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Comparing trunk/OOPSE/libmdtools/simulation_module.F90 (file contents):
Revision 1183 by gezelter, Fri May 21 15:58:48 2004 UTC vs.
Revision 1217 by gezelter, Tue Jun 1 21:45:22 2004 UTC

# Line 23 | Line 23 | module simulation
23    logical, save :: simulation_setup_complete = .false.
24  
25    integer, public, save :: nLocal, nGlobal
26 <  integer, public, save :: nGroup, nGroupGlobal
26 >  integer, public, save :: nGroups, nGroupGlobal
27    integer, public, save :: nExcludes_Global = 0
28    integer, public, save :: nExcludes_Local = 0
29    integer, allocatable, dimension(:,:), public :: excludesLocal
30    integer, allocatable, dimension(:),   public :: excludesGlobal
31    integer, allocatable, dimension(:),   public :: molMembershipList
32 <  integer, allocatable, dimension(:),   public :: groupList
33 <  integer, allocatable, dimension(:),   public :: groupStart
32 >  integer, allocatable, dimension(:),   public :: groupListRow
33 >  integer, allocatable, dimension(:),   public :: groupStartRow
34 >  integer, allocatable, dimension(:),   public :: groupListCol
35 >  integer, allocatable, dimension(:),   public :: groupStartCol
36 >  integer, allocatable, dimension(:),   public :: groupListLocal
37 >  integer, allocatable, dimension(:),   public :: groupStartLocal
38    integer, allocatable, dimension(:),   public :: nSkipsForAtom
39    integer, allocatable, dimension(:,:), public :: skipsForAtom
40 <  real(kind=dp), allocatable, dimension(:), public :: mfact
40 >  real(kind=dp), allocatable, dimension(:), public :: mfactRow
41 >  real(kind=dp), allocatable, dimension(:), public :: mfactCol
42 >  real(kind=dp), allocatable, dimension(:), public :: mfactLocal
43  
44    real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv
45    logical, public, save :: boxIsOrthorhombic
# Line 58 | Line 64 | contains
64    
65    subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, &
66         CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, &
67 <       CmolMembership, Cmfact, CnGroup, CgroupList, CgroupStart, &
67 >       CmolMembership, Cmfact, CnGroups, CglobalGroupMembership, &
68         status)    
69  
70      type (simtype) :: setThisSim
# Line 73 | Line 79 | contains
79      !!  Result status, success = 0, status = -1
80      integer, intent(out) :: status
81      integer :: i, j, me, thisStat, alloc_stat, myNode, id1, id2
82 <    integer :: gStart, gEnd, groupSize, biggestGroupSize, ia
82 >    integer :: ia
83  
84      !! mass factors used for molecular cutoffs
85      real ( kind = dp ), dimension(CnLocal) :: Cmfact
86 <    integer, intent(in):: CnGroup
87 <    integer, dimension(CnLocal),intent(in) :: CgroupList
88 <    integer, dimension(CnGroup),intent(in) :: CgroupStart
83 <    integer :: maxSkipsForAtom
86 >    integer, intent(in):: CnGroups
87 >    integer, dimension(CnGlobal), intent(in):: CglobalGroupMembership
88 >    integer :: maxSkipsForAtom, glPointer
89  
90   #ifdef IS_MPI
91      integer, allocatable, dimension(:) :: c_idents_Row
92      integer, allocatable, dimension(:) :: c_idents_Col
93 <    integer :: nrow
94 <    integer :: ncol
93 >    integer :: nAtomsInRow, nGroupsInRow, aid
94 >    integer :: nAtomsInCol, nGroupsInCol, gid
95   #endif  
96  
97      simulation_setup_complete = .false.
