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Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 673 by chuckv, Fri Aug 8 21:22:37 2003 UTC vs.
Revision 1217 by gezelter, Tue Jun 1 21:45:22 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.28 2003-08-08 21:22:37 chuckv Exp $, $Date: 2003-08-08 21:22:37 $, $Name: not supported by cvs2svn $, $Revision: 1.28 $
7	>	!! @version $Id: do_Forces.F90,v 1.68 2004-06-01 21:45:22 gezelter Exp $, $Date: 2004-06-01 21:45:22 $, $Name: not supported by cvs2svn $, $Revision: 1.68 $
8
9		module do_Forces
10		use force_globals
11		use simulation
12		use definitions
13		use atype_module
14	+	use switcheroo
15		use neighborLists
16		use lj
17		use sticky_pair
18		use dipole_dipole
19	+	use charge_charge
20		use reaction_field
21		use gb_pair
22		use vector_class
#	Line 29 | Line 31 | module do_Forces
31
32		#define __FORTRAN90
33		#include "fForceField.h"
34	+	#include "fSwitchingFunction.h"
35
36	<	logical, save :: do_forces_initialized = .false., haveRlist = .false.
36	>	INTEGER, PARAMETER:: PREPAIR_LOOP = 1
37	>	INTEGER, PARAMETER:: PAIR_LOOP    = 2
38	>
39	>	logical, save :: haveRlist = .false.
40	>	logical, save :: haveNeighborList = .false.
41		logical, save :: havePolicies = .false.
42	+	logical, save :: haveSIMvariables = .false.
43	+	logical, save :: havePropertyMap = .false.
44	+	logical, save :: haveSaneForceField = .false.
45		logical, save :: FF_uses_LJ
46		logical, save :: FF_uses_sticky
47	+	logical, save :: FF_uses_charges
48		logical, save :: FF_uses_dipoles
49		logical, save :: FF_uses_RF
50		logical, save :: FF_uses_GB
51		logical, save :: FF_uses_EAM
52	+	logical, save :: SIM_uses_LJ
53	+	logical, save :: SIM_uses_sticky
54	+	logical, save :: SIM_uses_charges
55	+	logical, save :: SIM_uses_dipoles
56	+	logical, save :: SIM_uses_RF
57	+	logical, save :: SIM_uses_GB
58	+	logical, save :: SIM_uses_EAM
59	+	logical, save :: SIM_requires_postpair_calc
60	+	logical, save :: SIM_requires_prepair_calc
61	+	logical, save :: SIM_uses_directional_atoms
62	+	logical, save :: SIM_uses_PBC
63	+	logical, save :: SIM_uses_molecular_cutoffs
64
65		real(kind=dp), save :: rlist, rlistsq
66
#	Line 45 | Line 68 | contains
68		public :: do_force_loop
69		public :: setRlistDF
70
71	+	#ifdef PROFILE
72	+	public :: getforcetime
73	+	real, save :: forceTime = 0
74	+	real :: forceTimeInitial, forceTimeFinal
75	+	integer :: nLoops
76	+	#endif
77	+
78	+	type :: Properties
79	+	logical :: is_lj     = .false.
80	+	logical :: is_sticky = .false.
81	+	logical :: is_dp     = .false.
82	+	logical :: is_gb     = .false.
83	+	logical :: is_eam    = .false.
84	+	logical :: is_charge = .false.
85	+	real(kind=DP) :: charge = 0.0_DP
86	+	real(kind=DP) :: dipole_moment = 0.0_DP
87	+	end type Properties
88	+
89	+	type(Properties), dimension(:),allocatable :: PropertyMap
90	+
91		contains
92
93		subroutine setRlistDF( this_rlist )
#	Line 55 | Line 98 | contains
98		rlistsq = rlist * rlist
99
100		haveRlist = .true.
58	–	if( havePolicies ) do_forces_initialized = .true.
101
102		end subroutine setRlistDF
103
104	+	subroutine createPropertyMap(status)
105	+	integer :: nAtypes
106	+	integer :: status
107	+	integer :: i
108	+	logical :: thisProperty
109	+	real (kind=DP) :: thisDPproperty
110	+
111	+	status = 0
112	+
113	+	nAtypes = getSize(atypes)
114	+
115	+	if (nAtypes == 0) then
116	+	status = -1
117	+	return
118	+	end if
119	+
120	+	if (.not. allocated(PropertyMap)) then
121	+	allocate(PropertyMap(nAtypes))
122	+	endif
123	+
124	+	do i = 1, nAtypes
125	+	call getElementProperty(atypes, i, "is_LJ", thisProperty)
126	+	PropertyMap(i)%is_LJ = thisProperty
127	+
128	+	call getElementProperty(atypes, i, "is_Charge", thisProperty)
129	+	PropertyMap(i)%is_Charge = thisProperty
130	+
131	+	if (thisProperty) then
132	+	call getElementProperty(atypes, i, "charge", thisDPproperty)
133	+	PropertyMap(i)%charge = thisDPproperty
134	+	endif
135	+
136	+	call getElementProperty(atypes, i, "is_DP", thisProperty)
137	+	PropertyMap(i)%is_DP = thisProperty
138	+
139	+	if (thisProperty) then
140	+	call getElementProperty(atypes, i, "dipole_moment", thisDPproperty)
141	+	PropertyMap(i)%dipole_moment = thisDPproperty
142	+	endif
143	+
144	+	call getElementProperty(atypes, i, "is_Sticky", thisProperty)
145	+	PropertyMap(i)%is_Sticky = thisProperty
146	+	call getElementProperty(atypes, i, "is_GB", thisProperty)
147	+	PropertyMap(i)%is_GB = thisProperty
148	+	call getElementProperty(atypes, i, "is_EAM", thisProperty)
149	+	PropertyMap(i)%is_EAM = thisProperty
150	+	end do
151	+
152	+	havePropertyMap = .true.
153	+
154	+	end subroutine createPropertyMap
155	+
156	+	subroutine setSimVariables()
157	+	SIM_uses_LJ = SimUsesLJ()
158	+	SIM_uses_sticky = SimUsesSticky()
159	+	SIM_uses_charges = SimUsesCharges()
160	+	SIM_uses_dipoles = SimUsesDipoles()
161	+	SIM_uses_RF = SimUsesRF()
162	+	SIM_uses_GB = SimUsesGB()
163	+	SIM_uses_EAM = SimUsesEAM()
164	+	SIM_requires_postpair_calc = SimRequiresPostpairCalc()
165	+	SIM_requires_prepair_calc = SimRequiresPrepairCalc()
166	+	SIM_uses_directional_atoms = SimUsesDirectionalAtoms()
167	+	SIM_uses_PBC = SimUsesPBC()
168	+	!SIM_uses_molecular_cutoffs = SimUsesMolecularCutoffs()
169	+
170	+	haveSIMvariables = .true.
171	+
172	+	return
173	+	end subroutine setSimVariables
174	+
175	+	subroutine doReadyCheck(error)
176	+	integer, intent(out) :: error
177	+
178	+	integer :: myStatus
179	+
180	+	error = 0
181	+
182	+	if (.not. havePropertyMap) then
183	+
184	+	myStatus = 0
185	+
186	+	call createPropertyMap(myStatus)
187	+
188	+	if (myStatus .ne. 0) then
189	+	write(default_error, *) 'createPropertyMap failed in do_Forces!'
190	+	error = -1
191	+	return
192	+	endif
193	+	endif
194	+
195	+	if (.not. haveSIMvariables) then
196	+	call setSimVariables()
197	+	endif
198	+
199	+	if (.not. haveRlist) then
200	+	write(default_error, *) 'rList has not been set in do_Forces!'
201	+	error = -1
202	+	return
203	+	endif
204	+
205	+	if (SIM_uses_LJ .and. FF_uses_LJ) then
206	+	if (.not. havePolicies) then
207	+	write(default_error, *) 'LJ mixing Policies have not been set in do_Forces!'
208	+	error = -1
209	+	return
210	+	endif
211	+	endif
212	+
213	+	if (.not. haveNeighborList) then
214	+	write(default_error, *) 'neighbor list has not been initialized in do_Forces!'
215	+	error = -1
216	+	return
217	+	end if
218	+
219	+	if (.not. haveSaneForceField) then
220	+	write(default_error, *) 'Force Field is not sane in do_Forces!'
221	+	error = -1
222	+	return
223	+	end if
224	+
225	+	#ifdef IS_MPI
226	+	if (.not. isMPISimSet()) then
227	+	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
228	+	error = -1
229	+	return
230	+	endif
231	+	#endif
232	+	return
233	+	end subroutine doReadyCheck
234	+
235	+
236		subroutine init_FF(LJMIXPOLICY, use_RF_c, thisStat)
237
238		integer, intent(in) :: LJMIXPOLICY
#	Line 83 | Line 257 | contains
257
258		FF_uses_LJ = .false.
259		FF_uses_sticky = .false.
260	+	FF_uses_charges = .false.
261		FF_uses_dipoles = .false.
262		FF_uses_GB = .false.
263		FF_uses_EAM = .false.
264
265		call getMatchingElementList(atypes, "is_LJ", .true., nMatches, MatchList)
266		if (nMatches .gt. 0) FF_uses_LJ = .true.
267	<
267	>
268	>	call getMatchingElementList(atypes, "is_Charge", .true., nMatches, MatchList)
269	>	if (nMatches .gt. 0) FF_uses_charges = .true.
270	>
271		call getMatchingElementList(atypes, "is_DP", .true., nMatches, MatchList)
272		if (nMatches .gt. 0) FF_uses_dipoles = .true.
273
#	Line 103 | Line 281 | contains
281		call getMatchingElementList(atypes, "is_EAM", .true., nMatches, MatchList)
282		if (nMatches .gt. 0) FF_uses_EAM = .true.
283
284	+	!! Assume sanity (for the sake of argument)
285	+	haveSaneForceField = .true.
286	+
287		!! check to make sure the FF_uses_RF setting makes sense
288
289		if (FF_uses_dipoles) then
#	Line 114 | Line 295 | contains
295		if (FF_uses_RF) then
296		write(default_error,*) 'Using Reaction Field with no dipoles?  Huh?'
297		thisStat = -1
298	+	haveSaneForceField = .false.
299		return
300		endif
301		endif
#	Line 128 | Line 310 | contains
310		case default
311		write(default_error,*) 'unknown LJ Mixing Policy!'
312		thisStat = -1
313	+	haveSaneForceField = .false.
314		return
315		end select
316		if (my_status /= 0) then
317		thisStat = -1
318	+	haveSaneForceField = .false.
319		return
320		end if
321	+	havePolicies = .true.
322		endif
323
324		if (FF_uses_sticky) then
325		call check_sticky_FF(my_status)
326		if (my_status /= 0) then
327		thisStat = -1
328	+	haveSaneForceField = .false.
329		return
330		end if
331		endif
332
333
334		if (FF_uses_EAM) then
335	<	call init_EAM_FF(my_status)
335	>	call init_EAM_FF(my_status)
336		if (my_status /= 0) then
337	+	write(default_error, *) "init_EAM_FF returned a bad status"
338		thisStat = -1
339	+	haveSaneForceField = .false.
340		return
341		end if
342		endif
343
156	–
157	–
344		if (FF_uses_GB) then
345		call check_gb_pair_FF(my_status)
346		if (my_status .ne. 0) then
347		thisStat = -1
348	+	haveSaneForceField = .false.
349		return
350		endif
351		endif
352
353		if (FF_uses_GB .and. FF_uses_LJ) then
354		endif
355	<	if (.not. do_forces_initialized) then
355	>	if (.not. haveNeighborList) then
356		!! Create neighbor lists
357	<	call expandNeighborList(getNlocal(), my_status)
357	>	call expandNeighborList(nLocal, my_status)
358		if (my_Status /= 0) then
359		write(default_error,*) "SimSetup: ExpandNeighborList returned error."
360		thisStat = -1
361		return
362		endif
363	+	haveNeighborList = .true.
364		endif
177	–
365
366	<	havePolicies = .true.
367	<	if( haveRlist ) do_forces_initialized = .true.
181	<
366	>
367	>
368		end subroutine init_FF
369
370
371		!! Does force loop over i,j pairs. Calls do_pair to calculates forces.
372		!------------------------------------------------------------->
373	<	subroutine do_force_loop(q, A, u_l, f, t, tau, pot, do_pot_c, do_stress_c, &
374	<	error)
373	>	subroutine do_force_loop(q, q_group, A, u_l, f, t, tau, pot, &
374	>	do_pot_c, do_stress_c, error)
375		!! Position array provided by C, dimensioned by getNlocal
376	<	real ( kind = dp ), dimension(3,getNlocal()) :: q
376	>	real ( kind = dp ), dimension(3, nLocal) :: q
377	>	!! molecular center-of-mass position array
378	>	real ( kind = dp ), dimension(3, nGroups) :: q_group
379		!! Rotation Matrix for each long range particle in simulation.
380	<	real( kind = dp), dimension(9,getNlocal()) :: A
380	>	real( kind = dp), dimension(9, nLocal) :: A
381		!! Unit vectors for dipoles (lab frame)
382	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
382	>	real( kind = dp ), dimension(3,nLocal) :: u_l
383		!! Force array provided by C, dimensioned by getNlocal
384	<	real ( kind = dp ), dimension(3,getNlocal()) :: f
384	>	real ( kind = dp ), dimension(3,nLocal) :: f
385		!! Torsion array provided by C, dimensioned by getNlocal
386	<	real( kind = dp ), dimension(3,getNlocal()) :: t
386	>	real( kind = dp ), dimension(3,nLocal) :: t
387	>
388		!! Stress Tensor
389		real( kind = dp), dimension(9) :: tau
390		real ( kind = dp ) :: pot
391		logical ( kind = 2) :: do_pot_c, do_stress_c
392		logical :: do_pot
393		logical :: do_stress
394	+	logical :: in_switching_region
395		#ifdef IS_MPI
396		real( kind = DP ) :: pot_local
397	<	integer :: nrow
398	<	integer :: ncol
397	>	integer :: nAtomsInRow
398	>	integer :: nAtomsInCol
399	>	integer :: nprocs
400	>	integer :: nGroupsInRow
401	>	integer :: nGroupsInCol
402		#endif
210	–	integer :: nlocal
403		integer :: natoms
404		logical :: update_nlist
405	<	integer :: i, j, jbeg, jend, jnab
405	>	integer :: i, j, jstart, jend, jnab
406	>	integer :: istart, iend
407	>	integer :: ia, jb, atom1, atom2
408		integer :: nlist
409	<	real( kind = DP ) ::  rijsq
410	<	real(kind=dp),dimension(3) :: d
409	>	real( kind = DP ) :: ratmsq, rgrpsq, rgrp, vpair, vij
410	>	real( kind = DP ) :: sw, dswdr, swderiv, mf
411	>	real(kind=dp),dimension(3) :: d_atm, d_grp, fpair, fij
412		real(kind=dp) :: rfpot, mu_i, virial
413	<	integer :: me_i
413	>	integer :: me_i, me_j, n_in_i, n_in_j
414		logical :: is_dp_i
415		integer :: neighborListSize
416		integer :: listerror, error
417		integer :: localError
418	+	integer :: propPack_i, propPack_j
419	+	integer :: loopStart, loopEnd, loop
420
421	<	real(kind=dp) :: listSkin = 1.0
421	>	real(kind=dp) :: listSkin = 1.0
422
226	–
423		!! initialize local variables
424	<
424	>
425		#ifdef IS_MPI
426		pot_local = 0.0_dp
427	<	nlocal = getNlocal()
428	<	nrow   = getNrow(plan_row)
429	<	ncol   = getNcol(plan_col)
427	>	nAtomsInRow   = getNatomsInRow(plan_atom_row)
428	>	nAtomsInCol   = getNatomsInCol(plan_atom_col)
429	>	nGroupsInRow  = getNgroupsInRow(plan_group_row)
430	>	nGroupsInCol  = getNgroupsInCol(plan_group_col)
431		#else
235	–	nlocal = getNlocal()
432		natoms = nlocal
433		#endif
434	<
435	<	call check_initialization(localError)
434	>
435	>	call doReadyCheck(localError)
436		if ( localError .ne. 0 ) then
437	<	call handleError("do_force_loop","Not Initialized")
437	>	call handleError("do_force_loop", "Not Initialized")
438		error = -1
439		return
440		end if
441		call zero_work_arrays()
442	<
442	>
443		do_pot = do_pot_c
444		do_stress = do_stress_c
445	<
250	<
445	>
446		! Gather all information needed by all force loops:
447
448		#ifdef IS_MPI
449	+
450	+	call gather(q, q_Row, plan_atom_row_3d)
451	+	call gather(q, q_Col, plan_atom_col_3d)
452
453	<	call gather(q,q_Row,plan_row3d)
454	<	call gather(q,q_Col,plan_col3d)
453	>	call gather(q_group, q_group_Row, plan_group_row_3d)
454	>	call gather(q_group, q_group_Col, plan_group_col_3d)
455
456	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
457	<	call gather(u_l,u_l_Row,plan_row3d)
458	<	call gather(u_l,u_l_Col,plan_col3d)
456	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
457	>	call gather(u_l, u_l_Row, plan_atom_row_3d)
458	>	call gather(u_l, u_l_Col, plan_atom_col_3d)
459
460	<	call gather(A,A_Row,plan_row_rotation)
461	<	call gather(A,A_Col,plan_col_rotation)
460	>	call gather(A, A_Row, plan_atom_row_rotation)
461	>	call gather(A, A_Col, plan_atom_col_rotation)
462		endif
463
464		#endif
267	–
268	–	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
269	–	!! See if we need to update neighbor lists
270	–	call checkNeighborList(nlocal, q, listSkin, update_nlist)
271	–	!! if_mpi_gather_stuff_for_prepair
272	–	!! do_prepair_loop_if_needed
273	–	!! if_mpi_scatter_stuff_from_prepair
274	–	!! if_mpi_gather_stuff_from_prepair_to_main_loop
275	–
276	–	!--------------------PREFORCE LOOP----------->>>>>>>>>>>>>>>>>>>>>>>>>>>
277	–	#ifdef IS_MPI
465
466	<	if (update_nlist) then
467	<
468	<	!! save current configuration, construct neighbor list,
469	<	!! and calculate forces
470	<	call saveNeighborList(nlocal, q)
471	<
472	<	neighborListSize = size(list)
473	<	nlist = 0
474	<
475	<	do i = 1, nrow
476	<	point(i) = nlist + 1
477	<
291	<	prepair_inner: do j = 1, ncol
292	<
293	<	if (skipThisPair(i,j)) cycle prepair_inner
294	<
295	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
296	<
297	<	if (rijsq < rlistsq) then
298	<
299	<	nlist = nlist + 1
300	<
301	<	if (nlist > neighborListSize) then
302	<	call expandNeighborList(nlocal, listerror)
303	<	if (listerror /= 0) then
304	<	error = -1
305	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
306	<	return
307	<	end if
308	<	neighborListSize = size(list)
309	<	endif
310	<
311	<	list(nlist) = j
312	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot_local)
313	<	endif
314	<	enddo prepair_inner
315	<	enddo
466	>	!! Begin force loop timing:
467	>	#ifdef PROFILE
468	>	call cpu_time(forceTimeInitial)
469	>	nloops = nloops + 1
470	>	#endif
471	>
472	>	loopEnd = PAIR_LOOP
473	>	if (FF_RequiresPrepairCalc() .and. SIM_requires_prepair_calc) then
474	>	loopStart = PREPAIR_LOOP
475	>	else
476	>	loopStart = PAIR_LOOP
477	>	endif
478
479	<	point(nrow + 1) = nlist + 1
318	<
319	<	else  !! (of update_check)
479	>	do loop = loopStart, loopEnd
480
481	<	! use the list to find the neighbors
482	<	do i = 1, nrow
483	<	JBEG = POINT(i)
484	<	JEND = POINT(i+1) - 1
485	<	! check thiat molecule i has neighbors
486	<	if (jbeg .le. jend) then
327	<
328	<	do jnab = jbeg, jend
329	<	j = list(jnab)
330	<
331	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
332	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
333	<	u_l, A, f, t, pot_local)
334	<
335	<	enddo
336	<	endif
337	<	enddo
338	<	endif
339	<
481	>	! See if we need to update neighbor lists
482	>	! (but only on the first time through):
483	>	if (loop .eq. loopStart) then
484	>	#ifdef IS_MPI
485	>	call checkNeighborList(nGroupsInRow, q_group_row, listSkin, &
486	>	update_nlist)
487		#else
488	<
489	<	if (update_nlist) then
488	>	call checkNeighborList(nGroups, q_group, listSkin, &
489	>	update_nlist)
490	>	#endif
491	>	endif
492
493	<	! save current configuration, contruct neighbor list,
494	<	! and calculate forces
495	<	call saveNeighborList(natoms, q)
493	>	if (update_nlist) then
494	>	!! save current configuration and construct neighbor list
495	>	#ifdef IS_MPI
496	>	call saveNeighborList(nGroupsInRow, q_group_row)
497	>	#else
498	>	call saveNeighborList(nGroups, q_group)
499	>	#endif
500	>	neighborListSize = size(list)
501	>	nlist = 0
502	>	endif
503
504	<	neighborListSize = size(list)
505	<
506	<	nlist = 0
507	<
508	<	do i = 1, natoms-1
509	<	point(i) = nlist + 1
510	<
355	<	prepair_inner: do j = i+1, natoms
356	<
357	<	if (skipThisPair(i,j))  cycle prepair_inner
358	<
359	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
360	<
504	>	istart = 1
505	>	#ifdef IS_MPI
506	>	iend = nGroupsInRow
507	>	#else
508	>	iend = nGroups - 1
509	>	#endif
510	>	outer: do i = istart, iend
511
512	<	if (rijsq < rlistsq) then
513	<
514	<
515	<	nlist = nlist + 1
516	<
517	<	if (nlist > neighborListSize) then
518	<	call expandNeighborList(natoms, listerror)
519	<	if (listerror /= 0) then
520	<	error = -1
521	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
522	<	return
523	<	end if
524	<	neighborListSize = size(list)
525	<	endif
526	<
527	<	list(nlist) = j
528	<
529	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
530	<	u_l, A, f, t, pot)
531	<
532	<	endif
533	<	enddo prepair_inner
534	<	enddo
385	<
386	<	point(natoms) = nlist + 1
387	<
388	<	else !! (update)
389	<
390	<	! use the list to find the neighbors
391	<	do i = 1, natoms-1
392	<	JBEG = POINT(i)
393	<	JEND = POINT(i+1) - 1
394	<	! check thiat molecule i has neighbors
395	<	if (jbeg .le. jend) then
396	<
397	<	do jnab = jbeg, jend
512	>	if (update_nlist) point(i) = nlist + 1
513	>
514	>	n_in_i = groupStartRow(i+1) - groupStartRow(i)
515	>
516	>	if (update_nlist) then
517	>	#ifdef IS_MPI
518	>	jstart = 1
519	>	jend = nGroupsInCol
520	>	#else
521	>	jstart = i+1
522	>	jend = nGroups
523	>	#endif
524	>	else
525	>	jstart = point(i)
526	>	jend = point(i+1) - 1
527	>	! make sure group i has neighbors
528	>	if (jstart .gt. jend) cycle outer
529	>	endif
530	>
531	>	do jnab = jstart, jend
532	>	if (update_nlist) then
533	>	j = jnab
534	>	else
535		j = list(jnab)
536	+	endif
537
400	–	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
401	–	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
402	–	u_l, A, f, t, pot)
403	–
404	–	enddo
405	–	endif
406	–	enddo
407	–	endif
408	–	#endif
409	–	!! Do rest of preforce calculations
410	–	!! do necessary preforce calculations
411	–	call do_preforce(nlocal,pot)
412	–	! we have already updated the neighbor list set it to false...
413	–	update_nlist = .false.
414	–	else
415	–	!! See if we need to update neighbor lists for non pre-pair
416	–	call checkNeighborList(nlocal, q, listSkin, update_nlist)
417	–	endif
418	–
419	–
420	–
421	–
422	–
423	–	!---------------------------------MAIN Pair LOOP->>>>>>>>>>>>>>>>>>>>>>>>>>>>
424	–
425	–
426	–
427	–
428	–
538		#ifdef IS_MPI
539	<
540	<	if (update_nlist) then
541	<
542	<	!! save current configuration, construct neighbor list,
543	<	!! and calculate forces
544	<	call saveNeighborList(nlocal, q)
545	<
546	<	neighborListSize = size(list)
547	<	nlist = 0
548	<
549	<	do i = 1, nrow
550	<	point(i) = nlist + 1
551	<
552	<	inner: do j = 1, ncol
553	<
554	<	if (skipThisPair(i,j)) cycle inner
555	<
556	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
557	<
558	<	if (rijsq < rlistsq) then
539	>	call get_interatomic_vector(q_group_Row(:,i), &
540	>	q_group_Col(:,j), d_grp, rgrpsq)
541	>	#else
542	>	call get_interatomic_vector(q_group(:,i), &
543	>	q_group(:,j), d_grp, rgrpsq)
544	>	#endif
545	>
546	>	if (rgrpsq < rlistsq) then
547	>	if (update_nlist) then
548	>	nlist = nlist + 1
549	>
550	>	if (nlist > neighborListSize) then
551	>	#ifdef IS_MPI
552	>	call expandNeighborList(nGroupsInRow, listerror)
553	>	#else
554	>	call expandNeighborList(nGroups, listerror)
555	>	#endif
556	>	if (listerror /= 0) then
557	>	error = -1
558	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
559	>	return
560	>	end if
561	>	neighborListSize = size(list)
562	>	endif
563	>
564	>	list(nlist) = j
565	>	endif
566
567	<	nlist = nlist + 1
568	<
569	<	if (nlist > neighborListSize) then
454	<	call expandNeighborList(nlocal, listerror)
455	<	if (listerror /= 0) then
456	<	error = -1
457	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
458	<	return
459	<	end if
460	<	neighborListSize = size(list)
567	>	if (loop .eq. PAIR_LOOP) then
568	>	vij = 0.0d0
569	>	fij(1:3) = 0.0d0
570		endif
571
572	<	list(nlist) = j
573	<
465	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
466	<	u_l, A, f, t, pot_local)
572	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
573	>	in_switching_region)
574
575	<	endif
576	<	enddo inner
577	<	enddo
575	>	n_in_j = groupStartCol(j+1) - groupStartCol(j)
576	>
577	>	do ia = groupStartRow(i), groupStartRow(i+1)-1
578	>
579	>	atom1 = groupListRow(ia)
580	>
581	>	inner: do jb = groupStartCol(j), groupStartCol(j+1)-1
582	>
583	>	atom2 = groupListCol(jb)
584	>
585	>	if (skipThisPair(atom1, atom2)) cycle inner
586
587	<	point(nrow + 1) = nlist + 1
588	<
589	<	else  !! (of update_check)
587	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
588	>	d_atm(1:3) = d_grp(1:3)
589	>	ratmsq = rgrpsq
590	>	else
591	>	#ifdef IS_MPI
592	>	call get_interatomic_vector(q_Row(:,atom1), &
593	>	q_Col(:,atom2), d_atm, ratmsq)
594	>	#else
595	>	call get_interatomic_vector(q(:,atom1), &
596	>	q(:,atom2), d_atm, ratmsq)
597	>	#endif
598	>	endif
599
600	<	! use the list to find the neighbors
601	<	do i = 1, nrow
602	<	JBEG = POINT(i)
603	<	JEND = POINT(i+1) - 1
604	<	! check thiat molecule i has neighbors
481	<	if (jbeg .le. jend) then
482	<
483	<	do jnab = jbeg, jend
484	<	j = list(jnab)
485	<
486	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
487	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
488	<	u_l, A, f, t, pot_local)
489	<
490	<	enddo
491	<	endif
492	<	enddo
493	<	endif
494	<
600	>	if (loop .eq. PREPAIR_LOOP) then
601	>	#ifdef IS_MPI
602	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
603	>	rgrpsq, d_grp, do_pot, do_stress, &
604	>	u_l, A, f, t, pot_local)
605		#else
606	<
607	<	if (update_nlist) then
608	<
609	<	! save current configuration, contruct neighbor list,
610	<	! and calculate forces
611	<	call saveNeighborList(natoms, q)
612	<
613	<	neighborListSize = size(list)
614	<
615	<	nlist = 0
616	<
617	<	do i = 1, natoms-1
618	<	point(i) = nlist + 1
619	<
510	<	inner: do j = i+1, natoms
511	<
512	<	if (skipThisPair(i,j))  cycle inner
513	<
514	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
515	<
606	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
607	>	rgrpsq, d_grp, do_pot, do_stress, &
608	>	u_l, A, f, t, pot)
609	>	#endif
610	>	else
611	>	#ifdef IS_MPI
612	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
613	>	do_pot, &
614	>	u_l, A, f, t, pot_local, vpair, fpair)
615	>	#else
616	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
617	>	do_pot,  &
618	>	u_l, A, f, t, pot, vpair, fpair)
619	>	#endif
620
621	<	if (rijsq < rlistsq) then
621	>	vij = vij + vpair
622	>	fij(1:3) = fij(1:3) + fpair(1:3)
623	>	endif
624	>	enddo inner
625	>	enddo
626
627	<	nlist = nlist + 1
628	<
629	<	if (nlist > neighborListSize) then
630	<	call expandNeighborList(natoms, listerror)
631	<	if (listerror /= 0) then
632	<	error = -1
633	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
634	<	return
635	<	end if
636	<	neighborListSize = size(list)
627	>	if (loop .eq. PAIR_LOOP) then
628	>	if (in_switching_region) then
629	>	swderiv = vij*dswdr/rgrp
630	>	fij(1) = fij(1) + swderiv*d_grp(1)
631	>	fij(2) = fij(2) + swderiv*d_grp(2)
632	>	fij(3) = fij(3) + swderiv*d_grp(3)
633	>
634	>	do ia=groupStartRow(i), groupStartRow(i+1)-1
635	>	atom1=groupListRow(ia)
636	>	mf = mfactRow(atom1)
637	>	#ifdef IS_MPI
638	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
639	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
640	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
641	>	#else
642	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
643	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
644	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
645	>	#endif
646	>	enddo
647	>
648	>	do jb=groupStartCol(j), groupStartCol(j+1)-1
649	>	atom2=groupListCol(jb)
650	>	mf = mfactCol(atom2)
651	>	#ifdef IS_MPI
652	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
653	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
654	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
655	>	#else
656	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
657	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
658	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
659	>	#endif
660	>	enddo
661	>	endif
662	>
663	>	if (do_stress) call add_stress_tensor(d_grp, fij)
664		endif
665	<
666	<	list(nlist) = j
667	<
533	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
534	<	u_l, A, f, t, pot)
535	<
536	<	endif
537	<	enddo inner
538	<	enddo
665	>	end if
666	>	enddo
667	>	enddo outer
668
669	<	point(natoms) = nlist + 1
670	<
671	<	else !! (update)
672	<
673	<	! use the list to find the neighbors
674	<	do i = 1, natoms-1
675	<	JBEG = POINT(i)
676	<	JEND = POINT(i+1) - 1
677	<	! check thiat molecule i has neighbors
678	<	if (jbeg .le. jend) then
679	<
551	<	do jnab = jbeg, jend
552	<	j = list(jnab)
553	<
554	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
555	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
556	<	u_l, A, f, t, pot)
557	<
558	<	enddo
669	>	if (update_nlist) then
670	>	#ifdef IS_MPI
671	>	point(nGroupsInRow + 1) = nlist + 1
672	>	#else
673	>	point(nGroups) = nlist + 1
674	>	#endif
675	>	if (loop .eq. PREPAIR_LOOP) then
676	>	! we just did the neighbor list update on the first
677	>	! pass, so we don't need to do it
678	>	! again on the second pass
679	>	update_nlist = .false.
680		endif
681	<	enddo
682	<	endif
681	>	endif
682	>
683	>	if (loop .eq. PREPAIR_LOOP) then
684	>	call do_preforce(nlocal, pot)
685	>	endif
686	>
687	>	enddo
688
689	<	#endif
689	>	!! Do timing
690	>	#ifdef PROFILE
691	>	call cpu_time(forceTimeFinal)
692	>	forceTime = forceTime + forceTimeFinal - forceTimeInitial
693	>	#endif
694
565	–	! phew, done with main loop.
566	–
695		#ifdef IS_MPI
696		!!distribute forces
697	<
697	>
698		f_temp = 0.0_dp
699	<	call scatter(f_Row,f_temp,plan_row3d)
699	>	call scatter(f_Row,f_temp,plan_atom_row_3d)
700		do i = 1,nlocal
701		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
702		end do
703	<
703	>
704		f_temp = 0.0_dp
705	<	call scatter(f_Col,f_temp,plan_col3d)
705	>	call scatter(f_Col,f_temp,plan_atom_col_3d)
706		do i = 1,nlocal
707		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
708		end do
709
710	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
710	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
711		t_temp = 0.0_dp
712	<	call scatter(t_Row,t_temp,plan_row3d)
712	>	call scatter(t_Row,t_temp,plan_atom_row_3d)
713		do i = 1,nlocal
714		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
715		end do
716		t_temp = 0.0_dp
717	<	call scatter(t_Col,t_temp,plan_col3d)
717	>	call scatter(t_Col,t_temp,plan_atom_col_3d)
718
719		do i = 1,nlocal
720		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
#	Line 595 | Line 723 | contains
723
724		if (do_pot) then
725		! scatter/gather pot_row into the members of my column
726	<	call scatter(pot_Row, pot_Temp, plan_row)
727	<
726	>	call scatter(pot_Row, pot_Temp, plan_atom_row)
727	>
728		! scatter/gather pot_local into all other procs
729		! add resultant to get total pot
730		do i = 1, nlocal
#	Line 604 | Line 732 | contains
732		enddo
733
734		pot_Temp = 0.0_DP
735	<
736	<	call scatter(pot_Col, pot_Temp, plan_col)
735	>
736	>	call scatter(pot_Col, pot_Temp, plan_atom_col)
737		do i = 1, nlocal
738		pot_local = pot_local + pot_Temp(i)
739		enddo
740	<
741	<	endif
740	>
741	>	endif
742		#endif
743	<
744	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
743	>
744	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
745
746	<	if (FF_uses_RF .and. SimUsesRF()) then
746	>	if (FF_uses_RF .and. SIM_uses_RF) then
747
748		#ifdef IS_MPI
749	<	call scatter(rf_Row,rf,plan_row3d)
750	<	call scatter(rf_Col,rf_Temp,plan_col3d)
749	>	call scatter(rf_Row,rf,plan_atom_row_3d)
750	>	call scatter(rf_Col,rf_Temp,plan_atom_col_3d)
751		do i = 1,nlocal
752		rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
753		end do
754		#endif
755
756	<	do i = 1, getNlocal()
757	<
756	>	do i = 1, nLocal
757	>
758		rfpot = 0.0_DP
759		#ifdef IS_MPI
760		me_i = atid_row(i)
761		#else
762		me_i = atid(i)
763		#endif
764	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
765	<	if ( is_DP_i ) then
766	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
764	>
765	>	if (PropertyMap(me_i)%is_DP) then
766	>
767	>	mu_i = PropertyMap(me_i)%dipole_moment
768	>
769		!! The reaction field needs to include a self contribution
770		!! to the field:
771	<	call accumulate_self_rf(i, mu_i, u_l)
771	>	call accumulate_self_rf(i, mu_i, u_l)
772		!! Get the reaction field contribution to the
773		!! potential and torques:
774		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 652 | Line 782 | contains
782		enddo
783		endif
784		endif
785	<
786	<
785	>
786	>
787		#ifdef IS_MPI
788	<
788	>
789		if (do_pot) then
790		pot = pot + pot_local
791		!! we assume the c code will do the allreduce to get the total potential
792		!! we could do it right here if we needed to...
793		endif
794	<
794	>
795		if (do_stress) then
796	<	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
796	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
797		mpi_comm_world,mpi_err)
798		call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
799		mpi_comm_world,mpi_err)
800		endif
801	<
801	>
802		#else
803	<
803	>
804		if (do_stress) then
805		tau = tau_Temp
806		virial = virial_Temp
807		endif
678	–
679	–	#endif
808
809	+	#endif
810	+
811		end subroutine do_force_loop
812	+
813	+	subroutine do_pair(i, j, rijsq, d, sw, do_pot, &
814	+	u_l, A, f, t, pot, vpair, fpair)
815
816	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
816	>	real( kind = dp ) :: pot, vpair, sw
817	>	real( kind = dp ), dimension(3) :: fpair
818	>	real( kind = dp ), dimension(nLocal)   :: mfact
819	>	real( kind = dp ), dimension(3,nLocal) :: u_l
820	>	real( kind = dp ), dimension(9,nLocal) :: A
821	>	real( kind = dp ), dimension(3,nLocal) :: f
822	>	real( kind = dp ), dimension(3,nLocal) :: t
823
824	<	real( kind = dp ) :: pot
686	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
687	<	real (kind=dp), dimension(9,getNlocal()) :: A
688	<	real (kind=dp), dimension(3,getNlocal()) :: f
689	<	real (kind=dp), dimension(3,getNlocal()) :: t
690	<
691	<	logical, intent(inout) :: do_pot, do_stress
824	>	logical, intent(inout) :: do_pot
825		integer, intent(in) :: i, j
826	<	real ( kind = dp ), intent(inout)    :: rijsq
826	>	real ( kind = dp ), intent(inout) :: rijsq
827		real ( kind = dp )                :: r
828		real ( kind = dp ), intent(inout) :: d(3)
696	–	logical :: is_LJ_i, is_LJ_j
697	–	logical :: is_DP_i, is_DP_j
698	–	logical :: is_GB_i, is_GB_j
699	–	logical :: is_EAM_i,is_EAM_j
700	–	logical :: is_Sticky_i, is_Sticky_j
829		integer :: me_i, me_j
830
831		r = sqrt(rijsq)
832	+	vpair = 0.0d0
833	+	fpair(1:3) = 0.0d0
834
835		#ifdef IS_MPI
706	–	if (tagRow(i) .eq. tagColumn(j)) then
707	–	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
708	–	endif
709	–
836		me_i = atid_row(i)
837		me_j = atid_col(j)
712	–
838		#else
714	–
839		me_i = atid(i)
840		me_j = atid(j)
717	–
841		#endif
842	<
843	<	if (FF_uses_LJ .and. SimUsesLJ()) then
844	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
845	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
846	<
847	<	if ( is_LJ_i .and. is_LJ_j ) &
848	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
842	>
843	>	if (FF_uses_LJ .and. SIM_uses_LJ) then
844	>
845	>	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
846	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
847	>	endif
848	>
849		endif
850	<
851	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
729	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
730	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
850	>
851	>	if (FF_uses_charges .and. SIM_uses_charges) then
852
853	<	if ( is_DP_i .and. is_DP_j ) then
854	<
734	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
735	<	do_pot, do_stress)
736	<	if (FF_uses_RF .and. SimUsesRF()) then
737	<	call accumulate_rf(i, j, r, u_l)
738	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
739	<	endif
740	<
853	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
854	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
855		endif
856	+
857		endif
858	+
859	+	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
860	+
861	+	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
862	+	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
863	+	do_pot)
864	+	if (FF_uses_RF .and. SIM_uses_RF) then
865	+	call accumulate_rf(i, j, r, u_l, sw)
866	+	call rf_correct_forces(i, j, d, r, u_l, sw, f, fpair)
867	+	endif
868	+	endif
869
870	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
870	>	endif
871
872	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
747	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
872	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
873
874	<	if ( is_Sticky_i .and. is_Sticky_j ) then
875	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
876	<	do_pot, do_stress)
874	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
875	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, A, f, t, &
876	>	do_pot)
877		endif
878	+
879		endif
880
881
882	<	if (FF_uses_GB .and. SimUsesGB()) then
882	>	if (FF_uses_GB .and. SIM_uses_GB) then
883	>
884	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
885	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
886	>	do_pot)
887	>	endif
888
889	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
759	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
889	>	endif
890
891	<	if ( is_GB_i .and. is_GB_j ) then
892	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
893	<	do_pot, do_stress)
891	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
892	>
893	>	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
894	>	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, &
895	>	do_pot)
896		endif
897	+
898		endif
899	<
767	<
768	<
769	<	if (FF_uses_EAM .and. SimUsesEAM()) then
770	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
771	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
772	<
773	<	if ( is_EAM_i .and. is_EAM_j ) &
774	<	call do_eam_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
775	<	endif
776	<
777	<
778	<
779	<
899	>
900		end subroutine do_pair
901
902	<
902	>	subroutine do_prepair(i, j, rijsq, d, sw, rcijsq, dc, &
903	>	do_pot, do_stress, u_l, A, f, t, pot)
904
905	<	subroutine do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
906	<	real( kind = dp ) :: pot
907	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
908	<	real (kind=dp), dimension(9,getNlocal()) :: A
909	<	real (kind=dp), dimension(3,getNlocal()) :: f
789	<	real (kind=dp), dimension(3,getNlocal()) :: t
905	>	real( kind = dp ) :: pot, sw
906	>	real( kind = dp ), dimension(3,nLocal) :: u_l
907	>	real (kind=dp), dimension(9,nLocal) :: A
908	>	real (kind=dp), dimension(3,nLocal) :: f
909	>	real (kind=dp), dimension(3,nLocal) :: t
910
911		logical, intent(inout) :: do_pot, do_stress
912		integer, intent(in) :: i, j
913	<	real ( kind = dp ), intent(inout)    :: rijsq
914	<	real ( kind = dp )                :: r
915	<	real ( kind = dp ), intent(inout) :: d(3)
913	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
914	>	real ( kind = dp )                :: r, rc
915	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
916
917		logical :: is_EAM_i, is_EAM_j
918
919		integer :: me_i, me_j
920
801	–	r = sqrt(rijsq)
802	–
921
922	<	#ifdef IS_MPI
923	<	if (tagRow(i) .eq. tagColumn(j)) then
924	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
925	<	endif
922	>	r = sqrt(rijsq)
923	>	if (SIM_uses_molecular_cutoffs) then
924	>	rc = sqrt(rcijsq)
925	>	else
926	>	rc = r
927	>	endif
928
929	+
930	+	#ifdef IS_MPI
931		me_i = atid_row(i)
932	<	me_j = atid_col(j)
933	<
812	<	#else
813	<
932	>	me_j = atid_col(j)
933	>	#else
934		me_i = atid(i)
935	<	me_j = atid(j)
816	<
935	>	me_j = atid(j)
936		#endif
937	<
938	<	if (FF_uses_EAM .and. SimUsesEAM()) then
820	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
821	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
937	>
938	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
939
940	<	if ( is_EAM_i .and. is_EAM_j ) &
940	>	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
941		call calc_EAM_prepair_rho(i, j, d, r, rijsq )
942	+
943		endif
944	<
944	>
945		end subroutine do_prepair
828	–
829	–
830	–
831	–
832	–	subroutine do_preforce(nlocal,pot)
833	–	integer :: nlocal
834	–	real( kind = dp ) :: pot
835	–
836	–	if (FF_uses_EAM .and. SimUsesEAM()) then
837	–	call calc_EAM_preforce_Frho(nlocal,pot)
838	–	endif
839	–
840	–
841	–	end subroutine do_preforce
842	–
843	–
844	–	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
845	–
846	–	real (kind = dp), dimension(3) :: q_i
847	–	real (kind = dp), dimension(3) :: q_j
848	–	real ( kind = dp ), intent(out) :: r_sq
849	–	real( kind = dp ) :: d(3), scaled(3)
850	–	integer i
851	–
852	–	d(1:3) = q_j(1:3) - q_i(1:3)
853	–
854	–	! Wrap back into periodic box if necessary
855	–	if ( SimUsesPBC() ) then
856	–
857	–	if( .not.boxIsOrthorhombic ) then
858	–	! calc the scaled coordinates.
859	–
860	–	scaled = matmul(HmatInv, d)
861	–
862	–	! wrap the scaled coordinates
863	–
864	–	scaled = scaled  - anint(scaled)
865	–
866	–
867	–	! calc the wrapped real coordinates from the wrapped scaled
868	–	! coordinates
869	–
870	–	d = matmul(Hmat,scaled)
871	–
872	–	else
873	–	! calc the scaled coordinates.
