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Merge pull request #648 from paulromano/hdf5-attribute

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Ability to read from attributes on HDF5 groups/datasets
This commit is contained in:
Sterling Harper 2016-05-15 12:50:31 -04:00
commit ba9a9c8507
5 changed files with 720 additions and 322 deletions
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918
src/hdf5_interface.F90
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4
src/initialize.F90
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@ -375,7 +375,7 @@ contains
! Check what type of file this is
file_id = file_open(argv(i), 'r', parallel=.true.)
call read_dataset(file_id, 'filetype', filetype)
call read_dataset(filetype, file_id, 'filetype')
call file_close(file_id)
! Set path and flag for type of run
@ -401,7 +401,7 @@ contains
! Check file type is a source file
file_id = file_open(argv(i), 'r', parallel=.true.)
call read_dataset(file_id, 'filetype', filetype)
call read_dataset(filetype, file_id, 'filetype')
call file_close(file_id)
if (filetype /= 'source') then
call fatal_error("Second file after restart flag must be a &

46
src/particle_restart.F90
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@ -34,7 +34,7 @@ contains
verbosity = 10
! Initialize the particle to be tracked
call p%initialize()
call p % initialize()
! Read in the restart information
call read_particle_restart(p, previous_run_mode)
@ -46,9 +46,9 @@ contains
select case (previous_run_mode)
case (MODE_EIGENVALUE)
particle_seed = ((current_batch - 1)*gen_per_batch + &
current_gen - 1)*n_particles + p%id
current_gen - 1)*n_particles + p % id
case (MODE_FIXEDSOURCE)
particle_seed = p%id
particle_seed = p % id
end select
call set_particle_seed(particle_seed)
@ -71,7 +71,7 @@ contains
integer :: int_scalar
integer(HID_T) :: file_id
character(MAX_WORD_LEN) :: mode
character(MAX_WORD_LEN) :: tempstr
! Write meessage
call write_message("Loading particle restart file " &
@ -81,32 +81,32 @@ contains
file_id = file_open(path_particle_restart, 'r')
! Read data from file
call read_dataset(file_id, 'filetype', int_scalar)
call read_dataset(file_id, 'revision', int_scalar)
call read_dataset(file_id, 'current_batch', current_batch)
call read_dataset(file_id, 'gen_per_batch', gen_per_batch)
call read_dataset(file_id, 'current_gen', current_gen)
call read_dataset(file_id, 'n_particles', n_particles)
call read_dataset(file_id, 'run_mode', mode)
select case (mode)
call read_dataset(tempstr, file_id, 'filetype')
call read_dataset(int_scalar, file_id, 'revision')
call read_dataset(current_batch, file_id, 'current_batch')
call read_dataset(gen_per_batch, file_id, 'gen_per_batch')
call read_dataset(current_gen, file_id, 'current_gen')
call read_dataset(n_particles, file_id, 'n_particles')
call read_dataset(tempstr, file_id, 'run_mode')
select case (tempstr)
case ('k-eigenvalue')
previous_run_mode = MODE_EIGENVALUE
case ('fixed source')
previous_run_mode = MODE_FIXEDSOURCE
end select
call read_dataset(file_id, 'id', p%id)
call read_dataset(file_id, 'weight', p%wgt)
call read_dataset(file_id, 'energy', p%E)
call read_dataset(file_id, 'energy_group', p%g)
call read_dataset(file_id, 'xyz', p%coord(1)%xyz)
call read_dataset(file_id, 'uvw', p%coord(1)%uvw)
call read_dataset(p % id, file_id, 'id')
call read_dataset(p % wgt, file_id, 'weight')
call read_dataset(p % E, file_id, 'energy')
call read_dataset(p % g, file_id, 'energy_group')
call read_dataset(p % coord(1) % xyz, file_id, 'xyz')
call read_dataset(p % coord(1) % uvw, file_id, 'uvw')
! Set particle last attributes
p%last_wgt = p%wgt
p%last_xyz = p%coord(1)%xyz
p%last_uvw = p%coord(1)%uvw
p%last_E = p%E
p%last_g = p%g
p % last_wgt = p % wgt
p % last_xyz = p % coord(1)%xyz
p % last_uvw = p % coord(1)%uvw
p % last_E = p % E
p % last_g = p % g
! Close hdf5 file
call file_close(file_id)

2
src/source.F90
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@ -53,7 +53,7 @@ contains
file_id = file_open(path_source, 'r', parallel=.true.)
! Read the file type
call read_dataset(file_id, "filetype", filetype)
call read_dataset(filetype, file_id, "filetype")
! Check to make sure this is a source file
if (filetype /= 'source') then

