From d6957a25240abd28b399dc78a2532b60dafbbc02 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 12 Dec 2013 22:54:42 -0500 Subject: [PATCH 01/15] Started writing script to download ACE files from NNDC site. --- data/get_nndc_data.py | 48 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100755 data/get_nndc_data.py diff --git a/data/get_nndc_data.py b/data/get_nndc_data.py new file mode 100755 index 0000000000..7bb3b2c6ea --- /dev/null +++ b/data/get_nndc_data.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python + +from __future__ import print_function +import tarfile +import urllib2 + +baseUrl = 'http://www.nndc.bnl.gov/endf/b7.1/aceFiles/' +files = ['ENDF-B-VII.1-neutron-293.6K.tar.gz', + 'ENDF-B-VII.1-neutron-300K.tar.gz', + 'ENDF-B-VII.1-neutron-900K.tar.gz', + 'ENDF-B-VII.1-neutron-1500K.tar.gz', + 'ENDF-B-VII.1-tsl.tar.gz'] +block_size = 16384 + +# ============================================================================== +# DOWNLOAD FILES FROM NNDC SITE + +filesComplete = [] +for f in files: + # Establish connection to URL + url = baseUrl + f + print('Downloading {0}... '.format(f), end='') + req = urllib2.urlopen(url) + + # Get file size from header + file_size = int(req.info().getheaders("Content-Length")[0]) + downloaded = 0 + + # Copy file to disk + with open(f, 'wb') as fh: + while True: + chunk = req.read(block_size) + if not chunk: break + fh.write(chunk) + downloaded += len(chunk) + status = "{0:10} [{1:3.2f}%]".format(downloaded, downloaded * 100. / file_size) + print(status + chr(8)*len(status), end='') + filesComplete.append(f) + +# ============================================================================== +# EXTRACT FILES FROM TGZ + +for f in files: + if not f in filesComplete: + continue + + with tarfile.open(f, 'r') as tgz: + tgz.extractall(path='nndc') From 6ba3c48c5af0a42950b3469d65b6dff5d1211c3d Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 19 Dec 2013 10:54:02 -0500 Subject: [PATCH 02/15] Check for file already downloaded. Rename xsdir. --- data/get_nndc_data.py | 25 ++++++++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) diff --git a/data/get_nndc_data.py b/data/get_nndc_data.py index 7bb3b2c6ea..0f943d684c 100755 --- a/data/get_nndc_data.py +++ b/data/get_nndc_data.py @@ -1,6 +1,8 @@ #!/usr/bin/env python from __future__ import print_function +import os +import os.path import tarfile import urllib2 @@ -19,22 +21,33 @@ filesComplete = [] for f in files: # Establish connection to URL url = baseUrl + f - print('Downloading {0}... '.format(f), end='') req = urllib2.urlopen(url) # Get file size from header - file_size = int(req.info().getheaders("Content-Length")[0]) + file_size = int(req.info().getheaders('Content-Length')[0]) downloaded = 0 + # Check if file already downloaded + if os.path.exists(f): + if os.path.getsize(f) == file_size: + print('Skipping ' + f) + continue + else: + overwrite = raw_input('Overwrite {0}? ([y]/n) '.format(f)) + if overwrite.lower().startswith('n'): + continue + # Copy file to disk + print('Downloading {0}... '.format(f), end='') with open(f, 'wb') as fh: while True: chunk = req.read(block_size) if not chunk: break fh.write(chunk) downloaded += len(chunk) - status = "{0:10} [{1:3.2f}%]".format(downloaded, downloaded * 100. / file_size) + status = '{0:10} [{1:3.2f}%]'.format(downloaded, downloaded * 100. / file_size) print(status + chr(8)*len(status), end='') + print('') filesComplete.append(f) # ============================================================================== @@ -44,5 +57,11 @@ for f in files: if not f in filesComplete: continue + # Extract files with tarfile.open(f, 'r') as tgz: tgz.extractall(path='nndc') + + # Give xsdir a unique name + xsdir = 'nndc/xsdir' + if os.path.exists(xsdir): + os.rename(xsdir, xsdir + '_' + f.strip('.tar.gz')) From e795b49f5c302b34b84161be382b11490bc2791c Mon Sep 17 00:00:00 2001 From: nhorelik Date: Fri, 31 Jan 2014 11:28:39 -0500 Subject: [PATCH 03/15] Updated data processing and viz documentation to include examples --- 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z$tarh44jq2K^HL4>D!MHevGzQ==Zwq) z*tI@z1o|H{IK@Voy^iwaXPogj2UQR-5)AS5X`lln4K)!