# | Line 1 | Line 1 | |
---|---|---|
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 90 | Line 94 | void SimSetup::createSim(void){ | |
94 | #endif // is_mpi | |
95 | ||
96 | void SimSetup::createSim(void){ | |
93 | – | int i, j, k, globalAtomIndex; |
97 | ||
98 | // gather all of the information from the Bass file | |
99 | ||
# | Line 100 | Line 103 | void SimSetup::createSim(void){ | |
103 | ||
104 | sysObjectsCreation(); | |
105 | ||
103 | – | // check on the post processing info |
104 | – | |
105 | – | finalInfoCheck(); |
106 | – | |
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 129 | Line 135 | void SimSetup::makeMolecules(void){ | |
135 | ||
136 | ||
137 | void SimSetup::makeMolecules(void){ | |
138 | < | int k, l; |
138 | > | int k; |
139 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
140 | molInit molInfo; | |
141 | DirectionalAtom* dAtom; | |
# | Line 551 | Line 557 | void SimSetup::gatherInfo(void){ | |
557 | ||
558 | ||
559 | void SimSetup::gatherInfo(void){ | |
560 | < | int i, j, k; |
560 | > | int i; |
561 | ||
562 | ensembleCase = -1; | |
563 | ffCase = -1; | |
# | Line 602 | 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 687 | 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 | < | |
694 | < | // get some of the tricky things that may still be in the globals |
695 | < | |
696 | < | double boxVector[3]; |
697 | < | if (globals->haveBox()){ |
698 | < | boxVector[0] = globals->getBox(); |
699 | < | boxVector[1] = globals->getBox(); |
700 | < | boxVector[2] = globals->getBox(); |
701 | < | |
702 | < | info[i].setBox(boxVector); |
703 | < | } |
704 | < | else if (globals->haveDensity()){ |
705 | < | double vol; |
706 | < | vol = (double) tot_nmol / globals->getDensity(); |
707 | < | boxVector[0] = pow(vol, (1.0 / 3.0)); |
708 | < | boxVector[1] = boxVector[0]; |
709 | < | boxVector[2] = boxVector[0]; |
710 | < | |
711 | < | info[i].setBox(boxVector); |
712 | < | } |
713 | < | else{ |
714 | < | if (!globals->haveBoxX()){ |
715 | < | sprintf(painCave.errMsg, |
716 | < | "SimSetup error, no periodic BoxX size given.\n"); |
717 | < | painCave.isFatal = 1; |
718 | < | simError(); |
719 | < | } |
720 | < | boxVector[0] = globals->getBoxX(); |
721 | < | |
722 | < | if (!globals->haveBoxY()){ |
723 | < | sprintf(painCave.errMsg, |
724 | < | "SimSetup error, no periodic BoxY size given.\n"); |
725 | < | painCave.isFatal = 1; |
726 | < | simError(); |
727 | < | } |
728 | < | boxVector[1] = globals->getBoxY(); |
729 | < | |
730 | < | if (!globals->haveBoxZ()){ |
731 | < | sprintf(painCave.errMsg, |
732 | < | "SimSetup error, no periodic BoxZ size given.\n"); |
733 | < | painCave.isFatal = 1; |
734 | < | simError(); |
735 | < | } |
736 | < | boxVector[2] = globals->getBoxZ(); |
737 | < | |
738 | < | info[i].setBox(boxVector); |
739 | < | } |
702 | > | |
703 | } | |
704 | < | |
704 | > | |
705 | //setup seed for random number generator | |
706 | int seedValue; | |
707 | ||
# | Line 842 | 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 887 | 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 | + | info[i].checkCutOffs(); |
857 | } | |
858 | ||
859 | #ifdef IS_MPI | |
# | Line 914 | Line 878 | void SimSetup::initSystemCoords(void){ | |
878 | if (worldRank == 0){ | |
879 | #endif //is_mpi | |
880 | inName = globals->getInitialConfig(); | |
917 | – | double* tempDouble = new double[1000000]; |
881 | fileInit = new InitializeFromFile(inName); | |
882 | #ifdef IS_MPI | |
883 | } | |
# | Line 932 | Line 895 | void SimSetup::initSystemCoords(void){ | |
895 | ||
896 | sprintf(painCave.errMsg, | |
897 | "Cannot intialize a parallel simulation without an initial configuration file.\n"); | |
898 | < | painCave.isFatal; |
898 | > | painCave.isFatal = 1;; |
899 | simError(); | |
900 | ||
901 | #else | |
# | Line 1158 | Line 1121 | void SimSetup::calcSysValues(void){ | |
1121 | } | |
1122 | ||
1123 | void SimSetup::calcSysValues(void){ | |
1124 | < | int i, j, k; |
1124 | > | int i; |
1125 | ||
1126 | int* molMembershipArray; | |
1127 | ||
# | Line 1257 | Line 1220 | void SimSetup::makeSysArrays(void){ | |
1220 | ||
1221 | ||
1222 | void SimSetup::makeSysArrays(void){ | |
1223 | < | int i, j, k, l; |
1223 | > | |
1224 | > | #ifndef IS_MPI |
1225 | > | int k, j; |
1226 | > | #endif // is_mpi |
1227 | > | int i, l; |
1228 | ||
1229 | Atom** the_atoms; | |
1230 | Molecule* the_molecules; | |
# | Line 1344 | Line 1311 | void SimSetup::makeIntegrator(void){ | |
1311 | NVT<RealIntegrator>* myNVT = NULL; | |
1312 | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; | |
1313 | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; | |
1314 | + | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1315 | ||
1316 | for (k = 0; k < nInfo; k++){ | |
1317 | switch (ensembleCase){ | |
# | Line 1447 | Line 1415 | void SimSetup::makeIntegrator(void){ | |
1415 | ||
1416 | if (globals->haveTauThermostat()) | |
1417 | myNPTf->setTauThermostat(globals->getTauThermostat()); | |
1418 | + | |
1419 | else{ | |
1420 | sprintf(painCave.errMsg, | |
1421 | "SimSetup error: If you use an NPT\n" | |
# | Line 1457 | Line 1426 | void SimSetup::makeIntegrator(void){ | |
1426 | ||
1427 | if (globals->haveTauBarostat()) | |
1428 | myNPTf->setTauBarostat(globals->getTauBarostat()); | |
1429 | + | |
1430 | else{ | |
1431 | sprintf(painCave.errMsg, | |
1432 | "SimSetup error: If you use an NPT\n" | |
# | Line 1468 | Line 1438 | void SimSetup::makeIntegrator(void){ | |
1438 | info->the_integrator = myNPTf; | |
1439 | break; | |
1440 | ||
1441 | + | case NPTxyz_ENS: |
1442 | + | if (globals->haveZconstraints()){ |
1443 | + | setupZConstraint(info[k]); |
1444 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1445 | + | } |
1446 | + | else |
1447 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1448 | + | |
1449 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1450 | + | |
1451 | + | if (globals->haveTargetPressure()) |
1452 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1453 | + | else{ |
1454 | + | sprintf(painCave.errMsg, |
1455 | + | "SimSetup error: If you use a constant pressure\n" |
1456 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1457 | + | painCave.isFatal = 1; |
1458 | + | simError(); |
1459 | + | } |
1460 | + | |
1461 | + | if (globals->haveTauThermostat()) |
1462 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1463 | + | else{ |
1464 | + | sprintf(painCave.errMsg, |
1465 | + | "SimSetup error: If you use an NPT\n" |
1466 | + | " ensemble, you must set tauThermostat.\n"); |
1467 | + | painCave.isFatal = 1; |
1468 | + | simError(); |
1469 | + | } |
1470 | + | |
1471 | + | if (globals->haveTauBarostat()) |
1472 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1473 | + | else{ |
1474 | + | sprintf(painCave.errMsg, |
1475 | + | "SimSetup error: If you use an NPT\n" |
1476 | + | " ensemble, you must set tauBarostat.\n"); |
1477 | + | painCave.isFatal = 1; |
1478 | + | simError(); |
1479 | + | } |
1480 | + | |
1481 | + | info->the_integrator = myNPTxyz; |
1482 | + | break; |
1483 | + | |
1484 | default: | |
1485 | sprintf(painCave.errMsg, | |
1486 | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |