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474 <span·class="k">fix·</span><span·class="nv·nv-Identifier">NPT</span><span·class="w">·</span><span·class="nv·nv-Identifier">ATOMS</span><span·class="w">·</span><span·class="n">npt</span><span·class="w">·</span><span·class="n">temp</span><span·class="w">·</span><span·class="m">300</span><span·class="n">.</span><span·class="w">·</span><span·class="m">300</span><span·class="n">.</span><span·class="w">·</span><span·class="m">100</span><span·class="w">·</span><span·class="n">iso</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">500</span>474 <span·class="k">fix·</span><span·class="nv·nv-Identifier">NPT</span><span·class="w">·</span><span·class="nv·nv-Identifier">ATOMS</span><span·class="w">·</span><span·class="n">npt</span><span·class="w">·</span><span·class="n">temp</span><span·class="w">·</span><span·class="m">300</span><span·class="n">.</span><span·class="w">·</span><span·class="m">300</span><span·class="n">.</span><span·class="w">·</span><span·class="m">100</span><span·class="w">·</span><span·class="n">iso</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">500</span>
475 <span·class="k">fix_modify·</span><span·class="nv·nv-Identifier">NPT</span><span·class="w">·</span><span·class="n">temp</span><span·class="w">·</span><span·class="n">TATOMS</span><span·class="w">·</span><span·class="n">press</span><span·class="w">·</span><span·class="n">thermo_press</span>475 <span·class="k">fix_modify·</span><span·class="nv·nv-Identifier">NPT</span><span·class="w">·</span><span·class="n">temp</span><span·class="w">·</span><span·class="n">TATOMS</span><span·class="w">·</span><span·class="n">press</span><span·class="w">·</span><span·class="n">thermo_press</span>
476 <span·class="k">fix·</span><span·class="nv·nv-Identifier">NVT</span><span·class="w">·</span><span·class="nv·nv-Identifier">DRUDES</span><span·class="w">·</span><span·class="n">nvt</span><span·class="w">·</span><span·class="n">temp</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">20</span>476 <span·class="k">fix·</span><span·class="nv·nv-Identifier">NVT</span><span·class="w">·</span><span·class="nv·nv-Identifier">DRUDES</span><span·class="w">·</span><span·class="n">nvt</span><span·class="w">·</span><span·class="n">temp</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">1</span><span·class="n">.</span><span·class="w">·</span><span·class="m">20</span>
477 <span·class="k">fix·</span><span·class="nv·nv-Identifier">INVERSE</span><span·class="w">·</span><span·class="nv·nv-Identifier">all</span><span·class="w">·</span><span·class="n">drude</span><span·class="o">/</span><span·class="n">transform</span><span·class="o">/</span><span·class="n">inverse</span>477 <span·class="k">fix·</span><span·class="nv·nv-Identifier">INVERSE</span><span·class="w">·</span><span·class="nv·nv-Identifier">all</span><span·class="w">·</span><span·class="n">drude</span><span·class="o">/</span><span·class="n">transform</span><span·class="o">/</span><span·class="n">inverse</span>
478 </pre></div>478 </pre></div>
479 </div>479 </div>
480 <p>Another·option·for·thermalizing·the·Drude·model·is·to·use·the480 <p>Another·option·for·thermalizing·the·Drude·model·is·to·use·the
481 temperature-grouped·Nose-Hoover·(TGNH)·thermostat·proposed·by·<a·class="reference·internal"·href="#tgnh-son"><span·class="std·std-ref">(Son)</span></a>.481 temperature-grouped·Nose-Hoover·(TGNH)·thermostat·proposed·by·<a·class="reference·internal"·href="fix_tgnh_drude.html#tgnh-son"><span·class="std·std-ref">(Son)</span></a>.
482 This·is·implemented·as·<a·class="reference·internal"·href="fix_tgnh_drude.html"><span·class="doc">fix·tgnvt/drude</span></a>·and·<a·class="reference·internal"·href="fix_tgnh_drude.html"><span·class="doc">fix·tgnpt/drude</span></a>.482 This·is·implemented·as·<a·class="reference·internal"·href="fix_tgnh_drude.html"><span·class="doc">fix·tgnvt/drude</span></a>·and·<a·class="reference·internal"·href="fix_tgnh_drude.html"><span·class="doc">fix·tgnpt/drude</span></a>.
483 It·separates·the·kinetic·energy·into·three·contributions:483 It·separates·the·kinetic·energy·into·three·contributions:
484 the·molecular·center·of·mass·(COM)·motion,·the·motion·of·atoms·or·atom-Drude·pairs·relative·to·molecular·COMs,484 the·molecular·center·of·mass·(COM)·motion,·the·motion·of·atoms·or·atom-Drude·pairs·relative·to·molecular·COMs,
485 and·the·relative·motion·of·atom-Drude·pairs.485 and·the·relative·motion·of·atom-Drude·pairs.
486 An·independent·Nose-Hoover·chain·is·applied·to·each·type·of·motion.486 An·independent·Nose-Hoover·chain·is·applied·to·each·type·of·motion.
487 When·TGNH·is·used,·the·temperatures·of·molecular,·atomic·and·Drude·motion·can·be·printed·out·with·<a·class="reference·internal"·href="thermo_style.html"><span·class="doc">thermo_style·command</span></a>·command.</p>487 When·TGNH·is·used,·the·temperatures·of·molecular,·atomic·and·Drude·motion·can·be·printed·out·with·<a·class="reference·internal"·href="thermo_style.html"><span·class="doc">thermo_style·command</span></a>·command.</p>
488 <p>NVT·simulation·with·TGNH·thermostat</p>488 <p>NVT·simulation·with·TGNH·thermostat</p>
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452 </div>452 </div>
453 <p>Example·input·scripts·available:·examples/PACKAGES/drude</p>453 <p>Example·input·scripts·available:·examples/PACKAGES/drude</p>
454 </section>454 </section>
455 <section·id="description">455 <section·id="description">
456 <h2>Description<a·class="headerlink"·href="#description"·title="Link·to·this·heading"></a></h2>456 <h2>Description<a·class="headerlink"·href="#description"·title="Link·to·this·heading"></a></h2>
457 <p>These·commands·are·variants·of·the·Nose-Hoover·fix·styles·<a·class="reference·internal"·href="fix_nh.html"><span·class="doc">fix·nvt</span></a>·and·<a·class="reference·internal"·href="fix_nh.html"><span·class="doc">fix·npt</span></a>·for·thermalized·Drude·polarizable457 <p>These·commands·are·variants·of·the·Nose-Hoover·fix·styles·<a·class="reference·internal"·href="fix_nh.html"><span·class="doc">fix·nvt</span></a>·and·<a·class="reference·internal"·href="fix_nh.html"><span·class="doc">fix·npt</span></a>·for·thermalized·Drude·polarizable
458 models.··They·apply·temperature-grouped·Nose-Hoover·thermostat·(TGNH)458 models.··They·apply·temperature-grouped·Nose-Hoover·thermostat·(TGNH)
459 proposed·by·<a·class="reference·internal"·href="Howto_drude2.html#tgnh-son"><span·class="std·std-ref">(Son)</span></a>.··When·there·are·fast·vibrational459 proposed·by·<a·class="reference·internal"·href="#tgnh-son"><span·class="std·std-ref">(Son)</span></a>.··When·there·are·fast·vibrational
460 modes·with·frequencies·close·to·Drude·oscillators·(e.g.·double·bonds·or460 modes·with·frequencies·close·to·Drude·oscillators·(e.g.·double·bonds·or
461 out-of-plane·torsions),·this·thermostat·can·provide·better·kinetic461 out-of-plane·torsions),·this·thermostat·can·provide·better·kinetic
462 energy·equipartitioning.</p>462 energy·equipartitioning.</p>
463 <p>The·difference·between·TGNH·and·the·original·Nose-Hoover·thermostat·is·that,463 <p>The·difference·between·TGNH·and·the·original·Nose-Hoover·thermostat·is·that,
464 TGNH·separates·the·kinetic·energy·of·the·group·into·three·contributions:464 TGNH·separates·the·kinetic·energy·of·the·group·into·three·contributions:
465 molecular·center·of·mass·(COM)·motion,465 molecular·center·of·mass·(COM)·motion,
466 motion·of·COM·of·atom-Drude·pairs·or·non-polarizable·atoms·relative·to·molecular·COM,466 motion·of·COM·of·atom-Drude·pairs·or·non-polarizable·atoms·relative·to·molecular·COM,
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./usr/share/doc/lammps/html/objects.inv
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Sphinx inventory
    
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160 }'}(=uGmPH\xe\xfܓ$)5N\x14E=\x17hp\x8qT?GSDLkmw\x1cg9\x16ȵ^;\x3@MEӵ8B)`\x12Fz=ƏE50\x1b\x1e\x1aq'B&\x1f*grsINU.]\x14i\x16\x0)j"\x15\x190q\x1fi\x12^\x1dǽ\x1f-j*XQQ5u\x1c.;7O0Ehp\xd7֖p\xc}$\x74t\x11K\x17f5`\x13¤\xd»     \x3\xdD\x19\x18`_܋1@\xbKÝOޥv4JWP\x0%H·~W!\xfUx>O蟏C\xd`\x1c;\x1a\x1eDy3Sg`\x8\x4160 }'}(=uGmPH\xe\xfܓ$)5N\x14E=\x17hp\x8qT?GSDLkmw\x1cg9\x16ȵ^;\x3@MEӵ8B)`\x12Fz=ƏE50\x1b\x1e\x1aq'B&\x1f*grsINU.]\x14i\x16\x0)j"\x15\x190q\x1fi\x12^\x1dǽ\x1f-j*XQQ5u\x1c.;7O0Ehp\xd7֖p\xc}$\x74t\x11K\x17f5`\x13¤\xd»     \x3\xdD\x19\x18`_܋1@\xbKÝOޥv4JWP\x0%H·~W!\xfUx>O蟏C\xd`\x1c;\x1a\x1eDy3Sg`\x8\x4
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