diff --git a/.gitattributes b/.gitattributes index ea8de3ecd..2709c11b2 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,8 +1,8 @@ # Auto detect text files and perform LF normalization * text=auto -examples_matlab_octave/* linguist-documentation -doc_matlab_octave/* linguist-documentation -doc_C++/* linguist-documentation +examples/octave/* linguist-documentation +doc/sphinx/octave/* linguist-documentation +doc/doxygen/cpp/* linguist-documentation *.html linguist-detectable=false *.htm linguist-detectable=false *.css linguist-detectable=false diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 05ab21a5b..ad98f9cc6 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -6,7 +6,7 @@ - ✅ Provide tests for your changes. - 📝 Use descriptive commit messages. - 📗 Update any related documentation and include any relevant screenshots. - - 📝 Add license information in the appropriate place. See MATLAB or C++ code for reference. + - 📝 Add license information in the appropriate place. See GNU Octave or C++ code for reference. SPDX-License-Identifier: GPL-3.0-or-later © 2008-2024 San Diego State University Research Foundation (SDSURF). diff --git a/.github/workflows/matlab-tests.yml b/.github/workflows/matlab-tests.yml index 72d2a4511..82578468f 100644 --- a/.github/workflows/matlab-tests.yml +++ b/.github/workflows/matlab-tests.yml @@ -33,8 +33,8 @@ jobs: with: test-results-junit: test-results/results.xml code-coverage-cobertura: code-coverage/coverage.xml - source-folder: src/matlab_octave - select-by-folder: tests/matlab_octave + source-folder: src/octave + select-by-folder: tests/octave strict: false use-parallel: false generate-summary: true diff --git a/.zenodo.json b/.zenodo.json index cb26ba44f..99f74a6de 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -157,7 +157,7 @@ "name": "GNU General Public License v3.0", "key": "gpl-3.0" }, - "language": "MATLAB/Octave", + "language": "Octave (MATLAB)", "url": "https://api.github.com/repos/jcorbino/mole", "subscribers_url": "https://api.github.com/repos/jcorbino/mole/subscribers", "created_at": "2017-08-12T19:03:04Z", diff --git a/CMakeLists.txt b/CMakeLists.txt index 2a900e579..29380576c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -149,10 +149,10 @@ set(LINK_LIBS ${ARMADILLO_LIBRARIES} # Add subdirectories add_subdirectory(src/cpp) add_subdirectory(tests/cpp) -add_subdirectory(tests/matlab_octave) +add_subdirectory(tests/octave) add_subdirectory(examples/cpp) # Custom target to build everything -add_custom_target(all_build DEPENDS mole_C++ tests_C++ examples_C++ tests_matlab_octave) +add_custom_target(all_build DEPENDS mole_C++ tests_C++ examples_C++ tests_octave) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 84d58b65d..7df2cde0e 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -59,7 +59,7 @@ The MOLE library follows a consistent structure across Octave and C++ implementa #### Octave Core Functions -Core functions are located in `src/matlab_octave/` and follow this pattern: +Core functions are located in `src/octave/` and follow this pattern: ```matlab function OUTPUT = functionName(k, m, dx, ...) @@ -157,7 +157,7 @@ When contributing core functionality, identify which category your contribution If adding a new operator, follow this checklist: -1. **Octave Implementation** (`src/matlab_octave/newoperator.m`): +1. **Octave Implementation** (`src/octave/newoperator.m`): ```matlab function OP = newoperator(k, m, dx) % Returns a new mimetic operator @@ -195,7 +195,7 @@ Examples are organized by PDE type in the `examples/` directory: ``` examples/ -├── matlab_octave/ # Octave examples +├── octave/ # Octave examples │ ├── elliptic1D.m # Basic examples │ ├── parabolic2D.m # 2D examples │ └── compact_operators/ # Specialized examples @@ -223,7 +223,7 @@ Organize your examples by PDE type: clc close all -addpath('../../src/matlab_octave') % REQUIRED: Add path to MOLE library +addpath('../../src/octave') % REQUIRED: Add path to MOLE library %% Problem Parameters % [Describe each parameter with physical meaning] @@ -404,7 +404,7 @@ $$ --- This example is implemented in: -- [Octave](https://github.com/csrc-sdsu/mole/blob/main/examples/matlab_octave/example_name.m) +- [Octave](https://github.com/csrc-sdsu/mole/blob/main/examples/octave/example_name.m) - [C++](https://github.com/csrc-sdsu/mole/blob/main/examples/cpp/example_name.cpp) *(if available)* #### Variants diff --git a/README.md b/README.md index 46b81d176..cfbe80b3e 100644 --- a/README.md +++ b/README.md @@ -126,7 +126,7 @@ make run_tests Octave equivalent of the C++ test suite. We recommend running these tests before using