# | Line 12 | Line 12 | |
---|---|---|
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(); | |
# | Line 66 | Line 76 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 80 | Line 96 | void SimSetup::createSim( void ){ | |
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 | } | |
# | Line 105 | Line 208 | void SimSetup::createSim( void ){ | |
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]; | |
# | Line 230 | Line 331 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 255 | Line 356 | void SimSetup::createSim( void ){ | |
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(); | |
# | Line 268 | Line 371 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 304 | Line 411 | void SimSetup::createSim( void ){ | |
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 | + | #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 | ||
# | Line 326 | Line 472 | void SimSetup::createSim( void ){ | |
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 | ||
# | Line 383 | Line 529 | void SimSetup::createSim( void ){ | |
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 | ||
# | Line 443 | Line 576 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 463 | Line 596 | void SimSetup::createSim( void ){ | |
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 | ); | |
# | Line 634 | Line 767 | void SimSetup::createSim( void ){ | |
767 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
768 | ||
769 | ||
770 | < | // // make the longe range forces and the integrator |
771 | < | |
772 | < | // new AllLong( simnfo ); |
773 | < | |
774 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
770 | > | // make the integrator |
771 | > | |
772 | > | |
773 | > | NVT* myNVT = NULL; |
774 | > | switch( ensembleCase ){ |
775 | ||
776 | + | case NVE_ENS: |
777 | + | new NVE( simnfo, the_ff ); |
778 | + | break; |
779 | ||
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") ){ | |
# | Line 683 | Line 846 | void SimSetup::makeMolecules( void ){ | |
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++){ | |
# | Line 707 | Line 877 | void SimSetup::makeMolecules( void ){ | |
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]; | |
# | Line 717 | Line 887 | void SimSetup::makeMolecules( void ){ | |
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); | |
# | Line 758 | Line 928 | void SimSetup::makeMolecules( void ){ | |
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 ){ | |
# | Line 775 | Line 945 | void SimSetup::makeMolecules( void ){ | |
945 | ||
946 | the_excludes[j+excludeOffset]->setPair( exI, exJ ); | |
947 | #else // isn't MPI | |
948 | + | |
949 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
950 | #endif //is_mpi | |
951 | } | |
# | Line 790 | Line 961 | void SimSetup::makeMolecules( void ){ | |
961 | ||
962 | if( currentBend->haveExtras() ){ | |
963 | ||
964 | < | extras = current_bend->getExtras(); |
964 | > | extras = currentBend->getExtras(); |
965 | current_extra = extras; | |
966 | ||
967 | while( current_extra != NULL ){ | |
# | Line 812 | Line 983 | void SimSetup::makeMolecules( void ){ | |
983 | ||
984 | default: | |
985 | sprintf( painCave.errMsg, | |
986 | < | "SimSetup Error: ghostVectorSource was neiter a " |
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() ); | |
# | Line 906 | Line 1077 | void SimSetup::makeMolecules( void ){ | |
1077 | ||
1078 | ||
1079 | the_molecules[i].initialize( info ); | |
1080 | + | |
1081 | + | |
1082 | atomOffset += info.nAtoms; | |
1083 | + | delete[] theBonds; |
1084 | + | delete[] theBends; |
1085 | + | delete[] theTorsions; |
1086 | } | |
1087 | ||
1088 | + | #ifdef IS_MPI |
1089 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1090 | + | MPIcheckPoint(); |
1091 | + | #endif // is_mpi |
1092 | + | |
1093 | // clean up the forcefield | |
1094 | the_ff->calcRcut(); | |
1095 | the_ff->cleanMe(); | |
1096 | + | |
1097 | } | |
1098 | ||
1099 | void SimSetup::initFromBass( void ){ |
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