diff --git a/src/core/ActionWithValue.h b/src/core/ActionWithValue.h
index 2bb744a9a81557e4ede0a1677a6a53f71954c2e9..15c03f59e888cfd404fc41f595263aae06a59b56 100644
--- a/src/core/ActionWithValue.h
+++ b/src/core/ActionWithValue.h
@@ -65,8 +65,6 @@ PLMD::Action you should use <b> the routines with the word component in the name
class ActionWithValue :
public virtual Action
{
-friend class VesselAccumulator;
-friend class VesselMoment;
private:
/// An array containing the values for this action
std::vector<Value*> values;
@@ -93,6 +91,7 @@ protected:
// -------- The action has multiple components ---------- //
+public:
/// Add a value with a name like label.name
void addComponent( const std::string& name );
/// Add a value with a name like label.name that has derivatives
@@ -101,6 +100,7 @@ protected:
void componentIsNotPeriodic( const std::string& name );
/// Set the value to be periodic with a particular domain
void componentIsPeriodic( const std::string& name, const std::string& min, const std::string& max );
+protected:
/// Return a pointer to the component by index
Value* getPntrToComponent(int i);
/// Return a pointer to the value by name
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index a8d11d5d2021ba7d6bac1fd7a0ee918e4b60e354..9b83aa7fb17cc39c84532aaa7884397d50345bd5 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -377,7 +377,7 @@ void MultiColvar::retrieveColvarWeight( const unsigned& j, Value& ww ){
ww.clearDerivatives(); ww.set(1.0);
}
-void MultiColvar::mergeDerivatives( const unsigned jcv, const Value& value_in, const double& df, const unsigned& vstart, Vessel* valout ){
+void MultiColvar::mergeDerivatives( const unsigned jcv, const Value& value_in, const double& df, const unsigned& vstart, vesselbase::Vessel* valout ){
plumed_assert( value_in.getNumberOfDerivatives()==3*colvar_atoms[jcv].getNumberActive()+9);
int thisatom, thispos, in=0; unsigned innat=colvar_atoms[jcv].getNumberActive();
diff --git a/src/multicolvar/MultiColvar.h b/src/multicolvar/MultiColvar.h
index eb9db602fdff1e84f3863426b7c67f2c6a472e98..38e90252b6ba15ec6c85b7c0b0d195cb430eba66 100644
--- a/src/multicolvar/MultiColvar.h
+++ b/src/multicolvar/MultiColvar.h
@@ -43,7 +43,7 @@ thereof, whtin it there is \ref AddingAMultiColvar "information" as to how to go
class MultiColvar :
public ActionAtomistic,
public ActionWithValue,
- public ActionWithVessel
+ public vesselbase::ActionWithVessel
{
private:
bool usepbc;
@@ -113,7 +113,7 @@ public:
/// Get the weight of the colvar
virtual void retrieveColvarWeight( const unsigned& i, Value& ww );
/// Merge the derivatives
- void mergeDerivatives( const unsigned j, const Value& value_in, const double& df, const unsigned& vstart, Vessel* valout );
+ void mergeDerivatives( const unsigned j, const Value& value_in, const double& df, const unsigned& vstart, vesselbase::Vessel* valout );
void mergeDerivatives( const unsigned j, const Value& value_in, const double& df, Value* valout );
/// Turn of atom requests when this colvar is deactivated cos its small
