git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14450 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_nh.html

@@ -170,7 +170,7 @@
 <li>one or more keyword/value pairs may be appended</li>
 </ul>
 <pre class="literal-block">
-keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>tchain</em> or <em>pchain</em> or <em>mtk</em> or <em>tloop</em> or <em>ploop</em> or <em>nreset</em> or <em>drag</em> or <em>dilate</em> or <em>scalexy</em> or <em>scaleyz</em> or <em>scalexz</em> or <em>flip</em> or <em>fixedpoint</em>
+keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>tchain</em> or <em>pchain</em> or <em>mtk</em> or <em>tloop</em> or <em>ploop</em> or <em>nreset</em> or <em>drag</em> or <em>dilate</em> or <em>scalexy</em> or <em>scaleyz</em> or <em>scalexz</em> or <em>flip</em> or <em>fixedpoint</em> or <em>update</em>
   <em>temp</em> values = Tstart Tstop Tdamp
     Tstart,Tstop = external temperature at start/end of run
     Tdamp = temperature damping parameter (time units)
@@ -201,6 +201,7 @@ keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em
   <em>flip</em> value = <em>yes</em> or <em>no</em> = allow or disallow box flips when it becomes highly skewed
   <em>fixedpoint</em> values = x y z
     x,y,z = perform barostat dilation/contraction around this point (distance units)
+  <em>update</em> value = <em>dipole</em> update dipole orientation (only for sphere variants)
 </pre>
 </div>
 <div class="section" id="examples">
@@ -235,12 +236,12 @@ correctly, the time-averaged temperature and stress tensor of the
 particles will match the target values specified by Tstart/Tstop and
 Pstart/Pstop.</p>
 <p>The equations of motion used are those of Shinoda et al in
-<a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
+<a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
-Martyna, Tobias and Klein in <a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a> with the strain
+Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span>(Martyna)</span></a> with the strain
 energy proposed by Parrinello and Rahman in
-<a class="reference internal" href="fix_nh_eff.html#parrinello"><span>(Parrinello)</span></a>.  The time integration schemes closely
+<a class="reference internal" href="#parrinello"><span>(Parrinello)</span></a>.  The time integration schemes closely
 follow the time-reversible measure-preserving Verlet and rRESPA
-integrators derived by Tuckerman et al in <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>.</p>
+integrators derived by Tuckerman et al in <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>.</p>
 <hr class="docutils" />
 <p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
 using the <em>temp</em> keyword.  Other thermostat-related keywords are
@@ -397,7 +398,7 @@ freedom. A value of 0 corresponds to no thermostatting of the
 barostat variables.</p>
 <p>The <em>mtk</em> keyword controls whether or not the correction terms due to
 Martyna, Tuckerman, and Klein are included in the equations of motion
-<a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a>.  Specifying <em>no</em> reproduces the original
+<a class="reference internal" href="#martyna"><span>(Martyna)</span></a>.  Specifying <em>no</em> reproduces the original
 Hoover barostat, whose volume probability distribution function
 differs from the true NPT and NPH ensembles by a factor of 1/V.  Hence
 using <em>yes</em> is more correct, but in many cases the difference is
@@ -406,7 +407,7 @@ negligible.</p>
 scheme at little extra cost.  The initial and final updates of the
 thermostat variables are broken up into <em>tloop</em> substeps, each of
 length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
-Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>.  The keyword <em>ploop</em>
+Suzuki-Yoshida scheme <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>.  The keyword <em>ploop</em>
 does the same thing for the barostat thermostat.</p>
 <p>The keyword <em>nreset</em> controls how often the reference dimensions used
 to define the strain energy are reset.  If this keyword is not used,
@@ -447,6 +448,11 @@ to <em>fixedpoint</em>, then the lower periodic boundaries will remain at
 far. In all cases, the particle trajectories are unaffected by the
 chosen value, except for a time-dependent constant translation of
 positions.</p>
+<p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
+orientation of the dipole moment of each particle is also updated
+during the time integration.  This option should be used for models
+where a dipole moment is assigned to finite-size particles,
+e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><em>atom_style hybrid sphere dipole</em></a> command.</p>
 <hr class="docutils" />
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -560,6 +566,18 @@ to undergo a slow random walk. This can be mitigated by resetting
 the momentum at infrequent intervals using the
 <a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command.</p>
 </div>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">This implementation has been shown to conserve linear momentum
+up to machine precision under NVT dynamics. Under NPT dynamics,
+for a system with zero initial total linear momentum, the total
+momentum fluctuates close to zero. It may occasionally undergo brief
+excursions to non-negligible values, before returning close to zero.
+Over long simulations, this has the effect of causing the center-of-mass
+to undergo a slow random walk. This can be mitigated by resetting
+the momentum at infrequent intervals using the
+<a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command.</p>
+</div>
 <hr class="docutils" />
 <p>The fix npt and fix nph commands can be used with rigid bodies or
 mixtures of rigid bodies and non-rigid particles (e.g. solvent).  But

doc/fix_nh.txt

@@ -26,7 +26,7 @@ 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 :l
-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 {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint}
+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 {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint} or {update}
   {temp} values = Tstart Tstop Tdamp
     Tstart,Tstop = external temperature at start/end of run
     Tdamp = temperature damping parameter (time units)
@@ -56,7 +56,8 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
   {scalexz} value = {yes} or {no} = scale xz with lz
   {flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed
   {fixedpoint} values = x y z
-    x,y,z = perform barostat dilation/contraction around this point (distance units) :pre
+    x,y,z = perform barostat dilation/contraction around this point (distance units)
+  {update} value = {dipole} update dipole orientation (only for sphere variants) :pre
 
 :ule
 
@@ -327,6 +328,13 @@ far. In all cases, the particle trajectories are unaffected by the
 chosen value, except for a time-dependent constant translation of
 positions.
 
+If the {update} keyword is used with the {dipole} value, then the
+orientation of the dipole moment of each particle is also updated
+during the time integration.  This option should be used for models
+where a dipole moment is assigned to finite-size particles,
+e.g. spheroids via use of the "atom_style hybrid sphere
+dipole"_atom_style.html command.
+
 :line
 
 NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can
@@ -450,6 +458,16 @@ to undergo a slow random walk. This can be mitigated by resetting
 the momentum at infrequent intervals using the
 "fix momentum"_fix_momentum.html command.
 
+NOTE: This implementation has been shown to conserve linear momentum
+up to machine precision under NVT dynamics. Under NPT dynamics,
+for a system with zero initial total linear momentum, the total
+momentum fluctuates close to zero. It may occasionally undergo brief
+excursions to non-negligible values, before returning close to zero. 
+Over long simulations, this has the effect of causing the center-of-mass
+to undergo a slow random walk. This can be mitigated by resetting
+the momentum at infrequent intervals using the
+"fix momentum"_fix_momentum.html command.
+
 :line
 
 The fix npt and fix nph commands can be used with rigid bodies or

doc/fix_nve_sphere.html

@@ -163,8 +163,8 @@ assumes point particles and only updates their position and velocity.</p>
 <p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
 orientation of the dipole moment of each particle is also updated
 during the time integration.  This option should be used for models
-where a dipole moment is assigned to particles via use of the
+where a dipole moment is assigned to finite-size particles,
-<a class="reference internal" href="atom_style.html"><em>atom_style dipole</em></a> command.</p>
+e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><em>atom_style hybrid sphere dipole</em></a> command.</p>
 <hr class="docutils" />
 <p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
 functionally the same as the corresponding style without the suffix.

doc/fix_nve_sphere.txt

@@ -39,8 +39,9 @@ assumes point particles and only updates their position and velocity.
 If the {update} keyword is used with the {dipole} value, then the
 orientation of the dipole moment of each particle is also updated
 during the time integration.  This option should be used for models
-where a dipole moment is assigned to particles via use of the
+where a dipole moment is assigned to finite-size particles,
-"atom_style dipole"_atom_style.html command.
+e.g. spheroids via use of the "atom_style hybrid sphere
+dipole"_atom_style.html command.
 
 :line