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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2 < #include <cstdlib>
3 < #include <cmath>
2 > #include <stdlib.h>
3 > #include <math.h>
4  
5   #ifdef IS_MPI
6   #include "mpiSimulation.hpp"
7   #include <unistd.h>
8   #endif //is_mpi
9  
10 + #ifdef PROFILE
11 + #include "mdProfile.hpp"
12 + #endif // profile
13 +
14   #include "Integrator.hpp"
15   #include "simError.h"
16  
17  
18 < Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){
19 <  
18 > template<typename T> Integrator<T>::Integrator(SimInfo* theInfo,
19 >                                               ForceFields* the_ff){
20    info = theInfo;
21    myFF = the_ff;
22    isFirst = 1;
# Line 21 | Line 25 | Integrator::Integrator( SimInfo *theInfo, ForceFields*
25    nMols = info->n_mol;
26  
27    // give a little love back to the SimInfo object
24 –  
25 –  if( info->the_integrator != NULL ) delete info->the_integrator;
26 –  info->the_integrator = this;
28  
29 <  nAtoms = info->n_atoms;
29 >  if (info->the_integrator != NULL){
30 >    delete info->the_integrator;
31 >  }
32  
33 <  std::cerr << "integ nAtoms = "  << nAtoms << "\n";
34 <
33 >  nAtoms = info->n_atoms;
34 >  integrableObjects = info->integrableObjects;
35 >
36    // check for constraints
37 <  
38 <  constrainedA    = NULL;
39 <  constrainedB    = NULL;
37 >
38 >  constrainedA = NULL;
39 >  constrainedB = NULL;
40    constrainedDsqr = NULL;
41 <  moving          = NULL;
42 <  moved           = NULL;
43 <  oldPos          = NULL;
44 <  
41 >  moving = NULL;
42 >  moved = NULL;
43 >  oldPos = NULL;
44 >
45    nConstrained = 0;
46  
47    checkConstraints();
48 +
49   }
50  
51 < Integrator::~Integrator() {
52 <  
48 <  if( nConstrained ){
51 > template<typename T> Integrator<T>::~Integrator(){
52 >  if (nConstrained){
53      delete[] constrainedA;
54      delete[] constrainedB;
55      delete[] constrainedDsqr;
# Line 53 | Line 57 | Integrator::~Integrator() {
57      delete[] moved;
58      delete[] oldPos;
59    }
56 –  
60   }
61  
62 < void Integrator::checkConstraints( void ){
60 <
61 <
62 > template<typename T> void Integrator<T>::checkConstraints(void){
63    isConstrained = 0;
64  
65 <  Constraint *temp_con;
66 <  Constraint *dummy_plug;
65 >  Constraint* temp_con;
66 >  Constraint* dummy_plug;
67    temp_con = new Constraint[info->n_SRI];
68    nConstrained = 0;
69    int constrained = 0;
70 <  
70 >
71    SRI** theArray;
72 <  for(int i = 0; i < nMols; i++){
73 <    
74 <    theArray = (SRI**) molecules[i].getMyBonds();
75 <    for(int j=0; j<molecules[i].getNBonds(); j++){
75 <      
72 >  for (int i = 0; i < nMols; i++){
73 >
74 >          theArray = (SRI * *) molecules[i].getMyBonds();
75 >    for (int j = 0; j < molecules[i].getNBonds(); j++){
76        constrained = theArray[j]->is_constrained();
77  
78 <      std::cerr << "Is the folowing bond constrained \n";
79 <      theArray[j]->printMe();
80 <      
81 <      if(constrained){
82 <        
83 <        std::cerr << "Yes\n";
78 >      if (constrained){
79 >        dummy_plug = theArray[j]->get_constraint();
80 >        temp_con[nConstrained].set_a(dummy_plug->get_a());
81 >        temp_con[nConstrained].set_b(dummy_plug->get_b());
82 >        temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
83  
84 <        dummy_plug = theArray[j]->get_constraint();
85 <        temp_con[nConstrained].set_a( dummy_plug->get_a() );
86 <        temp_con[nConstrained].set_b( dummy_plug->get_b() );
88 <        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
89 <        
90 <        nConstrained++;
91 <        constrained = 0;
92 <      }
93 <      else std::cerr << "No.\n";
84 >        nConstrained++;
85 >        constrained = 0;
86 >      }
87      }
88  
89 <    theArray = (SRI**) molecules[i].getMyBends();
90 <    for(int j=0; j<molecules[i].getNBends(); j++){
98 <      
89 >    theArray = (SRI * *) molecules[i].getMyBends();
90 >    for (int j = 0; j < molecules[i].getNBends(); j++){
91        constrained = theArray[j]->is_constrained();
92 <      
93 <      if(constrained){
94 <        
95 <        dummy_plug = theArray[j]->get_constraint();
96 <        temp_con[nConstrained].set_a( dummy_plug->get_a() );
97 <        temp_con[nConstrained].set_b( dummy_plug->get_b() );
98 <        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
99 <        
100 <        nConstrained++;
109 <        constrained = 0;
92 >
93 >      if (constrained){
94 >        dummy_plug = theArray[j]->get_constraint();
95 >        temp_con[nConstrained].set_a(dummy_plug->get_a());
