From f3b3c34f045463645d94b806a61a7a18a3869c2c Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 4 Dec 2008 16:15:03 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2282
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/delete_atoms.html | 17 ++++++++++++++---
 doc/delete_atoms.txt  | 17 ++++++++++++++---
 doc/fix_langevin.html |  2 +-
 doc/fix_langevin.txt  |  2 +-
 4 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/doc/delete_atoms.html b/doc/delete_atoms.html
index 1658779cd2..8e5fce55f0 100644
--- a/doc/delete_atoms.html
+++ b/doc/delete_atoms.html
@@ -15,7 +15,7 @@
 </P>
 <PRE>delete_atoms style args 
 </PRE>
-<UL><LI>style = <I>group</I> or <I>region</I> or <I>overlap</I> 
+<UL><LI>style = <I>group</I> or <I>region</I> or <I>overlap</I> or <I>porosity</I> 
 
 <PRE>  <I>group</I> args = group-ID
   <I>region</I> args = region-ID
@@ -23,7 +23,10 @@
     cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
     group1-ID = one atom in pair must be in this group
     group2-ID = other atom in pair must be in this group
-
+  <I>porosity</I> args = region-ID fraction seed
+    region-ID = region within which to perform deletions
+    fraction = delete this fraction of atoms
+    seed = random number seed (positive integer) 
 </PRE>
 
 </UL>
@@ -32,7 +35,8 @@
 <PRE>delete_atoms group edge
 delete_atoms region sphere
 delete_atoms overlap 0.3 all all
-delete_atoms overlap 0.5 solvent colloid 
+delete_atoms overlap 0.5 solvent colloid
+delete_atoms porosity cube 0.1 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -61,6 +65,13 @@ have occurred that no atom pairs within the cutoff will remain
 minimum number of atoms will be deleted, or that the same atoms will
 be deleted when running on different numbers of processors.
 </P>
+<P>For style <I>porosity</I> a specified <I>fraction</I> of atoms are deleted
+within the specified region.  For example, if fraction is 0.1, then
+10% of the atoms will be deleted.  The atoms to delete are chosen
+randomly.  There is no guarantee that the exact fraction of atoms will
+be deleted, or that the same atoms will be deleted when running on
+different numbers of processors.
+</P>
 <P>After atoms are deleted, if the system is not molecular (no bonds),
 then atom IDs are re-assigned so that they run from 1 to the number of
 atoms in the system.  This is not done for molecular systems, since it
diff --git a/doc/delete_atoms.txt b/doc/delete_atoms.txt
index add63b0b3a..ee99483af8 100644
--- a/doc/delete_atoms.txt
+++ b/doc/delete_atoms.txt
@@ -12,14 +12,17 @@ delete_atoms command :h3
 
 delete_atoms style args :pre
 
-style = {group} or {region} or {overlap} :ulb,l
+style = {group} or {region} or {overlap} or {porosity} :ulb,l
   {group} args = group-ID
   {region} args = region-ID
   {overlap} args = cutoff group1-ID group2-ID
     cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
     group1-ID = one atom in pair must be in this group
     group2-ID = other atom in pair must be in this group
-:pre
+  {porosity} args = region-ID fraction seed
+    region-ID = region within which to perform deletions
+    fraction = delete this fraction of atoms
+    seed = random number seed (positive integer) :pre
 :ule
 
 [Examples:]
@@ -27,7 +30,8 @@ style = {group} or {region} or {overlap} :ulb,l
 delete_atoms group edge
 delete_atoms region sphere
 delete_atoms overlap 0.3 all all
-delete_atoms overlap 0.5 solvent colloid :pre
+delete_atoms overlap 0.5 solvent colloid
+delete_atoms porosity cube 0.1 :pre
 
 [Description:]
 
@@ -56,6 +60,13 @@ have occurred that no atom pairs within the cutoff will remain
 minimum number of atoms will be deleted, or that the same atoms will
 be deleted when running on different numbers of processors.
 
+For style {porosity} a specified {fraction} of atoms are deleted
+within the specified region.  For example, if fraction is 0.1, then
+10% of the atoms will be deleted.  The atoms to delete are chosen
+randomly.  There is no guarantee that the exact fraction of atoms will
+be deleted, or that the same atoms will be deleted when running on
+different numbers of processors.
+
 After atoms are deleted, if the system is not molecular (no bonds),
 then atom IDs are re-assigned so that they run from 1 to the number of
 atoms in the system.  This is not done for molecular systems, since it
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index 16ac1bf03b..9e3e9e1fe1 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -23,7 +23,7 @@
 
 <LI>damp = damping parameter (time units) 
 
-<LI>seed = random # seed to use for white noise (positive integer) 
+<LI>seed = random number seed to use for white noise (positive integer) 
 
 <LI>zero or more keyword/value pairs may be appended 
 
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index 9c24106436..c6ddea6540 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -16,7 +16,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
 langevin = style name of this fix command :l
 Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
 damp = damping parameter (time units) :l
-seed = random # seed to use for white noise (positive integer) :l
+seed = random number seed to use for white noise (positive integer) :l
 
 zero or more keyword/value pairs may be appended :l
 keyword = {scale}