From daa2079565f9f79a5a6dd7e8e1e828e1660364a4 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Mon, 24 Jan 2022 22:13:39 +0000 Subject: [PATCH 01/31] added separate tests for each task --- .github/workflows/ci_tests.yml | 57 ++++++++++++++++++++++++++++++++-- tests/test_task_1.py | 49 +++++++++++++++++++++++++++++ tests/test_task_10.py | 49 +++++++++++++++++++++++++++++ tests/test_task_11.py | 49 +++++++++++++++++++++++++++++ tests/test_task_12.py | 49 +++++++++++++++++++++++++++++ tests/test_task_13.py | 50 +++++++++++++++++++++++++++++ tests/test_task_14.py | 50 +++++++++++++++++++++++++++++ tests/test_task_2.py | 49 +++++++++++++++++++++++++++++ tests/test_task_3.py | 49 +++++++++++++++++++++++++++++ tests/test_task_4.py | 55 ++++++++++++++++++++++++++++++++ tests/test_task_5.py | 49 +++++++++++++++++++++++++++++ tests/test_task_6.py | 49 +++++++++++++++++++++++++++++ tests/test_task_7.py | 49 +++++++++++++++++++++++++++++ tests/test_task_8.py | 50 +++++++++++++++++++++++++++++ tests/test_task_9.py | 49 +++++++++++++++++++++++++++++ 15 files changed, 750 insertions(+), 2 deletions(-) create mode 100644 tests/test_task_1.py create mode 100644 tests/test_task_10.py create mode 100644 tests/test_task_11.py create mode 100644 tests/test_task_12.py create mode 100644 tests/test_task_13.py create mode 100644 tests/test_task_14.py create mode 100644 tests/test_task_2.py create mode 100644 tests/test_task_3.py create mode 100644 tests/test_task_4.py create mode 100644 tests/test_task_5.py create mode 100644 tests/test_task_6.py create mode 100644 tests/test_task_7.py create mode 100644 tests/test_task_8.py create mode 100644 tests/test_task_9.py diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml index 0c41d62a..6e3352f6 100644 --- a/.github/workflows/ci_tests.yml +++ b/.github/workflows/ci_tests.yml @@ -23,6 +23,59 @@ jobs: - name: Checkout repository uses: actions/checkout@v2 - - name: run tests + - name: test task 1 run: | - pytest tests -v --cov=tasks/ --cov-report term --cov-report xml --junitxml=test-reports/junit.xml + pytest tests/test_task_1 -v + + - name: test task 2 + run: | + pytest tests/test_task_2 -v + + - name: test task 3 + run: | + pytest tests/test_task_3 -v + + - name: test task 4 + run: | + pytest tests/test_task_4 -v + + - name: test task 5 + run: | + pytest tests/test_task_5 -v + + - name: test task 6 + run: | + pytest tests/test_task_6 -v + + - name: test task 7 + run: | + pytest tests/test_task_7 -v + + - name: test task 8 + run: | + pytest tests/test_task_8 -v + + - name: test task 9 + run: | + pytest tests/test_task_9 -v + + - name: test task 10 + run: | + pytest tests/test_task_10 -v + + - name: test task 11 + run: | + pytest tests/test_task_11 -v + + - name: test task 12 + run: | + pytest tests/test_task_12 -v + + - name: test task 13 + run: | + pytest tests/test_task_13 -v + + - name: test task 14 + run: | + pytest tests/test_task_14 -v + diff --git a/tests/test_task_1.py b/tests/test_task_1.py new file mode 100644 index 00000000..96426195 --- /dev/null +++ b/tests/test_task_1.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_1(self): + for notebook in Path().rglob("tasks/tasks/task_01_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_10.py b/tests/test_task_10.py new file mode 100644 index 00000000..6ae16201 --- /dev/null +++ b/tests/test_task_10.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_10(self): + for notebook in Path().rglob("tasks/task_10_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_11.py b/tests/test_task_11.py new file mode 100644 index 00000000..490a05c2 --- /dev/null +++ b/tests/test_task_11.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_11(self): + for notebook in Path().rglob("tasks/task_11_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_12.py b/tests/test_task_12.py new file mode 100644 index 00000000..72f764d3 --- /dev/null +++ b/tests/test_task_12.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_12(self): + for notebook in Path().rglob("tasks/task_12_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_13.py b/tests/test_task_13.py new file mode 100644 index 00000000..d85331c2 --- /dev/null +++ b/tests/test_task_13.py @@ -0,0 +1,50 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + +# No module named 'openmc_model' + def test_task_13(self): + for notebook in Path().rglob("tasks/task_13_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_14.py b/tests/test_task_14.py new file mode 100644 index 00000000..a66355d2 --- /dev/null +++ b/tests/test_task_14.py @@ -0,0 +1,50 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + +# No module named 'openmc_model' + def test_task_14(self): + for notebook in Path().rglob("tasks/task_14_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_2.py b/tests/test_task_2.py new file mode 100644 index 00000000..deb003dc --- /dev/null +++ b/tests/test_task_2.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_2(self): + for notebook in Path().rglob("tasks/task_02_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_3.py b/tests/test_task_3.py new file mode 100644 index 00000000..8762c9bd --- /dev/null +++ b/tests/test_task_3.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_3(self): + for notebook in Path().rglob("tasks/task_03_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_4.py b/tests/test_task_4.py new file mode 100644 index 00000000..b2eeb8f5 --- /dev/null +++ b/tests/test_task_4.py @@ -0,0 +1,55 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_4(self): + for notebook in Path().rglob("tasks/task_04_*/1_.ipynb"): + nb, errors = _notebook_run(notebook) + assert errors == [] + for notebook in Path().rglob("tasks/task_04_*/4_.ipynb"): + nb, errors = _notebook_run(notebook) + assert errors == [] +# failing tasks +# 2_ring_source.ipynb -> no ring source in openmc 0.11 +# 3_plasma_source_plots.ipynb -> no ring source in openmc 0.11 +# 5_gamma_source_example.ipynb -> gamma outside of nuclear data energy range diff --git a/tests/test_task_5.py b/tests/test_task_5.py new file mode 100644 index 00000000..21e3f94e --- /dev/null +++ b/tests/test_task_5.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_5(self): + for notebook in Path().rglob("tasks/task_05_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_6.py b/tests/test_task_6.py new file mode 100644 index 00000000..9ca20f7b --- /dev/null +++ b/tests/test_task_6.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_6(self): + for notebook in Path().rglob("tasks/task_06_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_7.py b/tests/test_task_7.py new file mode 100644 index 00000000..15123efd --- /dev/null +++ b/tests/test_task_7.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_7(self): + for notebook in Path().rglob("tasks/task_07_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_8.py b/tests/test_task_8.py new file mode 100644 index 00000000..37735342 --- /dev/null +++ b/tests/test_task_8.py @@ -0,0 +1,50 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + +# ModuleNotFoundError: No module named 'statepoint_to_vtk' + def test_task_8(self): + for notebook in Path().rglob("tasks/task_08_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_9.py b/tests/test_task_9.py new file mode 100644 index 00000000..28cc1057 --- /dev/null +++ b/tests/test_task_9.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_9(self): + for notebook in Path().rglob("tasks/task_09_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] From 59b9b8bfa6c3282bc15d0fc3fbba67f4c1f4e6df Mon Sep 17 00:00:00 2001 From: Jonathan Date: Mon, 24 Jan 2022 22:14:07 +0000 Subject: [PATCH 02/31] removed old test script --- tests/test_all_tasks.py | 136 ---------------------------------------- 1 file changed, 136 deletions(-) delete mode 100644 tests/test_all_tasks.py diff --git a/tests/test_all_tasks.py b/tests/test_all_tasks.py deleted file mode 100644 index a1631c5f..00000000 --- a/tests/test_all_tasks.py +++ /dev/null @@ -1,136 +0,0 @@ - -""" -tests the create_isotope_plot from plotting_utils in the same way the examples -use the function. -""" - -import os -import sys -import unittest -from pathlib import Path - -import nbformat -from nbconvert.preprocessors import ExecutePreprocessor -from nbconvert.preprocessors.execute import CellExecutionError - - -def _notebook_run(path): - """ - Execute a notebook via nbconvert and collect output. - :returns (parsed nb object, execution errors) - """ - kernel_name = 'python%d' % sys.version_info[0] - this_file_directory = os.path.dirname(__file__) - errors = [] - - with open(path) as f: - nb = nbformat.read(f, as_version=4) - nb.metadata.get('kernelspec', {})['name'] = kernel_name - ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True - - try: - ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) - - except CellExecutionError as e: - if "SKIP" in e.traceback: - print(str(e.traceback).split("\n")[-2]) - else: - raise e - - return nb, errors - - -class test_tasks(unittest.TestCase): - - def test_task_1(self): - for notebook in Path().rglob("tasks/tasks/task_01_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_2(self): - for notebook in Path().rglob("tasks/task_02_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_3(self): - for notebook in Path().rglob("tasks/task_03_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_4(self): - for notebook in Path().rglob("tasks/task_04_*/1_.ipynb"): - nb, errors = _notebook_run(notebook) - assert errors == [] - for notebook in Path().rglob("tasks/task_04_*/4_.ipynb"): - nb, errors = _notebook_run(notebook) - assert errors == [] -# failing tasks -# 2_ring_source.ipynb -> no ring source in openmc 0.11 -# 3_plasma_source_plots.ipynb -> no ring source in openmc 0.11 -# 5_gamma_source_example.ipynb -> gamma outside of nuclear data energy range - - def test_task_5(self): - for notebook in Path().rglob("tasks/task_05_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_6(self): - for notebook in Path().rglob("tasks/task_06_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_7(self): - for notebook in Path().rglob("tasks/task_07_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - -# ModuleNotFoundError: No module named 'statepoint_to_vtk' -# def test_task_8(self): -# for notebook in Path().rglob("tasks/task_08_*/*.ipynb"): -# print(notebook) -# nb, errors = _notebook_run(notebook) -# assert errors == [] - - def test_task_9(self): - for notebook in Path().rglob("tasks/task_09_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_10(self): - for notebook in Path().rglob("tasks/task_10_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_11(self): - for notebook in Path().rglob("tasks/task_11_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_12(self): - for notebook in Path().rglob("tasks/task_12_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - -# No module named 'openmc_model' - # def test_task_13(self): - # for notebook in Path().rglob("tasks/task_13_*/*.ipynb"): - # print(notebook) - # nb, errors = _notebook_run(notebook) - # assert errors == [] - -# No module named 'openmc_model' - # def test_task_14(self): - # for notebook in Path().rglob("tasks/task_14_*/*.ipynb"): - # print(notebook) - # nb, errors = _notebook_run(notebook) - # assert errors == [] From ea83bac57085c245bcac1b4ff5a0a7fa1a6fa74d Mon Sep 17 00:00:00 2001 From: Jonathan Date: Mon, 24 Jan 2022 22:14:24 +0000 Subject: [PATCH 03/31] added gmsh to dockerfile --- Dockerfile | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index f7a48f01..a33634c0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -87,9 +87,14 @@ RUN apt-get --yes install libeigen3-dev \ # installing cadquery and jupyter RUN conda install jupyter -y && \ conda install -c conda-forge -c python python=3.8 && \ - conda install -c conda-forge -c cadquery cadquery=2.1 + # conda install -c conda-forge -c cadquery cadquery=2.2 + # commented out until next CQ release + conda install -c conda-forge -c cadquery cadquery=master # cadquery master dose not appear to show the .solid in the notebook +# Installing Gmsh +RUN conda install -c conda-forge gmsh +RUN apt-get install libxft2 # Python libraries used in the workshop RUN pip install cmake\ @@ -235,7 +240,7 @@ RUN cd /opt && \ cmake -Doptimize=on \ -Ddagmc=ON \ -DDAGMC_ROOT=/DAGMC \ - -DHDF5_PREFER_PARALLEL=off .. && \ + -DHDF5_PREFER_PARALLEL=off .. && \ make -j"$compile_cores" && \ make -j"$compile_cores" install && \ cd /opt/openmc/ && \ @@ -254,8 +259,7 @@ ENV OPENMC_CROSS_SECTIONS=/nuclear_data/cross_sections.xml RUN pip install neutronics_material_maker \ openmc-plasma-source \ remove_dagmc_tags \ - paramak \ - cad_to_h5m \ + # paramak \ stl_to_h5m \ openmc-dagmc-wrapper \ openmc-tally-unit-converter \ @@ -265,6 +269,10 @@ RUN pip install neutronics_material_maker \ dagmc_bounding_box \ openmc_mesh_tally_to_vtk +# installing from a branch that is still under development +RUN pip install https://github.com/fusion-energy/paramak/archive/adding_export_h5m_using_brep_gmsh_method.zip + + # an older version of openmc is need to provide an older executable # this particular exectuable allows an inital_source.h5 to be written # a specific openmc executable can be called using model.run(openmc_exec=path) From 686b53f1bce1b695b6b222c50b86bdab03e257cb Mon Sep 17 00:00:00 2001 From: Jonathan Date: Mon, 24 Jan 2022 22:51:43 +0000 Subject: [PATCH 04/31] updated tasks to work with brep gmsh workflow --- .../1_example_tritium_production.ipynb | 2 +- ...ronics_geometry_with_cell_tally_heat.ipynb | 41 +- ...aking_shapes_for_a_3d_mesh_tally_vtk.ipynb | 385 ++++++++++++- ...g_components_for_a_2d_mesh_tally_vtk.ipynb | 540 ++++++++++++++++-- ...r_a_2d_mesh_tally_and_matplotlib_png.ipynb | 79 ++- 5 files changed, 943 insertions(+), 104 deletions(-) diff --git a/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb b/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb index c17c79d1..2c4973a7 100644 --- a/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb +++ b/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb @@ -207,7 +207,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb index 21577890..b08a9047 100644 --- a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb +++ b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb @@ -29,7 +29,8 @@ " major_radius=450.,\n", " triangularity=0.55,\n", " elongation=2.,\n", - " rotation_angle=270\n", + " rotation_angle=180,\n", + " name='plasma'\n", ")\n", "\n", "blanket = paramak.BlanketFP(\n", @@ -38,11 +39,11 @@ " stop_angle=90,\n", " start_angle=-90,\n", " offset_from_plasma=40,\n", - " rotation_angle=270,\n", + " rotation_angle=180,\n", + " name='blanket'\n", ")\n", - "!rm blanket.stl\n", + "\n", "my_reactor = paramak.Reactor([plasma, blanket])\n", - "my_reactor.export_stl(['plasma.stl', 'blanket.stl'])\n", "my_reactor.show()" ] }, @@ -50,15 +51,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This section forms the neutronics model by combining the 3D model, the plasma source and some assigned materials. Additionally, the tallies to record the heating are specified. There are a few different methods of converting a CAD model into a neutronics model. Each method has pros and cons.\n", - "\n", - "The rector can also be converted from stl or stp to h5m format which is the 3D geometry format used by DAGMC to represent neutronics geometry.\n", + "This next code block exports the 3D reactor geometry as a DAGMC compatibile h5m file which can be used as a neutronics geometry. DAGMC is a neutronics code that allows particle transport on CAD geometry with various neutronics transport codes (including OpenMC).\n", "\n", - "stl-to-h5m can convert stl files to a h5m geometry\n", - "https://github.com/fusion-energy/stl_to_h5m\n", + "More details on DAGMC here https://svalinn.github.io/DAGMC/\n", "\n", - "cad-to-h5m can convert stp files to h5m geometry\n", - "https://github.com/fusion-energy/cad_to_h5m" + "This export will take a reasonable amount of time compared to other cells" ] }, { @@ -67,14 +64,8 @@ "metadata": {}, "outputs": [], "source": [ - "from stl_to_h5m import stl_to_h5m\n", "!rm dagmc.h5m\n", - "stl_to_h5m(\n", - " files_with_tags=[\n", - " ('blanket.stl', 'blanket'),\n", - " ],\n", - " h5m_filename='dagmc.h5m',\n", - ")" + "my_reactor.export_dagmc_h5m(filename='dagmc.h5m')" ] }, { @@ -99,7 +90,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The following code makes use of the previously created neutronics geometry (h5m file) and assigns actual materials to the material tags. Sets simulation intensity and specifies the neutronics results to record (know as tallies)." + "This section forms the neutronics model by combining the DAGMC model with a plasma source and some assigned materials. Additionally, the tallies to record the heating are specified. The code block also sets simulation intensity and specifies the neutronics results to record (know as tallies)." ] }, { @@ -111,15 +102,15 @@ "# this links the material tags in the dagmc h5m file with materials.\n", "# these materials are input as strings so they will be looked up in the\n", "# neutronics material maker package\n", - "material_tag_to_material_dict = {\n", - " 'blanket':'Li4SiO4',\n", - "}\n", "\n", - "geometry = odw.Geometry(h5m_filename='dagmc.h5m')\n", + "geometry = odw.Geometry(h5m_filename='dagmc.h5m', reflective_angles=(0, 180))\n", "\n", "materials = odw.Materials(\n", " h5m_filename='dagmc.h5m',\n", - " correspondence_dict=material_tag_to_material_dict\n", + " correspondence_dict={\n", + " 'mat_blanket':'Li4SiO4',\n", + " 'mat_plasma': 'DT_plasma'\n", + " }\n", ")\n", "\n", "tally1 = odw.CellTally(\n", @@ -267,7 +258,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.5" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb index 6e13bc76..0c552a6d 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -64,7 +64,7 @@ " (500, 300),\n", " (600, 20)\n", " ],\n", - " name='plasma',\n", + " name='blanket',\n", " rotation_angle=40,\n", " azimuth_placement_angle=[0, 45, 90, 135, 180, 225, 270, 315],\n", ")" @@ -79,14 +79,229 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Overwriting auto display for cadquery Workplane and Shape\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "3955b2abc1ff4ee8879a1f953ba247f6", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "HBox(children=(VBox(children=(HBox(children=(Checkbox(value=False, description='Axes', indent=False, _dom_clas…" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "my_reactor = paramak.Reactor([blanket, center_column])\n", "\n", - "my_reactor.export_stl()\n", - "\n", "my_reactor.show()" ] }, @@ -94,32 +309,126 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This section forms the neutronics model by combining the 3D model, the plasma source and some assigned materials. Additionally, the tallies to record the heating are specified. There are a few different methods of converting a CAD model into a neutronics model. Each method has pros and cons.\n", - "\n", - "The rector can also be converted from stl or stp to h5m format which is the 3D geometry format used by DAGMC to represent neutronics geometry.\n", - "\n", - "stl-to-h5m can convert stl files to a h5m geometry\n", - "https://github.com/fusion-energy/stl_to_h5m\n", - "\n", - "cad-to-h5m can convert stp files to h5m geometry\n", - "https://github.com/fusion-energy/cad_to_h5m" + "This section forms the neutronics model by combining the 3D model, the plasma source and some assigned materials. Additionally, the tallies to record the heating are specified." ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/jshim/brep_part_finder/brep_part_finder/core.py:75: UserWarning: No parts matching the specified volume +/- tolerances were found\n", + " warnings.warn(\n", + "/home/jshim/brep_part_finder/brep_part_finder/core.py:114: UserWarning: No parts matching the specified bounding boxes were found\n", + " warnings.warn(\"No parts matching the specified bounding boxes were found\")\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "volumes [(3, 1), (3, 2), (3, 3), (3, 4), (3, 5), (3, 6), (3, 7), (3, 8), (3, 9)]\n", + "Info : Meshing 1D...\n", + "Info : [ 0%] Meshing curve 1 (Circle)\n", + "Info : [ 10%] Meshing curve 2 (Circle)\n", + "Info : [ 10%] Meshing curve 3 (Circle)\n", + "Info : [ 10%] Meshing curve 4 (BSpline)\n", + "Info : [ 20%] Meshing curve 5 (Circle)\n", + "Info : [ 20%] Meshing curve 6 (Line)\n", + "Info : [ 20%] Meshing curve 7 (Circle)\n", + "Info : [ 30%] Meshing curve 8 (BSpline)\n", + "Info : [ 30%] Meshing curve 9 (BSpline)\n", + "Info : [ 30%] Meshing curve 10 (Circle)\n", + "Info : [ 40%] Meshing curve 11 (BSpline)\n", + "Info : [ 40%] Meshing curve 12 (BSpline)\n", + "Info : [ 40%] Meshing curve 13 (Circle)\n", + "Info : [ 50%] Meshing curve 14 (BSpline)\n", + "Info : [ 50%] Meshing curve 15 (BSpline)\n", + "Info : [ 50%] Meshing curve 16 (Circle)\n", + "Info : [ 60%] Meshing curve 17 (BSpline)\n", + "Info : [ 60%] Meshing curve 18 (BSpline)\n", + "Info : [ 60%] Meshing curve 19 (Circle)\n", + "Info : [ 70%] Meshing curve 20 (BSpline)\n", + "Info : [ 70%] Meshing curve 21 (BSpline)\n", + "Info : [ 70%] Meshing curve 22 (Circle)\n", + "Info : [ 80%] Meshing curve 23 (BSpline)\n", + "Info : [ 80%] Meshing curve 24 (BSpline)\n", + "Info : [ 80%] Meshing curve 25 (Circle)\n", + "Info : [ 90%] Meshing curve 26 (BSpline)\n", + "Info : [ 90%] Meshing curve 27 (BSpline)\n", + "Info : [ 90%] Meshing curve 28 (Circle)\n", + "Info : [100%] Meshing curve 29 (BSpline)\n", + "Info : [100%] Meshing curve 30 (BSpline)\n", + "Info : Done meshing 1D (Wall 0.55192s, CPU 0.556843s)\n", + "Info : Meshing 2D...\n", + "Info : [ 0%] Meshing surface 1 (Plane, MeshAdapt)\n", + "Info : [ 10%] Meshing surface 2 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 10%] Meshing surface 3 (Plane, MeshAdapt)\n", + "Info : [ 20%] Meshing surface 4 (Cylinder, MeshAdapt)\n", + "Info : [ 20%] Meshing surface 5 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 20%] Meshing surface 6 (Plane, MeshAdapt)\n", + "Info : [ 30%] Meshing surface 7 (Plane, MeshAdapt)\n", + "Info : [ 30%] Meshing surface 8 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 30%] Meshing surface 9 (Plane, MeshAdapt)\n", + "Info : [ 40%] Meshing surface 10 (Plane, MeshAdapt)\n", + "Info : [ 40%] Meshing surface 11 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 40%] Meshing surface 12 (Plane, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 13 (Plane, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 14 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 15 (Plane, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 16 (Plane, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 17 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 18 (Plane, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 19 (Plane, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 20 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 21 (Plane, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 22 (Plane, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 23 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 24 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 25 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 26 (Surface of Revolution, MeshAdapt)\n", + "Info : [100%] Meshing surface 27 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 28 (Plane, MeshAdapt)\n", + "Info : Done meshing 2D (Wall 32.0506s, CPU 32.0513s)\n", + "Info : 24134 nodes 49889 elements\n", + "Info : Writing '/tmp/volume_17r9qtjfn.stl'...