diff --git a/.github/workflows/quality.yml b/.github/workflows/quality.yml
index f563634..90634ac 100644
--- a/.github/workflows/quality.yml
+++ b/.github/workflows/quality.yml
@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: prefix-dev/setup-pixi@v0.8.8
         with:
-          pixi-version: v0.48.0
+          pixi-version: v0.66.0
       - run: pixi run fmt --check
       - run: pixi run lint
       - run: pixi run types
diff --git a/README.md b/README.md
index 09a58b8..33efebe 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ python examples/fsm_example.py data/sharada/06_diels_alder/ --calculator emt
 ```
 Note the EMT calculator should only be used for quick demonstrations/tests.
 
-## Tutorials 
+## Tutorials
 
 1. A Google Colab notebook example is available at:
 ```
@@ -51,11 +51,11 @@ The script:
 ```
 examples/fsm_example.py
 ```
-is a comprehensive and flexible tool that supports most ML-FSM functionality. 
+is a comprehensive and flexible tool that supports most ML-FSM functionality.
 
 Note: Users are responsible for installing their desired quantum chemistry backend, current calculators supported in fsm_example.py are [AIMNet2](https://github.com/isayevlab/AIMNet2), [MACEOFF23](https://github.com/ACEsuit/mace-off), [FAIR UMA](https://github.com/facebookresearch/fairchem), [TensorNet](https://github.com/torchmd/torchmd-net), [xTB](https://github.com/grimme-lab/xtb), [QChem](https://www.q-chem.com).
 
-3. Some ML potentials do not offer a native ASE interface. To accommodate these, a minimal example of custom ```ase.Calculator``` wrappers is provided in the ```examples/``` folder. This serves as templates for integrating arbitrary NNPs with ML-FSM   
+3. Some ML potentials do not offer a native ASE interface. To accommodate these, a minimal example of custom ```ase.Calculator``` wrappers is provided in the ```examples/``` folder. This serves as templates for integrating arbitrary NNPs with ML-FSM
 ## Usage
 For projects referencing algorithmic improvements to the FSM please cite:
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 8d6cefa..3091827 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx
 sphinx-autodoc-typehints
 numpydoc
-sphinx-rtd-theme
+furo
 myst-parser
diff --git a/docs/source/api.rst b/docs/source/api.rst
index 3205c73..7f28dd6 100644
--- a/docs/source/api.rst
+++ b/docs/source/api.rst
@@ -1,70 +1,90 @@
 API Reference
 =============
 
-This section contains the complete API reference for all modules in mlfsm.
+This section contains the complete API reference for all modules in ``mlfsm``.
+
+----
 
 Core Modules
 ------------
 
-Coordinates
-~~~~~~~~~~~
-.. automodule:: mlfsm.coords
+FreezingString (``mlfsm.cos``)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The main driver class that orchestrates string growth, interpolation, and node
+optimization throughout the FSM calculation.
+
+.. automodule:: mlfsm.cos
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
 
-The coordinates module provides objects and functionality for cartesian and redundant internal coordinates.
+----
+
+Interpolation (``mlfsm.interp``)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Provides :class:`~mlfsm.interp.Linear`, :class:`~mlfsm.interp.LST`, and
+:class:`~mlfsm.interp.RIC` interpolation schemes for generating reaction path
+nodes between endpoint geometries.
 
-Interpolation
-~~~~~~~~~~~~~
 .. automodule:: mlfsm.interp
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
 
-The interpolation module provides objects and funcitonality for various interpolation methods.
+----
 
-Optimization
-~~~~~~~~~~~~
-.. automodule:: mlfsm.opt
+Coordinates (``mlfsm.coords``)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Cartesian and redundant internal coordinate systems used during interpolation and
+back-transformation to Cartesian coordinates.
+
+.. automodule:: mlfsm.coords
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
 
-The opt module provides optimizer objects for various methods and coordinate systems.
+----
 
-Cos
-~~~~~~~~~~~~~~~~~
-.. automodule:: mlfsm.cos
+Optimization (``mlfsm.opt``)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Node-level optimizers that relax FSM images perpendicular to the current tangent
+direction using L-BFGS-B with explicit line search.
+
+.. automodule:: mlfsm.opt
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
 
-The cos module provides the main freezing string class
+----
+
+Geometry Utilities (``mlfsm.geom``)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Low-level vector operations and projection operators used throughout the FSM,
+including rigid-body alignment and translation/rotation projection.
 
-Geometry
-~~~~~~~~
 .. automodule:: mlfsm.geom
    :members:
    :undoc-members:
    :show-inheritance:
-   :special-members: __init__
 
-The geometry module has functions for manipulating geometries or calculating geometric quantities.
+----
+
+Utilities (``mlfsm.utils``)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Utility Modules
----------------
+Input/output helpers for loading reactant and product geometries and handling
+fixed-atom constraints.
 
-Utilities
-~~~~~~~~~
 .. automodule:: mlfsm.utils
    :members:
    :undoc-members:
    :show-inheritance:
-   :special-members: __init__
-
-Helper functions and utilities for common operations.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index d810b5f..fbf99d5 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -3,12 +3,9 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("../../mlfsm"))
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+sys.path.insert(0, os.path.abspath("../../src"))
 
 # -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "ML-FSM"
 copyright = "2025, Jonah Marks and Joe Gomes"
@@ -16,12 +13,14 @@
 release = "1.0.1"
 
 # -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
     "sphinx.ext.autodoc",
-    "sphinx.ext.autodoc.typehints",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
     "numpydoc",
     "myst_parser",
 ]
@@ -31,26 +30,17 @@
 templates_path = ["_templates"]
 exclude_patterns: list[str] = []
 
+# -- Intersphinx mapping -----------------------------------------------------
 
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_static_path = ["_static"]
-
-# Theme
-html_theme = "sphinx_rtd_theme"  # or 'furo' for a modern look
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "ase": ("https://wiki.fysik.dtu.dk/ase", None),
+}
 
-# Extensions
-extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.napoleon",  # for Google/NumPy docstrings
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.mathjax",
-]
+# -- Autodoc settings --------------------------------------------------------
 
-# Autodoc settings
 autodoc_default_options = {
     "members": True,
     "member-order": "bysource",
@@ -59,11 +49,24 @@
     "exclude-members": "__weakref__",
 }
 
-# Autosummary
+autodoc_typehints = "description"
 autosummary_generate = True
 
-# Napoleon settings (if using Google/NumPy docstrings)
+# -- Napoleon settings -------------------------------------------------------
+
 napoleon_google_docstring = True
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = False
 napoleon_include_private_with_doc = False
+
+# -- HTML output -------------------------------------------------------------
+
+html_theme = "furo"
+
+html_theme_options = {
+    "sidebar_hide_name": False,
+    "navigation_with_keys": True,
+    "top_of_page_button": "edit",
+}
+
+html_title = "ML-FSM"
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
index 4322aee..0bbdbcd 100644
--- a/docs/source/examples.rst
+++ b/docs/source/examples.rst
@@ -1,10 +1,162 @@
 Examples
 ========
 
-This section provides practical examples of using mlfsm.
+Quick Start — EMT Calculator
+-----------------------------
 
-.. toctree::
-   :maxdepth: 2
+The simplest way to test ML-FSM is with ASE's built-in EMT calculator.
+The example below runs a full FSM calculation on the Diels-Alder reaction
+included in the ``examples/data/`` directory. Note that the EMT calculator
+is only for quick tests and demonstrations and should not be used in
+serious TS searches.
 
-   examples/fsm_example.py
-   examples/FSM_Colab_AIMNet2.ipynb
+.. code-block:: python
+
+    from pathlib import Path
+    from ase.calculators.emt import EMT
+    from mlfsm.utils import load_xyz
+    from mlfsm.cos import FreezingString
+    from mlfsm.opt import CartesianOptimizer
+
+    reaction_dir = Path("examples/data/06_diels_alder")
+    reactant, product = load_xyz(reaction_dir)
+
+    # Set up the FSM with RIC interpolation (recommended)
+    fsm = FreezingString(reactant, product, nnodes_min=9, interp_method="ric")
+
+    # Set up the optimizer with an ASE calculator
+    optimizer = CartesianOptimizer(calc=EMT(), maxiter=1, maxls=3)
+
+    outdir = Path("fsm_output")
+    outdir.mkdir(exist_ok=True)
+
+    # Run the FSM loop
+    while fsm.growing:
+        fsm.grow()
+        fsm.optimize(optimizer)
+        fsm.write(outdir)
+
+    print(f"FSM finished in {fsm.ngrad} gradient evaluations")
+    print(f"TS guess written to {outdir}")
+
+Using Fixed Atoms
+-----------------
+
+To freeze part of the system (e.g., a scaffold or periodic image atoms), pass
+a zero-indexed array of atom indices. Fixed atoms are excluded from interpolation
+displacement and held stationary during node optimization.
+
+.. code-block:: python
+
+    import numpy as np
+    from mlfsm.utils import load_xyz_fixed
+    from mlfsm.cos import FreezingString
+
+    # Freeze atoms 0–11 (zero-indexed)
+    fixed = np.arange(0, 12)
+    reactant, product = load_xyz_fixed("examples/data/my_reaction", fixed)
+
+    fsm = FreezingString(reactant, product, nnodes_min=9, interp_method="ric")
+
+The ``FixAtoms`` constraint is propagated automatically through the FSM;
+:func:`~mlfsm.geom.project_trans_rot_fixed` is used for alignment and
+:class:`~mlfsm.opt.CartesianOptimizer` zeroes gradients on fixed atoms.
+
+Specifying a Step Size Directly
+---------------------------------
+
+Instead of setting ``nnodes_min``, you can pass an explicit Cartesian step
+size (in Angstrom). The number of nodes is then determined automatically from
+the path arc length.
+
+.. code-block:: python
+
+    fsm = FreezingString(reactant, product, stepsize=0.3, interp_method="ric")
+
+Choosing an Interpolation Method
+----------------------------------
+
+Three interpolation methods are available via the ``interp_method`` argument:
+
+.. list-table::
+   :header-rows: 1
+   :widths: 15 85
+
+   * - ``interp_method``
+     - Description
+   * - ``"ric"`` *(default)*
+     - Linear interpolation in redundant internal coordinates. Produces
+       physically realistic intermediate geometries and generally gives the
+       best TS guess quality.
+   * - ``"lst"``
+     - Linear Synchronous Transit. Interpolates pairwise interatomic distances
+       and minimises deviation from a Cartesian linear blend.
+   * - ``"cart"``
+     - Plain Cartesian linear interpolation. Fast but can produce unphysical
+       structures for large conformational changes.
+
+Using an ML Calculator (UMA Small 1.2)
+--------------------------------------
+
+ML-FSM is calculator-agnostic — any ASE-compatible calculator can be used as
+the gradient provider. Below is a minimal example using the UMA Small 1.2 model.
+
+.. code-block:: python
+
+    from pathlib import Path    
+    from fairchem.core import FAIRChemCalculator, pretrained_mlip
+    from mlfsm.utils import load_xyz
+    from mlfsm.cos import FreezingString
+    from mlfsm.opt import CartesianOptimizer
+
+    predictor = pretrained_mlip.get_predict_unit("uma-s-1p2")
+    calc = FAIRChemCalculator(predictor, task_name="omol")
+
+    reactant, product = load_xyz("examples/data/06_diels_alder")
+    fsm = FreezingString(reactant, product, nnodes_min=9, interp_method="ric")
+    optimizer = CartesianOptimizer(calc=calc, maxiter=1, maxls=3)
+
+    outdir = Path("fsm_output")
+    outdir.mkdir(exist_ok=True)
+
+    while fsm.growing:
+        fsm.grow()
+        fsm.optimize(optimizer)
+        fsm.write(outdir)
+
+Google Colab Tutorial
+---------------------
+See ``examples/FSM_Colab_AIMNet2.ipynb`` for an Colab notebook using AIMNet2.
+
+Example Reactions
+-----------------
+
+The ``examples/data/`` directory contains nine test reactions:
+
+.. list-table::
+   :header-rows: 1
+   :widths: 10 55
+
+   * - Folder
+     - Reaction
+   * - ``01_formaldehyde``
+     - H₂CO → H₂ + CO
+   * - ``02_isocyanate_water``
+     - Isocyanate + H₂O → carbamic acid
+   * - ``03_ethanal``
+     - Acetaldehyde keto–enol tautomerism
+   * - ``04_ethane_dehydrogenation``
+     - CH₃CH₃ → CH₂CH₂ + H₂
+   * - ``05_bicyclobutane``
+     - Bicyclo[1.1.0]butane → *trans*-butadiene
+   * - ``06_diels_alder``
+     - Parent Diels–Alder cycloaddition
+   * - ``07_hexadiene``
+     - *cis,cis*-2,4-hexadiene → 3,4-dimethylcyclobutene
+   * - ``08_alanine``
+     - Alanine dipeptide rearrangement
+   * - ``09_proton``
+     - Acid zeolite proton migration
+
+Each directory contains ``initial.xyz`` (reactant + product frames), ``chg``
+(molecular charge), and ``mult`` (spin multiplicity).
diff --git a/docs/source/index.rst b/docs/source/index.rst
index ff16533..1ae2f04 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -1,15 +1,29 @@
-mlfsm Documentation
-===================
+ML-FSM Documentation
+====================
 
-Welcome to ML-FSM's documentation! This package provides a calculator agnostic impleme.
+ML-FSM is a Python implementation of the **Freezing String Method** (FSM) for automated
+transition state (TS) guess generation. It supports multiple interpolation strategies
+including redundant internal coordinates (RIC), linear synchronous transit (LST), and
+Cartesian interpolation, and is designed to work with any ASE-compatible calculator,
+including machine learning interatomic potentials.
+
+Key features:
+
+- **RIC interpolation** — produces chemically realistic intermediate geometries and
+  enables larger interpolation step sizes with fewer optimization steps per cycle
+- **Calculator agnostic** — works with ML potentials (AIMNet2, MACE-OFF, TensorNet,
+  xTB, FAIR UMA) and quantum chemistry codes (Q-Chem via file I/O)
+- **Fixed-atom support** — freeze a subset of atoms during interpolation and optimization
+- **Flexible step-size control** — specify node count or an explicit Cartesian step size
+- **Open source** — MIT-licensed, installable from PyPI
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
    installation
-   api
    examples
+   api
 
 Indices and tables
 ==================
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 3d3603f..da614da 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -3,23 +3,60 @@ Installation
 
 Requirements
 ------------
-* Python 3.11+
-* NumPy 1.26+
-* ase 3.22+
-* scipy 1.13+
-* geometric 1.0.0+
-* networkx 3.0+
+
+- Python 3.11+
+- `NumPy <https://numpy.org>`_ ≥ 1.26
+- `ASE <https://wiki.fysik.dtu.dk/ase>`_ ≥ 3.22
+- `SciPy <https://scipy.org>`_ ≥ 1.13
+- `geomeTRIC <https://github.com/leeping/geomeTRIC>`_ ≥ 1.0.0
+- `NetworkX <https://networkx.org>`_ ≥ 3.0
 
 Install from PyPI
 -----------------
+
 .. code-block:: bash
 
    pip install mlfsm
 
-Install from source
+Install from Source
 -------------------
+To access the most recent features and bug fixes, install from source:
+
 .. code-block:: bash
 
    git clone https://github.com/thegomeslab/ML-FSM.git
    cd ML-FSM
    pip install -e .
+
+Optional: Calculator Dependencies
+--------------------------------------
+
+ML-FSM works with any ASE-compatible calculator including traditional QM and semi-empirical potential energy surfaces. 
+The following potentials have been tested and are supported out of the box via ``examples/fsm_example.py``:
+
+.. list-table::
+   :header-rows: 1
+   :widths: 20 45 35
+
+   * - Calculator
+     - Install
+     - Notes
+   * - **AIMNet2**
+     - .. code-block:: bash
+
+          git clone https://github.com/isayevlab/AIMNet2.git
+          cd AIMNET2
+          pip install -e .
+     - AIMNet2 pre-trained model.
+   * - **MACE**
+     - ``pip install mace-torch``
+     - Pre-trained models available via ``mace_off``
+   * - **FAIR UMA**
+     - ``pip install fairchem-core``
+     - Meta's Universal Model for Atoms
+   * - **xTB**
+     - ``mamba install xtb-python``
+     - GFN2-xTB semiempirical method
+   * - **Q-Chem**
+     - See `Q-Chem <https://www.q-chem.com>`_
+     - File-based I/O; requires a Q-Chem license
diff --git a/pixi.lock b/pixi.lock
index d55e174..8d861d8 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -6,130 +6,135 @@ environments:
     - url: https://conda.anaconda.org/pytorch/
     indexes:
     - https://pypi.org/simple
+    options:
+      pypi-prerelease-mode: if-necessary-or-explicit
     packages:
       linux-64:
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-3_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.7.9-hbd8a1cb_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-32_hfdb39a5_mkl.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-32_h372d94f_mkl.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.13.3-ha770c72_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.13.3-h48d6fc4_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.11.2-default_h0d58e46_1001.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h4ce23a2_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-32_hc41d3b0_mkl.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.1.0-hdb68285_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-6_h5875eb1_mkl.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-6_hfef963f_mkl.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.12.2-default_hafda6a7_1000.conda
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   license_family: MOZILLA
   purls: []
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+  size: 311150
+  timestamp: 1772476812121
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zeromq-4.3.5-h4818236_10.conda
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-  - krb5 >=1.21.3,<1.22.0a0
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+  - libcxx >=19
+  - krb5 >=1.22.2,<1.23.0a0
+  - libsodium >=1.0.21,<1.0.22.0a0
   license: MPL-2.0
   license_family: MOZILLA
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   depends:
-  - python >=3.9
+  - python >=3.10
+  - python
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   license_family: MIT
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   depends:
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-  - cffi >=1.11
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-  - python_abi 3.11.* *_cp311
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   license_family: BSD
   purls: []
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+  sha256: 9485ba49e8f47d2b597dd399e88f4802e100851b27c21d7525625b0b4025a5d9
+  md5: ab136e4c34e97f34fb621d2592a393d8
   depends:
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   - libzlib >=1.3.1,<2.0a0
   license: BSD-3-Clause
   license_family: BSD
   purls: []
-  size: 399979
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+  size: 433413
+  timestamp: 1764777166076
diff --git a/pyproject.toml b/pyproject.toml
index e5a2f2f..249bb3e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ lint = { cmd="ruff check . --fix" }
 types = { cmd="mypy ." }
 test = { cmd="pytest" }
 coverage = { cmd = "pytest --cov=src/mlfsm --cov-report=xml" }
-docs = { cmd="sphinx-build -b html docs/source docs/build" }
+docs = { cmd="python -m sphinx docs/source docs/build" }
 all = { depends-on = ["fmt", "lint", "types", "test", "docs"] }
 
 
@@ -65,7 +65,7 @@ pillow = "<11.3.0"
 sphinx = "*"
 sphinx-autodoc-typehints = "*"
 numpydoc = "*"
-sphinx-rtd-theme = "*"
+furo = "*"
 myst-parser = "*"
 
 [tool.ruff]
diff --git a/src/mlfsm/coords.py b/src/mlfsm/coords.py
index 895c225..10b5ab2 100644
--- a/src/mlfsm/coords.py
+++ b/src/mlfsm/coords.py
@@ -60,7 +60,7 @@ def qprint(self, atoms: Atoms) -> None:
             print(f"{name:15} = {coord.value(xyzb):15.8f}")
 
     def q(self, xyz: NDArray[np.float64]) -> NDArray[np.float64]:
-        """Return coordinate values in from Cartesian positions."""
+        """Return internal coordinate values from Cartesian positions."""
         xyzb = xyz * angs_to_bohr
         # return np.array([coord.value(xyzb) for coord in self.coords.values()], dtype=np.float64)
         return np.fromiter((coord.value(xyzb) for coord in self.coords.values()), dtype=np.float64)
diff --git a/src/mlfsm/cos.py b/src/mlfsm/cos.py
index b52ec8c..10b32a6 100644
--- a/src/mlfsm/cos.py
+++ b/src/mlfsm/cos.py
@@ -27,7 +27,50 @@
 
 
 class FreezingString:
-    """Implements the Freezing String Method."""
+    """Implements the Freezing String Method (FSM) for transition state guess generation.
+
+    The FSM grows two strings from the reactant and product endpoints toward each
+    other. At each iteration a new frontier node is placed by taking a step along
+    an interpolated path, optimized perpendicular to the local tangent direction,
+    and then frozen. The highest-energy node at convergence serves as the TS guess.
+
+    Parameters
+    ----------
+    reactant : ase.Atoms
+        Reactant geometry with an attached ASE calculator (optional at
+        construction; required before calling :meth:`optimize`).
+    product : ase.Atoms
+        Product geometry. Must have the same atom ordering as ``reactant``.
+    nnodes_min : int, optional
+        Nominal number of string nodes used to determine the interpolation
+        step size.  The actual node count may differ slightly depending on
+        the path arc length. Default is 10.
+    interp_method : {"ric", "lst", "cart"}
+        Interpolation scheme used to generate new frontier nodes:
+
+        * ``"ric"`` — redundant internal coordinates (recommended).
+        * ``"lst"`` — linear synchronous transit.
+        * ``"cart"`` — plain Cartesian linear interpolation.
+    ninterp : int, optional
+        Number of points used to discretize the dense interpolated path from
+        which frontier nodes are selected. Default is 100.
+    stepsize : float, optional
+        If > 0, sets the Cartesian step size (Å) explicitly and ignores
+        ``nnodes_min``. The step size is measured along the Cartesian
+        arc length of the initial linear interpolation. Default is 0.0
+        (derive step size from ``nnodes_min``).
+
+    Attributes
+    ----------
+    r_string, p_string : list[ase.Atoms]
+        Growing strings from the reactant and product ends.
+    r_energy, p_energy : list[float or None]
+        Energies at each node (``None`` until evaluated).
+    growing : bool
+        ``True`` while the two string ends have not yet converged.
+    ngrad : int
+        Total number of gradient evaluations performed so far.
+    """
 
     def __init__(
         self,
@@ -89,7 +132,16 @@ def __init__(
         self.coordsobj: Any = None
 
     def interpolate(self, outdir: Path | str) -> None:
-        """Generate and write interpolated string between current endpoints."""
+        """Generate and write the dense interpolated path between current frontier nodes.
+
+        Writes a single XYZ file named ``interp_<iteration>.xyz`` to ``outdir``.
+        Each frame comment line contains the cumulative arc-length value.
+
+        Parameters
+        ----------
+        outdir : path-like
+            Directory in which to write the interpolated path XYZ file.
+        """
         outfile = Path(outdir) / f"interp_{self.iteration:02d}.xyz"
 
         r_atoms = self.r_string[-1]
@@ -117,7 +169,14 @@ def interpolate(self, outdir: Path | str) -> None:
                     f.write(f"{atom} {x:.8f} {y:.8f} {z:.8f}\n")
 
     def grow(self) -> None:
-        """Grow the string by adding nodes from each end."""
+        """Grow the string by adding one new frontier node to each end.
+
+        Interpolates between the current frontier nodes, selects positions
+        one step-size inward from each end, and appends those nodes to
+        ``r_string`` and ``p_string`` with ``fix=False``. Sets
+        ``self.growing = False`` when the two frontiers are within one
+        step-size of each other.
+        """
         r_atoms = self.r_string[-1]
         p_atoms = self.p_string[-1]
 
@@ -238,7 +297,19 @@ def grow(self) -> None:
             self.p_nnodes = len(self.p_string)
 
     def optimize(self, optimizer: Any) -> None:
-        """Relax unfixed nodes on the hyperplane orthogonal to the local tangent direction."""
+        """Relax all unfixed frontier nodes perpendicular to the local tangent.
+
+        Evaluates energies for endpoint nodes that have not yet been computed,
+        then runs the optimizer on every unfixed node. After optimization each
+        node is frozen (``fix=True``) so it will not move in subsequent
+        iterations.
+
+        Parameters
+        ----------
+        optimizer : CartesianOptimizer or InternalsOptimizer
+            Optimizer instance whose ``calc`` attribute provides energies and
+            gradients via the ASE calculator interface.
+        """
         self.iteration += 1
         optimizer.coordsobj = self.coordsobj
 
@@ -284,7 +355,18 @@ def optimize(self, optimizer: Any) -> None:
             self.growing = False
 
     def write(self, outdir: Path | str) -> None:
-        """Write current string geometries and relative energies to an XYZ file."""
+        """Write the current string geometries and relative energies to an XYZ file.
+
+        Writes ``vfile_<iteration>.xyz`` to ``outdir``. Frame comment lines
+        contain the cumulative arc-length and relative energy (eV). On the
+        final iteration (``growing=False``) also writes the total gradient
+        count to ``ngrad.txt``.
+
+        Parameters
+        ----------
+        outdir : path-like
+            Directory in which to write output files.
+        """
         outdir = Path(outdir)
         outfile = outdir / f"vfile_{self.iteration:02d}.xyz"
         gradfile = outdir / "ngrad.txt"
diff --git a/src/mlfsm/interp.py b/src/mlfsm/interp.py
index 3a4eb22..f501d15 100644
--- a/src/mlfsm/interp.py
+++ b/src/mlfsm/interp.py
@@ -18,7 +18,24 @@
 
 @dataclass
 class Interpolate:
-    """Abstract base class for interpolation schemes between molecular geometries."""
+    """Abstract base class for interpolation schemes between molecular geometries.
+
+    Parameters
+    ----------
+    atoms1 : ase.Atoms
+        Starting (reactant-side) geometry.
+    atoms2 : ase.Atoms
+        Ending (product-side) geometry.
+    ninterp : int
+        Number of discrete frames to generate along the interpolated path.
+    gtol : float, optional
+        Gradient tolerance passed to the L-BFGS-B minimizer (used by
+        :class:`LST`). Default is 1e-4.
+    return_q : bool, optional
+        If ``True``, return interpolated internal coordinate vectors instead
+        of Cartesian positions. Only meaningful for :class:`RIC`. Default is
+        ``False``.
+    """
 
     atoms1: Atoms
     atoms2: Atoms
@@ -27,23 +44,31 @@ class Interpolate:
     return_q: bool = False
 
     def interpolate(self) -> NDArray[np.float32]:
-        """Abstract interpolationn routine-must be overridden."""
+        """Abstract interpolation routine — must be overridden by subclasses."""
         raise NotImplementedError
 
     def __call__(self) -> NDArray[np.float32]:
-        """Call the interpolation routine and returns interpolated geometries."""
+        """Call the interpolation routine and return interpolated geometries."""
         return self.interpolate()
 
 
 class Linear(Interpolate):
     """Linear interpolation of Cartesian coordinates.
 
-    Generates a reaction path by linearly interpolating Cartesian coordinates
-    between two endpoint geometries.
+    Generates a reaction path by linearly blending the Cartesian positions of
+    two endpoint geometries: ``(1-f)*xyz1 + f*xyz2`` for *f* in [0, 1]. Fast
+    but may produce unphysical geometries for large conformational changes.
     """
 
     def interpolate(self) -> NDArray[np.float32]:
-        """Compute linear interpolated path between two geometries."""
+        """Return linearly interpolated Cartesian path.
+
+        Returns
+        -------
+        NDArray[np.float32]
+            Array of shape ``(ninterp, natoms*3)`` with flattened Cartesian
+            coordinates for each interpolated frame.
+        """
         xyz1 = self.atoms1.get_positions()
         xyz2 = self.atoms2.get_positions()
 
@@ -56,11 +81,16 @@ def xab(f: float) -> NDArray[np.floating]:
 
 
 class LST(Interpolate):
-    """Linear Synchronous Transit (LST) interpolation method.
+    """Linear Synchronous Transit (LST) interpolation.
+
+    At each interpolation point *f*, minimizes the deviation from linearly
+    interpolated pairwise interatomic distances while remaining close to the
+    Cartesian linear blend. Produces more chemically realistic geometries than
+    plain Cartesian interpolation at moderate extra cost.
 
-    Halgren, Thomas A., and William N. Lipscomb.
-    "The synchronous transit method for determining reaction pathways and locating molecular transition states."
-    Chemical Physics Letters 49.2 (1977): 225 to 232.
+    References
+    ----------
+    Halgren, T. A.; Lipscomb, W. N. *Chem. Phys. Lett.* **1977**, *49*, 225-232.
     """
 
     def obj(
@@ -70,7 +100,28 @@ def obj(
         rab: Callable[[float], NDArray[np.floating]],
         xab: Callable[[float], NDArray[np.floating]],
     ) -> float:
-        """Objective function for LST interpolation."""
+        """Objective function minimized at each interpolation point.
+
+        Computes the weighted sum of squared deviations of pairwise distances
+        from their linearly interpolated target values, plus a small Cartesian
+        restraint to prevent rigid-body drift.
+
+        Parameters
+        ----------
+        x_c : NDArray
+            Flattened trial Cartesian coordinates.
+        f : float
+            Interpolation parameter in [0, 1].
+        rab : callable
+            Returns linearly interpolated pairwise distances at parameter *f*.
+        xab : callable
+            Returns linearly interpolated Cartesian coordinates at parameter *f*.
+
+        Returns
+        -------
+        float
+            Scalar objective value.
+        """
         x_c = x_c.reshape(-1, 3)
         rab_c = pdist(x_c)
         rab_i = rab(f)
@@ -79,7 +130,14 @@ def obj(
         return float((((rab_i - rab_c) ** 2) / rab_i**4).sum() + 5e-2 * ((x_i - x_c) ** 2).sum())
 
     def interpolate(self) -> NDArray[np.float32]:
-        """Generate interpolated structures using LST."""
+        """Return LST-interpolated path.
+
+        Returns
+        -------
+        NDArray[np.float32]
+            Array of shape ``(ninterp, natoms*3)`` with flattened Cartesian
+            coordinates for each frame.
+        """
         xyz1 = self.atoms1.get_positions()
         xyz2 = self.atoms2.get_positions()
         pdist_1 = pdist(xyz1)
@@ -109,14 +167,39 @@ def xab(f: float) -> NDArray[np.floating]:
 
 @dataclass
 class RIC(Interpolate):
-    """Interpolates in redundant internal coordinates (RIC)."""
+    """Redundant internal coordinate (RIC) interpolation.
+
+    Linearly interpolates between the reactant and product geometries in the
+    space of delocalized redundant internal coordinates (bonds, angles,
+    torsions, out-of-plane bends). The interpolated frames are then
+    back-transformed to Cartesian coordinates via iterative application of the
+    Wilson B-matrix. This scheme avoids the unphysical bond compressions that
+    can occur with Cartesian interpolation for large conformational changes.
+
+    Attributes
+    ----------
+    coords : Redundant
+        The redundant internal coordinate system built from both endpoints.
+    """
 
     def __post_init__(self) -> None:
-        """Initialize the RIC interpolator."""
+        """Build the shared redundant internal coordinate system."""
         self.coords = Redundant(self.atoms1, self.atoms2, verbose=False)
 
     def interpolate(self) -> NDArray[np.float32]:
-        """Generate interpolated structures using linear interpolation in RIC."""
+        """Return RIC-interpolated path in Cartesian (or internal) coordinates.
+
+        Torsion periodicity wrapping is applied automatically when the
+        interpolation crosses the ±π boundary.
+
+        Returns
+        -------
+        NDArray[np.float32]
+            If ``return_q`` is ``False`` (default): array of shape
+            ``(ninterp, natoms*3)`` with flattened Cartesian coordinates.
+            If ``return_q`` is ``True``: array of shape ``(ninterp, n_ics)``
+            with internal coordinate values.
+        """
         xyz1 = self.atoms1.get_positions()
         xyz2 = self.atoms2.get_positions()
         q1 = self.coords.q(xyz1)  # type ignore[no-untyped-call]
diff --git a/src/mlfsm/utils.py b/src/mlfsm/utils.py
index 2403ff5..958a984 100644
--- a/src/mlfsm/utils.py
+++ b/src/mlfsm/utils.py
@@ -1,7 +1,7 @@
 """Utility functions for reading input and checking numeric types."""
 
 from pathlib import Path
-from typing import Any
+from typing import Any, cast
 
 import numpy as np
 from ase import Atoms
@@ -13,17 +13,35 @@
 
 
 def load_xyz(reaction_dir: Path | str) -> tuple[Atoms, Atoms]:
-    """
-    Load reactant and product geometries from a directory.
+    """Load reactant and product geometries from a reaction directory.
+
+    Reads the first and last frames of ``initial.xyz`` and aligns them by
+    minimizing rigid-body rotation and translation via the Kabsch algorithm.
+
+    Parameters
+    ----------
+    reaction_dir : path-like
+        Directory containing ``initial.xyz``.  The file must have at least two
+        XYZ frames: the reactant (first) and the product (last).
 
-    Assumes a file named initial.xyz containing the reactant and product geometries.
+    Returns
+    -------
+    reactant : ase.Atoms
+        Reactant geometry after alignment.
+    product : ase.Atoms
+        Product geometry after alignment to the reactant.
+
+    Raises
+    ------
+    Exception
+        If ``initial.xyz`` does not exist in ``reaction_dir``.
     """
     xyz = Path(reaction_dir) / "initial.xyz"
     if not xyz.is_file():
         raise Exception(f"Input file {xyz} not found.")
     atoms = read(xyz, format="xyz", index=":")
-    reactant = atoms[0]
-    product = atoms[-1]
+    reactant = cast("Atoms", atoms[0])
+    product = cast("Atoms", atoms[-1])
     r_xyz, p_xyz = project_trans_rot(reactant.get_positions(), product.get_positions())
     reactant.set_positions(r_xyz.reshape(-1, 3))
     product.set_positions(p_xyz.reshape(-1, 3))
@@ -32,17 +50,39 @@ def load_xyz(reaction_dir: Path | str) -> tuple[Atoms, Atoms]:
 
 
 def load_xyz_fixed(reaction_dir: Path | str, fixed: NDArray[np.integer[Any]]) -> tuple[Atoms, Atoms]:
-    """
-    Load reactant and product geometries from a directory.
+    """Load reactant and product geometries with fixed-atom constraints applied.
+
+    Reads ``initial.xyz``, aligns the structures, and attaches an ASE
+    :class:`~ase.constraints.FixAtoms` constraint to both atoms objects so
+    that the specified atoms are held stationary during FSM optimization.
+    When ``fixed`` is empty the behaviour is identical to :func:`load_xyz`.
 
-    Assumes a file named initial.xyz containing the reactant and product geometries.
+    Parameters
+    ----------
+    reaction_dir : path-like
+        Directory containing ``initial.xyz``.
+    fixed : NDArray[int]
+        Zero-indexed array of atom indices to freeze.  Pass an empty array
+        (``np.array([], dtype=int)``) to apply no constraints.
+
+    Returns
+    -------
+    reactant : ase.Atoms
+        Reactant geometry with :class:`~ase.constraints.FixAtoms` applied.
+    product : ase.Atoms
+        Product geometry with :class:`~ase.constraints.FixAtoms` applied.
+
+    Raises
+    ------
+    Exception
+        If ``initial.xyz`` does not exist in ``reaction_dir``.
     """
     xyz = Path(reaction_dir) / "initial.xyz"
     if not xyz.is_file():
         raise Exception(f"Input file {xyz} not found.")
     atoms = read(xyz, format="xyz", index=":")
-    reactant = atoms[0]
-    product = atoms[-1]
+    reactant = cast("Atoms", atoms[0])
+    product = cast("Atoms", atoms[-1])
     if len(fixed) == 0:
         r_xyz, p_xyz = project_trans_rot(reactant.get_positions(), product.get_positions())
         reactant.set_positions(r_xyz.reshape(-1, 3))
@@ -59,10 +99,23 @@ def load_xyz_fixed(reaction_dir: Path | str, fixed: NDArray[np.integer[Any]]) ->
 
 
 def float_check(x: float) -> float:
-    """
-    Convert scalars, 0D arrays, or single element containers to a float.
+    """Convert a scalar, 0-D array, or single-element container to a Python float.
+
+    Parameters
+    ----------
+    x : float, ndarray, list, or tuple
+        Value to convert.  Must be a plain float, a 0-D NumPy array, or a
+        length-1 sequence.
+
+    Returns
+    -------
+    float
+        The converted value.
 
-    Leaves floats alone. Raises an error for anything else.
+    Raises
+    ------
+    TypeError
+        If ``x`` is a multi-element container or an unsupported type.
     """
     if isinstance(x, float):
         return x