Piattaforme Abilitanti per Griglie Computazionali a Elevate Prestazioni Orientate a Organizzazioni Virtuali Scalabili

Coordinatore scientifico: Prof. Marco Vanneschi

Macro obiettivo Macro obiettivo

Crescita competitiva sostenibileCrescita competitiva sostenibile

Programma strategico Programma strategico

Tecnologie abilitanti per la societa della Tecnologie abilitanti per la societa della conoscenzaconoscenza

Proposta progettuale attinente Proposta progettuale attinente

Reti e netputingReti e netputing

UR2 CNR - ISTM ---- WP13Sezione di Perugia c/o Dipartimento di Chimica, Via Elce di Sotto, 8 – 06123 Perugia

EPREPR

Istituto di Scienze e Tecnologie Istituto di Scienze e Tecnologie Molecolari (ISTM) – Sede di Milano, Molecolari (ISTM) – Sede di Milano, Sezioni di Padova e PerugiaSezioni di Padova e Perugia

Istituto di Metodologie Inorganiche e Istituto di Metodologie Inorganiche e dei Plasmi (IMIP) – Sede di dei Plasmi (IMIP) – Sede di Montelibretti, Sezione di BariMontelibretti, Sezione di Bari

Unità di Progetto “Calcolo e Reti ad Unità di Progetto “Calcolo e Reti ad Alte Prestazioni (HPCN)” dell’Ente per Alte Prestazioni (HPCN)” dell’Ente per le Nuove tecnologie, l’Energia e le Nuove tecnologie, l’Energia e l’Ambiente (ENEA)l’Ambiente (ENEA)

Dipartimenti universitariDipartimenti universitari

Dipartimento di Chimica, Università di Dipartimento di Chimica, Università di BariBariDipartimento di Chimica Fisica e Dipartimento di Chimica Fisica e Inorganica, Università di BolognaInorganica, Università di BolognaDipartimento di Chimica, Università di Dipartimento di Chimica, Università di Napoli “Federico II”Napoli “Federico II”Dipartimento di Chimica Inorganica, Dipartimento di Chimica Inorganica, Metallorganica ed Analitica, Università Metallorganica ed Analitica, Università di Padovadi PadovaDipartimento di Chimica, Università di Dipartimento di Chimica, Università di PerugiaPerugiaDipartimento di Ingegneria Civile ed Dipartimento di Ingegneria Civile ed Ambientale, Università di PerugiaAmbientale, Università di PerugiaDipartimento di Matematica ed Dipartimento di Matematica ed Informatica, Università di PerugiaInformatica, Università di Perugia

Progetto PQE2000

Grid Computing: tecnologie abilitanti e applicazioni Grid Computing: tecnologie abilitanti e applicazioni per eScienceper eScience

(MURST – Impiego del Fondo Speciale per lo Sviluppo della Ricerca (MURST – Impiego del Fondo Speciale per lo Sviluppo della Ricerca di Interesse Strategico – Tema: Società dell’Informazione)di Interesse Strategico – Tema: Società dell’Informazione)

ENACTS (European Network for Advanced Computing Technology for Science)

ENACTS partners

http://www.epcc.ac.uk/enacts

Grid in Computational Chemistry

The Grid environment represents a very promising The Grid environment represents a very promising computing resource for Computational Chemistrycomputing resource for Computational Chemistry

One of the most important Computational Chemistry One of the most important Computational Chemistry application is the use of Molecular Dynamics application is the use of Molecular Dynamics simulations for modelling natural phenomenasimulations for modelling natural phenomena

This application covers a wide range of systems This application covers a wide range of systems from simple (accurate interactions) to large from simple (accurate interactions) to large (approximate interactions) ones(approximate interactions) ones

The Grid allows to adapt on it the inner complexity The Grid allows to adapt on it the inner complexity of the various approaches adoptedof the various approaches adopted

Present state of the software of the project

The project software is articulated in three blocks of The project software is articulated in three blocks of programs suites: INTERACTION, DYNAMICS, programs suites: INTERACTION, DYNAMICS, OBSERVABLESOBSERVABLES

INTERACTION: ab initio calculations of the electronic INTERACTION: ab initio calculations of the electronic energy values (various packages for which the partner energy values (various packages for which the partner laboratories are often coauthors)laboratories are often coauthors)

DYNAMICS: dynamical calculations performed by DYNAMICS: dynamical calculations performed by integrating the equations of the nuclear motion (classical, integrating the equations of the nuclear motion (classical, quasiclassical or quantum mechanics approaches)quasiclassical or quantum mechanics approaches)

OBSERVABLES: evaluation of the macroscopic properties OBSERVABLES: evaluation of the macroscopic properties by manipulating the scattering matrix S and/or the by manipulating the scattering matrix S and/or the probability matrix P calculated in the DYNAMICS blockprobability matrix P calculated in the DYNAMICS block

Activity 1:The hardware and software inventory

Choice of the molecular virtual reality case Choice of the molecular virtual reality case studies studies

Write up of an inventory of the necessary Write up of an inventory of the necessary know how, of the programs to be know how, of the programs to be implemented, of the hardware to be grafted implemented, of the hardware to be grafted on the grid and of the available networking on the grid and of the available networking toolstools

Activity 2:The design of the grid cooperation model

Implementation of the basic elements of the collaborative Implementation of the basic elements of the collaborative work that a successful grid computing implieswork that a successful grid computing implies

Revision of the suites of computer codes used and declared Revision of the suites of computer codes used and declared available for the grid projectavailable for the grid project

Status of commercial software: modifications or Status of commercial software: modifications or extensions may require to be regulated at license levelextensions may require to be regulated at license level

These softwares may require to be implemented on These softwares may require to be implemented on machines on which they have never been implemented machines on which they have never been implemented

beforebefore

Activity 3:The structuring of the computing grid

Implementation of the computing grid for the Implementation of the computing grid for the virtual reality case studiesvirtual reality case studies

The networking of the cluster of machines The networking of the cluster of machines dedicated to the grid experiment will be dedicated to the grid experiment will be implementedimplemented

Basic metacomputing software tools will be Basic metacomputing software tools will be installed and testedinstalled and tested

Strong interactions with the workpackages Strong interactions with the workpackages devoted to the definition of the networking tools devoted to the definition of the networking tools and to their implementationand to their implementation

Activity 4:The molecular virtual reality demonstrators

Study of the characteristics of three a priori Study of the characteristics of three a priori simulators and selection of one of them for the simulators and selection of one of them for the construction of a demonstrator of grid calculations construction of a demonstrator of grid calculations in the field of molecular virtual realityin the field of molecular virtual reality

The three simulators will be concerned with:The three simulators will be concerned with: The simulation of a gas phase chemical processThe simulation of a gas phase chemical process The simulation of phase transitions for liquid cristalsThe simulation of phase transitions for liquid cristals The simulation of the functional properties of solid The simulation of the functional properties of solid

state materialsstate materials

Gant Diagram (only for temporary activities)

22 44 66 88 1010 1212 1414 1616 1818 2020 2222 2424 2626 2828 3030 3232 3434 3636

A. A. 11

XX XX XX XX XX XX

A. A. 22

XX XX XX XX XX XX

A. A. 33

XX XX XX XX XX XX XX XX

A. A. 44

XX XX XX XX XX XX XX XX XX XX XX

Activity plan

Activity/Activity/PartnerPartner

CNRCNR

PGPG

CNRCNR

MIMI

CNRCNR

PDPD

CNRCNR

BABA

INSTMINSTMPGPG

INSTMINSTMNANA

INSTMINSTMBOBO

ENEAENEA

Gas Gas Phase Phase SimulatorSimulator

xx xx xx XX

Liquid Liquid Crystals Crystals SimulatorSimulator

xx XX

Solid Solid State State SimulatorSimulator

XX xx xx

Scientific Scientific & Tech. & Tech. Coord.Coord.

XX

Financial Financial Coord.Coord. XX

Financial budget (Keuro)

Item/Item/

PartnerPartnerCNRCNR

PGPG

CNRCNR

MIMI

CNRCNR

PDPD

CNRCNR

BABA

INSTM INSTM PGPG

INSTMINSTMNANA

INSTMINSTMBOBO

ENEAENEA

CofinCofin 245.31245.31 139.97139.97 69.2069.20 154.95154.95 94.4994.49 95.0195.01 63.0063.00 51.6451.64

ContractsContracts 50.0050.00 20.0020.00 25.0025.00 35.0035.00

GeneralGeneral 90.0090.00 55.0055.00 60.0060.00 10.0010.00 40.0040.00 44.7244.72 40.0040.00 5.005.00

Instrum.Instrum. 70.0070.00 30.0030.00 30.0030.00 10.0010.00 30.0030.00 5.285.28 30.0030.00

Trav./Trav./

MeetingsMeetings40.0040.00 15.0015.00 10.0010.00 10.0010.00 25.0025.00 10.0010.00 20.0020.00

Total Total FundingsFundings

250.00250.00 100.00100.00 100.00100.00 50.0050.00 120.00120.00 60.0060.00 90.0090.00 40.0040.00

Total Total PartnerPartner

495.31495.31 239.97239.97 169.20169.20 204.95204.95 214.49214.49 155.01155.01 153.00153.00 91.6491.64

SIMBEX: SIMULATION OF MOLE-

CULAR BEAM EXPERIMENTS Project implementing Project implementing

an an a prioria priori molecular molecular simulation of crossed simulation of crossed molecular beam molecular beam experimentsexperiments Exper. Simul.

THE MOLECULAR SIMULATOR

A problem solving environment to simulate A problem solving environment to simulate chemical systems and processes using a chemical systems and processes using a priori atomic and molecular approachespriori atomic and molecular approaches

CHART FLOW of the SIMULATOR

SURFACESURFACEConstruction of the

Potential Energy Surface

DYNAMICSDYNAMICSDynamical properties

Calculation

PROPERTIESPROPERTIESCalculation of

Averaged quantities

Good

Results?no yes

end

MODULE 1

NOAre

ab initiocalculations

feasible

?

Areab initio

calculationsavailable

?

NO

YES

Applications usingab initio programs

for electronic structure

Useempirical data

fromdata bases

YES

Applicationsusing

fitting programs

2

1

AB INITIO ELECTRONIC ENERGIES

Orbital models (Hartree Fock, DFT)Orbital models (Hartree Fock, DFT) Many body (MCSCF, CI, COUPLED Many body (MCSCF, CI, COUPLED

CLUSTERS)CLUSTERS)

The H+ClCl fixed angle surface

POTENTIAL ENERGY SURFACES

Global methods (LEAST SQUARE Global methods (LEAST SQUARE FITTING, SPLINES, RKHS, LAGROBO)FITTING, SPLINES, RKHS, LAGROBO)

Local methods (SHEPARD Local methods (SHEPARD INTERPOLATION, MOVING LS) INTERPOLATION, MOVING LS)

MODULE 2

YESInitialsinglestate

?

Quantumdynamics

calculations

?

YES Applicationusing

time-dependentquantum

techniques

NO

Applications using classical and semi-classical dynamics

(trajectory) techniques

3

2

Application using time independent quantum techniques

TIME INDEPENDENT QUANTUM DYNAMICS

Define a reaction coordinate (spatial continuity Define a reaction coordinate (spatial continuity variable) and partition its range into small sectorsvariable) and partition its range into small sectors

Calculate the appropriate basis set for each sectorCalculate the appropriate basis set for each sector Expand the global wavefunction in the local basis Expand the global wavefunction in the local basis

set for each sector and average over the bound set for each sector and average over the bound coordinatescoordinates

Integrate the resulting set of coupled differential Integrate the resulting set of coupled differential cross sections in the reaction coordinatescross sections in the reaction coordinates

Apply asymptotic boundary conditions and Apply asymptotic boundary conditions and evaluate the S matrix elementsevaluate the S matrix elements

TIME DEPENDENT QUANTUM DYNAMICS

Use time as continuity variableUse time as continuity variable Propagate in time the system wavepacketPropagate in time the system wavepacket Analyze at each time step the wavepacket by Analyze at each time step the wavepacket by

expanding it into the product basis set in the expanding it into the product basis set in the product regionproduct region

When propagation is completed Fourier transform When propagation is completed Fourier transform from time to energy the expansion coefficients to from time to energy the expansion coefficients to derive the S matrix elementsderive the S matrix elements

TRAJECTORY TECHNIQUES

Define quantum like initial classical Define quantum like initial classical conditionsconditions

Integrate classical equations of motionsIntegrate classical equations of motions Discretize final results (eventually using Discretize final results (eventually using

classical action for semiclassical approaches)classical action for semiclassical approaches)

MODULE 3

NOState

specificosservablequantities

?

State to State

osservablequantities

?

NORate coefficients

Virtualmonitor

YES

Vibrational,Rotational,Angular

distributionsVirtual monitors

1

3

State specific cross section virtual monitors

AVERAGING

Time evolution (flux diagram, wavepacket Time evolution (flux diagram, wavepacket propagation, trajectories)propagation, trajectories)

Probabilities (state to state, state selected, global)Probabilities (state to state, state selected, global) Energy distributions (angular distributions, Energy distributions (angular distributions,

vibrational distributions, rotational distributions)vibrational distributions, rotational distributions) Vector correlations (two vector, three vector, …)Vector correlations (two vector, three vector, …) Cross sectionsCross sections Rate coefficientsRate coefficients

METACHEM

Metalaboratories for complex Metalaboratories for complex computational applications in computational applications in

Chemistry (COST in Chemistry Chemistry (COST in Chemistry Action D23)Action D23)

WHY METACHEM?

Modern advances in biology, medicine, Modern advances in biology, medicine, biotecnology, materials, ….. needs to be biotecnology, materials, ….. needs to be based on complex molecular simulations.based on complex molecular simulations.

It is impractical to convey in a single place It is impractical to convey in a single place all the competences, programs, computers all the competences, programs, computers necessary to carry out realistic simulations necessary to carry out realistic simulations of structures and processes.of structures and processes.

THE METALABORATORY

The Metalaboratory is a solution of the The Metalaboratory is a solution of the problem based upon a connection of the problem based upon a connection of the laboratories of various countries having laboratories of various countries having complementary competences grafted on a complementary competences grafted on a metacomputer system.metacomputer system.