5 |
|
#include <string> |
6 |
|
|
7 |
|
#include "SimSetup.hpp" |
8 |
+ |
#include "ReadWrite.hpp" |
9 |
|
#include "parse_me.h" |
10 |
|
#include "Integrator.hpp" |
11 |
|
#include "simError.h" |
23 |
|
#define NPTf_ENS 3 |
24 |
|
#define NPTim_ENS 4 |
25 |
|
#define NPTfm_ENS 5 |
25 |
– |
#define NVEZCONS_ENS 6 |
26 |
– |
#define NVTZCONS_ENS 7 |
27 |
– |
#define NPTiZCONS_ENS 8 |
28 |
– |
#define NPTfZCONS_ENS 9 |
29 |
– |
#define NPTimZCONS_ENS 10 |
30 |
– |
#define NPTfmZCONS_ENS 11 |
26 |
|
|
27 |
|
#define FF_DUFF 0 |
28 |
|
#define FF_LJ 1 |
97 |
|
int i, j, k, globalAtomIndex; |
98 |
|
|
99 |
|
// gather all of the information from the Bass file |
100 |
< |
|
100 |
> |
|
101 |
|
gatherInfo(); |
102 |
|
|
103 |
|
// creation of complex system objects |
105 |
|
sysObjectsCreation(); |
106 |
|
|
107 |
|
// check on the post processing info |
108 |
< |
|
108 |
> |
|
109 |
|
finalInfoCheck(); |
110 |
|
|
111 |
|
// initialize the system coordinates |
634 |
|
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
635 |
|
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
636 |
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
642 |
– |
|
643 |
– |
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
644 |
– |
else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
645 |
– |
else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS")) |
646 |
– |
ensembleCase = NPTiZCONS_ENS; |
647 |
– |
else if( !strcasecmp( ensemble, "NPTfZCONS")) ensembleCase = NPTfZCONS_ENS; |
648 |
– |
else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
649 |
– |
else if( !strcasecmp( ensemble, "NPTfmZCONS")) ensembleCase = NPTfmZCONS_ENS; |
650 |
– |
|
637 |
|
else{ |
638 |
|
sprintf( painCave.errMsg, |
639 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
889 |
|
void SimSetup::initSystemCoords( void ){ |
890 |
|
int i; |
891 |
|
|
892 |
< |
std::cerr << "Setting atom Coords\n"; |
892 |
> |
char* inName; |
893 |
|
|
894 |
+ |
|
895 |
|
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
896 |
|
|
897 |
|
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
902 |
|
#ifdef IS_MPI // is_mpi |
903 |
|
if( worldRank == 0 ){ |
904 |
|
#endif //is_mpi |
905 |
< |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
905 |
> |
inName = globals->getInitialConfig(); |
906 |
> |
double* tempDouble = new double[1000000]; |
907 |
> |
fileInit = new InitializeFromFile( inName ); |
908 |
|
#ifdef IS_MPI |
909 |
|
}else fileInit = new InitializeFromFile( NULL ); |
910 |
|
#endif |
1037 |
|
int i,k; |
1038 |
|
|
1039 |
|
// create the forceField |
1040 |
< |
|
1040 |
> |
|
1041 |
|
createFF(); |
1042 |
|
|
1043 |
|
// extract componentList |
1055 |
|
#endif //is_mpi |
1056 |
|
|
1057 |
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1058 |
< |
|
1058 |
> |
|
1059 |
|
makeSysArrays(); |
1060 |
|
|
1061 |
|
// make and initialize the molecules (all but atomic coordinates) |
1062 |
< |
|
1062 |
> |
|
1063 |
|
makeMolecules(); |
1064 |
|
|
1065 |
|
for(k=0; k<nInfo; k++){ |
1356 |
|
NPTf<RealIntegrator>* myNPTf = NULL; |
1357 |
|
NPTim<RealIntegrator>* myNPTim = NULL; |
1358 |
|
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1370 |
– |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1371 |
– |
ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1372 |
– |
ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1373 |
– |
ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1374 |
– |
ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1375 |
– |
ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1359 |
|
|
1360 |
|
for(k=0; k<nInfo; k++){ |
1361 |
|
|
1362 |
|
switch( ensembleCase ){ |
1363 |
|
|
1364 |
|
case NVE_ENS: |
