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  2. Mek-quake Queueing system - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Mek-quake_Queueing_system
    6 Jan 2021: Mek-quake Queueing system. From CUC3. Please write your thoughts about the mek-quake queueing system here. And please sign your posts! --Catherine 16:26, 21 June 2006 (BST). My thoughts are that what works best on most of the other clusters to keep
  3. Blacklisting Compilers - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Blacklisting_Compilers
    We also issue a waring reminding users they need to reconfigure if they have module loaded a new compiler. # ... To add a new ban, find the list for the appropriate compiler in CMakeLists.txt, then copy the above example, changing the condition and
  4. Wales Group Version control - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Wales_Group_Version_control
    6 Jan 2021: Note that Google Reader has a delay in updating the feeds, so you won't see new logs up to an hour after they are created and are visible with Firefox.
  5. GMIN MOVES module - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMIN_MOVES_module
    In short, a new parser is being developed by Kyle to allow the construction of a highly flexible move set. ... csw34> Temporary calls to new step taking routines for testing IF (NEWMOVEST) THEN!
  6. CamCASP/Programming/9 - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/9
    6 Jan 2021: New code: make_T_AO_mono 1 6.58 Old code: make_T_AO_mono 1 65.06. This speed-up occurs for all systems I've looked at.
  7. Optimising a path - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Optimising_a_path
    Eventually additions of new connections to the database will no longer reduce the rate constant.
  8. Talk:Catherine Pitt - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Talk:Catherine_Pitt
    6 Jan 2021: The ACML on tardis was already fixed (this is where I found the note) and I've done the new FFTW module on tardis (won't go live until I unleash
  9. Sorting a file by multiple columns - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Sorting_a_file_by_multiple_columns
    Sorting a file by multiple columns. From Docswiki. If you have a file you want to sort using multiple columns of numbers, the sort command is your new best friend!
  10. Python interface for GMIN/OPTIM - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Python_interface_for_GMIN/OPTIM
    Use the cmake option -DWITH_PYTHON. The goal of this interface is to allow for quick testing of new ideas before implementing them in Fortran.
  11. Environment modules - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Environment_modules
    6 Jan 2021: If you do module avail after loading the use.own module, you'll see there's a new section: /home/${USER}/privatemodules.
  12. Branching and Merging - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Branching_and_Merging
    trunk) as follows:. svn copy url-old url-new. where, for example, url-old is $SVN/trunk and url-new is $SVN/branches/your-new-branch-name. ... 5 then new functionality exists to help you (see the SVN manual for more information).
  13. Useful Python Scripts - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Useful_Python_Scripts
    6 Jan 2021: This is especially helpful when trying to reorder code for a cleaner flow, trying to remove issues leading to circular dependencies, or for becoming familiar with the structure of a new
  14. SuSE 10.1 workstation image - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/SuSE_10.1_workstation_image
    OpenSSH (SSH client) DONE. Pan (news client) DONE. Pine (mail/news client) DONE. ... rasmol (molecular visualisation) DONE. TeX/LaTeX (document preparation system) DONE. Thunderbird (mail/news client) DONE.
  15. Git-NECI - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Git-NECI
    6 Jan 2021: git checkout branchname' will allow you to swap branches, and 'git checkout -b newbranchname' will allow you to create a new branch. ... If you are in the middle of something, then want to work on something else, you can either create a new branch, or
  16. Calculating molecular properties - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_molecular_properties
    24663 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> $$$$$$ New timer profile $$$$$ List time 0.00959 Other: 0.00000 Electrostatic & VDW 0.00004 Other: 0.00000 Nonbond force 0.01572
  17. NECI-testcode - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/NECI-testcode
    6 Jan 2021: NECI-testcode. From CUC3. This is a new page to post info on how to migrate the test code between machines, as was done between discovery and scepter recently. ... Note that new benchmarks need to be produced if the number of cores changes as certain
  18. Mek-quake Queueing system - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Mek-quake_Queueing_system
    Mek-quake Queueing system. From Docswiki. Please write your thoughts about the mek-quake queueing system here. And please sign your posts! --Catherine 16:26, 21 June 2006 (BST). My thoughts are that what works best on most of the other clusters to
  19. Installing python modules - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Installing_python_modules
    6 Jan 2021: which adds /local/lib/python/site-packages to my PYTHONPATH (if the directory exists). This means I no longer have to worry about adding a new module to my PYTHONPATH.
  20. Pathsampling short paths - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Pathsampling_short_paths
    However, when you have the path.info file(s) from OPTIM you may not want to use them to start a new database -- instead, you can add them (one at a ... Systematically increasing the number of connections per minimum. Starting from an existing KTN, with
  21. Debugging odd transition states in OPTIM - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Debugging_odd_transition_states_in_OPTIM
    6 Jan 2021: In order to do so, new OPTIM keywords, DEBUG, DUMPNEBEOS, and DUMPNEBXYZ need to be added to print the NEB interpolated energy and coordinates in the files neb.xyz.31267.<n>,
  22. Git Workflow - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Git_Workflow
    Checkout the new repository and start writing the paper in the blank directory. ... else. All development should occur on branches. To create a new branch, run.
  23. Managing interactive jobs on cluster - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Managing_interactive_jobs_on_cluster
    pressing Shifto opens a new window with several options along with the corresponding letter that needs to be pressed to sort the top window based on a particular column.
  24. NECI Re-write - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/NECI_Re-write
    6 Jan 2021: Sets of defaults that can be called via a date. New memory book-keeping scheme in place. ... Currently the old routines just call the new ones with some of the options set to a default value.
  25. Local rigid body in OPTIM - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Local_rigid_body_in_OPTIM
    3. Introduce new subroutines GENRIGID_IMAGE_CTORIGID and GENRIGID_IMAGE_RIGIDTOC in genrigid.f90. 4. Edit newneb.f90 - after initial interpolation, we do coordinate transformation to local rigid body.
  26. Computing normal modes in angle-axis - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Computing_normal_modes_in_angle-axis
    For an example that is working look at newtip.f90. If you need to add a new potential, here are the steps you need to do:. ... See INERTIANTIP in newtip.f90 as an example. Edit subroutine COMPUTEINERTIA to add the call to your new inertia routine.
  27. Wales Group - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Wales_Group
    If you add a new page to this wiki, please provide a link to it in the Comprehensive Contents Page under the section you think most appropriate. ... Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
  28. Installing python modules - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Installing_python_modules
    which adds /local/lib/python/site-packages to my PYTHONPATH (if the directory exists). This means I no longer have to worry about adding a new module to my PYTHONPATH.

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