\n", + "Info : Done writing '/tmp/volume_17r9qtjfn.stl'\n", + "Info : Writing '/tmp/volume_2hfxtjt03.stl'...\n", + "Info : Done writing '/tmp/volume_2hfxtjt03.stl'\n", + "Info : Writing '/tmp/volume_3qlwtchp4.stl'...\n", + "Info : Done writing '/tmp/volume_3qlwtchp4.stl'\n", + "Info : Writing '/tmp/volume_4_omz93ti.stl'...\n", + "Info : Done writing '/tmp/volume_4_omz93ti.stl'\n", + "Info : Writing '/tmp/volume_5w5mf0r2n.stl'...\n", + "Info : Done writing '/tmp/volume_5w5mf0r2n.stl'\n", + "Info : Writing '/tmp/volume_67oxaamie.stl'...\n", + "Info : Done writing '/tmp/volume_67oxaamie.stl'\n", + "Info : Writing '/tmp/volume_71rvjpx0x.stl'...\n", + "Info : Done writing '/tmp/volume_71rvjpx0x.stl'\n", + "Info : Writing '/tmp/volume_88vts1mml.stl'...\n", + "Info : Done writing '/tmp/volume_88vts1mml.stl'\n", + "Info : Writing '/tmp/volume_95chc2uth.stl'...\n", + "Info : Done writing '/tmp/volume_95chc2uth.stl'\n", + "file /tmp/volume_17r9qtjfn.stl is watertight True\n" + ] + }, + { + "data": { + "text/plain": [ + "'dagmc.h5m'" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "from stl_to_h5m import stl_to_h5m\n", - "\n", - "stl_to_h5m(\n", - " files_with_tags=[\n", - " ('plasma.stl', 'mat_plasma'),\n", - " ('center_column.stl', 'mat_center_column')\n", - " ],\n", - " h5m_filename='dagmc.h5m',\n", - ")" + "my_reactor.export_dagmc_h5m()" ] }, { @@ -131,9 +440,23 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, - "outputs": [], + "outputs": [ + { + "ename": "ValueError", + "evalue": "material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column'].", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m/tmp/ipykernel_66164/1142178510.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[0mgeometry\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0modw\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGeometry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 18\u001b[0;31m materials = odw.Materials(\n\u001b[0m\u001b[1;32m 19\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 20\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmaterial_tag_to_material_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, h5m_filename, correspondence_dict)\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcorrespondence_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mh5m_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 24\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchecks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 25\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_openmc_materials\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopenmc_materials\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36mchecks\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;34mf\"contains the following material tags {materials_in_h5m}.\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 55\u001b[0m )\n\u001b[0;32m---> 56\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 57\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m\"graveyard\"\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mmaterials_in_h5m\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column']." + ] + } + ], "source": [ "# makes use of the previously created neutronics geometry (h5m file) and assigns\n", "# actual materials to the material tags. \n", @@ -146,7 +469,7 @@ "# these materials are input as strings so they will be looked up in the\n", "# neutronics material maker package\n", "material_tag_to_material_dict = {\n", - " 'mat_plasma': nmm.Material.from_library(name='DT_plasma'),\n", + " 'mat_blanket': nmm.Material.from_library(name='DT_plasma'),\n", " 'mat_center_column': nmm.Material.from_library(name='Li4SiO4'),\n", "}\n", "\n", @@ -293,7 +616,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb index ae1225a0..2a00f153 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -46,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -68,7 +68,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -92,9 +92,226 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Overwriting auto display for cadquery Workplane and Shape\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "8104656955214838ab77ce2008ab30a8", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "HBox(children=(VBox(children=(HBox(children=(Checkbox(value=False, description='Axes', indent=False, _dom_clas…" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "my_reactor = paramak.Reactor([blanket, pf_coil,center_column])\n", "\n", @@ -110,20 +327,48 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32;1m\n", + "*******************************************************************\n", + "****** Statistics on Transfer (Write) ******\u001b[0m\n", + "\u001b[32;1m\n", + "*******************************************************************\n", + "****** Transfer Mode = 0 I.E. As Is ******\u001b[0m\n", + "\u001b[32;1m****** Transferring Shape, ShapeType = 0 ******\u001b[0m\n" + ] + }, + { + "data": { + "text/html": [ + "my_reactor.stp
" + ], + "text/plain": [ + "/home/jshim/neutronics-workshop/tasks/task_12_CAD_mesh_fast_flux/my_reactor.stp" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32;1m** WorkSession : Sending all data\u001b[0m\n", + "\u001b[32;1m Step File Name : my_reactor.stp(3447 ents) Write Done\u001b[0m\n" + ] + } + ], "source": [ - "my_reactor.export_stp()\n", - "my_reactor.export_stl()\n", + "my_reactor.export_stp('my_reactor.stp')\n", "\n", "from IPython.display import FileLink\n", - "display(FileLink('blanket.stp'))\n", - "display(FileLink('pf_coil.stp'))\n", - "display(FileLink('center_column.stp'))\n", - "display(FileLink('blanket.stl'))\n", - "display(FileLink('pf_coil.stl'))\n", - "display(FileLink('center_column.stl'))" + "display(FileLink('my_reactor.stp'))" ] }, { @@ -135,20 +380,219 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/jshim/brep_part_finder/brep_part_finder/core.py:75: UserWarning: No parts matching the specified volume +/- tolerances were found\n", + " warnings.warn(\n", + "/home/jshim/brep_part_finder/brep_part_finder/core.py:114: UserWarning: No parts matching the specified bounding boxes were found\n", + " warnings.warn(\"No parts matching the specified bounding boxes were found\")\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Info : Meshing 1D...\n", + "Info : [ 0%] Meshing curve 1 (Circle)\n", + "Info : [ 10%] Meshing curve 2 (Circle)\n", + "Info : [ 10%] Meshing curve 3 (Line)\n", + "Info : [ 10%] Meshing curve 4 (Circle)\n", + "Info : [ 10%] Meshing curve 5 (Circle)\n", + "Info : [ 10%] Meshing curve 6 (Line)\n", + "Info : [ 10%] Meshing curve 7 (Circle)\n", + "Info : [ 10%] Meshing curve 8 (Line)\n", + "Info : [ 10%] Meshing curve 9 (Circle)\n", + "Info : [ 10%] Meshing curve 10 (Circle)\n", + "Info : [ 10%] Meshing curve 11 (Circle)\n", + "Info : [ 20%] Meshing curve 12 (BSpline)\n", + "Info : [ 20%] Meshing curve 13 (Circle)\n", + "Info : [ 20%] Meshing curve 14 (Circle)\n", + "Info : [ 20%] Meshing curve 15 (Circle)\n", + "Info : [ 20%] Meshing curve 16 (Circle)\n", + "Info : [ 20%] Meshing curve 17 (Circle)\n", + "Info : [ 20%] Meshing curve 18 (Line)\n", + "Info : [ 20%] Meshing curve 19 (Line)\n", + "Info : [ 20%] Meshing curve 20 (Circle)\n", + "Info : [ 20%] Meshing curve 21 (Circle)\n", + "Info : [ 20%] Meshing curve 22 (Circle)\n", + "Info : [ 30%] Meshing curve 23 (Line)\n", + "Info : [ 30%] Meshing curve 24 (Line)\n", + "Info : [ 30%] Meshing curve 25 (Circle)\n", + "Info : [ 30%] Meshing curve 26 (Circle)\n", + "Info : [ 30%] Meshing curve 27 (Circle)\n", + "Info : [ 30%] Meshing curve 28 (Circle)\n", + "Info : [ 30%] Meshing curve 29 (Circle)\n", + "Info : [ 30%] Meshing curve 30 (Line)\n", + "Info : [ 30%] Meshing curve 31 (Line)\n", + "Info 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MeshAdapt)\n", + "Info : [ 40%] Meshing surface 23 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 24 (Plane, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 25 (Plane, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 26 (Plane, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 27 (Sphere, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 28 (Plane, MeshAdapt)\n", + "Info : [ 50%] Meshing surface 29 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 30 (Plane, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 31 (Plane, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 32 (Plane, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 33 (Sphere, MeshAdapt)\n", + "Info : [ 60%] Meshing surface 34 (Plane, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 35 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 36 (Plane, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 37 (Plane, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 38 (Plane, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 39 (Sphere, MeshAdapt)\n", + "Info : [ 70%] Meshing surface 40 (Plane, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 41 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 42 (Plane, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 43 (Plane, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 44 (Plane, MeshAdapt)\n", + "Info : [ 80%] Meshing surface 45 (Sphere, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 46 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 47 (Surface of Revolution, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 48 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 49 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 50 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 51 (Sphere, MeshAdapt)\n", + "Info : [100%] Meshing surface 52 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 53 (Surface of Revolution, MeshAdapt)\n", + "Info : [100%] Meshing surface 54 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 55 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 56 (Plane, MeshAdapt)\n", + "Info : Done meshing 2D (Wall 14.6143s, CPU 14.6311s)\n", + "Info : 24024 nodes 50983 elements\n", + "Info : Writing '/tmp/volume_1_yuxossg.stl'...\n", + "Info : Done writing '/tmp/volume_1_yuxossg.stl'\n", + "Info : Writing '/tmp/volume_2d72ej6m7.stl'...\n", + "Info : Done writing '/tmp/volume_2d72ej6m7.stl'\n", + "Info : Writing '/tmp/volume_3eseweav4.stl'...\n", + "Info : Done writing '/tmp/volume_3eseweav4.stl'\n", + "Info : Writing '/tmp/volume_4fw4s7z6v.stl'...\n", + "Info : Done writing '/tmp/volume_4fw4s7z6v.stl'\n", + "Info : Writing '/tmp/volume_5v8kkgwcd.stl'...\n", + "Info : Done writing '/tmp/volume_5v8kkgwcd.stl'\n", + "Info : Writing '/tmp/volume_6ri1kpiz5.stl'...\n", + "Info : Done writing '/tmp/volume_6ri1kpiz5.stl'\n", + "Info : Writing '/tmp/volume_77467y6bm.stl'...\n", + "Info : Done writing '/tmp/volume_77467y6bm.stl'\n", + "Info : Writing '/tmp/volume_8bn6d5kqs.stl'...\n", + "Info : Done writing '/tmp/volume_8bn6d5kqs.stl'\n", + "Info : Writing '/tmp/volume_9jglwod6q.stl'...\n", + "Info : Done writing '/tmp/volume_9jglwod6q.stl'\n", + "Info : Writing '/tmp/volume_10udltgkpa.stl'...\n", + "Info : Done writing '/tmp/volume_10udltgkpa.stl'\n", + "file /tmp/volume_1_yuxossg.stl is watertight True\n", + "file /tmp/volume_2d72ej6m7.stl is watertight True\n" + ] + } + ], "source": [ - "from stl_to_h5m import stl_to_h5m\n", - "\n", - "stl_to_h5m(\n", - " files_with_tags=[\n", - " ('pf_coil.stl', 'mat_pf_coil'),\n", - " ('blanket.stl', 'mat_blanket'),\n", - " ('center_column.stl', 'mat_center_column')\n", - " ],\n", - " h5m_filename='dagmc.h5m',\n", - ")\n", + "my_reactor.export_dagmc_h5m('dagmc.h5m')\n", "\n", "import openmc_dagmc_wrapper as odw\n", "geometry = odw.Geometry(h5m_filename='dagmc.h5m')" @@ -167,9 +611,33 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/jshim/openmc-1/openmc/mixin.py:67: IDWarning: Another Surface instance already exists with id=9999.\n", + " warn(msg, IDWarning)\n", + "/home/jshim/openmc-1/openmc/mixin.py:67: IDWarning: Another Cell instance already exists with id=9999.\n", + " warn(msg, IDWarning)\n" + ] + }, + { + "ename": "ValueError", + "evalue": "material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column', 'mat_pf_coil'].", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m/tmp/ipykernel_66680/499989040.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[0mgeometry\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0modw\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGeometry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 18\u001b[0;31m materials = odw.Materials(\n\u001b[0m\u001b[1;32m 19\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 20\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmaterial_tag_to_material_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, h5m_filename, correspondence_dict)\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcorrespondence_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mh5m_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 24\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchecks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 25\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_openmc_materials\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopenmc_materials\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36mchecks\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;34mf\"contains the following material tags {materials_in_h5m}.\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 55\u001b[0m )\n\u001b[0;32m---> 56\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 57\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m\"graveyard\"\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mmaterials_in_h5m\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column', 'mat_pf_coil']." + ] + } + ], "source": [ "# makes use of the previously created neutronics geometry (h5m file) and assigns\n", "# actual materials to the material tags. \n", @@ -324,13 +792,10 @@ ] }, { - "cell_type": "code", - "execution_count": null, + "cell_type": "markdown", "metadata": {}, - "outputs": [], "source": [ - "from IPython.display import FileLink\n", - "display(FileLink('n,Xa)_on_2D_mesh_xz.vtk'))\n" + "The code block below provides a download link for a VTK which can be opened with Paraview\n" ] }, { @@ -338,7 +803,10 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "from IPython.display import FileLink\n", + "display(FileLink('n,Xa)_on_2D_mesh_xz.vtk'))" + ] } ], "metadata": { @@ -357,7 +825,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb index 74a5564e..9c661031 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb @@ -63,7 +63,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The next section defines the materials. This can be done using openmc.Materials or in this case strings that look up materials from the neutronics material maker." + "Exports the 3D geometry to a DAGMC neutronics geometry. The plasma is not included as not many neutron interactions occur in the low density plasma" ] }, { @@ -72,13 +72,7 @@ "metadata": {}, "outputs": [], "source": [ - "my_reactor.export_stp()\n", - "\n", - "from IPython.display import FileLink\n", - "display(FileLink('blanket.stp'))\n", - "display(FileLink('pf_coil.stp'))\n", - "display(FileLink('center_column.stp'))\n", - "display(FileLink('Graveyard.stp'))" + "my_reactor.export_dagmc_h5m('dagmc.h5m', exclude='plasma')" ] }, { @@ -100,7 +94,50 @@ "\n", "mat2 = Material.from_library(name='copper')\n", "\n", - "mat3 = Material.from_library(name='WC')" + "mat3 = Material.from_library(name='WC')\n", + "\n", + "mat4 = Material.from_library(name='eurofer')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This next section combines the geometry with the materials and specifies a few mesh tallies" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# makes use of the previously created neutronics geometry (h5m file) and assigns\n", + "# actual materials to the material tags. \n", + "\n", + "import openmc_dagmc_wrapper as odw\n", + "import neutronics_material_maker as nmm\n", + "\n", + "# this links the material tags in the dagmc h5m file with materials.\n", + "# these materials are input as strings so they will be looked up in the\n", + "# neutronics material maker package\n", + "material_tag_to_material_dict = {\n", + " 'mat_blanket': mat1,\n", + " 'mat_blanket_rear_wall':mat4,\n", + " 'mat_center_column_shield':mat3,\n", + " 'mat_divertor_lower':mat4,\n", + " 'mat_divertor_upper':mat4,\n", + " 'mat_firstwall':mat4,\n", + " 'mat_inboard_tf_coils':mat2,\n", + " 'mat_plasma':mat2 # todo remove\n", + "}\n", + "\n", + "geometry = odw.Geometry(h5m_filename='dagmc.h5m')\n", + "\n", + "materials = odw.Materials(\n", + " h5m_filename='dagmc.h5m',\n", + " correspondence_dict=material_tag_to_material_dict\n", + ")" ] }, { @@ -116,6 +153,7 @@ "metadata": {}, "outputs": [], "source": [ + "\n", "import openmc\n", "\n", "# initialises a new source object\n", @@ -135,7 +173,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This next section combines the geometry with the materials and specifies a few mesh tallies" + "Makes a 3D mesh tally" ] }, { @@ -143,8 +181,27 @@ "execution_count": null, "metadata": {}, "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "starts the simulation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, "source": [ - "#todo add mesh tallies, settings and run simulation" + "extracts the 3d mesh tally result and plots it as a vtk" ] }, { From 8bfda682c0611580abd9e34d77ce3f46f8aa1678 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Tue, 25 Jan 2022 09:04:35 +0000 Subject: [PATCH 05/31] seperate tests --- .circleci/config.yml | 59 ++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 54 insertions(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 054aeb46..699b00de 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -20,12 +20,61 @@ jobs: steps: - checkout + # - run: + # name: run tests + # no_output_timeout: 30m + # command: | + # cd .. + # pytest repo/tests -v + + - run: + name: test task 1 + command: pytest tests/test_task_1 -v + - run: + name: test task 2 + command: pytest tests/test_task_2 -v + - run: + name: test task 3 + command: pytest tests/test_task_3 -v + - run: + name: test task 4 + command: pytest tests/test_task_4 -v + - run: + name: test task 5 + command: pytest tests/test_task_5 -v + - run: + name: test task 6 + command: pytest tests/test_task_6 -v + - run: + name: test task 7 + command: pytest tests/test_task_7 -v + - run: + name: test task 8 + command: pytest tests/test_task_8 -v + - run: + name: test task 9 + command: pytest tests/test_task_9 -v - run: - name: run tests - no_output_timeout: 30m - command: | - cd .. - pytest repo/tests -v --cov=tasks/ --cov-report term --cov-report xml --junitxml=test-reports/junit.xml + name: test task 10 + command: pytest tests/test_task_10 -v + - run: + name: test task 11 + command: pytest tests/test_task_11 -v + - run: + name: test task 12 + command: pytest tests/test_task_12 -v + - run: + name: test task 13 + command: pytest tests/test_task_13 -v + - run: + name: test task 14 + command: pytest tests/test_task_14 -v + + + + + + - store_test_results: path: test-reports - store_artifacts: From 7ff7a060d8d7bbcdd31686af5680c8b37309f2b7 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Tue, 25 Jan 2022 09:06:48 +0000 Subject: [PATCH 06/31] changed file path for tests --- .circleci/config.yml | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 699b00de..bdc9e848 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -29,46 +29,46 @@ jobs: - run: name: test task 1 - command: pytest tests/test_task_1 -v + command: pytest tests/test_task_1.py -v - run: name: test task 2 - command: pytest tests/test_task_2 -v + command: pytest tests/test_task_2.py -v - run: name: test task 3 - command: pytest tests/test_task_3 -v + command: pytest tests/test_task_3.py -v - run: name: test task 4 - command: pytest tests/test_task_4 -v + command: pytest tests/test_task_4.py -v - run: name: test task 5 - command: pytest tests/test_task_5 -v + command: pytest tests/test_task_5.py -v - run: name: test task 6 - command: pytest tests/test_task_6 -v + command: pytest tests/test_task_6.py -v - run: name: test task 7 - command: pytest tests/test_task_7 -v + command: pytest tests/test_task_7.py -v - run: name: test task 8 - command: pytest tests/test_task_8 -v + command: pytest tests/test_task_8.py -v - run: name: test task 9 - command: pytest tests/test_task_9 -v + command: pytest tests/test_task_9.py -v - run: name: test task 10 - command: pytest tests/test_task_10 -v + command: pytest tests/test_task_10.py -v - run: name: test task 11 - command: pytest tests/test_task_11 -v + command: pytest tests/test_task_11.py -v - run: name: test task 12 - command: pytest tests/test_task_12 -v + command: pytest tests/test_task_12.py -v - run: name: test task 13 - command: pytest tests/test_task_13 -v + command: pytest tests/test_task_13.py -v - run: name: test task 14 - command: pytest tests/test_task_14 -v + command: pytest tests/test_task_14.py -v From f3539fc17589729fd5efaba2d15be6699d1c0eda Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Tue, 25 Jan 2022 09:15:36 +0000 Subject: [PATCH 07/31] [skip ci] tidy up testing files --- .circleci/config.yml | 17 ----------------- .github/workflows/ci_tests.yml | 28 ++++++++++++++-------------- 2 files changed, 14 insertions(+), 31 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index bdc9e848..d088a560 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -20,13 +20,6 @@ jobs: steps: - checkout - # - run: - # name: run tests - # no_output_timeout: 30m - # command: | - # cd .. - # pytest repo/tests -v - - run: name: test task 1 command: pytest tests/test_task_1.py -v @@ -69,13 +62,3 @@ jobs: - run: name: test task 14 command: pytest tests/test_task_14.py -v - - - - - - - - store_test_results: - path: test-reports - - store_artifacts: - path: test-reports diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml index 6e3352f6..dd69b5c9 100644 --- a/.github/workflows/ci_tests.yml +++ b/.github/workflows/ci_tests.yml @@ -25,57 +25,57 @@ jobs: - name: test task 1 run: | - pytest tests/test_task_1 -v + pytest tests/test_task_1.py -v - name: test task 2 run: | - pytest tests/test_task_2 -v + pytest tests/test_task_2.py -v - name: test task 3 run: | - pytest tests/test_task_3 -v + pytest tests/test_task_3.py -v - name: test task 4 run: | - pytest tests/test_task_4 -v + pytest tests/test_task_4.py -v - name: test task 5 run: | - pytest tests/test_task_5 -v + pytest tests/test_task_5.py -v - name: test task 6 run: | - pytest tests/test_task_6 -v + pytest tests/test_task_6.py -v - name: test task 7 run: | - pytest tests/test_task_7 -v + pytest tests/test_task_7.py -v - name: test task 8 run: | - pytest tests/test_task_8 -v + pytest tests/test_task_8.py -v - name: test task 9 run: | - pytest tests/test_task_9 -v + pytest tests/test_task_9.py -v - name: test task 10 run: | - pytest tests/test_task_10 -v + pytest tests/test_task_10.py -v - name: test task 11 run: | - pytest tests/test_task_11 -v + pytest tests/test_task_11.py -v - name: test task 12 run: | - pytest tests/test_task_12 -v + pytest tests/test_task_12.py -v - name: test task 13 run: | - pytest tests/test_task_13 -v + pytest tests/test_task_13.py -v - name: test task 14 run: | - pytest tests/test_task_14 -v + pytest tests/test_task_14.py -v From 0636d2f584441e2679264f6ac5f6d2a3c39be82f Mon Sep 17 00:00:00 2001 From: Jonathan Date: Wed, 26 Jan 2022 20:21:54 +0000 Subject: [PATCH 08/31] using updated openmc-source-plotter api --- Dockerfile | 2 +- .../1_point_source_plots.ipynb | 100 ++++++++---------- .../task_04_make_sources/2_ring_source.ipynb | 16 +-- .../3_plasma_source_plots.ipynb | 18 +++- .../5_gamma_source_example.ipynb | 25 +++-- 5 files changed, 81 insertions(+), 80 deletions(-) diff --git a/Dockerfile b/Dockerfile index f7a48f01..158a5f96 100644 --- a/Dockerfile +++ b/Dockerfile @@ -261,8 +261,8 @@ RUN pip install neutronics_material_maker \ openmc-tally-unit-converter \ regular_mesh_plotter \ spectrum_plotter \ - openmc_source_plotter \ dagmc_bounding_box \ + openmc_source_plotter \ openmc_mesh_tally_to_vtk # an older version of openmc is need to provide an older executable diff --git a/tasks/task_04_make_sources/1_point_source_plots.ipynb b/tasks/task_04_make_sources/1_point_source_plots.ipynb index c9486ea9..7887a18d 100644 --- a/tasks/task_04_make_sources/1_point_source_plots.ipynb +++ b/tasks/task_04_make_sources/1_point_source_plots.ipynb @@ -13,33 +13,9 @@ }, { "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/jshimwell/miniconda3/envs/openmc-dagmc/lib/python3.8/site-packages/IPython/core/display.py:724: UserWarning:\n", - "\n", - "Consider using IPython.display.IFrame instead\n", - "\n" - ] - }, - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "from IPython.display import HTML\n", "HTML('')" @@ -68,16 +44,16 @@ "outputs": [], "source": [ "# initialises a new source object\n", - "source = openmc.Source()\n", + "my_source = openmc.Source()\n", "\n", "# sets the location of the source to x=0 y=0 z=0\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", + "my_source.space = openmc.stats.Point((0, 0, 0))\n", "\n", "# sets the direction to isotropic\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source.angle = openmc.stats.Isotropic()\n", "\n", "# sets the energy distribution to 100% 14MeV neutrons\n", - "source.energy = openmc.stats.Discrete([14e6], [1])" + "my_source.energy = openmc.stats.Discrete([14e6], [1])" ] }, { @@ -95,8 +71,10 @@ "source": [ "import openmc_source_plotter as osp\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -112,16 +90,18 @@ "metadata": {}, "outputs": [], "source": [ - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source_2 = openmc.Source()\n", + "my_source_2.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_2.angle = openmc.stats.Isotropic()\n", "\n", "# Documentation on the Watt distribution is here\n", "# https://docs.openmc.org/en/stable/pythonapi/generated/openmc.data.WattEnergy.html\n", "source.energy = openmc.stats.Watt(a=988000.0, b=2.249e-06)\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source_2,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -137,16 +117,18 @@ "metadata": {}, "outputs": [], "source": [ - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source_3 = openmc.Source()\n", + "my_source_3.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_3.angle = openmc.stats.Isotropic()\n", "\n", "# Documentation on the Muir distribution is here\n", "# https://docs.openmc.org/en/stable/pythonapi/generated/openmc.stats.Muir.html\n", - "source.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)\n", + "my_source_3.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source_3,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -163,13 +145,15 @@ "outputs": [], "source": [ "# Creates an isotropic point source with monoenergetic 14MeV neutrons\n", - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", - "source.energy = openmc.stats.Discrete([14e6], [1])\n", + "my_source_4 = openmc.Source()\n", + "my_source_4.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_4.angle = openmc.stats.Isotropic()\n", + "my_source_4.energy = openmc.stats.Discrete([14e6], [1])\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_position_from_initial_source()" + "osp.plot_source_position(\n", + " source=my_source_4,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -186,13 +170,15 @@ "outputs": [], "source": [ "# Creates an isotropic point source with monoenergetic 14MeV neutrons\n", - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", - "source.energy = openmc.stats.Discrete([14e6], [1])\n", + "my_source_5 = openmc.Source()\n", + "my_source_5.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_5.angle = openmc.stats.Isotropic()\n", + "my_source_5.energy = openmc.stats.Discrete([14e6], [1])\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_direction_from_initial_source()" + "osp.plot_source_direction(\n", + " source=my_source_5,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -229,7 +215,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/2_ring_source.ipynb b/tasks/task_04_make_sources/2_ring_source.ipynb index 8fcfe1fe..31ddc070 100644 --- a/tasks/task_04_make_sources/2_ring_source.ipynb +++ b/tasks/task_04_make_sources/2_ring_source.ipynb @@ -44,7 +44,7 @@ "import openmc\n", "\n", "# initialises a new source object\n", - "source = openmc.Source()\n", + "my_source = openmc.Source()\n", "\n", "# the distribution of radius is just a single value\n", "radius = openmc.stats.Discrete([10], [1])\n", @@ -56,13 +56,13 @@ "angle = openmc.stats.Uniform(a=0., b=2* 3.14159265359)\n", "\n", "# this makes the ring source using the three distributions and a radius\n", - "source.space = openmc.stats.CylindricalIndependent(r=radius, phi=angle, z=z_values, origin=(0.0, 0.0, 0.0))\n", + "my_source.space = openmc.stats.CylindricalIndependent(r=radius, phi=angle, z=z_values, origin=(0.0, 0.0, 0.0))\n", "\n", "# sets the direction to isotropic\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source.angle = openmc.stats.Isotropic()\n", "\n", "# sets the energy distribution to a Muir distribution neutrons\n", - "source.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)" + "my_source.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)" ] }, { @@ -80,8 +80,10 @@ "source": [ "import openmc_source_plotter as osp\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_position_from_initial_source()" + "osp.plot_source_position(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -116,7 +118,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb index 859510b7..143da136 100644 --- a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb +++ b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb @@ -74,8 +74,10 @@ "source": [ "import openmc_source_plotter as osp\n", "\n", - "osp.create_initial_particles(my_source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -91,7 +93,10 @@ "metadata": {}, "outputs": [], "source": [ - "osp.plot_position_from_initial_source()" + "osp.plot_source_position(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -107,7 +112,10 @@ "metadata": {}, "outputs": [], "source": [ - "osp.plot_direction_from_initial_source()" + "osp.plot_source_direction(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -136,7 +144,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.5" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/5_gamma_source_example.ipynb b/tasks/task_04_make_sources/5_gamma_source_example.ipynb index bce6e156..e110f202 100644 --- a/tasks/task_04_make_sources/5_gamma_source_example.ipynb +++ b/tasks/task_04_make_sources/5_gamma_source_example.ipynb @@ -15,7 +15,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -54,18 +54,18 @@ "outputs": [], "source": [ "# initialises a new source object\n", - "source = openmc.Source()\n", + "my_source = openmc.Source()\n", "\n", "# sets the location of the source to x=0 y=0 z=0\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", + "my_source.space = openmc.stats.Point((0, 0, 0))\n", "\n", "# sets the direction to isotropic\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source.angle = openmc.stats.Isotropic()\n", "\n", "# sets the energy distribution to 50% 1.1MeV photons and 50% 1.3MeV photons\n", - "source.energy = openmc.stats.Discrete([1.1732e6,1.3325e6], [0.5, 0.5])\n", + "my_source.energy = openmc.stats.Discrete([1.1732e6,1.3325e6], [0.5, 0.5])\n", "\n", - "source.particle = 'photon'" + "my_source.particle = 'photon'" ] }, { @@ -86,9 +86,14 @@ "import openmc_source_plotter as osp\n", "\n", "# number_of_particles can be increased to sample more particles\n", - "osp.create_initial_particles(source, number_of_particles=1000, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "# this time we are setting the number of energy bins for the plot\n", - "osp.plot_energy_from_initial_source(energy_bins=np.linspace(0, 2e6, 50))" + "osp.plot_source_energy(\n", + " source=my_source,\n", + " number_of_particles=1000\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc',\n", + " energy_bins=np.linspace(0, 2e6, 50)\n", + ")\n", + "\n", + "# this time we are setting the number of energy bins for the plot\n" ] }, { @@ -125,7 +130,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, From 01bef62ffbcf82c717f68e36abe0ec04f98a6fc2 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Wed, 26 Jan 2022 20:50:55 +0000 Subject: [PATCH 09/31] types noticed after local testing --- Dockerfile | 2 ++ tasks/task_04_make_sources/1_point_source_plots.ipynb | 4 ++-- tasks/task_04_make_sources/2_ring_source.ipynb | 2 +- tasks/task_04_make_sources/3_plasma_source_plots.ipynb | 2 +- tasks/task_04_make_sources/4_neutron_tracks.ipynb | 2 +- tasks/task_04_make_sources/5_gamma_source_example.ipynb | 5 +++-- 6 files changed, 10 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 158a5f96..31f856bf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -29,6 +29,8 @@ # for local testing I tend to use this build command # docker build -t neutronics-workshop --build-arg compile_cores=14 --build-arg build_double_down=ON . +# and then run with this command +# docker run -p 8888:8888 neutronics-workshop # This can't be done currently as the base images uses conda installs for moab / dagmc which don't compile with OpenMC FROM ghcr.io/openmc-data-storage/miniconda3_4.9.2_endfb-7.1_nndc_tendl_2019:latest as dependencies diff --git a/tasks/task_04_make_sources/1_point_source_plots.ipynb b/tasks/task_04_make_sources/1_point_source_plots.ipynb index 7887a18d..78145915 100644 --- a/tasks/task_04_make_sources/1_point_source_plots.ipynb +++ b/tasks/task_04_make_sources/1_point_source_plots.ipynb @@ -96,7 +96,7 @@ "\n", "# Documentation on the Watt distribution is here\n", "# https://docs.openmc.org/en/stable/pythonapi/generated/openmc.data.WattEnergy.html\n", - "source.energy = openmc.stats.Watt(a=988000.0, b=2.249e-06)\n", + "my_source_2.energy = openmc.stats.Watt(a=988000.0, b=2.249e-06)\n", "\n", "osp.plot_source_energy(\n", " source=my_source_2,\n", @@ -215,7 +215,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/2_ring_source.ipynb b/tasks/task_04_make_sources/2_ring_source.ipynb index 31ddc070..9143423a 100644 --- a/tasks/task_04_make_sources/2_ring_source.ipynb +++ b/tasks/task_04_make_sources/2_ring_source.ipynb @@ -118,7 +118,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb index 143da136..a70eafb4 100644 --- a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb +++ b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb @@ -144,7 +144,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/4_neutron_tracks.ipynb b/tasks/task_04_make_sources/4_neutron_tracks.ipynb index affe6ab8..0314035d 100644 --- a/tasks/task_04_make_sources/4_neutron_tracks.ipynb +++ b/tasks/task_04_make_sources/4_neutron_tracks.ipynb @@ -204,7 +204,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/5_gamma_source_example.ipynb b/tasks/task_04_make_sources/5_gamma_source_example.ipynb index e110f202..c8ece5c7 100644 --- a/tasks/task_04_make_sources/5_gamma_source_example.ipynb +++ b/tasks/task_04_make_sources/5_gamma_source_example.ipynb @@ -84,11 +84,12 @@ "outputs": [], "source": [ "import openmc_source_plotter as osp\n", + "import numpy as np\n", "\n", "# number_of_particles can be increased to sample more particles\n", "osp.plot_source_energy(\n", " source=my_source,\n", - " number_of_particles=1000\n", + " number_of_particles=1000,\n", " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc',\n", " energy_bins=np.linspace(0, 2e6, 50)\n", ")\n", @@ -130,7 +131,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.9.5" } }, "nbformat": 4, From 5238896076be4030d807e919f1e136d19e773976 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Wed, 26 Jan 2022 23:12:16 +0000 Subject: [PATCH 10/31] switched to 3d mesh --- ...g_components_for_a_2d_mesh_tally_vtk.ipynb | 279 +++++++++++++----- 1 file changed, 204 insertions(+), 75 deletions(-) diff --git a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb index 2a00f153..2ffe72fa 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb @@ -105,7 +105,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "8104656955214838ab77ce2008ab30a8", + "model_id": "ecdb600c1f354e3ba931520b5c5e7764", "version_major": 2, "version_minor": 0 }, @@ -304,7 +304,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 4, @@ -340,7 +340,9 @@ "\u001b[32;1m\n", "*******************************************************************\n", "****** Transfer Mode = 0 I.E. As Is ******\u001b[0m\n", - "\u001b[32;1m****** Transferring Shape, ShapeType = 0 ******\u001b[0m\n" + "\u001b[32;1m****** Transferring Shape, ShapeType = 0 ******\u001b[0m\n", + "\u001b[32;1m** WorkSession : Sending all data\u001b[0m\n", + "\u001b[32;1m Step File Name : my_reactor.stp(3447 ents) Write Done\u001b[0m\n" ] }, { @@ -354,14 +356,6 @@ }, "metadata": {}, "output_type": "display_data" - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[32;1m** WorkSession : Sending all data\u001b[0m\n", - "\u001b[32;1m Step File Name : my_reactor.stp(3447 ents) Write Done\u001b[0m\n" - ] } ], "source": [ @@ -383,16 +377,6 @@ "execution_count": 6, "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/jshim/brep_part_finder/brep_part_finder/core.py:75: UserWarning: No parts matching the specified volume +/- tolerances were found\n", - " warnings.warn(\n", - "/home/jshim/brep_part_finder/brep_part_finder/core.py:114: UserWarning: No parts matching the specified bounding boxes were found\n", - " warnings.warn(\"No parts matching the specified bounding boxes were found\")\n" - ] - }, { "name": "stdout", "output_type": "stream", @@ -506,7 +490,7 @@ "Info : [100%] Meshing curve 106 (Circle)\n", "Info : [100%] Meshing curve 107 (Line)\n", "Info : [100%] Meshing curve 108 (Line)\n", - "Info : Done meshing 1D (Wall 0.0166881s, CPU 0.026631s)\n", + "Info : Done meshing 1D (Wall 0.0162452s, CPU 0.026592s)\n", "Info : Meshing 2D...\n", "Info : [ 0%] Meshing surface 1 (Cylinder, MeshAdapt)\n", "Info : [ 10%] Meshing surface 2 (Plane, MeshAdapt)\n", @@ -564,30 +548,38 @@ "Info : [100%] Meshing surface 54 (Plane, MeshAdapt)\n", "Info : [100%] Meshing surface 55 (Plane, MeshAdapt)\n", "Info : [100%] Meshing surface 56 (Plane, MeshAdapt)\n", - "Info : Done meshing 2D (Wall 14.6143s, CPU 14.6311s)\n", + "Info : Done meshing 2D (Wall 14.475s, CPU 14.4766s)\n", "Info : 24024 nodes 50983 elements\n", - "Info : Writing '/tmp/volume_1_yuxossg.stl'...\n", - "Info : Done writing '/tmp/volume_1_yuxossg.stl'\n", - "Info : Writing '/tmp/volume_2d72ej6m7.stl'...\n", - "Info : Done writing '/tmp/volume_2d72ej6m7.stl'\n", - "Info : Writing '/tmp/volume_3eseweav4.stl'...\n", - "Info : Done writing '/tmp/volume_3eseweav4.stl'\n", - "Info : Writing '/tmp/volume_4fw4s7z6v.stl'...\n", - "Info : Done writing '/tmp/volume_4fw4s7z6v.stl'\n", - "Info : Writing '/tmp/volume_5v8kkgwcd.stl'...\n", - "Info : Done writing '/tmp/volume_5v8kkgwcd.stl'\n", - "Info : Writing '/tmp/volume_6ri1kpiz5.stl'...\n", - "Info : Done writing '/tmp/volume_6ri1kpiz5.stl'\n", - "Info : Writing '/tmp/volume_77467y6bm.stl'...\n", - "Info : Done writing '/tmp/volume_77467y6bm.stl'\n", - "Info : Writing '/tmp/volume_8bn6d5kqs.stl'...\n", - "Info : Done writing '/tmp/volume_8bn6d5kqs.stl'\n", - "Info : Writing '/tmp/volume_9jglwod6q.stl'...\n", - "Info : Done writing '/tmp/volume_9jglwod6q.stl'\n", - "Info : Writing '/tmp/volume_10udltgkpa.stl'...\n", - "Info : Done writing '/tmp/volume_10udltgkpa.stl'\n", - "file /tmp/volume_1_yuxossg.stl is watertight True\n", - "file /tmp/volume_2d72ej6m7.stl is watertight True\n" + "Info : Writing '/tmp/volume_1ya905d6y.stl'...\n", + "Info : Done writing '/tmp/volume_1ya905d6y.stl'\n", + "Info : Writing '/tmp/volume_21713jqj7.stl'...\n", + "Info : Done writing '/tmp/volume_21713jqj7.stl'\n", + "Info : Writing '/tmp/volume_3fm04kflt.stl'...\n", + "Info : Done writing '/tmp/volume_3fm04kflt.stl'\n", + "Info : Writing '/tmp/volume_4ozp3ns7u.stl'...\n", + "Info : Done writing '/tmp/volume_4ozp3ns7u.stl'\n", + "Info : Writing '/tmp/volume_5vc_dm549.stl'...\n", + "Info : Done writing '/tmp/volume_5vc_dm549.stl'\n", + "Info : Writing '/tmp/volume_6xl62nv5j.stl'...\n", + "Info : Done writing '/tmp/volume_6xl62nv5j.stl'\n", + "Info : Writing '/tmp/volume_7p3fuo6bj.stl'...\n", + "Info : Done writing '/tmp/volume_7p3fuo6bj.stl'\n", + "Info : Writing '/tmp/volume_8fiwr678_.stl'...\n", + "Info : Done writing '/tmp/volume_8fiwr678_.stl'\n", + "Info : Writing '/tmp/volume_9i4o02pff.stl'...\n", + "Info : Done writing '/tmp/volume_9i4o02pff.stl'\n", + "Info : Writing '/tmp/volume_10qy8o513g.stl'...\n", + "Info : Done writing '/tmp/volume_10qy8o513g.stl'\n", + "file /tmp/volume_1ya905d6y.stl is watertight True\n", + "file /tmp/volume_21713jqj7.stl is watertight True\n", + "file /tmp/volume_3fm04kflt.stl is watertight True\n", + "file /tmp/volume_4ozp3ns7u.stl is watertight True\n", + "file /tmp/volume_5vc_dm549.stl is watertight True\n", + "file /tmp/volume_6xl62nv5j.stl is watertight True\n", + "file /tmp/volume_7p3fuo6bj.stl is watertight True\n", + "file /tmp/volume_8fiwr678_.stl is watertight True\n", + "file /tmp/volume_9i4o02pff.stl is watertight True\n", + "file /tmp/volume_10qy8o513g.stl is watertight True\n" ] } ], @@ -623,19 +615,6 @@ "/home/jshim/openmc-1/openmc/mixin.py:67: IDWarning: Another Cell instance already exists with id=9999.\n", " warn(msg, IDWarning)\n" ] - }, - { - "ename": "ValueError", - "evalue": "material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column', 'mat_pf_coil'].", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/tmp/ipykernel_66680/499989040.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[0mgeometry\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0modw\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGeometry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 18\u001b[0;31m materials = odw.Materials(\n\u001b[0m\u001b[1;32m 19\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 20\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmaterial_tag_to_material_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, h5m_filename, correspondence_dict)\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcorrespondence_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mh5m_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 24\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchecks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 25\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_openmc_materials\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopenmc_materials\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36mchecks\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;34mf\"contains the following material tags {materials_in_h5m}.\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 55\u001b[0m )\n\u001b[0;32m---> 56\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 57\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m\"graveyard\"\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mmaterials_in_h5m\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column', 'mat_pf_coil']." - ] } ], "source": [ @@ -671,7 +650,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -699,7 +678,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -708,11 +687,11 @@ "# finds bounding box size from the geometry size\n", "corners = DagmcBoundingBox('dagmc.h5m').corners()\n", "\n", - "tally1 = odw.MeshTally2D(\n", - " mesh_resolution=(100, 100),\n", + "tally1 = odw.MeshTally3D(\n", + " mesh_resolution=(100, 100, 100),\n", " bounding_box= corners,\n", " tally_type=\"(n,Xa)\",\n", - " plane='xz'\n", + " # plane='xz'\n", ")\n", "\n", "tallies = openmc.Tallies([tally1])" @@ -727,15 +706,118 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " %%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%\n", + " ############### %%%%%%%%%%%%%%%%%%%%%%%%\n", + " ################## %%%%%%%%%%%%%%%%%%%%%%%\n", + " ################### %%%%%%%%%%%%%%%%%%%%%%%\n", + " #################### %%%%%%%%%%%%%%%%%%%%%%\n", + " ##################### %%%%%%%%%%%%%%%%%%%%%\n", + " ###################### %%%%%%%%%%%%%%%%%%%%\n", + " ####################### %%%%%%%%%%%%%%%%%%\n", + " ####################### %%%%%%%%%%%%%%%%%\n", + " ###################### %%%%%%%%%%%%%%%%%\n", + " #################### %%%%%%%%%%%%%%%%%\n", + " ################# %%%%%%%%%%%%%%%%%\n", + " ############### %%%%%%%%%%%%%%%%\n", + " ############ %%%%%%%%%%%%%%%\n", + " ######## %%%%%%%%%%%%%%\n", + " %%%%%%%%%%%\n", + "\n", + " | The OpenMC Monte Carlo Code\n", + " Copyright | 2011-2021 MIT and OpenMC contributors\n", + " License | https://docs.openmc.org/en/latest/license.html\n", + " Version | 0.13.0-dev\n", + " Git SHA1 | 209fdd86ed14a16d4b73e9c44de8a9710a898e64\n", + " Date/Time | 2022-01-26 23:10:24\n", + " MPI Processes | 1\n", + " OpenMP Threads | 8\n", + "\n", + " Reading settings XML file...\n", + " Reading cross sections XML file...\n", + " Reading materials XML file...\n", + " Reading geometry XML file...\n", + "Using the DOUBLE-DOWN interface to Embree.\n", + "Loading file dagmc.h5m\n", + "Initializing the GeomQueryTool...\n", + "Using faceting tolerance: 0\n", + "Building acceleration data structures...\n", + "Implicit Complement assumed to be Vacuum\n", + " Reading Cu65 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Cu65.h5\n", + " Reading Cu63 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Cu63.h5\n", + " Reading Li6 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Li6.h5\n", + " Reading Li7 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Li7.h5\n", + " Reading Si28 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Si28.h5\n", + " Reading Si29 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Si29.h5\n", + " Reading Si30 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Si30.h5\n", + " Reading O16 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_O16.h5\n", + " Reading O18 from /home/jshim/nuc_data/cross_section_data/TENDL-2019_O18.h5\n", + " Reading O17 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_O17.h5\n", + " Minimum neutron data temperature: 294.0 K\n", + " Maximum neutron data temperature: 294.0 K\n", + " Reading tallies XML file...