void deactivateValue( const unsigned j );
diff --git a/src/multicolvar/VesselCVdens.cpp b/src/multicolvar/VesselCVdens.cpp
index d88d80a168ef65be44473873c1ad98a5d16c81bf..e9a5ecd91e9771bc66a2a54e32f6d49605e8b224 100644
--- a/src/multicolvar/VesselCVdens.cpp
+++ b/src/multicolvar/VesselCVdens.cpp
@@ -88,7 +88,7 @@ DENSITY SPECIES=20-500 REGION={SIGMA=0.1 VOLUME=r2}
//+ENDPLUMEDOC
-class VesselCVDens : public NormedSumVessel {
+class VesselCVDens : public vesselbase::NormedSumVessel {
private:
bool isDensity;
Value tmpval, tmpweight;
@@ -99,7 +99,7 @@ private:
HistogramBead bead;
public:
static void reserveKeyword( Keywords& keys );
- VesselCVDens( const VesselOptions& da );
+ VesselCVDens( const vesselbase::VesselOptions& da );
void getWeight( const unsigned& i, Value& weight );
void compute( const unsigned& i, const unsigned& j, Value& theval );
};
@@ -111,7 +111,7 @@ void VesselCVDens::reserveKeyword( Keywords& keys ){
"For more details on how this quantity is calculated see \\ref region.");
}
-VesselCVDens::VesselCVDens( const VesselOptions& da ) :
+VesselCVDens::VesselCVDens( const vesselbase::VesselOptions& da ) :
NormedSumVessel(da),
catom_pos(3),
not_in(false)
diff --git a/src/multicolvar/VesselMean.cpp b/src/multicolvar/VesselMean.cpp
index de6088d619d094483cbbb8e3bd6589aa1ffc799e..06be7c78da97217bda5012952ff69f0cc12cfeaf 100644
--- a/src/multicolvar/VesselMean.cpp
+++ b/src/multicolvar/VesselMean.cpp
@@ -26,12 +26,12 @@
namespace PLMD {
namespace multicolvar {
-class VesselMean : public NormedSumVessel {
+class VesselMean : public vesselbase::NormedSumVessel {
private:
MultiColvar* mycolv;
public:
static void reserveKeyword( Keywords& keys );
- VesselMean( const VesselOptions& da );
+ VesselMean( const vesselbase::VesselOptions& da );
void getWeight( const unsigned& i, Value& weight );
void compute( const unsigned& i, const unsigned& j, Value& theval );
};
@@ -42,7 +42,7 @@ void VesselMean::reserveKeyword( Keywords& keys ){
keys.reserveFlag("AVERAGE",false,"take the average value of these variables and store it in value called average.");
}
-VesselMean::VesselMean( const VesselOptions& da ) :
+VesselMean::VesselMean( const vesselbase::VesselOptions& da ) :
NormedSumVessel(da)
{
if( getAction()->isPeriodic() ) error("MEAN cannot be used with periodic variables");
diff --git a/src/multicolvar/VesselWithin.cpp b/src/multicolvar/VesselWithin.cpp
index 5558951c597f9aa29fca59285a109a146074b1c8..e864c7d2e6754902761b9d6424249a1a3391868c 100644
--- a/src/multicolvar/VesselWithin.cpp
+++ b/src/multicolvar/VesselWithin.cpp
@@ -28,13 +28,13 @@
namespace PLMD {
namespace multicolvar {
-class VesselWithin : public NormedSumVessel {
+class VesselWithin : public vesselbase::NormedSumVessel {
private:
MultiColvar* mycolv;
std::vector<HistogramBead> hist;
public:
static void reserveKeyword( Keywords& keys );
- VesselWithin( const VesselOptions& da );
+ VesselWithin( const vesselbase::VesselOptions& da );
void getWeight( const unsigned& i, Value& weight );
void compute( const unsigned& i, const unsigned& j, Value& theval );
