the enea experience in materials science...classical molecular dynamics simulations of 4000 copper...
TRANSCRIPT
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The ENEA experience in Materials Science
Massimo Celino
ENEA – C. R. CasacciaVia Anguillarese 30100123 Rome, Italy
Email: [email protected]
Hands on Training School on Molecular and Materials Science Grid ApplicationsICTP - Trieste31 march 2010
Computational MAterials Science and Technology LabCMAST Laboratory : www.afs.enea.it/project/cmast
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ENEA staff
M. Celino, S. Giusepponi, M. Gusso, R. Grena, P. Morvillo, G. Gianese, V. Rosato
S. Migliori, S. Raia, G. Bracco, S. Podda, A. Santoro, C. Sciò, A. Rocchi, A. Quintiliani
Molecular modeling activities
Support and maintenance of the ENEA GRID infrastructure
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• Based on:
–OpenAFS (shared filesystem)
–LSF Multicluster (resource manager)
ENEA GRID
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CASACCIACASACCIA
FRASCATIFRASCATI
S.TeresaS.Teresa
SaluggiaSaluggia
IspraIspra
BOLOGNABOLOGNA
PORTICIPORTICI
TRISAIATRISAIA
BRINDISIBRINDISI
ManfredoniaManfredonia
ENEA-GRID Computational & 3D Centers(more then 3600 core)
90>3000
400
140
30
#CPU/Core
45
New 192 core AMD 6 core
New 224 core
Intel Nehalem
ENEA GRID
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Parallel platforms in ENEA GRID
Hardware
• CRESCO HPC, Portici (NA) #125 in Top500 June 2008 (#2 in Italy) 17.1 Tflops, 300 hosts, 2720 cores, InfiniBand 4xDDR
• Other resources: ~100 hosts ~650 cpu
– AIX: IBM SP5 256 cpu (12 p575 1.5GHz, 16 cpu + 1 p595 1.9 Ghz, 64 cpu, 1.5 Tflops); SP4, 96 cpu, Frascati (Rome)
– SGI Altix 350 (IA64) 32 cpu Casaccia (Rome) & Onyx– Cray XD1 24 cpu Casaccia (Rome)– Linux clusters 32/x86_64; Apple cluster; Windows servers
Software
• Commercial codes (fluent, ansys, abaqus, nastran,...)
• Research codes and open source (CPMD, MCNP, OpenFoam,...)
• Computing environment s (Matlab, IDL, ...)
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HPC CRESCO HALL
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HPC CRESCO PLATFORM
Section 2(MPP)
256 Nodes blades IBM HS21 with 2 Xeon Quad-Core Clovertown E5345 (2.33GHz/1333MHz/8MB L2), 16 GB RAM total 2048 cores Intel ClovertownNew 28 Nodes (224 core) Nehalem 2.4 GHz
Portici LAN
SERVERS GPFS
4 Nodes IBM 3650
IBFC
High speed storage
2 GByte/s160 TByte IBM/
DDN 9550
Backup system
300 TByte IBM Tape Library TS3500 with 4 drives
SERVERS BACKUP
3 Nodes IBM 3650
FCIB
GARR(WAN)
Section 1(Large memory)42 Nodes SMP IBM x3850-M2 with 4 Xeon Quad-Core Tigerton E7330 (32/64 GByte RAM 2.4GHz/ 1066MHz/6MB L2) total 672 cores Intel Tigerton
Section 3(Special)
4 Nodes blades IBM QS21 con 2 Cell BE Processors 3.2 Ghz each.6 Nodes IBM x3755, 8 Core AMD 8222 FPGA VIRTEX54 Nodes IBM x 3755, 8 core AMD 8222 with NVIDIA Quadra FX 4500 X2 4 Nodes Windows 8 core 16 Byte RAM
4x10 Gbits 1000+1000 Mbits
35 Nodes for services
Servers for :• Front-end• installation
s• AFS
New 10 Nodes for tools
Tools:• Faro• Jobrama• Amaca
Interconnections InfiniBand
4XDDR
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Fluent
OpenFoam
Heart combustion
Commercial code
User Code
SOME CRESCO SPEEDUP
Open Source
User Code:HEART code for combustion
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Born in 1998 with 6 Italian geographic clusters
Main aim • Give to ENEA researchers an unified environment to use in an easy way heterogeneous computers and applications software• Build a homogeneous ICT infrastructure but with a distributed and delegated control • Integrate the ENEA-GRID with National and International GRIDS
Sensor nets
ENEA-GRIDwww.afs.enea.it/project/eneagrid
Data archivesColleagues & 3D
Softwarecatalogs
ComputersApplication
Fabric
Connectivity
Resource
Collective
User
THE ENEA GRID
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NETWORKNETWORK
DATA ACQUISITIONDATA ACQUISITION DATA ANALYSISDATA ANALYSIS
Cell Centered Data Base Cell Centered Data Base ““CCDB”CCDB”
IMAGINGIMAGINGINSTRUMENTSINSTRUMENTS
COMPUTATIONALCOMPUTATIONALRESOURCESRESOURCES
MULTI-SCALEMULTI-SCALEDATABASESDATABASES
ADVANCEDADVANCEDCOMPUTERCOMPUTERGRAPHICSGRAPHICS
ENEA GRID INFRASTRUCTURE
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AFS Geographical cross platform & File System
AIX SGI SUN CUDA Win Linux Cell Be FPGA
LSF
User programs and commercial codes
LSF multi-cluster as integrator
Graphical User Interface
Application Portal (ICA-Protocol)
ICAWEB
Qu
ality
of s
erv
ice
Mon
itorin
g, A
uto
matic
recovery
Accou
ntin
g
ENEA GRID Architecture
New
Application Portal (NX based)
newnew
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FARO (Fast Access to Remote Objects)
JOBRAMA (job monitoring)
AMACA (AFS Memorize And Check Application)
Visual tool able to scan the state of OpenAFS core components and report their condition, while signaling potential criticalities
HOMEMADE ENEA SERVICES
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From 1998 to 2009 Citrix for UNIX
AFS Geographical cross platform& File System
Load Leveler LSF
Graphic User Interface LSF multi-cluster as integrator
Telnet
User programs & commercial code
AFS Geographical cross platform& File System
Load Leveler LSF
Graphic User Interface LSF multi-cluster as integrator
Telnet
User programs & commercial code
ICAWEB
From 2008 to …… WEB FreeNX for UNIX
COMMERCIAL SOFTWARE
OpenSource SOFTWARE
ENEA-GRID SOFTWARE EVOLUTION
FARO
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FARO – Fast Access to Remote Objects
Built upon the user
FARO is the result of a software integration process where all the components interoperate in order to guarantee web access to remote resources, in a fast, secure and reliable way.
With FARO, researchers need only a reasonably modern web browser (with Java support), and every remote resource they use (from Xterm to desktops of remote Windows machines) will instantaneously reach their location.
Demo accepted in 5th EGEE USER FORUM (due in 11-15 April 2010)
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• Backend communicates with Job manager (LSF is currently implemented, but other schedulers can be integrated)• Frontend (web-applications) aggregates data and shows results
JOBRAMA
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The SPAGO approach
AIX
IRIXMacOS
CRAY
Altix Any Linux
Also, the service provider retains its autonomy!
Design Principle - Employs one or more proxy to execute grid commands on Wns without gLite.
- Shared file systems allow data sharing between proxies and WNs.
ENEA GRID
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Demo accepted in 5th EGEE USER FORUM (due in 11-15 April 2010)
FARO – CPMD
Interface towards the european GRID
Allows to submit CPMD jobs to the GRID.
The job is automatically executed on a GRID cluster supporting CPMD jobs
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CMAST Virtual Lab home page
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CMAST Virtual Lab home page
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ENEA-GRID access
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ACTIVITIES
CODES
• Hydrogen storage: MgH2
• Metallic membranes • Organic-inorganic adhesion• Liquid and amorphous AX2 systems
• Icosahedral order in undercooled metals• semiconductors• Tungsten and its alloys• CdS quantum dots• Materials under pressure• etc
• CPMD, CP2K, Quantum Expresso• GROMACS• Homemade for intermetallics and
semiconductors
PARTNERS
• University of Salerno, Rome “Tor Vergata”, Rome “La Sapienza”, Sassari, Camerino, Napoli, Perugia, etc
• CNR Avellino
• University of Lille, Strasbourg, Berlin, Zurich, Bath, Barkatullah
• ST Microelectronics• Ylichron• Numonyx• Tecnomarche• …
• Several ENEA groups
CMAST Virtual Lab
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Hydrogen storage
The remarkable ability of magnesium to store significant quantities of hydrogen has fostered intense research efforts in the last years in view of its future applications where light and safe hydrogen-storage media are needed. Magnesium material, characterized by light weight and low cost of production, can reversibly store about 7.7 wt% hydrogen (MgH2).
