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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 331 by chuckv, Thu Mar 13 00:33:18 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 1.17 2003-03-13 00:33:18 chuckv Exp $, $Date: 2003-03-13 00:33:18 $, $Name: not supported by cvs2svn $, $Revision: 1.17 $
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
16 <  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  
20   #ifdef IS_MPI
21    use mpiSimulation
# Line 22 | Line 23 | module do_Forces
23    implicit none
24    PRIVATE
25  
26 < !! Number of lj_atypes in lj_atype_list
27 <  integer, save :: n_atypes = 0
26 >  logical, save :: do_forces_initialized = .false.
27 >  logical, save :: FF_uses_LJ
28 >  logical, save :: FF_uses_sticky
29 >  logical, save :: FF_uses_dipoles
30 >  logical, save :: FF_uses_RF
31 >  logical, save :: FF_uses_GB
32 >  logical, save :: FF_uses_EAM
33  
28 – !! Global list of lj atypes in simulation
29 –  type (atype), pointer :: ListHead => null()
30 –  type (atype), pointer :: ListTail => null()
34  
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
108 <    real( kind = dp ), intent(in) :: epsilon
109 <    real( kind = dp ), intent(in) :: sigma
110 <    real( kind = dp ), intent(in) :: w0
111 <    real( kind = dp ), intent(in) :: v0
112 <    real( kind = dp ), intent(in) :: dipoleMoment
40 >  subroutine init_FF(thisStat)
41 >    integer, intent(out) :: thisStat  
42 >    integer :: my_status
43 >    character(len = 100) :: mix_Policy
44  
45 <    integer, intent(in) :: ident
46 <    integer, intent(out) :: status
47 <    integer, intent(in) :: is_Sticky
48 <    integer, intent(in) :: is_DP
49 <    integer, intent(in) :: is_GB
50 <    integer, intent(in) :: is_LJ
120 <
121 <
122 <    type (atype), pointer :: the_new_atype
123 <    integer :: alloc_error
124 <    integer :: atype_counter = 0
125 <    integer :: alloc_size
126 <    integer :: err_stat
127 <    status = 0
128 <
129 <
130 <
131 < ! allocate a new atype    
132 <    allocate(the_new_atype,stat=alloc_error)
133 <    if (alloc_error /= 0 ) then
134 <       status = -1
45 >    ! be a smarter subroutine.
46 >    mix_Policy = "FIXME"
47 >    thisStat = 0
48 >    call init_lj_FF(mix_Policy,my_status)
49 >    if (my_status /= 0) then
50 >       thisStat = -1
51         return
52      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 –
53      
54 < ! assume that this atype will be successfully added
55 <    the_new_atype%atype_ident = ident
56 <    the_new_atype%atype_number = n_lj_atypes + 1
54 >    call check_sticky_FF(my_status)
55 >    if (my_status /= 0) then
56 >       thisStat = -1
57 >       return
58 >    end if
59      
60 <    if ( is_Sticky /= 0 )    the_new_atype%is_Sticky   = .true.
61 <    if ( is_GB /= 0 )        the_new_atype%is_GB       = .true.
62 <    if ( is_LJ /= 0 )        the_new_atype%is_LJ       = .true.
157 <    if ( is_DP /= 0 )        the_new_atype%is_DP       = .true.
60 >    do_forces_initialized = .true.    
61 >    
62 >  end subroutine init_FF
63  
159 –    call add_atype(the_new_atype,ListHead,ListTail,err_stat)
160 –    if (err_stat /= 0 ) then
161 –       status = -1
162 –       return
163 –    endif
64  
165 –    n_atypes = n_atypes + 1
65  
66 <
67 <  end subroutine new_atype
68 <
69 <
70 <  subroutine init_FF(nComponents,ident, status)
71 < !! Number of components in ident array
72 <    integer, intent(inout) :: nComponents
73 < !! Array of identities nComponents long corresponding to
74 < !! ljatype ident.
75 <    integer, dimension(nComponents),intent(inout) :: ident
76 < !!  Result status, success = 0, error = -1
77 <    integer, intent(out) :: Status
78 <
79 <    integer :: alloc_stat
80 <
81 <    integer :: thisStat
82 <    integer :: i
83 <
84 <    integer :: myNode
66 >  !! Does force loop over i,j pairs. Calls do_pair to calculates forces.
67 >  !------------------------------------------------------------->
68 >  subroutine do_force_loop(q, A, u_l, f, t, tau, pot, do_pot_c, do_stress_c, &
69 >       error)
70 >    !! Position array provided by C, dimensioned by getNlocal
71 >    real ( kind = dp ), dimension(3,getNlocal()) :: q
72 >    !! Rotation Matrix for each long range particle in simulation.
73 >    real( kind = dp), dimension(9,getNlocal()) :: A    
74 >    !! Unit vectors for dipoles (lab frame)
75 >    real( kind = dp ), dimension(3,getNlocal()) :: u_l
76 >    !! Force array provided by C, dimensioned by getNlocal
77 >    real ( kind = dp ), dimension(3,getNlocal()) :: f
78 >    !! Torsion array provided by C, dimensioned by getNlocal
79 >    real( kind = dp ), dimension(3,getNlocal()) :: t    
80 >    !! Stress Tensor
81 >    real( kind = dp), dimension(9) :: tau  
82 >    real ( kind = dp ) :: pot
83 >    logical ( kind = 2) :: do_pot_c, do_stress_c
84 >    logical :: do_pot
85 >    logical :: do_stress
86   #ifdef IS_MPI
87 <    integer, allocatable, dimension(:) :: identRow
188 <    integer, allocatable, dimension(:) :: identCol
87 >    real( kind = DP ) :: pot_local
88      integer :: nrow
89      integer :: ncol
90   #endif
91 <    status = 0
92 <  
91 >    integer :: nlocal
92 >    integer :: natoms    
93 >    logical :: update_nlist  
94 >    integer :: i, j, jbeg, jend, jnab
95 >    integer :: nlist
96 >    real( kind = DP ) ::  rijsq, rlistsq, rcutsq, rlist, rcut
97 >    real(kind=dp),dimension(3) :: d
98 >    real(kind=dp) :: rfpot, mu_i, virial
99 >    integer :: me_i
100 >    logical :: is_dp_i
101 >    integer :: neighborListSize
102 >    integer :: listerror, error
103 >    integer :: localError
104  
105 <    
105 >    !! initialize local variables  
106  
107 < !! if were're not in MPI, we just update ljatypePtrList
108 < #ifndef IS_MPI
109 <    call create_IdentPtrlst(ident,ListHead,identPtrList,thisStat)
110 <    if ( thisStat /= 0 ) then
111 <       status = -1
112 <       return
113 <    endif
107 > #ifdef IS_MPI
108 >    nlocal = getNlocal()
109 >    nrow   = getNrow(plan_row)
110 >    ncol   = getNcol(plan_col)
111 > #else
112 >    nlocal = getNlocal()
113 >    natoms = nlocal
114 > #endif
115  
116 +    call getRcut(rcut,rc2=rcutsq)
117 +    call getRlist(rlist,rlistsq)
118      
119 < ! if were're in MPI, we also have to worry about row and col lists    
120 < #else
121 <  
209 < ! We can only set up forces if mpiSimulation has been setup.
210 <    if (.not. isMPISimSet()) then
211 <       write(default_error,*) "MPI is not set"
212 <       status = -1
119 >    call check_initialization(localError)
120 >    if ( localError .ne. 0 ) then
121 >       error = -1
122         return
123 <    endif
124 <    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
123 >    end if
124 >    call zero_work_arrays()
125  
126 <    allocate(identCol(ncol),stat=alloc_stat)
127 <    if (alloc_stat /= 0 ) then
227 <       status = -1
228 <       return
229 <    endif
126 >    do_pot = do_pot_c
127 >    do_stress = do_stress_c
128  
129 < !! Gather idents into row and column idents
232 <
233 <    call gather(ident,identRow,plan_row)
234 <    call gather(ident,identCol,plan_col)
129 >    ! Gather all information needed by all force loops:
130      
131 <  
237 < !! Create row and col pointer lists
238 <  
239 <    call create_IdentPtrlst(identRow,ListHead,identPtrListRow,thisStat)
240 <    if (thisStat /= 0 ) then
241 <       status = -1
242 <       return
243 <    endif
244 <  
245 <    call create_IdentPtrlst(identCol,ListHead,identPtrListColumn,thisStat)
246 <    if (thisStat /= 0 ) then
247 <       status = -1
248 <       return
249 <    endif
131 > #ifdef IS_MPI    
132  
133 < !! free temporary ident arrays
134 <    if (allocated(identCol)) then
135 <       deallocate(identCol)
136 <    end if
137 <    if (allocated(identCol)) then
138 <       deallocate(identRow)
133 >    call gather(q,q_Row,plan_row3d)
134 >    call gather(q,q_Col,plan_col3d)
135 >        
136 >    if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
137 >       call gather(u_l,u_l_Row,plan_row3d)
138 >       call gather(u_l,u_l_Col,plan_col3d)
139 >      
140 >       call gather(A,A_Row,plan_row_rotation)
141 >       call gather(A,A_Col,plan_col_rotation)
142      endif
143 <
143 >    
144   #endif
145      
146 <    call initForce_Modules(thisStat)
147 <    if (thisStat /= 0) then
148 <       status = -1
149 <       return
146 >    if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
147 >       !! See if we need to update neighbor lists
148 >       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)  
149 >       !! if_mpi_gather_stuff_for_prepair
150 >       !! do_prepair_loop_if_needed
151 >       !! if_mpi_scatter_stuff_from_prepair
152 >       !! if_mpi_gather_stuff_from_prepair_to_main_loop
153 >    else
154 >       !! See if we need to update neighbor lists
155 >       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)  
156      endif
266 –
267 – !! Create neighbor lists
268 –    call expandList(thisStat)
269 –    if (thisStat /= 0) then
270 –       status = -1
271 –       return
272 –    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
157      
286 –    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 –
322 –    
323 –    type(atype), pointer :: Atype_i
324 –    type(atype), pointer :: Atype_j
325 –
326 –
327 –
328 –
329 –  
330 –
158   #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 –    
159      
160 +    if (update_nlist) then
161 +      
162 +       !! save current configuration, construct neighbor list,
163 +       !! and calculate forces
164 +       call save_neighborList(q)
165 +      
166 +       neighborListSize = getNeighborListSize()
167 +       nlist = 0      
168 +      
169 +       do i = 1, nrow
170 +          point(i) = nlist + 1
171 +          
172 +          inner: do j = 1, ncol
173 +            
174 +             if (checkExcludes(i,j)) cycle inner
175 +            
176 +             call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
177 +            
178 +             if (rijsq <  rlistsq) then            
179 +                
180 +                nlist = nlist + 1
181 +                
182 +                if (nlist > neighborListSize) then
183 +                   call expandNeighborList(nlocal, listerror)
184 +                   if (listerror /= 0) then
185 +                      error = -1
186 +                      write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
187 +                      return
188 +                   end if
189 +                endif
190 +                
191 +                list(nlist) = j
192 +                                
193 +                if (rijsq <  rcutsq) then
194 +                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
195 +                endif
196 +             endif
197 +          enddo inner
198 +       enddo
199  
200 <     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)
200 >       point(nrow + 1) = nlist + 1
201        
202 < #endif          
472 <          
473 <           if (rijsq <  rlistsq) then
202 >    else  !! (of update_check)
203  
204 <              nlist = nlist + 1
204 >       ! use the list to find the neighbors
