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update doi Fixing typo Add ref sedfoam small modif
cgadal-papers · Mar 22, 2024 · d7559b7 · d7559b7
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diff --git a/AUTHORS.txt b/AUTHORS.txt
@@ -2,7 +2,7 @@ Project: LOCK_PLGC_MONOGRAPH
 
 List of authors:
 
- - Cyril Gadal <laurent.lacaze@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
+ - Cyril Gadal <cyril.gadal@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
 
  - Jean Schneider <[email protected]> Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine, CNRS, 54500, Nancy, France
 
@@ -20,7 +20,7 @@ List of authors:
 
  - Marie Rastello <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
 
- - Laurent Lacaze <cyril.gadal@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
+ - Laurent Lacaze <laurent.lacaze@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
 
 
 ----

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
@@ -3,7 +3,7 @@ Project title: Data used in 'Chapter 16. Particle-laden gravity currents: the lo
 Short project name: LOCK_PLGC_MONOGRAPH
 
 List of authors:
- - Cyril Gadal <laurent.lacaze@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
+ - Cyril Gadal <cyril.gadal@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
  - Jean Schneider <[email protected]> Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine, CNRS, 54500, Nancy, France
  - Cyrille Bonamy <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
  - Julien Chauchat <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
@@ -12,7 +12,7 @@ List of authors:
  - Matthieu Mercier <[email protected]> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
  - Florence Naaim <[email protected]> Univ. Grenoble Alpes, INRAE, CNRS, IRD, Grenoble INP, IGE, 38000 Grenoble, France
  - Marie Rastello <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
- - Laurent Lacaze <cyril.gadal@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
+ - Laurent Lacaze <laurent.lacaze@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
 
 Description
 -----------
@@ -30,7 +30,7 @@ The folder 'data/output_data' contains 287 netcdf4 files corresponding to each e
     - setup: setup used to acquire the data. See article.
     - dataset: Dataset classification of this run, See paper.
 
-   - dimensions(sizes): time(1801)
+   - dimensions(sizes): time(n)
 
    - variables(dimensions):
     - At(): Atwood number
@@ -63,8 +63,6 @@ The folder 'data/output_data' contains 287 netcdf4 files corresponding to each e
     - vs(): particle Stokes velocity
     - x_front('time',): front position vector
 
-   - groups:
-
 Variables can sometimes possess the following attributes:
   - unit: corresponding unit
   - std: error(s) on the given quantity, calculated by error propagation from measurement uncertainties using the `uncertainties` module (https://pythonhosted.org/uncertainties/) in Python.

diff --git a/PROJECT-META.yml b/PROJECT-META.yml
@@ -9,7 +9,7 @@ project:
       acronym: LOCK_PLGC_MONOGRAPH
 
    creator:
-      - Cyril Gadal <laurent.lacaze@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
+      - Cyril Gadal <cyril.gadal@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
       - Jean Schneider <[email protected]> Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine, CNRS, 54500, Nancy, France
       - Cyrille Bonamy <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
       - Julien Chauchat <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
@@ -18,7 +18,7 @@ project:
       - Matthieu Mercier <[email protected]> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
       - Florence Naaim <[email protected]> Univ. Grenoble Alpes, INRAE, CNRS, IRD, Grenoble INP, IGE, 38000 Grenoble, France
       - Marie Rastello <[email protected]> Univ. Grenoble Alpes, CNRS, Grenoble INP, LEGI, 38000 Grenoble, France
-      - Laurent Lacaze <cyril.gadal@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
+      - Laurent Lacaze <laurent.lacaze@imft.fr> Institut de Mécanique des Fluides de Toulouse (IMFT), Université de Toulouse, CNRS, Toulouse, France
 
    subject:
       - Experiments
@@ -45,7 +45,7 @@ project:
         - setup: setup used to acquire the data. See article.
         - dataset: Dataset classification of this run, See paper.
 
-       - dimensions(sizes): time(1801)
+       - dimensions(sizes): time(n)
 
        - variables(dimensions):
         - At(): Atwood number
@@ -78,21 +78,18 @@ project:
         - vs(): particle Stokes velocity
         - x_front('time',): front position vector
 
-       - groups:
-
     Variables can sometimes possess the following attributes:
       - unit: corresponding unit
       - std: error(s) on the given quantity, calculated by error propagation from measurement uncertainties using the `uncertainties` module (https://pythonhosted.org/uncertainties/) in Python.
       - comments: comments on the given quantity (definition, formulas, etc ..)
 
     In addition, the `analysis/analysis.py` script is used to generate the aforementioned NetCDF files from the original ones in `data/input_data`. The folder `paper` contains all source files of the article preprint, including Python codes to generate the article figures from the NetCDF files.
 
-    Finally, the CSV file 'dataset_summary.csv' offers a summary of all runs and corresponding experimental parameters,
-    allowing for easier access to the data.
+    Finally, the CSV file 'dataset_summary.csv' offers a summary of all runs and corresponding experimental parameters, allowing for easier access to the data.
 
    publisher:
 
-   date: 09/08/2023
+   date: 14/03/2024
 
    type:
       - dataset
@@ -103,9 +100,10 @@ project:
 
    # if the work is derived from...
    source:
-      - https://doi.org/10.48550/arXiv.2301.00192
+      - https://doi.org/10.1017/jfm.2023.762
       - https://doi.org/10.5281/zenodo.7487189
       - https://doi.org/10.1007/s00348-022-03562-y 
+      - https://doi.org/10.5194/gmd-10-4367-2017
 
    language: en-US
 

diff --git a/Readme.md b/Readme.md
@@ -1,6 +1,9 @@
 # PALAGRAM Monograph
 
-This repository contains the data and codes associated with the PALAGRAM consortium.
+This repository contains the data used in the research paper:
+
+> Gadal C., Schneider J., Bonamy C., Chauchat J., Dossmann Y., Kiesgen de Richter S., Mercier M. J., Naaim-Bouvet F., Rastello M., and Lacaze L. **Chapter 16: Particle-laden gravity currents: the lock-release slumping regime at the laboratory scale.** *Submitted to AGU Monograph.* 
+
 
 ## Repository organization
 
@@ -12,33 +15,76 @@ This repository contains the data and codes associated with the PALAGRAM consort
   │       └─── ... : NETCDF files
   │   └───output_data: processed data output by analysis.py (also contains input_data)
   │       └─── ... : NETCDF files
+  └───analysis:
+      └───analysis.py: analysis code, that reads input_data and writes output_data
   └───paper: contains source files for article
   │   └───figures: contains source figures
   │       └─── ... : PDF files
   │       └─── figure_scripts: contains figure scripts that reads data in data/output_data and writes figures in paper/figures
   │            └─── *.py : python scripts for figures
   │   └─── ... : various files (.tex, .bib, ...)
   │   └─── main.pdf : article preprint
-  └───analysis:
-      └───analysis.py: analysis code, that reads input_data and writes output_data
 
