Commit 328b7abe authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

correct various formatting issues flagged by sphinx

parent c3de3c14

doc/html/compute_xrd.html

+263 −63
Original line number Diff line number Diff line
@@ -225,69 +225,269 @@ The analytic approximation is computed using the formula 
<p>Coefficients parameterized by <a class="reference internal" href="#peng"><span class="std std-ref">(Peng)</span></a> are assigned for each

atom type designating the chemical symbol and charge of each atom

type. Valid chemical symbols for compute xrd are:</p>

<dl class="docutils">

<dt>H:    He1-:      He:      Li:    Li1+:</dt>

<dd><blockquote class="first">

<div><blockquote>

<div><dl class="docutils">

<dt>Be:    Be2+:       B:       C:    Cval:</dt>

<dd>N:       O:     O1-:       F:     F1-:</dd>

</dl>

<p>Ne:      Na:    Na1+:      Mg:    Mg2+:

Al:    Al3+:      Si:    Sival:   Si4+:</p>

<blockquote>

<div>P:       S:      Cl:    Cl1-:      Ar:

K:      Ca:    Ca2+:      Sc:    Sc3+:</div></blockquote>

<p>Ti:    Ti2+:    Ti3+:    Ti4+:       V:</p>

</div></blockquote>

<p>V2+:     V3+:     V5+:      Cr:    Cr2+:</p>

</div></blockquote>

<dl class="docutils">

<dt>Cr3+:      Mn:    Mn2+:    Mn3+:    Mn4+:</dt>

<dd>Fe:    Fe2+:    Fe3+:      Co:    Co2+:

Co:      Ni:    Ni2+:    Ni3+:      Cu:</dd>

</dl>

<p>Cu1+:    Cu2+:      Zn:    Zn2+:      Ga:

Ga3+:      Ge:    Ge4+:      As:      Se:</p>

<blockquote>

<div>Br:    Br1-:      Kr:      Rb:    Rb1+:

Sr:    Sr2+:       Y:     Y3+:      Zr:</div></blockquote>

<p>Zr4+:      Nb:    Nb3+:    Nb5+:      Mo:

Mo3+:    Mo5+:    Mo6+:      Tc:      Ru:

Ru3+:    Ru4+:      Rh:    Rh3+:    Rh4+:</p>

<blockquote>

<div>Pd:    Pd2+:    Pd4+:      Ag:    Ag1+:</div></blockquote>

<dl class="docutils">

<dt>Ag2+:      Cd:    Cd2+:      In:    In3+:</dt>

<dd>Sn:    Sn2+:    Sn4+:      Sb:    Sb3+:</dd>

<dt>Sb5+:      Te:       I:     I1-:      Xe:</dt>

<dd>Cs:    Cs1+:      Ba:    Ba2+:      La:</dd>

</dl>

<p>La3+:      Ce:    Ce3+:    Ce4+:      Pr:

Pr3+:    Pr4+:      Nd:    Nd3+:      Pm:

Pm3+:      Sm:    Sm3+:      Eu:    Eu2+:

Eu3+:      Gd:    Gd3+:      Tb:    Tb3+:</p>

<blockquote>

<div>Dy:    Dy3+:      Ho:    Ho3+:      Er:</div></blockquote>

<p>Er3+:      Tm:    Tm3+:      Yb:    Yb2+:

Yb3+:      Lu:    Lu3+:      Hf:    Hf4+:</p>

<blockquote>

<div>Ta:    Ta5+:       W:     W6+:      Re:

Os:    Os4+:      Ir:    Ir3+:    Ir4+:

Pt:    Pt2+:    Pt4+:      Au:    Au1+:</div></blockquote>

<p>Au3+:      Hg:    Hg1+:    Hg2+:      Tl:

Tl1+:    Tl3+:      Pb:    Pb2+:    Pb4+:</p>

<blockquote>

<div>Bi:    Bi3+:    Bi5+:      Po:      At:

Rn:      Fr:      Ra:    Ra2+:      Ac:</div></blockquote>

<dl class="docutils">

<dt>Ac3+:      Th:    Th4+:      Pa:       U:</dt>

<dd>U3+:     U4+:     U6+:      Np:    Np3+:</dd>

</dl>

<p class="last">Np4+:    Np6+:      Pu:    Pu3+:    Pu4+:

