84 |
|
|
85 |
|
real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
86 |
|
logical, public, save :: boxIsOrthorhombic |
87 |
< |
|
87 |
> |
|
88 |
|
public :: SimulationSetup |
89 |
|
public :: getNlocal |
90 |
|
public :: setBox |
105 |
|
public :: SimRequiresPrepairCalc |
106 |
|
public :: SimRequiresPostpairCalc |
107 |
|
|
108 |
< |
|
108 |
> |
|
109 |
|
contains |
110 |
< |
|
110 |
> |
|
111 |
|
subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, & |
112 |
|
CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, & |
113 |
|
CmolMembership, Cmfact, CnGroups, CglobalGroupMembership, & |
180 |
|
nGroupsInRow = getNgroupsInRow(plan_group_row) |
181 |
|
nGroupsInCol = getNgroupsInCol(plan_group_col) |
182 |
|
mynode = getMyNode() |
183 |
< |
|
183 |
> |
|
184 |
|
allocate(c_idents_Row(nAtomsInRow),stat=alloc_stat) |
185 |
|
if (alloc_stat /= 0 ) then |
186 |
|
status = -1 |
213 |
|
if (allocated(c_idents_Row)) then |
214 |
|
deallocate(c_idents_Row) |
215 |
|
endif |
216 |
< |
|
216 |
> |
|
217 |
|
#endif |
218 |
|
|
219 |
|
#ifdef IS_MPI |
252 |
|
status = -1 |
253 |
|
return |
254 |
|
endif |
255 |
< |
|
255 |
> |
|
256 |
|
glPointer = 1 |
257 |
|
|
258 |
|
do i = 1, nGroupsInRow |
291 |
|
|
292 |
|
call gather(mfactLocal, mfactRow, plan_atom_row) |
293 |
|
call gather(mfactLocal, mfactCol, plan_atom_col) |
294 |
< |
|
294 |
> |
|
295 |
|
if (allocated(mfactLocal)) then |
296 |
|
deallocate(mfactLocal) |
297 |
|
end if |
351 |
|
mfactRow(i) = Cmfact(i) |
352 |
|
mfactCol(i) = Cmfact(i) |
353 |
|
end do |
354 |
< |
|
354 |
> |
|
355 |
|
#endif |
356 |
|
|
357 |
|
|
358 |
< |
! We build the local atid's for both mpi and nonmpi |
358 |
> |
! We build the local atid's for both mpi and nonmpi |
359 |
|
do i = 1, nLocal |
360 |
< |
|
360 |
> |
|
361 |
|
me = getFirstMatchingElement(atypes, "c_ident", c_idents(i)) |
362 |
|
atid(i) = me |
363 |
< |
|
363 |
> |
|
364 |
|
enddo |
365 |
|
|
366 |
|
do i = 1, nExcludes_Local |
383 |
|
#ifdef IS_MPI |
384 |
|
do j = 1, nAtomsInRow |
385 |
|
#else |
386 |
< |
do j = 1, nLocal |
386 |
> |
do j = 1, nLocal |
387 |
|
#endif |
388 |
< |
nSkipsForAtom(j) = 0 |
388 |
> |
nSkipsForAtom(j) = 0 |
389 |
|
#ifdef IS_MPI |
390 |
< |
id1 = AtomRowToGlobal(j) |
390 |
> |
id1 = AtomRowToGlobal(j) |
391 |
|
#else |
392 |
< |
id1 = j |
392 |
> |
id1 = j |
393 |
|
#endif |
394 |
< |
do i = 1, nExcludes_Local |
395 |
< |
if (excludesLocal(1,i) .eq. id1 ) then |
396 |
< |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
394 |
> |
do i = 1, nExcludes_Local |
395 |
> |
if (excludesLocal(1,i) .eq. id1 ) then |
396 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
397 |
|
|
398 |
< |
if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
399 |
< |
maxSkipsForAtom = nSkipsForAtom(j) |
398 |
> |
if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
399 |
> |
maxSkipsForAtom = nSkipsForAtom(j) |
400 |
> |
endif |
401 |
|
endif |
402 |
< |
endif |
403 |
< |
if (excludesLocal(2,i) .eq. id1 ) then |
403 |
< |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
402 |
> |
if (excludesLocal(2,i) .eq. id1 ) then |
403 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
404 |
|
|
405 |
< |
if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
406 |
< |
maxSkipsForAtom = nSkipsForAtom(j) |
405 |
> |
if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
406 |
> |
maxSkipsForAtom = nSkipsForAtom(j) |
407 |
> |
endif |
408 |
|
endif |
409 |
< |
endif |
410 |
< |
end do |
410 |
< |
