compatible read_grav script including cell positions

99e1cb06 · Cristian Barrera-Hinojosa · 2858352e · 99e1cb06 · 99e1cb06 · 99e1cb06
Commit 99e1cb06 authored 4 years ago by Cristian Barrera-Hinojosa
--- a/bin/write_makefile.f90
+++ b/bin/write_makefile.f90
@@ -10,102 +10,139 @@ subroutine output_makefile(filename)
  format="(A)"
  open(unit=ilun,file=fileloc,form='formatted')
  write(ilun,format)"#############################################################################"
-  write(ilun,format)"# If you have problems with this makefile, contact Romain.Teyssier@gmail.com"
+  write(ilun,format)"# Contact: cbarrera.hinojosa@gmail.com "
  write(ilun,format)"#############################################################################"
  write(ilun,format)"# Compilation time parameters"
-  write(ilun,format)"NVECTOR = 64"
+  write(ilun,format)""
+  write(ilun,format)"# Do we want a debug build? 1=Yes, 0=No"
+  write(ilun,format)"DEBUG = 0"
+  write(ilun,format)"# Compiler flavor: GNU or INTEL"
+  write(ilun,format)"COMPILER = GNU"
+  write(ilun,format)"# Size of vector cache"
+  write(ilun,format)"NVECTOR = 32"
+  write(ilun,format)"# Number of dimensions"
  write(ilun,format)"NDIM = 3"
+  write(ilun,format)"# Float precision size"
  write(ilun,format)"NPRE = 8"
-  write(ilun,format)"NVAR = 5"
-  write(ilun,format)"NENER = 0"
+  write(ilun,format)"# hydro/mhd solver"
  write(ilun,format)"SOLVER = hydro"
-  write(ilun,format)"PATCH = "
+  write(ilun,format)"# Patch"
+  write(ilun,format)"PATCH ="
+  write(ilun,format)"# Use RT? 1=Yes, 0=No"
+  write(ilun,format)"RT = 0"
+  write(ilun,format)"# Use MPI? 1=Yes, 0=No"
+  write(ilun,format)"MPI = 1"
+  write(ilun,format)"MPIF90 = mpif90"
+  write(ilun,format)"# Root name of executable"
+  write(ilun,format)"EXEC = gramses"
+  write(ilun,format)"# Number of additional energies"
+  write(ilun,format)"NENER = 0"
+  write(ilun,format)"# Use Grackle cooling? 1=Yes, 0=No"
  write(ilun,format)"GRACKLE = 0"
-  write(ilun,format)"EXEC = ramses"
+  write(ilun,format)"# Number of metal species"
+  write(ilun,format)"NMETALS = 0"
+  write(ilun,format)"# ATON flages: Uncomment to enable ATON"
+  write(ilun,format)"ATON_FLAGS = #-DATON"
+  write(ilun,format)"# Number of ions for RT"
+  write(ilun,format)"NIONS = 0"
+  write(ilun,format)"# Number of photon groups for RT"
+  write(ilun,format)"NGROUPS = 0"
+  write(ilun,format)"# Number of passive scalars"
+  write(ilun,format)"NPSCAL = 0"
+  write(ilun,format)""
+  write(ilun,format)"# Compute NVAR"
+  write(ilun,format)"NVAR = 2+$(NDIM)"
+  write(ilun,format)"ifeq ($(SOLVER),mhd)"
+  write(ilun,format)"   NVAR = 8"
+  write(ilun,format)"endif"
+  write(ilun,format)"NVAR := $(NVAR)+$(NENER)+$(NPSCAL)+$(NMETALS)"
+  write(ilun,format)"ifeq ($(RT),1)"
+  write(ilun,format)"   NVAR := $(NVAR)+$(NIONS)"
+  write(ilun,format)"endif"
+  write(ilun,format)""
+  write(ilun,format)"# Set to one to use 'include ""mpif.h""' instead of more recent ""use mpi"""
+  write(ilun,format)"OLD_MPI_SUPPORT = 1"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"GITBRANCH = $(shell git rev-parse --abbrev-ref HEAD)"
