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exercises:2016_ethz_mmm:single_point_calculation [2016/02/25 11:55]
sclelia [Computation of the Lennard Jones curve]
exercises:2016_ethz_mmm:single_point_calculation [2016/02/25 12:17]
sclelia
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 ====== Computation of the Lennard Jones curve ====== ====== Computation of the Lennard Jones curve ======
  
-In this exercise you will compute the Lennard-Jones energy curve for a system of two Krypton atoms.\\ +In this exercise you will compute the Lennard-Jones energy curve for a system of two Krypton ​(Kr) atoms.\\ 
-In Part I you find the instructions for computing the energy of two Ar atoms at a distance $r=3.00 Å$.\\+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 $r$.\\ In Part II you find the instructions for getting the energy profile as a function of $r$.\\
-Additonal parameters for Xe 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.
  
 ===== Part I:  Single Point (Energy) calculation ===== ===== Part I:  Single Point (Energy) calculation =====
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         &​NONBONDED ​      ! parameters for the non bonded interactions         &​NONBONDED ​      ! parameters for the non bonded interactions
           &​LENNARD-JONES ! Lennard-Jones parameters           &​LENNARD-JONES ! Lennard-Jones parameters
-          atoms Ar Ar +          atoms Kr Kr 
-          EPSILON ​   [K_e] 119.8 +          EPSILON ​   [K_e] 164.56 
-          SIGMA [angstrom] ​  3.401+          SIGMA [angstrom] ​  3.601
           RCUT  [angstrom] ​ 25.0           RCUT  [angstrom] ​ 25.0
         &END LENNARD-JONES         &END LENNARD-JONES
       &END NONBONDED       &END NONBONDED
       &CHARGE       &CHARGE
-        ATOM Ar+        ATOM Kr
         CHARGE 0.0         CHARGE 0.0
       &END CHARGE       &END CHARGE
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     &​COORD ​               ​     &​COORD ​               ​
       UNIT angstrom       UNIT angstrom
-      ​Ar  0 0 0 +      ​Kr  0 0 0 
-      ​Ar  0 0+      ​Kr  0 0
     &END COORD     &END COORD
    &​END SUBSYS    &​END SUBSYS
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 === 2. Step === === 2. Step ===
-Run CP2K with the following ​arguments:+Submit a CP2K calculation ​with the following ​commands:
 <​code>​ <​code>​
-cp2k.popt -i energy.inp -o energy.out+bsub -n 1  mpirun ​cp2k.popt -i energy.inp -o energy.out
 </​code>​ </​code>​
  
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 ... ...
-  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): ​          ​0.003617048870059+some stufff
 ... ...
  
 +  ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): ​          ​0.003617048870059
 +...
 +some other stuff
 +...
   **** **** ****** ​ **  PROGRAM ENDED AT                 ​2014-01-20 12:​24:​18.154   **** **** ****** ​ **  PROGRAM ENDED AT                 ​2014-01-20 12:​24:​18.154
  ***** ** ***  *** **   ​PROGRAM RAN ON                       ​some_server.ethz.ch  ***** ** ***  *** **   ​PROGRAM RAN ON                       ​some_server.ethz.ch
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 </​code>​ </​code>​
  
-This is the energy (in Hartree) for a system of 2 Ar atoms at distance $ r=3.00 Å$+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, 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}} $ .
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 === 1. Step === === 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 Ar coordinates in order to get different starting distances.+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>​ <note important>​
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 To do so:  To do so: 
 <​code>​ <​code>​
-$ mv energy.out ​energy_dist3A.out+$ mv energy.out ​energy_dist4A.out
 </​code>​ </​code>​
  
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 | ...                  | ...    | ...        | | ...                  | ...    | ...        |
  
-This is the Lennard Jones energy curve for two Ar atoms.+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. By using any plotting program you can now get a representation of the energy profile.
  
 === 3. Step === === 3. Step ===
-Here are reported the LJ parameters for Xe atoms. Those are to replace the Ar parameters in the input file, along with your Xe coordinates that have to replace the Ar coordinates. A new LJ curve for Xe atoms can be now generated.+Here are reported the LJ parameters for Ne atoms. Those are to replace the Kr parameters in the input file, along with your Ne coordinates that have to replace the Kr coordinates. A new LJ curve for Ne atoms can be now generated.
  
 <​code>​ <​code>​
          &​NONBONDED ​            &​NONBONDED ​  
-          &​LENNARD-JONES ! Lennard-Jones ​Xe parameters +          &​LENNARD-JONES ! Lennard-Jones ​Ne parameters 
-           ​atoms ​Xe Xe  +           ​atoms ​Ne Ne  
-           ​EPSILON ​   [K_e] 232  +           ​EPSILON ​   [K_e] 36.831 ​ 
-           SIGMA [angstrom]  ​3.98+           SIGMA [angstrom]  ​2.775
            ​RCUT ​ [angstrom] 25.0            ​RCUT ​ [angstrom] 25.0
           &END LENNARD-JONES           &END LENNARD-JONES
          &​END NONBONDED          &​END NONBONDED
          &​CHARGE          &​CHARGE
-          ATOM Xe+          ATOM Ne
           CHARGE 0.0           CHARGE 0.0
          &​END CHARGE          &​END CHARGE
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 === 4. Step === === 4. Step ===
 Here are reported the combination rules for pairs unlike pairs, i.e. for pairs of non identical atoms. \\  Here are reported the combination rules for pairs unlike pairs, i.e. for pairs of non identical atoms. \\ 
-Once generated the ε and σ parameters for the couple ​Ar/Xe, generate once more the LJ dissociation curve. \\+Once generated the ε and σ parameters for the couple ​Kr/Ne, generate once more the LJ dissociation curve. \\
 Compare the "​mixed"​ curve to the two "​pure"​ curves and report the position and depth of the minimum. \\ Compare the "​mixed"​ curve to the two "​pure"​ curves and report the position and depth of the minimum. \\
  
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 <note tip> <note tip>
-Remember that you are running ​ with two different atom types. For this reason some of the input sections ​must be duplicated ​for the two kinds of atoms present+Remember that you are running ​ with two different atom types. For this reason some of the input sections ​MUST BE REPLICATED ​for the two kinds of atoms present
 </​note>​ </​note>​
  
-  * The " LENNARD-JONES " section must be present for all the three possible couples: ​Ar-ArXe-Xe and Xe-Ar.  Example: ​+  * The " LENNARD-JONES " section must be present for all the three possible couples: ​Kr-KrNe-Ne and Ne-Kr.  Example: ​
  
 <​code>​ <​code>​
       &​LENNARD-JONES ! Lennard-Jones parameters for Ar-Ar interaction       &​LENNARD-JONES ! Lennard-Jones parameters for Ar-Ar interaction
-          atoms Ar Ar +          atoms Kr Kr 
-          EPSILON ​   [K_e] 119.8 +          EPSILON ​   [K_e] 164.56 
-          SIGMA [angstrom] ​ 3.401+          SIGMA [angstrom] ​ 3.601
           RCUT  [angstrom] ​ 25.0           RCUT  [angstrom] ​ 25.0
       &END LENNARD-JONES       &END LENNARD-JONES
-      &​LENNARD-JONES ! Lennard-Jones ​Xe-Xe parameters +      &​LENNARD-JONES ! Lennard-Jones ​Ne-Ne parameters 
-           ​atoms ​Xe Xe  +           ​atoms ​Ne Ne  
-           ​EPSILON ​   [K_e] 232  +           ​EPSILON ​   [K_e] 36.831 ​ 
-           SIGMA [angstrom]  ​3.98+           SIGMA [angstrom]  ​2.775
            ​RCUT ​ [angstrom] 25.0            ​RCUT ​ [angstrom] 25.0
        &​END LENNARD-JONES        &​END LENNARD-JONES
-      &​LENNARD-JONES ! Lennard-Jones parameters for Ar-Xe interaction +      &​LENNARD-JONES ! Lennard-Jones parameters for Kr-Ne interaction 
-          atoms Ar Xe+          atoms Kr Ne
           EPSILON ​   [K_e] YOUR EPSILON           EPSILON ​   [K_e] YOUR EPSILON
           SIGMA [angstrom] ​ YOUR SIGMA           SIGMA [angstrom] ​ YOUR SIGMA
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 <​code>​ <​code>​
          &​CHARGE          &​CHARGE
-          ATOM Xe+          ATOM Ne
           CHARGE 0.0           CHARGE 0.0
          &​END CHARGE          &​END CHARGE
          &​CHARGE          &​CHARGE
-          ATOM Ar+          ATOM Kr
           CHARGE 0.0           CHARGE 0.0
          &​END CHARGE          &​END CHARGE
exercises/2016_ethz_mmm/single_point_calculation.txt · Last modified: 2016/02/25 12:17 by sclelia