Merge pull request #33 from MolSSI/docs

Deep modifications to adopt root users with a few new packages added

docs/compchem/ase_example.rst

@@ -57,7 +57,7 @@ paste it into your terminal and edit it to look like the following command line
 
 .. code-block:: bash
 
-    docker run --rm -w /home/molssi/temp -v .:/home/molssi/temp molssi/ase322-mamba141:latest /bin/bash -c "python test.inp"
+    docker run --rm -w /home -v $PWD:/home molssi/ase322-mamba141:latest /bin/bash -c "python test.inp"
 
 then press Enter. 
 
@@ -74,12 +74,6 @@ then press Enter.
     from the host system to the running container by default. For further details see the Apptainer 
     `documentation <https://apptainer.org/docs/user/latest/quick_start.html#working-with-files>`_.
 
-.. caution::
-
-    Ignore (usually many) wanings that you might get the first time a SIF file is being created.
-    This is because of Apptainer's `fakeroot <https://apptainer.org/docs/user/1.1/fakeroot.html>`_ 
-    feature which allows an unprivileged user to run containers as root by default.
-
 If nothing goes wrong, you should see the following lines in your terminal
 
 .. code-block:: bash
@@ -95,7 +89,7 @@ If nothing goes wrong, you should see the following lines in your terminal
 
     .. code-block:: bash
 
-        docker run --rm -w /home/molssi/temp -v .:/home/molssi/temp molssi/ase322-mamba141:latest /bin/bash -c "python test.inp >> test.out"
+        docker run --rm -w /home -v $PWD:/home molssi/ase322-mamba141:latest /bin/bash -c "python test.inp >> test.out"
     
     or
 

docs/compchem/index.rst

@@ -13,11 +13,14 @@ construct and run containerized computational chemistry software.
 
     ase322-mamba141
     ase_example
+    lammps-mamba141
+    lammps_example
+    mendeleev045-mamba141
     mopac220-mamba141
     mopac_example
-    psi4v180-mamba141-ase322
-    psi4-ase_example
     psi4v180-mamba141
     psi4_example
+    psi4v180-mamba141-ase322
+    psi4-ase_example
     pyscf221-mamba141
     pyscf_example

docs/compchem/lammps-mamba141.rst

@@ -0,0 +1,76 @@
+.. _lammps_mamba141:
+
+*********************************************************
+{{ lammps_mamba141.hub_specifications[0]["Source"].split("/")[-1] }}
+*********************************************************
+
+{% set title = lammps_mamba141.get("name") %}
+
+{{title}}
+=========================================================
+
+{% block content %}
+    {{ lammps_mamba141.description }}
+{% endblock content %}
+
+Source Specifications
+=====================
+
+{% block specifications %}
+    {% for dc in lammps_mamba141.source_specifications %}
+        {% for key, value in dc.items() %}
+            * **{{ key }}**: {{ value }}
+        {% endfor %}
+    {% endfor %}
+{% endblock specifications %}
+
+MolSSI Container Hub Specifications
+===================================
+
+{% block hub_specifications %}
+    {% for dc in lammps_mamba141.hub_specifications %}
+        {% for key, value in dc.items() %}
+            * **{{ key }}**: {{ value }}
+        {% endfor %}
+    {% endfor %}
+{% endblock hub_specifications %}
+
+* **Image pull command**:
+
+    .. code-block:: bash
+
+        {{ lammps_mamba141.docker_pull_command }}
+
+* **Container run command**:
+
+    .. code-block:: bash
+
+        {{ lammps_mamba141.docker_run_command }}
+
+{% block note %}
+{% if lammps_mamba141.note != "" %}
+.. note::
+
+        {{ lammps_mamba141.note }}
+{% endif %}
+{% endblock note %}
+
+Image Specifications
+====================
+
+{% block image_specifications %}
+    {% for dc in lammps_mamba141.image_specifications %}
+        {% for key, value in dc.items() %}
+            {% if dc[key] is string or dc[key] == "" %}
+                * **{{ key }}**: {{ value }}
+            {% else %}
+                * **{{ key }}**:
+                {% for key2 in dc[key] %}
+                    {% for key3, val3 in key2.items() %}
+                        + *{{ key3 }}*: {{ val3 }}
+                    {% endfor %}
+                {% endfor %}
+            {% endif %}
+        {% endfor %}
+    {% endfor %}
+{% endblock image_specifications %}

docs/compchem/lammps_example.rst

@@ -0,0 +1,114 @@
+.. _lammps_example:
+
+***************
+LAMMPS: Example
+***************
+
+Here, we demonstrate the non-interactive usage of the LAMMPS image recipe.
+
+Running LAMMPS Non-interactively
+================================
+
+First, let's create a temporary folder, ``temp`` in your **home** directory
+and ``cd`` to it
+
+.. code-block:: bash
+
+    mkdir ~/temp && cd ~/temp
+
+Use your favorite text editor to create a new input file. Let's call it **in.lj**
+and copy-paste the following code block into it and then, save it.
+
+.. code-block:: python
+
+    # 1) Initialization
+    units lj
+    dimension 3
+    atom_style atomic
+    pair_style lj/cut 2.5
+    boundary p p p
+
+    # 2) System definition
+    region simulation_box block -20 20 -20 20 -20 20
+    create_box 2 simulation_box
+    create_atoms 1 random 1500 341341 simulation_box
+    create_atoms 2 random 100 127569 simulation_box
+
+    # 3) Simulation settings
+    mass 1 1
+    mass 2 1
+    pair_coeff 1 1 1.0 1.0
+    pair_coeff 2 2 0.5 3.0
+
+    # 4) Visualization
+    thermo 10
+
+    # 5) Run
+    minimize 1.0e-4 1.0e-6 1000 10000
+
+This input file is borrowed from LAMMPS Tutorial 
+`page <https://lammpstutorials.github.io/sphinx/build/html/tutorials/lennardjones.html#the-input-script>`_
+and intends to run a molecular dynamics simulation of a Lennard-Jones
+binary fluid consisting of neutral dots with Langevin thermostat within the NVT ensemble.
+
+At this stage, the content of your directory should look like the following
+
+.. code-block:: bash
+
+    temp
+    └── in.lj
+
+Let's copy the docker run command from the `catalog <https://molssi.github.io/molssi-hub/compchem/lammps-mamba141.html>`_,
+paste it into a terminal and edit it to look like the following command line
+
+.. code-block:: bash
+
+    docker run --rm -w /home -v $(pwd):/home molssi/lammps-mamba141:latest /bin/bash -c "lmp_serial -in in.lj"
+
+then press Enter. If nothing goes wrong, you should see a long list of lines ending in
+
+.. code-block:: bash
+
+    Nlocal:           1600 ave        1600 max        1600 min
+    Histogram: 1 0 0 0 0 0 0 0 0 0
+    Nghost:            756 ave         756 max         756 min
+    Histogram: 1 0 0 0 0 0 0 0 0 0
+    Neighs:           2178 ave        2178 max        2178 min
+    Histogram: 1 0 0 0 0 0 0 0 0 0
+
+    Total # of neighbors = 2178
+    Ave neighs/atom = 1.36125
+    Neighbor list builds = 141
+    Dangerous builds = 1
+    Total wall time: 0:00:00
+
+.. note::
+
+    The same Docker image recipe can also be used with Apptainer (Singularity) to
+    obtain the same result via the following command
+
+    .. code-block:: bash
+
+        apptainer exec docker://molssi/lammps-mamba141:latest lmp_serial -in in.lj
+    
+    Note that Apptainer binds ``/home/$USER``, ``/tmp`` and current working directory (``$PWD``)
+    from the host system to the running container by default. For further details see the Apptainer 
+    `documentation <https://apptainer.org/docs/user/latest/quick_start.html#working-with-files>`_.
+
+By default, LAMMPS generates a **log.lammps** file with the auto-generated output upon finishing
+the job execution.
+
+.. note::
+
+    You can store the generated output in a separate output file by passing the ``-l <output_name>``
+    to the execution command as follows
+
+    .. code-block:: bash
+
+        docker run --rm -w /home -v $(pwd):/home molssi/lammps-mamba141:latest /bin/bash -c /bin/bash -c "lmp_serial -in in.lj -l log.out"
+    
+    or
+
+    .. code-block:: bash
+
+        apptainer exec docker://molssi/lammps-mamba141:latest lmp_serial -in in.lj -l log.out

docs/compchem/mendeleev045-mamba141.rst

@@ -0,0 +1,76 @@
+.. _mendeleev045_mamba141:
+
+*********************************************************
+{{ mendeleev045_mamba141.hub_specifications[0]["Source"].split("/")[-1] }}
+*********************************************************
+
+{% set title = mendeleev045_mamba141.get("name") %}
+
+{{title}}
+=========================================================
+
+{% block content %}
+    {{ mendeleev045_mamba141.description }}
+{% endblock content %}
+
+Source Specifications
+=====================
+
+{% block specifications %}
+    {% for dc in mendeleev045_mamba141.source_specifications %}
+        {% for key, value in dc.items() %}
+            * **{{ key }}**: {{ value }}
+        {% endfor %}
+    {% endfor %}
+{% endblock specifications %}
+
+MolSSI Container Hub Specifications
+===================================
+
+{% block hub_specifications %}
+    {% for dc in mendeleev045_mamba141.hub_specifications %}
+        {% for key, value in dc.items() %}
+            * **{{ key }}**: {{ value }}
+        {% endfor %}
+    {% endfor %}
+{% endblock hub_specifications %}
+
+* **Image pull command**:
+
+    .. code-block:: bash
+
+        {{ mendeleev045_mamba141.docker_pull_command }}
+
+* **Container run command**:
+
+    .. code-block:: bash
+
+        {{ mendeleev045_mamba141.docker_run_command }}
+
+{% block note %}
+{% if mendeleev045_mamba141.note != "" %}
+.. note::
+
+        {{ mendeleev045_mamba141.note }}
+{% endif %}
+{% endblock note %}
+
+Image Specifications
+====================
+
+{% block image_specifications %}
+    {% for dc in mendeleev045_mamba141.image_specifications %}
+        {% for key, value in dc.items() %}
+            {% if dc[key] is string or dc[key] == "" %}
+                * **{{ key }}**: {{ value }}
+            {% else %}
+                * **{{ key }}**:
+                {% for key2 in dc[key] %}
+                    {% for key3, val3 in key2.items() %}
+                        + *{{ key3 }}*: {{ val3 }}
+                    {% endfor %}
+                {% endfor %}
+            {% endif %}
+        {% endfor %}
+    {% endfor %}
+{% endblock image_specifications %}

docs/compchem/mopac_example.rst

@@ -54,30 +54,9 @@ paste it into your terminal and edit it to look like the following command line
 
 .. code-block:: bash
 
-    docker run --rm -w /home/molssi/temp -v $(pwd):/home/molssi/temp molssi/mopac220-mamba141:latest /bin/bash -c "mopac test.mop test.out"
+    docker run --rm -w /home -v $PWD:/home molssi/mopac220-mamba141:latest /bin/bash -c "mopac test.mop test.out"
 
-then press Enter. 
-
-.. note::
-
-    The same Docker image recipe can also be used with Apptainer (Singularity) to
-    obtain the same result via the following command
-
-    .. code-block:: bash
-
-        apptainer exec docker://molssi/mopac220-mamba141:latest mopac test.mop test.out
-    
-    Note that Apptainer binds ``/home/$USER``, ``/tmp`` and current working directory (``$PWD``)
-    from the host system to the running container by default. For further details see the Apptainer 
-    `documentation <https://apptainer.org/docs/user/latest/quick_start.html#working-with-files>`_.
-
-.. caution::
-
-    Ignore (usually many) wanings that you might get the first time a SIF file is being created.
-    This is because of Apptainer's `fakeroot <https://apptainer.org/docs/user/1.1/fakeroot.html>`_ 
-    feature which allows an unprivileged user to run containers as root by default.
-
-If nothing goes wrong, you should see the following lines in your terminal
+then press Enter. If nothing goes wrong, you should see the following lines in your terminal
 
 .. code-block:: bash
 
@@ -104,4 +83,17 @@ Your directory should now have the following structure
 
     .. code-block:: bash
 
-        * JOB ENDED NORMALLY *
+        * JOB ENDED NORMALLY *
+
+.. note::
+
+    The same Docker image recipe can also be used with Apptainer (Singularity) to
+    obtain the same result via the following command
+
+    .. code-block:: bash
+
+        apptainer exec docker://molssi/mopac220-mamba141:latest mopac test.mop test.out
+    
+    Note that Apptainer binds ``/home/$USER``, ``/tmp`` and current working directory (``$PWD``)
+    from the host system to the running container by default. For further details see the Apptainer 
+    `documentation <https://apptainer.org/docs/user/latest/quick_start.html#working-with-files>`_.