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--- exercises:2016_uzh_cmest:first_simulation_run [2016/09/22 08:53] – (Delete) exercises:2016_uzh_cmest:first_simulation_run renamed to exercises:2016_uzh_cmest:login tmueller
+++ exercises:2016_uzh_cmest:first_simulation_run [2020/08/21 10:15] (current) – external edit 127.0.0.1
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-This page is redirected to [[:exercises:2016_uzh_cmest:login]].
+====== Run your first simulation using CP2K ======
+When you check CP2K's [[::features]] and the outline of the lecture you will notice that there are many levels of theory, methods and possibilities to combine them. This results in a large number of possible options and coefficients to setup, control and tune a specific simulation.
+Together with the parameters for the numerical solvers this means that an average CP2K configuration file will contain quiet a number of options (even though for many others the default value will be applied) and not all of them will be discussed in the lecture or the exercises.
+The [[https://manual.cp2k.org/|CP2K Manual]] is the complete reference for all configuration options. Where appropriate you will find a reference to the respective paper when looking up a specific keyword/option.
+To get you started, we will do a simple exercise using Molecular Mechanics (that is: a classical approach). The point is to get familiar with the options, organizing and editing the input file and analyze the output.
+====== Computation of the Lennard Jones curve ======
+In this exercise you will compute the Lennard-Jones energy curve for a system of two Krypton (Kr) atoms using a Molecular Mechanics simulation rather than the analytical form of the potential.
+In Part I you find the instructions for computing the energy of two Kr atoms at a distance $r=4.00 Å$.
+In Part II you find the instructions for getting the energy profile as a function of $r$.
+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 by email, either as one PDF or as one file per plot (PNG, JPEG, or PDF format).
+===== Part I:  Single Point (Energy) calculation =====
+In this section a commented CP2K input example for a single point calculation is provided.
+Comments are added, they start with an exclamation mark '!'.
+=== 1. Step ===
+Load the CP2K module as shown before, create a directory ''ex1'' and change to it:
+<code>
+mkdir ex1
+cd ex1
+</code>
+Save the following input to a file named ''energy.inp'' (for example using ''$ vim energy.inp''):
+<code - energy.inp>
+&GLOBAL                  ! section to select the kind of calculation
+   RUN_TYPE ENERGY       ! select type of calculation. In this case: ENERGY (=Single point calculation)
+&END GLOBAL
+&FORCE_EVAL              ! section with parameters and system description
+  METHOD FIST            ! Molecular Mechanics method
+  &MM                    ! specification of MM parameters
+    &FORCEFIELD          ! parameters needed to describe the potential
+      &SPLINE
+        EMAX_SPLINE 10000    ! numeric parameter to ensure calculation stability. Should not be changed
+      &END SPLINE
+      &NONBONDED       ! parameters for the non bonded interactions
+        &LENNARD-JONES ! Lennard-Jones parameters
+          ATOMS Kr Kr
+          EPSILON    [K_e] 164.56
+          SIGMA [angstrom]   3.601
+          RCUT  [angstrom]  25.0
+        &END LENNARD-JONES
+      &END NONBONDED
+      &CHARGE
+        ATOM Kr
+        CHARGE 0.0
+      &END CHARGE
+    &END FORCEFIELD
+    &POISSON              ! solver for non periodic calculations
+      PERIODIC NONE
+      &EWALD
+        EWALD_TYPE none
+      &END EWALD
+    &END POISSON
+  &END MM
+  &SUBSYS                 ! system description
+    &CELL
+      ABC [angstrom] 10 10 10
+      PERIODIC NONE
+    &END CELL
+    &COORD
+      UNIT angstrom
+      Kr  0 0 0
+      Kr  4 0 0
+    &END COORD
+  &END SUBSYS
+&END FORCE_EVAL
+</code>
+<note tip>Instructions starting with an ampersand ''&'' start a //section// and **must** be terminated with an ''&END SECTION-NAME''. Other instructions are called //keywords//. The indentation is ignored but recommended for readability.</note>
+=== 2. Step ===
+Run a CP2K calculation with the following command:
+<code>
+$ cp2k.sopt -i energy.inp -o energy.out
+</code>
+<note tip>Alternatively you can run it using <code>$ cp2k.sopt -i energy.inp | tee energy.out</code> which will write the output simultaneously to a file ''energy.out'' and show it in the terminal.</note>
+=== 3. Step ===
+The output (''$ less energy.out'') should look like this:
+<code>
+[...]
+  **** **** ******  **  PROGRAM STARTED AT               2016-09-22 15:15:15.977
+ ***** ** ***  *** **   PROGRAM STARTED ON                                tcopt3
+ **    ****   ******    PROGRAM STARTED BY                             studentXX
+ ***** **    ** ** **   PROGRAM PROCESS ID                                112277
+  **** **  *******  **  PROGRAM STARTED IN          /data/students/studentXX/ex1
+[...]
+  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):          -0.000518941408898
+[...]
+ The number of warnings for this run is : 0
+ -------------------------------------------------------------------------------
+  **** **** ******  **  PROGRAM ENDED AT                 2016-09-22 15:15:16.027
+ ***** ** ***  *** **   PROGRAM RAN ON                                    tcopt3
+ **    ****   ******    PROGRAM RAN BY                                 studentXX
+ ***** **    ** ** **   PROGRAM PROCESS ID                                112277
+  **** **  *******  **  PROGRAM STOPPED IN          /data/students/studentXX/ex1
+</code>
+If you get the closing banner you know that CP2K finished.
+The following line tells you the result:
+<code>
+ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):             -0.000518941408898
+</code>
+This is the energy (in Hartree) for a system of 2 Kr atoms at distance $ r=4.00 Å$
+Note, that in the input-file ''EPSILON'' is given in units of //Kelvin//, whereas in the output the energy is printed in //Hartree//, which is the unit of energy in the system of atomic units (a.u.).
+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>Always check the number of warnings by looking at the line: <code>The number of warnings for this run is : ...</code>  If that number is not zero you **must** check the rest of the output for warnings and act accordingly, otherwise you may work with wrong results.</note>
+===== Part II: Computation of the LJ energy curve =====
+In this section a few scripts to get the LJ energy profiles are presented.
+=== 1. Step ===
+In order to get a good profile, a set of energy values as a function of the interatomic distance is needed. You can use the ''energy.inp'' input file and change the Kr coordinates in order to get different starting distances.
+<note important>
+The output file will be overwritten every time you run a calculation, unless you change its name.
+</note>
+To do so:
+<code>
+$ mv energy.out energy_dist4A.out
+</code>
+<note tip>
+If you run multiple calculations, it is always good to keep track of what you have done by producing an input and an output for every distance you are planning to run.
+</note>
+For doing so:
+<code>
+$ cp energy.inp energy_dist2A.inp
+</code>
+then edit the input file to update to the new coordinates (e.g. 2 Å) and rerun CP2K to produce a new output file:
+<code>
+$ cp2k.sopt -i energy_dist2A.inp -o energy_dist2A.out
+</code>
+=== 2. Step ===
+When you have tested a few distances, you can produce a table looking like:
+^ Input file      ^ Distance (Å)   ^ Energy   (Eh)       ^
+| energy_dist1A.inp    | 1      | ...        |
+| energy_dist2A.inp    | 2      | ...        |
+| energy_dist3A.inp    | 3      | ...        |
+| ...                  | ...    | ...        |
+This is the Lennard Jones energy curve for two Kr atoms.
+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 ===
+Now we do the same for Ne atoms: use the previous input file as a template and update the parameters according to the following:
+<code>
+         &NONBONDED
+           &LENNARD-JONES ! Lennard-Jones Ne parameters
+             ATOMS Ne Ne
+             EPSILON    [K_e] 36.831
+             SIGMA [angstrom]  2.775
+             RCUT  [angstrom] 25.0
+             &END LENNARD-JONES
+         &END NONBONDED
+         &CHARGE
+           ATOM Ne
+           CHARGE 0.0
+         &END CHARGE
+</code>
+Plot the energy curve again.
