| 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 |
< |
!! @version $Id: lj_FF.F90,v 1.9 2003-01-22 21:45:20 chuckv Exp $, $Date: 2003-01-22 21:45:20 $, $Name: not supported by cvs2svn $, $Revision: 1.9 $ |
| 5 |
> |
!! @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 $ |
| 6 |
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| 8 |
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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 |
| 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() |
| 57 |
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|
| 58 |
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|
| 59 |
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!! Neighbor list and commom arrays |
| 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 |
+ |
!! Row position array. |
| 71 |
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real( kind = dp ), allocatable, dimension(:,:) :: qRow |
| 72 |
+ |
!! Column position array. |
| 73 |
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real( kind = dp ), allocatable, dimension(:,:) :: qColumn |
| 74 |
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|
| 75 |
+ |
!! Row Force array. |
| 76 |
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real( kind = dp ), allocatable, dimension(:,:) :: fRow |
| 77 |
+ |
!! Column Force Array. |
| 78 |
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real( kind = dp ), allocatable, dimension(:,:) :: fColumn |
| 79 |
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|
| 80 |
< |
type (lj_atypePtr), dimension(:), allocatable :: identPtrListRow |
| 81 |
< |
type (lj_atypePtr), dimension(:), allocatable :: identPtrListColumn |
| 82 |
< |
#endif |
| 80 |
> |
!! Row potential energy array |
| 81 |
> |
real( kind = dp ), allocatable, dimension(:) :: eRow |
| 82 |
> |
!! Column potential energy array |
| 83 |
> |
real( kind = dp ), allocatable, dimension(:) :: eColumn |
| 84 |
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|
| 85 |
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|
| 86 |
+ |
!! Row lj_atype pointer list |
| 87 |
+ |
type (lj_atypePtr), dimension(:), pointer :: identPtrListRow => null() |
| 88 |
+ |
!! Column lj_atype pointer list |
| 89 |
+ |
type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null() |
| 90 |
+ |
#endif |
| 91 |
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|
| 82 |
– |
logical :: isljFFinit = .false. |
| 92 |
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|
| 93 |
+ |
!! Logical has lj force field module been initialized? |
| 94 |
+ |
logical, save :: isljFFinit = .false. |
| 95 |
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| 96 |
+ |
|
| 97 |
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!! Public methods and data |
| 98 |
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public :: new_lj_atype |
| 99 |
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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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contains |
| 107 |
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| 108 |
< |
subroutine new_lj_atype(ident,mass,epslon,sigma,status) |
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> |
subroutine new_lj_atype(ident,mass,epsilon,sigma,status) |
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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 |
| 116 |
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type (lj_atype), pointer :: lj_atype_ptr |
| 117 |
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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 |
| 134 |
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|
| 135 |
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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 |
| 169 |
– |
lj_atype_ptr => this_lj_atype |
| 170 |
– |
atype_counter = 1 |
| 181 |
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|
| 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 |
< |
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 |
|
calcLJMix("sigma",this_lj_atype%sigma, & |
| 213 |
< |
lj_atype_prt%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 |
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|
| 219 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 = & |
| 220 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma & |
| 221 |
< |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma |
| 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)%sigma6 = & |
| 225 |
< |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
| 226 |
< |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 & |
| 191 |
< |
* ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 |
| 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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|
| 193 |
– |
ljMix(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epslon = & |
| 194 |
– |
calcLJMix("epslon",this_lj_atype%epslon, & |
| 195 |
– |
lj_atype_prt%epslon) |
| 196 |
– |
|
| 228 |
|
! Advance to next pointer |
| 229 |
< |
lj_atype_ptr => lj_atype_ptr%next |
| 230 |
< |
atype_counter = atype_counter + 1 |
| 200 |
< |
|
| 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 |
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|
| 237 |
< |
|
| 205 |
< |
|
| 237 |
> |
write(*,*) "lj_atype_list now contains.." |
| 238 |
|
|
| 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 |
< |
lj_atype_ptr => this_lj_atype |
| 246 |
> |
|
| 247 |
|
! Increment number of atypes |
| 248 |
|
|
| 249 |
|
n_lj_atypes = n_lj_atypes + 1 |
| 250 |
|
|
| 251 |
|
! Set up self mixing |
| 252 |
|
|
| 215 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma = this_lj_atype%sigma |
| 216 |
– |
|
| 217 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma2 = ljMix(n_lj_atypes,n_lj_atypes)%sigma & |
| 218 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma |
| 219 |
– |
|
| 220 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%sigma6 = ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
| 221 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 & |
| 222 |
– |
* ljMix(n_lj_atypes,n_lj_atypes)%sigma2 |
| 223 |
– |
|
| 224 |
– |
ljMix(n_lj_atypes,n_lj_atypes)%epslon = this_lj_atype%epslon |
| 225 |
– |
|
| 226 |
– |
|
| 253 |
|
end subroutine new_lj_atype |
| 254 |
|
|
| 255 |
|
|
| 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 |
| 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) |
| 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 |
| 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) |
| 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 |
|
|
| 408 |
– |
|
| 490 |
|
end subroutine init_ljFF |
| 491 |
|
|
| 492 |
|
|
| 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() |
| 459 |
< |
|
| 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 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 |
|
|
| 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 |
| 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 |
|
|
| 528 |
– |
call check(update_nlist) |
| 529 |
– |
|
| 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 |
< |
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 |
|
|
| 668 |
|
call gather(q,qCol,plan_col3) |
| 669 |
|
#endif |
| 670 |
|
|
| 557 |
– |
#ifndef MPI |
| 671 |
|
|
| 559 |
– |
#endif |
| 560 |
– |
|
| 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 |
|
|
| 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 |
< |
#warning "Change how nlist size is done" |
| 732 |
> |
!! "Change how nlist size is done" |
| 733 |
|
write(DEFAULT_ERROR,*) "ERROR: nlist > list size" |
| 734 |
|
endif |
| 735 |
|
list(nlist) = 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 |
| 820 |
|
|
| 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 |
|
|
| 856 |
|
call scatter(fRow,f,plan_row3) |
| 857 |
|
|
| 858 |
|
call scatter(fCol,f_tmp,plan_col3) |
| 859 |
+ |
|
| 860 |
|
do i = 1,nlocal |
| 861 |
< |
do dim = 1,3 |
| 750 |
< |
f(dim,i) = f(dim,i) + f_tmp(dim,i) |
| 751 |
< |
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 |
|
|
| 777 |
– |
|
| 889 |
|
end subroutine do_lj_ff |
| 890 |
|
|
| 891 |
|
!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second |
| 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), pointer :: atype1 |
| 905 |
< |
type (lj_atype), intent(in), pointer :: 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 |
| 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 |
