diff --git a/src/bias/Bias.cpp b/src/bias/Bias.cpp
index 218998b1189237e48737f2905fbffeb5d2ba2d90..ea1526bbfb5a98efdb3b29d903802a7013ec341b 100644
--- a/src/bias/Bias.cpp
+++ b/src/bias/Bias.cpp
@@ -21,9 +21,9 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
 
-using namespace PLMD;
-using namespace PLMD::bias;
-using namespace std;
+
+namespace PLMD{
+namespace bias{
 
 Bias::Bias(const ActionOptions&ao):
 Action(ao),
@@ -49,4 +49,7 @@ void Bias::apply(){
   }
 }
 
+}
+}
+
 
diff --git a/src/cltools/SimpleMD.cpp b/src/cltools/SimpleMD.cpp
index 6788549d4f2adf8f4f2d5f9ab7657aff32b111d1..f5d9b36ac2ff242fd0e18fe2c0f7a7631ecacffb 100644
--- a/src/cltools/SimpleMD.cpp
+++ b/src/cltools/SimpleMD.cpp
@@ -30,7 +30,6 @@
 #include <vector>
 
 using namespace std;
-using namespace PLMD;
 
 namespace PLMD{
 namespace cltools{
diff --git a/src/core/Action.cpp b/src/core/Action.cpp
index d31212dd8a75165451069150c9a2a05c944e89a9..13088fab7f5a26c7c9b6f6dff6343ee08b91f326 100644
--- a/src/core/Action.cpp
+++ b/src/core/Action.cpp
@@ -28,7 +28,7 @@
 #include "ActionSet.h"
 #include <iostream>
 
-using namespace PLMD;
+namespace PLMD{
 
 Keywords ActionOptions::emptyKeys;
 
@@ -214,4 +214,5 @@ void Action::calculateFromPDB( const PDB& pdb ){
 }
 
 
+}
 
diff --git a/src/core/ActionPilot.cpp b/src/core/ActionPilot.cpp
index 7d10b9315f7b80f50437dd691fd11bf9267fe18f..161247ca360d85e7a99a6a736c47c93feeeb96e9 100644
--- a/src/core/ActionPilot.cpp
+++ b/src/core/ActionPilot.cpp
@@ -21,8 +21,8 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "ActionPilot.h"
 
-using namespace PLMD;
 using namespace std;
+namespace PLMD{
 
 void ActionPilot::registerKeywords(Keywords& keys){
 }
@@ -42,5 +42,6 @@ bool ActionPilot::onStep()const{
 int ActionPilot::getStride()const{
   return stride;
 }
+}
 
 
diff --git a/src/core/ActionRegister.cpp b/src/core/ActionRegister.cpp
index 7c5532d4a7fa9fecbb4f23d52e403ee39c9bd200..c69cbd53ea0b08adae7a960d7a88c91970c181c3 100644
--- a/src/core/ActionRegister.cpp
+++ b/src/core/ActionRegister.cpp
@@ -27,7 +27,7 @@
 
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 ActionRegister::~ActionRegister(){
   if(m.size()>0){
@@ -37,7 +37,7 @@ ActionRegister::~ActionRegister(){
   }
 }
 
-ActionRegister& PLMD::actionRegister(){
+ActionRegister& actionRegister(){
   static ActionRegister ans;
   return ans;
 }
@@ -106,7 +106,7 @@ bool ActionRegister::printTemplate( const std::string& action, bool include_opti
   }
 }
 
-std::ostream & PLMD::operator<<(std::ostream &log,const ActionRegister&ar){
+std::ostream & operator<<(std::ostream &log,const ActionRegister&ar){
   vector<string> s;
   for(ActionRegister::const_mIterator it=ar.m.begin();it!=ar.m.end();++it)
     s.push_back((*it).first);
@@ -125,3 +125,4 @@ std::ostream & PLMD::operator<<(std::ostream &log,const ActionRegister&ar){
 }
 
 
+}
diff --git a/src/core/ActionSet.cpp b/src/core/ActionSet.cpp
index 8f39a3aa1e23d5608868bbd012f8d49a67af9d9b..d1e2f62b335d9fa85215d40f2552ce34a28f03bc 100644
--- a/src/core/ActionSet.cpp
+++ b/src/core/ActionSet.cpp
@@ -22,7 +22,7 @@
 #include "ActionSet.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 ActionSet::ActionSet(PlumedMain&p):
 plumed(p){
@@ -48,3 +48,4 @@ std::string ActionSet::getLabelList() const{
 }
 
 
+}
diff --git a/src/core/ActionSetup.cpp b/src/core/ActionSetup.cpp
index 52118174be8ff30a654c10c330079e54e5512407..f7a333f178501350e88f3375b6347b275baeac6d 100644
--- a/src/core/ActionSetup.cpp
+++ b/src/core/ActionSetup.cpp
@@ -24,7 +24,7 @@
 #include "ActionSet.h"
 #include "tools/PlumedException.h"
 
-using namespace PLMD;
+namespace PLMD{
 
 ActionSetup::ActionSetup(const ActionOptions&ao):
   Action(ao)
@@ -42,3 +42,4 @@ void ActionSetup::registerKeywords( Keywords& keys ){
   keys.remove("LABEL");
 }
 
+}
diff --git a/src/core/ActionWithArguments.cpp b/src/core/ActionWithArguments.cpp
index b948ea69fa95b073402b48277687dc0676e18f2a..039c37f4199fb6a551720df8526f43dc1b51c8a0 100644
--- a/src/core/ActionWithArguments.cpp
+++ b/src/core/ActionWithArguments.cpp
@@ -25,7 +25,7 @@
 #include "ActionSet.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 void ActionWithArguments::registerKeywords(Keywords& keys){
   keys.reserve("compulsory","ARG","the input for this action is the output from one or more other actions. The particular output that you used is referenced using that action of interests label. If the label appears on its own then the value of the relevant Action is taken.  If * or *.* appears the information from all arguments is taken.  Some actions have multi-component outputs, each component of the output has a specific label so for instance an action labelled dist may have three componets x, y and z.  To take just the x component you should use dist.x, if you wish to take all three components then use dist.*");
@@ -183,3 +183,4 @@ double ActionWithArguments::getProjection(unsigned i,unsigned j)const{
 
 
 
+}
diff --git a/src/core/ActionWithValue.cpp b/src/core/ActionWithValue.cpp
index 92f4b28a3eed8aef315f64fb9fbaec84fda98fca..d09f53b3e502fa8eeeead68b70c2e82edc78cbd0 100644
--- a/src/core/ActionWithValue.cpp
+++ b/src/core/ActionWithValue.cpp
@@ -23,7 +23,7 @@
 #include "tools/PlumedException.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 void ActionWithValue::registerKeywords(Keywords& keys){
   keys.addFlag("NUMERICAL_DERIVATIVES", false, "calculate the derivatives for these quantities numerically");
@@ -185,3 +185,4 @@ void ActionWithValue::mergeFieldDerivatives( const std::vector<double>& derivati
       }
   }    
 }
+}
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index 794ca399e740efbdaaef6576d9a3fd0854f20649..9ecb186fe067d17ba44a7eb7546f947668f163a8 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -26,7 +26,6 @@
 #include <algorithm>
 #include <string>
 
-using namespace PLMD;
 using namespace std;
 
 namespace PLMD {
diff --git a/src/core/CLTool.cpp b/src/core/CLTool.cpp
index 405d2ce6a12adcb38a8fa552c68bf4a0194f9461..27fcee23ddedc2b72a6c14b18c9f0c078f184b96 100644
--- a/src/core/CLTool.cpp
+++ b/src/core/CLTool.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
 
-using namespace PLMD;
+namespace PLMD{
 
 Keywords CLToolOptions::emptyKeys;
 
@@ -185,3 +185,4 @@ bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ){
   setRemainingToDefault(out);
   return true;
 }
+}
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index 9dbb4e1f0d84761d2fa387e97a95fc8fb6d29523..228fff374e23a8c4cb4c65f38d3daa11d30610e1 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -34,7 +34,7 @@
 #include <algorithm>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 CLToolMain::CLToolMain():
 argc(0),
@@ -231,3 +231,4 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,PlumedCommunicator& p
   return 1;
 
