Document how to use Gromacs #79
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ptheywood
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Jan 31, 2022
…ich are much more manageable, with their own easier to find rendered pages. Closes #61 Whilst splitting this file into many smaller files, a number of additions and changes were made to the documentation, including: + Adds (basic) documentation for: + IBM XL compilers (Closes #61) + Amber (Part of #78) + EMAN2 + GRACE + Gromacs (Closes #37, part of #79) + NAMD + OpenMM + PLUMED + Singularity (Apptainer) (Closes #49) + Generic python information, with more detailed conda usage (Closes #47) + nvidia-smi (Closes #75) + HECBioSim project + IBM Collaboration project + Boost Module + FFTW module + NVTX library + PLUMED library + VTK + CMake + Make + Creates new `guides` section + Migrates the `profiling` documentation into the guides section + Migrates the `wanderings` about CUDA into the guides section + Adds some notes/warnings about potential WMLCE + RHEL 8 incompatibility. Larger changes still required (#63) + CSS/JS/_templates changes for a useful sidebar with the bootstrap theme with split source files + New issue #87 opened to consider replacing the theme to an actively maintained theme. + Removes relations.html from the sidebar, as styling issues were difficult to resolve nicely (Closes #77) + Adds sphinxext-rediraffe plugin for redirects for moved .html files (see conf.py) + Assorted RST improvements (links, crossrefs, quoteblocks, code-block, note, etc.) + Clarify module loads for RHEL 7 vs RHEL 8 where appropriate (Part of #73). + Assorted other improvements throughout the documentation History was a little messy, so has been squashed to avoid `.git` bloat.
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ptheywood
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Jan 31, 2022
…ich are much more manageable, with their own easier to find rendered pages. Closes #61 Whilst splitting this file into many smaller files, a number of additions and changes were made to the documentation, including: + Adds (basic) documentation for: + IBM XL compilers (Closes #61) + Amber (Part of #78) + EMAN2 + GRACE + Gromacs (Closes #37, part of #79) + NAMD + OpenMM + PLUMED + Singularity (Apptainer) (Closes #49) + Generic python information, with more detailed conda usage (Closes #47) + nvidia-smi (Closes #75) + HECBioSim project + IBM Collaboration project + Boost Module + FFTW module + NVTX library + PLUMED library + VTK + CMake + Make + Creates new `guides` section + Migrates the `profiling` documentation into the guides section + Migrates the `wanderings` about CUDA into the guides section + Adds some notes/warnings about potential WMLCE + RHEL 8 incompatibility. Larger changes still required (#63) + CSS/JS/_templates changes for a useful sidebar with the bootstrap theme with split source files + New issue #87 opened to consider replacing the theme to an actively maintained theme. + Removes relations.html from the sidebar, as styling issues were difficult to resolve nicely (Closes #77) + Adds sphinxext-rediraffe plugin for redirects for moved .html files (see conf.py) + Assorted RST improvements (links, crossrefs, quoteblocks, code-block, note, etc.) + Clarify module loads for RHEL 7 vs RHEL 8 where appropriate (Part of #73). + Assorted other improvements throughout the documentation + Adds the sphinx-copybutton plugin, for easy to copy code-block contents. History was a little messy, so has been squashed to avoid `.git` bloat.
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Now #67 is merged, the very basic Gromacs documentation can be exapended by editing software/applications/gromacs.rst |
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Closing this as the docs taskforce is being closed. The docs page can still be expanded if required with bede-speicifc additions if required. |
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Jun 7, 2022
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Talk to James Gebbie about how to use Gromacs and add the information to the docs
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