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exercises:2016_uzh_cmest:first_simulation_run [2016/09/22 14:35] – [Part II: Computation of the LJ energy curve] tmuellerexercises:2016_uzh_cmest:first_simulation_run [2016/09/28 13:26] – tmueller
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 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. 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 ====== ====== Computation of the Lennard Jones curve ======
  
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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 a proper PDF or directly in the email with the plots attached (as pictures in png, jpg, or pdf format). +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 ===== ===== Part I:  Single Point (Energy) calculation =====
  
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 &END FORCE_EVAL &END FORCE_EVAL
 </code> </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 === === 2. Step ===
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   **** **  *******  **  PROGRAM STARTED IN          /data/students/studentXX/ex1   **** **  *******  **  PROGRAM STARTED IN          /data/students/studentXX/ex1
 [...] [...]
-  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):           0.003617048870059+  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):          -0.000518941408898
 [...] [...]
  
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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>Always check the number of warnings by looking at the <code>The number of warnings for this run is : ...</code> line. If that number is not zero you **must** check the rest of the output for warnings and act accordingly.</note> 
  
 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>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 ===== ===== Part II: Computation of the LJ energy curve =====
    
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 Plot again the energy curve. Plot again the energy curve.
 +
 +====== Tips & Tricks ======
  
exercises/2016_uzh_cmest/first_simulation_run.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1