1 |
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!! Calculates Long Range forces Lennard-Jones interactions. |
2 |
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!! Corresponds to the force field defined in lj_FF.cpp |
3 |
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!! @author Charles F. Vardeman II |
4 |
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!! @author Matthew Meineke |
5 |
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!! @version $Id: lj_FF.F90,v 1.10 2003-01-24 21:36:52 chuckv Exp $, $Date: 2003-01-24 21:36:52 $, $Name: not supported by cvs2svn $, $Revision: 1.10 $ |
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module lj_ff |
10 |
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use simulation |
11 |
< |
use definitions, ONLY : dp, ndim |
11 |
> |
use definitions |
12 |
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#ifdef IS_MPI |
13 |
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use mpiSimulation |
14 |
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#endif |
21 |
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!! Starting Size for ljMixed Array |
22 |
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integer, parameter :: ljMixed_blocksize = 10 |
23 |
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|
24 |
+ |
!! Basic atom type for a Lennard-Jones Atom. |
25 |
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type, public :: lj_atype |
26 |
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private |
27 |
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sequence |
32 |
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!! Mass of Particle |
33 |
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real ( kind = dp ) :: mass = 0.0_dp |
34 |
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!! Lennard-Jones epslon |
35 |
< |
real ( kind = dp ) :: epslon = 0.0_dp |
35 |
> |
real ( kind = dp ) :: epsilon = 0.0_dp |
36 |
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!! Lennard-Jones Sigma |
37 |
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real ( kind = dp ) :: sigma = 0.0_dp |
38 |
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!! Lennard-Jones Sigma Squared |
51 |
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!! Global list of lj atypes in simulation |
52 |
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type (lj_atype), pointer :: lj_atype_list => null() |
53 |
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!! LJ mixing array |
54 |
< |
type (lj_atype), dimension(:,:), allocatable, pointer :: ljMixed =>null() |
54 |
> |
type (lj_atype), dimension(:,:), pointer :: ljMixed => null() |
55 |
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!! identity pointer list for force loop. |
56 |
< |
type (lj_atypePtr), dimension(:), allocatable :: identPtrList |
56 |
> |
type (lj_atypePtr), dimension(:), pointer :: identPtrList => null() |
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|
58 |
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|
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!! Neighbor list and commom arrays |
60 |
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!! This should eventally get moved to a neighbor list type |
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integer, allocatable, dimension(:) :: point |
62 |
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integer, allocatable, dimension(:) :: list |
63 |
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integer, parameter :: listMultiplier = 80 |
64 |
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integer :: nListAllocs = 0 |
65 |
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integer, parameter :: maxListAllocs = 5 |
66 |
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|
67 |
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#ifdef IS_MPI |
68 |
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! Universal routines: All types of force calculations will need these arrays |
69 |
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! Arrays specific to a type of force calculation should be declared in that module. |
70 |
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!! Row position array. |
71 |
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real( kind = dp ), allocatable, dimension(:,:) :: qRow |
72 |
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!! Column position array. |
73 |
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real( kind = dp ), allocatable, dimension(:,:) :: qColumn |
74 |
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|
75 |
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!! Row Force array. |
76 |
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real( kind = dp ), allocatable, dimension(:,:) :: fRow |
77 |
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!! Column Force Array. |
78 |
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real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
62 |
– |
#endif |
79 |
