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 NPT_ENS 2 |
20 |
+ |
|
21 |
+ |
#define FF_DUFF 0 |
22 |
+ |
#define FF_LJ 1 |
23 |
+ |
|
24 |
+ |
|
25 |
|
SimSetup::SimSetup(){ |
26 |
|
stamps = new MakeStamps(); |
27 |
|
globals = new Globals(); |
76 |
|
|
77 |
|
MakeStamps *the_stamps; |
78 |
|
Globals* the_globals; |
79 |
< |
int i, j; |
79 |
> |
int i, j, k, globalAtomIndex; |
80 |
> |
|
81 |
> |
int ensembleCase; |
82 |
> |
int ffCase; |
83 |
> |
|
84 |
> |
ensembleCase = -1; |
85 |
> |
ffCase = -1; |
86 |
|
|
87 |
|
// get the stamps and globals; |
88 |
|
the_stamps = stamps; |
96 |
|
// get the ones we know are there, yet still may need some work. |
97 |
|
n_components = the_globals->getNComponents(); |
98 |
|
strcpy( force_field, the_globals->getForceField() ); |
99 |
+ |
|
100 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 |
+ |
else{ |
103 |
+ |
sprintf( painCave.errMsg, |
104 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
105 |
+ |
force_field ); |
106 |
+ |
painCave.isFatal = 1; |
107 |
+ |
simError(); |
108 |
+ |
} |
109 |
+ |
|
110 |
+ |
// get the ensemble: |
111 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
112 |
+ |
|
113 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
114 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
115 |
+ |
else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
116 |
+ |
else{ |
117 |
+ |
sprintf( painCave.errMsg, |
118 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
119 |
+ |
"reverting to NVE for this simulation.\n", |
120 |
+ |
ensemble ); |
121 |
+ |
painCave.isFatal = 0; |
122 |
+ |
simError(); |
123 |
+ |
strcpy( ensemble, "NVE" ); |
124 |
+ |
ensembleCase = NVE_ENS; |
125 |
+ |
} |
126 |
|
strcpy( simnfo->ensemble, ensemble ); |
127 |
|
|
128 |
+ |
|
129 |
+ |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
130 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
131 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 |
+ |
// if (the_globals->haveTargetPressure()) |
133 |
+ |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 |
+ |
// else { |
135 |
+ |
// sprintf( painCave.errMsg, |
136 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
137 |
+ |
// " ensemble, you must set targetPressure.\n" |
138 |
+ |
// " This was found in the BASS file.\n"); |
139 |
+ |
// painCave.isFatal = 1; |
140 |
+ |
// simError(); |
141 |
+ |
// } |
142 |
+ |
|
143 |
+ |
// if (the_globals->haveTauThermostat()) |
144 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 |
+ |
// else if (the_globals->haveQmass()) |
146 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
147 |
+ |
// else { |
148 |
+ |
// sprintf( painCave.errMsg, |
149 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
150 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
151 |
+ |
// " Neither of these was found in the BASS file.\n"); |
152 |
+ |
// painCave.isFatal = 1; |
153 |
+ |
// simError(); |
154 |
+ |
// } |
155 |
+ |
|
156 |
+ |
// if (the_globals->haveTauBarostat()) |
157 |
+ |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 |
+ |
// else { |
159 |
+ |
// sprintf( painCave.errMsg, |
160 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
161 |
+ |
// " ensemble, you must set tauBarostat.\n" |
162 |
+ |
// " This was found in the BASS file.\n"); |
163 |
+ |
// painCave.isFatal = 1; |
164 |
+ |
// simError(); |
165 |
+ |
// } |
166 |
+ |
|
167 |
+ |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
169 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
170 |
+ |
|
171 |
+ |
// if (the_globals->haveTauThermostat()) |
172 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 |
+ |
// else if (the_globals->haveQmass()) |
174 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
175 |
+ |
// else { |
176 |
+ |
// sprintf( painCave.errMsg, |
177 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
178 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
179 |
+ |
// " Neither of these was found in the BASS file.\n"); |
180 |
+ |
// painCave.isFatal = 1; |
181 |
+ |
// simError(); |
182 |
+ |
// } |
183 |
+ |
|
184 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
185 |
|
simnfo->usePBC = the_globals->getPBC(); |
186 |
|
|
187 |
+ |
int usesDipoles = 0; |
188 |
+ |
switch( ffCase ){ |
189 |
|
|
190 |
+ |
case FF_DUFF: |
191 |
+ |
the_ff = new DUFF(); |
192 |
+ |
usesDipoles = 1; |
193 |
+ |
break; |
194 |
|
|
195 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
196 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
197 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
198 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
199 |
< |
else{ |
195 |
> |
case FF_LJ: |
196 |
> |
the_ff = new LJFF(); |
197 |
> |
break; |
198 |
> |
|
199 |
> |
default: |
200 |
|
sprintf( painCave.errMsg, |
201 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
98 |
< |
force_field ); |
201 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
202 |
|
painCave.isFatal = 1; |
203 |
|
simError(); |
204 |
|
} |
208 |
|
MPIcheckPoint(); |
209 |
|
#endif // is_mpi |
210 |
|
|
108 |
– |
|
109 |
– |
|
211 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
212 |
|
the_components = the_globals->getComponents(); |
213 |
|
components_nmol = new int[n_components]; |
331 |
|
simnfo->n_torsions = tot_torsions; |
332 |
|
simnfo->n_SRI = tot_SRI; |
333 |
|
simnfo->n_mol = tot_nmol; |
233 |
– |
|
334 |
|
|
335 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
336 |
+ |
|
337 |
|
#ifdef IS_MPI |
338 |
|
|
339 |
|
// divide the molecules among processors here. |
340 |
|
|
341 |
|
mpiSim = new mpiSimulation( simnfo ); |
342 |
|
|
241 |
– |
|
242 |
– |
|
343 |
|
globalIndex = mpiSim->divideLabor(); |
344 |
|
|
245 |
– |
|
246 |
– |
|
345 |
|
// set up the local variables |
346 |
|
|
347 |
|
int localMol, allMol; |
348 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
349 |
+ |
|
350 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
351 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
352 |
|
|
353 |
|
allMol = 0; |
354 |
|
localMol = 0; |
356 |
|
local_bonds = 0; |
357 |
|
local_bends = 0; |
358 |
|
local_torsions = 0; |
359 |
+ |
globalAtomIndex = 0; |
360 |
+ |
|
361 |
+ |
|
362 |
|
for( i=0; i<n_components; i++ ){ |
363 |
|
|
364 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
365 |
|
|
366 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
366 |
> |
if( mol2proc[allMol] == worldRank ){ |
367 |
|
|
368 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
369 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
371 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
372 |
|
localMol++; |
373 |
|
} |
374 |
< |
allMol++; |
374 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 |
> |
globalAtomIndex++; |
377 |
> |
} |
378 |
> |
|
379 |
> |
allMol++; |
380 |
|
} |
381 |
|
} |
382 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
383 |
|
|
276 |
– |
|
384 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
|
|
386 |
|
if( local_atoms != simnfo->n_atoms ){ |
387 |
|
sprintf( painCave.errMsg, |
388 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 |
< |
" localAtom (%d) are note equal.\n", |
389 |
> |
" localAtom (%d) are not equal.\n", |
390 |
|
simnfo->n_atoms, |
391 |
|
local_atoms ); |
392 |
|
painCave.isFatal = 1; |
411 |
|
Atom::createArrays(simnfo->n_atoms); |
412 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
413 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
414 |
+ |
int molIndex; |
415 |
|
|
416 |
+ |
// initialize the molecule's stampID's |
417 |
|
|
418 |
< |
if( simnfo->n_SRI ){ |
419 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
420 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
418 |
> |
#ifdef IS_MPI |
419 |
> |
|
420 |
> |
|
421 |
> |
molIndex = 0; |
422 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
423 |
> |
|
424 |
> |
if(mol2proc[i] == worldRank ){ |
425 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
426 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
