Merge pull request #23 from bc118/add_tests

Added unit tests for user input and other checks.
GOMC-WSU · Sep 24, 2023 · 649053e · 649053e
2 parents 85f56c2 + 392b7a2
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diff --git a/docs/getting_started/installation/installation.rst b/docs/getting_started/installation/installation.rst
@@ -3,11 +3,11 @@ Installation
 ============
 
 .. note::
-    The GOMC software need to be installed manually, outside of this Python install,
+    The GOMC >= v2.75 software need to be installed manually, outside of this Python install,
     with it's directory/path specified in the dihedral fit function.
 
-Recommended installation is with `mamba <https://github.com/mamba-org/mamba>`_
-------------------------------------------------------------------------------
+Installation with `mamba <https://github.com/mamba-org/mamba>`_ (Recommended)
+-----------------------------------------------------------------------------
 ::
 
     $ mamba install -c conda-forge mosdef-dihedral-fit
@@ -18,15 +18,9 @@ Install with `conda <https://repo.anaconda.com/miniconda/>`_
 
     $ conda install -c conda-forge mosdef-dihedral-fit
 
-There is an issue building MoSDeF-GOMC version 1.0.0 with ``conda`` or ``conda-forge``
-not extracting the latest ``conda`` build version. Therefore, the user can conduct
-the additional command below or install using ``mamba`` because ``mamba`` is using the correct build.::
 
-    $ conda install -c conda-forge sympy=1.10 garnett gsd pycifrw
-
-
-Install an editable version from the source code
-------------------------------------------------
+Install an editable version via the source code
+-----------------------------------------------
 
 It is common practice to utilize a pre-packaged ``Python`` distribution like
 `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ to
@@ -49,15 +43,15 @@ Install pre-commit
 
 To maintain uniform coding, this software utilizes the `pre-commit <https://pre-commit.com/>`_ package.
 
-To check all the files, you can run::
+To check all the files using pre-commit, run::
 
      $ pre-commit run --all-files
 
 
 Supported Python Versions
 -------------------------
 
-``Python 3.9`` is currently the only officially supported and tested version during the
+``Python 3.9 and 3.10`` are currently the only officially supported and tested version during the
 software development. Older versions of ``Python`` may work, but they are not guaranteed to work.
 
 Testing your installation

diff --git a/docs/getting_started/quick_start/quick_start.rst b/docs/getting_started/quick_start/quick_start.rst
@@ -5,7 +5,7 @@ Quick Start
 -----------
 
 .. note::
-    The GOMC software need to be installed manually, outside of this Python install,
+    The GOMC >= v2.75 software need to be installed manually, outside of this Python install,
     with it's directory/path specified in the dihedral fit function.
 
 These examples are provided as a python files, which the user can run and modifiy.

diff --git a/docs/index.rst b/docs/index.rst
@@ -9,9 +9,9 @@ dihedrals, then also analytically converts them to the periodic/`CHARMM <https:/
 Ryckaert-Bellemans (RB) torsion.
 
 The **MoSDeF-dihedral-fit** software produces dihedral fits for existing force fields, compatible with
-`GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu>`_ and
+`GPU Optimized Monte Carlo (GOMC) >= v2.75 <http://gomc.eng.wayne.edu>`_ and
 `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, with only tens of lines of python code,
-the `Gaussian <https://www.gaussin.com>`_ log files, and a **mol2** file.
+the `Gaussian 16 <https://www.gaussin.com>`_ log files, and a **mol2** file.
 
 .. note::
     Currently, this means that only the fourth (4th) cosine multiple or power is utilized in the dihedral fit.
@@ -24,21 +24,21 @@ the `Gaussian <https://www.gaussin.com>`_ log files, and a **mol2** file.
 
 The `MoSDeF-GOMC <https://github.com/GOMC-WSU/MoSDeF-GOMC/tree/master/mosdef_gomc>`_ software package is used
 for the Molecular Mechanics (MM) calculation, which utilizes 
-`GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu>`_, the
+`GPU Optimized Monte Carlo (GOMC) >= v2.75 <http://gomc.eng.wayne.edu>`_, the
 `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, and the
 `vmd-python <https://github.com/Eigenstate/vmd-python>`_ core software packages. For the Quantum Mechanics calculations,
-the **Gaussian** software is used, reading the **Gaussian** log files.
-From the **Gaussian** log file, a user created **mol2** file, and a few user inputs, this software automatically
+the **Gaussian 16** software is used, reading the **Gaussian 16** log files.
+From the **Gaussian 16** log file, a user created **mol2** file, and a few user inputs, this software automatically
 fits the desired dihedral, accounting for multiple dihedrals simultaneously. The software output provides
 a wide range of allowable dihedral fits with different cosine term combinations, including plots for visual reference;
 from this information, the user can then select the best dihedral fit for the specific application.
 Additionally, the 1-4 interactions for the force fields can be explicitly set in the force field XML file,
 allowing the flexibility that some other dihedral fitters lack. Lastly, the dihedral fits are compared by recalculating 
-the dihedral in **GOMC** and comparing it to the original **Gaussian** energies, ensuring a correct dihedral fit.  
+the dihedral in **GOMC >= v2.75** and comparing it to the original **Gaussian 16** energies, ensuring a correct dihedral fit.  
 
 
 **MoSDeF-dihedral-fit Highlights**:
-   #. With a **Gaussian** log file and a few user inputs, the user can easily fit a dihedral.
+   #. With a **Gaussian 16** log file and a few user inputs, the user can easily fit a dihedral.
 
    #. **MoSDeF-dihedral-fit** is designed to automate the dihedral fit
 

diff --git a/docs/overview/general_info.rst b/docs/overview/general_info.rst
@@ -12,9 +12,9 @@ dihedrals, then also analytically converts them to the periodic/`CHARMM <https:/
 Ryckaert-Bellemans (RB) torsion.
 
 The **MoSDeF-dihedral-fit** software produces dihedral fits for existing force fields, compatible with
-`GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu>`_ and
+`GPU Optimized Monte Carlo (GOMC) >= v2.75 <http://gomc.eng.wayne.edu>`_ and
 `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, with only tens of lines of python code,
-the `Gaussian <https://www.gaussin.com>`_ log files, and a **mol2** file.
+the `Gaussian 16 <https://www.gaussin.com>`_ log files, and a **mol2** file.
 
 .. note::
     Currently, this means that only the fourth (4th) cosine multiple or power is utilized in the dihedral fit.
@@ -30,14 +30,14 @@ for the Molecular Mechanics (MM) calculation, which utilizes
 `GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu>`_, the
 `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, and the
 `vmd-python <https://github.com/Eigenstate/vmd-python>`_ core software packages. For the Quantum Mechanics calculations,
-the **Gaussian** software is used, reading the **Gaussian** log files.
-From the **Gaussian** log file, a user created **mol2** file, and a few user inputs, this software automatically
+the **Gaussian 16** software is used, reading the **Gaussian 16** log files.
+From the **Gaussian 16** log file, a user created **mol2** file, and a few user inputs, this software automatically
 fits the desired dihedral, accounting for multiple dihedrals simultaneously. The software output provides
 a wide range of allowable dihedral fits with different cosine term combinations, including plots for visual reference;
 from this information, the user can then select the best dihedral fit for the specific application.
 Additionally, the 1-4 interactions for the force fields can be explicitly set in the force field XML file,
 allowing the flexibility that some other dihedral fitters lack. Lastly, the dihedral fits are compared by recalculating 
-the dihedral in **GOMC** and comparing it to the original **Gaussian** energies, ensuring a correct dihedral fit.  
+the dihedral in **GOMC >= v2.75** and comparing it to the original **Gaussian 16** energies, ensuring a correct dihedral fit.  
 
 
 
@@ -73,4 +73,4 @@ The **vmd-python** software is licensed by the Theoretical and Computational Bio
 
 The vmd-python website is https://github.com/Eigenstate/vmd-python
 
-The official VMD web page is http://www.ks.uiuc.edu/Research/vmd
+The official VMD web page is http://www.ks.uiuc.edu/Research/vmd
diff --git a/docs/reference/citing_mosdef_dihedral_fit_python.rst b/docs/reference/citing_mosdef_dihedral_fit_python.rst
@@ -47,7 +47,7 @@ Download as :download:`BibTeX <mosdef_dihedral_fit_zenodo.bib>` or :download:`RI
 
 
 
-Please also cite the **MoSDeF** software:
+Please also cite the following software:
 	* `mBuild <https://mbuild.mosdef.org/en/stable/>`_ -- A hierarchical, component based molecule builder
 
 	* `foyer <https://foyer.mosdef.org/en/stable/>`_ -- A package for atom-typing as well as applying and disseminating forcefields

diff --git a/docs/reference/credits.rst b/docs/reference/credits.rst
@@ -10,7 +10,7 @@ MoSDeF-dihedral-fit developers:
 
 **Nicholas Craven** - Developer
 
-**Christopher R. Iacovella** - Developer
+**Christopher R. Iacovella** - Advisor
 
 **Clare McCabe** - Advisor
 
@@ -19,6 +19,10 @@ MoSDeF-dihedral-fit developers:
 **Jeffrey Potoff** - Advisor and maintainer
 
 
-`MoSDeF-dihedral-fit <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit>`_ was developed and created as a collaborative effort between **Wayne State University** and **Vanderbilt University**, which included the `GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu>`_,`Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_, and `MoSDeF-GOMC <https://github.com/GOMC-WSU/MoSDeF-GOMC/tree/master/mosdef_gomc>`_ teams.
+`MoSDeF-dihedral-fit <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit>`_ was developed and created as a collaborative effort between **Wayne State University**, **Vanderbilt University**, and **Atomfold LLC** (`Atomfold LLC website <https://atomfold.com>`_).  
+
+**Wayne State University** developled the `GPU Optimized Monte Carlo (GOMC) <http://gomc.eng.wayne.edu>`_ engine, which is utilized in this software.
+
+Other collaboriative efforts between **Wayne State University** and **Vanderbilt University** include the `Molecular Simulation Design Framework (MoSDeF) <https://mosdef.org>`_ and `MoSDeF-GOMC <https://github.com/GOMC-WSU/MoSDeF-GOMC/tree/master/mosdef_gomc>`_ software, which are utilized in this software.
 
 The **MoSDeF-dihedral-fit** software was supported via National Science Foundation (**NSF**) grants OAC-1835713, OAC-1835874, and CBET-2052438.  Any statements stated or expressed are solely those of the **MoSDeF-dihedral-fit** software or developers and not the **NSF**.