From 02034c18298871b0e44c205fe6c1b3d9984a2c4b Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 17:42:03 +1000
Subject: [PATCH 01/23] (grtde) minor formatting adjustments

---
 src/setup/setup_grtde.f90 | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/setup/setup_grtde.f90 b/src/setup/setup_grtde.f90
index 903ef3927..5480a38d0 100644
--- a/src/setup/setup_grtde.f90
+++ b/src/setup/setup_grtde.f90
@@ -245,10 +245,10 @@ subroutine write_setupfile(filename)
  use setstar,      only:write_options_star
  use relaxstar,    only:write_options_relax
  character(len=*), intent(in) :: filename
- integer, parameter :: iunit = 20
+ integer :: iunit
 
  print "(a)",' writing setup options file '//trim(filename)
- open(unit=iunit,file=filename,status='replace',form='formatted')
+ open(newunit=iunit,file=filename,status='replace',form='formatted')
  write(iunit,"(a)") '# input file for tidal disruption setup'
 
  call write_options_star(star,iunit)
@@ -256,13 +256,12 @@ subroutine write_setupfile(filename)
  if (relax) call write_options_relax(iunit)
 
  write(iunit,"(/,a)") '# options for black hole and orbit'
-
- call write_inopt(mhole,          'mhole',          'mass of black hole (solar mass)',             iunit)
- call write_inopt(beta,           'beta',           'penetration factor',                          iunit)
- call write_inopt(ecc,            'ecc',            'eccentricity (1 for parabolic)',              iunit)
- call write_inopt(norbits,        'norbits',        'number of orbits',                            iunit)
- call write_inopt(dumpsperorbit,  'dumpsperorbit',  'number of dumps per orbit',                   iunit)
- call write_inopt(theta,          'theta',          'inclination of orbit (degrees)',              iunit)
+ call write_inopt(mhole,        'mhole',        'mass of black hole (solar mass)',iunit)
+ call write_inopt(beta,         'beta',         'penetration factor',             iunit)
+ call write_inopt(ecc,          'ecc',          'eccentricity (1 for parabolic)', iunit)
+ call write_inopt(norbits,      'norbits',      'number of orbits',               iunit)
+ call write_inopt(dumpsperorbit,'dumpsperorbit','number of dumps per orbit',      iunit)
+ call write_inopt(theta,        'theta',        'inclination of orbit (degrees)', iunit)
  close(iunit)
 
 end subroutine write_setupfile

From 92c10d36ca7dc4f5d71b360c47d35e5c1a35b2e8 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 17:46:18 +1000
Subject: [PATCH 02/23] (relax_star) relaxation procedure now restarts where it
 left off if phantomsetup is run again; added nice printout

---
 src/setup/relax_star.f90 | 132 +++++++++++++++++++++++++++++++++------
 1 file changed, 114 insertions(+), 18 deletions(-)

diff --git a/src/setup/relax_star.f90 b/src/setup/relax_star.f90
index 18107960f..9e56bebfc 100644
--- a/src/setup/relax_star.f90
+++ b/src/setup/relax_star.f90
@@ -61,13 +61,13 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
  use table_utils,     only:yinterp
  use deriv,           only:get_derivs_global
  use dim,             only:maxp,maxvxyzu,gr,gravity
- use part,            only:vxyzu,rad,eos_vars
+ use part,            only:vxyzu,rad,eos_vars,massoftype,igas
  use step_lf_global,  only:init_step,step
  use initial,         only:initialise
  use memory,          only:allocate_memory
  use energies,        only:compute_energies,ekin,epot,etherm
  use checksetup,      only:check_setup
- use io,              only:error,warning
+ use io,              only:error,warning,fatal,id,master
  use fileutils,       only:getnextfilename
  use readwrite_dumps, only:write_fulldump,init_readwrite_dumps
  use eos,             only:gamma,eos_outputs_mu
@@ -87,7 +87,7 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
  integer :: nits,nerr,nwarn,iunit,i1
  real    :: t,dt,dtmax,rmserr,rstar,mstar,tdyn
  real    :: entrop(nt),utherm(nt),mr(nt),rmax,dtext,dtnew
- logical :: converged,use_step
+ logical :: converged,use_step,restart
  logical, parameter :: fix_entrop = .true. ! fix entropy instead of thermal energy
  logical, parameter :: write_files = .true.
  character(len=20) :: filename,mylabel
@@ -107,7 +107,24 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
  mr = get_mr(rho,r)
  mstar = mr(nt)
  tdyn  = 2.*pi*sqrt(rstar**3/(32.*mstar))
- print*,'rstar  = ',rstar,' mstar = ',mstar, ' tdyn = ',tdyn
+ if (id==master) print*,'rstar = ',rstar,' mstar = ',mstar, ' tdyn = ',tdyn
+ !
+ ! see if we can restart or skip the relaxation process
+ ! based on a previous run
+ !
+ filename = 'relax'//trim(mylabel)//'_00000'
+ if (write_files) call init_readwrite_dumps()
+ call check_for_existing_file(filename,npart,massoftype(igas),&
+                              xyzh,vxyzu,restart,ierr)
+ !
+ ! quit with fatal error if non-matching file found, otherwise
+ ! this will be overwritten
+ !
+ if (write_files .and. ierr /= 0) then
+    if (id==master) print "(a)",' ERROR: pre-existing relaxed star dump(s) do not match'
+    call fatal('relax_star','please delete relax'//trim(mylabel)//'_* and restart...')
+ endif
+
  call set_options_for_relaxation(tdyn)
  call summary_initialise()
  !
@@ -154,20 +171,18 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
  !
  if (etherm > abs(epot)) then
     call error('relax_star','cannot relax star because it is unbound (etherm > epot)')
-    print*,' Etherm = ',etherm,' Epot = ',Epot
+    if (id==master) print*,' Etherm = ',etherm,' Epot = ',Epot
     if (maxvxyzu < 4) print "(/,a,/)",' *** Try compiling with ISOTHERMAL=no instead... ***'
     call restore_original_options(i1,npart)
     ierr = ierr_unbound
     return
  endif
- print "(/,3(a,1pg11.3),/,a,0pf6.2,a,es11.3,a,i4)",&
+ if (id==master) print "(/,3(a,1pg11.3),/,a,0pf6.2,a,es11.3,a,i4)",&
    ' RELAX-A-STAR-O-MATIC: Etherm:',etherm,' Epot:',Epot, ' R*:',maxval(r), &
    '       WILL stop WHEN: dens error < ',tol_dens,'% AND Ekin/Epot < ',tol_ekin,' OR Iter=',maxits
 
- filename = 'relax'//trim(mylabel)//'_00000'
  if (write_files) then
-    call init_readwrite_dumps()
-    if (len_trim(mylabel)==0) call write_fulldump(t,filename)
+    if (.not.restart) call write_fulldump(t,filename)
     open(newunit=iunit,file='relax'//trim(mylabel)//'.ev',status='replace')
     write(iunit,"(a)") '# nits,rmax,etherm,epot,ekin/epot,L2_{err}'
  endif
@@ -205,11 +220,13 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
     ! print information to screen
     !
     if (use_step) then
-       print "(a,es10.3,a,2pf6.2,2(a,1pg11.3))",' Relaxing star: t/dyn:',t/tdyn,', dens error:',rmserr,'%, R*:',rmax, &
+       if (id==master) print "(a,es10.3,a,2pf6.2,2(a,1pg11.3))",&
+        ' Relaxing star: t/dyn:',t/tdyn,', dens error:',rmserr,'%, R*:',rmax, &
         ' Ekin/Epot:',ekin/abs(epot)
     else
-       print "(a,i4,a,i4,a,2pf6.2,2(a,1pg11.3))",' Relaxing star: Iter',nits,'/',maxits, &
-             ', dens error:',rmserr,'%, R*:',rmax,' Ekin/Epot:',ekin/abs(epot)
+       if (id==master) print "(a,i4,a,i4,a,2pf6.2,2(a,1pg11.3))",&
+        ' Relaxing star: Iter',nits,'/',maxits, &
+        ', dens error:',rmserr,'%, R*:',rmax,' Ekin/Epot:',ekin/abs(epot)
     endif
     !
     ! additional diagnostic output, mainly for debugging/checking
@@ -222,20 +239,22 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
        !
        ! write dump files
        !
-       if (mod(nits,100)==0) then
+       if (mod(nits,100)==0 .or. ((nits==maxits .or. converged).and.nits > 1)) then
           filename = getnextfilename(filename)
           !
           ! before writing a file, set the real thermal energy profile
           ! so the file is useable as a starting file for the main calculation
           !
-          if (use_var_comp) call set_star_composition(use_var_comp,eos_outputs_mu(ieos_prev),&
-                                                      npart,xyzh,Xfrac,Yfrac,mu,mr,mstar,eos_vars,npin=i1)
+          if (use_var_comp) call set_star_composition(use_var_comp,&
+                                 eos_outputs_mu(ieos_prev),npart,xyzh,&
+                                 Xfrac,Yfrac,mu,mr,mstar,eos_vars,npin=i1)
 
-          if (maxvxyzu==4) call set_star_thermalenergy(ieos_prev,rho,pr,r,nt,npart,&
-             xyzh,vxyzu,rad,eos_vars,.true.,use_var_comp=.false.,initialtemp=1.e3,npin=i1)
+          if (maxvxyzu==4) call set_star_thermalenergy(ieos_prev,rho,pr,&
+                                r,nt,npart,xyzh,vxyzu,rad,eos_vars,.true.,&
+                                use_var_comp=.false.,initialtemp=1.e3,npin=i1)
 
           ! write relaxation snapshots
-          if (len_trim(mylabel)==0) call write_fulldump(t,filename)
+          if (write_files) call write_fulldump(t,filename)
 
           ! flush the relax.ev file
           call flush(iunit)
@@ -253,6 +272,13 @@ subroutine relax_star(nt,rho,pr,r,npart,xyzh,use_var_comp,Xfrac,Yfrac,mu,ierr,np
  if (.not.converged) then
     call warning('relax_star','relaxation did not converge, just reached max iterations')
     ierr = ierr_notconverged
+ else
+    if (id==master) print "(5(a,/))",&
+    "                             _                    _ ",&
+    "                    _ __ ___| | __ ___  _____  __| |",&
+    "                   | '__/ _ \ |/ _` \ \/ / _ \/ _` |",&
+    "                   | | |  __/ | (_| |>  <  __/ (_| |",&
+    "          o  o  o  |_|  \___|_|\__,_/_/\_\___|\__,_|  o  o  o"
  endif
  !
  ! unfake some things
@@ -397,6 +423,76 @@ subroutine set_options_for_relaxation(tdyn)
  if (gr) mass1 = 0. ! use Minkowski metric during relaxation
 
 end subroutine set_options_for_relaxation
+!----------------------------------------------------------------
+!+
+!  check if a previous snapshot exists of the relaxed star
+!+
+!----------------------------------------------------------------
+subroutine check_for_existing_file(filename,npart,mgas,xyzh,vxyzu,restart,ierr)
+ use dump_utils, only:open_dumpfile_r,read_header,dump_h,lenid,extract
+ use fileutils,  only:getnextfilename
+ use io,         only:idump,idisk1,id,nprocs,iprint
+ use readwrite_dumps, only:read_dump
+ character(len=*), intent(inout) :: filename
+ integer,          intent(in)    :: npart
+ real,             intent(in)    :: mgas
+ real,             intent(inout) :: xyzh(:,:),vxyzu(:,:)
+ logical,          intent(out)   :: restart
+ integer,          intent(out)   :: ierr
+ logical :: iexist,tagged
+ character(len=len(filename)) :: restart_file,filetmp
+ character(len=lenid) :: fileid
+ type(dump_h) :: hdr
+ integer :: npartfile
+ real :: hfactfile,tfile,mfile
+ !
+ ! check for the last file in the list relax_00000, relax_00001 etc
+ !
+ ierr = 0
+ iexist = .true.
+ filetmp = filename
+ restart_file = ''
+ restart = .false.
+ do while (iexist)
+    inquire(file=filetmp,exist=iexist)
+    if (iexist) then
+       restart_file = filetmp
+       filetmp = getnextfilename(filetmp)
+    endif
+ enddo
+ if (len_trim(restart_file) <= 0) return
+
+ print "(/,1x,a)",'>> RESTARTING relaxation from '//trim(restart_file)
+ call open_dumpfile_r(idump,restart_file,fileid,ierr)
+ call read_header(idump,hdr,tagged,ierr)
+ close(idump)
+ if (ierr /= 0) then
+    print "(a)",' ERROR: could not read file header'
+    return
+ else
+    call extract('nparttot',npartfile,hdr,ierr,default=0)
+    if (npartfile /= npart) then
+       print "(a,i0,a,i0)",' ERROR: np=',npartfile,' in '//&
+         trim(restart_file)//' differs from current np=',npart
+       ierr = 2
+       return
+    else
+       call extract('massoftype',mfile,hdr,ierr,default=0.)
+       if (abs(mfile-mgas) > epsilon(0.)) then
+          print "(a,es10.3,a,es10.3)",' ERROR: M=',npart*mfile,' in '//&
+            trim(restart_file)//' differs from current M=',npart*mgas
+          ierr = 3
+          return
+       else
+          restart = .true.
+          call read_dump(restart_file,tfile,hfactfile,&
+                         idisk1,iprint,id,nprocs,ierr)
+          filename = restart_file
+       endif
+    endif
+ endif
+
+end subroutine check_for_existing_file
 
 !--------------------------------------------------
 !+

From 747cd3364d6f9e048f9e9799d6bd8b1f38d71328 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 17:46:37 +1000
Subject: [PATCH 03/23] (set_star) cull unnecessary warning

---
 src/setup/set_star_utils.f90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/setup/set_star_utils.f90 b/src/setup/set_star_utils.f90
index 5d26826a0..07b62f29c 100644
--- a/src/setup/set_star_utils.f90
+++ b/src/setup/set_star_utils.f90
@@ -272,7 +272,6 @@ subroutine set_star_density(lattice,id,master,rmin,Rstar,Mstar,hfact,&
  if (npart_old /= 0 .and. massoftype(igas) > tiny(0.)) then
     n = nint(Mstar/massoftype(igas))
     mass_is_set = .true.
-    print "(a,i0)",' WARNING: particle mass is already set, using np = ',n
  endif
  !
  ! place particles in sphere

From 9ba25bc1ff0c402cc1d16bad7f6a26652257446c Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 22:42:18 +1000
Subject: [PATCH 04/23] (set_star) fixed errors with DEBUG=yes

---
 src/setup/set_star.f90       | 8 +++++++-
 src/setup/set_star_utils.f90 | 1 +
 src/setup/setup_binary.f90   | 5 +----
 src/setup/setup_star.f90     | 5 +----
 4 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/src/setup/set_star.f90 b/src/setup/set_star.f90
index 5724b83eb..a500a9169 100644
--- a/src/setup/set_star.f90
+++ b/src/setup/set_star.f90
@@ -49,7 +49,7 @@ module setstar
  end type star_t
 
  public :: star_t
- public :: set_defaults_star,set_star,shift_star
+ public :: set_star,shift_star
  public :: write_options_star,read_options_star,set_star_interactive
  public :: ikepler,imesa,ibpwpoly,ipoly,iuniform,ifromfile,ievrard
  public :: need_polyk
@@ -445,6 +445,9 @@ subroutine set_star_interactive(id,master,star,need_iso,use_var_comp,ieos,polyk)
  real,         intent(inout) :: polyk
  integer :: i
 
+ ! set defaults
+ call set_defaults_star(star)
+
  ! Select sphere & set default values
  do i = 1, nprofile_opts
     write(*,"(i2,')',1x,a)") i, profile_opt(i)
@@ -627,6 +630,9 @@ subroutine read_options_star(star,need_iso,ieos,polyk,db,nerr,label)
  character(len=*),          intent(in), optional :: label
  character(len=10) :: c
 
+ ! set defaults
+ call set_defaults_star(star)
+
  ! append optional label e.g. '1', '2'
  c = ''
  if (present(label)) c = trim(adjustl(label))
diff --git a/src/setup/set_star_utils.f90 b/src/setup/set_star_utils.f90
index 07b62f29c..a07d903c0 100644
--- a/src/setup/set_star_utils.f90
+++ b/src/setup/set_star_utils.f90
@@ -272,6 +272,7 @@ subroutine set_star_density(lattice,id,master,rmin,Rstar,Mstar,hfact,&
  if (npart_old /= 0 .and. massoftype(igas) > tiny(0.)) then
     n = nint(Mstar/massoftype(igas))
     mass_is_set = .true.
+    !print "(a,i0)",' WARNING: particle mass is already set, using np = ',n
  endif
  !
  ! place particles in sphere
diff --git a/src/setup/setup_binary.f90 b/src/setup/setup_binary.f90
index 1d33fa81e..7fd9a4087 100644
--- a/src/setup/setup_binary.f90
+++ b/src/setup/setup_binary.f90
@@ -51,7 +51,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
  use options,        only:iexternalforce
  use externalforces, only:iext_corotate,omega_corotate
  use io,             only:master
- use setstar,        only:set_star,set_defaults_star,shift_star
+ use setstar,        only:set_star,shift_star
  use eos,            only:X_in,Z_in,ieos
  use setup_params,   only:rhozero,npart_total
  use mpidomain,      only:i_belong
@@ -92,9 +92,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
  nstar = 2
  relax = .true.
  corotate = .false.
- do i=1,nstar
-    call set_defaults_star(star(i))
- enddo
  semi_major_axis = '10.'
  a    = 10.
  ecc  = 0.
diff --git a/src/setup/setup_star.f90 b/src/setup/setup_star.f90
index 356bc41ca..3eb33b4e5 100644
--- a/src/setup/setup_star.f90
+++ b/src/setup/setup_star.f90
@@ -71,7 +71,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use mpiutils,        only:reduceall_mpi
  use mpidomain,       only:i_belong
  use setup_params,    only:rhozero,npart_total
- use setstar,         only:set_star,set_defaults_star
+ use setstar,         only:set_star
  integer,           intent(in)    :: id
  integer,           intent(inout) :: npart
  integer,           intent(out)   :: npartoftype(:)
@@ -105,9 +105,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  X_in        = 0.74
  Z_in        = 0.02
  use_var_comp = .false.
-
- call set_defaults_star(star)
-
  !
  ! defaults needed for error checking
  !

From ca345c99672384fdacb12edebc72124f91644a75 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 22:42:56 +1000
Subject: [PATCH 05/23] (dens/force) fixed memory allocation issues when
 DEBUG=yes; use if (mpi)

---
 src/main/dens.F90  | 14 ++++++++++----
 src/main/force.F90 | 14 +++++++++-----
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/main/dens.F90 b/src/main/dens.F90
index bf666407f..71f4ba968 100644
--- a/src/main/dens.F90
+++ b/src/main/dens.F90
@@ -404,7 +404,10 @@ subroutine densityiterate(icall,npart,nactive,xyzh,vxyzu,divcurlv,divcurlB,Bevol
     enddo
  endif
 
- call recv_while_wait(stack_remote,xrecvbuf,irequestrecv,irequestsend,thread_complete,cell_counters,ncomplete_mpi)
+ if (mpi) then
+    call recv_while_wait(stack_remote,xrecvbuf,irequestrecv,&
+         irequestsend,thread_complete,cell_counters,ncomplete_mpi)
+ endif
 
  !$omp master
  call get_timings(t2,tcpu2)
@@ -422,6 +425,7 @@ subroutine densityiterate(icall,npart,nactive,xyzh,vxyzu,divcurlv,divcurlB,Bevol
 
  n_remote_its = 0
  iterations_finished = .false.
+ if (.not.mpi) iterations_finished = .true.
  !$omp end master
  !$omp barrier
 
@@ -469,11 +473,12 @@ subroutine densityiterate(icall,npart,nactive,xyzh,vxyzu,divcurlv,divcurlB,Bevol
        enddo
     endif igot_remote
 
-    call recv_while_wait(stack_waiting,xrecvbuf,irequestrecv,irequestsend,thread_complete,cell_counters,ncomplete_mpi)
+    if (mpi) call recv_while_wait(stack_waiting,xrecvbuf,irequestrecv,&
+             irequestsend,thread_complete,cell_counters,ncomplete_mpi)
     call reset_cell_counters(cell_counters)
     !$omp barrier
 
-    iam_waiting: if (stack_waiting%n > 0) then
+    iam_waiting: if (mpi .and. stack_waiting%n > 0) then
        !$omp do schedule(runtime)
        over_waiting: do i = 1, stack_waiting%n
           cell = stack_waiting%cells(i)
@@ -525,7 +530,8 @@ subroutine densityiterate(icall,npart,nactive,xyzh,vxyzu,divcurlv,divcurlB,Bevol
        enddo
     endif iam_waiting
 
-    call recv_while_wait(stack_remote,xrecvbuf,irequestrecv,irequestsend,thread_complete,cell_counters,ncomplete_mpi)
+    if (mpi) call recv_while_wait(stack_remote,xrecvbuf,irequestrecv,&
+             irequestsend,thread_complete,cell_counters,ncomplete_mpi)
 
     !$omp master
     if (reduceall_mpi('max',stack_redo%n) > 0) then
diff --git a/src/main/force.F90 b/src/main/force.F90
index 561362ab3..1d9100ffa 100644
--- a/src/main/force.F90
+++ b/src/main/force.F90
@@ -537,8 +537,11 @@ subroutine force(icall,npart,xyzh,vxyzu,fxyzu,divcurlv,divcurlB,Bevol,dBevol,&
     enddo
  endif
 
- call recv_while_wait(stack_remote,xrecvbuf,irequestrecv,irequestsend,thread_complete,cell_counters,ncomplete_mpi)
- call reset_cell_counters(cell_counters)
+ if (mpi) then
+    call recv_while_wait(stack_remote,xrecvbuf,irequestrecv,&
+         irequestsend,thread_complete,cell_counters,ncomplete_mpi)
+    call reset_cell_counters(cell_counters)
+ endif
 
  !$omp master
  call get_timings(t2,tcpu2)
@@ -547,7 +550,7 @@ subroutine force(icall,npart,xyzh,vxyzu,fxyzu,divcurlv,divcurlB,Bevol,dBevol,&
  !$omp end master
  !$omp barrier
 
- igot_remote: if (stack_remote%n > 0) then
+ igot_remote: if (mpi .and. stack_remote%n > 0) then
     !$omp do schedule(runtime)
     over_remote: do i = 1,stack_remote%n
        cell = get_cell(stack_remote,i)
@@ -587,9 +590,10 @@ subroutine force(icall,npart,xyzh,vxyzu,fxyzu,divcurlv,divcurlB,Bevol,dBevol,&
 
  endif igot_remote
 
- call recv_while_wait(stack_waiting,xrecvbuf,irequestrecv,irequestsend,thread_complete,cell_counters,ncomplete_mpi)
+ if (mpi) call recv_while_wait(stack_waiting,xrecvbuf,irequestrecv,&
+          irequestsend,thread_complete,cell_counters,ncomplete_mpi)
 
- iam_waiting: if (stack_waiting%n > 0) then
+ iam_waiting: if (mpi .and. stack_waiting%n > 0) then
     !$omp do schedule(runtime)
     over_waiting: do i = 1, stack_waiting%n
        cell = get_cell(stack_waiting,i)

From 000974ce2b198f526bd5634ab477154ad53e100d Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 22:55:21 +1000
Subject: [PATCH 06/23] (actions) compile+run phantomsetup with DEBUG=yes in
 github actions

---
 scripts/buildbot.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/buildbot.sh b/scripts/buildbot.sh
index c45abdfb9..beb1bd68c 100755
--- a/scripts/buildbot.sh
+++ b/scripts/buildbot.sh
@@ -321,9 +321,11 @@ for setup in $listofsetups; do
       colour=$white; # white (default)
       ncheck=$((ncheck + 1));
 
+      mydebug=''
       printf "Checking $setup ($target)... ";
       if [[ "$component" == "setup" ]]; then
          rm -f $phantomdir/bin/phantomsetup;
+         mydebug='DEBUG=yes' # compile phantomsetup with DEBUG=yes for setup test
          #make clean >& /dev/null;
       fi
       if [[ "$setup" == "blob" ]]; then
@@ -332,7 +334,7 @@ for setup in $listofsetups; do
       else
          mynowarn=$nowarn;
       fi
-      make SETUP=$setup $nolibs $mynowarn $maxp $target 1> $makeout 2> $errorlog; err=$?;
+      make SETUP=$setup $nolibs $mynowarn $maxp $target $mydebug 1> $makeout 2> $errorlog; err=$?;
       #--remove line numbers from error log files
       sed -e 's/90(.*)/90/g' -e 's/90:.*:/90/g' $errorlog | grep -v '/tmp' > $errorlog.tmp && mv $errorlog.tmp $errorlog;
       if [ $err -eq 0 ]; then

From c85fbac66d273c02621b83d11ccdeb1459da89bc Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 22:58:34 +1000
Subject: [PATCH 07/23] [header-bot] updated file headers

---
 src/setup/relax_star.f90  | 4 ++--
 src/setup/setup_grtde.f90 | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/setup/relax_star.f90 b/src/setup/relax_star.f90
index 9e56bebfc..65db5de98 100644
--- a/src/setup/relax_star.f90
+++ b/src/setup/relax_star.f90
@@ -18,8 +18,8 @@ module relaxstar
 !   - tol_dens : *% error in density to stop relaxation*
 !   - tol_ekin : *tolerance on ekin/epot to stop relaxation*
 !
-! :Dependencies: checksetup, damping, deriv, dim, energies, eos,
-!   externalforces, fileutils, infile_utils, initial, io, io_summary,
+! :Dependencies: checksetup, damping, deriv, dim, dump_utils, energies,
+!   eos, externalforces, fileutils, infile_utils, initial, io, io_summary,
 !   memory, options, part, physcon, ptmass, readwrite_dumps, setstar_utils,
 !   sortutils, step_lf_global, table_utils, units
 !
diff --git a/src/setup/setup_grtde.f90 b/src/setup/setup_grtde.f90
index 5480a38d0..72bf24033 100644
--- a/src/setup/setup_grtde.f90
+++ b/src/setup/setup_grtde.f90
@@ -18,11 +18,12 @@ module setup
 !   - ecc           : *eccentricity (1 for parabolic)*
 !   - mhole         : *mass of black hole (solar mass)*
 !   - norbits       : *number of orbits*
+!   - relax         : *relax star into hydrostatic equilibrium*
 !   - theta         : *inclination of orbit (degrees)*
 !
 ! :Dependencies: eos, externalforces, gravwaveutils, infile_utils, io,
-!   kernel, metric, mpidomain, part, physcon, setbinary, setstar,
-!   setup_params, timestep, units, vectorutils
+!   kernel, metric, mpidomain, part, physcon, relaxstar, setbinary,
+!   setstar, setup_params, timestep, units, vectorutils
 !
  use setstar, only:star_t
  implicit none

From 5d7fc0bbbed2071b576bf8bc51a4b32582a490a3 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Thu, 11 May 2023 23:18:29 +1000
Subject: [PATCH 08/23] (docs) updated docs for binary setup

---
 docs/binary.rst | 142 ++++++++++++++++++++++++++++++++++++------------
 1 file changed, 108 insertions(+), 34 deletions(-)

diff --git a/docs/binary.rst b/docs/binary.rst
index 41bb6b8f8..a6a7ec221 100644
--- a/docs/binary.rst
+++ b/docs/binary.rst
@@ -1,17 +1,37 @@
 Binary stars and common envelope evolution
 ============================================
 
-Using SETUP=binary
-------------------
-The one-stop-shop to setup a binary star simulation is to use SETUP=binary::
+Setting up and relaxing binary stars (the easy way)
+---------------------------------------------------
+The one-stop-shop to setup a binary star simulation is as follows::
 
-   ~/phantom/scripts/writemake.sh binary > Makefile
-   make setup
-   ./phantomsetup sim
+make a new directory and write a local Makefile
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-giving::
+::
 
-  -----------------------------------------------------------------
+   $ mkdir mybinarysim
+   $ cd mybinarysim
+   $ ~/phantom/scripts/writemake.sh binary > Makefile
+
+compile phantom and phantomsetup
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+   $ make
+   $ make setup
+   $ ls
+   Makefile    phantom*    phantomsetup*
+
+run phantomsetup
+~~~~~~~~~~~~~~~~
+
+::
+
+   ./phantomsetup sim
+
+   -----------------------------------------------------------------
    Welcome to the Ultimate Binary Setup
   -----------------------------------------------------------------
 
@@ -19,13 +39,17 @@ giving::
     Edit sim.setup and rerun phantomsetup
 
 
-This will create a file called sim.setup which contains setup options. Open this file in
-your favourite text editor to proceed...
+This will create a file called sim.setup which contains setup options.
+Open this file in your favourite text editor to proceed...
 
 
 Two sink particles in orbit
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The simplest is to setup two sink particles in a binary (iprofile=0), by amending the iprofile flags::
+----------------------------
+
+Set iprofile=0 for both stars in the .setup file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
 
    # options for star 1
               iprofile1 =           0    ! 0=Sink,1=Unif,2=Poly,3=Dens,4=KEPL,5=MESA,6=Pie
@@ -33,23 +57,30 @@ The simplest is to setup two sink particles in a binary (iprofile=0), by amendin
    # options for star 2
               iprofile2 =           0    ! 0=Sink,1=Unif,2=Poly,3=Dens,4=KEPL,5=MESA,6=Pie
 
-Then run phantomsetup again to rewrite the required options::
-
- $ ./phantomsetup sim
+run phantomsetup again to rewrite the required options
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-which will give::
+::
 
+ $ ./phantomsetup sim
+  ...
   ERROR: hacc1 not found
   ERROR: hacc2 not found
    2 error(s) during read of setup file: re-writing...
   writing setup options file sim.setup
    Edit sim.setup and rerun phantomsetup
 
-Run this again to finish the setup::
+run phantomsetup again to complete the setup
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+::
    ./phantomsetup sim
 
-This creates a sim.in file for the main code. You should edit the tmax and dtmax
+This creates a sim.in file for the main code.
+
+edit the .in file as desired
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+You should edit the tmax and dtmax
 to give the desired finishing time (tmax) and time between snapshots (dtmax)::
 
    cat sim.in
@@ -66,20 +97,30 @@ to give the desired finishing time (tmax) and time between snapshots (dtmax)::
                   f_acc =       0.500    ! particles < f_acc*h_acc accreted without checks
 
 
-After editing the .in file, proceed to run the simulation::
+run the simulation
+~~~~~~~~~~~~~~~~~~
+
+::
 
    make
    ./phantom sim
 
-and have a look at the outputs with splash::
+have a look at the outputs with splash
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
 
    splash sim_0*
 
 
 Two polytropes in orbit
-~~~~~~~~~~~~~~~~~~~~~~~~~
-The default is to setup-and-relax two polytropes and place them in orbit. For this edit
-your sim.setup file to give::
+------------------------
+The default is to setup two polytropes and place them in orbit.
+
+Edit .setup file to specify iprofile=2 for both stars
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
 
   # options for star 1
              iprofile1 =           2    ! 0=Sink,1=Unif,2=Poly,3=Dens,4=KEPL,5=MESA,6=Pie
@@ -92,9 +133,30 @@ your sim.setup file to give::
                 Mstar2 =       1.000    ! mass of star2
                 Rstar2 =       1.000    ! radius of star2
 
-Then run phantomsetup again to rewrite the required options::
+run phantomsetup again to rewrite the required options
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+  $ ./phantomsetup sim
+
+set the relaxation flag to true
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+   # relaxation options
+               relax =           T    ! relax stars into equilibrium
+            tol_ekin =   1.000E-07    ! tolerance on ekin/epot to stop relaxation
+            tol_dens =       1.000    ! % error in density to stop relaxation
+              maxits =        1000    ! maximum number of relaxation iterations
+
+run phantomsetup again
+~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+  $ ./phantomsetup sim
 
- $ ./phantomsetup sim
 
 This time you should see the automated relax-a-star procedure kick in::
 
@@ -104,15 +166,27 @@ This time you should see the automated relax-a-star procedure kick in::
     Relaxing star: Iter   2/1000, dens error: 10.97%, R*:  0.915     Ekin/Epot:  4.673E-03
     ...
 
-As previously, you can then just proceed to run the simulation after editing the sim.in file
-::
+restart the relaxation if needed
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The relaxation process will continue where it left off if you simply
+run phantomsetup again, stopping when the criteria above are met::
+
+  $ ./phantomsetup sim
+
+
+run the simulation after editing the sim.in file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+After successfully completing the setup process, you can proceed
+to run your Very Happy Binary Star Simulation^TM::
 
    ./phantom sim.in
 
 Two stars from MESA profiles
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-To use stellar profiles from the MESA code, select iprofile=5 in your .setup file
-and enter the name of the ascii data file containing the input profile
+-----------------------------
+
+select iprofile=5 in your .setup file and enter name of MESA file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Enter the name of the ascii data file containing the input profile
 (most files produced by MESA just work...)::
 
   # options for star 1
@@ -131,8 +205,8 @@ and enter the name of the ascii data file containing the input profile
 Notice that you do not get to set the particle resolution for the second star,
 since the mass of the particles is fixed by the mass and particle number in star 1.
 
-Replacing dense stellar cores with sink particles
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Replace dense stellar cores with sink particles (as necessary)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 In the options above you have the option to remove the dense core of the star
 which causes small timesteps in the code, and replace it with a softened point
 mass. The default option for this is isoftcore1=2 and isinkcore1=1.
@@ -140,8 +214,8 @@ mass. The default option for this is isoftcore1=2 and isinkcore1=1.
 For more details, see :doc:`Setting up a softened star <softstar>`
 
 
-Using SETUP=star and moddump_binary
-------------------------------------
+Setting up and relaxing binary stars (the old fashioned way)
+-------------------------------------------------------------
 See :doc:`Setting up stars and tidal disruption events <star>` for the older two-step procedure. The options available are
 identical, but with a bit more flexibility and without
 having to re-run the relaxation procedure over and over again.

