exercises:2016_ethz_mmm:single_point_calculation
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exercises:2016_ethz_mmm:single_point_calculation [2016/02/25 11:55] – [Computation of the Lennard Jones curve] sclelia | exercises:2016_ethz_mmm:single_point_calculation [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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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 |
- | 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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& | & | ||
& | & | ||
- | atoms Ar Ar | + | atoms Kr Kr |
- | EPSILON | + | EPSILON |
- | SIGMA [angstrom] | + | SIGMA [angstrom] |
RCUT [angstrom] | RCUT [angstrom] | ||
&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 | ||
Line 52: | Line 52: | ||
& | & | ||
UNIT angstrom | UNIT angstrom | ||
- | | + | |
- | | + | |
&END COORD | &END COORD | ||
& | & | ||
Line 60: | Line 60: | ||
=== 2. Step === | === 2. Step === | ||
- | Run CP2K with the following | + | Submit a CP2K calculation |
< | < | ||
- | $ cp2k.popt -i energy.inp -o energy.out | + | bsub -n 1 mpirun |
</ | </ | ||
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... | ... | ||
- | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): | + | some stufff |
... | ... | ||
+ | ENERGY| Total FORCE_EVAL ( FIST ) energy (a.u.): | ||
+ | ... | ||
+ | some other stuff | ||
+ | ... | ||
**** **** ****** | **** **** ****** | ||
***** ** *** *** ** | ***** ** *** *** ** | ||
Line 90: | Line 94: | ||
</ | </ | ||
- | 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 '' | Note, that in the input-file '' | ||
Line 99: | Line 103: | ||
=== 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 '' | + | 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> | <note important> | ||
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To do so: | To do so: | ||
< | < | ||
- | $ mv energy.out | + | $ mv energy.out |
</ | </ | ||
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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. |
< | < | ||
& | & | ||
- | & | + | & |
- | | + | |
- | | + | |
- | SIGMA [angstrom] | + | SIGMA [angstrom] |
| | ||
&END LENNARD-JONES | &END LENNARD-JONES | ||
& | & | ||
& | & | ||
- | ATOM Xe | + | ATOM Ne |
CHARGE 0.0 | CHARGE 0.0 | ||
& | & | ||
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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 | + | Once generated the ε and σ parameters for the couple |
Compare the " | Compare the " | ||
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<note tip> | <note tip> | ||
- | Remember that you are running | + | Remember that you are running |
</ | </ | ||
- | * The " LENNARD-JONES " section must be present for all the three possible couples: | + | * The " LENNARD-JONES " section must be present for all the three possible couples: |
< | < | ||
& | & | ||
- | atoms Ar Ar | + | atoms Kr Kr |
- | EPSILON | + | EPSILON |
- | SIGMA [angstrom] | + | SIGMA [angstrom] |
RCUT [angstrom] | RCUT [angstrom] | ||
&END LENNARD-JONES | &END LENNARD-JONES | ||
- | & | + | & |
- | | + | |
- | | + | |
- | SIGMA [angstrom] | + | SIGMA [angstrom] |
| | ||
& | & | ||
- | & | + | & |
- | atoms Ar Xe | + | atoms Kr Ne |
EPSILON | EPSILON | ||
SIGMA [angstrom] | SIGMA [angstrom] | ||
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< | < | ||
& | & | ||
- | ATOM Xe | + | ATOM Ne |
CHARGE 0.0 | CHARGE 0.0 | ||
& | & | ||
& | & | ||
- | ATOM Ar | + | ATOM Kr |
CHARGE 0.0 | CHARGE 0.0 | ||
& | & |
exercises/2016_ethz_mmm/single_point_calculation.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1