Merge pull request #31 from flindersuni/feature/lammps

Added LAMMPS Information Page

docs/source/index.rst

@@ -70,6 +70,7 @@ Table of Contents
 
     software/softwaresuitesoverview.rst
     software/ansys.rst
+    software/lammps.rst
     software/jupyter.rst
     software/singularity.rst
     software/matlab.rst

docs/source/software/lammps.rst

@@ -0,0 +1,55 @@
+------------------
+LAMMPS
+------------------
+=======
+Status
+=======
+LAMMPS was installed from the Development Branch on 7th Jan, 2022. 
+
+There are two versions of LAMMPS installed on DeepThought:
+
+1. A CPU only version, called lmp 
+2. a GPU only version, called lmp_gpu 
+
+*You cannot run the GPU enabled version without access to a GPU, as it will cause errors.*
+
+.. _LAMMPS: https://lammps.org
+
+
+=================
+Overview 
+=================
+From LAMMPS_:
+
+LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has 
+potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model 
+atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
+
+LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Many of its models have versions that 
+provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality. LAMMPS is distributed as an 
+open source code under the terms of the GPLv2. The current version can be downloaded here. Links are also included to older versions. All LAMMPS development is done via 
+GitHub, so all versions can also be accessed there. Periodic releases are also posted to SourceForge.
+
+==========================
+LAMMPS Installed Packages
+==========================
+
+The following is an extract from the ``lmp -h`` option, showing the enabled packages and capabilities of the LAMMPS installation.
+
+    ASPHERE ATC AWPMD BOCS BODY BROWNIAN CG-DNA CG-SDK CLASS2 COLLOID COLVARS 
+    COMPRESS CORESHELL DIELECTRIC DIFFRACTION DIPOLE DPD-BASIC DPD-MESO DPD-REACT 
+    DPD-SMOOTH DRUDE EFF EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX EXTRA-MOLECULE 
+    EXTRA-PAIR FEP GPU GRANULAR H5MD INTERLAYER KIM KSPACE LATBOLTZ LATTE MACHDYN 
+    MANIFOLD MANYBODY MC MDI MEAM MESONT MESSAGE MGPT MISC ML-HDNNP ML-IAP ML-PACE 
+    ML-QUIP ML-RANN ML-SNAP MOFFF MOLECULE MOLFILE MPIIO MSCG NETCDF OPENMP OPT 
+    ORIENT PERI PHONON PLUGIN PLUMED POEMS PTM PYTHON QEQ QMMM QTB REACTION REAXFF 
+    REPLICA RIGID SCAFACOS SHOCK SMTBQ SPH SPIN SRD TALLY UEF VORONOI VTK YAFF
+
+======================================
+LAMMPS Quickstart Command Line Guide
+======================================
+
+LAMMPS uses UCX and will require a custom mpirun invocation. The module system will warn you of this when you load the module. The following is a known good starting point:
+
+
+``mpirun -mca pml ucx --mca btl ^vader,tcp,uct -x UCX_NET_DEVICES=bond0 <program> <options>``

docs/source/software/softwaresuitesoverview.rst

@@ -15,9 +15,11 @@ List of Enterprise Software Suites
 .. _ANSYS: ansys.html
 .. _Singularity Containers: singularity.html 
 .. _MATLAB: matlab.html
+.. _LAMMPS: lammps.html
 
 1. `Jupyter Hub`_
 2. `ANSYS`_ 
-3. `Singularity Containers`_ 
-4. `MATLAB`_
+3. `LAMMPS`_
+4. `Singularity Containers`_ 
+5. `MATLAB`_