12 |
|
#include "mpiSimulation.hpp" |
13 |
|
#endif |
14 |
|
|
15 |
+ |
// some defines for ensemble and Forcefield cases |
16 |
+ |
|
17 |
+ |
#define NVE_ENS 0 |
18 |
+ |
#define NVT_ENS 1 |
19 |
+ |
#define NPTi_ENS 2 |
20 |
+ |
#define NPTf_ENS 3 |
21 |
+ |
|
22 |
+ |
|
23 |
+ |
#define FF_DUFF 0 |
24 |
+ |
#define FF_LJ 1 |
25 |
+ |
|
26 |
+ |
|
27 |
|
SimSetup::SimSetup(){ |
28 |
|
stamps = new MakeStamps(); |
29 |
|
globals = new Globals(); |
78 |
|
|
79 |
|
MakeStamps *the_stamps; |
80 |
|
Globals* the_globals; |
81 |
< |
int i, j; |
81 |
> |
int i, j, k, globalAtomIndex; |
82 |
> |
|
83 |
> |
int ensembleCase; |
84 |
> |
int ffCase; |
85 |
> |
|
86 |
> |
ensembleCase = -1; |
87 |
> |
ffCase = -1; |
88 |
|
|
89 |
|
// get the stamps and globals; |
90 |
|
the_stamps = stamps; |
98 |
|
// get the ones we know are there, yet still may need some work. |
99 |
|
n_components = the_globals->getNComponents(); |
100 |
|
strcpy( force_field, the_globals->getForceField() ); |
101 |
+ |
|
102 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
103 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
104 |
+ |
else{ |
105 |
+ |
sprintf( painCave.errMsg, |
106 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
107 |
+ |
force_field ); |
108 |
+ |
painCave.isFatal = 1; |
109 |
+ |
simError(); |
110 |
+ |
} |
111 |
+ |
|
112 |
+ |
// get the ensemble: |
113 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
114 |
+ |
|
115 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
116 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
117 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
118 |
+ |
ensembleCase = NPTi_ENS; |
119 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
120 |
+ |
else{ |
121 |
+ |
sprintf( painCave.errMsg, |
122 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
123 |
+ |
"reverting to NVE for this simulation.\n", |
124 |
+ |
ensemble ); |
125 |
+ |
painCave.isFatal = 0; |
126 |
+ |
simError(); |
127 |
+ |
strcpy( ensemble, "NVE" ); |
128 |
+ |
ensembleCase = NVE_ENS; |
129 |
+ |
} |
130 |
|
strcpy( simnfo->ensemble, ensemble ); |
131 |
|
|
132 |
+ |
|
133 |
+ |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
134 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
135 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
136 |
+ |
// if (the_globals->haveTargetPressure()) |
137 |
+ |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
138 |
+ |
// else { |
139 |
+ |
// sprintf( painCave.errMsg, |
140 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
141 |
+ |
// " ensemble, you must set targetPressure.\n" |
142 |
+ |
// " This was found in the BASS file.\n"); |
143 |
+ |
// painCave.isFatal = 1; |
144 |
+ |
// simError(); |
145 |
+ |
// } |
146 |
+ |
|
147 |
+ |
// if (the_globals->haveTauThermostat()) |
148 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
149 |
+ |
// else if (the_globals->haveQmass()) |
150 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
151 |
+ |
// else { |
152 |
+ |
// sprintf( painCave.errMsg, |
153 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
154 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
155 |
+ |
// " Neither of these was found in the BASS file.\n"); |
156 |
+ |
// painCave.isFatal = 1; |
157 |
+ |
// simError(); |
158 |
+ |
// } |
159 |
+ |
|
160 |
+ |
// if (the_globals->haveTauBarostat()) |
161 |
+ |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
162 |
+ |
// else { |
163 |
+ |
// sprintf( painCave.errMsg, |
164 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
165 |
+ |
// " ensemble, you must set tauBarostat.\n" |
166 |
+ |
// " This was found in the BASS file.\n"); |
167 |
+ |
// painCave.isFatal = 1; |
168 |
+ |
// simError(); |
169 |
+ |
// } |
170 |
+ |
|
171 |
+ |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
172 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
173 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
174 |
+ |
|
175 |
+ |
// if (the_globals->haveTauThermostat()) |
176 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
177 |
+ |
// else if (the_globals->haveQmass()) |
178 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
179 |
+ |
// else { |
180 |
+ |
// sprintf( painCave.errMsg, |
181 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
182 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
183 |
+ |
// " Neither of these was found in the BASS file.\n"); |
184 |
+ |
// painCave.isFatal = 1; |
185 |
+ |
// simError(); |
186 |
+ |
// } |
187 |
+ |
|
188 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
