Merge branch 'development' into massive_star_3d_analysis

.github/workflows/get_release_txt.py

@@ -26,9 +26,9 @@
                     txt = txt[m.end():].strip()
             else:
                 txt = ""
-                    
-            # we now need to substitute characters in the string so that 
-            # the action can deal with line breaks 
+
+            # we now need to substitute characters in the string so that
+            # the action can deal with line breaks
             txt = txt.replace('%', '%25')
             txt = txt.replace('\n', '%0A')
             txt = txt.replace('\r', '%0D')

.github/workflows/style.yml

@@ -0,0 +1,22 @@
+name: Style
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-style
+  cancel-in-progress: true
+
+jobs:
+  tabs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Tabs
+        run: .github/workflows/style/check_tabs.sh
+
+  trailing_whitespaces:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Trailing Whitespaces
+        run: .github/workflows/style/check_trailing_whitespaces.sh

.github/workflows/style/check_tabs.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.md" -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.nolint.H" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.nolint.H" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/\t/\ \ \ \ /g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTabs are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

.github/workflows/style/check_trailing_whitespaces.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+                  -o -path ./util/gcem \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.nolint.H" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.nolint.H" \
+                    -a ! -path "./networks/*/reaclib_rates.H" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/[[:blank:]]\+$//g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTrailing whitespaces at the end of a line are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

Diagnostics/DustCollapse/analytic.f90

@@ -1,6 +1,6 @@
 ! Print out the analytic solution for the homologous dust collapse problem,
 ! from Colgate and White 1966, ApJ, 143, 626.
-! 
+!
 ! This will yield r(t) as a function of t
 
 module constants_module
@@ -18,7 +18,7 @@ module constants_module
 
   ! we try to do equal timesteps, but eventually, the radius of the
   ! sphere is changing so quickly that we need to adjust the size of
-  ! the timestep.  The code will take nstep timesteps, with the 
+  ! the timestep.  The code will take nstep timesteps, with the
   ! initial timestep to be (t_f - t_i)/(nstep - 1).  Once the radius
   ! begins to change significantly, we will begin halving the timestep
   ! as needed.
@@ -111,7 +111,7 @@ function f(r,t) result (func)
   use constants_module
 
   implicit none
-  
+
   double precision, intent(in) :: r, t
   double precision :: func
 
@@ -130,7 +130,7 @@ function dfdr(r,t) result (dfuncdr)
   use constants_module
 
   implicit none
-  
+
   double precision, intent(in) :: r, t
   double precision :: dfuncdr
 
@@ -145,4 +145,4 @@ function dfdr(r,t) result (dfuncdr)
 end function dfdr
 
 
-  
+

Diagnostics/DustCollapse/analytic.txt

@@ -1,100 +1,100 @@
-  1.00000000000000002E-003   649909135.03119123     
-  2.00000001505167783E-003   649636489.29833126     
-  3.00000003010335563E-003   649181909.86863339     
-  4.00000004515503344E-003   648545142.11149800     
-  5.00000006020671125E-003   647725827.94719517     
-  6.00000007525838906E-003   646723505.15455902     
-  7.00000009031006686E-003   645537605.90191960     
-  8.00000010536174554E-003   644167454.93684888     
-  9.00000012041342334E-003   642612267.44508624     
-  1.00000001354651012E-002   640871146.53866076     
-  1.10000001505167790E-002   638943080.30864108     
-  1.20000001655684568E-002   636826938.57690644     
-  1.30000001806201346E-002   634521469.03385830     
-  1.40000001956718124E-002   632025293.06391215     
-  1.50000002107234902E-002   629336900.94825923     
-  1.60000002257751697E-002   626454646.57255840     
-  1.70000002408268493E-002   623376741.51493466     
-  1.80000002558785288E-002   620101248.48522842     
-  1.90000002709302084E-002   616626074.03659952     
-  2.00000002859818879E-002   612948960.51813209     
-  2.10000003010335674E-002   609067477.12493813     
-  2.20000003160852470E-002   604979010.01064956     
-  2.30000003311369265E-002   600680751.32512844     
-  2.40000003461886061E-002   596169687.06278419     
-  2.50000003612402856E-002   591442583.57983398     
-  2.60000003762919651E-002   586495972.61729527     
-  2.70000003913436447E-002   581326134.64072454     
-  2.80000004063953242E-002   575929080.27714694     
-  2.90000004214470038E-002   570300529.59325635     
-  3.00000004364986833E-002   564435888.91553104     
-  3.10000004515503629E-002   558330224.84078777     
-  3.20000004666020424E-002   551978235.02284503     
-  3.30000004816537185E-002   545374215.24478471     
-  3.40000004967053945E-002   538512022.19347811     
-  3.50000005117570706E-002   531385031.23928392     
-  3.60000005268087467E-002   523986088.38359386     
-  3.70000005418604228E-002   516307455.36294323     
-  3.80000005569120988E-002   508340746.68114388     
-  3.90000005719637749E-002   500076857.06765401     
-  4.00000005870154510E-002   491505877.51411915     
-  4.10000006020671270E-002   482616997.59909481     
-  4.20000006171188031E-002   473398391.23751330     
-  4.30000006321704792E-002   463837082.26100677     
-  4.40000006472221553E-002   453918785.24165601     
-  4.50000006622738313E-002   443627715.70000380     
-  4.60000006773255074E-002   432946362.08711797     
-  4.70000006923771835E-002   421855209.57271582     
-  4.80000007074288595E-002   410332402.41148412     
-  4.90000007224805356E-002   398353327.09658945     
-  5.00000007375322117E-002   385890092.01365507     
-  5.10000007525838878E-002   372910869.89102477     
-  5.20000007676355638E-002   359379055.40856612     
-  5.30000007826872399E-002   345252169.23859328     
-  5.40000007977389160E-002   330480407.04867899     
-  5.50000008127905921E-002   315004679.66142160     
-  5.60000008278422681E-002   298753904.09996289     
-  5.70000008428939442E-002   281641156.80718756     
-  5.80000008579456203E-002   263558033.79028088     
-  5.90000008729972963E-002   244366057.62596649     
-  6.00000008880489724E-002   223882951.33293855     
-  6.10000009031006485E-002   201859366.65185842     
-  6.20000009181523246E-002   177936241.02956882     
-  6.30000009332040006E-002   151557910.30957550     
-  6.40000009482556836E-002   121765291.35095723     
-  6.50000009633073667E-002   86559267.089058787     
-  6.55000009708332082E-002   65426461.293441042     
-  6.57500009745961289E-002   53302138.933172308     
-  6.60000009783590497E-002   39426676.852969810     
-  6.61250009802405031E-002   31420419.466817942     
-  6.61875009811812298E-002   26990556.317915626     
-  6.62500009821219565E-002   22141701.774704639     
-  6.63125009830626833E-002   16660747.853145797     
-  6.63437509835330536E-002   13545243.019599622     
-  6.63750009840034239E-002   10005961.472616604     
-  6.63906259842386021E-002   7977189.7376845730     
-  6.63984384843561981E-002   6859353.5722278254     
-  6.64062509844737942E-002   5640194.0016339840     
-  6.64140634845913902E-002   4269001.8157937871     
-  6.64179697346501813E-002   3494062.1127031618     
-  6.64218759847089724E-002   2619905.3127237577     
-  6.64238291097383748E-002   2123622.6108079469     
-  6.64257822347677773E-002   1559918.6189464168     
-  6.64267587972824786E-002   1236456.8137497872     
-  6.64272470785398222E-002   1057927.6240404730     
-  6.64277353597971659E-002   862738.15614189487     
-  6.64282236410545096E-002   642083.82668608800     
-  6.64284677816831814E-002   516374.94981919462     
-  6.64287119223118533E-002   372785.75911960861     
-  6.64288339926261961E-002   289635.30197500519     
-  6.64288950277833606E-002   243297.18415601959     
-  6.64289560629405251E-002   192010.14249639038     
-  6.64289865805191143E-002   163648.20723028996     
-  6.64290170980977035E-002   132563.58387729200     
-  6.64290476156762927E-002   97253.723591483620     
-  6.64290628744655803E-002   76985.780308764486     
-  6.64290705038602242E-002   65794.226798446252     
-  6.64290781332548680E-002   53550.730279557472     
-  6.64290857626495118E-002   39692.287404006805     
-  6.64290895773468337E-002   31781.040806673544     
-  6.64290933920441556E-002   22714.975861705043     
+  1.00000000000000002E-003   649909135.03119123
+  2.00000001505167783E-003   649636489.29833126
+  3.00000003010335563E-003   649181909.86863339
+  4.00000004515503344E-003   648545142.11149800
+  5.00000006020671125E-003   647725827.94719517
+  6.00000007525838906E-003   646723505.15455902
+  7.00000009031006686E-003   645537605.90191960
+  8.00000010536174554E-003   644167454.93684888
+  9.00000012041342334E-003   642612267.44508624
+  1.00000001354651012E-002   640871146.53866076
+  1.10000001505167790E-002   638943080.30864108
+  1.20000001655684568E-002   636826938.57690644
+  1.30000001806201346E-002   634521469.03385830
+  1.40000001956718124E-002   632025293.06391215
+  1.50000002107234902E-002   629336900.94825923
+  1.60000002257751697E-002   626454646.57255840
+  1.70000002408268493E-002   623376741.51493466
+  1.80000002558785288E-002   620101248.48522842
+  1.90000002709302084E-002   616626074.03659952
+  2.00000002859818879E-002   612948960.51813209
+  2.10000003010335674E-002   609067477.12493813
+  2.20000003160852470E-002   604979010.01064956
+  2.30000003311369265E-002   600680751.32512844
+  2.40000003461886061E-002   596169687.06278419
+  2.50000003612402856E-002   591442583.57983398
+  2.60000003762919651E-002   586495972.61729527
+  2.70000003913436447E-002   581326134.64072454
+  2.80000004063953242E-002   575929080.27714694
+  2.90000004214470038E-002   570300529.59325635
+  3.00000004364986833E-002   564435888.91553104
+  3.10000004515503629E-002   558330224.84078777
+  3.20000004666020424E-002   551978235.02284503
+  3.30000004816537185E-002   545374215.24478471
+  3.40000004967053945E-002   538512022.19347811
+  3.50000005117570706E-002   531385031.23928392
+  3.60000005268087467E-002   523986088.38359386
+  3.70000005418604228E-002   516307455.36294323
+  3.80000005569120988E-002   508340746.68114388
+  3.90000005719637749E-002   500076857.06765401
+  4.00000005870154510E-002   491505877.51411915
+  4.10000006020671270E-002   482616997.59909481
+  4.20000006171188031E-002   473398391.23751330
+  4.30000006321704792E-002   463837082.26100677
+  4.40000006472221553E-002   453918785.24165601
+  4.50000006622738313E-002   443627715.70000380
+  4.60000006773255074E-002   432946362.08711797
+  4.70000006923771835E-002   421855209.57271582
+  4.80000007074288595E-002   410332402.41148412
+  4.90000007224805356E-002   398353327.09658945
+  5.00000007375322117E-002   385890092.01365507
+  5.10000007525838878E-002   372910869.89102477
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+  5.30000007826872399E-002   345252169.23859328
+  5.40000007977389160E-002   330480407.04867899
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+  5.60000008278422681E-002   298753904.09996289
+  5.70000008428939442E-002   281641156.80718756
+  5.80000008579456203E-002   263558033.79028088
+  5.90000008729972963E-002   244366057.62596649
+  6.00000008880489724E-002   223882951.33293855
+  6.10000009031006485E-002   201859366.65185842
+  6.20000009181523246E-002   177936241.02956882
+  6.30000009332040006E-002   151557910.30957550
+  6.40000009482556836E-002   121765291.35095723
+  6.50000009633073667E-002   86559267.089058787
+  6.55000009708332082E-002   65426461.293441042
+  6.57500009745961289E-002   53302138.933172308
+  6.60000009783590497E-002   39426676.852969810
+  6.61250009802405031E-002   31420419.466817942
+  6.61875009811812298E-002   26990556.317915626
+  6.62500009821219565E-002   22141701.774704639
+  6.63125009830626833E-002   16660747.853145797
+  6.63437509835330536E-002   13545243.019599622
+  6.63750009840034239E-002   10005961.472616604
+  6.63906259842386021E-002   7977189.7376845730
+  6.63984384843561981E-002   6859353.5722278254
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+  6.64140634845913902E-002   4269001.8157937871
+  6.64179697346501813E-002   3494062.1127031618
+  6.64218759847089724E-002   2619905.3127237577
+  6.64238291097383748E-002   2123622.6108079469
+  6.64257822347677773E-002   1559918.6189464168
+  6.64267587972824786E-002   1236456.8137497872
+  6.64272470785398222E-002   1057927.6240404730
+  6.64277353597971659E-002   862738.15614189487
+  6.64282236410545096E-002   642083.82668608800
+  6.64284677816831814E-002   516374.94981919462
+  6.64287119223118533E-002   372785.75911960861
+  6.64288339926261961E-002   289635.30197500519
+  6.64288950277833606E-002   243297.18415601959
+  6.64289560629405251E-002   192010.14249639038
+  6.64289865805191143E-002   163648.20723028996
+  6.64290170980977035E-002   132563.58387729200
+  6.64290476156762927E-002   97253.723591483620
+  6.64290628744655803E-002   76985.780308764486
+  6.64290705038602242E-002   65794.226798446252
+  6.64290781332548680E-002   53550.730279557472
+  6.64290857626495118E-002   39692.287404006805
+  6.64290895773468337E-002   31781.040806673544
+  6.64290933920441556E-002   22714.975861705043

Diagnostics/Sedov/main.cpp

@@ -304,7 +304,7 @@ int main(int argc, char* argv[])
                                 e_bin[index] += (fab(i,j,k,rhoe_comp) / fab(i,j,k,dens_comp)) * vol;
 
                                 volcount[index] += vol;
-                                
+
                             }
                         }
                     }

Docs/preprocess_files.py

@@ -16,7 +16,7 @@ def strip_directives(filename, filepath, outpath):
     """
     Read in file, remove all preprocessor directives and output.
 
-    This is also going to switch square brackets initializing arrays to 
+    This is also going to switch square brackets initializing arrays to
     parentheses and remove the new-line characters
     """
 
@@ -43,7 +43,7 @@ def strip_directives(filename, filepath, outpath):
             continue
 
         # loop over files in subdirectories and run strip_directives on all
-        # C++ header files 
+        # C++ header files
         for f in sorted(os.listdir(os.path.join(rootdir, subdir))):
             if (f[-2:] == ".H"):
                 strip_directives(f, os.path.join(rootdir, subdir), outdir)

Docs/source/ConvertCheckpoint.rst

@@ -39,7 +39,7 @@ Now let’s suppose that you want to grow the domain by a factor of 8
 and cover that new larger domain with a level that is a factor of 2
 coarser than the existing level 0 grids.
 
-#. First, set ``DIM =`` in the GNUmakefile, and type ``make`` in the 
+#. First, set ``DIM =`` in the GNUmakefile, and type ``make`` in the
    ``Util/ConvertCheckpoint/`` directory.  This will
    make an executable from the ``Embiggen.cpp`` code.
 

Docs/source/EOS.rst

@@ -4,7 +4,7 @@ Equation of State
 
 Castro is written in a modular fashion so that the EOS
 can be supplied by the user.   No equations of state
-are distributed with Castro, instead they are part 
+are distributed with Castro, instead they are part
 of the separate `Microphysics repository <https://github.com/amrex-astro/Microphysics>`_.
 
 Most equations of state are written to take :math:`(\rho, T, X_k)` as