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Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 480 by chuckv, Tue Apr 8 17:16:22 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 1.12 2003-04-08 17:16:22 chuckv Exp $, $Date: 2003-04-08 17:16:22 $, $Name: not supported by cvs2svn $, $Revision: 1.12 $
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
23	+	use eam
24	+	use status
25		#ifdef IS_MPI
26		use mpiSimulation
27		#endif
#	Line 26 | 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.
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	+
67		public :: init_FF
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 )
94	+
95	+	real(kind=dp) :: this_rlist
96	+
97	+	rlist = this_rlist
98	+	rlistsq = rlist * rlist
99	+
100	+	haveRlist = .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 64 | 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 84 | 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
90	–	rrf = getRrf()
91	–	rt = getRt()
92	–	call initialize_dipole(rrf, rt)
290		if (FF_uses_RF) then
291		dielect = getDielect()
292	<	call initialize_rf(rrf, rt, dielect)
292	>	call initialize_rf(dielect)
293		endif
294		else
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
301	>	endif
302
303		if (FF_uses_LJ) then
304
107	–	call getRcut(rcut)
108	–
305		select case (LJMIXPOLICY)
306		case (LB_MIXING_RULE)
307	<	call init_lj_FF(LB_MIXING_RULE, rcut, my_status)
307	>	call init_lj_FF(LB_MIXING_RULE, my_status)
308		case (EXPLICIT_MIXING_RULE)
309	<	call init_lj_FF(EXPLICIT_MIXING_RULE, rcut, my_status)
309	>	call init_lj_FF(EXPLICIT_MIXING_RULE, my_status)
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	<
332	>
333	>
334	>	if (FF_uses_EAM) then
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	>
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
365
366	<	do_forces_initialized = .true.
367	<
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
183	–	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, rlistsq, rcutsq, rlist, rcut
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
422	+
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
205	–	nlocal = getNlocal()
432		natoms = nlocal
433		#endif
208	–
209	–	call getRcut(rcut,rc2=rcutsq)
210	–	call getRlist(rlist,rlistsq)
434
435	<	call check_initialization(localError)
435	>	call doReadyCheck(localError)
436		if ( localError .ne. 0 ) then
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
222	–
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
465
466	<	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
467	<	!! See if we need to update neighbor lists
468	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
469	<	!! if_mpi_gather_stuff_for_prepair
470	<	!! do_prepair_loop_if_needed
471	<	!! if_mpi_scatter_stuff_from_prepair
472	<	!! if_mpi_gather_stuff_from_prepair_to_main_loop
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	<	!! See if we need to update neighbor lists
249	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
476	>	loopStart = PAIR_LOOP
477		endif
478	<
478	>
479	>	do loop = loopStart, loopEnd
480	>
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	<
486	<	if (update_nlist) then
485	>	call checkNeighborList(nGroupsInRow, q_group_row, listSkin, &
486	>	update_nlist)
487	>	#else
488	>	call checkNeighborList(nGroups, q_group, listSkin, &
489	>	update_nlist)
490	>	#endif
491	>	endif
492
493	<	!! save current configuration, construct neighbor list,
494	<	!! and calculate forces
495	<	call saveNeighborList(nlocal, 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	<	nlist = 0
506	<
507	<	do i = 1, nrow
508	<	point(i) = nlist + 1
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 (update_nlist) point(i) = nlist + 1
513
514	<	inner: do j = 1, ncol
515	<
516	<	if (skipThisPair(i,j)) cycle inner
517	<
518	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
519	<
520	<	if (rijsq <  rlistsq) then
521	<
522	<	nlist = nlist + 1
523	<
524	<	if (nlist > neighborListSize) then
525	<	call expandNeighborList(nlocal, listerror)
526	<	if (listerror /= 0) then
527	<	error = -1
528	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
529	<	return
530	<	end if
531	<	neighborListSize = size(list)
532	<	endif
533	<
534	<	list(nlist) = j
535	<
288	<	if (rijsq <  rcutsq) then
289	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
290	<	u_l, A, f, t, pot_local)
291	<	endif
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
293	–	enddo inner
294	–	enddo
537
538	<	point(nrow + 1) = nlist + 1
539	<
540	<	else  !! (of update_check)
299	<
300	<	! use the list to find the neighbors
301	<	do i = 1, nrow
302	<	JBEG = POINT(i)
303	<	JEND = POINT(i+1) - 1
304	<	! check thiat molecule i has neighbors
305	<	if (jbeg .le. jend) then
306	<
307	<	do jnab = jbeg, jend
308	<	j = list(jnab)
309	<
310	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
311	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
312	<	u_l, A, f, t, pot_local)
313	<
314	<	enddo
315	<	endif
316	<	enddo
317	<	endif
318	<
538	>	#ifdef IS_MPI
539	>	call get_interatomic_vector(q_group_Row(:,i), &
540	>	q_group_Col(:,j), d_grp, rgrpsq)
541		#else
542	<
543	<	if (update_nlist) then
544	<
323	<	! save current configuration, contruct neighbor list,
324	<	! and calculate forces
325	<	call saveNeighborList(natoms, q)
326	<
327	<	neighborListSize = size(list)
328	<
329	<	nlist = 0
330	<
331	<	do i = 1, natoms-1
332	<	point(i) = nlist + 1
333	<
334	<	inner: do j = i+1, natoms
335	<
336	<	if (skipThisPair(i,j))  cycle inner
337	<
338	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
339	<
542	>	call get_interatomic_vector(q_group(:,i), &
543	>	q_group(:,j), d_grp, rgrpsq)
544	>	#endif
545
546	<	if (rijsq <  rlistsq) then
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
346	<	call expandNeighborList(natoms, listerror)
347	<	if (listerror /= 0) then
348	<	error = -1
349	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
350	<	return
351	<	end if
352	<	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
572	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
573	>	in_switching_region)
574
575	<	if (rijsq <  rcutsq) then
576	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
577	<	u_l, A, f, t, pot)
578	<	endif
579	<	endif
580	<	enddo inner
581	<	enddo
582	<
583	<	point(natoms) = nlist + 1
584	<
585	<	else !! (update)
368	<
369	<	! use the list to find the neighbors
370	<	do i = 1, natoms-1
371	<	JBEG = POINT(i)
372	<	JEND = POINT(i+1) - 1
373	<	! check thiat molecule i has neighbors
374	<	if (jbeg .le. jend) then
375	<
376	<	do jnab = jbeg, jend
377	<	j = list(jnab)
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	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
588	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
589	<	u_l, A, f, t, pot)
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	<	enddo
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	>	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	>	vij = vij + vpair
622	>	fij(1:3) = fij(1:3) + fpair(1:3)
623	>	endif
624	>	enddo inner
625	>	enddo
626	>
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	>	end if
666	>	enddo
667	>	enddo outer
668	>
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
390	–	! phew, done with main loop.
391	–
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 420 | 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 429 | 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 477 | 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
503	–
504	–	#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
511	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
512	<	real (kind=dp), dimension(9,getNlocal()) :: A
513	<	real (kind=dp), dimension(3,getNlocal()) :: f
514	<	real (kind=dp), dimension(3,getNlocal()) :: t
515	<
516	<	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)
521	–	logical :: is_LJ_i, is_LJ_j
522	–	logical :: is_DP_i, is_DP_j
523	–	logical :: is_GB_i, is_GB_j
524	–	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
530	–
836		me_i = atid_row(i)
837		me_j = atid_col(j)
533	–
838		#else
535	–
839		me_i = atid(i)
840		me_j = atid(j)
538	–
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
550	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
551	<	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	<
555	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
556	<	do_pot, do_stress)
557	<	if (FF_uses_RF .and. SimUsesRF()) then
558	<	call accumulate_rf(i, j, r, u_l)
559	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
560	<	endif
561	<
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)
568	<	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)
580	<	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	<
899	>
900		end subroutine do_pair
901
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 get_interatomic_vector(q_i, q_j, d, r_sq)
906	<
907	<	real (kind = dp), dimension(3) :: q_i
908	<	real (kind = dp), dimension(3) :: q_j
909	<	real ( kind = dp ), intent(out) :: r_sq
910	<	real( kind = dp ) :: d(3)
911	<	real( kind = dp ) :: d_old(3)
912	<	d(1:3) = q_i(1:3) - q_j(1:3)
913	<	d_old = d
914	<	! Wrap back into periodic box if necessary
915	<	if ( SimUsesPBC() ) then
916	<
917	<	d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,d(1:3)) * &
918	<	int(abs(d(1:3)/box(1:3)) + 0.5_dp)
919	<
920	<	endif
607	<	r_sq = dot_product(d,d)
608	<
609	<	end subroutine get_interatomic_vector
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, 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	>
921
922	<	subroutine check_initialization(error)
923	<	integer, intent(out) :: error
924	<
925	<	error = 0
926	<	! Make sure we are properly initialized.
