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ps4 - 10.675 Assignment#4 due In this problem set you will...

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10.675 Assignment #4 due 10/21/04 In this problem set, you will use Car-Parrinello Molecular Dynamics (CPMD) to calculate the adsorption energy of oxygen atom on the Si(100) surface and compare it to the experimental data that you can find. 1. Log on to NCSA from SecureCRT from your own machine by: ssh cu.ncsa.uiuc.edu usrname: password: or ssh [email protected] password 2. Before you submit the jobs, make sure you have the following files in your home directory (Of course you can put them to different folders and then specify the directory of different folder in your job script). You can copy these files from: /u/ac/hairong/public Executable cpmd: cpmd.x; Potentials for O and Si: O_BLYP_glue and Si_BLYP_glue; Input files for atomic oxygen, bare silicon surface, and adsorption of atomic oxygen on si(100): o, si_surf, and o_si_surf ; The script to run your job: mpi.ll (you can change the name as what you want). 3. The mpi.ll (listed as file 1 at the end of this document), is the shell script you should use to submit the jobs. The mpi.ll file is self-demonstrative, you need to modify it very easily and get cpmd to run. Here are some useful commands for ncsa operation: Submit the job: llsubmit filename Check status of your job: llq –u usrname Cancel your job: llcancel job number To check how many hours you have used: usage –u usrname ( P_usage will list how many hours you have used; Remember everybody has 250 hours for the whole semester) The above operations are related to queue system. If you just want to do single processor calculation, you can copy the script file mpi.ll as any other name such as script , use chmod +x script
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