102 |
|
// creation of complex system objects |
103 |
|
|
104 |
|
sysObjectsCreation(); |
105 |
– |
|
106 |
– |
// check on the post processing info |
107 |
– |
|
108 |
– |
finalInfoCheck(); |
105 |
|
|
106 |
|
// initialize the system coordinates |
107 |
|
|
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 |
|
|
696 |
|
} |
697 |
|
|
698 |
|
// check for the temperature set flag |
699 |
< |
|
699 |
> |
|
700 |
|
if (globals->haveTempSet()) |
701 |
|
info[i].setTemp = globals->getTempSet(); |
702 |
< |
|
703 |
< |
// get some of the tricky things that may still be in the globals |
704 |
< |
|
705 |
< |
double boxVector[3]; |
706 |
< |
if (globals->haveBox()){ |
707 |
< |
boxVector[0] = globals->getBox(); |
708 |
< |
boxVector[1] = globals->getBox(); |
709 |
< |
boxVector[2] = globals->getBox(); |
710 |
< |
|
711 |
< |
info[i].setBox(boxVector); |
712 |
< |
} |
713 |
< |
else if (globals->haveDensity()){ |
714 |
< |
double vol; |
715 |
< |
vol = (double) tot_nmol / globals->getDensity(); |
716 |
< |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
717 |
< |
boxVector[1] = boxVector[0]; |
718 |
< |
boxVector[2] = boxVector[0]; |
719 |
< |
|
720 |
< |
info[i].setBox(boxVector); |
721 |
< |
} |
722 |
< |
else{ |
723 |
< |
if (!globals->haveBoxX()){ |
724 |
< |
sprintf(painCave.errMsg, |
725 |
< |
"SimSetup error, no periodic BoxX size given.\n"); |
726 |
< |
painCave.isFatal = 1; |
727 |
< |
simError(); |
728 |
< |
} |
729 |
< |
boxVector[0] = globals->getBoxX(); |
730 |
< |
|
731 |
< |
if (!globals->haveBoxY()){ |
732 |
< |
sprintf(painCave.errMsg, |
733 |
< |
"SimSetup error, no periodic BoxY size given.\n"); |
734 |
< |
painCave.isFatal = 1; |
735 |
< |
simError(); |
736 |
< |
} |
737 |
< |
boxVector[1] = globals->getBoxY(); |
738 |
< |
|
739 |
< |
if (!globals->haveBoxZ()){ |
740 |
< |
sprintf(painCave.errMsg, |
741 |
< |
"SimSetup error, no periodic BoxZ size given.\n"); |
742 |
< |
painCave.isFatal = 1; |
743 |
< |
simError(); |
744 |
< |
} |
745 |
< |
boxVector[2] = globals->getBoxZ(); |
746 |
< |
|
747 |
< |
info[i].setBox(boxVector); |
748 |
< |
} |
702 |
> |
|
703 |
|
} |
704 |
< |
|
704 |
> |
|
705 |
|
//setup seed for random number generator |
706 |
|
int seedValue; |
707 |
|
|
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, |
850 |
|
theEst = globals->getEST(); |
851 |
|
} |
852 |
|
|
853 |
< |
info[i].setEcr(theEcr, theEst); |
853 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
854 |
|
} |
855 |
|
} |
856 |
|
} |
1414 |
|
|
1415 |
|
if (globals->haveTauThermostat()) |
1416 |
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1417 |
+ |
|
1418 |
|
else{ |
1419 |
|
sprintf(painCave.errMsg, |
1420 |
|
"SimSetup error: If you use an NPT\n" |
1425 |
|
|
1426 |
|
if (globals->haveTauBarostat()) |
1427 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1428 |
+ |
|
1429 |
|
else{ |
1430 |
|
sprintf(painCave.errMsg, |
1431 |
|
"SimSetup error: If you use an NPT\n" |