103 |
|
|
104 |
|
sysObjectsCreation(); |
105 |
|
|
106 |
+ |
// check on the post processing info |
107 |
+ |
|
108 |
+ |
finalInfoCheck(); |
109 |
+ |
|
110 |
|
// initialize the system coordinates |
111 |
|
|
112 |
|
if ( !initSuspend ){ |
116 |
|
info[0].currentTime = 0.0; |
117 |
|
} |
118 |
|
|
115 |
– |
// check on the post processing info |
116 |
– |
|
117 |
– |
finalInfoCheck(); |
118 |
– |
|
119 |
|
// make the output filenames |
120 |
|
|
121 |
|
makeOutNames(); |
699 |
|
|
700 |
|
if (globals->haveTempSet()) |
701 |
|
info[i].setTemp = globals->getTempSet(); |
702 |
+ |
|
703 |
+ |
// check for the extended State init |
704 |
+ |
|
705 |
+ |
info[i].useInitXSstate = globals->getUseInitXSstate(); |
706 |
+ |
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
707 |
|
|
708 |
|
} |
709 |
|
|
781 |
|
|
782 |
|
if (!globals->haveECR()){ |
783 |
|
sprintf(painCave.errMsg, |
784 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
785 |
< |
"box length for the electrostaticCutoffRadius.\n" |
781 |
< |
"I hope you have a very fast processor!\n"); |
784 |
> |
"SimSetup Warning: using default value of 15.0 angstroms" |
785 |
> |
"box length for the electrostaticCutoffRadius.\n"); |
786 |
|
painCave.isFatal = 0; |
787 |
|
simError(); |
788 |
< |
double smallest; |
785 |
< |
smallest = info[i].boxL[0]; |
786 |
< |
if (info[i].boxL[1] <= smallest) |
787 |
< |
smallest = info[i].boxL[1]; |
788 |
< |
if (info[i].boxL[2] <= smallest) |
789 |
< |
smallest = info[i].boxL[2]; |
790 |
< |
theEcr = 0.5 * smallest; |
788 |
> |
theEcr = 15.0; |
789 |
|
} |
790 |
|
else{ |
791 |
|
theEcr = globals->getECR(); |
818 |
|
if (usesDipoles){ |
819 |
|
if (!globals->haveECR()){ |
820 |
|
sprintf(painCave.errMsg, |
821 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
822 |
< |
"box length for the electrostaticCutoffRadius.\n" |
823 |
< |
"I hope you have a very fast processor!\n"); |
824 |
< |
painCave.isFatal = 0; |
825 |
< |
simError(); |
828 |
< |
double smallest; |
829 |
< |
smallest = info[i].boxL[0]; |
830 |
< |
if (info[i].boxL[1] <= smallest) |
831 |
< |
smallest = info[i].boxL[1]; |
832 |
< |
if (info[i].boxL[2] <= smallest) |
833 |
< |
smallest = info[i].boxL[2]; |
834 |
< |
theEcr = 0.5 * smallest; |
821 |
> |
"SimSetup Warning: using default value of 15.0 angstroms" |
822 |
> |
"box length for the electrostaticCutoffRadius.\n"); |
823 |
> |
painCave.isFatal = 0; |
824 |
> |
simError(); |
825 |
> |
theEcr = 15.0; |
826 |
|
} |
827 |
|
else{ |
828 |
|
theEcr = globals->getECR(); |
829 |
|
} |
830 |
< |
|
830 |
> |
|
831 |
|
if (!globals->haveEST()){ |
832 |
|
sprintf(painCave.errMsg, |
833 |
|
"SimSetup Warning: using default value of 0.05 * the " |
840 |
|
else{ |
841 |
|
theEst = globals->getEST(); |
842 |
|
} |
843 |
< |
|
843 |
> |
|
844 |
|
info[i].setDefaultEcr(theEcr, theEst); |
845 |
|
} |
846 |
|
} |
856 |
– |
info[i].checkCutOffs(); |
847 |
|
} |
858 |
– |
|
848 |
|
#ifdef IS_MPI |
849 |
|
strcpy(checkPointMsg, "post processing checks out"); |
850 |
|
MPIcheckPoint(); |
851 |
|
#endif // is_mpi |
852 |
|
} |
853 |
< |
|
853 |
> |
|
854 |
|
void SimSetup::initSystemCoords(void){ |
855 |
|
int i; |
856 |
|
|
878 |
|
delete fileInit; |
879 |
|
} |
880 |
|
else{ |
881 |
< |
#ifdef IS_MPI |
893 |
< |
|
881 |
> |
|
882 |
|
// no init from bass |
883 |
< |
|
883 |
> |
|
884 |
|
sprintf(painCave.errMsg, |
885 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
885 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
886 |
|
painCave.isFatal = 1;; |
887 |
|
simError(); |
888 |
< |
|
901 |
< |
#else |
902 |
< |
|
903 |
< |
initFromBass(); |
904 |
< |
|
905 |
< |
|
906 |
< |
#endif |
888 |
> |
|
889 |
|
} |
890 |
|
|
891 |
|
#ifdef IS_MPI |