+=== 4. Step ===
+Finally we look at the curve for Kr-Ne.
+The epsilon and sigma for the Lennard-Jones potential between Kr and Ne can be calculated using the parameters from the Kr-Kr and Ne-Ne interaction:
+$$ \sigma_{ij}= \sqrt{\sigma_i\sigma_j}$$ \\
+$$ \epsilon_{ij}= \sqrt{\epsilon_i\epsilon_j}$$
+Please note:
+  * The ''LENNARD-JONES'' section must be present for all the three possible couples now: Kr-Kr, Ne-Ne and Ne-Kr:
+<code>
+      &LENNARD-JONES ! Lennard-Jones parameters for Ar-Ar interaction
+        ATOMS Kr Kr
+        EPSILON    [K_e] 164.56
+        SIGMA [angstrom]  3.601
+        RCUT  [angstrom]  25.0
+      &END LENNARD-JONES
+      &LENNARD-JONES ! Lennard-Jones Ne-Ne parameters
+        ATOMS Ne Ne
+        EPSILON    [K_e] 36.831
+        SIGMA [angstrom]  2.775
+        RCUT  [angstrom] 25.0
+      &END LENNARD-JONES
+      &LENNARD-JONES ! Lennard-Jones parameters for Kr-Ne interaction
+        ATOMS Kr Ne
+        EPSILON    [K_e] YOUR EPSILON
+        SIGMA [angstrom]  YOUR SIGMA
+        RCUT  [angstrom]  25.0
+      &END LENNARD-JONES
+</code>
+  * The ''CHARGE'' section must be also duplicated:
+<code>
+         &CHARGE
+           ATOM Ne
+           CHARGE 0.0
+         &END CHARGE
+         &CHARGE
+           ATOM Kr
+           CHARGE 0.0
+         &END CHARGE
+</code>
+  * one of the atom kinds in the ''&COORD'' section must be set to Kr, the other to Ne.
+Plot again the energy curve.
+====== Tips & Tricks ======
+===== 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'' command:<code>
+$ grep "Total FORCE_EVAL" energy.out
+</code>which gives you:<code>
+ ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):             -0.000250281091139
+</code>
+  * Using the ''awk'' tool:<code>
+$ awk '/Total FORCE_EVAL/ { print $9; }' energy.out
+</code>which returns:<code>
+-0.000250281091139
+</code>''awk'' reads a given file line-by-line and splits a line into multiple fields (using whitespace as delimiter). The command above tells ''awk'' to look for the string ''Total FORCE_EVAL'' in a line and if found, print field number 9 of it, effectively returning the energy.
+===== Generating input files =====
+Many times you will have to run the same simulation with different parameters (here the distance).
+A simple way to generate the different input files is using shell scripting in combination with ''sed'' (the stream editor):
+<code>
+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 '/Total FORCE_EVAL/ { print $9; }' energy_${d}A.out
+done
+</code>
+  * The command ''seq 2 0.1 4'' generates the numbers ''2.0'', ''2.1'', ''2.2'', ... , ''4.0'' (try it out!)
+  * With ''for d in $(seq 2 0.1 4); do'' we use the shell to run all commands which follow once for every number (stored in ''$d'')
+  * ''sed -e "s|4 0 0|$d 0 0|" energy.inp'' looks for ''4 0 0'' in the file ''energy.inp'' (the original file from above) and replaces ''4 0 0'' by ''$d 0 0'' (that is: ''2.0'', ''2.1'', ''2.2'', ...)
+  * ... and using ''> energy_${d}A.out'' we redirect the output of the ''sed'' command to new files ''energy_2.0A.out'', ''energy_2.1A.out'', etc.
+  * Then we run ''cp2k.sopt'' as shown before on those new input files and write the output to new output files as well
+  * Using ''awk'' we extract the energy from the output file