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Commit JT 051118 before CEA

This commit is contained in:
julient31 2018-05-11 15:24:26 -06:00
parent eaaad3f6d5
commit 437e854741
15 changed files with 42 additions and 148 deletions
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70
examples/SPIN/read_restart/in.spin.read_data
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@ -1,6 +1,3 @@
<<<<<<< HEAD
<<<<<<< HEAD
# start a spin-lattice simulation from a data file
clear
units metal
dimension 3
@ -10,36 +7,13 @@ atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
read_data ../examples/SPIN/read_restart/Norm_randXY_8x8x32.data
=======
=======
# start a spin-lattice simulation from a data file
>>>>>>> Commit modifs before release 1 (03/26/18)
clear
units metal
dimension 3
boundary p p p
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
<<<<<<< HEAD
>>>>>>> Commit before meeting 032218
=======
read_data ../examples/SPIN/read_restart/Norm_randXY_8x8x32.data
>>>>>>> Commit modifs before release 1 (03/26/18)
mass 1 58.93
# define magneto-mechanical potentials and forces
<<<<<<< HEAD
<<<<<<< HEAD
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy ../examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 1.0 bin
neigh_modify every 1 check no delay 0
@ -51,32 +25,6 @@ fix 3 all nve/spin lattice yes
timestep 0.0001
# define outputs and computes
=======
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
=======
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
pair_coeff * * eam/alloy ../examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
>>>>>>> Commit modifs before release 1 (03/26/18)
neighbor 1.0 bin
neigh_modify every 1 check no delay 0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
<<<<<<< HEAD
# define outputs
>>>>>>> Commit before meeting 032218
=======
# define outputs and computes
>>>>>>> Commit modifs before release 1 (03/26/18)
compute out_mag all compute/spin
compute out_pe all pe
@ -92,21 +40,7 @@ thermo 10
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
thermo_modify format float %20.15g
<<<<<<< HEAD
<<<<<<< HEAD
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
run 100
=======
dump 1 all custom 1 dump.lammpstrj type x y z spx spy spz
run 10000
>>>>>>> Commit before meeting 032218
=======
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
run 100
>>>>>>> Commit modifs before release 1 (03/26/18)

6
examples/SPIN/read_restart/in.spin.restart
View File

@ -13,7 +13,7 @@ lattice fcc 3.54
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
read_dump ../examples/SPIN/Norm_randXY_8x8x32.dump 0 x y z box yes
read_dump ../examples/SPIN/read_restart/Norm_randXY_8x8x32.dump 0 x y z box yes
create_atoms 1 box
@ -27,9 +27,9 @@ velocity all create 200 4928459 rot yes dist gaussian
# define magneto-mechanical potentials and forces
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 1.0 bin
neigh_modify every 1 check no delay 0

4
examples/SPIN/read_restart/in.spin.write_restart
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@ -22,9 +22,9 @@ mass 1 58.93
set group all spin/random 31 1.72
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy ../examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20

5
src/SPIN/compute_spin.cpp
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@ -74,7 +74,7 @@ void ComputeSpin::init()
void ComputeSpin::compute_vector()
{
int i, index;
int i;
int countsp, countsptot;
double mag[4], magtot[4];
double magenergy, magenergytot;
@ -92,10 +92,7 @@ void ComputeSpin::compute_vector()
tempdenom = tempdenomtot = 0.0;
spintemperature = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double **sp = atom->sp;
double **fm = atom->fm;
double tx,ty,tz;

1
src/SPIN/fix_langevin_spin.cpp
View File

@ -117,7 +117,6 @@ void FixLangevinSpin::init()
{
// fix_langevin_spin has to be the last defined fix
int after = 0;
int flag_force = 0;
int flag_lang = 0;
for (int i = 0; i < modify->nfix; i++) {

18
src/SPIN/fix_nve_spin.cpp
View File

@ -258,14 +258,11 @@ void FixNVESpin::init()
void FixNVESpin::initial_integrate(int vflag)
{
double dtfm,msq,scale,fm2,fmsq,sp2,spsq,energy;
double spi[3], fmi[3];
double dtfm;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **sp = atom->sp;
double **fm = atom->fm;
double *rmass = atom->rmass;
double *mass = atom->mass;
int nlocal = atom->nlocal;
@ -422,17 +419,11 @@ void FixNVESpin::pre_neighbor()
void FixNVESpin::ComputeInteractionsSpin(int i)
{
const int nlocal = atom->nlocal;
double spi[3], fmi[3];
double **sp = atom->sp;
double **fm = atom->fm;
int eflag = 1;
int vflag = 0;
int pair_compute_flag = 1;
// force computation for spin i
spi[0] = sp[i][0];
@ -564,13 +555,12 @@ void FixNVESpin::AdvanceSingleSpin(int i)
int *sametag = atom->sametag;
double **sp = atom->sp;
double **fm = atom->fm;
double dtfm,msq,scale,fm2,fmsq,sp2,spsq,energy,dts2;
double msq,scale,fm2,energy,dts2;
double cp[3],g[3];
cp[0] = cp[1] = cp[2] = 0.0;
g[0] = g[1] = g[2] = 0.0;
fm2 = (fm[i][0]*fm[i][0])+(fm[i][1]*fm[i][1])+(fm[i][2]*fm[i][2]);
fmsq = sqrt(fm2);
energy = (sp[i][0]*fm[i][0])+(sp[i][1]*fm[i][1])+(sp[i][2]*fm[i][2]);
dts2 = dts*dts;
@ -622,10 +612,8 @@ void FixNVESpin::AdvanceSingleSpin(int i)
void FixNVESpin::final_integrate()
{
double dtfm,msq,scale,fm2,fmsq,energy;
double cp[3],g[3];
double dtfm;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;

