| 191 |
|
|
| 192 |
|
if( oldOrtho != orthoRhombic ){ |
| 193 |
|
|
| 194 |
< |
if( orthoRhombic ){ |
| 194 |
> |
if( orthoRhombic ) { |
| 195 |
|
sprintf( painCave.errMsg, |
| 196 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
| 196 |
> |
"\n\tOOPSE is switching from the default Non-Orthorhombic\n" |
| 197 |
|
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 198 |
|
"\tThis is usually a good thing, but if you wan't the\n" |
| 199 |
|
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 200 |
|
"\tvariable ( currently set to %G ) smaller.\n", |
| 201 |
|
orthoTolerance); |
| 202 |
+ |
painCave.severity = OOPSE_INFO; |
| 203 |
|
simError(); |
| 204 |
|
} |
| 205 |
|
else { |
| 206 |
|
sprintf( painCave.errMsg, |
| 207 |
< |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 207 |
> |
"\n\tOOPSE is switching from the faster Orthorhombic to the more\n" |
| 208 |
|
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 209 |
|
"\tThis is usually because the box has deformed under\n" |
| 210 |
|
"\tNPTf integration. If you wan't to live on the edge with\n" |
| 211 |
|
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 212 |
|
"\tvariable ( currently set to %G ) larger.\n", |
| 213 |
|
orthoTolerance); |
| 214 |
+ |
painCave.severity = OOPSE_WARNING; |
| 215 |
|
simError(); |
| 216 |
|
} |
| 217 |
|
} |
| 455 |
|
|
| 456 |
|
isError = 0; |
| 457 |
|
|
| 458 |
< |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
| 458 |
> |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
| 459 |
|
//it may not be a good idea to pass the address of first element in vector |
| 460 |
|
//since c++ standard does not require vector to be stored continuously in meomory |
| 461 |
|
//Most of the compilers will organize the memory of vector continuously |
| 462 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 463 |
|
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 464 |
< |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
| 465 |
< |
|
| 464 |
> |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
| 465 |
> |
|
| 466 |
|
if( isError ){ |
| 467 |
|
|
| 468 |
|
sprintf( painCave.errMsg, |
| 506 |
|
|
| 507 |
|
if( rCut > maxCutoff ){ |
| 508 |
|
sprintf( painCave.errMsg, |
| 509 |
< |
"cutoffRadius is too large for the current periodic box.\n" |
| 509 |
> |
"\n\tcutoffRadius is too large for the current periodic box.\n" |
| 510 |
|
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
| 511 |
|
"\tThis is larger than half of at least one of the\n" |
| 512 |
|
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 518 |
|
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 519 |
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 520 |
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 521 |
+ |
painCave.severity = OOPSE_ERROR; |
| 522 |
|
painCave.isFatal = 1; |
| 523 |
|
simError(); |
| 524 |
|
} |
| 525 |
|
} else { |
| 526 |
|
// initialize this stuff before using it, OK? |
| 527 |
|
sprintf( painCave.errMsg, |
| 528 |
< |
"Trying to check cutoffs without a box.\n" |
| 528 |
> |
"\n\tTrying to check cutoffs without a box.\n" |
| 529 |
|
"\tOOPSE should have better programmers than that.\n" ); |
| 530 |
+ |
painCave.severity = OOPSE_ERROR; |
| 531 |
|
painCave.isFatal = 1; |
| 532 |
|
simError(); |
| 533 |
|
} |
| 571 |
|
} |
| 572 |
|
|
| 573 |
|
|
| 574 |
< |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
| 575 |
< |
vector<int>& groupList, vector<int>& groupStart){ |
| 574 |
> |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
| 575 |
> |
vector<int>& FglobalGroupMembership, |
| 576 |
> |
vector<double>& mfact){ |
| 577 |
> |
|
| 578 |
|
Molecule* myMols; |
| 579 |
|
Atom** myAtoms; |
| 580 |
|
int numAtom; |
| 575 |
– |
int curIndex; |
| 581 |
|
double mtot; |
| 582 |
|
int numMol; |
| 583 |
|
int numCutoffGroups; |
| 589 |
|
double totalMass; |
| 590 |
|
|
| 591 |
|
mfact.clear(); |
| 592 |
< |
groupList.clear(); |
| 588 |
< |
groupStart.clear(); |
| 592 |
> |
FglobalGroupMembership.clear(); |
| 593 |
|
|
| 590 |
– |
//Be careful, fortran array begin at 1 |
| 591 |
– |
curIndex = 1; |
| 594 |
|
|
| 595 |
+ |
// Fix the silly fortran indexing problem |
| 596 |
+ |
#ifdef IS_MPI |
| 597 |
+ |
numAtom = mpiSim->getNAtomsGlobal(); |
| 598 |
+ |
#else |
| 599 |
+ |
numAtom = n_atoms; |
| 600 |
+ |
#endif |
| 601 |
+ |
for (int i = 0; i < numAtom; i++) |
| 602 |
+ |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
| 603 |
+ |
|
| 604 |
+ |
|
| 605 |
|
myMols = info->molecules; |
| 606 |
|
numMol = info->n_mol; |
| 607 |
|
for(int i = 0; i < numMol; i++){ |
| 608 |
|
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 609 |
< |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
| 610 |
< |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 609 |
> |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
| 610 |
> |
myCutoffGroup != NULL; |
| 611 |
> |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 612 |
|
|
| 613 |
|
totalMass = myCutoffGroup->getMass(); |
| 614 |
|
|
| 615 |
< |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 616 |
< |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 615 |
> |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
| 616 |
> |
cutoffAtom != NULL; |
| 617 |
> |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 618 |
|
mfact.push_back(cutoffAtom->getMass()/totalMass); |
| 605 |
– |
#ifdef IS_MPI |
| 606 |
– |
groupList.push_back(cutoffAtom->getGlobalIndex() + 1); |
| 607 |
– |
#else |
| 608 |
– |
groupList.push_back(cutoffAtom->getIndex() + 1); |
| 609 |
– |
#endif |
| 619 |
|
} |
| 620 |
< |
|
| 621 |
< |
groupStart.push_back(curIndex); |
| 613 |
< |
curIndex += myCutoffGroup->getNumAtom(); |
| 620 |
> |
} |
| 621 |
> |
} |
| 622 |
|
|
| 615 |
– |
}//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
| 616 |
– |
|
| 617 |
– |
}//end for(int i = 0; i < numMol; i++) |
| 618 |
– |
|
| 619 |
– |
|
| 620 |
– |
//The last cutoff group need more element to indicate the end of the cutoff |
| 621 |
– |
ngroup = groupStart.size(); |
| 623 |
|
} |
