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

Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.36 2003-10-30 18:59:20 gezelter Exp $, $Date: 2003-10-30 18:59:20 $, $Name: not supported by cvs2svn $, $Revision: 1.36 $
7	>	!! @version $Id: do_Forces.F90,v 1.63 2004-05-27 00:48:12 tim Exp $, $Date: 2004-05-27 00:48:12 $, $Name: not supported by cvs2svn $, $Revision: 1.63 $
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 46 | Line 69 | module do_Forces
69		public :: setRlistDF
70
71		#ifdef PROFILE
72	<	real(kind = dp) :: forceTime
73	<	real(kind = dp) :: forceTimeInitial, forceTimeFinal
74	<	real(kind = dp) :: globalForceTime
75	<	real(kind = dp) :: maxForceTime
53	<	integer, save :: nloops = 0
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 )
#	Line 63 | Line 98 | contains
98		rlistsq = rlist * rlist
99
100		haveRlist = .true.
66	–	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 91 | 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 111 | 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 122 | 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 136 | 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 156 | 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
165	–
166	–
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
186	–
365
366	<	havePolicies = .true.
367	<	if( haveRlist ) do_forces_initialized = .true.
190	<
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)
375	<	!! Position array provided by C, dimensioned by getNlocal
376	<	real ( kind = dp ), dimension(3,getNlocal()) :: q
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, 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
220	–	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		#else
244	–	nlocal = getNlocal()
432		natoms = nlocal
433		#endif
434	<
435	<	call check_initialization(localError)
434	>
435	>	call doReadyCheck(localError)
436		if ( localError .ne. 0 ) then
437	<	call handleError("do_force_loop","Not Initialized")
437	>	call handleError("do_force_loop", "Not Initialized")
438		error = -1
439		return
440		end if
441		call zero_work_arrays()
442	<
442	>
443		do_pot = do_pot_c
444		do_stress = do_stress_c
445	<
259	<
445	>
446		! Gather all information needed by all force loops:
447
448		#ifdef IS_MPI
449	+
450	+	call gather(q, q_Row, plan_atom_row_3d)
451	+	call gather(q, q_Col, plan_atom_col_3d)
452
453	<	call gather(q,q_Row,plan_row3d)
454	<	call gather(q,q_Col,plan_col3d)
453	>	call gather(q_group, q_group_Row, plan_group_row_3d)
454	>	call gather(q_group, q_group_Col, plan_group_col_3d)
455
456	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
457	<	call gather(u_l,u_l_Row,plan_row3d)
458	<	call gather(u_l,u_l_Col,plan_col3d)
456	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
457	>	call gather(u_l, u_l_Row, plan_atom_row_3d)
458	>	call gather(u_l, u_l_Col, plan_atom_col_3d)
459
460	<	call gather(A,A_Row,plan_row_rotation)
461	<	call gather(A,A_Col,plan_col_rotation)
460	>	call gather(A, A_Row, plan_atom_row_rotation)
461	>	call gather(A, A_Col, plan_atom_col_rotation)
462		endif
463
464		#endif
465	<
466	<	!! Begin force loop timing:
465	>
466	>	!! Begin force loop timing:
467		#ifdef PROFILE
468		call cpu_time(forceTimeInitial)
469		nloops = nloops + 1
470		#endif
282	–
283	–	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
284	–	!! See if we need to update neighbor lists
285	–	call checkNeighborList(nlocal, q, listSkin, update_nlist)
286	–	!! if_mpi_gather_stuff_for_prepair
287	–	!! do_prepair_loop_if_needed
288	–	!! if_mpi_scatter_stuff_from_prepair
289	–	!! if_mpi_gather_stuff_from_prepair_to_main_loop
290	–
291	–	!--------------------PREFORCE LOOP----------->>>>>>>>>>>>>>>>>>>>>>>>>>>
292	–	#ifdef IS_MPI
471
472	<	if (update_nlist) then
473	<
474	<	!! save current configuration, construct neighbor list,
475	<	!! and calculate forces
476	<	call saveNeighborList(nlocal, q)
299	<
300	<	neighborListSize = size(list)
301	<	nlist = 0
302	<
303	<	do i = 1, nrow
304	<	point(i) = nlist + 1
305	<
306	<	prepair_inner: do j = 1, ncol
307	<
308	<	if (skipThisPair(i,j)) cycle prepair_inner
309	<
310	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
311	<
312	<	if (rijsq < rlistsq) then
313	<
314	<	nlist = nlist + 1
315	<
316	<	if (nlist > neighborListSize) then
317	<	call expandNeighborList(nlocal, listerror)
318	<	if (listerror /= 0) then
319	<	error = -1
320	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
321	<	return
322	<	end if
323	<	neighborListSize = size(list)
324	<	endif
325	<
326	<	list(nlist) = j
327	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot_local)
328	<	endif
329	<	enddo prepair_inner
330	<	enddo
331	<
332	<	point(nrow + 1) = nlist + 1
333	<
334	<	else  !! (of update_check)
335	<
336	<	! use the list to find the neighbors
337	<	do i = 1, nrow
338	<	JBEG = POINT(i)
339	<	JEND = POINT(i+1) - 1
340	<	! check thiat molecule i has neighbors
341	<	if (jbeg .le. jend) then
342	<
343	<	do jnab = jbeg, jend
344	<	j = list(jnab)
345	<
346	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
347	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
348	<	u_l, A, f, t, pot_local)
349	<
350	<	enddo
351	<	endif
352	<	enddo
