CHANGELOG.md



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OpenGeoSys changelog

Unreleased
Please see the wiki-page

6.5.1
Changelog for OpenGeoSys 6.5.1


6.5.0
Changelog for OpenGeoSys 6.5.0

6.4.4
Changelog for OpenGeoSys 6.4.4

6.4.3
Changelog for OpenGeoSys 6.4.3

6.4.2
Changelog for OpenGeoSys 6.4.2

6.4.1
Changelog for OpenGeoSys 6.4.1

6.4.0
Changelog for OpenGeoSys 6.4.0

6.3.3
Changelog for OpenGeoSys 6.3.3

6.3.2
Changelog for OpenGeoSys 6.3.2

6.3.1
Changelog for OpenGeoSys 6.3.1

6.3.0
Changelog for OpenGeoSys 6.3.0

6.2.2
Changelog for OpenGeoSys 6.2.2

6.2.1
Changelog for OpenGeoSys 6.2.1

6.2.0
Changelog for OpenGeoSys 6.2.0

6.1.0
Changelog for OpenGeoSys 6.1.0

6.0.8
The highlight of the release is the implementation of the Lower-Interface
Elements for both the small deformation process (M) and hydro-mechanics process
(HM) allowing fractures to be incorporated in the solution domain.
For the liquid flow and two-phase flow processes several material models for the
fluids pressure, density, permeability, and viscosity were added.

Features

Implementation of hydro-mechanics (HM) with LIE. #1537-#1541

Implementation of small deformation (M) with LIE. #1452

Fracture constitutive models. #1434

Hydro-Mechanics process. #1508

First version of monolithic hydro-thermal process implementation with
Boussinesq approximation using constant viscosity. #1534

Two phase flow process with pp model implementation. #1530

Richards flow process implementation. #1473

Liquid process. #1468

Classes for relative permeability models. #1531

Classes for capillary models. #1517, #1578

Ehlers single-surface yield function constitutive relation model. #1556

Support scaling, GMRES, and Pardiso in Eigen linear solvers. #1509 #1510

Piecewise linear Monotonic curve and a generic curve parser. #1529

Support searching boundary nodes in MeshLib::NodeSearch. #1459

Support specifying the shape function order in process variables. #1503

Command line option --unbuffered-std-out to deactivate buffer for standard output. #1514

CMake option OGS_FATAL_ABORT for debugging. #1432

Set the default OGS_LOG_LEVEL to debug in release builds. #1522

Add integration order in input files. #1464

Migrated Data Explorer to Qt5. #1622, #1625

Benchmarks can be run on specific configurations only by using the new parameter
REQUIREMENTS in AddTest() (in CMake). #1610


Utilities
New utilities:

createQuadraticMesh #1500

convertToLinearMesh #1554

postLIE #1555


New features:

extend NodeReordering to correct ordering of nonlinear nodes #1519


Infrastructure

Ctest now works on Windows too by removing time-wrappers. #1480

Moved to public Jenkins instance at jenkins.opengeosys.org. #1505

Doxygen warnings parser in Jenkins will mark a build as unstable
if there are Doxygen warnings. #1585

Benchmarking on Jenkins now saves the standard output into a file for each
test. #1528


Fixes

Fix LocalToGlobalIndexMap with multiple variables and with multiple components. #1433 #1440

Fix PropertyVector<T*> for multi-component case. #1441

Fix checking IDs of nonlinear nodes. #1495

Fix incorrect use of getNumberOfBaseNodes(). #1515

Fix computing sparsity pattern for mixed shape function order cases. #1548

Fix that iterations and residuals were not printed when Eigen linear solver fails. #1499

Fix all of the Doxygen warnings in the code. #1569 #1573

Fix all of the input file/keyword documentation and its generation.


6.0.7

Features
The main features of this release is the implementation of two new processes,
the small deformation, and the heat conduction.  Some extensions were done to
the DOF table to be able to manage multi-component/multi-variable processes.
Also, during implementation of the Robin boundary conditions, the base classes
for boundary conditions were generalized.

Add small deformation process with linear elastic material model. The
implementation is based on the Kelvin mapping. #1340

Added B-Matrices and Kelvin mapping tools for deformation processes. #1359

Heat conduction process implementation. #1328

Finalize support for multicomponent boundary conditions adding configuration
parser. #1343

Added uniform Robin boundary condition. #1336

Added a generic natural boundary condition class. #1337

Added Robin boundary condition. #1336

Reworked the Parameter class. It now serves as a basis for BCs and ICs.
#1357, #1356

Added time-dependent Dirichlet BCs. #1380

Add calculation of surface flux, tests for groundwater flow. #1429

Implemented numerical Jacobian assembly for Newton-Raphson solver. #1352

Added the new parameter type "Group" which can be used for setting material
ID dependent values. #1426

Added fluid property class and several fluid density and viscosity models
based on it. #1398, #1435

Enabled solving of axially symmetric problems on 2D meshes for all currently
implemented processes. #1443

Added time measurement for assembly and solvers. #1322

Added named functions, out of which expressions can be built up at run-time
from the prj file, which can be used to output additional nodal quantities.
#1314, #1315

Added component-wise norms, and flexible convergence criteria for nonlinear
solvers. #1349, #1342

Restructured the time loop. #1364


Utilities
New utilities:

createNeumannBc: The tool integrates the given element property and writes
the computed data as a PropertyVector with the name node_aggregated_gwn
into the mesh. The tool also outputs an OGS-5 direct source term (Neumann
boundary condition) data file. #1346

scaleProperty for simple rescaling of mesh properties. #1347

convertGEO for geometric file conversion, e.g. gli to glm. #1360

swapNodeCoordinateAxes to swap node coordinate values, e.g. XY to XZ plane.
#1361
New feature:
Support tetrahedra types in generateStructuredMesh. #1353


Infrastructure

Migrated all important Jenkins jobs to script-based
Jenkins Pipeline
functionality.  For an introduction see
docs.opengeosys.org - Continuous Integration.
#1392, #1396, #1404, #1411, #1424, #1428, #1436

Moved CMake logic for packaging executable dependencies (such as shared libs)
to the install and package targets instead of running after each executable
gets build. #1458

Increase minimum clang compiler version to 3.5 in course of updating travis
build environment to Ubuntu LTS 14.04. #1448

Added a script that generates crosslinked Doxygen pages out of ctest input
files #1348


Fixes

Fix an issue that a shape vector was defined as a column vector. Corrected to
a row vector . #1288

Fix usage of boost::optional<T const&>, which has changed in version 1.61.
#1385

Fix Grid (enlarge bounding box to fit all points). #1369

Fix mapping of geometries to mesh surfaces. #1327. #1368

Fix transmitting raster data to element properties. #1347

Fixed missing XSD files in packages. #1410

Fix a shape vector to a row vector. #1288

Fix FEFLOW import. #1397

Fix NodeReordering to check ordering of each element. #1425

Fix builds linking shared VTK library. #1431

Fix global Newton iteration counter. #1341

Correct few loops over mesh nodes, which should run over the mesh subsets.
#1437

Fix shape function computation for 2D elements lying in the x-y-plane #1318

Fix AddTest, s.t. ctest now really checks results. #1325

Made Eigen preconditioner configurable. #1367


6.0.6

Features

Add external ode-solver interface with Sundials CVODE
library. #1109

Add piecewise linear curves parser to the project files. The curves are
specified by two vectors, the coordinates and values. They can be used for
example to map temporal dependencies (time-dependent boundary conditions) or
as approximations of coefficient dependencies (e.g. pressure-saturation
curves). #1149

Extend the LocalAssemblerInterface by adding default implementations of
pre/postTimestep and assembleJacobian functions. The current time and time
step size are passed in the preTimestep call to the particular processes. #1214

Add support multi-variable/multi-component in the DOF table interface and
extend the initial conditions to multi-components. #1224

Major rework of the general process interface. That also affects the
interface of concrete processes and local assemblers.
least squares optimization. #1145

Added functionality for the output of secondary variables. #1171

Added material properties for zeolite adsorption and Calcium oxide/hydroxide
reactions. #1178

Transferred the TES process, a monolithically coupled THC model for simulating
thermochemical energy storage devices, from OGS5. #1181

Introduced a general scheme for documenting OGS6 input file settings. #978
Added copy constructor for the class Surface, minor improvements in GeoLib. #1237

Added classes GeoLib::LineSegment and GeoLib::Polyline::SegmentIterator. #1139

GMSHInterface can handle stations as constraints. #1212

Added functionality to duplicate geometric data. #1229

Station names can be modified in Data Explorer #1273


Infrastructure


Fix circular dependencies on library level. This allows for dynamic linking
which is faster than static and can be used in debug builds, where the
compilation time is more important than the runtime.

Enable shared linking of ogs libraries. #1133

Break FileIO on ApplicationsLib dependency. #1138

Remove MeshLib on FileIO dependency. #1143, #1153

Cleanup some of AssemblerLib dependencies. #1166

Split AssemblerLib and move to MathLib and NumLib #1208

Move InsituLib to MeshLib #1208

Remove MathLib depends on NumLib #1208

Remove dependency of FileIO on Data Explorer #1302


Introduced Conan package manager for automatic fetching of build dependencies, #1141


Inconsistent formatting of tabs and spaces was finally resolved: now all
formatting, indentation and alignment, are done with four spaces. #1201


Windows 32-bit builds are disallowed because they are not supported.
Can be forced by setting OGS_32_BIT=ON. #1230


Simplified FindEigen.cmake, #1209


git diff --check is run in its own Travis job, #1207


Moved some IO implementations from FileIO to BaseLib/IO, GeoLib/IO, MeshLib/IO, #1182, #1235


Eigen is not optional anymore #1218


Removed OGS_USE_EIGENLIS CMake option. Use OGS_USE_LIS instead #1251


Fixes

Fix linking of Metis in MathLib. #1147

Fix memory leaks in GMSHInterface. #1212

Fix build with Lis #1267

Fixing several small issues with NetCDF import #1169

Restructure Applications related modules

Move DataHolderLib and FileIO under Applications #1279


Remove calling std::abort within libraries. Exceptions are thrown instead. #1245

Fix finding Boost with BOOST_ROOT CMake argument #1287

Fix linking of Sundials CVODE library #1197

Fixed issue where geometry names would be missing after merging geometries #1295


6.0.5

Features

Added an ODE solver library that can solve transient and nonlinear processes
(see http://doxygen.opengeosys.org/df/d35/group__ODESolver.html).
Move up common Process parts from particular GroundwaterFlow process
implementation. #951, #982
Separate Dirichlet boundary condition class implementation. #963
Split process output and post timestep. #998
Added pre- and postTimestep and -Iteration hooks to processes. #1094, #1100, #1101

New configuration tree parser

Checks configuration parameters more strictly, automatically prints error/warning messages.
Requires Boost >= 1.56 because of boost::optional with move semantics.
Command line argument --config-warnings-nonfatal that keeps OGS from terminating on warnings during
configuration file parsing (errors still makes it terminate).


Axis aligned bounding box:

Is now a from the right half-open interval.
Removed template from class declaration.


MeshLib: Class MeshElementGrid implements a grid data structure supporting search operations.
Added CMake option OGS_EIGEN_DYNAMIC_SHAPE_MATRICES that makes OGS use dynamically.
allocated shape matrices.
Added several cmake options for selecting which element types, dimensions and
orders to be built. Selecting only few element types speeds up compilation
significantly. #1092

Command line argument -l for OGS cli and testrunner to specify verbosity of logging. #1056

Added possibility to specify after which timesteps there shiuld be output.
Added possibility to specify timesteps of different size for use with
transient processes.


DataExplorer and utilities

Added command line tool for creating layered meshes from raster files
OGSFileConverter is now a separate library
Raster file to structured grid conversion can now convert pixel values in user-defined scalar arrays
All scalar arrays will be displayed in mesh information window in DataExplorer
Added generation of structured meshes to DataExplorer
Restructured mesh creation access in DataExplorer
Mesh layers can be added to existing meshes in DataExplorer
Rework tools:

CreateBoundaryConditionsAlongPolyline
AddTopLayer
ResetPropertyInPolygonalRegion
removeMeshElements


Infrastructure

Minimum Boost version: 1.56.0. #943
Boost requirement is now header-only. #940
Optional support for VTK 7. #1083

Test data is now a git submodule. #1000

In-code defined Jenkins jobs. #970
Use clang's address and undefined behaviour sanitizers on Jenkins now. #958


Documentation

Speed up builds with ccache, #938
Overview of the new non-linear, transient solver in [ODESolver](see
http://doxygen.opengeosys.org/df/d35/group__ODESolver.html) source code
documentation.


Fixes

Fix bugs in GeoLib:

lineSegmentIntersects.
Polygon::splitPolygonAtIntersection.
Grid.


GeoMapper: Refactoring few methods, c++11. #977
Rework FileIO::GMSH interface

Process geometries located other than in the x-y-plane.
Respect the scaling factor for Stations.
Fix memory leaks.
Added/modified tests for GML-, GMS- and TetGen-files.


6.0.4

Features

Parallel computing framework for FEM by using PETSc, which also includes

Parallel input of partitioned mesh data.
Parallel output of solutions by using pvtu data format.


New data structures for mesh properties are used everywhere replacing
Element's value member.
The penalty method to impose first-type boundary conditions was substituted
with a non-penalty method for LIS and Eigen linear solvers.
Support for multiple nodal variables is extended to the boundary conditions,
the sparsity pattern.
Passing of linear solver options from the project files is now possible.
The global matrix and global vector type of indices is consistent with the
linear solver library being used.


Infrastructure