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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 330 by gezelter, Wed Mar 12 23:15:46 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 1.16 2003-03-12 23:15:46 gezelter Exp $, $Date: 2003-03-12 23:15:46 $, $Name: not supported by cvs2svn $, $Revision: 1.16 $
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(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
114 <    real( kind = dp ), intent(in) :: epsilon
115 <    real( kind = dp ), intent(in) :: sigma
116 <    real( kind = dp ), intent(in) :: w0
117 <    real( kind = dp ), intent(in) :: v0
118 <    real( kind = dp ), intent(in) :: dipoleMoment
40 >  subroutine init_FF(thisStat)
41 >  
42 >    integer, intent(out) :: my_status
43 >    integer :: thisStat = 0
44  
45 <    integer, intent(in) :: ident
121 <    integer, intent(out) :: status
122 <    integer, intent(in) :: is_Sticky
123 <    integer, intent(in) :: is_DP
124 <    integer, intent(in) :: is_GB
125 <    integer, intent(in) :: is_LJ
45 >    ! be a smarter subroutine.
46  
47 <
48 <    type (atype), pointer :: the_new_atype
49 <    integer :: alloc_error
50 <    integer :: atype_counter = 0
131 <    integer :: alloc_size
132 <    integer :: err_stat
133 <    status = 0
134 <
135 <
136 <
137 < ! allocate a new atype    
138 <    allocate(the_new_atype,stat=alloc_error)
139 <    if (alloc_error /= 0 ) then
140 <       status = -1
47 >    
48 >    call init_lj_FF(my_status)
49 >    if (my_status /= 0) then
50 >       thisStat = -1
51         return
52      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
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.
163 <    if ( is_DP /= 0 )        the_new_atype%is_DP       = .true.
60 >    do_forces_initialized = .true.    
61 >    
62 >  end subroutine init_FF
63  
165    call add_atype(the_new_atype,ListHead,ListTail,err_stat)
166    if (err_stat /= 0 ) then
167       status = -1
168       return
169    endif
64  
171    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
194 <    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  
104 <    
104 >    !! initialize local variables  
105  
106 < !! if were're not in MPI, we just update ljatypePtrList
107 < #ifndef IS_MPI
108 <    call create_IdentPtrlst(ident,ListHead,identPtrList,thisStat)
109 <    if ( thisStat /= 0 ) then
110 <       status = -1
111 <       return
112 <    endif
106 > #ifdef IS_MPI
107 >    nlocal = getNlocal()
108 >    nrow   = getNrow(plan_row)
109 >    ncol   = getNcol(plan_col)
110 > #else
111 >    nlocal = getNlocal()
112 >    natoms = nlocal
113 > #endif
114  
115 +    call getRcut(rcut,rcut2=rcutsq)
116 +    call getRlist(rlist,rlistsq)
117      
118 < ! if were're in MPI, we also have to worry about row and col lists    
119 < #else
214 <  
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
219 <       return
220 <    endif
221 <    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
118 >    call check_initialization()
119 >    call zero_work_arrays()
120  
121 <    allocate(identCol(ncol),stat=alloc_stat)
122 <    if (alloc_stat /= 0 ) then
233 <       status = -1
234 <       return
235 <    endif
121 >    do_pot = do_pot_c
122 >    do_stress = do_stress_c
123  
124 < !! Gather idents into row and column idents
238 <
239 <    call gather(ident,identRow,plan_row)
240 <    call gather(ident,identCol,plan_col)
124 >    ! Gather all information needed by all force loops:
125      
126 <  
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
126 > #ifdef IS_MPI    
127  
128 < !! free temporary ident arrays
129 <    if (allocated(identCol)) then
130 <       deallocate(identCol)
131 <    end if
132 <    if (allocated(identCol)) then
133 <       deallocate(identRow)
128 >    call gather(q,q_Row,plan_row3d)
129 >    call gather(q,q_Col,plan_col3d)
130 >        
131 >    if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
132 >       call gather(u_l,u_l_Row,plan_row3d)
133 >       call gather(u_l,u_l_Col,plan_col3d)
134 >      
135 >       call gather(A,A_Row,plan_row_rotation)
136 >       call gather(A,A_Col,plan_col_rotation)
137      endif
138 <
138 >    
139   #endif
140      
141 <    call initForce_Modules(thisStat)
142 <    if (thisStat /= 0) then
143 <       status = -1
144 <       return
141 >    if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
142 >       !! See if we need to update neighbor lists
143 >       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)  
144 >       !! if_mpi_gather_stuff_for_prepair
145 >       !! do_prepair_loop_if_needed
146 >       !! if_mpi_scatter_stuff_from_prepair
147 >       !! if_mpi_gather_stuff_from_prepair_to_main_loop
148 >    else
149 >       !! See if we need to update neighbor lists
150 >       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)  
151      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
152      
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
153   #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
154      
155      if (update_nlist) then
156        
157 <       ! save current configuration, contruct neighbor list,
158 <       ! and calculate forces
157 >       !! save current configuration, construct neighbor list,
158 >       !! and calculate forces
159         call save_neighborList(q)
160        
161         neighborListSize = getNeighborListSize()
162 <       nlist = 0
162 >       nlist = 0      
163        
442       nrow = getNrow(plan_row)
443       ncol = getNcol(plan_col)
444       nlocal = getNlocal()
445      
164         do i = 1, nrow
165            point(i) = nlist + 1
448          Atype_i => identPtrListRow(i)%this
166            
167            inner: do j = 1, ncol
451             Atype_j => identPtrListColumn(j)%this
168              
169 <             call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),&
454 <                  rxij,ryij,rzij,rijsq,r)
169 >             if (checkExcludes(i,j)) cycle inner:
170              
171 <             ! skip the loop if the atoms are identical
457 <             if (mpi_cycle_jLoop(i,j)) cycle inner:
171 >             call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
172              
173               if (rijsq <  rlistsq) then            
174                  
175                  nlist = nlist + 1
176                  
177                  if (nlist > neighborListSize) then
178 <                   call expandList(listerror)
178 >                   call expandNeighborList(nlocal, listerror)
179                     if (listerror /= 0) then
180 <                      FFerror = -1
180 >                      error = -1
181                        write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
182                        return
183                     end if
184                  endif
185                  
186                  list(nlist) = j
187 <                
474 <                
187 >                                
188                  if (rijsq <  rcutsq) then
189 <                   call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
189 >                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
190                  endif
191               endif
192            enddo inner
# Line 481 | Line 194 | contains
194  
195         point(nrow + 1) = nlist + 1
196        
197 <    else !! (update)
197 >    else  !! (of update_check)
198  
199         ! use the list to find the neighbors
200         do i = 1, nrow
# Line 489 | Line 202 | contains
202            JEND = POINT(i+1) - 1
203            ! check thiat molecule i has neighbors
204            if (jbeg .le. jend) then
205 <
493 <             Atype_i => identPtrListRow(i)%this
205 >            
206               do jnab = jbeg, jend
207                  j = list(jnab)
208 <                Atype_j = identPtrListColumn(j)%this
209 <                call get_interatomic_vector(i,j,qRow(:,i),qCol(:,j),&
210 <                     rxij,ryij,rzij,rijsq,r)
211 <                
500 <                call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
208 >
209 >                call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
210 >                call do_pair(i, j, rijsq, d, do_pot, do_stress)
211 >
212               enddo
213            endif
214         enddo
215      endif
216 <
216 >    
217   #else
218      
219      if (update_nlist) then
# Line 514 | Line 225 | contains
225         neighborListSize = getNeighborListSize()
226         nlist = 0
227        
517    
228         do i = 1, natoms-1
229            point(i) = nlist + 1
230 <          Atype_i   => identPtrList(i)%this
521 <
230 >          
231            inner: do j = i+1, natoms
232 <             Atype_j   => identPtrList(j)%this
233 <             call get_interatomic_vector(i,j,q(:,i),q(:,j),&
234 <                  rxij,ryij,rzij,rijsq,r)
232 >            
233 >             if (checkExcludes(i,j)) cycle inner:
234 >            
235 >             call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
236            
237               if (rijsq <  rlistsq) then
238 <
238 >                
239                  nlist = nlist + 1
240                  
241                  if (nlist > neighborListSize) then
242 <                   call expandList(listerror)
242 >                   call expandList(natoms, listerror)
243                     if (listerror /= 0) then
244 <                      FFerror = -1
244 >                      error = -1
245                        write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
246                        return
247                     end if
248                  endif
249                  
250                  list(nlist) = j
251 <
542 <    
251 >                
252                  if (rijsq <  rcutsq) then
253 <                   call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
253 >                   call do_pair(i, j, rijsq, d, do_pot, do_stress)
254                  endif
255               endif
256            enddo inner
# Line 552 | Line 261 | contains
261      else !! (update)
262        