Pu6+:      Am:      Cm:      Bk:      Cf:tb(c=5,s=:)</p>

</dd>

</dl>

<table border="1" class="docutils">

<colgroup>

<col width="19%" />

<col width="19%" />

<col width="19%" />

<col width="23%" />

<col width="19%" />

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td>H</td>

<td>He1-</td>

<td>He</td>

<td>Li</td>

<td>Li1+</td>

</tr>

<tr class="row-even"><td>Be</td>

<td>Be2+</td>

<td>B</td>

<td>C</td>

<td>Cval</td>

</tr>

<tr class="row-odd"><td>N</td>

<td>O</td>

<td>O1-</td>

<td>F</td>

<td>F1-</td>

</tr>

<tr class="row-even"><td>Ne</td>

<td>Na</td>

<td>Na1+</td>

<td>Mg</td>

<td>Mg2+</td>

</tr>

<tr class="row-odd"><td>Al</td>

<td>Al3+</td>

<td>Si</td>

<td>Sival</td>

<td>Si4+</td>

</tr>

<tr class="row-even"><td>P</td>

<td>S</td>

<td>Cl</td>

<td>Cl1-</td>

<td>Ar</td>

</tr>

<tr class="row-odd"><td>K</td>

<td>Ca</td>

<td>Ca2+</td>

<td>Sc</td>

<td>Sc3+</td>

</tr>

<tr class="row-even"><td>Ti</td>

<td>Ti2+</td>

<td>Ti3+</td>

<td>Ti4+</td>

<td>V</td>

</tr>

<tr class="row-odd"><td>V2+</td>

<td>V3+</td>

<td>V5+</td>

<td>Cr</td>

<td>Cr2+</td>

</tr>

<tr class="row-even"><td>Cr3+</td>

<td>Mn</td>

<td>Mn2+</td>

<td>Mn3+</td>

<td>Mn4+</td>

</tr>

<tr class="row-odd"><td>Fe</td>

<td>Fe2+</td>

<td>Fe3+</td>

<td>Co</td>

<td>Co2+</td>

</tr>

<tr class="row-even"><td>Co</td>

<td>Ni</td>

<td>Ni2+</td>

<td>Ni3+</td>

<td>Cu</td>

</tr>

<tr class="row-odd"><td>Cu1+</td>

<td>Cu2+</td>

<td>Zn</td>

<td>Zn2+</td>

<td>Ga</td>

</tr>

<tr class="row-even"><td>Ga3+</td>

<td>Ge</td>

<td>Ge4+</td>

<td>As</td>

<td>Se</td>

</tr>

<tr class="row-odd"><td>Br</td>

<td>Br1-</td>

<td>Kr</td>

<td>Rb</td>

<td>Rb1+</td>

</tr>

<tr class="row-even"><td>Sr</td>

<td>Sr2+</td>

<td>Y</td>

<td>Y3+</td>

<td>Zr</td>

</tr>

<tr class="row-odd"><td>Zr4+</td>

<td>Nb</td>

<td>Nb3+</td>

<td>Nb5+</td>

<td>Mo</td>

</tr>

<tr class="row-even"><td>Mo3+</td>

<td>Mo5+</td>

<td>Mo6+</td>

<td>Tc</td>

<td>Ru</td>

</tr>

<tr class="row-odd"><td>Ru3+</td>

<td>Ru4+</td>

<td>Rh</td>

<td>Rh3+</td>

<td>Rh4+</td>

</tr>

<tr class="row-even"><td>Pd</td>

<td>Pd2+</td>

<td>Pd4+</td>

<td>Ag</td>

<td>Ag1+</td>

</tr>

<tr class="row-odd"><td>Ag2+</td>

<td>Cd</td>

<td>Cd2+</td>

<td>In</td>

<td>In3+</td>

</tr>

<tr class="row-even"><td>Sn</td>

<td>Sn2+</td>

<td>Sn4+</td>

<td>Sb</td>

<td>Sb3+</td>

</tr>

<tr class="row-odd"><td>Sb5+</td>

<td>Te</td>

<td>I</td>

<td>I1-</td>

<td>Xe</td>

</tr>

<tr class="row-even"><td>Cs</td>

<td>Cs1+</td>

<td>Ba</td>

<td>Ba2+</td>

<td>La</td>

</tr>

<tr class="row-odd"><td>La3+</td>

<td>Ce</td>

<td>Ce3+</td>

<td>Ce4+</td>

<td>Pr</td>

</tr>

<tr class="row-even"><td>Pr3+</td>

<td>Pr4+</td>

<td>Nd</td>

<td>Nd3+</td>

<td>Pm</td>

</tr>

<tr class="row-odd"><td>Pm3+</td>

<td>Sm</td>

<td>Sm3+</td>

<td>Eu</td>

<td>Eu2+</td>

</tr>

<tr class="row-even"><td>Eu3+</td>

<td>Gd</td>

<td>Gd3+</td>

<td>Tb</td>

<td>Tb3+</td>

</tr>

<tr class="row-odd"><td>Dy</td>

<td>Dy3+</td>

<td>Ho</td>

<td>Ho3+</td>

<td>Er</td>

</tr>

<tr class="row-even"><td>Er3+</td>

<td>Tm</td>

<td>Tm3+</td>

<td>Yb</td>

<td>Yb2+</td>

</tr>

<tr class="row-odd"><td>Yb3+</td>

<td>Lu</td>

<td>Lu3+</td>

<td>Hf</td>

<td>Hf4+</td>

</tr>

<tr class="row-even"><td>Ta</td>

<td>Ta5+</td>

<td>W</td>

<td>W6+</td>

<td>Re</td>

</tr>

<tr class="row-odd"><td>Os</td>

<td>Os4+</td>

<td>Ir</td>

<td>Ir3+</td>

<td>Ir4+</td>

</tr>

<tr class="row-even"><td>Pt</td>

<td>Pt2+</td>

<td>Pt4+</td>

<td>Au</td>

<td>Au1+</td>

</tr>

<tr class="row-odd"><td>Au3+</td>

<td>Hg</td>

<td>Hg1+</td>

<td>Hg2+</td>

<td>Tl</td>

</tr>

<tr class="row-even"><td>Tl1+</td>

<td>Tl3+</td>

<td>Pb</td>

<td>Pb2+</td>

<td>Pb4+</td>

</tr>

<tr class="row-odd"><td>Bi</td>

<td>Bi3+</td>

<td>Bi5+</td>

<td>Po</td>

<td>At</td>

</tr>

<tr class="row-even"><td>Rn</td>

<td>Fr</td>

<td>Ra</td>

<td>Ra2+</td>

<td>Ac</td>

</tr>

<tr class="row-odd"><td>Ac3+</td>

<td>Th</td>

<td>Th4+</td>

<td>Pa</td>

<td>U</td>

</tr>

<tr class="row-even"><td>U3+</td>

<td>U4+</td>

<td>U6+</td>

<td>Np</td>

<td>Np3+</td>

</tr>

<tr class="row-odd"><td>Np4+</td>

<td>Np6+</td>

<td>Pu</td>

<td>Pu3+</td>

<td>Pu4+</td>

</tr>

<tr class="row-even"><td>Pu6+</td>

<td>Am</td>

<td>Cm</td>

<td>Bk</td>

<td>Cf</td>

</tr>

</tbody>

</table>

<p>If the <em>echo</em> keyword is specified, compute xrd will provide extra

reporting information to the screen.</p>

<p><strong>Output info:</strong></p>

doc/html/fix_rx.html

+1 −1
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@@ -190,7 +190,7 @@ Note that more than min_steps ODE steps may be taken depending upon the ODE stif 
but no more than max_steps will be taken. If max_steps is reached, an error warning

is printed and the simulation is stopped.</p>

<p>After each ODE step, the solution error <em>e</em> is tested and weighted using the absTol

and relTol values. The error vector is weighted as <em>e</em> / (relTol * <a href="#id1"><span class="problematic" id="id2">|</span></a><em>u</em>| + absTol)

and relTol values. The error vector is weighted as <em>e</em> / (relTol * | <em>u</em> | + absTol)

where <em>u</em> is the solution vector. If the norm of the error is &lt;= 1, the solution is

accepted, <em>h</em> is increased by a proportional amount, and the next ODE step is begun.

Otherwise, <em>h</em> is shrunk and the ODE step is repeated.</p>

doc/html/fix_ti_spring.html

+1 −1
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@@ -198,7 +198,7 @@ thermodynamic integration.</p> 
thermodynamic integration, a non-zero total velocity will result in

divergencies during the integration due to the fact that the atoms are

&#8216;attatched&#8217; to its equilibrium positions by the Einstein

crystal. Check the option <em>zero</em> of <a class="reference external" href="fix_langevin_html">fix langevin</a>

crystal. Check the option <em>zero</em> of <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>

and <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a>. The use of the Nose-Hoover thermostat

(<a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>) is NOT recommended due to its well documented

issues with the canonical sampling of harmonic degrees of freedom

doc/html/neb.html

+4 −6
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@@ -412,12 +412,10 @@ and restart files.</p> 
this case), the print-out to the screen and master log.lammps file

contains a line of output, printed once every <em>Nevery</em> timesteps.  It

contains the timestep, the maximum force per replica, the maximum

force per atom (in any replica), potential gradients in the initial,</p>

<blockquote>

<div>final, and climbing replicas,</div></blockquote>

<p>the forward and backward energy barriers,

the total reaction coordinate (RDT), and

the normalized reaction coordinate and potential energy of each replica.</p>

force per atom (in any replica), potential gradients in the initial,

final, and climbing replicas, the forward and backward energy barriers,

the total reaction coordinate (RDT), and the normalized reaction

coordinate and potential energy of each replica.</p>

<p>The &#8220;maximum force per replica&#8221; is

the two-norm of the 3N-length force vector for the atoms in each

replica, maximized across replicas, which is what the <em>ftol</em> setting

doc/html/pair_lj_soft.html

+2 −2
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@@ -287,8 +287,8 @@ choices for the exponent are n = 2 or n = 1. For the remaining 
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are

appropriate choices. Plots of the LJ and Coulomb terms are shown

below, for lambda ranging from 1 to 0 every 0.1.</p>

<img alt="_images/lj_soft.jpg" class="align-center" src="_images/lj_soft.jpg" />

<img alt="_images/coul_soft.jpg" class="align-center" src="_images/coul_soft.jpg" />

<img alt="_images/lj_soft.jpg" src="_images/lj_soft.jpg" />

<img alt="_images/coul_soft.jpg" src="_images/coul_soft.jpg" />

<p>For the <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> pair styles,

the following coefficients must be defined for each pair of atoms

types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples

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