void printKeywords();
@@ -49,7 +49,7 @@ void VesselWithin::reserveKeyword( Keywords& keys ){
"\\ref histogrambead. The final values can be referenced using \\e label.between\\f$a\\f$&\\f$b\\f$.");
}
-VesselWithin::VesselWithin( const VesselOptions& da ) :
+VesselWithin::VesselWithin( const vesselbase::VesselOptions& da ) :
NormedSumVessel(da)
{
diff --git a/src/vessel-base/ActionWithVessel.cpp b/src/vessel-base/ActionWithVessel.cpp
index 39636948ae469698a9b05a47238d0eff916f7473..48a3902d2137e295d13301262b167d2cd1b6ef95 100644
--- a/src/vessel-base/ActionWithVessel.cpp
+++ b/src/vessel-base/ActionWithVessel.cpp
@@ -24,7 +24,8 @@
#include "VesselRegister.h"
using namespace std;
-using namespace PLMD;
+namespace PLMD{
+namespace vesselbase{
void ActionWithVessel::registerKeywords(Keywords& keys){
keys.add("optional","TOL","when accumulating sums quantities that contribute less than this will be ignored.");
@@ -206,3 +207,6 @@ void ActionWithVessel::calculateAllVessels( const int& stepn ){
void ActionWithVessel::retrieveDomain( std::string& min, std::string& max ){
plumed_massert(0, "If your function is periodic you need to add a retrieveDomain function so that ActionWithVessel can retrieve the domain");
}
+
+}
+}
diff --git a/src/vessel-base/ActionWithVessel.h b/src/vessel-base/ActionWithVessel.h
index fcf19aa061280164e117b725f9077004974e1584..22adc0ea7fab11b92a6eeda8981320818ca0ab82 100644
--- a/src/vessel-base/ActionWithVessel.h
+++ b/src/vessel-base/ActionWithVessel.h
@@ -29,9 +29,11 @@
#include <vector>
namespace PLMD{
+class Value;
+
+namespace vesselbase{
class Vessel;
-class Value;
/**
\ingroup MULTIINHERIT
@@ -169,4 +171,5 @@ Vessel* ActionWithVessel::getPntrToVessel( const unsigned& i ){
}
}
+}
#endif
diff --git a/src/vessel-base/NormedSumVessel.cpp b/src/vessel-base/NormedSumVessel.cpp
index ffe57499408510b35eec89bbff5b9638b77f689c..66d100e5449a59db6375ebda34400b122ef45c26 100644
--- a/src/vessel-base/NormedSumVessel.cpp
+++ b/src/vessel-base/NormedSumVessel.cpp
@@ -23,6 +23,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
NormedSumVessel::NormedSumVessel( const VesselOptions& da ):
VesselAccumulator(da),
@@ -95,3 +96,4 @@ void NormedSumVessel::finish( const double& tolerance ){
}
}
+}
diff --git a/src/vessel-base/NormedSumVessel.h b/src/vessel-base/NormedSumVessel.h
index 3af883a8d9dbd4ac3b37aa54cae8ae42d3c0943a..c111d8ff8b7458704d603a922f9f8bcc24dfdfb1 100644
--- a/src/vessel-base/NormedSumVessel.h
+++ b/src/vessel-base/NormedSumVessel.h
@@ -28,6 +28,7 @@
#include "VesselAccumulator.h"
namespace PLMD {
+namespace vesselbase{
class NormedSumVessel : public VesselAccumulator {
private:
@@ -49,5 +50,6 @@ public:
virtual void compute( const unsigned& , const unsigned& , Value& )=0;
};
+}
}
#endif
diff --git a/src/vessel-base/SumVessel.cpp b/src/vessel-base/SumVessel.cpp
index ddffb2e02f24ef3d5cfdfeaf0166bbde31f6599c..70923af22250fac479c0d07b14dc679c2c842294 100644
--- a/src/vessel-base/SumVessel.cpp
+++ b/src/vessel-base/SumVessel.cpp
@@ -23,6 +23,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
SumVessel::SumVessel( const VesselOptions& da ):
VesselAccumulator(da)
@@ -57,5 +58,6 @@ void SumVessel::finish( const double& tolerance ){
copy( myvalue2, getPntrToOutput(i) );
}
}
+}
}
diff --git a/src/vessel-base/SumVessel.h b/src/vessel-base/SumVessel.h
index e4b0306dc44d313f7d6161c425bfd36205e12110..feba6ed7ec75ab7877a94690376813a3ac8a05d7 100644
--- a/src/vessel-base/SumVessel.h
+++ b/src/vessel-base/SumVessel.h
@@ -28,6 +28,7 @@
#include "VesselAccumulator.h"
namespace PLMD {
+namespace vesselbase{
class SumVessel : public VesselAccumulator {
private:
@@ -44,5 +45,6 @@ public:
virtual double final_computations( const unsigned& , const double& , double& );
};
+}
}
#endif
diff --git a/src/vessel-base/Vessel.cpp b/src/vessel-base/Vessel.cpp
index 863a609a7b09587a71eb3f85e332d5650f0702cf..8721ef831915b61605716e7e7eaaa50053f8555b 100644
--- a/src/vessel-base/Vessel.cpp
+++ b/src/vessel-base/Vessel.cpp
@@ -26,6 +26,7 @@
#include "tools/Log.h"
namespace PLMD {
+namespace vesselbase{
VesselOptions::VesselOptions(const std::string& thisname, const std::string& params, ActionWithVessel* aa ):
myname(thisname),
@@ -63,3 +64,4 @@ void Vessel::error( const std::string& msg ){
}
}
+}
diff --git a/src/vessel-base/Vessel.h b/src/vessel-base/Vessel.h
index 1ab1ddeafbde78f8b6328ff81181fbf71ec61849..3e10eed44e8b6e88f71c0ac786a8b4c1b77a03a7 100644
--- a/src/vessel-base/Vessel.h
+++ b/src/vessel-base/Vessel.h
@@ -30,6 +30,11 @@
namespace PLMD{
+class PlumedCommunicator;
+class Log;
+
+namespace vesselbase{
+
/**
\ingroup TOOLBOX
Vessel is an abstract base class. The classes that inherit
@@ -40,8 +45,6 @@ on. This class is used in PLMD::ActionWithVessel.
class ActionWithVessel;
class Vessel;
-class Log;
-class PlumedCommunicator;
/// This class is used to pass the input to Vessels
class VesselOptions {
@@ -146,5 +149,6 @@ double Vessel::getBufferElement( const unsigned& i ) const {
return data_buffer[i];
}
+}
}
#endif
diff --git a/src/vessel-base/VesselAccumulator.cpp b/src/vessel-base/VesselAccumulator.cpp
index 951a13f75ba331b01a5866e1be2c42c1bc310a9f..8c9b0e59b7be1abcfe1abd6ed6b833762493f436 100644
--- a/src/vessel-base/VesselAccumulator.cpp
+++ b/src/vessel-base/VesselAccumulator.cpp
@@ -23,6 +23,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
VesselAccumulator::VesselAccumulator( const VesselOptions& da ):
VesselValueAccess(da),
@@ -65,4 +66,5 @@ bool VesselAccumulator::applyForce( std::vector<double>& forces ){
}
}
+}
diff --git a/src/vessel-base/VesselAccumulator.h b/src/vessel-base/VesselAccumulator.h
index 465e8e4983ee2fe6872e8e3e37a52ad85abbf274..9506d59dae3ca9c0b8c9342fa7fcf3e07331676b 100644
--- a/src/vessel-base/VesselAccumulator.h
+++ b/src/vessel-base/VesselAccumulator.h
@@ -28,6 +28,7 @@
#include "VesselValueAccess.h"
namespace PLMD {
+namespace vesselbase {
class VesselAccumulator : public VesselValueAccess {
private:
@@ -64,6 +65,7 @@ unsigned VesselAccumulator::getNumberOfValues() const {
}
+}
}
#endif
diff --git a/src/vessel-base/VesselLessThan.cpp b/src/vessel-base/VesselLessThan.cpp
