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Comparing trunk/OOPSE/libmdtools/do_Forces.F90 (file contents):
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 1199 by gezelter, Thu May 27 15:21:20 2004 UTC

#	Line 4 | Line 4
4
5		!! @author Charles F. Vardeman II
6		!! @author Matthew Meineke
7	<	!! @version $Id: do_Forces.F90,v 1.15 2003-04-11 15:16:59 gezelter Exp $, $Date: 2003-04-11 15:16:59 $, $Name: not supported by cvs2svn $, $Revision: 1.15 $
7	>	!! @version $Id: do_Forces.F90,v 1.64 2004-05-27 15:21:20 gezelter Exp $, $Date: 2004-05-27 15:21:20 $, $Name: not supported by cvs2svn $, $Revision: 1.64 $
8
9		module do_Forces
10		use force_globals
11		use simulation
12		use definitions
13		use atype_module
14	+	use switcheroo
15		use neighborLists
16		use lj
17		use sticky_pair
18		use dipole_dipole
19	+	use charge_charge
20		use reaction_field
21		use gb_pair
22	+	use vector_class
23	+	use eam
24	+	use status
25		#ifdef IS_MPI
26		use mpiSimulation
27		#endif
#	Line 26 | Line 31 | module do_Forces
31
32		#define __FORTRAN90
33		#include "fForceField.h"
34	+	#include "fSwitchingFunction.h"
35
36	<	logical, save :: do_forces_initialized = .false.
36	>	INTEGER, PARAMETER:: PREPAIR_LOOP = 1
37	>	INTEGER, PARAMETER:: PAIR_LOOP    = 2
38	>
39	>	logical, save :: haveRlist = .false.
40	>	logical, save :: haveNeighborList = .false.
41	>	logical, save :: havePolicies = .false.
42	>	logical, save :: haveSIMvariables = .false.
43	>	logical, save :: havePropertyMap = .false.
44	>	logical, save :: haveSaneForceField = .false.
45		logical, save :: FF_uses_LJ
46		logical, save :: FF_uses_sticky
47	+	logical, save :: FF_uses_charges
48		logical, save :: FF_uses_dipoles
49		logical, save :: FF_uses_RF
50		logical, save :: FF_uses_GB
51		logical, save :: FF_uses_EAM
52	+	logical, save :: SIM_uses_LJ
53	+	logical, save :: SIM_uses_sticky
54	+	logical, save :: SIM_uses_charges
55	+	logical, save :: SIM_uses_dipoles
56	+	logical, save :: SIM_uses_RF
57	+	logical, save :: SIM_uses_GB
58	+	logical, save :: SIM_uses_EAM
59	+	logical, save :: SIM_requires_postpair_calc
60	+	logical, save :: SIM_requires_prepair_calc
61	+	logical, save :: SIM_uses_directional_atoms
62	+	logical, save :: SIM_uses_PBC
63	+	logical, save :: SIM_uses_molecular_cutoffs
64
65	+	real(kind=dp), save :: rlist, rlistsq
66	+
67		public :: init_FF
68		public :: do_force_loop
69	+	public :: setRlistDF
70
71	+	#ifdef PROFILE
72	+	public :: getforcetime
73	+	real, save :: forceTime = 0
74	+	real :: forceTimeInitial, forceTimeFinal
75	+	integer :: nLoops
76	+	#endif
77	+
78	+	type :: Properties
79	+	logical :: is_lj     = .false.
80	+	logical :: is_sticky = .false.
81	+	logical :: is_dp     = .false.
82	+	logical :: is_gb     = .false.
83	+	logical :: is_eam    = .false.
84	+	logical :: is_charge = .false.
85	+	real(kind=DP) :: charge = 0.0_DP
86	+	real(kind=DP) :: dipole_moment = 0.0_DP
87	+	end type Properties
88	+
89	+	type(Properties), dimension(:),allocatable :: PropertyMap
90	+
91		contains
92	+
93	+	subroutine setRlistDF( this_rlist )
94	+
95	+	real(kind=dp) :: this_rlist
96	+
97	+	rlist = this_rlist
98	+	rlistsq = rlist * rlist
99	+
100	+	haveRlist = .true.
101	+
102	+	end subroutine setRlistDF
103	+
104	+	subroutine createPropertyMap(status)
105	+	integer :: nAtypes
106	+	integer :: status
107	+	integer :: i
108	+	logical :: thisProperty
109	+	real (kind=DP) :: thisDPproperty
110	+
111	+	status = 0
112	+
113	+	nAtypes = getSize(atypes)
114	+
115	+	if (nAtypes == 0) then
116	+	status = -1
117	+	return
118	+	end if
119	+
120	+	if (.not. allocated(PropertyMap)) then
121	+	allocate(PropertyMap(nAtypes))
122	+	endif
123	+
124	+	do i = 1, nAtypes
125	+	call getElementProperty(atypes, i, "is_LJ", thisProperty)
126	+	PropertyMap(i)%is_LJ = thisProperty
127	+
128	+	call getElementProperty(atypes, i, "is_Charge", thisProperty)
129	+	PropertyMap(i)%is_Charge = thisProperty
130	+
131	+	if (thisProperty) then
132	+	call getElementProperty(atypes, i, "charge", thisDPproperty)
133	+	PropertyMap(i)%charge = thisDPproperty
134	+	endif
135	+
136	+	call getElementProperty(atypes, i, "is_DP", thisProperty)
137	+	PropertyMap(i)%is_DP = thisProperty
138	+
139	+	if (thisProperty) then
140	+	call getElementProperty(atypes, i, "dipole_moment", thisDPproperty)
141	+	PropertyMap(i)%dipole_moment = thisDPproperty
142	+	endif
143	+
144	+	call getElementProperty(atypes, i, "is_Sticky", thisProperty)
145	+	PropertyMap(i)%is_Sticky = thisProperty
146	+	call getElementProperty(atypes, i, "is_GB", thisProperty)
147	+	PropertyMap(i)%is_GB = thisProperty
148	+	call getElementProperty(atypes, i, "is_EAM", thisProperty)
149	+	PropertyMap(i)%is_EAM = thisProperty
150	+	end do
151	+
152	+	havePropertyMap = .true.
153	+
154	+	end subroutine createPropertyMap
155	+
156	+	subroutine setSimVariables()
157	+	SIM_uses_LJ = SimUsesLJ()
158	+	SIM_uses_sticky = SimUsesSticky()
159	+	SIM_uses_charges = SimUsesCharges()
160	+	SIM_uses_dipoles = SimUsesDipoles()
161	+	SIM_uses_RF = SimUsesRF()
162	+	SIM_uses_GB = SimUsesGB()
163	+	SIM_uses_EAM = SimUsesEAM()
164	+	SIM_requires_postpair_calc = SimRequiresPostpairCalc()
165	+	SIM_requires_prepair_calc = SimRequiresPrepairCalc()
166	+	SIM_uses_directional_atoms = SimUsesDirectionalAtoms()
167	+	SIM_uses_PBC = SimUsesPBC()
168	+	!SIM_uses_molecular_cutoffs = SimUsesMolecularCutoffs()
169	+
170	+	haveSIMvariables = .true.