472	>	loopEnd = PAIR_LOOP
473	>	if (FF_RequiresPrepairCalc() .and. SIM_requires_prepair_calc) then
474	>	loopStart = PREPAIR_LOOP
475	>	else
476	>	loopStart = PAIR_LOOP
477		endif
354	–
355	–	#else
356	–
357	–	if (update_nlist) then
358	–
359	–	! save current configuration, contruct neighbor list,
360	–	! and calculate forces
361	–	call saveNeighborList(natoms, q)
362	–
363	–	neighborListSize = size(list)
364	–
365	–	nlist = 0
478
479	<	do i = 1, natoms-1
368	<	point(i) = nlist + 1
369	<
370	<	prepair_inner: do j = i+1, natoms
371	<
372	<	if (skipThisPair(i,j))  cycle prepair_inner
373	<
374	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
375	<
479	>	do loop = loopStart, loopEnd
480
481	<	if (rijsq < rlistsq) then
482	<
483	<
484	<	nlist = nlist + 1
485	<
382	<	if (nlist > neighborListSize) then
383	<	call expandNeighborList(natoms, listerror)
384	<	if (listerror /= 0) then
385	<	error = -1
386	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
387	<	return
388	<	end if
389	<	neighborListSize = size(list)
390	<	endif
391	<
392	<	list(nlist) = j
393	<
394	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
395	<	u_l, A, f, t, pot)
396	<
397	<	endif
398	<	enddo prepair_inner
399	<	enddo
481	>	! See if we need to update neighbor lists
482	>	! (but only on the first time through):
483	>	if (loop .eq. loopStart) then
484	>	call checkNeighborList(nGroups, q_group, listSkin, update_nlist)
485	>	endif
486
487	<	point(natoms) = nlist + 1
488	<
403	<	else !! (update)
404	<
405	<	! use the list to find the neighbors
406	<	do i = 1, natoms-1
407	<	JBEG = POINT(i)
408	<	JEND = POINT(i+1) - 1
409	<	! check thiat molecule i has neighbors
410	<	if (jbeg .le. jend) then
411	<
412	<	do jnab = jbeg, jend
413	<	j = list(jnab)
414	<
415	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
416	<	call do_prepair(i, j, rijsq, d, do_pot, do_stress, &
417	<	u_l, A, f, t, pot)
418	<
419	<	enddo
420	<	endif
421	<	enddo
422	<	endif
423	<	#endif
424	<	!! Do rest of preforce calculations
425	<	!! do necessary preforce calculations
426	<	call do_preforce(nlocal,pot)
427	<	! we have already updated the neighbor list set it to false...
428	<	update_nlist = .false.
429	<	else
430	<	!! See if we need to update neighbor lists for non pre-pair
431	<	call checkNeighborList(nlocal, q, listSkin, update_nlist)
432	<	endif
433	<
434	<
435	<
436	<
437	<
438	<	!---------------------------------MAIN Pair LOOP->>>>>>>>>>>>>>>>>>>>>>>>>>>>
439	<
440	<
441	<
442	<
443	<
487	>	if (update_nlist) then
488	>	!! save current configuration and construct neighbor list
489		#ifdef IS_MPI
490	<
491	<	if (update_nlist) then
490	>	call saveNeighborList(nGroupsInRow, q_group)
491	>	#else
492	>	call saveNeighborList(nGroups, q_group)
493	>	#endif
494	>	neighborListSize = size(list)
495	>	nlist = 0
496	>	endif
497
498	<	!! save current configuration, construct neighbor list,
499	<	!! and calculate forces
500	<	call saveNeighborList(nlocal, q)
501	<
502	<	neighborListSize = size(list)
503	<	nlist = 0
504	<
455	<	do i = 1, nrow
456	<	point(i) = nlist + 1
498	>	istart = 1
499	>	#ifdef IS_MPI
500	>	iend = nGroupsInRow
501	>	#else
502	>	iend = nGroups - 1
503	>	#endif
504	>	outer: do i = istart, iend
505
506	<	inner: do j = 1, ncol
507	<
508	<	if (skipThisPair(i,j)) cycle inner
509	<
510	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
511	<
512	<	if (rijsq < rlistsq) then
513	<
466	<	nlist = nlist + 1
467	<
468	<	if (nlist > neighborListSize) then
469	<	call expandNeighborList(nlocal, listerror)
470	<	if (listerror /= 0) then
471	<	error = -1
472	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
473	<	return
474	<	end if
475	<	neighborListSize = size(list)
476	<	endif
477	<
478	<	list(nlist) = j
479	<
480	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
481	<	u_l, A, f, t, pot_local)
482	<
483	<	endif
484	<	enddo inner
485	<	enddo
486	<
487	<	point(nrow + 1) = nlist + 1
488	<
489	<	else  !! (of update_check)
490	<
491	<	! use the list to find the neighbors
492	<	do i = 1, nrow
493	<	JBEG = POINT(i)
494	<	JEND = POINT(i+1) - 1
495	<	! check thiat molecule i has neighbors
496	<	if (jbeg .le. jend) then
497	<
498	<	do jnab = jbeg, jend
499	<	j = list(jnab)
500	<
501	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
502	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
503	<	u_l, A, f, t, pot_local)
504	<
505	<	enddo
506	<	endif
507	<	enddo
508	<	endif
509	<
506	>	if (update_nlist) point(i) = nlist + 1
507	>
508	>	n_in_i = groupStartRow(i+1) - groupStartRow(i)
509	>
510	>	if (update_nlist) then
511	>	#ifdef IS_MPI
512	>	jstart = 1
513	>	jend = nGroupsInCol
514		#else
515	<
516	<	if (update_nlist) then
517	<
518	<	! save current configuration, contruct neighbor list,
519	<	! and calculate forces
520	<	call saveNeighborList(natoms, q)
521	<
522	<	neighborListSize = size(list)
523	<
520	<	nlist = 0
521	<
522	<	do i = 1, natoms-1
523	<	point(i) = nlist + 1
515	>	jstart = i+1
516	>	jend = nGroups
517	>	#endif
518	>	else
519	>	jstart = point(i)
520	>	jend = point(i+1) - 1
521	>	! make sure group i has neighbors
522	>	if (jstart .gt. jend) cycle outer
523	>	endif
524
525	<	inner: do j = i+1, natoms
526	<
527	<	if (skipThisPair(i,j))  cycle inner
528	<
529	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
530	<
531	<
532	<	if (rijsq < rlistsq) then
525	>	do jnab = jstart, jend
526	>	if (update_nlist) then
527	>	j = jnab
528	>	else
529	>	j = list(jnab)
530	>	endif
531	>	#ifdef IS_MPI
532	>	call get_interatomic_vector(q_group_Row(:,i), &
533	>	q_group_Col(:,j), d_grp, rgrpsq)
534	>	#else
535	>	call get_interatomic_vector(q_group(:,i), &
536	>	q_group(:,j), d_grp, rgrpsq)
537	>	#endif
538	>	if (rgrpsq < rlistsq) then
539	>	if (update_nlist) then
540	>	nlist = nlist + 1
541	>
542	>	if (nlist > neighborListSize) then
543	>	#ifdef IS_MPI
544	>	call expandNeighborList(nGroupsInRow, listerror)
545	>	#else
546	>	call expandNeighborList(nGroups, listerror)
547	>	#endif
548	>	if (listerror /= 0) then
549	>	error = -1
550	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
551	>	return
552	>	end if
553	>	neighborListSize = size(list)
554	>	endif
555	>
556	>	list(nlist) = j
557	>	endif
558
559	<	nlist = nlist + 1
560	<
561	<	if (nlist > neighborListSize) then
537	<	call expandNeighborList(natoms, listerror)
538	<	if (listerror /= 0) then
539	<	error = -1
540	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
541	<	return
542	<	end if
543	<	neighborListSize = size(list)
559	>	if (loop .eq. PAIR_LOOP) then
560	>	vij = 0.0d0
561	>	fij(1:3) = 0.0d0
562		endif
563
564	<	list(nlist) = j
564	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
565	>	in_switching_region)
566
567	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
549	<	u_l, A, f, t, pot)
567	>	n_in_j = groupStartCol(j+1) - groupStartCol(j)
568
569	<	endif
570	<	enddo inner
571	<	enddo
569	>	do ia = groupStartRow(i), groupStartRow(i+1)-1
570	>
571	>	atom1 = groupListRow(ia)
572	>
573	>	inner: do jb = groupStartCol(j), groupStartCol(j+1)-1
574	>
575	>	atom2 = groupListCol(jb)
576	>
577	>	if (skipThisPair(atom1, atom2)) cycle inner
578	>
579	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
580	>	d_atm(1:3) = d_grp(1:3)
581	>	ratmsq = rgrpsq
582	>	else
583	>	#ifdef IS_MPI
584	>	call get_interatomic_vector(q_Row(:,atom1), &
585	>	q_Col(:,atom2), d_atm, ratmsq)
586	>	#else
587	>	call get_interatomic_vector(q(:,atom1), &
588	>	q(:,atom2), d_atm, ratmsq)
589	>	#endif
590	>	endif
591	>	if (loop .eq. PREPAIR_LOOP) then
592	>	#ifdef IS_MPI
593	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
594	>	rgrpsq, d_grp, do_pot, do_stress, &
595	>	u_l, A, f, t, pot_local)
596	>	#else
597	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
598	>	rgrpsq, d_grp, do_pot, do_stress, &
599	>	u_l, A, f, t, pot)
600	>	#endif
601	>	else
602	>	#ifdef IS_MPI
603	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
604	>	do_pot, &
605	>	u_l, A, f, t, pot_local, vpair, fpair)
606	>	#else
607	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
608	>	do_pot,  &
609	>	u_l, A, f, t, pot, vpair, fpair)
610	>	#endif
611	>	vij = vij + vpair
612	>	fij(1:3) = fij(1:3) + fpair(1:3)
613	>	endif
614	>	enddo inner
615	>	enddo
616	>
617	>	if (loop .eq. PAIR_LOOP) then
618	>	if (in_switching_region) then
619	>	swderiv = vij*dswdr/rgrp
620	>	fij(1) = fij(1) + swderiv*d_grp(1)
621	>	fij(2) = fij(2) + swderiv*d_grp(2)
622	>	fij(3) = fij(3) + swderiv*d_grp(3)
623	>
624	>	do ia=groupStartRow(i), groupStartRow(i+1)-1
625	>	atom1=groupListRow(ia)
626	>	mf = mfactRow(atom1)
627	>	#ifdef IS_MPI
628	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
629	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
630	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
631	>	#else
632	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
633	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
634	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
635	>	#endif
636	>	enddo
637	>
638	>	do jb=groupStartCol(j), groupStartCol(j+1)-1
639	>	atom2=groupListCol(jb)
640	>	mf = mfactCol(atom2)
641	>	#ifdef IS_MPI
642	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
643	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
644	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
645	>	#else
646	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
647	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
648	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
649	>	#endif
650	>	enddo
651	>	endif
652	>
653	>	if (do_stress) call add_stress_tensor(d_grp, fij)
654	>	endif
655	>	end if
656	>	enddo
657	>	enddo outer
658
659	<	point(natoms) = nlist + 1
660	<
661	<	else !! (update)
662	<
663	<	! use the list to find the neighbors
664	<	do i = 1, natoms-1
665	<	JBEG = POINT(i)
666	<	JEND = POINT(i+1) - 1
667	<	! check thiat molecule i has neighbors
668	<	if (jbeg .le. jend) then
669	<
566	<	do jnab = jbeg, jend
567	<	j = list(jnab)
568	<
569	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
570	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
571	<	u_l, A, f, t, pot)
572	<
573	<	enddo
659	>	if (update_nlist) then
660	>	#ifdef IS_MPI
661	>	point(nGroupsInRow + 1) = nlist + 1
662	>	#else
663	>	point(nGroups) = nlist + 1
664	>	#endif
665	>	if (loop .eq. PREPAIR_LOOP) then
666	>	! we just did the neighbor list update on the first
667	>	! pass, so we don't need to do it
668	>	! again on the second pass
669	>	update_nlist = .false.
