Re: need help on isothermal galaxy simulation with Gadget2

From: yanbin YANG <yanbin.yang_at_gmail.com>
Date: Tue, 24 Nov 2009 14:57:50 +0100

Dear Sander,

Many thanks! It's my fault, I didn't notice that small change in the
keyword, I copy
the Makefile from

      parameterfiles/galaxy.Makefile

where, the old keyword " -DISOTHERMAL " is used, instead of " ... _EQS".


it works now.

regards,
Yanbin.


Sander Valcke wrote:
>
> Dear Yang,
>
> I believe the correct flag to use is -DISOTHERM_EQS?
>
> regards,
>
> Sander
>
> yanbin YANG wrote:
>>
>> Dear all,
>>
>> I'm testing galaxy simulations with gadget2, the public version of
>> 2.0.4.
>>
>> When I run an isolate galaxy with *isothermal* gas, I find that, the
>> mean internal
>> energy of gas is kept increasing quickly, i.e., over 1 Gyr, by a
>> factor of >1000.
>> I think the gas in the simulation is not "isothermal". The
>> situation is even worse
>> when I run a galaxy collision, all the gas particle were so heated
>> and pushed out.
>>
>> I have compile the code with option of "-DISOTHERMAL". Could anyone help
>> me on this? Or point out where I have made a mistake. I have paste
>> the detailed
>> information of simulation below in case you have time to check.
>>
>>
>> Many thanks in advance!
>>
>> Yanbin YANG.
>>
>>
>>
>> PS, details of my simulation.
>>
>> ======================
>> CONTENT below
>> - Sect. 1) Setup of IC
>> - Sect. 2) Makefile I used.
>> - Sect. 3) parameter file for gadget.
>> ======================
>>
>>
>> Sect. 1) Setup of IC
>> --------------------
>> IC is an isolate galaxy that have been reached equilibrium. According
>> to the manual,
>> I have set the block of "u" to be zero. Actually, I set all gas
>> properties to be zero,
>> except the positions and velocities. Then specify the initial
>> temperature in
>> the parameter file.
>>
>>
>> Sect. 2) Make file I used.
>> #----------------------------------------------------------------------
>> # From the list below, please activate/deactivate the options that
>> # apply to your run. If you modify any of these options, make sure
>> # that you recompile the whole code by typing "make clean; make".
>> #
>> # Look at end of file for a brief guide to the compile-time options.
>> #----------------------------------------------------------------------
>>
>>
>> #--------------------------------------- Basic operation mode of code
>> #OPT += -DPERIODIC
>> OPT += -DUNEQUALSOFTENINGS
>> #--------------------------------------- Things that are always
>> recommended
>> OPT +=
>> -DPEANOHILBERT OPT
>> += -DWALLCLOCK
>> #--------------------------------------- TreePM Options
>> #OPT += -DPMGRID=256 #OPT +=
>> -DPLACEHIGHRESREGION=3 #OPT +=
>> -DENLARGEREGION=1.2 #OPT +=
>> -DASMTH=1.25 #OPT +=
>> -DRCUT=4.5
>> #--------------------------------------- Single/Double Precision
>> #OPT += -DDOUBLEPRECISION #OPT
>> += -DDOUBLEPRECISION_FFTW
>> #--------------------------------------- Time integration options
>> OPT += -DSYNCHRONIZATION
>> #OPT += -DFLEXSTEPS
>> #OPT += -DPSEUDOSYMMETRIC OPT
>> += -DNOSTOP_WHEN_BELOW_MINTIMESTEP #OPT +=
>> -DNOPMSTEPADJUSTMENT
>> #--------------------------------------- Output options
>> #OPT += -DHAVE_HDF5 #OPT +=
>> -DOUTPUTPOTENTIAL #OPT +=
>> -DOUTPUTACCELERATION #OPT +=
>> -DOUTPUTCHANGEOFENTROPY #OPT +=
>> -DOUTPUTTIMESTEP
>> #--------------------------------------- Things for special behaviour
>> #OPT += -DNOGRAVITY
>> #OPT += -DNOTREERND
>> #OPT += -DNOTYPEPREFIX_FFTW
>> #OPT += -DLONG_X=60
>> #OPT += -DLONG_Y=5
>> #OPT += -DLONG_Z=0.2
>> #OPT += -DTWODIMS
>> #OPT += -DSPH_BND_PARTICLES
>> #OPT += -DNOVISCOSITYLIMITER
>> OPT += -DCOMPUTE_POTENTIAL_ENERGY
>> #OPT += -DLONGIDS
>> OPT += -DISOTHERMAL
>> #OPT += -DSELECTIVE_NO_GRAVITY=2+4+8+16
>> #--------------------------------------- Testing and Debugging options
>> #OPT += -DFORCETEST=0.1
>> #--------------------------------------- Glass making
>> #OPT += -DMAKEGLASS=262144
>> #----------------------------------------------------------------------
>> # Here, select compile environment for the target machine. This may need
>> # adjustment, depending on your local system. Follow the examples to add
>> # additional target platforms, and to get things properly
>> compiled.
>> #----------------------------------------------------------------------
>> #--------------------------------------- Select some defaults
>>
>> CC = mpicc # sets the C-compiler
>> OPTIMIZE = -O2 -Wall -g # sets optimization and warning flags
>> MPICHLIB = -lmpich
>> #--------------------------------------- Select target computer
>>
>> SYSTYPE="MPA"
>> #SYSTYPE="Mako"
>> #SYSTYPE="Regatta"
>> #SYSTYPE="RZG_LinuxCluster"
>> #SYSTYPE="RZG_LinuxCluster-gcc"
>> #SYSTYPE="Opteron" #---------------------------------------
>> Adjust settings for target computer
>>
>> ifeq ($(SYSTYPE),"MPA")
>> CC = mpicc OPTIMIZE = -O3 -Wall GSL_INCL = -I/usr/include
>> GSL_LIBS = -L/usr/lib FFTW_INCL=
>> FFTW_LIBS= MPICHLIB = #HDF5INCL =
>> -I/opt/hdf5/include
>> #HDF5LIB = -L/opt/hdf5/lib -static -lhdf5 -lz
>> endif
>> ifeq ($(SYSTYPE),"Opteron")
>> CC = mpicc OPTIMIZE = -O3 -Wall -m64
>> GSL_INCL = -L/usr/local/include
>> GSL_LIBS = -L/usr/local/lib -static
>> FFTW_INCL= FFTW_LIBS=
>> MPICHLIB = HDF5INCL = -I/opt/hdf5/include
>> HDF5LIB = -L/opt/hdf5/lib -static -lhdf5 -lz
>> endif
>> ifeq ($(SYSTYPE),"Mako")
>> CC = mpicc # sets the C-compiler
>> OPTIMIZE = -O3 -march=athlon-mp -mfpmath=sse
>> GSL_INCL = GSL_LIBS
>> =
>> FFTW_INCL=
>> FFTW_LIBS= MPICHLIB
>> =
>> endif
>> ifeq ($(SYSTYPE),"Regatta")
>> CC = mpcc_r OPTIMIZE = -O5 -qstrict -qipa -q64
>> GSL_INCL = -I/afs/rzg/u/vrs/gsl_psi64/include
>> GSL_LIBS = -L/afs/rzg/u/vrs/gsl_psi64/lib FFTW_INCL=
>> -I/afs/rzg/u/vrs/fftw_psi64/include FFTW_LIBS=
>> -L/afs/rzg/u/vrs/fftw_psi64/lib -q64 -qipa MPICHLIB
>> = HDF5INCL =
>> -I/afs/rzg/u/vrs/hdf5_psi64/include HDF5LIB =
>> -L/afs/rzg/u/vrs/hdf5_psi64/lib -lhdf5 -lz
>> endif
>> ifeq ($(SYSTYPE),"RZG_LinuxCluster")
>> CC = mpicci OPTIMIZE = -O3 -ip # Note:
>> Don't use the "-rcd" optimization of Intel's compiler! (causes code
>> crashes)
>> GSL_INCL =
>> -I/afs/rzg/u/vrs/gsl_linux/include
>>
>> GSL_LIBS = -L/afs/rzg/u/vrs/gsl_linux/lib
>> -static
>> FFTW_INCL=
>> -I/afs/rzg/u/vrs/fftw_linux/include
>>
>> FFTW_LIBS=
>> -L/afs/rzg/u/vrs/fftw_linux/lib
>>
>> HDF5INCL =
>> -I/afs/rzg/u/vrs/hdf5_linux/include
>>
>> HDF5LIB = -L/afs/rzg/u/vrs/hdf5_linux/lib -static -lhdf5
>> -L/afs/rzg/u/vrs/zlib_linux/lib -lz
>> endif
>>
>>
>>
>> ifeq ($(SYSTYPE),"RZG_LinuxCluster-gcc")
>> CC = mpiccg OPTIMIZE = -Wall -g -O3
>> -march=pentium4
>> GSL_INCL = -I/afs/rzg/u/vrs/gsl_linux_gcc3.2/include
>> GSL_LIBS = -L/afs/rzg/u/vrs/gsl_linux_gcc3.2/lib FFTW_INCL=
>> -I/afs/rzg/u/vrs/fftw_linux_gcc3.2/include
>> FFTW_LIBS= -L/afs/rzg/u/vrs/fftw_linux_gcc3.2/lib HDF5INCL =
>> -I/afs/rzg/u/vrs/hdf5_linux/include HDF5LIB =
>> -L/afs/rzg/u/vrs/hdf5_linux/lib -static -lhdf5
>> -L/afs/rzg/u/vrs/zlib_linux/lib -lz
>> endif
>>
>>
>>
>> ifneq (HAVE_HDF5,$(findstring HAVE_HDF5,$(OPT)))
>> HDF5INCL = HDF5LIB
>> =
>> endif
>> OPTIONS = $(OPTIMIZE) $(OPT)
>>
>> EXEC = Gadget2
>>
>> OBJS = main.o run.o predict.o begrun.o endrun.o global.o \
>> timestep.o init.o restart.o io.o \
>> accel.o read_ic.o ngb.o \
>> system.o allocate.o density.o \
>> gravtree.o hydra.o driftfac.o \
>> domain.o allvars.o potential.o \
>> forcetree.o peano.o gravtree_forcetest.o \
>> pm_periodic.o pm_nonperiodic.o longrange.o INCL =
>> allvars.h proto.h tags.h Makefile
>>
>>
>> CFLAGS = $(OPTIONS) $(GSL_INCL) $(FFTW_INCL) $(HDF5INCL)
>>
>>
>> ifeq (NOTYPEPREFIX_FFTW,$(findstring NOTYPEPREFIX_FFTW,$(OPT))) #
>> fftw installed with type prefix?
>> FFTW_LIB = $(FFTW_LIBS) -lrfftw_mpi -lfftw_mpi -lrfftw
>> -lfftw
>> else
>>
>> ifeq (DOUBLEPRECISION_FFTW,$(findstring
>> DOUBLEPRECISION_FFTW,$(OPT))) FFTW_LIB
>> = $(FFTW_LIBS) -ldrfftw_mpi -ldfftw_mpi -ldrfftw
>> -ldfftw
>> else