171	+
172	+	return
173	+	end subroutine setSimVariables
174	+
175	+	subroutine doReadyCheck(error)
176	+	integer, intent(out) :: error
177	+
178	+	integer :: myStatus
179	+
180	+	error = 0
181	+
182	+	if (.not. havePropertyMap) then
183	+
184	+	myStatus = 0
185	+
186	+	call createPropertyMap(myStatus)
187	+
188	+	if (myStatus .ne. 0) then
189	+	write(default_error, *) 'createPropertyMap failed in do_Forces!'
190	+	error = -1
191	+	return
192	+	endif
193	+	endif
194	+
195	+	if (.not. haveSIMvariables) then
196	+	call setSimVariables()
197	+	endif
198	+
199	+	if (.not. haveRlist) then
200	+	write(default_error, *) 'rList has not been set in do_Forces!'
201	+	error = -1
202	+	return
203	+	endif
204	+
205	+	if (SIM_uses_LJ .and. FF_uses_LJ) then
206	+	if (.not. havePolicies) then
207	+	write(default_error, *) 'LJ mixing Policies have not been set in do_Forces!'
208	+	error = -1
209	+	return
210	+	endif
211	+	endif
212	+
213	+	if (.not. haveNeighborList) then
214	+	write(default_error, *) 'neighbor list has not been initialized in do_Forces!'
215	+	error = -1
216	+	return
217	+	end if
218	+
219	+	if (.not. haveSaneForceField) then
220	+	write(default_error, *) 'Force Field is not sane in do_Forces!'
221	+	error = -1
222	+	return
223	+	end if
224	+
225	+	#ifdef IS_MPI
226	+	if (.not. isMPISimSet()) then
227	+	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
228	+	error = -1
229	+	return
230	+	endif
231	+	#endif
232	+	return
233	+	end subroutine doReadyCheck
234	+
235
236		subroutine init_FF(LJMIXPOLICY, use_RF_c, thisStat)
237
#	Line 64 | Line 257 | contains
257
258		FF_uses_LJ = .false.
259		FF_uses_sticky = .false.
260	+	FF_uses_charges = .false.
261		FF_uses_dipoles = .false.
262		FF_uses_GB = .false.
263		FF_uses_EAM = .false.
264
265		call getMatchingElementList(atypes, "is_LJ", .true., nMatches, MatchList)
266		if (nMatches .gt. 0) FF_uses_LJ = .true.
267	<
267	>
268	>	call getMatchingElementList(atypes, "is_Charge", .true., nMatches, MatchList)
269	>	if (nMatches .gt. 0) FF_uses_charges = .true.
270	>
271		call getMatchingElementList(atypes, "is_DP", .true., nMatches, MatchList)
272		if (nMatches .gt. 0) FF_uses_dipoles = .true.
273
#	Line 84 | Line 281 | contains
281		call getMatchingElementList(atypes, "is_EAM", .true., nMatches, MatchList)
282		if (nMatches .gt. 0) FF_uses_EAM = .true.
283
284	+	!! Assume sanity (for the sake of argument)
285	+	haveSaneForceField = .true.
286	+
287		!! check to make sure the FF_uses_RF setting makes sense
288
289		if (FF_uses_dipoles) then
90	–	rrf = getRrf()
91	–	rt = getRt()
92	–	call initialize_dipole(rrf, rt)
290		if (FF_uses_RF) then
291		dielect = getDielect()
292	<	call initialize_rf(rrf, rt, dielect)
292	>	call initialize_rf(dielect)
293		endif
294		else
295		if (FF_uses_RF) then
296		write(default_error,*) 'Using Reaction Field with no dipoles?  Huh?'
297		thisStat = -1
298	+	haveSaneForceField = .false.
299		return
300		endif
301	<	endif
301	>	endif
302
303		if (FF_uses_LJ) then
304
107	–	call getRcut(rcut)
108	–
305		select case (LJMIXPOLICY)
306		case (LB_MIXING_RULE)
307	<	call init_lj_FF(LB_MIXING_RULE, rcut, my_status)
307	>	call init_lj_FF(LB_MIXING_RULE, my_status)
308		case (EXPLICIT_MIXING_RULE)
309	<	call init_lj_FF(EXPLICIT_MIXING_RULE, rcut, my_status)
309	>	call init_lj_FF(EXPLICIT_MIXING_RULE, my_status)
310		case default
311		write(default_error,*) 'unknown LJ Mixing Policy!'
312		thisStat = -1
313	+	haveSaneForceField = .false.
314		return
315		end select
316		if (my_status /= 0) then
317		thisStat = -1
318	+	haveSaneForceField = .false.
319		return
320		end if
321	+	havePolicies = .true.
322		endif
323
324		if (FF_uses_sticky) then
325		call check_sticky_FF(my_status)
326		if (my_status /= 0) then
327		thisStat = -1
328	+	haveSaneForceField = .false.
329		return
330		end if
331		endif
332	<
332	>
333	>
334	>	if (FF_uses_EAM) then
335	>	call init_EAM_FF(my_status)
336	>	if (my_status /= 0) then
337	>	write(default_error, *) "init_EAM_FF returned a bad status"
338	>	thisStat = -1
339	>	haveSaneForceField = .false.
340	>	return
341	>	end if
342	>	endif
343	>
344		if (FF_uses_GB) then
345		call check_gb_pair_FF(my_status)
346		if (my_status .ne. 0) then
347		thisStat = -1
348	+	haveSaneForceField = .false.
349		return
350		endif
351		endif
352
353		if (FF_uses_GB .and. FF_uses_LJ) then
354		endif
355	<	if (.not. do_forces_initialized) then
355	>	if (.not. haveNeighborList) then
356		!! Create neighbor lists
357	<	call expandNeighborList(getNlocal(), my_status)
357	>	call expandNeighborList(nLocal, my_status)
358		if (my_Status /= 0) then
359		write(default_error,*) "SimSetup: ExpandNeighborList returned error."
360		thisStat = -1
361		return
362		endif
363	+	haveNeighborList = .true.
364		endif
365
366	<	do_forces_initialized = .true.
367	<
366	>
367	>
368		end subroutine init_FF
369
370
371		!! Does force loop over i,j pairs. Calls do_pair to calculates forces.
372		!------------------------------------------------------------->
373	<	subroutine do_force_loop(q, A, u_l, f, t, tau, pot, do_pot_c, do_stress_c, &
374	<	error)
373	>	subroutine do_force_loop(q, q_group, A, u_l, f, t, tau, pot, &
374	>	do_pot_c, do_stress_c, error)
375		!! Position array provided by C, dimensioned by getNlocal
376	<	real ( kind = dp ), dimension(3,getNlocal()) :: q
376	>	real ( kind = dp ), dimension(3, nLocal) :: q
377	>	!! molecular center-of-mass position array
378	>	real ( kind = dp ), dimension(3, nGroups) :: q_group
379		!! Rotation Matrix for each long range particle in simulation.