670		endif
671	<	enddo
672	<	endif
671	>	endif
672	>
673	>	if (loop .eq. PREPAIR_LOOP) then
674	>	call do_preforce(nlocal, pot)
675	>	endif
676	>
677	>	enddo
678
679	<	#endif
579	<
580	<	! phew, done with main loop.
581	<
582	<	!! Do timing
679	>	!! Do timing
680		#ifdef PROFILE
681		call cpu_time(forceTimeFinal)
682		forceTime = forceTime + forceTimeFinal - forceTimeInitial
683	<	#endif
684	<
588	<
683	>	#endif
684	>
685		#ifdef IS_MPI
686		!!distribute forces
687	<
687	>
688		f_temp = 0.0_dp
689	<	call scatter(f_Row,f_temp,plan_row3d)
689	>	call scatter(f_Row,f_temp,plan_atom_row_3d)
690		do i = 1,nlocal
691		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
692		end do
693	<
693	>
694		f_temp = 0.0_dp
695	<	call scatter(f_Col,f_temp,plan_col3d)
695	>	call scatter(f_Col,f_temp,plan_atom_col_3d)
696		do i = 1,nlocal
697		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
698		end do
699
700	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
700	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
701		t_temp = 0.0_dp
702	<	call scatter(t_Row,t_temp,plan_row3d)
702	>	call scatter(t_Row,t_temp,plan_atom_row_3d)
703		do i = 1,nlocal
704		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
705		end do
706		t_temp = 0.0_dp
707	<	call scatter(t_Col,t_temp,plan_col3d)
707	>	call scatter(t_Col,t_temp,plan_atom_col_3d)
708
709		do i = 1,nlocal
710		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
#	Line 617 | Line 713 | contains
713
714		if (do_pot) then
715		! scatter/gather pot_row into the members of my column
716	<	call scatter(pot_Row, pot_Temp, plan_row)
717	<
716	>	call scatter(pot_Row, pot_Temp, plan_atom_row)
717	>
718		! scatter/gather pot_local into all other procs
719		! add resultant to get total pot
720		do i = 1, nlocal
#	Line 626 | Line 722 | contains
722		enddo
723
724		pot_Temp = 0.0_DP
725	<
726	<	call scatter(pot_Col, pot_Temp, plan_col)
725	>
726	>	call scatter(pot_Col, pot_Temp, plan_atom_col)
727		do i = 1, nlocal
728		pot_local = pot_local + pot_Temp(i)
729		enddo
730	<
731	<	endif
730	>
731	>	endif
732		#endif
733	<
734	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
733	>
734	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
735
736	<	if (FF_uses_RF .and. SimUsesRF()) then
736	>	if (FF_uses_RF .and. SIM_uses_RF) then
737
738		#ifdef IS_MPI
739	<	call scatter(rf_Row,rf,plan_row3d)
740	<	call scatter(rf_Col,rf_Temp,plan_col3d)
739	>	call scatter(rf_Row,rf,plan_atom_row_3d)
740	>	call scatter(rf_Col,rf_Temp,plan_atom_col_3d)
741		do i = 1,nlocal
742		rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
743		end do
744		#endif
745
746	<	do i = 1, getNlocal()
747	<
746	>	do i = 1, nLocal
747	>
748		rfpot = 0.0_DP
749		#ifdef IS_MPI
750		me_i = atid_row(i)
751		#else
752		me_i = atid(i)
753		#endif
754	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
755	<	if ( is_DP_i ) then
756	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
754	>
755	>	if (PropertyMap(me_i)%is_DP) then
756	>
757	>	mu_i = PropertyMap(me_i)%dipole_moment
758	>
759		!! The reaction field needs to include a self contribution
760		!! to the field:
761	<	call accumulate_self_rf(i, mu_i, u_l)
761	>	call accumulate_self_rf(i, mu_i, u_l)
762		!! Get the reaction field contribution to the
763		!! potential and torques:
764		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 674 | Line 772 | contains
772		enddo
773		endif
774		endif
775	<
776	<
775	>
776	>
777		#ifdef IS_MPI
778	<
778	>
779		if (do_pot) then
780		pot = pot + pot_local
781		!! we assume the c code will do the allreduce to get the total potential
782		!! we could do it right here if we needed to...