 }
+}
diff --git a/src/core/CLToolRegister.cpp b/src/core/CLToolRegister.cpp
index 7e2ca117300b3df0613b79bccf2591b6409e43d1..56ccbeadfb195157166c6a659a6effbb7ca81262 100644
--- a/src/core/CLToolRegister.cpp
+++ b/src/core/CLToolRegister.cpp
@@ -27,7 +27,7 @@
 
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 CLToolRegister::~CLToolRegister(){
   if(m.size()>0){
@@ -37,7 +37,7 @@ CLToolRegister::~CLToolRegister(){
   }
 }
 
-CLToolRegister& PLMD::cltoolRegister(){
+CLToolRegister& cltoolRegister(){
   static CLToolRegister ans;
   return ans;
 }
@@ -77,7 +77,7 @@ CLTool* CLToolRegister::create(const CLToolOptions&ao){
 }
 
 
-std::ostream & PLMD::operator<<(std::ostream &log,const CLToolRegister&ar){
+std::ostream & operator<<(std::ostream &log,const CLToolRegister&ar){
   vector<string> s(ar.list());
   for(unsigned i=0;i<s.size();i++) log<<"  "<<s[i]<<"\n";
   if(ar.disabled.size()>0){
@@ -111,3 +111,4 @@ vector<string> CLToolRegister::list()const{
 
 
 
+}
diff --git a/src/core/Colvar.cpp b/src/core/Colvar.cpp
index 33cf38032de9d2ea4d8215789e87185d2fe673c1..6c3a7c5c2a00acf0d53ec1307acd684007648ea4 100644
--- a/src/core/Colvar.cpp
+++ b/src/core/Colvar.cpp
@@ -24,7 +24,7 @@
 #include <string>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 Colvar::Colvar(const ActionOptions&ao):
 Action(ao),
@@ -97,3 +97,4 @@ void Colvar::setBoxDerivativesNoPbc(Value* v){
            v->getDerivative(3*i+2)));
   setBoxDerivatives(v,virial);
 }
+}
diff --git a/src/core/FlexibleBin.cpp b/src/core/FlexibleBin.cpp
index 4c9b037a2c6829fc4aa9da9e346c1f9727784c4c..d277128c117f04c5d051d6bd178b85075d82e033 100644
--- a/src/core/FlexibleBin.cpp
+++ b/src/core/FlexibleBin.cpp
@@ -27,7 +27,7 @@
 #include "tools/Matrix.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 
 FlexibleBin::FlexibleBin(int type, ActionWithArguments *paction,  double const &d ):type(type),paction(paction),sigma(d){
@@ -157,3 +157,5 @@ vector<double> FlexibleBin::getInverseMatrix() const{
 
 	return uppervec;  
 }
+
+}
diff --git a/src/core/GREX.cpp b/src/core/GREX.cpp
index 9abf4d60ec90f2916e802395ebbbbead64427b5b..0ce18bc78ca7ef8c46084fbee5a52eba2f5a0d81 100644
--- a/src/core/GREX.cpp
+++ b/src/core/GREX.cpp
@@ -27,7 +27,7 @@
 #include <sstream>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 GREX::GREX(PlumedMain&p):
   initialized(false),
@@ -156,3 +156,5 @@ void GREX::calculate(){
   }
   intracomm.Bcast(&foreignDeltaBias,1,0);
 }
+
+}
diff --git a/src/core/MDAtoms.cpp b/src/core/MDAtoms.cpp
index 018529454abf497ae8b875f1d2e270fd9ff39047..431c946338bd5558063889ce526e43f035f18fcc 100644
--- a/src/core/MDAtoms.cpp
+++ b/src/core/MDAtoms.cpp
@@ -25,7 +25,6 @@
 #include "tools/Tools.h"
 #include "tools/PlumedException.h"
 