427 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
428 |
> |
molIndex++; |
429 |
> |
} |
430 |
> |
} |
431 |
> |
|
432 |
> |
#else // is_mpi |
433 |
> |
|
434 |
> |
molIndex = 0; |
435 |
> |
globalAtomIndex = 0; |
436 |
> |
for(i=0; i<n_components; i++){ |
437 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
438 |
> |
the_molecules[molIndex].setStampID( i ); |
439 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
440 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 |
> |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 |
> |
globalAtomIndex++; |
444 |
> |
} |
445 |
> |
molIndex++; |
446 |
> |
} |
447 |
> |
} |
448 |
> |
|
449 |
> |
|
450 |
> |
#endif // is_mpi |
451 |
> |
|
452 |
> |
|
453 |
> |
if( simnfo->n_SRI ){ |
454 |
> |
|
455 |
> |
Exclude::createArray(simnfo->n_SRI); |
456 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
457 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 |
|
simnfo->globalExcludes = new int; |
459 |
< |
simnfo->n_exclude = tot_SRI; |
459 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
460 |
|
} |
461 |
|
else{ |
462 |
|
|
463 |
< |
the_excludes = new int[2]; |
464 |
< |
the_excludes[0] = 0; |
465 |
< |
the_excludes[1] = 0; |
463 |
> |
Exclude::createArray( 1 ); |
464 |
> |
the_excludes = new Exclude*; |
465 |
> |
the_excludes[0] = new Exclude(0); |
466 |
> |
the_excludes[0]->setPair( 0,0 ); |
467 |
|
simnfo->globalExcludes = new int; |
468 |
|
simnfo->globalExcludes[0] = 0; |
469 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
469 |
> |
simnfo->n_exclude = 0; |
470 |
|
} |
471 |
|
|
472 |
|
// set the arrays into the SimInfo object |
473 |
|
|
474 |
|
simnfo->atoms = the_atoms; |
475 |
< |
simnfo->sr_interactions = the_sris; |
475 |
> |
simnfo->molecules = the_molecules; |
476 |
|
simnfo->nGlobalExcludes = 0; |
477 |
|
simnfo->excludes = the_excludes; |
478 |
|
|
529 |
|
|
530 |
|
the_ff->setSimInfo( simnfo ); |
531 |
|
|
532 |
< |
makeAtoms(); |
532 |
> |
makeMolecules(); |
533 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
534 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
535 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
536 |
|
} |
537 |
|
|
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 |
– |
|
538 |
|
if (the_globals->getUseRF() ) { |
539 |
|
simnfo->useReactionField = 1; |
540 |
|
|
576 |
|
} |
577 |
|
simnfo->dielectric = the_globals->getDielectric(); |
578 |
|
} else { |
579 |
< |
if (simnfo->n_dipoles) { |
579 |
> |
if (usesDipoles) { |
580 |
|
|
581 |
|
if( !the_globals->haveECR() ){ |
582 |
|
sprintf( painCave.errMsg, |
583 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
583 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
584 |
|
"box length for the electrostaticCutoffRadius.\n" |
585 |
|
"I hope you have a very fast processor!\n"); |
586 |
|
painCave.isFatal = 0; |
596 |
|
|
597 |
|
if( !the_globals->haveEST() ){ |
598 |
|
sprintf( painCave.errMsg, |
599 |
< |
"SimSetup Warning: using default value of 5% of the" |
599 |
> |
"SimSetup Warning: using default value of 5%% of the " |
600 |
|
"electrostaticCutoffRadius for the " |
601 |
|
"electrostaticSkinThickness\n" |
602 |
|
); |
767 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
768 |
|
|
769 |
|
|
770 |
< |
// // make the longe range forces and the integrator |
770 |
> |
// make the integrator |
771 |
> |
|
772 |
> |
|
773 |
> |
NVT* myNVT = NULL; |
774 |
> |
switch( ensembleCase ){ |
775 |
|
|
776 |
< |
// new AllLong( simnfo ); |
776 |
> |
case NVE_ENS: |
777 |
> |
new NVE( simnfo, the_ff ); |
778 |
> |
break; |
779 |
|
|
780 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
781 |
< |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
782 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
783 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
780 |
> |
case NVT_ENS: |
781 |
> |
myNVT = new NVT( simnfo, the_ff ); |
782 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
783 |
> |
|
784 |
> |
if (the_globals->haveTauThermostat()) |
