# | Line 5 | Line 5 | |
---|---|---|
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" | |
# | Line 96 | Line 97 | void SimSetup::createSim(void){ | |
97 | int i, j, k, globalAtomIndex; | |
98 | ||
99 | // gather all of the information from the Bass file | |
100 | < | |
100 | > | |
101 | > | std::cerr << "gathering info\n"; |
102 | > | |
103 | gatherInfo(); | |
104 | ||
105 | // creation of complex system objects | |
106 | ||
107 | + | std::cerr << "creating system objects\n"; |
108 | + | |
109 | sysObjectsCreation(); | |
110 | ||
111 | // check on the post processing info | |
112 | ||
113 | + | std::cerr << "performing final info check.\n"; |
114 | + | |
115 | finalInfoCheck(); | |
116 | ||
117 | // initialize the system coordinates | |
118 | + | |
119 | + | std::cerr << "about to init coords\n"; |
120 | ||
121 | if( !isInfoArray ) initSystemCoords(); | |
122 | ||
# | Line 888 | Line 897 | void SimSetup::initSystemCoords( void ){ | |
897 | void SimSetup::initSystemCoords( void ){ | |
898 | int i; | |
899 | ||
900 | + | char* inName; |
901 | + | |
902 | std::cerr << "Setting atom Coords\n"; | |
903 | ||
904 | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); | |
# | Line 900 | Line 911 | void SimSetup::initSystemCoords( void ){ | |
911 | #ifdef IS_MPI // is_mpi | |
912 | if( worldRank == 0 ){ | |
913 | #endif //is_mpi | |
914 | < | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
914 | > | inName = globals->getInitialConfig(); |
915 | > | fileInit = new InitializeFromFile( inName ); |
916 | #ifdef IS_MPI | |
917 | }else fileInit = new InitializeFromFile( NULL ); | |
918 | #endif | |
# | Line 1033 | Line 1045 | void SimSetup::sysObjectsCreation( void ){ | |
1045 | int i,k; | |
1046 | ||
1047 | // create the forceField | |
1048 | < | |
1048 | > | |
1049 | createFF(); | |
1050 | ||
1051 | // extract componentList | |
# | Line 1051 | Line 1063 | void SimSetup::sysObjectsCreation( void ){ | |
1063 | #endif //is_mpi | |
1064 | ||
1065 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1066 | < | |
1066 | > | |
1067 | makeSysArrays(); | |
1068 | ||
1069 | // make and initialize the molecules (all but atomic coordinates) | |
1070 | < | |
1070 | > | |
1071 | makeMolecules(); | |
1072 | ||
1073 | for(k=0; k<nInfo; k++){ | |
# | Line 1358 | Line 1370 | void SimSetup::makeIntegrator( void ){ | |
1370 | switch( ensembleCase ){ | |
1371 | ||
1372 | case NVE_ENS: | |
1373 | < | if (haveZConstraint){ |
1374 | < | setupZConstraint(); |
1373 | > | if (globals->haveZconstraints()){ |
1374 | > | setupZConstraint(info[k]); |
1375 | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); | |
1376 | } | |
1377 | ||
# | Line 1368 | Line 1380 | void SimSetup::makeIntegrator( void ){ | |
1380 | break; | |
1381 | ||
1382 | case NVT_ENS: | |
1383 | < | if (haveZConstraint){ |
1384 | < | setupZConstraint(); |
1383 | > | if (globals->haveZconstraints()){ |
1384 | > | setupZConstraint(info[k]); |
1385 | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); | |
1386 | } | |
1387 | else | |
# | Line 1390 | Line 1402 | void SimSetup::makeIntegrator( void ){ | |
1402 | break; | |
1403 | ||
1404 | case NPTi_ENS: | |
1405 | < | if (haveZConstraint){ |
1406 | < | setupZConstraint(); |
1405 | > | if (globals->haveZconstraints()){ |
1406 | > | setupZConstraint(info[k]); |
1407 | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); | |
1408 | } | |
1409 | else | |
# | Line 1431 | Line 1443 | void SimSetup::makeIntegrator( void ){ | |
1443 | break; | |
1444 | ||
1445 | case NPTf_ENS: | |
1446 | < | if (haveZConstraint){ |
1447 | < | setupZConstraint(); |
1446 | > | if (globals->haveZconstraints()){ |
1447 | > | setupZConstraint(info[k]); |
1448 | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); | |
1449 | } | |
1450 | else | |
# | Line 1472 | Line 1484 | void SimSetup::makeIntegrator( void ){ | |
1484 | break; | |
1485 | ||
1486 | case NPTim_ENS: | |
1487 | < | if (haveZConstraint){ |
1488 | < | setupZConstraint(); |
1487 | > | if (globals->haveZconstraints()){ |
1488 | > | setupZConstraint(info[k]); |
1489 | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); | |
1490 | } | |
1491 | else | |
# | Line 1513 | Line 1525 | void SimSetup::makeIntegrator( void ){ | |
1525 | break; | |
1526 | ||
1527 | case NPTfm_ENS: | |
1528 | < | if (haveZConstraint){ |
1529 | < | setupZConstraint(); |
1528 | > | if (globals->haveZconstraints()){ |
1529 | > | setupZConstraint(info[k]); |
1530 | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); | |
1531 | } | |
1532 | else | |