From 82195da2787add626b57d3fd197917e24c2b1b38 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 09:53:44 +1000
Subject: [PATCH 09/23] (planetdisc) uninitialised variable error fixed in
 checksetup

---
 src/main/checksetup.F90        | 23 +++++++++++++++++++----
 src/main/extern_binary.f90     |  2 --
 src/main/externalforces.F90    |  2 --
 src/setup/phantomsetup.F90     |  3 ++-
 src/setup/setup_planetdisc.f90 |  3 +--
 5 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/main/checksetup.F90 b/src/main/checksetup.F90
index 1a9558eea..8bab8e06c 100644
--- a/src/main/checksetup.F90
+++ b/src/main/checksetup.F90
@@ -48,7 +48,7 @@ subroutine check_setup(nerror,nwarn,restart)
  use centreofmass,    only:get_centreofmass
  use options,         only:ieos,icooling,iexternalforce,use_dustfrac,use_hybrid
  use io,              only:id,master
- use externalforces,  only:accrete_particles,accradius1,iext_star,iext_corotate
+ use externalforces,  only:accrete_particles,update_externalforce,accradius1,iext_star,iext_corotate
  use timestep,        only:time
  use units,           only:G_is_unity,get_G_code
  use boundary,        only:xmin,xmax,ymin,ymax,zmin,zmax
@@ -301,11 +301,17 @@ subroutine check_setup(nerror,nwarn,restart)
 !--check for particles placed inside accretion boundaries
 !
  if (iexternalforce > 0 .and. .not.dorestart) then
+    call update_externalforce(iexternalforce,time,0.)
     nbad = 0
+    !$omp parallel do default(none) &
+    !$omp shared(npart,xyzh,massoftype,time,iexternalforce) &
+    !$omp private(i,accreted) &
+    !$omp reduction(+:nbad)
     do i=1,npart
        call accrete_particles(iexternalforce,xyzh(1,i),xyzh(2,i),xyzh(3,i),xyzh(4,i),massoftype(1),time,accreted)
        if (accreted) nbad = nbad + 1
     enddo
+    !$omp end parallel do
     if (nbad > 0) then
        print*,'WARNING: ',nbad,' of ',npart,' particles setup within the accretion boundary'
        nwarn = nwarn + 1
@@ -314,7 +320,7 @@ subroutine check_setup(nerror,nwarn,restart)
     hi = 0.
     call accrete_particles(iexternalforce,0.,0.,0.,hi,massoftype(1),time,accreted)
     !--if so, check for unresolved accretion radius
-    if (accreted .and. accradius1 < 0.5*hmin) then
+    if (accreted .and. accradius1 < 0.5*hmin .and. accradius1 > 0.) then
        print*,'WARNING: accretion radius is unresolved by a factor of hmin/racc = ',hmin/accradius1
        print*,'(this will cause the code to run needlessly slow)'
        nwarn = nwarn + 1
@@ -450,6 +456,10 @@ subroutine check_NaN(npart,array,label,nerror)
  integer :: nbad,i
 
  nbad = 0
+ !$omp parallel do default(none) schedule(static) &
+ !$omp shared(npart,array,label) &
+ !$omp private(i) &
+ !$omp reduction(+:nbad)
  do i=1,npart
     !--check for NaNs in xyzh
     if (any(isnan(array(:,i)))) then
@@ -457,6 +467,7 @@ subroutine check_NaN(npart,array,label,nerror)
        nbad = nbad + 1
     endif
  enddo
+ !$omp end parallel do
  if (nbad > 0) then
     print*,'ERROR: NaN in '//trim(label)//' on ',nbad,' of ',npart,' particles'
     nerror = nerror + 1
@@ -844,7 +855,6 @@ subroutine check_for_identical_positions(npart,xyzh,nbad)
  !
  allocate(index(npart))
  call indexxfunc(npart,r2func,xyzh,index)
-
  !
  ! check for identical positions. Stop checking as soon as non-identical
  ! positions are found.
@@ -852,6 +862,10 @@ subroutine check_for_identical_positions(npart,xyzh,nbad)
  nbad = 0
  itypei = igas
  itypej = igas
+ !$omp parallel do default(none) &
+ !$omp shared(npart,xyzh,index,maxphase,maxp,iphase) &
+ !$omp private(i,j,dx,dx2,itypei,itypej) &
+ !$omp reduction(+:nbad)
  do i=1,npart
     if (.not.isdead_or_accreted(xyzh(4,index(i)))) then
        j = i+1
@@ -864,7 +878,7 @@ subroutine check_for_identical_positions(npart,xyzh,nbad)
           dx2 = dot_product(dx,dx)
           if (dx2 < epsilon(dx2) .and. itypei==itypej) then
              nbad = nbad + 1
-             if (nbad <= 100) then
+             if (nbad <= 10) then
                 print*,'WARNING: particles of same type at same position: '
                 print*,' ',index(i),':',xyzh(1:3,index(i))
                 print*,' ',index(j),':',xyzh(1:3,index(j))
@@ -874,6 +888,7 @@ subroutine check_for_identical_positions(npart,xyzh,nbad)
        enddo
     endif
  enddo
+ !$omp end parallel do
 
  deallocate(index)
 
diff --git a/src/main/extern_binary.f90 b/src/main/extern_binary.f90
index 317f7894e..5c53956be 100644
--- a/src/main/extern_binary.f90
+++ b/src/main/extern_binary.f90
@@ -141,7 +141,6 @@ subroutine binary_force(xi,yi,zi,ti,fxi,fyi,fzi,phi)
  phi2 = -(1.-binarymassri)*dr2
  phi  = phi1 + phi2
 
- return
 end subroutine binary_force
 
 !----------------------------------------------
@@ -175,7 +174,6 @@ subroutine binary_posvel(ti,posmh,vels)
  vels(5) = -binarymassri*cos(ti)
  vels(6) = 0.
 
- return
 end subroutine binary_posvel
 
 !----------------------------------------------
diff --git a/src/main/externalforces.F90 b/src/main/externalforces.F90
index d8d13c633..940278203 100644
--- a/src/main/externalforces.F90
+++ b/src/main/externalforces.F90
@@ -26,8 +26,6 @@ module externalforces
  use extern_binary,   only:accradius1
  use extern_corotate, only:omega_corotate  ! so public from this module
  implicit none
- character(len=80), parameter, public :: &  ! module version
-    modid="$Id$"
 
  private
  public :: externalforce,externalforce_vdependent
diff --git a/src/setup/phantomsetup.F90 b/src/setup/phantomsetup.F90
index 0a3483788..6ee16474c 100644
--- a/src/setup/phantomsetup.F90
+++ b/src/setup/phantomsetup.F90
@@ -34,6 +34,7 @@ program phantomsetup
  use setup,           only:setpart
  use setup_params,    only:ihavesetupB,npart_total
  use checksetup,      only:check_setup
+ use timestep,        only:time
  use physcon,         only:pi
  use units,           only:set_units,print_units,c_is_unity
  use mpiutils,        only:init_mpi,finalise_mpi,reduceall_mpi
@@ -51,7 +52,7 @@ program phantomsetup
  integer, parameter          :: lenprefix = 120
  character(len=lenprefix)    :: fileprefix
  character(len=lenprefix+10) :: dumpfile,infile,evfile,logfile
- real                        :: time,pmassi
+ real                        :: pmassi
  logical                     :: iexist
 
  nprocs = 1    ! for MPI, this is not initialised until init_mpi, but an initialised value is required for init_part
diff --git a/src/setup/setup_planetdisc.f90 b/src/setup/setup_planetdisc.f90
index bcb29c68b..6f58bc2c6 100644
--- a/src/setup/setup_planetdisc.f90
+++ b/src/setup/setup_planetdisc.f90
@@ -191,7 +191,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
 !   vxyzu(3,i) = vxyzu(3,i) + vbinary(3)
 ! enddo
 
- return
 end subroutine setpart
 
 
@@ -205,7 +204,7 @@ subroutine write_setupfile(filename)
 
  print "(a)",' writing setup options file '//trim(filename)
  open(unit=iunit,file=filename,status='replace',form='formatted')
- write(iunit,"(a)") '# input file for gwdisc setup routines'
+ write(iunit,"(a)") '# input file for planetdisc setup routine'
 
  write(iunit,"(/,a)") '# resolution'
 

From ec052caef1f37fdb6cffe05532e0bf5ddadc97fc Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 10:05:58 +1000
Subject: [PATCH 10/23] (bondi) setup failures with DEBUG=yes fixed; remove
 ifdefs #55

---
 src/main/bondiexact.f90   |  3 +++
 src/setup/setup_bondi.F90 | 54 ++++++++++++++++++---------------------
 2 files changed, 28 insertions(+), 29 deletions(-)

diff --git a/src/main/bondiexact.f90 b/src/main/bondiexact.f90
index 46f14c724..7254d93d5 100644
--- a/src/main/bondiexact.f90
+++ b/src/main/bondiexact.f90
@@ -24,6 +24,9 @@ module bondiexact
  real, public  :: rcrit   = 5.
  real, private :: rhocrit = 1.
 
+ logical, public :: iswind = .false.
+ integer, public :: isol   = 0
+
  private
 
 contains
diff --git a/src/setup/setup_bondi.F90 b/src/setup/setup_bondi.F90
index 950ec8174..e29b990e2 100644
--- a/src/setup/setup_bondi.F90
+++ b/src/setup/setup_bondi.F90
@@ -25,30 +25,22 @@ module setup
 !
  use physcon,        only:pi
  use externalforces, only:accradius1,accradius1_hard
- use dim,            only:gr
-#ifdef GR
- use metric,         only:mass1
+ use dim,            only:gr,maxvxyzu
  use metric_tools,   only:imet_schwarzschild,imetric
-#else
  use externalforces, only:mass1
-#endif
  use setup_params,   only:rhozero,npart_total
  use io,             only:master,fatal
  use spherical,      only:set_sphere
  use options,        only:ieos,iexternalforce,nfulldump
  use timestep,       only:tmax,dtmax
  use centreofmass,   only:reset_centreofmass
- use units,          only:udist,umass,utime,set_units
+ use units,          only:set_units,get_G_code
  use physcon,        only:pc,solarm,gg
  use part,           only:xyzmh_ptmass,vxyz_ptmass,nptmass,ihacc,igas,set_particle_type,iboundary
  use stretchmap,     only:get_mass_r,rho_func
  use kernel,         only:radkern
  use prompting,      only:prompt
- use bondiexact,     only:get_bondi_solution,rcrit
-#ifdef GR
- use bondiexact,     only:isol,iswind
-#endif
-
+ use bondiexact,     only:get_bondi_solution,rcrit,isol,iswind
  implicit none
 
  public :: setpart
@@ -89,7 +81,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
 !-- Set code units
 !
  call set_units(G=1.d0,c=1.d0)
- print*,' gcode = ',gg*umass*utime**2/udist**3
+ print*,' G in code units = ',get_G_code()
 
 !
 !--Set general parameters
@@ -101,9 +93,10 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  rmax = 8.
  np   = 10000
 
-#ifdef GR
- if (imetric/=imet_schwarzschild) call fatal('setup_bondi','You are not using the Schwarzschild metric.')
-#endif
+ if (gr) then
+    if (imetric/=imet_schwarzschild) call fatal('setup_bondi',&
+       'You are not using the Schwarzschild metric.')
+ endif
 
 !
 !-- Read things from setup file
@@ -119,14 +112,16 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     endif
  elseif (id==master) then
     print "(a,/)",trim(filename)//' not found: using interactive setup'
-#ifdef GR
-    call prompt(' Enter solution type isol (1 = geodesic | 2 = sonic point flow) ',isol,1,2)
-    call prompt(' Do you want a wind (y/n)? ',iswind)
-#endif
+    if (gr) then
+       call prompt(' Enter solution type isol (1 = geodesic | 2 = sonic point flow) ',isol,1,2)
+       call prompt(' Do you want a wind (y/n)? ',iswind)
+    endif
     call prompt(' Enter inner edge: ',rmin,0.)
     call prompt(' Enter outer edge: ',rmax,rmin)
     call prompt(' Enter the desired number of particles: ',np,0)
     call write_setupfile(filename)
+    print*,' Edit '//trim(filename)//' and rerun phantomsetup'
+    stop
  endif
 
  if (gr) then
@@ -176,7 +171,8 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
 !--- Add stretched sphere
  npart = 0
  npart_total = 0
- call set_sphere('closepacked',id,master,rmin,rmax,psep,hfact,npart,xyzh,rhotab=rhotab,nptot=npart_total)
+ call set_sphere('closepacked',id,master,rmin,rmax,psep,hfact,npart,&
+                 xyzh,rhotab=rhotab,nptot=npart_total)
  massoftype(:) = totmass/npart
  print "(a,i0,/)",' npart = ',npart
 
@@ -187,7 +183,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     r = sqrt(dot_product(pos,pos))
     call get_bondi_solution(rhor,vr,ur,r,mass1,gamma)
     vxyzu(1:3,i) = vr*pos/r
-    vxyzu(4,i)   = ur
+    if (maxvxyzu >= 4) vxyzu(4,i) = ur
 
     if (set_boundary_particles) then
        if (r + radkern*xyzh(4,i)>rmax .or. r - radkern*xyzh(4,i)<rmin) then
@@ -238,10 +234,10 @@ subroutine write_setupfile(filename)
  open(unit=iunit,file=filename,status='replace',form='formatted')
  write(iunit,"(a)") '# input file for bondi setup routine'
  write(iunit,"(/,a)") '# solution type'
-#ifdef GR
- call write_inopt(isol,'isol','(1 = geodesic flow  |  2 = sonic point flow)',iunit)
- call write_inopt(iswind,'iswind','wind option (logical)',iunit)
-#endif
+ if (gr) then
+    call write_inopt(isol,'isol','(1 = geodesic flow  |  2 = sonic point flow)',iunit)
+    call write_inopt(iswind,'iswind','wind option (logical)',iunit)
+ endif
  call write_inopt(rmin,'rmin','inner edge',iunit)
  call write_inopt(rmax,'rmax','outer edge',iunit)
  call write_inopt(np,'np','desired number of particles (stretch-mapping will only give this approx.)',iunit)
@@ -264,10 +260,10 @@ subroutine read_setupfile(filename,ierr)
 
  print "(a)",' reading setup options from '//trim(filename)
  call open_db_from_file(db,filename,iunit,ierr)
-#ifdef GR
- call read_inopt(isol,  'isol',   db,ierr)
- call read_inopt(iswind,'iswind', db,ierr)
-#endif
+ if (gr) then
+    call read_inopt(isol,  'isol',   db,ierr)
+    call read_inopt(iswind,'iswind', db,ierr)
+ endif
  call read_inopt(rmin, 'rmin', db,ierr)
  call read_inopt(rmax, 'rmax', db,ierr)
  call read_inopt(np,   'np',   db,ierr)

From 7f6713e8e62897713f6d83aaed89efcb6bbfeb70 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 10:30:01 +1000
Subject: [PATCH 11/23] (torus) setup failures/out-of-bounds error fixed; added
 refs

---
 src/setup/setup_torus.f90 | 74 +++++++++++++++++++++------------------
 1 file changed, 40 insertions(+), 34 deletions(-)

diff --git a/src/setup/setup_torus.f90 b/src/setup/setup_torus.f90
index a6e53c440..ee410b98e 100644
--- a/src/setup/setup_torus.f90
+++ b/src/setup/setup_torus.f90
@@ -6,9 +6,19 @@
 !--------------------------------------------------------------------------!
 module setup
 !
-! this module does setup
+! Setup for a rotating torus, for simulations of
+! the magnetorotational instability and/or the
+! Papaloizoi-Pringle instbaility
 !
-! :References: None
+! Originally written over a few beers in collaboration
+! with Owen Matthews and Laure Fouchet. This shows.
+!
+! Most recently used in Nealon et al. (2018)
+!
+! :References:
+!  - Papaloizoi & Pringle (1984), MNRAS 208, 721
+!  - Zurek & Benz (1986), ApJ 308, 123
+!  - Nealon et al. (2018), MNRAS 474, 1737
 !
 ! :Owner: Daniel Price
 !
@@ -23,13 +33,14 @@ module setup
 
 contains
 
-subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
+subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,&
+           gamma,hfact,time,fileprefix)
  use part,         only:Bxyz,rhoh,hrho,mhd
- use part,         only:iphase,iamtype,igas,maxphase
+ use part,         only:igas
  use dim,          only:maxp,maxvxyzu
  use setup_params, only:ihavesetupB
  use physcon,      only:pi,au,solarm,solarr
- use units,        only:set_units
+ use units,        only:set_units,get_G_code
  integer,           intent(in)  :: id
  integer,           intent(out) :: npart
  integer,           intent(out) :: npartoftype(:)
@@ -39,19 +50,19 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  real,              intent(out) :: massoftype(:)
  real,              intent(in)  :: time
  character(len=20), intent(in)  :: fileprefix
- integer :: i,nrings,nlayers,iring,iz,ipart,npartphi,ii,iamtypei
- real :: Rtorus,dfac,Mstar,Mtorus,zmax,deltaz,bigG
+ integer :: i,nrings,nlayers,iring,iz,ipart,npartphi
+ real :: Rtorus,dfac,Mstar,Mtorus,zmax,deltaz
  real :: massp,r_in,r_out,deltar,polyn,np
- real :: ri,zi,rhofac,deltaphi,densi,pri
+ real :: ri,zi,rhofac,deltaphi,densi,pri,bigG
  real :: deltartemp,denstemp,rtemp,deltar0,dens0
- real :: omegai,v2onr,rcyl2,rcyl,rsph,rhosum,pmassi,pmassii
+ real :: omegai,v2onr,rcyl2,rcyl,rsph,rhosum,pmassi
  real :: beta,Bzi,dbeta,densmax,densmin
  real, parameter :: dndim = 1./3.
 
 ! call set_units(dist=au,mass=solarm,G=1.d0)
- bigG = 1.d0
- call set_units(dist=100.*solarr,mass=10.E6*solarm,G=bigG)
+ call set_units(dist=100.*solarr,mass=1.e7*solarm,G=1.d0)
 
+ bigG = get_G_code()
  Rtorus = 1.0
  dfac = 1.01
  Mstar = 1.0
@@ -61,7 +72,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  gamma = 5./3.
 
  print*,'Setup for beer-related torus thing (Owen, Laure)'
- print*,'maxvxyzu value: ',maxvxyzu
  print*,'particles: ',npart
 
 !
@@ -219,9 +229,9 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  enddo
 
  npart = ipart
- npartoftype(1) = ipart
+ npartoftype(igas) = ipart
  print*,'Mtorus = ',Mtorus,massp*npart
- massoftype(1) = Mtorus/real(npart)
+ massoftype(igas) = Mtorus/real(npart)
  print*,'Number of particles used',npart
 
  !
@@ -230,10 +240,9 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  !--set magnetic field using plasma beta
  beta = 100. !1.e4
  rhosum = 0.0
- pmassii = massoftype(igas)
- do ii=1,npart
-    if (maxphase==maxp) pmassii = massoftype(iamtype(iphase(ii)))
-    rhosum = rhosum + rhoh(xyzh(4,ii),pmassii)
+ pmassi = massoftype(igas)
+ do i=1,npart
+    rhosum = rhosum + rhoh(xyzh(4,i),pmassi)
  enddo
  rhosum = rhosum/npart
 
@@ -253,13 +262,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  !
  !--analytic velocities
  !
- pmassi   = massoftype(igas)
- iamtypei = igas
  do i=1,npart
-    if (maxphase==maxp) then
-       iamtypei = iamtype(iphase(i))
-       pmassi = massoftype(iamtypei)
-    endif
     densi = rhoh(xyzh(4,i),pmassi)
     Bzi   = sqrt(2.*polyk*densi**gamma/beta)
     rcyl2 = dot_product(xyzh(1:2,i),xyzh(1:2,i))
@@ -277,7 +280,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     vxyzu(3,i) = 0.
 
 ! Poloidal Field
-    if (mhd .and. iamtypei==igas) then
+    if (mhd) then
        Bxyz(3,i) = dbeta*(densi**2/rcyl &
                       + 2.*Mstar/(polyk*gamma)*densi**(3.-gamma) &
                       *(Rtorus/rcyl**3 - rcyl/rsph**3))
@@ -289,14 +292,16 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     endif
  enddo
 
-! Toroidal field
-
-
+! Toroidal field (not implemented)
 
  return
 
 contains
-
+!---------------------------------------------
+!+
+!  density function needed for Torus
+!+
+!---------------------------------------------
 real function rhofunc(rr,zz,polyn,dd,Mstar,R0)
  real, intent(in) :: rr,zz,polyn,dd,Mstar,R0
  real :: term
@@ -312,10 +317,12 @@ real function rhofunc(rr,zz,polyn,dd,Mstar,R0)
 
 end function rhofunc
 
-!
-!--sets several ring of particles above and below the midplane
-!  and around in phi
-!
+!---------------------------------------------
+!+
+!  setup several rings of particles above
+!  and below the midplane and around in phi
+!+
+!---------------------------------------------
 subroutine setring(npartphi,ipart,ri,deltar,deltaphi,densi)
  integer, intent(in)    :: npartphi
  integer, intent(inout) :: ipart
@@ -387,7 +394,6 @@ subroutine setring(npartphi,ipart,ri,deltar,deltaphi,densi)
     endif
     !print*,'zi = ',ri,zi,denszi,ipart
  enddo
-
 ! print*,'set ring: r = ',ri,' npart = ',ipart
 
 end subroutine setring

From 714edf82870e9db8c164ee9f077942e3099901f7 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 10:39:34 +1000
Subject: [PATCH 12/23] (quebec) setup failures with DEBUG=yes fixed

---
 src/setup/setup_quebec.f90 | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/setup/setup_quebec.f90 b/src/setup/setup_quebec.f90
index f6c0f5e9c..128b4c41c 100644
--- a/src/setup/setup_quebec.f90
+++ b/src/setup/setup_quebec.f90
@@ -32,8 +32,9 @@ module setup
 !  setup for uniform particle distributions
 !+
 !----------------------------------------------------------------
-subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
- use part,      only:maxvxyzu
+subroutine setpart(id,npart,npartoftype,xyzh,massoftype,&
+                   vxyzu,polyk,gamma,hfact,time,fileprefix)
+ use part,      only:maxvxyzu,igas
  use spherical, only:set_sphere,rho_func
  use io,        only:master
  use setup_params,   only:rhozero,npart_total
@@ -55,7 +56,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  real :: Rg_codeunits
  procedure(rho_func), pointer :: density_func
 
- call set_units(dist=solarr, mass=solarm, G=1.0)
+ call set_units(dist=solarr, mass=solarm, G=1.0d0)
 
 !
 !--parameters for this setup
@@ -82,9 +83,11 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
 !
  xyzh(:,:)  = 0.
  vxyzu(:,:) = 0.
+ polyk = 0.
 
  np    = min(10000000,int(2.0/3.0*size(xyzh(1,:)))) ! approx max number allowed in sphere given size(xyzh(1,:))
  npmax = np
+ np = 100000
  call prompt('Enter the approximate number of particles in the sphere ',np,0,npmax)
 
  totvol = 4./3.*pi*rmax**3
@@ -100,22 +103,21 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  npart_total = 0
 
  density_func => rhofunc
- call set_sphere('closepacked',id,master,rmin,rmax,psep,hfact,npart,xyzh,rhofunc=density_func,nptot=npart_total)
-
+ call set_sphere('closepacked',id,master,rmin,rmax,psep,&
+      hfact,npart,xyzh,rhofunc=density_func,nptot=npart_total)
 !
 !--set particle properties
 !
-
  npart_total = npart
  rhozero = total_mass / totvol
  print *, ' total mass = ',total_mass,' mean density = ',rhozero
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
  print *, ' npart = ',npart_total
 
- massoftype(1) = total_mass / npart_total
- print *, ' particle mass = ',massoftype(1)
+ massoftype(igas) = total_mass / npart_total
+ print *, ' particle mass = ',massoftype(igas)
  print *, ''
 
  ! convert Rg to code units
@@ -150,7 +152,11 @@ real function rhofunc(r)
  a = a / udist
 
  ! cgs units
- rhofunc = rho_crit * a * sin(r/a) / r
+ if (r > 0.) then
+    rhofunc = rho_crit * a * sin(r/a) / r
+ else
+    rhofunc = huge(0.)
+ endif
 
  ! convert to code units
  rhofunc = rhofunc / (umass / udist**3)

From e609998eaab45e514926b7e5589d93eef3f74ade Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 11:07:48 +1000
Subject: [PATCH 13/23] (readwrite_infile) #55 remove ifdefs; minor changes to
 wording

---
 src/main/readwrite_infile.F90 | 35 +++++++++--------------------------
 1 file changed, 9 insertions(+), 26 deletions(-)

diff --git a/src/main/readwrite_infile.F90 b/src/main/readwrite_infile.F90
index 4d57cf21c..3424975bf 100644
--- a/src/main/readwrite_infile.F90
+++ b/src/main/readwrite_infile.F90
@@ -82,7 +82,7 @@ module readwrite_infile
  use viscosity, only:irealvisc,shearparam,bulkvisc
  use part,      only:hfact,ien_type
  use io,        only:iverbose
- use dim,       only:do_radiation,nucleation
+ use dim,       only:do_radiation,nucleation,use_dust,use_dustgrowth
  implicit none
  logical :: incl_runtime2 = .false.
 
@@ -103,12 +103,8 @@ subroutine write_infile(infile,logfile,evfile,dumpfile,iwritein,iprint)
  use externalforces,  only:write_options_externalforces
  use damping,         only:write_options_damping
  use linklist,        only:write_inopts_link
-#ifdef DUST
  use dust,            only:write_options_dust
-#ifdef DUSTGROWTH
  use growth,          only:write_options_growth
-#endif
-#endif
 #ifdef PHOTO
  use photoevap,       only:write_options_photoevap
 #endif
@@ -196,7 +192,7 @@ subroutine write_infile(infile,logfile,evfile,dumpfile,iwritein,iprint)
 
  call write_inopts_link(iwritein)
 
- write(iwritein,"(/,a)") '# options controlling hydrodynamics, artificial dissipation'
+ write(iwritein,"(/,a)") '# options controlling hydrodynamics, shock capturing'
  if (maxalpha==maxp .and. nalpha > 0) then
     call write_inopt(alpha,'alpha','MINIMUM shock viscosity parameter',iwritein)
     call write_inopt(alphamax,'alphamax','MAXIMUM shock viscosity parameter',iwritein)
@@ -207,7 +203,7 @@ subroutine write_infile(infile,logfile,evfile,dumpfile,iwritein,iprint)
     call write_inopt(alphau,'alphau','shock conductivity parameter',iwritein)
  endif
  if (mhd) then
-    call write_inopt(alphaB,'alphaB','art. resistivity parameter',iwritein)
+    call write_inopt(alphaB,'alphaB','shock resistivity parameter',iwritein)
     call write_inopt(psidecayfac,'psidecayfac','div B diffusion parameter',iwritein)
     call write_inopt(overcleanfac,'overcleanfac','factor to increase cleaning speed (decreases time step)',iwritein)
     call write_inopt(hdivbbmax_max,'hdivbbmax_max','max factor to decrease cleaning timestep propto B/(h|divB|)',iwritein)
@@ -270,12 +266,8 @@ subroutine write_infile(infile,logfile,evfile,dumpfile,iwritein,iprint)
  call write_options_forcing(iwritein)
 #endif
 
-#ifdef DUST
- call write_options_dust(iwritein)
-#ifdef DUSTGROWTH
- call write_options_growth(iwritein)
-#endif
-#endif
+ if (use_dust) call write_options_dust(iwritein)
+ if (use_dustgrowth) call write_options_growth(iwritein)
 
 #ifdef PHOTO
  call write_options_photoevap(iwritein)
@@ -286,8 +278,6 @@ subroutine write_infile(infile,logfile,evfile,dumpfile,iwritein,iprint)
  call write_options_inject(iwritein)
 #endif
  if (nucleation) call write_options_dust_formation(iwritein)
-
- write(iwritein,"(/,a)") '# options for injecting/removing particles'
  call write_inopt(rkill,'rkill','deactivate particles outside this radius (<0 is off)',iwritein)
 
  if (sink_radiation) then
@@ -340,12 +330,8 @@ subroutine read_infile(infile,logfile,evfile,dumpfile)
 #endif
  use externalforces,  only:read_options_externalforces
  use linklist,        only:read_inopts_link
-#ifdef DUST
  use dust,            only:read_options_dust
-#ifdef DUSTGROWTH
  use growth,          only:read_options_growth
-#endif
-#endif
 #ifdef GR
  use metric,          only:read_options_metric
 #endif
@@ -362,7 +348,8 @@ subroutine read_infile(infile,logfile,evfile,dumpfile)
  use part,            only:mhd,nptmass
  use cooling,         only:read_options_cooling
  use ptmass,          only:read_options_ptmass
- use ptmass_radiation,   only:read_options_ptmass_radiation,isink_radiation,alpha_rad,iget_tdust,iray_resolution
+ use ptmass_radiation,   only:read_options_ptmass_radiation,isink_radiation,&
+                              alpha_rad,iget_tdust,iray_resolution
  use radiation_utils,    only:kappa_cgs
  use radiation_implicit, only:tol_rad,itsmax_rad,cv_type
  use damping,         only:read_options_damping
@@ -567,13 +554,9 @@ subroutine read_infile(infile,logfile,evfile,dumpfile)
        if (.not.imatch) call read_options_forcing(name,valstring,imatch,igotallturb,ierr)
 #endif
        if (.not.imatch) call read_inopts_link(name,valstring,imatch,igotalllink,ierr)
-#ifdef DUST
        !--Extract if one-fluid dust is used from the fileid
-       if (.not.imatch) call read_options_dust(name,valstring,imatch,igotalldust,ierr)
-#ifdef DUSTGROWTH
-       if (.not.imatch) call read_options_growth(name,valstring,imatch,igotallgrowth,ierr)
-#endif
-#endif
+       if (.not.imatch .and. use_dust) call read_options_dust(name,valstring,imatch,igotalldust,ierr)
+       if (.not.imatch .and. use_dustgrowth) call read_options_growth(name,valstring,imatch,igotallgrowth,ierr)
 #ifdef GR
        if (.not.imatch) call read_options_metric(name,valstring,imatch,igotallgr,ierr)
 #endif

From 32f072666232ef0c7500f69c3596c0d61245c0f6 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 11:08:22 +1000
Subject: [PATCH 14/23] (setup) failures with DEBUG=yes fixed

---
 src/setup/setup_alfvenwave.f90 | 30 +++++++++++++++----------
 src/setup/setup_kh.f90         | 11 ++++++----
 src/setup/setup_mhdrotor.f90   |  9 +++++---
 src/setup/setup_mhdwave.f90    | 40 +++++++++++++++++++---------------
 4 files changed, 54 insertions(+), 36 deletions(-)

diff --git a/src/setup/setup_alfvenwave.f90 b/src/setup/setup_alfvenwave.f90
index 8a302ffa8..2c54c12c8 100644
--- a/src/setup/setup_alfvenwave.f90
+++ b/src/setup/setup_alfvenwave.f90
@@ -53,17 +53,20 @@ module setup
 !  setup for MHD wave tests
 !+
 !----------------------------------------------------------------
-subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
+subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
+                   polyk,gamma,hfact,time,fileprefix)
  use dim,          only:maxvxyzu
  use setup_params, only:rhozero,ihavesetupB
  use unifdis,      only:set_unifdis,rho_func
- use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
- use part,         only:Bxyz,mhd,periodic
+ use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,&
+                        dxbound,dybound,dzbound
+ use part,         only:Bxyz,mhd,periodic,igas
  use io,           only:master
  use prompting,    only:prompt
  use mpiutils,     only:bcast_mpi
  use physcon,      only:pi
- use geometry,     only:igeom_rotated,igeom_cartesian,set_rotation_angles,coord_transform
+ use geometry,     only:igeom_rotated,igeom_cartesian,&
+                        set_rotation_angles,coord_transform
  use timestep,     only:tmax,dtmax
  use mpidomain,    only:i_belong
  integer,           intent(in)    :: id
@@ -75,7 +78,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  real,              intent(out)   :: polyk,gamma
  real,              intent(in)    :: hfact
  real,              intent(inout) :: time
- character(len=20), intent(in)    :: fileprefix
+ character(len=*),  intent(in)    :: fileprefix
  real :: deltax,totmass
  integer :: i,ierr,igeom
  real :: przero,uuzero,Bvec(3),vvec(3),Bnew(3),Bzero(3),vzero(3)
@@ -102,9 +105,13 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  !
  setupfile = trim(fileprefix)//'.setup'
  call read_setupfile(setupfile,gamma,ierr)
- if (ierr /= 0 .and. id==master) then
-    call interactive_setup()
-    call write_setupfile(setupfile,gamma)
+ if (ierr /= 0) then
+    if (id==master) then
+       call interactive_setup()
+       call write_setupfile(setupfile,gamma)
+       print*,' Edit '//trim(setupfile)//' and rerun phantomsetup'
+    endif
+    stop
  endif
  gamma = 5./3.
 !
@@ -148,6 +155,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     Bzero  = (/1.,0.,0./)
     vzero  = 0.
     uuzero = przero/(gam1*rhozero)
+    vwave  = sqrt(dot_product(Bzero,Bzero)/rhozero) ! Alfven speed
  end select
 
  call prim_to_cons(rhozero,vzero,Bzero,uuzero,q0)
@@ -159,8 +167,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
             '   vwave = ',f6.3,',         period = ',f6.3,/)
 
  call print_amplitudes(rhozero,drho,vzero,dv,Bzero,dB,uuzero,du)
- print*,' rhozero = ',rhozero,'dv = ',dv,' dB = ',dB
- print*,drho,rhozero*dv,dB,du,du + dot_product(vzero,dv) + dot_product(Bzero,dB)/rhozero
 
  if (maxvxyzu < 4) then
     polyk = przero/rhozero**gamma
@@ -188,11 +194,11 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
                      deltax,hfact,npart,xyzh,periodic,mask=i_belong)
  endif
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart
- print*,'npart = ',npart,' particle mass = ',massoftype(1)
+ print*,'npart = ',npart,' particle mass = ',massoftype(igas)
 
 
  do i=1,npart
diff --git a/src/setup/setup_kh.f90 b/src/setup/setup_kh.f90
index fb8f156c9..66d0172d3 100644
--- a/src/setup/setup_kh.f90
+++ b/src/setup/setup_kh.f90
@@ -38,12 +38,14 @@ module setup
 !  setup for uniform particle distributions
 !+
 !----------------------------------------------------------------
-subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
+subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
+                   polyk,gamma,hfact,time,fileprefix)
  use setup_params, only:npart_total
  use io,           only:master
  use options,      only:nfulldump
  use unifdis,      only:set_unifdis,rho_func
- use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
+ use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,&
+                        dxbound,dybound,dzbound
  use mpiutils,     only:bcast_mpi
  use part,         only:igas,periodic
  use prompting,    only:prompt
@@ -69,6 +71,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
 !
  time  = 0.
  gamma = 5./3
+ polyk = 0.
  filename= trim(fileprefix)//'.in'
  inquire(file=filename,exist=iexist)
  if (.not. iexist) then
@@ -100,12 +103,12 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
                   rhofunc=density_func,dir=2,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
  print*,' npart = ',npart,npart_total
 
  totmass = dy2*dxbound*dzbound*rho2 + (dybound-dy2)*dxbound*dzbound*rho1
  massoftype(igas) = totmass/npart_total
- print*,' particle mass = ',massoftype(1)
+ print*,' particle mass = ',massoftype(igas)
 
  do i=1,npart
     vxyzu(1,i) = v1 + Rfunc(xyzh(2,i))*(v2 - v1)
diff --git a/src/setup/setup_mhdrotor.f90 b/src/setup/setup_mhdrotor.f90
index 4382a7791..d33fb7148 100644
--- a/src/setup/setup_mhdrotor.f90
+++ b/src/setup/setup_mhdrotor.f90
@@ -29,12 +29,14 @@ module setup
 !  setup for uniform particle distributions
 !+
 !----------------------------------------------------------------
-subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
+subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
+                   polyk,gamma,hfact,time,fileprefix)
  use dim,          only:maxp,maxvxyzu,mhd
  use setup_params, only:npart_total,ihavesetupB
  use io,           only:master
  use unifdis,      only:set_unifdis
- use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
+ use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,&
+                        dxbound,dybound,dzbound
  use mpiutils,     only:bcast_mpi
  use part,         only:igas,Bxyz,periodic
  use prompting,    only:prompt
@@ -58,6 +60,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
 !
  time = 0.
  gamma = 1.4
+ polyk = 0.
 !
 !--set particles
 !
@@ -103,7 +106,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
                   rcylmax=rdisk,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
  print*,' npart = ',npart,npart_total
 
  totvol = (dxbound*dybound - pi*rdisk**2)*dzbound
diff --git a/src/setup/setup_mhdwave.f90 b/src/setup/setup_mhdwave.f90
index 07885f802..7a948e402 100644
--- a/src/setup/setup_mhdwave.f90
+++ b/src/setup/setup_mhdwave.f90
@@ -6,7 +6,8 @@
 !--------------------------------------------------------------------------!
 module setup
 !
-! Setup for simple MHD wave propagation test as per section 5.1 of Iwasaki (2015)
+! Setup for simple MHD wave propagation test
+! as per section 5.1 of Iwasaki (2015)
 !
 ! :References: None
 !
@@ -23,8 +24,8 @@ module setup
  implicit none
  public :: setpart
  !--private module variables
- integer                      :: npartx
- real                         :: plasmabzero
+ integer :: npartx
+ real    :: plasmabzero
 
  private
 
@@ -32,12 +33,11 @@ module setup
 
 !----------------------------------------------------------------
 !+
-!
-!
-!
+!  setup particles in uniform box with velocity perturbation
 !+
 !----------------------------------------------------------------
-subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
+subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
+                   polyk,gamma,hfact,time,fileprefix)
  use setup_params, only:rhozero,ihavesetupB
  use unifdis,      only:set_unifdis
  use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
@@ -111,11 +111,15 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
        if (id==master) call write_setupfile(filename)
        call fatal('setup','failed to read in all the data from .setup.  Aborting')
     endif
- elseif (id==master) then
-    print "(a,/)",trim(filename)//' not found: using interactive setup'
-    call prompt(' Enter number of particles in x ',npartx,8,nint((maxp)**(1/3.)))
-    call prompt(' Enter the plasma beta in the blast (this will adjust the magnetic field strength) ',plasmabzero)
-    call write_setupfile(filename)
+ else
+    if (id==master) then
+       print "(a,/)",trim(filename)//' not found: using interactive setup'
+       call prompt(' Enter number of particles in x ',npartx,8,nint((maxp)**(1/3.)))
+       call prompt(' Enter the plasma beta in the blast (this will adjust the magnetic field strength) ',plasmabzero)
+       call write_setupfile(filename)
+       print*,' Edit '//trim(filename)//' and rerun phantomsetup'
+    endif
+    stop
  endif
  call bcast_mpi(npartx)
  deltax = dxbound/npartx
@@ -126,14 +130,14 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
                   hfact,npart,xyzh,periodic,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart
- print*,'npart = ',npart,' particle mass = ',massoftype(1)
+ print*,'npart = ',npart,' particle mass = ',massoftype(igas)
 
  Bxyz = 0.0
- hzero = hfact*(massoftype(1)/rhozero)**(1./3.)
+ hzero = hfact*(massoftype(igas)/rhozero)**(1./3.)
  do i=1,npart
     vxyzu(1,i) = 0.01*exp(-(xyzh(1,i)/(3.0*hzero))**2)
     vxyzu(2,i) = 0.
@@ -161,9 +165,11 @@ subroutine write_setupfile(filename)
  open(unit=iunit,file=filename,status='replace',form='formatted')
  write(iunit,"(a)") '# input file for MHD Blast Wave setup routine'
  write(iunit,"(/,a)") '# dimensions'
- call write_inopt(npartx,'npartx','number of particles in x-direction',iunit)
+ call write_inopt(npartx,'npartx',&
+                 'number of particles in x-direction',iunit)
  write(iunit,"(/,a)") '# magnetic field strength'
- call write_inopt(plasmabzero,'plasmaB','plasma beta in the initial blast',iunit)
+ call write_inopt(plasmabzero,'plasmaB',&
+                  'plasma beta in the initial blast',iunit)
  close(iunit)
 
 end subroutine write_setupfile

From f8cbec555eb3c1a14919bd68e578bcc930ceac5d Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 11:37:45 +1000
Subject: [PATCH 15/23] (setup_binary) setup failures with DEBUG=yes fixed

---
 src/main/checksetup.F90     | 4 ++--
 src/setup/set_star.f90      | 2 +-
 src/setup/setup_binary.f90  | 5 ++++-
 src/setup/setup_mhdsine.f90 | 8 ++++----
 4 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/main/checksetup.F90 b/src/main/checksetup.F90
index 8bab8e06c..ad8ec0a16 100644
--- a/src/main/checksetup.F90
+++ b/src/main/checksetup.F90
@@ -95,11 +95,11 @@ subroutine check_setup(nerror,nwarn,restart)
     nwarn = nwarn + 1
  endif
 #endif
- if (hfact < 1. .or. hfact /= hfact) then
+ if (hfact < 1. .or. isnan(hfact)) then
     print*,'ERROR: hfact = ',hfact,', should be >= 1'
     nerror = nerror + 1
  endif
- if (polyk < 0. .or. polyk /= polyk) then
+ if (polyk < 0. .or. isnan(polyk)) then
     print*,'ERROR: polyk = ',polyk,', should be >= 0'
     nerror = nerror + 1
  endif
diff --git a/src/setup/set_star.f90 b/src/setup/set_star.f90
index a500a9169..7e6b0a8fe 100644
--- a/src/setup/set_star.f90
+++ b/src/setup/set_star.f90
@@ -49,7 +49,7 @@ module setstar
  end type star_t
 
  public :: star_t
- public :: set_star,shift_star
+ public :: set_star,set_defaults_star,shift_star
  public :: write_options_star,read_options_star,set_star_interactive
  public :: ikepler,imesa,ibpwpoly,ipoly,iuniform,ifromfile,ievrard
  public :: need_polyk
diff --git a/src/setup/setup_binary.f90 b/src/setup/setup_binary.f90
index 7fd9a4087..d089c8b18 100644
--- a/src/setup/setup_binary.f90
+++ b/src/setup/setup_binary.f90
@@ -51,7 +51,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
  use options,        only:iexternalforce
  use externalforces, only:iext_corotate,omega_corotate
  use io,             only:master
- use setstar,        only:set_star,shift_star
+ use setstar,        only:set_star,set_defaults_star,shift_star
  use eos,            only:X_in,Z_in,ieos
  use setup_params,   only:rhozero,npart_total
  use mpidomain,      only:i_belong
@@ -90,6 +90,9 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
  vxyzu(:,:) = 0.
  nptmass = 0
  nstar = 2
+ do i=1,nstar
+    call set_defaults_star(star(i))
+ enddo
  relax = .true.
  corotate = .false.
  semi_major_axis = '10.'
diff --git a/src/setup/setup_mhdsine.f90 b/src/setup/setup_mhdsine.f90
index 6df41870f..1b82b39de 100644
--- a/src/setup/setup_mhdsine.f90
+++ b/src/setup/setup_mhdsine.f90
@@ -29,14 +29,13 @@ module setup
 !  Sets up Bx = sin(2*pi*x), zero magnetic and velocity field otherwise
 !
 !  The amplitude should decay as exp(-eta * 4 * pi^2 * t)
-!
 !+
 !----------------------------------------------------------------
 subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
  use setup_params, only:rhozero,ihavesetupB
  use unifdis,      only:set_unifdis
  use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
- use part,         only:Bxyz,mhd,periodic
+ use part,         only:Bxyz,mhd,periodic,igas
  use io,           only:master
  use physcon,      only:pi
  use prompting,    only:prompt
@@ -77,6 +76,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     gamma = 5./3.
     gam1 = gamma - 1.
     uuzero = przero/(gam1*rhozero)
+    polyk = 0.
  else
     gamma = 1.
     polyk = przero/rhozero
@@ -94,11 +94,11 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
                   hfact,npart,xyzh,periodic,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart
- print*,'npart = ',npart,' particle mass = ',massoftype(1)
+ print*,'npart = ',npart,' particle mass = ',massoftype(igas)
 
  do i=1,npart
     vxyzu(1,i) = 0.

From 570e53d47d9a86494ad8a5c134da1b5d65b855a7 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 12:52:23 +1000
Subject: [PATCH 16/23] (phantomsetup) allow test as a job name

---
 src/main/boundary.f90      | 1 -
 src/setup/phantomsetup.F90 | 3 ---
 2 files changed, 4 deletions(-)

diff --git a/src/main/boundary.f90 b/src/main/boundary.f90
index 5f8e31d70..349cec742 100644
--- a/src/main/boundary.f90
+++ b/src/main/boundary.f90
@@ -138,7 +138,6 @@ subroutine cross_boundary(isperiodic,xyz,ncross)
     endif
  endif
 
- return
 end subroutine cross_boundary
 
 !-----------------------------------------------------------------------
diff --git a/src/setup/phantomsetup.F90 b/src/setup/phantomsetup.F90
index 6ee16474c..cd67ca8b2 100644
--- a/src/setup/phantomsetup.F90
+++ b/src/setup/phantomsetup.F90
@@ -80,9 +80,6 @@ program phantomsetup
     print*,'       (these are assigned automatically)'
     print "(/,a)",' e.g. "phantomsetup mysim"'
     stop
- elseif (fileprefix=='test') then
-    print*,'Error: cannot use ''test'' as the job name, please rename your .setup file'
-    stop
  endif
  infile = trim(fileprefix)//'.in'
  inquire(file=trim(infile),exist=iexist)

From b80dd129a24d9958fe66d7febb0da477d365049b Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 12:53:30 +1000
Subject: [PATCH 17/23] (setup) setup failures with DEBUG=yes fixed; general
 tidy up of setup routines

---
 src/setup/set_unifdis.f90           | 30 +++++++++-
 src/setup/setup_collidingclouds.f90 | 34 ++++--------
 src/setup/setup_disc.f90            |  2 +-
 src/setup/setup_radiativebox.f90    | 48 +++++-----------
 src/setup/setup_sedov.f90           | 59 +++++++-------------
 src/setup/setup_turb.f90            | 24 +++-----
 src/setup/setup_unifdis.f90         | 85 +++++++++--------------------
 src/setup/setup_wavedamp.f90        |  3 +-
 8 files changed, 112 insertions(+), 173 deletions(-)

diff --git a/src/setup/set_unifdis.f90 b/src/setup/set_unifdis.f90
index fb986eb68..d327b6865 100644
--- a/src/setup/set_unifdis.f90
+++ b/src/setup/set_unifdis.f90
@@ -19,7 +19,7 @@ module unifdis
  use stretchmap, only:rho_func
  implicit none
  public :: set_unifdis, get_ny_nz_closepacked, get_xyzmin_xyzmax_exact
- public :: is_valid_lattice, is_closepacked
+ public :: is_valid_lattice, is_closepacked, latticetype
 
  ! following lines of code allow an optional mask= argument
  ! to setup only certain subsets of the particle domain (used for MPI)
@@ -29,6 +29,11 @@ logical function mask_prototype(ip)
   end function mask_prototype
  end interface
 
+ integer, parameter, public :: i_cubic       = 1, &
+                               i_closepacked = 2, &
+                               i_hexagonal   = 3, &
+                               i_random      = 4
+
  public :: mask_prototype, mask_true, rho_func
 
  private
@@ -718,6 +723,29 @@ pure logical function is_valid_lattice(latticetype)
 
 end function is_valid_lattice
 
+!-------------------------------------------------------------
+!+
+!  utility function to give correct lattice string
+!  given integer lattice choice
+!+
+!-------------------------------------------------------------
+function latticetype(ilattice)
+ integer, intent(in) :: ilattice
+ character(len=11) :: latticetype
+
+ select case(ilattice)
+ case(i_random)
+    latticetype = 'random'
+ case(i_hexagonal)
+    latticetype = 'hexagonal'
+ case(i_closepacked)
+    latticetype = 'closepacked'
+ case default
+    latticetype = 'cubic'
+ end select
+
+end function latticetype
+
 !---------------------------------------------------------------
 !+
 !  check that the latticetype is closepacked
diff --git a/src/setup/setup_collidingclouds.f90 b/src/setup/setup_collidingclouds.f90
index 7e80f1c68..de7014b43 100644
--- a/src/setup/setup_collidingclouds.f90
+++ b/src/setup/setup_collidingclouds.f90
@@ -53,7 +53,6 @@ module setup
  real               :: r_crit_setup,h_acc_setup,h_soft_sinksink_setup,rho_crit_cgs_setup
  real(kind=8)       :: udist,umass
  logical            :: input_plasmaB
- character(len=20)  :: dist_unit,mass_unit
  character(len= 1), parameter :: labelx(4) = (/'x','y','z','r'/)
 
 contains
@@ -83,6 +82,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use mpidomain,    only:i_belong
  use ptmass,       only:icreate_sinks,r_crit,h_acc,h_soft_sinksink,rho_crit_cgs
  use cooling,      only:Tfloor
+ use setunits,     only:dist_unit,mass_unit
  integer,           intent(in)    :: id
  integer,           intent(inout) :: npart
  integer,           intent(out)   :: npartoftype(:)
@@ -335,10 +335,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     stop ! MPI, stop on other threads, interactive on master
  endif
  !
- !--units
- !
- call set_units(dist=udist,mass=umass,G=1.d0)
- !
  !--general parameters
  !
  time        = 0.
@@ -818,6 +814,7 @@ end subroutine KIcoolingcurve
 !----------------------------------------------------------------
 subroutine write_setupfile(filename)
  use infile_utils, only: write_inopt
+ use setunits,     only: write_options_units
  character(len=*), intent(in) :: filename
  integer, parameter           :: iunit = 20
  integer                      :: i,j
@@ -826,11 +823,11 @@ subroutine write_setupfile(filename)
  print "(a)",' writing setup options file '//trim(filename)
  open(unit=iunit,file=filename,status='replace',form='formatted')
  write(iunit,"(a)") '# input file for converging flows-in-box setup routines'
- write(iunit,"(/,a)") '# units'
- call write_inopt(dist_unit,'dist_unit','distance unit (e.g. pc)',iunit)
- call write_inopt(mass_unit,'mass_unit','mass unit (e.g. solarm)',iunit)
+ call write_options_units(iunit)
+
  write(iunit,"(/,a)") '# resolution'
  call write_inopt(np,'np','actual number of particles in cloud 1',iunit)
+
  write(iunit,"(/,a)") '# options for box'
  call write_inopt(dynamic_bdy,'dynamic_bdy','use dynamic boundary conditions',iunit)
  if (.not. dynamic_bdy) then
@@ -839,6 +836,7 @@ subroutine write_setupfile(filename)
        call write_inopt(xmaxi(j),labelx(j)//'max',labelx(j)//' max',iunit)
     enddo
  endif
+
  write(iunit,"(/,a)") '# Number of clouds'
  call write_inopt(Ncloud,'Ncloud','number of clouds',iunit)
  do i = 1,Ncloud
@@ -866,6 +864,7 @@ subroutine write_setupfile(filename)
     write(label,'(a,I1)') 'rms_mach',i
     call write_inopt(rms_mach(i),trim(label),'RMS Mach number of cloud turbulence (<0 for a fraction of Epot)',iunit)
  enddo
+
  write(iunit,"(/,a)") '# additional properties'
  call write_inopt(density_contrast,'density_contrast','density contrast',iunit)
  call write_inopt(T_bkg,'Temperature_medium','Temperature of the background',iunit)
@@ -880,6 +879,7 @@ subroutine write_setupfile(filename)
        call write_inopt(angB(j),trim(label),labelx(j)//'-angle of the magnetic field',iunit)
     enddo
  endif
+
  write(iunit,"(/,a)") '# Sink properties (values in .in file, if present, will take precedence)'
  call write_inopt(icreate_sinks_setup,'icreate_sinks','1: create sinks.  0: do not create sinks',iunit)
  if (icreate_sinks_setup==1) then
@@ -900,7 +900,7 @@ end subroutine write_setupfile
 subroutine read_setupfile(filename,ierr)
  use infile_utils, only: open_db_from_file,inopts,read_inopt,close_db
  use io,           only: error
- use units,        only: select_unit
+ use setunits,     only: read_options_and_set_units
  character(len=*), intent(in)  :: filename
  integer,          intent(out) :: ierr
  integer, parameter            :: iunit = 21
@@ -910,8 +910,8 @@ subroutine read_setupfile(filename,ierr)
 
  print "(a)",' reading setup options from '//trim(filename)
  call open_db_from_file(db,filename,iunit,ierr)
- call read_inopt(mass_unit,'mass_unit',db,ierr)
- call read_inopt(dist_unit,'dist_unit',db,ierr)
+ call read_options_and_set_units(db,nerr)
+
  call read_inopt(np,'np',db,ierr)
  call read_inopt(dynamic_bdy,'dynamic_bdy',db,ierr)
  if (.not. dynamic_bdy) then
@@ -973,18 +973,6 @@ subroutine read_setupfile(filename,ierr)
  endif
  call close_db(db)
 
- ! parse units
- call select_unit(mass_unit,umass,nerr)
- if (nerr /= 0) then
-    call error('setup_convergingflows','mass unit not recognised')
-    ierr = ierr + 1
- endif
- call select_unit(dist_unit,udist,nerr)
- if (nerr /= 0) then
-    call error('setup_convergingflows','length unit not recognised')
-    ierr = ierr + 1
- endif
-
  if (ierr > 0) then
     print "(1x,a,i2,a)",'Setup_convergingflows: ',nerr,' error(s) during read of setup file.  Re-writing.'
  endif
diff --git a/src/setup/setup_disc.f90 b/src/setup/setup_disc.f90
index 497e57e2d..574d37219 100644
--- a/src/setup/setup_disc.f90
+++ b/src/setup/setup_disc.f90
@@ -1009,6 +1009,7 @@ subroutine calculate_disc_mass()
  real :: Q_mintmp,disc_mtmp,annulus_mtmp
 
  totmass_gas  = 0.
+ disc_mdust = 0.
 
  do i=1,maxdiscs
     if (iuse_disc(i)) then
@@ -1346,7 +1347,6 @@ subroutine setup_discs(id,fileprefix,hfact,gamma,npart,polyk,&
 
              !--dust disc(s)
              do j=1,ndustlarge
-
                 npindustdisc = int(disc_mdust(i,j)/sum(disc_mdust(:,j))*np_dust(j))
                 itype = idust + j - 1
 
diff --git a/src/setup/setup_radiativebox.f90 b/src/setup/setup_radiativebox.f90
index 375f3f4b0..4e4c807be 100644
--- a/src/setup/setup_radiativebox.f90
+++ b/src/setup/setup_radiativebox.f90
@@ -31,13 +31,12 @@ module setup
 !   unifdis, units
 !
  use setup_params, only:rhozero
+ use dim,          only:gr
  implicit none
  public :: setpart
 
  integer :: npartx,ilattice,iradtype
  real    :: cs0,xmini,xmaxi,ymini,ymaxi,zmini,zmaxi
- character(len=20) :: dist_unit,mass_unit
- real(kind=8) :: udist,umass
 
  private
 
@@ -53,7 +52,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use io,            only:master,fatal,warning
  use unifdis,       only:set_unifdis
  use boundary,      only:xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound,set_boundary
-
  use physcon,       only:pi,mass_proton_cgs,kboltz,years,pc,solarm,c,Rg,steboltz
  use set_dust,      only:set_dustfrac
  use units,         only:set_units,unit_ergg,unit_velocity,unit_opacity,get_c_code,get_radconst_code
@@ -83,6 +81,8 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  real :: a,c_code,cv1,kappa_code,pmassi,Tref,xi0
  real :: rhoi,h0,rho0
 
+ call setup_setdefaults(id,polyk,gamma,xmin,xmax,ymin,ymax,zmin,zmax,npartx,cs0)
+
  filename=trim(fileprefix)//'.setup'
  inquire(file=filename,exist=iexist)
  if (iexist) then
@@ -93,18 +93,14 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
        stop
     endif
  elseif (id==master) then
-    call setup_setdefaults(&
-       id,polyk,gamma,xmin,xmax,ymin,ymax,zmin,zmax,mass_unit,dist_unit,&
-       npartx,cs0)
     call write_setupfile(filename,gamma)
     stop 'rerun phantomsetup after editing .setup file'
  else
     stop
  endif
  !
- ! set units and boundaries
+ ! set boundaries
  !
- call set_units(dist=udist,mass=umass,G=1.d0)
  call set_boundary(xmini,xmaxi,ymini,ymaxi,zmini,zmaxi)
  !
  ! setup particles
@@ -128,12 +124,12 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  end select
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
  print*,' npart = ',npart,npart_total
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart_total
- if (id==master) print*,' particle mass = ',massoftype(1)
+ if (id==master) print*,' particle mass = ',massoftype(igas)
  if (id==master) print*,' initial sound speed = ',cs0,' pressure = ',cs0**2/gamma
 
  vxyzu(1:3,:) = 0.
@@ -187,6 +183,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  case default
     call fatal('setup_radiativebox', 'radiation setup is not available')
  end select
+
 end subroutine setpart
 
 !------------------------------------------------------------------------
@@ -194,17 +191,16 @@ end subroutine setpart
 ! interactive setup
 !
 !------------------------------------------------------------------------
-subroutine setup_setdefaults(&
-   id,polyk,gamma,xmin,xmax,ymin,ymax,zmin,zmax,mass_unit,dist_unit,&
-   npartx,cs0)
+subroutine setup_setdefaults(id,polyk,gamma,xmin,xmax,ymin,ymax,zmin,zmax,&
+                             npartx,cs0)
  use io,        only:master
  use mpiutils,  only:bcast_mpi
  use options,   only:exchange_radiation_energy,limit_radiation_flux
+ use setunits,  only:mass_unit,dist_unit
  integer, intent(in)  :: id
  integer, intent(out) :: npartx
  real,    intent(in)  :: xmin,xmax,ymin,ymax,zmin,zmax
  real,    intent(out) :: polyk,gamma,cs0
- character(len=*),intent(out) :: mass_unit,dist_unit
 
  mass_unit = 'solarm'
  dist_unit = 'au'
@@ -233,6 +229,7 @@ subroutine setup_setdefaults(&
     call bcast_mpi(ilattice)
     call bcast_mpi(iradtype)
  endif
+
 end subroutine setup_setdefaults
 
 !------------------------------------------------------------------------
@@ -243,6 +240,7 @@ end subroutine setup_setdefaults
 subroutine write_setupfile(filename,gamma)
  use infile_utils, only:write_inopt
  use options,      only:exchange_radiation_energy,limit_radiation_flux
+ use setunits,     only:write_options_units
  character(len=*), intent(in) :: filename
  integer :: iunit
  real, intent(in) :: gamma
@@ -251,9 +249,7 @@ subroutine write_setupfile(filename,gamma)
  open(newunit=iunit,file=filename,status='replace',form='formatted')
  write(iunit,"(a)") '# input file for uniform setup routine'
 
- write(iunit,"(/,a)") '# units'
- call write_inopt(dist_unit,'dist_unit','distance unit (e.g. au)',iunit)
- call write_inopt(mass_unit,'mass_unit','mass unit (e.g. solarm)',iunit)
+ call write_options_units(iunit)
  !
  ! boundaries
  !
@@ -290,7 +286,7 @@ end subroutine write_setupfile
 !------------------------------------------------------------------------
 subroutine read_setupfile(filename,gamma,ierr)
  use infile_utils, only:open_db_from_file,inopts,read_inopt,close_db
- use units,        only:select_unit
+ use setunits,     only:read_options_and_set_units
  use io,           only:error
  use options,      only:exchange_radiation_energy,limit_radiation_flux
  character(len=*), intent(in)  :: filename
@@ -307,8 +303,7 @@ subroutine read_setupfile(filename,gamma,ierr)
  !
  ! units
  !
- call read_inopt(mass_unit,'mass_unit',db,errcount=nerr)
- call read_inopt(dist_unit,'dist_unit',db,errcount=nerr)
+ call read_options_and_set_units(db,nerr,gr)
  !
  ! boundaries
  !
@@ -331,19 +326,6 @@ subroutine read_setupfile(filename,gamma,ierr)
  call read_inopt(limit_radiation_flux,'flux_limiter',db,errcount=nerr)
 
  call close_db(db)
- !
- ! parse units
- !
- call select_unit(mass_unit,umass,nerr)
- if (nerr /= 0) then
-    call error('setup_unifdis','mass unit not recognised')
-    ierr = ierr + 1
- endif
- call select_unit(dist_unit,udist,nerr)
- if (nerr /= 0) then
-    call error('setup_unifdis','length unit not recognised')
-    ierr = ierr + 1
- endif
 
  if (nerr > 0) then
     print "(1x,i2,a)",nerr,' error(s) during read of setup file: re-writing...'
diff --git a/src/setup/setup_sedov.f90 b/src/setup/setup_sedov.f90
index 8b8ffb4ad..330345757 100644
--- a/src/setup/setup_sedov.f90
+++ b/src/setup/setup_sedov.f90
@@ -26,10 +26,8 @@ module setup
 
  private
  !--private module variables
- integer                      :: npartx
+ integer                      :: npartx,ilattice
  logical                      :: shuffle_parts
- character(len=20)            :: lattice
-
 
 contains
 
@@ -40,13 +38,12 @@ module setup
 !----------------------------------------------------------------
 subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact_out,time,fileprefix)
  use setup_params, only:rhozero
- use unifdis,      only:set_unifdis
+ use unifdis,      only:set_unifdis,latticetype,i_random,i_closepacked
  use io,           only:iprint,master,fatal
  use boundary,     only:xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
  use physcon,      only:pi
  use timestep,     only:tmax,dtmax
  use options,      only:alphau
- use prompting,    only:prompt
  use kernel,       only:wkern,cnormk,radkern2,hfact_default
  use part,         only:hfact,igas,periodic,set_particle_type
  use mpiutils,     only:bcast_mpi,reduceall_mpi
@@ -63,7 +60,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact_
  real,              intent(out)   :: vxyzu(:,:)
  real                             :: deltax,totmass,toten
  real                             :: enblast,gam1,uui,hsmooth,q2,r2
- integer                          :: i,maxp,maxvxyzu,ierr,ilattice
+ integer                          :: i,maxp,maxvxyzu,ierr
  character(len=100)               :: filename
  logical                          :: iexist
 !
@@ -78,6 +75,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact_
  maxp     = size(xyzh(1,:))
  maxvxyzu = size(vxyzu(:,1))
  npartx   = 50
+ ilattice = i_closepacked
 
  ! Read values from file if it exists, else prompt user for answers
  filename=trim(fileprefix)//'.setup'
@@ -90,26 +88,10 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact_
        call fatal('setup','failed to read in all the data from .setup.  Aborting')
     endif
  elseif (id==master) then
-    print "(a,/)",trim(filename)//' not found: using interactive setup'
-    call prompt(' Enter number of particles in x ',npartx,8,nint((maxp)**(1/3.)))
-
-    lattice  = 'cubic'
-    ilattice = 2
-    call prompt('Enter the type of particle lattice (1=random,2=cubic,3=closepacked,4=hexagonal)',ilattice,0,4)
-    if (ilattice==1) then
-       lattice = 'random'
-       shuffle_parts = .false.
-    elseif (ilattice==3) then
-       lattice = 'closepacked'
-    elseif (ilattice==4) then
-       lattice = 'hexagonal'
-    endif
-
-    shuffle_parts = .false.
-    if (ilattice==1) shuffle_parts = .true.
-    call prompt('Relax particles by shuffling?',shuffle_parts)
-
     call write_setupfile(filename)
+    stop 'rerun phantomsetup after editing .setup file'
+ else
+    stop
  endif
  call bcast_mpi(npartx)
  deltax = dxbound/npartx
@@ -126,7 +108,8 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact_
  gamma   = 5./3.
  gam1    = gamma - 1.
 
- call set_unifdis(trim(lattice),id,master,xmin,xmax,ymin,ymax,zmin,zmax,deltax,hfact,npart,xyzh,periodic,mask=i_belong)
+ call set_unifdis(latticetype(ilattice),id,master,xmin,xmax,ymin,ymax,zmin,zmax,&
+                  deltax,hfact,npart,xyzh,periodic,mask=i_belong)
 
  npartoftype(:) = 0
  npartoftype(igas) = npart
@@ -139,7 +122,8 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact_
     call set_particle_type(i,igas)
  enddo
  if (shuffle_parts) then
-    call shuffleparticles(iprint,npart,xyzh,massoftype(igas),duniform=rhozero,is_setup=.true.,prefix=trim(fileprefix))
+    call shuffleparticles(iprint,npart,xyzh,massoftype(igas),duniform=rhozero,&
+         is_setup=.true.,prefix=trim(fileprefix))
  endif
 
  toten = 0.
@@ -187,7 +171,7 @@ subroutine write_setupfile(filename)
  write(iunit,"(a)") '# input file for Sedov Blast Wave setup routine'
  write(iunit,"(/,a)") '# particle resolution & placement'
  call write_inopt(npartx,'npartx','number of particles in x-direction',iunit)
- call write_inopt(lattice,'lattice','particle lattice (random,cubic,closepacked,hcp,hexagonal)',iunit)
+ call write_inopt(ilattice,'lattice','particle lattice (1=cubic,2=closepacked,3=hcp,4=random)',iunit)
  call write_inopt(shuffle_parts,'shuffle_parts','relax particles by shuffling',iunit)
 
  close(iunit)
@@ -200,26 +184,25 @@ end subroutine write_setupfile
 !----------------------------------------------------------------
 subroutine read_setupfile(filename,ierr)
  use infile_utils, only: open_db_from_file,inopts,read_inopt,close_db
- use unifdis,      only: is_valid_lattice
  use io,           only: error
- use units,        only: select_unit
  character(len=*), intent(in)  :: filename
  integer,          intent(out) :: ierr
  integer, parameter            :: iunit = 21
  type(inopts), allocatable     :: db(:)
+ integer :: nerr
 
+ nerr = 0
  print "(a)",' reading setup options from '//trim(filename)
  call open_db_from_file(db,filename,iunit,ierr)
- call read_inopt(npartx,'npartx',db,ierr)
- call read_inopt(lattice,'lattice',db,ierr)
- if (ierr/=0 .or. .not. is_valid_lattice(trim(lattice))) then
-    print*, ' invalid lattice.  Setting to cubic.'
-    lattice = 'cubic'
+ call read_inopt(npartx,'npartx',db,errcount=nerr)
+ call read_inopt(ilattice,'lattice',db,ierr,min=1,max=4,errcount=nerr)
+ call read_inopt(shuffle_parts,'shuffle_parts',db,errcount=nerr)
+ if (nerr > 0) then
+    print "(1x,i2,a)",nerr,' error(s) during read of setup file: re-writing...'
+    ierr = nerr
  endif
- call read_inopt(shuffle_parts,'shuffle_parts',db,ierr)
-
  call close_db(db)
 
 end subroutine read_setupfile
-!----------------------------------------------------------------
+
 end module setup
diff --git a/src/setup/setup_turb.f90 b/src/setup/setup_turb.f90
index d8f898cb3..bbc8626da 100644
--- a/src/setup/setup_turb.f90
+++ b/src/setup/setup_turb.f90
@@ -41,10 +41,10 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use options,      only:use_dustfrac,nfulldump,beta
  use setup_params, only:rhozero,npart_total,ihavesetupB
  use io,           only:master
- use unifdis,      only:set_unifdis
+ use unifdis,      only:set_unifdis,latticetype
  use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
  use mpiutils,     only:bcast_mpi
- use part,         only:Bxyz,mhd,dustfrac,grainsize,graindens,ndusttypes,ndustsmall
+ use part,         only:Bxyz,mhd,dustfrac,grainsize,graindens,ndusttypes,ndustsmall,igas
  use physcon,      only:pi,solarm,pc,km
  use units,        only:set_units,udist,umass
  use prompting,    only:prompt
@@ -63,7 +63,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  real,              intent(inout) :: time
  character(len=20), intent(in)    :: fileprefix
  character(len=26)                :: filename
- integer :: ipart,i
+ integer :: i
  logical :: iexist
  real :: totmass,deltax
  real :: Bz_0
@@ -185,24 +185,16 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  npart = 0
  npart_total = 0
 
-
- select case(ilattice)
- case(2)
-    call set_unifdis('closepacked',id,master,xmin,xmax,ymin,ymax,zmin,zmax,deltax,hfact,npart,&
-                     xyzh,periodic,nptot=npart_total,mask=i_belong)
- case default
-    if (ilattice==1) print*,' error: chosen lattice not available, using cubic'
-    call set_unifdis('cubic',id,master,xmin,xmax,ymin,ymax,zmin,zmax,deltax,hfact,npart,&
-                     xyzh,periodic,nptot=npart_total,mask=i_belong)
- end select
+ call set_unifdis(latticetype(ilattice),id,master,xmin,xmax,ymin,ymax,zmin,zmax,&
+                  deltax,hfact,npart,xyzh,periodic,nptot=npart_total,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
- print *, ' npart = ',ipart,npart,npart_total
+ npartoftype(igas) = npart
+ print *, ' npart = ',npart,npart_total
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart_total
- print *, ' particle mass = ',massoftype(1)
+ print *, ' particle mass = ',massoftype(igas)
 
  do i=1,npart
     vxyzu(1:3,i) = 0.
diff --git a/src/setup/setup_unifdis.f90 b/src/setup/setup_unifdis.f90
index 0db04670e..680221812 100644
--- a/src/setup/setup_unifdis.f90
+++ b/src/setup/setup_unifdis.f90
@@ -32,7 +32,7 @@ module setup
 !   io, mpidomain, mpiutils, options, part, physcon, prompting, set_dust,
 !   setup_params, timestep, unifdis, units
 !
- use dim,          only:use_dust,mhd
+ use dim,          only:use_dust,mhd,gr
  use options,      only:use_dustfrac
  use setup_params, only:rhozero
  implicit none
@@ -40,8 +40,6 @@ module setup
 
  integer           :: npartx,ilattice
  real              :: cs0,xmini,xmaxi,ymini,ymaxi,zmini,zmaxi,Bzero
- character(len=20) :: dist_unit,mass_unit
- real(kind=8)      :: udist,umass
 
  !--change default defaults to reproduce the test from Section 5.6.7 of Price+(2018)
  logical :: BalsaraKim = .false.
@@ -59,15 +57,16 @@ module setup
 !+
 !----------------------------------------------------------------
 subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
- use dim,          only:maxvxyzu,h2chemistry,gr
+ use dim,          only:maxvxyzu,h2chemistry
  use setup_params, only:npart_total,ihavesetupB
  use io,           only:master
- use unifdis,      only:set_unifdis
+ use unifdis,      only:set_unifdis,latticetype
  use boundary,     only:xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound,set_boundary
  use part,         only:Bxyz,periodic,abundance,iHI,dustfrac,ndustsmall,ndusttypes,grainsize,graindens
  use physcon,      only:pi,mass_proton_cgs,kboltz,years,pc,solarm,micron
  use set_dust,     only:set_dustfrac
- use units,        only:set_units,unit_density
+ use setunits,     only:dist_unit,mass_unit
+ use units,        only:unit_density,udist
  use mpidomain,    only:i_belong
  use eos,          only:gmw
  use options,      only:icooling,alpha,alphau
@@ -122,10 +121,6 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  if (use_dust) then
     use_dustfrac = .true.
     dust_to_gas  = 0.01
-    ndustsmall   = 1
-    ndusttypes   = 1
-    grainsize(1) = 1.*micron/udist
-    graindens(1) = 3./unit_density
  endif
  if (BalsaraKim) then
     ! there is a typo in Price+ (2018) in stating the physical density;
@@ -185,13 +180,17 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     stop
  endif
  !
- ! set units and boundaries
+ ! set dust grain sizes
  !
- if (gr) then
-    call set_units(mass=umass,c=1.d0,G=1.d0)
- else
-    call set_units(dist=udist,mass=umass,G=1.d0)
+ if (use_dust) then
+    ndustsmall   = 1
+    ndusttypes   = 1
+    grainsize(1) = 1.*micron/udist
+    graindens(1) = 3./unit_density
  endif
+ !
+ ! set boundaries
+ !
  call set_boundary(xmini,xmaxi,ymini,ymaxi,zmini,zmaxi)
  !
  ! setup particles
@@ -200,23 +199,16 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  npart = 0
  npart_total = 0
 
- select case(ilattice)
- case(2)
-    call set_unifdis('closepacked',id,master,xmin,xmax,ymin,ymax,zmin,zmax,deltax,hfact,&
-                     npart,xyzh,periodic,nptot=npart_total,mask=i_belong)
- case default
-    if (ilattice /= 1) print*,' error: chosen lattice not available, using cubic'
-    call set_unifdis('cubic',id,master,xmin,xmax,ymin,ymax,zmin,zmax,deltax,hfact,npart,xyzh,&
-                     periodic,nptot=npart_total,mask=i_belong)
- end select
+ call set_unifdis(latticetype(ilattice),id,master,xmin,xmax,ymin,ymax,zmin,zmax,&
+                  deltax,hfact,npart,xyzh,periodic,nptot=npart_total,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
+ npartoftype(igas) = npart
  print*,' npart = ',npart,npart_total
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart_total
- if (id==master) print*,' particle mass = ',massoftype(1)
+ if (id==master) print*,' particle mass = ',massoftype(igas)
  if (id==master) print*,' initial sound speed = ',cs0,' pressure = ',cs0**2/gamma
 
  if (maxvxyzu < 4 .or. gamma <= 1.) then
@@ -249,6 +241,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     enddo
     ihavesetupB = .true.
  endif
+
 end subroutine setpart
 
 !------------------------------------------------------------------------
@@ -261,24 +254,12 @@ subroutine setup_interactive(id,polyk)
  use mpiutils,  only:bcast_mpi
  use dim,       only:maxp,maxvxyzu
  use prompting, only:prompt
- use units,     only:select_unit
+ use setunits,  only:set_units_interactive
  integer, intent(in)  :: id
  real,    intent(out) :: polyk
- integer              :: ierr
 
  if (id==master) then
-    ierr = 1
-    do while (ierr /= 0)
-       call prompt('Enter mass unit (e.g. solarm,jupiterm,earthm)',mass_unit)
-       call select_unit(mass_unit,umass,ierr)
-       if (ierr /= 0) print "(a)",' ERROR: mass unit not recognised'
-    enddo
-    ierr = 1
-    do while (ierr /= 0)
-       call prompt('Enter distance unit (e.g. au,pc,kpc,0.1pc)',dist_unit)
-       call select_unit(dist_unit,udist,ierr)
-       if (ierr /= 0) print "(a)",' ERROR: length unit not recognised'
-    enddo
+    call set_units_interactive(gr)
 
     call prompt('enter xmin boundary',xmini)
     call prompt('enter xmax boundary',xmaxi,xmini)
@@ -336,6 +317,7 @@ end subroutine setup_interactive
 !------------------------------------------------------------------------
 subroutine write_setupfile(filename)
  use infile_utils, only:write_inopt
+ use setunits,     only:write_options_units
  character(len=*), intent(in) :: filename
  integer :: iunit
 
@@ -343,9 +325,7 @@ subroutine write_setupfile(filename)
  open(newunit=iunit,file=filename,status='replace',form='formatted')
  write(iunit,"(a)") '# input file for uniform setup routine'
 
- write(iunit,"(/,a)") '# units'
- call write_inopt(dist_unit,'dist_unit','distance unit (e.g. au)',iunit)
- call write_inopt(mass_unit,'mass_unit','mass unit (e.g. solarm)',iunit)
+ call write_options_units(iunit)
  !
  ! boundaries
  !
@@ -381,8 +361,7 @@ end subroutine write_setupfile
 !------------------------------------------------------------------------
 subroutine read_setupfile(filename,ierr)
  use infile_utils, only:open_db_from_file,inopts,read_inopt,close_db
- use units,        only:select_unit
- use io,           only:error
+ use setunits,     only:read_options_and_set_units
  character(len=*), intent(in)  :: filename
  integer,          intent(out) :: ierr
  integer, parameter :: iunit = 21
@@ -396,8 +375,7 @@ subroutine read_setupfile(filename,ierr)
  !
  ! units
  !
- call read_inopt(mass_unit,'mass_unit',db,errcount=nerr)
- call read_inopt(dist_unit,'dist_unit',db,errcount=nerr)
+ call read_options_and_set_units(db,nerr,gr)
  !
  ! boundaries
  !
@@ -421,19 +399,6 @@ subroutine read_setupfile(filename,ierr)
  endif
  call read_inopt(ilattice,'ilattice',db,min=1,max=2,errcount=nerr)
  call close_db(db)
- !
- ! parse units
- !
- call select_unit(mass_unit,umass,nerr)
- if (nerr /= 0) then
-    call error('setup_unifdis','mass unit not recognised')
-    ierr = ierr + 1
- endif
- call select_unit(dist_unit,udist,nerr)
- if (nerr /= 0) then
-    call error('setup_unifdis','length unit not recognised')
-    ierr = ierr + 1
- endif
 
  if (nerr > 0) then
     print "(1x,i2,a)",nerr,' error(s) during read of setup file: re-writing...'
diff --git a/src/setup/setup_wavedamp.f90 b/src/setup/setup_wavedamp.f90
index 08320991d..8464bb638 100644
--- a/src/setup/setup_wavedamp.f90
+++ b/src/setup/setup_wavedamp.f90
@@ -109,6 +109,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use_ohm  = .false.
  use_hall = .false.
  use_ambi = .false.
+ ierr = 0
  !
  !--Prompt the user for relevant input to create .setup if file does not already exist
  !
@@ -223,7 +224,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  !--Convert to real values
  !
  if (realvals) then
-    !--matches dimensions of spereinbox
+    !--matches dimensions of sphereinbox
     udist = 1.d16
     umass = solarm
     call set_units(dist=udist,mass=umass,G=1.d0)

From 0aeb6aad30bdbd32e03847e398b22f6aaad5ac07 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 13:01:42 +1000
Subject: [PATCH 18/23] (hierarchical) seg fault/failure with DEBUG=yes fixed

---
 src/setup/set_hierarchical_utils.f90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/setup/set_hierarchical_utils.f90 b/src/setup/set_hierarchical_utils.f90
index 64b3240e0..699b72925 100644
--- a/src/setup/set_hierarchical_utils.f90
+++ b/src/setup/set_hierarchical_utils.f90
@@ -126,7 +126,7 @@ pure recursive subroutine recursive_splitting(sink_num, sink_list, split_list, s
  character(len=10) :: longests(max_hier_levels), new_splits(max_hier_levels)
  character(len=10) :: new_sink_list(max_hier_levels), longest_cut, sink_list_temp(max_hier_levels)
 
- sink_list_temp = sink_list
+ sink_list_temp(:) = sink_list(:)
 
  !print *, 'sink to generate: ', sink_list_temp
 
@@ -172,7 +172,7 @@ pure recursive subroutine recursive_splitting(sink_num, sink_list, split_list, s
     !print *, 'up to now splits are ', split_list
 
     ! Add new splits to split_list
-    do i=splits+1, splits+count
+    do i=splits+1, min(splits+count,size(split_list))
        split_list(i) = new_splits(i-splits)
     enddo
     splits = splits + count
@@ -197,7 +197,7 @@ pure recursive subroutine recursive_splitting(sink_num, sink_list, split_list, s
     !print *, split_list(:splits)
     !print *, splits
 
-    call recursive_splitting(count, new_sink_list(:count), split_list(:splits), splits)
+    call recursive_splitting(count, new_sink_list(:), split_list(:), splits)
 
  endif
 end subroutine recursive_splitting

From fb89f0e307aec4e91d9bf50ae3d9c0f29fa650d9 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 14:38:42 +1000
Subject: [PATCH 19/23] (setup) more failures with DEBUG=yes fixed; remove
 bcast_mpi as handled by write_setupfile followed by read_setupfile on all MPI
 threads

---
 src/main/checksetup.F90     |  3 ++-
 src/setup/set_units.f90     |  4 +--
 src/setup/setup_unifdis.f90 | 52 ++++++++++++-------------------------
 3 files changed, 21 insertions(+), 38 deletions(-)

diff --git a/src/main/checksetup.F90 b/src/main/checksetup.F90
index ad8ec0a16..71daa6caa 100644
--- a/src/main/checksetup.F90
+++ b/src/main/checksetup.F90
@@ -864,7 +864,8 @@ subroutine check_for_identical_positions(npart,xyzh,nbad)
  itypej = igas
  !$omp parallel do default(none) &
  !$omp shared(npart,xyzh,index,maxphase,maxp,iphase) &
- !$omp private(i,j,dx,dx2,itypei,itypej) &
+ !$omp firstprivate(itypei,itypej) &
+ !$omp private(i,j,dx,dx2) &
  !$omp reduction(+:nbad)
  do i=1,npart
     if (.not.isdead_or_accreted(xyzh(4,index(i)))) then
diff --git a/src/setup/set_units.f90 b/src/setup/set_units.f90
index a1cf40960..d622cd975 100644
--- a/src/setup/set_units.f90
+++ b/src/setup/set_units.f90
@@ -81,8 +81,8 @@ subroutine write_options_units(iunit,gr)
 
  ! units
  write(iunit,"(/,a)") '# units'
- call write_inopt(mass_unit,'mass_unit','mass unit (e.g. solarm)',iunit)
- if (nogr) call write_inopt(dist_unit,'dist_unit','distance unit (e.g. au)',iunit)
+ call write_inopt(mass_unit,'mass_unit','mass unit (e.g. solarm,jupiterm,1e6*solarm)',iunit)
+ if (nogr) call write_inopt(dist_unit,'dist_unit','distance unit (e.g. au,pc,kpc,0.1pc)',iunit)
 
 end subroutine write_options_units
 
diff --git a/src/setup/setup_unifdis.f90 b/src/setup/setup_unifdis.f90
index 680221812..1c372e851 100644
--- a/src/setup/setup_unifdis.f90
+++ b/src/setup/setup_unifdis.f90
@@ -62,7 +62,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use io,           only:master
  use unifdis,      only:set_unifdis,latticetype
  use boundary,     only:xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound,set_boundary
- use part,         only:Bxyz,periodic,abundance,iHI,dustfrac,ndustsmall,ndusttypes,grainsize,graindens
+ use part,         only:Bxyz,periodic,abundance,igas,iHI,dustfrac,ndustsmall,ndusttypes,grainsize,graindens
  use physcon,      only:pi,mass_proton_cgs,kboltz,years,pc,solarm,micron
  use set_dust,     only:set_dustfrac
  use setunits,     only:dist_unit,mass_unit
@@ -173,7 +173,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
        stop
     endif
  elseif (id==master) then
-    call setup_interactive(id,polyk)
+    call setup_interactive
     call write_setupfile(filename)
     stop 'rerun phantomsetup after editing .setup file'
  else
@@ -249,65 +249,47 @@ end subroutine setpart
 ! interactive setup
 !
 !------------------------------------------------------------------------
-subroutine setup_interactive(id,polyk)
+subroutine setup_interactive()
  use io,        only:master
- use mpiutils,  only:bcast_mpi
  use dim,       only:maxp,maxvxyzu
  use prompting, only:prompt
  use setunits,  only:set_units_interactive
- integer, intent(in)  :: id
- real,    intent(out) :: polyk
 
- if (id==master) then
-    call set_units_interactive(gr)
+ call set_units_interactive(gr)
 
-    call prompt('enter xmin boundary',xmini)
-    call prompt('enter xmax boundary',xmaxi,xmini)
-    call prompt('enter ymin boundary',ymini)
-    call prompt('enter ymax boundary',ymaxi,ymini)
-    call prompt('enter zmin boundary',zmini)
-    call prompt('enter zmax boundary',zmaxi,zmini)
- endif
+ call prompt('enter xmin boundary',xmini)
+ call prompt('enter xmax boundary',xmaxi,xmini)
+ call prompt('enter ymin boundary',ymini)
+ call prompt('enter ymax boundary',ymaxi,ymini)
+ call prompt('enter zmin boundary',zmini)
+ call prompt('enter zmax boundary',zmaxi,zmini)
  !
  ! number of particles
  !
- if (id==master) then
-    print*,' uniform setup... (max = ',nint((maxp)**(1/3.)),')'
-    call prompt('enter number of particles in x direction ',npartx,1)
- endif
- call bcast_mpi(npartx)
+ print*,' uniform setup... (max = ',nint((maxp)**(1/3.)),')'
+ call prompt('enter number of particles in x direction ',npartx,1)
  !
  ! mean density
  !
- if (id==master) call prompt(' enter density (gives particle mass)',rhozero,0.)
- call bcast_mpi(rhozero)
+ call prompt(' enter density (gives particle mass)',rhozero,0.)
  !
  ! sound speed in code units
  !
- if (id==master) then
-    call prompt(' enter sound speed in code units (sets polyk)',cs0,0.)
- endif
- call bcast_mpi(cs0)
+ call prompt(' enter sound speed in code units (sets polyk)',cs0,0.)
  !
  ! dust to gas ratio
  !
- if (use_dustfrac) then
-    call prompt('Enter dust to gas ratio',dust_to_gas,0.)
-    call bcast_mpi(dust_to_gas)
- endif
+ if (use_dustfrac) call prompt('Enter dust to gas ratio',dust_to_gas,0.)
  !
  ! magnetic field strength
  if (mhd .and. balsarakim) then
     call prompt('Enter magnetic field strength in code units ',Bzero,0.)
-    call bcast_mpi(Bzero)
  endif
  !
  ! type of lattice
  !
- if (id==master) then
-    call prompt(' select lattice type (1=cubic, 2=closepacked)',ilattice,1)
- endif
- call bcast_mpi(ilattice)
+ call prompt(' select lattice type (1=cubic, 2=closepacked)',ilattice,1)
+
 end subroutine setup_interactive
 
 !------------------------------------------------------------------------

From e7c97275be9a61705d8e8dc074e4d4cdd6518903 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 14:41:54 +1000
Subject: [PATCH 20/23] (taylorgreen) setup failure with DEBUG=yes fixed

---
 src/setup/setup_taylorgreen.f90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/setup/setup_taylorgreen.f90 b/src/setup/setup_taylorgreen.f90
index ca7214452..734395340 100644
--- a/src/setup/setup_taylorgreen.f90
+++ b/src/setup/setup_taylorgreen.f90
@@ -39,7 +39,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use physcon,      only:pi
  use prompting,    only:prompt
  use mpidomain,    only:i_belong
- use part,         only:periodic
+ use part,         only:periodic,igas
  integer,           intent(in)    :: id
  integer,           intent(inout) :: npart
  integer,           intent(out)   :: npartoftype(:)
@@ -50,7 +50,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  real,              intent(inout) :: time
  character(len=20), intent(in)    :: fileprefix
  real :: totmass,deltax,vzero,dz
- integer :: ipart,i,maxp,maxvxyzu,nx
+ integer :: i,maxp,maxvxyzu,nx
 !
 !--general parameters
 !
@@ -88,12 +88,12 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
                   hfact,npart,xyzh,periodic,nptot=npart_total,mask=i_belong)
 
  npartoftype(:) = 0
- npartoftype(1) = npart
- print*,' npart = ',ipart,npart,npart_total
+ npartoftype(igas) = npart
+ print*,' npart = ',npart,npart_total
 
  totmass = rhozero*dxbound*dybound*dzbound
  massoftype = totmass/npart_total
- print*,' particle mass = ',massoftype(1)
+ print*,' particle mass = ',massoftype(igas)
 
  vzero = 0.1
 

From 88340af6f9dd7ba362d80ba4a2832b043e9bc8bd Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 14:52:38 +1000
Subject: [PATCH 21/23] (setup) build failure in SETUP=mhdwave fixed

---
 src/setup/setup_mhdwave.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/setup/setup_mhdwave.f90 b/src/setup/setup_mhdwave.f90
index 7a948e402..d8e04d9bf 100644
--- a/src/setup/setup_mhdwave.f90
+++ b/src/setup/setup_mhdwave.f90
@@ -41,7 +41,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
  use setup_params, only:rhozero,ihavesetupB
  use unifdis,      only:set_unifdis
  use boundary,     only:set_boundary,xmin,ymin,zmin,xmax,ymax,zmax,dxbound,dybound,dzbound
- use part,         only:Bxyz,mhd,periodic
+ use part,         only:Bxyz,mhd,periodic,igas
  use io,           only:master,fatal
  use timestep,     only:dtmax,tmax
  use options,      only:nfulldump

From 0e055d23545c933187f6e15482a6dbeec7c6a8fc Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 16:22:33 +1000
Subject: [PATCH 22/23] (setup) remaining setup failures with DEBUG=yes fixed

---
 src/main/checksetup.F90         |  3 ++-
 src/setup/setup_bondiinject.f90 |  2 +-
 src/setup/setup_mhdblast.f90    | 21 ++++++++++-----------
 src/setup/setup_mhdwave.f90     |  1 +
 src/setup/setup_srblast.f90     | 28 +++++++++++-----------------
 5 files changed, 25 insertions(+), 30 deletions(-)

diff --git a/src/main/checksetup.F90 b/src/main/checksetup.F90
index 71daa6caa..fb8b187a7 100644
--- a/src/main/checksetup.F90
+++ b/src/main/checksetup.F90
@@ -54,6 +54,7 @@ subroutine check_setup(nerror,nwarn,restart)
  use boundary,        only:xmin,xmax,ymin,ymax,zmin,zmax
  use boundary_dyn,    only:dynamic_bdy,adjust_particles_dynamic_boundary
  use nicil,           only:n_nden
+ use metric_tools,    only:imetric,imet_minkowski
  integer, intent(out) :: nerror,nwarn
  logical, intent(in), optional :: restart
  integer      :: i,nbad,itype,iu,ndead
@@ -300,7 +301,7 @@ subroutine check_setup(nerror,nwarn,restart)
 !
 !--check for particles placed inside accretion boundaries
 !
- if (iexternalforce > 0 .and. .not.dorestart) then
+ if (iexternalforce > 0 .and. .not.dorestart .and. (.not.(gr .and. imetric==imet_minkowski))) then
     call update_externalforce(iexternalforce,time,0.)
     nbad = 0
     !$omp parallel do default(none) &
diff --git a/src/setup/setup_bondiinject.f90 b/src/setup/setup_bondiinject.f90
index acf4192c1..a6b724ab0 100644
--- a/src/setup/setup_bondiinject.f90
+++ b/src/setup/setup_bondiinject.f90
@@ -38,7 +38,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma_eos,hf
  use units,          only:set_units
  use inject,         only:init_inject,inject_particles,dtsphere,rin,drdp,iboundspheres
  use timestep,       only:tmax
- use io,             only:iprint
+ use io,             only:iprint,fatal
  use eos,            only:gamma
  use prompting,      only:prompt
  use metric_tools,   only:imet_schwarzschild,imetric
diff --git a/src/setup/setup_mhdblast.f90 b/src/setup/setup_mhdblast.f90
index 78c258a39..8c9d221ec 100644
--- a/src/setup/setup_mhdblast.f90
+++ b/src/setup/setup_mhdblast.f90
@@ -36,7 +36,7 @@ module setup
 !+
 !----------------------------------------------------------------
 subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
- use dim,          only:maxp,maxvxyzu,mhd
+ use dim,          only:maxvxyzu,mhd
  use setup_params, only:rhozero,ihavesetupB
  use unifdis,      only:set_unifdis
  use io,           only:master,fatal
@@ -44,10 +44,9 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use physcon,      only:pi
  use timestep,     only:tmax,dtmax
  use options,      only:nfulldump
- use prompting,    only:prompt
  use kernel,       only:wkern,cnormk,radkern2,hfact_default
  use part,         only:Bxyz,igas,periodic
- use mpiutils,     only:bcast_mpi,reduceall_mpi
+ use mpiutils,     only:reduceall_mpi
  use mpidomain,    only:i_belong
  integer,           intent(in)    :: id
  integer,           intent(out)   :: npart
@@ -84,6 +83,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  Rblast      = 0.125
  npartx      = 64
  gamma       = 1.4
+ polyk       = 0.
  plasmaB0    = 2.0*Pblast/(Bx*Bx + By*By + Bz*Bz)
  plasmaB     = plasmaB0
  ihavesetupB = .true.
@@ -106,12 +106,11 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
        call fatal('setup','failed to read in all the data from .setup.  Aborting')
     endif
  elseif (id==master) then
-    print "(a,/)",trim(filename)//' not found: using interactive setup'
-    call prompt(' Enter number of particles in x ',npartx,8,nint((maxp)**(1/3.)))
-    call prompt(' Enter the plasma beta in the blast (this will adjust the magnetic field strength) ',plasmaB)
     call write_setupfile(filename)
+    stop 'edit .setup file and try again'
+ else
+    stop
  endif
- call bcast_mpi(npartx)
  deltax = dxbound/npartx
  !
  ! Put particles on grid
@@ -145,10 +144,10 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     endif
  enddo
 