205 >       do i = 1, nrow
206 >          JBEG = POINT(i)
207 >          JEND = POINT(i+1) - 1
208 >          ! check thiat molecule i has neighbors
209 >          if (jbeg .le. jend) then
210 >            
211 >             do jnab = jbeg, jend
212 >                j = list(jnab)
213  
214 <              if (nlist > neighborListSize) then
215 <                 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
214 >                call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
215 >                call do_pair(i, j, rijsq, d, do_pot, do_stress)
216  
217 <              list(nlist) = j
218 <
217 >             enddo
218 >          endif
219 >       enddo
220 >    endif
221      
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
222   #else
223 <     point(natoms) = nlist + 1
224 < #endif
225 <
226 <  else !! (update)
223 >    
224 >    if (update_nlist) then
225 >      
226 >       ! save current configuration, contruct neighbor list,
227 >       ! and calculate forces
228 >       call save_neighborList(q)
229 >      
230 >       neighborListSize = getNeighborListSize()
231 >       nlist = 0
232 >      
233 >       do i = 1, natoms-1
234 >          point(i) = nlist + 1
235 >          
236 >          inner: do j = i+1, natoms
237 >            
238 >             if (checkExcludes(i,j)) cycle inner
239 >            
240 >             call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
241 >          
242 >             if (rijsq <  rlistsq) then
243 >                
244 >                nlist = nlist + 1
245 >                
246 >                if (nlist > neighborListSize) then
247 >                   call expandList(natoms, listerror)
248 >                   if (listerror /= 0) then
249 >                      error = -1
250 >                      write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
251 >                      return
252 >                   end if
253 >                endif
254 >                
255 >                list(nlist) = j
256 >                
257 >                if (rijsq <  rcutsq) then
258 >                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
259 >                endif
260 >             endif
261 >          enddo inner
262 >       enddo
263 >      
264 >       point(natoms) = nlist + 1
265 >      
266 >    else !! (update)
267 >      
268 >       ! use the list to find the neighbors
269 >       do i = 1, natoms-1
270 >          JBEG = POINT(i)
271 >          JEND = POINT(i+1) - 1
272 >          ! check thiat molecule i has neighbors
273 >          if (jbeg .le. jend) then
274 >            
275 >             do jnab = jbeg, jend
276 >                j = list(jnab)
277  
278 <     ! use the list to find the neighbors
279 <     do i = 1, nrow
505 <        JBEG = POINT(i)
506 <        JEND = POINT(i+1) - 1
507 <        ! check thiat molecule i has neighbors
508 <        if (jbeg .le. jend) then
278 >                call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
279 >                call do_pair(i, j, rijsq, d, do_pot, do_stress)
280  
281 +             enddo
282 +          endif
283 +       enddo
284 +    endif
285 +    
286 + #endif
287 +    
288 +    ! phew, done with main loop.
289 +    
290   #ifdef IS_MPI
511 –           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 –
533 –
534 –
535 – #ifdef IS_MPI
291      !!distribute forces
292 <
293 <    call scatter(fRow,f,plan_row3d)
294 <    call scatter(fCol,fTemp,plan_col3d)
540 <
292 >    
293 >    call scatter(f_Row,f,plan_row3d)
294 >    call scatter(f_Col,f_temp,plan_col3d)
295      do i = 1,nlocal
296 <       f(1:3,i) = f(1:3,i) + fTemp(1:3,i)
296 >       f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
297      end do
544 –
545 –    if (do_torque) then
546 –       call scatter(tRow,t,plan_row3d)
547 –       call scatter(tCol,tTemp,plan_col3d)
298      
299 +    if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
300 +       call scatter(t_Row,t,plan_row3d)
301 +       call scatter(t_Col,t_temp,plan_col3d)
302 +      
303         do i = 1,nlocal
304 <          t(1:3,i) = t(1:3,i) + tTemp(1:3,i)
304 >          t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
305         end do
306      endif
307 <
307 >    
308      if (do_pot) then
309         ! scatter/gather pot_row into the members of my column
310 <       call scatter(eRow,eTemp,plan_row)
310 >       call scatter(pot_Row, pot_Temp, plan_row)
311        
312         ! scatter/gather pot_local into all other procs
313         ! add resultant to get total pot
314         do i = 1, nlocal
315 <          pe_local = pe_local + eTemp(i)
315 >          pot_local = pot_local + pot_Temp(i)
316         enddo
317  
318 <       eTemp = 0.0E0_DP
319 <       call scatter(eCol,eTemp,plan_col)
318 >       pot_Temp = 0.0_DP
319 >
320 >       call scatter(pot_Col, pot_Temp, plan_col)
321         do i = 1, nlocal
322 <          pe_local = pe_local + eTemp(i)
322 >          pot_local = pot_local + pot_Temp(i)
323         enddo
324        
325 <       pe = pe_local
571 <    endif
572 < #else
573 < ! Copy local array into return array for c
574 <    f = fTemp
575 <    t = tTemp
325 >    endif    
326   #endif
327  
328 <    potE = pe
328 >    if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
329 >      
330 >       if (FF_uses_RF .and. SimUsesRF()) then
331 >          
332 > #ifdef IS_MPI
333 >          call scatter(rf_Row,rf,plan_row3d)
334 >          call scatter(rf_Col,rf_Temp,plan_col3d)
335 >          do i = 1,nlocal
336 >             rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
337 >          end do
338 > #endif
339 >          
340 >          do i = 1, getNlocal()
341  
342 <
581 <    if (do_stress) then
342 >             rfpot = 0.0_DP
343   #ifdef IS_MPI
344 <       mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, &
584 <            mpi_comm_world,mpi_err)
344 >             me_i = atid_row(i)
345   #else
346 <       tau = tauTemp
347 < #endif      
346 >             me_i = atid(i)
347 > #endif
348 >             call getElementProperty(atypes, me_i, "is_DP", is_DP_i)      
349 >             if ( is_DP_i ) then
350 >                call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
351 >                !! The reaction field needs to include a self contribution
352 >                !! to the field:
353 >                call accumulate_self_rf(i, mu_i, u_l)            
354 >                !! Get the reaction field contribution to the
355 >                !! potential and torques:
356 >                call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
357 > #ifdef IS_MPI
358 >                pot_local = pot_local + rfpot
359 > #else
360 >                pot = pot + rfpot
361 > #endif
362 >             endif            
363 >          enddo
364 >       endif
365      endif
366  
590 –  end subroutine do_force_loop
367  
368 + #ifdef IS_MPI
369  
370 +    if (do_pot) then
371 +       pot = pot_local
372 +       !! we assume the c code will do the allreduce to get the total potential
373 +       !! we could do it right here if we needed to...
374 +    endif
375  
376 +    if (do_stress) then
377 +       call mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, &
378 +            mpi_comm_world,mpi_err)
379 +       call mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, &
380 +            mpi_comm_world,mpi_err)
381 +    endif
382  
383 + #else
384  
385 +    if (do_stress) then
386 +       tau = tau_Temp
387 +       virial = virial_Temp
388 +    endif
389  
390 + #endif
391 +    
392 +  end subroutine do_force_loop
393  
394  
599 –
600 –
395   !! Calculate any pre-force loop components and update nlist if necessary.
396    subroutine do_preForce(updateNlist)
397      logical, intent(inout) :: updateNlist
# Line 606 | Line 400 | contains
400  
401    end subroutine do_preForce
402  
403 <
610 <
611 <
612 <
613 <
614 <
615 <
616 <
617 <
618 <
619 <
620 <
621 < !! Calculate any post force loop components, i.e. reaction field, etc.
403 >  !! Calculate any post force loop components, i.e. reaction field, etc.
404    subroutine do_postForce()
405  
406  
407  
408    end subroutine do_postForce
409  
410 +  subroutine do_pair(i, j, rijsq, d, do_pot, do_stress)
411  
412 +    real( kind = dp ) :: pot
413 +    real( kind = dp ), dimension(3,getNlocal()) :: u_l
414 +    real (kind=dp), dimension(9,getNlocal()) :: A
415 +    real (kind=dp), dimension(3,getNlocal()) :: f
416 +    real (kind=dp), dimension(3,getNlocal()) :: t
417  
418 +    logical, intent(inout) :: do_pot, do_stress
419 +    integer, intent(in) :: i, j
420 +    real ( kind = dp ), intent(inout)    :: rijsq
421 +    real ( kind = dp )                :: r
422 +    real ( kind = dp ), intent(inout) :: d(3)
423 +    logical :: is_LJ_i, is_LJ_j
424 +    logical :: is_DP_i, is_DP_j
425 +    logical :: is_Sticky_i, is_Sticky_j
426 +    integer :: me_i, me_j
427  
428 +    r = sqrt(rijsq)
429 +    
430 + #ifdef IS_MPI
431  
432 +    me_i = atid_row(i)
433 +    me_j = atid_col(j)
434  
435 + #else
436  
437 +    me_i = atid(i)
438 +    me_j = atid(j)
439  
440 + #endif
441  
442  
443 +    if (FF_uses_LJ .and. SimUsesLJ()) then
444 +       call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
445 +       call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
446 +      
447 +       if ( is_LJ_i .and. is_LJ_j ) &
448 +            call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
449 +    endif
450 +      
451  
452 <
453 <
454 <
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)
452 >    if (FF_uses_dipoles .and. SimUsesDipoles()) then
