Respond to @smharper comments on #684

openmc/data/library.py

@@ -23,7 +23,8 @@ class DataLibrary(object):
         root = ET.Element('cross_sections')
 
         # Determine common directory for library paths
-        common_dir = os.path.commonpath([lib['path'] for lib in self.libraries])
+        common_dir = os.path.dirname(os.path.commonprefix(
+            [lib['path'] for lib in self.libraries]))
         if common_dir == '':
             common_dir = '.'
 

src/angle_distribution.F90

@@ -1,8 +1,9 @@
 module angle_distribution
 
+  use hdf5, only: HID_T, HSIZE_T
+
   use constants, only: ZERO, ONE, HISTOGRAM, LINEAR_LINEAR
   use distribution_univariate, only: DistributionContainer, Tabular
-  use hdf5, only: HID_T, HSIZE_T
   use hdf5_interface, only: read_attribute, get_shape, read_dataset, &
        open_dataset, close_dataset
   use random_lcg, only: prn
@@ -81,9 +82,9 @@ contains
     dset_id = open_dataset(group_id, 'energy')
     call get_shape(dset_id, dims)
     n_energy = int(dims(1), 4)
-    allocate(this%energy(n_energy))
-    allocate(this%distribution(n_energy))
-    call read_dataset(this%energy, dset_id)
+    allocate(this % energy(n_energy))
+    allocate(this % distribution(n_energy))
+    call read_dataset(this % energy, dset_id)
     call close_dataset(dset_id)
 
     ! Get outgoing energy distribution data
@@ -105,8 +106,8 @@ contains
       end if
 
       ! Create and initialize tabular distribution
-      allocate(Tabular :: this%distribution(i)%obj)
-      select type (mudist => this%distribution(i)%obj)
+      allocate(Tabular :: this % distribution(i) % obj)
+      select type (mudist => this % distribution(i) % obj)
       type is (Tabular)
         mudist % interpolation = interp(i)
         allocate(mudist % x(n), mudist % p(n), mudist % c(n))

src/endf_header.F90

@@ -1,9 +1,10 @@
 module endf_header
 
+  use hdf5, only: HID_T, HSIZE_T
+
   use constants, only: ZERO, HISTOGRAM, LINEAR_LINEAR, LINEAR_LOG, &
        LOG_LINEAR, LOG_LOG
   use hdf5_interface
-  use hdf5, only: HID_T, HSIZE_T
   use search, only: binary_search
 
   implicit none
@@ -157,25 +158,25 @@ contains
 
     ! Determine number of regions
     nr = nint(xss(idx))
-    this%n_regions = nr
+    this % n_regions = nr
 
     ! Read interpolation region data
     if (nr > 0) then
-      allocate(this%nbt(nr))
-      allocate(this%int(nr))
-      this%nbt(:) = nint(xss(idx + 1 : idx + nr))
-      this%int(:) = nint(xss(idx + nr + 1 : idx + 2*nr))
+      allocate(this % nbt(nr))
+      allocate(this % int(nr))
+      this % nbt(:) = nint(xss(idx + 1 : idx + nr))
+      this % int(:) = nint(xss(idx + nr + 1 : idx + 2*nr))
     end if
 
     ! Determine number of pairs
     ne = int(XSS(idx + 2*nr + 1))
-    this%n_pairs = ne
+    this % n_pairs = ne
 
     ! Read (x,y) pairs
-    allocate(this%x(ne))
-    allocate(this%y(ne))
-    this%x(:) = xss(idx + 2*nr + 2 : idx + 2*nr + 1 + ne)
-    this%y(:) = xss(idx + 2*nr + 2 + ne : idx + 2*nr + 1 + 2*ne)
+    allocate(this % x(ne))
+    allocate(this % y(ne))
+    this % x(:) = xss(idx + 2*nr + 2 : idx + 2*nr + 1 + ne)
+    this % y(:) = xss(idx + 2*nr + 2 + ne : idx + 2*nr + 1 + 2*ne)
   end subroutine tabulated1d_from_ace
 
   subroutine tabulated1d_from_hdf5(this, dset_id)
@@ -185,19 +186,19 @@ contains
     real(8), allocatable :: xy(:,:)
     integer(HSIZE_T) :: dims(2)
 
-    call read_attribute(this%nbt, dset_id, 'breakpoints')
-    call read_attribute(this%int, dset_id, 'interpolation')
-    this%n_regions = size(this%nbt)
+    call read_attribute(this % nbt, dset_id, 'breakpoints')
+    call read_attribute(this % int, dset_id, 'interpolation')
+    this % n_regions = size(this % nbt)
 
     call get_shape(dset_id, dims)
-    this%n_pairs = int(dims(1), 4)
-    allocate(this%x(this%n_pairs))
-    allocate(this%y(this%n_pairs))
+    this % n_pairs = int(dims(1), 4)
+    allocate(this % x(this % n_pairs))
+    allocate(this % y(this % n_pairs))
 
     allocate(xy(dims(1), dims(2)))
     call read_dataset(xy, dset_id)
-    this%x(:) = xy(:,1)
-    this%y(:) = xy(:,2)
+    this % x(:) = xy(:,1)
+    this % y(:) = xy(:,2)
   end subroutine tabulated1d_from_hdf5
 
   pure function tabulated1d_evaluate(this, x) result(y)

src/energy_distribution.F90

@@ -1,9 +1,10 @@
 module energy_distribution
 
+  use hdf5
+
   use constants,     only: ZERO, ONE, HALF, TWO, PI, HISTOGRAM, LINEAR_LINEAR
   use endf_header,   only: Tabulated1D
   use hdf5_interface
-  use hdf5
   use math,          only: maxwell_spectrum, watt_spectrum
   use random_lcg,    only: prn
   use search,        only: binary_search

src/hdf5_interface.F90

@@ -10,13 +10,13 @@ module hdf5_interface
 ! can be combined into one simply accepting an assumed-shape array.
 !==============================================================================
 
-  use error, only: fatal_error
-  use tally_header, only: TallyResult
+  use, intrinsic :: ISO_C_BINDING
 
   use hdf5
   use h5lt
-  use, intrinsic :: ISO_C_BINDING
 
+  use error, only: fatal_error
+  use tally_header, only: TallyResult
 #ifdef PHDF5
   use message_passing, only: MPI_COMM_WORLD, MPI_INFO_NULL
 #endif

src/input_xml.F90

@@ -1,5 +1,7 @@
 module input_xml
 
+  use hdf5
+
   use cmfd_input,       only: configure_cmfd
   use constants
   use dict_header,      only: DictIntInt, ElemKeyValueCI
@@ -10,6 +12,7 @@ module input_xml
   use error,            only: fatal_error, warning
   use geometry_header,  only: Cell, Lattice, RectLattice, HexLattice
   use global
+  use hdf5_interface
   use list_header,      only: ListChar, ListInt, ListReal
   use mesh_header,      only: RegularMesh
   use multipole,        only: multipole_read
@@ -25,9 +28,6 @@ module input_xml
   use tally_initialize, only: add_tallies
   use xml_interface
 
-  use hdf5
-  use hdf5_interface
-
   implicit none
   save
 
@@ -2087,14 +2087,14 @@ contains
     call read_materials_xml(libraries, library_dict)
 
     ! Read continuous-energy cross sections
-    if (run_CE) then
+    if (run_CE .and. run_mode /= MODE_PLOTTING) then
       call time_read_xs%start()
       call read_ce_cross_sections(libraries, library_dict)
       call time_read_xs%stop()
     end if
 
     ! Normalize atom/weight percents
-    call normalize_ao()
+    if (run_mode /= MODE_PLOTTING) call normalize_ao()
 
     ! Clear dictionary
     call library_dict % clear()
@@ -3295,11 +3295,6 @@ contains
             ! If a specific nuclide was specified
             word = to_lower(sarray(j))
 
