| 11 |
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|
| 12 |
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type, public :: simtype |
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PRIVATE |
| 14 |
< |
SEQUENCE |
| 14 |
> |
! SEQUENCE |
| 15 |
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!! Number of particles on this processor |
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integer :: nLRparticles |
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!! Periodic Box |
| 38 |
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integer, allocatable, dimension(:) :: tag_column |
| 39 |
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#endif |
| 40 |
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|
| 41 |
< |
|
| 41 |
> |
!! WARNING: use_pbc hardcoded, fixme |
| 42 |
> |
logical :: use_pbc = .true. |
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logical :: setSim = .false. |
| 43 |
– |
|
| 44 |
– |
real( kind = dp ), allocatable(:,:),save :: q0 |
| 44 |
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|
| 45 |
+ |
!! array for saving previous positions for neighbor lists. |
| 46 |
+ |
real( kind = dp ), allocatable,dimension(:,:),save :: q0 |
| 47 |
+ |
|
| 48 |
+ |
|
| 49 |
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public :: check |
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public :: save_nlist |
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public :: wrap |
| 52 |
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public :: getBox |
| 53 |
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public :: getRcut |
| 54 |
< |
public :: setRcut |
| 54 |
> |
public :: getRlist |
| 55 |
> |
public :: getNlocal |
| 56 |
> |
public :: setSimulation |
| 57 |
> |
! public :: setRcut |
| 58 |
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|
| 59 |
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interface wrap |
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module procedure wrap_1d |
| 82 |
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real(kind = dp ), intent(in), dimension(3) :: box |
| 83 |
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real(kind = dp ), intent(in) :: rlist |
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real(kind = dp ), intent(in) :: rcut |
| 85 |
< |
|
| 85 |
> |
integer :: alloc_stat |
| 86 |
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if( setsim ) return ! simulation is already initialized |
| 87 |
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setSim = .true. |
| 88 |
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|
| 89 |
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thisSim%nLRParticles = nLRParticles |
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thisSim%box = box |
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thisSim%rlist = rlist |
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+ |
thisSIm%rlistsq = rlist * rlist |
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thisSim%rcut = rcut |
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thisSim%rcutsq = rcut * rcut |
| 95 |
< |
thisSim%rcut6 = rcutsq * rcutsq * rcutsq |
| 96 |
< |
|
| 95 |
> |
thisSim%rcut6 = thisSim%rcutsq * thisSim%rcutsq * thisSim%rcutsq |
| 96 |
> |
|
| 97 |
> |
if (.not. allocated(q0)) then |
| 98 |
> |
allocate(q0(3,nLRParticles),stat=alloc_stat) |
| 99 |
> |
endif |
| 100 |
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end subroutine setSimulation |
| 101 |
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|
| 102 |
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function getNparticles() result(nparticles) |
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end subroutine change_box_size |
| 114 |
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|
| 115 |
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|
| 116 |
< |
elemental function getBox_3d() result(thisBox) |
| 116 |
> |
function getBox_3d() result(thisBox) |
| 117 |
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real( kind = dp ), dimension(3) :: thisBox |
| 118 |
|
thisBox = thisSim%box |
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end function getBox_3d |
| 125 |
|
thisBox = thisSim%box(dim) |
