LibMultiScale & AMEL User Guidelibmultiscale.gforge.inria.fr/manual.pdf · component can be...

LibMultiScale & AMEL User Guide

Guillaume ANCIAUX

7 septembre 2007

Chapitre 1

Introduction

The LibMultiScale Library has been designed to be a high performance tool to study the mutiscale me-thods currently employed on material simulations. The component design of the project distinct the base codecomponents (Continuum mechanics code implemented through finite element, meshless, XFEM or moleculardynamics codes) from the coupling components. Other services like dumpers ( logging the state of the simu-lated system on files or memory, enabling filtering based on values averaging or geometrical criterion...), orstimulators that implement initial conditions (temperature, initial displacements) are provided.

At this day, the only stable coupling method is based on the Bridging Method. The molecular dynamicscomponent can be implemented by Lammps or Stamp while the Continuum mechanics component use a consti-tutive law based on the Cauchy-Born Rule and is implemented by a code developed in our team. The projectis actually maintained by Guillaume ANCIAUX.

1

Chapitre 2

Getting LibMultiScale and Compiling

Please consult the INSTALL.txt page for details on how to fully install LibMultiScale and its client AMEL(Atomistic Multi-domain coupling with External finite elements for LibMultiScale) that is downloadable at thepage :

http://gforge.inria.fr/docman/?group_id=915

The LibMultiScale Project is actually maintained by Guillaume ANCIAUX in a collaboration between theScalApplix Project, INRIA Futurs, and the CEA Ile-de-France (contract CEA/DIF N4600084494/P6H32). Thelicense that governs the LibMultiScale rights is a CECILL-C which can be consulted at the address :

http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html

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Chapitre 3

Preprocessing of the models

In order to use the LibMultiScale and its client AMEL, one should prepare the models wanted to be coupled.For instance, in the actual case, a mesh should be prepared and a mono-atomic crystal. In order to illustratethe discussion, we will describe the construction of a concrete case. The case studied will be a simple rectan-gular piece of material with a planar and circular(composed geometries) bridged zone. The figure 3.1 presentthe global aspect of such a coupled domain. It is a square domain with a side of L = 1000 · r0 where r0 isthe averaged inter-atomic distance. We firstly want to build an mono-atomic crystal of argon, meaning thatr0 = 1.22452143391761666.10−10. The bridged zone placed in the center of the domain would have an heightsize h = L/10 while length is l = L/3. Bridged zone size should not be smaller than 10r0 in order to avoid wavereflexions. Thus it represents a bridging size of L/100. In order to prevent reflexions, we use here a bridged sizeof 2L/100.

First we prepare the set of atoms constituting the crystal we want to modelize. Then we build the meshusing the appropriate tools. The numerical models are associated with configuration files that will be describedin the following.

L =

100

0 r0

l = L/3

h = L/10

Fig. 3.1 –

The different stages of this tutorial can be found in the examples directory of LibMultiScale release. Inorder to build the model we create a file casCustom that will initially contain the useful values we defined.The key words are not defined systematically in the following. For a full description, one should report to theglossary at the end of the document. Firstofall, we need a global section where models, and other importantdata will be assigned. This is done by opening a section block :

#general section

Section MultiScale RealUnits

3

...

endSection

The syntax is Section NAME UNITS, where the name is identified by the MultiScale and the units declarethe units used in the section. Inside of that block, we set the declaration of reusable variables. We naturallydefine the dimensions of the system by :

#definition of the global numbers

#inter-atomic distance

LET r0 = 1.2245214339176166619211e-10

#total domain size

LET L = 1000 * r0

#height of molecular domain

LET h = L / 10

#square width of molecular domain

LET l = L / 3

#the size of the bridged zone

LET bridgedSize = 2 * L / 100

#the dimensions of the coarsed zone

LET l2 = l + bridgedSize + h

LET h2 = bridgedSize + h

Any simulation will have to define its system dimension by :

DIMENSION 2

and the internal units system used by the codes. This precision is important as the base code componentsfor molecular mechanics have restricted unity systems.

UNITCODE RealUnits

The next section will explain how to configure the atomic section before the continuum section and its mesh.

3.1 preparing the crystal

In order to prepare the atomic zone, the first step in the construction is to build a squared/cubic zone fullof atoms adequately disposed. Then we will carve into that cubic zone to obtain the desired geometry. In ourconcrete case we want to modelize 2D Argon crystalline. We need to define a Bravais lattice. There are twoatoms in the reference Lattice, with coordinates (in reduced unities) :

0.0 0.0 0.5

0.5 0.5 0.5

The lattice is rectangular and follows the vectors :

1.22452143391761666e-10 0.0

0.0 2.1209333385024e-10 0.0

We will describe two ways to obtain that cubic zone. The first one will use Stamp to replicate BravaisLattice while the second will use a given script to generate input for Lammps.