-using namespace PLMD;
 using namespace std;
 
 namespace PLMD {
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 94fd95110e4363c688b3e61fb7f07cbfd3a3e0ad..f9f573ab2f7b5b15160b23ada75a88a9a44f2964 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -43,9 +43,10 @@
 #include "tools/Citations.h"
 #include "ExchangePatterns.h"
 
-using namespace PLMD;
 using namespace std;
 
+namespace PLMD{
+
 PlumedMain::PlumedMain():
   comm(*new PlumedCommunicator),
   dlloader(*new DLLoader),
@@ -625,6 +626,7 @@ void PlumedMain::runJobsAtEndOfCalculation(){
   }
 } 
 
+}
 
 
 //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
diff --git a/src/core/PlumedMainInitializer.cpp b/src/core/PlumedMainInitializer.cpp
index 67aca0d74b8bea243546ef395256af19c00f2341..d554ee0ff335f15b98a5e8e3025396ef15f36c69 100644
--- a/src/core/PlumedMainInitializer.cpp
+++ b/src/core/PlumedMainInitializer.cpp
@@ -23,8 +23,8 @@
 #include "tools/PlumedException.h"
 #include <cstdlib>
 
-using namespace PLMD;
 using namespace std;
+namespace PLMD{
 
 // !!!!!!!!!!!!!!!!!!!!!!    DANGER   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
 // THE FOLLOWING ARE UTILITIES WHICH ARE NECESSARY FOR DYNAMIC LOADING OF THE PLUMED KERNEL:
@@ -78,3 +78,4 @@ static class PlumedMainInitializer{
 }
 
 
+}
diff --git a/src/core/Value.cpp b/src/core/Value.cpp
index 32a7711866bc34a45b5daa18cc7a7923fbdce21c..e1940025ca7a891b1423b5a8c05193eadfa1fb63 100644
--- a/src/core/Value.cpp
+++ b/src/core/Value.cpp
@@ -28,7 +28,7 @@
 #include "Atoms.h"
 #include "PlumedMain.h"
 
-using namespace PLMD;
+namespace PLMD{
 
 Value::Value():
   action(NULL), 
@@ -152,7 +152,7 @@ ActionWithValue* Value::getPntrToAction(){
   return action;
 }
 
-void PLMD::copy( const Value& val1, Value& val2 ){
+void copy( const Value& val1, Value& val2 ){
   unsigned nder=val1.getNumberOfDerivatives();
   if( nder!=val2.getNumberOfDerivatives() ){ val2.resizeDerivatives( nder ); }
   val2.clearDerivatives();
@@ -160,7 +160,7 @@ void PLMD::copy( const Value& val1, Value& val2 ){
   val2.set( val1.get() );
 }
 
-void PLMD::copy( const Value& val1, Value* val2 ){
+void copy( const Value& val1, Value* val2 ){
   unsigned nder=val1.getNumberOfDerivatives();
   if( nder!=val2->getNumberOfDerivatives() ){ val2->resizeDerivatives( nder ); }
   val2->clearDerivatives();
@@ -168,12 +168,14 @@ void PLMD::copy( const Value& val1, Value* val2 ){
   val2->set( val1.get() );
 }
 
-void PLMD::add( const Value& val1, Value* val2 ){
+void add( const Value& val1, Value* val2 ){
   plumed_assert( val1.getNumberOfDerivatives()==val2->getNumberOfDerivatives() );
   for(unsigned i=0;i<val1.getNumberOfDerivatives();++i) val2->addDerivative( i, val1.getDerivative(i) );
   val2->set( val1.get() + val2->get() );
 }
 
+}
+
 
 
 
diff --git a/src/function/Function.cpp b/src/function/Function.cpp
index 8612cc6d305522099693ad7e3111c822d093646e..27e25d7a27b99f29c5b45c7ffcde427d9dda950b 100644
--- a/src/function/Function.cpp
+++ b/src/function/Function.cpp
@@ -21,9 +21,9 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Function.h"
 
