From e550f5120b3aff11ae376c601d921bd908743479 Mon Sep 17 00:00:00 2001
From: PabloPiaggi <ppiaggi@gmail.com>
Date: Tue, 22 May 2018 12:44:40 +0200
Subject: [PATCH] Updated docs
---
doc/src/compute_pair_entropy_atom.txt | 50 ++++++++++---------
.../{start.lmp => in.pairentropy} | 0
2 files changed, 26 insertions(+), 24 deletions(-)
rename examples/USER/misc/pair_entropy/{start.lmp => in.pairentropy} (100%)
diff --git a/doc/src/compute_pair_entropy_atom.txt b/doc/src/compute_pair_entropy_atom.txt
index 9a2dbb8f14..b9d63c8bc9 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
--
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