Merge branch 'development' into pynucastro_nse_table

.editorconfig

@@ -0,0 +1,62 @@
+# http://EditorConfig.org
+#
+# precedence of rules is bottom to top
+
+# this is the top-most EditorConfig file
+root = true
+
+
+[*.{c,h,cpp,hpp,H,py}]
+# 4 space indentation
+indent_style = space
+indent_size = 4
+
+# Clean up trailing whitespace
+trim_trailing_whitespace = true
+
+# unix-style newlines
+end_of_line = lf
+
+# newline ending in files
+insert_final_newline = true
+
+[networks/**/reaclib_rates.H]
+# some reaclib rate labels have trailing spaces
+trim_trailing_whitespace = false
+
+
+[*.md]
+# two end of line whitespaces are newlines without a paragraph
+trim_trailing_whitespace = false
+
+
+[*.rst]
+# Enforce UTF-8 encoding
+charset = utf-8
+
+# Unix-style newlines
+end_of_line = lf
+
+# Newline ending in files
+insert_final_newline = true
+
+# 3 space indentation
+indent_style = space
+indent_size = 3
+
+# Clean up trailing whitespace
+trim_trailing_whitespace = true
+
+[{Makefile,GNUmakefile,Make.*}]
+# TABs are part of its syntax
+indent_style = tab
+indent_size = unset
+
+
+[util/gcem/**]
+# don't mess with the gcem subtree
+indent_style = unset
+indent_size = unset
+trim_trailing_whitespace = unset
+end_of_line = unset
+insert_final_newline = unset

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Replaced tabs with spaces and trimmed trailing whitespace
+5a2247f598f88f80ad8b186188fccfd5537b18d3

.github/workflows/burn_cell_primordial_chem.yml

@@ -47,7 +47,7 @@ jobs:
             value2=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution.out)
 
             difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }')
-            
+
             if (( $(echo "$difference > $threshold" | bc -l) )); then
               echo "Line number: $line_number"
               echo "Value in test.out: $value1"

.github/workflows/create_release.yml

@@ -2,8 +2,8 @@ on:
   push:
     # Sequence of patterns matched against refs/tags
     tags:
-      - '[0-9][0-9].[0-9][0-9]' 
-  
+      - '[0-9][0-9].[0-9][0-9]'
+
 name: Create Release
 
 jobs:

.github/workflows/find_changed_files.py

@@ -28,7 +28,7 @@ def find_files(SHAs=None):
     if stderr is not None:
         raise Exception('git diff encountered an error')
 
-    files = [f for f in stdout.decode('utf-8').strip().split('\n') 
+    files = [f for f in stdout.decode('utf-8').strip().split('\n')
              if f.startswith('networks/')]
     print(files)
 

.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/macos_build_cell_primordial_chem.yml

@@ -11,7 +11,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          brew install cmake openmpi python3
+          brew install cmake openmpi python3 || true
+          brew link --overwrite [email protected]
 
       - name: Compile and run
         run: |

.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@v3
+      - name: Tabs
+        run: .github/workflows/style/check_tabs.sh
+
+  trailing_whitespaces:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - 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

CMakeLists.txt

@@ -32,13 +32,13 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/")
     set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
 
-    set (gamma_law_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include 
+    set (gamma_law_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/gamma_law
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null  
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants PARENT_SCOPE)
 
-    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkparamfile} 
+    execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkparamfile}
                     ${VODEparamfile} ${integrationparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
 
     set(gamma_law_sources ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/eos_data.cpp
@@ -57,12 +57,12 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
 
     #DO NOT change the order of the directories below!
-    set (primordial_chem_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include 
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/VODE ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/utils 
+    set (primordial_chem_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/VODE ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/utils
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces
                              ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/primordial_chem
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks 
-                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants 
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks
+                             ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants
                              PARENT_SCOPE)
 
     #we need to have extern_parameters.cpp be available at configure time
@@ -72,11 +72,11 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
     #to generate updated header files
 
     if(BUILD_UNIT_TEST)
-      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile} 
+      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile}
                       ${networkpcparamfile} ${networkparamfile} ${VODEparamfile} ${integrationparamfile} ${unittestparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
     else()
       #do not need paramfile and unittestparamfile
-      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkpcparamfile} 
+      execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkpcparamfile}
                       ${networkparamfile} ${VODEparamfile} ${integrationparamfile} " --use_namespace WORKING_DIRECTORY ${output_dir}/)
     endif()
 

EOS/breakout/actual_eos.H

@@ -130,7 +130,7 @@ void actual_eos (I input, T& state)
             }
         }
 
-        // Try to avoid the expensive log function.  Since we don't need entropy 
+        // Try to avoid the expensive log function.  Since we don't need entropy
         // in hydro solver, set it to an invalid but "nice" value for the plotfile.
         if constexpr (has_entropy<T>::value) {
             state.s = 1.0_rt;

EOS/eos_composition.H

@@ -26,7 +26,7 @@ struct eos_xderivs_t {
 /// The auxiliary state provides an alternate description to the composition,
 /// in terms of Ye, abar, and binding energy / nucleon
 ///
-template <class state_t> 
+template <class state_t>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void set_aux_comp_from_X(state_t& state) {
 

EOS/helmholtz/actual_eos.H

@@ -29,13 +29,13 @@ using namespace eos_rp;
 // derivatives), number density of electrons and positron pair (along
 // with their derivatives), adiabatic indices, specific heats, and
 // relativistically correct sound speed are also returned.
-// 
+//
 // this routine assumes planckian photons, an ideal gas of ions,
 // and an electron-positron gas with an arbitrary degree of relativity
 // and degeneracy. interpolation in a table of the helmholtz free energy
 // is used to return the electron-positron thermodynamic quantities.
 // all other derivatives are analytic.
-// 
+//
 // references: cox & giuli chapter 24 ; timmes & swesty apj 1999
 
 const std::string eos_name = "helmholtz";
@@ -510,7 +510,7 @@ void apply_ions (T& state)
     Real sion    = (pion * deni + eion) * tempi + kergavo * ytot1 * y;
     Real dsiondd = (dpiondd * deni - pion * deni * deni + deiondd) * tempi -
                    kergavo * deni * ytot1;
-    Real dsiondt = (dpiondt * deni + deiondt) * tempi -  
+    Real dsiondt = (dpiondt * deni + deiondt) * tempi -
                    (pion * deni + eion) * tempi * tempi +
                    1.5e0_rt * kergavo * tempi * ytot1;
 
@@ -759,7 +759,7 @@ void apply_coulomb_corrections (T& state)
         decoulda = s * dpcoulda;
         decouldz = s * dpcouldz;
 
-        s        = -avo_eos * kerg / (state.abar * plasg) * 
+        s        = -avo_eos * kerg / (state.abar * plasg) *
                     (1.5e0_rt * c2 * x - a2 * (b2 - 1.0e0_rt) * y);
         dscouldd = s * plasgdd;
         dscouldt = s * plasgdt;
@@ -1364,6 +1364,9 @@ void actual_eos_init ()
         for (int j = 0; j < jmax; ++j) {
             for (int i = 0; i < imax; ++i) {
                 std::getline(table, line);
+                if (line.empty()) {
+                    amrex::Error("Error reading free energy from helm_table.dat");
+                }
                 std::istringstream data(line);
                 data >> f_local[idx] >> f_local[idx+3] >> f_local[idx+1]
                      >> f_local[idx+4] >> f_local[idx+2] >> f_local[idx+5]
@@ -1377,6 +1380,9 @@ void actual_eos_init ()
         for (int j = 0; j < jmax; ++j) {
             for (int i = 0; i < imax; ++i) {
                 std::getline(table, line);
+                if (line.empty()) {
+                    amrex::Error("Error reading pressure derivative from helm_table.dat");
+                }
                 std::istringstream data(line);
                 data >> dpdf_local[idx] >> dpdf_local[idx+2]
                      >> dpdf_local[idx+1] >> dpdf_local[idx+3];
@@ -1389,6 +1395,9 @@ void actual_eos_init ()
         for (int j = 0; j < jmax; ++j) {
             for (int i = 0; i < imax; ++i) {
                 std::getline(table, line);
+                if (line.empty()) {
+                    amrex::Error("Error reading electron chemical potential from helm_table.dat");
+                }
                 std::istringstream data(line);
                 data >> ef_local[idx] >> ef_local[idx+2]
                      >> ef_local[idx+1] >> ef_local[idx+3];
@@ -1401,6 +1410,9 @@ void actual_eos_init ()
         for (int j = 0; j < jmax; ++j) {
             for (int i = 0; i < imax; ++i) {
                 std::getline(table, line);
+                if (line.empty()) {
+                    amrex::Error("Error reading number density from helm_table.dat");
+                }
                 std::istringstream data(line);
                 data >> xf_local[idx] >> xf_local[idx+2]
                      >> xf_local[idx+1] >> xf_local[idx+3];

EOS/polytrope/actual_eos.H

@@ -39,7 +39,7 @@ void actual_eos_init ()
     // Available pre-defined polytrope options:
 
     // 1: Non-relativistic, fully degenerate electron gas
-    // 2: Relativistic, fully degenerate electron gas 
+    // 2: Relativistic, fully degenerate electron gas
 
     if (polytrope_type > 0) {
         mu_e = polytrope_mu_e;
@@ -88,7 +88,7 @@ bool is_input_valid (I input)
 
 
 //---------------------------------------------------------------------------
-// Public interfaces 
+// Public interfaces
 //---------------------------------------------------------------------------
 
 inline