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This commit is contained in:
julient31
2018-01-15 11:39:44 -07:00
parent 38e940a392
commit 1e096d77ef
8 changed files with 127 additions and 97 deletions
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72
examples/SPIN/in.spin.bfo
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@ -3,14 +3,9 @@
###################
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 f
boundary p p p
#setting atom_style to spin:
atom_style spin
@ -21,8 +16,6 @@ atom_style spin
#why?
atom_modify map array
#newton off for pair spin in SEQNEI
#newton off off
###########################
#######Create atoms########
@ -30,49 +23,31 @@ atom_modify map array
#Lattice constant of sc Iron atoms of BFO
lattice sc 3.96
#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 17.0 0.0 17.0 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 2.50
#set group all spin 2.50 1.0 0.0 0.0
#Magnetic exchange interaction coefficient for bulk fcc Cobalt
pair_style pair/spin 5.7
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
pair_coeff * * exchange 5.7 -0.01575 0.0 1.965
#Magnetic interactions for BFO
#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 4.0 0.000109 1.0 1.0 1.0
#Mex10
pair_coeff * * me 4.0 0.00109 1.0 1.0 1.0
pair_style hybrid/overlay pair/spin/exchange 6.0 pair/spin/me 4.5
pair_coeff * * pair/spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * pair/spin/me me 4.5 0.00109 1.0 1.0 1.0
#pair_coeff * * pair/spin/soc/dmi dmi 4.5 0.001 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
neigh_modify every 10 check yes delay 20
#Magnetic field fix
#Type | Intensity (T or eV) | Direction
@ -81,17 +56,10 @@ fix 1 all force/spin anisotropy 0.0000035 0.0 0.0 1.0
#Fix Langevin spins (merging damping and temperature)
#Temp | Alpha_trans | Alpha_long | Seed
#fix 2 all langevin/spin 0.0 0.1 0.0 21
fix 2 all langevin/spin 0.0 0.1 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 1 500 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
fix 3 all integration/spin serial
#Setting the timestep for the simulation (in ps)
timestep 0.0001
@ -100,10 +68,26 @@ timestep 0.0001
#######run########
##################
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
#compute real time, total magnetization, magnetic energy, and spin temperature
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
variable magz equal c_out_mag[4]
variable magnorm equal c_out_mag[5]
variable emag equal c_out_mag[6]
variable tmag equal c_out_mag[7]
variable mag_force equal f_1
thermo 10
thermo_style custom step time v_magnorm v_emag temp etotal
thermo_modify format float %20.15g
#Dump the positions and spin directions of magnetic particles (vmd format)
dump 1 all custom 5000 dump_spin_BFO.lammpstrj type x y z spx spy spz
dump 1 all custom 100 dump_spin_BFO.lammpstrj type x y z spx spy spz
#Running the simulations for N timesteps
run 30000
#run 1
run 50000

24
examples/SPIN/in.spin.cobalt
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@ -5,8 +5,8 @@
clear
units metal
dimension 3
boundary p p p
#boundary p p f
#boundary p p p
boundary p p f
#newton off
@ -42,13 +42,14 @@ set group all spin/random 31 1.72
#set group all spin 1.72 0.0 0.0 1.0
#set group single_spin spin/random 11 1.72
velocity all create 200 4928459 rot yes dist gaussian
#velocity all create 200 4928459 rot yes dist gaussian
velocity all create 10 4928459 rot yes dist gaussian
#Magneto-mechanic interactions for bulk fcc Cobalt
#pair_style pair/spin/exchange 4.0
#pair_style eam/alloy
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
#pair_coeff * * ../Co_PurjaPun_2012.eam.alloy Co
@ -57,8 +58,9 @@ pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
#pair_coeff * * exchange 4.0 -0.0446928 0.003496 1.4885
#pair_coeff * * exchange 4.0 0.0 0.003496 1.4885
#pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
#pair_coeff * * pair/spin/exchange exchange 2.5 0.0446928 0.003496 1.4885
#pair_coeff * * pair/spin/exchange exchange 4.0 0.0 0.003496 1.4885
#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
@ -66,14 +68,13 @@ pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
#type i and j | interaction type | cutoff | K1 (eV) | K2 (adim) | K3 (Ang) (for SOC)
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.0 0.864159 2.13731
#Define a skin distance, update neigh list every
#neighbor 0.1 bin
#neigh_modify every 10 check yes delay 20
neighbor 0.1 bin
neigh_modify every 1 check no delay 0
neigh_modify every 10 check yes delay 20
#neighbor 1.0 bin
#neigh_modify every 1 check no delay 0
#Magnetic field fix
#Type | Intensity (T or eV) | Direction
@ -111,14 +112,13 @@ variable mag_force equal f_1
#variable test equal etotal-0.5*c_out_mag[6]
thermo 10
#thermo_style custom step time v_emag c_out_pe c_out_ke c_out_temp v_mag_force v_magnorm v_tmag etotal
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
thermo_style custom step time v_magnorm v_emag temp etotal
thermo_modify format float %20.15g
#Dump the positions and spin directions of magnetic particles (vmd format)
dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
#Running the simulations for N timesteps
#run 1
run 10000
#run 10000

2
src/SPIN/atom_vec_spin.cpp
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@ -45,7 +45,7 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
size_reverse = 6;
size_border = 11;
size_velocity = 3;
size_data_atom = 9; // to check later
size_data_atom = 9;
size_data_vel = 4;
xcol_data = 4;

20
src/SPIN/fix_integration_spin.cpp
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@ -85,6 +85,7 @@ FixIntegrationSpin::FixIntegrationSpin(LAMMPS *lmp, int narg, char **arg) :
magpair_flag = 0;
exch_flag = 0;
soc_neel_flag = soc_dmi_flag = 0;
me_flag = 0;
magforce_flag = 0;
zeeman_flag = aniso_flag = 0;
maglangevin_flag = 0;
@ -137,6 +138,9 @@ void FixIntegrationSpin::init()
} else if (strstr(force->pair_style,"pair/spin/soc/dmi")) {
soc_dmi_flag = 1;
lockpairspinsocdmi = (PairSpinSocDmi *) force->pair;
} else if (strstr(force->pair_style,"pair/spin/me")) {
me_flag = 1;
lockpairspinme = (PairSpinMe *) force->pair;
} else if (strstr(force->pair_style,"hybrid/overlay")) {
PairHybrid *lockhybrid = (PairHybrid *) force->pair;
int nhybrid_styles = lockhybrid->nstyles;
@ -151,6 +155,9 @@ void FixIntegrationSpin::init()
} else if (strstr(lockhybrid->keywords[ipair],"pair/spin/soc/dmi")) {
soc_dmi_flag = 1;
lockpairspinsocdmi = (PairSpinSocDmi *) lockhybrid->styles[ipair];
} else if (strstr(lockhybrid->keywords[ipair],"pair/spin/me")) {
me_flag = 1;
lockpairspinme = (PairSpinMe *) lockhybrid->styles[ipair];
}
}
} else error->all(FLERR,"Illegal fix integration/spin command");
@ -189,7 +196,7 @@ void FixIntegrationSpin::init()
if (mpi_flag) sectoring();
// grow tables for k and adv_list
// grow tables of stacking variables
stack_head = memory->grow(stack_head,nsectors,"integration/spin:stack_head");
stack_foot = memory->grow(stack_foot,nsectors,"integration/spin:stack_foot");
@ -461,6 +468,17 @@ void FixIntegrationSpin::ComputeInteractionsSpin(int ii)
}
}
if (me_flag) { // me
temp_cut = lockpairspinme->cut_spin_me[itype][jtype];
cut_2 = temp_cut*temp_cut;
if (rsq <= cut_2) {
eij[0] = rij[0]*inorm;
eij[1] = rij[1]*inorm;
eij[2] = rij[2]*inorm;
lockpairspinme->compute_me(i,j,eij,fmi,spi,spj);
}
}
}
if (magforce_flag) { // mag. forces

2
src/SPIN/fix_integration_spin.h
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@ -51,6 +51,7 @@ class FixIntegrationSpin : public Fix {
int magpair_flag; // magnetic pair flags
int exch_flag;
int soc_neel_flag, soc_dmi_flag;
int me_flag;
int magforce_flag; // magnetic force flags
int zeeman_flag, aniso_flag;
int maglangevin_flag; // magnetic langevin flags
@ -62,6 +63,7 @@ class FixIntegrationSpin : public Fix {
class PairSpinExchange *lockpairspinexchange;
class PairSpinSocNeel *lockpairspinsocneel;
class PairSpinSocDmi *lockpairspinsocdmi;
class PairSpinMe *lockpairspinme;
class FixForceSpin *lockforcespin;
class FixLangevinSpin *locklangevinspin;

94
src/SPIN/pair_spin_me.cpp
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@ -42,11 +42,12 @@ PairSpinMe::PairSpinMe(LAMMPS *lmp) : Pair(lmp)
{
hbar = force->hplanck/MY_2PI;
newton_pair_spin = 0; // no newton pair for now
//newton_pair_spin = 0; // no newton pair for now
// newton_pair = 0;
single_enable = 0;
me_flag = 0;
me_mech_flag = 0;
no_virial_fdotr_compute = 1;
}
@ -60,6 +61,7 @@ PairSpinMe::~PairSpinMe()
memory->destroy(cut_spin_me);
memory->destroy(ME);
memory->destroy(ME_mech);
memory->destroy(v_mex);
memory->destroy(v_mey);
memory->destroy(v_mez);
@ -150,7 +152,8 @@ void PairSpinMe::compute(int eflag, int vflag)
if (me_flag){
cut_me_2 = cut_spin_me[itype][jtype]*cut_spin_me[itype][jtype];
if (rsq <= cut_me_2){
compute_me(i,j,fmi,fmj,spi,spj);
compute_me(i,j,rij,fmi,spi,spj);
compute_me_mech(i,j,fi,spi,spj);
}
}
@ -161,14 +164,11 @@ void PairSpinMe::compute(int eflag, int vflag)
fm[i][1] += fmi[1];
fm[i][2] += fmi[2];
// if (newton_pair || j < nlocal) { => to be corrected
if (newton_pair_spin) {
if (newton_pair || j < nlocal) { // => to be corrected
// if (newton_pair_spin) {
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
fm[j][0] += fmj[0];
fm[j][1] += fmj[1];
fm[j][2] += fmj[2];
}
if (eflag) {
@ -189,30 +189,29 @@ void PairSpinMe::compute(int eflag, int vflag)
}
/* ---------------------------------------------------------------------- */
void PairSpinMe::compute_me(int i, int j, double fmi[3], double fmj[3], double spi[3], double spj[3])
void PairSpinMe::compute_me(int i, int j, double eij[3], double fmi[3], double spi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
itype = type[i];
jtype = type[j];
double **x = atom->x;
double meix,meiy,meiz;
double rx, ry, rz, inorm;
double rx, ry, rz;
double vx, vy, vz;
rx = x[j][0] - x[i][0];
ry = x[j][1] - x[i][1];
rz = x[j][2] - x[i][2];
inorm = 1.0/sqrt(rx*rx+ry*ry+rz*rz);
rx *= inorm;
ry *= inorm;
rz *= inorm;
rx = eij[0];
ry = eij[1];
rz = eij[2];
meix = v_mey[itype][jtype]*rz - v_mez[itype][jtype]*ry;
meiy = v_mez[itype][jtype]*rx - v_mex[itype][jtype]*rz;
meiz = v_mex[itype][jtype]*ry - v_mey[itype][jtype]*rx;
vx = v_mex[itype][jtype];
vy = v_mey[itype][jtype];
vz = v_mez[itype][jtype];
meix = vy*rz - vz*ry;
meiy = vz*rx - vx*rz;
meiz = vx*ry - vy*rx;
meix *= ME[itype][jtype];
meiy *= ME[itype][jtype];
@ -221,13 +220,39 @@ void PairSpinMe::compute_me(int i, int j, double fmi[3], double fmj[3], double
fmi[0] += spj[1]*meiz - spj[2]*meiy;
fmi[1] += spj[2]*meix - spj[0]*meiz;
fmi[2] += spj[0]*meiy - spj[1]*meix;
fmj[0] -= spi[1]*meiz - spi[2]*meiy;
fmj[1] -= spi[2]*meix - spi[0]*meiz;
fmj[2] -= spi[0]*meiy - spi[1]*meix;
}
/* ---------------------------------------------------------------------- */
void PairSpinMe::compute_me_mech(int i, int j, double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
itype = type[i];
jtype = type[j];
double meix,meiy,meiz;
double vx, vy, vz;
vx = v_mex[itype][jtype];
vy = v_mey[itype][jtype];
vz = v_mez[itype][jtype];
meix = spi[1]*spi[2] - spi[2]*spj[1];
meiy = spi[2]*spi[0] - spi[0]*spj[2];
meiz = spi[0]*spi[1] - spi[1]*spj[0];
meix *= ME_mech[itype][jtype];
meiy *= ME_mech[itype][jtype];
meiz *= ME_mech[itype][jtype];
fi[0] = meiy*vz - meiz*vy;
fi[1] = meiz*vx - meix*vz;
fi[2] = meix*vy - meiy*vx;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
@ -242,11 +267,12 @@ void PairSpinMe::allocate()
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cut_spin_me,n+1,n+1,"pair:cut_spin_me");
memory->create(ME,n+1,n+1,"pair:ME");
memory->create(v_mex,n+1,n+1,"pair:ME_vector_x");
memory->create(v_mey,n+1,n+1,"pair:ME_vector_y");
memory->create(v_mez,n+1,n+1,"pair:ME_vector_z");
memory->create(cut_spin_me,n+1,n+1,"pair/spin/me:cut_spin_me");
memory->create(ME,n+1,n+1,"pair/spin/me:ME");
memory->create(ME_mech,n+1,n+1,"pair/spin/me:ME_mech");
memory->create(v_mex,n+1,n+1,"pair/spin/me:ME_vector_x");
memory->create(v_mey,n+1,n+1,"pair/spin/me:ME_vector_y");
memory->create(v_mez,n+1,n+1,"pair/spin/me:ME_vector_z");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
@ -297,7 +323,7 @@ void PairSpinMe::coeff(int narg, char **arg)
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
const double rij = force->numeric(FLERR,arg[3]);
const double me = (force->numeric(FLERR,arg[4]))/hbar;
const double me = (force->numeric(FLERR,arg[4]));
double mex = force->numeric(FLERR,arg[5]);
double mey = force->numeric(FLERR,arg[6]);
double mez = force->numeric(FLERR,arg[7]);
@ -311,7 +337,8 @@ void PairSpinMe::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut_spin_me[i][j] = rij;
ME[i][j] = me;
ME[i][j] = me/hbar;
ME_mech[i][j] = me;
v_mex[i][j] = mex;
v_mey[i][j] = mey;
v_mez[i][j] = mez;
@ -337,12 +364,9 @@ void PairSpinMe::init_style()
neighbor->request(this,instance_me);
// check this half/full request => to be corrected/reviewed
#define FULLNEI
#if defined FULLNEI
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
#endif
}

6
src/SPIN/pair_spin_me.h
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@ -39,9 +39,11 @@ class PairSpinMe : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void compute_me(int, int, double fmi[3], double fmj[3], double spi[3], double spj[3]);
void compute_me(int, int, double [3], double [3], double [3], double [3]);
void compute_me_mech(int, int, double [3], double [3], double [3]);
int me_flag; // me flag
int me_mech_flag; // mech calculation flag
double cut_spin_me_global; // global me cutoff
double **cut_spin_me; // me cutoff distance
@ -50,7 +52,7 @@ class PairSpinMe : public Pair {
int newton_pair_spin;
double hbar;
double **ME; // me coeff in eV
double **ME, **ME_mech; // me coeff in eV
double **v_mex, **v_mey, **v_mez; // me direction
void allocate();

4
src/SPIN/pair_spin_soc_neel.h
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@ -39,8 +39,8 @@ class PairSpinSocNeel : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void compute_soc_neel(int, int, double, double eij[3], double fmi[3], double spi[3], double spj[3]);
void compute_soc_mech_neel(int, int, double, double eij[3], double fi[3], double spi[3], double spj[3]);
void compute_soc_neel(int, int, double, double [3], double [3], double [3], double [3]);
void compute_soc_mech_neel(int, int, double, double [3], double [3], double [3], double [3]);
int soc_neel_flag; // soc neel flag
int soc_mech_flag; // mech calculation flag