Merge branch 'development' into update_xrb_mixed

AMReX-Astro · Jul 18, 2024 · bca68ea · bca68ea
2 parents 1433028 + 6bc2822
commit bca68ea
Show file tree

Hide file tree

Showing 28 changed files with 8,118 additions and 268 deletions.
diff --git a/.zenodo.json b/.zenodo.json
@@ -2,29 +2,31 @@
     "creators": [
         {
             "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
+            "name": "Almgren, Ann",
+            "orcid": "0000-0003-2103-312X"
+        },
+        {
+            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+            "name": "Boyd, Brendan",
+            "orcid": "0000-0002-5419-9751"
+        },
+        {
             "name": "Fan, Doreen",
             "orcid": "0000-0002-3246-4315"
         },
         {
-            "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
-            "name": "Nonaka, Andy",
-            "orcid": "0000-0003-1791-0265"
+            "name": "Harpole, Alice",
+            "orcid": "0000-0002-1530-781X"
         },
         {
             "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
-            "name": "Almgren, Ann",
-            "orcid": "0000-0003-2103-312X"
+            "name": "Nonaka, Andy",
+            "orcid": "0000-0003-1791-0265"
         },
         {
-            "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
             "name": "Willcox, Donald",
             "orcid": "0000-0003-2300-5165"
         },
-        {
-            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
-            "name": "Harpole, Alice",
-            "orcid": "0000-0002-1530-781X"
-        },
         {
             "affiliation": "Department of Physics and Astronomy, Stony Brook University",
             "name": "Zingale, Michael",

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,27 @@
+# 24.07
+
+  * fix some AMReX namespace issues (#471)
+
+# 24.06
+
+  * added burning_cutoff_temperature_lo parameter (#465)
+
+  * fixed an OpenMP race condition in the diagnostics (#455)
+
+  * colorized the verbose stepping output (#463)
+
+  * added more CI checks (#458, #459, #462)
+
+  * fixed some clang-tidy issues (#443, #457)
+
+  * disallow OpenMP + GPUs (#456)
+
+  * documentation improvements (#450)
+
+  * fix a race condition in the build system dependencies (#448)
+
+  * add `eos_rh_t` in places to speed up the EOS calls (#446)
+
 # 24.05
 
   * some coverity, clang-tidy, and other compiler fixes (#430, #437,

diff --git a/Exec/science/wdconvect/ci-benchmarks/wdconvect_3d_extrema.out b/Exec/science/wdconvect/ci-benchmarks/wdconvect_3d_extrema.out
@@ -6,7 +6,7 @@
  velz                            -232072.20041           223669.30873
  magvel                           1.6659935689           283807.22726
  momentum                         1858344.5271       6.4467588594e+14
- vort                         3.7905619116e-13         0.089547619929
+ vort                          3.790561911e-13         0.089547619929
  rho                              73243.286692           2632585274.1
  rhoh                         1.2643451001e+21       6.4784804448e+27
  h                            1.7262264938e+16       2.4608815177e+18
@@ -26,7 +26,7 @@
  deltap                      -1.0176593093e+18       1.0748209947e+18
  deltaT                       -2.628445905e-07       9.4568318485e-08
  Pi                          -2.1314298456e+22       2.2695021217e+22
- pioverp0                    -1.3133053276e-05       1.3515909744e-05
+ pioverp0                    -1.3133053276e-05       1.3515909745e-05
  p0pluspi                     5.0885324496e+20       1.7639421276e+27
  gpix                        -2.8429127476e+16       3.1504856898e+16
  gpiy                        -2.1175608181e+16       1.9354104082e+16
@@ -50,6 +50,6 @@
  thermal                                     0                      0
  conductivity                                0                      0
  radial_velocity                 -214862.92054           228648.68391
- circ_velocity                2.4327330569e-15           273571.94181
+ circ_velocity                2.4412287111e-15           273571.94181
  sponge                          0.96289830721                      1
 
diff --git a/Exec/science/xrb_layered/README.md b/Exec/science/xrb_layered/README.md
@@ -4,6 +4,13 @@ Models the convection and burning in the envelope of a neutron star, where hydro
 has previously been depleted by the hot CNO cycle, leaving a pure helium layer at 
 large depths, where the burst will ignite.
 
+Appears in:
+
+  * `Hydrodynamical simulations of proton ingestion flashes in Type I X-ray Bursts`
+     Guichandut, S.; Zingale, M.; Cumming, A, 2023. 
+     https://arxiv.org/abs/2405.08952
+
+
 This is the multidimensional version of a calculation previously done in MESA in:
 
   * `The imprint of convection on Type I X-ray bursts: Pauses in photospheric
@@ -13,7 +20,6 @@ This is the multidimensional version of a calculation previously done in MESA in
 
 ## initial model
 
-* `xrb_layered_3cm.hse`
+* `toy_atm_hot_3cm.hse`
 
-An initial MESA model is placed into eulerian HSE using the lagrangian_planar routines
-from AMREX/initial_models. More detail in create_initial_model/README.md.
+Build using a MESA model as a guide. More details in `create_initial_model/`.
diff --git a/Exec/science/xrb_layered/create_initial_model/Initial_Model.ipynb b/Exec/science/xrb_layered/create_initial_model/Initial_Model.ipynb
diff --git a/Exec/science/xrb_layered/create_initial_model/README.md b/Exec/science/xrb_layered/create_initial_model/README.md
@@ -1,13 +1,11 @@
 ## MESA
 
-We first use MESA to create a model of a neutron star with mass $M=1.4M_\odot$ , radius $R=12$ km, and surface gravity $g=GM/R^2=1.29\times10^{14}$ g/cm $^2$ (MESA is Newtonian, and gravity has not been redshift-corrected). 
-
-We then accrete a column $y\sim 2\times 10^4$ g/cm $^{2}$ of iron. This will be the substrate/buffer below the burning region.
+We first use MESA to create a model of a neutron star with mass $M=1.4M_\odot$ , radius $R=12$ km, and surface gravity $g=GM/R^2=1.29\times10^{14}$ g/cm $^2$ (MESA is Newtonian, and gravity has not been redshift-corrected). Initially, the model is just an atmosphere of pure iron with a column depth of 5e9 g/cm2.
 
 We then accrete a "solar" mixture (70% hydrogen, 28% helium, 2% carbon-12) for a few days, until ignition in a helium layer. 
 
-The last two profiles of the MESA run (`profile37.data` & `profile38.data`) are copied in `mesa/`. These steps are all done in [github.com/simonguichandut/mesa\_mixed\_burst](https://github.com/simonguichandut/mesa_mixed_burst). The relevant run is `run/make_ignition_model_for_hydro/`. 
+The last two models of the MESA run (`profile4.data` & `profile5.data`) are copied in `mesa/`. These steps are all done in [github.com/simonguichandut/mesa\_mixed\_burst](https://github.com/simonguichandut/mesa_mixed_burst). The relevant run is `run/make_ignition_model_for_hydro/`. 
 
 ## Toy model
 
-See the notebook `Initial_Model.ipynb` for a detailed explanation of how we use the MESA model (profile37) to construct a simplified toy model, with a temperature kick at the bottom of the fuel layer. This is done in `toy_atm/`, which is a modified version of https://github.com/AMReX-Astro/initial_models/tree/main/toy_atm .
+See the notebook `Initial_Model.ipynb` for a detailed explanation of how we use the pre-igntion MESA model (profile4) to construct a simplified toy model, with a temperature kick at the bottom of the fuel layer. This is done in `toy_atm/`, which is a modified version of https://github.com/AMReX-Astro/initial_models/tree/main/toy_atm .