# | Line 1358 | Line 1358 | void SimSetup::makeIntegrator( void ){ | |
---|---|---|
1358 | switch( ensembleCase ){ | |
1359 | ||
1360 | case NVE_ENS: | |
1361 | < | if (haveZConstraint){ |
1362 | < | setupZConstraint(); |
1361 | > | if (globals->haveZconstraints()){ |
1362 | > | setupZConstraint(info[k]); |
1363 | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); | |
1364 | } | |
1365 | ||
# | Line 1368 | Line 1368 | void SimSetup::makeIntegrator( void ){ | |
1368 | break; | |
1369 | ||
1370 | case NVT_ENS: | |
1371 | < | if (haveZConstraint){ |
1372 | < | setupZConstraint(); |
1371 | > | if (globals->haveZconstraints()){ |
1372 | > | setupZConstraint(info[k]); |
1373 | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); | |
1374 | } | |
1375 | else | |
# | Line 1390 | Line 1390 | void SimSetup::makeIntegrator( void ){ | |
1390 | break; | |
1391 | ||
1392 | case NPTi_ENS: | |
1393 | < | if (haveZConstraint){ |
1394 | < | setupZConstraint(); |
1393 | > | if (globals->haveZconstraints()){ |
1394 | > | setupZConstraint(info[k]); |
1395 | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); | |
1396 | } | |
1397 | else | |
# | Line 1431 | Line 1431 | void SimSetup::makeIntegrator( void ){ | |
1431 | break; | |
1432 | ||
1433 | case NPTf_ENS: | |
1434 | < | if (haveZConstraint){ |
1435 | < | setupZConstraint(); |
1434 | > | if (globals->haveZconstraints()){ |
1435 | > | setupZConstraint(info[k]); |
1436 | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); | |
1437 | } | |
1438 | else | |
# | Line 1472 | Line 1472 | void SimSetup::makeIntegrator( void ){ | |
1472 | break; | |
1473 | ||
1474 | case NPTim_ENS: | |
1475 | < | if (haveZConstraint){ |
1476 | < | setupZConstraint(); |
1475 | > | if (globals->haveZconstraints()){ |
1476 | > | setupZConstraint(info[k]); |
1477 | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); | |
1478 | } | |
1479 | else | |
# | Line 1513 | Line 1513 | void SimSetup::makeIntegrator( void ){ | |
1513 | break; | |
1514 | ||
1515 | case NPTfm_ENS: | |
1516 | < | if (haveZConstraint){ |
1517 | < | setupZConstraint(); |
1516 | > | if (globals->haveZconstraints()){ |
1517 | > | setupZConstraint(info[k]); |
1518 | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); | |
1519 | } | |
1520 | else | |
# | Line 1589 | Line 1589 | void SimSetup::initFortran( void ){ | |
1589 | ||
1590 | } | |
1591 | ||
1592 | < | void SimSetup::setupZConstraint() |
1592 | > | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1593 | { | |
1594 | < | int k; |
1595 | < | |
1596 | < | for(k=0; k<nInfo; k++){ |
1597 | < | |
1598 | < | if(globals->haveZConsTime()){ |
1594 | > | int nZConstraints; |
1595 | > | ZconStamp** zconStamp; |
1596 | > | |
1597 | > | if(globals->haveZconstraintTime()){ |
1598 | ||
1599 | //add sample time of z-constraint into SimInfo's property list | |
1600 | DoubleData* zconsTimeProp = new DoubleData(); | |
1601 | < | zconsTimeProp->setID("zconstime"); |
1602 | < | zconsTimeProp->setData(globals->getZConsTime()); |
1603 | < | info[k].addProperty(zconsTimeProp); |
1601 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1602 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1603 | > | theInfo.addProperty(zconsTimeProp); |
1604 | } | |
1605 | else{ | |
1606 | sprintf( painCave.errMsg, | |
# | Line 1610 | Line 1609 | void SimSetup::setupZConstraint() | |
1609 | painCave.isFatal = 1; | |
1610 | simError(); | |
1611 | } | |
1612 | < | |
1613 | < | if(globals->haveIndexOfAllZConsMols()){ |
1614 | < | |
1615 | < | //add index of z-constraint molecules into SimInfo's property list |
1616 | < | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1617 | < | |
1618 | < | //sort the index |
1619 | < | sort(tempIndex.begin(), tempIndex.end()); |
1620 | < | |
1621 | < | IndexData* zconsIndex = new IndexData(); |
1622 | < | zconsIndex->setID("zconsindex"); |
1623 | < | zconsIndex->setIndexData(tempIndex); |
1624 | < | info[k].addProperty(zconsIndex); |
1625 | < | } |
1626 | < | else{ |
1627 | < | sprintf( painCave.errMsg, |
1629 | < | "SimSetup error: If you use an ZConstraint\n" |
1630 | < | " , you must set index of z-constraint molecules.\n"); |
1631 | < | painCave.isFatal = 1; |
1632 | < | simError(); |
1633 | < | |
1612 | > | |
1613 | > | // |
1614 | > | nZConstraints = globals->getNzConstraints(); |
1615 | > | zconStamp = globals->getZconStamp(); |
1616 | > | ZConsParaItem tempParaItem; |
1617 | > | |
1618 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1619 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1620 | > | |
1621 | > | for(int i = 0; i < nZConstraints; i++){ |
1622 | > | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1623 | > | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1624 | > | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1625 | > | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1626 | > | |
1627 | > | zconsParaData->addItem(tempParaItem); |
1628 | } | |
1629 | < | |
1629 | > | |
1630 | > | //sort the parameters by index of molecules |
1631 | > | zconsParaData->sortByIndex(); |
1632 | > | |
1633 | > | //push data into siminfo, therefore, we can retrieve later |
1634 | > | theInfo.addProperty(zconsParaData); |
1635 | > | |
1636 | > | //push zconsTol into siminfo, if user does not specify |
1637 | > | //value for zconsTol, a default value will be used |
1638 | > | DoubleData* zconsTol = new DoubleData(); |
1639 | > | zconsTol->setID(ZCONSTOL_ID); |
1640 | > | if(globals->haveZconsTol()){ |
1641 | > | zconsTol->setData(globals->getZconsTol()); |
1642 | > | } |
1643 | > | else{ |
1644 | > | double defaultZConsTol = 1E-6; |
1645 | > | sprintf( painCave.errMsg, |
1646 | > | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1647 | > | " , default value %f is used.\n", defaultZConsTol); |
1648 | > | painCave.isFatal = 0; |
1649 | > | simError(); |
1650 | > | |
1651 | > | zconsTol->setData(defaultZConsTol); |
1652 | > | } |
1653 | > | theInfo.addProperty(zconsTol); |
1654 | > | |
1655 | //Determine the name of ouput file and add it into SimInfo's property list | |
1656 | //Be careful, do not use inFileName, since it is a pointer which | |
1657 | //point to a string at master node, and slave nodes do not contain that string | |
1658 | ||
1659 | < | string zconsOutput(info[k].finalName); |
1659 | > | string zconsOutput(theInfo.finalName); |
1660 | ||
1661 | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; | |
1662 | ||
1663 | StringData* zconsFilename = new StringData(); | |
1664 | < | zconsFilename->setID("zconsfilename"); |
1664 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1665 | zconsFilename->setData(zconsOutput); | |
1666 | ||
1667 | < | info[k].addProperty(zconsFilename); |
1649 | < | } |
1667 | > | theInfo.addProperty(zconsFilename); |
1668 | } |
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