Add infrastructure for calibration of halo mass functions

.github/workflows/cicd.yml

@@ -54,7 +54,7 @@ jobs:
   ### Static executable and test codes
   Build-Executable-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -109,7 +109,7 @@ jobs:
   ### Non-static executable
   Build-Executable-Linux-Non-Static:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -151,7 +151,7 @@ jobs:
   ### Executable instrumented
   Build-Executables-Instrumented-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -180,7 +180,7 @@ jobs:
   ### Executable with dark matter only components
   Build-Executable-DMO-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -207,7 +207,7 @@ jobs:
   ### Executable MPI
   Build-Executables-MPI-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -238,7 +238,7 @@ jobs:
   ### Executable debugging
   Build-Executables-Debugging-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -265,7 +265,7 @@ jobs:
   ### Library
   Build-Library-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -338,7 +338,7 @@ jobs:
   ### Documentation
   Build-Documentation-Linux:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -368,7 +368,7 @@ jobs:
   ### Tools
   Build-Tools:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     needs: Build-Executable-Linux
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
@@ -585,7 +585,7 @@ jobs:
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o cloudy.exe' $GALACTICUS_EXEC_PATH/build.log`
           cd $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion}/src
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o autosps.exe' $GALACTICUS_EXEC_PATH/build.log`
-          cd $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion}/bin/
+          cd $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion}/src/
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o harmonize' $GALACTICUS_EXEC_PATH/build.log`
           cd $GALACTICUS_DATA_PATH
           zip -r toolsMacOS.zip \
@@ -765,7 +765,7 @@ jobs:
   # Watch for updates
   Watch-Updates:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -1516,7 +1516,7 @@ jobs:
   ## Emulation
   Emulation-Subhalos:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     needs: Build-Executable-DMO-Linux
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
@@ -1581,7 +1581,7 @@ jobs:
   ## Python Interface
   Python-Interface:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     needs: Build-Library-Linux
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."

.github/workflows/prChecks.yml

@@ -82,7 +82,7 @@ jobs:
   # Validate Perl scripts
   Validate-Perl-Scripts:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - uses: actions/checkout@v6
       - name: Check out repository analysis-perl
@@ -128,7 +128,7 @@ jobs:
   # Validate Perl modules
   Validate-Perl-Modules:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - uses: actions/checkout@v6
       - name: "Set environmental variables"
@@ -162,7 +162,7 @@ jobs:
   # Fortran static analysis
   Fortran-Static-Analysis:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - uses: actions/checkout@v6
       - name: "Set environmental variables"
@@ -192,7 +192,7 @@ jobs:
   # Embedded XML and LaTeX checks
   Embedded-XML-LaTeX:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - name: Check out repository code
         uses: actions/checkout@v6
@@ -248,7 +248,7 @@ jobs:
   # Spell check LaTeX files
   Spell-Check-LaTeX:
     runs-on: ubuntu-latest
-    container: ghcr.io/galacticusorg/buildenv:latest
+    container: ghcr.io/galacticusorg/buildenv:gfortranFinalization
     steps:
       - name: Check out repository code
         uses: actions/checkout@v6

.github/workflows/profile.yml

@@ -23,7 +23,7 @@ jobs:
   Profile-Model:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/galacticusorg/buildenv:latest
+      image: ghcr.io/galacticusorg/buildenv:gfortranFinalization
       options: --privileged
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."

.github/workflows/testCode.yml

@@ -39,7 +39,7 @@ jobs:
   Test-Code:
     runs-on: ${{ inputs.runner }}
     container:
-      image: ${{ startsWith( format('{0}',inputs.runner), 'ubuntu') && 'ghcr.io/galacticusorg/buildenv:latest' || '' }}
+      image: ${{ startsWith( format('{0}',inputs.runner), 'ubuntu') && 'ghcr.io/galacticusorg/buildenv:gfortranFinalization' || '' }}
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -77,9 +77,9 @@ jobs:
           set -o pipefail
           if [ ${{ inputs.mpi }} == 1 ]; then
            if [ ${{ inputs.expectCrash }} == 1 ]; then
-            ! mpirun -np 2 --allow-run-as-root ./${{ inputs.executable }} 2>&1 | tee test.log
+            ! mpirun --oversubscribe -np 2 --allow-run-as-root ./${{ inputs.executable }} 2>&1 | tee test.log
            else
-            mpirun -np 2 --allow-run-as-root ./${{ inputs.executable }} 2>&1 | tee test.log
+            mpirun --oversubscribe -np 2 --allow-run-as-root ./${{ inputs.executable }} 2>&1 | tee test.log
            fi
           else
            if [ ${{ inputs.expectCrash }} == 1 ]; then

.github/workflows/testModel.yml

@@ -64,7 +64,7 @@ jobs:
   Test-Model:
     runs-on: ${{ inputs.runner }}
     container:
-      image: ${{ startsWith( format('{0}',inputs.runner), 'ubuntu') && 'ghcr.io/galacticusorg/buildenv:latest' || '' }}
+      image: ${{ startsWith( format('{0}',inputs.runner), 'ubuntu') && 'ghcr.io/galacticusorg/buildenv:gfortranFinalization' || '' }}
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server."
@@ -158,7 +158,7 @@ jobs:
             false
            fi
            if [ ${{ inputs.mpi }} == 1 ]; then
-            mpirun -np  ${{ inputs.processesPerNode }} --allow-run-as-root ./Galacticus.exe ${{ inputs.file }} 2>&1 | tee test.log
+            mpirun --oversubscribe -np  ${{ inputs.processesPerNode }} --allow-run-as-root ./Galacticus.exe ${{ inputs.file }} 2>&1 | tee test.log
            else
             ./Galacticus.exe ${{ inputs.file }} 2>&1 | tee test.log
            fi

Makefile

@@ -114,11 +114,13 @@ endif
 ifeq '$(GALACTICUS_BUILD_OPTION)' 'gprof'
 FCFLAGS       += -pg
 FCFLAGS_NOOPT += -pg
+F77FLAGS      += -pg
 CFLAGS        += -pg
 CPPFLAGS      += -pg
 else
 FCFLAGS       += -g
 FCFLAGS_NOOPT += -g
+F77FLAGS      += -g
 CFLAGS        += -g
 CPPFLAGS      += -g
 endif
@@ -345,6 +347,11 @@ vpath %.cpp source
 $(BUILDPATH)/%.o : %.cpp $(BUILDPATH)/%.d $(BUILDPATH)/%.fl Makefile
 	$(CPPCOMPILER) -c $< -o $(BUILDPATH)/$*.o $(CPPFLAGS)
 
+# Rules for the QHull library. Use the C++17 standard for these files since they are not compatible with later C++ standards
+# (triggering 'template-id not allowed for constructor' errors)
+$(BUILDPATH)/qhull.o : source/qhull.cpp
+	$(CPPCOMPILER) -c source/qhull.cpp -o $(BUILDPATH)/qhull.o $(CPPFLAGS) -std=gnu++17
+
 # Rules for FFTLog library.
 source/FFTlog/cdgamma.f source/FFTlog/drfftb.f source/FFTlog/drffti.f source/FFTlog/drfftf.f: source/FFTlog/fftlog.f
 source/FFTlog/fftlog.f:
@@ -390,11 +397,15 @@ $(BUILDPATH)/FFTlog/%.o: ./source/FFTlog/%.f Makefile
 	@mkdir -p $(BUILDPATH)/moduleBuild
 	$(FCCOMPILER) -c $< -o $(BUILDPATH)/FFTlog/$*.o $(F77FLAGS) -Wno-argument-mismatch -std=legacy
 
-# Object (*.o) files are built by compiling Fortran (*.f) source files.
+# Object (*.o) files are built by compiling Fortran (*.[fF]) source files.
 vpath %.f source
 $(BUILDPATH)/%.o : %.f $(BUILDPATH)/%.d $(BUILDPATH)/%.fl Makefile
 	@mkdir -p $(BUILDPATH)/moduleBuild
 	$(FCCOMPILER) -c $< -o $(BUILDPATH)/$*.o $(F77FLAGS)
+vpath %.F source
+$(BUILDPATH)/%.o : %.F $(BUILDPATH)/%.d $(BUILDPATH)/%.fl Makefile
+	@mkdir -p $(BUILDPATH)/moduleBuild
+	$(FCCOMPILER) -c $< -o $(BUILDPATH)/$*.o $(F77FLAGS)
 
 # Special rules required for building some sources (unfortunate, but necessary....)
 # bivar.F90 doesn't like to be compiled with any optimization:
@@ -441,6 +452,13 @@ $(BUILDPATH)/%.d : ./source/%.f
 	else \
 	 mv $(BUILDPATH)/$*.d~ $(BUILDPATH)/$*.d ; \
 	fi
+$(BUILDPATH)/%.d : ./source/%.F
+	@echo $(BUILDPATH)/$*.o > $(BUILDPATH)/$*.d~
+	@if cmp -s $(BUILDPATH)/$*.d $(BUILDPATH)/$*.d~ ; then \
+	 rm $(BUILDPATH)/$*.d~ ; \
+	else \
+	 mv $(BUILDPATH)/$*.d~ $(BUILDPATH)/$*.d ; \
+	fi
 $(BUILDPATH)/%.d : ./source/%.c
 	@echo $(BUILDPATH)/$*.o > $(BUILDPATH)/$*.d~
 	@if cmp -s $(BUILDPATH)/$*.d $(BUILDPATH)/$*.d~ ; then \
@@ -462,6 +480,13 @@ $(BUILDPATH)/%.d : ./source/%.cpp
 	else \
 	 mv $*.d~ $*.d ; \
 	fi
+%.d : %.F
+	@echo $*.o > $*.d~
+	@if cmp -s $*.d $*.d~ ; then \
+	 rm $*.d~ ; \
+	else \
+	 mv $*.d~ $*.d ; \
+	fi
 %.d :
 	@if [ ! -f $*.d ]; then \
 	 mkdir -p `dirname $*.d`; \
@@ -486,6 +511,8 @@ $(BUILDPATH)/%.fl : ./source/%.F90
 	@touch $(BUILDPATH)/$*.fl
 $(BUILDPATH)/%.fl : ./source/%.f
 	@touch $(BUILDPATH)/$*.fl
+$(BUILDPATH)/%.fl : ./source/%.F
+	@touch $(BUILDPATH)/$*.fl
 $(BUILDPATH)/%.fl : ./source/%.c
 	@touch $(BUILDPATH)/$*.fl
 $(BUILDPATH)/%.fl : ./source/%.cpp

aux/words.dict

@@ -101,6 +101,7 @@ Dobbs
 Dodds
 Dopita
 Dorta
+Dopita
 Drlica
 Dutton
 Enzo
@@ -214,6 +215,7 @@ SEDs
 SIDM
 SNe
 SSPs
+Springer
 SZ
 Safranek
 Safronov
@@ -383,6 +385,7 @@ dielectronic
 differencing
 differentially
 differentiating
+digamma
 dilogarithm
 dilogarithms
 dima
@@ -559,6 +562,7 @@ normalizations
 normalizer
 normalizers
 octahedron
+octants
 octree
 octrees
 odes
@@ -608,6 +612,7 @@ photoionizations
 photometric
 piecewise
 polycyclic
+polygamma
 polylogarithm
 polylogarithms
 postprocess
@@ -764,6 +769,8 @@ unbuffered
 unclustered
 uncommented
 uncontracted
+underflow
+underflows
 undecorated
 underpredicts
 undersampling

constraints/pipelines/darkMatter/changesBohr2021.xml

@@ -0,0 +1,16 @@
+<changes>
+  <change type="replace" path="haloMassFunction">
+    <haloMassFunction value="shethTormen">
+      <a             value="0.7070"/> <!-- Sheth & Tormen (2002; http://adsabs.harvard.edu/abs/2002MNRAS.329...61S)  -->
+      <p             value="0.3000"/> <!-- Sheth & Tormen (2002; http://adsabs.harvard.edu/abs/2002MNRAS.329...61S)  -->
+      <normalization value="0.3658"/> <!-- Bohr et al. (2021; https://ui.adsabs.harvard.edu/abs/2021MNRAS.506..128B) -->
+    </haloMassFunction>
+  </change>
+  <change type="replace" path="powerSpectrumWindowFunction">
+    <powerSpectrumWindowFunction value="ETHOS">
+      <cW   value="3.79"/> <!-- Bohr et al. (2021; https://ui.adsabs.harvard.edu/abs/2021MNRAS.506..128B) -->
+      <beta value="3.46"/> <!-- Bohr et al. (2021; https://ui.adsabs.harvard.edu/abs/2021MNRAS.506..128B) -->
+    </powerSpectrumWindowFunction>
+  </change>
+  <change type="update" path="outputFileName" append="true" value="_Bohr2021"/>
+</changes>

constraints/pipelines/darkMatter/changesDespali2015.xml

@@ -0,0 +1,9 @@
+<changes>
+  <change type="replace" path="haloMassFunction">
+    <haloMassFunction value="despali2015"/>
+  </change>
+  <change type="replace" path="powerSpectrumWindowFunction">
+    <powerSpectrumWindowFunction value="topHat"/>
+  </change>
+  <change type="update" path="outputFileName" append="true" value="_Despali2015"/>
+</changes>

constraints/pipelines/darkMatter/changesTrue.xml

@@ -0,0 +1,4 @@
+<changes>
+  <change type="replaceWith" path="cosmologicalMassVariance" target="cosmologicalMassVariance/cosmologicalMassVariance"/>
+  <change type="update" path="outputFileName" append="true" value="_true"/>
+</changes>

constraints/pipelines/darkMatter/cosmology_COZMIC.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<parameters>
+  <formatVersion>2</formatVersion>
+  <lastModified revision="e9236b11f17f9c96b0cdac005d7945ac0febe7d5"/>
+
+  <!-- Cosmological parameters and options -->
+  <cosmologyFunctions  value="matterLambda"/>
+  <cosmologyParameters value="simple"       >
+    <HubbleConstant  value="70.000000"/>
+    <OmegaMatter     value=" 0.286000"/>
+    <OmegaDarkEnergy value=" 0.714000"/>
+    <OmegaBaryon     value=" 0.047000"/>
+    <temperatureCMB  value=" 2.725480"/>
+  </cosmologyParameters>
+
+</parameters>