Elmer version 8.0 is out

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raback
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Elmer version 8.0 is out

Post by raback » 05 May 2015, 10:09

Dear Elmer Users,

We are happy to announce a new Elmer major release 8.0.

The source code of the release is available in "release" branch of GitHub at https://github.com/ElmerCSC/elmerfem. You may retrieve the release at any later data using its tag by "git checkout release-8.0". There is also a fresh Windows version available at https://sourceforge.net/projects/elmerfem/.

The release notes list the most important new features of Elmer since the last official version 7.0 published on 31 May 2012. There have been thousands of code commits after that time. We have tried to maintain the development branch (trunk in svn, devel in git) stable and backward compatible. For that reason there has been very few official releases.However, as the use of Elmer expands to new areas where stability of code is more important we aim to have more regular official releases. For production runs the release branch is thus recommended.

Recently Elmer had been trasferred from using gnu autotools to cmake, and from using svn into git. These are important changes that enable the bright future of the code. However, here we list mainly the new features related to code functionality. The internal changes required in the cmake transition, package generaration and multithreading have been equally significant but they are omitted here. These may be relevant if you're developing the code but for standard users the inner workings of Elmer should not be of too much concern.

The core information on cmake and git transition has already been made separately available. For more information, see

http://goo.gl/oqRgtq
http://goo.gl/8qNaVM

Additionally the features related to Elmer/ICE branch of Elmer are not covered by these release notes.
The Elmer/ICE related information is well covered in its dedicated site at:

http://elmerice.elmerfem.org/

We would like to thank the developers outside CSC for many important contributions. Also there has been many users testing Elmer and sending bug reports. Without these efforts development of Elmer could not have been as fast.

Best regards,
ElmerTeam

Code: Select all

Elmer Release Notes for version 8.0
===================================

Previous release: 7.0
Period covered: 1 June 2012 - 28 April 2015 

New Finite elements
-------------------
- New edge element basis functions for H(curl):
  o 6-DOF triangle
  o 6-DOF quadrilateral
  o 12-DOF tetrahedron
  o 10-DOF pyramid
  o 8-DOF pyramid (use only for affine elements)
  o 15-DOF prism
  o 27-DOF hexahedron
- New face element basis functions for H(div):
  o 6-DOF triangle (BDM)
  o 6-DOF quadrilateral (ABF)
  o 12-DOF tetrahedron (BDM)
- Several new test cases relating to new edge and face elements added
- The documentation of face and edge elements created (Appendix F of ElmerSolver manual) 


Linear system solvers
---------------------
- FETI, Finite element tearing and interconnect
  o A domain decomposition method for solving large elliptic problems in parallel
  o MUMPS serial and QR of Cholmod may be used for nullspace detection of the local problems,
  o Add option 'Feti dump system=Logica', to dump the FETI system
    (K,f,R,B) to disk. Dump may also include inequality constraints.

- Support for Intel MKL (Pardiso) with WITH_MKL:BOOL=TRUE|FALSE CMake variable. 

  Allow some more control over the MKL Pardiso settings, especially setting the matrix
  type by using keyword 'Linear System Matrix Type', with choices    
  o 'general' or 'nonsymmetric'
  o 'postive definite'
  o 'symmetric idefinite'
  o 'structurally symmetric

  the last three also need the setting "Linear System Symmetric = True".
  If this keyword is not given, the matrix type is determined as    
  o "Linear System Symmetric=False" -> 'nonsymmetric'
  o "Linear System Symmetric=True" & "Linear System Positive
     Definite=true"  -> 'positive definite'
  o "Linear System Symmetric=True" & "Linear System Postive
     Definite=False" -> 'structurally symmetric'
    
  Note that the "Structurally Symmetric" mode of the MKL Pardiso can't handle
  (symmetric) indefinite matrices.