# Line 96 | Line 101 | contains
101  
102      nLocal = CnLocal
103      nGlobal = CnGlobal
104 <    nGroup = CnGroup
104 >    nGroups = CnGroups
105  
106      thisSim = setThisSim
107  
# Line 124 | Line 129 | contains
129         status = -1
130         return
131      endif
132 <    nrow = getNrow(plan_row)
133 <    ncol = getNcol(plan_col)
132 >    nAtomsInRow = getNatomsInRow(plan_atom_row)
133 >    nAtomsInCol = getNatomsInCol(plan_atom_col)
134 >    nGroupsInRow = getNgroupsInRow(plan_group_row)
135 >    nGroupsInCol = getNgroupsInCol(plan_group_col)
136      mynode = getMyNode()
137      
138 <    allocate(c_idents_Row(nrow),stat=alloc_stat)
138 >    allocate(c_idents_Row(nAtomsInRow),stat=alloc_stat)
139      if (alloc_stat /= 0 ) then
140         status = -1
141         return
142      endif
143  
144 <    allocate(c_idents_Col(ncol),stat=alloc_stat)
144 >    allocate(c_idents_Col(nAtomsInCol),stat=alloc_stat)
145      if (alloc_stat /= 0 ) then
146         status = -1
147         return
148      endif
149  
150 <    call gather(c_idents, c_idents_Row, plan_row)
151 <    call gather(c_idents, c_idents_Col, plan_col)
150 >    call gather(c_idents, c_idents_Row, plan_atom_row)
151 >    call gather(c_idents, c_idents_Col, plan_atom_col)
152  
153 <    do i = 1, nrow
153 >    do i = 1, nAtomsInRow
154         me = getFirstMatchingElement(atypes, "c_ident", c_idents_Row(i))
155         atid_Row(i) = me
156      enddo
157  
158 <    do i = 1, ncol
158 >    do i = 1, nAtomsInCol
159         me = getFirstMatchingElement(atypes, "c_ident", c_idents_Col(i))
160         atid_Col(i) = me
161      enddo
# Line 159 | Line 166 | contains
166      end if
167      if (allocated(c_idents_Row)) then
168         deallocate(c_idents_Row)
169 +    endif
170 +  
171 + #endif
172 +
173 + #ifdef IS_MPI
174 +    allocate(groupStartRow(nGroupsInRow+1),stat=alloc_stat)
175 +    if (alloc_stat /= 0 ) then
176 +       status = -1
177 +       return
178 +    endif
179 +    allocate(groupStartCol(nGroupsInCol+1),stat=alloc_stat)
180 +    if (alloc_stat /= 0 ) then
181 +       status = -1
182 +       return
183 +    endif
184 +    allocate(groupListRow(nAtomsInRow),stat=alloc_stat)
185 +    if (alloc_stat /= 0 ) then
186 +       status = -1
187 +       return
188 +    endif
189 +    allocate(groupListCol(nAtomsInCol),stat=alloc_stat)
190 +    if (alloc_stat /= 0 ) then
191 +       status = -1
192 +       return
193 +    endif
194 +    allocate(mfactRow(nAtomsInRow),stat=alloc_stat)
195 +    if (alloc_stat /= 0 ) then
196 +       status = -1
197 +       return
198 +    endif
199 +    allocate(mfactCol(nAtomsInCol),stat=alloc_stat)
200 +    if (alloc_stat /= 0 ) then
201 +       status = -1
202 +       return
203 +    endif
204 +    allocate(mfactLocal(nLocal),stat=alloc_stat)
205 +    if (alloc_stat /= 0 ) then
206 +       status = -1
207 +       return
208 +    endif
209 +    
210 +    glPointer = 1
211 +
212 +    do i = 1, nGroupsInRow
213 +
214 +       gid = GroupRowToGlobal(i)
215 +       groupStartRow(i) = glPointer      
216 +
217 +       do j = 1, nAtomsInRow
218 +          aid = AtomRowToGlobal(j)
219 +          if (CglobalGroupMembership(aid) .eq. gid) then
220 +             groupListRow(glPointer) = j
221 +             glPointer = glPointer + 1
222 +          endif
223 +       enddo
224 +    enddo
225 +    groupStartRow(nGroupsInRow+1) = nAtomsInRow + 1
226 +
227 +    glPointer = 1
228 +
229 +    do i = 1, nGroupsInCol
230 +
231 +       gid = GroupColToGlobal(i)
232 +       groupStartCol(i) = glPointer      
233 +
234 +       do j = 1, nAtomsInCol
235 +          aid = AtomColToGlobal(j)
236 +          if (CglobalGroupMembership(aid) .eq. gid) then
237 +             groupListCol(glPointer) = j
238 +             glPointer = glPointer + 1
239 +          endif
