info->setTemp){
213 >      if (info->getTime() >= currThermal){
214 >        thermalize();
215 >        currThermal += thermalTime;
216        }
217      }
218  
219 <    if( currTime >= currSample ){
220 <      dumpOut->writeDump( currTime );
219 >    if (info->getTime() >= currSample){
220 >      dumpOut->writeDump(info->getTime());
221        currSample += sampleTime;
222      }
223  
224 <    if( currTime >= currStatus ){
225 <      statOut->writeStat( currTime );
224 >    if (info->getTime() >= currStatus){
225 >      statOut->writeStat(info->getTime());
226        calcPot = 0;
227        calcStress = 0;
228        currStatus += statusTime;
229      }
230  
231 +    if (info->resetIntegrator){
232 +      if (info->getTime() >= currReset){
233 +        this->resetIntegrator();
234 +        currReset += resetTime;
235 +      }
236 +    }
237 +
238   #ifdef IS_MPI
239 <    strcpy( checkPointMsg,
254 <            "successfully took a time step." );
239 >    strcpy(checkPointMsg, "successfully took a time step.");
240      MPIcheckPoint();
241   #endif // is_mpi
257 –
242    }
243  
244 <  dumpOut->writeFinal(currTime);
244 >  dumpOut->writeFinal(info->getTime());
245  
246    delete dumpOut;
247    delete statOut;
248   }
249  
250 < void Integrator::integrateStep( int calcPot, int calcStress ){
251 <
268 <
269 <      
250 > template<typename T> void Integrator<T>::integrateStep(int calcPot,
251 >                                                       int calcStress){
252    // Position full step, and velocity half step
271 –
253    preMove();
254 +
255    moveA();
274 –  if( nConstrained ) constrainA();
256  
257 +  if (nConstrained){
258 +    constrainA();
259 +  }
260 +
261 +
262 + #ifdef IS_MPI
263 +  strcpy(checkPointMsg, "Succesful moveA\n");
264 +  MPIcheckPoint();
265 + #endif // is_mpi
266 +
267 +
268    // calc forces
269  
270 <  myFF->doForces(calcPot,calcStress);
270 >  calcForce(calcPot, calcStress);
271  
272 + #ifdef IS_MPI
273 +  strcpy(checkPointMsg, "Succesful doForces\n");
274 +  MPIcheckPoint();
275 + #endif // is_mpi
276 +
277 +
278    // finish the velocity  half step
279 <  
279 >
280    moveB();
281 <  if( nConstrained ) constrainB();
282 <  
281 >
282 >  if (nConstrained){
283 >    constrainB();
284 >  }
285 >
286 > #ifdef IS_MPI
287 >  strcpy(checkPointMsg, "Succesful moveB\n");
288 >  MPIcheckPoint();
289 > #endif // is_mpi
290   }
291  
292  
293 < void Integrator::moveA( void ){
294 <  
290 <  int i,j,k;
291 <  int atomIndex, aMatIndex;
293 > template<typename T> void Integrator<T>::moveA(void){
294 >  int i, j;
295    DirectionalAtom* dAtom;
296 <  double Tb[3];
297 <  double ji[3];
296 >  double Tb[3], ji[3];
297 >  double A[3][3], I[3][3];
298    double angle;
299 +  double vel[3], pos[3], frc[3];
300 +  double mass;
301  
302 +  for (i = 0; i < nAtoms; i++){
303 +    atoms[i]->getVel(vel);
304 +    atoms[i]->getPos(pos);
305 +    atoms[i]->getFrc(frc);
306  
307 +    mass = atoms[i]->getMass();
308  
309 <  for( i=0; i<nAtoms; i++ ){
310 <    atomIndex = i * 3;
311 <    aMatIndex = i * 9;
309 >    for (j = 0; j < 3; j++){
310 >      // velocity half step
311 >      vel[j] += (dt2 * frc[j] / mass) * eConvert;
312 >      // position whole step
313 >      pos[j] += dt * vel[j];
314 >    }
315  
316 <    // velocity half step
317 <    for( j=atomIndex; j<(atomIndex+3); j++ )
305 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
316 >    atoms[i]->setVel(vel);
317 >    atoms[i]->setPos(pos);
318  
319 <    // position whole step    
320 <    for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j];
309 <    
310 <    if( atoms[i]->isDirectional() ){
319 >    if (atoms[i]->isDirectional()){
320 >      dAtom = (DirectionalAtom *) atoms[i];
321  
312 –      dAtom = (DirectionalAtom *)atoms[i];
313 –          
322        // get and convert the torque to body frame
323 <      
324 <      Tb[0] = dAtom->getTx();
325 <      Tb[1] = dAtom->getTy();
326 <      Tb[2] = dAtom->getTz();
319 <      
320 <      dAtom->lab2Body( Tb );
321 <      
323 >
324 >      dAtom->getTrq(Tb);
325 >      dAtom->lab2Body(Tb);
326 >
327        // get the angular momentum, and propagate a half step
328 <      
329 <      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
330 <      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
331 <      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
332 <      
328 >
329 >      dAtom->getJ(ji);
330 >
331 >      for (j = 0; j < 3; j++)
332 >        ji[j] += (dt2 * Tb[j]) * eConvert;
333 >
334        // use the angular velocities to propagate the rotation matrix a
335        // full time step
336 <      
336 >
337 >      dAtom->getA(A);
338 >      dAtom->getI(I);
339 >
340        // rotate about the x-axis      
341 <      angle = dt2 * ji[0] / dAtom->getIxx();
342 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
343 <      
341 >      angle = dt2 * ji[0] / I[0][0];
342 >      this->rotate(1, 2, angle, ji, A);
343 >
344        // rotate about the y-axis
345 <      angle = dt2 * ji[1] / dAtom->getIyy();
346 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
347 <      
345 >      angle = dt2 * ji[1] / I[1][1];
346 >      this->rotate(2, 0, angle, ji, A);
347 >
348        // rotate about the z-axis
349 <      angle = dt * ji[2] / dAtom->getIzz();
350 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
351 <      
349 >      angle = dt * ji[2] / I[2][2];
350 >      this->rotate(0, 1, angle, ji, A);
351 >
352        // rotate about the y-axis
353 <      angle = dt2 * ji[1] / dAtom->getIyy();
354 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
355 <      
356 <       // rotate about the x-axis
357 <      angle = dt2 * ji[0] / dAtom->getIxx();
358 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
359 <      
360 <      dAtom->setJx( ji[0] );
361 <      dAtom->setJy( ji[1] );
362 <      dAtom->setJz( ji[2] );
353 >      angle = dt2 * ji[1] / I[1][1];
354 >      this->rotate(2, 0, angle, ji, A);
355 >
356 >      // rotate about the x-axis
357 >      angle = dt2 * ji[0] / I[0][0];
358 >      this->rotate(1, 2, angle, ji, A);
359 >
360 >
361 >      dAtom->setJ(ji);
362 >      dAtom->setA(A);
363      }
355 –    
364    }
365   }
366  
367  
368 < void Integrator::moveB( void ){
369 <  int i,j,k;
362 <  int atomIndex;
368 > template<typename T> void Integrator<T>::moveB(void){
369 >  int i, j;
370    DirectionalAtom* dAtom;
371 <  double Tb[3];
372 <  double ji[3];
371 >  double Tb[3], ji[3];
372 >  double vel[3], frc[3];
373 >  double mass;
374  
375 <  for( i=0; i<nAtoms; i++ ){
376 <    atomIndex = i * 3;
375 >  for (i = 0; i < nAtoms; i++){
376 >    atoms[i]->getVel(vel);
377 >    atoms[i]->getFrc(frc);
378  
379 +    mass = atoms[i]->getMass();
380 +
381      // velocity half step
382 <    for( j=atomIndex; j<(atomIndex+3); j++ )
383 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
382 >    for (j = 0; j < 3; j++)
383 >      vel[j] += (dt2 * frc[j] / mass) * eConvert;
384  
385 <    if( atoms[i]->isDirectional() ){
386 <      
387 <      dAtom = (DirectionalAtom *)atoms[i];
388 <      
389 <      // get and convert the torque to body frame
390 <      
391 <      Tb[0] = dAtom->getTx();
392 <      Tb[1] = dAtom->getTy();
393 <      Tb[2] = dAtom->getTz();
394 <      
395 <      dAtom->lab2Body( Tb );
396 <      
397 <      // get the angular momentum, and complete the angular momentum
398 <      // half step