189 |
|
simnfo->usePBC = the_globals->getPBC(); |
190 |
|
|
191 |
+ |
int usesDipoles = 0; |
192 |
+ |
switch( ffCase ){ |
193 |
|
|
194 |
+ |
case FF_DUFF: |
195 |
+ |
the_ff = new DUFF(); |
196 |
+ |
usesDipoles = 1; |
197 |
+ |
break; |
198 |
|
|
199 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
200 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
201 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
202 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
203 |
< |
else{ |
199 |
> |
case FF_LJ: |
200 |
> |
the_ff = new LJFF(); |
201 |
> |
break; |
202 |
> |
|
203 |
> |
default: |
204 |
|
sprintf( painCave.errMsg, |
205 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
98 |
< |
force_field ); |
205 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
206 |
|
painCave.isFatal = 1; |
207 |
|
simError(); |
208 |
|
} |
212 |
|
MPIcheckPoint(); |
213 |
|
#endif // is_mpi |
214 |
|
|
108 |
– |
|
109 |
– |
|
215 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
216 |
|
the_components = the_globals->getComponents(); |
217 |
|
components_nmol = new int[n_components]; |
335 |
|
simnfo->n_torsions = tot_torsions; |
336 |
|
simnfo->n_SRI = tot_SRI; |
337 |
|
simnfo->n_mol = tot_nmol; |
233 |
– |
|
338 |
|
|
339 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
340 |
+ |
|
341 |
|
#ifdef IS_MPI |
342 |
|
|
343 |
|
// divide the molecules among processors here. |
344 |
|
|
345 |
|
mpiSim = new mpiSimulation( simnfo ); |
346 |
|
|
241 |
– |
|
242 |
– |
|
347 |
|
globalIndex = mpiSim->divideLabor(); |
348 |
|
|
245 |
– |
|
246 |
– |
|
349 |
|
// set up the local variables |
350 |
|
|
351 |
|
int localMol, allMol; |
352 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
353 |
+ |
|
354 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
355 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
356 |
|
|
357 |
|
allMol = 0; |
358 |
|
localMol = 0; |
360 |
|
local_bonds = 0; |
361 |
|
local_bends = 0; |
362 |
|
local_torsions = 0; |
363 |
+ |
globalAtomIndex = 0; |
364 |
+ |
|
365 |
+ |
|
366 |
|
for( i=0; i<n_components; i++ ){ |
367 |
|
|
368 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
369 |
|
|
370 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
370 |
> |
if( mol2proc[allMol] == worldRank ){ |
371 |
|
|
372 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
373 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
375 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
376 |
|
localMol++; |
377 |
|
} |
378 |
< |
allMol++; |
378 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
379 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
380 |
> |
globalAtomIndex++; |
381 |
> |
} |
382 |
> |
|
383 |
> |
allMol++; |
384 |
|
} |
385 |
|
} |
386 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
387 |
|
|
276 |
– |
|
388 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
389 |
|
|
390 |
|
if( local_atoms != simnfo->n_atoms ){ |
391 |
|
sprintf( painCave.errMsg, |
392 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
393 |
< |
" localAtom (%d) are note equal.\n", |
393 |
> |
" localAtom (%d) are not equal.\n", |
394 |
|
simnfo->n_atoms, |
395 |
|
local_atoms ); |
396 |
|
painCave.isFatal = 1; |
415 |
|
Atom::createArrays(simnfo->n_atoms); |
416 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
417 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
418 |
+ |
int molIndex; |
419 |
|
|
420 |
+ |
// initialize the molecule's stampID's |
421 |
|
|
422 |
< |
if( simnfo->n_SRI ){ |
423 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
424 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
422 |
> |
#ifdef IS_MPI |
423 |
> |
|
424 |
> |
|
425 |
> |
molIndex = 0; |
426 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
427 |
> |
|
428 |
> |
if(mol2proc[i] == worldRank ){ |
429 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
430 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
431 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
432 |
> |
molIndex++; |
433 |
> |
} |
434 |
> |
} |
435 |
> |
|
436 |
> |
#else // is_mpi |
437 |
> |
|
438 |
> |
molIndex = 0; |
439 |
> |
globalAtomIndex = 0; |
440 |
> |
for(i=0; i<n_components; i++){ |
441 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
442 |
> |
the_molecules[molIndex].setStampID( i ); |
443 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
444 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
445 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
446 |
> |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
447 |
> |
globalAtomIndex++; |
448 |
> |
} |
449 |
> |
molIndex++; |
450 |
> |
} |
451 |
> |
} |
452 |
> |
|
453 |
> |
|
454 |
> |
#endif // is_mpi |
455 |
> |
|
456 |
> |
|
457 |
> |
if( simnfo->n_SRI ){ |
458 |
> |
|
459 |
> |
Exclude::createArray(simnfo->n_SRI); |
460 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
461 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
462 |
|
simnfo->globalExcludes = new int; |
463 |
< |
simnfo->n_exclude = tot_SRI; |
463 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
464 |
|
} |
465 |
|
else{ |
466 |
|
|
467 |
< |
the_excludes = new int[2]; |
468 |
< |
the_excludes[0] = 0; |
469 |
< |
the_excludes[1] = 0; |
467 |
> |
Exclude::createArray( 1 ); |
468 |
> |
the_excludes = new Exclude*; |
469 |
> |
the_excludes[0] = new Exclude(0); |
470 |
> |
the_excludes[0]->setPair( 0,0 ); |
471 |
|
simnfo->globalExcludes = new int; |
472 |
|
simnfo->globalExcludes[0] = 0; |
473 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
473 |
> |
simnfo->n_exclude = 0; |
474 |
|
} |
475 |
|
|
476 |
|
// set the arrays into the SimInfo object |
477 |
|
|
478 |
|
simnfo->atoms = the_atoms; |
479 |
< |
simnfo->sr_interactions = the_sris; |
479 |
> |
simnfo->molecules = the_molecules; |
480 |
|
simnfo->nGlobalExcludes = 0; |
481 |
|
simnfo->excludes = the_excludes; |
482 |
|
|
483 |
|
|
484 |
|
// get some of the tricky things that may still be in the globals |
485 |
|
|
486 |
< |
|
486 |
> |
double boxVector[3]; |
487 |
|
if( the_globals->haveBox() ){ |
488 |
< |
simnfo->box_x = the_globals->getBox(); |
489 |
< |
simnfo->box_y = the_globals->getBox(); |
490 |
< |
simnfo->box_z = the_globals->getBox(); |
488 |
> |
boxVector[0] = the_globals->getBox(); |
489 |
> |
boxVector[1] = the_globals->getBox(); |
490 |
> |
boxVector[2] = the_globals->getBox(); |
491 |
> |
|
492 |
> |
simnfo->setBox( boxVector ); |
493 |
|
} |
494 |
|
else if( the_globals->haveDensity() ){ |
495 |
|
|
496 |
|
double vol; |
497 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
498 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
499 |
< |
simnfo->box_y = simnfo->box_x; |
500 |
< |
simnfo->box_z = simnfo->box_x; |
498 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
499 |
> |
boxVector[1] = boxVector[0]; |
500 |
> |
boxVector[2] = boxVector[0]; |
501 |
> |
|
502 |
> |
simnfo->setBox( boxVector ); |
503 |
|
} |
504 |
|
else{ |
505 |
|
if( !the_globals->haveBoxX() ){ |
508 |
|
painCave.isFatal = 1; |
509 |
|
simError(); |
510 |
|
} |
511 |
< |
simnfo->box_x = the_globals->getBoxX(); |
511 |
> |
boxVector[0] = the_globals->getBoxX(); |
512 |
|
|
513 |
|
if( !the_globals->haveBoxY() ){ |
514 |
|
sprintf( painCave.errMsg, |
516 |
|
painCave.isFatal = 1; |
517 |
|
simError(); |
518 |
|
} |
519 |
< |
simnfo->box_y = the_globals->getBoxY(); |
519 |
> |
boxVector[1] = the_globals->getBoxY(); |
520 |
|
|
521 |
|
if( !the_globals->haveBoxZ() ){ |
522 |
|
sprintf( painCave.errMsg, |
524 |
|
painCave.isFatal = 1; |
525 |
|
simError(); |
526 |
|
} |
527 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
527 |
> |
boxVector[2] = the_globals->getBoxZ(); |
528 |
> |
|
529 |
> |
simnfo->setBox( boxVector ); |
530 |
|
} |
531 |
|
|
532 |
|
#ifdef IS_MPI |
539 |
|
|
540 |
|
the_ff->setSimInfo( simnfo ); |
541 |
|
|
542 |
< |
makeAtoms(); |
542 |
> |
makeMolecules(); |
543 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
544 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
545 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
546 |
|
} |
547 |
|
|
392 |
– |
if( tot_bonds ){ |
393 |
– |
makeBonds(); |
394 |
– |
} |
395 |
– |
|
396 |
– |
if( tot_bends ){ |
397 |
– |
makeBends(); |
398 |
– |
} |
399 |
– |
|
400 |
– |
if( tot_torsions ){ |
401 |
– |
makeTorsions(); |
402 |
– |
} |
403 |
– |
|
404 |
– |
|
548 |
|
if (the_globals->getUseRF() ) { |
549 |
|
simnfo->useReactionField = 1; |
550 |
|
|
556 |
|
painCave.isFatal = 0; |
557 |
|
simError(); |
558 |
|
double smallest; |
559 |
< |
smallest = simnfo->box_x; |
560 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
561 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 |
> |
smallest = simnfo->boxLx; |
560 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
561 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
562 |
|
simnfo->ecr = 0.5 * smallest; |
563 |
|
} else { |
564 |
|
simnfo->ecr = the_globals->getECR(); |
586 |
|
} |
587 |
|
simnfo->dielectric = the_globals->getDielectric(); |
588 |
|
} else { |
589 |
< |
if (simnfo->n_dipoles) { |
589 |
> |
if (usesDipoles) { |
590 |
|
|
591 |
|
if( !the_globals->haveECR() ){ |
592 |
|
sprintf( painCave.errMsg, |
593 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
593 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
594 |
|
"box length for the electrostaticCutoffRadius.\n" |
595 |
|
"I hope you have a very fast processor!\n"); |
596 |
|
painCave.isFatal = 0; |
597 |
|
simError(); |
598 |
|
double smallest; |
599 |
< |
smallest = simnfo->box_x; |
600 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
601 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
599 |
> |
smallest = simnfo->boxLx; |
600 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
601 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
602 |
|
simnfo->ecr = 0.5 * smallest; |
603 |
|
} else { |
604 |
|
simnfo->ecr = the_globals->getECR(); |
606 |
|
|
607 |
|
if( !the_globals->haveEST() ){ |
608 |
|
sprintf( painCave.errMsg, |
609 |
< |
"SimSetup Warning: using default value of 5% of the" |
609 |
> |
"SimSetup Warning: using default value of 5%% of the " |
610 |
|
"electrostaticCutoffRadius for the " |
611 |
|
"electrostaticSkinThickness\n" |
612 |
|
); |
777 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
778 |
|
|
779 |
|
|
780 |
< |
// // make the longe range forces and the integrator |
780 |
> |
// make the integrator |
781 |
> |
|
782 |
> |
|
783 |
> |
NVT* myNVT = NULL; |
784 |
> |
switch( ensembleCase ){ |
785 |
|
|
786 |
< |
// new AllLong( simnfo ); |
786 |
> |
case NVE_ENS: |
787 |
> |
new NVE( simnfo, the_ff ); |
788 |
> |
break; |
789 |
|
|
790 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
791 |
< |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
792 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
793 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
790 |
> |
case NVT_ENS: |
791 |
> |
myNVT = new NVT( simnfo, the_ff ); |
792 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
793 |
> |
|
794 |
> |
if (the_globals->haveTauThermostat()) |
795 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
796 |
> |
// else if (the_globals->haveQmass()) |
797 |
> |
// myNVT->setQmass(the_globals->getQmass()); |
798 |
> |
else { |
799 |
> |
sprintf( painCave.errMsg, |
800 |
> |
"SimSetup error: If you use the NVT\n" |
801 |
> |
" ensemble, you must set either tauThermostat or qMass.\n" |
802 |
> |
" Neither of these was found in the BASS file.\n"); |
803 |
> |
painCave.isFatal = 1; |
804 |
> |
simError(); |
805 |
> |
} |
806 |
> |
break; |
807 |
|
|
808 |
+ |
default: |
809 |
+ |
sprintf( painCave.errMsg, |
810 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
811 |
+ |
painCave.isFatal = 1; |
812 |
+ |
simError(); |
813 |
+ |
} |
814 |
|
|
815 |
|
|
816 |
+ |
#ifdef IS_MPI |
817 |
+ |
mpiSim->mpiRefresh(); |
818 |
+ |
#endif |
819 |
+ |
|
820 |
|
// initialize the Fortran |
821 |
< |
|
821 |
> |
|
822 |
> |
|
823 |
|
simnfo->refreshSim(); |
824 |
|
|
825 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
844 |
|
#endif // is_mpi |
845 |
|
} |
846 |
|
|
674 |
– |
void SimSetup::makeAtoms( void ){ |
847 |
|
|
848 |
< |
int i, j, k, index; |
677 |
< |
double ux, uy, uz, uSqr, u; |
678 |
< |
AtomStamp* current_atom; |
848 |
> |
void SimSetup::makeMolecules( void ){ |
849 |
|
|
850 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
851 |
+ |
molInit info; |
852 |
|
DirectionalAtom* dAtom; |
853 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
853 |
> |
LinkedAssign* extras; |
854 |
> |
LinkedAssign* current_extra; |
855 |
> |
AtomStamp* currentAtom; |
856 |
> |
BondStamp* currentBond; |
857 |
> |
BendStamp* currentBend; |
858 |
> |
TorsionStamp* currentTorsion; |
859 |
|
|
860 |
< |
lMolIndex = 0; |
861 |
< |
molIndex = 0; |
862 |
< |
index = 0; |
686 |
< |
for( i=0; i<n_components; i++ ){ |
860 |
> |
bond_pair* theBonds; |
861 |
> |
bend_set* theBends; |
862 |
> |
torsion_set* theTorsions; |
863 |
|
|
864 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
864 |
> |
|
865 |
> |
//init the forceField paramters |
866 |
|
|
867 |
< |
#ifdef IS_MPI |
691 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
692 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
693 |
< |
#endif // is_mpi |
867 |
> |
the_ff->readParams(); |
868 |
|
|
869 |
< |
molStart = index; |
870 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
697 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
698 |
< |
|
699 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
700 |
< |
if( current_atom->haveOrientation() ){ |
701 |
< |
|
702 |
< |
dAtom = new DirectionalAtom(index); |
703 |
< |
simnfo->n_oriented++; |
704 |
< |
the_atoms[index] = dAtom; |
705 |
< |
|
706 |
< |
ux = current_atom->getOrntX(); |
707 |
< |
uy = current_atom->getOrntY(); |
708 |
< |
uz = current_atom->getOrntZ(); |
709 |
< |
|
710 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
711 |
< |
|
712 |
< |
u = sqrt( uSqr ); |
713 |
< |
ux = ux / u; |
714 |
< |
uy = uy / u; |
715 |
< |
uz = uz / u; |
716 |
< |
|
717 |
< |
dAtom->setSUx( ux ); |
718 |
< |
dAtom->setSUy( uy ); |
719 |
< |
dAtom->setSUz( uz ); |
720 |
< |
} |
721 |
< |
else{ |
722 |
< |
the_atoms[index] = new GeneralAtom(index); |
723 |
< |
} |
724 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
725 |
< |
the_atoms[index]->setIndex( index ); |
726 |
< |
|
727 |
< |
// increment the index and repeat; |
728 |
< |
index++; |
729 |
< |
} |
730 |
< |
|
731 |
< |
molEnd = index -1; |
732 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
733 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
734 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
735 |
< |
the_molecules[lMolIndex].setStampID( i ); |
736 |
< |
lMolIndex++; |
869 |
> |
|
870 |
> |
// init the atoms |
871 |
|
|
872 |
< |
#ifdef IS_MPI |
873 |
< |
} |
874 |
< |
#endif //is_mpi |
875 |
< |
|
876 |
< |
molIndex++; |
743 |
< |
} |
744 |
< |
} |
745 |
< |
|
746 |
< |
#ifdef IS_MPI |
747 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
872 |
> |
double ux, uy, uz, u, uSqr; |
873 |
> |
|
874 |
> |
atomOffset = 0; |
875 |
> |
excludeOffset = 0; |
876 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
877 |
|
|
878 |
< |
delete[] globalIndex; |
878 |
> |
stampID = the_molecules[i].getStampID(); |
879 |
|
|
880 |
< |
mpiSim->mpiRefresh(); |
881 |
< |
#endif //IS_MPI |
882 |
< |
|
883 |
< |
the_ff->initializeAtoms(); |
884 |
< |
} |
880 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
881 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
882 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
883 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
884 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
885 |
|
|
886 |
< |
void SimSetup::makeBonds( void ){ |
887 |
< |
|
888 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
889 |
< |
bond_pair* the_bonds; |
890 |
< |
BondStamp* current_bond; |
762 |
< |
|
763 |
< |
the_bonds = new bond_pair[tot_bonds]; |
764 |
< |
index = 0; |
765 |
< |
offset = 0; |
766 |
< |
molIndex = 0; |
767 |
< |
|
768 |
< |
for( i=0; i<n_components; i++ ){ |
769 |
< |
|
770 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
771 |
< |
|
772 |
< |
#ifdef IS_MPI |
773 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
774 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
775 |
< |
#endif // is_mpi |
776 |
< |
|
777 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
778 |
< |
|
779 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
780 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
781 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
886 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
887 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
888 |
> |
info.myBonds = new Bond*[info.nBonds]; |
889 |
> |
info.myBends = new Bend*[info.nBends]; |
890 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
891 |
|
|
892 |
< |
exI = the_bonds[index].a; |
893 |
< |
exJ = the_bonds[index].b; |
894 |
< |
|
895 |
< |
// exclude_I must always be the smaller of the pair |
896 |
< |
if( exI > exJ ){ |
897 |
< |
tempEx = exI; |
898 |
< |
exI = exJ; |
899 |
< |
exJ = tempEx; |
900 |
< |
} |
901 |
< |
|
793 |
< |
|
794 |
< |
#ifdef IS_MPI |
795 |
< |
|
796 |
< |
the_excludes[index*2] = |
797 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
798 |
< |
the_excludes[index*2 + 1] = |
799 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
800 |
< |
|
801 |
< |
#else // isn't MPI |
802 |
< |
|
803 |
< |
the_excludes[index*2] = exI + 1; |
804 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
805 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
806 |
< |
#endif //is_mpi |
807 |
< |
|
808 |
< |
// increment the index and repeat; |
809 |
< |
index++; |
810 |
< |
} |
811 |
< |
offset += comp_stamps[i]->getNAtoms(); |
892 |
> |
theBonds = new bond_pair[info.nBonds]; |
893 |
> |
theBends = new bend_set[info.nBends]; |
894 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
895 |
> |
|
896 |
> |
// make the Atoms |
897 |
> |
|
898 |
> |
for(j=0; j<info.nAtoms; j++){ |
899 |
> |
|
900 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
901 |
> |
if( currentAtom->haveOrientation() ){ |
902 |
|
|
903 |
< |
#ifdef IS_MPI |
903 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
904 |
> |
simnfo->n_oriented++; |
905 |
> |
info.myAtoms[j] = dAtom; |
906 |
> |
|
907 |
> |
ux = currentAtom->getOrntX(); |
908 |
> |
uy = currentAtom->getOrntY(); |
909 |
> |
uz = currentAtom->getOrntZ(); |
910 |
> |
|
911 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
912 |
> |
|
913 |
> |
u = sqrt( uSqr ); |
914 |
> |
ux = ux / u; |
915 |
> |
uy = uy / u; |
916 |
> |
uz = uz / u; |
917 |
> |
|
918 |
> |
dAtom->setSUx( ux ); |
919 |
> |
dAtom->setSUy( uy ); |
920 |
> |
dAtom->setSUz( uz ); |
921 |
|
} |
922 |
< |
#endif //is_mpi |
922 |
> |
else{ |
923 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
924 |
> |
} |
925 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
926 |
> |
|
927 |
> |
#ifdef IS_MPI |
928 |
|
|
929 |
< |
molIndex++; |
930 |
< |
} |
931 |
< |
} |
929 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
930 |
> |
|
931 |
> |
#endif // is_mpi |
932 |
> |
} |
933 |
> |
|
934 |
> |
// make the bonds |
935 |
> |
for(j=0; j<info.nBonds; j++){ |
936 |
> |
|
937 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
938 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
939 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
940 |
|
|
941 |
< |
the_ff->initializeBonds( the_bonds ); |
942 |
< |
} |
941 |
> |
exI = theBonds[j].a; |
942 |
> |
exJ = theBonds[j].b; |
943 |
|
|
944 |
< |
void SimSetup::makeBends( void ){ |
945 |
< |
|
946 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
947 |
< |
bend_set* the_bends; |
948 |
< |
BendStamp* current_bend; |
949 |
< |
LinkedAssign* extras; |
830 |
< |
LinkedAssign* current_extra; |
831 |
< |
|
832 |
< |
|
833 |
< |
the_bends = new bend_set[tot_bends]; |
834 |
< |
index = 0; |
835 |
< |
offset = 0; |
836 |
< |
molIndex = 0; |
837 |
< |
for( i=0; i<n_components; i++ ){ |
838 |
< |
|
839 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
840 |
< |
|
944 |
> |
// exclude_I must always be the smaller of the pair |
945 |
> |
if( exI > exJ ){ |
946 |
> |
tempEx = exI; |
947 |
> |
exI = exJ; |
948 |
> |
exJ = tempEx; |
949 |
> |
} |
950 |
|
#ifdef IS_MPI |
951 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
952 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
953 |
< |
#endif // is_mpi |
951 |
> |
tempEx = exI; |
952 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
953 |
> |
tempEx = exJ; |
954 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
955 |
> |
|
956 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
957 |
> |
#else // isn't MPI |
958 |
|
|
959 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
959 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
960 |
> |
#endif //is_mpi |
961 |
> |
} |
962 |
> |
excludeOffset += info.nBonds; |
963 |
> |
|
964 |
> |
//make the bends |
965 |
> |
for(j=0; j<info.nBends; j++){ |
966 |
> |
|
967 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
968 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
969 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
970 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
971 |
|
|
972 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
849 |
< |
the_bends[index].a = current_bend->getA() + offset; |
850 |
< |
the_bends[index].b = current_bend->getB() + offset; |
851 |
< |
the_bends[index].c = current_bend->getC() + offset; |
852 |
< |
|
853 |
< |
if( current_bend->haveExtras() ){ |
972 |
> |
if( currentBend->haveExtras() ){ |
973 |
|
|
974 |
< |
extras = current_bend->getExtras(); |
975 |
< |
current_extra = extras; |
974 |
> |
extras = currentBend->getExtras(); |
975 |
> |
current_extra = extras; |
976 |
|
|
977 |
< |
while( current_extra != NULL ){ |
978 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
977 |
> |
while( current_extra != NULL ){ |
978 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
979 |
|
|
980 |
< |
switch( current_extra->getType() ){ |
980 |
> |
switch( current_extra->getType() ){ |
981 |
> |
|
982 |
> |
case 0: |
983 |
> |
theBends[j].ghost = |
984 |
> |
current_extra->getInt() + atomOffset; |
985 |
> |
theBends[j].isGhost = 1; |
986 |
> |
break; |
987 |
|
|
988 |
< |
case 0: |
989 |
< |
the_bends[index].ghost = |
990 |
< |
current_extra->getInt() + offset; |
991 |
< |
the_bends[index].isGhost = 1; |
992 |
< |
break; |
868 |
< |
|
869 |
< |
case 1: |
870 |
< |
the_bends[index].ghost = |
871 |
< |
(int)current_extra->getDouble() + offset; |
872 |
< |
the_bends[index].isGhost = 1; |
