Instalar 2LPT

(...)

• Paracompilar o código, você deve ter fftw-2.1.5 instalado em seu sistema. Para mais detalhes, consulte este post.

- To be able to compile the code, you should have FFTW 2.1.5 installed in your system
(go to fftw.org if you don't have it)

- If your installation of FFTW is not in the standard directory, change the first line
in 2lpt_ic.f to get the info file from the appropriate directory

- To compile the 2LPT code,

g77 -O3 -o 2lpt_ic.exe 2lpt_ic.f  -lsrfftw -lsfftw

the last two flags assume FFTW is installed in both single and double precision,
thus the "s" is appended to pick up the single precision version of the library.

- The code asks for a few parameters, in turn

Omega (Omega_m=dark+baryons) Omega_Lambda

h (Hubble in units of 100 km/s/Mpc)

Transfer function file (a CMBFAST file is assumed)

sigma8 at z=0

Box Dimensions in Mpc/h

redshift of the box (at which initial conditions are desired)

ZA (enter 0) or 2LPT (enter 1) initial conditions

Number of Files per Snapshot (this is from Gadget2, how many files you want the output in)

Output file

initialization (an integer to set the random number generator)

- An input file with default values is included, you can just run the code as

2lpt_ic.exe < input_test

to make sure it works after compilation. It will generate two ouput files, pos_test.0
and pos_test.1


- To change the number of particles you must edit the third line of the code (2lpt_ic.f)

Just change the integer j, The number of particles is Ngrid**3=(2*j)**3

- The output of the code includes a header appropriate for Gadget2 runs.

Instalar GADGET2

      Descrevo sucintamente os passos para instalação do código GADGET2 para simulações cosmológicas de N-corpos. Os passos aqui descritos foram adaptados de [1] e [2]. A instalação foi realizada em um Ubuntu 14.04.

Primeiramente, é importante ter instalados:

       $ sudo apt-get update
       $ sudo apt-get install build-essentials
       $ sudo apt-get install gfortran

      Precisaremos baixar o código GADGET aqui, a biblioteca GSL (GNU scientific library) aqui e a FFTW (fastest Fourier transform in the West library) aqui. Vamos descompactar o conteúdo de cada um desses arquivos para três pastas diferentes em HOME. Respectivamente, GADGET2, gsl-1.16 e fftw-2.1.5. Antes de trabalharmos com eles, vamos instalar a biblioteca MPI:

       $ sudo apt-get install libcr-dev mpich2 mpich2-doc

• Depois disso, vamos instalar a biblioteca GSL:

       $ cd gsl-1.16
       $ ./configure
       $ make
       $ sudo make install

• E então, a fftw:

       $ cd fftw-2.1.5
       $ ./configure --enable-mpi --enable-type-prefix --enable-float
       $ make
       $ sudo make install
       $ make clean
       $ ./configure --enable-mpi --enable-type-prefix

       $ make
       $ sudo make install

• Procure agora, dentro da pasta Gadget-2.0.7/Gadget2 o arquivo Makefile.Configure-o para que fique como:

#----------------------------------------------------------------------
# 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=128
#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
#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   +=  -DISOTHERM_EQS
#OPT   +=  -DADAPTIVE_GRAVSOFT_FORGAS
#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="OpteronMPA"
#SYSTYPE="OPA-Cluster32"
#SYSTYPE="OPA-Cluster64"


#--------------------------------------- Adjust settings for target computer

ifeq ($(SYSTYPE),"MPA")
CC       =  mpicc  
OPTIMIZE =  -O3 -Wall
GSL_INCL = -I/usr/local/include
GSL_LIBS = -L/usr/local/lib
FFTW_INCL= -I/usr/local/include
FFTW_LIBS= -L/usr/local/lib
MPICHLIB = -L/usr/lib
endif


ifeq ($(SYSTYPE),"OpteronMPA")
CC       =  mpicc  
OPTIMIZE =  -O3 -Wall -m64
GSL_INCL =  -L/usr/local/include
GSL_LIBS =  -L/usr/local/lib
FFTW_INCL=
FFTW_LIBS=
MPICHLIB =
HDF5INCL =  -I/opt/hdf5/include
HDF5LIB  =  -L/opt/hdf5/lib -lhdf5 -lz  -Wl,"-R /opt/hdf5/lib"
endif


ifeq ($(SYSTYPE),"OPA-Cluster32")
CC       =  mpicc  
OPTIMIZE =  -O3 -Wall
GSL_INCL =  -I/afs/rzg/bc-b/vrs/opteron32/include
GSL_LIBS =  -L/afs/rzg/bc-b/vrs/opteron32/lib  -Wl,"-R /afs/rzg/bc-b/vrs/opteron32/lib"
FFTW_INCL=  -I/afs/rzg/bc-b/vrs/opteron32/include
FFTW_LIBS=  -L/afs/rzg/bc-b/vrs/opteron32/lib
MPICHLIB =
HDF5INCL = 
HDF5LIB  =  -lhdf5 -lz
endif


ifeq ($(SYSTYPE),"OPA-Cluster64")
CC       =  mpicc  
OPTIMIZE =  -O3 -Wall -m64
GSL_INCL =  -I/afs/rzg/bc-b/vrs/opteron64/include
GSL_LIBS =  -L/afs/rzg/bc-b/vrs/opteron64/lib  -Wl,"-R /afs/rzg/bc-b/vrs/opteron64/lib"
FFTW_INCL=  -I/afs/rzg/bc-b/vrs/opteron64/include
FFTW_LIBS=  -L/afs/rzg/bc-b/vrs/opteron64/lib
MPICHLIB =
HDF5INCL = 
HDF5LIB  =  -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 =
HDF5INCL = 
HDF5LIB  =  -lhdf5 -lz
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  -Wl,"-R /afs/rzg/u/vrs/gsl_linux/lib"
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 -lhdf5 -lz  -Wl,"-R /afs/rzg/u/vrs/hdf5_linux/lib"
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  -Wl,"-R /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  -lhdf5 -lz  -Wl,"-R /afs/rzg/u/vrs/hdf5_linux/lib"
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)


#-----------------------------------------------------------------------
#
#   Brief guide to compile-time options of the code. More information
#   can be found in the code documentation.
#
# - PERIODIC:  
#     Set this if you want to have periodic boundary conditions.
#
# - UNEQUALSOFTENINGS:
#     Set this if you use particles with different gravitational
#     softening lengths.
#
# - PEANOHILBERT:   
#     This is a tuning option. When set, the code will bring the
#     particles after each domain decomposition into Peano-Hilbert
#     order. This improves cache utilization and performance.
# 
# - WALLCLOCK:      
#     If set, a wallclock timer is used by the code to measure internal
#     time consumption (see cpu-log file).  Otherwise, a timer that
#     measures consumed processor ticks is used.
#
# - PMGRID:    
#     This enables the TreePM method, i.e. the long-range force is
#     computed with a PM-algorithm, and the short range force with the
#     tree. The parameter has to be set to the size of the mesh that
#     should be used, (e.g. 64, 96, 128, etc). The mesh dimensions need
#     not necessarily be a power of two.  Note: If the simulation is
#     not in a periodic box, then a FFT method for vacuum boundaries is
#     employed, using an actual mesh with dimension twice(!) that
#     specified by PMGRID.
#
# - PLACEHIGHRESREGION:
#     If this option is set (will only work together with PMGRID), then
#     the long range force is computed in two stages: One Fourier-grid
#     is used to cover the whole simulation volume, allowing the
#     computation of the longe-range force.  A second Fourier mesh is
#     placed on the region occupied by "high-resolution" particles,
#     allowing the computation of an intermediate scale force. Finally,
#     the force on short scales is computed with the tree. This
#     procedure can be useful for "zoom-simulations", provided the
#     majority of particles (the high-res particles) are occupying only
#     a small fraction of the volume. To activate this option, the
#     parameter needs to be set to an integer bit mask that encodes the
#     particle types that make up the high-res particles.
#     For example, if types 0, 1, and 4 form the high-res
#     particles, set the parameter to PLACEHIGHRESREGION=19, because
#     2^0 + 2^1 + 2^4 = 19. The spatial region covered by the high-res
#     grid is determined automatically from the initial conditions.
#     Note: If a periodic box is used, the high-res zone may not intersect
#     the box boundaries.
#
# - ENLARGEREGION:
#     The spatial region covered by the high-res zone has a fixed size
#     during the simulation, which initially is set to the smallest
#     region that encompasses all high-res particles. Normally, the
#     simulation will be interrupted if high-res particles leave this
#     region in the course of the run. However, by setting this
#     parameter to a value larger than one, the size of the high-res
#     region can be expanded, providing a buffer region.  For example,
#     setting it to 1.4 will enlarge its side-length by 40% (it remains
#     centered on the high-res particles). Hence, with this setting, the
#     high-res region may expand or move by a limited amount.
#     Note: If SYNCHRONIZATION is activated, the code will be able to
#     continue even if high-res particles leave the initial high-res
#     grid. In this case, the code will update the size and position of
#     the grid that is placed onto the high-resolution region
#     automatically. To prevent that this potentially happens every
#     single PM step, one should nevertheless assign a value slightly
#     larger than 1 to ENLARGEREGION.
#
# - ASMTH:
#     This can be used to override the value assumed for the scale that
#     defines the long-range/short-range force-split in the TreePM
#     algorithm. The default value is 1.25, in mesh-cells.
#
# - RCUT:
#     This can be used to override the maximum radius in which the
#     short-range tree-force is evaluated (in case the TreePM algorithm
#     is used). The default value is 4.5, given in mesh-cells.
#
# - DOUBLEPRECISION:
#     This makes the code store and compute internal particle data in
#     double precision. Note that output files are nevertheless written
#     by converting the particle data to single precision.
#
# - DDOUBLEPRECISION_FFTW:
#     If this is set, the code will use the double-precision version of
#     FTTW, provided the latter has been explicitly installed with a
#     "d" prefix, and NOTYPEPREFIX_FFTW is not set. Otherwise the
#     single precision version ("s" prefix) is used.
#
# - SYNCHRONIZATION:
#     When this is set, particles are kept in a binary hierarchy of
#     timesteps and may only increase their timestep if the new
#     timestep will put them into synchronization with the higher time
#     level.
#
# - FLEXSTEPS:
#     This is an alternative to SYNCHRONIZATION. Particle timesteps are
#     here allowed to be integer multiples of the minimum timestep that
#     occurs among the particles, which in turn is rounded down to the
#     nearest power-of-two devision of the total simulated
#     timespan. This option distributes particles more evenly over
#     individual system timesteps, particularly once a simulation has
#     run for a while, and may then result in a reduction of work-load
#     imbalance losses.
#
# - PSEUDOSYMMETRIC:
#     When this option is set, the code will try to "anticipate"
#     timestep changes by extrapolating the change of the acceleration
#     into the future. This can in certain idealized cases improve the
#     long-term integration behaviour of periodic orbits, but should
#     make little or no difference in most real-world applications. May
#     only be used together with SYNCHRONIZATION.
#
# - NOSTOP_WHEN_BELOW_MINTIMESTEP:
#     If this is activated, the code will not terminate when the
#     timestep falls below the value of MinSizeTimestep specified in
#     the parameterfile. This is useful for runs where one wants to
#     enforce a constant timestep for all particles. This can be done
#     by activating this option, and by setting MinSizeTimestep and
#     MaxSizeTimestep to an equal value.
#
# - NOPMSTEPADJUSTMENT:
#     When this is set, the long-range timestep for the PM-force
#     computation (when the TreePM algorithm is used) is always
#     determined by MaxSizeTimeStep.  Otherwise, it is determined by
#     the MaxRMSDisplacement parameter, or MaxSizeTimeStep, whichever
#     gives the smaller step.
#
# - HAVE_HDF5:
#     If this is set, the code will be compiled with support for input
#     and output in the HDF5 format. You need to have the HDF5
#     libraries and headers installed on your computer for this option
#     to work. The HDF5 format can then be selected as format "3" in
#     Gadget's parameterfile.
#
# - OUTPUTPOTENTIAL:
#     This will make the code compute gravitational potentials for
#     all particles each time a snapshot file is generated. The values
#     are then included in the snapshot file. Note that the computation
#     of the values of the gravitational potential costs additional CPU.
#
# - OUTPUTACCELERATION:
#     This will include the physical acceleration of each particle in
#     snapshot files.
#
# - OUTPUTCHANGEOFENTROPY:
#     This will include the rate of change of entropy of gas particles
#     in snapshot files.
#
# - OUTPUTTIMESTEP: 
#     This will include the current timesteps of all particles in the
#     snapshot files.
#
# - NOGRAVITY     
#     This switches off gravity. Useful only for pure SPH simulations
#     in non-expanding space.
#
# - NOTREERND:      
#     If this is not set, the tree construction will succeed even when
#     there are a few particles at identical locations. This is done by
#     `rerouting' particles once the node-size has fallen below 1.0e-3
#     of the softening length. When this option is activated, this will
#     be surpressed and the tree construction will always fail if there
#     are particles at extremely close coordinates.
#
# - NOTYPEPREFIX_FFTW:
#     This is an option that signals that FFTW has been compiled
#     without the type-prefix option, i.e. no leading "d" or "s"
#     characters are used to access the library.
#
# - LONG_X/Y/Z:
#     These options can be used together with PERIODIC and NOGRAVITY only.
#     When set, the options define numerical factors that can be used to
#     distorts the periodic simulation cube into a parallelepiped of
#     arbitrary aspect ratio. This can be useful for idealized SPH tests.
#
# - TWODIMS:
#     This effectively switches of one dimension in SPH, i.e. the code
#     follows only 2d hydrodynamics in the xy-, yz-, or xz-plane. This
#     only works with NOGRAVITY, and if all coordinates of the third
#     axis are exactly equal. Can be useful for idealized SPH tests.
#
# - SPH_BND_PARTICLES:
#     If this is set, particles with a particle-ID equal to zero do not
#     receive any SPH acceleration. This can be useful for idealized
#     SPH tests, where these particles represent fixed "walls".
#
# - NOVISCOSITYLIMITER:  
#     If this is set, the code will not try to put an upper limit on
#     the viscous force in case an implausibly high pair-wise viscous
#     force (which may lead to a particle 'reflection' in case of poor
#     timestepping) should arise. Note: For proper settings of the
#     timestep parameters, this situation should not arise.
#
# - COMPUTE_POTENTIAL_ENERGY:
#     When this option is set, the code will compute the gravitational
#     potential energy each time a global statistics is computed. This
#     can be useful for testing global energy conservation.
#
# - LONGIDS:
#     If this is set, the code assumes that particle-IDs are stored as
#     64-bit long integers. This is only really needed if you want to
#     go beyond ~2 billion particles.
#
# - ISOTHERM_EQS:
#     This special option makes the gas behave like an isothermal gas
#     with equation of state P = cs^2 * rho. The sound-speed cs is set by
#     the thermal energy per unit mass in the intial conditions,
#     i.e. cs^2=u. If the value for u is zero, then the initial gas
#     temperature in the parameter file is used to define the sound speed
#     according to cs^2 = 3/2 kT/mp, where mp is the proton mass.
#
# - ADAPTIVE_GRAVSOFT_FORGAS:
#     When this option is set, the gravitational softening lengths used for
#     gas particles is tied to their SPH smoothing length. This can be useful
#     for dissipative collapse simulations. The option requires the setting
#     of UNEQUALSOFTENINGS.
#
# - SELECTIVE_NO_GRAVITY:
#     This can be used for special computations where one wants to
#     exclude certain particle types from receiving gravitational
#     forces. The particle types that are excluded in this fashion are
#     specified by a bit mask, in the same as for the PLACEHIGHRESREGION
#     option.
#
# - FORCETEST:      
#     This can be set to check the force accuracy of the code. The
#     option needs to be set to a number between 0 and 1 (e.g. 0.01),
#     which is taken to specify a random fraction of particles for
#     which at each timestep forces by direct summation are
#     computed. The normal tree-forces and the correct direct
#     summation forces are collected in a file. Note that the
#     simulation itself is unaffected by this option, but it will of
#     course run much(!) slower, especially if
#     FORCETEST*NumPart*NumPart >> NumPart. Note: Particle IDs must
#     be set to numbers >=1 for this to work.
#
# - MAKEGLASS
#     This option can be used to generate a glass-like particle
#     configuration. The value assigned gives the particle load,
#     which is initially generated as a Poisson sample and then
#     evolved towards a glass with the sign of gravity reversed.
#
#-----------------------------------------------------------------------
 

(...falta terminar...)

Instruções para GADGET2

Aqui, alguns tutoriais de instalação do simulator de N-body GADGET2:

https://elbrunz.wordpress.com/2012/01/07/my-first-gadget2-tests/

Gnuplot-iostream interface

Descritivo de como utilizar a linguagem c++ para manipular gráficos do GNUPlot.

http://www.stahlke.org/dan/gnuplot-iostream/