874	–
875	–	do i = 1, 3
876	–	scaled(i) = d(i) * HmatInv(i,i)
877	–
878	–	! wrap the scaled coordinates
879	–
880	–	scaled(i) = scaled(i) - anint(scaled(i))
881	–
882	–	! calc the wrapped real coordinates from the wrapped scaled
883	–	! coordinates
884	–
885	–	d(i) = scaled(i)*Hmat(i,i)
886	–	enddo
887	–	endif
888	–
889	–	endif
890	–
891	–	r_sq = dot_product(d,d)
892	–
893	–	end subroutine get_interatomic_vector
894	–
895	–	subroutine check_initialization(error)
896	–	integer, intent(out) :: error
897	–
898	–	error = 0
899	–	! Make sure we are properly initialized.
900	–	if (.not. do_forces_initialized) then
901	–	write(*,*) "Forces not initialized"
902	–	error = -1
903	–	return
904	–	endif
905	–
906	–	#ifdef IS_MPI
907	–	if (.not. isMPISimSet()) then
908	–	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
909	–	error = -1
910	–	return
911	–	endif
912	–	#endif
913	–
914	–	return
915	–	end subroutine check_initialization
916	–
917	–
918	–	subroutine zero_work_arrays()
919	–
920	–	#ifdef IS_MPI
921	–
922	–	q_Row = 0.0_dp
923	–	q_Col = 0.0_dp
924	–
925	–	u_l_Row = 0.0_dp
926	–	u_l_Col = 0.0_dp
927	–
928	–	A_Row = 0.0_dp
929	–	A_Col = 0.0_dp
930	–
931	–	f_Row = 0.0_dp
932	–	f_Col = 0.0_dp
933	–	f_Temp = 0.0_dp
934	–
935	–	t_Row = 0.0_dp
936	–	t_Col = 0.0_dp
937	–	t_Temp = 0.0_dp
946
947	<	pot_Row = 0.0_dp
948	<	pot_Col = 0.0_dp
949	<	pot_Temp = 0.0_dp
950	<
951	<	rf_Row = 0.0_dp
952	<	rf_Col = 0.0_dp
953	<	rf_Temp = 0.0_dp
947	>
948	>	subroutine do_preforce(nlocal,pot)
949	>	integer :: nlocal
950	>	real( kind = dp ) :: pot
951	>
952	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
953	>	call calc_EAM_preforce_Frho(nlocal,pot)
954	>	endif
955	>
956	>
957	>	end subroutine do_preforce
958	>
959	>
960	>	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
961	>
962	>	real (kind = dp), dimension(3) :: q_i
963	>	real (kind = dp), dimension(3) :: q_j
964	>	real ( kind = dp ), intent(out) :: r_sq
965	>	real( kind = dp ) :: d(3), scaled(3)
966	>	integer i
967	>
968	>	d(1:3) = q_j(1:3) - q_i(1:3)
969	>
970	>	! Wrap back into periodic box if necessary
971	>	if ( SIM_uses_PBC ) then
972	>
973	>	if( .not.boxIsOrthorhombic ) then
974	>	! calc the scaled coordinates.
975	>
976	>	scaled = matmul(HmatInv, d)
977	>
978	>	! wrap the scaled coordinates
979	>
980	>	scaled = scaled  - anint(scaled)
981	>
982	>
983	>	! calc the wrapped real coordinates from the wrapped scaled
984	>	! coordinates
985	>
986	>	d = matmul(Hmat,scaled)
987	>
988	>	else
989	>	! calc the scaled coordinates.
990	>
991	>	do i = 1, 3
992	>	scaled(i) = d(i) * HmatInv(i,i)
993	>
994	>	! wrap the scaled coordinates
995	>
996	>	scaled(i) = scaled(i) - anint(scaled(i))
997	>
998	>	! calc the wrapped real coordinates from the wrapped scaled
999	>	! coordinates
1000	>
1001	>	d(i) = scaled(i)*Hmat(i,i)
1002	>	enddo
1003	>	endif
1004	>
1005	>	endif
1006	>
1007	>	r_sq = dot_product(d,d)
1008	>
1009	>	end subroutine get_interatomic_vector
1010	>
1011	>	subroutine zero_work_arrays()
1012	>
1013	>	#ifdef IS_MPI
1014	>
1015	>	q_Row = 0.0_dp
1016	>	q_Col = 0.0_dp
1017
1018	+	q_group_Row = 0.0_dp
1019	+	q_group_Col = 0.0_dp
1020	+
1021	+	u_l_Row = 0.0_dp
1022	+	u_l_Col = 0.0_dp
1023	+
1024	+	A_Row = 0.0_dp
1025	+	A_Col = 0.0_dp
1026	+
1027	+	f_Row = 0.0_dp
1028	+	f_Col = 0.0_dp
1029	+	f_Temp = 0.0_dp
1030	+
1031	+	t_Row = 0.0_dp
1032	+	t_Col = 0.0_dp
1033	+	t_Temp = 0.0_dp
1034	+
1035	+	pot_Row = 0.0_dp
1036	+	pot_Col = 0.0_dp
1037	+	pot_Temp = 0.0_dp
1038	+
1039	+	rf_Row = 0.0_dp
1040	+	rf_Col = 0.0_dp
1041	+	rf_Temp = 0.0_dp
1042	+
1043		#endif
948	–
1044
1045	<	if (FF_uses_EAM .and. SimUsesEAM()) then
1046	<	call clean_EAM()
1047	<	endif
1048	<
1049	<
1050	<
1051	<
1052	<
1053	<	rf = 0.0_dp
1054	<	tau_Temp = 0.0_dp
1055	<	virial_Temp = 0.0_dp
1056	<	end subroutine zero_work_arrays
1057	<
1058	<	function skipThisPair(atom1, atom2) result(skip_it)
1059	<	integer, intent(in) :: atom1
1060	<	integer, intent(in), optional :: atom2
1061	<	logical :: skip_it
1062	<	integer :: unique_id_1, unique_id_2
1063	<	integer :: me_i,me_j
1064	<	integer :: i
1065	<
1066	<	skip_it = .false.
1067	<
1068	<	!! there are a number of reasons to skip a pair or a particle
1069	<	!! mostly we do this to exclude atoms who are involved in short
975	<	!! range interactions (bonds, bends, torsions), but we also need
976	<	!! to exclude some overcounted interactions that result from
977	<	!! the parallel decomposition
978	<
1045	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1046	>	call clean_EAM()
1047	>	endif
1048	>
1049	>	rf = 0.0_dp
1050	>	tau_Temp = 0.0_dp
1051	>	virial_Temp = 0.0_dp
1052	>	end subroutine zero_work_arrays
1053	>
1054	>	function skipThisPair(atom1, atom2) result(skip_it)
1055	>	integer, intent(in) :: atom1
1056	>	integer, intent(in), optional :: atom2
1057	>	logical :: skip_it
1058	>	integer :: unique_id_1, unique_id_2
1059	>	integer :: me_i,me_j
1060	>	integer :: i
1061	>
1062	>	skip_it = .false.
1063	>
1064	>	!! there are a number of reasons to skip a pair or a particle
1065	>	!! mostly we do this to exclude atoms who are involved in short
1066	>	!! range interactions (bonds, bends, torsions), but we also need
1067	>	!! to exclude some overcounted interactions that result from
1068	>	!! the parallel decomposition
1069	>
1070		#ifdef IS_MPI
1071	<	!! in MPI, we have to look up the unique IDs for each atom
1072	<	unique_id_1 = tagRow(atom1)
1071	>	!! in MPI, we have to look up the unique IDs for each atom
1072	>	unique_id_1 = AtomRowToGlobal(atom1)
1073		#else
1074	<	!! in the normal loop, the atom numbers are unique
1075	<	unique_id_1 = atom1
1074	>	!! in the normal loop, the atom numbers are unique
1075	>	unique_id_1 = atom1
1076		#endif
1077	<
1078	<	!! We were called with only one atom, so just check the global exclude
1079	<	!! list for this atom
1080	<	if (.not. present(atom2)) then
1081	<	do i = 1, nExcludes_global
1082	<	if (excludesGlobal(i) == unique_id_1) then
1083	<	skip_it = .true.
1084	<	return
1085	<	end if
1086	<	end do
1087	<	return
1088	<	end if
1089	<
1077	>
1078	>	!! We were called with only one atom, so just check the global exclude
1079	>	!! list for this atom
1080	>	if (.not. present(atom2)) then
1081	>	do i = 1, nExcludes_global
1082	>	if (excludesGlobal(i) == unique_id_1) then
1083	>	skip_it = .true.
1084	>	return
1085	>	end if
1086	>	end do
1087	>	return
1088	>	end if
1089	>
1090		#ifdef IS_MPI
1091	<	unique_id_2 = tagColumn(atom2)
1091	>	unique_id_2 = AtomColToGlobal(atom2)
1092		#else
1093	<	unique_id_2 = atom2
1093	>	unique_id_2 = atom2
1094		#endif
1095	<
1095	>
1096		#ifdef IS_MPI
1097	<	!! this situation should only arise in MPI simulations
1098	<	if (unique_id_1 == unique_id_2) then
1099	<	skip_it = .true.
1100	<	return
1101	<	end if
1102	<
1103	<	!! this prevents us from doing the pair on multiple processors
1104	<	if (unique_id_1 < unique_id_2) then
1105	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1106	<	skip_it = .true.
1107	<	return
1108	<	endif
1109	<	else
1110	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1111	<	skip_it = .true.
1112	<	return
1113	<	endif
1114	<	endif
1097	>	!! this situation should only arise in MPI simulations
1098	>	if (unique_id_1 == unique_id_2) then
1099	>	skip_it = .true.
1100	>	return
1101	>	end if
1102	>
1103	>	!! this prevents us from doing the pair on multiple processors
1104	>	if (unique_id_1 < unique_id_2) then
1105	>	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1106	>	skip_it = .true.
1107	>	return
1108	>	endif
1109	>	else
1110	>	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1111	>	skip_it = .true.
1112	>	return
1113	>	endif
1114	>	endif
1115		#endif
1116	+
1117	+	!! the rest of these situations can happen in all simulations:
1118	+	do i = 1, nExcludes_global
1119	+	if ((excludesGlobal(i) == unique_id_1) .or. &
1120	+	(excludesGlobal(i) == unique_id_2)) then
1121	+	skip_it = .true.
1122	+	return
1123	+	endif
1124	+	enddo
1125	+
1126	+	do i = 1, nSkipsForAtom(atom1)
1127	+	if (skipsForAtom(atom1, i) .eq. unique_id_2) then
1128	+	skip_it = .true.
1129	+	return
1130	+	endif
1131	+	end do
1132	+
1133	+	return
1134	+	end function skipThisPair
1135
1136	<	!! the rest of these situations can happen in all simulations:
1137	<	do i = 1, nExcludes_global
1138	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1139	<	(excludesGlobal(i) == unique_id_2)) then
1140	<	skip_it = .true.
1141	<	return
1142	<	endif
1143	<	enddo
1136	>	function FF_UsesDirectionalAtoms() result(doesit)
1137	>	logical :: doesit
1138	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1139	>	FF_uses_GB .or. FF_uses_RF
1140	>	end function FF_UsesDirectionalAtoms
1141	>
1142	>	function FF_RequiresPrepairCalc() result(doesit)
1143	>	logical :: doesit
1144	>	doesit = FF_uses_EAM
1145	>	end function FF_RequiresPrepairCalc
1146	>
1147	>	function FF_RequiresPostpairCalc() result(doesit)
1148	>	logical :: doesit
1149	>	doesit = FF_uses_RF
1150	>	end function FF_RequiresPostpairCalc
1151	>
1152	>	#ifdef PROFILE
1153	>	function getforcetime() result(totalforcetime)
1154	>	real(kind=dp) :: totalforcetime
1155	>	totalforcetime = forcetime
1156	>	end function getforcetime
1157	>	#endif
1158	>
1159	>	!! This cleans componets of force arrays belonging only to fortran
1160
1161	<	do i = 1, nExcludes_local
1162	<	if (excludesLocal(1,i) == unique_id_1) then
1163	<	if (excludesLocal(2,i) == unique_id_2) then
1164	<	skip_it = .true.
1165	<	return
1166	<	endif
1167	<	else
1168	<	if (excludesLocal(1,i) == unique_id_2) then
1169	<	if (excludesLocal(2,i) == unique_id_1) then
1170	<	skip_it = .true.
1171	<	return
1172	<	endif
1173	<	endif
1174	<	endif
1175	<	end do
1176	<
1177	<	return
1178	<	end function skipThisPair
1179	<
1180	<	function FF_UsesDirectionalAtoms() result(doesit)
1181	<	logical :: doesit
1182	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1183	<	FF_uses_GB .or. FF_uses_RF
1058	<	end function FF_UsesDirectionalAtoms
1059	<
1060	<	function FF_RequiresPrepairCalc() result(doesit)
1061	<	logical :: doesit
1062	<	doesit = FF_uses_EAM
1063	<	end function FF_RequiresPrepairCalc
1064	<
1065	<	function FF_RequiresPostpairCalc() result(doesit)
1066	<	logical :: doesit
1067	<	doesit = FF_uses_RF
1068	<	end function FF_RequiresPostpairCalc
1069	<
1070	<	!! This cleans componets of force arrays belonging only to fortran
1071	<
1161	>	subroutine add_stress_tensor(dpair, fpair)
1162	>
1163	>	real( kind = dp ), dimension(3), intent(in) :: dpair, fpair
1164	>
1165	>	! because the d vector is the rj - ri vector, and
1166	>	! because fx, fy, fz are the force on atom i, we need a
1167	>	! negative sign here:
1168	>
1169	>	tau_Temp(1) = tau_Temp(1) - dpair(1) * fpair(1)
1170	>	tau_Temp(2) = tau_Temp(2) - dpair(1) * fpair(2)
1171	>	tau_Temp(3) = tau_Temp(3) - dpair(1) * fpair(3)
1172	>	tau_Temp(4) = tau_Temp(4) - dpair(2) * fpair(1)
1173	>	tau_Temp(5) = tau_Temp(5) - dpair(2) * fpair(2)
1174	>	tau_Temp(6) = tau_Temp(6) - dpair(2) * fpair(3)
1175	>	tau_Temp(7) = tau_Temp(7) - dpair(3) * fpair(1)
1176	>	tau_Temp(8) = tau_Temp(8) - dpair(3) * fpair(2)
1177	>	tau_Temp(9) = tau_Temp(9) - dpair(3) * fpair(3)
1178	>
1179	>	virial_Temp = virial_Temp + &
1180	>	(tau_Temp(1) + tau_Temp(5) + tau_Temp(9))
1181	>
1182	>	end subroutine add_stress_tensor
1183	>
1184		end module do_Forces
1185	+

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