24 |
|
|
25 |
|
#define FF_DUFF 0 |
26 |
|
#define FF_LJ 1 |
27 |
+ |
#define FF_EAM 2 |
28 |
|
|
28 |
– |
|
29 |
|
SimSetup::SimSetup(){ |
30 |
+ |
|
31 |
+ |
isInfoArray = 0; |
32 |
+ |
nInfo = 1; |
33 |
+ |
|
34 |
|
stamps = new MakeStamps(); |
35 |
|
globals = new Globals(); |
36 |
|
|
37 |
+ |
|
38 |
|
#ifdef IS_MPI |
39 |
|
strcpy( checkPointMsg, "SimSetup creation successful" ); |
40 |
|
MPIcheckPoint(); |
45 |
|
delete stamps; |
46 |
|
delete globals; |
47 |
|
} |
48 |
+ |
|
49 |
+ |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
50 |
+ |
info = the_info; |
51 |
+ |
nInfo = theNinfo; |
52 |
+ |
isInfoArray = 1; |
53 |
+ |
} |
54 |
|
|
55 |
+ |
|
56 |
|
void SimSetup::parseFile( char* fileName ){ |
57 |
|
|
58 |
|
#ifdef IS_MPI |
410 |
|
have_extra =1; |
411 |
|
|
412 |
|
n_cells = (int)temp3 - 1; |
413 |
< |
cellx = info->boxLx / temp3; |
414 |
< |
celly = info->boxLy / temp3; |
415 |
< |
cellz = info->boxLz / temp3; |
413 |
> |
cellx = info->boxL[0] / temp3; |
414 |
> |
celly = info->boxL[1] / temp3; |
415 |
> |
cellz = info->boxL[2] / temp3; |
416 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
417 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
418 |
|
n_per_extra = (int)ceil( temp1 ); |
427 |
|
} |
428 |
|
else{ |
429 |
|
n_cells = (int)temp3; |
430 |
< |
cellx = info->boxLx / temp3; |
431 |
< |
celly = info->boxLy / temp3; |
432 |
< |
cellz = info->boxLz / temp3; |
430 |
> |
cellx = info->boxL[0] / temp3; |
431 |
> |
celly = info->boxL[1] / temp3; |
432 |
> |
cellz = info->boxL[2] / temp3; |
433 |
|
} |
434 |
|
|
435 |
|
current_mol = 0; |
598 |
|
|
599 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
600 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
601 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
602 |
|
else{ |
603 |
|
sprintf( painCave.errMsg, |
604 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
775 |
|
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
776 |
|
#endif //is_mpi |
777 |
|
|
778 |
+ |
double theEcr, theEst; |
779 |
|
|
780 |
|
if (globals->getUseRF() ) { |
781 |
|
info->useReactionField = 1; |
788 |
|
painCave.isFatal = 0; |
789 |
|
simError(); |
790 |
|
double smallest; |
791 |
< |
smallest = info->boxLx; |
792 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
793 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
794 |
< |
info->ecr = 0.5 * smallest; |
791 |
> |
smallest = info->boxL[0]; |
792 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
793 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
794 |
> |
theEcr = 0.5 * smallest; |
795 |
|
} else { |
796 |
< |
info->ecr = globals->getECR(); |
796 |
> |
theEcr = globals->getECR(); |
797 |
|
} |
798 |
|
|
799 |
|
if( !globals->haveEST() ){ |
803 |
|
); |
804 |
|
painCave.isFatal = 0; |
805 |
|
simError(); |
806 |
< |
info->est = 0.05 * info->ecr; |
806 |
> |
theEst = 0.05 * theEcr; |
807 |
|
} else { |
808 |
< |
info->est = globals->getEST(); |
808 |
> |
theEst= globals->getEST(); |
809 |
|
} |
810 |
+ |
|
811 |
+ |
info->setEcr( theEcr, theEst ); |
812 |
|
|
813 |
|
if(!globals->haveDielectric() ){ |
814 |
|
sprintf( painCave.errMsg, |
824 |
|
if (usesDipoles) { |
825 |
|
|
826 |
|
if( !globals->haveECR() ){ |
827 |
< |
sprintf( painCave.errMsg, |
828 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
829 |
< |
"box length for the electrostaticCutoffRadius.\n" |
830 |
< |
"I hope you have a very fast processor!\n"); |
831 |
< |
painCave.isFatal = 0; |
832 |
< |
simError(); |
833 |
< |
double smallest; |
834 |
< |
smallest = info->boxLx; |
835 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
836 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
837 |
< |
info->ecr = 0.5 * smallest; |
827 |
> |
sprintf( painCave.errMsg, |
828 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
829 |
> |
"box length for the electrostaticCutoffRadius.\n" |
830 |
> |
