mirror of https://gitlab.com/QEF/q-e.git
391 lines
20 KiB
HTML
391 lines
20 KiB
HTML
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</style>
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<title>molecularpdos.x: input description</title>
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</head>
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<body>
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<a name="__top__"></a><table style="border-width: 0; table-layout: auto; width: 100%; text-align: left; vertical-align: top; background: #00395a;">
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<tr><th style="margin: 3 3 3 10; background: #005789; background: linear-gradient(rgba(0,87,137,1),rgba(0,119,189,1)); color: #ffffee; ">
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<h1 style="margin: 10 10 10 15; text-align: left;"> Input File Description </h1>
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<h2 style="margin: 10 10 10 15; text-align: left;"> Program:
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molecularpdos.x / PWscf / Quantum Espresso<span style="font-weight: normal;"> (version: 6.4)</span>
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</h2>
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</th></tr>
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<tr><td style="padding: 10 3 3 3; background: #ffffff; color: #222222; ">
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<blockquote style="margin-bottom: 2em;">
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<h3>TABLE OF CONTENTS</h3>
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<blockquote>
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<p><a href="#idm3">INTRODUCTION</a></p>
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<p><a href="#idm9">&INPUTMOPDOS</a></p>
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<blockquote>
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<a href="#idm11">xmlfile_full</a> | <a href="#idm12">xmlfile_part</a> | <a href="#idm14">i_atmwfc_beg_full</a> | <a href="#idm17">i_atmwfc_end_full</a> | <a href="#idm20">i_atmwfc_beg_part</a> | <a href="#idm23">i_atmwfc_end_part</a> | <a href="#idm26">i_bnd_beg_full</a> | <a href="#idm29">i_bnd_end_full</a> | <a href="#idm32">i_bnd_beg_part</a> | <a href="#idm35">i_bnd_end_part</a> | <a href="#idm38">fileout</a> | <a href="#idm41">ngauss</a> | <a href="#idm44">degauss</a> | <a href="#idm48">Emin</a> | <a href="#idm49">Emax</a> | <a href="#idm52">DeltaE</a> | <a href="#idm55">kresolveddos</a>
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</blockquote>
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<p><a href="#idm58">Notes</a></p>
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<blockquote><a href="#idm59">Format of output files</a></blockquote>
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<blockquote><a href="#idm61">Important notices</a></blockquote>
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</blockquote>
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</blockquote>
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<blockquote>
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<a name="idm3"></a><h3>INTRODUCTION</h3>
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<blockquote><pre>
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<b>Purpose of molecularpdos.x:</b>
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Takes the projections onto orthogonalized atomic wavefunctions
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as computed by projwfc.x (see outdir/prefix.save/atomic_proj.xml)
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to build an LCAO-like representation of the eigenvalues of a system
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"full" and "part" of it (each should provide its own atomic_proj.xml file).
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Then the eigenvectors of the full system are projected onto the ones
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of the part. For example, to decompose the PDOS of an adsorbed molecule
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into its molecular orbital, as determined by a gas-phase calculation.
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Reference:
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An explanation of the keywords and the implementation
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is provided in Scientific Reports | 6:24603 (2016)
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<a href="http://dx.doi.org/10.1038/srep24603">DOI: 10.1038/srep24603</a> (Supp. Info).
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<b>Structure of the input data:</b>
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============================
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<b>&INPUTMOPDOS</b>
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...
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<b>/</b>
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</pre></blockquote>
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</blockquote>
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<a name="idm9"></a><a name="INPUTMOPDOS"></a><table border="0" width="100%" style="margin-bottom: 20;">
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<tr><th bgcolor="#ddcba6"><h2 style="margin: 10 10 10 15; text-align: left;"> Namelist: <span class="namelist"><span style="font-weight:normal">&</span>INPUTMOPDOS</span>
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</h2></th></tr>
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<tr><td style="text-align: left; background: #ffebc6; padding: 5 5 5 30; "><table style="border-color: #505087; border-style: solid; border-width: 0; margin-bottom: 10; table-layout: auto; width: 800;"><tbody><tr><td>
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<table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="white-space: nowrap; background: #ffff99; padding: 2 2 2 10; ">
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<a name="idm11"></a><a name="xmlfile_full"></a>xmlfile_full, <a name="idm12"></a><a name="xmlfile_part"></a>xmlfile_part</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">CHARACTER</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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xml files with atomic projections (produced by projwfc.x)
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for the full system and its molecular part
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm14"></a><a name="i_atmwfc_beg_full"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_atmwfc_beg_full</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 1
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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first atomic wavefunction of the full system
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considered for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm17"></a><a name="i_atmwfc_end_full"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_atmwfc_end_full</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0, i.e., all atomic wavefunctions
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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last atomic wavefunction of the full system
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considered for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm20"></a><a name="i_atmwfc_beg_part"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_atmwfc_beg_part</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 1
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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first atomic wavefunction of the molecular part
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considered for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm23"></a><a name="i_atmwfc_end_part"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_atmwfc_end_part</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0, i.e., all atomic wavefunctions
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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first atomic wavefunction of the molecular part
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considered for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm26"></a><a name="i_bnd_beg_full"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_bnd_beg_full</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 1
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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first eigenstate of the full system to be taken
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into account for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm29"></a><a name="i_bnd_end_full"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_bnd_end_full</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0, i.e., all eigenstates
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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last eigenstate of the full system to be taken
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into account for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm32"></a><a name="i_bnd_beg_part"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_bnd_beg_part</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 1
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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first eigenstate of the molecular part to be taken
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into account for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm35"></a><a name="i_bnd_end_part"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">i_bnd_end_part</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0, i.e., all eigenstates
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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last eigenstate of the molecular part to be taken
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into account for the projection
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm38"></a><a name="fileout"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">fileout</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">CHARACTER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 'molecularpdos'
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;"> prefix for output files containing molecular PDOS(E)
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm41"></a><a name="ngauss"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">ngauss</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">INTEGER</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
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Type of gaussian broadening:
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0 ... Simple Gaussian (default)
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1 ... Methfessel-Paxton of order 1
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-1 ... "cold smearing" (Marzari-Vanderbilt-DeVita-Payne)
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-99 ... Fermi-Dirac function
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm44"></a><a name="degauss"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">degauss</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">REAL</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0.0
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;"> gaussian broadening, Ry (not eV!)