873 |
< |
break; |
874 |
< |
|
875 |
< |
default: |
876 |
< |
sprintf( painCave.errMsg, |
877 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
878 |
< |
"double nor an int.\n" |
879 |
< |
"-->Bend[%d] in %s\n", |
880 |
< |
k, comp_stamps[i]->getID() ); |
881 |
< |
painCave.isFatal = 1; |
882 |
< |
simError(); |
883 |
< |
} |
884 |
< |
} |
988 |
> |
case 1: |
989 |
> |
theBends[j].ghost = |
990 |
> |
(int)current_extra->getDouble() + atomOffset; |
991 |
> |
theBends[j].isGhost = 1; |
992 |
> |
break; |
993 |
|
|
994 |
< |
else{ |
995 |
< |
|
996 |
< |
sprintf( painCave.errMsg, |
997 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
998 |
< |
" -->%s in Bend[%d] in %s\n", |
999 |
< |
current_extra->getlhs(), |
1000 |
< |
k, comp_stamps[i]->getID() ); |
1001 |
< |
painCave.isFatal = 1; |
894 |
< |
simError(); |
895 |
< |
} |
896 |
< |
|
897 |
< |
current_extra = current_extra->getNext(); |
994 |
> |
default: |
995 |
> |
sprintf( painCave.errMsg, |
996 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
997 |
> |
"double nor an int.\n" |
998 |
> |
"-->Bend[%d] in %s\n", |
999 |
> |
j, comp_stamps[stampID]->getID() ); |
1000 |
> |
painCave.isFatal = 1; |
1001 |
> |
simError(); |
1002 |
|
} |
1003 |
|
} |
1004 |
|
|
901 |
– |
if( !the_bends[index].isGhost ){ |
902 |
– |
|
903 |
– |
exI = the_bends[index].a; |
904 |
– |
exJ = the_bends[index].c; |
905 |
– |
} |
1005 |
|
else{ |
1006 |
|
|
1007 |
< |
exI = the_bends[index].a; |
1008 |
< |
exJ = the_bends[index].b; |
1007 |
> |
sprintf( painCave.errMsg, |
1008 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
1009 |
> |
" -->%s in Bend[%d] in %s\n", |
1010 |
> |
current_extra->getlhs(), |
1011 |
> |
j, comp_stamps[stampID]->getID() ); |
1012 |
> |
painCave.isFatal = 1; |
1013 |
> |
simError(); |
1014 |
|
} |
1015 |
|
|
1016 |
< |
// exclude_I must always be the smaller of the pair |
1017 |
< |
if( exI > exJ ){ |
1018 |
< |
tempEx = exI; |
1019 |
< |
exI = exJ; |
1020 |
< |
exJ = tempEx; |
1021 |
< |
} |
1016 |
> |
current_extra = current_extra->getNext(); |
1017 |
> |
} |
1018 |
> |
} |
1019 |
> |
|
1020 |
> |
if( !theBends[j].isGhost ){ |
1021 |
> |
|
1022 |
> |
exI = theBends[j].a; |
1023 |
> |
exJ = theBends[j].c; |
1024 |
> |
} |
1025 |
> |
else{ |
1026 |
> |
|
1027 |
> |
exI = theBends[j].a; |
1028 |
> |
exJ = theBends[j].b; |
1029 |
> |
} |
1030 |
> |
|
1031 |
> |
// exclude_I must always be the smaller of the pair |
1032 |
> |
if( exI > exJ ){ |
1033 |
> |
tempEx = exI; |
1034 |
> |
exI = exJ; |
1035 |
> |
exJ = tempEx; |
1036 |
> |
} |
1037 |
> |
#ifdef IS_MPI |
1038 |
> |
tempEx = exI; |
1039 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1040 |
> |
tempEx = exJ; |
1041 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1042 |
> |
|
1043 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1044 |
> |
#else // isn't MPI |
1045 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1046 |
> |
#endif //is_mpi |
1047 |
> |
} |
1048 |
> |
excludeOffset += info.nBends; |
1049 |
|
|
1050 |
+ |
for(j=0; j<info.nTorsions; j++){ |
1051 |
+ |
|
1052 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1053 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1054 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1055 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1056 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1057 |
+ |
|
1058 |
+ |
exI = theTorsions[j].a; |
1059 |
+ |
exJ = theTorsions[j].d; |
1060 |
|
|
1061 |
+ |
// exclude_I must always be the smaller of the pair |
1062 |
+ |
if( exI > exJ ){ |
1063 |
+ |
tempEx = exI; |
1064 |
+ |
exI = exJ; |
1065 |
+ |
exJ = tempEx; |
1066 |
+ |
} |
1067 |
|
#ifdef IS_MPI |
1068 |
< |
|
1069 |
< |
the_excludes[(index + tot_bonds)*2] = |
1070 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1071 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1072 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1073 |
< |
|
1068 |
> |
tempEx = exI; |
1069 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1070 |
> |
tempEx = exJ; |
1071 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1072 |
> |
|
1073 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1074 |
|
#else // isn't MPI |
1075 |
< |
|
929 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
930 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
931 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1075 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1076 |
|
#endif //is_mpi |
933 |
– |
|
934 |
– |
|
935 |
– |
// increment the index and repeat; |
936 |
– |
index++; |
937 |
– |
} |
938 |
– |
offset += comp_stamps[i]->getNAtoms(); |
939 |
– |
|
940 |
– |
#ifdef IS_MPI |
941 |
– |
} |
942 |
– |
#endif //is_mpi |
943 |
– |
|
944 |
– |
molIndex++; |
1077 |
|
} |
1078 |
< |
} |
1078 |
> |
excludeOffset += info.nTorsions; |
1079 |
> |
|
1080 |
> |
|
1081 |
> |
// send the arrays off to the forceField for init. |
1082 |
> |
|
1083 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1084 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1085 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1086 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1087 |
|
|
948 |
– |
#ifdef IS_MPI |
949 |
– |
sprintf( checkPointMsg, |
950 |
– |
"Successfully created the bends list.\n" ); |
951 |
– |
MPIcheckPoint(); |
952 |
– |
#endif // is_mpi |
953 |
– |
|
1088 |
|
|
1089 |
< |
the_ff->initializeBends( the_bends ); |
956 |
< |
} |
1089 |
> |
the_molecules[i].initialize( info ); |
1090 |
|
|
958 |
– |
void SimSetup::makeTorsions( void ){ |
1091 |
|
|
1092 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1093 |
< |
torsion_set* the_torsions; |
1094 |
< |
TorsionStamp* current_torsion; |
1092 |
> |
atomOffset += info.nAtoms; |
1093 |
> |
delete[] theBonds; |
1094 |
> |
delete[] theBends; |
1095 |
> |
delete[] theTorsions; |
1096 |
> |
} |
1097 |
|
|
964 |
– |
the_torsions = new torsion_set[tot_torsions]; |
965 |
– |
index = 0; |
966 |
– |
offset = 0; |
967 |
– |
molIndex = 0; |
968 |
– |
for( i=0; i<n_components; i++ ){ |
969 |
– |
|
970 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
971 |
– |
|
1098 |
|
#ifdef IS_MPI |
1099 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1100 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1101 |
< |
#endif // is_mpi |
1099 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1100 |
> |
MPIcheckPoint(); |
1101 |
> |
#endif // is_mpi |
1102 |
|
|
1103 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1103 |
> |
// clean up the forcefield |
1104 |
> |
the_ff->calcRcut(); |
1105 |
> |
the_ff->cleanMe(); |
1106 |
|
|
979 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
980 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
981 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
982 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
983 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
984 |
– |
|
985 |
– |
exI = the_torsions[index].a; |
986 |
– |
exJ = the_torsions[index].d; |
987 |
– |
|
988 |
– |
|
989 |
– |
// exclude_I must always be the smaller of the pair |
990 |
– |
if( exI > exJ ){ |
991 |
– |
tempEx = exI; |
992 |
– |
exI = exJ; |
993 |
– |
exJ = tempEx; |
994 |
– |
} |
995 |
– |
|
996 |
– |
|
997 |
– |
#ifdef IS_MPI |
998 |
– |
|
999 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1000 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
1001 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1002 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
1003 |
– |
|
1004 |
– |
#else // isn't MPI |
1005 |
– |
|
1006 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1007 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1008 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
1009 |
– |
#endif //is_mpi |
1010 |
– |
|
1011 |
– |
|
1012 |
– |
// increment the index and repeat; |
1013 |
– |
index++; |
1014 |
– |
} |
1015 |
– |
offset += comp_stamps[i]->getNAtoms(); |
1016 |
– |
|
1017 |
– |
#ifdef IS_MPI |
1018 |
– |
} |
1019 |
– |
#endif //is_mpi |
1020 |
– |
|
1021 |
– |
molIndex++; |
1022 |
– |
} |
1023 |
– |
} |
1024 |
– |
|
1025 |
– |
the_ff->initializeTorsions( the_torsions ); |
1107 |
|
} |
1108 |
|
|
1109 |
|
void SimSetup::initFromBass( void ){ |
1125 |
|
have_extra =1; |
1126 |
|
|
1127 |
|
n_cells = (int)temp3 - 1; |
1128 |
< |
cellx = simnfo->box_x / temp3; |
1129 |
< |
celly = simnfo->box_y / temp3; |
1130 |
< |
cellz = simnfo->box_z / temp3; |
1128 |
> |
cellx = simnfo->boxLx / temp3; |
1129 |
> |
celly = simnfo->boxLy / temp3; |
1130 |
> |
cellz = simnfo->boxLz / temp3; |
1131 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1132 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1133 |
|
n_per_extra = (int)ceil( temp1 ); |
1142 |
|
} |
1143 |
|
else{ |
1144 |
|
n_cells = (int)temp3; |
1145 |
< |
cellx = simnfo->box_x / temp3; |
1146 |
< |
celly = simnfo->box_y / temp3; |
1147 |
< |
cellz = simnfo->box_z / temp3; |
1145 |
> |
cellx = simnfo->boxLx / temp3; |
1146 |
> |
celly = simnfo->boxLy / temp3; |
1147 |
> |
cellz = simnfo->boxLz / temp3; |
1148 |
|
} |
1149 |
|
|
1150 |
|
current_mol = 0; |