Merge branch 'master' into cmake_misc
This commit is contained in:
Axel Kohlmeyer
1
.github/CODEOWNERS
vendored
1
.github/CODEOWNERS
vendored
@ -16,6 +16,7 @@ src/COMPRESS/* @akohlmey
|
||||
src/GPU/* @ndtrung81
|
||||
src/KOKKOS/* @stanmoore1
|
||||
src/KIM/* @ellio167
|
||||
src/LATTE/* @cnegre
|
||||
src/USER-CGDNA/* @ohenrich
|
||||
src/USER-CGSDK/* @akohlmey
|
||||
src/USER-COLVARS/* @giacomofiorin
|
||||
|
||||
@ -132,10 +132,10 @@ if(ENABLE_TESTING)
|
||||
endif(ENABLE_TESTING)
|
||||
|
||||
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
|
||||
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SNAP SRD
|
||||
KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA
|
||||
USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
|
||||
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
|
||||
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
|
||||
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
|
||||
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
|
||||
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
|
||||
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
|
||||
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
|
||||
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
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@ -306,8 +306,8 @@ if(PKG_LATTE)
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message(STATUS "LATTE not found - we will build our own")
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include(ExternalProject)
|
||||
ExternalProject_Add(latte_build
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URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz
|
||||
URL_MD5 cb86f1d2473ce00aa61ff6a023154b03
|
||||
URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
|
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URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb
|
||||
SOURCE_SUBDIR cmake
|
||||
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
|
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)
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||||
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||||
BIN
doc/src/Eqs/fix_integration_spin_stdecomposition.jpg
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BIN
doc/src/Eqs/fix_integration_spin_stdecomposition.jpg
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40
doc/src/Eqs/fix_integration_spin_stdecomposition.tex
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40
doc/src/Eqs/fix_integration_spin_stdecomposition.tex
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@ -0,0 +1,40 @@
|
||||
\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}
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||||
|
||||
%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);
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||||
\draw[line width=2pt, ->] (r) -- (s2);
|
||||
\draw[line width=2pt, ->] (s2) -- (v2);
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||||
|
||||
%Spin
|
||||
\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
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\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
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||||
\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] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
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||||
\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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||||
|
||||
\draw[line width=2pt,dashed, ->] (s01) -- (sN1);
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||||
\draw[line width=2pt, ->] (sN1) -- (sN);
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||||
\draw[line width=2pt, ->] (sN) -- (sN2);
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||||
\draw[line width=2pt,dashed, ->] (sN2) -- (s02);
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||||
|
||||
%from Global to Spin
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||||
\draw[line width=2pt, dashed, ->] (s1) -- (s01.west);
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\draw[line width=2pt, dashed, ->] (s1) -- (s02.west);
|
||||
|
||||
\end{tikzpicture}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/fix_langevin_spin_sLLG.jpg
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BIN
doc/src/Eqs/fix_langevin_spin_sLLG.jpg
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14
doc/src/Eqs/fix_langevin_spin_sLLG.tex
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14
doc/src/Eqs/fix_langevin_spin_sLLG.tex
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@ -0,0 +1,14 @@
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||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\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
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||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/force_spin_aniso.jpg
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BIN
doc/src/Eqs/force_spin_aniso.jpg
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After Width: | Height: | Size: 5.9 KiB |
11
doc/src/Eqs/force_spin_aniso.tex
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11
doc/src/Eqs/force_spin_aniso.tex
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@ -0,0 +1,11 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/force_spin_zeeman.jpg
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BIN
doc/src/Eqs/force_spin_zeeman.jpg
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Binary file not shown.
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After Width: | Height: | Size: 6.4 KiB |
11
doc/src/Eqs/force_spin_zeeman.tex
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11
doc/src/Eqs/force_spin_zeeman.tex
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@ -0,0 +1,11 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_entropy.jpg
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BIN
doc/src/Eqs/pair_entropy.jpg
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|
After Width: | Height: | Size: 8.7 KiB |
10
doc/src/Eqs/pair_entropy.tex
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10
doc/src/Eqs/pair_entropy.tex
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@ -0,0 +1,10 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
|
||||
$$
|
||||
s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr ,
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_entropy2.jpg
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BIN
doc/src/Eqs/pair_entropy2.jpg
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Binary file not shown.
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After Width: | Height: | Size: 8.3 KiB |
10
doc/src/Eqs/pair_entropy2.tex
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10
doc/src/Eqs/pair_entropy2.tex
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@ -0,0 +1,10 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
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||||
\thispagestyle{empty}
|
||||
|
||||
$$
|
||||
g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} ,
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_entropy3.jpg
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BIN
doc/src/Eqs/pair_entropy3.jpg
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Binary file not shown.
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After Width: | Height: | Size: 5.6 KiB |
10
doc/src/Eqs/pair_entropy3.tex
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10
doc/src/Eqs/pair_entropy3.tex
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@ -0,0 +1,10 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
|
||||
$$
|
||||
\bar{s}_S^i = \frac{\sum_j s_S^j + s_S^i}{N + 1} ,
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_spin_dmi_interaction.jpg
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BIN
doc/src/Eqs/pair_spin_dmi_interaction.jpg
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Binary file not shown.
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After Width: | Height: | Size: 6.2 KiB |
16
doc/src/Eqs/pair_spin_dmi_interaction.tex
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16
doc/src/Eqs/pair_spin_dmi_interaction.tex
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@ -0,0 +1,16 @@
|
||||
\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}
|
||||
\left( \vec{e}_{ij} \times \vec{D} \right)
|
||||
\cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right),
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
\vec{D}\left(r_{ij}\right)
|
||||
{\rm ~and~} \vec{D}\left(r_{ij}\right) = \vec{e}_{ij} \times \vec{D}
|
||||
BIN
doc/src/Eqs/pair_spin_exchange_forces.jpg
Normal file
BIN
doc/src/Eqs/pair_spin_exchange_forces.jpg
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After Width: | Height: | Size: 13 KiB |
14
doc/src/Eqs/pair_spin_exchange_forces.tex
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14
doc/src/Eqs/pair_spin_exchange_forces.tex
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@ -0,0 +1,14 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\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}
|
||||
BIN
doc/src/Eqs/pair_spin_exchange_function.jpg
Normal file
BIN
doc/src/Eqs/pair_spin_exchange_function.jpg
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After Width: | Height: | Size: 10 KiB |
13
doc/src/Eqs/pair_spin_exchange_function.tex
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13
doc/src/Eqs/pair_spin_exchange_function.tex
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@ -0,0 +1,13 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
{J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d}
|
||||
\right)^2 }\Theta (R_c - r_{ij}) \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_spin_exchange_interaction.jpg
Normal file
BIN
doc/src/Eqs/pair_spin_exchange_interaction.jpg
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After Width: | Height: | Size: 6.5 KiB |
11
doc/src/Eqs/pair_spin_exchange_interaction.tex
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doc/src/Eqs/pair_spin_exchange_interaction.tex
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@ -0,0 +1,11 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{exchange} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_spin_me_forces.jpg
Normal file
BIN
doc/src/Eqs/pair_spin_me_forces.jpg
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After Width: | Height: | Size: 13 KiB |
13
doc/src/Eqs/pair_spin_me_forces.tex
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13
doc/src/Eqs/pair_spin_me_forces.tex
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@ -0,0 +1,13 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\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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BIN
doc/src/Eqs/pair_spin_me_interaction.jpg
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12
doc/src/Eqs/pair_spin_me_interaction.tex
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12
doc/src/Eqs/pair_spin_me_interaction.tex
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@ -0,0 +1,12 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\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_neel_functions.jpg
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BIN
doc/src/Eqs/pair_spin_neel_functions.jpg
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13
doc/src/Eqs/pair_spin_neel_functions.tex
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doc/src/Eqs/pair_spin_neel_functions.tex
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@ -0,0 +1,13 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{eqnarray}
|
||||
g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\
|
||||
q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\
|
||||
q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber
|
||||
\end{eqnarray}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
BIN
doc/src/Eqs/pair_spin_neel_interaction.jpg
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BIN
doc/src/Eqs/pair_spin_neel_interaction.jpg
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After Width: | Height: | Size: 11 KiB |
16
doc/src/Eqs/pair_spin_neel_interaction.tex
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16
doc/src/Eqs/pair_spin_neel_interaction.tex
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@ -0,0 +1,16 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij}
|
||||
\cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
|
||||
+q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right)
|
||||
\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
|
||||
+ q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot
|
||||
{\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="11 May 2018 version">
|
||||
<META NAME="docnumber" CONTENT="22 Jun 2018 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -19,7 +19,7 @@
|
||||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
11 May 2018 version :c,h2
|
||||
22 Jun 2018 version :c,h2
|
||||
|
||||
Version info: :h3
|
||||
|
||||
|
||||
@ -129,12 +129,14 @@ region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
|
||||
|
||||
so that you do not have to define (or discard) a temporary variable X.
|
||||
|
||||
Additionally, the "immediate" expression may be followed by a colon,
|
||||
followed by a C-style format string, e.g. "%f" or "%.10g", which must be
|
||||
appropriate for formatting a double-precision floating-point value. The
|
||||
format string will be used to output the result of the variable evaluation,
|
||||
so you do not have to define a temporary "format-style variable"_variable.html.
|
||||
This may be used for formatting print output:
|
||||
Additionally, the "immediate" variable expression may be followed by a
|
||||
colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
|
||||
The format string must be appropriate for a double-precision
|
||||
floating-point value. The format string is used to output the result
|
||||
of the variable expression evaluation. If a format string is not
|
||||
specified a high-precision "%.20g" is used as the default.
|
||||
|
||||
This can be useful for formatting print output to a desired precion:
|
||||
|
||||
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
|
||||
|
||||
@ -592,6 +594,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
||||
"indent"_fix_indent.html,
|
||||
"latte"_fix_latte.html,
|
||||
"langevin (k)"_fix_langevin.html,
|
||||
"langevin/spin"_fix_langevin_spin.hmtl,
|
||||
"lineforce"_fix_lineforce.html,
|
||||
"momentum (k)"_fix_momentum.html,
|
||||
"move"_fix_move.html,
|
||||
@ -615,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
||||
"nve/line"_fix_nve_line.html,
|
||||
"nve/noforce"_fix_nve_noforce.html,
|
||||
"nve/sphere (o)"_fix_nve_sphere.html,
|
||||
"nve/spin"_fix_nve_spin.html,
|
||||
"nve/tri"_fix_nve_tri.html,
|
||||
"nvt (iko)"_fix_nh.html,
|
||||
"nvt/asphere (o)"_fix_nvt_asphere.html,
|
||||
@ -627,6 +631,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
||||
"planeforce"_fix_planeforce.html,
|
||||
"poems"_fix_poems.html,
|
||||
"pour"_fix_pour.html,
|
||||
"precession/spin"_fix_precession_spin.html,
|
||||
"press/berendsen"_fix_press_berendsen.html,
|
||||
"print"_fix_print.html,
|
||||
"property/atom (k)"_fix_property_atom.html,
|
||||
@ -833,6 +838,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"sna/atom"_compute_sna_atom.html,
|
||||
"snad/atom"_compute_sna_atom.html,
|
||||
"snav/atom"_compute_sna_atom.html,
|
||||
"spin"_compute_spin.html,
|
||||
"stress/atom"_compute_stress_atom.html,
|
||||
"temp (k)"_compute_temp.html,
|
||||
"temp/asphere"_compute_temp_asphere.html,
|
||||
@ -861,6 +867,7 @@ package"_Section_start.html#start_3.
|
||||
"dpd"_compute_dpd.html,
|
||||
"dpd/atom"_compute_dpd_atom.html,
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html,
|
||||
"entropy/atom"_compute_entropy_atom.html,
|
||||
"fep"_compute_fep.html,
|
||||
"force/tally"_compute_tally.html,
|
||||
"heat/flux/tally"_compute_tally.html,
|
||||
@ -1026,6 +1033,10 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"snap (k)"_pair_snap.html,
|
||||
"soft (go)"_pair_soft.html,
|
||||
"sw (giko)"_pair_sw.html,
|
||||
"spin/dmi"_pair_spin_dmi.html,
|
||||
"spin/exchange"_pair_spin_exchange.html,
|
||||
"spin/magelec"_pair_spin_magelec.html,
|
||||
"spin/neel"_pair_spin_neel.html,
|
||||
"table (gko)"_pair_table.html,
|
||||
"tersoff (giko)"_pair_tersoff.html,
|
||||
"tersoff/mod (gko)"_pair_tersoff_mod.html,
|
||||
|
||||
@ -36,7 +36,8 @@ This section describes how to perform common tasks using LAMMPS.
|
||||
6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
|
||||
6.25 "Polarizable models"_#howto_25
|
||||
6.26 "Adiabatic core/shell model"_#howto_26
|
||||
6.27 "Drude induced dipoles"_#howto_27 :all(b)
|
||||
6.27 "Drude induced dipoles"_#howto_27
|
||||
6.28 "Magnetic spins"_#howto_28 :all(b)
|
||||
|
||||
The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in "Section 7"_Section_example.html also show how to
|
||||
@ -2906,6 +2907,54 @@ with a Coulomb pair style. It may be useful to use {coul/long/cs} or
|
||||
similar from the CORESHELL package if the core and Drude particle come
|
||||
too close, which can cause numerical issues.
|
||||
|
||||
:line
|
||||
|
||||
6.28 Magnetic spins :link(howto_28),h4
|
||||
|
||||
The magnetic spin simualtions are enabled by the SPIN package, whose
|
||||
implementation is detailed in "Tranchida"_#Tranchida7.
|
||||
|
||||
The model representents the simulation of atomic magnetic spins coupled
|
||||
to lattice vibrations. The dynamics of those magnetic spins can be used
|
||||
to simulate a broad range a phenomena related to magneto-elasticity, or
|
||||
or to study the influence of defects on the magnetic properties of
|
||||
materials.
|
||||
|
||||
The magnetic spins are interacting with each others and with the
|
||||
lattice via pair interactions. Typically, the magnetic exchange
|
||||
interaction can be defined using the
|
||||
"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
|
||||
applies a magnetic torque to a given spin, considering the orientation
|
||||
of its neighboring spins and their relative distances.
|
||||
It also applies a force on the atoms as a function of the spin
|
||||
orientations and their associated inter-atomic distances.
|
||||
|
||||
The command "fix precession/spin"_fix_precession_spin.html allows to
|
||||
apply a constant magnetic torque on all the spins in the system. This
|
||||
torque can be an external magnetic field (Zeeman interaction), or an
|
||||
uniaxial magnetic anisotropy.
|
||||
|
||||
A Langevin thermostat can be applied to those magnetic spins using
|
||||
"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
|
||||
can be coupled to another Langevin thermostat applied to the atoms
|
||||
using "fix langevin"_fix_langevin.html in order to simulate
|
||||
thermostated spin-lattice system.
|
||||
|
||||
The magnetic Gilbert damping can also be applied using "fix
|
||||
langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
|
||||
the thermal energy of the Langevin thermostat, or to perform a
|
||||
relaxation of the magnetic configuration toward an equilibrium state.
|
||||
|
||||
All the computed magnetic properties can be outputed by two main
|
||||
commands. The first one is "compute spin"_compute_spin.html, that
|
||||
enables to evaluate magnetic averaged quantities, such as the total
|
||||
magnetization of the system along x, y, or z, the spin temperature, or
|
||||
the magnetic energy. The second command is "compute
|
||||
property/atom"_compute_property_atom.html. It enables to output all the
|
||||
per atom magnetic quantities. Typically, the orientation of a given
|
||||
magnetic spin, or the magnetic force acting on this spin.
|
||||
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
@ -2957,3 +3006,7 @@ Phys, 79, 926 (1983).
|
||||
|
||||
:link(howto-Lamoureux)
|
||||
[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
|
||||
|
||||
:link(Tranchida7)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
|
||||
@ -15,7 +15,7 @@ atom_style style args :pre
|
||||
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
|
||||
{dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
|
||||
{full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
|
||||
{sphere} or {tri} or {template} or {hybrid} :ulb,l
|
||||
{sphere} or {tri} or {template} or {hybrid} or {spin} :ulb,l
|
||||
args = none for any style except the following
|
||||
{body} args = bstyle bstyle-args
|
||||
bstyle = style of body particles
|
||||
@ -38,6 +38,7 @@ atom_style full
|
||||
atom_style body nparticle 2 10
|
||||
atom_style hybrid charge bond
|
||||
atom_style hybrid charge body nparticle 2 5
|
||||
atom_style spin
|
||||
atom_style template myMols
|
||||
atom_style tdpd 2 :pre
|
||||
|
||||
@ -89,6 +90,7 @@ quantities.
|
||||
{peri} | mass, volume | mesocopic Peridynamic models |
|
||||
{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
|
||||
{sphere} | diameter, mass, angular velocity | granular models |
|
||||
{spin} | magnetic moment | system with magnetic particles |
|
||||
{template} | template index, template atom | small molecules with fixed topology |
|
||||
{tri} | corner points, angular momentum | rigid bodies |
|
||||
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
|
||||
@ -175,6 +177,9 @@ used for calculating the field variables (e.g. stress and deformation)
|
||||
and a contact radius for calculating repulsive forces which prevent
|
||||
individual physical bodies from penetrating each other.
|
||||
|
||||
For the {spin} style, a magnetic spin is associated to each atom.
|
||||
Those spins have a norm (their magnetic moment) and a direction.
|
||||
|
||||
The {wavepacket} style is similar to {electron}, but the electrons may
|
||||
consist of several Gaussian wave packets, summed up with coefficients
|
||||
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
|
||||
@ -312,6 +317,8 @@ The {meso} style is part of the USER-SPH package for smoothed particle
|
||||
hydrodynamics (SPH). See "this PDF
|
||||
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
|
||||
|
||||
The {spin} style is part of the SPIN package.
|
||||
|
||||
The {wavepacket} style is part of the USER-AWPMD package for the
|
||||
"antisymmetrized wave packet MD method"_pair_awpmd.html.
