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IO, DRIVER: Allow for restart with different number of ghost zones.

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Now we can restart from restart snapshots with different number of ghost
zones. Also, remove the old restart snapshot format support from
read_datablocks_h5().

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
This commit is contained in:
Grzegorz Kowal 2019-02-11 11:02:36 -02:00
parent 6d421e6efb
commit 601adc8037
2 changed files with 116 additions and 108 deletions
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16
sources/driver.F90
View File

@ -41,7 +41,7 @@ program amun
use boundaries , only : print_boundaries, boundary_variables use boundaries , only : print_boundaries, boundary_variables
use coordinates , only : initialize_coordinates, finalize_coordinates use coordinates , only : initialize_coordinates, finalize_coordinates
use coordinates , only : print_coordinates use coordinates , only : print_coordinates
use coordinates , only : nb => bcells use coordinates , only : nn => bcells
use domains , only : initialize_domains, finalize_domains use domains , only : initialize_domains, finalize_domains
use equations , only : initialize_equations, finalize_equations use equations , only : initialize_equations, finalize_equations
use equations , only : print_equations use equations , only : print_equations
@ -284,7 +284,6 @@ program amun
call read_snapshot_parameter("eqsys" , eqsys , iret) call read_snapshot_parameter("eqsys" , eqsys , iret)
call read_snapshot_parameter("eos" , eos , iret) call read_snapshot_parameter("eos" , eos , iret)
call read_snapshot_parameter("ncells" , ncells , iret) call read_snapshot_parameter("ncells" , ncells , iret)
call read_snapshot_parameter("nghosts", nghosts, iret)
call read_snapshot_parameter("maxlev" , toplev , iret) call read_snapshot_parameter("maxlev" , toplev , iret)
call read_snapshot_parameter("rdims" , bdims , iret) call read_snapshot_parameter("rdims" , bdims , iret)
call read_snapshot_parameter("xmin" , xmin , iret) call read_snapshot_parameter("xmin" , xmin , iret)
@ -300,7 +299,6 @@ program amun
call get_parameter("equation_system" , eqsys ) call get_parameter("equation_system" , eqsys )
call get_parameter("equation_of_state", eos ) call get_parameter("equation_of_state", eos )
call get_parameter("ncells" , ncells ) call get_parameter("ncells" , ncells )
call get_parameter("nghosts" , nghosts)
call get_parameter("maxlev" , toplev ) call get_parameter("maxlev" , toplev )
call get_parameter("xblocks" , bdims(1)) call get_parameter("xblocks" , bdims(1))
call get_parameter("yblocks" , bdims(2)) call get_parameter("yblocks" , bdims(2))
@ -317,6 +315,10 @@ program amun
#endif /* NDIMS == 3 */ #endif /* NDIMS == 3 */
end if end if
! get the number of ghost zones
!
call get_parameter("nghosts", nghosts)
! get the execution termination parameters ! get the execution termination parameters
! !
call get_parameter("nmax", nmax) call get_parameter("nmax", nmax)
@ -346,9 +348,9 @@ program amun
ymin, ymax, zmin, zmax, master, iret) ymin, ymax, zmin, zmax, master, iret)
if (iret > 0) go to 170 if (iret > 0) go to 170
#if NDIMS == 3 #if NDIMS == 3
call initialize_blocks((/ nv, nv, nb, nb, nb /), master, iret) call initialize_blocks((/ nv, nv, nn, nn, nn /), master, iret)
#else /* NDIMS == 3 */ #else /* NDIMS == 3 */
call initialize_blocks((/ nv, nv, nb, nb, 1 /), master, iret) call initialize_blocks((/ nv, nv, nn, nn, 1 /), master, iret)
#endif /* NDIMS == 3 */ #endif /* NDIMS == 3 */
if (iret > 0) go to 160 if (iret > 0) go to 160
call initialize_operators(master, iret) call initialize_operators(master, iret)
@ -417,6 +419,10 @@ program amun
! !
call build_leaf_list() call build_leaf_list()
! update boundaries
!
call boundary_variables(time, dtnext)
else else
! generate the initial mesh, refine that mesh to the desired level according to ! generate the initial mesh, refine that mesh to the desired level according to

162
sources/io.F90
View File

@ -1993,7 +1993,7 @@ module io
integer(hid_t) :: gid integer(hid_t) :: gid
integer :: ierr, l integer :: ierr, l
integer :: lndims, lmblocks, lnleafs, llast_id integer :: lndims, lmblocks, lnleafs, llast_id
integer :: lncells, lnghost, lnproc, lnseeds integer :: lncells, lnproc, lnseeds
! local pointers ! local pointers
! !
@ -2030,7 +2030,6 @@ module io
call read_attribute(gid, 'nleafs' , lnleafs ) call read_attribute(gid, 'nleafs' , lnleafs )
call read_attribute(gid, 'last_id', llast_id) call read_attribute(gid, 'last_id', llast_id)
call read_attribute(gid, 'ncells' , lncells ) call read_attribute(gid, 'ncells' , lncells )
call read_attribute(gid, 'nghosts', lnghost )
call read_attribute(gid, 'nseeds' , lnseeds ) call read_attribute(gid, 'nseeds' , lnseeds )
call read_attribute(gid, 'step' , step ) call read_attribute(gid, 'step' , step )
call read_attribute(gid, 'isnap' , isnap ) call read_attribute(gid, 'isnap' , isnap )
@ -2062,13 +2061,6 @@ module io
, "The block dimensions do not match!" , "The block dimensions do not match!"
end if end if
! check the number of ghost layers
!
if (lnghost /= nghosts) then
write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "The number of ghost layers does not match!"
end if
! allocate space for seeds ! allocate space for seeds
! !
allocate(seeds(lnseeds)) allocate(seeds(lnseeds))
@ -2947,7 +2939,7 @@ module io
! !
use blocks , only : block_meta, block_data, list_data use blocks , only : block_meta, block_data, list_data
use blocks , only : append_datablock, link_blocks use blocks , only : append_datablock, link_blocks
use coordinates , only : nn => bcells use coordinates , only : nn => bcells, ng => nghosts
use equations , only : nv use equations , only : nv
use hdf5 , only : hid_t, hsize_t use hdf5 , only : hid_t, hsize_t
use hdf5 , only : h5gopen_f, h5gclose_f, h5lexists_f use hdf5 , only : h5gopen_f, h5gclose_f, h5lexists_f
@ -2971,7 +2963,7 @@ module io
character(len=16) :: bname character(len=16) :: bname
integer(hid_t) :: gid, bid integer(hid_t) :: gid, bid
integer(kind=4) :: l, i integer(kind=4) :: l, i
integer :: dblocks, ierr integer :: dblocks, ncells, nghosts, nc, nb, ne, status
! local arrays ! local arrays
! !
@ -2979,8 +2971,7 @@ module io
! local allocatable arrays ! local allocatable arrays
! !
integer(kind=4), dimension(:) , allocatable :: id real(kind=8), dimension(:,:,:,:,:), allocatable :: uu
real(kind=8) , dimension(:,:,:,:,:), allocatable :: uv, qv
! local parameters ! local parameters
! !
@ -2990,15 +2981,17 @@ module io
! !
! read the number of data blocks ! read the number of data blocks
! !
call h5gopen_f(fid, 'attributes', gid, ierr) call h5gopen_f(fid, 'attributes', gid, status)
if (ierr /= 0) then if (status /= 0) then
write(error_unit,"('[',a,']: ',a)") trim(loc) & write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot open the attribute group!" , "Cannot open the attribute group!"
return return
end if end if
call read_attribute(gid, 'dblocks', dblocks) call read_attribute(gid, 'dblocks', dblocks)
call h5gclose_f(gid, ierr) call read_attribute(gid, 'ncells' , ncells )
if (ierr /= 0) then call read_attribute(gid, 'nghosts', nghosts)
call h5gclose_f(gid, status)
if (status /= 0) then
write(error_unit,"('[',a,']: ',a)") trim(loc) & write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot close the attribute group!" , "Cannot close the attribute group!"
return return
@ -3010,73 +3003,42 @@ module io
! open the group 'datablocks' ! open the group 'datablocks'
! !
call h5gopen_f(fid, 'datablocks', gid, ierr) call h5gopen_f(fid, 'datablocks', gid, status)
if (ierr /= 0) then if (status /= 0) then
write(error_unit,"('[',a,']: ',a)") trim(loc) & write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot open the data block group!" , "Cannot open the data block group!"
return else
! prepare the number of cells in the stored blocks and corresponding indices
!
nc = ncells + 2 * nghosts
if (nghosts >= ng) then
nb = 1 + (nghosts - ng)
ne = nc - (nghosts - ng)
else
nb = 1 + (ng - nghosts)
ne = nn - (ng - nghosts)
end if end if
! fill out dimensions dm(:) ! fill out dimensions
! !
dm(1) = dblocks dm(1) = dblocks
dm(2) = nv dm(2) = nv
dm(3) = nn dm(3) = nc
dm(4) = nn dm(4) = nc
#if NDIMS == 3 #if NDIMS == 3
dm(5) = nn dm(5) = nc
#endif /* NDIMS == 3 */ #endif /* NDIMS == 3 */
! check if the old data format is used, otherwise use the new one ! allocate arrays for input data
! !
call h5lexists_f(gid, 'meta', flag, ierr) allocate(uu(3,dm(2),dm(3),dm(4),dm(5)), stat = status)
! restart files are in the old format ! check if allocation was successful
! !
if (flag) then if (status == 0) then
! allocate arrays to read data ! iterate over data blocks
!
allocate(id(dm(1)))
allocate(uv(dm(1),dm(2),dm(3),dm(4),dm(5)))
allocate(qv(dm(1),dm(2),dm(3),dm(4),dm(5)))
! read array data from the HDF5 file
!
call read_array(gid, 'meta', dm(1:1), id(:) )
call read_array(gid, 'uvar', dm(1:5), uv(:,:,:,:,:))
call read_array(gid, 'qvar', dm(1:5), qv(:,:,:,:,:))
! iterate over data blocks, allocate them and fill out their fields
!
do l = 1, dm(1)
! allocate and append to the end of the list a new datablock
!
call append_datablock(pdata)
! associate the corresponding meta block with the current data block
!
call link_blocks(block_array(id(l))%ptr, pdata)
! fill out the array of conservative and primitive variables
!
pdata%u(:,:,:,:) = uv(l,:,:,:,:)
pdata%q(:,:,:,:) = qv(l,:,:,:,:)
end do ! l = 1, dm(1)
! deallocate allocatable arrays
!
if (allocated(id)) deallocate(id)
if (allocated(uv)) deallocate(uv)
if (allocated(qv)) deallocate(qv)
! restart files are in the new format
!
else ! flag
! iterate over data blocks, allocate them and fill out their fields
! !
do l = 1, dm(1) do l = 1, dm(1)
@ -3090,7 +3052,8 @@ module io
! open the group for the current block fields ! open the group for the current block fields
! !
call h5gopen_f(gid, bname, bid, ierr) call h5gopen_f(gid, bname, bid, status)
if (status == 0) then
! get the id of the linked meta block ! get the id of the linked meta block
! !
@ -3100,27 +3063,66 @@ module io
! !
call link_blocks(block_array(i)%ptr, pdata) call link_blocks(block_array(i)%ptr, pdata)
! fill out the array of primitive and conservative variables ! read the data
! !
call read_array(bid, 'pvar' , dm(2:5), pdata%q (:,:,:,:)) call read_array(bid, 'pvar' , dm(2:5), uu(1,:,:,:,:))
call read_array(bid, 'cvar0', dm(2:5), pdata%u0(:,:,:,:)) call read_array(bid, 'cvar0', dm(2:5), uu(2,:,:,:,:))
call read_array(bid, 'cvar1', dm(2:5), pdata%u1(:,:,:,:)) call read_array(bid, 'cvar1', dm(2:5), uu(3,:,:,:,:))
! fill out the block arrays taking into account the change of nghosts
!
if (nghosts >= ng) then
#if NDIMS == 3
pdata%q (:,:,:,:) = uu(1,:,nb:ne,nb:ne,nb:ne)
pdata%u0(:,:,:,:) = uu(2,:,nb:ne,nb:ne,nb:ne)
pdata%u1(:,:,:,:) = uu(3,:,nb:ne,nb:ne,nb:ne)
#else /* NDIMS == 3 */
pdata%q (:,:,:,:) = uu(1,:,nb:ne,nb:ne, : )
pdata%u0(:,:,:,:) = uu(2,:,nb:ne,nb:ne, : )
pdata%u1(:,:,:,:) = uu(3,:,nb:ne,nb:ne, : )
#endif /* NDIMS == 3 */
else
#if NDIMS == 3
pdata%q (:,nb:ne,nb:ne,nb:ne) = uu(1,:,:,:,:)
pdata%u0(:,nb:ne,nb:ne,nb:ne) = uu(2,:,:,:,:)
pdata%u1(:,nb:ne,nb:ne,nb:ne) = uu(3,:,:,:,:)
#else /* NDIMS == 3 */
pdata%q (:,nb:ne,nb:ne, : ) = uu(1,:,:,:,:)
pdata%u0(:,nb:ne,nb:ne, : ) = uu(2,:,:,:,:)
pdata%u1(:,nb:ne,nb:ne, : ) = uu(3,:,:,:,:)
#endif /* NDIMS == 3 */
end if
! close the current data block group ! close the current data block group
! !
call h5gclose_f(bid, ierr) call h5gclose_f(bid, status)
if (status /= 0) then
write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot close group '", trim(bname), "'!"
end if
else
write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot open group '", trim(bname), "'!"
end if
end do ! l = 1, dm(1) end do ! l = 1, dm(1)
end if ! flag else ! allocate
write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot allocate temporary array!"
end if ! allocate
! deallocate allocatable arrays
!
if (allocated(uu)) deallocate(uu)
! close the data block group ! close the data block group
! !
call h5gclose_f(gid, ierr) call h5gclose_f(gid, status)
if (ierr /= 0) then if (status /= 0) then
write(error_unit,"('[',a,']: ',a)") trim(loc) & write(error_unit,"('[',a,']: ',a)") trim(loc) &
, "Cannot close the data block group!" , "Cannot close the data block group!"
return end if
end if end if
end if ! dblocks > 0 end if ! dblocks > 0