Merge remote-tracking branch 'origin' into Tillotson

Mega-merge-update
danieljprice · Sep 6, 2024 · 73c34cb · 73c34cb
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diff --git a/.mailmap b/.mailmap
@@ -123,5 +123,5 @@ 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]>
+Yann Bernard <[email protected]> Yrisch <[email protected]>
 David Bamba <[email protected]> DavidBamba <[email protected]>
diff --git a/AUTHORS b/AUTHORS
@@ -12,8 +12,8 @@ James Wurster <[email protected]>
 David Liptai <[email protected]>
 Lionel Siess <[email protected]>
 Fangyi (Fitz) Hu <[email protected]>
+Yann Bernard <[email protected]>
 Daniel Mentiplay <[email protected]>
-Yann Bernard <[email protected]>
 Megha Sharma <[email protected]>
 Arnaud Vericel <[email protected]>
 Mark Hutchison <[email protected]>
@@ -42,35 +42,36 @@ Sahl Rowther <[email protected]>
 Simon Glover <[email protected]>
 Thomas Reichardt <[email protected]>
 Jean-François Gonzalez <[email protected]>
-Madeline Overton <[email protected]>
 Christopher Russell <[email protected]>
-Jolien Malfait <[email protected]>
-Phantom benchmark bot <[email protected]>
+Madeline Overton <[email protected]>
 Alessia Franchini <[email protected]>
 Alex Pettitt <[email protected]>
+Jolien Malfait <[email protected]>
+Phantom benchmark bot <[email protected]>
 Kieran Hirsh <[email protected]>
 Nicole Rodrigues <[email protected]>
+Ana Lourdes Juarez <[email protected]>
+David Trevascus <[email protected]>
 Farzana Meru <[email protected]>
 Nicolás Cuello <[email protected]>
-David Trevascus <[email protected]>
-Miguel Gonzalez-Bolivar <[email protected]>
 Chris Nixon <[email protected]>
-Shunquan Huang <[email protected]>
-Joe Fisher <[email protected]>
+Miguel Gonzalez-Bolivar <[email protected]>
 Benoit Commercon <[email protected]>
-Zachary Pellow <[email protected]>
 Giulia Ballabio <[email protected]>
+Joe Fisher <[email protected]>
 Maxime Lombart <[email protected]>
 Orsola De Marco <[email protected]>
-Steven Rieder <[email protected]>
-Stéven Toupin <[email protected]>
-Taj Jankovič <[email protected]>
-Jeremy Smallwood <[email protected]>
+Shunquan Huang <[email protected]>
+Zachary Pellow <[email protected]>
 Ariel Chitan <[email protected]>
-Rebecca Martin <[email protected]>
-Jorge Cuadra <[email protected]>
-David Bamba <[email protected]>
-Shunquan Huang <[email protected]>
-Cox, Samuel <[email protected]>
 Chunliang Mu <[email protected]>
+Cox, Samuel <[email protected]>
+David Bamba <[email protected]>
 Hugh Griffiths <[email protected]>
+Jeremy Smallwood <[email protected]>
+Jorge Cuadra <[email protected]>
+Rebecca Martin <[email protected]>
+Shunquan Huang <[email protected]>
+Steven Rieder <[email protected]>
+Stéven Toupin <[email protected]>
+Taj Jankovič <[email protected]>
diff --git a/build/Makefile b/build/Makefile
@@ -528,7 +528,7 @@ SOURCES= physcon.f90 ${CONFIG} ${SRCKERNEL} io.F90 units.f90 \
          utils_system.f90 utils_mathfunc.f90 part.F90 ${DOMAIN} boundary.f90 boundary_dynamic.f90 utils_timing.f90 mpi_balance.F90 \
          setup_params.f90 timestep.f90 utils_dumpfiles.f90 utils_indtimesteps.F90 \
          utils_sort.f90 utils_supertimestep.F90 utils_tables.f90 utils_gravwave.f90 \
-         utils_sphNG.f90 utils_vectors.f90 utils_datafiles.f90 datafiles.f90 \
+         utils_sphNG.f90 utils_vectors.f90 utils_subgroup.f90 utils_kepler.f90 utils_datafiles.f90 datafiles.f90 \
          gitinfo.f90 ${SRCFASTMATH} random.f90 ${SRCEOS} cullendehnen.f90 ${SRCNIMHD} ${SRCGR} \
          checkoptions.F90 viscosity.f90 damping.f90 options.f90 cons2primsolver.f90 radiation_utils.f90 cons2prim.f90 \
          centreofmass.f90 ${SRCPOT} checkconserved.f90 \
@@ -538,7 +538,7 @@ SOURCES= physcon.f90 ${CONFIG} ${SRCKERNEL} io.F90 units.f90 \
          utils_deriv.f90 utils_implicit.f90 radiation_implicit.f90 ${SRCTURB} \
          ${SRCINJECT_DEPS} wind_equations.f90 wind.F90  \
          ${SRCKROME} memory.f90 ${SRCREADWRITE_DUMPS} ${SRCINJECT} \
-         H2regions.f90 utils_subgroup.f90 utils_kepler.f90 subgroup.f90 \
+         H2regions.f90 subgroup.f90 \
          quitdump.f90 ptmass.F90\
          readwrite_infile.F90 dens.F90 force.F90 deriv.F90 energies.F90 sort_particles.f90 \
          utils_shuffleparticles.F90 evwrite.f90 substepping.F90 step_leapfrog.F90 writeheader.F90 ${SRCAN} step_supertimestep.F90 \

diff --git a/build/Makefile_setups b/build/Makefile_setups
@@ -855,6 +855,15 @@ ifeq ($(SETUP), windtunnel)
     ANALYSIS=analysis_common_envelope.f90
 endif
 
+ifeq ($(SETUP), masstransfer)
+#   Wind tunnel setup
+    SETUPFILE= setup_masstransfer.f90
+    GRAVITY=yes
+    KNOWN_SETUP=yes
+    IND_TIMESTEPS=yes
+    ANALYSIS=analysis_common_envelope.f90
+endif
+
 ifeq ($(SETUP), jet)
 #   Jet simulation from Price, Tricco & Bate (2012)
     SETUPFILE= velfield_fromcubes.f90 setup_sphereinbox.f90

diff --git a/docs/external-utilities/index.rst b/docs/external-utilities/index.rst
@@ -6,6 +6,7 @@ There are several external utilities that are useful with Phantom.
 .. toctree::
    :maxdepth: 1
 
+   splash
    sarracen
    mcfost
    phantom-config

diff --git a/docs/external-utilities/splash.rst b/docs/external-utilities/splash.rst
@@ -0,0 +1,32 @@
+Splash
+======
+
+Splash is a free and open source visualisation tool for SPH data, developed closely alongside Phantom.
+
+- Docs: https://splash-viz.readthedocs.io/
+- Repo: https://github.com/danieljprice/splash
+
+Examples
+--------
+
+Plot column density render of all snapshots from a simulation::
+
+    splash -r density dump_0*
+
+Make an mp4 movie of the above, like so::
+
+    splash -r density dump_0* --movie
+
+which produces something like
+
+.. raw:: html
+
+    <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; height: auto;">
+       <iframe width="560" height="315" src="https://www.youtube.com/embed/bPurbeQNgvI" title="YouTube video player" frameborder="0" allow="accelerometer; encrypted-media; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+    </div>
+
+splash can also be used to plot the energy vs time files::
+
+   splash *.ev
+
+including automatic recognition of column labels
diff --git a/docs/user-guide/analysis.rst b/docs/user-guide/analysis.rst
@@ -7,7 +7,7 @@ Visualisation of Phantom output
 Dump files
 ~~~~~~~~~~
 
-That's what `splash <https://users.monash.edu.au/~splash>`_ is for! Use splash to interactively inspect the dump
+That's what `splash <https://github.com/danieljprice/splash>`_ is for! Use splash to interactively inspect the dump
 files produced by phantom, e.g.:
 
 .. code-block:: bash

diff --git a/docs/user-guide/dumpfile.rst b/docs/user-guide/dumpfile.rst
@@ -11,10 +11,10 @@ splash
 ~~~~~~
 For SPH simulations the raw data is not so useful since to visualise
 fields in a smooth manner one needs to use the SPH kernel. This is the
-purpose of `splash <https://users.monash.edu.au/~splash>`_, to enable you to produce smooth plots and visualisations
+purpose of `splash <https://github.com/danieljprice/splash>`_, to enable you to produce smooth plots and visualisations
 from the code. It reads the raw data files and gives you plots and visualisations::
 
-  splash file_00000 -r 6
+  splash file_00000 -r 6 --movie
 
 sarracen
 ~~~~~~~~

diff --git a/src/main/H2regions.f90 b/src/main/H2regions.f90
@@ -6,7 +6,10 @@
 !--------------------------------------------------------------------------!
 module HIIRegion
 !
-! Feedback from HII regions
+! HIIRegion
+! 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
 !
 ! :References: Fujii et al. (2021), Hopkins et al. (2012)
 !

diff --git a/src/main/cons2prim.f90 b/src/main/cons2prim.f90
@@ -20,7 +20,7 @@ module cons2prim
 !   Liptai & Price (2019), MNRAS 485, 819-842
 !   Ballabio et al. (2018), MNRAS 477, 2766-2771
 !
-! :Owner: Elisabeth Borchert
+! :Owner: Daniel Price
 !
 ! :Runtime parameters: None
 !

diff --git a/src/main/cooling_solver.f90 b/src/main/cooling_solver.f90
@@ -266,13 +266,26 @@ subroutine exact_cooling(ui, dudt, rho, dt, mu, gamma, Tdust, K2, kappa)
     !argument of Y^(-1) in eq 26
     dy = -Qref*dt*T_on_u/Tref
     y  = y + dy
+    !find new k for eq A7 (not necessarily the same as k for eq A5)
+    do while(y>yk .AND. k>1)
+       k = k-1
+       call calc_cooling_rate(Q, dlnQ_dlnT, rho, Tgrid(k), Tdust, mu, gamma, K2, kappa)
+       dlnQ_dlnT = log(Qi/Q)/log(Tgrid(k+1)/Tgrid(k))
+       Qi = Q
+       ! eqs A6 to get Yk
+       if (abs(dlnQ_dlnT-1.) < tol) then
+          yk = yk - Qref*Tgrid(k)/(Q*Tref)*log(Tgrid(k)/Tgrid(k+1))
+       else
+          yk = yk - Qref*Tgrid(k)/(Q*Tref*(1.-dlnQ_dlnT))*(1.-(Tgrid(k)/Tgrid(k+1))**(dlnQ_dlnT-1.))
+       endif
+    enddo
     !compute Yinv (eqs A7)
     if (abs(dlnQ_dlnT-1.) < tol) then
        Temp = max(Tgrid(k)*exp(-Q*Tref*(y-yk)/(Qref*Tgrid(k))),T_floor)
     else
        Yinv = 1.-(1.-dlnQ_dlnT)*Q*Tref/(Qref*Tgrid(k))*(y-yk)
        if (Yinv > 0.) then
-          Temp = Tgrid(k)*(Yinv**(1./(1.-dlnQ_dlnT)))
+          Temp = max(Tgrid(k)*(Yinv**(1./(1.-dlnQ_dlnT))),T_floor)
        else
           Temp = T_floor
        endif

diff --git a/src/main/energies.F90 b/src/main/energies.F90
@@ -72,7 +72,7 @@ subroutine compute_energies(t)
                           isdead_or_accreted,epot_sinksink,imacc,ispinx,ispiny,&
                           ispinz,mhd,gravity,poten,dustfrac,eos_vars,itemp,igasP,ics,&
                           nden_nimhd,eta_nimhd,iion,ndustsmall,graindens,grainsize,&
-                          iamdust,ndusttypes,rad,iradxi,gtgrad,group_info,n_group
+                          iamdust,ndusttypes,rad,iradxi,gtgrad,group_info,bin_info,n_group
  use part,           only:pxyzu,fxyzu,fext
  use gravwaveutils,  only:calculate_strain,calc_gravitwaves
  use centreofmass,   only:get_centreofmass_accel
@@ -83,7 +83,7 @@ subroutine compute_energies(t)
  use options,        only:iexternalforce,calc_erot,alpha,ieos,use_dustfrac
  use mpiutils,       only:reduceall_mpi
  use ptmass,         only:get_accel_sink_gas,use_regnbody
- use subgroup,     only:get_pot_subsys
+ use subgroup,       only:get_pot_subsys
  use viscosity,      only:irealvisc,shearfunc
  use nicil,          only:nicil_update_nimhd,nicil_get_halldrift,nicil_get_ambidrift, &
                      use_ohm,use_hall,use_ambi,n_data_out,n_warn,eta_constant
@@ -644,7 +644,7 @@ subroutine compute_energies(t)
  erad = reduceall_mpi('+',erad)
  if (nptmass > 1) then
     if (use_regnbody) then
-       call get_pot_subsys(n_group,group_info,xyzmh_ptmass,fxyz_ptmass,gtgrad,epot_sinksink)
+       call get_pot_subsys(n_group,group_info,bin_info,xyzmh_ptmass,vxyz_ptmass,fxyz_ptmass,gtgrad,epot_sinksink)
     endif
     epot = epot + epot_sinksink
  endif

diff --git a/src/main/evolve.F90 b/src/main/evolve.F90
@@ -91,7 +91,7 @@ subroutine evol(infile,logfile,evfile,dumpfile,flag)
                             xyzmh_ptmass,vxyz_ptmass,fxyz_ptmass,dptmass,gravity,iboundary, &
                             fxyz_ptmass_sinksink,ntot,poten,ndustsmall,accrete_particles_outside_sphere,&
                             linklist_ptmass,isionised,dsdt_ptmass,isdead_or_accreted
- use part,             only:n_group,n_ingroup,n_sing,group_info,nmatrix
+ use part,             only:n_group,n_ingroup,n_sing,group_info,bin_info,nmatrix
  use quitdump,         only:quit
  use ptmass,           only:icreate_sinks,ptmass_create,ipart_rhomax,pt_write_sinkev,calculate_mdot, &
                             set_integration_precision,ptmass_create_stars,use_regnbody,ptmass_create_seeds,&
@@ -143,7 +143,7 @@ subroutine evol(infile,logfile,evfile,dumpfile,flag)
  logical         :: use_global_dt
  integer         :: j,nskip,nskipped,nevwrite_threshold,nskipped_sink,nsinkwrite_threshold
  character(len=120) :: dumpfile_orig
- integer         :: dummy,istepHII
+ integer         :: dummy,istepHII,nptmass_old
 
  dummy = 0
 
@@ -279,7 +279,7 @@ subroutine evol(infile,logfile,evfile,dumpfile,flag)
     !  across all nodes
     nskip = int(ntot)
 #endif
-
+    nptmass_old = nptmass
     if (gravity .and. icreate_sinks > 0 .and. ipart_rhomax /= 0) then
        !
        ! creation of new sink particles
@@ -310,20 +310,21 @@ subroutine evol(infile,logfile,evfile,dumpfile,flag)
           istepHII = 2**nbinmax/HIIuprate
           if (istepHII==0) istepHII = 1
        endif
-       if (mod(istepfrac,istepHII)==0 .or. istepfrac==1 .or. (icreate_sinks == 2 .and. ipart_createstars /= 0)) then
+       if (mod(istepfrac,istepHII) == 0 .or. istepfrac == 1 .or. (icreate_sinks == 2 .and. ipart_createstars /= 0)) then
           call HII_feedback(nptmass,npart,xyzh,xyzmh_ptmass,vxyzu,isionised)
        endif
     endif
 
     ! Need to recompute the force when sink or stars are created
-    if (ipart_rhomax /= 0 .or. ipart_createseeds /= 0 .or. ipart_createstars /= 0) then
+    if (nptmass > nptmass_old .or. ipart_createseeds /= 0 .or. ipart_createstars /= 0) then
        if (use_regnbody) then
-          call group_identify(nptmass,n_group,n_ingroup,n_sing,xyzmh_ptmass,vxyz_ptmass,group_info,nmatrix)
+          call group_identify(nptmass,n_group,n_ingroup,n_sing,xyzmh_ptmass,vxyz_ptmass,group_info,bin_info,nmatrix,&
+                              new_ptmass=.true.,dtext=dtextforce)
           call get_force(nptmass,npart,0,1,time,dtextforce,xyzh,vxyzu,fext,xyzmh_ptmass,vxyz_ptmass,&
-                 fxyz_ptmass,dsdt_ptmass,0.,0.,dummy,.false.,linklist_ptmass,group_info=group_info)
+                 fxyz_ptmass,dsdt_ptmass,0.,0.,dummy,.false.,linklist_ptmass,bin_info,group_info=group_info)
        else
           call get_force(nptmass,npart,0,1,time,dtextforce,xyzh,vxyzu,fext,xyzmh_ptmass,vxyz_ptmass,&
-                fxyz_ptmass,dsdt_ptmass,0.,0.,dummy,.false.,linklist_ptmass)
+                fxyz_ptmass,dsdt_ptmass,0.,0.,dummy,.false.,linklist_ptmass,bin_info)
        endif
        if (ipart_createseeds /= 0) ipart_createseeds = 0 ! reset pointer to zero
        if (ipart_createstars /= 0) ipart_createstars = 0 ! reset pointer to zero

diff --git a/src/main/initial.F90 b/src/main/initial.F90
@@ -140,7 +140,7 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
                             epot_sinksink,get_ntypes,isdead_or_accreted,dustfrac,ddustevol,&
                             nden_nimhd,dustevol,rhoh,gradh, &
                             Bevol,Bxyz,dustprop,filfac,ddustprop,ndustsmall,iboundary,eos_vars,dvdx, &
-                            n_group,n_ingroup,n_sing,nmatrix,group_info,isionised
+                            n_group,n_ingroup,n_sing,nmatrix,group_info,bin_info,isionised
  use part,             only:pxyzu,dens,metrics,rad,radprop,drad,ithick
  use densityforce,     only:densityiterate
  use linklist,         only:set_linklist
@@ -221,7 +221,7 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
  use checkconserved,   only:get_conserv,etot_in,angtot_in,totmom_in,mdust_in
  use fileutils,        only:make_tags_unique
  use damping,          only:idamp
- use subgroup,         only:group_identify,init_subgroup
+ use subgroup,         only:group_identify,init_subgroup,update_kappa
  use HIIRegion,        only:iH2R,initialize_H2R,update_ionrates
  character(len=*), intent(in)  :: infile
  character(len=*), intent(out) :: logfile,evfile,dumpfile
@@ -517,9 +517,11 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
     ! compute initial sink-sink forces and get timestep
     if (use_regnbody) then
        call init_subgroup
-       call group_identify(nptmass,n_group,n_ingroup,n_sing,xyzmh_ptmass,vxyz_ptmass,group_info,nmatrix)
+       call group_identify(nptmass,n_group,n_ingroup,n_sing,xyzmh_ptmass,vxyz_ptmass,group_info,bin_info,nmatrix)
        call get_accel_sink_sink(nptmass,xyzmh_ptmass,fxyz_ptmass,epot_sinksink,dtsinksink,&
-                             iexternalforce,time,merge_ij,merge_n,dsdt_ptmass,group_info=group_info)
+                             iexternalforce,time,merge_ij,merge_n,dsdt_ptmass,&
+                             group_info=group_info,bin_info=bin_info)
+
     else
        call get_accel_sink_sink(nptmass,xyzmh_ptmass,fxyz_ptmass,epot_sinksink,dtsinksink,&
                              iexternalforce,time,merge_ij,merge_n,dsdt_ptmass)
@@ -536,8 +538,14 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
           if (ntypes > 1 .and. maxphase==maxp) then
              pmassi = massoftype(iamtype(iphase(i)))
           endif
-          call get_accel_sink_gas(nptmass,xyzh(1,i),xyzh(2,i),xyzh(3,i),xyzh(4,i),xyzmh_ptmass, &
-                   fext(1,i),fext(2,i),fext(3,i),poti,pmassi,fxyz_ptmass,dsdt_ptmass,fonrmax,dtphi2)
+          if (use_regnbody) then
+             call get_accel_sink_gas(nptmass,xyzh(1,i),xyzh(2,i),xyzh(3,i),xyzh(4,i),xyzmh_ptmass, &
+                                     fext(1,i),fext(2,i),fext(3,i),poti,pmassi,fxyz_ptmass,&
+                                     dsdt_ptmass,fonrmax,dtphi2,bin_info=bin_info)
+          else
+             call get_accel_sink_gas(nptmass,xyzh(1,i),xyzh(2,i),xyzh(3,i),xyzh(4,i),xyzmh_ptmass, &
+            fext(1,i),fext(2,i),fext(3,i),poti,pmassi,fxyz_ptmass,dsdt_ptmass,fonrmax,dtphi2)
+          endif
           dtsinkgas = min(dtsinkgas,C_force*1./sqrt(fonrmax),C_force*sqrt(dtphi2))
        endif
     enddo
@@ -552,6 +560,7 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
     !  Reduce dt over MPI tasks
     dtsinkgas = reduceall_mpi('min',dtsinkgas)
     dtextforce = reduceall_mpi('min',dtextforce)
+    if (use_regnbody) call update_kappa(xyzmh_ptmass,vxyz_ptmass,bin_info,group_info,n_group)
  endif
  call init_ptmass(nptmass,logfile)
  if (gravity .and. icreate_sinks > 0 .and. id==master) then

diff --git a/src/main/inject_randomwind.f90 b/src/main/inject_randomwind.f90
@@ -12,7 +12,7 @@ module inject
 ! :References:
 !   Trevascus et al. (2021), MNRAS 505, L21-L25
 !
-! :Owner: Shunquan Huang
+! :Owner: Daniel Price
 !
 ! :Runtime parameters:
 !   - delta_theta : *standard deviation for the gaussion distribution*