Merge pull request #351 from danieljprice/damping-bcs

Damping bcs

build/Makefile_qscripts

@@ -148,6 +148,9 @@ qscript:
         ifdef QEXTRA
 	   @echo '#PBS '$(QEXTRA)
         endif
+        ifdef QSTORAGE
+	   @echo '#PBS -l storage='$(QSTORAGE)
+        endif
 	@echo '## phantom jobs can be restarted:'
 	@echo '#PBS -r y'
         ifeq ($(PBSRESUBMIT),yes)

build/Makefile_systems

@@ -151,12 +151,13 @@ ifeq ($(SYSTEM), nci)
     ifeq ($(MPI),yes)
         NPAR=32
     endif
-    QPROJECT='fu7'
+    QPROJECT=$(PROJECT)
     QNAME='normal'
     WALLTIME='48:00:00'
     MPIEXEC='mpiexec -npernode 1'
     QNODES='ncpus='$(NPAR)
     QEXTRA='-l other=hyperthread'
+    QSTORAGE="gdata/$(QPROJECT)"
 endif
 
 ifeq ($(SYSTEM), gfortran)

docs/nci.rst

@@ -22,24 +22,26 @@ First edit your .bashrc file in your favourite text editor::
 Mine has::
 
    export SYSTEM=nci
+   export PROJECT=wk74
    export OMP_STACKSIZE=512M
    export OMP_NUM_THREADS=32
-   export PATH=$PATH:/scratch/fu7/splash/bin
-   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/scratch/fu7/splash/giza/lib
+   export SPLASH_DIR=/g/data/$PROJECT/splash
+   export PATH=$PATH:$SPLASH_DIR/bin
+   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SPLASH_DIR/giza/lib
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/apps/hdf5/1.10.5/lib
    export MAXP=2000000
    ulimit -s unlimited
    source ~/.modules
 
 If you are using phantom+mcfost, you will need the following lines::
 
-   export MCFOST_DIR=/scratch/fu7/mcfost-src/
+   export MCFOST_DIR=/g/data/$PROJECT/mcfost-src/
    export MCFOST_AUTO_UPDATE=0
-   export MCFOST_INSTALL=/scratch/fu7/mcfost/
+   export MCFOST_INSTALL=/g/data/$PROJECT/mcfost/
    export MCFOST_GIT=1
    export MCFOST_NO_XGBOOST=1
-   export MCFOST_LIBS=/scratch/fu7/mcfost
-   export MCFOST_UTILS=/scratch/fu7/mcfost/utils
+   export MCFOST_LIBS=/g/data/$PROJECT/mcfost
+   export MCFOST_UTILS=/g/data/$PROJECT/mcfost/utils
    export HDF5ROOT=/apps/hdf5/1.10.5/lib
 
 Then relevant modules in your .modules file::
@@ -55,12 +57,12 @@ Mine contains::
 
 where the last line is needed for git's large file storage (LFS) to work.
 
-Finally, make a shortcut to the /scratch filesystem::
+Finally, make a shortcut to the /g/data filesystem::
 
-   cd /scratch/fu7
+   cd /g/data/$PROJECT
    mkdir $USER
    cd
-   ln -s /scratch/fu7/$USER runs
+   ln -s /scratch/$PROJECT/$USER runs
    cd runs
    pwd -P
 
@@ -104,13 +106,14 @@ should produce something like::
   #PBS -l ncpus=48
   #PBS -N myrun
   #PBS -q normal
-  #PBS -P fu7
+  #PBS -P wk74
   #PBS -o tde.in.pbsout
   #PBS -j oe
   #PBS -m e
   #PBS -M daniel.price@monash.edu
   #PBS -l walltime=48:00:00
   #PBS -l mem=16G
+  #PBS -l storage=gdata/wk74
   #PBS -l other=hyperthread
   ## phantom jobs can be restarted:
   #PBS -r y

src/main/energies.F90

@@ -711,7 +711,7 @@ subroutine compute_energies(t)
 
  if (track_mass) then
     accretedmass = ev_data(iev_sum,iev_macc)
-    ev_data(iev_sum,iev_eacc) = accretedmass/accradius1 ! total accretion energy
+    if (accradius1 > 0.) ev_data(iev_sum,iev_eacc) = accretedmass/accradius1 ! total accretion energy
  endif
  if (track_lum) totlum = ev_data(iev_sum,iev_totlum)
 

src/main/initial.F90

@@ -152,10 +152,10 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
                             h_acc,r_crit,r_crit2,rho_crit,rho_crit_cgs,icreate_sinks, &
                             r_merge_uncond,r_merge_cond,r_merge_uncond2,r_merge_cond2,r_merge2
  use timestep,         only:time,dt,dtextforce,C_force,dtmax
+ use timestep_ind,     only:istepfrac
  use timing,           only:get_timings
 #ifdef IND_TIMESTEPS
- use timestep,         only:dtmax
- use timestep_ind,     only:istepfrac,ibinnow,maxbins,init_ibin
+ use timestep_ind,     only:ibinnow,maxbins,init_ibin
  use part,             only:ibin,ibin_old,ibin_wake,alphaind
  use readwrite_dumps,  only:dt_read_in
 #else
@@ -189,6 +189,8 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
  use dust_formation,   only:init_nucleation
 #ifdef INJECT_PARTICLES
  use inject,           only:init_inject,inject_particles
+ use partinject,       only:update_injected_particles
+ use timestep_ind,     only:nbinmax
 #endif
 #ifdef KROME
  use krome_interface,  only:initialise_krome
@@ -231,6 +233,7 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
  character(len=7) :: dust_label(maxdusttypes)
 #ifdef INJECT_PARTICLES
  character(len=len(dumpfile)) :: file1D
+ integer :: npart_old
 #endif
 
 
@@ -548,16 +551,10 @@ subroutine startrun(infile,logfile,evfile,dumpfile,noread)
     endif
     call rename('wind_profile1D.dat',trim(file1D))
  endif
+ npart_old = npart
  call inject_particles(time,0.,xyzh,vxyzu,xyzmh_ptmass,vxyz_ptmass,&
                        npart,npartoftype,dtinject)
-#ifdef GR
-! call update_injected_particles(npart_old,npart,istepfrac,nbinmax,time,dtmax,dt,dtinject)
- call init_metric(npart,xyzh,metrics,metricderivs)
- call prim2consall(npart,xyzh,metrics,vxyzu,dens,pxyzu,use_dens=.false.)
- if (iexternalforce > 0 .and. imetric /= imet_minkowski) then
-    call get_grforce_all(npart,xyzh,metrics,metricderivs,vxyzu,dens,fext,dtextforce) ! Not 100% sure if this is needed here
- endif
-#endif
+ call update_injected_particles(npart_old,npart,istepfrac,nbinmax,time,dtmax,dt,dtinject)
 #endif
 !
 !--set initial chemical abundance values