616	<	if (.not. do_forces_initialized) then
617	<	error = -1
618	<	return
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	<	if (.not. isMPISimSet()) then
932	<	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
933	<	error = -1
934	<	return
935	<	endif
627	<	#endif
628	<
629	<	return
630	<	end subroutine check_initialization
631	<
632	<
633	<	subroutine zero_work_arrays()
634	<
635	<	#ifdef IS_MPI
636	<
637	<	q_Row = 0.0_dp
638	<	q_Col = 0.0_dp
639	<
640	<	u_l_Row = 0.0_dp
641	<	u_l_Col = 0.0_dp
642	<
643	<	A_Row = 0.0_dp
644	<	A_Col = 0.0_dp
645	<
646	<	f_Row = 0.0_dp
647	<	f_Col = 0.0_dp
648	<	f_Temp = 0.0_dp
649	<
650	<	t_Row = 0.0_dp
651	<	t_Col = 0.0_dp
652	<	t_Temp = 0.0_dp
653	<
654	<	pot_Row = 0.0_dp
655	<	pot_Col = 0.0_dp
656	<	pot_Temp = 0.0_dp
657	<
658	<	rf_Row = 0.0_dp
659	<	rf_Col = 0.0_dp
660	<	rf_Temp = 0.0_dp
661	<
662	<	#endif
663	<
664	<	rf = 0.0_dp
665	<	tau_Temp = 0.0_dp
666	<	virial_Temp = 0.0_dp
667	<	end subroutine zero_work_arrays
668	<
669	<	function skipThisPair(atom1, atom2) result(skip_it)
670	<	integer, intent(in) :: atom1
671	<	integer, intent(in), optional :: atom2
672	<	logical :: skip_it
673	<	integer :: unique_id_1, unique_id_2
674	<	integer :: me_i,me_j
675	<	integer :: i
676	<
677	<	skip_it = .false.
678	<
679	<	!! there are a number of reasons to skip a pair or a particle
680	<	!! mostly we do this to exclude atoms who are involved in short
681	<	!! range interactions (bonds, bends, torsions), but we also need
682	<	!! to exclude some overcounted interactions that result from
683	<	!! the parallel decomposition
684	<
685	<	#ifdef IS_MPI
686	<	!! in MPI, we have to look up the unique IDs for each atom
687	<	unique_id_1 = tagRow(atom1)
688	<	#else
689	<	!! in the normal loop, the atom numbers are unique
690	<	unique_id_1 = atom1
691	<	#endif
692	<
693	<	!! We were called with only one atom, so just check the global exclude
694	<	!! list for this atom
695	<	if (.not. present(atom2)) then
696	<	do i = 1, nExcludes_global
697	<	if (excludesGlobal(i) == unique_id_1) then
698	<	skip_it = .true.
699	<	return
700	<	end if
701	<	end do
702	<	return
703	<	end if
704	<
705	<	#ifdef IS_MPI
706	<	unique_id_2 = tagColumn(atom2)
707	<	#else
708	<	unique_id_2 = atom2
930	>	#ifdef IS_MPI
931	>	me_i = atid_row(i)
932	>	me_j = atid_col(j)
933	>	#else
934	>	me_i = atid(i)
935	>	me_j = atid(j)
936		#endif
937	+
938	+	if (FF_uses_EAM .and. SIM_uses_EAM) then
939	+
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	+
945	+	end subroutine do_prepair
946	+
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
1044	+
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	<	!! this situation should only arise in MPI simulations
1072	<	if (unique_id_1 == unique_id_2) then
1073	<	skip_it = .true.
1074	<	return
1075	<	end if
717	<
718	<	!! this prevents us from doing the pair on multiple processors
719	<	if (unique_id_1 < unique_id_2) then
720	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
721	<	skip_it = .true.
722	<	return
723	<	endif
724	<	else
725	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
726	<	skip_it = .true.
727	<	return
728	<	endif
729	<	endif
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
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	+
1090	+	#ifdef IS_MPI
1091	+	unique_id_2 = AtomColToGlobal(atom2)
1092	+	#else
1093	+	unique_id_2 = atom2
1094	+	#endif
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
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
764	<	end function FF_UsesDirectionalAtoms
765	<
766	<	function FF_RequiresPrepairCalc() result(doesit)
767	<	logical :: doesit
768	<	doesit = FF_uses_EAM
769	<	end function FF_RequiresPrepairCalc
770	<
771	<	function FF_RequiresPostpairCalc() result(doesit)
772	<	logical :: doesit
773	<	doesit = FF_uses_RF
774	<	end function FF_RequiresPostpairCalc
775	<
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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