haloanalyzer is a mess

everythink should be checked and eventually written from scratch

Makefile

@@ -23,3 +23,4 @@ clean:
 	cd tools/conepartcreator/src ; make clean
 	cd tools/conegravcreator/src ; make clean
 	cd tools/conemapper/src ; make clean
+	rm -f mod/* obj/*

common/src/modreadhalo.f90

@@ -42,7 +42,8 @@ contains
        position_halo, velocity_halo, rmax_halo, identity_halo, npart_halo)
 
     use iso_fortran_env, only : ERROR_UNIT, OUTPUT_UNIT
-    use modconstant, only : IDKIND, type_common_metadata, type_parameter_pfof, type_info_ramses, type_info_cone_part
+    use modconstant, only : IDKIND, type_common_metadata, type_parameter_pfof
+    use type_info_ramses_mod, only : type_info_ramses, type_info_cone_part
     use fortran_hdf5_constants_m, only : H5_FILENAME_LEN, H5_STR_LEN
     use fortran_hdf5_manage_files_m, only : hdf5_close_file, hdf5_open_file 
     use fortran_hdf5_manage_groups_m, only : hdf5_close_group, hdf5_open_group
@@ -167,13 +168,14 @@ contains
     use fortran_hdf5_read_data_m
     use iso_fortran_env, only : ERROR_UNIT, OUTPUT_UNIT
     use modconstant, only : ERR_MSG_LEN, IDKIND, &
-         type_common_metadata, type_parameter_pfof, type_info_ramses, type_info_cone_part
+         type_common_metadata, type_parameter_pfof
+    use type_info_ramses_mod, only : type_info_ramses, type_info_cone_part
     use modmpicommons, only : type_info_process
     use modreadmeta, only : Read_meta_common, &
        Read_meta_halofinder_parameter, &
        Read_meta_info_cone, &
        Read_meta_info_ramses
-
+    use hdf5, only : HID_T
     
     type(type_info_process), intent(in) :: info_proc
     character(len=H5_FILENAME_LEN), intent(in) :: filename

tools/haloanalyzer/src/Makefile

 include ../../../Make.inc
 
-EXE = haloanalyzer
-
 COMMONDIR = ../../../common/src/
 OBJDIR=../../../obj/
 MODDIR=../../../mod/
-
 VPATH= $(COMMONDIR):.
 
-SRC = modhdf5.f90 \
-	modconstant.f90 \
+EXE = haloanalyzer.exe
+
+SRC = modconstant.f90 \
+	type_info_ramses_mod.f90 \
 	error_handling_mod.f90 \
 	type_particles_mod.f90 \
 	haloanalyzer_var_mod.f90 \
 	haloanalyzer_init_mod.f90 \
+	modvarcommons.f90 \
 	modmpicommons.f90 \
-	modvariable.f90 \
 	modreadmeta.f90 \
 	modreadhalo.f90 \
 	modfunctions.f90 \
@@ -39,20 +38,20 @@ $(OBJDIR)%.o:%.f90
 	@echo "--------------------------------"
 	@echo building $*.o with parameters \
 	FC=$(FC), FCFLAGS=$(FCFLAGS)
-	$(FC) -c $(FCFLAGS) $< -o $@ 
+	$(FC) -c $(FCFLAGS) $< -o $@
 
-# %.mod:%.f90
-# 	@echo "--------------------------------"
-# 	@echo building $*.mod with parameters \
-# 	FC=$(FC), FCFLAGS=$(FCFLAGS)
-# 	$(FC) -c $(FCFLAGS) $< 
+$(MODDIR)%.mod:%.f90
+	@echo "--------------------------------"
+	@echo building $*.mod with parameters \
+	FC=$(FC), FCFLAGS=$(FCFLAGS)
+	$(FC) -c $(FCFLAGS) $<
 
-all: release
+
+all: directories release
 release: $(EXE)
 debug: FCFLAGS = $(DEBUGFLAGS)
 debug: $(EXE)
 
-
 $(EXE) : gitversion $(OBJS)
 	@echo "--------------------------------"
 	@echo building $(EXE) 
@@ -63,12 +62,12 @@ cleanall :
 	@echo cleaning compiled objects, modules and executable
 	rm -f $(OBJDIR)*.o $(MODDIR)*.mod *~ $(EXE) $(COMMONDIR)/gitversion.h
 
-clean:
+clean :
 	@echo "--------------------------------"
-	@echo cleaning executable
-	rm -f  $(EXE)
-
+	@echo cleaning compiled objects, modules and executable 
+	rm -f $(EXE)
 
+# create file for git version
 gitversion: $(OBJ_GIT)
 ifneq ($(USE_GIT), )
 	@cd $(COMMONDIR) ;\
@@ -86,5 +85,4 @@ ${OBJDIR}:
 ${MODDIR}:
 	${MKDIR_P} $@
 
-
 .PHONY: gitversion clean cleanall directories all

tools/haloanalyzer/src/haloanalyzer.f90

-!=======================================================================
-! Author: Fabrice Roy (LUTH/CNRS/Observatoire de Paris)
-! Fabrice.Roy@obspm.fr
-!=======================================================================
+!------------------------------------------------------------------------------------------------------------------------------------
+! Copyright  2015 Fabrice Roy 
+!
+! Contact: fabrice.roy@obspm.fr
+!
+! This file is part of pFoF.
+!
+! pFoF is free software: you can redistribute it and/or modify
+! it under the terms of the GNU General Public License as published by
+! the Free Software Foundation, either version 3 of the License, or
+! (at your option) any later version.
+!
+! pFoF is distributed in the hope that it will be useful,
+! but WITHOUT ANY WARRANTY; without even the implied warranty of
+! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+! GNU General Public License for more details.
+! 
+! You should have received a copy of the GNU General Public License
+! along with pFoF. If not, see <http://www.gnu.org/licenses/>.
+
+!> @file
+!! Generic program reading a set of hdf5 halo files produced by pFoF
+! and analyzing them
+!! @brief
+!! 
+!! @author Fabrice Roy
 
-!=======================================================================
-! Generic program reading a set of hdf5 halo files produced by pFoF
+!> Generic program reading a set of hdf5 halo files produced by pFoF
 ! and analyzing them
 ! You can analyze either a subset of haloes by providing thier ID (analyzelist)
 ! or each halo in a subset of files by providing the name of the files (analyzefile)
-!=======================================================================
-Program haloanalyzer
+!------------------------------------------------------------------------------------------------------------------------------------
+program haloanalyzer
 
   use haloanalyzer_var_mod
   use modanalyzeengines
   use modfunctions
-  use modhdf5
+  use fortran_hdf5_manage_interface_m
+  use hdf5, only : HID_T
   implicit none
 
   type(list_of_var) :: var         ! list of the datasets needed for your analyzis
@@ -30,7 +52,7 @@ Program haloanalyzer
 
 
 #ifdef WITHMPI
-  Call Mpi_Init(mpierr)
+  call mpi_Init(mpierr)
 #endif
 
   call hdf5_init()
@@ -40,7 +62,7 @@ Program haloanalyzer
   var%vel = .false.   ! default is .true.
   var%id = .false.    ! default is .true.
 
-  call haloanalyzer_init(var, dm_particles)
+  call Haloanalyzer_init(var, dm_particles)
   
   ! The first argument is the name of the file containing the list of the ID of the haloes that you want to analyze
   ! The second argument is the name of your analyzis subroutine (defined in modfunctions.f90) 

tools/haloanalyzer/src/haloanalyzer_var_m.f90

+
+Module modvariable 
+#ifdef WITHMPI   
+Use mpi 
+#endif     
+! If you do not know the type of integer used for the ID, use h5dump on the first halo file.   
+! h5dump -d haloID test_halo_00000.h5   
+! This will print the dataset haloID containing the ID of each halo in the file.   
+! You should see something like   
+! HDF5 "test_halo_00000.h5" {   
+! DATASET "haloID" {   
+!    DATATYPE  H5T_STD_I64LE   
+! The datatype should contain the number of bits used, i.e. 32 for kind=4 or 64 for kind=8. 
+#ifdef LONGINT   
+Integer, parameter :: PRI = 8 
+#ifdef WITHMPI   
+Integer, parameter :: MPI_PRI = Mpi_Integer8 
+#endif 
+#else   
+Integer, parameter :: PRI = 4 
+#ifdef WITHMPI   
+Integer, parameter :: MPI_PRI = Mpi_Integer 
+#endif 
+#endif   !! Variables read from the HDF5 file   
+Integer(kind=PRI), dimension(:), allocatable :: id        ! id of the particles in the halo just read   
+Real(kind=4), dimension(:,:), allocatable :: pos  ! position of the particles in the halo just read   
+Real(kind=4), dimension(:,:), allocatable :: vel  ! velocities of the particles in the halo just read   
+Real(kind=4), dimension(:), allocatable :: mp   
+Integer(kind=PRI) :: currenthaloID ! haloID of the halo analyzed in your function   
+Integer(kind=4) :: currenthalo     ! index of the halo which varies from 1 to N where N is the total number of haloes you are analyzing   
+Integer(kind=4) :: nbhaloanalyzed  ! total number of haloes that you want to analyze 
+#ifdef WITHMPI   
+Integer :: procID   
+Integer :: procNB   
+Integer :: mpierr 
+#endif 
+End Module modvariable
+

tools/haloanalyzer/src/haloanalyzer_var_mod.f90

@@ -14,6 +14,19 @@ module haloanalyzer_var_mod
   !    DATATYPE  H5T_STD_I64LE
   ! The datatype should contain the number of bits used, i.e. 32 for kind=4 or 64 for kind=8.
 
+  implicit none
+   
+  private
+
+  public :: type_particles, &
+    type_var_list, &
+    type_info_proc, &
+    currenthalo, &
+    currenthaloID, &
+    nbhaloanalyzed
+
+
+
   type :: type_particles
      integer(kind=4) :: nb_part
      integer(kind=IDKIND), dimension(:), allocatable :: pfof_id        
@@ -46,4 +59,9 @@ module haloanalyzer_var_mod
      integer :: pnb
   end type type_info_proc
 
+  integer(kind=IDKIND) :: currenthaloID ! haloID of the halo analyzed in your function   
+  integer(kind=4) :: currenthalo     ! index of the halo which varies from 1 to N where N is the total number of haloes you are analyzing   
+  integer(kind=4) :: nbhaloanalyzed  ! total number of haloes that you want to analyze 
+  
+
 end module haloanalyzer_var_mod

tools/haloanalyzer/src/modanalyzeengines.f90

@@ -4,9 +4,7 @@
 !=======================================================================
 module modanalyzeengines
 
-  use modvariable
   use modfunctions
-  use modhdf5
   use modconstant, only : IDKIND, MPI_IDKIND
  
   implicit none

tools/haloanalyzer/src/modfunctions.f90

@@ -4,8 +4,9 @@
 !=======================================================================
 Module modfunctions
   
-  Use modvariable
+  use haloanalyzer_var_mod
 
+  implicit none
   !! WARNING: you can declare here the output variables you may want to deal with in the 
   !! main program, for instance if you want to write them in an output file.
   !! If the variable is an allocatable array, you have to allocate it the first
@@ -26,14 +27,14 @@ Contains
     Real(kind=8), dimension(3) :: x
     
     If(.not.Allocated(cmpos)) Then 
-       Allocate(cmpos(3,nbhaloanalyzed))
+      Allocate(cmpos(3,nbhaloanalyzed))
     End If
 
     np = size(pos,2)
     
     x = 0.d0
     Do ip = 1, np
-       x = x + pos(:,ip)
+      x = x + pos(:,ip)
     End Do
     
     cmpos(:,currenthalo) = x / real(np)