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Comparing trunk/OOPSE_old/src/mdtools/libmdCode/do_Forces.F90 (file contents):
Revision 297 by gezelter, Thu Mar 6 22:08:29 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 1.4 2003-03-06 22:08:29 gezelter Exp $, $Date: 2003-03-06 22:08:29 $, $Name: not supported by cvs2svn $, $Revision: 1.4 $
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 –
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(9,getNrow(plan_row)) :: ARow = 0.0_dp
66 –  real(kind = dp), dimension(9,getNcol(plan_col)) :: ACol = 0.0_dp  
67 –
68 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow = 0.0_dp
69 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol = 0.0_dp
70 –  real(kind = dp), dimension(3,getNlocal()) :: fTemp1 = 0.0_dp
71 –  real(kind = dp), dimension(3,getNlocal()) :: tTemp1 = 0.0_dp
72 –  real(kind = dp), dimension(3,getNlocal()) :: fTemp2 = 0.0_dp
73 –  real(kind = dp), dimension(3,getNlocal()) :: tTemp2 = 0.0_dp
74 –  real(kind = dp), dimension(3,getNlocal()) :: fTemp = 0.0_dp
75 –  real(kind = dp), dimension(3,getNlocal()) :: tTemp = 0.0_dp
76 –
77 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: tRow = 0.0_dp
78 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: tCol = 0.0_dp
79 –
80 –  real(kind = dp), dimension(3,getNrow(plan_row)) :: rflRow = 0.0_dp
81 –  real(kind = dp), dimension(3,getNcol(plan_col)) :: rflCol = 0.0_dp
82 –  real(kind = dp), dimension(3,getNlocal()) :: rflTemp = 0.0_dp
83 –
84 –  real(kind = dp), dimension(getNrow(plan_row)) :: eRow = 0.0_dp
85 –  real(kind = dp), dimension(getNcol(plan_col)) :: eCol = 0.0_dp
86 –
87 –  real(kind = dp), dimension(getNlocal()) :: eTemp = 0.0_dp
88 – #endif
89 –  real(kind = dp) :: pe = 0.0_dp
90 –  real(kind = dp), dimension(3,natoms) :: fTemp = 0.0_dp
91 –  real(kind = dp), dimension(3,natoms) :: tTemp = 0.0_dp
92 –  real(kind = dp), dimension(3,natoms) :: rflTemp = 0.0_dp
93 –  real(kind = dp), dimension(9) :: tauTemp = 0.0_dp
94 –
95 –  logical :: do_preForce  = .false.
96 –  logical :: do_postForce = .false.
97 –
98 –
99 –
100 – !! Public methods and data
101 –  public :: new_atype
102 –  public :: do_forceLoop
35    public :: init_FF
36 +  public :: do_force_loop
37  
105 –  
106 –
107 –
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
131 <    integer :: alloc_size
132 <    integer :: err_stat
133 <    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
143 –
144 – ! assign our new atype information
145 –    the_new_atype%mass        = mass
146 –    the_new_atype%epsilon     = epsilon
147 –    the_new_atype%sigma       = sigma
148 –    the_new_atype%sigma2      = sigma * sigma
149 –    the_new_atype%sigma6      = the_new_atype%sigma2 * the_new_atype%sigma2 &
150 –         * the_new_atype%sigma2
151 –    the_new_atype%w0       = w0
152 –    the_new_atype%v0       = v0
153 –    the_new_atype%dipoleMoment       = dipoleMoment
154 –
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.
163 <    if ( is_DP /= 0 )        the_new_atype%is_DP       = .true.
111 >    do_forces_initialized = .true.    
112 >    
113 >  end subroutine init_FF
114  
165 –    call add_atype(the_new_atype,ListHead,ListTail,err_stat)
166 –    if (err_stat /= 0 ) then
167 –       status = -1
168 –       return
169 –    endif
115  
171 –    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
194 <    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 <  
215 < ! We can only set up forces if mpiSimulation has been setup.
