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root/group/branches/no-template-branch/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 483 by gezelter, Wed Apr 9 04:06:43 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2 +
3   #include <cstring>
4   #include <iostream>
5   #include <fstream>
# Line 70 | Line 72 | void DumpWriter::writeDump( double currentTime ){
72    char tempBuffer[BUFFERSIZE];
73    char writeLine[BUFFERSIZE];
74  
75 <  int i, j, which_node, done, which_atom, local_index;
75 >  int i;
76 > #ifdef IS_MPI
77 >  int j, which_node, done, which_atom, local_index;
78 > #else //is_mpi
79 >  int nAtoms = entry_plug->n_atoms;
80 > #endif //is_mpi
81 >
82    double q[4];
83    DirectionalAtom* dAtom;
76 –  int nAtoms = entry_plug->n_atoms;
84    Atom** atoms = entry_plug->atoms;
85 +  double pos[3], vel[3];
86      
87  
88   #ifndef IS_MPI
89      
90    outFile << nAtoms << "\n";
91      
92 <  outFile << currentTime << "\t"
93 <          << entry_plug->box_x << "\t"
94 <          << entry_plug->box_y << "\t"
95 <          << entry_plug->box_z << "\n";
92 >  outFile << currentTime << ";\t"
93 >          << entry_plug->Hmat[0][0] << "\t"
94 >          << entry_plug->Hmat[1][0] << "\t"
95 >          << entry_plug->Hmat[2][0] << ";\t"
96 >
97 >          << entry_plug->Hmat[0][1] << "\t"
98 >          << entry_plug->Hmat[1][1] << "\t"
99 >          << entry_plug->Hmat[2][1] << ";\t"
100 >
101 >          << entry_plug->Hmat[0][2] << "\t"
102 >          << entry_plug->Hmat[1][2] << "\t"
103 >          << entry_plug->Hmat[2][2] << ";\n";
104      
105    for( i=0; i<nAtoms; i++ ){
106        
107 +    atoms[i]->getPos(pos);
108 +    atoms[i]->getVel(vel);
109  
110      sprintf( tempBuffer,
111               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
112               atoms[i]->getType(),
113 <             atoms[i]->getX(),
114 <             atoms[i]->getY(),
115 <             atoms[i]->getZ(),
116 <             atoms[i]->get_vx(),
117 <             atoms[i]->get_vy(),
118 <             atoms[i]->get_vz());
113 >             pos[0],
114 >             pos[1],
115 >             pos[2],
116 >             vel[0],
117 >             vel[1],
118 >             vel[2]);
119      strcpy( writeLine, tempBuffer );
120  
121      if( atoms[i]->isDirectional() ){
# Line 138 | Line 156 | void DumpWriter::writeDump( double currentTime ){
156    
157    if( worldRank == 0 ){
158      outFile << mpiSim->getTotAtoms() << "\n";
159 +  
160 +    outFile << currentTime << ";\t"
161 +            << entry_plug->Hmat[0][0] << "\t"
162 +            << entry_plug->Hmat[1][0] << "\t"
163 +            << entry_plug->Hmat[2][0] << ";\t"
164 +      
165 +            << entry_plug->Hmat[0][1] << "\t"
166 +            << entry_plug->Hmat[1][1] << "\t"
167 +            << entry_plug->Hmat[2][1] << ";\t"
168 +      
169 +            << entry_plug->Hmat[0][2] << "\t"
170 +            << entry_plug->Hmat[1][2] << "\t"
171 +            << entry_plug->Hmat[2][2] << ";\n";
172      
142 –    outFile << currentTime << "\t"
143 –            << entry_plug->box_x << "\t"
144 –            << entry_plug->box_y << "\t"
145 –            << entry_plug->box_z << "\n";
173      outFile.flush();
174      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
175        // Get the Node number which has this atom;
# Line 159 | Line 186 | void DumpWriter::writeDump( double currentTime ){
186          }
187          if (local_index != -1) {
188            //format the line
189 +          
190 +          atoms[local_index]->getPos(pos);
191 +          atoms[local_index]->getVel(vel);
192 +
193            sprintf( tempBuffer,
194                     "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
195                     atoms[local_index]->getType(),
196 <                   atoms[local_index]->getX(),
197 <                   atoms[local_index]->getY(),
198 <                   atoms[local_index]->getZ(),
199 <                   atoms[local_index]->get_vx(),
200 <                   atoms[local_index]->get_vy(),
201 <                   atoms[local_index]->get_vz()); // check here.
196 >                   pos[0],
197 >                   pos[1],
198 >                   pos[2],
199 >                   vel[0],
200 >                   vel[1],
201 >                   vel[2]); // check here.
202            strcpy( writeLine, tempBuffer );
203            
204            if( atoms[local_index]->isDirectional() ){
# Line 249 | Line 280 | void DumpWriter::writeDump( double currentTime ){
280        }
281        if (local_index != -1) {
282          //format the line
283 +
284 +        atoms[local_index]->getPos(pos);
285 +        atoms[local_index]->getVel(vel);
286 +
287          sprintf( tempBuffer,
288                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
289                   atoms[local_index]->getType(),
290 <                 atoms[local_index]->getX(),
291 <                 atoms[local_index]->getY(),
292 <                 atoms[local_index]->getZ(),
293 <                 atoms[local_index]->get_vx(),
294 <                 atoms[local_index]->get_vy(),
295 <                 atoms[local_index]->get_vz()); // check here.
290 >                 pos[0],
291 >                 pos[1],
292 >                 pos[2],
293 >                 vel[0],
294 >                 vel[1],
295 >                 vel[2]); // check here.
