A. Sozykin: Post-Processing the Results of Metastable States Molecular Dynamics Simulation

1. Post-processing the Results of
Metastable States Molecular
Dynamics Simulation
Brukhanov Vasilii, Krasnobaev Arsenii, Neustroeva
Natalia, Sozykin Andrey, Ushenin Konstantin
Ural-PDC 2016
Institute of Thermal Physics of UrB RAS, Yekaterinburg, Russia
Krasovskii Institute of Mathematics and Mechanics,
Yekaterinburg, Russia

2. Nucleation
Thermodynamic phase transition:
• Nucleation
• Collapse
Nucleation is widespread in both
nature and technological processes,
in which phase transitions occur
Nucleation types:
• Heterogeneous
• Homogeneous
2
Nucleation of carbon
dioxide bubbles
around a finger

3. Simulation Method
Molecular 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-Jones
Simulation software
• LAMMPS
3

4. LAMMPS
Molecular Dynamics Simulator
Open source code, GPL
The LAMMPS software is installed on the “URAN”
supercomputer
• GPU Support
LAMMPS does not support the methods of analysis of
metastable states, the calculation of the contact angle,
and tensor of pressure, and other
4

5. Example of Dump from LAMMPS
ITEM: 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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6. Homogeneous Nucleation
The gas mix of methane and
nitrogen
The model in the form of
cube with periodic boundary
conditions
The density is lowered by
stretch the cell and scaling of
coordinates of the particles
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7. Heterogeneous Nucleation
The liquid argon
Platinum surface
A gas bobble is formed near solid surface
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0 5 10 15 20 25 30 35 40
5
10
15
20
25
30
35
40
45 B
C
F1
F2
F3
B
A

8. Objectives
Postprocess the results of numerical experiments on MD
simulation made by LAMMPS
The 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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9. Algorithm
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10. Algorithm
a) 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 particles
c) Clustering:
• Unmarked cubes clustered by using the breadth-first search
algorithm
d) 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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11. Implementation
The algorithm was implemented using C++
Numerical experiments was carried out using specially prepared
test data for gas mixture
The 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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12. Implementation
Intel 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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13. Future Work
Accelerate the processing of data
with OpenMP and MPI
Calculate the contact angle
Calculate the tensor of pressure
Implement the programs as a plugin
to the LAMMPS
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0 5 10 15 20 25 30 35 40
5
10
15
20
25
30
35
40
45 F1
F2
F3
B
C
B
A

14. Thank you for your attention!