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 |
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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 |
> |
#ifdef IS_MPI |
13 |
> |
use mpiSimulation |
14 |
> |
#endif |
15 |
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implicit none |
16 |
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PRIVATE |
17 |
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|
18 |
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!! Number of lj_atypes in lj_atype_list |
19 |
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integer, save :: n_lj_atypes = 0 |
20 |
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|
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 |
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!! Basic atom type for a Lennard-Jones Atom. |
25 |
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type, public :: lj_atype |
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private |
27 |
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sequence |
28 |
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!! Unique number for place in linked list |
29 |
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integer :: atype_number = 0 |
30 |
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!! Unique indentifier number (ie atomic no, etc) |
31 |
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integer :: atype_ident = 0 |
32 |
< |
character(len = 15) :: name = "NULL" |
32 |
> |
!! Mass of Particle |
33 |
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real ( kind = dp ) :: mass = 0.0_dp |
34 |
< |
real ( kind = dp ) :: epslon = 0.0_dp |
34 |
> |
!! Lennard-Jones epslon |
35 |
> |
real ( kind = dp ) :: epsilon = 0.0_dp |
36 |
> |
!! Lennard-Jones Sigma |
37 |
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real ( kind = dp ) :: sigma = 0.0_dp |
38 |
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!! Lennard-Jones Sigma Squared |
39 |
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real ( kind = dp ) :: sigma2 = 0.0_dp |
40 |
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!! Lennard-Jones Sigma to sixth |
41 |
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real ( kind = dp ) :: sigma6 = 0.0_dp |
42 |
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!! Pointer for linked list creation |
43 |
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type (lj_atype), pointer :: next => null() |
44 |
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end type lj_atype |
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|
46 |
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!! Pointer type for atype ident array |
47 |
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type, public :: lj_atypePtr |
48 |
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type (lj_atype), pointer :: this => null() |
49 |
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end type lj_atypePtr |
50 |
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|
51 |
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!! Global list of lj atypes in simulation |
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type (lj_atype), pointer :: lj_atype_list => null() |
53 |
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!! LJ mixing array |
54 |
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type (lj_atype), dimension(:,:), pointer :: ljMixed => null() |
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!! identity pointer list for force loop. |
56 |
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type (lj_atypePtr), dimension(:), pointer :: identPtrList => null() |
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|
58 |
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|
59 |
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!! Neighbor list and commom arrays |
60 |
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!! This should eventally get moved to a neighbor list type |
61 |
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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 |
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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. |
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real( kind = dp ), allocatable, dimension(:,:) :: qRow |
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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. |
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real( kind = dp ), allocatable, dimension(:,:) :: fRow |
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!! Column Force Array. |
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real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
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|
80 |
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!! Row potential energy array |
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real( kind = dp ), allocatable, dimension(:) :: eRow |
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!! Column potential energy array |
83 |
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real( kind = dp ), allocatable, dimension(:) :: eColumn |
84 |
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|
85 |
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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 |
89 |
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type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null() |
90 |
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#endif |
91 |
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|
92 |
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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. |
95 |
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|
96 |
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|
97 |
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!! Public methods and data |
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public :: new_lj_atype |
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public :: do_lj_ff |
100 |
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public :: getLjPot |
101 |
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public :: init_ljFF |
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|
103 |
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|
104 |
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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(name,mass,epslon,sigma,status) |
26 |
< |
character( len = 15 ) :: name |
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 |
111 |
< |
real( kind = dp ), intent(in) :: sigam |
110 |
> |
real( kind = dp ), intent(in) :: epsilon |
111 |
> |
real( kind = dp ), intent(in) :: sigma |
112 |
> |
integer, intent(in) :: ident |
113 |
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integer, intent(out) :: status |
114 |
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|
115 |
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type (lj_atype), pointer :: this_lj_atype |
116 |
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type (lj_atype), pointer :: lj_atype_ptr |
117 |
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|
118 |
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type (lj_atype), dimension(:,:), pointer :: thisMix |
119 |
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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 |
123 |
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|
124 |
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status = 0 |
125 |
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|
126 |
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|
127 |
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|
128 |
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! allocate a new atype |
129 |
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allocate(this_lj_atype,stat=alloc_error) |
130 |
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if (alloc_error /= 0 ) then |
131 |
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status = -1 |
133 |
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end if |
134 |
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|
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! assign our new lj_atype information |
136 |
< |
this_lj_atype%name = name |
137 |
< |
this_lj_atype%mass = mass |
138 |
< |
this_lj_atype%epslon = epslon |
139 |
< |
this_lj_atype%sigma = sigma |
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 |
> |
* this_lj_atype%sigma2 |
142 |
> |
! assume that this atype will be successfully added |
143 |
> |
this_lj_atype%atype_ident = ident |
144 |
> |
this_lj_atype%atype_number = n_lj_atypes + 1 |
145 |
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|
146 |
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|
147 |
+ |
! First time through allocate a array of size ljMixed_blocksize |
148 |
+ |
if(.not. associated(ljMixed)) then |
149 |
+ |
