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Comparing trunk/OOPSE_old/src/mdtools/libmdCode/do_Forces.F90 (file contents):
Revision 295 by chuckv, Thu Mar 6 19:57:03 2003 UTC vs.
Revision 334 by gezelter, Thu Mar 13 17:45:54 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 1.3 2003-03-06 19:57:03 chuckv Exp $, $Date: 2003-03-06 19:57:03 $, $Name: not supported by cvs2svn $, $Revision: 1.3 $
7 > !! @version $Id: do_Forces.F90,v 1.19 2003-03-13 17:45:54 gezelter Exp $, $Date: 2003-03-13 17:45:54 $, $Name: not supported by cvs2svn $, $Revision: 1.19 $
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 –
34 –
35 –  logical, save :: firstTime = .True.
36 –
37 – !! Atype identity pointer lists
38 – #ifdef IS_MPI
39 – !! Row lj_atype pointer list
40 –  type (identPtrList), dimension(:), pointer :: identPtrListRow => null()
41 – !! Column lj_atype pointer list
42 –  type (identPtrList), dimension(:), pointer :: identPtrListColumn => null()
43 – #else
44 –  type(identPtrList ), dimension(:), pointer :: identPtrList => null()
45 – #endif
46 –
47 –
48 – !! Logical has lj force field module been initialized?
49 –  logical, save :: isFFinit = .false.
50 –
51 – !! Use periodic boundry conditions
52 –  logical :: wrap = .false.
53 –
54 – !! Potential energy global module variables
55 – #ifdef IS_MPI
56 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: qRow = 0.0_dp
57 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: qCol = 0.0_dp
58 –
59 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: muRow = 0.0_dp
60 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: muCol = 0.0_dp
61 –
62 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: u_lRow = 0.0_dp
63 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: u_lCol = 0.0_dp
64 –
65 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: ARow = 0.0_dp
66 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: ACol = 0.0_dp
67 –
68 –  
69 –
70 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow = 0.0_dp
71 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol = 0.0_dp
72 –
73 –
74 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: tRow = 0.0_dp
75 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: tCol = 0.0_dp
76 –
77 –
78 –
79 –  real(kind = dp), dimension(getNrow(plan_row)) :: eRow = 0.0_dp
80 –  real(kind = dp), dimension(getNcol(plan_col)) :: eCol = 0.0_dp
81 –
82 –  real(kind = dp), dimension(getNlocal()) :: eTemp = 0.0_dp
83 – #endif
84 –  real(kind = dp) :: pe = 0.0_dp
85 –  real(kind = dp), dimension(3,getNlocal()) :: fTemp = 0.0_dp
86 –  real(kind = dp), dimension(3,getNlocal()) :: tTemp = 0.0_dp
87 –  real(kind = dp), dimension(9) :: tauTemp = 0.0_dp
88 –
89 –  logical :: do_preForce  = .false.
90 –  logical :: do_postForce = .false.
91 –
92 –
93 –
94 – !! Public methods and data
95 –  public :: new_atype
96 –  public :: do_forceLoop
35    public :: init_FF
36 +  public :: do_force_loop
37  
99 –  
100 –
101 –
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
125 <    integer :: alloc_size
126 <    integer :: err_stat
127 <    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
137 –
138 – ! assign our new atype information
139 –    the_new_atype%mass        = mass
140 –    the_new_atype%epsilon     = epsilon
141 –    the_new_atype%sigma       = sigma
142 –    the_new_atype%sigma2      = sigma * sigma
143 –    the_new_atype%sigma6      = the_new_atype%sigma2 * the_new_atype%sigma2 &
144 –         * the_new_atype%sigma2
145 –    the_new_atype%w0       = w0
146 –    the_new_atype%v0       = v0
147 –    the_new_atype%dipoleMoment       = dipoleMoment
148 –
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.
157 <    if ( is_DP /= 0 )        the_new_atype%is_DP       = .true.
