6 |
|
use force_globals |
7 |
|
use vector_class |
8 |
|
use atype_module |
9 |
< |
use lj |
9 |
> |
use switcheroo |
10 |
|
#ifdef IS_MPI |
11 |
|
use mpiSimulation |
12 |
|
#endif |
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 :: nGroup, 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 |
30 |
> |
integer, allocatable, dimension(:), public :: excludesGlobal |
31 |
> |
integer, allocatable, dimension(:), public :: molMembershipList |
32 |
> |
integer, allocatable, dimension(:), public :: groupList |
33 |
> |
integer, allocatable, dimension(:), public :: groupStart |
34 |
> |
integer, allocatable, dimension(:), public :: nSkipsForAtom |
35 |
> |
integer, allocatable, dimension(:,:), public :: skipsForAtom |
36 |
> |
real(kind=dp), allocatable, dimension(:), public :: mfact |
37 |
|
|
38 |
< |
real(kind=dp), save :: rcut2 = 0.0_DP |
39 |
< |
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 |
< |
|
38 |
> |
real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
39 |
> |
logical, public, save :: boxIsOrthorhombic |
40 |
|
|
41 |
|
public :: SimulationSetup |
42 |
|
public :: getNlocal |
43 |
|
public :: setBox |
39 |
– |
public :: setBox_3d |
40 |
– |
public :: getBox |
41 |
– |
public :: setRcut |
42 |
– |
public :: getRcut |
43 |
– |
public :: getRlist |
44 |
– |
public :: getRrf |
45 |
– |
public :: getRt |
44 |
|
public :: getDielect |
45 |
|
public :: SimUsesPBC |
46 |
|
public :: SimUsesLJ |
47 |
+ |
public :: SimUsesCharges |
48 |
|
public :: SimUsesDipoles |
49 |
|
public :: SimUsesSticky |
50 |
|
public :: SimUsesRF |
53 |
|
public :: SimRequiresPrepairCalc |
54 |
|
public :: SimRequiresPostpairCalc |
55 |
|
public :: SimUsesDirectionalAtoms |
57 |
– |
|
58 |
– |
interface getBox |
59 |
– |
module procedure getBox_3d |
60 |
– |
module procedure getBox_1d |
61 |
– |
end interface |
56 |
|
|
63 |
– |
interface setBox |
64 |
– |
module procedure setBox_3d |
65 |
– |
module procedure setBox_1d |
66 |
– |
end interface |
67 |
– |
|
57 |
|
contains |
58 |
|
|
59 |
< |
subroutine SimulationSetup(setThisSim, nComponents, c_idents, & |
59 |
> |
subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, & |
60 |
|
CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, & |
61 |
+ |
CmolMembership, Cmfact, CnGroup, CgroupList, CgroupStart, & |
62 |
|
status) |
63 |
|
|
64 |
|
type (simtype) :: setThisSim |
65 |
< |
integer, intent(inout) :: nComponents |
66 |
< |
integer, dimension(nComponents),intent(inout) :: c_idents |
65 |
> |
integer, intent(inout) :: CnGlobal, CnLocal |
66 |
> |
integer, dimension(CnLocal),intent(inout) :: c_idents |
67 |
|
|
68 |
|
integer :: CnLocalExcludes |
69 |
|
integer, dimension(2,CnLocalExcludes), intent(in) :: CexcludesLocal |
70 |
|
integer :: CnGlobalExcludes |
71 |
|
integer, dimension(CnGlobalExcludes), intent(in) :: CexcludesGlobal |
72 |
+ |
integer, dimension(CnGlobal),intent(in) :: CmolMembership |
73 |
|
!! Result status, success = 0, status = -1 |
74 |
|
integer, intent(out) :: status |
75 |
< |
integer :: i, me, thisStat, alloc_stat, myNode |
75 |
> |
integer :: i, j, me, thisStat, alloc_stat, myNode, id1, id2 |
76 |
> |
integer :: gStart, gEnd, groupSize, biggestGroupSize, ia |
77 |
> |
|
78 |
> |
!! mass factors used for molecular cutoffs |
79 |
> |
real ( kind = dp ), dimension(CnLocal) :: Cmfact |
80 |
> |
integer, intent(in):: CnGroup |
81 |
> |
integer, dimension(CnLocal),intent(in) :: CgroupList |
82 |
> |
integer, dimension(CnGroup),intent(in) :: CgroupStart |
83 |
> |
integer :: maxSkipsForAtom |
84 |
> |
|
85 |
|
#ifdef IS_MPI |
86 |
|
integer, allocatable, dimension(:) :: c_idents_Row |
87 |
|
integer, allocatable, dimension(:) :: c_idents_Col |
93 |
|
status = 0 |
94 |
|
|
95 |
|
! copy C struct into fortran type |
96 |
+ |
|
97 |
+ |
nLocal = CnLocal |
98 |
+ |
nGlobal = CnGlobal |
99 |
+ |
nGroup = CnGroup |
100 |
+ |
|
101 |
|
thisSim = setThisSim |
97 |
– |
natoms = nComponents |
98 |
– |
rcut2 = thisSim%rcut * thisSim%rcut |
99 |
– |
rcut6 = rcut2 * rcut2 * rcut2 |
100 |
– |
rlist2 = thisSim%rlist * thisSim%rlist |
101 |
– |
box = thisSim%box |
102 |
|
|
103 |
|
nExcludes_Global = CnGlobalExcludes |
104 |
|
nExcludes_Local = CnLocalExcludes |
105 |
|
|
106 |
< |
call InitializeForceGlobals(natoms, thisStat) |
106 |
> |
call InitializeForceGlobals(nLocal, thisStat) |
107 |
|
if (thisStat /= 0) then |
108 |
+ |
write(default_error,*) "SimSetup: InitializeForceGlobals error" |
109 |
|
status = -1 |
110 |
|
return |
111 |
|
endif |
112 |
|
|
113 |
|
call InitializeSimGlobals(thisStat) |
114 |
|
if (thisStat /= 0) then |
115 |
+ |
write(default_error,*) "SimSetup: InitializeSimGlobals error" |
116 |
|
status = -1 |
117 |
|
return |
118 |
|
endif |
161 |
|
deallocate(c_idents_Row) |
162 |
|
endif |
163 |
|
|
164 |
< |
#else |
165 |
< |
do i = 1, nComponents |
164 |
> |
#endif |
165 |
> |
|
166 |
> |
! We build the local atid's for both mpi and nonmpi |
167 |
> |
do i = 1, nLocal |
168 |
|
|
169 |
|
me = getFirstMatchingElement(atypes, "c_ident", c_idents(i)) |
170 |
|
atid(i) = me |
171 |
|
|
172 |
|
enddo |
173 |
+ |
|
174 |
+ |
do i = 1, nExcludes_Local |
175 |
+ |
excludesLocal(1,i) = CexcludesLocal(1,i) |
176 |
+ |
excludesLocal(2,i) = CexcludesLocal(2,i) |
177 |
+ |
enddo |
178 |
+ |
|
179 |
+ |
maxSkipsForAtom = 0 |
180 |
+ |
do j = 1, nLocal |
181 |
+ |
nSkipsForAtom(j) = 0 |
182 |
+ |
#ifdef IS_MPI |
183 |
+ |
id1 = tagRow(j) |
184 |
+ |
#else |
185 |
+ |
id1 = j |
186 |
|
#endif |
187 |
+ |
do i = 1, nExcludes_Local |
188 |
+ |
if (excludesLocal(1,i) .eq. id1 ) then |
189 |
+ |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
190 |
|
|
191 |
< |
!! Create neighbor lists |
192 |
< |
call expandNeighborList(nComponents, thisStat) |
193 |
< |
if (thisStat /= 0) then |
194 |
< |
status = -1 |
191 |
> |
if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
192 |
> |
maxSkipsForAtom = nSkipsForAtom(j) |
193 |
> |
endif |
194 |
> |
endif |
195 |
> |
if (excludesLocal(2,i) .eq. id1 ) then |
196 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
197 |
> |
|
198 |
> |
if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
199 |
> |
maxSkipsForAtom = nSkipsForAtom(j) |
200 |
> |
endif |
201 |
> |
endif |
202 |
> |
end do |
203 |
> |
enddo |
204 |
> |
|
205 |
> |
allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat) |
206 |
> |
if (alloc_stat /= 0 ) then |
207 |
> |
write(*,*) 'Could not allocate skipsForAtom array' |
208 |
|
return |
209 |
|
endif |
210 |
|
|
211 |
< |
|
212 |
< |
do i = 1, nExcludes_Local |
213 |
< |
excludesLocal(1,i) = CexcludesLocal(1,i) |
214 |
< |
excludesLocal(2,i) = CexcludesLocal(2,i) |
211 |
> |
do j = 1, nLocal |
212 |
> |
nSkipsForAtom(j) = 0 |
213 |
> |
#ifdef IS_MPI |
214 |
> |
id1 = tagRow(j) |
215 |
> |
#else |
216 |
> |
id1 = j |
217 |
> |
#endif |
218 |
> |
do i = 1, nExcludes_Local |
219 |
> |
if (excludesLocal(1,i) .eq. id1 ) then |
220 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
221 |
> |
#ifdef IS_MPI |
222 |
> |
id2 = tagColumn(excludesLocal(2,i)) |
223 |
> |
#else |
224 |
> |
id2 = excludesLocal(2,i) |
