1 |
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#include <algorithm> |
2 |
< |
#include <cstdlib> |
2 |
> |
#include <stdlib.h> |
3 |
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#include <iostream> |
4 |
< |
#include <cmath> |
4 |
> |
#include <math.h> |
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#include <string> |
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#include <sprng.h> |
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|
7 |
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
21 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
24 |
+ |
#define NPTxyz_ENS 4 |
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|
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|
27 |
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#define FF_DUFF 0 |
28 |
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#define FF_LJ 1 |
29 |
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#define FF_EAM 2 |
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|
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using namespace std; |
32 |
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|
33 |
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/** |
34 |
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* Check whether dividend is divisble by divisor or not |
35 |
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*/ |
36 |
+ |
bool isDivisible(double dividend, double divisor){ |
37 |
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double tolerance = 0.000001; |
38 |
+ |
double quotient; |
39 |
+ |
double diff; |
40 |
+ |
int intQuotient; |
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|
42 |
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quotient = dividend / divisor; |
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|
44 |
+ |
if (quotient < 0) |
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quotient = -quotient; |
46 |
+ |
|
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intQuotient = int (quotient + tolerance); |
48 |
+ |
|
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diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
50 |
+ |
|
51 |
+ |
if (diff <= tolerance) |
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return true; |
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else |
54 |
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return false; |
55 |
+ |
} |
56 |
+ |
|
57 |
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SimSetup::SimSetup(){ |
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|
59 |
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initSuspend = false; |
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isInfoArray = 0; |
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nInfo = 1; |
62 |
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|
79 |
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info = the_info; |
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nInfo = theNinfo; |
81 |
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isInfoArray = 1; |
82 |
+ |
initSuspend = true; |
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} |
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|
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|
118 |
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#endif // is_mpi |
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|
120 |
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void SimSetup::createSim(void){ |
93 |
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int i, j, k, globalAtomIndex; |
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|
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// gather all of the information from the Bass file |
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|
133 |
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|
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// initialize the system coordinates |
135 |
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|
136 |
< |
if (!isInfoArray){ |
136 |
> |
if ( !initSuspend ){ |
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initSystemCoords(); |
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+ |
|
139 |
+ |
if( !(globals->getUseInitTime()) ) |
140 |
+ |
info[0].currentTime = 0.0; |
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} |
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|
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// make the output filenames |
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|
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|
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void SimSetup::makeMolecules(void){ |
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int k, l; |
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int k; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
581 |
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|
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|
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void SimSetup::gatherInfo(void){ |
584 |
< |
int i, j, k; |
584 |
> |
int i; |
585 |
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|
586 |
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ensembleCase = -1; |
587 |
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ffCase = -1; |
632 |
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else if (!strcasecmp(ensemble, "NPTf")){ |
633 |
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ensembleCase = NPTf_ENS; |
634 |
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} |
635 |
+ |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
636 |
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ensembleCase = NPTxyz_ENS; |
637 |
+ |
} |
638 |
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else{ |
639 |
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sprintf(painCave.errMsg, |
640 |
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"SimSetup Warning. Unrecognized Ensemble -> %s, " |
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simError(); |
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} |
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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())){ |
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sprintf(painCave.errMsg, |
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"Sample time is not divisible by dt \n"); |
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painCave.isFatal = 0; |
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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())){ |
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sprintf(painCave.errMsg, |
704 |
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"Status time is not divisible by dt\n"); |
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painCave.isFatal = 0; |
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simError(); |
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} |
708 |
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|
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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 |
+ |
simError(); |
714 |
+ |
} |
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"); |
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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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|
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for (i = 0; i < nInfo; i++){ |
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} |
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|
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// check for the temperature set flag |
752 |
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|
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|
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if (globals->haveTempSet()) |
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info[i].setTemp = globals->getTempSet(); |
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|
756 |
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// get some of the tricky things that may still be in the globals |
756 |
> |
// check for the extended State init |
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|
758 |
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double boxVector[3]; |
759 |
< |
if (globals->haveBox()){ |
760 |
< |
boxVector[0] = globals->getBox(); |
699 |
< |
boxVector[1] = globals->getBox(); |
700 |
< |
boxVector[2] = globals->getBox(); |
701 |
< |
|
702 |
< |
info[i].setBox(boxVector); |
703 |
< |
} |
704 |
< |
else if (globals->haveDensity()){ |
705 |
< |
double vol; |
706 |
< |
vol = (double) tot_nmol / globals->getDensity(); |
707 |
< |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
708 |
< |
boxVector[1] = boxVector[0]; |
709 |
< |
boxVector[2] = boxVector[0]; |
710 |
< |
|
711 |
< |
info[i].setBox(boxVector); |
712 |
< |
} |
713 |
< |
else{ |
714 |
< |
if (!globals->haveBoxX()){ |
715 |
< |
sprintf(painCave.errMsg, |
716 |
< |
"SimSetup error, no periodic BoxX size given.\n"); |
717 |
< |
painCave.isFatal = 1; |
718 |
< |
simError(); |
719 |
< |
} |
720 |
< |
boxVector[0] = globals->getBoxX(); |
721 |
< |
|
722 |
< |
if (!globals->haveBoxY()){ |
723 |
< |
sprintf(painCave.errMsg, |
724 |
< |
"SimSetup error, no periodic BoxY size given.\n"); |
725 |
< |
painCave.isFatal = 1; |
726 |
< |
simError(); |
727 |
< |
} |
728 |
< |
boxVector[1] = globals->getBoxY(); |
729 |
< |
|
730 |
< |
if (!globals->haveBoxZ()){ |
731 |
< |
sprintf(painCave.errMsg, |
732 |
< |
"SimSetup error, no periodic BoxZ size given.\n"); |
733 |
< |
painCave.isFatal = 1; |
734 |
< |
simError(); |
735 |
< |
} |
736 |
< |
boxVector[2] = globals->getBoxZ(); |
737 |
< |
|
738 |
< |
info[i].setBox(boxVector); |
739 |
< |
} |
758 |
> |
info[i].useInitXSstate = globals->getUseInitXSstate(); |
759 |
> |
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
760 |
> |
|
761 |
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} |
762 |
< |
|
762 |
> |
|
763 |
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//setup seed for random number generator |
764 |
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int seedValue; |
765 |
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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" |
818 |
< |
"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 |
|
painCave.isFatal = 0; |
840 |
|
simError(); |
841 |
< |
double smallest; |
822 |
< |
smallest = info[i].boxL[0]; |
823 |
< |
if (info[i].boxL[1] <= smallest) |
824 |
< |
smallest = info[i].boxL[1]; |
825 |
< |
if (info[i].boxL[2] <= smallest) |
826 |
< |
smallest = info[i].boxL[2]; |
827 |
< |
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(); |
856 |
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theEst = globals->getEST(); |
857 |
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} |
858 |
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|
859 |
< |
info[i].setEcr(theEcr, theEst); |
859 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
860 |
|
|
861 |
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if (!globals->haveDielectric()){ |
862 |
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sprintf(painCave.errMsg, |
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(); |
865 |
< |
double smallest; |
866 |
< |
smallest = info[i].boxL[0]; |
867 |
< |
if (info[i].boxL[1] <= smallest) |
868 |
< |
smallest = info[i].boxL[1]; |
869 |
< |
if (info[i].boxL[2] <= smallest) |
870 |
< |
smallest = info[i].boxL[2]; |
871 |
< |
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 |
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else{ |
894 |
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theEst = globals->getEST(); |
895 |
|
} |
896 |
< |
|
897 |
< |
info[i].setEcr(theEcr, theEst); |
896 |
> |
|
897 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
898 |
|
} |
899 |
|
} |
900 |
|
} |
894 |
– |
|
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 |
|
|
920 |
|
if (worldRank == 0){ |
921 |
|
#endif //is_mpi |
922 |
|
inName = globals->getInitialConfig(); |
917 |
– |
double* tempDouble = new double[1000000]; |
923 |
|
fileInit = new InitializeFromFile(inName); |
924 |
|
#ifdef IS_MPI |
925 |
|
} |
931 |
|
delete fileInit; |
932 |
|
} |
933 |
|
else{ |
934 |
< |
#ifdef IS_MPI |
930 |
< |
|
934 |
> |
|
935 |
|
// no init from bass |
936 |
< |
|
936 |
> |
|
937 |
|
sprintf(painCave.errMsg, |
938 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
939 |
< |
painCave.isFatal; |
938 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
939 |
> |
painCave.isFatal = 1;; |
940 |
|
simError(); |
941 |
< |
|
938 |
< |
#else |
939 |
< |
|
940 |
< |
initFromBass(); |
941 |
< |
|
942 |
< |
|
943 |
< |
#endif |
941 |
> |
|
942 |
|
} |
943 |
|
|
944 |
|
#ifdef IS_MPI |
1156 |
|
} |
1157 |
|
|
1158 |
|
void SimSetup::calcSysValues(void){ |
1159 |
< |
int i, j, k; |
1159 |
> |
int i; |
1160 |
|
|
1161 |
|
int* molMembershipArray; |
1162 |
|
|
1255 |
|
|
1256 |
|
|
1257 |
|
void SimSetup::makeSysArrays(void){ |
1258 |
< |
int i, j, k, l; |
1258 |
> |
|
1259 |
> |
#ifndef IS_MPI |
1260 |
> |
int k, j; |
1261 |
> |
#endif // is_mpi |
1262 |
> |
int i, l; |
1263 |
|
|
1264 |
|
Atom** the_atoms; |
1265 |
|
Molecule* the_molecules; |
1342 |
|
void SimSetup::makeIntegrator(void){ |
1343 |
|
int k; |
1344 |
|
|
1345 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1346 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1347 |
|
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1348 |
|
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1349 |
+ |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1350 |
|
|
1351 |
|
for (k = 0; k < nInfo; k++){ |
1352 |
|
switch (ensembleCase){ |
1353 |
|
case NVE_ENS: |
1354 |
|
if (globals->haveZconstraints()){ |
1355 |
|
setupZConstraint(info[k]); |
1356 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1356 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1357 |
|
} |
1358 |
< |
else |
1359 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1358 |
> |
else{ |
1359 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1360 |
> |
} |
1361 |
> |
|
1362 |
> |
info->the_integrator = myNVE; |
1363 |
|
break; |
1364 |
|
|
1365 |
|
case NVT_ENS: |
1381 |
|
painCave.isFatal = 1; |
1382 |
|
simError(); |
1383 |
|
} |
1384 |
+ |
|
1385 |
+ |
info->the_integrator = myNVT; |
1386 |
|
break; |
1387 |
|
|
1388 |
|
case NPTi_ENS: |
1424 |
|
painCave.isFatal = 1; |
1425 |
|
simError(); |
1426 |
|
} |
1427 |
+ |
|
1428 |
+ |
info->the_integrator = myNPTi; |
1429 |
|
break; |
1430 |
|
|
1431 |
|
case NPTf_ENS: |
1450 |
|
|
1451 |
|
if (globals->haveTauThermostat()) |
1452 |
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1453 |
+ |
|
1454 |
|
else{ |
1455 |
|
sprintf(painCave.errMsg, |
1456 |
|
"SimSetup error: If you use an NPT\n" |
1461 |
|
|
1462 |
|
if (globals->haveTauBarostat()) |
1463 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1464 |
+ |
|
1465 |
|
else{ |
1466 |
|
sprintf(painCave.errMsg, |
1467 |
|
"SimSetup error: If you use an NPT\n" |
1469 |
|
painCave.isFatal = 1; |
1470 |
|
simError(); |
1471 |
|
} |
1472 |
+ |
|
1473 |
+ |
info->the_integrator = myNPTf; |
1474 |
|
break; |
1475 |
|
|
1476 |
+ |
case NPTxyz_ENS: |
1477 |
+ |
if (globals->haveZconstraints()){ |
1478 |
+ |
setupZConstraint(info[k]); |
1479 |
+ |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1480 |
+ |
} |
1481 |
+ |
else |
1482 |
+ |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1483 |
+ |
|
1484 |
+ |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1485 |
+ |
|
1486 |
+ |
if (globals->haveTargetPressure()) |
1487 |
+ |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1488 |
+ |
else{ |
1489 |
+ |
sprintf(painCave.errMsg, |
1490 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1491 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1492 |
+ |
painCave.isFatal = 1; |
1493 |
+ |
simError(); |
1494 |
+ |
} |
1495 |
+ |
|
1496 |
+ |
if (globals->haveTauThermostat()) |
1497 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1498 |
+ |
else{ |
1499 |
+ |
sprintf(painCave.errMsg, |
1500 |
+ |
"SimSetup error: If you use an NPT\n" |
1501 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1502 |
+ |
painCave.isFatal = 1; |
1503 |
+ |
simError(); |
1504 |
+ |
} |
1505 |
+ |
|
1506 |
+ |
if (globals->haveTauBarostat()) |
1507 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1508 |
+ |
else{ |
1509 |
+ |
sprintf(painCave.errMsg, |
1510 |
+ |
"SimSetup error: If you use an NPT\n" |
1511 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1512 |
+ |
painCave.isFatal = 1; |
1513 |
+ |
simError(); |
1514 |
+ |
} |
1515 |
+ |
|
1516 |
+ |
info->the_integrator = myNPTxyz; |
1517 |
+ |
break; |
1518 |
+ |
|
1519 |
|
default: |
1520 |
|
sprintf(painCave.errMsg, |
1521 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |