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@ -536,11 +536,11 @@ package</A>.
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|||
<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (gko)</A></TD></TR>
|
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<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
|
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<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_smd_hertz.html">smd/hertz</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_smd_tlsph.html">smd/tlsph</A></TD><TD ><A HREF = "pair_smd_triangulated_surface.html">smd/triangulated/surface</A></TD><TD ><A HREF = "pair_smd_ulsph.html">smd/ulsph</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_mgpt.html">mgpt</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_smd_hertz.html">smd/hertz</A></TD><TD ><A HREF = "pair_smd_tlsph.html">smd/tlsph</A></TD><TD ><A HREF = "pair_smd_triangulated_surface.html">smd/triangulated/surface</A></TD><TD ><A HREF = "pair_smd_ulsph.html">smd/ulsph</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_smtbq.html">smtbq</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
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</TD></TR></TABLE></DIV>
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<HR>
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|
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@ -1795,12 +1795,12 @@
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<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
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</dt>
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</dl></td>
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<td style="width: 33%" valign="top"><dl>
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<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
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</dt>
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</dl></td>
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<td style="width: 33%" valign="top"><dl>
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<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
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</dt>
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|
@ -1818,6 +1818,10 @@
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</dt>
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<dt><a href="pair_mgpt.html#index-0">pair_style mgpt</a>
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</dt>
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<dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
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</dt>
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|
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|
@ -134,12 +134,19 @@ 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.
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</P>
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<P>IMPORTANT NOTE: For good performance, LAMMPS should be built with the
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compiler flags "-O3 -msse3 -funroll-loops" when including this pair
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style. The src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example
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machine Makefile with these options included as part of a standard MPI
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build. Note that as-is it will build with whatever low-level compiler
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(g++, icc, etc) is the default for your MPI installation.
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</P>
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<HR>
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<P><B>Mixing, shift, table tail correction, restart</B>:
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</P>
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<P>The (mgpt) pair style does not support the
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<A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options.
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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mix, shift, table, and tail options.
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</P>
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<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
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files</A>, since it is stored in potential files. Thus, you
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@ -154,8 +161,9 @@ script that reads a restart file.
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>mgpt</I> pair style is part of the USER-MGPT package and is only
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enabled if LAMMPS is built with that package.
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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 HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>The MGPT potentials require the <A HREF = "newton.html">newtion</A> setting to be
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"on" for pair style interactions.
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|
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@ -0,0 +1,272 @@
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>pair_style smtbq command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style smtbq
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style smtbq
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pair_coeff * * ffield.smtbq.Al2O3 O Al
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This pair stylecomputes a variable charge SMTB-Q (Second-Moment
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tight-Binding QEq) potential as described in <A HREF = "#SMTB-Q_1">SMTB-Q_1</A> and
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<A HREF = "#SMTB-Q_2">SMTB-Q_2</A>. Briefly, the energy of metallic-oxygen systems
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is given by three contributions:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_smtbq1.jpg">
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</CENTER>
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<P>where <I>E<sub>tot</sub></I> is the total potential energy of the system,
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<I>E<sub>ES</sub></I> is the electrostatic part of the total energy,
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<I>E<sub>OO</sub></I> is the interaction between oxygens and
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<I>E<sub>MO</sub></I> is a short-range interaction between metal and oxygen
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atoms. This interactions depend on interatomic distance
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<I>r<sub>ij</sub></I> and/or the charge <I>Q<sub>i</sub></I> of atoms
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<I>i</I>. Cut-off function enables smooth convergence to zero interaction.
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</P>
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<P>The parameters appearing in the upper expressions are set in the
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ffield.SMTBQ.Syst file where Syst corresponds to the selected system
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(e.g. field.SMTBQ.Al2O3). Exemples for TiO<sub>2</sub>,
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Al<sub>2</sub>O<sub>3</sub> are provided. A single pair_coeff command
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is used with the SMTBQ styles which provides the path to the potential
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file with parameters for needed elements. These are mapped to LAMMPS
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atom types by specifying additional arguments after the potential
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filename in the pair_coeff command. Note that atom type 1 must always
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correspond to oxygen atoms. As an example, to simulate a TiO2 system,
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atom type 1 has to be oxygen and atom type 2 Ti. The following
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pair_coeff command should then be used:
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</P>
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<PRE>pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
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</PRE>
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The electrostatic part of the energy consists of two components
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<P>self-energy of atom <I>i</I> in the form of a second order charge dependent
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polynomial and a long-range Coulombic electrostatic interaction. The
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latter uses the wolf summation method described in <A HREF = "#Wolf">Wolf</A>,
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spherically truncated at a longer cutoff, <I>R<sub>coul</sub></I>. The
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charge of each ion is modeled by an orbital Slater which depends on
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the principal quantum number (<I>n</I>) of the outer orbital shared by the
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ion.
