post update ibi

CHANGELOG.rst

@@ -30,6 +30,7 @@ Version 2022-dev
 -  use ndim vector instead of std::vector (#689)
 -  adapted tokenizer api (#693)
 -  made membervariable format consistent (#694)
+-  add ability to run ibi as a postupd method (#696)
 
 Version 2021.1 (released XX.03.21)
 ==================================

share/doc/methods.rst

@@ -663,17 +663,17 @@ unregularized version of IMC is applied.
 Internal degrees of freedom
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-For internal degrees of freedom, one can apply the IBI method. In that case,
-one also has to provide a setting_nonbonded file, which will be used to
-calculate the IMC matrix only from the nonbonded interactions.
+For internal degrees of freedom, one can apply the IBI method as a post update
+method.
 
 .. code:: xml
 
   <inverse>
     <imc>
-      <bonded_method>ibi</bonded_method>
-      <settings_nonbonded>settings-nonbonded.xml</settings_nonbonded>
+      <group>none</group>
     </imc>
+    <do_potential>0</do_potential>
+    <post_update>ibi</post_update>
   </inverse>
 
 Iterative Integral Equation methods

share/scripts/inverse/csg_table

@@ -82,6 +82,7 @@ postupd tag tag_file.sh
 postupd extrapolate postupd_extrapolate.sh
 postupd kbibi postupd_kbibi_correction.sh
 postupd cibi postupd_cibi_correction.sh
+postupd ibi postupd_ibi.sh
 
 # post add
 post add post_add.sh

share/scripts/inverse/imc_stat_generic.sh

@@ -27,11 +27,6 @@ EOF
 fi
 
 sim_prog="$(csg_get_property cg.inverse.program)"
-[[ -n $(csg_get_property --allow-empty cg.bonded.name) ]] && has_bonds=true || has_bonds=false
-bonded_method="$(csg_get_property cg.inverse.imc.bonded_method)"
-if [[ $has_bonds == true && $bonded_method == "ibi" ]]; then
-    settings_nonbonded="$(csg_get_property cg.inverse.imc.settings_nonbonded)"
-fi
 
 topol=$(csg_get_property --allow-empty cg.inverse.$sim_prog.imc.topol)
 [[ -z $topol ]] && topol=$(csg_get_property cg.inverse.$sim_prog.topol)
@@ -61,21 +56,8 @@ else
   #copy+resample all target dist in $this_dir
   for_all "non-bonded bonded" do_external resample target '$(csg_get_interaction_property inverse.target)' '$(csg_get_interaction_property name).dist.tgt'
 
-  if [[ $has_bonds == true ]]; then
-      if [[ $bonded_method == "imc" ]]; then
-          die "using IMC for bonded potentials is not implemented yet"
-      elif [[ $bonded_method == "ibi" ]]; then
-          msg "calculating regular distributions for ibi bonded upates"
-          critical csg_stat --options "$CSGXMLFILE" --top "$topol" --trj "$traj" \
-              --begin $equi_time --first-frame $first_frame --nt $tasks
-          msg "calculating correlations for imc updates"
-          critical csg_stat --do-imc --options "$settings_nonbonded" --top "$topol" --trj "$traj" \
-              --begin $equi_time --first-frame $first_frame --nt $tasks
-      fi
-  else
-      critical csg_stat --do-imc --options "$CSGXMLFILE" --top "$topol" --trj "$traj" \
-          --begin $equi_time --first-frame $first_frame --nt $tasks
-  fi
+  critical csg_stat --do-imc --options "$CSGXMLFILE" --top "$topol" --trj "$traj" \
+      --begin $equi_time --first-frame $first_frame --nt $tasks
 
   mark_done "imc_analysis"
 fi

share/scripts/inverse/postupd_cibi_correction.sh

@@ -1,6 +1,6 @@
 #! /bin/bash
 #
-# Copyright 2009-2017 The VOTCA Development Team (http://www.votca.org)
+# Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@ C-IBI: Targeting cumulative coordination within an iterative protocol
 to derive coarse-grained models of (multi-component) complex fluids,
 J. Chem. Phys. (in press).
 
-Usage: ${0##*/}
+Usage: ${0##*/} infile outfile
 EOF
    exit 0
 fi

share/scripts/inverse/postupd_ibi.sh

@@ -0,0 +1,55 @@
+#! /bin/bash
+#
+# Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+if [ "$1" = "--help" ]; then
+cat <<EOF
+${0##*/}, version %version%
+This script implemtents the function post update with the Inverse Boltzmann
+Method. This one is not like other post update methods in that the infile is ignored.
+
+Usage: ${0##*/} infile outfile
+EOF
+   exit 0
+fi
+
+name=$(csg_get_interaction_property name)
+bondtype="$(csg_get_interaction_property bondtype)"
+step_nr=$(get_current_step_nr)
+scheme=( $(csg_get_interaction_property inverse.do_potential) )
+scheme_nr=$(( (step_nr - 1 ) % ${#scheme[@]} ))
+postibi=( $(csg_get_interaction_property inverse.post_update_options.ibi.do) )
+postibi_nr=$(( (step_nr - 1 ) % ${#postibi[@]} ))
+
+if [[ ${postibi[$postibi_nr]} = 1 ]]; then
+
+    if [[ "${scheme[$scheme_nr]}" == 1 ]]; then
+        msg --color blue "WARNING: the potential ${name} has already been updated.
+This ibi post-update will overwrite the original update and all previous
+post-updates! You might want to set do_potential to 0."
+    fi
+
+    #update ibi
+    echo "Apply ibi post-update for interaction ${name}"
+    do_external resample target "$(csg_get_interaction_property inverse.target)" "${name}.dist.tgt"
+    kBT="$(csg_get_property cg.inverse.kBT)"
+    is_num "${kBT}" || die "${0##*/}: cg.inverse.kBT should be a number, but found '$kBT'"
+    do_external update ibi_pot "${name}.dist.tgt" "${name}.dist.new" "${name}.pot.cur" "${name}.dpot.pure_ibi" "${kBT}"
+    do_external potential shift --type "${bondtype}" "${name}.dpot.pure_ibi" "$2"
+else
+   echo "No ibi post-update for interaction ${name}"
+   do_external postupd dummy "$1" "$2"
+fi

share/scripts/inverse/postupd_kbibi_correction.sh

@@ -1,6 +1,6 @@
 #! /bin/bash
 #
-# Copyright 2009-2017 The VOTCA Development Team (http://www.votca.org)
+# Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -24,7 +24,7 @@ P. Ganguly, D. Mukherji, C. Junghans, N. F. A. van der Vegt,
 Kirkwood-Buff coarse-grained force fields for aqueous solutions,
 J. Chem. Theo. Comp., 8, 1802 (2012), doi:10.1021/ct3000958
 
-Usage: ${0##*/}
+Usage: ${0##*/} infile outfile
 EOF
    exit 0
 fi

share/scripts/inverse/prepare_iie.sh

@@ -28,13 +28,7 @@ fi
 sim_prog="$(csg_get_property cg.inverse.program)"
 method="$(csg_get_property cg.inverse.method)"
 initial_guess_method="$(csg_get_property "cg.inverse.${method}.initial_guess.method")"
-main_dir=$(get_main_dir)
-nb_interactions=$(csg_get_property --allow-empty cg.non-bonded.name)
-kBT="$(csg_get_property cg.inverse.kBT)"
-densities="$(csg_get_property cg.inverse.iie.densities)"
-n_intra="$(csg_get_property cg.inverse.iie.n_intra)"
 verbose=$(csg_get_property cg.inverse.iie.verbose)
-cut_off="$(csg_get_property cg.inverse.iie.cut_off)"
 
 if [ "${verbose}" == 'true' ]; then
     verbose_flag="--verbose"
@@ -52,6 +46,12 @@ case "$initial_guess_method" in
     for_all "bonded non-bonded" do_external prepare_single generic --use-bi
     ;;
 "ie")
+    main_dir=$(get_main_dir)
+    nb_interactions=$(csg_get_property --allow-empty cg.non-bonded.name)
+    kBT="$(csg_get_property cg.inverse.kBT)"
+    densities="$(csg_get_property cg.inverse.iie.densities)"
+    n_intra="$(csg_get_property cg.inverse.iie.n_intra)"
+    cut_off="$(csg_get_property cg.inverse.iie.cut_off)"
     # only for IE
     initial_guess_closure=$(csg_get_property "cg.inverse.${method}.initial_guess.closure")
     initial_guess_ignore_intra=$(csg_get_property "cg.inverse.${method}.initial_guess.ignore_intramolecular_correlation")

share/scripts/inverse/prepare_imc.sh

@@ -32,12 +32,17 @@ if [[ ${#names[@]} -gt 1 ]]; then
   msg --color blue "####################################################"
 fi
 
-
-[[ -n $(csg_get_property --allow-empty cg.bonded.name) ]] && has_bonds=true || has_bonds=false
-bonded_method="$(csg_get_property cg.inverse.imc.bonded_method)"
-
-if [[ $has_bonds == true && $bonded_method == "imc" ]]; then
-  die "using IMC for bonded potentials is not implemented yet"
-fi
+check_bonded_update() {
+  local do_potential=$(csg_get_interaction_property inverse.do_potential)
+  local imc_group=$(csg_get_interaction_property inverse.imc.group)
+  if [[ $do_potential != 0 ]] || [[ $imc_group != "none" ]]; then
+    die_msg="using IMC for bonded potentials is not implemented yet.\n"\
+"Make sure to set update_potential to 0 and imc.group to 'none' for\n"\
+"each bonded interaction. You can still use post_update ibi."
+    die "$die_msg"
+  fi
+}
+export -f check_bonded_update
+for_all "bonded" check_bonded_update
 
 do_external prepare generic

share/scripts/inverse/update_ibi_pot.pl

@@ -56,17 +56,43 @@
 (readin_table($cur_pot_file,@pot_r_cur,@pot_cur,@pot_flags_cur)) || die "$progname: error at readin_table\n";
 
 #should never happen due to resample, but better check
-die "Different grids \n" if (($r_aim[1]-$r_aim[0]-$r_cur[1]+$r_cur[0])>0.0001);
+die "Different grids \n" if (($r_aim[1]-$r_aim[0]-$r_cur[1]+$r_cur[0]) > 0.0001);
 die "Different start potential point \n" if (($r_aim[0]-$r_cur[0]) > 0.0001);
 die "Different end potential point \n" if ( $#r_aim != $#r_cur );
 
 my $outfile="$ARGV[3]";
 my @dpot;
 my @flag;
-my $value=0.0;
 
-#start from the end to make the begining have the last value
-for (my $i=$#r_aim;$i>=0;$i--){
+sub maxindex {
+  my( $aref, $idx_max ) = ( shift, 0 );
+  $aref->[$idx_max] > $aref->[$_] or $idx_max = $_ for 1 .. $#{$aref};
+  return $idx_max;
+}
+my $ndx_max_rdf_cur = maxindex(\@rdf_cur);
+
+#start from the middle and make the outside regions have the last valid value
+# go to end
+my $value=0.0;
+for (my $i=$ndx_max_rdf_cur;$i<=$#r_aim;$i++){
+  if (($rdf_aim[$i] > 1e-10) && ($rdf_cur[$i] > 1e-10)) {
+    $dpot[$i]=log($rdf_cur[$i]/$rdf_aim[$i])*$pref;
+    $flag[$i]="i";
+  } else {
+    $dpot[$i]=$value;
+    $flag[$i]="o";
+  }
+  if($pot_flags_cur[$i] =~ /[u]/) {
+    $dpot[$i]=$value;
+    $flag[$i]="o";
+  }
+  else {
+    $value=$dpot[$i];
+  }
+}
+# go to beginning
+$value=0.0;
+for (my $i=$ndx_max_rdf_cur-1;$i>=0;$i--){
   if (($rdf_aim[$i] > 1e-10) && ($rdf_cur[$i] > 1e-10)) {
     $dpot[$i]=log($rdf_cur[$i]/$rdf_aim[$i])*$pref;
     $flag[$i]="i";

share/scripts/inverse/update_imc.sh

@@ -32,20 +32,17 @@ do_external imc_stat $sim_prog
 default_reg=$(csg_get_property cg.inverse.imc.default_reg)
 is_num "${default_reg}" || die "${0##*/}: value of cg.inverse.imc.default_reg should be a number"
 
-[[ -n $(csg_get_property --allow-empty cg.bonded.name) ]] && has_bonds=true || has_bonds=false
-bonded_method="$(csg_get_property cg.inverse.imc.bonded_method)"
-
 imc_groups=$(csg_get_interaction_property --all inverse.imc.group)
 imc_groups=$(remove_duplicate $imc_groups)
 [[ -z ${imc_groups} ]] && die "${0##*/}: No imc groups defined"
 for group in $imc_groups; do
+  if [[ $group == "none" ]]; then
+    continue
+  fi
   reg="$(csg_get_property cg.inverse.imc.${group}.reg ${default_reg})" #filter me away
   is_num "${reg}" || die "${0##*/}: value of cg.inverse.imc.${group}.reg should be a number"
   msg "solving linear equations for imc group '$group' (regularization ${reg})"
   critical csg_imc_solve --imcfile "${group}.imc" --gmcfile "${group}.gmc" --idxfile "${group}.idx" --regularization "${reg}"
 done
 
-for_all "non-bonded" do_external update imc_single
-if [[ $has_bonds == true && $bonded_method == "ibi" ]]; then
-    for_all "bonded" do_external update ibi_single
-fi
+for_all "non-bonded bonded" do_external update imc_single

share/scripts/inverse/update_imc_single.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-# Copyright 2009-2019 The VOTCA Development Team (http://www.votca.org)
+# Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -30,8 +30,14 @@ step_nr=$(get_current_step_nr)
 scheme=( $(csg_get_interaction_property inverse.do_potential) )
 scheme_nr=$(( ( $step_nr - 1 ) % ${#scheme[@]} ))
 name=$(csg_get_interaction_property name)
+group=$(csg_get_interaction_property inverse.imc.group)
 
-if [ "${scheme[$scheme_nr]}" = 1 ]; then
+if [[ $group == "none" ]] && [[ ${scheme[$scheme_nr]} == 1 ]]; then
+    die_msg="for interaction $name the imc group is 'none' but\n"\
+"update_potential is non-zero. No imc update was calculated, so no update\n"\
+"can be made."
+    die "$die_msg"
+elif [[ ${scheme[$scheme_nr]} == 1 ]]; then
   echo "Update potential ${name} : yes"
   kBT=$(csg_get_property cg.inverse.kBT)
   is_num "${kBT}" || die "${0##*/}: cg.inverse.kBT should be a number, but found '$kBT'"
@@ -46,4 +52,3 @@ else
   step=$(csg_get_interaction_property step)
   do_external table dummy "${min}:${step}:${max}" "${name}.dpot.new"
 fi
-

share/xml/csg_defaults.xml.in

@@ -263,12 +263,6 @@
       <default_reg>0
         <DESC> default magnitude for regularization parameter if not given for the group explicitly, default =0</DESC>
       </default_reg>
-      <bonded_method>ibi
-        <DESC> method for calculating updates on the bonded interactions. ibi or imc (not implemented), default=ibi </DESC>
-      </bonded_method>
-      <settings_nonbonded>imc
-        <DESC> settings file to be used with csg_stat --do-imc. only needed if bonded_method=ibi</DESC>
-      </settings_nonbonded>
     </imc>
     <lammps>
       <DESC> general lammps specific options </DESC>
@@ -605,7 +599,7 @@
       <imc>
         <DESC>section containing inverse monte carlo specific options.</DESC>
         <group>
-          <DESC>Group of interaction. Cross-correlations of all members of a group are taken into account for calculating the update. If no cross correlations should be calculated, interactions have to be put into different groups.</DESC>
+          <DESC>Group of interaction. Cross-correlations of all members of a group are taken into account for calculating the update. If no cross correlations should be calculated, interactions have to be put into different groups. Group 'none' is completely ignored and update_potential needs to be zero for the respective interactions.</DESC>
         </group>
       </imc>
       <lammps>
@@ -703,6 +697,12 @@
             <DESC>Number of point to calculate the average from for the extrapolation</DESC>
           </points>
         </extrapolate>
+        <ibi>
+          <DESC>Contains all options of the IBI post-update script</DESC>
+          <do>1
+            <DESC>Update cycle for the IBI post-update (1 do, 0 do not). To do the post-update every third step specify "0 0 1", similar to do_potential</DESC>
+          </do>
+        </ibi>
         <kbibi>
           <DESC>Contains all options of the Kirkwood-Buff ramp corrections scripts</DESC>
           <do>1

src/tools/csg_stat_imc.cc

@@ -196,7 +196,9 @@ Imc::interaction_t *Imc::AddInteraction(tools::Property *p, bool is_bonded) {
       std::make_pair(name, std::make_unique<interaction_t>()));
   interaction_t *i = success.first->second.get();
   i->index_ = index;
-  getGroup(group)->interactions_.push_back(i);
+  if (group != "none") {
+    getGroup(group)->interactions_.push_back(i);
+  }
 
   i->is_bonded_ = is_bonded;
   i->step_ = p->get("step").as<double>();