From b68e56e9be678f2110ba5f1b6ada030d464c0c65 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 30 Nov 2022 19:10:46 -0500 Subject: [PATCH] (partially) apply clang-format --- src/ML-POD/fitpod.cpp | 4 +- src/ML-POD/mlpod.cpp | 22 ++-- src/ML-POD/mlpod.h | 260 ++++++++++++++++++++++-------------------- src/ML-POD/pair_pod.h | 2 +- 4 files changed, 152 insertions(+), 136 deletions(-) diff --git a/src/ML-POD/fitpod.cpp b/src/ML-POD/fitpod.cpp index 3c68bcd903..ce4c93bf50 100644 --- a/src/ML-POD/fitpod.cpp +++ b/src/ML-POD/fitpod.cpp @@ -728,7 +728,7 @@ void CFITPOD::read_data_files(std::string data_file, std::vector sp if (data.fraction >= 1.0) { if (comm->me == 0) 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); else error->all(FLERR,"data set is not found"); @@ -737,7 +737,7 @@ void CFITPOD::read_data_files(std::string data_file, std::vector sp } else { if (comm->me == 0) 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); else error->all(FLERR,"data set is not found"); diff --git a/src/ML-POD/mlpod.cpp b/src/ML-POD/mlpod.cpp index 4c6c21a272..52c6bf5670 100644 --- a/src/ML-POD/mlpod.cpp +++ b/src/ML-POD/mlpod.cpp @@ -32,8 +32,8 @@ using namespace LAMMPS_NS; using MathConst::MY_PI; -using MathSpecial::powint; using MathSpecial::cube; +using MathSpecial::powint; #define MAXLINE 1024 @@ -44,8 +44,8 @@ MLPOD::podstruct::podstruct() : { } -MLPOD::MLPOD(LAMMPS* _lmp, const std::string &pod_file, const std::string &coeff_file) - : Pointers(_lmp) +MLPOD::MLPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) : + Pointers(_lmp) { pod.besselparams = 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 - if (coeff_file != "") - read_coeff_file(coeff_file); + if (coeff_file != "") read_coeff_file(coeff_file); - if (pod.snaptwojmax > 0) { - InitSnap(); - } + if (pod.snaptwojmax > 0) { InitSnap(); } } MLPOD::~MLPOD() @@ -73,15 +70,15 @@ MLPOD::~MLPOD() memory->destroy(pod.elemindex); memory->destroy(pod.besselparams); memory->destroy(pod.coeff); - if (pod.ns2 > 0){ + if (pod.ns2 > 0) { memory->destroy(pod.Phi2); memory->destroy(pod.Lambda2); } - if (pod.ns3 > 0){ + if (pod.ns3 > 0) { memory->destroy(pod.Phi3); memory->destroy(pod.Lambda3); } - if (pod.ns4 > 0){ + if (pod.ns4 > 0) { memory->destroy(pod.Phi4); 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*/ ) { int i, j; diff --git a/src/ML-POD/mlpod.h b/src/ML-POD/mlpod.h index 83f090618e..123fa49fc7 100644 --- a/src/ML-POD/mlpod.h +++ b/src/ML-POD/mlpod.h @@ -25,23 +25,22 @@ #define DPOSV dposv_ extern "C" { - double DDOT(int *, double *, int *, double *, int *); - void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *, - int *); - void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *, - double *, double *, int *); - void DGETRF(int *, int *, double *, int *, int *, int *); - void DGETRI(int *, double *, int *, int *, double *, int *, int *); - void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *); - void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *); +double DDOT(int *, double *, int *, double *, int *); +void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *, + int *); +void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *, + double *, double *, int *); +void DGETRF(int *, int *, double *, int *, int *, int *); +void DGETRI(int *, double *, int *, int *, double *, int *, int *); +void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *); +void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *); } namespace LAMMPS_NS { class MLPOD : protected Pointers { -private: - + private: // functions for reading input files void read_pod(const std::string &pod_file); @@ -50,99 +49,106 @@ private: // functions for calculating/collating POD descriptors/coefficients for energies 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 podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, - int *ti, 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, - int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, int nrbf, int nabf, - int nelements, int natom, int Nij); + void podtally2b(double *eatom, double *fatom, double *eij, double *fij, int *ai, int *aj, int *ti, + 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, int *elemindex, int *pairnumsum, int *ai, int *aj, int *ti, int *tj, + int nrbf, int nabf, int nelements, int natom, int Nij); 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 rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti, int *tj, int *elemindex, - int *pdegree, int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, int natom); - double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, - double *coeff23, int *quadratic, int nc2, int nc3); - double quadratic_coefficients(double *c3, double *d3, double *coeff33, - int *quadratic, int nc3); + double *fatom3, double *rij, double *Phi, double *besselparams, double *tmpmem, + double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *aj, int *ti, + int *tj, int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3, + int nabf, int nelements, int Nij, int natom); + double quadratic_coefficients(double *c2, double *c3, double *d2, double *d3, double *coeff23, + int *quadratic, int nc2, 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 *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 quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2, double *d3, - double *coeff23, int *quadratic, int nc2, int nc3); + double quadratic_coefficients(double *ce2, double *ce3, double *c2, double *c3, double *d2, + double *d3, double *coeff23, int *quadratic, int nc2, int nc3); double quadratic_coefficients(double *ce3, double *c3, double *d3, double *coeff33, - int *quadratic, int nc3); - double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3, double *c4, - double *d2, double *d3, double *d4, double *coeff234, int *cubic, int nc2, int nc3, int nc4); - double cubic_coefficients(double *ce3, double *c3, double *d3, double *coeff333, int *cubic, int nc3); + int *quadratic, int nc3); + double cubic_coefficients(double *ce2, double *ce3, double *ce4, double *c2, double *c3, + double *c4, double *d2, double *d3, double *d4, double *coeff234, + 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 void snapSetup(int twojmax, int ntypes); void InitSnap(); - void snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray, double *rij, - double *wjelem, double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, - int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); - void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, - int *type, int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max, int nelements, - int twojmax, int inum); - 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 snapComputeUlist(double *Sr, double *Si, double *dSr, double *dSi, double *rootpqarray, + double *rij, double *wjelem, double *radelem, double rmin0, double rfac0, + double rcutfac, int *idxu_block, int *ti, int *tj, int twojmax, + int idxu_max, int ijnum, int switch_flag); + void snapZeroUarraytot2(double *Stotr, double *Stoti, double wself, int *idxu_block, int *type, + int *map, int *ai, int wselfall_flag, int chemflag, int idxu_max, + int nelements, int twojmax, int inum); + 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, - double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax, int idxu_max, - int idxz_max, int nelements, int bnorm_flag, int inum); + double *cglist, int *idxz, int *idxu_block, int *idxcg_block, int twojmax, + 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, - int *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max, int idxu_max, - int idxz_max, int nelements, int inum); - void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, - double *dulist_r, double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, - int *map, 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 *idxb, int *idxu_block, int *idxz_block, int twojmax, int idxb_max, + int idxu_max, int idxz_max, int nelements, int inum); + void snapComputeDbidrj(double *dblist, double *zlist_r, double *zlist_i, double *dulist_r, + double *dulist_i, int *idxb, int *idxu_block, int *idxz_block, int *map, + 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); 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 - void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, - double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); + void podradialbasis(double *rbf, double *xij, double *besselparams, double rin, double rmax, + int besseldegree, int inversedegree, int nbesselpars, int N); void pod1body(double *eatom, int *atomtype, int nelements, int natom); void podtally2b(double *eatom, double *eij, int *ai, int *ti, int *tj, int *elemindex, - int nelements, int nbf, int natom, int N); - void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex, int *pairnumsum, - int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements, int natom, int Nij); - void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi, double *besselparams, - double *tmpmem, double rin, double rcut, int *pairnumsum, int *atomtype, int *ai, int *ti, int *tj, - int *elemindex, int *pdegree, int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, int natom); - void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, - double *wjelem, double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, - int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); - void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, - int *ti, int *tj, int natom, int Nij); - void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, - int *ti, 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, - 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); + int nelements, int nbf, int natom, int N); + void pod3body(double *eatom, double *yij, double *e2ij, double *tmpmem, int *elemindex, + int *pairnumsum, int *ai, int *ti, int *tj, int nrbf, int nabf, int nelements, + int natom, int Nij); + void poddesc_ij(double *eatom1, double *eatom2, double *eatom3, double *rij, double *Phi, + double *besselparams, double *tmpmem, double rin, double rcut, int *pairnumsum, + int *atomtype, int *ai, int *ti, int *tj, int *elemindex, int *pdegree, + int nbesselpars, int nrbf2, int nrbf3, int nabf, int nelements, int Nij, + int natom); + void snapComputeUij(double *Sr, double *Si, double *rootpqarray, double *rij, double *wjelem, + double *radelem, double rmin0, double rfac0, double rcutfac, int *idxu_block, + int *ti, int *tj, int twojmax, int idxu_max, int ijnum, int switch_flag); + void snapdesc_ij(double *blist, double *rij, double *tmpmem, int *atomtype, int *ai, int *ti, + int *tj, int natom, int Nij); + void pod2body_force(double *force, double *fij, double *coeff2, int *ai, int *aj, int *ti, + 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, 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, - 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, - int *ti, 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, - 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); + 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, int *ti, + 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, 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, - 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 - void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin, double