molecular dynamics study of gas phase and gas surface reaction using md trajectory software complex l.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Molecular dynamics study of gas phase and gas-surface reaction using “MD Trajectory” software complex PowerPoint Presentation
Download Presentation
Molecular dynamics study of gas phase and gas-surface reaction using “MD Trajectory” software complex

Loading in 2 Seconds...

play fullscreen
1 / 55

Molecular dynamics study of gas phase and gas-surface reaction using “MD Trajectory” software complex - PowerPoint PPT Presentation


  • 199 Views
  • Uploaded on

Molecular dynamics study of gas phase and gas-surface reaction using “MD Trajectory” software complex. Michael Pogosbekian Valery Kovalev. Institute of Mechanics, M oscow S tate U niversity Dept. Mechanics and Mathematics, Moscow State University . MD Trajectory. Experimental DataBase.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Molecular dynamics study of gas phase and gas-surface reaction using “MD Trajectory” software complex' - glain


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
molecular dynamics study of gas phase and gas surface reaction using md trajectory software complex

Molecular dynamics study of gas phase and gas-surface reaction using “MD Trajectory” software complex

Michael Pogosbekian

Valery Kovalev

Institute of Mechanics, Moscow State University

Dept. Mechanics and Mathematics, Moscow State University

three levels of simulation

MD Trajectory

Experimental DataBase

Reaction rate :

Theoretical models

Three levels of simulation

AVOGADRO structure

Equilibrium chemical kinetics

One-temperature approach

Non-equilibrium chemical kinetics

Two-temperature approach

Computarized handbook

Models’ catalogue

Level chemical kinetics

“MD Trajectory”

where

– translational and vibrational temperatures

– vibrational states of reagents and products

two typical cases of the nonequilibrium conditions

MD Trajectory

Two typical cases of the nonequilibrium conditions

Boeing winged version of the Orbital Space Plane during reentry (T >> Tv)

Gas discharge (T << Tv)

software complex md trajectory

MD Trajectory

vibrational relaxation

exchange reaction

partial dissociation

full dissociation

Software complex “MD Trajectory”

Triatomic collisions

vibrational relaxation

exchange reaction

dissociation

where XY Î{AB, AC} and P - residual atom

Tetratomic collisions

where XY and WZ - diatomic molecule Ï{AB, CD}, MN - any diatomic molecule and P,Q - residual atoms

collision of a atom with bc molecule

classical trajectory method

Collision of A atom with BC molecule

Jacobi coordinate

relative B-C motion

relative A-BC motion

ABC motion as whole

where

slide6

classical trajectory method

Collision of A atom with BC molecule

Motion equations

where

numerical integration scheme of motion equations

MD Trajectory

Numerical integration scheme of motion equations

Kutta-Merson method

forth order approximation

automatic selection of integration step

(reduce calculation time for 10-30%)

error > max :

error < min :

max error min :

 =  / 2

 = 1.5 

 = 

r andom number generator uniformly distributed in 0 1

MD Trajectory

Main generator

Secondary generator

M.D. MacLaren – G.Marsaglia method

Random number generator uniformly distributed in (0,1)
results of trajectory calculations11

classical trajectory method

Level rate constants

Two-temperature rate constant

Results of trajectory calculations
potential energy surface

PES

Potential energy surface

Semiempirical methods

Generalized LEPS model

Method of diatomic complexes in molecules

Bond energy- bond order method

Ab-initio calculations

GAUSSIAN

MOLCAS

GAMESS (special version for INTEL platform - PC GAMESS)

generalized leps model

MD Trajectory

Generalized LEPS model

- dissociation energy

- Morse parameter

- equilibrium distance

- adjusted Sato parameter

analytical representation of pes

MD Trajectory

Analytical representation of PES

Many-body expansion method

One-particle term

– define the energy of

electronically excited atom

Two-particles term

– describe the potential curve of

diatomic molecule

Three-particles term

– define the interaction

at close internuclear distances

sorbie murrell function

MD Trajectory

Two-particles term

Three-particles term

Sorbie-Murrell function

– extended Rydberg function

where

– displacement from equilibrium distance

where

– bond number

– switching function

garcia lagana bond order function

MD Trajectory

Two-particles term

Three-particles term

Garcia-Lagana (bond-order) function

– polynomial of N-th order

where

– bond order coordinate

– polynomial of M-th order

where

aguado paniagua function

MD Trajectory

Two-particles term

Three-particles term

Aguado-Paniagua function

where

l = 2 or 3 for two- or three-particles term

– polynomial of M-th order

where

f eatures of software complex

MD Trajectory

Wide set of PES analytical functions

State-to-state rate constants

v, w - vibrational levels of reagent and product

Angle distribution of reaction products

Distribution products by vibrational and rotational numbers

Object oriented C++ code

XML – style for input & output data (LibXML library)

Save coordinate and pulses along of trajectory for subsequent demonstration purposes

Optimization of trajectory code for usage of cluster technologies based on MPI (Message Passing Interface)

Features of software complex
slide19

MD Trajectory

High performance supercomputer facilities

Moscow State University, cluster SCI - 36 CPUs total

Node configuration: Dual Pentium III/500MHz, 1Gb RAM, 3.2 Gb HDD

Network environment : SCI + Fast Ethernet

Russian Academy of Sciences, cluster MVS-1000M - 768 CPUs total

Node configuration: Dual Alpha 21264A/667MHz, 1Gb RAM, 15 Gb HDD

Network environment : Myrinet (2 Gb/s) + Fast Ethernet

parallel version of md trajectory

MD Trajectory

Module of

results visualization

Module of

task definition

Module of

data allocation

Module of

results processing

Trajectories calculation

module #1

Trajectories calculation

module #N

Data access layer

XML – files (LibXML2 library) PES, Tasks, Results

SQL Server (MySQL is planned)

Parallel version of “MD Trajectory”

Service layer - 1 muster process

Calculation layer - N slave processes

data access layer

MD Trajectory

WWW . XMLSOFT . ORG

Data Access Layer

Three kinds of input & output files

Input data – fixed size – rather simple structure – less than 1 Mb

Control Groupdescribes control function;

Molecule Groupcontains spectroscopic characteristic of diatomic molecules

PES Groupdescribes PES of the investigated system

Log file – dynamic size – rather simple structure – less than 10 Mb

Auxiliary information which can be required for calculation control and calculation continuation at the next time

Result file – dynamic size – very complex structure – up to 100 Mb

Two ways for realization of Data Access Layer

XML files. It is realized due to LibXML2 library

XML parser and toolkit of Gnome

DataBase connectivity module for MySQL Server is planned

slide22

MD Trajectory

MSU cluster

slide23

MD Trajectory

MSU cluster

slide24

CO + N  CN + O

Leading reaction in CN formation behind the shock wave front

in Martian atmosphere

A single experimental work for "short" temperature range

Absence of data at high temperatures

Experiment, L.B. Ibragimova

potential energy surface25

CO + N  CN + O

Potential energy surface

PES for

Modified LEPS model [1]

Sorbie-Murrell function [3]

based on ab-initio data [2,4]

Aguado-Paniagua function [4]

PES for

Generalized LEPS model [1]

References

1. K.J.Schmatjko and J.Wolfrum, Ber. Bunsen Phys. Chem., 1975, 79, pp.696-707

2. P.Halvick, J.C.Rayez, E.M.Evleth, J. Chem. Phys., 1984, 81, pp.728-737

3. SM.Simonson, N.Markovic, S.Nordholm and B.J.Persson, Chem. Phys., 1995, 200, pp.141-160

4. Andersson, N.Markovic and G.Nyman, Phys. Chem. Chem. Phys., 2000, 2, pp.613-620

slide28

CO + N  CN + O

Reaction cross-sections for CO(v,j)

slide31

CO + N  CN + O

Two-temperature rate constants

slide32

CO + N  CN + O

Nonequilibrium factor

slide33

CO + N  CN + O

Level rate constants

theoretical models for exchange reactions

MD Trajectory

Theoretical models for exchange reactions

 - model

Generalized Marrone-Treanor model (CVCV)

Theoretically informational model

slide39

MD Trajectory

Recombination processes

Eley-Rideal

Langmuir-Hinshelwood

Further development of “MD Trajectory”

Investigation of Gas-Surfaceprocesses

Design of thermal protection systems in space vehicles

Microelectronics applications

Heterogenous combustion

Main objectives

Recombination coefficient

Accomodation coefficient of chemical energy

Cite-specific effects and influence of top-layer surface structure

classical molecular dynamics

MD Trajectory

Classical molecular dynamics

Atoms are divided in two groups:

1. i = 1, … n (gas-phase atoms)

2. k = 1, … N (lattice atoms)

Total hamiltonian is:

The hamiltonian equations of motion are:

definition of initial conditions41

MD Trajectory

Collision scheme

Definition of initial conditions

Assumptions

flat surface

instead rough one

monocrystal

instead polycrystal

clear surface without adsorbed layer

Detailed description of classical molecular dynamics is represented in: Gert D. Billing Dynamics of Molecular Surface Interactions. New York, John Wiley&Sons, 2000, chapter 6, pp.93-102

definition of initial conditions42

MD Trajectory

Definition of initial conditions

For incident gas atom B:

where

- randomly distributed on the surface

For adsorbed gas atom A:

- randomly distributed on the surface

- the same as for atom B, where

For lattice atoms:

where

- equilibrium position

- surface temperature

- force constant for atom k

- phase angle, randomly distributed in

pes for b cristobalite

Oad + Ogas  O2

where

- separation distance,

- formal ionic charge, b – constant,

- adjustable parameters,

- number of valence shell electrons,

PES for b-cristobalite

B.P.Feuston, S.H.Garofalini Empirical three-body potential for vitreous silica. Journal of Chemical Physics, Vol. 89, No. 9, 1988. pp. 5818-5824

Modified form of the Born-Mayer-Huggins (BMH) potential:

where

for (

and

);

in other case.

where

- constants,

- angle subtended by

and

unit cell of b cristobalite lattice

Oad + Ogas  O2

Unit cell of b – cristobalite lattice

Ralph W.G. Wyckoff The crystal structure of the high temperature form of cristobalite (SiO2), American Journal of Science, Ser.5, Vol.9, 1925, pp.448-459

top layer structure of the b cristobalite surface

Oad + Ogas  O2

Top layer structure of the b – cristobalite surface

M.Cacciatore, M.Rutigliano, G.D.Billing Eley-Rideal and Lengmuir-Hinshelwod Recombination Coefficients for Oxygen on Silica Surfaces, Journal of Thermophysics and Heat Transfers, Vol. 13, No. 2, 1999, pp.195-203.

comparison of md calculations results for sio2

Oad + Ogas  O2

Comparison of MD calculations results for SiO2

Chemical energy accomodation coefficient in the Eley-Rideal recombination

md calculations results for sio2 surface

Oad + Ogas  O2

MD calculations results for SiO2 surface

Vibrational distribution of the formed O2 molecules in the Eley-Rideal reaction

md calculations results for sio2 surface49

Oad + Ogas  O2

MD calculations results for SiO2 surface

Vibrational distribution of the formed O2 molecules in the Eley-Rideal reaction

comparison of md calculation s results

Oad + Ogas  O2

Comparison of MD calculations results

Eley-Rideal recombination probability

comparison of md calculations results

Oad + Ogas  O2

Comparison of MD calculations results

Chemical energy accomodation coefficient in the Eley-Rideal recombination

md calculations results for sic surface

Oad + Ogas  O2

MD calculations results for SiC surface

Vibrational distribution of the formed O2 molecules in the Eley-Rideal reaction

md calculations results for sic surface54

Oad + Ogas  O2

MD calculations results for SiC surface

Vibrational distribution of the formed O2 molecules in the Eley-Rideal reaction