EGEE-II INFSO-RI-031688
Enabling Grids for E-sciencE
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THE COMPCHEM VO AND A GRID APPLICATION TO SPACECRAFT REENTRY
A. Laganà1, O. Gervasi2, A. Costantini1
B. 1 Department of Chemistry, University of Perugia, Perugia (I)
C. 2 Department of Mathematics and Computer Science, University of Perugia, Perugia (I)
About handling on the Grid quantum molecular knowledge related to molecular simulators
Authors: A. Laganà1, A. Costantini1, O. Gervasi2
Location: 1) Department of Chemistry, University of Perugia, Perugia, Italy
2) Department of Mathematics and Computer Science, University of Perugia, Perugia, Italy
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THE STARTING POINT
SIMBEX: design and implementation of a Simulator of Molecular Beam Experiments for atom diatom reactions using classical trajectories (demo at first EGEE meeting)
GEMS: design and partial implementation of a Grid Enabled Molecular Simulator using both quantum and classical trajectory methods to mimic molecular processes
GEMMS: design and feasibility studies of Grid Empowered Molecular and Matter Sciences in a cooperative fashion using in-house and commercial packages
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WORKFLOW OF SIMBEX
Interaction
Measurables
Dynamics
Virtual Monitor
Input
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The INTERACTION module
INTERACTION
DYNAMICS
Is therea suitable LEPS
Pes?
Import theLEPS parameters
NO
YES
START
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The DYNAMICS module
DYNAMICS
OBSERVABLES
Are classicaltrajectory
calculationsappro-priate?
NO
YES
TRAJ: application
performing atom diatom classical
trajectoryintegration
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TRAJECTORY DISTRIBUTION
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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GRIDIFYING the TRAJ kernel
TRAJ
return
Iterate over initial conditionsthe integration of individualtrajectories (ABCTRAJ, etc.)
Define quantities of generaluse
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The MEASURABLE module
OBSERVABLESNO
YES
Is the observable
a state-to-stateone?
DISTRIBUTIONS: VMfor scalar and vectorproduct distributions,
and state-to-state crosssections
Do calculated
and measuredproperties
agree?
END:EXTEND THE
CALCULATIONTO OTHER
PROPERTIES
YES NO END:TRY WITHANOTHER SURFACE
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THE VIRTUAL MONI-TORS BUILD IN REAL TIME THE PRODUCT ANGULAR DISTRIBU-TIONS OF THE VA-RIOUS CHANNELS
THE H+ICl REACTION
H+ICl→H + ICl
H+ICl→HCl+I
H+ICl→HI+Cl
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THE MOLECULAR BEAM EXPERIMENT of Perugia
MEASURABLES- Angular and time of flight product distributions
INFORMATION OBTAINABLE- Primary reaction products- Reaction mechanisms- Structure and life time of transients - Internal energy distribution of products- Key features of the potential
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From representation to simulation
REPRESENTATION OF EXPERIMENTAL
APPARATUSES
VISUALIZATION OF MOLECULAR STRUCTURES
SIMULATION OF MOLECULAR PROCESSES
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Types of molecular visualization
• Type of molecular representations:– Balls and Sticks (BS)
– Wire frame (WF)
– Space filling (SF)
– SF+WF
– Colored wire frame
• Properties
– Transparency
– Labels
• The atoms are colored using the RASMOL CPK coloring scheme
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A direct (versus the previous complex) mechanism for reactive processes
Simulation of molecular processes
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The analysis of the potential surface
The evolution of the arrier to reaction as a function of the collision angle
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EGEE-II INFSO-RI-031688 The minimum energy path (MEP) in the BO space
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EGEE-II INFSO-RI-031688 Fixed target geometry isoenergetic contours
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CONTOURS AND MEPS
A coordinate smoothlyconnecting reactants toproductsRemaining coordinatesare mutually orthogonal(bifurcations difficult tohandle)
LEPS surface
Isometric contours
Choosing a properset of coordinates
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PRESENT ADVANCES
EXTEND European collaboration to GEMS (Grid Enabled Molecular Simulations) using quantum means
• WG1 PHOTODYN: Computational photochemistry and photobiology
• WG2 QDYN: Quantum dynamics engines for Grid enabled molecular simulators
• WG3 ELAMS: E-science and Learning approaches in Molecular Science
• WG4 DECIQ: Code interoperability in Computational Quantum Chemistry
• WG5 CCWF: Computational Chemistry Workflows and Data Management
• WG6 AIMD4GRID: Ab initio Molecular Dynamics for the Grid
The D37 (GRIDCHEM) COST CMST action
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QUANTUM SCATTERING
EψHψ
tψ
iHψ
- time-independent: time is factored out of the wavefunction and the problem becomes a single energy stationary one
The wavefunction carries all the needed information on the scattering process.
- time-dependent: the time dependent Schrödinger equation is integrated at a given initial state by following the evolution in time of the wavepacket
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DYNAMICS module
DYNAMICS
OBSERVABLES
Is the calculation
single initial state?
NO NO
YES YES
TI: application carrying out
time-independentquantum
calculations(atom-diatom)
TD: application carrying out time-
dependent quantumcalculations
(atom-diatom)
TRAJ: application
using classical trajectory
calculations
Are classicaltrajectory
calculationsappro-priate?
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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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TIME DEPENDENT PSEUDOCODE
SEND “ready” status messageRECEIVE init_condintegrate in timegenerate the S matrix elementSEND “ready” status messageGOTO RECEIVE
Worker:
DO init_cond =1, N_initcond RECEIVE status message IF worker “ready” THEN SEND init_cond to worker ELSE GOTO RECEIVE endIF endDO
Master:
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Gridified time dependent method
TD
return
•Iterate over initial conditions•the integration over time•propagation (RWAVEPR, etc.)
Define quantities of generaluse
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Gridified time independent method
TI
return
Iterate over total energy value the integration of scattering
equations
Define quantities of generaluse including the integration
bed
Iterate over the reaction coor-dinate to build the interaction
matrix
Broadcast coupling matrix
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EGEE-II INFSO-RI-031688 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici
The N+N2 reaction
)',()(),()( 12
412
4 vNSNvNSN gg
A QUANTUM STUDY OF REACTIONS CONTRIBUTIONS TO HEAT DISSIPATION AROUND REENTERING SPACECRAFTS
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EGEE-II INFSO-RI-031688 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici
State to state probabilities
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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EGEE-II INFSO-RI-031688 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici
Threshold energies
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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●
●
Rate coefficients
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OUTLINE
• H+/D+ ions flowing through a carbon nanotube
• A quantum scattering problem solved using a 3D time-dependent technique (the problem has been already solved using classical approaches)
• Implementation of a quantum scattering formalism based on polar cylindrical coordinates to single out resonances, interferences and tunneling
A Model quantum problem
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-Carbon nanotubes are cylindrical aggregates of carbon atoms-They can be seen as a wrapped around plane of graphite.- The p orbitals of the carbon atoms are perpendicular to the C plane and and form an aromatic like layer.
THE NANOTUBES
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Carbon nanotubes are highly stable and show several highly interesting technological properties as new materials.
An interesting application is as hydrogen storage f.
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NANOTUBES AS QUANTUM SIEVES
- Nanotube have been considered for separation of mixtures of molecules of similar shape.-They can bind, in fact, differently to the internal part of the nanotube and alter the partition function.- Such an effect is expected to be particularly pronounced for H/D isotopic variants.
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SCATTERING IN CYLINDRICAL SYMMETRY PROBLEMS
In the nanotube problem the symmetry is about cylindricalThe most suitable coordinates are the polar cylindrical ones (r,,z) The projection of the total angular momentum on z is a good quantum number
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THE ELECTRONIC STRUCTURE
Most often DFT techniques are used to handle the problem (A.D. Becke, J. Chem. Phys. 1993, 98, 5648).
S. K. Gray et al calculated the bound states of an H2 molecule placed inside a carbon nanotube (with all its degrees of freedom) (T. Lu, E.M. Goldfield and S. K. Gray, J. Phys. Chem. B 2003, 107, 12989).
The ab initio calculation of the electronic structure of a carbon nanotube at the level of 'chemical accuracy' is highly demanding in terms of computational resources
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A FORCE FIELD APPROACH
The value of the parameters are (JACS 1995):
= 3.90310-5 h = 3.157 a0
612
r
σ
r
σ2εV
We used for our study an atom-atom additive semiempirical force field.
All interactions are formulated as van der Waals one between the H+ ion and the C atom.
The functional form used is a Lennard-Jones 6-12 :
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with k being the momentum along z.
iKθnK e)Rr
(ρJθ)ψ(r,
ikzeψ(z)
BASIS SET
R is the nanotube radius K is the angular momentum component on z
ρn is the nth zero of the Bessel function JK
The radial component is a Bessel function and the angular component is an imaginary expomential
The z component of the wavefunction is given by plane waves:
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RADIAL FUNCTION
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THE HAMILTONIAN
The Hamiltonian for a particle in cylindrical soordinates reads:
- By substituting f by r1/2f the first derivative disappears - By adopting cylindrical polar instead of cartesian coordinates it does appear a centripetal term towards the center of the cylinder- At non zero total angular momentum values the centripetal term is absorbed inside the cetrifugal one
z)θ,(r,V2m
H^
22^
with
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THE WAVEPACKET
- The initial (t=0) wavepacket is placed at one end of the nanotube- Its shape is that of an eigenfunction of the polar component of the Hamiltonian with a given component of the total angular momentum and a given radial excitation (that of the corresponding Bessel function)- Its z component is a Gaussian times a phase factor (corresponding to the linear momentum)
ikz2σ
)z(z
ee(z)2
20
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THE PROPAGATION
The wavepacket is propagated as usual using the propagator
)tiH(t
0
0
e)t(t,
U
- The potential operator is diagonal when represented on a grid
-Translation along z and r is dealt using a bidimensional Fourier transform
-Rotation (centrifugal term) is dealt using a one dimensional Fourier transform
-An absorbing imaginary potential is placed at both ends of the nanotube.
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OUTGOING FLUX MONITORING
)(,ˆˆ zzH
iF
where is a threshold Heaviside function and z is the point at which the analysis occurs (square
brackets indicate operator commutation)
At each time t of the propagation the expectation value of the flux operator is
calculated using the expression
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-0.003
-0.002
-0.001
0.000
0.001
L=0
-0.003
-0.002
-0.001
0.000
L=5
-0.003
-0.002
-0.001
0.000
L=10
Out
goin
g F
lux
0 500 1000 1500 2000-0.003
-0.002
-0.001
0.000
L=30
Time (atomic units)
OUTGOING FLUX PLOTS: angular momentum
H+ - Elong=0.04 h Etransv=0.01 h
An increase of the value of the angular momentum quantum number slightly delays the flux (the increase of the centrifugal potential pushes the wavepacket closer to the nanotube walls).
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-0.003
-0.002
-0.001
0.000
L=0
-0.003
-0.002
-0.001
0.000
L=5
Ou
tgo
ing
Flu
x
0 500 1000 1500 2000-0.003
-0.002
-0.001
0.000
L=10
Time (atomic units)
OUTGOING FLUX PLOTS: transversal excitation
H+ - Elong=0.04 h Etransv=0.03 h
Transversal excitation also slightly delays the flux and introduces some wiggles
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0 500 1000 1500 2000-0.004
-0.003
-0.002
-0.001
0.000
Ou
tgo
ing
Flu
x
L=0
Time (atomic units)
OUTGOING FLUX PLOTS: longitudinal energy
H+ - Elong=0.08 h Etransv=0.01 h
A doubling of the longitudinal energy shifts the flux of a factor √2.
