| 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(); |
| 703 |
> |
// check for the extended State init |
| 704 |
|
|
| 705 |
< |
if (!globals->haveBoxY()){ |
| 706 |
< |
sprintf(painCave.errMsg, |
| 707 |
< |
"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 |
|
|
| 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" |
| 827 |
< |
"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; |
| 831 |
< |
smallest = info[i].boxL[0]; |
| 832 |
< |
if (info[i].boxL[1] <= smallest) |
| 833 |
< |
smallest = info[i].boxL[1]; |
| 834 |
< |
if (info[i].boxL[2] <= smallest) |
| 835 |
< |
smallest = info[i].boxL[2]; |
| 836 |
< |
theEcr = 0.5 * smallest; |
| 788 |
> |
theEcr = 15.0; |
| 789 |
|
} |
| 790 |
|
else{ |
| 791 |
|
theEcr = globals->getECR(); |
| 803 |
|
theEst = globals->getEST(); |
| 804 |
|
} |
| 805 |
|
|
| 806 |
< |
info[i].setEcr(theEcr, theEst); |
| 806 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
| 807 |
|
|
| 808 |
|
if (!globals->haveDielectric()){ |
| 809 |
|
sprintf(painCave.errMsg, |
| 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(); |
| 874 |
< |
double smallest; |
| 875 |
< |
smallest = info[i].boxL[0]; |
| 876 |
< |
if (info[i].boxL[1] <= smallest) |
| 877 |
< |
smallest = info[i].boxL[1]; |
| 878 |
< |
if (info[i].boxL[2] <= smallest) |
| 879 |
< |
smallest = info[i].boxL[2]; |
| 880 |
< |
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 |
< |
|
| 844 |
< |
info[i].setEcr(theEcr, theEst); |
| 843 |
> |
|
| 844 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
| 845 |
|
} |
| 846 |
|
} |
| 847 |
|
} |
| 903 |
– |
|
| 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 |
| 938 |
< |
|
| 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 |
< |
|
| 946 |
< |
#else |
| 947 |
< |
|
| 948 |
< |
initFromBass(); |
| 949 |
< |
|
| 950 |
< |
|
| 951 |
< |
#endif |
| 888 |
> |
|
| 889 |
|
} |
| 890 |
|
|
| 891 |
|
#ifdef IS_MPI |
| 1397 |
|
|
| 1398 |
|
if (globals->haveTauThermostat()) |
| 1399 |
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
| 1400 |
+ |
|
| 1401 |
|
else{ |
| 1402 |
|
sprintf(painCave.errMsg, |
| 1403 |
|
"SimSetup error: If you use an NPT\n" |
| 1408 |
|
|
| 1409 |
|
if (globals->haveTauBarostat()) |
| 1410 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
| 1411 |
+ |
|
| 1412 |
|
else{ |
| 1413 |
|
sprintf(painCave.errMsg, |
| 1414 |
|
"SimSetup error: If you use an NPT\n" |
