commit JT 020818
- adding files for doc and reorg.
This commit is contained in:
julient31
BIN
doc/src/Eqs/fix_integration_spin_stdecomposition.jpg
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doc/src/Eqs/fix_integration_spin_stdecomposition.jpg
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doc/src/Eqs/fix_integration_spin_stdecomposition.tex
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doc/src/Eqs/fix_integration_spin_stdecomposition.tex
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\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm,tikz}
|
||||
\usetikzlibrary{automata,arrows,shapes,snakes}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{tikzpicture}
|
||||
|
||||
%Global
|
||||
\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
|
||||
\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
|
||||
\node (r) at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ };
|
||||
\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
|
||||
\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
|
||||
|
||||
\draw[line width=2pt, ->] (v1) -- (s1);
|
||||
\draw[line width=2pt, ->] (s1) -- (r);
|
||||
\draw[line width=2pt, ->] (r) -- (s2);
|
||||
\draw[line width=2pt, ->] (s2) -- (v2);
|
||||
|
||||
%Spin
|
||||
\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
|
||||
\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
|
||||
\node (sN) at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ };
|
||||
\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
|
||||
\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
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||||
|
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\draw[line width=2pt,dashed, ->] (s01) -- (sN1);
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\draw[line width=2pt, ->] (sN1) -- (sN);
|
||||
\draw[line width=2pt, ->] (sN) -- (sN2);
|
||||
\draw[line width=2pt,dashed, ->] (sN2) -- (s02);
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||||
|
||||
%from Global to Spin
|
||||
\draw[line width=2pt, dashed, ->] (s1) -- (s01.west);
|
||||
\draw[line width=2pt, dashed, ->] (s1) -- (s02.west);
|
||||
|
||||
\end{tikzpicture}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
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doc/src/Eqs/fix_langevin_spin_sLLG.jpg
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doc/src/Eqs/fix_langevin_spin_sLLG.jpg
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doc/src/Eqs/fix_langevin_spin_sLLG.tex
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doc/src/Eqs/fix_langevin_spin_sLLG.tex
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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, graphics, setspace}
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|
||||
\begin{document}
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||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left(
|
||||
\vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i}
|
||||
\times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
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doc/src/Eqs/force_spin_aniso.jpg
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doc/src/Eqs/force_spin_aniso.jpg
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doc/src/Eqs/force_spin_zeeman.jpg
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doc/src/Eqs/force_spin_zeeman.jpg
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doc/src/Eqs/pair_spin_exchange_forces.jpg
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doc/src/Eqs/pair_spin_exchange_forces.jpg
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doc/src/Eqs/pair_spin_exchange_forces.tex
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doc/src/Eqs/pair_spin_exchange_forces.tex
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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}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\vec{F}^{i} = \sum_{j}^{Neighbor} \frac{\partial {J} \left(r_{ij} \right)}{
|
||||
\partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{r}_{ij}
|
||||
~~{\rm and}~~ \vec{\omega}^{i} = \frac{1}{\hbar} \sum_{j}^{Neighbor} {J}
|
||||
\left(r_{ij} \right)\,\vec{s}_{j} \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
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doc/src/Eqs/pair_spin_exchange_function.jpg
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doc/src/Eqs/pair_spin_exchange_function.jpg
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doc/src/Eqs/pair_spin_exchange_interaction.jpg
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doc/src/Eqs/pair_spin_exchange_interaction.jpg
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doc/src/Eqs/pair_spin_me_forces.jpg
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doc/src/Eqs/pair_spin_me_forces.jpg
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doc/src/Eqs/pair_spin_me_forces.tex
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doc/src/Eqs/pair_spin_me_forces.tex
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\documentclass[preview]{standalone}
|
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\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\vec{F}^{i} = -\sum_{j}^{Neighbor} \left( \vec{s}_{i}\times \vec{s}_{j} \right)
|
||||
\times \vec{E} ~~{\rm and}~~ \vec{\omega}^{i} = -\frac{1}{\hbar}
|
||||
\sum_{j}^{Neighbor} \vec{s}_j \times \left(\vec{E}\times r_{ij} \right),\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_spin_me_interaction.jpg
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doc/src/Eqs/pair_spin_me_interaction.jpg
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doc/src/Eqs/pair_spin_me_interaction.tex
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doc/src/Eqs/pair_spin_me_interaction.tex
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\documentclass[preview]{standalone}
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||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times\vec{D}(r_{ij}) ~~{\rm and}~~
|
||||
\vec{F}_i = -\sum_{j}^{Neighb} \frac{\partial D(r_{ij})}{\partial r_{ij}} \left(\vec{s}_{i}\times \vec{s}_{j} \right) \cdot \vec{r}_{ij}, \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_spin_soc_dmi_interaction.jpg
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doc/src/Eqs/pair_spin_soc_dmi_interaction.jpg
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doc/src/Eqs/pair_spin_soc_dmi_interaction.tex
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doc/src/Eqs/pair_spin_soc_dmi_interaction.tex
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|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} \vec{D}\left(r_{ij}\right) \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
73
doc/src/pair_spin_me.txt
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73
doc/src/pair_spin_me.txt
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|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style pair/spin/me command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style pair/spin/me cutoff :pre
|
||||
|
||||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style pair/spin/me 4.5
|
||||
pair_coeff * * pair/spin/me me 4.5 0.00109 1.0 1.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {pair/spin/me} computes a magneto-electric interaction between
|
||||
pairs of magnetic spins. According to the derivation reported in
|
||||
"(Katsura)"_#Katsura1, this interaction is defined as:
|
||||
|
||||
:c,image(Eqs/pair_spin_me_interaction.jpg)
|
||||
|
||||
where si and sj are neighboring magnetic spins of two particles,
|
||||
rij = ri - rj is the normalized separation vector between the
|
||||
two particles, and E is an electric polarization vector.
|
||||
The norm and direction of E are giving the intensity and the
|
||||
direction of a screened dielectric atomic polarization (in eV).
|
||||
|
||||
From this magneto-electric interaction, each spin i will be submitted
|
||||
to a magnetic torque omega, and its associated atom can be submitted to a
|
||||
force F for spin-lattice calculations (see
|
||||
"fix_integration_spin"_fix_integration_spin.html), such as:
|
||||
|
||||
:c,image(Eqs/pair_spin_me_forces.jpg)
|
||||
|
||||
with h the Planck constant (in metal units).
|
||||
|
||||
More details about the derivation of these torques/forces are reported in
|
||||
"(Tranchida)"_#Tranchida1.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
All the {pair/spin} styles are part of the SPIN package.
|
||||
These styles are only enabled if LAMMPS was built with this package, and
|
||||
if the atom_style "spin" was declared.
|
||||
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
|
||||
"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html,
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Katsura1)
|
||||
[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)
|
||||
|
||||
:link(Tranchida1)
|
||||
[(Tranchida)] J. Tranchida, S.J. Plimpton, P. Thibaudeau, A.P. Thompson.
|
||||
arXiv preprint arXiv:1801.10233. (2018)
|
||||
82
doc/src/pair_spin_soc_dmi.txt
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82
doc/src/pair_spin_soc_dmi.txt
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@ -0,0 +1,82 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style pair/spin/soc/dmi command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style pair/spin/soc/dmi cutoff :pre
|
||||
|
||||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style pair/spin/soc/dmi 4.0
|
||||
pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0
|
||||
pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {pair/spin/soc/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction
|
||||
between pairs of magnetic spins:
|
||||
|
||||
:c,image(Eqs/pair_spin_soc_dmi_interaction.jpg)
|
||||
|
||||
where si and sj are two neighboring magnetic spins of two particles,
|
||||
rij = ri - rj is the inter-atomic distance between the two particles,
|
||||
and D(rij) is the DM vector defining the intensity and the
|
||||
sign of the exchange interaction.
|
||||
|
||||
This function is defined as:
|
||||
|
||||
:c,image(Eqs/pair_spin_exchange_function.jpg)
|
||||
|
||||
where a, b and d are the three constant coefficients defined in the associated
|
||||
"pair_coeff" command.
|
||||
|
||||
The coefficients a, b, and c need to be fitted so that the function above matches with
|
||||
the value of the DM interaction for the N neighbor shells taken
|
||||
into account.
|
||||
|
||||
Examples and more explanations about this function and its parametrization are reported
|
||||
in "(Tranchida)"_#Tranchida1.
|
||||
|
||||
From this DM interaction, each spin i will be submitted to a magnetic torque
|
||||
omega and its associated atom to a force F (for spin-lattice calculations only),
|
||||
such as:
|
||||
|
||||
:c,image(Eqs/pair_spin_soc_dmi_forces.jpg)
|
||||
|
||||
with h the Planck constant (in metal units).
|
||||
|
||||
More details about the derivation of these torques/forces are reported in
|
||||
"(Tranchida)"_#Tranchida1.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
All the {pair/spin} styles are part of the SPIN package.
|
||||
These styles are only enabled if LAMMPS was built with this package, and
|
||||
if the atom_style "spin" was declared.
|
||||
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
|
||||
"pair_eam"_pair_eam.html,
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Tranchida1)
|
||||
[(Tranchida)]https://arxiv.org/abs/1801.10233
|
||||
|
||||
55
examples/SPIN/bfo/in.spin.bfo
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55
examples/SPIN/bfo/in.spin.bfo
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@ -0,0 +1,55 @@
|
||||
# sc iron atoms in bismuth oxide
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice sc 3.96
|
||||
region box block 0.0 34.0 0.0 34.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for bfo
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
set group all spin/random 11 2.50
|
||||
|
||||
pair_style hybrid/overlay pair/spin/exchange 6.0 pair/spin/me 4.5
|
||||
pair_coeff * * pair/spin/exchange exchange 6.0 -0.01575 0.0 1.965
|
||||
pair_coeff * * pair/spin/me me 4.5 0.000109 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all force/spin anisotropy 0.0000035 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
|
||||
fix 3 all integration/spin lattice no
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 10
|
||||
|
||||
#dump 1 all custom 100 dump_spin_BFO.lammpstrj type x y z spx spy spz
|
||||
|
||||
run 10000
|
||||
|
||||
6006
examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy
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6006
examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy
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File diff suppressed because it is too large
Load Diff
59
examples/SPIN/cobalt/in.spin.cobalt
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59
examples/SPIN/cobalt/in.spin.cobalt
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@ -0,0 +1,59 @@
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
|
||||
fix 3 all integration/spin lattice yes
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 10
|
||||
|
||||
#dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
|
||||
|
||||
run 1000
|
||||
|
||||
6006
examples/SPIN/curie_temperature/Co_PurjaPun_2012.eam.alloy
Normal file
6006
examples/SPIN/curie_temperature/Co_PurjaPun_2012.eam.alloy
Normal file
File diff suppressed because it is too large
Load Diff
95
examples/SPIN/curie_temperature/compliance.py
Executable file
95
examples/SPIN/curie_temperature/compliance.py
Executable file
@ -0,0 +1,95 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# This file reads in the file log.lammps generated by the script ELASTIC/in.elastic
|
||||
# It prints out the 6x6 tensor of elastic constants Cij
|
||||
# followed by the 6x6 tensor of compliance constants Sij
|
||||
# It uses the same conventions as described in:
|
||||
# Sprik, Impey and Klein PRB (1984).
|
||||
# The units of Cij are whatever was used in log.lammps (usually GPa)
|
||||
# The units of Sij are the inverse of that (usually 1/GPa)
|
||||
|
||||
from numpy import zeros
|
||||
from numpy.linalg import inv
|
||||
|
||||
# define logfile layout
|
||||
|
||||
nvals = 21
|
||||
valpos = 4
|
||||
valstr = '\nElastic Constant C'
|
||||
|
||||
# define order of Cij in logfile
|
||||
|
||||
cindices = [0]*nvals
|
||||
cindices[0] = (0,0)
|
||||
cindices[1] = (1,1)
|
||||
cindices[2] = (2,2)
|
||||
cindices[3] = (0,1)
|
||||
cindices[4] = (0,2)
|
||||
cindices[5] = (1,2)
|
||||
cindices[6] = (3,3)
|
||||
cindices[7] = (4,4)
|
||||
cindices[8] = (5,5)
|
||||
cindices[9] = (0,3)
|
||||
cindices[10] = (0,4)
|
||||
cindices[11] = (0,5)
|
||||
cindices[12] = (1,3)
|
||||
cindices[13] = (1,4)
|
||||
cindices[14] = (1,5)
|
||||
cindices[15] = (2,3)
|
||||
cindices[16] = (2,4)
|
||||
cindices[17] = (2,5)
|
||||
cindices[18] = (3,4)
|
||||
cindices[19] = (3,5)
|
||||
cindices[20] = (4,5)
|
||||
|
||||
# open logfile
|
||||
|
||||
logfile = open("log.lammps",'r')
|
||||
|
||||
txt = logfile.read()
|
||||
|
||||
# search for 21 elastic constants
|
||||
|
||||
c = zeros((6,6))
|
||||
s2 = 0
|
||||
|
||||
for ival in range(nvals):
|
||||
s1 = txt.find(valstr,s2)
|
||||
if (s1 == -1):
|
||||
print "Failed to find elastic constants in log file"
|
||||
exit(1)
|
||||
s1 += 1
|
||||
s2 = txt.find("\n",s1)
|
||||
line = txt[s1:s2]
|
||||
# print line
|
||||
words = line.split()
|
||||
(i1,i2) = cindices[ival]
|
||||
c[i1,i2] = float(words[valpos])
|
||||
c[i2,i1] = c[i1,i2]
|
||||
|
||||
print "C tensor [GPa]"
|
||||
for i in range(6):
|
||||
for j in range(6):
|
||||
print "%10.8g " % c[i][j],
|
||||
print
|
||||
|
||||
# apply factor of 2 to columns of off-diagonal elements
|
||||
|
||||
for i in range(6):
|
||||
for j in range(3,6):
|
||||
c[i][j] *= 2.0
|
||||
|
||||
s = inv(c)
|
||||
|
||||
# apply factor of 1/2 to columns of off-diagonal elements
|
||||
|
||||
for i in range(6):
|
||||
for j in range(3,6):
|
||||
s[i][j] *= 0.5
|
||||
|
||||
print "S tensor [1/GPa]"
|
||||
for i in range(6):
|
||||
for j in range(6):
|
||||
print "%10.8g " % s[i][j],
|
||||
print
|
||||
|
||||
142
examples/SPIN/curie_temperature/displace.mod
Normal file
142
examples/SPIN/curie_temperature/displace.mod
Normal file
@ -0,0 +1,142 @@
|
||||
# NOTE: This script should not need to be
|
||||
# modified. See in.elastic for more info.
|
||||
#
|
||||
# Find which reference length to use
|
||||
|
||||
if "${dir} == 1" then &
|
||||
"variable len0 equal ${lx0}"
|
||||
if "${dir} == 2" then &
|
||||
"variable len0 equal ${ly0}"
|
||||
if "${dir} == 3" then &
|
||||
"variable len0 equal ${lz0}"
|
||||
if "${dir} == 4" then &
|
||||
"variable len0 equal ${lz0}"
|
||||
if "${dir} == 5" then &
|
||||
"variable len0 equal ${lz0}"
|
||||
if "${dir} == 6" then &
|
||||
"variable len0 equal ${ly0}"
|
||||
|
||||
# Reset box and simulation parameters
|
||||
|
||||
clear
|
||||
box tilt large
|
||||
read_restart restart.equil
|
||||
include potential.mod
|
||||
|
||||
# Negative deformation
|
||||
|
||||
variable delta equal -${up}*${len0}
|
||||
variable deltaxy equal -${up}*xy
|
||||
variable deltaxz equal -${up}*xz
|
||||
variable deltayz equal -${up}*yz
|
||||
if "${dir} == 1" then &
|
||||
"change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
|
||||
if "${dir} == 2" then &
|
||||
"change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
|
||||
if "${dir} == 3" then &
|
||||
"change_box all z delta 0 ${delta} remap units box"
|
||||
if "${dir} == 4" then &
|
||||
"change_box all yz delta ${delta} remap units box"
|
||||
if "${dir} == 5" then &
|
||||
"change_box all xz delta ${delta} remap units box"
|
||||
if "${dir} == 6" then &
|
||||
"change_box all xy delta ${delta} remap units box"
|
||||
|
||||
# Relax atoms positions
|
||||
|
||||
minimize ${etol} ${ftol} ${maxiter} ${maxeval}
|
||||
|
||||
# Obtain new stress tensor
|
||||
|
||||
variable tmp equal pxx
|
||||
variable pxx1 equal ${tmp}
|
||||
variable tmp equal pyy
|
||||
variable pyy1 equal ${tmp}
|
||||
variable tmp equal pzz
|
||||
variable pzz1 equal ${tmp}
|
||||
variable tmp equal pxy
|
||||
variable pxy1 equal ${tmp}
|
||||
variable tmp equal pxz
|
||||
variable pxz1 equal ${tmp}
|
||||
variable tmp equal pyz
|
||||
variable pyz1 equal ${tmp}
|
||||
|
||||
# Compute elastic constant from pressure tensor
|
||||
|
||||
variable C1neg equal ${d1}
|
||||
variable C2neg equal ${d2}
|
||||
variable C3neg equal ${d3}
|
||||
variable C4neg equal ${d4}
|
||||
variable C5neg equal ${d5}
|
||||
variable C6neg equal ${d6}
|
||||
|
||||
# Reset box and simulation parameters
|
||||
|
||||
clear
|
||||
box tilt large
|
||||
read_restart restart.equil
|
||||
include potential.mod
|
||||
|
||||
# Positive deformation
|
||||
|
||||
variable delta equal ${up}*${len0}
|
||||
variable deltaxy equal ${up}*xy
|
||||
variable deltaxz equal ${up}*xz
|
||||
variable deltayz equal ${up}*yz
|
||||
if "${dir} == 1" then &
|
||||
"change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
|
||||
if "${dir} == 2" then &
|
||||
"change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
|
||||
if "${dir} == 3" then &
|
||||
"change_box all z delta 0 ${delta} remap units box"
|
||||
if "${dir} == 4" then &
|
||||
"change_box all yz delta ${delta} remap units box"
|
||||
if "${dir} == 5" then &
|
||||
"change_box all xz delta ${delta} remap units box"
|
||||
if "${dir} == 6" then &
|
||||
"change_box all xy delta ${delta} remap units box"
|
||||
|
||||
# Relax atoms positions
|
||||
|
||||
minimize ${etol} ${ftol} ${maxiter} ${maxeval}
|
||||
|
||||
# Obtain new stress tensor
|
||||
|
||||
variable tmp equal pe
|
||||
variable e1 equal ${tmp}
|
||||
variable tmp equal press
|
||||
variable p1 equal ${tmp}
|
||||
variable tmp equal pxx
|
||||
variable pxx1 equal ${tmp}
|
||||
variable tmp equal pyy
|
||||
variable pyy1 equal ${tmp}
|
||||
variable tmp equal pzz
|
||||
variable pzz1 equal ${tmp}
|
||||
variable tmp equal pxy
|
||||
variable pxy1 equal ${tmp}
|
||||
variable tmp equal pxz
|
||||
variable pxz1 equal ${tmp}
|
||||
variable tmp equal pyz
|
||||
variable pyz1 equal ${tmp}
|
||||
|
||||
# Compute elastic constant from pressure tensor
|
||||
|
||||
variable C1pos equal ${d1}
|
||||
variable C2pos equal ${d2}
|
||||
variable C3pos equal ${d3}
|
||||
variable C4pos equal ${d4}
|
||||
variable C5pos equal ${d5}
|
||||
variable C6pos equal ${d6}
|
||||
|
||||
# Combine positive and negative
|
||||
|
||||
variable C1${dir} equal 0.5*(${C1neg}+${C1pos})
|
||||
variable C2${dir} equal 0.5*(${C2neg}+${C2pos})
|
||||
variable C3${dir} equal 0.5*(${C3neg}+${C3pos})
|
||||
variable C4${dir} equal 0.5*(${C4neg}+${C4pos})
|
||||
variable C5${dir} equal 0.5*(${C5neg}+${C5pos})
|
||||
variable C6${dir} equal 0.5*(${C6neg}+${C6pos})
|
||||
|
||||
# Delete dir to make sure it is not reused
|
||||
|
||||
variable dir delete
|
||||
59
examples/SPIN/curie_temperature/in.spin.cobalt
Normal file
59
examples/SPIN/curie_temperature/in.spin.cobalt
Normal file
@ -0,0 +1,59 @@
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
|
||||
fix 3 all integration/spin lattice yes
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 10
|
||||
|
||||
#dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
|
||||
|
||||
run 1000
|
||||
|
||||
204
examples/SPIN/curie_temperature/in.spin.curie_temperature
Normal file
204
examples/SPIN/curie_temperature/in.spin.curie_temperature
Normal file
@ -0,0 +1,204 @@
|
||||
# Compute elastic constant tensor for a crystal
|
||||
#
|
||||
# Written by Aidan Thompson (Sandia, athomps@sandia.gov)
|
||||
#
|
||||
# This script uses the following three include files.
|
||||
#
|
||||
# init.mod (must be modified for different crystal structures)
|
||||
# Define units, deformation parameters and initial
|
||||
# configuration of the atoms and simulation cell.
|
||||
#
|
||||
#
|
||||
# potential.mod (must be modified for different pair styles)
|
||||
# Define pair style and other attributes
|
||||
# not stored in restart file
|
||||
#
|
||||
#
|
||||
# displace.mod (displace.mod should not need to be modified)
|
||||
# Perform positive and negative box displacements
|
||||
# in direction ${dir} and size ${up}.
|
||||
# It uses the resultant changes
|
||||
# in stress to compute one
|
||||
# row of the elastic stiffness tensor
|
||||
#
|
||||
# Inputs variables:
|
||||
# dir = the Voigt deformation component
|
||||
# (1,2,3,4,5,6)
|
||||
# Global constants:
|
||||
# up = the deformation magnitude (strain units)
|
||||
# cfac = conversion from LAMMPS pressure units to
|
||||
# output units for elastic constants
|
||||
#
|
||||
#
|
||||
# To run this on a different system, it should only be necessary to
|
||||
# modify the files init.mod and potential.mod. In order to calculate
|
||||
# the elastic constants correctly, care must be taken to specify
|
||||
# the correct units in init.mod (units, cfac and cunits). It is also
|
||||
# important to verify that the minimization of energy w.r.t atom
|
||||
# positions in the deformed cell is fully converged.
|
||||
# One indication of this is that the elastic constants are insensitive
|
||||
# to the choice of the variable ${up} in init.mod. Another is to check
|
||||
# the final max and two-norm forces reported in the log file. If you know
|
||||
# that minimization is not required, you can set maxiter = 0.0 in
|
||||
# init.mod.
|
||||
#
|
||||
|
||||
include init.mod
|
||||
include potential.mod
|
||||
|
||||
# Compute initial state
|
||||
fix 3 all box/relax aniso 0.0
|
||||
minimize ${etol} ${ftol} ${maxiter} ${maxeval}
|
||||
|
||||
variable tmp equal pxx
|
||||
variable pxx0 equal ${tmp}
|
||||
variable tmp equal pyy
|
||||
variable pyy0 equal ${tmp}
|
||||
variable tmp equal pzz
|
||||
variable pzz0 equal ${tmp}
|
||||
variable tmp equal pyz
|
||||
variable pyz0 equal ${tmp}
|
||||
variable tmp equal pxz
|
||||
variable pxz0 equal ${tmp}
|
||||
variable tmp equal pxy
|
||||
variable pxy0 equal ${tmp}
|
||||
|
||||
variable tmp equal lx
|
||||
variable lx0 equal ${tmp}
|
||||
variable tmp equal ly
|
||||
variable ly0 equal ${tmp}
|
||||
variable tmp equal lz
|
||||
variable lz0 equal ${tmp}
|
||||
|
||||
# These formulas define the derivatives w.r.t. strain components
|
||||
# Constants uses $, variables use v_
|
||||
variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
|
||||
variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
|
||||
variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
|
||||
variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
|
||||
variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
|
||||
variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
|
||||
|
||||
displace_atoms all random ${atomjiggle} ${atomjiggle} ${atomjiggle} 87287 units box
|
||||
|
||||
# Write restart
|
||||
unfix 3
|
||||
write_restart restart.equil
|
||||
|
||||
# uxx Perturbation
|
||||
|
||||
variable dir equal 1
|
||||
include displace.mod
|
||||
|
||||
# uyy Perturbation
|
||||
|
||||
variable dir equal 2
|
||||
include displace.mod
|
||||
|
||||
# uzz Perturbation
|
||||
|
||||
variable dir equal 3
|
||||
include displace.mod
|
||||
|
||||
# uyz Perturbation
|
||||
|
||||
variable dir equal 4
|
||||
include displace.mod
|
||||
|
||||
# uxz Perturbation
|
||||
|
||||
variable dir equal 5
|
||||
include displace.mod
|
||||
|
||||
# uxy Perturbation
|
||||
|
||||
variable dir equal 6
|
||||
include displace.mod
|
||||
|
||||
# Output final values
|
||||
|
||||
variable C11all equal ${C11}
|
||||
variable C22all equal ${C22}
|
||||
variable C33all equal ${C33}
|
||||
|
||||
variable C12all equal 0.5*(${C12}+${C21})
|
||||
variable C13all equal 0.5*(${C13}+${C31})
|
||||
variable C23all equal 0.5*(${C23}+${C32})
|
||||
|
||||
variable C44all equal ${C44}
|
||||
variable C55all equal ${C55}
|
||||
variable C66all equal ${C66}
|
||||
|
||||
variable C14all equal 0.5*(${C14}+${C41})
|
||||
variable C15all equal 0.5*(${C15}+${C51})
|
||||
variable C16all equal 0.5*(${C16}+${C61})
|
||||
|
||||
variable C24all equal 0.5*(${C24}+${C42})
|
||||
variable C25all equal 0.5*(${C25}+${C52})
|
||||
variable C26all equal 0.5*(${C26}+${C62})
|
||||
|
||||
variable C34all equal 0.5*(${C34}+${C43})
|
||||
variable C35all equal 0.5*(${C35}+${C53})
|
||||
variable C36all equal 0.5*(${C36}+${C63})
|
||||
|
||||
variable C45all equal 0.5*(${C45}+${C54})
|
||||
variable C46all equal 0.5*(${C46}+${C64})
|
||||
variable C56all equal 0.5*(${C56}+${C65})
|
||||
|
||||
# Average moduli for cubic crystals
|
||||
|
||||
variable C11cubic equal (${C11all}+${C22all}+${C33all})/3.0
|
||||
variable C12cubic equal (${C12all}+${C13all}+${C23all})/3.0
|
||||
variable C44cubic equal (${C44all}+${C55all}+${C66all})/3.0
|
||||
|
||||
variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
|
||||
variable shearmodulus1 equal ${C44cubic}
|
||||
variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
|
||||
variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
|
||||
|
||||
# For Stillinger-Weber silicon, the analytical results
|
||||
# are known to be (E. R. Cowley, 1988):
|
||||
# C11 = 151.4 GPa
|
||||
# C12 = 76.4 GPa
|
||||
# C44 = 56.4 GPa
|
||||
|
||||
print "========================================="
|
||||
print "Components of the Elastic Constant Tensor"
|
||||
print "========================================="
|
||||
|
||||
print "Elastic Constant C11all = ${C11all} ${cunits}"
|
||||
print "Elastic Constant C22all = ${C22all} ${cunits}"
|
||||
print "Elastic Constant C33all = ${C33all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C12all = ${C12all} ${cunits}"
|
||||
print "Elastic Constant C13all = ${C13all} ${cunits}"
|
||||
print "Elastic Constant C23all = ${C23all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C44all = ${C44all} ${cunits}"
|
||||
print "Elastic Constant C55all = ${C55all} ${cunits}"
|
||||
print "Elastic Constant C66all = ${C66all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C14all = ${C14all} ${cunits}"
|
||||
print "Elastic Constant C15all = ${C15all} ${cunits}"
|
||||
print "Elastic Constant C16all = ${C16all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C24all = ${C24all} ${cunits}"
|
||||
print "Elastic Constant C25all = ${C25all} ${cunits}"
|
||||
print "Elastic Constant C26all = ${C26all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C34all = ${C34all} ${cunits}"
|
||||
print "Elastic Constant C35all = ${C35all} ${cunits}"
|
||||
print "Elastic Constant C36all = ${C36all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C45all = ${C45all} ${cunits}"
|
||||
print "Elastic Constant C46all = ${C46all} ${cunits}"
|
||||
print "Elastic Constant C56all = ${C56all} ${cunits}"
|
||||
|
||||
print "========================================="
|
||||
print "Average properties for a cubic crystal"
|
||||
print "========================================="
|
||||
|
||||
print "Bulk Modulus = ${bulkmodulus} ${cunits}"
|
||||
print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
|
||||
print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
|
||||
print "Poisson Ratio = ${poissonratio}"
|
||||
55
examples/SPIN/curie_temperature/init.mod
Normal file
55
examples/SPIN/curie_temperature/init.mod
Normal file
@ -0,0 +1,55 @@
|
||||
# NOTE: This script can be modified for different atomic structures,
|
||||
# units, etc. See in.spin.curie_temperature for more info.
|
||||
#
|
||||
|
||||
# Define the finite deformation size. Try several values of this
|
||||
# variable to verify that results do not depend on it.
|
||||
variable up equal 1.0e-6
|
||||
|
||||
# Define the amount of random jiggle for atoms
|
||||
# This prevents atoms from staying on saddle points
|
||||
variable atomjiggle equal 1.0e-5
|
||||
|
||||
# Uncomment one of these blocks, depending on what units
|
||||
# you are using in LAMMPS and for output
|
||||
|
||||
# metal units, elastic constants in eV/A^3
|
||||
#units metal
|
||||
#variable cfac equal 6.2414e-7
|
||||
#variable cunits string eV/A^3
|
||||
|
||||
# metal units, elastic constants in GPa
|
||||
units metal
|
||||
variable cfac equal 1.0e-4
|
||||
variable cunits string GPa
|
||||
|
||||
# real units, elastic constants in GPa
|
||||
#units real
|
||||
#variable cfac equal 1.01325e-4
|
||||
#variable cunits string GPa
|
||||
|
||||
# Define minimization parameters
|
||||
variable etol equal 0.0
|
||||
variable ftol equal 1.0e-10
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 1000
|
||||
variable dmax equal 1.0e-2
|
||||
|
||||
# generate the box and atom positions using a diamond lattice
|
||||
variable a equal 5.43
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#lattice diamond $a
|
||||
#region box prism 0 2.0 0 3.0 0 4.0 0.0 0.0 0.0
|
||||
#create_box 1 box
|
||||
#create_atoms 1 box
|
||||
|
||||
# Need to set mass (even for fixed lattice calculation, just to satisfy LAMMPS)
|
||||
mass 1 58.93
|
||||
|
||||
30
examples/SPIN/curie_temperature/potential.mod
Normal file
30
examples/SPIN/curie_temperature/potential.mod
Normal file
@ -0,0 +1,30 @@
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
# Choose potentials (spin or spin-lattice)
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
|
||||
air_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
# Setup minimization style
|
||||
min_style cg
|
||||
min_modify dmax ${dmax} line quadratic
|
||||
|
||||
# Setup output
|
||||
compute out_mag all compute/spin
|
||||
compute out_temp all temp
|
||||
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[7]
|
||||
|
||||
thermo_style custom step time v_magnorm v_tmag temp
|
||||
thermo 1
|
||||
|
||||
|
||||
#thermo 1
|
||||
#thermo_style custom step temp pe press pxx pyy pzz pxy pxz pyz lx ly lz vol
|
||||
#thermo_modify norm no
|
||||
6006
examples/SPIN/dev/Co_PurjaPun_2012.eam.alloy
Normal file
6006
examples/SPIN/dev/Co_PurjaPun_2012.eam.alloy
Normal file
File diff suppressed because it is too large
Load Diff
125
examples/SPIN/dev/in.spin.cobalt
Normal file
125
examples/SPIN/dev/in.spin.cobalt
Normal file
@ -0,0 +1,125 @@
|
||||
###################
|
||||
#######Init########
|
||||
###################
|
||||
|
||||
clear
|
||||
units metal
|
||||
dimension 3
|
||||
#boundary p p p
|
||||
boundary p p p
|
||||
|
||||
#newton off
|
||||
|
||||
#setting atom_style to spin:
|
||||
atom_style spin
|
||||
|
||||
#Define sort for paramagnetic simulations (if no pair interaction)
|
||||
#atom_modify sort 1000 4.0
|
||||
|
||||
atom_modify map array
|
||||
|
||||
###########################
|
||||
#######Create atoms########
|
||||
###########################
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#######################
|
||||
#######Settings########
|
||||
#######################
|
||||
|
||||
#isolating 1 atom into a group
|
||||
group single_spin id 10
|
||||
|
||||
#Setting one or more properties of one or more atoms.
|
||||
mass 1 58.93
|
||||
|
||||
#Setting spins orientation and moment
|
||||
set group all spin/random 31 1.72
|
||||
#set group all spin 1.72 0.0 0.0 1.0
|
||||
#set group single_spin spin/random 11 1.72
|
||||
|
||||
#velocity all create 200 4928459 rot yes dist gaussian
|
||||
velocity all create 200 4928459 rot yes dist gaussian
|
||||
|
||||
#Magneto-mechanic interactions for bulk fcc Cobalt
|
||||
#pair_style pair/spin/exchange 4.0
|
||||
#pair_style eam/alloy
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
|
||||
#pair_coeff * * ../Co_PurjaPun_2012.eam.alloy Co
|
||||
|
||||
#pair_style pair/spin/exchange 4.0
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
#pair_coeff * * exchange 4.0 -0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * exchange 4.0 0.0 0.003496 1.4885
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/exchange exchange 2.5 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/exchange exchange 4.0 0.0 0.003496 1.4885
|
||||
|
||||
#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
|
||||
#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
|
||||
#pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
|
||||
|
||||
#type i and j | interaction type | cutoff | K1 (eV) | K2 (adim) | K3 (Ang) (for SOC)
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.0 0.864159 2.13731
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
#fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.01 0.0 0.0 1.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
#fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
#fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all integration/spin lattice yes
|
||||
#fix 3 all integration/spin lattice no
|
||||
|
||||
#compute real time, total magnetization, magnetic energy, and spin temperature
|
||||
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
#variable test equal etotal-0.5*c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 10
|
||||
#run 1000
|
||||
|
||||
126
examples/SPIN/dev/in.spin.kagome
Normal file
126
examples/SPIN/dev/in.spin.kagome
Normal file
@ -0,0 +1,126 @@
|
||||
###################
|
||||
#######Init########
|
||||
###################
|
||||
|
||||
clear
|
||||
#setting units to metal (Ang, picosecs, eV, ...):
|
||||
units metal
|
||||
|
||||
#setting dimension of the system (N=2 or 3):
|
||||
dimension 3
|
||||
|
||||
#setting boundary conditions. (p for periodic, f for fixed, ...)
|
||||
boundary p p p
|
||||
#boundary f f f
|
||||
|
||||
#setting atom_style to spin:
|
||||
atom_style spin
|
||||
|
||||
#Define sort for paramagnetic simulations (if no pair interaction)
|
||||
#atom_modify sort 1000 4.0
|
||||
|
||||
#why?
|
||||
atom_modify map array
|
||||
|
||||
#newton off for pair spin in SEQNEI
|
||||
#newton off off
|
||||
|
||||
###########################
|
||||
#######Create atoms########
|
||||
###########################
|
||||
|
||||
#Lattice constant of fcc Cobalt
|
||||
lattice fcc 3.54
|
||||
#lattice sc 2.50
|
||||
|
||||
#Test Kagome
|
||||
#variable a equal sqrt(3.0)/8.0
|
||||
#variable b equal 3.0*sqrt(3.0)/8.0
|
||||
#variable c equal sqrt(3.0)/4.0
|
||||
|
||||
#lattice custom 2.5 a1 1.0 0.0 0.0 &
|
||||
# a2 0.0 1.0 0.0 &
|
||||
# a3 0.0 0.0 1.0 &
|
||||
# basis 0.0 $a 0.0 &
|
||||
# basis 0.25 $a 0.0 &
|
||||
# basis 0.375 0.0 0.0 &
|
||||
# basis 0.25 $b 0.0 &
|
||||
# basis 0.5 $b 0.0 &
|
||||
# basis 0.625 $c 0.0
|
||||
|
||||
#Defining a geometric region of space. Sets ID(user's choice), style(block, sphere, ...), then, args depends on the style chosen
|
||||
#(for block, one has x0, xf, y0, yf, z0, zf, in distance units)
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
|
||||
#Creating a simulation box based on the specified region. Entries: number of atom types and box ref.
|
||||
create_box 1 box
|
||||
|
||||
#Creating atoms (or molecules) on a lattice, or a single atom (or molecule), ...
|
||||
#Entries: atom type,
|
||||
create_atoms 1 box
|
||||
|
||||
#Replicating NxNxN the entire set of atoms
|
||||
#replicate 1 1 1
|
||||
|
||||
|
||||
#######################
|
||||
#######Settings########
|
||||
#######################
|
||||
|
||||
#Setting one or more properties of one or more atoms.
|
||||
#Setting mass
|
||||
mass 1 1.0
|
||||
#set group all mass 1.0
|
||||
#Setting spins orientation and moment
|
||||
#set group all spin/random 11 1.72
|
||||
set group all spin 1.72 1.0 0.0 0.0
|
||||
|
||||
#Magnetic exchange interaction coefficient for bulk fcc Cobalt
|
||||
pair_style pair/spin 4.0
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
|
||||
#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
|
||||
#pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 10 check yes delay 20
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 1.0 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy -0.1 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.1 0.0 1.0 0.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
#fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
fix 2 all langevin/spin 1.0 0.1 0.0 21
|
||||
#fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all nve/spin mpi
|
||||
|
||||
#compute real time, total magnetization, magnetic energy, and spin temperature
|
||||
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
|
||||
compute mag all compute/spin
|
||||
fix outmag all ave/time 1 1 10 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7] file mag_Co_nodamp.dat format %20.16g
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 100 dump_spin_T100.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 2000
|
||||
#run 1
|
||||
|
||||
88
examples/SPIN/read_restart/in.spin.read_data
Normal file
88
examples/SPIN/read_restart/in.spin.read_data
Normal file
@ -0,0 +1,88 @@
|
||||
###################
|
||||
#######Init########
|
||||
###################
|
||||
|
||||
clear
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
#boundary f f f
|
||||
|
||||
#setting atom_style to spin:
|
||||
atom_style spin
|
||||
|
||||
atom_modify map array
|
||||
|
||||
###########################
|
||||
#######Create atoms########
|
||||
###########################
|
||||
|
||||
read_data ../examples/SPIN/Norm_randXY_8x8x32_test.data
|
||||
|
||||
#######################
|
||||
#######Settings########
|
||||
#######################
|
||||
|
||||
#Setting one or more properties of one or more atoms.
|
||||
mass 1 58.93
|
||||
|
||||
#velocity all create 200 4928459 rot yes dist gaussian
|
||||
|
||||
#Magneto-mechanic interactions for bulk fcc Cobalt
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
|
||||
# cobalt eam potential
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
|
||||
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
#type i and j | interaction type | cutoff | K1 (eV) | K2 (adim) | K3 (Ang) (for SOC)
|
||||
pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 10 check yes delay 20
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all integration/spin serial
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 1 dump.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 10
|
||||
#run 10000
|
||||
|
||||
89
examples/SPIN/read_restart/in.spin.restart
Normal file
89
examples/SPIN/read_restart/in.spin.restart
Normal file
@ -0,0 +1,89 @@
|
||||
# read a dump file for a sim. of magnetic cobalt
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
|
||||
read_dump ../examples/SPIN/Norm_randXY_8x8x32.dump 0 x y z box yes
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#Setting spins orientation and moment
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
set group single_spin spin/random 11 1.72
|
||||
|
||||
velocity all create 200 4928459 rot yes dist gaussian
|
||||
|
||||
#Magneto-mechanic interactions for bulk fcc Cobalt
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
|
||||
# cobalt eam potential
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
|
||||
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
#type i and j | interaction type | cutoff | K1 (eV) | K2 (adim) | K3 (Ang) (for SOC)
|
||||
pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 10 check yes delay 20
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all integration/spin serial
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 20 dump.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 100
|
||||
#run 10000
|
||||
|
||||
55
examples/SPIN/skyrmion/in.spin.skyrmion
Normal file
55
examples/SPIN/skyrmion/in.spin.skyrmion
Normal file
@ -0,0 +1,55 @@
|
||||
# fcc cobalt in a 3d box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p f
|
||||
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 50.0 0.0 50.0 0.0 4.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
pair_style hybrid/overlay pair/spin/exchange 4.0 pair/spin/soc/dmi 2.6
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
pair_coeff * * pair/spin/soc/dmi dmi 2.6 0.01 0.0 0.0 1.0
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all force/spin anisotropy 0.0001 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
|
||||
fix 3 all integration/spin lattice no
|
||||
|
||||
timestep 0.0002
|
||||
|
||||
# define output and run
|
||||
|
||||
compute out_mag all compute/spin
|
||||
variable magz equal c_out_mag[4]
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable emag equal c_out_mag[6]
|
||||
variable tmag equal c_out_mag[7]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag etotal
|
||||
thermo 50
|
||||
|
||||
dump 1 all custom 50 dump_skyrmion.lammpstrj type x y z spx spy spz
|
||||
|
||||
run 10000
|
||||
|
||||
91
examples/SPIN/vmd/prepare_vmd.sh
Executable file
91
examples/SPIN/vmd/prepare_vmd.sh
Executable file
@ -0,0 +1,91 @@
|
||||
#!/bin/bash
|
||||
# example prepare_vmd.sh /home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj
|
||||
# you will get a return file
|
||||
|
||||
echo "vmd script for file $1 is preparing..."
|
||||
|
||||
timestamp(){
|
||||
date +%s
|
||||
}
|
||||
|
||||
TS=$(timestamp)
|
||||
FILE=view_${TS}.vmd
|
||||
|
||||
cat >${FILE} <<EOF
|
||||
proc vmd_draw_arrow {mol start end} {
|
||||
set middle [vecadd \$start [vecscale 0.9 [vecsub \$end \$start]]]
|
||||
graphics \$mol cylinder \$start \$middle radius 0.05
|
||||
graphics \$mol cone \$middle \$end radius 0.01 color 3
|
||||
}
|
||||
|
||||
proc vmd_draw_vector {args} {
|
||||
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
|
||||
# defaults
|
||||
set scale 2.0
|
||||
set res 50
|
||||
set radius 0.1
|
||||
set filled yes
|
||||
|
||||
if {[llength \$args] < 3} {
|
||||
error "wrong # args: should be \$usage"
|
||||
}
|
||||
set mol [lindex \$args 0]
|
||||
set center [lindex \$args 1]
|
||||
set vector [lindex \$args 2]
|
||||
if {[llength \$center] != 3 || [llength \$vector] != 3} {
|
||||
error "wrong type of args: should be \$usage"
|
||||
}
|
||||
|
||||
foreach {flag value} [lrange \$args 3 end] {
|
||||
switch -glob \$flag {
|
||||
scale {set scale \$value}
|
||||
res* {set res \$value}
|
||||
rad* {set radius \$value}
|
||||
fill* {set filled \$value}
|
||||
default {error "unknown option '\$flag': should be \$usage" }
|
||||
}
|
||||
}
|
||||
|
||||
set vechalf [vecscale [expr \$scale * 0.5] \$vector]
|
||||
return [list \\
|
||||
[graphics \$mol color yellow]\\
|
||||
[graphics \$mol cylinder [vecsub \$center \$vechalf]\\
|
||||
[vecadd \$center [vecscale 0.7 \$vechalf]] \\
|
||||
radius \$radius resolution \$res filled \$filled] \\
|
||||
[graphics \$mol color orange]\\
|
||||
[graphics \$mol cone [vecadd \$center [vecscale 0.6 \$vechalf]] \\
|
||||
[vecadd \$center \$vechalf] radius [expr \$radius * 2.5] \\
|
||||
resolution \$res]]
|
||||
}
|
||||
|
||||
proc vmd_draw_spin {args} {
|
||||
global molid
|
||||
graphics \$molid delete all
|
||||
set frame [molinfo \$molid get frame]
|
||||
set natoms [molinfo \$molid get numatoms]
|
||||
for {set i 0} {\$i < \$natoms} {incr i} {
|
||||
set sel [atomselect top "index \$i"]
|
||||
set coords [lindex [\$sel get {x y z}] \$molid]
|
||||
set velocities [lindex [\$sel get {vx vy vz}] \$molid]
|
||||
draw vector \$coords \$velocities
|
||||
set uvx [lindex [\$sel get {vx}] \$molid]
|
||||
set uvy [lindex [\$sel get {vy}] \$molid]
|
||||
set uvz [lindex [\$sel get {vz}] \$molid]
|
||||
\$sel set user [vecadd [vecadd [vecscale \$uvy \$uvy] [vecscale \$uvz \$uvz] ] [vecscale \$uvx \$uvx]]
|
||||
\$sel set user \$uvy
|
||||
#draw vector \$coords {0.0 uvy 0.0}
|
||||
}
|
||||
#pbc box -color 3
|
||||
}
|
||||
|
||||
proc enable_trace {} {
|
||||
global vmd_frame
|
||||
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
|
||||
}
|
||||
|
||||
set molid [mol addfile {$1} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
|
||||
scale by 0.5
|
||||
animate style Loop
|
||||
enable_trace
|
||||
EOF
|
||||
echo "$FILE is ready..."
|
||||
79
examples/SPIN/vmd/vmd_nano.vmd
Normal file
79
examples/SPIN/vmd/vmd_nano.vmd
Normal file
@ -0,0 +1,79 @@
|
||||
proc vmd_draw_arrow {mol start end} {
|
||||
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
|
||||
graphics $mol cylinder $start $middle radius 0.05
|
||||
graphics $mol cone $middle $end radius 0.01 color 3
|
||||
}
|
||||
|
||||
proc vmd_draw_vector {args} {
|
||||
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
|
||||
# defaults
|
||||
set scale 2.0
|
||||
set res 50
|
||||
set radius 0.1
|
||||
set filled yes
|
||||
|
||||
if {[llength $args] < 3} {
|
||||
error "wrong # args: should be $usage"
|
||||
}
|
||||
set mol [lindex $args 0]
|
||||
set center [lindex $args 1]
|
||||
set vector [lindex $args 2]
|
||||
if {[llength $center] != 3 || [llength $vector] != 3} {
|
||||
error "wrong type of args: should be $usage"
|
||||
}
|
||||
|
||||
foreach {flag value} [lrange $args 3 end] {
|
||||
switch -glob $flag {
|
||||
scale {set scale $value}
|
||||
res* {set res $value}
|
||||
rad* {set radius $value}
|
||||
fill* {set filled $value}
|
||||
default {error "unknown option '$flag': should be $usage" }
|
||||
}
|
||||
}
|
||||
|
||||
set vechalf [vecscale [expr $scale * 0.5] $vector]
|
||||
return [list \
|
||||
[graphics $mol color yellow]\
|
||||
[graphics $mol cylinder [vecsub $center $vechalf]\
|
||||
[vecadd $center [vecscale 0.7 $vechalf]] \
|
||||
radius $radius resolution $res filled $filled] \
|
||||
[graphics $mol color orange]\
|
||||
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
|
||||
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
|
||||
resolution $res]]
|
||||
}
|
||||
|
||||
proc vmd_draw_spin {args} {
|
||||
global molid
|
||||
graphics $molid delete all
|
||||
set frame [molinfo $molid get frame]
|
||||
set natoms [molinfo $molid get numatoms]
|
||||
for {set i 0} {$i < $natoms} {incr i} {
|
||||
set sel [atomselect top "index $i"]
|
||||
# set sel [atomselect top "index 1200"]
|
||||
set coords [lindex [$sel get {x y z}] $molid]
|
||||
set velocities [lindex [$sel get {vx vy vz}] $molid]
|
||||
draw vector $coords $velocities
|
||||
set uvx [lindex [$sel get {vx}] $molid]
|
||||
set uvy [lindex [$sel get {vy}] $molid]
|
||||
set uvz [lindex [$sel get {vz}] $molid]
|
||||
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
|
||||
$sel set user $uvy
|
||||
#draw vector $coords {0.0 uvy 0.0}
|
||||
}
|
||||
#pbc box -color 3
|
||||
}
|
||||
|
||||
proc enable_trace {} {
|
||||
global vmd_frame
|
||||
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
|
||||
}
|
||||
|
||||
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
|
||||
scale by 0.5
|
||||
animate style Loop
|
||||
enable_trace
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user