72
src/state_point.F90
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@ -703,25 +703,25 @@ contains
file_id = file_open(path_state_point, 'r', parallel=.true.)
! Read filetype
call read_dataset(file_id, "filetype", word)
call read_dataset(word, file_id, "filetype")
if (word /= 'statepoint') then
call fatal_error("OpenMC tried to restart from a non-statepoint file.")
end if
! Read revision number for state point file and make sure it matches with
! current version
call read_dataset(file_id, "revision", int_array(1))
call read_dataset(int_array(1), file_id, "revision")
if (int_array(1) /= REVISION_STATEPOINT) then
call fatal_error("State point version does not match current version &
&in OpenMC.")
end if
! Read and overwrite random number seed
call read_dataset(file_id, "seed", seed)
call read_dataset(seed, file_id, "seed")
! It is not impossible for a state point to be generated from a CE run but
! to be loaded in to an MG run (or vice versa), check to prevent that.
call read_dataset(file_id, "run_CE", sp_run_CE)
call read_dataset(sp_run_CE, file_id, "run_CE")
if (sp_run_CE == 0 .and. run_CE) then
call fatal_error("State point file is from multi-group run but &
& current run is continous-energy!")
@ -731,24 +731,24 @@ contains
end if
! Read and overwrite run information except number of batches
call read_dataset(file_id, "run_mode", word)
call read_dataset(word, file_id, "run_mode")
select case(word)
case ('fixed source')
run_mode = MODE_FIXEDSOURCE
case ('k-eigenvalue')
run_mode = MODE_EIGENVALUE
end select
call read_dataset(file_id, "n_particles", n_particles)
call read_dataset(file_id, "n_batches", int_array(1))
call read_dataset(n_particles, file_id, "n_particles")
call read_dataset(int_array(1), file_id, "n_batches")
! Take maximum of statepoint n_batches and input n_batches
n_batches = max(n_batches, int_array(1))
! Read batch number to restart at
call read_dataset(file_id, "current_batch", restart_batch)
call read_dataset(restart_batch, file_id, "current_batch")
! Check for source in statepoint if needed
call read_dataset(file_id, "source_present", int_array(1))
call read_dataset(int_array(1), file_id, "source_present")
if (int_array(1) == 1) then
source_present = .true.
else
@ -762,37 +762,37 @@ contains
! Read information specific to eigenvalue run
if (run_mode == MODE_EIGENVALUE) then
call read_dataset(file_id, "n_inactive", int_array(1))
call read_dataset(file_id, "gen_per_batch", gen_per_batch)
call read_dataset(file_id, "k_generation", &
k_generation(1:restart_batch*gen_per_batch))
call read_dataset(file_id, "entropy", &
entropy(1:restart_batch*gen_per_batch))
call read_dataset(file_id, "k_col_abs", k_col_abs)
call read_dataset(file_id, "k_col_tra", k_col_tra)
call read_dataset(file_id, "k_abs_tra", k_abs_tra)
call read_dataset(file_id, "k_combined", real_array(1:2))
call read_dataset(int_array(1), file_id, "n_inactive")
call read_dataset(gen_per_batch, file_id, "gen_per_batch")
call read_dataset(k_generation(1:restart_batch*gen_per_batch), &
file_id, "k_generation")
call read_dataset(entropy(1:restart_batch*gen_per_batch), &
file_id, "entropy")
call read_dataset(k_col_abs, file_id, "k_col_abs")
call read_dataset(k_col_tra, file_id, "k_col_tra")
call read_dataset(k_abs_tra, file_id, "k_abs_tra")
call read_dataset(real_array(1:2), file_id, "k_combined")
! Take maximum of statepoint n_inactive and input n_inactive
n_inactive = max(n_inactive, int_array(1))
! Read in to see if CMFD was on
call read_dataset(file_id, "cmfd_on", int_array(1))
call read_dataset(int_array(1), file_id, "cmfd_on")
! Read in CMFD info
if (int_array(1) == 1) then
cmfd_group = open_group(file_id, "cmfd")
call read_dataset(cmfd_group, "indices", cmfd%indices)
call read_dataset(cmfd_group, "k_cmfd", cmfd%k_cmfd(1:restart_batch))
call read_dataset(cmfd_group, "cmfd_src", cmfd%cmfd_src)
call read_dataset(cmfd_group, "cmfd_entropy", &
cmfd%entropy(1:restart_batch))
call read_dataset(cmfd_group, "cmfd_balance", &
cmfd%balance(1:restart_batch))
call read_dataset(cmfd_group, "cmfd_dominance", &
cmfd%dom(1:restart_batch))
call read_dataset(cmfd_group, "cmfd_srccmp", &
cmfd%src_cmp(1:restart_batch))
call read_dataset(cmfd % indices, cmfd_group, "indices")
call read_dataset(cmfd % k_cmfd(1:restart_batch), cmfd_group, "k_cmfd")
call read_dataset(cmfd % cmfd_src, cmfd_group, "cmfd_src")
call read_dataset(cmfd % entropy(1:restart_batch), cmfd_group, &
"cmfd_entropy")
call read_dataset(cmfd % balance(1:restart_batch), cmfd_group, &
"cmfd_balance")
call read_dataset(cmfd % dom(1:restart_batch), cmfd_group, &
"cmfd_dominance")
call read_dataset(cmfd % src_cmp(1:restart_batch), cmfd_group, &
"cmfd_srccmp")
call close_group(cmfd_group)
end if
end if
@ -812,14 +812,14 @@ contains
#endif
! Read number of realizations for global tallies
call read_dataset(file_id, "n_realizations", n_realizations, indep=.true.)
call read_dataset(n_realizations, file_id, "n_realizations", indep=.true.)
! Read global tally data
call read_dataset(file_id, "global_tallies", global_tallies)
! Check if tally results are present
tallies_group = open_group(file_id, "tallies")
call read_dataset(tallies_group, "tallies_present", int_array(1), &
call read_dataset(int_array(1), tallies_group, "tallies_present", &
indep=.true.)
! Read in sum and sum squared
@ -832,8 +832,8 @@ contains
tally_group = open_group(tallies_group, "tally " // &
trim(to_str(tally % id)))
call read_dataset(tally_group, "results", tally % results)
call read_dataset(tally_group, "n_realizations", &
tally % n_realizations)
call read_dataset(tally % n_realizations, tally_group, &
"n_realizations")
call close_group(tally_group)
end do TALLY_RESULTS
end if
@ -859,7 +859,7 @@ contains
file_id = file_open(path_source_point, 'r', parallel=.true.)
! Read file type
call read_dataset(file_id, "filetype", int_array(1))
call read_dataset(int_array(1), file_id, "filetype")
end if