hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/patches/patch.sh

@@ -0,0 +1,500 @@
+#! /usr/bin/env bash
+
+MANUAL="\
+
+Actions (choose one):
+  -h, --help
+                    print this help and exit
+  -p, --patch
+                    patch
+  -r, -R, --revert
+                    revert
+  -l, --list-engines
+                    print a list of available MD engines
+  -s, --save
+                    save, this needs *.preplumed files (*)
+  --save-originals
+                    same as save, but save also original files (*)
+  -n NEWENGINE, --new NEWENGINE
+                    create a new patch named NEWENGINE (*)
+  -i, --info
+                    output information on the patching procedure for a particular code                
+Options:
+  -e ENGINE, --engine ENGINE
+                    set MD engine to ENGINE (default: choose interactively)
+  -m MODE, --mode MODE (default: shared)
+                    set link mode to MODE, which can be either static, shared or runtime
+  --static
+                    same as --mode static
+  --shared
+                    same as --mode shared
+  --runtime
+                    same as --mode runtime
+  -d FILE, --diff FILE
+                    set the path to diff file (default: ROOT/patches/ENGINE.diff) (*)
+  -q, --quiet
+                    do not write logging information; useful with -i to print just
+                    the patching information
+  -I, --include
+                    use include files rather than symbolic links
+  -f, --force
+                    force patching (*)
+
+(*) These options are for developers or for testing only. Be sure to know what
+    you are doing before you use them.
+"
+
+prefix=""
+action=""
+engine=""
+diff=""
+mode=shared
+force=""
+include=""
+newpatch=
+
+multiple_actions=
+
+otherfiles=
+save_originals=
+quiet=
+mdroot=
+
+# default value:
+plumed_ignore_mpi=no
+
+for option
+do
+
+  prefix_option="$prefix$option"
+  prefix=""
+
+  case "$prefix_option" in
+    (--help|-h)         echo "$MANUAL" ; exit ;;
+    (--patch|-p)        test -n "$action" && multiple_actions=yes ; action=patch ;;
+    (--save|-s)         test -n "$action" && multiple_actions=yes ; action=save ;;
+    (--save-originals)  test -n "$action" && multiple_actions=yes ; action=save ; save_originals=yes ;;
+    (--revert|-R|-r)    test -n "$action" && multiple_actions=yes ; action=revert ;;
+    (--list-engines|-l) test -n "$action" && multiple_actions=yes ; action=list ;;
+    (--info|-i)         test -n "$action" && multiple_actions=yes ; action=info ;;
+    (--new=*)           test -n "$action" && multiple_actions=yes ; action=new ; newpatch="${prefix_option#--new=}" ;;
+    (--options)         test -n "$action" && multiple_actions=yes ; action=options ;;
+    (--description)     echo "patch an MD engine" ; exit ;;
+    (--engine=*) engine="${prefix_option#--engine=}" ;;
+    (--mdroot=*) mdroot="${prefix_option#--mdroot=}" ;;
+    (--mode=*) mode="${prefix_option#--mode=}" ;;
+    (--diff=*) diff="${prefix_option#--diff=}" ;;
+    (--engine|-e) prefix="--engine=" ;;
+    (--mdroot) prefix="--mdroot" ;;
+    (--root=*) prefix="--root="; PLUMED_ROOT="${prefix_option#--root=}" ;;
+    (--diff|-d) prefix="--diff=" ;;
+    (--mode|-m) prefix="--mode=" ;;
+    (--new|-n) prefix="--new=" ;;
+    (--static) mode=static ;;
+    (--shared) mode=shared ;;
+    (--runtime) mode=runtime ;;
+    (--force|-f) force=yes ;;
+    (--include|-I) include=yes ;;
+    (--quiet|-q) quiet=yes ;;
+    (*)
+      echo "ERROR: Unknown option $prefix_option. Use -h for help."
+      exit 1
+  esac
+done
+
+if [ -n "$mdroot" ] ; then
+  if ! cd "$mdroot" ; then
+    echo "ERROR: Directory $mdroot does not exist"
+    exit 1
+  fi
+fi
+
+if [ -n "$multiple_actions" ] ; then
+  echo "ERROR: Too many actions. -h for help"
+  exit 1
+fi
+
+if [ -z "$action" ] ; then
+  echo "Nothing to do. -h for help"
+  exit
+fi
+
+if [ "$action" = options ] ; then
+  echo "--help -h --patch -p --save -s --save-originals --revert -R -r --list-engines -l --info -i --new --options --description --engine --mdroot --mode --diff --engine -e --mdroot --root --diff -d --mode -m --new -n --static --shared --runtime --force -f --quiet -q --include"
+  exit 0
+fi
+
+test -n "$quiet" || echo "PLUMED patching tool"
+test -n "$quiet" || echo
+if [ -z "$PLUMED_ROOT" ]
+then
+  echo "ERROR: I cannot find PLUMED"
+  echo "Please set PLUMED_ROOT environment variable or use --root"
+  exit 1
+fi
+if [ ! -d "$PLUMED_ROOT/patches/" ]
+then
+  echo "ERROR: cannot find $PLUMED_ROOT/patches/ directory"
+  echo "Check your PLUMED_ROOT variable or --root option"
+  exit 1
+fi
+
+# build MD engines list
+
+mdlist=""
+for file in "$PLUMED_ROOT"/patches/*diff
+do
+  b="${file##*/}"
+  b="${b%.diff}"
+  mdlist="$mdlist $b"
+done
+
+if [ "$action" == list ]
+then
+  echo "Available MD engines:"
+  for file in "$PLUMED_ROOT"/patches/*diff
+  do
+    b="${file##*/}"
+    b="${b%.diff}"
+    echo "  $b"
+  done
+  exit
+fi
+
+if [ "$action" == new ]
+then
+  test -n "$quiet" || echo "Creating a new patch"
+  if [[ -e "$PLUMED_ROOT"/patches/"$newpatch".diff ]] ; then
+      echo "ERROR: patch $newpatch is already defined"
+      exit 1
+  fi
+  touch "$PLUMED_ROOT"/patches/"$newpatch".diff
+  test -n "$quiet" || echo "Created file $PLUMED_ROOT/patches/$newpatch.diff"
+  test -n "$quiet" || echo "Also consider the possibility of adding a $PLUMED_ROOT/patches/$newpatch.config file"
+  exit
+fi
+
+if [ -z "$engine" ]
+then
+  PS3="Choose the best matching code/version:"
+  select engine in $mdlist; do
+    if [[ -n "$engine" ]] ; then
+      break
+    else
+      echo "ERROR: choose in the list above or interrupt (^c)"
+    fi
+  done
+fi
+
+if [[ "$action" == patch || "$action" == revert ]]
+then
+  found=no
+  for engine_try in $mdlist ; do
+    if [[ "$engine" == "$engine_try" ]] ; then
+      found=yes
+    fi
+  done
+  if [[ "$found" == no ]] ; then
+    echo "WARNING: engine $engine not found, I will search for a close match"
+    for engine_try in $mdlist ; do
+      if [[ "${engine%.*}" == "${engine_try%.*}" ]] ; then
+        echo "WARNING: found $engine_try"
+        engine="$engine_try"
+      fi
+    done
+  fi
+fi
+
+if [ -z "$diff" ]
+then
+  diff="$PLUMED_ROOT/patches/${engine}.diff"
+fi
+if [ -z "$config" ]
+then
+  config="$PLUMED_ROOT/patches/${engine}.config"
+fi
+if [ -z "$otherfiles" ]
+then
+  test -d "$PLUMED_ROOT/patches/${engine}" && otherfiles="$PLUMED_ROOT/patches/${engine}/"
+fi
+
+test -n "$quiet" || echo "MD engine: $engine"
+test -n "$quiet" || echo "PLUMED location: $PLUMED_ROOT"
+test -n "$quiet" || echo "diff file: $diff"
+
+if [ -f "$config" ]
+then
+  test -n "$quiet" || echo "sourcing config file: $config"
+  # shellcheck disable=SC1090
+  source "$config"
+fi
+
+if [ -d "$otherfiles" ]
+then
+  test -n "$quiet" || echo "extra files located in: $otherfiles"
+fi
+
+case "$mode" in
+(static|shared|runtime) ;;
+(*)
+  echo "ERROR: I don't understand mode $mode"
+  exit 1
+esac
+
+
+case "$action" in
+  (patch)
+    if [ ! -e "$diff" ] ; then
+      echo "ERROR: MD engine not supported (or misspelled)"
+      exit 1
+    fi
+    if type -t plumed_preliminary_test 1>/dev/null ; then
+      if plumed_preliminary_test || [ "$force" ] ; then
+        echo >/dev/null
+      else
+        echo "ERROR: Preliminary test not passed."
+        echo "It seems that this is not $engine, or you are in the wrong directory"
+        echo "If you are sure about what you are doing, use -f"
+      exit 1
+      fi
+    fi
+    if [ -e Plumed.h ] || [ -e Plumed.inc ] || [ -e Plumed.cmake ]
+    then
+      if ( type -t plumed_before_revert 1>/dev/null || type -t plumed_after_revert 1>/dev/null) && ( type -t plumed_before_patch 1>/dev/null || type -t plumed_after_patch 1>/dev/null)
+      then
+        echo "ERROR: you have likely already patched, and your patch seems to need to be reverted."
+        echo "Revert first (-r)"
+        exit 1
+      else
+        echo "WARNING: you have likely already patched. Assuming that you can patch multiple times and continuing"
+      fi
+    fi
+    if [ ! -f "$PLUMED_ROOT/src/lib/Plumed.inc" ]
+    then
+      echo "ERROR: cannot find $PLUMED_ROOT/src/lib/Plumed.inc file"
+      echo "Compile plumed before patching"
+      exit 1
+    fi
+    if [ ! -f "$PLUMED_ROOT/src/lib/Plumed.cmake.$mode" ]
+    then
+      echo "ERROR: cannot find $PLUMED_ROOT/src/lib/Plumed.cmake.$mode file"
+      echo "Compile a $mode version of plumed before patching, or change patching mode [static|shared|runtime]"
+      exit 1
+    fi
+    if type -t plumed_before_patch 1>/dev/null ; then
+      test -n "$quiet" || echo "Executing plumed_before_patch function"
+      plumed_before_patch
+    fi
+    
+    if [[ -z $PLUMED_PATCH_NO_INCLUDE ]]; then
+      #PLUMED_PATCH_NO_INCLUDE is special for programs that have an embedded plumed integration
+      #and do not need the Plumed.h, Plumed.inc, and Plumed.cmake files
+      if test -n "$include" ; then
+        test -n "$quiet" || echo "Including Plumed.h, Plumed.inc, and Plumed.cmake ($mode mode)"
+        echo "#include \"$PLUMED_INCLUDEDIR/$PLUMED_PROGRAM_NAME/wrapper/Plumed.h\"" > Plumed.h
+        echo "include $PLUMED_ROOT/src/lib/Plumed.inc.$mode" > Plumed.inc
+        echo "include($PLUMED_ROOT/src/lib/Plumed.cmake.$mode)" > Plumed.cmake
+      else
+        test -n "$quiet" || echo "Linking Plumed.h, Plumed.inc, and Plumed.cmake ($mode mode)"
+        ln -fs "$PLUMED_INCLUDEDIR/$PLUMED_PROGRAM_NAME/wrapper/Plumed.h" Plumed.h
+        ln -fs "$PLUMED_ROOT/src/lib/Plumed.inc.$mode" Plumed.inc
+        ln -fs "$PLUMED_ROOT/src/lib/Plumed.cmake.$mode" Plumed.cmake
+      fi
+    fi
+
+    if [[ -n $PLUMED_PATCH_EXTRA_FILES ]]; then
+      for file in $PLUMED_PATCH_EXTRA_FILES; do
+        cp "${diff}/$file" "$file"
+      done
+    fi
+    if [ -d "$diff" ]; then
+      test -n "$quiet" || echo "Patching with on-the-fly diff from stored originals"
+      PREPLUMED=$(cd "$diff" ; find . -name "*.preplumed" | sort)
+      for bckfile in $PREPLUMED ; do
+        file="${bckfile%.preplumed}"
+        if test -e "$file" ; then
+          diff -U 5 "$diff/$bckfile" "$diff/$file" --label="$bckfile" --label="$file" |
+          patch -u -l -b -F 5 -N --suffix=.preplumed "$file"
+        else
+          echo "ERROR: File $file is missing"
+        fi
+      done
+    else
+      test -n "$quiet" || echo "Patching with stored diff"
+      bash "$diff"
+    fi
+
+    if [ "$PLUMED_IS_INSTALLED" = no  ] && [ "$mode" = shared ] ; then
+      echo ""
+      echo "You are patching in shared mode from a non installed PLUMED"
+      echo "Be warned that if you 'make clean' PLUMED the patched code won't work anymore"
+    fi
+
+    if [ "$mode" = runtime ] ; then
+      echo ""
+      echo "You are patching in runtime mode"
+      echo "Be warned that when you will run MD you will use the PLUMED version pointed at"
+      echo "by the PLUMED_KERNEL environment variable"
+    fi
+
+    if [ "$plumed_ignore_mpi" = no ] ; then
+      echo ""
+      if grep -q "D__PLUMED_HAS_MPI=1" "$PLUMED_ROOT"/src/config/compile_options.sh ; then
+        echo "PLUMED is compiled with MPI support so you can configure $engine with MPI" 
+      else
+        echo "PLUMED is compiled WITHOUT MPI support so you CANNOT configure $engine with MPI"
+      fi
+    fi
+
+    
+    if type -t plumed_after_patch 1>/dev/null ; then
+      test -n "$quiet" || echo "Executing plumed_after_patch function"
+      plumed_after_patch
+    fi
+
+  ;;
+  (info)
+    if type -t plumed_patch_info 1>/dev/null ; then
+      test -n "$quiet" || echo "Executing plumed_patch_info function"
+      plumed_patch_info
+    else
+      echo "No special info for this MD engine"
+    fi
+  ;;
+  (save)
+    if [[ -z $PLUMED_PATCH_NO_INCLUDE ]]; then
+      #PLUMED_PATCH_NO_INCLUDE is special for programs that have an embedded plumed integration
+      #and do not need the Plumed.h, Plumed.inc, and Plumed.cmake files
+      if [ ! -e Plumed.h ] || [ ! -e Plumed.inc ] || [ ! -e Plumed.cmake ]
+      then
+        echo "ERROR: I cannot find Plumed.h, Plumed.inc, and Plumed.cmake files. You have likely not patched yet."
+        exit 1
+      fi
+    fi
+    PREPLUMED=$(find . -name "*.preplumed" | sort)
+    for file in $PLUMED_PREPLUMED_IGNORE;
+    do
+      PREPLUMED=$(echo "$PREPLUMED" | grep -v "$file")
+    done
+
+    if ! test "$PREPLUMED" ; then
+      echo "ERROR: I cannot find any .preplumed file. There is nothing to save."
+      exit 1
+    fi
+    if type -t plumed_preliminary_test 1>/dev/null ; then
+      if plumed_preliminary_test || [ "$force" ] ; then
+        echo >/dev/null
+      else
+        echo "ERROR: Preliminary test not passed."
+        echo "It seems that this is not $engine, or you are in the wrong directory"
+        echo "If you are sure about what you are doing, use -f"
+      exit 1
+      fi
+    fi
+    test -n "$quiet" || echo "Saving your changes to $diff"
+    test -n "$quiet" || echo "Preplumed files:"
+    test -n "$quiet" || echo "$PREPLUMED"
+    if [[ -n $PLUMED_PATCH_EXTRA_FILES ]]; then
+      echo "Extra files:"
+      echo "$PLUMED_PATCH_EXTRA_FILES"
+    fi
+
+    if [ -d "$diff" ] && [ -z "$save_originals" ]; then
+      echo "This patch uses the dir format (originals are saved)"
+      echo "Are you sure you want to save the single diff?"
+      echo "Possible reasons to do it are:"
+      echo "* because of licence you do not want to store originals in plumed"
+      echo "* you do not want to do a big change on the diff files now"
+      answer=
+      PS3="Choose:"
+      select answer in single-diff originals ; do
+        if [[ -n "$answer" ]] ; then
+          break
+        else
+          echo "ERROR: choose in the list above or interrupt (^c)"
+        fi
+      done
+      if [ "$answer" = originals ] ; then
+        test -n "$quiet" || echo "saving originals"
+        save_originals=yes
+      else
+        test -n "$quiet" || echo "saving single diff file"
+      fi
+    fi
+    test -e "$diff" && rm -r "$diff"
+    for bckfile in $PREPLUMED ; do
+      file="${bckfile%.preplumed}"
+      if test -e "$file" ; then
+        if [ -n "$save_originals" ] ; then
+          xx="$diff/$file"
+          mkdir -p "${xx%/*}"
+          cp "$file" "$diff/$file"
+          cp "$bckfile" "$diff/$bckfile"
+        else
+          {
+            echo "patch -u -l -b -F 5 -N --suffix=.preplumed \"${file}\" << \\EOF_EOF"
+            diff -U 5 "${bckfile}" "$file" --label="$bckfile" --label="$file"
+            echo "EOF_EOF"
+          } >> "$diff"
+        fi
+      else
+        echo "ERROR: File $file is missing"
+      fi
+    done
+    if [[ -n $PLUMED_PATCH_EXTRA_FILES ]]; then
+      test -n "$quiet" || echo "saving extra files"
+      for file in $PLUMED_PATCH_EXTRA_FILES; do
+        xx=${diff}/$file
+        mkdir -p "${xx%/*}"
+        cp "$file" "${diff}/$file"
+      done
+    fi
+cat <<EOF
+* If you want your patch to perform some arbitrary action before/after
+* patching the diff files, just add a function named
+* plumed_before_patch/plumed_after_patch to the ${diff%diff}config file.
+* Do not forget to also add an equivalent plumed_before_revert/plumed_after_revert
+* function
+EOF
+  ;;
+  (revert)
+    if [ ! -e "$diff" ] ; then
+      echo "ERROR: MD engine not supported (or misspelled)"
+      exit 1
+    fi
+    if type -t plumed_before_revert 1>/dev/null ; then
+      test -n "$quiet" || echo "Executing plumed_before_revert function"
+      plumed_before_revert
+    fi
+    if [ ! -e Plumed.h ] || [ ! -e Plumed.inc ] || [ ! -e Plumed.cmake ]
+    then
+      echo "WARNING: I cannot find Plumed.h, Plumed.inc, and Plumed.cmake files. You have likely not patched yet."
+    else
+    test -n "$quiet" || echo "Removing Plumed.h, Plumed.inc, and Plumed.cmake"
+      rm Plumed.h Plumed.inc Plumed.cmake
+    fi
+    PREPLUMED=$(find . -name "*.preplumed")
+    if ! test "$PREPLUMED" ; then
+      echo "No .preplumed file found, nothing to restore."
+    else
+      test -n "$quiet" || echo "Reverting changes and touching reverted files"
+      for bckfile in $PREPLUMED ; do
+        file="${bckfile%.preplumed}"
+        mv "$bckfile" "$file"
+        touch "$file"
+      done
+    fi
+    if [[ -n $PLUMED_PATCH_EXTRA_FILES ]]; then
+      test -n "$quiet" || echo "Removing the extra files"
+      for file in $PLUMED_PATCH_EXTRA_FILES; do
+        rm -v "$file"
+      done
+    fi
+    if type -t plumed_after_revert 1>/dev/null ; then
+      test -n "$quiet" || echo "Executing plumed_after_revert function"
+      plumed_after_revert
+    fi
+esac
+
+
+

plumed/_lib/lib/plumed/patches/qespresso-5.0.2.config

@@ -0,0 +1,25 @@
+
+
+function plumed_preliminary_test(){
+# check if the README contains the word ESPRESSO and if qe has been already configured
+  grep -q ESPRESSO  README 1>/dev/null 2>/dev/null && test -f make.sys 
+}
+
+function plumed_before_patch(){
+cp make.sys make.sys.old
+PWD=`pwd`
+echo "include  ${PWD}/Plumed.inc ">make.sys
+awk '{if($1=="LIBS" && $2=="="){print $0" $(PLUMED_LOAD) "}else{print }}' make.sys.old >>make.sys
+}
+
+function plumed_after_revert(){
+  mv make.sys.old make.sys
+}
+
+function plumed_patch_info(){
+  echo ""
+  echo "For more information on Quantum Espresso you should visit http://www.quantum-espresso.org"
+}
+
+plumed_ignore_mpi=yes
+