git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15184 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/fix_orient.html

@@ -126,14 +126,18 @@
             
   <div class="section" id="fix-orient-fcc-command">
 <span id="index-0"></span><h1>fix orient/fcc command</h1>
+</div>
+<div class="section" id="fix-orient-bcc-command">
+<h1>fix orient/bcc command</h1>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">orient</span><span class="o">/</span><span class="n">fcc</span> <span class="n">nstats</span> <span class="nb">dir</span> <span class="n">alat</span> <span class="n">dE</span> <span class="n">cutlo</span> <span class="n">cuthi</span> <span class="n">file0</span> <span class="n">file1</span>
+<span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">orient</span><span class="o">/</span><span class="n">bcc</span> <span class="n">nstats</span> <span class="nb">dir</span> <span class="n">alat</span> <span class="n">dE</span> <span class="n">cutlo</span> <span class="n">cuthi</span> <span class="n">file0</span> <span class="n">file1</span>
 </pre></div>
 </div>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>nstats = print stats every this many steps, 0 = never</li>
 <li>dir = 0/1 for which crystal is used as reference</li>
-<li>alat = fcc cubic lattice constant (distance units)</li>
+<li>alat = fcc/bcc cubic lattice constant (distance units)</li>
 <li>dE = energy added to each atom (energy units)</li>
 <li>cutlo,cuthi = values between 0.0 and 1.0, cutlo &lt; cuthi</li>
 <li>file0,file1 = files that specify orientation of each grain</li>
@@ -141,6 +145,7 @@
 <div class="section" id="examples">
 <h2>Examples</h2>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">gb</span> <span class="nb">all</span> <span class="n">orient</span><span class="o">/</span><span class="n">fcc</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">4.032008</span> <span class="mf">0.001</span> <span class="mf">0.25</span> <span class="mf">0.75</span> <span class="n">xi</span><span class="o">.</span><span class="n">vec</span> <span class="n">chi</span><span class="o">.</span><span class="n">vec</span>
+<span class="n">fix</span> <span class="n">gb</span> <span class="nb">all</span> <span class="n">orient</span><span class="o">/</span><span class="n">bcc</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">2.882</span> <span class="mf">0.001</span> <span class="mf">0.25</span> <span class="mf">0.75</span> <span class="n">ngb</span><span class="o">.</span><span class="n">left</span> <span class="n">ngb</span><span class="o">.</span><span class="n">right</span>
 </pre></div>
 </div>
 </div>
@@ -150,8 +155,9 @@
 grain boundary which can be used to induce grain boundary migration
 (in the direction perpendicular to the grain boundary plane).  The
 motivation and explanation of this force and its application are
-described in <a class="reference internal" href="#janssens"><span class="std std-ref">(Janssens)</span></a>.  The force is only applied to
-atoms in the fix group.</p>
+described in <a class="reference internal" href="fix_orient_fcc.html#janssens"><span class="std std-ref">(Janssens)</span></a>. The adaptiation to bcc crystals
+is described in <a class="reference internal" href="#wicaksono1"><span class="std std-ref">(Wicaksono1)</span></a>. The computed force is only
+applied to atoms in the fix group.</p>
 <p>The basic idea is that atoms in one grain (on one side of the
 boundary) have a potential energy dE added to them.  Atoms in the
 other grain have 0.0 potential energy added.  Atoms near the boundary
@@ -169,19 +175,21 @@ system can displace during the simulation, and such motion should be
 accounted for in measuring the grain boundary velocity.</p>
 <p>The potential energy added to atom I is given by these formulas</p>
 <img alt="_images/fix_orient_fcc.jpg" class="align-center" src="_images/fix_orient_fcc.jpg" />
-<p>which are fully explained in <a class="reference internal" href="#janssens"><span class="std std-ref">(Janssens)</span></a>.  The order
-parameter Xi for atom I in equation (1) is a sum over the 12 nearest
-neighbors of atom I.  Rj is the vector from atom I to its neighbor J,
-and RIj is a vector in the reference (perfect) crystal.  That is, if
-dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
-Equation (2) gives the expected value of the order parameter XiIJ in
-the other grain.  Hi and lo cutoffs are defined in equations (3) and
-(4), using the input parameters <em>cutlo</em> and <em>cuthi</em> as thresholds to
-avoid adding grain boundary energy when the deviation in the order
-parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
-perfect crystal).  The added potential energy Ui for atom I is given
-in equation (6) where it is interpolated between 0 and dE using the
-two threshold Xi values and the Wi value of equation (5).</p>
+<p>which are fully explained in <a class="reference internal" href="fix_orient_fcc.html#janssens"><span class="std std-ref">(Janssens)</span></a>.  For fcc crystals
+this order parameter Xi for atom I in equation (1) is a sum over the
+12 nearest neighbors of atom I. For bcc crystals it is the
+corresponding sum of the 8 nearest neighbors. Rj is the vector from
+atom I to its neighbor J, and RIj is a vector in the reference
+(perfect) crystal.  That is, if dir = 0/1, then RIj is a vector to an
+atom coord from file 0/1.  Equation (2) gives the expected value of
+the order parameter XiIJ in the other grain.  Hi and lo cutoffs are
+defined in equations (3) and (4), using the input parameters <em>cutlo</em>
+and <em>cuthi</em> as thresholds to avoid adding grain boundary energy when
+the deviation in the order parameter from 0 or 1 is small (e.g. due to
+thermal fluctuations in a perfect crystal).  The added potential
+energy Ui for atom I is given in equation (6) where it is interpolated
+between 0 and dE using the two threshold Xi values and the Wi value of
+equation (5).</p>
 <p>The derivative of this energy expression gives the force on each atom
 which thus depends on the orientation of its neighbors relative to the
 2 grain orientations.  Only atoms near the grain boundary feel a net
@@ -196,14 +204,14 @@ effect of duplicate reference vector usage is small.</p>
 expense of the other.  A value of 0 means the first grain will shrink;
 a value of 1 means it will grow.  This assumes that <em>dE</em> is positive.
 The reverse will be true if <em>dE</em> is negative.</p>
-<p>The <em>alat</em> parameter is the cubic lattice constant for the fcc
+<p>The <em>alat</em> parameter is the cubic lattice constant for the fcc or bcc
 material and is only used to compute a cutoff distance of 1.57 * alat
-/ sqrt(2) for finding the 12 nearest neighbors of each atom (which
-should be valid for an fcc crystal).  A longer/shorter cutoff can be
-imposed by adjusting <em>alat</em>.  If a particular atom has less than 12
-neighbors within the cutoff, the order parameter of equation (1) is
-effectively multiplied by 12 divided by the actual number of neighbors
-within the cutoff.</p>
+/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom
+(which should be valid for an fcc or bcc crystal).  A longer/shorter
+cutoff can be imposed by adjusting <em>alat</em>.  If a particular atom has
+less than 12 or 8 neighbors within the cutoff, the order parameter of
+equation (1) is effectively multiplied by 12 or 8 divided by the
+actual number of neighbors within the cutoff.</p>
 <p>The <em>dE</em> parameter is the maximum amount of additional energy added to
 each atom in the grain which wants to shrink.</p>
 <p>The <em>cutlo</em> and <em>cuthi</em> parameters are used to reduce the force added
@@ -222,7 +230,8 @@ orientation.  The vector lengths should all be identical since an fcc
 lattice has a coordination number of 12.  Only 6 are listed due to
 symmetry, so the list must include one from each pair of
 equal-and-opposite neighbors.  A pair of orientation files for a
-Sigma=5 tilt boundary are show below.</p>
+Sigma=5 tilt boundary are shown below. A tutorial that can help for
+writing the orientation files is given in <a class="reference internal" href="#wicaksono2"><span class="std std-ref">(Wicaksono2)</span></a></p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
 <h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
@@ -246,7 +255,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
 <h2>Restrictions</h2>
 <p>This fix is part of the MISC package.  It is only enabled if LAMMPS
 was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
-<p>This fix should only be used with fcc lattices.</p>
+<p>This fix should only be used with fcc or bcc lattices.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>
@@ -255,6 +264,10 @@ was built with that package.  See the <a class="reference internal" href="Sectio
 <hr class="docutils" />
 <p id="janssens"><strong>(Janssens)</strong> Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature
 Materials, 5, 124-127 (2006).</p>
+<p id="wicaksono1"><strong>(Wicaksono1)</strong> Wicaksono, Sinclair, Militzer, Computational Materials
+Science, 117, 397-405 (2016).</p>
+<p id="wicaksono2"><strong>(Wicaksono2)</strong> Wicaksono, figshare,
+<a class="reference external" href="https://dx.doi.org/10.6084/m9.figshare.1488628.v1">https://dx.doi.org/10.6084/m9.figshare.1488628.v1</a> (2015).</p>
 <hr class="docutils" />
 <p>For illustration purposes, here are example files that specify a
 Sigma=5 &lt;100&gt; tilt boundary.  This is for a lattice constant of 3.5706