  write(ilun,format)"GITHASH = $(shell git log --pretty=format:'%H' -n 1)"
-  write(ilun,format)"GITREPO = $(shell git config --get remote.origin.url)"
+  write(ilun,format)"GITREMOTE = $(shell git config --get branch.$(GITBRANCH).remote)"
+  write(ilun,format)"GITREPO = $(shell git config --get remote.$(GITREMOTE).url)"
  write(ilun,format)"BUILDDATE = $(shell date +""%D-%T"")"
-  write(ilun,format)"DEFINES = -DNVECTOR=$(NVECTOR) -DNDIM=$(NDIM) -DNPRE=$(NPRE) -DNENER=$(NENER) -DNVAR=$(NVAR) \"
-  write(ilun,format)"          -DSOLVER$(SOLVER)"
+  write(ilun,format)"DEFINES = -DNVECTOR=$(NVECTOR) -DNDIM=$(NDIM) -DNPRE=$(NPRE) -DNENER=$(NENER) \"
+  write(ilun,format)"          -DNVAR=$(NVAR) -DSOLVER$(SOLVER) $(ATON_FLAGS)"
  write(ilun,format)"ifeq ($(GRACKLE),1)"
-  write(ilun,format)"DEFINES += -Dgrackle"
+  write(ilun,format)"   DEFINES += -Dgrackle"
+  write(ilun,format)"endif"
+  write(ilun,format)"ifeq ($(OLD_MPI_SUPPORT),1)"
+  write(ilun,format)"   DEFINES += -DMPI_OLD"
  write(ilun,format)"endif"
+  write(ilun,format)"ifeq ($(RT),1)"
+  write(ilun,format)"   DEFINES += -DRT -DNIONS=$(NIONS) -DNGROUPS=$(NGROUPS)"
+  write(ilun,format)"endif"
+  write(ilun,format)""
  write(ilun,format)"#############################################################################"
  write(ilun,format)"# Fortran compiler options and directives"
  write(ilun,format)""
-  write(ilun,format)"# --- No MPI, gfortran -------------------------------"
-  write(ilun,format)"F90 = gfortran -O3 -frecord-marker=4 -fbacktrace -ffree-line-length-none -g"
-  write(ilun,format)"FFLAGS = -x f95-cpp-input $(DEFINES) -DWITHOUTMPI"
-  write(ilun,format)""
-  write(ilun,format)"# --- No MPI, tau ----------------------------------"
-  write(ilun,format)"#F90 = tau_f90.sh -optKeepFiles -optPreProcess -optCPPOpts=$(DEFINES) -DWITHOUTMPI"
-  write(ilun,format)""
-  write(ilun,format)"# --- No MPI, pgf90 ----------------------------------"
-  write(ilun,format)"#F90 = pgf90"
-  write(ilun,format)"#FFLAGS = -Mpreprocess $(DEFINES) -DWITHOUTMPI"
-  write(ilun,format)""
-  write(ilun,format)"# --- No MPI, xlf ------------------------------------"
-  write(ilun,format)"#F90 = xlf"
-  write(ilun,format)"#FFLAGS = -WF,-DNDIM=$(NDIM),-DNPRE=$(NPRE),-DNVAR=$(NVAR),-DSOLVER$(SOLVER),-DWITHOUTMPI -qfree=f90 -qsuffix=f=f90 -qsuffix=cpp=f90"
-  write(ilun,format)""
-  write(ilun,format)"# --- No MPI, f90 ------------------------------------"
-  write(ilun,format)"#F90 = f90"
-  write(ilun,format)"#FFLAGS = -cpp $(DEFINES) -DWITHOUTMPI"
-  write(ilun,format)""
-  write(ilun,format)"# --- No MPI, ifort ----------------------------------"
-  write(ilun,format)"#F90 = ifort"
-  write(ilun,format)"#FFLAGS = -cpp $(DEFINES) -DWITHOUTMPI"
-  write(ilun,format)""
-  write(ilun,format)"# --- MPI, gfortran syntax ------------------------------"
-  write(ilun,format)"#F90 = mpif90 -frecord-marker=4 -O3 -ffree-line-length-none -g -fbacktrace "
-  write(ilun,format)"#FFLAGS = -x f95-cpp-input $(DEFINES)"
-  write(ilun,format)""
-  write(ilun,format)"# --- MPI, gfortran DEBUG syntax ------------------------------ "
-  write(ilun,format)"#F90 = mpif90 -frecord-marker=4 -ffree-line-length-none -fbacktrace -g -O -fbounds-check -Wuninitialized -Wall"
-  write(ilun,format)"#FFLAGS = -x f95-cpp-input -ffpe-trap=zero,underflow,overflow,invalid -finit-real=nan  $(DEFINES)    "
-  write(ilun,format)""
-  write(ilun,format)"# --- MPI, pgf90 syntax ------------------------------"
-  write(ilun,format)"#F90 = mpif90 -O3"
-  write(ilun,format)"#FFLAGS = -Mpreprocess $(DEFINES)"
-  write(ilun,format)""
-  write(ilun,format)"# --- MPI, ifort syntax ------------------------------"
-  write(ilun,format)"#F90 = mpif90"
-  write(ilun,format)"#FFLAGS = -cpp -fast $(DEFINES) -DNOSYSTEM"
-  write(ilun,format)""
-  write(ilun,format)"# --- MPI, ifort syntax, additional checks -----------"
-  write(ilun,format)"#F90 = mpif90"
-  write(ilun,format)"#FFLAGS = -warn all -O0 -g -traceback -fpe0 -ftrapuv -check bounds -cpp $(DEFINES) -DNOSYSTEM"
-  write(ilun,format)""
-  write(ilun,format)""
-  write(ilun,format)"# --- MPI, ifort syntax ------------------------------"
-  write(ilun,format)"#F90 = ftn"
-  write(ilun,format)"#FFLAGS = -xAVX -g -traceback -fpp -fast $(DEFINES) -DNOSYSTEM #-DRT "
+  write(ilun,format)"# GNU compiler (gfortran)"
+  write(ilun,format)"ifeq ($(COMPILER),GNU)"
+  write(ilun,format)"   FFLAGS = -x f95-cpp-input $(DEFINES) -std=legacy"
+  write(ilun,format)"   ifeq ($(MPI),1)"
+  write(ilun,format)"      F90 = $(MPIF90)"
+  write(ilun,format)"   else"
+  write(ilun,format)"      F90 = gfortran"
+  write(ilun,format)"      FFLAGS += -DWITHOUTMPI"
+  write(ilun,format)"   endif"
+  write(ilun,format)"   F90 += -frecord-marker=4 -fbacktrace -ffree-line-length-none -g -fimplicit-none"
+  write(ilun,format)"   ifeq ($(DEBUG),1)"
+  write(ilun,format)"      F90 += -O0 -fbounds-check -Wuninitialized -Wall"
+  write(ilun,format)"      FFLAGS += -ffpe-trap=zero,underflow,overflow,invalid -finit-real=nan"
+  write(ilun,format)"   else"
+  write(ilun,format)"      F90 += -O3"
+  write(ilun,format)"   endif"
+  write(ilun,format)"endif"
  write(ilun,format)""
-  write(ilun,format)"# --- MPI, ifort syntax, additional checks -----------"
-  write(ilun,format)"#F90 = ftn"
-  write(ilun,format)"#FFLAGS = -O3 -g -traceback -fpe0 -ftrapuv -cpp $(DEFINES) -DNOSYSTEM #-DRT"
+  write(ilun,format)"# Intel compiler"
+  write(ilun,format)"ifeq ($(COMPILER),INTEL)"
+  write(ilun,format)"   FFLAGS = -cpp $(DEFINES)"
+  write(ilun,format)"   ifeq ($(MPI),1)"
+  write(ilun,format)"      F90 = $(MPIF90)"
+  write(ilun,format)"      FFLAGS += -DNOSYSTEM"
+  write(ilun,format)"   else"
+  write(ilun,format)"      F90 = ifort"
+  write(ilun,format)"      FFLAGS += -DWITHOUTMPI"
+  write(ilun,format)"   endif"
+  write(ilun,format)"   F90 += -fp-model source"
+  write(ilun,format)"   ifeq ($(DEBUG),1)"
+  write(ilun,format)"      F90 += -warn all -O0 -g -traceback -check bounds"
+  write(ilun,format)"      FFLAGS += -fpe0 -ftrapuv -init=zero -init=snan -init=arrays"
+  write(ilun,format)"   else"
+  write(ilun,format)"      F90 += -O3"
+  write(ilun,format)"   endif"
+  write(ilun,format)"endif"
  write(ilun,format)""
  write(ilun,format)"#############################################################################"
  write(ilun,format)"MOD = mod"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"# MPI librairies"
-  write(ilun,format)"LIBMPI = "
+  write(ilun,format)"LIBMPI ="
  write(ilun,format)"#LIBMPI = -lfmpi -lmpi -lelan"
  write(ilun,format)""
  write(ilun,format)"# --- CUDA libraries, for Titane ---"
  write(ilun,format)"LIBCUDA = -L/opt/cuda/lib  -lm -lcuda -lcudart"
  write(ilun,format)""
  write(ilun,format)"ifeq ($(GRACKLE),1)"
-  write(ilun,format)"# Add include and library install path for grackle and hdf5 here"
-  write(ilun,format)"LIBS_GRACKLE = -L$(HOME)/local/lib -lgrackle -lhdf5 -lz -lgfortran -ldl"
-  write(ilun,format)"LIBS_OBJ     = -I$(HOME)/local/include -DCONFIG_BFLOAT_8 -DH5_USE_16_API -fPIC"
+  write(ilun,format)"   # Add include and library install path for grackle and hdf5 here"
+  write(ilun,format)"   LIBS_GRACKLE = -L$(HOME)/local/lib -lgrackle -lhdf5 -lz -lgfortran -ldl"
+  write(ilun,format)"   LIBS_OBJ     = -I$(HOME)/local/include -DCONFIG_BFLOAT_8 -DH5_USE_16_API -fPIC"
  write(ilun,format)"endif"
  write(ilun,format)"LIBS = $(LIBMPI) $(LIBS_GRACKLE)"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"# Sources directories are searched in this exact order"
-  write(ilun,format)"VPATH = $(shell [ -z $(PATCH) ] || find $(PATCH) -type d):../$(SOLVER):../aton:../hydro:../pm:../poisson:../amr"
+  write(ilun,format)"VPATH = $(shell [ -z $(PATCH) ] || find $(PATCH) -type d):../$(SOLVER):../aton:"
+  write(ilun,format)"ifeq ($(RT),1)"
+  write(ilun,format)"   VPATH += ../rt:"
+  write(ilun,format)"endif"
+  write(ilun,format)"VPATH += ../hydro:../pm:../poisson:../amr:../io"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"# All objects"
  write(ilun,format)"MODOBJ = amr_parameters.o amr_commons.o random.o pm_parameters.o pm_commons.o poisson_parameters.o gr_parameters.o gr_commons.o"
@@ -122,49 +159,60 @@ subroutine output_makefile(filename)
  write(ilun,format)"PMOBJ = init_part.o output_part.o rho_fine.o synchro_fine.o move_fine.o newdt_fine.o particle_tree.o \"
  write(ilun,format)"        add_list.o remove_list.o star_formation.o sink_particle.o feedback.o clump_finder.o clump_merger.o \"
  write(ilun,format)"        flag_formation_sites.o init_sink.o output_sink.o"
+  write(ilun,format)""
+  write(ilun,format)"# GR extra files for GR simulations"
+  write(ilun,format)"PMOBJ += move_fine_gr.o synchro_fine_gr.o"
+  write(ilun,format)""
  write(ilun,format)"# Poisson solver objects"
  write(ilun,format)"POISSONOBJ = init_poisson.o phi_fine_cg.o interpol_phi.o force_fine.o multigrid_coarse.o multigrid_fine_commons.o \"
  write(ilun,format)"             multigrid_fine_fine.o multigrid_fine_coarse.o gravana.o boundary_potential.o rho_ana.o output_poisson.o"
  write(ilun,format)""
  write(ilun,format)"# GR extra files for GR simulations"
  write(ilun,format)"POISSONOBJ += comp_gr_aij.o force_fine_gr.o init_poisson_gr.o interpol_gr_mat.o interpol_gr_pot.o \"
-  write(ilun,format)"		                                    multigrid_fine_commons_gr.o multigrid_fine_fine_gr_ln.o multigrid_fine_fine_gr_nl.o\"
+  write(ilun,format)"		      multigrid_fine_coarse_gr_nl.o multigrid_fine_commons_gr.o multigrid_fine_fine_gr_ln.o multigrid_fine_fine_gr_nl.o \"
  write(ilun,format)"			  source_fine_gr_aij_aij.o source_fine_gr_scalar.o source_fine_gr_vector.o"
-  write(ilun,format)"# force_fine_gr.o "
-  write(ilun,format)"# multigrid_fine_coarse_gr_nl.o "
-  write(ilun,format)""
  write(ilun,format)""
  write(ilun,format)"# Hydro objects"
  write(ilun,format)"HYDROOBJ = init_hydro.o init_flow_fine.o write_screen.o output_hydro.o courant_fine.o godunov_fine.o \"
  write(ilun,format)"           uplmde.o umuscl.o interpol_hydro.o godunov_utils.o condinit.o hydro_flag.o hydro_boundary.o \"
  write(ilun,format)"           boundana.o read_hydro_params.o synchro_hydro_fine.o"
+  write(ilun,format)""
+  write(ilun,format)""
+  write(ilun,format)""
+  write(ilun,format)""
  write(ilun,format)"# Patch objects"
  write(ilun,format)"sinclude $(PATCH)/Makefile"
  write(ilun,format)""
  write(ilun,format)"# All objects"
  write(ilun,format)"AMRLIB = $(AMROBJ) $(HYDROOBJ) $(PMOBJ) $(POISSONOBJ)"
+  write(ilun,format)"ifeq ($(RT),1)"
+  write(ilun,format)"   AMRLIB += $(RTOBJ)"
+  write(ilun,format)"endif"
  write(ilun,format)"# ATON objects"
  write(ilun,format)"ATON_MODOBJ = timing.o radiation_commons.o rad_step.o"
-  write(ilun,format)"ATON_OBJ = observe.o init_radiation.o rad_init.o rad_boundary.o rad_stars.o rad_backup.o ../aton/atonlib/libaton.a"
+  write(ilun,format)"ATON_OBJ = observe.o init_radiation.o rad_init.o rad_boundary.o rad_stars.o \"
+  write(ilun,format)"           rad_backup.o ../aton/atonlib/libaton.a"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"ramses:	$(MODOBJ) $(AMRLIB) ramses.o"
  write(ilun,format)"	$(F90) $(MODOBJ) $(AMRLIB) ramses.o -o $(EXEC)$(NDIM)d $(LIBS)"
  write(ilun,format)"	rm write_makefile.f90"
  write(ilun,format)"	rm write_patch.f90"
  write(ilun,format)"ramses_aton: $(MODOBJ) $(ATON_MODOBJ) $(AMRLIB) $(ATON_OBJ) ramses.o"
-  write(ilun,format)"	$(F90) $(MODOBJ) $(ATON_MODOBJ) $(AMRLIB) $(ATON_OBJ) ramses.o -o $(EXEC)$(NDIM)d $(LIBS) $(LIBCUDA)"
+  write(ilun,format)"	$(F90) $(MODOBJ) $(ATON_MODOBJ) $(AMRLIB) $(ATON_OBJ) ramses.o \"
+  write(ilun,format)"		-o $(EXEC)$(NDIM)d $(LIBS) $(LIBCUDA)"
  write(ilun,format)"	rm write_makefile.f90"
  write(ilun,format)"	rm write_patch.f90"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"write_gitinfo.o: FORCE"
-  write(ilun,format)"	$(F90) $(FFLAGS) -DPATCH=\'$(PATCH)\' -DGITBRANCH=\'$(GITBRANCH)\' -DGITHASH=\'""$(GITHASH)""\' \"
-  write(ilun,format)" -DGITREPO=\'$(GITREPO)\' -DBUILDDATE=\'""$(BUILDDATE)""\' -c ../amr/write_gitinfo.f90 -o $@		"
+  write(ilun,format)"	$(F90) $(FFLAGS) -DPATCH=\'$(PATCH)\' -DGITBRANCH=\'$(GITBRANCH)\' \"
+  write(ilun,format)"		-DGITHASH=\'""$(GITHASH)""\' -DGITREPO=\'$(GITREPO)\' \"
+  write(ilun,format)"		-DBUILDDATE=\'""$(BUILDDATE)""\' -c ../amr/write_gitinfo.f90 -o $@"
  write(ilun,format)"write_makefile.o: FORCE"
  write(ilun,format)"	../utils/scripts/cr_write_makefile.sh $(MAKEFILE_LIST)"
  write(ilun,format)"	$(F90) $(FFLAGS) -c write_makefile.f90 -o $@"
  write(ilun,format)"write_patch.o: FORCE"
  write(ilun,format)"	../utils/scripts/cr_write_patch.sh $(PATCH)"
-  write(ilun,format)"	$(F90) $(FFLAGS) -c write_patch.f90 -o $@"
+  write(ilun,format)"	$(F90) -O0 -c write_patch.f90 -o $@"
  write(ilun,format)"%.o:%.F"
  write(ilun,format)"	$(F90) $(FFLAGS) -c $^ -o $@ $(LIBS_OBJ)"
  write(ilun,format)"%.o:%.f90"
@@ -172,7 +220,7 @@ subroutine output_makefile(filename)
  write(ilun,format)"FORCE:"
  write(ilun,format)"#############################################################################"
  write(ilun,format)"clean:"
-  write(ilun,format)"	rm -f *.o *.$(MOD)"
+  write(ilun,format)"	rm -f *.o *.$(MOD) *.i"
  write(ilun,format)"#############################################################################"

  close(ilun)

--- a/poisson/output_poisson.f90
+++ b/poisson/output_poisson.f90
@@ -115,12 +115,12 @@ subroutine backup_poisson(filename)
                 end do

                 ! Write positions  ! Pos data in .amr files!
-!                 do ivar=1,ndim
-!                    do i=1,ncache
-!                        xdp(i)=xg(ind_grid(i),ivar)+xc(ind,ivar)
-!                    end do
-!                    write(ilun)xdp
-!                 end do
+                 do ivar=1,ndim
+                    do i=1,ncache
+                        xdp(i)=xg(ind_grid(i),ivar)+xc(ind,ivar)
+                    end do
+                    write(ilun)xdp
+                 end do
              end if

           end do

--- a/readgrav_gr.py
+++ b/readgrav_gr.py
+# This script read data from grav_ files and save to .npy
+# Fortran unformatted files seem to be composed with several blocks of different datatype.
+# Each block looks like this:
+# |(int) Size of DATA || (dtype) DATA ||(int) Size of DATA |
+
+import numpy as np
+from struct import *
+import time
+import sys
+
+t1=time.clock()
+#simulation details
+levelmin=int(sys.argv[3])
+levelmax=levelmin
+twotondim=8
+G=int(sys.argv[4])
+
+#files to be read
+path=sys.argv[1]
+#outpath=sys.argv[2]
+fileroot='grav_'+sys.argv[1][-6:-1]+'.out'
+numfiles=int(sys.argv[2])
+firstcount=1
+outfile=fileroot
+
+#internal variable
+datlis=[phi,f1,f2,f3,gr5,gr6,gr7,gr8,gr9,gr10,rho,gr_m1,gr_m2,gr_m3,gr_m4,x,y,z]=[[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[]]
+Ngrid=0
+for i in range(firstcount, firstcount+numfiles):
+    infile=fileroot+str(i).zfill(5)
+    with open(path+infile,'rb') as f:
+        content = f.read()
+    print('Reading '+path+infile+'  : '+str(time.clock()-t1)+' s')
+    pmin=0
+    pmax=48
+
+    ############ 'header info'############
+    info=unpack('i'*3*4,content[pmin:pmax])
+    [ncpu,ndim,nlevelmax,nboundary]=[info[1],info[4],info[7],info[10]]
+
+    ############ levels ############
+    for ilevel in range(levelmin,levelmax+1):
