git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10364 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_gld.html

@@ -21,8 +21,9 @@
 
 <LI>Tstart,Tstop = desired temperature at start/end of run (temperature units) 
 
-<LI>N_k = number of terms in the Prony series representation of the memory kernel
-seed = random number seed to use for white noise (positive integer) 
+<LI>N_k = number of terms in the Prony series representation of the memory kernel 
+
+<LI>seed = random number seed to use for white noise (positive integer) 
 
 <LI>series = <I>pprony</I> is presently the only available option 
 
@@ -35,9 +36,8 @@ seed = random number seed to use for white noise (positive integer)
 <PRE>keyword = <I>frozen</I> or <I>zero</I>
   <I>frozen</I> value = <I>no</I> or <I>yes</I>
     <I>no</I> = initialize extended variables using values drawn from equilibrium distribution at Tstart
-    <I>yes</I> = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature) 
-</PRE>
-<PRE>  <I>zero</I> value = <I>no</I> or <I>yes</I>
+    <I>yes</I> = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
+  <I>zero</I> value = <I>no</I> or <I>yes</I>
     <I>no</I> = do not set total random force to zero
     <I>yes</I> = set total random force to zero 
 </PRE>
@@ -58,6 +58,13 @@ Fluctuation-Dissipation Theorem.  The functional form of the memory
 kernel associated with the temporally non-local force is constrained
 to be a Prony series.
 </P>
+<P>IMPORTANT NOTE: While this fix bears many similarities to <A HREF = "fix_langevin.html">fix
+langevin</A>, it has one significant
+difference. Namely, <A HREF = "fix_gld.html">fix gld</A> performs time integration,
+whereas <A HREF = "fix_langevin.html">fix langevin</A> does NOT. To this end, the
+specification of another fix to perform time integration, such as <A HREF = "fix_nve.html">fix
+nve</A>, is NOT necessary.
+</P>
 <P>With this fix active, the force on the <I>j</I>th atom is given as
 </P>
 <CENTER><IMG SRC = "Eqs/fix_gld1.jpg">
@@ -89,13 +96,6 @@ the Newtonian and Langevin limits. Details of these limits, and the
 associated numerical concerns are discussed in
 <A HREF = "#Baczewski">(Baczewski)</A>.
 </P>
-<P>While this fix bears many similarities to <A HREF = "fix_langevin.html">fix
-langevin</A>, it has one significant
-difference. Namely, <A HREF = "fix_gld.html">fix gld</A> performs time integration,
-whereas <A HREF = "fix_langevin.html">fix langevin</A> does NOT. To this end, the
-specification of another fix to perform time integration, such as <A HREF = "fix_nve.html">fix
-nve</A>, is NOT necessary.
-</P>
 <P>The desired temperature at each timestep is ramped from <I>Tstart</I> to
 <I>Tstop</I> over the course of the next run.
 </P>
@@ -126,6 +126,8 @@ to zero by subtracting off an equal part of it from each atom in the
 group. As a result, the center-of-mass of a system with zero initial
 momentum will not drift over time.
 </P>
+<HR>
+
 <P><B>Restart, run start/stop, minimize info:</B>
 </P>
 <P>The instantaneous values of the extended variables are written to
@@ -135,6 +137,10 @@ do "exact" restarts with this fix, where the simulation continues on
 the same as if no restart had taken place. However, in a statistical
 sense, a restarted simulation should produce the same behavior.
 </P>
+<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various <A HREF = "Section_howto.html#howto_15">output commands</A>.  
+</P>
 <P>This fix can ramp its target temperature over multiple runs, using the
 <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
 <A HREF = "run.html">run</A> command for details of how to do this.
@@ -143,6 +149,10 @@ sense, a restarted simulation should produce the same behavior.
 </P>
 <P><B>Restrictions:</B> none
 </P>
+<P>This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_viscous.html">fix viscous</A>,

doc/fix_gld.txt

@@ -15,7 +15,7 @@ fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k key
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 gld = style name of this fix command :l
 Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
-N_k = number of terms in the Prony series representation of the memory kernel
+N_k = number of terms in the Prony series representation of the memory kernel :l
 seed = random number seed to use for white noise (positive integer) :l
 series = {pprony} is presently the only available option :l
 c_k = the weight of the kth term in the Prony series (mass per time units) :l
@@ -24,7 +24,7 @@ zero or more keyword/value pairs may be appended :l
 keyword = {frozen} or {zero}
   {frozen} value = {no} or {yes}
     {no} = initialize extended variables using values drawn from equilibrium distribution at Tstart
-    {yes} = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature) :pre
+    {yes} = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature)
   {zero} value = {no} or {yes}
     {no} = do not set total random force to zero
     {yes} = set total random force to zero :pre
@@ -45,6 +45,13 @@ Fluctuation-Dissipation Theorem.  The functional form of the memory
 kernel associated with the temporally non-local force is constrained
 to be a Prony series.
 
+IMPORTANT NOTE: While this fix bears many similarities to "fix
+langevin"_fix_langevin.html, it has one significant
+difference. Namely, "fix gld"_fix_gld.html performs time integration,
+whereas "fix langevin"_fix_langevin.html does NOT. To this end, the
+specification of another fix to perform time integration, such as "fix
+nve"_fix_nve.html, is NOT necessary.
+
 With this fix active, the force on the {j}th atom is given as
 
 :c,image(Eqs/fix_gld1.jpg)
@@ -76,13 +83,6 @@ the Newtonian and Langevin limits. Details of these limits, and the
 associated numerical concerns are discussed in
 "(Baczewski)"_#Baczewski.
 
-While this fix bears many similarities to "fix
-langevin"_fix_langevin.html, it has one significant
-difference. Namely, "fix gld"_fix_gld.html performs time integration,
-whereas "fix langevin"_fix_langevin.html does NOT. To this end, the
-specification of another fix to perform time integration, such as "fix
-nve"_fix_nve.html, is NOT necessary.
-
 The desired temperature at each timestep is ramped from {Tstart} to
 {Tstop} over the course of the next run.
 
@@ -113,6 +113,8 @@ to zero by subtracting off an equal part of it from each atom in the
 group. As a result, the center-of-mass of a system with zero initial
 momentum will not drift over time.
 
+:line
+
 [Restart, run start/stop, minimize info:]
 
 The instantaneous values of the extended variables are written to
@@ -122,6 +124,10 @@ do "exact" restarts with this fix, where the simulation continues on
 the same as if no restart had taken place. However, in a statistical
 sense, a restarted simulation should produce the same behavior.
 
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.  No global or per-atom quantities are stored by this fix for
+access by various "output commands"_Section_howto.html#howto_15.  
+
 This fix can ramp its target temperature over multiple runs, using the
 {start} and {stop} keywords of the "run"_run.html command.  See the
 "run"_run.html command for details of how to do this.
@@ -130,6 +136,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:] none
 
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
 [Related commands:]
 
 "fix langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html,