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|
80 |
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!! Row potential energy array |
81 |
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real( kind = dp ), allocatable, dimension(:) :: eRow |
82 |
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!! Column potential energy array |
83 |
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real( kind = dp ), allocatable, dimension(:) :: eColumn |
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|
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|
86 |
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!! Row lj_atype pointer list |
87 |
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type (lj_atypePtr), dimension(:), pointer :: identPtrListRow => null() |
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!! Column lj_atype pointer list |
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type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null() |
90 |
+ |
#endif |
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|
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|
93 |
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!! Logical has lj force field module been initialized? |
94 |
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logical, save :: isljFFinit = .false. |
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|
96 |
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|
97 |
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!! Public methods and data |
98 |
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public :: new_lj_atype |
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public :: do_lj_ff |
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public :: getLjPot |
101 |
< |
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101 |
> |
public :: init_ljFF |
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105 |
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106 |
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contains |
107 |
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108 |
< |
subroutine new_lj_atype(ident,mass,epslon,sigma,status) |
108 |
> |
subroutine new_lj_atype(ident,mass,epsilon,sigma,status) |
109 |
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real( kind = dp ), intent(in) :: mass |
110 |
< |
real( kind = dp ), intent(in) :: epslon |
110 |
> |
real( kind = dp ), intent(in) :: epsilon |
111 |
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real( kind = dp ), intent(in) :: sigma |
112 |
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integer, intent(in) :: ident |
113 |
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integer, intent(out) :: status |
115 |
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type (lj_atype), pointer :: this_lj_atype |
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type (lj_atype), pointer :: lj_atype_ptr |
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|
118 |
< |
type (lj_atype), allocatable, dimension(:,:), pointer :: thisMix |
119 |
< |
type (lj_atype), allocatable, dimension(:,:), pointer :: oldMix |
118 |
> |
type (lj_atype), dimension(:,:), pointer :: thisMix |
119 |
> |
type (lj_atype), dimension(:,:), pointer :: oldMix |
120 |
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integer :: alloc_error |
121 |
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integer :: atype_counter = 0 |
122 |
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integer :: alloc_size |
133 |
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end if |
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|
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! assign our new lj_atype information |
136 |
< |
this_lj_atype%mass = mass |
137 |
< |
this_lj_atype%epslon = epslon |
138 |
< |
this_lj_atype%sigma = sigma |
139 |
< |
this_lj_atype%sigma2 = sigma * sigma |
140 |
< |
this_lj_atype%sigma6 = this_lj_atype%sigma2 * this_lj_atype%sigma2 & |
136 |
> |
this_lj_atype%mass = mass |
137 |
> |
this_lj_atype%epsilon = epsilon |
138 |
> |
this_lj_atype%sigma = sigma |
139 |
> |
this_lj_atype%sigma2 = sigma * sigma |
140 |
> |
this_lj_atype%sigma6 = this_lj_atype%sigma2 * this_lj_atype%sigma2 & |
141 |
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* this_lj_atype%sigma2 |
142 |
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! assume that this atype will be successfully added |
143 |
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this_lj_atype%atype_ident = ident |
144 |
< |
this_lj_atype%number = n_lj_atypes + 1 |
144 |
> |
this_lj_atype%atype_number = n_lj_atypes + 1 |
145 |
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|
146 |
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|
147 |
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! First time through allocate a array of size ljMixed_blocksize |
155 |
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! If we have outgrown ljMixed_blocksize, allocate a new matrix twice the size and |
156 |
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! point ljMix at the new matrix. |
157 |
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else if( (n_lj_atypes + 1) > size(ljMixed)) then |
158 |
< |
alloc_size = 2*size(ljMix) |
158 |
> |
alloc_size = 2*size(ljMixed) |
159 |
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allocate(thisMix(alloc_size,alloc_size)) |
160 |
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if (alloc_error /= 0 ) then |
161 |
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status = -1 |
178 |
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! Find bottom of atype master list |
179 |
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! if lj_atype_list is null then we are at the top of the list. |
180 |
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if (.not. associated(lj_atype_list)) then |
153 |
– |
lj_atype_ptr => this_lj_atype |
154 |
– |
atype_counter = 1 |
181 |
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|
182 |
+ |
write(*,*) "Associating lists for first time" |
183 |
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|
184 |
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|
185 |
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this_lj_atype%atype_number = 1 |
186 |
+ |
|
187 |
+ |
ljMixed(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
188 |
+ |
|
189 |
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ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma & |
190 |
+ |
* ljMixed(n_lj_atypes,n_lj_atypes)%sigma |
191 |
+ |
|
192 |
+ |
ljMixed(n_lj_atypes,n_lj_atypes)%sigma6 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 & |
193 |
+ |
* ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 & |
194 |
+ |
* ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 |
195 |
+ |
|
196 |
+ |
ljMixed(n_lj_atypes,n_lj_atypes)%epsilon = this_lj_atype%epsilon |
197 |
+ |
|
198 |
+ |
lj_atype_list => this_lj_atype |
199 |
+ |
|
200 |
+ |
write(*,*) "lj_atype_list first time through -- ident", lj_atype_list%atype_ident |
201 |
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else ! we need to find the bottom of the list to insert new atype |
202 |
< |
lj_atype_ptr => lj_atype_list%next |
202 |
> |
write(*,*) "Second time through" |
203 |
> |
lj_atype_ptr => lj_atype_list |
204 |
> |
write(*,*) "lj_atype_ptr to next" |
205 |
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atype_counter = 1 |
206 |
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find_end: do |
207 |
< |
if (.not. associated(lj_atype_ptr%next)) then |
208 |
< |
exit find_end |
209 |
< |
end if |
207 |
> |
if (.not. associated(lj_atype_ptr)) exit find_end |
208 |
> |
|
209 |
> |
write(*,*) "Inside find_end-this ident", lj_atype_ptr%atype_ident |
210 |
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! Set up mixing for new atype and current atype in list |
211 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
211 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
212 |
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calcLJMix("sigma",this_lj_atype%sigma, & |
213 |
< |
lj_atype_prt%sigma) |
213 |
> |
lj_atype_ptr%sigma) |
214 |
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|
215 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
216 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
217 |
< |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
215 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
216 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
217 |
> |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
218 |
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|
219 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = & |
220 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
221 |
< |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
222 |
< |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
219 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = & |
220 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
221 |
> |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
222 |
> |
* ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
223 |
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|
224 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epslon = & |
225 |
< |
calcLJMix("epslon",this_lj_atype%epslon, & |
226 |
< |
lj_atype_prt%epslon) |
224 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epsilon = & |
225 |
> |
calcLJMix("epsilon",this_lj_atype%epsilon, & |
226 |
> |
lj_atype_ptr%epsilon) |
227 |
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|
228 |
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! Advance to next pointer |
229 |
< |
lj_atype_ptr => lj_atype_ptr%next |
230 |
< |
atype_counter = atype_counter + 1 |
184 |
< |
|
229 |
> |
lj_atype_ptr => lj_atype_ptr%next |
230 |
> |
atype_counter = atype_counter + 1 |
231 |
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end do find_end |
232 |
+ |
|
233 |
+ |
lj_atype_ptr => this_lj_atype |
234 |
+ |
write(*,*) "just added: ", lj_atype_ptr%atype_ident |
235 |
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end if |
236 |
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237 |
< |
|
189 |
< |
|
237 |
> |
write(*,*) "lj_atype_list now contains.." |
238 |
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|
239 |
+ |
lj_atype_ptr => lj_atype_list |
240 |
+ |
do while (associated(lj_atype_ptr)) |
241 |
+ |
write(*,*) "lj_atype_list contains ident", lj_atype_ptr%atype_ident |
242 |
+ |
lj_atype_ptr => lj_atype_ptr%next |
243 |
+ |
end do |
244 |
+ |
|
245 |
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! Insert new atype at end of list |
246 |
< |
lj_atype_ptr => this_lj_atype |
246 |
> |
|
247 |
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! Increment number of atypes |
248 |
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|
249 |
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n_lj_atypes = n_lj_atypes + 1 |
250 |
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251 |
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! Set up self mixing |
252 |
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|
199 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
200 |
– |
|
201 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma2 = ljMix(n_lj_atypes,n_lj_atypes)%sigma & |
202 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma |
203 |
– |
|
204 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma6 = ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
205 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
206 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 |
207 |
– |
|
208 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%epslon = this_lj_atype%epslon |
209 |
– |
|
210 |
– |
|
253 |
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end subroutine new_lj_atype |
254 |
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|
255 |
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|
256 |
< |
subroutine init_ljFF() |
256 |
> |
subroutine init_ljFF(nComponents,ident, status) |
257 |
> |
!! Number of components in ident array |
258 |
> |
integer, intent(inout) :: nComponents |
259 |
> |
!! Array of identities nComponents long corresponding to |
260 |
> |
!! ljatype ident. |
261 |
> |
integer, dimension(nComponents),intent(inout) :: ident |
262 |
> |
!! Result status, success = 0, error = -1 |
263 |
> |
integer, intent(out) :: Status |
264 |
|
|
265 |
+ |
integer :: alloc_stat |
266 |
|
|
267 |
+ |
integer :: thisStat |
268 |
+ |
integer :: i |
269 |
|
#ifdef IS_MPI |
270 |
+ |
integer, allocatable, dimension(:) :: identRow |
271 |
+ |
integer, allocatable, dimension(:) :: identCol |
272 |
+ |
integer :: nrow |
273 |
+ |
integer :: ncol |
274 |
+ |
integer :: alloc_stat |
275 |
+ |
#endif |
276 |
+ |
status = 0 |
277 |
|
|
278 |
+ |
write(*,*) "Initializing ljFF" |
279 |
+ |
!! if were're not in MPI, we just update ljatypePtrList |
280 |
+ |
#ifndef IS_MPI |
281 |
+ |
call new_ljatypePtrList(nComponents,ident,identPtrList,thisStat) |
282 |
+ |
if ( thisStat /= 0 ) then |
283 |
+ |
status = -1 |
284 |
+ |
return |
285 |
+ |
endif |
286 |
+ |
write(*,*) "component pointer list initialized" |
287 |
+ |
!! Allocate pointer lists |
288 |
+ |
allocate(point(nComponents),stat=alloc_stat) |
289 |
+ |
if (alloc_stat /=0) then |
290 |
+ |
status = -1 |
291 |
+ |
return |
292 |
+ |
endif |
293 |
+ |
|
294 |
+ |
allocate(list(nComponents*listMultiplier),stat=alloc_stat) |
295 |
+ |
if (alloc_stat /=0) then |
296 |
+ |
status = -1 |
297 |
+ |
return |
298 |
+ |
endif |
299 |
|
|
300 |
+ |
! if were're in MPI, we also have to worry about row and col lists |
301 |
+ |
#else |
302 |
+ |
! We can only set up forces if mpiSimulation has been setup. |
303 |
+ |
if (.not. isMPISimSet()) then |
304 |
+ |
status = -1 |
305 |
+ |
return |
306 |
+ |
endif |
307 |
+ |
nrow = getNrow() |
308 |
+ |
ncol = getNcol() |
309 |
+ |
!! Allocate temperary arrays to hold gather information |
310 |
+ |
allocate(identRow(nrow),stat=alloc_stat) |
311 |
+ |
if (alloc_stat /= 0 ) then |
312 |
+ |
status = -1 |
313 |
+ |
return |
314 |
+ |
endif |
315 |
+ |
|
316 |
+ |
allocate(identCol(ncol),stat=alloc_stat) |
317 |
+ |
if (alloc_stat /= 0 ) then |
318 |
+ |
status = -1 |
319 |
+ |
return |
320 |
+ |
endif |
321 |
+ |
!! Gather idents into row and column idents |
322 |
+ |
call gather(ident,identRow,plan_row) |
323 |
+ |
call gather(ident,identCol,plan_col) |
324 |
+ |
|
325 |
+ |
!! Create row and col pointer lists |
326 |
+ |
call new_ljatypePtrList(nrow,identRow,identPtrListRow,thisStat) |
327 |
+ |
if (thisStat /= 0 ) then |
328 |
+ |
status = -1 |
329 |
+ |
return |
330 |
+ |
endif |
331 |
+ |
|
332 |
+ |
call new_ljatypePtrList(ncol,identCol,identPtrListCol,thisStat) |
333 |
+ |
if (thisStat /= 0 ) then |
334 |
+ |
status = -1 |
335 |
+ |
return |
336 |
+ |
endif |
337 |
+ |
|
338 |
+ |
!! free temporary ident arrays |
339 |
+ |
deallocate(identCol) |
340 |
+ |
deallocate(identRow) |
341 |
+ |
|
342 |
+ |
!! Allocate Simulation arrays |
343 |
+ |
!! NOTE: This bit of code should be fixed, it can cause large |
344 |
+ |
!! memory fragmentation if call repeatedly |
345 |
+ |
|
346 |
+ |
if (.not.allocated(qRow)) then |
347 |
+ |
allocate(qRow(3,nrow),stat=alloc_stat) |
348 |
+ |
if (alloc_stat /= 0 ) then |
349 |
+ |
status = -1 |
350 |
+ |
return |
351 |
+ |
endif |
352 |
+ |
else |
353 |
+ |
deallocate(qrow) |
354 |
+ |
allocate(qRow(3,nrow),stat=alloc_stat) |
355 |
+ |
if (alloc_stat /= 0 ) then |
356 |
+ |
status = -1 |
357 |
+ |
return |
358 |
+ |
endif |
359 |
+ |
endif |
360 |
+ |
|
361 |
+ |
if (.not.allocated(3,qCol)) then |
362 |
+ |
allocate(qCol(ncol),stat=alloc_stat) |
363 |
+ |
if (alloc_stat /= 0 ) then |
364 |
+ |
status = -1 |
365 |
+ |
return |
366 |
+ |
endif |
367 |
+ |
else |
368 |
+ |
deallocate(qCol) |
369 |
+ |
allocate(qCol(3,ncol),stat=alloc_stat) |
370 |
+ |
if (alloc_stat /= 0 ) then |
371 |
+ |
status = -1 |
372 |
+ |
return |
373 |
+ |
endif |
374 |
+ |
endif |
375 |
+ |
|
376 |
+ |
if (.not.allocated(fRow)) then |
377 |
+ |
allocate(fRow(3,nrow),stat=alloc_stat) |
378 |
+ |
if (alloc_stat /= 0 ) then |
379 |
+ |
status = -1 |
380 |
+ |
return |
381 |
+ |
endif |
382 |
+ |
else |
383 |
+ |
deallocate(fRow) |
384 |
+ |
allocate(fRow(3,nrow),stat=alloc_stat) |
385 |
+ |
if (alloc_stat /= 0 ) then |
386 |
+ |
status = -1 |
387 |
+ |
return |
388 |
+ |
endif |
389 |
+ |
endif |
390 |
+ |
|
391 |
+ |
if (.not.allocated(fCol)) then |
392 |
+ |
allocate(fCol(3,ncol),stat=alloc_stat) |
393 |
+ |
if (alloc_stat /= 0 ) then |
394 |
+ |
status = -1 |
395 |
+ |
return |
396 |
+ |
endif |
397 |
+ |
else |
398 |
+ |
deallocate(fCol) |
399 |
+ |
allocate(fCol(3,ncol),stat=alloc_stat) |
400 |
+ |
if (alloc_stat /= 0 ) then |
401 |
+ |
status = -1 |
402 |
+ |
return |
403 |
+ |
endif |
404 |
+ |
endif |
405 |
+ |
|
406 |
+ |
if (.not.allocated(eRow)) then |
407 |
+ |
allocate(eRow(nrow),stat=alloc_stat) |
408 |
+ |
if (alloc_stat /= 0 ) then |
409 |
+ |
status = -1 |
410 |
+ |
return |
411 |
+ |
endif |
412 |
+ |
else |
413 |
+ |
deallocate(eRow) |
414 |
+ |
allocate(eRow(nrow),stat=alloc_stat) |
415 |
+ |
if (alloc_stat /= 0 ) then |
416 |
+ |
status = -1 |
417 |
+ |
return |
418 |
+ |
endif |
419 |
+ |
endif |
420 |
+ |
|
421 |
+ |
if (.not.allocated(eCol)) then |
422 |
+ |
allocate(eCol(ncol),stat=alloc_stat) |
423 |
+ |
if (alloc_stat /= 0 ) then |
424 |
+ |
status = -1 |
425 |
+ |
return |
426 |
+ |
endif |
427 |
+ |
else |
428 |
+ |
deallocate(eCol) |
429 |
+ |
allocate(eCol(ncol),stat=alloc_stat) |
430 |
+ |
if (alloc_stat /= 0 ) then |
431 |
+ |
status = -1 |
432 |
+ |
return |
433 |
+ |
endif |
434 |
+ |
endif |
435 |
|
|
436 |
+ |
if (.not.allocated(eTemp)) then |
437 |
+ |
allocate(eTemp(nComponents),stat=alloc_stat) |
438 |
+ |
if (alloc_stat /= 0 ) then |
439 |
+ |
status = -1 |
440 |
+ |
return |
441 |
+ |
endif |
442 |
+ |
else |
443 |
+ |
deallocate(eTemp) |
444 |
+ |
allocate(eTemp(nComponets),stat=alloc_stat) |
445 |
+ |
if (alloc_stat /= 0 ) then |
446 |
+ |
status = -1 |
447 |
+ |
return |
448 |
+ |
endif |
449 |
+ |
endif |
450 |
+ |
|
451 |
+ |
|
452 |
+ |
!! Allocate neighbor lists for mpi simulations. |
453 |
+ |
if (.not. allocated(point)) then |
454 |
+ |
allocate(point(nrow),stat=alloc_stat) |
455 |
+ |
if (alloc_stat /=0) then |
456 |
+ |
status = -1 |
457 |
+ |
return |
458 |
+ |
endif |
459 |
+ |
|
460 |
+ |
allocate(list(ncol*listMultiplier),stat=alloc_stat) |
461 |
+ |
if (alloc_stat /=0) then |
462 |
+ |
status = -1 |
463 |
+ |
return |
464 |
+ |
endif |
465 |
+ |
else |
466 |
+ |
deallocate(list) |
467 |
+ |
deallocate(point) |
468 |
+ |
allocate(point(nrow),stat=alloc_stat) |
469 |
+ |
if (alloc_stat /=0) then |
470 |
+ |
status = -1 |
471 |
+ |
return |
472 |
+ |
endif |
473 |
+ |
|
474 |
+ |
allocate(list(ncol*listMultiplier),stat=alloc_stat) |
475 |
+ |
if (alloc_stat /=0) then |
476 |
+ |
status = -1 |
477 |
+ |
return |
478 |
+ |
endif |
479 |
+ |
endif |
480 |
+ |
|
481 |
|
#endif |
482 |
+ |
|
483 |
+ |
|
484 |
+ |
do i = 1, nComponents |
485 |
+ |
write(*,*) "Ident pointer list ident: ", identPtrList(i)%this%atype_ident |
486 |
+ |
end do |
487 |
|
|
488 |
+ |
isljFFinit = .true. |
489 |
+ |
|
490 |
|
end subroutine init_ljFF |
491 |
|
|
492 |
+ |
|
493 |
+ |
|
494 |
+ |
|
495 |
+ |
|
496 |
|
!! Takes an ident array and creates an atype pointer list |
497 |
|
!! based on those identities |
498 |
|
subroutine new_ljatypePtrList(mysize,ident,PtrList,status) |
499 |
|
integer, intent(in) :: mysize |
500 |
< |
integer, intent(in) :: ident |
500 |
> |
integer,dimension(:), intent(in) :: ident |
501 |
|
integer, optional :: status |
502 |
< |
type(lj_atypePtr), dimension(:) :: PtrList |
502 |
> |
type(lj_atypePtr), dimension(:), pointer :: PtrList |
503 |
|
|
504 |
|
integer :: thisIdent |
505 |
|
integer :: i |
508 |
|
|
509 |
|
if (present(status)) status = 0 |
510 |
|
|
511 |
+ |
write(*,*) "Creating new ljatypePtrList...." |
512 |
|
! First time through, allocate list |
513 |
< |
if (.not.(allocated)) then |
513 |
> |
if (.not.associated(PtrList)) then |
514 |
> |
write(*,*) "allocating pointer list...." |
515 |
|
allocate(PtrList(mysize)) |
516 |
|
else |
517 |
|
! We want to creat a new ident list so free old list |
518 |
< |
deallocate(PrtList) |
518 |
> |
deallocate(PtrList) |
519 |
|
allocate(PtrList(mysize)) |
520 |
|
endif |
521 |
|
|
522 |
|
! Match pointer list |
523 |
+ |
write(*,*) "Doing ident search" |
524 |
|
do i = 1, mysize |
525 |
|
thisIdent = ident(i) |
526 |
+ |
write(*,*) "Calling getLJatype for ident ", thisIdent |
527 |
|
call getLJatype(thisIdent,tmpPtr) |
528 |
|
|
529 |
|
if (.not. associated(tmpPtr)) then |
530 |
+ |
write(*,*) "tmpptr was not associated" |
531 |
|
status = -1 |
532 |
|
return |
533 |
|
endif |
541 |
|
!! returns a null pointer if error |
542 |
|
subroutine getLJatype(ident,ljAtypePtr) |
543 |
|
integer, intent(in) :: ident |
544 |
< |
type (lj_atype), intent(out),pointer :: ljAtypePtr => null() |
269 |
< |
|
544 |
> |
type (lj_atype), pointer :: ljAtypePtr |
545 |
|
type (lj_atype), pointer :: tmplj_atype_ptr => null() |
546 |
|
|
547 |
+ |
write(*,*) "Finding ljAtype for ident ", ident |
548 |
+ |
ljAtypePtr => null() |
549 |
+ |
|
550 |
|
if(.not. associated(lj_atype_list)) return |
551 |
|
|
552 |
|
! Point at head of list. |
553 |
+ |
write(*,*) "Searching at head of list" |
554 |
|
tmplj_atype_ptr => lj_atype_list |
555 |
|
find_ident: do |
556 |
|
if (.not.associated(tmplj_atype_ptr)) then |
557 |
+ |
write(*,*) "Find_ident, pointer not associated" |
558 |
|
exit find_ident |
559 |
< |
else if( lj_atype_ptr%atype_ident == ident) |
559 |
> |
else if( tmplj_atype_ptr%atype_ident == ident) then |
560 |
|
ljAtypePtr => tmplj_atype_ptr |
561 |
|
exit find_ident |
562 |
|
endif |
563 |
|
tmplj_atype_ptr => tmplj_atype_ptr%next |
564 |
|
end do find_ident |
565 |
|
|
566 |
+ |
|
567 |
+ |
|
568 |
+ |
|
569 |
|
end subroutine getLJatype |
570 |
|
|
571 |
|
|
572 |
< |
! FORCE routine |
572 |
> |
!! FORCE routine Calculates Lennard Jones forces. |
573 |
|
!-------------------------------------------------------------> |
574 |
|
subroutine do_lj_ff(q,f,potE,do_pot) |
575 |
< |
real ( kind = dp ), dimension(ndim,) :: q |
576 |
< |
real ( kind = dp ), dimension(ndim,nLRparticles) :: f |
575 |
> |
!! Position array provided by C, dimensioned by getNlocal |
576 |
> |
real ( kind = dp ), dimension(3,getNlocal()) :: q |
577 |
> |
!! Force array provided by C, dimensioned by getNlocal |
578 |
> |
real ( kind = dp ), dimension(3,getNlocal()) :: f |
579 |
|
real ( kind = dp ) :: potE |
580 |
|
logical ( kind = 2) :: do_pot |
581 |
+ |
|
582 |
+ |
type(lj_atype), pointer :: ljAtype_i |
583 |
+ |
type(lj_atype), pointer :: ljAtype_j |
584 |
+ |
|
585 |
|
#ifdef MPI |
586 |
< |
real( kind = DP ), dimension(3,ncol) :: efr |
586 |
> |
real( kind = DP ), dimension(3,getNcol()) :: efr |
587 |
|
real( kind = DP ) :: pot_local |
588 |
|
#else |
589 |
< |
! real( kind = DP ), dimension(3,natoms) :: efr |
589 |
> |
real( kind = DP ), dimension(3,getNlocal()) :: efr |
590 |
|
#endif |
591 |
|
|
592 |
|
real( kind = DP ) :: pe |
593 |
< |
logical, :: update_nlist |
593 |
> |
logical :: update_nlist |
594 |
|
|
595 |
|
|
596 |
|
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
599 |
|
integer :: tag_i,tag_j |
600 |
|
real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
601 |
|
real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
602 |
+ |
real( kind = DP ) :: rlistsq, rcutsq,rlist,rcut |
603 |
|
|
604 |
+ |
! a rig that need to be fixed. |
605 |
+ |
#ifdef IS_MPI |
606 |
+ |
logical :: newtons_thrd = .true. |
607 |
+ |
real( kind = dp ) :: pe_local |
608 |
+ |
integer :: nlocal |
609 |
+ |
#endif |
610 |
|
integer :: nrow |
611 |
|
integer :: ncol |
612 |
+ |
integer :: natoms |
613 |
|
|
614 |
+ |
! Make sure we are properly initialized. |
615 |
+ |
if (.not. isljFFInit) then |
616 |
+ |
write(default_error,*) "ERROR: lj_FF has not been properly initialized" |
617 |
+ |
return |
618 |
+ |
endif |
619 |
+ |
#ifdef IS_MPI |
620 |
+ |
if (.not. isMPISimSet()) then |
621 |
+ |
write(default_error,*) "ERROR: mpiSimulation has not been properly initialized" |
622 |
+ |
return |
623 |
+ |
endif |
624 |
+ |
#endif |
625 |
|
|
626 |
< |
|
626 |
> |
!! initialize local variables |
627 |
> |
natoms = getNlocal() |
628 |
> |
call getRcut(rcut,rcut2=rcutsq) |
629 |
> |
call getRlist(rlist,rlistsq) |
630 |
|
#ifndef IS_MPI |
631 |
|
nrow = natoms - 1 |
632 |
|
ncol = natoms |
633 |
|
#else |
634 |
+ |
nrow = getNrow(plan_row) |
635 |
+ |
ncol = getNcol(plan_col) |
636 |
+ |
nlocal = natoms |
637 |
|
j_start = 1 |
638 |
|
#endif |
639 |
|
|
640 |
< |
call check(update_nlist) |
640 |
> |
|
641 |
> |
!! See if we need to update neighbor lists |
642 |
> |
call check(q,update_nlist) |
643 |
|
|
644 |
+ |
!--------------WARNING........................... |
645 |
+ |
! Zero variables, NOTE:::: Forces are zeroed in C |
646 |
+ |
! Zeroing them here could delete previously computed |
647 |
+ |
! Forces. |
648 |
+ |
!------------------------------------------------ |
