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<div class="section" id="pair-style-mgpt-command">
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<span id="index-0"></span><h1>pair_style mgpt command<a class="headerlink" href="#pair-style-mgpt-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style mgpt
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</pre></div>
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</div>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style mgpt
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pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
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cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
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cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
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pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
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pair_coeff * * parmin potin Omega volpress yes nbody 12
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
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(<a class="reference internal" href="#moriarty1"><span>Moriarty1</span></a>) provides a first-principles approach to
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multi-ion interatomic potentials in d-band transition metals, with a
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volume-dependent, real-space total-energy functional for the N-ion
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elemental bulk material in the form</p>
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<img alt="_images/pair_mgpt.jpg" class="align-center" src="_images/pair_mgpt.jpg" />
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<p>where the prime on each summation sign indicates the exclusion of all
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self-interaction terms from the summation. The leading volume term
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E_vol as well as the two-ion central-force pair potential v_2 and the
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three- and four-ion angular-force potentials, v_3 and v_4, depend
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explicitly on the atomic volume Omega, but are structure independent
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and transferable to all bulk ion configurations, either ordered or
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disordered, and with of without the presence of point and line
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defects. The simplified model GPT or MGPT (<a class="reference internal" href="#moriarty2"><span>Moriarty2</span></a>,
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<a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>), which retains the form of E_tot and permits
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more efficient large-scale atomistic simulations, derives from the GPT
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through a series of systematic approximations applied to E_vol and the
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potentials v_n that are valid for mid-period transition metals with
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nearly half-filled d bands.</p>
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<p>Both analytic (<a class="reference internal" href="#moriarty2"><span>Moriarty2</span></a>) and matrix
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(<a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>) representations of MGPT have been developed.
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In the more general matrix representation, which can also be applied
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to f-band actinide metals and permits both canonical and non-canonical
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d/f bands, the multi-ion potentials are evaluated on the fly during a
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simulation through d- or f-state matrix multiplication, and the forces
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that move the ions are determined analytically. Fast matrix-MGPT
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algorithms have been developed independently by Glosli
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(<a class="reference internal" href="#glosli"><span>Glosli</span></a>, <a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>) and by Oppelstrup
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(<a class="reference internal" href="#oppelstrup"><span>Oppelstrup</span></a>)</p>
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<p>The <em>mgpt</em> pair style calculates forces, energies, and the total
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energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm.
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Input potential and control data are entered through the
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<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. Each material treated requires
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input parmin and potin potential files, as shown in the above
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examples, as well as specification by the user of the initial atomic
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volume Omega through pair_coeff. At the beginning of a time step in
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any simulation, the total volume of the simulation cell V should
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always be equal to Omega*N, where N is the number of metal ions
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present, taking into account the presence of any vacancies and/or
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interstitials in the case of a solid. In a constant-volume
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simulation, which is the normal mode of operation for the <em>mgpt</em> pair
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style, Omega, V and N all remain constant throughout the simulation
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and thus are equal to their initial values. In a constant-stress
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simulation, the cell volume V will change (slowly) as the simulation
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proceeds. After each time step, the atomic volume should be updated
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by the code as Omega = V/N. In addition, the volume term E_vol and
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the potentials v_2, v_3 and v_4 have to be removed at the end of the
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time step, and then respecified at the new value of Omega. In all
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smulations, Omega must remain within the defined volume range for
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E_vol and the potentials for the given material.</p>
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<p>The default option volpress yes in the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
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command includes all volume derivatives of E_tot required to calculate
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the stress tensor and pressure correctly. The option volpress no
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disregards the pressure contribution resulting from the volume term
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E_vol, and can be used for testing and analysis purposes. The
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additional optional variable nbody controls the specific terms in
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E_tot that are calculated. The default option and the normal option
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for mid-period transition and actinide metals is nbody 1234 for which
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all four terms in E_tot are retained. The option nbody 12, for
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example, retains only the volume term and the two-ion pair potential
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term and can be used for GPT series-end transition metals that can be
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well described without v_3 and v_4. The nbody option can also be used
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to test or analyze the contribution of any of the four terms in E_tot
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to a given calculated property.</p>
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<p>The <em>mgpt</em> pair style makes extensive use of matrix algebra and
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includes optimized kernels for the BlueGene/Q architecture and the
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Intel/AMD (x86) architectures. When compiled with the appropriate
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compiler and compiler switches (-msse3 on x86, and using the IBM XL
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compiler on BG/Q), these optimized routines are used automatically.
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For BG/Q machines, building with the default Makefile for that
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architecture (e.g., “make bgq”) should enable the optimized algebra
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routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
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(build with “make mpi_fastmgpt”) enables the fast algebra routines.
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The user will be informed in the output files of the matrix kernels in
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use. To further improve speed, on x86 the option precision single can
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be added to the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command line, which
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improves speed (up to a factor of two) at the cost of doing matrix
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calculations with 7 digit precision instead of the default 16. For
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consistency the default option can be specified explicitly by the
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option precision double.</p>
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<p>All remaining potential and control data are contained with the parmin
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and potin files, including cutoffs, atomic mass, and other basic MGPT
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variables. Specific MGPT potential data for the transition metals
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tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
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and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
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directory. The stored files are, respectively, Ta4.mgpt.parmin,
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Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
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Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
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V6.1.mgpt.potin . Useful corresponding informational “README” files
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on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
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potentials directory. These latter files indicate the volume mesh and
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range for each potential and give appropriate references for the
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potentials. It is expected that MGPT potentials for additional
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materials will be added over time.</p>
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<p>Useful example MGPT scripts are given in the examples/USER/mgpt
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directory. These scripts show the necessary steps to perform
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constant-volume calculations and simulations. It is strongly
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recommended that the user work through and understand these examples
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before proceeding to more complex simulations.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">For good performance, LAMMPS should be built with the compiler
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flags “-O3 -msse3 -funroll-loops” when including this pair style. The
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src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example machine Makefile
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with these options included as part of a standard MPI build. Note
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that as-is it will build with whatever low-level compiler (g++, icc,
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etc) is the default for your MPI installation.</p>
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</div>
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<hr class="docutils" />
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<p><strong>Mixing, shift, table tail correction, restart</strong>:</p>
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<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
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mix, shift, table, and tail options.</p>
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<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
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needs to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.</p>
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<p>This pair style can only be used via the <em>pair</em> keyword of the
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<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
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<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This pair style is part of the USER-MGPT package and is only enabled
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if LAMMPS is built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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<p>The MGPT potentials require the <a class="reference internal" href="newton.html"><em>newtion</em></a> setting to be
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“on” for pair style interactions.</p>
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<p>The stored parmin and potin potential files provided with LAMMPS in
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the “potentials” directory are written in Rydberg atomic units, with
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energies in Rydbergs and distances in Bohr radii. The <em>mgpt</em> pair
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style converts Rydbergs to Hartrees to make the potential files
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compatible with LAMMPS electron <a class="reference internal" href="units.html"><em>units</em></a>.</p>
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<p>The form of E_tot used in the <em>mgpt</em> pair style is only appropriate
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for elemental bulk solids and liquids. This includes solids with
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point and extended defects such as vacancies, interstitials, grain
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boundaries and dislocations. Alloys and free surfaces, however,
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require significant modifications, which are not included in the
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<em>mgpt</em> pair style. Likewise, the <em>hybrid</em> pair style is not allowed,
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where MGPT would be used for some atoms but not for others.</p>
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<p>Electron-thermal effects are not included in the standard MGPT
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potentials provided in the “potentials” directory, where the
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potentials have been constructed at zero electron temperature.
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Physically, electron-thermal effects may be important in 3d (e.g., V)
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and 4d (e.g., Mo) transition metals at high temperatures near melt and
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above. It is expected that temperature-dependent MGPT potentials for
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such cases will be added over time.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The options defaults for the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command are
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volpress yes, nbody 1234, and precision double.</p>
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<hr class="docutils" />
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<p id="moriarty1"><strong>(Moriarty1)</strong> Moriarty, Physical Review B, 38, 3199 (1988).</p>
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<p id="moriarty2"><strong>(Moriarty2)</strong> Moriarty, Physical Review B, 42, 1609 (1990).
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Moriarty, Physical Review B 49, 12431 (1994).</p>
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<p id="moriarty3"><strong>(Moriarty3)</strong> Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
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Journal of Materials Research, 21, 563 (2006).</p>
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<p id="glosli"><strong>(Glosli)</strong> Glosli, unpublished, 2005.
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Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
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Series, 46, 254 (2006).</p>
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<p id="oppelstrup"><strong>(Oppelstrup)</strong> Oppelstrup, unpublished, 2015.
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Oppelstrup and Moriarty, to be published.</p>
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