1365 |
< |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1365 |
> |
if (globals->haveZconstraints()){ |
1366 |
> |
setupZConstraint(info[k]); |
1367 |
> |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1368 |
> |
} |
1369 |
> |
|
1370 |
> |
else |
1371 |
> |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1372 |
|
break; |
1373 |
|
|
1374 |
|
case NVT_ENS: |
1375 |
< |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1375 |
> |
if (globals->haveZconstraints()){ |
1376 |
> |
setupZConstraint(info[k]); |
1377 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1378 |
> |
} |
1379 |
> |
else |
1380 |
> |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1381 |
> |
|
1382 |
|
myNVT->setTargetTemp(globals->getTargetTemp()); |
1383 |
|
|
1384 |
|
if (globals->haveTauThermostat()) |
1394 |
|
break; |
1395 |
|
|
1396 |
|
case NPTi_ENS: |
1397 |
< |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1398 |
< |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1397 |
> |
if (globals->haveZconstraints()){ |
1398 |
> |
setupZConstraint(info[k]); |
1399 |
> |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1400 |
> |
} |
1401 |
> |
else |
1402 |
> |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1403 |
> |
|
1404 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1405 |
|
|
1406 |
|
if (globals->haveTargetPressure()) |
1407 |
|
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1435 |
|
break; |
1436 |
|
|
1437 |
|
case NPTf_ENS: |
1438 |
< |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1438 |
> |
if (globals->haveZconstraints()){ |
1439 |
> |
setupZConstraint(info[k]); |
1440 |
> |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1441 |
> |
} |
1442 |
> |
else |
1443 |
> |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1444 |
> |
|
1445 |
|
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1446 |
|
|
1447 |
|
if (globals->haveTargetPressure()) |
1476 |
|
break; |
1477 |
|
|
1478 |
|
case NPTim_ENS: |
1479 |
< |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1480 |
< |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1479 |
> |
if (globals->haveZconstraints()){ |
1480 |
> |
setupZConstraint(info[k]); |
1481 |
> |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1482 |
> |
} |
1483 |
> |
else |
1484 |
> |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1485 |
> |
|
1486 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1487 |
|
|
1488 |
|
if (globals->haveTargetPressure()) |
1489 |
|
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1517 |
|
break; |
1518 |
|
|
1519 |
|
case NPTfm_ENS: |
1520 |
< |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1521 |
< |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1520 |
> |
if (globals->haveZconstraints()){ |
1521 |
> |
setupZConstraint(info[k]); |
1522 |
> |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1523 |
> |
} |
1524 |
> |
else |
1525 |
> |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1526 |
> |
|
1527 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1528 |
|
|
1529 |
|
if (globals->haveTargetPressure()) |
1530 |
|
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1548 |
|
|
1549 |
|
if( globals->haveTauBarostat() ) |
1550 |
|
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1532 |
– |
else{ |
1533 |
– |
sprintf( painCave.errMsg, |
1534 |
– |
"SimSetup error: If you use an NPT\n" |
1535 |
– |
" ensemble, you must set tauBarostat.\n"); |
1536 |
– |
painCave.isFatal = 1; |
1537 |
– |
simError(); |
1538 |
– |
} |
1539 |
– |
break; |
1540 |
– |
|
1541 |
– |
case NVEZCONS_ENS: |
1542 |
– |
|
1543 |
– |
|
1544 |
– |
//setup index of z-constraint molecules, z-constraint sampel time |
