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 |
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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 |
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// get the stamps and globals; |
88 |
|
the_stamps = stamps; |
96 |
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// get the ones we know are there, yet still may need some work. |
97 |
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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 |
< |
|
191 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
192 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
193 |
< |
else{ |
190 |
> |
case FF_DUFF: |
191 |
> |
the_ff = new DUFF(); |
192 |
> |
usesDipoles = 1; |
193 |
> |
break; |
194 |
> |
|
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", |
96 |
< |
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 |
|
|
106 |
– |
|
107 |
– |
|
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; |
231 |
– |
|
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 |
|
|
239 |
– |
|
240 |
– |
|
343 |
|
globalIndex = mpiSim->divideLabor(); |
344 |
|
|
345 |
|
// set up the local variables |
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( mol2proc[j] == worldRank ){ |
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 |
|
|
274 |
– |
|
384 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
|
|
386 |
|
if( local_atoms != simnfo->n_atoms ){ |
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 |
|
} |
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 |
|
} |
452 |
|
|
453 |
|
if( simnfo->n_SRI ){ |
454 |
|
|
337 |
– |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 |
– |
|
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 |
|
|
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_Ex" ) ) new Symplectic( simnfo, the_ff ); |
781 |
< |
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 |
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 ){ |
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 |
|
} |
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() ); |
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 ){ |