| 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" ); |
| 50 |
|
delete stamps; |
| 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 |
|
|
| 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, " |
| 1309 |
|
NPTf<RealIntegrator>* myNPTf = NULL; |
| 1310 |
|
NPTim<RealIntegrator>* myNPTim = NULL; |
| 1311 |
|
NPTfm<RealIntegrator>* myNPTfm = NULL; |
| 1312 |
< |
|
| 1312 |
> |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
| 1313 |
> |
|
| 1314 |
> |
cerr << "setting integrator" <<endl; |
| 1315 |
> |
|
| 1316 |
|
switch( ensembleCase ){ |
| 1317 |
|
|
| 1318 |
|
case NVE_ENS: |
| 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"); |