240 +       enddo
241 +    enddo
242 +    groupStartCol(nGroupsInCol+1) = nAtomsInCol + 1
243 +
244 +    mfactLocal = Cmfact        
245 +
246 +    call gather(mfactLocal,      mfactRow,      plan_atom_row)
247 +    call gather(mfactLocal,      mfactCol,      plan_atom_col)
248 +    
249 +    if (allocated(mfactLocal)) then
250 +       deallocate(mfactLocal)
251 +    end if
252 + #else
253 +    allocate(groupStartRow(nGroups+1),stat=alloc_stat)
254 +    if (alloc_stat /= 0 ) then
255 +       status = -1
256 +       return
257 +    endif
258 +    allocate(groupStartCol(nGroups+1),stat=alloc_stat)
259 +    if (alloc_stat /= 0 ) then
260 +       status = -1
261 +       return
262 +    endif
263 +    allocate(groupListRow(nLocal),stat=alloc_stat)
264 +    if (alloc_stat /= 0 ) then
265 +       status = -1
266 +       return
267      endif
268 +    allocate(groupListCol(nLocal),stat=alloc_stat)
269 +    if (alloc_stat /= 0 ) then
270 +       status = -1
271 +       return
272 +    endif
273 +    allocate(mfactRow(nLocal),stat=alloc_stat)
274 +    if (alloc_stat /= 0 ) then
275 +       status = -1
276 +       return
277 +    endif
278 +    allocate(mfactCol(nLocal),stat=alloc_stat)
279 +    if (alloc_stat /= 0 ) then
280 +       status = -1
281 +       return
282 +    endif
283 +    allocate(mfactLocal(nLocal),stat=alloc_stat)
284 +    if (alloc_stat /= 0 ) then
285 +       status = -1
286 +       return
287 +    endif
288 +
289 +    glPointer = 1
290 +    do i = 1, nGroups
291 +       groupStartRow(i) = glPointer      
292 +       groupStartCol(i) = glPointer
293 +       do j = 1, nLocal
294 +          if (CglobalGroupMembership(j) .eq. i) then
295 +             groupListRow(glPointer) = j
296 +             groupListCol(glPointer) = j
297 +             glPointer = glPointer + 1
298 +          endif
299 +       enddo
300 +    enddo
301 +    groupStartRow(nGroups+1) = nLocal + 1
302 +    groupStartCol(nGroups+1) = nLocal + 1
303 +
304 +    do i = 1, nLocal
305 +       mfactRow(i) = Cmfact(i)
306 +       mfactCol(i) = Cmfact(i)
307 +    end do
308      
309   #endif
310  
311 +
312   ! We build the local atid's for both mpi and nonmpi
313      do i = 1, nLocal
314        
# Line 176 | Line 322 | contains
322         excludesLocal(2,i) = CexcludesLocal(2,i)
323      enddo
324  
325 + #ifdef IS_MPI
326 +    allocate(nSkipsForAtom(nAtomsInRow), stat=alloc_stat)
327 + #else
328 +    allocate(nSkipsForAtom(nLocal), stat=alloc_stat)
329 + #endif
330 +    if (alloc_stat /= 0 ) then
331 +       thisStat = -1
332 +       write(*,*) 'Could not allocate nSkipsForAtom array'
333 +       return
334 +    endif
335 +
336      maxSkipsForAtom = 0
337 + #ifdef IS_MPI
338 +    do j = 1, nAtomsInRow
339 + #else
340      do j = 1, nLocal
341 + #endif
342         nSkipsForAtom(j) = 0
343   #ifdef IS_MPI
344 <       id1 = tagRow(j)
344 >       id1 = AtomRowToGlobal(j)
345   #else
346         id1 = j
347   #endif
# Line 202 | Line 363 | contains
363         end do
364      enddo
365  
366 + #ifdef IS_MPI
367 +    allocate(skipsForAtom(nAtomsInRow, maxSkipsForAtom), stat=alloc_stat)
368 + #else
369      allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat)
370 + #endif
371      if (alloc_stat /= 0 ) then
372         write(*,*) 'Could not allocate skipsForAtom array'
373         return
374      endif
375  
376 + #ifdef IS_MPI
377 +    do j = 1, nAtomsInRow
378 + #else
379      do j = 1, nLocal
380 + #endif
381         nSkipsForAtom(j) = 0
382   #ifdef IS_MPI
383 <       id1 = tagRow(j)
383 >       id1 = AtomRowToGlobal(j)
384   #else
385         id1 = j
386   #endif
387         do i = 1, nExcludes_Local
388            if (excludesLocal(1,i) .eq. id1 ) then
389               nSkipsForAtom(j) = nSkipsForAtom(j) + 1
390 < #ifdef IS_MPI
391 <             id2 = tagColumn(excludesLocal(2,i))
