16 |
|
|
17 |
|
// some defines for ensemble and Forcefield cases |
18 |
|
|
19 |
< |
#define NVE_ENS 0 |
20 |
< |
#define NVT_ENS 1 |
21 |
< |
#define NPTi_ENS 2 |
22 |
< |
#define NPTf_ENS 3 |
23 |
< |
#define NPTim_ENS 4 |
24 |
< |
#define NPTfm_ENS 5 |
25 |
< |
#define NVEZCONS_ENS 6 |
26 |
< |
|
19 |
> |
#define NVE_ENS 0 |
20 |
> |
#define NVT_ENS 1 |
21 |
> |
#define NPTi_ENS 2 |
22 |
> |
#define NPTf_ENS 3 |
23 |
> |
#define NPTim_ENS 4 |
24 |
> |
#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 |
31 |
|
|
32 |
|
#define FF_DUFF 0 |
33 |
|
#define FF_LJ 1 |
627 |
|
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
628 |
|
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
629 |
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
630 |
+ |
|
631 |
|
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
632 |
+ |
else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
633 |
+ |
else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) |
634 |
+ |
ensembleCase = NPTiZCONS_ENS; |
635 |
+ |
else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; |
636 |
+ |
else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
637 |
+ |
else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_ENS; |
638 |
+ |
|
639 |
|
else{ |
640 |
|
sprintf( painCave.errMsg, |
641 |
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
1322 |
|
NPTim<RealIntegrator>* myNPTim = NULL; |
1323 |
|
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1324 |
|
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1325 |
+ |
ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1326 |
+ |
ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1327 |
+ |
ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1328 |
+ |
ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1329 |
+ |
ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1330 |
|
|
1331 |
|
cerr << "setting integrator" <<endl; |
1332 |
|
|
1493 |
|
break; |
1494 |
|
|
1495 |
|
case NVEZCONS_ENS: |
1479 |
– |
{ |
1496 |
|
|
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 |
– |
} |
1497 |
|
|
1498 |
< |
//Determine the name of ouput file and add it into SimInfo's property list |
1499 |
< |
//Be careful, do not use inFileName, since it is a pointer which |
1500 |
< |
//point to a string at master node, and slave nodes do not contain that string |
1501 |
< |
|
1502 |
< |
string zconsOutput(info->finalName); |
1503 |
< |
|
1504 |
< |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1505 |
< |
|
1506 |
< |
StringData* zconsFilename = new StringData(); |
1507 |
< |
zconsFilename->setID("zconsfilename"); |
1508 |
< |
zconsFilename->setData(zconsOutput); |
1498 |
> |
//setup index of z-constraint molecules, z-constraint sampel time |
1499 |
> |
//and z-constraint force output name. These parameter should be known |
1500 |
> |
//before constructing the z-constraint integrator |
1501 |
> |
setupZConstraint(); |
1502 |
> |
|
1503 |
> |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1504 |
> |
|
1505 |
> |
break; |
1506 |
> |
|
1507 |
> |
|
1508 |
> |
case NVTZCONS_ENS: |
1509 |
> |
|
1510 |
> |
setupZConstraint(); |
1511 |
> |
|
1512 |
> |
myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff ); |
1513 |
> |
myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1514 |
|
|
1515 |
< |
info->addProperty(zconsFilename); |
1515 |
> |
if (globals->haveTauThermostat()) |
1516 |
> |
myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1517 |
> |
|
1518 |
> |
else { |
1519 |
> |
sprintf( painCave.errMsg, |
1520 |
> |
"SimSetup error: If you use the NVT\n" |
1521 |
> |
" ensemble, you must set tauThermostat.\n"); |
1522 |
> |
painCave.isFatal = 1; |
1523 |
> |
simError(); |
1524 |
> |
} |
1525 |
> |
break; |
1526 |
> |
|
1527 |
> |
case NPTiZCONS_ENS: |
1528 |
> |
|
1529 |
> |
setupZConstraint(); |
1530 |
> |
|
1531 |
> |
myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff ); |
