Merge branch 'master' into merge

Fitz-Hu · Jan 11, 2024 · e5f46f2 · e5f46f2
2 parents e3495cf + 8a8e100
commit e5f46f2
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diff --git a/.github/workflows/mpi.yml b/.github/workflows/mpi.yml
@@ -19,7 +19,7 @@ jobs:
           - yes
         ntasks:
           - 1
-          - 4
+          - 2
         input: # [SETUP, phantom_tests]
           - ['test', '']
           - ['testkd', '']
@@ -43,7 +43,7 @@ jobs:
 
     env:
       OMP_STACKSIZE: 512M
-      OMP_NUM_THREADS: 4
+      OMP_NUM_THREADS: 2
 
     steps:
 

diff --git a/.mailmap b/.mailmap
@@ -21,12 +21,13 @@ Rebecca Nealon <[email protected]> Nealon <[email protected]
 Alex Pettitt <[email protected]> Alex <[email protected]>
 Alex Pettitt <[email protected]> <[email protected]>
 Alex Pettitt <[email protected]> <[email protected]>
-Terrence Tricco <[email protected]>
-<[email protected]> <[email protected]>
-<[email protected]> <tricco@solo.(none)>
-<[email protected]> <tricco@rin.(none)>
-<[email protected]> <[email protected]>
-<[email protected]> <[email protected]>
+<[email protected]> <[email protected]>
+<[email protected]> <[email protected]>
+<[email protected]> <tricco@solo.(none)>
+<[email protected]> <tricco@rin.(none)>
+<[email protected]> <[email protected]>
+<[email protected]> <[email protected]>
+Terrence Tricco <[email protected]> <[email protected]> 
 James Wurster <[email protected]> James Wurster <[email protected]>
 James Wurster <[email protected]> jameswurster <[email protected]>
 James Wurster <[email protected]> jameswurster <[email protected]>
@@ -46,12 +47,12 @@ Stéven Toupin <[email protected]> stoupin <devnull@localhost>
 Guillaume Laibe <[email protected]> glaibe <[email protected]>
 Guillaume Laibe <[email protected]> glaibe <[email protected]>
 Alice Cerioli <[email protected]> ALICE CERIOLI <[email protected]>
+Alice Cerioli <[email protected]> <[email protected]>
 Thomas Reichardt <[email protected]>
 Thomas Reichardt <[email protected]> Thomas  Reichardt <[email protected]>
 Thomas Reichardt <[email protected]> Mr Thomas Reichardt <[email protected]>
 Roberto Iaconi <[email protected]> Roberto Iaconi <rxi552@raijin6.(none)>
 Roberto Iaconi <[email protected]> Roberto Iaconi <[email protected]>
-Alice Cerioli <[email protected]> <[email protected]>
 Daniel Mentiplay <[email protected]> <[email protected]>
 Daniel Mentiplay <[email protected]> <[email protected]>
 Daniel Mentiplay <[email protected]> <[email protected]>
@@ -72,10 +73,15 @@ Enrico Ragusa <[email protected]> <[email protected]>
 Enrico Ragusa <[email protected]> <[email protected]>
 Kieran Hirsh <[email protected]> <[email protected]>
 Giulia Ballabio <[email protected]> Giulia Ballabio <[email protected]>
+Mats Esseldeurs <[email protected]>
+Mats Esseldeurs <[email protected]> <[email protected]>
+Mats Esseldeurs <[email protected]> <[email protected]>
 Lionel Siess <[email protected]>
 Lionel Siess <[email protected]> <[email protected]>
 Lionel Siess <[email protected]> <[email protected]>
 Lionel Siess <[email protected]> <[email protected]>
+Mats Esseldeurs <[email protected]>
+Mats Esseldeurs <[email protected]> <[email protected]>
 David Liptai <[email protected]> <[email protected]>
 David Liptai <[email protected]> <[email protected]>
 David Liptai <[email protected]> <[email protected]>
@@ -85,8 +91,13 @@ Fangyi (Fitz) Hu <[email protected]> Fitz-Hu <[email protected]
 Fangyi (Fitz) Hu <[email protected]> root <root@Heartie的小电脑.localdomain>
 Fangyi (Fitz) Hu <[email protected]> root <root@Heartie的小电脑.localdomain>
 Fangyi (Fitz) Hu <[email protected]> fitzHu <[email protected]>
+Fangyi (Fitz) Hu <[email protected]> Fitz Hu <[email protected]>
+Fangyi (Fitz) Hu <[email protected]> fhu <[email protected]>
 Megha Sharma <[email protected]> Megha Sharma <[email protected]>
 Megha Sharma <[email protected]> megha sharma <[email protected]>
+Megha Sharma <[email protected]> Megha Sharma <[email protected]>
+Megha Sharma <[email protected]> Megha Sharma <[email protected]>
+Megha Sharma <[email protected]> Megha Sharma <[email protected]> 
 Mike Lau <[email protected]> Mike Lau <[email protected]>
 Elisabeth Borchert <[email protected]> emborchert <[email protected]>
 Ward Homan <[email protected]> ward <[email protected]>
@@ -103,3 +114,9 @@ Sahl Rowther <[email protected]> <[email protected]>
 Sahl Rowther <[email protected]> sahl95 <[email protected]>
 Caitlyn Hardiman <[email protected]> caitlynhardiman <[email protected]>
 Amena Faruqi <[email protected]> <[email protected]>
+Amena Faruqi <[email protected]> Amena Faruqi <[email protected]>
+Alison Young <[email protected]> Alison Young <[email protected]>
+Simone Ceppi <[email protected]> Simone Ceppi <[email protected]>
+Mats Esseldeurs <[email protected]> mats esseldeurs <[email protected]>
+Mats Esseldeurs <[email protected]> MatsEsseldeurs <[email protected]>
+Nicolás Cuello <[email protected]> Nicolas Cuello <[email protected]>
diff --git a/AUTHORS b/AUTHORS
@@ -11,34 +11,30 @@ Conrad Chan <[email protected]>
 James Wurster <[email protected]>
 David Liptai <[email protected]>
 Lionel Siess <[email protected]>
+Fangyi (Fitz) Hu <[email protected]>
 Daniel Mentiplay <[email protected]>
+Megha Sharma <[email protected]>
 Arnaud Vericel <[email protected]>
 Mark Hutchison <[email protected]>
-Fitz Hu <[email protected]>
-Megha Sharma <[email protected]>
 Rebecca Nealon <[email protected]>
 Elisabeth Borchert <[email protected]>
 Ward Homan <[email protected]>
 Christophe Pinte <[email protected]>
-Fangyi (Fitz) Hu <[email protected]>
-Megha Sharma <[email protected]>
-Terrence Tricco <[email protected]>
+Terrence Tricco <[email protected]>
+Simone Ceppi <[email protected]>
+Mats Esseldeurs <[email protected]>
 Mats Esseldeurs <[email protected]>
 Stephane Michoulier <[email protected]>
-Simone Ceppi <[email protected]>
-MatsEsseldeurs <[email protected]>
+Spencer Magnall <[email protected]>
 Caitlyn Hardiman <[email protected]>
 Enrico Ragusa <[email protected]>
-Spencer Magnall <[email protected]>
-fhu <[email protected]>
 Sergei Biriukov <[email protected]>
 Cristiano Longarini <[email protected]>
 Giovanni Dipierro <[email protected]>
 Roberto Iaconi <[email protected]>
+Amena Faruqi <[email protected]>
 Hauke Worpel <[email protected]>
 Alison Young <[email protected]>
-Simone Ceppi <[email protected]>
-Amena Faruqi <[email protected]>
 Stephen Neilson <[email protected]>
 Martina Toscani <[email protected]>
 Benedetta Veronesi <[email protected]>
@@ -53,26 +49,20 @@ Jolien Malfait <[email protected]>
 Phantom benchmark bot <[email protected]>
 Kieran Hirsh <[email protected]>
 Nicole Rodrigues <[email protected]>
-Amena Faruqi <[email protected]>
 David Trevascus <[email protected]>
 Farzana Meru <[email protected]>
+Nicolás Cuello <[email protected]>
 Chris Nixon <[email protected]>
-Megha Sharma <[email protected]>
-Nicolas Cuello <[email protected]>
+Miguel Gonzalez-Bolivar <[email protected]>
 Benoit Commercon <[email protected]>
 Giulia Ballabio <[email protected]>
 Joe Fisher <[email protected]>
 Maxime Lombart <[email protected]>
-Megha Sharma <megha@dyn-49-127-43-125.its.monash.edu.au>
+Mike Lau <mike.lau@h-its.org>
 Orsola De Marco <[email protected]>
-Terrence Tricco <[email protected]>
 Zachary Pellow <[email protected]>
 s-neilson <[email protected]>
-Alison Young <[email protected]>
 Cox, Samuel <[email protected]>
 Jorge Cuadra <[email protected]>
-Miguel Gonzalez-Bolivar <[email protected]>
-Nicolás Cuello <[email protected]>
 Steven Rieder <[email protected]>
 Stéven Toupin <[email protected]>
-mats esseldeurs <[email protected]>
diff --git a/build/Makefile b/build/Makefile
@@ -244,10 +244,6 @@ ifeq ($(NONIDEALMHD), yes)
     FPPFLAGS += -DNONIDEALMHD
 endif
 