216 <    if (.not. isMPISimSet()) then
217 <       write(default_error,*) "MPI is not set"
218 <       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)
222 <    ncol = getNcol(plan_col)
223 <    mynode = getMyNode()
224 < !! Allocate temperary arrays to hold gather information
225 <    allocate(identRow(nrow),stat=alloc_stat)
226 <    if (alloc_stat /= 0 ) then
227 <       status = -1
228 <       return
229 <    endif
174 >    end if
175 >    call zero_work_arrays()
176  
177 <    allocate(identCol(ncol),stat=alloc_stat)
178 <    if (alloc_stat /= 0 ) then
233 <       status = -1
234 <       return
235 <    endif
177 >    do_pot = do_pot_c
178 >    do_stress = do_stress_c
179  
180 < !! Gather idents into row and column idents
238 <
239 <    call gather(ident,identRow,plan_row)
240 <    call gather(ident,identCol,plan_col)
180 >    ! Gather all information needed by all force loops:
181      
182 <  
243 < !! Create row and col pointer lists
244 <  
245 <    call create_IdentPtrlst(identRow,ListHead,identPtrListRow,thisStat)
246 <    if (thisStat /= 0 ) then
247 <       status = -1
248 <       return
249 <    endif
250 <  
251 <    call create_IdentPtrlst(identCol,ListHead,identPtrListColumn,thisStat)
252 <    if (thisStat /= 0 ) then
253 <       status = -1
254 <       return
255 <    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
272 –
273 – !! Create neighbor lists
274 –    call expandList(thisStat)
275 –    if (thisStat /= 0) then
276 –       status = -1
277 –       return
278 –    endif
279 –
280 –    isFFinit = .true.
281 –
282 –
283 –  end subroutine init_FF
284 –
285 –
286 –
287 –
288 –  subroutine initForce_Modules(thisStat)
289 –    integer, intent(out) :: thisStat
290 –    integer :: my_status
208      
292 –    thisStat = 0
293 –    call init_lj_FF(ListHead,my_status)
294 –    if (my_status /= 0) then
295 –       thisStat = -1
296 –       return
297 –    end if
298 –
299 –  end subroutine initForce_Modules
300 –
301 –
302 –
303 –
304 – !! FORCE routine Calculates Lennard Jones forces.
305 – !------------------------------------------------------------->
306 –  subroutine do_force_loop(q,A,mu,u_l,f,t,tau,potE,do_pot,FFerror)
307 – !! Position array provided by C, dimensioned by getNlocal
308 –    real ( kind = dp ), dimension(3,getNlocal()) :: q
309 –  !! Rotation Matrix for each long range particle in simulation.
310 –    real( kind = dp), dimension(9,getNlocal()) :: A
311 –
312 –  !! Magnitude dipole moment
313 –    real( kind = dp ), dimension(3,getNlocal()) :: mu
314 –  !! Unit vectors for dipoles (lab frame)
315 –    real( kind = dp ), dimension(3,getNlocal()) :: u_l
316 – !! Force array provided by C, dimensioned by getNlocal
317 –    real ( kind = dp ), dimension(3,getNlocal()) :: f
318 – !! Torsion array provided by C, dimensioned by getNlocal
319 –    real( kind = dp ), dimension(3,getNlocal()) :: t
320 –
321 – !! Stress Tensor
322 –    real( kind = dp), dimension(9) :: tau
323 –
324 –    real ( kind = dp ) :: potE
325 –    logical ( kind = 2) :: do_pot
326 –    integer :: FFerror
327 –
328 –    
329 –    type(atype), pointer :: Atype_i
330 –    type(atype), pointer :: Atype_j
331 –
332 –
333 –
334 –
335 –  
336 –
209   #ifdef IS_MPI
338 –  real( kind = DP ) :: pot_local
339 –
340 – !! Local arrays needed for MPI
341 –
342 – #endif
343 –
344 –
345 –
346 –  real( kind = DP )   :: pe
347 –  logical             :: update_nlist
348 –
349 –
350 –  integer ::  i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2
351 –  integer :: nlist
352 –  integer :: j_start
353 –
354 –  real( kind = DP ) ::  r_ij, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp
355 –
356 –  real( kind = DP ) ::  rx_ij, ry_ij, rz_ij, rijsq
357 –  real( kind = DP ) ::  rlistsq, rcutsq,rlist,rcut
358 –
359 –  real( kind = DP ) :: dielectric = 0.0_dp
360 –
361 – ! a rig that need to be fixed.
362 – #ifdef IS_MPI
363 –  real( kind = dp ) :: pe_local
364 –  integer :: nlocal
365 – #endif
366 –  integer :: nrow
367 –  integer :: ncol
368 –  integer :: natoms
369 –  integer :: neighborListSize
370 –  integer :: listerror
371 – !! should we calculate the stress tensor
372 –  logical  :: do_stress = .false.
373 –
374 –
375 –  FFerror = 0
376 –
377 – ! Make sure we are properly initialized.
378 –  if (.not. isFFInit) then
379 –     write(default_error,*) "ERROR: lj_FF has not been properly initialized"
380 –     FFerror = -1
381 –     return
382 –  endif
383 – #ifdef IS_MPI
384 –    if (.not. isMPISimSet()) then
385 –     write(default_error,*) "ERROR: mpiSimulation has not been properly initialized"
386 –     FFerror = -1
387 –     return
388 –  endif
389 – #endif
390 –
391 – !! initialize local variables  
392 –  natoms = getNlocal()
393 –  call getRcut(rcut,rcut2=rcutsq)
394 –  call getRlist(rlist,rlistsq)
395 –
396 – !! Find ensemble
397 –  if (isEnsemble("NPT")) do_stress = .true.
398 – !! set to wrap
399 –  if (isPBC()) wrap = .true.
400 –
401 –
402 –
403 –  
404 – !! See if we need to update neighbor lists
405 –  call check(q,update_nlist)
406 –
407 – !--------------WARNING...........................
408 – ! Zero variables, NOTE:::: Forces are zeroed in C
409 – ! Zeroing them here could delete previously computed
410 – ! Forces.
411 – !------------------------------------------------
412 –  call zero_module_variables()
413 –
414 –
415 – ! communicate MPI positions
416 – #ifdef IS_MPI    
417 –    call gather(q,qRow,plan_row3d)
418 –    call gather(q,qCol,plan_col3d)
419 –
420 –    call gather(mu,muRow,plan_row3d)
421 –    call gather(mu,muCol,plan_col3d)
422 –
423 –    call gather(u_l,u_lRow,plan_row3d)
424 –    call gather(u_l,u_lCol,plan_col3d)
425 –
426 –    call gather(A,ARow,plan_row_rotation)
427 –    call gather(A,ACol,plan_col_rotation)
428 – #endif
429 –
430 –
431 – #ifdef IS_MPI
210      
211      if (update_nlist) then
212        
213 <       ! save current configuration, contruct neighbor list,
214 <       ! and calculate forces
213 >       !! save current configuration, construct neighbor list,
214 >       !! and calculate forces
215         call save_neighborList(q)
216        
217         neighborListSize = getNeighborListSize()
218 <       nlist = 0
218 >       nlist = 0      
219        
442 –       nrow = getNrow(plan_row)
443 –       ncol = getNcol(plan_col)
444 –       nlocal = getNlocal()
445 –      
220         do i = 1, nrow
221            point(i) = nlist + 1
448 –          Atype_i => identPtrListRow(i)%this
222            
223            inner: do j = 1, ncol
451 –             Atype_j => identPtrListColumn(j)%this
224              
225 <             call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),&
454 <                  rxij,ryij,rzij,rijsq,r)
225 >             if (checkExcludes(i,j)) cycle inner
226              
227 <             ! skip the loop if the atoms are identical
457 <             if (mpi_cycle_jLoop(i,j)) cycle inner:
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 expandList(listerror)
234 >                   call expandNeighborList(nlocal, listerror)
235                     if (listerror /= 0) then
236 <                      FFerror = -1
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 <                
474 <                
243 >                                
244                  if (rijsq <  rcutsq) then
245 <                   call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
245 >                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
246                  endif
247               endif
248            enddo inner
# Line 481 | Line 250 | contains
250  
251         point(nrow + 1) = nlist + 1
252        
253 <    else !! (update)
253 >    else  !! (of update_check)
254  
255         ! use the list to find the neighbors
256         do i = 1, nrow
# Line 489 | Line 258 | contains
258            JEND = POINT(i+1) - 1
259            ! check thiat molecule i has neighbors
260            if (jbeg .le. jend) then
261 <
493 <             Atype_i => identPtrListRow(i)%this
261 >            
262               do jnab = jbeg, jend
263                  j = list(jnab)
264 <                Atype_j = identPtrListColumn(j)%this
265 <                call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),&
266 <                     rxij,ryij,rzij,rijsq,r)
267 <                
500 <                call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
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               enddo
269            endif
270         enddo
271      endif
272 <
272 >    
273   #else
274      
275      if (update_nlist) then
# Line 514 | Line 281 | contains
281         neighborListSize = getNeighborListSize()
282         nlist = 0
283        
517 –    
284         do i = 1, natoms-1
285            point(i) = nlist + 1
286 <          Atype_i   => identPtrList(i)%this
521 <
286 >          
287            inner: do j = i+1, natoms
288 <             Atype_j   => identPtrList(j)%this
289 <             call get_interatomic_vector(i,j,q(:,i),q(:,j),&
290 <                  rxij,ryij,rzij,rijsq,r)
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 <
294 >                
295                  nlist = nlist + 1
296                  
297                  if (nlist > neighborListSize) then
298 <                   call expandList(listerror)
298 >                   call expandList(natoms, listerror)
299                     if (listerror /= 0) then
300 <                      FFerror = -1
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 <
542 <    
307 >                
308                  if (rijsq <  rcutsq) then
309 <                   call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
309 >                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
310                  endif
311               endif
312            enddo inner
# Line 552 | Line 317 | contains
317      else !! (update)
318        
319         ! use the list to find the neighbors
320 <       do i = 1, nrow
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              
561 –             Atype_i => identPtrList(i)%this
326               do jnab = jbeg, jend
327                  j = list(jnab)
564 –                Atype_j = identPtrList(j)%this
565 –                call get_interatomic_vector(i,j,q(:,i),q(:,j),&
566 –                     rxij,ryij,rzij,rijsq,r)
567 –                call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
568 –             enddo
569 –          endif
570 –       enddo
571 –    endif
328  
329 < #endif
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 < #ifdef IS_MPI
577 <    !! distribute all reaction field stuff (or anything for post-pair):
578 <    call scatter(rflRow,rflTemp1,plan_row3d)
579 <    call scatter(rflCol,rflTemp2,plan_col3d)
580 <    do i = 1,nlocal
581 <       rflTemp(1:3,i) = rflTemp1(1:3,i) + rflTemp2(1:3,i)
582 <    end do
583 < #endif
584 <
585 < ! This is the post-pair loop:
586 < #ifdef IS_MPI
587 <
588 <    if (system_has_postpair_atoms) then
589 <       do i = 1, nlocal
590 <          Atype_i => identPtrListRow(i)%this
591 <          call do_postpair(i, Atype_i)
332 >             enddo
333 >          endif
334         enddo
335      endif
336 <
337 < #else
338 <
339 <    if (system_has_postpair_atoms) then
340 <       do i = 1, natoms
599 <          Atype_i => identPtr(i)%this
600 <          call do_postpair(i, Atype_i)
601 <       enddo
602 <    endif
603 <
604 < #endif
605 <
606 <
607 <
608 <
336 >    
337 > #endif
338 >    
339 >    ! phew, done with main loop.
340 >    
341   #ifdef IS_MPI
342      !!distribute forces
343 <
344 <    call scatter(fRow,fTemp1,plan_row3d)
345 <    call scatter(fCol,fTemp2,plan_col3d)
614 <
615 <
343 >    
344 >    call scatter(f_Row,f,plan_row3d)
345 >    call scatter(f_Col,f_temp,plan_col3d)
346      do i = 1,nlocal
347 <       fTemp(1:3,i) = fTemp1(1:3,i) + fTemp2(1:3,i)
347 >       f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
348      end do
619 –
620 –    if (do_torque) then
621 –       call scatter(tRow,tTemp1,plan_row3d)
622 –       call scatter(tCol,tTemp2,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 <          tTemp(1:3,i) = tTemp1(1:3,i) + tTemp2(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
646 <    endif
647 < #else
648 < ! Copy local array into return array for c
649 <    f = f+fTemp
650 <    t = 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 <
656 <    if (do_stress) then
393 >             rfpot = 0.0_DP
394   #ifdef IS_MPI
395 <       mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, &
659 <            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  
665 –  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.
677 <  subroutine do_preForce(updateNlist)
678 <    logical, intent(inout) :: updateNlist
679 <
680 <
681 <
682 <  end subroutine do_preForce
683 <
684 <
685 <
686 <
687 <
688 <
689 <
690 <
691 <
692 <
693 <
694 <
695 <
696 < !! Calculate any post force loop components, i.e. reaction field, etc.
697 <  subroutine do_postForce()
698 <
699 <
700 <
701 <  end subroutine do_postForce
702 <
703 <
704 <
705 <
706 <
707 <
708 <
709 <
710 <
711 <
712 <
713 <
714 <
715 <
716 <
717 <
718 <
719 <  subroutine do_pair(atype_i,atype_j,i,j,r_ij,rx_ij,ry_ij,rz_ij)
720 <    type (atype ), pointer, intent(inout) :: atype_i
721 <    type (atype ), pointer, intent(inout) :: atype_j
722 <    integer :: i
723 <    integer :: j
724 <    real ( kind = dp ), intent(inout) :: rx_ij
725 <    real ( kind = dp ), intent(inout) :: ry_ij
726 <    real ( kind = dp ), intent(inout) :: rz_ij
727 <
728 <
729 <    real( kind = dp ) :: fx = 0.0_dp
730 <    real( kind = dp ) :: fy = 0.0_dp
731 <    real( kind = dp ) :: fz = 0.0_dp  
732 <  
733 <    real( kind = dp ) ::  drdx = 0.0_dp
734 <    real( kind = dp ) ::  drdy = 0.0_dp
735 <    real( kind = dp ) ::  drdz = 0.0_dp
463 >    r = sqrt(rijsq)
464      
465 + #ifdef IS_MPI
466  
467 <    if (Atype_i%is_LJ .and. Atype_j%is_LJ) then
468 <       call getLJForce(r,pot,dudr,ljAtype_i,ljAtype_j,fx,fy,fz)
740 <    endif
467 >    me_i = atid_row(i)
468 >    me_j = atid_col(j)
469  
742 –    if (Atype_i%is_dp .and. Atype_j%is_dp) then
743 –
744 – #ifdef IS_MPI
745 –       call dipole_dipole(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, &
746 –            ulRow(:,i), ulCol(:,j), rt, rrf, pot)
470   #else
748 –       call dipole_dipole(i, j, atype_i, atype_j, rx_ij, ry_ij, rz_ij, r_ij, &
749 –            ul(:,i), ul(:,j), rt, rrf, pot)
750 – #endif
471  
472 <       if (do_reaction_field) then
473 < #ifdef IS_MPI
474 <          call accumulate_rf(i, j, r_ij, rflRow(:,i), rflCol(:j), &
755 <               ulRow(:i), ulCol(:,j), rt, rrf)
756 < #else
757 <          call accumulate_rf(i, j, r_ij, rfl(:,i), rfl(:j), &
758 <               ul(:,i), ul(:,j), rt, rrf)
472 >    me_i = atid(i)
473 >    me_j = atid(j)
474 >
475   #endif
760 –       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 <    if (Atype_i%is_sticky .and. Atype_j%is_sticky) then
488 <       call getstickyforce(r,pot,dudr,ljAtype_i,ljAtype_j)
489 <    endif
768 <
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
775 < #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
795 <                
796 <                fRow(1,j) = fRow(1,j) + fx
797 <                fRow(2,j) = fRow(2,j) + fy
798 <                fRow(3,j) = fRow(3,j) + fz
799 < #else
800 <                fTemp(1,j) = fTemp(1,j) - fx
801 <                fTemp(2,j) = fTemp(2,j) - fy
802 <                fTemp(3,j) = fTemp(3,j) - fz
803 <                fTemp(1,i) = fTemp(1,i) + fx
804 <                fTemp(2,i) = fTemp(2,i) + fy
805 <                fTemp(3,i) = fTemp(3,i) + fz
806 < #endif
807 <                
808 <                if (do_stress) then
809 <                   tauTemp(1) = tauTemp(1) + fx * rxij
810 <                   tauTemp(2) = tauTemp(2) + fx * ryij
811 <                   tauTemp(3) = tauTemp(3) + fx * rzij
812 <                   tauTemp(4) = tauTemp(4) + fy * rxij
813 <                   tauTemp(5) = tauTemp(5) + fy * ryij
814 <                   tauTemp(6) = tauTemp(6) + fy * rzij
815 <                   tauTemp(7) = tauTemp(7) + fz * rxij
816 <                   tauTemp(8) = tauTemp(8) + fz * ryij
817 <                   tauTemp(9) = tauTemp(9) + fz * rzij
818 <                endif
819 <
820 <
821 <
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 <
827 <
828 <
829 <
830 <
831 <
832 <
833 <
834 <
835 <
836 <
837 <
838 <
839 <  subroutine get_interatomic_vector(q_i,q_j,rx_ij,ry_ij,rz_ij,r_sq,r_ij)
840 < !---------------- Arguments-------------------------------
841 <   !! index i
842 <
843 <    !! 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
846 –    !! x component of vector between i and j
847 –    real ( kind = dp ), intent(out)  :: rx_ij
848 –    !! y component of vector between i and j
849 –    real ( kind = dp ), intent(out)  :: ry_ij
850 –    !! z component of vector between i and j
851 –    real ( kind = dp ), intent(out)  :: rz_ij
852 –    !! magnitude of r squared
523      real ( kind = dp ), intent(out) :: r_sq
854 –    !! magnitude of vector r between atoms i and j.
