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Comparing trunk/OOPSE/libmdtools/simulation_module.F90 (file contents):
Revision 491 by mmeineke, Fri Apr 11 18:46:37 2003 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 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), save :: rcut2 = 0.0_DP
45 <  real(kind=dp), save :: rcut6 = 0.0_DP
32 <  real(kind=dp), save :: rlist2 = 0.0_DP
33 <  real(kind=dp), public, dimension(3), save :: box
34 <
44 >  real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv
45 >  logical, public, save :: boxIsOrthorhombic
46    
47    public :: SimulationSetup
48    public :: getNlocal
49    public :: setBox
39 –  public :: setBox_3d
40 –  public :: getBox
41 –  public :: setRcut
42 –  public :: getRcut
43 –  public :: getRlist
44 –  public :: getRrf
45 –  public :: getRt
50    public :: getDielect
51    public :: SimUsesPBC
52    public :: SimUsesLJ
53 +  public :: SimUsesCharges
54    public :: SimUsesDipoles
55    public :: SimUsesSticky
56    public :: SimUsesRF
# Line 54 | Line 59 | module simulation
59    public :: SimRequiresPrepairCalc
60    public :: SimRequiresPostpairCalc
61    public :: SimUsesDirectionalAtoms
57 –
58 –  interface getBox
59 –     module procedure getBox_3d
60 –     module procedure getBox_1d
61 –  end interface
62    
63 –  interface setBox
64 –     module procedure setBox_3d
65 –     module procedure setBox_1d
66 –  end interface
67 –  
63   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 83 | 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 98 | Line 102 | contains
102  
103      nLocal = CnLocal
104      nGlobal = CnGlobal
105 +    nGroups = CnGroups
106  
107      thisSim = setThisSim
103 –    rcut2 = thisSim%rcut * thisSim%rcut
104 –    rcut6 = rcut2 * rcut2 * rcut2
105 –    rlist2 = thisSim%rlist * thisSim%rlist
106 –    box = thisSim%box
108  
109      nExcludes_Global = CnGlobalExcludes
110      nExcludes_Local = CnLocalExcludes
# Line 129 | 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 165 | 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
176 – #endif
317  
178 –
179 –
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 +    do j = 1, nLocal
325 +       nSkipsForAtom(j) = 0
326 + #ifdef IS_MPI
327 +       id1 = AtomRowToGlobal(j)
328 + #else
329 +       id1 = j
330 + #endif
331 +       do i = 1, nExcludes_Local
332 +          if (excludesLocal(1,i) .eq. id1 ) then
333 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
334 +
335 +             if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then
336 +                maxSkipsForAtom = nSkipsForAtom(j)
337 +             endif
338 +          endif
339 +          if (excludesLocal(2,i) .eq. id1 ) then
340 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
341 +
342 +             if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then
343 +                maxSkipsForAtom = nSkipsForAtom(j)
344 +             endif
345 +          endif
346 +       end do
347 +    enddo
348 +
349 +    allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat)
350 +    if (alloc_stat /= 0 ) then
351 +       write(*,*) 'Could not allocate skipsForAtom array'
352 +       return
353 +    endif
354 +
355 +    do j = 1, nLocal
356 +       nSkipsForAtom(j) = 0
357 + #ifdef IS_MPI
358 +       id1 = AtomRowToGlobal(j)
359 + #else
360 +       id1 = j
361 + #endif
362 +       do i = 1, nExcludes_Local
363 +          if (excludesLocal(1,i) .eq. id1 ) then
364 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
365 + #ifdef IS_MPI
366 +             id2 = AtomColToGlobal(excludesLocal(2,i))
367 + #else
368 +             id2 = excludesLocal(2,i)
369 + #endif
370 +             skipsForAtom(j, nSkipsForAtom(j)) = id2
371 +          endif
372 +          if (excludesLocal(2, i) .eq. id2 ) then
373 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
374 + #ifdef IS_MPI
375 +             id2 = AtomColToGlobal(excludesLocal(1,i))
376 + #else
377 +             id2 = excludesLocal(1,i)
378 + #endif
379 +             skipsForAtom(j, nSkipsForAtom(j)) = id2
380 +          endif
381 +       end do
382 +    enddo
383      
384      do i = 1, nExcludes_Global
385         excludesGlobal(i) = CexcludesGlobal(i)
# Line 188 | Line 387 | contains
387  
388      do i = 1, nGlobal
389         molMemberShipList(i) = CmolMembership(i)
390 <     enddo
391 <
390 >    enddo
391 >    
392      if (status == 0) simulation_setup_complete = .true.
393      
394    end subroutine SimulationSetup
395    
396 <  subroutine setBox_3d(new_box_size)
397 <    real(kind=dp), dimension(3) :: new_box_size
396 >  subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic)
397 >    real(kind=dp), dimension(3,3) :: cHmat, cHmatInv
398 >    integer :: cBoxIsOrthorhombic
399      integer :: smallest, status, i
200 –
201 –    thisSim%box = new_box_size
202 –    box = thisSim%box
203 –
204 –    return    
205 –  end subroutine setBox_3d
206 –
207 –  subroutine setBox_1d(dim, new_box_size)
208 –    integer :: dim, status
209 –    real(kind=dp) :: new_box_size
210 –    thisSim%box(dim) = new_box_size
211 –    box(dim) = thisSim%box(dim)
212 –  end subroutine setBox_1d
213 –
214 –  subroutine setRcut(new_rcut, status)
215 –    real(kind = dp) :: new_rcut
216 –    integer :: myStatus, status
217 –    thisSim%rcut = new_rcut
218 –    rcut2 = thisSim%rcut * thisSim%rcut
219 –    rcut6 = rcut2 * rcut2 * rcut2
220 –    status = 0
221 –    return
222 –  end subroutine setRcut
223 –
224 –  function getBox_3d() result(thisBox)
225 –    real( kind = dp ), dimension(3) :: thisBox
226 –    thisBox = thisSim%box
227 –  end function getBox_3d
228 –  
229 –  function getBox_1d(dim) result(thisBox)
230 –    integer, intent(in) :: dim
231 –    real( kind = dp ) :: thisBox
400      
401 <    thisBox = thisSim%box(dim)
402 <  end function getBox_1d
403 <    
404 <  subroutine getRcut(thisrcut,rc2,rc6,status)
405 <    real( kind = dp ), intent(out) :: thisrcut
406 <    real( kind = dp ), intent(out), optional :: rc2
407 <    real( kind = dp ), intent(out), optional :: rc6
240 <    integer, optional :: status
241 <
242 <    if (present(status)) status = 0
401 >    Hmat = cHmat
402 >    HmatInv = cHmatInv
403 >    if (cBoxIsOrthorhombic .eq. 0 ) then
404 >       boxIsOrthorhombic = .false.
405 >    else
406 >       boxIsOrthorhombic = .true.
407 >    endif
408      
409 <    if (.not.simulation_setup_complete ) then
410 <       if (present(status)) status = -1
246 <       return
247 <    end if
248 <    
249 <    thisrcut = thisSim%rcut
250 <    if(present(rc2)) rc2 = rcut2
251 <    if(present(rc6)) rc6 = rcut6
252 <  end subroutine getRcut
253 <  
254 <  subroutine getRlist(thisrlist,rl2,status)
255 <    real( kind = dp ), intent(out) :: thisrlist
256 <    real( kind = dp ), intent(out), optional :: rl2
409 >    return    
410 >  end subroutine setBox
411  
258 –    integer, optional :: status
259 –
260 –    if (present(status)) status = 0
261 –
262 –    if (.not.simulation_setup_complete ) then
263 –       if (present(status)) status = -1
264 –       return
265 –    end if
266 –    
267 –    thisrlist = thisSim%rlist
268 –    if(present(rl2)) rl2 = rlist2
269 –  end subroutine getRlist
270 –
271 –  function getRrf() result(rrf)
272 –    real( kind = dp ) :: rrf
273 –    rrf = thisSim%rrf
274 –    write(*,*) 'getRrf = ', rrf, thisSim%rrf
275 –  end function getRrf
276 –  
277 –  function getRt() result(rt)
278 –    real( kind = dp ) :: rt
279 –    rt = thisSim%rt
280 –  end function getRt
281 –
412    function getDielect() result(dielect)
413      real( kind = dp ) :: dielect
414      dielect = thisSim%dielect
# Line 299 | Line 429 | contains
429      doesit = thisSim%SIM_uses_sticky
430    end function SimUsesSticky
431  
432 +  function SimUsesCharges() result(doesit)
433 +    logical :: doesit
434 +    doesit = thisSim%SIM_uses_charges
435 +  end function SimUsesCharges
436 +
437    function SimUsesDipoles() result(doesit)
438      logical :: doesit
439      doesit = thisSim%SIM_uses_dipoles
# Line 342 | Line 477 | contains
477      thisStat = 0
478      
479      call FreeSimGlobals()    
480 +
481 +    allocate(nSkipsForAtom(nLocal), stat=alloc_stat)
482 +    if (alloc_stat /= 0 ) then
483 +       thisStat = -1
484 +       return
485 +    endif
486      
487      allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat)
488      if (alloc_stat /= 0 ) then
# Line 367 | Line 508 | contains
508      
509      !We free in the opposite order in which we allocate in.
510  
511 +    if (allocated(skipsForAtom)) deallocate(skipsForAtom)
512 +    if (allocated(mfactCol)) deallocate(mfactCol)
513 +    if (allocated(mfactRow)) deallocate(mfactRow)
514 +    if (allocated(groupListCol)) deallocate(groupListCol)    
515 +    if (allocated(groupListRow)) deallocate(groupListRow)    
516 +    if (allocated(groupStartCol)) deallocate(groupStartCol)
517 +    if (allocated(groupStartRow)) deallocate(groupStartRow)    
518      if (allocated(molMembershipList)) deallocate(molMembershipList)    
519      if (allocated(excludesGlobal)) deallocate(excludesGlobal)
520      if (allocated(excludesLocal)) deallocate(excludesLocal)
521 <
521 >    
522    end subroutine FreeSimGlobals
523 <
523 >  
524    pure function getNlocal() result(n)
525      integer :: n
526      n = nLocal
527    end function getNlocal
380 –
528    
529 +  
530   end module simulation

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