- Updated Hypre & Trilinos interfaces.
  o HYPRE parameter 'BoomerAMG Strong Threshold'
  o Add interface to Hypre AMS preconditoner.
  o In Trilinos added possibility to pass node coordinates to ML 
    (set "aggregation: aux: enable" in the ML parameter list)

- Direct solvers
  o Default to MUMPS for parallel direct solver
  o Default to Umfpack for serial runs

- Keep MPI alive even if #cores=1, e.g. allow, f.ex., use of MUMPS solver in serial runs
  with MPI-linked executable.  

- GCR iteration
  o  Recompute the true residual when restarting and check the accuracy of
     the iterated residual norm when the convergence criterion is met

- Stopping creteria
  o Add option to use |Ax-b|/(|A||x|+|b|) as stopping criteria.
  o Componentwise and normwise relative backward errors may be used as stopping criteria for linear solvers.

- Add 'mumpslocal' direct solver option (has some additional functionality to 'mumps')

- Possibility to scale the solution optimally before going to linear systems solution. 

- Added namespace 'mglowest:' to the linear solvers used for the lowest level in all multigrid methods.

- Converge tolerances related to the block preconditioning may now be adjusted adaptively during the
  solution process if the keyword "Linear System Adaptive Tolerance" is given.

- Enable saving of ConstraintMatrix mainly for debugging purposes. 

- Added Matrix_t field  "PrecValues(:)"; use this when factorizing ILUs
  instead of "Values", if defined by user. The "PrecValues" may be
  update elementwise using DefaultUpdatePrec(P), and it is by default
  scaled by the same scaling as the "Values" field.


Mesh interpolation and manipulation
-----------------------------------
- Internal LoadMesh functionality
  o Eliminates the need of old "eio" library. 
  o Othewise the functionality is maintained.

- Discontinuous Meshes:
  o It is now possible to introduce discontinuous boundaries to the mesh at the time of reading the mesh. 
    At the boundaries the nodes are doubled which may be used to introduce discontinuities on the fields.
  o For the discontinuity projectors may be applied to restore the continuity, or to set jump conditions 
    on the boundary. Keyword is "Discontinuous Boundary = Logical True" in BC section.  
  o There are many test cases with prefix "DisContBoundary". 

- Internal mesh extrusion that can be applied also in parallel. 
  o May remove meshing bottle-necks by allowing efficient mesh generation from 2D foot-prints. 
  o It is possible to have a desired distribution of elements in the extruded direction. 
  o Min and max coordinate in the extruded direction may be given.
  o Several options to tweak how the entities are treated and numbered in extrusion. 

- Projectors
  o Projectors to ensure the the continuity of fields over nonconformal (or conformal) mesh interfaces.
  o Both node-to-surface (strong) and surface-to-surface 
     (weak, galerkin, mortar) type of projectors available
  o A tailored projector family "Level Projector" for cases where exact match between interface meshes 
    may be found at some lower dimensional surface (or line)
  o Various strategies implemented (flat, rotational, radial) implemented to allow flattening of interface meshes.
    The flattened interface meshes allow more accurate projection since there is no faceting of the meshes.
  o Rotational projectors may be periodic or antiperiodic.
  o Also edge degrees of freedom may be projected. 


Nonlinear system features
-------------------------
- Nonlinear Timestepping
  o Improved Newmark time integration scheme so that the terms related to previous timestep also 
    use previous stiffness matrix and force vector. This may yield better accuracy for nonlinear 
    problems in time. 

- FCT, Flux Corrected Transport
  o A preliminary version of monotonicity preserving scheme 
     (see e.g. Dimitri Kuzmin et al.)
  o Requires global access to mass matrix and is applicable only to transient scalar problems. 
  o Activation by "Linear System FCT = Logical True" to advection-diffusion type of equation 
    (with Crank-Nicholsen time discreation).

- Soft Limiters:
  o Changed the way how soft limiters can be applied so that the residual is computed within the assembly loop. 
    This makes it possible to apply soft limiters also to nonlinear cases.
   
- Slave Solver strategy for coupled problems
  o Any solver can have "Slave Solvers" which are solved within the DefaultInitialize slot 
    of the primary solver. This makes it possible to implement efficient coupling methods
    for nonlinear problems, also accounting step-size control.

- Add keyword "Nonlinear System Compute Change in Scaled System = Logical". The
  purpose is to allow linear & nonlinear convergence measure matching when
  "Nonlinear System Convergence Measure = residual"

- Modified the linesearch and made it more easily usable with legacy solvers. 
  o At minimum, just include 
     "IF( DefaultLinesearch() ) GOTO 100" 
     where the goto address is the start of the assembly process. 


Other libtary functionality
---------------------------
- Table input:
  o Specification "Cubic Monotone" implemented to sif-file table input.
     This keeps the cubic spline monotone, if the input is monotone.
            
- ListGetFun: 
  o Subroutine that may be called internall by an argument still maintaining the standard GetReal sif syntax. 
  o Enabled optional computation of derivatives in ListGetFun. 

- Added possibility to obtain the keyword for which an User Defined Function is called for
  Using "ListGetActiveName()" function.

- Added possibility to output information on several partitions when running in parallel using keyword
  "Max Output Partition" of type Integer. 

- Added functions "GetRealVector" and "GetComplexVector" to allow for easier definition 
  of vector valued keywords within user modules. Also works for "Equals" and "Opposes"
  statements. 

- Added Component list type for entities not related to mesh. E.g.
  electric circuits, chemical reactions etc. 
  Use GetComponent() to get these from the list. 

- Created a new way to compare to reference solution where the user may give Solver-specific 
  "Reference Norm". Case is passed when all reference norms are passed within given tolerance. 
  Also added possibility to compare to analytical solution when making tests in addition to 
  precomputed reference norm. Keywords for this is "Reference Solution" of type Real. 

- Simple geometric clustering methods implemented for future internal partitioning.

- Implicit friction model where the tangential traction is set to be the normal traction 
  multiplied by a signed friction coefficient. Works yet properly only in 2D. 

- Enable setting of BCs (and body forces) such that constant value is enforced on the BC 
  (or body force). One node is used as the "supernode" and other rows are lumped to this 
  row. The other nodal dofs will get the same value as the one in the supernode.

- Adding a keyword in sif to change bodywise element type definitions for solvers. 
  The used convention is given in Body section in the following form, 
  Solver n: Element = String, where String is the conventional element type definition.

- Any real valued keyword may be normalized by area (or volume) by giving 
  keyword 'keyword normalize by area' (or volume) resulting to the value of 
  'keyword' being divided by the area (volume) at the time of calling. The area should be the
  operator for BCs and for other field (material, body, body force) the volume should apply. 

- A utility to set just one node in boundary/body force section to make floating potentials unique.

- More versatile saving of linear systems. Called with keyword 'Linear System Save'.

- Possibilitty to add default boundary condition with keyword 
  'Default Target = Logical' in BC section.

- ListGetRealAtIP function routine to also deal with computing data at IPs.

- Added ListCheckPrefix keyword for checking whether keyword with given prefix exists. 
  Also added ListCheckPrefixAny* routines for checking if a keyword with the given prefix 
  in any BC, Body Force, Body or IC.

- Various ListCheckAny* functions to make it possible to simplify many solver modules. 

- Added function for checking whether a keyword with a given prefix exists, ListCheckPrefix. 
  As there can be multiple corresponding keywords to this it does not make sense to get the value.
  A typical use could be to check for existance of keywords of style 'prefix '//TRIM(VarName).

- Keyword > Exec Condition < for Solver section implemented to allow setting of condition 
  that determinenes whether a solver will be executed. A positive number is regarded to be True. 

- Added possibility to enforce steady-state execution within transient simulation by setting 
  > Steady State Condition < flag to a positive number. 

- Saving and restarting works also with global variables. Also there is a better chance that they 
  will work with non-nodal fields. Restart may be selective such that 'Restart Variable i', 
  i=1,2,3,.. may be optionally given in the Simulation section. 

- Global variable for periodic problems 'Periodic Time'. Time period may be set by 
  "Simulation Block" keyword 'Time Period', the default is inifite. This makes it easy to have 
  parameters with cyclic dependence. 

- Add a "Solver" section flag "Enforce Exact Dirichlet BCs" (default: true), setting
  this to false restores old behaviour concerning Dirichlet BC & external constraint
  interaction.

- Improvements for p-elements
  o Try to apply p-element basis & integration schemes only
    to Solvers that ask for p-elements
  o Enable p-basis for "Mesh Level=n" generated meshes


ElmerSolver Solver modules
---------------------------
- MagnetocDynamics: 
  o CalcFields: can also compute derived fields for initial 2D nodal potential.
  o Improved logic when to compute Jfix field and its BCs. 
  o The nonlinear iteration can now use the stopping criterion ||b-A(V)V|| / ||b|| with V the 
    current nonlinear iterate. 
  o The use of new Piola transformed elements can now be activated from a sif file for stationary and 
    transient cases. 
  o Anisotropic electric conductivity should now be handled correctly for any type of conductivity 
    tensor (even nonsymmetric)
  o Calculate votages, torque and moment of inertia. 
  o Add block solution for (MagnetoDynamics style) implemted for A-V formualation 
    (no other matrix blocks assumed).
  o CalcFields: support for stranded coils current density and electric fields computation. 
    A possibility to calculate JxB, that is the magnetic force.
  o Added a functionality to compute the Average Magnetic Flux, Average Magnetic Flux Density 
    and Magnetic Flux Area on a given boundary.
  o Added the so called classical Low-Frequency Model to MagnetoDynamics module for taking 
    eddy currents into account in lamination stacks.
  o Harmonic: Added low frequency and wide-frequency band models for taking eddies in laminate 
    stacks into account
  o Adding a possibility to use rotation matrix in MagnetoDynamics. 
    This could be used to transform the anisotropic material property tensors.
  o Added a foil coil which is now a regognized option as a coil model.

- MagneticDynamics2D: 
  o New solver with similar functionality as with the MagnetoDynamics solver but for 2D nodal elemenets
  o Harmonic and steady state versions available. 
  o Also cylindrically symmetric cases may be treated.

- VectorHelmholz:
  o New solver that can be used to study vector valued wave problems in electromagnetics.
  o Solver includes shifted matrix for ILU preconditioning. The solver can use both the 
    simplest and lowest non-affine edge elements. 
  o Includes also VectorHelmholtzCalcFields to compute postprocessed fields. 

- WaveSolver: 
  o New preliminary solver for the classical transient wave equation for scalar potential.

- HarmonicLoss: 
  o New solver that can be make on on-the-fly fourier transform and estimate the componentwise 
    harmonic losses. Losses can be linear or quadratic with frequency. 

- StatCurrentSolver: 
  o Implemented nonlinearity for StatCurrentSolver 

- ParticleAcvector:
  o When advecting particles may compute path integrals over the particle track

- HeatSolver: 
  o Implemented 'Infinity BC Temperature' for HeatSolver that assumes infinately large conducting domain.
 
- ResultOutputSolver: 
  o A hack to save results automatically also in vtu format by just giving the "Post File" the suffix ".vtu".
  o Added support of Elmer elements 820 and 827 to VtuOutputSolver.
  o Vtu output format can now also save discontinuous fields where each node is saved separately 
     for each element. The keyword for this is "Discontinuous Galerkin = True". Note that the resulting 
     VTU files may be huge!
  o In VtuOutputSolver enable saving and omitting of halo elements in parallel output. 
    New logical keywords introduced 'Skip Halo Elements' and 'Save Halo Elements Only'.
  o In vtu format enables saving of only boundaries or bulk elements.
    Activated by new keywords 'Save Boundaries Only' and 'Save Bulk Only'.
  o Include information about possible discontinuity of the mesh in the filename of vtu files.
  o Introduced two new keywords, "Save Elemental Fields" and "Save Nodal Fields" in VTU 
     format. The default for both is "True". 
  o Added a mask condition that may be used to pick the elements and nodes to be saved in 
     VTU format in ResultOutputSolver.
  o Added default names for physical bodies/BCs in case of Gmsh output.

- ElasticSolver:
  o The spring BC definition is now given in terms of the pseudo-traction vector
  o Surface traction BCs can now be defined using the conventional terms even for large displacements. 
  o Enhanced postprocessing features to inlude principal strain computation

- StressSolver:
  o Added namespace for stress computation to allow different linear system settings.
  o Nonlinear Linesearch added to linear elasticity solver

- SaveData
  o SaveDependence: New auxiliary subroutine for saving functional forms in a 1D table.

- SaveParticleData:
  o Added Gsmh output for the particles.

- IsoSurfaceSolver:
  o New Solver for saving isolines or isosurfaces of given field as a mesh. 
    Also saving of .geo files for Gmsh for further meshing. 

- DataToFieldSolver:
  o Given data in scattered points fit a field to the data. In the case of noisy or missing 
    data diffusion may be added for regularization. 

- Acoustics: 
  o New Solver for the linearized NS equations in the frequency domain.

- CompessibleNS
  o New Solver for large-amplitude acoustics in time domain.

- CoilSolver: 
  o A preliminary solver that may be used to set currents for closed open and closed coils. 
    The current may be normalized to given density, or other heuristic methods may be 
    used to make the current distribution more uniform. 

ElmerGUI
---------
- New XML files for menu defitions: 
  o vectorhelmholtz.xml: Wave equation for electric/magnetic fields
  o magnetodynamics2d.xml
- New keyword settings in meny
  o bicgstabl polynomial order setting
  o vanka as choice for preconditioner
- Generate sif automatically when saving a mesh or exiting
- Group similar boundary conditions in ElmerGUI for more compact sifs. 
- Possibility to use ParaView in post processing in ElmerGUI. The PATH environment variable
  of the workstation should point to the bin directory of PV.

ElmerGrid
---------
- ElmerGrid export:
  o Basic Gmsh output to ElmerGrid. 
  o Ascii XML VTK writer. The purpose of this is to provide an alternative way to view 
    the meshes and partitioning prior to actually computing anything.

- ElmerGrid import:
  o Preserves names of entities also for Gmsh mesh format.
  o GiD import extended for two additional elementtypes.
  o Adopted Comsol input to the new style of .mphtxt files for geometric entity names

- ElmerGrid partitioning:
  o Improved partitioning so that the user may use dual graph instead of the nodal graph to 
     make the partitioning. This is invoked with flag '-partdual'.
  o Memory savings implemented by directly constructing sparse matrices (for Metis). 
  o Implemented new hierarchical partitioning routine that can be used to first 
    partition boundary elements with Metis, and thereafter the remaining bulk elements. 
    The user may also extend the partitioned boundary with additional element layers to the 
    bulk elements (default is one).
  o Improved on partitioning routines for rotational and constrained problems. 
  o Enabled hybrid partitioning where the connected elements may be partitioned using 1D 
     partitioning and the rest of the elements are partitioned with Metis.
  o First version of halo in z-direction, testing still incomplete.
  o Enabled even partitioning with the -partitioning flag. 

- Other features:
  o Enabled that the checking of parent elements for bc elements in partitioning is done only 
     optionally using new -partbcoptim flag. 
  o Enabled constant helicity when extruding meshes. 
  o New style of selective extrusion where the materials to be extruded may be handpicked for each layer  

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