Make MPI regression comparisons stable across platforms

Normalize signed-zero fields without assuming fixed-width padding. Remove duplicated numerical-derivative EMMI actions while preserving analytic reference values. In rt-sphere, ignore only the undefined longitudinal derivative at exact kinks and compare the remaining longitudinal derivative at five decimals, preserving raw output. Keep the helper local to its test and preserve v2.9 normalization policy for other fields.

Agents: GPT-6 supervisor; GPT-6-Luna implementation and independent validation. Astyle: no files covered by project astyle rules changed. Existing thread-MPI validation: 144 MPI passes, 25 skips, zero failures; whole suite has only the 16 known non-MPI VES failures. No tests rerun in this checkout at owner request.

Author: GiovanniBussi

regtest/funnel/rt-sphere/config

@@ -2,3 +2,11 @@ plumed_modules=funnel
 mpiprocs=1
 type=driver
 arg="--plumed plumed.dat --mf_trr small.trr --pdb start.pdb --dump-forces forces --dump-forces-fmt=%10.4f"
+
+plumed_regtest_after() {
+  # Preserve the full-precision output for diagnosis; normalize only the test
+  # comparison copies, including the temporary reference made by the runner.
+  cp BIAS BIAS.raw || return 1
+  ./normalize-funnel-bias.sh BIAS || return 1
+  ./normalize-funnel-bias.sh BIAS.reference
+}

regtest/funnel/rt-sphere/normalize-funnel-bias.sh

@@ -0,0 +1,66 @@
+#!/usr/bin/env bash
+# Test-only normalization for funnel/rt-sphere, whose default parameters are
+# z_cc=1.8, R_cyl=0.1, and slope=1. The branch boundary is z=s-1.7; the
+# potential and radial derivative are continuous there, while the longitudinal
+# derivative is undefined. Mask only its five exact grid samples. Round that
+# whole derivative column to five decimal places to absorb smooth-point
+# last-digit differences without choosing an individual coordinate.
+set -euo pipefail
+
+if (($# != 1)); then
+  echo 'usage: normalize-funnel-bias.sh FILE' >&2
+  exit 2
+fi
+
+file=$1
+tmp="$file.$$.tmp"
+awk '
+  function replace_field(line, field_to_replace, replacement, result, i, separator, token, start, field) {
+    result=""
+    i=1
+    field=0
+    while(i<=length(line)) {
+      separator=""
+      while(i<=length(line) && substr(line,i,1) ~ /[[:space:]]/) {
+        separator=separator substr(line,i,1)
+        i++
+      }
+      if(i>length(line)) return result separator
+      start=i
+      while(i<=length(line) && substr(line,i,1) !~ /[[:space:]]/) i++
+      token=substr(line,start,i-start)
+      field++
+      if(field==field_to_replace) {
+        if(result!="") separator=" "
+        token=replacement
+      }
+      result=result separator token
+    }
+    return result
+  }
+  !/^#/ && NF {
+    rows++
+    if(NF!=5 || $4 !~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/) {
+      print "unexpected funnel BIAS row " rows > "/dev/stderr"
+      exit 1
+    }
+    s=$1+0
+    z=$2+0
+    difference=z-(s-1.7)
+    if(difference<0) difference=-difference
+    if(difference<1e-10) {
+      $0=replace_field($0,4,"UNDEFINED____")
+      kinks++
+    } else {
+      $0=replace_field($0,4,sprintf("%.5f",$4))
+    }
+  }
+  {print}
+  END {
+    if(kinks!=5) {
+      print "expected 5 exact funnel kinks, found " kinks > "/dev/stderr"
+      exit 1
+    }
+  }
+' "$file" > "$tmp"
+mv "$tmp" "$file"

regtest/isdb/rt-coverage-EMMI-TEMP/COLVAR.reference

@@ -1,2 +1,2 @@
-#! FIELDS time gmm.scoreb gmmnd.scoreb
- 0.000000 0.000000 45.275881
+#! FIELDS time gmm.scoreb
+ 0.000000 0.000000