111 >    do_forces_initialized = .true.    
112 >    
113 >  end subroutine init_FF
114  
159 –    call add_atype(the_new_atype,ListHead,ListTail,err_stat)
160 –    if (err_stat /= 0 ) then
161 –       status = -1
162 –       return
163 –    endif
115  
165 –    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
188 <    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
201 <       status = -1
202 <       return
203 <    endif
204 <
205 <    
206 < ! if were're in MPI, we also have to worry about row and col lists    
158 > #ifdef IS_MPI
159 >    nlocal = getNlocal()
160 >    nrow   = getNrow(plan_row)
161 >    ncol   = getNcol(plan_col)
162   #else
163 <  
164 < ! We can only set up forces if mpiSimulation has been setup.
165 <    if (.not. isMPISimSet()) then
211 <       write(default_error,*) "MPI is not set"
212 <       status = -1
213 <       return
214 <    endif
215 <    nrow = getNrow(plan_row)
216 <    ncol = getNcol(plan_col)
217 <    mynode = getMyNode()
218 < !! Allocate temperary arrays to hold gather information
219 <    allocate(identRow(nrow),stat=alloc_stat)
220 <    if (alloc_stat /= 0 ) then
221 <       status = -1
222 <       return
223 <    endif
163 >    nlocal = getNlocal()
164 >    natoms = nlocal
165 > #endif
166  
167 <    allocate(identCol(ncol),stat=alloc_stat)
168 <    if (alloc_stat /= 0 ) then
227 <       status = -1
228 <       return
229 <    endif
230 <
231 < !! Gather idents into row and column idents
232 <
233 <    call gather(ident,identRow,plan_row)
234 <    call gather(ident,identCol,plan_col)
167 >    call getRcut(rcut,rc2=rcutsq)
168 >    call getRlist(rlist,rlistsq)
169      
170 <  
171 < !! Create row and col pointer lists
172 <  
239 <    call create_IdentPtrlst(identRow,ListHead,identPtrListRow,thisStat)
240 <    if (thisStat /= 0 ) then
241 <       status = -1
170 >    call check_initialization(localError)
171 >    if ( localError .ne. 0 ) then
172 >       error = -1
173         return
243 –    endif
244 –  
245 –    call create_IdentPtrlst(identCol,ListHead,identPtrListColumn,thisStat)
246 –    if (thisStat /= 0 ) then
247 –       status = -1
248 –       return
249 –    endif
250 –
251 – !! free temporary ident arrays
252 –    if (allocated(identCol)) then
253 –       deallocate(identCol)
174      end if
175 <    if (allocated(identCol)) then
176 <       deallocate(identRow)
177 <    endif
175 >    call zero_work_arrays()
176 >
177 >    do_pot = do_pot_c
178 >    do_stress = do_stress_c
179  
180 < #endif
180 >    ! Gather all information needed by all force loops:
181      
182 <    call initForce_Modules(thisStat)
262 <    if (thisStat /= 0) then
263 <       status = -1
264 <       return
265 <    endif
182 > #ifdef IS_MPI    
183  
184 < !! Create neighbor lists
185 <    call expandList(thisStat)
186 <    if (thisStat /= 0) then
187 <       status = -1
188 <       return
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
273 –
274 –    isFFinit = .true.
275 –
276 –
277 –  end subroutine init_FF
278 –
279 –
280 –
281 –
282 –  subroutine initForce_Modules(thisStat)
283 –    integer, intent(out) :: thisStat
284 –    integer :: my_status
194      
195 <    thisStat = 0
287 <    call init_lj_FF(ListHead,my_status)
288 <    if (my_status /= 0) then
289 <       thisStat = -1
290 <       return
291 <    end if
292 <
293 <  end subroutine initForce_Modules
294 <
295 <
296 <
297 <
298 < !! FORCE routine Calculates Lennard Jones forces.
299 < !------------------------------------------------------------->
300 <  subroutine do__force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror)
301 < !! Position array provided by C, dimensioned by getNlocal
302 <    real ( kind = dp ), dimension(3,getNlocal()) :: q
303 <  !! Rotation Matrix for each long range particle in simulation.
304 <    real( kind = dp), dimension(9,getNlocal()) :: A
305 <
306 <  !! Magnitude dipole moment
307 <    real( kind = dp ), dimension(3,getNlocal()) :: mu
308 <  !! Unit vectors for dipoles (lab frame)
309 <    real( kind = dp ), dimension(3,getNlocal()) :: u_l
310 < !! Force array provided by C, dimensioned by getNlocal
311 <    real ( kind = dp ), dimension(3,getNlocal()) :: f
312 < !! Torsion array provided by C, dimensioned by getNlocal
313 <    real( kind = dp ), dimension(3,getNlocal()) :: t
314 <
315 < !! Stress Tensor
316 <    real( kind = dp), dimension(9) :: tau
317 <
318 <    real ( kind = dp ) :: potE
319 <    logical ( kind = 2) :: do_pot
320 <    integer :: FFerror
321 <
195 > #endif
196      
197 <    type(atype), pointer :: Atype_i
198 <    type(atype), pointer :: Atype_j
199 <
200 <
201 <
202 <
203 <  
204 <
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
332 –  real( kind = DP ) :: pot_local
333 –
334 – !! Local arrays needed for MPI
335 –
336 – #endif
337 –
338 –
339 –
340 –  real( kind = DP )   :: pe
341 –  logical             :: update_nlist
342 –
343 –
344 –  integer ::  i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2
345 –  integer :: nlist
346 –  integer :: j_start
347 –
348 –  real( kind = DP ) ::  r_ij, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp
349 –
350 –  real( kind = DP ) ::  rx_ij, ry_ij, rz_ij, rijsq
351 –  real( kind = DP ) ::  rlistsq, rcutsq,rlist,rcut
352 –
353 –  real( kind = DP ) :: dielectric = 0.0_dp
354 –
355 – ! a rig that need to be fixed.
356 – #ifdef IS_MPI
357 –  real( kind = dp ) :: pe_local
358 –  integer :: nlocal
359 – #endif
360 –  integer :: nrow
361 –  integer :: ncol
362 –  integer :: natoms
363 –  integer :: neighborListSize
364 –  integer :: listerror
365 – !! should we calculate the stress tensor
366 –  logical  :: do_stress = .false.
367 –
368 –
369 –  FFerror = 0
370 –
371 – ! Make sure we are properly initialized.
372 –  if (.not. isFFInit) then
373 –     write(default_error,*) "ERROR: lj_FF has not been properly initialized"
374 –     FFerror = -1
375 –     return
376 –  endif
377 – #ifdef IS_MPI
378 –    if (.not. isMPISimSet()) then
379 –     write(default_error,*) "ERROR: mpiSimulation has not been properly initialized"
380 –     FFerror = -1
381 –     return
382 –  endif
383 – #endif
384 –
385 – !! initialize local variables  
386 –  natoms = getNlocal()
387 –  call getRcut(rcut,rcut2=rcutsq)
388 –  call getRlist(rlist,rlistsq)
389 –
390 – !! Find ensemble
391 –  if (isEnsemble("NPT")) do_stress = .true.
392 – !! set to wrap
393 –  if (isPBC()) wrap = .true.
394 –
395 –
396 – #ifndef IS_MPI
397 –  nrow = natoms - 1
398 –  ncol = natoms
399 – #else
400 –  nrow = getNrow(plan_row)
401 –  ncol = getNcol(plan_col)
402 –  nlocal = natoms
403 –  j_start = 1
404 – #endif
405 –
406 –  
407 – !! See if we need to update neighbor lists
408 –  call check(q,update_nlist)
409 –
410 – !--------------WARNING...........................
411 – ! Zero variables, NOTE:::: Forces are zeroed in C
412 – ! Zeroing them here could delete previously computed
413 – ! Forces.