rcut, - int besseldegree, int inversedegree, int nbesselpars, int N); + void podeigenvaluedecomposition(double *Phi, double *Lambda, double *besselparams, double rin, + 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 *lmp) : Pointers(lmp){}; @@ -183,16 +189,17 @@ public: // variables declaring number of snapshots, descriptors, and combinations int nbesselpars = 3; - int ns2, ns3, ns4; // number of snapshots for radial basis functions for linear POD potentials - int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials - int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials - int nd1, nd2, nd3, nd4; // number of descriptors for linear 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 ns2, ns3, + ns4; // number of snapshots for radial basis functions for linear POD potentials + int nc2, nc3, nc4; // number of chemical combinations for linear POD potentials + int nbf1, nbf2, nbf3, nbf4; // number of basis functions for linear POD potentials + int nd1, nd2, nd3, nd4; // number of descriptors for linear 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 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; double snaprfac0; double snapelementradius[10]; @@ -208,8 +215,8 @@ public: int idxcg_max; int ntypes; int nelements; - int ndoubles; // number of multi-element pairs - int ntriples; // number of multi-element triplets + int ndoubles; // number of multi-element pairs + int ntriples; // number of multi-element triplets int bnormflag; int chemflag; int switchflag; @@ -222,7 +229,7 @@ public: double rcutfac; double rcutmax; - int *map; // map types to [0,nelements) + int *map; // map types to [0,nelements) int *idx_max; int *idxz; int *idxz_block; @@ -245,16 +252,16 @@ public: // 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, 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, 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 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 podArrayErrorNorm(double *a, double *b, int n); void podArraySetValue(double *y, double a, 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 podArrayMax(double *a, int n); double podArraySum(double *a, int n); @@ -262,42 +269,53 @@ public: int podArrayMax(int *a, int n); 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 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_inverse(double *invA, double *A1, double *A2, double *A3); // functions for calculating energy and force descriptors - void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, - int *pairlist, int *pairnumsum, int *atomtype, int *alist, int inum, int dim); + void podNeighPairs(double *xij, double *x, int *ai, int *aj, int *ti, int *tj, int *pairlist, + int *pairnumsum, int *atomtype, int *alist, int inum, int dim); 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); - void quadratic_descriptors(double* d23, double *dd23, double* d2, double *d3, double* dd2, double *dd3, - int M2, int M3, int N); - void quadratic_descriptors(double* d33, double *dd33, double *d3, double *dd3, int M3, int N); - void cubic_descriptors(double* d234, double *dd234, double* d2, double *d3, double *d4, - double* dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N); - void cubic_descriptors(double* d333, double *Dd333, double *d3, double *Dd3, int M3, int N); - double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp, 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); + int *alist, int *pairlist, int *pairnum, int *pairnumsum, int *tmpint, + int natom, int Nij); + void quadratic_descriptors(double *d23, double *dd23, double *d2, double *d3, double *dd2, + double *dd3, int M2, int M3, int N); + void quadratic_descriptors(double *d33, double *dd33, double *d3, double *dd3, int M3, int N); + void cubic_descriptors(double *d234, double *dd234, double *d2, double *d3, double *d4, + double *dd2, double *dd3, double *dd4, int M2, int M3, int M4, int N); + void cubic_descriptors(double *d333, double *Dd333, double *d3, double *Dd3, int M3, int N); + double calculate_energyforce(double *force, double *gd, double *gdd, double *coeff, double *tmp, + 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 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 lammpsNeighPairs(double *rij, double **x, double rcutsq, int *idxi, int *ai, int *aj, int *ti, int *tj, - int *pairnumsum, int *atomtype, int *numneigh, int *ilist, int **jlist, int inum); - 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); + 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 *pairnumsum, int *atomtype, int *numneigh, int *ilist, + int **jlist, int inum); + 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 *energycoeff, double *forcecoeff, double *gd, double *gdall, double *coeff); - void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem, int *pairnumsum, - 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, 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); + double calculate_energy(double *energycoeff, double *forcecoeff, double *gd, double *gdall, + double *coeff); + void calculate_force(double *force, double *effectivecoeff, double *rij, double *tmpmem, + int *pairnumsum, 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, + 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 @@ -306,10 +324,8 @@ public: double *Q; double *A; double *b; - }; } // namespace LAMMPS_NS #endif - diff --git a/src/ML-POD/pair_pod.h b/src/ML-POD/pair_pod.h index c47ead1496..62b6e99f3b 100644 --- a/src/ML-POD/pair_pod.h +++ b/src/ML-POD/pair_pod.h @@ -72,7 +72,7 @@ class PairPOD : public Pair { int *ti; // types of atoms I 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