INELASTIC AND REACTIVE INELASTIC AND REACTIVE ELE-MENTARY PROCESSES IN ELE-MENTARY PROCESSES IN

ATOM- DIATOM, DIATOM-ATOM- DIATOM, DIATOM-DIATOM COLLISIONS AND DIATOM COLLISIONS AND

BEYONDBEYONDAntonio Laganà*

Dipartimento di Chimica

University of Perugia

lag@unipg.it

*Antonio Riganelli, Dimitris Skouteris, Leonardo Pacifici, Noelia Faginas Lago, Stefano Crocchianti

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MULTISCALE SIMULATIONS

Electronic structure

Kinetics of non elementary processes

Macroscopic properties of realistic systems

Fluid dynamics, electrodynamics, etc.

Nuclear dynamics

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SUMMARY

• A priori molecular simulations: theoretical means

• The N + N2 collisions: beyond quasiclassical

• The need for accurate potential energy surfaces• Some diatom-diatom, atom-polyatom processes• Towards complex molecular systems• Concurrent computing • Metalaboratories for molecular calculations• Grid enabled molecular simulators

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AC (f) + B (reactive)

A + B + C (dissociative)

The atom-diatom case

TRAJECTORY CALCULATIONS

The Hamilton equations

Integrate the above differential equations from a given configuration of the reactants until a final reactive, non reactive or dissociation configuration is reached

dRx/dt=PRx/µA,BC

drx/dt=Prx/µBC

dPRx/dt=-∂V/∂Rx

dPrx/dt=-∂V/∂rx dry/dt=Pry/µBC drz/dt=Prz/µBC

dRy/dt=PRy/µA,BC dRz/dt=PRz/µA,BC

dPry/dt=-∂V/∂ry dPrz/dt=-∂V/∂rz

dPRy/dt=-∂V/∂Ry

dPRz/dt=-∂V/∂Rz

A + BC (i) AB (f) + C (reactive)

A + BC (f) (non reactive)

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QUANTUM METHODS

Time dependent

Time independent

{W} – set of position vectors of the nuclei or any other choice of coordinatesHn - nuclear Hamiltonian

Factor out time and choose a different continuity va-riable (or transformation from reactants to products)

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THE DYNAMICAL QUANTITIES

• PROBABILITY: Pif=Nif/N or =|Sif|2

• CROSS SECTION: σif=πb2maxPif

• RATE COEFFICIENTS: averaging σif(E) over discrete distributions and integrating over continuous distributions

Reaction and Molecular Dynamics, Springer, 2000

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• N + N2 , H+H2, O+O2

• H2+OH, H2+H2, OH+HCl, OH+CO

• Cl + CH4

RECENT DYNAMICAL STUDIES

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Nitrogen atom Nitrogen molecule reaction

)',()(),()( 12

412

4 vNSNvNSN gg

Previous calculations: extended quasiclassical trajectory calculations of state to state rate coefficients (available for distribution)

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: exact quantum calculations

Zero total angular momentum

Time dependent approach in Jacobi coordinates

Initial quantum states v=0-5 j=0,1,2

Collision energy interval

Iterations: ~2000

LEPS surface

2NN

E=1.359-1.759 eV

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THE TIME DEPENDENT METHOD

Collocate the wavepacket

Time propagate the wavepacket

Carry out its analysis at the

product asymptote

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: state to state probabilities2NN

0.146 eV

0.433 eV

0.717 eV

0.997 eV

E(v)

V=0

V=1

V=2

V=3

1.270 eV

1.543eV

V=4

V=5

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: threshold energies2NN

1.359 eV

0.950 eV

0.772 eV

0.199 eV

Etr

V=0

V=1

V=2

V=4

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Product vibrational distributions (1.65 eV)

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Time dependent 3D

Time independent RIOS

2NN

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RIOS: state to state probabilities (v=0)

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RIOS vs 3D product vibrational distributions

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State specific probabilities. Effect of rotation

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FITTING A NEW POTENTIAL ENERGY SURFACE (PES)

• Fit the parameters of the PES to ab initio data • Adopt process coordinates instead of arrangement

coordinates (like Jacobi coordinates) • Use bond order (BO) variables defined as

nij=exp[-βij(rij-reij)]

and their polar version

ρ=[n122 + n23

2]½ α=atan(n23/n12)

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OH + HCl

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POLYATOMIC REACTION FUNCTIONAL FORMS

• ROtating BO (ROBO) and Largest Angle Generalization ROBO (LAGROBO).

• Many Process Expansion (MPE)

W=ξWξVξ

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MOVING TO LARGER SYSTEMS

• Simplify the interaction

• Decompose the domain

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THE FORCE FIELD

• The most popular formulations of force fields separate intra- from inter-molecular forces

• Intramolecular terms are associated to functional forms fitted to ab initio data

• Intermolecular are expressed as sums of two body semiempirical (usually of the Lennard Johnes type) functionals

Interaction representation

Many body expansion truncated to the second term Two body interactions are of the atom(ion) – atom(ion) type

Portability among different systems

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EnergyEnergy minimizationminimizationArArnnCC66HH66

Isomer (1|1)

Isomer (2|0)

-665C3v(2|0)2

-711D6h(1|1)2

-356C6v(1 0׀ )1

E(1/cm)GPIsomern

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OTHER NEW GLOBAL POTENTIALSOTHER NEW GLOBAL POTENTIALS1. Atom-bond pseudo two-body (Pirani et al.)

2. Full Bond Order potential (ALLBO) (Laganà et al.)

nkl is the Bond Order variable of the kl atomic pair

)exp( kle

klkl rrn

V ({r}) = ∑k∑mLkm(rkm,,αkm)

L = Lennard Johnes potential, k = atom index, m = bond index

P = Bond order potential, k = atom index, l = bond index

V ({r}) = ∑k∑lL kl (nkl)

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CONCURRENCY IN MOLECULAR CALCULATIONS

1. NATURAL CONCURRENCY

FROM EXTENSIVE TRAJECTORY CALCULATIONS

2. MULTILEVEL CONCURRENCY IN QUANTUM CALCULATIONS

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SISD (Single Instruction stream Single Data

stream)

CU PU MM

CU Control Unit

PU Processing Unit

MM Memory Module

IS DS

IS Instruction stream

DS Data stream

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SIMD (Master - workers)

CU

PU1

PU2

PUn

MM1

MM2

MMn

IS

DS1

DS2

DSn

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MIMD (Cooperative workers)

CU PU1

PU2

PUn

MM1

MM2

MMn

DS1

DS2

DSn

CU

CU

IS1

IS2

ISn

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MPI QUASICLASSICAL PSEUDOCODE

SEND “ready” status messageRECEIVE seedintegrate trajectoryupdate indicatorsSEND “ready” status messageGOTO RECEIVE

Worker:

DO traj_index =1, traj_number RECEIVE status message IF worker “ready” THEN generate seed SEND seed to worker ELSE GOTO RECEIVE endIF endDO

Master:

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COLLABORATIVE INITIATIVES TO DEVELOP REALISTIC A PRIORI

SIMULATORS

• Innovative approaches to chemical (as well as to physical, aerospace, medicinal, biological, etc.) problems need the cooperation of knowledge and computer resources.

• The concentration of human and hardware resources is no longer practical for logistic, economic and psycological reasons.

METACHEM

Metalaboratories for complex computational applications in

Chemistry

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THE METALABORATORY

• The METALABORATORY is a cluster of geographically distributed laboratories having complementary expertise and software programs and having some hardware resources grafted on a computing grid.

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THE STRUCTURE OF A METALABORATORY

• Several computational science laboratories acting as reservoirs of specific expertise relevant to the realization of a given project.

• One particularly skilled computer science laboratory (or Large Scale Computing Facility) acting as the regulator of the grid.

• Other laboratories having complementary expertises (for example an experimental laboratory).

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ONGOING MOLECULAR SCIENCE

METALABORATORIES• CI Calculations (Carsky).• DIRAC (Faegri).• SIMBEX (Gervasi)• Atmospheric processes (Aguilar)• Elchem (Laganà)• Chemical knowledge (Rossi)

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The CHEMISTRY community

Simbex

Murqm

Dirac

Elchem

Dysts

Comovit

Icab

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LABS per NATIONALITY (51)

1 Isr,Pl,Sk,Nl

2 Cz,Ch, Fr, Dk, A, Sw, No

3 Hu

4 Gr

5 E

6 D, Uk,

9 I

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SIMBEX: SIMUL. MOLECULAR BEAM

EXPERIMENTS • Managing an a priori

simulation to be inter- faced with the experi- ment in crossed mole- cular beam measure- ments

Exper. Simul.

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REQUEST: a potential fitted to beam experiments

Interaction

Observables

SUPPLY: the potential and related monitors

Dynamics

YES

NO Theoretical and experimental results agree?

The GEMS.0 demo application

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The INTERACTION module

INTERACTION

DYNAMICS

Is therea suitable Pes?

Are ab initiocalculationsavailable?

Are ab initiocalculations

feasible?

Ab initio applicationusing programs forelectronic structure

Application using fitting programs to

generate a PESroutine

Import thePES routine

NO

NO NO

YES YES YES

Force field-application taking

empirical data from

database to generate a PES

START

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The DYNAMICS module

DYNAMICS

OBSERVABLES

Are quantumdynamics

calculationsinappropriate?

Is the calculation

single initial state?

NO NO

YES YES

TI: application carrying out

time-independentquantum

calculations

TD: application carrying out time-

dependent quantumcalculations

ABCtraj: quasiclassical

trajectorycalculations

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The OBSERVABLES module

OBSERVABLESNO NO

YES YES

Is the observable

a state-to-stateobservable?

Is theobservable

a state specificobservable?

