[liggghts] 01/04: Merge.

Anton Gladky gladk at moszumanska.debian.org
Sat Jan 16 23:59:38 UTC 2016


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gladk pushed a commit to branch master
in repository liggghts.

commit 8d004a60715a1cd61300b826a71a2d8c7b211cc5
Merge: 0592532 3697863
Author: Anton Gladky <gladk at debian.org>
Date:   Sun Jan 17 00:49:22 2016 +0100

    Merge.

 README                                             |   27 +-
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 doc/Manual.txt                                     |    2 +-
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 doc/atom_style.html                                |    5 +
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 doc/change_box.html                                |    2 +-
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 doc/compute_ke_multisphere.html                    |   59 +
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 doc/compute_pair_gran_local.html                   |   28 +-
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 doc/compute_pe.html                                |    5 +-
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 doc/compute_pe_atom.html                           |    3 +
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 doc/compute_reduce.html                            |    2 +-
 doc/compute_reduce.txt                             |    2 +-
 doc/compute_rigid.html                             |    5 +-
 doc/compute_rigid.txt                              |    5 +-
 doc/create_atoms.html                              |   13 +-
 doc/create_atoms.txt                               |   13 +-
 doc/dump.html                                      |    7 +-
 doc/dump.txt                                       |    7 +-
 doc/dump_custom_vtk.html                           |   21 +-
 doc/dump_custom_vtk.txt                            |   21 +-
 doc/fix_ave_spatial.html                           |    2 +-
 doc/fix_ave_spatial.txt                            |    2 +-
 doc/fix_buoyancy.html                              |   95 +
 doc/fix_buoyancy.txt                               |   85 +
 doc/fix_deform.html                                |    2 +-
 doc/fix_deform.txt                                 |    2 +-
 doc/fix_dt_reset.html                              |    2 +-
 doc/fix_dt_reset.txt                               |    2 +-
 doc/fix_heat_gran_conduction.html                  |   13 +-
 doc/fix_heat_gran_conduction.txt                   |   12 +-
 doc/fix_insert_pack.html                           |    6 +-
 doc/fix_insert_pack.txt                            |    6 +-
 doc/fix_insert_stream.html                         |    5 +-
 doc/fix_insert_stream.txt                          |    2 +-
 doc/fix_mesh_surface.html                          |   96 +-
 doc/fix_mesh_surface.txt                           |   86 +-
 doc/fix_mesh_surface_stress.html                   |    4 +-
 doc/fix_mesh_surface_stress.txt                    |    4 +-
 doc/fix_move.html                                  |    2 +-
 doc/fix_move.txt                                   |    2 +-
 doc/fix_move_mesh.html                             |   14 +-
 doc/fix_move_mesh.txt                              |   14 +-
 doc/fix_multisphere.html                           |  101 ++
 doc/fix_multisphere.txt                            |   98 ++
 doc/fix_particledistribution_discrete.html         |   48 +-
 doc/fix_particledistribution_discrete.txt          |   48 +-
 doc/fix_particletemplate_multisphere.html          |  148 ++
 doc/fix_particletemplate_multisphere.txt           |  127 ++
 doc/fix_particletemplate_sphere.html               |   36 +-
 doc/fix_particletemplate_sphere.txt                |   35 +-
 doc/fix_poems.html                                 |    2 +-
 doc/fix_poems.txt                                  |    2 +-
 doc/fix_wall_gran.html                             |    6 +
 doc/fix_wall_gran.txt                              |    6 +
 doc/fix_wall_reflect.html                          |    4 +-
 doc/fix_wall_reflect.txt                           |    4 +-
 doc/gran_cohesion_easo_capillary_viscous.html      |  162 ++
 doc/gran_cohesion_easo_capillary_viscous.txt       |  155 ++
 doc/gran_cohesion_sjkr.html                        |    4 +-
 doc/gran_cohesion_sjkr.txt                         |    4 +-
 doc/gran_cohesion_sjkr2.html                       |    4 +-
 doc/gran_cohesion_sjkr2.txt                        |    4 +-
 doc/gran_cohesion_washino_capillary_viscous.html   |  154 ++
 doc/gran_cohesion_washino_capillary_viscous.txt    |  148 ++
 doc/gran_model_hertz.html                          |   22 +-
 doc/gran_model_hertz.txt                           |   22 +-
 doc/gran_model_hertz_stiffness.html                |   25 +-
 doc/gran_model_hertz_stiffness.txt                 |   26 +-
 doc/gran_model_hooke.html                          |   28 +-
 doc/gran_model_hooke.txt                           |   28 +-
 doc/gran_model_hooke_stiffness.html                |   16 +-
 doc/gran_model_hooke_stiffness.txt                 |   16 +-
 doc/gran_rolling_friction_epsd.html                |   10 +-
 doc/gran_rolling_friction_epsd.txt                 |   10 +-
 ..._epsd.html => gran_rolling_friction_epsd3.html} |   14 +-
 ...on_epsd.txt => gran_rolling_friction_epsd3.txt} |   15 +-
 doc/gran_surface_sphere.html                       |   29 +
 doc/gran_surface_sphere.txt                        |   24 +
 doc/gran_tangential_history.html                   |   32 +-
 doc/gran_tangential_history.txt                    |   29 +-
 doc/liggghts_2.X_tutorial.html                     |    2 +-
 doc/liggghts_2.X_tutorial.txt                      |    2 +-
 doc/pair_gran.html                                 |    2 +-
 doc/pair_gran.txt                                  |    2 +-
