Release Notes
Contents
Minor Developments 1.Nodal vectors output on elements. Element_nodal_value_flag has been implemented in Output_data. If specified, nodal values will be projected and plotted as element variables. 2.Improvement in mesh smoothing algorithm for both mesh generation and adaptivity 3.Add Group_no (group number) and Mat_no (material number) to history point output 4.Update zero volume error message for mechanical elements 5.The main .dat file has been added to the manifest. 6.Output variables set file write and read. When parageo is run with -check option, it will generate this file with the output variable names and their default output flags. The alias values are redefinable by the user, and next time parageo is run (without -check flag) the variables will be output with the aliases etc. 7.Output_iterations_plotfile keyword has been added to Control_data. Defines the number of iterations to plot, starting with the first iteration. 8.Adhesion models 2 and 3 in implicit 9.Part geometry contact stress output disabled 10.IX-ParaGeo a.Changes for IX-ParaGeo release testing
Bugfixes 1.Thermal strains have been disabled in implicit geostatic 2.Add load factor to surface pressure in Peaceman model 3.Improvements to stress dependent aperture and conductivity models for dual search and single search contact 4.Contact slip added to 3D tangential state variables 5.Minor updates and corrections to parallel implicit contact and restart 6.Compaction curve generation – only ouput summary from rank 0 7.Time step cutting fixed for implicit coupled and parallel 8.Corrections to contact depth update and pore force, normal and tangential stress conductivities 9.Fixed issue with Fault_set data which returned an error message “Surface # is external and cannot be split” 10.Parameter_definition names to allow prefix of group names 11.Parallel reference set data fixed to show all requested properties 12.Pore pressure contribution fixed for out-of-contact facet 13.Surface section: Ensure node coordinates are defined if not present in the .geo file 14.SR3R model corrected stress update 15.Minor correction to read expression for data file parametric expressions 16.Compaction curve generation: Only output summary from rank 0 17.Improvements to handling geostatic pore pressure for implicit 18.Change of format for numbers written in .sed and .spat files to avoid truncation of large numbers 19.Corrected variable names for Bond3 model
Manual 5.1 •Restructuring of the reference manual pages to be consistent with PGEdit classification of data structures. •ParaGeo Reference manual has been updated with new developments. •Minor updates and corrections.
Examples Updated: \Tutorial_Examples 1.MEM_001 – MEM Workflow a.Case04c & 04d – Implicit-Implicit HM Modelling – minor updates to include adhesion in contact
2.MAT_004 – Modelling Creep in Shales and Chalks a.Case02 – Power law with accelerated creep for high q
Tutorial Files Examples Updated: \Tutorial_Examples 1.MEM_001 – MEM Workflow b.Case04c & 04d – Implicit-Implicit HM Modelling – minor updates to include adhesion in contact
2.MAT_004 – Modelling Creep in Shales and Chalks c.Case02 – Power law with accelerated creep for high q
|
Manual 5.0 New Examples: \ParaGeo_Validation_Examples 1.Val_004d – Billet Upsetting a.Case02 Herschel-Bulkley 2.Val_006 – Well Geothermal – U-Shaped Closed-Loop Well System
\ParaGeo_Examples 3.Ex_008 – Well Element: a.Case03 – U-Shaped Geothermal well with multiple well completions b.Case04 – Influence of Skin factor on well elements using the Peaceman model 4.Ex_011 – Parameterised boundary
\Tutorial_Examples 5.Mat_001d – Mechanical compaction models 6.Geol_003 – Geological modelling for TET meshes a.Case02 – Forward model from a non-final restoration point 7.MEM_001 – MEM Workflow a.Case04c & 04d – Implicit-Implicit HM Modelling b.Case05 – Mapping of results to spatial surface and output to plot file
Examples Updated: \Abaqus Format Tutorial Examples 8.Abaq_Mech_001 – Mechanical Analysis Introduction a.Case 1A – Base Case Description
\Tutorial_Examples 9.MEM_001 – MEM Workflow a.Case03a, 03b, 04, 04_coarse, 04b – “Well_type” keyword has been added to Well_definition data structures
