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Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 650 by chuckv, Thu Jul 24 19:57:35 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.25 2003-07-24 19:57:35 chuckv Exp $, $Date: 2003-07-24 19:57:35 $, $Name: not supported by cvs2svn $, $Revision: 1.25 $
7	>	!! @version $Id: do_Forces.F90,v 1.56 2004-05-12 14:29:24 gezelter Exp $, $Date: 2004-05-12 14:29:24 $, $Name: not supported by cvs2svn $, $Revision: 1.56 $
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 28 | Line 31 | module do_Forces
31
32		#define __FORTRAN90
33		#include "fForceField.h"
34	+	#include "fSwitchingFunction.h"
35
36	<	logical, save :: do_forces_initialized = .false., haveRlist = .false.
36	>	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
#	Line 44 | Line 65 | contains
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 )
#	Line 54 | Line 95 | contains
95		rlistsq = rlist * rlist
96
97		haveRlist = .true.
57	–	if( havePolicies ) do_forces_initialized = .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 82 | 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 102 | 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
#	Line 113 | Line 292 | contains
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
#	Line 127 | Line 307 | contains
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. do_forces_initialized) then
352	>	if (.not. haveNeighborList) then
353		!! Create neighbor lists
354	<	call expandNeighborList(getNlocal(), my_status)
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	<	havePolicies = .true.
364	<	if( haveRlist ) do_forces_initialized = .true.
168	<
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)
372	<	!! Position array provided by C, dimensioned by getNlocal
373	<	real ( kind = dp ), dimension(3,getNlocal()) :: q
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,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	+	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
197	–	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
406	<	real(kind=dp),dimension(3) :: d
405	>	real( kind = DP ) :: ratmsq, rgrpsq, rgrp, vpair, vab
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
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
416	>	real(kind=dp) :: listSkin = 1.0
417
213	–
418		!! initialize local variables
419	<
419	>
420		#ifdef IS_MPI
421		pot_local = 0.0_dp
218	–	nlocal = getNlocal()
422		nrow   = getNrow(plan_row)
423		ncol   = getNcol(plan_col)
424	+	nrow_group   = getNrowGroup(plan_row)
425	+	ncol_group   = getNcolGroup(plan_col)
426		#else
222	–	nlocal = getNlocal()
427		natoms = nlocal
428		#endif
429	<
430	<	call check_initialization(localError)
429	>
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 250 | 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, listSkin, 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	<
477	<	!--------------------PREFORCE LOOP----------->>>>>>>>>>>>>>>>>>>>>>>>>>>
476	>
477	>	!--------------------PREFORCE LOOP----------->>>>>>>>>>>>>>>>>>>>>>>>>>>
478		#ifdef IS_MPI
263	–
264	–	if (update_nlist) then
479
480	<	!! save current configuration, construct neighbor list,
267	<	!! and calculate forces
268	<	call saveNeighborList(nlocal, q)
269	<
270	<	neighborListSize = size(list)
271	<	nlist = 0
272	<
273	<	do i = 1, nrow
274	<	point(i) = nlist + 1
480	>	if (update_nlist) then
481
482	<	prepair_inner: do j = 1, ncol
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	<	if (skipThisPair(i,j)) cycle prepair_inner
279	<
280	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
281	<
282	<	if (rijsq < rlistsq) then
493	>	do j = 1, ncol_group
494
495	<	nlist = nlist + 1
495	>	call get_interatomic_vector(q_group_Row(:,i), &
496	>	q_group_Col(:,j), d_grp, rgrpsq)
497
498	<	if (nlist > neighborListSize) then
499	<	call expandNeighborList(nlocal, listerror)
500	<	if (listerror /= 0) then
501	<	error = -1
502	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
503	<	return
504	<	end if
505	<	neighborListSize = size(list)
506	<	endif
507	<
508	<	list(nlist) = j
509	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot_local)
510	<	endif
511	<	enddo prepair_inner
512	<	enddo
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	<	point(nrow + 1) = nlist + 1
517	<
518	<	else  !! (of update_check)
516	>	prepair_inner: do jb = groupStart(j), groupStart(j+1)-1
517	>	atom2 = groupList(jb)
518	>
519	>	if (skipThisPair(atom1, atom2)) cycle prepair_inner
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	<	! use the list to find the neighbors
529	<	do i = 1, nrow
530	<	JBEG = POINT(i)
531	<	JEND = POINT(i+1) - 1
532	<	! check thiat molecule i has neighbors
533	<	if (jbeg .le. jend) then
534	<
535	<	do jnab = jbeg, jend
536	<	j = list(jnab)
528	>	enddo prepair_inner
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	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
551	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
552	<	u_l, A, f, t, pot_local)
553	<
554	<	enddo
555	<	endif
556	<	enddo
557	<	endif
558	<
559	<	#else
560	<
561	<	if (update_nlist) then
550	>	do jb = groupStart(j), groupStart(j+1)-1
551	>	atom2 = groupList(jb)
552	>
553	>	call get_interatomic_vector(q_Row(:,atom1), &
554	>	q_Col(:,atom2), d_atm, ratmsq)
555	>
556	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
557	>	rgrpsq, d_grp, do_pot, do_stress, &
558	>	u_l, A, f, t, pot_local)
559	>
560	>	enddo
561	>	enddo
562	>	enddo
563	>	endif
564	>	enddo
565	>	endif
566
567	<	! save current configuration, contruct neighbor list,
568	<	! and calculate forces
569	<	call saveNeighborList(natoms, q)
332	<
333	<	neighborListSize = size(list)
334	<
335	<	nlist = 0
336	<
337	<	do i = 1, natoms-1
338	<	point(i) = nlist + 1
567	>	#else
568	>
569	>	if (update_nlist) then
570
571	<	prepair_inner: do j = i+1, natoms
571	>	!! save current configuration, construct neighbor list,
572	>	!! and calculate forces
573	>
574	>	call saveNeighborList(nGroup, q_group)
575	>
576	>	neighborListSize = size(list)
577	>	nlist = 0
578	>
579	>	do i = 1, nGroup-1
580	>	point(i) = nlist + 1
581
582	<	if (skipThisPair(i,j))  cycle prepair_inner
343	<
344	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
345	<
346	<
347	<	if (rijsq < rlistsq) then
582	>	do j = i+1, nGroup
583
584	<	nlist = nlist + 1
585	<
351	<	if (nlist > neighborListSize) then
352	<	call expandNeighborList(natoms, listerror)
353	<	if (listerror /= 0) then
354	<	error = -1
355	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
356	<	return
357	<	end if
358	<	neighborListSize = size(list)
359	<	endif
584	>	call get_interatomic_vector(q_group(:,i), &
585	>	q_group(:,j), d_grp, rgrpsq)
586
587	<	list(nlist) = j
587	>	if (rgrpsq < rlistsq) then
588	>	nlist = nlist + 1
589	>
590	>	if (nlist > neighborListSize) then
591	>	call expandNeighborList(nGroup, listerror)
592	>	if (listerror /= 0) then
593	>	error = -1
594	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
595	>	return
596	>	end if
597	>	neighborListSize = size(list)
598	>	endif
599	>
600	>	list(nlist) = j
601	>
602	>	do ia = groupStart(i), groupStart(i+1)-1
603	>	atom1 = groupList(ia)
604	>
605	>	prepair_inner: do jb = groupStart(j), groupStart(j+1)-1
606	>	atom2 = groupList(jb)
607	>
608	>	if (skipThisPair(atom1, atom2)) cycle prepair_inner
609	>
610	>	call get_interatomic_vector(q(:,atom1), &
611	>	q(:,atom2), d_atm, ratmsq)
612	>
613	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
614	>	rgrpsq, d_grp, do_pot, do_stress, &
615	>	u_l, A, f, t, pot)
616	>
617	>	enddo prepair_inner
618	>	enddo
619	>	end if
620	>	enddo
621	>	enddo
622	>	point(nGroup) = nlist + 1
623	>
624	>	else  !! (of update_check)
625	>
626	>	! use the list to find the neighbors
627	>	do i = 1, nGroup-1
628	>	JBEG = POINT(i)
629	>	JEND = POINT(i+1) - 1
630	>	! check that group i has neighbors
631	>	if (jbeg .le. jend) then
632
633	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
634	<	u_l, A, f, t, pot)
635	<
633	>	do jnab = jbeg, jend
634	>	j = list(jnab)
635	>
636	>	do ia = groupStart(i), groupStart(i+1)-1
637	>	atom1 = groupList(ia)
638	>
639	>	do jb = groupStart(j), groupStart(j+1)-1
640	>	atom2 = groupList(jb)
641	>
642	>	call get_interatomic_vector(q(:,atom1), &
643	>	q(:,atom2), d_atm, ratmsq)
644	>
645	>	call do_prepair(atom1, atom2, ratmsq, d_atm, &
646	>	rgrpsq, d_grp, do_pot, do_stress, &
647	>	u_l, A, f, t, pot)
648	>
649	>	enddo
650	>	enddo
651	>	enddo
652		endif
653	<	enddo prepair_inner
654	<	enddo
653	>	enddo
654	>	endif
655
370	–	point(natoms) = nlist + 1
371	–
372	–	else !! (update)
373	–
374	–	! use the list to find the neighbors
375	–	do i = 1, natoms-1
376	–	JBEG = POINT(i)
377	–	JEND = POINT(i+1) - 1
378	–	! check thiat molecule i has neighbors
379	–	if (jbeg .le. jend) then
380	–
381	–	do jnab = jbeg, jend
382	–	j = list(jnab)
383	–
384	–	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
385	–	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
386	–	u_l, A, f, t, pot)
387	–
388	–	enddo
389	–	endif
390	–	enddo
391	–	endif
656		#endif
657	<	!! Do rest of preforce calculations
658	<	call do_preforce(nlocal,pot)
657	>
658	>	!! Do rest of preforce calculations
659	>	!! do necessary preforce calculations
660	>	call do_preforce(nlocal,pot)
661	>	! we have already updated the neighbor list set it to false...
662	>	update_nlist = .false.
663		else
664		!! See if we need to update neighbor lists for non pre-pair
665	<	call checkNeighborList(nlocal, q, listSkin, update_nlist)
665	>	call checkNeighborList(nGroup, q_group, listSkin, update_nlist)
666		endif
667	<
668	<
669	<
402	<
403	<
404	<	!---------------------------------MAIN Pair LOOP->>>>>>>>>>>>>>>>>>>>>>>>>>>>
405	<
406	<
407	<
408	<
409	<
667	>
668	>	!---------------------------------MAIN Pair LOOP->>>>>>>>>>>>>
669	>
670		#ifdef IS_MPI
671
672		if (update_nlist) then
673
674		!! save current configuration, construct neighbor list,
675		!! and calculate forces
416	–	call saveNeighborList(nlocal, q)
676
677	+	call saveNeighborList(nGroup, q_group)
678	+
679		neighborListSize = size(list)
680		nlist = 0
681
682	<	do i = 1, nrow
682	>	do i = 1, nrow_group
683		point(i) = nlist + 1
684
685	<	inner: do j = 1, ncol
685	>	do j = 1, ncol_group
686
687	<	if (skipThisPair(i,j)) cycle inner
688	<
428	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
687	>	call get_interatomic_vector(q_group_Row(:,i), &
688	>	q_group_Col(:,j), d_grp, rgrpsq)
689
690	<	if (rijsq < rlistsq) then
431	<
690	>	if (rgrpsq < rlistsq) then
691		nlist = nlist + 1
692
693		if (nlist > neighborListSize) then
694	<	call expandNeighborList(nlocal, listerror)
694	>	call expandNeighborList(nGroup, listerror)
695		if (listerror /= 0) then
696		error = -1
697		write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
#	Line 442 | Line 701 | contains
701		endif