|
||||
|
||||
|
||||
130
doc/src/compute_entropy_atom.txt
Normal file
130
doc/src/compute_entropy_atom.txt
Normal file
@ -0,0 +1,130 @@
|
||||
"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
|
||||
|
||||
compute entropy/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command :l
|
||||
entropy/atom = style name of this compute command :l
|
||||
sigma = width of gaussians used in the g(r) smoothening :l
|
||||
cutoff = cutoff for the g(r) calculation :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {avg} or {local}
|
||||
{avg} values = {yes} or {no} cutoff2
|
||||
{yes} = average the pair entropy over neighbors
|
||||
{no} = do not average the pair entropy over neighbors
|
||||
cutoff2 = cutoff for the averaging over neighbors
|
||||
{local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all entropy/atom 0.25 5.
|
||||
compute 1 all entropy/atom 0.25 5. avg yes 5.
|
||||
compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the pair entropy fingerprint for
|
||||
each atom in the group. The fingerprint is useful to distinguish between
|
||||
ordered and disordered environments, for instance liquid and solid-like
|
||||
environments, or glassy and crystalline-like environments. Some
|
||||
applications could be the identification of grain boundaries, a
|
||||
melt-solid interface, or a solid cluster emerging from the melt.
|
||||
The advantage of this parameter over others is that no a priori
|
||||
information about the solid structure is required.
|
||||
|
||||
This parameter for atom i is computed using the following formula from
|
||||
"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton ,
|
||||
|
||||
:c,image(Eqs/pair_entropy.jpg)
|
||||
|
||||
where r is a distance, g(r) is the radial distribution function of atom
|
||||
i and rho is the density of the system. The g(r) computed for each
|
||||
atom i can be noisy and therefore it is smoothened using:
|
||||
|
||||
:c,image(Eqs/pair_entropy2.jpg)
|
||||
|
||||
where the sum in j goes through the neighbors of atom i, and sigma is a
|
||||
parameter to control the smoothening.
|
||||
|
||||
The input parameters are {sigma} the smoothening parameter, and the
|
||||
{cutoff} for the calculation of g(r).
|
||||
|
||||
If the keyword {avg} has the setting {yes}, then this compute also
|
||||
averages the parameter over the neighbors of atom i according to:
|
||||
|
||||
:c,image(Eqs/pair_entropy3.jpg)
|
||||
|
||||
where the sum j goes over the neighbors of atom i and N is the number
|
||||
of neighbors. This procedure provides a sharper distinction between
|
||||
order and disorder environments. In this case the input parameter
|
||||
{cutoff2} is the cutoff for the averaging over the neighbors and
|
||||
must also be specified.
|
||||
|
||||
If the {avg yes} option is used, the effective cutoff of the neighbor
|
||||
list should be {cutoff}+{cutoff2} and therefore it might be necessary
|
||||
to increase the skin of the neighbor list with:
|
||||
|
||||
neighbor skin bin :pre
|
||||
|
||||
See "neighbor"_neighbor.html for details.
|
||||
|
||||
If the {local yes} option is used, the g(r) is normalized by the
|
||||
local density around each atom, that is to say the density around each
|
||||
atom is the number of neighbors within the neighbor list cutoff divided
|
||||
by the corresponding volume. This option can be useful when dealing with
|
||||
inhomogeneus systems such as those that have surfaces.
|
||||
|
||||
Here are typical input parameters for fcc aluminum (lattice
|
||||
constant 4.05 Angstroms),
|
||||
|
||||
compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre
|
||||
|
||||
and for bcc sodium (lattice constant 4.23 Angstroms),
|
||||
|
||||
compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre
|
||||
|
||||
|
||||
[Output info:]
|
||||
|
||||
By default, this compute calculates the pair entropy value for each
|
||||
atom as a per-atom vector, which can be accessed by any command that
|
||||
uses per-atom values from a compute as input. See "Section
|
||||
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The pair entropy values have units of the Boltzmann constant. They are
|
||||
always negative, and lower values (lower entropy) correspond to more
|
||||
ordered environments.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute cna/atom"_compute_cna_atom.html
|
||||
"compute centro/atom"_compute_centro_atom.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The default values for the optional keywords are avg = no and local = no.
|
||||
|
||||
:line
|
||||
|
||||
:link(Piaggi)
|
||||
[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).
|
||||
|
||||
:link(Nettleton)
|
||||
[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958).
|
||||
@ -19,6 +19,7 @@ input = one or more atom attributes :l
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
sp, spx, spy, spz, fmx, fmy, fmz,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
@ -46,6 +47,9 @@ input = one or more atom attributes :l
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipole moment of atom
|
||||
mu = magnitude of dipole moment of atom
|
||||
sp = atomic magnetic spin moment
|
||||
spx, spy, spz = direction of the atomic magnetic spin
|
||||
fmx, fmy, fmz = magnetic force
|
||||
radius,diameter = radius,diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
@ -82,7 +86,8 @@ input = one or more atom attributes :l
|
||||
|
||||
compute 1 all property/atom xs vx fx mux
|
||||
compute 2 all property/atom type
|
||||
compute 1 all property/atom ix iy iz :pre
|
||||
compute 1 all property/atom ix iy iz
|
||||
compute 3 all property/atom sp spx spy spz :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -152,6 +157,10 @@ The vector or array values will be in whatever "units"_units.html the
|
||||
corresponding attribute is in, e.g. velocity units for vx, charge
|
||||
units for q, etc.
|
||||
|
||||
For the spin quantities, sp is in the units of the Bohr magneton, spx,
|
||||
spy, and spz are adimentional quantities, and fmx, fmy and fmz are
|
||||
given in rad.THz.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
78
doc/src/compute_spin.txt
Normal file
78
doc/src/compute_spin.txt
Normal file
@ -0,0 +1,78 @@
|
||||
"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
|
||||
|
||||
compute spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID compute/spin :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
compute/spin = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute out_mag all compute/spin :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates magnetic quantities for a system
|
||||
of atoms having spins.
|
||||
|
||||
This compute calculates 6 magnetic quantities.
|
||||
|
||||
The three first quantities are the x,y and z coordinates of the total magnetization.
|
||||
|
||||
The fourth quantity is the norm of the total magnetization.
|
||||
|
||||
The fifth quantity is the magnetic energy.
|
||||
|
||||
The sixth one is referred to as the spin temperature, according
|
||||
to the work of "(Nurdin)"_#Nurdin1.
|
||||
|
||||
The simplest way to output the results of the compute spin calculation
|
||||
is to define some of the quantities as variables, and to use the thermo and
|
||||
thermo_style commands, for example:
|
||||
|
||||
compute out_mag all compute/spin :pre
|
||||
|
||||
variable mag_z equal c_out_mag\[3\]
|
||||
variable mag_norm equal c_out_mag\[4\]
|
||||
variable temp_mag equal c_out_mag\[6\] :pre
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
|
||||
|
||||
This serie of commands evaluates the total magnetization along z, the norm of
|
||||
the total magnetization, and the magnetic temperature. Three variables are
|
||||
assigned to those quantities. The thermo and thermo_style commands print them
|
||||
every 10 timesteps.
|
||||
|
||||
|
||||
[Output info:]
|
||||
|
||||
The array values are "intensive". The array values will be in
|
||||
metal units ("units"_units.html).
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {spin} compute is part of the SPIN package.
|
||||
This compute is only enabled if LAMMPS was built with this package.
|
||||
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
The atom_style has to be "spin" for this compute to be valid.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Nurdin1)
|
||||
[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
|
||||
|
||||
@ -31,6 +31,7 @@ Computes :h1
|
||||
compute_dpd
|
||||
compute_dpd_atom
|
||||
compute_edpd_temp_atom
|
||||
compute_entropy_atom
|
||||
compute_erotate_asphere
|
||||
compute_erotate_rigid
|
||||
compute_erotate_sphere
|
||||
@ -95,6 +96,7 @@ Computes :h1
|
||||
compute_smd_ulsph_stress
|
||||
compute_smd_vol
|
||||
compute_sna_atom
|
||||
compute_spin
|
||||
compute_stress_atom
|
||||
compute_tally
|
||||
compute_tdpd_cc_atom
|
||||
|
||||
@ -35,8 +35,11 @@ fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box :pre
|
||||
[Description:]
|
||||
|
||||
Reset the timestep size every N steps during a run, so that no atom
|
||||
moves further than Xmax, based on current atom velocities and forces,
|
||||
and (optionally) no atom's kinetic energy changes by more than Emax.
|
||||
moves further than the specified {Xmax} distance, based on current
|
||||
atom velocities and forces. Optionally an additional criterion is
|
||||
imposed by the {emax} keyword, so that no atom's kinetic energy
|
||||
changes by more than the specified {Emax}.
|
||||
|
||||
This can be useful when starting from a configuration with overlapping
|
||||
atoms, where forces will be large. Or it can be useful when running
|
||||
an impact simulation where one or more high-energy atoms collide with
|
||||
@ -52,9 +55,12 @@ current velocity and force. Since performing this calculation exactly
|
||||
would require the solution to a quartic equation, a cheaper estimate
|
||||
is generated. The estimate is conservative in that the atom's
|
||||
displacement is guaranteed not to exceed {Xmax}, though it may be
|
||||
smaller. Also, if the {Emax} value is given, for each atom, the
|
||||
timestep is limited to a value that allows the atom's kinetic energy
|
||||
to change by at most {Emax}.
|
||||
smaller.
|
||||
|
||||
In addition if the {emax} keyword is used, the specified {Emax} value
|
||||
is enforced as a limit on how much an atom's kinetic energy can
|
||||
change. If the timestep required is even smaller than for the {Xmax}
|
||||
displacement, then the smaller timestep is used.
|
||||
|
||||
Given this putative timestep for each atom, the minimum timestep value
|
||||
across all atoms is computed. Then the {Tmin} and {Tmax} bounds are
|
||||
@ -93,4 +99,5 @@ minimization"_minimize.html.
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults is units = lattice, and no kinetic energy change limit.
|
||||
The option defaults are units = lattice, and no emax kinetic energy
|
||||
limit.
|
||||
|
||||
102
doc/src/fix_langevin_spin.txt
Normal file
102
doc/src/fix_langevin_spin.txt
Normal file
@ -0,0 +1,102 @@
|
||||
"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
|
||||
|
||||
fix langevin/spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID langevin/spin T Tdamp seed :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
langevin/spin = style name of this fix command :l
|
||||
T = desired temperature of the bath (temperature units, K in metal units) :l
|
||||
Tdamp = transverse magnetic damping parameter (adim) :l
|
||||
seed = random number seed to use for white noise (positive integer) :l
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 2 all langevin/spin 300.0 0.01 21 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the
|
||||
magnetic spins associated to the atoms.
|
||||
Used with "fix nve/spin"_fix_nve_spin.html, this command performs
|
||||
Brownian dynamics (BD).
|
||||
A random torque and a transverse dissipation are applied to each spin i according to
|
||||
the following stochastic differential equation:
|
||||
|
||||
:c,image(Eqs/fix_langevin_spin_sLLG.jpg)
|
||||
|
||||
with lambda the transverse damping, and eta a random verctor.
|
||||
This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
|
||||
equation.
|
||||
|
||||
The components of eta are drawn from a Gaussian probability law. Their amplitude
|
||||
is defined as a proportion of the temperature of the external thermostat T (in K
|
||||
in metal units).
|
||||
|
||||
More details about this implementation are reported in "(Tranchida)"_#Tranchida2.
|
||||
|
||||
Note: due to the form of the sLLG equation, this fix has to be defined just
|
||||
before the nve/spin fix (and after all other magnetic fixes).
|
||||
As an example:
|
||||
|
||||
fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 300.0 0.01 21
|
||||
fix 3 all nve/spin lattice yes :pre
|
||||
|
||||
is correct, but defining a force/spin command after the langevin/spin command
|
||||
would give an error message.
|
||||
|
||||
Note: The random # {seed} must be a positive integer. A Marsaglia random
|
||||
number generator is used. Each processor uses the input seed to
|
||||
generate its own unique seed and its own stream of random numbers.
|
||||
Thus the dynamics of the system will not be identical on two runs on
|
||||
different numbers of processors.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. Because the state of the random number generator
|
||||
is not saved in restart files, this means you cannot do "exact"
|
||||
restarts with this fix, where the simulation continues on the same as
|
||||
if no restart had taken place. However, in a statistical sense, a
|
||||
restarted simulation should produce the same behavior.
|
||||
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {langevin/spin} fix is part of the SPIN package.
|
||||
This style is only enabled if LAMMPS was built with this package.
|
||||
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
The numerical integration has to be performed with {fix nve/spin}
|
||||
when {fix langevin/spin} is enabled.
|
||||
|
||||
This fix has to be the last defined magnetic fix before the time
|
||||
integration fix (e.g. {fix nve/spin}).
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Mayergoyz1)
|
||||
[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)
|
||||
|
||||
:link(Tranchida2)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
76
doc/src/fix_nve_spin.txt
Normal file
76
doc/src/fix_nve_spin.txt
Normal file
@ -0,0 +1,76 @@
|
||||
"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
|
||||
|
||||
fix nve/spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID nve/spin keyword values :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
nve/spin = style name of this fix command :l
|
||||
keyword = {lattice} :l
|
||||
{lattice} value = {no} or {yes} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
fix 1 all nve/spin lattice no :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Perform a symplectic integration for the spin or spin-lattice system.
|
||||
|
||||
The {lattice} keyword defines if the spins are integrated on a lattice
|
||||
of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
|
||||
|
||||
By default (lattice = yes), a spin-lattice integration is performed.
|
||||
|
||||
The {nve/spin} fix applies a Suzuki-Trotter decomposition to
|
||||
the equations of motion of the spin lattice system, following the scheme:
|
||||
|
||||
:c,image(Eqs/fix_integration_spin_stdecomposition.jpg)
|
||||
|
||||
according to the implementation reported in "(Omelyan)"_#Omelyan1.
|
||||
|
||||
A sectoring method enables this scheme for parallel calculations.
|
||||
The implementation of this sectoring algorithm is reported
|
||||
in "(Tranchida)"_#Tranchida1.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix style can only be used if LAMMPS was built with the
|
||||
SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info on packages.
|
||||
|
||||
To use the spin algorithm, it is necessary to define a map with
|
||||
the atom_modify command. Typically, by adding the command:
|
||||
|
||||
atom_modify map array :pre
|
||||
|
||||
before you create the simulation box. Note that the keyword "hash"
|
||||
instead of "array" is also valid.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Omelyan1)
|
||||
[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett.
|
||||
86(5), 898. (2001).
|
||||
|
||||
:link(Tranchida1)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
87
doc/src/fix_precession_spin.txt
Normal file
87
doc/src/fix_precession_spin.txt
Normal file
@ -0,0 +1,87 @@
|
||||
"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
|
||||
|
||||
fix precession/spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group precession/spin style args :pre
|
||||
|
||||
ID, group are documented in "fix"_fix.html command :ulb,l
|
||||
precession/spin = style name of this fix command :l
|
||||
style = {zeeman} or {anisotropy} :l
|
||||
{zeeman} args = H x y z
|
||||
H = intensity of the magnetic field (in Tesla)
|
||||
x y z = vector direction of the field
|
||||
{anisotropy} args = K x y z
|
||||
K = intensity of the magnetic anisotropy (in eV)
|
||||
x y z = vector direction of the anisotropy :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Impose a force torque to each magnetic spin in the group.
|
||||
|
||||
Style {zeeman} is used for the simulation of the interaction
|
||||
between the magnetic spins in the defined group and an external
|
||||
magnetic field:
|
||||
|
||||
:c,image(Eqs/force_spin_zeeman.jpg)
|
||||
|
||||
with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
|
||||
in metal units).
|
||||
|
||||
Style {anisotropy} is used to simulate an easy axis or an easy plane
|
||||
for the magnetic spins in the defined group:
|
||||
|
||||
:c,image(Eqs/force_spin_aniso.jpg)
|
||||
|
||||
with n defining the direction of the anisotropy, and K (in eV) its intensity.
|
||||
If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
|
||||
|
||||
In both cases, the choice of (x y z) imposes the vector direction for the force.
|
||||
Only the direction of the vector is important; it's length is ignored.
|
||||
|
||||
Both styles can be combined within one single command line.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
By default, the energy associated to this fix is not added to the potential
|
||||
energy of the system.
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this fix
|
||||
to add this magnetic potential energy to the potential energy of the system,
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes :pre
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15.
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {precession/spin} style is part of the SPIN package.
|
||||
This style is 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
|
||||
|
||||
[Default:] none
|
||||
@ -61,6 +61,7 @@ Fixes :h1
|
||||
fix_langevin
|
||||
fix_langevin_drude
|
||||
fix_langevin_eff
|
||||
fix_langevin_spin
|
||||
fix_latte
|
||||
fix_lb_fluid
|
||||
fix_lb_momentum
|
||||
@ -99,6 +100,7 @@ Fixes :h1
|
||||
fix_nve_manifold_rattle
|
||||
fix_nve_noforce
|
||||
fix_nve_sphere
|
||||
fix_nve_spin
|
||||
fix_nve_tri
|
||||
fix_nvk
|
||||
fix_nvt_asphere
|
||||
@ -114,6 +116,7 @@ Fixes :h1
|
||||
fix_planeforce
|
||||
fix_poems
|
||||
fix_pour
|
||||
fix_precession_spin
|
||||
fix_press_berendsen
|
||||
fix_print
|
||||
fix_property_atom
|
||||
|
||||
@ -176,6 +176,7 @@ fix_ipi.html
|
||||
fix_langevin.html
|
||||
fix_langevin_drude.html
|
||||
fix_langevin_eff.html
|
||||
fix_langevin_spin.html
|
||||
fix_latte.html
|
||||
fix_lb_fluid.html
|
||||
fix_lb_momentum.html
|
||||
@ -213,6 +214,7 @@ fix_nve_line.html
|
||||
fix_nve_manifold_rattle.html
|
||||
fix_nve_noforce.html
|
||||
fix_nve_sphere.html
|
||||
fix_nve_spin.html
|
||||
fix_nve_tri.html
|
||||
fix_nvk.html
|
||||
fix_nvt_asphere.html
|
||||
@ -229,6 +231,7 @@ fix_pimd.html
|
||||
fix_planeforce.html
|
||||
fix_poems.html
|
||||
fix_pour.html
|
||||
fix_precession_spin.html
|
||||
fix_press_berendsen.html
|
||||
fix_print.html
|
||||
fix_property_atom.html
|
||||
@ -317,6 +320,7 @@ compute_displace_atom.html
|
||||
compute_dpd.html
|
||||
compute_dpd_atom.html
|
||||
compute_edpd_temp_atom.html
|
||||
compute_entropy_atom.html
|
||||
compute_erotate_asphere.html
|
||||
compute_erotate_rigid.html
|
||||
compute_erotate_sphere.html
|
||||
@ -381,6 +385,7 @@ compute_smd_ulsph_strain_rate.html
|
||||
compute_smd_ulsph_stress.html
|
||||
compute_smd_vol.html
|
||||
compute_sna_atom.html
|
||||
compute_spin.html
|
||||
compute_stress_atom.html
|
||||
compute_tally.html
|
||||
compute_tdpd_cc_atom.html
|
||||
@ -506,6 +511,10 @@ pair_sph_lj.html
|
||||
pair_sph_rhosum.html
|
||||
pair_sph_taitwater.html
|
||||
pair_sph_taitwater_morris.html
|
||||
pair_spin_dmi.html
|
||||
pair_spin_exchange.html
|
||||
pair_spin_magelec.html
|
||||
pair_spin_neel.html
|
||||
pair_srp.html
|
||||
pair_sw.html
|
||||
pair_table.html
|
||||
|
||||
@ -23,15 +23,15 @@ pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
|
||||
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
|
||||
pair_coeff * * rebo CH.airebo NULL NULL C
|
||||
pair_coeff * * tersoff BNC.tersoff B N NULL
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
|
||||
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
|
||||
pair_coeff 1 1 coul/shield 0.70
|
||||
pair_coeff 1 2 coul/shield 0.69498201415576216335
|
||||
pair_coeff 2 2 coul/shield 0.69
|
||||
pair_coeff 2 2 coul/shield 0.69 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {ilp/graphene/hbn} style computes the registry-dependent interlayer
|
||||
potential (RDILP) potential as described in "(Leven)"_#Leven and
|
||||
potential (ILP) potential as described in "(Leven)"_#Leven and
|
||||
"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
|
||||
in "(Kolmogorov)"_#Kolmogorov2.
|
||||
|
||||
@ -61,13 +61,13 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
|
||||
are fitted with taper function by setting the cutoff equal to 16.0
|
||||
Angstrom. Using different cutoff or taper function should be careful.
|
||||
|
||||
NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented,
|
||||
BNCH-old.ILP contains the parameters published in "(Leven)"_#Leven and
|
||||
"(Maaravi)"_#Maaravi2, which is only suitable for long-range
|
||||
interaction. The parameters in BNCH.ILP provides a good description both
|
||||
for short- and long-range interaction. This is useful for simulations in
|
||||
the high pressure (small interlayer distances) regime. The comparison of
|
||||
two sets of parameters can be found in "(Ouyang)"_#Ouyang.
|
||||
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials
|
||||
are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description
|
||||
in both short- and long-range interaction regime, while the old ILP parameters
|
||||
published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for
|
||||
long-range interaction regime. This feature is essential for simulations in
|
||||
high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance).
|
||||
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
|
||||
|
||||
This potential must be used in combination with hybrid/overlay.
|
||||
Other interactions can be set to zero using pair_style {none}.
|
||||
@ -101,12 +101,12 @@ units, if your simulation does not use {metal} units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_none"_pair_none.html
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html
|
||||
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html
|
||||
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html
|
||||
"pair_style pair_coul_shield"_pair_coul_shield.html
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
|
||||
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
|
||||
"pair_style pair_coul_shield"_pair_coul_shield.html.
|
||||
|
||||
[Default:] tap_flag = 1
|
||||
|
||||
@ -121,5 +121,5 @@ units, if your simulation does not use {metal} units.
|
||||
:link(Kolmogorov2)
|
||||
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
|
||||
:link(Ouyang)
|
||||
[(Ouyang)] W. Ouyang, D. Mandelli, O. Hod, M. Urbakh, In preparation.
|
||||
:link(Ouyang1)
|
||||
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
|
||||
|
||||
@ -27,7 +27,7 @@ pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi
|
||||
The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi (KC)
|
||||
interaction potential as described in "(Kolmogorov)"_#Kolmogorov1.
|
||||
No simplification is made,
|
||||
|
||||
@ -51,6 +51,15 @@ and {rcut} are included in the parameter file. {S} is designed to
|
||||
facilitate scaling of energies. {rcut} is designed to build the neighbor
|
||||
list for calculating the normals for each atom pair.
|
||||
|
||||
NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC)
|
||||
is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides
|
||||
a good description in both short- and long-range interaction regime,
|
||||
while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1
|
||||
are only suitable for long-range interaction regime.
|
||||
This feature is essential for simulations in high-pressure regime
|
||||
(i.e., the interlayer distance smaller than the equilibrium distance).
|
||||
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2.
|
||||
|
||||
This potential must be used in combination with hybrid/overlay.
|
||||
Other interactions can be set to zero using pair_style {none}.
|
||||
|
||||
@ -83,11 +92,11 @@ units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_none"_pair_none.html
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html
|
||||
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html
|
||||
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_none"_pair_none.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
|
||||
|
||||
[Default:] tap_flag = 0
|
||||
|
||||
@ -95,3 +104,6 @@ units.
|
||||
|
||||
:link(Kolmogorov1)
|
||||
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
|
||||
:link(Ouyang2)
|
||||
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
|
||||
|
||||
66
doc/src/pair_spin_dmi.txt
Normal file
66
doc/src/pair_spin_dmi.txt
Normal file
@ -0,0 +1,66 @@
|
||||
"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 spin/dmi command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style spin/dmi cutoff :pre
|
||||
|
||||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style spin/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 {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction
|
||||
between pairs of magnetic spins:
|
||||
|
||||
:c,image(Eqs/pair_spin_dmi_interaction.jpg)
|
||||
|
||||
where si and sj are two neighboring magnetic spins of two particles,
|
||||
eij = (ri - rj)/|ri-rj| is the normalized separation vector between the
|
||||
two particles, and D is the DM vector defining the intensity and the
|
||||
sign of the interaction.
|
||||
|
||||
Examples and more explanations about this interaction and its parametrization are
|
||||
reported in "(Tranchida)"_#Tranchida5.
|
||||
|
||||
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).
|
||||
|
||||
More details about the derivation of these torques/forces are reported in
|
||||
"(Tranchida)"_#Tranchida5.
|
||||
|
||||
: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(Tranchida5)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
82
doc/src/pair_spin_exchange.txt
Normal file
82
doc/src/pair_spin_exchange.txt
Normal file
@ -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 spin/exchange command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style spin/exchange cutoff :pre
|
||||
|
||||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
|
||||
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {spin/exchange} computes the exchange interaction between
|
||||
pairs of magnetic spins:
|
||||
|
||||
:c,image(Eqs/pair_spin_exchange_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 J(rij) is a function 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 d need to be fitted so that the function above matches with
|
||||
the value of the exchange interaction for the N neighbor shells taken into account.
|
||||
|
||||
Examples and more explanations about this function and its parametrization are reported
|
||||
in "(Tranchida)"_#Tranchida3.
|
||||
|
||||
From this exchange 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_nve_spin"_fix_nve_spin.html),
|
||||
such as:
|
||||
|
||||
:c,image(Eqs/pair_spin_exchange_forces.jpg)
|
||||
|
||||
with h the Planck constant (in metal units).
|
||||
|
||||
More details about the derivation of these torques/forces are reported in
|
||||
"(Tranchida)"_#Tranchida3.
|
||||
|
||||
: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(Tranchida3)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
73
doc/src/pair_spin_magelec.txt
Normal file
73
doc/src/pair_spin_magelec.txt
Normal file
@ -0,0 +1,73 @@
|
||||
"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 spin/me command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style spin/me cutoff :pre
|
||||
|
||||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style spin/me 4.5
|
||||
pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {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,
|
||||
eij = (ri - rj)/|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_nve_spin"_fix_nve_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)"_#Tranchida4.
|
||||
|
||||
: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(Tranchida4)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
81
doc/src/pair_spin_neel.txt
Normal file
81
doc/src/pair_spin_neel.txt
Normal file
@ -0,0 +1,81 @@
|
||||
"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 spin/neel command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style spin/neel cutoff :pre
|
||||
|
||||
cutoff = global cutoff pair (distance in metal units) :ulb,l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style spin/neel 4.0
|
||||
pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {spin/neel} computes the Neel pair anisotropy model
|
||||
between pairs of magnetic spins:
|
||||
|
||||
:c,image(Eqs/pair_spin_neel_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,
|
||||
eij = (ri - rj)/|ri-rj| is their normalized separation vector
|
||||
and g1, q1 and q2 are three functions defining the intensity of the
|
||||
dipolar and quadrupolar contributions, with:
|
||||
|
||||
:c,image(Eqs/pair_spin_neel_functions.jpg)
|
||||
|
||||
With the functions g(rij) and q(rij) defined and fitted according to the same
|
||||
Bethe-Slater function used to fit the exchange interaction:
|
||||
|
||||
: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 d need to be fitted so that the function above matches with
|
||||
the values of the magneto-elastic constant of the materials at stake.
|
||||
|
||||
Examples and more explanations about this function and its parametrization are reported
|
||||
in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in
|
||||
future work.
|
||||
|
||||
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).
|
||||
|
||||
More details about the derivation of these torques/forces are reported in
|
||||
"(Tranchida)"_#Tranchida6.
|
||||
|
||||
: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(Tranchida6)
|
||||
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
arXiv preprint arXiv:1801.10233, (2018).
|
||||
@ -97,6 +97,10 @@ Pair Styles :h1
|
||||
pair_sph_rhosum
|
||||
pair_sph_taitwater
|
||||
pair_sph_taitwater_morris
|
||||
pair_spin_dmi
|
||||
pair_spin_exchange
|
||||
pair_spin_magelec
|
||||
pair_spin_neel
|
||||
pair_srp
|
||||
pair_sw
|
||||
pair_table
|
||||
|
||||
@ -305,9 +305,15 @@ string parameter is quoted.
|
||||
For the {format} style, an equal-style variable is specified along
|
||||
with a C-style format string, e.g. "%f" or "%.10g", which must be
|
||||
appropriate for formatting a double-precision floating-point value.
|
||||
This allows an equal-style variable to be formatted specifically for
|
||||
output as a string, e.g. by the "print"_print.html command, if the
|
||||
default format "%.15g" has too much precision.
|
||||
The default format is "%.15g". This variable style allows an
|
||||
equal-style variable to be formatted precisely when it is evaluated.
|
||||
|
||||
If you simply wish to print a variable value with desired precision to
|
||||
the screen or logfile via the "print"_print.html or "fix
|
||||
print"_fix_print.html commands, you can also do this by specifying an
|
||||
"immediate" variable with a trailing colon and format string, as part
|
||||
of the string argument of those commands. This is explained in
|
||||
"Section 3.2"_Section_commands.html#cmd_2.
|
||||
|
||||
For the {getenv} style, a single string is assigned to the variable
|
||||
which should be the name of an environment variable. When the
|
||||
|
||||
BIN
doc/utils/txt2html/txt2html
Executable file
BIN
doc/utils/txt2html/txt2html
Executable file
Binary file not shown.
53
examples/SPIN/bfo/in.spin.bfo
Normal file
53
examples/SPIN/bfo/in.spin.bfo
Normal file
@ -0,0 +1,53 @@
|
||||
# layer sc iron atoms (in the [001] plane) in bismuth oxide
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p f
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
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 spin/exchange 6.0 spin/magelec 4.5
|
||||
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
|
||||
pair_coeff * * spin/magelec magelec 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 precession/spin anisotropy 0.0000033 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 3 all nve/spin lattice no
|
||||
|
||||
timestep 0.0002
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 5000
|
||||
212
examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
Normal file
212
examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# layer sc iron atoms (in the [001] plane) in bismuth oxide
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p f
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice sc 3.96
|
||||
Lattice spacing in x,y,z = 3.96 3.96 3.96
|
||||
region box block 0.0 34.0 0.0 34.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 5780 atoms
|
||||
Time spent = 0.0013566 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for bfo
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
set group all spin/random 11 2.50
|
||||
5780 settings made for spin/random
|
||||
|
||||
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
|
||||
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
|
||||
pair_coeff * * spin/magelec magelec 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 precession/spin anisotropy 0.0000033 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 3 all nve/spin lattice no
|
||||
|
||||
timestep 0.0002
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.1
|
||||
ghost atom cutoff = 6.1
|
||||
binsize = 3.05, bins = 45 45 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair spin/magelec, perpetual, copy from (1)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes
|
||||
