exercises:2016_uzh_cmest:first_simulation_run
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exercises:2016_uzh_cmest:first_simulation_run [2016/09/22 14:12] – [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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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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&END FORCE_EVAL | &END FORCE_EVAL | ||
</ | </ | ||
+ | |||
+ | <note tip> | ||
=== 2. Step === | === 2. Step === | ||
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**** ** ******* | **** ** ******* | ||
[...] | [...] | ||
- | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): | + | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): |
[...] | [...] | ||
Line 117: | Line 118: | ||
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: | ||
Line 131: | Line 130: | ||
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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^ Input file ^ Distance (Å) ^ Energy | ^ Input file ^ Distance (Å) ^ Energy | ||
| energy_dist1A.inp | | energy_dist1A.inp | ||
- | | energy_dist1.5A.inp | ||
| energy_dist2A.inp | | energy_dist2A.inp | ||
- | | energy_dist2.5A.inp | ||
| energy_dist3A.inp | | energy_dist3A.inp | ||
| ... | ... | ... | | | ... | ... | ... | | ||
Line 178: | Line 176: | ||
By using any plotting program you can now get a representation of the energy profile. | By using any plotting program you can now get a representation of the energy profile. | ||
+ | Choose a an appropriate minimum distance and step size. | ||
=== 3. Step === | === 3. Step === | ||
- | Here are reported | + | Now we do the same for Ne atoms: use the previous |
< | < | ||
& | & | ||
- | | + | & |
- | atoms Ne Ne | + | ATOMS Ne Ne |
- | | + | |
- | | + | |
- | | + | |
- | &END LENNARD-JONES | + | |
& | & | ||
& | & | ||
- | | + | ATOM Ne |
- | CHARGE 0.0 | + | |
& | & | ||
</ | </ | ||
+ | |||
+ | Plot the energy curve again. | ||
=== 4. Step === | === 4. Step === | ||
- | Here are reported | + | |
- | Once generated the ε and σ parameters | + | Finally we look at the curve for Kr-Ne. |
- | Compare | + | |
+ | The epsilon | ||
$$ \sigma_{ij}= \sqrt{\sigma_i\sigma_j}$$ \\ | $$ \sigma_{ij}= \sqrt{\sigma_i\sigma_j}$$ \\ | ||
$$ \epsilon_{ij}= \sqrt{\epsilon_i\epsilon_j}$$ | $$ \epsilon_{ij}= \sqrt{\epsilon_i\epsilon_j}$$ | ||
- | <note tip> | + | Please |
- | Remember that you are running | + | |
- | </ | + | |
- | * The " | + | * The '' |
< | < | ||
& | & | ||
- | atoms Kr Kr | + | ATOMS Kr Kr |
- | EPSILON | + | EPSILON |
- | SIGMA [angstrom] | + | SIGMA [angstrom] |
- | RCUT [angstrom] | + | RCUT [angstrom] |
&END LENNARD-JONES | &END LENNARD-JONES | ||
& | & | ||
- | | + | ATOMS Ne Ne |
- | | + | EPSILON |
- | | + | SIGMA [angstrom] |
- | | + | RCUT [angstrom] 25.0 |
- | | + | &END LENNARD-JONES |
& | & | ||
- | atoms Kr Ne | + | ATOMS Kr Ne |
- | EPSILON | + | EPSILON |
- | SIGMA [angstrom] | + | SIGMA [angstrom] |
- | RCUT [angstrom] | + | RCUT [angstrom] |
- | &END LENNARD-JONES | + | &END LENNARD-JONES |
</ | </ | ||
- | * The " | + | * The '' |
< | < | ||
& | & | ||
- | | + | ATOM Ne |
- | CHARGE 0.0 | + | |
& | & | ||
& | & | ||
- | | + | ATOM Kr |
- | CHARGE 0.0 | + | |
& | & | ||
</ | </ | ||
- | ===== Questions | + | * one of the atom kinds in the ''& |
- | * Sketch | + | |
- | * Report, for both curves, | + | Plot again the energy curve. |
- | * What are the major differences between | + | |
+ | ====== | ||
+ | |||
+ | ===== 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 | ||
+ | |||
+ | < | ||
+ | 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.1474553521.txt.gz · Last modified: 2020/08/21 10:15 (external edit)