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root/group/trunk/OOPSE/libmdtools/do_Forces.F90

Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.17 2003-07-02 21:26:55 mmeineke Exp $, $Date: 2003-07-02 21:26:55 $, $Name: not supported by cvs2svn $, $Revision: 1.17 $
7	>	!! @version $Id: do_Forces.F90,v 1.67 2004-06-01 18:42:58 gezelter Exp $, $Date: 2004-06-01 18:42:58 $, $Name: not supported by cvs2svn $, $Revision: 1.67 $
8
9		module do_Forces
10		use force_globals
11		use simulation
12		use definitions
13		use atype_module
14	+	use switcheroo
15		use neighborLists
16		use lj
17		use sticky_pair
18		use dipole_dipole
19	+	use charge_charge
20		use reaction_field
21		use gb_pair
22	+	use vector_class
23	+	use eam
24	+	use status
25		#ifdef IS_MPI
26		use mpiSimulation
27		#endif
#	Line 26 | Line 31 | module do_Forces
31
32		#define __FORTRAN90
33		#include "fForceField.h"
34	+	#include "fSwitchingFunction.h"
35
36	<	logical, save :: do_forces_initialized = .false.
36	>	INTEGER, PARAMETER:: PREPAIR_LOOP = 1
37	>	INTEGER, PARAMETER:: PAIR_LOOP    = 2
38	>
39	>	logical, save :: haveRlist = .false.
40	>	logical, save :: haveNeighborList = .false.
41	>	logical, save :: havePolicies = .false.
42	>	logical, save :: haveSIMvariables = .false.
43	>	logical, save :: havePropertyMap = .false.
44	>	logical, save :: haveSaneForceField = .false.
45		logical, save :: FF_uses_LJ
46		logical, save :: FF_uses_sticky
47	+	logical, save :: FF_uses_charges
48		logical, save :: FF_uses_dipoles
49		logical, save :: FF_uses_RF
50		logical, save :: FF_uses_GB
51		logical, save :: FF_uses_EAM
52	+	logical, save :: SIM_uses_LJ
53	+	logical, save :: SIM_uses_sticky
54	+	logical, save :: SIM_uses_charges
55	+	logical, save :: SIM_uses_dipoles
56	+	logical, save :: SIM_uses_RF
57	+	logical, save :: SIM_uses_GB
58	+	logical, save :: SIM_uses_EAM
59	+	logical, save :: SIM_requires_postpair_calc
60	+	logical, save :: SIM_requires_prepair_calc
61	+	logical, save :: SIM_uses_directional_atoms
62	+	logical, save :: SIM_uses_PBC
63	+	logical, save :: SIM_uses_molecular_cutoffs
64
65	+	real(kind=dp), save :: rlist, rlistsq
66	+
67		public :: init_FF
68		public :: do_force_loop
69	+	public :: setRlistDF
70
71	+	#ifdef PROFILE
72	+	public :: getforcetime
73	+	real, save :: forceTime = 0
74	+	real :: forceTimeInitial, forceTimeFinal
75	+	integer :: nLoops
76	+	#endif
77	+
78	+	type :: Properties
79	+	logical :: is_lj     = .false.
80	+	logical :: is_sticky = .false.
81	+	logical :: is_dp     = .false.
82	+	logical :: is_gb     = .false.
83	+	logical :: is_eam    = .false.
84	+	logical :: is_charge = .false.
85	+	real(kind=DP) :: charge = 0.0_DP
86	+	real(kind=DP) :: dipole_moment = 0.0_DP
87	+	end type Properties
88	+
89	+	type(Properties), dimension(:),allocatable :: PropertyMap
90	+
91		contains
92
93	+	subroutine setRlistDF( this_rlist )
94	+
95	+	real(kind=dp) :: this_rlist
96	+
97	+	rlist = this_rlist
98	+	rlistsq = rlist * rlist
99	+
100	+	haveRlist = .true.
101	+
102	+	end subroutine setRlistDF
103	+
104	+	subroutine createPropertyMap(status)
105	+	integer :: nAtypes
106	+	integer :: status
107	+	integer :: i
108	+	logical :: thisProperty
109	+	real (kind=DP) :: thisDPproperty
110	+
111	+	status = 0
112	+
113	+	nAtypes = getSize(atypes)
114	+
115	+	if (nAtypes == 0) then
116	+	status = -1
117	+	return
118	+	end if
119	+
120	+	if (.not. allocated(PropertyMap)) then
121	+	allocate(PropertyMap(nAtypes))
122	+	endif
123	+
124	+	do i = 1, nAtypes
125	+	call getElementProperty(atypes, i, "is_LJ", thisProperty)
126	+	PropertyMap(i)%is_LJ = thisProperty
127	+
128	+	call getElementProperty(atypes, i, "is_Charge", thisProperty)
129	+	PropertyMap(i)%is_Charge = thisProperty
130	+
131	+	if (thisProperty) then
132	+	call getElementProperty(atypes, i, "charge", thisDPproperty)
133	+	PropertyMap(i)%charge = thisDPproperty
134	+	endif
135	+
136	+	call getElementProperty(atypes, i, "is_DP", thisProperty)
137	+	PropertyMap(i)%is_DP = thisProperty
138	+
139	+	if (thisProperty) then
140	+	call getElementProperty(atypes, i, "dipole_moment", thisDPproperty)
141	+	PropertyMap(i)%dipole_moment = thisDPproperty
142	+	endif
143	+
144	+	call getElementProperty(atypes, i, "is_Sticky", thisProperty)
145	+	PropertyMap(i)%is_Sticky = thisProperty
146	+	call getElementProperty(atypes, i, "is_GB", thisProperty)
147	+	PropertyMap(i)%is_GB = thisProperty
148	+	call getElementProperty(atypes, i, "is_EAM", thisProperty)
149	+	PropertyMap(i)%is_EAM = thisProperty
150	+	end do
151	+
152	+	havePropertyMap = .true.
153	+
154	+	end subroutine createPropertyMap
155	+
156	+	subroutine setSimVariables()
157	+	SIM_uses_LJ = SimUsesLJ()
158	+	SIM_uses_sticky = SimUsesSticky()
159	+	SIM_uses_charges = SimUsesCharges()
160	+	SIM_uses_dipoles = SimUsesDipoles()
161	+	SIM_uses_RF = SimUsesRF()
162	+	SIM_uses_GB = SimUsesGB()
163	+	SIM_uses_EAM = SimUsesEAM()
164	+	SIM_requires_postpair_calc = SimRequiresPostpairCalc()
165	+	SIM_requires_prepair_calc = SimRequiresPrepairCalc()
166	+	SIM_uses_directional_atoms = SimUsesDirectionalAtoms()
167	+	SIM_uses_PBC = SimUsesPBC()
168	+	!SIM_uses_molecular_cutoffs = SimUsesMolecularCutoffs()
169	+
170	+	haveSIMvariables = .true.