Step Time v_magnorm v_emag Temp TotEng
|
||||
0 0 0.010071723 -0.13298298 0 -0.12034311
|
||||
50 0.01 0.0098643821 -1.3898985 0 -1.3772103
|
||||
100 0.02 0.0096526211 -2.6381677 0 -2.6254222
|
||||
150 0.03 0.0094342235 -3.8784006 0 -3.8656019
|
||||
200 0.04 0.0092074832 -5.111441 0 -5.0986001
|
||||
250 0.05 0.0089713115 -6.3380611 0 -6.3251904
|
||||
300 0.06 0.0087256081 -7.5587787 0 -7.5458894
|
||||
350 0.07 0.0084715548 -8.7738491 0 -8.7609521
|
||||
400 0.08 0.008211486 -9.9833855 0 -9.9704932
|
||||
450 0.09 0.0079483243 -11.18751 0 -11.174637
|
||||
500 0.1 0.0076849713 -12.386462 0 -12.37362
|
||||
550 0.11 0.007424064 -13.580633 0 -13.567832
|
||||
600 0.12 0.0071680699 -14.770519 0 -14.757759
|
||||
650 0.13 0.0069192726 -15.956579 0 -15.943853
|
||||
700 0.14 0.0066793495 -17.139049 0 -17.126343
|
||||
750 0.15 0.0064488038 -18.317803 0 -18.305099
|
||||
800 0.16 0.0062267571 -19.492336 0 -19.479616
|
||||
850 0.17 0.0060112235 -20.661925 0 -20.649176
|
||||
900 0.18 0.0057995251 -21.825931 0 -21.813141
|
||||
950 0.19 0.0055886511 -22.98413 0 -22.971297
|
||||
1000 0.2 0.0053757923 -24.136967 0 -24.124095
|
||||
1050 0.21 0.0051592263 -25.285621 0 -25.272717
|
||||
1100 0.22 0.0049391661 -26.431928 0 -26.419004
|
||||
1150 0.23 0.0047179149 -27.578212 0 -27.565281
|
||||
1200 0.24 0.0044991004 -28.727051 0 -28.714128
|
||||
1250 0.25 0.0042864034 -29.880967 0 -29.868062
|
||||
1300 0.26 0.0040824475 -31.042054 0 -31.029173
|
||||
1350 0.27 0.0038883007 -32.21165 0 -32.198795
|
||||
1400 0.28 0.0037036595 -33.390159 0 -33.377326
|
||||
1450 0.29 0.0035274815 -34.577121 0 -34.564302
|
||||
1500 0.3 0.0033587207 -35.771483 0 -35.758672
|
||||
1550 0.31 0.0031969501 -36.971996 0 -36.95919
|
||||
1600 0.32 0.0030429081 -38.177601 0 -38.164801
|
||||
1650 0.33 0.0028989804 -39.387757 0 -39.374962
|
||||
1700 0.34 0.0027692024 -40.602665 0 -40.589873
|
||||
1750 0.35 0.0026581403 -41.823341 0 -41.81054
|
||||
1800 0.36 0.0025686991 -43.05145 0 -43.038628
|
||||
1850 0.37 0.002500124 -44.288966 0 -44.276111
|
||||
1900 0.38 0.0024477804 -45.537752 0 -45.52486
|
||||
1950 0.39 0.0024050049 -46.799255 0 -46.786336
|
||||
2000 0.4 0.0023657031 -48.074388 0 -48.061466
|
||||
2050 0.41 0.0023260844 -49.363587 0 -49.350695
|
||||
2100 0.42 0.0022848329 -50.666866 0 -50.654039
|
||||
2150 0.43 0.0022419759 -51.983781 0 -51.971055
|
||||
2200 0.44 0.0021972506 -53.31336 0 -53.300764
|
||||
2250 0.45 0.0021488322 -54.654121 0 -54.641676
|
||||
2300 0.46 0.0020929483 -56.004207 0 -55.991918
|
||||
2350 0.47 0.0020244601 -57.361586 0 -57.349442
|
||||
2400 0.48 0.001938225 -58.72428 0 -58.712247
|
||||
2450 0.49 0.0018309419 -60.09064 0 -60.078671
|
||||
2500 0.5 0.0017030436 -61.459658 0 -61.447705
|
||||
2550 0.51 0.0015599449 -62.831213 0 -62.819237
|
||||
2600 0.52 0.0014117554 -64.206088 0 -64.194074
|
||||
2650 0.53 0.0012709942 -65.585701 0 -65.573657
|
||||
2700 0.54 0.0011490452 -66.971565 0 -66.959515
|
||||
2750 0.55 0.001053009 -68.364663 0 -68.352635
|
||||
2800 0.56 0.00098415327 -69.765002 0 -69.753017
|
||||
2850 0.57 0.00093809306 -71.171532 0 -71.159598
|
||||
2900 0.58 0.00090656933 -72.58234 0 -72.570459
|
||||
2950 0.59 0.00088069677 -73.994931 0 -73.983099
|
||||
3000 0.6 0.00085472643 -75.406507 0 -75.39472
|
||||
3050 0.61 0.00082842902 -76.814319 0 -76.802575
|
||||
3100 0.62 0.00080642618 -78.216074 0 -78.204373
|
||||
3150 0.63 0.00079463972 -79.610246 0 -79.598589
|
||||
3200 0.64 0.0007962304 -80.996103 0 -80.984494
|
||||
3250 0.65 0.00080980411 -82.37346 0 -82.361903
|
||||
3300 0.66 0.00083070982 -83.742356 0 -83.730855
|
||||
3350 0.67 0.00085389185 -85.102808 0 -85.091374
|
||||
3400 0.68 0.00087624091 -86.454619 0 -86.443259
|
||||
3450 0.69 0.00089741986 -87.797089 0 -87.785814
|
||||
3500 0.7 0.00091910796 -89.12875 0 -89.117567
|
||||
3550 0.71 0.00094318459 -90.447312 0 -90.436232
|
||||
3600 0.72 0.00096989367 -91.750008 0 -91.739046
|
||||
3650 0.73 0.00099713096 -93.034224 0 -93.023402
|
||||
3700 0.74 0.0010212995 -94.298186 0 -94.287529
|
||||
3750 0.75 0.0010391164 -95.5414 0 -95.530926
|
||||
3800 0.76 0.0010491462 -96.764626 0 -96.754338
|
||||
3850 0.77 0.0010521238 -97.969346 0 -97.95923
|
||||
3900 0.78 0.0010500324 -99.156875 0 -99.146899
|
||||
3950 0.79 0.0010447043 -100.32743 0 -100.31756
|
||||
4000 0.8 0.0010368986 -101.4796 0 -101.46978
|
||||
4050 0.81 0.0010263632 -102.61044 0 -102.60064
|
||||
4100 0.82 0.0010126933 -103.71619 0 -103.70639
|
||||
4150 0.83 0.00099631895 -104.79338 0 -104.78358
|
||||
4200 0.84 0.0009789075 -105.8398 0 -105.82998
|
||||
4250 0.85 0.00096287608 -106.85496 0 -106.84515
|
||||
4300 0.86 0.00095034023 -107.84011 0 -107.83029
|
||||
4350 0.87 0.00094219078 -108.7976 0 -108.78778
|
||||
4400 0.88 0.00093779428 -109.73016 0 -109.72031
|
||||
4450 0.89 0.0009354459 -110.63996 0 -110.63008
|
||||
4500 0.9 0.00093342614 -111.52805 0 -111.51812
|
||||
4550 0.91 0.0009311077 -112.39417 0 -112.38416
|
||||
4600 0.92 0.00092926689 -113.23706 0 -113.22697
|
||||
4650 0.93 0.00092921566 -114.05512 0 -114.04495
|
||||
4700 0.94 0.00093142598 -114.84701 0 -114.83675
|
||||
4750 0.95 0.00093479851 -115.61197 0 -115.60164
|
||||
4800 0.96 0.0009369799 -116.3499 0 -116.33951
|
||||
4850 0.97 0.00093516768 -117.06128 0 -117.05084
|
||||
4900 0.98 0.00092684411 -117.74695 0 -117.73645
|
||||
4950 0.99 0.00091046222 -118.40798 0 -118.39742
|
||||
5000 1 0.00088619957 -119.04554 0 -119.03492
|
||||
Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms
|
||||
|
||||
Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 24.227 | 24.227 | 24.227 | 0.0 | 18.88
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.081048 | 0.081048 | 0.081048 | 0.0 | 0.06
|
||||
Output | 39.796 | 39.796 | 39.796 | 0.0 | 31.02
|
||||
Modify | 64.112 | 64.112 | 64.112 | 0.0 | 49.97
|
||||
Other | | 0.08788 | | | 0.07
|
||||
|
||||
Nlocal: 5780 ave 5780 max 5780 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1065 ave 1065 max 1065 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 92480 ave 92480 max 92480 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 92480
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:02:08
|
||||
212
examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
Normal file
212
examples/SPIN/bfo/log.11May18.spin.bfo.g++.4
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# layer sc iron atoms (in the [001] plane) in bismuth oxide
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p f
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice sc 3.96
|
||||
Lattice spacing in x,y,z = 3.96 3.96 3.96
|
||||
region box block 0.0 34.0 0.0 34.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 5780 atoms
|
||||
Time spent = 0.000355959 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for bfo
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
set group all spin/random 11 2.50
|
||||
5780 settings made for spin/random
|
||||
|
||||
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
|
||||
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
|
||||
pair_coeff * * spin/magelec magelec 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 precession/spin anisotropy 0.0000033 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 3 all nve/spin lattice no
|
||||
|
||||
timestep 0.0002
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.1
|
||||
ghost atom cutoff = 6.1
|
||||
binsize = 3.05, bins = 45 45 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair spin/magelec, perpetual, copy from (1)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes
|
||||
Step Time v_magnorm v_emag Temp TotEng
|
||||
0 0 0.010071723 -0.13298298 0 -0.12034311
|
||||
50 0.01 0.0098643821 -1.3898985 0 -1.3772103
|
||||
100 0.02 0.009652621 -2.6381677 0 -2.6254222
|
||||
150 0.03 0.0094342234 -3.8784007 0 -3.8656019
|
||||
200 0.04 0.009207483 -5.1114411 0 -5.0986001
|
||||
250 0.05 0.0089713114 -6.3380611 0 -6.3251904
|
||||
300 0.06 0.0087256079 -7.5587787 0 -7.5458894
|
||||
350 0.07 0.0084715546 -8.7738491 0 -8.7609521
|
||||
400 0.08 0.0082114858 -9.9833855 0 -9.9704932
|
||||
450 0.09 0.0079483242 -11.18751 0 -11.174637
|
||||
500 0.1 0.0076849711 -12.386462 0 -12.37362
|
||||
550 0.11 0.0074240638 -13.580633 0 -13.567832
|
||||
600 0.12 0.0071680697 -14.770519 0 -14.757759
|
||||
650 0.13 0.0069192724 -15.956579 0 -15.943853
|
||||
700 0.14 0.0066793493 -17.139049 0 -17.126343
|
||||
750 0.15 0.0064488035 -18.317803 0 -18.305099
|
||||
800 0.16 0.0062267569 -19.492336 0 -19.479616
|
||||
850 0.17 0.0060112233 -20.661925 0 -20.649176
|
||||
900 0.18 0.005799525 -21.825931 0 -21.813141
|
||||
950 0.19 0.0055886511 -22.98413 0 -22.971297
|
||||
1000 0.2 0.0053757923 -24.136967 0 -24.124095
|
||||
1050 0.21 0.0051592265 -25.285621 0 -25.272717
|
||||
1100 0.22 0.0049391664 -26.431928 0 -26.419004
|
||||
1150 0.23 0.0047179153 -27.578212 0 -27.565281
|
||||
1200 0.24 0.0044991009 -28.727051 0 -28.714128
|
||||
1250 0.25 0.0042864039 -29.880967 0 -29.868062
|
||||
1300 0.26 0.004082448 -31.042054 0 -31.029174
|
||||
1350 0.27 0.0038883012 -32.21165 0 -32.198795
|
||||
1400 0.28 0.0037036599 -33.390159 0 -33.377326
|
||||
1450 0.29 0.0035274817 -34.577121 0 -34.564302
|
||||
1500 0.3 0.0033587208 -35.771483 0 -35.758672
|
||||
1550 0.31 0.0031969501 -36.971996 0 -36.95919
|
||||
1600 0.32 0.0030429079 -38.177601 0 -38.164801
|
||||
1650 0.33 0.0028989801 -39.387757 0 -39.374962
|
||||
1700 0.34 0.0027692022 -40.602666 0 -40.589873
|
||||
1750 0.35 0.0026581401 -41.823341 0 -41.81054
|
||||
1800 0.36 0.002568699 -43.05145 0 -43.038628
|
||||
1850 0.37 0.0025001242 -44.288966 0 -44.276111
|
||||
1900 0.38 0.0024477808 -45.537752 0 -45.52486
|
||||
1950 0.39 0.0024050056 -46.799255 0 -46.786336
|
||||
2000 0.4 0.002365704 -48.074388 0 -48.061466
|
||||
2050 0.41 0.0023260854 -49.363587 0 -49.350695
|
||||
2100 0.42 0.002284834 -50.666866 0 -50.654039
|
||||
2150 0.43 0.0022419771 -51.983781 0 -51.971055
|
||||
2200 0.44 0.0021972518 -53.31336 0 -53.300764
|
||||
2250 0.45 0.0021488333 -54.654121 0 -54.641676
|
||||
2300 0.46 0.0020929494 -56.004207 0 -55.991918
|
||||
2350 0.47 0.0020244612 -57.361586 0 -57.349441
|
||||
2400 0.48 0.0019382262 -58.72428 0 -58.712247
|
||||
2450 0.49 0.001830943 -60.090639 0 -60.078671
|
||||
2500 0.5 0.0017030446 -61.459658 0 -61.447704
|
||||
2550 0.51 0.0015599459 -62.831213 0 -62.819237
|
||||
2600 0.52 0.0014117562 -64.206088 0 -64.194074
|
||||
2650 0.53 0.001270995 -65.5857 0 -65.573657
|
||||
2700 0.54 0.001149046 -66.971565 0 -66.959515
|
||||
2750 0.55 0.0010530098 -68.364663 0 -68.352635
|
||||
2800 0.56 0.00098415418 -69.765002 0 -69.753017
|
||||
2850 0.57 0.00093809402 -71.171532 0 -71.159598
|
||||
2900 0.58 0.00090657031 -72.58234 0 -72.570459
|
||||
2950 0.59 0.00088069773 -73.994931 0 -73.983099
|
||||
3000 0.6 0.00085472731 -75.406507 0 -75.39472
|
||||
3050 0.61 0.00082842975 -76.814319 0 -76.802575
|
||||
3100 0.62 0.00080642669 -78.216074 0 -78.204373
|
||||
3150 0.63 0.00079464 -79.610246 0 -79.59859
|
||||
3200 0.64 0.00079623049 -80.996103 0 -80.984494
|
||||
3250 0.65 0.00080980416 -82.373461 0 -82.361903
|
||||
3300 0.66 0.00083070997 -83.742356 0 -83.730856
|
||||
3350 0.67 0.00085389223 -85.102809 0 -85.091374
|
||||
3400 0.68 0.00087624159 -86.454619 0 -86.44326
|
||||
3450 0.69 0.00089742086 -87.79709 0 -87.785815
|
||||
3500 0.7 0.00091910931 -89.12875 0 -89.117568
|
||||
3550 0.71 0.00094318635 -90.447312 0 -90.436233
|
||||
3600 0.72 0.00096989594 -91.750008 0 -91.739047
|
||||
3650 0.73 0.00099713386 -93.034224 0 -93.023403
|
||||
3700 0.74 0.0010213031 -94.298186 0 -94.287529
|
||||
3750 0.75 0.0010391209 -95.541401 0 -95.530926
|
||||
3800 0.76 0.0010491514 -96.764626 0 -96.754339
|
||||
3850 0.77 0.0010521296 -97.969347 0 -97.959231
|
||||
3900 0.78 0.0010500386 -99.156876 0 -99.146899
|
||||
3950 0.79 0.0010447106 -100.32743 0 -100.31756
|
||||
4000 0.8 0.0010369046 -101.4796 0 -101.46978
|
||||
4050 0.81 0.0010263688 -102.61044 0 -102.60064
|
||||
4100 0.82 0.0010126985 -103.71619 0 -103.70639
|
||||
4150 0.83 0.00099632366 -104.79338 0 -104.78358
|
||||
4200 0.84 0.00097891183 -105.8398 0 -105.82998
|
||||
4250 0.85 0.00096288003 -106.85496 0 -106.84515
|
||||
4300 0.86 0.00095034371 -107.84011 0 -107.83029
|
||||
4350 0.87 0.00094219371 -108.7976 0 -108.78778
|
||||
4400 0.88 0.00093779663 -109.73016 0 -109.72031
|
||||
4450 0.89 0.00093544766 -110.63996 0 -110.63008
|
||||
4500 0.9 0.00093342739 -111.52805 0 -111.51812
|
||||
4550 0.91 0.00093110855 -112.39417 0 -112.38416
|
||||
4600 0.92 0.00092926746 -113.23706 0 -113.22697
|
||||
4650 0.93 0.00092921608 -114.05512 0 -114.04495
|
||||
4700 0.94 0.0009314263 -114.84701 0 -114.83675
|
||||
4750 0.95 0.0009347987 -115.61197 0 -115.60164
|
||||
4800 0.96 0.00093697985 -116.3499 0 -116.33951
|
||||
4850 0.97 0.00093516726 -117.06128 0 -117.05084
|
||||
4900 0.98 0.00092684316 -117.74695 0 -117.73645
|
||||
4950 0.99 0.00091046061 -118.40798 0 -118.39742
|
||||
5000 1 0.00088619727 -119.04554 0 -119.03492
|
||||
Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms
|
||||
|
||||
Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.2804 | 6.3487 | 6.4569 | 2.7 | 17.09
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.15385 | 0.27957 | 0.36215 | 14.6 | 0.75
|
||||
Output | 10.573 | 10.784 | 10.994 | 4.8 | 29.03
|
||||
Modify | 19.48 | 19.707 | 19.925 | 3.7 | 53.06
|
||||
Other | | 0.02255 | | | 0.06
|
||||
|
||||
Nlocal: 1445 ave 1445 max 1445 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 555 ave 555 max 555 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 23120 ave 23120 max 23120 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 92480
|
||||
Ave neighs/atom = 16
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:37
|
||||
6006
examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy
Normal file
6006
examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,5 @@
|
||||
2.503 0.01476
|
||||
3.54 0.001497
|
||||
4.33 0.001578
|
||||
5.01 -0.001224
|
||||
5.597 0.000354
|
||||
32
examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py
Normal file
32
examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py
Normal file
@ -0,0 +1,32 @@
|
||||
#Program fitting the exchange interaction
|
||||
#Model curve: Bethe-Slater function
|
||||
import numpy as np, pylab, tkinter
|
||||
import matplotlib.pyplot as plt
|
||||
from scipy.optimize import curve_fit
|
||||
from decimal import *
|
||||
|
||||
print("Loop begin")
|
||||
|
||||
#Definition of the Bethe-Slater function
|
||||
def func(x,a,b,c):
|
||||
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
|
||||
|
||||
#Exchange coeff table (data to fit)
|
||||
rdata, Jdata = np.loadtxt('exchange_fcc_cobalt.dat', usecols=(0,1), unpack=True)
|
||||
plt.plot(rdata, Jdata, 'b-', label='data')
|
||||
|
||||
#Perform the fit
|
||||
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
|
||||
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
|
||||
|
||||
#Print the fitted params
|
||||
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
|
||||
|
||||
#Ploting the result
|
||||
plt.xlabel('r_ij')
|
||||
pylab.xlim([0,6.5])
|
||||
plt.ylabel('J_ij')
|
||||
plt.legend()
|
||||
plt.show()
|
||||
|
||||
print("Loop end")
|
||||
63
examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
Normal file
63
examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
Normal file
@ -0,0 +1,63 @@
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
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 fcc cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
thermo_style custom f_1
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
|
||||
thermo 50
|
||||
|
||||
#compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 1000
|
||||
142
examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
Normal file
142
examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
Normal file
@ -0,0 +1,142 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
Lattice spacing in x,y,z = 3.54 3.54 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000651121 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for fcc cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
500 settings made for spin
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
thermo_style custom f_1
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
|
||||
thermo 50
|
||||
|
||||
#compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.59954
|
||||
ghost atom cutoff = 6.59954
|
||||
binsize = 3.29977, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes
|
||||
Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
|
||||
0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636
|
||||
50 0.005 0.049785486 0 0 1 -187.94112 95.094679 -2372.4636
|
||||
100 0.01 0.049785486 0 0 1 -187.94071 81.578321 -2372.4636
|
||||
150 0.015 0.049785486 0 0 1 -187.93912 62.802727 -2372.4636
|
||||
200 0.02 0.049785486 0 0 1 -187.93551 43.35108 -2372.4636
|
||||
250 0.025 0.049785486 0 0 1 -187.92942 27.749821 -2372.4636
|
||||
300 0.03 0.049785486 0 0 1 -187.92118 19.149389 -2372.4636
|
||||
350 0.035 0.049785486 0 0 1 -187.91199 18.453387 -2372.4636
|
||||
400 0.04 0.049785486 0 0 1 -187.90364 24.249423 -2372.4636
|
||||
450 0.045 0.049785486 0 0 1 -187.89806 33.548008 -2372.4636
|
||||
500 0.05 0.049785486 0 0 1 -187.89668 42.973172 -2372.4636
|
||||
550 0.055 0.049785486 0 0 1 -187.9 49.902539 -2372.4636
|
||||
600 0.06 0.049785486 0 0 1 -187.90735 53.166772 -2372.4636
|
||||
650 0.065 0.049785486 0 0 1 -187.91706 53.153416 -2372.4636
|
||||
700 0.07 0.049785486 0 0 1 -187.92692 51.377187 -2372.4636
|
||||
750 0.075 0.049785486 0 0 1 -187.9348 49.725449 -2372.4636
|
||||
800 0.08 0.049785486 0 0 1 -187.93921 49.663576 -2372.4636
|
||||
850 0.085 0.049785486 0 0 1 -187.93974 51.681567 -2372.4636
|
||||
900 0.09 0.049785486 0 0 1 -187.937 55.166554 -2372.4636
|
||||
950 0.095 0.049785486 0 0 1 -187.93239 58.718232 -2372.4636
|
||||
1000 0.1 0.049785486 0 0 1 -187.92755 60.75567 -2372.4636
|
||||
Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.142 | 2.142 | 2.142 | 0.0 | 51.86
|
||||
Neigh | 0.0094573 | 0.0094573 | 0.0094573 | 0.0 | 0.23
|
||||
Comm | 0.023293 | 0.023293 | 0.023293 | 0.0 | 0.56
|
||||
Output | 0.00031972 | 0.00031972 | 0.00031972 | 0.0 | 0.01
|
||||
Modify | 1.9488 | 1.9488 | 1.9488 | 0.0 | 47.18
|
||||
Other | | 0.006488 | | | 0.16
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 24065 ave 24065 max 24065 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 48130 ave 48130 max 48130 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48130
|
||||
Ave neighs/atom = 96.26
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
142
examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
Normal file
142
examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
Normal file
@ -0,0 +1,142 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
Lattice spacing in x,y,z = 3.54 3.54 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000240088 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for fcc cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
500 settings made for spin
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
thermo_style custom f_1
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
|
||||
thermo 50
|
||||
|
||||
#compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.59954
|
||||
ghost atom cutoff = 6.59954
|
||||
binsize = 3.29977, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes
|
||||
Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
|
||||
0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636
|
||||
50 0.005 0.049785486 0 0 1 -187.94101 95.174807 -2372.4636
|
||||
100 0.01 0.049785486 0 0 1 -187.94029 81.854304 -2372.4636
|
||||
150 0.015 0.049785486 0 0 1 -187.93834 63.270938 -2372.4636
|
||||
200 0.02 0.049785486 0 0 1 -187.93446 43.867262 -2372.4636
|
||||
250 0.025 0.049785486 0 0 1 -187.92831 28.075261 -2372.4636
|
||||
300 0.03 0.049785486 0 0 1 -187.92031 19.046222 -2372.4636
|
||||
350 0.035 0.049785486 0 0 1 -187.91161 17.79071 -2372.4636
|
||||
400 0.04 0.049785486 0 0 1 -187.9039 23.079994 -2372.4636
|
||||
450 0.045 0.049785486 0 0 1 -187.89895 32.127316 -2372.4636
|
||||
500 0.05 0.049785486 0 0 1 -187.89801 41.709644 -2372.4636
|
||||
550 0.055 0.049785486 0 0 1 -187.90146 49.246292 -2372.4636
|
||||
600 0.06 0.049785486 0 0 1 -187.90859 53.465535 -2372.4636
|
||||
650 0.065 0.049785486 0 0 1 -187.91778 54.522857 -2372.4636
|
||||
700 0.07 0.049785486 0 0 1 -187.9269 53.635521 -2372.4636
|
||||
750 0.075 0.049785486 0 0 1 -187.93396 52.419678 -2372.4636
|
||||
800 0.08 0.049785486 0 0 1 -187.9376 52.176558 -2372.4636
|
||||
850 0.085 0.049785486 0 0 1 -187.93744 53.380592 -2372.4636
|
||||
900 0.09 0.049785486 0 0 1 -187.93412 55.551378 -2372.4636
|
||||
950 0.095 0.049785486 0 0 1 -187.92902 57.540047 -2372.4636
|
||||
1000 0.1 0.049785486 0 0 1 -187.92378 58.088674 -2372.4636
|
||||
Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.54717 | 0.57392 | 0.58784 | 2.1 | 33.48
|
||||
Neigh | 0.0023484 | 0.0025793 | 0.0026793 | 0.3 | 0.15
|
||||
Comm | 0.058548 | 0.073335 | 0.10006 | 5.9 | 4.28
|
||||
Output | 0.00042272 | 0.00079203 | 0.0018559 | 0.0 | 0.05
|
||||
Modify | 1.0577 | 1.0611 | 1.0625 | 0.2 | 61.90
|
||||
Other | | 0.00239 | | | 0.14
|
||||
|
||||
Nlocal: 125 ave 133 max 116 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 1099 ave 1108 max 1091 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Neighs: 6032.5 ave 6417 max 5489 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
FullNghs: 12065 ave 13062 max 10970 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
|
||||
Total # of neighbors = 48260
|
||||
Ave neighs/atom = 96.52
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
1
examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy
Symbolic link
1
examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../cobalt_fcc/Co_PurjaPun_2012.eam.alloy
|
||||
32
examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py
Normal file
32
examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py
Normal file
@ -0,0 +1,32 @@
|
||||
#Program fitting the exchange interaction
|
||||
#Model curve: Bethe-Slater function
|
||||
import numpy as np, pylab, tkinter
|
||||
import matplotlib.pyplot as plt
|
||||
from scipy.optimize import curve_fit
|
||||
from decimal import *
|
||||
|
||||
print("Loop begin")
|
||||
|
||||
#Definition of the Bethe-Slater function
|
||||
def func(x,a,b,c):
|
||||
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
|
||||
|
||||
#Exchange coeff table (data to fit)
|
||||
rdata, Jdata = np.loadtxt('exchange_hcp_co.dat', usecols=(0,1), unpack=True)
|
||||
plt.plot(rdata, Jdata, 'b-', label='data')
|
||||
|
||||
#Perform the fit
|
||||
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
|
||||
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
|
||||
|
||||
#Print the fitted params
|
||||
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
|
||||
|
||||
#Ploting the result
|
||||
plt.xlabel('r_ij')
|
||||
pylab.xlim([0,6.5])
|
||||
plt.ylabel('J_ij')
|
||||
plt.legend()
|
||||
plt.show()
|
||||
|
||||
print("Loop end")
|
||||
@ -0,0 +1,9 @@
|
||||
2.25569176882662 73.37931034482759
|
||||
2.3817863397548162 47.99999999999999
|
||||
2.4518388791593697 34.39080459770115
|
||||
2.507880910683012 31.816091954022987
|
||||
2.5359019264448337 28.137931034482747
|
||||
2.5779334500875657 25.011494252873554
|
||||
2.6339754816112086 19.126436781609186
|
||||
2.760070052539404 13.241379310344826
|
||||
3.5446584938704033 6.068965517241367
|
||||
59
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
Normal file
59
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
Normal file
@ -0,0 +1,59 @@
|
||||
# hcp cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
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 hcp cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 3 all nve/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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 10
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 2000
|
||||
318
examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
Normal file
318
examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
Normal file
@ -0,0 +1,318 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# hcp cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000801802 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for hcp cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
500 settings made for spin
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 3 all nve/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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 10
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.59954
|
||||
ghost atom cutoff = 6.59954
|
||||
binsize = 3.29977, bins = 4 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes
|
||||
Step Time v_magnorm v_emag Temp TotEng
|
||||
0 0 1 -187.29499 100.00543 -2375.8943
|
||||
10 0.001 1 -187.29714 99.845593 -2375.8943
|
||||
20 0.002 1 -187.30356 99.367234 -2375.8943
|
||||
30 0.003 1 -187.31419 98.573996 -2375.8943
|
||||
40 0.004 1 -187.32896 97.472027 -2375.8943
|
||||
50 0.005 1 -187.34772 96.069944 -2375.8943
|
||||
60 0.006 1 -187.37032 94.378764 -2375.8943
|
||||
70 0.007 1 -187.39656 92.411827 -2375.8943
|
||||
80 0.008 1 -187.4262 90.184697 -2375.8943
|
||||
90 0.009 1 -187.459 87.715037 -2375.8943
|
||||
100 0.01 1 -187.49466 85.022479 -2375.8943
|
||||
110 0.011 1 -187.53289 82.128462 -2375.8943
|
||||
120 0.012 1 -187.57334 79.05606 -2375.8943
|
||||
130 0.013 1 -187.61568 75.82979 -2375.8943
|
||||
140 0.014 1 -187.65953 72.475403 -2375.8943
|
||||
150 0.015 1 -187.70453 69.019658 -2375.8943
|
||||
160 0.016 1 -187.75028 65.490086 -2375.8943
|
||||
170 0.017 1 -187.79642 61.914735 -2375.8943
|
||||
180 0.018 1 -187.84254 58.321911 -2375.8943
|
||||
190 0.019 1 -187.88828 54.739907 -2375.8943
|
||||
200 0.02 1 -187.93324 51.196728 -2375.8943
|
||||
210 0.021 1 -187.97708 47.719812 -2375.8943
|
||||
220 0.022 1 -188.01947 44.335762 -2375.8943
|
||||
230 0.023 1 -188.06003 41.07007 -2375.8943
|
||||
240 0.024 1 -188.09853 37.946852 -2375.8944
|
||||
250 0.025 1 -188.13457 34.988599 -2375.8944
|
||||
260 0.026 1 -188.16795 32.215943 -2375.8944
|
||||
270 0.027 1 -188.19851 29.647465 -2375.8944
|
||||
280 0.028 1 -188.22593 27.299481 -2375.8944
|
||||
290 0.029 1 -188.25011 25.185896 -2375.8944
|
||||
300 0.03 1 -188.27095 23.318075 -2375.8945
|
||||
310 0.031 1 -188.2883 21.70475 -2375.8945
|
||||
320 0.032 1 -188.30213 20.35194 -2375.8945
|
||||
330 0.033 1 -188.31251 19.262946 -2375.8945
|
||||
340 0.034 1 -188.31928 18.438347 -2375.8945
|
||||
350 0.035 1 -188.32258 17.876036 -2375.8945
|
||||
360 0.036 1 -188.32249 17.571322 -2375.8945
|
||||
370 0.037 1 -188.31913 17.517032 -2375.8945
|
||||
380 0.038 1 -188.31264 17.703653 -2375.8945
|
||||
390 0.039 1 -188.30321 18.119513 -2375.8945
|
||||
400 0.04 1 -188.29102 18.750969 -2375.8945
|
||||
410 0.041 1 -188.2763 19.582631 -2375.8945
|
||||
420 0.042 1 -188.25929 20.597597 -2375.8945
|
||||
430 0.043 1 -188.24025 21.777699 -2375.8945
|
||||
440 0.044 1 -188.21945 23.103765 -2375.8945
|
||||
450 0.045 1 -188.19719 24.555878 -2375.8946
|
||||
460 0.046 1 -188.17368 26.113643 -2375.8946
|
||||
470 0.047 1 -188.1493 27.756439 -2375.8946
|
||||
480 0.048 1 -188.12429 29.463677 -2375.8946
|
||||
490 0.049 1 -188.09895 31.21504 -2375.8946
|
||||
500 0.05 1 -188.07354 32.990713 -2375.8946
|
||||
510 0.051 1 -188.04832 34.771601 -2375.8945
|
||||
520 0.052 1 -188.02358 36.539517 -2375.8945
|
||||
530 0.053 1 -187.99951 38.27736 -2375.8945
|
||||
540 0.054 1 -187.97636 39.969275 -2375.8945
|
||||
550 0.055 1 -187.95437 41.600775 -2375.8945
|
||||
560 0.056 1 -187.93364 43.158863 -2375.8944
|
||||
570 0.057 1 -187.9144 44.632119 -2375.8944
|
||||
580 0.058 1 -187.89669 46.010765 -2375.8944
|
||||
590 0.059 1 -187.88074 47.286714 -2375.8944
|
||||
600 0.06 1 -187.86658 48.453573 -2375.8944
|
||||
610 0.061 1 -187.85422 49.506668 -2375.8943
|
||||
620 0.062 1 -187.84377 50.443021 -2375.8943
|
||||
630 0.063 1 -187.8352 51.261297 -2375.8943
|
||||
640 0.064 1 -187.8285 51.961764 -2375.8943
|
||||
650 0.065 1 -187.8236 52.54622 -2375.8943
|
||||
660 0.066 1 -187.8205 53.017899 -2375.8943
|
||||
670 0.067 1 -187.81909 53.381374 -2375.8943
|
||||
680 0.068 1 -187.81926 53.64244 -2375.8943
|
||||
690 0.069 1 -187.82092 53.807997 -2375.8943
|
||||
700 0.07 1 -187.82391 53.885909 -2375.8943
|
||||
710 0.071 1 -187.82814 53.884865 -2375.8943
|
||||
720 0.072 1 -187.83339 53.814238 -2375.8943
|
||||
730 0.073 1 -187.83952 53.68392 -2375.8943
|
||||
740 0.074 1 -187.84635 53.504185 -2375.8943
|
||||
750 0.075 1 -187.85375 53.285525 -2375.8943
|
||||
760 0.076 1 -187.86153 53.038494 -2375.8943
|
||||
770 0.077 1 -187.86952 52.773567 -2375.8943
|
||||
780 0.078 1 -187.87758 52.500994 -2375.8943
|
||||
790 0.079 1 -187.88549 52.230655 -2375.8943
|
||||
800 0.08 1 -187.89313 51.971933 -2375.8943
|
||||
810 0.081 1 -187.90035 51.733593 -2375.8943
|
||||
820 0.082 1 -187.90702 51.523671 -2375.8943
|
||||
830 0.083 1 -187.91302 51.349376 -2375.8943
|
||||
840 0.084 1 -187.91824 51.217006 -2375.8943
|
||||
850 0.085 1 -187.9226 51.131875 -2375.8943
|
||||
860 0.086 1 -187.92602 51.098259 -2375.8943
|
||||
870 0.087 1 -187.92844 51.119356 -2375.8943
|
||||
880 0.088 1 -187.92979 51.197261 -2375.8943
|
||||
890 0.089 1 -187.93011 51.332955 -2375.8943
|
||||
900 0.09 1 -187.92937 51.526314 -2375.8943
|
||||
910 0.091 1 -187.92757 51.77613 -2375.8943
|
||||
920 0.092 1 -187.92475 52.080145 -2375.8943
|
||||
930 0.093 1 -187.92096 52.435106 -2375.8943
|
||||
940 0.094 1 -187.91624 52.836825 -2375.8943
|
||||
950 0.095 1 -187.91068 53.280251 -2375.8943
|
||||
960 0.096 1 -187.90435 53.759559 -2375.8943
|
||||
970 0.097 1 -187.89734 54.268246 -2375.8943
|
||||
980 0.098 1 -187.88981 54.799223 -2375.8943
|
||||
990 0.099 1 -187.88185 55.344928 -2375.8943
|
||||
1000 0.1 1 -187.87357 55.897438 -2375.8943
|
||||
1010 0.101 1 -187.86511 56.448585 -2375.8943
|
||||
1020 0.102 1 -187.8566 56.990069 -2375.8943
|
||||
1030 0.103 1 -187.84817 57.513575 -2375.8943
|
||||
1040 0.104 1 -187.83995 58.010887 -2375.8943
|
||||
1050 0.105 1 -187.83208 58.474004 -2375.8943
|
||||
1060 0.106 1 -187.8247 58.89524 -2375.8943
|
||||
1070 0.107 1 -187.81789 59.267328 -2375.8943
|
||||
1080 0.108 1 -187.81177 59.583518 -2375.8943
|
||||
1090 0.109 1 -187.80646 59.837665 -2375.8943
|
||||
1100 0.11 1 -187.80204 60.024306 -2375.8943
|
||||
1110 0.111 1 -187.79861 60.138734 -2375.8943
|
||||
1120 0.112 1 -187.79625 60.177056 -2375.8943
|
||||
1130 0.113 1 -187.79497 60.136244 -2375.8943
|
||||
1140 0.114 1 -187.79485 60.014176 -2375.8943
|
||||
1150 0.115 1 -187.7959 59.809665 -2375.8943
|
||||
1160 0.116 1 -187.79811 59.52248 -2375.8943
|
||||
1170 0.117 1 -187.80157 59.153353 -2375.8943
|
||||
1180 0.118 1 -187.80618 58.703971 -2375.8943
|
||||
1190 0.119 1 -187.81193 58.176956 -2375.8943
|
||||
1200 0.12 1 -187.81879 57.575849 -2375.8943
|
||||
1210 0.121 1 -187.82668 56.905072 -2375.8943
|
||||
1220 0.122 1 -187.83554 56.169878 -2375.8943
|
||||
1230 0.123 1 -187.84528 55.376297 -2375.8943
|
||||
1240 0.124 1 -187.85581 54.53107 -2375.8943
|
||||
1250 0.125 1 -187.86702 53.641573 -2375.8943
|
||||
1260 0.126 1 -187.8788 52.715739 -2375.8943
|
||||
1270 0.127 1 -187.89103 51.761969 -2375.8943
|
||||
1280 0.128 1 -187.90358 50.789036 -2375.8943
|
||||
1290 0.129 1 -187.91632 49.805988 -2375.8943
|
||||
1300 0.13 1 -187.92911 48.822045 -2375.8943
|
||||
1310 0.131 1 -187.94182 47.846491 -2375.8943
|
||||
1320 0.132 1 -187.95428 46.888574 -2375.8943
|
||||
1330 0.133 1 -187.96643 45.957394 -2375.8943
|
||||
1340 0.134 1 -187.9781 45.061794 -2375.8943
|
||||
1350 0.135 1 -187.9892 44.210263 -2375.8943
|
||||
1360 0.136 1 -187.99955 43.410832 -2375.8943
|
||||
1370 0.137 1 -188.00907 42.670979 -2375.8943
|
||||
1380 0.138 1 -188.01767 41.997547 -2375.8943
|
||||
1390 0.139 1 -188.02525 41.396655 -2375.8943
|
||||
1400 0.14 1 -188.03177 40.873631 -2375.8944
|
||||
1410 0.141 1 -188.03711 40.432952 -2375.8944
|
||||
1420 0.142 1 -188.04124 40.078172 -2375.8944
|
||||
1430 0.143 1 -188.04413 39.811902 -2375.8944
|
||||
1440 0.144 1 -188.04575 39.635775 -2375.8944
|
||||
1450 0.145 1 -188.04607 39.550435 -2375.8943
|
||||
1460 0.146 1 -188.04515 39.555512 -2375.8943
|
||||
1470 0.147 1 -188.04298 39.649651 -2375.8943
|
||||
1480 0.148 1 -188.03961 39.830523 -2375.8943
|
||||
1490 0.149 1 -188.03508 40.094865 -2375.8943
|
||||
1500 0.15 1 -188.02944 40.438519 -2375.8943
|
||||
1510 0.151 1 -188.02275 40.856491 -2375.8943
|
||||
1520 0.152 1 -188.01515 41.343019 -2375.8943
|
||||
1530 0.153 1 -188.00671 41.891643 -2375.8943
|
||||
1540 0.154 1 -187.99753 42.495295 -2375.8943
|
||||
1550 0.155 1 -187.98772 43.14639 -2375.8943
|
||||
1560 0.156 1 -187.9774 43.836918 -2375.8943
|
||||
