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

Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 891 by mmeineke, Fri Dec 19 20:36:35 2003 UTC vs.
Revision 1208 by gezelter, Fri May 28 15:21:37 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.40 2003-12-19 20:36:35 mmeineke Exp $, $Date: 2003-12-19 20:36:35 $, $Name: not supported by cvs2svn $, $Revision: 1.40 $
7	>	!! @version $Id: do_Forces.F90,v 1.66 2004-05-28 15:21:37 gezelter Exp $, $Date: 2004-05-28 15:21:37 $, $Name: not supported by cvs2svn $, $Revision: 1.66 $
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
#	Line 29 | 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	>	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
#	Line 52 | Line 75 | contains
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 )
#	Line 62 | Line 98 | contains
98		rlistsq = rlist * rlist
99
100		haveRlist = .true.
65	–	if( havePolicies ) do_forces_initialized = .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 90 | 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 110 | 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
#	Line 121 | Line 295 | contains
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
#	Line 135 | Line 310 | contains
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
#	Line 155 | Line 334 | contains
334		if (FF_uses_EAM) then
335		call init_EAM_FF(my_status)
336		if (my_status /= 0) then
337	<	write(*,*) "init_EAM_FF returned a bad status"
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
164	–
165	–
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
185	–
365
366	<	havePolicies = .true.
367	<	if( haveRlist ) do_forces_initialized = .true.
189	<
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
219	–	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
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	<
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
243	–	nlocal = getNlocal()
434		natoms = nlocal
435		#endif
436	<
437	<	call check_initialization(localError)
436	>
437	>	call doReadyCheck(localError)
438		if ( localError .ne. 0 ) then
439	<	call handleError("do_force_loop","Not Initialized")
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	<
258	<
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	<	!! Begin force loop timing:
467	>
468	>	!! Begin force loop timing:
469		#ifdef PROFILE
470		call cpu_time(forceTimeInitial)
471		nloops = nloops + 1
472		#endif
281	–
282	–	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
283	–	!! See if we need to update neighbor lists
284	–	call checkNeighborList(nlocal, q, listSkin, update_nlist)
285	–	!! if_mpi_gather_stuff_for_prepair
286	–	!! do_prepair_loop_if_needed
287	–	!! if_mpi_scatter_stuff_from_prepair
288	–	!! if_mpi_gather_stuff_from_prepair_to_main_loop
289	–
290	–	!--------------------PREFORCE LOOP----------->>>>>>>>>>>>>>>>>>>>>>>>>>>
291	–	#ifdef IS_MPI
473
474	<	if (update_nlist) then
475	<
476	<	!! save current configuration, construct neighbor list,
477	<	!! and calculate forces
478	<	call saveNeighborList(nlocal, q)
479	<
299	<	neighborListSize = size(list)
300	<	nlist = 0
301	<
302	<	do i = 1, nrow
303	<	point(i) = nlist + 1
304	<
305	<	prepair_inner: do j = 1, ncol
306	<
307	<	if (skipThisPair(i,j)) cycle prepair_inner
308	<
309	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
310	<
311	<	if (rijsq < rlistsq) then
312	<
313	<	nlist = nlist + 1
314	<
315	<	if (nlist > neighborListSize) then
316	<	call expandNeighborList(nlocal, listerror)
317	<	if (listerror /= 0) then
318	<	error = -1
319	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
320	<	return
321	<	end if
322	<	neighborListSize = size(list)
323	<	endif
324	<
325	<	list(nlist) = j
326	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot_local)
327	<	endif
328	<	enddo prepair_inner
329	<	enddo
474	>	loopEnd = PAIR_LOOP
475	>	if (FF_RequiresPrepairCalc() .and. SIM_requires_prepair_calc) then
476	>	loopStart = PREPAIR_LOOP
477	>	else
478	>	loopStart = PAIR_LOOP
479	>	endif
480
481	<	point(nrow + 1) = nlist + 1
482	<
333	<	else  !! (of update_check)
481	>	do loop = loopStart, loopEnd
482	>	write(*,*) 'doign loop ', loop
483
484	<	! use the list to find the neighbors
485	<	do i = 1, nrow
486	<	JBEG = POINT(i)
487	<	JEND = POINT(i+1) - 1
488	<	! check thiat molecule i has neighbors
489	<	if (jbeg .le. jend) then
341	<
342	<	do jnab = jbeg, jend
343	<	j = list(jnab)
344	<
345	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
346	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
347	<	u_l, A, f, t, pot_local)
348	<
349	<	enddo
350	<	endif
351	<	enddo
352	<	endif
353	<
484	>	! See if we need to update neighbor lists
485	>	! (but only on the first time through):
486	>	if (loop .eq. loopStart) then
487	>	#ifdef IS_MPI
488	>	call checkNeighborList(nGroupsInRow, q_group_row, listSkin, &
489	>	update_nlist)
490		#else
491	<
492	<	if (update_nlist) then
491	>	call checkNeighborList(nGroups, q_group, listSkin, &
492	>	update_nlist)
493	>	#endif
494	>	endif
495
496	<	! save current configuration, contruct neighbor list,
