diff --git a/doc/src/fix_ave_grid.rst b/doc/src/fix_ave_grid.rst index 5760bb4508..da0d1f957b 100644 --- a/doc/src/fix_ave_grid.rst +++ b/doc/src/fix_ave_grid.rst @@ -129,12 +129,12 @@ overlays the simulation box. For 2d simulations, *Nz* must be 1. The very coarse compared to the particle count, or very fine. If one or more of the values = 1, then bins are 2d planes or 1d slices of the simulation domain. Note that if the total number of grid cells is -small, it may be more efficient to use the doc:`fix ave/chunk +small, it may be more efficient to use the :doc:`fix ave/chunk ` command which can treat a grid defined by the :doc:`compute chunk/atom ` command as a global grid where each processor owns a copy of all the grid cells. If *Nx* = *Ny* = *Nz* = 1 is used, the same calculation would be more -efficiently performed by the doc:`fix ave/atom ` +efficiently performed by the :doc:`fix ave/atom ` command. If the simulation box size or shape changes during a simulation, the diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 67600af62d..a9d21bab9b 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -1441,7 +1441,7 @@ timestep that the variable needs the tallies. An input script can also request variables be evaluated before or after or in between runs, e.g. by including them in a :doc:`print ` command. -LAMMPS keeps track of all of this as it performs a doc:`run ` or +LAMMPS keeps track of all of this as it performs a :doc:`run ` or :doc:`minimize ` simulation, as well as in between simulations. An error will be generated if you attempt to evaluate a variable when LAMMPS knows it cannot produce accurate values. For @@ -1453,7 +1453,7 @@ command, then an error will occur. However, there are two special cases to be aware when a variable requires invocation of a compute (directly or indirectly). The first -is if the variable is evaluated before the first doc:`run ` or +is if the variable is evaluated before the first :doc:`run ` or :doc:`minimize ` command in the input script. In this case, LAMMPS will generate an error. This is because many computes require initializations which have not yet taken place. One example is the @@ -1463,10 +1463,10 @@ energy or virial quantities; these values are not tallied until the first simulation begins. The second special case is when a variable that depends on a compute -is evaluated in between doc:`run ` or :doc:`minimize ` +is evaluated in between :doc:`run ` or :doc:`minimize ` commands. It is possible for other input script commands issued following the previous run, but before the variable is evaluated, to -change the system. For example, the doc:`delete_atoms ` +change the system. For example, the :doc:`delete_atoms ` command could be used to remove atoms. Since the compute will not re-initialize itself until the next simulation or it may depend on energy/virial computations performed before the system was changed, it