diff --git a/doc/src/compute_pair_entropy_atom.txt b/doc/src/compute_pair_entropy_atom.txt index 9a2dbb8f1408bff15545ff4e4acd60075a7e8ac6..b9d63c8bc9832d4a593fa1b5f174a068a5ee5443 100644 --- a/doc/src/compute_pair_entropy_atom.txt +++ b/doc/src/compute_pair_entropy_atom.txt @@ -10,25 +10,26 @@ compute pentropy/atom command :h3 [Syntax:] -compute ID group-ID pentropy/atom sigma cutoff :l -compute ID group-ID pentropy/atom sigma cutoff avg yes/no cutoff2 ... :pre +compute ID group-ID pentropy/atom sigma cutoff keyword value ... :pre ID, group-ID are documented in "compute"_compute.html command :l pentropy/atom = style name of this compute command :l sigma = width of gaussians used in the g(r) smoothening :l cutoff = cutoff for the g(r) calculation :l one or more keyword/value pairs may be appended :l -{avg} yes/no cutoff2 - avg = {no} or {yes} - {no} = do not average the pair entropy over neighbors +keyword = {avg} or {local} + {avg} values = {yes} or {no} cutoff2 {yes} = average the pair entropy over neighbors - cutoff2 = cutoff for the averaging over neighbors :pre + {no} = do not average the pair entropy over neighbors + cutoff2 = cutoff for the averaging over neighbors + {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre :ule [Examples:] -compute 1 all pentropy/atom 0.25 5. :pre -compute 1 all pentropy/atom 0.25 5. avg yes 5. :pre +compute 1 all pentropy/atom 0.25 5. +compute 1 all pentropy/atom 0.25 5. avg yes 5. +compute 1 all pentropy/atom 0.125 7.3 avg yes 5.1 local yes :pre [Description:] @@ -77,11 +78,21 @@ neighbor skin bin :pre See "neighbor"_neighbor.html for details. -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -{centro/atom} style. +If the {local yes} option is used, the g(r) is normalized by the +local density around each atom, that is to say the density around each +atom is the number of neighbors within the neighbor list cutoff divided +by the corresponding volume. This option can be useful when dealing with +inhomogeneus systems such as those that have surfaces. + +Here are typical input parameters for fcc aluminum (lattice + constant 4.05 Angstroms), + +compute 1 all pentropy/atom 0.25 5.7 avg yes 3.7 :pre + +and for bcc sodium (lattice constant 4.23 Angstroms), + +compute 1 all pentropy/atom 0.25 7.3 avg yes 5.1 :pre + [Output info:] @@ -95,15 +106,6 @@ The pair entropy values have units of the Boltzmann constant. They are always negative, and lower values (lower entropy) correspond to more ordered environments. -Here are typical input parameters for fcc aluminum (lattice - constant 4.05 Angstroms), - -compute 1 all pentropy/atom 0.25 5.7 avg yes 3.7 :pre - -and for bcc sodium (lattice constant 4.23 Angstroms), - -compute 1 all pentropy/atom 0.25 7.3 avg yes 5.1 :pre - [Restrictions:] none [Related commands:] @@ -113,12 +115,12 @@ compute 1 all pentropy/atom 0.25 7.3 avg yes 5.1 :pre [Default:] -The default value for the optional keyword is avg = no. +The default values for the optional keywords are avg = no and local = no. :line :link(Piaggi) [(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017). -:link(Nettleton} +:link(Nettleton) [(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958). diff --git a/examples/USER/misc/pair_entropy/start.lmp b/examples/USER/misc/pair_entropy/in.pairentropy similarity index 100% rename from examples/USER/misc/pair_entropy/start.lmp rename to examples/USER/misc/pair_entropy/in.pairentropy