Project ID: plumID:20.024
Stderr for source: Alanine-dipeptide/plumed.dat
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WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">>
WARNING: "core/Atoms.h" does not exist anymore in  version >=2.10, you should change your code.
../GAMBES.J3PI09.cpp: In member function ‘virtual void PLMD::bias::GAMBES::prepare()’:
../GAMBES.J3PI09.cpp:224:37: warning: ‘void PLMD::PlumedMain::DeprecatedAtoms::setCollectEnergy(bool) const’ is deprecated [-Wdeprecated-declarations]
224 |   plumed.getAtoms().setCollectEnergy(true);
|   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
In file included from ../GAMBES.J3PI09.cpp:22:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:111:10: note: declared here
111 |     void setCollectEnergy(bool b) const;
|          ^~~~~~~~~~~~~~~~
../GAMBES.J3PI09.cpp: In member function ‘virtual void PLMD::bias::GAMBES::calculate()’:
../GAMBES.J3PI09.cpp:230:36: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKbT() const’ is deprecated: Use Action::getkBT() N.B. this function also reads the TEMP keyword from the input for you. [-Wdeprecated-declarations]
230 |   beta = 1/plumed.getAtoms().getKbT();
|            ~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from ../GAMBES.J3PI09.cpp:22:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:105:12: note: declared here
105 |     double getKbT() const ;
|            ^~~~~~
../GAMBES.J3PI09.cpp:231:63: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKBoltzmann() const’ is deprecated: Use Action::getKBoltzmann(). [-Wdeprecated-declarations]
231 |   if(temp>0.0){ beta = 1/(temp*plumed.getAtoms().getKBoltzmann()) ; }
|                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from ../GAMBES.J3PI09.cpp:22:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:103:12: note: declared here
103 |     double getKBoltzmann() const ;
|            ^~~~~~~~~~~~~
../GAMBES.J3PI09.cpp:250:57: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getEnergy() const’ is deprecated [-Wdeprecated-declarations]
250 |   if(iter==0){energy_offset= plumed.getAtoms().getEnergy();}
|                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from ../GAMBES.J3PI09.cpp:22:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:113:12: note: declared here
113 |     double getEnergy() const ;
|            ^~~~~~~~~
../GAMBES.J3PI09.cpp:251:44: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getEnergy() const’ is deprecated [-Wdeprecated-declarations]
251 |   double energy=plumed.getAtoms().getEnergy() - energy_offset;
|                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from ../GAMBES.J3PI09.cpp:22:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:113:12: note: declared here
113 |     double getEnergy() const ;
|            ^~~~~~~~~