exercises:2015_ethz_mmm:c2h2_bond_energy
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exercises:2015_ethz_mmm:c2h2_bond_energy [2015/02/27 08:53] – yakutovich | exercises:2015_ethz_mmm:c2h2_bond_energy [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== C2H2 and C2H4 bond energy ====== | ====== C2H2 and C2H4 bond energy ====== | ||
<note warning> | <note warning> | ||
- | Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run: | + | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: |
- | < | + | |
- | you@eulerX ~$ ./ | + | you@eulerX ~$ module load courses mmm vmd |
- | </code> | + | |
- | ** Pay attention to the output of this program. It may give you some helpful information** | + | you@eulerX ~$ mmm-init |
+ | </note> | ||
- | If you don't have the file " | ||
- | < | ||
- | you@eulerX ~$ unzip update_functionlibrary.zip | ||
- | you@eulerX ~$ chmod 755 update_functionlibrary | ||
- | </ | ||
- | Or if you are working on the remote computer you can also do the following: | ||
- | < | ||
- | you@eulerX ~$ wget http:// | ||
- | you@eulerX ~$ unzip exercises: | ||
- | you@eulerX ~$ chmod 755 update_functionlibrary | ||
- | </ | ||
- | </ | ||
- | <note important> | + | <note important> |
< | < | ||
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</ | </ | ||
- | **and to submit the job chain:** | + | **and to submit the job:** |
< | < | ||
- | you@eulerX ~$ bsub < c2h2.a.chain | + | you@eulerX ~$ bsub < jobname |
</ | </ | ||
</ | </ | ||
Line 126: | Line 115: | ||
# | # | ||
# loads the functions | # loads the functions | ||
- | # this script uses the functions: | + | # this script uses the functions: |
# | # | ||
module load new cp2k | module load new cp2k | ||
- | . ~/Scripts/myfunctions.bash | + | . /cluster/apps/ |
Line 141: | Line 130: | ||
# | # | ||
- | for n in `list -5 5` | + | for n in `m_list |
do | do | ||
- | dist_cc=`change | + | dist_cc=`m_change |
- | c2=`add $dist_hc $dist_cc ` | + | c2=`m_sum $dist_hc $dist_cc` |
- | h2=`add $c2 $dist_hc ` | + | h2=`m_sum $c2 $dist_hc ` |
# | # | ||
# replaces coordinates in the input | # replaces coordinates in the input | ||
# | # | ||
- | | + | |
# | # | ||
# Runs cp2k | # Runs cp2k | ||
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# gets the energy from the output (in a.u.) | # gets the energy from the output (in a.u.) | ||
# | # | ||
- | energy=` | + | energy=` |
echo $dist_cc $energy | echo $dist_cc $energy | ||
# | # | ||
Line 172: | Line 161: | ||
mv c2h2.*.inp c2h2.*.out Logs | mv c2h2.*.inp c2h2.*.out Logs | ||
rm RUN* *restart* | rm RUN* *restart* | ||
+ | |||
+ | |||
</ | </ | ||
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# | # | ||
# loads the functions | # loads the functions | ||
- | # this script uses the functions: | + | # this script uses the functions: |
# | # | ||
module load new cp2k | module load new cp2k | ||
- | . ~/ | + | #. ~/ |
+ | . / | ||
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# | # | ||
- | for n in `list -5 5` | + | for n in `m_list |
do | do | ||
- | dist_cc=`change | + | dist_cc=`m_change |
- | c2=`add $dist_hcx $dist_cc` | + | c2=`m_sum $dist_hcx $dist_cc` |
- | h3=`add $c2 $dist_hcx ` | + | h3=`m_sum $c2 $dist_hcx ` |
# | # | ||
# replaces coordinates in the input | # replaces coordinates in the input | ||
# | # | ||
- | | + | |
# | # | ||
# Runs cp2k | # Runs cp2k | ||
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# gets the energy from the output (in a.u.) | # gets the energy from the output (in a.u.) | ||
# | # | ||
- | energy=` | + | energy=` |
echo $dist_cc $energy | echo $dist_cc $energy | ||
# | # | ||
Line 307: | Line 299: | ||
mv c2h4.*.inp c2h4.*.out Logs | mv c2h4.*.inp c2h4.*.out Logs | ||
rm RUN* *restart* | rm RUN* *restart* | ||
- | | + | |
+ | | ||
</ | </ | ||
exercises/2015_ethz_mmm/c2h2_bond_energy.1425027231.txt.gz · Last modified: 2020/08/21 10:14 (external edit)