399 <      
400 <      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
401 <      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
402 <      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
403 <      
393 <      dAtom->setJx( ji[0] );
394 <      dAtom->setJy( ji[1] );
395 <      dAtom->setJz( ji[2] );
385 >    atoms[i]->setVel(vel);
386 >
387 >    if (atoms[i]->isDirectional()){
388 >      dAtom = (DirectionalAtom *) atoms[i];
389 >
390 >      // get and convert the torque to body frame      
391 >
392 >      dAtom->getTrq(Tb);
393 >      dAtom->lab2Body(Tb);
394 >
395 >      // get the angular momentum, and propagate a half step
396 >
397 >      dAtom->getJ(ji);
398 >
399 >      for (j = 0; j < 3; j++)
400 >        ji[j] += (dt2 * Tb[j]) * eConvert;
401 >
402 >
403 >      dAtom->setJ(ji);
404      }
405    }
398 –
406   }
407  
408 < void Integrator::preMove( void ){
409 <  int i;
408 > template<typename T> void Integrator<T>::preMove(void){
409 >  int i, j;
410 >  double pos[3];
411  
412 <  if( nConstrained ){
412 >  if (nConstrained){
413 >    for (i = 0; i < nAtoms; i++){
414 >      atoms[i]->getPos(pos);
415  
416 <    for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
416 >      for (j = 0; j < 3; j++){
417 >        oldPos[3 * i + j] = pos[j];
418 >      }
419 >    }
420    }
421 < }  
421 > }
422  
423 < void Integrator::constrainA(){
424 <
412 <  int i,j,k;
423 > template<typename T> void Integrator<T>::constrainA(){
424 >  int i, j, k;
425    int done;
426 +  double posA[3], posB[3];
427 +  double velA[3], velB[3];
428    double pab[3];
429    double rab[3];
430    int a, b, ax, ay, az, bx, by, bz;
# Line 422 | Line 436 | void Integrator::constrainA(){
436    double gab;
437    int iteration;
438  
439 <
426 <  
427 <  for( i=0; i<nAtoms; i++){
428 <    
439 >  for (i = 0; i < nAtoms; i++){
440      moving[i] = 0;
441 <    moved[i]  = 1;
441 >    moved[i] = 1;
442    }
443  
444    iteration = 0;
445    done = 0;
446 <  while( !done && (iteration < maxIteration )){
436 <
446 >  while (!done && (iteration < maxIteration)){
447      done = 1;
448 <    for(i=0; i<nConstrained; i++){
439 <
448 >    for (i = 0; i < nConstrained; i++){
449        a = constrainedA[i];
450        b = constrainedB[i];
442 –      
443 –      ax = (a*3) + 0;
444 –      ay = (a*3) + 1;
445 –      az = (a*3) + 2;
451  
452 <      bx = (b*3) + 0;
453 <      by = (b*3) + 1;
454 <      bz = (b*3) + 2;
452 >      ax = (a * 3) + 0;
453 >      ay = (a * 3) + 1;
454 >      az = (a * 3) + 2;
455  
456 <      if( moved[a] || moved[b] ){
457 <        
458 <        pab[0] = pos[ax] - pos[bx];
454 <        pab[1] = pos[ay] - pos[by];
455 <        pab[2] = pos[az] - pos[bz];
456 >      bx = (b * 3) + 0;
457 >      by = (b * 3) + 1;
458 >      bz = (b * 3) + 2;
459  
460 <        //periodic boundary condition
460 >      if (moved[a] || moved[b]){
461 >        atoms[a]->getPos(posA);
462 >        atoms[b]->getPos(posB);
463  
464 <        info->wrapVector( pab );
464 >        for (j = 0; j < 3; j++)
465 >          pab[j] = posA[j] - posB[j];
466  
467 <        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
467 >        //periodic boundary condition
468  
469 <        rabsq = constrainedDsqr[i];
464 <        diffsq = rabsq - pabsq;
469 >        info->wrapVector(pab);
470  
471 <        // the original rattle code from alan tidesley
467 <        if (fabs(diffsq) > (tol*rabsq*2)) {
468 <          rab[0] = oldPos[ax] - oldPos[bx];
469 <          rab[1] = oldPos[ay] - oldPos[by];
470 <          rab[2] = oldPos[az] - oldPos[bz];
471 >        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
472  
473 <          info->wrapVector( rab );
473 >        rabsq = constrainedDsqr[i];
474 >        diffsq = rabsq - pabsq;
475  
476 <          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
476 >        // the original rattle code from alan tidesley
477 >        if (fabs(diffsq) > (tol * rabsq * 2)){
478 >          rab[0] = oldPos[ax] - oldPos[bx];
479 >          rab[1] = oldPos[ay] - oldPos[by];
480 >          rab[2] = oldPos[az] - oldPos[bz];
481  
482 <          rpabsq = rpab * rpab;
482 >          info->wrapVector(rab);
483  
484 +          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
485  
486 <          if (rpabsq < (rabsq * -diffsq)){
486 >          rpabsq = rpab * rpab;
487  
488 +
489 +          if (rpabsq < (rabsq * -diffsq)){
490   #ifdef IS_MPI
491 <            a = atoms[a]->getGlobalIndex();
492 <            b = atoms[b]->getGlobalIndex();
491 >            a = atoms[a]->getGlobalIndex();
492 >            b = atoms[b]->getGlobalIndex();
493   #endif //is_mpi
494 <            sprintf( painCave.errMsg,
495 <                     "Constraint failure in constrainA at atom %d and %d.\n",
496 <                     a, b );
497 <            painCave.isFatal = 1;
498 <            simError();
499 <          }
494 >            sprintf(painCave.errMsg,
495 >                    "Constraint failure in constrainA at atom %d and %d.\n", a,
496 >                    b);
497 >            painCave.isFatal = 1;
498 >            simError();
499 >          }
500  
501 <          rma = 1.0 / atoms[a]->getMass();
502 <          rmb = 1.0 / atoms[b]->getMass();
501 >          rma = 1.0 / atoms[a]->getMass();
502 >          rmb = 1.0 / atoms[b]->getMass();
503  
504 <          gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
504 >          gab = diffsq / (2.0 * (rma + rmb) * rpab);
505  
506            dx = rab[0] * gab;
507            dy = rab[1] * gab;
508            dz = rab[2] * gab;
509  
510 <          pos[ax] += rma * dx;
511 <          pos[ay] += rma * dy;
512 <          pos[az] += rma * dz;
510 >          posA[0] += rma * dx;
511 >          posA[1] += rma * dy;
512 >          posA[2] += rma * dz;
513  
514 <          pos[bx] -= rmb * dx;
506 <          pos[by] -= rmb * dy;
507 <          pos[bz] -= rmb * dz;
514 >          atoms[a]->setPos(posA);
515  
516 +          posB[0] -= rmb * dx;
517 +          posB[1] -= rmb * dy;
518 +          posB[2] -= rmb * dz;
519 +
520 +          atoms[b]->setPos(posB);
521 +
522            dx = dx / dt;
523            dy = dy / dt;
524            dz = dz / dt;
525  
526 <          vel[ax] += rma * dx;
514 <          vel[ay] += rma * dy;
515 <          vel[az] += rma * dz;
526 >          atoms[a]->getVel(velA);
527  
528 <          vel[bx] -= rmb * dx;
529 <          vel[by] -= rmb * dy;
530 <          vel[bz] -= rmb * dz;
528 >          velA[0] += rma * dx;
529 >          velA[1] += rma * dy;
530 >          velA[2] += rma * dz;
531  
532 <          moving[a] = 1;
533 <          moving[b] = 1;
534 <          done = 0;
535 <        }
532 >          atoms[a]->setVel(velA);
533 >
534 >          atoms[b]->getVel(velB);
535 >
536 >          velB[0] -= rmb * dx;
537 >          velB[1] -= rmb * dy;
538 >          velB[2] -= rmb * dz;
539 >
540 >          atoms[b]->setVel(velB);
541 >
542 >          moving[a] = 1;
543 >          moving[b] = 1;
544 >          done = 0;
545 >        }
546        }
547      }
548 <    
549 <    for(i=0; i<nAtoms; i++){
529 <      
548 >
549 >    for (i = 0; i < nAtoms; i++){
550        moved[i] = moving[i];
551        moving[i] = 0;
552      }
# Line 534 | Line 554 | void Integrator::constrainA(){
554      iteration++;
555    }
556  
557 <  if( !done ){
558 <
559 <    sprintf( painCave.errMsg,
560 <             "Constraint failure in constrainA, too many iterations: %d\n",
541 <             iteration );
557 >  if (!done){
558 >    sprintf(painCave.errMsg,
559 >            "Constraint failure in constrainA, too many iterations: %d\n",
560 >            iteration);
561      painCave.isFatal = 1;
562      simError();
563    }
545 –
564   }
565  
566 < void Integrator::constrainB( void ){
567 <  
550 <  int i,j,k;
566 > template<typename T> void Integrator<T>::constrainB(void){
567 >  int i, j, k;
568    int done;
569 +  double posA[3], posB[3];
570 +  double velA[3], velB[3];
571    double vxab, vyab, vzab;
572    double rab[3];
573    int a, b, ax, ay, az, bx, by, bz;
# Line 559 | Line 578 | void Integrator::constrainB( void ){
578    double gab;
579    int iteration;
580  
581 <  for(i=0; i<nAtoms; i++){
581 >  for (i = 0; i < nAtoms; i++){
582      moving[i] = 0;
583      moved[i] = 1;
584    }
585  
586    done = 0;
587    iteration = 0;
588 <  while( !done && (iteration < maxIteration ) ){
570 <
588 >  while (!done && (iteration < maxIteration)){
589      done = 1;
590  
591 <    for(i=0; i<nConstrained; i++){
574 <      
591 >    for (i = 0; i < nConstrained; i++){
592        a = constrainedA[i];
593        b = constrainedB[i];
594  
595 <      ax = (a*3) + 0;
596 <      ay = (a*3) + 1;
597 <      az = (a*3) + 2;
595 >      ax = (a * 3) + 0;
596 >      ay = (a * 3) + 1;
597 >      az = (a * 3) + 2;
598  
599 <      bx = (b*3) + 0;
600 <      by = (b*3) + 1;
601 <      bz = (b*3) + 2;
599 >      bx = (b * 3) + 0;
600 >      by = (b * 3) + 1;
601 >      bz = (b * 3) + 2;
602  
603 <      if( moved[a] || moved[b] ){
604 <        
605 <        vxab = vel[ax] - vel[bx];
589 <        vyab = vel[ay] - vel[by];
590 <        vzab = vel[az] - vel[bz];
603 >      if (moved[a] || moved[b]){
604 >        atoms[a]->getVel(velA);
605 >        atoms[b]->getVel(velB);
606  
607 <        rab[0] = pos[ax] - pos[bx];
608 <        rab[1] = pos[ay] - pos[by];
609 <        rab[2] = pos[az] - pos[bz];
595 <        
596 <        info->wrapVector( rab );
597 <        
598 <        rma = 1.0 / atoms[a]->getMass();
599 <        rmb = 1.0 / atoms[b]->getMass();
607 >        vxab = velA[0] - velB[0];
608 >        vyab = velA[1] - velB[1];
609 >        vzab = velA[2] - velB[2];
610  
611 <        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
612 <          
603 <        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
611 >        atoms[a]->getPos(posA);
612 >        atoms[b]->getPos(posB);
613  
614 <        if (fabs(gab) > tol) {
615 <          
607 <          dx = rab[0] * gab;
608 <          dy = rab[1] * gab;
609 <          dz = rab[2] * gab;
610 <          
611 <          vel[ax] += rma * dx;
612 <          vel[ay] += rma * dy;
613 <          vel[az] += rma * dz;
614 >        for (j = 0; j < 3; j++)
615 >          rab[j] = posA[j] - posB[j];
616  
617 <          vel[bx] -= rmb * dx;
618 <          vel[by] -= rmb * dy;
619 <          vel[bz] -= rmb * dz;
620 <          
621 <          moving[a] = 1;
622 <          moving[b] = 1;
623 <          done = 0;
624 <        }
617 >        info->wrapVector(rab);
618 >
619 >        rma = 1.0 / atoms[a]->getMass();
620 >        rmb = 1.0 / atoms[b]->getMass();
621 >
622 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
623 >
624 >        gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
625 >
626 >        if (fabs(gab) > tol){
627 >          dx = rab[0] * gab;
628 >          dy = rab[1] * gab;
629 >          dz = rab[2] * gab;
630 >
631 >          velA[0] += rma * dx;
632 >          velA[1] += rma * dy;
633 >          velA[2] += rma * dz;
634 >
635 >          atoms[a]->setVel(velA);
636 >
637 >          velB[0] -= rmb * dx;
