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@ -2001,15 +2001,17 @@ periodic box. By holding the two regions at different temperatures
with a <a class="reference internal" href="#howto-13"><span class="std std-ref">thermostatting fix</span></a>, the energy
added to the hot region should equal the energy subtracted from the
cold region and be proportional to the heat flux moving between the
regions. See the paper by <a class="reference internal" href="#ikeshoji"><span class="std std-ref">Ikeshoji and Hafskjold</span></a> for
details of this idea. Note that thermostatting fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, and <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> store the cumulative energy they
regions. See the papers by <a class="reference internal" href="#howto-ikeshoji"><span class="std std-ref">Ikeshoji and Hafskjold</span></a>
and <a class="reference internal" href="#howto-wirnsberger"><span class="std std-ref">Wirnsberger et al</span></a> for details of this idea.
Note that thermostatting fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, and <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> store the cumulative energy they
add/subtract.</p>
<p>Alternatively, as a second method, the <a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>
command can used in place of thermostats on each of two regions to
add/subtract specified amounts of energy to both regions. In both
cases, the resulting temperatures of the two regions can be monitored
with the &#8220;compute temp/region&#8221; command and the temperature profile of
the intermediate region can be monitored with the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.</p>
<p>Alternatively, as a second method, the <a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a> or
<a class="reference internal" href="fix_ehex.html"><span class="doc">fix ehex</span></a> commands can be used in place of thermostats
on each of two regions to add/subtract specified amounts of energy to
both regions. In both cases, the resulting temperatures of the two
regions can be monitored with the &#8220;compute temp/region&#8221; command and
the temperature profile of the intermediate region can be monitored
with the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a> and <a class="reference internal" href="compute_ke_atom.html"><span class="doc">compute ke/atom</span></a> commands.</p>
<p>The third method is to perform a reverse non-equilibrium MD simulation
using the <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>
command which implements the rNEMD algorithm of Muller-Plathe.
@ -2782,8 +2784,10 @@ too close, which can cause numerical issues.</p>
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
<p id="horn"><strong>(Horn)</strong> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).</p>
<p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
<p id="howto-ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).</p>
<p id="howto-wirnsberger"><strong>(Wirnsberger)</strong> Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).</p>
<p id="howto-mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<p id="howto-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909