171	+
172	+	return
173	+	end subroutine setSimVariables
174	+
175	+	subroutine doReadyCheck(error)
176	+	integer, intent(out) :: error
177	+
178	+	integer :: myStatus
179	+
180	+	error = 0
181	+
182	+	if (.not. havePropertyMap) then
183	+
184	+	myStatus = 0
185	+
186	+	call createPropertyMap(myStatus)
187	+
188	+	if (myStatus .ne. 0) then
189	+	write(default_error, *) 'createPropertyMap failed in do_Forces!'
190	+	error = -1
191	+	return
192	+	endif
193	+	endif
194	+
195	+	if (.not. haveSIMvariables) then
196	+	call setSimVariables()
197	+	endif
198	+
199	+	if (.not. haveRlist) then
200	+	write(default_error, *) 'rList has not been set in do_Forces!'
201	+	error = -1
202	+	return
203	+	endif
204	+
205	+	if (SIM_uses_LJ .and. FF_uses_LJ) then
206	+	if (.not. havePolicies) then
207	+	write(default_error, *) 'LJ mixing Policies have not been set in do_Forces!'
208	+	error = -1
209	+	return
210	+	endif
211	+	endif
212	+
213	+	if (.not. haveNeighborList) then
214	+	write(default_error, *) 'neighbor list has not been initialized in do_Forces!'
215	+	error = -1
216	+	return
217	+	end if
218	+
219	+	if (.not. haveSaneForceField) then
220	+	write(default_error, *) 'Force Field is not sane in do_Forces!'
221	+	error = -1
222	+	return
223	+	end if
224	+
225	+	#ifdef IS_MPI
226	+	if (.not. isMPISimSet()) then
227	+	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
228	+	error = -1
229	+	return
230	+	endif
231	+	#endif
232	+	return
233	+	end subroutine doReadyCheck
234	+
235	+
236		subroutine init_FF(LJMIXPOLICY, use_RF_c, thisStat)
237
238		integer, intent(in) :: LJMIXPOLICY
#	Line 64 | Line 257 | contains
257
258		FF_uses_LJ = .false.
259		FF_uses_sticky = .false.
260	+	FF_uses_charges = .false.
261		FF_uses_dipoles = .false.
262		FF_uses_GB = .false.
263		FF_uses_EAM = .false.
264
265		call getMatchingElementList(atypes, "is_LJ", .true., nMatches, MatchList)
266		if (nMatches .gt. 0) FF_uses_LJ = .true.
267	<
267	>
268	>	call getMatchingElementList(atypes, "is_Charge", .true., nMatches, MatchList)
269	>	if (nMatches .gt. 0) FF_uses_charges = .true.
270	>
271		call getMatchingElementList(atypes, "is_DP", .true., nMatches, MatchList)
272		if (nMatches .gt. 0) FF_uses_dipoles = .true.
273
#	Line 84 | Line 281 | contains
281		call getMatchingElementList(atypes, "is_EAM", .true., nMatches, MatchList)
282		if (nMatches .gt. 0) FF_uses_EAM = .true.
283
284	+	!! Assume sanity (for the sake of argument)
285	+	haveSaneForceField = .true.
286	+
287		!! check to make sure the FF_uses_RF setting makes sense
288
289		if (FF_uses_dipoles) then
90	–	rrf = getRrf()
91	–	rt = getRt()
92	–	call initialize_dipole(rrf, rt)
290		if (FF_uses_RF) then
291		dielect = getDielect()
292	<	call initialize_rf(rrf, rt, dielect)
292	>	call initialize_rf(dielect)
293		endif
294		else
295		if (FF_uses_RF) then
296		write(default_error,*) 'Using Reaction Field with no dipoles?  Huh?'
297		thisStat = -1
298	+	haveSaneForceField = .false.
299		return
300		endif
301	<	endif
301	>	endif
302
303		if (FF_uses_LJ) then
304
107	–	call getRcut(rcut)
108	–
305		select case (LJMIXPOLICY)
306		case (LB_MIXING_RULE)
307	<	call init_lj_FF(LB_MIXING_RULE, rcut, my_status)
307	>	call init_lj_FF(LB_MIXING_RULE, my_status)
308		case (EXPLICIT_MIXING_RULE)
309	<	call init_lj_FF(EXPLICIT_MIXING_RULE, rcut, my_status)
309	>	call init_lj_FF(EXPLICIT_MIXING_RULE, my_status)
310		case default
311		write(default_error,*) 'unknown LJ Mixing Policy!'
312		thisStat = -1
313	+	haveSaneForceField = .false.
314		return
315		end select
316		if (my_status /= 0) then
317		thisStat = -1
318	+	haveSaneForceField = .false.
319		return
320		end if
321	+	havePolicies = .true.
322		endif
323
324		if (FF_uses_sticky) then
325		call check_sticky_FF(my_status)
326		if (my_status /= 0) then
327		thisStat = -1
328	+	haveSaneForceField = .false.
329		return
330		end if
331		endif
332	<
332	>
333	>
334	>	if (FF_uses_EAM) then
335	>	call init_EAM_FF(my_status)
336	>	if (my_status /= 0) then
337	>	write(default_error, *) "init_EAM_FF returned a bad status"
338	>	thisStat = -1
339	>	haveSaneForceField = .false.
340	>	return
341	>	end if
342	>	endif
343	>
344		if (FF_uses_GB) then
345		call check_gb_pair_FF(my_status)
346		if (my_status .ne. 0) then
347		thisStat = -1
348	+	haveSaneForceField = .false.
349		return
350		endif
351		endif
352
353		if (FF_uses_GB .and. FF_uses_LJ) then
354		endif
355	<	if (.not. do_forces_initialized) then
355	>	if (.not. haveNeighborList) then
356		!! Create neighbor lists
357	<	call expandNeighborList(getNlocal(), my_status)
357	>	call expandNeighborList(nLocal, my_status)
358		if (my_Status /= 0) then
359		write(default_error,*) "SimSetup: ExpandNeighborList returned error."
360		thisStat = -1
361		return
362		endif
363	+	haveNeighborList = .true.
364		endif
365
366	<	do_forces_initialized = .true.
367	<
366	>
367	>
368		end subroutine init_FF
369
370
371		!! Does force loop over i,j pairs. Calls do_pair to calculates forces.
372		!------------------------------------------------------------->
373	<	subroutine do_force_loop(q, A, u_l, f, t, tau, pot, do_pot_c, do_stress_c, &
374	<	error)
373	>	subroutine do_force_loop(q, q_group, A, u_l, f, t, tau, pot, &
374	>	do_pot_c, do_stress_c, error)
375		!! Position array provided by C, dimensioned by getNlocal
376	<	real ( kind = dp ), dimension(3,getNlocal()) :: q
376	>	real ( kind = dp ), dimension(3, nLocal) :: q
377	>	!! molecular center-of-mass position array
378	>	real ( kind = dp ), dimension(3, nGroups) :: q_group
379		!! Rotation Matrix for each long range particle in simulation.
380	<	real( kind = dp), dimension(9,getNlocal()) :: A
380	>	real( kind = dp), dimension(9, nLocal) :: A
381		!! Unit vectors for dipoles (lab frame)
382	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
382	>	real( kind = dp ), dimension(3,nLocal) :: u_l
383		!! Force array provided by C, dimensioned by getNlocal
384	<	real ( kind = dp ), dimension(3,getNlocal()) :: f
384	>	real ( kind = dp ), dimension(3,nLocal) :: f
385		!! Torsion array provided by C, dimensioned by getNlocal
386	<	real( kind = dp ), dimension(3,getNlocal()) :: t
386	>	real( kind = dp ), dimension(3,nLocal) :: t
387	>
388		!! Stress Tensor
389		real( kind = dp), dimension(9) :: tau
390		real ( kind = dp ) :: pot
391		logical ( kind = 2) :: do_pot_c, do_stress_c
392		logical :: do_pot
393		logical :: do_stress
394	+	logical :: in_switching_region
395		#ifdef IS_MPI
396		real( kind = DP ) :: pot_local
397	<	integer :: nrow
398	<	integer :: ncol
397	>	integer :: nAtomsInRow
398	>	integer :: nAtomsInCol
399	>	integer :: nprocs
400	>	integer :: nGroupsInRow
401	>	integer :: nGroupsInCol
402		#endif
183	–	integer :: nlocal
403		integer :: natoms
404		logical :: update_nlist
405	<	integer :: i, j, jbeg, jend, jnab
405	>	integer :: i, j, jstart, jend, jnab
406	>	integer :: istart, iend
407	>	integer :: ia, jb, atom1, atom2
408		integer :: nlist
409	<	real( kind = DP ) ::  rijsq, rlistsq, rcutsq, rlist, rcut
410	<	real(kind=dp),dimension(3) :: d
409	>	real( kind = DP ) :: ratmsq, rgrpsq, rgrp, vpair, vij
410	>	real( kind = DP ) :: sw, dswdr, swderiv, mf
411	>	real(kind=dp),dimension(3) :: d_atm, d_grp, fpair, fij
412		real(kind=dp) :: rfpot, mu_i, virial
413	<	integer :: me_i
413	>	integer :: me_i, me_j, n_in_i, n_in_j
414		logical :: is_dp_i
415		integer :: neighborListSize
416		integer :: listerror, error
417		integer :: localError
418	+	integer :: propPack_i, propPack_j
419	+	integer :: loopStart, loopEnd, loop
420
421	+	real(kind=dp) :: listSkin = 1.0
422	+
423		!! initialize local variables
424	<
424	>
425		#ifdef IS_MPI
426		pot_local = 0.0_dp
427	<	nlocal = getNlocal()
428	<	nrow   = getNrow(plan_row)
429	<	ncol   = getNcol(plan_col)
427	>	nAtomsInRow   = getNatomsInRow(plan_atom_row)
428	>	nAtomsInCol   = getNatomsInCol(plan_atom_col)
429	>	nGroupsInRow  = getNgroupsInRow(plan_group_row)
430	>	nGroupsInCol  = getNgroupsInCol(plan_group_col)
431	>	write(*,*) nAtomsInRow, nAtomsInCol, nGroupsInRow, nGroupsInCol
432	>	write(*,*) pot_local
433		#else
205	–	nlocal = getNlocal()
434		natoms = nlocal
435		#endif
208	–
209	–	call getRcut(rcut,rc2=rcutsq)
210	–	call getRlist(rlist,rlistsq)
436
437	<	call check_initialization(localError)
437	>	call doReadyCheck(localError)
438		if ( localError .ne. 0 ) then
439	+	call handleError("do_force_loop", "Not Initialized")
440		error = -1
441		return
442		end if
443		call zero_work_arrays()
444	<
444	>
445		do_pot = do_pot_c
446		do_stress = do_stress_c
447	<
447	>
448		! Gather all information needed by all force loops:
449
450		#ifdef IS_MPI
451	+
452	+	call gather(q, q_Row, plan_atom_row_3d)
453	+	call gather(q, q_Col, plan_atom_col_3d)
454
455	<	call gather(q,q_Row,plan_row3d)
456	<	call gather(q,q_Col,plan_col3d)
455	>	call gather(q_group, q_group_Row, plan_group_row_3d)
456	>	call gather(q_group, q_group_Col, plan_group_col_3d)
457
458	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
459	<	call gather(u_l,u_l_Row,plan_row3d)
460	<	call gather(u_l,u_l_Col,plan_col3d)
458	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
459	>	call gather(u_l, u_l_Row, plan_atom_row_3d)
460	>	call gather(u_l, u_l_Col, plan_atom_col_3d)
461
462	<	call gather(A,A_Row,plan_row_rotation)
463	<	call gather(A,A_Col,plan_col_rotation)
462	>	call gather(A, A_Row, plan_atom_row_rotation)
463	>	call gather(A, A_Col, plan_atom_col_rotation)
464		endif
465
466		#endif
467
468	<	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
469	<	!! See if we need to update neighbor lists
470	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
471	<	!! if_mpi_gather_stuff_for_prepair
472	<	!! do_prepair_loop_if_needed
473	<	!! if_mpi_scatter_stuff_from_prepair
474	<	!! if_mpi_gather_stuff_from_prepair_to_main_loop
468	>	!! Begin force loop timing:
469	>	#ifdef PROFILE
470	>	call cpu_time(forceTimeInitial)
471	>	nloops = nloops + 1
472	>	#endif
473	>
474	>	loopEnd = PAIR_LOOP
475	>	if (FF_RequiresPrepairCalc() .and. SIM_requires_prepair_calc) then
476	>	loopStart = PREPAIR_LOOP
477		else
478	<	!! See if we need to update neighbor lists
248	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
478	>	loopStart = PAIR_LOOP
479		endif
480	<
480	>
481	>	do loop = loopStart, loopEnd
482	>
483	>	! See if we need to update neighbor lists
484	>	! (but only on the first time through):
485	>	if (loop .eq. loopStart) then
486		#ifdef IS_MPI
487	<
488	<	if (update_nlist) then
487	>	call checkNeighborList(nGroupsInRow, q_group_row, listSkin, &
488	>	update_nlist)
489	>	#else
490	>	call checkNeighborList(nGroups, q_group, listSkin, &
491	>	update_nlist)
492	>	#endif
493	>	endif
494
495	<	!! save current configuration, construct neighbor list,
496	<	!! and calculate forces
497	<	call saveNeighborList(nlocal, q)
495	>	if (update_nlist) then
496	>	!! save current configuration and construct neighbor list
497	>	#ifdef IS_MPI
498	>	call saveNeighborList(nGroupsInRow, q_group_row)
499	>	#else
500	>	call saveNeighborList(nGroups, q_group)
501	>	#endif
502	>	neighborListSize = size(list)
503	>	nlist = 0
504	>	endif
505
506	<	neighborListSize = size(list)
507	<	nlist = 0
508	<
509	<	do i = 1, nrow
510	<	point(i) = nlist + 1
506	>	istart = 1
507	>	#ifdef IS_MPI
508	>	iend = nGroupsInRow
509	>	#else
510	>	iend = nGroups - 1
511	>	#endif
512	>	outer: do i = istart, iend
513	>
514	>	if (update_nlist) point(i) = nlist + 1
515
516	<	inner: do j = 1, ncol
517	<
518	<	if (skipThisPair(i,j)) cycle inner
519	<
520	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
521	<
522	<	if (rijsq <  rlistsq) then
523	<
524	<	nlist = nlist + 1
525	<
526	<	if (nlist > neighborListSize) then
527	<	call expandNeighborList(nlocal, listerror)
528	<	if (listerror /= 0) then
529	<	error = -1
530	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
531	<	return
532	<	end if
533	<	neighborListSize = size(list)
534	<	endif
535	<
536	<	list(nlist) = j
537	<
287	<	if (rijsq <  rcutsq) then
288	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
289	<	u_l, A, f, t, pot_local)
290	<	endif
516	>	n_in_i = groupStartRow(i+1) - groupStartRow(i)
517	>
518	>	if (update_nlist) then
519	>	#ifdef IS_MPI
520	>	jstart = 1
521	>	jend = nGroupsInCol
522	>	#else
523	>	jstart = i+1
524	>	jend = nGroups
525	>	#endif
526	>	else
527	>	jstart = point(i)
528	>	jend = point(i+1) - 1
529	>	! make sure group i has neighbors
530	>	if (jstart .gt. jend) cycle outer
531	>	endif
532	>
533	>	do jnab = jstart, jend
534	>	if (update_nlist) then
535	>	j = jnab
536	>	else
537	>	j = list(jnab)
538		endif
292	–	enddo inner
293	–	enddo
539
540	<	point(nrow + 1) = nlist + 1
541	<
542	<	else  !! (of update_check)
298	<
299	<	! use the list to find the neighbors
300	<	do i = 1, nrow
301	<	JBEG = POINT(i)
302	<	JEND = POINT(i+1) - 1
303	<	! check thiat molecule i has neighbors
304	<	if (jbeg .le. jend) then
305	<
306	<	do jnab = jbeg, jend
307	<	j = list(jnab)
308	<
309	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
310	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
311	<	u_l, A, f, t, pot_local)
312	<
313	<	enddo
314	<	endif
315	<	enddo
316	<	endif
317	<
540	>	#ifdef IS_MPI
541	>	call get_interatomic_vector(q_group_Row(:,i), &
542	>	q_group_Col(:,j), d_grp, rgrpsq)
543		#else
544	<
545	<	if (update_nlist) then
546	<
322	<	! save current configuration, contruct neighbor list,
323	<	! and calculate forces
324	<	call saveNeighborList(natoms, q)
325	<
326	<	neighborListSize = size(list)
327	<
328	<	nlist = 0
329	<
330	<	do i = 1, natoms-1
331	<	point(i) = nlist + 1
332	<
333	<	inner: do j = i+1, natoms
334	<
335	<	if (skipThisPair(i,j))  cycle inner
336	<
337	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
338	<
544	>	call get_interatomic_vector(q_group(:,i), &
545	>	q_group(:,j), d_grp, rgrpsq)
546	>	#endif
547
548	<	if (rijsq <  rlistsq) then
548	>	if (rgrpsq < rlistsq) then
549	>	if (update_nlist) then
550	>	nlist = nlist + 1
551	>
552	>	if (nlist > neighborListSize) then
553	>	#ifdef IS_MPI
554	>	call expandNeighborList(nGroupsInRow, listerror)
555	>	#else
556	>	call expandNeighborList(nGroups, listerror)
557	>	#endif
558	>	if (listerror /= 0) then
559	>	error = -1
560	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
561	>	return
562	>	end if
563	>	neighborListSize = size(list)
564	>	endif
565	>
566	>	list(nlist) = j
567	>	endif
568
569	<	nlist = nlist + 1
570	<
571	<	if (nlist > neighborListSize) then
345	<	call expandNeighborList(natoms, listerror)
346	<	if (listerror /= 0) then
347	<	error = -1
348	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
349	<	return
350	<	end if
351	<	neighborListSize = size(list)
569	>	if (loop .eq. PAIR_LOOP) then
570	>	vij = 0.0d0
571	>	fij(1:3) = 0.0d0
572		endif
573
574	<	list(nlist) = j
574	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
575	>	in_switching_region)
576
577	<	if (rijsq <  rcutsq) then
578	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
579	<	u_l, A, f, t, pot)
580	<	endif
581	<	endif
582	<	enddo inner
583	<	enddo
584	<
585	<	point(natoms) = nlist + 1
586	<
587	<	else !! (update)
367	<
368	<	! use the list to find the neighbors
369	<	do i = 1, natoms-1
370	<	JBEG = POINT(i)
371	<	JEND = POINT(i+1) - 1
372	<	! check thiat molecule i has neighbors
373	<	if (jbeg .le. jend) then
374	<
375	<	do jnab = jbeg, jend
376	<	j = list(jnab)
577	>	n_in_j = groupStartCol(j+1) - groupStartCol(j)
578	>
579	>	do ia = groupStartRow(i), groupStartRow(i+1)-1
580	>
581	>	atom1 = groupListRow(ia)
582	>
583	>	inner: do jb = groupStartCol(j), groupStartCol(j+1)-1
584	>
585	>	atom2 = groupListCol(jb)
586	>
587	>	if (skipThisPair(atom1, atom2)) cycle inner
588
589	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
590	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
591	<	u_l, A, f, t, pot)
589	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
590	>	d_atm(1:3) = d_grp(1:3)
591	>	ratmsq = rgrpsq
592	>	else
593	>	#ifdef IS_MPI
594	>	call get_interatomic_vector(q_Row(:,atom1), &
595	>	q_Col(:,atom2), d_atm, ratmsq)
596	>	#else
597	>	call get_interatomic_vector(q(:,atom1), &
598	>	q(:,atom2), d_atm, ratmsq)
599	>	#endif
600	>	endif
601	>	#ifdef IS_MPI
602	>	write(*,'(a20,2i8,es12.3,2i8)') 'atom1, atom2, pot = ', atom1, atom2, ratmsq, AtomRowToGlobal(atom1), AtomColToGlobal(atom2)
603	>	#endif
604
605	<	enddo
605	>	if (loop .eq. PREPAIR_LOOP) then
606	>	#ifdef IS_MPI
607	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
608	>	rgrpsq, d_grp, do_pot, do_stress, &
609	>	u_l, A, f, t, pot_local)
610	>	#else
611	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
612	>	rgrpsq, d_grp, do_pot, do_stress, &
613	>	u_l, A, f, t, pot)
614	>	#endif
615	>	else
616	>	#ifdef IS_MPI
617	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
618	>	do_pot, &
619	>	u_l, A, f, t, pot_local, vpair, fpair)
620	>	write(*,'(a20,2i11,2es12.3)') 'atom1, atom2, pot = ', atom1, atom2, pot_local, vpair
621	>	#else
622	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
623	>	do_pot,  &
624	>	u_l, A, f, t, pot, vpair, fpair)
625	>	#endif
626	>
627	>	vij = vij + vpair
628	>	fij(1:3) = fij(1:3) + fpair(1:3)
629	>	endif
630	>	enddo inner
631	>	enddo
632	>
633	>	if (loop .eq. PAIR_LOOP) then
634	>	if (in_switching_region) then
635	>	swderiv = vij*dswdr/rgrp
636	>	fij(1) = fij(1) + swderiv*d_grp(1)
637	>	fij(2) = fij(2) + swderiv*d_grp(2)
638	>	fij(3) = fij(3) + swderiv*d_grp(3)
639	>
640	>	do ia=groupStartRow(i), groupStartRow(i+1)-1
641	>	atom1=groupListRow(ia)
642	>	mf = mfactRow(atom1)
643	>	#ifdef IS_MPI
644	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
645	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
646	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
647	>	#else
648	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
649	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
650	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
651	>	#endif
652	>	enddo
653	>
654	>	do jb=groupStartCol(j), groupStartCol(j+1)-1
655	>	atom2=groupListCol(jb)
656	>	mf = mfactCol(atom2)
657	>	#ifdef IS_MPI
658	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
659	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
660	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
661	>	#else
662	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
663	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
664	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
665	>	#endif
666	>	enddo
667	>	endif
668	>
669	>	if (do_stress) call add_stress_tensor(d_grp, fij)
670	>	endif
671	>	end if
672	>	enddo
673	>	enddo outer
674	>
675	>	if (update_nlist) then
676	>	#ifdef IS_MPI
677	>	point(nGroupsInRow + 1) = nlist + 1
678	>	#else
679	>	point(nGroups) = nlist + 1
680	>	#endif
681	>	if (loop .eq. PREPAIR_LOOP) then
682	>	! we just did the neighbor list update on the first
683	>	! pass, so we don't need to do it
684	>	! again on the second pass
685	>	update_nlist = .false.
686		endif
687	<	enddo
688	<	endif
687	>	endif
688	>
689	>	if (loop .eq. PREPAIR_LOOP) then
690	>	call do_preforce(nlocal, pot)
691	>	endif
692	>
693	>	enddo
694
695	<	#endif
695	>	!! Do timing
696	>	#ifdef PROFILE
697	>	call cpu_time(forceTimeFinal)
698	>	forceTime = forceTime + forceTimeFinal - forceTimeInitial
699	>	#endif
700
389	–	! phew, done with main loop.
390	–
701		#ifdef IS_MPI
702		!!distribute forces
703	<
703	>
704		f_temp = 0.0_dp
705	<	call scatter(f_Row,f_temp,plan_row3d)
705	>	call scatter(f_Row,f_temp,plan_atom_row_3d)
706		do i = 1,nlocal
707		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
708		end do
709	<
709	>
710		f_temp = 0.0_dp
711	<	call scatter(f_Col,f_temp,plan_col3d)
711	>	call scatter(f_Col,f_temp,plan_atom_col_3d)
712		do i = 1,nlocal
713		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
714		end do
715
716	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
716	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
717		t_temp = 0.0_dp
718	<	call scatter(t_Row,t_temp,plan_row3d)
718	>	call scatter(t_Row,t_temp,plan_atom_row_3d)
719		do i = 1,nlocal
720		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
721		end do
722		t_temp = 0.0_dp
723	<	call scatter(t_Col,t_temp,plan_col3d)
723	>	call scatter(t_Col,t_temp,plan_atom_col_3d)
724
725		do i = 1,nlocal
726		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
#	Line 419 | Line 729 | contains
729
730		if (do_pot) then
731		! scatter/gather pot_row into the members of my column
732	<	call scatter(pot_Row, pot_Temp, plan_row)
733	<
732	>	call scatter(pot_Row, pot_Temp, plan_atom_row)
733	>
734		! scatter/gather pot_local into all other procs
735		! add resultant to get total pot
736		do i = 1, nlocal
#	Line 428 | Line 738 | contains
738		enddo
739
740		pot_Temp = 0.0_DP
741	<
742	<	call scatter(pot_Col, pot_Temp, plan_col)
741	>
742	>	call scatter(pot_Col, pot_Temp, plan_atom_col)
743		do i = 1, nlocal
744		pot_local = pot_local + pot_Temp(i)
745		enddo
436	–
437	–	endif
438	–	#endif
439	–
440	–	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
746
747	<	if (FF_uses_RF .and. SimUsesRF()) then
747	>	endif
748	>	#endif
749	>
750	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
751	>
752	>	if (FF_uses_RF .and. SIM_uses_RF) then
753
754		#ifdef IS_MPI
755	<	call scatter(rf_Row,rf,plan_row3d)
756	<	call scatter(rf_Col,rf_Temp,plan_col3d)
755	>	call scatter(rf_Row,rf,plan_atom_row_3d)
756	>	call scatter(rf_Col,rf_Temp,plan_atom_col_3d)
757		do i = 1,nlocal
758		rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
759		end do
760		#endif
761
762	<	do i = 1, getNlocal()
763	<
762	>	do i = 1, nLocal
763	>
764		rfpot = 0.0_DP
765		#ifdef IS_MPI
766		me_i = atid_row(i)
767		#else
768		me_i = atid(i)
769		#endif
770	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
771	<	if ( is_DP_i ) then
772	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
770	>
771	>	if (PropertyMap(me_i)%is_DP) then
772	>
773	>	mu_i = PropertyMap(me_i)%dipole_moment
774	>
775		!! The reaction field needs to include a self contribution
776		!! to the field:
777	<	call accumulate_self_rf(i, mu_i, u_l)
777	>	call accumulate_self_rf(i, mu_i, u_l)
778		!! Get the reaction field contribution to the
779		!! potential and torques:
780		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 476 | Line 788 | contains
788		enddo
789		endif
790		endif
791	<
792	<
791	>
792	>
793		#ifdef IS_MPI
794	<
794	>
795		if (do_pot) then
796		pot = pot + pot_local
797		!! we assume the c code will do the allreduce to get the total potential
798		!! we could do it right here if we needed to...
799		endif
800	<
800	>
801		if (do_stress) then
802	<	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
802	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
803		mpi_comm_world,mpi_err)
804		call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
805		mpi_comm_world,mpi_err)
806		endif
807	<
807	>
808		#else
809	<
809	>
810		if (do_stress) then
811		tau = tau_Temp
812		virial = virial_Temp
813		endif
502	–
503	–	#endif
814
815	+	#endif
816	+
817		end subroutine do_force_loop
818	+
819	+	subroutine do_pair(i, j, rijsq, d, sw, do_pot, &
820	+	u_l, A, f, t, pot, vpair, fpair)
821
822	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
822	>	real( kind = dp ) :: pot, vpair, sw
823	>	real( kind = dp ), dimension(3) :: fpair
824	>	real( kind = dp ), dimension(nLocal)   :: mfact
825	>	real( kind = dp ), dimension(3,nLocal) :: u_l
826	>	real( kind = dp ), dimension(9,nLocal) :: A
827	>	real( kind = dp ), dimension(3,nLocal) :: f
828	>	real( kind = dp ), dimension(3,nLocal) :: t
829
830	<	real( kind = dp ) :: pot
510	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
511	<	real (kind=dp), dimension(9,getNlocal()) :: A
512	<	real (kind=dp), dimension(3,getNlocal()) :: f
513	<	real (kind=dp), dimension(3,getNlocal()) :: t
514	<
515	<	logical, intent(inout) :: do_pot, do_stress
830	>	logical, intent(inout) :: do_pot
831		integer, intent(in) :: i, j
832	<	real ( kind = dp ), intent(inout)    :: rijsq
832	>	real ( kind = dp ), intent(inout) :: rijsq
833		real ( kind = dp )                :: r
834		real ( kind = dp ), intent(inout) :: d(3)
520	–	logical :: is_LJ_i, is_LJ_j
521	–	logical :: is_DP_i, is_DP_j
522	–	logical :: is_GB_i, is_GB_j
523	–	logical :: is_Sticky_i, is_Sticky_j
835		integer :: me_i, me_j
836
837		r = sqrt(rijsq)
838	+	vpair = 0.0d0
839	+	fpair(1:3) = 0.0d0
840
528	–
529	–
841		#ifdef IS_MPI
842	<	if (tagRow(i) .eq. tagColumn(j)) then
843	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
842	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
843	>	write(0,*) 'do_pair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
844		endif
534	–
845		me_i = atid_row(i)
846		me_j = atid_col(j)
537	–
847		#else
539	–
848		me_i = atid(i)
849		me_j = atid(j)
542	–
850		#endif
851	+
852	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
853	+
854	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
855	+	!write(*,*) 'calling lj with'
856	+	!write(*,*) i, j, r, rijsq
857	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
858	+	!write(*,'(3es12.3)') sw, vpair, pot
859	+	!write(*,*)
860
861	<	if (FF_uses_LJ .and. SimUsesLJ()) then
862	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
863	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
548	<
549	<	if ( is_LJ_i .and. is_LJ_j ) &
550	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
861	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
862	>	endif
863	>
864		endif
865	<
866	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
554	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
555	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
865	>
866	>	if (FF_uses_charges .and. SIM_uses_charges) then
867
868	<	if ( is_DP_i .and. is_DP_j ) then
869	<
559	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
560	<	do_pot, do_stress)
561	<	if (FF_uses_RF .and. SimUsesRF()) then
562	<	call accumulate_rf(i, j, r, u_l)
563	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
564	<	endif
565	<
868	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
869	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
870		endif
871	+
872		endif
873	+
874	+	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
875	+
876	+	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
877	+	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
878	+	do_pot)
879	+	if (FF_uses_RF .and. SIM_uses_RF) then
880	+	call accumulate_rf(i, j, r, u_l, sw)
881	+	call rf_correct_forces(i, j, d, r, u_l, sw, f, fpair)
882	+	endif
883	+	endif
884
885	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
885	>	endif
886
887	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
572	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
887	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
888
889	<	if ( is_Sticky_i .and. is_Sticky_j ) then
890	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
891	<	do_pot, do_stress)
889	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
890	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, A, f, t, &
891	>	do_pot)
892		endif
893	+
894		endif
895
896
897	<	if (FF_uses_GB .and. SimUsesGB()) then
582	<
583	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
584	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
897	>	if (FF_uses_GB .and. SIM_uses_GB) then
898
899	<	if ( is_GB_i .and. is_GB_j ) then
900	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
901	<	do_pot, do_stress)
899	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
900	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
901	>	do_pot)
902		endif
590	–	endif
591	–
592	–	end subroutine do_pair
903
904	<
595	<	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
596	<
597	<	real (kind = dp), dimension(3) :: q_i
598	<	real (kind = dp), dimension(3) :: q_j
599	<	real ( kind = dp ), intent(out) :: r_sq
600	<	real( kind = dp ) :: d(3), scaled(3)
601	<	integer i
602	<
603	<	d(1:3) = q_j(1:3) - q_i(1:3)
604	<
605	<	! Wrap back into periodic box if necessary
606	<	if ( SimUsesPBC() ) then
904	>	endif
905
906	<	if( .not.boxIsOrthorhombic ) then
907	<	! calc the scaled coordinates.
908	<
909	<	scaled = matmul(HmatInv, d)
910	<
613	<	! wrap the scaled coordinates
614	<
615	<	scaled = scaled  - anint(scaled)
616	<
617	<
618	<	! calc the wrapped real coordinates from the wrapped scaled
619	<	! coordinates
620	<
621	<	d = matmul(Hmat,scaled)
622	<
623	<	else
624	<	! calc the scaled coordinates.
625	<
626	<	do i = 1, 3
627	<	scaled(i) = d(i) * HmatInv(i,i)
628	<
629	<	! wrap the scaled coordinates
630	<
631	<	scaled(i) = scaled(i) - anint(scaled(i))
632	<
633	<	! calc the wrapped real coordinates from the wrapped scaled
634	<	! coordinates
635	<
636	<	d(i) = scaled(i)*Hmat(i,i)
637	<	enddo
906	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
907	>
908	>	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
909	>	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, &
910	>	do_pot)
911		endif
912
913		endif
914
915	<	r_sq = dot_product(d,d)
643	<
644	<	end subroutine get_interatomic_vector
645	<
646	<	subroutine check_initialization(error)
647	<	integer, intent(out) :: error
648	<
649	<	error = 0
650	<	! Make sure we are properly initialized.
651	<	if (.not. do_forces_initialized) then
652	<	error = -1
653	<	return
654	<	endif
915	>	end subroutine do_pair
916
917	<	#ifdef IS_MPI
918	<	if (.not. isMPISimSet()) then
658	<	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
659	<	error = -1
660	<	return
661	<	endif
662	<	#endif
663	<
664	<	return
665	<	end subroutine check_initialization
917	>	subroutine do_prepair(i, j, rijsq, d, sw, rcijsq, dc, &
918	>	do_pot, do_stress, u_l, A, f, t, pot)
919
920	<
921	<	subroutine zero_work_arrays()
922	<
923	<	#ifdef IS_MPI
920	>	real( kind = dp ) :: pot, sw
921	>	real( kind = dp ), dimension(3,nLocal) :: u_l
922	>	real (kind=dp), dimension(9,nLocal) :: A
923	>	real (kind=dp), dimension(3,nLocal) :: f
924	>	real (kind=dp), dimension(3,nLocal) :: t
925	>
926	>	logical, intent(inout) :: do_pot, do_stress
927	>	integer, intent(in) :: i, j
928	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
929	>	real ( kind = dp )                :: r, rc
930	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
931	>
932	>	logical :: is_EAM_i, is_EAM_j
933	>
934	>	integer :: me_i, me_j
935	>
936
937	<	q_Row = 0.0_dp
938	<	q_Col = 0.0_dp
939	<
940	<	u_l_Row = 0.0_dp
941	<	u_l_Col = 0.0_dp
942	<
943	<	A_Row = 0.0_dp
679	<	A_Col = 0.0_dp
680	<
681	<	f_Row = 0.0_dp
682	<	f_Col = 0.0_dp
683	<	f_Temp = 0.0_dp
684	<
685	<	t_Row = 0.0_dp
686	<	t_Col = 0.0_dp
687	<	t_Temp = 0.0_dp
688	<
689	<	pot_Row = 0.0_dp
690	<	pot_Col = 0.0_dp
691	<	pot_Temp = 0.0_dp
937	>	r = sqrt(rijsq)
938	>	if (SIM_uses_molecular_cutoffs) then
939	>	rc = sqrt(rcijsq)
940	>	else
941	>	rc = r
942	>	endif
943	>
944
693	–	rf_Row = 0.0_dp
694	–	rf_Col = 0.0_dp
695	–	rf_Temp = 0.0_dp
696	–
697	–	#endif
698	–
699	–	rf = 0.0_dp
700	–	tau_Temp = 0.0_dp
701	–	virial_Temp = 0.0_dp
702	–	end subroutine zero_work_arrays
703	–
704	–	function skipThisPair(atom1, atom2) result(skip_it)
705	–	integer, intent(in) :: atom1
706	–	integer, intent(in), optional :: atom2
707	–	logical :: skip_it
708	–	integer :: unique_id_1, unique_id_2
709	–	integer :: me_i,me_j
710	–	integer :: i
711	–
712	–	skip_it = .false.
