Merge remote-tracking branch 'upstream/develop' into hex_lattice

Conflicts:
	src/relaxng/geometry.rnc
This commit is contained in:
Sterling Harper 2014-11-22 00:32:55 -05:00
commit 1abb821bd6
25 changed files with 516 additions and 34 deletions

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@ -4,6 +4,292 @@
State Point Binary File Specifications
======================================
-----------
Revision 13
-----------
**integer(4) FILETYPE_STATEPOINT**
Flags whether this file is a statepoint file or a particle restart file.
**integer(4) REVISION_STATEPOINT**
Revision of the binary state point file. Any time a change is made in the
format of the state-point file, this integer is incremented.
**integer(4) VERSION_MAJOR**
Major version number for OpenMC
**integer(4) VERSION_MINOR**
Minor version number for OpenMC
**integer(4) VERSION_RELEASE**
Release version number for OpenMC
**character(19) time_stamp**
Date and time the state point was written.
**character(255) path**
Absolute path to directory containing input files.
**integer(8) seed**
Pseudo-random number generator seed.
**integer(4) run_mode**
run mode used. The modes are described in constants.F90.
**integer(8) n_particles**
Number of particles used per generation.
**integer(4) current_batch**
The number of batches already simulated.
if (run_mode == MODE_EIGENVALUE)
**integer(4) n_inactive**
Number of inactive batches
**integer(4) gen_per_batch**
Number of generations per batch for criticality calculations
*do i = 1, current_batch \* gen_per_batch*
**real(8) k_generation(i)**
k-effective for the i-th total generation
*do i = 1, current_batch \* gen_per_batch*
**real(8) entropy(i)**
Shannon entropy for the i-th total generation
**real(8) k_col_abs**
Sum of product of collision/absorption estimates of k-effective
**real(8) k_col_tra**
Sum of product of collision/track-length estimates of k-effective
**real(8) k_abs_tra**
Sum of product of absorption/track-length estimates of k-effective
**real(8) k_combined(2)**
Mean and standard deviation of a combined estimate of k-effective
**integer(4) cmfd_on**
Flag that cmfd is on
if (cmfd_on)
**integer(4) cmfd % indices**
Indices for cmfd mesh (i,j,k,g)
**real(8) cmfd % k_cmfd(1:current_batch)**
CMFD eigenvalues
**real(8) cmfd % src(1:G,1:I,1:J,1:K)**
CMFD fission source
**real(8) cmfd % entropy(1:current_batch)**
CMFD estimate of Shannon entropy
**real(8) cmfd % balance(1:current_batch)**
RMS of the residual neutron balance equation on CMFD mesh
**real(8) cmfd % dom(1:current_batch)**
CMFD estimate of dominance ratio
**real(8) cmfd % scr_cmp(1:current_batch)**
RMS comparison of difference between OpenMC and CMFD fission source
**integer(4) n_meshes**
Number of meshes in tallies.xml file
*do i = 1, n_meshes*
**integer(4) meshes(i) % id**
Unique ID of mesh.
**integer(4) meshes(i) % type**
Type of mesh.
**integer(4) meshes(i) % n_dimension**
Number of dimensions for mesh (2 or 3).
**integer(4) meshes(i) % dimension(:)**
Number of mesh cells in each dimension.
**real(8) meshes(i) % lower_left(:)**
Coordinates of lower-left corner of mesh.
**real(8) meshes(i) % upper_right(:)**
Coordinates of upper-right corner of mesh.
**real(8) meshes(i) % width(:)**
Width of each mesh cell in each dimension.
**integer(4) n_tallies**
*do i = 1, n_tallies*
**integer(4) tallies(i) % id**
Unique ID of tally.
**integer(4) tallies(i) % n_realizations**
Number of realizations for the i-th tally.
**integer(4) size(tallies(i) % scores, 1)**
Total number of score bins for the i-th tally
**integer(4) size(tallies(i) % scores, 2)**
Total number of filter bins for the i-th tally
**integer(4) tallies(i) % n_filters**
*do j = 1, tallies(i) % n_filters*
**integer(4) tallies(i) % filter(j) % type**
Type of tally filter.
**integer(4) tallies(i) % filter(j) % n_bins**
Number of bins for filter.
**integer(4)/real(8) tallies(i) % filter(j) % bins(:)**
Value for each filter bin of this type.
**integer(4) tallies(i) % n_nuclide_bins**
Number of nuclide bins. If none are specified, this is just one.
*do j = 1, tallies(i) % n_nuclide_bins*
**integer(4) tallies(i) % nuclide_bins(j)**
Values of specified nuclide bins
**integer(4) tallies(i) % n_score_bins**
Number of scoring bins.
*do j = 1, tallies(i) % n_score_bins*
**integer(4) tallies(i) % score_bins(j)**
Values of specified scoring bins (e.g. SCORE_FLUX).
*do j = 1, tallies(i) % n_score_bins*
**integer(4) tallies(i) % scatt_order(j)**
Scattering Order specified scoring bins.
**integer(4) tallies(i) % n_score_bins**
Number of scoring bins without accounting for those added by
the scatter-pn command.
**integer(4) source_present**
Flag indicated if source bank is present in the file
**integer(4) n_realizations**
Number of realizations for global tallies.
**integer(4) N_GLOBAL_TALLIES**
Number of global tally scores
*do i = 1, N_GLOBAL_TALLIES*
**real(8) global_tallies(i) % sum**
Accumulated sum for the i-th global tally
**real(8) global_tallies(i) % sum_sq**
Accumulated sum of squares for the i-th global tally
**integer(4) tallies_on**
Flag indicated if tallies are present in the file.
if (tallies_on > 0)
*do i = 1, n_tallies*
*do k = 1, size(tallies(i) % scores, 2)*
*do j = 1, size(tallies(i) % scores, 1)*
**real(8) tallies(i) % scores(j,k) % sum**
Accumulated sum for the j-th score and k-th filter of the
i-th tally
**real(8) tallies(i) % scores(j,k) % sum_sq**
Accumulated sum of squares for the j-th score and k-th
filter of the i-th tally
if (run_mode == MODE_EIGENVALUE and source_present)
*do i = 1, n_particles*
**real(8) source_bank(i) % wgt**
Weight of the i-th source particle
**real(8) source_bank(i) % xyz(1:3)**
Coordinates of the i-th source particle.
**real(8) source_bank(i) % uvw(1:3)**
Direction of the i-th source particle
**real(8) source_bank(i) % E**
Energy of the i-th source particle.
-----------
Revision 12
-----------

