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using namespace std; |
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|
33 |
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/** |
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* Check whether dividend is divisble by divisor or not |
35 |
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*/ |
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bool isDivisible(double dividend, double divisor){ |
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double tolerance = 0.000001; |
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double quotient; |
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double diff; |
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int intQuotient; |
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|
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quotient = dividend / divisor; |
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|
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if (quotient < 0) |
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quotient = -quotient; |
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|
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intQuotient = int (quotient + tolerance); |
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|
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diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
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|
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if (diff <= tolerance) |
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return true; |
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else |
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return false; |
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} |
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|
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SimSetup::SimSetup(){ |
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|
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initSuspend = false; |
127 |
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|
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sysObjectsCreation(); |
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|
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// check on the post processing info |
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|
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finalInfoCheck(); |
133 |
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|
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// initialize the system coordinates |
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|
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if ( !initSuspend ){ |
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if( !(globals->getUseInitTime()) ) |
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info[0].currentTime = 0.0; |
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} |
114 |
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|
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// check on the post processing info |
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|
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finalInfoCheck(); |
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|
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// make the output filenames |
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|
689 |
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" Please give nMol in the components.\n"); |
690 |
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painCave.isFatal = 1; |
691 |
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simError(); |
692 |
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} |
693 |
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|
694 |
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//check whether sample time, status time, thermal time and reset time are divisble by dt |
695 |
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if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
696 |
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sprintf(painCave.errMsg, |
697 |
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"Sample time is not divisible by dt \n"); |
698 |
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painCave.isFatal = 0; |
699 |
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simError(); |
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} |
701 |
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|
702 |
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if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
703 |
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sprintf(painCave.errMsg, |
704 |
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"Status time is not divisible by dt\n"); |
705 |
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painCave.isFatal = 0; |
706 |
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simError(); |
707 |
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} |
708 |
+ |
|
709 |
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if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
710 |
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sprintf(painCave.errMsg, |
711 |
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"Thermal time is not divisible by dt\n"); |
712 |
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painCave.isFatal = 0; |
713 |
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simError(); |
714 |
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} |
715 |
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|
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if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
717 |
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sprintf(painCave.errMsg, |
718 |
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"Reset time is not divisible by dt\n"); |
719 |
+ |
painCave.isFatal = 0; |
720 |
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simError(); |
721 |
+ |
} |
722 |
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|
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// set the status, sample, and thermal kick times |
724 |
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|
834 |
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|
835 |
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if (!globals->haveECR()){ |
836 |
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sprintf(painCave.errMsg, |
837 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
838 |
< |
"box length for the electrostaticCutoffRadius.\n" |
786 |
< |
"I hope you have a very fast processor!\n"); |
837 |
> |
"SimSetup Warning: using default value of 15.0 angstroms" |
838 |
> |
"box length for the electrostaticCutoffRadius.\n"); |
839 |
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painCave.isFatal = 0; |
840 |
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simError(); |
841 |
< |
double smallest; |
790 |
< |
smallest = info[i].boxL[0]; |
791 |
< |
if (info[i].boxL[1] <= smallest) |
792 |
< |
smallest = info[i].boxL[1]; |
793 |
< |
if (info[i].boxL[2] <= smallest) |
794 |
< |
smallest = info[i].boxL[2]; |
795 |
< |
theEcr = 0.5 * smallest; |
841 |
> |
theEcr = 15.0; |
842 |
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} |
843 |
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else{ |
844 |
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theEcr = globals->getECR(); |
871 |
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if (usesDipoles){ |
872 |
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if (!globals->haveECR()){ |
873 |
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sprintf(painCave.errMsg, |
874 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
875 |
< |
"box length for the electrostaticCutoffRadius.\n" |
876 |
< |
"I hope you have a very fast processor!\n"); |
877 |
< |
painCave.isFatal = 0; |
878 |
< |
simError(); |
833 |
< |
double smallest; |
834 |
< |
smallest = info[i].boxL[0]; |
835 |
< |
if (info[i].boxL[1] <= smallest) |
836 |
< |
smallest = info[i].boxL[1]; |
837 |
< |
if (info[i].boxL[2] <= smallest) |
838 |
< |
smallest = info[i].boxL[2]; |
839 |
< |
theEcr = 0.5 * smallest; |
874 |
> |
"SimSetup Warning: using default value of 15.0 angstroms" |
875 |
> |
"box length for the electrostaticCutoffRadius.\n"); |
876 |
> |
painCave.isFatal = 0; |
877 |
> |
simError(); |
878 |
> |
theEcr = 15.0; |
879 |
|
} |
880 |
|
else{ |
881 |
|
theEcr = globals->getECR(); |
882 |
|
} |
883 |
< |
|
883 |
> |
|
884 |
|
if (!globals->haveEST()){ |
885 |
|
sprintf(painCave.errMsg, |
886 |
|
"SimSetup Warning: using default value of 0.05 * the " |
893 |
|
else{ |
894 |
|
theEst = globals->getEST(); |
895 |
|
} |
896 |
< |
|
896 |
> |
|
897 |
|
info[i].setDefaultEcr(theEcr, theEst); |
898 |
|
} |
899 |
|
} |
861 |
– |
|
862 |
– |
if( !initSuspend ) |
863 |
– |
info[i].checkCutOffs(); |
900 |
|
} |
865 |
– |
|
901 |
|
#ifdef IS_MPI |
902 |
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strcpy(checkPointMsg, "post processing checks out"); |
903 |
|
MPIcheckPoint(); |
904 |
|
#endif // is_mpi |
905 |
|
} |
906 |
< |
|
906 |
> |
|
907 |
|
void SimSetup::initSystemCoords(void){ |
908 |
|
int i; |
909 |
|
|
931 |
|
delete fileInit; |
932 |
|
} |
933 |
|
else{ |
934 |
< |
#ifdef IS_MPI |
935 |
< |
|
936 |
< |
// no init from bass |
902 |
< |
|
934 |
> |
|
935 |
> |
// no init from bass |
936 |
> |
|
937 |
|
sprintf(painCave.errMsg, |
938 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
938 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
939 |
|
painCave.isFatal = 1;; |
940 |
|
simError(); |
941 |
< |
|
908 |
< |
#else |
909 |
< |
|
910 |
< |
initFromBass(); |
911 |
< |
|
912 |
< |
|
913 |
< |
#endif |
941 |
> |
|
942 |
|
} |
943 |
|
|
944 |
|
#ifdef IS_MPI |