497	<	! and calculate forces
498	<	call saveNeighborList(natoms, q)
496	>	if (update_nlist) then
497	>	!! save current configuration and construct neighbor list
498	>	#ifdef IS_MPI
499	>	call saveNeighborList(nGroupsInRow, q_group_row)
500	>	#else
501	>	call saveNeighborList(nGroups, q_group)
502	>	#endif
503	>	neighborListSize = size(list)
504	>	nlist = 0
505	>	endif
506
507	<	neighborListSize = size(list)
508	<
509	<	nlist = 0
510	<
511	<	do i = 1, natoms-1
512	<	point(i) = nlist + 1
513	<
369	<	prepair_inner: do j = i+1, natoms
370	<
371	<	if (skipThisPair(i,j))  cycle prepair_inner
372	<
373	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
374	<
507	>	istart = 1
508	>	#ifdef IS_MPI
509	>	iend = nGroupsInRow
510	>	#else
511	>	iend = nGroups - 1
512	>	#endif
513	>	outer: do i = istart, iend
514
515	<	if (rijsq < rlistsq) then
516	<
517	<
518	<	nlist = nlist + 1
519	<
520	<	if (nlist > neighborListSize) then
521	<	call expandNeighborList(natoms, listerror)
383	<	if (listerror /= 0) then
384	<	error = -1
385	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
386	<	return
387	<	end if
388	<	neighborListSize = size(list)
389	<	endif
390	<
391	<	list(nlist) = j
392	<
393	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
394	<	u_l, A, f, t, pot)
395	<
396	<	endif
397	<	enddo prepair_inner
398	<	enddo
399	<
400	<	point(natoms) = nlist + 1
401	<
402	<	else !! (update)
403	<
404	<	! use the list to find the neighbors
405	<	do i = 1, natoms-1
406	<	JBEG = POINT(i)
407	<	JEND = POINT(i+1) - 1
408	<	! check thiat molecule i has neighbors
409	<	if (jbeg .le. jend) then
410	<
411	<	do jnab = jbeg, jend
412	<	j = list(jnab)
413	<
414	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
415	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
416	<	u_l, A, f, t, pot)
417	<
418	<	enddo
419	<	endif
420	<	enddo
421	<	endif
422	<	#endif
423	<	!! Do rest of preforce calculations
424	<	!! do necessary preforce calculations
425	<	call do_preforce(nlocal,pot)
426	<	! we have already updated the neighbor list set it to false...
427	<	update_nlist = .false.
428	<	else
429	<	!! See if we need to update neighbor lists for non pre-pair
430	<	call checkNeighborList(nlocal, q, listSkin, update_nlist)
431	<	endif
432	<
433	<
434	<
435	<
436	<
437	<	!---------------------------------MAIN Pair LOOP->>>>>>>>>>>>>>>>>>>>>>>>>>>>
438	<
439	<
440	<
441	<
442	<
515	>	write(*,*) 'doing ', i
516	>
517	>	if (update_nlist) point(i) = nlist + 1
518	>
519	>	n_in_i = groupStartRow(i+1) - groupStartRow(i)
520	>
521	>	if (update_nlist) then
522		#ifdef IS_MPI
523	<
524	<	if (update_nlist) then
525	<	!! save current configuration, construct neighbor list,
526	<	!! and calculate forces
527	<	call saveNeighborList(nlocal, q)
528	<
529	<	neighborListSize = size(list)
530	<	nlist = 0
531	<
532	<	do i = 1, nrow
533	<	point(i) = nlist + 1
523	>	jstart = 1
524	>	jend = nGroupsInCol
525	>	#else
526	>	jstart = i+1
527	>	jend = nGroups
528	>	#endif
529	>	else
530	>	jstart = point(i)
531	>	jend = point(i+1) - 1
532	>	! make sure group i has neighbors
533	>	if (jstart .gt. jend) cycle outer
534	>	endif
535
536	<	inner: do j = 1, ncol
537	<
538	<	if (skipThisPair(i,j)) cycle inner
539	<
540	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
461	<
462	<	if (rijsq < rlistsq) then
463	<
464	<	nlist = nlist + 1
465	<
466	<	if (nlist > neighborListSize) then
467	<	call expandNeighborList(nlocal, listerror)
468	<	if (listerror /= 0) then
469	<	error = -1
470	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
471	<	return
472	<	end if
473	<	neighborListSize = size(list)
474	<	endif
475	<
476	<	list(nlist) = j
477	<
478	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
479	<	u_l, A, f, t, pot_local)
480	<
536	>	do jnab = jstart, jend
537	>	if (update_nlist) then
538	>	j = jnab
539	>	else
540	>	j = list(jnab)
541		endif
482	–	enddo inner
483	–	enddo
542
543	<	point(nrow + 1) = nlist + 1
544	<
545	<	else  !! (of update_check)
488	<
489	<	! use the list to find the neighbors
490	<	do i = 1, nrow
491	<	JBEG = POINT(i)
492	<	JEND = POINT(i+1) - 1
493	<	! check thiat molecule i has neighbors
494	<	if (jbeg .le. jend) then
495	<
496	<	do jnab = jbeg, jend
497	<	j = list(jnab)
498	<
499	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
500	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
501	<	u_l, A, f, t, pot_local)
502	<
503	<	enddo
504	<	endif
505	<	enddo
506	<	endif
507	<
543	>	#ifdef IS_MPI
544	>	call get_interatomic_vector(q_group_Row(:,i), &
545	>	q_group_Col(:,j), d_grp, rgrpsq)
546		#else
547	<
548	<	if (update_nlist) then
547	>	call get_interatomic_vector(q_group(:,i), &
548	>	q_group(:,j), d_grp, rgrpsq)
549	>	#endif
550
551	<	! save current configuration, contruct neighbor list,
552	<	! and calculate forces
553	<	call saveNeighborList(natoms, q)
554	<
555	<	neighborListSize = size(list)
556	<
557	<	nlist = 0
558	<
559	<	do i = 1, natoms-1
560	<	point(i) = nlist + 1
561	<
562	<	inner: do j = i+1, natoms
563	<
564	<	if (skipThisPair(i,j))  cycle inner
565	<