-!!$            ! Append default_xs specifier to nuclide if needed
-!!$            if ((default_xs /= '') .and. (.not. ends_with(sarray(j), 'c'))) then
-!!$              word = trim(word) // "." // trim(default_xs)
-!!$            end if
-
             ! Search through nuclides
             pair_list => nuclide_dict % keys()
             do while (associated(pair_list))

src/nuclide_header.F90

@@ -2,13 +2,14 @@ module nuclide_header
 
   use, intrinsic :: ISO_FORTRAN_ENV
 
+  use hdf5,        only: HID_T, HSIZE_T, SIZE_T, h5iget_name_f
+  use h5lt,        only: h5ltpath_valid_f
+
   use constants
   use dict_header, only: DictIntInt
   use endf,        only: reaction_name, is_fission, is_disappearance
   use endf_header, only: Function1D, Constant1D, Polynomial, Tabulated1D
   use error,       only: fatal_error, warning
-  use hdf5,        only: HID_T, HSIZE_T, SIZE_T, h5iget_name_f
-  use h5lt,        only: h5ltpath_valid_f
   use hdf5_interface, only: read_attribute, open_group, close_group, &
        open_dataset, read_dataset, close_dataset, get_shape
   use list_header, only: ListInt

src/product_header.F90

@@ -1,10 +1,11 @@
 module product_header
 
+  use hdf5, only: HID_T
+
   use angleenergy_header, only: AngleEnergyContainer
   use constants, only: ZERO, MAX_WORD_LEN, EMISSION_PROMPT, EMISSION_DELAYED, &
        EMISSION_TOTAL, NEUTRON, PHOTON
   use endf_header, only: Tabulated1D, Function1D, Constant1D, Polynomial
-  use hdf5, only: HID_T
   use hdf5_interface, only: read_attribute, open_group, close_group, &
        open_dataset, close_dataset, read_dataset
   use random_lcg, only: prn

src/reaction_header.F90

@@ -1,6 +1,7 @@
 module reaction_header
 
   use hdf5,           only: HID_T, HSIZE_T
+
   use hdf5_interface, only: read_attribute, open_group, close_group, &
        open_dataset, read_dataset, close_dataset, get_shape
   use product_header, only: ReactionProduct

src/secondary_correlated.F90

@@ -1,9 +1,10 @@
 module secondary_correlated
 
+  use hdf5, only: HID_T, HSIZE_T
+
   use angleenergy_header, only: AngleEnergy
   use constants, only: ZERO, ONE, HALF, TWO, HISTOGRAM, LINEAR_LINEAR
   use distribution_univariate, only: DistributionContainer, Tabular
-  use hdf5, only: HID_T, HSIZE_T
   use hdf5_interface, only: get_shape, read_attribute, open_dataset, &
        read_dataset, close_dataset
   use random_lcg, only: prn

src/secondary_kalbach.F90

@@ -1,8 +1,9 @@
 module secondary_kalbach
 
+  use hdf5, only: HID_T, HSIZE_T
+
   use angleenergy_header, only: AngleEnergy
   use constants, only: ZERO, HALF, ONE, TWO, HISTOGRAM, LINEAR_LINEAR
-  use hdf5, only: HID_T, HSIZE_T
   use hdf5_interface, only: read_attribute, read_dataset, open_dataset, &
        close_dataset, get_shape
   use random_lcg, only: prn

src/secondary_nbody.F90

@@ -1,8 +1,9 @@
 module secondary_nbody
 
+  use hdf5,               only: HID_T
+
   use angleenergy_header, only: AngleEnergy
   use constants,          only: ONE, TWO, PI
-  use hdf5,               only: HID_T
   use hdf5_interface,     only: read_attribute
   use math,               only: maxwell_spectrum
   use random_lcg,         only: prn

src/secondary_uncorrelated.F90

@@ -1,13 +1,14 @@
 module secondary_uncorrelated
 
+  use h5lt, only: h5ltpath_valid_f
+  use hdf5, only: HID_T
+
   use angle_distribution, only: AngleDistribution
   use angleenergy_header, only: AngleEnergy
   use constants, only: ONE, TWO, MAX_WORD_LEN
   use energy_distribution, only: EnergyDistribution, LevelInelastic, &
        ContinuousTabular, MaxwellEnergy, Evaporation, WattEnergy, DiscretePhoton
   use error, only: warning
-  use h5lt, only: h5ltpath_valid_f
-  use hdf5, only: HID_T
   use hdf5_interface, only: read_attribute, open_group, close_group
   use random_lcg, only: prn