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 [2016/09/28 13:26] – tmueller | ||
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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.): |
[...] | [...] | ||
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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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^ 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 | ||
| ... | ... | ... | | | ... | ... | ... | | ||
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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 the LJ energy curve for the two set of parameters ($\sigma$ and $\epsilon$) provided. | + | |
- | * Report, for both curves, the minimum energy distance and the depth of the minimum. | + | Plot again the energy curve. |
- | * What are the major differences between the curves? How do they relate to the sets of parameters provided? | + | |
+ | ====== Tips & Tricks ====== | ||
exercises/2016_uzh_cmest/first_simulation_run.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1