We present a new code based on the Molecular Dynamics' Theory CP2K.

Downloading the code

What can be downloaded ?

The source of CP2K is open and freely available for everybody under the GPL license.

Installation instructions can be found on the wiki and in the INSTALL.md file which is part of the download.

The sparse matrix library DBCSR is part of CP2K, and made available standalone at the DBCSR page.

Available versions of CP2K

Development Version	Released Version
Most recent All new features Potentially unstable / buggy only available via Git	Older Stable, no ongoing development All major functionality in good shape Only rare backports of bug fixes (as time permits)

Looking at the version history might help you to decide.

How to download

From an official release

Sources of released versions are available at our GitHub project page. Alternatively, precompiled single node, optimised CP2K versions for Linux with or without OpenMP support are available as well.

From a Distribution

From a third party

Debian/Ubuntu alternative: http://packages.mccode.org/
Windows: https://github.com/brhr-iwao/CP2K_for_Windows

Git Access

The code in Git is under constant development. Check the Dashboard for current issues.

The Git (git) program must be installed on your machine for this to work.

Initial checkout

The latest and all prior versions are available from the CP2K GitHub repository.

To clone the current master:

git clone --recursive https://github.com/cp2k/cp2k.git cp2k

or to directly checkout a branch (check the CP2K GitHub project page for available branches):

git clone --recursive -b support/v6.1 https://github.com/cp2k/cp2k.git cp2k

Keeping your clone up-to-date (Git >= 2.14)

Set the following once on your CP2K Git clone. It will tell Git to automatically update included submodules as well and to always use rebase instead of merge.

Executing the code

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.
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.

Part I: Single Point (Energy) calculation

In this section a commented CP2K input example for a single point calculation is provided. Comments are added and signaled with '!'.

1. Step

Save the following input to a file named energy.inp

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
        &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

2. Step

Submit a CP2K calculation with the following commands:

bsub -n 1  mpirun cp2k.popt -i energy.inp -o energy.out

3. Step

Afterwards the file energy.out will look like this:

 **** **** ******  **  PROGRAM STARTED AT                2014-01-20 11:32:08.142
 ***** ** ***  *** **   PROGRAM STARTED ON                   some_server.ethz.ch
 **    ****   ******    PROGRAM STARTED BY                                   you
 ***** **    ** ** **   PROGRAM PROCESS ID                                 24183
 **** **  *******  **  PROGRAM STARTED IN                     /home/you/XERCISES

...
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 RAN ON                       some_server.ethz.ch
 **    ****   ******    PROGRAM RAN BY                                       you
 ***** **    ** ** **   PROGRAM PROCESS ID                                 24993
  **** **  *******  **  PROGRAM STOPPED IN                   /home/you/EXERCISES

If you get the closing Banner you know that cp2k worked. The following line tells you the result:

ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.):              0.003617048870059

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_{b} = 3.1668154 \cdot 10^{- 6} \frac{E_{H}}{K}

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.

The output file will be rewritten every time you run a calculation, unless you change its name.

To do so:

$ mv energy.out energy_dist4A.out

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.

For doing so:

$ cp energy.inp energy_dist2A.inp

then edit the input file with the new coordinates (e.g. 2 Å). you can now run CP2K and produce the output file:

$ cp2k.popt -i energy_dist2A.inp -o energy_dist2A.out

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.

3. Step

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.

         &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

4. Step

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 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.

σ_{i j} = \sqrt{σ_{i} σ_{j}}

ϵ_{i j} = \sqrt{ϵ_{i} ϵ_{j}}

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

The “ LENNARD-JONES ” section must be present for all the three possible couples: Kr-Kr, Ne-Ne and Ne-Kr. Example:

      &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

The “ CHARGE ” section must be also duplicated:

         &CHARGE
          ATOM Ne
          CHARGE 0.0
         &END CHARGE
         &CHARGE
          ATOM Kr
          CHARGE 0.0
         &END CHARGE

Questions

Sketch the LJ energy curve for the two set of parameters ( $σ$ and $ϵ$ ) provided.
Report, for both curves, the minimum energy distance and the depth of the minimum.
What are the major differences between the curves? How do they relate to the sets of parameters provided?

Reference: https://www.cp2k.org/exercises:2016_ethz_mmm:single_point_calculation

Since 18/01/2017

The Molecular Dynamics' Code CP2K

What can be downloaded ?

Available versions of CP2K

How to download

From an official release

From a Distribution

From a third party

Git Access

Initial checkout

Keeping your clone up-to-date (Git >= 2.14)

Computation of the Lennard Jones curve

Part I: Single Point (Energy) calculation

1. Step

2. Step

3. Step

Part II: Computation of the LJ energy curve

1. Step

2. Step

3. Step

4. Step

Questions

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Since 18/01/2017

The Molecular Dynamics' Code CP2K

What can be downloaded ?

Available versions of CP2K

How to download

From an official release

From a Distribution

From a third party

Git Access

Initial checkout

Keeping your clone up-to-date (Git >= 2.14)

Computation of the Lennard Jones curve

Part I: Single Point (Energy) calculation

1. Step

2. Step

3. Step

Part II: Computation of the LJ energy curve

1. Step

2. Step

3. Step

4. Step

Questions

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Post a Comment

0 Comments

Labels

Popular Posts

How to run CRYSTAL17

Modeling a metal-oxide interface (Crystal Code)

Introduction to calculations using Siesta code

ARTICLES

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