Merge pull request lammps#4761 from akohlmey/collected-small-fixes

akohlmey · web-flow · commit c5998396f2cf · 2025-11-04T20:11:21.000-05:00
Collected small changes and fixes
diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml
@@ -19,7 +19,7 @@ jobs:
   build:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-13
+    runs-on: macos-15-intel
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst
@@ -24,6 +24,13 @@ started to create problems with modern C++ compilers.  LAMMPS version
 download and compile this version, if you want to use any of these
 packages.
 
+.. toctree::
+   :maxdepth: 0
+   :hidden:
+   :glob:
+
+   atc_*
+
 Neighbor style and comm mode multi/old
 --------------------------------------
 
diff --git a/doc/src/atc_add_molecule.rst b/doc/src/atc_add_molecule.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_add_species.rst b/doc/src/atc_add_species.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_atom_element_map.rst b/doc/src/atc_atom_element_map.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_atom_weight.rst b/doc/src/atc_atom_weight.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_atomic_charge.rst b/doc/src/atc_atomic_charge.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_boundary_dynamics.rst b/doc/src/atc_boundary_dynamics.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_boundary_faceset.rst b/doc/src/atc_boundary_faceset.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_boundary_type.rst b/doc/src/atc_boundary_type.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_consistent_fe_initialization.rst b/doc/src/atc_consistent_fe_initialization.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_control_localized_lambda.rst b/doc/src/atc_control_localized_lambda.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_control_momentum.rst b/doc/src/atc_control_momentum.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_control_thermal.rst b/doc/src/atc_control_thermal.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_decomposition.rst b/doc/src/atc_decomposition.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_electron_integration.rst b/doc/src/atc_electron_integration.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_equilibrium_start.rst b/doc/src/atc_equilibrium_start.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_extrinsic_exchange.rst b/doc/src/atc_extrinsic_exchange.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_fe_md_boundary.rst b/doc/src/atc_fe_md_boundary.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_filter_scale.rst b/doc/src/atc_filter_scale.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_filter_type.rst b/doc/src/atc_filter_type.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_fix.rst b/doc/src/atc_fix.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_fix_flux.rst b/doc/src/atc_fix_flux.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_hardy_computes.rst b/doc/src/atc_hardy_computes.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_hardy_fields.rst b/doc/src/atc_hardy_fields.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_hardy_gradients.rst b/doc/src/atc_hardy_gradients.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_hardy_kernel.rst b/doc/src/atc_hardy_kernel.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_hardy_on_the_fly.rst b/doc/src/atc_hardy_on_the_fly.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_hardy_rates.rst b/doc/src/atc_hardy_rates.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_initial.rst b/doc/src/atc_initial.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_internal_element_set.rst b/doc/src/atc_internal_element_set.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_internal_quadrature.rst b/doc/src/atc_internal_quadrature.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_kernel_bandwidth.rst b/doc/src/atc_kernel_bandwidth.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_lumped_lambda_solve.rst b/doc/src/atc_lumped_lambda_solve.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mask_direction.rst b/doc/src/atc_mask_direction.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mass_matrix.rst b/doc/src/atc_mass_matrix.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_material.rst b/doc/src/atc_material.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_add_to_nodeset.rst b/doc/src/atc_mesh_add_to_nodeset.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_create.rst b/doc/src/atc_mesh_create.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_create_elementset.rst b/doc/src/atc_mesh_create_elementset.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_create_faceset_box.rst b/doc/src/atc_mesh_create_faceset_box.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_create_faceset_plane.rst b/doc/src/atc_mesh_create_faceset_plane.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_create_nodeset.rst b/doc/src/atc_mesh_create_nodeset.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_delete_elements.rst b/doc/src/atc_mesh_delete_elements.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_nodeset_to_elementset.rst b/doc/src/atc_mesh_nodeset_to_elementset.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_output.rst b/doc/src/atc_mesh_output.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_quadrature.rst b/doc/src/atc_mesh_quadrature.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_read.rst b/doc/src/atc_mesh_read.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_mesh_write.rst b/doc/src/atc_mesh_write.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_output.rst b/doc/src/atc_output.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_output_boundary_integral.rst b/doc/src/atc_output_boundary_integral.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_output_contour_integral.rst b/doc/src/atc_output_contour_integral.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_output_nodeset.rst b/doc/src/atc_output_nodeset.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_output_volume_integral.rst b/doc/src/atc_output_volume_integral.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_pair_interactions.rst b/doc/src/atc_pair_interactions.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_poisson_solver.rst b/doc/src/atc_poisson_solver.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_read_restart.rst b/doc/src/atc_read_restart.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_remove_molecule.rst b/doc/src/atc_remove_molecule.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_remove_source.rst b/doc/src/atc_remove_source.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_remove_species.rst b/doc/src/atc_remove_species.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_reset_atomic_reference.rst b/doc/src/atc_reset_atomic_reference.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_reset_time.rst b/doc/src/atc_reset_time.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_sample_frequency.rst b/doc/src/atc_sample_frequency.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_set_reference_pe.rst b/doc/src/atc_set_reference_pe.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_source.rst b/doc/src/atc_source.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_source_integration.rst b/doc/src/atc_source_integration.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_temperature_definition.rst b/doc/src/atc_temperature_definition.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_time_filter.rst b/doc/src/atc_time_filter.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_time_integration.rst b/doc/src/atc_time_integration.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_track_displacement.rst b/doc/src/atc_track_displacement.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_unfix.rst b/doc/src/atc_unfix.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_unfix_flux.rst b/doc/src/atc_unfix_flux.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_write_atom_weights.rst b/doc/src/atc_write_atom_weights.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/atc_write_restart.rst b/doc/src/atc_write_restart.rst
@@ -0,0 +1 @@
+fix_atc.rst
diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst
@@ -0,0 +1,9 @@
+fix atc command
+===============
+
+.. meta::
+   :http-equiv=Refresh: 5; url=Commands_removed.html#atc-awpmd-and-poems-packages
+
+.. deprecated:: 10Sep2025
+
+The ATC package and the `fix atc` command have been removed from LAMMPS.
diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst
diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst
diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst
diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst
diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst
diff --git a/src/EXTRA-FIX/fix_smd.cpp b/src/EXTRA-FIX/fix_smd.cpp
diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
diff --git a/src/region_block.cpp b/src/region_block.cpp
diff --git a/src/region_cone.cpp b/src/region_cone.cpp
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
diff --git a/src/region_ellipsoid.cpp b/src/region_ellipsoid.cpp
diff --git a/src/region_prism.cpp b/src/region_prism.cpp
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