3.2 Generating with Stamp

In the following we may define by = 2.1209333385024.10−10. The basic information concerning a crystal issynthetized in a file called FAtomes. A more precise description of this Stamp file can be found in the StampDocumentation. For the desired crystal, this file is :

4

*******************************************

***** les unites sont le MKS **************

** sauf les masses sont molaires(Kg/mol) **

*******************************************

nbAtomes 1

nom AR

masse 39.95e-3

sigma 0.11e-9

epsilon 1.6567944e-21

interPotentiel PotentielLJ

****************************

**** coordonnees du motif 1.23157195294235e-10 **

****************************

Motif

1.22452143391761666e-10 0.0 0.0

0.0 2.1209333385024e-10 0.0

0.0 0.0 7e-10

***********************************

**** coordonnees reduires [0..1] **

* X **** Y ***** Z *****At ********

***********************************

Structure

2

0.0 0.0 0.5 AR

0.5 0.5 0.5 AR

Then a Stamp configuration file must be produced. In the same way, the appropriate structure of this filecan be found in the Stamp documentation. We give here an example :

FichierAtomes config-stamp/FAtomes2D

LongueurInput angstrom

TempsInput ps

TemperatureInput K

EnergieInput eV

EnergieOutput eV

Ensemble NVE

Schema verlet

Structure Fichier

Decoupage 474 81 1

Potentiel LJ

Rcut 2.93885144140227

Trequis 0.0

Deltatemps 0.001

RandSeed 17

ConditionX Libre

ConditionY Libre

ConditionZ Libre

*EcrireStatProc 1

StepLimit 40000

StepAvg 200

Protection 100

The Decoupage keyword control how many times the Bravais lattice is duplicated in each directions. Ac-counting the bridging zone size, a rectangular zone with dimensions l′ × h′ needs to be filled with atoms :

l′ × h′ = (l + bridgedSize + h) × (bridgedSize + h) (3.1)

= (L · 136/300) × (L · 12/100) (3.2)

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The rounded-off (ceiled) rectangular zone should be :

l′ × h′ = 474r0 × 140r0

We then determine the lattice factors :

fx = 474 fy = 140 · 0.5773502691896277986 = 81

3.3 Generating with Script application

That second method will produce an input file for Lammps. In the crystalgen directory there exist scriptshelpful to produce crystal input files for Lammps. The interesting one for the described example is gencrystal-lammps.pl. The various scripts for pre/post treatment can be found on the project page1. We first need toprovide a bravais lattice basis vectors file :

argon2D.bravais:

1.22452143391761666 0 0

0 2.1209333385024 0

0 0 7

Then we need to provide the list of atoms present in an unity lattice in reduced coordinates :

maille-argon2D.xyz:

2

ARGN

AR 0.0 0.0 0.5

AR 0.5 0.5 0.5

Then calling the following command generate the input file for Lammps :

./gencrystal-lammps.pl argon2D.bravais maille-argon2D.xyz 474 81 1 > custom.lammps

Then a lammps configuration file must be provided. Let it be in.lj.custom with the following containing :

# 2d Lennard-Jones Argon

units real

dimension 2

atom_style atomic

boundary s s p

read_data config-lammps/data.custom

#velocity all create 80.0 87287 loop geom

pair_style lj/cut 2.93885144140227

pair_coeff 1 1 0.238492861193117 1.1 2.93885144140227

neighbor 0.4 bin

neigh_modify every 20 check no

fix 1 all nve

restart 1000 restart.lammps

thermo 10

run 50

Remark : here the run keyword is present. For use with LibMultiScale it should not be present as it isLibMultiScale who will performs the integration steps.

1http ://gforge.inria.fr/projects/libmultiscale/

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3.4 Carving the coarse model geometry

We have prepared a rectangular 2D crystal. We want to control the dimensions using the LibMultiScalefacilities. To do that, we must complete our configuration file adding a dedicated section. The coarse geometricdescription will be a cube described by its corner :

GEOMETRY CUBE 2 -l2/2 l2/2 -h2/2 h2/2 0 0

The syntax is GEOMETRY ID TYPE DIMENSION PARAMETERS. Parameters are described in the glossary. Thegeometries can be defined anywhere in the configuration files, as well as variables declarations.

#Stamp section

Section Stamp RealUnits

DOMAIN_NAME md

STAMP_FILE config-stamp/CAScfcCustom

GEOMETRY 4 CUBE 2 -l2/2 l2/2 \\

-h2/2 h2/2 0 0

DOMAIN_GEOMETRY 4

DOMAIN_BOUNDARY_GEOMETRY 4

endSection

#Lammps section

Section Lammps RealUnits

DOMAIN_NAME md

LAMMPS_FILE config-lammps/in.lj.custom

GEOMETRY 4 CUBE 2 -l2/2 l2/2 \\

-h2/2 h2/2 0 0

DOMAIN_GEOMETRY 4


endSection

In this sections we defined the name of the domain by section DOMAIN_NAME name, the configuration file usedwith STAMP/LAMMPS_FILE filename, and the geometry of the domain by DOMAIN_GEOMETRY ID. The boundarymust be provided also, but practically it is used in the coupling process, and then need not to be coherent atthis stage. Then the total geometry is assigned also to the boundary. We now have to declare the model in theglobal section by adding MD_CODE STAMP 0 or MD_CODE LAMMPS 0 (where 0 is the declared ID of the model)giving the global configuration file :

#general section




LET r0 = 1.2245214339176166619211e-10

#total domain size

LET L = 1000 * r0


LET h = L / 10


LET l = L / 3





LET h2 = bridgedSize + h

DIMENSION 2

UNITCODE RealUnits

MD_CODE STAMP 0

DUMPER PARAVIEW 1

endSection

#Stamp section


DOMAIN_NAME md


GEOMETRY 4 CUBE 2 -l2/2 l2/2 -h2/2 h2/2 0 0

DOMAIN_GEOMETRY 4


endSection

7

Fig. 3.2 – Coarsed crystal domain generated at stage 1. Distance unities are angstroems.