702
703		list(nlist) = j
445	–
446	–	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
447	–	u_l, A, f, t, pot_local)
704
705	<	endif
706	<	enddo inner
707	<	enddo
705	>	vab = 0.0d0
706	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
707	>	in_switching_region)
708	>
709	>	do ia = groupStart(i), groupStart(i+1)-1
710	>	atom1 = groupList(ia)
711	>
712	>	inner: do jb = groupStart(j), groupStart(j+1)-1
713	>	atom2 = groupList(jb)
714
715	<	point(nrow + 1) = nlist + 1
715	>	if (skipThisPair(atom1, atom2)) cycle inner
716	>
717	>	call get_interatomic_vector(q_Row(:,atom1), &
718	>	q_Col(:,atom2), d_atm, ratmsq)
719	>
720	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
721	>	do_pot, do_stress, &
722	>	u_l, A, f, t, pot_local, vpair)
723	>
724	>	vab = vab + vpair
725	>	enddo inner
726	>	enddo
727	>
728	>	if (in_switching_region) then
729	>	swderiv = vab*dswdr/rgrp
730	>
731	>	do ia=groupStart(i), groupStart(i+1)-1
732	>	atom1=groupList(ia)
733	>	mf = mfact(atom1)
734	>	f_Row(1,atom1) = f_Row(1,atom1) - swderiv*d_grp(1)*mf
735	>	f_Row(2,atom1) = f_Row(2,atom1) - swderiv*d_grp(2)*mf
736	>	f_Row(3,atom1) = f_Row(3,atom1) - swderiv*d_grp(3)*mf
737	>	enddo
738	>
739	>	do jb=groupStart(j), groupStart(j+1)-1
740	>	atom2=groupList(jb)
741	>	mf = mfact(atom2)
742	>	f_Col(1,atom2) = f_Col(1,atom2) + swderiv*d_grp(1)*mf
743	>	f_Col(2,atom2) = f_Col(2,atom2) + swderiv*d_grp(2)*mf
744	>	f_Col(3,atom2) = f_Col(3,atom2) + swderiv*d_grp(3)*mf
745	>	enddo
746	>	endif
747	>
748	>	end if
749	>	enddo
750	>	enddo
751	>	point(nrow_group + 1) = nlist + 1
752
753		else  !! (of update_check)
754	<
754	>
755		! use the list to find the neighbors
756	<	do i = 1, nrow
756	>	do i = 1, nrow_group
757		JBEG = POINT(i)
758		JEND = POINT(i+1) - 1
759	<	! check thiat molecule i has neighbors
759	>	! check that group i has neighbors
760		if (jbeg .le. jend) then
761
762		do jnab = jbeg, jend
763		j = list(jnab)
764	+
765	+	call get_interatomic_vector(q_group_Row(:,i), &
766	+	q_group_Col(:,j), d_grp, rgrpsq)
767	+
768	+	vab = 0.0d0
769	+	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
770	+	in_switching_region)
771	+
772	+	do ia = groupStart(i), groupStart(i+1)-1
773	+	atom1 = groupList(ia)
774	+
775	+	do jb = groupStart(j), groupStart(j+1)-1
776	+	atom2 = groupList(jb)
777	+	write(*,*) 'doing ', atom1, atom2
778	+
779	+	call get_interatomic_vector(q_Row(:,atom1), &
780	+	q_Col(:,atom2), d_atm, ratmsq)
781	+
782	+	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
783	+	do_pot, do_stress, &
784	+	u_l, A, f, t, pot_local, vpair)
785	+
786	+	vab = vab + vpair
787	+
788	+	enddo
789	+	enddo
790	+
791	+	if (in_switching_region) then
792	+	swderiv = vab*dswdr/rgrp
793	+
794	+	do ia=groupStart(i), groupStart(i+1)-1
795	+	atom1=groupList(ia)
796	+	mf = mfact(atom1)
797	+	f_Row(1,atom1) = f_Row(1,atom1) - swderiv*d_grp(1)*mf
798	+	f_Row(2,atom1) = f_Row(2,atom1) - swderiv*d_grp(2)*mf
799	+	f_Row(3,atom1) = f_Row(3,atom1) - swderiv*d_grp(3)*mf
800	+	enddo
801	+
802	+	do jb=groupStart(j), groupStart(j+1)-1
803	+	atom2=groupList(jb)
804	+	mf = mfact(atom2)
805	+	f_Col(1,atom2) = f_Col(1,atom2) + swderiv*d_grp(1)*mf
806	+	f_Col(2,atom2) = f_Col(2,atom2) + swderiv*d_grp(2)*mf
807	+	f_Col(3,atom2) = f_Col(3,atom2) + swderiv*d_grp(3)*mf
808	+	enddo
809	+	endif
810
467	–	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
468	–	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
469	–	u_l, A, f, t, pot_local)
470	–
811		enddo
812		endif
813		enddo
814		endif
815
816		#else
817	<
817	>
818		if (update_nlist) then
819
820	<	! save current configuration, contruct neighbor list,
821	<	! and calculate forces
482	<	call saveNeighborList(natoms, q)
820	>	!! save current configuration, construct neighbor list,
821	>	!! and calculate forces
822
823	+	call saveNeighborList(nGroup, q_group)
824	+
825		neighborListSize = size(list)
826	<
486	<	nlist = 0
826	>	nlist = 0
827
828	<	do i = 1, natoms-1
828	>	do i = 1, nGroup-1
829		point(i) = nlist + 1
830
831	<	inner: do j = i+1, natoms
831	>	do j = i+1, nGroup
832
833	<	if (skipThisPair(i,j))  cycle inner
834	<
835	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
836	<
497	<
498	<	if (rijsq < rlistsq) then
499	<
833	>	call get_interatomic_vector(q_group(:,i), &
834	>	q_group(:,j), d_grp, rgrpsq)
835	>
836	>	if (rgrpsq < rlistsq) then
837		nlist = nlist + 1
838	<
838	>
839		if (nlist > neighborListSize) then
840	<	call expandNeighborList(natoms, listerror)
840	>	call expandNeighborList(nGroup, listerror)
841		if (listerror /= 0) then
842		error = -1
843		write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
#	Line 510 | Line 847 | contains
847		endif
848
849		list(nlist) = j
850	+
851	+	vab = 0.0d0
852	+	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
853	+	in_switching_region)
854
855	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
856	<	u_l, A, f, t, pot)
857	<
858	<	endif
859	<	enddo inner
855	>	do ia = groupStart(i), groupStart(i+1)-1
856	>	atom1 = groupList(ia)
857	>
858	>	inner: do jb = groupStart(j), groupStart(j+1)-1
859	>	atom2 = groupList(jb)
860	>
861	>	if (skipThisPair(atom1, atom2)) cycle inner
862	>
863	>	call get_interatomic_vector(q(:,atom1), &
864	>	q(:,atom2), d_atm, ratmsq)
865	>
866	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
867	>	do_pot, do_stress, &
868	>	u_l, A, f, t, pot, vpair)
869	>
870	>	vab = vab + vpair
