pabloprf · pabloprf · Oct 15, 2025 · Aug 6, 2025 · Aug 6, 2025 · Aug 6, 2025
diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,6 @@
 */scratch/*
 *.DS_Store*
 config_user.json
-.DS_Store
 *.egg-info/
 docs/build/
 *.bat

diff --git a/docs/capabilities/misc_capabilities.rst b/docs/capabilities/misc_capabilities.rst
@@ -10,7 +10,7 @@ Miscellaneous
 Interpret Tokamak equilibrium
 -----------------------------
 
-MITIM has a quick g-eqdsk file reader and visualizer that is based on the ``omfit-classes`` package.
+MITIM has a quick g-eqdsk file reader and visualizer that is based on the ``megpy`` package.
 
 To open and plot a g-eqdsk file:
 
@@ -47,7 +47,7 @@ To open and plot an ``input.gacode`` file:
 .. code-block:: python
 
 	from mitim_tools.gacode_tools import PROFILEStools
-	p = PROFILEStools.PROFILES_GACODE(file)
+	p = PROFILEStools.gacode_state(file)
 	p.plot()
 
 It will plot results in a notebook-like plot with different tabs:

diff --git a/docs/capabilities/optimization.rst b/docs/capabilities/optimization.rst
@@ -44,7 +44,7 @@ Select the location of the MITIM namelist (see :ref:`Understanding the MITIM nam
 .. code-block:: python
 
    folder    = Path('MITIM-fusion/tests/scratch/mitim_tut')
-   namelist  = Path('MITIM-fusion/templates/main.namelist.json')
+   namelist  = Path('MITIM-fusion/templates/namelist.optimization.yaml')
 
 Then create your custom optimization object as a child of the parent ``STRATEGYtools.opt_evaluator`` class.
 You only need to modify what operations need to occur inside the ``run()`` (where operations/simulations happen) and ``scalarized_objective()`` (to define what is the target to maximize) methods.
@@ -105,7 +105,7 @@ Now we can create and launch the MITIM optimization process from the beginning (
 
 .. code-block:: python
 
-   MITIM_BO = STRATEGYtools.MITIM_BO( opt_fun1D, cold_startYN = True )
+   MITIM_BO = STRATEGYtools.MITIM_BO( opt_fun1D, cold_start = True )
    MITIM_BO.run()
 
 Once finished, we can plot the results easily with:
@@ -118,7 +118,7 @@ Once finished, we can plot the results easily with:
 Understanding the MITIM namelist
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Checkout file ``MITIM-fusion/templates/main.namelist.json``, which has comprehensive comments.
+Checkout file ``MITIM-fusion/templates/namelist.optimization.yaml``, which has comprehensive comments.
 
 *Under development*
 

diff --git a/docs/capabilities/tglf_capabilities.rst b/docs/capabilities/tglf_capabilities.rst
@@ -68,30 +68,31 @@ To generate the input files (input.tglf) to TGLF at each radial location, MITIM
 
 .. code-block:: python
 
-    cdf = tglf.prep(folder,inputgacode=inputgacode_file,cold_start=False )
+    _ = tglf.prep(inputgacode_file,folder,cold_start=False)
 
-.. tip::
 
-    The ``.prep()`` method, when applied to a case that starts with an input.gacode file, launches a `TGYRO` run for a "zero" iteration to generate *input.tglf* at specific ``rho`` locations from the *input.gacode*. This method to generate input files is inspired by how the `OMFIT framework <https://omfit.io/index.html>`_ works.
+Now, we are ready to run TGLF. Once the ``prep()`` command has finished, one can run TGLF with different settings and assumptions.
+That is why, at this point, a sub-folder name for this specific run can be provided. Similarly to the ``prep()`` command, a ``cold_start`` flag can be provided.
+
+The set of control inputs to TGLF (saturation rule, electromagnetic effects, basis functions, etc.) are provided following the following sequential logic:
+
+1. Each code has a set of default settings, which for TGLF are specified in ``templates/input.tglf.controls``. This is the base namelist of settings that will be used if no other specification is provided.
+2. Then, a ``code_settings`` argument can be provided to the ``run()`` command. This argument refers to a specific set of settings that are specified in ``templates/input.tglf.models.yaml``, and that will overwrite the default settings in ``input.tglf.controls``.
+3. Finally, an ``extraOptions`` argument can be provided to the ``run()`` command, which is a dictionary of specific settings to change from the previous two steps.
 