We also added a DUMPER keyword to request the creation of a dumper component with implementationthrough PARAV IEW output (the first parameter is the frequency at which the dumper should generateoutputs).

Then, launching the command ./AMEL casCustom 1 would produce in ../analysis directory the initialdumps in VTK Xml format2. The figure 3.2 illustrate what should be obtained at this stage.

Remark : The main difference between Lammps and Stamp component is the internal unit system used.Lammps have an internal system that use angstroem metric system unit. Stamp uses SI metric system unit.The difference is notified by the command UNITCODE option (option = AtomUnits/RealUnits)

In order to refine the geometric description, we have to use composed geometries. In that manner, we candecompose the total atomic geometry in three geometries as presented by the figure 3.3. Two circles with radiush2/2 and centers (−l/2, 0) and (l/2, 0) respectively, and a rectangle with (−l/2,−h/2), (−l/2, h/2),(l/2,−h/2)and (l/2, h/2) as corners. This can be done by the following definitions :

#Stamp section


DOMAIN_NAME md


#definition of sub geometries

#values used to define the half circles and the central square

LET ANGLE1 = pi/2

LET ANGLE2 = 3 * ANGLE1

GEOMETRY 2 BALL 2 -l/2 0 0 h2/2 ANGLE1 ANGLE2

GEOMETRY 3 BALL 2 l/2 0 0 h2/2 ANGLE2 ANGLE1

GEOMETRY 4 CUBE 2 -l/2 l/2 -h2/2 h2/2 0 0

#union of the geometries

GEOMETRY 5 UNION 2 3


DOMAIN_GEOMETRY 6


endSection

We have prepared the crystal for the multi-scale model. We now have to focus on the preparation of thecontinuum domain.

3.5 Preparing the mesh

The current way used to prepare the final mesh needs the software Gmsh3that can build 2D/3D meshes. Wecan consider a scale factor that will be passed to LibMultiScale as a parameter. This is an option for convenientbuild of the mesh. We then consider that L = 2.

2readable by the opensource software ParaView3Any mesh generator software that produce readable formats for LibMesh should work fine with LibMultiScale.

8

Fig. 3.3 – refined molecular domain.

The first stage of building consists in placing the relevant boundary points of the domain. These points willbe added for the external boundary :

(−1,−1) (−1, 1) (1,−1) (1, 1)

and for the internal boundaries :

(−0.33,−0.1) (−0.33, 0.1) (0.33,−0.1) (0.33, 0.1)

Then we have to introduce the points to define the bridged zone by the points :

(−0.33,−0.14) (−0.33, 0.14) (0.33,−0.14) (0.33, 0.14)

Finally, in order to describe the curvatures we define the points :

(−0.43, 0) (−0.47, 0) (0.43, 0) (0.47, 0)

The Gmsh file you should obtain is :

Point(1) = {-1,-1,0,0.1};

Point(2) = {-1,1,0,0.1};

Point(3) = {1,-1,0,0.1};

Point(4) = {1,1,0,0.1};

Point(5) = {-0.33,-0.1,0,0.1};

Point(6) = {-0.33,0.1,0,0.1};

Point(7) = {0.33,-0.1,0,0.1};

Point(8) = {0.33,0.1,0,0.1};

Point(9) = {-0.33,-0.14,0,0.1};

Point(10) = {-0.33,0.14,0,0.1};

Point(11) = {0.33,-0.14,0,0.1};

Point(12) = {0.33,0.14,0,0.1};

Point(13) = {-0.43,0,0,0.1};

Point(14) = {-0.47,0,0,0.1};

Point(15) = {0.43,0,0,0.1};

Point(16) = {0.47,0,0,0.1};

Point(17) = {-0.33,0,0,0.1};

Point(18) = {0.33,0,0,0.1};

Now, we have to build the segments, and then the surfaces in order to let Gmsh generate the elements. Thefollowing lines constitute the geometric information of the continuum domain (eventually, they can be builtusing the graphical interface of Gmsh) :

9

Fig. 3.4 – skeleton points for the mesh that should be obtained

Circle(1) = {8,18,15};

Circle(2) = {15,18,7};

Circle(5) = {10,17,14};

Circle(6) = {6,17,13};

Circle(7) = {13,17,5};

Circle(8) = {9,17,14};

Circle(9) = {11,18,16};

Circle(10) = {12,18,16};

Line(11) = {6,8};

Line(12) = {5,7};

Line(13) = {9,11};

Line(14) = {10,12};

Line Loop(15) = {10,-9,-13,8,-5,14};