# | Line 1589 | Line 1601 | void SimSetup::initFortran( void ){ | |
1601 | ||
1602 | } | |
1603 | ||
1604 | < | void SimSetup::setupZConstraint() |
1604 | > | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1605 | { | |
1606 | < | int k; |
1607 | < | |
1608 | < | for(k=0; k<nInfo; k++){ |
1609 | < | |
1598 | < | if(globals->haveZConsTime()){ |
1606 | > | int nZConstraints; |
1607 | > | ZconStamp** zconStamp; |
1608 | > | |
1609 | > | if(globals->haveZconstraintTime()){ |
1610 | ||
1611 | //add sample time of z-constraint into SimInfo's property list | |
1612 | DoubleData* zconsTimeProp = new DoubleData(); | |
1613 | < | zconsTimeProp->setID("zconstime"); |
1614 | < | zconsTimeProp->setData(globals->getZConsTime()); |
1615 | < | info[k].addProperty(zconsTimeProp); |
1613 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1614 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1615 | > | theInfo.addProperty(zconsTimeProp); |
1616 | } | |
1617 | else{ | |
1618 | sprintf( painCave.errMsg, | |
# | Line 1610 | Line 1621 | void SimSetup::setupZConstraint() | |
1621 | painCave.isFatal = 1; | |
1622 | simError(); | |
1623 | } | |
1624 | < | |
1625 | < | if(globals->haveIndexOfAllZConsMols()){ |
1626 | < | |
1627 | < | //add index of z-constraint molecules into SimInfo's property list |
1628 | < | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1629 | < | |
1630 | < | //sort the index |
1631 | < | sort(tempIndex.begin(), tempIndex.end()); |
1632 | < | |
1633 | < | IndexData* zconsIndex = new IndexData(); |
1634 | < | zconsIndex->setID("zconsindex"); |
1635 | < | zconsIndex->setIndexData(tempIndex); |
1636 | < | info[k].addProperty(zconsIndex); |
1624 | > | |
1625 | > | // |
1626 | > | nZConstraints = globals->getNzConstraints(); |
1627 | > | zconStamp = globals->getZconStamp(); |
1628 | > | ZConsParaItem tempParaItem; |
1629 | > | |
1630 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1631 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1632 | > | |
1633 | > | for(int i = 0; i < nZConstraints; i++){ |
1634 | > | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1635 | > | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1636 | > | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1637 | > | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1638 | > | |
1639 | > | zconsParaData->addItem(tempParaItem); |
1640 | } | |
1641 | < | else{ |
1642 | < | sprintf( painCave.errMsg, |
1643 | < | "SimSetup error: If you use an ZConstraint\n" |
1644 | < | " , you must set index of z-constraint molecules.\n"); |
1645 | < | painCave.isFatal = 1; |
1646 | < | simError(); |
1647 | < | |
1641 | > | |
1642 | > | //sort the parameters by index of molecules |
1643 | > | zconsParaData->sortByIndex(); |
1644 | > | |
1645 | > | //push data into siminfo, therefore, we can retrieve later |
1646 | > | theInfo.addProperty(zconsParaData); |
1647 | > | |
1648 | > | //push zconsTol into siminfo, if user does not specify |
1649 | > | //value for zconsTol, a default value will be used |
1650 | > | DoubleData* zconsTol = new DoubleData(); |
1651 | > | zconsTol->setID(ZCONSTOL_ID); |
1652 | > | if(globals->haveZconsTol()){ |
1653 | > | zconsTol->setData(globals->getZconsTol()); |
1654 | } | |
1655 | < | |
1655 | > | else{ |
1656 | > | double defaultZConsTol = 1E-6; |
1657 | > | sprintf( painCave.errMsg, |
1658 | > | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1659 | > | " , default value %f is used.\n", defaultZConsTol); |
1660 | > | painCave.isFatal = 0; |
1661 | > | simError(); |
1662 | > | |
1663 | > | zconsTol->setData(defaultZConsTol); |
1664 | > | } |
1665 | > | theInfo.addProperty(zconsTol); |
1666 | > | |
1667 | //Determine the name of ouput file and add it into SimInfo's property list | |
1668 | //Be careful, do not use inFileName, since it is a pointer which | |
1669 | //point to a string at master node, and slave nodes do not contain that string | |
1670 | ||
1671 | < | string zconsOutput(info[k].finalName); |
1671 | > | string zconsOutput(theInfo.finalName); |
1672 | ||
1673 | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; | |
1674 | ||
1675 | StringData* zconsFilename = new StringData(); | |
1676 | < | zconsFilename->setID("zconsfilename"); |
1676 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1677 | zconsFilename->setData(zconsOutput); | |
1678 | ||
1679 | < | info[k].addProperty(zconsFilename); |
1649 | < | } |
1679 | > | theInfo.addProperty(zconsFilename); |
1680 | } |
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