223 < #else
390 >             ! exclude lists have global ID's so this line is
391 >             ! the same in MPI and non-MPI
392               id2 = excludesLocal(2,i)
225 – #endif
393               skipsForAtom(j, nSkipsForAtom(j)) = id2
394            endif
395 <          if (excludesLocal(2, i) .eq. id2 ) then
395 >          if (excludesLocal(2, i) .eq. id1 ) then
396               nSkipsForAtom(j) = nSkipsForAtom(j) + 1
397 < #ifdef IS_MPI
398 <             id2 = tagColumn(excludesLocal(1,i))
232 < #else
397 >             ! exclude lists have global ID's so this line is
398 >             ! the same in MPI and non-MPI
399               id2 = excludesLocal(1,i)
234 – #endif
400               skipsForAtom(j, nSkipsForAtom(j)) = id2
401            endif
402         end do
# Line 245 | Line 410 | contains
410         molMemberShipList(i) = CmolMembership(i)
411      enddo
412      
248 –    biggestGroupSize = 0
249 –    do i = 1, nGroup
250 –       groupStart(i) = CgroupStart(i)
251 –       groupSize = 0
252 –       gStart = groupStart(i)      
253 –       if (i .eq. nGroup) then
254 –          gEnd = nLocal
255 –       else
256 –          gEnd = CgroupStart(i+1) - 1
257 –       endif
258 –       do ia = gStart, gEnd
259 –          groupList(ia) = CgroupList(ia)
260 –          groupSize = groupSize + 1
261 –       enddo
262 –       if (groupSize .gt. biggestGroupSize) biggestGroupSize = groupSize      
263 –    enddo
264 –    groupStart(nGroup+1) = nLocal+1
265 –
266 –    do i = 1, nLocal
267 –       mfact(i) = Cmfact(i)
268 –    enddo    
269 –    
413      if (status == 0) simulation_setup_complete = .true.
414      
415    end subroutine SimulationSetup
# Line 355 | Line 498 | contains
498      thisStat = 0
499      
500      call FreeSimGlobals()    
358 –
359 –    allocate(nSkipsForAtom(nLocal), stat=alloc_stat)
360 –    if (alloc_stat /= 0 ) then
361 –       thisStat = -1
362 –       return
363 –    endif
501      
502      allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat)
503      if (alloc_stat /= 0 ) then
# Line 379 | Line 516 | contains
516         thisStat = -1
517         return
518      endif
382 –
383 –    allocate(groupStart(nGroup+1), stat=alloc_stat)
384 –    if (alloc_stat /= 0 ) then
385 –       thisStat = -1
386 –       return
387 –    endif
388 –
389 –    allocate(groupList(nLocal), stat=alloc_stat)
390 –    if (alloc_stat /= 0 ) then
391 –       thisStat = -1
392 –       return
393 –    endif
394 –
395 –    allocate(mfact(nLocal), stat=alloc_stat)
396 –    if (alloc_stat /= 0 ) then
397 –       thisStat = -1
398 –       return
399 –    endif
519      
520    end subroutine InitializeSimGlobals
521    
# Line 405 | Line 524 | contains
524      !We free in the opposite order in which we allocate in.
525  
526      if (allocated(skipsForAtom)) deallocate(skipsForAtom)
527 <    if (allocated(mfact)) deallocate(mfact)
528 <    if (allocated(groupList)) deallocate(groupList)    
529 <    if (allocated(groupStart)) deallocate(groupStart)    
527 >    if (allocated(nSkipsForAtom)) deallocate(nSkipsForAtom)
528 >    if (allocated(mfactLocal)) deallocate(mfactLocal)
529 >    if (allocated(mfactCol)) deallocate(mfactCol)
530 >    if (allocated(mfactRow)) deallocate(mfactRow)
531 >    if (allocated(groupListCol)) deallocate(groupListCol)    
532 >    if (allocated(groupListRow)) deallocate(groupListRow)    
533 >    if (allocated(groupStartCol)) deallocate(groupStartCol)
534 >    if (allocated(groupStartRow)) deallocate(groupStartRow)    
535      if (allocated(molMembershipList)) deallocate(molMembershipList)    
536      if (allocated(excludesGlobal)) deallocate(excludesGlobal)
537      if (allocated(excludesLocal)) deallocate(excludesLocal)

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