enddo |
409 |
> |
end do |
410 |
> |
enddo |
411 |
|
|
412 |
|
#ifdef IS_MPI |
413 |
< |
allocate(skipsForAtom(nAtomsInRow, maxSkipsForAtom), stat=alloc_stat) |
413 |
> |
allocate(skipsForAtom(nAtomsInRow, maxSkipsForAtom), stat=alloc_stat) |
414 |
|
#else |
415 |
< |
allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat) |
415 |
> |
allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat) |
416 |
|
#endif |
417 |
< |
if (alloc_stat /= 0 ) then |
418 |
< |
write(*,*) 'Could not allocate skipsForAtom array' |
419 |
< |
return |
420 |
< |
endif |
417 |
> |
if (alloc_stat /= 0 ) then |
418 |
> |
write(*,*) 'Could not allocate skipsForAtom array' |
419 |
> |
return |
420 |
> |
endif |
421 |
|
|
422 |
|
#ifdef IS_MPI |
423 |
< |
do j = 1, nAtomsInRow |
423 |
> |
do j = 1, nAtomsInRow |
424 |
|
#else |
425 |
< |
do j = 1, nLocal |
425 |
> |
do j = 1, nLocal |
426 |
|
#endif |
427 |
< |
nSkipsForAtom(j) = 0 |
427 |
> |
nSkipsForAtom(j) = 0 |
428 |
|
#ifdef IS_MPI |
429 |
< |
id1 = AtomRowToGlobal(j) |
429 |
> |
id1 = AtomRowToGlobal(j) |
430 |
|
#else |
431 |
< |
id1 = j |
431 |
> |
id1 = j |
432 |
|
#endif |
433 |
< |
do i = 1, nExcludes_Local |
434 |
< |
if (excludesLocal(1,i) .eq. id1 ) then |
435 |
< |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
436 |
< |
! exclude lists have global ID's so this line is |
437 |
< |
! the same in MPI and non-MPI |
438 |
< |
id2 = excludesLocal(2,i) |
439 |
< |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
440 |
< |
endif |
441 |
< |
if (excludesLocal(2, i) .eq. id1 ) then |
442 |
< |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
443 |
< |
! exclude lists have global ID's so this line is |
444 |
< |
! the same in MPI and non-MPI |
445 |
< |
id2 = excludesLocal(1,i) |
446 |
< |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
447 |
< |
endif |
448 |
< |
end do |
449 |
< |
enddo |
450 |
< |
|
451 |
< |
do i = 1, nExcludes_Global |
452 |
< |
excludesGlobal(i) = CexcludesGlobal(i) |
453 |
< |
enddo |
433 |
> |
do i = 1, nExcludes_Local |
434 |
> |
if (excludesLocal(1,i) .eq. id1 ) then |
435 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
436 |
> |
! exclude lists have global ID's so this line is |
437 |
> |
! the same in MPI and non-MPI |
438 |
> |
id2 = excludesLocal(2,i) |
439 |
> |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
440 |
> |
endif |
441 |
> |
if (excludesLocal(2, i) .eq. id1 ) then |
442 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
443 |
> |
! exclude lists have global ID's so this line is |
444 |
> |
! the same in MPI and non-MPI |
445 |
> |
id2 = excludesLocal(1,i) |
446 |
> |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
447 |
> |
endif |
448 |
> |
end do |
449 |
> |
enddo |
450 |
|
|
451 |
< |
do i = 1, nGlobal |
452 |
< |
molMemberShipList(i) = CmolMembership(i) |
453 |
< |
enddo |
458 |
< |
|
459 |
< |
if (status == 0) simulation_setup_complete = .true. |
460 |
< |
|
461 |
< |
end subroutine SimulationSetup |
462 |
< |
|
463 |
< |
subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
464 |
< |
real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
465 |
< |
integer :: cBoxIsOrthorhombic |
466 |
< |
integer :: smallest, status, i |
467 |
< |
|
468 |
< |
Hmat = cHmat |
469 |
< |
HmatInv = cHmatInv |
470 |
< |
if (cBoxIsOrthorhombic .eq. 0 ) then |
471 |
< |
boxIsOrthorhombic = .false. |
472 |
< |
else |
473 |
< |
boxIsOrthorhombic = .true. |
474 |
< |
endif |
475 |
< |
|
476 |
< |
return |
477 |
< |
