Post-Processing the Results of Metastable States Molecular Dynamics Simulation

Post-processing the Results of Metastable States Molecular

Dynamics SimulationBrukhanov Vasilii, Krasnobaev Arsenii, Neustroeva

Natalia, Sozykin Andrey, Ushenin Konstantin

Ural-PDC 2016

Institute of Thermal Physics of UrB RAS, Yekaterinburg, RussiaKrasovskii Institute of Mathematics and Mechanics,

Yekaterinburg, Russia

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NucleationThermodynamic phase transition:• Nucleation• CollapseNucleation is widespread in both nature and technological processes, in which phase transitions occurNucleation types:• Heterogeneous• Homogeneous Nucleation of carbon

dioxide bubbles around a finger

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Simulation MethodMolecular dynamics (MD) simulations

• Allows to determine the change of coordinates of particles and their velocities in time

• Allows to determine various physical quantities, for example, temperature, pressure, etc.

Model of interaction between nonpolar molecules

• A potential of Lennard-JonesSimulation software

• LAMMPS

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LAMMPSMolecular Dynamics SimulatorOpen source code, GPLThe LAMMPS software is installed on the “URAN” supercomputer

• GPU SupportLAMMPS does not support the methods of analysis of metastable states, the calculation of the contact angle, and tensor of pressure, and other

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Example of Dump from LAMMPSITEM: ATOMS id type x y z c_ca 31127 1 2.33568 3.57123 6.70623 1.73666 56470 1 1.24006 3.57133 6.00946 1.56173 62858 1 2.32967 3.11241 5.77479 1.86667 111855 1 2.92656 2.74577 4.95696 1.86967 49955 1 1.79124 2.51865 4.93426 1.61828 48568 1 2.33431 1.67614 5.04784 1.12719 30615 1 2.92933 2.95744 7.39322 2.41488 104830 1 2.18763 2.11816 6.03591 1.14954 31146 1 1.22668 1.25918 7.63858 1.66225 75567 1 3.26946 1.74535 5.53318 1.30432 32009 1 1.9777 3.76021 4.93877 1.16815 123176 1 0.759058 1.31996 4.86576 1.38175 75767 1 3.04665 1.81611 7.72417 2.01346

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Homogeneous NucleationThe gas mix of methane and nitrogenThe model in the form of cube with periodic boundary conditionsThe density is lowered by stretch the cell and scaling of coordinates of the particles

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Heterogeneous Nucleation The liquid argonPlatinum surfaceA gas bobble is formed near solid surface

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ObjectivesPostprocess the results of numerical experiments on MD simulation made by LAMMPSThe gas mixture in cells with periodic boundaries

• Find empty cluster with maximum radius• Evaluate parameters of the cluster:

• volume• coordinates of mass center• particles density distribution

Liquid argon between surface of solid frame• Compute the contact angle• Compute the tensor of pressure

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Algorithm

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Algorithma) Discretization space:

• The model space is divided into equal cells, which are cubes with sides parallel to the model sides

b) Shading:• Shading all the cubes, which centers are less than the distance Rnearest

from the particlesc) Clustering:

• Unmarked cubes clustered by using the breadth-first search algorithmd) Finding the cluster center :

• Are defined the most extreme cells for this clusters in all three dimensions and calculates the center of the cluster

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ImplementationThe algorithm was implemented using C++Numerical experiments was carried out using specially prepared test data for gas mixtureThe speed on a single core of Intel Xeon X5675 processor was 440 seconds

• 1 frame• 1M particles• 300 cubes of partition per particle

• It is enough for practical use of the program with the frame number of 100–200

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ImplementationIntel VTune Amplifier investigation

• 94% - shading • 2% - clustering using the breadth-first search • 1% - other tasks (discretization, cluster center finding,

input/output, etc.)

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Future WorkAccelerate the processing of data with OpenMP and MPICalculate the contact angleCalculate the tensor of pressureImplement the programs as a plugin to the LAMMPS

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Thank you for your attention!