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Comparing trunk/OOPSE/libmdtools/simulation_module.F90 (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1206 by tim, Thu May 27 19:51:18 2004 UTC

# Line 6 | Line 6 | module simulation
6    use force_globals
7    use vector_class
8    use atype_module
9 +  use switcheroo
10   #ifdef IS_MPI
11    use mpiSimulation
12   #endif
# Line 15 | Line 16 | module simulation
16  
17   #define __FORTRAN90
18   #include "fSimulation.h"
19 + #include "fSwitchingFunction.h"
20  
21 <  type (simtype), public :: thisSim
21 >  type (simtype), public, save :: thisSim
22  
23    logical, save :: simulation_setup_complete = .false.
24  
25    integer, public, save :: nLocal, nGlobal
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
30 >  integer, allocatable, dimension(:),   public :: excludesGlobal
31 >  integer, allocatable, dimension(:),   public :: molMembershipList
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 :: 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 36 | Line 50 | module simulation
50    public :: getDielect
51    public :: SimUsesPBC
52    public :: SimUsesLJ
53 +  public :: SimUsesCharges
54    public :: SimUsesDipoles
55    public :: SimUsesSticky
56    public :: SimUsesRF
# Line 49 | Line 64 | contains
64    
65    subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, &
66         CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, &
67 <       CmolMembership, &
67 >       CmolMembership, Cmfact, CnGroups, CgroupList, CgroupStart, &
68         status)    
69  
70      type (simtype) :: setThisSim
# Line 63 | Line 78 | contains
78      integer, dimension(CnGlobal),intent(in) :: CmolMembership
79      !!  Result status, success = 0, status = -1
80      integer, intent(out) :: status
81 <    integer :: i, me, thisStat, alloc_stat, myNode
81 >    integer :: i, j, me, thisStat, alloc_stat, myNode, id1, id2
82 >    integer :: ia
83 >
84 >    !! mass factors used for molecular cutoffs
85 >    real ( kind = dp ), dimension(CnLocal) :: Cmfact
86 >    integer, intent(in):: CnGroups
87 >    integer, dimension(CnLocal),intent(in) :: CgroupList
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 78 | Line 102 | contains
102  
103      nLocal = CnLocal
104      nGlobal = CnGlobal
105 +    nGroups = CnGroups
106  
107      thisSim = setThisSim
108  
# Line 105 | 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 141 | 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        
313         me = getFirstMatchingElement(atypes, "c_ident", c_idents(i))
314         atid(i) = me
315    
316      enddo
152 – #endif
317  
154 –
155 –
318      do i = 1, nExcludes_Local
319         excludesLocal(1,i) = CexcludesLocal(1,i)
320         excludesLocal(2,i) = CexcludesLocal(2,i)
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 = AtomRowToGlobal(j)
332 + #else
333 +       id1 = j
334 + #endif
335 +       do i = 1, nExcludes_Local
336 +          if (excludesLocal(1,i) .eq. id1 ) then
337 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
338 +
339 +             if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then
340 +                maxSkipsForAtom = nSkipsForAtom(j)
341 +             endif
342 +          endif
343 +          if (excludesLocal(2,i) .eq. id1 ) then
344 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
345 +
346 +             if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then
347 +                maxSkipsForAtom = nSkipsForAtom(j)
348 +             endif
349 +          endif
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 = 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 +             ! exclude lists have global ID's so this line is
378 +             ! the same in MPI and non-MPI
379 +             id2 = excludesLocal(2,i)
380 +             skipsForAtom(j, nSkipsForAtom(j)) = id2
381 +          endif
382 +          if (excludesLocal(2, i) .eq. id2 ) then
383 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
384 +             ! exclude lists have global ID's so this line is
385 +             ! the same in MPI and non-MPI
386 +             id2 = excludesLocal(1,i)
387 +             skipsForAtom(j, nSkipsForAtom(j)) = id2
388 +          endif
389 +       end do
390 +    enddo
391      
392      do i = 1, nExcludes_Global
393         excludesGlobal(i) = CexcludesGlobal(i)
# Line 164 | Line 395 | contains
395  
396      do i = 1, nGlobal
397         molMemberShipList(i) = CmolMembership(i)
398 <     enddo
399 <
398 >    enddo
399 >    
400      if (status == 0) simulation_setup_complete = .true.
401      
402    end subroutine SimulationSetup
# Line 206 | Line 437 | contains
437      doesit = thisSim%SIM_uses_sticky
438    end function SimUsesSticky
439  
440 +  function SimUsesCharges() result(doesit)
441 +    logical :: doesit
442 +    doesit = thisSim%SIM_uses_charges
443 +  end function SimUsesCharges
444 +
445    function SimUsesDipoles() result(doesit)
446      logical :: doesit
447      doesit = thisSim%SIM_uses_dipoles
# Line 249 | Line 485 | contains
485      thisStat = 0
486      
487      call FreeSimGlobals()    
488 +
489 +    allocate(nSkipsForAtom(nLocal), stat=alloc_stat)
490 +    if (alloc_stat /= 0 ) then
491 +       thisStat = -1
492 +       return
493 +    endif
494      
495      allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat)
496      if (alloc_stat /= 0 ) then
# Line 274 | Line 516 | contains
516      
517      !We free in the opposite order in which we allocate in.
518  
519 +    if (allocated(skipsForAtom)) deallocate(skipsForAtom)
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)
529 <
529 >    
530    end subroutine FreeSimGlobals
531 <
531 >  
532    pure function getNlocal() result(n)
533      integer :: n
534      n = nLocal
535    end function getNlocal
287 –
536    
537 +  
538   end module simulation

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