263         ! use the list to find the neighbors
264 <       do i = 1, nrow
264 >       do i = 1, natoms-1
265            JBEG = POINT(i)
266            JEND = POINT(i+1) - 1
267            ! check thiat molecule i has neighbors
268            if (jbeg .le. jend) then
269              
561             Atype_i => identPtrList(i)%this
270               do jnab = jbeg, jend
271                  j = list(jnab)
272 <                Atype_j = identPtrList(j)%this
273 <                call get_interatomic_vector(i,j,q(:,i),q(:,j),&
274 <                     rxij,ryij,rzij,rijsq,r)
275 <                call do_pair(Atype_i,Atype_j,i,j,r,rxij,ryij,rzij)
272 >
273 >                call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
274 >                call do_pair(i, j, rijsq, d, do_pot, do_stress)
275 >
276               enddo
277            endif
278         enddo
279      endif
280 <
280 >    
281   #endif
282 <
283 <
284 < #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:
282 >    
283 >    ! phew, done with main loop.
284 >    
285   #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)
592       enddo
593    endif
594
595 #else
596
597    if (system_has_postpair_atoms) then
598       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
609 #ifdef IS_MPI
286      !!distribute forces
287 <
288 <    call scatter(fRow,fTemp1,plan_row3d)
289 <    call scatter(fCol,fTemp2,plan_col3d)
614 <
615 <
287 >    
288 >    call scatter(f_Row,f,plan_row3d)
289 >    call scatter(f_Col,f_temp,plan_col3d)
290      do i = 1,nlocal
291 <       fTemp(1:3,i) = fTemp1(1:3,i) + fTemp2(1:3,i)
291 >       f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
292      end do
619
620    if (do_torque) then
621       call scatter(tRow,tTemp1,plan_row3d)
622       call scatter(tCol,tTemp2,plan_col3d)
293      
294 +    if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
295 +       call scatter(t_Row,t,plan_row3d)
296 +       call scatter(t_Col,t_temp,plan_col3d)
297 +      
298         do i = 1,nlocal
299 <          tTemp(1:3,i) = tTemp1(1:3,i) + tTemp2(1:3,i)
299 >          t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
300         end do
301      endif
302 <
302 >    
303      if (do_pot) then
304         ! scatter/gather pot_row into the members of my column
305 <       call scatter(eRow,eTemp,plan_row)
305 >       call scatter(pot_Row, pot_Temp, plan_row)
306        
307         ! scatter/gather pot_local into all other procs
308         ! add resultant to get total pot
309         do i = 1, nlocal
310 <          pe_local = pe_local + eTemp(i)
310 >          pot_local = pot_local + pot_Temp(i)
311         enddo
312  
313 <       eTemp = 0.0E0_DP
314 <       call scatter(eCol,eTemp,plan_col)
313 >       pot_Temp = 0.0_DP
314 >
315 >       call scatter(pot_Col, pot_Temp, plan_col)
316         do i = 1, nlocal
317 <          pe_local = pe_local + eTemp(i)
317 >          pot_local = pot_local + pot_Temp(i)
318         enddo
319        
320 <       pe = pe_local
646 <    endif
647 < #else
648 < ! Copy local array into return array for c
649 <    f = f+fTemp
650 <    t = t+tTemp
320 >    endif    
321   #endif
322  
323 <    potE = pe
323 >    if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
324 >      
325 >       if (FF_uses_RF .and. SimUsesRF()) then
326 >          
327 > #ifdef IS_MPI
328 >          call scatter(rf_Row,rf,plan_row3d)
329 >          call scatter(rf_Col,rf_Temp,plan_col3d)
330 >          do i = 1,nlocal
331 >             rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
332 >          end do
333 > #endif
334 >          
335 >          do i = 1, getNlocal()
336  
337 <
656 <    if (do_stress) then
337 >             rfpot = 0.0_DP
338   #ifdef IS_MPI
339 <       mpi_allreduce = (tau,tauTemp,9,mpi_double_precision,mpi_sum, &
659 <            mpi_comm_world,mpi_err)
339 >             me_i = atid_row(i)
340   #else
341 <       tau = tauTemp
342 < #endif      
341 >             me_i = atid(i)
342 > #endif
343 >             call getElementProperty(atypes, me_i, "is_DP", is_DP_i)      
344 >             if ( is_DP_i ) then
345 >                call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
346 >                !! The reaction field needs to include a self contribution
347 >                !! to the field:
348 >                call accumulate_self_rf(i, mu_i, u_l)            
349 >                !! Get the reaction field contribution to the
350 >                !! potential and torques:
351 >                call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
352 > #ifdef IS_MPI
353 >                pot_local = pot_local + rfpot
354 > #else
355 >                pot = pot + rfpot
356 > #endif
357 >             endif            
358 >          enddo
359 >       endif
360      endif
361  
665  end subroutine do_force_loop
362  
363 + #ifdef IS_MPI
364  
365 +    if (do_pot) then
366 +       pot = pot_local
367 +       !! we assume the c code will do the allreduce to get the total potential
368 +       !! we could do it right here if we needed to...