785 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
786 |
> |
else if (the_globals->haveQmass()) |
787 |
> |
myNVT->setQmass(the_globals->getQmass()); |
788 |
> |
else { |
789 |
> |
sprintf( painCave.errMsg, |
790 |
> |
"SimSetup error: If you use the NVT\n" |
791 |
> |
" ensemble, you must set either tauThermostat or qMass.\n" |
792 |
> |
" Neither of these was found in the BASS file.\n"); |
793 |
> |
painCave.isFatal = 1; |
794 |
> |
simError(); |
795 |
> |
} |
796 |
> |
break; |
797 |
> |
|
798 |
> |
default: |
799 |
> |
sprintf( painCave.errMsg, |
800 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
801 |
> |
painCave.isFatal = 1; |
802 |
> |
simError(); |
803 |
> |
} |
804 |
|
|
805 |
|
|
806 |
+ |
#ifdef IS_MPI |
807 |
+ |
mpiSim->mpiRefresh(); |
808 |
+ |
#endif |
809 |
|
|
810 |
|
// initialize the Fortran |
811 |
< |
|
811 |
> |
|
812 |
> |
|
813 |
|
simnfo->refreshSim(); |
814 |
|
|
815 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
837 |
|
|
838 |
|
void SimSetup::makeMolecules( void ){ |
839 |
|
|
840 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
840 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
841 |
|
molInit info; |
842 |
|
DirectionalAtom* dAtom; |
843 |
+ |
LinkedAssign* extras; |
844 |
+ |
LinkedAssign* current_extra; |
845 |
|
AtomStamp* currentAtom; |
846 |
|
BondStamp* currentBond; |
847 |
|
BendStamp* currentBend; |
848 |
|
TorsionStamp* currentTorsion; |
849 |
+ |
|
850 |
+ |
bond_pair* theBonds; |
851 |
+ |
bend_set* theBends; |
852 |
+ |
torsion_set* theTorsions; |
853 |
+ |
|
854 |
|
|
855 |
|
//init the forceField paramters |
856 |
|
|
857 |
|
the_ff->readParams(); |
858 |
|
|
859 |
|
|
860 |
< |
// init the molecules |
860 |
> |
// init the atoms |
861 |
|
|
862 |
+ |
double ux, uy, uz, u, uSqr; |
863 |
+ |
|
864 |
|
atomOffset = 0; |
865 |
+ |
excludeOffset = 0; |
866 |
|
for(i=0; i<simnfo->n_mol; i++){ |
867 |
|
|
868 |
|
stampID = the_molecules[i].getStampID(); |
871 |
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
872 |
|
info.nBends = comp_stamps[stampID]->getNBends(); |
873 |
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
874 |
< |
|
874 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
875 |
> |
|
876 |
|
info.myAtoms = &the_atoms[atomOffset]; |
877 |
+ |
info.myExcludes = &the_excludes[excludeOffset]; |
878 |
|
info.myBonds = new Bond*[info.nBonds]; |
879 |
|
info.myBends = new Bend*[info.nBends]; |
880 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
880 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
881 |
|
|
882 |
|
theBonds = new bond_pair[info.nBonds]; |
883 |
|
theBends = new bend_set[info.nBends]; |
887 |
|
|
888 |
|
for(j=0; j<info.nAtoms; j++){ |
889 |
|
|
890 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
890 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
891 |
|
if( currentAtom->haveOrientation() ){ |
892 |
|
|
893 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
922 |
|
} |
923 |
|
|
924 |
|
// make the bonds |
925 |
< |
for(j=0; j<nBonds; j++){ |
925 |
> |
for(j=0; j<info.nBonds; j++){ |
926 |
|
|
927 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
928 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
929 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
930 |
|
|
931 |
< |
exI = theBonds[i].a; |
932 |
< |
exJ = theBonds[i].b; |
931 |
> |
exI = theBonds[j].a; |
932 |
> |
exJ = theBonds[j].b; |
933 |
|
|
934 |
|
// exclude_I must always be the smaller of the pair |
935 |
|
if( exI > exJ ){ |
938 |
|
exJ = tempEx; |
939 |
|
} |
940 |
|
#ifdef IS_MPI |
941 |
< |
|
942 |
< |
the_excludes[index*2] = |
943 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
944 |
< |
the_excludes[index*2 + 1] = |
770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
941 |
> |
tempEx = exI; |
942 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
943 |
> |
tempEx = exJ; |
944 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
945 |
|
|
946 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
