ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/simulation_module.F90
(Generate patch)

Comparing trunk/OOPSE/libmdtools/simulation_module.F90 (file contents):
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 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 :: natoms
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, nGlobal, nLocal, c_idents, &
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
71 <    integer, intent(inout) :: nGlobal, nLocal
72 <    integer, dimension(nLocal),intent(inout) :: c_idents
71 >    integer, intent(inout) :: CnGlobal, CnLocal
72 >    integer, dimension(CnLocal),intent(inout) :: c_idents
73  
74      integer :: CnLocalExcludes
75      integer, dimension(2,CnLocalExcludes), intent(in) :: CexcludesLocal
76      integer :: CnGlobalExcludes
77      integer, dimension(CnGlobalExcludes), intent(in) :: CexcludesGlobal
78 <    integer, dimension(nGlobal),intent(in) :: CmolMembership
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.
99      status = 0
100  
101      ! copy C struct into fortran type
102 +
103 +    nLocal = CnLocal
104 +    nGlobal = CnGlobal
105 +    nGroups = CnGroups
106 +
107      thisSim = setThisSim
99 –    natoms = nLocal
100 –    rcut2 = thisSim%rcut * thisSim%rcut
101 –    rcut6 = rcut2 * rcut2 * rcut2
102 –    rlist2 = thisSim%rlist * thisSim%rlist
103 –    box = thisSim%box
108  
109      nExcludes_Global = CnGlobalExcludes
110      nExcludes_Local = CnLocalExcludes
111  
112 <    call InitializeForceGlobals(natoms, thisStat)
112 >    call InitializeForceGlobals(nLocal, thisStat)
113      if (thisStat /= 0) then
114         write(default_error,*) "SimSetup: InitializeForceGlobals error"
115         status = -1
# Line 126 | 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 162 | 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
228 +    groupStartCol(nGroupsInCol+1) = nAtomsInCol
229 +    call gather(groupListLocal,  groupListRow,  plan_atom_row)
230 +    call gather(groupListLocal,  groupListCol,  plan_atom_col)
231 +    call gather(mfactLocal,      mfactRow,      plan_atom_row)
232 +    call gather(mfactLocal,      mfactCol,      plan_atom_col)
233      
234 +    if (allocated(mfactLocal)) then
235 +       deallocate(mfactLocal)
236 +    end if
237 +    if (allocated(groupListLocal)) then
238 +       deallocate(groupListLocal)
239 +    endif
240 +    if (allocated(groupStartLocal)) then
241 +       deallocate(groupStartLocal)
242 +    endif
243   #else
244 +    allocate(groupStartRow(nGroups+1),stat=alloc_stat)
245 +    if (alloc_stat /= 0 ) then
246 +       status = -1
247 +       return
248 +    endif
249 +    allocate(groupStartCol(nGroups+1),stat=alloc_stat)
250 +    if (alloc_stat /= 0 ) then
251 +       status = -1
252 +       return
253 +    endif
254 +    allocate(groupListRow(nLocal),stat=alloc_stat)
255 +    if (alloc_stat /= 0 ) then
256 +       status = -1
257 +       return
258 +    endif
259 +    allocate(groupListCol(nLocal),stat=alloc_stat)
260 +    if (alloc_stat /= 0 ) then
261 +       status = -1
262 +       return
263 +    endif
264 +    allocate(mfactRow(nLocal),stat=alloc_stat)
265 +    if (alloc_stat /= 0 ) then
266 +       status = -1
267 +       return
268 +    endif
269 +    allocate(mfactCol(nLocal),stat=alloc_stat)
270 +    if (alloc_stat /= 0 ) then
271 +       status = -1
272 +       return
273 +    endif
274 +    do i = 1, nGroups
275 +       groupStartRow(i) = CgroupStart(i)
276 +       groupStartCol(i) = CgroupStart(i)
277 +    end do
278 +    groupStartRow(nGroups+1) = nLocal
279 +    groupStartCol(nGroups+1) = nLocal
280 +    do i = 1, nLocal
281 +       groupListRow(i) = CgroupList(i)
282 +       groupListCol(i) = CgroupList(i)
283 +       mfactRow(i) = Cmfact(i)
284 +       mfactCol(i) = Cmfact(i)
285 +    end do
286 +    
287 + #endif
288 +
289 +
290 + ! We build the local atid's for both mpi and nonmpi
291      do i = 1, nLocal
292        
293         me = getFirstMatchingElement(atypes, "c_ident", c_idents(i))
294         atid(i) = me
295    
296      enddo
173 – #endif
297  
175 –
176 –
298      do i = 1, nExcludes_Local
299         excludesLocal(1,i) = CexcludesLocal(1,i)
300         excludesLocal(2,i) = CexcludesLocal(2,i)
