Merge branch 'v2.3' into v2.4

CHANGES/v2.3.md

@@ -205,10 +205,13 @@ For developers:
 
 For users:
 - GROMACS patch updated to gromacs-2016.4
+- Solved a bug in \ref ERMSD leading to incorrect results when using non-default length units (e.g. with `UNITS LENGTH=A`).
 
 For developers:
 - Regtest script also reports when exitcode different from zero is returned.
 - Patch script reports errors returning a nonzero exit code.
 - cppcheck update to 1.81
+- Solved small bug in stored PLUMED_ROOT directory as obtained from statically patched MD codes.
+  Namely, the compilation directory was stored rather than the installation one.
 
 

regtest/basic/rt-ermsd2/Makefile

+include ../../scripts/test.make

regtest/basic/rt-ermsd2/colvar.reference

+#! FIELDS time e e2
+ 0.000000   0.00078   0.00000
+ 1.000000   0.61839   0.10157
+ 2.000000   0.58178   0.08616
+ 3.000000   0.83629   0.09939
+ 4.000000   0.79844   0.11675
+ 5.000000   0.82803   0.10357
+ 6.000000   0.87762   0.10627
+ 7.000000   0.79849   0.06094
+ 8.000000   0.90058   0.11108
+ 9.000000   1.02312   0.04906

regtest/basic/rt-ermsd2/config

+type=driver
+# this is to test a different name
+#arg="--plumed plumed.dat --mf_xtc samples.xtc"
+#arg="--plumed plumed.dat --igro broken.gro"
+#arg="--plumed plumed.dat --igro before.gro"
+arg="--plumed plumed.dat --mf_xtc traj.xtc"

regtest/basic/rt-ermsd2/plumed.dat

+UNITS LENGTH=A
+MOLINFO STRUCTURE=ref.pdb
+
+e: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb
+
+e2: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb PAIRS=1,2,1,3,1,4,2,3,2,4,3,4
+
+DUMPDERIVATIVES ARG=e,e2 FILE=der FMT=%9.3f
+
+PRINT ARG=e,e2 FILE=colvar FMT=%9.5f
+
+# ne: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb NUMERICAL_DERIVATIVES
+
+# ne2: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb PAIRS=1,2,1,3,1,4,2,3,2,4,3,4 NUMERICAL_DERIVATIVES
+
+# DUMPDERIVATIVES ARG=e,ne FILE=nder
+
+

src/colvar/ERMSD.cpp

@@ -176,7 +176,7 @@ ERMSD::ERMSD(const ActionOptions&ao):
 // shift to count from zero
   for(unsigned i=0; i<pairs_.size(); ++i) pairs_[i]--;
 
-  ermsd.setReference(reference_positions,pairs_,cutoff);
+  ermsd.setReference(reference_positions,pairs_,cutoff/atoms.getUnits().getLength());
 
   requestAtoms(atoms_);
   derivs.resize(natoms);
@@ -204,9 +204,10 @@ void ERMSD::calculate() {
 // Notice that this might have problems when having 2 RNA molecules (hybridization).
 
   ermsdist=ermsd.calculate(getPositions(),fake_pbc,derivs,virial);
-  setValue(ermsdist);
+  const double scale=atoms.getUnits().getLength();
+  setValue(ermsdist*scale);
 
-  for(unsigned i=0; i<derivs.size(); ++i) {setAtomsDerivatives(i,derivs[i]);}
+  for(unsigned i=0; i<derivs.size(); ++i) {setAtomsDerivatives(i,derivs[i]*scale);}
 
   setBoxDerivativesNoPbc();
 

src/lib/Makefile

@@ -94,7 +94,7 @@ install-build:
 	mkdir -p install/
 	$(MAKE) PLUMED_INSTALL=Install all
 ifdef LD_RO
-	$(MAKE) install/kernel.o
+	$(MAKE) PLUMED_INSTALL=Install install/kernel.o
 endif
 # modulefile
 	@cat modulefile.in | \
@@ -222,7 +222,7 @@ endif
 ifdef LD_RO
 	cp install/kernel.o "$(DESTDIR)$(libdir)/$(program_name)/obj/kernel.o"
 else
-	../maketools/copyobjects "$(DESTDIR)$(libdir)/$(program_name)/obj/k" $(OBJ_KERNEL)
+	../maketools/copyobjects "$(DESTDIR)$(libdir)/$(program_name)/obj/k" $(subst ../config/Config.o,../config/ConfigInstall.o,$(OBJ_KERNEL))
 endif
 	cp $(OBJ_WRAPPER) "$(DESTDIR)$(libdir)/$(program_name)/obj/PlumedStatic.o"
 	cp $(OBJ_DYNAMIC_WRAPPER) "$(DESTDIR)$(libdir)/$(program_name)/obj/Plumed.o"