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 |
– |
|
7 |
|
#include "SimSetup.hpp" |
8 |
|
#include "ReadWrite.hpp" |
9 |
|
#include "parse_me.h" |
21 |
|
#define NVT_ENS 1 |
22 |
|
#define NPTi_ENS 2 |
23 |
|
#define NPTf_ENS 3 |
24 |
+ |
#define NPTxyz_ENS 4 |
25 |
|
|
26 |
+ |
|
27 |
|
#define FF_DUFF 0 |
28 |
|
#define FF_LJ 1 |
29 |
|
#define FF_EAM 2 |
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 |
|
|
103 |
|
|
104 |
|
sysObjectsCreation(); |
105 |
|
|
102 |
– |
// check on the post processing info |
103 |
– |
|
104 |
– |
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 |
|
|
607 |
|
} |
608 |
|
else if (!strcasecmp(ensemble, "NPTf")){ |
609 |
|
ensembleCase = NPTf_ENS; |
610 |
+ |
} |
611 |
+ |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
612 |
+ |
ensembleCase = NPTxyz_ENS; |
613 |
|
} |
614 |
|
else{ |
615 |
|
sprintf(painCave.errMsg, |
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 |
694 |
< |
|
695 |
< |
double boxVector[3]; |
696 |
< |
if (globals->haveBox()){ |
697 |
< |
boxVector[0] = globals->getBox(); |
698 |
< |
boxVector[1] = globals->getBox(); |
699 |
< |
boxVector[2] = globals->getBox(); |
703 |
> |
// check for the extended State init |
704 |
|
|
705 |
< |
info[i].setBox(boxVector); |
706 |
< |
} |
707 |
< |
else if (globals->haveDensity()){ |
704 |
< |
double vol; |
705 |
< |
vol = (double) tot_nmol / globals->getDensity(); |
706 |
< |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
707 |
< |
boxVector[1] = boxVector[0]; |
708 |
< |
boxVector[2] = boxVector[0]; |
709 |
< |
|
710 |
< |
info[i].setBox(boxVector); |
711 |
< |
} |
712 |
< |
else{ |
713 |
< |
if (!globals->haveBoxX()){ |
714 |
< |
sprintf(painCave.errMsg, |
715 |
< |
"SimSetup error, no periodic BoxX size given.\n"); |
716 |
< |
painCave.isFatal = 1; |
717 |
< |
simError(); |
718 |
< |
} |
719 |
< |
boxVector[0] = globals->getBoxX(); |
720 |
< |
|
721 |
< |
if (!globals->haveBoxY()){ |
722 |
< |
sprintf(painCave.errMsg, |
723 |
< |
"SimSetup error, no periodic BoxY size given.\n"); |
724 |
< |
painCave.isFatal = 1; |
725 |
< |
simError(); |
726 |
< |
} |
727 |
< |
boxVector[1] = globals->getBoxY(); |
728 |
< |
|
729 |
< |
if (!globals->haveBoxZ()){ |
730 |
< |
sprintf(painCave.errMsg, |
731 |
< |
"SimSetup error, no periodic BoxZ size given.\n"); |
732 |
< |
painCave.isFatal = 1; |
733 |
< |
simError(); |
734 |
< |
} |
735 |
< |
boxVector[2] = globals->getBoxZ(); |
736 |
< |
|
737 |
< |
info[i].setBox(boxVector); |
738 |
< |
} |
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 |
1318 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1319 |
|
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1320 |
|
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1321 |
+ |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1322 |
|
|
1323 |
|
for (k = 0; k < nInfo; k++){ |
1324 |
|
switch (ensembleCase){ |
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" |
1443 |
|
} |
1444 |
|
|
1445 |
|
info->the_integrator = myNPTf; |
1446 |
+ |
break; |
1447 |
+ |
|
1448 |
+ |
case NPTxyz_ENS: |
1449 |
+ |
if (globals->haveZconstraints()){ |
1450 |
+ |
setupZConstraint(info[k]); |
1451 |
+ |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1452 |
+ |
} |
1453 |
+ |
else |
1454 |
+ |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1455 |
+ |
|
1456 |
+ |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1457 |
+ |
|
1458 |
+ |
if (globals->haveTargetPressure()) |
1459 |
+ |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1460 |
+ |
else{ |
1461 |
+ |
sprintf(painCave.errMsg, |
1462 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1463 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1464 |
+ |
painCave.isFatal = 1; |
1465 |
+ |
simError(); |
1466 |
+ |
} |
1467 |
+ |
|
1468 |
+ |
if (globals->haveTauThermostat()) |
1469 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1470 |
+ |
else{ |
1471 |
+ |
sprintf(painCave.errMsg, |
1472 |
+ |
"SimSetup error: If you use an NPT\n" |
1473 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1474 |
+ |
painCave.isFatal = 1; |
1475 |
+ |
simError(); |
1476 |
+ |
} |
1477 |
+ |
|
1478 |
+ |
if (globals->haveTauBarostat()) |
1479 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1480 |
+ |
else{ |
1481 |
+ |
sprintf(painCave.errMsg, |
1482 |
+ |
"SimSetup error: If you use an NPT\n" |
1483 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1484 |
+ |
painCave.isFatal = 1; |
1485 |
+ |
simError(); |
1486 |
+ |
} |
1487 |
+ |
|
1488 |
+ |
info->the_integrator = myNPTxyz; |
1489 |
|
break; |
1490 |
|
|
1491 |
|
default: |