566	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
567	<
568	<
569	<	if (rijsq < rlistsq) then
551	>	if (rgrpsq < rlistsq) then
552	>	if (update_nlist) then
553	>	nlist = nlist + 1
554	>
555	>	if (nlist > neighborListSize) then
556	>	#ifdef IS_MPI
557	>	call expandNeighborList(nGroupsInRow, listerror)
558	>	#else
559	>	call expandNeighborList(nGroups, listerror)
560	>	#endif
561	>	if (listerror /= 0) then
562	>	error = -1
563	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
564	>	return
565	>	end if
566	>	neighborListSize = size(list)
567	>	endif
568	>
569	>	list(nlist) = j
570	>	endif
571
572	<	nlist = nlist + 1
573	<
574	<	if (nlist > neighborListSize) then
535	<	call expandNeighborList(natoms, listerror)
536	<	if (listerror /= 0) then
537	<	error = -1
538	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
539	<	return
540	<	end if
541	<	neighborListSize = size(list)
572	>	if (loop .eq. PAIR_LOOP) then
573	>	vij = 0.0d0
574	>	fij(1:3) = 0.0d0
575		endif
576
577	<	list(nlist) = j
577	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
578	>	in_switching_region)
579
580	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
547	<	u_l, A, f, t, pot)
580	>	n_in_j = groupStartCol(j+1) - groupStartCol(j)
581
582	<	endif
583	<	enddo inner
584	<	enddo
582	>	do ia = groupStartRow(i), groupStartRow(i+1)-1
583	>
584	>	atom1 = groupListRow(ia)
585	>
586	>	inner: do jb = groupStartCol(j), groupStartCol(j+1)-1
587	>
588	>	atom2 = groupListCol(jb)
589	>
590	>	if (skipThisPair(atom1, atom2)) cycle inner
591	>
592	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
593	>	d_atm(1:3) = d_grp(1:3)
594	>	ratmsq = rgrpsq
595	>	else
596	>	#ifdef IS_MPI
597	>	call get_interatomic_vector(q_Row(:,atom1), &
598	>	q_Col(:,atom2), d_atm, ratmsq)
599	>	#else
600	>	call get_interatomic_vector(q(:,atom1), &
601	>	q(:,atom2), d_atm, ratmsq)
602	>	#endif
603	>	endif
604	>	if (loop .eq. PREPAIR_LOOP) then
605	>	#ifdef IS_MPI
606	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
607	>	rgrpsq, d_grp, do_pot, do_stress, &
608	>	u_l, A, f, t, pot_local)
609	>	#else
610	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
611	>	rgrpsq, d_grp, do_pot, do_stress, &
612	>	u_l, A, f, t, pot)
613	>	#endif
614	>	else
615	>	#ifdef IS_MPI
616	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
617	>	do_pot, &
618	>	u_l, A, f, t, pot_local, vpair, fpair)
619	>	#else
620	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
621	>	do_pot,  &
622	>	u_l, A, f, t, pot, vpair, fpair)
623	>	#endif
624	>	vij = vij + vpair
625	>	fij(1:3) = fij(1:3) + fpair(1:3)
626	>	endif
627	>	enddo inner
628	>	enddo
629	>
630	>	if (loop .eq. PAIR_LOOP) then
631	>	if (in_switching_region) then
632	>	swderiv = vij*dswdr/rgrp
633	>	fij(1) = fij(1) + swderiv*d_grp(1)
634	>	fij(2) = fij(2) + swderiv*d_grp(2)
635	>	fij(3) = fij(3) + swderiv*d_grp(3)
636	>
637	>	do ia=groupStartRow(i), groupStartRow(i+1)-1
638	>	atom1=groupListRow(ia)
639	>	mf = mfactRow(atom1)
640	>	#ifdef IS_MPI
641	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
642	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
643	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
644	>	#else
645	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
646	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
647	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
648	>	#endif
649	>	enddo
650	>
651	>	do jb=groupStartCol(j), groupStartCol(j+1)-1
652	>	atom2=groupListCol(jb)
653	>	mf = mfactCol(atom2)
654	>	#ifdef IS_MPI
655	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
656	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
657	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
658	>	#else
659	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
660	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
661	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
662	>	#endif
663	>	enddo
664	>	endif
665	>
666	>	if (do_stress) call add_stress_tensor(d_grp, fij)
667	>	endif
668	>	end if
669	>	enddo
670	>	enddo outer
671
672	<	point(natoms) = nlist + 1
673	<
674	<	else !! (update)
675	<
676	<	! use the list to find the neighbors
677	<	do i = 1, natoms-1
678	<	JBEG = POINT(i)
679	<	JEND = POINT(i+1) - 1
680	<	! check thiat molecule i has neighbors
681	<	if (jbeg .le. jend) then
682	<
564	<	do jnab = jbeg, jend
565	<	j = list(jnab)
566	<
567	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
568	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
569	<	u_l, A, f, t, pot)
570	<
571	<	enddo
672	>	if (update_nlist) then
673	>	#ifdef IS_MPI
674	>	point(nGroupsInRow + 1) = nlist + 1
675	>	#else
676	>	point(nGroups) = nlist + 1
677	>	#endif
678	>	if (loop .eq. PREPAIR_LOOP) then
679	>	! we just did the neighbor list update on the first
680	>	! pass, so we don't need to do it
681	>	! again on the second pass
682	>	update_nlist = .false.
683		endif
684	<	enddo
685	<	endif
684	>	endif
685	>
686	>	if (loop .eq. PREPAIR_LOOP) then
687	>	call do_preforce(nlocal, pot)
688	>	endif
689	>
690	>	enddo
691
692	<	#endif
577	<
578	<	! phew, done with main loop.
579	<
580	<	!! Do timing
692	>	!! Do timing
693		#ifdef PROFILE
694		call cpu_time(forceTimeFinal)
695		forceTime = forceTime + forceTimeFinal - forceTimeInitial
696	<	#endif
697	<
586	<
696	>	#endif
697	>
698		#ifdef IS_MPI
699		!!distribute forces
700	<
700	>
701		f_temp = 0.0_dp
702	<	call scatter(f_Row,f_temp,plan_row3d)
702	>	call scatter(f_Row,f_temp,plan_atom_row_3d)
703		do i = 1,nlocal
704		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
705		end do
706	<
706	>
707		f_temp = 0.0_dp
708	<	call scatter(f_Col,f_temp,plan_col3d)
708	>	call scatter(f_Col,f_temp,plan_atom_col_3d)
709		do i = 1,nlocal
710		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
711		end do
712
713	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
713	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
714		t_temp = 0.0_dp
715	<	call scatter(t_Row,t_temp,plan_row3d)
715	>	call scatter(t_Row,t_temp,plan_atom_row_3d)
716		do i = 1,nlocal
717		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
718		end do
719		t_temp = 0.0_dp
720	<	call scatter(t_Col,t_temp,plan_col3d)
720	>	call scatter(t_Col,t_temp,plan_atom_col_3d)
721
722		do i = 1,nlocal
723		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
#	Line 615 | Line 726 | contains
726
727		if (do_pot) then
728		! scatter/gather pot_row into the members of my column
729	<	call scatter(pot_Row, pot_Temp, plan_row)
730	<
729	>	call scatter(pot_Row, pot_Temp, plan_atom_row)
730	>
731		! scatter/gather pot_local into all other procs
732		! add resultant to get total pot
733		do i = 1, nlocal
#	Line 624 | Line 735 | contains
735		enddo
736
737		pot_Temp = 0.0_DP
738	<
739	<	call scatter(pot_Col, pot_Temp, plan_col)
738	>
739	>	call scatter(pot_Col, pot_Temp, plan_atom_col)
740		do i = 1, nlocal
741		pot_local = pot_local + pot_Temp(i)
742		enddo
743	<
744	<	endif
743	>
744	>	endif
745		#endif
746	<
747	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
746	>
747	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
748
749	<	if (FF_uses_RF .and. SimUsesRF()) then
749	>	if (FF_uses_RF .and. SIM_uses_RF) then
750
751		#ifdef IS_MPI
752	<	call scatter(rf_Row,rf,plan_row3d)
753	<	call scatter(rf_Col,rf_Temp,plan_col3d)
752	>	call scatter(rf_Row,rf,plan_atom_row_3d)
753	>	call scatter(rf_Col,rf_Temp,plan_atom_col_3d)
754		do i = 1,nlocal
755		rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
756		end do
757		#endif
758
759	<	do i = 1, getNlocal()
760	<
759	>	do i = 1, nLocal
760	>
761		rfpot = 0.0_DP
762		#ifdef IS_MPI
763		me_i = atid_row(i)
764		#else
765		me_i = atid(i)
766		#endif
767	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
768	<	if ( is_DP_i ) then
769	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
767	>
768	>	if (PropertyMap(me_i)%is_DP) then
769	>
770	>	mu_i = PropertyMap(me_i)%dipole_moment
771	>
772		!! The reaction field needs to include a self contribution
773		!! to the field:
774	<	call accumulate_self_rf(i, mu_i, u_l)
774	>	call accumulate_self_rf(i, mu_i, u_l)
775		!! Get the reaction field contribution to the
776		!! potential and torques:
777		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 672 | Line 785 | contains
785		enddo
786		endif
787		endif
788	<
789	<
788	>
789	>
790		#ifdef IS_MPI
791	<
791	>
792		if (do_pot) then
793		pot = pot + pot_local
794		!! we assume the c code will do the allreduce to get the total potential
795		!! we could do it right here if we needed to...
