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Implemented lists instead of multidim arrays

This commit is contained in:
Aidan Thompson 2019-06-11 18:24:02 -06:00
parent 960a975e2a
commit 0559e155f2
6 changed files with 566 additions and 714 deletions
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7
src/SNAP/compute_sna_atom.cpp
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@ -247,13 +247,12 @@ void ComputeSNAAtom::compute_peratom()
snaptr->compute_ui(ninside);
snaptr->compute_zi();
snaptr->compute_bi();
snaptr->copy_bi2bvec();
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
sna[i][icoeff] = snaptr->bvec[icoeff];
sna[i][icoeff] = snaptr->blist[icoeff];
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr->bvec[icoeff];
double bi = snaptr->blist[icoeff];
// diagonal element of quadratic matrix
@ -262,7 +261,7 @@ void ComputeSNAAtom::compute_peratom()
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
sna[i][ncount++] = bi*snaptr->bvec[jcoeff];
sna[i][ncount++] = bi*snaptr->blist[jcoeff];
}
}
} else {

34
src/SNAP/compute_snad_atom.cpp
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@ -266,7 +266,6 @@ void ComputeSNADAtom::compute_peratom()
snaptr->compute_zi();
if (quadraticflag) {
snaptr->compute_bi();
snaptr->copy_bi2bvec();
}
for (int jj = 0; jj < ninside; jj++) {
@ -275,7 +274,6 @@ void ComputeSNADAtom::compute_peratom()
snaptr->wj[jj],
snaptr->rcutij[jj]);
snaptr->compute_dbidrj();
snaptr->copy_dbi2dbvec();
// Accumulate -dBi/dRi, -dBi/dRj
@ -283,12 +281,12 @@ void ComputeSNADAtom::compute_peratom()
double *snadj = snad[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snadi[icoeff] += snaptr->dbvec[icoeff][0];
snadi[icoeff+yoffset] += snaptr->dbvec[icoeff][1];
snadi[icoeff+zoffset] += snaptr->dbvec[icoeff][2];
snadj[icoeff] -= snaptr->dbvec[icoeff][0];
snadj[icoeff+yoffset] -= snaptr->dbvec[icoeff][1];
snadj[icoeff+zoffset] -= snaptr->dbvec[icoeff][2];
snadi[icoeff] += snaptr->dblist[icoeff][0];
snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
snadj[icoeff] -= snaptr->dblist[icoeff][0];
snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
}
if (quadraticflag) {
@ -297,10 +295,10 @@ void ComputeSNADAtom::compute_peratom()
snadj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr->bvec[icoeff];
double bix = snaptr->dbvec[icoeff][0];
double biy = snaptr->dbvec[icoeff][1];
double biz = snaptr->dbvec[icoeff][2];
double bi = snaptr->blist[icoeff];
double bix = snaptr->dblist[icoeff][0];
double biy = snaptr->dblist[icoeff][1];
double biz = snaptr->dblist[icoeff][2];
// diagonal elements of quadratic matrix
@ -319,12 +317,12 @@ void ComputeSNADAtom::compute_peratom()
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr->dbvec[jcoeff][0]
+ bix*snaptr->bvec[jcoeff];
double dbytmp = bi*snaptr->dbvec[jcoeff][1]
+ biy*snaptr->bvec[jcoeff];
double dbztmp = bi*snaptr->dbvec[jcoeff][2]
+ biz*snaptr->bvec[jcoeff];
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+ bix*snaptr->blist[jcoeff];
double dbytmp = bi*snaptr->dblist[jcoeff][1]
+ biy*snaptr->blist[jcoeff];
double dbztmp = bi*snaptr->dblist[jcoeff][2]
+ biz*snaptr->blist[jcoeff];
snadi[ncount] += dbxtmp;
snadi[ncount+yoffset] += dbytmp;

46
src/SNAP/compute_snav_atom.cpp
View File

@ -260,7 +260,6 @@ void ComputeSNAVAtom::compute_peratom()
snaptr->compute_zi();
if (quadraticflag) {
snaptr->compute_bi();
snaptr->copy_bi2bvec();
}
for (int jj = 0; jj < ninside; jj++) {
@ -270,7 +269,6 @@ void ComputeSNAVAtom::compute_peratom()
snaptr->wj[jj],
snaptr->rcutij[jj]);
snaptr->compute_dbidrj();
snaptr->copy_dbi2dbvec();
// Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj
@ -278,18 +276,18 @@ void ComputeSNAVAtom::compute_peratom()
double *snavj = snav[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snavi[icoeff] += snaptr->dbvec[icoeff][0]*xtmp;
snavi[icoeff+nperdim] += snaptr->dbvec[icoeff][1]*ytmp;
snavi[icoeff+2*nperdim] += snaptr->dbvec[icoeff][2]*ztmp;
snavi[icoeff+3*nperdim] += snaptr->dbvec[icoeff][1]*ztmp;
snavi[icoeff+4*nperdim] += snaptr->dbvec[icoeff][0]*ztmp;
snavi[icoeff+5*nperdim] += snaptr->dbvec[icoeff][0]*ytmp;
snavj[icoeff] -= snaptr->dbvec[icoeff][0]*x[j][0];
snavj[icoeff+nperdim] -= snaptr->dbvec[icoeff][1]*x[j][1];
snavj[icoeff+2*nperdim] -= snaptr->dbvec[icoeff][2]*x[j][2];
snavj[icoeff+3*nperdim] -= snaptr->dbvec[icoeff][1]*x[j][2];
snavj[icoeff+4*nperdim] -= snaptr->dbvec[icoeff][0]*x[j][2];
snavj[icoeff+5*nperdim] -= snaptr->dbvec[icoeff][0]*x[j][1];
snavi[icoeff] += snaptr->dblist[icoeff][0]*xtmp;
snavi[icoeff+nperdim] += snaptr->dblist[icoeff][1]*ytmp;
snavi[icoeff+2*nperdim] += snaptr->dblist[icoeff][2]*ztmp;
snavi[icoeff+3*nperdim] += snaptr->dblist[icoeff][1]*ztmp;
snavi[icoeff+4*nperdim] += snaptr->dblist[icoeff][0]*ztmp;
snavi[icoeff+5*nperdim] += snaptr->dblist[icoeff][0]*ytmp;
snavj[icoeff] -= snaptr->dblist[icoeff][0]*x[j][0];
snavj[icoeff+nperdim] -= snaptr->dblist[icoeff][1]*x[j][1];
snavj[icoeff+2*nperdim] -= snaptr->dblist[icoeff][2]*x[j][2];
snavj[icoeff+3*nperdim] -= snaptr->dblist[icoeff][1]*x[j][2];
snavj[icoeff+4*nperdim] -= snaptr->dblist[icoeff][0]*x[j][2];
snavj[icoeff+5*nperdim] -= snaptr->dblist[icoeff][0]*x[j][1];
}
if (quadraticflag) {
@ -298,10 +296,10 @@ void ComputeSNAVAtom::compute_peratom()
snavj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr->bvec[icoeff];
double bix = snaptr->dbvec[icoeff][0];
double biy = snaptr->dbvec[icoeff][1];
double biz = snaptr->dbvec[icoeff][2];
double bi = snaptr->blist[icoeff];
double bix = snaptr->dblist[icoeff][0];
double biy = snaptr->dblist[icoeff][1];
double biz = snaptr->dblist[icoeff][2];
// diagonal element of quadratic matrix
@ -325,12 +323,12 @@ void ComputeSNAVAtom::compute_peratom()
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr->dbvec[jcoeff][0]
+ bix*snaptr->bvec[jcoeff];
double dbytmp = bi*snaptr->dbvec[jcoeff][1]
+ biy*snaptr->bvec[jcoeff];
double dbztmp = bi*snaptr->dbvec[jcoeff][2]
+ biz*snaptr->bvec[jcoeff];
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+ bix*snaptr->blist[jcoeff];
double dbytmp = bi*snaptr->dblist[jcoeff][1]
+ biy*snaptr->blist[jcoeff];
double dbztmp = bi*snaptr->dblist[jcoeff][2]
+ biz*snaptr->blist[jcoeff];
snavi[ncount] += dbxtmp*xtmp;
snavi[ncount+nperdim] += dbytmp*ytmp;
snavi[ncount+2*nperdim] += dbztmp*ztmp;

8
src/SNAP/pair_snap.cpp
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@ -166,17 +166,14 @@ void PairSNAP::compute(int eflag, int vflag)
}
}
// compute Ui, Zi, and Bi for atom I
// compute Ui, Yi for atom I
snaptr->compute_ui(ninside);
snaptr->compute_zi();
// for neighbors of I within cutoff:
// compute Fij = dEi/dRj = -dEi/dRi
// add to Fi, subtract from Fj
// compute beta_i*Z_i = Y_i
snaptr->compute_yi(beta[ii]);
for (int jj = 0; jj < ninside; jj++) {
@ -310,10 +307,9 @@ void PairSNAP::compute_bispectrum()
snaptr->compute_ui(ninside);
snaptr->compute_zi();
snaptr->compute_bi();
snaptr->copy_bi2bvec();
for (int k = 0; k < ncoeff; k++)
bispectrum[ii][k] = snaptr->bvec[k];
bispectrum[ii][k] = snaptr->blist[k];
}
}

1160
src/SNAP/sna.cpp
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File diff suppressed because it is too large Load Diff

25
src/SNAP/sna.h
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@ -26,7 +26,6 @@ namespace LAMMPS_NS {
struct SNA_ZINDICES {
int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju;
double betaj;
};
struct SNA_BINDICES {
@ -51,19 +50,20 @@ public:
void compute_ui(int);
void compute_zi();
void compute_yi(const double*);
void compute_yterm(int, int, int, const double*);
void compute_bi();
void copy_bi2bvec();
// functions for derivatives
void compute_duidrj(double*, double, double);
void compute_dbidrj();
void compute_deidrj(double*);
void copy_dbi2dbvec();
double compute_sfac(double, double);
double compute_dsfac(double, double);
double* bvec, ** dbvec;
double* blist;
double** dblist;
double** rij;
int* inside;
double* wj;
@ -73,31 +73,17 @@ public:
void grow_rij(int);
int twojmax, diagonalstyle;
double*** uarraytot_r, *** uarraytot_i;
double***** zarray_r, ***** zarray_i;
double*** yarray_r, *** yarray_i;
double*** uarray_r, *** uarray_i;
private:
double rmin0, rfac0;
// use indexlist instead of loops, constructor generates these
// data for bispectrum coefficients
SNA_ZINDICES* idxz;
SNA_BINDICES* idxb;
int idxcg_max, idxu_max, idxz_max, idxb_max;
// data for bispectrum coefficients
double***** cgarray;
double** rootpqarray;
double*** barray;
// derivatives of data
double**** duarray_r, **** duarray_i;
double**** dbarray;
double* cglist;
int*** idxcg_block;
@ -121,9 +107,6 @@ private:
void destroy_twojmax_arrays();
void init_clebsch_gordan();
void init_rootpqarray();
void jtostr(char*, int);
void mtostr(char*, int, int);
void print_clebsch_gordan(FILE*);
void zero_uarraytot();
void addself_uarraytot(double);
void add_uarraytot(double, double, double);