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> |
5 |
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#include <string> |
6 |
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#include <sprng.h> |
7 |
– |
|
7 |
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#include "SimSetup.hpp" |
8 |
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#include "ReadWrite.hpp" |
9 |
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#include "parse_me.h" |
21 |
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#define NVT_ENS 1 |
22 |
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#define NPTi_ENS 2 |
23 |
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#define NPTf_ENS 3 |
24 |
< |
#define NPTim_ENS 4 |
26 |
< |
#define NPTfm_ENS 5 |
24 |
> |
#define NPTxyz_ENS 4 |
25 |
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|
26 |
+ |
|
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 |
31 |
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using namespace std; |
32 |
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|
33 |
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SimSetup::SimSetup(){ |
34 |
+ |
|
35 |
+ |
initSuspend = false; |
36 |
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isInfoArray = 0; |
37 |
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nInfo = 1; |
38 |
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|
55 |
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info = the_info; |
56 |
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nInfo = theNinfo; |
57 |
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isInfoArray = 1; |
58 |
+ |
initSuspend = true; |
59 |
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} |
60 |
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|
61 |
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|
94 |
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#endif // is_mpi |
95 |
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|
96 |
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void SimSetup::createSim(void){ |
95 |
– |
int i, j, k, globalAtomIndex; |
97 |
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|
98 |
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// gather all of the information from the Bass file |
99 |
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|
103 |
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|
104 |
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sysObjectsCreation(); |
105 |
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|
105 |
– |
// check on the post processing info |
106 |
– |
|
107 |
– |
finalInfoCheck(); |
108 |
– |
|
106 |
|
// initialize the system coordinates |
107 |
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|
108 |
< |
if (!isInfoArray){ |
108 |
> |
if ( !initSuspend ){ |
109 |
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initSystemCoords(); |
110 |
+ |
|
111 |
+ |
if( !(globals->getUseInitTime()) ) |
112 |
+ |
info[0].currentTime = 0.0; |
113 |
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} |
114 |
+ |
|
115 |
+ |
// check on the post processing info |
116 |
+ |
|
117 |
+ |
finalInfoCheck(); |
118 |
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|
119 |
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// make the output filenames |
120 |
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|
135 |
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|
136 |
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|
137 |
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void SimSetup::makeMolecules(void){ |
138 |
< |
int k, l; |
138 |
> |
int k; |
139 |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
140 |
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molInit molInfo; |
141 |
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DirectionalAtom* dAtom; |
557 |
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|
558 |
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|
559 |
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void SimSetup::gatherInfo(void){ |
560 |
< |
int i, j, k; |
560 |
> |
int i; |
561 |
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|
562 |
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ensembleCase = -1; |
563 |
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ffCase = -1; |
608 |
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else if (!strcasecmp(ensemble, "NPTf")){ |
609 |
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ensembleCase = NPTf_ENS; |
610 |
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} |
611 |
< |
else if (!strcasecmp(ensemble, "NPTim")){ |
612 |
< |
ensembleCase = NPTim_ENS; |
609 |
< |
} |
610 |
< |
else if (!strcasecmp(ensemble, "NPTfm")){ |
611 |
< |
ensembleCase = NPTfm_ENS; |
611 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
612 |
> |
ensembleCase = NPTxyz_ENS; |
613 |
|
} |
614 |
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else{ |
615 |
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sprintf(painCave.errMsg, |
689 |
|
info[i].thermalTime = globals->getThermalTime(); |
690 |
|
} |
691 |
|
|
692 |
< |
// check for the temperature set flag |
692 |
> |
info[i].resetIntegrator = 0; |
