After the spatially-averaged velocity field has been subtracted from each atom, the temperature is calculated by the formula KE = dim/2 N k @@ -106,8 +107,8 @@ needed, the subtracted degrees-of-freedom can be altered using the
See this howto section of the manual for a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a -thermostatting fix will effectively implement a PUT, as described in -(Evans). +thermostatting fix, as explained there, will effectively implement a +profile-unbiased thermostat (PUT), as described in (Evans).
Output info:
diff --git a/doc/compute_temp_profile.txt b/doc/compute_temp_profile.txt index dc7a530588..e1dd975198 100644 --- a/doc/compute_temp_profile.txt +++ b/doc/compute_temp_profile.txt @@ -60,7 +60,8 @@ When a temperature is computed, the velocity for the set of atoms that are both in the compute group and in the same spatial bin is summed to compute an average velocity for the bin. This bias velocity is then subtracted from the velocities of individual atoms in the bin to yield -a thermal velocity. +a thermal velocity for each atom. Note that if there is only one +atom in the bin, it's thermal velocity will thus be 0.0. After the spatially-averaged velocity field has been subtracted from each atom, the temperature is calculated by the formula KE = dim/2 N k @@ -98,8 +99,8 @@ needed, the subtracted degrees-of-freedom can be altered using the See "this howto section"_Section_howto.html#4_16 of the manual for a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a -thermostatting fix will effectively implement a PUT, as described in -"(Evans)"_#Evans. +thermostatting fix, as explained there, will effectively implement a +profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans. [Output info:] diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html index a59e2e4e0c..b0b128a62d 100644 --- a/doc/neigh_modify.html +++ b/doc/neigh_modify.html @@ -133,6 +133,17 @@ could potentially overflow the list. This threshold is set by the one value which tells LAMMPS the maximum number of neighbor's one atom can have. +IMPORTANT NOTE: LAMMPS can crash without an error message if the +number of neighbors for a single particle is larger than the page +setting, which means it is much, much larger than the one setting. +This is because LAMMPS doesn't error check these limits for every +pairwise interaction (too costly), but only after all the particle's +neighbors have been found. This problem usually means something is +very wrong with the way you've setup your problem (particle spacing, +cutoff length, neighbor skin distance, etc). If you really expect +that many neighbors per particle, then boost the one and page +settings accordingly. +
The binsize option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for neighbor style bin, LAMMPS uses bins diff --git a/doc/neigh_modify.txt b/doc/neigh_modify.txt index 3fff0f65c4..51282b20fc 100644 --- a/doc/neigh_modify.txt +++ b/doc/neigh_modify.txt @@ -128,6 +128,17 @@ could potentially overflow the list. This threshold is set by the {one} value which tells LAMMPS the maximum number of neighbor's one atom can have. +IMPORTANT NOTE: LAMMPS can crash without an error message if the +number of neighbors for a single particle is larger than the {page} +setting, which means it is much, much larger than the {one} setting. +This is because LAMMPS doesn't error check these limits for every +pairwise interaction (too costly), but only after all the particle's +neighbors have been found. This problem usually means something is +very wrong with the way you've setup your problem (particle spacing, +cutoff length, neighbor skin distance, etc). If you really expect +that many neighbors per particle, then boost the {one} and {page} +settings accordingly. + The {binsize} option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins