Merge branch 'master' of https://bitbucket.org/danielprice/phantom

AUTHORS

@@ -28,12 +28,13 @@ Christopher Russell <crussell@udel.edu>
 Alessia Franchini <alessia.franchini@unlv.edu>
 Alex Pettitt <alex@astro1.sci.hokudai.ac.jp>
 Lionel Siess <lionel.siess@astro.ulb.ac.be>
+Daniel Price <dprice@cantab.net>
 Enrico Ragusa <er198@leicester.ac.uk>
 Kieran Hirsh <kieran.hirsh1@monash.edu>
 Nicole Rodrigues <nicole.rodrigues@monash.edu>
+Sergei Biriukov <svbiriukov@gmail.com>
 Chris Nixon <cjn@leicester.ac.uk>
 Nicolas Cuello <cuellonicolas@gmail.com>
-Sergei Biriukov <svbiriukov@gmail.com>
 Benoit Commercon <benoit.commercon@gmail.com>
 Giulia Ballabio <giulia.ballabio2@studenti.unimi.it>
 Hauke Worpel <hauke@ursa.aip.de>
@@ -44,7 +45,6 @@ Rebecca Nealon <rebecca.nealon@leicester.ac.uk>
 Zachary Pellow <zpel1@student.monash.edu>
 Alison Young <ayoung@astro.ex.ac.uk>
 Cox, Samuel <sc676@leicester.ac.uk>
-Daniel Price <dprice@cantab.net>
 Hauke WOrpel <hworpel@aip.de>
 Jorge Cuadra <jcuadra@astro.puc.cl>
 Lionel Siess <Lionel.Siess@ulb.ac.be>

build/Makefile

@@ -1,6 +1,6 @@
 #--------------------------------------------------------------------------!
 # The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-# Copyright (c) 2007-2018 The Authors (see AUTHORS)                        !
+# Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 # See LICENCE file for usage and distribution conditions                   !
 # http://users.monash.edu.au/~dprice/phantom                               !
 #--------------------------------------------------------------------------!
@@ -22,7 +22,7 @@
 .KEEP_STATE:
 
 PHANTOM_VERSION_MAJOR=1
-PHANTOM_VERSION_MINOR=3
+PHANTOM_VERSION_MINOR=4
 PHANTOM_VERSION_MICRO=0
 VERSION=$(PHANTOM_VERSION_MAJOR).$(PHANTOM_VERSION_MINOR).$(PHANTOM_VERSION_MICRO)
 

docs/gitinfo.rst

@@ -34,9 +34,7 @@ Install git-lfs
 ---------------
 
 In order to read large datafiles stored in the phantom git repo, you
-will need git-lfs installed:
-
-::
+will need git-lfs installed::
 
    git lfs install
 

docs/nci.rst

@@ -3,25 +3,24 @@ Getting started on the NCI supercomputer (Australian National Supercomputing Fac
 
 Apply for an account at http://nci.org.au
 
-If you are in Daniel Price’s research group, request to join projects
-“fu7” and “pt4”
+If you are in Daniel Price’s research group, request to join project “fu7”
 
 Log in 
 -------
 
 ::
 
-   ssh -Y USERNAME@gadi.nci.org.au
+   ssh -Y USER@gadi.nci.org.au
 
 Make a shortcut to the /short filesystem
 ----------------------------------------
 
 ::
 
-   cd /short/pt4
-   mkdir USERNAME
+   cd /scratch/fu7
+   mkdir $USER
    cd
-   ln -s /short/pt4/USERNAME runs
+   ln -s /scratch/fu7/$USER runs
    cd runs
    pwd -P
 
@@ -52,4 +51,4 @@ more info
 ---------
 
 For more information on the actual machine `read the
-userguide <https://opus.nci.org.au/display/Help/Gadi+User+Guide>`__
+userguide <https://opus.nci.org.au/display/Help/Preparing+for+Gadi>`__

docs/releasenotes.rst

@@ -1,8 +1,18 @@
 Release notes
 =============
 
-Current development version - v1.4.0 - XXth August 2019
--------------------------------------------------------
+Current development version - v1.x.x
+-------------------------------------
+
+Physics
+~~~~~~~
+
+Performance
+~~~~~~~~~~~
+
+
+v1.4.0 - 20th January 2020 - 1b48489
+------------------------------------
 
 Physics
 ~~~~~~~
@@ -17,6 +27,8 @@ Physics
 -  warning added about particles with zero sound speed
 -  preliminary work to incorporate Shen (2012) equation of state for
    Neutron stars
+-  Support for multi grain dust with multiple large grain species
+-  (non-ideal MHD) updated nicil cosmic ray ionisation library to V1.2.6
 
 Setup
 ~~~~~
@@ -39,6 +51,14 @@ Bugs
    problem with extern_binary
 -  Default units changed in galaxies setup to avoid momentum
    conservation warning
+-  bug fixes for barotropic ieos=8
+-  bug fix with fatal error for particles with energy equal to zero (now a warning)
+-  (pyphantom) Added try statements to avoid errors when loading utherm, temperature and bxyz
+-  (ptmass) bug fix in bookkeeping of why sink was not created
+-  (test_derivs) more precise test of artificial viscosity terms for DISC_VISCOSITY=no,
+-  passes test suite when KERNEL=quintic
+-  MPI thread-safe downloading of datafiles
+-  BUG FIX with memory allocation for dvdx; possibly affecting viscosity switch if DISC_VISCOSITY=no
 