+aZd>3=i8=4Z-2`#fP8_V NHT2Zq-LMY*{{WX%y`_ * [1]_ `Scipy `_ @@ -41,6 +41,55 @@ Plotting in 2D .. image:: ../_images/atr.png :height: 200px +See below for a simple example of a plots xml file that demonstrates the +capabilities of 2D slice plots. Here we assume that there is a ``geometry.xml`` +file containing 7 cells. + +.. code-block:: xml + + + + + + myplot + 0 0 + 10 10 + 2000 2000 + 0 0 0 + + + + + + + 1 3 4 5 6 + + + + + + +In this example, OpenMC will produce a plot named ``myplot.ppm`` when run in +plotting mode. The picture will be on the xy-plane, depicting the rectangle +between points (-5,-5) and (5,5) with 2000 pixels along each dimension. The +color of each pixel is determined by placing a particle at the center of that +pixel and using OpenMC's internal ``find_cell`` routine (the same one used for +particle tracking during simulation) to determine the cell and material at that +location. In this example, pixels are 10/2000=0.005 cm wide, so points will be +at (-4.9975,-4.9975), (-4.9950,-4.9975), (-4.9925,-4.9975), etc. This is pointed +out to demonstrate that this plot may miss any features smaller than 0.005 cm, +since they could exist between pixel centers. More pixels can be used to resolve +finer features, but could result in larger files. + +The ``background``, ``col_spec``, and ``mask`` elements define how to set pixel +colors based on the cell ids at each pixel center. In this example, RGB colors +are specified for cells 1,2,3,4, and 7, a random color will be assigned to cells +5 and 6, and a black background color (``rgb="0 0 0"``) will be applied to +locations where no cell is defined. However, the ``mask`` element here says that +only cells 1,3,4,5, and 6 should be displayed, with other cells taking a white +color (``rgb="255 255 255"``), which overrides the ``col_spec`` for cell 2 and +the random color assigned to cell 7. + After running OpenMC to obtain PPM files, images should be saved to another format before using them elsewhere. This cuts down the size of the file by orders of magnitude. Most image viewers and editors that can view PPM images @@ -53,7 +102,7 @@ Ubuntu: ``sudo apt-get install imagemagick``). Images are then converted like: .. code-block:: sh - convert plot.ppm plot.png + convert myplot.ppm myplot.png Plotting in 3D -------------- @@ -61,10 +110,37 @@ Plotting in 3D .. image:: ../_images/3dgeomplot.png :height: 200px +See below for a simple example of a plots xml file that demonstrates the +capabilities of 3D voxel plots. + +.. code-block:: xml + + + + + + myplot + 0 0 0 + 10 10 10 + 500 500 500 + + + + +Voxel plots are built the same way 2D slice plots are, by determining the cell +or material id of a particle at the center of each voxel. In this example, the +space covered is the cube between the points (-5,-5,-5) and (5,5,5), with voxel +centers 10/500 = 0.02 cm apart. The binary VOXEL files that are produced do not +specify any color - instead containing only material or cell ids (material id +in this example) - and thus the ``background``, ``col_spec``, and ``mask`` +elements are not used. If no cell is found at a voxel center, an id of -1 is +stored. + The binary VOXEL files output by OpenMC can not be viewed directly by any existing viewers. In order to view them, they must be converted into a standard -mesh format that can be viewed in ParaView, Visit, etc. The provided utility -voxel.py accomplishes this for SILO: +mesh format that can be viewed in ParaView, Visit, etc. This typically will +compress the size of the file significantly. The provided utility voxel.py +accomplishes this for SILO: .. code-block:: sh @@ -88,13 +164,21 @@ or Users can process the binary into any other format if desired by following the example of voxel.py. For the binary file structure, see :ref:`devguide_voxel`. +Once processed into a standard 3D file format, colors and masks can be defined +using the stored id numbers to better explore the geometry. The process for +doing this will depend on the 3D viewer, but should be straightforward. + +.. image:: ../_images/3dba.png + :height: 200px + .. note:: 3D voxel plotting can be very computer intensive for the viewing program (Visit, Paraview, etc.) if the number of voxels is large (>10 million or so). Thus if you want an accurate picture that renders smoothly, consider using only one voxel in a certain direction. For - instance, the 3D pin lattice figure above was generated with a - 500x500x1 voxel mesh, which allows for resolution of the cylinders - without wasting too many voxels on the axial dimension. + instance, the 3D pin lattice figure at the beginning of this section + was generated with a 500x500x1 voxel mesh, which allows for resolution + of the cylinders without wasting too many voxels on the axial + dimension. ------------------- From 5d0b98835d2ca1101b4d11a273bfa1ff12530ff7 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Mon, 17 Feb 2014 17:30:02 -0500 Subject: [PATCH 04/15] Extract files to subdirectories. Add pre-generated cross_sections.xml. --- data/cross_sections_nndc.xml | 1716 ++++++++++++++++++++++++++++++++++ data/get_nndc_data.py | 17 +- 2 files changed, 1727 insertions(+), 6 deletions(-) create mode 100644 data/cross_sections_nndc.xml diff --git a/data/cross_sections_nndc.xml b/data/cross_sections_nndc.xml new file mode 100644 index 0000000000..2e421d7ab0 --- /dev/null +++ b/data/cross_sections_nndc.xml @@ -0,0 +1,1716 @@ + + + ascii + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/data/get_nndc_data.py b/data/get_nndc_data.py index 0f943d684c..c9279add6b 100755 --- a/data/get_nndc_data.py +++ b/data/get_nndc_data.py @@ -2,7 +2,8 @@ from __future__ import print_function import os -import os.path +import shutil +import subprocess import tarfile import urllib2 @@ -31,6 +32,7 @@ for f in files: if os.path.exists(f): if os.path.getsize(f) == file_size: print('Skipping ' + f) + filesComplete.append(f) continue else: overwrite = raw_input('Overwrite {0}? ([y]/n) '.format(f)) @@ -58,10 +60,13 @@ for f in files: continue # Extract files + suffix = f[f.rindex('-') + 1:].rstrip('.tar.gz') with tarfile.open(f, 'r') as tgz: - tgz.extractall(path='nndc') + print('Extracting {0}...'.format(f)) + tgz.extractall(path='nndc/' + suffix) - # Give xsdir a unique name - xsdir = 'nndc/xsdir' - if os.path.exists(xsdir): - os.rename(xsdir, xsdir + '_' + f.strip('.tar.gz')) +# ============================================================================== +# COPY CROSS_SECTIONS.XML + +print('Copying cross_sections_nndc.xml...') +shutil.copyfile('cross_sections_nndc.xml', 'nndc/cross_sections.xml') From 6edd3934fbb3071f5f98c005a72ba0c4171b17ae Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Mon, 17 Feb 2014 17:46:10 -0500 Subject: [PATCH 05/15] Update installation guide with information about NNDC data. --- docs/source/usersguide/install.rst | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst index 164b0151be..ff33d9a6c6 100644 --- a/docs/source/usersguide/install.rst +++ b/docs/source/usersguide/install.rst @@ -264,10 +264,27 @@ Cross Section Configuration In order to run a simulation with OpenMC, you will need cross section data for each nuclide in your problem. Since OpenMC uses ACE format cross sections, you -can use nuclear data that was processed with NJOY, such as that distributed with -MCNP_ or Serpent_. The TALYS-based evaluated nuclear data library, TENDL_, is +can use nuclear data that was processed with NJOY_, such as that distributed +with MCNP_ or Serpent_. Several sources provide free processed ACE data as +described below. The TALYS-based evaluated nuclear data library, TENDL_, is also openly available in ACE format. +Using ENDF/B-VII.1 Cross Sections from NNDC +------------------------------------------- + +The NNDC_ provides ACE data from the ENDF/B-VII.1 neutron and thermal scattering +sublibraries at four temperatures processed using NJOY_. To use this data with +OpenMC, a script is provided with OpenMC that will automatically download, +extract, and set up a confiuration file: + +.. code-block:: sh + + cd openmc/data + python get_nndc_data.py + +At this point, you should set the :envvar:`CROSS_SECTIONS` environment variable +to the absolute path of the file ``openmc/data/nndc/cross_sections.xml``. + Using JEFF Cross Sections from OECD/NEA --------------------------------------- @@ -314,6 +331,8 @@ distribution to the location of the Serpent cross sections. Then, either set the environment variable to the absolute path of the ``cross_sections_serpent.xml`` file. +.. _NJOY: http://t2.lanl.gov/nis/codes.shtml +.. _NNDC: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html .. _NEA: http://www.oecd-nea.org .. _JEFF: http://www.oecd-nea.org/dbdata/jeff/ .. _here: http://www.oecd-nea.org/dbdata/pubs/jeff312-cd.html From 1fb2bb96f6c31ac33bfde36b33a48929906eebf1 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Tue, 18 Feb 2014 17:47:20 -0500 Subject: [PATCH 06/15] Updated data/readme.rst. --- data/readme.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/data/readme.rst b/data/readme.rst index d975723b52..03685491d0 100644 --- a/data/readme.rst +++ b/data/readme.rst @@ -15,6 +15,9 @@ work with a few common cross section sources. - **cross_sections_ascii.xml** -- This file matches ENDF/B-VII.0 cross sections distributed with MCNP5 / MCNP6 beta. +- **cross_sections_nndc.xml** -- This file matches ENDF/B-VII.1 cross sections + distributed from the `NNDC website`_. + - **cross_sections_serpent.xml** -- This file matches ENDF/B-VII.0 cross sections distributed with Serpent 1.1.7. @@ -31,3 +34,4 @@ element in your settings.xml, or set the CROSS_SECTIONS environment variable to the full path of the cross_sections.xml file. .. _user's guide: http://mit-crpg.github.io/openmc/usersguide/install.html#cross-section-configuration +.. _NNDC website: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html From b102b71809a3f9baf62046ef8e1bd291bedad8e5 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Tue, 18 Feb 2014 17:55:40 -0500 Subject: [PATCH 07/15] Added HDF5 files to .gitignore. --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 9f720f9894..2dae450d08 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,6 @@ src/templates/*.f90 # Test results error file results_error.dat + +# HDF5 files +*.h5 From a96c6ad47463aa26cbbc13c01c9b99f46b5f4f75 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Wed, 19 Feb 2014 18:02:18 -0500 Subject: [PATCH 08/15] Ask user to delete downloaded tgz files. --- data/get_nndc_data.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/data/get_nndc_data.py b/data/get_nndc_data.py index c9279add6b..0fd1a98894 100755 --- a/data/get_nndc_data.py +++ b/data/get_nndc_data.py @@ -4,6 +4,7 @@ from __future__ import print_function import os import shutil import subprocess +import sys import tarfile import urllib2 @@ -70,3 +71,19 @@ for f in files: print('Copying cross_sections_nndc.xml...') shutil.copyfile('cross_sections_nndc.xml', 'nndc/cross_sections.xml') + +# ============================================================================== +# PROMPT USER TO DELETE .TAR.GZ FILES + +# Ask user to delete +if sys.version_info[0] < 3: + response = raw_input('Delete *.tar.gz files? ([y]/n) ') +else: + response = input('Delete *.tar.gz files? ([y]/n) ') + +# Delete files if requested +if not response or response.lower().startswith('y'): + for f in files: + if os.path.exists(f): + print('Removing {0}...'.format(f)) + os.remove(f) From 3f6913ba6ed110f324d1a0afabe4b68a368f4dd1 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Wed, 19 Feb 2014 18:12:38 -0500 Subject: [PATCH 09/15] Make get_nndc_data.py compatible with Python 3. --- data/get_nndc_data.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/data/get_nndc_data.py b/data/get_nndc_data.py index 0fd1a98894..2e76401a4b 100755 --- a/data/get_nndc_data.py +++ b/data/get_nndc_data.py @@ -6,7 +6,11 @@ import shutil import subprocess import sys import tarfile -import urllib2 + +try: + from urllib.request import urlopen +except ImportError: + from urllib2 import urlopen baseUrl = 'http://www.nndc.bnl.gov/endf/b7.1/aceFiles/' files = ['ENDF-B-VII.1-neutron-293.6K.tar.gz', @@ -23,7 +27,7 @@ filesComplete = [] for f in files: # Establish connection to URL url = baseUrl + f - req = urllib2.urlopen(url) + req = urlopen(url) # Get file size from header file_size = int(req.info().getheaders('Content-Length')[0]) @@ -36,7 +40,10 @@ for f in files: filesComplete.append(f) continue else: - overwrite = raw_input('Overwrite {0}? ([y]/n) '.format(f)) + if sys.version_info[0] < 3: + overwrite = raw_input('Overwrite {0}? ([y]/n) '.format(f)) + else: + overwrite = input('Overwrite {0}? ([y]/n) '.format(f)) if overwrite.lower().startswith('n'): continue From 6dda6baeb3adee9497f70c09482d4d4e39314356 Mon Sep 17 00:00:00 2001 From: Bryan Herman Date: Thu, 20 Feb 2014 16:32:28 -0500 Subject: [PATCH 10/15] updated documentation --- docs/source/usersguide/input.rst | 49 +++++++++++++++++++++++++++----- 1 file changed, 42 insertions(+), 7 deletions(-) diff --git a/docs/source/usersguide/input.rst b/docs/source/usersguide/input.rst index 28ba30c23e..362197439d 100644 --- a/docs/source/usersguide/input.rst +++ b/docs/source/usersguide/input.rst @@ -348,8 +348,10 @@ attributes/sub-elements: The ```` element indicates at what batches a state point file should be written. A state point file can be used to restart a run or to get -tally results at any batch. This element has the following -attributes/sub-elements: +tally results at any batch. The default behavior when using this tag is to +write out the source bank in the state_point file. This behavior can be +customized by using the ```` element. This element has the +following attributes/sub-elements: :batches: A list of integers separated by spaces indicating at what batches a state @@ -364,19 +366,52 @@ attributes/sub-elements: *Default*: None +```` Element +-------------------------- + +The ```` element indicates at what batches the source bank +should be written. The source bank can be either written out within a state +point file or separately in a source point file. This element has the following +attributes/sub-elements: + + :batches: + A list of integers separated by spaces indicating at what batches a state + point file should be written. It should be noted that if source_separate + tag is not set to "true", this list must be a subset of state point batches. + + *Default*: Last batch only + + :interval: + A single integer :math:`n` indicating that a state point should be written + every :math:`n` batches. This option can be given in lieu of listing + batches explicitly. It should be noted that if source_separate tag is not + set to "true", this value should produce a list of batches that is a subset + of state point batches. + + *Default*: None + :source_separate: - If this element is set to "true", a separate binary source file will be + If this element is set to "true", a separate binary source point file will be written. Otherwise, the source sites will be written in the state point directly. *Default*: false - :source_write: If this element is set to "false", source sites are not written - to the state point file. This can substantially reduce the size of state - points if large numbers of particles per batch are used. + :source_write: + If this element is set to "false", source sites are not written + to the state point or source point file. This can substantially reduce the + size of state points if large numbers of particles per batch are used. *Default*: true + :overwrite_latest: + If this element is set to "true", a source point file containing + the source bank will be written out to a separate file named + ``source.binary`` or ``source.h5`` depending on if HDF5 is enabled. + This file will be overwritten at every single batch so that the latest + source bank will be available. It should be noted that a user can set both + this element to "true" and specify batches to write a permanent source bank. + ```` Element ------------------------------ @@ -1052,7 +1087,7 @@ sub-elements: the PNG format can often times reduce the file size by orders of magnitude without any loss of image quality. Likewise, high-resolution voxel files produced by OpenMC can be quite large, - but the equivalent SILO files will be significantly smaller. + but the equivalent SILO files will by significantly smaller. *Default*: "slice" From 9acc8ff366969813276d71bc59eb451e13bca7fa Mon Sep 17 00:00:00 2001 From: Bryan Herman Date: Thu, 20 Feb 2014 17:48:13 -0500 Subject: [PATCH 11/15] deleted unused data file --- tests/test_sourcepoint_latest/results_test.dat | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 tests/test_sourcepoint_latest/results_test.dat diff --git a/tests/test_sourcepoint_latest/results_test.dat b/tests/test_sourcepoint_latest/results_test.dat deleted file mode 100644 index 00a65f913b..0000000000 --- a/tests/test_sourcepoint_latest/results_test.dat +++ /dev/null @@ -1,2 +0,0 @@ -k-combined: -3.011353E-01 2.854556E-03 From e3a45bce3b090949ad2b4901f64ca48f55af3a1a Mon Sep 17 00:00:00 2001 From: Bryan Herman Date: Thu, 20 Feb 2014 18:32:51 -0500 Subject: [PATCH 12/15] updated results file for source point latest test --- tests/test_sourcepoint_latest/results_true.dat | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/test_sourcepoint_latest/results_true.dat b/tests/test_sourcepoint_latest/results_true.dat index 748df0351e..00a65f913b 100644 --- a/tests/test_sourcepoint_latest/results_true.dat +++ b/tests/test_sourcepoint_latest/results_true.dat @@ -1,3 +1,2 @@ k-combined: -0.000000E+00 0.000000E+00 --9.438655E-02 -4.436810E+00 -2.416825E+00 +3.011353E-01 2.854556E-03 From e63746cdb8247308e9cd5a64ba07029cbf402b7b Mon Sep 17 00:00:00 2001 From: Bryan Herman Date: Fri, 21 Feb 2014 10:21:32 -0500 Subject: [PATCH 13/15] added cleanup script to remove all binary files from directories --- tests/cleanup.bash | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100755 tests/cleanup.bash diff --git a/tests/cleanup.bash b/tests/cleanup.bash new file mode 100755 index 0000000000..d23b166a26 --- /dev/null +++ b/tests/cleanup.bash @@ -0,0 +1,14 @@ +# This simple script ensures that all binary +# output files have been deleted in all the +# folders. This can occur if a previous error +# occurred and the test suite was rerun without +# deleting left over binary files. This will +# cause an assertion error in some of the +# tests. +for i in ./*; do + if [ -d "$i" ]; then + cd $i + rm -f *.binary *.h5 + cd .. + fi +done From d1a42b79ce8b6c485ed80b025d5df70aa8bf0d26 Mon Sep 17 00:00:00 2001 From: Bryan Herman Date: Fri, 21 Feb 2014 10:50:18 -0500 Subject: [PATCH 14/15] fixed deleting binary files --- tests/test_sourcepoint_restart/test_sourcepoint_restart.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_sourcepoint_restart/test_sourcepoint_restart.py b/tests/test_sourcepoint_restart/test_sourcepoint_restart.py index a4387405b8..9b2e3185f9 100644 --- a/tests/test_sourcepoint_restart/test_sourcepoint_restart.py +++ b/tests/test_sourcepoint_restart/test_sourcepoint_restart.py @@ -126,7 +126,7 @@ def test_results_serial(): def teardown(): output = glob.glob(pwd + '/statepoint.7.*') - output += glob.glob(pwd + '/sourcepoint.7.*') + output += glob.glob(pwd + '/source.7.*') output.append(pwd + '/results_test.dat') for f in output: if os.path.exists(f): From 411aea322dddb42ca66975e600d7a7de6490e971 Mon Sep 17 00:00:00 2001 From: Bryan Herman Date: Fri, 21 Feb 2014 14:14:56 -0500 Subject: [PATCH 15/15] restructured sourcepoint restart test --- tests/test_sourcepoint_restart/results.py | 2 +- .../test_sourcepoint_restart/results_true.dat | 3378 ++++++++--------- tests/test_sourcepoint_restart/settings.xml | 4 +- .../test_sourcepoint_restart.py | 46 +- 4 files changed, 1713 insertions(+), 1717 deletions(-) diff --git a/tests/test_sourcepoint_restart/results.py b/tests/test_sourcepoint_restart/results.py index d0b3a55e04..f4c32a893f 100644 --- a/tests/test_sourcepoint_restart/results.py +++ b/tests/test_sourcepoint_restart/results.py @@ -11,7 +11,7 @@ import statepoint if len(sys.argv) > 1: sp = statepoint.StatePoint(sys.argv[1]) else: - sp = statepoint.StatePoint('statepoint.7.binary') + sp = statepoint.StatePoint('statepoint.10.binary') sp.read_results() # extract tally results and convert to vector diff --git a/tests/test_sourcepoint_restart/results_true.dat b/tests/test_sourcepoint_restart/results_true.dat index f2b97af34d..ad94d76457 100644 --- a/tests/test_sourcepoint_restart/results_true.dat +++ b/tests/test_sourcepoint_restart/results_true.dat @@ -1,16 +1,16 @@ k-combined: -0.000000E+00 0.000000E+00 +3.011353E-01 2.854556E-03 tally 1: -3.000000E-03 -5.000000E-06 -1.350207E-03 -9.349751E-07 --7.677912E-05 -4.241317E-07 --3.387424E-04 -1.343262E-07 -1.215119E-03 -9.127703E-07 +8.000000E-03 +1.600000E-05 +6.192275E-04 +1.370333E-06 +-8.662964E-04 +7.279501E-07 +-1.041312E-05 +3.860351E-07 +4.821963E-03 +5.791161E-06 0.000000E+00 0.000000E+00 0.000000E+00 @@ -41,16 +41,16 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 -3.000000E-03 -9.000000E-06 -1.889613E-04 -3.570639E-08 -2.320049E-04 -5.382627E-08 -1.491658E-03 -2.225044E-06 -1.817087E-03 -2.362232E-06 +1.100000E-02 +3.300000E-05 +4.387087E-03 +7.410082E-06 +1.860042E-03 +2.867148E-06 +3.399756E-03 +5.784483E-06 +5.116596E-03 +6.752240E-06 0.000000E+00 0.000000E+00 0.000000E+00 @@ -59,6 +59,18 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 +3.028119E-04 +9.169503E-08 +1.000000E-03 +1.000000E-06 +5.438971E-04 +2.958240E-07 +-5.626399E-05 +3.165637E-09 +-4.136011E-04 +1.710658E-07 +6.013419E-04 +3.616120E-07 0.000000E+00 0.000000E+00 0.000000E+00 @@ -69,6 +81,16 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 +5.000000E-03 +1.300000E-05 +3.577754E-03 +6.496319E-06 +1.890975E-03 +1.788514E-06 +9.937593E-04 +4.944395E-07 +1.803302E-03 +1.626040E-06 0.000000E+00 0.000000E+00 0.000000E+00 @@ -139,38 +161,16 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -8.000000E-03 -4.000000E-05 -1.075518E-03 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+2.829537E-06 0.000000E+00 0.000000E+00 0.000000E+00 @@ -1963,134 +2203,14 @@ tally 1: 0.000000E+00 2.000000E-03 2.000000E-06 -1.439409E-03 -1.103682E-06 -6.555229E-04 -5.306118E-07 -7.043819E-05 -4.155385E-07 -1.226302E-03 -7.521585E-07 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -1.000000E-03 -1.000000E-06 -4.295537E-04 -1.845164E-07 --2.232254E-04 -4.982957E-08 --4.461813E-04 -1.990778E-07 -3.121671E-04 -9.744828E-08 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -2.000000E-03 -4.000000E-06 -1.440797E-04 -2.075896E-08 -1.581861E-03 -2.502285E-06 -7.101262E-04 -5.042792E-07 -6.019679E-04 -3.623653E-07 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 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+2.096746E-07 +6.016549E-04 +1.809943E-07 0.000000E+00 0.000000E+00 0.000000E+00 @@ -2122,57 +2242,25 @@ tally 1: 0.000000E+00 0.000000E+00 7.000000E-03 -2.900000E-05 -4.675157E-03 -1.278192E-05 -2.215224E-03 -3.397777E-06 -1.088961E-03 -2.486687E-06 -3.344373E-03 -6.674880E-06 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -2.000000E-03 -4.000000E-06 --2.660370E-04 -7.077569E-08 --7.919915E-04 -6.272506E-07 -2.842468E-04 -8.079625E-08 -9.141350E-04 -4.598136E-07 -0.000000E+00 -0.000000E+00 +1.700000E-05 +5.770569E-03 +1.116420E-05 +4.074122E-03 +5.715629E-06 +2.739484E-03 +2.864833E-06 +3.630946E-03 +2.739811E-06 +0.000000E+00 +0.000000E+00 +0.000000E+00 +0.000000E+00 +0.000000E+00 +0.000000E+00 +0.000000E+00 +0.000000E+00 +3.028119E-04 +9.169503E-08 0.000000E+00 0.000000E+00 0.000000E+00 @@ -2193,6 +2281,16 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 +1.000000E-02 +2.600000E-05 +3.940359E-03 +1.345990E-05 +4.066207E-03 +4.701591E-06 +2.653786E-03 +1.896780E-06 +3.626422E-03 +2.904169E-06 0.000000E+00 0.000000E+00 0.000000E+00 @@ -2201,16 +2299,18 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 +8.948660E-04 +8.007852E-07 1.000000E-03 1.000000E-06 -6.738077E-05 -4.540168E-09 --4.931897E-04 -2.432361E-07 --1.003064E-04 -1.006137E-08 -3.009839E-04 -9.059133E-08 +8.049124E-04 +6.478840E-07 +4.718259E-04 +2.226197E-07 +9.635598E-05 +9.284475E-09 +9.084356E-04 +8.252553E-07 0.000000E+00 0.000000E+00 0.000000E+00 @@ -2221,116 +2321,16 @@ tally 1: 0.000000E+00 0.000000E+00 0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 -0.000000E+00 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b/tests/test_sourcepoint_restart/settings.xml index 5fee23d67e..c405186fb7 100644 --- a/tests/test_sourcepoint_restart/settings.xml +++ b/tests/test_sourcepoint_restart/settings.xml @@ -1,8 +1,8 @@ - - + + 10 diff --git a/tests/test_sourcepoint_restart/test_sourcepoint_restart.py b/tests/test_sourcepoint_restart/test_sourcepoint_restart.py index 9b2e3185f9..0eaf1198cc 100644 --- a/tests/test_sourcepoint_restart/test_sourcepoint_restart.py +++ b/tests/test_sourcepoint_restart/test_sourcepoint_restart.py @@ -24,49 +24,49 @@ def test_run(): assert returncode == 0 def test_created_statepoint(): - statepoint = glob.glob(pwd + '/statepoint.7.