783		endif
784	<
784	>
785		if (do_stress) then
786	<	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
786	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
787		mpi_comm_world,mpi_err)
788		call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
789		mpi_comm_world,mpi_err)
790		endif
791	<
791	>
792		#else
793	<
793	>
794		if (do_stress) then
795		tau = tau_Temp
796		virial = virial_Temp
797		endif
798	<
798	>
799		#endif
702	–
703	–	#ifdef PROFILE
704	–	if (do_pot) then
705	–
706	–	#ifdef IS_MPI
707	–
800
709	–	call printCommTime()
710	–
711	–	call mpi_allreduce(forceTime,globalForceTime,1,MPI_DOUBLE_PRECISION, &
712	–	mpi_sum,mpi_comm_world,mpi_err)
713	–
714	–	call mpi_allreduce(forceTime,maxForceTime,1,MPI_DOUBLE_PRECISION, &
715	–	MPI_MAX,mpi_comm_world,mpi_err)
716	–
717	–	call mpi_comm_size( MPI_COMM_WORLD, nprocs,mpi_err)
718	–
719	–	if (getMyNode() == 0) then
720	–	write(*,*) "Total processor time spent in force calculations is: ", globalForceTime
721	–	write(*,*) "Total Time spent in force loop per processor is: ", globalforceTime/nprocs
722	–	write(*,*) "Maximum force time on any processor is: ", maxForceTime
723	–	end if
724	–	#else
725	–	write(*,*) "Time spent in force loop is: ", forceTime
726	–	#endif
727	–
728	–
729	–	endif
730	–
731	–	#endif
732	–
801		end subroutine do_force_loop
802	+
803	+	subroutine do_pair(i, j, rijsq, d, sw, do_pot, &
804	+	u_l, A, f, t, pot, vpair, fpair)
805
806	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
806	>	real( kind = dp ) :: pot, vpair, sw
807	>	real( kind = dp ), dimension(3) :: fpair
808	>	real( kind = dp ), dimension(nLocal)   :: mfact
809	>	real( kind = dp ), dimension(3,nLocal) :: u_l
810	>	real( kind = dp ), dimension(9,nLocal) :: A
811	>	real( kind = dp ), dimension(3,nLocal) :: f
812	>	real( kind = dp ), dimension(3,nLocal) :: t
813
814	<	real( kind = dp ) :: pot
738	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
739	<	real (kind=dp), dimension(9,getNlocal()) :: A
740	<	real (kind=dp), dimension(3,getNlocal()) :: f
741	<	real (kind=dp), dimension(3,getNlocal()) :: t
742	<
743	<	logical, intent(inout) :: do_pot, do_stress
814	>	logical, intent(inout) :: do_pot
815		integer, intent(in) :: i, j
816	<	real ( kind = dp ), intent(inout)    :: rijsq
816	>	real ( kind = dp ), intent(inout) :: rijsq
817		real ( kind = dp )                :: r
818		real ( kind = dp ), intent(inout) :: d(3)
748	–	logical :: is_LJ_i, is_LJ_j
749	–	logical :: is_DP_i, is_DP_j
750	–	logical :: is_GB_i, is_GB_j
751	–	logical :: is_EAM_i,is_EAM_j
752	–	logical :: is_Sticky_i, is_Sticky_j
819		integer :: me_i, me_j
820
821		r = sqrt(rijsq)
822	+	vpair = 0.0d0
823	+	fpair(1:3) = 0.0d0
824
825		#ifdef IS_MPI
826	<	if (tagRow(i) .eq. tagColumn(j)) then
827	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
826	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
827	>	write(0,*) 'do_pair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
828		endif
761	–
829		me_i = atid_row(i)
830		me_j = atid_col(j)
764	–
831		#else
766	–
832		me_i = atid(i)
833		me_j = atid(j)
769	–
834		#endif
835	+
836	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
837	+
838	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
839	+	!write(*,*) 'calling lj with'
840	+	!write(*,*) i, j, r, rijsq
841	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
842	+	!write(*,'(3es12.3)') sw, vpair, pot
843	+	!write(*,*)
844
845	<	if (FF_uses_LJ .and. SimUsesLJ()) then
846	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
847	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
775	<
776	<	if ( is_LJ_i .and. is_LJ_j ) &
777	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
845	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
846	>	endif
847	>
848		endif
849	<
850	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
781	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
782	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
849	>
850	>	if (FF_uses_charges .and. SIM_uses_charges) then
851
852	<	if ( is_DP_i .and. is_DP_j ) then
853	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
786	<	do_pot, do_stress)
787	<	if (FF_uses_RF .and. SimUsesRF()) then
788	<	call accumulate_rf(i, j, r, u_l)
789	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
790	<	endif
791	<
852	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
853	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
854		endif
855	+
856		endif
857	+
858	+	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
859	+
860	+	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
861	+	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
862	+	do_pot)
863	+	if (FF_uses_RF .and. SIM_uses_RF) then
864	+	call accumulate_rf(i, j, r, u_l, sw)
865	+	call rf_correct_forces(i, j, d, r, u_l, sw, f, fpair)
866	+	endif
867	+	endif
868
869	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
869	>	endif
870
871	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
798	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
871	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
872
873	<	if ( is_Sticky_i .and. is_Sticky_j ) then
874	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
875	<	do_pot, do_stress)
873	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
874	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, A, f, t, &
875	>	do_pot)
876		endif
877	+
878		endif
879
880
881	<	if (FF_uses_GB .and. SimUsesGB()) then
808	<
809	<
810	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
811	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
881	>	if (FF_uses_GB .and. SIM_uses_GB) then
882
883	<	if ( is_GB_i .and. is_GB_j ) then
884	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
885	<	do_pot, do_stress)
883	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
884	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
885	>	do_pot)
886		endif
817	–	endif
818	–
887
888	<
889	<	if (FF_uses_EAM .and. SimUsesEAM()) then
890	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
891	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
892	<
893	<	if ( is_EAM_i .and. is_EAM_j ) &
