hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/scripts/config.sh

@@ -0,0 +1,126 @@
+#! /usr/bin/env bash
+
+MANUAL="\
+
+Options:
+  -h, --help
+                    print this help and exit
+  -q, --quiet
+                    don't write anything, just return true of false
+  show
+                    dump a full configuration file
+  has [word1 [word2]..]
+                    check if plumed has features words
+  module [word1 [word2]..]
+                    check if plumed has enables modules words
+  makefile_conf
+                    dumps the Makefile.conf file
+
+Examples:
+
+Check if plumed as dlopen enabled
+> plumed config has dlopen
+Check if plumed as dlopen AND zlib enabled
+> plumed config has dlopen zlib
+Check if plumed as module colvar active
+> plumed config module colvar
+"
+
+# notice that the relative path of config.txt is also
+# hardcoded in a comment written in the log from src/core/PlumedMain.cpp
+# if you change it here, also change it there!
+configfile="$PLUMED_ROOT"/src/config/config.txt
+
+quiet=no
+list=no
+checklist=""
+for opt
+do
+  case "$opt" in
+  (--help|-h) echo "$MANUAL" ; exit ;;
+  (--description)
+    echo "inquire plumed about how it was configure"
+    exit 0
+    ;;
+  (--options)
+    echo "--help -h --description --options --quiet -q --version -v show has module mpiexec makefile_conf python_bin"
+    exit 0
+    ;;
+  (--quiet|-q) quiet=yes ;;
+  (--version|-v) action=version ;;
+  (show)
+    cat "$configfile"
+    exit 0
+    ;;
+  (has) action=has ;;
+  (module) action=module ;;
+  (python_bin) action=python_bin ;;
+  (mpiexec) action=mpiexec ;;
+  (makefile_conf)
+    cat "$configfile" | awk '{if($1=="makefile_conf") { gsub("^makefile_conf ",""); print} }'
+    exit 0
+    ;;
+  (*)
+    checklist="$checklist $opt"
+  esac
+done
+
+if test -z "$checklist" && ( test "$action" = show  || test  "$action" = has || test "$action" = module)
+then
+  test "$quiet" = no && echo "nothing to do"
+  exit 1
+fi
+
+case $action in
+(has|module)
+  retval=0
+  for check in $checklist
+  do
+  
+  ff=$(
+    cat "$configfile" |
+    awk -v action="$action" -v check="$check" '{ if($1==action && $2==check){ print $3;exit } }'
+  )
+  
+  if test "$ff" = on ; then
+    test "$quiet" = no && echo "$check on"
+  elif test "$ff" = off ; then
+    test "$quiet" = no && echo "$check off"
+    retval=1
+  else
+    test "$quiet" = no && echo "$check not found"
+    retval=1
+  fi
+  
+  done
+  
+  exit $retval
+ ;;
+(version)
+  long=$(cat "$configfile" | grep -v \# | awk '{ if($1=="version" && $2=="long") print $3 }')
+  git=$(cat "$configfile" | grep -v \# | awk '{ if($1=="version" && $2=="git") print $3 }')
+  echo "Version: $long (git: $git)"
+ ;;
+(python_bin)
+  py=$(cat "$configfile" | grep -v \# | awk '{ if($1=="python_bin") print $2 }')
+  if test -n "$py" ; then
+    retval=0
+    test "$quiet" = no && echo "$py"
+  else
+    retval=1
+    test "$quiet" = no && echo "python not found"
+  fi
+  exit $retval
+;;
+(mpiexec)
+  mpi=$(cat "$configfile" | grep -v \# | awk '{ if($1=="mpiexec") { sub(" *mpiexec ","",$0);  print} }')
+  if test -n "$mpi" ; then
+    retval=0
+    test "$quiet" = no && echo "$mpi"
+  else
+    retval=1
+    test "$quiet" = no && echo "mpiexec not found"
+  fi
+  exit $retval
+esac
+

plumed/_lib/lib/plumed/scripts/mklib.sh

@@ -0,0 +1,175 @@
+#! /usr/bin/env bash
+
+if [ "$1" = --description ] ; then
+  echo "compile one or more *.cpp files into a shared library"
+fi
+
+MANUAL='Compile one or more *.cpp files into a shared library.