RATE: virtual monitor (VM)

for thermal ratecoefficients

CROSS: VM for statespecific cross sections,

rate constants and maps of

product intensity

DISTRIBUTIONS: VMfor scalar and vectorproduct distributions,

and state-to-state crosssections

Do calculated

and measuredproperties

agree?END

YES

INTERACTION

NO

Beam VM for Intensity in the

Lab frame

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The Virtual monitors

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THE PROTOTYPE COMPUTING GRID

• The computers that the participating laboratories will put outside the firewall to be clustered on the network and act as a single virtual parallel machine.

• The running version (not the ones under develop-ment) of the relevant codes that the participating laboratories will implement to run concurrently on the grid for the project.

• The distribution software to allocate the different tasks on the most suitable machines

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Demo deployment layout

• Sites

– GILDA testbed sites, in which INFN Grid 2.2.0 (fully compatible with LCG 2.2.0) middleware is installed.

• Key services

– Resource Broker: grid004.ct.infn.it– Computing Element: ce.grid.unipg.it– User Interface: ui.grid.unipg.it– GENIUS Portal: https://genius.ct.infn.it– CompChem VOMS

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The testbed sites• The Chemistry Department of the University of Perugia has been

included in the sponsor and the testbed site list • The Chemistry Department node is made by a cluster of 14 nodes (2

proc. Intel Pentium III, 2G RAM, 40G HD) + Computing Element + LCNGFG server

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Demo scale of usage• Number of jobs: 10 per day

• Storage: 100KB – 50GB depending on the type of computational engine used and the chemical system studied:

– Trajectory calculations: <100KB

– Time Dependent Quantum: 10GB

– Time Independent Quantum: 50GB

• RAM: 100KB – 2GB

– Trajectory calculations: <100K

– Time Dependent Quantum: 1GB

– Time Independent Quantum: 2GB

• Success rate: 98%

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EGEE

Grid

Usage of LCG-2 middleware services

GEMS

Application

Deployment

Server

Resource Broker

Computing Element

MPI

GEMS

programGEMS

programGEMS

programGEMS

programs

Working nodes

License Server

•Outbound connectivity

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The grid added value• SOFTWARE INTEGRATION INTO DISTRIBUTED

WORKFLOWS: assemble applications out of various (different or complementary) distributed competences coordinated via the grid.

• COMPUTATIONAL CAMPAIGNS: evaluate properties depending on the fate of few out of millions or more events by distributing the computations on the grid

• COLLABORATIVE ENGINEERING OF KNOWLEDGE:

handle (when is the case also in a privacy protecting fashion) chemical information and knowledge including training and production of new knowledge.

SIMBEX: a research/educational tool for the simulation of elementary chemical reaction

•High interactivity

•Advanced visualization

•In deep insight into the chemical mechansm

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GRID PROJECTS

• GRID.IT: the Italian project on grid platforms

• EGEE: the European production grid

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GRID.IT

INFN

ASI

CNIT

The Italian GRID

CNR

Università

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Programming Environment

High-level servicesHigh-level servicesKnowledge services, Data bases, Scientific libraries, Image processing, …Knowledge services, Data bases, Scientific libraries, Image processing, …

Domain-specific Problem Solving Environments (PSEs)

High-performance, Grid-aware component-based High-performance, Grid-aware component-based programming model and toolsprogramming model and tools

Resource management, Performance tools, Security, VO, …Resource management, Performance tools, Security, VO, …

Next Generation MiddlewareNext Generation Middleware

Basic infrastructure - standards (OGSA-compliant)

Software technology of Grid.it

Applications (Chemistry, Biology, Earth science, etc.)

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PG

MI

PD

BO

BA

NA

RM

ChemGrid.it: a Grid model for ChemistryComp. Center

UPV

UBCESCA

Comp. Center

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ChemGrid: the PG configuration

Access to GRID.IT

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• The VO CompChem has been created to register to the VO:http://grid-cnaf.infn.it/index.php?

voregister&type=1• The implementation of the Grid Molecular Simulator prototype has

prompted a modification of the EGEE infrastructure in order to guarantee the strong need for real-time interaction with the Grid

• The prototype will be rewritten in XML (instead of PHP) to be included in the Genius application testbed to demonstrate the power of the Grid.

• We attended the following EGEE events:– EGEE Generic Applications Advisory Panel (EGAAP), First Meeting,

Geneva, June 14th, 2004– EGEE NA4 Open Meeting, Catania, July 14-16, 2004

The outcomes of CompChem

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COLLABORATIONS INFORMATICS M. Vanneschi, R. Baraglia, Pisa (Italy) O. Gervasi, S. Tasso, Perugia (Italy) CHEMISTRY G.G. Balint-Kurti, Bristol (UK) E. Garcia, Vitoria (Spain) M. Alberti, Barcelona (Spain) G. Parker, Norman (USA) SIMBEX EU COST CHEMISTRY GROUP

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CONCLUSIONS

• Rigorous dynamical calculations are becoming routinely feasible for polyatomic systems

• Molecular dynamics treatments are tackling extremely complex systems

• Dynamical treatments are becoming essential part of multiscale approaches on the computing Grid

• Research must adopt a service oriented orgnization to become sustainable

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