 doc/region.html                                    |    2 +-
 doc/region.txt                                     |    2 +-
 doc/set.html                                       |   45 +-
 doc/set.txt                                        |   45 +-
 doc/thermo_modify.html                             |    7 +-
 doc/thermo_modify.txt                              |    7 +-
 doc/variable.html                                  |    6 +-
 doc/variable.txt                                   |    6 +-
 doc/velocity.html                                  |   10 +-
 doc/velocity.txt                                   |   10 +-
 .../ParScale/heatTransferBed_paScal/cleanscript    |    1 +
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 .../heatTransferBed_paScal/pascal/0/radius.json    |    4 +-
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 .../data/stone1.multisphere                        |   50 +
 .../multisphere_stone_restitution/data/stone1.test |    2 +
 .../multisphere_stone_restitution/in.multisphere   |   65 +
 .../multisphere_stone_restitution/post/.gitignore  |    0
 .../multisphere_stone_restitution/postscript       |    7 +
 src/ASPHERE/fix_nve_asphere.cpp                    |   33 +-
 src/CMakeLists.txt                                 |  139 +-
 src/MAKE/Makefile.fedora_vtk_fpic                  |    2 +-
 ...ic_debug_vtk => Makefile.fedora_vtk_fpic_debug} |   17 +-
 src/MAKE/Makefile.ubuntuVTK                        |   18 +-
 src/MAKE/Makefile.ubuntuVTK6                       |   16 +-
 src/MAKE/Makefile.ubuntuVTK_debug                  |   22 +-
 src/MAKE/Makefile.ubuntuVTK_fpic                   |    7 +-
 ...buntuVTK_fpic => Makefile.ubuntuVTK_fpic_debug} |   20 +-
 ...le.ubuntuVTK_fpic => Makefile.ubuntu_15p10_vtk} |   17 +-
 ...ntuVTK_fpic => Makefile.ubuntu_15p10_vtk_debug} |   21 +-
 ...untuVTK_fpic => Makefile.ubuntu_15p10_vtk_fpic} |   13 +-
 src/Make.sh                                        |   23 +-
 src/PASCAL/Install.sh                              |    2 +-
 src/PASCAL/fix_pascal_couple.cpp                   |    2 +-
 src/POEMS/fix_poems.cpp                            | 1101 ++++++------
 src/POEMS/fix_poems.h                              |   99 +-
 src/RIGID/fix_rigid.cpp                            |    2 +-
 src/WINDOWS/GenerateHeaders.bat                    |   16 +
 src/WINDOWS/extra/dirent.h                         |  372 ++++
 src/WINDOWS/extra/erf.h                            |   20 +
 src/WINDOWS/extra/erf_namd.c                       |  345 ++++
 src/WINDOWS/extra/fftw2/FFTW2dll.dll               |  Bin 0 -> 263168 bytes
 src/WINDOWS/extra/fftw2/FFTW2dll.lib               |  Bin 0 -> 22998 bytes
 src/WINDOWS/extra/fftw2/FFTW2st.lib                |  Bin 0 -> 404572 bytes
 src/WINDOWS/extra/fftw2/RFFTW2dll.dll              |  Bin 0 -> 481792 bytes
 src/WINDOWS/extra/fftw2/RFFTW2dll.lib              |  Bin 0 -> 35830 bytes
 src/WINDOWS/extra/fftw2/RFFTW2st.lib               |  Bin 0 -> 337962 bytes
 src/WINDOWS/extra/fftw2/fftw.h                     |  421 +++++
 src/WINDOWS/extra/fftw2/x64/FFTW2dll.dll           |  Bin 0 -> 228864 bytes
 src/WINDOWS/extra/fftw2/x64/FFTW2dll.lib           |  Bin 0 -> 9588 bytes
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 src/WINDOWS/extra/inttypes.h                       |  305 ++++
 src/WINDOWS/extra/sleep.cpp                        |   10 +
 src/WINDOWS/extra/sleep.h                          |    1 +
 src/WINDOWS/extra/stdint.h                         |  247 +++
 src/WINDOWS/extra/sys/time.h                       |   28 +
 src/WINDOWS/extra/unistd.h                         |    4 +
 src/abstract_mesh.h                                |    6 +-
 src/associative_pointer_array.h                    |   12 +-
 src/associative_pointer_array_I.h                  |   37 +-
 src/atom.cpp                                       |   26 +-
 src/atom.h                                         |    2 +-
 src/atom_vec_sph.cpp                               |    3 +-
 src/atom_vec_sph.h                                 |    3 +-
 src/atom_vec_sphere.cpp                            |    2 +
 src/bounding_box.cpp                               |   32 +-
 src/bounding_box.h                                 |   32 +-
 src/cfd_datacoupling_mpi.cpp                       |    4 +-
 src/cfd_datacoupling_mpi.h                         |    8 +-
 src/{properties.h => cfd_datacoupling_simple.h}    |   32 +-
 src/cfd_regionmodel_none.cpp                       |    4 +-
 src/change_box.cpp                                 |    4 +-
 src/cleanAllNonSpherical.sh                        |    2 +
 src/cleanAllParScale.sh                            |    3 +
 src/cohesion_model_easo_capillary_viscous.h        |  471 +++++
 src/cohesion_model_sjkr.h                          |    8 +-
 src/cohesion_model_sjkr2.h                         |    8 +-
 src/cohesion_model_washino_capillary_viscous.h     |  491 ++++++
 src/comm.cpp                                       |    4 +
 src/comm_I.h                                       |    4 +-
 src/compute_cna_atom.cpp                           |    4 +-
 ...roperties.h => compute_erotate_multisphere.cpp} |   47 +-
 ...{properties.h => compute_erotate_multisphere.h} |   48 +-
 src/compute_group_group.cpp                        |    2 +-
 src/{properties.h => compute_ke_multisphere.cpp}   |   58 +-
 src/{properties.h => compute_ke_multisphere.h}     |   47 +-
 src/compute_pair_gran_local.cpp                    |  137 +-
 src/compute_pair_gran_local.h                      |   37 +-
 src/compute_rigid.cpp                              |  181 ++
 src/{debug_liggghts.h => compute_rigid.h}          |   46 +-
 src/compute_surface.cpp                            |    4 +-
 src/contact_interface.h                            |   20 +-
 src/contact_model_constants.h                      |    4 +-
 src/contact_models.cpp                             |    6 +-
 src/contact_models.h                               |  117 +-
 src/container.h                                    |    3 +-
 src/container_base.cpp                             |   39 +-
 src/container_base.h                               |   37 +-
 src/container_base_I.h                             |   13 +-
 src/create_atoms.cpp                               |   34 +-
 src/create_atoms.h                                 |    2 +
 src/custom_value_tracker.cpp                       |   21 +-
 src/custom_value_tracker.h                         |   21 +-
 src/custom_value_tracker_I.h                       |   75 +-
 src/debug_liggghts.h                               |    1 +
 src/displace_atoms.cpp                             |    4 +-
 src/domain_wedge_dummy.h                           |    3 +-
 src/dump_custom.cpp                                |    4 +-
 src/dump_custom_vtk.cpp                            |    4 +-
 src/dump_mesh_stl.cpp                              |   41 +-
 src/dump_mesh_stl.h                                |    3 +-
 src/dump_mesh_vtk.cpp                              |    1 +
 src/dump_movie.cpp                                 |    2 +-
 src/fix.cpp                                        |    7 +-
 src/fix.h                                          |    4 +-
 src/fix_ave_correlate.cpp                          |    2 +-
 src/fix_ave_euler.cpp                              |   23 +-
 src/fix_ave_histo.cpp                              |    2 +-
 src/fix_ave_spatial.cpp                            |    6 +-
 src/fix_ave_time.cpp                               |    2 +-
 src/fix_buoyancy.cpp                               |  327 ++++
 src/{fix_freeze.h => fix_buoyancy.h}               |   62 +-
 src/fix_cfd_coupling_convection_species.cpp        |  253 +++
 ...rce.h => fix_cfd_coupling_convection_species.h} |   52 +-
 src/fix_cfd_coupling_force.cpp                     |   93 +-
 src/fix_cfd_coupling_force.h                       |    7 +-
 src/fix_cfd_coupling_force_implicit.cpp            |   88 +-
 src/fix_cfd_coupling_force_implicit.h              |   10 +
 src/fix_check_timestep_gran.cpp                    |    4 +-
 src/fix_check_timestep_sph.cpp                     |    2 +-
 src/fix_contact_history.cpp                        |   14 +-
 src/fix_contact_history.h                          |   39 +-
 src/fix_deform.cpp                                 |    2 +-
 src/fix_dt_reset.cpp                               |    2 +-
 src/fix_dummy.h                                    |   78 -
 src/fix_freeze.cpp                                 |   14 +-
 src/fix_freeze.h                                   |    2 +
 src/fix_heat_gran.cpp                              |    6 +-
 src/fix_heat_gran_conduction.cpp                   |    4 +-
 src/fix_heat_gran_conduction.h                     |    2 +-
 src/fix_insert.cpp                                 |  149 +-
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 src/fix_insert_pack.cpp                            |   48 +-
 src/fix_insert_pack.h                              |    8 +-
 src/fix_insert_stream.cpp                          |   52 +-
 src/fix_insert_stream.h                            |   15 +-
 src/fix_massflow_mesh.cpp                          |   14 +-
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 src/fix_mesh.cpp                                   |  145 +-
 src/fix_mesh.h                                     |   17 +-
 src/fix_mesh_surface.cpp                           |   46 +-
 src/fix_mesh_surface.h                             |    3 +-
 src/fix_mesh_surface_stress.cpp                    |    4 +-
 src/fix_mesh_surface_stress_servo.cpp              |   13 +-
 src/fix_mesh_surface_stress_servo.h                |    3 +-
 src/fix_move.cpp                                   |    2 +-
 src/fix_move_mesh.cpp                              |    3 +-
 src/fix_move_mesh.h                                |    3 +-
 src/fix_multisphere.cpp                            | 1098 ++++++++++++
 src/fix_multisphere.h                              |  232 ++-
 src/fix_multisphere_comm_I.h                       |    1 +
 src/fix_neighlist_mesh.cpp                         |   25 +-
 src/fix_neighlist_mesh.h                           |    5 +-
 src/fix_nve_sphere.cpp                             |   34 +-
 src/fix_nve_sphere.h                               |    4 +
 src/fix_particledistribution_discrete.cpp          |   47 +-
 src/fix_particledistribution_discrete.h            |    7 +
 src/fix_print.cpp                                  |    2 +-
 src/fix_property_atom.cpp                          |    4 +-
 src/fix_property_atom.h                            |    8 +-
 src/fix_property_atom_tracer.cpp                   |    4 +
 src/fix_property_global.h                          |    8 +-
 src/fix_remove.h                                   |    1 +
 src/fix_rigid.cpp                                  |    2 +-
 src/fix_scalar_transport_equation.h                |    3 +
 src/fix_sph.cpp                                    |    2 +-
 src/fix_template_multiplespheres.cpp               |  564 ++++++
 ...ate_sphere.h => fix_template_multiplespheres.h} |  123 +-
 src/fix_template_multisphere.cpp                   |  656 +++++++
 ...sport_equation.h => fix_template_multisphere.h} |   96 +-
 src/fix_template_sphere.cpp                        |   37 +-
 src/fix_template_sphere.h                          |   13 +-
 src/fix_wall.cpp                                   |    2 +-
 src/fix_wall_gran.cpp                              |  132 +-
 src/fix_wall_gran.h                                |   10 +-
 src/fix_wall_gran_base.h                           |   34 +-
 src/general_container.h                            |   23 +-
 src/general_container_I.h                          |   62 +-
 src/global_properties.cpp                          |  136 +-
 src/global_properties.h                            |   16 +-
