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exercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/22 14:18] – dpasseroneexercises:2018_ethz_mmm:lennard_jones_cluster_2018 [2018/02/23 08:48] – dpasserone
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 +<note tip>
 +All files of this exercise be downloaded directly from the wiki: {{exercise_1.1.zip|}} 
 +</note>
  
-<code> +Download the 1.1 exercise into your **EXERCISES** folder and unzip it. 
-max@qmobile:~$ cp2k.ssmp -i file.inp -o file.out +
-</code>  +
- +
  
 <code> <code>
-================================================================== +max@qmobile:~$ cd ; cd EXERCISES 
-m_addcolumn +max@qmobile:~$ wget http://www.cp2k.org/_media/exercises:2018_ethz_mmm:exercise_1.1.zip 
-Description: +max@qmobile:~$ unzip exercises:2018_ethz_mmm:exercise_1.1.zip 
-        add a column at the left of a file, the same string in every line. +max@qmobile:~$ cd exercise_1.1
-Usage: +
-        m_addcolumn string < file > file.out +
-================================================================== +
- +
- +
-================================================================== +
-m_cutlines +
-Description: +
-        Cuts lines l1..l2, l3..l4, l5..l6 away from a file +
-Usage: +
-        m_cutlines l1 l2 l3 l4 l5 l6 ...  < file > modified_file +
-================================================================== +
- +
- +
-================================================================== +
-m_domyslab +
-Description: +
-        starting from a unit cell file with Element x y z columns, generate a nx ny nz cell. The parameter d is the nearest neighbor distance, and the cell lengths Lx, Ly, Lz are in the same units as in the unit cell file. Since d is used to multiply all coordinates, the unit cell coordinates are meant to be in nearest neighbor units. +
-Usage: +
-        m_domyslab Lx Ly Lz d nx ny nz < unitcell > slab.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_interpolate +
-Description: +
-        Returns a list of real numbers that interpolates two given extremes A and B with n+1 points (from A=0 to B=n) +
-Usage: +
-        m_interpolate xa xb n +
-================================================================== +
- +
- +
-================================================================== +
-m_multiply +
-Description: +
-        Returns the product of two numbers +
-Usage: +
-        m_multiply num1 num2 +
-================================================================== +
- +
- +
-================================================================== +
-m_overlayer +
-Description: +
-        Replaces the 4th column (z coordinate) of a file with a user-given new z coordinate. +
-Usage: +
-        m_overlayer newz < overlayer.xyz > newoverlayer.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_replace +
-Description: +
-        Replaces all occurrencies of an "oldstring" in a file with a "newstring" string +
-Usage: +
-        m_replace "oldstring" "newstring" < oldfile > newfile +
-================================================================== +
- +
- +
-================================================================== +
-m_trimlines +
-Description: +
-        trims around lines l1..l2, l3..l4, l5..l6 of +
-Usage: +
-        m_trimlines l1 l2 l3 l4 l5 l6 ...  < file > modified_file +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzcenter +
- +
- +
-Description: +
-        Centers a sample in the directions specified by a 1, and not in those specified by a 0 +
-Usage: +
-        m_xyzcenter flagx flagy flagz < cell.xyz > cell_center.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzminmax +
-Description: +
-        This function returns the maximum and minimum X (or Y, or Z) value from a XYZ file +
-Usage: +
-        m_xyzminmax x|y|z < file.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzrefold +
- +
-Description: +
-        Refolds a sample according to periodic boundary conditions in all directions marked by 1 +
-        The cell is defined by a,b,c in the second line of the xyz file +
-Usage: +
-        m_xyzrefold markx marky markz < filein.xyz > fileout.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyztranslate +
- +
-Description: +
-        Translates all coordinates of a xyz file by a given vector. +
-Usage: +
-        m_xyztranslate tx ty tz < filein.xyz > fileout.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_atan2 +
-Description: +
-        Returns the angle in degrees between the positive X-axis of a plane and the point given by the coordinates (x,y) on it: +
- +
-\ +
- \ +
-  * (x,y) +
-   \ +
-    \ +
-     \_______ +
-      \      | +
-       \angle| +
-      --\----------------------> +
-         \                     X +
- +
-Usage: +
-        m_atan2 x y +
-================================================================== +
- +
- +
-================================================================== +
-m_distance +
-Description: +
-        Computes the distance between two points +
-Usage: +
-        m_distance x1 y1 z1 x2 y2 z2 +
-================================================================== +
- +
- +
-================================================================== +
-m_functions.bash +
-================================================================== +
- +
- +
-================================================================== +
-m_lattice +
- +
-Description: +
-        Replicates a cell in 3 directions and generates a sample with the cell lengths a b c in the second line +
-        IT ONLY READS THE LINES WITH EXACTLY 4 COLUMNS (atomic index, x, y, z) +
-Usage: +
-        m_lattice [Atom] cellx celly cellz nx ny nz < cell > sample.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_norm +
-Please specify three arguments +
-Description: +
-        Returns the norm of a vector +
-Usage: +
-        m_norm x y z +
- +
-================================================================== +
- +
- +
-================================================================== +
-m_pdbtorsion +
-Description: +
-        Returns torsion defined by 4 atoms in a pdb file +
-                           Atom4 +
-                            / +
-             <-.           / +
-           angle\         / +
-     Atom2-------|-----Atom3 +
-      /      \__/ +
-     / +
-    / +
- Atom1 +
- +
-Usage: +
-        m_pdbtorsion n1 n2 n3 n4 file +
-================================================================== +
- +
- +
-================================================================== +
-m_scalar +
-Description: +
-        Returns scalar product of two vectos +
-Usage: +
-        m_scalar x1 y1 z1 x2 y2 z2 +
-================================================================== +
- +
- +
-================================================================== +
-m_unitvec +
-Description: +
-        Returns a normalized input vector +
-Usage: +
-        m_unitvec x y z +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzcountframes +
-Description: +
-        This function counts the number of frames in a trajectory +
-Usage: +
-        m_xyzcountframes file.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyznatoms +
-Description: +
-        This function returns the number of atoms in a given XYZ file +
-Usage: +
-        m_xyznatoms < file.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzrescale +
- +
-Description: +
-        Rescales all coordinates of a xyz file by a given factor. If the cell is given in the second line it is multiplied by the same factor +
-Usage: +
-        m_xyzrescale factor < filein.xyz > fileout.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzzhistogram +
-Description: +
-        This function makes a z histogram of a trajectory +
-Usage: +
-        m_xyzzhistogram n_intervals n_atoms z_min z_max +
-================================================================== +
- +
- +
-================================================================== +
-m_change +
-Please specify three arguments +
-Description: +
-        Adds a delta times an integer to a central value +
-Usage: +
-        m_change x0 n delta +
-================================================================== +
- +
- +
-================================================================== +
-m_divide +
-Description: +
-        Returns the ratio of two numbers +
-Usage: +
-        m_ratio num1 num2 +
-================================================================== +
- +
- +
-================================================================== +
-m_getcolumn +
-Description: +
-        Greps a string from a file and gets the last instance; then takes the nth column +
-Usage: +
-        m_getcolumn "STRING" column < file +
-================================================================== +
- +
- +
-================================================================== +
-m_list +
-Please specify two arguments +
-Description: +
-        Creates an ordered list of numbers between two integers +
-Usage: +
-        m_list nmin nmax +
-================================================================== +
- +
- +
-================================================================== +
-m_onecolumn +
-Description: +
-        parse a file and write all words as a single column +
-Usage: +
-        m_onecolumn < file +
-================================================================== +
- +
- +
-================================================================== +
-m_pdbvecjoin +
-Description: +
-        Returns a vector joining  two atoms in a pdb file +
-Usage: +
-        m_pdbvecjoin at1 at2 pdbfile +
-================================================================== +
- +
- +
-================================================================== +
-m_sum +
-Description: +
-        Returns the sum of two numbers +
-Usage: +
-        m_sum num1 num2 +
-================================================================== +
- +
- +
-================================================================== +
-m_vecprod +
-Description: +
-        Returns vector product of two vectors +
-Usage: +
-        m_vecprod x1 y1 z1 x2 y2 z2 +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzframes +
-Description: +
-        This function takes frames from a xyz file +
-Usage: +
-        m_takeslides first_frame last_frame file.xyz  (with last_frame=all, until the end) +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzrand +
- +
-Description: +
-        Randomizes a file xyz from -delta/2 to delta/2 +
-Usage: +
-        m_xyzrand delta < file.xyz +
-================================================================== +
- +
- +
-================================================================== +
-m_xyzsort +
- +
-Description: +
-        Sorts a xyz file according to z, y, x coordinates (z is inverted) +
-Usage: +
-        m_xyzsort < file.xyz > filesorted.xyz +
-================================================================== +
- +
- +
 </code> </code>
  
  
-Download the 1.1 exercise into your $HOME folder and unzip it.  
- 
-<code> 
-you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_1.1.zip 
-you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_1.1.zip 
-</code> 
-<!-- 
-<note tip> 
-All files of this exercise be downloaded from the wiki: {{exercise_1.1.zip|}}  
-</note> 
  
 In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster: In this exercise you will test the Lennard-Jones potential. In particular, we will focus on the system described in the following paper about the energy landscape of the 38 atom Lennard-Jones cluster:
 <note tip>{{ :exercises:2017_ethz_mmm:1999_the_double-funnel_energy_landscape_of_the_38-atom_lennard-jones_cluster.pdf |}} <note tip>{{ :exercises:2017_ethz_mmm:1999_the_double-funnel_energy_landscape_of_the_38-atom_lennard-jones_cluster.pdf |}}
 </note> </note>
-Login to euler using your nethz credentials. + 
-Then go to the directory "exercise_1.1". +The command to run cp2k is the following (with a generic **file.inp** input file): 
 <code> <code>
-you@eulerX ~$ cd exercise_1.1+max@qmobile:~$ cp2k.ssmp -i file.inp -o file.out 
 +</code> 
  
- 
-</code> 
  
 ===== Geometry optimization  ===== ===== Geometry optimization  =====
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 <note important>NOTE ON THE UNITS: CP2K USES SO CALLED "atomic units". Meaning that the resulting energies are expressed in Hartree,  <note important>NOTE ON THE UNITS: CP2K USES SO CALLED "atomic units". Meaning that the resulting energies are expressed in Hartree, 
 **1 Hartree=27.2114 eV**.  **1 Hartree=27.2114 eV**. 
-In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in "temperature" units (there is a Boltzmann constant to make units work...). **The sigma value is in Angstrom.**+In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in "temperature" units (there is a Boltzmann constant K_b to make units work...). <code>1 Kelvin*K_b=3.2E-6 Hartree</code>. Using this conversion factor you can transform the epsilon value into Hartree, and the total energy can be expressed in units of epsilon.  **The sigma value is in Angstrom.**
 </note> </note>
 <note tip> <note tip>
-  - load the module with the special m_* bash functions and initialize the module: <code>module load courses mmm ; mmm-init </code> +  - randomize the coordinate files **fcc.xyz** (which represents the "cubic" structure) <code>m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</code>Do the same with **ico.xyz** which represents the icosahedral structure. You can look at all files with **vmd**. 
-  - randomize the coordinate files **fcc.xyz**  <code>m_xyzrand 1.0 < fcc.xyz > fcc_rand.xyz</code> . Do the same with ico.xyz +  - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values. 
-  - extract the q4 order parameter from **fcc.xyz** and from **fcc_rand.xyz** and compare the values.<code>module load new gcc/4.8.2 python/2.7.12   +  - <code> python stein.py file.xyz </code>You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. You will also be asked **"value of l"** This means the symmetry of the order parameter, which is **l=4** in this case.
-python stein.py file.xyz </code>. You will be asked the cutoff radius for the neighbors, it is **1.391** in sigma units. **You should input it in Angstrom**. +
   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>   - before running the simulation, copy the input coordinate file into in.xyz <code>cp fcc_rand.xyz in.xyz</code>
-  - run cp2k <code>module load cp2k</code>(this has only to be done once)<code>cp2k.popt -i geo_opt.inp -o geo_opt.out </code>  +  - Before running cp2k, check if the file **OPT-pos-1.xyz** is already present from a previous run. In that case remove or delete it accordingly. It contains the trajectory of the optimization. 
-  - in the output file, note the final energy, **transform it in the unit of the paper (epsilon units)** +  - run cp2k  <code>cp2k.ssmp -i geo_opt.inp | tee geo_opt.out </code> (to see the output on the screen as well), or **AS AN ALTERNATIVE** <code>cp2k.ssmp -i geo_opt.inp > geo_opt.out </code> (to retain the output in the geo_opt.out file only)  
-  - load vmd module and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)+  - in the output file, grep the final energy <code>grep "ENERGY|“ geo_opt.out</code> and transform it in the unit of the paper (epsilon units) 
 +  - Open vmd and play with the optimization trajectory <code>vmd OPT-pos-1.xyz</code> (ask the teacher)
   - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <code>./myq4 OPT-pos-1.xyz > fcc.ene.q4</code>    - apply the script **myq4** to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory. <code>./myq4 OPT-pos-1.xyz > fcc.ene.q4</code> 
   - plot q4 and energies with **gnuplot** (ask the teacher)   - plot q4 and energies with **gnuplot** (ask the teacher)
   - have a look at the myq4 script <code>nano myq4</code>   - have a look at the myq4 script <code>nano myq4</code>
   - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: <code>mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC</code>   - repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example: <code>mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC</code>
-  - finally, run the bash script <code>./curve</code>. Look inside, and try to understand what you get. +  - Run the bash script <code>./curve</code>Look inside, and try to understand what you get.  
 +  - create a FCC_OUT subdirectory (**mkdir FCC_OUT ; cd FCC_OUT**) and copy there the files you want to keep; then go back one dir (**cd ..**), delete all the OPT* files (**rm OPT* **) and repeat the exercise with ico.xyz
  
 </note> </note>
 +
 +
 +
 +
 +
 +
 +
 +
  
  
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 <note tip>Assignment:  <note tip>Assignment: 
   - Report the energy of the minima, compare it with the ones of the initial configurations.    - Report the energy of the minima, compare it with the ones of the initial configurations. 
 +  - After converting the energy into "epsilon" units, estimate the number of bonds in the cluster, assuming a pairwise interaction.
   - Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?   - Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?
   - Report the value of the order parameter of the minumum, and discuss what you see   - Report the value of the order parameter of the minumum, and discuss what you see
   - Use "gnuplot" to make the output of "./curve" understandable, discuss the results.   - Use "gnuplot" to make the output of "./curve" understandable, discuss the results.
 </note> </note>
--->+
exercises/2018_ethz_mmm/lennard_jones_cluster_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1