-using namespace PLMD;
-using namespace PLMD::function;
 using namespace std;
+namespace PLMD{
+namespace function{
 
 void Function::registerKeywords(Keywords& keys){
   Action::registerKeywords(keys);
@@ -78,3 +78,5 @@ void Function::apply(){
     getPntrToArgument(i)->addForce(f[i]);
   }
 }
+}
+}
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index 77f33b1f644fd80d777d12c1337c1c86c6c070de..4f8de058190d7cbb2f82cdba6a82ddfbc2c3745f 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -29,7 +29,6 @@
 #include "tools/Units.h"
 #include <cstdio>
 
-using namespace PLMD;
 using namespace std;
 
 namespace PLMD
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index d7d4f9e0ae6f2ca241d43ea04510820504645d8a..3c6ec29d8615dfcae5ae73eee597abea1bc17af6 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -34,7 +34,6 @@
 #include <string>
 
 using namespace std;
-using namespace PLMD;
 
 namespace PLMD {
 namespace generic{
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index 366c399a2d7fdc6f037f058c8713bac747365224..6b7c3c129d34945102f995a8db5393e8118ef405 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -29,8 +29,8 @@
 #include <string>
 
 using namespace std;
-using namespace PLMD;
-using namespace PLMD::multicolvar;
+namespace PLMD{
+namespace multicolvar{
 
 void MultiColvar::registerKeywords( Keywords& keys ){
   Action::registerKeywords( keys );
@@ -467,3 +467,5 @@ void MultiColvar::apply(){
     }
   }
 }
+}
+}
diff --git a/src/multicolvar/MultiColvar.h b/src/multicolvar/MultiColvar.h
index a82f45a0a62d59732eff5d2088f92d278ce12840..02cd5632d7a4516f760027c63ec540c4b0df215f 100644
--- a/src/multicolvar/MultiColvar.h
+++ b/src/multicolvar/MultiColvar.h
@@ -32,8 +32,6 @@
 namespace PLMD {
 namespace multicolvar {
 
-class MultiColvar;
-
 /**
 \ingroup INHERIT
 This is the abstract base class to use for creating distributions of colvars and functions
diff --git a/src/multicolvar/SecondaryStructureRMSD.cpp b/src/multicolvar/SecondaryStructureRMSD.cpp
index 8520ec7a9b4eee381b5f99bf53497c24b6a3dcee..c8b08dd4e32dabca9c2eb8881d8679b327520175 100644
--- a/src/multicolvar/SecondaryStructureRMSD.cpp
+++ b/src/multicolvar/SecondaryStructureRMSD.cpp
@@ -25,9 +25,9 @@
 #include "tools/RMSD.h"
 #include "tools/DRMSD.h"
 
-using namespace PLMD::multicolvar;
 
 namespace PLMD {
+namespace multicolvar{
 
 void SecondaryStructureRMSD::registerKeywords( Keywords& keys ){
   MultiColvar::registerKeywords( keys );
@@ -146,3 +146,4 @@ bool SecondaryStructureRMSD::usingRMSD() const {
 }
 
 }
+}
diff --git a/src/tools/Angle.cpp b/src/tools/Angle.cpp
index 64900ec43d1b964c48f9301b06cf2696b684f49d..afbf1f9a3636bedf98ab5eaa1eff61adc6d942ba 100644
--- a/src/tools/Angle.cpp
+++ b/src/tools/Angle.cpp
@@ -23,7 +23,7 @@
 #include "Tools.h"
 #include <cmath>
 
-using namespace PLMD;
+namespace PLMD{
 
 double Angle::compute(const Vector& v1,const Vector& v2)const{
     return std::acos(dotProduct(v1,v2)/(v1.modulo()*v2.modulo()));
@@ -65,3 +65,4 @@ double Angle::compute(const Vector& v1,const Vector& v2,Vector& d1,Vector& d2)co
     return std::acos(dpnn);
 }
 
+}
diff --git a/src/tools/Citations.cpp b/src/tools/Citations.cpp
index aebf931c90c18ecd776354916f4e634a81f5cadd..2618ec39dd94470871836f7c50aff05ac98a0917 100644
--- a/src/tools/Citations.cpp
+++ b/src/tools/Citations.cpp
@@ -25,7 +25,7 @@
 #include <iostream>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 std::string Citations::cite(const std::string & item){
   unsigned i;
@@ -38,10 +38,11 @@ std::string Citations::cite(const std::string & item){
   return ret;
 }
 
-std::ostream & PLMD::operator<<(std::ostream &log,const Citations&cit){
+std::ostream & operator<<(std::ostream &log,const Citations&cit){
   for(unsigned i=0;i<cit.items.size();++i)
     log<<"  ["<<i+1<<"] "<<cit.items[i]<<"\n";
   return log;
 }
+}
 
 
diff --git a/src/tools/DLLoader.cpp b/src/tools/DLLoader.cpp
index a614d8cd5157dea47ac54892aac6e8e3b7252bb7..59ab3b0813134a888cee4feea962620d990e885c 100644
--- a/src/tools/DLLoader.cpp
+++ b/src/tools/DLLoader.cpp
@@ -26,7 +26,7 @@
 #include <dlfcn.h>
 #endif
 
-using namespace PLMD;
+namespace PLMD{
 
 bool DLLoader::installed(){
 #ifdef __PLUMED_HAS_DLOPEN
@@ -81,3 +81,4 @@ DLLoader&DLLoader::operator=(const DLLoader&dl){
 
 
 
+}
diff --git a/src/tools/DRMSD.cpp b/src/tools/DRMSD.cpp
index 89cc38c188294ec207ddd45bdcad191895d21e49..6897052b700583bc969e464b9462bd508d43e471 100644
--- a/src/tools/DRMSD.cpp
+++ b/src/tools/DRMSD.cpp
@@ -25,7 +25,7 @@
 #include <cmath>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 void DRMSD::setFromPDB(const PDB&pdb, double lbound, double ubound){
   setReference(pdb.getPositions(), lbound, ubound);
@@ -90,3 +90,4 @@ double DRMSD::calculate(const std::vector<Vector> & positions, const Pbc& pbc,
 }
 
 
+}
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index b787859a75ad9137b8cf3a8e274161f2d919356c..6561e20d39fad6a8f140962a5c9c317657f3492f 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -33,7 +33,7 @@
 #include "KernelFunctions.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 Grid::Grid(const std::string& funcl, std::vector<Value*> args, const vector<std::string> & gmin, 
            const vector<std::string> & gmax, const vector<unsigned> & nbin, bool dospline, bool usederiv, bool doclear){
@@ -622,3 +622,4 @@ void SparseGrid::writeToFile(PlumedOFile& ofile){
    ofile.printField();
  }
 }
+}
diff --git a/src/tools/HistogramBead.cpp b/src/tools/HistogramBead.cpp
index 9bfadc7237ba4ce42ab718f0622f8330b35d10d5..267a8abe3fd3072f773797a5f6bfb85396dd7e17 100644
--- a/src/tools/HistogramBead.cpp
+++ b/src/tools/HistogramBead.cpp
@@ -25,7 +25,7 @@
 #include "Tools.h"
 #include "Keywords.h"
 
-using namespace PLMD;
+namespace PLMD{
 
 //+PLUMEDOC INTERNAL histogrambead 
 /*
@@ -188,3 +188,4 @@ double HistogramBead::calculate( double x, double& df ) const {
   return f;
 }     
 
+}
diff --git a/src/tools/Kearsley.cpp b/src/tools/Kearsley.cpp
index bf3e589c2b74ac97ac79e06cb2a658188fa0f4e0..d3dd5571225d2c9405170d56db8d7181f8a265df 100644
--- a/src/tools/Kearsley.cpp
+++ b/src/tools/Kearsley.cpp
@@ -30,7 +30,7 @@
 #include "Random.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 // put some notes
 
@@ -874,3 +874,4 @@ for(l=0;l<3;l++){
 
 	exit(0);
 }
+}
diff --git a/src/tools/Keywords.cpp b/src/tools/Keywords.cpp
index 171e9843399650b190a93de67a0d20a98f9580b2..186b219a568c627ee281bc2d698b7b7aa2452af6 100644
--- a/src/tools/Keywords.cpp
+++ b/src/tools/Keywords.cpp
@@ -24,7 +24,7 @@
 #include "Tools.h"
 #include <iostream>
 