894	<	call do_eam_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
895	<	endif
896	<
897	<
898	<
831	<
888	>	endif
889	>
890	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
891	>
892	>	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
893	>	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, &
894	>	do_pot)
895	>	endif
896	>
897	>	endif
898	>
899		end subroutine do_pair
900
901	+	subroutine do_prepair(i, j, rijsq, d, sw, rcijsq, dc, &
902	+	do_pot, do_stress, u_l, A, f, t, pot)
903
904	<
905	<	subroutine do_prepair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
906	<	real( kind = dp ) :: pot
907	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
908	<	real (kind=dp), dimension(9,getNlocal()) :: A
840	<	real (kind=dp), dimension(3,getNlocal()) :: f
841	<	real (kind=dp), dimension(3,getNlocal()) :: t
904	>	real( kind = dp ) :: pot, sw
905	>	real( kind = dp ), dimension(3,nLocal) :: u_l
906	>	real (kind=dp), dimension(9,nLocal) :: A
907	>	real (kind=dp), dimension(3,nLocal) :: f
908	>	real (kind=dp), dimension(3,nLocal) :: t
909
910		logical, intent(inout) :: do_pot, do_stress
911		integer, intent(in) :: i, j
912	<	real ( kind = dp ), intent(inout)    :: rijsq
913	<	real ( kind = dp )                :: r
914	<	real ( kind = dp ), intent(inout) :: d(3)
912	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
913	>	real ( kind = dp )                :: r, rc
914	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
915
916		logical :: is_EAM_i, is_EAM_j
917
918		integer :: me_i, me_j
919
920	<	r = sqrt(rijsq)
920	>
921	>	r = sqrt(rijsq)
922	>	if (SIM_uses_molecular_cutoffs) then
923	>	rc = sqrt(rcijsq)
924	>	else
925	>	rc = r
926	>	endif
927
928
929		#ifdef IS_MPI
930	<	if (tagRow(i) .eq. tagColumn(j)) then
931	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
930	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
931	>	write(0,*) 'do_prepair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
932		endif
933
934		me_i = atid_row(i)
#	Line 867 | Line 940 | contains
940		me_j = atid(j)
941
942		#endif
943	<
944	<	if (FF_uses_EAM .and. SimUsesEAM()) then
872	<	call getElementProperty(atypes, me_i, "is_EAM", is_EAM_i)
873	<	call getElementProperty(atypes, me_j, "is_EAM", is_EAM_j)
943	>
944	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
945
946	<	if ( is_EAM_i .and. is_EAM_j ) &
946	>	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
947		call calc_EAM_prepair_rho(i, j, d, r, rijsq )
877	–	endif
878	–
879	–	end subroutine do_prepair
880	–
881	–
882	–
883	–
884	–	subroutine do_preforce(nlocal,pot)
885	–	integer :: nlocal
886	–	real( kind = dp ) :: pot
887	–
888	–	if (FF_uses_EAM .and. SimUsesEAM()) then
889	–	call calc_EAM_preforce_Frho(nlocal,pot)
890	–	endif
891	–
892	–
893	–	end subroutine do_preforce
894	–
895	–
896	–	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
897	–
898	–	real (kind = dp), dimension(3) :: q_i
899	–	real (kind = dp), dimension(3) :: q_j
900	–	real ( kind = dp ), intent(out) :: r_sq
901	–	real( kind = dp ) :: d(3), scaled(3)
902	–	integer i
903	–
904	–	d(1:3) = q_j(1:3) - q_i(1:3)
905	–
906	–	! Wrap back into periodic box if necessary
907	–	if ( SimUsesPBC() ) then
908	–
909	–	if( .not.boxIsOrthorhombic ) then
910	–	! calc the scaled coordinates.
911	–
912	–	scaled = matmul(HmatInv, d)
913	–
914	–	! wrap the scaled coordinates
915	–
916	–	scaled = scaled  - anint(scaled)
917	–
918	–
919	–	! calc the wrapped real coordinates from the wrapped scaled
920	–	! coordinates
921	–
922	–	d = matmul(Hmat,scaled)
923	–
924	–	else
925	–	! calc the scaled coordinates.
926	–
927	–	do i = 1, 3
928	–	scaled(i) = d(i) * HmatInv(i,i)
929	–
930	–	! wrap the scaled coordinates
931	–
932	–	scaled(i) = scaled(i) - anint(scaled(i))
933	–
934	–	! calc the wrapped real coordinates from the wrapped scaled
935	–	! coordinates
936	–
937	–	d(i) = scaled(i)*Hmat(i,i)
938	–	enddo
939	–	endif
940	–
941	–	endif
942	–
943	–	r_sq = dot_product(d,d)
944	–
945	–	end subroutine get_interatomic_vector
946	–
947	–	subroutine check_initialization(error)
948	–	integer, intent(out) :: error
949	–
950	–	error = 0
951	–	! Make sure we are properly initialized.
952	–	if (.not. do_forces_initialized) then
953	–	write(*,*) "Forces not initialized"
954	–	error = -1
955	–	return
956	–	endif
957	–
958	–	#ifdef IS_MPI
959	–	if (.not. isMPISimSet()) then
960	–	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
961	–	error = -1
962	–	return
963	–	endif
964	–	#endif
965	–
966	–	return
967	–	end subroutine check_initialization
968	–
969	–
970	–	subroutine zero_work_arrays()
971	–
972	–	#ifdef IS_MPI
973	–
974	–	q_Row = 0.0_dp
975	–	q_Col = 0.0_dp
976	–
977	–	u_l_Row = 0.0_dp
978	–	u_l_Col = 0.0_dp
979	–
980	–	A_Row = 0.0_dp
981	–	A_Col = 0.0_dp
982	–
983	–	f_Row = 0.0_dp
984	–	f_Col = 0.0_dp
985	–	f_Temp = 0.0_dp
948
949	<	t_Row = 0.0_dp
950	<	t_Col = 0.0_dp
951	<	t_Temp = 0.0_dp
949	>	endif
950	>
951	>	end subroutine do_prepair
952
953	<	pot_Row = 0.0_dp
954	<	pot_Col = 0.0_dp
955	<	pot_Temp = 0.0_dp
953	>
954	>	subroutine do_preforce(nlocal,pot)
955	>	integer :: nlocal
956	>	real( kind = dp ) :: pot
957	>
958	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
959	>	call calc_EAM_preforce_Frho(nlocal,pot)
960	>	endif
961	>
962	>
963	>	end subroutine do_preforce
964	>
965	>
966	>	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
967	>
968	>	real (kind = dp), dimension(3) :: q_i
969	>	real (kind = dp), dimension(3) :: q_j
970	>	real ( kind = dp ), intent(out) :: r_sq
971	>	real( kind = dp ) :: d(3), scaled(3)
972	>	integer i
973	>
974	>	d(1:3) = q_j(1:3) - q_i(1:3)
975	>
976	>	! Wrap back into periodic box if necessary
977	>	if ( SIM_uses_PBC ) then
978	>
979	>	if( .not.boxIsOrthorhombic ) then
980	>	! calc the scaled coordinates.
981	>
982	>	scaled = matmul(HmatInv, d)
983	>
984	>	! wrap the scaled coordinates
985	>
986	>	scaled = scaled  - anint(scaled)
987	>
988	>
989	>	! calc the wrapped real coordinates from the wrapped scaled
990	>	! coordinates
991	>
992	>	d = matmul(Hmat,scaled)
993	>
994	>	else
995	>	! calc the scaled coordinates.
996	>
997	>	do i = 1, 3
998	>	scaled(i) = d(i) * HmatInv(i,i)
999	>
1000	>	! wrap the scaled coordinates
1001	>
1002	>	scaled(i) = scaled(i) - anint(scaled(i))
1003	>
1004	>	! calc the wrapped real coordinates from the wrapped scaled
1005	>	! coordinates
1006	>
1007	>	d(i) = scaled(i)*Hmat(i,i)
1008	>	enddo
1009	>	endif
1010	>
1011	>	endif
1012	>
1013	>	r_sq = dot_product(d,d)
1014	>
1015	>	end subroutine get_interatomic_vector
1016	>
1017	>	subroutine zero_work_arrays()
1018	>
1019	>	#ifdef IS_MPI
1020	>
1021	>	q_Row = 0.0_dp
1022	>	q_Col = 0.0_dp
1023
1024	<	rf_Row = 0.0_dp
1025	<	rf_Col = 0.0_dp
1026	<	rf_Temp = 0.0_dp
1027	<
1024	>	q_group_Row = 0.0_dp
1025	>	q_group_Col = 0.0_dp
1026	>
1027	>	u_l_Row = 0.0_dp
1028	>	u_l_Col = 0.0_dp
1029	>
1030	>	A_Row = 0.0_dp
1031	>	A_Col = 0.0_dp
1032	>
1033	>	f_Row = 0.0_dp
1034	>	f_Col = 0.0_dp
1035	>	f_Temp = 0.0_dp
1036	>
1037	>	t_Row = 0.0_dp
1038	>	t_Col = 0.0_dp
1039	>	t_Temp = 0.0_dp
1040	>
1041	>	pot_Row = 0.0_dp
1042	>	pot_Col = 0.0_dp
1043	>	pot_Temp = 0.0_dp
1044	>
1045	>	rf_Row = 0.0_dp
1046	>	rf_Col = 0.0_dp
1047	>	rf_Temp = 0.0_dp
1048	>
1049		#endif
1000	–
1050
1051	<	if (FF_uses_EAM .and. SimUsesEAM()) then
1052	<	call clean_EAM()
1053	<	endif
1054	<
1055	<
1056	<
1057	<
1058	<
1059	<	rf = 0.0_dp
1060	<	tau_Temp = 0.0_dp
1061	<	virial_Temp = 0.0_dp
1062	<	end subroutine zero_work_arrays
1063	<
1064	<	function skipThisPair(atom1, atom2) result(skip_it)
1065	<	integer, intent(in) :: atom1
1066	<	integer, intent(in), optional :: atom2
1067	<	logical :: skip_it
1068	<	integer :: unique_id_1, unique_id_2
1069	<	integer :: me_i,me_j
1070	<	integer :: i
1071	<
1072	<	skip_it = .false.
1073	<
1074	<	!! there are a number of reasons to skip a pair or a particle
1075	<	!! mostly we do this to exclude atoms who are involved in short
1027	<	!! range interactions (bonds, bends, torsions), but we also need
1028	<	!! to exclude some overcounted interactions that result from
1029	<	!! the parallel decomposition
1030	<
1051	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
1052	>	call clean_EAM()
1053	>	endif
1054	>
1055	>	rf = 0.0_dp
1056	>	tau_Temp = 0.0_dp
1057	>	virial_Temp = 0.0_dp
1058	>	end subroutine zero_work_arrays
1059	>
1060	>	function skipThisPair(atom1, atom2) result(skip_it)
1061	>	integer, intent(in) :: atom1
1062	>	integer, intent(in), optional :: atom2
1063	>	logical :: skip_it
1064	>	integer :: unique_id_1, unique_id_2
1065	>	integer :: me_i,me_j
1066	>	integer :: i
1067	>
1068	>	skip_it = .false.
1069	>
1070	>	!! there are a number of reasons to skip a pair or a particle
1071	>	!! mostly we do this to exclude atoms who are involved in short
1072	>	!! range interactions (bonds, bends, torsions), but we also need
1073	>	!! to exclude some overcounted interactions that result from
1074	>	!! the parallel decomposition
1075	>
1076		#ifdef IS_MPI
1077	<	!! in MPI, we have to look up the unique IDs for each atom
1078	<	unique_id_1 = tagRow(atom1)
1077	>	!! in MPI, we have to look up the unique IDs for each atom
1078	>	unique_id_1 = AtomRowToGlobal(atom1)
1079		#else
1080	<	!! in the normal loop, the atom numbers are unique
1081	<	unique_id_1 = atom1
1080	>	!! in the normal loop, the atom numbers are unique
1081	>	unique_id_1 = atom1
1082		#endif
1083	<
1084	<	!! We were called with only one atom, so just check the global exclude
1085	<	!! list for this atom
1086	<	if (.not. present(atom2)) then
1087	<	do i = 1, nExcludes_global
1088	<	if (excludesGlobal(i) == unique_id_1) then
1089	<	skip_it = .true.
1090	<	return
1091	<	end if
1092	<	end do
1093	<	return
1094	<	end if
1095	<
1083	>
1084	>	!! We were called with only one atom, so just check the global exclude
1085	>	!! list for this atom
1086	>	if (.not. present(atom2)) then
1087	>	do i = 1, nExcludes_global
1088	>	if (excludesGlobal(i) == unique_id_1) then
1089	>	skip_it = .true.
1090	>	return
1091	>	end if
1092	>	end do
1093	>	return
1094	>	end if
1095	>
1096		#ifdef IS_MPI
1097	<	unique_id_2 = tagColumn(atom2)
1097	>	unique_id_2 = AtomColToGlobal(atom2)
1098		#else
1099	<	unique_id_2 = atom2
1099	>	unique_id_2 = atom2
1100		#endif
1101	<
1101	>
1102		#ifdef IS_MPI
1103	<	!! this situation should only arise in MPI simulations
1104	<	if (unique_id_1 == unique_id_2) then
1105	<	skip_it = .true.
1106	<	return
1107	<	end if
1108	<
1109	<	!! this prevents us from doing the pair on multiple processors
1110	<	if (unique_id_1 < unique_id_2) then
1111	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1112	<	skip_it = .true.
1113	<	return
1114	<	endif
1115	<	else
1116	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1117	<	skip_it = .true.
1118	<	return
1119	<	endif
1120	<	endif
1103	>	!! this situation should only arise in MPI simulations
1104	>	if (unique_id_1 == unique_id_2) then
1105	>	skip_it = .true.
1106	>	return
1107	>	end if
1108	>
1109	>	!! this prevents us from doing the pair on multiple processors
1110	>	if (unique_id_1 < unique_id_2) then
1111	>	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1112	>	skip_it = .true.
1113	>	return
1114	>	endif
1115	>	else
1116	>	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1117	>	skip_it = .true.
1118	>	return
1119	>	endif
1120	>	endif
1121		#endif
1122	+
1123	+	!! the rest of these situations can happen in all simulations:
1124	+	do i = 1, nExcludes_global
1125	+	if ((excludesGlobal(i) == unique_id_1) .or. &
1126	+	(excludesGlobal(i) == unique_id_2)) then
1127	+	skip_it = .true.
1128	+	return
1129	+	endif
1130	+	enddo
1131	+
1132	+	do i = 1, nSkipsForAtom(unique_id_1)
1133	+	if (skipsForAtom(unique_id_1, i) .eq. unique_id_2) then
1134	+	skip_it = .true.
1135	+	return
1136	+	endif
1137	+	end do
1138	+
1139	+	return
1140	+	end function skipThisPair
1141
1142	<	!! the rest of these situations can happen in all simulations:
1143	<	do i = 1, nExcludes_global
1144	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1145	<	(excludesGlobal(i) == unique_id_2)) then
1146	<	skip_it = .true.
1147	<	return
1148	<	endif
1149	<	enddo
1142	>	function FF_UsesDirectionalAtoms() result(doesit)
1143	>	logical :: doesit
1144	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1145	>	FF_uses_GB .or. FF_uses_RF
1146	>	end function FF_UsesDirectionalAtoms
1147	>
1148	>	function FF_RequiresPrepairCalc() result(doesit)
1149	>	logical :: doesit
1150	>	doesit = FF_uses_EAM
1151	>	end function FF_RequiresPrepairCalc
1152	>
1153	>	function FF_RequiresPostpairCalc() result(doesit)
1154	>	logical :: doesit
1155	>	doesit = FF_uses_RF
1156	>	end function FF_RequiresPostpairCalc
1157	>
1158	>	#ifdef PROFILE
1159	>	function getforcetime() result(totalforcetime)
1160	>	real(kind=dp) :: totalforcetime
1161	>	totalforcetime = forcetime
1162	>	end function getforcetime
1163	>	#endif
1164	>
1165	>	!! This cleans componets of force arrays belonging only to fortran
1166
1167	<	do i = 1, nExcludes_local
1168	<	if (excludesLocal(1,i) == unique_id_1) then
1169	<	if (excludesLocal(2,i) == unique_id_2) then
1170	<	skip_it = .true.
1171	<	return
1172	<	endif
1173	<	else
1174	<	if (excludesLocal(1,i) == unique_id_2) then
1175	<	if (excludesLocal(2,i) == unique_id_1) then
1176	<	skip_it = .true.
1177	<	return
1178	<	endif
1179	<	endif
1180	<	endif
1181	<	end do
1182	<
1183	<	return
1184	<	end function skipThisPair
1185	<
1186	<	function FF_UsesDirectionalAtoms() result(doesit)
1187	<	logical :: doesit
1188	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1189	<	FF_uses_GB .or. FF_uses_RF
1190	<	end function FF_UsesDirectionalAtoms
1111	<
1112	<	function FF_RequiresPrepairCalc() result(doesit)
1113	<	logical :: doesit
1114	<	doesit = FF_uses_EAM
1115	<	end function FF_RequiresPrepairCalc
1116	<
1117	<	function FF_RequiresPostpairCalc() result(doesit)
1118	<	logical :: doesit
1119	<	doesit = FF_uses_RF
1120	<	end function FF_RequiresPostpairCalc
1121	<
1122	<	!! This cleans componets of force arrays belonging only to fortran
1123	<
1167	>	subroutine add_stress_tensor(dpair, fpair)
1168	>
1169	>	real( kind = dp ), dimension(3), intent(in) :: dpair, fpair
1170	>
1171	>	! because the d vector is the rj - ri vector, and
1172	>	! because fx, fy, fz are the force on atom i, we need a
1173	>	! negative sign here:
1174	>
1175	>	tau_Temp(1) = tau_Temp(1) - dpair(1) * fpair(1)
1176	>	tau_Temp(2) = tau_Temp(2) - dpair(1) * fpair(2)
1177	>	tau_Temp(3) = tau_Temp(3) - dpair(1) * fpair(3)
1178	>	tau_Temp(4) = tau_Temp(4) - dpair(2) * fpair(1)
1179	>	tau_Temp(5) = tau_Temp(5) - dpair(2) * fpair(2)
1180	>	tau_Temp(6) = tau_Temp(6) - dpair(2) * fpair(3)
1181	>	tau_Temp(7) = tau_Temp(7) - dpair(3) * fpair(1)
1182	>	tau_Temp(8) = tau_Temp(8) - dpair(3) * fpair(2)
1183	>	tau_Temp(9) = tau_Temp(9) - dpair(3) * fpair(3)
1184	>
1185	>	!write(*,'(6es12.3)')  fpair(1:3), tau_Temp(1), tau_Temp(5), tau_temp(9)
1186	>	virial_Temp = virial_Temp + &
1187	>	(tau_Temp(1) + tau_Temp(5) + tau_Temp(9))
1188	>
1189	>	end subroutine add_stress_tensor
1190	>
1191		end module do_Forces
1192	+

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