649 |
|
#ifndef IS_MPI |
650 |
< |
nloops = nloops + 1 |
651 |
< |
pot = 0.0E0_DP |
652 |
< |
f = 0.0E0_DP |
332 |
< |
e = 0.0E0_DP |
650 |
> |
! nloops = nloops + 1 |
651 |
> |
pe = 0.0E0_DP |
652 |
> |
|
653 |
|
#else |
654 |
|
f_row = 0.0E0_DP |
655 |
|
f_col = 0.0E0_DP |
656 |
|
|
657 |
< |
pot_local = 0.0E0_DP |
657 |
> |
pe_local = 0.0E0_DP |
658 |
|
|
659 |
< |
e_row = 0.0E0_DP |
660 |
< |
e_col = 0.0E0_DP |
661 |
< |
e_tmp = 0.0E0_DP |
659 |
> |
eRow = 0.0E0_DP |
660 |
> |
eCol = 0.0E0_DP |
661 |
> |
eTemp = 0.0E0_DP |
662 |
|
#endif |
663 |
|
efr = 0.0E0_DP |
664 |
|
|
665 |
|
! communicate MPI positions |
666 |
|
#ifdef MPI |
667 |
< |
call gather(q,q_row,plan_row3) |
668 |
< |
call gather(q,q_col,plan_col3) |
667 |
> |
call gather(q,qRow,plan_row3) |
668 |
> |
call gather(q,qCol,plan_col3) |
669 |
|
#endif |
670 |
|
|
351 |
– |
#ifndef MPI |
671 |
|
|
353 |
– |
#endif |
354 |
– |
|
672 |
|
if (update_nlist) then |
673 |
|
|
674 |
|
! save current configuration, contruct neighbor list, |
675 |
|
! and calculate forces |
676 |
< |
call save_nlist() |
676 |
> |
call save_nlist(q) |
677 |
|
|
678 |
|
nlist = 0 |
679 |
|
|
682 |
|
do i = 1, nrow |
683 |
|
point(i) = nlist + 1 |
684 |
|
#ifdef MPI |
685 |
< |
tag_i = tag_row(i) |
686 |
< |
rxi = q_row(1,i) |
687 |
< |
ryi = q_row(2,i) |
688 |
< |
rzi = q_row(3,i) |
685 |
> |
ljAtype_i => identPtrListRow(i)%this |
686 |
> |
tag_i = tagRow(i) |
687 |
> |
rxi = qRow(1,i) |
688 |
> |
ryi = qRow(2,i) |
689 |
> |
rzi = qRow(3,i) |
690 |
|
#else |
691 |
+ |
ljAtype_i => identPtrList(i)%this |
692 |
|
j_start = i + 1 |
693 |
|
rxi = q(1,i) |
694 |
|
ryi = q(2,i) |
697 |
|
|
698 |
|
inner: do j = j_start, ncol |
699 |
|
#ifdef MPI |
700 |
< |
tag_j = tag_col(j) |
700 |
> |
! Assign identity pointers and tags |
701 |
> |
ljAtype_j => identPtrListColumn(j)%this |
702 |
> |
tag_j = tagCol(j) |
703 |
|
if (newtons_thrd) then |
704 |
|
if (tag_i <= tag_j) then |
705 |
|
if (mod(tag_i + tag_j,2) == 0) cycle inner |
708 |
|
endif |
709 |
|
endif |
710 |
|
|
711 |
< |
rxij = wrap(rxi - q_col(1,j), 1) |
712 |
< |
ryij = wrap(ryi - q_col(2,j), 2) |
713 |
< |
rzij = wrap(rzi - q_col(3,j), 3) |
711 |
> |
rxij = wrap(rxi - qCol(1,j), 1) |
712 |
> |
ryij = wrap(ryi - qCol(2,j), 2) |
713 |
> |
rzij = wrap(rzi - qCol(3,j), 3) |
714 |
|
#else |
715 |
< |
|
715 |
> |
ljAtype_j => identPtrList(j)%this |
716 |
|
rxij = wrap(rxi - q(1,j), 1) |
717 |
|
ryij = wrap(ryi - q(2,j), 2) |
718 |
|
rzij = wrap(rzi - q(3,j), 3) |
721 |
|
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
722 |
|
|
723 |
|
#ifdef MPI |
724 |
< |
if (rijsq <= rlstsq .AND. & |
724 |
> |
if (rijsq <= rlistsq .AND. & |
725 |
|
tag_j /= tag_i) then |
726 |
|
#else |
727 |
< |
if (rijsq < rlstsq) then |
727 |
> |
if (rijsq < rlistsq) then |
728 |
|
#endif |
729 |
|
|
730 |
|
nlist = nlist + 1 |
731 |
|
if (nlist > size(list)) then |
732 |
< |
call info("FORCE_LJ","error size list smaller then nlist") |
733 |
< |
write(msg,*) "nlist size(list)", nlist, size(list) |
413 |
< |
call info("FORCE_LJ",msg) |
414 |
< |
#ifdef MPI |
415 |
< |
call mpi_abort(MPI_COMM_WORLD,mpi_err) |
416 |
< |
#endif |
417 |
< |
stop |
732 |
> |
!! "Change how nlist size is done" |
733 |
> |
write(DEFAULT_ERROR,*) "ERROR: nlist > list size" |
734 |
|
endif |
735 |
|
list(nlist) = j |
736 |
|
|
739 |
|
|
740 |
|
r = dsqrt(rijsq) |
741 |
|
|
742 |
< |
call LJ_mix(r,pot,dudr,d2,i,j) |
742 |
> |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
743 |
|
|
744 |
|
#ifdef MPI |
745 |
< |
e_row(i) = e_row(i) + pot*0.5 |
746 |
< |
e_col(i) = e_col(i) + pot*0.5 |
745 |
> |
eRow(i) = eRow(i) + pot*0.5 |
746 |
> |
eCol(i) = eCol(i) + pot*0.5 |
747 |
|
#else |
748 |
|
pe = pe + pot |
749 |
|
#endif |
760 |
|
|
761 |
|
|
762 |
|
#ifdef MPI |
763 |
< |
f_col(dim,j) = f_col(dim,j) - ftmp |
764 |
< |
f_row(dim,i) = f_row(dim,i) + ftmp |
763 |
> |
fCol(dim,j) = fCol(dim,j) - ftmp |
764 |
> |
fRow(dim,i) = fRow(dim,i) + ftmp |
765 |
|
#else |
766 |
|
|
767 |
|
f(dim,j) = f(dim,j) - ftmp |
789 |
|
! check thiat molecule i has neighbors |
790 |
|
if (jbeg .le. jend) then |
791 |
|
#ifdef MPI |
792 |
< |
rxi = q_row(1,i) |
793 |
< |
ryi = q_row(2,i) |
794 |
< |
rzi = q_row(3,i) |
792 |
> |
ljAtype_i => identPtrListRow(i)%this |
793 |
> |
rxi = qRow(1,i) |
794 |
> |
ryi = qRow(2,i) |
795 |
> |
rzi = qRow(3,i) |
796 |
|
#else |
797 |
+ |
ljAtype_i => identPtrList(i)%this |
798 |
|
rxi = q(1,i) |
799 |
|
ryi = q(2,i) |
800 |
|
rzi = q(3,i) |
802 |
|
do jnab = jbeg, jend |
803 |
|
j = list(jnab) |
804 |
|
#ifdef MPI |
805 |
< |
rxij = wrap(rxi - q_col(1,j), 1) |
806 |
< |
ryij = wrap(ryi - q_col(2,j), 2) |
807 |
< |
rzij = wrap(rzi - q_col(3,j), 3) |
805 |
> |
ljAtype_j = identPtrListColumn(j)%this |
806 |
> |
rxij = wrap(rxi - q_col(1,j), 1) |
807 |
> |
ryij = wrap(ryi - q_col(2,j), 2) |
808 |
> |
rzij = wrap(rzi - q_col(3,j), 3) |
809 |
|
#else |
810 |
< |
rxij = wrap(rxi - q(1,j), 1) |
811 |
< |
ryij = wrap(ryi - q(2,j), 2) |
812 |
< |
rzij = wrap(rzi - q(3,j), 3) |
810 |
> |
ljAtype_j = identPtrList(j)%this |
811 |
> |
rxij = wrap(rxi - q(1,j), 1) |
812 |
> |
ryij = wrap(ryi - q(2,j), 2) |
813 |
> |
rzij = wrap(rzi - q(3,j), 3) |
814 |
|
#endif |
815 |
|
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
816 |
|
|
818 |
|
|
819 |
|
r = dsqrt(rijsq) |
820 |
|
|
821 |
< |
call LJ_mix(r,pot,dudr,d2,i,j) |
821 |
> |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
822 |
|
#ifdef MPI |
823 |
< |
e_row(i) = e_row(i) + pot*0.5 |
824 |
< |
e_col(i) = e_col(i) + pot*0.5 |
823 |
> |
eRow(i) = eRow(i) + pot*0.5 |
824 |
> |
eCol(i) = eCol(i) + pot*0.5 |
825 |
|
#else |
826 |
< |
if (do_pot) pe = pe + pot |
826 |
> |
pe = pe + pot |
827 |
|
#endif |
828 |
|
|
829 |
|
|
836 |
|
drdx1 = efr(dim,j) / r |
837 |
|
ftmp = dudr * drdx1 |
838 |
|
#ifdef MPI |
839 |
< |
f_col(dim,j) = f_col(dim,j) - ftmp |
840 |
< |
f_row(dim,i) = f_row(dim,i) + ftmp |
839 |
> |
fCol(dim,j) = fCol(dim,j) - ftmp |
840 |
> |
fRow(dim,i) = fRow(dim,i) + ftmp |
841 |
|
#else |
842 |
|
f(dim,j) = f(dim,j) - ftmp |
843 |
|
f(dim,i) = f(dim,i) + ftmp |
853 |
|
|
854 |
|
#ifdef MPI |
855 |
|
!!distribute forces |
856 |
< |
call scatter(f_row,f,plan_row3) |
856 |
> |
call scatter(fRow,f,plan_row3) |
857 |
|
|
858 |
< |
call scatter(f_col,f_tmp,plan_col3) |
858 |
> |
call scatter(fCol,f_tmp,plan_col3) |
859 |
> |
|
860 |
|
do i = 1,nlocal |
861 |
< |
do dim = 1,3 |
541 |
< |
f(dim,i) = f(dim,i) + f_tmp(dim,i) |
542 |
< |
end do |
861 |
> |
f(1:3,i) = f(1:3,i) + f_tmp(1:3,i) |
862 |
|
end do |
863 |
|
|
864 |
|
|
870 |
|
! scatter/gather pot_local into all other procs |
871 |
|
! add resultant to get total pot |
872 |
|
do i = 1, nlocal |
873 |
< |
pot_local = pot_local + e_tmp(i) |
873 |
> |
pe_local = pe_local + e_tmp(i) |
874 |
|
enddo |
875 |
|
if (newtons_thrd) then |
876 |
|
e_tmp = 0.0E0_DP |
877 |
|
call scatter(e_col,e_tmp,plan_col) |
878 |
|
do i = 1, nlocal |
879 |
< |
pot_local = pot_local + e_tmp(i) |
879 |
> |
pe_local = pe_local + e_tmp(i) |
880 |
|
enddo |
881 |
|
endif |
882 |
|
endif |
883 |
+ |
potE = pe_local |
884 |
|
#endif |
885 |
|
|
886 |
+ |
potE = pe |
887 |
|
|
888 |
|
|
568 |
– |
|
889 |
|
end subroutine do_lj_ff |
890 |
|
|
891 |
< |
!! Calculates the potential between two lj particles, optionally returns second |
891 |
> |
!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second |
892 |
|
!! derivatives. |
893 |
|
subroutine getLjPot(r,pot,dudr,atype1,atype2,d2,status) |
894 |
|
! arguments |
901 |
|
!! Second Derivative, optional, used mainly for normal mode calculations. |
902 |
|
real( kind = dp ), intent(out), optional :: d2 |
903 |
|
|
904 |
< |
type (lj_atype), intent(in) :: atype1 |
905 |
< |
type (lj_atype), intent(in) :: atype2 |
904 |
> |
type (lj_atype), pointer :: atype1 |
905 |
> |
type (lj_atype), pointer :: atype2 |
906 |
|
|
907 |
|
integer, intent(out), optional :: status |
908 |
|
|
910 |
|
real( kind = dp ) :: sigma |
911 |
|
real( kind = dp ) :: sigma2 |
912 |
|
real( kind = dp ) :: sigma6 |
913 |
< |
real( kind = dp ) :: epslon |
913 |
> |
real( kind = dp ) :: epsilon |
914 |
|
|
915 |
|
real( kind = dp ) :: rcut |
916 |
|
real( kind = dp ) :: rcut2 |
935 |
|
if (present(status)) status = 0 |
936 |
|
|
937 |
|
! Look up the correct parameters in the mixing matrix |
938 |
< |
sigma = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma |
939 |
< |
sigma2 = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma2 |
940 |
< |
sigma6 = ljMixed(atype1%atype_ident,atype2_atype_ident)%sigma6 |
941 |
< |
epslon = ljMixed(atype1%atype_ident,atype2_atype_ident)%epslon |
938 |
> |
sigma = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma |
939 |
> |
sigma2 = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma2 |
940 |
> |
sigma6 = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma6 |
941 |
> |
epsilon = ljMixed(atype1%atype_ident,atype2%atype_ident)%epsilon |
942 |
|
|
943 |
|
|
944 |
|
|
958 |
|
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
959 |
|
|
960 |
|
if (r.le.rcut) then |
961 |
< |
u = 4.0E0_DP * epsilon * (t12 - t6) + delta |
961 |
> |
pot = 4.0E0_DP * epsilon * (t12 - t6) + delta |
962 |
|
dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r |
963 |
|
if(doSec) d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r |
964 |
|
else |
965 |
< |
u = 0.0E0_DP |
965 |
> |
pot = 0.0E0_DP |
966 |
|
dudr = 0.0E0_DP |
967 |
|
if(doSec) d2 = 0.0E0_DP |
968 |
|
endif |
974 |
|
end subroutine getLjPot |
975 |
|
|
976 |
|
|
977 |
< |
!! Calculates the mixing for sigma or epslon based on character string |
977 |
> |
!! Calculates the mixing for sigma or epslon based on character string for initialzition of mixing array. |
978 |
|
function calcLJMix(thisParam,param1,param2,status) result(myMixParam) |
979 |
|
character(len=*) :: thisParam |
980 |
|
real(kind = dp) :: param1 |
991 |
|
|
992 |
|
case ("sigma") |
993 |
|
myMixParam = 0.5_dp * (param1 + param2) |
994 |
< |
case ("epslon") |
994 |
> |
case ("epsilon") |
995 |
|
myMixParam = sqrt(param1 * param2) |
996 |
|
case default |
997 |
|
status = -1 |