+
+Usage:
+
+  plumed mklib [options] files1.cpp [file2.cpp ...]
+
+Options:
+  -h, --help
+                         Print this help and exit
+  -o LIBNAME, --out LIBNAME
+                         Name of the output library. If missing, the name
+                         of the first input file will me used, with its
+                         suffix properly adjusted.
+  -n                     No-clobber mode, similar to `mv -n`.
+                         Does not overwrite an existing library.
+                         If the library exists when the command is started,
+                         skip also the compilation phase.
+
+Environment variables:
+  PLUMED_MKLIB_CFLAGS    Extra compile time flags to be used
+  PLUMED_MKLIB_LDFLAGS   Extra link time flags (and libraries) to be used
+'
+
+OPTIONS="--description --options -h --help -o --out -n"
+
+if [ $# == 0 ]
+then
+  echo "ERROR"
+  echo "type 'plumed mklib file1.cpp [file2.cpp etc]'"
+  exit 1
+fi
+
+source "$PLUMED_ROOT"/src/config/compile_options.sh
+
+prefix=""
+lib=""
+no_clobber=""
+files=() # empty array
+for opt
+do
+  prefixopt="$prefix$opt"
+  prefix=""
+  case "$prefixopt" in
+    (-o|--out) prefix="--out=";;
+    (-h|--help) echo "$MANUAL" ; exit ;;
+    (--options) echo "$OPTIONS" ; exit ;;
+    (--out=*) lib="${prefixopt#--out=}";;
+    (-n) no_clobber=yes;;
+    (-*)
+      echo "ERROR: Unknown option $opt. Use --help for help."
+      exit 1 ;;
+    (*)
+      files+=("${prefixopt}");;
+  esac
+done
+
+if [ ${#files[@]} = 0 ] ; then
+  echo ERROR
+  echo "pass at least one file"
+  exit 1
+fi
+
+if [ -z "$lib" ]
+then
+  firstfile="${files[0]}"
+  lib="${firstfile%%.cpp}".$soext
+fi
+
+recompile=no
+for file in "${files[@]}"
+do
+  if ! test $lib -nt $file ;
+  then
+    recompile=yes
+  fi
+done
+
+if test -z "$no_clobber" ; then
+  recompile=yes
+fi
+
+if test $recompile = no ; then
+  echo "$lib is already up to date"
+  exit 0
+fi
+
+rm -f "$lib"
+
+toRemove=""
+remover() {
+  #if compilation fails or crashes the trap will delete the temporary files
+  for f in $toRemove; do
+    rm -rf "${f}"
+  done
+}
+trap "remover" EXIT
+objs=""
+
+tmpdir=$(mktemp -d "plumed_mklib.XXXXXX")
+
+toRemove="${toRemove} $tmpdir"
+
+for file in "${files[@]}"
+do
+
+  if [[ "$file" != *.cpp ]] ;
+  then
+    echo "ERROR"
+    echo "type 'plumed mklib file1.cpp [file2.cpp etc]'"
+    exit 1
+  fi
+
+  obj="${file%%.cpp}".o
+  
+  if [ ! -f "$file" ]
+  then
+    echo "ERROR: I cannot find file $file"
+    exit 1
+  fi
+  #adding a simple tmpfile, to preprocess "in place" the input file,
+  #this assumes the user has write permission in the current directory
+  #which should be true since we are going to compile and output something here
+  tmpfile=$(mktemp "${file%.cpp}.XXXXXX")
+  mv "${tmpfile}" "${tmpfile}.cpp"
+  tmpfile=${tmpfile}.cpp
+  cp "${file}" "${tmpfile}"
+  toRemove="${toRemove} ${tmpfile} ${tmpfile}.bak"
+  #this deprecates the shortcut to action register
+  if grep -q '^#include "\(bias\|colvar\|function\|sasa\|vatom\)\/ActionRegister.h"' "${tmpfile}"; then
+     >&2 echo 'WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">>'
+     sed -i.bak 's%^#include ".*/ActionRegister.h"%#include "core/ActionRegister.h"%g' "${tmpfile}"
+  fi
+  #this deprecates the shortcut to CLtoolregister
+  if grep -q '^#include "\(cltools\)\/CLToolRegister.h"' "${tmpfile}"; then
+     >&2  echo 'WARNING: using a legacy  CLToolRegister.h include path, please use <<#include "core/CLToolRegister.h">>'
+     sed -i.bak 's%^#include ".*/CLToolRegister.h"%#include "core/CLToolRegister.h"%g' "${tmpfile}"
+  fi
+  #this removes "#include "core/Atoms.h" and makes the compilation failing on the calls of Atoms
+  #instead of on the include
+  if grep -q '^#include\s*"core/Atoms.h"' "${tmpfile}"; then
+     #\s match anly type of white space
+     >&2  echo 'WARNING: "core/Atoms.h" does not exist anymore in  version >=2.10, you should change your code.'
+     sed -i.bak '/^#include\s*"core\/Atoms.h"/d' "${tmpfile}"
+  fi
+  rm -f "$tmpdir/$obj"
+
+  eval "$compile" "$PLUMED_MKLIB_CFLAGS" -o "$tmpdir/$obj" "$tmpfile" || {
+    echo "ERROR: compiling $file"
+    exit 1
+  }
+
+  objs="$objs $tmpdir/$obj"
+
+done
+
+link_command="$link_uninstalled"
+
+if test "$PLUMED_IS_INSTALLED" = yes; then
+  link_command="$link_installed"
+fi
+
+eval "$link_command" "$PLUMED_MKLIB_LDFLAGS" $objs -o "$tmpdir/$lib"
+
+if test -n "$no_clobber" ; then
+  # || true is necessary with recent coreutils
+  mv -n "$tmpdir/$lib" $lib || true
+else
+  mv "$tmpdir/$lib" $lib
+fi

plumed/_lib/lib/plumed/scripts/newcv.sh

@@ -0,0 +1,26 @@
+#! /usr/bin/env bash
+
+if [ "$1" = --description ] ; then
+  echo "create a new collective variable from a template"
+  exit 0
+fi
+
+if [ "$1" = --options ] ; then
+  echo "--description --options"
+  exit 0
+fi
+
+if [ $# != 2 ] ;
+then
+  echo "ERROR"
+  echo "type 'plumed newcv directive classname'"
+  echo "E.g. 'plumed newcv TORSION Torsion'"
+  exit 1
+fi
+
+directive=$1
+classname=$2
+
+sed "s/TEMPLATE/$directive/g
+     s/Template/$classname/g" "$PLUMED_ROOT"/src/colvar/Template.cpp > ${classname}.cpp
+

plumed/_lib/lib/plumed/scripts/partial_tempering.sh

@@ -0,0 +1,319 @@
+#! /usr/bin/env bash
+# vim:ft=awk
+if [ "$1" = --description ] ; then
+  echo "scale parameters in a gromacs topology to implement solute or partial tempering"
+  exit 0
+fi
+
+if [ "$1" = --options ] ; then
+  echo "--description --gromacs4 --help -h --options"
+  exit 0
+fi
+
+if [ "$1" = --help ] || [ "$1" = -h ] ; then
+  cat <<EOF
+Usage:
+
+  plumed partial_tempering [--gromacs4] scale < processed.top
+
+where scale is the Hamiltonian scaling factor and
+processed.top is a post-processed topology file (i.e. produced with grompp -pp)
+where each "hot" atom has a "_" appended to the atom type, e.g.:
+
+     1 amber99_43_     1    RC5    O5'      1    -0.6223         16   ; qtot -0.6223
+
+Notice that the section that should be edited is the [atoms] section for all the
+molecules that you wish to affect (typically only for the solute, but you may also
+want to change solvent parameters).
+
+Also remember to first produce the processed.top file with grompp -pp. Editing a normal
+topol.top file will not work, because it does not contain all the parameters.
+The processed.top file should not have any "#include" statement.
+
+# produce a processed topology
+grompp -pp
+# choose the "hot" atoms
+vi processed.top
+# generate the actual topology
+plumed partial_tempering \$scale < processed.top > topol\$i.top
+
+WARNING: It's not very robust and there might be force-field dependent issues!
+A few tests are strongly suggested.
+
+WARNING: This script requires gawk to be available on your system.
+
+1. Compare partial_tempering with scale=1.0 to non-scaled force field. E.g.
+grompp -o topol-unscaled.tpr
+grompp -pp
+vi processed.top # choose the "hot" atoms appending "_". You can choose whatever.
+plumed partial_tempering 1.0 < processed.top > topol-scaled.top # scale with factor 1
+grompp -p topol-scaled.top -o topol-scaled.tpr
+# Then do a rerun on a trajectory
+mdrun -s topol-unscaled.tpr -rerun rerun.trr
+mdrun -s topol-scaled.tpr -rerun rerun.trr
+# and compare the resuling energy files. they should be identical
+
+2. Compare partial_tempering with scale=0.5 to non-scaled force field.
+Repeat the same procedure but using "plumed partial_tempering 0.5".
+Choose all the atoms in all the relevant [atoms] sections (e.g. solute, solvent and ions).
+In the two resulting energy files you should see:
+long range electrostatics, LJ, and dihedral energy is *half* in the scaled case
+all other terms (bonds/bends) are identical.
+
+EOF
+  exit
+fi
+
+gromacs5=1
+
+if [ "$1" == --gromacs4 ] ; then
+  gromacs5=0
+  shift
+fi
+
+gawk -v scale=$1 -v gromacs5=$gromacs5 '
+BEGIN{
+  combrule=1;
+}
+function recname()
+{
+     if($1=="[" && $3=="]") return $2;
+     return "";
+}
+function error(msg)
+{
+     print "ERROR:",msg > "/dev/stderr" ;
+     exit;
+}
+function warning(msg)
+{
+     print "WARNING:",msg | "cat 1>&2"
+}
+function find_matching_torsion(params,atype, a1,a2,a3,a4,iswitch,progression,test,array,param,countX,bestCountX,bestMatch)
+{
+   progression=NR
+   bestCountX=5
+   for(iswitch=0;iswitch<32;iswitch++){
+     countX=0
+     if(iswitch%2==0){
+       a1=atype[1]; a2=atype[2]; a3=atype[3]; a4=atype[4];
+     } else {
+       a1=atype[4]; a2=atype[3]; a3=atype[2]; a4=atype[1];
+     }
+     if(int(iswitch/2)%2==1){ a1="X"; countX++; }
+     if(int(iswitch/4)%2==1){ a2="X"; countX++; }
+     if(int(iswitch/8)%2==1){ a3="X"; countX++; }
+     if(int(iswitch/16)%2==1){a4="X"; countX++; }
+     test=a1"-"a2"-"a3"-"a4"-"$5;
+     if(test in params){
+       split(params[test],array,":");
+       bestMatch=0;
+       if(gromacs5) {
+         if(countX<bestCountX || (countX==bestCountX && array[1]<progression)) bestMatch=1
+       } else {
+         if(array[1]<progression) bestMatch=1;
+       }
+       if(bestMatch){
+         progression=array[1];
+         bestCountX=countX
+         param=params[test];
+       }
+     }
+   }
+   return param;
+}
+{
+# This is the suffix for "hot" atoms:
+  suffix="_";
+
+# format for writing parameters
+  CONVFMT="%.12g"
+
+##### PARSING DATABASE #####
+# store comments:
+  comments="";
+  if(a=match($0,";")) comments=substr($0,a);
+# remove comments:
+  gsub(";.*","");
+# echo empty line
+  if(NF==0){
+    print comments;
+    next;
+  }
+# set name of current block
+  if(recname() ) rec=recname();
+# set defaults for nb interactions
+  if(rec=="defaults" && NF==5) combrule=$2;
+# if we are in atomtypes section, check which fields are present
+# use same heuristics as in src/kernel/toppush.c
+  if(rec=="atomtypes" && NF>=4){
+    if((length($4)==1 && $4~"[a-zA-Z]")){
+      bondtypefield=1;
+      epsilonfield=6;
+    }
+    else if((length($6)==1 && $6~"[a-zA-Z]")){
+      bondtypefield=2;
+      epsilonfield=8;
+    }
+    else if((length($5)==1 && $5~"[a-zA-Z]")){
+      if(substr($2,0,1) ~"[a-zA-Z]"){
+        bondtypefield=2;
+        epsilonfield=7;
+      } else {
+        bondtypefield=1;
+        epsilonfield=7;
+      }
+    } else error("in atomtypes");
+    if(epsilonfield!=NF) error("in atomtypes");
+# NOTE: OPLS uses bond types, thus we have to save the bondtype
+# For other force fields (e.g. AMBER) atomtype is used as bondtype
+# and column two is ignored (it is just atomic number).