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OUTGOING FLUX PLOTS: isotopic effectD+, Elong = 0.04 h, Etrasv = 0.01 h
A doubling of the mass shifts the flux of a factor √2
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THE EXTENDED WORKFLOW
In an extended approach the whole workflow is considered including
• the generation of the potential energy values and their functional representation
• the integration of full (classical) dimensional motion equations for many atom systems
• statistical averaging to build observable quantities
• visual techniques to single out relevant patterns
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Extended INTERACTION module
INTERACTION
DYNAMICS
Is therea suitable Pes?
Are ab initiocalculationsavailable?
Are ab initiocalculations
feasible?
CALL SUPSIMCALL FITTING Import the
PES routine
NO NO NO
YES YES YES
Take force fielddata and
procedures from relateddatabases
START
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Gridified Ab initio approach
SUPSIM
return
Iterate over the systemgeometries geometries
the call of ab initio suitesof codes (GAMESS, etc)
Define the characteristics of the ab initio calculation, the coordinates used and the
Variable’s intervals
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Gridified FITTING portal
FITTING
Return
Are asym-ptotic values
accurate?
Are remai-ning valuesinaccurate?
Do ab initiovalues have the
proper sym-metry?
Enforce the propersymmetry
Application using fitting programs to
generate a PESroutine
Modify asym-ptotic values
NO NONO
Modify short andlong range values
YES YESYES
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EXTENDED DYNAMICS module
DYNAMICS
OBSERVABLES
Is the calculation
single initial state?
NONO
YES YES
TI: application carrying out
time-independentquantum
calculations(atom-diatom)
TD: application carrying out time-
dependent quantumcalculations
(atom-diatom)
TRAJ: application
using classical few body trajectory
calculations
Are classicaltrajectory
calculationsappro-priate?
DL_POLY: application
using classical mechanics to
many body systems
Is it A many
Bodyproblem?
YES
NO
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Extended MEASURABLES module
OBSERVABLESNO NO
YES YES
Is the observable
a state-to-stateone?
Is theobservable
a state specificonee?
VM for thermal and thermodynamic pro-
perties including Molecular Virtual
Reality tools
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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IONIC BIOLOGICAL CHANNELS
They are usually schematized as a sequence of:• Entrance gate• Bilayer pore• Selectivity filter
• Biological ionic channels play an important role in the control of ionic cellular concentrations and in synapses
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ION FLOW THROUGH NANOTUBES
A nanotube model can be used to understand the ionic conductivity of cations (like Na+ or K+) through cellular membranes.
A life science application to the understanding of cellular micropores
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THE CARBON NANOTUBE AS A MODEL
WE CONSIDERED THE CNT AS A MODEL FOR BIOLOGICAL IONIC CHANNELS THOUGH IT HAS AN INTEREST PER SE AS AN ELECTRONIC DEVICE
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CNT IONIC PERMEABILITY SIMULATION
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FORWARD LOOKS
• New distribution models• More complex molecular simulations• Integration of molecular and atmospheric
simulations• Virtual laboratories• VO economies
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ELAPSED TIMES
0
100
200
300
400
500
600
700
800
900
1000
1 2 3 4 5 6 7 8
Numero nodi
Ela
pse
d t
ime
/sec
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SPEEDUPS
0
1
2
3
4
5
6
7
8
9
1 2 3 4 5 6 7 8
Numero nodi
Sp
eed
up
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•A SOLVATED ION
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benzene microsolvation
Simulation of microsolvation of benzene with rare gas atoms.
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AIR POLLUTION SIMULATION
CPM10 Concentration from CHIMERE-aerosols
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EGEE and gLite are registered trademarks
THE COMPCHEM VO AND A GRID APPLICATION TO SPACECRAFT REENTRY
A. Laganà1, O. Gervasi2, A. Costantini1
B. 1 Department of Chemistry, University of Perugia, Perugia (I)
C. 2 Department of Mathematics and Computer Science, University of Perugia, Perugia (I)
Go to VRML animation
flame spectroscopy
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VO CREDIT SYSTEM