Biodyn – User manual
Contents
1. 17 Biodyn User manual Running tests from imported models The follow step to the setting of the properties and imposition of the conditions and the subsequent creation of the mesh is the solution of the problem created If the user has correctly introduced the data and the mesh has a good quality without slices null volume elements no overlapped or repeated nodes or element Biodyn can run the test Files View Geometry Utilities Data Mesh Help eo PS OD o Ve Once all the data was right E 09 00 P IS as lata inserted and the mesh was been created correctly user can run the problem ter that is possible to control and follow the process evolution with this remarked tool Delete result files Figure 11 Calculate command and View process info tool From the toolbar select Calculate gt Calculate The program will start to solve the problem If the user wants it is possible to visualize some information about the status of the computation Calculate gt View process info Biodyn will plot on screen the information about the test run and ulterior information about the convergence of the calculation If some error occurs Biodyn will print on screen the information about it Pue 182. General Conditions Inlet amp Oulet Fluid Conditions Fluid Velocity Data Profile appearence Maximum Peak Velocity m sec 0 7 v Velocity misse Welocity Profile time variation gustomized Profile Pressure Da Systolic max Pressure mmHg 1201 Diastolic min Pressure mmHg 80 0 Pressure Profile time Version use D Wall Data Assign wall to layer Body Data Assian body to layer Import Model Export Current Model Figure 7 Inlet amp Outlet Fluid Conditions window Velocity Data 53 Red circles indicate the combo windows for the assignation of different types of velocity or pressure profiles These combos in the green circles are used to assign automatically the properties to the layers This combos are turned on only if the check button in the orange circles are activated Blue circles indicates the check button for the activation of the customized profile e Maximum Peak Velocity is the maximum value that the peak of flow can reach The dimension is in m sec and the default value is set to 0 7m sec e Velocity profile this field permits to select how the flow changes along the time It is possible to choose a standard pulse profile a sinusoidal profile or a linear one e Customized Profile if the user turns on this field the button EDIT is turned on Picking this button the user can introduce manually the points of that describe the profile tr
3. E compassfem cnd Fichero cnd 15 07 201018 14 F5599B7E B compassfem bas Fichero bas 15 07 2010 18 14 00000000 Total 1 carpeta y 874 836 octetos en en 5 ficheros Figure 1 Biodyn rar installation files These entire files will be put in the same directory that before in order to run Biodyn automatically when Tdyn is launched After that it is necessary to actualize some GiD properties and conditions To do this please unzip the file gid groups conds rar User could find in the following directory C Program Files Compass Tdyn11 0 5 problemtypes common_lib compass or similar directory a folder named gid_groups_conds User has to substitute this folder with gid_groups_conds rar unzipped Biodyn User manual Ie AAA Archivo rdenes Herramientas Favoritos Opciones Ayuda EFTETTE o R IU A adir Extraeren Comprobar Ver Eliminar Buscar Asistente Informaci n Buscarvirus Comentario Proteger auto extra ble E B gid_groups_conds rar gid_groups_conds archivo RAR tama o descomprimido 29 831 694 octetos Nombre amp Tama o Comprimido Tipo Modificado CRC32 Be E E A E TEMERE di ve Folder 06 02 2012 11 19 e utils Folder 06 02 2012 11 19 Dsre Folder 06 02 2012 11 19 du msgs Folder 06 02 2012 11 19 e images Folder 06 02 2012 11 19 e gid_groups_conds_utils Folder 06 02 2012 11 19 Le gid groups conds full Folder 06 02 2012 11 19 4 gid
4. etc Another important function available is the interpolator the syntax to use is Interpolate 4t f t t f t t3 f t3 t that permit to introduce the value of the pressure in any instant of time Assign Pressure to layer activating this option is possible to assign automatically the properties set before to a layer The layers available appear in the window just on the right of the check button Wall Data Assign wall to layer activating this option is possible to assign automatically the properties set before to a layer The layers available appear in the window just on the right of the check button The wall is the part of the vessel in which the velocity of flow has null value It is usually assigned to the wall vessel Body Data Assign Body to layer activating this option is possible to assign automatically the properties set before to a layer The layers available appear in the window just on the right of the check button The body is the fluid part of the vessel It represents the blood In this part the velocity is free but all the fluid properties are assigned 15 Biodyn User manual Storing data and importing data Biodyn is thought to simplify the analysis of the fluid dynamic simulation especially for blood fluid experiment In many cases is very useful to reproduce many times the same conditions for different geometries or cases In order to make easier this process of experiments reproduction
5. groups conds Folder 06 02 2012 11 19 la writecalcfile tcl 2 628 2 628 Fichero tcl 25 02 2011 19 09 EA58F712 la units xml 16 772 3480 XML Document 20 12 201015 39 C5F599BA A units tcl 12 040 12040 Fichero tcl 25 02 201119 09 E6099FFE A transform tcl 3 552 3 552 Fichero tcl 25 02 2011 19 09 04785C1E A tclIndex 69 943 5373 Fichero 28 01 2011 18 43 25C86889 A reports tcl 15 173 15173 Fichero tcl 25 02 201119 09 44D1A7D3 A post tcl 11 462 11462 Fichero tcl 25 02 201119 09 BB9284A6 A pkgIndextci 917 498 Fichero tcl 25 02 201119 09 9BDC3EE3 a param_creator tcl 15 310 15 310 Fichero tcl 25 02 2011 19 09 31096753 la local_axes tcl 4 269 4 269 Fichero tcl 25 02 2011 19 09 7AFLEDBO la groups tcl 10 933 10 933 Fichero tcl 25 02 2011 19 09 F76EB6B6 3 gid_groups_conds_32 dll 2 139 648 696 367 Application Extens 25 02 2011 19 08 00EA312F la gid groups conds tcl 63 580 63 580 Fichero tcl 25 02 2011 19 09 92515CCD f igid groups conds fsl 13 363200 12 496 850 Fichero fsl 11 01 2011 18 14 F17272AD a function editor tcl 7 642 7 642 Fichero tcl 25 02 2011 19 09 D7AGEEFB 3 draw post tcl 114 687 114 687 Fichero tcl 25 02 201119 09 ECC7AEEE a conditions tcl 34242 34 42 Fichero tcl 25 02 2011 19 09 5D69CAA1 _FOSSIL_ 3 722 240 569 481 Fichero 11 01 2011 15 29 AAFB14A3 eeu Total 8 carpetas y 19 608 238 octetos en 18 ficheros Figure 2 gid_groups_conds rar data folder Biodyn User manual Biodyn Wiza
6. 31 0 64 91 91 0 66 90 50 0 58 89 43 0 70 88 30 0 72 87 32 0 74 86 55 0 76 85 70 0 78 84 85 0 80 84 43 0 82 83 55 0 84 83 44 0 86 83 00 0 88 82 73 0 90 82 57 0 92 82 14 0 94 81 85 0 96 81 28 0 98 80 71 1 00 80 574 Diastolic min Pres From the window ditor is possible to introduce many kinds of function In the example the function interpolate is used Pressure Profle ti E Customized Assign presse to Wall Data Assign wall to layd Body Data Assign body to la Ok Import Model Export Current Model Cancel Figure 8 Introduction of customized velocity data Pressure Data e Systolic max Pressure is the maximum value that the peak of pressure can reach The dimension is expressed in mmHg and the default value is set to 120 e Diastolic min Pressure is the minimum value that the peak of pressure can reach The dimension is expressed in mmHg and the default value is set to 80 e Pressure Profile this field permits to select how the flow changes along the time It is possible to choose a standard pulse profile a sinusoidal profile or a linear one e Customized Profile if the user turns on this field the button EDIT is turned on Picking this 14 Biodyn User manual button the user can introduce manually the points of that describe the profile trough a Function Editor The user can use different kind of function like sinus exponential logarithmic etc
7. Biodyn User manual Bio Uyn Multiphysic Analysis in Bio Engineering Applications User manual Version 0 2 2 International Center for Numerical Methods in Engineering CIMNE Biodyn User manual International Center for Numerical Methods in Engneering Edificio C1 Campus Norte UPC Gran Capit n s n 08034 Barcelona Spain www cimne upc es Noviembre 24 11 2011 BioDYN User Manual CIMNE BIOMENG CIMNE BIOMEDICAL ENGINEERING DEPARTAMENT The Authors Biodyn User manual Historial Document Version Date Participants Remarks V0 1 25 11 2011 MB ES CG JG V0 2 01 02 2012 MB ES CG JG V 0 2 2 06 02 2012 MB ES CG JG Clara Garcia CG Eduardo Soudah ES Julio Garcia JG Maurizio Bordone MB Summary Introducir dci Da 4 Biodyn Installation ii ici 5 lore o A O ECO CESE E 7 Analysis SMN dt ete mets 9 General ConditiN ce E 11 Inlet amp Outlet Fluid Conditions sinirika nennen tnmen nnne nns aa e EKSE Saa EE EEE Eai 13 Mesh creation and r nning tests ss tala id bid ida 17 Running tests from imported Models miii A A a debe EC Sexes duc 18 Figures Figure 1 Biodyn rar installation files coconnnccocnoncnnnnonononannnnnnnnnnnononnnnnnnnnnnnnnno nn REDE RERA REED ED nnns seen neni aia Da nn nnn 5 Figure 2 gid groups conds rar data folder enne nnne dad dia ende nain dea 6 Fip re 3 Blodyn WIZaFd oet e tete aida 7 Figure 4 Biodyn Wizard opened The progra
8. Biodyn has the option to export and import the data setting In the lower bar of the wizard window the central buttons permit to save the conditions set like showed in the previous paragraphs Biodyn could export the data storing them in an xml file Importing the data from the xml file all the ancient data will be replaced for the charged ones Bil ES Analysis Definition General Conditions Inlet amp Oulet Fluid Conditions Fluid Velocity Data Profile appearence Maximum Peak Velocity m sec 10 7 V Velocity m sec Velocity Profile time variation Pulse B d C Customized Profile In the inferior side of the wizard there are the buttons for the exportation and the importation Assign velocity to layer inlet E Pressure Data Systolic max Pressure mmHg 1 20 0 0 Diastolic min Pressure mmHg 180 0 Pressure Profile time Variation Pulse P Pressure mmHg of the settings C Customized Profile properties and Assign pressure to layer Oulet condition of the simulation Wall Data Assign wall to layer Wall Body Data Assign body to layer Blood lt Import Model AJ NExport Current Model A Figure 9 Import and Export tools of Biodyn Wizard 16 Biodyn User manual Mesh creation and running tests If the model charged does not have a mesh the user has to generate the mesh in order to permit to the Biodyn solver to obtain the results To create
9. General Data Heartbeat Rate bpm 60 0 Cycles Number 1 Y Time Step sec 0 001 Initial Steps 25 Automatic Layer Assignment Tools Habilitated Please check correct layer names and properties Import Model Export Current Model Cancel Figure 6 General Condition Window 12 Through these 3 fields user can modify the name of the material or the physical properties of the fluid Density and Viscosity In Biodyn standard values of blood are charged by default but it is possible to select also water or air Heartbeat and Cycle number set the duration of the simulation and the frequency of the pulsatile flow This 2 values set the time step of 1 iteration and the first step for which will be saved the results In this window the user can visualize the information about the layer present in the model of the Project If the project does not have any layers the Biodyn advise the user with this warning If the layers present in the model are 4 in accord to the Biodyn model of solution the program will advertise the ser with this other message Biodyn User manual Inlet amp Outlet Fluid Conditions The third window allows defining the condition of inlet and outlet of the simulation In the left column are showed the data available in the right column Biodyn plots automatically the selected profile of velocity and pressure Analysis Definition
10. ation or to reproduce atypical situations different to the physiological and standard ones The first column of data is so organized Blood Fluid Data e Material Name From this menu user could charge the common values for 3 biologic fluid blood air and water changing this field Biodyn will update Density and Viscosity value automatically next fields e Density is the value of the density of the fluid used by Biodyn It is expressed in kg m the default value is 1040 e Viscosity is the other property of the fluid of the simulation Its default value is set on 0 0035 and the dimension is expressed in kg m sec General data e Heartbeat Rate is the period of one cardiac cycle expressed in beat per minutes bpm this value modifies the duration of the simulation For example if the bpm are 60 the cycle will take 1 second If the heartbeat is 90 bpm the cardiac cycle will take 0 666 seconds If Customized velocity or pressure are activated this data will be ignored e Cycles Number this value that is 1 by default indicate the number of cardiac cycles that the program will perform This number also modify the total time of the simulation the time set in the previous field is multiplied for the number of cycle indicated in this space e Time Step this value expressed in second is the dimension of the time step for one iteration of the computational solution e Initial Step is the first step in which will be written the first resul
11. ee structure with a root and branches directed to the sheets with different relationships between the elements This structure allows adding elements in a very efficient way In Biodyn a user friendly and easy platform all the data information introduced using the help window will be automatically actualized in the interface that will be available from the toolbar of the program This GUI based on a tree structure was developed with the intention of make easy the data flow and the information management 1 WWww compassis com compass Productos Tdyn Biodyn User manual Biodyn Installation Once the user has installed Tdyn software he can import Biodyn rar file in the directory where compassfem problem type is installed as showed in the following example C Program Files Compass Tdyn11 0 5 problemtypes CompassFEM11 0 compassfem gid In the user will find Biodyn directory compassfem_default spd compassfem xml compassfem tcl compassfem cnd compassfem bas Archivo rdenes Herramientas Favoritos Opciones Ayuda EF A 40 A adir Extraeren Comprobar Ver Eliminar Buscar Asistente Informaci n Buscarvirus Comentario Proteger auto extra ble Nombre Y Tama o Comprimido Tipo Modificado ng Folder e biodyn Folder 01 02 2012 17 15 7 compassfem default spd Fichero spd 20 05 201115 36 997BB101 compassfem xml E XML Document 25 02 201119 09 33E75F49 compassfem tcl Fichero tcl 15 03 201114 55 BE6829B8
12. ids After that is possible to choose if Biodyn will work in 3 or 2 Gravity dimensions Negative Y direction 2 Negative Z direction Another Units Units system Int system SI Geometry units m La Figure 5 Analysis definition windows from here users set the generic data of the process Biodyn User manual In the left windows the tree structure contains all the possible options modifiable user has only to pick upon one of them to choose it and immediately on the right side the option chose will appear Gravity field permits to determine the direction of the gravity force The last field available is the Units Here is possible to choose the system of units and finally to decide the unit used by the program Is meter m is selected all the geometries created in the Biodyn environment will have that dimension Change the unit will be useful when for example the user has to work with an imported geometry and the dimensions of that geometry are expressed in millimetres or other ones 10 Biodyn User manual General Conditions The second window of the wizard contains the fields of the fluid properties and the general data of the problem The program charge by default some values those value are the most used in the scientific literature and in the numerical or experimental simulations Anyway the user can modify those values in order to perform a personalized simul
13. m will charge the default values sesseeeeee 8 Figure 5 Analysis definition windows from here users set the generic data of the process 9 Figure 6 General Condition Window cssccccccecessessnsecesececsesesnaaecececeseeseauaecesecuseesesaeaeceeecsseeseasaeenesesseeeegs 12 Figure 7 Inlet amp Outlet Fluid Conditions window cc cccccccecsssessaececececeeseseaeceeecssessesasaeceeeceseesesaeaeeeeeesseeees 13 Figure 8 Introduction of customized velocity data oocccononocooooncnnononanonnnnnnnncnnnonononnnnnnnnnannn no aa aa Dana ea ian Dos 14 Figure 9 Import and Export tools of Biodyn Wizard esses eene nnn nnn nnne 16 Figure 10 Mesh Generation eei tee ceder Estee ced eara taco lee cede caesa snc eed eee Seasmecdtescdeceessunente 17 Figure 11 Calculate command and View process info tool oooooooococccnccnnononoonnncnncnnnanonononnnnncnnnan aa a aa ae ea ea ai anos 18 Biodyn User manual Introduction Biodyn is a medical application contained in Tdyn software Tdyn is an environment for computational fluid dynamics CFD multi physics simulation and fluid structure interaction calculations based on the leading stabilized finite element method FIC FEM Tdyn includes different modules that allow solving Heat Transfer in both solid and fluids Turbulence Advection of Species in fluids and solids and Free Surface problems using
14. nal va Fluid Flow in Fluids Gravity O Negative Y direction 2 Negative Z direction O Another Units Units system Int system SI Iv Geometry units m v Figure 4 Biodyn Wizard opened The program will charge the default values The wizard for the model creation of Biodyn is structured in three principal windows e Analysis definition e General Conditions e Inlet amp Outlet Fluid Conditions Biodyn User manual Analysis definition The first step is to decide and to define the type of analysis to simulate Trough a very simple tree structure the user will define the type of analysis using the menu Simulation Type e Fluid Dynamics Analysis e Coupled Fluid Structural Analysis User can also define the dimension of the simulation in other words the user has the possibility to work in 2D or in 3D To do this user has to use the menu Fluid Simulation Dimension e 3DFlow e 2Dflow Bill ES Analysis Definition General Conditions Inlet amp Oulet Fluid Conditions First step is Problem Definition decided the Select atvpe of problem elected Problem type of C v Simulation Type Y amp User Defined Problem simulation to uHd Dynemi diysis Y Fluid Dynamics Analysis perform zy Coupled Fluid Structural Analysis Y 3D Flow C Y 3 Fluid Simulation Dimension we Flow in Fluids zL3D Flo oe Linear Static Analysis gt 2D Flow oe Internal OX Fluid A Flow in Flu
15. ough a Function Editor The user can use different kind of function like sinus exponential logarithmic etc etc Another important function available is the interpolator the syntax to 13 Biodyn User manual use is Interpolate t f t1 t f t t3 f t3 t that permit to introduce the value of the velocity in any instant of time e Assign velocity to layer activating this option is possible to assign automatically the properties set before to a layer The layers available appear in the window just on the right of the check button If some layer are repeated Biodyn will advertise the user with a waring in order to correct the mistake of assignation BioDyn Gle zx jJ Analysis Definition General Conditions Inlet amp Oulet Fluid Conditions If the Customized i Profile check button Fig is turned on the Edit Velocity Data Profile appearence button is active Picking it the Maximum Peak Velocity m sec 0 7 v Velocity m sec E 8 Function Editor pops Velocity Profile iime va ation amizer up Cg Customized Profile CHuv Assign velocity to Te l e Pressure Data Systolic max Preg 68 0 16 72 10 0 18 70 65 0 20 70 00 0 22 70 92 0 24 72 76 0 26 77 89 0 28 85 78 0 30 97 63X 32 106 0 0 34 110 79 0 36 113 0 0 38 113 42 0 40 114 0 0 42 113 15 0 44 113 32 0 46 108 56 N 48 101 18 0 50 95 40 0 52 94 15 0 54 94 15 0 56 95 84 0 58 95 40 0 60 95 00 0 62 93
16. rd When the user launches Biodyn the program automatically opens the wizard From here the user will start to set the data and the properties of the tests that the user wants to run Otherwise if the user want to import a model is necessary to call the wizard from the toolbar To do this choose from toolbar Data gt Biodyn Models En AED Files View Geometry Utilities Mesh Calculate Reports Postprocess Help OB SlIBwWwH Problemtype amp x From sd user a 3 Import export materials charge the Biodyn wizard ao Q Start data om 488 Groups P a E Data o a Data intemal O Check properties entiti Biodyn will automatically A as read all the information 47 related to the present 3 e model ak AU eb qeS M x of 124 E A A Figure 3 Biodyn Wizard The wizard automatically pops up charging the default setting and reading all the information present in the model in use User can now start to modify data and properties in order to customize the test Biodyn User manual Gil ES Analysis Definition General Conditions Inlet amp Oulet Fluid Conditions Problem Definition Select a type of problem Selected Problern v Simulation Type Y User Defined Problem gt Fluid Dynamics Analysis oe Fluid Dynamics Analysis Coupled Fluid Structural Analysis v 3D Flow vy Fluid Simulation Dimension V Flow in Fluids 3D Flow Y Linear Static Analysis gt 2D Flow Y Inter
17. t calculated The wizard also shows the information about the layers presents in the model charged by Biodyn That information is showed in the right column The layers are an easy way to separate the geometries in different zones in order to assign every geometrical entity to a separated layer Layers permit to visualize only the part of the geometry that the user wants to use and assign to it properties or conditions in an independent way If the model does not have any layers or has not enough layers for a correct simulation the wizard advises the user and the automatic assignment will be turned off 11 Biodyn User manual E BioDyn Sc Analysis Definition General Conditions Inlet amp Oulet Fluid Conditions General layer option Fluid Data Material Name Blood Density kg m3 1040 iscosity ka m s 0 0035 Heartbeat Rate bpm 60 0 Cycles Number 1 ime 0 00 Initial Steps ere are not enough layers in the model to assign data automatically Remember to assign geometry to layers manually using the program menus Import Model Export Current Model Cancel K e Biodyn i Analysis Definition General Conditions Inlet amp Oulet Fluid Conditions General layer option Fluid Data Layers Information Material Name Blood M zm superficie Density kg m3 1040 Volumen trad Viscosity ka m s 0 0035 SS
18. the mesh te user has only to select from the toolbar of Biodyn the route Mesh gt Generate Mesh Otherwise with the keys Ctrl g The user now has to define the size of the element and finally mesh the geometry From the toolbar is it possible to set other advanced option for expert users T n Project UNNAMED m m et LA Files View Geometry Utilities Data Calculate Reports Postprocess Help OO Gba reas T Structured gt e semiStructured b Ja ME Cartesian P gm Boundary layer If the model does not have any mesh user o Sai A Elementtype gt must generate the mesh of the model To do O E SS Mesh criteria this it is necessary to select from the toolbar A ESOS this option or press Ctrl g la KE Draw d Lu OO O AA X Nx gt CE Ge Ct g P Os Erase Tee Sa wen Je s na a hk y gt E lt I RA x K 2 1 qualit Aa al A Mesh options from model po SA Scale assigned sizes e Es WEN Generate mesh element size Maximum element site fas Mesher window presents some basic options The most important one is the size of the mesh criteria delete results elements of the mesh 9 Mesh all surfaces V Delete result files O Mesh surfaces in active layers By default Biodyn will propose a value but it Mesh using default options can be modified by the user unstructured size transitions slow RS 0 5 EH Generate Cancel Figure 10 Mesh Generation
19. the same stabilised scheme mentioned above Tdyn also offers advanced solvers for beams shells and solid structures and includes cutting edge tools for solving fluid structure interaction FSI problems The different analyses available in Tdyn are fully integrated in an advanced graphic user interface GUI for geometry and data definition mesh generation and post processing the analysis results The Tdyn GUI uses a versatile tree like interface for data managing allowing an easy control of the whole process of entering the analysis data Biodyn application allows the creation of models for the blood flow analysis in veins and arteries For an easy use of Biodyn a user friendly interface was created The wizard also allows some modifications of advanced options for the problem definition Trough the wizard is so possible the creation of the model and the setting of its properties step by step This tool is thought to support and to make easier the creation and the solution of blood flow models The information created in Biodyn will be stored in a XML database XML language offers many advantages for the data and information management e XML was accepted for world software leaders and also supports Unicode and it is a recommendation W3C e Syntax rules are simple logic concise and easy to use XML documents are readable clear and easy to create e The information is stored in text format e The elements of a XML document set up a tr
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