allocate(thisMix(ljMixed_blocksize,ljMixed_blocksize)) |
150 |
+ |
if (alloc_error /= 0 ) then |
151 |
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status = -1 |
152 |
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return |
153 |
+ |
end if |
154 |
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ljMixed => thisMix |
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 |
+ |
else if( (n_lj_atypes + 1) > size(ljMixed)) then |
158 |
+ |
alloc_size = 2*size(ljMixed) |
159 |
+ |
allocate(thisMix(alloc_size,alloc_size)) |
160 |
+ |
if (alloc_error /= 0 ) then |
161 |
+ |
status = -1 |
162 |
+ |
return |
163 |
+ |
end if |
164 |
+ |
! point oldMix at old ljMixed array |
165 |
+ |
oldMix => ljMixed |
166 |
+ |
! Copy oldMix into new Mixed array |
167 |
+ |
thisMix = oldMix |
168 |
+ |
! Point ljMixed at new array |
169 |
+ |
ljMixed => thisMix |
170 |
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! Free old array so we don't have a memory leak |
171 |
+ |
deallocate(oldMix) |
172 |
+ |
endif |
173 |
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|
174 |
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|
175 |
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|
176 |
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|
177 |
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|
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 |
181 |
< |
lj_atype_ptr => this_lj_atype |
181 |
> |
|
182 |
> |
write(*,*) "Associating lists for first time" |
183 |
> |
|
184 |
> |
|
185 |
> |
this_lj_atype%atype_number = 1 |
186 |
> |
|
187 |
> |
ljMixed(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
188 |
> |
|
189 |
> |
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 |
> |
else ! we need to find the bottom of the list to insert new atype |
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 |
57 |
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else ! we need to find the bottom of the list |
58 |
– |
lj_atype_ptr => lj_atype_list%next |
206 |
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find_end: do |
207 |
< |
if (.not. associated(lj_atype_ptr%next)) then |
208 |
< |
exit find_end |
209 |
< |
end if |
210 |
< |
lj_atype_ptr => lj_atype_ptr%next |
207 |
> |
if (.not. associated(lj_atype_ptr)) exit find_end |
208 |
> |
|
209 |
> |
write(*,*) "Inside find_end-this ident", lj_atype_ptr%atype_ident |
210 |
> |
! Set up mixing for new atype and current atype in list |
211 |
> |
ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma = & |
212 |
> |
calcLJMix("sigma",this_lj_atype%sigma, & |
213 |
> |
lj_atype_ptr%sigma) |
214 |
> |
|
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 |
> |
|
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 |
> |
|
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 |
> |
|
228 |
> |
! Advance to next pointer |
229 |
> |
lj_atype_ptr => lj_atype_ptr%next |
230 |
> |
atype_counter = atype_counter + 1 |
231 |
|
end do find_end |
232 |
+ |
|
233 |
+ |
lj_atype_ptr => this_lj_atype |
234 |
+ |
write(*,*) "just added: ", lj_atype_ptr%atype_ident |
235 |
|
end if |
236 |
+ |
|
237 |
+ |
write(*,*) "lj_atype_list now contains.." |
238 |
|
|
239 |
< |
lj_atype_ptr => this_lj_atype |
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 |
+ |
! Insert new atype at end of list |
246 |
+ |
|
247 |
+ |
! Increment number of atypes |
248 |
+ |
|
249 |
+ |
n_lj_atypes = n_lj_atypes + 1 |
250 |
+ |
|
251 |
+ |
! Set up self mixing |
252 |
+ |
|
253 |
|
end subroutine new_lj_atype |
254 |
|
|
71 |
– |
subroutine add_lj_atype() |
255 |
|
|
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 |
< |
end subroutine add_lj_atype |
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 |
< |
subroutine do_lj_ff(q,f,potE) |
295 |
< |
real ( kind = dp ), dimension(ndim,) :: q |
296 |
< |
real ( kind = dp ), dimension(ndim,nLRparticles) :: f |
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,dimension(:), intent(in) :: ident |
501 |
> |
integer, optional :: status |
502 |
> |
type(lj_atypePtr), dimension(:), pointer :: PtrList |
503 |
> |
|
504 |
> |
integer :: thisIdent |
505 |
> |
integer :: i |
506 |
> |
integer :: alloc_error |
507 |
> |
type (lj_atype), pointer :: tmpPtr |
508 |
> |
|
509 |
> |
if (present(status)) status = 0 |
510 |
> |
|
511 |
> |
write(*,*) "Creating new ljatypePtrList...." |
512 |
> |
! First time through, allocate list |
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(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 |
534 |
> |
|
535 |
> |
PtrList(i)%this => tmpPtr |
536 |
> |
end do |
537 |
> |
|
538 |
> |
end subroutine new_ljatypePtrList |
539 |
> |
|
540 |
> |
!! Finds a lj_atype based upon numerical ident |
541 |
> |
!! returns a null pointer if error |
542 |
> |
subroutine getLJatype(ident,ljAtypePtr) |
543 |
> |
integer, intent(in) :: ident |
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( 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 Calculates Lennard Jones forces. |
573 |
> |
!-------------------------------------------------------------> |
574 |
> |
subroutine do_lj_ff(q,f,potE,do_pot) |
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,getNcol()) :: efr |
587 |
+ |
real( kind = DP ) :: pot_local |
588 |
+ |
#else |
589 |
+ |
real( kind = DP ), dimension(3,getNlocal()) :: efr |
590 |
+ |
#endif |
591 |
+ |
|
592 |
+ |
real( kind = DP ) :: pe |
593 |
+ |
logical :: update_nlist |
594 |
|
|
595 |
|
|
596 |
+ |
integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
597 |
+ |
integer :: nlist |
598 |
+ |
integer :: j_start |
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 |
+ |
!! 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 |
+ |
|
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 |
+ |
pe = 0.0E0_DP |
652 |
+ |
|
653 |
+ |
#else |
654 |
+ |
f_row = 0.0E0_DP |
655 |
+ |
f_col = 0.0E0_DP |
656 |
+ |
|
657 |
+ |
pe_local = 0.0E0_DP |
658 |
+ |
|
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,qRow,plan_row3) |
668 |
+ |
call gather(q,qCol,plan_col3) |
669 |
+ |
#endif |
670 |
+ |
|
671 |
+ |
|
672 |
+ |
if (update_nlist) then |
673 |
+ |
|
674 |
+ |
! save current configuration, contruct neighbor list, |
675 |
+ |
! and calculate forces |
676 |
+ |
call save_nlist(q) |
677 |
+ |
|
678 |
+ |
nlist = 0 |
679 |
+ |
|
680 |
+ |
|
681 |
+ |
|
682 |
+ |
do i = 1, nrow |
683 |
+ |
point(i) = nlist + 1 |
684 |
+ |
#ifdef MPI |
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) |
695 |
+ |
rzi = q(3,i) |
696 |
+ |
#endif |
697 |
+ |
|
698 |
+ |
inner: do j = j_start, ncol |
699 |
+ |
#ifdef MPI |
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 |
706 |
+ |
else |
707 |
+ |
if (mod(tag_i + tag_j,2) == 1) cycle inner |
708 |
+ |
endif |
709 |
+ |
endif |
710 |
+ |
|
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 |
+ |
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) |
719 |
+ |
|
720 |
+ |
#endif |
721 |
+ |
rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
722 |
+ |
|
723 |
+ |
#ifdef MPI |
724 |
+ |
if (rijsq <= rlistsq .AND. & |
725 |
+ |
tag_j /= tag_i) then |
726 |
+ |
#else |
727 |
+ |
if (rijsq < rlistsq) then |
728 |
+ |
#endif |
729 |
+ |
|
730 |
+ |
nlist = nlist + 1 |
731 |
+ |
if (nlist > size(list)) then |
732 |
+ |
!! "Change how nlist size is done" |
733 |
+ |
write(DEFAULT_ERROR,*) "ERROR: nlist > list size" |
734 |
+ |
endif |
735 |
+ |
list(nlist) = j |
736 |
+ |
|
737 |
+ |
|
738 |
+ |
if (rijsq < rcutsq) then |
739 |
+ |
|
740 |
+ |
r = dsqrt(rijsq) |
741 |
+ |
|
742 |
+ |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
743 |
+ |
|
744 |
+ |
#ifdef MPI |
745 |
+ |
eRow(i) = eRow(i) + pot*0.5 |
746 |
+ |
eCol(i) = eCol(i) + pot*0.5 |
747 |
+ |
#else |
748 |
+ |
pe = pe + pot |
749 |
+ |
#endif |
750 |
+ |
|
751 |
+ |
efr(1,j) = -rxij |
752 |
+ |
efr(2,j) = -ryij |
753 |
+ |
efr(3,j) = -rzij |
754 |
+ |
|
755 |
+ |
do dim = 1, 3 |
756 |
+ |
|
757 |
+ |
|
758 |
+ |
drdx1 = efr(dim,j) / r |
759 |
+ |
ftmp = dudr * drdx1 |
760 |
+ |
|
761 |
+ |
|
762 |
+ |
#ifdef MPI |
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 |
768 |
+ |
f(dim,i) = f(dim,i) + ftmp |
769 |
+ |
|
770 |
+ |
#endif |
771 |
+ |
enddo |
772 |
+ |
endif |
773 |
+ |
endif |
774 |
+ |
enddo inner |
775 |
+ |
enddo |
776 |
+ |
|
777 |
+ |
#ifdef MPI |
778 |
+ |
point(nrow + 1) = nlist + 1 |
779 |
+ |
#else |
780 |
+ |
point(natoms) = nlist + 1 |
781 |
+ |
#endif |
782 |
+ |
|
783 |
+ |
else |
784 |
+ |
|
785 |
+ |
! use the list to find the neighbors |
786 |
+ |
do i = 1, nrow |
787 |
+ |
JBEG = POINT(i) |
788 |
+ |
JEND = POINT(i+1) - 1 |
789 |
+ |
! check thiat molecule i has neighbors |
790 |
+ |
if (jbeg .le. jend) then |
791 |
+ |
#ifdef MPI |
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) |
801 |
+ |
#endif |
802 |
+ |
do jnab = jbeg, jend |
803 |
+ |
j = list(jnab) |
804 |
+ |
#ifdef MPI |
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 |
+ |
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 |
+ |
|
817 |
+ |
if (rijsq < rcutsq) then |
818 |
+ |
|
819 |
+ |
r = dsqrt(rijsq) |
820 |
+ |
|
821 |
+ |
