exercises:2017_ethz_mmm:single_point_calculation
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— | exercises:2017_ethz_mmm:single_point_calculation [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== 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 '' | ||
+ | |||
+ | <code - energy.inp> | ||
+ | & | ||
+ | | ||
+ | &END GLOBAL | ||
+ | & | ||
+ | METHOD FIST ! Molecular Mechanics method | ||
+ | & | ||
+ | & | ||
+ | &SPLINE | ||
+ | EMAX_SPLINE 10000 ! numeric parameter to ensure calculation stability. Should not be changed | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | atoms Kr Kr | ||
+ | EPSILON | ||
+ | SIGMA [angstrom] | ||
+ | RCUT [angstrom] | ||
+ | &END LENNARD-JONES | ||
+ | &END NONBONDED | ||
+ | &CHARGE | ||
+ | ATOM Kr | ||
+ | CHARGE 0.0 | ||
+ | &END CHARGE | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | | ||
+ | &EWALD | ||
+ | EWALD_TYPE none | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | & | ||
+ | &CELL | ||
+ | ABC [angstrom] 10 10 10 | ||
+ | | ||
+ | &END CELL | ||
+ | & | ||
+ | UNIT angstrom | ||
+ | Kr 0 0 0 | ||
+ | Kr 4 0 0 | ||
+ | &END COORD | ||
+ | & | ||
+ | &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: | ||
+ | < | ||
+ | **** **** ****** | ||
+ | ***** ** *** *** ** | ||
+ | | ||
+ | ***** ** ** ** ** | ||
+ | **** ** ******* | ||
+ | |||
+ | ... | ||
+ | some stufff | ||
+ | ... | ||
+ | |||
+ | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): | ||
+ | ... | ||
+ | some other stuff | ||
+ | ... | ||
+ | **** **** ****** | ||
+ | ***** ** *** *** ** | ||
+ | | ||
+ | ***** ** ** ** ** | ||
+ | **** ** ******* | ||
+ | </ | ||
+ | |||
+ | 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.): | ||
+ | </ | ||
+ | |||
+ | 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 '' | ||
+ | |||
+ | ===== 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 '' | ||
+ | |||
+ | <note important> | ||
+ | The output file will be rewritten every time you run a calculation, | ||
+ | </ | ||
+ | |||
+ | To do so: | ||
+ | < | ||
+ | $ mv energy.out energy_dist4A.out | ||
+ | </ | ||
+ | |||
+ | <note tip> | ||
+ | If you run multiple calculations, | ||
+ | </ | ||
+ | |||
+ | 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 | ||
+ | | energy_dist1A.inp | ||
+ | | energy_dist2A.inp | ||
+ | | energy_dist3A.inp | ||
+ | | ... | ... | ... | | ||
+ | |||
+ | 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. | ||
+ | |||
+ | < | ||
+ | & | ||
+ | & | ||
+ | atoms Ne Ne | ||
+ | | ||
+ | SIGMA [angstrom] | ||
+ | | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | & | ||
+ | ATOM Ne | ||
+ | CHARGE 0.0 | ||
+ | & | ||
+ | </ | ||
+ | |||
+ | === 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 " | ||
+ | |||
+ | $$ \sigma_{ij}= \sqrt{\sigma_i\sigma_j}$$ \\ | ||
+ | $$ \epsilon_{ij}= \sqrt{\epsilon_i\epsilon_j}$$ | ||
+ | |||
+ | <note tip> | ||
+ | Remember that you are running | ||
+ | </ | ||
+ | |||
+ | * The " LENNARD-JONES " section must be present for all the three possible couples: Kr-Kr, Ne-Ne and Ne-Kr. | ||
+ | |||
+ | < | ||
+ | & | ||
+ | atoms Kr Kr | ||
+ | EPSILON | ||
+ | SIGMA [angstrom] | ||
+ | RCUT [angstrom] | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Ne Ne | ||
+ | | ||
+ | SIGMA [angstrom] | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | atoms Kr Ne | ||
+ | EPSILON | ||
+ | SIGMA [angstrom] | ||
+ | RCUT [angstrom] | ||
+ | &END LENNARD-JONES | ||
+ | </ | ||
+ | |||
+ | * The " CHARGE " section must be also duplicated: | ||
+ | |||
+ | < | ||
+ | & | ||
+ | ATOM Ne | ||
+ | CHARGE 0.0 | ||
+ | & | ||
+ | & | ||
+ | ATOM Kr | ||
+ | CHARGE 0.0 | ||
+ | & | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== Questions ===== | ||
+ | * Sketch the LJ energy curve for the two set of parameters ($\sigma$ and $\epsilon$) 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? | ||