Dropped thermforce iteration method (fixes #172)

.travis.yml

@@ -62,7 +62,6 @@ env:
     - CSG_MDRUN_STEPS=500 TEST=spce/simplex/density J=4
     - CSG_MDRUN_STEPS=500 TEST=spce/simplex/pressure J=4
     - CSG_MDRUN_STEPS=500 TEST=spce/simplex/simple J=4
-    - CSG_MDRUN_STEPS=500 TEST=spce/tf J=4
     - CSG_MDRUN_STEPS=500 TEST=urea-water/ibi J=4
     - CSG_MDRUN_STEPS=500 TEST=urea-water/kb-ibi J=4
 

CHANGELOG.md

@@ -3,6 +3,7 @@ For more detailed information about the changes see the history of the [reposito
 ## Version 1.4-dev
  * dropped support for gromacs-4 and clean up
  * dropped multi_g_rdf script
+ * dropped thermforce iteration method
 
 ## Version 1.3_rc1 _SuperUzma_ (released 23.09.15)
 

share/scripts/inverse/csg_table

@@ -1,5 +1,5 @@
 #
-# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
+# Copyright 2009-2015 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.
@@ -27,16 +27,13 @@ csg master inverse.sh
 prepare ibi prepare_generic.sh
 prepare imc prepare_imc.sh
 prepare generic prepare_generic.sh
-prepare tf prepare_generic.sh
 prepare optimizer prepare_optimizer.sh
 prepare re prepare_re.sh
 prepare_single ibi prepare_generic_single.sh
 prepare_single imc prepare_generic_single.sh
-prepare_single tf prepare_generic_single.sh
 prepare_single optimizer prepare_optimizer_single.sh
 initstep ibi initialize_step_generic.sh
 initstep imc initialize_step_generic.sh
-initstep tf initialize_step_generic.sh
 initstep optimizer initialize_step_optimizer.sh
 initstep re initialize_step_re.sh
 
@@ -50,7 +47,6 @@ update ibm update_ibm.sh
 # TODO: think about name add_pot, is other name maybe better
 add_pot ibi add_pot_generic.sh
 add_pot imc add_pot_generic.sh
-add_pot tf add_pot_generic.sh
 add_pot optimizer dummy.sh
 add_pot re dummy.sh
 
@@ -59,19 +55,16 @@ add_pot re dummy.sh
 # pre update
 pre_update ibi dummy.sh
 pre_update imc dummy.sh
-pre_update tf dummy.sh
 pre_update optimizer dummy.sh
 pre_update re pre_update_re.sh
 
 # post update
 post_update ibi post_update_generic.sh
 post_update imc post_update_generic.sh
-post_update tf post_update_generic.sh
 post_update optimizer dummy.sh
 post_update re post_update_generic.sh
 post_update_single ibi post_update_generic_single.sh
 post_update_single imc post_update_generic_single.sh
-post_update_single tf post_update_generic_single.sh
 post_update_single re post_update_re_single.sh
 
 #post update scripts
@@ -124,11 +117,6 @@ solve numpy linsolve.py
 
 imc purify imc_purify.sh
 
-# tf specific stuff
-update tf update_tf.sh
-update tf_single update_tf_single.sh
-calc thermforce calc_thermforce.sh
-
 # optimzer(generic) stuff
 optimizer prepare_state optimizer_prepare_state.sh
 optimizer parameters_to_potential optimizer_parameters_to_potential.sh

share/scripts/inverse/functions_common.sh

@@ -280,8 +280,6 @@ csg_get_interaction_property () { #gets an interaction property from the xml fil
       done
       [[ -z $ret ]] && die "${FUNCNAME[0]}: Could not find a bonded definition with name '$bondname' in the mapping file(s) '$mapping'. Make sure to use the same name in the settings file (or --ia-name when calling from csg_call) and the mapping file."
       echo "$ret"
-    elif [[ -n $CSGXMLFILE && $(csg_get_property --allow-empty cg.inverse.method) = "tf" ]]; then
-      echo "thermforce"
     else
       echo "$bondtype"
     fi
@@ -294,7 +292,7 @@ csg_get_interaction_property () { #gets an interaction property from the xml fil
 
   #map bondtype back to tags in xml file (for csg_call)
   case "$bondtype" in
-    "non-bonded"|"thermforce")
+    "non-bonded")
       xmltype="non-bonded";;
     "bonded"|"bond"|"angle"|"dihedral")
       xmltype="bonded";;

share/scripts/inverse/postupd_pressure.sh

@@ -29,8 +29,6 @@ fi
 
 [[ -f $2 ]] && die "${0##*/}: $2 is already there"
 
-[[ $(csg_get_interaction_property bondtype) = "thermforce" ]] && die "${0##*/}: pressure correction for thermforce makes no sense!"
-
 step_nr="$(get_current_step_nr)"
 sim_prog="$(csg_get_property cg.inverse.program)"
 [[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for ${sim_prog} is not implemented yet!"

share/scripts/inverse/potential_extrapolate.sh

@@ -35,7 +35,7 @@ EOF
 
 clean="no"
 pot_type="$2"
-pot_types="non-bonded bond thermforce angle dihedral"
+pot_types="non-bonded bond angle dihedral"
 avg_points=3
 
 ### begin parsing options
@@ -77,8 +77,6 @@ if [[ $pot_type = "non-bonded"  ]]; then
   intermediate="$(critical mktemp "${input}.onlyleft.XXXXX")"
   do_external table extrapolate --function exponential --avgpoints $avg_points --region left "${input}" "${intermediate}"
   do_external table extrapolate --function constant --avgpoints 1 --region right "${intermediate}" "${output}"
-elif [[ $pot_type = "thermforce" ]]; then
-  do_external table extrapolate --function constant --avgpoints $avg_points --region leftright "${input}" "${output}"
 elif [[ $pot_type = "bond"  || $pot_type = "angle" || $pot_type = "dihedral" ]]; then
   do_external table extrapolate --function linear --avgpoints $avg_points --region leftright "${input}" "${output}"
 else

share/scripts/inverse/potential_shift.pl

@@ -76,7 +76,7 @@
 (readin_table($infile,@r,@dpot,@flag,$comments)) || die "$progname: error at readin_table\n";
 
 my $zero=undef;
-if (( "$type" eq "non-bonded" ) or ("$type" eq "thermforce" )) {
+if ( "$type" eq "non-bonded" ) {
   $zero=$dpot[$#r];
 } 
 elsif (( "$type" eq "bond" ) or ("$type" eq "dihedral") or ("$type" eq "angle") or ("$type" eq "bonded")) {

share/scripts/inverse/potential_to_gromacs.sh

@@ -103,7 +103,7 @@ if [[ $tabtype = "non-bonded" ]]; then
   elif [[ -z $tablend ]]; then
     die "${0##*/}: cg.inverse.gromacs.table_end was not defined in xml seeting file"
   fi
-elif [[ $tabtype = "bond" || $tabtype = "thermforce" ]]; then
+elif [[ $tabtype = "bond" ]]; then
   tablend="$(csg_get_property cg.inverse.gromacs.table_end)"
 elif [[ $tabtype = "angle" ]]; then
   tablend=180

share/scripts/inverse/prepare_generic_single.sh

@@ -47,28 +47,19 @@ if [[ -f ${main_dir}/${name}.pot.in ]]; then
 else
   target=$(csg_get_interaction_property inverse.target)
   msg "Using initial guess from dist ${target} for ${name}"
-  if [[ $bondtype = "thermforce" ]]; then
-    #therm force is resampled later and as one want to symetrize 1d density
-    cp_from_main_dir --rename "$(csg_get_interaction_property inverse.target)" "${name}.dist.tgt" 
-    #initial guess from density
-    raw="$(critical mktemp -u ${name}.pot.new.raw.XXX)"
-    do_external calc thermforce ${name}.dist.tgt ${raw}
-    do_external table change_flag "${raw}" "${output}"
-  else
-    #resample target dist
-    do_external resample target "$(csg_get_interaction_property inverse.target)" "${name}.dist.tgt" 
-    # initial guess from rdf
-    raw="$(critical mktemp ${name}.pot.new.raw.XXX)"
-    kbt="$(csg_get_property cg.inverse.kBT)"
-    dist_min="$(csg_get_property cg.inverse.dist_min)"
-    do_external dist invert --type "${bondtype}" --kbT "${kbt}" --min "${dist_min}" ${name}.dist.tgt ${raw}
-    smooth="$(critical mktemp ${name}.pot.new.smooth.XXX)"
-    critical csg_resample --in ${raw} --out ${smooth} --grid ${min}:${step}:${max} --comment "${comment}"
-    extrapolate="$(critical mktemp ${name}.pot.new.extrapolate.XXX)"
-    do_external potential extrapolate --type "$bondtype" "${smooth}" "${extrapolate}"
-    shifted="$(critical mktemp ${name}.pot.new.shifted.XXX)"
-    do_external potential shift --type "${bondtype}" ${extrapolate} ${shifted}
-    do_external table change_flag "${shifted}" "${output}"
-  fi
+  #resample target dist
+  do_external resample target "$(csg_get_interaction_property inverse.target)" "${name}.dist.tgt" 
+  # initial guess from rdf
+  raw="$(critical mktemp ${name}.pot.new.raw.XXX)"
+  kbt="$(csg_get_property cg.inverse.kBT)"
+  dist_min="$(csg_get_property cg.inverse.dist_min)"
+  do_external dist invert --type "${bondtype}" --kbT "${kbt}" --min "${dist_min}" ${name}.dist.tgt ${raw}
+  smooth="$(critical mktemp ${name}.pot.new.smooth.XXX)"
+  critical csg_resample --in ${raw} --out ${smooth} --grid ${min}:${step}:${max} --comment "${comment}"
+  extrapolate="$(critical mktemp ${name}.pot.new.extrapolate.XXX)"
+  do_external potential extrapolate --type "$bondtype" "${smooth}" "${extrapolate}"
+  shifted="$(critical mktemp ${name}.pot.new.shifted.XXX)"
+  do_external potential shift --type "${bondtype}" ${extrapolate} ${shifted}
+  do_external table change_flag "${shifted}" "${output}"
 fi
 

share/scripts/inverse/table_to_xvg.pl

@@ -49,7 +49,7 @@
 --max MAX             Replace all pot value bigger MAX by MAX 
 
 
-Possible types: non-bonded (=C12), bond, thermforce, C12, C6, CB, angle, dihedral
+Possible types: non-bonded (=C12), bond, C12, C6, CB, angle, dihedral
 
 Examples:
 * $progname --type bond table.in table_b0.xvg
@@ -130,9 +130,6 @@
   $begin=-180;
   $end=180;
 }
-elsif ( "$type" eq "thermforce" ){
-  $fmt="%15.10e   %15.10e %15.10e\n";
-}
 else{
   die "$progname: Unsupported type of interatction: $type -> go and implement it\n";
 }