638 >          velB[1] -= rmb * dy;
639 >          velB[2] -= rmb * dz;
640 >
641 >          atoms[b]->setVel(velB);
642 >
643 >          moving[a] = 1;
644 >          moving[b] = 1;
645 >          done = 0;
646 >        }
647        }
648      }
649  
650 <    for(i=0; i<nAtoms; i++){
650 >    for (i = 0; i < nAtoms; i++){
651        moved[i] = moving[i];
652        moving[i] = 0;
653      }
654 <    
654 >
655      iteration++;
656    }
657  
658 <  if( !done ){
659 <
660 <  
661 <    sprintf( painCave.errMsg,
638 <             "Constraint failure in constrainB, too many iterations: %d\n",
639 <             iteration );
658 >  if (!done){
659 >    sprintf(painCave.errMsg,
660 >            "Constraint failure in constrainB, too many iterations: %d\n",
661 >            iteration);
662      painCave.isFatal = 1;
663      simError();
664 <  }
643 <
664 >  }
665   }
666  
667 <
668 <
669 <
670 <
650 <
651 <
652 < void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
653 <                         double A[9] ){
654 <
655 <  int i,j,k;
667 > template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
668 >                                                double angle, double ji[3],
669 >                                                double A[3][3]){
670 >  int i, j, k;
671    double sinAngle;
672    double cosAngle;
673    double angleSqr;
# Line 664 | Line 679 | void Integrator::rotate( int axes1, int axes2, double
679  
680    // initialize the tempA
681  
682 <  for(i=0; i<3; i++){
683 <    for(j=0; j<3; j++){
684 <      tempA[j][i] = A[3*i + j];
682 >  for (i = 0; i < 3; i++){
683 >    for (j = 0; j < 3; j++){
684 >      tempA[j][i] = A[i][j];
685      }
686    }
687  
688    // initialize the tempJ
689  
690 <  for( i=0; i<3; i++) tempJ[i] = ji[i];
691 <  
690 >  for (i = 0; i < 3; i++)
691 >    tempJ[i] = ji[i];
692 >
693    // initalize rot as a unit matrix
694  
695    rot[0][0] = 1.0;
# Line 683 | Line 699 | void Integrator::rotate( int axes1, int axes2, double
699    rot[1][0] = 0.0;
700    rot[1][1] = 1.0;
701    rot[1][2] = 0.0;
702 <  
702 >
703    rot[2][0] = 0.0;
704    rot[2][1] = 0.0;
705    rot[2][2] = 1.0;
706 <  
706 >
707    // use a small angle aproximation for sin and cosine
708  
709 <  angleSqr  = angle * angle;
709 >  angleSqr = angle * angle;
710    angleSqrOver4 = angleSqr / 4.0;
711    top = 1.0 - angleSqrOver4;
712    bottom = 1.0 + angleSqrOver4;
# Line 703 | Line 719 | void Integrator::rotate( int axes1, int axes2, double
719  
720    rot[axes1][axes2] = sinAngle;
721    rot[axes2][axes1] = -sinAngle;
722 <  
722 >
723    // rotate the momentum acoording to: ji[] = rot[][] * ji[]
724 <  
725 <  for(i=0; i<3; i++){
724 >
725 >  for (i = 0; i < 3; i++){
726      ji[i] = 0.0;
727 <    for(k=0; k<3; k++){
727 >    for (k = 0; k < 3; k++){
728        ji[i] += rot[i][k] * tempJ[k];
729      }
730    }
# Line 721 | Line 737 | void Integrator::rotate( int axes1, int axes2, double
737    // calculation as:
738    //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
739  
740 <  for(i=0; i<3; i++){
741 <    for(j=0; j<3; j++){
742 <      A[3*j + i] = 0.0;
743 <      for(k=0; k<3; k++){
744 <        A[3*j + i] += tempA[i][k] * rot[j][k];
740 >  for (i = 0; i < 3; i++){
741 >    for (j = 0; j < 3; j++){
742 >      A[j][i] = 0.0;
743 >      for (k = 0; k < 3; k++){
744 >        A[j][i] += tempA[i][k] * rot[j][k];
745        }
746      }
747    }
748   }
749 +
750 + template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
751 +  myFF->doForces(calcPot, calcStress);
752 + }
753 +
754 + template<typename T> void Integrator<T>::thermalize(){
755 +  tStats->velocitize();
756 + }

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