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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 1206 by tim, Thu May 27 19:51:18 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, CgroupList, CgroupStart, &
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
86 >    integer, intent(in):: CnGroups
87      integer, dimension(CnLocal),intent(in) :: CgroupList
88 <    integer, dimension(CnGroup),intent(in) :: CgroupStart
88 >    integer, dimension(CnGroups),intent(in) :: CgroupStart
89      integer :: maxSkipsForAtom
90  
91   #ifdef IS_MPI
92      integer, allocatable, dimension(:) :: c_idents_Row
93      integer, allocatable, dimension(:) :: c_idents_Col
94 <    integer :: nrow
95 <    integer :: ncol
94 >    integer :: nAtomsInRow, nGroupsInRow
95 >    integer :: nAtomsInCol, nGroupsInCol
96   #endif  
97  
98      simulation_setup_complete = .false.
# Line 96 | Line 102 | contains
102  
103      nLocal = CnLocal
104      nGlobal = CnGlobal
105 <    nGroup = CnGroup
105 >    nGroups = CnGroups
106  
107      thisSim = setThisSim
108  
# Line 124 | Line 130 | contains
130         status = -1
131         return
132      endif
133 <    nrow = getNrow(plan_row)
134 <    ncol = getNcol(plan_col)
133 >    nAtomsInRow = getNatomsInRow(plan_atom_row)
134 >    nAtomsInCol = getNatomsInCol(plan_atom_col)
135 >    nGroupsInRow = getNgroupsInRow(plan_group_row)
136 >    nGroupsInCol = getNgroupsInCol(plan_group_col)
137      mynode = getMyNode()
138      
139 <    allocate(c_idents_Row(nrow),stat=alloc_stat)
139 >    allocate(c_idents_Row(nAtomsInRow),stat=alloc_stat)
140      if (alloc_stat /= 0 ) then
141         status = -1
142         return
143      endif
144  
145 <    allocate(c_idents_Col(ncol),stat=alloc_stat)
145 >    allocate(c_idents_Col(nAtomsInCol),stat=alloc_stat)
146      if (alloc_stat /= 0 ) then
147         status = -1
148         return
149      endif
150  
151 <    call gather(c_idents, c_idents_Row, plan_row)
152 <    call gather(c_idents, c_idents_Col, plan_col)
151 >    call gather(c_idents, c_idents_Row, plan_atom_row)
152 >    call gather(c_idents, c_idents_Col, plan_atom_col)
153  
154 <    do i = 1, nrow
154 >    do i = 1, nAtomsInRow
155         me = getFirstMatchingElement(atypes, "c_ident", c_idents_Row(i))
156         atid_Row(i) = me
157      enddo
158  
159 <    do i = 1, ncol
159 >    do i = 1, nAtomsInCol
160         me = getFirstMatchingElement(atypes, "c_ident", c_idents_Col(i))
161         atid_Col(i) = me
162      enddo
# Line 160 | Line 168 | contains
168      if (allocated(c_idents_Row)) then
169         deallocate(c_idents_Row)
170      endif
171 +  
172 + #endif
173 +
174 + #ifdef IS_MPI
175 +    allocate(groupStartRow(nGroupsInRow+1),stat=alloc_stat)
176 +    if (alloc_stat /= 0 ) then
177 +       status = -1
178 +       return
179 +    endif
180 +    allocate(groupStartCol(nGroupsInCol+1),stat=alloc_stat)
181 +    if (alloc_stat /= 0 ) then
182 +       status = -1
183 +       return
184 +    endif
185 +    allocate(groupListRow(nAtomsInRow),stat=alloc_stat)
186 +    if (alloc_stat /= 0 ) then
187 +       status = -1
188 +       return
189 +    endif
190 +    allocate(groupListCol(nAtomsInCol),stat=alloc_stat)
191 +    if (alloc_stat /= 0 ) then
192 +       status = -1
193 +       return
194 +    endif
195 +    allocate(mfactRow(nAtomsInRow),stat=alloc_stat)
196 +    if (alloc_stat /= 0 ) then
197 +       status = -1
198 +       return
199 +    endif
200 +    allocate(mfactCol(nAtomsInCol),stat=alloc_stat)
201 +    if (alloc_stat /= 0 ) then
202 +       status = -1
203 +       return
204 +    endif
205 +    allocate(groupStartLocal(nGroups), stat=alloc_stat)
206 +    if (alloc_stat /= 0 ) then
207 +       status = -1
208 +       return
209 +    endif
210 +    allocate(groupListLocal(nLocal), stat=alloc_stat)
211 +    if (alloc_stat /= 0 ) then
212 +       status = -1
213 +       return
214 +    endif    
215 +    allocate(mfactLocal(nLocal), stat=alloc_stat)
216 +    if (alloc_stat /= 0 ) then
217 +       status = -1
218 +       return
219 +    endif    
220 +            
221 +    groupStartLocal = CgroupStart
222 +    groupListLocal = CgroupList
223 +    mfactLocal = Cmfact        
224 +            
225 +    call gather(groupStartLocal, groupStartRow, plan_group_row)
226 +    call gather(groupStartLocal, groupStartCol, plan_group_col)  
227 +    groupStartRow(nGroupsInRow+1) = nAtomsInRow + 1
228 +    groupStartCol(nGroupsInCol+1) = nAtomsInCol + 1
229 +    call gather(groupListLocal,  groupListRow,  plan_atom_row)
230 +    call gather(groupListLocal,  groupListCol,  plan_atom_col)
231 +
232 +    ! C passes us groupList as globalID numbers for the atoms
233 +    ! we need to remap these onto the row and column ids on this
234 +    ! processor.  This is a linear search, but is only done once
235 +    ! (we hope)
236 +
237 +    do i = 1, nAtomsInRow
238 +       do j = 1, nAtomsInRow
239 +          if (AtomRowToGlobal(j) .eq. groupListRow(i)) then
240 +             groupListRow(i) = j
241 +          endif
242 +       enddo
243 +    enddo
244 +    do i = 1, nAtomsInCol
245 +       do j = 1, nAtomsInCol
246 +          if (AtomColToGlobal(j) .eq. groupListCol(i)) then
247 +             groupListCol(i) = j
248 +          endif
249 +       enddo
250 +    enddo
251 +    call gather(mfactLocal,      mfactRow,      plan_atom_row)
252 +    call gather(mfactLocal,      mfactCol,      plan_atom_col)
253      
254 +    if (allocated(mfactLocal)) then
255 +       deallocate(mfactLocal)
256 +    end if
257 +    if (allocated(groupListLocal)) then
258 +       deallocate(groupListLocal)
259 +    endif
260 +    if (allocated(groupStartLocal)) then
261 +       deallocate(groupStartLocal)
262 +    endif
263 + #else
264 +    allocate(groupStartRow(nGroups+1),stat=alloc_stat)
265 +    if (alloc_stat /= 0 ) then
266 +       status = -1
267 +       return
268 +    endif
269 +    allocate(groupStartCol(nGroups+1),stat=alloc_stat)
270 +    if (alloc_stat /= 0 ) then
271 +       status = -1
272 +       return
273 +    endif
274 +    allocate(groupListRow(nLocal),stat=alloc_stat)
275 +    if (alloc_stat /= 0 ) then
276 +       status = -1
277 +       return
278 +    endif
279 +    allocate(groupListCol(nLocal),stat=alloc_stat)
280 +    if (alloc_stat /= 0 ) then
281 +       status = -1
282 +       return
283 +    endif
284 +    allocate(mfactRow(nLocal),stat=alloc_stat)
285 +    if (alloc_stat /= 0 ) then
286 +       status = -1
287 +       return
288 +    endif
289 +    allocate(mfactCol(nLocal),stat=alloc_stat)
290 +    if (alloc_stat /= 0 ) then
291 +       status = -1
292 +       return
293 +    endif
294 +    do i = 1, nGroups
295 +       groupStartRow(i) = CgroupStart(i)
296 +       groupStartCol(i) = CgroupStart(i)
297 +    end do
298 +    groupStartRow(nGroups+1) = nLocal + 1
299 +    groupStartCol(nGroups+1) = nLocal + 1
300 +    do i = 1, nLocal
301 +       groupListRow(i) = CgroupList(i)
302 +       groupListCol(i) = CgroupList(i)
303 +       mfactRow(i) = Cmfact(i)
304 +       mfactCol(i) = Cmfact(i)
305 +    end do
306 +    
307   #endif