8
src/SPIN/fix_nve_spin.h
View File

@ -80,10 +80,10 @@ friend class PairSpin;
// stacking variables for sectoring algorithm
int *stack_head; // index of first atom in backward_stacks
int *stack_foot; // index of first atom in forward_stacks
int *backward_stacks; // index of next atom in backward stack
int *forward_stacks; // index of next atom in forward stack
int *stack_head; // index of first atom in backward_stacks
int *stack_foot; // index of first atom in forward_stacks
int *backward_stacks; // index of next atom in backward stack
int *forward_stacks; // index of next atom in forward stack
};

1
src/SPIN/fix_precession_spin.cpp
View File

@ -183,7 +183,6 @@ void FixPrecessionSpin::post_force(int vflag)
double **fm = atom->fm;
double spi[3], fmi[3];
const int nlocal = atom->nlocal;
double scalar;
eflag = 0;
emag = 0.0;

22
src/SPIN/pair_spin_dmi.cpp
View File

@ -283,9 +283,9 @@ void PairSpinDmi::compute(int eflag, int vflag)
// compute magnetic and mechanical components of soc_dmi
if (rsq <= local_cut2) {
compute_dmi(i,j,rsq,eij,fmi,spi,spj);
compute_dmi(i,j,eij,fmi,spj);
if (lattice_flag) {
compute_dmi_mech(i,j,fi,spi,spj);
compute_dmi_mech(fi);
}
}
@ -321,23 +321,19 @@ void PairSpinDmi::compute(int eflag, int vflag)
void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
{
const int nlocal = atom->nlocal;
int *type = atom->type;
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
double xi[3], rij[3], eij[3];
double spi[3], spj[3];
double spj[3];
int iexchange, idmi, ineel, ime;
int i,j,jj,inum,jnum,itype,jtype;
int i,j,jnum,itype,jtype;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, inorm;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -345,10 +341,6 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
i = ilist[ii];
itype = type[i];
spi[0] = sp[i][0];
spi[1] = sp[i][1];
spi[2] = sp[i][2];
xi[0] = x[i][0];
xi[1] = x[i][1];
xi[2] = x[i][2];
@ -378,7 +370,7 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype];
if (rsq <= local_cut2) {
compute_dmi(i,j,rsq,eij,fmi,spi,spj);
compute_dmi(i,j,eij,fmi,spj);
}
}
@ -389,7 +381,7 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
compute the dmi interaction between spin i and spin j
------------------------------------------------------------------------- */
void PairSpinDmi::compute_dmi(int i, int j, double rsq, double eij[3], double fmi[3], double spi[3], double spj[3])
void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
@ -410,7 +402,7 @@ void PairSpinDmi::compute_dmi(int i, int j, double rsq, double eij[3], double fm
compute the mechanical force due to the dmi interaction between atom i and atom j
------------------------------------------------------------------------- */
void PairSpinDmi::compute_dmi_mech(int i, int j, double fi[3], double spi[3], double spj[3])
void PairSpinDmi::compute_dmi_mech(double fi[3])
{
fi[0] += 0.0;
fi[1] += 0.0;

4
src/SPIN/pair_spin_dmi.h
View File

@ -37,8 +37,8 @@ class PairSpinDmi : public PairSpin {
void compute(int, int);
void compute_single_pair(int, double *);
void compute_dmi(int, int, double, double *, double *, double *, double *);
void compute_dmi_mech(int, int, double *, double *, double *);
void compute_dmi(int, int, double *, double *, double *);
void compute_dmi_mech(double *);
void write_restart(FILE *);
void read_restart(FILE *);