947 |
|
#else // isn't MPI |
773 |
– |
|
774 |
– |
the_excludes[index*2] = exI + 1; |
775 |
– |
the_excludes[index*2 + 1] = exJ + 1; |
776 |
– |
// fortran index from 1 (hence the +1 in the indexing) |
948 |
|
|
949 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
950 |
|
#endif //is_mpi |
951 |
< |
|
952 |
< |
} |
951 |
> |
} |
952 |
> |
excludeOffset += info.nBonds; |
953 |
|
|
954 |
< |
|
955 |
< |
|
956 |
< |
|
957 |
< |
|
958 |
< |
|
959 |
< |
|
960 |
< |
|
789 |
< |
|
790 |
< |
|
791 |
< |
|
792 |
< |
|
793 |
< |
|
794 |
< |
|
795 |
< |
|
796 |
< |
void SimSetup::makeAtoms( void ){ |
797 |
< |
|
798 |
< |
int i, j, k, index; |
799 |
< |
double ux, uy, uz, uSqr, u; |
800 |
< |
AtomStamp* current_atom; |
801 |
< |
|
802 |
< |
DirectionalAtom* dAtom; |
803 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
804 |
< |
|
805 |
< |
lMolIndex = 0; |
806 |
< |
molIndex = 0; |
807 |
< |
index = 0; |
808 |
< |
for( i=0; i<n_components; i++ ){ |
809 |
< |
|
810 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
811 |
< |
|
812 |
< |
#ifdef IS_MPI |
813 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
814 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
815 |
< |
#endif // is_mpi |
816 |
< |
|
817 |
< |
molStart = index; |
818 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
819 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
954 |
> |
//make the bends |
955 |
> |
for(j=0; j<info.nBends; j++){ |
956 |
> |
|
957 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
958 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
959 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
960 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
961 |
|
|
962 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
822 |
< |
if( current_atom->haveOrientation() ){ |
962 |
> |
if( currentBend->haveExtras() ){ |
963 |
|
|
964 |
< |
dAtom = new DirectionalAtom(index); |
965 |
< |
simnfo->n_oriented++; |
826 |
< |
the_atoms[index] = dAtom; |
964 |
> |
extras = currentBend->getExtras(); |
965 |
> |
current_extra = extras; |
966 |
|
|
967 |
< |
ux = current_atom->getOrntX(); |
968 |
< |
uy = current_atom->getOrntY(); |
969 |
< |
uz = current_atom->getOrntZ(); |
970 |
< |
|
971 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
972 |
< |
|
973 |
< |
u = sqrt( uSqr ); |
974 |
< |
ux = ux / u; |
975 |
< |
uy = uy / u; |
976 |
< |
uz = uz / u; |
977 |
< |
|
978 |
< |
dAtom->setSUx( ux ); |
979 |
< |
dAtom->setSUy( uy ); |
980 |
< |
dAtom->setSUz( uz ); |
981 |
< |
} |
982 |
< |
else{ |
983 |
< |
the_atoms[index] = new GeneralAtom(index); |
984 |
< |
} |
985 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
986 |
< |
the_atoms[index]->setIndex( index ); |
987 |
< |
|
988 |
< |
// increment the index and repeat; |
989 |
< |
index++; |
990 |
< |
} |
991 |
< |
|
992 |
< |
molEnd = index -1; |
993 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
855 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
856 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
857 |
< |
the_molecules[lMolIndex].setStampID( i ); |
858 |
< |
lMolIndex++; |
859 |
< |
|
860 |
< |
#ifdef IS_MPI |
861 |
< |
} |
862 |
< |
#endif //is_mpi |
863 |
< |
|
864 |
< |
molIndex++; |
865 |
< |
} |
866 |
< |
} |
867 |
< |
|
868 |
< |
#ifdef IS_MPI |
869 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
870 |
< |
|
871 |
< |
delete[] globalIndex; |
872 |
< |
|
873 |
< |
mpiSim->mpiRefresh(); |
874 |
< |
#endif //IS_MPI |
967 |
> |
while( current_extra != NULL ){ |
968 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
969 |
> |
|
970 |
> |
switch( current_extra->getType() ){ |
971 |
> |
|
972 |
> |
case 0: |
973 |
> |
theBends[j].ghost = |
974 |
> |
current_extra->getInt() + atomOffset; |
975 |
> |
theBends[j].isGhost = 1; |
976 |
> |
break; |
977 |
> |
|
978 |
> |
case 1: |
979 |
> |
theBends[j].ghost = |
980 |
> |
(int)current_extra->getDouble() + atomOffset; |
981 |
> |
theBends[j].isGhost = 1; |
982 |
> |
break; |
983 |