414 – !------------------------------------------------
415 –  call zero_module_variables()
416 –
417 –
418 – ! communicate MPI positions
419 – #ifdef IS_MPI    
420 –    call gather(q,qRow,plan_row3d)
421 –    call gather(q,qCol,plan_col3d)
422 –
423 –    call gather(mu,muRow,plan_row3d)
424 –    call gather(mu,muCol,plan_col3d)
425 –
426 –    call gather(u_l,u_lRow,plan_row3d)
427 –    call gather(u_l,u_lCol,plan_col3d)
428 –
429 –    call gather(A,ARow,plan_row_rotation)
430 –    call gather(A,ACol,plan_col_rotation)
431 – #endif
432 –
433 –
434 –  if (update_nlist) then
435 –
436 –     ! save current configuration, contruct neighbor list,
437 –     ! and calculate forces
438 –     call save_neighborList(q)
439 –    
440 –     neighborListSize = getNeighborListSize()
441 –     nlist = 0
442 –    
210      
211 +    if (update_nlist) then
212 +      
213 +       !! save current configuration, construct neighbor list,
214 +       !! and calculate forces
215 +       call saveNeighborList(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 (skipThisPair(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 <     do i = 1, nrow
446 <        point(i) = nlist + 1
447 < #ifdef IS_MPI
448 <        Atype_i => identPtrListRow(i)%this
449 <        tag_i = tagRow(i)
450 < #else
451 <        Atype_i   => identPtrList(i)%this
452 <        j_start = i + 1
453 < #endif
454 <
455 <        inner: do j = j_start, ncol
456 < ! Assign identity pointers and tags
457 < #ifdef IS_MPI
458 <           Atype_j => identPtrListColumn(j)%this
459 <          
460 <           call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),&
461 <                rxij,ryij,rzij,rijsq,r)
462 < !! For mpi, use newtons 3rd law when building neigbor list
463 < !! Also check to see the particle i != j.
464 <           if (mpi_cycle_jLoop(i,j)) cycle inner:
465 <
466 < #else          
467 <           Atype_j   => identPtrList(j)%this
468 <           call get_interatomic_vector(i,j,q(:,i),q(:,j),&
469 <                rxij,ryij,rzij,rijsq,r)
251 >       point(nrow + 1) = nlist + 1
252        
253 < #endif          
472 <          
473 <           if (rijsq <  rlistsq) then
253 >    else  !! (of update_check)
254  
255 <              nlist = nlist + 1
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 <              if (nlist > neighborListSize) then
266 <                 call expandList(listerror)
479 <                 if (listerror /= 0) then
480 <                    FFerror = -1
481 <                    write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
482 <                    return
483 <                 end if
484 <              endif
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 <              list(nlist) = j
269 <
268 >             enddo
269 >          endif
270 >       enddo
271 >    endif
272      
489 –              if (rijsq <  rcutsq) then
490 –                 call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
491 –              endif
492 –          enddo inner
493 –     enddo
494 –
495 – #ifdef IS_MPI
496 –     point(nrow + 1) = nlist + 1
273   #else
274 <     point(natoms) = nlist + 1
275 < #endif
276 <
277 <  else !! (update)
278 <
279 <     ! use the list to find the neighbors
280 <     do i = 1, nrow
281 <        JBEG = POINT(i)
282 <        JEND = POINT(i+1) - 1
283 <        ! check thiat molecule i has neighbors
284 <        if (jbeg .le. jend) then
274 >    
275 >    if (update_nlist) then
276 >      
277 >       ! save current configuration, contruct neighbor list,
278 >       ! and calculate forces
279 >       call saveNeighborList(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 (skipThisPair(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 < #ifdef IS_MPI
330 <           ljAtype_i => identPtrListRow(i)%this
512 < #else
513 <           ljAtype_i => identPtrList(i)%this
514 < #endif
515 <           do jnab = jbeg, jend
516 <              j = list(jnab)
517 < #ifdef IS_MPI
518 <              ljAtype_j = identPtrListColumn(j)%this
519 <              call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),&
520 <                   rxij,ryij,rzij,rijsq,r)
521 <              
522 < #else
523 <              ljAtype_j = identPtrList(j)%this
524 <              call get_interatomic_vector(i,j,q(:,i),q(:,j),&
525 <                   rxij,ryij,rzij,rijsq,r)
526 < #endif
527 <              call do_pair(i,j,r,rxij,ryij,rzij)
528 <          enddo
529 <       endif
530 <    enddo
531 < endif
532 <
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 <
332 >             enddo
333 >          endif
334 >       enddo
335 >    endif
336 >    
337 > #endif
338 >    
339 >    ! phew, done with main loop.
340 >    
341   #ifdef IS_MPI
342      !!distribute forces
343 <
344 <    call scatter(fRow,f,plan_row3d)
345 <    call scatter(fCol,fTemp,plan_col3d)
540 <
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) + fTemp(1:3,i)
347 >       f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
348      end do
544 –
545 –    if (do_torque) then
546 –       call scatter(tRow,t,plan_row3d)
547 –       call scatter(tCol,tTemp,plan_col3d)
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) + tTemp(1:3,i)
355 >          t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
356         end do
357      endif
358 <
358 >    
359      if (do_pot) then
360         ! scatter/gather pot_row into the members of my column
361 <       call scatter(eRow,eTemp,plan_row)
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 <          pe_local = pe_local + eTemp(i)
366 >          pot_local = pot_local + pot_Temp(i)
367         enddo
368  
369 <       eTemp = 0.0E0_DP
370 <       call scatter(eCol,eTemp,plan_col)
369 >       pot_Temp = 0.0_DP
370 >
371 >       call scatter(pot_Col, pot_Temp, plan_col)
372         do i = 1, nlocal
373 <          pe_local = pe_local + eTemp(i)
373 >          pot_local = pot_local + pot_Temp(i)
374         enddo
375        
376 <       pe = pe_local
571 <    endif
572 < #else
573 < ! Copy local array into return array for c
574 <    f = fTemp
575 <    t = tTemp
376 >    endif    
377   #endif
378  
379 <    potE = pe
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 <
581 <    if (do_stress) then
393 >             rfpot = 0.0_DP
394   #ifdef IS_MPI
395 <       mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, &
584 <            mpi_comm_world,mpi_err)
395 >             me_i = atid_row(i)
396   #else
397 <       tau = tauTemp
398 < #endif      
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  
590 –  end subroutine do_force_loop
418  
419 + #ifdef IS_MPI
420  
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 +    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 + #else
435  
436 +    if (do_stress) then
437 +       tau = tau_Temp
438 +       virial = virial_Temp
439 +    endif
440  
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 ) :: 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 +    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 < !! Calculate any pre-force loop components and update nlist if necessary.
464 <  subroutine do_preForce(updateNlist)
465 <    logical, intent(inout) :: updateNlist
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 <  end subroutine do_preForce
472 >    me_i = atid(i)
473 >    me_j = atid(j)
474  
475 + #endif
476  
477  
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 <
488 <
489 <
615 <
616 <
617 <
618 <
619 <
620 <
621 < !! Calculate any post force loop components, i.e. reaction field, etc.