308  
309 +
310   ! We build the local atid's for both mpi and nonmpi
311      do i = 1, nLocal
312        
# Line 177 | Line 321 | contains
321      enddo
322  
323      maxSkipsForAtom = 0
324 + #ifdef IS_MPI
325 +    do j = 1, nAtomsInRow
326 + #else
327      do j = 1, nLocal
328 + #endif
329         nSkipsForAtom(j) = 0
330   #ifdef IS_MPI
331 <       id1 = tagRow(j)
331 >       id1 = AtomRowToGlobal(j)
332   #else
333         id1 = j
334   #endif
# Line 202 | Line 350 | contains
350         end do
351      enddo
352  
353 + #ifdef IS_MPI
354 +    allocate(skipsForAtom(nAtomsInRow, maxSkipsForAtom), stat=alloc_stat)
355 + #else
356      allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat)
357 + #endif
358      if (alloc_stat /= 0 ) then
359         write(*,*) 'Could not allocate skipsForAtom array'
360         return
361      endif
362  
363 + #ifdef IS_MPI
364 +    do j = 1, nAtomsInRow
365 + #else
366      do j = 1, nLocal
367 + #endif
368         nSkipsForAtom(j) = 0
369   #ifdef IS_MPI
370 <       id1 = tagRow(j)
370 >       id1 = AtomRowToGlobal(j)
371   #else
372         id1 = j
373   #endif
374         do i = 1, nExcludes_Local
375            if (excludesLocal(1,i) .eq. id1 ) then
376               nSkipsForAtom(j) = nSkipsForAtom(j) + 1
377 < #ifdef IS_MPI
378 <             id2 = tagColumn(excludesLocal(2,i))
223 < #else
377 >             ! exclude lists have global ID's so this line is
378 >             ! the same in MPI and non-MPI
379               id2 = excludesLocal(2,i)
225 – #endif
380               skipsForAtom(j, nSkipsForAtom(j)) = id2
381            endif
382            if (excludesLocal(2, i) .eq. id2 ) then
383               nSkipsForAtom(j) = nSkipsForAtom(j) + 1
384 < #ifdef IS_MPI
385 <             id2 = tagColumn(excludesLocal(1,i))
232 < #else
384 >             ! exclude lists have global ID's so this line is
385 >             ! the same in MPI and non-MPI
386               id2 = excludesLocal(1,i)
234 – #endif
387               skipsForAtom(j, nSkipsForAtom(j)) = id2
388            endif
389         end do
# Line 245 | Line 397 | contains
397         molMemberShipList(i) = CmolMembership(i)
398      enddo
399      
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 –    
400      if (status == 0) simulation_setup_complete = .true.
401      
402    end subroutine SimulationSetup
# Line 379 | Line 509 | contains
509         thisStat = -1
510         return
511      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
512      
513    end subroutine InitializeSimGlobals
514    
# Line 405 | Line 517 | contains
517      !We free in the opposite order in which we allocate in.
518  
519      if (allocated(skipsForAtom)) deallocate(skipsForAtom)
520 <    if (allocated(mfact)) deallocate(mfact)
521 <    if (allocated(groupList)) deallocate(groupList)    
522 <    if (allocated(groupStart)) deallocate(groupStart)    
520 >    if (allocated(mfactCol)) deallocate(mfactCol)
521 >    if (allocated(mfactRow)) deallocate(mfactRow)
522 >    if (allocated(groupListCol)) deallocate(groupListCol)    
523 >    if (allocated(groupListRow)) deallocate(groupListRow)    
524 >    if (allocated(groupStartCol)) deallocate(groupStartCol)
525 >    if (allocated(groupStartRow)) deallocate(groupStartRow)    
526      if (allocated(molMembershipList)) deallocate(molMembershipList)    
527      if (allocated(excludesGlobal)) deallocate(excludesGlobal)
528      if (allocated(excludesLocal)) deallocate(excludesLocal)

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