Loading doc/src/compute_pair_entropy_atom.txt +26 −24 Original line number Diff line number Diff line Loading @@ -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:] Loading Loading @@ -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:] Loading @@ -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:] Loading @@ -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). examples/USER/misc/pair_entropy/start.lmp→examples/USER/misc/pair_entropy/in.pairentropy +0 −0 File moved. View file Loading
doc/src/compute_pair_entropy_atom.txt +26 −24 Original line number Diff line number Diff line Loading @@ -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:] Loading Loading @@ -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:] Loading @@ -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:] Loading @@ -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).
examples/USER/misc/pair_entropy/start.lmp→examples/USER/misc/pair_entropy/in.pairentropy +0 −0 File moved. View file
