Add CNAME and noJekyl

CNAME

@@ -1 +1 @@
-https://qtchem.github.io/ChemToolsCUDA/
+cugbasis.qcdevs.org

_sources/installation.rst.txt

@@ -3,20 +3,6 @@
 Installation
 ############
 
-Downloading Code
-================
-
-The latest code can be obtained through theochem (https://github.com/qtchem/CuGBasis) in Github,
-
-.. code-block:: bash
-
-   git clone https://github.com/qtchem/CuGBasis.git
-
-   # Get the dependencies in ./libs/ folder
-   git submodule update --init --recursive
-
-
-
 Dependencies
 ============
 
@@ -25,20 +11,54 @@ The following dependencies will be necessary for cuGBasis to build properly,
 * CMake>=3.24: (https://cmake.org/)
 * CUDA/DRIVERS/NVCC/CUDA-TOOLKIT: (https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
 * Python>=3.7: (http://www.python.org/)
+
+The following Python dependencies are necessary:
+
 * NumPy >= 1.16.0: http://www.numpy.org/
 * Pybind11 on python: (https://github.com/pybind/pybind11)
 * IOData on python: (https://github.com/theochem/iodata)
 
+These python dependencies can be installed via:
+
+.. code-block:: bash
+
+    pip install numpy pybind11 qc-iodata
+
 For testing the following are required to be installed on the Python system:
 
 * PyTest >= 5.4.3: (https://docs.pytest.org/ <https://docs.pytest.org/)
 * GBasis: (https://github.com/theochem/gbasis)
 * ChemTools: (https://github.com/theochem/chemtools)
 
-The following Eigen package will automatically be tried to linked if CMake could not find the package already.
+These can be installed via:
+
+.. code-block:: bash
+
+    pip install pytest
+    pip install git+https://github.com/theochem/gbasis.git
+    pip install git+https://github.com/theochem/chemtools.git
+
+
+The following Eigen package will automatically be linked if CMake could not find the package already.
 
 * Eigen>=3: (https://eigen.tuxfamily.org/index.php?title=Main_Page)
 
+
+Downloading Code
+================
+
+The user must obtain the latest code from theochem (https://github.com/theochem/cugbasis) in Github,
+As well, as obtain the dependencies from running the `git submodule` command.
+
+.. code-block:: bash
+
+   git clone https://github.com/theochem/CuGBasis.git
+
+   # Get the dependencies in ./libs/ folder
+   git submodule update --init --recursive
+
+
+
 Installation
 ============
 
@@ -78,7 +98,7 @@ The following is the set of instructions for creating a Python environment insid
 and installing cuGBasis. It's important to compile/install cuGBasis with a GPU enabled.
 It is recommended that CMake version be greater than 3.24 (see below).
 Note that different Cuda environments can be loaded, but here we will load Cuda 11.7 version.
-It's important to load the required depedencies before creating the python environment
+It's important to load the required dependencies before creating the python environment
 so that the same compiler is used when creating the Python virtual environment, and when
 installing (this may not be required but is hypothesized to may cause future errors).
 

conventions.html

@@ -52,8 +52,8 @@
               <p class="caption" role="heading"><span class="caption-text">User documentation:</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#downloading-code">Downloading Code</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#dependencies">Dependencies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#downloading-code">Downloading Code</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#id1">Installation</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="installation.html#python-binding">Python Binding</a></li>
 <li class="toctree-l3"><a class="reference internal" href="installation.html#c">C++</a></li>
@@ -106,6 +106,10 @@
 <p class="caption" role="heading"><span class="caption-text">Example Tutorials:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="quick_start.html#Installation-cuGBasis-on-Colab">Installation cuGBasis on Colab</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="quick_start.html#Enable-GPU">Enable GPU</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="quick_start.html#Constructing-Molecule-Object">Constructing Molecule Object</a></li>
 <li class="toctree-l2"><a class="reference internal" href="quick_start.html#Electron-Density">Electron Density</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="quick_start.html#Molecular-Integration-and-Dipole-Moment">Molecular Integration and Dipole Moment</a></li>
@@ -117,6 +121,11 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="critical_points.html">QTAIM Critical Points</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="critical_points.html#Installation-cuGBasis-on-Colab">Installation cuGBasis on Colab</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="critical_points.html#Enable-GPU">Enable GPU</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="critical_points.html#Load-the-Molecule">Load the Molecule</a></li>
 <li class="toctree-l2"><a class="reference internal" href="critical_points.html#Using-Default-Initial-Guess">Using Default Initial Guess</a></li>
 <li class="toctree-l2"><a class="reference internal" href="critical_points.html#Challenging-Cases">Challenging Cases</a></li>
 </ul>

critical_points.html

@@ -53,8 +53,8 @@
               <p class="caption" role="heading"><span class="caption-text">User documentation:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#downloading-code">Downloading Code</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#dependencies">Dependencies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#downloading-code">Downloading Code</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#id1">Installation</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="installation.html#python-binding">Python Binding</a></li>
 <li class="toctree-l3"><a class="reference internal" href="installation.html#c">C++</a></li>
@@ -107,6 +107,10 @@
 <p class="caption" role="heading"><span class="caption-text">Example Tutorials:</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="quick_start.html#Installation-cuGBasis-on-Colab">Installation cuGBasis on Colab</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="quick_start.html#Enable-GPU">Enable GPU</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="quick_start.html#Constructing-Molecule-Object">Constructing Molecule Object</a></li>
 <li class="toctree-l2"><a class="reference internal" href="quick_start.html#Electron-Density">Electron Density</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="quick_start.html#Molecular-Integration-and-Dipole-Moment">Molecular Integration and Dipole Moment</a></li>
@@ -118,6 +122,11 @@
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">QTAIM Critical Points</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#Installation-cuGBasis-on-Colab">Installation cuGBasis on Colab</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#Enable-GPU">Enable GPU</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#Load-the-Molecule">Load the Molecule</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#Using-Default-Initial-Guess">Using Default Initial Guess</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#Challenging-Cases">Challenging Cases</a></li>
 </ul>
@@ -160,10 +169,45 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <p><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></p>
+  <p><a class="reference external" href="https://colab.research.google.com/github/theochem/cuGBasis/blob/main/examples/critical_points.ipynb"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></a></p>
 <section id="QTAIM-Critical-Points">
 <h1>QTAIM Critical Points<a class="headerlink" href="#QTAIM-Critical-Points" title="Permalink to this heading"></a></h1>
 <p>This example illustrates how to find the QTAIM critical points and bond-paths using ChemTools and cuGBasis. This is precisely when the gradient of the electron density <span class="math notranslate nohighlight">\(\nabla \rho = 0\)</span> is zero. The first step is to load the wavefunction information using cuGBasis.</p>
+<section id="Installation-cuGBasis-on-Colab">
+<h2>Installation cuGBasis on Colab<a class="headerlink" href="#Installation-cuGBasis-on-Colab" title="Permalink to this heading"></a></h2>
+<p>The user can skip this step if they aren’t using Google Colab.</p>
+<p>Installation of cuGBasis is rather simple, given that the user has CMake, and CUDA installed.</p>
+<section id="Enable-GPU">
+<h3>Enable GPU<a class="headerlink" href="#Enable-GPU" title="Permalink to this heading"></a></h3>
+<p>On Google Colab, the GPU needs to be enabled. The user should do the following:</p>
+<p>Click on Runtime -&gt; Change runtime type -&gt; T4 GPU</p>
+<div class="nbinput nblast docutils container">
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
+</pre></div>
+</div>
+<div class="input_area highlight-ipython2 notranslate"><div class="highlight"><pre><span></span><span class="c1">#@title **Installing Horton, ChemTools and cuGBasis</span>
+<span class="c1">#@markdown It may take a few minutes! Make sure to enable GPU</span>
+<span class="o">!</span>pip<span class="w"> </span>install<span class="w"> </span>-q<span class="w"> </span>condacolab
+<span class="kn">import</span> <span class="nn">condacolab</span>
+<span class="n">condacolab</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
+<span class="o">!</span>pip<span class="w"> </span>install<span class="w"> </span>numpy<span class="w"> </span>matplotlib<span class="w"> </span>scipy<span class="w"> </span>pybind11<span class="w"> </span>qc-iodata
+<span class="o">!</span>pip<span class="w"> </span>install<span class="w"> </span>git+https://github.com/theochem/grid.git
+<span class="o">!</span>mamba<span class="w"> </span>install<span class="w"> </span>-c<span class="w"> </span>theochem<span class="w"> </span>horton
+<span class="o">!</span>pip<span class="w"> </span>install<span class="w"> </span>git+https://github.com/theochem/chemtools.git@refs/pull/59/head
+<span class="o">!</span>git<span class="w"> </span>clone<span class="w"> </span>https://www.github.com/theochem/cuGBasis
+<span class="o">%</span><span class="k">cd</span> cuGBasis
+<span class="o">!</span>git<span class="w"> </span>submodule<span class="w"> </span>update<span class="w"> </span>--init<span class="w"> </span>--recursive
+<span class="o">!</span>ls
+<span class="o">!</span>pip<span class="w"> </span>install<span class="w"> </span>-v<span class="w"> </span>.
+<span class="o">%</span><span class="k">cd</span> examples/
+</pre></div>
+</div>
+</div>
+</section>
+</section>
+<section id="Load-the-Molecule">
+<h2>Load the Molecule<a class="headerlink" href="#Load-the-Molecule" title="Permalink to this heading"></a></h2>
+<p>The first step is to load the wavefunction information using cuGBasis.</p>
 <div class="nbinput nblast docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
 </pre></div>
@@ -182,6 +226,7 @@ <h1>QTAIM Critical Points<a class="headerlink" href="#QTAIM-Critical-Points" tit
 </pre></div>
 </div>
 </div>
+</section>
 <section id="Using-Default-Initial-Guess">
 <h2>Using Default Initial Guess<a class="headerlink" href="#Using-Default-Initial-Guess" title="Permalink to this heading"></a></h2>
 <p>In this example, we will provide only the atomic coordinates and it will generate initial guesses where the gradient of the electron density is close to zero. This should roughly be near the center of each atom, inbetween any two atoms and between three/four atoms. The electron density, gradient and hessian are obtained from cuGBasis and use is given to the ChemTools algorithm for efficiently finding the critical points and then find the bond-paths for all bond-critical points.</p>
@@ -309,7 +354,7 @@ <h2>Using Default Initial Guess<a class="headerlink" href="#Using-Default-Initia
 <div class="prompt empty docutils container">
 </div>
 <div class="output_area docutils container">
-<img alt="_images/critical_points_7_0.png" src="_images/critical_points_7_0.png" />
+<img alt="_images/critical_points_10_0.png" src="_images/critical_points_10_0.png" />
 </div>
 </div>
 </section>
@@ -427,7 +472,7 @@ <h2>Challenging Cases<a class="headerlink" href="#Challenging-Cases" title="Perm
 <div class="prompt empty docutils container">
 </div>
 <div class="output_area docutils container">
-<img alt="_images/critical_points_12_0.png" src="_images/critical_points_12_0.png" />
+<img alt="_images/critical_points_15_0.png" src="_images/critical_points_15_0.png" />
 </div>
 </div>
 </section>

critical_points.ipynb

@@ -5,9 +5,7 @@
    "id": "d4c8aca925071ae4",
    "metadata": {},
    "source": [
-    "<a target=\"_blank\" href=\"https://colab.research.google.com/github/theochem/cuGBasis/blob/main/examples/critical_points_collab.ipynb\">\n",
-    "  <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
-    "</a>"
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/theochem/cuGBasis/blob/main/examples/critical_points.ipynb)"
    ]
   },
   {
@@ -23,6 +21,57 @@
     "when the gradient of the electron density $\\nabla \\rho = 0$ is zero. The first step is to load the wavefunction information using cuGBasis."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "b7038844c933e1c7",
+   "metadata": {},
+   "source": [
+    "## Installation cuGBasis on Colab\n",
+    "\n",
+    "The user can skip this step if they aren't using Google Colab. \n",
+    "\n",
+    "Installation of cuGBasis is rather simple, given that the user has CMake, and CUDA installed. \n",
+    "\n",
+    "### Enable GPU \n",
+    "On Google Colab, the GPU needs to be enabled. The user should do the following:\n",
+    "\n",
+    "Click on Runtime -> Change runtime type -> T4 GPU\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "610dc9b99028d6a7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#@title **Installing Horton, ChemTools and cuGBasis\n",
+    "#@markdown It may take a few minutes! Make sure to enable GPU \n",
+    "!pip install -q condacolab\n",
+    "import condacolab\n",
+    "condacolab.install()\n",
+    "!pip install numpy matplotlib scipy pybind11 qc-iodata\n",
+    "!pip install git+https://github.com/theochem/grid.git\n",
+    "!mamba install -c theochem horton\n",
+    "!pip install git+https://github.com/theochem/chemtools.git@refs/pull/59/head\n",
+    "!git clone https://www.github.com/theochem/cuGBasis\n",
+    "%cd cuGBasis\n",
+    "!git submodule update --init --recursive\n",
+    "!ls\n",
+    "!pip install -v .\n",
+    "%cd examples/"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9a5aede76dfa5af5",
+   "metadata": {},
+   "source": [
+    "## Load the Molecule\n",
+    "\n",
+    " The first step is to load the wavefunction information using cuGBasis."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

generating_cube_files.html

@@ -52,8 +52,8 @@
               <p class="caption" role="heading"><span class="caption-text">User documentation:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#downloading-code">Downloading Code</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#dependencies">Dependencies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#downloading-code">Downloading Code</a></li>
 <li class="toctree-l2"><a class="reference internal" href="installation.html#id1">Installation</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="installation.html#python-binding">Python Binding</a></li>
 <li class="toctree-l3"><a class="reference internal" href="installation.html#c">C++</a></li>
@@ -106,6 +106,10 @@
 <p class="caption" role="heading"><span class="caption-text">Example Tutorials:</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick Start</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="quick_start.html#Installation-cuGBasis-on-Colab">Installation cuGBasis on Colab</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="quick_start.html#Enable-GPU">Enable GPU</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="quick_start.html#Constructing-Molecule-Object">Constructing Molecule Object</a></li>
 <li class="toctree-l2"><a class="reference internal" href="quick_start.html#Electron-Density">Electron Density</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="quick_start.html#Molecular-Integration-and-Dipole-Moment">Molecular Integration and Dipole Moment</a></li>
@@ -117,6 +121,11 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="critical_points.html">QTAIM Critical Points</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="critical_points.html#Installation-cuGBasis-on-Colab">Installation cuGBasis on Colab</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="critical_points.html#Enable-GPU">Enable GPU</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="critical_points.html#Load-the-Molecule">Load the Molecule</a></li>
 <li class="toctree-l2"><a class="reference internal" href="critical_points.html#Using-Default-Initial-Guess">Using Default Initial Guess</a></li>
 <li class="toctree-l2"><a class="reference internal" href="critical_points.html#Challenging-Cases">Challenging Cases</a></li>
 </ul>