871	>
872	>	enddo inner
873	>	enddo
874	>
875	>	if (in_switching_region) then
876	>	swderiv = vab*dswdr/rgrp
877	>	do ia=groupStart(i), groupStart(i+1)-1
878	>	atom1=groupList(ia)
879	>	mf = mfact(atom1)
880	>	f(1,atom1) = f(1,atom1) - swderiv*d_grp(1)*mf
881	>	f(2,atom1) = f(2,atom1) - swderiv*d_grp(2)*mf
882	>	f(3,atom1) = f(3,atom1) - swderiv*d_grp(3)*mf
883	>	enddo
884	>
885	>	do jb=groupStart(j), groupStart(j+1)-1
886	>	atom2=groupList(jb)
887	>	mf = mfact(atom2)
888	>	f(1,atom2) = f(1,atom2) + swderiv*d_grp(1)*mf
889	>	f(2,atom2) = f(2,atom2) + swderiv*d_grp(2)*mf
890	>	f(3,atom2) = f(3,atom2) + swderiv*d_grp(3)*mf
891	>	enddo
892	>	endif
893	>
894	>	end if
895	>	enddo
896		enddo
897	+	point(nGroup) = nlist + 1
898
899	<	point(natoms) = nlist + 1
899	>	else  !! (of update_check)
900
523	–	else !! (update)
524	–
901		! use the list to find the neighbors
902	<	do i = 1, natoms-1
902	>	do i = 1, nGroup-1
903		JBEG = POINT(i)
904		JEND = POINT(i+1) - 1
905	<	! check thiat molecule i has neighbors
905	>	! check that group i has neighbors
906		if (jbeg .le. jend) then
907
908		do jnab = jbeg, jend
909		j = list(jnab)
910
911	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
912	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
537	<	u_l, A, f, t, pot)
911	>	call get_interatomic_vector(q_group(:,i), &
912	>	q_group(:,j), d_grp, rgrpsq)
913
914	+	vab = 0.0d0
915	+
916	+	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
917	+	in_switching_region)
918	+
919	+	do ia = groupStart(i), groupStart(i+1)-1
920	+	atom1 = groupList(ia)
921	+
922	+	do jb = groupStart(j), groupStart(j+1)-1
923	+	atom2 = groupList(jb)
924	+
925	+	call get_interatomic_vector(q(:,atom1), &
926	+	q(:,atom2), d_atm, ratmsq)
927	+
928	+	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
929	+	do_pot, do_stress, &
930	+	u_l, A, f, t, pot, vpair)
931	+
932	+	vab = vab + vpair
933	+
934	+	enddo
935	+	enddo
936	+
937	+	if (in_switching_region) then
938	+	swderiv = vab*dswdr/rgrp
939	+
940	+	do ia=groupStart(i), groupStart(i+1)-1
941	+	atom1=groupList(ia)
942	+	mf = mfact(atom1)
943	+	f(1,atom1) = f(1,atom1) - swderiv*d_grp(1)*mf
944	+	f(2,atom1) = f(2,atom1) - swderiv*d_grp(2)*mf
945	+	f(3,atom1) = f(3,atom1) - swderiv*d_grp(3)*mf
946	+	enddo
947	+
948	+	do jb=groupStart(j), groupStart(j+1)-1
949	+	atom2=groupList(jb)
950	+	mf = mfact(atom2)
951	+	f(1,atom2) = f(1,atom2) + swderiv*d_grp(1)*mf
952	+	f(2,atom2) = f(2,atom2) + swderiv*d_grp(2)*mf
953	+	f(3,atom2) = f(3,atom2) + swderiv*d_grp(3)*mf
954	+	enddo
955	+	endif
956		enddo
957		endif
958		enddo
959		endif
960	<
960	>
961		#endif
962
963		! phew, done with main loop.
964
965	+	!! Do timing
966	+	#ifdef PROFILE
967	+	call cpu_time(forceTimeFinal)
968	+	forceTime = forceTime + forceTimeFinal - forceTimeInitial
969	+	#endif
970	+
971		#ifdef IS_MPI
972		!!distribute forces
973	<
973	>
974		f_temp = 0.0_dp
975		call scatter(f_Row,f_temp,plan_row3d)
976		do i = 1,nlocal
977		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
978		end do
979	<
979	>
980		f_temp = 0.0_dp
981		call scatter(f_Col,f_temp,plan_col3d)
982		do i = 1,nlocal
983		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
984		end do
985
986	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
986	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
987		t_temp = 0.0_dp
988		call scatter(t_Row,t_temp,plan_row3d)
989		do i = 1,nlocal
#	Line 577 | Line 1000 | contains
1000		if (do_pot) then
1001		! scatter/gather pot_row into the members of my column
1002		call scatter(pot_Row, pot_Temp, plan_row)
1003	<
1003	>
1004		! scatter/gather pot_local into all other procs
1005		! add resultant to get total pot
1006		do i = 1, nlocal
#	Line 585 | Line 1008 | contains
1008		enddo
1009
1010		pot_Temp = 0.0_DP
1011	<
1011	>
1012		call scatter(pot_Col, pot_Temp, plan_col)
1013		do i = 1, nlocal
1014		pot_local = pot_local + pot_Temp(i)
1015		enddo
1016	<
1017	<	endif
1016	>
1017	>	endif
1018		#endif
1019	<
1020	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
1019	>
1020	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
1021
1022	<	if (FF_uses_RF .and. SimUsesRF()) then
1022	>	if (FF_uses_RF .and. SIM_uses_RF) then
1023
1024		#ifdef IS_MPI
1025		call scatter(rf_Row,rf,plan_row3d)
#	Line 606 | Line 1029 | contains
1029		end do
1030		#endif
1031
1032	<	do i = 1, getNlocal()
1033	<
1032	>	do i = 1, nLocal
1033	>
1034		rfpot = 0.0_DP
1035		#ifdef IS_MPI
1036		me_i = atid_row(i)
1037		#else
1038		me_i = atid(i)
1039		#endif
1040	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
1041	<	if ( is_DP_i ) then
1042	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
1040	>
1041	>	if (PropertyMap(me_i)%is_DP) then
1042	>
1043	>	mu_i = PropertyMap(me_i)%dipole_moment
1044	>
1045		!! The reaction field needs to include a self contribution
1046		!! to the field:
1047	<	call accumulate_self_rf(i, mu_i, u_l)
1047	>	call accumulate_self_rf(i, mu_i, u_l)
1048		!! Get the reaction field contribution to the
1049		!! potential and torques:
1050		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 633 | Line 1058 | contains
1058		enddo
1059		endif
1060		endif
1061	<
1062	<
1061	>
1062	>
1063		#ifdef IS_MPI
1064	<
1064	>
1065		if (do_pot) then
1066		pot = pot + pot_local
1067		!! we assume the c code will do the allreduce to get the total potential
1068		!! we could do it right here if we needed to...
1069		endif
1070	<
1070	>
1071		if (do_stress) then
1072	<	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
1072	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
1073		mpi_comm_world,mpi_err)
1074		call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
1075		mpi_comm_world,mpi_err)
1076		endif
1077	<
1077	>
1078		#else
1079	<
1079	>
1080		if (do_stress) then
1081		tau = tau_Temp
1082		virial = virial_Temp
1083		endif
1084	<
1084	>
1085		#endif
1086
1087	+
1088		end subroutine do_force_loop
1089
1090	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
1090	>
1091	>	subroutine do_pair(i, j, rijsq, d, sw, do_pot, do_stress, &
1092	>	u_l, A, f, t, pot, vpair)
1093
1094	<	real( kind = dp ) :: pot
1095	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
1096	<	real (kind=dp), dimension(9,getNlocal()) :: A
1097	<	real (kind=dp), dimension(3,getNlocal()) :: f
1098	<	real (kind=dp), dimension(3,getNlocal()) :: t
1094	>	real( kind = dp ) :: pot, vpair, sw
1095	>	real( kind = dp ), dimension(nLocal)   :: mfact
1096	>	real( kind = dp ), dimension(3,nLocal) :: u_l
1097	>	real( kind = dp ), dimension(9,nLocal) :: A
1098	>	real( kind = dp ), dimension(3,nLocal) :: f
1099	>	real( kind = dp ), dimension(3,nLocal) :: t
1100
1101		logical, intent(inout) :: do_pot, do_stress
1102		integer, intent(in) :: i, j
1103	<	real ( kind = dp ), intent(inout)    :: rijsq
1103	>	real ( kind = dp ), intent(inout) :: rijsq
1104		real ( kind = dp )                :: r
1105		real ( kind = dp ), intent(inout) :: d(3)
677	–	logical :: is_LJ_i, is_LJ_j
678	–	logical :: is_DP_i, is_DP_j
679	–	logical :: is_GB_i, is_GB_j
680	–	logical :: is_EAM_i,is_EAM_j
681	–	logical :: is_Sticky_i, is_Sticky_j
1106		integer :: me_i, me_j
1107
1108		r = sqrt(rijsq)
1109	+	vpair = 0.0d0
1110
1111		#ifdef IS_MPI
1112		if (tagRow(i) .eq. tagColumn(j)) then
1113		write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
1114		endif
690	–
1115		me_i = atid_row(i)
1116		me_j = atid_col(j)
693	–
1117		#else
695	–
1118		me_i = atid(i)
1119		me_j = atid(j)
698	–
1120		#endif
1121	+
1122	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
1123	+
1124	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
1125	+	!write(*,*) 'calling lj with'
1126	+	!write(*,*) i, j, r, rijsq
1127	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
1128	+	!write(*,'(3es12.3)') sw, vpair, pot
1129	+	!write(*,*)
1130
1131	<	if (FF_uses_LJ .and. SimUsesLJ()) then
1132	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
1133	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
704	<
705	<	if ( is_LJ_i .and. is_LJ_j ) &
706	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
707	<	endif
708	<
709	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
710	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
711	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
1131	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, pot, f, do_pot, &
1132	>	do_stress)
1133	>	endif
1134
1135	<	if ( is_DP_i .and. is_DP_j ) then
1136	<
1137	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
1135	>	endif
1136	>
1137	>	if (FF_uses_charges .and. SIM_uses_charges) then
1138	>
1139	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
1140	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, pot, f, do_pot, &
1141	>	do_stress)
1142	>	endif
1143	>
1144	>	endif
1145	>
1146	>	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
1147	>
1148	>	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
1149	>	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, pot, u_l, f, t, &
1150		do_pot, do_stress)
1151	<	if (FF_uses_RF .and. SimUsesRF()) then
1152	<	call accumulate_rf(i, j, r, u_l)
1153	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
1154	<	endif
721	<
1151	>	if (FF_uses_RF .and. SIM_uses_RF) then
1152	>	call accumulate_rf(i, j, r, u_l, sw)
1153	>	call rf_correct_forces(i, j, d, r, u_l, sw, f, do_stress)
1154	>	endif
1155		endif
1156	+
1157		endif
1158
1159	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
1159	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
1160
1161	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
1162	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
729	<
730	<	if ( is_Sticky_i .and. is_Sticky_j ) then
731	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
1161	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
1162	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, pot, A, f, t, &
1163		do_pot, do_stress)
1164		endif
1165	+
1166		endif
1167
1168
1169	<	if (FF_uses_GB .and. SimUsesGB()) then
738	<
739	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
740	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
1169	>	if (FF_uses_GB .and. SIM_uses_GB) then
1170
1171	<	if ( is_GB_i .and. is_GB_j ) then
1172	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
1171	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
1172	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, pot, u_l, f, t, &
1173		do_pot, do_stress)
1174		endif
746	–	endif
747	–
1175
1176	<
1177	<	if (FF_uses_EAM .and. SimUsesEAM()) then
1178	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
1179	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
1180	<
1181	<	if ( is_EAM_i .and. is_EAM_j ) &
1182	<	call do_eam_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
1183	<	endif
1184	<
1185	<
1186	<
760	<
1176	>	endif
1177	>
1178	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1179	>
1180	>	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
1181	>	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, pot, f, &
1182	>	do_pot, do_stress)
1183	>	endif
1184	>
1185	>	endif
1186	>
1187		end subroutine do_pair
1188
1189	<
1190	<
765	<	subroutine do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
1189	>	subroutine do_prepair(i, j, rijsq, d, rcijsq, dc, &
1190	>	do_pot, do_stress, u_l, A, f, t, pot)
1191		real( kind = dp ) :: pot
1192	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
1193	<	real (kind=dp), dimension(9,getNlocal()) :: A
1194	<	real (kind=dp), dimension(3,getNlocal()) :: f
1195	<	real (kind=dp), dimension(3,getNlocal()) :: t
1192	>	real( kind = dp ), dimension(3,nLocal) :: u_l
1193	>	real (kind=dp), dimension(9,nLocal) :: A
1194	>	real (kind=dp), dimension(3,nLocal) :: f
1195	>	real (kind=dp), dimension(3,nLocal) :: t
1196
1197		logical, intent(inout) :: do_pot, do_stress
1198		integer, intent(in) :: i, j
1199	<	real ( kind = dp ), intent(inout)    :: rijsq
1200	<	real ( kind = dp )                :: r
1201	<	real ( kind = dp ), intent(inout) :: d(3)
1199	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
1200	>	real ( kind = dp )                :: r, rc
1201	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
1202
1203		logical :: is_EAM_i, is_EAM_j
1204
1205		integer :: me_i, me_j
1206
1207	<	r = sqrt(rijsq)
1207	>
1208	>	r = sqrt(rijsq)
1209	>	if (SIM_uses_molecular_cutoffs) then
1210	>	rc = sqrt(rcijsq)
1211	>	else
1212	>	rc = r
1213	>	endif
1214
1215	+
1216		#ifdef IS_MPI
1217		if (tagRow(i) .eq. tagColumn(j)) then
1218		write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
#	Line 795 | Line 1227 | contains
1227		me_j = atid(j)
1228
1229		#endif
1230	<
1231	<	if (FF_uses_EAM .and. SimUsesEAM()) then
1232	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
1233	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
802	<
803	<	if ( is_EAM_i .and. is_EAM_j ) &
1230	>
1231	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1232	>
1233	>	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
1234		call calc_EAM_prepair_rho(i, j, d, r, rijsq )
1235	+
1236		endif
1237	<	end subroutine do_prepair
1237	>
1238	>	end subroutine do_prepair
1239
1240
1241
1242
1243	<	subroutine do_preforce(nlocal,pot)
1244	<	integer :: nlocal
1245	<	real( kind = dp ) :: pot
1246	<
1247	<	if (FF_uses_EAM .and. SimUsesEAM()) then
1243	>	subroutine do_preforce(nlocal,pot)
1244	>	integer :: nlocal
1245	>	real( kind = dp ) :: pot
1246	>
1247	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1248		call calc_EAM_preforce_Frho(nlocal,pot)
1249		endif
1250	<
1251	<
1252	<	end subroutine do_preforce
1253	<
1254	<
1255	<	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
1256	<
1257	<	real (kind = dp), dimension(3) :: q_i
1258	<	real (kind = dp), dimension(3) :: q_j
1259	<	real ( kind = dp ), intent(out) :: r_sq
1260	<	real( kind = dp ) :: d(3), scaled(3)
1261	<	integer i
1262	<
1263	<	d(1:3) = q_j(1:3) - q_i(1:3)
1264	<
1265	<	! Wrap back into periodic box if necessary
1266	<	if ( SimUsesPBC() ) then
835	<
836	<	if( .not.boxIsOrthorhombic ) then
837	<	! calc the scaled coordinates.
838	<
839	<	scaled = matmul(HmatInv, d)
840	<
841	<	! wrap the scaled coordinates
842	<
843	<	scaled = scaled  - anint(scaled)
844	<
845	<
846	<	! calc the wrapped real coordinates from the wrapped scaled
847	<	! coordinates
848	<
849	<	d = matmul(Hmat,scaled)
850	<
851	<	else
852	<	! calc the scaled coordinates.
853	<
854	<	do i = 1, 3
855	<	scaled(i) = d(i) * HmatInv(i,i)
856	<
857	<	! wrap the scaled coordinates
858	<
859	<	scaled(i) = scaled(i) - anint(scaled(i))
860	<
861	<	! calc the wrapped real coordinates from the wrapped scaled
862	<	! coordinates
863	<
864	<	d(i) = scaled(i)*Hmat(i,i)
865	<	enddo
866	<	endif
867	<
868	<	endif
869	<
870	<	r_sq = dot_product(d,d)
871	<
872	<	end subroutine get_interatomic_vector
873	<
874	<	subroutine check_initialization(error)
875	<	integer, intent(out) :: error
876	<
877	<	error = 0
878	<	! Make sure we are properly initialized.
879	<	if (.not. do_forces_initialized) then
880	<	error = -1
881	<	return
882	<	endif
883	<
884	<	#ifdef IS_MPI
885	<	if (.not. isMPISimSet()) then
886	<	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
887	<	error = -1
888	<	return
889	<	endif
890	<	#endif
891	<
892	<	return
893	<	end subroutine check_initialization
894	<
895	<
896	<	subroutine zero_work_arrays()
897	<
898	<	#ifdef IS_MPI
899	<
900	<	q_Row = 0.0_dp
901	<	q_Col = 0.0_dp
902	<
903	<	u_l_Row = 0.0_dp
904	<	u_l_Col = 0.0_dp
905	<
906	<	A_Row = 0.0_dp
907	<	A_Col = 0.0_dp
908	<
909	<	f_Row = 0.0_dp
910	<	f_Col = 0.0_dp
911	<	f_Temp = 0.0_dp
1250	>
1251	>
1252	>	end subroutine do_preforce
1253	>
1254	>
1255	>	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
1256	>
1257	>	real (kind = dp), dimension(3) :: q_i
1258	>	real (kind = dp), dimension(3) :: q_j
1259	>	real ( kind = dp ), intent(out) :: r_sq
1260	>	real( kind = dp ) :: d(3), scaled(3)
1261	>	integer i
1262	>
1263	>	d(1:3) = q_j(1:3) - q_i(1:3)
1264	>
1265	>	! Wrap back into periodic box if necessary
1266	>	if ( SIM_uses_PBC ) then
1267
1268	<	t_Row = 0.0_dp
1269	<	t_Col = 0.0_dp
1270	<	t_Temp = 0.0_dp
1268	>	if( .not.boxIsOrthorhombic ) then
1269	>	! calc the scaled coordinates.
1270	>
1271	>	scaled = matmul(HmatInv, d)
1272	>
1273	>	! wrap the scaled coordinates
1274	>
1275	>	scaled = scaled  - anint(scaled)
1276	>
1277	>
1278	>	! calc the wrapped real coordinates from the wrapped scaled
1279	>	! coordinates
1280	>
1281	>	d = matmul(Hmat,scaled)
1282	>
1283	>	else
1284	>	! calc the scaled coordinates.
1285	>
1286	>	do i = 1, 3
1287	>	scaled(i) = d(i) * HmatInv(i,i)
1288	>
1289	>	! wrap the scaled coordinates
1290	>
1291	>	scaled(i) = scaled(i) - anint(scaled(i))
1292	>
1293	>	! calc the wrapped real coordinates from the wrapped scaled
1294	>	! coordinates
1295	>
1296	>	d(i) = scaled(i)*Hmat(i,i)
1297	>	enddo
1298	>	endif
1299	>
1300	>	endif
1301	>
1302	>	r_sq = dot_product(d,d)
1303	>
1304	>	end subroutine get_interatomic_vector
1305
1306	<	pot_Row = 0.0_dp
1307	<	pot_Col = 0.0_dp
1308	<	pot_Temp = 0.0_dp
1306	>	subroutine zero_work_arrays()
1307	>
1308	>	#ifdef IS_MPI
1309	>
1310	>	q_Row = 0.0_dp
1311	>	q_Col = 0.0_dp
1312
1313	<	rf_Row = 0.0_dp
1314	<	rf_Col = 0.0_dp
1315	<	rf_Temp = 0.0_dp
1316	<
1313	>	q_group_Row = 0.0_dp
1314	>	q_group_Col = 0.0_dp
1315	>
1316	>	u_l_Row = 0.0_dp
1317	>	u_l_Col = 0.0_dp
1318	>
1319	>	A_Row = 0.0_dp
1320	>	A_Col = 0.0_dp
1321	>
1322	>	f_Row = 0.0_dp
1323	>	f_Col = 0.0_dp
1324	>	f_Temp = 0.0_dp
1325	>
1326	>	t_Row = 0.0_dp
1327	>	t_Col = 0.0_dp
1328	>	t_Temp = 0.0_dp
1329	>
1330	>	pot_Row = 0.0_dp
1331	>	pot_Col = 0.0_dp
1332	>	pot_Temp = 0.0_dp
1333	>
1334	>	rf_Row = 0.0_dp
1335	>	rf_Col = 0.0_dp
1336	>	rf_Temp = 0.0_dp
1337	>
1338		#endif
1339	<
1340	<	rf = 0.0_dp
1341	<	tau_Temp = 0.0_dp
1342	<	virial_Temp = 0.0_dp
1343	<	end subroutine zero_work_arrays
1344	<
1345	<	function skipThisPair(atom1, atom2) result(skip_it)
1346	<	integer, intent(in) :: atom1
1347	<	integer, intent(in), optional :: atom2
1348	<	logical :: skip_it
1349	<	integer :: unique_id_1, unique_id_2
1350	<	integer :: me_i,me_j
1351	<	integer :: i
1352	<
1353	<	skip_it = .false.
1354	<
1355	<	!! there are a number of reasons to skip a pair or a particle
1356	<	!! mostly we do this to exclude atoms who are involved in short
1357	<	!! range interactions (bonds, bends, torsions), but we also need
1358	<	!! to exclude some overcounted interactions that result from
1359	<	!! the parallel decomposition
1360	<
1339	>
1340	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1341	>	call clean_EAM()
1342	>	endif
1343	>
1344	>	rf = 0.0_dp
1345	>	tau_Temp = 0.0_dp
1346	>	virial_Temp = 0.0_dp
1347	>	end subroutine zero_work_arrays
1348	>
1349	>	function skipThisPair(atom1, atom2) result(skip_it)
1350	>	integer, intent(in) :: atom1
1351	>	integer, intent(in), optional :: atom2
1352	>	logical :: skip_it
1353	>	integer :: unique_id_1, unique_id_2
1354	>	integer :: me_i,me_j
1355	>	integer :: i
1356	>
1357	>	skip_it = .false.
1358	>
1359	>	!! there are a number of reasons to skip a pair or a particle
1360	>	!! mostly we do this to exclude atoms who are involved in short
1361	>	!! range interactions (bonds, bends, torsions), but we also need
1362	>	!! to exclude some overcounted interactions that result from
1363	>	!! the parallel decomposition
1364	>
1365		#ifdef IS_MPI
1366	<	!! in MPI, we have to look up the unique IDs for each atom
1367	<	unique_id_1 = tagRow(atom1)
1366	>	!! in MPI, we have to look up the unique IDs for each atom
1367	>	unique_id_1 = tagRow(atom1)
1368		#else
1369	<	!! in the normal loop, the atom numbers are unique
1370	<	unique_id_1 = atom1
1369	>	!! in the normal loop, the atom numbers are unique
1370	>	unique_id_1 = atom1
1371		#endif
1372	<
1373	<	!! We were called with only one atom, so just check the global exclude
1374	<	!! list for this atom
1375	<	if (.not. present(atom2)) then
1376	<	do i = 1, nExcludes_global
1377	<	if (excludesGlobal(i) == unique_id_1) then
1378	<	skip_it = .true.
1379	<	return
1380	<	end if
1381	<	end do
1382	<	return
1383	<	end if
1384	<
1372	>
1373	>	!! We were called with only one atom, so just check the global exclude
1374	>	!! list for this atom
1375	>	if (.not. present(atom2)) then
1376	>	do i = 1, nExcludes_global
1377	>	if (excludesGlobal(i) == unique_id_1) then
1378	>	skip_it = .true.
1379	>	return
1380	>	end if
1381	>	end do
1382	>	return
1383	>	end if
1384	>
1385		#ifdef IS_MPI
1386	<	unique_id_2 = tagColumn(atom2)
1386	>	unique_id_2 = tagColumn(atom2)
1387		#else
1388	<	unique_id_2 = atom2
1388	>	unique_id_2 = atom2
1389		#endif
1390	<
1390	>
1391		#ifdef IS_MPI
1392	<	!! this situation should only arise in MPI simulations
1393	<	if (unique_id_1 == unique_id_2) then
1394	<	skip_it = .true.
1395	<	return
1396	<	end if
1397	<
1398	<	!! this prevents us from doing the pair on multiple processors
1399	<	if (unique_id_1 < unique_id_2) then
1400	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1401	<	skip_it = .true.
1402	<	return
1403	<	endif
1404	<	else
1405	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1406	<	skip_it = .true.
1407	<	return
1408	<	endif
1409	<	endif
1392	>	!! this situation should only arise in MPI simulations
1393	>	if (unique_id_1 == unique_id_2) then
1394	>	skip_it = .true.
1395	>	return
1396	>	end if
1397	>
1398	>	!! this prevents us from doing the pair on multiple processors
1399	>	if (unique_id_1 < unique_id_2) then
1400	>	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1401	>	skip_it = .true.
1402	>	return
1403	>	endif
1404	>	else
1405	>	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1406	>	skip_it = .true.
1407	>	return
1408	>	endif
1409	>	endif
1410		#endif
1411	+
1412	+	!! the rest of these situations can happen in all simulations:
1413	+	do i = 1, nExcludes_global
1414	+	if ((excludesGlobal(i) == unique_id_1) .or. &
1415	+	(excludesGlobal(i) == unique_id_2)) then
1416	+	skip_it = .true.
1417	+	return
1418	+	endif
1419	+	enddo
1420	+
1421	+	do i = 1, nExcludes_local
1422	+	if (excludesLocal(1,i) == unique_id_1) then
1423	+	if (excludesLocal(2,i) == unique_id_2) then
1424	+	skip_it = .true.
1425	+	return
1426	+	endif
1427	+	else
1428	+	if (excludesLocal(1,i) == unique_id_2) then
1429	+	if (excludesLocal(2,i) == unique_id_1) then
1430	+	skip_it = .true.
1431	+	return
1432	+	endif
1433	+	endif
1434	+	endif
1435	+	end do
1436	+
1437	+	return
1438	+	end function skipThisPair
1439
1440	<	!! the rest of these situations can happen in all simulations:
1441	<	do i = 1, nExcludes_global
1442	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1443	<	(excludesGlobal(i) == unique_id_2)) then
1444	<	skip_it = .true.
1445	<	return
1446	<	endif
1447	<	enddo
1448	<
1449	<	do i = 1, nExcludes_local
1450	<	if (excludesLocal(1,i) == unique_id_1) then
1451	<	if (excludesLocal(2,i) == unique_id_2) then
1452	<	skip_it = .true.
1453	<	return
1454	<	endif
1455	<	else
1456	<	if (excludesLocal(1,i) == unique_id_2) then
1457	<	if (excludesLocal(2,i) == unique_id_1) then
1458	<	skip_it = .true.
1459	<	return
1460	<	endif
1461	<	endif
1462	<	endif
1463	<	end do
1464	<
1020	<	return
1021	<	end function skipThisPair
1022	<
1023	<	function FF_UsesDirectionalAtoms() result(doesit)
1024	<	logical :: doesit
1025	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1026	<	FF_uses_GB .or. FF_uses_RF
1027	<	end function FF_UsesDirectionalAtoms
1028	<
1029	<	function FF_RequiresPrepairCalc() result(doesit)
1030	<	logical :: doesit
1031	<	doesit = FF_uses_EAM
1032	<	end function FF_RequiresPrepairCalc
1033	<
1034	<	function FF_RequiresPostpairCalc() result(doesit)
1035	<	logical :: doesit
1036	<	doesit = FF_uses_RF
1037	<	end function FF_RequiresPostpairCalc
1038	<
1440	>	function FF_UsesDirectionalAtoms() result(doesit)
1441	>	logical :: doesit
1442	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1443	>	FF_uses_GB .or. FF_uses_RF
1444	>	end function FF_UsesDirectionalAtoms
1445	>
1446	>	function FF_RequiresPrepairCalc() result(doesit)
1447	>	logical :: doesit
1448	>	doesit = FF_uses_EAM
1449	>	end function FF_RequiresPrepairCalc
1450	>
1451	>	function FF_RequiresPostpairCalc() result(doesit)
1452	>	logical :: doesit
1453	>	doesit = FF_uses_RF
1454	>	end function FF_RequiresPostpairCalc
1455	>
1456	>	#ifdef PROFILE
1457	>	function getforcetime() result(totalforcetime)
1458	>	real(kind=dp) :: totalforcetime
1459	>	totalforcetime = forcetime
1460	>	end function getforcetime
1461	>	#endif
1462	>
1463	>	!! This cleans componets of force arrays belonging only to fortran
1464	>
1465		end module do_Forces

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