17
src/SPIN/pair_spin_exchange.cpp
View File

@ -273,7 +273,7 @@ void PairSpinExchange::compute(int eflag, int vflag)
// compute exchange interaction
if (rsq <= local_cut2) {
compute_exchange(i,j,rsq,fmi,spi,spj);
compute_exchange(i,j,rsq,fmi,spj);
if (lattice_flag) {
compute_exchange_mech(i,j,rsq,eij,fi,spi,spj);
}
@ -316,22 +316,19 @@ void PairSpinExchange::compute(int eflag, int vflag)
void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
{
const int nlocal = atom->nlocal;
int *type = atom->type;
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
double xi[3], rij[3];
double spi[3], spj[3];
double spj[3];
int iexchange, idmi, ineel, ime;
int i,j,jj,inum,jnum,itype,jtype;
int i,j,jnum,itype,jtype;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -339,10 +336,6 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
i = ilist[ii];
itype = type[i];
spi[0] = sp[i][0];
spi[1] = sp[i][1];
spi[2] = sp[i][2];
xi[0] = x[i][0];
xi[1] = x[i][1];
xi[2] = x[i][2];
@ -367,7 +360,7 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
if (rsq <= local_cut2) {
compute_exchange(i,j,rsq,fmi,spi,spj);
compute_exchange(i,j,rsq,fmi,spj);
}
}
@ -378,7 +371,7 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
compute exchange interaction between spins i and j
------------------------------------------------------------------------- */
void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3], double spi[3], double spj[3])
void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;

2
src/SPIN/pair_spin_exchange.h
View File

@ -37,7 +37,7 @@ class PairSpinExchange : public PairSpin {
void compute(int, int);
void compute_single_pair(int, double *);
void compute_exchange(int, int, double, double *, double *, double *);
void compute_exchange(int, int, double, double *, double *);
void compute_exchange_mech(int, int, double, double *, double *, double *, double *);
void write_restart(FILE *);

18
src/SPIN/pair_spin_me.cpp
View File

@ -282,7 +282,7 @@ void PairSpinMe::compute(int eflag, int vflag)
// compute me interaction
if (rsq <= local_cut2) {
compute_me(i,j,rsq,eij,fmi,spi,spj);
compute_me(i,j,rsq,eij,fmi,spj);
if (lattice_flag) {
compute_me_mech(i,j,fi,spi,spj);
}
@ -320,23 +320,19 @@ void PairSpinMe::compute(int eflag, int vflag)
void PairSpinMe::compute_single_pair(int ii, double fmi[3])
{
const int nlocal = atom->nlocal;
int *type = atom->type;
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
double xi[3], rij[3], eij[3];
double spi[3], spj[3];
double spj[3];
int iexchange, idmi, ineel, ime;
int i,j,jj,inum,jnum,itype,jtype;
int i,j,jnum,itype,jtype;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, inorm;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -344,10 +340,6 @@ void PairSpinMe::compute_single_pair(int ii, double fmi[3])
i = ilist[ii];
itype = type[i];
spi[0] = sp[i][0];
spi[1] = sp[i][1];
spi[2] = sp[i][2];
xi[0] = x[i][0];
xi[1] = x[i][1];
xi[2] = x[i][2];
@ -378,7 +370,7 @@ void PairSpinMe::compute_single_pair(int ii, double fmi[3])
eij[2] = inorm*rij[2];
if (rsq <= local_cut2) {
compute_me(i,j,rsq,eij,fmi,spi,spj);
compute_me(i,j,rsq,eij,fmi,spj);
}
}
@ -386,7 +378,7 @@ void PairSpinMe::compute_single_pair(int ii, double fmi[3])
/* ---------------------------------------------------------------------- */
void PairSpinMe::compute_me(int i, int j, double rsq, double eij[3], double fmi[3], double spi[3], double spj[3])
void PairSpinMe::compute_me(int i, int j, double rsq, double eij[3], double fmi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;

2
src/SPIN/pair_spin_me.h
View File

@ -37,7 +37,7 @@ class PairSpinMe : public PairSpin {
void compute(int, int);
void compute_single_pair(int, double *);
void compute_me(int, int, double, double *, double *, double *, double *);
void compute_me(int, int, double, double *, double *, double *);
void compute_me_mech(int, int, double *, double *, double *);
void write_restart(FILE *);

10
src/SPIN/pair_spin_neel.cpp
View File

@ -326,7 +326,6 @@ void PairSpinNeel::compute(int eflag, int vflag)
void PairSpinNeel::compute_single_pair(int ii, double fmi[3])
{
const int nlocal = atom->nlocal;
int *type = atom->type;
double **x = atom->x;
double **sp = atom->sp;
@ -335,13 +334,11 @@ void PairSpinNeel::compute_single_pair(int ii, double fmi[3])
double xi[3], rij[3], eij[3];
double spi[3], spj[3];
int iexchange, idmi, ineel, ime;
int i,j,jj,inum,jnum,itype,jtype;
int i,j,jnum,itype,jtype;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, rd, inorm;
double rsq, inorm;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -379,6 +376,9 @@ void PairSpinNeel::compute_single_pair(int ii, double fmi[3])
rij[2] = x[j][2] - xi[2];
rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
inorm = 1.0/sqrt(rsq);
eij[0] = inorm*rij[0];
eij[1] = inorm*rij[1];
eij[2] = inorm*rij[2];
if (rsq <= local_cut2) {
compute_neel(i,j,rsq,eij,fmi,spi,spj);