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Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 1197 by gezelter, Wed May 26 16:41:23 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.4 2003-03-24 21:55:34 gezelter Exp $, $Date: 2003-03-24 21:55:34 $, $Name: not supported by cvs2svn $, $Revision: 1.4 $
7	>	!! @version $Id: do_Forces.F90,v 1.62 2004-05-26 16:41:23 gezelter Exp $, $Date: 2004-05-26 16:41:23 $, $Name: not supported by cvs2svn $, $Revision: 1.62 $
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. haveNeighborList) then
356	+	!! Create neighbor lists
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	<
367	<	do_forces_initialized = .true.
146	<
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, nGroup) :: 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	<	#ifdef IS_MPI
394	>	logical :: in_switching_region
395	>	#ifdef IS_MPI
396		real( kind = DP ) :: pot_local
397		integer :: nrow
398		integer :: ncol
399	+	integer :: nprocs
400	+	integer :: nrow_group
401	+	integer :: ncol_group
402		#endif
175	–	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	<	nlocal = getNlocal()
426	>	pot_local = 0.0_dp
427		nrow   = getNrow(plan_row)
428		ncol   = getNcol(plan_col)
429	+	nrow_group   = getNrowGroup(plan_row)
430	+	ncol_group   = getNcolGroup(plan_col)
431		#else
196	–	nlocal = getNlocal()
432		natoms = nlocal
433		#endif
199	–
200	–	call getRcut(rcut,rc2=rcutsq)
201	–	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	<
445	>
446		! Gather all information needed by all force loops:
447
448		#ifdef IS_MPI
449	+
450	+	call gather(q, q_Row, plan_row3d)
451	+	call gather(q, q_Col, plan_col3d)
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_row_Group_3d)
454	>	call gather(q_group, q_group_Col, plan_col_Group_3d)
455
456	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
456	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
457		call gather(u_l,u_l_Row,plan_row3d)
458		call gather(u_l,u_l_Col,plan_col3d)
459
#	Line 227 | Line 463 | contains
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
239	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
476	>	loopStart = PAIR_LOOP
477		endif
478	<
479	<	#ifdef IS_MPI
480	<
481	<	if (update_nlist) then
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	>	call checkNeighborList(nGroup, q_group, listSkin, update_nlist)
485	>	endif
486	>
487	>	if (update_nlist) then
488	>	!! save current configuration and construct neighbor list
489	>	call saveNeighborList(nGroup, q_group)
490	>	neighborListSize = size(list)
491	>	nlist = 0
492	>	endif
493
494	<	!! save current configuration, construct neighbor list,
495	<	!! and calculate forces
496	<	call saveNeighborList(q)
497	<
498	<	neighborListSize = size(list)
499	<	nlist = 0
500	<
253	<	do i = 1, nrow
254	<	point(i) = nlist + 1
494	>	istart = 1
495	>	#ifdef IS_MPI
496	>	iend = nrow_group
497	>	#else
498	>	iend = nGroup - 1
499	>	#endif
500	>	outer: do i = istart, iend
501
502	<	inner: do j = 1, ncol
503	<
504	<	if (skipThisPair(i,j)) cycle inner
505	<
506	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
507	<
508	<	if (rijsq <  rlistsq) then
509	<
264	<	nlist = nlist + 1
265	<
266	<	if (nlist > neighborListSize) then
267	<	call expandNeighborList(nlocal, listerror)
268	<	if (listerror /= 0) then
269	<	error = -1
270	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
271	<	return
272	<	end if
273	<	neighborListSize = size(list)
274	<	endif
275	<
276	<	list(nlist) = j
277	<
278	<	if (rijsq <  rcutsq) then
279	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
280	<	u_l, A, f, t,pot)
281	<	endif
282	<	endif
283	<	enddo inner
284	<	enddo
285	<
286	<	point(nrow + 1) = nlist + 1
287	<
288	<	else  !! (of update_check)
289	<
290	<	! use the list to find the neighbors
291	<	do i = 1, nrow
292	<	JBEG = POINT(i)
293	<	JEND = POINT(i+1) - 1
294	<	! check thiat molecule i has neighbors
295	<	if (jbeg .le. jend) then
296	<
297	<	do jnab = jbeg, jend
298	<	j = list(jnab)
299	<
300	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
301	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
302	<	u_l, A, f, t,pot)
303	<
304	<	enddo
305	<	endif
306	<	enddo
307	<	endif
308	<
502	>	if (update_nlist) point(i) = nlist + 1
503	>
504	>	n_in_i = groupStart(i+1) - groupStart(i)
505	>
506	>	if (update_nlist) then
507	>	#ifdef IS_MPI
508	>	jstart = 1
509	>	jend = ncol_group
510		#else
511	<
512	<	if (update_nlist) then
513	<
514	<	! save current configuration, contruct neighbor list,
515	<	! and calculate forces
516	<	call saveNeighborList(q)
517	<
518	<	neighborListSize = size(list)
519	<
319	<	nlist = 0
320	<
321	<	do i = 1, natoms-1
322	<	point(i) = nlist + 1
511	>	jstart = i+1
512	>	jend = nGroup
513	>	#endif
514	>	else
515	>	jstart = point(i)
516	>	jend = point(i+1) - 1
517	>	! make sure group i has neighbors
518	>	if (jstart .gt. jend) cycle outer
519	>	endif
520
521	<	inner: do j = i+1, natoms
522	<
523	<	if (skipThisPair(i,j))  cycle inner
524	<
525	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
526	<
527	<
528	<	if (rijsq <  rlistsq) then
521	>	do jnab = jstart, jend
522	>	if (update_nlist) then
523	>	j = jnab
524	>	else
525	>	j = list(jnab)
526	>	endif
527	>	#ifdef IS_MPI
528	>	call get_interatomic_vector(q_group_Row(:,i), &
529	>	q_group_Col(:,j), d_grp, rgrpsq)
530	>	#else
531	>	call get_interatomic_vector(q_group(:,i), &
532	>	q_group(:,j), d_grp, rgrpsq)
533	>	#endif
534	>	if (rgrpsq < rlistsq) then
535	>	if (update_nlist) then
536	>	nlist = nlist + 1
537	>
538	>	if (nlist > neighborListSize) then
539	>	call expandNeighborList(nGroup, listerror)
540	>	if (listerror /= 0) then
541	>	error = -1
542	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
543	>	return
544	>	end if
545	>	neighborListSize = size(list)
546	>	endif
547	>
548	>	list(nlist) = j
549	>	endif
550
551	<	nlist = nlist + 1
552	<
553	<	if (nlist > neighborListSize) then
336	<	call expandNeighborList(natoms, listerror)
337	<	if (listerror /= 0) then
338	<	error = -1
339	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
340	<	return
341	<	end if
342	<	neighborListSize = size(list)
551	>	if (loop .eq. PAIR_LOOP) then
552	>	vij = 0.0d0
553	>	fij(1:3) = 0.0d0
554		endif
555
556	<	list(nlist) = j
556	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
557	>	in_switching_region)
558
559	<	if (rijsq <  rcutsq) then
560	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
561	<	u_l, A, f, t,pot)
559	>	n_in_j = groupStart(j+1) - groupStart(j)
560	>
561	>	do ia = groupStart(i), groupStart(i+1)-1
562	>
563	>	atom1 = groupList(ia)
564	>
565	>	inner: do jb = groupStart(j), groupStart(j+1)-1
566	>
567	>	atom2 = groupList(jb)
568	>
569	>	if (skipThisPair(atom1, atom2)) cycle inner
570	>
571	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
572	>	d_atm(1:3) = d_grp(1:3)
573	>	ratmsq = rgrpsq
574	>	else
575	>	#ifdef IS_MPI
576	>	call get_interatomic_vector(q_Row(:,atom1), &
577	>	q_Col(:,atom2), d_atm, ratmsq)
578	>	#else
579	>	call get_interatomic_vector(q(:,atom1), &
580	>	q(:,atom2), d_atm, ratmsq)
581	>	#endif
582	>	endif
583	>	if (loop .eq. PREPAIR_LOOP) then
584	>	#ifdef IS_MPI
585	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
586	>	rgrpsq, d_grp, do_pot, do_stress, &
587	>	u_l, A, f, t, pot_local)
588	>	#else
589	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
590	>	rgrpsq, d_grp, do_pot, do_stress, &
591	>	u_l, A, f, t, pot)
592	>	#endif
593	>	else
594	>	#ifdef IS_MPI
595	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
596	>	do_pot, &
597	>	u_l, A, f, t, pot_local, vpair, fpair)
598	>	#else
599	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
600	>	do_pot,  &
601	>	u_l, A, f, t, pot, vpair, fpair)
602	>	#endif
603	>	vij = vij + vpair
604	>	fij(1:3) = fij(1:3) + fpair(1:3)
605	>	endif
606	>	enddo inner
607	>	enddo
608	>
609	>	if (loop .eq. PAIR_LOOP) then
610	>	if (in_switching_region) then
611	>	swderiv = vij*dswdr/rgrp
612	>	fij(1) = fij(1) + swderiv*d_grp(1)
613	>	fij(2) = fij(2) + swderiv*d_grp(2)
614	>	fij(3) = fij(3) + swderiv*d_grp(3)
615	>
616	>	do ia=groupStart(i), groupStart(i+1)-1
617	>	atom1=groupList(ia)
618	>	mf = mfact(atom1)
619	>	#ifdef IS_MPI
620	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
621	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
622	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
623	>	#else
624	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
625	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
626	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
627	>	#endif
628	>	enddo
629	>
630	>	do jb=groupStart(j), groupStart(j+1)-1
631	>	atom2=groupList(jb)
632	>	mf = mfact(atom2)
633	>	#ifdef IS_MPI
634	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
635	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
636	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
637	>	#else
638	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
639	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
640	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
641	>	#endif
642	>	enddo
643	>	endif
644	>
645	>	if (do_stress) call add_stress_tensor(d_grp, fij)
646		endif
647	<	endif
648	<	enddo inner
649	<	enddo
647	>	end if
648	>	enddo
649	>	enddo outer
650
651	<	point(natoms) = nlist + 1
652	<
653	<	else !! (update)
654	<
655	<	! use the list to find the neighbors
656	<	do i = 1, natoms-1
657	<	JBEG = POINT(i)
658	<	JEND = POINT(i+1) - 1
659	<	! check thiat molecule i has neighbors
660	<	if (jbeg .le. jend) then
661	<
366	<	do jnab = jbeg, jend
367	<	j = list(jnab)
368	<
369	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
370	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
371	<	u_l, A, f, t,pot)
372	<
373	<	enddo
651	>	if (update_nlist) then
652	>	#ifdef IS_MPI
653	>	point(nrow_group + 1) = nlist + 1
654	>	#else
655	>	point(nGroup) = nlist + 1
656	>	#endif
657	>	if (loop .eq. PREPAIR_LOOP) then
658	>	! we just did the neighbor list update on the first
659	>	! pass, so we don't need to do it
660	>	! again on the second pass
661	>	update_nlist = .false.
662		endif
663	<	enddo
664	<	endif
663	>	endif
664	>
665	>	if (loop .eq. PREPAIR_LOOP) then
666	>	call do_preforce(nlocal, pot)
667	>	endif
668	>
669	>	enddo
670
671	<	#endif
671	>	!! Do timing
672	>	#ifdef PROFILE
673	>	call cpu_time(forceTimeFinal)
674	>	forceTime = forceTime + forceTimeFinal - forceTimeInitial
675	>	#endif
676
380	–	! phew, done with main loop.
381	–
677		#ifdef IS_MPI
678		!!distribute forces
679
680	<	call scatter(f_Row,f,plan_row3d)
680	>	f_temp = 0.0_dp
681	>	call scatter(f_Row,f_temp,plan_row3d)
682	>	do i = 1,nlocal
683	>	f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
684	>	end do
685	>
686	>	f_temp = 0.0_dp
687		call scatter(f_Col,f_temp,plan_col3d)
688		do i = 1,nlocal
689		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
690		end do
691
692	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
693	<	call scatter(t_Row,t,plan_row3d)
692	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
693	>	t_temp = 0.0_dp
694	>	call scatter(t_Row,t_temp,plan_row3d)
695	>	do i = 1,nlocal
696	>	t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
697	>	end do
698	>	t_temp = 0.0_dp
699		call scatter(t_Col,t_temp,plan_col3d)
700
701		do i = 1,nlocal
#	Line 406 | Line 712 | contains
712		do i = 1, nlocal
713		pot_local = pot_local + pot_Temp(i)
714		enddo
715	<
716	<	pot_Temp = 0.0_DP
717	<
715	>
716	>	pot_Temp = 0.0_DP
717	>
718		call scatter(pot_Col, pot_Temp, plan_col)
719		do i = 1, nlocal
720		pot_local = pot_local + pot_Temp(i)
721		enddo
722
723	<	endif
723	>	endif
724		#endif
725	<
726	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
725	>
726	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
727
728	<	if (FF_uses_RF .and. SimUsesRF()) then
728	>	if (FF_uses_RF .and. SIM_uses_RF) then
729
730		#ifdef IS_MPI
731		call scatter(rf_Row,rf,plan_row3d)
#	Line 429 | Line 735 | contains
735		end do
736		#endif
737
738	<	do i = 1, getNlocal()
739	<
738	>	do i = 1, nLocal
739	>
740		rfpot = 0.0_DP
741		#ifdef IS_MPI
742		me_i = atid_row(i)
743		#else
744		me_i = atid(i)
745		#endif
746	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
747	<	if ( is_DP_i ) then
748	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
746	>
747	>	if (PropertyMap(me_i)%is_DP) then
748	>
749	>	mu_i = PropertyMap(me_i)%dipole_moment
750	>
751		!! The reaction field needs to include a self contribution
752		!! to the field:
753	<	call accumulate_self_rf(i, mu_i, u_l)
753	>	call accumulate_self_rf(i, mu_i, u_l)
754		!! Get the reaction field contribution to the
755		!! potential and torques:
756		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 456 | Line 764 | contains
764		enddo
765		endif
766		endif
767	<
768	<
767	>
768	>
769		#ifdef IS_MPI
770	<
770	>
771		if (do_pot) then
772	<	pot = pot_local
772	>	pot = pot + pot_local
773		!! we assume the c code will do the allreduce to get the total potential
774		!! we could do it right here if we needed to...
775		endif
776	<
776	>
777		if (do_stress) then
778	<	call mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, &
778	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
779		mpi_comm_world,mpi_err)
780	<	call mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, &
780	>	call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
781		mpi_comm_world,mpi_err)
782		endif
783	<
783	>
784		#else
785	<
785	>
786		if (do_stress) then
787		tau = tau_Temp
788		virial = virial_Temp
789		endif
482	–
483	–	#endif
790
791	+	#endif
792	+
793		end subroutine do_force_loop
794	+
795	+	subroutine do_pair(i, j, rijsq, d, sw, do_pot, &
796	+	u_l, A, f, t, pot, vpair, fpair)
797
798	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t,pot)
798	>	real( kind = dp ) :: pot, vpair, sw
799	>	real( kind = dp ), dimension(3) :: fpair
800	>	real( kind = dp ), dimension(nLocal)   :: mfact
801	>	real( kind = dp ), dimension(3,nLocal) :: u_l
802	>	real( kind = dp ), dimension(9,nLocal) :: A
803	>	real( kind = dp ), dimension(3,nLocal) :: f
804	>	real( kind = dp ), dimension(3,nLocal) :: t
805
806	<	real( kind = dp ) :: pot
490	<	real( kind = dp ), dimension(:,:) :: u_l
491	<	real (kind=dp), dimension(:,:) :: A
492	<	real (kind=dp), dimension(:,:) :: f
493	<	real (kind=dp), dimension(:,:) :: t
494	<
495	<	logical, intent(inout) :: do_pot, do_stress
806	>	logical, intent(inout) :: do_pot
807		integer, intent(in) :: i, j
808	<	real ( kind = dp ), intent(inout)    :: rijsq
808	>	real ( kind = dp ), intent(inout) :: rijsq
809		real ( kind = dp )                :: r
810		real ( kind = dp ), intent(inout) :: d(3)
500	–	logical :: is_LJ_i, is_LJ_j
501	–	logical :: is_DP_i, is_DP_j
502	–	logical :: is_GB_i, is_GB_j
503	–	logical :: is_Sticky_i, is_Sticky_j
811		integer :: me_i, me_j
812
813		r = sqrt(rijsq)
814	+	vpair = 0.0d0
815	+	fpair(1:3) = 0.0d0
816
817		#ifdef IS_MPI
818	<
818	>	if (tagRow(i) .eq. tagColumn(j)) then
819	>	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
820	>	endif
821		me_i = atid_row(i)
822		me_j = atid_col(j)
512	–
823		#else
514	–
824		me_i = atid(i)
825		me_j = atid(j)
517	–
826		#endif
827	+
828	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
829	+
830	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
831	+	!write(*,*) 'calling lj with'
832	+	!write(*,*) i, j, r, rijsq
833	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
834	+	!write(*,'(3es12.3)') sw, vpair, pot
835	+	!write(*,*)
836
837	<	if (FF_uses_LJ .and. SimUsesLJ()) then
838	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
839	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
523	<
524	<	if ( is_LJ_i .and. is_LJ_j ) &
525	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
837	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
838	>	endif
839	>
840		endif
841	<
842	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
529	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
530	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
841	>
842	>	if (FF_uses_charges .and. SIM_uses_charges) then
843
844	<	if ( is_DP_i .and. is_DP_j ) then
845	<
534	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
535	<	do_pot, do_stress)
536	<	if (FF_uses_RF .and. SimUsesRF()) then
537	<	call accumulate_rf(i, j, r, u_l)
538	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
539	<	endif
540	<
844	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
845	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
846		endif
847	+
848		endif
849	+
850	+	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
851	+
852	+	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
853	+	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
854	+	do_pot)
855	+	if (FF_uses_RF .and. SIM_uses_RF) then
856	+	call accumulate_rf(i, j, r, u_l, sw)
857	+	call rf_correct_forces(i, j, d, r, u_l, sw, f, fpair)
858	+	endif
859	+	endif
860
861	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
861	>	endif
862
863	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