713	–
714	–	!! there are a number of reasons to skip a pair or a particle
715	–	!! mostly we do this to exclude atoms who are involved in short
716	–	!! range interactions (bonds, bends, torsions), but we also need
717	–	!! to exclude some overcounted interactions that result from
718	–	!! the parallel decomposition
719	–
945		#ifdef IS_MPI
946	<	!! in MPI, we have to look up the unique IDs for each atom
947	<	unique_id_1 = tagRow(atom1)
946	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
947	>	write(0,*) 'do_prepair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
948	>	endif
949	>
950	>	me_i = atid_row(i)
951	>	me_j = atid_col(j)
952	>
953		#else
954	<	!! in the normal loop, the atom numbers are unique
955	<	unique_id_1 = atom1
954	>
955	>	me_i = atid(i)
956	>	me_j = atid(j)
957	>
958		#endif
959	+
960	+	if (FF_uses_EAM .and. SIM_uses_EAM) then
961	+
962	+	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
963	+	call calc_EAM_prepair_rho(i, j, d, r, rijsq )
964	+
965	+	endif
966	+
967	+	end subroutine do_prepair
968	+
969	+
970	+	subroutine do_preforce(nlocal,pot)
971	+	integer :: nlocal
972	+	real( kind = dp ) :: pot
973	+
974	+	if (FF_uses_EAM .and. SIM_uses_EAM) then
975	+	call calc_EAM_preforce_Frho(nlocal,pot)
976	+	endif
977	+
978	+
979	+	end subroutine do_preforce
980	+
981	+
982	+	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
983	+
984	+	real (kind = dp), dimension(3) :: q_i
985	+	real (kind = dp), dimension(3) :: q_j
986	+	real ( kind = dp ), intent(out) :: r_sq
987	+	real( kind = dp ) :: d(3), scaled(3)
988	+	integer i
989	+
990	+	d(1:3) = q_j(1:3) - q_i(1:3)
991	+
992	+	! Wrap back into periodic box if necessary
993	+	if ( SIM_uses_PBC ) then
994	+
995	+	if( .not.boxIsOrthorhombic ) then
996	+	! calc the scaled coordinates.
997	+
998	+	scaled = matmul(HmatInv, d)
999	+
1000	+	! wrap the scaled coordinates
1001	+
1002	+	scaled = scaled  - anint(scaled)
1003	+
1004	+
1005	+	! calc the wrapped real coordinates from the wrapped scaled
1006	+	! coordinates
1007	+
1008	+	d = matmul(Hmat,scaled)
1009	+
1010	+	else
1011	+	! calc the scaled coordinates.
1012	+
1013	+	do i = 1, 3
1014	+	scaled(i) = d(i) * HmatInv(i,i)
1015	+
1016	+	! wrap the scaled coordinates
1017	+
1018	+	scaled(i) = scaled(i) - anint(scaled(i))
1019	+
1020	+	! calc the wrapped real coordinates from the wrapped scaled
1021	+	! coordinates
1022	+
1023	+	d(i) = scaled(i)*Hmat(i,i)
1024	+	enddo
1025	+	endif
1026	+
1027	+	endif
1028	+
1029	+	r_sq = dot_product(d,d)
1030	+
1031	+	end subroutine get_interatomic_vector
1032	+
1033	+	subroutine zero_work_arrays()
1034	+
1035	+	#ifdef IS_MPI
1036	+
1037	+	q_Row = 0.0_dp
1038	+	q_Col = 0.0_dp
1039
1040	<	!! We were called with only one atom, so just check the global exclude
1041	<	!! list for this atom
1042	<	if (.not. present(atom2)) then
1043	<	do i = 1, nExcludes_global
1044	<	if (excludesGlobal(i) == unique_id_1) then
1045	<	skip_it = .true.
1046	<	return
1047	<	end if
1048	<	end do
1049	<	return
1050	<	end if
1051	<
1040	>	q_group_Row = 0.0_dp
1041	>	q_group_Col = 0.0_dp
1042	>
1043	>	u_l_Row = 0.0_dp
1044	>	u_l_Col = 0.0_dp
1045	>
1046	>	A_Row = 0.0_dp
1047	>	A_Col = 0.0_dp
1048	>
1049	>	f_Row = 0.0_dp
1050	>	f_Col = 0.0_dp
1051	>	f_Temp = 0.0_dp
1052	>
1053	>	t_Row = 0.0_dp
1054	>	t_Col = 0.0_dp
1055	>	t_Temp = 0.0_dp
1056	>
1057	>	pot_Row = 0.0_dp
1058	>	pot_Col = 0.0_dp
1059	>	pot_Temp = 0.0_dp
1060	>
1061	>	rf_Row = 0.0_dp
1062	>	rf_Col = 0.0_dp
1063	>	rf_Temp = 0.0_dp
1064	>
1065	>	#endif
1066	>
1067	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1068	>	call clean_EAM()
1069	>	endif
1070	>
1071	>	rf = 0.0_dp
1072	>	tau_Temp = 0.0_dp
1073	>	virial_Temp = 0.0_dp
1074	>	end subroutine zero_work_arrays
1075	>
1076	>	function skipThisPair(atom1, atom2) result(skip_it)
1077	>	integer, intent(in) :: atom1
1078	>	integer, intent(in), optional :: atom2
1079	>	logical :: skip_it
1080	>	integer :: unique_id_1, unique_id_2
1081	>	integer :: me_i,me_j
1082	>	integer :: i
1083	>
1084	>	skip_it = .false.
