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Comparing trunk/OOPSE_old/src/mdtools/libmdCode/do_Forces.F90 (file contents):
Revision 293 by mmeineke, Thu Mar 6 16:07:57 2003 UTC vs.
Revision 332 by gezelter, Thu Mar 13 15:28:43 2003 UTC

# Line 1 | Line 1
1 + !! do_Forces.F90
2 + !! module do_Forces
3   !! Calculates Long Range forces.
4 +
5   !! @author Charles F. Vardeman II
6   !! @author Matthew Meineke
7 < !! @version $Id: do_Forces.F90,v 1.2 2003-03-06 16:07:55 mmeineke Exp $, $Date: 2003-03-06 16:07:55 $, $Name: not supported by cvs2svn $, $Revision: 1.2 $
7 > !! @version $Id: do_Forces.F90,v 1.18 2003-03-13 15:28:43 gezelter Exp $, $Date: 2003-03-13 15:28:43 $, $Name: not supported by cvs2svn $, $Revision: 1.18 $
8  
9  
10  
11   module do_Forces
12    use simulation
13    use definitions
14 <  use generic_atypes
15 <  use neighborLists
16 <  
17 <  use lj_FF
18 <  use sticky_FF
19 <  use dp_FF
17 <  use gb_FF
14 >  use atype_module
15 >  use neighborLists  
16 >  use lj
17 >  use sticky_pair
18 >  use dipole_dipole
19 >  use reaction_field
20  
21   #ifdef IS_MPI
22    use mpiSimulation
# Line 22 | Line 24 | module do_Forces
24    implicit none
25    PRIVATE
26  
27 < !! Number of lj_atypes in lj_atype_list
28 <  integer, save :: n_atypes = 0
27 >  logical, save :: do_forces_initialized = .false.
28 >  logical, save :: FF_uses_LJ
29 >  logical, save :: FF_uses_sticky
30 >  logical, save :: FF_uses_dipoles
31 >  logical, save :: FF_uses_RF
32 >  logical, save :: FF_uses_GB
33 >  logical, save :: FF_uses_EAM
34  
28 !! Global list of lj atypes in simulation
29  type (atype), pointer :: ListHead => null()
30  type (atype), pointer :: ListTail => null()
31
32
33 !! LJ mixing array  
34 !  type (lj_atype), dimension(:,:), pointer :: ljMixed => null()
35
36
37  logical, save :: firstTime = .True.
38
39 !! Atype identity pointer lists
40 #ifdef IS_MPI
41 !! Row lj_atype pointer list
42  type (identPtrList), dimension(:), pointer :: identPtrListRow => null()
43 !! Column lj_atype pointer list
44  type (identPtrList), dimension(:), pointer :: identPtrListColumn => null()
45 #else
46  type(identPtrList ), dimension(:), pointer :: identPtrList => null()
47 #endif
48
49
50 !! Logical has lj force field module been initialized?
51  logical, save :: isFFinit = .false.
52
53
54 !! Public methods and data
55  public :: new_atype
56  public :: do_forceLoop
57  public :: getLjPot
35    public :: init_FF
36 +  public :: do_force_loop
37  
60  
61
62
38   contains
39  
40 < !! Adds a new lj_atype to the list.
41 <  subroutine new_atype(ident,mass,epsilon,sigma, &
42 <       is_LJ,is_Sticky,is_DP,is_GB,w0,v0,dipoleMoment,status)
43 <    real( kind = dp ), intent(in) :: mass
44 <    real( kind = dp ), intent(in) :: epsilon
45 <    real( kind = dp ), intent(in) :: sigma
46 <    real( kind = dp ), intent(in) :: w0
47 <    real( kind = dp ), intent(in) :: v0
48 <    real( kind = dp ), intent(in) :: dipoleMoment
40 >  subroutine init_FF(LJ_mix_policy, use_RF_c, thisStat)
41 >    logical(kind = 2), intent(in) :: use_RF_c
42 >    logical :: use_RF_f
43 >    integer, intent(out) :: thisStat  
44 >    integer :: my_status, nMatches
45 >    character(len = 100) :: LJ_mix_Policy
46 >    integer, pointer :: MatchList(:)
47 >    
48 >    !! Fortran's version of a cast:
49 >    use_RF_f = use_RF_c
50  
51 <    integer, intent(in) :: ident
52 <    integer, intent(out) :: status
53 <    integer, intent(in) :: is_Sticky
54 <    integer, intent(in) :: is_DP
55 <    integer, intent(in) :: is_GB
56 <    integer, intent(in) :: is_LJ
51 >    !! assume things are copacetic, unless they aren't
52 >    thisStat = 0
53 >    
54 >    !! init_FF is called *after* all of the atom types have been
55 >    !! defined in atype_module using the new_atype subroutine.
56 >    !!
57 >    !! this will scan through the known atypes and figure out what
58 >    !! interactions are used by the force field.    
59  
60 +    FF_uses_LJ = .false.
61 +    FF_uses_sticky = .false.
62 +    FF_uses_dipoles = .false.
63 +    FF_uses_GB = .false.
64 +    FF_uses_EAM = .false.
65 +    
66 +    call getMatchingElementList(atypes, "is_LJ", .true., nMatches, MatchList)
67 +    deallocate(MatchList)
68 +    if (nMatches .gt. 0) FF_uses_LJ = .true.
69  
70 <    type (atype), pointer :: the_new_atype
71 <    integer :: alloc_error
72 <    integer :: atype_counter = 0
86 <    integer :: alloc_size
87 <    integer :: err_stat
88 <    status = 0
70 >    call getMatchingElementList(atypes, "is_DP", .true., nMatches, MatchList)
71 >    deallocate(MatchList)
72 >    if (nMatches .gt. 0) FF_uses_dipoles = .true.
