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(partially) apply clang-format

This commit is contained in:
Axel Kohlmeyer 2022-11-30 19:10:46 -05:00
parent c0a01ae19b
commit b68e56e9be
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GPG Key ID: D9B44E93BF0C375A
4 changed files with 152 additions and 136 deletions
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4
src/ML-POD/fitpod.cpp
View File

@ -728,7 +728,7 @@ void CFITPOD::read_data_files(std::string data_file, std::vector<std::string> sp
if (data.fraction >= 1.0) { if (data.fraction >= 1.0) {
if (comm->me == 0) if (comm->me == 0)
utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n"); utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n");
if ((int) traindata.data_path.size() > 1) if (traindata.data_path.size() > 1)
get_data(traindata, species); get_data(traindata, species);
else else
error->all(FLERR,"data set is not found"); error->all(FLERR,"data set is not found");
@ -737,7 +737,7 @@ void CFITPOD::read_data_files(std::string data_file, std::vector<std::string> sp
} else { } else {
if (comm->me == 0) if (comm->me == 0)
utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n"); utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n");
if ((int) data.data_path.size() > 1) if (data.data_path.size() > 1)
get_data(data, species); get_data(data, species);
else else
error->all(FLERR,"data set is not found"); error->all(FLERR,"data set is not found");

22
src/ML-POD/mlpod.cpp
View File

@ -32,8 +32,8 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using MathConst::MY_PI; using MathConst::MY_PI;
using MathSpecial::powint;
using MathSpecial::cube; using MathSpecial::cube;
using MathSpecial::powint;
#define MAXLINE 1024 #define MAXLINE 1024
@ -44,8 +44,8 @@ MLPOD::podstruct::podstruct() :
{ {
} }
MLPOD::MLPOD(LAMMPS* _lmp, const std::string &pod_file, const std::string &coeff_file) MLPOD::MLPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) :
: Pointers(_lmp) Pointers(_lmp)
{ {
pod.besselparams = nullptr; pod.besselparams = nullptr;
pod.pbc = nullptr; pod.pbc = nullptr;
@ -56,12 +56,9 @@ MLPOD::MLPOD(LAMMPS* _lmp, const std::string &pod_file, const std::string &coeff
// read pod coefficient file to podstruct // read pod coefficient file to podstruct
if (coeff_file != "") if (coeff_file != "") read_coeff_file(coeff_file);
read_coeff_file(coeff_file);
if (pod.snaptwojmax > 0) { if (pod.snaptwojmax > 0) { InitSnap(); }
InitSnap();
}
} }
MLPOD::~MLPOD() MLPOD::~MLPOD()
@ -73,15 +70,15 @@ MLPOD::~MLPOD()
memory->destroy(pod.elemindex); memory->destroy(pod.elemindex);
memory->destroy(pod.besselparams); memory->destroy(pod.besselparams);
memory->destroy(pod.coeff); memory->destroy(pod.coeff);
if (pod.ns2 > 0){ if (pod.ns2 > 0) {
memory->destroy(pod.Phi2); memory->destroy(pod.Phi2);
memory->destroy(pod.Lambda2); memory->destroy(pod.Lambda2);
} }
if (pod.ns3 > 0){ if (pod.ns3 > 0) {
memory->destroy(pod.Phi3); memory->destroy(pod.Phi3);
memory->destroy(pod.Lambda3); memory->destroy(pod.Lambda3);
} }
if (pod.ns4 > 0){ if (pod.ns4 > 0) {
memory->destroy(pod.Phi4); memory->destroy(pod.Phi4);
memory->destroy(pod.Lambda4); memory->destroy(pod.Lambda4);
} }
@ -107,6 +104,9 @@ MLPOD::~MLPOD()
} }
} }
// clang-format off
void MLPOD::print_matrix(const char *desc, int m, int n, double **a, int /*lda*/ ) void MLPOD::print_matrix(const char *desc, int m, int n, double **a, int /*lda*/ )
{ {
int i, j; int i, j;

260
src/ML-POD/mlpod.h
View File

@ -25,23 +25,22 @@
#define DPOSV dposv_ #define DPOSV dposv_
extern "C" { extern "C" {
double DDOT(int *, double *, int *, double *, int *); double DDOT(int *, double *, int *, double *, int *);
void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *, void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *,
int *); int *);
void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *, void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *,
double *, double *, int *); double *, double *, int *);
void DGETRF(int *, int *, double *, int *, int *, int *); void DGETRF(int *, int *, double *, int *, int *, int *);
void DGETRI(int *, double *, int *, int *, double *, int *, int *); void DGETRI(int *, double *, int *, int *, double *, int *, int *);
void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *); void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *);
void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *); void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *);