Line Loop(16) = {11,1,2,-12,-7,-6};

Plane Surface(17) = {15,16};

Line(18) = {4,3};

Line(19) = {1,2};

Line(20) = {2,4};

Line(21) = {3,1};

Line Loop(22) = {18,21,19,20};

Plane Surface(23) = {22,15};

Now, one could play with the weights in order to inform Gmsh of the surfacic constraints on elements wewant to maintain. Typically we want the mesh to be well refined near the center of the domain, i.e. the futureatomic zone. In that manner we affect weights of 0.01 to points 5 to 12. Now using the Gmsh mesh constructionfacility we may obtain the result presented on the figure 3.6 by typing :

gmesh -o mymesh.unv -format unv -2 file.geo

where file.geo is the file containing all the precedent geometric informations. Then a mesh file formatted withUNV standard loadable by LibMesh is produced. This file should be placed in LibMultiScale/run/config-libmesh/

in the standard file tree place.

Remark : one can refine in a different way by playing with the weights placed onto the initial points. Creatingother internal surfaces allow refinement to be better controlled. For example, setting the same weight to all pointsinduce the mesh presented by figure 3.6.

10

Fig. 3.5 – segment and surfaces for the mesh that should be obtained

We open a new section block with name LibMesh :

#LibMesh section

Section LibMesh RealUnits

...

endSection

Then we need to set the name of the domain :

DOMAIN_NAME mymesh

Then we have to set the size of the domain. The global size has been decided to be L = 1000r0.Then we notify the file that the libMesh will have to load :

MESH_FILE config-libmesh/mymesh.unv L/2

The following parameter is the scaling factor. It is set in order to scale the mesh file to the real domain size.As we choose L = 2 in the mesh file, we may want to scale by half the real domain size.

We also have to describe the geometry of the domain. This is done using the substraction operator andthe shrink operator. The shrink operator takes any basic geometry (no combined geometries) and reduces itfollowing given parameters. The geometry declaration take the form :

#full domain cube

GEOMETRY 17 CUBE 2 -L/2 L/2 -L/2 L/2 0 0

#shrinking the two circles

GEOMETRY 18 SHRINK 5 bridgedSize 0 0

#shrinking the central cube only on the y axis

GEOMETRY 19 SHRINK 4 0 bridgedSize 0


GEOMETRY 21 SUB 17 20

DOMAIN_GEOMETRY 21


11

Fig. 3.6 – Final mesh obtained by Gmsh

We have to define the constitutive relation that need to be used as well as the mass of the monoatomiccrystal. We want to use a constitutive law defined by the Cauchy-Born rule with a lennard-jones potential. Weprecise the parameters by :

CONSTITUTIVELAW CAUCHY-BORN 2.1*r0

LENNARDJONES r0 1.6567944e-21 0.11e-9 [lattice_file]

MASS 39.95e-3

For the Cauchy-Born constitutive law to work well, one should specify a bravais lattice section into a givenfile (or in the same file as the LibMesh section if no file name was specified). This section should look like :

#crystal section

Section Lattice RealUnits

LET sqrt3 = 1.732050807568877294

BRAVAIS 0 r0 0.0 0.0

BRAVAIS 1 r0/2 r0/2*sqrt3 0.0

ATOMTYPE Ar 39.95e-3 0

NBATOM 1

ATOM Ar 0.0 0.0 0.0

endSection

which is the declaration of a mono-atomic crystal of Argon with two atoms per lattice.

Also, the atomic mass is required in order to compute the cauchy-born rule. And finally we declare thetimestep that will be used :

TIMESTEP 1e-15

In order to dump the finite element domain, the same way that we did for the molecular dynamics model,we have to declare it in the global section adding :

ELAST_CODE LIBMESH 1

At the stage 3, the configuration file should look like :

File Edit Options Buffers Tools Help

#global section



12


LET r0 = 1.2245214339176166619211e-10

#total domain size

LET L = 1000 * r0


LET h = L / 10.


LET l = L / 3





LET h2 = 2*bridgedSize + h

DIMENSION 2

UNITCODE RealUnits

MD_CODE STAMP 0


DUMPER PARAVIEW 1

endSection

#Stamp section


DOMAIN_NAME md




LET ANGLE1 = pi/2


GEOMETRY 2 BALL 2 -l/2 0 0 h2/2 ANGLE1 ANGLE2

GEOMETRY 3 BALL 2 l/2 0 0 h2/2 ANGLE2 ANGLE1

GEOMETRY 4 CUBE 2 -l/2 l/2 -h2/2 h2/2 0 0




DOMAIN_GEOMETRY 6


endSection

#LibMesh section




DOMAIN_NAME mymesh






DOMAIN_GEOMETRY 21


LENNARDJONES r0 1.6567944e-21 0.11e-9

TIMESTEP 1e-15

MASS 39.95e-3

endSection

#crystal section

Section Lattice RealUnits

LET sqrt3 = 1.732050807568877294

BRAVAIS 0 r0 0.0 0.0

13

BRAVAIS 1 r0/2 r0/2*sqrt3 0.0

ATOMTYPE Ar 39.95e-3 0

NBATOM 1

ATOM Ar 0.0 0.0 0.0

endSection

Reusing the command ./AMEL casCustom 1 will now produce one more vtu file describing the continuummodel giving the result presented by figure 3.7.

