From 15b6eeb0115fbb803c6c054124d29beee4ce58d9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Sat, 8 Aug 2009 22:59:06 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3033 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_langevin.html | 31 +++++++++++++++++++++++++------ doc/fix_langevin.txt | 32 +++++++++++++++++++++++++------- 2 files changed, 50 insertions(+), 13 deletions(-) diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index b52b1ca3a0..a165aa8d6a 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -27,10 +27,13 @@
  • zero or more keyword/value pairs may be appended -
    keyword = scale
+
    keyword = scale or tally
   scale values = type ratio
     type = atom type (1-N)
-    ratio = factor by which to scale the damping coefficient 
+    ratio = factor by which to scale the damping coefficient
+  tally values = no or yes
+    no = do not tally the energy added/subtracted to atoms
+    yes = do tally the energy added/subtracted to atoms 
 
    
 
 
@@ -139,6 +142,13 @@ particle mass in Ff, unlike fix viscous.  Thus the mass and size of
 different atom types should be accounted for in the choice of ratio
 values.
 
    
+
    The keyword tally enables the calculation of the cummulative energy
+added/subtracted to the atoms as they are thermostatted.  Effectively
+it is the energy exchanged between the infinite thermal reservoir and
+the particles.  As described below, this energy can then be printed
+out or added to the potential energy of the system to monitor energy
+conservation.
+
    
 
    Restart, fix_modify, output, run start/stop, minimize info:
 
    
 
    No information about this fix is written to binary restart
@@ -154,8 +164,18 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
    
-
    No global scalar or vector or per-atom quantities are stored by this
-fix for access by various output commands.
+
    The fix_modify energy option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of thermodynamic
+output.  Note that use of this option requires
+setting the tally keyword to yes.
+
    
+
    The cummulative energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various output
+commands.  The scalar value calculated by
+this fix is "extensive", meaning it scales with the number of atoms in
+the simulation.  Note that use of this option requires setting the
+tally keyword to yes.
 
    
 
    This fix can ramp its target temperature over multiple runs, using the
 start and stop keywords of the run command.  See the
@@ -172,8 +192,7 @@ viscous, fix nvt
 
    
 
    Default:
 
    
-
    The option defaults are axes = 1 1 1, scale = 1.0 for all types, no
-region, and weight = 1.0.
+
    The option defaults are scale = 1.0 for all types and tally = no.
 
    
 
    
 
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index b4a888592d..4ee610166a 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -17,12 +17,14 @@ 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 number seed to use for white noise (positive integer) :l
-
 zero or more keyword/value pairs may be appended :l
-keyword = {scale}
+keyword = {scale} or {tally}
   {scale} values = type ratio
     type = atom type (1-N)
-    ratio = factor by which to scale the damping coefficient :pre
+    ratio = factor by which to scale the damping coefficient
+  {tally} values = {no} or {yes}
+    {no} = do not tally the energy added/subtracted to atoms
+    {yes} = do tally the energy added/subtracted to atoms :pre
 :ule
 
 [Examples:]
@@ -130,6 +132,13 @@ particle mass in Ff, unlike fix {viscous}.  Thus the mass and size of
 different atom types should be accounted for in the choice of ratio
 values.
 
+The keyword {tally} enables the calculation of the cummulative energy
+added/subtracted to the atoms as they are thermostatted.  Effectively
+it is the energy exchanged between the infinite thermal reservoir and
+the particles.  As described below, this energy can then be printed
+out or added to the potential energy of the system to monitor energy
+conservation.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
@@ -145,8 +154,18 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-No global scalar or vector or per-atom quantities are stored by this
-fix for access by various "output commands"_Section_howto.html#4_15.
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.  Note that use of this option requires
+setting the {tally} keyword to {yes}.
+
+The cummulative energy change due to this fix is stored as a scalar
+quantity, which can be accessed by various "output
+commands"_Section_howto.html#4_15.  The scalar value calculated by
+this fix is "extensive", meaning it scales with the number of atoms in
+the simulation.  Note that use of this option requires setting the
+{tally} keyword to {yes}.
 
 This fix can ramp its target temperature over multiple runs, using the
 {start} and {stop} keywords of the "run"_run.html command.  See the
@@ -163,8 +182,7 @@ viscous"_fix_viscous.html, "fix nvt"_fix_nvt.html
 
 [Default:]
 
-The option defaults are axes = 1 1 1, scale = 1.0 for all types, no
-region, and weight = 1.0.
+The option defaults are scale = 1.0 for all types and tally = no.
 
 :line