547	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
863	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
864
865	<	if ( is_Sticky_i .and. is_Sticky_j ) then
866	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
867	<	do_pot, do_stress)
865	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
866	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, A, f, t, &
867	>	do_pot)
868		endif
869	+
870		endif
871
872
873	<	if (FF_uses_GB .and. SimUsesGB()) then
557	<
558	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
559	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
873	>	if (FF_uses_GB .and. SIM_uses_GB) then
874
875	<	if ( is_GB_i .and. is_GB_j ) then
876	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
877	<	do_pot, do_stress)
875	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
876	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
877	>	do_pot)
878		endif
565	–	endif
566	–
567	–	end subroutine do_pair
879
880	<
570	<	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
571	<
572	<	real (kind = dp), dimension(3) :: q_i
573	<	real (kind = dp), dimension(3) :: q_j
574	<	real ( kind = dp ), intent(out) :: r_sq
575	<	real( kind = dp ) :: d(3)
576	<	real( kind = dp ) :: d_old(3)
577	<	d(1:3) = q_i(1:3) - q_j(1:3)
578	<	d_old = d
579	<	! Wrap back into periodic box if necessary
580	<	if ( SimUsesPBC() ) then
880	>	endif
881
882	<	d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,d(1:3)) * &
583	<	int(abs(d(1:3)/box(1:3)) + 0.5_dp)
882	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
883
884	+	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
885	+	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, &
886	+	do_pot)
887	+	endif
888	+
889		endif
586	–	r_sq = dot_product(d,d)
587	–
588	–	end subroutine get_interatomic_vector
589	–
590	–	subroutine check_initialization(error)
591	–	integer, intent(out) :: error
890
891	<	error = 0
594	<	! Make sure we are properly initialized.
595	<	if (.not. do_forces_initialized) then
596	<	error = -1
597	<	return
598	<	endif
891	>	end subroutine do_pair
892
893	<	#ifdef IS_MPI
894	<	if (.not. isMPISimSet()) then
602	<	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
603	<	error = -1
604	<	return
605	<	endif
606	<	#endif
607	<
608	<	return
609	<	end subroutine check_initialization
893	>	subroutine do_prepair(i, j, rijsq, d, sw, rcijsq, dc, &
894	>	do_pot, do_stress, u_l, A, f, t, pot)
895
896	<
897	<	subroutine zero_work_arrays()
898	<
899	<	#ifdef IS_MPI
896	>	real( kind = dp ) :: pot, sw
897	>	real( kind = dp ), dimension(3,nLocal) :: u_l
898	>	real (kind=dp), dimension(9,nLocal) :: A
899	>	real (kind=dp), dimension(3,nLocal) :: f
900	>	real (kind=dp), dimension(3,nLocal) :: t
901	>
902	>	logical, intent(inout) :: do_pot, do_stress
903	>	integer, intent(in) :: i, j
904	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
905	>	real ( kind = dp )                :: r, rc
906	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
907	>
908	>	logical :: is_EAM_i, is_EAM_j
909	>
910	>	integer :: me_i, me_j
911	>
912
913	<	q_Row = 0.0_dp
914	<	q_Col = 0.0_dp
915	<
916	<	u_l_Row = 0.0_dp
917	<	u_l_Col = 0.0_dp
918	<
919	<	A_Row = 0.0_dp
623	<	A_Col = 0.0_dp
624	<
625	<	f_Row = 0.0_dp
626	<	f_Col = 0.0_dp
627	<	f_Temp = 0.0_dp
628	<
629	<	t_Row = 0.0_dp
630	<	t_Col = 0.0_dp
631	<	t_Temp = 0.0_dp
632	<
633	<	pot_Row = 0.0_dp
634	<	pot_Col = 0.0_dp
635	<	pot_Temp = 0.0_dp
913	>	r = sqrt(rijsq)
914	>	if (SIM_uses_molecular_cutoffs) then
915	>	rc = sqrt(rcijsq)
916	>	else
917	>	rc = r
918	>	endif
919	>
920
637	–	rf_Row = 0.0_dp
638	–	rf_Col = 0.0_dp
639	–	rf_Temp = 0.0_dp
640	–
641	–	#endif
642	–
643	–	rf = 0.0_dp
644	–	tau_Temp = 0.0_dp
645	–	virial_Temp = 0.0_dp
646	–
647	–	end subroutine zero_work_arrays
648	–
649	–	function skipThisPair(atom1, atom2) result(skip_it)
650	–	integer, intent(in) :: atom1
651	–	integer, intent(in), optional :: atom2
652	–	logical :: skip_it
653	–	integer :: unique_id_1, unique_id_2
654	–	integer :: me_i,me_j
655	–	integer :: i
656	–
657	–	skip_it = .false.
658	–
659	–	!! there are a number of reasons to skip a pair or a particle
660	–	!! mostly we do this to exclude atoms who are involved in short
661	–	!! range interactions (bonds, bends, torsions), but we also need
662	–	!! to exclude some overcounted interactions that result from
663	–	!! the parallel decomposition
664	–
921		#ifdef IS_MPI
922	<	!! in MPI, we have to look up the unique IDs for each atom
923	<	unique_id_1 = tagRow(atom1)
922	>	if (tagRow(i) .eq. tagColumn(j)) then
923	>	write(0,*) 'do_prepair is doing', i , j, tagRow(i), tagColumn(j)
924	>	endif
925	>
926	>	me_i = atid_row(i)
927	>	me_j = atid_col(j)
928	>
929		#else
930	<	!! in the normal loop, the atom numbers are unique
931	<	unique_id_1 = atom1
930	>
931	>	me_i = atid(i)
932	>	me_j = atid(j)
933	>
934		#endif
935	<
936	<	!! We were called with only one atom, so just check the global exclude
937	<	!! list for this atom
938	<	if (.not. present(atom2)) then
939	<	do i = 1, nExcludes_global
940	<	if (excludesGlobal(i) == unique_id_1) then
941	<	skip_it = .true.
942	<	return
943	<	end if
944	<	end do
945	<	return
946	<	end if
947	<
948	<	#ifdef IS_MPI
949	<	unique_id_2 = tagColumn(atom2)
950	<	#else
951	<	unique_id_2 = atom2
952	<	#endif
953	<
935	>
936	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
937	>
938	>	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
939	>	call calc_EAM_prepair_rho(i, j, d, r, rijsq )
940	>
941	>	endif
942	>
943	>	end subroutine do_prepair
944	>
945	>
946	>	subroutine do_preforce(nlocal,pot)
947	>	integer :: nlocal
948	>	real( kind = dp ) :: pot
949	>
950	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
951	>	call calc_EAM_preforce_Frho(nlocal,pot)
952	>	endif
953	>
954	>
955	>	end subroutine do_preforce
956	>
957	>
958	>	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
959	>
960	>	real (kind = dp), dimension(3) :: q_i
961	>	real (kind = dp), dimension(3) :: q_j
962	>	real ( kind = dp ), intent(out) :: r_sq
963	>	real( kind = dp ) :: d(3), scaled(3)
964	>	integer i
965	>
966	>	d(1:3) = q_j(1:3) - q_i(1:3)
967	>
968	>	! Wrap back into periodic box if necessary
969	>	if ( SIM_uses_PBC ) then
970	>
971	>	if( .not.boxIsOrthorhombic ) then
972	>	! calc the scaled coordinates.
973	>
974	>	scaled = matmul(HmatInv, d)
975	>
976	>	! wrap the scaled coordinates
977	>
978	>	scaled = scaled  - anint(scaled)
979	>
980	>
981	>	! calc the wrapped real coordinates from the wrapped scaled
982	>	! coordinates
983	>
984	>	d = matmul(Hmat,scaled)
985	>
986	>	else
987	>	! calc the scaled coordinates.
988	>
989	>	do i = 1, 3
990	>	scaled(i) = d(i) * HmatInv(i,i)
991	>
992	>	! wrap the scaled coordinates
993	>
994	>	scaled(i) = scaled(i) - anint(scaled(i))
995	>
996	>	! calc the wrapped real coordinates from the wrapped scaled
997	>	! coordinates
998	>
999	>	d(i) = scaled(i)*Hmat(i,i)
1000	>	enddo
1001	>	endif
1002	>
1003	>	endif
1004	>
1005	>	r_sq = dot_product(d,d)
1006	>
1007	>	end subroutine get_interatomic_vector
1008	>
1009	>	subroutine zero_work_arrays()
1010	>
1011		#ifdef IS_MPI
1012	<	!! this situation should only arise in MPI simulations
1013	<	if (unique_id_1 == unique_id_2) then
1014	<	skip_it = .true.
695	<	return
696	<	end if
697	<
698	<	!! this prevents us from doing the pair on multiple processors
699	<	if (unique_id_1 < unique_id_2) then
700	<	if (mod(unique_id_1 + unique_id_2,2) == 0) skip_it = .true.
701	<	return
702	<	else
703	<	if (mod(unique_id_1 + unique_id_2,2) == 1) skip_it = .true.
704	<	return
705	<	endif
706	<	#endif
1012	>
1013	>	q_Row = 0.0_dp
1014	>	q_Col = 0.0_dp
1015
1016	<	!! the rest of these situations can happen in all simulations:
1017	<	do i = 1, nExcludes_global
1018	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1019	<	(excludesGlobal(i) == unique_id_2)) then
1020	<	skip_it = .true.
1021	<	return
1022	<	endif
1023	<	enddo
1016	>	q_group_Row = 0.0_dp
1017	>	q_group_Col = 0.0_dp
1018	>
1019	>	u_l_Row = 0.0_dp
1020	>	u_l_Col = 0.0_dp
1021	>
1022	>	A_Row = 0.0_dp
1023	>	A_Col = 0.0_dp
1024	>
1025	>	f_Row = 0.0_dp
1026	>	f_Col = 0.0_dp
1027	>	f_Temp = 0.0_dp
1028	>
1029	>	t_Row = 0.0_dp
1030	>	t_Col = 0.0_dp
1031	>	t_Temp = 0.0_dp
1032	>
1033	>	pot_Row = 0.0_dp
1034	>	pot_Col = 0.0_dp
1035	>	pot_Temp = 0.0_dp
1036	>
1037	>	rf_Row = 0.0_dp
1038	>	rf_Col = 0.0_dp
1039	>	rf_Temp = 0.0_dp
1040	>
1041	>	#endif
1042
1043	<	do i = 1, nExcludes_local
1044	<	if (excludesLocal(1,i) == unique_id_1) then
1045	<	if (excludesLocal(2,i) == unique_id_2) then
1046	<	skip_it = .true.
1047	<	return
1048	<	endif
1049	<	else
1050	<	if (excludesLocal(1,i) == unique_id_2) then
1051	<	if (excludesLocal(2,i) == unique_id_1) then
1052	<	skip_it = .true.
1053	<	return
1054	<	endif
1055	<	endif
1056	<	endif
1057	<	end do
1058	<
1059	<	return
1060	<	end function skipThisPair
1043	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1044	>	call clean_EAM()
1045	>	endif
1046	>
1047	>	rf = 0.0_dp
1048	>	tau_Temp = 0.0_dp
1049	>	virial_Temp = 0.0_dp
1050	>	end subroutine zero_work_arrays
1051	>
1052	>	function skipThisPair(atom1, atom2) result(skip_it)
1053	>	integer, intent(in) :: atom1
1054	>	integer, intent(in), optional :: atom2
1055	>	logical :: skip_it
1056	>	integer :: unique_id_1, unique_id_2
1057	>	integer :: me_i,me_j
1058	>	integer :: i
1059	>
1060	>	skip_it = .false.
1061	>
1062	>	!! there are a number of reasons to skip a pair or a particle
1063	>	!! mostly we do this to exclude atoms who are involved in short
1064	>	!! range interactions (bonds, bends, torsions), but we also need
1065	>	!! to exclude some overcounted interactions that result from
1066	>	!! the parallel decomposition
1067	>
1068	>	#ifdef IS_MPI
1069	>	!! in MPI, we have to look up the unique IDs for each atom
1070	>	unique_id_1 = tagRow(atom1)
1071	>	#else
1072	>	!! in the normal loop, the atom numbers are unique
1073	>	unique_id_1 = atom1
1074	>	#endif
1075	>
1076	>	!! We were called with only one atom, so just check the global exclude
1077	>	!! list for this atom
1078	>	if (.not. present(atom2)) then
1079	>	do i = 1, nExcludes_global
1080	>	if (excludesGlobal(i) == unique_id_1) then
1081	>	skip_it = .true.
1082	>	return
1083	>	end if
1084	>	end do
1085	>	return
1086	>	end if
1087	>
1088	>	#ifdef IS_MPI
1089	>	unique_id_2 = tagColumn(atom2)
1090	>	#else
1091	>	unique_id_2 = atom2
1092	>	#endif
1093	>
1094	>	#ifdef IS_MPI
1095	>	!! this situation should only arise in MPI simulations
1096	>	if (unique_id_1 == unique_id_2) then
1097	>	skip_it = .true.
1098	>	return
1099	>	end if
1100	>
1101	>	!! this prevents us from doing the pair on multiple processors
1102	>	if (unique_id_1 < unique_id_2) then
1103	>	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1104	>	skip_it = .true.
1105	>	return
1106	>	endif
1107	>	else
1108	>	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1109	>	skip_it = .true.
1110	>	return
1111	>	endif
1112	>	endif
1113	>	#endif
1114	>
1115	>	!! the rest of these situations can happen in all simulations:
1116	>	do i = 1, nExcludes_global
1117	>	if ((excludesGlobal(i) == unique_id_1) .or. &
1118	>	(excludesGlobal(i) == unique_id_2)) then
1119	>	skip_it = .true.
1120	>	return
1121	>	endif
1122	>	enddo
1123	>
1124	>	do i = 1, nSkipsForAtom(unique_id_1)
1125	>	if (skipsForAtom(unique_id_1, i) .eq. unique_id_2) then
1126	>	skip_it = .true.
1127	>	return
1128	>	endif
1129	>	end do
1130	>
1131	>	return
1132	>	end function skipThisPair
1133	>
1134	>	function FF_UsesDirectionalAtoms() result(doesit)
1135	>	logical :: doesit
1136	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1137	>	FF_uses_GB .or. FF_uses_RF
1138	>	end function FF_UsesDirectionalAtoms
1139	>
1140	>	function FF_RequiresPrepairCalc() result(doesit)
1141	>	logical :: doesit
1142	>	doesit = FF_uses_EAM
1143	>	end function FF_RequiresPrepairCalc
1144	>
1145	>	function FF_RequiresPostpairCalc() result(doesit)
1146	>	logical :: doesit
1147	>	doesit = FF_uses_RF
1148	>	end function FF_RequiresPostpairCalc
1149	>
1150	>	#ifdef PROFILE
1151	>	function getforcetime() result(totalforcetime)
1152	>	real(kind=dp) :: totalforcetime
1153	>	totalforcetime = forcetime
1154	>	end function getforcetime
1155	>	#endif
1156	>
1157	>	!! This cleans componets of force arrays belonging only to fortran
1158
1159	<	function FF_UsesDirectionalAtoms() result(doesit)
1160	<	logical :: doesit
1161	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1162	<	FF_uses_GB .or. FF_uses_RF
1163	<	end function FF_UsesDirectionalAtoms
1164	<
1165	<	function FF_RequiresPrepairCalc() result(doesit)
1166	<	logical :: doesit
1167	<	doesit = FF_uses_EAM
1168	<	end function FF_RequiresPrepairCalc
1169	<
1170	<	function FF_RequiresPostpairCalc() result(doesit)
1171	<	logical :: doesit
1172	<	doesit = FF_uses_RF
1173	<	end function FF_RequiresPostpairCalc
1174	<
1159	>	subroutine add_stress_tensor(dpair, fpair)
1160	>
1161	>	real( kind = dp ), dimension(3), intent(in) :: dpair, fpair
1162	>
1163	>	! because the d vector is the rj - ri vector, and
1164	>	! because fx, fy, fz are the force on atom i, we need a
1165	>	! negative sign here:
1166	>
1167	>	tau_Temp(1) = tau_Temp(1) - dpair(1) * fpair(1)
1168	>	tau_Temp(2) = tau_Temp(2) - dpair(1) * fpair(2)
1169	>	tau_Temp(3) = tau_Temp(3) - dpair(1) * fpair(3)
1170	>	tau_Temp(4) = tau_Temp(4) - dpair(2) * fpair(1)
1171	>	tau_Temp(5) = tau_Temp(5) - dpair(2) * fpair(2)
1172	>	tau_Temp(6) = tau_Temp(6) - dpair(2) * fpair(3)
1173	>	tau_Temp(7) = tau_Temp(7) - dpair(3) * fpair(1)
1174	>	tau_Temp(8) = tau_Temp(8) - dpair(3) * fpair(2)
1175	>	tau_Temp(9) = tau_Temp(9) - dpair(3) * fpair(3)
1176	>
1177	>	!write(*,'(6es12.3)')  fpair(1:3), tau_Temp(1), tau_Temp(5), tau_temp(9)
1178	>	virial_Temp = virial_Temp + &
1179	>	(tau_Temp(1) + tau_Temp(5) + tau_Temp(9))
1180	>
1181	>	end subroutine add_stress_tensor
1182	>
1183		end module do_Forces
1184	+

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