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Added a lot of boilerplate for inner data, not working yet

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This commit is contained in:
Aidan Thompson
2022-03-10 18:40:59 -07:00
parent adef6bd10c
commit 11d3b13e31
14 changed files with 101 additions and 50 deletions
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22
src/ML-IAP/mliap_descriptor_snap.cpp
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@ -46,7 +46,8 @@ MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ndescriptors = snaptr->ncoeff;
}
@ -162,10 +163,12 @@ void MLIAPDescriptorSNAP::compute_forces(class MLIAPData* data)
int j = snaptr->inside[jj];
if (chemflag)
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
else
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, 0);
snaptr->rcutij[jj], jj, 0,
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_deidrj(fij);
@ -236,10 +239,12 @@ void MLIAPDescriptorSNAP::compute_force_gradients(class MLIAPData* data)
if (chemflag)
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
else
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, 0);
snaptr->rcutij[jj], jj, 0,
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_dbidrj();
@ -309,10 +314,12 @@ void MLIAPDescriptorSNAP::compute_descriptor_gradients(class MLIAPData* data)
for (int jj = 0; jj < ninside; jj++) {
if (chemflag)
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
else
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, 0);
snaptr->rcutij[jj], jj, 0,
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_dbidrj();
@ -361,6 +368,7 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
for (int i = 0; i < nelements; i++) delete[] elements[i];
delete[] elements;

1
src/ML-IAP/mliap_descriptor_snap.h
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@ -39,6 +39,7 @@ class MLIAPDescriptorSNAP : public MLIAPDescriptor {
int twojmax, switchflag, bzeroflag;
int chemflag, bnormflag, wselfallflag;
int switchinnerflag;
double rfac0, rmin0;
};

4
src/ML-SNAP/compute_sna_atom.cpp
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@ -54,6 +54,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
nelements = 1;
// offset by 1 to match up with types
@ -138,7 +139,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
size_peratom_cols = ncoeff;

1
src/ML-SNAP/compute_sna_atom.h
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@ -44,6 +44,7 @@ class ComputeSNAAtom : public Compute {
double *wjelem;
int *map; // map types to [0,nelements)
int nelements, chemflag;
int switchinnerflag;
class SNA *snaptr;
double cutmax;
int quadraticflag;

7
src/ML-SNAP/compute_snad_atom.cpp
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@ -54,6 +54,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
nelements = 1;
// process required arguments
@ -136,7 +137,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nperdim = ncoeff;
@ -300,7 +302,8 @@ void ComputeSNADAtom::compute_peratom()
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr->inside[jj];
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj], jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_dbidrj();
// Accumulate -dBi/dRi, -dBi/dRj

1
src/ML-SNAP/compute_snad_atom.h
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@ -46,6 +46,7 @@ class ComputeSNADAtom : public Compute {
double *wjelem;
int *map; // map types to [0,nelements)
int nelements, chemflag;
int switchinnerflag;
class SNA *snaptr;
double cutmax;
int quadraticflag;

7
src/ML-SNAP/compute_snap.cpp
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@ -61,6 +61,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
nelements = 1;
// process required arguments
@ -148,7 +149,8 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nperdim = ncoeff;
@ -354,7 +356,8 @@ void ComputeSnap::compute_array()
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr->inside[jj];
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj], jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_dbidrj();
// Accumulate dBi/dRi, -dBi/dRj

1
src/ML-SNAP/compute_snap.h
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@ -46,6 +46,7 @@ class ComputeSnap : public Compute {
double *wjelem;
int *map; // map types to [0,nelements)
int nelements, chemflag;
int switchinnerflag;
class SNA *snaptr;
double cutmax;
int quadraticflag;

7
src/ML-SNAP/compute_snav_atom.cpp
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@ -53,6 +53,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
nelements = 1;
// process required arguments
@ -131,7 +132,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nperdim = ncoeff;
@ -294,7 +296,8 @@ void ComputeSNAVAtom::compute_peratom()
const int j = snaptr->inside[jj];
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj], jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_dbidrj();
// Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj

1
src/ML-SNAP/compute_snav_atom.h
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@ -46,6 +46,7 @@ class ComputeSNAVAtom : public Compute {
double *wjelem;
int *map; // map types to [0,nelements)
int nelements, chemflag;
int switchinnerflag;
class SNA *snaptr;
int quadraticflag;
};

11
src/ML-SNAP/pair_snap.cpp
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@ -174,10 +174,13 @@ void PairSNAP::compute(int eflag, int vflag)
int j = snaptr->inside[jj];
if (chemflag)
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, snaptr->element[jj]);
snaptr->rcutij[jj], jj, snaptr->element[jj],
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
else
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj],jj, 0);
snaptr->rcutij[jj], jj, 0,
// snaptr->rinnerij[jj], snaptr->drinnerij[jj],jj);
0.0, 1.0);
snaptr->compute_deidrj(fij);
@ -403,7 +406,8 @@ void PairSNAP::coeff(int narg, char **arg)
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag, nelements);
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
if (ncoeff != snaptr->ncoeff) {
if (comm->me == 0)
@ -626,6 +630,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
chunksize = 32768;
parallel_thresh = 8192;

