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get rid of non-standard variable-length arrays in ML-RANN package

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This commit is contained in:
Axel Kohlmeyer
2025-02-05 23:39:13 -05:00
parent 2ae07ec1cb
commit 97e7baf33f
4 changed files with 123 additions and 115 deletions
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54
src/ML-RANN/rann_fingerprint_bond.cpp
View File

@ -36,6 +36,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
using namespace LAMMPS_NS::RANN;
static constexpr double SMALL = 1.0e-12;
Fingerprint_bond::Fingerprint_bond(PairRANN *_pair) : Fingerprint(_pair)
{
n_body_type = 3;
@ -317,7 +319,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax+12];
std::vector<double> row(kmax+12, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
int p = kmax;
int countmb=((mlength)*(mlength+1))>>1;
// calculate interpolation expr, rinvs and dfc, for each neighbor
@ -354,13 +357,13 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
expr[jj][p+1]=dely*rinvs;
expr[jj][p+2]=delz*rinvs;
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
if (expr[jj][p]*expr[jj][p] < SMALL) {
expr[jj][p] = 0.000001;
}
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
expr[jj][p+1] = 0.000001;
}
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
expr[jj][p+2] = 0.000001;
}
expr[jj][p+3] = -dfc*expr[jj][p];
@ -377,7 +380,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
int kb = kmax;
int mb = mlength;
count = startingneuron;
double Bb[mb];
std::vector<double> Bb(mb, 0.0);
double dBbx;
double dBby;
double dBbz;
@ -397,7 +400,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
}
for (n=0;n<kb;n++) {
for (a1=0;a1<mb;a1++) {
Bb[a1]=0;
Bb[a1]=0.0;
}
ai = n;
double y1 = alpha_k[ai]/re;
@ -409,7 +412,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
continue;
}
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -419,10 +422,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
}
}
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
double Bg[mb];
for (a1=0;a1<mb;a1++) {
Bg[a1]=0;
}
std::vector<double> Bg(mb, 0.0);
ai = n;
double y1 = alpha_k[ai]/re;
//loop over ktype to get Bg
@ -433,7 +433,7 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
continue;
}
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -450,8 +450,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
if (atomtypes[2] != nelements && atomtypes[2] != jtype) {
continue;
}
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -477,8 +477,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
continue;
}
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -512,8 +512,8 @@ void Fingerprint_bond::do3bodyfeatureset_singleneighborloop(double * features,do
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
continue;
}
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -572,16 +572,18 @@ void Fingerprint_bond::do3bodyfeatureset_doubleneighborloop(double * features,do
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax];
double y[jnum][3];
double ri[jnum];
double dfc[jnum];
std::vector<double> row(kmax, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
std::vector<double> yrow(3, 0.0);
std::vector<std::vector<double>> y(jnum, yrow);
std::vector<double> ri(jnum, 0.0);
std::vector<double> dfc(jnum, 0.0);
int kb = kmax;
int mb = mlength;
double c41[kmax];
double c51[kmax];
double c61[kmax];
double ct[kmax];
std::vector<double> c41(kmax, 0.0);
std::vector<double> c51(kmax, 0.0);
std::vector<double> c61(kmax, 0.0);
std::vector<double> ct(kmax, 0.0);
for (jj = 0; jj < jnum; jj++) {
jtype = tn[jj];
if (jtypes != nelements && jtypes != jtype && ktypes != nelements && ktypes != jtype) {

67
src/ML-RANN/rann_fingerprint_bondscreened.cpp
View File

@ -36,6 +36,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
using namespace LAMMPS_NS::RANN;
static constexpr double SMALL = 1.0e-12;
Fingerprint_bondscreened::Fingerprint_bondscreened(PairRANN *_pair) : Fingerprint(_pair)
{
n_body_type = 3;
@ -319,7 +321,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax+12];
std::vector<double> row(kmax+12, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
int p = kmax;
int countmb=((mlength)*(mlength+1))>>1;
// calculate interpolation expr, rinvs and dfc, for each neighbor
@ -358,13 +361,13 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
expr[jj][p+1]=dely*rinvs;
expr[jj][p+2]=delz*rinvs;
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
if (expr[jj][p]*expr[jj][p] < SMALL) {
expr[jj][p] = 0.000001;
}
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
expr[jj][p+1] = 0.000001;
}
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
expr[jj][p+2] = 0.000001;
}
expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj];
@ -381,20 +384,20 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
int kb = kmax;
int mb = mlength;
count = startingneuron;
double Bb[mb];
std::vector<double> Bb(mb, 0.0);
double dBbx;
double dBby;
double dBbz;
double dBbx1[mb];
double dBby1[mb];
double dBbz1[mb];
std::vector<double> dBbx1(mb, 0.0);
std::vector<double> dBby1(mb, 0.0);
std::vector<double> dBbz1(mb, 0.0);
double yprod;
for (mcount=0;mcount<countmb;mcount++) {
int *M = Mf[mcount];
int *_coeffx = coeffx[mcount];
int *_coeffy = coeffy[mcount];
int *_coeffz = coeffz[mcount];
int *_coeff = coeff[mcount];
int *_coeffy = coeffy[mcount];
int *_coeffz = coeffz[mcount];
int *_coeff = coeff[mcount];
a = mb+1;
for (a1=0;a1<mb;a1++) {
if (Mf[mcount][a1+1]==0) {
@ -420,7 +423,7 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
continue;
}
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -430,10 +433,7 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
}
}
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
double Bg[mb];
for (a1=0;a1<mb;a1++) {
Bg[a1]=0;
}
std::vector<double> Bg(mb, 0.0);
ai = n;
double y1 = alpha_k[ai]/re;
//loop over ktype to get Bg
@ -445,7 +445,7 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
continue;
}
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -463,8 +463,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
if (atomtypes[2] != nelements && atomtypes[2] != jtype) {
continue;
}
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -500,8 +500,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
continue;
}
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -545,8 +545,8 @@ void Fingerprint_bondscreened::do3bodyfeatureset_singleneighborloop(double * fea
if (atomtypes[1] != nelements && atomtypes[1] != jtype) {
continue;
}
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -615,17 +615,20 @@ void Fingerprint_bondscreened::do3bodyfeatureset_doubleneighborloop(double * fea
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax];
double y[jnum][3];
double ri[jnum];
double dfc[jnum];
std::vector<double> row(kmax, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
std::vector<double> yrow(3, 0.0);
std::vector<std::vector<double>> y(jnum, yrow);
std::vector<double> ri(jnum, 0.0);
std::vector<double> dfc(jnum, 0.0);
int kb = kmax;
int mb = mlength;
double Bijk[kb][mb];
double c41[kmax];
double c51[kmax];
double c61[kmax];
double ct[kmax];
std::vector<double> brow(mb, 0.0);
std::vector<std::vector<double>> Bijk(kb, brow);
std::vector<double> c41(kmax, 0.0);
std::vector<double> c51(kmax, 0.0);
std::vector<double> c61(kmax, 0.0);
std::vector<double> ct(kmax, 0.0);
for (jj = 0; jj < jnum; jj++) {
if (Bij[jj]==false) {continue;}
jtype = tn[jj];

60
src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp
View File

@ -35,6 +35,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
using namespace LAMMPS_NS::RANN;
static constexpr double SMALL = 1.0e-12;
Fingerprint_bondscreenedspin::Fingerprint_bondscreenedspin(PairRANN *_pair) : Fingerprint(_pair)
{
n_body_type = 3;
@ -320,7 +322,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax+12];
std::vector<double> row(kmax+12, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
int p = kmax;
int countmb=((mlength)*(mlength+1))>>1;
double *si = sim->s[i];
@ -360,13 +363,13 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
expr[jj][p+1]=dely*rinvs;
expr[jj][p+2]=delz*rinvs;
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
if (expr[jj][p]*expr[jj][p] < SMALL) {
expr[jj][p] = 0.000001;
}
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
expr[jj][p+1] = 0.000001;
}
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
expr[jj][p+2] = 0.000001;
}
expr[jj][p+3] = -dfc*expr[jj][p]-dSikx[jj];
@ -383,8 +386,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
int kb = kmax;
int mb = mlength;
count = startingneuron;
double Bb[mb];
double Bbs[mb];
std::vector<double> Bb(mb, 0.0);
std::vector<double> Bbs(mb, 0.0);
double dBbx;
double dBby;
double dBbz;
@ -421,7 +424,7 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -432,12 +435,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
}
}
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
double Bg[mb];
double Bgs[mb];
for (a1=0;a1<mb;a1++) {
Bg[a1]=0;
Bgs[a1]=0;
}
std::vector<double> Bg(mb, 0.0);
std::vector<double> Bgs(mb, 0.0);
ai = n;
double y1 = alpha_k[ai]/re;
//loop over ktype to get Bg
@ -452,7 +451,7 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -474,8 +473,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
j = jl[jj];
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -517,8 +516,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
j = jl[jj];
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -568,8 +567,8 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_singleneighborloop(double *
j = jl[jj];
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -641,18 +640,21 @@ void Fingerprint_bondscreenedspin::do3bodyfeatureset_doubleneighborloop(double *
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax];
double y[jnum][3];
double ri[jnum];
double dfc[jnum];
std::vector<double> row(kmax, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
std::vector<double> yrow(3, 0.0);
std::vector<std::vector<double>> y(jnum, yrow);
std::vector<double> ri(jnum, 0.0);
std::vector<double> dfc(jnum, 0.0);
int kb = kmax;
int mb = mlength;
double Bijk[kb][mb];
double c41[kmax];
double c51[kmax];
double c61[kmax];
double ct[kmax];
double *si = sim->s[i];
std::vector<double> brow(mb, 0.0);
std::vector<std::vector<double>> Bijk(kb, brow);
std::vector<double> c41(kmax, 0.0);
std::vector<double> c51(kmax, 0.0);
std::vector<double> c61(kmax, 0.0);
std::vector<double> ct(kmax, 0.0);
for (jj = 0; jj < jnum; jj++) {
if (Bij[jj]==false) {continue;}
jtype = tn[jj];

57
src/ML-RANN/rann_fingerprint_bondspin.cpp
View File

@ -35,6 +35,8 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
using namespace LAMMPS_NS::RANN;
static constexpr double SMALL = 1.0e-12;
Fingerprint_bondspin::Fingerprint_bondspin(PairRANN *_pair) : Fingerprint(_pair)
{
n_body_type = 3;
@ -317,7 +319,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax+12];
std::vector<double> row(kmax+12, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
int p = kmax;
int countmb=((mlength)*(mlength+1))>>1;
double *si = sim->s[i];
@ -355,13 +358,13 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
expr[jj][p+1]=dely*rinvs;
expr[jj][p+2]=delz*rinvs;
//Hack to avoid nan when x y or z component of radial vector is exactly 0. Shouldn't affect accuracy.
if (expr[jj][p]*expr[jj][p]<0.000000000001) {
if (expr[jj][p]*expr[jj][p] < SMALL) {
expr[jj][p] = 0.000001;
}
if (expr[jj][p+1]*expr[jj][p+1]<0.000000000001) {
if (expr[jj][p+1]*expr[jj][p+1] < SMALL) {
expr[jj][p+1] = 0.000001;
}
if (expr[jj][p+2]*expr[jj][p+2]<0.000000000001) {
if (expr[jj][p+2]*expr[jj][p+2] < SMALL) {
expr[jj][p+2] = 0.000001;
}
expr[jj][p+3] = -dfc*expr[jj][p];
@ -378,8 +381,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
int kb = kmax;
int mb = mlength;
count = startingneuron;
double Bb[mb];
double Bbs[mb];
std::vector<double> Bb(mb, 0.0);
std::vector<double> Bbs(mb, 0.0);
double dBbx;
double dBby;
double dBbz;
@ -415,7 +418,7 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -426,12 +429,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
}
}
if (atomtypes[1]!=atomtypes[2]) {//Bb!=Bg
double Bg[mb];
double Bgs[mb];
for (a1=0;a1<mb;a1++) {
Bg[a1]=0;
Bgs[a1]=0;
}
std::vector<double> Bg(mb, 0.0);
std::vector<double> Bgs(mb, 0.0);
ai = n;
double y1 = alpha_k[ai]/re;
//loop over ktype to get Bg
@ -445,7 +444,7 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double yprod = expr[jj][ai];
double *y4 = &expr[jj][p];
double *y4 = expr[jj].data() + p;
for (a2=0;a2<a;a2++) {
yprod *= y4[M[a2+1]];
}
@ -466,8 +465,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
j = jl[jj];
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -502,8 +501,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
j = jl[jj];
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -546,8 +545,8 @@ void Fingerprint_bondspin::do3bodyfeatureset_singleneighborloop(double * feature
j = jl[jj];
double *sj = sim->s[j];
double sp = si[0]*sj[0]+si[1]*sj[1]+si[2]*sj[2];
double *y3 = &expr[jj][p+3];
double *y4 = &expr[jj][p];
double *y3 = expr[jj].data() + p + 3;
double *y4 = expr[jj].data() + p;
ai = n;
yprod = expr[jj][ai];
for (a2=0;a2<a;a2++) {
@ -612,16 +611,18 @@ void Fingerprint_bondspin::do3bodyfeatureset_doubleneighborloop(double * feature
i = ilist[ii];
itype = pair->map[type[i]];
int f = pair->net[itype].dimensions[0];
double expr[jnum][kmax];
double y[jnum][3];
double ri[jnum];
double dfc[jnum];
std::vector<double> row(kmax, 0.0);
std::vector<std::vector<double>> expr(jnum, row);
std::vector<double> yrow(3, 0.0);
std::vector<std::vector<double>> y(jnum, yrow);
std::vector<double> ri(jnum, 0.0);
std::vector<double> dfc(jnum, 0.0);
int kb = kmax;
int mb = mlength;
double c41[kmax];
double c51[kmax];
double c61[kmax];
double ct[kmax];
std::vector<double> c41(kmax, 0.0);
std::vector<double> c51(kmax, 0.0);
std::vector<double> c61(kmax, 0.0);
std::vector<double> ct(kmax, 0.0);
double *si = sim->s[i];
for (jj = 0; jj < jnum; jj++) {
jtype = tn[jj];