103 |
|
|
104 |
|
sysObjectsCreation(); |
105 |
|
|
106 |
– |
// check on the post processing info |
107 |
– |
|
108 |
– |
finalInfoCheck(); |
109 |
– |
|
106 |
|
// initialize the system coordinates |
107 |
|
|
108 |
|
if ( !initSuspend ){ |
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(); |
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(); |
702 |
|
|
703 |
< |
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]; |
703 |
> |
// check for the extended State init |
704 |
|
|
705 |
< |
info[i].setBox(boxVector); |
706 |
< |
} |
707 |
< |
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 |
< |
} |
705 |
> |
info[i].useInitXSstate = globals->getUseInitXSstate(); |
706 |
> |
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
707 |
> |
|
708 |
|
} |
709 |
< |
|
709 |
> |
|
710 |
|
//setup seed for random number generator |
711 |
|
int seedValue; |
712 |
|
|
810 |
|
theEst = globals->getEST(); |
811 |
|
} |
812 |
|
|
813 |
< |
info[i].setEcr(theEcr, theEst); |
813 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
814 |
|
|
815 |
|
if (!globals->haveDielectric()){ |
816 |
|
sprintf(painCave.errMsg, |
855 |
|
theEst = globals->getEST(); |
856 |
|
} |
857 |
|
|
858 |
< |
info[i].setEcr(theEcr, theEst); |
858 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
859 |
|
} |
860 |
|
} |
861 |
+ |
|
862 |
+ |
if( !initSuspend ) |
863 |
+ |
info[i].checkCutOffs(); |
864 |
|
} |
865 |
|
|
866 |
|
#ifdef IS_MPI |
1422 |
|
|
1423 |
|
if (globals->haveTauThermostat()) |
1424 |
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1425 |
+ |
|
1426 |
|
else{ |
1427 |
|
sprintf(painCave.errMsg, |
1428 |
|
"SimSetup error: If you use an NPT\n" |
1433 |
|
|
1434 |
|
if (globals->haveTauBarostat()) |
1435 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1436 |
+ |
|
1437 |
|
else{ |
1438 |
|
sprintf(painCave.errMsg, |
1439 |
|
"SimSetup error: If you use an NPT\n" |