-using namespace PLMD;
+namespace PLMD{
 
 Keywords::KeyType::KeyType( const std::string& type ){
   if( type=="compulsory" ){
@@ -489,3 +489,4 @@ void Keywords::destroyData(){
    booldefs.clear(); numdefs.clear(); atomtags.clear();
 }
 
+}
diff --git a/src/tools/LatticeReduction.cpp b/src/tools/LatticeReduction.cpp
index 28c785f740b810e425a90bb303f96d73d248f88e..70b548f5cae4360f53becae4cbb61c12cdffdf07 100644
--- a/src/tools/LatticeReduction.cpp
+++ b/src/tools/LatticeReduction.cpp
@@ -22,7 +22,7 @@
 #include "PlumedException.h"
 #include "LatticeReduction.h"
 
-using namespace PLMD;
+namespace PLMD{
 
 void LatticeReduction::sort(Vector v[3]){
   for(int i=0;i<3;i++) for(int j=i+1;j<3;j++) if(modulo2(v[i])>modulo2(v[j])){
@@ -189,3 +189,4 @@ bool LatticeReduction::isReduced(const Tensor&t){
   return true;
 }
 
+}
diff --git a/src/tools/NeighborList.cpp b/src/tools/NeighborList.cpp
index ebfc18a020905f01c3a3a2195b2e58e5b872d977..6e87131a29a3e6d2b5ca5597dd362fc1ee755480 100644
--- a/src/tools/NeighborList.cpp
+++ b/src/tools/NeighborList.cpp
@@ -27,7 +27,7 @@
 #include "Tools.h"
 #include "NeighborList.h"
 
-using namespace PLMD;
+namespace PLMD{
 using namespace std;
 
 NeighborList::NeighborList(const vector<AtomNumber>& list0, const vector<AtomNumber>& list1,
@@ -194,3 +194,4 @@ vector<unsigned> NeighborList::getNeighbors(unsigned index) {
  return neighbors;
 }
 
+}
diff --git a/src/tools/OptimalAlignment.cpp b/src/tools/OptimalAlignment.cpp
index 245a08571746766c1b3b1925bec5ad4eeddb7fb7..f3ffe587692f9f6b014e11ce9ce9acd5f23b1aa8 100644
--- a/src/tools/OptimalAlignment.cpp
+++ b/src/tools/OptimalAlignment.cpp
@@ -28,7 +28,7 @@
 #include "Random.h"
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 OptimalAlignment::OptimalAlignment( const  std::vector<double>  & align, const  std::vector<double>  & displace, const std::vector<Vector> & p0, const std::vector<Vector> & p1 , Log &log )
 :log(log){
@@ -392,3 +392,4 @@ double OptimalAlignment::weightedFindiffTest( bool rmsd){
 
 
 
+}
diff --git a/src/tools/Pbc.cpp b/src/tools/Pbc.cpp
index e39655fe83be17cd481f2beb69c2f184290cc4aa..382b059f540d19db78d96be3d35ffbf0037d08ef 100644
--- a/src/tools/Pbc.cpp
+++ b/src/tools/Pbc.cpp
@@ -24,7 +24,7 @@
 #include "PlumedException.h"
 #include "LatticeReduction.h"
 
-using namespace PLMD;
+namespace PLMD{
 
 Pbc::Pbc():
   type(unset)
@@ -138,3 +138,4 @@ const Tensor& Pbc::getInvBox()const{
 
 
 
+}
diff --git a/src/tools/PlumedCommunicator.cpp b/src/tools/PlumedCommunicator.cpp
index f9a54102b049c08a4919a178f8c0565024b59c54..e08ae20d311a8faa9ad50e73e6de533311a90e58 100644
--- a/src/tools/PlumedCommunicator.cpp
+++ b/src/tools/PlumedCommunicator.cpp
@@ -24,7 +24,6 @@
 #include "PlumedException.h"
 
 using namespace std;
-using namespace PLMD;
 