1570 0.157 1 -187.9667 44.558553 -2375.8943
|
||||
1580 0.158 1 -187.95576 45.302751 -2375.8943
|
||||
1590 0.159 1 -187.94466 46.060862 -2375.8943
|
||||
1600 0.16 1 -187.93356 46.824226 -2375.8943
|
||||
1610 0.161 1 -187.92257 47.584289 -2375.8943
|
||||
1620 0.162 1 -187.91183 48.332703 -2375.8943
|
||||
1630 0.163 1 -187.90145 49.061422 -2375.8943
|
||||
1640 0.164 1 -187.89155 49.762798 -2375.8943
|
||||
1650 0.165 1 -187.88222 50.429671 -2375.8943
|
||||
1660 0.166 1 -187.87357 51.055445 -2375.8943
|
||||
1670 0.167 1 -187.86569 51.634167 -2375.8943
|
||||
1680 0.168 1 -187.85864 52.160588 -2375.8943
|
||||
1690 0.169 1 -187.85249 52.630219 -2375.8943
|
||||
1700 0.17 1 -187.8473 53.039377 -2375.8943
|
||||
1710 0.171 1 -187.84311 53.385221 -2375.8943
|
||||
1720 0.172 1 -187.83994 53.665778 -2375.8943
|
||||
1730 0.173 1 -187.83781 53.879954 -2375.8943
|
||||
1740 0.174 1 -187.83671 54.027539 -2375.8943
|
||||
1750 0.175 1 -187.83663 54.109201 -2375.8943
|
||||
1760 0.176 1 -187.83753 54.126472 -2375.8943
|
||||
1770 0.177 1 -187.83941 54.081708 -2375.8943
|
||||
1780 0.178 1 -187.8422 53.97806 -2375.8943
|
||||
1790 0.179 1 -187.84584 53.819424 -2375.8943
|
||||
1800 0.18 1 -187.85025 53.610389 -2375.8943
|
||||
1810 0.181 1 -187.85535 53.356163 -2375.8943
|
||||
1820 0.182 1 -187.86105 53.06251 -2375.8943
|
||||
1830 0.183 1 -187.86723 52.735671 -2375.8943
|
||||
1840 0.184 1 -187.87384 52.382262 -2375.8943
|
||||
1850 0.185 1 -187.88075 52.009201 -2375.8943
|
||||
1860 0.186 1 -187.88784 51.623613 -2375.8943
|
||||
1870 0.187 1 -187.89501 51.232726 -2375.8943
|
||||
1880 0.188 1 -187.90214 50.843782 -2375.8943
|
||||
1890 0.189 1 -187.90912 50.463929 -2375.8943
|
||||
1900 0.19 1 -187.91585 50.100133 -2375.8943
|
||||
1910 0.191 1 -187.92222 49.759075 -2375.8943
|
||||
1920 0.192 1 -187.92814 49.447064 -2375.8943
|
||||
1930 0.193 1 -187.93351 49.169949 -2375.8943
|
||||
1940 0.194 1 -187.93826 48.933036 -2375.8943
|
||||
1950 0.195 1 -187.94232 48.741013 -2375.8943
|
||||
1960 0.196 1 -187.94561 48.597888 -2375.8943
|
||||
1970 0.197 1 -187.94809 48.506926 -2375.8943
|
||||
1980 0.198 1 -187.94972 48.470605 -2375.8943
|
||||
1990 0.199 1 -187.95047 48.490576 -2375.8943
|
||||
2000 0.2 1 -187.95033 48.567643 -2375.8943
|
||||
Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms
|
||||
|
||||
Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.9958 | 4.9958 | 4.9958 | 0.0 | 47.40
|
||||
Neigh | 0.020741 | 0.020741 | 0.020741 | 0.0 | 0.20
|
||||
Comm | 0.05899 | 0.05899 | 0.05899 | 0.0 | 0.56
|
||||
Output | 1.1598 | 1.1598 | 1.1598 | 0.0 | 11.00
|
||||
Modify | 4.2885 | 4.2885 | 4.2885 | 0.0 | 40.69
|
||||
Other | | 0.01522 | | | 0.14
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2444 ave 2444 max 2444 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27041 ave 27041 max 27041 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 54082 ave 54082 max 54082 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 54082
|
||||
Ave neighs/atom = 108.164
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:10
|
||||
318
examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
Normal file
318
examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
Normal file
@ -0,0 +1,318 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# hcp cobalt in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000241518 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for hcp cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
#set group all spin/random 31 1.72
|
||||
set group all spin 1.72 0.0 0.0 1.0
|
||||
500 settings made for spin
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 3 all nve/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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 10
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.59954
|
||||
ghost atom cutoff = 6.59954
|
||||
binsize = 3.29977, bins = 4 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes
|
||||
Step Time v_magnorm v_emag Temp TotEng
|
||||
0 0 1 -187.29499 100.00543 -2375.8943
|
||||
10 0.001 1 -187.29721 99.841045 -2375.8943
|
||||
20 0.002 1 -187.30385 99.349208 -2375.8943
|
||||
30 0.003 1 -187.31485 98.533905 -2375.8943
|
||||
40 0.004 1 -187.33011 97.401749 -2375.8943
|
||||
50 0.005 1 -187.34949 95.961938 -2375.8943
|
||||
60 0.006 1 -187.37283 94.22618 -2375.8943
|
||||
70 0.007 1 -187.39992 92.208606 -2375.8943
|
||||
80 0.008 1 -187.43051 89.92566 -2375.8943
|
||||
90 0.009 1 -187.46434 87.39597 -2375.8943
|
||||
100 0.01 1 -187.5011 84.640195 -2375.8943
|
||||
110 0.011 1 -187.54047 81.680862 -2375.8943
|
||||
120 0.012 1 -187.5821 78.542172 -2375.8943
|
||||
130 0.013 1 -187.62564 75.249797 -2375.8943
|
||||
140 0.014 1 -187.67069 71.830656 -2375.8943
|
||||
150 0.015 1 -187.71686 68.312673 -2375.8943
|
||||
160 0.016 1 -187.76377 64.724523 -2375.8943
|
||||
170 0.017 1 -187.81099 61.095365 -2375.8943
|
||||
180 0.018 1 -187.85814 57.454566 -2375.8943
|
||||
190 0.019 1 -187.90481 53.831412 -2375.8943
|
||||
200 0.02 1 -187.95061 50.254822 -2375.8943
|
||||
210 0.021 1 -187.99517 46.753056 -2375.8943
|
||||
220 0.022 1 -188.03812 43.353428 -2375.8943
|
||||
230 0.023 1 -188.07913 40.082023 -2375.8943
|
||||
240 0.024 1 -188.11787 36.963429 -2375.8943
|
||||
250 0.025 1 -188.15409 34.020481 -2375.8943
|
||||
260 0.026 1 -188.1875 31.27403 -2375.8943
|
||||
270 0.027 1 -188.21782 28.74271 -2375.8943
|
||||
280 0.028 1 -188.2449 26.44276 -2375.8943
|
||||
290 0.029 1 -188.26857 24.387875 -2375.8943
|
||||
300 0.03 1 -188.28877 22.589076 -2375.8944
|
||||
310 0.031 1 -188.30529 21.054615 -2375.8944
|
||||
320 0.032 1 -188.31814 19.789913 -2375.8944
|
||||
330 0.033 1 -188.3273 18.797563 -2375.8944
|
||||
340 0.034 1 -188.33284 18.077336 -2375.8944
|
||||
350 0.035 1 -188.33478 17.626237 -2375.8945
|
||||
360 0.036 1 -188.33319 17.438611 -2375.8945
|
||||
370 0.037 1 -188.32824 17.506247 -2375.8945
|
||||
380 0.038 1 -188.32007 17.818564 -2375.8945
|
||||
390 0.039 1 -188.30888 18.362769 -2375.8945
|
||||
400 0.04 1 -188.2949 19.124086 -2375.8945
|
||||
410 0.041 1 -188.27837 20.085983 -2375.8945
|
||||
420 0.042 1 -188.25957 21.230423 -2375.8945
|
||||
430 0.043 1 -188.23868 22.538112 -2375.8945
|
||||
440 0.044 1 -188.21604 23.988778 -2375.8945
|
||||
450 0.045 1 -188.19195 25.561447 -2375.8945
|
||||
460 0.046 1 -188.16672 27.234703 -2375.8945
|
||||
470 0.047 1 -188.14064 28.986964 -2375.8946
|
||||
480 0.048 1 -188.11402 30.796738 -2375.8946
|
||||
490 0.049 1 -188.08713 32.642869 -2375.8945
|
||||
500 0.05 1 -188.06032 34.504776 -2375.8945
|
||||
510 0.051 1 -188.03383 36.362662 -2375.8945
|
||||
520 0.052 1 -188.00793 38.197721 -2375.8945
|
||||
530 0.053 1 -187.98284 39.992314 -2375.8945
|
||||
540 0.054 1 -187.95884 41.730127 -2375.8945
|
||||
550 0.055 1 -187.93612 43.396298 -2375.8945
|
||||
560 0.056 1 -187.91489 44.97754 -2375.8945
|
||||
570 0.057 1 -187.89524 46.462224 -2375.8945
|
||||
580 0.058 1 -187.87735 47.840443 -2375.8945
|
||||
590 0.059 1 -187.8613 49.104064 -2375.8945
|
||||
600 0.06 1 -187.84719 50.246744 -2375.8945
|
||||
610 0.061 1 -187.83509 51.26393 -2375.8944
|
||||
620 0.062 1 -187.82506 52.152839 -2375.8944
|
||||
630 0.063 1 -187.81706 52.912413 -2375.8944
|
||||
640 0.064 1 -187.81109 53.543272 -2375.8944
|
||||
650 0.065 1 -187.80708 54.047636 -2375.8944
|
||||
660 0.066 1 -187.80499 54.429234 -2375.8944
|
||||
670 0.067 1 -187.8047 54.693202 -2375.8944
|
||||
680 0.068 1 -187.80613 54.845965 -2375.8944
|
||||
690 0.069 1 -187.80914 54.895106 -2375.8944
|
||||
700 0.07 1 -187.81356 54.849238 -2375.8944
|
||||
710 0.071 1 -187.81923 54.71786 -2375.8943
|
||||
720 0.072 1 -187.82608 54.511181 -2375.8943
|
||||
730 0.073 1 -187.83388 54.239987 -2375.8943
|
||||
740 0.074 1 -187.84244 53.91548 -2375.8943
|
||||
750 0.075 1 -187.85158 53.549112 -2375.8943
|
||||
760 0.076 1 -187.86112 53.152433 -2375.8943
|
||||
770 0.077 1 -187.87086 52.736925 -2375.8943
|
||||
780 0.078 1 -187.88063 52.313858 -2375.8943
|
||||
790 0.079 1 -187.89026 51.894138 -2375.8943
|
||||
800 0.08 1 -187.89958 51.488169 -2375.8943
|
||||
810 0.081 1 -187.90842 51.105725 -2375.8943
|
||||
820 0.082 1 -187.91663 50.755829 -2375.8943
|
||||
830 0.083 1 -187.92411 50.446651 -2375.8943
|
||||
840 0.084 1 -187.93071 50.185404 -2375.8943
|
||||
850 0.085 1 -187.93637 49.978262 -2375.8943
|
||||
860 0.086 1 -187.94099 49.830307 -2375.8943
|
||||
870 0.087 1 -187.9445 49.745473 -2375.8943
|
||||
880 0.088 1 -187.94685 49.726517 -2375.8943
|
||||
890 0.089 1 -187.94802 49.774999 -2375.8943
|
||||
900 0.09 1 -187.94799 49.891282 -2375.8943
|
||||
910 0.091 1 -187.94678 50.074549 -2375.8943
|
||||
920 0.092 1 -187.94441 50.322833 -2375.8943
|
||||
930 0.093 1 -187.94093 50.633063 -2375.8943
|
||||
940 0.094 1 -187.93639 51.001126 -2375.8943
|
||||
950 0.095 1 -187.93089 51.421938 -2375.8943
|
||||
960 0.096 1 -187.9245 51.889531 -2375.8943
|
||||
970 0.097 1 -187.91733 52.397148 -2375.8943
|
||||
980 0.098 1 -187.9095 52.937345 -2375.8943
|
||||
990 0.099 1 -187.90113 53.502108 -2375.8943
|
||||
1000 0.1 1 -187.89236 54.082966 -2375.8943
|
||||
1010 0.101 1 -187.88332 54.671115 -2375.8943
|
||||
1020 0.102 1 -187.87415 55.257545 -2375.8943
|
||||
1030 0.103 1 -187.86501 55.833162 -2375.8943
|
||||
1040 0.104 1 -187.85602 56.388915 -2375.8943
|
||||
1050 0.105 1 -187.84734 56.915918 -2375.8943
|
||||
1060 0.106 1 -187.83909 57.405575 -2375.8943
|
||||
1070 0.107 1 -187.83143 57.849686 -2375.8943
|
||||
1080 0.108 1 -187.82446 58.240564 -2375.8943
|
||||
1090 0.109 1 -187.8183 58.571132 -2375.8943
|
||||
1100 0.11 1 -187.81306 58.835016 -2375.8943
|
||||
1110 0.111 1 -187.80883 59.026633 -2375.8943
|
||||
1120 0.112 1 -187.8057 59.141258 -2375.8943
|
||||
1130 0.113 1 -187.80372 59.17509 -2375.8943
|
||||
1140 0.114 1 -187.80295 59.125305 -2375.8943
|
||||
1150 0.115 1 -187.80341 58.990092 -2375.8943
|
||||
1160 0.116 1 -187.80515 58.76868 -2375.8943
|
||||
1170 0.117 1 -187.80814 58.461352 -2375.8943
|
||||
1180 0.118 1 -187.81244 58.069457 -2375.8943
|
||||
1190 0.119 1 -187.81794 57.595377 -2375.8944
|
||||
1200 0.12 1 -187.82458 57.042514 -2375.8944
|
||||
1210 0.121 1 -187.83233 56.415256 -2375.8944
|
||||
1220 0.122 1 -187.84112 55.718931 -2375.8944
|
||||
1230 0.123 1 -187.85086 54.959744 -2375.8944
|
||||
1240 0.124 1 -187.86145 54.144707 -2375.8944
|
||||
1250 0.125 1 -187.87277 53.281562 -2375.8944
|
||||
1260 0.126 1 -187.88471 52.378686 -2375.8944
|
||||
1270 0.127 1 -187.89713 51.445 -2375.8944
|
||||
1280 0.128 1 -187.9099 50.489858 -2375.8944
|
||||
1290 0.129 1 -187.92288 49.522943 -2375.8944
|
||||
1300 0.13 1 -187.93591 48.554147 -2375.8944
|
||||
1310 0.131 1 -187.94886 47.593456 -2375.8944
|
||||
1320 0.132 1 -187.96157 46.650829 -2375.8944
|
||||
1330 0.133 1 -187.97391 45.736073 -2375.8944
|
||||
1340 0.134 1 -187.98573 44.858733 -2375.8944
|
||||
1350 0.135 1 -187.99691 44.027964 -2375.8944
|
||||
1360 0.136 1 -188.00731 43.252426 -2375.8944
|
||||
1370 0.137 1 -188.01678 42.540178 -2375.8943
|
||||
1380 0.138 1 -188.02529 41.898568 -2375.8943
|
||||
1390 0.139 1 -188.0327 41.334152 -2375.8943
|
||||
1400 0.14 1 -188.03894 40.852606 -2375.8943
|
||||
1410 0.141 1 -188.04396 40.45866 -2375.8944
|
||||
1420 0.142 1 -188.04768 40.156041 -2375.8944
|
||||
1430 0.143 1 -188.05007 39.947416 -2375.8944
|
||||
1440 0.144 1 -188.05107 39.834367 -2375.8944
|
||||
1450 0.145 1 -188.0507 39.817378 -2375.8944
|
||||
1460 0.146 1 -188.04898 39.895828 -2375.8944
|
||||
1470 0.147 1 -188.04595 40.068005 -2375.8945
|
||||
1480 0.148 1 -188.04164 40.331129 -2375.8945
|
||||
1490 0.149 1 -188.03603 40.681394 -2375.8945
|
||||
1500 0.15 1 -188.02929 41.114003 -2375.8945
|
||||
1510 0.151 1 -188.02148 41.623259 -2375.8945
|
||||
1520 0.152 1 -188.0127 42.20263 -2375.8945
|
||||
1530 0.153 1 -188.00302 42.844846 -2375.8945
|
||||
1540 0.154 1 -187.99255 43.541977 -2375.8945
|
||||
1550 0.155 1 -187.98148 44.285554 -2375.8945
|
||||
1560 0.156 1 -187.96989 45.066666 -2375.8945
|
||||
1570 0.157 1 -187.95793 45.876084 -2375.8945
|
||||
1580 0.158 1 -187.94574 46.704378 -2375.8945
|
||||
1590 0.159 1 -187.93346 47.542032 -2375.8945
|
||||
1600 0.16 1 -187.92122 48.379564 -2375.8945
|
||||
1610 0.161 1 -187.90916 49.207642 -2375.8945
|
||||
1620 0.162 1 -187.89742 50.0172 -2375.8945
|
||||
1630 0.163 1 -187.88613 50.799541 -2375.8945
|
||||
1640 0.164 1 -187.87536 51.546446 -2375.8944
|
||||
1650 0.165 1 -187.86531 52.250265 -2375.8944
|
||||
1660 0.166 1 -187.85604 52.904001 -2375.8944
|
||||
1670 0.167 1 -187.84765 53.501394 -2375.8944
|
||||
1680 0.168 1 -187.84021 54.036987 -2375.8944
|
||||
1690 0.169 1 -187.83379 54.506178 -2375.8944
|
||||
1700 0.17 1 -187.82846 54.905273 -2375.8944
|
||||
1710 0.171 1 -187.82424 55.231514 -2375.8944
|
||||
1720 0.172 1 -187.82117 55.483104 -2375.8944
|
||||
1730 0.173 1 -187.81922 55.659221 -2375.8944
|
||||
1740 0.174 1 -187.81843 55.760007 -2375.8944
|
||||
1750 0.175 1 -187.81881 55.786556 -2375.8944
|
||||
1760 0.176 1 -187.82029 55.740888 -2375.8944
|
||||
1770 0.177 1 -187.82284 55.625916 -2375.8944
|
||||
1780 0.178 1 -187.82639 55.445397 -2375.8944
|
||||
1790 0.179 1 -187.83088 55.203871 -2375.8944
|
||||
1800 0.18 1 -187.83623 54.906597 -2375.8944
|
||||
1810 0.181 1 -187.84235 54.559471 -2375.8944
|
||||
1820 0.182 1 -187.84913 54.168949 -2375.8944
|
||||
1830 0.183 1 -187.85646 53.741952 -2375.8943
|
||||
1840 0.184 1 -187.86424 53.28578 -2375.8943
|
||||
1850 0.185 1 -187.87239 52.807988 -2375.8943
|
||||
1860 0.186 1 -187.88077 52.3163 -2375.8943
|
||||
1870 0.187 1 -187.88925 51.81851 -2375.8943
|
||||
1880 0.188 1 -187.89772 51.322368 -2375.8943
|
||||
1890 0.189 1 -187.90605 50.835483 -2375.8943
|
||||
1900 0.19 1 -187.91415 50.365218 -2375.8943
|
||||
1910 0.191 1 -187.92189 49.9186 -2375.8943
|
||||
1920 0.192 1 -187.92917 49.502222 -2375.8943
|
||||
1930 0.193 1 -187.93591 49.122167 -2375.8943
|
||||
1940 0.194 1 -187.94198 48.783928 -2375.8943
|
||||
1950 0.195 1 -187.94737 48.492348 -2375.8943
|
||||
1960 0.196 1 -187.95199 48.25154 -2375.8943
|
||||
1970 0.197 1 -187.95576 48.064862 -2375.8943
|
||||
1980 0.198 1 -187.95866 47.934875 -2375.8943
|
||||
1990 0.199 1 -187.96065 47.863314 -2375.8943
|
||||
2000 0.2 1 -187.96171 47.851079 -2375.8943
|
||||
Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms
|
||||
|
||||
Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s
|
||||
96.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2934 | 1.3683 | 1.432 | 4.2 | 31.09
|
||||
Neigh | 0.005039 | 0.0053418 | 0.0054908 | 0.2 | 0.12
|
||||
Comm | 0.12642 | 0.1922 | 0.26891 | 11.6 | 4.37
|
||||
Output | 0.39256 | 0.40875 | 0.43431 | 2.5 | 9.29
|
||||
Modify | 2.395 | 2.4202 | 2.4352 | 1.0 | 54.99
|
||||
Other | | 0.006007 | | | 0.14
|
||||
|
||||
Nlocal: 125 ave 130 max 122 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 1324 ave 1330 max 1316 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 6747 ave 6959 max 6652 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
FullNghs: 13494 ave 14060 max 13186 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 53976
|
||||
Ave neighs/atom = 107.952
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
15009
examples/SPIN/iron/Fe_Mishin2006.eam.alloy
Normal file
15009
examples/SPIN/iron/Fe_Mishin2006.eam.alloy
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,5 @@
|
||||
2.4824 0.01948336
|
||||
2.8665 0.01109
|
||||
4.0538 -0.0002176
|
||||
4.753 -0.001714
|
||||
4.965 -0.001986
|
||||
32
examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py
Normal file
32
examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py
Normal file
@ -0,0 +1,32 @@
|
||||
#Program fitting the exchange interaction
|
||||
#Model curve: Bethe-Slater function
|
||||
import numpy as np, pylab, tkinter
|
||||
import matplotlib.pyplot as plt
|
||||
from scipy.optimize import curve_fit
|
||||
from decimal import *
|
||||
|
||||
print("Loop begin")
|
||||
|
||||
#Definition of the Bethe-Slater function
|
||||
def func(x,a,b,c):
|
||||
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
|
||||
|
||||
#Exchange coeff table (data to fit)
|
||||
rdata, Jdata = np.loadtxt('exchange_bcc_iron.dat', usecols=(0,1), unpack=True)
|
||||
plt.plot(rdata, Jdata, 'b-', label='data')
|
||||
|
||||
#Perform the fit
|
||||
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
|
||||
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
|
||||
|
||||
#Print the fitted params
|
||||
