Commit 003c2088 authored by LAMBERT Jean-charles's avatar LAMBERT Jean-charles

manuals + smooth installation w/wo NEMO

parent 8165d781
......@@ -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()
#
......@@ -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})
......
.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
.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
.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
.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
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