796		endif
797	<
797	>
798		if (do_stress) then
799	<	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
799	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
800		mpi_comm_world,mpi_err)
801		call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
802		mpi_comm_world,mpi_err)
803		endif
804	<
804	>
805		#else
806	<
806	>
807		if (do_stress) then
808		tau = tau_Temp
809		virial = virial_Temp
810		endif
811
812		#endif
813	<
701	<
702	<
813	>
814		end subroutine do_force_loop
815	+
816	+	subroutine do_pair(i, j, rijsq, d, sw, do_pot, &
817	+	u_l, A, f, t, pot, vpair, fpair)
818
819	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
819	>	real( kind = dp ) :: pot, vpair, sw
820	>	real( kind = dp ), dimension(3) :: fpair
821	>	real( kind = dp ), dimension(nLocal)   :: mfact
822	>	real( kind = dp ), dimension(3,nLocal) :: u_l
823	>	real( kind = dp ), dimension(9,nLocal) :: A
824	>	real( kind = dp ), dimension(3,nLocal) :: f
825	>	real( kind = dp ), dimension(3,nLocal) :: t
826
827	<	real( kind = dp ) :: pot
708	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
709	<	real (kind=dp), dimension(9,getNlocal()) :: A
710	<	real (kind=dp), dimension(3,getNlocal()) :: f
711	<	real (kind=dp), dimension(3,getNlocal()) :: t
712	<
713	<	logical, intent(inout) :: do_pot, do_stress
827	>	logical, intent(inout) :: do_pot
828		integer, intent(in) :: i, j
829	<	real ( kind = dp ), intent(inout)    :: rijsq
829	>	real ( kind = dp ), intent(inout) :: rijsq
830		real ( kind = dp )                :: r
831		real ( kind = dp ), intent(inout) :: d(3)
718	–	logical :: is_LJ_i, is_LJ_j
719	–	logical :: is_DP_i, is_DP_j
720	–	logical :: is_GB_i, is_GB_j
721	–	logical :: is_EAM_i,is_EAM_j
722	–	logical :: is_Sticky_i, is_Sticky_j
832		integer :: me_i, me_j
833
834		r = sqrt(rijsq)
835	+	vpair = 0.0d0
836	+	fpair(1:3) = 0.0d0
837
838		#ifdef IS_MPI
839	<	if (tagRow(i) .eq. tagColumn(j)) then
840	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
839	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
840	>	write(0,*) 'do_pair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
841		endif
731	–
842		me_i = atid_row(i)
843		me_j = atid_col(j)
734	–
844		#else
736	–
845		me_i = atid(i)
846		me_j = atid(j)
739	–
847		#endif
848	+
849	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
850	+
851	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
852	+	!write(*,*) 'calling lj with'
853	+	!write(*,*) i, j, r, rijsq
854	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
855	+	!write(*,'(3es12.3)') sw, vpair, pot
856	+	!write(*,*)
857
858	<	if (FF_uses_LJ .and. SimUsesLJ()) then
859	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
860	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
745	<
746	<	if ( is_LJ_i .and. is_LJ_j ) &
747	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
858	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
859	>	endif
860	>
861		endif
862	<
863	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
751	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
752	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
862	>
863	>	if (FF_uses_charges .and. SIM_uses_charges) then
864
865	<	if ( is_DP_i .and. is_DP_j ) then
866	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
756	<	do_pot, do_stress)
757	<	if (FF_uses_RF .and. SimUsesRF()) then
758	<	call accumulate_rf(i, j, r, u_l)
759	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
760	<	endif
761	<
865	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
866	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
867		endif
868	+
869		endif
870	+
871	+	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
872	+
873	+	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
874	+	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
875	+	do_pot)
876	+	if (FF_uses_RF .and. SIM_uses_RF) then
877	+	call accumulate_rf(i, j, r, u_l, sw)
878	+	call rf_correct_forces(i, j, d, r, u_l, sw, f, fpair)
879	+	endif
880	+	endif
881
882	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
882	>	endif
883
884	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
768	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
884	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
885
886	<	if ( is_Sticky_i .and. is_Sticky_j ) then
887	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
888	<	do_pot, do_stress)
886	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
887	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, A, f, t, &
888	>	do_pot)
889		endif
890	+
891		endif
892
893
894	<	if (FF_uses_GB .and. SimUsesGB()) then
894	>	if (FF_uses_GB .and. SIM_uses_GB) then
895	>
896	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
897	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
898	>	do_pot)
899	>	endif
900
901	<
780	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
781	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
901	>	endif
902
903	<	if ( is_GB_i .and. is_GB_j ) then
904	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
905	<	do_pot, do_stress)
903	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
904	>
905	>	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
906	>	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, &
907	>	do_pot)
908		endif
909	+
910		endif
911	<
789	<
790	<
791	<	if (FF_uses_EAM .and. SimUsesEAM()) then
792	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
793	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
794	<
795	<	if ( is_EAM_i .and. is_EAM_j ) &
796	<	call do_eam_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
797	<	endif
798	<
799	<
800	<
801	<
911	>
912		end subroutine do_pair
913
914	+	subroutine do_prepair(i, j, rijsq, d, sw, rcijsq, dc, &
915	+	do_pot, do_stress, u_l, A, f, t, pot)
916
917	<
918	<	subroutine do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
919	<	real( kind = dp ) :: pot
920	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
921	<	real (kind=dp), dimension(9,getNlocal()) :: A
810	<	real (kind=dp), dimension(3,getNlocal()) :: f
811	<	real (kind=dp), dimension(3,getNlocal()) :: t
917	>	real( kind = dp ) :: pot, sw
918	>	real( kind = dp ), dimension(3,nLocal) :: u_l
919	>	real (kind=dp), dimension(9,nLocal) :: A
920	>	real (kind=dp), dimension(3,nLocal) :: f
921	>	real (kind=dp), dimension(3,nLocal) :: t
922
923		logical, intent(inout) :: do_pot, do_stress
924		integer, intent(in) :: i, j
925	<	real ( kind = dp ), intent(inout)    :: rijsq
926	<	real ( kind = dp )                :: r
927	<	real ( kind = dp ), intent(inout) :: d(3)
925	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
926	>	real ( kind = dp )                :: r, rc
927	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
928
929		logical :: is_EAM_i, is_EAM_j
930
931		integer :: me_i, me_j
932
933	<	r = sqrt(rijsq)
933	>
934	>	r = sqrt(rijsq)
935	>	if (SIM_uses_molecular_cutoffs) then
936	>	rc = sqrt(rcijsq)
937	>	else
938	>	rc = r
939	>	endif
940
941
942		#ifdef IS_MPI
943	<	if (tagRow(i) .eq. tagColumn(j)) then
944	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
943	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
944	>	write(0,*) 'do_prepair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
945		endif
946
947		me_i = atid_row(i)
#	Line 837 | Line 953 | contains
953		me_j = atid(j)
954
955		#endif
956	<
957	<	if (FF_uses_EAM .and. SimUsesEAM()) then
842	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
843	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
956	>
957	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
958
959	<	if ( is_EAM_i .and. is_EAM_j ) &
959	>	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
960		call calc_EAM_prepair_rho(i, j, d, r, rijsq )
961	+
962		endif
963	<
963	>
964		end subroutine do_prepair
850	–
851	–
852	–
853	–
854	–	subroutine do_preforce(nlocal,pot)
855	–	integer :: nlocal
856	–	real( kind = dp ) :: pot
857	–
858	–	if (FF_uses_EAM .and. SimUsesEAM()) then
859	–	call calc_EAM_preforce_Frho(nlocal,pot)
860	–	endif
861	–
862	–
863	–	end subroutine do_preforce
864	–
865	–
866	–	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
867	–
868	–	real (kind = dp), dimension(3) :: q_i
869	–	real (kind = dp), dimension(3) :: q_j
870	–	real ( kind = dp ), intent(out) :: r_sq
871	–	real( kind = dp ) :: d(3), scaled(3)
872	–	integer i
873	–
874	–	d(1:3) = q_j(1:3) - q_i(1:3)
875	–
876	–	! Wrap back into periodic box if necessary
877	–	if ( SimUsesPBC() ) then
878	–
879	–	if( .not.boxIsOrthorhombic ) then
880	–	! calc the scaled coordinates.
