Added tilt factor scaling and fixed-point features to fix box/relax

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8471 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_box_relax.html

@@ -20,13 +20,18 @@
 <LI>box/relax = style name of this fix command 
 
 <PRE>one or more keyword value pairs may be appended
-keyword = <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>nreset</I> or <I>vmax</I> or <I>dilate</I>
+keyword = <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>nreset</I> or <I>vmax</I> or <I>dilate</I> or <I>scaleyz</I> or <I>scalexz</I> or <I>scalexy</I> or <I>fixedpoint</I> 
   <I>iso</I> or <I>aniso</I> or <I>tri</I> value = Ptarget = desired pressure (pressure units)
   <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> value = Ptarget = desired pressure (pressure units)
   <I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
   <I>nreset</I> value = reset reference cell every this many minimizer iterations
   <I>vmax</I> value = fraction = max allowed volume change in one iteration
   <I>dilate</I> value = <I>all</I> or <I>partial</I> 
+  <I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
+  <I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
+  <I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
+  <I>fixedpoint</I> values = x y z
+    x,y,z = perform relaxation dilation/contraction around this point (distance units) 
 </PRE>
 
 </UL>
@@ -82,6 +87,27 @@ re-scaled.  This can be useful for leaving the coordinates of atoms in
 a solid substrate unchanged and controlling the pressure of a
 surrounding fluid.
 </P>
+<P>The <I>scaleyz</I>, <I>scalexz</I>, and <I>scalexy</I> keywords control whether or
+not the corresponding tilt factors are scaled with the associated box
+dimensions when relaxing triclinic periodic cells.  The default
+values <I>yes</I> will turn on scaling, which corresponds to adjusting the
+linear dimensions of the cell while preserving its shape.  Choosing
+<I>no</I> ensures that the tilt factors are not scaled with the box
+dimensions. See below for restrictions and default values in different
+situations. In older versions of LAMMPS, scaling of tilt factors was
+not performed. The old behavior can be recovered by setting all three
+scale keywords to <I>no</I>.
+</P>
+<P>The <I>fixedpoint</I> keyword specifies the fixed point for cell relaxation.
+By default, it is the center of the box.  Whatever point is
+chosen will not move during the simulation.  For example, if the lower
+periodic boundaries pass through (0,0,0), and this point is provided
+to <I>fixedpoint</I>, then the lower periodic boundaries will remain at
+(0,0,0), while the upper periodic boundaries will move twice as
+far. In all cases, the particle positions at each iteration are 
+unaffected by the chosen value, except that all particles are 
+displaced by the same amount, different on each iteration.
+</P>
 <P>IMPORTANT NOTE: Appling an external pressure to tilt dimensions <I>xy</I>,
 <I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
 tilt dimensions, i.e. a dramatically deformed simulation box.  This
@@ -302,6 +328,12 @@ available if the simulation domain is non-orthogonal.  The
 simulation box is orthogonal or non-orthogonal (triclinic) and explain
 the meaning of the xy,xz,yz tilt factors.
 </P>
+<P>The <I>scaleyz yes</I> and <I>scalexz yes</I> keyword/value pairs can not be used
+for 2D simulations. <I>scaleyz yes</I>, <I>scalexz yes</I>, and <I>scalexy yes</I> options
+can only be used if the 2nd dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+<I>tri</I>, <I>yz</I>, <I>xz</I>, and <I>xy</I>.
+</P>
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "minimize.html">minimize</A>

doc/fix_box_relax.txt

@@ -15,13 +15,20 @@ fix ID group-ID box/relax keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 box/relax = style name of this fix command :l
 one or more keyword value pairs may be appended
-keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate}
+keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint} 
   {iso} or {aniso} or {tri} value = Ptarget = desired pressure (pressure units)
   {x} or {y} or {z} or {xy} or {yz} or {xz} value = Ptarget = desired pressure (pressure units)
   {couple} = {none} or {xyz} or {xy} or {yz} or {xz}
   {nreset} value = reset reference cell every this many minimizer iterations
   {vmax} value = fraction = max allowed volume change in one iteration
-  {dilate} value = {all} or {partial} :pre
+  {dilate} value = {all} or {partial} 
+  {scaleyz} value = {yes} or {no} = scale yz with lz
+  {scalexz} value = {yes} or {no} = scale xz with lz
+  {scalexy} value = {yes} or {no} = scale xy with ly
+  {fixedpoint} values = x y z
+    x,y,z = perform relaxation dilation/contraction around this point (distance units) :pre
+
+
 :ule
 
 [Examples:]
@@ -76,6 +83,27 @@ re-scaled.  This can be useful for leaving the coordinates of atoms in
 a solid substrate unchanged and controlling the pressure of a
 surrounding fluid.
 
+The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or
+not the corresponding tilt factors are scaled with the associated box
+dimensions when relaxing triclinic periodic cells.  The default
+values {yes} will turn on scaling, which corresponds to adjusting the
+linear dimensions of the cell while preserving its shape.  Choosing
+{no} ensures that the tilt factors are not scaled with the box
+dimensions. See below for restrictions and default values in different
+situations. In older versions of LAMMPS, scaling of tilt factors was
+not performed. The old behavior can be recovered by setting all three
+scale keywords to {no}.
+
+The {fixedpoint} keyword specifies the fixed point for cell relaxation.
+By default, it is the center of the box.  Whatever point is
+chosen will not move during the simulation.  For example, if the lower
+periodic boundaries pass through (0,0,0), and this point is provided
+to {fixedpoint}, then the lower periodic boundaries will remain at
+(0,0,0), while the upper periodic boundaries will move twice as
+far. In all cases, the particle positions at each iteration are 
+unaffected by the chosen value, except that all particles are 
+displaced by the same amount, different on each iteration.
+
 IMPORTANT NOTE: Appling an external pressure to tilt dimensions {xy},
 {xz}, {yz} can sometimes result in arbitrarily large values of the
 tilt dimensions, i.e. a dramatically deformed simulation box.  This
@@ -296,6 +324,12 @@ available if the simulation domain is non-orthogonal.  The
 simulation box is orthogonal or non-orthogonal (triclinic) and explain
 the meaning of the xy,xz,yz tilt factors.
 
+The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used
+for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options
+can only be used if the 2nd dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+{tri}, {yz}, {xz}, and {xy}.
+
 [Related commands:]
 
 "fix npt"_fix_nh.html, "minimize"_minimize.html

doc/fix_nh.html

@@ -28,7 +28,7 @@
 <LI>style_name = <I>nvt</I> or <I>npt</I> or <I>nph</I> 
 
 <PRE>one or more keyword value pairs may be appended
-keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I> or <I>scaleyz</I> or <I>scalexz</I> or <I>scalexy</I>
+keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I> or <I>scaleyz</I> or <I>scalexz</I> or <I>scalexy</I> or <I>fixedpoint</I>
   <I>temp</I> values = Tstart Tstop Tdamp
     Tstart,Tstop = external temperature at start/end of run
     Tdamp = temperature damping parameter (time units)

doc/fix_nh.txt

@@ -19,7 +19,7 @@ fix ID group-ID style_name keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 style_name = {nvt} or {npt} or {nph} :l
 one or more keyword value pairs may be appended
-keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scaleyz} or {scalexz} or {scalexy}
+keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint}
   {temp} values = Tstart Tstop Tdamp
     Tstart,Tstop = external temperature at start/end of run
     Tdamp = temperature damping parameter (time units)