 Performance
 ~~~~~~~~~~~

scripts/HEADER-module

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-THISYEAR The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

scripts/HEADER-program

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-THISYEAR The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

scripts/header.pl

@@ -412,6 +412,8 @@ sub write_module_header {
             print "!\n$gen";
          }
       } else {
+         my $thisyear = 1900 + (localtime)[5];;
+         $_ =~ s/THISYEAR/$thisyear/;
          print $_;
       }
    }

src/main/boundary.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/bowen_dust.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/centreofmass.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/checkoptions.F90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/checksetup.F90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!
@@ -141,6 +141,7 @@ subroutine check_setup(nerror,nwarn,restart)
        itype = iamtype(iphase(i))
        if (itype < 1 .or. itype > maxtypes) then
           nbad = nbad + 1
+          if (nbad < 10) print*,'ERROR: unknown particle type ',itype,' on particle ',i
        else
           ncount(itype) = ncount(itype) + 1
        endif
@@ -150,21 +151,11 @@ subroutine check_setup(nerror,nwarn,restart)
        nerror = nerror + 1
     endif
     if (any(ncount /= npartoftype)) then
-       print*,'ncount=',ncount,'; npartoftype=',npartoftype
+       print*,'n(via iphase)=',ncount
+       print*,'npartoftype  =',npartoftype
        print*,'ERROR: sum of types in iphase is not equal to npartoftype'
        nerror = nerror + 1
     endif
-!
-!--If boundary particles are present, then only gas and boundary particles may exist
-!
-    if (npartoftype(iboundary) > 0) then
-       do i = 1,maxtypes
-          if (npartoftype(i) > 0 .and. (i/=igas .and. i/=iboundary)) then
-             print*, 'Error in setup: boundary particles cannot coexist with non-gas particles'
-             nerror = nerror + 1
-          endif
-       enddo
-    endif
  endif
 !
 !--should not have negative or zero smoothing lengths in initial setup
@@ -609,10 +600,11 @@ end subroutine check_setup_dustgrid
 
 subroutine check_for_identical_positions(npart,xyzh,nbad)
  use sortutils, only:indexxfunc,r2func
+ use part,      only:maxphase,maxp,iphase,igas,iamtype
  integer, intent(in)  :: npart
  real,    intent(in)  :: xyzh(:,:)
  integer, intent(out) :: nbad
- integer :: i,j
+ integer :: i,j,itypei,itypej
  real    :: dx(3),dx2
  integer, allocatable :: index(:)
  !
@@ -626,16 +618,23 @@ subroutine check_for_identical_positions(npart,xyzh,nbad)
  ! positions are found.
  !
  nbad = 0
+ itypei = igas
+ itypej = igas
  do i=1,npart
     j = i+1
     dx2 = 0.
+    if (maxphase==maxp) itypei = iamtype(iphase(index(i)))
     do while (dx2 < epsilon(dx2) .and. j < npart)
        dx = xyzh(1:3,index(i)) - xyzh(1:3,index(j))
+       if (maxphase==maxp) itypej = iamtype(iphase(index(j)))
        dx2 = dot_product(dx,dx)
-       if (dx2 < epsilon(dx2)) then
+       if (dx2 < epsilon(dx2) .and. itypei==itypej) then
           nbad = nbad + 1
-          if (nbad <= 100) print*,'WARNING: particles ',index(i),' and ',index(j),&
-             ' at same position ',xyzh(1:3,index(i)),xyzh(1:3,index(j))
+          if (nbad <= 100) 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))
+          endif
        endif
        j = j + 1
     enddo

src/main/commons.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/config.F90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!
@@ -171,7 +171,7 @@ module dim
 
  ! Maximum number of particle types
  !
- integer, parameter :: maxtypes = 7 + maxdustlarge - 1
+ integer, parameter :: maxtypes = 7 + 2*maxdustlarge - 1
 
  !
  ! Number of dimensions, where it is needed

src/main/coolfunc.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/cooling.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/damping.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!

src/main/datafiles.f90

@@ -1,6 +1,6 @@
 !--------------------------------------------------------------------------!
 ! The Phantom Smoothed Particle Hydrodynamics code, by Daniel Price et al. !
-! Copyright (c) 2007-2019 The Authors (see AUTHORS)                        !
+! Copyright (c) 2007-2020 The Authors (see AUTHORS)                        !
 ! See LICENCE file for usage and distribution conditions                   !
 ! http://phantomsph.bitbucket.io/                                          !
 !--------------------------------------------------------------------------!