380	<	real( kind = dp), dimension(9,getNlocal()) :: A
380	>	real( kind = dp), dimension(9, nLocal) :: A
381		!! Unit vectors for dipoles (lab frame)
382	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
382	>	real( kind = dp ), dimension(3,nLocal) :: u_l
383		!! Force array provided by C, dimensioned by getNlocal
384	<	real ( kind = dp ), dimension(3,getNlocal()) :: f
384	>	real ( kind = dp ), dimension(3,nLocal) :: f
385		!! Torsion array provided by C, dimensioned by getNlocal
386	<	real( kind = dp ), dimension(3,getNlocal()) :: t
386	>	real( kind = dp ), dimension(3,nLocal) :: t
387	>
388		!! Stress Tensor
389		real( kind = dp), dimension(9) :: tau
390		real ( kind = dp ) :: pot
391		logical ( kind = 2) :: do_pot_c, do_stress_c
392		logical :: do_pot
393		logical :: do_stress
394	+	logical :: in_switching_region
395		#ifdef IS_MPI
396		real( kind = DP ) :: pot_local
397	<	integer :: nrow
398	<	integer :: ncol
397	>	integer :: nAtomsInRow
398	>	integer :: nAtomsInCol
399	>	integer :: nprocs
400	>	integer :: nGroupsInRow
401	>	integer :: nGroupsInCol
402		#endif
183	–	integer :: nlocal
403		integer :: natoms
404		logical :: update_nlist
405	<	integer :: i, j, jbeg, jend, jnab
405	>	integer :: i, j, jstart, jend, jnab
406	>	integer :: istart, iend
407	>	integer :: ia, jb, atom1, atom2
408		integer :: nlist
409	<	real( kind = DP ) ::  rijsq, rlistsq, rcutsq, rlist, rcut
410	<	real(kind=dp),dimension(3) :: d
409	>	real( kind = DP ) :: ratmsq, rgrpsq, rgrp, vpair, vij
410	>	real( kind = DP ) :: sw, dswdr, swderiv, mf
411	>	real(kind=dp),dimension(3) :: d_atm, d_grp, fpair, fij
412		real(kind=dp) :: rfpot, mu_i, virial
413	<	integer :: me_i
413	>	integer :: me_i, me_j, n_in_i, n_in_j
414		logical :: is_dp_i
415		integer :: neighborListSize
416		integer :: listerror, error
417		integer :: localError
418	+	integer :: propPack_i, propPack_j
419	+	integer :: loopStart, loopEnd, loop
420
421	+	real(kind=dp) :: listSkin = 1.0
422	+
423		!! initialize local variables
424	<
424	>
425		#ifdef IS_MPI
426		pot_local = 0.0_dp
427	<	nlocal = getNlocal()
428	<	nrow   = getNrow(plan_row)
429	<	ncol   = getNcol(plan_col)
427	>	nAtomsInRow   = getNatomsInRow(plan_atom_row)
428	>	nAtomsInCol   = getNatomsInCol(plan_atom_col)
429	>	nGroupsInRow  = getNgroupsInRow(plan_group_row)
430	>	nGroupsInCol  = getNgroupsInCol(plan_group_col)
431		#else
205	–	nlocal = getNlocal()
432		natoms = nlocal
433		#endif
208	–
209	–	call getRcut(rcut,rc2=rcutsq)
210	–	call getRlist(rlist,rlistsq)
434
435	<	call check_initialization(localError)
435	>	call doReadyCheck(localError)
436		if ( localError .ne. 0 ) then
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	<
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	<	if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
467	<	!! See if we need to update neighbor lists
468	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
469	<	!! if_mpi_gather_stuff_for_prepair
470	<	!! do_prepair_loop_if_needed
471	<	!! if_mpi_scatter_stuff_from_prepair
472	<	!! if_mpi_gather_stuff_from_prepair_to_main_loop
466	>	!! Begin force loop timing:
467	>	#ifdef PROFILE
468	>	call cpu_time(forceTimeInitial)
469	>	nloops = nloops + 1
470	>	#endif
471	>
472	>	loopEnd = PAIR_LOOP
473	>	if (FF_RequiresPrepairCalc() .and. SIM_requires_prepair_calc) then
474	>	loopStart = PREPAIR_LOOP
475		else
476	<	!! See if we need to update neighbor lists
248	<	call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)
476	>	loopStart = PAIR_LOOP
477		endif
478	<
478	>
479	>	do loop = loopStart, loopEnd
480	>
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	>	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	<
262	<	do i = 1, nrow
263	<	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	<
514	<	nlist = nlist + 1
515	<
516	<	if (nlist > neighborListSize) then
517	<	call expandNeighborList(nlocal, listerror)
518	<	if (listerror /= 0) then
519	<	error = -1
520	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
521	<	return
522	<	end if
523	<	neighborListSize = size(list)
524	<	endif
525	<
526	<	list(nlist) = j
527	<
528	<	if (rijsq <  rcutsq) then
529	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
289	<	u_l, A, f, t, pot_local)
290	<	endif
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	>	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	>	do jnab = jstart, jend
526	>	if (update_nlist) then
527	>	j = jnab
528	>	else
529	>	j = list(jnab)
530		endif
292	–	enddo inner
293	–	enddo
531
532	<	point(nrow + 1) = nlist + 1
533	<
534	<	else  !! (of update_check)
298	<
299	<	! use the list to find the neighbors
300	<	do i = 1, nrow
301	<	JBEG = POINT(i)
302	<	JEND = POINT(i+1) - 1
303	<	! check thiat molecule i has neighbors
304	<	if (jbeg .le. jend) then
305	<
306	<	do jnab = jbeg, jend
307	<	j = list(jnab)
308	<
309	<	call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
310	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
311	<	u_l, A, f, t, pot_local)
312	<
313	<	enddo
314	<	endif
315	<	enddo
316	<	endif
317	<
532	>	#ifdef IS_MPI
533	>	call get_interatomic_vector(q_group_Row(:,i), &
534	>	q_group_Col(:,j), d_grp, rgrpsq)
535		#else
536	<
537	<	if (update_nlist) then
538	<
322	<	! save current configuration, contruct neighbor list,
323	<	! and calculate forces
324	<	call saveNeighborList(natoms, q)
325	<
326	<	neighborListSize = size(list)
327	<
328	<	nlist = 0
329	<
330	<	do i = 1, natoms-1
331	<	point(i) = nlist + 1
332	<
333	<	inner: do j = i+1, natoms
334	<
335	<	if (skipThisPair(i,j))  cycle inner
336	<
337	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
338	<
536	>	call get_interatomic_vector(q_group(:,i), &
537	>	q_group(:,j), d_grp, rgrpsq)
538	>	#endif
539
540	<	if (rijsq <  rlistsq) then
540	>	if (rgrpsq < rlistsq) then
541	>	if (update_nlist) then
542	>	nlist = nlist + 1
543	>
544	>	if (nlist > neighborListSize) then
545	>	#ifdef IS_MPI
546	>	call expandNeighborList(nGroupsInRow, listerror)
547	>	#else
548	>	call expandNeighborList(nGroups, listerror)
549	>	#endif
550	>	if (listerror /= 0) then
551	>	error = -1
552	>	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
553	>	return
554	>	end if
555	>	neighborListSize = size(list)
556	>	endif
557	>
558	>	list(nlist) = j
559	>	endif
560
561	<	nlist = nlist + 1
562	<
563	<	if (nlist > neighborListSize) then
345	<	call expandNeighborList(natoms, listerror)
346	<	if (listerror /= 0) then
347	<	error = -1
348	<	write(DEFAULT_ERROR,*) "ERROR: nlist > list size and max allocations exceeded."