- write(*,'(2x,a,3Es11.4)')'Magnetic field (Bx,By,Bz): ',Bx,By,Bz
- write(*,'(2x,a,2Es11.4)')'Pressure in blast, medium: ',Pblast,Pmed
- write(*,'(2x,a,2Es11.4)')'Plasma beta in blast, medium: ',plasmaB,2.0*Pmed/(Bx*Bx + By*By + Bz*Bz)
- write(*,'(2x,a, Es11.4)')'Initial blast radius: ',Rblast
+ write(*,'(2x,a,3es11.4)')'Magnetic field (Bx,By,Bz): ',Bx,By,Bz
+ write(*,'(2x,a,2es11.4)')'Pressure in blast, medium: ',Pblast,Pmed
+ write(*,'(2x,a,2es11.4)')'Plasma beta in blast, medium: ',plasmaB,2.0*Pmed/(Bx*Bx + By*By + Bz*Bz)
+ write(*,'(2x,a, es11.4)')'Initial blast radius: ',Rblast
 
 end subroutine setpart
 
diff --git a/src/setup/setup_mhdwave.f90 b/src/setup/setup_mhdwave.f90
index d8e04d9bf..05db82219 100644
--- a/src/setup/setup_mhdwave.f90
+++ b/src/setup/setup_mhdwave.f90
@@ -92,6 +92,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,&
     gamma = 5./3.
     gam1 = gamma - 1.
     uuzero = przero/(gam1*rhozero)
+    polyk = przero/rhozero**gamma
  else
     gamma = 1.
     polyk = przero/rhozero
diff --git a/src/setup/setup_srblast.f90 b/src/setup/setup_srblast.f90
index 566f4a0eb..67ca3cb11 100644
--- a/src/setup/setup_srblast.f90
+++ b/src/setup/setup_srblast.f90
@@ -41,7 +41,7 @@ module setup
 !+
 !----------------------------------------------------------------
 subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,time,fileprefix)
- use dim,          only:maxp,maxvxyzu,gr
+ use dim,          only:maxvxyzu,gr
  use setup_params, only:rhozero
  use unifdis,      only:set_unifdis
  use io,           only:master,fatal
@@ -49,10 +49,9 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  use physcon,      only:pi
  use timestep,     only:tmax,dtmax
  use options,      only:nfulldump
- use prompting,    only:prompt
  use kernel,       only:hfact_default
  use part,         only:igas,periodic
- use mpiutils,     only:bcast_mpi,reduceall_mpi
+ use mpiutils,     only:reduceall_mpi
  use units,        only:set_units
  use mpidomain,    only:i_belong
  integer,           intent(in)    :: id
@@ -80,7 +79,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  !
  ! Must have G=c=1 in relativity
  !
- call set_units(G=1.,c=1.)
+ call set_units(G=1.d0,c=1.d0)
 
  !
  ! General parameters
@@ -89,6 +88,7 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
  hfact       = hfact_default
  rhozero     = 1.0
  gamma       = 5./3.
+ polyk       = 0.
 
  !
  ! Default setup parameters
@@ -125,17 +125,11 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
        call fatal('setup','failed to read in all the data from .setup.  Aborting')
     endif
  elseif (id==master) then
-    print "(a,/)",trim(filename)//' not found: using interactive setup'
-    call prompt(' Enter number of particles in x ',npartx,8,nint((maxp)**(1/3.)))
-    call prompt(' Enter pressure in blast ',Pblast,0.)
-    call prompt(' Enter pressure in medium ',Pmed,0.)
-    call prompt(' Enter size of box ',boxsize,0.)
-    call prompt(' Enter radius of blast ',Rblast,0.,boxsize/2.)
-    call prompt(' IC smoothing factor (in terms of particle spacing) ',smoothfac)
     call write_setupfile(filename)
+    stop 'edit .setup file and try again'
+ else
+    stop
  endif
- call bcast_mpi(npartx)
-
  !
  ! Set boundaries
  !
@@ -167,9 +161,9 @@ subroutine setpart(id,npart,npartoftype,xyzh,massoftype,vxyzu,polyk,gamma,hfact,
     vxyzu(4,i) = (ublast-umed)/(1. + exp((r-Rblast)/del)) + umed
  enddo
 
- write(*,'(2x,a,2Es11.4)')'Pressure in blast, medium: ',Pblast,Pmed
- write(*,'(2x,a, Es11.4)')'Initial blast radius: ',Rblast
- write(*,'(2x,a, Es11.4)')'Initial blast energy: ',toten
+ write(*,'(2x,a,2es11.4)') 'Pressure in blast, medium: ',Pblast,Pmed
+ write(*,'(2x,a, es11.4)') 'Initial blast radius: ',Rblast
+ write(*,'(2x,a, es11.4)') 'Initial blast energy: ',toten
 
 end subroutine setpart
 
@@ -221,5 +215,5 @@ subroutine read_setupfile(filename,ierr)
  call close_db(db)
 
 end subroutine read_setupfile
-!----------------------------------------------------------------
+
 end module setup

From 8a8024bd55938bfbfdeb48f2e30f0fa086cd8d98 Mon Sep 17 00:00:00 2001
From: Daniel Price <daniel.price@monash.edu>
Date: Fri, 12 May 2023 16:24:37 +1000
Subject: [PATCH 23/23] [header-bot] updated file headers

---
 src/main/readwrite_infile.F90       |  2 +-
 src/setup/phantomsetup.F90          |  2 +-
 src/setup/set_units.f90             |  4 ++--
 src/setup/setup_bondi.F90           |  2 +-
 src/setup/setup_collidingclouds.f90 |  5 ++---
 src/setup/setup_mhdblast.f90        |  4 ++--
 src/setup/setup_mhdwave.f90         |  4 +---
 src/setup/setup_radiativebox.f90    | 28 +++++++++++++---------------
 src/setup/setup_sedov.f90           |  8 ++++----
 src/setup/setup_srblast.f90         |  4 ++--
 src/setup/setup_unifdis.f90         |  4 +---
 11 files changed, 30 insertions(+), 37 deletions(-)

diff --git a/src/main/readwrite_infile.F90 b/src/main/readwrite_infile.F90
index 3424975bf..31cbf3084 100644
--- a/src/main/readwrite_infile.F90
+++ b/src/main/readwrite_infile.F90
@@ -17,7 +17,7 @@ module readwrite_infile
 !   - C_cour             : *Courant number*
 !   - C_force            : *dt_force number*
 !   - alpha              : *shock viscosity parameter*
-!   - alphaB             : *art. resistivity parameter*
+!   - alphaB             : *shock resistivity parameter*
 !   - alphamax           : *MAXIMUM shock viscosity parameter*
 !   - alphau             : *shock conductivity parameter*
 !   - avdecayconst       : *decay time constant for viscosity switches*
diff --git a/src/setup/phantomsetup.F90 b/src/setup/phantomsetup.F90
index cd67ca8b2..7026c3c90 100644
--- a/src/setup/phantomsetup.F90
+++ b/src/setup/phantomsetup.F90
@@ -17,7 +17,7 @@ program phantomsetup
 ! :Dependencies: boundary, checksetup, dim, eos, fileutils, gravwaveutils,
 !   io, krome_interface, memory, mpidomain, mpiutils, options, part,
 !   physcon, readwrite_dumps, readwrite_infile, setBfield, setup,
-!   setup_params, systemutils, units
+!   setup_params, systemutils, timestep, units
 !
  use memory,          only:allocate_memory,deallocate_memory
  use dim,             only:tagline,maxp,maxvxyzu,mpi,&
diff --git a/src/setup/set_units.f90 b/src/setup/set_units.f90
index d622cd975..e3a950bd6 100644
--- a/src/setup/set_units.f90
+++ b/src/setup/set_units.f90
@@ -14,8 +14,8 @@ module setunits
 ! :Owner: Daniel Price
 !
 ! :Runtime parameters:
-!   - dist_unit : *distance unit (e.g. au)*
-!   - mass_unit : *mass unit (e.g. solarm)*
+!   - dist_unit : *distance unit (e.g. au,pc,kpc,0.1pc)*
+!   - mass_unit : *mass unit (e.g. solarm,jupiterm,1e6*solarm)*
 !
 ! :Dependencies: infile_utils, io, prompting, units
 !
diff --git a/src/setup/setup_bondi.F90 b/src/setup/setup_bondi.F90
index e29b990e2..78389239f 100644
--- a/src/setup/setup_bondi.F90
+++ b/src/setup/setup_bondi.F90
@@ -20,7 +20,7 @@ module setup
 !   - rmin   : *inner edge*
 !
 ! :Dependencies: bondiexact, centreofmass, dim, externalforces,
-!   infile_utils, io, kernel, metric, metric_tools, options, part, physcon,
+!   infile_utils, io, kernel, metric_tools, options, part, physcon,
 !   prompting, setup_params, spherical, stretchmap, timestep, units
 !
  use physcon,        only:pi
diff --git a/src/setup/setup_collidingclouds.f90 b/src/setup/setup_collidingclouds.f90
index de7014b43..34884af92 100644
--- a/src/setup/setup_collidingclouds.f90
+++ b/src/setup/setup_collidingclouds.f90
@@ -18,12 +18,10 @@ module setup
 !   - Ncloud             : *number of clouds*
 !   - Temperature_medium : *Temperature of the background*
 !   - density_contrast   : *density contrast*
-!   - dist_unit          : *distance unit (e.g. pc)*
 !   - dynamic_bdy        : *use dynamic boundary conditions*
 !   - h_acc              : *accretion radius (code units)*
 !   - h_soft_sinksink    : *sink-sink softening radius (code units)*
 !   - icreate_sinks      : *1: create sinks.  0: do not create sinks*
-!   - mass_unit          : *mass unit (e.g. solarm)*
 !   - np                 : *actual number of particles in cloud 1*
 !   - plasmaB            : *plasma beta*
 !   - r_crit             : *critical radius (code units)*
@@ -31,7 +29,8 @@ module setup
 !
 ! :Dependencies: boundary, boundary_dyn, cooling, datafiles, dim, eos,
 !   infile_utils, io, kernel, mpidomain, options, part, physcon, prompting,
-!   ptmass, setup_params, spherical, timestep, unifdis, units, velfield
+!   ptmass, setunits, setup_params, spherical, timestep, unifdis, units,
+!   velfield
 !
  use part,         only:mhd
  use dim,          only:maxvxyzu,maxp_hard
diff --git a/src/setup/setup_mhdblast.f90 b/src/setup/setup_mhdblast.f90
index 8c9d221ec..721e84ece 100644
--- a/src/setup/setup_mhdblast.f90
+++ b/src/setup/setup_mhdblast.f90
@@ -17,8 +17,8 @@ module setup
 !   - plasmaB : *plasma beta in the initial blast*
 !
 ! :Dependencies: boundary, dim, infile_utils, io, kernel, mpidomain,
-!   mpiutils, options, part, physcon, prompting, setup_params, timestep,
-!   unifdis, units
+!   mpiutils, options, part, physcon, setup_params, timestep, unifdis,
+!   units
 !
  implicit none
  public :: setpart
diff --git a/src/setup/setup_mhdwave.f90 b/src/setup/setup_mhdwave.f90
index 05db82219..495b8f668 100644
--- a/src/setup/setup_mhdwave.f90
+++ b/src/setup/setup_mhdwave.f90
@@ -13,9 +13,7 @@ module setup
 !
 ! :Owner: James Wurster
 !
-! :Runtime parameters:
-!   - npartx  : *number of particles in x-direction*
-!   - plasmaB : *plasma beta in the initial blast*
+! :Runtime parameters: None
 !
 ! :Dependencies: boundary, infile_utils, io, kernel, mpidomain, mpiutils,
 !   options, part, physcon, prompting, setup_params, timestep, unifdis,
diff --git a/src/setup/setup_radiativebox.f90 b/src/setup/setup_radiativebox.f90
index 4e4c807be..0850a5624 100644
--- a/src/setup/setup_radiativebox.f90
+++ b/src/setup/setup_radiativebox.f90
@@ -13,22 +13,20 @@ module setup
 ! :Owner: Sergei Biriukov
 !
 ! :Runtime parameters:
-!   - cs0       : *initial sound speed in code units*
-!   - dist_unit : *distance unit (e.g. au)*
-!   - ilattice  : *lattice type (1=cubic, 2=closepacked)*
-!   - mass_unit : *mass unit (e.g. solarm)*
-!   - nx        : *number of particles in x direction*
-!   - rhozero   : *initial density in code units*
-!   - xmax      : *xmax boundary*
-!   - xmin      : *xmin boundary*
-!   - ymax      : *ymax boundary*
-!   - ymin      : *ymin boundary*
-!   - zmax      : *zmax boundary*
-!   - zmin      : *zmin boundary*
+!   - cs0      : *initial sound speed in code units*
+!   - ilattice : *lattice type (1=cubic, 2=closepacked)*
+!   - nx       : *number of particles in x direction*
+!   - rhozero  : *initial density in code units*
+!   - xmax     : *xmax boundary*
+!   - xmin     : *xmin boundary*
+!   - ymax     : *ymax boundary*
+!   - ymin     : *ymin boundary*
+!   - zmax     : *zmax boundary*
+!   - zmin     : *zmin boundary*
 !
-! :Dependencies: boundary, eos, infile_utils, io, kernel, mpidomain,
-!   mpiutils, options, part, physcon, set_dust, setup_params, timestep,
-!   unifdis, units
+! :Dependencies: boundary, dim, eos, infile_utils, io, kernel, mpidomain,
+!   mpiutils, options, part, physcon, set_dust, setunits, setup_params,
+!   timestep, unifdis, units
 !
  use setup_params, only:rhozero
  use dim,          only:gr
diff --git a/src/setup/setup_sedov.f90 b/src/setup/setup_sedov.f90
index 330345757..bc3ea4814 100644
--- a/src/setup/setup_sedov.f90
+++ b/src/setup/setup_sedov.f90
@@ -10,16 +10,16 @@ module setup
 !
 ! :References: None
 !
-! :Owner: James Wurster
+! :Owner: Daniel Price
 !
 ! :Runtime parameters:
-!   - lattice       : *particle lattice (random,cubic,closepacked,hcp,hexagonal)*
+!   - lattice       : *particle lattice (1=cubic,2=closepacked,3=hcp,4=random)*
 !   - npartx        : *number of particles in x-direction*
 !   - shuffle_parts : *relax particles by shuffling*
 !
 ! :Dependencies: boundary, infile_utils, io, kernel, mpidomain, mpiutils,
-!   options, part, physcon, prompting, setup_params, timestep, unifdis,
-!   units, utils_shuffleparticles
+!   options, part, physcon, setup_params, timestep, unifdis,
+!   utils_shuffleparticles
 !
  implicit none
  public :: setpart
diff --git a/src/setup/setup_srblast.f90 b/src/setup/setup_srblast.f90
index 67ca3cb11..f2c51e692 100644
--- a/src/setup/setup_srblast.f90
+++ b/src/setup/setup_srblast.f90
@@ -21,8 +21,8 @@ module setup
 !   - smoothfac : *IC smoothing factor (in terms of particle spacing)*
 !
 ! :Dependencies: boundary, dim, infile_utils, io, kernel, mpidomain,
-!   mpiutils, options, part, physcon, prompting, setup_params, timestep,
-!   unifdis, units
+!   mpiutils, options, part, physcon, setup_params, timestep, unifdis,
+!   units
 !
  implicit none
  public :: setpart
diff --git a/src/setup/setup_unifdis.f90 b/src/setup/setup_unifdis.f90
index 1c372e851..44b4ad316 100644
--- a/src/setup/setup_unifdis.f90
+++ b/src/setup/setup_unifdis.f90
@@ -15,10 +15,8 @@ module setup
 ! :Runtime parameters:
 !   - Bzero       : *magnetic field strength in code units*
 !   - cs0         : *initial sound speed in code units*
-!   - dist_unit   : *distance unit (e.g. au)*
 !   - dust_to_gas : *dust-to-gas ratio*
 !   - ilattice    : *lattice type (1=cubic, 2=closepacked)*
-!   - mass_unit   : *mass unit (e.g. solarm)*
 !   - nx          : *number of particles in x direction*
 !   - rhozero     : *initial density in code units*
 !   - xmax        : *xmax boundary*
@@ -29,7 +27,7 @@ module setup
 !   - zmin        : *zmin boundary*
 !
 ! :Dependencies: boundary, cooling, cooling_ism, dim, eos, infile_utils,
-!   io, mpidomain, mpiutils, options, part, physcon, prompting, set_dust,
+!   io, mpidomain, options, part, physcon, prompting, set_dust, setunits,
 !   setup_params, timestep, unifdis, units
 !
  use dim,          only:use_dust,mhd,gr