 src/granular_pair_style.cpp                        |    3 +-
 src/granular_pair_style.h                          |    5 +-
 src/granular_styles.cpp                            |    3 +-
 src/input.cpp                                      |   15 +-
 src/input_mesh_tet.cpp                             |    2 +-
 src/input_mesh_tri.cpp                             |   30 +-
 src/input_mesh_tri.h                               |    5 +-
 src/input_multisphere.cpp                          |  192 +++
 src/{superquadric.h => input_multisphere.h}        |   28 +-
 src/lammps.cpp                                     |   14 +-
 src/library_cfd_coupling.h                         |    4 +-
 src/lmpwindows.h                                   |   12 +-
 src/math_extra_liggghts.h                          |   51 +-
 src/memory.cpp                                     |    6 +-
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 src/modify.cpp                                     |   12 +-
 src/mpi_liggghts.h                                 |    4 +-
 src/multi_node_mesh.h                              |   12 +-
 src/multi_node_mesh_I.h                            |   10 +-
 src/multi_vector_container.h                       |    3 +-
 src/multisphere.cpp                                |  623 +++++++
 src/multisphere.h                                  |  236 +++
 src/{cfd_regionmodel_none.cpp => multisphere_I.h}  |  158 +-
 src/multisphere_parallel.h                         |    2 +-
 src/neigh_bond.cpp                                 |   16 +-
 src/neigh_gran.cpp                                 |    9 +-
 src/neighbor.cpp                                   |    1 +
 src/normal_model_hertz.h                           |   65 +-
 src/normal_model_hertz_stiffness.h                 |   45 +-
 src/normal_model_hooke.h                           |   65 +-
 src/normal_model_hooke_hysteresis.h                |   44 +-
 src/normal_model_hooke_stiffness.h                 |   43 +-
 src/os_specific.h                                  |    3 +-
 src/pair_gran.cpp                                  |    6 +-
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 src/pair_gran_base.h                               |   85 +-
 src/pair_gran_proxy.cpp                            |   10 +-
 src/pair_gran_proxy.h                              |   11 +-
 src/pair_hybrid.cpp                                |    3 +
 src/pair_sph.cpp                                   |    3 +-
 src/pair_sph.h                                     |    3 +-
 src/particleToInsert.cpp                           |   77 +-
 src/particleToInsert.h                             |   18 +-
 src/particleToInsert_multisphere.cpp               |  287 ++++
 ...conduction.h => particleToInsert_multisphere.h} |   64 +-
 src/primitive_wall.h                               |    3 +-
 src/primitive_wall_definitions.h                   |    3 +-
 src/properties.cpp                                 |  101 ++
 src/properties.h                                   |    6 +-
 src/property_registry.cpp                          |   16 +-
 src/property_registry.h                            |   14 +-
 src/read_data.cpp                                  |   10 +-
 src/read_restart.cpp                               |    4 +-
 src/reader.cpp                                     |    2 +-
 src/region.cpp                                     |   40 +-
 src/region.h                                       |    1 +
 src/region_mesh_tet.cpp                            |  528 +++++-
 src/region_mesh_tet.h                              |   40 +-
 src/region_neighbor_list.cpp                       |  519 ++++++
 src/region_neighbor_list.h                         |  174 ++
 src/region_wedge.cpp                               |    5 +-
 src/region_wedge.h                                 |    3 +-
 src/rolling_model_cdt.h                            |   27 +-
 src/rolling_model_epsd.h                           |  116 +-
 src/rolling_model_epsd2.h                          |   21 +-
 ...{rolling_model_epsd.h => rolling_model_epsd3.h} |   33 +-
 src/scalar_container.h                             |    3 +-
 src/set.cpp                                        |   49 +-
 src/settings.h                                     |    2 +-
 src/style_cohesion_model.h                         |    2 +
 src/style_compute.h                                |    3 +
 src/style_contact_model.h                          |  255 +++
 src/style_fix.h                                    |    5 +
 src/style_rolling_model.h                          |    1 +
 src/superquadric_flag.h                            |    5 +
 src/surface_mesh.h                                 |   25 +-
 src/surface_mesh_I.h                               |  210 ++-
 src/surface_model_default.h                        |   24 +-
 src/tangential_model_history.h                     |   98 +-
 src/tangential_model_no_history.h                  |   67 +-
 src/thermo.cpp                                     |   16 +-
 src/thermo.h                                       |    1 +
 src/tracking_mesh_I.h                              |    3 +-
 src/tri_mesh.h                                     |   30 +-
 src/tri_mesh_I.h                                   |    3 +-
 src/variable.cpp                                   |   17 +-
 src/vector_container.h                             |    7 +-
 src/vector_liggghts.h                              |   95 +-
 src/velocity.cpp                                   |  210 ++-
 src/velocity.h                                     |    3 +
 src/version_liggghts.h                             |    2 +-
 src/version_liggghts.txt                           |    2 +-
 src/write_data.cpp                                 |    2 +-
 src/write_restart.cpp                              |   14 +-
 439 files changed, 16375 insertions(+), 47830 deletions(-)