   ```
 
-## Workflow
+## Data organization
+
+The CSV file `dataset_summary.csv` offers a summary of all runs and corresponding experimental parameters, allowing for easier access to the data.
+
+The folder `data/output_data` contains 287 netcdf4 files corresponding to each experimental run used in the paper. For each run, the structure of the NetCDF file is the following:
+- attributes:
+  - particle_type: particle type used (silica sand, glass beads, etc..)
+  - label: filename
+  - lab: lab where this run has been performed
+  - run_oldID: Old filename, corresponding to the experimental notebook
+  - author: author(s) that acquired this run
+  - setup: setup used to acquire the data. See article.
+  - dataset: Dataset classification of this run, See paper.
+
+- dimensions(sizes): time(n)
 
-One can work separately on the analysis (`analysis.py`), or the figures. While changing and running analysis.py, `output_data` are automatically updated. Figure scripts then needs to be re-run to update them (Use `figure_scripts/run_all.py` to update them all).
+- variables(dimensions):
+  - At(): Atwood number
+  - Fr(): Froude number (adi. initial current velocity)
+  - H0(): initial heavy fluid height inside the lock
+  - H_a(): ambient fluid height outside the lock
+  - L0(): streamwise lock length
+  - L_1(): streamwise tank length after the lock
+  - Re(): Reynolds number
+  - S(): Settling number
+  - St(): Stokes number
+  - T_a(): ambient temperature
+  - T_f(): heavy fluid temperature inside the lock
+  - W0(): crossstream lock width
+  - a(): lock aspect ratio
+  - alpha(): bottom slope
+  - d(): particle diameter
+  - gprime(): specific gravity
+  - lamb(): adi. attenuation parameter
+  - nu_a(): ambient viscosity
+  - nu_f(): heavy fluid lock viscosity
+  - phi(): initial particle volume fraction inside the lock
+  - rho_a(): ambient fluid density
+  - rho_c(): heavy fluid mix density inside the lock
+  - rho_f(): 
+  - rho_p(): particle density
+  - t('time',): time vector
+  - t0(): characteristic timescale, t0 = L0/u0
+  - u0(): characteristic velocity scale, u0 = sqrt(gprime*H0)
+  - vs(): particle Stokes velocity
+  - x_front('time',): front position vector
 
-### Working on the repo
+Variables can sometimes possess the following attributes:
+  - unit: corresponding unit
+  - std: error(s) on the given quantity, calculated by error propagation from measurement uncertainties using the `uncertainties` module (https://pythonhosted.org/uncertainties/) in Python.
+  - comments: comments on the given quantity (definition, formulas, etc ..)
 
-If you have git installed, clone the repository: `git clone [email protected]:Cgadal/palagram_monograph.git`.
+## Related works
 
-> **Warning**: When working locally, please create and work on a separate branch, different from `main`. 
+- Gadal, C., Mercier, M. J., Rastello, M., & Lacaze, L. (2023). Slumping regime in lock-release turbidity currents. *Journal of Fluid Mechanics*, 974, A4. [doi:10.1017/jfm.2023.762](https://doi.org/10.1017/jfm.2023.762) 
 
-Then:
+- Gadal, C., Mercier, M., Rastello, M., & Lacaze, L. (2023). Data used in 'Slumping regime in lock-release turbidity currents' [Data set]. In Journal of Fluid Mechanics (Vol. 974, p. A4). *Zenodo*. https://doi.org/10.5281/zenodo.10058946
 
-- commit your work
-- pull to update the `main` branch
-- merge the `main` branch with your work branch and solve potential conflicts
-- only then, push on the distant repo (GitHub)
+- Schneider, J., Dossmann, Y., Farges, O. et al. Investigation of particle laden gravity currents using the light attenuation technique. *Exp Fluids*, 64, 23 (2023). [doi:10.1007/s00348-022-03562-y](https://doi.org/10.1007/s00348-022-03562-y)
 
-If you don't have git installed, you won't be able to work on the repo. You can still download the whole content by clicking on the green <> code button, or simply clicking [here](https://github.com/Cgadal/palagram_monograph/archive/refs/heads/main.zip).
+- Chauchat, J., Cheng, Z., Nagel, T., Bonamy, C., and Hsu, T.-J. (2017) SedFoam-2.0: a 3-D two-phase flow numerical model for sediment transport, *Geosci. Model Dev.*, 10, 4367-4392, [doi:10.5194/gmd-10-4367-2017](https://doi.org/10.5194/gmd-10-4367-2017) and [github](https://github.com/sedfoam/sedfoam)
diff --git a/paper/main.aux b/paper/main.aux
@@ -27,7 +27,7 @@
 \newlabel{eq:Xt_slope}{{6}{6}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Particle-Laden Gravity Currents}{6}{}\protected@file@percent }
 \newlabel{sec:intro_PLGC}{{1.2}{6}}
-\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces \textbf  {Experimental set-ups used in this study.} (a--c) Sketches of the three experimental set-ups. Below are shown snapshots of corresponding experimental images: (d--h) Set-up 1, $\alpha = 7^\circ $, $\phi \sim 3\nobreakspace  {}\%$, ${S}t=0.027$; (i--k) Set-up 2, $\alpha = 45.4^\circ $, $\phi \sim 1.5\nobreakspace  {}\%$, ${S}t=0.06 $; (l--p) Set-up 3, $\alpha = 0^\circ $, $\phi \sim 55\%$, ${S}t \equiv 0$. Below the horizontal black line are shown snapshots of a numerical simulation using SedFoan: (q--v) $\alpha = 45.4^\circ $, $\phi \sim 1.7\nobreakspace  {}\%$, $\mathcal  {S}t=0.06$.\relax }}{7}{}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces \textbf  {Experimental set-ups used in this study.} (a--c) Sketches of the three experimental set-ups. Below are shown snapshots of corresponding experimental images: (d--h) Set-up 1, $\alpha = 7^\circ $, $\phi \sim 3\nobreakspace  {}\%$, ${S}t=0.027$; (i--k) Set-up 2, $\alpha = 45.4^\circ $, $\phi \sim 1.5\nobreakspace  {}\%$, ${S}t=0.06 $; (l--p) Set-up 3, $\alpha = 0^\circ $, $\phi \sim 55\%$, ${S}t \equiv 0$. Below the horizontal black line are shown snapshots of a numerical simulation using SedFoam: (q--v) $\alpha = 45.4^\circ $, $\phi \sim 1.7\nobreakspace  {}\%$, $\mathcal  {S}t=0.06$.\relax }}{7}{}\protected@file@percent }
 \providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
 \newlabel{fig:fig1}{{1}{7}}
 \citation{Schneider2023}

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