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Application of Gaussian package to chemical reaction studies. M. Sterzel 1 T. Szepieniec 1 , W. Piskorz 2 , F. Zawada 2 1 ACC CYFRONET AGH 2 Depatment of Chemistry, Jagiellonian University EGEE User Forum, Manchester 1 1 th May 2007. Outlook. Aim of this talk - PowerPoint PPT Presentation
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EGEE-II INFSO-RI-031688
Enabling Grids for E-sciencE
www.eu-egee.org
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Application of Gaussian package to chemical reaction studies
M. Sterzel1
T. Szepieniec1, W. Piskorz2, F. Zawada2
1ACC CYFRONET AGH2Depatment of Chemistry, Jagiellonian University
EGEE User Forum, Manchester 11th May 2007
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 2
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Outlook
• Aim of this talk– To demonstrate Grid application to chemical reaction studies
• Parts of the talk topics– Commercial Software on the Grid– Gaussian VO– Chemical reaction – basics– Sample calculations– Final Remarks
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 3
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Commercial Software
• Commercial Software – why bother about it?– Used by majority of scientists to conduct research– Faster implementation of new computational methods– Better user support– More frequent bug fixes
• Why Gausian?– Large number of computational methods implemented– One of the first ab-initio codes– The most popular among communities– User friendly– Available on many platforms along with GUI
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 4
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Gaussian VO
• Invented and operated by ACC CYFRONET• All license issues confirmed with Gaussian Inc,• Open for every EGEE user• Any compuing centre with proper Gaussian
license may support it (4 supporting centres, another 3 in the line)
• 20 users since the start in September 2006• VO manager – Mariusz Sterzel
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 5
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Gaussian VO – participation
As a user:• Register at:
https://voms.cyf-kr.edu.pl:8443/vo/gaussian/vomrs
• Accept Gaussian VO license requirements• Wait for VOMRS admin acceptance• voms-proxy-init --vo gaussian and you are ready to use the
program...
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 6
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Gaussian VO – participation
As a user:• Register at:
https://voms.cyf-kr.edu.pl:8443/vo/gaussian/vomrs
• Accept Gaussian VO license requirements• Wait for VOMRS admin acceptance• voms-proxy-init --vo gaussian and you are ready to use the
program...
As a participating centre:• Just sent an e-mail concerning participation to VO manager• After confirmation of the license status at your centre with
Gaussian Inc, detailed informations concerning set-up will be sent back to you
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 7
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Becaming a user
gaussian VO Registration
[-] gaussian Registration Home. Registration (Phase I). Groups and Group Roles. Institutions & Sites. Required Personal Info. Certificate Authorities
Registration (Phase I)
Welcome to the gaussian VO user registration phase I page.
All fields on this page are required. After submitting this form,a confirmation email will be sent within 24 hours with furtherinstructions. If you fail to follow the instructions within 10days, your registration will be discarded and you will have tore-register.
If you don't receive the confirmation email, please check youremail address in VOMRS and change it if necessary. If it wascorrect, contact the VO administrator .
Email address :
Grid job submission rights : fullfull
Personal Information
First name:
Last name:
Phone:
Submit Cancel
You are logged in as /C=XX/O=GRID/O=Important/CN=Jon Doe - Gaussian
C=XX/O=GRID/CN=Important Grid CA
on.doe important.domain
Jon
Doe
+00 00 123 4567
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 8
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Future work
• Web portal with a plug-in for Gaussian
• Parallel version of the code
• Integration with other chemical packages
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 9
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
H—CN CN—H
Chemical reactions
... a process that results interconversion of molecules
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 10
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Points of interest:– Structure of substrates and products– Structure of active complex at TS– Reaction path
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 11
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Points of interest:– Structure of substrates and products– Structure of active complex at TS– Reaction path(s)
Reactionpath
substrate(s) product(s)
Transition State (TS)
Energy
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 12
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Energy
substrate(s)product(s)
A+B C
DIntermediateproduct
TS1
TS2
E(TS1) > E(TS2)
Reactionpath
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 13
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Energy
Possible reaction paths;More intermediate products
Reaction path
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 14
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Main problem – TS determination
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 15
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Main problem – TS determination
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 16
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Main problem – TS determination
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 17
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Main problem – TS determination
E
‘reaction coordinate’
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 18
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
Main problem – TS determination
‘reaction coordinate’
E
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 19
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Chemical reactions
TS verification – vibrational analysis – one imaginary frequency!
i1203 cm-1
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 20
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Sample calculations
N2O braking on oxide surfaces – possible mechanisms
• Electron transfer
6. (O-)--X+--(O-) X + O2
1. N2O + X 2. N2O(s) + X X+--N2O-
4. X+--N2O- X+--(O-) + N25. (O-)--X+--(O-)
e- transfer
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 21
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Sample calculations
N2O braking on oxide surfaces – possible mechanisms
• An Oxygen transfer
1. N2O(g) N2O(s) 2. N2O(s) + X X--O--N2
4. O-X-O 5. O--O-X 6. X + O2
4. X-O
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 22
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Sample calculations
Vac
uu
m
Oxi
de
slab
Adsorbed N2O
Slab construction
Oxi
de
slab
Matrix generation
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 23
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Sample calculations
• Reaction paths:
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 24
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Sample calculations
• Reaction paths:
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 25
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Sample calculations
Computational details:– Gaussian 03 D.01– BP86 functional– Basis set of double-ζ quality
Timings:– CPU time for SP calculation – approx 7 hours– 15 paths – 10-50 energy points on each path– In total about 250 energy poits calcutated
Work still in progress...
Mariusz Sterzel EGEE User Forum Manchester May 11th 2007 26
Enabling Grids for E-sciencE
EGEE-II INFSO-RI-031688
Summary
• Chemical reaction studies require huge computational resources
• Data point on energy surfaces are collected separately
• With a little of work the whole process can be automated