"I hope you have a very fast processor!\n"); |
831 |
> |
painCave.isFatal = 0; |
832 |
> |
simError(); |
833 |
> |
double smallest; |
834 |
> |
smallest = info->boxL[0]; |
835 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
836 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
837 |
> |
theEcr = 0.5 * smallest; |
838 |
|
} else { |
839 |
< |
info->ecr = globals->getECR(); |
839 |
> |
theEcr = globals->getECR(); |
840 |
|
} |
841 |
|
|
842 |
|
if( !globals->haveEST() ){ |
843 |
< |
sprintf( painCave.errMsg, |
844 |
< |
"SimSetup Warning: using default value of 5%% of the " |
845 |
< |
"electrostaticCutoffRadius for the " |
846 |
< |
"electrostaticSkinThickness\n" |
847 |
< |
); |
848 |
< |
painCave.isFatal = 0; |
849 |
< |
simError(); |
850 |
< |
info->est = 0.05 * info->ecr; |
843 |
> |
sprintf( painCave.errMsg, |
844 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
845 |
> |
"electrostaticCutoffRadius for the " |
846 |
> |
"electrostaticSkinThickness\n" |
847 |
> |
); |
848 |
> |
painCave.isFatal = 0; |
849 |
> |
simError(); |
850 |
> |
theEst = 0.05 * theEcr; |
851 |
|
} else { |
852 |
< |
info->est = globals->getEST(); |
852 |
> |
theEst= globals->getEST(); |
853 |
|
} |
854 |
+ |
|
855 |
+ |
info->setEcr( theEcr, theEst ); |
856 |
|
} |
857 |
|
} |
858 |
|
|
875 |
|
#ifdef IS_MPI |
876 |
|
}else fileInit = new InitializeFromFile( NULL ); |
877 |
|
#endif |
878 |
< |
fileInit->read_xyz( info ); // default velocities on |
878 |
> |
fileInit->readInit( info ); // default velocities on |
879 |
|
|
880 |
|
delete fileInit; |
881 |
|
} |
1043 |
|
|
1044 |
|
case FF_LJ: |
1045 |
|
the_ff = new LJFF(); |
1046 |
+ |
break; |
1047 |
+ |
|
1048 |
+ |
case FF_EAM: |
1049 |
+ |
the_ff = new EAM_FF(); |
1050 |
|
break; |
1051 |
|
|
1052 |
|
default: |
1298 |
|
|
1299 |
|
void SimSetup::makeIntegrator( void ){ |
1300 |
|
|
1301 |
< |
NVT* myNVT = NULL; |
1302 |
< |
NPTi* myNPTi = NULL; |
1303 |
< |
NPTf* myNPTf = NULL; |
1304 |
< |
NPTim* myNPTim = NULL; |
1305 |
< |
NPTfm* myNPTfm = NULL; |
1301 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1302 |
> |
NPTi<RealIntegrator>* myNPTi = NULL; |
1303 |
> |
NPTf<RealIntegrator>* myNPTf = NULL; |
1304 |
> |
NPTim<RealIntegrator>* myNPTim = NULL; |
1305 |
> |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1306 |
|
|
1307 |
|
switch( ensembleCase ){ |
1308 |
|
|
1309 |
|
case NVE_ENS: |
1310 |
< |
new NVE( info, the_ff ); |
1310 |
> |
new NVE<RealIntegrator>( info, the_ff ); |
1311 |
|
break; |
1312 |
|
|
1313 |
|
case NVT_ENS: |
1314 |
< |
myNVT = new NVT( info, the_ff ); |
1314 |
> |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1315 |
|
myNVT->setTargetTemp(globals->getTargetTemp()); |
1316 |
|
|
1317 |
|
if (globals->haveTauThermostat()) |
1327 |
|
break; |
1328 |
|
|
1329 |
|
case NPTi_ENS: |
1330 |
< |
myNPTi = new NPTi( info, the_ff ); |
1330 |
> |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1331 |
|
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1332 |
|
|
1333 |
|
if (globals->haveTargetPressure()) |
1362 |
|
break; |
1363 |
|
|
1364 |
|
case NPTf_ENS: |
1365 |
< |
myNPTf = new NPTf( info, the_ff ); |
1365 |
> |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1366 |
|
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1367 |
|
|
1368 |
|
if (globals->haveTargetPressure()) |
1397 |
|
break; |
1398 |
|
|
1399 |
|
case NPTim_ENS: |
1400 |
< |
myNPTim = new NPTim( info, the_ff ); |
1400 |
> |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1401 |
|
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1402 |
|
|
1403 |
|
if (globals->haveTargetPressure()) |
1432 |
|
break; |
1433 |
|
|
1434 |
|
case NPTfm_ENS: |
1435 |
< |
myNPTfm = new NPTfm( info, the_ff ); |
1435 |
> |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1436 |
|
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1437 |
|
|
1438 |
|
if (globals->haveTargetPressure()) |