# Open SourceMolecular Dynamics

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exercises:2016_ethz_mmm:single_point_calculation

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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 12:02]sclelia Both sides previous revision Previous revision 2016/02/25 12:17 sclelia 2016/02/25 12:02 sclelia 2016/02/25 11:55 sclelia [Computation of the Lennard Jones curve] 2016/02/03 09:54 external edit 2016/02/25 12:17 sclelia 2016/02/25 12:02 sclelia 2016/02/25 11:55 sclelia [Computation of the Lennard Jones curve] 2016/02/03 09:54 external edit Last revision Both sides next revision Line 1: Line 1: ====== 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 ===== Line 27: Line 27: &​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 Line 52: Line 52: &​COORD ​               ​ &​COORD ​               ​ UNIT angstrom UNIT angstrom - ​Ar  0 0 0 + ​Kr  0 0 0 - ​Ar  3 0 0 + ​Kr  4 0 0 &END COORD &END COORD &​END SUBSYS &​END SUBSYS Line 75: Line 75: ... ... - 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 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 ''​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 $k_\text{b} = 3.1668154 \cdot 10^{-6} \frac{E_\text{H}}{\text{K}}$ . 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 ''​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. ​ Line 107: Line 111: To do so: To do so: <​code>​ <​code>​ - $mv energy.out ​energy_dist3A.out +$ mv energy.out ​energy_dist4A.out ​ Line 133: Line 137: | ...                  | ...    | ...        | | ...                  | ...    | ...        | - 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 Line 156: Line 160: === 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. \\ Line 163: Line 167: - 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 ​ - * The " LENNARD-JONES " section must be present for all the three possible couples: ​Ar-Ar, Xe-Xe and Xe-Ar.  Example: ​ + * The " LENNARD-JONES " section must be present for all the three possible couples: ​Kr-Kr, Ne-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 Line 193: Line 197: <​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 