\n", + " Preparing distributed cell instances...\n", + " Writing summary.h5 file...\n", + " Maximum neutron transport energy: 20000000.0 eV for Li6\n", + "\n", + " ===============> FIXED SOURCE TRANSPORT SIMULATION <===============\n", + "\n", + " Simulating batch 1\n", + " Simulating batch 2\n", + " Simulating batch 3\n", + " Simulating batch 4\n", + " Simulating batch 5\n", + " Simulating batch 6\n", + " Simulating batch 7\n", + " Simulating batch 8\n", + " Simulating batch 9\n", + " Simulating batch 10\n", + " Creating state point statepoint.10.h5...\n", + "\n", + " =======================> TIMING STATISTICS <=======================\n", + "\n", + " Total time for initialization = 9.6893e-01 seconds\n", + " Reading cross sections = 8.6679e-01 seconds\n", + " Total time in simulation = 7.1340e-01 seconds\n", + " Time in transport only = 6.7301e-01 seconds\n", + " Time in active batches = 7.1340e-01 seconds\n", + " Time accumulating tallies = 1.8198e-02 seconds\n", + " Time writing statepoints = 2.0861e-02 seconds\n", + " Total time for finalization = 9.6260e-01 seconds\n", + " Total time elapsed = 2.6586e+00 seconds\n", + " Calculation Rate (active) = 28034.7 particles/second\n", + "\n", + " ============================> RESULTS <============================\n", + "\n", + " Leakage Fraction = 0.51210 +/- 0.00313\n", + "\n" + ] + } + ], "source": [ "import openmc_plasma_source as ops\n", "\n", "settings = odw.FusionSettings()\n", - "settings.batches = 4\n", - "settings.particles = 1000\n", + "settings.batches = 10\n", + "settings.particles = 2000\n", "\n", "# assigns a ring source of DT energy neutrons to the source using the\n", "# openmc_plasma_source package, more details here\n", @@ -766,9 +848,36 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{1: Tally\n", + "\tID =\t1\n", + "\tName =\t(n,Xa)_on_3D_mesh\n", + "\tFilters =\tMeshFilter\n", + "\tNuclides =\ttotal\n", + "\tScores =\t['(n,Xa)']\n", + "\tEstimator =\ttracklength}\n", + "tally.size 1000000\n", + "tally [0. 0. 0. ... 0. 0. 0.]\n", + "Writing n_Xa_on_3D_mesh.vtk\n" + ] + }, + { + "data": { + "text/plain": [ + "'n_Xa_on_3D_mesh.vtk'" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "from openmc_mesh_tally_to_vtk import write_mesh_tally_to_vtk\n", "# importing a package for converting regular mesh tallies to vtk files\n", @@ -776,18 +885,18 @@ "\n", "\n", "# assumes you have a statepoint file from the OpenMC simulation\n", - "statepoint = openmc.StatePoint('statepoint.4.h5')\n", + "statepoint = openmc.StatePoint(statepoint_file)\n", "\n", "# this shows the tallies present in the statepoint file\n", "print(statepoint.tallies)\n", "\n", "# loads up a tally from the statepoint using it's name\n", - "my_tally = statepoint.get_tally(name='(n,Xa)_on_2D_mesh_xz')\n", + "my_tally = statepoint.get_tally(name='(n,Xa)_on_3D_mesh')\n", "\n", "# converts the tally result into a VTK file\n", "write_mesh_tally_to_vtk(\n", " tally=my_tally,\n", - " filename = \"(n,Xa)_on_2D_mesh_xz.vtk\",\n", + " filename = \"n_Xa_on_3D_mesh.vtk\",\n", ")" ] }, @@ -800,13 +909,33 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 19, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "n_Xa_on_3D_mesh.vtk
" + ], + "text/plain": [ + "/home/jshim/neutronics-workshop/tasks/task_12_CAD_mesh_fast_flux/n_Xa_on_3D_mesh.vtk" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "from IPython.display import FileLink\n", - "display(FileLink('n,Xa)_on_2D_mesh_xz.vtk'))" + "display(FileLink('n_Xa_on_3D_mesh.vtk'))" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { From 101b4f39f30b5ce724a9d101b811fe2204e27c93 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Wed, 26 Jan 2022 23:13:40 +0000 Subject: [PATCH 11/31] added brep fiels --- .gitignore | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 8e76279a..87f40abe 100644 --- a/.gitignore +++ b/.gitignore @@ -1,20 +1,21 @@ - +# openmc files *.xml - tallies.out - *.h5 +# DAGMC files *.h5m +# Cubit files *.trelis - *.jou - +*.log *.cub +# Python library files *.so +# Paraview files *.vtk *.vtp *.pvtp @@ -26,8 +27,9 @@ __pycache__/ .ipynb_checkpoints/ +# CAD files +*.brep *.stl *.stp *.svg -*.log *.png \ No newline at end of file From 692a432296fe77f736d15b94222bb00eb7620bf2 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Wed, 26 Jan 2022 23:18:37 +0000 Subject: [PATCH 12/31] make ring source 180 degrees --- tasks/task_04_make_sources/1_point_source_plots.ipynb | 2 +- tasks/task_04_make_sources/2_ring_source.ipynb | 2 +- tasks/task_04_make_sources/3_plasma_source_plots.ipynb | 2 +- tasks/task_04_make_sources/4_neutron_tracks.ipynb | 2 +- tasks/task_04_make_sources/5_gamma_source_example.ipynb | 2 +- ...ulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb | 6 +++--- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/tasks/task_04_make_sources/1_point_source_plots.ipynb b/tasks/task_04_make_sources/1_point_source_plots.ipynb index c9486ea9..553c1ab8 100644 --- a/tasks/task_04_make_sources/1_point_source_plots.ipynb +++ b/tasks/task_04_make_sources/1_point_source_plots.ipynb @@ -229,7 +229,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/2_ring_source.ipynb b/tasks/task_04_make_sources/2_ring_source.ipynb index 8fcfe1fe..8acb1ad0 100644 --- a/tasks/task_04_make_sources/2_ring_source.ipynb +++ b/tasks/task_04_make_sources/2_ring_source.ipynb @@ -116,7 +116,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb index 859510b7..f2350a7a 100644 --- a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb +++ b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb @@ -136,7 +136,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.5" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/4_neutron_tracks.ipynb b/tasks/task_04_make_sources/4_neutron_tracks.ipynb index affe6ab8..0314035d 100644 --- a/tasks/task_04_make_sources/4_neutron_tracks.ipynb +++ b/tasks/task_04_make_sources/4_neutron_tracks.ipynb @@ -204,7 +204,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/5_gamma_source_example.ipynb b/tasks/task_04_make_sources/5_gamma_source_example.ipynb index bce6e156..c1c53767 100644 --- a/tasks/task_04_make_sources/5_gamma_source_example.ipynb +++ b/tasks/task_04_make_sources/5_gamma_source_example.ipynb @@ -125,7 +125,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb index b08a9047..f7ea8d2b 100644 --- a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb +++ b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb @@ -126,9 +126,9 @@ "settings.batches = 1\n", "settings.particles = 100\n", "\n", - "# assigns a ring source of DT energy neutrons to the source using the\n", - "# openmc_plasma_source package\n", - "settings.source = ops.FusionRingSource(fuel=\"DT\", radius=350)\n", + "# assigns a ring source of DT energy neutrons to the source using the openmc_plasma_source package.\n", + "# This source has a 14MeV neutron energy, with a radius of 350cm and is half a ring (0 to 180 degrees)\n", + "settings.source = ops.FusionRingSource(fuel=\"DT\", radius=350, angles=(0, 3.14))\n", "\n", "my_model = openmc.Model(\n", " materials=materials, geometry=geometry, settings=settings, tallies=tallies\n", From 34634ab7fa77fc23fd3475b16682d13746fcebbe Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Tue, 1 Feb 2022 17:54:30 +0000 Subject: [PATCH 13/31] started on ww addition --- .../1_minimal_weight_window_example.py | 134 ++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 tasks/task_13_variance_reduction/1_minimal_weight_window_example.py diff --git a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py new file mode 100644 index 00000000..fde64ebd --- /dev/null +++ b/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py @@ -0,0 +1,134 @@ +import openmc +import matplotlib.pyplot as plt + +# MATERIALS + +# creates two materials, one is a neutron multiplier (lead) and the other a tritium breeder (lithium) +mats = openmc.Materials() + +breeder_material = openmc.Material(name="breeder") +breeder_material.add_element('Li', 1, percent_type='ao') +breeder_material.set_density('g/cm3', 2.0) + +multiplier_material = openmc.Material(name="multiplier") +multiplier_material.add_element('Pb', 1, percent_type='ao') +multiplier_material.set_density('g/cm3', 11.0) + +mats = [breeder_material, multiplier_material] + + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=50) +sph2 = openmc.Sphere(r=90, boundary_type='vacuum') +plane1 = openmc.XPlane(20) + +# cells +breeder_cell = openmc.Cell(region=+sph1 & -sph2 & -plane1) +breeder_cell.fill = breeder_material + +multiplier_cell = openmc.Cell(region=+sph1 & -sph2 & +plane1) +multiplier_cell.fill = multiplier_material + +inner_vacuum_cell = openmc.Cell(region=-sph1) + +universe = openmc.Universe(cells=[inner_vacuum_cell, breeder_cell, multiplier_cell]) + +geom = openmc.Geometry(universe) + +# Create mesh which will be used for tally and weight window +my_mesh = openmc.RegularMesh() +mesh_height = 4 # number of cells in the X and Z dimensions +mesh_width = mesh_height +my_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension +my_mesh.lower_left = [-200, -200, -200] # physical limits (corners) of the mesh +my_mesh.upper_right = [200, 200, 200] + +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 50 +sett.particle = "neutron" +sett.run_mode = 'fixed source' + +lower_ww_bounds=[] +energy_bins = [] +upper_ww_bounds=[] +for mesh_element in range(mesh_height * mesh_width): + print(mesh_element) + energy_bins.append(1.1) + energy_bins.append(1e9) + lower_ww_bounds.append(1) + lower_ww_bounds.append(10) + upper_ww_bounds.append(40) + upper_ww_bounds.append(30) + # lower_ww_bounds.append() + +# docs on ww https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh =my_mesh, + lower_ww_bounds=lower_ww_bounds, + energy_bins=energy_bins, + upper_ww_bounds=upper_ww_bounds +) + +sett.weight_windows = ww + + + +# creates a 14MeV point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +sett.source = source + + + + + + +tallies = openmc.Tallies() +# Create mesh filter for tally +mesh_filter = openmc.MeshFilter(my_mesh) +mesh_tally = openmc.Tally(name='tallies_on_mesh') +mesh_tally.filters = [mesh_filter] +mesh_tally.scores = ['flux', 'absorption', '(n,2n)'] # change flux to absorption +tallies.append(mesh_tally) + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# plt.show(universe.plot(width=(180, 180), basis='xz')) + +# # deletes old files +# !rm summary.h5 +# !rm statepoint.*.h5 + +# runs the simulation +output_filename = model.run() + +# open the results file +results = openmc.StatePoint(output_filename) + +# access the flux tally +my_tally = results.get_tally(scores=['flux']) +my_slice = my_tally.get_slice(scores=['flux']) +my_slice.mean.shape = (mesh_width, mesh_height) + +fig = plt.subplot() + +# when plotting the 2d data, added the extent is required. +# otherwise the plot uses the index of the 2d data arrays +# as the x y axis +fig.imshow(my_slice.mean, extent=[-200,200,-200,200], vmin=1e-9, vmax=1) + +plt.show() + +# notice that neutrons are produced and emitted isotropically from a point source. +# There is a slight increase in flux within the neutron multiplier. From 088a852b06650614716b8ca11d5d164d573ab4c2 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Wed, 2 Feb 2022 18:04:00 +0000 Subject: [PATCH 14/31] started on spectra example --- .../1_minimal_weight_window_example.py | 110 ++++++++------- .../2_minimal_weight_window_example.py | 129 ++++++++++++++++++ 2 files changed, 183 insertions(+), 56 deletions(-) create mode 100644 tasks/task_13_variance_reduction/2_minimal_weight_window_example.py diff --git a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py index fde64ebd..3fd3c7ce 100644 --- a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py +++ b/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py @@ -3,102 +3,95 @@ # MATERIALS -# creates two materials, one is a neutron multiplier (lead) and the other a tritium breeder (lithium) +# creates a single material mats = openmc.Materials() -breeder_material = openmc.Material(name="breeder") -breeder_material.add_element('Li', 1, percent_type='ao') -breeder_material.set_density('g/cm3', 2.0) +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) -multiplier_material = openmc.Material(name="multiplier") -multiplier_material.add_element('Pb', 1, percent_type='ao') -multiplier_material.set_density('g/cm3', 11.0) - -mats = [breeder_material, multiplier_material] +mats = [shielding_material] # GEOMETRY # surfaces -sph1 = openmc.Sphere(r=50) -sph2 = openmc.Sphere(r=90, boundary_type='vacuum') -plane1 = openmc.XPlane(20) +sph1 = openmc.Sphere(r=200, boundary_type='vacuum') # cells -breeder_cell = openmc.Cell(region=+sph1 & -sph2 & -plane1) -breeder_cell.fill = breeder_material - -multiplier_cell = openmc.Cell(region=+sph1 & -sph2 & +plane1) -multiplier_cell.fill = multiplier_material +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material -inner_vacuum_cell = openmc.Cell(region=-sph1) - -universe = openmc.Universe(cells=[inner_vacuum_cell, breeder_cell, multiplier_cell]) +universe = openmc.Universe(cells=[shield_cell]) geom = openmc.Geometry(universe) # Create mesh which will be used for tally and weight window -my_mesh = openmc.RegularMesh() -mesh_height = 4 # number of cells in the X and Z dimensions -mesh_width = mesh_height -my_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension -my_mesh.lower_left = [-200, -200, -200] # physical limits (corners) of the mesh -my_mesh.upper_right = [200, 200, 200] +my_ww_mesh = openmc.RegularMesh() +mesh_height = 10 # number of mesh elements in the Y direction +mesh_width = 10 # number of mesh elements in the X direction +my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension +my_ww_mesh.lower_left = [-100, -100, -100] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [100, 100, 100] + -# SETTINGS -# Instantiate a Settings object -sett = openmc.Settings() -sett.batches = 100 -sett.inactive = 0 -sett.particles = 50 -sett.particle = "neutron" -sett.run_mode = 'fixed source' lower_ww_bounds=[] -energy_bins = [] upper_ww_bounds=[] -for mesh_element in range(mesh_height * mesh_width): - print(mesh_element) - energy_bins.append(1.1) - energy_bins.append(1e9) - lower_ww_bounds.append(1) - lower_ww_bounds.append(10) - upper_ww_bounds.append(40) - upper_ww_bounds.append(30) - # lower_ww_bounds.append() +for mesh_element in range(1, (mesh_height * mesh_width)+1): + if mesh_element > (mesh_height * mesh_width) *0.5: + lower_ww_bounds.append(0.001) + upper_ww_bounds.append(0.7) + else: + lower_ww_bounds.append(-1) + upper_ww_bounds.append(-1) + # docs on ww https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows ww = openmc.WeightWindows( - mesh =my_mesh, + mesh =my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, lower_ww_bounds=lower_ww_bounds, - energy_bins=energy_bins, - upper_ww_bounds=upper_ww_bounds + particle_type='neutron', + energy_bins=(0.0, 100_000_000.0), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 ) -sett.weight_windows = ww - - # creates a 14MeV point source source = openmc.Source() source.space = openmc.stats.Point((0, 0, 0)) source.angle = openmc.stats.Isotropic() source.energy = openmc.stats.Discrete([14e6], [1]) -sett.source = source +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' +sett.weight_windows = ww +# Create mesh which will be used for tally and weight window +my_tally_mesh = openmc.RegularMesh() +my_tally_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension +my_tally_mesh.lower_left = [-100, -100, -100] # physical limits (corners) of the mesh +my_tally_mesh.upper_right = [100, 100, 100] tallies = openmc.Tallies() # Create mesh filter for tally -mesh_filter = openmc.MeshFilter(my_mesh) -mesh_tally = openmc.Tally(name='tallies_on_mesh') +mesh_filter = openmc.MeshFilter(my_tally_mesh) +mesh_tally = openmc.Tally(name='flux_on_mesh') mesh_tally.filters = [mesh_filter] -mesh_tally.scores = ['flux', 'absorption', '(n,2n)'] # change flux to absorption +mesh_tally.scores = ['flux'] tallies.append(mesh_tally) # combines the geometry, materials, settings and tallies to create a neutronics model @@ -120,13 +113,18 @@ my_tally = results.get_tally(scores=['flux']) my_slice = my_tally.get_slice(scores=['flux']) my_slice.mean.shape = (mesh_width, mesh_height) - fig = plt.subplot() # when plotting the 2d data, added the extent is required. # otherwise the plot uses the index of the 2d data arrays # as the x y axis -fig.imshow(my_slice.mean, extent=[-200,200,-200,200], vmin=1e-9, vmax=1) +fig.imshow(my_slice.mean, extent=[-200,200,-200,200], vmin=1e-5, vmax=28) +plt.show() + +fig.imshow(my_slice.std_dev, extent=[-200,200,-200,200])#, vmin=1e-7, vmax=1) + +# np.amax(my_slice.mean) +28 plt.show() diff --git a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py new file mode 100644 index 00000000..7fa9990c --- /dev/null +++ b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py @@ -0,0 +1,129 @@ +import openmc +import matplotlib.pyplot as plt + +# MATERIALS + +# creates a single material +mats = openmc.Materials() + +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) + +mats = [shielding_material] + + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=200, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material + +universe = openmc.Universe(cells=[shield_cell]) + +geom = openmc.Geometry(universe) + +# Create mesh which will be used for tally and weight window +my_ww_mesh = openmc.RegularMesh() +mesh_height = 10 # number of mesh elements in the Y direction +mesh_width = 10 # number of mesh elements in the X direction +my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension +my_ww_mesh.lower_left = [-100, -100, -100] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [100, 100, 100] + + + + +lower_ww_bounds=[] +upper_ww_bounds=[] +for mesh_element in range(1, (mesh_height * mesh_width)+1): + if mesh_element > (mesh_height * mesh_width) *0.5: + lower_ww_bounds.append(0.001) + upper_ww_bounds.append(0.7) + else: + lower_ww_bounds.append(-1) + upper_ww_bounds.append(-1) + + +# docs on ww https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh =my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, + lower_ww_bounds=lower_ww_bounds, + particle_type='neutron', + energy_bins=(0.0, 100_000_000.0), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 +) + + +# creates a 14MeV point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) + +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' +sett.weight_windows = ww + + + + +#creates an empty tally object +tallies = openmc.Tallies() + + +# sets up filters for the tallies +neutron_particle_filter = openmc.ParticleFilter(['neutron']) +energy_bins = openmc.mgxs.GROUP_STRUCTURES['CCFE-709'] +energy_filter = openmc.EnergyFilter(energy_bins) + +# setup the filters for the surface tally +front_surface_filter = openmc.SurfaceFilter(sph1) +# detects when particles across the surface + +front_surface_spectra_tally = openmc.Tally(name='front_surface_spectra_tally') +front_surface_spectra_tally.scores = ['current'] +front_surface_spectra_tally.filters = [front_surface_filter, neutron_particle_filter, energy_filter] +tallies.append(front_surface_spectra_tally) + + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# plt.show(universe.plot(width=(180, 180), basis='xz')) + +# # deletes old files +# !rm summary.h5 +# !rm statepoint.*.h5 + +# runs the simulation +output_filename = model.run() + +# open the results file +results = openmc.StatePoint(output_filename) +my_tally = results.get_tally(name="front_surface_spectra_tally") + +from spectrum_plotter import plot_spectrum_from_tally + +test_plot = plot_spectrum_from_tally( + spectrum={"neutron spectra": my_tally}, + volume=1, + x_label="Energy [MeV]", + y_label="Flux [n/cm^2s]", + x_scale="linear", + y_scale="linear", + title="example plot 1", + filename="example_spectra_from_tally_matplotlib.png", +) \ No newline at end of file From 38b61d5423f36a3ad1b7f2d453987ce45b2307b3 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Fri, 4 Feb 2022 11:21:53 +0000 Subject: [PATCH 15/31] simple sphere working --- .../2_minimal_weight_window_example.py | 67 +++++++++++-------- .../sphere_otf/orig/with_ww/make_vtk.py | 16 +++++ .../sphere_otf/orig/without_ww/make_vtk.py | 16 +++++ 3 files changed, 71 insertions(+), 28 deletions(-) create mode 100644 tasks/task_13_variance_reduction/sphere_otf/orig/with_ww/make_vtk.py create mode 100644 tasks/task_13_variance_reduction/sphere_otf/orig/without_ww/make_vtk.py diff --git a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py index 7fa9990c..e78ee14c 100644 --- a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py +++ b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py @@ -1,5 +1,5 @@ import openmc -import matplotlib.pyplot as plt +import os # MATERIALS @@ -18,9 +18,12 @@ # surfaces sph1 = openmc.Sphere(r=200, boundary_type='vacuum') +plane1 = openmc.YPlane(y0=-1, boundary_type='reflective') +plane2 = openmc.YPlane(y0=1, boundary_type='reflective') + # cells -shield_cell = openmc.Cell(region=-sph1) +shield_cell = openmc.Cell(region=-sph1 & +plane1 & -plane2) shield_cell.fill = shielding_material universe = openmc.Universe(cells=[shield_cell]) @@ -29,29 +32,34 @@ # Create mesh which will be used for tally and weight window my_ww_mesh = openmc.RegularMesh() -mesh_height = 10 # number of mesh elements in the Y direction -mesh_width = 10 # number of mesh elements in the X direction +mesh_height = 5 # number of mesh elements in the Y direction +mesh_width = 5 # number of mesh elements in the X direction my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension -my_ww_mesh.lower_left = [-100, -100, -100] # physical limits (corners) of the mesh -my_ww_mesh.upper_right = [100, 100, 100] - +my_ww_mesh.lower_left = [-100, -1, -100] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [100, 1, 100] +lower_ww_bounds = [ + -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, +] -lower_ww_bounds=[] -upper_ww_bounds=[] -for mesh_element in range(1, (mesh_height * mesh_width)+1): - if mesh_element > (mesh_height * mesh_width) *0.5: - lower_ww_bounds.append(0.001) - upper_ww_bounds.append(0.7) - else: - lower_ww_bounds.append(-1) - upper_ww_bounds.append(-1) +upper_ww_bounds = [ + 0.1, 0.1, 0.1, 0.1, 0.1, + 0.1, 0.2, 0.2, 0.2, 0.1, + 0.1, 0.2, -1, 0.2, 0.1, + 0.1, 0.2, 0.2, 0.2, 0.1, + 0.1, 0.1, 0.1, 0.1, 0.1, +] -# docs on ww https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +# docs for ww are here +# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows ww = openmc.WeightWindows( - mesh =my_ww_mesh, + mesh=my_ww_mesh, upper_ww_bounds=upper_ww_bounds, lower_ww_bounds=lower_ww_bounds, particle_type='neutron', @@ -76,8 +84,7 @@ sett.source = source sett.run_mode = 'fixed source' sett.weight_windows = ww - - +sett.particles = 'neutron' #creates an empty tally object @@ -105,8 +112,9 @@ # plt.show(universe.plot(width=(180, 180), basis='xz')) # # deletes old files -# !rm summary.h5 -# !rm statepoint.*.h5 +os.remove('summary.h5') +os.remove('statepoint.100.h5') + # runs the simulation output_filename = model.run() @@ -119,11 +127,14 @@ test_plot = plot_spectrum_from_tally( spectrum={"neutron spectra": my_tally}, - volume=1, x_label="Energy [MeV]", - y_label="Flux [n/cm^2s]", - x_scale="linear", - y_scale="linear", + y_label="Current [n/source_particle]", + x_scale="log", + y_scale="log", title="example plot 1", - filename="example_spectra_from_tally_matplotlib.png", -) \ No newline at end of file + required_units="neutron / source_particle", + plotting_package="plotly", + filename="example_spectra_from_tally_matplotlib.html", +) + +test_plot.show() \ No newline at end of file diff --git a/tasks/task_13_variance_reduction/sphere_otf/orig/with_ww/make_vtk.py b/tasks/task_13_variance_reduction/sphere_otf/orig/with_ww/make_vtk.py new file mode 100644 index 00000000..9789a23a --- /dev/null +++ b/tasks/task_13_variance_reduction/sphere_otf/orig/with_ww/make_vtk.py @@ -0,0 +1,16 @@ +from openmc_mesh_tally_to_vtk import write_mesh_tally_to_vtk +import openmc + +# assumes you have a statepoint file from the OpenMC simulation +statepoint = openmc.StatePoint('statepoint.2.h5') + +print(statepoint.tallies) + +# assumes the statepoint file has a RegularMesh tally with a certain name +my_tally = statepoint.get_tally(id=10) + +# converts the tally result into a VTK file +write_mesh_tally_to_vtk( + tally=my_tally, + filename = "vtk_file_from_openmc_mesh.vtk", +) \ No newline at end of file diff --git a/tasks/task_13_variance_reduction/sphere_otf/orig/without_ww/make_vtk.py b/tasks/task_13_variance_reduction/sphere_otf/orig/without_ww/make_vtk.py new file mode 100644 index 00000000..9789a23a --- /dev/null +++ b/tasks/task_13_variance_reduction/sphere_otf/orig/without_ww/make_vtk.py @@ -0,0 +1,16 @@ +from openmc_mesh_tally_to_vtk import write_mesh_tally_to_vtk +import openmc + +# assumes you have a statepoint file from the OpenMC simulation +statepoint = openmc.StatePoint('statepoint.2.h5') + +print(statepoint.tallies) + +# assumes the statepoint file has a RegularMesh tally with a certain name +my_tally = statepoint.get_tally(id=10) + +# converts the tally result into a VTK file +write_mesh_tally_to_vtk( + tally=my_tally, + filename = "vtk_file_from_openmc_mesh.vtk", +) \ No newline at end of file From f50edc977dddb206f722cb3af71af82991423264 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Fri, 4 Feb 2022 17:41:03 +0000 Subject: [PATCH 16/31] got spectrum example working --- .../1_minimal_weight_window_example.py | 141 ++++++++-------- .../2_minimal_weight_window_example.py | 104 +++++++----- .../3_minimal_weight_window_example.py | 150 ++++++++++++++++++ .../weight_window_values.py | 4 + 4 files changed, 292 insertions(+), 107 deletions(-) create mode 100644 tasks/task_13_variance_reduction/3_minimal_weight_window_example.py create mode 100644 tasks/task_13_variance_reduction/weight_window_values.py diff --git a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py index 3fd3c7ce..4987f21e 100644 --- a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py +++ b/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py @@ -1,4 +1,5 @@ import openmc +import os import matplotlib.pyplot as plt # MATERIALS @@ -13,11 +14,10 @@ mats = [shielding_material] - # GEOMETRY # surfaces -sph1 = openmc.Sphere(r=200, boundary_type='vacuum') +sph1 = openmc.Sphere(r=250, boundary_type='vacuum') # cells shield_cell = openmc.Cell(region=-sph1) @@ -27,44 +27,12 @@ geom = openmc.Geometry(universe) -# Create mesh which will be used for tally and weight window -my_ww_mesh = openmc.RegularMesh() -mesh_height = 10 # number of mesh elements in the Y direction -mesh_width = 10 # number of mesh elements in the X direction -my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension -my_ww_mesh.lower_left = [-100, -100, -100] # physical limits (corners) of the mesh -my_ww_mesh.upper_right = [100, 100, 100] - - - - -lower_ww_bounds=[] -upper_ww_bounds=[] -for mesh_element in range(1, (mesh_height * mesh_width)+1): - if mesh_element > (mesh_height * mesh_width) *0.5: - lower_ww_bounds.append(0.001) - upper_ww_bounds.append(0.7) - else: - lower_ww_bounds.append(-1) - upper_ww_bounds.append(-1) - - -# docs on ww https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows -ww = openmc.WeightWindows( - mesh =my_ww_mesh, - upper_ww_bounds=upper_ww_bounds, - lower_ww_bounds=lower_ww_bounds, - particle_type='neutron', - energy_bins=(0.0, 100_000_000.0), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) - survival_ratio=5 -) - - -# creates a 14MeV point source +# creates a 14MeV neutron point source source = openmc.Source() source.space = openmc.stats.Point((0, 0, 0)) source.angle = openmc.stats.Isotropic() source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' # SETTINGS @@ -75,58 +43,103 @@ sett.particles = 500 sett.source = source sett.run_mode = 'fixed source' -sett.weight_windows = ww -# Create mesh which will be used for tally and weight window +# Create mesh which will be used for the tally my_tally_mesh = openmc.RegularMesh() -my_tally_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension -my_tally_mesh.lower_left = [-100, -100, -100] # physical limits (corners) of the mesh -my_tally_mesh.upper_right = [100, 100, 100] - - +my_tally_mesh.dimension = [25, 1, 25] # only 1 cell in the Y dimension +my_tally_mesh.lower_left = [-120, -1, -120] # physical limits (corners) of the mesh +my_tally_mesh.upper_right = [120, 1, 120] -tallies = openmc.Tallies() # Create mesh filter for tally mesh_filter = openmc.MeshFilter(my_tally_mesh) mesh_tally = openmc.Tally(name='flux_on_mesh') mesh_tally.filters = [mesh_filter] mesh_tally.scores = ['flux'] +#creates an empty tally object +tallies = openmc.Tallies() tallies.append(mesh_tally) # combines the geometry, materials, settings and tallies to create a neutronics model model = openmc.model.Model(geom, mats, sett, tallies) -# plt.show(universe.plot(width=(180, 180), basis='xz')) - -# # deletes old files -# !rm summary.h5 -# !rm statepoint.*.h5 - -# runs the simulation -output_filename = model.run() +# runs the simulation with weight windows +output_no_ww_filename = model.run() # open the results file -results = openmc.StatePoint(output_filename) +results_no_ww = openmc.StatePoint(output_no_ww_filename) # access the flux tally -my_tally = results.get_tally(scores=['flux']) -my_slice = my_tally.get_slice(scores=['flux']) -my_slice.mean.shape = (mesh_width, mesh_height) +my_tally_no_ww = results_no_ww.get_tally(scores=['flux']) +my_slice_no_ww = my_tally_no_ww.get_slice(scores=['flux']) +my_slice_no_ww.mean.shape = (25, 25) fig = plt.subplot() # when plotting the 2d data, added the extent is required. # otherwise the plot uses the index of the 2d data arrays # as the x y axis -fig.imshow(my_slice.mean, extent=[-200,200,-200,200], vmin=1e-5, vmax=28) -plt.show() +fig.imshow(my_slice_no_ww.mean, extent=[-120,120,-120,120], vmin=1e-5, vmax=10) +plt.savefig('no_ww.png') +# plt.show() + + -fig.imshow(my_slice.std_dev, extent=[-200,200,-200,200])#, vmin=1e-7, vmax=1) +# Create mesh which will be used for tally and weight window +my_ww_mesh = openmc.RegularMesh() +my_ww_mesh.dimension = [25, 25, 25] +my_ww_mesh.lower_left = [-120, -120, -120] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [120, 120, 120] + +# imports values for weight windows +from weight_window_values import upper_ww_bounds, lower_ww_bounds + +# docs for ww are here +# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh=my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, + lower_ww_bounds=lower_ww_bounds, + particle_type='neutron', + energy_bins=(0.0, 100_000_000.), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 +) +# sets the weight windows define to be used in the simulation +sett.weight_windows = ww -# np.amax(my_slice.mean) -28 +# deletes old files +try: + os.remove('summary.h5') +except OSError: + pass -plt.show() +# as each particle history is now longer due to the splitting that occurs with +# weight windows. Running the same number of batches would therefore take more +# time. To make a fair comparison the batch has been reduce to 20 as this takes +# a similar amount of time as 100 without weight windows +sett.batches=20 -# notice that neutrons are produced and emitted isotropically from a point source. -# There is a slight increase in flux within the neutron multiplier. + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# runs the simulation with weight windows +output_ww_filename = model.run() + + + + +# open the results file +results_ww = openmc.StatePoint(output_ww_filename) + +# access the flux tally +my_tally_ww = results_ww.get_tally(scores=['flux']) +my_slice_ww = my_tally_ww.get_slice(scores=['flux']) +my_slice_ww.mean.shape = (25, 25) +fig = plt.subplot() + +# when plotting the 2d data, added the extent is required. +# otherwise the plot uses the index of the 2d data arrays +# as the x y axis +fig.imshow(my_slice_ww.mean, extent=[-120,120,-120,120], vmin=1e-5, vmax=10) +plt.savefig('ww.png') +# plt.show() diff --git a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py index e78ee14c..b596489d 100644 --- a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py +++ b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py @@ -1,5 +1,7 @@ import openmc import os +from spectrum_plotter import plot_spectrum_from_tally + # MATERIALS @@ -30,43 +32,6 @@ geom = openmc.Geometry(universe) -# Create mesh which will be used for tally and weight window -my_ww_mesh = openmc.RegularMesh() -mesh_height = 5 # number of mesh elements in the Y direction -mesh_width = 5 # number of mesh elements in the X direction -my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension -my_ww_mesh.lower_left = [-100, -1, -100] # physical limits (corners) of the mesh -my_ww_mesh.upper_right = [100, 1, 100] - - -lower_ww_bounds = [ - -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -] - -upper_ww_bounds = [ - 0.1, 0.1, 0.1, 0.1, 0.1, - 0.1, 0.2, 0.2, 0.2, 0.1, - 0.1, 0.2, -1, 0.2, 0.1, - 0.1, 0.2, 0.2, 0.2, 0.1, - 0.1, 0.1, 0.1, 0.1, 0.1, -] - - -# docs for ww are here -# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows -ww = openmc.WeightWindows( - mesh=my_ww_mesh, - upper_ww_bounds=upper_ww_bounds, - lower_ww_bounds=lower_ww_bounds, - particle_type='neutron', - energy_bins=(0.0, 100_000_000.0), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) - survival_ratio=5 -) - # creates a 14MeV point source source = openmc.Source() @@ -83,8 +48,7 @@ sett.particles = 500 sett.source = source sett.run_mode = 'fixed source' -sett.weight_windows = ww -sett.particles = 'neutron' +# sett.particles = 'neutrons' #creates an empty tally object @@ -113,7 +77,7 @@ # # deletes old files os.remove('summary.h5') -os.remove('statepoint.100.h5') +os.remove(f'statepoint.{sett.batches}.h5') # runs the simulation @@ -121,12 +85,66 @@ # open the results file results = openmc.StatePoint(output_filename) -my_tally = results.get_tally(name="front_surface_spectra_tally") +my_analogy_tally = results.get_tally(name="front_surface_spectra_tally") + + + + + + +# Create mesh which will be used for tally and weight window +my_ww_mesh = openmc.RegularMesh() +mesh_height = 5 # number of mesh elements in the Y direction +mesh_width = 5 # number of mesh elements in the X direction +my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension +my_ww_mesh.lower_left = [-100, -1, -100] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [100, 1, 100] + + +lower_ww_bounds = [ + 0.1, 0.1, 0.1, 0.1, 0.1, + 0.1, 0.2, 0.2, 0.2, 0.1, + 0.1, 0.2, -1, 0.2, 0.1, + 0.1, 0.2, 0.2, 0.2, 0.1, + 0.1, 0.1, 0.1, 0.1, 0.1, +] + +upper_ww_bounds = [ + 0.2, 0.2, 0.2, 0.2, 0.2, + 0.2, 0.4, 0.4, 0.4, 0.2, + 0.2, 0.4, -1, 0.4, 0.2, + 0.2, 0.4, 0.4, 0.4, 0.2, + 0.2, 0.2, 0.2, 0.2, 0.2, +] + + +# docs for ww are here +# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh=my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, + lower_ww_bounds=lower_ww_bounds, + particle_type='neutron', + energy_bins=(0.0, 100_000_000.0), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 +) +sett.weight_windows = ww + + +# # deletes old files +os.remove('summary.h5') +os.remove(f'statepoint.{sett.batches}.h5') + +output_filename = model.run() + +# open the results file +ww_results = openmc.StatePoint(output_filename) +my_weight_window_tally = ww_results.get_tally(name="front_surface_spectra_tally") + -from spectrum_plotter import plot_spectrum_from_tally test_plot = plot_spectrum_from_tally( - spectrum={"neutron spectra": my_tally}, + spectrum={"analogy": my_analogy_tally, 'my_weight_window_tally': my_weight_window_tally}, x_label="Energy [MeV]", y_label="Current [n/source_particle]", x_scale="log", diff --git a/tasks/task_13_variance_reduction/3_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/3_minimal_weight_window_example.py new file mode 100644 index 00000000..e8c72a7a --- /dev/null +++ b/tasks/task_13_variance_reduction/3_minimal_weight_window_example.py @@ -0,0 +1,150 @@ +import openmc +import os +from spectrum_plotter import plot_spectrum_from_tally + + +# MATERIALS + +# creates a single material +mats = openmc.Materials() + +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) + +mats = [shielding_material] + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=250, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material + +universe = openmc.Universe(cells=[shield_cell]) + +geom = openmc.Geometry(universe) + + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' + + +#creates an empty tally object +tallies = openmc.Tallies() + + +# setup the filters for the surface tally +# detects neutrons (not photons) +neutron_particle_filter = openmc.ParticleFilter(['neutron']) +# detects when particles across the surface +front_surface_filter = openmc.SurfaceFilter(sph1) +energy_bins = openmc.mgxs.GROUP_STRUCTURES['CCFE-709'] +energy_filter = openmc.EnergyFilter(energy_bins) + +front_surface_spectra_tally = openmc.Tally(name='front_surface_spectra_tally') +front_surface_spectra_tally.scores = ['current'] +front_surface_spectra_tally.filters = [front_surface_filter, neutron_particle_filter, energy_filter] +tallies.append(front_surface_spectra_tally) + + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# deletes old files +try: + os.remove('summary.h5') + os.remove('statepoint.*.h5') +except OSError: + pass + + +# runs the simulation without weight windows +output_filename = model.run() + +# open the results file +results = openmc.StatePoint(output_filename) +my_analogy_tally = results.get_tally(name="front_surface_spectra_tally") + + + +# Create mesh which will be used for the weight windows +my_ww_mesh = openmc.RegularMesh() + +my_ww_mesh.dimension = [25, 25, 25] +my_ww_mesh.lower_left = [-120, -120, -120] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [120, 120, 120] + +# imports values for weight windows +from weight_window_values import upper_ww_bounds, lower_ww_bounds + + +# docs for ww are here +# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh=my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, + lower_ww_bounds=lower_ww_bounds, + particle_type='neutron', + energy_bins=(0.0, 100_000_000.), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 +) +# sets the weight windows define to be used in the simulation +sett.weight_windows = ww + +# deletes old files +try: + os.remove('summary.h5') +except OSError: + pass + +# as each particle history is now longer due to the splitting that occurs with +# weight windows. Running the same number of batches would therefore take more +# time. To make a fair comparison the batch has been reduce to 20 as this takes +# a similar amount of time as 100 without weight windows +sett.batches=20 + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# runs the simulation with weight windows +output_ww_filename = model.run() + +# open the results file +ww_results = openmc.StatePoint(output_ww_filename) +my_weight_window_tally = ww_results.get_tally(name="front_surface_spectra_tally") + + +# this function plots the neutron spectrum and requires spectrum_plotter to be installed +# pip install spectrum_plotter +test_plot = plot_spectrum_from_tally( + spectrum={"analogy": my_analogy_tally, 'my_weight_window_tally': my_weight_window_tally}, + x_label="Energy [MeV]", + y_label="Current [n/source_particle]", + x_scale="log", + y_scale="log", + title="example plot 1", + required_units="neutron / source_particle", + plotting_package="plotly", + filename="example_spectra_from_tally_matplotlib.html", +) + +# loads up the plot in a webbrowser +test_plot.show() diff --git a/tasks/task_13_variance_reduction/weight_window_values.py b/tasks/task_13_variance_reduction/weight_window_values.py new file mode 100644 index 00000000..e749b1d4 --- /dev/null +++ b/tasks/task_13_variance_reduction/weight_window_values.py @@ -0,0 +1,4 @@ + +lower_ww_bounds = [-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 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Mon Sep 17 00:00:00 2001 From: Jonathan Date: Sun, 6 Feb 2022 21:58:13 +0000 Subject: [PATCH 17/31] [skip ci] moved tasks 13 and 14 --- tasks/README.md | 5 +++-- .../1_techniques_for_sampling_design_space.ipynb | 0 .../README.md | 0 .../openmc_model.py | 0 .../plotting_tools.py | 0 .../run_all.sh | 0 .../README.md | 0 .../openmc_model.py | 0 .../parameter_study_optimisation.ipynb | 0 .../run_all.sh | 0 10 files changed, 3 insertions(+), 2 deletions(-) rename tasks/{task_13_parameter_study_sampling => task_14_parameter_study_sampling}/1_techniques_for_sampling_design_space.ipynb (100%) rename tasks/{task_13_parameter_study_sampling => task_14_parameter_study_sampling}/README.md (100%) rename tasks/{task_13_parameter_study_sampling => task_14_parameter_study_sampling}/openmc_model.py (100%) rename tasks/{task_13_parameter_study_sampling => task_14_parameter_study_sampling}/plotting_tools.py (100%) rename tasks/{task_13_parameter_study_sampling => task_14_parameter_study_sampling}/run_all.sh (100%) rename tasks/{task_14_parameter_study_optimisation => task_15_parameter_study_optimisation}/README.md (100%) rename tasks/{task_14_parameter_study_optimisation => task_15_parameter_study_optimisation}/openmc_model.py (100%) rename tasks/{task_14_parameter_study_optimisation => task_15_parameter_study_optimisation}/parameter_study_optimisation.ipynb (100%) rename tasks/{task_14_parameter_study_optimisation => task_15_parameter_study_optimisation}/run_all.sh (100%) diff --git a/tasks/README.md b/tasks/README.md index 211bd514..e5c63f29 100644 --- a/tasks/README.md +++ b/tasks/README.md @@ -13,5 +13,6 @@ | [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) | | [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating | | | [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux | | -| [Task 13 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | | -| [Task 14 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_parameter_study_optimisation) | Data science machine learning approaches | | +| [Task 13 - Variance reduction](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_variance_reduction) | Variance reduction with weight windows | | +| [Task 14 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | | +| [Task 15 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_optimisation) | Data science machine learning approaches | | diff --git a/tasks/task_13_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb b/tasks/task_14_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb similarity index 100% rename from tasks/task_13_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb rename to tasks/task_14_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb diff --git a/tasks/task_13_parameter_study_sampling/README.md b/tasks/task_14_parameter_study_sampling/README.md similarity index 100% rename from tasks/task_13_parameter_study_sampling/README.md rename to tasks/task_14_parameter_study_sampling/README.md diff --git a/tasks/task_13_parameter_study_sampling/openmc_model.py b/tasks/task_14_parameter_study_sampling/openmc_model.py similarity index 100% rename from tasks/task_13_parameter_study_sampling/openmc_model.py rename to tasks/task_14_parameter_study_sampling/openmc_model.py diff --git a/tasks/task_13_parameter_study_sampling/plotting_tools.py b/tasks/task_14_parameter_study_sampling/plotting_tools.py similarity index 100% rename from tasks/task_13_parameter_study_sampling/plotting_tools.py rename to tasks/task_14_parameter_study_sampling/plotting_tools.py diff --git a/tasks/task_13_parameter_study_sampling/run_all.sh b/tasks/task_14_parameter_study_sampling/run_all.sh similarity index 100% rename from tasks/task_13_parameter_study_sampling/run_all.sh rename to tasks/task_14_parameter_study_sampling/run_all.sh diff --git a/tasks/task_14_parameter_study_optimisation/README.md b/tasks/task_15_parameter_study_optimisation/README.md similarity index 100% rename from tasks/task_14_parameter_study_optimisation/README.md rename to tasks/task_15_parameter_study_optimisation/README.md diff --git a/tasks/task_14_parameter_study_optimisation/openmc_model.py b/tasks/task_15_parameter_study_optimisation/openmc_model.py similarity index 100% rename from tasks/task_14_parameter_study_optimisation/openmc_model.py rename to tasks/task_15_parameter_study_optimisation/openmc_model.py diff --git a/tasks/task_14_parameter_study_optimisation/parameter_study_optimisation.ipynb b/tasks/task_15_parameter_study_optimisation/parameter_study_optimisation.ipynb similarity index 100% rename from tasks/task_14_parameter_study_optimisation/parameter_study_optimisation.ipynb rename to tasks/task_15_parameter_study_optimisation/parameter_study_optimisation.ipynb diff --git a/tasks/task_14_parameter_study_optimisation/run_all.sh b/tasks/task_15_parameter_study_optimisation/run_all.sh similarity index 100% rename from tasks/task_14_parameter_study_optimisation/run_all.sh rename to tasks/task_15_parameter_study_optimisation/run_all.sh From 41f05752670a7085f02ff4139bcb47b9cb56241c Mon Sep 17 00:00:00 2001 From: Jonathan Date: Sun, 6 Feb 2022 22:23:36 +0000 Subject: [PATCH 18/31] [skip ci] split example into two sections --- .../2_minimal_weight_window_example.py | 158 ------------------ .../2_minimal_weight_window_example.py} | 63 +++---- .../3_minimal_weight_window_example.py | 0 .../ww/1_minimal_weight_window_example.py | 86 ++++++++++ 4 files changed, 105 insertions(+), 202 deletions(-) delete mode 100644 tasks/task_13_variance_reduction/2_minimal_weight_window_example.py rename tasks/task_13_variance_reduction/{1_minimal_weight_window_example.py => no_ww/2_minimal_weight_window_example.py} (77%) rename tasks/task_13_variance_reduction/{ => spectra}/3_minimal_weight_window_example.py (100%) create mode 100644 tasks/task_13_variance_reduction/ww/1_minimal_weight_window_example.py diff --git a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py deleted file mode 100644 index b596489d..00000000 --- a/tasks/task_13_variance_reduction/2_minimal_weight_window_example.py +++ /dev/null @@ -1,158 +0,0 @@ -import openmc -import os -from spectrum_plotter import plot_spectrum_from_tally - - -# MATERIALS - -# creates a single material -mats = openmc.Materials() - -shielding_material = openmc.Material(name="breeder") -shielding_material.add_nuclide('Fe56', 1, percent_type='ao') -shielding_material.set_density('g/cm3', 7) - -mats = [shielding_material] - - - -# GEOMETRY - -# surfaces -sph1 = openmc.Sphere(r=200, boundary_type='vacuum') -plane1 = openmc.YPlane(y0=-1, boundary_type='reflective') -plane2 = openmc.YPlane(y0=1, boundary_type='reflective') - - -# cells -shield_cell = openmc.Cell(region=-sph1 & +plane1 & -plane2) -shield_cell.fill = shielding_material - -universe = openmc.Universe(cells=[shield_cell]) - -geom = openmc.Geometry(universe) - - -# creates a 14MeV point source -source = openmc.Source() -source.space = openmc.stats.Point((0, 0, 0)) -source.angle = openmc.stats.Isotropic() -source.energy = openmc.stats.Discrete([14e6], [1]) - -# SETTINGS - -# Instantiate a Settings object -sett = openmc.Settings() -sett.batches = 100 -sett.inactive = 0 -sett.particles = 500 -sett.source = source -sett.run_mode = 'fixed source' -# sett.particles = 'neutrons' - - -#creates an empty tally object -tallies = openmc.Tallies() - - -# sets up filters for the tallies -neutron_particle_filter = openmc.ParticleFilter(['neutron']) -energy_bins = openmc.mgxs.GROUP_STRUCTURES['CCFE-709'] -energy_filter = openmc.EnergyFilter(energy_bins) - -# setup the filters for the surface tally -front_surface_filter = openmc.SurfaceFilter(sph1) -# detects when particles across the surface - -front_surface_spectra_tally = openmc.Tally(name='front_surface_spectra_tally') -front_surface_spectra_tally.scores = ['current'] -front_surface_spectra_tally.filters = [front_surface_filter, neutron_particle_filter, energy_filter] -tallies.append(front_surface_spectra_tally) - - -# combines the geometry, materials, settings and tallies to create a neutronics model -model = openmc.model.Model(geom, mats, sett, tallies) - -# plt.show(universe.plot(width=(180, 180), basis='xz')) - -# # deletes old files -os.remove('summary.h5') -os.remove(f'statepoint.