369 +    endif
370  
371 +    if (do_stress) then
372 +       call mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, &
373 +            mpi_comm_world,mpi_err)
374 +       call mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, &
375 +            mpi_comm_world,mpi_err)
376 +    endif
377  
378 + #else
379  
380 +    if (do_stress) then
381 +       tau = tau_Temp
382 +       virial = virial_Temp
383 +    endif
384  
385 + #endif
386 +    
387 +  end subroutine do_force_loop
388  
389  
674
675
390   !! Calculate any pre-force loop components and update nlist if necessary.
391    subroutine do_preForce(updateNlist)
392      logical, intent(inout) :: updateNlist
# Line 681 | Line 395 | contains
395  
396    end subroutine do_preForce
397  
398 <
685 <
686 <
687 <
688 <
689 <
690 <
691 <
692 <
693 <
694 <
695 <
696 < !! Calculate any post force loop components, i.e. reaction field, etc.
398 >  !! Calculate any post force loop components, i.e. reaction field, etc.
399    subroutine do_postForce()
400  
401  
402  
403    end subroutine do_postForce
404  
405 +  subroutine do_pair(i, j, rijsq, d, do_pot, do_stress)
406  
407 +    real( kind = dp ) :: pot
408 +    real( kind = dp ), dimension(3,getNlocal()) :: u_l
409 +    real (kind=dp), dimension(9,getNlocal()) :: A
410 +    real (kind=dp), dimension(3,getNlocal()) :: f
411 +    real (kind=dp), dimension(3,getNlocal()) :: t
412  
413 +    logical, intent(inout) :: do_pot, do_stress
414 +    integer, intent(in) :: i, j
415 +    real ( kind = dp ), intent(in)    :: rijsq
416 +    real ( kind = dp )                :: r
417 +    real ( kind = dp ), intent(inout) :: d(3)
418 +    logical :: is_LJ_i, is_LJ_j
419 +    logical :: is_DP_i, is_DP_j
420 +    logical :: is_Sticky_i, is_Sticky_j
421 +    integer :: me_i, me_j
422  
423 <
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
423 >    r = sqrt(rijsq)
424      
425 + #ifdef IS_MPI
426  
427 <    if (Atype_i%is_LJ .and. Atype_j%is_LJ) then
428 <       call getLJForce(r,pot,dudr,ljAtype_i,ljAtype_j,fx,fy,fz)
740 <    endif
427 >    me_i = atid_row(i)
428 >    me_j = atid_col(j)
429  
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)
430   #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
431  
432 <       if (do_reaction_field) then
433 < #ifdef IS_MPI
434 <          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)
432 >    me_i = atid(i)
433 >    me_j = atid(j)
434 >
435   #endif
760       endif
436  
437  
438 +    if (FF_uses_LJ .and. SimUsesLJ()) then
439 +       call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
440 +       call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
441 +      
442 +       if ( is_LJ_i .and. is_LJ_j ) &
443 +            call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
444      endif
445 +      
446  
447 <    if (Atype_i%is_sticky .and. Atype_j%is_sticky) then
448 <       call getstickyforce(r,pot,dudr,ljAtype_i,ljAtype_j)
449 <    endif
768 <
447 >    if (FF_uses_dipoles .and. SimUsesDipoles()) then
448 >       call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
449 >       call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
450        
451 < #ifdef IS_MPI
452 <                eRow(i) = eRow(i) + pot*0.5
453 <                eCol(i) = eCol(i) + pot*0.5
454 < #else
455 <                    pe = pe + pot
775 < #endif                
451 >       if ( is_DP_i .and. is_DP_j ) then
452 >          
453 >          call do_dipole_pair(i, j, d, r, pot, u_l, f, t, do_pot, do_stress)
454 >          
455 >          if (FF_uses_RF .and. SimUsesRF()) then
456              
457 <                drdx = -rxij / r
458 <                drdy = -ryij / r
459 <                drdz = -rzij / r
460 <                
461 <                fx = dudr * drdx
462 <                fy = dudr * drdy
463 <                fz = dudr * drdz
457 >             call accumulate_rf(i, j, r, u_l)