881	–
882	–	scaled = matmul(HmatInv, d)
883	–
884	–	! wrap the scaled coordinates
885	–
886	–	scaled = scaled  - anint(scaled)
887	–
888	–
889	–	! calc the wrapped real coordinates from the wrapped scaled
890	–	! coordinates
891	–
892	–	d = matmul(Hmat,scaled)
893	–
894	–	else
895	–	! calc the scaled coordinates.
896	–
897	–	do i = 1, 3
898	–	scaled(i) = d(i) * HmatInv(i,i)
899	–
900	–	! wrap the scaled coordinates
901	–
902	–	scaled(i) = scaled(i) - anint(scaled(i))
903	–
904	–	! calc the wrapped real coordinates from the wrapped scaled
905	–	! coordinates
906	–
907	–	d(i) = scaled(i)*Hmat(i,i)
908	–	enddo
909	–	endif
910	–
911	–	endif
912	–
913	–	r_sq = dot_product(d,d)
914	–
915	–	end subroutine get_interatomic_vector
916	–
917	–	subroutine check_initialization(error)
918	–	integer, intent(out) :: error
919	–
920	–	error = 0
921	–	! Make sure we are properly initialized.
922	–	if (.not. do_forces_initialized) then
923	–	write(*,*) "Forces not initialized"
924	–	error = -1
925	–	return
926	–	endif
927	–
928	–	#ifdef IS_MPI
929	–	if (.not. isMPISimSet()) then
930	–	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
931	–	error = -1
932	–	return
933	–	endif
934	–	#endif
935	–
936	–	return
937	–	end subroutine check_initialization
938	–
939	–
940	–	subroutine zero_work_arrays()
941	–
942	–	#ifdef IS_MPI
943	–
944	–	q_Row = 0.0_dp
945	–	q_Col = 0.0_dp
946	–
947	–	u_l_Row = 0.0_dp
948	–	u_l_Col = 0.0_dp
949	–
950	–	A_Row = 0.0_dp
951	–	A_Col = 0.0_dp
952	–
953	–	f_Row = 0.0_dp
954	–	f_Col = 0.0_dp
955	–	f_Temp = 0.0_dp
956	–
957	–	t_Row = 0.0_dp
958	–	t_Col = 0.0_dp
959	–	t_Temp = 0.0_dp
965
966	<	pot_Row = 0.0_dp
967	<	pot_Col = 0.0_dp
968	<	pot_Temp = 0.0_dp
969	<
970	<	rf_Row = 0.0_dp
971	<	rf_Col = 0.0_dp
972	<	rf_Temp = 0.0_dp
966	>
967	>	subroutine do_preforce(nlocal,pot)
968	>	integer :: nlocal
969	>	real( kind = dp ) :: pot
970	>
971	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
972	>	call calc_EAM_preforce_Frho(nlocal,pot)
973	>	endif
974	>
975	>
976	>	end subroutine do_preforce
977	>
978	>
979	>	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
980	>
981	>	real (kind = dp), dimension(3) :: q_i
982	>	real (kind = dp), dimension(3) :: q_j
983	>	real ( kind = dp ), intent(out) :: r_sq
984	>	real( kind = dp ) :: d(3), scaled(3)
985	>	integer i
986	>
987	>	d(1:3) = q_j(1:3) - q_i(1:3)
988	>
989	>	! Wrap back into periodic box if necessary
990	>	if ( SIM_uses_PBC ) then
991	>
992	>	if( .not.boxIsOrthorhombic ) then
993	>	! calc the scaled coordinates.
994	>
995	>	scaled = matmul(HmatInv, d)
996	>
997	>	! wrap the scaled coordinates
998	>
999	>	scaled = scaled  - anint(scaled)
1000	>
1001	>
1002	>	! calc the wrapped real coordinates from the wrapped scaled
1003	>	! coordinates
1004	>
1005	>	d = matmul(Hmat,scaled)
1006	>
1007	>	else
1008	>	! calc the scaled coordinates.
