diff --git a/.gitignore b/.gitignore
index 87dd35caa..a42251c4e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -110,3 +110,5 @@ valgrind*
**/.DS_Store
**/*.vim
**/*.cbp
+
+.idea
diff --git a/BUILDING.md b/BUILDING.md
index 0ccc9a7f4..806b00afa 100644
--- a/BUILDING.md
+++ b/BUILDING.md
@@ -1,42 +1,42 @@
-# Building CoastalME from source
-
-
-Build requirements
---------------------------------------------------------------------------------
-
-The minimum requirements to build CoastalME are:
-
-- CMake >= 3.16, and an associated build system (make, ninja, Visual Studio, etc.)
-- GDAL >= 2.1
-- C++11
-- F2008 compiler
-
-
-CMake (CoastalME versions >= 3.5.0)
---------------------------------------------------------------------------------
-
-Since version 3.5.0, CoastalME can be built using the CMake build system.
-With the CMake build system you can compile and install CoastalME on more or less any
-platform. After unpacking the source distribution archive (or cloning the repository)
-step into the source tree:
-
- cd CoastalME-{VERSION}
-
-Create a build directory and step into it:
-
-
- mkdir build
- cd build
-
-From the build directory you can now configure CMake, build and install the binaries:
-
-
- cmake ..
- cmake --build .
- cmake --build . --target install
-
-Note:
-
- For a minimal build, add these options to the initial ``cmake`` command: ``...``.
- To enable specific DEBUG drivers, add ``....`` or ``...``.
+# Building CoastalME from source
+
+
+Build requirements
+--------------------------------------------------------------------------------
+
+The minimum requirements to build CoastalME are:
+
+- CMake >= 3.16, and an associated build system (make, ninja, Visual Studio, etc.)
+- GDAL >= 2.1
+- C++11
+- F2008 compiler
+
+
+CMake (CoastalME versions >= 3.5.0)
+--------------------------------------------------------------------------------
+
+Since version 3.5.0, CoastalME can be built using the CMake build system.
+With the CMake build system you can compile and install CoastalME on more or less any
+platform. After unpacking the source distribution archive (or cloning the repository)
+step into the source tree:
+
+ cd CoastalME-{VERSION}
+
+Create a build directory and step into it:
+
+
+ mkdir build
+ cd build
+
+From the build directory you can now configure CMake, build and install the binaries:
+
+
+ cmake ..
+ cmake --build .
+ cmake --build . --target install
+
+Note:
+
+ For a minimal build, add these options to the initial ``cmake`` command: ``...``.
+ To enable specific DEBUG drivers, add ``....`` or ``...``.
\ No newline at end of file
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index 83589b77c..1c661eb9e 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -1,135 +1,135 @@
-# Code of Conduct
-
-This code of conduct governs how we behave in any CoastalME forum or event and
-whenever we will be judged by our actions. We expect it to be honored by everyone
-who participates in the CoastalME community formally or informally, or claims any
-affiliation with the project.
-
-Introduction
--------------
-
-This code of conduct governs how we behave in any CoastalME forum or event and
-whenever we will be judged by our actions. We expect it to be honored by
-everyone who participates in the CoastalME community formally or informally, or
-claims any affiliation with the CoastalME project.
-
-It applies to in-person events (such as conferences and related social events),
-IRC, public and private mailing lists, the issue tracker, the wiki, blogs,
-Twitter, and any other forums which the community uses for communication and
-interactions.
-
-This code is not exhaustive or complete. It serves to distill our common
-understanding of a collaborative, shared environment and goals. We expect it to
-be followed in spirit as much as in the letter, so that it can enrich all of
-us and the technical communities in which we participate.
-
-Diversity Statement
--------------------
-
-CoastalME welcomes and encourages participation by everyone. We are committed to
-being a community that everyone feels good about joining, and we will always
-work to treat everyone well. No matter how you identify yourself or how others
-perceive you: we welcome you.
-Specific Guidelines
-
-We strive to:
-
-- Be open.
-
- We invite anyone to participate in our community. We preferably use public
- methods of communication for project-related messages, unless discussing
- something sensitive. This applies to messages for help or project-related
- support, too; not only is a public support request much more likely to result
- in an answer to a question, it also makes sure that any inadvertent mistakes
- made by people answering will be more easily detected and corrected.
-
-- Be empathetic, welcoming, friendly, and patient.
-
- We work together to resolve conflict, assume good intentions, and do our best
- to act in an empathetic fashion. We may all experience some frustration from
- time to time, but we do not allow frustration to turn into a personal attack.
- A community where people feel uncomfortable or threatened is not a productive
- one. Note that we have a multi-cultural, multi-lingual community and some of
- us are non-native speakers. We should be respectful when dealing with other
- community members as well as with people outside our community.
-
-- Be collaborative.
-
- Our work will be used by other people, and in turn we will depend on the work
- of others. When we make something for the benefit of CoastalME, we are willing to
- explain to others how it works, so that they can build on the work to make it
- even better. Any decision we make will affect users and colleagues, and we
- take those consequences seriously when making decisions.
-
-- Be inquisitive.
-
- Nobody knows everything! Asking questions early avoids many problems later,
- so questions are encouraged, though they may be directed to the appropriate
- forum. Those who are asked should be responsive and helpful, within the
- context of our shared goal of improving CoastalME.
-
-- Be careful in the words that we choose.
-
- Whether we are participating as professionals or volunteers, we value
- professionalism in all interactions, and take responsibility for our own
- speech. Be kind to others. Do not insult or put down other participants.
-
-- Be concise.
-
- Keep in mind that what you write once will be read by hundreds of persons.
- Writing a short email means people can understand the conversation as
- efficiently as possible. Short emails should always strive to be empathetic,
- welcoming, friendly and patient. When a long explanation is necessary,
- consider adding a summary.
-
- Try to bring new ideas to a conversation so that each mail adds something
- unique to the thread, keeping in mind that the rest of the thread still
- contains the other messages with arguments that have already been made.
-
- Try to stay on topic, especially in discussions that are already fairly large.
-
-- Step down considerately.
-
- Members of every project come and go. When somebody leaves or disengages
- from the project they should tell people they are leaving and take the proper
- steps to ensure that others can pick up where they left off. In doing so,
- they should remain respectful of those who continue to participate in the
- project and should not misrepresent the project's goals or achievements.
- Likewise, community members should respect any individual's choice to leave
- the project.
-
-Anti-Harassment
----------------
-
-Harassment and other exclusionary behavior are not acceptable.
-This includes, but is not limited to:
-
-- Personal insults or discriminatory jokes and language, especially those using racist or sexist terms.
-- Offensive comments, excessive or unnecessary profanity.
-- Intimidation, violent threats or demands.
-- Sustained disruption of sessions or events.
-- Stalking, harassing photography or recording.
-- Unwelcome physical contact or sexual attention.
-- Repeated harassment of others. In general, if someone asks you to stop, then stop.
-- Posting (or threatening to post) other people's personally identifying information ("doxing").
-- Sharing private content, such as emails sent privately or non-publicly, or unlogged forums such as IRC channel history.
-- Advocating for, or encouraging, any of the above behavior.
-
-Reporting Guidelines
---------------------
-
-If you believe someone is breaking this code of conduct, you may reply to them,
-and point to this code of conduct. Such messages may be in public or in private,
-whatever is most appropriate. Assume good faith; it is more likely that
-participants are unaware of their bad behavior than that they intentionally try
-to degrade the quality of the discussion. Should there be difficulties in
-dealing with the situation, you may report your concerns to event staff, a forum
-leader or the CoastalME Board. Serious or persistent offenders may be expelled from
-the event or forum by event organizers or forum leaders.
-
-To privately email the code of conduct committee leadership use coc@osgeo.org.
-
-Credits
--------
-
+# Code of Conduct
+
+This code of conduct governs how we behave in any CoastalME forum or event and
+whenever we will be judged by our actions. We expect it to be honored by everyone
+who participates in the CoastalME community formally or informally, or claims any
+affiliation with the project.
+
+Introduction
+-------------
+
+This code of conduct governs how we behave in any CoastalME forum or event and
+whenever we will be judged by our actions. We expect it to be honored by
+everyone who participates in the CoastalME community formally or informally, or
+claims any affiliation with the CoastalME project.
+
+It applies to in-person events (such as conferences and related social events),
+IRC, public and private mailing lists, the issue tracker, the wiki, blogs,
+Twitter, and any other forums which the community uses for communication and
+interactions.
+
+This code is not exhaustive or complete. It serves to distill our common
+understanding of a collaborative, shared environment and goals. We expect it to
+be followed in spirit as much as in the letter, so that it can enrich all of
+us and the technical communities in which we participate.
+
+Diversity Statement
+-------------------
+
+CoastalME welcomes and encourages participation by everyone. We are committed to
+being a community that everyone feels good about joining, and we will always
+work to treat everyone well. No matter how you identify yourself or how others
+perceive you: we welcome you.
+Specific Guidelines
+
+We strive to:
+
+- Be open.
+
+ We invite anyone to participate in our community. We preferably use public
+ methods of communication for project-related messages, unless discussing
+ something sensitive. This applies to messages for help or project-related
+ support, too; not only is a public support request much more likely to result
+ in an answer to a question, it also makes sure that any inadvertent mistakes
+ made by people answering will be more easily detected and corrected.
+
+- Be empathetic, welcoming, friendly, and patient.
+
+ We work together to resolve conflict, assume good intentions, and do our best
+ to act in an empathetic fashion. We may all experience some frustration from
+ time to time, but we do not allow frustration to turn into a personal attack.
+ A community where people feel uncomfortable or threatened is not a productive
+ one. Note that we have a multi-cultural, multi-lingual community and some of
+ us are non-native speakers. We should be respectful when dealing with other
+ community members as well as with people outside our community.
+
+- Be collaborative.
+
+ Our work will be used by other people, and in turn we will depend on the work
+ of others. When we make something for the benefit of CoastalME, we are willing to
+ explain to others how it works, so that they can build on the work to make it
+ even better. Any decision we make will affect users and colleagues, and we
+ take those consequences seriously when making decisions.
+
+- Be inquisitive.
+
+ Nobody knows everything! Asking questions early avoids many problems later,
+ so questions are encouraged, though they may be directed to the appropriate
+ forum. Those who are asked should be responsive and helpful, within the
+ context of our shared goal of improving CoastalME.
+
+- Be careful in the words that we choose.
+
+ Whether we are participating as professionals or volunteers, we value
+ professionalism in all interactions, and take responsibility for our own
+ speech. Be kind to others. Do not insult or put down other participants.
+
+- Be concise.
+
+ Keep in mind that what you write once will be read by hundreds of persons.
+ Writing a short email means people can understand the conversation as
+ efficiently as possible. Short emails should always strive to be empathetic,
+ welcoming, friendly and patient. When a long explanation is necessary,
+ consider adding a summary.
+
+ Try to bring new ideas to a conversation so that each mail adds something
+ unique to the thread, keeping in mind that the rest of the thread still
+ contains the other messages with arguments that have already been made.
+
+ Try to stay on topic, especially in discussions that are already fairly large.
+
+- Step down considerately.
+
+ Members of every project come and go. When somebody leaves or disengages
+ from the project they should tell people they are leaving and take the proper
+ steps to ensure that others can pick up where they left off. In doing so,
+ they should remain respectful of those who continue to participate in the
+ project and should not misrepresent the project's goals or achievements.
+ Likewise, community members should respect any individual's choice to leave
+ the project.
+
+Anti-Harassment
+---------------
+
+Harassment and other exclusionary behavior are not acceptable.
+This includes, but is not limited to:
+
+- Personal insults or discriminatory jokes and language, especially those using racist or sexist terms.
+- Offensive comments, excessive or unnecessary profanity.
+- Intimidation, violent threats or demands.
+- Sustained disruption of sessions or events.
+- Stalking, harassing photography or recording.
+- Unwelcome physical contact or sexual attention.
+- Repeated harassment of others. In general, if someone asks you to stop, then stop.
+- Posting (or threatening to post) other people's personally identifying information ("doxing").
+- Sharing private content, such as emails sent privately or non-publicly, or unlogged forums such as IRC channel history.
+- Advocating for, or encouraging, any of the above behavior.
+
+Reporting Guidelines
+--------------------
+
+If you believe someone is breaking this code of conduct, you may reply to them,
+and point to this code of conduct. Such messages may be in public or in private,
+whatever is most appropriate. Assume good faith; it is more likely that
+participants are unaware of their bad behavior than that they intentionally try
+to degrade the quality of the discussion. Should there be difficulties in
+dealing with the situation, you may report your concerns to event staff, a forum
+leader or the CoastalME Board. Serious or persistent offenders may be expelled from
+the event or forum by event organizers or forum leaders.
+
+To privately email the code of conduct committee leadership use coc@osgeo.org.
+
+Credits
+-------
+
CoastalME re-uses the `OSGeo Code of Conduct `__
\ No newline at end of file
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index d2d3a4041..824ac64c9 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,36 +1,36 @@
-# How to contribute?
-
-There are several ways for developers and users to contribute to CoastalME:
-
-- [Contributing code](#contributing-code)
-- [Filing high-quality reports](#filing-high-quality-reports)
-- [Improving documentation](#improving-documentation)
-- [Credits](#credits)
-
-## Contributing code
-
-Minor changes to CoastalME, such as bug fixes, may be made by opening a GitHub pull request.
-
-Major changes should be discussed on the [CoastalME Discussions](https://github.com/apayo/CoastalME/discussions/19#discussion-7445785) and may require the drafting of a RFC (request for comment) document.
-
-CoastalME's policy on substantial code additions is documented at [rfc_process.md](/development/rfc_process.md).
-
-## Filing high-quality issue reports
-
-Using the GitHub [issue reports](https://github.com/apayo/CoastalME/issues) at the Master repository.
-
-## Improving documentation
-
-CoastalME's documentation includes C++ [API documentation](https://codedocs.xyz/apayo/CoastalME/) built automatically from source comments using Doxygen and [CodeDocx.XYZ](https://codedocs.xyz) files containing manually-edited content.
-
-To be correctly parsed, the documentation should follow the [Doxygen block documentation style](https://doxygen.nl/manual/docblocks.html#specialblock)
-
- /*! \brief Brief description.
- * Brief description continued.
- *
- * Detailed description starts here.
- */
-
-## Credits
-
+# How to contribute?
+
+There are several ways for developers and users to contribute to CoastalME:
+
+- [Contributing code](#contributing-code)
+- [Filing high-quality reports](#filing-high-quality-reports)
+- [Improving documentation](#improving-documentation)
+- [Credits](#credits)
+
+## Contributing code
+
+Minor changes to CoastalME, such as bug fixes, may be made by opening a GitHub pull request.
+
+Major changes should be discussed on the [CoastalME Discussions](https://github.com/apayo/CoastalME/discussions/19#discussion-7445785) and may require the drafting of a RFC (request for comment) document.
+
+CoastalME's policy on substantial code additions is documented at [rfc_process.md](/development/rfc_process.md).
+
+## Filing high-quality issue reports
+
+Using the GitHub [issue reports](https://github.com/apayo/CoastalME/issues) at the Master repository.
+
+## Improving documentation
+
+CoastalME's documentation includes C++ [API documentation](https://codedocs.xyz/apayo/CoastalME/) built automatically from source comments using Doxygen and [CodeDocx.XYZ](https://codedocs.xyz) files containing manually-edited content.
+
+To be correctly parsed, the documentation should follow the [Doxygen block documentation style](https://doxygen.nl/manual/docblocks.html#specialblock)
+
+ /*! \brief Brief description.
+ * Brief description continued.
+ *
+ * Detailed description starts here.
+ */
+
+## Credits
+
This section has been largely inspired by https://github.com/OSGeo/gdal
\ No newline at end of file
diff --git a/LICENSE.md b/LICENSE.md
index 8566c3cc9..d929fb5e0 100644
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -1,78 +1,78 @@
-
-# CoastalME Licensing
-
-This file attempts to include all licenses that apply within the CoastalME
-source tree, in particular any that are supposed to be exposed to the end user
-for credit requirements for instance. The contents of this file can be
-displayed from CostalME GitHub Master repository with filename LICENSE.MD
-
-- [CoastalME General](#coastalme-general)
-- [GDAL-OGR General](#gdal-ogr-general)
-- [CSHORE General](#cshore-general)
-
-
-## CoastalME General
-
-The text shown below should be added to all source code.
-
-
- This file is part of CoastalME, the Coastal Modelling Environment.
-
- CoastalME is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
-
- This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-
-https://github.com/apayo/CoastalME
-
-## GDAL-OGR General
-
-In general GDAL/OGR is licensed under an MIT style license with the
-following terms:
-
-Permission is hereby granted, free of charge, to any person obtaining a
-copy of this software and associated documentation files (the "Software"),
-to deal in the Software without restriction, including without limitation
-the rights to use, copy, modify, merge, publish, distribute, sublicense,
-and/or sell copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included
-in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.
-
-https://github.com/OSGeo/gdal
-
-## CSHORE General
-
-MIT License
-
-Copyright (c) Microsoft Corporation.
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE
-
+
+# CoastalME Licensing
+
+This file attempts to include all licenses that apply within the CoastalME
+source tree, in particular any that are supposed to be exposed to the end user
+for credit requirements for instance. The contents of this file can be
+displayed from CostalME GitHub Master repository with filename LICENSE.MD
+
+- [CoastalME General](#coastalme-general)
+- [GDAL-OGR General](#gdal-ogr-general)
+- [CSHORE General](#cshore-general)
+
+
+## CoastalME General
+
+The text shown below should be added to all source code.
+
+
+ This file is part of CoastalME, the Coastal Modelling Environment.
+
+ CoastalME is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+
+https://github.com/apayo/CoastalME
+
+## GDAL-OGR General
+
+In general GDAL/OGR is licensed under an MIT style license with the
+following terms:
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+https://github.com/OSGeo/gdal
+
+## CSHORE General
+
+MIT License
+
+Copyright (c) Microsoft Corporation.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE
+
https://github.com/erdc/cshore
\ No newline at end of file
diff --git a/README.md b/README.md
index be92f91d4..90e9b124e 100644
--- a/README.md
+++ b/README.md
@@ -65,7 +65,19 @@ If you see error messages about missing software (for example, telling you that
Run make install `make install`. This will create an executable file called cme in the CoastalME folder.
-Edit cme.ini to tell CoastalME which input file to read (for example, in/test_suite/minimal_wave_angle_230/minimal.dat). You'll need to make sure that the "Path for output" listed in cme.ini (for example, out/test_suite/minimal_wave_angle_230) exists. If it doesn't exist, then create it: `mkdir -p out/test_suite/minimal_wave_angle_230/`.
+CoastalME supports two configuration file formats: `.ini` (legacy) and `.yaml` (modern).
+
+**Using YAML format (recommended)**:
+Edit `cme.yaml` to specify input and output paths. Example:
+```yaml
+input_data_file: in/test_suite/minimal_wave_angle_230/minimal.yaml
+output_path: out/test_suite/minimal_wave_angle_230/
+```
+
+**Using legacy .ini format**:
+Edit `cme.ini` to tell CoastalME which input file to read (for example, in/test_suite/minimal_wave_angle_230/minimal.dat). You'll need to make sure that the "Path for output" listed in cme.ini (for example, out/test_suite/minimal_wave_angle_230) exists. If it doesn't exist, then create it: `mkdir -p out/test_suite/minimal_wave_angle_230/`.
+
+**Note**: CoastalME will automatically detect which format to use. If both `cme.yaml` and `cme.ini` exist, `cme.yaml` takes priority.
Run cme `./cme`. Output will appear in the "Path for output" folder.
diff --git a/TO_DO_LIST.md b/TO_DO_LIST.md
index f42c643bc..32295d033 100644
--- a/TO_DO_LIST.md
+++ b/TO_DO_LIST.md
@@ -1,118 +1,118 @@
-# TO DO LIST
-
-089 is max (also using github permalinks to code lines)
-
-## Table of contents
-- [Documentation]{#documentation)
-- [User input](#user-input)
-- [Error handling](#error-handling)
-- [Theory/Efficiency](#theory-efficiency)
-- [Output](#output)
-- [Completed](#completed)
-
-## Documentation
-- TODO 001 [Add more information about all classes]
-- TODO 007 [Need more info re. setup and surge from Manuel]
-
-## User input
-- TODO 000 [Should user input be split in two main files]
-- TODO 011 Should this constant be a user input?
- [1](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/cme.h#L600-L602)
- [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/simulation.cpp#L211)
- [3](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/simulation.cpp#L371)
-- TODO 036 [Read in changed deep water wave values](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/init_grid.cpp#L177)
-- TODO 030 [Do we also need to be able to input landform sub-categories?] [code](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L750)
-- TODO 027 [Sort out GDAL problem with raster reference units](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L537)
-- TODO 022 [Get intervention update working](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_intervention.cpp#L32)
-- TODO 042 [Should we have a smallest valid input for KLS in the CERC equation?] [code](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/read_input.cpp#L2378-L2380)
-- TODO 045 [Method of getting depth of closure value needs to be a user input] [code](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/simulation.h#L771)
-- TODO 049 [Handle other command line parameters e.g. path to .ini file, path to datafile](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/utils.cpp#L125)
-- TODO 035 [Also handle other EPSG for vector spatial reference systems](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_vector.cpp#L492)
-- TODO 054 [Choose more files to omit from "usual" raster output]
-- TODO 069 [Enable ability to represent intervention structures which have their foundation embedded in consolidated sediment. In other words, with the elevation of the base of the intervention structure *below* the top of all consolidated sediment layers. Will need some sanity checking of elevations]
-- TODO 071 [If the user input file format is changed, write a Python script to convert from the old file format to the new]
-- TODO 083 [Get all three kinds of sediment input events working correctly]
-
-## Error handling
-- TODO 038 [Do better error handling if insufficient memory]
-- TODO 004 [Improve error handling of situation where we have a valid shadow zone but cannot find a neighbouring cell which is 'under' the coastline](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_shadow_zones.cpp#L490)
-- TODO 006 [Check GDALGridCreate() with only start-of-coast or an end-of-coast profiles](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L214)
-- TODO 009 [Decide what to do when we have eroded down to basement](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L214)
-- TODO 017 [Extra safety check needed, make sure that each point is within valid grid](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L146)
-- TODO 018 [Improve situation where new landwards point on parallel profile is not within the raster grid](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L222) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L394)
-- TODO 019 [Improve situation where Dean profile has a near-zero elevation difference](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L286) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L394)
-- TODO 020 [Check calculation of elevation of coast point of Dean parallel profile](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L949) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L1435)
-- TODO 021 [Improve situation where all layers have zero thickness](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_cliff_collapse.cpp#L819)
-- TODO 025 [Improve situation where this point has only zero thickness layers](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L195) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L508)
-- TODO 026 [Check situation where cell in parallel profile is not in a polygon](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L495)
-- TODO 028 [Give a warning if raster input layer has several bands](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L605)
-- TODO 038 [Do better error handling if insufficient memory](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L71)
-- TODO 053 [Improve handling of situation where landward elevation of profile is -ve](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L1581)
-- TODO 055 [Maybe add a safety check?]
-- TODO 080 [Do we get -ve breaking wave heights here?]
-- TODO 084 [Improve handling of situation where consecutive profile points are same distance from shoreline]
-
-## Theory/Efficiency
-- TODO 002 [Do we really need D50 for drift landform class? What do we need for drift?](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/assign_landforms.cpp#L346)
-- TODO 005 [Maybe give every coast point a value for end-of-profile wave height and direction instead of for deep water wave height and direction](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L58)
-- TODO 010 [Do we also need to update the active zone cells?](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L1828)
-- TODO 012 [Change finding of adjacent polygons, and calculation of the length of shared normals, when we make polygon seaward length determined by depth of closure](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_polygons.cpp#L504)
-- TODO 013 [Change calculation (need user input?) of coastline smoothing convexity threshold](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L119)
-- TODO 014 [Profile spacing, vould try gradually increasing the profile spacing with increasing concavity, and decreasing the profile spacing with increasing convexity](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L396)
-- TODO 016 [Check mass balance for recirculating unconsolidated sediment option](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_sediment_movement.cpp#L539)
-- TODO 023 [Only calculate shore platform erosion if cell is in a polygon](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L51)
-- TODO 024 [Should we calculate platform erosion on a profile that has hit dry land?](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L124)
-- TODO 044 [Implement estuaries. Before we can do this, we will need to deal with multiple coastlines. Will need to get working where profile hits another profile which belongs to a different coast object.](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L1478) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L1537)
-- TODO 037 [Need more info on nFindIndex](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/interpolate.cpp#L103-L121)
-- TODO 051 [Implement other ways of calculating depth of closure, see TODO 045](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/utils.cpp#L2482-L2493)
-- TODO 056 [Check this please Andres]
-- TODO 059 [Implement dune landform class]
-- TODO 060 [Remove 'magic numbers' from code here]
-- TODO 061 [Is this safety check to depth of breaking a reasonable thing to do?]
-- TODO 066 [Should this be for all layers? Check]
-- TODO 067 [Is this ever non-zero? Check]
-- TODO 070 [Change CShore to use allocatable arrays (https://fortran-lang.org/en/learn/best_practices/allocatable_arrays/) so that the number of points in the CShore output profiles can either be a user input, or determined by e.g. the physical length of the profile]
-- TODO 075 [What if bedrock protrudes above Dean profile?]
-- TODO 076 [When doing parallel profiles, start from the profile which is closest to a right angle with the coast]
-- TODO 077 [As traverse between the bounding profiles creating parallel profiles, gradually change the parallel profile orientation based on distance weighting of two bounding profiles]
-- TODO 078 [At present, we don't allow cliff collapse onto interventions. Is this realistic? Should it change with different types of intervention?]
-- TODO 089 [Why do we get patches of sediment in the sea?]
- TODO 086 [Try alternatives to GDALGridCreate(), e.g. https://gts.sourceforge.net/index.html, https://doc.cgal.org/latest/Triangulation_2/index.html#Chapter_2D_Triangulations]
- TODO 088 [In (almost) all whole-grid loops, immediately continue if cell is hinterland (but not when calculating cliff collapse)]
-
-## Output
-- TODO 065 [Get GPKG output working]
-- TODO 063 [Add NetCDF support, see https://trac.osgeo.org/gdal/wiki/NetCDF]
-- TODO 064 [Add support for grids that are not oriented N-S and W-E, but are still rectangular (will need to add a transformation in the reading and writing process, the first to bring it to the local base and the second to save it in global coordinates)]
-- TODO 031 [Get raster slice output working with multiple slices](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L1122-L1125)
-- TODO 032 [Improve output scaling for DBL_NODATA situation](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L1617)
-- TODO 033 [Also test and configure (e.g. by passing open() options) other vector output file formats](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_utils.cpp#L893)
-- TODO 034 [Also test and configure (e.g. by passing open() options) other raster output file formats](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_utils.cpp#L1642)
-- TODO 043 [When outputting profiles, how do we deal with randomness of profile spacing (since profile location is determined by curvature)?]
-- TODO 052 [Improve saving of profiles and parallel profiles]
-- TODO 062 [Show end-of-iteration number of cells with sediment somewhere]
-- TODO 068 [Only show output in log file that is relevant to processes being simulated]
-- TODO 074 [Output history of what landforms are on a particular cell or cells. User inputs cell(s), how?]
-- TODO 082 [Also show m_dStartIterUnconsFineAllCells etc. in log file]
-
-## Completed
-- TODO 003 [Make coastline curvature moving window size a user input DONE in 1.1.22]
-- TODO 046 [Why is cliff collapse eroded during deposition (three size classes) no longer calculated? DONE IN 1.1.22]
-- TODO 058 [Dave to check this DONE in 1.1.22]
-- TODO 039 [Rewrite reading of multiple random number seeds DONE in 1.2.1, 8 Nov 2024]
-- TODO 041 [Read in SWL per-timestep]
-- BUG 002 [Useless output e.g. clay layers even if no clay input DONE in 1.1.21]
-- BUG 003 [Use mean SWL for elevations of Dean profiles DONE in 1.2.1, 27 Nov 2024]
-- BUG 004 [Don't smooth intervention coastline DONE 1.2.1, 27 Nov 2024]
-- TODO 073 [If output dir does not exist, then create it (ask user first) DONE 1.2.2, 28 Nov 2024]
-- TODO 047 [Where is the GDAL description for the deep water wave stations vector file? DONE 1.2.3, 2 Dec 2024]
-- TODO 048 [Where is the GDAL description for the flood input locations point or vector file? DONE 1.2.3, 2 Dec 2024]
-- TODO 027 [Sort out GDAL problem with raster reference units DONE 1.2.3, 2 Dec 2024]
-- TODO 079 [Do sanity checking on wave and tide input DONE 1.2.3, 2 Dec 2024]
-- TODO 072 [CShore crashes occasionally, is it because of -ve Z values here? DONE 1.2.3, 2 Dec 2024]
-- TODO 050 [Update for recent versions of Windows DONE 1.2.3, 2 Dec 2024]
-- TODO 037 [Need more info on nFindIndex() DONE 1.2.3, 2 Dec 2024]
-- [Improve coast normals DONE 1.2.3, 20 Dec 2024]
-- TODO 057 [Check this please Manuel DONE 1.2.4, 4 Jan 2025]
-- TODO 087 [Is there a problem if profile is not long enough for user-input depth of closure? DONE 1.3.0 2 Feb 2025]
-
+# TO DO LIST
+
+089 is max (also using github permalinks to code lines)
+
+## Table of contents
+- [Documentation]{#documentation)
+- [User input](#user-input)
+- [Error handling](#error-handling)
+- [Theory/Efficiency](#theory-efficiency)
+- [Output](#output)
+- [Completed](#completed)
+
+## Documentation
+- TODO 001 [Add more information about all classes]
+- TODO 007 [Need more info re. setup and surge from Manuel]
+
+## User input
+- TODO 000 [Should user input be split in two main files]
+- TODO 011 Should this constant be a user input?
+ [1](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/cme.h#L600-L602)
+ [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/simulation.cpp#L211)
+ [3](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/simulation.cpp#L371)
+- TODO 036 [Read in changed deep water wave values](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/init_grid.cpp#L177)
+- TODO 030 [Do we also need to be able to input landform sub-categories?] [code](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L750)
+- TODO 027 [Sort out GDAL problem with raster reference units](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L537)
+- TODO 022 [Get intervention update working](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_intervention.cpp#L32)
+- TODO 042 [Should we have a smallest valid input for KLS in the CERC equation?] [code](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/read_input.cpp#L2378-L2380)
+- TODO 045 [Method of getting depth of closure value needs to be a user input] [code](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/simulation.h#L771)
+- TODO 049 [Handle other command line parameters e.g. path to .ini file, path to datafile](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/utils.cpp#L125)
+- TODO 035 [Also handle other EPSG for vector spatial reference systems](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_vector.cpp#L492)
+- TODO 054 [Choose more files to omit from "usual" raster output]
+- TODO 069 [Enable ability to represent intervention structures which have their foundation embedded in consolidated sediment. In other words, with the elevation of the base of the intervention structure *below* the top of all consolidated sediment layers. Will need some sanity checking of elevations]
+- TODO 071 [If the user input file format is changed, write a Python script to convert from the old file format to the new]
+- TODO 083 [Get all three kinds of sediment input events working correctly]
+
+## Error handling
+- TODO 038 [Do better error handling if insufficient memory]
+- TODO 004 [Improve error handling of situation where we have a valid shadow zone but cannot find a neighbouring cell which is 'under' the coastline](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_shadow_zones.cpp#L490)
+- TODO 006 [Check GDALGridCreate() with only start-of-coast or an end-of-coast profiles](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L214)
+- TODO 009 [Decide what to do when we have eroded down to basement](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L214)
+- TODO 017 [Extra safety check needed, make sure that each point is within valid grid](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L146)
+- TODO 018 [Improve situation where new landwards point on parallel profile is not within the raster grid](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L222) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L394)
+- TODO 019 [Improve situation where Dean profile has a near-zero elevation difference](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L286) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L394)
+- TODO 020 [Check calculation of elevation of coast point of Dean parallel profile](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L949) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_within_polygon.cpp#L1435)
+- TODO 021 [Improve situation where all layers have zero thickness](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_cliff_collapse.cpp#L819)
+- TODO 025 [Improve situation where this point has only zero thickness layers](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L195) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L508)
+- TODO 026 [Check situation where cell in parallel profile is not in a polygon](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L495)
+- TODO 028 [Give a warning if raster input layer has several bands](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L605)
+- TODO 038 [Do better error handling if insufficient memory](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L71)
+- TODO 053 [Improve handling of situation where landward elevation of profile is -ve](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L1581)
+- TODO 055 [Maybe add a safety check?]
+- TODO 080 [Do we get -ve breaking wave heights here?]
+- TODO 084 [Improve handling of situation where consecutive profile points are same distance from shoreline]
+
+## Theory/Efficiency
+- TODO 002 [Do we really need D50 for drift landform class? What do we need for drift?](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/assign_landforms.cpp#L346)
+- TODO 005 [Maybe give every coast point a value for end-of-profile wave height and direction instead of for deep water wave height and direction](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L58)
+- TODO 010 [Do we also need to update the active zone cells?](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/calc_waves.cpp#L1828)
+- TODO 012 [Change finding of adjacent polygons, and calculation of the length of shared normals, when we make polygon seaward length determined by depth of closure](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_polygons.cpp#L504)
+- TODO 013 [Change calculation (need user input?) of coastline smoothing convexity threshold](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L119)
+- TODO 014 [Profile spacing, vould try gradually increasing the profile spacing with increasing concavity, and decreasing the profile spacing with increasing convexity](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L396)
+- TODO 016 [Check mass balance for recirculating unconsolidated sediment option](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_beach_sediment_movement.cpp#L539)
+- TODO 023 [Only calculate shore platform erosion if cell is in a polygon](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L51)
+- TODO 024 [Should we calculate platform erosion on a profile that has hit dry land?](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/do_shore_platform_erosion.cpp#L124)
+- TODO 044 [Implement estuaries. Before we can do this, we will need to deal with multiple coastlines. Will need to get working where profile hits another profile which belongs to a different coast object.](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L1478) [2](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/create_profiles.cpp#L1537)
+- TODO 037 [Need more info on nFindIndex](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/interpolate.cpp#L103-L121)
+- TODO 051 [Implement other ways of calculating depth of closure, see TODO 045](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/utils.cpp#L2482-L2493)
+- TODO 056 [Check this please Andres]
+- TODO 059 [Implement dune landform class]
+- TODO 060 [Remove 'magic numbers' from code here]
+- TODO 061 [Is this safety check to depth of breaking a reasonable thing to do?]
+- TODO 066 [Should this be for all layers? Check]
+- TODO 067 [Is this ever non-zero? Check]
+- TODO 070 [Change CShore to use allocatable arrays (https://fortran-lang.org/en/learn/best_practices/allocatable_arrays/) so that the number of points in the CShore output profiles can either be a user input, or determined by e.g. the physical length of the profile]
+- TODO 075 [What if bedrock protrudes above Dean profile?]
+- TODO 076 [When doing parallel profiles, start from the profile which is closest to a right angle with the coast]
+- TODO 077 [As traverse between the bounding profiles creating parallel profiles, gradually change the parallel profile orientation based on distance weighting of two bounding profiles]
+- TODO 078 [At present, we don't allow cliff collapse onto interventions. Is this realistic? Should it change with different types of intervention?]
+- TODO 089 [Why do we get patches of sediment in the sea?]
+ TODO 086 [Try alternatives to GDALGridCreate(), e.g. https://gts.sourceforge.net/index.html, https://doc.cgal.org/latest/Triangulation_2/index.html#Chapter_2D_Triangulations]
+ TODO 088 [In (almost) all whole-grid loops, immediately continue if cell is hinterland (but not when calculating cliff collapse)]
+
+## Output
+- TODO 065 [Get GPKG output working]
+- TODO 063 [Add NetCDF support, see https://trac.osgeo.org/gdal/wiki/NetCDF]
+- TODO 064 [Add support for grids that are not oriented N-S and W-E, but are still rectangular (will need to add a transformation in the reading and writing process, the first to bring it to the local base and the second to save it in global coordinates)]
+- TODO 031 [Get raster slice output working with multiple slices](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L1122-L1125)
+- TODO 032 [Improve output scaling for DBL_NODATA situation](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_raster.cpp#L1617)
+- TODO 033 [Also test and configure (e.g. by passing open() options) other vector output file formats](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_utils.cpp#L893)
+- TODO 034 [Also test and configure (e.g. by passing open() options) other raster output file formats](https://github.com/coastalme/coastalme/blob/730a0be2274de02125681ab3e14424dbbfadbaeb/src/gis_utils.cpp#L1642)
+- TODO 043 [When outputting profiles, how do we deal with randomness of profile spacing (since profile location is determined by curvature)?]
+- TODO 052 [Improve saving of profiles and parallel profiles]
+- TODO 062 [Show end-of-iteration number of cells with sediment somewhere]
+- TODO 068 [Only show output in log file that is relevant to processes being simulated]
+- TODO 074 [Output history of what landforms are on a particular cell or cells. User inputs cell(s), how?]
+- TODO 082 [Also show m_dStartIterUnconsFineAllCells etc. in log file]
+
+## Completed
+- TODO 003 [Make coastline curvature moving window size a user input DONE in 1.1.22]
+- TODO 046 [Why is cliff collapse eroded during deposition (three size classes) no longer calculated? DONE IN 1.1.22]
+- TODO 058 [Dave to check this DONE in 1.1.22]
+- TODO 039 [Rewrite reading of multiple random number seeds DONE in 1.2.1, 8 Nov 2024]
+- TODO 041 [Read in SWL per-timestep]
+- BUG 002 [Useless output e.g. clay layers even if no clay input DONE in 1.1.21]
+- BUG 003 [Use mean SWL for elevations of Dean profiles DONE in 1.2.1, 27 Nov 2024]
+- BUG 004 [Don't smooth intervention coastline DONE 1.2.1, 27 Nov 2024]
+- TODO 073 [If output dir does not exist, then create it (ask user first) DONE 1.2.2, 28 Nov 2024]
+- TODO 047 [Where is the GDAL description for the deep water wave stations vector file? DONE 1.2.3, 2 Dec 2024]
+- TODO 048 [Where is the GDAL description for the flood input locations point or vector file? DONE 1.2.3, 2 Dec 2024]
+- TODO 027 [Sort out GDAL problem with raster reference units DONE 1.2.3, 2 Dec 2024]
+- TODO 079 [Do sanity checking on wave and tide input DONE 1.2.3, 2 Dec 2024]
+- TODO 072 [CShore crashes occasionally, is it because of -ve Z values here? DONE 1.2.3, 2 Dec 2024]
+- TODO 050 [Update for recent versions of Windows DONE 1.2.3, 2 Dec 2024]
+- TODO 037 [Need more info on nFindIndex() DONE 1.2.3, 2 Dec 2024]
+- [Improve coast normals DONE 1.2.3, 20 Dec 2024]
+- TODO 057 [Check this please Manuel DONE 1.2.4, 4 Jan 2025]
+- TODO 087 [Is there a problem if profile is not long enough for user-input depth of closure? DONE 1.3.0 2 Feb 2025]
+
diff --git a/cme.ini b/cme.ini
index 61dcba4db..4060e515f 100644
--- a/cme.ini
+++ b/cme.ini
@@ -2,7 +2,7 @@
;
; Initialization file for CoastalME
;
-; Copyright (C) 2024 David Favis-Mortlock and Andres Payo
+; Copyright (C) 2025 David Favis-Mortlock and Andres Payo
;
;=====================================================================================================================
;
@@ -17,10 +17,11 @@
; Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
;
;======================================================================================================================
-Input data file (path and name) : /Users/wilfchun/Documents/GitHub/CoastalME/CoastalME_data_local/CSE/Thorpness/in/thorpness.yaml
+Input data file (path and name) : in/test_suite/minimal_cons_wave_angle_230/minimal.dat
;======================================================================================================================
-Path for output :/Users/wilfchun/Documents/GitHub/CoastalME/CoastalME_data_local/CSE/Thorpness/out/
+
+Path for output : out/test_suite/minimal_cons_wave_angle_230/
;======================================================================================================================
diff --git a/cme.ini.THORPNESS b/cme.ini.THORPNESS
new file mode 100644
index 000000000..61dcba4db
--- /dev/null
+++ b/cme.ini.THORPNESS
@@ -0,0 +1,29 @@
+;======================================================================================================================
+;
+; Initialization file for CoastalME
+;
+; Copyright (C) 2024 David Favis-Mortlock and Andres Payo
+;
+;=====================================================================================================================
+;
+; This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public
+; License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later
+; version.
+;
+; This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+;
+; You should have received a copy of the GNU General Public License along with this program; if not, write to the Free
+; Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+;
+;======================================================================================================================
+Input data file (path and name) : /Users/wilfchun/Documents/GitHub/CoastalME/CoastalME_data_local/CSE/Thorpness/in/thorpness.yaml
+
+;======================================================================================================================
+Path for output :/Users/wilfchun/Documents/GitHub/CoastalME/CoastalME_data_local/CSE/Thorpness/out/
+
+;======================================================================================================================
+
+; Uncomment if email notification required. This only works on Linux, and if configured for mail sending
+#Email address for messages (Linux only) :
+
diff --git a/cme.yaml b/cme.yaml
new file mode 100644
index 000000000..3e3b33f2b
--- /dev/null
+++ b/cme.yaml
@@ -0,0 +1,32 @@
+#======================================================================================================================
+#
+# CoastalME initialization file (YAML format)
+#
+# Copyright (C) 2024 David Favis-Mortlock and Andres Payo
+#
+#=====================================================================================================================
+#
+# This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public
+# License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+# warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with this program; if not, write to the Free
+# Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+#
+#======================================================================================================================
+
+# Path to the main input configuration file (.dat or .yaml)
+# Can be absolute or relative to the directory containing this file
+input_data_file: in/test_suite/minimal_cons_wave_angle_230/minimal.dat
+
+# Path for output files
+# Can be absolute or relative to the directory containing this file
+# IMPORTANT: A trailing slash is required
+output_path: out/test_suite/minimal_cons_wave_angle_230/
+
+# Email address for notification messages (optional, Linux only)
+# Uncomment to enable email notifications
+# email_address: user@example.com
diff --git a/in/test_suite/minimal_cons_wave_angle_230/minimal.qgs b/in/test_suite/minimal_cons_wave_angle_230/minimal.qgs
index 10593d9cb..500b70a43 100644
--- a/in/test_suite/minimal_cons_wave_angle_230/minimal.qgs
+++ b/in/test_suite/minimal_cons_wave_angle_230/minimal.qgs
@@ -1,5 +1,5 @@
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