forked from lijiext/lammps
Commit JT 051319
- added a cubic anisotropy in fix_precession_spin - added associated doc and examples - corrected neb/spin commands in doc/src/ - added tools/spin/ description
This commit is contained in:
julient31
parent
a7c9560dc1
commit
11f223416c
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@ -83,7 +83,7 @@ An alphabetic list of all general LAMMPS commands.
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"molecule"_molecule.html,
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"ndx2group"_group2ndx.html,
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"neb"_neb.html,
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"neb_spin"_neb_spin.html,
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"neb/spin"_neb_spin.html,
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"neigh_modify"_neigh_modify.html,
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"neighbor"_neighbor.html,
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"newton"_newton.html,
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Binary file not shown.
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After Width: | Height: | Size: 25 KiB |
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@ -0,0 +1,21 @@
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\documentclass[preview]{standalone}
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\usepackage{varwidth}
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\usepackage[utf8x]{inputenc}
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\usepackage{amsmath,amssymb,amsthm,bm}
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\begin{document}
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\begin{varwidth}{50in}
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\begin{equation}
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\bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
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\Big[
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\left(\vec{s}_{i} \cdot \vec{n1} \right)^2
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\left(\vec{s}_{i} \cdot \vec{n2} \right)^2 +
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\left(\vec{s}_{i} \cdot \vec{n2} \right)^2
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\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 +
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\left(\vec{s}_{i} \cdot \vec{n1} \right)^2
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\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big]
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+K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
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\left(\vec{s}_{i} \cdot \vec{n2} \right)^2
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\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber
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\end{equation}
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\end{varwidth}
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\end{document}
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@ -77,6 +77,7 @@ Post-processing tools :h3
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"python"_#pythontools,
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"reax"_#reax_tool,
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"smd"_#smd,
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"spin"_#spin,
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"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
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Miscellaneous tools :h3
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@ -511,6 +512,20 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
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:line
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spin tool :h4,link(spin)
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The spin sub-directory contains a C file interpolate.c which can
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be compiled and used to perform a cubic polynomial interpolation of
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the MEP following a GNEB calculation.
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See the README file in tools/spin/interpolate_gneb for more details.
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This tool was written by the SPIN package author, Julien
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Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
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Ivanov, at University of Iceland (ali5 at hi.is).
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:line
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vim tool :h4,link(vim)
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The files in the tools/vim directory are add-ons to the VIM editor
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@ -62,12 +62,12 @@ Commands :h1
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mass
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message
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min_modify
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min_spin
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min/spin
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min_style
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minimize
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molecule
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neb
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neb_spin
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neb/spin
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neigh_modify
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neighbor
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newton
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@ -14,19 +14,23 @@ fix ID group precession/spin style args :pre
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ID, group are documented in "fix"_fix.html command :ulb,l
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precession/spin = style name of this fix command :l
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style = {zeeman} or {anisotropy} :l
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style = {zeeman} or {anisotropy} or {cubic} :l
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{zeeman} args = H x y z
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H = intensity of the magnetic field (in Tesla)
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x y z = vector direction of the field
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{anisotropy} args = K x y z
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K = intensity of the magnetic anisotropy (in eV)
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x y z = vector direction of the anisotropy :pre
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{cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
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K1 and K2c = intensity of the magnetic anisotropy (in eV)
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n1x to n3z = three direction vectors of the cubic anisotropy :pre
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:ule
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[Examples:]
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fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
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fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0
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fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
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fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
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fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
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[Description:]
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@ -50,10 +54,29 @@ for the magnetic spins in the defined group:
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with n defining the direction of the anisotropy, and K (in eV) its intensity.
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If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
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In both cases, the choice of (x y z) imposes the vector direction for the force.
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Only the direction of the vector is important; it's length is ignored.
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Style {cubic} is used to simulate a cubic anisotropy, with three
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possible easy axis for the magnetic spins in the defined group:
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Both styles can be combined within one single command line.
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:c,image(Eqs/fix_spin_cubic.jpg)
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with K1 and K2c (in eV) the intensity coefficients and
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n1, n2 and n3 defining the three anisotropic directions
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defined by the command (from n1x to n3z).
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For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
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iron type anisotropy (easy axis along the (001)-type cube
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edges), and K1 > 0 defines a nickel type anisotropy (easy axis
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along the (111)-type cube diagonals).
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K2^c > 0 also defines easy axis along the (111)-type cube
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diagonals.
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See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
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anisotropies.
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In all cases, the choice of (x y z) only imposes the vector
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directions for the forces. Only the direction of the vector is
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important; it's length is ignored (the entered vectors are
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normalized).
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Those styles can be combined within one single command line.
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:line
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@ -85,3 +108,9 @@ package"_Build_package.html doc page for more info.
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"atom_style spin"_atom_style.html
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[Default:] none
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:line
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:link(Skomski1)
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[(Skomski)] Skomski, R. (2008). Simple models of magnetism.
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Oxford University Press.
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@ -6,7 +6,7 @@
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:line
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neb command :h3
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neb/spin command :h3
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[Syntax:]
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@ -0,0 +1,60 @@
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# bcc iron in a 3d periodic box
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clear
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units metal
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atom_style spin
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dimension 3
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boundary p p p
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# necessary for the serial algorithm (sametag)
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atom_modify map array
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lattice bcc 2.8665
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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create_box 1 box
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create_atoms 1 box
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# setting mass, mag. moments, and interactions for bcc iron
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mass 1 55.845
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set group all spin 2.2 -1.0 0.0 0.0
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velocity all create 100 4928459 rot yes dist gaussian
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pair_style hybrid/overlay eam/alloy spin/exchange 3.5
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pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
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pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
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neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.0 21
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fix 3 all nve/spin lattice yes
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timestep 0.0001
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# compute and output options
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compute out_mag all spin
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compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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variable magx equal c_out_mag[1]
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variable magy equal c_out_mag[2]
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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variable tmag equal c_out_mag[6]
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thermo_style custom step time v_magx v_magy v_magz v_magnorm v_tmag v_emag pe etotal
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thermo 50
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
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run 2000
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# min_style spin
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# min_modify alpha_damp 1.0 discrete_factor 10
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# minimize 1.0e-16 1.0e-16 10000 10000
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@ -0,0 +1,60 @@
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# fcc nickel in a 3d periodic box
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clear
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units metal
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atom_style spin
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dimension 3
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boundary p p p
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# necessary for the serial algorithm (sametag)
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atom_modify map array
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lattice fcc 3.524
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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create_box 1 box
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create_atoms 1 box
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# setting mass, mag. moments, and interactions for cobalt
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mass 1 58.69
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set group all spin/random 31 0.63
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#set group all spin 0.63 0.0 0.0 1.0
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velocity all create 100 4928459 rot yes dist gaussian
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pair_style hybrid/overlay eam/alloy spin/exchange 4.0
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pair_coeff * * eam/alloy Ni99.eam.alloy Ni
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pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
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neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 &
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zeeman 0.0 0.0 0.0 1.0
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fix_modify 1 energy yes
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fix 2 all langevin/spin 0.0 0.0 21
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fix 3 all nve/spin lattice yes
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timestep 0.0001
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# compute and output options
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compute out_mag all spin
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compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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variable tmag equal c_out_mag[6]
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thermo_style custom step time v_magnorm v_emag temp v_tmag etotal
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thermo 50
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
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run 2000
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@ -156,6 +156,8 @@
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/fix_nve_spin.h
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/fix_precession_spin.cpp
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/fix_precession_spin.h
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/fix_setforce_spin.cpp
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/fix_setforce_spin.h
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/min_spin.cpp
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/min_spin.h
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/neb_spin.cpp
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@ -25,8 +25,8 @@
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#include <cstdio>
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#include <cstdlib>
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#include <cstring>
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#include "atom.h"
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#include "error.h"
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#include "domain.h"
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#include "error.h"
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#include "fix_precession_spin.h"
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@ -35,6 +35,7 @@
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#include "math_const.h"
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#include "memory.h"
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#include "modify.h"
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#include "neigh_list.h"
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#include "respa.h"
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#include "update.h"
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#include "variable.h"
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@ -71,8 +72,12 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm
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Ka = 0.0;
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nax = nay = naz = 0.0;
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Kax = Kay = Kaz = 0.0;
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k1c = k2c = 0.0;
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nc1x = nc1y = nc1z = 0.0;
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nc2x = nc2y = nc2z = 0.0;
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nc3x = nc3y = nc3z = 0.0;
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zeeman_flag = aniso_flag = 0;
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zeeman_flag = aniso_flag = cubic_flag = 0;
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int iarg = 3;
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while (iarg < narg) {
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@ -92,14 +97,61 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm
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nay = force->numeric(FLERR,arg[iarg+3]);
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naz = force->numeric(FLERR,arg[iarg+4]);
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iarg += 5;
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} else if (strcmp(arg[iarg],"cubic") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix precession/spin command");
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cubic_flag = 1;
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k1c = force->numeric(FLERR,arg[iarg+1]);
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k2c = force->numeric(FLERR,arg[iarg+2]);
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nc1x = force->numeric(FLERR,arg[iarg+3]);
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nc1y = force->numeric(FLERR,arg[iarg+4]);
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nc1z = force->numeric(FLERR,arg[iarg+5]);
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nc2x = force->numeric(FLERR,arg[iarg+6]);
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nc2y = force->numeric(FLERR,arg[iarg+7]);
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nc2z = force->numeric(FLERR,arg[iarg+8]);
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nc3x = force->numeric(FLERR,arg[iarg+9]);
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nc3y = force->numeric(FLERR,arg[iarg+10]);
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nc3z = force->numeric(FLERR,arg[iarg+11]);
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iarg += 12;
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} else error->all(FLERR,"Illegal precession/spin command");
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}
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// normalize vectors
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double inorm;
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if (zeeman_flag) {
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inorm = 1.0/sqrt(nhx*nhx + nhy*nhy + nhz*nhz);
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nhx *= inorm;
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nhy *= inorm;
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nhz *= inorm;
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}
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if (aniso_flag) {
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inorm = 1.0/sqrt(nax*nax + nay*nay + naz*naz);
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nax *= inorm;
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nay *= inorm;
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naz *= inorm;
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}
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if (cubic_flag) {
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inorm = 1.0/sqrt(nc1x*nc1x + nc1y*nc1y + nc1z*nc1z);
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nc1x *= inorm;
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nc1y *= inorm;
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nc1z *= inorm;
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inorm = 1.0/sqrt(nc2x*nc2x + nc2y*nc2y + nc2z*nc2z);
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nc2x *= inorm;
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nc2y *= inorm;
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nc2z *= inorm;
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inorm = 1.0/sqrt(nc3x*nc3x + nc3y*nc3y + nc3z*nc3z);
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nc3x *= inorm;
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nc3y *= inorm;
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nc3z *= inorm;
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}
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degree2rad = MY_PI/180.0;
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time_origin = update->ntimestep;
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eflag = 0;
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emag = 0.0;
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eprec = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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@ -130,8 +182,12 @@ void FixPrecessionSpin::init()
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const double mub = 5.78901e-5; // in eV/T
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const double gyro = mub/hbar; // in rad.THz/T
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H_field *= gyro; // in rad.THz
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Ka /= hbar; // in rad.THz
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// convert field quantities to rad.THz
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H_field *= gyro;
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Kah = Ka/hbar;
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k1ch = k1c/hbar;
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k2ch = k2c/hbar;
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if (strstr(update->integrate_style,"respa")) {
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ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
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@ -188,15 +244,17 @@ void FixPrecessionSpin::post_force(int /* vflag */)
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set_magneticprecession(); // update mag. field if time-dep.
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}
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double **sp = atom->sp;
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int *mask = atom->mask;
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double **fm = atom->fm;
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double spi[3], fmi[3];
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double **sp = atom->sp;
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const int nlocal = atom->nlocal;
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double spi[3], fmi[3], epreci;
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eflag = 0;
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emag = 0.0;
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eprec = 0.0;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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epreci = 0.0;
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spi[0] = sp[i][0];
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spi[1] = sp[i][1];
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spi[2] = sp[i][2];
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@ -204,34 +262,39 @@ void FixPrecessionSpin::post_force(int /* vflag */)
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if (zeeman_flag) { // compute Zeeman interaction
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compute_zeeman(i,fmi);
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emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
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epreci -= hbar*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
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}
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if (aniso_flag) { // compute magnetic anisotropy
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compute_anisotropy(spi,fmi);
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emag -= 0.5*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
|
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epreci -= compute_anisotropy_energy(spi);
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||||
}
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||||
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||||
if (cubic_flag) { // compute cubic anisotropy
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||||
compute_cubic(spi,fmi);
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||||
epreci -= compute_cubic_energy(spi);
|
||||
}
|
||||
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||||
eprec += epreci;
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fm[i][0] += fmi[0];
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||||
fm[i][1] += fmi[1];
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||||
fm[i][2] += fmi[2];
|
||||
}
|
||||
emag *= hbar;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double fmi[3])
|
||||
{
|
||||
if (zeeman_flag) {
|
||||
compute_zeeman(i,fmi);
|
||||
}
|
||||
if (aniso_flag) {
|
||||
compute_anisotropy(spi,fmi);
|
||||
int *mask = atom->mask;
|
||||
if (mask[i] & groupbit) {
|
||||
if (zeeman_flag) compute_zeeman(i,fmi);
|
||||
if (aniso_flag) compute_anisotropy(spi,fmi);
|
||||
if (cubic_flag) compute_cubic(spi,fmi);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPrecessionSpin::compute_zeeman(int i, double fmi[3])
|
||||
|
|
@ -254,6 +317,16 @@ void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3])
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixPrecessionSpin::compute_anisotropy_energy(double spi[3])
|
||||
{
|
||||
double energy = 0.0;
|
||||
double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2];
|
||||
energy = Ka*scalar*scalar;
|
||||
return energy;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
|
||||
{
|
||||
if (ilevel == ilevel_respa) post_force(vflag);
|
||||
|
|
@ -269,12 +342,70 @@ void FixPrecessionSpin::set_magneticprecession()
|
|||
hz = H_field*nhz;
|
||||
}
|
||||
if (aniso_flag) {
|
||||
Kax = 2.0*Ka*nax;
|
||||
Kay = 2.0*Ka*nay;
|
||||
Kaz = 2.0*Ka*naz;
|
||||
Kax = 2.0*Kah*nax;
|
||||
Kay = 2.0*Kah*nay;
|
||||
Kaz = 2.0*Kah*naz;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute cubic aniso energy of spin i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixPrecessionSpin::compute_cubic_energy(double spi[3])
|
||||
{
|
||||
double energy = 0.0;
|
||||
double skx,sky,skz;
|
||||
|
||||
skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z;
|
||||
sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z;
|
||||
skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z;
|
||||
|
||||
energy = k1c*(skx*skx*sky*sky + sky*sky*skz*skz + skx*skx*skz*skz);
|
||||
energy += k2c*skx*skx*sky*sky*skz*skz;
|
||||
|
||||
return energy;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute cubic anisotropy interaction for spin i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixPrecessionSpin::compute_cubic(double spi[3], double fmi[3])
|
||||
{
|
||||
double skx,sky,skz,skx2,sky2,skz2;
|
||||
double four1,four2,four3,fourx,foury,fourz;
|
||||
double six1,six2,six3,sixx,sixy,sixz;
|
||||
|
||||
skx = spi[0]*nc1x+spi[1]*nc1y+spi[2]*nc1z;
|
||||
sky = spi[0]*nc2x+spi[1]*nc2y+spi[2]*nc2z;
|
||||
skz = spi[0]*nc3x+spi[1]*nc3y+spi[2]*nc3z;
|
||||
|
||||
skx2 = skx*skx;
|
||||
sky2 = sky*sky;
|
||||
skz2 = skz*skz;
|
||||
|
||||
four1 = 2.0*skx*(sky2+skz2);
|
||||
four2 = 2.0*sky*(skx2+skz2);
|
||||
four3 = 2.0*skz*(skx2+sky2);
|
||||
|
||||
fourx = k1ch*(nc1x*four1 + nc2x*four2 + nc3x*four3);
|
||||
foury = k1ch*(nc1y*four1 + nc2y*four2 + nc3y*four3);
|
||||
fourz = k1ch*(nc1z*four1 + nc2z*four2 + nc3z*four3);
|
||||
|
||||
six1 = 2.0*skx*sky2*skz2;
|
||||
six2 = 2.0*sky*skx2*skz2;
|
||||
six3 = 2.0*skz*skx2*sky2;
|
||||
|
||||
sixx = k2ch*(nc1x*six1 + nc2x*six2 + nc3x*six3);
|
||||
sixy = k2ch*(nc1y*six1 + nc2y*six2 + nc3y*six3);
|
||||
sixz = k2ch*(nc1z*six1 + nc2z*six2 + nc3z*six3);
|
||||
|
||||
fmi[0] += fourx + sixx;
|
||||
fmi[1] += foury + sixy;
|
||||
fmi[2] += fourz + sixz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
potential energy in magnetic field
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
@ -284,10 +415,10 @@ double FixPrecessionSpin::compute_scalar()
|
|||
// only sum across procs one time
|
||||
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(&emag,&emag_all,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_Allreduce(&eprec,&eprec_all,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return emag_all;
|
||||
return eprec_all;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
|
|||
|
|
@ -39,10 +39,19 @@ class FixPrecessionSpin : public Fix {
|
|||
void min_post_force(int);
|
||||
double compute_scalar();
|
||||
|
||||
int zeeman_flag, aniso_flag;
|
||||
int zeeman_flag, aniso_flag, cubic_flag;
|
||||
void compute_single_precession(int, double *, double *);
|
||||
void compute_zeeman(int, double *);
|
||||
|
||||
// uniaxial aniso calculations
|
||||
|
||||
void compute_anisotropy(double *, double *);
|
||||
double compute_anisotropy_energy(double *);
|
||||
|
||||
// cubic aniso calculations
|
||||
|
||||
void compute_cubic(double *, double *);
|
||||
double compute_cubic_energy(double *);
|
||||
|
||||
protected:
|
||||
int style; // style of the magnetic precession
|
||||
|
|
@ -52,7 +61,7 @@ class FixPrecessionSpin : public Fix {
|
|||
int ilevel_respa;
|
||||
int time_origin;
|
||||
int eflag;
|
||||
double emag, emag_all;
|
||||
double eprec, eprec_all;
|
||||
|
||||
int varflag;
|
||||
int magfieldstyle;
|
||||
|
|
@ -67,10 +76,19 @@ class FixPrecessionSpin : public Fix {
|
|||
|
||||
// magnetic anisotropy intensity and direction
|
||||
|
||||
double Ka;
|
||||
double Ka; // aniso const. in eV
|
||||
double Kah; // aniso const. in rad.THz
|
||||
double nax, nay, naz;
|
||||
double Kax, Kay, Kaz; // temp. force variables
|
||||
|
||||
// cubic anisotropy intensity
|
||||
|
||||
double k1c,k2c; // cubic const. in eV
|
||||
double k1ch,k2ch; // cubic const. in rad.THz
|
||||
double nc1x,nc1y,nc1z;
|
||||
double nc2x,nc2y,nc2z;
|
||||
double nc3x,nc3y,nc3z;
|
||||
|
||||
void set_magneticprecession();
|
||||
|
||||
};
|
||||
|
|
|
|||
|
|
@ -39,6 +39,7 @@ pymol_asphere convert LAMMPS output of ellipsoids to PyMol format
|
|||
python Python scripts for post-processing LAMMPS output
|
||||
reax Tools for analyzing output of ReaxFF simulations
|
||||
smd convert Smooth Mach Dynamics triangles to VTK
|
||||
spin perform a cubic polynomial interpolation of a GNEB MEP
|
||||
vim add-ons to VIM editor for editing LAMMPS input scripts
|
||||
xmgrace a collection of scripts to generate xmgrace plots
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue