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Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC vs.
Revision 1183 by gezelter, Fri May 21 15:58:48 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.5 2003-03-31 21:50:59 chuckv Exp $, $Date: 2003-03-31 21:50:59 $, $Name: not supported by cvs2svn $, $Revision: 1.5 $
7	>	!! @version $Id: do_Forces.F90,v 1.60 2004-05-21 15:58:40 gezelter Exp $, $Date: 2004-05-21 15:58:40 $, $Name: not supported by cvs2svn $, $Revision: 1.60 $
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	>	logical, save :: haveRlist = .false.
37	>	logical, save :: haveNeighborList = .false.
38	>	logical, save :: havePolicies = .false.
39	>	logical, save :: haveSIMvariables = .false.
40	>	logical, save :: havePropertyMap = .false.
41	>	logical, save :: haveSaneForceField = .false.
42		logical, save :: FF_uses_LJ
43		logical, save :: FF_uses_sticky
44	+	logical, save :: FF_uses_charges
45		logical, save :: FF_uses_dipoles
46		logical, save :: FF_uses_RF
47		logical, save :: FF_uses_GB
48		logical, save :: FF_uses_EAM
49	+	logical, save :: SIM_uses_LJ
50	+	logical, save :: SIM_uses_sticky
51	+	logical, save :: SIM_uses_charges
52	+	logical, save :: SIM_uses_dipoles
53	+	logical, save :: SIM_uses_RF
54	+	logical, save :: SIM_uses_GB
55	+	logical, save :: SIM_uses_EAM
56	+	logical, save :: SIM_requires_postpair_calc
57	+	logical, save :: SIM_requires_prepair_calc
58	+	logical, save :: SIM_uses_directional_atoms
59	+	logical, save :: SIM_uses_PBC
60	+	logical, save :: SIM_uses_molecular_cutoffs
61
62	+	real(kind=dp), save :: rlist, rlistsq
63	+
64		public :: init_FF
65		public :: do_force_loop
66	+	public :: setRlistDF
67
68	+	#ifdef PROFILE
69	+	public :: getforcetime
70	+	real, save :: forceTime = 0
71	+	real :: forceTimeInitial, forceTimeFinal
72	+	integer :: nLoops
73	+	#endif
74	+
75	+	type :: Properties
76	+	logical :: is_lj     = .false.
77	+	logical :: is_sticky = .false.
78	+	logical :: is_dp     = .false.
79	+	logical :: is_gb     = .false.
80	+	logical :: is_eam    = .false.
81	+	logical :: is_charge = .false.
82	+	real(kind=DP) :: charge = 0.0_DP
83	+	real(kind=DP) :: dipole_moment = 0.0_DP
84	+	end type Properties
85	+
86	+	type(Properties), dimension(:),allocatable :: PropertyMap
87	+
88		contains
89
90	+	subroutine setRlistDF( this_rlist )
91	+
92	+	real(kind=dp) :: this_rlist
93	+
94	+	rlist = this_rlist
95	+	rlistsq = rlist * rlist
96	+
97	+	haveRlist = .true.
98	+
99	+	end subroutine setRlistDF
100	+
101	+	subroutine createPropertyMap(status)
102	+	integer :: nAtypes
103	+	integer :: status
104	+	integer :: i
105	+	logical :: thisProperty
106	+	real (kind=DP) :: thisDPproperty
107	+
108	+	status = 0
109	+
110	+	nAtypes = getSize(atypes)
111	+
112	+	if (nAtypes == 0) then
113	+	status = -1
114	+	return
115	+	end if
116	+
117	+	if (.not. allocated(PropertyMap)) then
118	+	allocate(PropertyMap(nAtypes))
119	+	endif
120	+
121	+	do i = 1, nAtypes
122	+	call getElementProperty(atypes, i, "is_LJ", thisProperty)
123	+	PropertyMap(i)%is_LJ = thisProperty
124	+
125	+	call getElementProperty(atypes, i, "is_Charge", thisProperty)
126	+	PropertyMap(i)%is_Charge = thisProperty
127	+
128	+	if (thisProperty) then
129	+	call getElementProperty(atypes, i, "charge", thisDPproperty)
130	+	PropertyMap(i)%charge = thisDPproperty
131	+	endif
132	+
133	+	call getElementProperty(atypes, i, "is_DP", thisProperty)
134	+	PropertyMap(i)%is_DP = thisProperty
135	+
136	+	if (thisProperty) then
137	+	call getElementProperty(atypes, i, "dipole_moment", thisDPproperty)
138	+	PropertyMap(i)%dipole_moment = thisDPproperty
139	+	endif
140	+
141	+	call getElementProperty(atypes, i, "is_Sticky", thisProperty)
142	+	PropertyMap(i)%is_Sticky = thisProperty
143	+	call getElementProperty(atypes, i, "is_GB", thisProperty)
144	+	PropertyMap(i)%is_GB = thisProperty
145	+	call getElementProperty(atypes, i, "is_EAM", thisProperty)
146	+	PropertyMap(i)%is_EAM = thisProperty
147	+	end do
148	+
149	+	havePropertyMap = .true.
150	+
151	+	end subroutine createPropertyMap
152	+
153	+	subroutine setSimVariables()
154	+	SIM_uses_LJ = SimUsesLJ()
155	+	SIM_uses_sticky = SimUsesSticky()
156	+	SIM_uses_charges = SimUsesCharges()
157	+	SIM_uses_dipoles = SimUsesDipoles()
158	+	SIM_uses_RF = SimUsesRF()
159	+	SIM_uses_GB = SimUsesGB()
160	+	SIM_uses_EAM = SimUsesEAM()
161	+	SIM_requires_postpair_calc = SimRequiresPostpairCalc()
162	+	SIM_requires_prepair_calc = SimRequiresPrepairCalc()
163	+	SIM_uses_directional_atoms = SimUsesDirectionalAtoms()
164	+	SIM_uses_PBC = SimUsesPBC()
165	+	!SIM_uses_molecular_cutoffs = SimUsesMolecularCutoffs()
166	+
167	+	haveSIMvariables = .true.
168	+
169	+	return
170	+	end subroutine setSimVariables
171	+
172	+	subroutine doReadyCheck(error)
173	+	integer, intent(out) :: error
174	+
175	+	integer :: myStatus
176	+
177	+	error = 0
178	+
179	+	if (.not. havePropertyMap) then
180	+
181	+	myStatus = 0
182	+
183	+	call createPropertyMap(myStatus)
184	+
185	+	if (myStatus .ne. 0) then
186	+	write(default_error, *) 'createPropertyMap failed in do_Forces!'
187	+	error = -1
188	+	return
189	+	endif
190	+	endif
191	+
192	+	if (.not. haveSIMvariables) then
193	+	call setSimVariables()
194	+	endif
195	+
196	+	if (.not. haveRlist) then
197	+	write(default_error, *) 'rList has not been set in do_Forces!'
198	+	error = -1
199	+	return
200	+	endif
201	+
202	+	if (SIM_uses_LJ .and. FF_uses_LJ) then
203	+	if (.not. havePolicies) then
204	+	write(default_error, *) 'LJ mixing Policies have not been set in do_Forces!'
205	+	error = -1
206	+	return
207	+	endif
208	+	endif
209	+
210	+	if (.not. haveNeighborList) then
211	+	write(default_error, *) 'neighbor list has not been initialized in do_Forces!'
212	+	error = -1
213	+	return
214	+	end if
215	+
216	+	if (.not. haveSaneForceField) then
217	+	write(default_error, *) 'Force Field is not sane in do_Forces!'
218	+	error = -1
219	+	return
220	+	end if
221	+
222	+	#ifdef IS_MPI
223	+	if (.not. isMPISimSet()) then
224	+	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
225	+	error = -1
226	+	return
227	+	endif
228	+	#endif
229	+	return
230	+	end subroutine doReadyCheck
231	+
232	+
233		subroutine init_FF(LJMIXPOLICY, use_RF_c, thisStat)
234
235		integer, intent(in) :: LJMIXPOLICY
#	Line 64 | Line 254 | contains
254
255		FF_uses_LJ = .false.
256		FF_uses_sticky = .false.
257	+	FF_uses_charges = .false.
258		FF_uses_dipoles = .false.
259		FF_uses_GB = .false.
260		FF_uses_EAM = .false.
261
262		call getMatchingElementList(atypes, "is_LJ", .true., nMatches, MatchList)
263		if (nMatches .gt. 0) FF_uses_LJ = .true.
264	<
264	>
265	>	call getMatchingElementList(atypes, "is_Charge", .true., nMatches, MatchList)
266	>	if (nMatches .gt. 0) FF_uses_charges = .true.
267	>
268		call getMatchingElementList(atypes, "is_DP", .true., nMatches, MatchList)
269		if (nMatches .gt. 0) FF_uses_dipoles = .true.
270
#	Line 84 | Line 278 | contains
278		call getMatchingElementList(atypes, "is_EAM", .true., nMatches, MatchList)
279		if (nMatches .gt. 0) FF_uses_EAM = .true.
280
281	+	!! Assume sanity (for the sake of argument)
282	+	haveSaneForceField = .true.
283	+
284		!! check to make sure the FF_uses_RF setting makes sense
285
286		if (FF_uses_dipoles) then
90	–	rrf = getRrf()
91	–	rt = getRt()
92	–	call initialize_dipole(rrf, rt)
287		if (FF_uses_RF) then
288		dielect = getDielect()
289	<	call initialize_rf(rrf, rt, dielect)
289	>	call initialize_rf(dielect)
290		endif
291		else
292		if (FF_uses_RF) then
293		write(default_error,*) 'Using Reaction Field with no dipoles?  Huh?'
294		thisStat = -1
295	+	haveSaneForceField = .false.
296		return
297		endif
298	<	endif
298	>	endif
299
300		if (FF_uses_LJ) then
301
107	–	call getRcut(rcut)
108	–
302		select case (LJMIXPOLICY)
303		case (LB_MIXING_RULE)
304	<	call init_lj_FF(LB_MIXING_RULE, rcut, my_status)
304	>	call init_lj_FF(LB_MIXING_RULE, my_status)
305		case (EXPLICIT_MIXING_RULE)
306	<	call init_lj_FF(EXPLICIT_MIXING_RULE, rcut, my_status)
306	>	call init_lj_FF(EXPLICIT_MIXING_RULE, my_status)
307		case default
308		write(default_error,*) 'unknown LJ Mixing Policy!'
309		thisStat = -1
310	+	haveSaneForceField = .false.
311		return
312		end select
313		if (my_status /= 0) then
314		thisStat = -1
315	+	haveSaneForceField = .false.
316		return
317		end if
318	+	havePolicies = .true.
319		endif
320
321		if (FF_uses_sticky) then
322		call check_sticky_FF(my_status)
323		if (my_status /= 0) then
324		thisStat = -1
325	+	haveSaneForceField = .false.
326		return
327		end if
328		endif
329	<
329	>
330	>
331	>	if (FF_uses_EAM) then
332	>	call init_EAM_FF(my_status)
333	>	if (my_status /= 0) then
334	>	write(default_error, *) "init_EAM_FF returned a bad status"
335	>	thisStat = -1
336	>	haveSaneForceField = .false.
337	>	return
338	>	end if
339	>	endif
340	>
341		if (FF_uses_GB) then
342		call check_gb_pair_FF(my_status)
343		if (my_status .ne. 0) then
344		thisStat = -1
345	+	haveSaneForceField = .false.
346		return
347		endif
348		endif
349
350		if (FF_uses_GB .and. FF_uses_LJ) then
351		endif
352	+	if (.not. haveNeighborList) then
353	+	!! Create neighbor lists
354	+	call expandNeighborList(nLocal, my_status)
355	+	if (my_Status /= 0) then
356	+	write(default_error,*) "SimSetup: ExpandNeighborList returned error."
357	+	thisStat = -1
358	+	return
359	+	endif
360	+	haveNeighborList = .true.
361	+	endif
362
363	<
364	<	do_forces_initialized = .true.
146	<
363	>
364	>
365		end subroutine init_FF
366
367
368		!! Does force loop over i,j pairs. Calls do_pair to calculates forces.
369		!------------------------------------------------------------->
370	<	subroutine do_force_loop(q, A, u_l, f, t, tau, pot, do_pot_c, do_stress_c, &
371	<	error)
370	>	subroutine do_force_loop(q, q_group, A, u_l, f, t, tau, pot, &
371	>	do_pot_c, do_stress_c, error)
372		!! Position array provided by C, dimensioned by getNlocal
373	<	real ( kind = dp ), dimension(3,getNlocal()) :: q
373	>	real ( kind = dp ), dimension(3, nLocal) :: q
374	>	!! molecular center-of-mass position array
375	>	real ( kind = dp ), dimension(3, nGroup) :: q_group
376		!! Rotation Matrix for each long range particle in simulation.
377	<	real( kind = dp), dimension(9,getNlocal()) :: A
377	>	real( kind = dp), dimension(9, nLocal) :: A
378		!! Unit vectors for dipoles (lab frame)
379	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
379	>	real( kind = dp ), dimension(3,nLocal) :: u_l
380		!! Force array provided by C, dimensioned by getNlocal
381	<	real ( kind = dp ), dimension(3,getNlocal()) :: f
381	>	real ( kind = dp ), dimension(3,nLocal) :: f
382		!! Torsion array provided by C, dimensioned by getNlocal
383	<	real( kind = dp ), dimension(3,getNlocal()) :: t
383	>	real( kind = dp ), dimension(3,nLocal) :: t
384	>
385		!! Stress Tensor
386		real( kind = dp), dimension(9) :: tau
387		real ( kind = dp ) :: pot
388		logical ( kind = 2) :: do_pot_c, do_stress_c
389		logical :: do_pot
390		logical :: do_stress
391	<	#ifdef IS_MPI
391	>	logical :: in_switching_region
392	>	#ifdef IS_MPI
393		real( kind = DP ) :: pot_local
394		integer :: nrow
395		integer :: ncol
396	+	integer :: nprocs
397	+	integer :: nrow_group
398	+	integer :: ncol_group
399		#endif
175	–	integer :: nlocal
400		integer :: natoms
401		logical :: update_nlist
402		integer :: i, j, jbeg, jend, jnab
403	+	integer :: ia, jb, atom1, atom2
404		integer :: nlist
405	<	real( kind = DP ) ::  rijsq, rlistsq, rcutsq, rlist, rcut
406	<	real(kind=dp),dimension(3) :: d
405	>	real( kind = DP ) :: ratmsq, rgrpsq, rgrp, vpair, vij
406	>	real( kind = DP ) :: sw, dswdr, swderiv, mf
407	>	real(kind=dp),dimension(3) :: d_atm, d_grp
408		real(kind=dp) :: rfpot, mu_i, virial
409	<	integer :: me_i
409	>	integer :: me_i, me_j, n_in_i, n_in_j
410		logical :: is_dp_i
411		integer :: neighborListSize
412		integer :: listerror, error
413		integer :: localError
414	+	integer :: propPack_i, propPack_j
415
416	+	real(kind=dp) :: listSkin = 1.0
417	+
418		!! initialize local variables
419	<
419	>
420		#ifdef IS_MPI
421	<	nlocal = getNlocal()
421	>	pot_local = 0.0_dp
422		nrow   = getNrow(plan_row)
423		ncol   = getNcol(plan_col)
424	+	nrow_group   = getNrowGroup(plan_row)
425	+	ncol_group   = getNcolGroup(plan_col)
426		#else
196	–	nlocal = getNlocal()
427		natoms = nlocal
428		#endif
199	–
200	–	call getRcut(rcut,rc2=rcutsq)
201	–	call getRlist(rlist,rlistsq)
429
430	<	call check_initialization(localError)
430	>	call doReadyCheck(localError)
431		if ( localError .ne. 0 ) then
432	+	call handleError("do_force_loop", "Not Initialized")
433		error = -1
434		return
435		end if
436		call zero_work_arrays()
437	<
437	>
438		do_pot = do_pot_c
439		do_stress = do_stress_c
440	<
440	>
441		! Gather all information needed by all force loops:
442
443		#ifdef IS_MPI
444	+
445	+	call gather(q, q_Row, plan_row3d)
446	+	call gather(q, q_Col, plan_col3d)
447
448	<	call gather(q,q_Row,plan_row3d)
449	<	call gather(q,q_Col,plan_col3d)
448	>	call gather(q_group, q_group_Row, plan_row_Group_3d)
449	>	call gather(q_group, q_group_Col, plan_col_Group_3d)
450
451	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
451	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
452		call gather(u_l,u_l_Row,plan_row3d)
453		call gather(u_l,u_l_Col,plan_col3d)
454
#	Line 227 | Line 458 | contains
458
459		#endif
460
461	<	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
461	>	!! Begin force loop timing:
462	>	#ifdef PROFILE
463	>	call cpu_time(forceTimeInitial)
464	>	nloops = nloops + 1
465	>	#endif
466	>
467	>	if (FF_RequiresPrepairCalc() .and. SIM_requires_prepair_calc) then
468		!! See if we need to update neighbor lists
469	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
469	>
470	>	call checkNeighborList(nGroup, q_group, listSkin, update_nlist)
471	>
472		!! if_mpi_gather_stuff_for_prepair
473		!! do_prepair_loop_if_needed
474		!! if_mpi_scatter_stuff_from_prepair
475		!! if_mpi_gather_stuff_from_prepair_to_main_loop
476	<	else
477	<	!! See if we need to update neighbor lists
478	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
476	>
477	>	!--------------------PREFORCE LOOP----------->>>>>>>>>>>>>>>>>>>>>>>>>>>
478	>	#ifdef IS_MPI
479	>
480	>	if (update_nlist) then
481	>
482	>	!! save current configuration, construct neighbor list,
483	>	!! and calculate forces
484	>
485	>	call saveNeighborList(nGroup, q_group)
486	>
487	>	neighborListSize = size(list)
488	>	nlist = 0
489	>
490	>	do i = 1, nrow_group
491	>	point(i) = nlist + 1
492	>
493	>	do j = 1, ncol_group
494	>
495	>	call get_interatomic_vector(q_group_Row(:,i), &
496	>	q_group_Col(:,j), d_grp, rgrpsq)
497	>
498	>	if (rgrpsq < rlistsq) then
499	>	nlist = nlist + 1
500	>
501	>	if (nlist > neighborListSize) then
502	>	call expandNeighborList(nGroup, listerror)
503	>	if (listerror /= 0) then
504	>	error = -1
505	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
506	>	return
507	>	end if
508	>	neighborListSize = size(list)
509	>	endif
510	>
511	>	list(nlist) = j
512	>
513	>	do ia = groupStart(i), groupStart(i+1)-1
514	>	atom1 = groupList(ia)
515	>
516	>	prepair_inner1: do jb = groupStart(j), groupStart(j+1)-1
517	>	atom2 = groupList(jb)
518	>
519	>	if (skipThisPair(atom1, atom2)) cycle prepair_inner1
520	>
521	>	call get_interatomic_vector(q_Row(:,atom1), &
522	>	q_Col(:,atom2), d_atm, ratmsq)
523	>
524	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
525	>	rgrpsq, d_grp, do_pot, do_stress, &
526	>	u_l, A, f, t, pot_local)
527	>
528	>	enddo prepair_inner1
529	>	enddo
530	>	end if
531	>	enddo
532	>	enddo
533	>	point(nrow_group + 1) = nlist + 1
534	>
535	>	else  !! (of update_check)
536	>
537	>	! use the list to find the neighbors
538	>	do i = 1, nrow_group
539	>	JBEG = POINT(i)
540	>	JEND = POINT(i+1) - 1
541	>	! check that group i has neighbors
542	>	if (jbeg .le. jend) then
543	>
544	>	do jnab = jbeg, jend
545	>	j = list(jnab)
546	>
547	>	do ia = groupStart(i), groupStart(i+1)-1
548	>	atom1 = groupList(ia)
549	>
550	>	prepair_inner2: do jb = groupStart(j), groupStart(j+1)-1
551	>	atom2 = groupList(jb)
552	>
553	>	if (skipThisPair(atom1, atom2)) cycle prepair_inner2
554	>
555	>	call get_interatomic_vector(q_Row(:,atom1), &
556	>	q_Col(:,atom2), d_atm, ratmsq)
557	>
558	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
559	>	rgrpsq, d_grp, do_pot, do_stress, &
560	>	u_l, A, f, t, pot_local)
561	>
562	>	enddo prepair_inner2
563	>	enddo
564	>	enddo
565	>	endif
566	>	enddo
567	>	endif
568	>
569	>	#else
570	>
571	>	if (update_nlist) then
572	>
573	>	!! save current configuration, construct neighbor list,
574	>	!! and calculate forces
575	>
576	>	call saveNeighborList(nGroup, q_group)
577	>
578	>	neighborListSize = size(list)
579	>	nlist = 0
580	>
581	>	do i = 1, nGroup-1
582	>	point(i) = nlist + 1
583	>
584	>	do j = i+1, nGroup
585	>
586	>	call get_interatomic_vector(q_group(:,i), &
587	>	q_group(:,j), d_grp, rgrpsq)
588	>
589	>	if (rgrpsq < rlistsq) then
590	>	nlist = nlist + 1
591	>
592	>	if (nlist > neighborListSize) then
593	>	call expandNeighborList(nGroup, listerror)
594	>	if (listerror /= 0) then
595	>	error = -1
596	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
597	>	return
598	>	end if
599	>	neighborListSize = size(list)
600	>	endif
601	>
602	>	list(nlist) = j
603	>
604	>	do ia = groupStart(i), groupStart(i+1)-1
605	>	atom1 = groupList(ia)
606	>
607	>	prepair_inner1: do jb = groupStart(j), groupStart(j+1)-1
608	>	atom2 = groupList(jb)
609	>
610	>	if (skipThisPair(atom1, atom2)) cycle prepair_inner1
611	>
612	>	call get_interatomic_vector(q(:,atom1), &
613	>	q(:,atom2), d_atm, ratmsq)
614	>
615	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
616	>	rgrpsq, d_grp, do_pot, do_stress, &
617	>	u_l, A, f, t, pot)
618	>
619	>	enddo prepair_inner1
620	>	enddo
621	>	end if
622	>	enddo
623	>	enddo
624	>	point(nGroup) = nlist + 1
625	>
626	>	else  !! (of update_check)
627	>
628	>	! use the list to find the neighbors
629	>	do i = 1, nGroup-1
630	>	JBEG = POINT(i)
631	>	JEND = POINT(i+1) - 1
632	>	! check that group i has neighbors
633	>	if (jbeg .le. jend) then
634	>
635	>	do jnab = jbeg, jend
636	>	j = list(jnab)
637	>
638	>	do ia = groupStart(i), groupStart(i+1)-1
639	>	atom1 = groupList(ia)
640	>
641	>	prepair_inner2: do jb = groupStart(j), groupStart(j+1)-1
642	>	atom2 = groupList(jb)
643	>
644	>	if (skipThisPair(atom1, atom2)) cycle prepair_inner2
645	>
646	>	call get_interatomic_vector(q(:,atom1), &
647	>	q(:,atom2), d_atm, ratmsq)
648	>
649	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
650	>	rgrpsq, d_grp, do_pot, do_stress, &
651	>	u_l, A, f, t, pot)
652	>
653	>	enddo prepair_inner2
654	>	enddo
655	>	enddo
656	>	endif
657	>	enddo
658	>	endif
659	>
660	>	#endif
661	>
662	>	!! Do rest of preforce calculations
663	>	!! do necessary preforce calculations
664	>	call do_preforce(nlocal,pot)
665	>	! we have already updated the neighbor list set it to false...
666	>	update_nlist = .false.
667	>	else
668	>	!! See if we need to update neighbor lists for non pre-pair
669	>	call checkNeighborList(nGroup, q_group, listSkin, update_nlist)
670		endif
671
672	+	!---------------------------------MAIN Pair LOOP->>>>>>>>>>>>>
673	+
674		#ifdef IS_MPI
675
676		if (update_nlist) then
677
678		!! save current configuration, construct neighbor list,
679		!! and calculate forces
248	–	call saveNeighborList(q)
680
681	+	call saveNeighborList(nGroup, q_group)
682	+
683		neighborListSize = size(list)
684		nlist = 0
685
686	<	do i = 1, nrow
686	>	do i = 1, nrow_group
687	>
688		point(i) = nlist + 1
689	+
690	+	n_in_i = groupStart(i+1) - groupStart(i)
691
692	<	inner: do j = 1, ncol
692	>	do j = 1, ncol_group
693
694	<	if (skipThisPair(i,j)) cycle inner
694	>	call get_interatomic_vector(q_group_Row(:,i), &
695	>	q_group_Col(:,j), d_grp, rgrpsq)
696
697	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
261	<
262	<	if (rijsq <  rlistsq) then
263	<
697	>	if (rgrpsq < rlistsq) then
698		nlist = nlist + 1
699
700		if (nlist > neighborListSize) then
701	<	call expandNeighborList(nlocal, listerror)
701	>	call expandNeighborList(nGroup, listerror)
702		if (listerror /= 0) then
703		error = -1
704		write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
#	Line 274 | Line 708 | contains
708		endif
709
710		list(nlist) = j
711	<
712	<	if (rijsq <  rcutsq) then
713	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
714	<	u_l, A, f, t,pot)
711	>
712	>	vij = 0.0d0
713	>
714	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
715	>	in_switching_region)
716	>
717	>	n_in_j = groupStart(j+1) - groupStart(j)
718	>
719	>	do ia = groupStart(i), groupStart(i+1)-1
720	>	atom1 = groupList(ia)
721	>
722	>	inner1: do jb = groupStart(j), groupStart(j+1)-1
723	>	atom2 = groupList(jb)
724	>
725	>	if (skipThisPair(atom1, atom2)) cycle inner1
726	>
727	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
728	>	d_atm(1:3) = d_grp(1:3)
729	>	ratmsq = rgrpsq
730	>	else
731	>	call get_interatomic_vector(q_Row(:,atom1), &
732	>	q_Col(:,atom2), d_atm, ratmsq)
733	>	endif
734	>
735	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
736	>	do_pot, do_stress, &
737	>	u_l, A, f, t, pot_local, vpair)
738	>
739	>	vij = vij + vpair
740	>	enddo inner1
741	>	enddo
742	>
743	>	if (in_switching_region) then
744	>	swderiv = vij*dswdr/rgrp
745	>
746	>	do ia=groupStart(i), groupStart(i+1)-1
747	>	atom1=groupList(ia)
748	>	mf = mfact(atom1)
749	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
750	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
751	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
752	>	enddo
753	>
754	>	do jb=groupStart(j), groupStart(j+1)-1
755	>	atom2=groupList(jb)
756	>	mf = mfact(atom2)
757	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
758	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
759	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
760	>	enddo
761		endif
762	<	endif
763	<	enddo inner
762	>
763	>	end if
764	>	enddo
765		enddo
766
767	<	point(nrow + 1) = nlist + 1
767	>	point(nrow_group + 1) = nlist + 1
768
769		else  !! (of update_check)
770	<
770	>
771		! use the list to find the neighbors
772	<	do i = 1, nrow
772	>	do i = 1, nrow_group
773	>
774	>	n_in_i = groupStart(i+1) - groupStart(i)
775	>
776		JBEG = POINT(i)
777		JEND = POINT(i+1) - 1
778	<	! check thiat molecule i has neighbors
778	>	! check that group i has neighbors
779		if (jbeg .le. jend) then
780
781		do jnab = jbeg, jend
782		j = list(jnab)
783	+
784	+	call get_interatomic_vector(q_group_Row(:,i), &
785	+	q_group_Col(:,j), d_grp, rgrpsq)
786	+
787	+	vij = 0.0d0
788	+	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
789	+	in_switching_region)
790	+
791	+	n_in_j = groupStart(j+1) - groupStart(j)
792	+
793	+	do ia = groupStart(i), groupStart(i+1)-1
794	+	atom1 = groupList(ia)
795	+
796	+	inner2: do jb = groupStart(j), groupStart(j+1)-1
797	+	atom2 = groupList(jb)
798	+
799	+	if (skipThisPair(atom1, atom2)) cycle inner2
800
801	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
802	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
803	<	u_l, A, f, t,pot)
801	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
802	>	d_atm(1:3) = d_grp(1:3)
803	>	ratmsq = rgrpsq
804	>	else
805	>	call get_interatomic_vector(q_Row(:,atom1), &
806	>	q_Col(:,atom2), d_atm, ratmsq)
807	>	endif
808	>
809	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
810	>	do_pot, do_stress, &
811	>	u_l, A, f, t, pot_local, vpair)
812	>
813	>	vij = vij + vpair
814	>
815	>	enddo inner2
816	>	enddo
817	>
818	>	if (in_switching_region) then
819	>	swderiv = vij*dswdr/rgrp
820	>
821	>	do ia=groupStart(i), groupStart(i+1)-1
822	>	atom1=groupList(ia)
823	>	mf = mfact(atom1)
824	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
825	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
826	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
827	>	enddo
828	>
829	>	do jb=groupStart(j), groupStart(j+1)-1
830	>	atom2=groupList(jb)
831	>	mf = mfact(atom2)
832	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
833	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
834	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
835	>	enddo
836	>	endif
837
838		enddo
839		endif
#	Line 307 | Line 841 | contains
841		endif
842
843		#else
844	<
844	>
845		if (update_nlist) then
846
847	<	! save current configuration, contruct neighbor list,
848	<	! and calculate forces
315	<	call saveNeighborList(q)
847	>	!! save current configuration, construct neighbor list,
848	>	!! and calculate forces
849
850	+	call saveNeighborList(nGroup, q_group)
851	+
852		neighborListSize = size(list)
853	<
319	<	nlist = 0
853	>	nlist = 0
854
855	<	do i = 1, natoms-1
855	>	do i = 1, nGroup-1
856	>
857		point(i) = nlist + 1
858	+	n_in_i = groupStart(i+1) - groupStart(i)
859
860	<	inner: do j = i+1, natoms
860	>	do j = i+1, nGroup
861
862	<	if (skipThisPair(i,j))  cycle inner
863	<
864	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
865	<
330	<
331	<	if (rijsq <  rlistsq) then
332	<
862	>	call get_interatomic_vector(q_group(:,i), &
863	>	q_group(:,j), d_grp, rgrpsq)
864	>
865	>	if (rgrpsq < rlistsq) then
866		nlist = nlist + 1
867	<
867	>
868		if (nlist > neighborListSize) then
869	<	call expandNeighborList(natoms, listerror)
869	>	call expandNeighborList(nGroup, listerror)
870		if (listerror /= 0) then
871		error = -1
872		write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
#	Line 343 | Line 876 | contains
876		endif
877
878		list(nlist) = j
879	+
880	+	vij = 0.0d0
881	+
882	+	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
883	+	in_switching_region)
884
885	<	if (rijsq <  rcutsq) then
886	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
887	<	u_l, A, f, t,pot)
885	>	n_in_j = groupStart(j+1) - groupStart(j)
886	>
887	>	do ia = groupStart(i), groupStart(i+1)-1
888	>	atom1 = groupList(ia)
889	>
890	>	inner1: do jb = groupStart(j), groupStart(j+1)-1
891	>	atom2 = groupList(jb)
892	>
893	>	if (skipThisPair(atom1, atom2)) cycle inner1
894	>
895	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
896	>	d_atm(1:3) = d_grp(1:3)
897	>	ratmsq = rgrpsq
898	>	else
899	>	call get_interatomic_vector(q(:,atom1), &
900	>	q(:,atom2), d_atm, ratmsq)
901	>	endif
902	>
903	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
904	>	do_pot, do_stress, &
905	>	u_l, A, f, t, pot, vpair)
906	>
907	>	vij = vij + vpair
908	>
909	>	enddo inner1
910	>	enddo
911	>
912	>	if (in_switching_region) then
913	>	swderiv = vij*dswdr/rgrp
914	>	do ia=groupStart(i), groupStart(i+1)-1
915	>	atom1=groupList(ia)
916	>	mf = mfact(atom1)
917	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
918	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
919	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
920	>	enddo
921	>
922	>	do jb=groupStart(j), groupStart(j+1)-1
923	>	atom2=groupList(jb)
924	>	mf = mfact(atom2)
925	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
926	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
927	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
928	>	enddo
929		endif
930	<	endif
931	<	enddo inner
930	>
931	>	end if
932	>	enddo
933		enddo
934	+	point(nGroup) = nlist + 1
935
936	<	point(natoms) = nlist + 1
936	>	else  !! (of update_check)
937
357	–	else !! (update)
358	–
938		! use the list to find the neighbors
939	<	do i = 1, natoms-1
939	>	do i = 1, nGroup-1
940	>
941	>	n_in_i = groupStart(i+1) - groupStart(i)
942	>
943		JBEG = POINT(i)
944		JEND = POINT(i+1) - 1
945	<	! check thiat molecule i has neighbors
945	>	! check that group i has neighbors
946		if (jbeg .le. jend) then
947
948		do jnab = jbeg, jend
949		j = list(jnab)
950	+
951	+	call get_interatomic_vector(q_group(:,i), &
952	+	q_group(:,j), d_grp, rgrpsq)
953
954	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
955	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
956	<	u_l, A, f, t,pot)
954	>	vij = 0.0d0
955	>
956	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
957	>	in_switching_region)
958	>
959	>	n_in_j = groupStart(j+1) - groupStart(j)
960	>
961	>	do ia = groupStart(i), groupStart(i+1)-1
962	>	atom1 = groupList(ia)
963	>
964	>	inner2: do jb = groupStart(j), groupStart(j+1)-1
965	>	atom2 = groupList(jb)
966
967	+	if (skipThisPair(atom1, atom2)) cycle inner2
968	+
969	+	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
970	+	d_atm(1:3) = d_grp(1:3)
971	+	ratmsq = rgrpsq
972	+	else
973	+	call get_interatomic_vector(q(:,atom1), &
974	+	q(:,atom2), d_atm, ratmsq)
975	+	endif
976	+
977	+	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
978	+	do_pot, do_stress, &
979	+	u_l, A, f, t, pot, vpair)
980	+
981	+	vij = vij + vpair
982	+
983	+	enddo inner2
984	+	enddo
985	+
986	+	if (in_switching_region) then
987	+	swderiv = vij*dswdr/rgrp
988	+
989	+	do ia=groupStart(i), groupStart(i+1)-1
990	+	atom1=groupList(ia)
991	+	mf = mfact(atom1)
992	+	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
993	+	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
994	+	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
995	+	enddo
996	+
997	+	do jb=groupStart(j), groupStart(j+1)-1
998	+	atom2=groupList(jb)
999	+	mf = mfact(atom2)
1000	+	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
1001	+	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
1002	+	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
1003	+	enddo
1004	+	endif
1005		enddo
1006		endif
1007		enddo
#	Line 379 | Line 1011 | contains
1011
1012		! phew, done with main loop.
1013
1014	+	!! Do timing
1015	+	#ifdef PROFILE
1016	+	call cpu_time(forceTimeFinal)
1017	+	forceTime = forceTime + forceTimeFinal - forceTimeInitial
1018	+	#endif
1019	+
1020		#ifdef IS_MPI
1021		!!distribute forces
1022	<
1022	>
1023		f_temp = 0.0_dp
1024		call scatter(f_Row,f_temp,plan_row3d)
1025		do i = 1,nlocal
1026		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
1027		end do
1028	<
1028	>
1029		f_temp = 0.0_dp
1030		call scatter(f_Col,f_temp,plan_col3d)
1031		do i = 1,nlocal
1032		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
1033		end do
1034
1035	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
1035	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
1036		t_temp = 0.0_dp
1037		call scatter(t_Row,t_temp,plan_row3d)
1038		do i = 1,nlocal
#	Line 417 | Line 1055 | contains
1055		do i = 1, nlocal
1056		pot_local = pot_local + pot_Temp(i)
1057		enddo
1058	<
1059	<	pot_Temp = 0.0_DP
1060	<
1058	>
1059	>	pot_Temp = 0.0_DP
1060	>
1061		call scatter(pot_Col, pot_Temp, plan_col)
1062		do i = 1, nlocal
1063		pot_local = pot_local + pot_Temp(i)
1064		enddo
1065
1066	<	endif
1066	>	endif
1067		#endif
1068	<
1069	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
1068	>
1069	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
1070
1071	<	if (FF_uses_RF .and. SimUsesRF()) then
1071	>	if (FF_uses_RF .and. SIM_uses_RF) then
1072
1073		#ifdef IS_MPI
1074		call scatter(rf_Row,rf,plan_row3d)
#	Line 440 | Line 1078 | contains
1078		end do
1079		#endif
1080
1081	<	do i = 1, getNlocal()
1082	<
1081	>	do i = 1, nLocal
1082	>
1083		rfpot = 0.0_DP
1084		#ifdef IS_MPI
1085		me_i = atid_row(i)
1086		#else
1087		me_i = atid(i)
1088		#endif
1089	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
1090	<	if ( is_DP_i ) then
1091	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
1089	>
1090	>	if (PropertyMap(me_i)%is_DP) then
1091	>
1092	>	mu_i = PropertyMap(me_i)%dipole_moment
1093	>
1094		!! The reaction field needs to include a self contribution
1095		!! to the field:
1096	<	call accumulate_self_rf(i, mu_i, u_l)
1096	>	call accumulate_self_rf(i, mu_i, u_l)
1097		!! Get the reaction field contribution to the
1098		!! potential and torques:
1099		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 467 | Line 1107 | contains
1107		enddo
1108		endif
1109		endif
1110	<
1111	<
1110	>
1111	>
1112		#ifdef IS_MPI
1113	<
1113	>
1114		if (do_pot) then
1115	<	write(*,*) "Fortran is on pot:, pot, pot_local ", pot,pot_local
476	<	pot = pot_local
1115	>	pot = pot + pot_local
1116		!! we assume the c code will do the allreduce to get the total potential
1117		!! we could do it right here if we needed to...
1118		endif
1119	<
1119	>
1120		if (do_stress) then
1121	<	call mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, &
1121	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
1122		mpi_comm_world,mpi_err)
1123	<	call mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, &
1123	>	call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
1124		mpi_comm_world,mpi_err)
1125		endif
1126	<
1126	>
1127		#else
1128	<
1128	>
1129		if (do_stress) then
1130		tau = tau_Temp
1131		virial = virial_Temp
1132		endif
1133	<
1133	>
1134		#endif
1135
1136	+
1137		end subroutine do_force_loop
1138
1139	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t,pot)
1139	>
1140	>	subroutine do_pair(i, j, rijsq, d, sw, do_pot, do_stress, &
1141	>	u_l, A, f, t, pot, vpair)
1142
1143	<	real( kind = dp ) :: pot
1144	<	real( kind = dp ), dimension(:,:) :: u_l
1145	<	real (kind=dp), dimension(:,:) :: A
1146	<	real (kind=dp), dimension(:,:) :: f
1147	<	real (kind=dp), dimension(:,:) :: t
1143	>	real( kind = dp ) :: pot, vpair, sw
1144	>	real( kind = dp ), dimension(nLocal)   :: mfact
1145	>	real( kind = dp ), dimension(3,nLocal) :: u_l
1146	>	real( kind = dp ), dimension(9,nLocal) :: A
1147	>	real( kind = dp ), dimension(3,nLocal) :: f
1148	>	real( kind = dp ), dimension(3,nLocal) :: t
1149
1150		logical, intent(inout) :: do_pot, do_stress
1151		integer, intent(in) :: i, j
1152	<	real ( kind = dp ), intent(inout)    :: rijsq
1152	>	real ( kind = dp ), intent(inout) :: rijsq
1153		real ( kind = dp )                :: r
1154		real ( kind = dp ), intent(inout) :: d(3)
512	–	logical :: is_LJ_i, is_LJ_j
513	–	logical :: is_DP_i, is_DP_j
514	–	logical :: is_GB_i, is_GB_j
515	–	logical :: is_Sticky_i, is_Sticky_j
1155		integer :: me_i, me_j
1156
1157		r = sqrt(rijsq)
1158	+	vpair = 0.0d0
1159
1160		#ifdef IS_MPI
1161	<
1161	>	if (tagRow(i) .eq. tagColumn(j)) then
1162	>	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
1163	>	endif
1164		me_i = atid_row(i)
1165		me_j = atid_col(j)
524	–
1166		#else
526	–
1167		me_i = atid(i)
1168		me_j = atid(j)
529	–
1169		#endif
1170	+
1171	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
1172	+
1173	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
1174	+	!write(*,*) 'calling lj with'
1175	+	!write(*,*) i, j, r, rijsq
1176	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
1177	+	!write(*,'(3es12.3)') sw, vpair, pot
1178	+	!write(*,*)
1179
1180	<	if (FF_uses_LJ .and. SimUsesLJ()) then
1181	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
1182	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
1183	<
536	<	if ( is_LJ_i .and. is_LJ_j ) &
537	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
1180	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, pot, f, do_pot, &
1181	>	do_stress)
1182	>	endif
1183	>
1184		endif
1185	<
1186	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
541	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
542	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
1185	>
1186	>	if (FF_uses_charges .and. SIM_uses_charges) then
1187
1188	<	if ( is_DP_i .and. is_DP_j ) then
1189	<
1190	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
1188	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
1189	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, pot, f, do_pot, &
1190	>	do_stress)
1191	>	endif
1192	>
1193	>	endif
1194	>
1195	>	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
1196	>
1197	>	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
1198	>	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, pot, u_l, f, t, &
1199		do_pot, do_stress)
1200	<	if (FF_uses_RF .and. SimUsesRF()) then
1201	<	call accumulate_rf(i, j, r, u_l)
1202	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
1203	<	endif
552	<
1200	>	if (FF_uses_RF .and. SIM_uses_RF) then
1201	>	call accumulate_rf(i, j, r, u_l, sw)
1202	>	call rf_correct_forces(i, j, d, r, u_l, sw, f, do_stress)
1203	>	endif
1204		endif
1205	+
1206		endif
1207
1208	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
1208	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
1209
1210	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
1211	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
560	<
561	<	if ( is_Sticky_i .and. is_Sticky_j ) then
562	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
1210	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
1211	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, pot, A, f, t, &
1212		do_pot, do_stress)
1213		endif
1214	+
1215		endif
1216
1217
1218	<	if (FF_uses_GB .and. SimUsesGB()) then
569	<
570	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
571	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
1218	>	if (FF_uses_GB .and. SIM_uses_GB) then
1219
1220	<	if ( is_GB_i .and. is_GB_j ) then
1221	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
1220	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
1221	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, pot, u_l, f, t, &
1222		do_pot, do_stress)
1223		endif
577	–	endif
578	–
579	–	end subroutine do_pair
1224
1225	<
582	<	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
583	<
584	<	real (kind = dp), dimension(3) :: q_i
585	<	real (kind = dp), dimension(3) :: q_j
586	<	real ( kind = dp ), intent(out) :: r_sq
587	<	real( kind = dp ) :: d(3)
588	<	real( kind = dp ) :: d_old(3)
589	<	d(1:3) = q_i(1:3) - q_j(1:3)
590	<	d_old = d
591	<	! Wrap back into periodic box if necessary
592	<	if ( SimUsesPBC() ) then
1225	>	endif
1226
1227	<	d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,d(1:3)) * &
595	<	int(abs(d(1:3)/box(1:3)) + 0.5_dp)
1227	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1228
1229	+	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
1230	+	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, pot, f, &
1231	+	do_pot, do_stress)
1232	+	endif
1233	+
1234		endif
598	–	r_sq = dot_product(d,d)
599	–
600	–	end subroutine get_interatomic_vector
601	–
602	–	subroutine check_initialization(error)
603	–	integer, intent(out) :: error
1235
1236	<	error = 0
1237	<	! Make sure we are properly initialized.