MOLE to ensure proper setup. ```matlab -make run_matlab_octave_tests +make run_octave_tests ``` ## Examples diff --git a/doc/doxygen/matlab_octave/README.md b/doc/doxygen/matlab_octave/README.md deleted file mode 100644 index 596e8f112..000000000 --- a/doc/doxygen/matlab_octave/README.md +++ /dev/null @@ -1 +0,0 @@ -This folder contains **generated** documentation of *MOLE's* MATLAB/Octave version via a tool called [M2HTML](https://www.gllmflndn.com/software/matlab/m2html). Please note that we do not regularly update this documentation. diff --git a/doc/sphinx/Makefile b/doc/sphinx/Makefile index d00af8b62..303d509df 100644 --- a/doc/sphinx/Makefile +++ b/doc/sphinx/Makefile @@ -44,6 +44,7 @@ help: # Doxygen documentation doc-doxygen: @echo "Generating Doxygen documentation..." + @mkdir -p $(DOXYDIR) @cd ../.. && doxygen Doxyfile @if [ ! -d "$(DOXYXML)" ]; then \ echo "Error: Doxygen XML output directory not found at $(DOXYXML)"; \ diff --git a/doc/sphinx/octave/README.md b/doc/sphinx/octave/README.md new file mode 100644 index 000000000..e5b3f95f7 --- /dev/null +++ b/doc/sphinx/octave/README.md @@ -0,0 +1 @@ +This folder contains **generated** documentation of *MOLE's* Octave version via a tool called [M2HTML](https://www.gllmflndn.com/software/matlab/m2html). Please note that we do not regularly update this documentation. diff --git a/doc/doxygen/matlab_octave/alpha.png b/doc/sphinx/octave/alpha.png similarity index 100% rename from doc/doxygen/matlab_octave/alpha.png rename to doc/sphinx/octave/alpha.png diff --git a/doc/doxygen/matlab_octave/c++.png b/doc/sphinx/octave/c++.png similarity index 100% rename from doc/doxygen/matlab_octave/c++.png rename to doc/sphinx/octave/c++.png diff --git a/doc/doxygen/matlab_octave/c.png b/doc/sphinx/octave/c.png similarity index 100% rename from doc/doxygen/matlab_octave/c.png rename to doc/sphinx/octave/c.png diff --git a/doc/doxygen/matlab_octave/demoicon.gif b/doc/sphinx/octave/demoicon.gif similarity index 100% rename from doc/doxygen/matlab_octave/demoicon.gif rename to doc/sphinx/octave/demoicon.gif diff --git a/doc/doxygen/matlab_octave/down.png b/doc/sphinx/octave/down.png similarity index 100% rename from doc/doxygen/matlab_octave/down.png rename to doc/sphinx/octave/down.png diff --git a/doc/doxygen/matlab_octave/doxysearch.php b/doc/sphinx/octave/doxysearch.php similarity index 100% rename from doc/doxygen/matlab_octave/doxysearch.php rename to doc/sphinx/octave/doxysearch.php diff --git a/doc/doxygen/matlab_octave/fortran.png b/doc/sphinx/octave/fortran.png similarity index 100% rename from doc/doxygen/matlab_octave/fortran.png rename to doc/sphinx/octave/fortran.png diff --git a/doc/doxygen/matlab_octave/hp.png b/doc/sphinx/octave/hp.png similarity index 100% rename from doc/doxygen/matlab_octave/hp.png rename to doc/sphinx/octave/hp.png diff --git a/doc/doxygen/matlab_octave/index.html b/doc/sphinx/octave/index.html similarity index 77% rename from doc/doxygen/matlab_octave/index.html rename to doc/sphinx/octave/index.html index 1226961cc..7775bab6d 100644 --- a/doc/doxygen/matlab_octave/index.html +++ b/doc/sphinx/octave/index.html @@ -5,19 +5,19 @@ MOLE's Documentation - + - + -This is a MATLAB/Octave Documentation by M2HTML.
+This is a Octave Documentation by M2HTML (Compatible with MATLAB).
Go to menu.html for the documentation of all -the MATLAB/Octave functions. +the Octave functions.
diff --git a/doc/doxygen/matlab_octave/left.png b/doc/sphinx/octave/left.png similarity index 100% rename from doc/doxygen/matlab_octave/left.png rename to doc/sphinx/octave/left.png diff --git a/doc/doxygen/matlab_octave/linux.png b/doc/sphinx/octave/linux.png similarity index 100% rename from doc/doxygen/matlab_octave/linux.png rename to doc/sphinx/octave/linux.png diff --git a/doc/doxygen/matlab_octave/m2html.css b/doc/sphinx/octave/m2html.css similarity index 100% rename from doc/doxygen/matlab_octave/m2html.css rename to doc/sphinx/octave/m2html.css diff --git a/doc/doxygen/matlab_octave/matlabicon.gif b/doc/sphinx/octave/matlabicon.gif similarity index 100% rename from doc/doxygen/matlab_octave/matlabicon.gif rename to doc/sphinx/octave/matlabicon.gif diff --git a/doc/doxygen/matlab_octave/menu.html b/doc/sphinx/octave/menu.html similarity index 72% rename from doc/doxygen/matlab_octave/menu.html rename to doc/sphinx/octave/menu.html index ccb79eff7..69334724a 100644 --- a/doc/doxygen/matlab_octave/menu.html +++ b/doc/sphinx/octave/menu.html @@ -2,9 +2,9 @@ "http://www.w3.org/TR/REC-html40/loose.dtd"> - MATLAB/Octave Index - - + Octave Index (compatible with MATLAB) + + @@ -12,11 +12,11 @@ -

MATLAB/Octave Index

-

MATLAB/Octave Directories

+

Octave Index

+

Octave Directories

- +
  • mole_Octave
  • +
    Generated by m2html © 2005
    diff --git a/doc/doxygen/matlab_octave/mex.png b/doc/sphinx/octave/mex.png similarity index 100% rename from doc/doxygen/matlab_octave/mex.png rename to doc/sphinx/octave/mex.png diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/DI2.html b/doc/sphinx/octave/mole_Octave/DI2.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/DI2.html rename to doc/sphinx/octave/mole_Octave/DI2.html index e7802a11f..e789335e8 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/DI2.html +++ b/doc/sphinx/octave/mole_Octave/DI2.html @@ -15,7 +15,7 @@ - +

    DI2

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/DI3.html b/doc/sphinx/octave/mole_Octave/DI3.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/DI3.html rename to doc/sphinx/octave/mole_Octave/DI3.html index c42c4de80..21307c3fe 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/DI3.html +++ b/doc/sphinx/octave/mole_Octave/DI3.html @@ -15,7 +15,7 @@ - +

    DI3

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/GI1.html b/doc/sphinx/octave/mole_Octave/GI1.html similarity index 98% rename from doc/doxygen/matlab_octave/mole_MATLAB/GI1.html rename to doc/sphinx/octave/mole_Octave/GI1.html index 944f5c94f..12de4188b 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/GI1.html +++ b/doc/sphinx/octave/mole_Octave/GI1.html @@ -15,7 +15,7 @@ - +

    GI1

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/GI13.html b/doc/sphinx/octave/mole_Octave/GI13.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/GI13.html rename to doc/sphinx/octave/mole_Octave/GI13.html index bb33ab1bc..6c27ca0b4 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/GI13.html +++ b/doc/sphinx/octave/mole_Octave/GI13.html @@ -15,7 +15,7 @@ - +

    GI13

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/GI2.html b/doc/sphinx/octave/mole_Octave/GI2.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/GI2.html rename to doc/sphinx/octave/mole_Octave/GI2.html index 5a16b2b1d..d5c3924ee 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/GI2.html +++ b/doc/sphinx/octave/mole_Octave/GI2.html @@ -15,7 +15,7 @@ - +

    GI2

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/curl2D.html b/doc/sphinx/octave/mole_Octave/curl2D.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/curl2D.html rename to doc/sphinx/octave/mole_Octave/curl2D.html index b5dc4874a..221a0d3a1 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/curl2D.html +++ b/doc/sphinx/octave/mole_Octave/curl2D.html @@ -15,7 +15,7 @@ - +

    curl2D

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div.html b/doc/sphinx/octave/mole_Octave/div.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div.html rename to doc/sphinx/octave/mole_Octave/div.html index 60055c211..ac21a09da 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div.html +++ b/doc/sphinx/octave/mole_Octave/div.html @@ -15,7 +15,7 @@ - +

    div

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div2D.html b/doc/sphinx/octave/mole_Octave/div2D.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div2D.html rename to doc/sphinx/octave/mole_Octave/div2D.html index 98845a3e5..5657bcde0 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div2D.html +++ b/doc/sphinx/octave/mole_Octave/div2D.html @@ -15,7 +15,7 @@ - +

    div2D

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div2DCurv.html b/doc/sphinx/octave/mole_Octave/div2DCurv.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div2DCurv.html rename to doc/sphinx/octave/mole_Octave/div2DCurv.html index 40bb6ad13..46c5f8f40 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div2DCurv.html +++ b/doc/sphinx/octave/mole_Octave/div2DCurv.html @@ -15,7 +15,7 @@ - +

    div2DCurv

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div2DNonUniform.html b/doc/sphinx/octave/mole_Octave/div2DNonUniform.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div2DNonUniform.html rename to doc/sphinx/octave/mole_Octave/div2DNonUniform.html index 07a1389cf..15dd61d8b 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div2DNonUniform.html +++ b/doc/sphinx/octave/mole_Octave/div2DNonUniform.html @@ -15,7 +15,7 @@ - +

    div2DNonUniform

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div3D.html b/doc/sphinx/octave/mole_Octave/div3D.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div3D.html rename to doc/sphinx/octave/mole_Octave/div3D.html index 3cd42c901..9d8807ed4 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div3D.html +++ b/doc/sphinx/octave/mole_Octave/div3D.html @@ -15,7 +15,7 @@ - +

    div3D

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div3DCurv.html b/doc/sphinx/octave/mole_Octave/div3DCurv.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div3DCurv.html rename to doc/sphinx/octave/mole_Octave/div3DCurv.html index 0fa90b7be..096534a62 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div3DCurv.html +++ b/doc/sphinx/octave/mole_Octave/div3DCurv.html @@ -15,7 +15,7 @@ - +

    div3DCurv

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/div3DNonUniform.html b/doc/sphinx/octave/mole_Octave/div3DNonUniform.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/div3DNonUniform.html rename to doc/sphinx/octave/mole_Octave/div3DNonUniform.html index 0803cdd51..863cee10d 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/div3DNonUniform.html +++ b/doc/sphinx/octave/mole_Octave/div3DNonUniform.html @@ -15,7 +15,7 @@ - +

    div3DNonUniform

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/divNonUniform.html b/doc/sphinx/octave/mole_Octave/divNonUniform.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/divNonUniform.html rename to doc/sphinx/octave/mole_Octave/divNonUniform.html index db34afe7b..3b1760a10 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/divNonUniform.html +++ b/doc/sphinx/octave/mole_Octave/divNonUniform.html @@ -15,7 +15,7 @@ - +

    divNonUniform

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/grad.html b/doc/sphinx/octave/mole_Octave/grad.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/grad.html rename to doc/sphinx/octave/mole_Octave/grad.html index 4330b1ba8..bb5af2d6e 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/grad.html +++ b/doc/sphinx/octave/mole_Octave/grad.html @@ -15,7 +15,7 @@ - +

    grad

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/grad2D.html b/doc/sphinx/octave/mole_Octave/grad2D.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/grad2D.html rename to doc/sphinx/octave/mole_Octave/grad2D.html index ac053988b..a6832aad2 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/grad2D.html +++ b/doc/sphinx/octave/mole_Octave/grad2D.html @@ -15,7 +15,7 @@ - +

    grad2D

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/grad2DCurv.html b/doc/sphinx/octave/mole_Octave/grad2DCurv.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/grad2DCurv.html rename to doc/sphinx/octave/mole_Octave/grad2DCurv.html index 86f382323..e36c5515b 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/grad2DCurv.html +++ b/doc/sphinx/octave/mole_Octave/grad2DCurv.html @@ -15,7 +15,7 @@ - +

    grad2DCurv

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/grad2DNonUniform.html b/doc/sphinx/octave/mole_Octave/grad2DNonUniform.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/grad2DNonUniform.html rename to doc/sphinx/octave/mole_Octave/grad2DNonUniform.html index 19536ffa3..bcc2024bd 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/grad2DNonUniform.html +++ b/doc/sphinx/octave/mole_Octave/grad2DNonUniform.html @@ -15,7 +15,7 @@ - +

    grad2DNonUniform

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    grad3D

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/grad3DCurv.html b/doc/sphinx/octave/mole_Octave/grad3DCurv.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/grad3DCurv.html rename to doc/sphinx/octave/mole_Octave/grad3DCurv.html index a86e17407..4a90e3a96 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/grad3DCurv.html +++ b/doc/sphinx/octave/mole_Octave/grad3DCurv.html @@ -15,7 +15,7 @@ - +

    grad3DCurv

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/grad3DNonUniform.html b/doc/sphinx/octave/mole_Octave/grad3DNonUniform.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/grad3DNonUniform.html rename to doc/sphinx/octave/mole_Octave/grad3DNonUniform.html index 098e08612..46db99138 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/grad3DNonUniform.html +++ b/doc/sphinx/octave/mole_Octave/grad3DNonUniform.html @@ -15,7 +15,7 @@ - +

    grad3DNonUniform

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/gradNonUniform.html b/doc/sphinx/octave/mole_Octave/gradNonUniform.html similarity index 99% rename from doc/doxygen/matlab_octave/mole_MATLAB/gradNonUniform.html rename to doc/sphinx/octave/mole_Octave/gradNonUniform.html index 9eccb5d44..322baf29a 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/gradNonUniform.html +++ b/doc/sphinx/octave/mole_Octave/gradNonUniform.html @@ -15,7 +15,7 @@ - +

    gradNonUniform

    diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/graph.dot b/doc/sphinx/octave/mole_Octave/graph.dot similarity index 100% rename from doc/doxygen/matlab_octave/mole_MATLAB/graph.dot rename to doc/sphinx/octave/mole_Octave/graph.dot diff --git a/doc/doxygen/matlab_octave/mole_MATLAB/graph.html b/doc/sphinx/octave/mole_Octave/graph.html similarity index 98% rename from doc/doxygen/matlab_octave/mole_MATLAB/graph.html rename to doc/sphinx/octave/mole_Octave/graph.html index 1f4d7684c..a8c879184 100644 --- a/doc/doxygen/matlab_octave/mole_MATLAB/graph.html +++ b/doc/sphinx/octave/mole_Octave/graph.html @@ -2,9 +2,9 @@ "http://www.w3.org/TR/REC-html40/loose.dtd"> - Dependency Graph for mole_MATLAB - - + Dependency Graph for mole_Octave + + @@ -12,10 +12,10 @@ -

    Dependency Graph for mole_MATLAB

    +

    Dependency Graph for mole_Octave

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    gridGen

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    +

    Index for mole_Octave

    Functions