622 <  subroutine do_postForce()
623 <
624 <
625 <
626 <  end subroutine do_postForce
627 <
628 <
629 <
630 <
631 <
632 <
633 <
634 <
635 <
636 <
637 <
638 <
639 <
640 <
641 <
642 <
643 <
644 <  subroutine do_pair(atype_i,atype_j,i,j,r_ij,rx_ij,ry_ij,rz_ij)
645 <    type (atype ), pointer, intent(inout) :: atype_i
646 <    type (atype ), pointer, intent(inout) :: atype_j
647 <    integer :: i
648 <    integer :: j
649 <    real ( kind = dp ), intent(inout) :: rx_ij
650 <    real ( kind = dp ), intent(inout) :: ry_ij
651 <    real ( kind = dp ), intent(inout) :: rz_ij
652 <
653 <
654 <    real( kind = dp ) :: fx = 0.0_dp
655 <    real( kind = dp ) :: fy = 0.0_dp
656 <    real( kind = dp ) :: fz = 0.0_dp  
657 <
658 <    real( kind = dp ) ::  drdx = 0.0_dp
659 <    real( kind = dp ) ::  drdy = 0.0_dp
660 <    real( kind = dp ) ::  drdz = 0.0_dp
661 <    
662 <
663 <
664 <
665 <
666 <
667 <    call getLJForce(r,pot,dudr,ljAtype_i,ljAtype_j)
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 < #ifdef IS_MPI
492 <                eRow(i) = eRow(i) + pot*0.5
493 <                eCol(i) = eCol(i) + pot*0.5
494 < #else
495 <                    pe = pe + pot
674 < #endif                
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 <                drdx = -rxij / r
498 <                drdy = -ryij / r
499 <                drdz = -rzij / r
500 <                
501 <                fx = dudr * drdx
502 <                fy = dudr * drdy
503 <                fz = dudr * drdz
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 <
508 <
509 <
510 <
511 <                
512 < #ifdef IS_MPI
513 <                fCol(1,j) = fCol(1,j) - fx
514 <                fCol(2,j) = fCol(2,j) - fy
515 <                fCol(3,j) = fCol(3,j) - fz
694 <                
695 <                fRow(1,j) = fRow(1,j) + fx
696 <                fRow(2,j) = fRow(2,j) + fy
697 <                fRow(3,j) = fRow(3,j) + fz
698 < #else
699 <                fTemp(1,j) = fTemp(1,j) - fx
700 <                fTemp(2,j) = fTemp(2,j) - fy
701 <                fTemp(3,j) = fTemp(3,j) - fz
702 <                fTemp(1,i) = fTemp(1,i) + fx
703 <                fTemp(2,i) = fTemp(2,i) + fy
704 <                fTemp(3,i) = fTemp(3,i) + fz
705 < #endif
706 <                
707 <                if (do_stress) then
708 <                   tauTemp(1) = tauTemp(1) + fx * rxij
709 <                   tauTemp(2) = tauTemp(2) + fx * ryij
710 <                   tauTemp(3) = tauTemp(3) + fx * rzij
711 <                   tauTemp(4) = tauTemp(4) + fy * rxij
712 <                   tauTemp(5) = tauTemp(5) + fy * ryij
713 <                   tauTemp(6) = tauTemp(6) + fy * rzij
714 <                   tauTemp(7) = tauTemp(7) + fz * rxij
715 <                   tauTemp(8) = tauTemp(8) + fz * ryij
716 <                   tauTemp(9) = tauTemp(9) + fz * rzij
717 <                endif
718 <
719 <
720 <
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  
519 <
520 <
726 <
727 <
728 <
729 <
730 <
731 <
732 <
733 <
734 <
735 <
736 <
737 <
738 <  subroutine get_interatomic_vector(q_i,q_j,rx_ij,ry_ij,rz_ij,r_sq,r_ij)
739 < !---------------- Arguments-------------------------------
740 <   !! index i
741 <
742 <    !! Position array
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
745 –    !! x component of vector between i and j
746 –    real ( kind = dp ), intent(out)  :: rx_ij
747 –    !! y component of vector between i and j
748 –    real ( kind = dp ), intent(out)  :: ry_ij
749 –    !! z component of vector between i and j
750 –    real ( kind = dp ), intent(out)  :: rz_ij
751 –    !! magnitude of r squared
523      real ( kind = dp ), intent(out) :: r_sq
753 –    !! magnitude of vector r between atoms i and j.
