Merge pull request #579 from danieljprice/mega-merge

Merge #566, #572 and #578

.mailmap

@@ -96,14 +96,16 @@ 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]>
+Mike Lau <[email protected]> Mike Lau <[email protected]>
+Mike Lau <[email protected]> Mike Lau <[email protected]>
 Elisabeth Borchert <[email protected]> emborchert <[email protected]>
 Ward Homan <[email protected]> ward <[email protected]>
 Ward Homan <[email protected]> wardhoman <[email protected]>
 Benedetta Veronesi <[email protected]> benedetta veronesi <[email protected]>
 Benedetta Veronesi <[email protected]> <[email protected]>
 Phantom benchmark bot <[email protected]> Ubuntu <[email protected]>
 Stephane Michoulier <[email protected]> StephaneMichoulier <[email protected]>
+Stephane Michoulier <[email protected]> MICHOULIER Stephane <smichoulier@sidus11>
 Jolien Malfait <[email protected]> Jolien128 <[email protected]>
 Martina Toscani <[email protected]> <[email protected]>
 Martina Toscani <[email protected]> <[email protected]>
@@ -115,4 +117,11 @@ 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]>
+Madeline Overton <[email protected]> Madeline Nicole Overton <[email protected]>
+Madeline Overton <[email protected]> Madeline Overton <[email protected]>
 Nicolás Cuello <[email protected]> Nicolas Cuello <[email protected]>
+Rebecca Martin <[email protected]> rebeccagmartin <[email protected]>
+Stephen Nielson <[email protected]> s-neilson <[email protected]>
+Stephen Nielson <[email protected]> Stephen Neilson <[email protected]>
+Yann Bernard <[email protected]> Yrisch <[email protected]>
+David Bamba <[email protected]> DavidBamba <[email protected]>

AUTHORS

@@ -6,14 +6,14 @@
 # Edit .mailmap if your name or email are wrong         #
 #-------------------------------------------------------#
 Daniel Price <[email protected]>
-Mike Lau <mike.lau@monash.edu>
+Mike Lau <mike.lau@h-its.org>
 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]>
-Yrisch <[email protected]>
+Yann Bernard <[email protected]>
 Megha Sharma <[email protected]>
 Arnaud Vericel <[email protected]>
 Mark Hutchison <[email protected]>
@@ -26,50 +26,50 @@ Terrence Tricco <[email protected]>
 Stephane Michoulier <[email protected]>
 Simone Ceppi <[email protected]>
 Spencer Magnall <[email protected]>
-Caitlyn Hardiman <[email protected]>
 Enrico Ragusa <[email protected]>
+Caitlyn Hardiman <[email protected]>
 Cristiano Longarini <[email protected]>
 Sergei Biriukov <[email protected]>
 Giovanni Dipierro <[email protected]>
 Roberto Iaconi <[email protected]>
 Amena Faruqi <[email protected]>
 Hauke Worpel <[email protected]>
 Alison Young <[email protected]>
-Stephen Neilson <36410751+s-neilson@users.noreply.github.com>
+Stephen Nielson <stephen.neilson@students.mq.edu.au>
 Martina Toscani <[email protected]>
 Benedetta Veronesi <[email protected]>
-Sahl Rowther <[email protected]>
 Simon Glover <[email protected]>
+Sahl Rowther <[email protected]>
 Thomas Reichardt <[email protected]>
 Jean-François Gonzalez <[email protected]>
 Christopher Russell <[email protected]>
-Alessia Franchini <alessia.franchini@unlv.edu>
+Madeline Overton <overtm2@unlv.nevada.edu>
 Alex Pettitt <[email protected]>
-Jolien Malfait <[email protected]>
 Phantom benchmark bot <[email protected]>
-Kieran Hirsh <[email protected]>
-Mike Lau <[email protected]>
+Jolien Malfait <[email protected]>
+Alessia Franchini <[email protected]>
 Nicole Rodrigues <[email protected]>
-David Trevascus <dtre10@student.monash.edu>
+Kieran Hirsh <kieran.hirsh1@monash.edu>
 Farzana Meru <[email protected]>
+David Trevascus <[email protected]>
 Nicolás Cuello <[email protected]>
 Chris Nixon <[email protected]>
 Miguel Gonzalez-Bolivar <[email protected]>
-Benoit Commercon <[email protected]>
-Giulia Ballabio <[email protected]>
-Joe Fisher <[email protected]>
 Maxime Lombart <[email protected]>
-Orsola De Marco <[email protected]>
 Zachary Pellow <[email protected]>
-s-neilson <[email protected]>
-Ariel Chitan <[email protected]>
-Chunliang Mu <[email protected]>
-Cox, Samuel <[email protected]>
+Orsola De Marco <[email protected]>
+Joe Fisher <[email protected]>
+Benoit Commercon <[email protected]>
+Giulia Ballabio <[email protected]>
+Rebecca Martin <[email protected]>
+Jorge Cuadra <[email protected]>
 Hugh Griffiths <[email protected]>
 Jeremy Smallwood <[email protected]>
-Jorge Cuadra <[email protected]>
-MICHOULIER Stephane <smichoulier@sidus11>
+David Bamba <[email protected]>
+Cox, Samuel <[email protected]>
+Chunliang Mu <[email protected]>
+Shunquan Huang <[email protected]>
 Steven Rieder <[email protected]>
 Stéven Toupin <[email protected]>
 Taj Jankovič <[email protected]>
-rebeccagmartin <[email protected].com>
+Ariel Chitan <arielchitan@gmail.com>

build/Makefile

@@ -488,7 +488,7 @@ ifdef METRIC
 else
     SRCMETRIC= metric_minkowski.f90
 endif
-SRCGR=inverse4x4.f90 einsteintk_utils.f90 $(SRCMETRIC) metric_tools.f90 utils_gr.f90 interpolate3D.f90 tmunu2grid.f90
+SRCGR=inverse4x4.f90 metric_et_utils.f90 einsteintk_utils.f90 $(SRCMETRIC) metric_tools.f90 utils_gr.f90 interpolate3D.f90 tmunu2grid.f90
 #
 # chemistry and cooling
 #
@@ -1230,6 +1230,24 @@ combinedustdumps: checksys checkparams $(OBJCDD)
 cleancombinedustdumps:
 	rm -f $(BINDIR)/combinedustdumps
 
+#----------------------------------------------------
+# these are the sources for the tabulate_metric tility
+.PHONY: tabulate_metric
+SRCTAB= io.F90 utils_infiles.f90 metric_${METRIC}.f90 metric_et_utils.f90 tabulate_metric.f90 #metric_tools.F90
+OBJTAB1= $(SRCTAB:.F90=.o)
+OBJTAB= $(OBJTAB1:.f90=.o)
+
+tabulate_metric: checksys $(OBJTAB)
+	@echo ""
+	@echo "tabulate_metric: Because grids are great"
+	@echo ""
+	$(FC) $(FFLAGS) -o $(BINDIR)/$@ $(OBJTAB)
+
+cleantabulatemetric:
+	rm -f $(BINDIR)/tabulate_metric
+
+
+
 
 include Makefile_qscripts
 

build/Makefile_setups

@@ -77,7 +77,17 @@ endif
 ifeq ($(SETUP), asteroidwind)
 #   asteroid emitting a wind (Trevascus et al. 2021)
     SETUPFILE=setup_asteroidwind.f90
-    SRCINJECT=utils_binary.f90 inject_asteroidwind.f90
+    SRCINJECT=utils_binary.f90 inject_randomwind.f90
+    IND_TIMESTEPS=yes
+    CONST_AV=yes
+    ISOTHERMAL=yes
+    KNOWN_SETUP=yes
+endif
+
+ifeq ($(SETUP), randomwind)
+#   asteroid emitting a wind (Trevascus et al. 2021)
+    SETUPFILE=setup_disc.f90
+    SRCINJECT=utils_binary.f90 inject_randomwind.f90
     IND_TIMESTEPS=yes
     CONST_AV=yes
     ISOTHERMAL=yes

docs/developer-guide/datafiles.rst

@@ -8,7 +8,7 @@ order for your modules to be portable.
 Small files
 -----------
 
-For *very small files* (under 1Mb), you can simply add these to the git
+For *very small files* (under 100Kb), you can simply add these to the git
 repository in a subdirectory of the phantom/data directory:
 
 ::

src/main/H2regions.f90

@@ -6,21 +6,17 @@
 !--------------------------------------------------------------------------!
 module HIIRegion
 !
-! HIIRegion
+! Feedback from HII regions
 !
 ! :References: Fujii et al. (2021), Hopkins et al. (2012)
 !
-! :Owner: Yrisch
+! :Owner: Yann Bernard
 !
 ! :Runtime parameters: None
 !
 ! :Dependencies: dim, eos, infile_utils, io, linklist, part, physcon,
 !   sortutils, timing, units
 !
-! contains routines to model HII region expansion due to ionization and radiation pressure..
-! routine originally made by Hopkins et al. (2012),reused by Fujii et al. (2021)
-! and adapted in Phantom by Yann Bernard
-
  implicit none
 
  public :: update_ionrates,update_ionrate, HII_feedback,initialize_H2R,read_options_H2R,write_options_H2R
@@ -52,17 +48,18 @@ module HIIRegion
 
 contains
 
- !-----------------------------------------------------------------------
- !+
- !  Initialise stellar feedbacks
- !+
- !-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+!+
+!  Initialise stellar feedbacks
+!+
+!-----------------------------------------------------------------------
 subroutine initialize_H2R
  use io,      only:iprint,iverbose,id,master
  use part,    only:isionised
  use units,   only:udist,umass,utime
  use physcon, only:mass_proton_cgs,kboltz,pc,eV,solarm
- use eos    , only:gmw,gamma
+ use eos,     only:gmw,gamma
+
  isionised(:)=.false.
  !calculate the useful constant in code units
  mH = gmw*mass_proton_cgs
@@ -85,15 +82,14 @@ subroutine initialize_H2R
     write(iprint,"(a,es18.10,es18.10)") " Max strögrem radius (code/pc)   : ", Rst_max, Rmax
     write(iprint,"(a,es18.10,es18.10)") " Min feedback mass   (code/Msun) : ", Minmass, Mmin
  endif
- return
+
 end subroutine initialize_H2R
 
 !-----------------------------------------------------------------------
 !+
 !  Calculation of the the ionizing photon rate of all stars (Only for restart)
 !+
 !-----------------------------------------------------------------------
-
 subroutine update_ionrates(nptmass,xyzmh_ptmass,h_acc)
  use io,     only:iprint,iverbose
  use units,  only:umass
@@ -104,6 +100,7 @@ subroutine update_ionrates(nptmass,xyzmh_ptmass,h_acc)
  real,    intent(in)    :: h_acc
  real    :: logmi,log_Q,mi,hi
  integer :: i
+
  nHIIsources = 0
  !$omp parallel do default(none) &
  !$omp shared(xyzmh_ptmass,iprint,iverbose,umass)&
@@ -122,7 +119,7 @@ subroutine update_ionrates(nptmass,xyzmh_ptmass,h_acc)
        xyzmh_ptmass(irstrom,i)  = -1.
        nHIIsources = nHIIsources + 1
        if (iverbose >= 0) then
-          write(iprint,"(/a,es18.10,es18.10/)")"Massive stars detected : Log Q, Mass : ",log_Q,mi
+          write(iprint,"(/a,es18.10,es18.10/)") "Massive stars detected : Log Q, Mass : ",log_Q,mi
        endif
     else
        xyzmh_ptmass(irateion,i) = -1.
@@ -133,9 +130,14 @@ subroutine update_ionrates(nptmass,xyzmh_ptmass,h_acc)
  if (iverbose > 1) then
     write(iprint,"(/a,i8/)") "nb_feedback sources : ",nHIIsources
  endif
- return
+
 end subroutine update_ionrates
 
+!-----------------------------------------------------------------------
+!+
+!  update the ionizing photon rate
+!+
+!-----------------------------------------------------------------------
 subroutine update_ionrate(i,xyzmh_ptmass,h_acc)
  use io,     only:iprint,iverbose
  use units,  only:umass
@@ -145,6 +147,7 @@ subroutine update_ionrate(i,xyzmh_ptmass,h_acc)
  real,    intent(inout) :: xyzmh_ptmass(:,:)
  real,    intent(in)    :: h_acc
  real    :: logmi,log_Q,mi,hi
+
  mi = xyzmh_ptmass(4,i)
  hi = xyzmh_ptmass(ihacc,i)
  if (mi > Minmass .and. hi < h_acc) then
@@ -156,7 +159,7 @@ subroutine update_ionrate(i,xyzmh_ptmass,h_acc)
     xyzmh_ptmass(irstrom,i)  = -1.
     nHIIsources = nHIIsources + 1
     if (iverbose >= 0) then
-       write(iprint,"(/a,es18.10,es18.10/)")"Massive stars detected : Log Q, Mass : ",log_Q,mi
+       write(iprint,"(/a,es18.10,es18.10/)") "Massive stars detected : Log Q, Mass : ",log_Q,mi
     endif
  else
     xyzmh_ptmass(irateion,i) = -1.
@@ -166,15 +169,14 @@ subroutine update_ionrate(i,xyzmh_ptmass,h_acc)
  if (iverbose > 1) then
     write(iprint,"(/a,i8/)") "nb_feedback sources : ",nHIIsources
  endif
- return
-end subroutine update_ionrate
 
- !-----------------------------------------------------------------------
- !+
- !  Main subroutine : Application of the HII feedback using Hopkins's like prescription
- !+
- !-----------------------------------------------------------------------
+end subroutine update_ionrate
 
+!-----------------------------------------------------------------------
+!+
+!  Main subroutine : Application of the HII feedback using Hopkins's like prescription
+!+
+!-----------------------------------------------------------------------
 subroutine HII_feedback(nptmass,npart,xyzh,xyzmh_ptmass,vxyzu,isionised,dt)
  use part,       only:rhoh,massoftype,ihsoft,igas,irateion,isdead_or_accreted,&
                       irstrom
@@ -268,10 +270,10 @@ subroutine HII_feedback(nptmass,npart,xyzh,xyzmh_ptmass,vxyzu,isionised,dt)
           r_in = sqrt((xi-xyzh(1,j))**2 + (yi-xyzh(2,j))**2 + (zi-xyzh(3,j))**2)
           mHII = ((4.*pi*(r**3-r_in**3)*rhoh(xyzh(4,j),pmass))/3)
           if (mHII>3*pmass) then
-!$omp parallel do default(none) &
-!$omp shared(mHII,listneigh,xyzh,sigd,dt) &
-!$omp shared(mH,vxyzu,log_Qi,hv_on_c,npartin,pmass,xi,yi,zi) &
-!$omp private(j,dx,dy,dz,vkx,vky,vkz,xj,yj,zj,r,taud)
+             !$omp parallel do default(none) &
+             !$omp shared(mHII,listneigh,xyzh,sigd,dt) &
+             !$omp shared(mH,vxyzu,log_Qi,hv_on_c,npartin,pmass,xi,yi,zi) &
+             !$omp private(j,dx,dy,dz,vkx,vky,vkz,xj,yj,zj,r,taud)
              do k=1,npartin
                 j = listneigh(1)
                 xj = xyzh(1,j)
@@ -290,35 +292,48 @@ subroutine HII_feedback(nptmass,npart,xyzh,xyzmh_ptmass,vxyzu,isionised,dt)
                 vxyzu(2,j) = vxyzu(2,j) +  vky*dt
                 vxyzu(3,j) = vxyzu(3,j) +  vkz*dt
              enddo
-!$omp end parallel do
+             !$omp end parallel do
           endif
        endif
     enddo
  endif
  call get_timings(t2,tcpu2)
  call increment_timer(itimer_HII,t2-t1,tcpu2-tcpu1)
- return
+
 end subroutine HII_feedback
 
+!-----------------------------------------------------------------------
+!+
+!  write options to input file
+!+
+!-----------------------------------------------------------------------
 subroutine write_options_H2R(iunit)
  use infile_utils, only:write_inopt
  use physcon,      only:solarm
  integer, intent(in) :: iunit
- write(iunit,"(/,a)") '# options controlling HII region expansion feedback'
- if (iH2R>0) then
+
+ if (iH2R > 0) then
+    write(iunit,"(/,a)") '# options controlling HII region expansion feedback'
     call write_inopt(iH2R, 'iH2R', "enable the HII region expansion feedback in star forming reigon", iunit)
     call write_inopt(Mmin, 'Mmin', "Minimum star mass to trigger HII region (MSun)", iunit)
     call write_inopt(Rmax, 'Rmax', "Maximum radius for HII region (pc)", iunit)
  endif
+
 end subroutine write_options_H2R
 
+!-----------------------------------------------------------------------
+!+
+!  read options from input file
+!+
+!-----------------------------------------------------------------------
 subroutine read_options_H2R(name,valstring,imatch,igotall,ierr)
  use io,         only:fatal
  character(len=*), intent(in)  :: name,valstring
  logical,          intent(out) :: imatch,igotall
  integer,          intent(out) :: ierr
  integer, save :: ngot = 0
  character(len=30), parameter  :: label = 'read_options_H2R'
+
  imatch = .true.
  select case(trim(name))
  case('iH2R')
@@ -337,6 +352,7 @@ subroutine read_options_H2R(name,valstring,imatch,igotall,ierr)
     imatch = .true.
  end select
  igotall = (ngot >= 3)
+
 end subroutine read_options_H2R
 
 end module HIIRegion