301      enddo
302 +
303 +    maxSkipsForAtom = 0
304 +    do j = 1, nLocal
305 +       nSkipsForAtom(j) = 0
306 + #ifdef IS_MPI
307 +       id1 = AtomRowToGlobal(j)
308 + #else
309 +       id1 = j
310 + #endif
311 +       do i = 1, nExcludes_Local
312 +          if (excludesLocal(1,i) .eq. id1 ) then
313 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
314 +
315 +             if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then
316 +                maxSkipsForAtom = nSkipsForAtom(j)
317 +             endif
318 +          endif
319 +          if (excludesLocal(2,i) .eq. id1 ) then
320 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
321 +
322 +             if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then
323 +                maxSkipsForAtom = nSkipsForAtom(j)
324 +             endif
325 +          endif
326 +       end do
327 +    enddo
328 +
329 +    allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat)
330 +    if (alloc_stat /= 0 ) then
331 +       write(*,*) 'Could not allocate skipsForAtom array'
332 +       return
333 +    endif
334 +
335 +    do j = 1, nLocal
336 +       nSkipsForAtom(j) = 0
337 + #ifdef IS_MPI
338 +       id1 = AtomRowToGlobal(j)
339 + #else
340 +       id1 = j
341 + #endif
342 +       do i = 1, nExcludes_Local
343 +          if (excludesLocal(1,i) .eq. id1 ) then
344 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
345 + #ifdef IS_MPI
346 +             id2 = AtomColToGlobal(excludesLocal(2,i))
347 + #else
348 +             id2 = excludesLocal(2,i)
349 + #endif
350 +             skipsForAtom(j, nSkipsForAtom(j)) = id2
351 +          endif
352 +          if (excludesLocal(2, i) .eq. id2 ) then
353 +             nSkipsForAtom(j) = nSkipsForAtom(j) + 1
354 + #ifdef IS_MPI
355 +             id2 = AtomColToGlobal(excludesLocal(1,i))
356 + #else
357 +             id2 = excludesLocal(1,i)
358 + #endif
359 +             skipsForAtom(j, nSkipsForAtom(j)) = id2
360 +          endif
361 +       end do
362 +    enddo
363      
364      do i = 1, nExcludes_Global
365         excludesGlobal(i) = CexcludesGlobal(i)
# Line 185 | Line 367 | contains
367  
368      do i = 1, nGlobal
369         molMemberShipList(i) = CmolMembership(i)
188 –       ! write(0,*) 'molMembershipList(',i,') = ', molMemberShipList(i)
370      enddo
371 <
371 >    
372      if (status == 0) simulation_setup_complete = .true.
373      
374    end subroutine SimulationSetup
375    
376 <  subroutine setBox_3d(new_box_size)
377 <    real(kind=dp), dimension(3) :: new_box_size
376 >  subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic)
377 >    real(kind=dp), dimension(3,3) :: cHmat, cHmatInv
378 >    integer :: cBoxIsOrthorhombic
379      integer :: smallest, status, i
198 –
199 –    thisSim%box = new_box_size
200 –    box = thisSim%box
201 –
202 –    return    
203 –  end subroutine setBox_3d
204 –
205 –  subroutine setBox_1d(dim, new_box_size)
206 –    integer :: dim, status
207 –    real(kind=dp) :: new_box_size
208 –    thisSim%box(dim) = new_box_size
209 –    box(dim) = thisSim%box(dim)
210 –  end subroutine setBox_1d
211 –
212 –  subroutine setRcut(new_rcut, status)
213 –    real(kind = dp) :: new_rcut
214 –    integer :: myStatus, status
215 –    thisSim%rcut = new_rcut
216 –    rcut2 = thisSim%rcut * thisSim%rcut
217 –    rcut6 = rcut2 * rcut2 * rcut2
218 –    status = 0
219 –    return
220 –  end subroutine setRcut
221 –
222 –  function getBox_3d() result(thisBox)
223 –    real( kind = dp ), dimension(3) :: thisBox
224 –    thisBox = thisSim%box
225 –  end function getBox_3d
226 –  
227 –  function getBox_1d(dim) result(thisBox)
228 –    integer, intent(in) :: dim
229 –    real( kind = dp ) :: thisBox
380      
381 <    thisBox = thisSim%box(dim)
382 <  end function getBox_1d
383 <    
384 <  subroutine getRcut(thisrcut,rc2,rc6,status)
385 <    real( kind = dp ), intent(out) :: thisrcut
386 <    real( kind = dp ), intent(out), optional :: rc2
387 <    real( kind = dp ), intent(out), optional :: rc6
238 <    integer, optional :: status
239 <
240 <    if (present(status)) status = 0
381 >    Hmat = cHmat
382 >    HmatInv = cHmatInv
383 >    if (cBoxIsOrthorhombic .eq. 0 ) then
384 >       boxIsOrthorhombic = .false.
385 >    else
386 >       boxIsOrthorhombic = .true.
387 >    endif
388      
389 <    if (.not.simulation_setup_complete ) then
390 <       if (present(status)) status = -1
244 <       return
245 <    end if
246 <    
247 <    thisrcut = thisSim%rcut
248 <    if(present(rc2)) rc2 = rcut2
249 <    if(present(rc6)) rc6 = rcut6
250 <  end subroutine getRcut
251 <  
252 <  subroutine getRlist(thisrlist,rl2,status)
253 <    real( kind = dp ), intent(out) :: thisrlist
254 <    real( kind = dp ), intent(out), optional :: rl2
389 >    return    
390 >  end subroutine setBox
391  
256 –    integer, optional :: status
257 –
258 –    if (present(status)) status = 0
259 –
260 –    if (.not.simulation_setup_complete ) then
261 –       if (present(status)) status = -1
262 –       return
263 –    end if
264 –    
265 –    thisrlist = thisSim%rlist
266 –    if(present(rl2)) rl2 = rlist2
267 –  end subroutine getRlist
268 –
269 –  function getRrf() result(rrf)
270 –    real( kind = dp ) :: rrf
271 –    rrf = thisSim%rrf
272 –    write(*,*) 'getRrf = ', rrf, thisSim%rrf
273 –  end function getRrf
274 –  
275 –  function getRt() result(rt)
276 –    real( kind = dp ) :: rt
277 –    rt = thisSim%rt
278 –  end function getRt
279 –
392    function getDielect() result(dielect)
393      real( kind = dp ) :: dielect
394      dielect = thisSim%dielect
# Line 297 | Line 409 | contains
409      doesit = thisSim%SIM_uses_sticky
410    end function SimUsesSticky
411  
412 +  function SimUsesCharges() result(doesit)
413 +    logical :: doesit
414 +    doesit = thisSim%SIM_uses_charges
415 +  end function SimUsesCharges
416 +
417    function SimUsesDipoles() result(doesit)
418      logical :: doesit
419      doesit = thisSim%SIM_uses_dipoles
# Line 340 | Line 457 | contains
457      thisStat = 0
458      
459      call FreeSimGlobals()    
460 +
461 +    allocate(nSkipsForAtom(nLocal), stat=alloc_stat)
462 +    if (alloc_stat /= 0 ) then
463 +       thisStat = -1
464 +       return
465 +    endif
466      
467      allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat)
468      if (alloc_stat /= 0 ) then
# Line 353 | Line 476 | contains
476         return
477      endif
478  
479 <    allocate(molMembershipList(getNlocal()), stat=alloc_stat)
479 >    allocate(molMembershipList(nGlobal), stat=alloc_stat)
480      if (alloc_stat /= 0 ) then
481         thisStat = -1
482         return
# Line 365 | Line 488 | contains
488      
489      !We free in the opposite order in which we allocate in.
490  
491 +    if (allocated(skipsForAtom)) deallocate(skipsForAtom)
492 +    if (allocated(mfactCol)) deallocate(mfactCol)
493 +    if (allocated(mfactRow)) deallocate(mfactRow)
494 +    if (allocated(groupListCol)) deallocate(groupListCol)    
495 +    if (allocated(groupListRow)) deallocate(groupListRow)    
496 +    if (allocated(groupStartCol)) deallocate(groupStartCol)
497 +    if (allocated(groupStartRow)) deallocate(groupStartRow)    
498      if (allocated(molMembershipList)) deallocate(molMembershipList)    
499      if (allocated(excludesGlobal)) deallocate(excludesGlobal)
500      if (allocated(excludesLocal)) deallocate(excludesLocal)
501 <
501 >    
502    end subroutine FreeSimGlobals
503 <
504 <  pure function getNlocal() result(nlocal)
505 <    integer :: nlocal
506 <    nlocal = natoms
503 >  
504 >  pure function getNlocal() result(n)
505 >    integer :: n
506 >    n = nLocal
507    end function getNlocal
378 –
508    
509 +  
510   end module simulation

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines