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<title>NWChem Version 3.3.1 Release Notes</title>
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<link rel="stylesheet" type="text/css" href="../shared/nwchem_basic.css">
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</head>
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<body text="#000000" bgcolor="#FFFFFF" link="blue" alink="blue" vlink="blue">
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<table width="700"><tr><td>
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<br>
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<table>
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<tbody>
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<tr>
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<td align="left" width="325"><img src="../images/nwchem_logo_dark.gif" border=0 width=200 alt="NWChem - computational chemistry on parallel computers"></td>
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<td align="right" width="325" valign="bottom">
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<a href="../nwchem_main.html">NWChem Home</a> |
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<a href="../disclaimer.html">Security & Privacy</a> |
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<a href="http://www.pnl.gov" target="_blank">PNNL</a>
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</td>
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</tr>
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</tbody>
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</table>
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<hr>
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<h1>NWChem Version 3.3 and 3.3.1 Release Notes</h1>
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<p>
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<font color="red">NOTE:</font> These release notes are not a
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substitute for reading the
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<a href="../doc/user/index.html">
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User Manual</a>! They are meant to give
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a thumbnail sketch of the new capabilities and bug fixes that
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are available in NWChem Version 3.3. When there is a conflict
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between the release notes and the
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<a href="../doc/user/index.html">
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User Manual</a>, the
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<a href="../doc/user/index.html">
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User Manual</a> takes precedence.
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<p>
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<font color="red">NWChem 3.3.1</font> <a href="#331">changes</a> from
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NWChem 3.3
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<p>
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Several new major capabilities are available in NWChem, including several
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new modules. The new modules are:
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<ul>
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<li> Car-Parrinello simulations (the PSPW module),</li>
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<li> Python interface (the PYTHON module), and</li>
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<li> analysis of trajectory information during a molecular dynamics
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calculation and of ESP calculations(the ANALYSIS module).</li>
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</ul>
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For each of these capabilities, the user is referred to the
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<a href="../doc/user/index.html">
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User Manual</a> for more information.
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<p>
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Additional major additions to the capabilities include:
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<ul>
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<li> GIAO NMR chemical shift capabilities for closed shells
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(GIAO in the PROPERTY module),</li>
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<li> The DRIVER module has been greatly improved, with many
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new features,</li>
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<li> Several new DFT functionals have been added:
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<ul>
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<li> Exchange Perdew91, Gill96, and PBE96 functionals</li>
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<li> Correlation PBE96 functional</li>
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<li> Exchange-Correlation Becke97, Becke97-1, and HCTH functionals</li>
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</ul></li>
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<li> The ElectroStatic Potential (ESP) module has several new features,</li>
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<li> Automatic recognition of molecular symmetry (AUTOSYM in the GEOMETRY module),</li>
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<li> Addition of Hondo 1e- energy and gradient integrals,</li>
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<li> Increased accuracy in the integral API.</li>
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</ul>
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Again, for each of these capabilities, the user is referred to the
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<a href="../doc/user/index.html">
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User Manual</a> for more information.
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<p>
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Listed below are the other major and many minor changes for
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each module with significant changes. These descriptions are somewhat
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terse and more information is generally available in the
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<a href="../doc/user/index.html">
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User Manual</a>.
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<p>
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<b>Task level directives:</b>
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<ul>
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<li> Unrecognized directives will now cause NWChem to stop and
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print an error message </li>
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<li> Task analysis added for MD runs</li>
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<li> Task python added for python interface</li>
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<li> Task pspw added for pseudopotential plane-wave (Car-Parrinello) runs</li>
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</ul>
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<p>
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<b>Initial orbital Guess:</b>
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<ul>
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<li>New code from Paul Sherwood to generate reasonable initial atomic
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guesses for heavy elements with ECPs. This generates guess densities
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for those atoms that previously didn't work and produces much better
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guess densities than the previous version. </li>
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<li>The atomic guess code now generates f orbital density fragments in the
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correct order for both cartesian and spherical basis sets.</li>
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<li>Higher accuracy is now used in the initial guess to accomodate large
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basis sets. If linear dependencies are found, even higher accuracy
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is used.</li>
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<li>Users are warned if initial guess can lead to symmetry problems.</li>
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<li><font color="red">BUG FIX:</font> UHF projections of small basis sets
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to large basis sets will now work</li>
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</ul>
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<p>
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<b>Basis Sets:</b>
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<ul>
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<li>Basis set library has been updated to include all new basis sets at the
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<a href="http://www.emsl.pnl.gov/forms/basisform.html">
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EMSL Gaussian Basis Set Order Form page of David Feller</a></li>
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<li><font color="red">BUG FIX:</font> Some of the Stuttgart ECPs which had the
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coefficients and exponents switched are now correct.</li>
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</ul>
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<p>
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<b>Geometry:</b>
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<ul>
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<li>Extended redundant internals to allow user constraints.</li>
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<li>Adjustable geometries.</li>
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<li>AUTOZ is now the default.</li>
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<li>A tolerance is now available in SYMMETRY directive of GEOMETRY directive.</li>
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<li>AUTOSYM is now available (with a tolerance) on the GEOMETRY line directive.</li>
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<li>Optional velocity input for Car Parinello code.</li>
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<li>More robust z-matrix code.</li>
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<li>C<sub>7</sub> and D<sub>6</sub> symmetries are properly set up.</li>
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</ul>
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<p>
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<b>DFT:</b>
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<ul>
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<li>Introduced X Perdew91, Gill96, and PB96 functionals.</li>
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<li>Introduced C PB96 functional.</li>
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<li>Introduced XC Becke97, Becke97-1, and HCTH.</li>
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<li>DFT is now able to use spherical basis functions as well as cartesian.</li>
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<li>DFT gradients can now use the Texas integrals.</li>
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<li>Linear scaling is acheived in the exchange contribution when charge
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fitting basis sets are used with hybrid density functionals.</li>
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<li>If the vectors directive is used with SCF or DFT and a problem occurs,
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the atomic guess will be used.</li>
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<li>Lebedev grids have been significantly modified.</li>
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<li>Delley weights are no longer allowed.</li>
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<li>Modified grid input: you can now add <atom tag> nrad nang accqrad.</li>
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<li>Better screening on the exchange correlation numerical grid, which improves
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performance by at least 20%.</li>
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<li>Default convergence parameters was modified to produce more robust results.</li>
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<li>Introduced check on integrated density: a warning message is printed if
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the claimed accuracy criteria for the XC numerical grid are not met.</li>
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<li>Default finite difference step for nuclear hessian generation for DFT
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changed to 0.01 au and for all other methods it is 0.001 au.</li>
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<li><font color="red">BUG FIX:</font> In cases in which the spin polarization
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is large in open shell systems, wrong wave functions and gradients were obtained
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using Perdew86 C functionals. This has been fixed.</li>
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<li><font color="red">BUG FIX:</font> If the user has a CD fitting basis set with
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a shell larger than any shell in the AO basis set, the program would stop.
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This no longer applies.</li>
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<li><font color="red">BUG FIX:</font> All hybrid functionals were giving incorrect
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results when using open shell wavefunctions because the total density was being
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used instead of separate alpha and beta Hartree-Fock exchange contributions.
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This is now fixed. (It was also fixed in later releases of 3.2.1.)</li>
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</ul>
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<p>
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<b>SCF:</b>
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<ul>
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<li>Eliminated or tightened screening options to make integral selection threshold
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more consistent between file and direct routines.</li>
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<li>Improved precision in linear solve to stabilize direct SCF.</li>
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<li>If the vectors directive is used with SCF or DFT and a problem occurs,
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the atomic guess will be used.</li>
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</ul>
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<p>
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<b>Driver:</b>
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<ul>
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<li>Revamped Driver capabilities.</li>
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<li>Ensure constraints are imposed after geometry step.</li>
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<li>Extended redundant internals to allow user constraints.</li>
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<li>AUTOZ is now the default.</li>
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</ul>
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<p>
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<b>Properties:</b>
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<ul>
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<li>Note that spherical functions do not work yet with properties.</li>
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<li>Input for the NBO program are produced.</li>
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<li>Addition of GIAO NMR chemical shift calculations.</li>
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<li>Added "all" keyword.</li>
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<li><font color="red">BUG FIX:</font>Property package will correctly skip
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property evaluation for generally contracted basis sets and basis sets with
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pure sp functions (to get the properties use the "segement" keyword when
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specifying a basis set).</li>
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</ul>
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<p>
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<b>MP2:</b>
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<ul>
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<li>TIGHT directive MP2 for higher precision energy and gradients</li>
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<li><font color="red">BUG FIX:</font> Non-abelian point groups are now
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handled properly in the MP2 gradient code.</li>
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<li>Make RI-MP2 compute SCF reference if it is not already done
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(or done with sufficient accuracy).</li>
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<li><font color="red">BUG FIX:</font> RIMP2 - Fix overflow memory problem
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for large jobs.</li>
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</ul>
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<p>
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<b>Hessian and Frequencies:</b>
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<ul>
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<li>Default finite difference step for nuclear hessian generation for DFT
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changed to 0.01 au and for all other methods it is 0.001 au.</li>
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<li><font color="red">BUG FIX:</font> Numerical hessian restarts now work properly.</li>
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</ul>
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<p>
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<b>ESP:</b>
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<ul>
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<li>Use of fast routines for ESP calculations.</li>
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<li>Write name.xyz and name.plt file (plot with gOpenMol).</li>
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<li>Write name.er file to recover previous runs.</li>
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<li>Write name.q file with partial charges.</li>
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<li>Added Schwarz screening - screen option in ESP block.</li>
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<li>Added option to read in previous esp grid, if name.grid is present, it will
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automatically get used unless you give a command recalculate.</li>
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<li>Print atom radii.</li>
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<li>Additional constraint options.</li>
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</ul>
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<p>
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<b>Prepare module:</b>
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<ul>
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<li>Changed topology and restart format printed out.</li>
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<li>New ALTLOC, MODEL, LINK, and CHAIN commands.</li>
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<li>Allow comment lines in sequence file - begin line with #.</li>
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<li>Always recalculate grid if ESP required on a fragment.</li>
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<li>Implement 'modify segment' and 'update lists' commands.</li>
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<li>Force PDB link cards.</li>
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<li>Add modify commands for bonded interaction parameters.</li>
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<li>Recode pre_mklist to allow and identify multiple node (greater than 3)
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bonded interactions.</li>
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<li>Automatically identifies cysteine-sulphur bridges.</li>
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<li>Default HIS to HID for amber when reading PDB without hydrogens.</li>
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<li>Write out segment charges when writing topology file.</li>
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<li>Add support for DNA and RNA with AMBER force field.</li>
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<li>Add ignore keyword so that bonded parameters between quantum atoms do not
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need to be defined in the database.</li>
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<li>Make 1.0 default scaling for ESP fitted charges.</li>
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<li><font color="red">BUG FIX:</font>Multiple node bonded interaction error
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takes care of itself.</li>
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<li><font color="red">BUG FIX:</font>If last segment was a single atom,
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the atom would be lost. This is now fixed.</li>
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<li><font color="red">KNOWN BUG:</font>In some systems, when converting a
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restart file to a PDB file, the restart file gets corrupted. This is fixed in
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version 3.3.1.</li>
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</ul>
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<p>
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<b>MD:</b>
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<ul>
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<li>Changed topology format - cannot use old files with the new code!!
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<li>Added ability to analyze the trajectory on the fly - see the ANALYSIS module of
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User Manual.</li>
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<li>Implement periodic boundary conditions for bonded interactions.</li>
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<li>Improved load balancing.</li>
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<li>Dynamic assignment of subset of nodes for performing the FFT calculation.</li>
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<li>Split PME calculation now default - see pme keyword in MD block.</li>
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<li>Improved periodic boundary condition scheme.</li>
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<li>Exclude constraints between atoms fixed in space - improves reliability of
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Shake algorithm.</li>
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<li>Remove the restriction that bonded interactions can involve
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atoms on at most two segments.</li>
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<li>Improved printing SHAKE dev-too-large error message identifying the atoms that
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are involved.</li>
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<li><font color="red">BUG FIX:</font> Fix J-Box or I-Box is Illegal problem.
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Prevent dimension problems if box index list from previous run
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exceeds current dimension.</li>
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</ul>
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<p>
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<b>Integral changes:</b>
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<ul>
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<li>Inclusion of energy and gradient one-electron integrals from HONDO.</li>
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<li>Turn off SP integral code due to accuracy problems.</li>
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<li>Several fixes to the integral code with respect to memory and bugs in TEXAS when
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high angular momentum and large exponents are present in the basis set.</li>
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<li>Fix of ECP integral bug when the ECP contained a zero r-exponent.</li>
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<li>Routines for relativistic integral code (include?)</li>
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<li>Generates relativistic one-electron integrals (include?)</li>
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</ul>
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<p>
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<b>Tests, manuals and misc script changes:</b>
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<ul>
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<li>Updated User's Manual to reflect new and modified functionality in NWChem.</li>
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<li>QA tests have been updated to reflect the new functionality in NWChem.</li>
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<li>Updated scripts to run NWChem in LoadLeveller and NQE and to test results.</li>
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<li>Addition of some scripts to create animated gifs based on using RASMOL and
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files printed out by NWChem during optimizations and frequency calculations.</li>
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<li>Updates in the Programmer's Manual (much more is still left to come!).</li>
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</ul>
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<p>
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<b>Installation availability:</b>
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<p>
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The current tested platforms and O/S versions are:
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<ul>
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<li> IBM SP with P2SC nodes, AIX 4.2.1, and PSSP 2.3 </li>
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<li> IBM SP with silver nodes (SMP nodes with two 604e processors),
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AIX 4.3.2, and PSSP 3.1. </li>
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<li> IBM RS6000 workstation, AIX 3.2, 4.1. and 4.3 </li>
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<li> Cray T3E, 2.0.4.61 UNICOSMK </li>
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<li> SGI R8000/10000, IRIX 6.2, 6.5 </li>
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<li> SGI R4000, IRIX 5.3 </li>
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<li> SUN workstations, SunOS 4.1.3 and Solaris 5.5 </li>
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<li> Compaq DEC alpha workstion (600 MHz EV6), Digital UNIX V4.0E
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Rev. 1091, DEC C V5.8-009, Digital Fortran V5.2 </li>
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<li> Linux. Since there are at least 8 popular distributions of the
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Linux operating system and numerous others in existence, including
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downloading everything and building your own Linux OS, it is
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impossible to test all possible versions of Linux with NWChem. NWChem
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Release 3.3 has been tested on Slackware 3.4, 3.5, 4.0, RedHat 5.1,
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5.2, and 6.0, Mandrake based on RedHat 6.0, and LinuxPPC 4.0 for the
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Power PC Macintosh. These all use the EGCS compilers at different
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levels. Those distributed from Slackware are somewhat different than
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those distributed from RedHat but the code is configured to run on all
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of them. The Linux Alpha version 5.2 from Red Hat fails to compile
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the code as well as the beta release of the Digital Fortran compiler
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for Linux based Alpha systems.</li>
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</ul>
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<font color="red">NOTE:</font>In releases of NWChem prior to 3.3 additional processes had
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to be created on workstation clusters to support remote access to
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shared memory. This is no longer the case. The TCGMSG process
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group file just needs to refer to processes running NWChem.