1238	<	if (.not. do_forces_initialized) then
1239	<	error = -1
1240	<	return
1236	>	end subroutine do_pair
1237	>
1238	>	subroutine do_prepair(i, j, rijsq, d, rcijsq, dc, &
1239	>	do_pot, do_stress, u_l, A, f, t, pot)
1240	>	real( kind = dp ) :: pot
1241	>	real( kind = dp ), dimension(3,nLocal) :: u_l
1242	>	real (kind=dp), dimension(9,nLocal) :: A
1243	>	real (kind=dp), dimension(3,nLocal) :: f
1244	>	real (kind=dp), dimension(3,nLocal) :: t
1245	>
1246	>	logical, intent(inout) :: do_pot, do_stress
1247	>	integer, intent(in) :: i, j
1248	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
1249	>	real ( kind = dp )                :: r, rc
1250	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
1251	>
1252	>	logical :: is_EAM_i, is_EAM_j
1253	>
1254	>	integer :: me_i, me_j
1255	>
1256	>
1257	>	r = sqrt(rijsq)
1258	>	if (SIM_uses_molecular_cutoffs) then
1259	>	rc = sqrt(rcijsq)
1260	>	else
1261	>	rc = r
1262		endif
1263	+
1264
1265		#ifdef IS_MPI
1266	<	if (.not. isMPISimSet()) then
1267	<	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
1268	<	error = -1
1269	<	return
1270	<	endif
1266	>	if (tagRow(i) .eq. tagColumn(j)) then
1267	>	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
1268	>	endif
1269	>
1270	>	me_i = atid_row(i)
1271	>	me_j = atid_col(j)
1272	>
1273	>	#else
1274	>
1275	>	me_i = atid(i)
1276	>	me_j = atid(j)
1277	>
1278		#endif
1279
1280	<	return
621	<	end subroutine check_initialization
1280	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1281
1282	<
1283	<	subroutine zero_work_arrays()
1284	<
1285	<	#ifdef IS_MPI
1286	<
1287	<	q_Row = 0.0_dp
1288	<	q_Col = 0.0_dp
1289	<
1290	<	u_l_Row = 0.0_dp
1291	<	u_l_Col = 0.0_dp
1292	<
1293	<	A_Row = 0.0_dp
1294	<	A_Col = 0.0_dp
1295	<
1296	<	f_Row = 0.0_dp
1297	<	f_Col = 0.0_dp
1298	<	f_Temp = 0.0_dp
1282	>	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
1283	>	call calc_EAM_prepair_rho(i, j, d, r, rijsq )
1284	>
1285	>	endif
1286	>
1287	>	end subroutine do_prepair
1288	>
1289	>
1290	>
1291	>
1292	>	subroutine do_preforce(nlocal,pot)
1293	>	integer :: nlocal
1294	>	real( kind = dp ) :: pot
1295	>
1296	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1297	>	call calc_EAM_preforce_Frho(nlocal,pot)
1298	>	endif
1299	>
1300	>
1301	>	end subroutine do_preforce
1302	>
1303	>
1304	>	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
1305	>
1306	>	real (kind = dp), dimension(3) :: q_i
1307	>	real (kind = dp), dimension(3) :: q_j
1308	>	real ( kind = dp ), intent(out) :: r_sq
1309	>	real( kind = dp ) :: d(3), scaled(3)
1310	>	integer i
1311	>
1312	>	d(1:3) = q_j(1:3) - q_i(1:3)
1313	>
1314	>	! Wrap back into periodic box if necessary
1315	>	if ( SIM_uses_PBC ) then
1316
1317	<	t_Row = 0.0_dp
1318	<	t_Col = 0.0_dp
1319	<	t_Temp = 0.0_dp
1317	>	if( .not.boxIsOrthorhombic ) then
1318	>	! calc the scaled coordinates.
1319	>
1320	>	scaled = matmul(HmatInv, d)
1321	>
1322	>	! wrap the scaled coordinates
1323	>
1324	>	scaled = scaled  - anint(scaled)
1325	>
1326	>
1327	>	! calc the wrapped real coordinates from the wrapped scaled
1328	>	! coordinates
1329	>
1330	>	d = matmul(Hmat,scaled)
1331	>
1332	>	else
1333	>	! calc the scaled coordinates.
1334	>
1335	>	do i = 1, 3
1336	>	scaled(i) = d(i) * HmatInv(i,i)
1337	>
1338	>	! wrap the scaled coordinates
1339	>
1340	>	scaled(i) = scaled(i) - anint(scaled(i))
1341	>
1342	>	! calc the wrapped real coordinates from the wrapped scaled
1343	>	! coordinates
1344	>
1345	>	d(i) = scaled(i)*Hmat(i,i)
1346	>	enddo
1347	>	endif
1348	>
1349	>	endif
1350	>
1351	>	r_sq = dot_product(d,d)
1352	>
1353	>	end subroutine get_interatomic_vector
1354
1355	<	pot_Row = 0.0_dp
1356	<	pot_Col = 0.0_dp
1357	<	pot_Temp = 0.0_dp
1355	>	subroutine zero_work_arrays()
1356	>
1357	>	#ifdef IS_MPI
1358	>
1359	>	q_Row = 0.0_dp
1360	>	q_Col = 0.0_dp
1361
1362	<	rf_Row = 0.0_dp
1363	<	rf_Col = 0.0_dp
1364	<	rf_Temp = 0.0_dp
1365	<
1362	>	q_group_Row = 0.0_dp
1363	>	q_group_Col = 0.0_dp
1364	>
1365	>	u_l_Row = 0.0_dp
1366	>	u_l_Col = 0.0_dp
1367	>
1368	>	A_Row = 0.0_dp
1369	>	A_Col = 0.0_dp
1370	>
1371	>	f_Row = 0.0_dp
1372	>	f_Col = 0.0_dp
1373	>	f_Temp = 0.0_dp
1374	>
1375	>	t_Row = 0.0_dp
1376	>	t_Col = 0.0_dp
1377	>	t_Temp = 0.0_dp
1378	>
1379	>	pot_Row = 0.0_dp
1380	>	pot_Col = 0.0_dp
1381	>	pot_Temp = 0.0_dp
1382	>
1383	>	rf_Row = 0.0_dp
1384	>	rf_Col = 0.0_dp
1385	>	rf_Temp = 0.0_dp
1386	>
1387		#endif
1388	<
1389	<	rf = 0.0_dp
1390	<	tau_Temp = 0.0_dp
1391	<	virial_Temp = 0.0_dp
1392	<
1393	<	end subroutine zero_work_arrays
1394	<
1395	<	function skipThisPair(atom1, atom2) result(skip_it)
1396	<	integer, intent(in) :: atom1
1397	<	integer, intent(in), optional :: atom2
1398	<	logical :: skip_it
1399	<	integer :: unique_id_1, unique_id_2
1400	<	integer :: me_i,me_j
1401	<	integer :: i
1402	<
1403	<	skip_it = .false.
1404	<
1405	<	!! there are a number of reasons to skip a pair or a particle
1406	<	!! mostly we do this to exclude atoms who are involved in short
1407	<	!! range interactions (bonds, bends, torsions), but we also need
1408	<	!! to exclude some overcounted interactions that result from
1409	<	!! the parallel decomposition
1410	<
1388	>
1389	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1390	>	call clean_EAM()
1391	>	endif
1392	>
1393	>	rf = 0.0_dp
1394	>	tau_Temp = 0.0_dp
1395	>	virial_Temp = 0.0_dp
1396	>	end subroutine zero_work_arrays
1397	>
1398	>	function skipThisPair(atom1, atom2) result(skip_it)
1399	>	integer, intent(in) :: atom1
1400	>	integer, intent(in), optional :: atom2
1401	>	logical :: skip_it
1402	>	integer :: unique_id_1, unique_id_2
1403	>	integer :: me_i,me_j
1404	>	integer :: i
1405	>
1406	>	skip_it = .false.
1407	>
1408	>	!! there are a number of reasons to skip a pair or a particle
1409	>	!! mostly we do this to exclude atoms who are involved in short
1410	>	!! range interactions (bonds, bends, torsions), but we also need
1411	>	!! to exclude some overcounted interactions that result from
1412	>	!! the parallel decomposition
1413	>
1414		#ifdef IS_MPI
1415	<	!! in MPI, we have to look up the unique IDs for each atom
1416	<	unique_id_1 = tagRow(atom1)
1415	>	!! in MPI, we have to look up the unique IDs for each atom
1416	>	unique_id_1 = tagRow(atom1)
1417		#else
1418	<	!! in the normal loop, the atom numbers are unique
1419	<	unique_id_1 = atom1
1418	>	!! in the normal loop, the atom numbers are unique
1419	>	unique_id_1 = atom1
1420		#endif
1421	<
1422	<	!! We were called with only one atom, so just check the global exclude
1423	<	!! list for this atom
1424	<	if (.not. present(atom2)) then
1425	<	do i = 1, nExcludes_global
1426	<	if (excludesGlobal(i) == unique_id_1) then
1427	<	skip_it = .true.
1428	<	return
1429	<	end if
1430	<	end do
1431	<	return
1432	<	end if
1433	<
1421	>
1422	>	!! We were called with only one atom, so just check the global exclude
1423	>	!! list for this atom
1424	>	if (.not. present(atom2)) then
1425	>	do i = 1, nExcludes_global
1426	>	if (excludesGlobal(i) == unique_id_1) then
1427	>	skip_it = .true.
1428	>	return
1429	>	end if
1430	>	end do
1431	>	return
1432	>	end if
1433	>
1434		#ifdef IS_MPI
1435	<	unique_id_2 = tagColumn(atom2)
1435	>	unique_id_2 = tagColumn(atom2)
1436		#else
1437	<	unique_id_2 = atom2
1437	>	unique_id_2 = atom2
1438		#endif
1439	<
1439	>
1440		#ifdef IS_MPI
1441	<	!! this situation should only arise in MPI simulations
1442	<	if (unique_id_1 == unique_id_2) then
1443	<	skip_it = .true.
1444	<	return
1445	<	end if
1446	<
1447	<	!! this prevents us from doing the pair on multiple processors
1448	<	if (unique_id_1 < unique_id_2) then
1449	<	if (mod(unique_id_1 + unique_id_2,2) == 0) skip_it = .true.
1450	<	return
1451	<	else
1452	<	if (mod(unique_id_1 + unique_id_2,2) == 1) skip_it = .true.
1453	<	return
1454	<	endif
1441	>	!! this situation should only arise in MPI simulations
1442	>	if (unique_id_1 == unique_id_2) then
1443	>	skip_it = .true.
1444	>	return
1445	>	end if
1446	>
1447	>	!! this prevents us from doing the pair on multiple processors
1448	>	if (unique_id_1 < unique_id_2) then
1449	>	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1450	>	skip_it = .true.
1451	>	return
1452	>	endif
1453	>	else
1454	>	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1455	>	skip_it = .true.
1456	>	return
1457	>	endif
1458	>	endif
1459		#endif
1460	<
1461	<	!! the rest of these situations can happen in all simulations:
1462	<	do i = 1, nExcludes_global
1463	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1464	<	(excludesGlobal(i) == unique_id_2)) then
1465	<	skip_it = .true.
1466	<	return
1467	<	endif
1468	<	enddo
1460	>
1461	>	!! the rest of these situations can happen in all simulations:
1462	>	do i = 1, nExcludes_global
1463	>	if ((excludesGlobal(i) == unique_id_1) .or. &
1464	>	(excludesGlobal(i) == unique_id_2)) then
1465	>	skip_it = .true.
1466	>	return
1467	>	endif
1468	>	enddo
1469	>
1470	>	do i = 1, nSkipsForAtom(unique_id_1)
1471	>	if (skipsForAtom(unique_id_1, i) .eq. unique_id_2) then
1472	>	skip_it = .true.
1473	>	return
1474	>	endif
1475	>	end do
1476	>
1477	>	return
1478	>	end function skipThisPair
1479
1480	<	do i = 1, nExcludes_local
1481	<	if (excludesLocal(1,i) == unique_id_1) then
1482	<	if (excludesLocal(2,i) == unique_id_2) then
1483	<	skip_it = .true.
1484	<	return
1485	<	endif
1486	<	else
1487	<	if (excludesLocal(1,i) == unique_id_2) then
1488	<	if (excludesLocal(2,i) == unique_id_1) then
1489	<	skip_it = .true.
1490	<	return
1491	<	endif
1492	<	endif
1493	<	endif
1494	<	end do
1495	<
1496	<	return
1497	<	end function skipThisPair
1498	<
1499	<	function FF_UsesDirectionalAtoms() result(doesit)
1500	<	logical :: doesit
1501	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1502	<	FF_uses_GB .or. FF_uses_RF
1503	<	end function FF_UsesDirectionalAtoms
1504	<
754	<	function FF_RequiresPrepairCalc() result(doesit)
755	<	logical :: doesit
756	<	doesit = FF_uses_EAM
757	<	end function FF_RequiresPrepairCalc
758	<
759	<	function FF_RequiresPostpairCalc() result(doesit)
760	<	logical :: doesit
761	<	doesit = FF_uses_RF
762	<	end function FF_RequiresPostpairCalc
763	<
1480	>	function FF_UsesDirectionalAtoms() result(doesit)
1481	>	logical :: doesit
1482	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1483	>	FF_uses_GB .or. FF_uses_RF
1484	>	end function FF_UsesDirectionalAtoms
1485	>
1486	>	function FF_RequiresPrepairCalc() result(doesit)
1487	>	logical :: doesit
1488	>	doesit = FF_uses_EAM
1489	>	end function FF_RequiresPrepairCalc
1490	>
1491	>	function FF_RequiresPostpairCalc() result(doesit)
1492	>	logical :: doesit
1493	>	doesit = FF_uses_RF
1494	>	end function FF_RequiresPostpairCalc
1495	>
1496	>	#ifdef PROFILE
1497	>	function getforcetime() result(totalforcetime)
1498	>	real(kind=dp) :: totalforcetime
1499	>	totalforcetime = forcetime
1500	>	end function getforcetime
1501	>	#endif
1502	>
1503	>	!! This cleans componets of force arrays belonging only to fortran
1504	>
1505		end module do_Forces

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