96 >        temp_con[nConstrained].set_b(dummy_plug->get_b());
97 >        temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
98 >
99 >        nConstrained++;
100 >        constrained = 0;
101        }
102      }
103  
104 <    theArray = (SRI**) molecules[i].getMyTorsions();
105 <    for(int j=0; j<molecules[i].getNTorsions(); j++){
115 <      
104 >    theArray = (SRI * *) molecules[i].getMyTorsions();
105 >    for (int j = 0; j < molecules[i].getNTorsions(); j++){
106        constrained = theArray[j]->is_constrained();
107 <      
108 <      if(constrained){
109 <        
110 <        dummy_plug = theArray[j]->get_constraint();
111 <        temp_con[nConstrained].set_a( dummy_plug->get_a() );
112 <        temp_con[nConstrained].set_b( dummy_plug->get_b() );
113 <        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
114 <        
115 <        nConstrained++;
126 <        constrained = 0;
107 >
108 >      if (constrained){
109 >        dummy_plug = theArray[j]->get_constraint();
110 >        temp_con[nConstrained].set_a(dummy_plug->get_a());
111 >        temp_con[nConstrained].set_b(dummy_plug->get_b());
112 >        temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
113 >
114 >        nConstrained++;
115 >        constrained = 0;
116        }
117      }
118    }
119  
120 <  if(nConstrained > 0){
121 <    
120 >
121 >  if (nConstrained > 0){
122      isConstrained = 1;
123  
124 <    if(constrainedA != NULL )    delete[] constrainedA;
125 <    if(constrainedB != NULL )    delete[] constrainedB;
126 <    if(constrainedDsqr != NULL ) delete[] constrainedDsqr;
124 >    if (constrainedA != NULL)
125 >      delete[] constrainedA;
126 >    if (constrainedB != NULL)
127 >      delete[] constrainedB;
128 >    if (constrainedDsqr != NULL)
129 >      delete[] constrainedDsqr;
130  
131 <    constrainedA =    new int[nConstrained];
132 <    constrainedB =    new int[nConstrained];
131 >    constrainedA = new int[nConstrained];
132 >    constrainedB = new int[nConstrained];
133      constrainedDsqr = new double[nConstrained];
134 <    
135 <    for( int i = 0; i < nConstrained; i++){
144 <      
134 >
135 >    for (int i = 0; i < nConstrained; i++){
136        constrainedA[i] = temp_con[i].get_a();
137        constrainedB[i] = temp_con[i].get_b();
138        constrainedDsqr[i] = temp_con[i].get_dsqr();
148 –
139      }
140  
141 <    
142 <    // save oldAtoms to check for lode balanceing later on.
143 <    
141 >
142 >    // save oldAtoms to check for lode balancing later on.
143 >
144      oldAtoms = nAtoms;
145 <    
145 >
146      moving = new int[nAtoms];
147 <    moved  = new int[nAtoms];
147 >    moved = new int[nAtoms];
148  
149 <    oldPos = new double[nAtoms*3];
149 >    oldPos = new double[nAtoms * 3];
150    }
151 <  
151 >
152    delete[] temp_con;
153   }
154  
155  
156 < void Integrator::integrate( void ){
156 > template<typename T> void Integrator<T>::integrate(void){
157  
158 <  int i, j;                         // loop counters
159 <
160 <  double runTime     = info->run_time;
171 <  double sampleTime  = info->sampleTime;
172 <  double statusTime  = info->statusTime;
158 >  double runTime = info->run_time;
159 >  double sampleTime = info->sampleTime;
160 >  double statusTime = info->statusTime;
161    double thermalTime = info->thermalTime;
162 +  double resetTime = info->resetTime;
163  
164 +  double difference;
165    double currSample;
166    double currThermal;
167    double currStatus;
168 <  double currTime;
168 >  double currReset;
169  
170    int calcPot, calcStress;
181 –  int isError;
171  
172 +  tStats = new Thermo(info);
173 +  statOut = new StatWriter(info);
174 +  dumpOut = new DumpWriter(info);
175  
184 –
185 –  tStats   = new Thermo( info );
186 –  statOut  = new StatWriter( info );
187 –  dumpOut  = new DumpWriter( info );
188 –
176    atoms = info->atoms;
190 –  DirectionalAtom* dAtom;
177  
178    dt = info->dt;
179    dt2 = 0.5 * dt;
180  
181 +  readyCheck();
182 +
183 +  // remove center of mass drift velocity (in case we passed in a configuration
184 +  // that was drifting
185 +  tStats->removeCOMdrift();
186 +
187 +  // initialize the retraints if necessary
188 +  if (info->useThermInt) {
189 +    myFF->initRestraints();
190 +  }
191 +
192    // initialize the forces before the first step
193  
194 <  myFF->doForces(1,1);
194 >  calcForce(1, 1);
195    
196 <  if( info->setTemp ){
197 <    
198 <    tStats->velocitize();
196 >  if (nConstrained){
197 >    preMove();
198 >    constrainA();
199 >    calcForce(1, 1);
200 >    constrainB();
201    }
202    
203 <  dumpOut->writeDump( 0.0 );
204 <  statOut->writeStat( 0.0 );
205 <  
203 >  if (info->setTemp){
204 >    thermalize();
205 >  }
206 >
207    calcPot     = 0;
208    calcStress  = 0;
209 <  currSample  = sampleTime;
210 <  currThermal = thermalTime;
211 <  currStatus  = statusTime;
212 <  currTime    = 0.0;;
209 >  currSample  = sampleTime + info->getTime();
210 >  currThermal = thermalTime+ info->getTime();
211 >  currStatus  = statusTime + info->getTime();
212 >  currReset   = resetTime  + info->getTime();
213  
214 +  dumpOut->writeDump(info->getTime());
215 +  statOut->writeStat(info->getTime());
216  
215 –  readyCheck();
217  
218   #ifdef IS_MPI
219 <  strcpy( checkPointMsg,
219 <          "The integrator is ready to go." );
219 >  strcpy(checkPointMsg, "The integrator is ready to go.");
220    MPIcheckPoint();
221   #endif // is_mpi
222  
223 <
224 <  pos  = Atom::getPosArray();
225 <  vel  = Atom::getVelArray();
226 <  frc  = Atom::getFrcArray();
227 <
228 <  while( currTime < runTime ){
229 <
230 <    if( (currTime+dt) >= currStatus ){
223 >  while (info->getTime() < runTime && !stopIntegrator()){
224 >    difference = info->getTime() + dt - currStatus;
225 >    if (difference > 0 || fabs(difference) < 1e-4 ){
226        calcPot = 1;
227        calcStress = 1;
228      }
229  
230 <    std::cerr << currTime << "\n";
230 > #ifdef PROFILE
231 >    startProfile( pro1 );
232 > #endif
233 >    
234 >    integrateStep(calcPot, calcStress);
235  
236 <    integrateStep( calcPot, calcStress );
237 <      
239 <    currTime += dt;
236 > #ifdef PROFILE
237 >    endProfile( pro1 );
238  
239 <    if( info->setTemp ){
240 <      if( currTime >= currThermal ){
241 <        tStats->velocitize();
242 <        currThermal += thermalTime;
239 >    startProfile( pro2 );
240 > #endif // profile
241 >
242 >    info->incrTime(dt);
243 >
244 >    if (info->setTemp){
245 >      if (info->getTime() >= currThermal){
246 >        thermalize();
247 >        currThermal += thermalTime;
248        }
249      }
250  
251 <    if( currTime >= currSample ){
252 <      dumpOut->writeDump( currTime );
251 >    if (info->getTime() >= currSample){
252 >      dumpOut->writeDump(info->getTime());
253        currSample += sampleTime;
254      }
255  
256 <    if( currTime >= currStatus ){
257 <      statOut->writeStat( currTime );
258 <      calcPot = 0;
256 >    if (info->getTime() >= currStatus){
257 >      statOut->writeStat(info->getTime());
258 >      statOut->writeRaw(info->getTime());
259 >      calcPot = 0;
260        calcStress = 0;
261        currStatus += statusTime;
262 <    }
262 >    }
263  
264 +    if (info->resetIntegrator){
265 +      if (info->getTime() >= currReset){
266 +        this->resetIntegrator();
267 +        currReset += resetTime;
268 +      }
269 +    }
270 +    
271 + #ifdef PROFILE
272 +    endProfile( pro2 );
273 + #endif //profile
274 +
275   #ifdef IS_MPI
276 <    strcpy( checkPointMsg,
262 <            "successfully took a time step." );
276 >    strcpy(checkPointMsg, "successfully took a time step.");
277      MPIcheckPoint();
278   #endif // is_mpi
265 –
279    }
280  
281 <  dumpOut->writeFinal(currTime);
281 >  // dump out a file containing the omega values for the final configuration
282 >  if (info->useThermInt)
283 >    myFF->dumpzAngle();
284 >  
285  
286    delete dumpOut;
287    delete statOut;
288   }
289  
290 < void Integrator::integrateStep( int calcPot, int calcStress ){
291 <
276 <
277 <      
290 > template<typename T> void Integrator<T>::integrateStep(int calcPot,
291 >                                                       int calcStress){
292    // Position full step, and velocity half step
293  
294 + #ifdef PROFILE
295 +  startProfile(pro3);
296 + #endif //profile
297 +
298    preMove();
299 +
300 + #ifdef PROFILE
301 +  endProfile(pro3);
302 +
303 +  startProfile(pro4);
304 + #endif // profile
305 +
306    moveA();
282 –  //if( nConstrained ) constrainA();
307  
308 + #ifdef PROFILE
309 +  endProfile(pro4);
310 +  
311 +  startProfile(pro5);
312 + #endif//profile
313 +
314 +
315 + #ifdef IS_MPI
316 +  strcpy(checkPointMsg, "Succesful moveA\n");
317 +  MPIcheckPoint();
318 + #endif // is_mpi
319 +
320    // calc forces
321 +  calcForce(calcPot, calcStress);
322  
323 <  myFF->doForces(calcPot,calcStress);
323 > #ifdef IS_MPI
324 >  strcpy(checkPointMsg, "Succesful doForces\n");
325 >  MPIcheckPoint();
326 > #endif // is_mpi
327  
328 <  // finish the velocity  half step
329 <  
290 <  moveB();
291 <  if( nConstrained ) constrainB();
292 <  
