Create charmm/47.2 module

MPI/charmm/LICENSE

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+23 March 2023
+
+To : Dr. Spencer Bliven (LICENSEE)
+Email : spencer.bliven@psi.ch
+
+1) HARVARD grants to LICENSEE a non-exclusive, and non-transferable license to use CHARMM 47
+(Copyright  1984, 1987, 1991, 1992, 1994, 1995, 1996, 1997, 1998, 1999, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 
+by the President & Fellows of Harvard University), a system of computer
+programs for macromolecular energy minimization and dynamics, including
+the source code and associated documentation furnished hereunder
+(hereinafter called CHARMM), upon the terms and conditions hereinafter
+set out and until LICENSEE discontinues use of CHARMM. Use of CHARMM is
+restricted to the LICENSEE and direct collaborators at his/her
+institution who have agreed to accept the terms of this license.
+
+2) LICENSEE acknowledges that CHARMM is a research tool still in the
+development stage, that it is being supplied "as is" without any
+accompanying services or improvements from HARVARD and that the program
+is distributed to enable others to utilize CHARMM in their scholarly
+activities.
+
+3) HARVARD makes no representations or warranties, express or implied. By
+way of example, but not limitation, HARVARD makes no representations or
+warranties of merchantability or fitness for any particular purpose or
+that the use of the licensed software components or documentation will
+not infringe any patents, copyrights, trademarks or other rights. HARVARD
+shall have no liability nor be liable for any direct, indirect or
+consequential damages with respect to any claim by LICENSEE or any third
+party on account of or arising from this Agreement or use of CHARMM.
+
+4) LICENSEE agrees that it will use CHARMM (and any modifications,
+improvements, or derivatives to CHARMM that LICENSEE may create) solely
+for internal, non-commercial purposes. The term "non-commercial," as used
+in this Agreement, means academic or other not-for-profit scholarly
+research which (a) is not undertaken for profit, or (b) is not intended
+to produce works, services, or data for commercial use, or (c) is neither
+conducted, nor funded, by a person or an entity engaged in the commercial
+use, application or exploitation of works similar to CHARMM, unless such
+funding confers no commercial rights to the funding person or entity.
+
+5) The LICENSEE shall not disclose in any form either the delivered
+CHARMM or any modifications or derivative works based on CHARMM to third
+parties without prior written authorization from The CHARMM Development
+Project. If the LICENSEE receives a request to furnish all or any portion
+of CHARMM to any third party, he/she will not fulfill such a request and
+will refer it in writing to The CHARMM Development Project. LICENSEE
+agrees that this license is for his/her research at the present location
+along, as listed on the address above; if he/she moves to another
+location, a new license must be issued or the program returned to The
+CHARMM Development Project.
+
+6) LICENSEE agrees to notify HARVARD of any modifications, improvements,
+or derivatives made to CHARMM, as described in Section 4, above. Any
+modifications or derivative works based on CHARMM are considered part of
+CHARMM and ownership thereof is retained by HARVARD. Reports of such
+modifications or derivative works are to be made to HARVARD.
+
+7) The LICENSEE may make a reasonable number of copies of CHARMM for
+internal use for the purposes of backup, maintenance of CHARMM or the
+development of derivative works based on CHARMM. These additional copies
+will carry the copyright notice and will be controlled by this license,
+and will be destroyed by the LICENSEE upon termination of the license.
+
+8) Ownership of all rights, including copyright in CHARMM and in any
+material associated therewith, shall at all times remain with HARVARD,
+and LICENSEE agrees to preserve same. LICENSEE agrees not to use any
+portion of CHARMM in any machine-readable form outside CHARMM, nor to
+make any copies except for its internal use, without prior written
+consent of HARVARD. LICENSEE agrees to place the appropriate copyright
+notice on any such copies.
+
+9) This Agreement shall be construed, interpreted and applied in
+accordance with the Commonwealth of Massachusetts, and any legal action
+arising out of this Agreement or use of CHARMM shall be filed in a court
+of the Commonwealth of Massachusetts.
+
+10) Nothing in this Agreement shall be construed as conferring rights to
+use in advertising, publicity or otherwise any trademark or the name of
+"HARVARD."
+
+11) LICENSEE agrees that any reports or publication of results obtained
+with CHARMM will acknowledge its use by an appropriate citation. Until
+further notice this would refer to the CHARMM program and to the papers:
+B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S.
+Swaminathan, and M. Karplus, CHARMM: A Program for Macromolecular Energy,
+Minimization, and Dynamics Calculations, J. Comp. Chem., 4, 187-217
+(1983); and B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L.
+Nilsson, R. J. Petrella, B. Roux, Y. Won, M. Karplus, et al., CHARMM: The
+Biomolecular Simulation Program, J. Comput. Chem., 30, 1545-1614 (2009).
+
+Agreed to and signed electronically on 23 March 2023 by
+
+Dr. Spencer Bliven
+Scientific Computing, Theory, and Data
+Paul Scherrer Institute
+
+Email: spencer.bliven@psi.ch
+
+

MPI/charmm/README.md

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+# CHARMM
+
+## Installation
+
+1. [Request a license](https://charmm.chemistry.harvard.edu/)
+
+Here is the brief description I submitted: "PSI is a federal research institute
+in Switzerland. Charmm will be installed on the HPC cluster, upon request from
+structural biology groups."
+
+2. Following accepting the license I got a [download
+link](http://charmm.chemistry.harvard.edu/download_charmm.php) by email.
+
+3. Save the tarball as `/opt/psi/var/distfiles/charmm-47.2.tar.gz` (converting
+from `c${V_MAJOR}b${V_MINOR}.tar.gz`
+
+4. Run `./build`
+
+5. Check the output directory for symlinks. These seem to come from
+post_install, but I don't have time to debug the script more so I'm going to
+just copy the directories manually.
+

MPI/charmm/build

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+#!/usr/bin/env modbuild 
+
+pbuild::add_to_group 'MPI'
+
+
+# STUB URL. This should be manually downloaded and placed in /opt/psi/var/distfiles/
+pbuild::set_download_url "http://psi.ch/manual_download/charmm-${V_MAJOR}.${V_MINOR}.tar.gz"
+
+pbuild::pre_configure() {
+  pbuild::add_configure_args "--with-X11"
+  pbuild::add_configure_args "--with-gamus"
+
+  if pbuild::use_flag gpu ; then
+    pbuild::add_configure_args "--with-domdec_gpu"
+    pbuild::add_configure_args "--with-blade"
+  else # pbuild::use_flag cpu
+    pbuild::add_configure_args "--with-repdstr"
+  fi
+
+}
+
+pbuild::post_install() {
+  cp "$BUILDBLOCK_DIR/LICENSE" "$PREFIX/"
+  rm -f "$PREFIX/source" "$PREFIX/tool"  # remove symlink (rc10 issue?)
+  for dir in doc test support; do
+    rm -f "$PREFIX/$dir"  # remove symlink
+    cp -rf "$SRC_DIR/${dir}" "$PREFIX/"
+  done
+}

MPI/charmm/files/variants

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+charmm/47.2_cpu	unstable	gcc/10.4.0 openmpi/4.1.4_slurm b:cmake/3.23.2
+charmm/47.2_gpu	unstable	gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2

MPI/charmm/modulefile

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+#%Module1.0
+
+module-whatis		"Chemistry at HARvard Macromolecular Mechanics"
+module-url		"https://academiccharmm.org/"
+module-license		"Academic license. See CHARMM_PREFIX/LICENSE"
+module-maintainer	"Spencer Bliven <spencer.bliven@psi.ch>"
+module-help		"
+A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models.
+
+This is the Academic version of CHARMM.
+"