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<p>
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<hr>
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<p>
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<a name="331"></a>
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<center><h2>Changes from NWChem 3.3 to NWChem 3.3.1</h2></center>
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<p>
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<ul>
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<li>Fix for PB96 functionals. <font color="red">Note that all previous
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calculations with this functional are incorrect. Do NOT rely on results
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using any version previous to 3.3.1</font></li>
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<li>Slightly looser value of EPREC in DRIVER for DFT
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calculations. (5e-6 instead of 1e-7)</li>
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<li>Improved screening on the grid for DFT which only effects large
|
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calculations (usually those that have molecules that are "spread
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out").</li>
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<li>The periodic boundary conditions for an MD run now checks
|
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for images more than one cell away.</li>
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<li>Fix in the PREPARE module so that some solvents that were
|
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not being written out correctly in the PDB file now are.</li>
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<li>Fix in the solvate box command.</li>
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<li>Fix for periodic boundary conditions for solvation.</li>
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<li>Fix for the passing of character strings in the PSPW code. </li>
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<li>Dramatically improved parallel efficiency of the Lagrange
|
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multipliers and the non-local pseudopotentials on high-latency
|
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parallel platforms in the PSPW code.</li>
|
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<li>Improved persistence of tolerance changes when linear
|
|
dependence is found. This had caused some convergence
|
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problems.</li>
|
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<li>Improved eigensolver for large linear dependencies.
|
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<font color="red"> Please note that the current algorithm in PEigS requires
|
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more memory. You may need to increase the
|
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amount of memory needed for a particular calcuation. This problem
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will be rectified in the next version.</font></li>
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<li>The TIGHT option has replaced AOTOL and MOTOL in MP2 (undocumented
|
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feature of version 3.3).</li>
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<li>Fix in the CCSD calculation to add some synchronization which
|
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provided more stability.</li>
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<li>Fix for message passing with Linux. This fixes a
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<a href="../support/known_bugs.3.3.html#8">known performance problem</a>.</li>
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<li>Modifications in the GA tools which were causing performance
|
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problems between workstations.</li>
|
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<li>Fix tools makefiles to allow for larger than 2 GB files on the
|
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SP and to fix a diagonalization problem which was causing problems
|
|
with the scalability of DFT.</li>
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<li>Fix for the T3E makefile so that the make works cleanly.
|
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<li>Work arounds to LAPI problems that have been identified on
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the SP. The symptoms generally showed up as jobs that
|
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would hang.</li>
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<li>Additional printing of information in the ecce.out file to
|
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be compatible with Ecce 1.5.</li>
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<li>The examples directory has been updated and the tests
|
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directory has been deleted because the input files were
|
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obsolete.</li>
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</ul>
|
|
<p>
|
|
<hr>
|
|
<font size="0">
|
|
<center>
|
|
<a href="../nwchem_main.html">NWChem</a> |
|
|
<a href="../capabilities/nwchem_capab.html">Capabilities</a> |
|
|
<a href="../platforms/platforms.html">Platforms</a> |
|
|
<a href="../download.html">Download</a> |
|
|
<a href="../doc/user/index.html">User's Manual</a> |
|
|
<a href="../doc/prog/index.html">Programmer's Manual</a> |
|
|
<a href="index.html">Release Notes</a> |
|
|
<a href="../support/faq/NWChem_FAQ.html">FAQ</a>
|
|
</center>
|
|
<br>
|
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<center>
|
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<a href="../support/known_bugs.html">Known Bugs</a> |
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<a href="../support/support.html">Support</a> |
|
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<a href="../training/training.html">Tutorial</a> |
|
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<a href="../contributors.html">Contributors</a> |
|
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<a href="../benchmarks/index.html">Benchmarks</a> |
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<a href="http://www.emsl.pnl.gov/forms/search_nwchem.html">Search</a> |
|
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<a href="http://www.emsl.pnl.gov/docs/mssg/index.html">Mol Sci. Soft. Group</a> |
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<a href="../citation.html">Citation</a>
|
|
</center>
|
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</font>
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<hr>
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Contact: <a href="mailto:ms3distribution@emsl.pnl.gov">NWChem Support</a><br>
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Updated: March 8, 2005
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