855 –    real ( kind = dp ), intent(out) :: r_ij
856 –    !! wrap into periodic box.
857 –    logical, intent(in) :: wrap
858 –
859 – !--------------- Local Variables---------------------------
860 –    !! Distance between i and j
524      real( kind = dp ) :: d(3)
862 – !---------------- END DECLARATIONS-------------------------
525  
864 –
865 – ! Find distance between i and j
526      d(1:3) = q_i(1:3) - q_j(1:3)
867 –
868 – ! Wrap back into periodic box if necessary
869 –    if ( wrap ) then
870 –       d(1:3) = d(1:3) - thisSim%box(1:3) * sign(1.0_dp,thisSim%box(1:3)) * &
871 –            int(abs(d(1:3)/thisSim%box(1:3) + 0.5_dp)
872 –    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)
877 <
878 < !   Set each component for force calculation
879 <    rx_ij = d(1)
880 <    ry_ij = d(2)
881 <    rz_ij = d(3)
882 <
883 <
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
892 <    fTemp = 0.0_dp
893 <    tTemp = 0.0_dp
894 < #else
895 <    qRow = 0.0_dp
896 <    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  
599 < #ifdef IS_MPI
600 < !! Function to properly build neighbor lists in MPI using newtons 3rd law.
601 < !! We don't want 2 processors doing the same i j pair twice.
602 < !! Also checks to see if i and j are the same particle.
603 <  function mpi_cycle_jLoop(i,j) result(do_cycle)
604 < !--------------- Arguments--------------------------
605 < ! Index i
606 <    integer,intent(in) :: i
931 < ! Index j
932 <    integer,intent(in) :: j
933 < ! Result do_cycle
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 >  function checkExcludes(atom1,atom2) result(do_cycle)
604 >    
605 >    integer,intent(in) :: atom1
606 >    integer,intent(in), optional :: atom2
607      logical :: do_cycle
608 < !--------------- Local variables--------------------
609 <    integer :: tag_i
937 <    integer :: tag_j
938 < !--------------- END DECLARATIONS------------------    
939 <    tag_i = tagRow(i)
940 <    tag_j = tagColumn(j)
608 >    integer :: unique_id_1, unique_id_2
609 >    integer :: i, j
610  
611 <    do_cycle = .false.
611 >    do_cycle = .false.
612 >    
613 > #ifdef IS_MPI
614 >    unique_id_1 = tagRow(atom1)
615 > #else
616 >    unique_id_1 = tag(atom1)
617 > #endif
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 <    if (tag_i == tag_j) then
630 >    !! we return if atom2 not present here.
631 >    
632 > #ifdef IS_MPI
633 >    unique_id_2 = tagColumn(atom2)
634 > #else
635 >    unique_id_2 = tag(atom2)
636 > #endif
637 >    
638 >    if (unique_id_1 == unique_id_2) then
639         do_cycle = .true.
640         return
641      end if
642 <
643 <    if (tag_i < tag_j) then
644 <       if (mod(tag_i + tag_j,2) == 0) do_cycle = .true.
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(tag_i + tag_j,2) == 1) do_cycle = .true.
647 >       if (mod(unique_id_1 + unique_id_2,2) == 1) do_cycle = .true.
648      endif
649 <  end function mpi_cycle_jLoop
650 < #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 +  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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