349	<	return
350	<	end if
351	<	neighborListSize = size(list)
561	>	if (loop .eq. PAIR_LOOP) then
562	>	vij = 0.0d0
563	>	fij(1:3) = 0.0d0
564		endif
565
566	<	list(nlist) = j
566	>	call get_switch(rgrpsq, sw, dswdr, rgrp, group_switch, &
567	>	in_switching_region)
568
569	<	if (rijsq <  rcutsq) then
570	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
571	<	u_l, A, f, t, pot)
569	>	n_in_j = groupStartCol(j+1) - groupStartCol(j)
570	>
571	>	do ia = groupStartRow(i), groupStartRow(i+1)-1
572	>
573	>	atom1 = groupListRow(ia)
574	>
575	>	inner: do jb = groupStartCol(j), groupStartCol(j+1)-1
576	>
577	>	atom2 = groupListCol(jb)
578	>
579	>	if (skipThisPair(atom1, atom2)) cycle inner
580	>
581	>	if ((n_in_i .eq. 1).and.(n_in_j .eq. 1)) then
582	>	d_atm(1:3) = d_grp(1:3)
583	>	ratmsq = rgrpsq
584	>	else
585	>	#ifdef IS_MPI
586	>	call get_interatomic_vector(q_Row(:,atom1), &
587	>	q_Col(:,atom2), d_atm, ratmsq)
588	>	#else
589	>	call get_interatomic_vector(q(:,atom1), &
590	>	q(:,atom2), d_atm, ratmsq)
591	>	#endif
592	>	endif
593	>	if (loop .eq. PREPAIR_LOOP) then
594	>	#ifdef IS_MPI
595	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
596	>	rgrpsq, d_grp, do_pot, do_stress, &
597	>	u_l, A, f, t, pot_local)
598	>	#else
599	>	call do_prepair(atom1, atom2, ratmsq, d_atm, sw, &
600	>	rgrpsq, d_grp, do_pot, do_stress, &
601	>	u_l, A, f, t, pot)
602	>	#endif
603	>	else
604	>	#ifdef IS_MPI
605	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
606	>	do_pot, &
607	>	u_l, A, f, t, pot_local, vpair, fpair)
608	>	#else
609	>	call do_pair(atom1, atom2, ratmsq, d_atm, sw, &
610	>	do_pot,  &
611	>	u_l, A, f, t, pot, vpair, fpair)
612	>	#endif
613	>	vij = vij + vpair
614	>	fij(1:3) = fij(1:3) + fpair(1:3)
615	>	endif
616	>	enddo inner
617	>	enddo
618	>
619	>	if (loop .eq. PAIR_LOOP) then
620	>	if (in_switching_region) then
621	>	swderiv = vij*dswdr/rgrp
622	>	fij(1) = fij(1) + swderiv*d_grp(1)
623	>	fij(2) = fij(2) + swderiv*d_grp(2)
624	>	fij(3) = fij(3) + swderiv*d_grp(3)
625	>
626	>	do ia=groupStartRow(i), groupStartRow(i+1)-1
627	>	atom1=groupListRow(ia)
628	>	mf = mfactRow(atom1)
629	>	#ifdef IS_MPI
630	>	f_Row(1,atom1) = f_Row(1,atom1) + swderiv*d_grp(1)*mf
631	>	f_Row(2,atom1) = f_Row(2,atom1) + swderiv*d_grp(2)*mf
632	>	f_Row(3,atom1) = f_Row(3,atom1) + swderiv*d_grp(3)*mf
633	>	#else
634	>	f(1,atom1) = f(1,atom1) + swderiv*d_grp(1)*mf
635	>	f(2,atom1) = f(2,atom1) + swderiv*d_grp(2)*mf
636	>	f(3,atom1) = f(3,atom1) + swderiv*d_grp(3)*mf
637	>	#endif
638	>	enddo
639	>
640	>	do jb=groupStartCol(j), groupStartCol(j+1)-1
641	>	atom2=groupListCol(jb)
642	>	mf = mfactCol(atom2)
643	>	#ifdef IS_MPI
644	>	f_Col(1,atom2) = f_Col(1,atom2) - swderiv*d_grp(1)*mf
645	>	f_Col(2,atom2) = f_Col(2,atom2) - swderiv*d_grp(2)*mf
646	>	f_Col(3,atom2) = f_Col(3,atom2) - swderiv*d_grp(3)*mf
647	>	#else
648	>	f(1,atom2) = f(1,atom2) - swderiv*d_grp(1)*mf
649	>	f(2,atom2) = f(2,atom2) - swderiv*d_grp(2)*mf
650	>	f(3,atom2) = f(3,atom2) - swderiv*d_grp(3)*mf
651	>	#endif
652	>	enddo
653	>	endif
654	>
655	>	if (do_stress) call add_stress_tensor(d_grp, fij)
656		endif
657	<	endif
658	<	enddo inner
659	<	enddo
657	>	end if
658	>	enddo
659	>	enddo outer
660
661	<	point(natoms) = nlist + 1
662	<
663	<	else !! (update)
664	<
665	<	! use the list to find the neighbors
666	<	do i = 1, natoms-1
667	<	JBEG = POINT(i)
668	<	JEND = POINT(i+1) - 1
669	<	! check thiat molecule i has neighbors
670	<	if (jbeg .le. jend) then
671	<
375	<	do jnab = jbeg, jend
376	<	j = list(jnab)
377	<
378	<	call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
379	<	call do_pair(i, j, rijsq, d, do_pot, do_stress, &
380	<	u_l, A, f, t, pot)
381	<
382	<	enddo
661	>	if (update_nlist) then
662	>	#ifdef IS_MPI
663	>	point(nGroupsInRow + 1) = nlist + 1
664	>	#else
665	>	point(nGroups) = nlist + 1
666	>	#endif
667	>	if (loop .eq. PREPAIR_LOOP) then
668	>	! we just did the neighbor list update on the first
669	>	! pass, so we don't need to do it
670	>	! again on the second pass
671	>	update_nlist = .false.
672		endif
673	<	enddo
674	<	endif
673	>	endif
674	>
675	>	if (loop .eq. PREPAIR_LOOP) then
676	>	call do_preforce(nlocal, pot)
677	>	endif
678	>
679	>	enddo
680
681	<	#endif
681	>	!! Do timing
682	>	#ifdef PROFILE
683	>	call cpu_time(forceTimeFinal)
684	>	forceTime = forceTime + forceTimeFinal - forceTimeInitial
685	>	#endif
686
389	–	! phew, done with main loop.