1
src/ML-SNAP/pair_snap.h
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@ -59,6 +59,7 @@ class PairSNAP : public Pair {
double **scale; // for thermodynamic integration
int twojmax, switchflag, bzeroflag, bnormflag;
int chemflag, wselfallflag;
int switchinnerflag;
int chunksize,parallel_thresh;
double rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters

62
src/ML-SNAP/sna.cpp
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@ -103,7 +103,7 @@ using namespace MathSpecial;
j = |j1-j2|, |j1-j2|+2,...,j1+j2-2,j1+j2
[1] Albert Bartok-Partay, "Gaussian Approximation..."
Doctoral Thesis, Cambrindge University, (2009)
Doctoral Thesis, Cambridge University, (2009)
[2] D. A. Varshalovich, A. N. Moskalev, and V. K. Khersonskii,
"Quantum Theory of Angular Momentum," World Scientific (1988)
@ -112,14 +112,15 @@ using namespace MathSpecial;
SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
double rmin0_in, int switch_flag_in, int bzero_flag_in,
int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in) : Pointers(lmp)
int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in,
int nelements_in, int switch_inner_flag_in) : Pointers(lmp)
{
wself = 1.0;
rfac0 = rfac0_in;
rmin0 = rmin0_in;
switch_flag = switch_flag_in;
switch_inner_flag = 0;
switch_inner_flag = switch_inner_flag_in;
bzero_flag = bzero_flag_in;
chem_flag = chem_flag_in;
bnorm_flag = bnorm_flag_in;
@ -142,6 +143,8 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in,
inside = nullptr;
wj = nullptr;
rcutij = nullptr;
rinnerij = nullptr;
drinnerij = nullptr;
element = nullptr;
nmax = 0;
idxz = nullptr;
@ -171,7 +174,11 @@ SNA::~SNA()
memory->destroy(inside);
memory->destroy(wj);
memory->destroy(rcutij);
memory->destroy(element);
if (switch_inner_flag) {
memory->destroy(rinnerij);
memory->destroy(drinnerij);
}
if (chem_flag) memory->destroy(element);
memory->destroy(ulist_r_ij);
memory->destroy(ulist_i_ij);
delete[] idxz;
@ -308,7 +315,6 @@ void SNA::init()
init_rootpqarray();
}
void SNA::grow_rij(int newnmax)
{
if (newnmax <= nmax) return;
@ -319,14 +325,22 @@ void SNA::grow_rij(int newnmax)
memory->destroy(inside);
memory->destroy(wj);
memory->destroy(rcutij);
memory->destroy(element);
if (switch_inner_flag) {
memory->destroy(rinnerij);
memory->destroy(drinnerij);
}
if (chem_flag) memory->destroy(element);
memory->destroy(ulist_r_ij);
memory->destroy(ulist_i_ij);
memory->create(rij, nmax, 3, "pair:rij");
memory->create(inside, nmax, "pair:inside");
memory->create(wj, nmax, "pair:wj");
memory->create(rcutij, nmax, "pair:rcutij");
memory->create(element, nmax, "sna:element");
if (switch_inner_flag) {
memory->create(rinnerij, nmax, "pair:rinnerij");
memory->create(drinnerij, nmax, "pair:drinnerij");
}
if (chem_flag) memory->create(element, nmax, "sna:element");
memory->create(ulist_r_ij, nmax, idxu_max, "sna:ulist_ij");
memory->create(ulist_i_ij, nmax, idxu_max, "sna:ulist_ij");
}
@ -360,9 +374,9 @@ void SNA::compute_ui(int jnum, int ielem)
compute_uarray(x, y, z, z0, r, j);
if (chem_flag)
add_uarraytot(r, wj[j], rcutij[j], j, element[j]);
add_uarraytot(r, wj[j], rcutij[j], j, element[j], rinnerij[j], drinnerij[j]);
else
add_uarraytot(r, wj[j], rcutij[j], j, 0);
add_uarraytot(r, wj[j], rcutij[j], j, 0, rinnerij[j], drinnerij[j]);
}
}
@ -952,7 +966,8 @@ void SNA::compute_dbidrj()
calculate derivative of Ui w.r.t. atom j
------------------------------------------------------------------------- */
void SNA::compute_duidrj(double* rij, double wj, double rcut, int jj, int jelem)
void SNA::compute_duidrj(double* rij, double wj, double rcut, int jj,
int jelem, double rinner, double drinner)
{
double rsq, r, x, y, z, z0, theta0, cs, sn;
double dz0dr;
@ -970,7 +985,7 @@ void SNA::compute_duidrj(double* rij, double wj, double rcut, int jj, int jelem)
dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq;
elem_duarray = jelem;
compute_duarray(x, y, z, z0, r, dz0dr, wj, rcut, jj);
compute_duarray(x, y, z, z0, r, dz0dr, wj, rcut, jj, rinner, drinner);
}
/* ---------------------------------------------------------------------- */
@ -999,18 +1014,17 @@ void SNA::zero_uarraytot(int ielem)
add Wigner U-functions for one neighbor to the total
------------------------------------------------------------------------- */
void SNA::add_uarraytot(double r, double wj, double rcut, int jj, int jelem)
void SNA::add_uarraytot(double r, double wj, double rcut, int jj, int jelem,
double rinner, double drinner)
{
double sfac;
double rinner = 0.0;
double drinner = 1.0;
sfac = compute_sfac(r, rcut);
sfac *= wj;
if (switch_inner_flag)
sfac *= compute_sfac_inner(r, rinner, drinner);
double* ulist_r = ulist_r_ij[jj];
double* ulist_i = ulist_i_ij[jj];
@ -1123,7 +1137,8 @@ void SNA::compute_uarray(double x, double y, double z,
void SNA::compute_duarray(double x, double y, double z,
double z0, double r, double dz0dr,
double wj, double rcut, int jj)
double wj, double rcut, int jj,
double rinner, double drinner)
{
double r0inv;
double a_r, a_i, b_r, b_i;
@ -1254,11 +1269,9 @@ void SNA::compute_duarray(double x, double y, double z,
double dsfac = compute_dsfac(r, rcut);
if (switch_inner_flag) {
double rinner = 0.0;
double drinner = 1.0;
sfac *= compute_sfac_inner(r, rinner, drinner);
dsfac *= compute_dsfac_inner(r, rinner, drinner);
double sfac_inner = compute_sfac_inner(r, rinner, drinner);
dsfac = dsfac*sfac_inner + sfac*compute_dsfac_inner(r, rinner, drinner);
sfac *= sfac_inner;
}
sfac *= wj;
@ -1323,7 +1336,12 @@ double SNA::memory_usage()
bytes += (double)nmax * sizeof(int); // inside
bytes += (double)nmax * sizeof(double); // wj
bytes += (double)nmax * sizeof(double); // rcutij
if (switch_inner_flag) {
bytes += (double)nmax * sizeof(double); // rinnerij
bytes += (double)nmax * sizeof(double); // drinnerij
}
if (chem_flag) bytes += (double)nmax * sizeof(int); // element
return bytes;
}
/* ---------------------------------------------------------------------- */

25
src/ML-SNAP/sna.h
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@ -33,7 +33,7 @@ struct SNA_BINDICES {
class SNA : protected Pointers {
public:
SNA(LAMMPS *, double, int, double, int, int, int, int, int, int);
SNA(LAMMPS *, double, int, double, int, int, int, int, int, int, int);
SNA(LAMMPS *lmp) : Pointers(lmp){};
~SNA() override;
@ -53,7 +53,7 @@ class SNA : protected Pointers {
// functions for derivatives
void compute_duidrj(double *, double, double, int, int);
void compute_duidrj(double *, double, double, int, int, double, double);
void compute_dbidrj();
void compute_deidrj(double *);
double compute_sfac(double, double);
@ -64,12 +64,14 @@ class SNA : protected Pointers {
double *blist;
double **dblist;
double **rij;
int *inside;
double *wj;
double *rcutij;
int *element; // index on [0,nelements)
int nmax;
double **rij; // short rij list
int *inside; // short neighbor list
double *wj; // short weight list
double *rcutij; // short cutoff list
double *rinnerij; // short inner cutoff list
double *drinnerij;// short inner range list
int *element; // short element list [0,nelements)
int nmax; // allocated size of short lists
void grow_rij(int);
@ -90,7 +92,7 @@ class SNA : protected Pointers {
int ***idxcg_block;
double *ulisttot_r, *ulisttot_i;
double **ulist_r_ij, **ulist_i_ij;
double **ulist_r_ij, **ulist_i_ij; // short u list
int *idxu_block;
double *zlist_r, *zlist_i;
@ -107,11 +109,12 @@ class SNA : protected Pointers {
void print_clebsch_gordan();
void init_rootpqarray();
void zero_uarraytot(int);
void add_uarraytot(double, double, double, int, int);
void add_uarraytot(double, double, double, int, int, double, double);
void compute_uarray(double, double, double, double, double, int);
double deltacg(int, int, int);
void compute_ncoeff();
void compute_duarray(double, double, double, double, double, double, double, double, int);
void compute_duarray(double, double, double, double, double, double,
double, double, int, double, double);
// Sets the style for the switching function
// 0 = none