Fig. 3.7 – Full domain

3.6 Preparing the bridging zone

At this step of the construction we have defined both models. The coupling is activated by the simplekeyword

BRIDGING_CODE TYPE ID1 ID2 OPTIONS...

The bridging that will be described is based on the Bridging Method (the only one stable at this time). Weneed to manage a Bridged Zone where the DOFs of both domains will be weighted.

The detection of the DOFs involved in the bridging zone is made by a simple test : any DOFs for whichits initial position is inside the intersection of both model geometries, is considered as a coupled DOF. Theponderation process has a detached procedure. In order to help the LibMultiScale to know the shape of theweighting gradients, the user have to provide a geometry ID. This geometry can be composed only by operatorUNION. All primitive are accepted. We then have to describe the Bridging Zone by four sub geometries :

GEOMETRY 100 CUBE 2 -l/2 l/2 -h2/2 -h/2 0 0

GEOMETRY 101 CUBE 2 -l/2 l/2 h/2 h2/2 0 0

GEOMETRY 102 BALL 2 -l/2 0 h/2 h2/2 ANGLE1 ANGLE2

GEOMETRY 103 BALL 2 l/2 0 h/2 h2/2 ANGLE2 ANGLE1




BRIDGING_CODE BRIDGING 0 1 106

14

If we submit this configuration file, AMEL generates additional VTU files :

– recatomesatoms weigth.vtu– recelemsmesh weigth.vtu– grid.vtu– fictifsatomesatoms weigth.vtu– fictifselemsmesh weigth.vtu– grid-fictifs.vtuThe two first ones are presented by figures 3.8 and 3.9. It presents the DOFs that were detected inside of the

bridging zone based on the geometric description given. And the color field represents the associated weight.

Fig. 3.8 – Mesh part detected inside if the bridging zone at stage4

Fig. 3.9 – Atoms detected inside if the bridging zone at stage4

It can be seen that it did not worked correctly. Due to the curvature of the circles, atoms may have beeninside of both domain geometric description, but not inside of the desired elements. Then the LibMultiScalehave selected additional elements creating the “elemental picks” around the mesh. Additionally some nodeshave a weight of zero indicating that there were not inside the Bridging Zone geometry (default weight is zero).

Then, as a reaction to the problem, one should reduce with a delta parameter the atomic domain and growequivalently the bridging zone geometry.

The grid VTU dump files are the grids used to speed up the computation of atom-element association.Concerning the other files, they treat a part of the coupling we did not approach until now. On a geometry

like the one presented, boundary conditions cannot be maintained on the free surfaces4. The surface effectinvolved can be controlled by the coupling component. This is the goal of the boundary geometries in themolecular dynamics cases. One should define a zone where the atoms are concerned by the force field rupturenear the free surface. Then the coupling component will detect these atoms and owning elements to imposeto these atoms a displacement interpolated by the continuum domain. The two last “fictifs” files present the

4in simpler geometries, periodic boundary conditions could be applied, or truncated potential

15

detection. As we declared the boundary geometry to be the same as the domains, then all the atoms in thebridged zone will have an imposed displacement. We must refine the boundary geometry to conform the wantedatoms (i.e. free surface within a given cutoff radius range).

The total configuration file at stage 5 would be :

#global section




LET r0 = 1.2245214339176166619211e-10

#total domain size

LET L = 1000 * r0


LET h = L / 10.


LET l = L / 3





LET h2 = 2*bridgedSize + h

#delta parameter

LET delta = r0/6

DIMENSION 2

UNITCODE RealUnits

MD_CODE STAMP 0


GEOMETRY 100 CUBE 2 -l/2 l/2 -h2/2-delta -h/2 0 0

GEOMETRY 101 CUBE 2 -l/2 l/2 h/2 h2/2+delta 0 0

GEOMETRY 102 BALL 2 -l/2 0 h/2 h2/2+delta ANGLE1 ANGLE2

GEOMETRY 103 BALL 2 l/2 0 h/2 h2/2+delta ANGLE2 ANGLE1




BRIDGING_CODE BELYTSCHKO 0 1 106

DUMPER PARAVIEW 1

endSection

#Stamp section


DOMAIN_NAME md




LET ANGLE1 = pi/2


GEOMETRY 2 BALL 2 -l/2 0 0 h2/2-delta ANGLE1 ANGLE2

GEOMETRY 3 BALL 2 l/2 0 0 h2/2-delta ANGLE2 ANGLE1

GEOMETRY 4 CUBE 2 -l/2 l/2 -h2/2-delta h2/2-delta 0 0




#definition of the boundary

LET rcut = r0 * 2.6

16

GEOMETRY 7 SHRINK 5 rcut 0 0

GEOMETRY 8 SHRINK 4 0 rcut 0


GEOMETRY 10 GROW 5 r0 0 0

GEOMETRY 11 GROW 4 0 r0 0



DOMAIN_GEOMETRY 6


endSection

#LibMesh section




DOMAIN_NAME mymesh






DOMAIN_GEOMETRY 21


LENNARDJONES r0 1.6567944e-21 0.11e-9

TIMESTEP 1e-15

MASS 39.95e-3

endSection

The user must control that the ponderation is correct, that the surface effect will affect the appropriateatoms. All the configuration of the model was done in a sequential aspect. Simulation can yet be launchedchangeing the number of step to the desired one :

./AMEL casCustom 10000

The description of the stimulation and dumpers needed to alter and monitor the simulation is given in theglossary. Concerning the processor mapping, the user can consult the next section.

3.7 Configuring the distribution over a cluster of processors

At this day, there is only one type of distribution possible. Two models cannot coexist on the same processor.More precisely, each processor will be the host for one model and only one model as a UNIX processus. Thenthe option for the user is to decide how many processors are attributed on a given model. This is done by thekeyword PROCESSORS. A sample configuration using 4 processors, 3 for the MD model and 1 for the FEmodel should be :

COM DISTRIBUTED

PROCESSORS 1 3

PROCESSORS 0 1

where the COM keyword expose the mapping solution. As we said, this is actually the only one available.

17

Chapitre 4

Keyword list

In this chapter are described all the rules and keywords for the parser of AMEL.

4.1 Section syntax

A section should be declared as follow :

Section NAME UNITS

...

endSection

where the name of the section is specified by NAME, and UNITS specify the units that will be used in thatsection. This is mandatory in order to have an automatic units conversion, ensuring common config files fordifferent internal units (hence for different codes). UNITS can have the value RealUnits (S.I.) and AtomUnits(angstroems,...).

4.2 Variable declaration

LET varname = mathexpression

This is used to declare any reusable variable in the configuration files. The variables are defined in thereading order. If a keyword, like MD CODE or ELAST CODE is placed, the variables defined in the calledsection will be defined for the next line of the currect section.

PRINT var

Used to dump the value of a variable. Debug usage for preparation of the domains, geometry ... etc.

4.3 Geometry keywords

GEOMETRY ID TYPE OPTIONS ...

The description of the different types follows now.

Declaration of a BALL geometry.

GEOMETRY ID BALL 1 CX RMIN RMAX

GEOMETRY ID BALL 2 CX CY RMIN RMAX TMIN TMAX

GEOMETRY ID BALL 3 CX CY CZ RMIN RMAX TMIN TMAX PMIN PMAX

The declaration is dimension dependant. Considering the spherical coordinates, RMIN,RMAX from theradius offset. TMIN TMAX, the angle offset for teta coordinate. PMIN, PMAX, is the angle offset on the lastcoordinate.

Declaration of a CUBE geometry

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GEOMETRIE 1 CUBE 2 0 5 0 5 0 2 GEOMETRIE 1 CUBE 2 0 5 0 5 2 2

Fig. 4.1 – Here are presented the geometries declared for two different use of the hole parameter.

GEOMETRY ID CUBE 1 XMIN XMAX HX

GEOMETRY ID CUBE 2 XMIN XMAX YMIN YMAX HX HY

GEOMETRY ID CUBE 3 XMIN XMAX YMIN YMAX ZMIN ZMAX HX HY HZ

The declaration is demention dependant. The parameters are the coordinates of the bounding box. The lastparameters (HX,HY,HZ), specify a possible hole in the bounding box allowing various geometries like presentedby figure 4.1.

Declaration of an ELLIPSOID geometry

GEOMETRY ID ELLISPOID 1 CX A1

GEOMETRY ID ELLISPOID 2 CX CY A1 A2

GEOMETRY ID ELLISPOID 3 CX CY CZ A1 A2 A3

CX,CY,CZ specify the center of the ellipsoid. the parameters A1, A2 and A3 specify the axis length of theellipsoid.

Declaration of a composed geometry

GEOMETRY ID INTER ID1 ID2

GEOMETRY ID UNION ID1 ID2

GEOMETRY ID SUB ID1 ID2

INTER produce the intersection of geometries ID1 and ID2 while UNION produce their union. SUB sub-stract the geometry ID2 from the ID1 geometry.

Shrinking/Growing a geometry

GEOMETRY ID SHRINK ID1 FX FY FY

GEOMETRY ID GROW ID1 FX FY FZ

The FX,FY,FZ parameters should positive. Only composed geometries, CUBE and BALL may be used bythis operator. In the BALL case, only FX is relevant, modifying the RMAX value. In cube case, the boundingbox is reduced in each direction following FX,FY,FZ.

4.4 Atomic domain keywords

Giving the domain name :

DOMAIN_NAME name

Defining the domain geometries :

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DOMAIN_GEOMETRY ID

DOMAIN_BOUNDARY_GEOMETRY ID

This is the total domain geometric description and the boundary geometry. The boundary geometry is onlyused by the coupling components to correct surface effects.

Setting behavior for parallel optimisation (optional).

MIGRATION value

value can be enable or disable. It has sense only for parallel simulations. By default it is enabled. At presenttime this keyword is deprecated.

4.4.1 Lammps keywords

LAMMPS FILE config-file

4.4.2 Stamp keywords

STAMP FILE config-file

4.4.3 MD1D keywords

This model works only in 1D.

RCUT value

Defines the cutoff range for the potential.

R0 value

Defines the interatomic distance of the simulated monoatomic crystal.

NUM_ATOMES value

Defines the number of atoms wanted. The generated crystal will be centered.

MASS value

Defines the atomic mass.

TIMESTEP value

Defines the timestep of simulation.

EPSILON value

SIGMA value

Defines the parameters for the Lennard-Jones potential.

4.4.4 DummyMD keywords

This model is used to replay a saved simulation. Thus a model have to be reloaded and then frames areread instead of calculated.

DUMMY_TYPE type

Specify the type of simulation to reload. It can be LAMMPS, LAMMPS or MD1D.

DUMMY_FILE file

Specify the config file used to initiate the domain. It is hence a STAMP or LAMMPS or MD1D configurationfile.

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4.5 Continuum keywords

Giving the domain name :

DOMAIN_NAME name

Defining the domain geometries :

DOMAIN_GEOMETRY ID

DOMAIN_BOUNDARY_GEOMETRY ID

This is the total domain geometric description and the boundary geometry. The boundary geometry is onlyused by the coupling components to correct surface effects.

ELEM_SIZE value value2D value3D

This specify the uniform size of the elements in each direction. This is used for automatic grid meshing ofthe continuum domain.

CONSTITUTIVELAW type params

This specify to the constitutive law controller that is wanted. At present time, possible values for type areCAUCHY-BORN and LAME.For CAUCHY-BORN type, one parameter has to be specified and is a cutoff radius. A command line specifyingpotential to be used is then required.For LAME type, lame parameters are required ( Poisson modulus should be precised first ).

TIMESTEP value

Specify the explicit timestep value.

LENNARDJONES r0 epsilon sigma lattice_file

Specify the parameters for the lennard jones parameter. First one is interatomic distance and others areclassical lennard-jones parameters. If lattice file is specified then the Lattice section is searched in that file.Otherwise the lattice section is searched in the current file.

ANALYTIC_EAM a p re ksi q lattice_file

Specify the parameters for the analytic eam potential. The computed potential has the formula :

W =∑

i6=j

a exp(−p(rij

re− 1)) + ksi

√

∑

i6=j

exp(−2q(rij

re− 1))

EAM potential_file lattice_file

Specify the parameters for the eam potential. The potential file has the standard format described at theaddress http://www4.eas.asu.edu/cms/potentials/main/main.htm

MASS value

Mass used to compute initial density.

MESH_FILE file_name scalefactor

This notify the filename of the mesh to be loaded. Then the mesh will be scaled by the given factor.

SHIFT x y z

This will translate the nodes by the vector (x,y,z), giving opportunity to tune the mesh position with atoms.

RESTART_FILE filename

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Specify a file to reload positions, velocity and forces stored at a given state. It should be a zipped xml filewith valid tags. Such files can be generated by dumpers (see Dumper section).

RELOAD_PARTITION filename

not yet documented

BOUNDARY_CONDITION geom_id type regexp1D egexp2D regexp3D

The boundary conditions specified by this option affect the geometry given by the geom id parameter. Theboundary conditions can actually be of two types : DISP or PBC.

– DISP imposes a given displacement given by the regular expression that should be like ux = 2 uy =0 uz = 0.

– PBC declares a periodic boundary condition. It is functional only for auto-generated meshes (grid meshes).Then a fusion of different nodes is operated in order to have a periodic behavior of the simulation.the regexp parameters specify the dimensions in which this operation is to be performed (example :X = 1 Y = 0 Z = 0 for a periodic boundary condition along X axis).

PRESSION value

This is used to apply a pression onto the X-Z surfaces of a continuum domain. The value of the pression isto be precised in the used code units (no automatic conversion). Obviously this option was created for a reallyspecific job. Not to be used commonly.

4.6 Lattice keywords

This following keywords are to be used into a Lattice section.

BRAVAIS coordinate axisx axisy axisz

Specify a bravais vector identified by coordinate. There should be as much bravais vectors as the dimensionof the space.

ATOMTYPE type mass charge

Declare one atom type that is to be associated with mass and charge.

NBATOM value

Specify the number of atoms into the lattice. There should be as use of ATOM keyword (see the following)as NBATOM specify.

ATOM type x y z

Declare one atom into the lattice. The coordinates are lattice relative. Type parameter should refer to aprevious declaration by ATOMTYPE.

4.7 Global keywords

This keywords should be used in the MultiScale section (which should be unique for a given case).

UNITCODE value

This command is used to specify the internal units that will be used. The possible values are AtomsUnitsand RealUnits.

MD_CODE type ID conffile

This keyword defines a molecular dynamics domain. The type defines the code that will be used to computethe trajectories of the atoms (MD1D, LAMMPS, STAMP or DUMMY). The ID parameter identify by a numberthe domain hence declared. The conffile parameter specify where to find the information about the configurationof this domain, which will have to contain a section about that type of domain. If no file is specified, then thecurrent file is parsed for such a section.

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ELAST_CODE type ID conffile

Idem for continuum mechanics code. Values for type can only be LIBMESH at present time.

BRIDGING_CODE TYPE IDMD IDCONTINUUM geomID [GRID_DIVISIONX value]

[GRID_DIVISIONY value]

[GRID_DIVISIONZ value]

This keyword declares a bridging zone coupled by a method of type TYPE. Types can be :– BELYTSCHKOFULL : belytschko method but with no condensation of the constraint matrix. Functional

only in sequential.– BELYTSCHKO : belytschko method but with condensation of the constraint matrix. It is the more

generic approach.IDMD and IDCONTINUUM are domain identifiers that must have been introduced by the command

MD CODE and ELAST CODE respectively. The geomID identify a geometry that will be used for the des-cription of the weighting functions.

In the computation of the association between atoms and finite elements, a spatial grid is used to speed upthe research. The optional GRID DIVISIONX parameters define the granularity of such a spatial grid alongthe X-axis. Idem for the GRID DIVISIONY and GRID DIVISIONZ parameters.

4.8 Dumper keywords

Declaration of a dump component :

DUMPER TYPE FREQUENCY OPTIONS ...

all dumper have their frequency to be specified. The options may change one to an other. Still, there aregeneral options :

– FILTERGEOM geom id : used to request a filter on geometrical criterion. Only dofs into the specifiedgeometry will be dumped.

– FILTERDISP value : The criterion for filter is base on the displacement field. If the displacement value,in absolute, exceed the given value, then the dof is dumped.

– FILTERVEL value : same thing for velocity field.– FILTERFORCE value : same thing for force field.– PREFIX dir : specify the directory where the dumped file should be created. Default is ../analysis/The Paraview Dumper :

DUMPER PARAVIEW FREQUENCY [DISP] [VEL] [FORCE] [CONSTRAINT]

[BASE64] [TEXT] [ID] [MASS]

[PROC] [COMPRESSED] [P0]

the options are explained :

DISP : request dumping the displacements

VEL : request dumpin the velocities

PROC : request dumping the distribution

FORCE : request dumping the force/acceleration field

CONSTRAINT : request dumping the constraint field

DEFORMATION : request dumping the deformation field (only for continuum)

BASE64 : request using in the base64 mode(default)

TEXT : request dumping in the text mode

COMPRESSED : compression of dumped file is activated (only if zlib support has been compiled)

ID : internal identity number of each dof is dumped as a normal field used for debugging only

MASS : mass associated with each dof is dumped

P0 : initial position is dumped

DUMPER EPSN FREQUENCY xml_file

Unmaintained.

DUMPER DUMPER1D FREQUENCY

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Produce 1D dump files analysable via gnuplot scripts. the script analysePVF.pl should be used to producevideos or fig files.

DUMPER FIG FREQUENCY

If libMesh has been compiled with the fig support this should produce (only in sequential) a valid xfig file(helpfull to produce documentation)

DUMPER SCOTCH FREQUENCY

This will produce (in sequential only) scotch graph format files. Mainly used in internal to produce graphtaking into account the coupling stage.

DUMPER DUMPERECIN FREQUENCY

This will produce a single txt file with the kinetic energy for each timestep.

DUMPER XYZ FREQUENCY

This will produce an XYZ file for the atoms (only).

DUMPER LAMMPS FREQUENCY

This will produce a lammps file for the atoms (only). This file will be loadable for a simulation using lammpsmodule.

DUMPER RESTART FREQUENCY

This will produce restart files for the used codes. One restart file produced by lammps may not be used withStamp. The format is xml with dedicated tags and optionally (depend on the compilation of LibMultiScale)gzipped.

4.9 Stimulation keywords

This presents all the stimulation that is possible to inject.

STIMULATION type options

This declares the use of a given stimulation. There are two kinds, initial and permanent stimulation. Thefollowing details the principal types.

STIMULATION GAUSS lWave intensity geometryID

This produces an initial displacement with a gaussian expression onto a given geometry. The value atthe exponential term is given by lWave while the intensity value modify the factor against the exponential(intensity · e−(2πr/lWave)2 where r is the distance to the center of the given geometry).

STIMULATION SIN lWave intensity geometryID

This produces an initial velocity field following a sinusoid function intensity · sin(2πr/lWave).

STIMULATION MODULATE lWave intensity geometryID

This produces a modulation over the actual displacement by a given frequency. The applied formula isu+ = intensity · cos(2πr/lWave).

STIMULATION RAZ

This is used when restarting a situation. One may want to reset displacement, velocities, forced to zero. theinitial positions are then set

STIMULATION MATIERELANCEE axe intensity geomID

This produce a uniaxial velocity field over the given geometry. The velocity field follows a gradient orientedalong a given axes (1=x, 2=y, 3=z) growing from the center of the geometry to the external surfaces. Theintensity is the higher value imposed.

STIMULATION STABILISE

This implements the stabilization algorithm of Melh (minimization heuristic that kill velocities which donot follow the potential slope).

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4.10 Parallel keywords

In order to declare the distribution over a cluster, one should set the following keywords.

COM DISTRIBUTED

PROCESSOR ID_DOMAIN nb_procs

In the future, other methods of distribution, accounting to the geometrical situation will be available.

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