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="white-space: nowrap; background: #ffff99; padding: 2 2 2 10; ">
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<a name="idm48"></a><a name="Emin"></a>Emin, <a name="idm49"></a><a name="Emax"></a>Emax</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">REAL</td>
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</tr>
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<tr>
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<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
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<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> (band extrema)
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</td>
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</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;"> min & max energy (eV) for DOS plot
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</pre></blockquote></td></tr>
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</table>
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
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<a name="idm52"></a><a name="DeltaE"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
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<tr>
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<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">DeltaE</th>
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<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">REAL</td>
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</tr>
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|
<tr>
|
|
<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
|
|
<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> 0.01
|
|
</td>
|
|
</tr>
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<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;"> energy grid step (eV)
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|
</pre></blockquote></td></tr>
|
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</table>
|
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<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
|
|
<a name="idm55"></a><a name="kresolveddos"></a><table width="100%" style="border-color: #b5b500; border-style: solid; border-width: 2; margin-bottom: 10; table-layout: auto; background-color: #FFFFFF;">
|
|
<tr>
|
|
<th align="left" valign="top" width="20%" style="background: #ffff99; padding: 2 2 2 10; ">kresolveddos</th>
|
|
<td style="text-align: left; vertical-align: top; background: #ffffc3; padding: 2 2 2 5; ">LOGICAL</td>
|
|
</tr>
|
|
<tr>
|
|
<td style="text-align: right; vertical-align: top; background: #ffffc3; padding: 2 10 2 10; "><i>Default:</i></td>
|
|
<td style="text-align: left; vertical-align: top; background: #fff3d9; padding: 2 2 2 5; "> .false.
|
|
</td>
|
|
</tr>
|
|
<tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
|
|
if .true. the k-resolved DOS is computed: not summed over
|
|
all k-points but written as a function of the k-point index.
|
|
In this case all k-point weights are set to unity
|
|
</pre></blockquote></td></tr>
|
|
</table>
|
|
<div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
|
|
</td></tr></tbody></table></td></tr>
|
|
</table>
|
|
<blockquote>
|
|
<a name="idm58"><h3>Notes</h3></a>
|
|
<blockquote>
|
|
<a name="idm59"><h4>Format of output files</h4></a>
|
|
<blockquote><pre>
|
|
Projections are written to standard output.
|
|
|
|
The molecular projected DOS is written to the file "fileout".mopdos.
|
|
|
|
* The format for the spin-unpolarized case is:
|
|
index_of_molecular_orbital E MOPDOS(E)
|
|
...
|
|
|
|
* The format for the collinear, spin-polarized case is:
|
|
index_of_molecular_orbital E MOPDOSup(E) MOPDOSdw(E)
|
|
...
|
|
|
|
The file "fileout".mopdos_tot contains the sum
|
|
over the molecular orbitals.
|
|
|
|
* The format for the spin-unpolarized case is:
|
|
E MOPDOS(E)
|
|
...
|
|
|
|
* The format for the collinear, spin-polarized case is:
|
|
E MOPDOSup(E) MOPDOSdw(E)
|
|
...
|
|
|
|
All DOS(E) are in states/eV plotted vs E in eV
|
|
</pre></blockquote>
|
|
</blockquote>
|
|
<blockquote>
|
|
<a name="idm61"><h4>Important notices</h4></a>
|
|
<blockquote><pre>
|
|
* The atomic wavefunctions identified by the ranges
|
|
i_atmwfc_beg_full:i_atmwfc_end_full (full system) and
|
|
i_atmwfc_beg_part:i_atmwfc_end_part (molecular part)
|
|
should correspond to the same atomic states. See the
|
|
header of the output of projwfc.x for more information.
|
|
|
|
* If using k-points, the same unit cell and the same
|
|
k-points should be used in computing the molecular part,
|
|
unless you really know what you are doing.
|
|
|
|
* The tetrahedron method is presently not implemented.
|
|
|
|
* Gaussian broadening is used in all cases
|
|
(with ngauss and degauss values from input).
|
|
</pre></blockquote>
|
|
</blockquote>
|
|
</blockquote>
|
|
</td></tr>
|
|
</table>
|
|
<small>
|
|
This file has been created by helpdoc utility on Thu Nov 28 10:42:25 CET 2019.
|
|
</small>
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</body>
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</html>
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