390	–
687		#ifdef IS_MPI
688		!!distribute forces
689	<
689	>
690		f_temp = 0.0_dp
691	<	call scatter(f_Row,f_temp,plan_row3d)
691	>	call scatter(f_Row,f_temp,plan_atom_row_3d)
692		do i = 1,nlocal
693		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
694		end do
695	<
695	>
696		f_temp = 0.0_dp
697	<	call scatter(f_Col,f_temp,plan_col3d)
697	>	call scatter(f_Col,f_temp,plan_atom_col_3d)
698		do i = 1,nlocal
699		f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
700		end do
701
702	<	if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
702	>	if (FF_UsesDirectionalAtoms() .and. SIM_uses_directional_atoms) then
703		t_temp = 0.0_dp
704	<	call scatter(t_Row,t_temp,plan_row3d)
704	>	call scatter(t_Row,t_temp,plan_atom_row_3d)
705		do i = 1,nlocal
706		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
707		end do
708		t_temp = 0.0_dp
709	<	call scatter(t_Col,t_temp,plan_col3d)
709	>	call scatter(t_Col,t_temp,plan_atom_col_3d)
710
711		do i = 1,nlocal
712		t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
#	Line 419 | Line 715 | contains
715
716		if (do_pot) then
717		! scatter/gather pot_row into the members of my column
718	<	call scatter(pot_Row, pot_Temp, plan_row)
719	<
718	>	call scatter(pot_Row, pot_Temp, plan_atom_row)
719	>
720		! scatter/gather pot_local into all other procs
721		! add resultant to get total pot
722		do i = 1, nlocal
#	Line 428 | Line 724 | contains
724		enddo
725
726		pot_Temp = 0.0_DP
727	<
728	<	call scatter(pot_Col, pot_Temp, plan_col)
727	>
728	>	call scatter(pot_Col, pot_Temp, plan_atom_col)
729		do i = 1, nlocal
730		pot_local = pot_local + pot_Temp(i)
731		enddo
732	<
733	<	endif
732	>
733	>	endif
734		#endif
735	<
736	<	if (FF_RequiresPostpairCalc() .and. SimRequiresPostpairCalc()) then
735	>
736	>	if (FF_RequiresPostpairCalc() .and. SIM_requires_postpair_calc) then
737
738	<	if (FF_uses_RF .and. SimUsesRF()) then
738	>	if (FF_uses_RF .and. SIM_uses_RF) then
739
740		#ifdef IS_MPI
741	<	call scatter(rf_Row,rf,plan_row3d)
742	<	call scatter(rf_Col,rf_Temp,plan_col3d)
741	>	call scatter(rf_Row,rf,plan_atom_row_3d)
742	>	call scatter(rf_Col,rf_Temp,plan_atom_col_3d)
743		do i = 1,nlocal
744		rf(1:3,i) = rf(1:3,i) + rf_Temp(1:3,i)
745		end do
746		#endif
747
748	<	do i = 1, getNlocal()
749	<
748	>	do i = 1, nLocal
749	>
750		rfpot = 0.0_DP
751		#ifdef IS_MPI
752		me_i = atid_row(i)
753		#else
754		me_i = atid(i)
755		#endif
756	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
757	<	if ( is_DP_i ) then
758	<	call getElementProperty(atypes, me_i, "dipole_moment", mu_i)
756	>
757	>	if (PropertyMap(me_i)%is_DP) then
758	>
759	>	mu_i = PropertyMap(me_i)%dipole_moment
760	>
761		!! The reaction field needs to include a self contribution
762		!! to the field:
763	<	call accumulate_self_rf(i, mu_i, u_l)
763	>	call accumulate_self_rf(i, mu_i, u_l)
764		!! Get the reaction field contribution to the
765		!! potential and torques:
766		call reaction_field_final(i, mu_i, u_l, rfpot, t, do_pot)
#	Line 476 | Line 774 | contains
774		enddo
775		endif
776		endif
777	<
778	<
777	>
778	>
779		#ifdef IS_MPI
780	<
780	>
781		if (do_pot) then
782		pot = pot + pot_local
783		!! we assume the c code will do the allreduce to get the total potential
784		!! we could do it right here if we needed to...
785		endif
786	<
786	>
787		if (do_stress) then
788	<	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
788	>	call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
789		mpi_comm_world,mpi_err)
790		call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
791		mpi_comm_world,mpi_err)
792		endif
793	<
793	>
794		#else
795	<
795	>
796		if (do_stress) then
797		tau = tau_Temp
798		virial = virial_Temp
799		endif
502	–
503	–	#endif
800
801	+	#endif
802	+
803		end subroutine do_force_loop
804	+
805	+	subroutine do_pair(i, j, rijsq, d, sw, do_pot, &
806	+	u_l, A, f, t, pot, vpair, fpair)
807
808	<	subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
808	>	real( kind = dp ) :: pot, vpair, sw
809	>	real( kind = dp ), dimension(3) :: fpair
810	>	real( kind = dp ), dimension(nLocal)   :: mfact
811	>	real( kind = dp ), dimension(3,nLocal) :: u_l
812	>	real( kind = dp ), dimension(9,nLocal) :: A
813	>	real( kind = dp ), dimension(3,nLocal) :: f
814	>	real( kind = dp ), dimension(3,nLocal) :: t
815
816	<	real( kind = dp ) :: pot
510	<	real( kind = dp ), dimension(3,getNlocal()) :: u_l
511	<	real (kind=dp), dimension(9,getNlocal()) :: A
512	<	real (kind=dp), dimension(3,getNlocal()) :: f
513	<	real (kind=dp), dimension(3,getNlocal()) :: t
514	<
515	<	logical, intent(inout) :: do_pot, do_stress
816	>	logical, intent(inout) :: do_pot
817		integer, intent(in) :: i, j
818	<	real ( kind = dp ), intent(inout)    :: rijsq
818	>	real ( kind = dp ), intent(inout) :: rijsq
819		real ( kind = dp )                :: r
820		real ( kind = dp ), intent(inout) :: d(3)
520	–	logical :: is_LJ_i, is_LJ_j
521	–	logical :: is_DP_i, is_DP_j
522	–	logical :: is_GB_i, is_GB_j
523	–	logical :: is_Sticky_i, is_Sticky_j
821		integer :: me_i, me_j
822
823		r = sqrt(rijsq)
824	+	vpair = 0.0d0
825	+	fpair(1:3) = 0.0d0
826
528	–
529	–
827		#ifdef IS_MPI
828	<	if (tagRow(i) .eq. tagColumn(j)) then
829	<	write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
828	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
829	>	write(0,*) 'do_pair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
830		endif
534	–
831		me_i = atid_row(i)
832		me_j = atid_col(j)
537	–
833		#else
539	–
834		me_i = atid(i)
835		me_j = atid(j)
542	–
836		#endif
837	+
838	+	if (FF_uses_LJ .and. SIM_uses_LJ) then
839	+
840	+	if ( PropertyMap(me_i)%is_LJ .and. PropertyMap(me_j)%is_LJ ) then
841	+	!write(*,*) 'calling lj with'
842	+	!write(*,*) i, j, r, rijsq
843	+	!write(*,'(3es12.3)') d(1), d(2), d(3)
844	+	!write(*,'(3es12.3)') sw, vpair, pot