1545 |
– |
//and z-constraint force output name. These parameter should be known |
1546 |
– |
//before constructing the z-constraint integrator |
1547 |
– |
setupZConstraint(); |
1548 |
– |
|
1549 |
– |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1550 |
– |
|
1551 |
– |
break; |
1552 |
– |
|
1553 |
– |
|
1554 |
– |
case NVTZCONS_ENS: |
1555 |
– |
|
1556 |
– |
setupZConstraint(); |
1557 |
– |
|
1558 |
– |
myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1559 |
– |
myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1560 |
– |
|
1561 |
– |
if (globals->haveTauThermostat()) |
1562 |
– |
myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1563 |
– |
|
1564 |
– |
else { |
1565 |
– |
sprintf( painCave.errMsg, |
1566 |
– |
"SimSetup error: If you use the NVT\n" |
1567 |
– |
" ensemble, you must set tauThermostat.\n"); |
1568 |
– |
painCave.isFatal = 1; |
1569 |
– |
simError(); |
1570 |
– |
} |
1571 |
– |
break; |
1572 |
– |
|
1573 |
– |
case NPTiZCONS_ENS: |
1574 |
– |
|
1575 |
– |
setupZConstraint(); |
1576 |
– |
|
1577 |
– |
myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1578 |
– |
myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1579 |
– |
|
1580 |
– |
if (globals->haveTargetPressure()) |
1581 |
– |
myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1582 |
– |
else { |
1583 |
– |
sprintf( painCave.errMsg, |
1584 |
– |
"SimSetup error: If you use a constant pressure\n" |
1585 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1586 |
– |
painCave.isFatal = 1; |
1587 |
– |
simError(); |
1588 |
– |
} |
1589 |
– |
|
1590 |
– |
if( globals->haveTauThermostat() ) |
1591 |
– |
myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1592 |
– |
else{ |
1593 |
– |
sprintf( painCave.errMsg, |
1594 |
– |
"SimSetup error: If you use an NPT\n" |
1595 |
– |
" ensemble, you must set tauThermostat.\n"); |
1596 |
– |
painCave.isFatal = 1; |
1597 |
– |
simError(); |
1598 |
– |
} |
1599 |
– |
|
1600 |
– |
if( globals->haveTauBarostat() ) |
1601 |
– |
myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1602 |
– |
else{ |
1603 |
– |
sprintf( painCave.errMsg, |
1604 |
– |
"SimSetup error: If you use an NPT\n" |
1605 |
– |
" ensemble, you must set tauBarostat.\n"); |
1606 |
– |
painCave.isFatal = 1; |
1607 |
– |
simError(); |
1608 |
– |
} |
1609 |
– |
|
1610 |
– |
break; |
1611 |
– |
|
1612 |
– |
case NPTfZCONS_ENS: |
1613 |
– |
|
1614 |
– |
setupZConstraint(); |
1615 |
– |
|
1616 |
– |
myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1617 |
– |
myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1618 |
– |
|
1619 |
– |
if (globals->haveTargetPressure()) |
1620 |
– |
myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1621 |
– |
else { |
1622 |
– |
sprintf( painCave.errMsg, |
1623 |
– |
"SimSetup error: If you use a constant pressure\n" |
1624 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1625 |
– |
painCave.isFatal = 1; |
1626 |
– |
simError(); |
1627 |
– |
} |
1628 |
– |
|
1629 |
– |
if( globals->haveTauThermostat() ) |
1630 |
– |
myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1551 |
|
else{ |
1552 |
|
sprintf( painCave.errMsg, |
1553 |
|
"SimSetup error: If you use an NPT\n" |
1634 |
– |
" ensemble, you must set tauThermostat.\n"); |
1635 |
– |
painCave.isFatal = 1; |
1636 |
– |
simError(); |
1637 |
– |
} |
1638 |
– |
|
1639 |
– |
if( globals->haveTauBarostat() ) |
1640 |
– |
myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1641 |
– |
else{ |
1642 |
– |
sprintf( painCave.errMsg, |
1643 |
– |
"SimSetup error: If you use an NPT\n" |
1554 |
|
" ensemble, you must set tauBarostat.\n"); |
1555 |
|
painCave.isFatal = 1; |
1556 |
|
simError(); |
1647 |
– |
} |
1648 |
– |
|
1649 |
– |
break; |
1650 |
– |
|
1651 |
– |
case NPTimZCONS_ENS: |
1652 |
– |
|
1653 |
– |
setupZConstraint(); |
1654 |
– |
|
1655 |
– |
myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1656 |
– |
myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1657 |
– |
|
1658 |
– |
if (globals->haveTargetPressure()) |
1659 |
– |
myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1660 |
– |
else { |
1661 |
– |
sprintf( painCave.errMsg, |
1662 |
– |
"SimSetup error: If you use a constant pressure\n" |
1663 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1664 |
– |
painCave.isFatal = 1; |
1665 |
– |
simError(); |
1557 |
|
} |
1667 |
– |
|
1668 |
– |
if( globals->haveTauThermostat() ) |
1669 |
– |
myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1670 |
– |
else{ |
1671 |
– |
sprintf( painCave.errMsg, |
1672 |
– |
"SimSetup error: If you use an NPT\n" |
1673 |
– |
" ensemble, you must set tauThermostat.\n"); |
1674 |
– |
painCave.isFatal = 1; |
1675 |
– |
simError(); |
1676 |
– |
} |
1677 |
– |
|
1678 |
– |
if( globals->haveTauBarostat() ) |
1679 |
– |
myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1680 |
– |
else{ |
1681 |
– |
sprintf( painCave.errMsg, |
1682 |
– |
"SimSetup error: If you use an NPT\n" |
1683 |
– |
" ensemble, you must set tauBarostat.\n"); |
1684 |
– |
painCave.isFatal = 1; |
1685 |
– |
simError(); |
1686 |
– |
} |
1687 |
– |
|
1558 |
|
break; |
1559 |
|
|
1690 |
– |
case NPTfmZCONS_ENS: |
1691 |
– |
|
1692 |
– |
setupZConstraint(); |
1693 |
– |
|
1694 |
– |
myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1695 |
– |
myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1696 |
– |
|
1697 |
– |
if (globals->haveTargetPressure()) |
1698 |
– |
myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1699 |
– |
else { |
1700 |
– |
sprintf( painCave.errMsg, |
1701 |
– |
"SimSetup error: If you use a constant pressure\n" |
1702 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1703 |
– |
painCave.isFatal = 1; |
1704 |
– |
simError(); |
1705 |
– |
} |
1706 |
– |
|
1707 |
– |
if( globals->haveTauThermostat() ) |
1708 |
– |
myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1709 |
– |
else{ |
1710 |
– |
sprintf( painCave.errMsg, |
1711 |
– |
"SimSetup error: If you use an NPT\n" |
1712 |
– |
" ensemble, you must set tauThermostat.\n"); |
1713 |
– |
painCave.isFatal = 1; |
1714 |
– |
simError(); |
1715 |
– |
} |
1716 |
– |
|
1717 |
– |
if( globals->haveTauBarostat() ) |
1718 |
– |
myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1719 |
– |
else{ |
1720 |
– |
sprintf( painCave.errMsg, |
1721 |
– |
"SimSetup error: If you use an NPT\n" |
1722 |
– |
" ensemble, you must set tauBarostat.\n"); |
1723 |
– |
painCave.isFatal = 1; |
1724 |
– |
simError(); |
1725 |
– |
} |
1726 |
– |
break; |
1727 |
– |
|
1728 |
– |
|
1729 |
– |
|
1560 |
|
default: |
1561 |
|
sprintf( painCave.errMsg, |
1562 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1593 |
|
|
1594 |
|
} |
1595 |
|
|
1596 |
< |
void SimSetup::setupZConstraint() |
1596 |
> |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1597 |
|
{ |
1598 |
< |
int k; |
1599 |
< |
|
1600 |
< |
for(k=0; k<nInfo; k++){ |
1601 |
< |
|
1772 |
< |
if(globals->haveZConsTime()){ |
1598 |
> |
int nZConstraints; |
1599 |
> |
ZconStamp** zconStamp; |
1600 |
> |
|
1601 |
> |
if(globals->haveZconstraintTime()){ |
1602 |
|
|
1603 |
|
//add sample time of z-constraint into SimInfo's property list |
1604 |
|
DoubleData* zconsTimeProp = new DoubleData(); |
1605 |
< |
zconsTimeProp->setID("zconstime"); |
1606 |
< |
zconsTimeProp->setData(globals->getZConsTime()); |
1607 |
< |
info[k].addProperty(zconsTimeProp); |
1605 |
> |
zconsTimeProp->setID(ZCONSTIME_ID); |
1606 |
> |
zconsTimeProp->setData(globals->getZconsTime()); |
1607 |
> |
theInfo.addProperty(zconsTimeProp); |
1608 |
|
} |
1609 |
|
else{ |
1610 |
|
sprintf( painCave.errMsg, |
1613 |
|
painCave.isFatal = 1; |
1614 |
|
simError(); |
1615 |
|
} |
1616 |
< |
|
1617 |
< |
if(globals->haveIndexOfAllZConsMols()){ |
1618 |
< |
|
1619 |
< |
//add index of z-constraint molecules into SimInfo's property list |
1620 |
< |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1621 |
< |
|
1622 |
< |
//sort the index |
1623 |
< |
sort(tempIndex.begin(), tempIndex.end()); |
1624 |
< |
|
1625 |
< |
IndexData* zconsIndex = new IndexData(); |
1626 |
< |
zconsIndex->setID("zconsindex"); |
1627 |
< |
zconsIndex->setIndexData(tempIndex); |
1628 |
< |
info[k].addProperty(zconsIndex); |
1616 |
> |
|
1617 |
> |
// |
1618 |
> |
nZConstraints = globals->getNzConstraints(); |
1619 |
> |
theInfo.nZconstraints = nZConstraints; |
1620 |
> |
|
1621 |
> |
zconStamp = globals->getZconStamp(); |
1622 |
> |
ZConsParaItem tempParaItem; |
1623 |
> |
|
1624 |
> |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1625 |
> |
zconsParaData->setID(ZCONSPARADATA_ID); |
1626 |
> |
|
1627 |
> |
for(int i = 0; i < nZConstraints; i++){ |
1628 |
> |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1629 |
> |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1630 |
> |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1631 |
> |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1632 |
> |
|
1633 |
> |
zconsParaData->addItem(tempParaItem); |
1634 |
|
} |
1635 |
< |
else{ |
1636 |
< |
sprintf( painCave.errMsg, |
1637 |
< |
"SimSetup error: If you use an ZConstraint\n" |
1638 |
< |
" , you must set index of z-constraint molecules.\n"); |
1639 |
< |
painCave.isFatal = 1; |
1640 |
< |
simError(); |
1641 |
< |
|
1635 |
> |
|
1636 |
> |
//sort the parameters by index of molecules |
1637 |
> |
zconsParaData->sortByIndex(); |
1638 |
> |
|
1639 |
> |
//push data into siminfo, therefore, we can retrieve later |
1640 |
> |
theInfo.addProperty(zconsParaData); |
1641 |
> |
|
1642 |
> |
//push zconsTol into siminfo, if user does not specify |
1643 |
> |
//value for zconsTol, a default value will be used |
1644 |
> |
DoubleData* zconsTol = new DoubleData(); |
1645 |
> |
zconsTol->setID(ZCONSTOL_ID); |
1646 |
> |
if(globals->haveZconsTol()){ |
1647 |
> |
zconsTol->setData(globals->getZconsTol()); |
1648 |
|
} |
1649 |
< |
|
1649 |
> |
else{ |
1650 |
> |
double defaultZConsTol = 1E-6; |
1651 |
> |
sprintf( painCave.errMsg, |
1652 |
> |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1653 |
> |
" , default value %f is used.\n", defaultZConsTol); |
1654 |
> |
painCave.isFatal = 0; |
1655 |
> |
simError(); |
1656 |
> |
|
1657 |
> |
zconsTol->setData(defaultZConsTol); |
1658 |
> |
} |
1659 |
> |
theInfo.addProperty(zconsTol); |
1660 |
> |
|
1661 |
|
//Determine the name of ouput file and add it into SimInfo's property list |
1662 |
|
//Be careful, do not use inFileName, since it is a pointer which |
1663 |
|
//point to a string at master node, and slave nodes do not contain that string |
1664 |
|
|
1665 |
< |
string zconsOutput(info[k].finalName); |
1665 |
> |
string zconsOutput(theInfo.finalName); |
1666 |
|
|
1667 |
|
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1668 |
|
|
1669 |
|
StringData* zconsFilename = new StringData(); |
1670 |
< |
zconsFilename->setID("zconsfilename"); |
1670 |
> |
zconsFilename->setID(ZCONSFILENAME_ID); |
1671 |
|
zconsFilename->setData(zconsOutput); |
1672 |
|
|
1673 |
< |
info[k].addProperty(zconsFilename); |
1823 |
< |
} |
1673 |
> |
theInfo.addProperty(zconsFilename); |
1674 |
|
} |