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</P>
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<P>Interaction between oxygen, <I>E<sub>OO</sub></I>, consists of two parts,
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an attractive and a repulsive part. The attractive part is effective
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only at short range (< r<sub>2</sub><sup>OO</sup>). The attractive
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contribution was optimized to study surfaces reconstruction
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(e.g. <A HREF = "#SMTB-Q_2">SMTB-Q_2</A> in TiO<sub>2</sub>) and is not necessary
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for oxide bulk modeling. The repulsive part is the Pauli interaction
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between the electron clouds of oxygen. The Pauli repulsion and the
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coulombic electrostatic interaction have same cut off value. In the
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ffield.SMTBQ.Syst, the keyword <I>'buck'</I> allows to consider only the
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repulsive O-O interactions. The keyword <I>'buckPlusAttr'</I> allows to
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consider the repulsive and the attractive O-O interactions.
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</P>
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<P>The short-range interaction between metal-oxygen, <I>E<sub>MO</sub></I> is
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based on the second moment approximation of the density of states with
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a N-body potential for the band energy term,
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<I>E<sup>i</sup><sub>cov</sub></I>, and a Born-Mayer type repulsive terms
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as indicated by the keyword <I>'second_moment'</I> in the
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ffield.SMTBQ.Syst. The energy band term is given by:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_smtbq2.jpg">
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</CENTER>
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<P>where <I>η<sub>i</sub></I> is the stoichiometry of atom <I>i</I>,
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<I>δQ<sub>i</sub></I> is the charge delocalization of atom <I>i</I>,
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compared to its formal charge
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<I>Q<sup>F</sup><sub>i</sub></I>. n<sub>0</sub>, the number of hybridized
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orbitals, is calculated with to the atomic orbitals shared
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<I>d<sub>i</sub></I> and the stoichiometry
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<I>η<sub>i</sub></I>. <I>r<sub>c1</sub></I> and <I>r<sub>c2</sub></I> are the two
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cutoff radius around the fourth neighbors in the cutoff function.
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</P>
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<P>In the formalism used here, <I>ξ<sup>0</sup></I> is the energy
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parameter. <I>ξ<sup>0</sup></I> is in tight-binding approximation the
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hopping integral between the hybridized orbitals of the cation and the
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anion. In the literature we find many ways to write the hopping
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integral depending on whether one takes the point of view of the anion
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or cation. These are equivalent vision. The correspondence between the
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two visions is explained in appendix A of the article in the
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SrTiO<sub>3</sub> <A HREF = "#SMTB-Q_3">SMTB-Q_3</A> (parameter <I>β</I> shown in
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this article is in fact the <I>β<sub>O</sub></I>). To summarize the
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relationship between the hopping integral <I>ξ<sup>0</sup></I> and the
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others, we have in an oxide C<sub>n</sub>O<sub>m</sub> the following
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relationship:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_smtbq3.jpg">
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</CENTER>
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<P>Thus parameter μ, indicated above, is given by : μ = (√n
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+ √m) ⁄ 2
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</P>
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<P>The potential offers the possibility to consider the polarizability of
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the electron clouds of oxygen by changing the slater radius of the
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charge density around the oxygens through the parameters <I>rBB, rB and
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rS</I> in the ffield.SMTBQ.Syst. This change in radius is performed
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according to the method developed by E. Maras
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<A HREF = "#SMTB-Q_2">SMTB-Q_2</A>. This method needs to determine the number of
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nearest neighbors around the oxygen. This calculation is based on
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first (<I>r<sub>1n</sub></I>) and second (<I>r<sub>2n</sub></I>) distances
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neighbors.
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</P>
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<P>The SMTB-Q potential is a variable charge potential. The equilibrium
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charge on each atom is calculated by the electronegativity
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equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for further detail. One
|
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can adjust the frequency, the maximum number of iterative loop and the
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convergence of the equilibrium charge calculation. To obtain the
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energy conservation in NVE thermodynamic ensemble, we recommend to use
|
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a convergence parameter in the interval 10<sup>-5</sup> -
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10<sup>-6</sup> eV.
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</P>
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<P>The ffield.SMTBQ.Syst files are provided for few systems. They consist
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of nine parts and the lines beginning with '#' are comments (note that
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the number of comment lines matter). The first sections are on the
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potential parameters and others are on the simulation options and
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might be modified. Keywords are character type and must be enclosed in
|
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quotation marks ('').
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</P>
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<P>1) Number of different element in the oxide:
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</P>
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<UL><LI>N<sub>elem</sub>= 2 or 3
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<LI>Divided line
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</UL>
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<P>2) Atomic parameters
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</P>
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For the anion (oxygen)
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<UL><LI>Name of element (char) and stoichiometry in oxide
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<LI>Formal charge and mass of element
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<LI>Principal quantic number of outer orbital (<I>n</I>), electronegativity (<I>χ<sup>0</sup><sub>i</simulationub></I>) and hardness (<I>J<sup>0</sup><sub>i</sub></I>)
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<LI> Ionic radius parameters : max coordination number (<I>coordBB</I> = 6 by default), bulk coordination number <I>(coordB)</I>, surface coordination number <I>(coordS)</I> and <I>rBB, rB and rS</I> the slater radius for each coordination number. (<b>note : If you don't want to change the slater radius, use three identical radius values</b>)
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<LI>Number of orbital shared by the element in the oxide (<I>d<sub>i</sub></I>)
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<LI>Divided line
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</UL>
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<P>For each cations (metal):
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</P>
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||||
<UL><LI>Name of element (char) and stoichiometry in oxide
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<LI>Formal charge and mass of element
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<LI>Number of electron in outer orbital <I>(ne)</I>, electronegativity (<I>χ<sup>0</sup><sub>i</simulationub></I>), hardness (<I>J<sup>0</sup><sub>i</sub></I>) and <I>r<sub>Salter</sub></I> the slater radius for the cation.
|
||||
<LI>Number of orbitals shared by the elements in the oxide (<I>d<sub>i</sub></I>)
|
||||
<LI>Divided line
|
||||
</UL>
|
||||
<P>3) Potential parameters:
|
||||
</P>
|
||||
<UL><LI>Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
|
||||
<LI>Potential parameter: <pre><br/> If type of potential is 'second_moment' : <I>A (eV)</I>, <I>p</I>, <I>ξ<sup>0</sup></I> (eV) and <I>q</I> <br/> <I>r<sub>c1</sub></I> (Å), <I>r<sub>c2</sub></I> (Å) and <I>r<sub>0</sub></I> (Å) <br/> If type of potential is 'buck' : <I>C</I> (eV) and <I>ρ</I> (Å) <br/> If type of potential is 'buckPlusAttr' : <I>C</I> (eV) and <I>ρ</I> (Å) <br/> <I>D</I> (eV), <I>B</I> (Å<sup>-1</sup>), <I>r<sub>1</sub><sup>OO</sup></I> (Å) and <I>r<sub>2</sub><sup>OO</sup></I> (Å) </pre>
|
||||
<LI>Divided line
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</UL>
|
||||
<P>4) Tables parameters:
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||||
</P>
|
||||
<UL><LI>Cutoff radius for the Coulomb interaction (<I>R<sub>coul</sub></I>)
|
||||
<LI>Starting radius (<I>r<sub>min</sub></I> = 1,18845 Å) and increments (<I>dr</I> = 0,001 Å) for creating the potential table.
|
||||
<LI>Divided line
|
||||
</UL>
|
||||
<P>5) Rick model parameter:
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||||
</P>
|
||||
<UL><LI><I>Nevery</I> : parameter to set the frequency (<I>1/Nevery</I>) of the charge resolution. The charges are evaluated each <I>Nevery</I> time steps.
|
||||
<LI>Max number of iterative loop (<I>loopmax</I>) and precision criterion (<I>prec</I>) in eV of the charge resolution
|
||||
<LI>Divided line
|
||||
</UL>
|
||||
<P>6) Coordination parameter:
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||||
</P>
|
||||
<UL><LI>First (<I>r<sub>1n</sub></I>) and second (<I>r<sub>2n</sub></I>) neighbor distances in Å
|
||||
<LI>Divided line
|
||||
</UL>
|
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<P>7) Charge initialization mode:
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</P>
|
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<UL><LI>Keyword (<I>QInitMode</I>) and initial oxygen charge (<I>Q<sub>init</sub></I>). If keyword = 'true', all oxygen charges are initially set equal to <I>Q<sub>init</sub></I>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using <A HREF = "#read_data.html">read_data</A> command.
|
||||
<LI>Divided line
|
||||
</UL>
|
||||
8) Mode for the electronegativity equalization (Qeq)
|
||||
|
||||
<UL><LI>Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
|
||||
<LI>Parameter if necessary
|
||||
<LI>Divided line
|
||||
</UL>
|
||||
9) Verbose
|
||||
|
||||
<UL><LI>If you want the code to work in verbose mode or not : 'true' or 'false'
|
||||
<LI>If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and <I>N<sub>Energy</sub></I>. This option writes in file every <I>N<sub>Energy</sub></I> time step. If the value is 'false' then <I>N<sub>Energy</sub></I> = 0. The file take into account the possibility to have several QEq group <I>g</I> then it writes: time step, number of atoms in group <I>g</I>, electrostatic part of energy, <I>E<sub>ES</sub></I>, the interaction between oxygen, <I>E<sub>OO</sub></I>, and short range metal-oxygen interaction, <I>E<sub>MO</sub></I>.
|
||||
<LI>If you want to print in file 'Electroneg_component.txt' the electronegativity component (<I>∂E<sub>tot</sub> ⁄∂Q<sub>i</sub></I>) or not: 'true' or 'false' and <I>N<sub>Electroneg</sub></I>.This option writes in file every <I>N<sub>Electroneg</sub></I> time step. If the value is 'false' then <I>N<sub>Electroneg</sub></I> = 0. The file consist in atom number <I>i</I>, atom type (1 for oxygen and # higher than 1 for metal), atom position: <I>x</I>, <I>y</I> and <I>z</I>, atomic charge of atom <I>i</I>, electrostatic part of atom <I>i</I> electronegativity, covalent part of atom <I>i</I> electronegativity, the hopping integral of atom <I>i</I> <I>(Zβ<sup>2</sup>)<sub>i<sub></I> and box electronegativity.
|
||||
</UL>
|
||||
<P>IMPORTANT NOTE: This last option slows down the calculation
|
||||
dramatically. Use only with a single processor simulation.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info:</B>
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
mix, shift, table, and tail options.
|
||||
</P>
|
||||
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
|
||||
files</A>, since it is stored in potential files. Thus, you
|
||||
needs to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
</P>
|
||||
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
||||
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
||||
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restriction:</B>
|
||||
</P>
|
||||
<P>This pair style is part of the USER-SMTBQ package and is only enabled
|
||||
if LAMMPS is built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>This potential requires using atom type 1 for oxygen and atom type
|
||||
higher than 1 for metal atoms.
|
||||
</P>
|
||||
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
|
||||
for pair interactions.
|
||||
</P>
|
||||
<P>The SMTB-Q potential files provided with LAMMPS (see the potentials
|
||||
directory) are parameterized for metal <A HREF = "unit.html">units</A>.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Citing this work:</B>
|
||||
</P>
|
||||
<P>Please cite related publication: N. Salles, O. Politano, E. Amzallag
|
||||
and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "SMTB-Q_1"></A>
|
||||
|
||||
<P><B>(SMTB-Q_1)</B> N. Salles, O. Politano, E. Amzallag, R. Tetot,
|
||||
Comput. Mater. Sci. 111 (2016) 181-189
|
||||
</P>
|
||||
<A NAME = "SMTB-Q_2"></A>
|
||||
|
||||
<P><B>(SMTB-Q_2)</B> E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
|
||||
H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
|
||||
</P>
|
||||
<A NAME = "SMTB-Q_3"></A>
|
||||
|
||||
<P><B>(SMTB-Q_3)</B> R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
|
||||
Science 616, 19-8722 28 (2013)
|
||||
</P>
|
||||
<A NAME = "Wolf"></A>
|
||||
|
||||
<P><B>(Wolf)</B> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
|
||||
Phys, 110, 8254 (1999).
|
||||
</P>
|
||||
<A NAME = "Rick"></A>
|
||||
|
||||
<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
|
||||
(1994).
|
||||
</P>
|
||||
</HTML>
|
Loading…
Reference in New Issue