From f6c92890f1cc1cfde524cba585d32e87e825f30d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 28 Nov 2011 17:25:54 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7234 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_python.html | 6 +++--- doc/Section_python.txt | 6 +++--- doc/fix_addforce.html | 4 ++-- doc/fix_addforce.txt | 2 +- doc/fix_aveforce.html | 4 ++-- doc/fix_aveforce.txt | 2 +- doc/fix_langevin.html | 21 ++++++++++++++++++++- doc/fix_langevin.txt | 20 +++++++++++++++++++- doc/pair_comb.html | 2 +- doc/pair_comb.txt | 2 +- 10 files changed, 53 insertions(+), 16 deletions(-) diff --git a/doc/Section_python.html b/doc/Section_python.html index 92de682b05..b968a2baa7 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -176,7 +176,7 @@ by Argonne National Labs. From within the mpich directory, type

-
./configure --enable-sharedlib=gcc
+
./configure --enable-shared
 make
 make install 
 

@@ -189,8 +189,8 @@ static and shared MPI library.  This will be fine for running LAMMPS
 from Python since it only uses the shared library.  But if you now try
 to build LAMMPS by itself as a stand-alone program (cd lammps/src;
 make foo) or build other codes that expect to link against libmpich.a,
-then those builds will typically fail if the linker uses libmpich.so
-instead.  This means you will need to remove the file
+then those builds may fail if the linker uses libmpich.so instead.  If
+this happens, it means you will need to remove the file
 /usr/local/lib/libmich.so before building LAMMPS again as a
 stand-alone code.
 

diff --git a/doc/Section_python.txt b/doc/Section_python.txt
index dbf4700819..8f2aae4567 100644
--- a/doc/Section_python.txt
+++ b/doc/Section_python.txt
@@ -172,7 +172,7 @@ by Argonne National Labs.  From within the mpich directory, type
 
 :link(mpich,http://www-unix.mcs.anl.gov/mpi)
 
-./configure --enable-sharedlib=gcc
+./configure --enable-shared
 make
 make install :pre
 
@@ -185,8 +185,8 @@ static and shared MPI library.  This will be fine for running LAMMPS
 from Python since it only uses the shared library.  But if you now try
 to build LAMMPS by itself as a stand-alone program (cd lammps/src;
 make foo) or build other codes that expect to link against libmpich.a,
-then those builds will typically fail if the linker uses libmpich.so
-instead.  This means you will need to remove the file
+then those builds may fail if the linker uses libmpich.so instead.  If
+this happens, it means you will need to remove the file
 /usr/local/lib/libmich.so before building LAMMPS again as a
 stand-alone code.
 
diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html
index 4fe72468f1..05b679d66b 100644
--- a/doc/fix_addforce.html
+++ b/doc/fix_addforce.html
@@ -23,8 +23,8 @@
 
 
  • fx,fy,fz = force component values (force units) 
 
-
  • any of fx,fy,fz can be a variable (see below) 
-
+
      any of fx,fy,fz can be a variable (see below) 
+
    
 
  • zero or more keyword/value pairs may be appended to args 
 
 
  • keyword = region or energy 
diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt
index e2c6e2e1fc..b20a696071 100644
--- a/doc/fix_addforce.txt
+++ b/doc/fix_addforce.txt
@@ -16,7 +16,7 @@ fix ID group-ID addforce fx fy fz keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 addforce = style name of this fix command :l
 fx,fy,fz = force component values (force units) :l
-any of fx,fy,fz can be a variable (see below) :l
+  any of fx,fy,fz can be a variable (see below) :pre
 zero or more keyword/value pairs may be appended to args :l
 keyword = {region} or {energy} :l
   {region} value = region-ID
diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html
index d2f9355090..3aae86bb54 100644
--- a/doc/fix_aveforce.html
+++ b/doc/fix_aveforce.html
@@ -23,8 +23,8 @@
 
 
  • fx,fy,fz = force component values (force units) 
 
-
  • any of fx,fy,fz can be a variable (see below) 
-
+
      any of fx,fy,fz can be a variable (see below) 
+
    
 
  • zero or more keyword/value pairs may be appended to args 
 
 
  • keyword = region  
diff --git a/doc/fix_aveforce.txt b/doc/fix_aveforce.txt
index b8db603c51..bae11d47d4 100644
--- a/doc/fix_aveforce.txt
+++ b/doc/fix_aveforce.txt
@@ -16,7 +16,7 @@ fix ID group-ID aveforce fx fy fz keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 aveforce = style name of this fix command :l
 fx,fy,fz = force component values (force units) :l
-any of fx,fy,fz can be a variable (see below) :l
+  any of fx,fy,fz can be a variable (see below) :pre
 zero or more keyword/value pairs may be appended to args :l
 keyword = {region}  :l
   {region} value = region-ID
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index 17fefcd560..d19ae2ff44 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -21,6 +21,8 @@
 
 
  • Tstart,Tstop = desired temperature at start/end of run (temperature units) 
 
+
      Tstart can be a variable (see below) 
+
    
 
  • damp = damping parameter (time units) 
 
 
  • seed = random number seed to use for white noise (positive integer) 
@@ -33,7 +35,7 @@
     no = do not thermostat rotational degrees of freedom via the angular momentum
     yes = do thermostat rotational degrees of freedom via the angular momentum
   omega value = no or yes
-    no = do not thermostat rotational degrees of freedom via then angular velocity
+    no = do not thermostat rotational degrees of freedom via the angular velocity
     yes = do thermostat rotational degrees of freedom via the angular velocity
   scale values = type ratio
     type = atom type (1-N)
@@ -113,6 +115,23 @@ thermostatting.
 
    The desired temperature at each timestep is a ramped value during the
 run from Tstart to Tstop.
 
    
+
    Tstart can be specified as an equal-style or atom-style
+variable.  In this case, the Tstop setting is
+ignored.  If the value is a variable, it should be specified as
+v_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+target temperature.
+
    
+
    Equal-style variables can specify formulas with various mathematical
+functions, and include thermo_style command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
    
+
    Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent
+temperature with optional time-dependence as well.
+
    
 
    Like other fixes that perform thermostatting, this fix can be used
 with compute commands that remove a "bias" from the
 atom velocities.  E.g. removing the center-of-mass velocity from a
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index 63fd2135f8..085bcdccd6 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -15,6 +15,7 @@ fix ID group-ID langevin Tstart Tstop damp seed keyword values ... :pre
 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
+  Tstart can be a variable (see below) :pre
 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
@@ -23,7 +24,7 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
     {no} = do not thermostat rotational degrees of freedom via the angular momentum
     {yes} = do thermostat rotational degrees of freedom via the angular momentum
   {omega} value = {no} or {yes}
-    {no} = do not thermostat rotational degrees of freedom via then angular velocity
+    {no} = do not thermostat rotational degrees of freedom via the angular velocity
     {yes} = do thermostat rotational degrees of freedom via the angular velocity
   {scale} values = type ratio
     type = atom type (1-N)
@@ -102,6 +103,23 @@ thermostatting.
 The desired temperature at each timestep is a ramped value during the
 run from {Tstart} to {Tstop}.
 
+{Tstart} can be specified as an equal-style or atom-style
+"variable"_variable.html.  In this case, the {Tstop} setting is
+ignored.  If the value is a variable, it should be specified as
+v_name, where name is the variable name.  In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+target temperature.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include "thermo_style"_thermo_style.html command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent temperature.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus it is easy to specify a spatially-dependent
+temperature with optional time-dependence as well.
+
 Like other fixes that perform thermostatting, this fix can be used
 with "compute commands"_compute.html that remove a "bias" from the
 atom velocities.  E.g. removing the center-of-mass velocity from a
diff --git a/doc/pair_comb.html b/doc/pair_comb.html
index 71e245c9e6..55ec1beb1e 100644
--- a/doc/pair_comb.html
+++ b/doc/pair_comb.html
@@ -252,7 +252,7 @@ Phillpot, Phys Rev B, 81, 125328 (2010).
 
    
 
 
-
    (Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141
+
    (Rick) S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
 (1994).
 
    
 
diff --git a/doc/pair_comb.txt b/doc/pair_comb.txt
index ed625ba629..9ec7ede788 100644
--- a/doc/pair_comb.txt
+++ b/doc/pair_comb.txt
@@ -244,7 +244,7 @@ Phillpot, Phys Rev B, 81, 125328 (2010).
 [(Tersoff)] J. Tersoff, Phys Rev B, 37, 6991 (1988).
 
 :link(Rick)
-[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141
+[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
 (1994).
 
 :link(Wolf)