forked from lijiext/lammps
correct various formatting issues flagged by sphinx
This commit is contained in:
Axel Kohlmeyer
parent
c3de3c142f
commit
328b7abeaa
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@ -225,69 +225,269 @@ The analytic approximation is computed using the formula
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<p>Coefficients parameterized by <a class="reference internal" href="#peng"><span class="std std-ref">(Peng)</span></a> are assigned for each
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atom type designating the chemical symbol and charge of each atom
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type. Valid chemical symbols for compute xrd are:</p>
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<dl class="docutils">
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<dt>H: He1-: He: Li: Li1+:</dt>
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<dd><blockquote class="first">
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<div><blockquote>
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<div><dl class="docutils">
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<dt>Be: Be2+: B: C: Cval:</dt>
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<dd>N: O: O1-: F: F1-:</dd>
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</dl>
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<p>Ne: Na: Na1+: Mg: Mg2+:
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Al: Al3+: Si: Sival: Si4+:</p>
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<blockquote>
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<div>P: S: Cl: Cl1-: Ar:
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K: Ca: Ca2+: Sc: Sc3+:</div></blockquote>
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<p>Ti: Ti2+: Ti3+: Ti4+: V:</p>
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</div></blockquote>
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<p>V2+: V3+: V5+: Cr: Cr2+:</p>
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</div></blockquote>
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<dl class="docutils">
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<dt>Cr3+: Mn: Mn2+: Mn3+: Mn4+:</dt>
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<dd>Fe: Fe2+: Fe3+: Co: Co2+:
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Co: Ni: Ni2+: Ni3+: Cu:</dd>
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</dl>
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<p>Cu1+: Cu2+: Zn: Zn2+: Ga:
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Ga3+: Ge: Ge4+: As: Se:</p>
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<blockquote>
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<div>Br: Br1-: Kr: Rb: Rb1+:
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Sr: Sr2+: Y: Y3+: Zr:</div></blockquote>
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<p>Zr4+: Nb: Nb3+: Nb5+: Mo:
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Mo3+: Mo5+: Mo6+: Tc: Ru:
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Ru3+: Ru4+: Rh: Rh3+: Rh4+:</p>
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<blockquote>
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<div>Pd: Pd2+: Pd4+: Ag: Ag1+:</div></blockquote>
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<dl class="docutils">
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<dt>Ag2+: Cd: Cd2+: In: In3+:</dt>
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<dd>Sn: Sn2+: Sn4+: Sb: Sb3+:</dd>
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<dt>Sb5+: Te: I: I1-: Xe:</dt>
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<dd>Cs: Cs1+: Ba: Ba2+: La:</dd>
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</dl>
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<p>La3+: Ce: Ce3+: Ce4+: Pr:
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Pr3+: Pr4+: Nd: Nd3+: Pm:
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Pm3+: Sm: Sm3+: Eu: Eu2+:
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Eu3+: Gd: Gd3+: Tb: Tb3+:</p>
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<blockquote>
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<div>Dy: Dy3+: Ho: Ho3+: Er:</div></blockquote>
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<p>Er3+: Tm: Tm3+: Yb: Yb2+:
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Yb3+: Lu: Lu3+: Hf: Hf4+:</p>
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<blockquote>
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<div>Ta: Ta5+: W: W6+: Re:
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Os: Os4+: Ir: Ir3+: Ir4+:
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Pt: Pt2+: Pt4+: Au: Au1+:</div></blockquote>
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<p>Au3+: Hg: Hg1+: Hg2+: Tl:
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Tl1+: Tl3+: Pb: Pb2+: Pb4+:</p>
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<blockquote>
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<div>Bi: Bi3+: Bi5+: Po: At:
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Rn: Fr: Ra: Ra2+: Ac:</div></blockquote>
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<dl class="docutils">
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<dt>Ac3+: Th: Th4+: Pa: U:</dt>
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<dd>U3+: U4+: U6+: Np: Np3+:</dd>
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</dl>
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<p class="last">Np4+: Np6+: Pu: Pu3+: Pu4+:
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Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:)</p>
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</dd>
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</dl>
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<table border="1" class="docutils">
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<colgroup>
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<col width="19%" />
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<col width="19%" />
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<col width="19%" />
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<col width="23%" />
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<col width="19%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>H</td>
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<td>He1-</td>
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<td>He</td>
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<td>Li</td>
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<td>Li1+</td>
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</tr>
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<tr class="row-even"><td>Be</td>
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<td>Be2+</td>
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<td>B</td>
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<td>C</td>
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<td>Cval</td>
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</tr>
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<tr class="row-odd"><td>N</td>
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<td>O</td>
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<td>O1-</td>
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<td>F</td>
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<td>F1-</td>
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</tr>
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<tr class="row-even"><td>Ne</td>
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<td>Na</td>
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<td>Na1+</td>
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<td>Mg</td>
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<td>Mg2+</td>
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</tr>
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<tr class="row-odd"><td>Al</td>
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<td>Al3+</td>
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<td>Si</td>
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<td>Sival</td>
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<td>Si4+</td>
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</tr>
