# | Line 1 | Line 1 | |
---|---|---|
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" | |
# | Line 14 | Line 16 | |
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 | < | |
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 | |
34 | #define FF_EAM 2 | |
35 | + | |
36 | + | using namespace std; |
37 | ||
38 | SimSetup::SimSetup(){ | |
39 | ||
# | Line 618 | Line 627 | void SimSetup::gatherInfo( void ){ | |
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, " | |
# | Line 1303 | Line 1321 | void SimSetup::makeIntegrator( void ){ | |
1321 | NPTf<RealIntegrator>* myNPTf = NULL; | |
1322 | NPTim<RealIntegrator>* myNPTim = NULL; | |
1323 | NPTfm<RealIntegrator>* myNPTfm = NULL; | |
1324 | < | |
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 | > | |
1333 | switch( ensembleCase ){ | |
1334 | ||
1335 | case NVE_ENS: | |
# | Line 1465 | Line 1491 | void SimSetup::makeIntegrator( void ){ | |
1491 | simError(); | |
1492 | } | |
1493 | break; | |
1494 | + | |
1495 | + | case NVEZCONS_ENS: |
1496 | ||
1497 | + | |
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 | + | 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 | + | 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"); | |
# | Line 1501 | Line 1716 | void SimSetup::initFortran( void ){ | |
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 | + | } |
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