1 |
+ |
#include <algorithm> |
2 |
|
#include <cstdlib> |
3 |
|
#include <iostream> |
4 |
|
#include <cmath> |
5 |
+ |
#include <string> |
6 |
|
|
7 |
|
#include "SimSetup.hpp" |
8 |
|
#include "parse_me.h" |
22 |
|
#define NPTf_ENS 3 |
23 |
|
#define NPTim_ENS 4 |
24 |
|
#define NPTfm_ENS 5 |
25 |
+ |
#define NVEZCONS_ENS 6 |
26 |
|
|
27 |
|
|
28 |
|
#define FF_DUFF 0 |
29 |
|
#define FF_LJ 1 |
30 |
+ |
#define FF_EAM 2 |
31 |
|
|
32 |
+ |
using namespace std; |
33 |
|
|
34 |
|
SimSetup::SimSetup(){ |
35 |
+ |
|
36 |
+ |
isInfoArray = 0; |
37 |
+ |
nInfo = 1; |
38 |
+ |
|
39 |
|
stamps = new MakeStamps(); |
40 |
|
globals = new Globals(); |
41 |
|
|
42 |
+ |
|
43 |
|
#ifdef IS_MPI |
44 |
|
strcpy( checkPointMsg, "SimSetup creation successful" ); |
45 |
|
MPIcheckPoint(); |
51 |
|
delete globals; |
52 |
|
} |
53 |
|
|
54 |
+ |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
55 |
+ |
info = the_info; |
56 |
+ |
nInfo = theNinfo; |
57 |
+ |
isInfoArray = 1; |
58 |
+ |
} |
59 |
+ |
|
60 |
+ |
|
61 |
|
void SimSetup::parseFile( char* fileName ){ |
62 |
|
|
63 |
|
#ifdef IS_MPI |
415 |
|
have_extra =1; |
416 |
|
|
417 |
|
n_cells = (int)temp3 - 1; |
418 |
< |
cellx = info->boxLx / temp3; |
419 |
< |
celly = info->boxLy / temp3; |
420 |
< |
cellz = info->boxLz / temp3; |
418 |
> |
cellx = info->boxL[0] / temp3; |
419 |
> |
celly = info->boxL[1] / temp3; |
420 |
> |
cellz = info->boxL[2] / temp3; |
421 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
422 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
423 |
|
n_per_extra = (int)ceil( temp1 ); |
432 |
|
} |
433 |
|
else{ |
434 |
|
n_cells = (int)temp3; |
435 |
< |
cellx = info->boxLx / temp3; |
436 |
< |
celly = info->boxLy / temp3; |
437 |
< |
cellz = info->boxLz / temp3; |
435 |
> |
cellx = info->boxL[0] / temp3; |
436 |
> |
celly = info->boxL[1] / temp3; |
437 |
> |
cellz = info->boxL[2] / temp3; |
438 |
|
} |
439 |
|
|
440 |
|
current_mol = 0; |
603 |
|
|
604 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
605 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
606 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
607 |
|
else{ |
608 |
|
sprintf( painCave.errMsg, |
609 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
623 |
|
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
624 |
|
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
625 |
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
626 |
+ |
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
627 |
|
else{ |
628 |
|
sprintf( painCave.errMsg, |
629 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
781 |
|
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
782 |
|
#endif //is_mpi |
783 |
|
|
784 |
+ |
double theEcr, theEst; |
785 |
|
|
786 |
|
if (globals->getUseRF() ) { |
787 |
|
info->useReactionField = 1; |
794 |
|
painCave.isFatal = 0; |
795 |
|
simError(); |
796 |
|
double smallest; |
797 |
< |
smallest = info->boxLx; |
798 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
799 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
800 |
< |
info->ecr = 0.5 * smallest; |
797 |
> |
smallest = info->boxL[0]; |
798 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
799 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
800 |
> |
theEcr = 0.5 * smallest; |
801 |
|
} else { |
802 |
< |
info->ecr = globals->getECR(); |
802 |
> |
theEcr = globals->getECR(); |
803 |
|
} |
804 |
|
|
805 |
|
if( !globals->haveEST() ){ |
809 |
|
); |
810 |
|
painCave.isFatal = 0; |
811 |
|
simError(); |
812 |
< |
info->est = 0.05 * info->ecr; |
812 |
> |
theEst = 0.05 * theEcr; |
813 |
|
} else { |
814 |
< |
info->est = globals->getEST(); |
814 |
> |
theEst= globals->getEST(); |
815 |
|
} |
816 |
+ |
|
817 |
+ |
info->setEcr( theEcr, theEst ); |
818 |
|
|
819 |
|
if(!globals->haveDielectric() ){ |
820 |
|
sprintf( painCave.errMsg, |
830 |
|
if (usesDipoles) { |
831 |
|
|
832 |
|
if( !globals->haveECR() ){ |
833 |
< |
sprintf( painCave.errMsg, |
834 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
835 |
< |
"box length for the electrostaticCutoffRadius.\n" |
836 |
< |
"I hope you have a very fast processor!\n"); |
837 |
< |
painCave.isFatal = 0; |
838 |
< |
simError(); |
839 |
< |
double smallest; |
840 |
< |
smallest = info->boxLx; |
841 |
< |
if (info->boxLy <= smallest) smallest = info->boxLy; |
842 |
< |
if (info->boxLz <= smallest) smallest = info->boxLz; |
843 |
< |
info->ecr = 0.5 * smallest; |
833 |
> |
sprintf( painCave.errMsg, |
834 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
835 |
> |
"box length for the electrostaticCutoffRadius.\n" |
836 |
> |
"I hope you have a very fast processor!\n"); |
837 |
> |
painCave.isFatal = 0; |
838 |
> |
simError(); |
839 |
> |
double smallest; |
840 |
> |
smallest = info->boxL[0]; |
841 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
842 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
843 |
> |
theEcr = 0.5 * smallest; |
844 |
|
} else { |
845 |
< |
info->ecr = globals->getECR(); |
845 |
> |
theEcr = globals->getECR(); |
846 |
|
} |
847 |
|
|
848 |
|
if( !globals->haveEST() ){ |
849 |
< |
sprintf( painCave.errMsg, |
850 |
< |
"SimSetup Warning: using default value of 5%% of the " |
851 |
< |
"electrostaticCutoffRadius for the " |
852 |
< |
"electrostaticSkinThickness\n" |
853 |
< |
); |
854 |
< |
painCave.isFatal = 0; |
855 |
< |
simError(); |
856 |
< |
info->est = 0.05 * info->ecr; |
849 |
> |
sprintf( painCave.errMsg, |
850 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
851 |
> |
"electrostaticCutoffRadius for the " |
852 |
> |
"electrostaticSkinThickness\n" |
853 |
> |
); |
854 |
> |
painCave.isFatal = 0; |
855 |
> |
simError(); |
856 |
> |
theEst = 0.05 * theEcr; |
857 |
|
} else { |
858 |
< |
info->est = globals->getEST(); |
858 |
> |
theEst= globals->getEST(); |
859 |
|
} |
860 |
+ |
|
861 |
+ |
info->setEcr( theEcr, theEst ); |
862 |
|
} |
863 |
|
} |
864 |
|
|
881 |
|
#ifdef IS_MPI |
882 |
|
}else fileInit = new InitializeFromFile( NULL ); |
883 |
|
#endif |
884 |
< |
fileInit->read_xyz( info ); // default velocities on |
884 |
> |
fileInit->readInit( info ); // default velocities on |
885 |
|
|
886 |
|
delete fileInit; |
887 |
|
} |
1051 |
|
the_ff = new LJFF(); |
1052 |
|
break; |
1053 |
|
|
1054 |
+ |
case FF_EAM: |
1055 |
+ |
the_ff = new EAM_FF(); |
1056 |
+ |
break; |
1057 |
+ |
|
1058 |
|
default: |
1059 |
|
sprintf( painCave.errMsg, |
1060 |
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1304 |
|
|
1305 |
|
void SimSetup::makeIntegrator( void ){ |
1306 |
|
|
1307 |
< |
NVT* myNVT = NULL; |
1308 |
< |
NPTi* myNPTi = NULL; |
1309 |
< |
NPTf* myNPTf = NULL; |
1310 |
< |
NPTim* myNPTim = NULL; |
1311 |
< |
NPTfm* myNPTfm = NULL; |
1312 |
< |
|
1307 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1308 |
> |
NPTi<RealIntegrator>* myNPTi = NULL; |
1309 |
> |
NPTf<RealIntegrator>* myNPTf = NULL; |
1310 |
> |
NPTim<RealIntegrator>* myNPTim = NULL; |
1311 |
> |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1312 |
> |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1313 |
> |
|
1314 |
> |
cerr << "setting integrator" <<endl; |
1315 |
> |
|
1316 |
|
switch( ensembleCase ){ |
1317 |
|
|
1318 |
|
case NVE_ENS: |
1319 |
< |
new NVE( info, the_ff ); |
1319 |
> |
new NVE<RealIntegrator>( info, the_ff ); |
1320 |
|
break; |
1321 |
|
|
1322 |
|
case NVT_ENS: |
