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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15031 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-05-11 20:36:18 +00:00
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8 changed files with 80 additions and 73 deletions
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32
doc/html/Section_commands.html
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@ -1182,10 +1182,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="23%" />
<col width="23%" />
<col width="21%" />
<col width="24%" />
<col width="30%" />
<col width="25%" />
<col width="31%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><span class="doc">awpmd/cut</span></a></td>
@ -1194,38 +1194,38 @@ if <a class="reference internal" href="Section_start.html#start-3"><span class="
<td><a class="reference internal" href="pair_coul_diel.html"><span class="doc">coul/diel (o)</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">coul/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_dpd_conservative.html"><span class="doc">dpd/conservative</span></a></td>
<td><a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">dpd/fdt</span></a></td>
<td><a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">dpd/fdt/energy</span></a></td>
<td><a class="reference internal" href="pair_eam.html"><span class="doc">eam/cd (o)</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_eam.html"><span class="doc">eam/cd (o)</span></a></td>
<td><a class="reference internal" href="pair_edip.html"><span class="doc">edip (o)</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_edip.html"><span class="doc">edip (o)</span></a></td>
<td><a class="reference internal" href="pair_eff.html"><span class="doc">eff/cut</span></a></td>
<td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss/cut</span></a></td>
<td><a class="reference internal" href="pair_mdf.html"><span class="doc">lennard/mdf</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><span class="doc">lennard/mdf</span></a></td>
<td><a class="reference internal" href="pair_list.html"><span class="doc">list</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_list.html"><span class="doc">list</span></a></td>
<td><a class="reference internal" href="pair_charmm.html"><span class="doc">lj/charmm/coul/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/cut/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/long/soft (o)</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/cut/dipole/sf (go)</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/cut/dipole/sf (go)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_thole.html"><span class="doc">lj/cut/thole/long (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/tip4p/long/soft (o)</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/tip4p/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_mdf.html"><span class="doc">lj/mdf</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><span class="doc">lj/mdf</span></a></td>
<td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk (gko)</span></a></td>
<td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/long (go)</span></a></td>
<td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/msm (o)</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/msm (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_sf.html"><span class="doc">lj/sf (o)</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_sf.html"><span class="doc">lj/sf (o)</span></a></td>
<td><a class="reference internal" href="pair_meam_spline.html"><span class="doc">meam/spline</span></a></td>
<td><a class="reference internal" href="pair_meam_sw_spline.html"><span class="doc">meam/sw/spline</span></a></td>
<td><a class="reference internal" href="pair_mgpt.html"><span class="doc">mgpt</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_mgpt.html"><span class="doc">mgpt</span></a></td>
<td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/smooth/linear</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/smooth/linear</span></a></td>
<td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/soft</span></a></td>
<td><a class="reference internal" href="pair_multi_lucy.html"><span class="doc">multi/lucy</span></a></td>
<td><a class="reference internal" href="pair_quip.html"><span class="doc">quip</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>

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@ -2101,7 +2101,7 @@ more details.</p>
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>
<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a>
<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>
<a class="reference internal" href="pair_dpd_conservative.html"><span class="doc">pair_dpd/conservative</span></a>
<span class="xref doc">pair_dpd/conservative</span>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair_dpd/fdt</span></a>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair_dpd/fdt/energy</span></a>, examples/USER/dpd</p>
<p>Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),

40
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@ -648,31 +648,31 @@ KOKKOS, o = USER-OMP, t = OPT.
These are additional pair styles in USER packages, which can be used
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/conservative <pair_dpd_conservative>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`eam/cd (o) <pair_eam>` | :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lennard/mdf <pair_mdf>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` | :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` | :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/sdk/coul/msm (o) <pair_sdk>` | :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`mgpt <pair_mgpt>` | :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`quip <pair_quip>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` | :doc:`eam/cd (o) <pair_eam>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | :doc:`lennard/mdf <pair_mdf>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` | :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` | :doc:`lj/sdk/coul/msm (o) <pair_sdk>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` | :doc:`mgpt <pair_mgpt>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`quip <pair_quip>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` | :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
----------

26
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@ -542,17 +542,21 @@ There are several options for outputting atom coordinates. The *x*\ ,
appropriate distance :doc:`units <units>` (Angstroms, sigma, etc). Use
*xs*\ , *ys*\ , *zs* if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. Use
*xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that using *xu*\ , *yu*\ , *zu* means that the
coordinate values may be far outside the box bounds printed with the
snapshot. Using *xsu*\ , *ysu*\ , *zsu* is similar to using *xu*\ , *yu*\ , *zu*\ ,
except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.
(tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed
in :ref:`Section howto 6.12 <howto_12>`.
Use *xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has
passed thru a periodic boundary one or more times, the value is
printed for what the coordinate would be if it had not been wrapped
back into the periodic box. Note that using *xu*\ , *yu*\ , *zu* means
that the coordinate values may be far outside the box bounds printed
with the snapshot. Using *xsu*\ , *ysu*\ , *zsu* is similar to using
*xu*\ , *yu*\ , *zu*\ , except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
have the corresponding cooordinate increased or decreased by 1.0.
The image flags can be printed directly using the *ix*\ , *iy*\ , *iz*
attributes. For periodic dimensions, they specify which image of the

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@ -590,17 +590,20 @@ atom velocity and force and atomic charge.</p>
appropriate distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> (Angstroms, sigma, etc). Use
<em>xs</em>, <em>ys</em>, <em>zs</em> if you want the coordinates &#8220;scaled&#8221; to the box size,
so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. Use
<em>xu</em>, <em>yu</em>, <em>zu</em> if you want the coordinates &#8220;unwrapped&#8221; by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that using <em>xu</em>, <em>yu</em>, <em>zu</em> means that the
coordinate values may be far outside the box bounds printed with the
snapshot. Using <em>xsu</em>, <em>ysu</em>, <em>zsu</em> is similar to using <em>xu</em>, <em>yu</em>, <em>zu</em>,
except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.</p>
(tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed
in <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">Section howto 6.12</span></a>.</p>
<p>Use <em>xu</em>, <em>yu</em>, <em>zu</em> if you want the coordinates &#8220;unwrapped&#8221; by the
image flags for each atom. Unwrapped means that if the atom has
passed thru a periodic boundary one or more times, the value is
printed for what the coordinate would be if it had not been wrapped
back into the periodic box. Note that using <em>xu</em>, <em>yu</em>, <em>zu</em> means
that the coordinate values may be far outside the box bounds printed
with the snapshot. Using <em>xsu</em>, <em>ysu</em>, <em>zsu</em> is similar to using
<em>xu</em>, <em>yu</em>, <em>zu</em>, except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
have the corresponding cooordinate increased or decreased by 1.0.</p>
<p>The image flags can be printed directly using the <em>ix</em>, <em>iy</em>, <em>iz</em>
attributes. For periodic dimensions, they specify which image of the
simulation box the atom is considered to be in. An image of 0 means

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@ -153,7 +153,7 @@
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Use the Muller-Plathe algorithm described in <a class="reference internal" href="#muller-plathe"><span class="std std-ref">this paper</span></a> to exchange kinetic energy between two particles
<p>Use the Muller-Plathe algorithm described in <a class="reference internal" href="fix_viscosity.html#muller-plathe"><span class="std std-ref">this paper</span></a> to exchange kinetic energy between two particles
in different regions of the simulation box every N steps. This
induces a temperature gradient in the system. As described below this
enables the thermal conductivity of a material to be calculated. This
@ -202,7 +202,7 @@ swaps is computed by the fix and can be output. Dividing this
quantity by time and the cross-sectional area of the simulation box
yields a heat flux. The ratio of heat flux to the slope of the
temperature profile is proportional to the thermal conductivity of the
fluid, in appropriate units. See the <a class="reference internal" href="#muller-plathe"><span class="std std-ref">Muller-Plathe paper</span></a> for details.</p>
fluid, in appropriate units. See the <a class="reference internal" href="fix_viscosity.html#muller-plathe"><span class="std std-ref">Muller-Plathe paper</span></a> for details.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If your system is periodic in the direction of the heat flux,

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@ -1800,10 +1800,6 @@
</dt>
<dt><a href="pair_dpd_conservative.html#index-0">pair_style dpd/conservative</a>
</dt>
<dt><a href="pair_dpd_fdt.html#index-0">pair_style dpd/fdt</a>
</dt>
@ -1915,12 +1911,12 @@
<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
</dt>
@ -1950,6 +1946,10 @@
</dt>
<dt><a href="pair_multi_lucy.html#index-0">pair_style multi/lucy</a>
</dt>
<dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
</dt>

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