{sett.batches}.h5') - - -# runs the simulation -output_filename = model.run() - -# open the results file -results = openmc.StatePoint(output_filename) -my_analogy_tally = results.get_tally(name="front_surface_spectra_tally") - - - - - - -# Create mesh which will be used for tally and weight window -my_ww_mesh = openmc.RegularMesh() -mesh_height = 5 # number of mesh elements in the Y direction -mesh_width = 5 # number of mesh elements in the X direction -my_ww_mesh.dimension = [mesh_width, 1, mesh_height] # only 1 cell in the Y dimension -my_ww_mesh.lower_left = [-100, -1, -100] # physical limits (corners) of the mesh -my_ww_mesh.upper_right = [100, 1, 100] - - -lower_ww_bounds = [ - 0.1, 0.1, 0.1, 0.1, 0.1, - 0.1, 0.2, 0.2, 0.2, 0.1, - 0.1, 0.2, -1, 0.2, 0.1, - 0.1, 0.2, 0.2, 0.2, 0.1, - 0.1, 0.1, 0.1, 0.1, 0.1, -] - -upper_ww_bounds = [ - 0.2, 0.2, 0.2, 0.2, 0.2, - 0.2, 0.4, 0.4, 0.4, 0.2, - 0.2, 0.4, -1, 0.4, 0.2, - 0.2, 0.4, 0.4, 0.4, 0.2, - 0.2, 0.2, 0.2, 0.2, 0.2, -] - - -# docs for ww are here -# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows -ww = openmc.WeightWindows( - mesh=my_ww_mesh, - upper_ww_bounds=upper_ww_bounds, - lower_ww_bounds=lower_ww_bounds, - particle_type='neutron', - energy_bins=(0.0, 100_000_000.0), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) - survival_ratio=5 -) -sett.weight_windows = ww - - -# # deletes old files -os.remove('summary.h5') -os.remove(f'statepoint.{sett.batches}.h5') - -output_filename = model.run() - -# open the results file -ww_results = openmc.StatePoint(output_filename) -my_weight_window_tally = ww_results.get_tally(name="front_surface_spectra_tally") - - - -test_plot = plot_spectrum_from_tally( - spectrum={"analogy": my_analogy_tally, 'my_weight_window_tally': my_weight_window_tally}, - x_label="Energy [MeV]", - y_label="Current [n/source_particle]", - x_scale="log", - y_scale="log", - title="example plot 1", - required_units="neutron / source_particle", - plotting_package="plotly", - filename="example_spectra_from_tally_matplotlib.html", -) - -test_plot.show() \ No newline at end of file diff --git a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/no_ww/2_minimal_weight_window_example.py similarity index 77% rename from tasks/task_13_variance_reduction/1_minimal_weight_window_example.py rename to tasks/task_13_variance_reduction/no_ww/2_minimal_weight_window_example.py index 4987f21e..b681ded8 100644 --- a/tasks/task_13_variance_reduction/1_minimal_weight_window_example.py +++ b/tasks/task_13_variance_reduction/no_ww/2_minimal_weight_window_example.py @@ -36,15 +36,6 @@ # SETTINGS -# Instantiate a Settings object -sett = openmc.Settings() -sett.batches = 100 -sett.inactive = 0 -sett.particles = 500 -sett.source = source -sett.run_mode = 'fixed source' - - # Create mesh which will be used for the tally my_tally_mesh = openmc.RegularMesh() my_tally_mesh.dimension = [25, 1, 25] # only 1 cell in the Y dimension @@ -60,29 +51,6 @@ tallies = openmc.Tallies() tallies.append(mesh_tally) -# combines the geometry, materials, settings and tallies to create a neutronics model -model = openmc.model.Model(geom, mats, sett, tallies) - -# runs the simulation with weight windows -output_no_ww_filename = model.run() - -# open the results file -results_no_ww = openmc.StatePoint(output_no_ww_filename) - -# access the flux tally -my_tally_no_ww = results_no_ww.get_tally(scores=['flux']) -my_slice_no_ww = my_tally_no_ww.get_slice(scores=['flux']) -my_slice_no_ww.mean.shape = (25, 25) -fig = plt.subplot() - -# when plotting the 2d data, added the extent is required. -# otherwise the plot uses the index of the 2d data arrays -# as the x y axis -fig.imshow(my_slice_no_ww.mean, extent=[-120,120,-120,120], vmin=1e-5, vmax=10) -plt.savefig('no_ww.png') -# plt.show() - - # Create mesh which will be used for tally and weight window my_ww_mesh = openmc.RegularMesh() @@ -103,20 +71,29 @@ energy_bins=(0.0, 100_000_000.), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) survival_ratio=5 ) -# sets the weight windows define to be used in the simulation -sett.weight_windows = ww -# deletes old files -try: - os.remove('summary.h5') -except OSError: - pass +# Instantiate a Settings object +sett = openmc.Settings() # as each particle history is now longer due to the splitting that occurs with # weight windows. Running the same number of batches would therefore take more # time. To make a fair comparison the batch has been reduce to 20 as this takes # a similar amount of time as 100 without weight windows -sett.batches=20 + +sett.batches = 20 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' +# sets the weight windows define to be used in the simulation +sett.weight_windows = ww + +# # deletes old files +# try: +# os.remove('summary.h5') +# except OSError: +# pass + # combines the geometry, materials, settings and tallies to create a neutronics model @@ -126,8 +103,6 @@ output_ww_filename = model.run() - - # open the results file results_ww = openmc.StatePoint(output_ww_filename) @@ -140,6 +115,6 @@ # when plotting the 2d data, added the extent is required. # otherwise the plot uses the index of the 2d data arrays # as the x y axis -fig.imshow(my_slice_ww.mean, extent=[-120,120,-120,120], vmin=1e-5, vmax=10) +fig.imshow(my_slice_ww.mean, extent=[-120,120,-120,120])#, vmin=1e-5, vmax=10) plt.savefig('ww.png') -# plt.show() +plt.show() \ No newline at end of file diff --git a/tasks/task_13_variance_reduction/3_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/spectra/3_minimal_weight_window_example.py similarity index 100% rename from tasks/task_13_variance_reduction/3_minimal_weight_window_example.py rename to tasks/task_13_variance_reduction/spectra/3_minimal_weight_window_example.py diff --git a/tasks/task_13_variance_reduction/ww/1_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/ww/1_minimal_weight_window_example.py new file mode 100644 index 00000000..a55ad5d4 --- /dev/null +++ b/tasks/task_13_variance_reduction/ww/1_minimal_weight_window_example.py @@ -0,0 +1,86 @@ +import openmc +import os +import matplotlib.pyplot as plt + +# MATERIALS + +# creates a single material +mats = openmc.Materials() + +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) + +mats = [shielding_material] + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=250, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material + +universe = openmc.Universe(cells=[shield_cell]) + +geom = openmc.Geometry(universe) + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' + + +# Create mesh which will be used for the tally +my_tally_mesh = openmc.RegularMesh() +my_tally_mesh.dimension = [25, 1, 25] # only 1 cell in the Y dimension +my_tally_mesh.lower_left = [-120, -1, -120] # physical limits (corners) of the mesh +my_tally_mesh.upper_right = [120, 1, 120] + +# Create mesh filter for tally +mesh_filter = openmc.MeshFilter(my_tally_mesh) +mesh_tally = openmc.Tally(name='flux_on_mesh') +mesh_tally.filters = [mesh_filter] +mesh_tally.scores = ['flux'] +#creates an empty tally object +tallies = openmc.Tallies() +tallies.append(mesh_tally) + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# runs the simulation with weight windows +output_no_ww_filename = model.run() + +# open the results file +results_no_ww = openmc.StatePoint(output_no_ww_filename) + +# access the flux tally +my_tally_no_ww = results_no_ww.get_tally(scores=['flux']) +my_slice_no_ww = my_tally_no_ww.get_slice(scores=['flux']) +my_slice_no_ww.mean.shape = (25, 25) +fig = plt.subplot() + +# when plotting the 2d data, added the extent is required. +# otherwise the plot uses the index of the 2d data arrays +# as the x y axis +fig.imshow(my_slice_no_ww.mean, extent=[-120,120,-120,120])#, vmin=1e-5, vmax=10) +plt.savefig('no_ww.png') +plt.show() + + + From 96d31375c9fdb6becdaf712b1adb41147075c83f Mon Sep 17 00:00:00 2001 From: Jonathan Date: Sun, 13 Feb 2022 17:45:38 +0000 Subject: [PATCH 19/31] renamed files --- ...w_example.py => 1_minimal_weight_window_mesh_tally_example.py} | 0 ...window_example.py => 2_no_weight_window_mesh_tally_example.py} | 0 ...ample.py => 3_minimal_weight_window__spectra_tally_example.py} | 0 .../{sphere_otf => xml_examples}/orig/with_ww/make_vtk.py | 0 .../{sphere_otf => xml_examples}/orig/without_ww/make_vtk.py | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename tasks/task_13_variance_reduction/{ww/1_minimal_weight_window_example.py => 1_minimal_weight_window_mesh_tally_example.py} (100%) rename tasks/task_13_variance_reduction/{no_ww/2_minimal_weight_window_example.py => 2_no_weight_window_mesh_tally_example.py} (100%) rename tasks/task_13_variance_reduction/{spectra/3_minimal_weight_window_example.py => 3_minimal_weight_window__spectra_tally_example.py} (100%) rename tasks/task_13_variance_reduction/{sphere_otf => xml_examples}/orig/with_ww/make_vtk.py (100%) rename tasks/task_13_variance_reduction/{sphere_otf => xml_examples}/orig/without_ww/make_vtk.py (100%) diff --git a/tasks/task_13_variance_reduction/ww/1_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/1_minimal_weight_window_mesh_tally_example.py similarity index 100% rename from tasks/task_13_variance_reduction/ww/1_minimal_weight_window_example.py rename to tasks/task_13_variance_reduction/1_minimal_weight_window_mesh_tally_example.py diff --git a/tasks/task_13_variance_reduction/no_ww/2_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/2_no_weight_window_mesh_tally_example.py similarity index 100% rename from tasks/task_13_variance_reduction/no_ww/2_minimal_weight_window_example.py rename to tasks/task_13_variance_reduction/2_no_weight_window_mesh_tally_example.py diff --git a/tasks/task_13_variance_reduction/spectra/3_minimal_weight_window_example.py b/tasks/task_13_variance_reduction/3_minimal_weight_window__spectra_tally_example.py similarity index 100% rename from tasks/task_13_variance_reduction/spectra/3_minimal_weight_window_example.py rename to tasks/task_13_variance_reduction/3_minimal_weight_window__spectra_tally_example.py diff --git a/tasks/task_13_variance_reduction/sphere_otf/orig/with_ww/make_vtk.py b/tasks/task_13_variance_reduction/xml_examples/orig/with_ww/make_vtk.py similarity index 100% rename from tasks/task_13_variance_reduction/sphere_otf/orig/with_ww/make_vtk.py rename to tasks/task_13_variance_reduction/xml_examples/orig/with_ww/make_vtk.py diff --git a/tasks/task_13_variance_reduction/sphere_otf/orig/without_ww/make_vtk.py b/tasks/task_13_variance_reduction/xml_examples/orig/without_ww/make_vtk.py similarity index 100% rename from tasks/task_13_variance_reduction/sphere_otf/orig/without_ww/make_vtk.py rename to tasks/task_13_variance_reduction/xml_examples/orig/without_ww/make_vtk.py From 6db59e024de856d343e2abe03c30d7cf405c0c97 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Mon, 14 Feb 2022 00:05:14 +0000 Subject: [PATCH 20/31] added draft task for activation and tally traacking --- tasks/README.md | 5 +- ..._example_transmutation_isotope_build_up.py | 96 +++++++++++++++++++ ...techniques_for_sampling_design_space.ipynb | 0 .../README.md | 0 .../openmc_model.py | 0 .../plotting_tools.py | 0 .../run_all.sh | 0 .../README.md | 0 .../openmc_model.py | 0 .../parameter_study_optimisation.ipynb | 0 .../run_all.sh | 0 11 files changed, 99 insertions(+), 2 deletions(-) create mode 100644 tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py rename tasks/{task_14_parameter_study_sampling => task_15_parameter_study_sampling}/1_techniques_for_sampling_design_space.ipynb (100%) rename tasks/{task_14_parameter_study_sampling => task_15_parameter_study_sampling}/README.md (100%) rename tasks/{task_14_parameter_study_sampling => task_15_parameter_study_sampling}/openmc_model.py (100%) rename tasks/{task_14_parameter_study_sampling => task_15_parameter_study_sampling}/plotting_tools.py (100%) rename tasks/{task_14_parameter_study_sampling => task_15_parameter_study_sampling}/run_all.sh (100%) rename tasks/{task_15_parameter_study_optimisation => task_16_parameter_study_optimisation}/README.md (100%) rename tasks/{task_15_parameter_study_optimisation => task_16_parameter_study_optimisation}/openmc_model.py (100%) rename tasks/{task_15_parameter_study_optimisation => task_16_parameter_study_optimisation}/parameter_study_optimisation.ipynb (100%) rename tasks/{task_15_parameter_study_optimisation => task_16_parameter_study_optimisation}/run_all.sh (100%) diff --git a/tasks/README.md b/tasks/README.md index e5c63f29..0014e5a8 100644 --- a/tasks/README.md +++ b/tasks/README.md @@ -14,5 +14,6 @@ | [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating | | | [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux | | | [Task 13 - Variance reduction](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_variance_reduction) | Variance reduction with weight windows | | -| [Task 14 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | | -| [Task 15 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_optimisation) | Data science machine learning approaches | | +| [Task 14 - Activation and transmutation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_activation_transmutation) | Actionation of material, evolution of materials, tallies as a function of time, burn up, transmutation and isotope creation | | +| [Task 15 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | | +| [Task 16 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_parameter_study_optimisation) | Data science machine learning approaches | | diff --git a/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py b/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py new file mode 100644 index 00000000..0df5c3bd --- /dev/null +++ b/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py @@ -0,0 +1,96 @@ +import openmc +import openmc.deplete +import matplotlib.pyplot as plt +import math + +iron_sphere_radius = 250 + +# MATERIALS + +mats = openmc.Materials() + +# makes a simple material from Iron +shielding_material = openmc.Material(name="shielding_material") +shielding_material.add_element('Fe', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7.7) +shielding_material.volume = (4/3) * math.pi * iron_sphere_radius**3 +shielding_material.depletable = True + +materials = openmc.Materials([shielding_material]) +materials.export_to_xml() + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=iron_sphere_radius, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material +shield_cell.volume = (4/3) * math.pi * sph1.r**3 + +universe = openmc.Universe(cells=[shield_cell]) + +geometry = openmc.Geometry(universe) + + + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +settings = openmc.Settings() +settings.batches = 2 +settings.inactive = 0 +settings.particles = 500 +settings.source = source +settings.run_mode = 'fixed source' + + +tallies = openmc.Tallies() + +# added a cell tally for tritium production +cell_filter = openmc.CellFilter(shield_cell) +tbr_tally = openmc.Tally(name='TBR') +tbr_tally.filters = [cell_filter] +tbr_tally.scores = ['(n,Xt)'] # Where X is a wildcard character, this catches any tritium production +tallies.append(tbr_tally) + + +# run python generate_endf71_chain.py from the openmc-dev/data repo +chain_filename = '/home/jshim/data-shimwell/depletion/chain_endfb71.xml' +chain = openmc.deplete.Chain.from_xml(chain_filename) + +geometry.export_to_xml() +settings.export_to_xml() +tallies.export_to_xml() # running in depletion mode doesn't write out the tallies file +materials.export_to_xml() +model = openmc.model.Model(geometry, materials, settings, tallies) + +operator = openmc.deplete.Operator(model, chain_filename) + +time_steps = [3600, 86400, 3600, 86400, 3600] +source_rates = [1.e12, 0, 1.e12, 0, 1e12] + +integrator = openmc.deplete.PredictorIntegrator(operator, time_steps, source_rates) + +integrator.integrate() + +results = openmc.deplete.ResultsList.from_hdf5("depletion_results.h5") + +print(results.get_atoms('1', 'Co60')) + +# could be used material results.export_to_materials(1) could be used to plot + + +for counter in [0,1,2,3,4,5]: + sp = openmc.StatePoint(f'openmc_simulation_n{counter}.h5') + tbr_tally = sp.get_tally(name='TBR') + print(tbr_tally.mean, tbr_tally.std_dev) diff --git a/tasks/task_14_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb b/tasks/task_15_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb similarity index 100% rename from tasks/task_14_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb rename to tasks/task_15_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb diff --git a/tasks/task_14_parameter_study_sampling/README.md b/tasks/task_15_parameter_study_sampling/README.md similarity index 100% rename from tasks/task_14_parameter_study_sampling/README.md rename to tasks/task_15_parameter_study_sampling/README.md diff --git a/tasks/task_14_parameter_study_sampling/openmc_model.py b/tasks/task_15_parameter_study_sampling/openmc_model.py similarity index 100% rename from tasks/task_14_parameter_study_sampling/openmc_model.py rename to tasks/task_15_parameter_study_sampling/openmc_model.py diff --git a/tasks/task_14_parameter_study_sampling/plotting_tools.py b/tasks/task_15_parameter_study_sampling/plotting_tools.py similarity index 100% rename from tasks/task_14_parameter_study_sampling/plotting_tools.py rename to tasks/task_15_parameter_study_sampling/plotting_tools.py diff --git a/tasks/task_14_parameter_study_sampling/run_all.sh b/tasks/task_15_parameter_study_sampling/run_all.sh similarity index 100% rename from tasks/task_14_parameter_study_sampling/run_all.sh rename to tasks/task_15_parameter_study_sampling/run_all.sh diff --git a/tasks/task_15_parameter_study_optimisation/README.md b/tasks/task_16_parameter_study_optimisation/README.md similarity index 100% rename from tasks/task_15_parameter_study_optimisation/README.md rename to tasks/task_16_parameter_study_optimisation/README.md diff --git a/tasks/task_15_parameter_study_optimisation/openmc_model.py b/tasks/task_16_parameter_study_optimisation/openmc_model.py similarity index 100% rename from tasks/task_15_parameter_study_optimisation/openmc_model.py rename to tasks/task_16_parameter_study_optimisation/openmc_model.py diff --git a/tasks/task_15_parameter_study_optimisation/parameter_study_optimisation.ipynb b/tasks/task_16_parameter_study_optimisation/parameter_study_optimisation.ipynb similarity index 100% rename from tasks/task_15_parameter_study_optimisation/parameter_study_optimisation.ipynb rename to tasks/task_16_parameter_study_optimisation/parameter_study_optimisation.ipynb diff --git a/tasks/task_15_parameter_study_optimisation/run_all.sh b/tasks/task_16_parameter_study_optimisation/run_all.sh similarity index 100% rename from tasks/task_15_parameter_study_optimisation/run_all.sh rename to tasks/task_16_parameter_study_optimisation/run_all.sh From 3f651ed173116f80a28131129379d2ced16a1ebf Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 14 Feb 2022 17:56:11 +0000 Subject: [PATCH 21/31] updating to openmc 0.13.0 --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 31f856bf..1250eaa3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -227,8 +227,8 @@ RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Libr # installs OpenMc from source RUN cd /opt && \ # git clone --single-branch --branch model_lib_fix --depth 1 https://github.com/fusion-energy/openmc.git && \ - git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git && \ - # git clone --single-branch --branch v0.12.1 --depth 1 https://github.com/openmc-dev/openmc.git && \ + # git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git && \ + git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git && \ cd openmc && \ # this commit is from this PR https://github.com/openmc-dev/openmc/pull/1900 git checkout 0157dc219ff8dca814859b3140c6cef1e78cdee1 && \ From fd320d7e30c06c1a610f7098169acefb1d60085c Mon Sep 17 00:00:00 2001 From: Jonathan Date: Mon, 14 Feb 2022 23:41:26 +0000 Subject: [PATCH 22/31] [skip ci] removed commit checkout for openmc --- Dockerfile | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1250eaa3..60cd6aa9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -186,8 +186,8 @@ RUN if [ "$build_double_down" = "ON" ] ; \ mkdir build ; \ cd build ; \ cmake .. -DMOAB_DIR=/MOAB \ - -DCMAKE_INSTALL_PREFIX=.. \ - -DEMBREE_DIR=/embree ; \ + -DCMAKE_INSTALL_PREFIX=.. \ + -DEMBREE_DIR=/embree ; \ make -j"$compile_cores" ; \ make -j"$compile_cores" install ; \ rm -rf /double-down/build /double-down/double-down ; \ @@ -230,8 +230,6 @@ RUN cd /opt && \ # git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git && \ git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git && \ cd openmc && \ - # this commit is from this PR https://github.com/openmc-dev/openmc/pull/1900 - git checkout 0157dc219ff8dca814859b3140c6cef1e78cdee1 && \ mkdir build && \ cd build && \ cmake -Doptimize=on \ @@ -257,15 +255,17 @@ RUN pip install neutronics_material_maker \ openmc-plasma-source \ remove_dagmc_tags \ paramak \ - cad_to_h5m \ - stl_to_h5m \ + brep_to_h5m \ + brep_part_finder \ openmc-dagmc-wrapper \ openmc-tally-unit-converter \ regular_mesh_plotter \ spectrum_plotter \ dagmc_bounding_box \ openmc_source_plotter \ - openmc_mesh_tally_to_vtk + openmc_mesh_tally_to_vtk \ + cad_to_h5m \ + stl_to_h5m # an older version of openmc is need to provide an older executable # this particular exectuable allows an inital_source.h5 to be written From 4c5769f0c1f8f15f884feb26a4433dbf7b9c7678 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Thu, 17 Feb 2022 21:25:26 +0000 Subject: [PATCH 23/31] tidied up activation examples --- ..._example_transmutation_isotope_build_up.py | 38 ++++---- .../2_example_tally_change_with_burnup.py | 91 +++++++++++++++++++ 2 files changed, 110 insertions(+), 19 deletions(-) create mode 100644 tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py diff --git a/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py b/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py index 0df5c3bd..383c7bba 100644 --- a/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py +++ b/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py @@ -11,7 +11,7 @@ # makes a simple material from Iron shielding_material = openmc.Material(name="shielding_material") -shielding_material.add_element('Fe', 1, percent_type='ao') +shielding_material.add_nuclide('Co59', 1, percent_type='ao') shielding_material.set_density('g/cm3', 7.7) shielding_material.volume = (4/3) * math.pi * iron_sphere_radius**3 shielding_material.depletable = True @@ -47,7 +47,7 @@ # Instantiate a Settings object settings = openmc.Settings() -settings.batches = 2 +settings.batches = 5 settings.inactive = 0 settings.particles = 500 settings.source = source @@ -56,13 +56,6 @@ tallies = openmc.Tallies() -# added a cell tally for tritium production -cell_filter = openmc.CellFilter(shield_cell) -tbr_tally = openmc.Tally(name='TBR') -tbr_tally.filters = [cell_filter] -tbr_tally.scores = ['(n,Xt)'] # Where X is a wildcard character, this catches any tritium production -tallies.append(tbr_tally) - # run python generate_endf71_chain.py from the openmc-dev/data repo chain_filename = '/home/jshim/data-shimwell/depletion/chain_endfb71.xml' @@ -70,27 +63,34 @@ geometry.export_to_xml() settings.export_to_xml() -tallies.export_to_xml() # running in depletion mode doesn't write out the tallies file +# tallies.export_to_xml() # running in depletion mode doesn't write out the tallies file materials.export_to_xml() model = openmc.model.Model(geometry, materials, settings, tallies) operator = openmc.deplete.Operator(model, chain_filename) -time_steps = [3600, 86400, 3600, 86400, 3600] -source_rates = [1.e12, 0, 1.e12, 0, 1e12] -integrator = openmc.deplete.PredictorIntegrator(operator, time_steps, source_rates) +time_steps = [365*24*60*60] * 5 +source_rates = [1e9]*5 # 1GW + +integrator = openmc.deplete.PredictorIntegrator( + operator=operator, timesteps=time_steps,source_rates=source_rates +) integrator.integrate() results = openmc.deplete.ResultsList.from_hdf5("depletion_results.h5") -print(results.get_atoms('1', 'Co60')) +times, number_of_co60_atoms = results.get_atoms('1', 'Co60') -# could be used material results.export_to_materials(1) could be used to plot +import matplotlib.pyplot as plt + +fig, ax = plt.subplots() +ax.plot(times, number_of_co60_atoms) -for counter in [0,1,2,3,4,5]: - sp = openmc.StatePoint(f'openmc_simulation_n{counter}.h5') - tbr_tally = sp.get_tally(name='TBR') - print(tbr_tally.mean, tbr_tally.std_dev) +ax.set(xlabel='time (s)', ylabel='Number of atoms', + title='Build up of atoms saturates when decay is equal to activation this occurs at circa 5 half lives') +ax.grid() +plt.savefig('atoms.png') +plt.show() \ No newline at end of file diff --git a/tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py b/tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py new file mode 100644 index 00000000..6d89931e --- /dev/null +++ b/tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py @@ -0,0 +1,91 @@ +import openmc +import openmc.deplete +import matplotlib.pyplot as plt +import math + +lithium_orthosilicate_radius = 250 + +# MATERIALS + +mats = openmc.Materials() + +# makes a simple material from Iron +shielding_material = openmc.Material(name="shielding_material") +shielding_material.add_elements_from_formula('Li4SiO4') +shielding_material.set_density('g/cm3', 2.5) +shielding_material.volume = (4/3) * math.pi * lithium_orthosilicate_radius**3 +shielding_material.depletable = True + +materials = openmc.Materials([shielding_material]) +materials.export_to_xml() + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=lithium_orthosilicate_radius, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material +shield_cell.volume = (4/3) * math.pi * sph1.r**3 + +universe = openmc.Universe(cells=[shield_cell]) + +geometry = openmc.Geometry(universe) + + + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +settings = openmc.Settings() +settings.batches = 2 +settings.inactive = 0 +settings.particles = 500 +settings.source = source +settings.run_mode = 'fixed source' + + +tallies = openmc.Tallies() + +# added a cell tally for tritium production +cell_filter = openmc.CellFilter(shield_cell) +tbr_tally = openmc.Tally(name='TBR') +tbr_tally.filters = [cell_filter] +tbr_tally.scores = ['(n,Xt)'] # Where X is a wildcard character, this catches any tritium production +tallies.append(tbr_tally) + + +# run python generate_endf71_chain.py from the openmc-dev/data repo +chain_filename = '/home/jshim/data-shimwell/depletion/chain_endfb71.xml' +chain = openmc.deplete.Chain.from_xml(chain_filename) + +geometry.export_to_xml() +settings.export_to_xml() +tallies.export_to_xml() # running in depletion mode doesn't write out the tallies file +materials.export_to_xml() +model = openmc.model.Model(geometry, materials, settings, tallies) + +operator = openmc.deplete.Operator(model, chain_filename) + + +time_steps = [365*24*60*60] * 5 # 5 steps of 5 years in seconds +source_rates = [1e9]*5 # 1GW + + +integrator = openmc.deplete.PredictorIntegrator(operator, time_steps, source_rates) + +integrator.integrate() + +for counter in [0,1,2,3,4,5]: + sp = openmc.StatePoint(f'openmc_simulation_n{counter}.h5') + tbr_tally = sp.get_tally(name='TBR') + print(tbr_tally.mean, tbr_tally.std_dev) From e75b0c88078ca366800b2ed8ba100f440a1eb08f Mon Sep 17 00:00:00 2001 From: Jonathan Date: Thu, 17 Feb 2022 22:35:01 +0000 Subject: [PATCH 24/31] updated docker added new install script --- Dockerfile | 13 +- install_scripts/build_embree.sh | 108 ---------- ...nda_cadquery_openmc_dagmc_trelis_plugin.sh | 190 ----------------- .../install_openmc_embree_double_down.sh | 177 ---------------- .../install_openmc_ubuntu_18.04.sh | 194 ------------------ .../install_openmc_ubuntu_20.04.sh | 118 +++++++++++ 6 files changed, 120 insertions(+), 680 deletions(-) delete mode 100755 install_scripts/build_embree.sh delete mode 100644 install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh delete mode 100644 install_scripts/install_openmc_embree_double_down.sh delete mode 100644 install_scripts/install_openmc_ubuntu_18.04.sh create mode 100644 install_scripts/install_openmc_ubuntu_20.04.sh diff --git a/Dockerfile b/Dockerfile index 60cd6aa9..adbcaa9c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -60,8 +60,6 @@ RUN apt-get --yes install libeigen3-dev \ hdf5-tools \ imagemagick \ cmake \ - # libeigen3-dev required for DAGMC - libeigen3-dev \ # libnetcdf-dev is needed to allow NETCDF on MOAB which helps with tet meshes in OpenMC libnetcdf-dev \ # libtbb-dev required for DAGMC @@ -150,7 +148,7 @@ RUN if [ "$build_double_down" = "ON" ] ; \ # Clone and install MOAB RUN mkdir MOAB && \ cd MOAB && \ - git clone --single-branch --branch 5.3.0 --depth 1 https://bitbucket.org/fathomteam/moab.git && \ + git clone --single-branch --branch 5.3.1 --depth 1 https://bitbucket.org/fathomteam/moab.git && \ mkdir build && \ cd build && \ cmake ../moab -DENABLE_HDF5=ON \ @@ -197,12 +195,7 @@ RUN if [ "$build_double_down" = "ON" ] ; \ # DAGMC version develop install from source RUN mkdir DAGMC && \ cd DAGMC && \ - git clone --single-branch --branch develop https://github.com/svalinn/DAGMC.git && \ - # git clone --single-branch --branch develop --depth 1 https://github.com/svalinn/DAGMC.git && \ - cd DAGMC && \ - # this commit is from this PR https://github.com/svalinn/DAGMC/pull/786 - git checkout fbd0cdbad100a0fd8d80de42321e69d09fdd67f4 && \ - cd .. && \ + git clone --single-branch --branch v3.2.1 --depth 1 https://github.com/svalinn/DAGMC.git && \ mkdir build && \ cd build && \ cmake ../DAGMC -DBUILD_TALLY=ON \ @@ -226,8 +219,6 @@ RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Libr # installs OpenMc from source RUN cd /opt && \ - # git clone --single-branch --branch model_lib_fix --depth 1 https://github.com/fusion-energy/openmc.git && \ - # git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git && \ git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git && \ cd openmc && \ mkdir build && \ diff --git a/install_scripts/build_embree.sh b/install_scripts/build_embree.sh deleted file mode 100755 index 0753924c..00000000 --- a/install_scripts/build_embree.sh +++ /dev/null @@ -1,108 +0,0 @@ -#!/bin/bash -set -eu - -function build_embree() { - if [ -d $PWD/embree ] ; then - echo "Embree installed" - return - fi - - # make embree - git clone https://github.com/embree/embree - cd embree - echo "EMBREE being installed in "$EMBREE_DIR - mkdir bld - cd bld - cmake .. -DCMAKE_INSTALL_PREFIX=.. -DEMBREE_ISPC_SUPPORT=OFF - make -j4 - make install - cd .. - cd .. -} - -function build_double() { - if [ -d $PWD/double-down ] ; then - echo "double down already installed" - return - fi - echo $EMBREE_DIR - # make double down - git clone https://github.com/pshriwise/double-down - cd double-down - export DD_DIR=$PWD - mkdir bld - cd bld - cmake .. -DCMAKE_INSTALL_PREFIX=.. -DMOAB_DIR=$MOAB_DIR -DEMBREE_DIR=$EMBREE_DIR -DEMBREE_ROOT=$EMBREE_DIR - make -j4 - make install - cd .. - cd .. -} - -function build_dagmc() { - if [ -d $PWD/dagmc ] ; then - echo "dagmc already built" - return - fi - # make dagmc - git clone https://github.com/svalinn/dagmc - cd dagmc - mkdir bld - cd bld - cmake .. -DMOAB_DIR=$MOAB_DIR -DBUILD_STATIC_LIBS=OFF -DDOUBLE_DOWN=ON -DDOUBLE_DOWN_DIR=$DD_DIR -DCMAKE_INSTALL_PREFIX=.. - make -j4 - make install - cd .. - cd .. -} - -function build_openmc() { - if [ -d $PWD/openmc ] ; then - echo "openmc already built" - return - fi - # make dagmc - git clone https://github.com/openmc-dev/openmc - cd openmc - mkdir bld - cd bld - cmake .. -Ddagmc=ON -DDAGMC_DIR=$DAGMC_DIR -DCMAKE_INSTALL_PREFIX=$OPENMC_INSTALL_DIR - make -j4 - make install - cd .. - cd .. -} - -# need to know where MOAB is -if [ -z $MOAB_DIR ] ; then - echo "Must set MOAB_DIR outside the script" - echo "i.e. export MOAB_DIR=/path/to/moab" - exit 1 -fi - -# need to know where to install openmc is -if [ -z $OPENMC_INSTALL_DIR ] ; then - echo "Must set OPENMC_INSTALL_DIR outside the script" - echo "i.e. export MOAB_DIR=/path/to/moab" - echo " or OPENMC_DIR=/path/to/thing/" - exit 1 -fi - -export DAGMC_DIR=$PWD/dagmc/lib/cmake -export EMBREE_DIR=$PWD/embree/lib/cmake/embree-3.12.1 -export DD_DIR=$PWD/double-down/lib/cmake - -sudo apt-get install cmake-curses-gui -sudo apt-get install libtbb-dev -sudo apt-get install libglfw3-dev -sudo apt-get install libeigen3-dev - -build_embree -build_double -build_dagmc -build_openmc - -# all done -echo "all done" - - diff --git a/install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh b/install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh deleted file mode 100644 index b33667dc..00000000 --- a/install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh +++ /dev/null @@ -1,190 +0,0 @@ - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - -sudo apt-get install --yes wget - -# Miniconda - -# wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -# bash Miniconda3-py37_4.8.3-Linux-x86_64.sh -# conda init -# conda create -y --name cq -# conda activate cq -# conda clean --all -# conda install -c conda-forge -c python python=3.7.8 -# conda clean --all -# conda install -c conda-forge -c cadquery cadquery=2 - - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - - -sudo apt-get --yes install gfortran -sudo apt-get --yes install g++ -sudo apt-get --yes install cmake -sudo apt-get --yes install libhdf5-dev - -sudo apt-get install -y python3 -sudo apt-get install -y python3-pip -sudo apt-get install -y python3-dev -sudo apt-get install -y python3-tk - -sudo apt-get install --yes imagemagick -sudo apt-get install --yes hdf5-tools -sudo apt-get install --yes paraview -sudo apt-get install --yes eog -sudo apt-get install --yes libsilo-dev -sudo apt-get install --yes git - -sudo apt-get --yes install dpkg -sudo apt-get --yes install libxkbfile1 -sudo apt-get --yes install -f -sudo apt-get --yes install libblas-dev -sudo apt-get --yes install liblapack-dev - -sudo apt-get install libeigen3-dev - -sudo apt-get --yes install libnetcdf-dev -sudo apt-get --yes install libnetcdf13 - -sudo apt remove -y cmake -pip3 install cmake -# need cmake version 3.18.2 - -pip3 install numpy pandas six h5py Matplotlib uncertainties lxml scipy cython vtk pytest -pip3 install codecov pytest-cov pylint plotly tqdm pyside2 ghalton==0.6.1 - -pip3 install neutronics_material_maker - -cd ~ -git clone https://github.com/njoy/NJOY2016 -cd NJOY2016 -mkdir build -cd build -cmake -Dstatic=on .. && make 2>/dev/null -sudo make install - -MOAB_INSTALL_DIR=$HOME/MOAB -DAGMC_INSTALL_DIR=$HOME/DAGMC -set -ex - -echo 'export MOAB_INSTALL_DIR=$HOME/MOAB' >> ~/.bashrc -echo 'export DAGMC_INSTALL_DIR=$HOME/DAGMC' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc - -pip3 install cython - -cd ~ -mkdir MOAB -cd MOAB -git clone -b Version5.1.0 https://bitbucket.org/fathomteam/moab/ -mkdir build -cd build -# this installs without netcdf but with pymoab -#cmake ../moab -DENABLE_HDF5=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_PYMOAB=ON -# this installs with netcdf but without pymoab -cmake ../moab -DENABLE_HDF5=ON -DENABLE_MPI=off -DENABLE_NETCDF=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -make -j2 -make -j install -# this 2nd build is required which is a shame -# this is to be used if you want pymoab -# cmake ../moab -DBUILD_SHARED_LIBS=OFF -# otherwise if you want netcdf -cmake ../moab -DBUILD_SHARED_LIBS=OFF -make -j install - -LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/MOAB/bin' >> ~/.bashrc - -cd ~ -mkdir DAGMC -cd DAGMC -git clone -b develop https://github.com/svalinn/dagmc -mkdir build -cd build -cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -make -j install -LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/DAGMC/bin' >> ~/.bashrc - -# OpenMC Install, this must be installed to /opt/openmc, `parametric_plasma_source` python module has this path hard-coded -cd /opt -sudo git clone --recurse-submodules https://github.com/openmc-dev/openmc.git -cd /opt/openmc -sudo chmod 777 -R openmc -sudo git checkout develop -sudo mkdir build -sudo chmod 777 build -cd build -cmake -Ddagmc=ON -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -# cmake -Ddagmc=ON -Ddebug=on -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -sudo make -j2 -sudo make -j install -cd /opt -sudo chmod 777 -R openmc -cd /opt/openmc/ -pip install -e . - -cd ~ -git clone https://github.com/openmc-dev/data.git -cd data -python3 convert_fendl.py -python3 convert_tendl.py -python3 convert_nndc71.py - -OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2017-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2019-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml' >> ~/.bashrc - - -# OPENMC_CROSS_SECTION library - -# Single cross-section library - -# change filepaths to desired library cross_sections.xml file -OPENMC_CROSS_SECTIONS=~/data/nndc-b7.1-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS=~/data/nndc-b7.1-hdf5/cross_sections.xml' >> ~/.bashrc - -# Combined cross-section library - -# cd ~/data -# python3 combine_libraries.py -l fendl-3.1d-hdf5/cross_sections.xml nndc-b7.1-hdf5/cross_sections.xml tendl-2019-hdf5/cross_sections.xml -o combined_cross_sections.xml -# OPENMC_CROSS_SECTIONS=~/data/combined_cross_sections.xml -# echo 'export OPENMC_CROSS_SECTIONS=~/data/combined_cross_sections.xml' >> ~/.bashrc - - -# Trelis - -# Download Trelis-16.5.4-Lin64.deb -# Add Trelis-16.5.4-Lin64.deb to /opt folder - -# cd /opt -# sudo dpkg -i Trelis-16.5.4-Lin64.deb - - -# Trelis-DAGMC Plugin - -cd ~ -sudo apt-get install openfortivpn -sudo apt install curl - -# Download svalinn-plugin-16.5-u18.04.tgz from https://uwmadison.app.box.com/v/dagmc-trelis -# Add svalinn-plugin-16.5-u18.04.tgz to /opt/Trelis-16.5/bin/plugins - -cd /opt/Trelis-16.5/bin/plugins -sudo tar xzf svalinn-plugin-16.5-u18.04.tgz - -cd /opt/Trelis-16.5/bin -sudo bash plugins/svalinn/install.sh - -PATH=$PATH:/opt/Trelis-16.5/bin -echo 'export PATH=$PATH:/opt/Trelis-16.5/bin' >> ~/.bashrc - -LD_LIBRARY_PATH=/opt/Trelis-16.5/bin/plugins/svalinn:$LD_LIBRARY_PATH -echo 'export LD_LIBRARY_PATH=/opt/Trelis-16.5/bin/plugins/svalinn:$LD_LIBRARY_PATH' >> ~/.bashrc \ No newline at end of file diff --git a/install_scripts/install_openmc_embree_double_down.sh b/install_scripts/install_openmc_embree_double_down.sh deleted file mode 100644 index b2150bf2..00000000 --- a/install_scripts/install_openmc_embree_double_down.sh +++ /dev/null @@ -1,177 +0,0 @@ - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - -# Install dependencies from Debian package manager -sudo apt-get install --yes wget \ - git \ - gfortran \ - g++ \ - cmake \ - mpich \ - libmpich-dev \ - libhdf5-serial-dev \ - libhdf5-mpich-dev \ - imagemagick \ - autoremove \ - clean - -# Miniconda -wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -bash Miniconda3-py37_4.8.3-Linux-x86_64.sh -conda init -conda create -y --name cq -conda activate cq -conda clean --all -conda install -c conda-forge -c cadquery cadquery=master -conda install gxx_linux-64 - -# required pacakges identified from openmc travis.yml -sudo apt-get --yes install mpich \ - libmpich-dev \ - libhdf5-serial-dev \ - libhdf5-mpich-dev \ - libblas-dev \ - liblapack-dev \ - imagemagick - -# needed to allow NETCDF on MOAB which helps with tet meshes in OpenMC -sudo apt-get --yes install libnetcdf-dev - -# eigen3 needed for DAGMC -sudo apt-get --yes install libeigen3-dev - -# dependancies used in the workshop -sudo apt-get -y install git -sudo apt-get --yes install hdf5-tools - -# new version needed for openmc compile -pip install cmake - - -# Python libraries used in the workshop -pip install plotly tqdm ghalton==0.6.1 noisyopt scikit-optimize \ - inference-tools adaptive vtk itkwidgets nest_asyncio \ - neutronics_material_maker parametric-plasma-source pytest \ - pytest-cov - -# needed for moab -pip install cython - -# needed for openmc -pip install --upgrade numpy - - -# install addition packages required for DAGMC -sudo apt-get --yes install libeigen3-dev \ - libblas-dev \ - liblapack-dev \ - libnetcdf-dev \ - libtbb-dev \ - libglfw3-dev - -# needed for CadQuery functionality -sudo apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev \ - freeglut3-dev libosmesa6 libosmesa6-dev \ - libgles2-mesa-dev - - -export compile_cores=2 - -# Clone and install Embree -git clone --single-branch --branch master https://github.com/embree/embree -cd embree -mkdir build -cd build -cmake .. -DCMAKE_INSTALL_PREFIX=.. \ - -DEMBREE_ISPC_SUPPORT=OFF -make -j"$compile_cores" -make -j"$compile_cores" install - - -cd ~ -mkdir MOAB -cd MOAB -git clone --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ -mkdir build -cd build -# this installs without netcdf but with pymoab -#cmake ../moab -DENABLE_HDF5=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_PYMOAB=ON -cmake ../moab -DENABLE_HDF5=ON \ - -DENABLE_NETCDF=ON \ - -DBUILD_SHARED_LIBS=OFF \ - -DENABLE_FORTRAN=OFF \ - -DCMAKE_INSTALL_PREFIX=$HOME/MOAB -make -j"$compile_cores" -make -j"$compile_cores" install -# this 2nd build is required and includes pymoab -cmake ../moab -DBUILD_SHARED_LIBS=ON \ - -DENABLE_HDF5=ON \ - -DENABLE_PYMOAB=ON \ - -DENABLE_BLASLAPACK=OFF \ - -DENABLE_FORTRAN=OFF \ - -DCMAKE_INSTALL_PREFIX=$HOME/MOAB -make -j"$compile_cores" -make -j"$compile_cores" install -cd pymoab -bash install.sh -python setup.py install - -# Clone and install Double-Down -cd ~ -git clone https://github.com/pshriwise/double-down -cd double-down -mkdir build -cd build -cmake .. -DCMAKE_INSTALL_PREFIX=.. \ - -DMOAB_DIR=$HOME/MOAB \ - -DEMBREE_DIR=$HOME/embree/lib/cmake/embree-3.12.1 -make -j"$compile_cores" -make -j"$compile_cores" install - -# DAGMC install -cd ~ -mkdir DAGMC -cd DAGMC -git clone --single-branch --branch develop https://github.com/svalinn/dagmc -mkdir build -cd build -cmake ../dagmc -DBUILD_TALLY=ON \ - -DCMAKE_INSTALL_PREFIX=$HOME/DAGMC \ - -DMOAB_DIR=$HOME/MOAB # this might need changing to /home/username/MOAB -make -j"$compile_cores" install - -export DAGMC_INSTALL_DIR=$HOME/DAGMC -export LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH -export LD_LIBRARY_PATH=/opt/Trelis-16.5/bin/plugins/svalinn:$LD_LIBRARY_PATH - -# installs OpenMc from source -cd /opt -git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git -sudo chmod -R 777 openmc -cd openmc -mkdir build -cd build -cmake -Ddagmc=ON \ - -DDAGMC_DIR=$HOME/DAGMC/build \ - -DHDF5_PREFER_PARALLEL=OFF .. -make -j"$compile_cores" -sudo make -j"$compile_cores" install -cd /opt/openmc/ -pip install . - -# Clone and install NJOY2016 -cd ~ -git clone https://github.com/njoy/NJOY2016 --branch master --single-branch -cd NJOY2016 -mkdir build -cd build -cmake -Dstatic=on .. -make 2>/dev/null -sudo make install - -# clone and download nuclear data -git clone --single-branch --branch master https://github.com/openmc-dev/data.git -python3 data/convert_nndc71.py -python3 data/convert_tendl.py -python3 data/data/combine_libraries.py -l data/nndc-b7.1-hdf5/cross_sections.xml data/tendl-2019-hdf5/cross_sections.xml -o data/cross_sections.xml diff --git a/install_scripts/install_openmc_ubuntu_18.04.sh b/install_scripts/install_openmc_ubuntu_18.04.sh deleted file mode 100644 index 0c79f548..00000000 --- a/install_scripts/install_openmc_ubuntu_18.04.sh +++ /dev/null @@ -1,194 +0,0 @@ - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - -sudo apt-get --yes install gfortran -sudo apt-get --yes install g++ -sudo apt-get --yes install cmake -sudo apt-get --yes install libhdf5-dev - -sudo apt-get install -y python3 -sudo apt-get install -y python3-pip -sudo apt-get install -y python3-dev -sudo apt-get install -y python3-tk - -sudo apt-get install --yes imagemagick -sudo apt-get install --yes hdf5-tools -sudo apt-get install --yes paraview -sudo apt-get install --yes eog -sudo apt-get install --yes wget -sudo apt-get install --yes libsilo-dev -sudo apt-get install --yes git - -sudo apt-get --yes install dpkg -sudo