1 |
|
#include <algorithm> |
2 |
< |
#include <cstdlib> |
2 |
> |
#include <stdlib.h> |
3 |
|
#include <iostream> |
4 |
< |
#include <cmath> |
4 |
> |
#include <math.h> |
5 |
|
#include <string> |
6 |
|
#include <sprng.h> |
7 |
|
#include "SimSetup.hpp" |
31 |
|
using namespace std; |
32 |
|
|
33 |
|
SimSetup::SimSetup(){ |
34 |
+ |
|
35 |
+ |
initSuspend = false; |
36 |
|
isInfoArray = 0; |
37 |
|
nInfo = 1; |
38 |
|
|
55 |
|
info = the_info; |
56 |
|
nInfo = theNinfo; |
57 |
|
isInfoArray = 1; |
58 |
+ |
initSuspend = true; |
59 |
|
} |
60 |
|
|
61 |
|
|
102 |
|
// creation of complex system objects |
103 |
|
|
104 |
|
sysObjectsCreation(); |
102 |
– |
|
103 |
– |
// check on the post processing info |
104 |
– |
|
105 |
– |
finalInfoCheck(); |
105 |
|
|
106 |
|
// initialize the system coordinates |
107 |
|
|
108 |
< |
if (!isInfoArray){ |
108 |
> |
if ( !initSuspend ){ |
109 |
|
initSystemCoords(); |
110 |
|
|
111 |
|
if( !(globals->getUseInitTime()) ) |
112 |
|
info[0].currentTime = 0.0; |
113 |
|
} |
114 |
|
|
115 |
+ |
// check on the post processing info |
116 |
+ |
|
117 |
+ |
finalInfoCheck(); |
118 |
+ |
|
119 |
|
// make the output filenames |
120 |
|
|
121 |
|
makeOutNames(); |
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 |
703 |
> |
// check for the extended State init |
704 |
|
|
705 |
< |
double boxVector[3]; |
706 |
< |
if (globals->haveBox()){ |
707 |
< |
boxVector[0] = globals->getBox(); |
705 |
< |
boxVector[1] = globals->getBox(); |
706 |
< |
boxVector[2] = globals->getBox(); |
707 |
< |
|
708 |
< |
info[i].setBox(boxVector); |
709 |
< |
} |
710 |
< |
else if (globals->haveDensity()){ |
711 |
< |
double vol; |
712 |
< |
vol = (double) tot_nmol / globals->getDensity(); |
713 |
< |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
714 |
< |
boxVector[1] = boxVector[0]; |
715 |
< |
boxVector[2] = boxVector[0]; |
716 |
< |
|
717 |
< |
info[i].setBox(boxVector); |
718 |
< |
} |
719 |
< |
else{ |
720 |
< |
if (!globals->haveBoxX()){ |
721 |
< |
sprintf(painCave.errMsg, |
722 |
< |
"SimSetup error, no periodic BoxX size given.\n"); |
723 |
< |
painCave.isFatal = 1; |
724 |
< |
simError(); |
725 |
< |
} |
726 |
< |
boxVector[0] = globals->getBoxX(); |
727 |
< |
|
728 |
< |
if (!globals->haveBoxY()){ |
729 |
< |
sprintf(painCave.errMsg, |
730 |
< |
"SimSetup error, no periodic BoxY size given.\n"); |
731 |
< |
painCave.isFatal = 1; |
732 |
< |
simError(); |
733 |
< |
} |
734 |
< |
boxVector[1] = globals->getBoxY(); |
735 |
< |
|
736 |
< |
if (!globals->haveBoxZ()){ |
737 |
< |
sprintf(painCave.errMsg, |
738 |
< |
"SimSetup error, no periodic BoxZ size given.\n"); |
739 |
< |
painCave.isFatal = 1; |
740 |
< |
simError(); |
741 |
< |
} |
742 |
< |
boxVector[2] = globals->getBoxZ(); |
743 |
< |
|
744 |
< |
info[i].setBox(boxVector); |
745 |
< |
} |
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 |
|
|
810 |
|
theEst = globals->getEST(); |
811 |
|
} |
812 |
|
|
813 |
< |
info[i].setEcr(theEcr, theEst); |
813 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
814 |
|
|
815 |
|
if (!globals->haveDielectric()){ |
816 |
|
sprintf(painCave.errMsg, |
855 |
|
theEst = globals->getEST(); |
856 |
|
} |
857 |
|
|
858 |
< |
info[i].setEcr(theEcr, theEst); |
858 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
859 |
|
} |
860 |
|
} |
861 |
+ |
|
862 |
+ |
if( !initSuspend ) |
863 |
+ |
info[i].checkCutOffs(); |
864 |
|
} |
865 |
|
|
866 |
|
#ifdef IS_MPI |
1422 |
|
|
1423 |
|
if (globals->haveTauThermostat()) |
1424 |
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1425 |
+ |
|
1426 |
|
else{ |
1427 |
|
sprintf(painCave.errMsg, |
1428 |
|
"SimSetup error: If you use an NPT\n" |
1433 |
|
|
1434 |
|
if (globals->haveTauBarostat()) |
1435 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1436 |
+ |
|
1437 |
|
else{ |
1438 |
|
sprintf(painCave.errMsg, |
1439 |
|
"SimSetup error: If you use an NPT\n" |