Merge pull request #417 from votca/imc_regularization_fix

imc: make regularization group based

share/scripts/inverse/functions_common.sh

@@ -885,6 +885,7 @@ check_for_obsolete_xml_options() { #check xml file for obsolete options
     cg.non-bonded.inverse.espresso.index1 cg.non-bonded.inverse.espresso.index2 cg.inverse.espresso.success \
     cg.inverse.espresso.scriptdir cg.non-bonded.inverse.post_update_options.kbibi.type \
     cg.inverse.imc.numpy.bin cg.inverse.imc.octave.bin cg.inverse.imc.matlab.bin cg.inverse.imc.solver \
+    cg.non-bonded.inverse.imc.reg \
     ; do
     [[ -z "$(csg_get_property --allow-empty $i)" ]] && continue #filter me away
     new=""
@@ -909,6 +910,8 @@ check_for_obsolete_xml_options() { #check xml file for obsolete options
 	new="${i}.type";;
       cg.inverse.convergence_check_options.limit)
         new="cg.inverse.convergence_check.limit";;
+      cg.non-bonded.inverse.imc.reg)
+        new="cg.inverse.imc.<group>.reg";;
     esac
     [[ -n $new ]] && new="has been renamed to $new" || new="has been removed"
     die "${FUNCNAME[0]}: The xml option $i $new\nPlease remove the obsolete options from the xmlfile"

share/scripts/inverse/update_imc.sh

@@ -29,13 +29,17 @@ fi
 sim_prog="$(csg_get_property cg.inverse.program)"
 do_external imc_stat $sim_prog
 
+default_reg=$(csg_get_property cg.inverse.imc.default_reg)
+is_num "${default_reg}" || die "${0##*/}: value of cg.inverse.imc.default_reg should be a number"
+
 imc_groups=$(csg_get_interaction_property --all inverse.imc.group)
 imc_groups=$(remove_duplicate $imc_groups)
 [[ -z ${imc_groups} ]] && die "${0##*/}: No imc groups defined"
-reg="$(csg_get_interaction_property --all inverse.imc.reg)"
 for group in $imc_groups; do
   # currently this is a hack! need to create combined array
-  msg "solving linear equations for imc group '$group'"
+  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_imcrepack --in ${group} --out ${group}.packed
   critical csg_imc_solve --imcfile "${group}.packed.imc" --gmcfile "${group}.packed.gmc" --regularization "${reg}" --outputfile "${group}.packed.sol"
   critical csg_imcrepack --in ${group}.packed --unpack ${group}.packed.sol

share/xml/csg_defaults.xml.in

@@ -260,6 +260,9 @@
     </hoomd-blue>
     <imc>
       <DESC> general imc specific options </DESC>
+      <default_reg>0
+        <DESC> default magnitude for regularization parameter if not given for the group explicitly, default =0</DESC>
+      </default_reg>
     </imc>
     <lammps>
       <DESC> general lammps specific options </DESC>
@@ -538,9 +541,6 @@
         <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>
         </group>
-        <reg>0
-          <DESC> magnitude for regularization parameter, default =0</DESC>
-        </reg>
       </imc>
       <lammps>
         <DESC>lammps specific options for this interations</DESC>