ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
This commit is contained in:
sjplimp
2016-05-11 20:36:18 +00:00
parent 3e4b83abaa
commit 8caee4c0e1
8 changed files with 80 additions and 73 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
doc/html/Section_commands.html
View File

@ -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> 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"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="23%" /> <col width="21%" />
<col width="23%" />
<col width="24%" /> <col width="24%" />
<col width="30%" /> <col width="25%" />
<col width="31%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><span class="doc">awpmd/cut</span></a></td> <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> <td><a class="reference internal" href="pair_coul_diel.html"><span class="doc">coul/diel (o)</span></a></td>
</tr> </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> <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</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_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>
<tr class="row-odd"><td><a class="reference internal" href="pair_eam.html"><span class="doc">eam/cd (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_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_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_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>
<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><span class="doc">lennard/mdf</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_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_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/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>
<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> <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_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_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_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>
<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> <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_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 (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/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>
<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/msm (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_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_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_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>
<tr class="row-even"><td><a class="reference internal" href="pair_mgpt.html"><span class="doc">mgpt</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/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_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> <td><a class="reference internal" href="pair_quip.html"><span class="doc">quip</span></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td> <tr class="row-odd"><td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>

2
doc/html/Section_packages.html
View File

@ -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="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_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="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</span></a>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair_dpd/fdt/energy</span></a>, examples/USER/dpd</p> <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), <p>Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),

50
doc/html/_sources/Section_commands.txt
View File

@ -648,31 +648,31 @@ KOKKOS, o = USER-OMP, t = OPT.
These are additional pair styles in USER packages, which can be used These are additional pair styles in USER packages, which can be used
if :ref:`LAMMPS is built with the appropriate package <start_3>`. 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:`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:`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:`eam/cd (o) <pair_eam>` | :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | | :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | :doc:`lennard/mdf <pair_mdf>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :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:`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/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/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/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/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/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:`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:`mgpt <pair_mgpt>` | :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`quip <pair_quip>` | | :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:`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:`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:`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>` | | :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
---------- ----------

26
doc/html/_sources/dump.txt
View File

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

25
doc/html/dump.html
View File

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

4
doc/html/fix_thermal_conductivity.html
View File

@ -153,7 +153,7 @@
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 in different regions of the simulation box every N steps. This
induces a temperature gradient in the system. As described below this induces a temperature gradient in the system. As described below this
enables the thermal conductivity of a material to be calculated. 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 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 yields a heat flux. The ratio of heat flux to the slope of the
temperature profile is proportional to the thermal conductivity 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"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">If your system is periodic in the direction of the heat flux, <p class="last">If your system is periodic in the direction of the heat flux,

12
doc/html/genindex.html
View File

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

2
doc/html/searchindex.js
View File

File diff suppressed because one or more lines are too long