+        ############ nboundary+ncpu ############
+        for ibound in range(1,nboundary+ncpu+1):
+            pmin0=pmax
+            pmax0=pmin0+4*3*2
+            info=unpack('i'*3*2,content[pmin0:pmax0])
+            [currlevel,ncache]=[info[1],info[4]]
+            Ngrid+=ncache*twotondim
+            #print pmin0, pmax0, currlevel, ncache
+            if ncache==0:
+                pmax=pmax0
+                continue
+            ############ twotondim ############
+            for ind in range(1,twotondim+1):
+                j=0
+                ############ parameters ############
+                for N in ([1,2,3,4,5,6,7,8,9,10,11,12,13,14,15]):
+                    ipar=datlis[j]
+                    pmin=pmax0+(8*N-4)+(N-1)*8*ncache
+                    pmax=pmin+ncache*8
+                    #print(pmin,pmax,ncache)
+                    info=unpack('d'*ncache,content[pmin:pmax])
+                    for floatelem in info:
+                        ipar.append(floatelem)
+                    j=j+1
+                    #pmax=pmax+4
+                    #print ind, pmin, pmax, ncache
+                pmax0=pmax+4
+            pmax=pmax0
+    f.close()
+
+print('Transposing: '+str(time.clock()-t1)+' s')
+datlis=np.transpose(datlis)
+#print('Deleting repeating elements: '+str(time.clock()-t1)+' s')
+#datlis=np.vstack({tuple(row) for row in datlis})
+#print('Saving to '+path+outfile+'  : '+str(time.clock()-t1)+' s')
+#np.save(path+outfile,datlis)
+
+print('Mapping to tuple: '+str(time.clock()-t1)+' s')
+datlis=map(tuple,datlis)
+
+print('Finding set of values: '+str(time.clock()-t1)+' s')
+datlis=set(datlis)
+
+print('Mapping back to array: '+str(time.clock()-t1)+' s')
+datlis=map(tuple,datlis)
+
+data=np.zeros((G**3,18))
+for i in range(len(data)):
+    print(i)
+    data[i][0]=datlis[i][0]
+    data[i][1]=datlis[i][1]
+    data[i][2]=datlis[i][2]
+    data[i][3]=datlis[i][3]
+    data[i][4]=datlis[i][4]
+    data[i][5]=datlis[i][5]
+    data[i][6]=datlis[i][6]
+    data[i][7]=datlis[i][7]
+    data[i][8]=datlis[i][8]
+    data[i][9]=datlis[i][9]
+    data[i][10]=datlis[i][10]
+    data[i][11]=datlis[i][11]
+    data[i][12]=datlis[i][12]
+    data[i][13]=datlis[i][13]
+    data[i][14]=datlis[i][14]
+    data[i][15]=datlis[i][15]
+    data[i][16]=datlis[i][16]
+    data[i][17]=datlis[i][17]
+
+print('Saving to '+path+outfile+'  : '+str(time.clock()-t1)+' s')
+np.save(path+outfile,data)
+
+print('Done : '+str(time.clock()-t1)+' s, N = %d'%(len(datlis)))
+sys.exit()
--- a/submit.sh
+++ b/submit.sh
-#!/bin/sh
-
-#SBATCH -n 16
-#SBATCH -t 00:05:00
-#SBATCH -J gramses
-#SBATCH -o ./logs/%j.log
-#SBATCH -e ./logs/%j.err
-#SBATCH -p cosma
-#SBATCH -A durham
-#SBATCH --exclusive
-
-# prepare
-module purge
-module load intel_comp
-module load intel_mpi
-# module load hdfview
-unset I_MPI_HYDRA_BOOTSTRAP
-
-# compile
-#make clean && make
-
-# run
-mpirun -np $SLURM_NTASKS ./bin/ramses3d ./namelist/gr_test.nml
-
-# report
-echo ""
-sacct -j $SLURM_JOBID --format=JobID,JobName,Partition,AllocCPUS,Elapsed,ExitCode
-exit