 namespace PLMD{
 
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index 108ac893e90c14fa78d4287dacfc8ddee8c993a1..599962c10e7d86f9a061fa06c671c2d5c647beb1 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -28,7 +28,7 @@
 #include <iostream>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 RMSD::RMSD(const RMSD & oldrmsd):
   alignmentMethod(oldrmsd.alignmentMethod),
@@ -158,3 +158,4 @@ double RMSD::simpleAlignment(const  std::vector<double>  & align,
       }
       return ret;
 }
+}
diff --git a/src/tools/Random.cpp b/src/tools/Random.cpp
index 9cc9363b6b0d023b70509b377a3e5e80dd52dc2e..ad7a54b3dc1e83caf61002a0aebf2cd9b57cff80 100644
--- a/src/tools/Random.cpp
+++ b/src/tools/Random.cpp
@@ -25,7 +25,7 @@
 #include <sstream>
 #include <iostream>
 
-using namespace PLMD;
+namespace PLMD{
 
 const double Random::fact=5.9604644775390625e-8;     /* 1 / 2^24  */
 const double Random::EPS=3.0e-16;
@@ -145,3 +145,4 @@ double Random::Gaussian(){
 	return v2*fac;
 }
 
+}
diff --git a/src/tools/Stopwatch.cpp b/src/tools/Stopwatch.cpp
index 2f6815ab685dd6268af4e6f3458534e6c023c814..57d92745d4663554377bc612d63df839663d8853 100644
--- a/src/tools/Stopwatch.cpp
+++ b/src/tools/Stopwatch.cpp
@@ -42,18 +42,15 @@ clock_gettime (#define __CLOCK_GETTIME):
 #include <sys/time.h>
 #endif
 
-using namespace PLMD;
 using namespace std;
 
-// this is needed for friend operators
 namespace PLMD{
 
+// this is needed for friend operators
 std::ostream& operator<<(std::ostream&os,const Stopwatch&sw){
   return sw.log(os);
 }
 
-}
-
 Stopwatch::Time::operator double()const{
   return sec+0.000000001*nsec;
 }
@@ -158,6 +155,8 @@ std::ostream& Stopwatch::log(std::ostream&os)const{
   return os;
 }
 
+}
+
 
 
 
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
index d4b12b2b79eb86319f33f1015e67c9d96bbadee9..68cc1dc917ce564ac8fd8afd93ea362791a24e98 100644
--- a/src/tools/SwitchingFunction.cpp
+++ b/src/tools/SwitchingFunction.cpp
@@ -26,7 +26,7 @@
 #include <limits>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
 //+PLUMEDOC INTERNAL switchingfunction 
 /*
@@ -213,5 +213,7 @@ void SwitchingFunction::printKeywords( Log& log ) const {
   skeys.print(log);
 }
 
+}
+
 
 
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index 1393b49b5cdde8a11bb54db8f271c67ecb3c453c..0a5c20b221a491e4f00ed5c092c20d3496d81d07 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -27,8 +27,8 @@
 #include <cstring>
 #include <dirent.h>
 
-using namespace PLMD;
 using namespace std;
+namespace PLMD{
 
 bool Tools::convert(const string & str,int & t){
         istringstream istr(str.c_str());
@@ -257,3 +257,5 @@ void Tools::stripLeadingAndTrailingBlanks( std::string& str ){
   std::size_t last=str.find_last_not_of(' ');
   if( first<last ) str=str.substr(first,last+1);
 }
+
+}
diff --git a/src/tools/Torsion.cpp b/src/tools/Torsion.cpp
index 426deca00f85481761f9b7d23136c1e5b5a208ab..dd7a6ecf57e7a610bb4fc528af8436cf8721b80d 100644
--- a/src/tools/Torsion.cpp
+++ b/src/tools/Torsion.cpp
@@ -25,7 +25,7 @@
 #include <cmath>
 #include <iostream>
 
-using namespace PLMD;
+namespace PLMD{
 
 double Torsion::compute(const Vector& v1,const Vector& v2,const Vector& v3)const{
     const Vector nv2(v2*(1.0/v2.modulo()));
@@ -81,5 +81,7 @@ double Torsion::compute(const Vector& v1,const Vector& v2,const Vector& v3,Vecto
   return torsion;
 }
 
+}
+