Open SourceMolecular Dynamics

Site Tools

exercises:2019_uzh_acpc2:ex01

Differences

This shows you the differences between two versions of the page.

 exercises:2019_uzh_acpc2:ex01 [2019/04/17 08:29]jglan [Background] exercises:2019_uzh_acpc2:ex01 [2019/05/02 07:34]jglan Both sides previous revision Previous revision 2019/05/02 07:34 jglan 2019/04/18 07:22 jglan 2019/04/17 08:30 jglan [Background] 2019/04/17 08:29 jglan [Background] 2019/04/17 08:27 jglan [Lennard-Jones liquids] 2019/04/09 09:12 jglan created Next revision Previous revision 2019/05/02 07:34 jglan 2019/04/18 07:22 jglan 2019/04/17 08:30 jglan [Background] 2019/04/17 08:29 jglan [Background] 2019/04/17 08:27 jglan [Lennard-Jones liquids] 2019/04/09 09:12 jglan created Line 14: Line 14: ====== Background ====== ====== Background ====== - You are expected to carry out an MD simulation of Lennard-Jones fluid containing mono-atomic + You are expected to carry out an MD simulation of Lennard-Jones ​(L-J) fluid containing mono-atomic particles. The [[https://​en.wikipedia.org/​wiki/​Lennard-Jones_potential | L-J potential ]] energy expression used is particles. The [[https://​en.wikipedia.org/​wiki/​Lennard-Jones_potential | L-J potential ]] energy expression used is Line 23: Line 23: distance between atoms i and j. distance between atoms i and j. - [[https://​en.wikipedia.org/​wiki/​Periodic_boundary_conditions|Periodic boundary conditions]] should be used in this simulation. The atom near the ”edge” of the simulation box interacts with atoms contained in the neighboring image of the box. In computer simulations,​ one of these is the original simulation box, and others are copies called images. During the simulation, only the properties of the original simulation box need to be recorded and propagated. The minimum-image convention is a common form of PBC particle bookkeeping in which each individual particle in the simulation interacts with the closest image of the remaining particles in the system. To prevent artifacts, it requires a cut-off value of rij for the L-J potential. For realistic results, the cut-off should be less than the half of the simulation box size and over σ Radial distribution + [[https://​en.wikipedia.org/​wiki/​Periodic_boundary_conditions|Periodic boundary conditions ​(PBC)]] should be used in this simulation. The atom near the ”edge” of the simulation box interacts with atoms contained in the neighboring image of the box. In computer simulations,​ one of these is the original simulation box, and others are copies called images. During the simulation, only the properties of the original simulation box need to be recorded and propagated. The minimum-image convention is a common form of PBC particle bookkeeping in which each individual particle in the simulation interacts with the closest image of the remaining particles in the system. To prevent artifacts, it requires a cut-off value of rij for the L-J potential. For realistic results, the cut-off should be less than the half of the simulation box size and over σ Radial distribution function, (or pair correlation function) $g(r)$ in a system of particles (atoms, molecules, colloids, function, (or pair correlation function) $g(r)$ in a system of particles (atoms, molecules, colloids, etc.), describes how density varies as a function of distance from a reference particle. etc.), describes how density varies as a function of distance from a reference particle. Line 216: Line 216: <​code>​ <​code>​ - $cp2k.sopt -i argon.inp -o argon.out ​ +$ cp2k.popt -i argon.inp -o argon.out ​ ​ Line 498: Line 498: TIMECON 1000 TIMECON 1000 &END NOSE &END NOSE + &END THERMOSTAT &​END MD &​END MD