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<tr class="row-even"><td>P</td>
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<td>S</td>
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<td>Cl</td>
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<td>Cl1-</td>
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<td>Ar</td>
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</tr>
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<tr class="row-odd"><td>K</td>
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<td>Ca</td>
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<td>Ca2+</td>
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<td>Sc</td>
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<td>Sc3+</td>
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</tr>
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<tr class="row-even"><td>Ti</td>
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<td>Ti2+</td>
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<td>Ti3+</td>
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<td>Ti4+</td>
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<td>V</td>
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</tr>
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<tr class="row-odd"><td>V2+</td>
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<td>V3+</td>
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<td>V5+</td>
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<td>Cr</td>
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<td>Cr2+</td>
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</tr>
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<tr class="row-even"><td>Cr3+</td>
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<td>Mn</td>
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<td>Mn2+</td>
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<td>Mn3+</td>
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<td>Mn4+</td>
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</tr>
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<tr class="row-odd"><td>Fe</td>
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<td>Fe2+</td>
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<td>Fe3+</td>
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<td>Co</td>
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<td>Co2+</td>
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</tr>
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<tr class="row-even"><td>Co</td>
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<td>Ni</td>
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<td>Ni2+</td>
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<td>Ni3+</td>
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<td>Cu</td>
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</tr>
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<tr class="row-odd"><td>Cu1+</td>
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<td>Cu2+</td>
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<td>Zn</td>
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<td>Zn2+</td>
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<td>Ga</td>
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</tr>
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<tr class="row-even"><td>Ga3+</td>
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<td>Ge</td>
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<td>Ge4+</td>
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<td>As</td>
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<td>Se</td>
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</tr>
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<tr class="row-odd"><td>Br</td>
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<td>Br1-</td>
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<td>Kr</td>
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<td>Rb</td>
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<td>Rb1+</td>
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</tr>
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<tr class="row-even"><td>Sr</td>
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<td>Sr2+</td>
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<td>Y</td>
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<td>Y3+</td>
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<td>Zr</td>
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</tr>
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<tr class="row-odd"><td>Zr4+</td>
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<td>Nb</td>
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<td>Nb3+</td>
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<td>Nb5+</td>
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<td>Mo</td>
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</tr>
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<tr class="row-even"><td>Mo3+</td>
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<td>Mo5+</td>
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<td>Mo6+</td>
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<td>Tc</td>
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<td>Ru</td>
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</tr>
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<tr class="row-odd"><td>Ru3+</td>
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<td>Ru4+</td>
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<td>Rh</td>
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<td>Rh3+</td>
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<td>Rh4+</td>
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</tr>
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<tr class="row-even"><td>Pd</td>
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<td>Pd2+</td>
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<td>Pd4+</td>
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<td>Ag</td>
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<td>Ag1+</td>
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</tr>
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<tr class="row-odd"><td>Ag2+</td>
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<td>Cd</td>
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<td>Cd2+</td>
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<td>In</td>
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<td>In3+</td>
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</tr>
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<tr class="row-even"><td>Sn</td>
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<td>Sn2+</td>
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<td>Sn4+</td>
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<td>Sb</td>
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<td>Sb3+</td>
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</tr>
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<tr class="row-odd"><td>Sb5+</td>
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<td>Te</td>
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<td>I</td>
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<td>I1-</td>
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<td>Xe</td>
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</tr>
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<tr class="row-even"><td>Cs</td>
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<td>Cs1+</td>
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<td>Ba</td>
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<td>Ba2+</td>
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<td>La</td>
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</tr>
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<tr class="row-odd"><td>La3+</td>
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<td>Ce</td>
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<td>Ce3+</td>
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<td>Ce4+</td>
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<td>Pr</td>
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</tr>
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<tr class="row-even"><td>Pr3+</td>
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<td>Pr4+</td>
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<td>Nd</td>
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<td>Nd3+</td>
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<td>Pm</td>
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</tr>
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<tr class="row-odd"><td>Pm3+</td>
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<td>Sm</td>
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<td>Sm3+</td>
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<td>Eu</td>
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<td>Eu2+</td>
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</tr>
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<tr class="row-even"><td>Eu3+</td>
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<td>Gd</td>
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<td>Gd3+</td>
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<td>Tb</td>
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<td>Tb3+</td>
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</tr>
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<tr class="row-odd"><td>Dy</td>
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<td>Dy3+</td>
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<td>Ho</td>
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<td>Ho3+</td>
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<td>Er</td>
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</tr>
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<tr class="row-even"><td>Er3+</td>
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<td>Tm</td>
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<td>Tm3+</td>
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<td>Yb</td>
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<td>Yb2+</td>
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</tr>
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<tr class="row-odd"><td>Yb3+</td>
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<td>Lu</td>
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<td>Lu3+</td>
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<td>Hf</td>
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<td>Hf4+</td>
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</tr>
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<tr class="row-even"><td>Ta</td>
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<td>Ta5+</td>
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<td>W</td>
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<td>W6+</td>
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<td>Re</td>
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</tr>
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<tr class="row-odd"><td>Os</td>
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<td>Os4+</td>
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<td>Ir</td>
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<td>Ir3+</td>
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<td>Ir4+</td>
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</tr>
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<tr class="row-even"><td>Pt</td>
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<td>Pt2+</td>
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<td>Pt4+</td>
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<td>Au</td>
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<td>Au1+</td>
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</tr>
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<tr class="row-odd"><td>Au3+</td>
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<td>Hg</td>
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<td>Hg1+</td>
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<td>Hg2+</td>
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<td>Tl</td>
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</tr>
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<tr class="row-even"><td>Tl1+</td>
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<td>Tl3+</td>
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<td>Pb</td>
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<td>Pb2+</td>
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<td>Pb4+</td>
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</tr>
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<tr class="row-odd"><td>Bi</td>
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<td>Bi3+</td>
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<td>Bi5+</td>
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<td>Po</td>
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<td>At</td>
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</tr>
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<tr class="row-even"><td>Rn</td>
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<td>Fr</td>
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<td>Ra</td>
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<td>Ra2+</td>
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<td>Ac</td>
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</tr>
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<tr class="row-odd"><td>Ac3+</td>
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<td>Th</td>
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<td>Th4+</td>
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<td>Pa</td>
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<td>U</td>
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</tr>
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<tr class="row-even"><td>U3+</td>
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<td>U4+</td>
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<td>U6+</td>
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<td>Np</td>
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<td>Np3+</td>
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</tr>
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<tr class="row-odd"><td>Np4+</td>
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<td>Np6+</td>
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<td>Pu</td>
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<td>Pu3+</td>
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<td>Pu4+</td>
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</tr>
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<tr class="row-even"><td>Pu6+</td>
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<td>Am</td>
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<td>Cm</td>
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<td>Bk</td>
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<td>Cf</td>
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</tr>
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</tbody>
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</table>
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<p>If the <em>echo</em> keyword is specified, compute xrd will provide extra
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reporting information to the screen.</p>
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<p><strong>Output info:</strong></p>
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@ -190,7 +190,7 @@ Note that more than min_steps ODE steps may be taken depending upon the ODE stif
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but no more than max_steps will be taken. If max_steps is reached, an error warning
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is printed and the simulation is stopped.</p>
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<p>After each ODE step, the solution error <em>e</em> is tested and weighted using the absTol
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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)
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and relTol values. The error vector is weighted as <em>e</em> / (relTol * | <em>u</em> | + absTol)
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where <em>u</em> is the solution vector. If the norm of the error is <= 1, the solution is
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accepted, <em>h</em> is increased by a proportional amount, and the next ODE step is begun.
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Otherwise, <em>h</em> is shrunk and the ODE step is repeated.</p>
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@ -198,7 +198,7 @@ thermodynamic integration.</p>
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thermodynamic integration, a non-zero total velocity will result in
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divergencies during the integration due to the fact that the atoms are
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‘attatched’ to its equilibrium positions by the Einstein
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crystal. Check the option <em>zero</em> of <a class="reference external" href="fix_langevin_html">fix langevin</a>
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crystal. Check the option <em>zero</em> of <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>
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and <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a>. The use of the Nose-Hoover thermostat
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(<a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>) is NOT recommended due to its well documented
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issues with the canonical sampling of harmonic degrees of freedom
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@ -412,12 +412,10 @@ and restart files.</p>
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this case), the print-out to the screen and master log.lammps file
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contains a line of output, printed once every <em>Nevery</em> timesteps. It
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contains the timestep, the maximum force per replica, the maximum
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force per atom (in any replica), potential gradients in the initial,</p>
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<blockquote>
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<div>final, and climbing replicas,</div></blockquote>
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<p>the forward and backward energy barriers,
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the total reaction coordinate (RDT), and
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the normalized reaction coordinate and potential energy of each replica.</p>
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force per atom (in any replica), potential gradients in the initial,
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final, and climbing replicas, the forward and backward energy barriers,
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the total reaction coordinate (RDT), and the normalized reaction
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coordinate and potential energy of each replica.</p>
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<p>The “maximum force per replica” is
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the two-norm of the 3N-length force vector for the atoms in each
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replica, maximized across replicas, which is what the <em>ftol</em> setting
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|
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@ -287,8 +287,8 @@ choices for the exponent are n = 2 or n = 1. For the remaining
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coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
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appropriate choices. Plots of the LJ and Coulomb terms are shown
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below, for lambda ranging from 1 to 0 every 0.1.</p>
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<img alt="_images/lj_soft.jpg" class="align-center" src="_images/lj_soft.jpg" />
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<img alt="_images/coul_soft.jpg" class="align-center" src="_images/coul_soft.jpg" />
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<img alt="_images/lj_soft.jpg" src="_images/lj_soft.jpg" />
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<img alt="_images/coul_soft.jpg" src="_images/coul_soft.jpg" />
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<p>For the <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> pair styles,
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the following coefficients must be defined for each pair of atoms
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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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@ -40,8 +40,6 @@ compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre
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fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd
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fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre
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:pre
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[Description:]
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Define a computation that calculates x-ray diffraction intensity as described
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|
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@ -107,48 +105,48 @@ Coefficients parameterized by "(Peng)"_#Peng are assigned for each
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atom type designating the chemical symbol and charge of each atom
|
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type. Valid chemical symbols for compute xrd are:
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|
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H: He1-: He: Li: Li1+:
|
||||
Be: Be2+: B: C: Cval:
|
||||
N: O: O1-: F: F1-:
|
||||
Ne: Na: Na1+: Mg: Mg2+:
|
||||
Al: Al3+: Si: Sival: Si4+:
|
||||
P: S: Cl: Cl1-: Ar:
|
||||
K: Ca: Ca2+: Sc: Sc3+:
|
||||
Ti: Ti2+: Ti3+: Ti4+: V:
|
||||
V2+: V3+: V5+: Cr: Cr2+:
|
||||
Cr3+: Mn: Mn2+: Mn3+: Mn4+:
|
||||
Fe: Fe2+: Fe3+: Co: Co2+:
|
||||
Co: Ni: Ni2+: Ni3+: Cu:
|
||||
Cu1+: Cu2+: Zn: Zn2+: Ga:
|
||||
Ga3+: Ge: Ge4+: As: Se:
|
||||
Br: Br1-: Kr: Rb: Rb1+:
|
||||
Sr: Sr2+: Y: Y3+: Zr:
|
||||
Zr4+: Nb: Nb3+: Nb5+: Mo:
|
||||
Mo3+: Mo5+: Mo6+: Tc: Ru:
|
||||
Ru3+: Ru4+: Rh: Rh3+: Rh4+:
|
||||
Pd: Pd2+: Pd4+: Ag: Ag1+:
|
||||
Ag2+: Cd: Cd2+: In: In3+:
|
||||
Sn: Sn2+: Sn4+: Sb: Sb3+:
|
||||
Sb5+: Te: I: I1-: Xe:
|
||||
Cs: Cs1+: Ba: Ba2+: La:
|
||||
La3+: Ce: Ce3+: Ce4+: Pr:
|
||||
Pr3+: Pr4+: Nd: Nd3+: Pm:
|
||||
Pm3+: Sm: Sm3+: Eu: Eu2+:
|
||||
Eu3+: Gd: Gd3+: Tb: Tb3+:
|
||||
Dy: Dy3+: Ho: Ho3+: Er:
|
||||
Er3+: Tm: Tm3+: Yb: Yb2+:
|
||||
Yb3+: Lu: Lu3+: Hf: Hf4+:
|
||||
Ta: Ta5+: W: W6+: Re:
|
||||
Os: Os4+: Ir: Ir3+: Ir4+:
|
||||
Pt: Pt2+: Pt4+: Au: Au1+:
|
||||
Au3+: Hg: Hg1+: Hg2+: Tl:
|
||||
Tl1+: Tl3+: Pb: Pb2+: Pb4+:
|
||||
Bi: Bi3+: Bi5+: Po: At:
|
||||
Rn: Fr: Ra: Ra2+: Ac:
|
||||
Ac3+: Th: Th4+: Pa: U:
|
||||
U3+: U4+: U6+: Np: Np3+:
|
||||
Np4+: Np6+: Pu: Pu3+: Pu4+:
|
||||
Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:)
|
||||
H| He1-| He| Li| Li1+|
|
||||
Be| Be2+| B| C| Cval|
|
||||
N| O| O1-| F| F1-|
|
||||
Ne| Na| Na1+| Mg| Mg2+|
|
||||
Al| Al3+| Si| Sival| Si4+|
|
||||