1009	>
1010	>	do i = 1, 3
1011	>	scaled(i) = d(i) * HmatInv(i,i)
1012	>
1013	>	! wrap the scaled coordinates
1014	>
1015	>	scaled(i) = scaled(i) - anint(scaled(i))
1016	>
1017	>	! calc the wrapped real coordinates from the wrapped scaled
1018	>	! coordinates
1019	>
1020	>	d(i) = scaled(i)*Hmat(i,i)
1021	>	enddo
1022	>	endif
1023	>
1024	>	endif
1025	>
1026	>	r_sq = dot_product(d,d)
1027	>
1028	>	end subroutine get_interatomic_vector
1029	>
1030	>	subroutine zero_work_arrays()
1031	>
1032	>	#ifdef IS_MPI
1033	>
1034	>	q_Row = 0.0_dp
1035	>	q_Col = 0.0_dp
1036
1037	+	q_group_Row = 0.0_dp
1038	+	q_group_Col = 0.0_dp
1039	+
1040	+	u_l_Row = 0.0_dp
1041	+	u_l_Col = 0.0_dp
1042	+
1043	+	A_Row = 0.0_dp
1044	+	A_Col = 0.0_dp
1045	+
1046	+	f_Row = 0.0_dp
1047	+	f_Col = 0.0_dp
1048	+	f_Temp = 0.0_dp
1049	+
1050	+	t_Row = 0.0_dp
1051	+	t_Col = 0.0_dp
1052	+	t_Temp = 0.0_dp
1053	+
1054	+	pot_Row = 0.0_dp
1055	+	pot_Col = 0.0_dp
1056	+	pot_Temp = 0.0_dp
1057	+
1058	+	rf_Row = 0.0_dp
1059	+	rf_Col = 0.0_dp
1060	+	rf_Temp = 0.0_dp
1061	+
1062		#endif
970	–
1063
1064	<	if (FF_uses_EAM .and. SimUsesEAM()) then
1065	<	call clean_EAM()
1066	<	endif
1067	<
1068	<
1069	<
1070	<
1071	<
1072	<	rf = 0.0_dp
1073	<	tau_Temp = 0.0_dp
1074	<	virial_Temp = 0.0_dp
1075	<	end subroutine zero_work_arrays
1076	<
1077	<	function skipThisPair(atom1, atom2) result(skip_it)
1078	<	integer, intent(in) :: atom1
1079	<	integer, intent(in), optional :: atom2
1080	<	logical :: skip_it
1081	<	integer :: unique_id_1, unique_id_2
1082	<	integer :: me_i,me_j
1083	<	integer :: i
1084	<
1085	<	skip_it = .false.
1086	<
1087	<	!! there are a number of reasons to skip a pair or a particle
1088	<	!! mostly we do this to exclude atoms who are involved in short
997	<	!! range interactions (bonds, bends, torsions), but we also need
998	<	!! to exclude some overcounted interactions that result from
999	<	!! the parallel decomposition
1000	<
1064	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1065	>	call clean_EAM()
1066	>	endif
1067	>
1068	>	rf = 0.0_dp
1069	>	tau_Temp = 0.0_dp
1070	>	virial_Temp = 0.0_dp
1071	>	end subroutine zero_work_arrays
1072	>
1073	>	function skipThisPair(atom1, atom2) result(skip_it)
1074	>	integer, intent(in) :: atom1
1075	>	integer, intent(in), optional :: atom2
1076	>	logical :: skip_it
1077	>	integer :: unique_id_1, unique_id_2
1078	>	integer :: me_i,me_j
1079	>	integer :: i
1080	>
1081	>	skip_it = .false.
1082	>
1083	>	!! there are a number of reasons to skip a pair or a particle
1084	>	!! mostly we do this to exclude atoms who are involved in short
1085	>	!! range interactions (bonds, bends, torsions), but we also need
1086	>	!! to exclude some overcounted interactions that result from
1087	>	!! the parallel decomposition
1088	>
1089		#ifdef IS_MPI
1090	<	!! in MPI, we have to look up the unique IDs for each atom
1091	<	unique_id_1 = tagRow(atom1)
1090	>	!! in MPI, we have to look up the unique IDs for each atom
1091	>	unique_id_1 = AtomRowToGlobal(atom1)
1092		#else
1093	<	!! in the normal loop, the atom numbers are unique
1094	<	unique_id_1 = atom1
1093	>	!! in the normal loop, the atom numbers are unique
1094	>	unique_id_1 = atom1
1095		#endif
1096	<
1097	<	!! We were called with only one atom, so just check the global exclude
1098	<	!! list for this atom
1099	<	if (.not. present(atom2)) then
1100	<	do i = 1, nExcludes_global
1101	<	if (excludesGlobal(i) == unique_id_1) then
1102	<	skip_it = .true.
1103	<	return
1104	<	end if
1105	<	end do
1106	<	return
1107	<	end if
1108	<
1096	>
1097	>	!! We were called with only one atom, so just check the global exclude
1098	>	!! list for this atom
1099	>	if (.not. present(atom2)) then
1100	>	do i = 1, nExcludes_global
1101	>	if (excludesGlobal(i) == unique_id_1) then
1102	>	skip_it = .true.
1103	>	return
1104	>	end if
1105	>	end do
1106	>	return
1107	>	end if
1108	>
1109		#ifdef IS_MPI
1110	<	unique_id_2 = tagColumn(atom2)
1110	>	unique_id_2 = AtomColToGlobal(atom2)
1111		#else
1112	<	unique_id_2 = atom2
1112	>	unique_id_2 = atom2
1113		#endif
1114	<
1114	>
1115		#ifdef IS_MPI
1116	<	!! this situation should only arise in MPI simulations
1117	<	if (unique_id_1 == unique_id_2) then
1118	<	skip_it = .true.
1119	<	return
1120	<	end if
1121	<
1122	<	!! this prevents us from doing the pair on multiple processors
1123	<	if (unique_id_1 < unique_id_2) then
1124	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1125	<	skip_it = .true.
1126	<	return
1127	<	endif
1128	<	else
1129	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1130	<	skip_it = .true.
1131	<	return
1132	<	endif
1133	<	endif
1116	>	!! this situation should only arise in MPI simulations
1117	>	if (unique_id_1 == unique_id_2) then
1118	>	skip_it = .true.
