Merge branch 'v2.0-fixes' into v2.0

src/tools/DLLoader.cpp

@@ -20,7 +20,6 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "DLLoader.h"
-#include "Exception.h"
 
 #ifdef __PLUMED_HAS_DLOPEN
 #include <dlfcn.h>

src/tools/DLLoader.h

@@ -53,7 +53,7 @@ public:
   void* load(const std::string&);
 /// Returns the last error in dynamic loader
   const std::string & error();
-/// Returs true if the dynamic loader is available (on some systems it may not).
+/// Returns true if the dynamic loader is available (on some systems it may not).
   static bool installed();
 };
 

src/tools/Exception.h

@@ -59,6 +59,12 @@ extensive error message can be added.
   if(a<=0) plumed_error();
   if(a<=0) plumed_merror("a should be larger than zero");
 \endverbatim
+The additional macros
+plumed_dbg_assert() and plumed_dbg_massert() are similar
+to plumed_assert() and plumed_massert() respectively, but the corresponding
+check is only performed when NDEBUG macro is not defined. They should
+be used when the check is expensive and should be skipped in production
+code.
 
 By default, execution is terminated imediately and a message is printed on stderr.
 
@@ -133,7 +139,7 @@ public:
 /// Conditionally print file/line/function information and exit when NDEBUG flag is not present
 #define plumed_dbg_assert(test) if(!(test)) throw PLMD::Exception("assertion failed " #test,__FILE__,__LINE__,__PRETTY_FUNCTION__)
 /// \relates PLMD::Exception
-/// Conditionally print file/line/function information plus msg and exit when NDEBUG flast is not present
+/// Conditionally print file/line/function information plus msg and exit when NDEBUG flag is not present
 #define plumed_dbg_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
 #endif
 

src/tools/Log.h

@@ -26,8 +26,6 @@
 
 namespace PLMD{
 
-class Communicator;
-
 /// Class containing the log stream.
 ///
 /// It is similar to a FILE stream. It allows a printf() function, and

src/tools/Units.h

@@ -26,10 +26,18 @@
 
 namespace PLMD{
 
-/// Small utility class.
-/// It has no implemented methods, and all its data are public.
-/// It just simplify the syntax of functions which should pass the
-/// value of all the units.
+/**
+\ingroup TOOLBOX
+Small utility class that contains information about units.
+
+This class can be used to contain in a single place all the
+information about units. Units are expressed in terms of
+standard PLUMED units, i.e. kj/mol, nm, and ps.
+Units can be set as double or as string. In the latter case,
+one can also use strings such as kcal/mol.
+
+
+*/
 class Units{
 /// Units for energy, expressed in kj/mol (e.g. 4.184 means kcal/mol)
   double energy;
@@ -41,19 +49,40 @@ class Units{
   double time;
   std::string timeString;
 public:
-// Constructor, setting default values (1.0)
+/// Constructor, setting default values (1.0)
   Units();
+/// Set energy units from string.
+/// Also understands the following strings:
+/// kj/mol, kcal/mol, j/mol, and eV.
   void setEnergy(const std::string &);
+/// Set time units from string.
+/// Also understands the following strings:
+/// ps, ns, fs.
   void setTime(const std::string &);
+/// Set lengh units from string.
+/// Also understands the following strings:
+/// nm, A, um.
   void setLength(const std::string &);
-  void setEnergy(const double);
-  void setTime(const double);
-  void setLength(const double);
+/// Set energy units from double.
+/// Should be specified in units of kj/mol (e.g. 4.184 means kcal/mol)
+  void setEnergy(double);
+/// Set time units from double.
+/// Should be specified in units of ps (e.g. 0.001 means fs)
+  void setTime(double);
+/// Set lenght units from double.
+/// Should be specified in units of nm (e.g. 0.1 means A)
+  void setLength(double);
+/// Get energy units as double.
   const double & getEnergy()const;
+/// Get length units as double.
   const double & getLength()const;
+/// Get time units as double.
   const double & getTime()const;
+/// Get energy units as string.
   const std::string & getEnergyString()const;
+/// Get length units as string.
   const std::string & getLengthString()const;
+/// Get time units as string.
   const std::string & getTimeString()const;
 };