Others: 10.ParaGeo Reference manual has been updated with new developments 11.Minor updates and corrections
Tutorial Files New Examples: \ParaGeo_Validation_Examples 1.Val_004d – Billet Upsetting a.Case02 Herschel-Bulkley 2.Val_006 – Well Geothermal – U-Shaped Closed-Loop Well System
\ParaGeo_Examples 3.Ex_008 – Well Element: a.Case03 – U-Shaped Geothermal well with multiple well completions b.Case04 – Influence of Skin factor on well elements using the Peaceman model 4.Ex_011 – Parameterised boundary
\Tutorial_Examples 5.Mat_001d – Mechanical compaction models 6.Geol_003 – Geological modelling for TET meshes a.Case02 – Forward model from a non-final restoration point 7.MEM_001 – MEM Workflow a.Case04c & 04d – Implicit-Implicit HM Modelling b.Case05 – Mapping of results to spatial surface and output to plot file
Examples Updated: \Abaqus Format Tutorial Examples 8.Abaq_Mech_001 – Mechanical Analysis Introduction a.Case 1A – Base Case Description
\ParaGeo_Validation_Examples 9.Val_004b Strip Footing Collapse - 2D, Implicit, TPM6M 10.Val_004c Cook's Membrane - 2D, Implicit, QPM8M
\Tutorial_Examples 11.MEM_001 – MEM Workflow a.Case03a, 03b, 04, 04_coarse, 04b – “Well_type” keyword has been added to Well_definition data structures
Snippet Libraries Updated Snippet Libraries: 1.ParaGeo_Reference_5_0 oWell (Injector + Producer) added oWell (Distributed completion) added oParam. Boundary (Linear) added oParam. Boundary (Quadratic) added oHistory Point (Contact) added oGeostatic Data (Target Stresses) added oContact Surface (Single Search) added oMaterial Data (Mech. Comp. Athy) added oMaterial Data (Mech. Comp. Schneider) added oMaterial Data (2 surface bond3) added oMaterial Data (SR3S 2 surface) added oMaterial Data all previous snippets have been modified so that they only add the relevant material properties
2.ParaGeo_Utilities_5_0 oOutput to Coordinate System added
|
Developments 1.Implicit node→node contact with friction 2.Well element with flow and thermal models 3.Implicit transformed freedoms including for contact and parallel analysis 4.Enhancements to parameterised boundaries: a.Extend functionality for usage outside GeoInv b.Implementation of axis distribution c.Enable sedimentation with parameterised boundaries d.Enable remeshing with parameterised boundaries e.Enable usage of multiple parameterised boundaries f.Parallel implementation 5.ParaGeo – PFLOTRAN Interface (Beta Version) a.One-way coupling b.Memory or ASCII file transfer c.Mapping between disparate mesh discretisations d.Mapping on Faults e.Generic build functionality enabling geomechanics solver to included as a .dll or .so 6.SR3S two-surface constitutive model with destructuration 7.Add bond formation and destructuration to SR4 and SR3 models to enable simulation of brittle structures in mechanical compaction settings for geological applications 8.Athy and Schneider compaction models for streamlined hardening law definition 9.Output of variables in cylindrical and transformed cartesian coordinate systems
Minor Developments 1.Enhancement of Time step growth models for implicit fields 2.Contact a.Contact Dual_search_flag to enable contact search for a specific surfaces in a contact set rather than all surfaces b.Contact thermal models as function of property tables (Normal stress, aperture, etc) c.History output for contact nodes 3.Geostatic a.Multi-stage geostatic initialisation with target stresses 4.Couple freedoms: a.Output of couple freedoms codes to plot file b.Allow couple freedoms in partially exposed / partially in contact surfaces c.Allow couple freedoms with surfaces separated by a gap 5.MeshGeometry a.Enhancements to Abaqus → ParaGeo conversion with added Abaqus keywords *SURFACE and *NSET and *ELSET made of several previously defined components. 6.Tidy up write of control data structures when generating a .dat file (e.g. Abaqus to ParaGeo, Restoration to Forward, etc) 7.Read Eclipse EGRID/UNRST and FEGRID and FUNRST files and output hdf5 plot files 8.IX_ParaGeo a.Evaluation of state variables at list of reservoir points identified by IX 9.Mesh Generation: a.Improve robustness of surface facet search for non-conforming background meshes 10.Enhancements to 3D sedimentation: a.Sedimentation regions for removal of patches with removal based on number or removal based on area b.Surface ponds defined by one line or two lines c.Improved procedure for identification of orientation of new surfaces d.Enhance deposition with minimum thickness with identification of correction of coordinates of lines defining the intersection with existing top surface e.Extend deposition line insertion to account for overhanging sediment ahead of anticline 11.Enhancements to 3D pinchout: a.Restructuring and optimisation of 3-D parallel implementation b.Improvements to facet search algorithm (reduce likelihood of extrapolation) c.Implementation of optional additional statistics via Output_flag d.Minor enhancement to mesh gen for flat surfaces with 2 lines
Bugfixes 1.Trigger error messages for non-valid contact models (e.g. tangential Morh-Coulomb in implicit node to facet) only if the properties are being used in the simulation 2.Enforce output of contact aperture to the plot file even if the value is 0 (mostly affecting initial plots) 3.Spatial grid output of material systems 4.Geometry conversion from Zmap import with mixtures of 3-noded and 4-noded facets 5.Manifest files missing extensions 6.History surface called in parallel even with no elements
|
Minor Developments 1.Update to Dirichlet treatment for PETSC (assemble rhs on first solve) 2.Additional checks for load control data 3.Herschel-Bulkley viscoplasticity: Allow spatial distribution of K, Sig0 and Exponent n 4.Implicit orthotropic and transverse isotropy (including Voight definition) 5.Reduce tolerance in vector norm from QSMALL (10E-10) to SMALL (10E-15) for geometry operations 6.Add Host name to banner together with Bin Wang’s suggestions
Bugfixes 1.Ensure 64bit group name assignments can be used in all assignments (issue in spatial boundary) 2.Spatial grid dependent element variables in parallel not output
|
Minor Developments - All (General) 1.Allow all element variables to be used for spatial tables + additional checks 2.Minor improvements to Petsc solve for linear thermal/flow problems 3.Minor Improvement to RHS norm computation and auto-setting of Petsc Resolve tolerance 4.Minor improvement to geostatic with embedded fracture
Minor Developments - IX-ParaGeo 1.Updates for iterative-implicit coupling
Bugfixes - All (General) 1.Minor correction to implicit poroelasticity 2.Minor issue at some domain interfaces for parallel contact 3.Ensure prescribed element pore pressure transferred to nodal values for implicit mechanical field 4.Minor bugfix for parallel well flow 5.Ensure material grids are available in sequential analysis (issue arising from memory optimisation) 6.Ensure prescribed values for wells are always fully set in parallel for Mumps (issue arising from memory optimisation) 7.Minor fortran compatibility issues highlighted from GNU compiler build
Bugfixes - IX-ParaGeo 1.EDFM parallel mapping after memory optimisation (deleted inactive contact surfaces) 2.Minor changes in parallel arising from previous memory optimisation
Geotest 1.Create permission for directories when running geotest 2.Enhancements for IX-ParaGeo regression testing 3.Allow creation of subdirectories of test problems
|
Minor Developments 1.Updated algorithm of accumulated offset for node-node contact. The new algorithm outputs the difference in displacement of the two opposing nodes regardless of current contact state. The previous algorithm would reset to zero if contact was lost. Not that accumulated offset is a post-processing variable and does not change the stress update algorithm
Bugfixes 1.Minor improvement to hysteretic elastic model 4 (to improve robustness of the loading/unloading state check)
|
Developments 1.Parallel: Optimisation of all operations relating to creating domain data subsequent to domain decomposition 2.Petsc Solver: Modified so that by default prescribed freedoms are retained and assembled into the global matrix to improve performance of gamg and hypre pre-conditioners 3.Geological: Restoration to Forward for cases with faulted basal horizon (limited to non-intersecting faults crossing the whole model) 4.Geological: Initial implementation of 3D pinchout prevention 5.Generation of Pflotran mesh data from a ParaGeo geometry 6.ParaGeo-IX: Coupling IX to Implicit Geomechanical field and allow Iterative coupling methods
Minor Developments 1.Geological: Several enhancements in restoration to forward to ensure minor or no edits to the generated data file 2.Allow specification of petsc_resolve_tol (default 1E-4) for skipping resolve if the RHS norm is low 3.Additional data checks for time dependent hardening 4.Change element centre coordinate output to be optionally in the original coordinates (Element_centre_out_flag=2) 5.Geological: Sedimentation on part boundaries in 3D 6.New option for water level → Partial_saturation_flag 2 – Treats sediment above water level as fully saturated
Bugfixes 1.Regional Stress Regime (RSR) output changed to use range 0 - 3 2.Minor bugs to contact 3D 3.Fix fatal error when more than 1 reference set is defined 4.Gather/scatter initialisation data compatibility with memory optimisation 5.Compatibility of facies gather/scatter with memory optimisation 6.Several minor issues with spatial surface and read .plt file 7.Parallel analysis with dependent variables: Dependent variables not output to plot file 8.Spatial table size not defined error message 9.Add error message if no materials defined 10.Geological: Correct local coordinate system definition required for non-flat part boundaries 11.Geological: Change of written number output format during restoration 2 forward to avoid small rounding errors for large coordinate numbers 12.Issue with adaptivity when the region does not encompass the full domain
Manual 4.3.0 1.New: Tutorial example Geol_003 demonstrating restoration to forward simulation workflow for 3D models with TET meshes. The model is built from Zmap data and HEX to TET conversion is demonstrated 2.New: Tutorial Wellbore_002 – Casing Collapse due to Shear at Salt/Sandstone Bedding Plane 3.New: Tutorial Mech_005 - Formation of Salt Diapirs in 2D (Bench Scale) 4.Case 1 - Base Case with Extension only 5.Case 2 - Extension and Compression with Sedimentation 6.Case 3 - Formation of Turtle Back Structures 7.Update: Tutorial Wellbore_001 Case01 – Inclusion of time-dependent cement hardening material data and diagenetic shrinkage data 8.Update: Tutorial Hm_005 Case 1 and Case 2 9.Update: Tutorial Geol_002 Case02, Case03a, Case03b and Geol_002b Case 01, Case02, Case04 - Addition of Partial_saturation_flag in the Water_level_data data structure 10.Minor updates and corrections
Tutorial Files 1.New: Files for tutorial example Geol_003 have been added 2.New: Files for tutorial example Wellbore_002 have been added 3.New: Files for tutorial examples Mech_005 Case 1, Case 2 and Case 3 have been added 4.Update: Files for tutorial Wellbore_001 Case01 have been updated 5.Update: Files for tutorial Hm_005 Case 1 and Case 2 have been updated 6.Update: Files for tutorial Geol_002 Case02, Case03a and Case03b have been updated 7.Update: Files for tutorial Geol_002b Case01, Case02 and Case04 have been updated
|
Minor Developments 1.Diagenesis reaction model based on time 2.Allow EDFM cell ID to be defined in the data 3.Export of Abaqus files (geometry data) 4.Water level for partial saturation (sediment above water level) 5.Minor improvements to element centroid output a.Support for additional element types b.Improvement in precision c.Optional output of .corelt files with original coordinates i.Element_centre_out_flag 1 – current coordinates ii.Element_centre_out_flag 2 – original coordinates 6.Allow parameter definition to be used within time curves
Bugfixes 1.Minor IX changes for Linux build 2.Parallel Geostatic gather operation (in optimised memory code) 3.Restoration decompaction timing with adaptivity 4.Cement shrinkage mainly due to chemical change rather than temperature 5.Centroids for pyramidal and prismatic elements 6.Implicit model Petsc error (Nevan) 7.Parallel: MPI issue in Parageo v 4.2 8.Issue with water table located below top surface 9.Salt thermo-mechanical wellbore model: temperature stays constant
Manual 4.2.1 1.Minor updates and corrections.
|
Developments 1.Adaptivity enabled in TET restorations 2.Parallel tied contact surfaces (couple freedoms) 3.Pre-analysis Data check a.Control table read and output 4.Allow usage of Deactivation_data to model erosion for cases with water table 5.Spatial surface output 6.Optimisation of Memory for large implicit problems. Particular focus on: a.Gather/scatter optimisation b.Solver: Distributed pre-solve for Petsc c.Dynamic table allocation and usage
Minor Developments 1.State variables a.Add K0 as state variable b.Additional state variables for SR3, SR4 and CC models 2.Time dependent hardening table 3.Output of manifest file 4.Enhancement of spatial grid output with simplified data definition 5.Spatial_table: allow time as dependent variable 6.Spatial_table: Allow multiple variables in a single table for tables with single dependent variable 7.Minor updates to depth update frequency check 8.Changes to mapping for cases with facies and adaptivity 9.Simplification of contact stress output a.Scaling by 2 no longer performed
Bugfixes 1.Include K0 and/or G as state variables in poroelastic models so can vary spatially 2.Parallelize master-slave coupled surfaces (e.g. fault) 3.Time step drop below min. in parallel 4.Issue with pore pressure plot on groups deactivated for porous flow 5.Calculation of Coulomb stress ratio on faults 6.Enhancement to spatial surface stress ratio reporting 7.Issue with reading multiple spatial surfaces 8.Contact tangential stress output in plt file 9.EDFM one-way coupling parallel issue 10. Error when performing a HEX boundary extraction from a restored geometry 11. Allow definition of porosity via parameter_definition 12. Correction to point history output of ’Pore_nod’ and ‘Temp_nod’ with contact active 13. Apply pore pressure for implicit Elastic Single Step Solve 14. Implicit spatial density correction 15. Allow_plot added to grp_stat 16. Fix to parallel output of spatial surface when the surface does not intersect the model 17. Missing files added to manifest 18. Only allow Data_check read if -check specified 19. Improvement of error messages for spatial table 20. Mechanical pore pressure loading for implicit 8-noded Hexa 21. Well output for iterative coupling 22. Parallel: termination of simulation if minimum time step reached 23. HEX 2 TET conversion segmentation error 24. Sedimentation and adaptivity depth update 25. Remove contact output scaling for stress 26. Minor changes for thermal-only and porous flow-only analysis when stratigraphy defined 27. Read .plt with multiple spatial surfaces 28. Corrected sign convention for spatial surface coulomb stress 29. Improve method for assigning contact freedoms at nodes for parallel 30. readplt copy_mech, oneapi2023 compile fixes
Manual 4.2.0 1.New: reference page for “Tied Contact (Master-Slave Couple freedoms)” in “Contact Data” 2.New: reference page for “Variables Output_list” in “Output Data” 3.Update: reference page for “Variables List” 4.New: ParaGeo example Ex_012 demonstrating mapping of 3D grids into 2D models 5.New: tutorial example MEM_002 demonstrating workflow for initialisation of MEM models with salt formations 6.New: tutorial example MESH_002 demonstrating unstructured 3D mesh generation in ParaGeo 7.New: tutorial example Geol_002b_Case03 demonstrating modelling of erosion within restoration to forward simulation workflow 8.Update: ParaGeo example Ex_002 Case01and Case01rst 9.Update: tutorial example MEM_001 Case03a, 03b, 04, 04b - Inclusion of water level data and spatial boundary data in conjunction with initial nodal pore pressure spatial grid data 10. Minor updates and corrections
Tutorials Files 1.New: Files for Ex_012 have been added 2.New: Files for MEM_002 have been added 3.New: Files for MESH_002 have been added 4.New: Files for Geol_002b_Case03 have been added 5.Update: Files for Ex_002 Case01and Case01rst have been updated 6.Update: Files for MEM_001 Case03a, 03b, 04, 04b have been updated 7.Update: Files for MEM_001 Case01, 01b, 02 have been updated with minor corrections and results from 4.2.0 version
|
Developments 1.64 Bit Solver Implementation (Mumps and Petsc) a.Implemented for all fields (geomechanical, porous flow and thermal) b.Pre-solve procedures updated to speed up and reduce memory c.hdf5 interface functions to allowing both 32bit and 64bit integers d.Optimisation of equation numbering to reduce memory/communication for petsc e.Integration of petsc version 3.18.5 with Hypre preconditioners f.Integration with hdf5 version 1.12.1 g.Integration with Mumps 5.5.1 2.Spatial surface 3.Read plot file utility (Read_plt_file data structure) 4.Conversion .inp to Part_geometry
Minor Developments 1.Speed up reading of .spat files 2.Re-integrate procedure for generating more dense smoothing of part geometry surfaces from coarse surfaces 3.Implement adaptive curvature sets for 3-D tessellated surfaces 4.Allow a specifically named petsc_options.set
Bugfixes 1.Check and resolve missing sat_dens on individual domains 2.Minor improvement to 3-D surface mesh generator 3.Prescribed Boundary - Ensure auto-generated transformed freedoms are re-initialised after a remesh
Manual 4.1.0 1.New: added links to data structures reference pages when mentioned in the tutorials 2.New: reference pages for new data structures Spatial_surface and Read_plt_file 3.Update: Additional info within Solver_control page 4.Update: Minor updates and corrections
|
Developments 1.Mapping from 3D spatial grids to 2D models
Minor Developments 1.Make contact aperture model 5 minimum aperture consistent with user defined value 2.Mesh to Geometry - Convert 3-D surface elements to: a.If TYPE=GEOMETRY, ParaGeo will convert these to NSET for use b.If TYPE=GROUP, ParaGeo will convert these to TSET for use 3.Mesh to Geometry: Allow specification of tolerance for surface splitting by facet angle (*CONVERSION OPTIONS, SURFACE SPLIT ANGLE=value)
Bugfixes 1.Allow 32-character names to assigned kerogen properties during sedimentation 2.HEX to TET conversion: allow for surfaces with existing 3-node facets 3.Mesh to Geometry - Correct input for "Conversion Options: Surface Split" 4.Extend prescribed_boundary background element search for isolated surface nodes 5.Correct parallel surface history for contact nodes 6.Fixed memory issue in parallel 3D TET forward model
Manual 4.0.1 1.New: index for tutorial examples in table format including pictures to facilitate reference. 2.New: ParaGeo example Ex_010 demonstrating modelling of faults in a continuum manner for flow modelling 3.Update: minor corrections
Tutorials Files 1.New: Files for Ex_010 have been added 2.Update: files for GeoInv_002 have been updated with a keyword change
|
Developments 1.Optimisation of memory for parallel analysis 2.Contact mechanics formulated in terms of effective stresses (previously formulated in terms of total stresses) 3.Permeability enhancement for continuum fault modelling 4.Restoration to Forward conversion for 3D TET models without faults
Minor Developments 1.Improve handling of path names on Linux 2.Add -v (version) option to ParaGeo 3.Allow history output for contact points that are not in contact (useful for fracture opening cases) History_surface->Contact_state_flag 4.Improve method of average pressure formulation (not more generally used average volume strain formation) for 3-D Tetrahedra 5.Speed up parallel initialisation of surface data structures 6.Contact flow aperture model (for opening fractures) 7.EDFM fracture insertion: implement specific offset algorithm for EDFM fractures (Edfm_offset_type and Edfm_offset_codes) 8.Improve mapping for spatial grids and Hexahedral meshes when background element not found 9.Deposition of HEX elements: prevent deposition of isolated elements (as these are prone to instability) 10. Sedimentation_data: Add output flag for plot file 11. Addition of facies to group data and sedimentation data 12. Normal displacement constraint for 2D part geometry
Bugfixes 1.Issue with generation of EDFM models with Fracman fractures 2.Mapping of facies, force update of facies assignment after adaptivity 3.Fix to a 3D model memory issue related to spatial grids 4.Missing time curve data in Rest to Forward generated data file 5.Fixes to Hex to TET conversion 6.Elastic property did not follow facies definition when only one group is present
|