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exercise:mm_uzh:chp_cu111 [2014/06/30 11:14] – talirzexercise:mm_uzh:chp_cu111 [2014/06/30 14:05] – talirz
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   - Visualize an optimized slab with vmd, draw the simulation box and create a replica along x,y and z to familiarize yourself with the geometry. Why is the //slab geometry// used in atomistic simulations? What are the relevant convergence parameters? (2P)   - Visualize an optimized slab with vmd, draw the simulation box and create a replica along x,y and z to familiarize yourself with the geometry. Why is the //slab geometry// used in atomistic simulations? What are the relevant convergence parameters? (2P)
-  - The initial geometries were cut from a perfect bulk Cu crystal. Why do they still need to be optimized? Do //all// of them need to be optimized?+  - The initial geometries were cut from a perfect bulk Cu crystal. Why do they still need to be optimized? 
 +  - **BONUS** Do //all// of them need to be optimized?
   - How many layers are required to achieve a bulk environment in the center of the slab? //Hint:// Study the energy $\triangle E(N)$ as a function of $N$. You may want to use the script ''analyze-slabs.sh''.   - How many layers are required to achieve a bulk environment in the center of the slab? //Hint:// Study the energy $\triangle E(N)$ as a function of $N$. You may want to use the script ''analyze-slabs.sh''.
   - Calculate the surface energy $\sigma$ of Cu(111).   - Calculate the surface energy $\sigma$ of Cu(111).
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   - Before your start, look inside ''equilibrate.in'' and define the initial temperature. What type of [[http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD.html#desc_ENSEMBLE|ensemble]] are we using? Why aren't we using the NVE ensemble? (2P)   - Before your start, look inside ''equilibrate.in'' and define the initial temperature. What type of [[http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD.html#desc_ENSEMBLE|ensemble]] are we using? Why aren't we using the NVE ensemble? (2P)
   - The simulation time in ''equilibrate.in'' is 1 ns, which may be longer than required. While the simulation is running, monitor the temperature and the atomic structure (see hint below) to find out when the system reaches equilibrium.   - The simulation time in ''equilibrate.in'' is 1 ns, which may be longer than required. While the simulation is running, monitor the temperature and the atomic structure (see hint below) to find out when the system reaches equilibrium.
-  - Explain, why the average value of the temperature $\langle T \rangle$ must converge to $T_m$ in equilibrium. Calculate $\rangle T \rangle$ for the equilibrated system and compare against the [[https://sites.google.com/site/eampotentials/Cu|literature value]] calculated for this potential. //Note:// An error of 2-3% is still expected due to finite size effects. (2P)+  - Explain, why the average value of the temperature $\langle T \rangle$ must converge to $T_m$ in equilibrium. Calculate $\langle T \rangle$ for the equilibrated system and compare against the [[https://sites.google.com/site/eampotentials/Cu|literature value]] calculated for this potential. //Note:// An error of 2-3% is still expected due to finite size effects. (2P)
   - What happens if you choose $T_0$ much lower (or larger) than $T_m$? Describe qualitatively the expected effects in the atomic structure as well in the temperature as a function of simulation time.   - What happens if you choose $T_0$ much lower (or larger) than $T_m$? Describe qualitatively the expected effects in the atomic structure as well in the temperature as a function of simulation time.
 </note> </note>
exercises/2014_uzh_molsim/chp_cu111.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1