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 |
+ |
#define FF_DUFF 0 |
23 |
+ |
#define FF_LJ 1 |
24 |
+ |
|
25 |
+ |
|
26 |
|
SimSetup::SimSetup(){ |
27 |
|
stamps = new MakeStamps(); |
28 |
|
globals = new Globals(); |
77 |
|
|
78 |
|
MakeStamps *the_stamps; |
79 |
|
Globals* the_globals; |
80 |
< |
int i, j; |
80 |
> |
int i, j, k, globalAtomIndex; |
81 |
> |
|
82 |
> |
int ensembleCase; |
83 |
> |
int ffCase; |
84 |
> |
|
85 |
> |
ensembleCase = -1; |
86 |
> |
ffCase = -1; |
87 |
|
|
88 |
|
// get the stamps and globals; |
89 |
|
the_stamps = stamps; |
97 |
|
// get the ones we know are there, yet still may need some work. |
98 |
|
n_components = the_globals->getNComponents(); |
99 |
|
strcpy( force_field, the_globals->getForceField() ); |
100 |
+ |
|
101 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
102 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
103 |
+ |
else{ |
104 |
+ |
sprintf( painCave.errMsg, |
105 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
106 |
+ |
force_field ); |
107 |
+ |
painCave.isFatal = 1; |
108 |
+ |
simError(); |
109 |
+ |
} |
110 |
+ |
|
111 |
+ |
// get the ensemble: |
112 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
113 |
+ |
|
114 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
115 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
116 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
117 |
+ |
ensembleCase = NPTi_ENS; |
118 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
119 |
+ |
else{ |
120 |
+ |
sprintf( painCave.errMsg, |
121 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
122 |
+ |
"reverting to NVE for this simulation.\n", |
123 |
+ |
ensemble ); |
124 |
+ |
painCave.isFatal = 0; |
125 |
+ |
simError(); |
126 |
+ |
strcpy( ensemble, "NVE" ); |
127 |
+ |
ensembleCase = NVE_ENS; |
128 |
+ |
} |
129 |
|
strcpy( simnfo->ensemble, ensemble ); |
130 |
|
|
131 |
+ |
|
132 |
+ |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
133 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
134 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
135 |
+ |
// if (the_globals->haveTargetPressure()) |
136 |
+ |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
137 |
+ |
// else { |
138 |
+ |
// sprintf( painCave.errMsg, |
139 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
140 |
+ |
// " ensemble, you must set targetPressure.\n" |
141 |
+ |
// " This was found in the BASS file.\n"); |
142 |
+ |
// painCave.isFatal = 1; |
143 |
+ |
// simError(); |
144 |
+ |
// } |
145 |
+ |
|
146 |
+ |
// if (the_globals->haveTauThermostat()) |
147 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
148 |
+ |
// else if (the_globals->haveQmass()) |
149 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
150 |
+ |
// else { |
151 |
+ |
// sprintf( painCave.errMsg, |
152 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
153 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
154 |
+ |
// " Neither of these was found in the BASS file.\n"); |
155 |
+ |
// painCave.isFatal = 1; |
156 |
+ |
// simError(); |
157 |
+ |
// } |
158 |
+ |
|
159 |
+ |
// if (the_globals->haveTauBarostat()) |
160 |
+ |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
161 |
+ |
// else { |
162 |
+ |
// sprintf( painCave.errMsg, |
163 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
164 |
+ |
// " ensemble, you must set tauBarostat.\n" |
165 |
+ |
// " This was found in the BASS file.\n"); |
166 |
+ |
// painCave.isFatal = 1; |
167 |
+ |
// simError(); |
168 |
+ |
// } |
169 |
+ |
|
170 |
+ |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
171 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
172 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
173 |
+ |
|
174 |
+ |
// if (the_globals->haveTauThermostat()) |
175 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
176 |
+ |
// else if (the_globals->haveQmass()) |
177 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
178 |
+ |
// else { |
179 |
+ |
// sprintf( painCave.errMsg, |
180 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
181 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
182 |
+ |
// " Neither of these was found in the BASS file.\n"); |
183 |
+ |
// painCave.isFatal = 1; |
184 |
+ |
// simError(); |
185 |
+ |
// } |
186 |
+ |
|
187 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
188 |
|
simnfo->usePBC = the_globals->getPBC(); |
189 |
|
|
190 |
+ |
int usesDipoles = 0; |
191 |
+ |
switch( ffCase ){ |
192 |
|
|
193 |
+ |
case FF_DUFF: |
194 |
+ |
the_ff = new DUFF(); |
195 |
+ |
usesDipoles = 1; |
196 |
+ |
break; |
197 |
|
|
198 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
199 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
200 |
< |
else{ |
198 |
> |
case FF_LJ: |
199 |
> |
the_ff = new LJFF(); |
200 |
> |
break; |
201 |
> |
|
202 |
> |
default: |
203 |
|
sprintf( painCave.errMsg, |
204 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
96 |
< |
force_field ); |
204 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
205 |
|
painCave.isFatal = 1; |
206 |
|
simError(); |
207 |
|
} |
210 |
|
strcpy( checkPointMsg, "ForceField creation successful" ); |
211 |
|
MPIcheckPoint(); |
212 |
|
#endif // is_mpi |
105 |
– |
|
106 |
– |
|
213 |
|
|
214 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
215 |
|
the_components = the_globals->getComponents(); |
334 |
|
simnfo->n_torsions = tot_torsions; |
335 |
|
simnfo->n_SRI = tot_SRI; |
336 |
|
simnfo->n_mol = tot_nmol; |
231 |
– |
|
337 |
|
|
338 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
339 |
+ |
|
340 |
|
#ifdef IS_MPI |
341 |
|
|
342 |
|
// divide the molecules among processors here. |
343 |
|
|
344 |
|
mpiSim = new mpiSimulation( simnfo ); |
345 |
|
|
239 |
– |
|
240 |
– |
|
346 |
|
globalIndex = mpiSim->divideLabor(); |
347 |
|
|
348 |
|
// set up the local variables |
359 |
|
local_bonds = 0; |
360 |
|
local_bends = 0; |
361 |
|
local_torsions = 0; |
362 |
+ |
globalAtomIndex = 0; |
363 |
+ |
|
364 |
+ |
|
365 |
|
for( i=0; i<n_components; i++ ){ |
366 |
|
|
367 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
368 |
|
|
369 |
< |
if( mol2proc[j] == worldRank ){ |
369 |
> |
if( mol2proc[allMol] == worldRank ){ |
370 |
|
|
371 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
372 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
374 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
375 |
|
localMol++; |
376 |
|
} |
377 |
< |
allMol++; |
377 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
378 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
379 |
> |
globalAtomIndex++; |
380 |
> |
} |
381 |
> |
|
382 |
> |
allMol++; |
383 |
|
} |
384 |
|
} |
385 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
386 |
|
|
274 |
– |
|
387 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
388 |
|
|
389 |
|
if( local_atoms != simnfo->n_atoms ){ |
427 |
|
if(mol2proc[i] == worldRank ){ |
428 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
429 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
430 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
431 |
|
molIndex++; |
432 |
|
} |
433 |
|
} |
435 |
|
#else // is_mpi |
436 |
|
|
437 |
|
molIndex = 0; |
438 |
+ |
globalAtomIndex = 0; |
439 |
|
for(i=0; i<n_components; i++){ |
440 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
441 |
|
the_molecules[molIndex].setStampID( i ); |
442 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
443 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
444 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
445 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
446 |
+ |
globalAtomIndex++; |
447 |
+ |
} |
448 |
|
molIndex++; |
449 |
|
} |
450 |
|
} |
482 |
|
|
483 |
|
// get some of the tricky things that may still be in the globals |
484 |
|
|
485 |
< |
|
485 |
> |
double boxVector[3]; |
486 |
|
if( the_globals->haveBox() ){ |
487 |
< |
simnfo->box_x = the_globals->getBox(); |
488 |
< |
simnfo->box_y = the_globals->getBox(); |
489 |
< |
simnfo->box_z = the_globals->getBox(); |
487 |
> |
boxVector[0] = the_globals->getBox(); |
488 |
> |
boxVector[1] = the_globals->getBox(); |
489 |
> |
boxVector[2] = the_globals->getBox(); |
490 |
> |
|
491 |
> |
simnfo->setBox( boxVector ); |
492 |
|
} |
493 |
|
else if( the_globals->haveDensity() ){ |
494 |
|
|
495 |
|
double vol; |
496 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
497 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
498 |
< |
simnfo->box_y = simnfo->box_x; |
499 |
< |
simnfo->box_z = simnfo->box_x; |
497 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
498 |
> |
boxVector[1] = boxVector[0]; |
499 |
> |
boxVector[2] = boxVector[0]; |
500 |
> |
|
501 |
> |
simnfo->setBox( boxVector ); |
502 |
|
} |
503 |
|
else{ |
504 |
|
if( !the_globals->haveBoxX() ){ |
507 |
|
painCave.isFatal = 1; |
508 |
|
simError(); |
509 |
|
} |
510 |
< |
simnfo->box_x = the_globals->getBoxX(); |
510 |
> |
boxVector[0] = the_globals->getBoxX(); |
511 |
|
|
512 |
|
if( !the_globals->haveBoxY() ){ |
513 |
|
sprintf( painCave.errMsg, |
515 |
|
painCave.isFatal = 1; |
516 |
|
simError(); |
517 |
|
} |
518 |
< |
simnfo->box_y = the_globals->getBoxY(); |
518 |
> |
boxVector[1] = the_globals->getBoxY(); |
519 |
|
|
520 |
|
if( !the_globals->haveBoxZ() ){ |
521 |
|
sprintf( painCave.errMsg, |
523 |
|
painCave.isFatal = 1; |
524 |
|
simError(); |
525 |
|
} |
526 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
526 |
> |
boxVector[2] = the_globals->getBoxZ(); |
527 |
> |
|
528 |
> |
simnfo->setBox( boxVector ); |
529 |
|
} |
530 |
|
|
531 |
|
#ifdef IS_MPI |
555 |
|
painCave.isFatal = 0; |
556 |
|
simError(); |
557 |
|
double smallest; |
558 |
< |
smallest = simnfo->box_x; |
559 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
560 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
558 |
> |
smallest = simnfo->boxLx; |
559 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
560 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
561 |
|
simnfo->ecr = 0.5 * smallest; |
562 |
|
} else { |
563 |
|
simnfo->ecr = the_globals->getECR(); |
585 |
|
} |
586 |
|
simnfo->dielectric = the_globals->getDielectric(); |
587 |
|
} else { |
588 |
< |
if (simnfo->n_dipoles) { |
588 |
> |
if (usesDipoles) { |
589 |
|
|
590 |
|
if( !the_globals->haveECR() ){ |
591 |
|
sprintf( painCave.errMsg, |
592 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
592 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
593 |
|
"box length for the electrostaticCutoffRadius.\n" |
594 |
|
"I hope you have a very fast processor!\n"); |
595 |
|
painCave.isFatal = 0; |
596 |
|
simError(); |
597 |
|
double smallest; |
598 |
< |
smallest = simnfo->box_x; |
599 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
600 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
598 |
> |
smallest = simnfo->boxLx; |
599 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
600 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
601 |
|
simnfo->ecr = 0.5 * smallest; |
602 |
|
} else { |
603 |
|
simnfo->ecr = the_globals->getECR(); |
605 |
|
|
606 |
|
if( !the_globals->haveEST() ){ |
607 |
|
sprintf( painCave.errMsg, |
608 |
< |
"SimSetup Warning: using default value of 5% of the" |
608 |
> |
"SimSetup Warning: using default value of 5%% of the " |
609 |
|
"electrostaticCutoffRadius for the " |
610 |
|
"electrostaticSkinThickness\n" |
611 |
|
); |
776 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
777 |
|
|
778 |
|
|
779 |
< |
// // make the longe range forces and the integrator |
779 |
> |
// make the integrator |
780 |
> |
|
781 |
> |
|
782 |
> |
NVT* myNVT = NULL; |
783 |
> |
switch( ensembleCase ){ |
784 |
|
|
785 |
< |
// new AllLong( simnfo ); |
785 |
> |
case NVE_ENS: |
786 |
> |
new NVE( simnfo, the_ff ); |
787 |
> |
break; |
788 |
|
|
789 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
790 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
789 |
> |
case NVT_ENS: |
790 |
> |
myNVT = new NVT( simnfo, the_ff ); |
791 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
792 |
|
|
793 |
+ |
if (the_globals->haveTauThermostat()) |
794 |
+ |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
795 |
+ |
// else if (the_globals->haveQmass()) |
796 |
+ |
// myNVT->setQmass(the_globals->getQmass()); |
797 |
+ |
else { |
798 |
+ |
sprintf( painCave.errMsg, |
799 |
+ |
"SimSetup error: If you use the NVT\n" |
800 |
+ |
" ensemble, you must set either tauThermostat or qMass.\n" |
801 |
+ |
" Neither of these was found in the BASS file.\n"); |
802 |
+ |
painCave.isFatal = 1; |
803 |
+ |
simError(); |
804 |
+ |
} |
805 |
+ |
break; |
806 |
+ |
|
807 |
+ |
default: |
808 |
+ |
sprintf( painCave.errMsg, |
809 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
810 |
+ |
painCave.isFatal = 1; |
811 |
+ |
simError(); |
812 |
+ |
} |
813 |
+ |
|
814 |
+ |
|
815 |
|
#ifdef IS_MPI |
816 |
|
mpiSim->mpiRefresh(); |
817 |
|
#endif |
1124 |
|
have_extra =1; |
1125 |
|
|
1126 |
|
n_cells = (int)temp3 - 1; |
1127 |
< |
cellx = simnfo->box_x / temp3; |
1128 |
< |
celly = simnfo->box_y / temp3; |
1129 |
< |
cellz = simnfo->box_z / temp3; |
1127 |
> |
cellx = simnfo->boxLx / temp3; |
1128 |
> |
celly = simnfo->boxLy / temp3; |
1129 |
> |
cellz = simnfo->boxLz / temp3; |
1130 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1131 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1132 |
|
n_per_extra = (int)ceil( temp1 ); |
1141 |
|
} |
1142 |
|
else{ |
1143 |
|
n_cells = (int)temp3; |
1144 |
< |
cellx = simnfo->box_x / temp3; |
1145 |
< |
celly = simnfo->box_y / temp3; |
1146 |
< |
cellz = simnfo->box_z / temp3; |
1144 |
> |
cellx = simnfo->boxLx / temp3; |
1145 |
> |
celly = simnfo->boxLy / temp3; |
1146 |
> |
cellz = simnfo->boxLz / temp3; |
1147 |
|
} |
1148 |
|
|
1149 |
|
current_mol = 0; |