From b7238e42e1947bbc6bf74af5545c04ddadac3cf7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 27 Aug 2009 18:51:09 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3122 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_nvt.html | 44 ++++++++++++++++++++++++++++++----------- doc/fix_nvt.txt | 43 +++++++++++++++++++++++++++++----------- doc/minimize.html | 2 +- doc/minimize.txt | 2 +- doc/reset_timestep.html | 4 ++-- doc/reset_timestep.txt | 4 ++-- 6 files changed, 69 insertions(+), 30 deletions(-) diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index 886eca926d..074842546e 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -25,16 +25,17 @@
  • zero or more keyword/value pairs may be appended -
  • keyword = drag +
  • keyword = drag or chain -
      drag value = drag factor added to thermostat (0.0 = no drag) 
+
      drag value = drag factor added to thermostat (0.0 = no drag)
+  chain value = yes or no 
 
    
 
 
 
    Examples:
 
    
 
    fix 1 all nvt 300.0 300.0 100.0
-fix 1 all nvt 300.0 300.0 100.0 drag 0.2 
+fix 1 all nvt 300.0 300.0 100.0 drag 0.2 chain no 
 
    
 
    Description:
 
    
@@ -55,15 +56,29 @@ example, a value of 100.0 means to relax the temperature in a timespan
 of (roughly) 100 time units (tau or fmsec or psec - see the
 units command).
 
    
+
    The chain keyword determines whether Nose/Hoover chains are used or
+not.  If chain is specified as no, then the original Nose/Hoover
+formulation is used.  If chain is specified as yes, which is the
+default, then chains as described in (Martyna) are used
+which include extra non-physical variables which couple to the
+thermostat.  Nose/Hoover chains provide a more robust NVT integrator,
+overcoming non-ergodic sampling issues and energy oscillations found
+with ordinary Nose/Hoover dynamics.  Our implementation uses one chain
+and integrates the equations of motion via a Trotter expansion good to
+2nd order accuracy in the timestep size.
+
    
 
    In some cases (e.g. for solids) the temperature of the system can
-oscillate undesirably when a Nose/Hoover thermostat is applied.  The
-optional drag keyword will damp these oscillations, although it
-alters the Nose/Hoover equations.  A value of 0.0 (no drag) leaves the
-Nose/Hoover formalism unchanged.  A non-zero value adds a drag term;
-the larger the value specified, the greater the damping effect.
-Performing a short run and monitoring the temperature is the best way
-to determine if the drag term is working.  Typically a value between
-0.2 to 2.0 is sufficient to damp oscillations after a few periods.
+oscillate undesirably when a Nose/Hoover thermostat is applied, though
+this should be less of a problem if Nose/Hoover chains are used.  The
+optional drag keyword will damp these oscillations in an ad-hoc
+fashion, by altering the Nose/Hoover equations so that they no longer
+exactly sample the canonical ensemble.  A value of 0.0 (no drag)
+leaves the Nose/Hoover formalism unchanged.  A non-zero value adds a
+drag term; the larger the value specified, the greater the damping
+effect.  Performing a short run and monitoring the temperature is the
+best way to determine if the drag term is working.  Typically a value
+between 0.2 to 2.0 is sufficient to damp oscillations after a few
+periods.
 
    
 
    IMPORTANT NOTE: Unlike the fix temp/berendsen
 command which performs thermostatting but NO time integration, this
@@ -159,7 +174,7 @@ temp/rescale, fix langevin,
 
    
 
    Default:
 
    
-
    The keyword defaults are drag = 0.0.
+
    The keyword defaults are drag = 0.0 and chain = yes.
 
    
 
    
 
@@ -167,4 +182,9 @@ temp/rescale, fix langevin,
 
 
    (Hoover) Hoover, Phys Rev A, 31, 1695 (1985).
 
    
+
+
+
    (Martyna) Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
+Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
+
    
 
diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt
index 01c2284078..55555a3169 100644
--- a/doc/fix_nvt.txt
+++ b/doc/fix_nvt.txt
@@ -18,14 +18,15 @@ Tstart,Tstop = desired temperature at start/end of run :l
 Tdamp = temperature damping parameter (time units) :l
 
 zero or more keyword/value pairs may be appended :l
-keyword = {drag} :l
-  {drag} value = drag factor added to thermostat (0.0 = no drag) :pre
+keyword = {drag} or {chain} :l
+  {drag} value = drag factor added to thermostat (0.0 = no drag)
+  {chain} value = {yes} or {no} :pre
 :ule
 
 [Examples:]
 
 fix 1 all nvt 300.0 300.0 100.0
-fix 1 all nvt 300.0 300.0 100.0 drag 0.2 :pre
+fix 1 all nvt 300.0 300.0 100.0 drag 0.2 chain no :pre
 
 [Description:]
 
@@ -46,15 +47,29 @@ example, a value of 100.0 means to relax the temperature in a timespan
 of (roughly) 100 time units (tau or fmsec or psec - see the
 "units"_units.html command).
 
+The {chain} keyword determines whether Nose/Hoover chains are used or
+not.  If {chain} is specified as {no}, then the original Nose/Hoover
+formulation is used.  If {chain} is specified as {yes}, which is the
+default, then chains as described in "(Martyna)"_#Martyna are used
+which include extra non-physical variables which couple to the
+thermostat.  Nose/Hoover chains provide a more robust NVT integrator,
+overcoming non-ergodic sampling issues and energy oscillations found
+with ordinary Nose/Hoover dynamics.  Our implementation uses one chain
+and integrates the equations of motion via a Trotter expansion good to
+2nd order accuracy in the timestep size.
+
 In some cases (e.g. for solids) the temperature of the system can
-oscillate undesirably when a Nose/Hoover thermostat is applied.  The
-optional {drag} keyword will damp these oscillations, although it
-alters the Nose/Hoover equations.  A value of 0.0 (no drag) leaves the
-Nose/Hoover formalism unchanged.  A non-zero value adds a drag term;
-the larger the value specified, the greater the damping effect.
-Performing a short run and monitoring the temperature is the best way
-to determine if the drag term is working.  Typically a value between
-0.2 to 2.0 is sufficient to damp oscillations after a few periods.
+oscillate undesirably when a Nose/Hoover thermostat is applied, though
+this should be less of a problem if Nose/Hoover chains are used.  The
+optional {drag} keyword will damp these oscillations in an ad-hoc
+fashion, by altering the Nose/Hoover equations so that they no longer
+exactly sample the canonical ensemble.  A value of 0.0 (no drag)
+leaves the Nose/Hoover formalism unchanged.  A non-zero value adds a
+drag term; the larger the value specified, the greater the damping
+effect.  Performing a short run and monitoring the temperature is the
+best way to determine if the drag term is working.  Typically a value
+between 0.2 to 2.0 is sufficient to damp oscillations after a few
+periods.
 
 IMPORTANT NOTE: Unlike the "fix temp/berendsen"_fix_berendsen.html
 command which performs thermostatting but NO time integration, this
@@ -150,9 +165,13 @@ temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,
 
 [Default:]
 
-The keyword defaults are drag = 0.0.
+The keyword defaults are drag = 0.0 and chain = yes.
 
 :line
 
 :link(Hoover)
 [(Hoover)] Hoover, Phys Rev A, 31, 1695 (1985).
+
+:link(Martyna)
+[(Martyna)] Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
+Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
diff --git a/doc/minimize.html b/doc/minimize.html
index cead66fa87..b6a19b21f1 100644
--- a/doc/minimize.html
+++ b/doc/minimize.html
@@ -18,7 +18,7 @@
 
    • etol = stopping tolerance for energy (unitless)
 
    • ftol = stopping tolerance for force (force units)
 
    • maxiter = max iterations of minimizer
-
    • maxeval = max number of total force/energy evaluations 
+
    • maxeval = max number of force/energy evaluations 
 
    
 
    Examples:
 
    
diff --git a/doc/minimize.txt b/doc/minimize.txt
index 6633083b09..5939cbf56b 100644
--- a/doc/minimize.txt
+++ b/doc/minimize.txt
@@ -15,7 +15,7 @@ minimize etol ftol maxiter maxeval :pre
 etol = stopping tolerance for energy (unitless)
 ftol = stopping tolerance for force (force units)
 maxiter = max iterations of minimizer
-maxeval = max number of total force/energy evaluations :ul
+maxeval = max number of force/energy evaluations :ul
 
 [Examples:]
 
diff --git a/doc/reset_timestep.html b/doc/reset_timestep.html
index 0514441c53..5fae614f9a 100644
--- a/doc/reset_timestep.html
+++ b/doc/reset_timestep.html
@@ -45,8 +45,8 @@ write.  See the undump command or fix
 ave/spatial.  Also fix
 dt/reset and fix deposit.
diff --git a/doc/reset_timestep.txt b/doc/reset_timestep.txt
index f8eb41cb13..9953fd4c52 100644
--- a/doc/reset_timestep.txt
+++ b/doc/reset_timestep.txt
@@ -42,8 +42,8 @@ write.  See the "undump"_undump.html command or "restart
 if necessary.  New specifications for dump and restart files can be
 given after the reset_timestep command is used.
 
-This command cannot be used when any fixes are defined that keeps
-track of elapsed time to perform time-dependent operations.  Examples
+This command cannot be used when any fixes are defined that keep track
+of elapsed time to perform time-dependent operations.  Examples
 include the "ave" fixes such as "fix
 ave/spatial"_fix_ave_spatial.html.  Also "fix
 dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html.