73  
74 +    call getMatchingElementList(atypes, "is_Sticky", .true., nMatches, &
75 +         MatchList)
76 +    deallocate(MatchList)
77 +    if (nMatches .gt. 0) FF_uses_Sticky = .true.
78 +    
79 +    call getMatchingElementList(atypes, "is_GB", .true., nMatches, MatchList)
80 +    deallocate(MatchList)
81 +    if (nMatches .gt. 0) FF_uses_GB = .true.
82  
83 +    call getMatchingElementList(atypes, "is_EAM", .true., nMatches, MatchList)
84 +    deallocate(MatchList)
85 +    if (nMatches .gt. 0) FF_uses_EAM = .true.
86  
87 < ! allocate a new atype    
88 <    allocate(the_new_atype,stat=alloc_error)
89 <    if (alloc_error /= 0 ) then
90 <       status = -1
87 >    !! check to make sure the use_RF setting makes sense
88 >    if (use_RF_f) then
89 >       if (FF_uses_dipoles) then
90 >          FF_uses_RF = .true.
91 >          call initialize_rf()
92 >       else
93 >          write(default_error,*) 'Using Reaction Field with no dipoles?  Huh?'
94 >          thisStat = -1
95 >          return
96 >       endif
97 >    endif
98 >    
99 >    call init_lj_FF(LJ_mix_Policy, my_status)
100 >    if (my_status /= 0) then
101 >       thisStat = -1
102         return
103      end if
98
99 ! assign our new atype information
100    the_new_atype%mass        = mass
101    the_new_atype%epsilon     = epsilon
102    the_new_atype%sigma       = sigma
103    the_new_atype%sigma2      = sigma * sigma
104    the_new_atype%sigma6      = the_new_atype%sigma2 * the_new_atype%sigma2 &
105         * the_new_atype%sigma2
106    the_new_atype%w0       = w0
107    the_new_atype%v0       = v0
108    the_new_atype%dipoleMoment       = dipoleMoment
109
104      
105 < ! assume that this atype will be successfully added
106 <    the_new_atype%atype_ident = ident
107 <    the_new_atype%atype_number = n_lj_atypes + 1
105 >    call check_sticky_FF(my_status)
106 >    if (my_status /= 0) then
107 >       thisStat = -1
108 >       return
109 >    end if
110      
111 <    if ( is_Sticky /= 0 )    the_new_atype%is_Sticky   = .true.
112 <    if ( is_GB /= 0 )        the_new_atype%is_GB       = .true.
113 <    if ( is_LJ /= 0 )        the_new_atype%is_LJ       = .true.
118 <    if ( is_DP /= 0 )        the_new_atype%is_DP       = .true.
111 >    do_forces_initialized = .true.    
112 >    
113 >  end subroutine init_FF
114  
120    call add_atype(the_new_atype,ListHead,ListTail,err_stat)
121    if (err_stat /= 0 ) then
122       status = -1
123       return
124    endif
115  
126    n_atypes = n_atypes + 1
116  
117 <
118 <  end subroutine new_atype
119 <
120 <
121 <  subroutine init_FF(nComponents,ident, status)
122 < !! Number of components in ident array
123 <    integer, intent(inout) :: nComponents
124 < !! Array of identities nComponents long corresponding to
125 < !! ljatype ident.
126 <    integer, dimension(nComponents),intent(inout) :: ident
127 < !!  Result status, success = 0, error = -1
128 <    integer, intent(out) :: Status
129 <
130 <    integer :: alloc_stat
131 <
132 <    integer :: thisStat
133 <    integer :: i
134 <
135 <    integer :: myNode
117 >  !! Does force loop over i,j pairs. Calls do_pair to calculates forces.
118 >  !------------------------------------------------------------->
119 >  subroutine do_force_loop(q, A, u_l, f, t, tau, pot, do_pot_c, do_stress_c, &
120 >       error)
121 >    !! Position array provided by C, dimensioned by getNlocal
122 >    real ( kind = dp ), dimension(3,getNlocal()) :: q
123 >    !! Rotation Matrix for each long range particle in simulation.
124 >    real( kind = dp), dimension(9,getNlocal()) :: A    
125 >    !! Unit vectors for dipoles (lab frame)
126 >    real( kind = dp ), dimension(3,getNlocal()) :: u_l
127 >    !! Force array provided by C, dimensioned by getNlocal
128 >    real ( kind = dp ), dimension(3,getNlocal()) :: f
129 >    !! Torsion array provided by C, dimensioned by getNlocal
130 >    real( kind = dp ), dimension(3,getNlocal()) :: t    
131 >    !! Stress Tensor
132 >    real( kind = dp), dimension(9) :: tau  
133 >    real ( kind = dp ) :: pot
134 >    logical ( kind = 2) :: do_pot_c, do_stress_c
135 >    logical :: do_pot
136 >    logical :: do_stress
137   #ifdef IS_MPI
138 <    integer, allocatable, dimension(:) :: identRow
149 <    integer, allocatable, dimension(:) :: identCol
138 >    real( kind = DP ) :: pot_local
139      integer :: nrow
140      integer :: ncol
141   #endif
142 <    status = 0
143 <  
142 >    integer :: nlocal
143 >    integer :: natoms    
144 >    logical :: update_nlist  
145 >    integer :: i, j, jbeg, jend, jnab
146 >    integer :: nlist
147 >    real( kind = DP ) ::  rijsq, rlistsq, rcutsq, rlist, rcut
148 >    real(kind=dp),dimension(3) :: d
149 >    real(kind=dp) :: rfpot, mu_i, virial
150 >    integer :: me_i
151 >    logical :: is_dp_i
152 >    integer :: neighborListSize
153 >    integer :: listerror, error
154 >    integer :: localError
155  
156 <    
156 >    !! initialize local variables  
157  
158 < !! if were're not in MPI, we just update ljatypePtrList
159 < #ifndef IS_MPI
160 <    call create_IdentPtrlst(ident,ListHead,identPtrList,thisStat)
161 <    if ( thisStat /= 0 ) then
162 <       status = -1
163 <       return
164 <    endif
158 > #ifdef IS_MPI
159 >    nlocal = getNlocal()
160 >    nrow   = getNrow(plan_row)
161 >    ncol   = getNcol(plan_col)
162 > #else
163 >    nlocal = getNlocal()
164 >    natoms = nlocal
165 > #endif
166  
167 +    call getRcut(rcut,rc2=rcutsq)
168 +    call getRlist(rlist,rlistsq)
169      
170 < ! if were're in MPI, we also have to worry about row and col lists    
171 < #else
172 <  
170 < ! We can only set up forces if mpiSimulation has been setup.
