first commit

Makefile

@@ -0,0 +1,101 @@
+########## User-definable stuff ##########
+#
+###Compiler and compilation options
+COMP_SER = gcc
+COMP_MPI = mpicc
+OPTIONS = -Wall -O3
+#
+### Behavioural flags
+#Use double precision integer (enable in general)
+DEFINEFLAGS += -D_LONGIDS
+#Generate debug help. Only useful for development
+DEFINEFLAGS += -D_DEBUG
+#Use double precision floating point? Set to "yes" or "no"
+USE_SINGLE_PRECISION = yes
+#Use OMP parallelization? Set to "yes" or "no"
+USE_OMP = yes
+#Use MPI parallelization? Set to "yes" or "no"
+USE_MPI = yes
+#
+###Path to libraries and headers
+###If two or more of the dependencies reside in the same paths, only
+###one instance is necessary.
+#GSL
+GSL_INC = -I/home/damonge/include
+GSL_LIB = -L/home/damonge/lib
+#FFTW
+FFTW_INC = 
+FFTW_LIB = 
+#cfitsio
+FITS_INC = 
+FITS_LIB = 
+#
+########## End of user-definable ##########
+
+ifeq ($(strip $(USE_OMP)),yes)
+OPTIONS += -fopenmp
+DEFINEFLAGS += -D_HAVE_OMP
+endif #OMP
+
+ifeq ($(strip $(USE_MPI)),yes)
+DEFINEFLAGS += -D_HAVE_MPI
+COMP_PAR = $(COMP_MPI)
+else #MPI
+COMP_PAR = $(COMP_SER)
+endif #MPI
+
+ifeq ($(strip $(USE_SINGLE_PRECISION)),yes)
+DEFINEFLAGS += -D_SPREC
+
+ifeq ($(strip $(USE_OMP)),yes)
+LIB_FFTW += -lfftw3f_omp
+endif #OMP
+ifeq ($(strip $(USE_MPI)),yes)
+LIB_FFTW += -lfftw3f_mpi
+endif #MPI
+LIB_FFTW += -lfftw3f
+
+else #SINGLE_PRECISION
+
+ifeq ($(strip $(USE_OMP)),yes)
+LIB_FFTW += -lfftw3_omp
+endif #OMP
+ifeq ($(strip $(USE_MPI)),yes)
+LIB_FFTW += -lfftw3_mpi
+endif #MPI
+LIB_FFTW += -lfftw3
+
+endif #SINGLE_PRECISION
+
+
+OPTIONS += $(DEFINEFLAGS)
+
+INC_ALL = -I./src $(GSL_INC) $(FFTW_INC) $(FITS_INC)
+LIB_ALL = $(GSL_LIB) $(FFTW_LIB) $(FITS_LIB) -lgsl -lgslcblas $(LIB_FFTW) -lcfitsio -lm
+
+COMMONO = src/common.o
+COSMOMADO = src/cosmo_mad.o
+COSMOO = src/cosmo.o
+FOURIERO = src/fourier.o
+GRIDO = src/grid_tools.o
+IOO = src/io.o
+MAIN = src/main.c
+OFILES = $(COMMONO) $(COSMOMADO) $(COSMOO) $(FOURIERO) $(GRIDO) $(IOO)
+
+EXEC = CoLoRe
+
+default : $(EXEC)
+
+%.o : %.c
+	$(COMP_CC) $(OPTIONS) $(INC_ALL) -c $< -o $@
+
+$(OFILES) : COMP_CC := $(COMP_PAR)
+
+$(EXEC) : $(OFILES)
+	$(COMP_PAR) $(OPTIONS) $(INC_ALL) $(OFILES) $(MAIN) -o $(EXEC) $(LIB_ALL)
+
+clean :
+	rm -f src/*.o
+
+cleaner : 
+	rm -f *~ src/*.o src/*~  $(EXEC)

README

@@ -0,0 +1,89 @@
+CoLoRe - Cosmological Lognormal Realizations
+
+
+1 Methods.
+
+CoLoRe is a parallel C code for generating fast mock realizations
+of a given galaxy sample using a lognormal model for the matter density.
+The process is as follows:
+ 1) Generate a Gaussian realization of the linearized density field at
+    z=0, as well as the corresponding linear radial velocity field.
+    This is done in a Cartesian grid.
+ 2) Calculate the redshift of each grid point and linearly evolve
+    the density and velocity to that redshift. Include a linear galaxy
+    bias (redshift-dependent) in the evolution of the overdensity field.
+ 3) Log-normalize the density field and poisson-sample it using an
+    input N(z). Each source is randomly placed inside its cell.
+ 4) Compute the cosmological redshift and angular coordinates for each
+    source, and introduce redshift-space distortions based on the local
+    value of the velocity field.
+ 5) Write sources to file.
+
+The source code can be found in the folder "src/"
+
+When in doubt, bear in mind that by default CoLoRe uses the following units:
+ - Lenghts: Mpc/h
+ - Angles: degrees
+
+
+2 Compilation and usage.
+
+To compile CoLoRe, open the Makefile and edit it according to your
+system. The default options (except for the paths to the external
+libraries) should work for most systems. CoLoRe may be very memory-
+demanding. To minimize the memory overhead use single precision
+floating point (USE_PRECISION = yes).
+
+OpenMP parallelization is enabled by setting the option USE_OMP
+to "yes".
+
+MPI parallelization is enabled by setting the option USE_MPI
+to "yes".
+
+CoLoRe uses 3 external packages:
+ - GSL. The GNU Scientific Library (tested for versions 3.*)
+ - FFTW. The Fastest Fourier Transform of the West (versions 3.*)
+ - CFITSIO. FITS format library.
+The paths to the corresponding headers and libraries should be correctly
+set in the Makefile.
+
+Once the Makefile has been editted, typing 'make' should generate
+the executable 'CoLoRe'. To run CoLoRe just type
+
+> mpirun -np <number-of-nodes> ./CoLoRe <param_file>
+
+where <param_file> is the path to the parameter file described in
+section 3.
+
+
+3 Parameter file.
+
+The behaviour of CoLoRe is mainly controlled by the input param file. The
+param file is basically a set of name-value pairs. Any blank lines, and
+anything beyond a #-symbol will be ignored. We provide a sample param
+file (param_sample.ini) that includes all the input parameters needed by
+CoLoRe. The comments included in this file explain the meaning and
+functionality of these parameters.
+
+
+4 Output.
+
+The main output of CoLoRe is a catalogue of sources written either
+as ASCII or FITS files. Each source is characterized by 4 quantities:
+ - Z0 -> cosmological redshift (without RSDs)
+ - RA -> right ascension
+ - DEC -> declination
+ - RSD -> RSD contribution to the redshift
+          (i.e. true redshift = Z0 + RSD).
+
+
+5 License:
+CoLoRe is distributed under the GPL license (see COPYING in the root
+directory). We kindly ask you to report the program's website
+"https://github.com/damonge/CoLoRe" when using it.
+
+
+6 Contact:
+Regarding bugs, suggestions, questions or petitions, feel free to contact
+the author:
+    David Alonso: [email protected]

param_sample.ini

@@ -0,0 +1,46 @@
+###File names
+#Output prefix. Output will be in prefix_<node ID>.<fits/txt>
+prefix_out= out
+#Output format. Select FITS or ASCII
+output_format= FITS
+#Path to power spectrum at z=0. Power spectrum file must
+#be in CAMB format: k (h/Mpc), P(k) (Mpc/h)^3.
+pk_filename= test_files/Pk_CAMB_test.dat
+#Path to N(z) file. Should contain two columns
+# 1-> z, 2-> dN(z)/dz*dOmega
+# with dN/dzdOmega in units of deg^-2
+nz_filename= test_files/Nz_test.txt
+#Path to bias file. Should contain two columns
+# 1-> z, 2-> b(z)
+bias_filename= test_files/Bz_test.txt
+
+###Cosmological parameters
+#Non-relativistic matter
+omega_M= 0.3
+#Dark energy
+omega_L= 0.7
+#Baryons
+omega_B= 0.049
+#Hubble parameter (in units of 100 km/s/Mpc)
+h= 0.67
+#Dark energy equation of state
+w= -1.0
+#Primordial scalar spectral index
+ns= 0.96
+#Power spectrum normalization
+sigma_8= 0.8
+
+###Redshift range
+z_min= 0.1
+z_max= 0.5
+
+###Extra Gaussian smoothing scale [Mpc/h] (set to a
+#negative value if you don't want any smoothing)
+r_smooth= 2.
+
+###Grid resolution.
+#Will use a Cartesian grid with n_grid^3 cells
+n_grid= 128
+
+###RNG seed
+seed= 1001