293 < }
328 > #ifdef PROFILE
329 >  endProfile( pro5 );
330  
331 +  startProfile( pro6 );
332 + #endif //profile
333  
334 < void Integrator::moveA( void ){
297 <  
298 <  int i,j,k;
299 <  int atomIndex, aMatIndex;
300 <  DirectionalAtom* dAtom;
301 <  double Tb[3];
302 <  double ji[3];
303 <  double angle;
304 <  double A[3][3], At[3][3];
334 >  // finish the velocity  half step
335  
336 +  moveB();
337  
338 <  for( i=0; i<nAtoms; i++ ){
339 <    atomIndex = i * 3;
340 <    aMatIndex = i * 9;
338 > #ifdef PROFILE
339 >  endProfile(pro6);
340 > #endif // profile
341  
342 <    // velocity half step
343 <    for( j=atomIndex; j<(atomIndex+3); j++ )
344 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
342 > #ifdef IS_MPI
343 >  strcpy(checkPointMsg, "Succesful moveB\n");
344 >  MPIcheckPoint();
345 > #endif // is_mpi
346 > }
347  
348  
349 <    // position whole step    
350 <    for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j];
349 > template<typename T> void Integrator<T>::moveA(void){
350 >  size_t i, j;
351 >  DirectionalAtom* dAtom;
352 >  double Tb[3], ji[3];
353 >  double vel[3], pos[3], frc[3];
354 >  double mass;
355 >  double omega;
356 >
357 >  for (i = 0; i < integrableObjects.size() ; i++){
358 >    integrableObjects[i]->getVel(vel);
359 >    integrableObjects[i]->getPos(pos);
360 >    integrableObjects[i]->getFrc(frc);
361      
362 +    mass = integrableObjects[i]->getMass();
363  
364 <    if( atoms[i]->isDirectional() ){
364 >    for (j = 0; j < 3; j++){
365 >      // velocity half step
366 >      vel[j] += (dt2 * frc[j] / mass) * eConvert;
367 >      // position whole step
368 >      pos[j] += dt * vel[j];
369 >    }
370  
371 <      dAtom = (DirectionalAtom *)atoms[i];
372 <          
371 >    integrableObjects[i]->setVel(vel);
372 >    integrableObjects[i]->setPos(pos);
373 >
374 >    if (integrableObjects[i]->isDirectional()){
375 >
376        // get and convert the torque to body frame
325 –      
326 –      Tb[0] = dAtom->getTx();
327 –      Tb[1] = dAtom->getTy();
328 –      Tb[2] = dAtom->getTz();
377  
378 <      dAtom->lab2Body( Tb );
378 >      integrableObjects[i]->getTrq(Tb);
379 >      integrableObjects[i]->lab2Body(Tb);
380  
381        // get the angular momentum, and propagate a half step
333 –      
334 –      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
335 –      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
336 –      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
337 –      
338 –      // use the angular velocities to propagate the rotation matrix a
339 –      // full time step
340 –      
341 –      // rotate about the x-axis      
342 –      angle = dt2 * ji[0] / dAtom->getIxx();
343 –      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
382  
383 <      // rotate about the y-axis
346 <      angle = dt2 * ji[1] / dAtom->getIyy();
347 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
348 <      
349 <      // rotate about the z-axis
350 <      angle = dt * ji[2] / dAtom->getIzz();
351 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
352 <      
353 <      // rotate about the y-axis
354 <      angle = dt2 * ji[1] / dAtom->getIyy();
355 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
356 <      
357 <       // rotate about the x-axis
358 <      angle = dt2 * ji[0] / dAtom->getIxx();
359 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
360 <      
361 <      dAtom->setJx( ji[0] );
362 <      dAtom->setJy( ji[1] );
363 <      dAtom->setJz( ji[2] );
383 >      integrableObjects[i]->getJ(ji);
384  
385 <      std::cerr << "Amat[" << i << "]\n";
386 <      info->printMat9( &Amat[aMatIndex] );
387 <          
388 <      std::cerr << "ji[" << i << "]\t"
389 <                << ji[0] << "\t"
390 <                << ji[1] << "\t"
371 <                << ji[2] << "\n";
372 <          
385 >      for (j = 0; j < 3; j++)
386 >        ji[j] += (dt2 * Tb[j]) * eConvert;
387 >
388 >      this->rotationPropagation( integrableObjects[i], ji );
389 >
390 >      integrableObjects[i]->setJ(ji);
391      }
374 –    
392    }
393 +
394 +  if (nConstrained){
395 +    constrainA();
396 +  }
397   }
398  
399  
400 < void Integrator::moveB( void ){
401 <  int i,j,k;
402 <  int atomIndex, aMatIndex;
403 <  DirectionalAtom* dAtom;
404 <  double Tb[3];
384 <  double ji[3];
400 > template<typename T> void Integrator<T>::moveB(void){
401 >  int i, j;
402 >  double Tb[3], ji[3];
403 >  double vel[3], frc[3];
404 >  double mass;
405  
406 <  for( i=0; i<nAtoms; i++ ){
407 <    atomIndex = i * 3;
408 <    aMatIndex = i * 9;