| 126 |
|
end function getBox_dim |
| 127 |
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|
| 128 |
< |
subroutine check(update_nlist) |
| 129 |
< |
|
| 128 |
> |
subroutine check(q,update_nlist) |
| 129 |
> |
real( kind = dp ), dimension(:,:) :: q |
| 130 |
|
integer :: i |
| 131 |
|
real( kind = DP ) :: dispmx |
| 132 |
|
logical, intent(out) :: update_nlist |
| 133 |
|
real( kind = DP ) :: dispmx_tmp |
| 134 |
< |
|
| 134 |
> |
real( kind = dp ) :: skin_thickness |
| 135 |
> |
integer :: natoms |
| 136 |
> |
|
| 137 |
> |
natoms = thisSim%nLRparticles |
| 138 |
> |
skin_thickness = thisSim%rlist |
| 139 |
|
dispmx = 0.0E0_DP |
| 126 |
– |
|
| 140 |
|
!! calculate the largest displacement of any atom in any direction |
| 141 |
|
|
| 142 |
|
#ifdef MPI |
| 143 |
|
dispmx_tmp = 0.0E0_DP |
| 144 |
< |
do i = 1, nlocal |
| 144 |
> |
do i = 1, thisSim%nLRparticles |
| 145 |
|
dispmx_tmp = max( abs ( q(1,i) - q0(1,i) ), dispmx ) |
| 146 |
|
dispmx_tmp = max( abs ( q(2,i) - q0(2,i) ), dispmx ) |
| 147 |
|
dispmx_tmp = max( abs ( q(3,i) - q0(3,i) ), dispmx ) |
| 149 |
|
call mpi_allreduce(dispmx_tmp,dispmx,1,mpi_double_precision, & |
| 150 |
|
mpi_max,mpi_comm_world,mpi_err) |
| 151 |
|
#else |
| 152 |
< |
do i = 1, natoms |
| 152 |
> |
|
| 153 |
> |
do i = 1, thisSim%nLRparticles |
| 154 |
|
dispmx = max( abs ( q(1,i) - q0(1,i) ), dispmx ) |
| 155 |
|
dispmx = max( abs ( q(2,i) - q0(2,i) ), dispmx ) |
| 156 |
|
dispmx = max( abs ( q(3,i) - q0(3,i) ), dispmx ) |
| 173 |
|
|
| 174 |
|
if (.not. allocated(q0)) then |
| 175 |
|
allocate(q0(3,list_size)) |
| 176 |
< |
else if( list_size > size(q0)) |
| 176 |
> |
else if( list_size > size(q0)) then |
| 177 |
|
deallocate(q0) |
| 178 |
|
allocate(q0(3,list_size)) |
| 179 |
|
endif |
| 200 |
|
return |
| 201 |
|
end function wrap_1d |
| 202 |
|
|
| 203 |
< |
elemental function wrap_3d(r) result(this_wrap) |
| 203 |
> |
function wrap_3d(r) result(this_wrap) |
| 204 |
|
real( kind = dp ), dimension(3), intent(in) :: r |
| 205 |
|
real( kind = dp ), dimension(3) :: this_wrap |
| 206 |
|
|
| 207 |
|
|
| 208 |
|
if (use_pbc) then |
| 209 |
|
! this_wrap = r - box(dim)*dsign(1.0E0_DP,r)*int(abs(r/box(dim)) + 0.5E0_DP) |
| 210 |
< |
this_wrap(1:3) = r(1:3) - box(1:3)*nint(r(1:3)/box(1:3)) |
| 210 |
> |
this_wrap = r - thisSim%box*nint(r/thisSim%box) |
| 211 |
|
else |
| 212 |
|
this_wrap = r |
| 213 |
|
endif |
| 214 |
|
end function wrap_3d |
| 215 |
|
|
| 216 |
< |
|
| 217 |
< |
|
| 216 |
> |
|
| 217 |
> |
|
| 218 |
|
subroutine getRcut(thisrcut,rcut2,rcut6,status) |
| 219 |
|
real( kind = dp ), intent(out) :: thisrcut |
| 220 |
|
real( kind = dp ), intent(out), optional :: rcut2 |
| 221 |
< |
real( kind = dp ), intent(out), optional :: thisrcut6 |
| 221 |
> |
real( kind = dp ), intent(out), optional :: rcut6 |
| 222 |
|
integer, optional :: status |
| 223 |
|
|
| 224 |
|
if (present(status)) status = 0 |
| 228 |
|
return |
| 229 |
|
end if |
| 230 |
|
|
| 231 |
< |
thisrcut = rcut |
| 232 |
< |
if(present(rcut2)) rcut2 = rcutsq |
| 233 |
< |
if(present(rcut2)) rcut6 = rcut_6 |
| 231 |
> |
thisrcut = thisSim%rcut |
| 232 |
> |
if(present(rcut2)) rcut2 = thisSim%rcutsq |
| 233 |
> |
if(present(rcut6)) rcut6 = thisSim%rcut6 |
| 234 |
|
|
| 235 |
|
end subroutine getRcut |
| 236 |
|
|
| 237 |
+ |
|
| 238 |
+ |
|
| 239 |
+ |
|
| 240 |
+ |
subroutine getRlist(thisrlist,rlist2,status) |
| 241 |
+ |
real( kind = dp ), intent(out) :: thisrlist |
| 242 |
+ |
real( kind = dp ), intent(out), optional :: rlist2 |
| 243 |
|
|
| 244 |
+ |
integer, optional :: status |
| 245 |
|
|
| 246 |
+ |
if (present(status)) status = 0 |
| 247 |
|
|
| 248 |
+ |
if (.not.setSim ) then |
| 249 |
+ |
if (present(status)) status = -1 |
| 250 |
+ |
return |
| 251 |
+ |
end if |
| 252 |
+ |
|
| 253 |
+ |
thisrlist = thisSim%rlist |
| 254 |
+ |
if(present(rlist2)) rlist2 = thisSim%rlistsq |
| 255 |
+ |
|
| 256 |
+ |
|
| 257 |
+ |
end subroutine getRlist |
| 258 |
+ |
|
| 259 |
+ |
|
| 260 |
+ |
|
| 261 |
+ |
pure function getNlocal() result(nlocal) |
| 262 |
+ |
integer :: nlocal |
| 263 |
+ |
nlocal = thisSim%nLRparticles |
| 264 |
+ |
end function getNlocal |
| 265 |
+ |
|
| 266 |
+ |
|
| 267 |
+ |
|
| 268 |
|
end module simulation |
