Update examples and re-run with PetIBM-0.5.1 container (#1)

* Remove examples not super useful

* Remove unneeded files

* (tgv) Run/Update example for petibm-0.5.1 container

* (ns) Run/Update example for petibm-0.5.1 container

* (ibpm) Run/Update examples for petibm-0.5.1 container

* (decoupled, flat plate) Run/Update examples for petibm-0.5.1 container

* (decoupled, cylRe100) Run/Update examples for petibm-0.5.1 container

* (decoupled, flapping) Run/Update example for petibm-0.5.1 container

* (decoupled, oscillating) Run/Update example for petibm-0.5.1 container

* (decoupled, cylRe550) Run/Update example for petibm-0.5.1 container

* (decoupled, cylRe40) Add example for petibm-0.5.1 container

* (decoupled, sphere) Revise/update examples for petibm-0.5.1 container

* Add digitized data from Dutsch et al. (1998)

* Update copyright year

* Fix typo in data value

* Add conda env file for post-processing scripts

* Update readme

* Remove inline equations from readme

* Fix figure links

* Add decoupledibpm example using Aggregation AMG

* Small updates to figures (ibpm, cylRe100)

* Add more vorticity figures (flapping wing)

* Select correct max cl deviation

* Revise tgv example

* Add convergence analysis oscillating cyl Re=100

* Calculate slope using the lstsq method in log

* Update color scheme and fix typo

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2019, Olivier Mesnard
+Copyright (c) 2019-2022, Olivier Mesnard
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -4,37 +4,47 @@
 [![Docker Hub](https://img.shields.io/badge/hosted-docker--hub-informational.svg)](https://hub.docker.com/repository/docker/barbagroup/petibm)
 [![Singularity Hub](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/3692)
 
-## Dependencies
+The repository includes examples of flow simulation with [PetIBM](https://github.com/barbagroup/PetIBM).
+Each example provides the set of input data and the python post-processing scripts.
 
-Package version last used indicated between parenthesis.
+## Requirements
 
-* [PetIBM](https://github.com/barbagroup/PetIBM) (`0.4.2`)
-  * [OpenMPI](https://www.open-mpi.org) (`3.1.4`)
-  * [PETSc](https://www.mcs.anl.gov/petsc) (`3.11.4`)
-  * [CUDA Toolkit](https://developer.nvidia.com/cuda-toolkit-archive) (`10.1`)
-  * [AmgX](https://github.com/NVIDIA/AMGX) (commit `cf285c1`)
-* [PetibmPy](https://github.com/mesnardo/petibmpy) (`develop`)
+To run the examples, you can either install PetIBM on your machine or use our Docker image.
+
+To install PetIBM locally, please refer to [these instructions](https://barbagroup.github.io/PetIBM/dc/df1/md_doc_markdowns_installation.html).
+
+To pull the Docker image (tag is last used to run these examples):
+
+```shell
+docker pull docker pull barbagroup/petibm:0.5.1-GPU-OpenMPI-xenial
+```
+
+To post-process the numerical solution, we provide python scripts.
+To install the packages required to execute the scripts, we recommend creating a `conda` environment with:
+
+```
+conda env create --name=petibm-example --file=environment.yml
+```
+
+Note that most examples are set to solve the Poisson system on a GPU using the NVIDIA AmgX library and require a CUDA-capable GPU device.
+Of course, you can always modify the configuration files to run all solvers on CPUs.
 
 ## List of examples
 
+* [2D array of decaying vortices at Re=10](examples/taylorgreenvortices) (convergence analysis)
 * Navier-Stokes solver
-  * Convergence analysis (2D lid-driven cavity flow at Reynolds number 100)
-  * 2D lid-driven cavity flow at Reynolds numbers 100, 1000, 3200, and 5000
+  * [2D lid-driven cavity flow at Re=100, 1000, 3200, and 5000](examples/navierstokes)
 * Immersed boundary projection method (IBPM)
-  * 2D flow around an impulsively started cylinder at Reynolds numbers 40, 550, and 3000
-  * 2D unsteady flow around a stationary cylinder at Reynolds number 100
+  * [2D flow around an impulsively started circular cylinder at Re=40, 550, and 3000](examples/ibpm)
+  * [2D unsteady flow past a stationary circular cylinder at Re=100](examples/ibpm/cylinder2dRe100)
 * Decoupled IBPM
-  * 2D unsteady flow around a stationary cylinder at Reynolds number 100
-  * 2D flow around an impulsively started cylinder at Reynolds number 550.
-  * 2D flapping wing at Reynolds number 75
-  * 2D flow around an inline oscillating cylinder at Reynolds number 100
-  * 3D steady flow around an inclined flat plate at Reynolds number 100
-  * 3D steady-flow around a sphere at Reynolds numbers 50, 100, 150, 200, 250, and 300
-  * 3D unsteady flow around a sphere at Reynolds number 350
-
-## Contact
-
-Please e-mail [Olivier Mesnard](mailto:[email protected]) if you have any questions, suggestions, or feedback.
-
-To report bugs, please use the GitHub issue tracking system.
+  * [2D flow around an impulsively started circular cylinder at Re=40 and 550](examples/decoupledibpm)
+  * [2D unsteady flow past a stationary circular cylinder at Re=100](examples/decoupledibpm/cylinder2dRe100)
+  * [2D flapping wing at Re=75](examples/decoupledibpm/flapping2dRe75)
+  * [2D flow around an inline oscillating cylinder at Re=100 and KC=5](examples/decoupledibpm/oscillatingcylinder2dRe100)
+  * [3D steady flow around an inclined flat plate at Re=100](examples/decoupledibpm/flatplate3dRe100)
+  * [3D steady flow around a sphere at Re=50, 100, 150, 200, 250, and 300](examples/decoupledibpm/sphere3d)
+  * [3D unsteady flow around a sphere at Re=350](examples/decoupledibpm/sphere3d/Re350)
+
+To report bugs or ask questions, please use the GitHub issue tracking system.
 We also welcome pull-requests.

data/dutsch_et_al_1998/u_phi=180_x=-0.6.csv

@@ -0,0 +1,29 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-component of the velocity
+# at phase angle 180 degrees and at location x/D=-0.6.
+# Data digitized from Fig. 9 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+-0.08771929824561475, -0.9974358974358972
+-0.14912280701754455, -0.8948717948717946
+-0.22222222222222276, -0.797435897435897
+-0.37426900584795386, -0.6948717948717944
+-0.49122807017543924, -0.5948717948717943
+-0.38304093567251507, -0.48974358974358934
+0.035087719298244835, -0.39487179487179436
+0.5701754385964906, -0.2923076923076917
+0.8947368421052633, -0.1948717948717944
+1.0643274853801152, 0.21025641025641084
+0.874269005847951, 0.3051282051282057
+0.42105263157894646, 0.40769230769230813
+-0.1988304093567259, 0.5051282051282054
+-0.6081871345029246, 0.6025641025641026
+-0.6169590643274858, 0.6974358974358974
+-0.5760233918128659, 0.8
+-0.4122807017543866, 0.9025641025641027
+-0.22222222222222276, 1.0025641025641026

data/dutsch_et_al_1998/u_phi=180_x=0.0.csv

@@ -0,0 +1,21 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 180 degrees and at location x/D=0.0.
+# Data digitized from Fig. 9 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+-0.2463768115942031, -0.997455470737914
+-0.3159420289855073, -0.8956743002544534
+-0.4086956521739131, -0.7964376590330791
+-0.6144927536231883, -0.6972010178117054
+-0.7217391304347827, -0.5954198473282448
+-0.7768115942028988, 0.60559796437659
+-0.5913043478260873, 0.704834605597964
+-0.41449275362318816, 0.8066157760814245
+-0.30144927536231925, 0.9007633587786255
+-0.2376811594202901, 1.002544529262086

data/dutsch_et_al_1998/u_phi=180_x=0.6.csv

@@ -0,0 +1,30 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 180 degrees and at location x/D=0.6.
+# Data digitized from Fig. 9 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+-0.06588579795021943, -0.9948652118100139
+-0.03367496339677878, -0.8921694480102711
+-0.06588579795021987, -0.7971758664955089
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+-0.045387994143485155, 0.804878048780487
+-0.0717423133235724, 0.9050064184852367

data/dutsch_et_al_1998/u_phi=180_x=1.2.csv

@@ -0,0 +1,31 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 180 degrees and at location x/D=1.2.
+# Data digitized from Fig. 9 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+0.057268722466960575, -0.9999999999999996
+0.05726872246696102, -0.8943298969072169
+0.08663729809104304, -0.7989690721649485
+0.13950073421439102, -0.6984536082474229
+0.14243759177679927, -0.5927835051546393
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+0.245227606461087, -0.38659793814432963
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+0.3303964757709257, -0.09536082474226837
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+0.2775330396475777, 0.10824742268041243
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+0.28928046989721157, 0.30670103092783485
+0.25991189427312866, 0.40721649484536093
+0.21585903083700497, 0.5077319587628866
+0.17474302496328953, 0.6082474226804121
+0.11013215859030856, 0.7036082474226802
+0.08076358296622654, 0.8041237113402061
+0.05139500734214408, 0.904639175257732

data/dutsch_et_al_1998/u_phi=210_x=-0.6.csv

@@ -0,0 +1,31 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 210 degrees and at location x/D=-0.6.
+# Data digitized from Fig. 10 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+-0.026548672566371945, -0.9999999999999998
+-0.03834808259587019, -0.8990944372574383
+-0.03834808259587019, -0.7981888745148766
+-0.10619469026548733, -0.7024579560155233
+-0.18584070796460228, -0.6015523932729616
+-0.23598820058997072, -0.505821474773609
+-0.1268436578171097, -0.4049159120310475
+0.1445427728613562, -0.30142302716688163
+0.46607669616519143, -0.20310478654592434
+0.7020648967551617, -0.09961190168175871
+0.9410029498525061, 0.10219922380336444
+0.7020648967551617, 0.19793014230271688
+0.303834808259587, 0.2988357050452787
+-0.05604719764011845, 0.4023285899094441
+-0.2802359882005909, 0.4954721862871928
+-0.33038348082595914, 0.5963777490297542
+-0.33923303834808327, 0.6946959896507119
+-0.22418879056047203, 0.8007761966364816
+-0.17699115044247815, 0.8990944372574389
+-0.05604719764011845, 0.9974126778783963

data/dutsch_et_al_1998/u_phi=210_x=0.0.csv

@@ -0,0 +1,25 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 210 degrees and at location x/D=0.0.
+# Data digitized from Fig. 10 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+-0.2419825072886299, -1
+-0.29154518950437325, -0.9002557544757033
+-0.36734693877551017, -0.8030690537084402
+-0.4431486880466471, -0.703324808184143
+-0.3236151603498545, -0.6035805626598467
+0.3002915451895043, -0.4987212276214834
+0.8921282798833823, -0.40409207161125327
+0.9475218658892133, 0.39897698209718646
+0.28862973760932986, 0.49872122762148374
+-0.376093294460641, 0.5984654731457801
+-0.45481049562682196, 0.7007672634271103
+-0.3877551020408161, 0.8005115089514068
+-0.26239067055393583, 0.9028132992327369
+-0.2653061224489792, 1

data/dutsch_et_al_1998/u_phi=210_x=0.6.csv

@@ -0,0 +1,22 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 210 degrees and at location x/D=0.6.
+# Data digitized from Fig. 10 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+-0.18432510885341058, -1.0076335877862594
+-0.1901306240928884, -0.9058524173027989
+-0.22496371552975347, -0.8040712468193378
+-0.2046444121915818, -0.7099236641221369
+-0.2597968069666181, -0.6055979643765901
+0.48330914368650246, -0.5063613231552162
+0.4252539912917275, 0.4936386768447839
+-0.25399129172714074, 0.5979643765903309
+-0.2685050798258346, 0.6972010178117051
+-0.24238026124818557, 0.7989821882951657
+-0.21915820029027566, 0.9033078880407127