> |
|
984 |
> |
default: |
985 |
> |
sprintf( painCave.errMsg, |
986 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
987 |
> |
"double nor an int.\n" |
988 |
> |
"-->Bend[%d] in %s\n", |
989 |
> |
j, comp_stamps[stampID]->getID() ); |
990 |
> |
painCave.isFatal = 1; |
991 |
> |
simError(); |
992 |
> |
} |
993 |
> |
} |
994 |
|
|
995 |
< |
the_ff->initializeAtoms(); |
996 |
< |
} |
997 |
< |
|
998 |
< |
void SimSetup::makeBonds( void ){ |
999 |
< |
|
1000 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1001 |
< |
bond_pair* the_bonds; |
1002 |
< |
BondStamp* current_bond; |
1003 |
< |
|
885 |
< |
the_bonds = new bond_pair[tot_bonds]; |
886 |
< |
index = 0; |
887 |
< |
offset = 0; |
888 |
< |
molIndex = 0; |
889 |
< |
|
890 |
< |
for( i=0; i<n_components; i++ ){ |
891 |
< |
|
892 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
893 |
< |
|
894 |
< |
#ifdef IS_MPI |
895 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
896 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
897 |
< |
#endif // is_mpi |
898 |
< |
|
899 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
900 |
< |
|
901 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
902 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
903 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
904 |
< |
|
905 |
< |
exI = the_bonds[index].a; |
906 |
< |
exJ = the_bonds[index].b; |
907 |
< |
|
908 |
< |
// exclude_I must always be the smaller of the pair |
909 |
< |
if( exI > exJ ){ |
910 |
< |
tempEx = exI; |
911 |
< |
exI = exJ; |
912 |
< |
exJ = tempEx; |
995 |
> |
else{ |
996 |
> |
|
997 |
> |
sprintf( painCave.errMsg, |
998 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
999 |
> |
" -->%s in Bend[%d] in %s\n", |
1000 |
> |
current_extra->getlhs(), |
1001 |
> |
j, comp_stamps[stampID]->getID() ); |
1002 |
> |
painCave.isFatal = 1; |
1003 |
> |
simError(); |
1004 |
|
} |
914 |
– |
|
1005 |
|
|
1006 |
< |
#ifdef IS_MPI |
917 |
< |
|
918 |
< |
the_excludes[index*2] = |
919 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
920 |
< |
the_excludes[index*2 + 1] = |
921 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
922 |
< |
|
923 |
< |
#else // isn't MPI |
924 |
< |
|
925 |
< |
the_excludes[index*2] = exI + 1; |
926 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
927 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
928 |
< |
#endif //is_mpi |
929 |
< |
|
930 |
< |
// increment the index and repeat; |
931 |
< |
index++; |
1006 |
> |
current_extra = current_extra->getNext(); |
1007 |
|
} |
1008 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1008 |
> |
} |
1009 |
> |
|
1010 |
> |
if( !theBends[j].isGhost ){ |
1011 |
> |
|
1012 |
> |
exI = theBends[j].a; |
1013 |
> |
exJ = theBends[j].c; |
1014 |
> |
} |
1015 |
> |
else{ |
1016 |
|
|
1017 |
< |
#ifdef IS_MPI |
1017 |
> |
exI = theBends[j].a; |
1018 |
> |
exJ = theBends[j].b; |
1019 |
|
} |
937 |
– |
#endif //is_mpi |
1020 |
|
|
1021 |
< |
molIndex++; |
1022 |
< |
} |
1023 |
< |
} |
1021 |
> |
// exclude_I must always be the smaller of the pair |
1022 |
> |
if( exI > exJ ){ |
1023 |
> |
tempEx = exI; |
1024 |
> |
exI = exJ; |
1025 |
> |
exJ = tempEx; |
1026 |
> |
} |
1027 |
> |
#ifdef IS_MPI |
1028 |
> |
tempEx = exI; |
1029 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1030 |
> |
tempEx = exJ; |
1031 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1032 |
> |
|
1033 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1034 |
> |
#else // isn't MPI |
1035 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1036 |
> |
#endif //is_mpi |
1037 |
> |
} |
1038 |
> |
excludeOffset += info.nBends; |
1039 |
|
|
1040 |
< |
the_ff->initializeBonds( the_bonds ); |
1041 |
< |
} |
1040 |
> |
for(j=0; j<info.nTorsions; j++){ |
1041 |
> |
|
1042 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1043 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1044 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1045 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1046 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1047 |
