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Commit modifs before release 2 (04/02/18)
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@ -36,7 +36,8 @@ This section describes how to perform common tasks using LAMMPS.
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6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
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6.25 "Polarizable models"_#howto_25
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6.26 "Adiabatic core/shell model"_#howto_26
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6.27 "Drude induced dipoles"_#howto_27 :all(b)
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6.27 "Drude induced dipoles"_#howto_27
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6.28 "Magnetic spins"_#howto_28 :all(b)
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The example input scripts included in the LAMMPS distribution and
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highlighted in "Section 7"_Section_example.html also show how to
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@ -2837,6 +2838,7 @@ CS-Info # header of additional section :pre
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4 2
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5 3
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6 3
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The interactions between the
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7 4
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8 4
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(...) :pre
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@ -2906,6 +2908,54 @@ with a Coulomb pair style. It may be useful to use {coul/long/cs} or
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similar from the CORESHELL package if the core and Drude particle come
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too close, which can cause numerical issues.
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:line
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6.28 Magnetic spins :link(howto_28),h4
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The magnetic spin simualtions are enabled by the SPIN package, whose
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implementation is detailed in "Tranchida"_#Tranchida7.
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The model representents the simulation of atomic magnetic spins coupled
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to lattice vibrations. The dynamics of those magnetic spins can be used
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to simulate a broad range a phenomena related to magneto-elasticity, or
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or to study the influence of defects on the magnetic properties of
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materials.
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The magnetic spins are interacting with each others and with the
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lattice via pair interactions. Typically, the magnetic exchange
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interaction can be defined using the
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"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
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applies a magnetic torque to a given spin, considering the orientation
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of its neighboring spins and their relative distances.
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It also applies a force on the atoms as a function of the spin
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orientations and their associated inter-atomic distances.
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The command "fix precession/spin"_fix_precession_spin.html allows to
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apply a constant magnetic torque on all the spins in the system. This
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torque can be an external magnetic field (Zeeman interaction), or an
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uniaxial magnetic anisotropy.
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A Langevin thermostat can be applied to those magnetic spins using
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"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
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can be coupled to another Langevin thermostat applied to the atoms
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using "fix langevin"_fix_langevin.html in order to simulate
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thermostated spin-lattice system.
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The magnetic Gilbert damping can also be applied using "fix
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langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
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the thermal energy of the Langevin thermostat, or to perform a
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relaxation of the magnetic configuration toward an equilibrium state.
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All the computed magnetic properties can be outputed by two main
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commands. The first one is "compute spin"_compute_spin.html, that
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enables to evaluate magnetic averaged quantities, such as the total
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magnetization of the system along x, y, or z, the spin temperature, or
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the magnetic energy. The second command is "compute
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property/atom"_compute_property_atom.html. It enables to output all the
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per atom magnetic quantities. Typically, the orientation of a given
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magnetic spin, or the magnetic force acting on this spin.
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:line
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:line
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@ -2957,3 +3007,7 @@ Phys, 79, 926 (1983).
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:link(howto-Lamoureux)
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[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
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:link(Tranchida7)
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[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
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arXiv preprint arXiv:1801.10233, (2018).
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@ -19,6 +19,7 @@ input = one or more atom attributes :l
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x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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sp, spx, spy, spz, fmx, fmy, fmz,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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shapex,shapey, shapez,
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@ -46,6 +47,9 @@ input = one or more atom attributes :l
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q = atom charge
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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sp = atomic magnetic spin moment
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spx, spy, spz = direction of the atomic magnetic spin
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fmx, fmy, fmz = magnetic force
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radius,diameter = radius,diameter of spherical particle
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omegax,omegay,omegaz = angular velocity of spherical particle
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angmomx,angmomy,angmomz = angular momentum of aspherical particle
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@ -82,7 +86,8 @@ input = one or more atom attributes :l
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compute 1 all property/atom xs vx fx mux
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compute 2 all property/atom type
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compute 1 all property/atom ix iy iz :pre
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compute 1 all property/atom ix iy iz
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compute 3 all property/atom sp spx spy spz :pre
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[Description:]
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@ -152,6 +157,10 @@ The vector or array values will be in whatever "units"_units.html the
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corresponding attribute is in, e.g. velocity units for vx, charge
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units for q, etc.
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For the spin quantities, sp is in the units of the Bohr magneton, spx,
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spy, and spz are adimentional quantities, and fmx, fmy and fmz are
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given in rad.THz.
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[Restrictions:] none
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[Related commands:]
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@ -6,22 +6,22 @@
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:line
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fix integration/spin command :h3
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fix nve/spin command :h3
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[Syntax:]
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fix ID group-ID integration/spin keyword values :pre
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fix ID group-ID nve/spin keyword values :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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integration/spin = style name of this fix command :l
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nve/spin = style name of this fix command :l
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keyword = {lattice} :l
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{lattice} value = {no} or {yes} :pre
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:ule
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[Examples:]
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fix 3 all integration/spin lattice yes
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fix 1 all integration/spin lattice no :pre
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fix 3 all nve/spin lattice yes
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fix 1 all nve/spin lattice no :pre
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[Description:]
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@ -32,7 +32,7 @@ of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
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By default (lattice = yes), a spin-lattice integration is performed.
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The {integration/spin} fix applies a Suzuki-Trotter decomposition to
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The {nve/spin} fix applies a Suzuki-Trotter decomposition to
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the equations of motion of the spin lattice system, following the scheme:
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:c,image(Eqs/fix_integration_spin_stdecomposition.jpg)
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@ -51,9 +51,8 @@ This fix style can only be used if LAMMPS was built with the
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SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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When the spin algorithm is used for serial calculations, it is
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necessary to define a map via the atom_modify command.
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Typically, by adding the command:
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To use the spin algorithm, it is necessary to define a map with
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the atom_modify command. Typically, by adding the command:
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atom_modify map array :pre
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@ -6,14 +6,14 @@
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:line
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fix force/spin command :h3
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fix precession/spin command :h3
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[Syntax:]
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fix ID group force/spin style args :pre
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fix ID group precession/spin style args :pre
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ID, group are documented in "fix"_fix.html command :ulb,l
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force/spin = style name of this fix command :l
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precession/spin = style name of this fix command :l
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style = {zeeman} or {aniso} :l
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{zeeman} args = H x y z
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H = intensity of the magnetic field (in Tesla)
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@ -25,8 +25,8 @@ style = {zeeman} or {aniso} :l
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[Examples:]
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fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
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fix 1 all force/spin aniso 0.001 0.0 0.0 1.0 :pre
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fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
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fix 1 all precession/spin aniso 0.001 0.0 0.0 1.0 :pre
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[Description:]
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@ -61,7 +61,7 @@ files"_restart.html.
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[Restrictions:]
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The {force/spin} style is part of the SPIN package.
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The {precession/spin} style is part of the SPIN package.
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This style is only enabled if LAMMPS was built with this package, and
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if the atom_style "spin" was declared.
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See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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@ -54,4 +54,4 @@ thermo 10
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compute outsp all property/atom spx spy spz sp fmx fmy fmz
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dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
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run 20000
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run 2000
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@ -67,6 +67,8 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) :
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sector_flag = NONE;
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mech_flag = 1;
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nlocal_max = 0;
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// checking if map array or hash is defined
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if (atom->map_style == 0)
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@ -220,11 +222,14 @@ void FixNVESpin::init()
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if (sector_flag) sectoring();
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// init. size tables of stacking variables (sectoring)
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nlocal_max = atom->nlocal;
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stack_head = memory->grow(stack_head,nsectors,"NVE/spin:stack_head");
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stack_foot = memory->grow(stack_foot,nsectors,"NVE/spin:stack_foot");
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forward_stacks = memory->grow(forward_stacks,atom->nmax,"NVE/spin:forward_stacks");
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backward_stacks = memory->grow(backward_stacks,atom->nmax,"NVE/spin:backward_stacks");
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forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks");
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backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks");
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if (nlocal_max == 0)
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error->all(FLERR,"Incorrect value of nlocal_max");
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}
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@ -359,6 +364,12 @@ void FixNVESpin::pre_neighbor()
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double **x = atom->x;
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int nlocal = atom->nlocal;
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if (nlocal_max < nlocal) { // grow linked lists if necessary
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nlocal_max = nlocal;
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forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks");
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backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks");
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}
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for (int j = 0; j < nsectors; j++) {
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stack_head[j] = -1;
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stack_foot[j] = -1;
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@ -455,7 +466,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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temp_cut = 0.0;
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if (exch_flag) { // exchange
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if (exch_flag) { // exchange
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temp_cut = lockpairspinexchange->cut_spin_exchange[itype][jtype];
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cut_2 = temp_cut*temp_cut;
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if (rsq <= cut_2) {
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@ -474,7 +485,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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}
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}
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if (soc_dmi_flag) { // soc_dmi
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if (soc_dmi_flag) { // soc_dmi
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temp_cut = lockpairspinsocdmi->cut_soc_dmi[itype][jtype];
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cut_2 = temp_cut*temp_cut;
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if (rsq <= cut_2) {
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@ -482,7 +493,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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}
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}
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if (me_flag) { // me
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if (me_flag) { // me
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temp_cut = lockpairspinme->cut_spin_me[itype][jtype];
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cut_2 = temp_cut*temp_cut;
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if (rsq <= cut_2) {
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@ -496,19 +507,19 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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}
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if (magprecession_flag) { // magnetic precession
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if (zeeman_flag) { // zeeman
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if (zeeman_flag) { // zeeman
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lockprecessionspin->compute_zeeman(i,fmi);
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}
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if (aniso_flag) { // aniso
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if (aniso_flag) { // aniso
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lockprecessionspin->compute_anisotropy(i,spi,fmi);
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}
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}
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if (maglangevin_flag) { // mag. langevin
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if (tdamp_flag) { // transverse damping
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if (maglangevin_flag) { // mag. langevin
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if (tdamp_flag) { // transverse damping
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locklangevinspin->add_tdamping(spi,fmi);
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}
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if (temp_flag) { // spin temperature
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if (temp_flag) { // spin temperature
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locklangevinspin->add_temperature(fmi);
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}
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}
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@ -522,7 +533,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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}
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/* ----------------------------------------------------------------------
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divide each domain into sectors
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divide each domain into 8 sectors
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---------------------------------------------------------------------- */
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void FixNVESpin::sectoring()
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@ -11,6 +11,11 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ------------------------------------------------------------------------
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Contributing authors: Julien Tranchida (SNL)
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Aidan Thompson (SNL)
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(nve/spin,FixNVESpin)
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@ -44,13 +49,15 @@ class FixNVESpin : public Fix {
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void pre_neighbor();
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protected:
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int sector_flag; // sector_flag = 0 if serial algorithm
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// sector_flag = 1 if parallel algorithm
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int mech_flag; // mech_flag = 0 if spins only
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// mech_flag = 1 if spin-lattice calc.
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int sector_flag; // sector_flag = 0 if serial algorithm
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// sector_flag = 1 if parallel algorithm
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int mech_flag; // mech_flag = 0 if spins only
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// mech_flag = 1 if spin-lattice calc.
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double dtv, dtf, dts; // velocity, force, and spin timesteps
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double dtv, dtf, dts; // velocity, force, and spin timesteps
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int nlocal_max; // max value of nlocal (for lists size)
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int magpair_flag; // magnetic pair flags
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int exch_flag;
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int soc_neel_flag, soc_dmi_flag;
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