data/dutsch_et_al_1998/u_phi=210_x=1.2.csv

@@ -0,0 +1,31 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 210 degrees and at location x/D=1.2.
+# Data digitized from Fig. 10 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+0.008645533141210748, -1.0025252525252526
+0.031700288184438374, -0.9015151515151514
+0.06628242074928004, -0.8055555555555556
+0.10951008645533156, -0.7045454545454544
+0.16138328530259383, -0.606060606060606
+0.24783861671469776, -0.5075757575757576
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+0.1181556195965423, 0.6944444444444444
+0.04899135446685898, 0.7954545454545454
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data/dutsch_et_al_1998/u_phi=330_x=-0.6.csv

@@ -0,0 +1,32 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 330 degrees and at location x/D=-0.6.
+# Data digitized from Fig. 11 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+0.061764705882353166, -1.0025839793281666
+0.05294117647058849, -0.8992248062015511
+0.00588235294117645, -0.7984496124031013
+-0.03823529411764692, -0.6976744186046517
+-0.08529411764705852, -0.5968992248062022
+-0.09999999999999964, -0.5012919896640833
+-0.1352941176470579, -0.4005167958656337
+-0.20588235294117574, -0.3049095607235146
+-0.23235294117646976, -0.20155038759689958
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+-0.1999999999999993, 0.29715762273901747
+-0.14411764705882302, 0.39793281653746715
+-0.12058823529411722, 0.4987080103359167
+-0.07058823529411695, 0.5994832041343662
+-0.07058823529411695, 0.7002583979328159
+-0.09411764705882275, 0.8010335917312654
+-0.011764705882352011, 0.9043927648578804
+0.011764705882353343, 1.0025839793281648

data/dutsch_et_al_1998/u_phi=330_x=0.0.csv

@@ -0,0 +1,21 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 330 degrees and at location x/D=0.0.
+# Data digitized from Fig. 11 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+0.07536231884057987, -0.8978021167533281
+0.1855072463768117, -0.6994689678061734
+0.3130434782608704, -0.6003945864218021
+0.3565217391304354, -0.5012132610539515
+0.2521739130434786, -0.4043883910462074
+0.2434782608695656, 0.3971493896817492
+0.32753623188405845, 0.4937345576575577
+0.41159420289855086, 0.5979533134196258
+0.26376811594202954, 0.6999225578050666
+0.10434782608695681, 1.002924364789615

data/dutsch_et_al_1998/u_phi=330_x=0.6.csv

@@ -0,0 +1,20 @@
+# Experimental data from Dutsch et al. (1998).
+# Vertical profile of the x-velocity
+# at phase angle 330 degrees and at location x/D=0.6.
+# Data digitized from Fig. 11 of Cai et al. (2016)
+# by [email protected] on Feb. 14, 2020 (using WebPlotDigitizer).
+#
+# References:
+# * Dütsch, H., Durst, F., Becker, S., & Lienhart, H. (1998). Low-Reynolds-number flow around an oscillating circular cylinder at low Keulegan–Carpenter numbers. Journal of Fluid Mechanics, 360, 249-271.
+# * Cai, S. G., Ouahsine, A., Favier, J., & Hoarau, Y. (2016). Improved implicit immersed boundary method via operator splitting. In Computational Methods for Solids and Fluids (pp. 49-66). Springer, Cham.
+#
+# u, y
+0.25507246376811565, -0.9974522292993631
+0.3971014492753624, -0.9006369426751593
+0.6173913043478256, -0.7936305732484079
+0.9014492753623187, -0.6993630573248408
+0.8202898550724633, -0.5974522292993629
+0.7304347826086954, 0.602547770700637
+0.8376811594202893, 0.7019108280254778
+0.6202898550724636, 0.8063694267515922
+0.39420289855072443, 0.9082802547770701