inelastic and reactive ele- mentary processes in atom- diatom, diatom-diatom collisions and beyond...
TRANSCRIPT
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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
*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
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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.
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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.
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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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