# Open SourceMolecular Dynamics

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exercises:2015_ethz_mmm:surface_cu

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 exercises:2015_ethz_mmm:surface_cu [2015/02/06 17:49]127.0.0.1 external edit exercises:2015_ethz_mmm:surface_cu [2015/03/19 22:17] (current)yakutovich [Surface energies of Copper high-symmetry surfaces] 2015/03/19 22:17 yakutovich [Surface energies of Copper high-symmetry surfaces] 2015/03/13 15:25 dpasserone 2015/03/06 10:58 yakutovich 2015/03/06 10:51 yakutovich 2015/03/06 10:36 dpasserone 2015/03/06 10:28 yakutovich 2015/03/06 10:27 yakutovich 2015/03/06 10:25 yakutovich 2015/03/06 09:20 yakutovich 2015/03/06 02:18 dpasserone 2015/03/04 00:57 dpasserone 2015/03/04 00:53 dpasserone 2015/03/04 00:49 dpasserone 2015/02/06 17:49 external edit Next revision Previous revision 2015/03/19 22:17 yakutovich [Surface energies of Copper high-symmetry surfaces] 2015/03/13 15:25 dpasserone 2015/03/06 10:58 yakutovich 2015/03/06 10:51 yakutovich 2015/03/06 10:36 dpasserone 2015/03/06 10:28 yakutovich 2015/03/06 10:27 yakutovich 2015/03/06 10:25 yakutovich 2015/03/06 09:20 yakutovich 2015/03/06 02:18 dpasserone 2015/03/04 00:57 dpasserone 2015/03/04 00:53 dpasserone 2015/03/04 00:49 dpasserone 2015/02/06 17:49 external edit Line 1: Line 1: + ====== Surface energies of Copper high-symmetry surfaces ====== ====== Surface energies of Copper high-symmetry surfaces ====== + + + TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: + + you@eulerX ~$module load courses mmm vmd + + you@eulerX ~$ mmm-init + ​ + + + ​ **REMEMBER: this is the command to load the  module for the cp2k program:** + + + you@eulerX ~$module load new cp2k + ​ + + **and to submit the job:** + + + you@eulerX ~$ bsub < jobname +  ​ +  ​ + + + {{:​exercises:​2015_ethz_mmm:​lect2_surf.001.jpg?​nolink&​400|}} + + ---- + + {{:​exercises:​2015_ethz_mmm:​lect2_surf.002.jpg?​400|}} + + ---- + + {{:​exercises:​2015_ethz_mmm:​lect2_surf.003.jpg?​400|}} + + In this exercise we will compute the surface energies of Cu using the EAM potential. In this exercise we will compute the surface energies of Cu using the EAM potential. As a reference, we report the table from the Gross book: As a reference, we report the table from the Gross book: Line 5: Line 41: {{screen_shot_2014-03-07_at_6.55.49_am.png?​direct&​500 |http://​example.com|External Link}} {{screen_shot_2014-03-07_at_6.55.49_am.png?​direct&​500 |http://​example.com|External Link}} + ---- + * Download all the necessary files from  from the wiki: {{exercise_3.1.zip|exercise_3.1.zip}} (**all inputs are commented**) in your home directory and unzip it: + + you@eulerX ~$wget http://​www.cp2k.org/​_media/​exercises:​2015_ethz_mmm:​exercise_3.1.zip + you@eulerX ~$ unzip exercises:​2015_ethz_mmm:​exercise_3.1.zip + you@eulerX ~$cd exercise_3.1 + ​ + * Run the optimizations 100.inp, 110.inp, 111.inp and the bulk. + + you@eulerX exercise_3.1$ bsub cp2k.popt -i 100.inp -o 100.out + you@eulerX exercise_3.1$bsub cp2k.popt -i 110.inp -o 110.out + you@eulerX exercise_3.1$ bsub cp2k.popt -i 111.inp -o 111.out + you@eulerX exercise_3.1$bsub cp2k.popt -i bulk.inp -o bulk.out + ​ + * While geometry optimization is running you can have a look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. In vmd it is also possible to open a console, and give the command **pbc set { a b c 90 90 90 }** where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization. + + you@eulerX exercise_3.1$ vmd 100.xyz + you@eulerX exercise_3.1$vmd 110.xyz + you@eulerX exercise_3.1$ vmd 111.xyz + ​ - ​- Copy the files from  from the wiki: {{exercise_3.1.zip|exercise_3.1.zip}} (**all inputs are commented**) into a new