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Commit modifs before release 1 (03/26/18)

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This commit is contained in:
julient31
2018-03-26 13:30:36 -06:00
parent 08bc115380
commit a315599bac
36 changed files with 6660 additions and 598 deletions
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80
src/SPIN/atom_vec_spin.cpp
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@ -1,4 +1,5 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -43,14 +44,13 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
size_forward = 7;
size_reverse = 6;
size_border = 11;
size_border = 10;
size_velocity = 3;
size_data_atom = 9;
size_data_vel = 4;
xcol_data = 4;
forceclearflag = 1;
atom->mumag_flag = 1;
atom->sp_flag = 1;
}
@ -83,7 +83,6 @@ void AtomVecSpin::grow(int n)
// allocating mag. quantities
mumag = memory->grow(atom->mumag,nmax,"atom:mumag");
sp = memory->grow(atom->sp,nmax,4,"atom:sp");
fm = memory->grow(atom->fm,nmax*comm->nthreads,3,"atom:fm");
@ -101,7 +100,7 @@ void AtomVecSpin::grow_reset()
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
mumag = atom->mumag; sp = atom->sp; fm = atom->fm;
sp = atom->sp; fm = atom->fm;
}
@ -122,7 +121,6 @@ void AtomVecSpin::copy(int i, int j, int delflag)
v[j][1] = v[i][1];
v[j][2] = v[i][2];
mumag[j] = mumag[i];
sp[j][0] = sp[i][0];
sp[j][1] = sp[i][1];
sp[j][2] = sp[i][2];
@ -381,7 +379,6 @@ int AtomVecSpin::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = mumag[j];
buf[m++] = sp[j][0];
buf[m++] = sp[j][1];
buf[m++] = sp[j][2];
@ -405,7 +402,6 @@ int AtomVecSpin::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = mumag[j];
buf[m++] = sp[j][0];
buf[m++] = sp[j][1];
buf[m++] = sp[j][2];
@ -438,7 +434,6 @@ int AtomVecSpin::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = mumag[j];
buf[m++] = sp[j][0];
buf[m++] = sp[j][1];
buf[m++] = sp[j][2];
@ -466,7 +461,6 @@ int AtomVecSpin::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = mumag[j];
buf[m++] = sp[j][0];
buf[m++] = sp[j][1];
buf[m++] = sp[j][2];
@ -487,7 +481,6 @@ int AtomVecSpin::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = mumag[j];
buf[m++] = sp[j][0];
buf[m++] = sp[j][1];
buf[m++] = sp[j][2];
@ -521,7 +514,6 @@ int AtomVecSpin::pack_border_hybrid(int n, int *list, double *buf)
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = mumag[j];
buf[m++] = sp[j][0];
buf[m++] = sp[j][1];
buf[m++] = sp[j][2];
@ -547,7 +539,6 @@ void AtomVecSpin::unpack_border(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
mumag[i] = buf[m++];
sp[i][0] = buf[m++];
sp[i][1] = buf[m++];
sp[i][2] = buf[m++];
@ -577,7 +568,6 @@ void AtomVecSpin::unpack_border_vel(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
mumag[i] = buf[m++];
sp[i][0] = buf[m++];
sp[i][1] = buf[m++];
sp[i][2] = buf[m++];
@ -603,7 +593,6 @@ int AtomVecSpin::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++) {
mumag[i] = buf[m++];
sp[i][0] = buf[m++];
sp[i][1] = buf[m++];
sp[i][2] = buf[m++];
@ -632,7 +621,6 @@ int AtomVecSpin::pack_exchange(int i, double *buf)
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = mumag[i];
buf[m++] = sp[i][0];
buf[m++] = sp[i][1];
buf[m++] = sp[i][2];
@ -665,7 +653,6 @@ int AtomVecSpin::unpack_exchange(double *buf)
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
mumag[nlocal] = buf[m++];
sp[nlocal][0] = buf[m++];
sp[nlocal][1] = buf[m++];
sp[nlocal][2] = buf[m++];
@ -722,7 +709,6 @@ int AtomVecSpin::pack_restart(int i, double *buf)
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = mumag[i];
buf[m++] = sp[i][0];
buf[m++] = sp[i][1];
buf[m++] = sp[i][2];
@ -761,7 +747,6 @@ int AtomVecSpin::unpack_restart(double *buf)
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
mumag[nlocal] = buf[m++];
sp[nlocal][0] = buf[m++];
sp[nlocal][1] = buf[m++];
sp[nlocal][2] = buf[m++];
@ -800,7 +785,6 @@ void AtomVecSpin::create_atom(int itype, double *coord)
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
mumag[nlocal] = 0.0;
sp[nlocal][0] = 0.0;
sp[nlocal][1] = 0.0;
sp[nlocal][2] = 0.0;
@ -824,18 +808,20 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values)
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
mumag[nlocal] = atof(values[2]);
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
sp[nlocal][0] = atof(values[6]);
sp[nlocal][1] = atof(values[7]);
sp[nlocal][2] = atof(values[8]);
sp[nlocal][3] = sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);
sp[nlocal][3] = atof(values[2]);
sp[nlocal][0] = atof(values[5]);
sp[nlocal][1] = atof(values[6]);
sp[nlocal][2] = atof(values[7]);
double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);
sp[nlocal][0] *= inorm;
sp[nlocal][1] *= inorm;
sp[nlocal][2] *= inorm;
image[nlocal] = imagetmp;
@ -854,13 +840,17 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values)
int AtomVecSpin::data_atom_hybrid(int nlocal, char **values)
{
mumag[nlocal] = atof(values[0]);
sp[nlocal][0] = atof(values[1]);
sp[nlocal][1] = atof(values[2]);
sp[nlocal][2] = atof(values[3]);
sp[nlocal][3] = sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);
sp[nlocal][0] = atof(values[0]);
sp[nlocal][1] = atof(values[1]);
sp[nlocal][2] = atof(values[2]);
double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);
sp[nlocal][0] *= inorm;
sp[nlocal][1] *= inorm;
sp[nlocal][2] *= inorm;
sp[nlocal][3] = atof(values[3]);
return 4;
}
@ -875,17 +865,16 @@ void AtomVecSpin::pack_data(double **buf)
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(type[i]).d;
buf[i][2] = mumag[i];
buf[i][2] = sp[i][3];
buf[i][3] = x[i][0];
buf[i][4] = x[i][1];
buf[i][5] = x[i][2];
buf[i][6] = sp[i][0];
buf[i][7] = sp[i][1];
buf[i][8] = sp[i][2];
buf[i][9] = sp[i][3];
buf[i][10] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][11] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][12] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
buf[i][9] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][10] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][11] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
@ -895,13 +884,13 @@ void AtomVecSpin::pack_data(double **buf)
int AtomVecSpin::pack_data_hybrid(int i, double *buf)
{
buf[0] = mumag[i];
buf[1] = sp[i][0];
buf[2] = sp[i][1];
buf[3] = sp[i][2];
buf[4] = sp[i][3];
return 5;
buf[0] = sp[i][0];
buf[1] = sp[i][1];
buf[2] = sp[i][2];
buf[3] = sp[i][3];
return 4;
}
/* ----------------------------------------------------------------------
@ -947,7 +936,6 @@ bigint AtomVecSpin::memory_usage()
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
if (atom->memcheck("mumag")) bytes += memory->usage(mumag,nmax);
if (atom->memcheck("sp")) bytes += memory->usage(sp,nmax,4);
if (atom->memcheck("fm")) bytes += memory->usage(fm,nmax*comm->nthreads,3);