1323 |
< |
myNVT = new NVT( info, the_ff ); |
1323 |
> |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1324 |
|
myNVT->setTargetTemp(globals->getTargetTemp()); |
1325 |
|
|
1326 |
|
if (globals->haveTauThermostat()) |
1336 |
|
break; |
1337 |
|
|
1338 |
|
case NPTi_ENS: |
1339 |
< |
myNPTi = new NPTi( info, the_ff ); |
1339 |
> |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1340 |
|
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1341 |
|
|
1342 |
|
if (globals->haveTargetPressure()) |
1371 |
|
break; |
1372 |
|
|
1373 |
|
case NPTf_ENS: |
1374 |
< |
myNPTf = new NPTf( info, the_ff ); |
1374 |
> |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1375 |
|
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1376 |
|
|
1377 |
|
if (globals->haveTargetPressure()) |
1406 |
|
break; |
1407 |
|
|
1408 |
|
case NPTim_ENS: |
1409 |
< |
myNPTim = new NPTim( info, the_ff ); |
1409 |
> |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1410 |
|
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1411 |
|
|
1412 |
|
if (globals->haveTargetPressure()) |
1441 |
|
break; |
1442 |
|
|
1443 |
|
case NPTfm_ENS: |
1444 |
< |
myNPTfm = new NPTfm( info, the_ff ); |
1444 |
> |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1445 |
|
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 |
|
|
1447 |
|
if (globals->haveTargetPressure()) |
1474 |
|
simError(); |
1475 |
|
} |
1476 |
|
break; |
1477 |
+ |
|
1478 |
+ |
case NVEZCONS_ENS: |
1479 |
+ |
{ |
1480 |
|
|
1481 |
+ |
if(globals->haveZConsTime()){ |
1482 |
+ |
|
1483 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1484 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1485 |
+ |
zconsTimeProp->setID("zconstime"); |
1486 |
+ |
zconsTimeProp->setData(globals->getZConsTime()); |
1487 |
+ |
info->addProperty(zconsTimeProp); |
1488 |
+ |
} |
1489 |
+ |
else{ |
1490 |
+ |
sprintf( painCave.errMsg, |
1491 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1492 |
+ |
" , you must set sample time.\n"); |
1493 |
+ |
painCave.isFatal = 1; |
1494 |
+ |
simError(); |
1495 |
+ |
} |
1496 |
+ |
|
1497 |
+ |
if(globals->haveIndexOfAllZConsMols()){ |
1498 |
+ |
|
1499 |
+ |
//add index of z-constraint molecules into SimInfo's property list |
1500 |
+ |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1501 |
+ |
sort(tempIndex.begin(), tempIndex.end()); |
1502 |
+ |
|
1503 |
+ |
IndexData* zconsIndex = new IndexData(); |
1504 |
+ |
zconsIndex->setID("zconsindex"); |
1505 |
+ |
zconsIndex->setIndexData(tempIndex); |
1506 |
+ |
info->addProperty(zconsIndex); |
1507 |
+ |
} |
1508 |
+ |
else{ |
1509 |
+ |
sprintf( painCave.errMsg, |
1510 |
+ |
"SimSetup error: If you use an ZConstraint\n" |
1511 |
+ |
" , you must set index of z-constraint molecules.\n"); |
1512 |
+ |
painCave.isFatal = 1; |
1513 |
+ |
simError(); |
1514 |
+ |
|
1515 |
+ |
} |
1516 |
+ |
|
1517 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1518 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1519 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1520 |
+ |
|
1521 |
+ |
string zconsOutput(info->finalName); |
1522 |
+ |
|
1523 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1524 |
+ |
|
1525 |
+ |
StringData* zconsFilename = new StringData(); |
1526 |
+ |
zconsFilename->setID("zconsfilename"); |
1527 |
+ |
zconsFilename->setData(zconsOutput); |
1528 |
+ |
|
1529 |
+ |
info->addProperty(zconsFilename); |
1530 |
+ |
|
1531 |
+ |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1532 |
+ |
|
1533 |
+ |
break; |
1534 |
+ |
} |
1535 |
+ |
|
1536 |
|
default: |
1537 |
|
sprintf( painCave.errMsg, |
1538 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |