# | Line 1 | Line 1 | |
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1 | #include <algorithm> | |
2 | < | #include <cstdlib> |
2 | > | #include <stdlib.h> |
3 | #include <iostream> | |
4 | < | #include <cmath> |
4 | > | #include <math.h> |
5 | #include <string> | |
6 | #include <sprng.h> | |
7 | – | |
7 | #include "SimSetup.hpp" | |
8 | #include "ReadWrite.hpp" | |
9 | #include "parse_me.h" | |
# | Line 22 | Line 21 | |
21 | #define NVT_ENS 1 | |
22 | #define NPTi_ENS 2 | |
23 | #define NPTf_ENS 3 | |
24 | + | #define NPTxyz_ENS 4 |
25 | ||
26 | + | |
27 | #define FF_DUFF 0 | |
28 | #define FF_LJ 1 | |
29 | #define FF_EAM 2 | |
# | Line 30 | Line 31 | SimSetup::SimSetup(){ | |
31 | using namespace std; | |
32 | ||
33 | SimSetup::SimSetup(){ | |
34 | + | |
35 | + | initSuspend = false; |
36 | isInfoArray = 0; | |
37 | nInfo = 1; | |
38 | ||
# | Line 52 | Line 55 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi | |
55 | info = the_info; | |
56 | nInfo = theNinfo; | |
57 | isInfoArray = 1; | |
58 | + | initSuspend = true; |
59 | } | |
60 | ||
61 | ||
# | Line 99 | Line 103 | void SimSetup::createSim(void){ | |
103 | ||
104 | sysObjectsCreation(); | |
105 | ||
102 | – | // check on the post processing info |
103 | – | |
104 | – | finalInfoCheck(); |
105 | – | |
106 | // initialize the system coordinates | |
107 | ||
108 | < | if (!isInfoArray){ |
108 | > | if ( !initSuspend ){ |
109 | initSystemCoords(); | |
110 | ||
111 | if( !(globals->getUseInitTime()) ) | |
112 | info[0].currentTime = 0.0; | |
113 | } | |
114 | ||
115 | + | // check on the post processing info |
116 | + | |
117 | + | finalInfoCheck(); |
118 | + | |
119 | // make the output filenames | |
120 | ||
121 | makeOutNames(); | |
# | Line 604 | Line 608 | void SimSetup::gatherInfo(void){ | |
608 | else if (!strcasecmp(ensemble, "NPTf")){ | |
609 | ensembleCase = NPTf_ENS; | |
610 | } | |
611 | + | else if (!strcasecmp(ensemble, "NPTxyz")){ |
612 | + | ensembleCase = NPTxyz_ENS; |
613 | + | } |
614 | else{ | |
615 | sprintf(painCave.errMsg, | |
616 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 689 | Line 696 | void SimSetup::gatherInfo(void){ | |
696 | } | |
697 | ||
698 | // check for the temperature set flag | |
699 | < | |
699 | > | |
700 | if (globals->haveTempSet()) | |
701 | info[i].setTemp = globals->getTempSet(); | |
702 | < | |
696 | < | // get some of the tricky things that may still be in the globals |
697 | < | |
698 | < | double boxVector[3]; |
699 | < | if (globals->haveBox()){ |
700 | < | boxVector[0] = globals->getBox(); |
701 | < | boxVector[1] = globals->getBox(); |
702 | < | boxVector[2] = globals->getBox(); |
703 | < | |
704 | < | info[i].setBox(boxVector); |
705 | < | } |
706 | < | else if (globals->haveDensity()){ |
707 | < | double vol; |
708 | < | vol = (double) tot_nmol / globals->getDensity(); |
709 | < | boxVector[0] = pow(vol, (1.0 / 3.0)); |
710 | < | boxVector[1] = boxVector[0]; |
711 | < | boxVector[2] = boxVector[0]; |
712 | < | |
713 | < | info[i].setBox(boxVector); |
714 | < | } |
715 | < | else{ |
716 | < | if (!globals->haveBoxX()){ |
717 | < | sprintf(painCave.errMsg, |
718 | < | "SimSetup error, no periodic BoxX size given.\n"); |
719 | < | painCave.isFatal = 1; |
720 | < | simError(); |
721 | < | } |
722 | < | boxVector[0] = globals->getBoxX(); |
723 | < | |
724 | < | if (!globals->haveBoxY()){ |