*') - assert len(statepoint) == 1 + statepoint = glob.glob(pwd + '/statepoint.*') + assert len(statepoint) == 2 assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5') sourcepoint = glob.glob(pwd + '/source.7.*') assert len(sourcepoint) == 1 assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5') def test_results(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/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 + os.remove(statepoint[0]) def test_restart_form1(): statepoint = glob.glob(pwd + '/statepoint.7.*') + sourcepoint = glob.glob(pwd + '/source.7.*') openmc_path = pwd + '/../../src/openmc' if int(NoseMPI.mpi_np) > 0: proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path, - '-r', statepoint[0]], + '-r', statepoint[0], sourcepoint[0]], stderr=STDOUT, stdout=PIPE) else: - proc = Popen([openmc_path, '-r', statepoint[0]], stderr=STDOUT, stdout=PIPE) + proc = Popen([openmc_path, '-r', statepoint[0], sourcepoint[0]], stderr=STDOUT, stdout=PIPE) print(proc.communicate()[0]) returncode = proc.returncode assert returncode == 0 def test_created_statepoint_form1(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/statepoint.10.*') assert len(statepoint) == 1 assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5') - sourcepoint = glob.glob(pwd + '/source.7.*') - assert len(sourcepoint) == 1 - assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5') def test_results_form1(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/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 + os.remove(statepoint[0]) def test_restart_form2(): statepoint = glob.glob(pwd + '/statepoint.7.*') @@ -74,50 +74,46 @@ def test_restart_form2(): openmc_path = pwd + '/../../src/openmc' if int(NoseMPI.mpi_np) > 0: proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path, - '--restart', statepoint[0], source[0]], + '--restart', statepoint[0], sourcepoint[0]], stderr=STDOUT, stdout=PIPE) else: - proc = Popen([openmc_path, '--restart', statepoint[0]], + proc = Popen([openmc_path, '--restart', statepoint[0], sourcepoint[0]], stderr=STDOUT, stdout=PIPE) print(proc.communicate()[0]) returncode = proc.returncode assert returncode == 0 def test_created_statepoint_form2(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/statepoint.10.*') assert len(statepoint) == 1 assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5') - sourcepoint = glob.glob(pwd + '/source.7.*') - assert len(sourcepoint) == 1 - assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5') def test_results_form2(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/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 + os.remove(statepoint[0]) def test_restart_serial(): statepoint = glob.glob(pwd + '/statepoint.7.*') + sourcepoint = glob.glob(pwd + '/source.7.*') openmc_path = pwd + '/../../src/openmc' - proc = Popen([openmc_path, '--restart', statepoint[0]], + proc = Popen([openmc_path, '--restart', statepoint[0], sourcepoint[0]], stderr=STDOUT, stdout=PIPE) print(proc.communicate()[0]) returncode = proc.returncode assert returncode == 0 def test_created_statepoint_serial(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/statepoint.10.*') assert len(statepoint) == 1 assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5') - sourcepoint = glob.glob(pwd + '/source.7.*') - assert len(sourcepoint) == 1 - assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5') def test_results_serial(): - statepoint = glob.glob(pwd + '/statepoint.7.*') + statepoint = glob.glob(pwd + '/statepoint.10.*') call(['python', 'results.py', statepoint[0]]) compare = filecmp.cmp('results_test.dat', 'results_true.dat') if not compare: @@ -125,8 +121,8 @@ def test_results_serial(): assert compare def teardown(): - output = glob.glob(pwd + '/statepoint.7.*') - output += glob.glob(pwd + '/source.7.*') + output = glob.glob(pwd + '/statepoint.*') + output += glob.glob(pwd + '/source.*') output.append(pwd + '/results_test.dat') for f in output: if os.path.exists(f):