Merge branch 'namd' into 'master'

Add NAMD module

See merge request Pmodules/buildblocks!51

MPI/NAMD/README.md

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+NAMD
+----
+
+This directory (and /opt/psi/MPI/NAMD) is reserved for a future compiled version of NAMD.
+
+We currently use pre-compiled binaries. These are located in Tools/NAMD.
+
+

Tools/NAMD/README.md

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+NAMD
+----
+
+NAMD uses a non-commercial license. A disclaimer is printed when the module is loaded.
+
+Installation
+============
+
+[Release Notes](https://www.ks.uiuc.edu/Research/namd/cvs/notes.html)
+
+1. A NAMD account is needed to download binaries
+2. Create new directory `/opt/psi/MPI/NAMD/$VERSION`
+3. Download the latest binary.
+   - Use `NAMD_$VERSION_Linux-x86_64-verbs-smp-CUDA.tar.gz` for _gpu
+   - Use `NAMD_$VERSION_Linux-x86_64-verbs-smp.tar.gz` for non-gpu
+
+4. Unpack to the new directory with `tar -xzvf NAMD*.tar.gz --strip-components=1 -C /opt/psi/MPI/NAMD/$VERSION`
+5. Clean up:
+
+    mkdir bin
+    find . -maxdepth 1 -executable -type f -exec mv '{}' bin ';'
+
+6. Add new variant to files/variants
+7. Run the build-script to install the modulefile and to set the release
+

Tools/NAMD/build

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+#!/usr/bin/env modbuild
+
+# Binary distribution with manual installation. See README.md
+
+pbuild::add_to_group 'Tools'
+
+pbuild::prep() {
+    :
+}
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    :
+}
+

Tools/NAMD/files/variants

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+NAMD/2.13  unstable    
+NAMD/2.13_gpu  unstable    cuda/9.2.148

Tools/NAMD/modulefile

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+#%Module1.0
+
+
+set disclaimer {NAMD is available for Non-Commercial Use only. Before using, please review the
+license (http://www.ks.uiuc.edu/Research/namd/license.html). You should also
+acknowledge the developers:
+
+    "NAMD was developed by the Theoretical and Computational Biophysics Group
+    in the Beckman Institute for Advanced Science and Technology at the
+    University of Illinois at Urbana-Champaign."
+
+And cite the reference:
+
+    James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad
+    Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant
+    Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of
+    Computational Chemistry, 26:1781-1802, 2005. abstract, journal
+
+And link the website: http://www.ks.uiuc.edu/Research/namd/}
+
+module-whatis		"Scalable Molecular Dynamics Software"
+module-url		"http://www.ks.uiuc.edu/Research/namd/"
+module-license		"NAMD Non-Commercial License (http://www.ks.uiuc.edu/Research/namd/license.html)"
+module-maintainer	"Spencer Bliven <spencer.bliven@psi.ch"
+module-help		"NAMD is a parallel molecular dynamics code designed for high-performance
+simulation of large biomolecular systems. Based on Charm++ parallel objects,
+NAMD scales to hundreds of cores for typical simulations and beyond 500,000
+cores for the largest simulations. NAMD uses the popular molecular graphics
+program VMD for simulation setup and trajectory analysis, but is also
+file-compatible with AMBER, CHARMM, and X-PLOR.
+
+${disclaimer}"
+
+puts stderr $disclaimer