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@ -757,7 +757,10 @@ Each ``<cell>`` element can have the following attributes or sub-elements:
is on the negative side of surface 3 and the positive side of surface 5, the
bounding surfaces would be given as "-3 5".
*Default*: None
.. note:: The surface attribute/element can be omitted to make a cell fill
its entire universe.
*Default*: No surfaces
:rotation:
If the cell is filled with a universe, this element specifies the angles in
@ -1245,7 +1248,7 @@ implemented in openMC:
``<plot>`` Element
------------------
Each plot must contain a combination of the following attributes or
Each plot is specified by a combination of the following attributes or
sub-elements:
:id:
@ -1266,6 +1269,18 @@ sub-elements:
*Default*: ``cell``
:level:
Universe depth to plot at (optional). This parameter controls how many
universe levels deep to pull cell and material ids from when setting plot
colors. If a given location does not have as many levels as specified,
colors will be taken from the lowest level at that location. For example, if
``level`` is set to zero colors will be taken from top-level (universe zero)
cells only. However, if ``level`` is set to 1 colors will be taken from
cells in universes that fill top-level fill-cells, and from top-level cells
that contain materials.
*Default*: Whatever the deepest universe is in the model
:origin:
Specifies the (x,y,z) coordinate of the center of the plot. Should be three
floats separated by spaces.

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@ -11,7 +11,7 @@ module constants
integer, parameter :: VERSION_RELEASE = 1
! Revision numbers for binary files
integer, parameter :: REVISION_STATEPOINT = 12
integer, parameter :: REVISION_STATEPOINT = 13
integer, parameter :: REVISION_PARTICLE_RESTART = 1
! Binary file types

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@ -23,6 +23,7 @@ module eigenvalue
reset_result
use tracking, only: transport
implicit none
private
public :: run_eigenvalue

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@ -3,6 +3,8 @@ module endf
use constants
use string, only: to_str
implicit none
contains
!===============================================================================

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@ -5,6 +5,8 @@ module energy_grid
use list_header, only: ListReal
use output, only: write_message
implicit none
contains
!===============================================================================

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@ -11,6 +11,8 @@ module fixed_source
use tally, only: synchronize_tallies, setup_active_usertallies
use tracking, only: transport
implicit none
contains
subroutine run_fixedsource()