458 >             call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
459 >            
460 >          endif
461 >          
462 >       endif
463 >    endif
464  
465 +    if (FF_uses_Sticky .and. SimUsesSticky()) then
466  
467 <
468 <
469 <
470 <
471 <                
472 < #ifdef IS_MPI
473 <                fCol(1,j) = fCol(1,j) - fx
474 <                fCol(2,j) = fCol(2,j) - fy
475 <                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 <
467 >       call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
468 >       call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
469 >      
470 >       if ( is_Sticky_i .and. is_Sticky_j ) then
471 >          call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
472 >               do_pot, do_stress)
473 >       endif
474 >    endif
475 >      
476    end subroutine do_pair
477  
478  
479 <
480 <
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
479 >  subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
480 >    
481      real (kind = dp), dimension(3) :: q_i
482      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
483      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
484      real( kind = dp ) :: d(3)
862 !---------------- END DECLARATIONS-------------------------
485  
864
865 ! Find distance between i and j
486      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
487      
488 < !   Find Magnitude of the vector
488 >    ! Wrap back into periodic box if necessary
489 >    if ( SimUsesPBC() ) then
490 >       d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,box(1:3)) * &
491 >            int(abs(d(1:3)/box(1:3) + 0.5_dp))
492 >    endif
493 >    
494      r_sq = dot_product(d,d)
495 <    r_ij = sqrt(r_sq)
495 >        
496 >  end subroutine get_interatomic_vector
497  
498 < !   Set each component for force calculation
499 <    rx_ij = d(1)
880 <    ry_ij = d(2)
881 <    rz_ij = d(3)
498 >  subroutine check_initialization(error)
499 >    integer, intent(out) :: error
500  
501 +    error = 0
502 +    ! Make sure we are properly initialized.
503 +    if (.not. do_Forces_initialized) then
504 +       write(default_error,*) "ERROR: do_Forces has not been initialized!"
505 +       error = -1
506 +       return
507 +    endif
508 + #ifdef IS_MPI
509 +    if (.not. isMPISimSet()) then
510 +       write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
511 +       error = -1
512 +       return
513 +    endif
514 + #endif
515  
516 <  end subroutine get_interatomic_vector
516 >    return
517 >  end subroutine check_initialization
518  
519 <  subroutine zero_module_variables()
519 >  
520 >  subroutine zero_work_arrays()
521 >    
522 > #ifdef IS_MPI
523  
524 < #ifndef IS_MPI
525 <
890 <    pe = 0.0E0_DP
891 <    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
524 >    q_Row = 0.0_dp
525 >    q_Col = 0.0_dp  
526      
527 <    muRow = 0.0_dp
528 <    muCol = 0.0_dp
527 >    u_l_Row = 0.0_dp
528 >    u_l_Col = 0.0_dp
529      
530 <    u_lRow = 0.0_dp
531 <    u_lCol = 0.0_dp
530 >    A_Row = 0.0_dp
531 >    A_Col = 0.0_dp
532      
533 <    ARow = 0.0_dp
534 <    ACol = 0.0_dp
535 <    
536 <    fRow = 0.0_dp
537 <    fCol = 0.0_dp
538 <    
539 <  
911 <    tRow = 0.0_dp
912 <    tCol = 0.0_dp
533 >    f_Row = 0.0_dp
534 >    f_Col = 0.0_dp
535 >    f_Temp = 0.0_dp
536 >      
537 >    t_Row = 0.0_dp
538 >    t_Col = 0.0_dp
539 >    t_Temp = 0.0_dp
540  
541 <  
541 >    pot_Row = 0.0_dp
542 >    pot_Col = 0.0_dp
543 >    pot_Temp = 0.0_dp
544  
916    eRow = 0.0_dp
917    eCol = 0.0_dp
918    eTemp = 0.0_dp
545   #endif
546  
547 <  end subroutine zero_module_variables
547 >    tau_Temp = 0.0_dp
548 >    virial_Temp = 0.0_dp
549 >    
550 >  end subroutine zero_work_arrays
551 >  
552  
553 < #ifdef IS_MPI
554 < !! Function to properly build neighbor lists in MPI using newtons 3rd law.
555 < !! We don't want 2 processors doing the same i j pair twice.
556 < !! Also checks to see if i and j are the same particle.
557 <  function mpi_cycle_jLoop(i,j) result(do_cycle)
558 < !--------------- Arguments--------------------------
559 < ! Index i
560 <    integer,intent(in) :: i
561 < ! Index j
562 <    integer,intent(in) :: j
563 < ! Result do_cycle
553 >  !! Function to properly build neighbor lists in MPI using newtons 3rd law.
554 >  !! We don't want 2 processors doing the same i j pair twice.
555 >  !! Also checks to see if i and j are the same particle.
556 >
557 >  function checkExcludes(atom1,atom2) result(do_cycle)
558 >    !--------------- Arguments--------------------------
559 >    ! Index i
560 >    integer,intent(in) :: atom1
561 >    ! Index j
562 >    integer,intent(in), optional :: atom2
563 >    ! Result do_cycle
564      logical :: do_cycle
565 < !--------------- Local variables--------------------
565 >    !--------------- Local variables--------------------
566      integer :: tag_i
567      integer :: tag_j
568 < !--------------- END DECLARATIONS------------------    
569 <    tag_i = tagRow(i)
570 <    tag_j = tagColumn(j)
568 >    integer :: i, j
569 >    !--------------- END DECLARATIONS------------------  
570 >    do_cycle = .false.
571 >    
572 > #ifdef IS_MPI
573 >    tag_i = tagRow(atom1)
574 > #else
575 >    tag_i = tag(atom1)
576 > #endif
577 >    
578 >    !! Check global excludes first
579 >    if (.not. present(atom2)) then
580 >       do i = 1, nExcludes_global
581 >          if (excludeGlobal(i) == tag_i) then
582 >             do_cycle = .true.
583 >             return
584 >          end if
585 >       end do
586 >       return !! return after checking globals
587 >    end if
588  
589 <    do_cycle = .false.
590 <
589 >    !! we return if atom2 not present here.
590 >    tag_j = tagColumn(atom2)
591 >    
592      if (tag_i == tag_j) then
593         do_cycle = .true.
594         return
595      end if
596 <
596 >    
597      if (tag_i < tag_j) then
598         if (mod(tag_i + tag_j,2) == 0) do_cycle = .true.
599         return
600      else                
601         if (mod(tag_i + tag_j,2) == 1) do_cycle = .true.
602      endif
603 <  end function mpi_cycle_jLoop
604 < #endif
603 >            
604 >    do i = 1, nExcludes_local
605 >       if ((tag_i == excludesLocal(1,i)) .and. (excludesLocal(2,i) < 0)) then
606 >          do_cycle = .true.
607 >          return
608 >       end if
609 >    end do
610 >    
611 >    
612 >  end function checkExcludes
613  
614 +  function FF_UsesDirectionalAtoms() result(doesit)
615 +    logical :: doesit
616 +    doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
617 +         FF_uses_GB .or. FF_uses_RF
618 +  end function FF_UsesDirectionalAtoms
619 +  
620 +  function FF_RequiresPrepairCalc() result(doesit)
621 +    logical :: doesit
622 +    doesit = FF_uses_EAM
623 +  end function FF_RequiresPrepairCalc
624 +  
625 +  function FF_RequiresPostpairCalc() result(doesit)
626 +    logical :: doesit
627 +    doesit = FF_uses_RF
628 +  end function FF_RequiresPostpairCalc
629 +  
630   end module do_Forces

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