-Now, we are ready to run TGLF. Once the ``prep()`` command has finished, one can run TGLF with different settings and assumptions. That is why, at this point, a sub-folder name for this specific run can be provided. Similarly to the ``prep()`` command, a ``cold_start`` flag can be provided.
-The set of control inputs to TGLF (like saturation rule, electromagnetic effects, etc.) are provided in two ways.
-First, the argument ``TGLFsettings`` indicates the base case to start with.
-The user is referred to ``templates/input.tglf.models.json`` to understand the meaning of each setting, and ``templates/input.tglf.controls`` for the default setup.
-Second, the argument ``extraOptions`` can be passed as a dictionary of variables to change.
 For example, the following two commands will run TGLF with saturation rule number 2 with and without electromagnetic effets. After each ``run()`` command, a ``read()`` is needed, to populate the *tglf.results* dictionary with the TGLF outputs (``label`` refers to the dictionary key for each run):
 
 .. code-block:: python
 
-    tglf.run( subFolderTGLF = 'yes_em_folder', 
-              TGLFsettings  = 5,
-              extraOptions  = {},
+    tglf.run( subfolder = 'yes_em_folder', 
+              code_settings  = 'SAT2',
+              extraOptions  = {'USE_BPER':True},
               cold_start       = False )
 
     tglf.read( label = 'yes_em' )
 
-    tglf.run( subFolderTGLF = 'no_em_folder', 
-              TGLFsettings  = 5,
+    tglf.run( subfolder = 'no_em_folder', 
+              code_settings  = 'SAT2',
               extraOptions  = {'USE_BPER':False},
               cold_start       = False )
 
@@ -139,7 +140,7 @@ Similarly as in the previous section, you need to run the ``prep()`` command, bu
 
 .. code-block:: python
 
-    cdf = tglf.prep(folder,cold_start=False)
+    cdf = tglf.prep_using_tgyro(folder,cold_start=False)
 
 .. note::
 
@@ -168,7 +169,7 @@ If you have a input.tglf file already, you can still use this script to run it.
     inputtglf_file   = Path('MITIM-fusion/tests/data/input.tglf')
 
     tglf = TGLFtools.TGLF()
-    tglf.prep_from_tglf( folder, inputtglf_file, input_gacode = inputgacode_file )
+    tglf.prep_from_file( folder, inputtglf_file, input_gacode = inputgacode_file )
 
 The rest of the workflow is identical, including ``.run()``, ``.read()`` and ``.plot()``.
 
@@ -190,7 +191,7 @@ The rest of the workflow is identical, including ``.run()``, ``.read()`` and ``.
         inputtglf_file   = Path('MITIM-fusion/tests/data/input.tglf')
 
         tglf = TGLFtools.TGLF()
-        tglf.prep_from_tglf( folder, inputtglf_file )
+        tglf.prep_from_file( folder, inputtglf_file )
         tglf.read (folder = f'{folder}/', label = 'yes_em' )
         tglf.plot( labels = ['yes_em'] )
 
@@ -215,26 +216,4 @@ Run 1D scans of TGLF input parameter
 TGLF aliases
 ------------
 
-MITIM provides a few useful aliases, including for the TGLF tools:
-
-- To plot results that exist in a folder ``run1/``, with or without a suffix and with or without an input.gacode file (for normalizations):
-
-    .. code-block:: bash
-
-        mitim_plot_tglf run1/
-        mitim_plot_tglf run1/ --suffix _0.55 --gacode input.gacode
-
-
-- To run TGLF in a folder ``run1/`` using input file ``input.tglf``, with or without an input.gacode file (for normalizations):
-
-    .. code-block:: bash
-
-        mitim_run_tglf --folder run1/ --tglf input.tglf
-        mitim_run_tglf --folder run1/ --tglf input.tglf --gacode input.gacode
-
-- To run a parameter scan in a folder ``scan1/`` using input file ``input.tglf``, with or without an input.gacode file (for normalizations):
-
-    .. code-block:: bash
-
-        mitim_run_tglf --folder scan1/ --tglf input.tglf --gacode input.gacode --scan RLTS_2
-
+MITIM provides a few useful aliases, including for the TGLF tools: :ref:`Shell Scripts`
diff --git a/docs/capabilities/tgyro_capabilities.rst b/docs/capabilities/tgyro_capabilities.rst
@@ -35,7 +35,7 @@ Create a PROFILES class from the input.gacode file:
 
 .. code-block:: python
 
-	profiles = PROFILEStools.PROFILES_GACODE(gacode_file)
+	profiles = PROFILEStools.gacode_state(gacode_file)
 
 .. tip::
 
@@ -83,7 +83,7 @@ Now TGYRO can be run:
                PredictionSet         = PredictionSet,
                TGLFsettings          = TGLFsettings,
                TGYRO_solver_options  = solver,
-               Physics_options = physics_options)
+               TGYRO_physics_options = physics_options)
 
 Read:
 
@@ -120,7 +120,7 @@ Create a profiles class with the `input.gacode` file that TGYRO used to run and
 	gacode_file = Path('MITIM-fusion/tests/data/input.gacode')
 	folder      = Path('MITIM-fusion/tests/scratch/tgyro_tut/run1')
 
-	profiles    = PROFILEStools.PROFILES_GACODE(gacode_file)
+	profiles    = PROFILEStools.gacode_state(gacode_file)
 	tgyro_out   = TGYROtools.TGYROoutput(folder,profiles=profiles)
 
 Plot results:
@@ -133,11 +133,5 @@ Plot results:
 TGYRO aliases
 -------------
 
-MITIM provides a few useful aliases, including for the TGYRO tools:
-
-- To plot results that exist in a folder ``run1/``:
-
-    .. code-block:: bash
-
-        mitim_plot_tgyro run1/
+MITIM provides a few useful aliases, including for the TGYRO tools: :ref:`Shell Scripts`
 
diff --git a/docs/capabilities/transp_capabilities.rst b/docs/capabilities/transp_capabilities.rst
@@ -123,24 +123,5 @@ If TRANSP has already been run and the .CDF results file already exists (``cdf_f
 TRANSP aliases
 --------------
 
-MITIM provides a few useful aliases, including for the TRANSP tools:
-
-- To read TRANSP results in CDF files (which stores the results in the ``cdfs`` list. First run can be plotted with ``cdfs[0].plot``):
-
-    .. code-block:: bash
-
-        mitim_read_transp 12345A01.CDF 12345A02.CDF
-
-- To interact with the TRANSP globus grid:
-
-    .. code-block:: bash
-
-		# To check status of runs under username pablorf
-		mitim_trcheck pablorf
-
-		# To remove from the grid CMOD run numbers 88664P01, 88664P03 from user pablorf
-		mitim_trclean 88664P CMOD --numbers 1,3
-
-		# To get results file (intermediate or final) from CMOD run 152895P01 from user pablorf
-		mitim_trlook 152895P01 CMOD
+MITIM provides a few useful aliases, including for the TRANSP tools: :ref:`Shell Scripts`
 
diff --git a/docs/capabilities/vitals_capabilities.rst b/docs/capabilities/vitals_capabilities.rst
@@ -38,8 +38,8 @@ As a starting point of VITALS, you need to prepare and run TGLF for the base cas
 	rho              = 0.5
 
 	tglf = TGLFtools.TGLF( rhos = [ rho ] )
-	cdf = tglf.prep( folder, inputgacode = inputgacode_file)
-	tglf.run( subFolderTGLF = 'run_base', TGLFsettings = 5)
+	cdf = tglf.prep( inputgacode_file, folder )
+	tglf.run( subfolder = 'run_base', code_settings = 'SAT3')
 	tglf.read( label = 'run_base' )
 
 
@@ -120,7 +120,7 @@ Once the VITALS object has been created, parameters such as the TGLF control inp
 
 .. code-block:: python
 
-	vitals_fun.TGLFparameters['TGLFsettings']  = 5
+	vitals_fun.TGLFparameters['code_settings']  = 'SAT3'
 	vitals_fun.TGLFparameters['extraOptions']  = {}
 
 .. note::

diff --git a/docs/faq.rst b/docs/faq.rst
@@ -30,7 +30,7 @@ Issues during MITIM installation
 
    .. code-block:: console
 
-      pip3 install -e MITIM-fusion\[pyqt\] --no-cache
+      pip3 install -e MITIM-fusion\[pyqt\] --no-cache-dir
 
 Issues during MITIM tests
 -------------------------
@@ -61,9 +61,3 @@ Issues during MITIM tests
 
    Make sure you that, if you have keys, you have added them to authorized_keys in both server and tunnel machines.
 
-
-
-Issues during PORTALS simulations
----------------------------------
-
-Nothing here yet.
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,8 +1,8 @@
 MITIM: a toolbox for modeling tasks in plasma physics and fusion energy
 =======================================================================
 
-The **MITIM** (MIT Integrated Modeling) is a versatile and user-friendly Python library designed for *plasma physics* and *fusion energy* researchers, distributed as the `MITIM-fusion  <https://github.com/pabloprf/MITIM-fusion>`_ GitHub repository.
-Developed in 2018 by `Pablo Rodriguez-Fernandez <https://www.pablorf.com/>`_ at the MIT Plasma Science and Fusion Center, this light-weight, command-line,
+The **MITIM** (MIT Integrated Modeling) is a versatile and user-friendly Python library designed for plasma physics and fusion energy researchers, distributed as the `MITIM-fusion  <https://github.com/pabloprf/MITIM-fusion>`_ GitHub repository.
+Spearheaded by `Pablo Rodriguez-Fernandez <https://www.pablorf.com/>`_ at the MIT Plasma Science and Fusion Center, this light-weight, command-line,
 object-oriented toolbox streamlines the execution and interpretation of physics models and simplifies complex optimization tasks.
 
 MITIM stands out for its modular nature, making it particularly useful for integrating models with optimization workflows.
@@ -28,7 +28,7 @@ Overview
 --------
 
 Developed at the MIT Plasma Science and Fusion Center, MITIM emerged in 2023 as a progression from the PORTALS project (*Performance Optimization of Reactors via Training of Active Learning Surrogates*).
-This evolution marks a significant enhancement in our approach to transport and optimization in plasma physics research.
+This evolution marked a significant enhancement in our approach to transport and optimization in plasma physics research.
 
 MITIM's core functionality revolves around the standalone execution of codes and the nuanced interpretation of results through object-oriented Python scripts.
 This enables researchers to seamlessly integrate these scripts into custom surrogate-based optimization frameworks,

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -36,13 +36,6 @@ Use ``pip`` to install all the required MITIM requirements:
    The optional argument ``[pyqt]`` added in the intallation command above must only be used if the machine allows for graphic interfaces.
    If running in a computing cluster, remove that flag.
    The ``pyqt`` package is used to create condensed figures into a single notebook when interpreting and plotting simulation results.
-
-   If you wish to install all capabilities (including compatibility with `OMFIT <https://omfit.io/>`_), it is recommended that ``pip`` is run as follows:
-
-   .. code-block:: console
-
-      pip3 install -e MITIM-fusion[pyqt,omfit]
-
 
 If you were unsuccessful in the installation, check out our :ref:`Frequently Asked Questions` section.
 
@@ -53,11 +46,11 @@ User configuration
 In ``MITIM-fusion/templates/``, there is a ``config_user_example.json`` with specifications of where to run certain codes and what the login requirements are.
 There are also options to specify the default verbose level and the default DPI for the figures in notebooks.
 Users need to specify their own configurations in a file that follows the same structure.
-There are different options to handle this config file.
+There are different options to handle this config file:
 
 1. Create a new file named ``config_user.json`` **in the same folder** ``MITIM-fusion/templates/``. MITIM will automatically look for this file when running the code.
 2. Create a new file anywhere in your machine. Then, **set the environment variable** ``MITIM_CONFIG`` to the path of this file. MITIM will automatically look for this file when running the code.
-3. Create a new file anywhere in your machine. **Do this at the beginning of your script**:
+3. Create a new file anywhere in your machine. Then, **add these lines at the beginning of your script**:
 
    .. code-block:: python
 
@@ -87,29 +80,46 @@ In this example, the ``identity`` option is only required if you are running in
    {
       "preferences": {
          "tglf":             "engaging",
+         "neo":              "local",
          "tgyro":            "perlmutter",
          "verbose_level":    "5",
          "dpi_notebook":     "80"
       },
+    "local": {
+        "machine":    "local",
+        "username":   "YOUR_USERNAME",
+        "scratch":    "/Users/YOUR_USERNAME/scratch/",
+        "modules":    "",
+        "cores_per_node":  8,
+        "gpus_per_node": 0
+    },
       "engaging": {
          "machine":          "eofe7.mit.edu", 
          "username":         "YOUR_USERNAME",
          "scratch":          "/pool001/YOUR_USERNAME/scratch/",
+         "modules":          "",
+         "cores_per_node":   64,
+         "gpus_per_node":     0,
          "slurm": {
             "partition":    "sched_mit_psfc",
+            "exclusive":    false,
             "exclude":      "node584"
             }
       },
       "perlmutter": {
          "machine":          "perlmutter.nersc.gov", 
          "username":         "YOUR_USERNAME",
          "scratch":          "/pscratch/sd/p/YOUR_USERNAME/scratch/",
+         "modules":          "",
          "identity":         "/Users/YOUR_USERNAME/.ssh/id_rsa_nersc",
+         "cores_per_node":   32,
+         "gpus_per_node":     4,
          "slurm": {
                "account":      "YOUR_ACCOUNT",
                "partition":    "YOUR_PARTITION",
                "constraint":   "gpu",
-               "mem":          "4GB" 
+               "mem":          "4GB",
+               "email":        "optional@email"
             }
       }
    }
@@ -119,20 +129,15 @@ MITIM will attempt to create SSH and SFTP connections to that machine, and will
 
 .. attention::
 
-   Note that MITIM does not maintain or develop the simulation codes that are used within it, such as those from `GACODE <http://gafusion.github.io/doc/index.html>`_ or `TRANSP <hhttps://transp.pppl.gov/index.html>`_. It assumes that proper permissions have been obtained and that working versions of those codes exist in the machine configured to run them.
+   Note that MITIM does not maintain or develop the simulation codes that are used within it, such as those from `GACODE <https://gacode.io/>`_ or `TRANSP <https://transp.pppl.gov/index.html>`_. It assumes that proper permissions have been obtained and that working versions of those codes exist in the machine configured to run them.
 
 Please note that MITIM will try to run the codes with standard commands that the shell must understand.
 For example, to run the TGLF code, MITIM will want to execute the command ``tglf`` in the *eofe7.mit.edu* machine as specified in the example above.
 There are several ways to make sure that the shell understands the command:
 
-.. dropdown:: 1. Source at shell initialization (recommended)
+.. dropdown:: 1. Send specific commands per code (recommended)
 
-   Is the commands are available upon login in that machine (e.g. in your personal ``.bashrc`` file), MITIM will be able to run them.
-   Please note that aliases are usually not available in non-interactive shells, and it is recommended to use full paths and to avoid print (echo) statements.
-
-.. dropdown:: 2. Send specific commands per code
-
-   Finally, you can populate the ``modules`` option per machine in your ``config_user.json`` file. For example:
+   You can populate the ``modules`` option per machine in your ``config_user.json`` file. For example:
 
    .. code-block:: console
 
@@ -142,10 +147,13 @@ There are several ways to make sure that the shell understands the command:
          ...
       }
 
-
    Note that you can the same machine listed several times in your ``config_user.json`` file, with different ``modules`` options per code.
    You just need to give it a different name per code.
 
+.. dropdown:: 2. Source at shell initialization
+
+   If the commands are available upon login in that machine (e.g. in your personal ``.bashrc`` file), MITIM will be able to run them.
+   Please note that aliases are usually not available in non-interactive shells, and it is recommended to use full paths and to avoid print (echo) statements.
 
 
 License and contributions