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Chemshell License Page: Chemshell ChemShell ChemShell is a computational chemistry environment for standard quantum chemical or force field calculations, including hybrid QM/MM calculations. ChemShell includes interfaces to various QM and MM codes, and is designed to deal with the communication and data handling, whilst energy evaluations are undertaken by external codes. Versions 3.5 and 3.6 has been compiled on BlueWonder the using the Intel compilers suite and Intel MPI. ChemShell can provide interfaces to the following stand alone codes, many of which are also installed on the Hartree Centre systems. • GAMESS-UK • MNDO • TURBOMOLE • GAUSSIAN • Molpro • Orca • NWChem • DMol3 • DL_POLY • CHARMM • GULP • GROMOS License Currently for use by one research group only. Whilst the software is free for academic usage there are limitations within the license agreement which must be strictly adhered to by users. A copy of the full license can be found on the Web site. The license covers the ChemShell code, not the stand alone quantum chemistry or MD codes to which ChemShell provides interfaces. You can download a copy of the Academic Licence form (PDF - 123kB - link opens in a new window)which should be completed and faxed to Paul Sherwood on +44 1925 603634. For payment details please see the instructions (PDF - 64kB - link opens in a new window). In case of any problems with payment, please contact Laura Johnston. UK academic groups should use the Royalty Free licence (PDF - 138kB - link opens in a new window) and do not need to make a payment. For commercial licencing, or for any further information please contact Paul Sherwood. - 1 - Page: Chemshell Acknowledging Publications making use of the software should contain an acknowledgement by making reference to: 1. ChemShell, a Computational Chemistry Shell, see http://www.chemshell.org If the program has been locally modified, the nature of the modifications should be outlined. If the QM/MM implementation within ChemShell has been used to obtain the results, please provide a citation to the following publication: 1. "QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis" P. Sherwood, A. H. de Vries, M. F. Guest, G. Schreckenbach, C. R. A. Catlow, S. A. French, A. A. Sokol, S. T. Bromley, W. Thiel, A. J. Turner, S. Billeter, F. Terstegen, S. Thiel, J. Kendrick, S. C. Rogers, J. Casci, M. Watson, F. King, E. Karlsen, M. Sjøvoll, A. Fahmi, A. Schäfer, Ch. Lennartz, J. Mol. Struct. (Theochem.) 2003, 632, 1, mentioning, where appropriate the authors of the specific programs used. If the DL-FIND geometry optimiser was used within ChemShell, please cite: 1. "DL-FIND: an Open-Source Geometry Optimizer for Atomistic Simulations" Johannes Kästner, Joanne M. Carr, Thomas W. Keal, Walter Thiel, Adrian Wander, Paul Sherwood, J. Phys. Chem. A, 2009, 113, 11856. Running on the Invicta or Napier. The Chemshell -p flag is used to set the number of cores in parallel jobs. The following example scripts can be modified to submit jobs to SGE. Jobs that fit on a single Intel compute node (16 or fewer cores on Invicta, 24 or fewer on Napier) can use the smp.pe parallel environment. For example the following script defines a 2 core job (with input file inner.chm) running on a single 16-core node: #!/bin/bash #BSUB -J ChemShell #BSUB -o stdout.%J.txt #BSUB -e stderr.%J.txt #BSUB -R "span[ptile=24]" #BSUB -n 48 #BSUB -W 0:20 cd $LS_SUBCWD - 2 - Page: Chemshell #Load modules source /etc/profile.d/modules.sh module load chemshell # count how many processors are allocated NP=0 for TOKEN in $LSB_HOSTS do ((NP++)) done # execute ChemShell mpiexec.hydra -np $NP chemsh.x INPUT.chm > OUTPUT.out Further info Further information can be found on the ChemShell web site http://www.stfc.ac.uk/ cse/36254.aspx including the Chemshell Manual, tutorials and details of the chemsh- users email list which can be used to post queries to seek help. - 3 -.
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