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@ -83,7 +83,8 @@ contains
end if
end do SURFACE_LOOP
! If we've reached here, then the sense matched on every surface
! If we've reached here, then the sense matched on every surface or there
! are no surfaces.
in_cell = .true.
end function simple_cell_contains

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@ -435,7 +435,6 @@ contains
i = i + 1
case ('-t', '-track', '--track')
write_all_tracks = .true.
i = i + 1
case default
call fatal_error("Unknown command line option: " // argv(i))
end select

View file

@ -1012,17 +1012,18 @@ contains
call fatal_error("Cannot specify material and fill simultaneously")
end if
! Check to make sure that surfaces were specified
if (.not. check_for_node(node_cell, "surfaces")) then
call fatal_error("No surfaces specified for cell " &
&// trim(to_str(c % id)))
end if
! Allocate array for surfaces and copy
n = get_arraysize_integer(node_cell, "surfaces")
if (check_for_node(node_cell, "surfaces")) then
n = get_arraysize_integer(node_cell, "surfaces")
else
n = 0
end if
c % n_surfaces = n
allocate(c % surfaces(n))
call get_node_array(node_cell, "surfaces", c % surfaces)
if (n > 0) then
allocate(c % surfaces(n))
call get_node_array(node_cell, "surfaces", c % surfaces)
end if
! Rotation matrix
if (check_for_node(node_cell, "rotation")) then
@ -2916,16 +2917,14 @@ contains
end select
! Set output file path
filename = "plot"
filename = trim(to_str(pl % id)) // "_plot"
if (check_for_node(node_plot, "filename")) &
call get_node_value(node_plot, "filename", filename)
select case (pl % type)
case (PLOT_TYPE_SLICE)
pl % path_plot = trim(path_input) // trim(to_str(pl % id)) // &
"_" // trim(filename) // ".ppm"
pl % path_plot = trim(path_input) // trim(filename) // ".ppm"
case (PLOT_TYPE_VOXEL)
pl % path_plot = trim(path_input) // trim(to_str(pl % id)) // &
"_" // trim(filename) // ".voxel"
pl % path_plot = trim(path_input) // trim(filename) // ".voxel"
end select
! Copy plot pixel size
@ -3005,6 +3004,18 @@ contains
end if
end if
! Copy plot cell universe level
if (check_for_node(node_plot, "level")) then
call get_node_value(node_plot, "level", pl % level)
if (pl % level < 0) then
call fatal_error("Bad universe level in plot " &
&// trim(to_str(pl % id)))
end if
else
pl % level = PLOT_LEVEL_LOWEST
end if
! Copy plot color type and initialize all colors randomly
temp_str = "cell"
if (check_for_node(node_plot, "color")) &

View file

@ -1463,6 +1463,12 @@ contains
! Plot id
write(ou,100) "Plot ID:", trim(to_str(pl % id))
! Plot filename
write(ou,100) "Plot file:", trim(pl % path_plot)
! Plot level
write(ou,100) "Universe depth:", trim(to_str(pl % level))
! Plot type
if (pl % type == PLOT_TYPE_SLICE) then
write(ou,100) "Plot Type:", "Slice"

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@ -7,7 +7,7 @@ module plot
use global
use mesh, only: get_mesh_indices
use output, only: write_message
use particle_header, only: deallocate_coord, Particle
use particle_header, only: deallocate_coord, Particle, LocalCoord
use plot_header
use ppmlib, only: Image, init_image, allocate_image, &
deallocate_image, set_pixel
@ -32,7 +32,7 @@ contains
! Display output message
call write_message("Processing plot " // trim(to_str(pl % id)) &
&// "...", 5)
&// ": " // trim(pl % path_plot) // " ...", 5)
if (pl % type == PLOT_TYPE_SLICE) then
! create 2d image
@ -58,7 +58,9 @@ contains
integer, intent(out) :: id
logical :: found_cell
type(Cell), pointer :: c => null()
integer :: level
type(Cell), pointer :: c => null()
type(LocalCoord), pointer :: coord => null()
call deallocate_coord(p % coord0 % next)
p % coord => p % coord0
@ -66,6 +68,16 @@ contains
call find_cell(p, found_cell)
if (check_overlaps) call check_cell_overlap(p)
! Loop through universes and stop on any specified level
level = 0
coord => p % coord0
do
if (level == pl % level) exit
if (.not. associated(coord % next)) exit
coord => coord % next
level = level + 1
end do
if (.not. found_cell) then
! If no cell, revert to default color
rgb = pl % not_found % rgb
@ -73,19 +85,23 @@ contains
else
if (pl % color_by == PLOT_COLOR_MATS) then
! Assign color based on material
c => cells(p % coord % cell)
c => cells(coord % cell)
if (c % material == MATERIAL_VOID) then
! By default, color void cells white
rgb = 255
id = -1
else if (c % type == CELL_FILL) then
! If we stopped on a middle universe level, treat as if not found
rgb = pl % not_found % rgb
id = -1
else
rgb = pl % colors(c % material) % rgb
id = materials(c % material) % id
end if
else if (pl % color_by == PLOT_COLOR_CELLS) then
! Assign color based on cell
rgb = pl % colors(p % coord % cell) % rgb
id = cells(p % coord % cell) % id
rgb = pl % colors(coord % cell) % rgb
id = cells(coord % cell) % id
else
rgb = 0
id = -1

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@ -27,6 +27,7 @@ module plot_header
integer :: basis ! direction of plot slice
integer :: pixels(3) ! pixel width/height of plot slice
integer :: meshlines_width ! pixel width of meshlines
integer :: level ! universe depth to plot the cells of
type(StructuredMesh), pointer :: meshlines_mesh => null() ! mesh to plot
type(ObjectColor) :: meshlines_color ! Color for meshlines
type(ObjectColor) :: not_found ! color for positions where no cell found
@ -36,6 +37,9 @@ module plot_header
! Plot type
integer, parameter :: PLOT_TYPE_SLICE = 1
integer, parameter :: PLOT_TYPE_VOXEL = 2
! Plot level
integer, parameter :: PLOT_LEVEL_LOWEST = -1
! Plot basis plane
integer, parameter :: PLOT_BASIS_XY = 1

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@ -7,7 +7,7 @@ element geometry {
(element material { ( xsd:int | "void" ) } |
attribute material { ( xsd:int | "void" ) })
) &
(element surfaces { list { xsd:int+ } } | attribute surfaces { list { xsd:int+ } }) &
(element surfaces { list { xsd:int* } } | attribute surfaces { list { xsd:int* } })? &
(element rotation { list { xsd:double+ } } | attribute rotation { list { xsd:double+ } })? &
(element translation { list { xsd:double+ } } | attribute translation { list { xsd:double+ } })?
}*

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@ -7,6 +7,7 @@ element plots {
attribute type { "slice" | "voxel" })? &
(element color { ( "cell" | "mat" | "material" ) } |
attribute color { ( "cell" | "mat" | "material" ) })? &
(element level { xsd:int } | attribute level { xsd:int })? &
(element origin { list { xsd:double+ } } |
attribute origin { list { xsd:double+ } })? &
(element width { list { xsd:double+ } } |

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@ -3,6 +3,8 @@ module search
use constants
use error, only: fatal_error
implicit none
integer, parameter :: MAX_ITERATION = 64
interface binary_search

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@ -83,7 +83,6 @@ contains
! Write run information
call sp % write_data(run_mode, "run_mode")
call sp % write_data(n_particles, "n_particles")
call sp % write_data(n_batches, "n_batches")
! Write out current batch number
call sp % write_data(current_batch, "current_batch")
@ -306,7 +305,7 @@ contains
! Set filename
filename = trim(path_output) // 'source.' // &
& zero_padded(current_batch, count_digits(n_batches))
#ifdef HDF5
filename = trim(filename) // '.h5'
#else
@ -568,14 +567,15 @@ contains
! Read and overwrite run information except number of batches
call sp % read_data(run_mode, "run_mode")
call sp % read_data(n_particles, "n_particles")
call sp % read_data(int_array(1), "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 sp % read_data(restart_batch, "current_batch")
if (restart_batch > n_batches) then
call fatal_error("The number batches specified in settings.xml is fewer &
& than the number of batches in the given statepoint file.")
end if
! Read information specific to eigenvalue run
if (run_mode == MODE_EIGENVALUE) then
call sp % read_data(int_array(1), "n_inactive")

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@ -16,6 +16,8 @@ module tracking
use track_output, only: initialize_particle_track, write_particle_track, &
finalize_particle_track
implicit none
contains
!===============================================================================

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@ -6,7 +6,7 @@ from collections import OrderedDict
import numpy as np
import scipy.stats
REVISION_STATEPOINT = 12
REVISION_STATEPOINT = 13
filter_types = {1: 'universe', 2: 'material', 3: 'cell', 4: 'cellborn',
5: 'surface', 6: 'mesh', 7: 'energyin', 8: 'energyout'}
@ -182,7 +182,6 @@ class StatePoint(object):
# Read run information
self.run_mode = self._get_int(path='run_mode')[0]
self.n_particles = self._get_long(path='n_particles')[0]
self.n_batches = self._get_int(path='n_batches')[0]
# Read current batch
self.current_batch = self._get_int(path='current_batch')[0]

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@ -0,0 +1,17 @@
<?xml version="1.0"?>
<geometry>
<cell id="11" universe="11" material="1"/>
<cell id="12" universe="12" material="2" surfaces=""/>
<lattice id="21" type="rect" dimension="2 2" lower_left="-2.0 -2.0"
width="2.0 2.0" outside="2">
<universes>
11 12
12 11
</universes>
</lattice>
<surface id="101" type="z-cylinder" coeffs="0.0 0.0 5.0" boundary="vacuum"/>
<cell id="101" universe="0" fill="21" surfaces="-101"/>
</geometry>

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@ -0,0 +1,14 @@
<?xml version="1.0"?>
<materials>
<material id="1">
<density value="4.5" units="g/cc" />
<nuclide name="U-235" xs="71c" ao="1.0" />
</material>
<material id="2">
<density value="4.5" units="g/cc" />
<nuclide name="U-238" xs="71c" ao="1.0" />
</material>
</materials>

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@ -0,0 +1,25 @@
#!/usr/bin/env python
import sys
# import statepoint
sys.path.insert(0, '../../src/utils')
import statepoint
# read in statepoint file
if len(sys.argv) > 1:
sp = statepoint.StatePoint(sys.argv[1])
else:
sp = statepoint.StatePoint('statepoint.10.binary')
sp.read_results()
# set up output string
outstr = ''
# write out k-combined
outstr += 'k-combined:\n'
outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
# write results to file
with open('results_test.dat','w') as fh:
fh.write(outstr)

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@ -0,0 +1,2 @@
k-combined:
9.998895E-02 2.846817E-04

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@ -0,0 +1,16 @@
<?xml version="1.0"?>
<settings>
<eigenvalue>
<batches>10</batches>
<inactive>5</inactive>
<particles>1000</particles>
</eigenvalue>
<source>
<space type="box">
<parameters>-4 -4 -4 4 4 4</parameters>
</space>
</source>
</settings>

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@ -0,0 +1,59 @@
#!/usr/bin/env python
import os
from subprocess import Popen, STDOUT, PIPE, call
import filecmp
import glob
from optparse import OptionParser
parser = OptionParser()
parser.add_option('--mpi_exec', dest='mpi_exec', default='')
parser.add_option('--mpi_np', dest='mpi_np', default='3')
parser.add_option('--exe', dest='exe')
(opts, args) = parser.parse_args()
cwd = os.getcwd()
def test_run():
if opts.mpi_exec != '':
proc = Popen([opts.mpi_exec, '-np', opts.mpi_np, opts.exe, cwd],
stderr=STDOUT, stdout=PIPE)
else:
proc = Popen([opts.exe, cwd], stderr=STDOUT, stdout=PIPE)
print(proc.communicate()[0])
returncode = proc.returncode
assert returncode == 0, 'OpenMC did not exit successfully.'
def test_created_statepoint():
statepoint = glob.glob(os.path.join(cwd, 'statepoint.10.*'))
assert len(statepoint) == 1, 'Either multiple or no statepoint files exist.'
assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5'),\
'Statepoint file is not a binary or hdf5 file.'
def test_results():
statepoint = glob.glob(os.path.join(cwd, 'statepoint.10.*'))
call(['python', 'results.py', statepoint[0]])
compare = filecmp.cmp('results_test.dat', 'results_true.dat')
if not compare:
os.rename('results_test.dat', 'results_error.dat')
assert compare, 'Results do not agree.'
def teardown():
output = glob.glob(os.path.join(cwd, 'statepoint.10.*'))
output.append(os.path.join(cwd, 'results_test.dat'))
for f in output:
if os.path.exists(f):
os.remove(f)
if __name__ == '__main__':
# test for openmc executable
if opts.exe is None:
raise Exception('Must specify OpenMC executable from command line with --exe.')
# run tests
try:
test_run()
test_created_statepoint()
test_results()
finally:
teardown()