New OGS release 5.5

Announcements
1

Dear all,

OpenGeoSys version 5.5 has just been released. This version includes
- a new OGS-ChemApp interface
- a new reaction-interface / toolbox with general functionalities for coupling of reaction codes to OGS
- some routines of the Geochemcalc-Toolbox by DL for water density and gas-phase / water phase equilibria
- updates to the KineticReaction routine of OGS including NAPL-dissolution and mineral dissolution / precipitation models
- several updates to the OGS-Phreeqc interface
- several minor things related to the coupling of heat and conservative / reactive mass transport (temperature dependent diffusion, dispersion, biodegradation models, etc.)

You can find the release notes and some additional information at https://svn.ufz.de/ogs/wiki/ReleaseNotes

Bests, Christof

···

--
_______________________________________
Dr. Christof Beyer
Institute of Geosciences
Geohydromodelling
Christian-Albrechts-University Kiel
Ludewig-Meyn-Str. 10
24118 Kiel
Germany

phone: +49(0)431-8803172
fax: +49(0)431-8807606
mobile: +49(0)176-24297908
email: christof.beyer@gpi.uni-kiel.de
home: http://www.ifg.uni-kiel.de/
_______________________________________

2

Dear All,

We are planning to release a new version of OGS5, which includes the following improvements

Fix constrained
#227 opened 6 days ago by waltherm

Parallelization scheme with two MPI groups (STEP 2) (FINAL STEP)
#226 opened 13 days ago by hobit03

Parallelization scheme with two MPI groups (STEP 1)
#223 opened on Nov 3 by hobit03

critical fix for constrained BC
#220 opened on Oct 22 by waltherm

Better mac redistributable package
#218 opened on Oct 20 by bilke

Return the value directly from a function.
#211 opened on Sep 2 by wenqing

Add Reynolds fluid visco EOS case 30
#210 opened on Sep 1 by fabienma

Considered the Neumann BC applied at the axisymmetric axis.
#209 opened on Aug 31 by wenqing

Correct seepage
#207 opened on Aug 25 by waltherm

fix a bug in VTU putput with MPI
#206 opened on Aug 25 by norihiro-w

Forgot to add CelsiusZeroInKelvin in one temperature.
#205 opened on Aug 24 by wenqing

Fixed a bug in the binary IO of element stresses.
#204 opened on Aug 24 by wenqing

Open-sourcing: Removed Bulirsch-Stoer, added SUNDIALS CVode
#201 opened on Aug 5 by chleh

fix a bug in checking a constrained BC flag with MPI
#200 opened on Aug 5 by norihiro-w

Removed preprocessors for physical constants
#199 opened on Aug 4 by wenqing

Another round of CMake improvements
#198 opened on Jul 31 by bilke

Re-structured CSolidProperties
#195 opened on Jul 30 by wenqing

Re-structured class CSolidProperties
#194 opened on Jul 30 by wenqing

Re-strutured class CFluidProperties
#193 opened on Jul 30 by wenqing

Fix cmake mkl 2
#192 opened on Jul 28 by bilke

Fix cmake mkl
#191 opened on Jul 23 by norihiro-w

Open sourcing OGS
#190 opened on Jul 20 by bilke

Enable output element stresses at specified time step by RELOAD
#189 opened on Jul 17 by wenqing

Fix compiling errors for OGS_FEM_MPI with MSVC
#188 opened on Jul 16 by norihiro-w

There are also other PRs to be merged soon, and the target repository could be the open source one: https://github.com/ufz/ogs5

Best regards,

Wenqing

3

Dear Christoph,

Happy new year!

As mentioned in my last email, we are going to merge the development branch in our private github repository to the svn repository for a new version. After benchmarking, I found the several benchmarks in C directory failed in the result comparison. Would you please checkout branch 'develop' in our github repository and confirm the results obtained with the changes by Lars for the open source release? Two commit are identified that correspond to the failed benchmarks:

···

-----------------------------------
Commit: Replaced NR::zbrent by an LGPL-ed implementation, SHA: eb82d8eeabb0d975417fd7342f9553889c249ba6
(https://github.com/envinf/ogs5-trunk/commit/eb82d8eeabb0d975417fd7342f9553889c249ba6\)
Failed benchmark:
CB_FILECOMPARE_C/ChemAppCoupling/Wagrien_BatchEqui_PVLE_CAP/wagrien_1D (Failed)

-----------------------------------
Commit: Removed numerical recipes implementations. SHA:98a7b89e65cb299527768c2581b4c5cf3f561b61
(https://github.com/envinf/ogs5-trunk/commit/98a7b89e65cb299527768c2581b4c5cf3f561b61\)
Failed benchmarks:
          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)
          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)

If you cannot access our github repository, I can send you two zip files of source code that contain the two commits.

All the best for you and your family in the year of 2016.

Wenqing
On 12/15/2015 02:06 PM, Wenqing Wang wrote:

Dear All,

We are planning to release a new version of OGS5, which includes the following improvements

Fix constrained
#227 opened 6 days ago by waltherm

Parallelization scheme with two MPI groups (STEP 2) (FINAL STEP)
#226 opened 13 days ago by hobit03

Parallelization scheme with two MPI groups (STEP 1)
#223 opened on Nov 3 by hobit03

critical fix for constrained BC
#220 opened on Oct 22 by waltherm

Better mac redistributable package
#218 opened on Oct 20 by bilke

Return the value directly from a function.
#211 opened on Sep 2 by wenqing

Add Reynolds fluid visco EOS case 30
#210 opened on Sep 1 by fabienma

Considered the Neumann BC applied at the axisymmetric axis.
#209 opened on Aug 31 by wenqing

Correct seepage
#207 opened on Aug 25 by waltherm

fix a bug in VTU putput with MPI
#206 opened on Aug 25 by norihiro-w

Forgot to add CelsiusZeroInKelvin in one temperature.
#205 opened on Aug 24 by wenqing

Fixed a bug in the binary IO of element stresses.
#204 opened on Aug 24 by wenqing

Open-sourcing: Removed Bulirsch-Stoer, added SUNDIALS CVode
#201 opened on Aug 5 by chleh

fix a bug in checking a constrained BC flag with MPI
#200 opened on Aug 5 by norihiro-w

Removed preprocessors for physical constants
#199 opened on Aug 4 by wenqing

Another round of CMake improvements
#198 opened on Jul 31 by bilke

Re-structured CSolidProperties
#195 opened on Jul 30 by wenqing

Re-structured class CSolidProperties
#194 opened on Jul 30 by wenqing

Re-strutured class CFluidProperties
#193 opened on Jul 30 by wenqing

Fix cmake mkl 2
#192 opened on Jul 28 by bilke

Fix cmake mkl
#191 opened on Jul 23 by norihiro-w

Open sourcing OGS
#190 opened on Jul 20 by bilke

Enable output element stresses at specified time step by RELOAD
#189 opened on Jul 17 by wenqing

Fix compiling errors for OGS_FEM_MPI with MSVC
#188 opened on Jul 16 by norihiro-w

There are also other PRs to be merged soon, and the target repository could be the open source one: GitHub - ufz/ogs5: OpenGeoSys THM/C simulator version 5

Best regards,

Wenqing

4

This release includes the most part of contributions from the developers of OGS5 in the last half year.

# 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.
  <blockquote>
      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)
  </blockquote>

# Changlog
  <blockquote>
     Removed all warnings
#231 opened 6 days ago by wenqing

Fix velocity calculation in TNEQ process
#230 opened 7 days ago by chleh

Fixed a bug in the unit of the gas constant for the EOS of Peng-Robinson
#229 opened 8 days ago by wenqing

Fixed a bug in the mass matrix calculation
#228 opened 12 days ago by wenqing

Fix constrained
#227 opened on Dec 9, 2015 by waltherm

Parallelization scheme with two MPI groups (STEP 2) (FINAL STEP)
#226 opened on Dec 2, 2015 by hobit03

Enabled the MPI version for the coupling between H2 and T or C
#224 opened on Nov 5, 2015 by wenqing

Parallelization scheme with two MPI groups (STEP 1)
#223 opened on Nov 3, 2015 by hobit03

Parallel computing of HM/H2M/THM/TH2M modelling
#222 opened on Oct 29, 2015 by wenqing

critical fix for constrained BC
#220 opened on Oct 22, 2015 by waltherm

Better mac redistributable package
#218 opened on Oct 20, 2015 by bilke

StableErrorAdaptive needs maximum overall coupling error, gets it now.
#216 opened on Oct 19, 2015 by waltherm

Added a warning about adjusting the linear solver setting.
#215 opened on Oct 9, 2015 by wenqing

Return the value directly from a function.
#211 opened on Sep 2, 2015 by wenqing

Add Reynolds fluid visco EOS case 30
#210 opened on Sep 1, 2015 by fabienma

Considered the Neumann BC applied at the axisymmetric axis.
#209 opened on Aug 31, 2015 by wenqing

Correct seepage
#207 opened on Aug 25, 2015 by waltherm

fix a bug in VTU putput with MPI
#206 opened on Aug 25, 2015 by norihiro-w

Forgot to add CelsiusZeroInKelvin in one temperature.
#205 opened on Aug 24, 2015 by wenqing

Fixed a bug in the binary IO of element stresses.
#204 opened on Aug 24, 2015 by wenqing

Open-sourcing: Removed Bulirsch-Stoer, added SUNDIALS CVode
#201 opened on Aug 5, 2015 by chleh

fix a bug in checking a constrained BC flag with MPI
#200 opened on Aug 5, 2015 by norihiro-w

Removed preprocessors for physical constants
#199 opened on Aug 4, 2015 by wenqing

Another round of CMake improvements
#198 opened on Jul 31, 2015 by bilke

Re-structured CSolidProperties
#195 opened on Jul 30, 2015 by wenqing

Re-structured class CSolidProperties
#194 opened on Jul 30, 2015 by wenqing

Re-strutured class CFluidProperties
#193 opened on Jul 30, 2015 by wenqing

Fix cmake mkl 2
#192 opened on Jul 28, 2015 by bilke

Fix cmake mkl
#191 opened on Jul 23, 2015 by norihiro-w

Open sourcing OGS
#190 opened on Jul 20, 2015 by bilke

Enable output element stresses at specified time step by RELOAD
#189 opened on Jul 17, 2015 by wenqing

Fix compiling errors for OGS_FEM_MPI with MSVC
#188 opened on Jul 16, 2015 by norihiro-w
  </blockquote>