> |
|
1048 |
> |
exI = theTorsions[j].a; |
1049 |
> |
exJ = theTorsions[j].d; |
1050 |
|
|
1051 |
< |
void SimSetup::makeBends( void ){ |
1051 |
> |
// exclude_I must always be the smaller of the pair |
1052 |
> |
if( exI > exJ ){ |
1053 |
> |
tempEx = exI; |
1054 |
> |
exI = exJ; |
1055 |
> |
exJ = tempEx; |
1056 |
> |
} |
1057 |
> |
#ifdef IS_MPI |
1058 |
> |
tempEx = exI; |
1059 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1060 |
> |
tempEx = exJ; |
1061 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1062 |
> |
|
1063 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1064 |
> |
#else // isn't MPI |
1065 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1066 |
> |
#endif //is_mpi |
1067 |
> |
} |
1068 |
> |
excludeOffset += info.nTorsions; |
1069 |
|
|
1070 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1071 |
< |
bend_set* the_bends; |
950 |
< |
BendStamp* current_bend; |
951 |
< |
LinkedAssign* extras; |
952 |
< |
LinkedAssign* current_extra; |
953 |
< |
|
1070 |
> |
|
1071 |
> |
// send the arrays off to the forceField for init. |
1072 |
|
|
1073 |
< |
the_bends = new bend_set[tot_bends]; |
1074 |
< |
index = 0; |
1075 |
< |
offset = 0; |
1076 |
< |
molIndex = 0; |
959 |
< |
for( i=0; i<n_components; i++ ){ |
960 |
< |
|
961 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1073 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1074 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1075 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1076 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1077 |
|
|
963 |
– |
#ifdef IS_MPI |
964 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
965 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
966 |
– |
#endif // is_mpi |
1078 |
|
|
1079 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
969 |
< |
|
970 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
971 |
< |
the_bends[index].a = current_bend->getA() + offset; |
972 |
< |
the_bends[index].b = current_bend->getB() + offset; |
973 |
< |
the_bends[index].c = current_bend->getC() + offset; |
974 |
< |
|
975 |
< |
if( current_bend->haveExtras() ){ |
976 |
< |
|
977 |
< |
extras = current_bend->getExtras(); |
978 |
< |
current_extra = extras; |
979 |
< |
|
980 |
< |
while( current_extra != NULL ){ |
981 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
982 |
< |
|
983 |
< |
switch( current_extra->getType() ){ |
984 |
< |
|
985 |
< |
case 0: |
986 |
< |
the_bends[index].ghost = |
987 |
< |
current_extra->getInt() + offset; |
988 |
< |
the_bends[index].isGhost = 1; |
989 |
< |
break; |
990 |
< |
|
991 |
< |
case 1: |
992 |
< |
the_bends[index].ghost = |
993 |
< |
(int)current_extra->getDouble() + offset; |
994 |
< |
the_bends[index].isGhost = 1; |
995 |
< |
break; |
996 |
< |
|
997 |
< |
default: |
998 |
< |
sprintf( painCave.errMsg, |
999 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
1000 |
< |
"double nor an int.\n" |
1001 |
< |
"-->Bend[%d] in %s\n", |
1002 |
< |
k, comp_stamps[i]->getID() ); |
1003 |
< |
painCave.isFatal = 1; |
1004 |
< |
simError(); |
1005 |
< |
} |
1006 |
< |
} |
1007 |
< |
|
1008 |
< |
else{ |
1009 |
< |
|
1010 |
< |
sprintf( painCave.errMsg, |
1011 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
1012 |
< |
" -->%s in Bend[%d] in %s\n", |
1013 |
< |
current_extra->getlhs(), |
1014 |
< |
k, comp_stamps[i]->getID() ); |
1015 |
< |
painCave.isFatal = 1; |
1016 |
< |
simError(); |
1017 |
< |
} |
1018 |
< |
|
1019 |
< |
current_extra = current_extra->getNext(); |
1020 |
< |
} |
1021 |
< |
} |
1022 |
< |
|
1023 |
< |
if( !the_bends[index].isGhost ){ |
1024 |
< |
|
1025 |
< |
exI = the_bends[index].a; |
1026 |
< |
exJ = the_bends[index].c; |
1027 |
< |
} |
1028 |
< |
else{ |
1029 |
< |
|
1030 |
< |
exI = the_bends[index].a; |
1031 |
< |
exJ = the_bends[index].b; |
1032 |
< |
} |
1033 |
< |
|
1034 |
< |
// exclude_I must always be the smaller of the pair |
1035 |
< |
if( exI > exJ ){ |
1036 |
< |
tempEx = exI; |
1037 |
< |
exI = exJ; |
1038 |
< |
exJ = tempEx; |
1039 |
< |
} |
1079 |
> |
the_molecules[i].initialize( info ); |
1080 |
|
|
1081 |
|
|
1082 |
< |
#ifdef IS_MPI |
1083 |
< |
|
1084 |
< |
the_excludes[(index + tot_bonds)*2] = |
1085 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1046 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1047 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1048 |
< |
|
1049 |
< |
#else // isn't MPI |
1050 |
< |
|
1051 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
1052 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1053 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1054 |
< |
#endif //is_mpi |
1055 |
< |
|
1056 |
< |
|
1057 |
< |
// increment the index and repeat; |
1058 |
< |
index++; |
1059 |
< |
} |
1060 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1061 |
< |
|
1062 |
< |
#ifdef IS_MPI |
1063 |
< |
} |
1064 |
< |
#endif //is_mpi |
1065 |
< |
|
1066 |
< |
molIndex++; |
1067 |
< |
} |
1082 |
> |
atomOffset += info.nAtoms; |
1083 |
> |
delete[] theBonds; |
1084 |
> |
delete[] theBends; |
1085 |
> |
delete[] theTorsions; |
1086 |
|
} |
1087 |
|
|
1088 |
|
#ifdef IS_MPI |
1089 |
< |
sprintf( checkPointMsg, |
1072 |
< |
"Successfully created the bends list.\n" ); |
1089 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1090 |
|
MPIcheckPoint(); |
1091 |
|
#endif // is_mpi |
1075 |
– |
|
1092 |
|
|
1093 |
< |
the_ff->initializeBends( the_bends ); |
1094 |
< |
} |
1093 |
> |
// clean up the forcefield |
1094 |
> |
the_ff->calcRcut(); |
1095 |
> |
the_ff->cleanMe(); |
1096 |
|
|
1080 |
– |
void SimSetup::makeTorsions( void ){ |
1081 |
– |
|
1082 |
– |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1083 |
– |
torsion_set* the_torsions; |
1084 |
– |
TorsionStamp* current_torsion; |
1085 |
– |
|
1086 |
– |
the_torsions = new torsion_set[tot_torsions]; |
1087 |
– |
index = 0; |
1088 |
– |
offset = 0; |
1089 |
– |
molIndex = 0; |
1090 |
– |
for( i=0; i<n_components; i++ ){ |
1091 |
– |
|
1092 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
1093 |
– |
|
1094 |
– |
#ifdef IS_MPI |
1095 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
1096 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
1097 |
– |
#endif // is_mpi |
1098 |
– |
|
1099 |
– |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1100 |
– |
|
1101 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
1102 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
1103 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
1104 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
1105 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
1106 |
– |
|
1107 |
– |
exI = the_torsions[index].a; |
1108 |
– |
exJ = the_torsions[index].d; |
1109 |
– |
|
1110 |
– |
|
1111 |
– |
// exclude_I must always be the smaller of the pair |
1112 |
– |
if( exI > exJ ){ |
1113 |
– |
tempEx = exI; |
1114 |
– |
exI = exJ; |
1115 |
– |
exJ = tempEx; |
1116 |
– |
} |
1117 |
– |
|
1118 |
– |
|
1119 |
– |
#ifdef IS_MPI |
1120 |
– |
|
1121 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1122 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
1123 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1124 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
1125 |
– |
|
1126 |
– |
#else // isn't MPI |
1127 |
– |
|
1128 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1129 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1130 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
1131 |
– |
#endif //is_mpi |
1132 |
– |
|
1133 |
– |
|
1134 |
– |
// increment the index and repeat; |
1135 |
– |
index++; |
1136 |
– |
} |
1137 |
– |
offset += comp_stamps[i]->getNAtoms(); |
1138 |
– |
|
1139 |
– |
#ifdef IS_MPI |
1140 |
– |
} |
1141 |
– |
#endif //is_mpi |
1142 |
– |
|
1143 |
– |
molIndex++; |
1144 |
– |
} |
1145 |
– |
} |
1146 |
– |
|
1147 |
– |
the_ff->initializeTorsions( the_torsions ); |
1097 |
|
} |
1098 |
|
|
1099 |
|
void SimSetup::initFromBass( void ){ |