845	+	!write(*,*)
846
847	<	if (FF_uses_LJ .and. SimUsesLJ()) then
848	<	call getElementProperty(atypes, me_i, "is_LJ", is_LJ_i)
849	<	call getElementProperty(atypes, me_j, "is_LJ", is_LJ_j)
548	<
549	<	if ( is_LJ_i .and. is_LJ_j ) &
550	<	call do_lj_pair(i, j, d, r, rijsq, pot, f, do_pot, do_stress)
847	>	call do_lj_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
848	>	endif
849	>
850		endif
851	<
852	<	if (FF_uses_dipoles .and. SimUsesDipoles()) then
554	<	call getElementProperty(atypes, me_i, "is_DP", is_DP_i)
555	<	call getElementProperty(atypes, me_j, "is_DP", is_DP_j)
851	>
852	>	if (FF_uses_charges .and. SIM_uses_charges) then
853
854	<	if ( is_DP_i .and. is_DP_j ) then
855	<
559	<	call do_dipole_pair(i, j, d, r, rijsq, pot, u_l, f, t, &
560	<	do_pot, do_stress)
561	<	if (FF_uses_RF .and. SimUsesRF()) then
562	<	call accumulate_rf(i, j, r, u_l)
563	<	call rf_correct_forces(i, j, d, r, u_l, f, do_stress)
564	<	endif
565	<
854	>	if (PropertyMap(me_i)%is_Charge .and. PropertyMap(me_j)%is_Charge) then
855	>	call do_charge_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, do_pot)
856		endif
857	+
858		endif
859	+
860	+	if (FF_uses_dipoles .and. SIM_uses_dipoles) then
861	+
862	+	if ( PropertyMap(me_i)%is_DP .and. PropertyMap(me_j)%is_DP) then
863	+	call do_dipole_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
864	+	do_pot)
865	+	if (FF_uses_RF .and. SIM_uses_RF) then
866	+	call accumulate_rf(i, j, r, u_l, sw)
867	+	call rf_correct_forces(i, j, d, r, u_l, sw, f, fpair)
868	+	endif
869	+	endif
870
871	<	if (FF_uses_Sticky .and. SimUsesSticky()) then
871	>	endif
872
873	<	call getElementProperty(atypes, me_i, "is_Sticky", is_Sticky_i)
572	<	call getElementProperty(atypes, me_j, "is_Sticky", is_Sticky_j)
873	>	if (FF_uses_Sticky .and. SIM_uses_sticky) then
874
875	<	if ( is_Sticky_i .and. is_Sticky_j ) then
876	<	call do_sticky_pair(i, j, d, r, rijsq, A, pot, f, t, &
877	<	do_pot, do_stress)
875	>	if ( PropertyMap(me_i)%is_Sticky .and. PropertyMap(me_j)%is_Sticky) then
876	>	call do_sticky_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, A, f, t, &
877	>	do_pot)
878		endif
879	+
880		endif
881
882
883	<	if (FF_uses_GB .and. SimUsesGB()) then
582	<
583	<	call getElementProperty(atypes, me_i, "is_GB", is_GB_i)
584	<	call getElementProperty(atypes, me_j, "is_GB", is_GB_j)
883	>	if (FF_uses_GB .and. SIM_uses_GB) then
884
885	<	if ( is_GB_i .and. is_GB_j ) then
886	<	call do_gb_pair(i, j, d, r, rijsq, u_l, pot, f, t, &
887	<	do_pot, do_stress)
885	>	if ( PropertyMap(me_i)%is_GB .and. PropertyMap(me_j)%is_GB) then
886	>	call do_gb_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, u_l, f, t, &
887	>	do_pot)
888		endif
590	–	endif
591	–
592	–	end subroutine do_pair
889
890	<
595	<	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
596	<
597	<	real (kind = dp), dimension(3) :: q_i
598	<	real (kind = dp), dimension(3) :: q_j
599	<	real ( kind = dp ), intent(out) :: r_sq
600	<	real( kind = dp ) :: d(3)
601	<	real( kind = dp ) :: d_old(3)
602	<	d(1:3) = q_j(1:3) - q_i(1:3)
603	<	d_old = d
604	<	! Wrap back into periodic box if necessary
605	<	if ( SimUsesPBC() ) then
890	>	endif
891
892	<	d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,d(1:3)) * &
608	<	int(abs(d(1:3)/box(1:3)) + 0.5_dp)
892	>	if (FF_uses_EAM .and. SIM_uses_EAM) then
893
894	+	if ( PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) then
895	+	call do_eam_pair(i, j, d, r, rijsq, sw, vpair, fpair, pot, f, &
896	+	do_pot)
897	+	endif
898	+
899		endif
611	–	r_sq = dot_product(d,d)
612	–
613	–	end subroutine get_interatomic_vector
614	–
615	–	subroutine check_initialization(error)
616	–	integer, intent(out) :: error
900
901	<	error = 0
619	<	! Make sure we are properly initialized.
620	<	if (.not. do_forces_initialized) then
621	<	error = -1
622	<	return
623	<	endif
901	>	end subroutine do_pair
902
903	<	#ifdef IS_MPI
904	<	if (.not. isMPISimSet()) then
627	<	write(default_error,*) "ERROR: mpiSimulation has not been initialized!"
628	<	error = -1
629	<	return
630	<	endif
631	<	#endif
632	<
633	<	return
634	<	end subroutine check_initialization
903	>	subroutine do_prepair(i, j, rijsq, d, sw, rcijsq, dc, &
904	>	do_pot, do_stress, u_l, A, f, t, pot)
905
906	<
907	<	subroutine zero_work_arrays()
908	<
909	<	#ifdef IS_MPI
906	>	real( kind = dp ) :: pot, sw
907	>	real( kind = dp ), dimension(3,nLocal) :: u_l
908	>	real (kind=dp), dimension(9,nLocal) :: A
909	>	real (kind=dp), dimension(3,nLocal) :: f
910	>	real (kind=dp), dimension(3,nLocal) :: t
911	>
912	>	logical, intent(inout) :: do_pot, do_stress
913	>	integer, intent(in) :: i, j
914	>	real ( kind = dp ), intent(inout)    :: rijsq, rcijsq
915	>	real ( kind = dp )                :: r, rc
916	>	real ( kind = dp ), intent(inout) :: d(3), dc(3)
917	>
918	>	logical :: is_EAM_i, is_EAM_j
919	>
920	>	integer :: me_i, me_j
921	>
922
923	<	q_Row = 0.0_dp
924	<	q_Col = 0.0_dp
925	<
926	<	u_l_Row = 0.0_dp
927	<	u_l_Col = 0.0_dp
928	<
929	<	A_Row = 0.0_dp
648	<	A_Col = 0.0_dp
649	<
650	<	f_Row = 0.0_dp
651	<	f_Col = 0.0_dp
652	<	f_Temp = 0.0_dp
653	<
654	<	t_Row = 0.0_dp
655	<	t_Col = 0.0_dp
656	<	t_Temp = 0.0_dp
657	<
658	<	pot_Row = 0.0_dp
659	<	pot_Col = 0.0_dp
660	<	pot_Temp = 0.0_dp
923	>	r = sqrt(rijsq)
924	>	if (SIM_uses_molecular_cutoffs) then
925	>	rc = sqrt(rcijsq)
926	>	else
927	>	rc = r
928	>	endif
929	>
930
662	–	rf_Row = 0.0_dp
663	–	rf_Col = 0.0_dp
664	–	rf_Temp = 0.0_dp
665	–
666	–	#endif
667	–
668	–	rf = 0.0_dp
669	–	tau_Temp = 0.0_dp
670	–	virial_Temp = 0.0_dp
671	–	end subroutine zero_work_arrays
672	–
673	–	function skipThisPair(atom1, atom2) result(skip_it)
674	–	integer, intent(in) :: atom1
675	–	integer, intent(in), optional :: atom2
676	–	logical :: skip_it
677	–	integer :: unique_id_1, unique_id_2
678	–	integer :: me_i,me_j
679	–	integer :: i
680	–
681	–	skip_it = .false.