1532 |
> |
myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1533 |
> |
|
1534 |
> |
if (globals->haveTargetPressure()) |
1535 |
> |
myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1536 |
> |
else { |
1537 |
> |
sprintf( painCave.errMsg, |
1538 |
> |
"SimSetup error: If you use a constant pressure\n" |
1539 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1540 |
> |
painCave.isFatal = 1; |
1541 |
> |
simError(); |
1542 |
> |
} |
1543 |
> |
|
1544 |
> |
if( globals->haveTauThermostat() ) |
1545 |
> |
myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1546 |
> |
else{ |
1547 |
> |
sprintf( painCave.errMsg, |
1548 |
> |
"SimSetup error: If you use an NPT\n" |
1549 |
> |
" ensemble, you must set tauThermostat.\n"); |
1550 |
> |
painCave.isFatal = 1; |
1551 |
> |
simError(); |
1552 |
> |
} |
1553 |
> |
|
1554 |
> |
if( globals->haveTauBarostat() ) |
1555 |
> |
myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1556 |
> |
else{ |
1557 |
> |
sprintf( painCave.errMsg, |
1558 |
> |
"SimSetup error: If you use an NPT\n" |
1559 |
> |
" ensemble, you must set tauBarostat.\n"); |
1560 |
> |
painCave.isFatal = 1; |
1561 |
> |
simError(); |
1562 |
> |
} |
1563 |
> |
|
1564 |
> |
break; |
1565 |
> |
|
1566 |
> |
case NPTfZCONS_ENS: |
1567 |
> |
|
1568 |
> |
setupZConstraint(); |
1569 |
> |
|
1570 |
> |
myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff ); |
1571 |
> |
myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1572 |
> |
|
1573 |
> |
if (globals->haveTargetPressure()) |
1574 |
> |
myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1575 |
> |
else { |
1576 |
> |
sprintf( painCave.errMsg, |
1577 |
> |
"SimSetup error: If you use a constant pressure\n" |
1578 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1579 |
> |
painCave.isFatal = 1; |
1580 |
> |
simError(); |
1581 |
> |
} |
1582 |
> |
|
1583 |
> |
if( globals->haveTauThermostat() ) |
1584 |
> |
myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1585 |
> |
else{ |
1586 |
> |
sprintf( painCave.errMsg, |
1587 |
> |
"SimSetup error: If you use an NPT\n" |
1588 |
> |
" ensemble, you must set tauThermostat.\n"); |
1589 |
> |
painCave.isFatal = 1; |
1590 |
> |
simError(); |
1591 |
> |
} |
1592 |
> |
|
1593 |
> |
if( globals->haveTauBarostat() ) |
1594 |
> |
myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1595 |
> |
else{ |
1596 |
> |
sprintf( painCave.errMsg, |
1597 |
> |
"SimSetup error: If you use an NPT\n" |
1598 |
> |
" ensemble, you must set tauBarostat.\n"); |
1599 |
> |
painCave.isFatal = 1; |
1600 |
> |
simError(); |
1601 |
> |
} |
1602 |
> |
|
1603 |
> |
break; |
1604 |
|
|
1605 |
< |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1606 |
< |
|
1605 |
> |
case NPTimZCONS_ENS: |
1606 |
> |
|
1607 |
> |
setupZConstraint(); |
1608 |
> |
|
1609 |
> |
myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff ); |
1610 |
> |
myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1611 |
> |
|
1612 |
> |
if (globals->haveTargetPressure()) |
1613 |
> |
myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1614 |
> |
else { |
1615 |
> |
sprintf( painCave.errMsg, |
1616 |
> |
"SimSetup error: If you use a constant pressure\n" |
1617 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1618 |
> |
painCave.isFatal = 1; |
1619 |
> |
simError(); |
1620 |
> |
} |
1621 |
> |
|
1622 |
> |
if( globals->haveTauThermostat() ) |
1623 |
> |
myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1624 |
> |
else{ |
1625 |
> |
sprintf( painCave.errMsg, |
1626 |
> |
"SimSetup error: If you use an NPT\n" |
1627 |
> |
" ensemble, you must set tauThermostat.\n"); |
1628 |
> |
painCave.isFatal = 1; |
1629 |
> |
simError(); |
1630 |
> |
} |
1631 |
> |
|
1632 |
> |
if( globals->haveTauBarostat() ) |
1633 |
> |
myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1634 |
> |
else{ |
1635 |
> |
sprintf( painCave.errMsg, |
1636 |
> |
"SimSetup error: If you use an NPT\n" |
1637 |
> |
" ensemble, you must set tauBarostat.\n"); |
1638 |
> |
painCave.isFatal = 1; |
1639 |
> |
simError(); |
1640 |
> |
} |
1641 |
> |
|
1642 |
|
break; |
1643 |
+ |
|
1644 |
+ |
case NPTfmZCONS_ENS: |
1645 |
+ |
|
1646 |
+ |
setupZConstraint(); |
1647 |
+ |
|
1648 |
+ |
myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff ); |
1649 |
+ |
myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1650 |
+ |
|
1651 |
+ |
if (globals->haveTargetPressure()) |
1652 |
+ |
myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1653 |
+ |
else { |
1654 |
+ |
sprintf( painCave.errMsg, |
1655 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1656 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1657 |
+ |
painCave.isFatal = 1; |
1658 |
+ |
simError(); |
1659 |
|
} |
1660 |
|
|
1661 |
+ |
if( globals->haveTauThermostat() ) |
1662 |
+ |
myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1663 |
+ |
else{ |
1664 |
+ |
sprintf( painCave.errMsg, |
1665 |
+ |
"SimSetup error: If you use an NPT\n" |
1666 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1667 |
+ |
painCave.isFatal = 1; |
1668 |
+ |
simError(); |
1669 |
+ |
} |
1670 |
+ |
|
1671 |
+ |
if( globals->haveTauBarostat() ) |
1672 |
+ |
myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1673 |
+ |
else{ |
1674 |
+ |
sprintf( painCave.errMsg, |
1675 |
+ |
"SimSetup error: If you use an NPT\n" |
1676 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1677 |
+ |
painCave.isFatal = 1; |
1678 |
+ |
simError(); |
1679 |
+ |
} |
1680 |
+ |
break; |
1681 |
+ |
|
1682 |
+ |
|
1683 |
+ |
|
1684 |
|
default: |
1685 |
|
sprintf( painCave.errMsg, |
1686 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1716 |
|
#endif // is_mpi |
1717 |
|
|
1718 |
|
} |
1719 |
+ |
|
1720 |
+ |
void SimSetup::setupZConstraint() |
1721 |
+ |
{ |
1722 |
+ |
if(globals->haveZConsTime()){ |
1723 |
+ |
|
1724 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1725 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1726 |
+ |
zconsTimeProp->setID("zconstime"); |
1727 |
+ |
zconsTimeProp->setData(globals->getZConsTime()); |
1728 |
+ |
info->addProperty(zconsTimeProp); |
1729 |
+ |
} |
1730 |
+ |
else{ |
1731 |
+ |
sprintf( painCave.errMsg, |
1732 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1733 |
+ |
" , you must set sample time.\n"); |
1734 |
+ |
painCave.isFatal = 1; |
1735 |
+ |
simError(); |
1736 |
+ |
} |
1737 |
+ |
|
1738 |
+ |
if(globals->haveIndexOfAllZConsMols()){ |
1739 |
+ |
|
1740 |
+ |
//add index of z-constraint molecules into SimInfo's property list |
1741 |
+ |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1742 |
+ |
|
1743 |
+ |
//sort the index |
1744 |
+ |
sort(tempIndex.begin(), tempIndex.end()); |
1745 |
+ |
|
1746 |
+ |
IndexData* zconsIndex = new IndexData(); |
1747 |
+ |
zconsIndex->setID("zconsindex"); |
1748 |
+ |
zconsIndex->setIndexData(tempIndex); |
1749 |
+ |
info->addProperty(zconsIndex); |
1750 |
+ |
} |
1751 |
+ |
else{ |
1752 |
+ |
sprintf( painCave.errMsg, |
1753 |
+ |
"SimSetup error: If you use an ZConstraint\n" |
1754 |
+ |
" , you must set index of z-constraint molecules.\n"); |
1755 |
+ |
painCave.isFatal = 1; |
1756 |
+ |
simError(); |
1757 |
+ |
|
1758 |
+ |
} |
1759 |
+ |
|
1760 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1761 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1762 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1763 |
+ |
|
1764 |
+ |
string zconsOutput(info->finalName); |
1765 |
+ |
|
1766 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1767 |
+ |
|
1768 |
+ |
StringData* zconsFilename = new StringData(); |
1769 |
+ |
zconsFilename->setID("zconsfilename"); |
1770 |
+ |
zconsFilename->setData(zconsOutput); |
1771 |
+ |
|
1772 |
+ |
info->addProperty(zconsFilename); |
1773 |
+ |
|
1774 |
+ |
} |