296          strcpy( writeLine, tempBuffer );
297          
298          if( atoms[local_index]->isDirectional() ){
# Line 307 | Line 342 | void DumpWriter::writeDump( double currentTime ){
342   #endif // is_mpi
343   }
344  
345 < void DumpWriter::writeFinal(){
345 > void DumpWriter::writeFinal(double finalTime){
346  
347    char finalName[500];
348    ofstream finalOut;
# Line 318 | Line 353 | void DumpWriter::writeFinal(){
353  
354    double q[4];
355    DirectionalAtom* dAtom;
321 –  int nAtoms = entry_plug->n_atoms;
356    Atom** atoms = entry_plug->atoms;
357 <  int i, j, which_node, done, game_over, which_atom, local_index;
357 >  int i;
358 > #ifdef IS_MPI
359 >  int j, which_node, done, which_atom, local_index;
360 > #else //is_mpi
361 >  int nAtoms = entry_plug->n_atoms;
362 > #endif //is_mpi
363    
364 +  double pos[3], vel[3];
365    
366   #ifdef IS_MPI
367    if(worldRank == 0 ){
# Line 353 | Line 393 | void DumpWriter::writeFinal(){
393      
394    finalOut << nAtoms << "\n";
395      
396 <  finalOut << entry_plug->box_x << "\t"
397 <           << entry_plug->box_y << "\t"
398 <           << entry_plug->box_z << "\n";
396 >  finalOut << finalTime << ";\t"
397 >           << entry_plug->Hmat[0][0] << "\t"
398 >           << entry_plug->Hmat[1][0] << "\t"
399 >           << entry_plug->Hmat[2][0] << ";\t"
400 >    
401 >           << entry_plug->Hmat[0][1] << "\t"
402 >           << entry_plug->Hmat[1][1] << "\t"
403 >           << entry_plug->Hmat[2][1] << ";\t"
404 >    
405 >           << entry_plug->Hmat[0][2] << "\t"
406 >           << entry_plug->Hmat[1][2] << "\t"
407 >           << entry_plug->Hmat[2][2] << ";\n";
408    
409    for( i=0; i<nAtoms; i++ ){
410        
411 +    atoms[i]->getPos(pos);
412 +    atoms[i]->getVel(vel);
413 +    
414      sprintf( tempBuffer,
415               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
416               atoms[i]->getType(),
417 <             atoms[i]->getX(),
418 <             atoms[i]->getY(),
419 <             atoms[i]->getZ(),
420 <             atoms[i]->get_vx(),
421 <             atoms[i]->get_vy(),
422 <             atoms[i]->get_vz());
417 >             pos[0],
418 >             pos[1],
419 >             pos[2],
420 >             vel[0],
421 >             vel[1],
422 >             vel[2]);
423      strcpy( writeLine, tempBuffer );
424  
425      if( atoms[i]->isDirectional() ){
# Line 411 | Line 463 | void DumpWriter::writeFinal(){
463    if( worldRank == 0 ){
464      finalOut << mpiSim->getTotAtoms() << "\n";
465      
466 <    finalOut << entry_plug->box_x << "\t"
467 <            << entry_plug->box_y << "\t"
468 <            << entry_plug->box_z << "\n";
466 >    finalOut << finalTime << ";\t"
467 >             << entry_plug->Hmat[0][0] << "\t"
468 >             << entry_plug->Hmat[1][0] << "\t"
469 >             << entry_plug->Hmat[2][0] << ";\t"
470 >      
471 >             << entry_plug->Hmat[0][1] << "\t"
472 >             << entry_plug->Hmat[1][1] << "\t"
473 >             << entry_plug->Hmat[2][1] << ";\t"
474 >      
475 >             << entry_plug->Hmat[0][2] << "\t"
476 >             << entry_plug->Hmat[1][2] << "\t"
477 >             << entry_plug->Hmat[2][2] << ";\n";
478      
479      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
480        // Get the Node number which has this molecule:
# Line 427 | Line 488 | void DumpWriter::writeFinal(){
488          for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
489            if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
490          }
491 <        if (local_index != -1) {        
491 >        if (local_index != -1) {    
492 >
493 >          atoms[local_index]->getPos(pos);
494 >          atoms[local_index]->getVel(vel);
495 >          
496            sprintf( tempBuffer,
497                     "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
498                     atoms[local_index]->getType(),
499 <                   atoms[local_index]->getX(),
500 <                   atoms[local_index]->getY(),
501 <                   atoms[local_index]->getZ(),
502 <                   atoms[local_index]->get_vx(),
503 <                   atoms[local_index]->get_vy(),
504 <                   atoms[local_index]->get_vz());
499 >                   pos[0],
500 >                   pos[1],
501 >                   pos[2],
502 >                   vel[0],
503 >                   vel[1],
504 >                   vel[2]);
505            strcpy( writeLine, tempBuffer );
506            
507            if( atoms[local_index]->isDirectional() ){
# Line 516 | Line 581 | void DumpWriter::writeFinal(){
581        }
582        if (local_index != -1) {
583  
584 +        atoms[local_index]->getPos(pos);
585 +        atoms[local_index]->getVel(vel);
586 +
587          //format the line
588          sprintf( tempBuffer,
589                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
590                   atoms[local_index]->getType(),
591 <                 atoms[local_index]->getX(),
592 <                 atoms[local_index]->getY(),
593 <                 atoms[local_index]->getZ(),
594 <                 atoms[local_index]->get_vx(),
595 <                 atoms[local_index]->get_vy(),
596 <                 atoms[local_index]->get_vz()); // check here.
591 >                 pos[0],
592 >                 pos[1],
593 >                 pos[2],
594 >                 vel[0],
595 >                 vel[1],
596 >                 vel[2]); // check here.
597          strcpy( writeLine, tempBuffer );
598          
599          if( atoms[local_index]->isDirectional() ){

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