manuals + smooth installation w/wo NEMO

CMakeLists.txt

@@ -13,7 +13,9 @@
 # ============================================================================
 
 cmake_minimum_required(VERSION 2.6)
- 
+
+cmake_policy(SET CMP0054 NEW)
+
 # project name
 project (uns_projects)
 
@@ -123,7 +125,7 @@ include_directories (${EXTRA_INCLUDES})
 if ( FALCON_INSTALLED )
   include_directories (${DEHNEN}/falcON/utils/inc ${DEHNEN}/falcON/inc)
 endif()
-include_directories (${UNSIOPATH}/lib ${UNSIOPATH}/include ${UNSIOPATH}/include/uns $ENV{NEMO}/inc $ENV{NEMO}/inc/uns $ENV{NEMO}/lib)
+include_directories (${UNSIOPATH}/lib ${UNSIOPATH}/include ${UNSIOPATH}/include/nemo ${UNSIOPATH}/include/uns $ENV{NEMO}/inc $ENV{NEMO}/inc/uns $ENV{NEMO}/lib)
 include_directories (/usr/include/malloc)
 
 # Make sure the linker can find the Hello library once it is built.
@@ -132,18 +134,18 @@ link_directories ( ${UNSIOPATH}/${LIB_SUFFIX} ${UNSIOPATH}/lib ${UNSIOPATH}/lib6
 # ----------------------------------------------------------
 # Install SETUP
 # ----------------------------------------------------------
-
 mark_as_advanced(CMAKE_INSTALL_PREFIX)
 
-if (CMAKE_INSTALL_PREFIX STREQUAL $ENV{NEMO} )
+if ( "XX${CMAKE_INSTALL_PREFIX}" STREQUAL "XX$ENV{NEMO}" )
   SET(PREFIX_LIB lib)
 else()
   SET(PREFIX_LIB ${LIB_SUFFIX})
 endif()
-if (NOT CMAKE_INSTALL_PREFIX) 
+
+if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) 
   set (CMAKE_INSTALL_PREFIX ${UNSIOPATH})
 endif()
-MESSAGE( STATUS "--------> CMAKE_INSTALL_PREFIX =" ${CMAKE_INSTALL_PREFIX})
+MESSAGE( STATUS "--------> CMAKE_INSTALL_PREFIX =" ${CMAKE_INSTALL_PREFIX} )
 
 if (OSX)
   MESSAGE(STATUS "\nAfter running \"make install\", do not forget to set your environment variable DYLD_LIBRARY_PATH using command:\n\n export DYLD_LIBRARY_PATH=${CMAKE_INSTALL_PREFIX}/lib\n")
@@ -179,6 +181,12 @@ else ()
    FILE(GLOB execpp_sources ${PROJECT_SOURCE_DIR}/src/*.cc)
 endif ()
 # build cpp executables according to the source
+if (NEMO_INSTALLED)
+  set (LINK_NEMO "-lnemo")
+else ()
+    set (LINK_NEMO "")
+endif()
+
 FOREACH(exe_cpp ${execpp_sources})
 
   get_filename_component(exe ${exe_cpp} NAME_WE)
@@ -190,12 +198,12 @@ FOREACH(exe_cpp ${execpp_sources})
          # with fits
          # target_link_libraries (${exe} JCLprojects JCLutils cpgplot pgplot.a ${FC_GFORT_LIB} ${FC_G77_LIB}  CCfits cfitsio X11 nemo unsio WDutils falcON gomp ${LIBBOOST} pthread dl)
          # without fits
-         target_link_libraries (${exe} JCLprojects JCLutils cpgplot pgplot.a ${FC_GFORT_LIB} ${FC_G77_LIB} X11 nemo unsio WDutils falcON gomp ${LIBBOOST} pthread dl)
+	 target_link_libraries (${exe} JCLprojects JCLutils cpgplot pgplot.a ${FC_GFORT_LIB} ${FC_G77_LIB} X11 ${LINK_NEMO} unsio WDutils falcON gomp ${LIBBOOST} pthread dl)
   else ()
     # with fits
 	  # target_link_libraries (${exe} JCLprojects JCLutils ${FC_GFORT_LIB} ${FC_G77_LIB} CCfits cfitsio nemo unsio gomp ${LIBBOOST} dl)
     # without fits
-	  target_link_libraries (${exe} JCLprojects JCLutils ${FC_GFORT_LIB} ${FC_G77_LIB} nemo unsio gomp ${LIBBOOST} dl)
+    target_link_libraries (${exe} JCLprojects JCLutils ${FC_GFORT_LIB} ${FC_G77_LIB} ${LINK_NEMO} unsio gomp ${LIBBOOST} dl)
   endif ()
   INSTALL(TARGETS ${exe} RUNTIME  DESTINATION bin)
 
@@ -214,19 +222,20 @@ ENDIF(OSX)
 # 
 # install bin targets
 FOREACH(exe_cpp ${execpp_sources})
-
   get_filename_component(exe ${exe_cpp} NAME_WE)
   #INSTALL(PROGRAMS  ${PROJECT_BINARY_DIR}/bin/${exe}     DESTINATION bin)
 ENDFOREACH(exe_cpp ${execpp_sources})
 
 INSTALL(FILES  ${PROJECT_BINARY_DIR}/lib/libJCLutils.${SOEXT} DESTINATION ${PREFIX_LIB})
 INSTALL(FILES  ${PROJECT_BINARY_DIR}/lib/libJCLprojects.${SOEXT} DESTINATION ${PREFIX_LIB})
-INSTALL(FILES  ${PROJECT_SOURCE_DIR}/man/uns_2dplot.1 DESTINATION man/man1)
-INSTALL(FILES  ${PROJECT_SOURCE_DIR}/man/uns_stack.1 DESTINATION man/man1)
-INSTALL(FILES  ${PROJECT_SOURCE_DIR}/man/uns2uns.1 DESTINATION man/man1)
-INSTALL(FILES  ${PROJECT_SOURCE_DIR}/man/uns_projects.1 DESTINATION man/man1)
 INSTALL(FILES  ${PROJECT_SOURCE_DIR}/lib/utils/nemodep/cfalcon.h DESTINATION inc/uns)
 INSTALL(FILES  ${PROJECT_SOURCE_DIR}/lib/utils/csnaptools.h DESTINATION inc/uns)
 INSTALL(FILES  ${PROJECT_SOURCE_DIR}/lib/projects/nemodep/crectify.h DESTINATION inc/uns)
 INSTALL(FILES  ${PROJECT_SOURCE_DIR}/lib/utils/ctimer.h DESTINATION inc/uns)
+
+# Manuals
+FILE(GLOB manuals  ${PROJECT_SOURCE_DIR}/man/*.1)
+FOREACH(install_man ${manuals})
+  INSTALL(FILES  ${install_man}  DESTINATION man/man1)
+ENDFOREACH()
 #

cmake/FindUNSIO.cmake

@@ -34,20 +34,20 @@ if (NOT UNSIO_SETUP)
   endif ()
 
   if (NOT UNSIO_FOUND) # try system 
-    MESSAGE (STATUS "Trying UNSIOLIB = " ${UNSIOLIB} "  from system=/usr/lib64" )
-    find_library(UNSIOLIB NAMES unsio PATHS /usr/lib64)
+    MESSAGE (STATUS "Trying UNSIOLIB = " ${UNSIOLIB} "  from system=/usr/${LIB_SUFFIX}" )
+    find_library(UNSIOLIB NAMES unsio PATHS /usr/${LIB_SUFFIX})
     if ( NOT  ${UNSIOLIB} STREQUAL  UNSIOLIB-NOTFOUND)
       MESSAGE(STATUS "Found UNSIOLIB in system =" ${UNSIOLIB})
       SET(UNSIO_FOUND TRUE)
       SET(UNSIOPATH /usr)
-      MESSAGE(STATUS "UNSIO found in /usr/lib64")
+      MESSAGE(STATUS "UNSIO found in /usr/${LIB_SUFFIX}")
     else ()
-      MESSAGE(STATUS "UNSIO not found in /usr/lib64")
+      MESSAGE(STATUS "UNSIO not found in /usr/${LIB_SUFFIX}")
     endif()
   endif()
 
   if (NOT UNSIO_FOUND) # try $HOME/local
-    find_library(UNSIOLIB NAMES unsio PATHS $ENV{HOME}/local/unsio/lib64)
+    find_library(UNSIOLIB NAMES unsio PATHS $ENV{HOME}/local/unsio/${LIB_SUFFIX})
     MESSAGE (STATUS "UNSIOLIB = " ${UNSIOLIB} " -- "  $ENV{HOME})
     if (NOT  ${UNSIOLIB} STREQUAL  UNSIOLIB-NOTFOUND)
       MESSAGE(STATUS "Found UNSIOLIB in $ENV{HOME}/local/unsio/ =" ${UNSIOLIB})

man/uns2uns.1

-.TH uns2uns 1NEMO "July 05, 2011"
+.TH uns2uns 1NEMO "March 17, 2020"
 .SH NAME
-uns2uns a universal converting tool for UNS snapshots.
+uns2uns \- a universal converting tool for UNS snapshots.
 
 .SH SYNOPSIS
 \fBuns2uns in=\fPuns_input\fB out=\fPuns_output\fB
@@ -23,14 +23,14 @@ There are two kinds of nbody file structure:
 - \fBrange\fP file structure (\fIRFS\fP), like NEMO, where  data are identified
   by range of indexes (ex 0:999 for the disk and 1000:9999  for the halo).  
 .TP 0
-- \fBcomponent\fP file structure (\fICFS\fP), like GADGET, where data are identified by
+- \fBcomponent\fP file structure (\fICFS\fP), like GADGET or RAMSES where data are identified by
   component name (disk, gas, halo, stars, bulge, bndry).
 .SH PARAMETERS
 The following parameters are recognized.
 .TP 12
 \fBin=\fP\fIuns input file\fP
-Currently, the following input files are supported: Nemo,Gadget 2 &
-1, list of files, sqlite3 uns data base
+Currently, the following input files are supported: Nemo, Gadget3,
+Gadget2, Gadget1, RAMSES, list of files, sqlite3 uns data base
 .TP
 \fBout=\fP\fIuns output file\fP
 Output data will be written to \fIout_file\fP in the format type
@@ -48,7 +48,7 @@ select=gas@0:1000+disk@300:400). For more details, see EXAMPLES below.
 .TP
 \fBtype=\fP\fIuns type format\fP
 we specify here the type of the output file.
-Currently, the following output files are supported: nemo, gadget2
+Currently, the following output files are supported: nemo, gadget2, gadget3
 .TP
 \fBbits=\fP\fIphysical quantities to saved\fP
 If this parameter is left blank, then all physical quantities will be
@@ -71,6 +71,9 @@ values:
   'T'  temperature
 
   ex: bits=xRH will save positions, densities and hsml
+  
+  (see also : 
+https://projets.lam.fr/projects/unsio/wiki/UnsioVariablesUtilisation#How-to-select-data-at-loading)
 
 .SH EXAMPLES
 In the following examples, we assume that \fIfileg2\fP is a GADGET2 file,
@@ -110,6 +113,8 @@ output files will have a trailing number.
 
 .SH SEE ALSO
 snapmask(1NEMO), snapcopy(1NEMO), snapshot(5NEMO), uns_info(1NEMO)
+.TP
+https://projets.lam.fr/projects/unsio/wiki
 
 .SH AUTHOR
 Jean-Charles LAMBERT
@@ -117,5 +122,6 @@ Jean-Charles LAMBERT
 .nf
 .ta +1i +4i
 05-Jul-11	V1.0 created	JCL
+17-Mar-20	V2.0 bugs fixed	JCL
 .fi
 

man/uns_2dplot.1

-.TH UNS_2DPLOT 1NEMO "November 9, 2010"
+.TH UNS_2DPLOT 1NEMO "March 17, 2020"
 .SH NAME
 uns_2dplot \- create a 2D image of an UNS file
 .SH SYNOPSIS
@@ -12,19 +12,28 @@ that you  get, looks like the one you get with glnemo2(see man
 glnemo2) on gas particles.
 .PP
 The computation of all gaussian is multithreaded and the number of threads used can be
-selected from the command line. It requires BOOST thread api for compilation.
+selected from the command line.
 
 .SH PARAMETERS
 The following parameters are recognized.
 .TP 24
 \fBin=\fP\fIuns input file\fP
-Currently, the following input files are supported: Nemo,Gadget 2 &
-1, list of files
+Currently, the following input files are supported: Nemo regular, Nemo
+piped, Gadget3, Gadget2, Gadget1, Ramses, list of files
 .TP
 \fBselect=\fP\fIselect-particles\fP
 Select particles. Sets of particles must be selected using the : range operator, separated by a comma. 
 E.g. select=0:9,10:19 would select two sets of 10 particles, or by component (gas,halo,stars,bulge,disk,bndry)
-[all] 
+[all]
+.TP
+\fBprop=\fP\fproperties to display (metal,age,temp,rho)\fP
+In case of structured snapshots like Gagdet or Ramses, you can select
+the properties you want to display (metal,age,temp,rho). By default it
+displays accumulated density of particles in the light of see.
+.TP
+\fBpsort=\fP\f sort properties\fP
+sort properties according to 0:none, 1:min, 2:max. The default is [0]
+no sorting. 
 .TP
 \fBdev=\fP\fIoutput-image-file\fP
 you specify here the output name of the image which will be automatically saved in GIF
@@ -60,6 +69,18 @@ select as true if you want to display particles in ZY plan. Default is
 \fBcom=\fP\fIcenter-of-mass?\fP
 center according to center if mass. Default is [t].
 .TP
+\fBhsml=\fP\fIuse hydro smooth length\fP
+Use hydro smooth length if exists, default [f] false
+.TP
+\fBcb=\fP\fItoggle color map\fP
+default is false [f]
+.TP
+\fBcmap=\fP\fIselect color map\fP
+available color maps 0:rainbow, 1:heat, 2:gray, default is [0]
+.TP
+\fBitf=\fP\fIimage transfer function\fP
+image transer function 0:linear, 1:logarithmic, 2:square-root, default [1]
+.TP
 \fBsview=\fP\fIsingle-display-view?\fP
 if true, only one image will be created for all requested plan
 xy|xz|zy. If false, and if a name is given to 'dev' parameter, then a
@@ -95,12 +116,16 @@ display some verbose log [f]
 .TP
 .TP
 .SH SEE ALSO
-snapplot(1NEMO), snapgrid(1NEMO), snapshot(5NEMO), glnemo2(1NEMO)
+snapplot(1NEMO), snapgrid(1NEMO), snapshot(5NEMO), glnemo2(1NEMO),
+uns_projects(1NEMO)
+.TP
+https://projets.lam.fr/projects/unsio/wiki
 .SH AUTHOR
 Jean-Charles LAMBERT
 .SH HISTORY
 .nf
 .ta +1i +4i
 09-Nov-10	V1.0 public release	JCL
+17-Mar-20	V2.0 bugs fixes		JCL
 .fi
 

man/uns_projects.1

-.TH UNS_PROJECTS 1NEMO "05 Dec 2011"
+.TH uns_projects 1NEMO "March 17, 2020"
 
 .SH DESCRIPTION
-\fIuns_projects\fP is a set of programs based on uns technology. (see
-man unsiof for fortran API).
+\fIuns_projects\fP is a set of programs based on unsio
+technology. (see https://projets.lam.fr/projects/unsio/wiki)
 
 .SH PROJECTS
 
@@ -12,14 +12,17 @@ man unsiof for fortran API).
 \fBuns2uns\fP converts an uns snapshot to another uns format (see man
 uns2uns)
 .TP
-\fBuns_tonemo\fP converts an uns snapshot to NEMO format
+\fBuns_tonemo\fP converts an uns snapshot to NEMO format (see man uns_tonemo)
 .TP
 \fBuns_2dplot\fP plots particles positions of an uns snapshot (see man
 uns_2dplot)
 .TP
-\fBuns_stack\fP stacks two uns snapshot (see man uns_stack)
+\fBuns_density\fP computes local density on an uns snapshot (see man uns_density)
+.TP
+\fBuns_addgravity\fP adds acceleration and potential of an uns
+snapshot (see man uns_addgravity)
 .TP
-\fBuns_density\fP computes local density on an uns snapshot
+\fBuns_stack\fP stacks two uns snapshot (see man uns_stack)
 .TP
 \fBuns_glindex2nemo\fP saves in NEMO format, particles pos,vel and
 mass, selected from a  list of particles identifiers stored in a file,
@@ -29,25 +32,21 @@ and created with glnemo2 program
 .TP
 \fBuns_mover\fP uns version of mover program
 .TP
-\fBuns_addgravity\fP adds acceleration and potential on a uns snapshot
-.TP
 \fBuns_barangle\fP detects bar angle of an uns snapshot (experimental
 but works fine)
 
-
-
-
-
-
-
-
 .SH SEE ALSO
 unsiof, snapshot(5NEMO)
+
+https://projets.lam.fr/projects/unsio/wiki
+ 
 .SH AUTHOR
 Jean-Charles LAMBERT
 .SH HISTORY
 .nf
 .ta +1i +4i
 05-Dec-11	V1.0 created	JCL
+17-Mar-20	V2.0 manual updated	JCL
+
 .fi
 

man/uns_tonemo.1

-.TH UNS_ 1NEMO "April 2, 2010"
+.TH uns_tonemo 1NEMO "March 17, 2020"
 .SH NAME
-uns_stack \- superimpose two UNS N-body snapshots
+uns_tonemo \- convert UNS N-body snapshots to NEMO snapshot
 .SH SYNOPSIS
-\fBuns_stack in1=\fPin_file1 \fBin2=\fPin_file2 \fBout=\fPout_file [parameter=value] .\|.\|.
+\fBuns_tonemo in=\fPin_file \fBout=\fPout_file [parameter=value] .\|.\|.
 .SH DESCRIPTION
-\fIuns_stack\fP reads in two UNS N-body systems and outputs one containing
-particles from both.  It may be used to set up collisions by
-specifying offsets in position and velocity space.
-.PP
-If more than two snapshots need to be stacked, multiple runs of \fIuns_stack\fP.
-would be needed
+\fIuns_tonemo\fP reads a compatible UNS snapshot and save it in
+NEMO format
 .SH PARAMETERS
 The following parameters are recognized.
 .TP 24
-\fBin1=\fP\fIin_file1\fP
-.TP
-\fBin2=\fP\fIin_file2\fP
-Input data will be read from these files, which must be in
-\fIUNS\fP format (currently Nemo and Gadget2 are supported).  Only the
-first frames are used. Both input snapshot must have the same file format.
-
+\fBin=\fP\fIuns input file snapshot\fP
+give as input a compatible UNS file snapshot (Nemo, Gadget, Ramses...)
 Default: \fIrequired\fP.
 .TP
 \fBout=\fP\fIout_file\fP
-Output data will be written to \fIout_file\fP. The out file format
-will be the same as input file format.
+Output file name. You can give a filename or "-" (to pipe with
+another NEMO program). Default: \fIrequired\fP.
 .TP
-\fBdeltar=\fP\fIrel_position\fP
-Relative position of first snapshot w.r.t. second.
-Default: \fB0.0,0.0,0.0\fP.
+\fBtimes=\fP\fItime-range\fP
+Select time [all]
 .TP
-\fBdeltav=\fP\fIrel_velocity\fP
-Relative velocity of first snapshot w.r.t. second.
-Default: \fB0.0,0.0,0.0\fP.
+\fBfirst=\fP\fIboolean\fP
+if true, add a trailing number to the first output file [f]
 .TP
-\fBshift=1|2\fP
-Shift system1 or system2?  If the final system is shifted with center
-of mass moved to the center, this option is not relevant anymore.
-Default: \fB1\fP.
-.TP
-\fBzerocm=\fP\fIzero_cm_flag\fP
-If true, translate to center of mass before output.
-Default: \fBfalse\fP. 
+\fBoffset=\fP\fItime offset\fP
+ +/- time offset between two consecutives snapshots [0.01]
 .TP
 \fBverbose=\fP\fIflag\fP
-If true, give some verbose output.
-Default: \fBTrue\fP.
+If true, give some verbose output [t].
 .TP
 .SH SEE ALSO
-snapstack(1NEMO), snapadd(1NEMO), snapshot(5NEMO)
+uns2uns(1NEMO), uns_projects(1NEMO), snapshot(5NEMO)
+.TP
+https://projets.lam.fr/projects/unsio/wiki
 .SH AUTHOR
 Jean-Charles LAMBERT
 .SH HISTORY
 .nf
 .ta +1i +4i
-02-Apr-10	V1.0 created	JCL
+17-Mar-20	V2.0 manual created	JCL
 .fi