RMSD: reformulate two loops so their omp simd pragmas can be honoured (plumed#1438)

* RMSD: reformulate two loops so their omp simd pragmas can be honoured

A plain `./configure && make` fails on any machine whose default C++ compiler is
clang: configure enables OpenMP automatically, and src/tools/Makefile appends
-Werror, so the vectorizer's refusal is fatal.

    RMSD.cpp:1443:35: error: loop not vectorized: the optimizer was unable to
    perform the requested transformation; the transformation might be disabled or
    specified as part of an unsupported transformation ordering
    [-Werror,-Wpass-failed=transform-warning]
    RMSD.cpp:1487:35: error: (the same, in getDDistanceDReference)

Both are attributed to the opening line of the enclosing function, which hides
the loop at fault. Each of the two functions contains exactly one
`#pragma omp simd`, so the attribution is unambiguous: the loops at lines 1479
and 1530.

The pragma is kept. The loop body is rewritten so the compiler can act on it:
the loop-invariant `(ddist_dc*-csum)` is hoisted into a named Vector, and the
Vector expression is expanded into its three components. Both loops now
vectorize at width 4, confirmed with -Rpass=loop-vectorize, instead of being
refused.

Alternatives measured with clang 20.1.1, all on the same tree:

    braces around the if body                       still fails
    hoisting the invariant only                     still fails
    binding `Vector& dv=derivatives[iat]`           still fails
    flatten to `double*` + manual 3-way unroll      vectorizes, but the pointer
                                                    is UB when n==0
    per-component `derivatives[iat][k]`             vectorizes   <- chosen

The Vector arithmetic creates temporaries the vectorizer cannot see through, and
naming the element through a reference reintroduces them; only the direct
per-component form works.

No other pragma in the file is touched. The other eight active ones already
vectorize. Two more, on identically shaped std::vector<Vector> loops at lines
1339 and 1426, were commented out long ago because they gave wrong results with
the Intel compiler; these two had the same shape.

Behaviour is unchanged, and the 17 regtests that exercise these paths pass,
including rt-rmsd-displace, which is the align != displace case that actually
enters the modified branch.

This is the same class of problem as plumed#1437. It escapes CI because no job builds
clang with OpenMP enabled: the Linux workflow uses gcc and icpx, and macsimple
uses AppleClang without libomp, where `#pragma omp simd` is inert.

* RMSD: also unswitch getDistance's reduction loop

The first commit fixed the two loops that fail at -O3. Building PLUMED with
mpicxx at -O2 shows a third one, which -O3 happens to vectorize:

    RMSD.cpp:1361:22: error: loop not vectorized: the optimizer was unable to
    perform the requested transformation [-Werror,-Wpass-failed=transform-warning]

The remark is attributed to getDistance()'s opening line; the pragma is the
`omp simd reduction(+:localDist)` at line 1374. Its body branches on alEqDis
and safe, both of which are loop-invariant members, so the loop carries a
per-iteration test the vectorizer will not always unswitch by itself.

Hoisting the two branches out of the loop makes it vectorize at -O2 as well.
This is a pure unswitching: both conditions are invariant, the summation order
is unchanged, and the arithmetic is untouched, so results are bit-identical.

Measured on this file with clang 20.1.1, counting -Wpass-failed diagnostics
(-march makes no difference at any level):

    -O level     before    after
    -O0            0         0
    -O1            5         4
    -Os            8         7
    -O2            3         0
    -O3            2         0

-O1 and -Os remain non-clean, but not for a reason any source change can fix:
clang's loop vectorizer is effectively disabled there, so every `omp simd` in
the file is refused, including the ones that are perfectly good at -O2. Making
PLUMED buildable at those levels would mean not combining -Werror with
-Wpass-failed in the module makefiles; that is a build-system decision and is
deliberately left out of this PR.

Author: aalhossary

src/tools/RMSD.cpp

@@ -1371,13 +1371,16 @@ double RMSDCoreData::getDistance( const bool squared) {
   } else {
     localDist=eigenvals[0]+rr00+rr11;
   }
-  #pragma omp simd reduction(+:localDist)
-  for(unsigned iat=0; iat<n; iat++) {
-    if(alEqDis) {
-      if(safe) {
+  if(alEqDis) {
+    if(safe) {
+      #pragma omp simd reduction(+:localDist)
+      for(unsigned iat=0; iat<n; iat++) {
         localDist+=align[iat]*modulo2(d[iat]);
       }
-    } else {
+    }
+  } else {
+    #pragma omp simd reduction(+:localDist)
+    for(unsigned iat=0; iat<n; iat++) {
       localDist+=displace[iat]*modulo2(d[iat]);
     }
   }
@@ -1475,11 +1478,16 @@ std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
     }
   }
 
-  if(!alEqDis)
+  if(!alEqDis) {
+    const Vector shift=ddist_dcpositions-csum;
     #pragma omp simd
     for(unsigned iat=0; iat<n; iat++) {
-      derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcpositions-csum)*align[iat]);
+      const double a=align[iat];
+      derivatives[iat][0]=prefactor*(derivatives[iat][0]+shift[0]*a);
+      derivatives[iat][1]=prefactor*(derivatives[iat][1]+shift[1]*a);
+      derivatives[iat][2]=prefactor*(derivatives[iat][2]+shift[2]*a);
     }
+  }
 
   return derivatives;
 }
@@ -1526,11 +1534,16 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
     }
   }
 
-  if(!alEqDis)
+  if(!alEqDis) {
+    const Vector shift=ddist_dcreference-csum;
     #pragma omp simd
     for(unsigned iat=0; iat<n; iat++) {
-      derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcreference-csum)*align[iat]);
+      const double a=align[iat];
+      derivatives[iat][0]=prefactor*(derivatives[iat][0]+shift[0]*a);
+      derivatives[iat][1]=prefactor*(derivatives[iat][1]+shift[1]*a);
+      derivatives[iat][2]=prefactor*(derivatives[iat][2]+shift[2]*a);
     }
+  }
 
   return derivatives;
 }