453 >       call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
454 >       call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
455        
456 < #ifdef IS_MPI
457 <                eRow(i) = eRow(i) + pot*0.5
458 <                eCol(i) = eCol(i) + pot*0.5
459 < #else
460 <                    pe = pe + pot
674 < #endif                
456 >       if ( is_DP_i .and. is_DP_j ) then
457 >          
458 >          call do_dipole_pair(i, j, d, r, pot, u_l, f, t, do_pot, do_stress)
459 >          
460 >          if (FF_uses_RF .and. SimUsesRF()) then
461              
462 <                drdx = -rxij / r
463 <                drdy = -ryij / r
464 <                drdz = -rzij / r
465 <                
466 <                fx = dudr * drdx
467 <                fy = dudr * drdy
468 <                fz = dudr * drdz
462 >             call accumulate_rf(i, j, r, u_l)
463 >             call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
464 >            
465 >          endif
466 >          
467 >       endif
468 >    endif
469  
470 +    if (FF_uses_Sticky .and. SimUsesSticky()) then
471  
472 <
473 <
474 <
475 <
476 <                
477 < #ifdef IS_MPI
478 <                fCol(1,j) = fCol(1,j) - fx
479 <                fCol(2,j) = fCol(2,j) - fy
480 <                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 <
472 >       call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
473 >       call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
474 >      
475 >       if ( is_Sticky_i .and. is_Sticky_j ) then
476 >          call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
477 >               do_pot, do_stress)
478 >       endif
479 >    endif
480 >      
481    end subroutine do_pair
482  
483  
484 <
485 <
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
484 >  subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
485 >    
486      real (kind = dp), dimension(3) :: q_i
487      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
488      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
489      real( kind = dp ) :: d(3)
761 – !---------------- END DECLARATIONS-------------------------
490  
763 –
764 – ! Find distance between i and j
491      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
492      
493 < !   Find Magnitude of the vector
493 >    ! Wrap back into periodic box if necessary
494 >    if ( SimUsesPBC() ) then
495 >       d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,box(1:3)) * &
496 >            int(abs(d(1:3)/box(1:3) + 0.5_dp))
497 >    endif
498 >    
499      r_sq = dot_product(d,d)
500 <    r_ij = sqrt(r_sq)
500 >        
501 >  end subroutine get_interatomic_vector
502  
503 < !   Set each component for force calculation
504 <    rx_ij = d(1)
779 <    ry_ij = d(2)
780 <    rz_ij = d(3)
503 >  subroutine check_initialization(error)
504 >    integer, intent(out) :: error
505  
506 +    error = 0
507 +    ! Make sure we are properly initialized.
508 +    if (.not. do_Forces_initialized) then
509 +       write(default_error,*) "ERROR: do_Forces has not been initialized!"
510 +       error = -1
511 +       return
512 +    endif
513 + #ifdef IS_MPI
514 +    if (.not. isMPISimSet()) then
515 +       write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
516 +       error = -1
517 +       return
518 +    endif
519 + #endif
520  
521 <  end subroutine get_interatomic_vector
521 >    return
522 >  end subroutine check_initialization
523  
524 <  subroutine zero_module_variables()
524 >  
525 >  subroutine zero_work_arrays()
526 >    
527 > #ifdef IS_MPI
528  
529 < #ifndef IS_MPI
530 <
789 <    pe = 0.0E0_DP
790 <    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
529 >    q_Row = 0.0_dp
530 >    q_Col = 0.0_dp  
531      
532 <    muRow = 0.0_dp
533 <    muCol = 0.0_dp
532 >    u_l_Row = 0.0_dp
533 >    u_l_Col = 0.0_dp
534      
535 <    u_lRow = 0.0_dp
536 <    u_lCol = 0.0_dp
535 >    A_Row = 0.0_dp
536 >    A_Col = 0.0_dp
537      
538 <    ARow = 0.0_dp
539 <    ACol = 0.0_dp
540 <    
541 <    fRow = 0.0_dp
542 <    fCol = 0.0_dp
543 <    
544 <  
810 <    tRow = 0.0_dp
811 <    tCol = 0.0_dp
538 >    f_Row = 0.0_dp
539 >    f_Col = 0.0_dp
540 >    f_Temp = 0.0_dp
541 >      
542 >    t_Row = 0.0_dp
543 >    t_Col = 0.0_dp
544 >    t_Temp = 0.0_dp
545  
546 <  
546 >    pot_Row = 0.0_dp
547 >    pot_Col = 0.0_dp
548 >    pot_Temp = 0.0_dp
549  
815 –    eRow = 0.0_dp
816 –    eCol = 0.0_dp
817 –    eTemp = 0.0_dp
550   #endif
551  
552 <  end subroutine zero_module_variables
552 >    tau_Temp = 0.0_dp
553 >    virial_Temp = 0.0_dp
554 >    
555 >  end subroutine zero_work_arrays
556 >  
557  
558 < #ifdef IS_MPI
559 < !! Function to properly build neighbor lists in MPI using newtons 3rd law.
560 < !! We don't want 2 processors doing the same i j pair twice.
561 < !! Also checks to see if i and j are the same particle.
562 <  function mpi_cycle_jLoop(i,j) result(do_cycle)
563 < !--------------- Arguments--------------------------
564 < ! Index i
565 <    integer,intent(in) :: i
566 < ! Index j
567 <    integer,intent(in) :: j
568 < ! Result do_cycle
558 >  !! Function to properly build neighbor lists in MPI using newtons 3rd law.
559 >  !! We don't want 2 processors doing the same i j pair twice.
560 >  !! Also checks to see if i and j are the same particle.
561 >
562 >  function checkExcludes(atom1,atom2) result(do_cycle)
563 >    !--------------- Arguments--------------------------
564 >    ! Index i
565 >    integer,intent(in) :: atom1
566 >    ! Index j
567 >    integer,intent(in), optional :: atom2
568 >    ! Result do_cycle
569      logical :: do_cycle
570 < !--------------- Local variables--------------------
570 >    !--------------- Local variables--------------------
571      integer :: tag_i
572      integer :: tag_j
573 < !--------------- END DECLARATIONS------------------    
574 <    tag_i = tagRow(i)
575 <    tag_j = tagColumn(j)
573 >    integer :: i, j
574 >    !--------------- END DECLARATIONS------------------  
575 >    do_cycle = .false.
576 >    
577 > #ifdef IS_MPI
578 >    tag_i = tagRow(atom1)
579 > #else
580 >    tag_i = tag(atom1)
581 > #endif
582 >    
583 >    !! Check global excludes first
584 >    if (.not. present(atom2)) then
585 >       do i = 1, nExcludes_global
586 >          if (excludeGlobal(i) == tag_i) then
587 >             do_cycle = .true.
588 >             return
589 >          end if
590 >       end do
591 >       return !! return after checking globals
592 >    end if
593  
594 <    do_cycle = .false.
595 <
594 >    !! we return if atom2 not present here.
595 >    tag_j = tagColumn(atom2)
596 >    
597      if (tag_i == tag_j) then
598         do_cycle = .true.
599         return
600      end if
601 <
601 >    
602      if (tag_i < tag_j) then
603         if (mod(tag_i + tag_j,2) == 0) do_cycle = .true.
604         return
605      else                
606         if (mod(tag_i + tag_j,2) == 1) do_cycle = .true.
607      endif
608 <  end function mpi_cycle_jLoop
609 < #endif
608 >            
609 >    do i = 1, nExcludes_local
610 >       if ((tag_i == excludesLocal(1,i)) .and. (excludesLocal(2,i) < 0)) then
611 >          do_cycle = .true.
612 >          return
613 >       end if
614 >    end do
615 >    
616 >    
617 >  end function checkExcludes
618  
619 +  function FF_UsesDirectionalAtoms() result(doesit)
620 +    logical :: doesit
621 +    doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
622 +         FF_uses_GB .or. FF_uses_RF
623 +  end function FF_UsesDirectionalAtoms
624 +  
625 +  function FF_RequiresPrepairCalc() result(doesit)
626 +    logical :: doesit
627 +    doesit = FF_uses_EAM
628 +  end function FF_RequiresPrepairCalc
629 +  
630 +  function FF_RequiresPostpairCalc() result(doesit)
631 +    logical :: doesit
632 +    doesit = FF_uses_RF
633 +  end function FF_RequiresPostpairCalc
634 +  
635   end module do_Forces

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