5.8 with freesteam storage

A release just for Francescos paper.

Version 5.8

Changelog

Clang format for some files and a new tag of 5.8

• #122 by wenqing Fixed bugs in the excavation modelling in the coupled HM processes
• #121 by wenqing Enable $EPSILON for ST that is is consistent with BCs
• #120 by Thomas-TK Not enough memory available in the heap for unconfined models
• #119 by Thomas-TK Replaced the tab indentation with four spaces
• #118 by wenqing clean the source code
• #117 by wenqing IAPWS models of water density and viscosity
• #116 by wenqing Unify the temperaure unit
• #115 by wenqing Several improvements
• #114 by wenqing Changed the term of LiquidFlow for time unit scaling factor
• #113 by wenqing Fix a bug and some warning, and clean some code
• #112 by wenqing CFEMesh::GenerateHighOrderNodes(): Fixed a bug when 1D elements mixed with 3D elements
• #111 by wenqing Updated README with quickstart and build instructions.
• #109 by bilke [CFiniteElementStd::CalcSaturation] Initialize mfp_vector[i]->Fem_Ele_Std for variable dependent fluid properties
• #108 by wenqing $EPSILON in the bc-file can replace the automatically calculated search length
• #107 by Thomas-TK VTP + PVD output for particles if output option is set as PVD
• #106 by Thomas-TK Improvment and bugfixing in CFiniteElementVec
• #105 by wenqing Missing Header (WIN7, VS2015)
• #104 by Thomas-TK A workaround for 2D-XZ model setup
• #103 by Thomas-TK Clean CFiniteElementVec::GlobalAssembly_RHS()
• #102 by wenqing Removed the duplicated computation of saturation extrapolation
  please review
• #101 by wenqing Re-organized some includes and removed pieces of unused code
  please review
• #100 by wenqing Changed the member initialization and some names of CFiniteElementVec
  please review
• #99 by wenqing Fixed one benchmark and deactivated the other failed twos
• #98 by wenqing Updated the year of copyright
  Added a utility of mHM2OGS
• #96 by wenqing Replaced the piece of source code for finding path with an existing function
• #95 by wenqing Fixed some compilation warnings and removed unused source code
• #94 by wenqing Fixed a bug in CFiniteElementStd::Assemble_RHS_M()
• #93 by wenqing Changed a variable name in void CSourceTerm::FaceIntegration
• #92 by wenqing Fixed a bug in face integration
• #91 by wenqing [FromJM] Added the coordinates of the nodes on polyline in Tecplot output under USE_PETSC
• #90 by wenqing [From Jobst] Enabled the variable output polyline along polyline for parallel computing by using PETSc
• #89 by wenqing Corrected MSVC condition in cmake for msvc 2010
• #88 by wenqing Reactivate the functionality of deactivating elements during setting of source terms
• #87 by wenqing changed index in CaPrinSrtDir in rf_msp_new.cpp
• #86 by VinayGK Bugfix of the automatic calculation of the search radius.
• #84 by bilke Corrected the output of fluid properties
• #83 by wenqing Update Cmake petsc script

Data Explorer (for OGS-5)

Placeholder release for attaching Data Explorer for OGS-5 binaries.

5.7.1

New features/changes

• Process
  • New keyword $CONSTANT in PCS to set the user provided value to node values (#15)
  • Improvements of TES/TNEQ (#40, #68)
  • New Minkley and Burgers solid material models (#46)
  • Support nonlinear flow in LIQUID_FLOW (#51)
  • allow to run non-GEMS processes with OGS-GEMS build (#67)
• Output
  • new output format type CSV for point and polyline (#13)
  • support MMP_VALUES and MFP_VALUES in PVD output (#14)
  • add tensor output to VTK point data (#36)
• Efficiency
  • Speedup of shape function computations (#38)
• CMake
  • removed OGS_FEM_* CMake options. Please use new CMake options OGS_CONFIG, OGS_LSOLVER, and OGS_CHEMSOLVER (#4, #18)
  • accept user provided PROCESSOR_COUNT CMake option (#43)
• Misc.
  • Formatted entire code with clang-format (#16)
  • Automatic build check using Travis CI (#30)
  • Mingw 64-Bit builds and package naming with git information (#47)

Fixed bugs

• bug fix in the monolithic scheme of HM coupled with T in the staggered manner (#5)
• fix output directory for vtk partical files (#6)
• fix the reloading solution functionality with MPI (#7)
• skip comment lines in OUT files (#10)
• fix a segmentation fault with invalid element value names in PVD output (#12)
• critical bug fix in NONLINEAR time stepping (#17)
• fix a bug in applying DIRECT bc and st for mass transport (#41)
• remove output of extra "ZONE" (#42)
• fix BENCHMARK_DIR CMake option (#44)
• bug fix and improvement in the parallel computing with PETSc (#50)
• bug fix in calculating the first time step length with adaptive time stepping (#62)

New benchmarks

Deactivated benchmarks

• ECLIPSE_DUMUX/kinetic_CO2phase_generation_E100/CO2phase_gen_E100
• ECLIPSE_DUMUX/kinetic_CO2phase_generation_E300/CO2phase_gen_E300
• ECLIPSE_DUMUX/1phase_radialflow_1phase_transport/1pf_1pt
• ECLIPSE_DUMUX/2phase_flow_2phase_tracertransport/2pf_2pt

5.7.0

New major features

1. Parallelization scheme with two MPI communication groups for coupled chemical reaction, mass transport and hydraulic processes (by Wenkui).
2. Parallel computing of HM/H2M/THM/TH2M modelling with PETSs (by Wenqing), and the related three benchmarks by Peter Vogel at BGR
3. MPI version for the coupling between H2 and T or C (by Wenqing)
4. Neumann BC at the axisymmetric axis (By Wenqing)
5. Enabled element stress output at specified time step by RELOAD (By >Wenqing)

Improvements

1. Licence for open source release and CMake improvements (By Lars).
2. Several important bug fixings (by Nori, Marc and Christoph)
3. Removed all warnings (By Wenqing)

Deactivated benchmarks

In order to prepare a open source release, the source code of ODE solver has been removed (Bulirsch-Stoer). Therefore some benchmarks that use this ODE failed with this release, and they are deactivated from the current benchmarking list. Hopefully they could be fixed by Christof in the next release. Those who need to conduction the computation of the similar problems are suggested to use version 5.6.0 as an instead.

42 - BG_FILECOMPARE_ECLIPSE_DUMUX/kinetic_CO2phase_generation_E100/CO2phase_gen_E100 (Failed) 44 - BG_FILECOMPARE_ECLIPSE_DUMUX/kinetic_CO2phase_generation_E300/CO2phase_gen_E300 (Failed) 48 - CB_FILECOMPARE_C/1D_isofrac/1d_isofrac_AS (Failed) 50 - CB_FILECOMPARE_C/1D_isofrac/1d_isofrac (Failed) 54 - CB_LONG_FILECOMPARE_C/FG_3ports/rt1 (Failed) 60 - CB_FILECOMPARE_C/ChemAppCoupling/slow_kin_cap_act_precalc/cmp8 (Failed) 62 - CB_FILECOMPARE_C/ChemAppCoupling/Wagrien_BatchEqui_PVLE_CAP/wagrien_1D (Failed) 63 - CB_BENCHMARK_C/Engesgaard/2Kin/slow_kin_pqc/pds (Failed) 64 - CB_FILECOMPARE_C/Engesgaard/2Kin/slow_kin_pqc/pds (Failed) 65 - CB_BENCHMARK_C/Engesgaard/2Kin/slow_kin_pqc_krc/pds (Failed) 66 - CB_FILECOMPARE_C/Engesgaard/2Kin/slow_kin_pqc_krc/pds (Failed) 67 - CB_BENCHMARK_C/Engesgaard/Additional_pqc_output/pds (Failed) 68 - CB_FILECOMPARE_C/Engesgaard/Additional_pqc_output/pds (Failed) 69 - CB_BENCHMARK_C/Engesgaard/equi/calcite_pqc_volume/pds (Failed) 70 - CB_FILECOMPARE_C/Engesgaard/equi/calcite_pqc_volume/pds (Failed) 71 - CB_BENCHMARK_C/Engesgaard/equi/calcite_pqc_weight/pds (Failed) 72 - CB_FILECOMPARE_C/Engesgaard/equi/calcite_pqc_weight/pds (Failed) 73 - CB_BENCHMARK_C/Engesgaard/Kin/fast_kin_pqc/pds (Failed) 74 - CB_FILECOMPARE_C/Engesgaard/Kin/fast_kin_pqc/pds (Failed) 75 - CB_BENCHMARK_C/Engesgaard/Kin/fast_kin_pqc_krc/pds (Failed) 76 - CB_FILECOMPARE_C/Engesgaard/Kin/fast_kin_pqc_krc/pds (Failed) 77 - CB_BENCHMARK_C/Engesgaard/Kin/slow_kin_pqc/pds (Failed) 78 - CB_FILECOMPARE_C/Engesgaard/Kin/slow_kin_pqc/pds (Failed) 79 - CB_BENCHMARK_C/Engesgaard/Kin/slow_kin_pqc_krc/pds (Failed) 80 - CB_FILECOMPARE_C/Engesgaard/Kin/slow_kin_pqc_krc/pds (Failed) 82 - CB_FILECOMPARE_C/NAPL-dissolution/1D_NAPL-diss_dissolution/1D_TPF_resS_trans (Failed) 108 - CB_FILECOMPARE_C/Poro-Perm_Update/Lagneau_Batch/pds (Failed) 110 - CB_FILECOMPARE_C/ReactDeact/1D_isofrac_deac1/1d_isofrac (Failed) 112 - CB_FILECOMPARE_C/ReactDeact/1D_isofrac_deac1/1d_isofrac_AS (Failed) 114 - CB_FILECOMPARE_C/ReactDeact/1D_isofrac_deac2/1d_isofrac (Failed) 116 - CB_FILECOMPARE_C/ReactDeact/1D_isofrac_deac2/1d_isofrac_AS (Failed) 118 - CB_FILECOMPARE_C/ReactDeact/1D_isofrac_deac3/1d_isofrac (Failed) 120 - CB_FILECOMPARE_C/ReactDeact/1D_isofrac_deac3/1d_isofrac_AS (Failed) 122 - CB_LONG_FILECOMPARE_C/ReactDeact/FG_3ports_deac_3/rt1 (Failed) 126 - CB_FILECOMPARE_TCR/Temperature_BacGrowth/bact_growth_new (Failed) 132 - CB_FILECOMPARE_TCR/Temperature_NAPLdiss_Csat/TCE_10C_new (Failed) 134 - CB_FILECOMPARE_TCR/Temperature_NAPLdiss_PhaseDiff/TCE_10C_new (Failed) 148 - HS_FILECOMPARE_C/1d_xylene_degradation/h2_line (Failed) 150 - HS_LONG_FILECOMPARE_C/1d_TCEaufEisen/1d_TCE_Ion (Failed)