6 |
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use force_globals |
7 |
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use vector_class |
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use atype_module |
9 |
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use switcheroo |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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|
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#define __FORTRAN90 |
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#include "fSimulation.h" |
19 |
+ |
#include "fSwitchingFunction.h" |
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|
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type (simtype), public, save :: thisSim |
22 |
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|
23 |
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logical, save :: simulation_setup_complete = .false. |
24 |
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|
25 |
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integer, public, save :: nLocal, nGlobal |
26 |
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integer, public, save :: nGroups, nGroupGlobal |
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integer, public, save :: nExcludes_Global = 0 |
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integer, public, save :: nExcludes_Local = 0 |
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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 |
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|
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real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
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logical, public, save :: boxIsOrthorhombic |
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|
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subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, & |
66 |
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CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, & |
67 |
< |
CmolMembership, & |
67 |
> |
CmolMembership, Cmfact, CnGroups, CgroupList, CgroupStart, & |
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status) |
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|
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type (simtype) :: setThisSim |
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integer, dimension(CnGlobal),intent(in) :: CmolMembership |
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!! Result status, success = 0, status = -1 |
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integer, intent(out) :: status |
81 |
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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 |
> |
|
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#ifdef IS_MPI |
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integer, allocatable, dimension(:) :: c_idents_Row |
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integer, allocatable, dimension(:) :: c_idents_Col |
94 |
< |
integer :: nrow |
95 |
< |
integer :: ncol |
94 |
> |
integer :: nAtomsInRow, nGroupsInRow |
95 |
> |
integer :: nAtomsInCol, nGroupsInCol |
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#endif |
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|
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simulation_setup_complete = .false. |
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|
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nLocal = CnLocal |
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nGlobal = CnGlobal |
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nGroups = CnGroups |
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|
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thisSim = setThisSim |
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|
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status = -1 |
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return |
132 |
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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) |
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mynode = getMyNode() |
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|
139 |
< |
allocate(c_idents_Row(nrow),stat=alloc_stat) |
139 |
> |
allocate(c_idents_Row(nAtomsInRow),stat=alloc_stat) |
140 |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
145 |
< |
allocate(c_idents_Col(ncol),stat=alloc_stat) |
145 |
> |
allocate(c_idents_Col(nAtomsInCol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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) |
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|
154 |
< |
do i = 1, nrow |
154 |
> |
do i = 1, nAtomsInRow |
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me = getFirstMatchingElement(atypes, "c_ident", c_idents_Row(i)) |
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atid_Row(i) = me |
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enddo |
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|
159 |
< |
do i = 1, ncol |
159 |
> |
do i = 1, nAtomsInCol |
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me = getFirstMatchingElement(atypes, "c_ident", c_idents_Col(i)) |
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atid_Col(i) = me |
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enddo |
168 |
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if (allocated(c_idents_Row)) then |
169 |
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deallocate(c_idents_Row) |
170 |
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endif |
171 |
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|
172 |
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#endif |
173 |
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|
174 |
+ |
#ifdef IS_MPI |
175 |
+ |
allocate(groupStartRow(nGroupsInRow+1),stat=alloc_stat) |
176 |
+ |
if (alloc_stat /= 0 ) then |
177 |
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status = -1 |
178 |
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return |
179 |
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endif |
180 |
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allocate(groupStartCol(nGroupsInCol+1),stat=alloc_stat) |
181 |
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if (alloc_stat /= 0 ) then |
182 |
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status = -1 |
183 |
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return |
184 |
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endif |
185 |
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allocate(groupListRow(nAtomsInRow),stat=alloc_stat) |
186 |
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if (alloc_stat /= 0 ) then |
187 |
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status = -1 |
188 |
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return |
189 |
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endif |
190 |
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allocate(groupListCol(nAtomsInCol),stat=alloc_stat) |
191 |
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if (alloc_stat /= 0 ) then |
192 |
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status = -1 |
193 |
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return |
194 |
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endif |
195 |
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allocate(mfactRow(nAtomsInRow),stat=alloc_stat) |
196 |
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if (alloc_stat /= 0 ) then |
197 |
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status = -1 |
198 |
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return |
199 |
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endif |
200 |
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allocate(mfactCol(nAtomsInCol),stat=alloc_stat) |
201 |
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if (alloc_stat /= 0 ) then |
202 |
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status = -1 |
203 |
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return |
204 |
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endif |
205 |
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allocate(groupStartLocal(nGroups), stat=alloc_stat) |
206 |
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if (alloc_stat /= 0 ) then |
207 |
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status = -1 |
208 |
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return |
209 |
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endif |
210 |
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allocate(groupListLocal(nLocal), stat=alloc_stat) |
211 |
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if (alloc_stat /= 0 ) then |
212 |
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status = -1 |
213 |
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return |
214 |
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endif |
215 |
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allocate(mfactLocal(nLocal), stat=alloc_stat) |
216 |
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if (alloc_stat /= 0 ) then |
217 |
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status = -1 |
218 |
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return |
219 |
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endif |
220 |
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|
221 |
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groupStartLocal = CgroupStart |
222 |
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groupListLocal = CgroupList |
223 |
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mfactLocal = Cmfact |
224 |
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|
225 |
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call gather(groupStartLocal, groupStartRow, plan_group_row) |
226 |
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call gather(groupStartLocal, groupStartCol, plan_group_col) |
227 |
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groupStartRow(nGroupsInRow+1) = nAtomsInRow + 1 |
228 |
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groupStartCol(nGroupsInCol+1) = nAtomsInCol + 1 |
229 |
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call gather(groupListLocal, groupListRow, plan_atom_row) |
230 |
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call gather(groupListLocal, groupListCol, plan_atom_col) |
231 |
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|
232 |
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! C passes us groupList as globalID numbers for the atoms |
233 |
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! we need to remap these onto the row and column ids on this |
234 |
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! processor. This is a linear search, but is only done once |
235 |
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! (we hope) |
236 |
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|
237 |
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do i = 1, nAtomsInRow |
238 |
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do j = 1, nAtomsInRow |
239 |
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if (AtomRowToGlobal(j) .eq. groupListRow(i)) then |
240 |
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groupListRow(i) = j |
241 |
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endif |
242 |
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enddo |
243 |
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enddo |
244 |
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do i = 1, nAtomsInCol |
245 |
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do j = 1, nAtomsInCol |
246 |
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if (AtomColToGlobal(j) .eq. groupListCol(i)) then |
247 |
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groupListCol(i) = j |
248 |
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endif |
249 |
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enddo |
250 |
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enddo |
251 |
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call gather(mfactLocal, mfactRow, plan_atom_row) |
252 |
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call gather(mfactLocal, mfactCol, plan_atom_col) |
253 |
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|
254 |
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if (allocated(mfactLocal)) then |
255 |
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deallocate(mfactLocal) |
256 |
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end if |
257 |
+ |
if (allocated(groupListLocal)) then |
258 |
+ |
deallocate(groupListLocal) |
259 |
+ |
endif |
260 |
+ |
if (allocated(groupStartLocal)) then |
261 |
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deallocate(groupStartLocal) |
262 |
+ |
endif |
263 |
+ |
#else |
264 |
+ |
allocate(groupStartRow(nGroups+1),stat=alloc_stat) |
265 |
+ |
if (alloc_stat /= 0 ) then |
266 |
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status = -1 |
267 |
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return |
268 |
+ |
endif |
269 |
+ |
allocate(groupStartCol(nGroups+1),stat=alloc_stat) |
270 |
+ |
if (alloc_stat /= 0 ) then |
271 |
+ |
status = -1 |
272 |
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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 |
|
|
315 |
|
|
316 |
|
enddo |
317 |
|
|
156 |
– |
|
157 |
– |
|
158 |
– |
|
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) |
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 |
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 |
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 |
295 |
– |
|
536 |
|
|
537 |
+ |
|
538 |
|
end module simulation |