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 |
< |
ExtendedSystem* the_extendedsystem; |
80 |
< |
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; |
97 |
|
n_components = the_globals->getNComponents(); |
98 |
|
strcpy( force_field, the_globals->getForceField() ); |
99 |
|
|
100 |
< |
// get the ensemble and set up an extended system if we need it: |
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() ); |
87 |
– |
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
– |
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
– |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 |
– |
if (the_globals->haveTargetPressure()) |
91 |
– |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 |
– |
else { |
93 |
– |
sprintf( painCave.errMsg, |
94 |
– |
"SimSetup error: If you use the constant pressure\n" |
95 |
– |
" ensemble, you must set targetPressure.\n" |
96 |
– |
" This was found in the BASS file.\n"); |
97 |
– |
painCave.isFatal = 1; |
98 |
– |
simError(); |
99 |
– |
} |
112 |
|
|
113 |
< |
if (the_globals->haveTauThermostat()) |
114 |
< |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
115 |
< |
else if (the_globals->haveQmass()) |
116 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
105 |
< |
else { |
106 |
< |
sprintf( painCave.errMsg, |
107 |
< |
"SimSetup error: If you use one of the constant temperature\n" |
108 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
109 |
< |
" Neither of these was found in the BASS file.\n"); |
110 |
< |
painCave.isFatal = 1; |
111 |
< |
simError(); |
112 |
< |
} |
113 |
< |
|
114 |
< |
if (the_globals->haveTauBarostat()) |
115 |
< |
the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 |
< |
else { |
117 |
< |
sprintf( painCave.errMsg, |
118 |
< |
"SimSetup error: If you use the constant pressure\n" |
119 |
< |
" ensemble, you must set tauBarostat.\n" |
120 |
< |
" This was found in the BASS file.\n"); |
121 |
< |
painCave.isFatal = 1; |
122 |
< |
simError(); |
123 |
< |
} |
124 |
< |
|
125 |
< |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
126 |
< |
the_extendedsystem = new ExtendedSystem( simnfo ); |
127 |
< |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
128 |
< |
|
129 |
< |
if (the_globals->haveTauThermostat()) |
130 |
< |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 |
< |
else if (the_globals->haveQmass()) |
132 |
< |
the_extendedsystem->setQmass(the_globals->getQmass()); |
133 |
< |
else { |
134 |
< |
sprintf( painCave.errMsg, |
135 |
< |
"SimSetup error: If you use one of the constant temperature\n" |
136 |
< |
" ensembles, you must set either tauThermostat or qMass.\n" |
137 |
< |
" Neither of these was found in the BASS file.\n"); |
138 |
< |
painCave.isFatal = 1; |
139 |
< |
simError(); |
140 |
< |
} |
141 |
< |
|
142 |
< |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
143 |
< |
} else { |
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", |
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 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
189 |
< |
the_ff = new TraPPE_ExFF(); |
188 |
> |
switch( ffCase ){ |
189 |
> |
|
190 |
> |
case FF_DUFF: |
191 |
> |
the_ff = new DUFF(); |
192 |
|
usesDipoles = 1; |
193 |
< |
} |
194 |
< |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
195 |
< |
else{ |
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", |
166 |
< |
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 |
|
|
176 |
– |
|
177 |
– |
|
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; |
301 |
– |
|
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 |
|
|
309 |
– |
|
310 |
– |
|
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 |
|
|
344 |
– |
|
384 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
|
|
386 |
|
if( local_atoms != simnfo->n_atoms ){ |
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 |
|
} |
479 |
|
|
480 |
|
// get some of the tricky things that may still be in the globals |
481 |
|
|
482 |
< |
|
482 |
> |
double boxVector[3]; |
483 |
|
if( the_globals->haveBox() ){ |
484 |
< |
simnfo->box_x = the_globals->getBox(); |
485 |
< |
simnfo->box_y = the_globals->getBox(); |
486 |
< |
simnfo->box_z = the_globals->getBox(); |
484 |
> |
boxVector[0] = the_globals->getBox(); |
485 |
> |
boxVector[1] = the_globals->getBox(); |
486 |
> |
boxVector[2] = the_globals->getBox(); |
487 |
> |
|
488 |
> |
simnfo->setBox( boxVector ); |
489 |
|
} |
490 |
|
else if( the_globals->haveDensity() ){ |
491 |
|
|
492 |
|
double vol; |
493 |
|
vol = (double)tot_nmol / the_globals->getDensity(); |
494 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
495 |
< |
simnfo->box_y = simnfo->box_x; |
496 |
< |
simnfo->box_z = simnfo->box_x; |
494 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
495 |
> |
boxVector[1] = boxVector[0]; |
496 |
> |
boxVector[2] = boxVector[0]; |
497 |
> |
|
498 |
> |
simnfo->setBox( boxVector ); |
499 |
|
} |
500 |
|
else{ |
501 |
|
if( !the_globals->haveBoxX() ){ |
504 |
|
painCave.isFatal = 1; |
505 |
|
simError(); |
506 |
|
} |
507 |
< |
simnfo->box_x = the_globals->getBoxX(); |
507 |
> |
boxVector[0] = the_globals->getBoxX(); |
508 |
|
|
509 |
|
if( !the_globals->haveBoxY() ){ |
510 |
|
sprintf( painCave.errMsg, |
512 |
|
painCave.isFatal = 1; |
513 |
|
simError(); |
514 |
|
} |
515 |
< |
simnfo->box_y = the_globals->getBoxY(); |
515 |
> |
boxVector[1] = the_globals->getBoxY(); |
516 |
|
|
517 |
|
if( !the_globals->haveBoxZ() ){ |
518 |
|
sprintf( painCave.errMsg, |
520 |
|
painCave.isFatal = 1; |
521 |
|
simError(); |
522 |
|
} |
523 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
523 |
> |
boxVector[2] = the_globals->getBoxZ(); |
524 |
> |
|
525 |
> |
simnfo->setBox( boxVector ); |
526 |
|
} |
527 |
|
|
528 |
|
#ifdef IS_MPI |
552 |
|
painCave.isFatal = 0; |
553 |
|
simError(); |
554 |
|
double smallest; |
555 |
< |
smallest = simnfo->box_x; |
556 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
557 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
555 |
> |
smallest = simnfo->boxLx; |
556 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
557 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
558 |
|
simnfo->ecr = 0.5 * smallest; |
559 |
|
} else { |
560 |
|
simnfo->ecr = the_globals->getECR(); |
592 |
|
painCave.isFatal = 0; |
593 |
|
simError(); |
594 |
|
double smallest; |
595 |
< |
smallest = simnfo->box_x; |
596 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
597 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
595 |
> |
smallest = simnfo->boxLx; |
596 |
> |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
597 |
> |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
598 |
|
simnfo->ecr = 0.5 * smallest; |
599 |
|
} else { |
600 |
|
simnfo->ecr = the_globals->getECR(); |
773 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
774 |
|
|
775 |
|
|
776 |
< |
// // make the longe range forces and the integrator |
776 |
> |
// make the integrator |
777 |
> |
|
778 |
> |
|
779 |
> |
NVT* myNVT = NULL; |
780 |
> |
switch( ensembleCase ){ |
781 |
|
|
782 |
< |
// new AllLong( simnfo ); |
782 |
> |
case NVE_ENS: |
783 |
> |
new NVE( simnfo, the_ff ); |
784 |
> |
break; |
785 |
|
|
786 |
+ |
case NVT_ENS: |
787 |
+ |
myNVT = new NVT( simnfo, the_ff ); |
788 |
+ |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
789 |
|
|
790 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
791 |
< |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
792 |
< |
std::cerr << "called new Symplecic\n"; |
793 |
< |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
794 |
< |
} |
795 |
< |
else if( !strcmp( force_field, "LJ" ) ){ |
796 |
< |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
797 |
< |
std::cerr << "called new Verlet\n"; |
798 |
< |
fprintf( stderr, "called new Verlet. stderr\n" ); |
799 |
< |
} |
800 |
< |
else { |
801 |
< |
std::cerr << "I'm a bug.\n"; |
802 |
< |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
790 |
> |
if (the_globals->haveTauThermostat()) |
791 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
792 |
> |
// else if (the_globals->haveQmass()) |
793 |
> |
// myNVT->setQmass(the_globals->getQmass()); |
794 |
> |
else { |
795 |
> |
sprintf( painCave.errMsg, |
796 |
> |
"SimSetup error: If you use the NVT\n" |
797 |
> |
" ensemble, you must set either tauThermostat or qMass.\n" |
798 |
> |
" Neither of these was found in the BASS file.\n"); |
799 |
> |
painCave.isFatal = 1; |
800 |
> |
simError(); |
801 |
> |
} |
802 |
> |
break; |
803 |
> |
|
804 |
> |
default: |
805 |
> |
sprintf( painCave.errMsg, |
806 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
807 |
> |
painCave.isFatal = 1; |
808 |
> |
simError(); |
809 |
|
} |
810 |
+ |
|
811 |
+ |
|
812 |
|
#ifdef IS_MPI |
813 |
|
mpiSim->mpiRefresh(); |
814 |
|
#endif |
1121 |
|
have_extra =1; |
1122 |
|
|
1123 |
|
n_cells = (int)temp3 - 1; |
1124 |
< |
cellx = simnfo->box_x / temp3; |
1125 |
< |
celly = simnfo->box_y / temp3; |
1126 |
< |
cellz = simnfo->box_z / temp3; |
1124 |
> |
cellx = simnfo->boxLx / temp3; |
1125 |
> |
celly = simnfo->boxLy / temp3; |
1126 |
> |
cellz = simnfo->boxLz / temp3; |
1127 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1128 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1129 |
|
n_per_extra = (int)ceil( temp1 ); |
1138 |
|
} |
1139 |
|
else{ |
1140 |
|
n_cells = (int)temp3; |
1141 |
< |
cellx = simnfo->box_x / temp3; |
1142 |
< |
celly = simnfo->box_y / temp3; |
1143 |
< |
cellz = simnfo->box_z / temp3; |
1141 |
> |
cellx = simnfo->boxLx / temp3; |
1142 |
> |
celly = simnfo->boxLy / temp3; |
1143 |
> |
cellz = simnfo->boxLz / temp3; |
1144 |
|
} |
1145 |
|
|
1146 |
|
current_mol = 0; |