forked from lijiext/lammps
First version of the spin tutorial (2)
Examples (example/SPIN), for BFO and Co
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<script type="text/javascript"
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src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
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</script>
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<script type="text/x-mathjax-config">
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MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
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</script>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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Tutorial for the SPIN package in LAMMPS :h3
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This tutorial explains how to use the spin dynamics in LAMMPS,
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and to perform spin and spin--lattice simulations using the
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SPIN package. As an illustration, input files are documented.
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First of all, LAMMPS has to be compiled with the SPIN package
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activated. Then, the data file and input scripts have to be
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modified to include the magnetic spins and to handle them.
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:line
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[Overview of the spin and spin--lattice dynamics]
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At the atomic scale, magnetic materials can be seen as ensemble of
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atoms, each one of them carying a magnetic moment, refered to as its
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atomic spin. In ref "Antropov"_#Antropov, a formalism allowing to
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simulate approximate classical spins, and to couple them to lattice
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vibrations was introduced. Each of these spins is simulated via a
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classical vector, associated to each magnetic atom, and whose
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trajectory is defined by an equation of motion.
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Lattice vibrations are simulated by the usual equations of MD.
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A mechanical potential (EAM, Finnis-Siclair, or Dudarev-Derlet) ensure
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the cohesion of the particles. The coupling between the magnetic and
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lattice degrees of freedom is performed via the inter-atomic dependence
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of the magnetic interactions.
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:ole
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:line
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[Preparation of the data file]
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For the mechanical potentials, the data file is similar to a standard LAMMPS
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data file for {atom_style full}. The DPs and the {harmonic bonds} connecting
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them to their DC should appear in the data file as normal atoms and bonds.
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For the magnetic interactions, no data file is necessary, every interaction
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input will be define in the input file. :pre
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:line
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[Basic input file]
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Up to know, spin simulations only accept the metal units.
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The atom style should be set to {spin}, so that you
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can define atomic spin vectors.
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The set group command defines the Lande factor (the norm) of
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the magnetic vectors in a given group, and their initial
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oriantation. The command is:
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set group A B C D E F :pre
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with A, B, C, D, E, and F the following input parameters:
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A is set to all, or to the number of a specific and pre-defined
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group of atoms,
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B is set to {spin} or {spin/random}, depending on if the spins of
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the group have to be initialized in a particulat direction, or randomly.
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If B is defined as {spin}, the C is the Lande factor for the spins of
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the group, and [D,E,F] is the vector giving the direction for the
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initialization.
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If B is defined as {spin/random}, C is a number giving the seed for the random
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difinition of the directions, and D is the Lande factor of the spins
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in this group. E and F are not defined.
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Examples:
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set group all spin 1.72 1.0 0.0 0.0
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set group all spin/random 11 1.72
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setting the initial direction of all spins, with a Lande factor of 1.72,
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and either in the x direction, or randomly. :l
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The pair style has to be set to {pair/spin}. The command is
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pair_style pair/spin A
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with A a global radius cutoff.
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The different pair interactions and their associated coefficients can then be
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defined via the pair coeff command.
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pair_coeff A B C D E F G H
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where A and B are setting the pair concerned by this pair coeff command.
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For example, A=1 and B=2 to set the pair coefficients between spins of
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type 1 and spins of type 2. Use {*} for setting a pair coeffcient between
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all pairs of spins.
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C defines the type of the interaction. It can be set to {exchange} for an
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exchange interaction, {dmi} for a Dzyaloshinskii-Moriya (DM) interaction, or to
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{me} for a magneto-electric (ME) interaction.
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If C is set to {exchange}, D is the radius cutoff (in Angtrom) associated
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to the exchange interaction, and E, F and G are the three parameters of the
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Bethe--Slater function (E in eV, F without dimension, and G in Angtrom).
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H is not defined.
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If C is set to {dmi}, D is the radius cutoff (in Angtrom) associated to the DM
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interaction, E is the intensity of the interaction in eV (which is also the
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norm of the DM vector), and [F, G, H] are giving the direction of the DM
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vector.
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If C is set to {me}, D is the radius cutoff (in Angtrom) associated to the ME
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interaction, E is the intensity of the interaction in eV (which corresponds to
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the intensity of the electric polarization), and [F, G, H] are giving the
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direction of the polarization vector.
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Examples:
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pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
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pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
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are setting an exchange interaction between every type of spins, with a radius
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cutoff of 4.0 Angtrom, and E=0.0446928 eV, F=0.003496, and G=1.4885 Angtrom as
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coefficient for the associated Bethe--Slater function, and a DM interaction
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with a radius cutoff of 2.6 Angtrom, an intensity of 0.001 eV and a DM vector
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in the direction [0.0 0.0 1.0]. :l
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A fix has to be set to {force/spin} to define local magnetic forces, like the Zeeman
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interaction or an anisotropic interaction. The command is:
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fix A B C D E F G H
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with A the label of the associated fix, B defining to which group of spins the
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force is applied to, C defined as {force/spin} for magnetic local fixes, and
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D defining the type of this fix. D can be equal to {zeeman} for a Zeeman interaction,
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or to {anisotropy} for an anisotropic interaction.
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If D is set to {zeeman}, then E gives the intensity of the applied magnetic field (in
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Tesla), and [F, G, H] the direction of this field.
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If is set to {anisotropy}, hen E gives the intensity of the anisotropic field (in eV),
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and [F, G, H] the direction of this anisotropy.
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Examples:
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fix 1 all force/spin zeeman 1.0 0.0 0.0 1.0
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fix 2 all force/spin anisotropy 0.001 0.0 1.0 0.0
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are setting two fixes, the first one, labelled 1, is applied to all spins and defines
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a Zeeman interaction corresponding to a field of 1 Tesla in the z direction, whereas
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the second fix, labelled 2, is also applied to all spins, and defines a uniaxial
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anisotropy of intensity 0.001 eV, in the direction y. :l
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To simulate the temperature effects, a fix has to be set to {langevin/spin}. The command
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is
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fix A B C D E F G
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where A is the label of the associated fix, B defines to which spins the fix is applied,
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and C is set equal to {langevin/spin}. Then, D defines the temperature of the random bath
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(in K), E is the transverse magnetic damping (no dimension), F is a longitudinal magnetic
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damping, and G the seed for the random variables.
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Note: the transverse damping is not implemented into LAMMPS yet. It is necessary for
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micromagnetic simulations only.
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Examples:
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fix 2 all langevin/spin 300.0 0.01 0.0 21
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is setting a fix labelled as 2, which is connecting all spins to a random bath. The temperature
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of this bath is set to 300 K, and the value of the transverse Gilbert damping is set to 0.01.
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The seed is set to 21.
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For LAMMPS to understand that the motion of spins has to be taken into account, one has to set
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a fix to {nve/spin}. The command is:
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fix A B C D
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with A the label of this fix, B defining to which group of atoms this fix is applied to, C has
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to be set to {nve/spin}, and D can be set to {serial} for a serial calculation, with one
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processor only, or to {mpi} for a parallel calculation, with N processors.
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Example:
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fix 3 all nve/spin mpi
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is setting a fix labelled 3, and applies it to all the particles. The calculation is running in
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parallel as the option {mpi} is defined.
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Two main outputs of the computed magnetic quntities can be performed.
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The first one is via a compute and a fix options. The compute command is defined as:
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compute A B C
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with A the label of this compute, B to which group of particles it is applied to, and finally,
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the option {compute/spin} has to be set.
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This compute is associated to a fix to define the output frequency and format. A typical command is:
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fix A B C D E F G H
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where A is the label of the fix, B the group of particles it is applied to, C defines the type of the
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output fix, for example we chose to use {ave/time}, which can output every N timesteps, and perform
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a time average over those steps. D, E, and F are the usual command of {ave/time}. G stands for the
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magnetic quantities that are computed by {compute/spin}. Those quantities are:
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c_mag[1] Physical time (in ps)
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c_mag[2] Magnetization along x (adim)
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c_mag[3] Magnetization along y (adim)
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c_mag[4] Magnetization along z (adim)
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c_mag[5] Magnetization Norm (adim)
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c_mag[6] Magnetic energy (in eV)
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c_mag[7] Spin temperature (in K)
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And H stands for the output format, and is defined as in other .
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Example:
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compute 1 all compute/spin
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fix 3 all ave/time 1 1 10 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7]
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file mag_output.dat format %20.16g
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is defining a compute of the magnetic quantities applied to all spins. The fix then outputs
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every magnetic quantities every 10 time steps without performing any time average. These
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quantities are stored in a file called mag_output.dat, with a special format (defined by %20.16g)
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It is also possible to output the evolution of the spin configuration. This can be done with
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the dump command. The only difference with a regular dump command is that the velocities
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vi are replaced by the spin components spi.
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Example:
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dump 1 all custom 100 dump_spin.lammpstrj type x y z spx spy spz
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is dumping every 100 timesteps the spin configuration in a file called dump_spin.lammpstrj.
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:line
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:link(Antropov)
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[(Antropov)] Antropov, Katsnelson, Harmon, Van Schilfgaarde, and Kusnezov, Phys Rev B, 54(2), 1019 (1996)
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@ -0,0 +1,109 @@
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###################
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#######Init########
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###################
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clear
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#setting units to metal (Ang, picosecs, eV, ...):
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units metal
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#setting dimension of the system (N=2 or 3):
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dimension 3
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#setting boundary conditions. (p for periodic, f for fixed, ...)
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boundary p p f
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#setting atom_style to spin:
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atom_style spin
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#Define sort for paramagnetic simulations (if no pair interaction)
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#atom_modify sort 1000 4.0
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#why?
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atom_modify map array
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#newton off for pair spin in SEQNEI
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#newton off off
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###########################
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#######Create atoms########
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###########################
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#Lattice constant of sc Iron atoms of BFO
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lattice sc 3.96
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#Defining a geometric region of space. Sets ID(user's choice), style(block, sphere, ...), then, args depends on the style chosen
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#(for block, one has x0, xf, y0, yf, z0, zf, in distance units)
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region box block 0.0 17.0 0.0 17.0 0.0 5.0
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#Creating a simulation box based on the specified region. Entries: number of atom types and box ref.
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create_box 1 box
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#Creating atoms (or molecules) on a lattice, or a single atom (or molecule), ...
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#Entries: atom type,
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create_atoms 1 box
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#Replicating NxNxN the entire set of atoms
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#replicate 1 1 1
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#######################
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#######Settings########
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#######################
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#Setting one or more properties of one or more atoms.
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#Setting mass
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mass 1 1.0
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#set group all mass 1.0
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#Setting spins orientation and moment
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set group all spin/random 11 2.50
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#set group all spin 2.50 1.0 0.0 0.0
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#Magnetic exchange interaction coefficient for bulk fcc Cobalt
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pair_style pair/spin 5.7
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#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
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pair_coeff * * exchange 5.7 -0.01575 0.0 1.965
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#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
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#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
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#pair_coeff * * me 4.0 0.000109 1.0 1.0 1.0
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#Mex10
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pair_coeff * * me 4.0 0.00109 1.0 1.0 1.0
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#Define a skin distance, update neigh list every
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#neighbor 1.0 bin
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#neigh_modify every 10 check yes delay 20
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neighbor 0.0 bin
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neigh_modify every 1 check no delay 0
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#Magnetic field fix
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#Type | Intensity (T or eV) | Direction
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#fix 1 all force/spin zeeman 1.0 0.0 0.0 1.0
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fix 1 all force/spin anisotropy 0.0000035 0.0 0.0 1.0
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#Fix Langevin spins (merging damping and temperature)
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#Temp | Alpha_trans | Alpha_long | Seed
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#fix 2 all langevin/spin 0.0 0.1 0.0 21
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fix 2 all langevin/spin 0.0 0.1 0.0 21
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#fix 2 all langevin/spin 0.0 0.0 0.0 21
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#Magnetic integration fix
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fix 3 all nve/spin mpi
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#compute real time, total magnetization, magnetic energy, and spin temperature
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#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
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compute mag all compute/spin
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fix outmag all ave/time 1 1 500 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7] file mag_BFO.dat format %20.16g
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#Setting the timestep for the simulation (in ps)
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timestep 0.0001
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##################
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#######run########
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##################
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#Dump the positions and spin directions of magnetic particles (vmd format)
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dump 1 all custom 5000 dump_spin_BFO.lammpstrj type x y z spx spy spz
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#Running the simulations for N timesteps
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run 30000
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#run 1
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@ -0,0 +1,126 @@
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###################
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#######Init########
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###################
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clear
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#setting units to metal (Ang, picosecs, eV, ...):
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units metal
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#setting dimension of the system (N=2 or 3):
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dimension 3
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#setting boundary conditions. (p for periodic, f for fixed, ...)
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boundary p p p
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#boundary f f f
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#setting atom_style to spin:
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atom_style spin
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#Define sort for paramagnetic simulations (if no pair interaction)
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#atom_modify sort 1000 4.0
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#why?
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atom_modify map array
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#newton off for pair spin in SEQNEI
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#newton off off
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###########################
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#######Create atoms########
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###########################
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#Lattice constant of fcc Cobalt
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lattice fcc 3.54
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#lattice sc 2.50
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#Test Kagome
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#variable a equal sqrt(3.0)/8.0
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#variable b equal 3.0*sqrt(3.0)/8.0
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#variable c equal sqrt(3.0)/4.0
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#lattice custom 2.5 a1 1.0 0.0 0.0 &
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# a2 0.0 1.0 0.0 &
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# a3 0.0 0.0 1.0 &
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# basis 0.0 $a 0.0 &
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# basis 0.25 $a 0.0 &
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# basis 0.375 0.0 0.0 &
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# basis 0.25 $b 0.0 &
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# basis 0.5 $b 0.0 &
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# basis 0.625 $c 0.0
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#Defining a geometric region of space. Sets ID(user's choice), style(block, sphere, ...), then, args depends on the style chosen
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#(for block, one has x0, xf, y0, yf, z0, zf, in distance units)
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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#Creating a simulation box based on the specified region. Entries: number of atom types and box ref.
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create_box 1 box
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#Creating atoms (or molecules) on a lattice, or a single atom (or molecule), ...
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#Entries: atom type,
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create_atoms 1 box
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#Replicating NxNxN the entire set of atoms
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#replicate 1 1 1
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#######################
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#######Settings########
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#######################
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#Setting one or more properties of one or more atoms.
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#Setting mass
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mass 1 1.0
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#set group all mass 1.0
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#Setting spins orientation and moment
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#set group all spin/random 11 1.72
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set group all spin 1.72 1.0 0.0 0.0
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#Magnetic exchange interaction coefficient for bulk fcc Cobalt
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pair_style pair/spin 4.0
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#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
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pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
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#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
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#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
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#pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
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#Define a skin distance, update neigh list every
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 10 check yes delay 20
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 1.0 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy -0.1 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.1 0.0 1.0 0.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
#fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
fix 2 all langevin/spin 1.0 0.1 0.0 21
|
||||
#fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all nve/spin mpi
|
||||
|
||||
#compute real time, total magnetization, magnetic energy, and spin temperature
|
||||
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
|
||||
compute mag all compute/spin
|
||||
fix outmag all ave/time 1 1 10 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7] file mag_Co_nodamp.dat format %20.16g
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 100 dump_spin_T100.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 2000
|
||||
#run 1
|
||||
|
||||
|
|
@ -0,0 +1,126 @@
|
|||
###################
|
||||
#######Init########
|
||||
###################
|
||||
|
||||
clear
|
||||
#setting units to metal (Ang, picosecs, eV, ...):
|
||||
units metal
|
||||
|
||||
#setting dimension of the system (N=2 or 3):
|
||||
dimension 3
|
||||
|
||||
#setting boundary conditions. (p for periodic, f for fixed, ...)
|
||||
boundary p p p
|
||||
#boundary f f f
|
||||
|
||||
#setting atom_style to spin:
|
||||
atom_style spin
|
||||
|
||||
#Define sort for paramagnetic simulations (if no pair interaction)
|
||||
#atom_modify sort 1000 4.0
|
||||
|
||||
#why?
|
||||
atom_modify map array
|
||||
|
||||
#newton off for pair spin in SEQNEI
|
||||
#newton off off
|
||||
|
||||
###########################
|
||||
#######Create atoms########
|
||||
###########################
|
||||
|
||||
#Lattice constant of fcc Cobalt
|
||||
lattice fcc 3.54
|
||||
#lattice sc 2.50
|
||||
|
||||
#Test Kagome
|
||||
#variable a equal sqrt(3.0)/8.0
|
||||
#variable b equal 3.0*sqrt(3.0)/8.0
|
||||
#variable c equal sqrt(3.0)/4.0
|
||||
|
||||
#lattice custom 2.5 a1 1.0 0.0 0.0 &
|
||||
# a2 0.0 1.0 0.0 &
|
||||
# a3 0.0 0.0 1.0 &
|
||||
# basis 0.0 $a 0.0 &
|
||||
# basis 0.25 $a 0.0 &
|
||||
# basis 0.375 0.0 0.0 &
|
||||
# basis 0.25 $b 0.0 &
|
||||
# basis 0.5 $b 0.0 &
|
||||
# basis 0.625 $c 0.0
|
||||
|
||||
#Defining a geometric region of space. Sets ID(user's choice), style(block, sphere, ...), then, args depends on the style chosen
|
||||
#(for block, one has x0, xf, y0, yf, z0, zf, in distance units)
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
|
||||
#Creating a simulation box based on the specified region. Entries: number of atom types and box ref.
|
||||
create_box 1 box
|
||||
|
||||
#Creating atoms (or molecules) on a lattice, or a single atom (or molecule), ...
|
||||
#Entries: atom type,
|
||||
create_atoms 1 box
|
||||
|
||||
#Replicating NxNxN the entire set of atoms
|
||||
#replicate 1 1 1
|
||||
|
||||
|
||||
#######################
|
||||
#######Settings########
|
||||
#######################
|
||||
|
||||
#Setting one or more properties of one or more atoms.
|
||||
#Setting mass
|
||||
mass 1 1.0
|
||||
#set group all mass 1.0
|
||||
#Setting spins orientation and moment
|
||||
#set group all spin/random 11 1.72
|
||||
set group all spin 1.72 1.0 0.0 0.0
|
||||
|
||||
#Magnetic exchange interaction coefficient for bulk fcc Cobalt
|
||||
pair_style pair/spin 4.0
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
|
||||
#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
|
||||
#pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 10 check yes delay 20
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 1.0 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy -0.1 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.1 0.0 1.0 0.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
#fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
fix 2 all langevin/spin 1.0 0.1 0.0 21
|
||||
#fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all nve/spin mpi
|
||||
|
||||
#compute real time, total magnetization, magnetic energy, and spin temperature
|
||||
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
|
||||
compute mag all compute/spin
|
||||
fix outmag all ave/time 1 1 10 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7] file mag_Co_nodamp.dat format %20.16g
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 100 dump_spin_T100.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 2000
|
||||
#run 1
|
||||
|
||||
|
|
@ -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 3.0
|
||||
set res 5
|
||||
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_spin_T100.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
|
||||
scale by 0.5
|
||||
animate style Loop
|
||||
enable_trace
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue