Added Vashishta potential
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14117 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
@ -887,6 +887,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"tip4p/cut (o)"_pair_coul.html,
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"tip4p/cut (o)"_pair_coul.html,
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"tip4p/long (o)"_pair_coul.html,
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"tip4p/long (o)"_pair_coul.html,
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"tri/lj (o)"_pair_tri_lj.html,
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"tri/lj (o)"_pair_tri_lj.html,
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"vashishta"_pair_vashishta.html,
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"yukawa (go)"_pair_yukawa.html,
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"yukawa (go)"_pair_yukawa.html,
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"yukawa/colloid (go)"_pair_yukawa_colloid.html,
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"yukawa/colloid (go)"_pair_yukawa_colloid.html,
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"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
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"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
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@ -80,6 +80,7 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential
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srd: stochastic rotation dynamics (SRD) particles as solvent
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srd: stochastic rotation dynamics (SRD) particles as solvent
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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tri: triangular particles in rigid bodies :tb(s=:)
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tri: triangular particles in rigid bodies :tb(s=:)
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vashishta: models using the Vashishta potential
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Here is how you might run and visualize one of the sample problems:
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Here is how you might run and visualize one of the sample problems:
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@ -200,6 +200,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
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"pair_style tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
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"pair_style tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
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"pair_style tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
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"pair_style tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
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"pair_style tri/lj"_pair_tri_lj.html - LJ potential between triangles
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"pair_style tri/lj"_pair_tri_lj.html - LJ potential between triangles
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"pair_style vashishta"_pair_vahishta.html - Vashishta 2-body and 3-body potential
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"pair_style yukawa"_pair_yukawa.html - Yukawa potential
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"pair_style yukawa"_pair_yukawa.html - Yukawa potential
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"pair_style yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
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"pair_style yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
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"pair_style zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
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"pair_style zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
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211
doc/pair_vashishta.html
Normal file
211
doc/pair_vashishta.html
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@ -0,0 +1,211 @@
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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 vashishta 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 vashishta
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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 vashishta
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pair_coeff * * SiC.vashishta Si C
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>vashishta</I> style computes the combined 2-body and 3-body
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family of potentials developed in the group of Vashishta and
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co-workers. By combining repulsive, screened Coulombic,
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screened charge-dipole, and dispersion interactions with a
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bond-angle energy based on the Stillinger-Weber potential,
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this potential has been used to describe a variety of inorganic
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compounds, including SiO2 <A HREF = "#Vashishta1990">Vashishta1990</A>,
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SiC <A HREF = "#Vashishta2007">Vashishta2007</A>,
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and InP <A HREF = "#Branicio2009">Branicio2009</A>.
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</P>
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<P>The potential for the energy U of a system of atoms is
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</P>
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<CENTER><IMG SRC = "Eqs/pair_vashishta.jpg">
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</CENTER>
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<P>where we follow the notation used in <A HREF = "#Branicio2009">Branicio2009</A>.
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U2 is a two-body term and U3 is a three-body term. The
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summation over two-body terms is over all neighbors J within
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a cutoff distance = <I>rc</I>. The twobody terms are shifted and
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tilted by a linear function so that the energy and force are
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both zero at <I>rc</I>. The summation over three-body terms
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is over all neighbors J and K within a cut-off distance = <I>r0</I>,
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where the exponential screening function becomes zero.
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</P>
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<P>Only a single pair_coeff command is used with the <I>vashishta</I> style which
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specifies a Vashishta potential file with parameters for all
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needed elements. These are mapped to LAMMPS atom types by specifying
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N additional arguments after the filename in the pair_coeff command,
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where N is the number of LAMMPS atom types:
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</P>
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<UL><LI>filename
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<LI>N element names = mapping of Vashishta elements to atom types
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</UL>
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<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
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to specify the path for the potential file.
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</P>
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<P>As an example, imagine a file SiC.vashishta has parameters for
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Si and C. If your LAMMPS simulation has 4 atoms types and you want
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the 1st 3 to be Si, and the 4th to be C, you would use the following
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pair_coeff command:
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</P>
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<PRE>pair_coeff * * SiC.vashishta Si Si Si C
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</PRE>
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<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
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element in the file. The final C argument maps LAMMPS atom type 4
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to the C element in the file. If a mapping value is specified as
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NULL, the mapping is not performed. This can be used when a <I>vashishta</I>
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potential is used as part of the <I>hybrid</I> pair style. The NULL values
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are placeholders for atom types that will be used with other
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potentials.
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</P>
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<P>Vashishta files in the <I>potentials</I> directory of the LAMMPS
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distribution have a ".vashishta" suffix. Lines that are not blank or
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comments (starting with #) define parameters for a triplet of
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elements. The parameters in a single entry correspond to the two-body
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and three-body coefficients in the formulae above:
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</P>
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<UL><LI>element 1 (the center atom in a 3-body interaction)
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<LI>element 2
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<LI>element 3
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<LI>H (energy units)
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<LI>eta
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<LI>Zi (electron charge units)
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<LI>Zj (electron charge units)
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<LI>lambda1 (distance units)
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<LI>D (energy units)
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<LI>lambda4 (distance units)
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<LI>W (energy units)
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<LI>rc (distance units)
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<LI>B (energy units)
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<LI>gamma
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<LI>r0 (distance units)
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<LI>C
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<LI>costheta0
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</UL>
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<P>The non-annotated parameters are unitless.
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The Vashishta potential file must contain entries for all the
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elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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simulation; LAMMPS ignores those entries.
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For a single-element simulation, only a single entry is required
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(e.g. SiSiSi). For a two-element simulation, the file must contain 8
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entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
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specify parameters for all permutations of the two elements
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interacting in three-body configurations. Thus for 3 elements, 27
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entries would be required, etc.
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</P>
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<P>Depending on the particular version of the Vashishta potential,
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the values of these parameters may be keyed to the identities of
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zero, one, two, or three elements.
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In order to make the input file format unambiguous, general,
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and simple to code,
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LAMMPS uses a slightly confusing method for specifying parameters.
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All parameters are divided into two classes: two-body and three-body.
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Two-body and three-body parameters are handled differently,
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as described below.
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The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
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They appear in the above formulae with two subscripts.
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The parameters Zi and Zj are also classified as two-body parameters,
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even though they only have 1 subscript.
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The three-body parameters are B, C, costheta0.
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They appear in the above formulae with three subscripts.
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Two-body and three-body parameters are handled differently,
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as described below.
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</P>
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<P>The first element in each entry is the center atom
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in a three-body interaction, while the second and third elements
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are two neighbor atoms. Three-body parameters for a central atom I
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and two neighbors J and K are taken from the IJK entry.
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Note that even though three-body parameters do not depend on the order of
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J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
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The user must ensure that these values are equal.
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Two-body parameters for an atom I interacting with atom J are taken from
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the IJJ entry, where the 2nd and 3rd
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elements are the same. Thus the two-body parameters
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for Si interacting with C come from the SiCC entry. Note that even
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though two-body parameters (except possibly gamma and r0 in U3)
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do not depend on the order of the two elements,
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LAMMPS will get the Si-C value from the SiCC entry
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and the C-Si value from the CSiSi entry. The user must ensure
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that these values are equal. Two-body parameters appearing
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in entries where the 2nd and 3rd elements are different are
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stored but never used. It is good practice to enter zero for
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these values. Note that the three-body function U3 above
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contains the two-body parameters gamma and r0. So U3 for a
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central C atom bonded to an Si atom and a second C atom
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will take three-body parameters from the CSiC entry, but
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two-body parameters from the CCC and CSiSi entries.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS as
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described above from values in the potential file.
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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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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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This pair style is part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
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</P>
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<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
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for pair interactions.
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</P>
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<P>The Vashishta potential files provided with LAMMPS (see the
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potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
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You can use the Vashishta potential with any LAMMPS units, but you would need
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to create your own Vashishta potential file with coefficients listed in the
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appropriate units if your simulation doesn't use "metal" units.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Vashishta1990"></A>
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<P><B>(Vashishta1990)</B> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
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</P>
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<A NAME = "Vashishta2007"></A>
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<P><B>(Vashishta2007)</B> P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
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</P>
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<A NAME = "Branicio2009"></A>
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<P><B>(Branicio2009)</B> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
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</P>
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</HTML>
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204
doc/pair_vashishta.txt
Normal file
204
doc/pair_vashishta.txt
Normal file
@ -0,0 +1,204 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style vashishta command :h3
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[Syntax:]
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pair_style vashishta :pre
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[Examples:]
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pair_style vashishta
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pair_coeff * * SiC.vashishta Si C :pre
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[Description:]
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The {vashishta} style computes the combined 2-body and 3-body
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family of potentials developed in the group of Vashishta and
|
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|
co-workers. By combining repulsive, screened Coulombic,
|
||||||
|
screened charge-dipole, and dispersion interactions with a
|
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|
bond-angle energy based on the Stillinger-Weber potential,
|
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this potential has been used to describe a variety of inorganic
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compounds, including SiO2 "Vashishta1990"_#Vashishta1990,
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SiC "Vashishta2007"_#Vashishta2007,
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and InP "Branicio2009"_#Branicio2009.
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The potential for the energy U of a system of atoms is
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:c,image(Eqs/pair_vashishta.jpg)
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where we follow the notation used in "Branicio2009"_#Branicio2009.
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U2 is a two-body term and U3 is a three-body term. The
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summation over two-body terms is over all neighbors J within
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a cutoff distance = {rc}. The twobody terms are shifted and
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tilted by a linear function so that the energy and force are
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both zero at {rc}. The summation over three-body terms
|
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|
is over all neighbors J and K within a cut-off distance = {r0},
|
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where the exponential screening function becomes zero.
|
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Only a single pair_coeff command is used with the {vashishta} style which
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specifies a Vashishta potential file with parameters for all
|
||||||
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needed elements. These are mapped to LAMMPS atom types by specifying
|
||||||
|
N additional arguments after the filename in the pair_coeff command,
|
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where N is the number of LAMMPS atom types:
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filename
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N element names = mapping of Vashishta elements to atom types :ul
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See the "pair_coeff"_pair_coeff.html doc page for alternate ways
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to specify the path for the potential file.
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As an example, imagine a file SiC.vashishta has parameters for
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Si and C. If your LAMMPS simulation has 4 atoms types and you want
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the 1st 3 to be Si, and the 4th to be C, you would use the following
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pair_coeff command:
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pair_coeff * * SiC.vashishta Si Si Si C :pre
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The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
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element in the file. The final C argument maps LAMMPS atom type 4
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to the C element in the file. If a mapping value is specified as
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NULL, the mapping is not performed. This can be used when a {vashishta}
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potential is used as part of the {hybrid} pair style. The NULL values
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||||||
|
are placeholders for atom types that will be used with other
|
||||||
|
potentials.
|
||||||
|
|
||||||
|
Vashishta files in the {potentials} directory of the LAMMPS
|
||||||
|
distribution have a ".vashishta" suffix. Lines that are not blank or
|
||||||
|
comments (starting with #) define parameters for a triplet of
|
||||||
|
elements. The parameters in a single entry correspond to the two-body
|
||||||
|
and three-body coefficients in the formulae above:
|
||||||
|
|
||||||
|
element 1 (the center atom in a 3-body interaction)
|
||||||
|
element 2
|
||||||
|
element 3
|
||||||
|
H (energy units)
|
||||||
|
eta
|
||||||
|
Zi (electron charge units)
|
||||||
|
Zj (electron charge units)
|
||||||
|
lambda1 (distance units)
|
||||||
|
D (energy units)
|
||||||
|
lambda4 (distance units)
|
||||||
|
W (energy units)
|
||||||
|
rc (distance units)
|
||||||
|
B (energy units)
|
||||||
|
gamma
|
||||||
|
r0 (distance units)
|
||||||
|
C
|
||||||
|
costheta0 :ul
|
||||||
|
|
||||||
|
The non-annotated parameters are unitless.
|
||||||
|
The Vashishta potential file must contain entries for all the
|
||||||
|
elements listed in the pair_coeff command. It can also contain
|
||||||
|
entries for additional elements not being used in a particular
|
||||||
|
simulation; LAMMPS ignores those entries.
|
||||||
|
For a single-element simulation, only a single entry is required
|
||||||
|
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
|
||||||
|
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
|
||||||
|
specify parameters for all permutations of the two elements
|
||||||
|
interacting in three-body configurations. Thus for 3 elements, 27
|
||||||
|
entries would be required, etc.
|
||||||
|
|
||||||
|
Depending on the particular version of the Vashishta potential,
|
||||||
|
the values of these parameters may be keyed to the identities of
|
||||||
|
zero, one, two, or three elements.
|
||||||
|
In order to make the input file format unambiguous, general,
|
||||||
|
and simple to code,
|
||||||
|
LAMMPS uses a slightly confusing method for specifying parameters.
|
||||||
|
All parameters are divided into two classes: two-body and three-body.
|
||||||
|
Two-body and three-body parameters are handled differently,
|
||||||
|
as described below.
|
||||||
|
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
|
||||||
|
They appear in the above formulae with two subscripts.
|
||||||
|
The parameters Zi and Zj are also classified as two-body parameters,
|
||||||
|
even though they only have 1 subscript.
|
||||||
|
The three-body parameters are B, C, costheta0.
|
||||||
|
They appear in the above formulae with three subscripts.
|
||||||
|
Two-body and three-body parameters are handled differently,
|
||||||
|
as described below.
|
||||||
|
|
||||||
|
The first element in each entry is the center atom
|
||||||
|
in a three-body interaction, while the second and third elements
|
||||||
|
are two neighbor atoms. Three-body parameters for a central atom I
|
||||||
|
and two neighbors J and K are taken from the IJK entry.
|
||||||
|
Note that even though three-body parameters do not depend on the order of
|
||||||
|
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
|
||||||
|
The user must ensure that these values are equal.
|
||||||
|
Two-body parameters for an atom I interacting with atom J are taken from
|
||||||
|
the IJJ entry, where the 2nd and 3rd
|
||||||
|
elements are the same. Thus the two-body parameters
|
||||||
|
for Si interacting with C come from the SiCC entry. Note that even
|
||||||
|
though two-body parameters (except possibly gamma and r0 in U3)
|
||||||
|
do not depend on the order of the two elements,
|
||||||
|
LAMMPS will get the Si-C value from the SiCC entry
|
||||||
|
and the C-Si value from the CSiSi entry. The user must ensure
|
||||||
|
that these values are equal. Two-body parameters appearing
|
||||||
|
in entries where the 2nd and 3rd elements are different are
|
||||||
|
stored but never used. It is good practice to enter zero for
|
||||||
|
these values. Note that the three-body function U3 above
|
||||||
|
contains the two-body parameters gamma and r0. So U3 for a
|
||||||
|
central C atom bonded to an Si atom and a second C atom
|
||||||
|
will take three-body parameters from the CSiC entry, but
|
||||||
|
two-body parameters from the CCC and CSiSi entries.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||||
|
|
||||||
|
For atom type pairs I,J and I != J, where types I and J correspond to
|
||||||
|
two different element types, mixing is performed by LAMMPS as
|
||||||
|
described above from values in the potential file.
|
||||||
|
|
||||||
|
This pair style does not support the "pair_modify"_pair_modify.html
|
||||||
|
shift, table, and tail options.
|
||||||
|
|
||||||
|
This pair style does not write its information to "binary restart
|
||||||
|
files"_restart.html, since it is stored in potential files. Thus, you
|
||||||
|
need to re-specify the pair_style and pair_coeff commands in an input
|
||||||
|
script that reads a restart file.
|
||||||
|
|
||||||
|
This pair style can only be used via the {pair} keyword of the
|
||||||
|
"run_style respa"_run_style.html command. It does not support the
|
||||||
|
{inner}, {middle}, {outer} keywords.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
[Restrictions:]
|
||||||
|
|
||||||
|
This pair style is part of the MANYBODY package. It is only enabled
|
||||||
|
if LAMMPS was built with that package (which it is by default). See
|
||||||
|
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||||
|
|
||||||
|
This pair style requires the "newton"_newton.html setting to be "on"
|
||||||
|
for pair interactions.
|
||||||
|
|
||||||
|
The Vashishta potential files provided with LAMMPS (see the
|
||||||
|
potentials directory) are parameterized for metal "units"_units.html.
|
||||||
|
You can use the Vashishta potential with any LAMMPS units, but you would need
|
||||||
|
to create your own Vashishta potential file with coefficients listed in the
|
||||||
|
appropriate units if your simulation doesn't use "metal" units.
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"pair_coeff"_pair_coeff.html
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
:link(Vashishta1990)
|
||||||
|
[(Vashishta1990)] P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
|
||||||
|
|
||||||
|
:link(Vashishta2007)
|
||||||
|
[(Vashishta2007)] P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
|
||||||
|
|
||||||
|
:link(Branicio2009)
|
||||||
|
[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
|
||||||
|
|
||||||
@ -98,6 +98,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent
|
|||||||
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
|
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
|
||||||
streitz: Streitz-Mintmire potential for Al2O3
|
streitz: Streitz-Mintmire potential for Al2O3
|
||||||
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
||||||
|
vashishta: models using the Vashishta potential
|
||||||
voronoi: test of Voronoi tesselation in compute voronoi/atom
|
voronoi: test of Voronoi tesselation in compute voronoi/atom
|
||||||
|
|
||||||
Here is a src/Make.py command which will perform a parallel build of a
|
Here is a src/Make.py command which will perform a parallel build of a
|
||||||
|
|||||||
38
examples/vashishta/InP.vashishta
Executable file
38
examples/vashishta/InP.vashishta
Executable file
@ -0,0 +1,38 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
|
||||||
|
#
|
||||||
|
# Vashishta potential file for InP, Branicio, Rino, Gan and Tsuzuki,
|
||||||
|
# J. Phys Condensed Matter 21 (2009) 095002
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
In In In 273.584 7 -1.21 -1.21 4.5 0.0 2.75
|
||||||
|
0.0 6.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
P P P 1813.06 7 1.21 1.21 4.5 52.7067 2.75
|
||||||
|
0.0 6.0 0.0 0.0 0.0 0.0 -0.333333333333
|
||||||
|
|
||||||
|
In P P 4847.09 9 1.21 -1.21 4.5 26.3533 2.75
|
||||||
|
270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333
|
||||||
|
|
||||||
|
P In In 4847.09 9 1.21 -1.21 4.5 26.3533 2.75
|
||||||
|
270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333
|
||||||
|
|
||||||
|
In In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
In P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
P In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
P P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
41
examples/vashishta/SiO.1990.vashishta
Executable file
41
examples/vashishta/SiO.1990.vashishta
Executable file
@ -0,0 +1,41 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo, Phys. Rev. B 41, 12197 (1990).
|
||||||
|
#
|
||||||
|
# Vashishta potential file for SiO2, P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo,
|
||||||
|
# Phys. Rev. B 41, 12197 (1990).
|
||||||
|
#
|
||||||
|
# These parameters, some inferred indirectly, give a good
|
||||||
|
# match to the energy-volume curve for alpha-quartz in Fig. 2 of the paper.
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
#
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
Si Si Si 0.82023 11 1.6 1.6 999 0.0 4.43
|
||||||
|
0.0 10.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O O 743.848 7 -0.8 -0.8 999 22.1179 4.43
|
||||||
|
0.0 10.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si Si 163.859 9 -0.8 1.6 999 44.2357 4.43
|
||||||
|
0.0 10.0 20.146 1.0 2.60 0.0 -0.77714596
|
||||||
|
|
||||||
|
Si O O 163.859 9 1.6 -0.8 999 44.2357 4.43
|
||||||
|
0.0 10.0 5.0365 1.0 2.60 0.0 -0.333333333333
|
||||||
|
|
||||||
|
Si O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
26
examples/vashishta/data.quartz
Normal file
26
examples/vashishta/data.quartz
Normal file
@ -0,0 +1,26 @@
|
|||||||
|
# SiO2 alpha quartz
|
||||||
|
|
||||||
|
9 atoms
|
||||||
|
2 atom types
|
||||||
|
|
||||||
|
0 4.913400 xlo xhi
|
||||||
|
0 4.255129 ylo yhi
|
||||||
|
0 5.405200 zlo zhi
|
||||||
|
-2.456700 0.0 0.0 xy xz yz
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 28.0855
|
||||||
|
2 15.9994
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 2.308807 0.000000 3.603467
|
||||||
|
2 1 -1.154403 1.999485 1.801733
|
||||||
|
3 1 -1.154403 -1.999485 0.000000
|
||||||
|
4 2 1.375998 1.140800 4.245244
|
||||||
|
5 2 -1.675961 0.621249 7.848711
|
||||||
|
6 2 0.299963 -1.762049 6.046977
|
||||||
|
7 2 0.299963 1.762049 -4.245244
|
||||||
|
8 2 -1.675961 -0.621249 -0.64177
|
||||||
|
9 2 1.375998 -1.140800 -2.443511
|
||||||
75
examples/vashishta/in.indiumphosphide
Normal file
75
examples/vashishta/in.indiumphosphide
Normal file
@ -0,0 +1,75 @@
|
|||||||
|
# calculate the energy volume curve for InP zincblende
|
||||||
|
|
||||||
|
# define volume range and filename
|
||||||
|
|
||||||
|
variable ndelta equal 100
|
||||||
|
variable volatom_min equal 20.0
|
||||||
|
variable volatom_max equal 29.0
|
||||||
|
variable evsvolfile string evsvol.dat
|
||||||
|
|
||||||
|
# set up cell
|
||||||
|
|
||||||
|
units metal
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
# setup loop variables for box volume
|
||||||
|
|
||||||
|
variable amin equal ${volatom_min}^(1/3)*2
|
||||||
|
variable delta equal (${volatom_max}-${volatom_min})/${ndelta}
|
||||||
|
variable scale equal (${delta}/v_volatom+1)^(1/3)
|
||||||
|
|
||||||
|
# set up 8 atom InP zincblende unit cell
|
||||||
|
|
||||||
|
lattice diamond ${amin}
|
||||||
|
|
||||||
|
region box prism &
|
||||||
|
0 1 &
|
||||||
|
0 1 &
|
||||||
|
0 1 &
|
||||||
|
0 0 0
|
||||||
|
|
||||||
|
create_box 2 box
|
||||||
|
|
||||||
|
create_atoms 1 box &
|
||||||
|
basis 5 2 &
|
||||||
|
basis 6 2 &
|
||||||
|
basis 7 2 &
|
||||||
|
basis 8 2
|
||||||
|
|
||||||
|
mass 1 114.76
|
||||||
|
mass 2 30.98
|
||||||
|
|
||||||
|
# choose potential
|
||||||
|
|
||||||
|
pair_style vashishta
|
||||||
|
pair_coeff * * InP.vashishta In P
|
||||||
|
|
||||||
|
# setup neighbor style
|
||||||
|
|
||||||
|
neighbor 1.0 nsq
|
||||||
|
neigh_modify once no every 1 delay 0 check yes
|
||||||
|
|
||||||
|
# setup output
|
||||||
|
|
||||||
|
thermo_style custom step temp pe press vol
|
||||||
|
thermo_modify norm no
|
||||||
|
variable volatom equal vol/atoms
|
||||||
|
variable eatom equal pe/atoms
|
||||||
|
print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}
|
||||||
|
|
||||||
|
# loop over range of volumes
|
||||||
|
|
||||||
|
label loop
|
||||||
|
variable i loop ${ndelta}
|
||||||
|
|
||||||
|
change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap
|
||||||
|
|
||||||
|
# calculate energy
|
||||||
|
# no energy minimization needed for zincblende
|
||||||
|
|
||||||
|
run 0
|
||||||
|
print "${volatom} ${eatom}" append ${evsvolfile}
|
||||||
|
|
||||||
|
next i
|
||||||
|
jump SELF loop
|
||||||
28
examples/vashishta/in.sio2
Normal file
28
examples/vashishta/in.sio2
Normal file
@ -0,0 +1,28 @@
|
|||||||
|
# test Vashishta potential for quartz
|
||||||
|
|
||||||
|
units metal
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.quartz
|
||||||
|
|
||||||
|
replicate 4 4 4
|
||||||
|
velocity all create 2000.0 277387 mom yes
|
||||||
|
displace_atoms all move 0.05 0.9 0.4 units box
|
||||||
|
|
||||||
|
pair_style vashishta
|
||||||
|
pair_coeff * * SiO.1990.vashishta Si O
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 10
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
thermo 10
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz
|
||||||
|
#dump_modify 1 element Si O
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
38
potentials/InP.vashishta
Executable file
38
potentials/InP.vashishta
Executable file
@ -0,0 +1,38 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
|
||||||
|
#
|
||||||
|
# Vashishta potential file for InP, Branicio, Rino, Gan and Tsuzuki,
|
||||||
|
# J. Phys Condensed Matter 21 (2009) 095002
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
In In In 273.584 7 -1.21 -1.21 4.5 0.0 2.75
|
||||||
|
0.0 6.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
P P P 1813.06 7 1.21 1.21 4.5 52.7067 2.75
|
||||||
|
0.0 6.0 0.0 0.0 0.0 0.0 -0.333333333333
|
||||||
|
|
||||||
|
In P P 4847.09 9 1.21 -1.21 4.5 26.3533 2.75
|
||||||
|
270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333
|
||||||
|
|
||||||
|
P In In 4847.09 9 1.21 -1.21 4.5 26.3533 2.75
|
||||||
|
270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333
|
||||||
|
|
||||||
|
In In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
In P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
P In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
P P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
@ -100,3 +100,4 @@ sw Stillinger-Weber potential
|
|||||||
tersoff Tersoff potential
|
tersoff Tersoff potential
|
||||||
tersoff.mod modified Tersoff potential
|
tersoff.mod modified Tersoff potential
|
||||||
tersoff.zbl Tersoff with ZBL core
|
tersoff.zbl Tersoff with ZBL core
|
||||||
|
vashishta Vashishta 2-body and 3-body potential
|
||||||
|
|||||||
41
potentials/SiC.vashishta
Executable file
41
potentials/SiC.vashishta
Executable file
@ -0,0 +1,41 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: P. Vashishta, R. K. Kalia, A. Nakano, and J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
|
||||||
|
#
|
||||||
|
# Vashishta potential file for SiC, P. Vashishta, R. K. Kalia, A. Nakano,
|
||||||
|
# and J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
#
|
||||||
|
# Note: Value of D here equals D/2 in paper
|
||||||
|
#
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
C C C 471.74538 7 -1.201 -1.201 5.0 0.0 3.0
|
||||||
|
0.0 7.35 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si Si Si 23.67291 7 1.201 1.201 5.0 15.575 3.0
|
||||||
|
0.0 7.35 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
C Si Si 447.09026 9 -1.201 1.201 5.0 7.7874 3.0
|
||||||
|
61.4694 7.35 9.003 1.0 2.90 5.0 -0.333333333333
|
||||||
|
|
||||||
|
Si C C 447.09026 9 1.201 -1.201 5.0 7.7874 3.0
|
||||||
|
61.4694 7.35 9.003 1.0 2.90 5.0 -0.333333333333
|
||||||
|
|
||||||
|
C C Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
C Si C 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si C Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si Si C 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
41
potentials/SiO.1990.vashishta
Executable file
41
potentials/SiO.1990.vashishta
Executable file
@ -0,0 +1,41 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo, Phys. Rev. B 41, 12197 (1990).
|
||||||
|
#
|
||||||
|
# Vashishta potential file for SiO2, P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo,
|
||||||
|
# Phys. Rev. B 41, 12197 (1990).
|
||||||
|
#
|
||||||
|
# These parameters, some inferred indirectly, give a good
|
||||||
|
# match to the energy-volume curve for alpha-quartz in Fig. 2 of the paper.
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
#
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
Si Si Si 0.82023 11 1.6 1.6 999 0.0 4.43
|
||||||
|
0.0 10.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O O 743.848 7 -0.8 -0.8 999 22.1179 4.43
|
||||||
|
0.0 10.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si Si 163.859 9 -0.8 1.6 999 44.2357 4.43
|
||||||
|
0.0 10.0 20.146 1.0 2.60 0.0 -0.77714596
|
||||||
|
|
||||||
|
Si O O 163.859 9 1.6 -0.8 999 44.2357 4.43
|
||||||
|
0.0 10.0 5.0365 1.0 2.60 0.0 -0.333333333333
|
||||||
|
|
||||||
|
Si O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
38
potentials/SiO.1994.vashishta
Executable file
38
potentials/SiO.1994.vashishta
Executable file
@ -0,0 +1,38 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Nakano, Kalia, and Vashishta, J. Non-Crystal. Solids, v. 171, p. 157 (1994)
|
||||||
|
#
|
||||||
|
# Vashishta potential file for SiO2, Nakano, Kalia, and Vashishta,
|
||||||
|
# J. Non-Crystal. Solids, v. 171, p. 157 (1994)
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
#
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
Si Si Si 0.80603 11 1.76 1.76 4.43 0.0 2.5
|
||||||
|
0.0 5.5 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O O 730.17 7 -0.88 -0.88 4.43 26.7447 2.5
|
||||||
|
0.0 5.5 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si Si 160.849 9 -0.88 1.76 4.43 53.4894 2.5
|
||||||
|
0.0 5.5 19.972 1.0 2.60 0.0 -0.77714596
|
||||||
|
|
||||||
|
Si O O 160.849 9 1.76 -0.88 4.43 53.4894 2.5
|
||||||
|
0.0 5.5 4.993 1.0 2.60 0.0 -0.333333333333
|
||||||
|
|
||||||
|
Si O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
37
potentials/SiO.1997.vashishta
Executable file
37
potentials/SiO.1997.vashishta
Executable file
@ -0,0 +1,37 @@
|
|||||||
|
# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Broughton, Meli,Vashishta,and Kalia, Phys Rev B, v. 56, p. 611 (1997)
|
||||||
|
#
|
||||||
|
# Vashishta potential file for SiO2, Broughton, Meli,Vashishta,and Kalia, Phys Rev B, v. 56, p. 611 (1997)
|
||||||
|
#
|
||||||
|
# These entries are in LAMMPS "metal" units:
|
||||||
|
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
|
||||||
|
# lambda1, lambda4, rc, r0, gamma = Angstroms;
|
||||||
|
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
|
||||||
|
# other quantities are unitless
|
||||||
|
#
|
||||||
|
# element1 element2 element3
|
||||||
|
# H eta Zi Zj lambda1 D lambda4
|
||||||
|
# W rc B gamma r0 C cos(theta)
|
||||||
|
|
||||||
|
Si Si Si 0.15500 11 0.7872 0.7872 4.43 0.0 2.5
|
||||||
|
0.0 5.5 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O O 140.38 7 -0.3936 -0.3936 4.43 5.3504 2.5
|
||||||
|
0.0 5.5 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si Si 30.923 9 -0.3936 0.7872 4.43 10.701 2.5
|
||||||
|
0.0 5.5 19.972 1.0 2.60 0.0 -0.80593
|
||||||
|
|
||||||
|
Si O O 30.923 9 0.7872 -0.3936 4.43 10.701 2.5
|
||||||
|
0.0 5.5 4.993 1.0 2.60 0.0 -0.333333333333
|
||||||
|
|
||||||
|
Si O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
Si Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
|
||||||
|
O O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
|
0.0 0.0 0.0 0.0 0.0 0.0 0.0
|
||||||
619
src/MANYBODY/pair_vashishta.cpp
Executable file
619
src/MANYBODY/pair_vashishta.cpp
Executable file
@ -0,0 +1,619 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing author: Aidan Thompson (SNL)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "math.h"
|
||||||
|
#include "stdio.h"
|
||||||
|
#include "stdlib.h"
|
||||||
|
#include "string.h"
|
||||||
|
#include "pair_vashishta.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_request.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
//using namespace MathConst;
|
||||||
|
|
||||||
|
#define MAXLINE 1024
|
||||||
|
#define DELTA 4
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
|
||||||
|
{
|
||||||
|
single_enable = 0;
|
||||||
|
restartinfo = 0;
|
||||||
|
one_coeff = 1;
|
||||||
|
manybody_flag = 1;
|
||||||
|
|
||||||
|
nelements = 0;
|
||||||
|
elements = NULL;
|
||||||
|
nparams = maxparam = 0;
|
||||||
|
params = NULL;
|
||||||
|
elem2param = NULL;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
check if allocated, since class can be destructed when incomplete
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
PairVashishta::~PairVashishta()
|
||||||
|
{
|
||||||
|
if (elements)
|
||||||
|
for (int i = 0; i < nelements; i++) delete [] elements[i];
|
||||||
|
delete [] elements;
|
||||||
|
memory->destroy(params);
|
||||||
|
memory->destroy(elem2param);
|
||||||
|
|
||||||
|
if (allocated) {
|
||||||
|
memory->destroy(setflag);
|
||||||
|
memory->destroy(cutsq);
|
||||||
|
delete [] map;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::compute(int eflag, int vflag)
|
||||||
|
{
|
||||||
|
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
|
||||||
|
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
|
||||||
|
tagint itag,jtag;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||||
|
double rsq,rsq1,rsq2;
|
||||||
|
double delr1[3],delr2[3],fj[3],fk[3];
|
||||||
|
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||||
|
|
||||||
|
evdwl = 0.0;
|
||||||
|
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||||
|
else evflag = vflag_fdotr = 0;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double **f = atom->f;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
int *type = atom->type;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
int newton_pair = force->newton_pair;
|
||||||
|
|
||||||
|
inum = list->inum;
|
||||||
|
ilist = list->ilist;
|
||||||
|
numneigh = list->numneigh;
|
||||||
|
firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// loop over full neighbor list of my atoms
|
||||||
|
|
||||||
|
for (ii = 0; ii < inum; ii++) {
|
||||||
|
i = ilist[ii];
|
||||||
|
itag = tag[i];
|
||||||
|
itype = map[type[i]];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
|
||||||
|
// two-body interactions, skip half of them
|
||||||
|
|
||||||
|
jlist = firstneigh[i];
|
||||||
|
jnum = numneigh[i];
|
||||||
|
|
||||||
|
for (jj = 0; jj < jnum; jj++) {
|
||||||
|
j = jlist[jj];
|
||||||
|
j &= NEIGHMASK;
|
||||||
|
jtag = tag[j];
|
||||||
|
|
||||||
|
if (itag > jtag) {
|
||||||
|
if ((itag+jtag) % 2 == 0) continue;
|
||||||
|
} else if (itag < jtag) {
|
||||||
|
if ((itag+jtag) % 2 == 1) continue;
|
||||||
|
} else {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = map[type[j]];
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
ijparam = elem2param[itype][jtype][jtype];
|
||||||
|
if (rsq > params[ijparam].cutsq) continue;
|
||||||
|
|
||||||
|
twobody(¶ms[ijparam],rsq,fpair,eflag,evdwl);
|
||||||
|
|
||||||
|
f[i][0] += delx*fpair;
|
||||||
|
f[i][1] += dely*fpair;
|
||||||
|
f[i][2] += delz*fpair;
|
||||||
|
f[j][0] -= delx*fpair;
|
||||||
|
f[j][1] -= dely*fpair;
|
||||||
|
f[j][2] -= delz*fpair;
|
||||||
|
|
||||||
|
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||||
|
evdwl,0.0,fpair,delx,dely,delz);
|
||||||
|
}
|
||||||
|
|
||||||
|
jnumm1 = jnum - 1;
|
||||||
|
|
||||||
|
for (jj = 0; jj < jnumm1; jj++) {
|
||||||
|
j = jlist[jj];
|
||||||
|
j &= NEIGHMASK;
|
||||||
|
jtype = map[type[j]];
|
||||||
|
ijparam = elem2param[itype][jtype][jtype];
|
||||||
|
delr1[0] = x[j][0] - xtmp;
|
||||||
|
delr1[1] = x[j][1] - ytmp;
|
||||||
|
delr1[2] = x[j][2] - ztmp;
|
||||||
|
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||||
|
if (rsq1 >= params[ijparam].cutsq2) continue;
|
||||||
|
|
||||||
|
for (kk = jj+1; kk < jnum; kk++) {
|
||||||
|
k = jlist[kk];
|
||||||
|
k &= NEIGHMASK;
|
||||||
|
ktype = map[type[k]];
|
||||||
|
ikparam = elem2param[itype][ktype][ktype];
|
||||||
|
ijkparam = elem2param[itype][jtype][ktype];
|
||||||
|
|
||||||
|
delr2[0] = x[k][0] - xtmp;
|
||||||
|
delr2[1] = x[k][1] - ytmp;
|
||||||
|
delr2[2] = x[k][2] - ztmp;
|
||||||
|
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||||
|
if (rsq2 >= params[ikparam].cutsq2) continue;
|
||||||
|
|
||||||
|
threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
|
||||||
|
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
|
||||||
|
|
||||||
|
f[i][0] -= fj[0] + fk[0];
|
||||||
|
f[i][1] -= fj[1] + fk[1];
|
||||||
|
f[i][2] -= fj[2] + fk[2];
|
||||||
|
f[j][0] += fj[0];
|
||||||
|
f[j][1] += fj[1];
|
||||||
|
f[j][2] += fj[2];
|
||||||
|
f[k][0] += fk[0];
|
||||||
|
f[k][1] += fk[1];
|
||||||
|
f[k][2] += fk[2];
|
||||||
|
|
||||||
|
if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (vflag_fdotr) virial_fdotr_compute();
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::allocate()
|
||||||
|
{
|
||||||
|
allocated = 1;
|
||||||
|
int n = atom->ntypes;
|
||||||
|
|
||||||
|
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||||
|
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||||
|
|
||||||
|
map = new int[n+1];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
global settings
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::settings(int narg, char **arg)
|
||||||
|
{
|
||||||
|
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
set coeffs for one or more type pairs
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::coeff(int narg, char **arg)
|
||||||
|
{
|
||||||
|
int i,j,n;
|
||||||
|
|
||||||
|
if (!allocated) allocate();
|
||||||
|
|
||||||
|
if (narg != 3 + atom->ntypes)
|
||||||
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
|
||||||
|
// insure I,J args are * *
|
||||||
|
|
||||||
|
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
|
||||||
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
|
||||||
|
// read args that map atom types to elements in potential file
|
||||||
|
// map[i] = which element the Ith atom type is, -1 if NULL
|
||||||
|
// nelements = # of unique elements
|
||||||
|
// elements = list of element names
|
||||||
|
|
||||||
|
if (elements) {
|
||||||
|
for (i = 0; i < nelements; i++) delete [] elements[i];
|
||||||
|
delete [] elements;
|
||||||
|
}
|
||||||
|
elements = new char*[atom->ntypes];
|
||||||
|
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
|
||||||
|
|
||||||
|
nelements = 0;
|
||||||
|
for (i = 3; i < narg; i++) {
|
||||||
|
if (strcmp(arg[i],"NULL") == 0) {
|
||||||
|
map[i-2] = -1;
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
for (j = 0; j < nelements; j++)
|
||||||
|
if (strcmp(arg[i],elements[j]) == 0) break;
|
||||||
|
map[i-2] = j;
|
||||||
|
if (j == nelements) {
|
||||||
|
n = strlen(arg[i]) + 1;
|
||||||
|
elements[j] = new char[n];
|
||||||
|
strcpy(elements[j],arg[i]);
|
||||||
|
nelements++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// read potential file and initialize potential parameters
|
||||||
|
|
||||||
|
read_file(arg[2]);
|
||||||
|
setup();
|
||||||
|
|
||||||
|
// clear setflag since coeff() called once with I,J = * *
|
||||||
|
|
||||||
|
n = atom->ntypes;
|
||||||
|
for (int i = 1; i <= n; i++)
|
||||||
|
for (int j = i; j <= n; j++)
|
||||||
|
setflag[i][j] = 0;
|
||||||
|
|
||||||
|
// set setflag i,j for type pairs where both are mapped to elements
|
||||||
|
|
||||||
|
int count = 0;
|
||||||
|
for (int i = 1; i <= n; i++)
|
||||||
|
for (int j = i; j <= n; j++)
|
||||||
|
if (map[i] >= 0 && map[j] >= 0) {
|
||||||
|
setflag[i][j] = 1;
|
||||||
|
count++;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
init specific to this pair style
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::init_style()
|
||||||
|
{
|
||||||
|
if (atom->tag_enable == 0)
|
||||||
|
error->all(FLERR,"Pair style Vashishta requires atom IDs");
|
||||||
|
if (force->newton_pair == 0)
|
||||||
|
error->all(FLERR,"Pair style Vashishta requires newton pair on");
|
||||||
|
|
||||||
|
// need a full neighbor list
|
||||||
|
|
||||||
|
int irequest = neighbor->request(this);
|
||||||
|
neighbor->requests[irequest]->half = 0;
|
||||||
|
neighbor->requests[irequest]->full = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
init for one type pair i,j and corresponding j,i
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairVashishta::init_one(int i, int j)
|
||||||
|
{
|
||||||
|
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||||
|
|
||||||
|
return cutmax;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::read_file(char *file)
|
||||||
|
{
|
||||||
|
int params_per_line = 17;
|
||||||
|
char **words = new char*[params_per_line+1];
|
||||||
|
|
||||||
|
memory->sfree(params);
|
||||||
|
params = NULL;
|
||||||
|
nparams = maxparam = 0;
|
||||||
|
|
||||||
|
// open file on proc 0
|
||||||
|
|
||||||
|
FILE *fp;
|
||||||
|
if (comm->me == 0) {
|
||||||
|
fp = force->open_potential(file);
|
||||||
|
if (fp == NULL) {
|
||||||
|
char str[128];
|
||||||
|
sprintf(str,"Cannot open Vashishta potential file %s",file);
|
||||||
|
error->one(FLERR,str);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// read each set of params from potential file
|
||||||
|
// one set of params can span multiple lines
|
||||||
|
// store params if all 3 element tags are in element list
|
||||||
|
|
||||||
|
int n,nwords,ielement,jelement,kelement;
|
||||||
|
char line[MAXLINE],*ptr;
|
||||||
|
int eof = 0;
|
||||||
|
|
||||||
|
while (1) {
|
||||||
|
if (comm->me == 0) {
|
||||||
|
ptr = fgets(line,MAXLINE,fp);
|
||||||
|
if (ptr == NULL) {
|
||||||
|
eof = 1;
|
||||||
|
fclose(fp);
|
||||||
|
} else n = strlen(line) + 1;
|
||||||
|
}
|
||||||
|
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||||
|
if (eof) break;
|
||||||
|
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||||
|
|
||||||
|
// strip comment, skip line if blank
|
||||||
|
|
||||||
|
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||||
|
nwords = atom->count_words(line);
|
||||||
|
if (nwords == 0) continue;
|
||||||
|
|
||||||
|
// concatenate additional lines until have params_per_line words
|
||||||
|
|
||||||
|
while (nwords < params_per_line) {
|
||||||
|
n = strlen(line);
|
||||||
|
if (comm->me == 0) {
|
||||||
|
ptr = fgets(&line[n],MAXLINE-n,fp);
|
||||||
|
if (ptr == NULL) {
|
||||||
|
eof = 1;
|
||||||
|
fclose(fp);
|
||||||
|
} else n = strlen(line) + 1;
|
||||||
|
}
|
||||||
|
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||||
|
if (eof) break;
|
||||||
|
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||||
|
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||||
|
nwords = atom->count_words(line);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nwords != params_per_line)
|
||||||
|
error->all(FLERR,"Incorrect format in Vashishta potential file");
|
||||||
|
|
||||||
|
// words = ptrs to all words in line
|
||||||
|
|
||||||
|
nwords = 0;
|
||||||
|
words[nwords++] = strtok(line," \t\n\r\f");
|
||||||
|
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
|
||||||
|
|
||||||
|
// ielement,jelement,kelement = 1st args
|
||||||
|
// if all 3 args are in element list, then parse this line
|
||||||
|
// else skip to next entry in file
|
||||||
|
|
||||||
|
for (ielement = 0; ielement < nelements; ielement++)
|
||||||
|
if (strcmp(words[0],elements[ielement]) == 0) break;
|
||||||
|
if (ielement == nelements) continue;
|
||||||
|
for (jelement = 0; jelement < nelements; jelement++)
|
||||||
|
if (strcmp(words[1],elements[jelement]) == 0) break;
|
||||||
|
if (jelement == nelements) continue;
|
||||||
|
for (kelement = 0; kelement < nelements; kelement++)
|
||||||
|
if (strcmp(words[2],elements[kelement]) == 0) break;
|
||||||
|
if (kelement == nelements) continue;
|
||||||
|
|
||||||
|
// load up parameter settings and error check their values
|
||||||
|
|
||||||
|
if (nparams == maxparam) {
|
||||||
|
maxparam += DELTA;
|
||||||
|
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
|
||||||
|
"pair:params");
|
||||||
|
}
|
||||||
|
|
||||||
|
params[nparams].ielement = ielement;
|
||||||
|
params[nparams].jelement = jelement;
|
||||||
|
params[nparams].kelement = kelement;
|
||||||
|
params[nparams].bigh = atof(words[3]);
|
||||||
|
params[nparams].eta = atof(words[4]);
|
||||||
|
params[nparams].zi = atof(words[5]);
|
||||||
|
params[nparams].zj = atof(words[6]);
|
||||||
|
params[nparams].lambda1 = atof(words[7]);
|
||||||
|
params[nparams].bigd = atof(words[8]);
|
||||||
|
params[nparams].lambda4 = atof(words[9]);
|
||||||
|
params[nparams].bigw = atof(words[10]);
|
||||||
|
params[nparams].cut = atof(words[11]);
|
||||||
|
params[nparams].bigb = atof(words[12]);
|
||||||
|
params[nparams].gamma = atof(words[13]);
|
||||||
|
params[nparams].r0 = atof(words[14]);
|
||||||
|
params[nparams].bigc = atof(words[15]);
|
||||||
|
params[nparams].costheta = atof(words[16]);
|
||||||
|
|
||||||
|
if (params[nparams].bigb < 0.0 || params[nparams].gamma < 0.0 ||
|
||||||
|
params[nparams].r0 < 0.0 || params[nparams].bigc < 0.0 ||
|
||||||
|
params[nparams].bigh < 0.0 || params[nparams].eta < 0.0 ||
|
||||||
|
params[nparams].lambda1 < 0.0 || params[nparams].bigd < 0.0 ||
|
||||||
|
params[nparams].lambda4 < 0.0 || params[nparams].bigw < 0.0 ||
|
||||||
|
params[nparams].cut < 0.0)
|
||||||
|
error->all(FLERR,"Illegal Vashishta parameter");
|
||||||
|
|
||||||
|
nparams++;
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] words;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::setup()
|
||||||
|
{
|
||||||
|
int i,j,k,m,n;
|
||||||
|
|
||||||
|
// set elem2param for all triplet combinations
|
||||||
|
// must be a single exact match to lines read from file
|
||||||
|
// do not allow for ACB in place of ABC
|
||||||
|
|
||||||
|
memory->destroy(elem2param);
|
||||||
|
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
|
||||||
|
|
||||||
|
for (i = 0; i < nelements; i++)
|
||||||
|
for (j = 0; j < nelements; j++)
|
||||||
|
for (k = 0; k < nelements; k++) {
|
||||||
|
n = -1;
|
||||||
|
for (m = 0; m < nparams; m++) {
|
||||||
|
if (i == params[m].ielement && j == params[m].jelement &&
|
||||||
|
k == params[m].kelement) {
|
||||||
|
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
|
||||||
|
n = m;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
|
||||||
|
elem2param[i][j][k] = n;
|
||||||
|
}
|
||||||
|
|
||||||
|
// compute parameter values derived from inputs
|
||||||
|
|
||||||
|
// set cutsq using shortcut to reduce neighbor list for accelerated
|
||||||
|
// calculations. cut must remain unchanged as it is a potential parameter
|
||||||
|
|
||||||
|
for (m = 0; m < nparams; m++) {
|
||||||
|
params[m].cutsq = params[m].cut * params[m].cut;
|
||||||
|
params[m].cutsq2 = params[m].r0 * params[m].r0;
|
||||||
|
|
||||||
|
params[m].lam1inv = 1.0/params[m].lambda1;
|
||||||
|
params[m].lam4inv = 1.0/params[m].lambda4;
|
||||||
|
params[m].zizj = params[m].zi*params[m].zj * force->qqr2e;
|
||||||
|
// Note that bigd does not have 1/2 factor
|
||||||
|
params[m].mbigd = params[m].bigd;
|
||||||
|
params[m].heta = params[m].bigh*params[m].eta;
|
||||||
|
params[m].big2b = 2.0*params[m].bigb;
|
||||||
|
params[m].big6w = 6.0*params[m].bigw;
|
||||||
|
|
||||||
|
params[m].rcinv = 1.0/params[m].cut;
|
||||||
|
params[m].rc2inv = 1.0/params[m].cutsq;
|
||||||
|
params[m].rc4inv = params[m].rc2inv*params[m].rc2inv;
|
||||||
|
params[m].rc6inv = params[m].rc2inv*params[m].rc4inv;
|
||||||
|
params[m].rceta = pow(params[m].rcinv,params[m].eta);
|
||||||
|
params[m].lam1rc = params[m].cut*params[m].lam1inv;
|
||||||
|
params[m].lam4rc = params[m].cut*params[m].lam4inv;
|
||||||
|
params[m].vrcc2 = params[m].zizj*params[m].rcinv *
|
||||||
|
exp(-params[m].lam1rc);
|
||||||
|
params[m].vrcc3 = params[m].mbigd*params[m].rc4inv *
|
||||||
|
exp(-params[m].lam4rc);
|
||||||
|
params[m].vrc = params[m].bigh*params[m].rceta +
|
||||||
|
params[m].vrcc2 - params[m].vrcc3 -
|
||||||
|
params[m].bigw*params[m].rc6inv;
|
||||||
|
|
||||||
|
params[m].dvrc1 = params[m].heta*params[m].rceta*params[m].rcinv;
|
||||||
|
params[m].dvrc2 = params[m].vrcc2 *
|
||||||
|
(params[m].rcinv+params[m].lam1inv);
|
||||||
|
params[m].dvrc3 = params[m].vrcc3 *
|
||||||
|
(4.0*params[m].rcinv+params[m].lam4inv);
|
||||||
|
params[m].dvrc4 = params[m].big6w*params[m].rc6inv *
|
||||||
|
params[m].rcinv;
|
||||||
|
params[m].dvrc = params[m].dvrc3 + params[m].dvrc4 -
|
||||||
|
params[m].dvrc1 - params[m].dvrc2;
|
||||||
|
params[m].c5 = params[m].cut*params[m].dvrc - params[m].vrc;
|
||||||
|
}
|
||||||
|
|
||||||
|
// set cutmax to max of all params
|
||||||
|
|
||||||
|
cutmax = 0.0;
|
||||||
|
for (m = 0; m < nparams; m++) {
|
||||||
|
if (params[m].cut > cutmax) cutmax = params[m].cut;
|
||||||
|
if (params[m].r0 > cutmax) cutmax = params[m].r0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::twobody(Param *param, double rsq, double &fforce,
|
||||||
|
int eflag, double &eng)
|
||||||
|
{
|
||||||
|
double r,rinvsq,r4inv,r6inv,reta,lam1r,lam4r;
|
||||||
|
double vc2,vc3,vo2;
|
||||||
|
|
||||||
|
r = sqrt(rsq);
|
||||||
|
rinvsq = 1.0/rsq;
|
||||||
|
r4inv = rinvsq*rinvsq;
|
||||||
|
r6inv = rinvsq*r4inv;
|
||||||
|
reta = pow(r,-param->eta);
|
||||||
|
lam1r = r*param->lam1inv;
|
||||||
|
lam4r = r*param->lam4inv;
|
||||||
|
vc2 = param->zizj*exp(-lam1r)/r;
|
||||||
|
vc3 = param->mbigd*r4inv*exp(-lam4r);
|
||||||
|
vo2 = param->bigh*reta + vc2 - vc3 - param->bigw*r6inv;
|
||||||
|
|
||||||
|
fforce = (param->dvrc*r - (4.0*vc3 + lam4r*vc3+param->big6w*r6inv-
|
||||||
|
param->heta*reta - vc2-lam1r*vc2)) * rinvsq;
|
||||||
|
if (eflag) eng = vo2 - r*param->dvrc + param->c5;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairVashishta::threebody(Param *paramij, Param *paramik, Param *paramijk,
|
||||||
|
double rsq1, double rsq2,
|
||||||
|
double *delr1, double *delr2,
|
||||||
|
double *fj, double *fk, int eflag, double &eng)
|
||||||
|
{
|
||||||
|
double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
|
||||||
|
double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
|
||||||
|
double rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2,pcsinv,pcsinvsq,pcs;
|
||||||
|
double facang,facang12,csfacang,csfac1,csfac2;
|
||||||
|
|
||||||
|
r1 = sqrt(rsq1);
|
||||||
|
rinvsq1 = 1.0/rsq1;
|
||||||
|
rainv1 = 1.0/(r1 - paramij->r0);
|
||||||
|
gsrainv1 = paramij->gamma * rainv1;
|
||||||
|
gsrainvsq1 = gsrainv1*rainv1/r1;
|
||||||
|
expgsrainv1 = exp(gsrainv1);
|
||||||
|
|
||||||
|
r2 = sqrt(rsq2);
|
||||||
|
rinvsq2 = 1.0/rsq2;
|
||||||
|
rainv2 = 1.0/(r2 - paramik->r0);
|
||||||
|
gsrainv2 = paramik->gamma * rainv2;
|
||||||
|
gsrainvsq2 = gsrainv2*rainv2/r2;
|
||||||
|
expgsrainv2 = exp(gsrainv2);
|
||||||
|
|
||||||
|
rinv12 = 1.0/(r1*r2);
|
||||||
|
cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
|
||||||
|
delcs = cs - paramijk->costheta;
|
||||||
|
delcssq = delcs*delcs;
|
||||||
|
pcsinv = paramijk->bigc*delcssq + 1.0;
|
||||||
|
pcsinvsq = pcsinv*pcsinv;
|
||||||
|
pcs = delcssq/pcsinv;
|
||||||
|
|
||||||
|
facexp = expgsrainv1*expgsrainv2;
|
||||||
|
|
||||||
|
facrad = paramijk->bigb * facexp * pcs;
|
||||||
|
frad1 = facrad*gsrainvsq1;
|
||||||
|
frad2 = facrad*gsrainvsq2;
|
||||||
|
facang = paramijk->big2b * facexp * delcs/pcsinvsq;
|
||||||
|
facang12 = rinv12*facang;
|
||||||
|
csfacang = cs*facang;
|
||||||
|
csfac1 = rinvsq1*csfacang;
|
||||||
|
|
||||||
|
fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
|
||||||
|
fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
|
||||||
|
fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
|
||||||
|
|
||||||
|
csfac2 = rinvsq2*csfacang;
|
||||||
|
|
||||||
|
fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12;
|
||||||
|
fk[1] = delr2[1]*(frad2+csfac2)-delr1[1]*facang12;
|
||||||
|
fk[2] = delr2[2]*(frad2+csfac2)-delr1[2]*facang12;
|
||||||
|
|
||||||
|
if (eflag) eng = facrad;
|
||||||
|
}
|
||||||
122
src/MANYBODY/pair_vashishta.h
Executable file
122
src/MANYBODY/pair_vashishta.h
Executable file
@ -0,0 +1,122 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef PAIR_CLASS
|
||||||
|
|
||||||
|
PairStyle(vashishta,PairVashishta)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_PAIR_Vashishta_H
|
||||||
|
#define LMP_PAIR_Vashishta_H
|
||||||
|
|
||||||
|
#include "pair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class PairVashishta : public Pair {
|
||||||
|
public:
|
||||||
|
PairVashishta(class LAMMPS *);
|
||||||
|
virtual ~PairVashishta();
|
||||||
|
virtual void compute(int, int);
|
||||||
|
void settings(int, char **);
|
||||||
|
void coeff(int, char **);
|
||||||
|
virtual double init_one(int, int);
|
||||||
|
virtual void init_style();
|
||||||
|
|
||||||
|
protected:
|
||||||
|
struct Param {
|
||||||
|
double bigb,gamma,r0,bigc,costheta;
|
||||||
|
double bigh,eta,zi,zj;
|
||||||
|
double lambda1,bigd,mbigd,lambda4,bigw,cut;
|
||||||
|
double lam1inv,lam4inv,zizj,heta,big2b,big6w;
|
||||||
|
double rcinv,rc2inv,rc4inv,rc6inv,rceta;
|
||||||
|
double cutsq2,cutsq;
|
||||||
|
double lam1rc,lam4rc,vrcc2,vrcc3,vrc;
|
||||||
|
double dvrc1,dvrc2,dvrc3,dvrc4,dvrc,c5;
|
||||||
|
int ielement,jelement,kelement;
|
||||||
|
};
|
||||||
|
|
||||||
|
double cutmax; // max cutoff for all elements
|
||||||
|
int nelements; // # of unique elements
|
||||||
|
char **elements; // names of unique elements
|
||||||
|
int ***elem2param; // mapping from element triplets to parameters
|
||||||
|
int *map; // mapping from atom types to elements
|
||||||
|
int nparams; // # of stored parameter sets
|
||||||
|
int maxparam; // max # of parameter sets
|
||||||
|
Param *params; // parameter set for an I-J-K interaction
|
||||||
|
|
||||||
|
virtual void allocate();
|
||||||
|
void read_file(char *);
|
||||||
|
void setup();
|
||||||
|
void twobody(Param *, double, double &, int, double &);
|
||||||
|
void threebody(Param *, Param *, Param *, double, double, double *, double *,
|
||||||
|
double *, double *, int, double &);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Incorrect args for pair coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Pair style Vashishta requires atom IDs
|
||||||
|
|
||||||
|
This is a requirement to use the Vashishta potential.
|
||||||
|
|
||||||
|
E: Pair style Vashishta requires newton pair on
|
||||||
|
|
||||||
|
See the newton command. This is a restriction to use the Vashishta
|
||||||
|
potential.
|
||||||
|
|
||||||
|
E: All pair coeffs are not set
|
||||||
|
|
||||||
|
All pair coefficients must be set in the data file or by the
|
||||||
|
pair_coeff command before running a simulation.
|
||||||
|
|
||||||
|
E: Cannot open Vashishta potential file %s
|
||||||
|
|
||||||
|
The specified Vashishta potential file cannot be opened. Check that the path
|
||||||
|
and name are correct.
|
||||||
|
|
||||||
|
E: Incorrect format in Vashishta potential file
|
||||||
|
|
||||||
|
Incorrect number of words per line in the potential file.
|
||||||
|
|
||||||
|
E: Illegal Vashishta parameter
|
||||||
|
|
||||||
|
One or more of the coefficients defined in the potential file is
|
||||||
|
invalid.
|
||||||
|
|
||||||
|
E: Potential file has duplicate entry
|
||||||
|
|
||||||
|
The potential file for a Vashishta or Tersoff potential has more than
|
||||||
|
one entry for the same 3 ordered elements.
|
||||||
|
|
||||||
|
E: Potential file is missing an entry
|
||||||
|
|
||||||
|
The potential file for a Vashishta or Tersoff potential does not have a
|
||||||
|
needed entry.
|
||||||
|
|
||||||
|
*/
|
||||||
Reference in New Issue
Block a user