Merge branch 'v2.2'

CHANGES/v2.2.txt

@@ -117,6 +117,8 @@ For users:
 - Optimisations (activation of the dependencies, secondary structures, DRMSD)
 - Fixed a performance regression with RMSD=OPTIMAL-FAST
 - Fixed a bug in the normalization of kernel functions (relevant for \ref HISTOGRAM).
+- Fixed a regression introduced in v2.2 that was making \ref METAD with non-MPI multiple walkers crash
+  if reading frequently. See \issue{190}
 - Updated patch for gromacs 5.1
 - Possibility to control manual generation (including pdf) from ./configure. Pdf manual is now off
   by default. Notice that on travis CI it is still generated.

regtest/basic/rt-mpi6c/Makefile

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

regtest/basic/rt-mpi6c/config

+mpiprocs=3
+type=driver
+# this is to test a different name
+arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --multi 3"

regtest/basic/rt-mpi6c/plumed.0.dat

+_SET_SUFFIX .a
+c: DISTANCE ATOMS=1,2
+d: DISTANCE ATOMS=2,3
+
+# this is a dummy file, just to enable checking
+PRINT FILE=colvar ARG=c
+
+# the HILLS file are not really checked here since non-mpi walkers are not reproducible
+# however, this example crashes
+single: METAD ARG=c,d SIGMA=0.1,0.2 HEIGHT=0.1 PACE=2  WALKERS_ID=0 WALKERS_DIR=. WALKERS_N=3 WALKERS_RSTRIDE=1
+

regtest/basic/rt-mpi6c/plumed.1.dat

+_SET_SUFFIX .a
+c: DISTANCE ATOMS=1,2
+d: DISTANCE ATOMS=2,3
+
+single: METAD ARG=c,d SIGMA=0.1,0.2 HEIGHT=0.1 PACE=2  WALKERS_ID=1 WALKERS_DIR=. WALKERS_N=3 WALKERS_RSTRIDE=1
+

regtest/basic/rt-mpi6c/plumed.2.dat

+_SET_SUFFIX .a
+c: DISTANCE ATOMS=1,2
+d: DISTANCE ATOMS=2,3
+
+single: METAD ARG=c,d SIGMA=0.1,0.2 HEIGHT=0.1 PACE=2 WALKERS_ID=2 WALKERS_DIR=. WALKERS_N=3 WALKERS_RSTRIDE=1
+

src/core/PlumedMain.cpp

@@ -499,6 +499,7 @@ void PlumedMain::readInputFile(std::string str){
   IFile ifile;
   ifile.link(*this);
   ifile.open(str);
+  ifile.allowNoEOL();
   std::vector<std::string> words;
   while(Tools::getParsedLine(ifile,words) && words[0]!="ENDPLUMED") readInputWords(words);
   log.printf("END FILE: %s\n",str.c_str());

src/tools/IFile.cpp

@@ -187,7 +187,8 @@ IFile& IFile::scanField(){
 
 IFile::IFile():
   inMiddleOfField(false),
-  ignoreFields(false)
+  ignoreFields(false),
+  noEOL(false)
 {
 }
 
@@ -198,9 +199,8 @@ IFile::~IFile(){
 IFile& IFile::getline(std::string &str){
   char tmp=0;
   str="";
-// I comment out this (see note below on commented fgetpos):
-// fpos_t pos;
-// fgetpos(fp,&pos);
+  fpos_t pos;
+  fgetpos(fp,&pos);
   while(llread(&tmp,1)==1 && tmp && tmp!='\n' && tmp!='\r' && !eof && !err){
     str+=tmp;
   }
@@ -208,11 +208,12 @@ IFile& IFile::getline(std::string &str){
     llread(&tmp,1);
     plumed_massert(tmp=='\n',"plumed only accepts \\n (unix) or \\r\\n (dos) new lines");
   }
-  if(eof){
-    if(str.length()>0) eof=false;
-  } else if(err || tmp!='\n'){
+ if(eof && noEOL){
+   if(str.length()>0) eof=false;
+ } else if(eof || err || tmp!='\n'){
     eof = true;
     str="";
+    if(!err) fsetpos(fp,&pos);
 // there was a fsetpos here that apparently is not necessary
 //  fsetpos(fp,&pos);
 // I think it was necessary to have rewind working correctly
@@ -245,4 +246,8 @@ void IFile::allowIgnoredFields(){
   ignoreFields=true;
 }
 
+void IFile::allowNoEOL(){
+  noEOL=true;
+}
+
 }

src/tools/IFile.h

@@ -55,6 +55,8 @@ public virtual FileBase{
   bool inMiddleOfField;
 /// Set to true if you want to allow fields to be ignored in the read in file
   bool ignoreFields;
+/// Set to true to allow files without end-of-line at the end
+  bool noEOL;
 /// Advance to next field (= read one line)
   IFile& advanceField();
 /// Find field index by name
@@ -93,6 +95,10 @@ Typically used as
   IFile& scanField(Value* val);
 /// Allow some of the fields in the input to be ignored
   void allowIgnoredFields();
+/// Allow files without EOL at the end.
+/// This in practice should be only used when opening
+/// plumed input files
+  void allowNoEOL();
 };
 
 }