Commit e00544c8 authored by Steve Plimpton's avatar Steve Plimpton
Browse files

Merge branch 'gridcomm-tiled' of github.com:lammps/lammps into gridcomm-tiled

parents ecec36cc d2a66cc9
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.gitattributes

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.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore

.github/codecov.yml

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comment: false
coverage:
  notify:
    slack:
      default:
        url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
        threshold: 10%
        only_pulls: false
        branches:
          - "master"
        flags:
          - "unit"
        paths:
          - "src"
  status:
    project:
        default:
            branches:
              - "master"
            paths:
              - "src"
            informational: true
    patch:
        default:
            branches:
              - "master"
            paths:
              - "src"
            informational: true
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@@ -23,14 +23,17 @@ if(ENABLE_TESTING)
        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
      include(CheckCXXCompilerFlag)
      set(CMAKE_CUSTOM_LINKER_DEFAULT default)
      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER)
      check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER)
      check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER)
      if(HAVE_LLD_LINKER)
      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
      check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
      check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
      find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
      find_program(HAVE_GOLD_LINKER_BIN ld.gold)
      find_program(HAVE_BFD_LINKER_BIN ld.bfd)
      if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
        set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
      elseif(HAVE_GOLD_LINKER)
      elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
        set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
      elseif(HAVE_BFD_LINKER)
      elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
        set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
      endif()
      set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
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@@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
   incorrect periodic images of atoms in interaction lists.  To avoid, either use
   :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.

*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*

   Since LAMMPS stores topology data with individual atoms, all atoms
   comprising a bond, angle, dihedral or improper must be present on any
   sub-domain that "owns" the atom with the information, either as a
   local or a ghost atom. The communication cutoff is what determines up
   to what distance from a sub-domain boundary ghost atoms are created.
   The communication cutoff is by default the largest non-bonded cutoff
   plus the neighbor skin distance, but for short or non-bonded cutoffs
   and/or long bonds, this may not be sufficient. This warning indicates
   that there is an increased risk of a simulation stopping unexpectedly
   because of Bond/Angle/Dihedral/Improper atoms missing.  It can be
   silenced by manually setting the communication cutoff via
   :doc:`comm_modify cutoff <comm_modify>`.  However, since the
   heuristic used to determine the estimate is not always accurate, it
   is not changed automatically and the warning may be ignored depending
   on the specific system being simulated.

*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
   Self-explanatory.

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@@ -77,7 +77,7 @@ The colloid-solvent interaction energy is given by
   \left[ 1 - \frac{\left(5 ~ a^6+45~a^4~r^2+63~a^2~r^4+15~r^6\right) \sigma^6}
   {15 \left(a-r\right)^6 \left( a+r \right)^6} \right], \quad r < r_c

where :math:A_{cs}` is the Hamaker constant, *a* is the radius of the colloidal
where :math:`A_{cs}` is the Hamaker constant, *a* is the radius of the colloidal
particle, and :math:`r_c` is the cutoff.  This formula is derived from the
colloid-colloid interaction, letting one of the particle sizes go to
zero.
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