Project ID: plumID:21.005
Stderr for source: SF-prof/plumed_structure_factor_OO.dat
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WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">>
../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp: In static member function ‘static void PLMD::colvar::StructureFactor_sphericallyAveraged::registerKeywords(PLMD::Keywords&)’:
../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp:77:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
77 | keys.addOutputComponent("Sk","default","the instantaneous structure factor averaged over a k-shell");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:27,
from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25,
from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25,
from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24,
from ../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp:6:
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp: In constructor ‘PLMD::colvar::StructureFactor_sphericallyAveraged::StructureFactor_sphericallyAveraged(const PLMD::ActionOptions&)’:
../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp:184:41: warning: ‘int PLMD::PlumedMain::DeprecatedAtoms::getNatoms() const’ is deprecated [-Wdeprecated-declarations]
184 | NumAtom_=plumed.getAtoms().getNatoms();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from ../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp:8:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:106:9: note: declared here
106 | int getNatoms() const ;
| ^~~~~~~~~
../codes/StructureFactor_sphericallyAveraged.Y63YEj.cpp:190:108: warning: ‘int PLMD::PlumedMain::DeprecatedAtoms::getNatoms() const’ is deprecated [-Wdeprecated-declarations]
190 | log.printf(" over a total of N_tot=%d, considering a number of atoms N=%d\n",plumed.getAtoms().getNatoms(),NumAtom_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/home/runner/opt/include/plumed_master/core/PlumedMain.h:106:9: note: declared here
106 | int getNatoms() const ;
| ^~~~~~~~~
Assembler messages:
Fatal error: can't create plumed_mklib.Vo0FNp/../codes/StructureFactor_sphericallyAveraged.o: No such file or directory
terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError'
what():
(core/PlumedMain.cpp:1502) void PLMD::PlumedMain::load(const std::string&)
An error happened while executing command env PLUMED_ROOT='/home/runner/opt/lib/plumed_master' PLUMED_VERSION='2.11.0-dev' PLUMED_HTMLDIR='/home/runner/opt/share/doc/plumed_master' PLUMED_INCLUDEDIR='/home/runner/opt/include' PLUMED_PROGRAM_NAME='plumed_master' PLUMED_IS_INSTALLED='yes' "/home/runner/opt/lib/plumed_master"/scripts/mklib.sh -n -o ./../codes/StructureFactor_sphericallyAveraged.2.11.0-dev.so ../codes/StructureFactor_sphericallyAveraged.cpp
[fv-az1371-234:38281] *** Process received signal ***
[fv-az1371-234:38281] Signal: Aborted (6)
[fv-az1371-234:38281] Signal code: (-6)
[fv-az1371-234:38281] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7f6b9b245330]
[fv-az1371-234:38281] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7f6b9b29eb2c]
[fv-az1371-234:38281] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7f6b9b24527e]
[fv-az1371-234:38281] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7f6b9b2288ff]
[fv-az1371-234:38281] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ff5)[0x7f6b9b6a5ff5]
[fv-az1371-234:38281] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb0da)[0x7f6b9b6bb0da]
[fv-az1371-234:38281] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x7f6b9b6a5a55]
[fv-az1371-234:38281] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5a6f)[0x7f6b9b6a5a6f]
[fv-az1371-234:38281] [ 8] plumed_master(+0x146dd)[0x562cd305b6dd]
[fv-az1371-234:38281] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7f6b9b22a1ca]
[fv-az1371-234:38281] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7f6b9b22a28b]
[fv-az1371-234:38281] [11] plumed_master(+0x15365)[0x562cd305c365]
[fv-az1371-234:38281] *** End of error message ***