1085	>
1086	>	!! there are a number of reasons to skip a pair or a particle
1087	>	!! mostly we do this to exclude atoms who are involved in short
1088	>	!! range interactions (bonds, bends, torsions), but we also need
1089	>	!! to exclude some overcounted interactions that result from
1090	>	!! the parallel decomposition
1091	>
1092		#ifdef IS_MPI
1093	<	unique_id_2 = tagColumn(atom2)
1093	>	!! in MPI, we have to look up the unique IDs for each atom
1094	>	unique_id_1 = AtomRowToGlobal(atom1)
1095		#else
1096	<	unique_id_2 = atom2
1096	>	!! in the normal loop, the atom numbers are unique
1097	>	unique_id_1 = atom1
1098		#endif
1099	<
1099	>
1100	>	!! We were called with only one atom, so just check the global exclude
1101	>	!! list for this atom
1102	>	if (.not. present(atom2)) then
1103	>	do i = 1, nExcludes_global
1104	>	if (excludesGlobal(i) == unique_id_1) then
1105	>	skip_it = .true.
1106	>	return
1107	>	end if
1108	>	end do
1109	>	return
1110	>	end if
1111	>
1112		#ifdef IS_MPI
1113	<	!! this situation should only arise in MPI simulations
1114	<	if (unique_id_1 == unique_id_2) then
1115	<	skip_it = .true.
750	<	return
751	<	end if
752	<
753	<	!! this prevents us from doing the pair on multiple processors
754	<	if (unique_id_1 < unique_id_2) then
755	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
756	<	skip_it = .true.
757	<	return
758	<	endif
759	<	else
760	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
761	<	skip_it = .true.
762	<	return
763	<	endif
764	<	endif
1113	>	unique_id_2 = AtomColToGlobal(atom2)
1114	>	#else
1115	>	unique_id_2 = atom2
1116		#endif
1117	+
1118	+	#ifdef IS_MPI
1119	+	!! this situation should only arise in MPI simulations
1120	+	if (unique_id_1 == unique_id_2) then
1121	+	skip_it = .true.
1122	+	return
1123	+	end if
1124	+
1125	+	!! this prevents us from doing the pair on multiple processors
1126	+	if (unique_id_1 < unique_id_2) then
1127	+	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1128	+	skip_it = .true.
1129	+	return
1130	+	endif
1131	+	else
1132	+	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1133	+	skip_it = .true.
1134	+	return
1135	+	endif
1136	+	endif
1137	+	#endif
1138	+
1139	+	!! the rest of these situations can happen in all simulations:
1140	+	do i = 1, nExcludes_global
1141	+	if ((excludesGlobal(i) == unique_id_1) .or. &
1142	+	(excludesGlobal(i) == unique_id_2)) then
1143	+	skip_it = .true.
1144	+	return
1145	+	endif
1146	+	enddo
1147	+
1148	+	do i = 1, nSkipsForAtom(atom1)
1149	+	if (skipsForAtom(atom1, i) .eq. unique_id_2) then
1150	+	skip_it = .true.
1151	+	return
1152	+	endif
1153	+	end do
1154	+
1155	+	return
1156	+	end function skipThisPair
1157
1158	<	!! the rest of these situations can happen in all simulations:
1159	<	do i = 1, nExcludes_global
1160	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1161	<	(excludesGlobal(i) == unique_id_2)) then
1162	<	skip_it = .true.
1163	<	return
1164	<	endif
1165	<	enddo
1158	>	function FF_UsesDirectionalAtoms() result(doesit)
1159	>	logical :: doesit
1160	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1161	>	FF_uses_GB .or. FF_uses_RF
1162	>	end function FF_UsesDirectionalAtoms
1163	>
1164	>	function FF_RequiresPrepairCalc() result(doesit)
1165	>	logical :: doesit
1166	>	doesit = FF_uses_EAM
1167	>	end function FF_RequiresPrepairCalc
1168	>
1169	>	function FF_RequiresPostpairCalc() result(doesit)
1170	>	logical :: doesit
1171	>	doesit = FF_uses_RF
1172	>	end function FF_RequiresPostpairCalc
1173	>
1174	>	#ifdef PROFILE
1175	>	function getforcetime() result(totalforcetime)
1176	>	real(kind=dp) :: totalforcetime
1177	>	totalforcetime = forcetime
1178	>	end function getforcetime
1179	>	#endif
1180	>
1181	>	!! This cleans componets of force arrays belonging only to fortran
1182
1183	<	do i = 1, nExcludes_local
1184	<	if (excludesLocal(1,i) == unique_id_1) then
1185	<	if (excludesLocal(2,i) == unique_id_2) then
1186	<	skip_it = .true.
1187	<	return
1188	<	endif
1189	<	else
1190	<	if (excludesLocal(1,i) == unique_id_2) then
1191	<	if (excludesLocal(2,i) == unique_id_1) then
1192	<	skip_it = .true.
1193	<	return
1194	<	endif
1195	<	endif
1196	<	endif
1197	<	end do
1198	<
1199	<	return
1200	<	end function skipThisPair
1201	<
1202	<	function FF_UsesDirectionalAtoms() result(doesit)
1203	<	logical :: doesit
1204	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1205	<	FF_uses_GB .or. FF_uses_RF
1206	<	end function FF_UsesDirectionalAtoms
800	<
801	<	function FF_RequiresPrepairCalc() result(doesit)
802	<	logical :: doesit
803	<	doesit = FF_uses_EAM
804	<	end function FF_RequiresPrepairCalc
805	<
806	<	function FF_RequiresPostpairCalc() result(doesit)
807	<	logical :: doesit
808	<	doesit = FF_uses_RF
809	<	end function FF_RequiresPostpairCalc
810	<
1183	>	subroutine add_stress_tensor(dpair, fpair)
1184	>
1185	>	real( kind = dp ), dimension(3), intent(in) :: dpair, fpair
1186	>
1187	>	! because the d vector is the rj - ri vector, and
1188	>	! because fx, fy, fz are the force on atom i, we need a
1189	>	! negative sign here:
1190	>
1191	>	tau_Temp(1) = tau_Temp(1) - dpair(1) * fpair(1)
1192	>	tau_Temp(2) = tau_Temp(2) - dpair(1) * fpair(2)
1193	>	tau_Temp(3) = tau_Temp(3) - dpair(1) * fpair(3)
1194	>	tau_Temp(4) = tau_Temp(4) - dpair(2) * fpair(1)
1195	>	tau_Temp(5) = tau_Temp(5) - dpair(2) * fpair(2)
1196	>	tau_Temp(6) = tau_Temp(6) - dpair(2) * fpair(3)
1197	>	tau_Temp(7) = tau_Temp(7) - dpair(3) * fpair(1)
1198	>	tau_Temp(8) = tau_Temp(8) - dpair(3) * fpair(2)
1199	>	tau_Temp(9) = tau_Temp(9) - dpair(3) * fpair(3)
1200	>
1201	>	!write(*,'(6es12.3)')  fpair(1:3), tau_Temp(1), tau_Temp(5), tau_temp(9)
1202	>	virial_Temp = virial_Temp + &
1203	>	(tau_Temp(1) + tau_Temp(5) + tau_Temp(9))
1204	>
1205	>	end subroutine add_stress_tensor
1206	>
1207		end module do_Forces
1208	+

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