682	–
683	–	!! there are a number of reasons to skip a pair or a particle
684	–	!! mostly we do this to exclude atoms who are involved in short
685	–	!! range interactions (bonds, bends, torsions), but we also need
686	–	!! to exclude some overcounted interactions that result from
687	–	!! the parallel decomposition
688	–
931		#ifdef IS_MPI
932	<	!! in MPI, we have to look up the unique IDs for each atom
933	<	unique_id_1 = tagRow(atom1)
932	>	if (AtomRowToGlobal(i) .eq. AtomColToGlobal(j)) then
933	>	write(0,*) 'do_prepair is doing', i , j, AtomRowToGlobal(i), AtomColToGlobal(j)
934	>	endif
935	>
936	>	me_i = atid_row(i)
937	>	me_j = atid_col(j)
938	>
939		#else
940	<	!! in the normal loop, the atom numbers are unique
941	<	unique_id_1 = atom1
942	<	#endif
943	<
697	<	!! We were called with only one atom, so just check the global exclude
698	<	!! list for this atom
699	<	if (.not. present(atom2)) then
700	<	do i = 1, nExcludes_global
701	<	if (excludesGlobal(i) == unique_id_1) then
702	<	skip_it = .true.
703	<	return
704	<	end if
705	<	end do
706	<	return
707	<	end if
708	<
709	<	#ifdef IS_MPI
710	<	unique_id_2 = tagColumn(atom2)
711	<	#else
712	<	unique_id_2 = atom2
940	>
941	>	me_i = atid(i)
942	>	me_j = atid(j)
943	>
944		#endif
945	+
946	+	if (FF_uses_EAM .and. SIM_uses_EAM) then
947	+
948	+	if (PropertyMap(me_i)%is_EAM .and. PropertyMap(me_j)%is_EAM) &
949	+	call calc_EAM_prepair_rho(i, j, d, r, rijsq )
950	+
951	+	endif
952	+
953	+	end subroutine do_prepair
954	+
955	+
956	+	subroutine do_preforce(nlocal,pot)
957	+	integer :: nlocal
958	+	real( kind = dp ) :: pot
959	+
960	+	if (FF_uses_EAM .and. SIM_uses_EAM) then
961	+	call calc_EAM_preforce_Frho(nlocal,pot)
962	+	endif
963	+
964	+
965	+	end subroutine do_preforce
966	+
967	+
968	+	subroutine get_interatomic_vector(q_i, q_j, d, r_sq)
969	+
970	+	real (kind = dp), dimension(3) :: q_i
971	+	real (kind = dp), dimension(3) :: q_j
972	+	real ( kind = dp ), intent(out) :: r_sq
973	+	real( kind = dp ) :: d(3), scaled(3)
974	+	integer i
975	+
976	+	d(1:3) = q_j(1:3) - q_i(1:3)
977	+
978	+	! Wrap back into periodic box if necessary
979	+	if ( SIM_uses_PBC ) then
980	+
981	+	if( .not.boxIsOrthorhombic ) then
982	+	! calc the scaled coordinates.
983	+
984	+	scaled = matmul(HmatInv, d)
985	+
986	+	! wrap the scaled coordinates
987	+
988	+	scaled = scaled  - anint(scaled)
989	+
990	+
991	+	! calc the wrapped real coordinates from the wrapped scaled
992	+	! coordinates
993	+
994	+	d = matmul(Hmat,scaled)
995	+
996	+	else
997	+	! calc the scaled coordinates.
998	+
999	+	do i = 1, 3
1000	+	scaled(i) = d(i) * HmatInv(i,i)
1001	+
1002	+	! wrap the scaled coordinates
1003	+
1004	+	scaled(i) = scaled(i) - anint(scaled(i))
1005	+
1006	+	! calc the wrapped real coordinates from the wrapped scaled
1007	+	! coordinates
1008	+
1009	+	d(i) = scaled(i)*Hmat(i,i)
1010	+	enddo
1011	+	endif
1012	+
1013	+	endif
1014	+
1015	+	r_sq = dot_product(d,d)
1016	+
1017	+	end subroutine get_interatomic_vector
1018	+
1019	+	subroutine zero_work_arrays()
1020	+
1021	+	#ifdef IS_MPI
1022	+
1023	+	q_Row = 0.0_dp
1024	+	q_Col = 0.0_dp
1025
1026	+	q_group_Row = 0.0_dp
1027	+	q_group_Col = 0.0_dp
1028	+
1029	+	u_l_Row = 0.0_dp
1030	+	u_l_Col = 0.0_dp
1031	+
1032	+	A_Row = 0.0_dp
1033	+	A_Col = 0.0_dp
1034	+
1035	+	f_Row = 0.0_dp
1036	+	f_Col = 0.0_dp
1037	+	f_Temp = 0.0_dp
1038	+
1039	+	t_Row = 0.0_dp
1040	+	t_Col = 0.0_dp
1041	+	t_Temp = 0.0_dp
1042	+
1043	+	pot_Row = 0.0_dp
1044	+	pot_Col = 0.0_dp
1045	+	pot_Temp = 0.0_dp
1046	+
1047	+	rf_Row = 0.0_dp
1048	+	rf_Col = 0.0_dp
1049	+	rf_Temp = 0.0_dp
1050	+
1051	+	#endif
1052	+
1053	+	if (FF_uses_EAM .and. SIM_uses_EAM) then
1054	+	call clean_EAM()
1055	+	endif
1056	+
1057	+	rf = 0.0_dp
1058	+	tau_Temp = 0.0_dp
1059	+	virial_Temp = 0.0_dp
1060	+	end subroutine zero_work_arrays
1061	+
1062	+	function skipThisPair(atom1, atom2) result(skip_it)
1063	+	integer, intent(in) :: atom1
1064	+	integer, intent(in), optional :: atom2
1065	+	logical :: skip_it
1066	+	integer :: unique_id_1, unique_id_2
1067	+	integer :: me_i,me_j
1068	+	integer :: i
1069	+
1070	+	skip_it = .false.
1071	+
1072	+	!! there are a number of reasons to skip a pair or a particle
1073	+	!! mostly we do this to exclude atoms who are involved in short
1074	+	!! range interactions (bonds, bends, torsions), but we also need
1075	+	!! to exclude some overcounted interactions that result from
1076	+	!! the parallel decomposition
1077	+
1078		#ifdef IS_MPI
1079	<	!! this situation should only arise in MPI simulations
1080	<	if (unique_id_1 == unique_id_2) then
1081	<	skip_it = .true.