-ifeq ($(H2CHEM), yes)
-    FPPFLAGS += -DH2CHEM
-endif
-
 ifeq ($(DISC_VISCOSITY), yes)
     FPPFLAGS += -DDISC_VISCOSITY
 endif
@@ -468,7 +464,8 @@ OBJDIR=obj
 # external forces
 #
 ifeq (X$(SRCPOTS), X)
-SRCPOTS= extern_corotate.f90 \
+SRCPOTS= extern_gr.F90 \
+         extern_corotate.f90 \
          extern_binary.f90 \
          extern_spiral.f90 \
          extern_lensethirring.f90 \
@@ -478,6 +475,7 @@ SRCPOTS= extern_corotate.f90 \
          extern_densprofile.f90 \
          extern_staticsine.f90 \
          extern_gwinspiral.f90 \
+         extern_geopot.f90 \
          externalforces.f90
 endif
 ifeq (X$(SRCPOT), X)
@@ -487,8 +485,9 @@ endif
 # metrics for GR
 #
 ifeq ($(GR),yes)
-    SRCPOT=extern_gr.F90 $(SRCPOTS:externalforces.f90=externalforces_gr.f90)
+    SRCPOT=$(SRCPOTS:externalforces.f90=externalforces_gr.f90)
 endif
+
 ifdef METRIC
     SRCMETRIC= metric_${METRIC}.f90
 else
@@ -570,16 +569,14 @@ ifeq ($(UNAME), Darwin)
 endif
 
 
+ifeq ($(KROME), krome)
 	@echo ""
 	@echo "=============== CHEMISTRY ==============="
 	@echo ""
-ifeq ($(KROME), krome)
 	@echo "krome coupling status = enabled"
-else
-	@echo "krome coupling status = disabled"
-endif
 	@echo ""
 	@echo "========================================="
+endif
 	@sh ../scripts/phantom_version_gen.sh "$(IDFLAGS)"
 	@echo ""
 	@echo "The Phantom is here (in $(BINDIR)/phantom)"
@@ -622,14 +619,14 @@ SRCDUMP= physcon.f90 ${CONFIG} ${SRCKERNEL} utils_omp.F90 io.F90 units.f90 \
          utils_dumpfiles.f90 utils_vectors.f90 utils_mathfunc.f90 \
          utils_datafiles.f90 utils_filenames.f90 utils_system.f90 utils_tables.f90 datafiles.f90 gitinfo.f90 \
          centreofmass.f90 \
-         timestep.f90 ${SRCEOS} cullendehnen.f90 dust_formation.F90 \
+         timestep.f90 ${SRCEOS} cullendehnen.f90 dust_formation.f90 \
          ${SRCGR} ${SRCPOT} \
          memory.F90 \
          utils_sphNG.f90 \
          setup_params.f90 ${SRCFASTMATH} checkoptions.F90 \
          viscosity.f90 damping.f90 options.f90 checkconserved.f90 prompting.f90 ${SRCDUST} \
          ${SRCREADWRITE_DUMPS} \
-         utils_sort.f90 sort_particles.F90
+         utils_sort.f90 sort_particles.f90
 OBJDUMP1= $(SRCDUMP:.f90=.o)
 OBJDUMP= $(OBJDUMP1:.F90=.o)
 
@@ -1327,7 +1324,7 @@ getdims:
 	@echo $(MAXP)
 
 get_setup_opts:
-	@echo "${GR:yes=GR} ${METRIC} ${MHD:yes=MHD} ${NONIDEALMHD:yes=non-ideal} ${DUST:yes=dust} ${GRAVITY:yes=self-gravity} ${RADIATION:yes=radiation}  ${H2CHEM:yes=H2_Chemistry} ${DISC_VISCOSITY:yes=disc_viscosity} ${ISOTHERMAL:yes=isothermal} ${PERIODIC:yes=periodic}" | xargs | sed -e 's/ /, /g' -e 's/_/ /g'
+	@echo "${GR:yes=GR} ${METRIC} ${MHD:yes=MHD} ${NONIDEALMHD:yes=non-ideal} ${DUST:yes=dust} ${GRAVITY:yes=self-gravity} ${RADIATION:yes=radiation} ${DISC_VISCOSITY:yes=disc_viscosity} ${ISOTHERMAL:yes=isothermal} ${PERIODIC:yes=periodic}" | xargs | sed -e 's/ /, /g' -e 's/_/ /g'
 
 get_setup_file:
 	@echo "$(SETUPFILE)"

diff --git a/build/Makefile_defaults_gfortran b/build/Makefile_defaults_gfortran
@@ -12,7 +12,7 @@
 #  endif
 #
 FC= gfortran
-FFLAGS+= -O3 -Wall -Wno-unused-dummy-argument -frecord-marker=4 -gdwarf-2 \
+FFLAGS+= -O3 -Wall -Wno-unused-dummy-argument -frecord-marker=4 -g \
         -finline-functions-called-once -finline-limit=1500 -funroll-loops -ftree-vectorize \
         -std=f2008 -fall-intrinsics
 DBLFLAG= -fdefault-real-8 -fdefault-double-8

diff --git a/build/Makefile_defaults_ifort b/build/Makefile_defaults_ifort
@@ -15,8 +15,8 @@ KNOWN_SYSTEM=yes
 
 # for ifort version 18+ -openmp flag is obsolete
 IFORT_VERSION_MAJOR=${shell ifort -v 2>&1 | head -1 | cut -d' ' -f 3 | cut -d'.' -f 1}
-ifeq ($(shell [ $(IFORT_VERSION_MAJOR) -gt 17 ] && echo true),true)
-    OMPFLAGS= -qopenmp
+ifeq ($(shell [ $(IFORT_VERSION_MAJOR) -lt 17 ] && echo true),true)
+    OMPFLAGS= -openmp
 else
-    OMPFLAGS = -openmp
+    OMPFLAGS = -qopenmp
 endif
diff --git a/build/Makefile_setups b/build/Makefile_setups
@@ -776,7 +776,7 @@ ifeq ($(SETUP), dustystar)
     FPPFLAGS= -DDUST_NUCLEATION -DSTAR
     SETUPFILE= setup_star.f90
     MODFILE= utils_binary.f90 set_binary.f90 moddump_binary.f90
-    ANALYSIS= ${SRCNIMHD} utils_summary.o utils_omp.o ptmass.o energies.o analysis_common_envelope.f90 dust_formation.F90
+    ANALYSIS= ${SRCNIMHD} utils_summary.o utils_omp.o ptmass.o energies.o analysis_common_envelope.f90 dust_formation.f90
     KNOWN_SETUP=yes
     MAXP=10000000
     GRAVITY=yes

diff --git a/docs/examples.rst b/docs/examples.rst
@@ -17,3 +17,4 @@ This section contains some examples of physical problems that you can solve with
    density
    hierarchicalsystems
    selfgravity_gravitationalinstability
+   wind
-Original file line number
+Diff line change
@@ Expand Up @@
        density
        hierarchicalsystems
        selfgravity_gravitationalinstability
+       wind