apt-get --yes install libxkbfile1 -sudo apt-get --yes install -f -sudo apt-get --yes install libblas-dev -sudo apt-get --yes install liblapack-dev - -# needed to allow NETCDF on MOAB which helps with tet meshes in OpenMC -sudo apt-get --yes install libnetcdf-dev -sudo apt-get --yes install libnetcdf13 - -# needed for newest version of openmc with dagmc -sudo apt remove -y cmake -pip3 install cmake==3.12.0 - -pip3 install numpy --user -pip3 install pandas --user -pip3 install six --user -pip3 install h5py --user -pip3 install Matplotlib --user -pip3 install uncertainties --user -pip3 install lxml --user -pip3 install scipy --user -pip3 install cython --user -pip3 install vtk --user -pip3 install pytest --user -pip3 install codecov --user -pip3 install pytest-cov --user -pip3 install pylint --user -pip3 install plotly --user -pip3 install tqdm --user -pip3 install pyside2 --user # required by openmc plotter -pip3 install ghalton==0.6.1 - -# needed for workshop tasks -pip3 install neutronics_material_maker --user - -# Clone and install NJOY2016 -cd ~ -git clone https://github.com/njoy/NJOY2016 #/opt/NJOY2016 -cd NJOY2016 -mkdir build -cd build -cmake -Dstatic=on .. && make 2>/dev/null -sudo make install - - -sudo rm /usr/bin/python -sudo ln -s /usr/bin/python3 /usr/bin/python - -# MOAB Variables -MOAB_INSTALL_DIR=$HOME/MOAB - -# DAGMC Variables -DAGMC_INSTALL_DIR=$HOME/DAGMC -set -ex - -echo 'export MOAB_INSTALL_DIR=$HOME/MOAB' >> ~/.bashrc -echo 'export DAGMC_INSTALL_DIR=$HOME/DAGMC' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc -# echo '$PATH:/openmc/build/bin/' >> ~/.bashrc - -pip install cython - -# MOAB Install -cd ~ -mkdir MOAB -cd MOAB -git clone -b Version5.1.0 https://bitbucket.org/fathomteam/moab/ -mkdir build -cd build -# this installs without netcdf but with pymoab -#cmake ../moab -DENABLE_HDF5=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_PYMOAB=ON -# this installs with netcdf but without pymoab -cmake ../moab -DENABLE_HDF5=ON -DENABLE_MPI=off -DENABLE_NETCDF=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -make -j -make -j install -# this 2nd build is required which is a shame -# this is to be used if you want pymoab -# cmake ../moab -DBUILD_SHARED_LIBS=OFF -# otherwise if you want netcdf -cmake ../moab -DBUILD_SHARED_LIBS=OFF -make -j install - -# if you installed pymoab run these two commands as well -# cd pymoab -# python3 setup.py install --user - -#needs setting in bashrc -LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/MOAB/bin' >> ~/.bashrc - - -# DAGMC Install -cd ~ -mkdir DAGMC -cd DAGMC -git clone -b develop https://github.com/svalinn/dagmc -mkdir build -cd build -# cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_EXE=ON -# cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -DBUILD_STATIC_LIBS=OFF -cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -make -j install -# rm -rf $HOME/DAGMC/dagmc -#needs setting in bashrc -LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/DAGMC/bin' >> ~/.bashrc - - -# OpenMC Install -cd /opt -sudo git clone https://github.com/mit-crpg/openmc.git --recursive -cd /opt/openmc -sudo git checkout develop -sudo mkdir build -sudo chmod 777 build -cd build -cmake -Doptimize=on -Ddagmc=ON -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -# cmake -Ddagmc=ON -Ddebug=on -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -sudo make -sudo make install -cd /opt/openmc/ -sudo python3 setup.py develop --user - - -# Nuclear data install -cd ~ -git clone https://github.com/openmc-dev/data.git -cd data -python3 convert_fendl.py -python3 convert_tendl.py -python3 convert_nndc71.py - - -OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2017-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2019-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml' >> ~/.bashrc - -OPENMC_CROSS_SECTIONS=~/data/tendl-2017-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS=~/data/tendl-2019-hdf5/cross_sections.xml' >> ~/.bashrc - - - -RUN git clone https://github.com/openmc-dev/plotter.git -echo 'export PATH=$PATH:/plotter/' >> ~/.bashrc - - - - -# dependancies for the occ_faceter -sudo apt-get --yes update && apt-get --yes upgrade -sudo apt-get --yes install libcgal-dev -sudo apt-get --yes install software-properties-common -sudo add-apt-repository -y ppa:freecad-maintainers/freecad-stable -sudo apt-get --yes install libocc*dev -sudo apt-get --yes install occ* -sudo apt-get --yes install libtbb-dev - -# install the occ_faceter, this currently uses a branch that could be merged -cd ~ -git clone https://github.com/makeclean/occ_faceter.git -cd occ_faceter -mkdir build && cd build -cmake .. -DCMAKE_INSTALL_PREFIX=.. -make -make install -sudo cp /occ_faceter/bin/steps2h5m /bin -sudo cp /occ_faceter/bin/occ_faceter /bin diff --git a/install_scripts/install_openmc_ubuntu_20.04.sh b/install_scripts/install_openmc_ubuntu_20.04.sh new file mode 100644 index 00000000..7a51e14a --- /dev/null +++ b/install_scripts/install_openmc_ubuntu_20.04.sh @@ -0,0 +1,118 @@ + +# install openmc with dagmc embree and double down into a new conda enviroment +# packages are compiled in this install script using all available CPU cores. +# to reduce the core usage to 2 replace -j commands with -j2 + + +sudo apt-get --yes update +apt-get --yes upgrade + + +# install dependancies +sudo apt-get install libeigen3-dev +sudo apt-get install git +sudo apt-get install wget +sudo apt-get install gfortran +sudo apt-get install g++ +sudo apt-get install mpich +sudo apt-get install libmpich-dev +sudo apt-get install libhdf5-serial-dev +sudo apt-get install libhdf5-mpich-dev +sudo apt-get install hdf5-tools +sudo apt-get install imagemagick +sudo apt-get install cmake +sudo apt-get install libeigen3-dev +sudo apt-get install libnetcdf-dev +sudo apt-get install libtbb-dev +sudo apt-get install libgles2-mesa-dev + +# install conda, creates new python enviroment and activates it +cd ~ +wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +bash Miniconda3-latest-Linux-x86_64.sh +conda create --name openmc-dagmc python=3.8 +conda activate openmc-dagmc + +# install python dependancies +conda install numpy +conda install cython + +# installs embree +cd ~ +git clone --shallow-submodules --single-branch --branch v3.12.2 --depth 1 https://github.com/embree/embree.git +cd embree +mkdir build +cd build +cmake .. -DCMAKE_INSTALL_PREFIX=.. -DEMBREE_ISPC_SUPPORT=OFF +make -j +make -j install + +# install moab +cd ~ +mkdir MOAB +cd MOAB +git clone --single-branch --branch 5.3.1 --depth 1 https://bitbucket.org/fathomteam/moab.git +mkdir build +cd build +cmake ../moab -DENABLE_HDF5=ON -DENABLE_NETCDF=ON -DENABLE_FORTRAN=OFF -DENABLE_BLASLAPACK=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/MOAB +make -j +sudo make -j install +cmake ../moab -DENABLE_HDF5=ON -DENABLE_PYMOAB=ON -DENABLE_FORTRAN=OFF -DBUILD_SHARED_LIBS=ON -DENABLE_BLASLAPACK=OFF -DCMAKE_INSTALL_PREFIX=/MOAB +sudo make -j install +cd pymoab +sudo bash install.sh +sudo python setup.py install + + +# add to new dirs to the path +echo 'export PATH="$HOME/MOAB/bin:$PATH"' >> ~/.bashrc +echo 'export LD_LIBRARY_PATH="$HOME/MOAB/lib:$LD_LIBRARY_PATH"' >> ~/.bashrc +source ~/.bashrc + +# install Double-Down +cd ~ +git clone --shallow-submodules --single-branch --branch v1.0.0 --depth 1 https://github.com/pshriwise/double-down.git +cd double-down +mkdir build +cd build +cmake .. -DMOAB_DIR=$HOME/MOAB -DCMAKE_INSTALL_PREFIX=.. -DEMBREE_DIR=$HOME/embree +make -j +make -j install + + +# DAGMC version develop install from source +cd ~ +mkdir DAGMC +cd DAGMC +# git clone --single-branch --branch 3.2.1-rc1 --depth 1 https://github.com/svalinn/DAGMC.git +git clone --single-branch --branch v3.2.1 --depth 1 https://github.com/svalinn/DAGMC.git +mkdir build +cd build +cmake ../DAGMC -DBUILD_TALLY=ON -DMOAB_DIR=$HOME/MOAB -DDOUBLE_DOWN=ON -DBUILD_STATIC_EXE=OFF -DBUILD_STATIC_LIBS=OFF -DCMAKE_INSTALL_PREFIX=$HOME/DAGMC/ -DDOUBLE_DOWN_DIR=$HOME/double-down +make -j install + +# add to new dirs to the path +echo 'export PATH="$HOME/DAGMC/bin:$PATH"' >> ~/.bashrc +echo 'export LD_LIBRARY_PATH="$HOME/DAGMC/lib:$LD_LIBRARY_PATH"' >> ~/.bashrc +source ~/.bashrc + +# installs OpenMC +cd ~ +git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git +cd openmc +mkdir build +cd build +cmake -Doptimize=on -Ddagmc=ON -DDAGMC_ROOT=$HOME/DAGMC -DHDF5_PREFER_PARALLEL=off .. +make -j +make -j install +cd .. +pip install . + +# install WMP nuclear data +RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Library_v1.1.tar.gz +tar -xf WMP_Library_v1.1.tar.gz -C + +# installs TENDL and ENDF nuclear data. Performed after openmc install as +# openmc is needed to write the cross_Sections.xml file +pip install openmc_data_downloader +openmc_data_downloader -d nuclear_data -l ENDFB-7.1-NNDC TENDL-2019 -p neutron photon -e all -i H3 --no-overwrite From f2f03feb7ea8d917c1ecd37bdc224ab4f0f8053d Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 24 Feb 2022 16:48:42 +0000 Subject: [PATCH 25/31] [skip ci] changed h5m filename to avoid overwritting --- ...aking_shapes_for_a_3d_mesh_tally_vtk.ipynb | 359 +----------------- ...g_components_for_a_2d_mesh_tally_vtk.ipynb | 2 +- ...r_a_2d_mesh_tally_and_matplotlib_png.ipynb | 6 +- 3 files changed, 13 insertions(+), 354 deletions(-) diff --git a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb index 0c552a6d..4342186e 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -79,226 +79,9 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Overwriting auto display for cadquery Workplane and Shape\n" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "3955b2abc1ff4ee8879a1f953ba247f6", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(VBox(children=(HBox(children=(Checkbox(value=False, description='Axes', indent=False, _dom_clas…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "my_reactor = paramak.Reactor([blanket, center_column])\n", "\n", @@ -314,119 +97,9 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/jshim/brep_part_finder/brep_part_finder/core.py:75: UserWarning: No parts matching the specified volume +/- tolerances were found\n", - " warnings.warn(\n", - "/home/jshim/brep_part_finder/brep_part_finder/core.py:114: UserWarning: No parts matching the specified bounding boxes were found\n", - " warnings.warn(\"No parts matching the specified bounding boxes were found\")\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "volumes [(3, 1), (3, 2), (3, 3), (3, 4), (3, 5), (3, 6), (3, 7), (3, 8), (3, 9)]\n", - "Info : Meshing 1D...\n", - "Info : [ 0%] Meshing curve 1 (Circle)\n", - "Info : [ 10%] Meshing curve 2 (Circle)\n", - "Info : [ 10%] Meshing curve 3 (Circle)\n", - "Info : [ 10%] Meshing curve 4 (BSpline)\n", - "Info : [ 20%] Meshing curve 5 (Circle)\n", - "Info : [ 20%] Meshing curve 6 (Line)\n", - "Info : [ 20%] Meshing curve 7 (Circle)\n", - "Info : [ 30%] Meshing curve 8 (BSpline)\n", - "Info : [ 30%] Meshing curve 9 (BSpline)\n", - "Info : [ 30%] Meshing curve 10 (Circle)\n", - "Info : [ 40%] Meshing curve 11 (BSpline)\n", - "Info : [ 40%] Meshing curve 12 (BSpline)\n", - "Info : [ 40%] Meshing curve 13 (Circle)\n", - "Info : [ 50%] Meshing curve 14 (BSpline)\n", - "Info : [ 50%] Meshing curve 15 (BSpline)\n", - "Info : [ 50%] Meshing curve 16 (Circle)\n", - "Info : [ 60%] Meshing curve 17 (BSpline)\n", - "Info : [ 60%] Meshing curve 18 (BSpline)\n", - "Info : [ 60%] Meshing curve 19 (Circle)\n", - "Info : [ 70%] Meshing curve 20 (BSpline)\n", - "Info : [ 70%] Meshing curve 21 (BSpline)\n", - "Info : [ 70%] Meshing curve 22 (Circle)\n", - "Info : [ 80%] Meshing curve 23 (BSpline)\n", - "Info : [ 80%] Meshing curve 24 (BSpline)\n", - "Info : [ 80%] Meshing curve 25 (Circle)\n", - "Info : [ 90%] Meshing curve 26 (BSpline)\n", - "Info : [ 90%] Meshing curve 27 (BSpline)\n", - "Info : [ 90%] Meshing curve 28 (Circle)\n", - "Info : [100%] Meshing curve 29 (BSpline)\n", - "Info : [100%] Meshing curve 30 (BSpline)\n", - "Info : Done meshing 1D (Wall 0.55192s, CPU 0.556843s)\n", - "Info : Meshing 2D...\n", - "Info : [ 0%] Meshing surface 1 (Plane, MeshAdapt)\n", - "Info : [ 10%] Meshing surface 2 (Surface of Revolution, MeshAdapt)\n", - "Info : [ 10%] Meshing surface 3 (Plane, MeshAdapt)\n", - "Info : [ 20%] Meshing surface 4 (Cylinder, MeshAdapt)\n", - "Info : [ 20%] Meshing surface 5 (Surface of Revolution, MeshAdapt)\n", - "Info : [ 20%] Meshing surface 6 (Plane, MeshAdapt)\n", - "Info : [ 30%] Meshing surface 7 (Plane, MeshAdapt)\n", - "Info : [ 30%] Meshing surface 8 (Surface of Revolution, MeshAdapt)\n", - "Info : [ 30%] Meshing surface 9 (Plane, MeshAdapt)\n", - "Info : [ 40%] Meshing surface 10 (Plane, MeshAdapt)\n", - 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"Info : [100%] Meshing surface 27 (Plane, MeshAdapt)\n", - "Info : [100%] Meshing surface 28 (Plane, MeshAdapt)\n", - "Info : Done meshing 2D (Wall 32.0506s, CPU 32.0513s)\n", - "Info : 24134 nodes 49889 elements\n", - "Info : Writing '/tmp/volume_17r9qtjfn.stl'...\n", - "Info : Done writing '/tmp/volume_17r9qtjfn.stl'\n", - "Info : Writing '/tmp/volume_2hfxtjt03.stl'...\n", - "Info : Done writing '/tmp/volume_2hfxtjt03.stl'\n", - "Info : Writing '/tmp/volume_3qlwtchp4.stl'...\n", - "Info : Done writing '/tmp/volume_3qlwtchp4.stl'\n", - "Info : Writing '/tmp/volume_4_omz93ti.stl'...\n", - "Info : Done writing '/tmp/volume_4_omz93ti.stl'\n", - "Info : Writing '/tmp/volume_5w5mf0r2n.stl'...\n", - "Info : Done writing '/tmp/volume_5w5mf0r2n.stl'\n", - "Info : Writing '/tmp/volume_67oxaamie.stl'...\n", - "Info : Done writing '/tmp/volume_67oxaamie.stl'\n", - "Info : Writing '/tmp/volume_71rvjpx0x.stl'...\n", - "Info : Done writing '/tmp/volume_71rvjpx0x.stl'\n", - "Info : Writing '/tmp/volume_88vts1mml.stl'...\n", - "Info : Done writing '/tmp/volume_88vts1mml.stl'\n", - "Info : Writing '/tmp/volume_95chc2uth.stl'...\n", - "Info : Done writing '/tmp/volume_95chc2uth.stl'\n", - "file /tmp/volume_17r9qtjfn.stl is watertight True\n" - ] - }, - { - "data": { - "text/plain": [ - "'dagmc.h5m'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "my_reactor.export_dagmc_h5m()" ] @@ -440,23 +113,9 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "ValueError", - "evalue": "material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column'].", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/tmp/ipykernel_66164/1142178510.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[0mgeometry\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0modw\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGeometry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 18\u001b[0;31m materials = odw.Materials(\n\u001b[0m\u001b[1;32m 19\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'dagmc.h5m'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 20\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmaterial_tag_to_material_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, h5m_filename, correspondence_dict)\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcorrespondence_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcorrespondence_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mh5m_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 24\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchecks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 25\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_openmc_materials\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopenmc_materials\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/Materials.py\u001b[0m in \u001b[0;36mchecks\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;34mf\"contains the following material tags {materials_in_h5m}.\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 55\u001b[0m )\n\u001b[0;32m---> 56\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 57\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m\"graveyard\"\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mmaterials_in_h5m\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: material with tag mat_blanket was not found in the dagmc h5m file. The DAGMC file dagmc.h5m contains the following material tags ['mat_center_column']." - ] - } - ], + "outputs": [], "source": [ "# makes use of the previously created neutronics geometry (h5m file) and assigns\n", "# actual materials to the material tags. \n", @@ -616,7 +275,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.8.12" } }, "nbformat": 4, diff --git a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb index 2ffe72fa..4e64b5f9 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb @@ -954,7 +954,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.8.12" } }, "nbformat": 4, diff --git a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb index 9c661031..e10f1593 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb @@ -72,7 +72,7 @@ "metadata": {}, "outputs": [], "source": [ - "my_reactor.export_dagmc_h5m('dagmc.h5m', exclude='plasma')" + "my_reactor.export_dagmc_h5m('dagmc_3.h5m', exclude='plasma')" ] }, { @@ -132,7 +132,7 @@ " 'mat_plasma':mat2 # todo remove\n", "}\n", "\n", - "geometry = odw.Geometry(h5m_filename='dagmc.h5m')\n", + "geometry = odw.Geometry(h5m_filename='dagmc_3.h5m')\n", "\n", "materials = odw.Materials(\n", " h5m_filename='dagmc.h5m',\n", @@ -270,7 +270,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.8.12" } }, "nbformat": 4, From 9193440f0eb26920580a81b2aada8cd9e407405a Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 24 Feb 2022 16:56:05 +0000 Subject: [PATCH 26/31] added cool props --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 897e50c8..7c0f6462 100644 --- a/Dockerfile +++ b/Dockerfile @@ -247,7 +247,7 @@ ENV OPENMC_CROSS_SECTIONS=/nuclear_data/cross_sections.xml # python packages from the neutronics workflow -RUN pip install neutronics_material_maker \ +RUN pip install neutronics_material_maker[density] \ openmc-plasma-source \ remove_dagmc_tags \ openmc-dagmc-wrapper \ From 31b68d54060b7d4f1da56c59ebf3c02070f46d42 Mon Sep 17 00:00:00 2001 From: Jonathan Date: Sun, 27 Feb 2022 02:01:10 +0000 Subject: [PATCH 27/31] [skip ci] added paramak_develop isntall --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7c0f6462..cc59f3ea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -258,7 +258,7 @@ RUN pip install neutronics_material_maker[density] \ openmc_mesh_tally_to_vtk # installing a development version of the paramak that allows exporting to h5m files -RUN conda install -c fusion-energy -c cadquery -c conda-forge +RUN conda install -c fusion-energy -c cadquery -c conda-forge paramak_develop # an older version of openmc is need to provide an older executable From fd1e256dcf49e74127e6a751e59aef01633df25b Mon Sep 17 00:00:00 2001 From: shimwell Date: Mon, 28 Feb 2022 00:06:47 +0000 Subject: [PATCH 28/31] increased time outs --- tests/test_task_11.py | 2 +- tests/test_task_12.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_task_11.py b/tests/test_task_11.py index 490a05c2..1373d2e0 100644 --- a/tests/test_task_11.py +++ b/tests/test_task_11.py @@ -26,7 +26,7 @@ def _notebook_run(path): with open(path) as f: nb = nbformat.read(f, as_version=4) nb.metadata.get('kernelspec', {})['name'] = kernel_name - ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=900) #, allow_errors=True try: ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) diff --git a/tests/test_task_12.py b/tests/test_task_12.py index 72f764d3..c4a3f238 100644 --- a/tests/test_task_12.py +++ b/tests/test_task_12.py @@ -26,7 +26,7 @@ def _notebook_run(path): with open(path) as f: nb = nbformat.read(f, as_version=4) nb.metadata.get('kernelspec', {})['name'] = kernel_name - ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=900) #, allow_errors=True try: ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) From c1f925d5fa55efe8ae236650fbad5258916cfb99 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 28 Feb 2022 09:36:03 +0000 Subject: [PATCH 29/31] added extra tasks to table --- README.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index d6190f4b..17c1f45e 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,6 @@ some motivation for learning neutronics.

- :point_right: [Try the workshop in your browser](https://neutronics-workshop-4zf6u4tg6a-lz.a.run.app/) # History @@ -38,8 +37,6 @@ also welcome as pull requests to the develop branch. The resource has proven most useful as it is one of the few open source and accessible fusion neutronics training resources. - - ## Installation There are video tutorials for this section which accompany the step by step @@ -54,7 +51,6 @@ instructions below. [Windows](https://hub.docker.com/editions/community/docker-ce-desktop-windows), including the part where you enable docker use as a non-root user. - 2. Pull the docker image from the store by typing the following command in a terminal window, or Windows users might prefer PowerShell. @@ -128,5 +124,7 @@ map which is great for working through the workshop with colleagues. | [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) | | [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating | | | [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux | | -| [Task 13 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | | -| [Task 14 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_parameter_study_optimisation) | Data science machine learning approaches | | +| [Task 13 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows | | +| [Task 14 - Activation transmutation](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_14_activation_transmutation) | Isotope build up and tally variation as a function of time | | +| [Task 15 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies | | +| [Task 16 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_parameter_study_optimisation) | Data science machine learning approaches | | From ecd8f405e51cf2d07edde6c66b0eeb0d53bf6062 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Mon, 28 Feb 2022 10:01:06 +0000 Subject: [PATCH 30/31] reduced mesh size to speed up meshing --- ...imulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb index f7ea8d2b..b6f0955b 100644 --- a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb +++ b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb @@ -65,7 +65,7 @@ "outputs": [], "source": [ "!rm dagmc.h5m\n", - "my_reactor.export_dagmc_h5m(filename='dagmc.h5m')" + "my_reactor.export_dagmc_h5m(filename='dagmc.h5m', min_mesh_size=10, max_mesh_size=20)" ] }, { @@ -258,7 +258,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.8.12" } }, "nbformat": 4, From 42c9e24bf58c4d00f82232d7e7a9dae333ee5d7f Mon Sep 17 00:00:00 2001 From: shimwell Date: Mon, 28 Feb 2022 21:08:49 +0000 Subject: [PATCH 31/31] corrected dagmc filename --- ..._making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb index e10f1593..717ef647 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb @@ -135,7 +135,7 @@ "geometry = odw.Geometry(h5m_filename='dagmc_3.h5m')\n", "\n", "materials = odw.Materials(\n", - " h5m_filename='dagmc.h5m',\n", + " h5m_filename='dagmc_3.h5m',\n", " correspondence_dict=material_tag_to_material_dict\n", ")" ]