P| S| Cl| Cl1-| Ar|
|
||||
K| Ca| Ca2+| Sc| Sc3+|
|
||||
Ti| Ti2+| Ti3+| Ti4+| V|
|
||||
V2+| V3+| V5+| Cr| Cr2+|
|
||||
Cr3+| Mn| Mn2+| Mn3+| Mn4+|
|
||||
Fe| Fe2+| Fe3+| Co| Co2+|
|
||||
Co| Ni| Ni2+| Ni3+| Cu|
|
||||
Cu1+| Cu2+| Zn| Zn2+| Ga|
|
||||
Ga3+| Ge| Ge4+| As| Se|
|
||||
Br| Br1-| Kr| Rb| Rb1+|
|
||||
Sr| Sr2+| Y| Y3+| Zr|
|
||||
Zr4+| Nb| Nb3+| Nb5+| Mo|
|
||||
Mo3+| Mo5+| Mo6+| Tc| Ru|
|
||||
Ru3+| Ru4+| Rh| Rh3+| Rh4+|
|
||||
Pd| Pd2+| Pd4+| Ag| Ag1+|
|
||||
Ag2+| Cd| Cd2+| In| In3+|
|
||||
Sn| Sn2+| Sn4+| Sb| Sb3+|
|
||||
Sb5+| Te| I| I1-| Xe|
|
||||
Cs| Cs1+| Ba| Ba2+| La|
|
||||
La3+| Ce| Ce3+| Ce4+| Pr|
|
||||
Pr3+| Pr4+| Nd| Nd3+| Pm|
|
||||
Pm3+| Sm| Sm3+| Eu| Eu2+|
|
||||
Eu3+| Gd| Gd3+| Tb| Tb3+|
|
||||
Dy| Dy3+| Ho| Ho3+| Er|
|
||||
Er3+| Tm| Tm3+| Yb| Yb2+|
|
||||
Yb3+| Lu| Lu3+| Hf| Hf4+|
|
||||
Ta| Ta5+| W| W6+| Re|
|
||||
Os| Os4+| Ir| Ir3+| Ir4+|
|
||||
Pt| Pt2+| Pt4+| Au| Au1+|
|
||||
Au3+| Hg| Hg1+| Hg2+| Tl|
|
||||
Tl1+| Tl3+| Pb| Pb2+| Pb4+|
|
||||
Bi| Bi3+| Bi5+| Po| At|
|
||||
Rn| Fr| Ra| Ra2+| Ac|
|
||||
Ac3+| Th| Th4+| Pa| U|
|
||||
U3+| U4+| U6+| Np| Np3+|
|
||||
Np4+| Np6+| Pu| Pu3+| Pu4+|
|
||||
Pu6+| Am| Cm| Bk| Cf :tb(c=5,s=|)
|
||||
|
||||
If the {echo} keyword is specified, compute xrd will provide extra
|
||||
reporting information to the screen.
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ but no more than max_steps will be taken. If max_steps is reached, an error warn
|
|||
is printed and the simulation is stopped.
|
||||
|
||||
After each ODE step, the solution error {e} is tested and weighted using the absTol
|
||||
and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol)
|
||||
and relTol values. The error vector is weighted as {e} / (relTol * | {u} | + absTol)
|
||||
where {u} is the solution vector. If the norm of the error is <= 1, the solution is
|
||||
accepted, {h} is increased by a proportional amount, and the next ODE step is begun.
|
||||
Otherwise, {h} is shrunk and the ODE step is repeated.
|
||||
|
|
|
|||
|
|
@ -86,7 +86,7 @@ NOTE: It is importante to keep the center of mass fixed during the
|
|||
thermodynamic integration, a non-zero total velocity will result in
|
||||
divergencies during the integration due to the fact that the atoms are
|
||||
'attatched' to its equilibrium positions by the Einstein
|
||||
crystal. Check the option {zero} of "fix langevin"_fix_langevin_html
|
||||
crystal. Check the option {zero} of "fix langevin"_fix_langevin.html
|
||||
and "velocity"_velocity.html. The use of the Nose-Hoover thermostat
|
||||
("fix nvt"_fix_nh.html) is NOT recommended due to its well documented
|
||||
issues with the canonical sampling of harmonic degrees of freedom
|
||||
|
|
|
|||
|
|
@ -319,10 +319,9 @@ this case), the print-out to the screen and master log.lammps file
|
|||
contains a line of output, printed once every {Nevery} timesteps. It
|
||||
contains the timestep, the maximum force per replica, the maximum
|
||||
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.
|
||||
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.
|
||||
|
||||
The "maximum force per replica" is
|
||||
the two-norm of the 3N-length force vector for the atoms in each
|
||||
|
|
|
|||
|
|
@ -134,7 +134,8 @@ 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.
|
||||
|
||||
:c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
|
||||
:image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
|
||||
:c
|
||||
|
||||
For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
|
||||
the following coefficients must be defined for each pair of atoms
|
||||
|
|
|
|||
Loading…
Reference in New Issue