693 |
> |
if( globals->haveResetTime() ){ |
694 |
> |
info[i].resetTime = globals->getResetTime(); |
695 |
> |
info[i].resetIntegrator = 1; |
696 |
> |
} |
697 |
|
|
698 |
+ |
// check for the temperature set flag |
699 |
+ |
|
700 |
|
if (globals->haveTempSet()) |
701 |
|
info[i].setTemp = globals->getTempSet(); |
702 |
< |
|
696 |
< |
// get some of the tricky things that may still be in the globals |
697 |
< |
|
698 |
< |
double boxVector[3]; |
699 |
< |
if (globals->haveBox()){ |
700 |
< |
boxVector[0] = globals->getBox(); |
701 |
< |
boxVector[1] = globals->getBox(); |
702 |
< |
boxVector[2] = globals->getBox(); |
703 |
< |
|
704 |
< |
info[i].setBox(boxVector); |
705 |
< |
} |
706 |
< |
else if (globals->haveDensity()){ |
707 |
< |
double vol; |
708 |
< |
vol = (double) tot_nmol / globals->getDensity(); |
709 |
< |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
710 |
< |
boxVector[1] = boxVector[0]; |
711 |
< |
boxVector[2] = boxVector[0]; |
712 |
< |
|
713 |
< |
info[i].setBox(boxVector); |
714 |
< |
} |
715 |
< |
else{ |
716 |
< |
if (!globals->haveBoxX()){ |
717 |
< |
sprintf(painCave.errMsg, |
718 |
< |
"SimSetup error, no periodic BoxX size given.\n"); |
719 |
< |
painCave.isFatal = 1; |
720 |
< |
simError(); |
721 |
< |
} |
722 |
< |
boxVector[0] = globals->getBoxX(); |
723 |
< |
|
724 |
< |
if (!globals->haveBoxY()){ |
725 |
< |
sprintf(painCave.errMsg, |
726 |
< |
"SimSetup error, no periodic BoxY size given.\n"); |
727 |
< |
painCave.isFatal = 1; |
728 |
< |
simError(); |
729 |
< |
} |
730 |
< |
boxVector[1] = globals->getBoxY(); |
731 |
< |
|
732 |
< |
if (!globals->haveBoxZ()){ |
733 |
< |
sprintf(painCave.errMsg, |
734 |
< |
"SimSetup error, no periodic BoxZ size given.\n"); |
735 |
< |
painCave.isFatal = 1; |
736 |
< |
simError(); |
737 |
< |
} |
738 |
< |
boxVector[2] = globals->getBoxZ(); |
739 |
< |
|
740 |
< |
info[i].setBox(boxVector); |
741 |
< |
} |
702 |
> |
|
703 |
|
} |
704 |
< |
|
704 |
> |
|
705 |
|
//setup seed for random number generator |
706 |
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int seedValue; |
707 |
|
|
805 |
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theEst = globals->getEST(); |
806 |
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} |
807 |
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|
808 |
< |
info[i].setEcr(theEcr, theEst); |
808 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
809 |
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|
810 |
|
if (!globals->haveDielectric()){ |
811 |
|
sprintf(painCave.errMsg, |
850 |
|
theEst = globals->getEST(); |
851 |
|
} |
852 |
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|
853 |
< |
info[i].setEcr(theEcr, theEst); |
853 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
854 |
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} |
855 |
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} |
856 |
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} |
877 |
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if (worldRank == 0){ |
878 |
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#endif //is_mpi |
879 |
|
inName = globals->getInitialConfig(); |
919 |
– |
double* tempDouble = new double[1000000]; |
880 |
|
fileInit = new InitializeFromFile(inName); |
881 |
|
#ifdef IS_MPI |
882 |
|
} |
894 |
|
|
895 |
|
sprintf(painCave.errMsg, |
896 |
|
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
897 |
< |
painCave.isFatal; |
897 |
> |
painCave.isFatal = 1;; |
898 |
|
simError(); |
899 |
|
|
900 |
|
#else |
1120 |
|
} |
1121 |
|
|
1122 |
|
void SimSetup::calcSysValues(void){ |
1123 |
< |
int i, j, k; |
1123 |
> |
int i; |
1124 |
|
|
1125 |
|
int* molMembershipArray; |
1126 |
|
|
1219 |
|
|
1220 |
|
|
1221 |
|
void SimSetup::makeSysArrays(void){ |
1222 |
< |
int i, j, k, l; |
1222 |
> |
|
1223 |
> |
#ifndef IS_MPI |
1224 |
> |
int k, j; |
1225 |
> |
#endif // is_mpi |
1226 |
> |
int i, l; |
1227 |
|
|
1228 |
|
Atom** the_atoms; |
1229 |
|
Molecule* the_molecules; |
1306 |
|
void SimSetup::makeIntegrator(void){ |
1307 |
|
int k; |
1308 |
|
|
1309 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1310 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1311 |
< |
NPTi<RealIntegrator>* myNPTi = NULL; |
1312 |
< |
NPTf<RealIntegrator>* myNPTf = NULL; |
1313 |
< |
NPTim<RealIntegrator>* myNPTim = NULL; |
1349 |
< |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1311 |
> |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1312 |
> |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1313 |
> |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1314 |
|
|
1315 |
|
for (k = 0; k < nInfo; k++){ |
1316 |
|
switch (ensembleCase){ |
1317 |
|
case NVE_ENS: |
1318 |
|
if (globals->haveZconstraints()){ |
1319 |
|
setupZConstraint(info[k]); |
1320 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1320 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1321 |
|
} |
1322 |
< |
else |
1323 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1322 |
> |
else{ |
1323 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1324 |
> |
} |
1325 |
> |
|
1326 |
> |
info->the_integrator = myNVE; |
1327 |
|
break; |
1328 |
|
|
1329 |
|
case NVT_ENS: |
1345 |
|
painCave.isFatal = 1; |
1346 |
|
simError(); |
1347 |
|
} |
1348 |
+ |
|
1349 |
+ |
info->the_integrator = myNVT; |
1350 |
|
break; |
1351 |
|
|
1352 |
|
case NPTi_ENS: |
1353 |
|
if (globals->haveZconstraints()){ |
1354 |
|
setupZConstraint(info[k]); |
1355 |
< |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff); |
1355 |
> |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1356 |
|
} |
1357 |
|
else |
1358 |
< |
myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff); |
1358 |
> |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1359 |
|
|
1360 |
|
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1361 |
|
|
1388 |
|
painCave.isFatal = 1; |
1389 |
|
simError(); |
1390 |
|
} |
1391 |
+ |
|
1392 |
+ |
info->the_integrator = myNPTi; |
1393 |
|
break; |
1394 |
|
|
1395 |
|
case NPTf_ENS: |
1396 |
|
if (globals->haveZconstraints()){ |
1397 |
|
setupZConstraint(info[k]); |
1398 |
< |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1398 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1399 |
|
} |
1400 |
|
else |
1401 |
< |
myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1401 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1402 |
|
|
1403 |
|
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1404 |
|
|
1431 |
|
painCave.isFatal = 1; |
1432 |
|
simError(); |
1433 |
|
} |
1434 |
+ |
|
1435 |
+ |
info->the_integrator = myNPTf; |
1436 |
|
break; |
1437 |
|
|
1438 |
< |
case NPTim_ENS: |
1438 |
> |
case NPTxyz_ENS: |
1439 |
|
if (globals->haveZconstraints()){ |
1440 |
|
setupZConstraint(info[k]); |
1441 |
< |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1441 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1442 |
|
} |
1443 |
|
else |
1444 |
< |
myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1444 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1445 |
|
|
1446 |
< |
myNPTim->setTargetTemp(globals->getTargetTemp()); |
1446 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1447 |
|
|
1448 |
|
if (globals->haveTargetPressure()) |
1449 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1449 |
> |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1450 |
|
else{ |
1451 |
|
sprintf(painCave.errMsg, |
1452 |
|
"SimSetup error: If you use a constant pressure\n" |
1453 |
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
1454 |
|
painCave.isFatal = 1; |
1455 |
|
simError(); |
1456 |
< |
} |
1456 |
> |
} |
1457 |
|
|
1458 |
|
if (globals->haveTauThermostat()) |
1459 |
< |
myNPTim->setTauThermostat(globals->getTauThermostat()); |
1459 |
> |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1460 |
|
else{ |
1461 |
|
sprintf(painCave.errMsg, |
1462 |
|
"SimSetup error: If you use an NPT\n" |
1466 |
|
} |
1467 |
|
|
1468 |
|
if (globals->haveTauBarostat()) |
1469 |
< |
myNPTim->setTauBarostat(globals->getTauBarostat()); |
1469 |
> |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1470 |
|
else{ |
1471 |
|
sprintf(painCave.errMsg, |
1472 |
|
"SimSetup error: If you use an NPT\n" |
1474 |
|
painCave.isFatal = 1; |
1475 |
|
simError(); |
1476 |
|
} |
1504 |
– |
break; |
1477 |
|
|
1478 |
< |
case NPTfm_ENS: |
1507 |
< |
if (globals->haveZconstraints()){ |
1508 |
< |
setupZConstraint(info[k]); |
1509 |
< |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1510 |
< |
} |
1511 |
< |
else |
1512 |
< |
myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1513 |
< |
|
1514 |
< |
myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1515 |
< |
|
1516 |
< |
if (globals->haveTargetPressure()) |
1517 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1518 |
< |
else{ |
1519 |
< |
sprintf(painCave.errMsg, |
1520 |
< |
"SimSetup error: If you use a constant pressure\n" |
1521 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1522 |
< |
painCave.isFatal = 1; |
1523 |
< |
simError(); |
1524 |
< |
} |
1525 |
< |
|
1526 |
< |
if (globals->haveTauThermostat()) |
1527 |
< |
myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1528 |
< |
else{ |
1529 |
< |
sprintf(painCave.errMsg, |
1530 |
< |
"SimSetup error: If you use an NPT\n" |
1531 |
< |
" ensemble, you must set tauThermostat.\n"); |
1532 |
< |
painCave.isFatal = 1; |
1533 |
< |
simError(); |
1534 |
< |
} |
1535 |
< |
|
1536 |
< |
if (globals->haveTauBarostat()) |
1537 |
< |
myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1538 |
< |
else{ |
1539 |
< |
sprintf(painCave.errMsg, |
1540 |
< |
"SimSetup error: If you use an NPT\n" |
1541 |
< |
" ensemble, you must set tauBarostat.\n"); |
1542 |
< |
painCave.isFatal = 1; |
1543 |
< |
simError(); |
1544 |
< |
} |
1478 |
> |
info->the_integrator = myNPTxyz; |
1479 |
|
break; |
1480 |
|
|
1481 |
|
default: |
1549 |
|
} |
1550 |
|
theInfo.addProperty(zconsTol); |
1551 |
|
|
1552 |
< |
//set Force Substraction Policy |
1552 |
> |
//set Force Subtraction Policy |
1553 |
|
StringData* zconsForcePolicy = new StringData(); |
1554 |
|
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1555 |
|
|
1558 |
|
} |
1559 |
|
else{ |
1560 |
|
sprintf(painCave.errMsg, |
1561 |
< |
"ZConstraint Warning: User does not set force substraction policy, " |
1561 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
1562 |
|
"PolicyByMass is used\n"); |
1563 |
|
painCave.isFatal = 0; |
1564 |
|
simError(); |