About handling on the Grid quantum molecular knowledge related to molecular simulators

EGEE-II INFSO-RI-031688

Enabling Grids for E-sciencE

www.eu-egee.org

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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




WORKFLOW OF SIMBEX

Interaction

Measurables

Dynamics

Virtual Monitor

Input




The INTERACTION module

INTERACTION

DYNAMICS

Is therea suitable LEPS

Pes?

Import theLEPS parameters

NO

YES

START




The DYNAMICS module

DYNAMICS

OBSERVABLES

Are classicaltrajectory

calculationsappro-priate?

NO

YES

TRAJ: application

performing atom diatom classical

trajectoryintegration




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:




GRIDIFYING the TRAJ kernel

TRAJ

return

Iterate over initial conditionsthe integration of individualtrajectories (ABCTRAJ, etc.)

Define quantities of generaluse




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




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




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




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




A direct (versus the previous complex) mechanism for reactive processes

Simulation of molecular processes




The analysis of the potential surface

The evolution of the arrier to reaction as a function of the collision angle



EGEE-II INFSO-RI-031688 The minimum energy path (MEP) in the BO space



EGEE-II INFSO-RI-031688 Fixed target geometry isoenergetic contours




CONTOURS AND MEPS

A coordinate smoothlyconnecting reactants toproductsRemaining coordinatesare mutually orthogonal(bifurcations difficult tohandle)

LEPS surface

Isometric contours

Choosing a properset of coordinates




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




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




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






THE TIME DEPENDENT METHOD

Collocate the wavepacket

Time propagate the wavepacket

Carry out its analysis at the

product asymptote




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:




Gridified time dependent method

TD

return

•Iterate over initial conditions•the integration over time•propagation (RWAVEPR, etc.)

Define quantities of generaluse




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



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




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




Threshold energies

1.359 eV

0.950 eV

0.772 eV

0.199 eV

Etr

V=0

V=1

V=2

V=4




●

●

Rate coefficients




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




-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




Carbon nanotubes are highly stable and show several highly interesting technological properties as new materials.

An interesting application is as hydrogen storage f.




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.




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




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




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 :




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:




RADIAL FUNCTION




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




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




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.




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




-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).




-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


Transversal excitation also slightly delays the flux and introduces some wiggles




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


A doubling of the longitudinal energy shifts the flux of a factor √2.




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




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




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




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




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




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



DL_POLY: application

using classical mechanics to

many body systems

Is it A many

Bodyproblem?

YES

NO




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




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




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




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




CNT IONIC PERMEABILITY SIMULATION




FORWARD LOOKS

• New distribution models• More complex molecular simulations• Integration of molecular and atmospheric

simulations• Virtual laboratories• VO economies




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




SPEEDUPS

0

1

2

3

4

5

6

7

8

9

1 2 3 4 5 6 7 8

Numero nodi

Sp

eed

up




•A SOLVATED ION




benzene microsolvation

Simulation of microsolvation of benzene with rare gas atoms.




AIR POLLUTION SIMULATION

CPM10 Concentration from CHIMERE-aerosols



www.eu-egee.org

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)

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flame spectroscopy




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About handling on the Grid quantum molecular knowledge related to molecular simulators