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
|
||||
|
||||
#Ploting the result
|
||||
plt.xlabel('r_ij')
|
||||
pylab.xlim([0,6.5])
|
||||
plt.ylabel('J_ij')
|
||||
plt.legend()
|
||||
plt.show()
|
||||
|
||||
print("Loop end")
|
||||
19
examples/SPIN/iron/fe_dd.dat
Normal file
19
examples/SPIN/iron/fe_dd.dat
Normal file
@ -0,0 +1,19 @@
|
||||
6 8
|
||||
Optimal parameter set
|
||||
1 4.100199340884814 F
|
||||
2 1.565647547483517 F
|
||||
1 0.9332056681088162 T 3.000000000000000
|
||||
2 -1.162558782567700 T 2.866666666666670
|
||||
3 -0.3502026949249225 T 2.733333333333330
|
||||
4 0.4287820835430028 T 2.600000000000000
|
||||
5 4.907925057809273 T 2.400000000000000
|
||||
6 -5.307049068415304 T 2.300000000000000
|
||||
1 -0.1960674387419232 F 4.100000000000000
|
||||
2 0.3687525935422963 F 3.800000000000000
|
||||
3 -1.505333614924853 F 3.500000000000000
|
||||
4 4.948907078156191 T 3.200000000000000
|
||||
5 -4.894613262753399 T 2.900000000000000
|
||||
6 3.468897724782442 T 2.600000000000000
|
||||
7 -1.792218099820337 T 2.400000000000000
|
||||
8 80.22069592246987 T 2.300000000000000
|
||||
|
||||
56
examples/SPIN/iron/in.spin.iron
Normal file
56
examples/SPIN/iron/in.spin.iron
Normal file
@ -0,0 +1,56 @@
|
||||
# bcc iron in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice bcc 2.8665
|
||||
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 bcc iron
|
||||
|
||||
mass 1 55.845
|
||||
|
||||
set group all spin/random 31 2.2
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
|
||||
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
|
||||
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
run 50000
|
||||
1115
examples/SPIN/iron/log.11May18.spin.iron.g++.1
Normal file
1115
examples/SPIN/iron/log.11May18.spin.iron.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
1115
examples/SPIN/iron/log.11May18.spin.iron.g++.4
Normal file
1115
examples/SPIN/iron/log.11May18.spin.iron.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
30006
examples/SPIN/nickel/Ni99.eam.alloy
Normal file
30006
examples/SPIN/nickel/Ni99.eam.alloy
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,5 @@
|
||||
2.492 0.0028027
|
||||
3.524 0.0000816
|
||||
4.316 0.0003537
|
||||
4.984 0.0001632
|
||||
5.572 0.0000408
|
||||
@ -0,0 +1,5 @@
|
||||
2.495 8.3
|
||||
3.524 -3.99
|
||||
4.31 0.998
|
||||
4.99 -0.955
|
||||
5.56 0.213
|
||||
33
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py
Normal file
33
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py
Normal file
@ -0,0 +1,33 @@
|
||||
# program fitting the exchange interaction
|
||||
# model curve: Bethe-Slater function
|
||||
import numpy as np, pylab, tkinter
|
||||
import matplotlib.pyplot as plt
|
||||
from scipy.optimize import curve_fit
|
||||
from decimal import *
|
||||
|
||||
print("Loop begin")
|
||||
|
||||
# definition of the Bethe-Slater function
|
||||
def func(x,a,b,c):
|
||||
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
|
||||
|
||||
# exchange coeff table (data to fit)
|
||||
rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True)
|
||||
plt.plot(rdata, Jdata, 'b-', label='data')
|
||||
|
||||
# perform the fit
|
||||
popt, pcov = curve_fit(func, rdata, Jdata, bounds=([0.0,-1.0,0.0], [100.,5.,5.]))
|
||||
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
|
||||
|
||||
# print the fitted parameters
|
||||
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
|
||||
|
||||
# ploting the result
|
||||
plt.xlabel('r_ij')
|
||||
pylab.xlim([0.0,6.5])
|
||||
#pylab.ylim([-2.0,10.0])
|
||||
plt.ylabel('J_ij')
|
||||
plt.legend()
|
||||
plt.show()
|
||||
|
||||
print("Loop end")
|
||||
58
examples/SPIN/nickel/in.spin.nickel
Normal file
58
examples/SPIN/nickel/in.spin.nickel
Normal file
@ -0,0 +1,58 @@
|
||||
# fcc nickel in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.524
|
||||
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 58.69
|
||||
|
||||
set group all spin/random 31 0.63
|
||||
#set group all spin 0.63 0.0 0.0 1.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Ni99.eam.alloy Ni
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp v_tmag etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
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]
|
||||
|
||||
run 2000
|
||||
|
||||
157
examples/SPIN/nickel/log.11May18.spin.nickel.g++.1
Normal file
157
examples/SPIN/nickel/log.11May18.spin.nickel.g++.1
Normal file
@ -0,0 +1,157 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# fcc nickel in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.524
|
||||
Lattice spacing in x,y,z = 3.524 3.524 3.524
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000804186 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.69
|
||||
|
||||
set group all spin/random 31 0.63
|
||||
500 settings made for spin/random
|
||||
#set group all spin 0.63 0.0 0.0 1.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Ni99.eam.alloy Ni
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp v_tmag etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
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]
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.90375
|
||||
ghost atom cutoff = 5.90375
|
||||
binsize = 2.95187, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes
|
||||
Step Time v_magnorm v_emag Temp v_tmag TotEng
|
||||
0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018
|
||||
50 0.005 0.028733807 0.070491717 101.47879 -56307.038 -2218.1018
|
||||
100 0.01 0.028733815 -0.70937134 101.7311 5851.6355 -2218.1018
|
||||
150 0.015 0.028733823 -1.853981 99.63039 2395.8677 -2218.1018
|
||||
200 0.02 0.028733828 -3.2679239 94.850105 1482.3486 -2218.1018
|
||||
250 0.025 0.028733824 -4.863967 88.444584 1100.7396 -2218.1018
|
||||
300 0.03 0.028733807 -6.5763457 82.689581 899.56642 -2218.1018
|
||||
350 0.035 0.028733783 -8.3489158 80.108798 768.64457 -2218.1018
|
||||
400 0.04 0.028733763 -10.120216 82.374947 670.03091 -2218.1018
|
||||
450 0.045 0.028733755 -11.828932 89.814597 593.77931 -2218.1018
|
||||
500 0.05 0.028733762 -13.423712 101.39613 535.03371 -2218.1018
|
||||
550 0.055 0.028733783 -14.866724 115.07399 489.92024 -2218.1018
|
||||
600 0.06 0.028733801 -16.135279 128.57849 458.66654 -2218.1018
|
||||
650 0.065 0.028733804 -17.222838 140.22402 440.11437 -2218.1018
|
||||
700 0.07 0.028733795 -18.154813 149.61295 425.91356 -2218.1018
|
||||
750 0.075 0.028733781 -18.996903 157.5814 412.82654 -2218.1018
|
||||
800 0.08 0.028733768 -19.804249 164.92075 407.77954 -2218.1018
|
||||
850 0.085 0.028733752 -20.579151 171.67278 406.84726 -2218.1018
|
||||
900 0.09 0.028733728 -21.294277 177.67238 399.69633 -2218.1018
|
||||
950 0.095 0.028733715 -21.943945 183.2621 389.92281 -2218.1018
|
||||
1000 0.1 0.02873374 -22.551277 188.99284 383.19592 -2218.1018
|
||||
1050 0.105 0.028733783 -23.120147 194.51391 375.87245 -2218.1018
|
||||
1100 0.11 0.028733792 -23.602325 198.18631 365.37753 -2218.1018
|
||||
1150 0.115 0.028733774 -23.976048 199.04022 354.04863 -2218.1018
|
||||
1200 0.12 0.02873376 -24.31575 198.41999 346.40397 -2218.1018
|
||||
1250 0.125 0.028733759 -24.718347 198.3669 343.1701 -2218.1018
|
||||
1300 0.13 0.028733765 -25.189073 199.57949 336.90052 -2218.1018
|
||||
1350 0.135 0.028733774 -25.650252 201.45897 329.07023 -2218.1018
|
||||
1400 0.14 0.028733785 -26.042702 203.6926 327.97373 -2218.1018
|
||||
1450 0.145 0.028733791 -26.373965 206.80469 327.38747 -2218.1018
|
||||
1500 0.15 0.028733791 -26.691802 211.43923 322.75885 -2218.1018
|
||||
1550 0.155 0.028733794 -27.021573 217.10969 315.55781 -2218.1018
|
||||
1600 0.16 0.028733792 -27.344066 222.16052 310.6743 -2218.1018
|
||||
1650 0.165 0.028733788 -27.640017 225.28449 310.49671 -2218.1018
|
||||
1700 0.17 0.028733803 -27.907241 226.37676 310.9389 -2218.1018
|
||||
1750 0.175 0.028733828 -28.143477 226.31095 313.28034 -2218.1018
|
||||
1800 0.18 0.028733833 -28.363397 226.43633 317.31668 -2218.1018
|
||||
1850 0.185 0.028733811 -28.58153 227.36287 318.98645 -2218.1018
|
||||
1900 0.19 0.028733796 -28.785208 228.39889 316.9972 -2218.1018
|
||||
1950 0.195 0.028733826 -28.9724 228.84666 309.8027 -2218.1018
|
||||
2000 0.2 0.02873386 -29.175039 228.918 297.88519 -2218.1018
|
||||
Loop time of 10.033 on 1 procs for 2000 steps with 500 atoms
|
||||
|
||||
Performance: 1.722 ns/day, 13.935 hours/ns, 199.342 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.909 | 3.909 | 3.909 | 0.0 | 38.96
|
||||
Neigh | 0.031031 | 0.031031 | 0.031031 | 0.0 | 0.31
|
||||
Comm | 0.046559 | 0.046559 | 0.046559 | 0.0 | 0.46
|
||||
Output | 2.4087 | 2.4087 | 2.4087 | 0.0 | 24.01
|
||||
Modify | 3.625 | 3.625 | 3.625 | 0.0 | 36.13
|
||||
Other | | 0.01268 | | | 0.13
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19508 ave 19508 max 19508 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 39016 ave 39016 max 39016 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 39016
|
||||
Ave neighs/atom = 78.032
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:10
|
||||
157
examples/SPIN/nickel/log.11May18.spin.nickel.g++.4
Normal file
157
examples/SPIN/nickel/log.11May18.spin.nickel.g++.4
Normal file
@ -0,0 +1,157 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# fcc nickel in a 3d periodic box
|
||||
|
||||
clear
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.524
|
||||
Lattice spacing in x,y,z = 3.524 3.524 3.524
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000523567 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.69
|
||||
|
||||
set group all spin/random 31 0.63
|
||||
500 settings made for spin/random
|
||||
#set group all spin 0.63 0.0 0.0 1.0
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Ni99.eam.alloy Ni
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp v_tmag etotal
|
||||
thermo 50
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
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]
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.90375
|
||||
ghost atom cutoff = 5.90375
|
||||
binsize = 2.95187, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes
|
||||
Step Time v_magnorm v_emag Temp v_tmag TotEng
|
||||
0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018
|
||||
50 0.005 0.028733805 0.25324083 98.741633 -15727.749 -2218.1018
|
||||
100 0.01 0.028733812 -0.37320751 97.073875 11244.373 -2218.1018
|
||||
150 0.015 0.028733819 -1.3971549 94.073447 3250.0517 -2218.1018
|
||||
200 0.02 0.028733825 -2.7238372 89.419944 1838.752 -2218.1018
|
||||
250 0.025 0.028733829 -4.2684428 84.07494 1304.3675 -2218.1018
|
||||
300 0.03 0.028733824 -5.9636712 80.06368 1025.7815 -2218.1018
|
||||
350 0.035 0.02873381 -7.7386326 79.366702 844.49729 -2218.1018
|
||||
400 0.04 0.028733802 -9.5148059 83.052751 715.20758 -2218.1018
|
||||
450 0.045 0.028733806 -11.234935 91.282747 621.75552 -2218.1018
|
||||
500 0.05 0.02873381 -12.875184 103.49836 550.04479 -2218.1018
|
||||
550 0.055 0.028733808 -14.413473 118.16526 495.70417 -2218.1018
|
||||
600 0.06 0.028733803 -15.812466 132.83837 461.35805 -2218.1018
|
||||
650 0.065 0.028733808 -17.061311 145.41049 444.38951 -2218.1018
|
||||
700 0.07 0.028733818 -18.181903 154.83414 438.85866 -2218.1018
|
||||
750 0.075 0.028733823 -19.176259 160.58645 436.90462 -2218.1018
|
||||
800 0.08 0.028733825 -20.035157 163.02829 429.73193 -2218.1018
|
||||
850 0.085 0.028733825 -20.806548 164.4197 419.73763 -2218.1018
|
||||
900 0.09 0.028733829 -21.571419 167.8571 411.59699 -2218.1018
|
||||
950 0.095 0.028733825 -22.365879 175.00875 402.66175 -2218.1018
|
||||
1000 0.1 0.028733821 -23.133464 184.68305 391.05824 -2218.1018
|
||||
1050 0.105 0.028733833 -23.770507 193.83795 379.23354 -2218.1018
|
||||
1100 0.11 0.02873385 -24.249882 200.5039 372.08521 -2218.1018
|
||||
1150 0.115 0.028733864 -24.630489 204.46984 367.92135 -2218.1018
|
||||
1200 0.12 0.028733877 -24.956281 205.96624 363.72367 -2218.1018
|
||||
1250 0.125 0.028733884 -25.227332 205.18503 361.09236 -2218.1018
|
||||
1300 0.13 0.028733877 -25.43568 202.76969 359.10924 -2218.1018
|
||||
1350 0.135 0.028733868 -25.588748 199.85462 358.69556 -2218.1018
|
||||
1400 0.14 0.028733866 -25.723582 197.99165 360.27856 -2218.1018
|
||||
1450 0.145 0.028733851 -25.866283 198.30283 360.46623 -2218.1018
|
||||
1500 0.15 0.028733812 -26.014569 200.95517 354.66722 -2218.1018
|
||||
1550 0.155 0.02873379 -26.192673 205.95485 348.37935 -2218.1018
|
||||
1600 0.16 0.028733795 -26.444059 212.87557 345.53576 -2218.1018
|
||||
1650 0.165 0.028733838 -26.75551 219.86449 338.9224 -2218.1018
|
||||
1700 0.17 0.028733868 -27.068513 224.47868 327.81241 -2218.1018
|
||||
1750 0.175 0.028733862 -27.344118 225.62318 319.85486 -2218.1018
|
||||
1800 0.18 0.028733849 -27.57563 224.07463 320.07064 -2218.1018
|
||||
1850 0.185 0.028733852 -27.774274 221.70618 323.12599 -2218.1018
|
||||
1900 0.19 0.028733864 -27.967999 220.53947 322.9504 -2218.1018
|
||||
1950 0.195 0.028733863 -28.173041 221.61407 318.63401 -2218.1018
|
||||
2000 0.2 0.028733853 -28.362177 224.22281 310.55185 -2218.1018
|
||||
Loop time of 3.95094 on 4 procs for 2000 steps with 500 atoms
|
||||
|
||||
Performance: 4.374 ns/day, 5.487 hours/ns, 506.208 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0289 | 1.0467 | 1.0811 | 2.0 | 26.49
|
||||
Neigh | 0.0079527 | 0.0081946 | 0.0084369 | 0.2 | 0.21
|
||||
Comm | 0.094456 | 0.13311 | 0.15138 | 6.2 | 3.37
|
||||
Output | 0.69702 | 0.71998 | 0.74483 | 2.1 | 18.22
|
||||
Modify | 2.0107 | 2.0383 | 2.0598 | 1.3 | 51.59
|
||||
Other | | 0.004668 | | | 0.12
|
||||
|
||||
Nlocal: 125 ave 132 max 120 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 1099 ave 1104 max 1092 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 4876.5 ave 5100 max 4721 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
FullNghs: 9753 ave 10296 max 9362 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 39012
|
||||
Ave neighs/atom = 78.024
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
1
examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
Symbolic link
1
examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../cobalt_fcc/Co_PurjaPun_2012.eam.alloy
|
||||
8207
examples/SPIN/read_restart/Norm_randXY_8x8x32.data
Normal file
8207
examples/SPIN/read_restart/Norm_randXY_8x8x32.data
Normal file
File diff suppressed because it is too large
Load Diff
45
examples/SPIN/read_restart/in.spin.read_data
Normal file
45
examples/SPIN/read_restart/in.spin.read_data
Normal file
@ -0,0 +1,45 @@
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 10 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]
|
||||
|
||||
run 100
|
||||
49
examples/SPIN/read_restart/in.spin.restart
Normal file
49
examples/SPIN/read_restart/in.spin.restart
Normal file
@ -0,0 +1,49 @@
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 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]
|
||||
|
||||
run 100
|
||||
55
examples/SPIN/read_restart/in.spin.write_restart
Normal file
55
examples/SPIN/read_restart/in.spin.write_restart
Normal file
@ -0,0 +1,55 @@
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
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
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice no
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 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]
|
||||
|
||||
run 1000
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
|
||||
112
examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1
Normal file
112
examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1
Normal file
@ -0,0 +1,112 @@
|
||||
LAMMPS (11 May 2018)
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
orthogonal box = (0 0 0) to (28.32 28.32 113.28)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8192 atoms
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 10 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]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 8 8 31
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
|
||||
Step Time v_magnorm v_emag v_tmag Temp TotEng
|
||||
0 0 0.980832325249102 -2984.9466433509 51.7121203365409 0 -38881.8459242429
|
||||
10 0.001 0.980832325038224 -2984.94800197308 52.2550760237226 0.00128259392155095 -38881.8459243688
|
||||
20 0.002 0.980832322622779 -2984.95196908579 53.4253029071033 0.0050206854169363 -38881.8459246487
|
||||
30 0.003 0.980832317889283 -2984.95826684048 55.1488791221993 0.0109316238061975 -38881.8459250502
|
||||
40 0.004 0.980832310888481 -2984.96649810512 57.3217709603901 0.0186091353316915 -38881.8459255204
|
||||
50 0.005 0.980832301939686 -2984.97619813381 59.8271487572311 0.0275752699737783 -38881.8459260027
|
||||
60 0.006 0.980832291654664 -2984.98688847988 62.5518654049861 0.0373348857300743 -38881.8459264498
|
||||
70 0.007 0.980832280861627 -2984.99812400566 65.3978892661935 0.0474235455824994 -38881.845926824
|
||||
80 0.008 0.980832270462785 -2985.00952679611 68.286219599829 0.0574425858114516 -38881.8459271072
|
||||
90 0.009 0.980832261284587 -2985.02080458573 71.1539714621652 0.0670788260497413 -38881.8459272915
|
||||
100 0.01 0.980832253960703 -2985.03175506188 73.9486358176052 0.0761100787140068 -38881.8459273845
|
||||
Loop time of 12.4286 on 1 procs for 100 steps with 8192 atoms
|
||||
|
||||
Performance: 0.070 ns/day, 345.239 hours/ns, 8.046 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0123 | 4.0123 | 4.0123 | 0.0 | 32.28
|
||||
Neigh | 3.005 | 3.005 | 3.005 | 0.0 | 24.18
|
||||
Comm | 0.041798 | 0.041798 | 0.041798 | 0.0 | 0.34
|
||||
Output | 1.8465 | 1.8465 | 1.8465 | 0.0 | 14.86
|
||||
Modify | 3.5157 | 3.5157 | 3.5157 | 0.0 | 28.29
|
||||
Other | | 0.007261 | | | 0.06
|
||||
|
||||
Nlocal: 8192 ave 8192 max 8192 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 14621 ave 14621 max 14621 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 573440 ave 573440 max 573440 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1146880
|
||||
Ave neighs/atom = 140
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:12
|
||||
112
examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
Normal file
112
examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4
Normal file
@ -0,0 +1,112 @@
|
||||
LAMMPS (11 May 2018)
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
read_data Norm_randXY_8x8x32.data
|
||||
orthogonal box = (0 0 0) to (28.32 28.32 113.28)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
8192 atoms
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs and computes
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 10 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]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 8 8 31
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.994 | 8.25 Mbytes
|
||||
Step Time v_magnorm v_emag v_tmag Temp TotEng
|
||||
0 0 0.980832325249103 -2984.9466433509 51.7121203365411 0 -38881.8459242507
|
||||
10 0.001 0.980832325329477 -2984.94800197307 52.2550778515409 0.00128259391683994 -38881.8459243698
|
||||
20 0.002 0.980832324654401 -2984.95196908569 53.4253110612179 0.00502068532291255 -38881.8459246487
|
||||
30 0.003 0.98083232312993 -2984.95826683995 55.148898005011 0.0109316232931419 -38881.84592505
|
||||
40 0.004 0.980832320808156 -2984.9664981035 57.3218040934977 0.0186091337978305 -38881.8459255198
|
||||
50 0.005 0.980832317596783 -2984.97619813016 59.827198436387 0.0275752665472358 -38881.8459260035
|
||||
60 0.006 0.980832313514709 -2984.98688847322 62.5519331668858 0.037334879488755 -38881.84592645
|
||||
70 0.007 0.980832309220414 -2984.99812399537 65.3979760533737 0.0474235360022736 -38881.8459268243
|
||||
80 0.008 0.980832304490479 -2985.00952678209 68.2863250613635 0.0574425728014485 -38881.8459271068
|
||||
90 0.009 0.980832299379824 -2985.02080456789 71.1540940309591 0.0670788096168283 -38881.8459272917
|
||||
100 0.01 0.980832294622694 -2985.03175503971 73.9487734241296 0.0761100584457276 -38881.8459273851
|
||||
Loop time of 3.6612 on 4 procs for 100 steps with 8192 atoms
|
||||
|
||||
Performance: 0.236 ns/day, 101.700 hours/ns, 27.313 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0622 | 1.076 | 1.0936 | 1.1 | 29.39
|
||||
Neigh | 0.77462 | 0.79542 | 0.81798 | 1.9 | 21.73
|
||||
Comm | 0.024701 | 0.066122 | 0.10261 | 11.1 | 1.81
|
||||
Output | 0.50304 | 0.51253 | 0.52111 | 0.9 | 14.00
|
||||
Modify | 1.2006 | 1.2082 | 1.2205 | 0.7 | 33.00
|
||||
Other | | 0.002962 | | | 0.08
|
||||
|
||||
Nlocal: 2048 ave 2095 max 1981 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 5765 ave 5832 max 5718 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 143360 ave 146361 max 139058 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
FullNghs: 286720 ave 293300 max 277340 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
||||
Total # of neighbors = 1146880
|
||||
Ave neighs/atom = 140
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
117
examples/SPIN/read_restart/log.11May18.spin.restart.g++.1
Normal file
117
examples/SPIN/read_restart/log.11May18.spin.restart.g++.1
Normal file
@ -0,0 +1,117 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
restoring atom style spin from restart
|
||||
orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style spin/exchange from restart
|
||||
500 atoms
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 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]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 4 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes
|
||||
Step Time v_magnorm v_emag v_tmag Temp TotEng
|
||||
1000 0 0.106120063678768 -11.8110267448938 5244.87332482316 0 -2206.81097898043
|
||||
1010 0.001 0.106120047478105 -11.8198467887534 5263.87502105137 0.136650312456579 -2206.81097929055
|
||||
1020 0.002 0.106120026430373 -11.8460960518731 5267.29822866382 0.542282409605327 -2206.81098022997
|
||||
1030 0.003 0.106120005015917 -11.8891434078861 5252.95323564256 1.204018338139 -2206.81098172551
|
||||
1040 0.004 0.106119988532653 -11.9479778701641 5220.88508622311 2.10120884995911 -2206.81098371047
|
||||
1050 0.005 0.10611998133687 -12.021242685853 5172.58549378915 3.20622445795757 -2206.81098610701
|
||||
1060 0.006 0.10611998489458 -12.107271344148 5110.57395203849 4.48535975411235 -2206.81098879725
|
||||
1070 0.007 0.106119996964771 -12.204156761765 5038.48903231346 5.9003121044977 -2206.81099161183
|
||||
1080 0.008 0.106120013042521 -12.3098695046152 4961.0327167967 7.4104497466856 -2206.81099434653
|
||||
1090 0.009 0.106120029236234 -12.4224157835754 4883.3210922213 8.97568980540163 -2206.81099680117
|
||||
1100 0.01 0.106120044071404 -12.5400036896932 4809.88136080052 10.559459821976 -2206.81099883104
|
||||
Loop time of 0.833234 on 1 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 1.037 ns/day, 23.145 hours/ns, 120.014 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.26558 | 0.26558 | 0.26558 | 0.0 | 31.87
|
||||
Neigh | 0.21352 | 0.21352 | 0.21352 | 0.0 | 25.62
|
||||
Comm | 0.0057988 | 0.0057988 | 0.0057988 | 0.0 | 0.70
|
||||
Output | 0.12463 | 0.12463 | 0.12463 | 0.0 | 14.96
|
||||
Modify | 0.22275 | 0.22275 | 0.22275 | 0.0 | 26.73
|
||||
Other | | 0.0009537 | | | 0.11
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2534 ave 2534 max 2534 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 36500 ave 36500 max 36500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 73000 ave 73000 max 73000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 73000
|
||||
Ave neighs/atom = 146
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
118
examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
Normal file
118
examples/SPIN/read_restart/log.11May18.spin.restart.g++.4
Normal file
@ -0,0 +1,118 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# start a spin-lattice simulation from a data file
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
read_restart restart_hcp_cobalt.equil
|
||||
WARNING: Restart file used different # of processors (../read_restart.cpp:723)
|
||||
restoring atom style spin from restart
|
||||
orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style spin/exchange from restart
|
||||
500 atoms
|
||||
|
||||
# setting mass, mag. moments, and interactions
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all nve/spin lattice yes
|
||||
timestep 0.0001
|
||||
|
||||
# define outputs
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 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]
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.49954
|
||||
ghost atom cutoff = 7.49954
|
||||
binsize = 3.74977, bins = 4 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair eam/alloy, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes
|
||||
Step Time v_magnorm v_emag v_tmag Temp TotEng
|
||||
1000 0 0.106120063678768 -11.8110267448939 5244.87332482316 0 -2206.81097898003
|
||||
1010 0.001 0.106120030254187 -11.8198467883806 5263.87550015043 0.136650306637598 -2206.81097929055
|
||||
1020 0.002 0.106119996655714 -11.8460960476455 5267.299198699 0.542282344092749 -2206.81098022997
|
||||
1030 0.003 0.106119967407682 -11.8891433919665 5252.95473019843 1.20401809237154 -2206.81098172552
|
||||
1040 0.004 0.106119960016585 -11.9479778326021 5220.88686874944 2.10120827278397 -2206.81098371049
|
||||
1050 0.005 0.106119961252471 -12.0212426191481 5172.58712301374 3.20622343988728 -2206.81098610703
|
||||
1060 0.006 0.106119967598995 -12.1072712483404 5110.57504803718 4.48535830705751 -2206.81098879724
|
||||
1070 0.007 0.106119967669058 -12.2041566468564 5038.48927079832 5.90031039867811 -2206.81099161179
|
||||
1080 0.008 0.106119969263395 -12.3098693905406 4961.03212459716 7.41044810751949 -2206.8109943465
|
||||
1090 0.009 0.106119960964075 -12.4224156966204 4883.31968289062 8.97568865379831 -2206.81099680112
|
||||
1100 0.01 0.106119945605273 -12.5400036591612 4809.87930844463 10.5594596175303 -2206.81099883101
|
||||
Loop time of 0.304678 on 4 procs for 100 steps with 500 atoms
|
||||
|
||||
Performance: 2.836 ns/day, 8.463 hours/ns, 328.215 timesteps/s
|
||||
98.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.071445 | 0.073018 | 0.074151 | 0.4 | 23.97
|
||||
Neigh | 0.054448 | 0.055709 | 0.057528 | 0.5 | 18.28
|
||||
Comm | 0.0061178 | 0.0074609 | 0.0090766 | 1.2 | 2.45
|
||||
Output | 0.037489 | 0.038586 | 0.039952 | 0.5 | 12.66
|
||||
Modify | 0.12826 | 0.12954 | 0.13065 | 0.3 | 42.52
|
||||
Other | | 0.0003686 | | | 0.12
|
||||
|
||||
Nlocal: 125 ave 129 max 120 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 1387 ave 1392 max 1383 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 9125 ave 9428 max 8740 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
FullNghs: 18250 ave 18834 max 17520 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 73000
|
||||
Ave neighs/atom = 146
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
119
examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1
Normal file
119
examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1
Normal file
@ -0,0 +1,119 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.00027585 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
500 settings made for spin/random
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice no
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 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]
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 7 11 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes
|
||||
Step Time v_magnorm v_emag Temp TotEng
|
||||
0 0 0.076558814 1.7982359 0 1.7982359
|
||||
100 0.01 0.079107243 0.56368447 0 0.56368447
|
||||
200 0.02 0.08225862 -0.42421042 0 -0.42421042
|
||||
300 0.03 0.08397714 -1.4964948 0 -1.4964948
|
||||
400 0.04 0.084704989 -2.6740652 0 -2.6740652
|
||||
500 0.05 0.087486342 -4.2043382 0 -4.2043382
|
||||
600 0.06 0.09187261 -5.6687169 0 -5.6687169
|
||||
700 0.07 0.096925249 -6.937499 0 -6.937499
|
||||
800 0.08 0.098988236 -8.2456715 0 -8.2456715
|
||||
900 0.09 0.10434092 -10.111953 0 -10.111953
|
||||
1000 0.1 0.10612006 -11.811027 0 -11.811027
|
||||
Loop time of 2.60215 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 3.320 ns/day, 7.228 hours/ns, 384.297 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.35178 | 0.35178 | 0.35178 | 0.0 | 13.52
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.014421 | 0.014421 | 0.014421 | 0.0 | 0.55
|
||||
Output | 1.2046 | 1.2046 | 1.2046 | 0.0 | 46.29
|
||||
Modify | 1.0274 | 1.0274 | 1.0274 | 0.0 | 39.48
|
||||
Other | | 0.004006 | | | 0.15
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1221 ave 1221 max 1221 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 10000 ave 10000 max 10000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10000
|
||||
Ave neighs/atom = 20
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
119
examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4
Normal file
119
examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4
Normal file
@ -0,0 +1,119 @@
|
||||
LAMMPS (11 May 2018)
|
||||
# fcc cobalt in a 3d periodic box
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
lattice hcp 2.5071
|
||||
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000257969 secs
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
500 settings made for spin/random
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 100.0 0.01 21
|
||||
|
||||
fix 3 all nve/spin lattice no
|
||||
timestep 0.0001
|
||||
|
||||
# compute and output options
|
||||
|
||||
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[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag temp etotal
|
||||
thermo 100
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 100 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]
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 20 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.1
|
||||
ghost atom cutoff = 4.1
|
||||
binsize = 2.05, bins = 7 11 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair spin/exchange, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.367 | 6.367 | 6.367 Mbytes
|
||||
Step Time v_magnorm v_emag Temp TotEng
|
||||
0 0 0.076558814 1.7982359 0 1.7982359
|
||||
100 0.01 0.081414414 0.70545723 0 0.70545723
|
||||
200 0.02 0.084519539 -0.33171078 0 -0.33171078
|
||||
300 0.03 0.089334139 -1.3988283 0 -1.3988283
|
||||
400 0.04 0.092873722 -2.8519371 0 -2.8519371
|
||||
500 0.05 0.0970839 -4.1531164 0 -4.1531164
|
||||
600 0.06 0.099626132 -5.7993765 0 -5.7993765
|
||||
700 0.07 0.10467169 -7.3011333 0 -7.3011333
|
||||
800 0.08 0.10893493 -8.6918141 0 -8.6918141
|
||||
900 0.09 0.11389657 -10.236174 0 -10.236174
|
||||
1000 0.1 0.1180057 -11.896933 0 -11.896933
|
||||
Loop time of 1.05012 on 4 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 8.228 ns/day, 2.917 hours/ns, 952.272 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.08972 | 0.090456 | 0.091872 | 0.3 | 8.61
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.016958 | 0.018047 | 0.019791 | 0.8 | 1.72
|
||||
Output | 0.36286 | 0.37483 | 0.38975 | 1.6 | 35.69
|
||||
Modify | 0.55131 | 0.56541 | 0.57702 | 1.3 | 53.84
|
||||
Other | | 0.001374 | | | 0.13
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 597.5 ave 600 max 595 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2500 ave 2500 max 2500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10000
|
||||
Ave neighs/atom = 20
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_restart restart_hcp_cobalt.equil
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
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
|
||||
|
||||
|
||||
|
||||
6006
examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs
Normal file
6006
examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs
Normal file
File diff suppressed because it is too large
Load Diff
8211
examples/USER/misc/entropy/data.interface
Normal file
8211
examples/USER/misc/entropy/data.interface
Normal file
File diff suppressed because it is too large
Load Diff
34
examples/USER/misc/entropy/in.entropy
Normal file
34
examples/USER/misc/entropy/in.entropy
Normal file
@ -0,0 +1,34 @@
|
||||
echo both
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.interface
|
||||
mass 1 22.98977
|
||||
|
||||
neigh_modify delay 10 every 1
|
||||
pair_style eam/fs
|
||||
pair_coeff * * Na_MendelevM_2014.eam.fs Na
|
||||
timestep 0.002
|
||||
thermo 500
|
||||
|
||||
neighbor 4. bin
|
||||
|
||||
# Define computes
|
||||
# Global density, no average
|
||||
compute 1 all entropy/atom 0.25 7.75
|
||||
# Local density, no average
|
||||
compute 2 all entropy/atom 0.25 7.75 local yes
|
||||
# Global density, average over neighbors
|
||||
compute 3 all entropy/atom 0.25 7.75 avg yes 5.
|
||||
# Local density, average over neighbors
|
||||
compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes
|
||||
|
||||
dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4
|
||||
|
||||
|
||||
fix 1 all nph x 1. 1. 10.
|
||||
fix 2 all temp/csvr 350. 350. 0.1 64582
|
||||
|
||||
run 1000
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user