call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j) |
822 |
+ |
#ifdef MPI |
823 |
+ |
eRow(i) = eRow(i) + pot*0.5 |
824 |
+ |
eCol(i) = eCol(i) + pot*0.5 |
825 |
+ |
#else |
826 |
+ |
pe = pe + pot |
827 |
+ |
#endif |
828 |
+ |
|
829 |
+ |
|
830 |
+ |
efr(1,j) = -rxij |
831 |
+ |
efr(2,j) = -ryij |
832 |
+ |
efr(3,j) = -rzij |
833 |
+ |
|
834 |
+ |
do dim = 1, 3 |
835 |
+ |
|
836 |
+ |
drdx1 = efr(dim,j) / r |
837 |
+ |
ftmp = dudr * drdx1 |
838 |
+ |
#ifdef MPI |
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 |
844 |
+ |
#endif |
845 |
+ |
enddo |
846 |
+ |
endif |
847 |
+ |
enddo |
848 |
+ |
endif |
849 |
+ |
enddo |
850 |
+ |
endif |
851 |
+ |
|
852 |
+ |
|
853 |
+ |
|
854 |
+ |
#ifdef MPI |
855 |
+ |
!!distribute forces |
856 |
+ |
call scatter(fRow,f,plan_row3) |
857 |
+ |
|
858 |
+ |
call scatter(fCol,f_tmp,plan_col3) |
859 |
+ |
|
860 |
+ |
do i = 1,nlocal |
861 |
+ |
f(1:3,i) = f(1:3,i) + f_tmp(1:3,i) |
862 |
+ |
end do |
863 |
+ |
|
864 |
+ |
|
865 |
+ |
|
866 |
+ |
if (do_pot) then |
867 |
+ |
! scatter/gather pot_row into the members of my column |
868 |
+ |
call scatter(e_row,e_tmp,plan_row) |
869 |
+ |
|
870 |
+ |
! scatter/gather pot_local into all other procs |
871 |
+ |
! add resultant to get total pot |
872 |
+ |
do i = 1, nlocal |
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 |
+ |
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 |
+ |
|
889 |
|
end subroutine do_lj_ff |
890 |
|
|
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 |
895 |
+ |
!! Length of vector between particles |
896 |
+ |
real( kind = dp ), intent(in) :: r |
897 |
+ |
!! Potential Energy |
898 |
+ |
real( kind = dp ), intent(out) :: pot |
899 |
+ |
!! Derivatve wrt postion |
900 |
+ |
real( kind = dp ), intent(out) :: dudr |
901 |
+ |
!! Second Derivative, optional, used mainly for normal mode calculations. |
902 |
+ |
real( kind = dp ), intent(out), optional :: d2 |
903 |
+ |
|
904 |
+ |
type (lj_atype), pointer :: atype1 |
905 |
+ |
type (lj_atype), pointer :: atype2 |
906 |
|
|
907 |
+ |
integer, intent(out), optional :: status |
908 |
|
|
909 |
+ |
! local Variables |
910 |
+ |
real( kind = dp ) :: sigma |
911 |
+ |
real( kind = dp ) :: sigma2 |
912 |
+ |
real( kind = dp ) :: sigma6 |
913 |
+ |
real( kind = dp ) :: epsilon |
914 |
+ |
|
915 |
+ |
real( kind = dp ) :: rcut |
916 |
+ |
real( kind = dp ) :: rcut2 |
917 |
+ |
real( kind = dp ) :: rcut6 |
918 |
+ |
real( kind = dp ) :: r2 |
919 |
+ |
real( kind = dp ) :: r6 |
920 |
+ |
|
921 |
+ |
real( kind = dp ) :: t6 |
922 |
+ |
real( kind = dp ) :: t12 |
923 |
+ |
real( kind = dp ) :: tp6 |
924 |
+ |
real( kind = dp ) :: tp12 |
925 |
+ |
real( kind = dp ) :: delta |
926 |
+ |
|
927 |
+ |
logical :: doSec = .false. |
928 |
+ |
|
929 |
+ |
integer :: errorStat |
930 |
+ |
|
931 |
+ |
!! Optional Argument Checking |
932 |
+ |
! Check to see if we need to do second derivatives |
933 |
+ |
|
934 |
+ |
if (present(d2)) doSec = .true. |
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 |
+ |
epsilon = ljMixed(atype1%atype_ident,atype2%atype_ident)%epsilon |
942 |
+ |
|
943 |
+ |
|
944 |
+ |
|
945 |
+ |
call getRcut(rcut,rcut2=rcut2,rcut6=rcut6,status=errorStat) |
946 |
+ |
|
947 |
+ |
r2 = r * r |
948 |
+ |
r6 = r2 * r2 * r2 |
949 |
+ |
|
950 |
+ |
t6 = sigma6/ r6 |
951 |
+ |
t12 = t6 * t6 |
952 |
+ |
|
953 |
+ |
|
954 |
+ |
|
955 |
+ |
tp6 = sigma6 / rcut6 |
956 |
+ |
tp12 = tp6*tp6 |
957 |
+ |
|
958 |
+ |
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
959 |
+ |
|
960 |
+ |
if (r.le.rcut) then |
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 |
+ |
pot = 0.0E0_DP |
966 |
+ |
dudr = 0.0E0_DP |
967 |
+ |
if(doSec) d2 = 0.0E0_DP |
968 |
+ |
endif |
969 |
+ |
|
970 |
+ |
return |
971 |
+ |
|
972 |
+ |
|
973 |
+ |
|
974 |
+ |
end subroutine getLjPot |
975 |
+ |
|
976 |
+ |
|
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 |
981 |
+ |
real(kind = dp) :: param2 |
982 |
+ |
real(kind = dp ) :: myMixParam |
983 |
+ |
integer, optional :: status |
984 |
+ |
|
985 |
+ |
|
986 |
+ |
myMixParam = 0.0_dp |
987 |
+ |
|
988 |
+ |
if (present(status)) status = 0 |
989 |
+ |
|
990 |
+ |
select case (thisParam) |
991 |
+ |
|
992 |
+ |
case ("sigma") |
993 |
+ |
myMixParam = 0.5_dp * (param1 + param2) |
994 |
+ |
case ("epsilon") |
995 |
+ |
myMixParam = sqrt(param1 * param2) |
996 |
+ |
case default |
997 |
+ |
status = -1 |
998 |
+ |
end select |
999 |
+ |
|
1000 |
+ |
end function calcLJMix |
1001 |
+ |
|
1002 |
+ |
|
1003 |
+ |
|
1004 |
|
end module lj_ff |