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whitespace cleanup

This commit is contained in:
Axel Kohlmeyer 2017-09-20 11:13:13 -04:00
parent e7d042ba1a
commit ad25a95297
5 changed files with 87 additions and 87 deletions
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2
examples/snap/Mo_Chen_PRM2017.snap
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@ -2,6 +2,6 @@
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# Generated by Materials Virtual Lab
# Definition of SNAP potential.
pair_style snap
pair_style snap
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo

2
potentials/Mo_Chen_PRM2017.snap
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@ -1,6 +1,6 @@
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# Generated by Materials Virtual Lab
# Definition of SNAP potential.
pair_style snap
pair_style snap
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo

2
potentials/Ta06A.snap
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@ -2,7 +2,7 @@
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73

4
potentials/W_2940_2017_2_He_JW2013.snap
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@ -8,8 +8,8 @@ variable zblz equal 74
# Specify hybrid with SNAP, ZBL, and long-range Coulomb
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here

164
src/compute_centro_atom.cpp
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@ -39,7 +39,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
distsq(NULL), nearest(NULL), centro(NULL)
{
if (narg < 4 || narg > 6)
if (narg < 4 || narg > 6)
error->all(FLERR,"Illegal compute centro/atom command");
if (strcmp(arg[3],"fcc") == 0) nnn = 12;
@ -49,13 +49,13 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
// default values
axes_flag = 0;
// optional keywords
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"axes") == 0) {
if (iarg+2 > narg)
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute centro/atom command3");
if (strcmp(arg[iarg+1],"yes") == 0) axes_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) axes_flag = 0;
@ -70,7 +70,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
if (!axes_flag) size_peratom_cols = 0;
else size_peratom_cols = 10;
nmax = 0;
maxneigh = 0;
}
@ -205,98 +205,98 @@ void ComputeCentroAtom::compute_peratom()
}
// check whether to include local crystal symmetry axes
if (!axes_flag) {
// if not nnn neighbors, centro = 0.0
// if not nnn neighbors, centro = 0.0
if (n < nnn) {
centro[i] = 0.0;
continue;
}
if (n < nnn) {
centro[i] = 0.0;
continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2(nnn,n,distsq,nearest);
select2(nnn,n,distsq,nearest);
// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
// pairs = squared length of each R
// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
// pairs = squared length of each R
n = 0;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
pairs[n++] = delx*delx + dely*dely + delz*delz;
n = 0;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
pairs[n++] = delx*delx + dely*dely + delz*delz;
}
}
}
}
} else {
// calculate local crystal symmetry axes
// calculate local crystal symmetry axes
// rsq1, rsq2 are two smallest values of R^2
// R1, R2 are corresponding vectors Ri - Rj
// R3 is normal to R1, R2
// rsq1, rsq2 are two smallest values of R^2
// R1, R2 are corresponding vectors Ri - Rj
// R3 is normal to R1, R2
double rsq1,rsq2;
double rsq1,rsq2;
double* r1 = &array_atom[i][1];
double* r2 = &array_atom[i][4];
double* r3 = &array_atom[i][7];
if (n < nnn) {
centro[i] = 0.0;
MathExtra::zero3(r1);
MathExtra::zero3(r2);
MathExtra::zero3(r3);
continue;
}
double* r1 = &array_atom[i][1];
double* r2 = &array_atom[i][4];
double* r3 = &array_atom[i][7];
if (n < nnn) {
centro[i] = 0.0;
MathExtra::zero3(r1);
MathExtra::zero3(r2);
MathExtra::zero3(r3);
continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2(nnn,n,distsq,nearest);
select2(nnn,n,distsq,nearest);
n = 0;
rsq1 = rsq2 = cutsq;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
double rsq = delx*delx + dely*dely + delz*delz;
pairs[n++] = rsq;
if (rsq < rsq2) {
if (rsq < rsq1) {
rsq2 = rsq1;
MathExtra::copy3(r1, r2);
rsq1 = rsq;
MathExtra::sub3(x[jj],x[kk],r1);
} else {
rsq2 = rsq;
MathExtra::sub3(x[jj],x[kk],r2);
}
n = 0;
rsq1 = rsq2 = cutsq;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
double rsq = delx*delx + dely*dely + delz*delz;
pairs[n++] = rsq;
if (rsq < rsq2) {
if (rsq < rsq1) {
rsq2 = rsq1;
MathExtra::copy3(r1, r2);
rsq1 = rsq;
MathExtra::sub3(x[jj],x[kk],r1);
} else {
rsq2 = rsq;
MathExtra::sub3(x[jj],x[kk],r2);
}
}
}
}
}
}
MathExtra::cross3(r1,r2,r3);
MathExtra::norm3(r1);
MathExtra::norm3(r2);
MathExtra::norm3(r3);
MathExtra::cross3(r1,r2,r3);
MathExtra::norm3(r1);
MathExtra::norm3(r2);
MathExtra::norm3(r3);
}
// store nhalf smallest pair distances in 1st nhalf locations of pairs
select(nhalf,npairs,pairs);
// centrosymmetry = sum of nhalf smallest squared values
value = 0.0;
@ -306,9 +306,9 @@ void ComputeCentroAtom::compute_peratom()
} else {
centro[i] = 0.0;
if (axes_flag) {
MathExtra::zero3(&array_atom[i][1]);
MathExtra::zero3(&array_atom[i][4]);
MathExtra::zero3(&array_atom[i][7]);
MathExtra::zero3(&array_atom[i][1]);
MathExtra::zero3(&array_atom[i][4]);
MathExtra::zero3(&array_atom[i][7]);
}
}
}
@ -319,7 +319,7 @@ void ComputeCentroAtom::compute_peratom()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
array_atom[i][0] = centro[i];
array_atom[i][0] = centro[i];
}
}