diff --cc src/container_base.cpp
index b3ca2b5,1b43ea7..89c2497
--- a/src/container_base.cpp
+++ b/src/container_base.cpp
@@@ -97,10 -83,10 +100,11 @@@ using namespace LAMMPS_NS
    : id_(0),
      communicationType_(COMM_TYPE_MANUAL),
      refFrame_(REF_FRAME_UNDEFINED),
 +>>>>>>> upstream/3.0.0
      restartType_(RESTART_TYPE_UNDEFINED),
      scalePower_(-1),
-     useDefault_(false)
+     useDefault_(false),
+     container_statistics_raw_data_(0)
    {
            setProperties(_id, _comm, _ref,_restart,_scalePower);
    }
diff --cc src/container_base.h
index 51d5b3d,bb10d52..45930bb
--- a/src/container_base.h
+++ b/src/container_base.h
@@@ -132,20 -143,16 +147,20 @@@ namespace LAMMPS_N
  
       protected:
  
 +<<<<<<< HEAD
 +          ContainerBase(char *_id, char* _comm, char* _ref, char *_restart,int _scalePower);
 +=======
            ContainerBase(const char *_id, const char* _comm, const char* _ref, const char *_restart,int _scalePower);
 +>>>>>>> upstream/3.0.0
            ContainerBase(ContainerBase const &orig);
  
-           inline bool isScaleInvariant();
-           inline bool isTranslationInvariant();
-           inline bool isRotationInvariant();
+           inline bool isScaleInvariant() const;
+           inline bool isTranslationInvariant() const;
+           inline bool isRotationInvariant() const;
  
-           inline bool decidePackUnpackOperation(int operation,bool scale,bool translate, bool rotate);
+           inline bool decidePackUnpackOperation(int operation,bool scale,bool translate, bool rotate) const;
  
-           inline bool decideCommOperation(int operation);
+           inline bool decideCommOperation(int operation) const;
  
            inline bool decideCreateNewElements(int operation);
  
diff --cc src/read_data.cpp
index 8d8318c,64bc34d..696beb0
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@@ -640,17 -636,10 +640,17 @@@ void ReadData::header(int flag, int add
    parse_keyword(1,flag);
    for (n = 0; n < NSECTIONS; n++)
      if (strcmp(keyword,section_keywords[n]) == 0) break;
 +<<<<<<< HEAD
 +  if (n == NSECTIONS && me == 0) {	//- new from patch 17May2012
 +    char str[128];
 +    sprintf(str,"Unknown identifier in data file: %s",keyword);
 +    error->one(FLERR,str);	//- new from patch 17May2012
 +=======
    if (n == NSECTIONS && me == 0) {
-     char str[128];
+     char str[512];
      sprintf(str,"Unknown identifier in data file: %s",keyword);
      error->one(FLERR,str);
 +>>>>>>> upstream/3.0.0
    }
  
    // error check on consistency of header values

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/liggghts.git



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