| 102 |
|
// creation of complex system objects |
| 103 |
|
|
| 104 |
|
sysObjectsCreation(); |
| 105 |
+ |
|
| 106 |
+ |
// check on the post processing info |
| 107 |
+ |
|
| 108 |
+ |
finalInfoCheck(); |
| 109 |
|
|
| 110 |
|
// initialize the system coordinates |
| 111 |
|
|
| 115 |
|
if( !(globals->getUseInitTime()) ) |
| 116 |
|
info[0].currentTime = 0.0; |
| 117 |
|
} |
| 114 |
– |
|
| 115 |
– |
// check on the post processing info |
| 116 |
– |
|
| 117 |
– |
finalInfoCheck(); |
| 118 |
|
|
| 119 |
|
// make the output filenames |
| 120 |
|
|
| 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 |
|
} |
| 847 |
|
} |
| 857 |
– |
|
| 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 |
| 892 |
< |
|
| 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 |
< |
|
| 900 |
< |
#else |
| 901 |
< |
|
| 902 |
< |
initFromBass(); |
| 903 |
< |
|
| 904 |
< |
|
| 905 |
< |
#endif |
| 888 |
> |
|
| 889 |
|
} |
| 890 |
|
|
| 891 |
|
#ifdef IS_MPI |
