forked from lijiext/lammps
Changes for coupling magnetomech:
- hybrid_overlay friend with fix_nve_spin - modif of the allocation of pair classes in fix_nve_spin - modif input file for hybrid/overlay eam - spin/pair - new file for cobalt eam potentials
This commit is contained in:
julient31
parent
45ea7b3cc7
commit
f5ff30df83
File diff suppressed because it is too large
Load Diff
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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
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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 0.001 0.0 0.0 1.0
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#fix 1 all force/spin anisotropy -0.1 0.0 0.0 1.0
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#fix 1 all force/spin anisotropy 0.1 0.0 1.0 0.0
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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 1.0 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 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
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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 100 dump_spin_T100.lammpstrj type x y z spx spy spz
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#Running the simulations for N timesteps
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run 2000
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#run 1
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@ -0,0 +1,111 @@
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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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#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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#######################
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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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#Magneto-mechanic interactions for bulk fcc Cobalt
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pair_style hybrid/overlay eam/alloy pair/spin 4.0
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pair_coeff * * eam/alloy ../Co_PurjaPun_2012.eam.alloy Co
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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 * * pair/spin 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
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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 10.0 0.0 0.0 1.0
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#fix 1 all force/spin anisotropy 0.001 0.0 0.0 1.0
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#fix 1 all force/spin anisotropy -0.1 0.0 0.0 1.0
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#fix 1 all force/spin anisotropy 0.1 0.0 1.0 0.0
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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 1.0 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 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
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#Setting the timestep for the simulation (in ps)
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timestep 0.00001
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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 100 dump_spin_MM.lammpstrj type x y z spx spy spz
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#Running the simulations for N timesteps
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run 10000
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#run 1
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19
in.cobalt
19
in.cobalt
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@ -32,21 +32,6 @@ atom_modify map array
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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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@ -59,10 +44,6 @@ create_box 1 box
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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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@ -34,6 +34,7 @@
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#include "memory.h"
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#include "fix_force_spin.h"
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#include "fix_langevin_spin.h"
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#include "pair_hybrid.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -114,7 +115,21 @@ void FixNVESpin::init()
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memory->create(fmi,3,"nves:fmi");
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memory->create(fmj,3,"nves:fmj");
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lockpairspin = (PairSpin *) force->pair;
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if (strstr(force->pair_style,"pair/spin")) {
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lockpairspin = (PairSpin *) force->pair;
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} else if (strstr(force->pair_style,"hybrid/overlay")) {
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PairHybrid *lockhybrid = (PairHybrid *) force->pair;
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int nhybrid_styles = lockhybrid->nstyles;
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int ipair;
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for (ipair = 0; ipair < nhybrid_styles; ipair++) {
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if (strstr(lockhybrid->keywords[ipair],"pair/spin")) {
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lockpairspin = (PairSpin *) lockhybrid->styles[ipair];
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}
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}
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} else error->all(FLERR,"Illegal fix nve/spin command");
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// check errors, and handle simple hybrid (not overlay)
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int iforce;
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for (iforce = 0; iforce < modify->nfix; iforce++)
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@ -125,15 +140,29 @@ void FixNVESpin::init()
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if (strstr(modify->fix[iforce]->style,"langevin/spin")) break;
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locklangevinspin = (FixLangevinSpin *) modify->fix[iforce];
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exch_flag = lockpairspin->exch_flag;
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dmi_flag = lockpairspin->dmi_flag;
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me_flag = lockpairspin->me_flag;
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if (lockpairspin->exch_flag == 1) {
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exch_flag = lockpairspin->exch_flag;
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}
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if (lockpairspin->dmi_flag == 1) {
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dmi_flag = lockpairspin->dmi_flag;
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}
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if (lockpairspin->me_flag == 1) {
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me_flag = lockpairspin->me_flag;
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}
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zeeman_flag = lockforcespin->zeeman_flag;
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aniso_flag = lockforcespin->aniso_flag;
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if (lockforcespin->zeeman_flag == 1) {
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zeeman_flag = lockforcespin->zeeman_flag;
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}
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if (lockforcespin->aniso_flag == 1) {
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aniso_flag = lockforcespin->aniso_flag;
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}
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tdamp_flag = locklangevinspin->tdamp_flag;
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temp_flag = locklangevinspin->temp_flag;
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if (locklangevinspin->tdamp_flag == 1) {
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tdamp_flag = locklangevinspin->tdamp_flag;
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}
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if (locklangevinspin->temp_flag == 1){
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temp_flag = locklangevinspin->temp_flag;
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}
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if (mpi_flag == 1) {
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sectoring();
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@ -173,7 +202,6 @@ void FixNVESpin::initial_integrate(int vflag)
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int *type = atom->type;
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int *mask = atom->mask;
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// update half v all particles
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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@ -193,7 +221,6 @@ void FixNVESpin::initial_integrate(int vflag)
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x[i][2] += 0.5 * dtv * v[i][2];
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}
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}
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if (extra == SPIN) {
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if (mpi_flag == 1) {
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@ -236,7 +263,7 @@ void FixNVESpin::initial_integrate(int vflag)
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} else error->all(FLERR,"Illegal fix nve/spin command");
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}
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// update x for all particles
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// update half x for all particles
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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x[i][0] += 0.5 * dtv * v[i][0];
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@ -279,10 +306,13 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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int *type = atom->type;
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const int newton_pair = force->newton_pair;
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inum = lockpairspin->list->inum;
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ilist = lockpairspin->list->ilist;
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numneigh = lockpairspin->list->numneigh;
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firstneigh = lockpairspin->list->firstneigh;
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// add test here
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if (exch_flag == 1 || dmi_flag == 1 || me_flag == 1 ) {
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inum = lockpairspin->list->inum;
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ilist = lockpairspin->list->ilist;
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numneigh = lockpairspin->list->numneigh;
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firstneigh = lockpairspin->list->firstneigh;
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}
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double xtmp,ytmp,ztmp;
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double rsq,rd,delx,dely,delz;
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@ -350,6 +380,7 @@ void FixNVESpin::ComputeInteractionsSpin(int ii)
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lockpairspin->compute_me(i,j,fmi,fmj,spi,spj);
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}
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}
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}
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// post force
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@ -47,6 +47,7 @@ class FixNVESpin : public FixNVE {
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int zeeman_flag, aniso_flag;
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int tdamp_flag, temp_flag;
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class PairHybrid *lockhybrid;
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class PairSpin *lockpairspin;
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class FixForceSpin *lockforcespin;
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class FixLangevinSpin *locklangevinspin;
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@ -39,7 +39,6 @@ PairSpin::PairSpin(LAMMPS *lmp) : Pair(lmp)
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exch_flag = 0;
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dmi_flag = 0;
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me_flag = 0;
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}
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/* ---------------------------------------------------------------------- */
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@ -364,7 +363,8 @@ void PairSpin::coeff(int narg, char **arg)
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if (count == 0) error->all(FLERR,"Incorrect args in pair_style command");
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} else if (strcmp(arg[2],"dmi")==0) {
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if (narg != 8) error->all(FLERR,"Incorrect args in pair_style command");
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dmi_flag = 1;
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dmi_flag = 1;
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int ilo,ihi,jlo,jhi;
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force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
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force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
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@ -426,7 +426,8 @@ void PairSpin::coeff(int narg, char **arg)
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if (count == 0) error->all(FLERR,"Incorrect args in pair_style command");
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} else error->all(FLERR,"Incorrect args in pair_style command");
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//Check if Jex [][] still works for Ferrimagnetic exchange
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// check if Jex [][] still works for Ferrimagnetic exchange
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}
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@ -31,6 +31,7 @@ class PairHybrid : public Pair {
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friend class FixOMP;
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friend class Force;
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friend class Respa;
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friend class FixNVESpin;
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friend class Info;
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public:
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PairHybrid(class LAMMPS *);
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@ -70,7 +70,7 @@ proc enable_trace {} {
|
|||
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
|
||||
}
|
||||
|
||||
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump_spin_BFO.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
|
||||
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump_spin_MM.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