754 –    real ( kind = dp ), intent(out) :: r_ij
755 –    !! wrap into periodic box.
756 –    logical, intent(in) :: wrap
757 –
758 – !--------------- Local Variables---------------------------
759 –    !! Distance between i and j
524      real( kind = dp ) :: d(3)
761 – !---------------- END DECLARATIONS-------------------------
525  
763 –
764 – ! Find distance between i and j
526      d(1:3) = q_i(1:3) - q_j(1:3)
766 –
767 – ! Wrap back into periodic box if necessary
768 –    if ( wrap ) then
769 –       d(1:3) = d(1:3) - thisSim%box(1:3) * sign(1.0_dp,thisSim%box(1:3)) * &
770 –            int(abs(d(1:3)/thisSim%box(1:3) + 0.5_dp)
771 –    end if
527      
528 < !   Find Magnitude of the vector
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 <    r_ij = sqrt(r_sq)
776 <
777 < !   Set each component for force calculation
778 <    rx_ij = d(1)
779 <    ry_ij = d(2)
780 <    rz_ij = d(3)
781 <
782 <
535 >        
536    end subroutine get_interatomic_vector
537  
538 <  subroutine zero_module_variables()
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 < #ifndef IS_MPI
549 > #ifdef IS_MPI
550 >    if (.not. isMPISimSet()) then
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  
560 <    pe = 0.0E0_DP
561 <    tauTemp = 0.0_dp
791 <    fTemp = 0.0_dp
792 <    tTemp = 0.0_dp
793 < #else
794 <    qRow = 0.0_dp
795 <    qCol = 0.0_dp
560 >  
561 >  subroutine zero_work_arrays()
562      
563 <    muRow = 0.0_dp
564 <    muCol = 0.0_dp
563 > #ifdef IS_MPI
564 >
565 >    q_Row = 0.0_dp
566 >    q_Col = 0.0_dp  
567      
568 <    u_lRow = 0.0_dp
569 <    u_lCol = 0.0_dp
568 >    u_l_Row = 0.0_dp
569 >    u_l_Col = 0.0_dp
570      
571 <    ARow = 0.0_dp
572 <    ACol = 0.0_dp
571 >    A_Row = 0.0_dp
572 >    A_Col = 0.0_dp
573      
574 <    fRow = 0.0_dp
575 <    fCol = 0.0_dp
576 <    
577 <  
578 <    tRow = 0.0_dp
579 <    tCol = 0.0_dp
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 <  
582 >    pot_Row = 0.0_dp
583 >    pot_Col = 0.0_dp
584 >    pot_Temp = 0.0_dp
585  
586 <    eRow = 0.0_dp
587 <    eCol = 0.0_dp
588 <    eTemp = 0.0_dp
586 >    rf_Row = 0.0_dp
587 >    rf_Col = 0.0_dp
588 >    rf_Temp = 0.0_dp
589 >
590   #endif
591  
592 <  end subroutine zero_module_variables
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 >  function skipThisPair(atom1, atom2) result(skip_it)
599 >    
600 >    integer, intent(in) :: atom1
601 >    integer, intent(in), optional :: atom2
602 >    logical :: skip_it
603 >    integer :: unique_id_1, unique_id_2
604 >    integer :: i
605  
606 < #ifdef IS_MPI
823 < !! Function to properly build neighbor lists in MPI using newtons 3rd law.
824 < !! We don't want 2 processors doing the same i j pair twice.
825 < !! Also checks to see if i and j are the same particle.
826 <  function mpi_cycle_jLoop(i,j) result(do_cycle)
827 < !--------------- Arguments--------------------------
828 < ! Index i
829 <    integer,intent(in) :: i
830 < ! Index j
831 <    integer,intent(in) :: j
832 < ! Result do_cycle
833 <    logical :: do_cycle
834 < !--------------- Local variables--------------------
835 <    integer :: tag_i
836 <    integer :: tag_j
837 < !--------------- END DECLARATIONS------------------    
838 <    tag_i = tagRow(i)
839 <    tag_j = tagColumn(j)
606 >    skip_it = .false.
607  
608 <    do_cycle = .false.
609 <
610 <    if (tag_i == tag_j) then
611 <       do_cycle = .true.
608 >    !! there are a number of reasons to skip a pair or a particle
609 >    !! mostly we do this to exclude atoms who are involved in short
610 >    !! range interactions (bonds, bends, torsions), but we also need
611 >    !! to exclude some overcounted interactions that result from
612 >    !! the parallel decomposition
613 >    
614 > #ifdef IS_MPI
615 >    !! in MPI, we have to look up the unique IDs for each atom
616 >    unique_id_1 = tagRow(atom1)
617 > #else
618 >    !! in the normal loop, the atom numbers are unique
619 >    unique_id_1 = atom1
620 > #endif
621 >    
622 >    !! We were called with only one atom, so just check the global exclude
623 >    !! list for this atom
624 >    if (.not. present(atom2)) then
625 >       do i = 1, nExcludes_global
626 >          if (excludesGlobal(i) == unique_id_1) then
627 >             skip_it = .true.
628 >             return
629 >          end if
630 >       end do
631 >       return
632 >    end if
633 >    
634 > #ifdef IS_MPI
635 >    unique_id_2 = tagColumn(atom2)
636 > #else
637 >    unique_id_2 = atom2
638 > #endif
639 >    
640 > #ifdef IS_MPI
641 >    !! this situation should only arise in MPI simulations
642 >    if (unique_id_1 == unique_id_2) then
643 >       skip_it = .true.
644         return
645      end if
646 <
647 <    if (tag_i < tag_j) then
648 <       if (mod(tag_i + tag_j,2) == 0) do_cycle = .true.
646 >    
647 >    !! this prevents us from doing the pair on multiple processors
648 >    if (unique_id_1 < unique_id_2) then
649 >       if (mod(unique_id_1 + unique_id_2,2) == 0) skip_it = .true.
650         return
651      else                
652 <       if (mod(tag_i + tag_j,2) == 1) do_cycle = .true.
652 >       if (mod(unique_id_1 + unique_id_2,2) == 1) skip_it = .true.
653      endif
854 –  end function mpi_cycle_jLoop
654   #endif
655  
656 +    !! the rest of these situations can happen in all simulations:
657 +    do i = 1, nExcludes_global      
658 +       if ((excludesGlobal(i) == unique_id_1) .or. &
659 +            (excludesGlobal(i) == unique_id_2)) then
660 +          skip_it = .true.
661 +          return
662 +       endif
663 +    enddo
664 +    
665 +    do i = 1, nExcludes_local
666 +       if (excludesLocal(1,i) == unique_id_1) then
667 +          if (excludesLocal(2,i) == unique_id_2) then
668 +             skip_it = .true.
669 +             return
670 +          endif
671 +       else
672 +          if (excludesLocal(1,i) == unique_id_2) then
673 +             if (excludesLocal(2,i) == unique_id_1) then
674 +                skip_it = .true.
675 +                return
676 +             endif
677 +          endif
678 +       endif
679 +    end do
680 +    
681 +    return
682 +  end function skipThisPair
683 +
684 +  function FF_UsesDirectionalAtoms() result(doesit)
685 +    logical :: doesit
686 +    doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
687 +         FF_uses_GB .or. FF_uses_RF
688 +  end function FF_UsesDirectionalAtoms
689 +  
690 +  function FF_RequiresPrepairCalc() result(doesit)
691 +    logical :: doesit
692 +    doesit = FF_uses_EAM
693 +  end function FF_RequiresPrepairCalc
694 +  
695 +  function FF_RequiresPostpairCalc() result(doesit)
696 +    logical :: doesit
697 +    doesit = FF_uses_RF
698 +  end function FF_RequiresPostpairCalc
699 +  
700   end module do_Forces

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