} }
namespace LAMMPS_NS { namespace LAMMPS_NS {
class MLPOD : protected Pointers { class MLPOD : protected Pointers {
private: private:
// functions for reading input files // functions for reading input files
void read_pod(const std::string &pod_file); void read_pod(const std::string &pod_file);
@ -50,99 +49,106 @@ private:
// functions for calculating/collating POD descriptors/coefficients for energies // functions for calculating/collating POD descriptors/coefficients for energies
void podradialbasis(double *rbf, double *drbf, double *xij, double *besselparams, double rin, void podradialbasis(double *rbf, double *drbf, double *xij, double *besselparams, double rin,
double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); double rmax, int besseldegree, int inversedegree, int nbesselpars, int N);
void pod1body(double *eatom, double *fatom, int *atomtype, int nelements, int natom); void pod1body(double *eatom, double *fatom, int *atomtype, int nelements, int natom);
void podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, void podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, int *ti,
int *ti, int *tj, int *elemindex, int nelements, int nbf, int natom, int N); int *tj, int *elemindex, int nelements, int nbf, int natom, int N);
void pod3body(double *eatom, double *fatom, double *rij, double *e2ij, double *f2ij, double *tmpmem, void pod3body(double *eatom, double *fatom, double *rij, double *e2ij, double *f2ij,
int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, int nrbf, int nabf, double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj,
int nelements, int natom, int Nij); int nrbf, int nabf, int nelements, int natom, int Nij);
void poddesc(double *eatom1, double *fatom1, double *eatom2, double *fatom2, double *eatom3, void poddesc(double *eatom1, double *fatom1, double *eatom2, double *fatom2, double *eatom3,
double *fatom3, double *rij, double *Phi, double *besselparams, double *tmpmem, double rin, double *fatom3, double *rij, double *Phi, double *besselparams, double *tmpmem,
double rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti, int *tj, int *elemindex, double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti,
int *pdegree, int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, int natom); int *tj, int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3,
double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, int nabf, int nelements, int Nij, int natom);
double *coeff23, int *quadratic, int nc2, int nc3); double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, double *coeff23,
double quadratic_coefficients(double *c3, double *d3, double *coeff33, int *quadratic, int nc2, int nc3);
int *quadratic, int nc3); double quadratic_coefficients(double *c3, double *d3, double *coeff33, int *quadratic, int nc3);
double cubic_coefficients(double *c2, double *c3, double *c4, double *d2, double *d3, double *d4, double cubic_coefficients(double *c2, double *c3, double *c4, double *d2, double *d3, double *d4,
double *coeff234, int *cubic, int nc2, int nc3, int nc4); double *coeff234, int *cubic, int nc2, int nc3, int nc4);
double cubic_coefficients(double *c3, double *d3, double *coeff333, int *cubic, int nc3); double cubic_coefficients(double *c3, double *d3, double *coeff333, int *cubic, int nc3);
double quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2, double *d3, double quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2,
double *coeff23, int *quadratic, int nc2, int nc3); double *d3, double *coeff23, int *quadratic, int nc2, int nc3);
double quadratic_coefficients(double *ce3, double *c3, double *d3, double *coeff33, double quadratic_coefficients(double *ce3, double *c3, double *d3, double *coeff33,
int *quadratic, int nc3); int *quadratic, int nc3);
double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3, double *c4, double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3,
double *d2, double *d3, double *d4, double *coeff234, int *cubic, int nc2, int nc3, int nc4); double *c4, double *d2, double *d3, double *d4, double *coeff234,
double cubic_coefficients(double *ce3, double *c3, double *d3, double *coeff333, int *cubic, int nc3); int *cubic, int nc2, int nc3, int nc4);
double cubic_coefficients(double *ce3, double *c3, double *d3, double *coeff333, int *cubic,
int nc3);
// functions for calculating/collating SNAP descriptors/coefficients for energies // functions for calculating/collating SNAP descriptors/coefficients for energies
void snapSetup(int twojmax, int ntypes); void snapSetup(int twojmax, int ntypes);
void InitSnap(); void InitSnap();
void snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray, double *rij, void snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray,
double *wjelem, double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, double *rij, double *wjelem, double *radelem, double rmin0, double rfac0,
int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); double rcutfac, int *idxu_block, int *ti, int *tj, int twojmax,
void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, int idxu_max, int ijnum, int switch_flag);
int *type, int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max, int nelements, void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, int *type,
int twojmax, int inum); int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max,
void snapAddUarraytot(double *Stotr, double *Stoti, double *Sr, int nelements, int twojmax, int inum);
double *Si, int *map, int *ai, int *tj, int idxu_max, int inum, int ijnum, int chemflag); void snapAddUarraytot(double *Stotr, double *Stoti, double *Sr, double *Si, int *map, int *ai,
int *tj, int idxu_max, int inum, int ijnum, int chemflag);
void snapComputeZi2(double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, void snapComputeZi2(double *zlist_r, double *zlist_i, double *Stotr, double *Stoti,
double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax, int idxu_max, double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax,
int idxz_max, int nelements, int bnorm_flag, int inum); int idxu_max, int idxz_max, int nelements, int bnorm_flag, int inum);
void snapComputeBi1(double *blist, double *zlist_r, double *zlist_i, double *Stotr, double *Stoti, void snapComputeBi1(double *blist, double *zlist_r, double *zlist_i, double *Stotr, double *Stoti,
int *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max, int idxu_max, int *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max,
int idxz_max, int nelements, int inum); int idxu_max, int idxz_max, int nelements, int inum);
void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, double *dulist_r,
double *dulist_r, double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, int *map,
int *map, int *ai, int *tj, int twojmax, int idxb_max, int idxu_max, int idxz_max, int *ai, int *tj, int twojmax, int idxb_max, int idxu_max, int idxz_max,
int nelements, int bnorm_flag, int chemflag, int inum, int ijnum); int nelements, int bnorm_flag, int chemflag, int inum, int ijnum);
void snapdesc(double *blist, double *bd, double *rij, double *tmpmem, int *atomtype, int *ai, void snapdesc(double *blist, double *bd, double *rij, double *tmpmem, int *atomtype, int *ai,
int *aj, int *ti, int *tj, int natom, int Nij); int *aj, int *ti, int *tj, int natom, int Nij);
// functions for calculating/collating POD descriptors/coefficients for forces // functions for calculating/collating POD descriptors/coefficients for forces
void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, double rmax,
double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); int besseldegree, int inversedegree, int nbesselpars, int N);
void pod1body(double *eatom, int *atomtype, int nelements, int natom); void pod1body(double *eatom, int *atomtype, int nelements, int natom);
void podtally2b(double *eatom, double *eij, int *ai, int *ti, int *tj, int *elemindex, void podtally2b(double *eatom, double *eij, int *ai, int *ti, int *tj, int *elemindex,
int nelements, int nbf, int natom, int N); int nelements, int nbf, int natom, int N);
void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex, int *pairnumsum, void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex,
int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); int *pairnumsum, int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements,
void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi, double *besselparams, int natom, int Nij);
double *tmpmem, double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *ti, int *tj, void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi,
int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, int natom); double *besselparams, double *tmpmem, double rin, double rcut, int *pairnumsum,
void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, int *atomtype, int *ai, int *ti, int *tj, int *elemindex, int *pdegree,
double *wjelem, double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij,
int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); int natom);
void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, double *wjelem,
int *ti, int *tj, int natom, int Nij); double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block,
void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag);
int *ti, int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, int *ti,
void pod3body_force(double *force, double *yij, double *e2ij, double *f2ij, double *coeff3, double *tmpmem, int *tj, int natom, int Nij);
int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, int nrbf, int nabf, void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti,
int nelements, int natom, int Nij); int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij);
void snapTallyForce(double *force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, int ijnum, void pod3body_force(double *force, double *yij, double *e2ij, double *f2ij, double *coeff3,
int ncoeff, int ntype); double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti,
int *tj, int nrbf, int nabf, int nelements, int natom, int Nij);
void snapTallyForce(double *force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti,
int ijnum, int ncoeff, int ntype);
void pod4body_force(double *force, double *rij, double *coeff4, double *tmpmem, int *atomtype, void pod4body_force(double *force, double *rij, double *coeff4, double *tmpmem, int *atomtype,
int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij);
void pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, void pod2body_force(double **force, double *fij, double *coeff2, int *ai, int *aj, int *ti,
int *ti, int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij); int *tj, int *elemindex, int nelements, int nbf, int natom, int Nij);
void pod3body_force(double **force, double *yij, double *e2ij, double *f2ij, double *coeff3, double *tmpmem, void pod3body_force(double **force, double *yij, double *e2ij, double *f2ij, double *coeff3,
int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, int nrbf, int nabf, double *tmpmem, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti,
int nelements, int natom, int Nij); int *tj, int nrbf, int nabf, int nelements, int natom, int Nij);
void snapTallyForce(double **force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti, int ijnum, void snapTallyForce(double **force, double *dbdr, double *coeff4, int *ai, int *aj, int *ti,
int ncoeff, int ntype); int ijnum, int ncoeff, int ntype);
void pod4body_force(double **force, double *rij, double *coeff4, double *tmpmem, int *atomtype, void pod4body_force(double **force, double *rij, double *coeff4, double *tmpmem, int *atomtype,
int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij);
// eigenproblem functions // eigenproblem functions
void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin, double rcut, void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin,
int besseldegree, int inversedegree, int nbesselpars, int N); double rcut, int besseldegree, int inversedegree, int nbesselpars,
int N);
public: public:
MLPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file); MLPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file);
MLPOD(LAMMPS *lmp) : Pointers(lmp){}; MLPOD(LAMMPS *lmp) : Pointers(lmp){};
@ -183,16 +189,17 @@ public:
// variables declaring number of snapshots, descriptors, and combinations // variables declaring number of snapshots, descriptors, and combinations
int nbesselpars = 3; int nbesselpars = 3;
int ns2, ns3, ns4; // number of snapshots for radial basis functions for linear POD potentials int ns2, ns3,
int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials ns4; // number of snapshots for radial basis functions for linear POD potentials
int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials
int nd1, nd2, nd3, nd4; // number of descriptors for linear POD potentials int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials
int nd22, nd23, nd24, nd33, nd34, nd44; // number of descriptors for quadratic POD potentials int nd1, nd2, nd3, nd4; // number of descriptors for linear POD potentials
int nd234, nd333, nd444; // number of descriptors for cubic POD potentials int nd22, nd23, nd24, nd33, nd34, nd44; // number of descriptors for quadratic POD potentials
int nd234, nd333, nd444; // number of descriptors for cubic POD potentials
int nrbf3, nabf3, nrbf4, nabf4; int nrbf3, nabf3, nrbf4, nabf4;
int nd, nd1234; int nd, nd1234;
int snaptwojmax; // also used to tell if SNAP is used when allocating/deallocating int snaptwojmax; // also used to tell if SNAP is used when allocating/deallocating
int snapchemflag; int snapchemflag;
double snaprfac0; double snaprfac0;
double snapelementradius[10]; double snapelementradius[10];
@ -208,8 +215,8 @@ public:
int idxcg_max; int idxcg_max;
int ntypes; int ntypes;
int nelements; int nelements;
int ndoubles; // number of multi-element pairs int ndoubles; // number of multi-element pairs
int ntriples; // number of multi-element triplets int ntriples; // number of multi-element triplets
int bnormflag; int bnormflag;
int chemflag; int chemflag;
int switchflag; int switchflag;
@ -222,7 +229,7 @@ public:
double rcutfac; double rcutfac;
double rcutmax; double rcutmax;
int *map; // map types to [0,nelements) int *map; // map types to [0,nelements)
int *idx_max; int *idx_max;
int *idxz; int *idxz;
int *idxz_block; int *idxz_block;
@ -245,16 +252,16 @@ public:
// functions for collecting/collating arrays // functions for collecting/collating arrays
void print_matrix(const char* desc, int m, int n, int* a, int lda ); void print_matrix(const char *desc, int m, int n, int *a, int lda);
void print_matrix(const char* desc, int m, int n, double* a, int lda ); void print_matrix(const char *desc, int m, int n, double *a, int lda);
void print_matrix(const char* desc, int m, int n, double **a, int lda ); void print_matrix(const char *desc, int m, int n, double **a, int lda);
void podMatMul(double *c, double *a, double *b, int r1, int c1, int c2); void podMatMul(double *c, double *a, double *b, int r1, int c1, int c2);
void podCumsum(int* output, int* input, int length); void podCumsum(int *output, int *input, int length);
double podArrayNorm(double *a, int n); double podArrayNorm(double *a, int n);
double podArrayErrorNorm(double *a, double *b, int n); double podArrayErrorNorm(double *a, double *b, int n);
void podArraySetValue(double *y, double a, int n); void podArraySetValue(double *y, double a, int n);
void podArrayCopy(double *y, double *x, int n); void podArrayCopy(double *y, double *x, int n);
void podArrayFill(int* output, int start, int length); void podArrayFill(int *output, int start, int length);
double podArrayMin(double *a, int n); double podArrayMin(double *a, int n);
double podArrayMax(double *a, int n); double podArrayMax(double *a, int n);
double podArraySum(double *a, int n); double podArraySum(double *a, int n);
@ -262,42 +269,53 @@ public:
int podArrayMax(int *a, int n); int podArrayMax(int *a, int n);
void podKron(double *C, double *A, double *B, double alpha, int M1, int M2); void podKron(double *C, double *A, double *B, double alpha, int M1, int M2);
void rotation_matrix(double *Rmat, double alpha, double beta, double gamma); void rotation_matrix(double *Rmat, double alpha, double beta, double gamma);
void triclinic_lattice_conversion(double *a, double *b, double *c, double *A, double *B, double *C); void triclinic_lattice_conversion(double *a, double *b, double *c, double *A, double *B,
double *C);
void matrix33_multiplication(double *xrot, double *Rmat, double *x, int natom); void matrix33_multiplication(double *xrot, double *Rmat, double *x, int natom);
void matrix33_inverse(double *invA, double *A1, double *A2, double *A3); void matrix33_inverse(double *invA, double *A1, double *A2, double *A3);
// functions for calculating energy and force descriptors // functions for calculating energy and force descriptors
void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, int *pairlist,
int *pairlist, int *pairnumsum, int *atomtype, int *alist, int inum, int dim); int *pairnumsum, int *atomtype, int *alist, int inum, int dim);
void linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, int *atomtype, void linear_descriptors(double *gd, double *efatom, double *y, double *tmpmem, int *atomtype,
int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, int natom, int Nij); int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint,
void quadratic_descriptors(double* d23, double *dd23, double* d2, double *d3, double* dd2, double *dd3, int natom, int Nij);
int M2, int M3, int N); void quadratic_descriptors(double *d23, double *dd23, double *d2, double *d3, double *dd2,
void quadratic_descriptors(double* d33, double *dd33, double *d3, double *dd3, int M3, int N); double *dd3, int M2, int M3, int N);
void cubic_descriptors(double* d234, double *dd234, double* d2, double *d3, double *d4, void quadratic_descriptors(double *d33, double *dd33, double *d3, double *dd3, int M3, int N);
double* dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N); void cubic_descriptors(double *d234, double *dd234, double *d2, double *d3, double *d4,
void cubic_descriptors(double* d333, double *Dd333, double *d3, double *Dd3, int M3, int N); double *dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N);
double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp, int natom); void cubic_descriptors(double *d333, double *Dd333, double *d3, double *Dd3, int M3, int N);
double energyforce_calculation(double *f, double *gd, double *gdd, double *coeff, double *y, int *atomtype, double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp,
int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, int natom, int Nij); int natom);
double energyforce_calculation(double *f, double *gd, double *gdd, double *coeff, double *y,
int *atomtype, int *alist, int *pairlist, int *pairnum,
int *pairnumsum, int *tmpint, int natom, int Nij);
// functions for calculating energies and forces // functions for calculating energies and forces
void podNeighPairs(double *rij, double *x, int *idxi, int *ai, int *aj, int *ti, int *tj, void podNeighPairs(double *rij, double *x, int *idxi, int *ai, int *aj, int *ti, int *tj,
int *pairnumsum, int *atomtype, int *jlist, int *alist, int inum); int *pairnumsum, int *atomtype, int *jlist, int *alist, int inum);
int lammpsNeighPairs(double *rij, double **x, double rcutsq, int *idxi, int *ai, int *aj, int *ti, int *tj, int lammpsNeighPairs(double *rij, double **x, double rcutsq, int *idxi, int *ai, int *aj, int *ti,
int *pairnumsum, int *atomtype, int *numneigh, int *ilist, int **jlist, int inum); int *tj, int *pairnumsum, int *atomtype, int *numneigh, int *ilist,
void linear_descriptors_ij(double *gd, double *eatom, double *rij, double *tmpmem, int *pairnumsum, int **jlist, int inum);
int *atomtype, int *ai, int *ti, int *tj, int natom, int Nij); void linear_descriptors_ij(double *gd, double *eatom, double *rij, double *tmpmem,
int *pairnumsum, int *atomtype, int *ai, int *ti, int *tj, int natom,
int Nij);
double calculate_energy(double *effectivecoeff, double *gd, double *coeff); double calculate_energy(double *effectivecoeff, double *gd, double *coeff);
double calculate_energy(double *energycoeff, double *forcecoeff, double *gd, double *gdall, double *coeff); double calculate_energy(double *energycoeff, double *forcecoeff, double *gd, double *gdall,
void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem, int *pairnumsum, double *coeff);
int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem,
void calculate_force(double **force, double *effectivecoeff, double *rij, double *tmpmem, int *pairnumsum, int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti,
int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); int *tj, int natom, int Nij);
double energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff, double *gd, double *rij, void calculate_force(double **force, double *effectivecoeff, double *rij, double *tmpmem,
double *tmpmem, int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj, int natom, int Nij); int *pairnumsum, int *atomtype, int *idxi, int *ai, int *aj, int *ti,
int *tj, int natom, int Nij);
double energyforce_calculation(double *force, double *podcoeff, double *effectivecoeff,
double *gd, double *rij, double *tmpmem, int *pairnumsum,
int *atomtype, int *idxi, int *ai, int *aj, int *ti, int *tj,
int natom, int Nij);
// variables used in eigenvaluedecomposition // variables used in eigenvaluedecomposition
@ -306,10 +324,8 @@ public:
double *Q; double *Q;
double *A; double *A;
double *b; double *b;
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS
#endif #endif

2
src/ML-POD/pair_pod.h
View File

@ -72,7 +72,7 @@ class PairPOD : public Pair {
int *ti; // types of atoms I for all pairs (I, J) int *ti; // types of atoms I for all pairs (I, J)
int *tj; // types of atoms J for all pairs (I, J) int *tj; // types of atoms J for all pairs (I, J)
bool peratom_warn; // print warning about missing per-atom energies or stresses bool peratom_warn; // print warning about missing per-atom energies or stresses
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS