Update to ogs5py 1.0

Author: MuellerSeb

LICENSE.txt

@@ -0,0 +1,30 @@
+Copyright (c) 2019, OpenGeoSys Community (http://www.opengeosys.org)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+3. All advertising materials mentioning features or use of this software
+   must display the following acknowledgement:
+   This product includes software developed by the OpenGeoSys Community.
+4. Neither the name of the OpenGeoSys Community nor the
+   names of its contributors may be used to endorse or promote products
+   derived from this software without specific prior written permission.
+5. Attribute the OpenGeoSys Community, preferably citing an appropriate
+   paper listed on the OpenGeoSys Community homepage:
+   http://www.opengeosys.org/papers
+
+THIS SOFTWARE IS PROVIDED BY THE OpenGeoSys Community ''AS IS'' AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE OpenGeoSys Community BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,46 +1,35 @@
-Welcome to the ogs5py benchmarks
-================================
-
-Purpose
--------
-Most of the OGS5 benchmarks were rewritten into a ogs5py-script in this repository.
-
-The following were skipped:
-
-+ `HT_EOS`   (folder) \*.bat files to copy stuff... uarg.. (maybe rewrite with ogs5py)
-+ `bact_growth_new`    #THERMAL in mfp
-+ `HT_var_density_1D`    $AREA in mmp
-+ `thm_quad`    $STORATIVITY in mmp
-+ `viscosity_yaws`    $AREA in mmp
-+ `uc_pris`    GLI not valid (SRF not present for VOLUME)
-+ `brand_m1_l1`    GLI not valid (TIN and Polylines at the same time[?])
-+ `2d_h_us_line_Warrick`    lonesome mmp
-+ `model_1`    $AREA in msh (not supported by ogs5py)
-
-The following benchmarks have multiple sub keywords in some files, which is
-not convertable to a ogs5py script at the moment. Therefore the following are skipped as well:
-
-+ `lag2d`    repeated NEIGHBOR (cct)
-+ `decal`    repeated NEIGHBOR (cct)
-+ `2D1P_transport`    repeated POROSITY (mmp)
-+ `Nuklidtransport`    repeated MASS_DISPERSION (mmp)
-+ `cement2d`    repeated KINETIC_GEM (gem)
-+ `model_1`    repeated DAT_TYPE (out)
-+ `Leakage`    repeated TIM_TYPE (out)
-+ `CO2-FLOW`    repeated DAT_TYPE (out)
-+ `2pf_2pt`    repeated SIMULATOR (pcs)
-
-
-Generation
-----------
+# Welcome to the ogs5py benchmarks
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/GeoStat-Framework/ogs5py/master/docs/source/pics/OGS.png" alt="ogs5py-LOGO" width="251px"/>
+</p>
+
+## Purpose
+
+To get in touch with [``ogs5py``][ogs5_link], most of the OGS5 benchmarks were rewritten into a ogs5py-script in this repository.
+These benchmarks can be seen as a smorgasbord to provide a starting point for your own ogs5py model.
+
+You can clone this repository with:
+
+    git clone https://github.com/GeoStat-Framework/ogs5py_benchmarks.git
+
+Or simply download it as a [zip-file][zip].
+
+The original Benchmarks can be found here: https://github.com/ufz/ogs5-benchmarks
+
+
+## Generation
 
 The scripts were generated with the python script
 
         gen_benchmark_scripts.py
-        
+
 You can run all generated scripts for testing with the python script
- 
+
         run_ogs5py_scripts.py
 
 
-Created January 2019, Copyright Sebastian Müller 2019
+Copyright Sebastian Müller 2019
+
+[ogs5_link]: https://github.com/GeoStat-Framework/ogs5py
+[zip]: https://github.com/GeoStat-Framework/ogs5py_benchmarks/archive/master.zip

benchmarks/Anisotropy/moleculardiffusion/soil_layer.gli

@@ -1,4 +1,4 @@
-|-------------- Written with ogs5py --------------|
+|------------------ Written with ogs5py ------------------|
 #POINTS
 0 0.0 1.0 0.0 $NAME POINT0 $MD 0.05
 1 0.0 0.0 0.0 $NAME POINT1 $MD 0.05
@@ -265,4 +265,4 @@
   $POLYLINES
    POLYLINE6
 #STOP
-|-- Written with ogs5py (0.6.1) on: 2019-01-22_19-37-18 --|
+|-- Written with ogs5py (1.0.0.rc1) on: 2019-08-22_15-03-32 --|

benchmarks/Anisotropy/moleculardiffusion/soil_layer.msh

@@ -1153,4 +1153,4 @@
 734 6 tri 324 162 161     
 735 6 tri 324 163 162     
 #STOP
-|-- Written with ogs5py (0.6.1) on: 2019-01-22_19-37-18 --|
+|-- Written with ogs5py (1.0.0.rc1) on: 2019-08-22_15-03-32 --|

benchmarks/Anisotropy/moleculardiffusion/soil_layer.py

@@ -6,6 +6,18 @@
     task_id='soil_layer',
     output_dir='out',
 )
+model.msh.read_file('soil_layer.msh')
+model.gli.read_file('soil_layer.gli')
+model.pcs.add_block(
+    main_key='PROCESS',
+    PCS_TYPE='LIQUID_FLOW',
+    NUM_TYPE='NEW',
+)
+model.pcs.add_block(
+    main_key='PROCESS',
+    PCS_TYPE='MASS_TRANSPORT',
+    NUM_TYPE='NEW',
+)
 model.bc.add_block(
     main_key='BOUNDARY_CONDITION',
     PCS_TYPE='LIQUID_FLOW',
@@ -34,7 +46,6 @@
     GEO_TYPE=['POLYLINE', 'POLYLINE11'],
     DIS_TYPE=['CONSTANT', 1.0],
 )
-model.gli.read_file('soil_layer.gli')
 model.ic.add_block(
     main_key='INITIAL_CONDITION',
     PCS_TYPE='LIQUID_FLOW',
@@ -56,19 +67,8 @@
     GEO_TYPE=['POLYLINE', 'POLYLINE11'],
     DIS_TYPE=['CONSTANT', 1.0],
 )
-model.mcp.add_block(
-    main_key='COMPONENT_PROPERTIES',
-    NAME='Tracer',
-    MOBILE=1,
-    TRANSPORT_PHASE=0,
-    DIFFUSION=[1, 6e-10],
-)
-model.mfp.add_block(
-    main_key='FLUID_PROPERTIES',
-    FLUID_TYPE='LIQUID',
-    PCS_TYPE='PRESSURE1',
-    DENSITY=[1, 1000.0],
-    VISCOSITY=[1, 0.001],
+model.st.add_block(
+    main_key='SOURCE_TERM',
 )
 model.mmp.add_block(
     main_key='MEDIUM_PROPERTIES',
@@ -154,7 +154,6 @@
     MASS_DISPERSION=[1, 0.0, 0.0],
     DENSITY=[1, 2000.0],
 )
-model.msh.read_file('soil_layer.msh')
 model.msp.add_block(
     main_key='SOLID_PROPERTIES',
     DENSITY=[1, 2000.0],
@@ -239,6 +238,20 @@
         [1, 0.00118799939],
     ],
 )
+model.mfp.add_block(
+    main_key='FLUID_PROPERTIES',
+    FLUID_TYPE='LIQUID',
+    PCS_TYPE='PRESSURE1',
+    DENSITY=[1, 1000.0],
+    VISCOSITY=[1, 0.001],
+)
+model.mcp.add_block(
+    main_key='COMPONENT_PROPERTIES',
+    NAME='Tracer',
+    MOBILE=1,
+    TRANSPORT_PHASE=0,
+    DIFFUSION=[1, 6e-10],
+)
 model.num.add_block(
     main_key='NUMERICS',
     PCS_TYPE='LIQUID_FLOW',
@@ -251,29 +264,6 @@
     LINEAR_SOLVER=[2, 6, 1e-14, 1000, 0.5, 1, 2],
     ELE_GAUSS_POINTS=3,
 )
-model.out.add_block(
-    main_key='OUTPUT',
-    NOD_VALUES=[
-        ['PRESSURE1'],
-        ['Tracer'],
-    ],
-    GEO_TYPE='DOMAIN',
-    TIM_TYPE=['STEPS', 1],
-    DAT_TYPE='PVD',
-)
-model.pcs.add_block(
-    main_key='PROCESS',
-    PCS_TYPE='LIQUID_FLOW',
-    NUM_TYPE='NEW',
-)
-model.pcs.add_block(
-    main_key='PROCESS',
-    PCS_TYPE='MASS_TRANSPORT',
-    NUM_TYPE='NEW',
-)
-model.st.add_block(
-    main_key='SOURCE_TERM',
-)
 model.tim.add_block(
     main_key='TIME_STEPPING',
     PCS_TYPE='LIQUID_FLOW',
@@ -288,5 +278,15 @@
     TIME_START=0.0,
     TIME_END=300000000.0,
 )
+model.out.add_block(
+    main_key='OUTPUT',
+    NOD_VALUES=[
+        ['PRESSURE1'],
+        ['Tracer'],
+    ],
+    GEO_TYPE='DOMAIN',
+    TIM_TYPE=['STEPS', 1],
+    DAT_TYPE='PVD',
+)
 model.write_input()
 model.run_model()

benchmarks/Anisotropy/permeability/soil_layer.gli

@@ -1,4 +1,4 @@
-|-------------- Written with ogs5py --------------|
+|------------------ Written with ogs5py ------------------|
 #POINTS
 0 0.0 1.0 0.0 $NAME POINT0 $MD 0.05
 1 0.0 0.0 0.0 $NAME POINT1 $MD 0.05
@@ -265,4 +265,4 @@
   $POLYLINES
    POLYLINE6
 #STOP
-|-- Written with ogs5py (0.6.1) on: 2019-01-22_19-37-18 --|
+|-- Written with ogs5py (1.0.0.rc1) on: 2019-08-22_15-03-32 --|

benchmarks/Anisotropy/permeability/soil_layer.msh

@@ -1153,4 +1153,4 @@
 734 6 tri 324 162 161     
 735 6 tri 324 163 162     
 #STOP
-|-- Written with ogs5py (0.6.1) on: 2019-01-22_19-37-18 --|
+|-- Written with ogs5py (1.0.0.rc1) on: 2019-08-22_15-03-32 --|

benchmarks/Anisotropy/permeability/soil_layer.py

@@ -6,6 +6,18 @@
     task_id='soil_layer',
     output_dir='out',
 )
+model.msh.read_file('soil_layer.msh')
+model.gli.read_file('soil_layer.gli')
+model.pcs.add_block(
+    main_key='PROCESS',
+    PCS_TYPE='LIQUID_FLOW',
+    NUM_TYPE='NEW',
+)
+model.pcs.add_block(
+    main_key='PROCESS',
+    PCS_TYPE='MASS_TRANSPORT',
+    NUM_TYPE='NEW',
+)
 model.bc.add_block(
     main_key='BOUNDARY_CONDITION',
     PCS_TYPE='LIQUID_FLOW',
@@ -34,7 +46,6 @@
     GEO_TYPE=['POLYLINE', 'POLYLINE11'],
     DIS_TYPE=['CONSTANT', 1.0],
 )
-model.gli.read_file('soil_layer.gli')
 model.ic.add_block(
     main_key='INITIAL_CONDITION',
     PCS_TYPE='LIQUID_FLOW',
@@ -56,19 +67,8 @@
     GEO_TYPE=['POLYLINE', 'POLYLINE11'],
     DIS_TYPE=['CONSTANT', 1.0],
 )
-model.mcp.add_block(
-    main_key='COMPONENT_PROPERTIES',
-    NAME='Tracer',
-    MOBILE=1,
-    TRANSPORT_PHASE=0,
-    DIFFUSION=[1, 6e-10],
-)
-model.mfp.add_block(
-    main_key='FLUID_PROPERTIES',
-    FLUID_TYPE='LIQUID',
-    PCS_TYPE='PRESSURE1',
-    DENSITY=[1, 1000.0],
-    VISCOSITY=[1, 0.001],
+model.st.add_block(
+    main_key='SOURCE_TERM',
 )
 model.mmp.add_block(
     main_key='MEDIUM_PROPERTIES',
@@ -154,7 +154,6 @@
     MASS_DISPERSION=[1, 0.0, 0.0],
     DENSITY=[1, 2000.0],
 )
-model.msh.read_file('soil_layer.msh')
 model.msp.add_block(
     main_key='SOLID_PROPERTIES',
     DENSITY=[1, 2000.0],
@@ -183,6 +182,20 @@
     main_key='SOLID_PROPERTIES',
     DENSITY=[1, 2000.0],
 )
+model.mfp.add_block(
+    main_key='FLUID_PROPERTIES',
+    FLUID_TYPE='LIQUID',
+    PCS_TYPE='PRESSURE1',
+    DENSITY=[1, 1000.0],
+    VISCOSITY=[1, 0.001],
+)
+model.mcp.add_block(
+    main_key='COMPONENT_PROPERTIES',
+    NAME='Tracer',
+    MOBILE=1,
+    TRANSPORT_PHASE=0,
+    DIFFUSION=[1, 6e-10],
+)
 model.num.add_block(
     main_key='NUMERICS',
     PCS_TYPE='LIQUID_FLOW',
@@ -195,29 +208,6 @@
     LINEAR_SOLVER=[2, 6, 1e-14, 1000, 0.5, 1, 2],
     ELE_GAUSS_POINTS=3,
 )
-model.out.add_block(
-    main_key='OUTPUT',
-    NOD_VALUES=[
-        ['PRESSURE1'],
-        ['Tracer'],
-    ],
-    GEO_TYPE='DOMAIN',
-    TIM_TYPE=['STEPS', 1],
-    DAT_TYPE='PVD',
-)
-model.pcs.add_block(
-    main_key='PROCESS',
-    PCS_TYPE='LIQUID_FLOW',
-    NUM_TYPE='NEW',
-)
-model.pcs.add_block(
-    main_key='PROCESS',
-    PCS_TYPE='MASS_TRANSPORT',
-    NUM_TYPE='NEW',
-)
-model.st.add_block(
-    main_key='SOURCE_TERM',
-)
 model.tim.add_block(
     main_key='TIME_STEPPING',
     PCS_TYPE='LIQUID_FLOW',
@@ -232,5 +222,15 @@
     TIME_START=0.0,
     TIME_END=300000000.0,
 )
+model.out.add_block(
+    main_key='OUTPUT',
+    NOD_VALUES=[
+        ['PRESSURE1'],
+        ['Tracer'],
+    ],
+    GEO_TYPE='DOMAIN',
+    TIM_TYPE=['STEPS', 1],
+    DAT_TYPE='PVD',
+)
 model.write_input()
 model.run_model()