225 |
> |
#endif |
226 |
> |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
227 |
> |
endif |
228 |
> |
if (excludesLocal(2, i) .eq. id2 ) then |
229 |
> |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
230 |
> |
#ifdef IS_MPI |
231 |
> |
id2 = tagColumn(excludesLocal(1,i)) |
232 |
> |
#else |
233 |
> |
id2 = excludesLocal(1,i) |
234 |
> |
#endif |
235 |
> |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
236 |
> |
endif |
237 |
> |
end do |
238 |
|
enddo |
239 |
|
|
240 |
|
do i = 1, nExcludes_Global |
241 |
|
excludesGlobal(i) = CexcludesGlobal(i) |
242 |
|
enddo |
243 |
|
|
244 |
+ |
do i = 1, nGlobal |
245 |
+ |
molMemberShipList(i) = CmolMembership(i) |
246 |
+ |
enddo |
247 |
+ |
|
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 |
+ |
|
270 |
|
if (status == 0) simulation_setup_complete = .true. |
271 |
|
|
272 |
|
end subroutine SimulationSetup |
273 |
|
|
274 |
< |
subroutine setBox_3d(new_box_size) |
275 |
< |
real(kind=dp), dimension(3) :: new_box_size |
274 |
> |
subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
275 |
> |
real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
276 |
> |
integer :: cBoxIsOrthorhombic |
277 |
|
integer :: smallest, status, i |
278 |
< |
|
279 |
< |
thisSim%box = new_box_size |
280 |
< |
box = thisSim%box |
281 |
< |
|
282 |
< |
smallest = 1 |
283 |
< |
do i = 2, 3 |
284 |
< |
if (new_box_size(i) .lt. new_box_size(smallest)) smallest = i |
202 |
< |
end do |
203 |
< |
if (thisSim%rcut .gt. 0.5_dp * new_box_size(smallest)) & |
204 |
< |
call setRcut(0.5_dp * new_box_size(smallest), status) |
205 |
< |
return |
206 |
< |
end subroutine setBox_3d |
207 |
< |
|
208 |
< |
subroutine setBox_1d(dim, new_box_size) |
209 |
< |
integer :: dim, status |
210 |
< |
real(kind=dp) :: new_box_size |
211 |
< |
thisSim%box(dim) = new_box_size |
212 |
< |
box(dim) = thisSim%box(dim) |
213 |
< |
if (thisSim%rcut .gt. 0.5_dp * new_box_size) & |
214 |
< |
call setRcut(0.5_dp * new_box_size, status) |
215 |
< |
end subroutine setBox_1d |
216 |
< |
|
217 |
< |
subroutine setRcut(new_rcut, status) |
218 |
< |
real(kind = dp) :: new_rcut |
219 |
< |
integer :: myStatus, status |
220 |
< |
thisSim%rcut = new_rcut |
221 |
< |
rcut2 = thisSim%rcut * thisSim%rcut |
222 |
< |
rcut6 = rcut2 * rcut2 * rcut2 |
223 |
< |
myStatus = 0 |
224 |
< |
call LJ_new_rcut(new_rcut, myStatus) |
225 |
< |
if (myStatus .ne. 0) then |
226 |
< |
write(default_error, *) 'LJ module refused our rcut!' |
227 |
< |
status = -1 |
228 |
< |
return |
278 |
> |
|
279 |
> |
Hmat = cHmat |
280 |
> |
HmatInv = cHmatInv |
281 |
> |
if (cBoxIsOrthorhombic .eq. 0 ) then |
282 |
> |
boxIsOrthorhombic = .false. |
283 |
> |
else |
284 |
> |
boxIsOrthorhombic = .true. |
285 |
|
endif |
230 |
– |
status = 0 |
231 |
– |
return |
232 |
– |
end subroutine setRcut |
233 |
– |
|
234 |
– |
function getBox_3d() result(thisBox) |
235 |
– |
real( kind = dp ), dimension(3) :: thisBox |
236 |
– |
thisBox = thisSim%box |
237 |
– |
end function getBox_3d |
238 |
– |
|
239 |
– |
function getBox_1d(dim) result(thisBox) |
240 |
– |
integer, intent(in) :: dim |
241 |
– |
real( kind = dp ) :: thisBox |
286 |
|
|
287 |
< |
thisBox = thisSim%box(dim) |
288 |
< |
end function getBox_1d |
245 |
< |
|
246 |
< |
subroutine getRcut(thisrcut,rc2,rc6,status) |
247 |
< |
real( kind = dp ), intent(out) :: thisrcut |
248 |
< |
real( kind = dp ), intent(out), optional :: rc2 |
249 |
< |
real( kind = dp ), intent(out), optional :: rc6 |
250 |
< |
integer, optional :: status |
287 |
> |
return |
288 |
> |
end subroutine setBox |
289 |
|
|
252 |
– |
if (present(status)) status = 0 |
253 |
– |
|
254 |
– |
if (.not.simulation_setup_complete ) then |
255 |
– |
if (present(status)) status = -1 |
256 |
– |
return |
257 |
– |
end if |
258 |
– |
|
259 |
– |
thisrcut = thisSim%rcut |
260 |
– |
if(present(rc2)) rc2 = rcut2 |
261 |
– |
if(present(rc6)) rc6 = rcut6 |
262 |
– |
end subroutine getRcut |
263 |
– |
|
264 |
– |
subroutine getRlist(thisrlist,rl2,status) |
265 |
– |
real( kind = dp ), intent(out) :: thisrlist |
266 |
– |
real( kind = dp ), intent(out), optional :: rl2 |
267 |
– |
|
268 |
– |
integer, optional :: status |
269 |
– |
|
270 |
– |
if (present(status)) status = 0 |
271 |
– |
|
272 |
– |
if (.not.simulation_setup_complete ) then |
273 |
– |
if (present(status)) status = -1 |
274 |
– |
return |
275 |
– |
end if |
276 |
– |
|
277 |
– |
thisrlist = thisSim%rlist |
278 |
– |
if(present(rl2)) rl2 = rlist2 |
279 |
– |
end subroutine getRlist |
280 |
– |
|
281 |
– |
function getRrf() result(rrf) |
282 |
– |
real( kind = dp ) :: rrf |
283 |
– |
rrf = thisSim%rrf |
284 |
– |
write(*,*) 'getRrf = ', rrf, thisSim%rrf |
285 |
– |
end function getRrf |
286 |
– |
|
287 |
– |
function getRt() result(rt) |
288 |
– |
real( kind = dp ) :: rt |
289 |
– |
rt = thisSim%rt |
290 |
– |
end function getRt |
291 |
– |
|
290 |
|
function getDielect() result(dielect) |
291 |
|
real( kind = dp ) :: dielect |
292 |
|
dielect = thisSim%dielect |
307 |
|
doesit = thisSim%SIM_uses_sticky |
308 |
|
end function SimUsesSticky |
309 |
|
|
310 |
+ |
function SimUsesCharges() result(doesit) |
311 |
+ |
logical :: doesit |
312 |
+ |
doesit = thisSim%SIM_uses_charges |
313 |
+ |
end function SimUsesCharges |
314 |
+ |
|
315 |
|
function SimUsesDipoles() result(doesit) |
316 |
|
logical :: doesit |
317 |
|
doesit = thisSim%SIM_uses_dipoles |
355 |
|
thisStat = 0 |
356 |
|
|
357 |
|
call FreeSimGlobals() |
358 |
+ |
|
359 |
+ |
allocate(nSkipsForAtom(nLocal), stat=alloc_stat) |
360 |
+ |
if (alloc_stat /= 0 ) then |
361 |
+ |
thisStat = -1 |
362 |
+ |
return |
363 |
+ |
endif |
364 |
|
|
365 |
|
allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat) |
366 |
|
if (alloc_stat /= 0 ) then |
373 |
|
thisStat = -1 |
374 |
|
return |
375 |
|
endif |
376 |
+ |
|
377 |
+ |
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
378 |
+ |
if (alloc_stat /= 0 ) then |
379 |
+ |
thisStat = -1 |
380 |
+ |
return |
381 |
+ |
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 |
400 |
|
|
401 |
|
end subroutine InitializeSimGlobals |
402 |
|
|
403 |
|
subroutine FreeSimGlobals() |
404 |
|
|
405 |
|
!We free in the opposite order in which we allocate in. |
406 |
< |
|
406 |
> |
|
407 |
> |
if (allocated(skipsForAtom)) deallocate(skipsForAtom) |
408 |
> |
if (allocated(mfact)) deallocate(mfact) |
409 |
> |
if (allocated(groupList)) deallocate(groupList) |
410 |
> |
if (allocated(groupStart)) deallocate(groupStart) |
411 |
> |
if (allocated(molMembershipList)) deallocate(molMembershipList) |
412 |
|
if (allocated(excludesGlobal)) deallocate(excludesGlobal) |
413 |
|
if (allocated(excludesLocal)) deallocate(excludesLocal) |
414 |
< |
|
414 |
> |
|
415 |
|
end subroutine FreeSimGlobals |
416 |
< |
|
417 |
< |
pure function getNlocal() result(nlocal) |
418 |
< |
integer :: nlocal |
419 |
< |
nlocal = natoms |
416 |
> |
|
417 |
> |
pure function getNlocal() result(n) |
418 |
> |
integer :: n |
419 |
> |
n = nLocal |
420 |
|
end function getNlocal |
383 |
– |
|
421 |
|
|
422 |
+ |
|
423 |
|
end module simulation |