Project ID: plumID:23.034
Stderr for source: full_model/plumed.dat
Download: zipped raw stdout - zipped raw stderr
#! Only the first 1000 rows of the error file are shown below #! To inspect the full error file, please download the zipped raw stderr file above WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">> In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tools.h:27, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:28, 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 PairOrientationalEntropy.nKsWGv.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tensor.h:98: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 98 | #pragma acc enter data copyin(this[0:1], d, d[0:n*m-1]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tensor.h:102: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 102 | #pragma acc exit data delete( d[0:n*m-1], d, this[0:1]) | In file included from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:27: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:94: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 94 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:100: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 100 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:102: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 102 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:108: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 108 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:112: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 112 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:116: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 116 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:120: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 120 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:123: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 123 | #pragma acc routine seq | In file included from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:27: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:100: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 100 | #pragma acc enter data copyin(this[0:1],sz,data[0:sz]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:103: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 103 | #pragma acc exit data delete(data[0:sz],sz,this[0:1]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:117: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 117 | #pragma acc enter data copyin(this[0:1]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:123: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 123 | #pragma acc exit data delete( this[0:1]) | PairOrientationalEntropy.nKsWGv.cpp: In constructor ‘PLMD::colvar::PairOrientationalEntropy::PairOrientationalEntropy(const PLMD::ActionOptions&)’: PairOrientationalEntropy.nKsWGv.cpp:193:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator, int>::value_type’ {aka ‘int’} [-Wsign-compare] 193 | for(unsigned int i=0;i<nhist_[0];i++) { PairOrientationalEntropy.nKsWGv.cpp:194:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 194 | for(unsigned int j=0;j<nhist_[1];j++) { PairOrientationalEntropy.nKsWGv.cpp:252:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 252 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:256:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 256 | for(unsigned i=0;i<nhist_[1];++i){ PairOrientationalEntropy.nKsWGv.cpp: In member function ‘virtual void PLMD::colvar::PairOrientationalEntropy::calculate()’: PairOrientationalEntropy.nKsWGv.cpp:511:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 511 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:512:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 512 | for(unsigned j=0;j<nhist_[1];++j){ PairOrientationalEntropy.nKsWGv.cpp:523:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 523 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:524:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 524 | for(unsigned j=0;j<nhist_[1];++j){ PairOrientationalEntropy.nKsWGv.cpp:562:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 562 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:563:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 563 | for(unsigned j=0;j<nhist_[1];++j){ PairOrientationalEntropy.nKsWGv.cpp:581:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 581 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:582:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 582 | for(unsigned j=0;j<nhist_[1];++j){ PairOrientationalEntropy.nKsWGv.cpp:593:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 593 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:594:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 594 | for(unsigned j=0;j<nhist_[1];++j){ PairOrientationalEntropy.nKsWGv.cpp: In member function ‘double PLMD::colvar::PairOrientationalEntropy::integrate(PLMD::Matrix , std::vector ) const’: PairOrientationalEntropy.nKsWGv.cpp:626:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 626 | for(unsigned i=1;i<(nhist_[0]-1);++i){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:627:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 627 | for(unsigned j=1;j<(nhist_[1]-1);++j){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:632:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 632 | for(unsigned i=1;i<(nhist_[0]-1);++i){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:636:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 636 | for(unsigned j=1;j<(nhist_[1]-1);++j){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp: In member function ‘PLMD::Vector PLMD::colvar::PairOrientationalEntropy::integrate(PLMD::Matrix<PLMD::VectorGeneric<3> >, std::vector ) const’: PairOrientationalEntropy.nKsWGv.cpp:653:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 653 | for(unsigned i=1;i<(nhist_[0]-1);++i){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:654:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 654 | for(unsigned j=1;j<(nhist_[1]-1);++j){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:659:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 659 | for(unsigned i=1;i<(nhist_[0]-1);++i){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:663:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 663 | for(unsigned