406 >  for (i = 0; i < integrableObjects.size(); i++){
407 >    integrableObjects[i]->getVel(vel);
408 >    integrableObjects[i]->getFrc(frc);
409  
410 +    mass = integrableObjects[i]->getMass();
411 +
412      // velocity half step
413 <    for( j=atomIndex; j<(atomIndex+3); j++ )
414 <      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
413 >    for (j = 0; j < 3; j++)
414 >      vel[j] += (dt2 * frc[j] / mass) * eConvert;
415  
416 <
417 <    if( atoms[i]->isDirectional() ){
418 <      
419 <      dAtom = (DirectionalAtom *)atoms[i];
398 <      
416 >    integrableObjects[i]->setVel(vel);
417 >
418 >    if (integrableObjects[i]->isDirectional()){
419 >
420        // get and convert the torque to body frame
400 –      
401 –      Tb[0] = dAtom->getTx();
402 –      Tb[1] = dAtom->getTy();
403 –      Tb[2] = dAtom->getTz();
404 –      
405 –      std::cerr << "TrqB[" << i << "]\t"
406 –                << Tb[0] << "\t"
407 –                << Tb[1] << "\t"
408 –                << Tb[2] << "\n";
421  
422 <      dAtom->lab2Body( Tb );
423 <      
412 <      // get the angular momentum, and complete the angular momentum
413 <      // half step
414 <      
415 <      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
416 <      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
417 <      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
418 <      
419 <      dAtom->setJx( ji[0] );
420 <      dAtom->setJy( ji[1] );
421 <      dAtom->setJz( ji[2] );
422 >      integrableObjects[i]->getTrq(Tb);
423 >      integrableObjects[i]->lab2Body(Tb);
424  
425 +      // get the angular momentum, and propagate a half step
426  
427 <      std::cerr << "Amat[" << i << "]\n";
428 <      info->printMat9( &Amat[aMatIndex] );
429 <          
430 <      std::cerr << "ji[" << i << "]\t"
431 <                << ji[0] << "\t"
432 <                << ji[1] << "\t"
433 <                << ji[2] << "\n";
427 >      integrableObjects[i]->getJ(ji);
428 >
429 >      for (j = 0; j < 3; j++)
430 >        ji[j] += (dt2 * Tb[j]) * eConvert;
431 >
432 >
433 >      integrableObjects[i]->setJ(ji);
434      }
435    }
436  
437 +  if (nConstrained){
438 +    constrainB();
439 +  }
440   }
441  
442 < void Integrator::preMove( void ){
443 <  int i;
442 > template<typename T> void Integrator<T>::preMove(void){
443 >  int i, j;
444 >  double pos[3];
445  
446 <  if( nConstrained ){
446 >  if (nConstrained){
447 >    for (i = 0; i < nAtoms; i++){
448 >      atoms[i]->getPos(pos);
449  
450 <    for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
450 >      for (j = 0; j < 3; j++){
451 >        oldPos[3 * i + j] = pos[j];
452 >      }
453 >    }
454    }
455 < }  
455 > }
456  
457 < void Integrator::constrainA(){
458 <
447 <  int i,j,k;
457 > template<typename T> void Integrator<T>::constrainA(){
458 >  int i, j;
459    int done;
460 +  double posA[3], posB[3];
461 +  double velA[3], velB[3];
462    double pab[3];
463    double rab[3];
464    int a, b, ax, ay, az, bx, by, bz;
# Line 457 | Line 470 | void Integrator::constrainA(){
470    double gab;
471    int iteration;
472  
473 <  for( i=0; i<nAtoms; i++){
461 <    
473 >  for (i = 0; i < nAtoms; i++){
474      moving[i] = 0;
475 <    moved[i]  = 1;
475 >    moved[i] = 1;
476    }
477  
478    iteration = 0;
479    done = 0;
480 <  while( !done && (iteration < maxIteration )){
469 <
480 >  while (!done && (iteration < maxIteration)){
481      done = 1;
482 <    for(i=0; i<nConstrained; i++){
472 <
482 >    for (i = 0; i < nConstrained; i++){
483        a = constrainedA[i];
484        b = constrainedB[i];
475 –      
476 –      ax = (a*3) + 0;
477 –      ay = (a*3) + 1;
478 –      az = (a*3) + 2;
485  
486 <      bx = (b*3) + 0;
487 <      by = (b*3) + 1;
488 <      bz = (b*3) + 2;
486 >      ax = (a * 3) + 0;
487 >      ay = (a * 3) + 1;
488 >      az = (a * 3) + 2;
489  
490 <      if( moved[a] || moved[b] ){
491 <        
492 <        pab[0] = pos[ax] - pos[bx];
487 <        pab[1] = pos[ay] - pos[by];
488 <        pab[2] = pos[az] - pos[bz];
490 >      bx = (b * 3) + 0;
491 >      by = (b * 3) + 1;
492 >      bz = (b * 3) + 2;
493  
494 <        //periodic boundary condition
494 >      if (moved[a] || moved[b]){
495 >        atoms[a]->getPos(posA);
496 >        atoms[b]->getPos(posB);
497  
498 <        info->wrapVector( pab );
498 >        for (j = 0; j < 3; j++)
499 >          pab[j] = posA[j] - posB[j];
500  
501 <        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
501 >        //periodic boundary condition
502  
503 <        rabsq = constrainedDsqr[i];
497 <        diffsq = rabsq - pabsq;
503 >        info->wrapVector(pab);
504  
505 <        // the original rattle code from alan tidesley
500 <        if (fabs(diffsq) > (tol*rabsq*2)) {
501 <          rab[0] = oldPos[ax] - oldPos[bx];
502 <          rab[1] = oldPos[ay] - oldPos[by];
503 <          rab[2] = oldPos[az] - oldPos[bz];
505 >        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
506  
507 <          info->wrapVector( rab );
507 >        rabsq = constrainedDsqr[i];
508 >        diffsq = rabsq - pabsq;
509  
510 <          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
510 >        // the original rattle code from alan tidesley
511 >        if (fabs(diffsq) > (tol * rabsq * 2)){
512 >          rab[0] = oldPos[ax] - oldPos[bx];
513 >          rab[1] = oldPos[ay] - oldPos[by];
514 >          rab[2] = oldPos[az] - oldPos[bz];
515  
516 <          rpabsq = rpab * rpab;
516 >          info->wrapVector(rab);
517  
518 +          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
519  
520 <          if (rpabsq < (rabsq * -diffsq)){
520 >          rpabsq = rpab * rpab;
521  
522 +
523 +          if (rpabsq < (rabsq * -diffsq)){
524   #ifdef IS_MPI
525 <            a = atoms[a]->getGlobalIndex();
526 <            b = atoms[b]->getGlobalIndex();
525 >            a = atoms[a]->getGlobalIndex();
526 >            b = atoms[b]->getGlobalIndex();
527   #endif //is_mpi
528 <            sprintf( painCave.errMsg,
529 <                     "Constraint failure in constrainA at atom %d and %d.\n",
530 <                     a, b );
531 <            painCave.isFatal = 1;
532 <            simError();
533 <          }
528 >            sprintf(painCave.errMsg,
529 >                    "Constraint failure in constrainA at atom %d and %d.\n", a,
530 >                    b);
531 >            painCave.isFatal = 1;
532 >            simError();
533 >          }
534  
535 <          rma = 1.0 / atoms[a]->getMass();
536 <          rmb = 1.0 / atoms[b]->getMass();
535 >          rma = 1.0 / atoms[a]->getMass();
536 >          rmb = 1.0 / atoms[b]->getMass();
537  
538 <          gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
538 >          gab = diffsq / (2.0 * (rma + rmb) * rpab);
539  
540            dx = rab[0] * gab;
541            dy = rab[1] * gab;
542            dz = rab[2] * gab;
543  
544 <          pos[ax] += rma * dx;
545 <          pos[ay] += rma * dy;
546 <          pos[az] += rma * dz;
544 >          posA[0] += rma * dx;
545 >          posA[1] += rma * dy;
546 >          posA[2] += rma * dz;
547  
548 <          pos[bx] -= rmb * dx;
539 <          pos[by] -= rmb * dy;
540 <          pos[bz] -= rmb * dz;
548 >          atoms[a]->setPos(posA);
549  
550 +          posB[0] -= rmb * dx;
551 +          posB[1] -= rmb * dy;
552 +          posB[2] -= rmb * dz;
553 +
554 +          atoms[b]->setPos(posB);
555 +
556            dx = dx / dt;
557            dy = dy / dt;
558            dz = dz / dt;
559  
560 <          vel[ax] += rma * dx;
547 <          vel[ay] += rma * dy;
548 <          vel[az] += rma * dz;
560 >          atoms[a]->getVel(velA);
561  
562 <          vel[bx] -= rmb * dx;
563 <          vel[by] -= rmb * dy;
564 <          vel[bz] -= rmb * dz;
562 >          velA[0] += rma * dx;
563 >          velA[1] += rma * dy;
564 >          velA[2] += rma * dz;
565  
566 <          moving[a] = 1;
567 <          moving[b] = 1;
568 <          done = 0;
569 <        }
566 >          atoms[a]->setVel(velA);
567 >
568 >          atoms[b]->getVel(velB);
569 >
570 >          velB[0] -= rmb * dx;
571 >          velB[1] -= rmb * dy;
572 >          velB[2] -= rmb * dz;
573 >
574 >          atoms[b]->setVel(velB);
575 >
576 >          moving[a] = 1;
577 >          moving[b] = 1;
578 >          done = 0;
579 >        }
580        }
581      }
582 <    
583 <    for(i=0; i<nAtoms; i++){
562 <      
582 >
583 >    for (i = 0; i < nAtoms; i++){
584        moved[i] = moving[i];
585        moving[i] = 0;
586      }
# Line 567 | Line 588 | void Integrator::constrainA(){
588      iteration++;
589    }
590  
591 <  if( !done ){
592 <
593 <    sprintf( painCave.errMsg,
594 <             "Constraint failure in constrainA, too many iterations: %d\n",
574 <             iteration );
591 >  if (!done){
592 >    sprintf(painCave.errMsg,
593 >            "Constraint failure in constrainA, too many iterations: %d\n",
594 >            iteration);
595      painCave.isFatal = 1;
596      simError();
597    }
598  
599   }
600  
601 < void Integrator::constrainB( void ){
602 <  
583 <  int i,j,k;
601 > template<typename T> void Integrator<T>::constrainB(void){
602 >  int i, j;
603    int done;
604 +  double posA[3], posB[3];
605 +  double velA[3], velB[3];
606    double vxab, vyab, vzab;
607    double rab[3];
608    int a, b, ax, ay, az, bx, by, bz;
609    double rma, rmb;
610    double dx, dy, dz;
611 <  double rabsq, pabsq, rvab;
591 <  double diffsq;
611 >  double rvab;
612    double gab;
613    int iteration;
614  
615 <  for(i=0; i<nAtoms; i++){
615 >  for (i = 0; i < nAtoms; i++){
616      moving[i] = 0;
617      moved[i] = 1;
618    }
619  
620    done = 0;
621    iteration = 0;
622 <  while( !done && (iteration < maxIteration ) ){
603 <
622 >  while (!done && (iteration < maxIteration)){
623      done = 1;
624  
625 <    for(i=0; i<nConstrained; i++){
607 <      
625 >    for (i = 0; i < nConstrained; i++){
626        a = constrainedA[i];
627        b = constrainedB[i];
628  
629 <      ax = (a*3) + 0;
630 <      ay = (a*3) + 1;
631 <      az = (a*3) + 2;
614 <
615 <      bx = (b*3) + 0;
616 <      by = (b*3) + 1;
617 <      bz = (b*3) + 2;
629 >      ax = (a * 3) + 0;
630 >      ay = (a * 3) + 1;
631 >      az = (a * 3) + 2;
632  
633 <      if( moved[a] || moved[b] ){
634 <        
635 <        vxab = vel[ax] - vel[bx];
622 <        vyab = vel[ay] - vel[by];
623 <        vzab = vel[az] - vel[bz];
633 >      bx = (b * 3) + 0;
634 >      by = (b * 3) + 1;
635 >      bz = (b * 3) + 2;
636  
637 <        rab[0] = pos[ax] - pos[bx];
638 <        rab[1] = pos[ay] - pos[by];
639 <        rab[2] = pos[az] - pos[bz];
628 <        
629 <        info->wrapVector( rab );
630 <        
631 <        rma = 1.0 / atoms[a]->getMass();
632 <        rmb = 1.0 / atoms[b]->getMass();
637 >      if (moved[a] || moved[b]){
638 >        atoms[a]->getVel(velA);
639 >        atoms[b]->getVel(velB);
640  
641 <        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
642 <          
643 <        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
641 >        vxab = velA[0] - velB[0];
642 >        vyab = velA[1] - velB[1];
643 >        vzab = velA[2] - velB[2];
644  
645 <        if (fabs(gab) > tol) {
646 <          
640 <          dx = rab[0] * gab;
641 <          dy = rab[1] * gab;
642 <          dz = rab[2] * gab;
643 <          
644 <          vel[ax] += rma * dx;
645 <          vel[ay] += rma * dy;
646 <          vel[az] += rma * dz;
645 >        atoms[a]->getPos(posA);
646 >        atoms[b]->getPos(posB);
647  
648 <          vel[bx] -= rmb * dx;
649 <          vel[by] -= rmb * dy;
650 <          vel[bz] -= rmb * dz;
651 <          
652 <          moving[a] = 1;
653 <          moving[b] = 1;
654 <          done = 0;
655 <        }
648 >        for (j = 0; j < 3; j++)
649 >          rab[j] = posA[j] - posB[j];
650 >
651 >        info->wrapVector(rab);
652 >
653 >        rma = 1.0 / atoms[a]->getMass();
654 >        rmb = 1.0 / atoms[b]->getMass();
655 >
656 >        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
657 >
658 >        gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
659 >
660 >        if (fabs(gab) > tol){
661 >          dx = rab[0] * gab;
662 >          dy = rab[1] * gab;
663 >          dz = rab[2] * gab;
664 >
665 >          velA[0] += rma * dx;
666 >          velA[1] += rma * dy;
667 >          velA[2] += rma * dz;
668 >
669 >          atoms[a]->setVel(velA);
670 >
671 >          velB[0] -= rmb * dx;
672 >          velB[1] -= rmb * dy;
673 >          velB[2] -= rmb * dz;
674 >
675 >          atoms[b]->setVel(velB);
676 >
677 >          moving[a] = 1;
678 >          moving[b] = 1;
679 >          done = 0;
680 >        }
681        }
682      }
683  
684 <    for(i=0; i<nAtoms; i++){
684 >    for (i = 0; i < nAtoms; i++){
685        moved[i] = moving[i];
686        moving[i] = 0;
687      }
688 <    
688 >
689      iteration++;
690    }
691  
692 <  if( !done ){
693 <
694 <  
695 <    sprintf( painCave.errMsg,
671 <             "Constraint failure in constrainB, too many iterations: %d\n",
672 <             iteration );
692 >  if (!done){
693 >    sprintf(painCave.errMsg,
694 >            "Constraint failure in constrainB, too many iterations: %d\n",
695 >            iteration);
696      painCave.isFatal = 1;
697      simError();
698 <  }
676 <
698 >  }
699   }
700  
701 + template<typename T> void Integrator<T>::rotationPropagation
702 + ( StuntDouble* sd, double ji[3] ){
703  
704 +  double angle;
705 +  double A[3][3], I[3][3];
706 +  int i, j, k;
707  
708 +  // use the angular velocities to propagate the rotation matrix a
709 +  // full time step
710  
711 +  sd->getA(A);
712 +  sd->getI(I);