+    bondtype[$1]=$bondtypefield;
+  }
+
+# storing dihedraltypes:
+  if(rec=="dihedraltypes" && ($5==1 || $5==2 || $5==3 || $5==4 || $5==5 || $5==9)){
+    if($5==1 || $5==4 || $5==9) string=":"$6" "$7" "$8;
+    else if($5==2) string=":"$6" "$7;
+    else if($5==3) string=":"$6" "$7" "$8" "$9" "$10" "$11;
+    else if($5==5) string=":"$6" "$7" "$8" "$9;
+    type=$1"-"$2"-"$3"-"$4"-"$5
+    if(type in params) params[type]=params[type]string;
+    else               params[type]=NR""string;
+# parameters are commented since they are used inline
+    print "; LINE("NR")",$0,comments
+    next;
+  }
+
+##### SCANNING #####
+# in case new list of atoms for a new molecule, delete the present list
+  if(recname()=="atoms"){
+    delete list_of_atoms;
+    n_of_atoms=0;
+  }
+# detect amber type of each atom
+  if(rec=="atoms" && NF>6){
+     name=$2;
+     gsub(suffix"$","",name)
+     ato[$1]=name;
+  }
+
+##### PRINTING #####
+# DIHEDRALS
+  if(rec=="dihedrals" && ($5==1 || $5==2 || $5==3 || $5==4 || $5==5 || $5==9) ){
+    found1=0; found4=0;
+    for(j=0;j<n_of_atoms;j++) {
+      if($1==list_of_atoms[j]) found1=1;
+      if($4==list_of_atoms[j]) found4=1;
+    }
+    sscale=1.0;
+    if(found1)sscale*=sqrt(scale);
+    if(found4)sscale*=sqrt(scale);
+
+# this is the case in which dihedrals are online:
+     if(NF>5){
+       printf($1" "$2" "$3" "$4" "$5" ");
+       if($5==1 || $5==4 || $5==9){
+                                   if(NF!=8) error("dihedrals with type 1,4,9 should have 8 fields");
+                                   printf($6" "$7*sscale" "$8);
+       } else if($5==2) {
+                                   if(NF!=7) error("dihedrals with type 2 should have 7 fields");
+                                   printf($6" "$7*sscale);
+       } else if($5==3) {
+                                   if(NF!=11) error("dihedrals with type 3 should have 11 fields");
+                                   printf($6*sscale" "$7*sscale" "$8*sscale" "$9*sscale" "$10*sscale" "$11*sscale);
+       } else if($5==5) {
+                                   if(NF!=9) error("dihedrals with type 5 should have 9 fields");
+                                   printf($6*sscale" "$7*sscale" "$8*sscale" "$9*sscale);
+       } else error("dihedrals with more than 5 fields should be 1,2,3,4,5 or 9");
+       printf(" "comments"\n");
+# this is the case in which we have to search the database
+     } else if(NF==5){
+       param="";
+       atype[1]=bondtype[ato[$1]]
+       atype[2]=bondtype[ato[$2]]
+       atype[3]=bondtype[ato[$3]]
+       atype[4]=bondtype[ato[$4]]
+
+       param=find_matching_torsion(params,atype);
+       
+       
+    n=split(param,array,":");
+    if(n<=1) error("params not found "$1" "$2" "$3" "$4" "$5" "atype[1]" "atype[2]" "atype[3]" "atype[4]);
+    if($5!=9 && n!=2){
+# in case of multiple dihedrals !=9, all parameters should be the same, otherwise I suspect there is some problem
+      for(i=3;i<=n;i++){
+        if((array[i]-array[2])**2>1e-20) error("multiple dihedrals !=9: parameters "array[i]" and "array[2]" are different\n");
+      }
+# then, I just take one of the instances
+      param=array[1]":"array[2];
+      n=split(param,array,":");
+    }
+    
+    printf("; parameters for types %s %s %s %s at LINE(%s)\n",atype[1],atype[2],atype[3],atype[4],array[1]);
+    for(i=2;i<=n;i++){
+      printf($1" "$2" "$3" "$4" "$5" ");
+      split(array[i],array1," ");
+      if($5==1 || $5==4 || $5==9){
+                                  printf(array1[1]" "array1[2]*sscale" "array1[3]);
+      } else if($5==2) {
+                                  printf(array1[1]" "array1[2]*sscale);
+      } else if($5==3) {
+                                  printf(array1[1]*sscale" "array1[2]*sscale" "array1[3]*sscale" "array1[4]*sscale" "array1[5]*sscale" "array1[6]*sscale);
+      } else if($5==5) {
+                                  printf(array1[1]*sscale" "array1[2]*sscale" "array1[3]*sscale" "array1[4]*sscale);
+      } else error("dihedrals with more than 5 fields should be 1,2,3,4,5 or 9");
+      printf(comments);
+      printf("\n");
+    }
+   } else error("dihedrals should have at least 5 fields");
+# PAIRS
+  } else if(rec=="pairs" && ($3==1 || $3==2) && NF>3 ){
+    found1=0; found2=0;
+    for(j=0;j<n_of_atoms;j++) {
+      if($1==list_of_atoms[j]) found1=1;
+      if($2==list_of_atoms[j]) found2=1;
+    }
+    scaleq1=1.0;
+    scaleq2=1.0;
+    if(found1)scaleq1*=sqrt(scale);
+    if(found2)scaleq2*=sqrt(scale);
+    scale2=1.0; # scaling for second to last column
+    if(combrule==1) scale2=scaleq1*scaleq2;
+    if($3==1) {
+      print $1,$2,$3,scale2*$4,scaleq1*scaleq2*$5," ; scaled";
+    }
+    if($3==2) {
+      print $1,$2,$3,$4,scaleq1*$5,scaleq2*$6,scale2*$7,scaleq1*scaleq2*$8," ; scaled";
+    }
+# ATOMTYPES
+  } else if(rec=="atomtypes" && NF>=4){
+    scale2=1.0; # scaling for second to last column
+    if(combrule==1) scale2=scale;
+    for(i=1;i<NF;i++)printf($i" "); print $NF,comments;
+    printf($1""suffix" "bondtype[$1]" ");
+    from=3;
+    if(NF==6) from=2; # GROMOS does not store bondtype by default, so we should add one column
+    for(i=from;i<NF-1;i++)printf($i" "); print scale2*$(NF-1),scale*$NF," ; scaled";
+# ATOMTYPES (PAIRS)
+  } else if((rec=="pairtypes" || rec=="nonbond_params") && NF>=5){
+    scale2=1.0; # scaling for second to last column
+    if(combrule==1) scale2=scale;
+    print $1,$2,$3,$4,$5,comments
+    print $1""suffix,$2,$3,sqrt(scale2)*$4,sqrt(scale)*$5," ; scaled";
+    print $1,$2""suffix,$3,sqrt(scale2)*$4,sqrt(scale)*$5," ; scaled";
+    print $1""suffix,$2""suffix,$3,scale2*$4,scale*$5," ; scaled";
+# ATOMS
+  } else if(rec=="atoms" && NF>=7){
+     if($2~".*"suffix"$"){
+       if(NF>=8) print $1,$2,$3,$4,$5,$6,$7*sqrt(scale),$8,comments;
+       if(NF==7) print $1,$2,$3,$4,$5,$6,$7*sqrt(scale),comments;
+       list_of_atoms[n_of_atoms]=$1;
+       n_of_atoms++;
+     }
+     else print $0
+# EVERYTHING ELSE (just print)
+  } else print $0,comments
+}
+'
+

plumed/_lib/lib/plumed/scripts/patch.sh

@@ -0,0 +1,4 @@
+#! /usr/bin/env bash
+
+"${PLUMED_ROOT}"/patches/patch.sh "$@"
+