1082	<	return
1083	<	end if
721	<
722	<	!! this prevents us from doing the pair on multiple processors
723	<	if (unique_id_1 < unique_id_2) then
724	<	if (mod(unique_id_1 + unique_id_2,2) == 0) then
725	<	skip_it = .true.
726	<	return
727	<	endif
728	<	else
729	<	if (mod(unique_id_1 + unique_id_2,2) == 1) then
730	<	skip_it = .true.
731	<	return
732	<	endif
733	<	endif
1079	>	!! in MPI, we have to look up the unique IDs for each atom
1080	>	unique_id_1 = AtomRowToGlobal(atom1)
1081	>	#else
1082	>	!! in the normal loop, the atom numbers are unique
1083	>	unique_id_1 = atom1
1084		#endif
1085	+
1086	+	!! We were called with only one atom, so just check the global exclude
1087	+	!! list for this atom
1088	+	if (.not. present(atom2)) then
1089	+	do i = 1, nExcludes_global
1090	+	if (excludesGlobal(i) == unique_id_1) then
1091	+	skip_it = .true.
1092	+	return
1093	+	end if
1094	+	end do
1095	+	return
1096	+	end if
1097	+
1098	+	#ifdef IS_MPI
1099	+	unique_id_2 = AtomColToGlobal(atom2)
1100	+	#else
1101	+	unique_id_2 = atom2
1102	+	#endif
1103	+
1104	+	#ifdef IS_MPI
1105	+	!! this situation should only arise in MPI simulations
1106	+	if (unique_id_1 == unique_id_2) then
1107	+	skip_it = .true.
1108	+	return
1109	+	end if
1110	+
1111	+	!! this prevents us from doing the pair on multiple processors
1112	+	if (unique_id_1 < unique_id_2) then
1113	+	if (mod(unique_id_1 + unique_id_2,2) == 0) then
1114	+	skip_it = .true.
1115	+	return
1116	+	endif
1117	+	else
1118	+	if (mod(unique_id_1 + unique_id_2,2) == 1) then
1119	+	skip_it = .true.
1120	+	return
1121	+	endif
1122	+	endif
1123	+	#endif
1124	+
1125	+	!! the rest of these situations can happen in all simulations:
1126	+	do i = 1, nExcludes_global
1127	+	if ((excludesGlobal(i) == unique_id_1) .or. &
1128	+	(excludesGlobal(i) == unique_id_2)) then
1129	+	skip_it = .true.
1130	+	return
1131	+	endif
1132	+	enddo
1133	+
1134	+	do i = 1, nSkipsForAtom(unique_id_1)
1135	+	if (skipsForAtom(unique_id_1, i) .eq. unique_id_2) then
1136	+	skip_it = .true.
1137	+	return
1138	+	endif
1139	+	end do
1140	+
1141	+	return
1142	+	end function skipThisPair
1143
1144	<	!! the rest of these situations can happen in all simulations:
1145	<	do i = 1, nExcludes_global
1146	<	if ((excludesGlobal(i) == unique_id_1) .or. &
1147	<	(excludesGlobal(i) == unique_id_2)) then
1148	<	skip_it = .true.
1149	<	return
1150	<	endif
1151	<	enddo
1144	>	function FF_UsesDirectionalAtoms() result(doesit)
1145	>	logical :: doesit
1146	>	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1147	>	FF_uses_GB .or. FF_uses_RF
1148	>	end function FF_UsesDirectionalAtoms
1149	>
1150	>	function FF_RequiresPrepairCalc() result(doesit)
1151	>	logical :: doesit
1152	>	doesit = FF_uses_EAM
1153	>	end function FF_RequiresPrepairCalc
1154	>
1155	>	function FF_RequiresPostpairCalc() result(doesit)
1156	>	logical :: doesit
1157	>	doesit = FF_uses_RF
1158	>	end function FF_RequiresPostpairCalc
1159	>
1160	>	#ifdef PROFILE
1161	>	function getforcetime() result(totalforcetime)
1162	>	real(kind=dp) :: totalforcetime
1163	>	totalforcetime = forcetime
1164	>	end function getforcetime
1165	>	#endif
1166	>
1167	>	!! This cleans componets of force arrays belonging only to fortran
1168
1169	<	do i = 1, nExcludes_local
1170	<	if (excludesLocal(1,i) == unique_id_1) then
1171	<	if (excludesLocal(2,i) == unique_id_2) then
1172	<	skip_it = .true.
1173	<	return
1174	<	endif
1175	<	else
1176	<	if (excludesLocal(1,i) == unique_id_2) then
1177	<	if (excludesLocal(2,i) == unique_id_1) then
1178	<	skip_it = .true.
1179	<	return
1180	<	endif
1181	<	endif
1182	<	endif
1183	<	end do
1184	<
1185	<	return
1186	<	end function skipThisPair
1187	<
1188	<	function FF_UsesDirectionalAtoms() result(doesit)
1189	<	logical :: doesit
1190	<	doesit = FF_uses_dipoles .or. FF_uses_sticky .or. &
1191	<	FF_uses_GB .or. FF_uses_RF
1192	<	end function FF_UsesDirectionalAtoms
769	<
770	<	function FF_RequiresPrepairCalc() result(doesit)
771	<	logical :: doesit
772	<	doesit = FF_uses_EAM
773	<	end function FF_RequiresPrepairCalc
774	<
775	<	function FF_RequiresPostpairCalc() result(doesit)
776	<	logical :: doesit
777	<	doesit = FF_uses_RF
778	<	end function FF_RequiresPostpairCalc
779	<
1169	>	subroutine add_stress_tensor(dpair, fpair)
1170	>
1171	>	real( kind = dp ), dimension(3), intent(in) :: dpair, fpair
1172	>
1173	>	! because the d vector is the rj - ri vector, and
1174	>	! because fx, fy, fz are the force on atom i, we need a
1175	>	! negative sign here:
1176	>
1177	>	tau_Temp(1) = tau_Temp(1) - dpair(1) * fpair(1)
1178	>	tau_Temp(2) = tau_Temp(2) - dpair(1) * fpair(2)
1179	>	tau_Temp(3) = tau_Temp(3) - dpair(1) * fpair(3)
1180	>	tau_Temp(4) = tau_Temp(4) - dpair(2) * fpair(1)
1181	>	tau_Temp(5) = tau_Temp(5) - dpair(2) * fpair(2)
1182	>	tau_Temp(6) = tau_Temp(6) - dpair(2) * fpair(3)
1183	>	tau_Temp(7) = tau_Temp(7) - dpair(3) * fpair(1)
1184	>	tau_Temp(8) = tau_Temp(8) - dpair(3) * fpair(2)
1185	>	tau_Temp(9) = tau_Temp(9) - dpair(3) * fpair(3)
1186	>
1187	>	!write(*,'(6es12.3)')  fpair(1:3), tau_Temp(1), tau_Temp(5), tau_temp(9)
1188	>	virial_Temp = virial_Temp + &
1189	>	(tau_Temp(1) + tau_Temp(5) + tau_Temp(9))
1190	>
1191	>	end subroutine add_stress_tensor
1192	>
1193		end module do_Forces
1194	+

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