713  
714 +  if (sd->isLinear()) {
715 +    i = sd->linearAxis();
716 +    j = (i+1)%3;
717 +    k = (i+2)%3;
718 +    
719 +    angle = dt2 * ji[j] / I[j][j];
720 +    this->rotate( k, i, angle, ji, A );
721  
722 +    angle = dt * ji[k] / I[k][k];
723 +    this->rotate( i, j, angle, ji, A);
724  
725 < void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
726 <                         double A[9] ){
725 >    angle = dt2 * ji[j] / I[j][j];
726 >    this->rotate( k, i, angle, ji, A );
727  
728 <  int i,j,k;
728 >  } else {
729 >    // rotate about the x-axis
730 >    angle = dt2 * ji[0] / I[0][0];
731 >    this->rotate( 1, 2, angle, ji, A );
732 >    
733 >    // rotate about the y-axis
734 >    angle = dt2 * ji[1] / I[1][1];
735 >    this->rotate( 2, 0, angle, ji, A );
736 >    
737 >    // rotate about the z-axis
738 >    angle = dt * ji[2] / I[2][2];
739 >    sd->addZangle(angle);
740 >    this->rotate( 0, 1, angle, ji, A);
741 >    
742 >    // rotate about the y-axis
743 >    angle = dt2 * ji[1] / I[1][1];
744 >    this->rotate( 2, 0, angle, ji, A );
745 >    
746 >    // rotate about the x-axis
747 >    angle = dt2 * ji[0] / I[0][0];
748 >    this->rotate( 1, 2, angle, ji, A );
749 >    
750 >  }
751 >  sd->setA( A  );
752 > }
753 >
754 > template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
755 >                                                double angle, double ji[3],
756 >                                                double A[3][3]){
757 >  int i, j, k;
758    double sinAngle;
759    double cosAngle;
760    double angleSqr;
# Line 695 | Line 764 | void Integrator::rotate( int axes1, int axes2, double
764    double tempA[3][3];
765    double tempJ[3];
766  
698 –
767    // initialize the tempA
768  
769 <  for(i=0; i<3; i++){
770 <    for(j=0; j<3; j++){
771 <      tempA[j][i] = A[3*i+j];
769 >  for (i = 0; i < 3; i++){
770 >    for (j = 0; j < 3; j++){
771 >      tempA[j][i] = A[i][j];
772      }
773    }
774  
775    // initialize the tempJ
776  
777 <  for( i=0; i<3; i++) tempJ[i] = ji[i];
778 <  
777 >  for (i = 0; i < 3; i++)
778 >    tempJ[i] = ji[i];
779 >
780    // initalize rot as a unit matrix
781  
782    rot[0][0] = 1.0;
# Line 717 | Line 786 | void Integrator::rotate( int axes1, int axes2, double
786    rot[1][0] = 0.0;
787    rot[1][1] = 1.0;
788    rot[1][2] = 0.0;
789 <  
789 >
790    rot[2][0] = 0.0;
791    rot[2][1] = 0.0;
792    rot[2][2] = 1.0;
793 <  
793 >
794    // use a small angle aproximation for sin and cosine
795  
796 <  angleSqr  = angle * angle;
796 >  angleSqr = angle * angle;
797    angleSqrOver4 = angleSqr / 4.0;
798    top = 1.0 - angleSqrOver4;
799    bottom = 1.0 + angleSqrOver4;
# Line 737 | Line 806 | void Integrator::rotate( int axes1, int axes2, double
806  
807    rot[axes1][axes2] = sinAngle;
808    rot[axes2][axes1] = -sinAngle;
809 <  
809 >
810    // rotate the momentum acoording to: ji[] = rot[][] * ji[]
811 <  
812 <  for(i=0; i<3; i++){
811 >
812 >  for (i = 0; i < 3; i++){
813      ji[i] = 0.0;
814 <    for(k=0; k<3; k++){
814 >    for (k = 0; k < 3; k++){
815        ji[i] += rot[i][k] * tempJ[k];
816      }
817    }
818  
819 <  // rotate the Rotation matrix acording to:
819 >  // rotate the Rotation matrix acording to:
820    //            A[][] = A[][] * transpose(rot[][])
821  
822  
# Line 755 | Line 824 | void Integrator::rotate( int axes1, int axes2, double
824    // calculation as:
825    //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
826  
827 <  for(i=0; i<3; i++){
828 <    for(j=0; j<3; j++){
829 <      A[3*j+i] = 0.0;
830 <      for(k=0; k<3; k++){
831 <        A[3*j+i] += tempA[i][k] * rot[j][k];
827 >  for (i = 0; i < 3; i++){
828 >    for (j = 0; j < 3; j++){
829 >      A[j][i] = 0.0;
830 >      for (k = 0; k < 3; k++){
831 >        A[j][i] += tempA[i][k] * rot[j][k];
832        }
833      }
834    }
835   }
836 +
837 + template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
838 +  myFF->doForces(calcPot, calcStress);
839 + }
840 +
841 + template<typename T> void Integrator<T>::thermalize(){
842 +  tStats->velocitize();
843 + }
844 +
845 + template<typename T> double Integrator<T>::getConservedQuantity(void){
846 +  return tStats->getTotalE();
847 + }
848 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
849 +  //By default, return a null string
850 +  //The reason we use string instead of char* is that if we use char*, we will
851 +  //return a pointer point to local variable which might cause problem
852 +  return string();
853 + }

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