1119	>	return
1120	>	end if
1121	>
1122	>	!! this prevents us from doing the pair on multiple processors
1123	>	if (unique_id_1 < unique_id_2) then
1124	>	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1125	>	skip_it = .true.
1126	>	return
1127	>	endif
1128	>	else
1129	>	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1130	>	skip_it = .true.
1131	>	return
1132	>	endif
1133	>	endif
1134		#endif
1135	+
1136	+	!! the rest of these situations can happen in all simulations:
1137	+	do i = 1, nExcludes_global
1138	+	if ((excludesGlobal(i) == unique_id_1) .or. &
1139	+	(excludesGlobal(i) == unique_id_2)) then
1140	+	skip_it = .true.
1141	+	return
1142	+	endif
1143	+	enddo
1144	+
1145	+	do i = 1, nSkipsForAtom(atom1)
1146	+	if (skipsForAtom(atom1, i) .eq. unique_id_2) then
1147	+	skip_it = .true.
1148	+	return
1149	+	endif
1150	+	end do
1151	+
1152	+	return
1153	+	end function skipThisPair
1154
1155	<	!! the rest of these situations can happen in all simulations:
1156	<	do i = 1, nExcludes_global
1157	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1158	<	(excludesGlobal(i) == unique_id_2)) then
1159	<	skip_it = .true.
1160	<	return
1161	<	endif
1162	<	enddo
1163	<
1164	<	do i = 1, nExcludes_local
1165	<	if (excludesLocal(1,i) == unique_id_1) then
1166	<	if (excludesLocal(2,i) == unique_id_2) then
1167	<	skip_it = .true.
1168	<	return
1169	<	endif
1170	<	else
1064	<	if (excludesLocal(1,i) == unique_id_2) then
1065	<	if (excludesLocal(2,i) == unique_id_1) then
1066	<	skip_it = .true.
1067	<	return
1068	<	endif
1069	<	endif
1070	<	endif
1071	<	end do
1072	<
1073	<	return
1074	<	end function skipThisPair
1075	<
1076	<	function FF_UsesDirectionalAtoms() result(doesit)
1077	<	logical :: doesit
1078	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1079	<	FF_uses_GB .or. FF_uses_RF
1080	<	end function FF_UsesDirectionalAtoms
1081	<
1082	<	function FF_RequiresPrepairCalc() result(doesit)
1083	<	logical :: doesit
1084	<	doesit = FF_uses_EAM
1085	<	end function FF_RequiresPrepairCalc
1086	<
1087	<	function FF_RequiresPostpairCalc() result(doesit)
1088	<	logical :: doesit
1089	<	doesit = FF_uses_RF
1090	<	end function FF_RequiresPostpairCalc
1091	<
1155	>	function FF_UsesDirectionalAtoms() result(doesit)
1156	>	logical :: doesit
1157	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1158	>	FF_uses_GB .or. FF_uses_RF
1159	>	end function FF_UsesDirectionalAtoms
1160	>
1161	>	function FF_RequiresPrepairCalc() result(doesit)
1162	>	logical :: doesit
1163	>	doesit = FF_uses_EAM
1164	>	end function FF_RequiresPrepairCalc
1165	>
1166	>	function FF_RequiresPostpairCalc() result(doesit)
1167	>	logical :: doesit
1168	>	doesit = FF_uses_RF
1169	>	end function FF_RequiresPostpairCalc
1170	>
1171		#ifdef PROFILE
1172	<	function getforcetime() result(totalforcetime)
1173	<	real(kind=dp) :: totalforcetime
1174	<	totalforcetime = forcetime
1175	<	end function getforcetime
1172	>	function getforcetime() result(totalforcetime)
1173	>	real(kind=dp) :: totalforcetime
1174	>	totalforcetime = forcetime
1175	>	end function getforcetime
1176		#endif
1177	+
1178	+	!! This cleans componets of force arrays belonging only to fortran
1179
1180	<	!! This cleans componets of force arrays belonging only to fortran
1181	<
1180	>	subroutine add_stress_tensor(dpair, fpair)
1181	>
1182	>	real( kind = dp ), dimension(3), intent(in) :: dpair, fpair
1183	>
1184	>	! because the d vector is the rj - ri vector, and
1185	>	! because fx, fy, fz are the force on atom i, we need a
1186	>	! negative sign here:
1187	>
1188	>	tau_Temp(1) = tau_Temp(1) - dpair(1) * fpair(1)
1189	>	tau_Temp(2) = tau_Temp(2) - dpair(1) * fpair(2)
1190	>	tau_Temp(3) = tau_Temp(3) - dpair(1) * fpair(3)
1191	>	tau_Temp(4) = tau_Temp(4) - dpair(2) * fpair(1)
1192	>	tau_Temp(5) = tau_Temp(5) - dpair(2) * fpair(2)
1193	>	tau_Temp(6) = tau_Temp(6) - dpair(2) * fpair(3)
1194	>	tau_Temp(7) = tau_Temp(7) - dpair(3) * fpair(1)
1195	>	tau_Temp(8) = tau_Temp(8) - dpair(3) * fpair(2)
1196	>	tau_Temp(9) = tau_Temp(9) - dpair(3) * fpair(3)
1197	>
1198	>	!write(*,'(6es12.3)')  fpair(1:3), tau_Temp(1), tau_Temp(5), tau_temp(9)
1199	>	virial_Temp = virial_Temp + &
1200	>	(tau_Temp(1) + tau_Temp(5) + tau_Temp(9))
1201	>
1202	>	end subroutine add_stress_tensor
1203	>
1204		end module do_Forces
1205	+

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