j=1;j<(nhist_[1]-1);++j){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp: In member function ‘PLMD::Tensor PLMD::colvar::PairOrientationalEntropy::integrate(PLMD::Matrix<PLMD::TensorGeneric<3, 3> >, std::vector ) const’: PairOrientationalEntropy.nKsWGv.cpp:680:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 680 | for(unsigned i=1;i<(nhist_[0]-1);++i){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:681:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 681 | for(unsigned j=1;j<(nhist_[1]-1);++j){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:686:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 686 | for(unsigned i=1;i<(nhist_[0]-1);++i){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp:690:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 690 | for(unsigned j=1;j<(nhist_[1]-1);++j){ | ~^~~~~~~~~~~~~~ PairOrientationalEntropy.nKsWGv.cpp: In member function ‘void PLMD::colvar::PairOrientationalEntropy::outputGofr(PLMD::Matrix , const char*)’: PairOrientationalEntropy.nKsWGv.cpp:705:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 705 | for(unsigned i=0;i<nhist_[0];++i){ PairOrientationalEntropy.nKsWGv.cpp:706:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 706 | for(unsigned j=0;j<nhist_[1];++j){ WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">> In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tools.h:27, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:28, 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 ManyAnglePlus.at8WeS.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tensor.h:98: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 98 | #pragma acc enter data copyin(this[0:1], d, d[0:n*m-1]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tensor.h:102: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 102 | #pragma acc exit data delete( d[0:n*m-1], d, this[0:1]) | In file included from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:27: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:94: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 94 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:100: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 100 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:102: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 102 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:108: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 108 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:112: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 112 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:116: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 116 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:120: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 120 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:123: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 123 | #pragma acc routine seq | In file included from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:27: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:100: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 100 | #pragma acc enter data copyin(this[0:1],sz,data[0:sz]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:103: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 103 | #pragma acc exit data delete(data[0:sz],sz,this[0:1]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:117: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 117 | #pragma acc enter data copyin(this[0:1]) | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Matrix.h:123: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 123 | #pragma acc exit data delete( this[0:1]) | In file included from ManyAnglePlus.at8WeS.cpp:26: /home/runner/opt/include/plumed_master/tools/Angle.h:43: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 43 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/tools/Angle.h:46: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 46 | #pragma acc routine seq | ManyAnglePlus.at8WeS.cpp: In static member function ‘static void PLMD::colvar::ManyAngle::registerKeywords(PLMD::Keywords&)’: ManyAnglePlus.at8WeS.cpp:95:26: 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] 95 | keys.addOutputComponent("mean","default","Return the 1st moment of angle variable"); //(Z) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:27: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:268:8: note: declared here 268 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr ); | ^~~~~~~~~~~~~~~~~~ ManyAnglePlus.at8WeS.cpp:96:26: 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] 96 | keys.addOutputComponent("moment2","default","Return the 2nd moment of angle variable"); //(Z) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:268:8: note: declared here 268 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr ); | ^~~~~~~~~~~~~~~~~~ ManyAnglePlus.at8WeS.cpp: In constructor ‘PLMD::colvar::ManyAngle::ManyAngle(const PLMD::ActionOptions&)’: ManyAnglePlus.at8WeS.cpp:67:27: warning: ‘PLMD::colvar::ManyAngle::moment2’ will be initialized after [-Wreorder] 67 | bool pbc, serial, mean, moment2; | ^~~~~~~ ManyAnglePlus.at8WeS.cpp:67:13: warning: ‘bool PLMD::colvar::ManyAngle::serial’ [-Wreorder] 67 | bool pbc, serial, mean, moment2; | ^~~~~~ ManyAnglePlus.at8WeS.cpp:99:1: warning: when initialized here [-Wreorder] 99 | ManyAngle::ManyAngle(const ActionOptions&ao): | ^~~~~~~~~ ManyAnglePlus.at8WeS.cpp:123:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 123 | if(mean) addComponentWithDerivatives("mean"); componentIsNotPeriodic("mean"); moments[0]=getPntrToComponent("mean"); // (Z) | ^~ ManyAnglePlus.at8WeS.cpp:123:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 123 | if(mean) addComponentWithDerivatives("mean"); componentIsNotPeriodic("mean"); moments[0]=getPntrToComponent("mean"); // (Z) | ^~~~~~~~~~~~~~~~~~~~~~ ManyAnglePlus.at8WeS.cpp:124:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 124 | if(moment2) addComponentWithDerivatives("moment2"); componentIsNotPeriodic("moment2"); moments[1]=getPntrToComponent("moment2"); // (Z) | ^~ ManyAnglePlus.at8WeS.cpp:124:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 124 | if(moment2) addComponentWithDerivatives("moment2"); componentIsNotPeriodic("moment2"); moments[1]=getPntrToComponent("moment2"); // (Z) | ^~~~~~~~~~~~~~~~~~~~~~ </pre>