end subroutine setBox |
451 |
> |
do i = 1, nExcludes_Global |
452 |
> |
excludesGlobal(i) = CexcludesGlobal(i) |
453 |
> |
enddo |
454 |
|
|
455 |
< |
function getDielect() result(dielect) |
456 |
< |
real( kind = dp ) :: dielect |
457 |
< |
dielect = thisSim%dielect |
482 |
< |
end function getDielect |
483 |
< |
|
484 |
< |
function SimUsesPBC() result(doesit) |
485 |
< |
logical :: doesit |
486 |
< |
doesit = thisSim%SIM_uses_PBC |
487 |
< |
end function SimUsesPBC |
455 |
> |
do i = 1, nGlobal |
456 |
> |
molMemberShipList(i) = CmolMembership(i) |
457 |
> |
enddo |
458 |
|
|
459 |
< |
function SimUsesDirectionalAtoms() result(doesit) |
490 |
< |
logical :: doesit |
491 |
< |
doesit = thisSim%SIM_uses_dipoles .or. thisSim%SIM_uses_sticky .or. & |
492 |
< |
thisSim%SIM_uses_GayBerne .or. thisSim%SIM_uses_Shapes |
493 |
< |
end function SimUsesDirectionalAtoms |
459 |
> |
if (status == 0) simulation_setup_complete = .true. |
460 |
|
|
461 |
< |
function SimUsesLennardJones() result(doesit) |
496 |
< |
logical :: doesit |
497 |
< |
doesit = thisSim%SIM_uses_LennardJones |
498 |
< |
end function SimUsesLennardJones |
461 |
> |
end subroutine SimulationSetup |
462 |
|
|
463 |
< |
function SimUsesElectrostatics() result(doesit) |
464 |
< |
logical :: doesit |
465 |
< |
doesit = thisSim%SIM_uses_Electrostatics |
466 |
< |
end function SimUsesElectrostatics |
463 |
> |
subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
464 |
> |
real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
465 |
> |
integer :: cBoxIsOrthorhombic |
466 |
> |
integer :: smallest, status, i |
467 |
|
|
468 |
< |
function SimUsesCharges() result(doesit) |
469 |
< |
logical :: doesit |
470 |
< |
doesit = thisSim%SIM_uses_Charges |
471 |
< |
end function SimUsesCharges |
468 |
> |
Hmat = cHmat |
469 |
> |
HmatInv = cHmatInv |
470 |
> |
if (cBoxIsOrthorhombic .eq. 0 ) then |
471 |
> |
boxIsOrthorhombic = .false. |
472 |
> |
else |
473 |
> |
boxIsOrthorhombic = .true. |
474 |
> |
endif |
475 |
|
|
476 |
< |
function SimUsesDipoles() result(doesit) |
477 |
< |
logical :: doesit |
512 |
< |
doesit = thisSim%SIM_uses_Dipoles |
513 |
< |
end function SimUsesDipoles |
476 |
> |
return |
477 |
> |
end subroutine setBox |
478 |
|
|
479 |
< |
function SimUsesSticky() result(doesit) |
480 |
< |
logical :: doesit |
481 |
< |
doesit = thisSim%SIM_uses_Sticky |
482 |
< |
end function SimUsesSticky |
519 |
< |
|
520 |
< |
function SimUsesGayBerne() result(doesit) |
521 |
< |
logical :: doesit |
522 |
< |
doesit = thisSim%SIM_uses_GayBerne |
523 |
< |
end function SimUsesGayBerne |
524 |
< |
|
525 |
< |
function SimUsesEAM() result(doesit) |
526 |
< |
logical :: doesit |
527 |
< |
doesit = thisSim%SIM_uses_EAM |
528 |
< |
end function SimUsesEAM |
479 |
> |
function getDielect() result(dielect) |
480 |
> |
real( kind = dp ) :: dielect |
481 |
> |
dielect = thisSim%dielect |
482 |
> |
end function getDielect |
483 |
|
|
484 |
< |
function SimUsesShapes() result(doesit) |
485 |
< |
logical :: doesit |
486 |
< |
doesit = thisSim%SIM_uses_Shapes |
487 |
< |
end function SimUsesShapes |
484 |
> |
function SimUsesPBC() result(doesit) |
485 |
> |
logical :: doesit |
486 |
> |
doesit = thisSim%SIM_uses_PBC |
487 |
> |
end function SimUsesPBC |
488 |
|
|
489 |
< |
function SimUsesFLARB() result(doesit) |
490 |
< |
logical :: doesit |
491 |
< |
doesit = thisSim%SIM_uses_FLARB |
492 |
< |
end function SimUsesFLARB |
489 |
> |
function SimUsesDirectionalAtoms() result(doesit) |
490 |
> |
logical :: doesit |
491 |
> |
doesit = thisSim%SIM_uses_dipoles .or. thisSim%SIM_uses_sticky .or. & |
492 |
> |
thisSim%SIM_uses_GayBerne .or. thisSim%SIM_uses_Shapes |
493 |
> |
end function SimUsesDirectionalAtoms |
494 |
|
|
495 |
< |
function SimUsesRF() result(doesit) |
496 |
< |
logical :: doesit |
497 |
< |
doesit = thisSim%SIM_uses_RF |
498 |
< |
end function SimUsesRF |
495 |
> |
function SimUsesLennardJones() result(doesit) |
496 |
> |
logical :: doesit |
497 |
> |
doesit = thisSim%SIM_uses_LennardJones |
498 |
> |
end function SimUsesLennardJones |
499 |
|
|
500 |
< |
function SimRequiresPrepairCalc() result(doesit) |
501 |
< |
logical :: doesit |
502 |
< |
doesit = thisSim%SIM_uses_EAM |
503 |
< |
end function SimRequiresPrepairCalc |
500 |
> |
function SimUsesElectrostatics() result(doesit) |
501 |
> |
logical :: doesit |
502 |
> |
doesit = thisSim%SIM_uses_Electrostatics |
503 |
> |
end function SimUsesElectrostatics |
504 |
|
|
505 |
< |
function SimRequiresPostpairCalc() result(doesit) |
506 |
< |
logical :: doesit |
507 |
< |
doesit = thisSim%SIM_uses_RF |
508 |
< |
end function SimRequiresPostpairCalc |
554 |
< |
|
555 |
< |
subroutine InitializeSimGlobals(thisStat) |
556 |
< |
integer, intent(out) :: thisStat |
557 |
< |
integer :: alloc_stat |
558 |
< |
|
559 |
< |
thisStat = 0 |
560 |
< |
|
561 |
< |
call FreeSimGlobals() |
562 |
< |
|
563 |
< |
allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat) |
564 |
< |
if (alloc_stat /= 0 ) then |
565 |
< |
thisStat = -1 |
566 |
< |
return |
567 |
< |
endif |
568 |
< |
|
569 |
< |
allocate(excludesGlobal(nExcludes_Global), stat=alloc_stat) |
570 |
< |
if (alloc_stat /= 0 ) then |
571 |
< |
thisStat = -1 |
572 |
< |
return |
573 |
< |
endif |
505 |
> |
function SimUsesCharges() result(doesit) |
506 |
> |
logical :: doesit |
507 |
> |
doesit = thisSim%SIM_uses_Charges |
508 |
> |
end function SimUsesCharges |
509 |
|
|
510 |
< |
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
511 |
< |
if (alloc_stat /= 0 ) then |
512 |
< |
thisStat = -1 |
513 |
< |
return |
579 |
< |
endif |
580 |
< |
|
581 |
< |
end subroutine InitializeSimGlobals |
582 |
< |
|
583 |
< |
subroutine FreeSimGlobals() |
584 |
< |
|
585 |
< |
!We free in the opposite order in which we allocate in. |
510 |
> |
function SimUsesDipoles() result(doesit) |
511 |
> |
logical :: doesit |
512 |
> |
doesit = thisSim%SIM_uses_Dipoles |
513 |
> |
end function SimUsesDipoles |
514 |
|
|
515 |
< |
if (allocated(skipsForAtom)) deallocate(skipsForAtom) |
516 |
< |
if (allocated(nSkipsForAtom)) deallocate(nSkipsForAtom) |
517 |
< |
if (allocated(mfactLocal)) deallocate(mfactLocal) |
518 |
< |
if (allocated(mfactCol)) deallocate(mfactCol) |
519 |
< |
if (allocated(mfactRow)) deallocate(mfactRow) |
520 |
< |
if (allocated(groupListCol)) deallocate(groupListCol) |
521 |
< |
if (allocated(groupListRow)) deallocate(groupListRow) |
522 |
< |
if (allocated(groupStartCol)) deallocate(groupStartCol) |
523 |
< |
if (allocated(groupStartRow)) deallocate(groupStartRow) |
524 |
< |
if (allocated(molMembershipList)) deallocate(molMembershipList) |
525 |
< |
if (allocated(excludesGlobal)) deallocate(excludesGlobal) |
526 |
< |
if (allocated(excludesLocal)) deallocate(excludesLocal) |
527 |
< |
|
528 |
< |
end subroutine FreeSimGlobals |
529 |
< |
|
530 |
< |
pure function getNlocal() result(n) |
531 |
< |
integer :: n |
532 |
< |
n = nLocal |
533 |
< |
end function getNlocal |
534 |
< |
|
535 |
< |
end module simulation |
515 |
> |
function SimUsesSticky() result(doesit) |
516 |
> |
logical :: doesit |
517 |
> |
doesit = thisSim%SIM_uses_Sticky |
518 |
> |
end function SimUsesSticky |
519 |
> |
|
520 |
> |
function SimUsesGayBerne() result(doesit) |
521 |
> |
logical :: doesit |
522 |
> |
doesit = thisSim%SIM_uses_GayBerne |
523 |
> |
end function SimUsesGayBerne |
524 |
> |
|
525 |
> |
function SimUsesEAM() result(doesit) |
526 |
> |
logical :: doesit |
527 |
> |
doesit = thisSim%SIM_uses_EAM |
528 |
> |
end function SimUsesEAM |
529 |
> |
|
530 |
> |
function SimUsesShapes() result(doesit) |
531 |
> |
logical :: doesit |
532 |
> |
doesit = thisSim%SIM_uses_Shapes |
533 |
> |
end function SimUsesShapes |
534 |
> |
|
535 |
> |
function SimUsesFLARB() result(doesit) |
536 |
> |
logical :: doesit |
537 |
> |
doesit = thisSim%SIM_uses_FLARB |
538 |
> |
end function SimUsesFLARB |
539 |
> |
|
540 |
> |
function SimUsesRF() result(doesit) |
541 |
> |
logical :: doesit |
542 |
> |
doesit = thisSim%SIM_uses_RF |
543 |
> |
end function SimUsesRF |
544 |
> |
|
545 |
> |
function SimRequiresPrepairCalc() result(doesit) |
546 |
> |
logical :: doesit |
547 |
> |
doesit = thisSim%SIM_uses_EAM |
548 |
> |
end function SimRequiresPrepairCalc |
549 |
> |
|
550 |
> |
function SimRequiresPostpairCalc() result(doesit) |
551 |
> |
logical :: doesit |
552 |
> |
doesit = thisSim%SIM_uses_RF |
553 |
> |
end function SimRequiresPostpairCalc |
554 |
> |
|
555 |
> |
subroutine InitializeSimGlobals(thisStat) |
556 |
> |
integer, intent(out) :: thisStat |
557 |
> |
integer :: alloc_stat |
558 |
> |
|
559 |
> |
thisStat = 0 |
560 |
> |
|
561 |
> |
call FreeSimGlobals() |
562 |
> |
|
563 |
> |
allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat) |
564 |
> |
if (alloc_stat /= 0 ) then |
565 |
> |
thisStat = -1 |
566 |
> |
return |
567 |
> |
endif |
568 |
> |
|
569 |
> |
allocate(excludesGlobal(nExcludes_Global), stat=alloc_stat) |
570 |
> |
if (alloc_stat /= 0 ) then |
571 |
> |
thisStat = -1 |
572 |
> |
return |
573 |
> |
endif |
574 |
> |
|
575 |
> |
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
576 |
> |
if (alloc_stat /= 0 ) then |
577 |
> |
thisStat = -1 |
578 |
> |
return |
579 |
> |
endif |
580 |
> |
|
581 |
> |
end subroutine InitializeSimGlobals |
582 |
> |
|
583 |
> |
subroutine FreeSimGlobals() |
584 |
> |
|
585 |
> |
!We free in the opposite order in which we allocate in. |
586 |
> |
|
587 |
> |
if (allocated(skipsForAtom)) deallocate(skipsForAtom) |
588 |
> |
if (allocated(nSkipsForAtom)) deallocate(nSkipsForAtom) |
589 |
> |
if (allocated(mfactLocal)) deallocate(mfactLocal) |
590 |
> |
if (allocated(mfactCol)) deallocate(mfactCol) |
591 |
> |
if (allocated(mfactRow)) deallocate(mfactRow) |
592 |
> |
if (allocated(groupListCol)) deallocate(groupListCol) |
593 |
> |
if (allocated(groupListRow)) deallocate(groupListRow) |
594 |
> |
if (allocated(groupStartCol)) deallocate(groupStartCol) |
595 |
> |
if (allocated(groupStartRow)) deallocate(groupStartRow) |
596 |
> |
if (allocated(molMembershipList)) deallocate(molMembershipList) |
597 |
> |
if (allocated(excludesGlobal)) deallocate(excludesGlobal) |
598 |
> |
if (allocated(excludesLocal)) deallocate(excludesLocal) |
599 |
> |
|
600 |
> |
end subroutine FreeSimGlobals |
601 |
> |
|
602 |
> |
pure function getNlocal() result(n) |
603 |
> |
integer :: n |
604 |
> |
n = nLocal |
605 |
> |
end function getNlocal |
606 |
> |
|
607 |
> |
end module simulation |