directory + * Compute the three surface energies: you need to compute the area, subtract bulk contribution,​ take care of the units. - - Use the batch **run_cp2k_lattice** to run a chain of simulations on a Cu bulk system. From the output **lat.out** check the lattice constant corresponding to minimum cohesive energy **PER ATOM** (divide by the number of particles, find it out!), you will need it later + ​* Unordered List ItemIn ​the class we will learn how to compute the Wulff crystal from these three numbers. - - Run the optimizations 100.inp, 110.inp, 111.inp ---- look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. + ​* Basically, you should edit the input file "​DP",​ replacing ​ **"​PUT_HERE_THE_XXX_SURFACE_ENERGY"​** with corresponding ​surface ​energy. Note that for the {100} and {110} surfaces you need to edit **TWO** lines each: the program takes care of assigning the surface energy to equivalent surfaces (like (010)) but since it was developed for island on surfaces it does not do it automatically in all directions. ​**z** direction is treated differently in this program. - - In vmd, you can also open a console, and give the command **pbc set { a b c 90 90 90 }**  where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization. + ​* At this point, you can run the sowos program: - - Compute the three surface energies: you need to compute the area, subtract bulk contribution,​ take care of the units. + - ​- In the class we will learn how to compute the Wulff crystal from these three numbers. + you@eulerX exercise_3.1$​./​sowos.v02.00.02.x - ​- Basically, you should edit the input file "​DP",​ replacing ​the column beginning with **"​PUT_HERE_THE_XXX_SURFACE_ENERGY"​** with quantities that are proportional to the three surface ​free energies (see Wulff theorem). Note that for the {100} and {110} surfaces you need to edit **TWO** lines each, since the **z** direction is treated differently in this program. + ​ - ​- At this point, you run the program ​with the command **./​sowos.v02.00.02.x** + ​* There will be many output files. Important are: - ​- There will be many output files. Important are + - the atomistic model **out.atomistic-inside-gnuplot.xyz** which will contain many atoms if you chose a proportionality constant in the file DP which is too large. If you appropriately modify it (how?) you can have a xyz file to be opened in vmd. - - * the atomistic model **out.atomistic-inside-gnuplot.xyz** which will contain many atoms if you chose a proportionality constant in the file DP which is too large. If you appropriately modify it (how?) you can have a xyz file to be opened in vmd. + - the **out.plot-gnuplot.plt** file. You can open it with gnuplot: - - * the **out.plot-gnuplot.plt** file. If you launch ​gnuplot, then "**load "​out.plot-gnuplot.plt"​** a plot of the crystal will be shown. To have it more or less to scale in all directions: **set xrange [-80:80];set yrange [-80:80]; set view equal xyz; replot** + - ​- * you can rotate with the mouse! + you@eulerX exercise_3.1$ ​gnuplot + gnuplot> ​load "​out.plot-gnuplot.plt"​ + gnuplot> ​set xrange [-80:80] + gnuplot> ​set yrange ​[-80:80] + gnuplot> ​set view equal xyz + gnuplot> ​replot + ​ + * you can rotate with the mouse! - <​note ​important>**Assignment: use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system!**​ + <​note ​tip> + Assignment: use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system! + ​documentation on **SOWOS** can be found at [[http://​www.danielescopece84.altervista.org/​sowos.html|the web site of Daniele Scopece]]​documentation on **SOWOS** can be found at [[http://​www.danielescopece84.altervista.org/​sowos.html|the web site of Daniele Scopece]]