171 <    if (.not. isMPISimSet()) then
172 <       write(default_error,*) "MPI is not set"
173 <       status = -1
170 >    call check_initialization(localError)
171 >    if ( localError .ne. 0 ) then
172 >       error = -1
173         return
174 <    endif
175 <    nrow = getNrow(plan_row)
177 <    ncol = getNcol(plan_col)
178 <    mynode = getMyNode()
179 < !! Allocate temperary arrays to hold gather information
180 <    allocate(identRow(nrow),stat=alloc_stat)
181 <    if (alloc_stat /= 0 ) then
182 <       status = -1
183 <       return
184 <    endif
174 >    end if
175 >    call zero_work_arrays()
176  
177 <    allocate(identCol(ncol),stat=alloc_stat)
178 <    if (alloc_stat /= 0 ) then
188 <       status = -1
189 <       return
190 <    endif
177 >    do_pot = do_pot_c
178 >    do_stress = do_stress_c
179  
180 < !! Gather idents into row and column idents
193 <
194 <    call gather(ident,identRow,plan_row)
195 <    call gather(ident,identCol,plan_col)
180 >    ! Gather all information needed by all force loops:
181      
182 <  
198 < !! Create row and col pointer lists
199 <  
200 <    call create_IdentPtrlst(identRow,ListHead,identPtrListRow,thisStat)
201 <    if (thisStat /= 0 ) then
202 <       status = -1
203 <       return
204 <    endif
205 <  
206 <    call create_IdentPtrlst(identCol,ListHead,identPtrListColumn,thisStat)
207 <    if (thisStat /= 0 ) then
208 <       status = -1
209 <       return
210 <    endif
182 > #ifdef IS_MPI    
183  
184 < !! free temporary ident arrays
185 <    if (allocated(identCol)) then
186 <       deallocate(identCol)
187 <    end if
188 <    if (allocated(identCol)) then
189 <       deallocate(identRow)
184 >    call gather(q,q_Row,plan_row3d)
185 >    call gather(q,q_Col,plan_col3d)
186 >        
187 >    if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
188 >       call gather(u_l,u_l_Row,plan_row3d)
189 >       call gather(u_l,u_l_Col,plan_col3d)
190 >      
191 >       call gather(A,A_Row,plan_row_rotation)
192 >       call gather(A,A_Col,plan_col_rotation)
193      endif
194 <
194 >    
195   #endif
196      
197 <    call initForce_Modules(thisStat)
198 <    if (thisStat /= 0) then
199 <       status = -1
200 <       return
197 >    if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
198 >       !! See if we need to update neighbor lists
199 >       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)  
200 >       !! if_mpi_gather_stuff_for_prepair
201 >       !! do_prepair_loop_if_needed
202 >       !! if_mpi_scatter_stuff_from_prepair
203 >       !! if_mpi_gather_stuff_from_prepair_to_main_loop
204 >    else
205 >       !! See if we need to update neighbor lists
206 >       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)  
207      endif
208 +    
209 + #ifdef IS_MPI
210 +    
211 +    if (update_nlist) then
212 +      
213 +       !! save current configuration, construct neighbor list,
214 +       !! and calculate forces
215 +       call save_neighborList(q)
216 +      
217 +       neighborListSize = getNeighborListSize()
218 +       nlist = 0      
219 +      
220 +       do i = 1, nrow
221 +          point(i) = nlist + 1
222 +          
223 +          inner: do j = 1, ncol
224 +            
225 +             if (checkExcludes(i,j)) cycle inner
226 +            
227 +             call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
228 +            
229 +             if (rijsq <  rlistsq) then            
230 +                
231 +                nlist = nlist + 1
232 +                
233 +                if (nlist > neighborListSize) then
234 +                   call expandNeighborList(nlocal, listerror)
235 +                   if (listerror /= 0) then
236 +                      error = -1
237 +                      write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
238 +                      return
239 +                   end if
240 +                endif
241 +                
242 +                list(nlist) = j
243 +                                
244 +                if (rijsq <  rcutsq) then
245 +                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
246 +                endif
247 +             endif
248 +          enddo inner
249 +       enddo
250  
251 < !! Create neighbor lists
252 <    call expandList(thisStat)
253 <    if (thisStat /= 0) then
231 <       status = -1
232 <       return
233 <    endif
251 >       point(nrow + 1) = nlist + 1
252 >      
253 >    else  !! (of update_check)
254  
255 <    isFFinit = .true.
255 >       ! use the list to find the neighbors
256 >       do i = 1, nrow
257 >          JBEG = POINT(i)
258 >          JEND = POINT(i+1) - 1
259 >          ! check thiat molecule i has neighbors
260 >          if (jbeg .le. jend) then
261 >            
262 >             do jnab = jbeg, jend
263 >                j = list(jnab)
264  
265 +                call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
266 +                call do_pair(i, j, rijsq, d, do_pot, do_stress)
267  
268 <  end subroutine init_FF
269 <
270 <
271 <
242 <
243 <  subroutine initForce_Modules(thisStat)
244 <    integer, intent(out) :: thisStat
245 <    integer :: my_status
268 >             enddo
269 >          endif
270 >       enddo
271 >    endif
272      
273 <    thisStat = 0
274 <    call init_lj_FF(ListHead,my_status)
275 <    if (my_status /= 0) then
276 <       thisStat = -1
277 <       return
278 <    end if
273 > #else
274 >    
275 >    if (update_nlist) then
276 >      
277 >       ! save current configuration, contruct neighbor list,
278 >       ! and calculate forces
279 >       call save_neighborList(q)
280 >      
281 >       neighborListSize = getNeighborListSize()
282 >       nlist = 0
283 >      
284 >       do i = 1, natoms-1
285 >          point(i) = nlist + 1
286 >          
287 >          inner: do j = i+1, natoms
288 >            
289 >             if (checkExcludes(i,j)) cycle inner
290 >            
291 >             call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
292 >          
293 >             if (rijsq <  rlistsq) then
294 >                
295 >                nlist = nlist + 1
296 >                
297 >                if (nlist > neighborListSize) then
298 >                   call expandList(natoms, listerror)
299 >                   if (listerror /= 0) then
300 >                      error = -1
301 >                      write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
302 >                      return
303 >                   end if
304 >                endif
305 >                
306 >                list(nlist) = j
307 >                
308 >                if (rijsq <  rcutsq) then
309 >                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
310 >                endif
311 >             endif
312 >          enddo inner
313 >       enddo
314 >      
315 >       point(natoms) = nlist + 1
316 >      
317 >    else !! (update)
318 >      
319 >       ! use the list to find the neighbors
320 >       do i = 1, natoms-1
321 >          JBEG = POINT(i)
322 >          JEND = POINT(i+1) - 1
323 >          ! check thiat molecule i has neighbors
324 >          if (jbeg .le. jend) then
325 >            
326 >             do jnab = jbeg, jend
327 >                j = list(jnab)
328  
329 <  end subroutine initForce_Modules
329 >                call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
330 >                call do_pair(i, j, rijsq, d, do_pot, do_stress)
331  
332 <
333 <
334 <
335 < !! FORCE routine Calculates Lennard Jones forces.
260 < !------------------------------------------------------------->
261 <  subroutine do__force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror)
262 < !! Position array provided by C, dimensioned by getNlocal
263 <    real ( kind = dp ), dimension(3,getNlocal()) :: q
264 <  !! Rotation Matrix for each long range particle in simulation.
265 <    real( kind = dp), dimension(9,getNlocal()) :: A
266 <
267 <  !! Magnitude dipole moment
268 <    real( kind = dp ), dimension(3,getNlocal()) :: mu
269 <  !! Unit vectors for dipoles (lab frame)
270 <    real( kind = dp ), dimension(3,getNlocal()) :: u_l
271 < !! Force array provided by C, dimensioned by getNlocal
272 <    real ( kind = dp ), dimension(3,getNlocal()) :: f
273 < !! Torsion array provided by C, dimensioned by getNlocal
274 <    real( kind = dp ), dimension(3,getNlocal()) :: t
275 <
276 < !! Stress Tensor
277 <    real( kind = dp), dimension(9) :: tau
278 <    real( kind = dp), dimension(9) :: tauTemp
279 <    real ( kind = dp ) :: potE
280 <    logical ( kind = 2) :: do_pot
281 <    integer :: FFerror
282 <
332 >             enddo
333 >          endif
334 >       enddo
335 >    endif
336      
337 <    type(atype), pointer :: Atype_i
338 <    type(atype), pointer :: Atype_j
337 > #endif
338 >    
339 >    ! phew, done with main loop.
340 >    
341 > #ifdef IS_MPI
342 >    !!distribute forces
343 >    
344 >    call scatter(f_Row,f,plan_row3d)
345 >    call scatter(f_Col,f_temp,plan_col3d)
346 >    do i = 1,nlocal
347 >       f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
348 >    end do
349 >    
350 >    if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
351 >       call scatter(t_Row,t,plan_row3d)
352 >       call scatter(t_Col,t_temp,plan_col3d)
353 >      
354 >       do i = 1,nlocal
355 >          t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
356 >       end do
357 >    endif
358 >    
359 >    if (do_pot) then
360 >       ! scatter/gather pot_row into the members of my column
361 >       call scatter(pot_Row, pot_Temp, plan_row)
362 >      
363 >       ! scatter/gather pot_local into all other procs
364 >       ! add resultant to get total pot
365 >       do i = 1, nlocal
366 >          pot_local = pot_local + pot_Temp(i)
367 >       enddo
368  
369 +       pot_Temp = 0.0_DP
370  
371 +       call scatter(pot_Col, pot_Temp, plan_col)
372 +       do i = 1, nlocal
373 +          pot_local = pot_local + pot_Temp(i)
374 +       enddo
375 +      
376 +    endif    
377 + #endif
378  
379 +    if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
380 +      
381 +       if (FF_uses_RF .and. SimUsesRF()) then
382 +          
383 + #ifdef IS_MPI
384 +          call scatter(rf_Row,rf,plan_row3d)
385 +          call scatter(rf_Col,rf_Temp,plan_col3d)
386 +          do i = 1,nlocal
387 +             rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
388 +          end do
389 + #endif
390 +          
391 +          do i = 1, getNlocal()
392  
393 <  
291 <
393 >             rfpot = 0.0_DP
394   #ifdef IS_MPI
395 <  real( kind = DP ) :: pot_local
395 >             me_i = atid_row(i)
396 > #else
397 >             me_i = atid(i)
398 > #endif
399 >             call getElementProperty(atypes, me_i, "is_DP", is_DP_i)      
400 >             if ( is_DP_i ) then
401 >                call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
402 >                !! The reaction field needs to include a self contribution
403 >                !! to the field:
404 >                call accumulate_self_rf(i, mu_i, u_l)            
405 >                !! Get the reaction field contribution to the
406 >                !! potential and torques:
407 >                call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
408 > #ifdef IS_MPI
409 >                pot_local = pot_local + rfpot
410 > #else
411 >                pot = pot + rfpot
412 > #endif
413 >             endif            
414 >          enddo
415 >       endif
416 >    endif
417  
295 !! Local arrays needed for MPI
296  real(kind = dp), dimension(3,getNrow(plan_row)) :: qRow = 0.0_dp
297  real(kind = dp), dimension(3,getNcol(plan_col)) :: qCol = 0.0_dp
418  
419 <  real(kind = dp), dimension(3,getNrow(plan_row)) :: muRow = 0.0_dp
300 <  real(kind = dp), dimension(3,getNcol(plan_col)) :: muCol = 0.0_dp
419 > #ifdef IS_MPI
420  
421 <  real(kind = dp), dimension(3,getNrow(plan_row)) :: u_lRow = 0.0_dp
422 <  real(kind = dp), dimension(3,getNcol(plan_col)) :: u_lCol = 0.0_dp
421 >    if (do_pot) then
422 >       pot = pot_local
423 >       !! we assume the c code will do the allreduce to get the total potential
424 >       !! we could do it right here if we needed to...
425 >    endif
426  
427 <  real(kind = dp), dimension(3,getNrow(plan_row)) :: ARow = 0.0_dp
428 <  real(kind = dp), dimension(3,getNcol(plan_col)) :: ACol = 0.0_dp
427 >    if (do_stress) then
428 >       call mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, &
429 >            mpi_comm_world,mpi_err)
430 >       call mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, &
431 >            mpi_comm_world,mpi_err)
432 >    endif
433  
434 <  
434 > #else
435  
436 <  real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow = 0.0_dp
437 <  real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol = 0.0_dp
438 <  real(kind = dp), dimension(3,getNlocal()) :: fMPITemp = 0.0_dp
436 >    if (do_stress) then
437 >       tau = tau_Temp
438 >       virial = virial_Temp
439 >    endif
440  
441 <  real(kind = dp), dimension(3,getNrow(plan_row)) :: tRow = 0.0_dp
442 <  real(kind = dp), dimension(3,getNcol(plan_col)) :: tCol = 0.0_dp
443 <  real(kind = dp), dimension(3,getNlocal()) :: tMPITemp = 0.0_dp
441 > #endif
442 >    
443 >  end subroutine do_force_loop
444  
445 +  subroutine do_pair(i, j, rijsq, d, do_pot, do_stress)
446  
447 <  real(kind = dp), dimension(getNrow(plan_row)) :: eRow = 0.0_dp
448 <  real(kind = dp), dimension(getNcol(plan_col)) :: eCol = 0.0_dp
447 >    real( kind = dp ) :: pot
448 >    real( kind = dp ), dimension(3,getNlocal()) :: u_l
449 >    real (kind=dp), dimension(9,getNlocal()) :: A
450 >    real (kind=dp), dimension(3,getNlocal()) :: f
451 >    real (kind=dp), dimension(3,getNlocal()) :: t
452  
453 <  real(kind = dp), dimension(getNlocal()) :: eTemp = 0.0_dp
453 >    logical, intent(inout) :: do_pot, do_stress
454 >    integer, intent(in) :: i, j
455 >    real ( kind = dp ), intent(inout)    :: rijsq
456 >    real ( kind = dp )                :: r
457 >    real ( kind = dp ), intent(inout) :: d(3)
458 >    logical :: is_LJ_i, is_LJ_j
459 >    logical :: is_DP_i, is_DP_j
460 >    logical :: is_Sticky_i, is_Sticky_j
461 >    integer :: me_i, me_j
462  
463 < #endif
463 >    r = sqrt(rijsq)
464 >    
465 > #ifdef IS_MPI
466  
467 +    me_i = atid_row(i)
468 +    me_j = atid_col(j)
469  
470 + #else
471  
472 <  real( kind = DP )   :: pe
473 <  logical             :: update_nlist
472 >    me_i = atid(i)
473 >    me_j = atid(j)
474  
475 + #endif
476  
332  integer ::  i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2
333  integer :: nlist
334  integer :: j_start
335  integer :: tag_i,tag_j
336  real( kind = DP ) ::  r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp
337  real( kind = dp ) :: fx,fy,fz
338  real( kind = DP ) ::  drdx, drdy, drdz
339  real( kind = DP ) ::  rxi, ryi, rzi, rxij, ryij, rzij, rijsq
340  real( kind = DP ) ::  rlistsq, rcutsq,rlist,rcut
477  
478 <  real( kind = DP ) :: dielectric = 0.0_dp
478 >    if (FF_uses_LJ .and. SimUsesLJ()) then
479 >       call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
480 >       call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
481 >      
482 >       if ( is_LJ_i .and. is_LJ_j ) &
483 >            call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
484 >    endif
485 >      
486  
487 < ! a rig that need to be fixed.
488 < #ifdef IS_MPI
489 <  logical :: newtons_thrd = .true.
490 <  real( kind = dp ) :: pe_local
491 <  integer :: nlocal
492 < #endif
493 <  integer :: nrow
494 <  integer :: ncol
495 <  integer :: natoms
496 <  integer :: neighborListSize
497 <  integer :: listerror
498 < !! should we calculate the stress tensor
499 <  logical  :: do_stress = .false.
487 >    if (FF_uses_dipoles .and. SimUsesDipoles()) then
488 >       call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
489 >       call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
490 >      
491 >       if ( is_DP_i .and. is_DP_j ) then
492 >          
493 >          call do_dipole_pair(i, j, d, r, pot, u_l, f, t, do_pot, do_stress)
494 >          
495 >          if (FF_uses_RF .and. SimUsesRF()) then
496 >            
497 >             call accumulate_rf(i, j, r, u_l)
498 >             call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
499 >            
500 >          endif
501 >          
502 >       endif
503 >    endif
504  
505 +    if (FF_uses_Sticky .and. SimUsesSticky()) then
506  
507 <  FFerror = 0
507 >       call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
508 >       call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
509 >      
510 >       if ( is_Sticky_i .and. is_Sticky_j ) then
511 >          call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
512 >               do_pot, do_stress)
513 >       endif
514 >    endif
515 >      
516 >  end subroutine do_pair
517  
518 < ! Make sure we are properly initialized.
519 <  if (.not. isFFInit) then
520 <     write(default_error,*) "ERROR: lj_FF has not been properly initialized"
521 <     FFerror = -1
522 <     return
523 <  endif
518 >
519 >  subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
520 >    
521 >    real (kind = dp), dimension(3) :: q_i
522 >    real (kind = dp), dimension(3) :: q_j
523 >    real ( kind = dp ), intent(out) :: r_sq
524 >    real( kind = dp ) :: d(3)
525 >
526 >    d(1:3) = q_i(1:3) - q_j(1:3)
527 >    
528 >    ! Wrap back into periodic box if necessary
529 >    if ( SimUsesPBC() ) then
530 >       d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,box(1:3)) * &
531 >            int(abs(d(1:3)/box(1:3) + 0.5_dp))
532 >    endif
533 >    
534 >    r_sq = dot_product(d,d)
535 >        
536 >  end subroutine get_interatomic_vector
537 >
538 >  subroutine check_initialization(error)
539 >    integer, intent(out) :: error
540 >    
541 >    error = 0
542 >    ! Make sure we are properly initialized.
543 >    if (.not. do_forces_initialized) then
544 >       write(default_error,*) "ERROR: do_Forces has not been initialized!"
545 >       error = -1
546 >       return
547 >    endif
548 >
549   #ifdef IS_MPI
550      if (.not. isMPISimSet()) then
551 <     write(default_error,*) "ERROR: mpiSimulation has not been properly initialized"
552 <     FFerror = -1
553 <     return
554 <  endif
551 >       write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
552 >       error = -1
553 >       return
554 >    endif
555   #endif
556 +    
557 +    return
558 +  end subroutine check_initialization
559  
375 !! initialize local variables  
376  natoms = getNlocal()
377  call getRcut(rcut,rcut2=rcutsq)
378  call getRlist(rlist,rlistsq)
379 !! Find ensemble
380  if (isEnsemble("NPT")) do_stress = .true.
381
382 #ifndef IS_MPI
383  nrow = natoms - 1
384  ncol = natoms
385 #else
386  nrow = getNrow(plan_row)
387  ncol = getNcol(plan_col)
388  nlocal = natoms
389  j_start = 1
390 #endif
391
560    
561 < !! See if we need to update neighbor lists
562 <  call check(q,update_nlist)
563 < !  if (firstTime) then
396 < !     update_nlist = .true.
397 < !     firstTime = .false.
398 < !  endif
561 >  subroutine zero_work_arrays()
562 >    
563 > #ifdef IS_MPI
564  
565 < !--------------WARNING...........................
566 < ! Zero variables, NOTE:::: Forces are zeroed in C
567 < ! Zeroing them here could delete previously computed
568 < ! Forces.
569 < !------------------------------------------------
570 < #ifndef IS_MPI
571 < !  nloops = nloops + 1
572 <  pe = 0.0E0_DP
565 >    q_Row = 0.0_dp
566 >    q_Col = 0.0_dp  
567 >    
568 >    u_l_Row = 0.0_dp
569 >    u_l_Col = 0.0_dp
570 >    
571 >    A_Row = 0.0_dp
572 >    A_Col = 0.0_dp
573 >    
574 >    f_Row = 0.0_dp
575 >    f_Col = 0.0_dp
576 >    f_Temp = 0.0_dp
577 >      
578 >    t_Row = 0.0_dp
579 >    t_Col = 0.0_dp
580 >    t_Temp = 0.0_dp
581  
582 < #else
583 <    fRow = 0.0E0_DP
584 <    fCol = 0.0E0_DP
582 >    pot_Row = 0.0_dp
583 >    pot_Col = 0.0_dp
584 >    pot_Temp = 0.0_dp
585  
586 <    pe_local = 0.0E0_DP
586 >    rf_Row = 0.0_dp
587 >    rf_Col = 0.0_dp
588 >    rf_Temp = 0.0_dp
589  
415    eRow = 0.0E0_DP
416    eCol = 0.0E0_DP
417    eTemp = 0.0E0_DP
590   #endif
591  
592 < ! communicate MPI positions
593 < #ifdef IS_MPI    
594 <    call gather(q,qRow,plan_row3d)
595 <    call gather(q,qCol,plan_col3d)
592 >    rf = 0.0_dp
593 >    tau_Temp = 0.0_dp
594 >    virial_Temp = 0.0_dp
595 >    
596 >  end subroutine zero_work_arrays
597 >  
598  
599 <    call gather(mu,muRow,plan_row3d)
600 <    call gather(mu,muCol,plan_col3d)
599 >  !! Function to properly build neighbor lists in MPI using newtons 3rd law.
600 >  !! We don't want 2 processors doing the same i j pair twice.
601 >  !! Also checks to see if i and j are the same particle.
602  
603 <    call gather(u_l,u_lRow,plan_row3d)
429 <    call gather(u_l,u_lCol,plan_col3d)
430 <
431 <    call gather(A,ARow,plan_row_rotation)
432 <    call gather(A,ACol,plan_col_rotation)
433 <
434 < #endif
435 <
436 <
437 <  if (update_nlist) then
438 <
439 <     ! save current configuration, contruct neighbor list,
440 <     ! and calculate forces
441 <     call save_neighborList(q)
442 <    
443 <     neighborListSize = getNeighborListSize()
444 <     nlist = 0
445 <    
603 >  function checkExcludes(atom1,atom2) result(do_cycle)
604      
605 +    integer,intent(in) :: atom1
606 +    integer,intent(in), optional :: atom2
607 +    logical :: do_cycle
608 +    integer :: unique_id_1, unique_id_2
609 +    integer :: i, j
610  
611 <     do i = 1, nrow
612 <        point(i) = nlist + 1
611 >    do_cycle = .false.
612 >    
613   #ifdef IS_MPI
614 <        ljAtype_i => identPtrListRow(i)%this
452 <        tag_i = tagRow(i)
453 <        rxi = qRow(1,i)
454 <        ryi = qRow(2,i)
455 <        rzi = qRow(3,i)
614 >    unique_id_1 = tagRow(atom1)
615   #else
616 <        ljAtype_i   => identPtrList(i)%this
458 <        j_start = i + 1
459 <        rxi = q(1,i)
460 <        ryi = q(2,i)
461 <        rzi = q(3,i)
616 >    unique_id_1 = tag(atom1)
617   #endif
618 <
619 <        inner: do j = j_start, ncol
620 < #ifdef IS_MPI
621 < ! Assign identity pointers and tags
622 <           ljAtype_j => identPtrListColumn(j)%this
623 <           tag_j = tagColumn(j)
624 <           if (newtons_thrd) then
625 <              if (tag_i <= tag_j) then
626 <                 if (mod(tag_i + tag_j,2) == 0) cycle inner
627 <              else                
628 <                 if (mod(tag_i + tag_j,2) == 1) cycle inner
474 <              endif
475 <           endif
476 <
477 <           rxij = wrap(rxi - qCol(1,j), 1)
478 <           ryij = wrap(ryi - qCol(2,j), 2)
479 <           rzij = wrap(rzi - qCol(3,j), 3)
480 < #else          
481 <           ljAtype_j   => identPtrList(j)%this
482 <           rxij = wrap(rxi - q(1,j), 1)
483 <           ryij = wrap(ryi - q(2,j), 2)
484 <           rzij = wrap(rzi - q(3,j), 3)
485 <      
486 < #endif          
487 <           rijsq = rxij*rxij + ryij*ryij + rzij*rzij
618 >    
619 >    !! Check global excludes first
620 >    if (.not. present(atom2)) then
621 >       do i = 1, nExcludes_global
622 >          if (excludesGlobal(i) == unique_id_1) then
623 >             do_cycle = .true.
624 >             return
625 >          end if
626 >       end do
627 >       return !! return after checking globals
628 >    end if
629  
630 < #ifdef IS_MPI
490 <             if (rijsq <=  rlistsq .AND. &
491 <                  tag_j /= tag_i) then
492 < #else
493 <          
494 <             if (rijsq <  rlistsq) then
495 < #endif
496 <            
497 <              nlist = nlist + 1
498 <              if (nlist > neighborListSize) then
499 <                 call expandList(listerror)
500 <                 if (listerror /= 0) then
501 <                    FFerror = -1
502 <                    write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
503 <                    return
504 <                 end if
505 <              endif
506 <              list(nlist) = j
507 <
630 >    !! we return if atom2 not present here.
631      
509              if (rijsq <  rcutsq) then
510                
511                 r = dsqrt(rijsq)
512      
513                 call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j)
514      
632   #ifdef IS_MPI
633 <                eRow(i) = eRow(i) + pot*0.5
517 <                eCol(i) = eCol(i) + pot*0.5
633 >    unique_id_2 = tagColumn(atom2)
634   #else
635 <                    pe = pe + pot
520 < #endif                
521 <            
522 <                drdx = -rxij / r
523 <                drdy = -ryij / r
524 <                drdz = -rzij / r
525 <                
526 <                fx = dudr * drdx
527 <                fy = dudr * drdy
528 <                fz = dudr * drdz
529 <                
530 < #ifdef IS_MPI
531 <                fCol(1,j) = fCol(1,j) - fx
532 <                fCol(2,j) = fCol(2,j) - fy
533 <                fCol(3,j) = fCol(3,j) - fz
534 <                
535 <                fRow(1,j) = fRow(1,j) + fx
536 <                fRow(2,j) = fRow(2,j) + fy
537 <                fRow(3,j) = fRow(3,j) + fz
538 < #else
539 <                f(1,j) = f(1,j) - fx
540 <                f(2,j) = f(2,j) - fy
541 <                f(3,j) = f(3,j) - fz
542 <                f(1,i) = f(1,i) + fx
543 <                f(2,i) = f(2,i) + fy
544 <                f(3,i) = f(3,i) + fz
635 >    unique_id_2 = tag(atom2)
636   #endif
546                
547                if (do_stress) then
548                   tauTemp(1) = tauTemp(1) + fx * rxij
549                   tauTemp(2) = tauTemp(2) + fx * ryij
550                   tauTemp(3) = tauTemp(3) + fx * rzij
551                   tauTemp(4) = tauTemp(4) + fy * rxij
552                   tauTemp(5) = tauTemp(5) + fy * ryij
553                   tauTemp(6) = tauTemp(6) + fy * rzij
554                   tauTemp(7) = tauTemp(7) + fz * rxij
555                   tauTemp(8) = tauTemp(8) + fz * ryij
556                   tauTemp(9) = tauTemp(9) + fz * rzij
557                endif
558             endif
559          enddo inner
560     enddo
561
562 #ifdef IS_MPI
563     point(nrow + 1) = nlist + 1
564 #else
565     point(natoms) = nlist + 1
566 #endif
567
568  else
569
570     ! use the list to find the neighbors
571     do i = 1, nrow
572        JBEG = POINT(i)
573        JEND = POINT(i+1) - 1
574        ! check thiat molecule i has neighbors
575        if (jbeg .le. jend) then
576 #ifdef IS_MPI
577           ljAtype_i => identPtrListRow(i)%this
578           rxi = qRow(1,i)
579           ryi = qRow(2,i)
580           rzi = qRow(3,i)
581 #else
582           ljAtype_i   => identPtrList(i)%this
583           rxi = q(1,i)
584           ryi = q(2,i)
585           rzi = q(3,i)
586 #endif
587           do jnab = jbeg, jend
588              j = list(jnab)
589 #ifdef IS_MPI
590              ljAtype_j = identPtrListColumn(j)%this
591              rxij = wrap(rxi - qCol(1,j), 1)
592              ryij = wrap(ryi - qCol(2,j), 2)
593              rzij = wrap(rzi - qCol(3,j), 3)
594 #else
595              ljAtype_j = identPtrList(j)%this
596              rxij = wrap(rxi - q(1,j), 1)
597              ryij = wrap(ryi - q(2,j), 2)
598              rzij = wrap(rzi - q(3,j), 3)
599 #endif
600              rijsq = rxij*rxij + ryij*ryij + rzij*rzij
601              
602              if (rijsq <  rcutsq) then
603
604                 r = dsqrt(rijsq)
605                
606                 call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j)
607 #ifdef IS_MPI
608                eRow(i) = eRow(i) + pot*0.5
609                eCol(i) = eCol(i) + pot*0.5
610 #else
611                pe = pe + pot
612 #endif                
613  
614                drdx = -rxij / r
615                drdy = -ryij / r
616                drdz = -rzij / r
617                
618                fx = dudr * drdx
619                fy = dudr * drdy
620                fz = dudr * drdz
621                
622 #ifdef IS_MPI
623                fCol(1,j) = fCol(1,j) - fx
624                fCol(2,j) = fCol(2,j) - fy
625                fCol(3,j) = fCol(3,j) - fz
626                
627                fRow(1,j) = fRow(1,j) + fx
628                fRow(2,j) = fRow(2,j) + fy
629                fRow(3,j) = fRow(3,j) + fz
630 #else
631                f(1,j) = f(1,j) - fx
632                f(2,j) = f(2,j) - fy
633                f(3,j) = f(3,j) - fz
634                f(1,i) = f(1,i) + fx
635                f(2,i) = f(2,i) + fy
636                f(3,i) = f(3,i) + fz
637 #endif
638                
639                if (do_stress) then
640                   tauTemp(1) = tauTemp(1) + fx * rxij
641                   tauTemp(2) = tauTemp(2) + fx * ryij
642                   tauTemp(3) = tauTemp(3) + fx * rzij
643                   tauTemp(4) = tauTemp(4) + fy * rxij
644                   tauTemp(5) = tauTemp(5) + fy * ryij
645                   tauTemp(6) = tauTemp(6) + fy * rzij
646                   tauTemp(7) = tauTemp(7) + fz * rxij
647                   tauTemp(8) = tauTemp(8) + fz * ryij
648                   tauTemp(9) = tauTemp(9) + fz * rzij
649                endif
650                
651                
652             endif
653          enddo
654       endif
655    enddo
656 endif
657
658
659
660 #ifdef IS_MPI
661    !!distribute forces
662
663    call scatter(fRow,f,plan_row3d)
664    call scatter(fCol,fMPITemp,plan_col3d)
665
666    do i = 1,nlocal
667       f(1:3,i) = f(1:3,i) + fMPITemp(1:3,i)
668    end do
669
670
671    call scatter(tRow,t,plan_row3d)
672    call scatter(tCol,tMPITemp,plan_col3d)
637      
638 <    do i = 1,nlocal
639 <       t(1:3,i) = t(1:3,i) + tMPITemp(1:3,i)
638 >    if (unique_id_1 == unique_id_2) then
639 >       do_cycle = .true.
640 >       return
641 >    end if
642 >    
643 >    if (unique_id_1 < unique_id_2) then
644 >       if (mod(unique_id_1 + unique_id_2,2) == 0) do_cycle = .true.
645 >       return
646 >    else                
647 >       if (mod(unique_id_1 + unique_id_2,2) == 1) do_cycle = .true.
648 >    endif
649 >    
650 >    do i = 1, nExcludes_local
651 >       if ((unique_id_1 == excludesLocal(1,i)) .and.  &
652 >            (excludesLocal(2,i) < 0)) then
653 >          do_cycle = .true.
654 >          return
655 >       end if
656      end do
657 +    
658 +  end function checkExcludes
659  
660 <
661 <    if (do_pot) then
662 <       ! scatter/gather pot_row into the members of my column
663 <       call scatter(eRow,eTemp,plan_row)
664 <      
665 <       ! scatter/gather pot_local into all other procs
666 <       ! add resultant to get total pot
667 <       do i = 1, nlocal
668 <          pe_local = pe_local + eTemp(i)
669 <       enddo
670 <       if (newtons_thrd) then
671 <          eTemp = 0.0E0_DP
672 <          call scatter(eCol,eTemp,plan_col)
673 <          do i = 1, nlocal
674 <             pe_local = pe_local + eTemp(i)
675 <          enddo
694 <       endif
695 <       pe = pe_local
696 <    endif
697 <
698 < #endif
699 <
700 <    potE = pe
701 <
702 <
703 <    if (do_stress) then
704 < #ifdef IS_MPI
705 <       mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, &
706 <            mpi_comm_world,mpi_err)
707 < #else
708 <       tau = tauTemp
709 < #endif      
710 <    endif
711 <
712 <
713 <  end subroutine do_force_loop
714 <
715 <
716 <
660 >  function FF_UsesDirectionalAtoms() result(doesit)
661 >    logical :: doesit
662 >    doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
663 >         FF_uses_GB .or. FF_uses_RF
664 >  end function FF_UsesDirectionalAtoms
665 >  
666 >  function FF_RequiresPrepairCalc() result(doesit)
667 >    logical :: doesit
668 >    doesit = FF_uses_EAM
669 >  end function FF_RequiresPrepairCalc
670 >  
671 >  function FF_RequiresPostpairCalc() result(doesit)
672 >    logical :: doesit
673 >    doesit = FF_uses_RF
674 >  end function FF_RequiresPostpairCalc
675 >  
676   end module do_Forces

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