index 58930505117167f15a805f20008e01c788d91e76..79a51c645bdf1a8c6583bf4642c45d18e55cd244 100644
--- a/src/vessel-base/VesselLessThan.cpp
+++ b/src/vessel-base/VesselLessThan.cpp
@@ -26,6 +26,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
class VesselLessThan : public SumVessel {
private:
@@ -69,3 +70,4 @@ double VesselLessThan::compute( const unsigned& i, const double& val, double& df
}
}
+}
diff --git a/src/vessel-base/VesselMin.cpp b/src/vessel-base/VesselMin.cpp
index ca12ce1fb072f59dce111c5a4e61ee714d07eb62..145f9cce74c3222fc2d114d021b8f790d4421d13 100644
--- a/src/vessel-base/VesselMin.cpp
+++ b/src/vessel-base/VesselMin.cpp
@@ -24,6 +24,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
class VesselMin : public SumVessel {
private:
@@ -76,3 +77,4 @@ double VesselMin::final_computations( const unsigned& i, const double& valin, do
}
}
+}
diff --git a/src/vessel-base/VesselMoment.cpp b/src/vessel-base/VesselMoment.cpp
index 151d53b12fea4058ba6aa40c9c4e159b2b0d6445..d7c846569556122574c46c20bf204f0095a4a9e5 100644
--- a/src/vessel-base/VesselMoment.cpp
+++ b/src/vessel-base/VesselMoment.cpp
@@ -25,6 +25,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
class VesselMoment : public VesselStoreAllValues {
private:
@@ -131,3 +132,4 @@ bool VesselMoment::applyForce( std::vector<double>& forces ){
}
}
+}
diff --git a/src/vessel-base/VesselMoreThan.cpp b/src/vessel-base/VesselMoreThan.cpp
index 495c9806a22e68d7906985acb4271115108c771b..16b7ded5b921cc22956af5ecdc97f9c590257444 100644
--- a/src/vessel-base/VesselMoreThan.cpp
+++ b/src/vessel-base/VesselMoreThan.cpp
@@ -26,6 +26,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
class VesselMoreThan : public SumVessel {
private:
@@ -70,3 +71,4 @@ double VesselMoreThan::compute( const unsigned& i, const double& val, double& df
}
}
+}
diff --git a/src/vessel-base/VesselRegister.cpp b/src/vessel-base/VesselRegister.cpp
index eaa75759ee745cafbd1c361573bc84ef38746dd7..f57bfc05529018ab7d1ff4897c2cb56a8a247deb 100644
--- a/src/vessel-base/VesselRegister.cpp
+++ b/src/vessel-base/VesselRegister.cpp
@@ -23,6 +23,7 @@
#include "VesselRegister.h"
namespace PLMD{
+namespace vesselbase{
VesselRegister::~VesselRegister(){
if(m.size()>0){
@@ -68,3 +69,4 @@ Keywords VesselRegister::getKeywords(){
}
}
+}
diff --git a/src/vessel-base/VesselRegister.h b/src/vessel-base/VesselRegister.h
index 84a7aaaf4d394f32454a72bd6da5b18014331247..c4f15d66be25f0e3ad5a60baba5edc50f24130ca 100644
--- a/src/vessel-base/VesselRegister.h
+++ b/src/vessel-base/VesselRegister.h
@@ -30,6 +30,7 @@
#include "Tools/Keywords.h"
namespace PLMD{
+namespace vesselbase{
class Vessel;
class VesselOptions;
@@ -63,11 +64,12 @@ VesselRegister& vesselRegister();
#define PLUMED_REGISTER_VESSEL(classname,keyword) \
static class classname##RegisterMe{ \
- static PLMD::Vessel * create(const PLMD::VesselOptions&da){return new classname(da);} \
+ static PLMD::vesselbase::Vessel * create(const PLMD::vesselbase::VesselOptions&da){return new classname(da);} \
public: \
- classname##RegisterMe(){PLMD::vesselRegister().add(keyword,create,classname::reserveKeyword);}; \
- ~classname##RegisterMe(){PLMD::vesselRegister().remove(create);}; \
+ classname##RegisterMe(){PLMD::vesselbase::vesselRegister().add(keyword,create,classname::reserveKeyword);}; \
+ ~classname##RegisterMe(){PLMD::vesselbase::vesselRegister().remove(create);}; \
} classname##RegisterMeObject;
+}
}
#endif
diff --git a/src/vessel-base/VesselStoreAllValues.cpp b/src/vessel-base/VesselStoreAllValues.cpp
index 14e7653e14c6c048fcc809bde13b02968917ba7f..15428743e4aff4f76c37365c7f4ba2f5a48e5a47 100644
--- a/src/vessel-base/VesselStoreAllValues.cpp
+++ b/src/vessel-base/VesselStoreAllValues.cpp
@@ -23,6 +23,7 @@
#include "VesselStoreAllValues.h"
namespace PLMD {
+namespace vesselbase{
VesselStoreAllValues::VesselStoreAllValues( const VesselOptions& da ):
VesselValueAccess(da)
@@ -48,4 +49,5 @@ bool VesselStoreAllValues::calculate( const unsigned& i, const double& tolerance
}
+}
diff --git a/src/vessel-base/VesselStoreAllValues.h b/src/vessel-base/VesselStoreAllValues.h
index cd3bccc50c352e3904c271015ba14e9f99d9b90f..42f8844eb54d88f0b1a9b0bce9fe50131c13ffc2 100644
--- a/src/vessel-base/VesselStoreAllValues.h
+++ b/src/vessel-base/VesselStoreAllValues.h
@@ -28,6 +28,7 @@
#include "VesselValueAccess.h"
namespace PLMD {
+namespace vesselbase{
class VesselStoreAllValues : public VesselValueAccess {
public:
@@ -41,5 +42,6 @@ public:
virtual void local_resizing()=0;
};
+}
}
#endif
diff --git a/src/vessel-base/VesselSum.cpp b/src/vessel-base/VesselSum.cpp
index 537718903297ea1839ed2416931b8a01997ed7ac..1855f2de4b3ccfc853de3e350a8e3ace026fbaa1 100644
--- a/src/vessel-base/VesselSum.cpp
+++ b/src/vessel-base/VesselSum.cpp
@@ -24,6 +24,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
class VesselSum : public SumVessel {
public:
@@ -51,3 +52,4 @@ double VesselSum::compute( const unsigned& i, const double& val, double& df ){
}
}
+}
diff --git a/src/vessel-base/VesselValueAccess.cpp b/src/vessel-base/VesselValueAccess.cpp
index ab38908782d502e8f227dbf104617b6e5debf43b..78fb425e77aef1f9752f05b1d5c4e95fe5b87202 100644
--- a/src/vessel-base/VesselValueAccess.cpp
+++ b/src/vessel-base/VesselValueAccess.cpp
@@ -23,6 +23,7 @@
#include "ActionWithVessel.h"
namespace PLMD {
+namespace vesselbase{
VesselValueAccess::VesselValueAccess( const VesselOptions& da ) :
Vessel(da)
@@ -42,3 +43,4 @@ void VesselValueAccess::setValueSizes( const std::vector<unsigned>& val_sizes ){
}
}
+}
diff --git a/src/vessel-base/VesselValueAccess.h b/src/vessel-base/VesselValueAccess.h
index a89a9983b5b77240952fd27c9af52e3781cc603b..7efd2d444e82e63301ad71d76e630499d9ea03ca 100644
--- a/src/vessel-base/VesselValueAccess.h
+++ b/src/vessel-base/VesselValueAccess.h
@@ -29,6 +29,7 @@
#include "core/Value.h"
namespace PLMD {
+namespace vesselbase{
class VesselValueAccess : public Vessel {
private:
@@ -66,5 +67,6 @@ double VesselValueAccess::getValue( const unsigned& icv ) const {
return getBufferElement( value_starts[icv] );
}
+}
}
#endif