>>
>> FFTW_LIB = $(FFTW_LIBS) -lsrfftw_mpi -lsfftw_mpi -lsrfftw
>> -lsfftw
>> endif
>>
>> endif
>>
>>
>>
>> LIBS = $(HDF5LIB) -g $(MPICHLIB) $(GSL_LIBS) -lgsl -lgslcblas
>> -lm $(FFTW_LIB)
>>
>> $(EXEC): $(OBJS)
>> $(CC) $(OBJS) $(LIBS) -o $(EXEC)
>> $(OBJS): $(INCL)
>>
>>
>> clean:
>> rm -f $(OBJS) $(EXEC)
>>
>>
>>
>>
>>
>> Sect. 3) my parameter file
>>
>> % Relevant
>> files
>>
>>
>> InitCondFile gdMRv9Ae.go.10.00C
>> OutputDir gdMRv9Ae/
>> EnergyFile energy.txt
>> InfoFile info.txt TimingsFile timings.txt
>> CpuFile cpu.txt RestartFile restart
>> SnapshotFileBase gdMRv9Ae
>>
>> OutputListFilename gdMRv9Ae/output_list.txt
>>
>> % CPU time -limit
>>
>> TimeLimitCPU 360000 % = 10 hours
>> ResubmitOn 0 ResubmitCommand my-scriptfile
>> % Code options
>>
>>
>> ICFormat 1
>> SnapFormat 1
>> ComovingIntegrationOn 0
>>
>> TypeOfTimestepCriterion 0
>> OutputListOn 0
>> PeriodicBoundariesOn 0
>>
>> % Caracteristics of run
>>
>> TimeBegin 0.0 % Begin of the simulation
>> TimeMax 3.0 % End of the simulation
>> Omega0 0
>> OmegaLambda 0
>> OmegaBaryon 0
>> HubbleParam 0.7
>> BoxSize 0
>>
>> % Output frequency
>>
>> TimeBetSnapshot 0.006
>> TimeOfFirstSnapshot 0 CpuTimeBetRestartFile 3600.0 ; here
>> in seconds
>> TimeBetStatistics 0.05
>> NumFilesPerSnapshot 1
>> NumFilesWrittenInParallel 1
>>
>>
>>
>> % Accuracy of time integration
>>
>> ErrTolIntAccuracy 0.025
>>
>> CourantFac 0.15 MaxSizeTimestep 0.005
>> MinSizeTimestep 0.0001
>>
>>
>>
>>
>> % Tree algorithm, force accuracy, domain update frequency
>>
>> ErrTolTheta 0.3 TypeOfOpeningCriterion
>> 1 ErrTolForceAcc 0.005
>> TreeDomainUpdateFrequency 0.1
>>
>>
>> % Further parameters of SPH
>>
>> DesNumNgb 40
>> MaxNumNgbDeviation 2
>> ArtBulkViscConst 3.8
>> InitGasTemp 10000 % always ignored if set to 0
>> MinGasTemp 10000
>> % Memory allocation
>>
>> PartAllocFactor 9.5
>> TreeAllocFactor 9.5
>> BufferSize 100 % in MByte
>>
>>
>> % System of units
>>
>> UnitLength_in_cm 3.085678e21 ; 1.0 kpc
>> UnitMass_in_g 1.989e43 ; 1.0e10 solar masses
>> UnitVelocity_in_cm_per_s 1e5 ; 1 km/sec
>> GravityConstantInternal 0
>> %
>> Softening lengths
>>
>> MinGasHsmlFractional 0.25
>>
>> SofteningGas 0.5
>> SofteningHalo 0.5
>> SofteningDisk 0.5
>> SofteningBulge 0.5 SofteningStars 0.5
>> SofteningBndry 0.5 SofteningGasMaxPhys 0.5
>> SofteningHaloMaxPhys 0.5
>> SofteningDiskMaxPhys 0.5
>> SofteningBulgeMaxPhys 0.5
>> SofteningStarsMaxPhys 0.5
>> SofteningBndryMaxPhys 0.5
>>
>>
>>
>>
>> MaxRMSDisplacementFac 0.2
>>
>>
>>
>>
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>
Received on 2009-11-24 14:58:00

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