However, further research is needed since Mg has a high operation temperature and slow absorption kinetics that prevent for the moment the use in practical applications. For these reasons a detailed study of the interface between Mg and MgH2 is needed to characterize the dynamics of hydrogen at the
interface. Thanks to Amelia Montone, ENEA TEPSI Project
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Hydrogen desorption
Starting configuration
Mg surface
MgH2 surface
InterfaceLx= 6.21 Å
Ly= 50.30 Å
Lz= 15.10 Å
MgH2:
60 Mg atoms + 120 H atoms
Idrogeno
Magnesio
Mg: 72 atoms
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Catalyst, T= 400 K
Hydrogen desorption
T= 700 K
0
100
200
300
400
500
0 200 400 600 800 1000
CRESCO: ~ 8 sec – 150 PE ~ 3 sec – 576 PE
CPMD
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Peptide on carbon nanostructures
PEPTIDEPeptide sequence HWSAWWIRSNQS taken from the exeperimental work of Wang et al (Nat Mater 2003)
Modeling of the initial peptide folding by MD simulations in water and energy monimization starting from a totally unfolded atomic structureGROMACS code with OPLS-AA force field
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GRAFENE
PEPTIDE
Rigid docking between folded peptide and carbon surface by means of genetic
algorithm
Peptide on carbon nanostructures
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Peptide on carbon nanostructures
MD relaxation in water of the best peptide-carbon surface complexes to adjust geometrical matching and to further optimize the binding energy
Car Parrinello molecular dynamics to characterize the electronic structure and better define the contact regions
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Peptide on carbon nanostructures
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Peptide on carbon nanostructures
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Liquid and amorphous AX2 materials
Initial configuration
Final configuration:• few homopolar bonds Si-Si• most of the Si atoms have tetrahedral coordination
Diffusion coefficient
Total neutron structure factor
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First Sharp Diffraction Peak in AX2 liquids
500 atoms studied with about 600 cores: 8 sec per time step
Liquid and amorphous AX2 materials
C. Massobrio, M. Celino, P. S. Salmon, R. A. Martin, M. Micoulaut, A. Pasquarello, “Atomic structure of the two intermediate phase glasses SiSe4 and GeSe4”, Phys. Rev. B 79, 174201 (2009)
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Even in simple liquids the short range order may differ from that of crystalline solids.
Undercoolings as large as 20% of the melting temperature is observed for a great variety of different metals.
Icosahedral short range order is postulated in the melts to explain the large undercoolings of pure metals.
A commons approach is to characterize the liquid metal by starting from the analysis of the single icosahedra and its deformations.
Icosahedral short range order
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13 atoms
55 atoms
147 atoms
The potential energy, by using for example the Lennard-Jones interatomic potential, for the 13 atom icosahedra cluster is about 8% smaller than corresponding fcc and hcp structure.
Icosahedral short range order
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∑ +=i
iB
iRc EEE
( ) 21
1/22
−= ∑ −−
j
rrqiB
oijeE ξ( )∑ −−=j
rrpiR
oijAeE 1/
Classical Molecular Dynamics simulations of 4000 copper atoms
Constant temperature and constant pressure simulations
Interatomic potential:
Molecular dynamics
Cleri, Rosato, PRB 48 (1), pp. 22-33, 2003
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Experimental melting temperatureTm=1356 K
Temperature of interest:Liquid: T= 1450 K Undercooled: T=1150 K
<5% of difference with experimental densities
MD: D=3.90 10-5 cm2/sec at T=1400 K
Exp: D=3.97 10-5 cm2/sec at Tm=1356 K
Molecular dynamics temperature in the NPT ensemble
Molecular dynamics
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Neutron Structure Factor
Room pressure
Pair correlation function
Bond angle distribution
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Temperatures MD simulations:Liquid: T= 1450 K Undercooled: T=1150 K
Experimental results:
T= 1142 K ; P= 0.3 GPaT= 1167 K ; P= 0.7 GPaT= 1253 K ; P= 1.4 GPaT= 1333 K ; P= 3.3 GPa
T= 1150 K
ExperimentsMD
Experiments:F. Coppari et al. J. Phys. 121 (2008) 042009
Bond angle distribution
Radial distribution function
High pressure
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Common neighbour analysis
Three indeces jkl specifies the local environment of a pair of atoms:
j = the number of neighbors common to both atoms
k = the number of bonds between the common neighbors
l = the number of bonds in the longest continuous chain formed by the k bonds between common neighbors
For example:
555 icosahedral order
421 fcc order
421 and 422 hcp order
Ref: Clarke and Jónsonn (PRE 93)
ICOSAHEDRAL cluster has the central atom characterized by 12 nearest neighbor atoms with 555 environment
N555 = 12
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Icosahedral symmetry
N555= 12T= 1150 K
P= 0.3 GPa Perc: 0.40
P= 3.3 GPa Perc: 0.72
T= 1150 K
P= 0.3 GPa Perc: 0.14
P= 3.3 GPa Perc: 0.29
T= 1450 K
N555
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Icosahedral symmetry
N555
T= 1150 K
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FCC symmetry
Opposite behaviour for the FCC symmetry
M. Celino, F. Coppari, A. Di Cicco, “Pressure effects on icosahedral short range order in undercooled copper” Solid State Science 12 (2010) 179-182