Makefile build support for USER-ADIOS and build documentation

doc/src/Build_extras.txt

@@ -37,6 +37,7 @@ This is the list of packages that may require additional steps.
 "POEMS"_#poems,
 "PYTHON"_#python,
 "VORONOI"_#voronoi,
+"USER-ADIOS"_#user-adios,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
 "USER-COLVARS"_#user-colvars,
@@ -576,6 +577,28 @@ the lib/voronoi/Makefile.lammps file.
 
 :line
 
+USER-ADIOS package :h4,link(user-adios)
+
+The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2, version 2.3.1 or newer.
+Make sure that you have ADIOS built with/without MPI if you build LAMMPS with/without MPI, respectively.
+
+[CMake build]:
+
+-D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
+-D PKG_USER-ADIOS=yes     :pre
+
+[Traditional make]:
+
+Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
+
+make yes-user-adios                       :pre
+
+otherwise, set ADIOS2_DIR environment variable when turning on the package:
+
+ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed :pre
+
+:line
+
 USER-ATC package :h4,link(user-atc)
 
 The USER-ATC package requires the MANYBODY package also be installed.

doc/src/Build_package.txt

@@ -48,6 +48,7 @@ packages:
 "POEMS"_Build_extras.html#poems,
 "PYTHON"_Build_extras.html#python,
 "VORONOI"_Build_extras.html#voronoi,
+"USER-ADIOS"_Build_extras.html#user-adios,
 "USER-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,
 "USER-COLVARS"_Build_extras.html#user-colvars,

doc/src/Packages_details.txt

@@ -63,6 +63,7 @@ as contained in the file name.
 "SRD"_#PKG-SRD,
 "VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
 
+"USER-ADIOS"_#PKG-USER-ADIOS,
 "USER-ATC"_#PKG-USER-ATC,
 "USER-AWPMD"_#PKG-USER-AWPMD,
 "USER-BOCS"_#PKG-USER-BOCS,
@@ -975,6 +976,31 @@ examples/voronoi :ul
 
 :line
 
+USER-ADIOS package :link(PKG-USER-ADIOS),h4
+
+[Contents:]
+
+ADIOS is a high-performance I/O library. This package implements the 
+dump "atom/adios" and dump "custom/adios" commands to write data using
+the ADIOS library. 
+
+[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-adios on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-ADIOS: filenames -> commands
+src/USER-ADIOS/README
+examples/USER/adios
+https://github.com/ornladios/ADIOS2 :ul
+
+:line
+
 USER-ATC package :link(PKG-USER-ATC),h4
 
 [Contents:]

doc/src/Packages_user.txt

@@ -38,6 +38,7 @@ int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
+"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
 "USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
 "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no

src/Makefile

@@ -58,7 +58,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  molecule mpiio mscg opt peri poems \
 	  python qeq replica rigid shock snap spin srd voronoi
 
-PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
+PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
 	   user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
 	   user-intel user-lb user-manifold user-meamc user-meso \
 	   user-mgpt user-misc user-mofff user-molfile \

src/USER-ADIOS/Install.sh

@@ -30,60 +30,64 @@ done
 
 if (test $1 = 1) then
 
-#  if (test -z "$ADIOS_DIR") then
+  CONFIGSCRIPT=none
-#    if command -v adios_config; then 
+  if ( test `which adios2-config` ) then
-#        ADIOS_DIR=`adios_config -d`
+    CONFIGSCRIPT=adios2-config
-#    else
+  elif ( ! test -z "$ADIOS2_DIR" ) then
-#      echo "ERROR: ADIOS_DIR environment variable needs to point to ADIOS" \
+    if ( test `which $ADIOS2_DIR/bin/adios2-config` ) then
-#           " installation directory or adios_config should be in PATH"
+      CONFIGSCRIPT=$ADIOS2_DIR/bin/adios2-config
-#    fi
+    else
-#  fi
+      echo "ERROR: ADIOS2_DIR environment variable is set but" \
-#  ADIOS_INC=-I${ADIOS_DIR}/include
+           "\$ADIOS2_DIR/bin/adios2-config does not exist"
-#  ADIOS_LIB=`${ADIOS_DIR}/bin/adios_config -l`
+    fi
-#  
+  elif ( ! test -z "$ADIOS_DIR" ) then
-#  echo "adios_SYSINC=${ADIOS_INC}
+    if ( test `which $ADIOS_DIR/bin/adios2-config` ) then
-#adios_SYSLIB=${ADIOS_LIB}
+      CONFIGSCRIPT=$ADIOS_DIR/bin/adios2-config
-#adios_SYSPATH=${ADIOS_DIR}
+    else
-#" > ../Makefile.adios 
+      echo "ERROR: ADIOS_DIR environment variable is set but" \
-
+           "\$ADIOS_DIR/bin/adios2-config does not exist"
-
+    fi
-  if (test -e ../Makefile.package) then
+  else
-    sed -i -e 's/[^ \t]*adios[^ \t]* //g' ../Makefile.package
+    echo "ERROR: ADIOS2_DIR environment variable must point to ADIOS 2.x" \
-    sed -i -e 's/-DLMP_ADIOS //g' ../Makefile.package
+         "installation directory or adios2-config should be in PATH"
-    sed -i -e '/^adios_SYS.*$/d' ../Makefile.package
-#    sed -i -e '4 i \
-#adios_SYSINC='"${ADIOS_INC}"'
-#' ../Makefile.package
-#    sed -i -e '5 i \
-#adios_SYSLIB='"${ADIOS_LIB}"'
-#' ../Makefile.package
-#    sed -i -e '6 i \
-#adios_SYSPATH='"${ADIOS_DIR}"'
-#' ../Makefile.package
-    sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_ADIOS |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(adios_SYSINC) |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(adios_SYSLIB) |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(adios_SYSPATH) |' ../Makefile.package
   fi
 
-  if (test -e ../Makefile.package.settings) then
+  if [ "$CONFIGSCRIPT" != "none" ]; then 
-    sed -i -e '/^include.*adios.*$/d' ../Makefile.package.settings
+    ADIOS2_INC=`$CONFIGSCRIPT --cxx-flags`
-    # multiline form needed for BSD sed on Macs
+    ADIOS2_LIB=`$CONFIGSCRIPT --cxx-libs`
-    sed -i -e '4 i \
+  
-include ..\/..\/lib\/adios\/Makefile.lammps
+    echo "adios_SYSINC=${ADIOS2_INC}
+adios_SYSLIB=${ADIOS2_LIB}
+" > Makefile.lammps
+
+
+    if (test -e ../Makefile.package) then
+      sed -i -e 's/[^ \t]*adios[^ \t]* //g' ../Makefile.package
+      sed -i -e '/^adios_SYS.*$/d' ../Makefile.package
+      sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(adios_SYSINC) |' ../Makefile.package
+      sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(adios_SYSLIB) |' ../Makefile.package
+    fi
+
+    if (test -e ../Makefile.package.settings) then
+      sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings
+      # multiline form needed for BSD sed on Macs
+      sed -i -e '4 i \
+include ../USER-ADIOS/Makefile.lammps
 ' ../Makefile.package.settings
+    fi
   fi
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*adios[^ \t]* //g' ../Makefile.package
-    sed -i -e 's/-DLMP_ADIOS //g' ../Makefile.package
     sed -i -e '/^adios_SYS.*$/d' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*adios.*$/d' ../Makefile.package.settings
+    sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings
   fi
 
+  rm -f Makefile.lammps
+
 fi