725 | < | sprintf(painCave.errMsg, |
726 | < | "SimSetup error, no periodic BoxY size given.\n"); |
727 | < | painCave.isFatal = 1; |
728 | < | simError(); |
729 | < | } |
730 | < | boxVector[1] = globals->getBoxY(); |
731 | < | |
732 | < | if (!globals->haveBoxZ()){ |
733 | < | sprintf(painCave.errMsg, |
734 | < | "SimSetup error, no periodic BoxZ size given.\n"); |
735 | < | painCave.isFatal = 1; |
736 | < | simError(); |
737 | < | } |
738 | < | boxVector[2] = globals->getBoxZ(); |
739 | < | |
740 | < | info[i].setBox(boxVector); |
741 | < | } |
702 | > | |
703 | } | |
704 | < | |
704 | > | |
705 | //setup seed for random number generator | |
706 | int seedValue; | |
707 | ||
# | Line 844 | Line 805 | void SimSetup::finalInfoCheck(void){ | |
805 | theEst = globals->getEST(); | |
806 | } | |
807 | ||
808 | < | info[i].setEcr(theEcr, theEst); |
808 | > | info[i].setDefaultEcr(theEcr, theEst); |
809 | ||
810 | if (!globals->haveDielectric()){ | |
811 | sprintf(painCave.errMsg, | |
# | Line 889 | Line 850 | void SimSetup::finalInfoCheck(void){ | |
850 | theEst = globals->getEST(); | |
851 | } | |
852 | ||
853 | < | info[i].setEcr(theEcr, theEst); |
853 | > | info[i].setDefaultEcr(theEcr, theEst); |
854 | } | |
855 | } | |
856 | } | |
# | Line 1349 | Line 1310 | void SimSetup::makeIntegrator(void){ | |
1310 | NVT<RealIntegrator>* myNVT = NULL; | |
1311 | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; | |
1312 | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; | |
1313 | + | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1314 | ||
1315 | for (k = 0; k < nInfo; k++){ | |
1316 | switch (ensembleCase){ | |
# | Line 1471 | Line 1433 | void SimSetup::makeIntegrator(void){ | |
1433 | } | |
1434 | ||
1435 | info->the_integrator = myNPTf; | |
1436 | + | break; |
1437 | + | |
1438 | + | case NPTxyz_ENS: |
1439 | + | if (globals->haveZconstraints()){ |
1440 | + | setupZConstraint(info[k]); |
1441 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1442 | + | } |
1443 | + | else |
1444 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1445 | + | |
1446 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1447 | + | |
1448 | + | if (globals->haveTargetPressure()) |
1449 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1450 | + | else{ |
1451 | + | sprintf(painCave.errMsg, |
1452 | + | "SimSetup error: If you use a constant pressure\n" |
1453 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1454 | + | painCave.isFatal = 1; |
1455 | + | simError(); |
1456 | + | } |
1457 | + | |
1458 | + | if (globals->haveTauThermostat()) |
1459 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1460 | + | else{ |
1461 | + | sprintf(painCave.errMsg, |
1462 | + | "SimSetup error: If you use an NPT\n" |
1463 | + | " ensemble, you must set tauThermostat.\n"); |
1464 | + | painCave.isFatal = 1; |
1465 | + | simError(); |
1466 | + | } |
1467 | + | |
1468 | + | if (globals->haveTauBarostat()) |
1469 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1470 | + | else{ |
1471 | + | sprintf(painCave.errMsg, |
1472 | + | "SimSetup error: If you use an NPT\n" |
1473 | + | " ensemble, you must set tauBarostat.\n"); |
1474 | + | painCave.isFatal = 1; |
1475 | + | simError(); |
1476 | + | } |
1477 | + | |
1478 | + | info->the_integrator = myNPTxyz; |
1479 | break; | |
1480 | ||
1481 | default: |
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