exercises:2016_uzh_cmest:first_simulation_run
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exercises:2016_uzh_cmest:first_simulation_run [2016/09/22 14:36] – [Part I: Single Point (Energy) calculation] tmueller | exercises:2016_uzh_cmest:first_simulation_run [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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To get you started, we will do a simple exercise using Molecular Mechanics (that is: a classical approach). The point is to get familiar with the options, organizing and editing the input file and analyze the output. | To get you started, we will do a simple exercise using Molecular Mechanics (that is: a classical approach). The point is to get familiar with the options, organizing and editing the input file and analyze the output. | ||
+ | |||
====== Computation of the Lennard Jones curve ====== | ====== Computation of the Lennard Jones curve ====== | ||
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Additonal parameters for Neon (Ne) and combination rules to obtain new parameters are provided in Part III and IV. | Additonal parameters for Neon (Ne) and combination rules to obtain new parameters are provided in Part III and IV. | ||
- | You are expected to hand in the respective plots plus answers to the questions. The format can be either | + | You are expected to hand in the respective plots by email, |
===== Part I: Single Point (Energy) calculation ===== | ===== Part I: Single Point (Energy) calculation ===== | ||
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**** ** ******* | **** ** ******* | ||
[...] | [...] | ||
- | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): | + | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): |
[...] | [...] | ||
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If you get the closing banner you know that CP2K finished. | If you get the closing banner you know that CP2K finished. | ||
- | |||
- | <note warning> | ||
The following line tells you the result: | The following line tells you the result: | ||
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To convert from //Kelvin// to //Hartree// you have to multiply with the Boltzmann constant $ k_\text{b} = 3.1668154 \cdot 10^{-6} \frac{E_\text{H}}{\text{K}} $ . | To convert from //Kelvin// to //Hartree// you have to multiply with the Boltzmann constant $ k_\text{b} = 3.1668154 \cdot 10^{-6} \frac{E_\text{H}}{\text{K}} $ . | ||
+ | <note warning> | ||
===== Part II: Computation of the LJ energy curve ===== | ===== Part II: Computation of the LJ energy curve ===== | ||
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Plot again the energy curve. | Plot again the energy curve. | ||
+ | ====== Tips & Tricks ====== | ||
+ | |||
+ | ===== Parsing the output ===== | ||
+ | |||
+ | Many times you will have to get some value out of a simulation output, in this case, the energy. | ||
+ | This can achieved in a number of ways: | ||
+ | |||
+ | * Using the '' | ||
+ | $ grep "Total FORCE_EVAL" | ||
+ | </ | ||
+ | | ||
+ | </ | ||
+ | * Using the '' | ||
+ | $ awk '/ | ||
+ | </ | ||
+ | -0.000250281091139 | ||
+ | </ | ||
+ | |||
+ | ===== Generating input files ===== | ||
+ | |||
+ | Many times you will have to run the same simulation with different parameters (here the distance). | ||
+ | |||
+ | A simple way to generate the different input files is using shell scripting in combination with '' | ||
+ | |||
+ | < | ||
+ | for d in $(seq 2 0.1 4); do | ||
+ | sed -e "s|4 0 0|${d} 0 0|" energy.inp > energy_${d}A.inp | ||
+ | cp2k.sopt -i energy_${d}A.inp -o energy_${d}A.out | ||
+ | awk '/ | ||
+ | done | ||
+ | </ | ||
+ | |||
+ | * The command '' | ||
+ | * With '' | ||
+ | * '' | ||
+ | * ... and using ''> | ||
+ | * Then we run '' | ||
+ | * Using '' |
exercises/2016_uzh_cmest/first_simulation_run.1474554991.txt.gz · Last modified: 2020/08/21 10:15 (external edit)