apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -32,8 +32,8 @@ class ComputePODAtom : public Compute {
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void init_list(int, class NeighList *) override;
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void compute_peratom() override;
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double memory_usage() override;
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh,
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double rcutsq, int i);
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
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int *numneigh, double rcutsq, int i);
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void map_element2type(int narg, char **arg, int nelements);
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private:
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@ -45,14 +45,14 @@ class ComputePODAtom : public Compute {
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int nij;
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int nijmax;
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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char **elements;
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int *map;
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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};
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} // namespace LAMMPS_NS
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@ -32,8 +32,8 @@ class ComputePODGlobal : public Compute {
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void init_list(int, class NeighList *) override;
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void compute_array() override;
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double memory_usage() override;
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh,
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double rcutsq, int i);
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
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int *numneigh, double rcutsq, int i);
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void map_element2type(int narg, char **arg, int nelements);
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private:
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@ -44,14 +44,14 @@ class ComputePODGlobal : public Compute {
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int nij;
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int nijmax;
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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char **elements;
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int *map;
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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};
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} // namespace LAMMPS_NS
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@ -32,8 +32,8 @@ class ComputePODLocal : public Compute {
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void init_list(int, class NeighList *) override;
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void compute_array() override;
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double memory_usage() override;
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh,
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double rcutsq, int i);
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
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int *numneigh, double rcutsq, int i);
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void map_element2type(int narg, char **arg, int nelements);
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private:
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@ -44,14 +44,14 @@ class ComputePODLocal : public Compute {
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int nij;
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int nijmax;
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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char **elements;
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int *map;
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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};
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} // namespace LAMMPS_NS
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@ -32,8 +32,8 @@ class ComputePODDAtom : public Compute {
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void init_list(int, class NeighList *) override;
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void compute_peratom() override;
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double memory_usage() override;
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh,
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double rcutsq, int i);
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void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
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int *numneigh, double rcutsq, int i);
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void map_element2type(int narg, char **arg, int nelements);
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private:
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@ -45,14 +45,14 @@ class ComputePODDAtom : public Compute {
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int nij;
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int nijmax;
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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double *tmpmem; // temporary memory
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double *rij; // (xj - xi) for all pairs (I, J)
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char **elements;
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int *map;
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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int *ai; // IDs of atoms I for all pairs (I, J)
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int *aj; // IDs of atoms J for all pairs (I, J)
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int *ti; // types of atoms I for all pairs (I, J)
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int *tj; // types of atoms J for all pairs (I, J)
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};
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} // namespace LAMMPS_NS
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@ -25,26 +25,26 @@
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#define DPOSV dposv_
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extern "C" {
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double DDOT(int *, double *, int *, double *, int *);
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void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *,
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int *);
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void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *,
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double *, double *, int *);
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void DGETRF(int *, int *, double *, int *, int *, int *);
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void DGETRI(int *, double *, int *, int *, double *, int *, int *);
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void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *);
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void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *);
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double DDOT(int *, double *, int *, double *, int *);
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void DGEMV(char *, int *, int *, double *, double *, int *, double *, int *, double *, double *,
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int *);
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void DGEMM(char *, char *, int *, int *, int *, double *, double *, int *, double *, int *,
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double *, double *, int *);
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void DGETRF(int *, int *, double *, int *, int *, int *);
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void DGETRI(int *, double *, int *, int *, double *, int *, int *);
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void DSYEV(char *, char *, int *, double *, int *, double *, double *, int *, int *);
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void DPOSV(char *, int *, int *, double *, int *, double *, int *, int *);
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}
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namespace LAMMPS_NS {
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class EAPOD : protected Pointers {
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private:
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private:
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int indexmap3(int *indx, int n1, int n2, int n3, int N1, int N2);
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int crossindices(int *dabf1, int nabf1, int nrbf1, int nebf1,
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int *dabf2, int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12);
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int crossindices(int *ind1, int *ind2, int *dabf1, int nabf1, int nrbf1, int nebf1,
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int *dabf2, int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12);
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int crossindices(int *dabf1, int nabf1, int nrbf1, int nebf1, int *dabf2, int nabf2, int nrbf2,
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int nebf2, int dabf12, int nrbf12);
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int crossindices(int *ind1, int *ind2, int *dabf1, int nabf1, int nrbf1, int nebf1, int *dabf2,
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int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12);
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void init3bodyarray(int *np, int *pq, int *pc, int Pa3);
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@ -60,17 +60,19 @@ private:
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void eigenvaluedecomposition(double *Phi, double *Lambda, int N);
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void myneighbors(double *rij, double *x, int *ai, int *aj, int *ti, int *tj,
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int *jlist, int *pairnumsum, int *atomtype, int *alist, int i);
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void myneighbors(double *rij, double *x, int *ai, int *aj, int *ti, int *tj, int *jlist,
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int *pairnumsum, int *atomtype, int *alist, int i);
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void radialbasis(double *rbf, double *rbfx, double *rbfy, double *rbfz, double *rij, double *besselparams, double rin,
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double rmax, int besseldegree, int inversedegree, int nbesselpars, int N);
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void radialbasis(double *rbf, double *rbfx, double *rbfy, double *rbfz, double *rij,
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double *besselparams, double rin, double rmax, int besseldegree,
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int inversedegree, int nbesselpars, int N);
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void angularbasis(double *abf, double *abfx, double *abfy, double *abfz, double *rij, double *tm, int *pq, int N, int K);
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void angularbasis(double *abf, double *abfx, double *abfy, double *abfz, double *rij, double *tm,
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int *pq, int N, int K);
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void radialangularbasis(double *sumU, double *U, double *Ux, double *Uy, double *Uz,
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double *rbf, double *rbfx, double *rbfy, double *rbfz, double *abf,
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double *abfx, double *abfy, double *abfz, int *atomtype, int N, int K, int M, int Ne);
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void radialangularbasis(double *sumU, double *U, double *Ux, double *Uy, double *Uz, double *rbf,
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double *rbfx, double *rbfy, double *rbfz, double *abf, double *abfx,
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double *abfy, double *abfz, int *atomtype, int N, int K, int M, int Ne);
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void MatMul(double *c, double *a, double *b, int r1, int c1, int c2);
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@ -80,19 +82,18 @@ private:
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void mvproduct(double *fij, double *c, double *dd, int N, int ndesc);
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public:
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public:
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std::vector<std::string> species;
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double rin;
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double rcut;
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int true4BodyDesc;
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int nelements; // number of elements
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int nelements; // number of elements
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int pbc[3];
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int *elemindex ;
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int *elemindex;
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int onebody; // one-body descriptors
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int onebody; // one-body descriptors
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int besseldegree;
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int inversedegree;
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int pdegree[2];
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@ -100,44 +101,45 @@ public:
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int timing;
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double comptime[20];
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double besselparams[3];
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double *Phi ; // eigenvectors
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double *Lambda ; // eigenvalues
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double *coeff; // coefficients
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double *Phi; // eigenvectors
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double *Lambda; // eigenvalues
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double *coeff; // coefficients
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//double *newcoeff ; // coefficients
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double *tmpmem;
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// environmental variables
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int nClusters; // number of environment clusters
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int nComponents; // number of principal components
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int nClusters; // number of environment clusters
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int nComponents; // number of principal components
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//int nNeighbors; // numbe of neighbors
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int Mdesc; // number of base descriptors
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int Mdesc; // number of base descriptors
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double *Proj; // PCA Projection matrix
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double *Centroids; // centroids of the clusters
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double *bd; // base descriptors
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double *bdd; // derivatives of the base descriptors with respect to the atomic positions
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double *pd; // multi-environment descriptors
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double *pdd; // derivative of the multi-environment descriptors with respect to the atomic positions
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double *Proj; // PCA Projection matrix
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double *Centroids; // centroids of the clusters
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double *bd; // base descriptors
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double *bdd; // derivatives of the base descriptors with respect to the atomic positions
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double *pd; // multi-environment descriptors
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double *
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pdd; // derivative of the multi-environment descriptors with respect to the atomic positions
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int nproj; // number of elements in projection matrix (nComponents * Mdesc * nelements)
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int ncentroids; // number of centroids (nComponents * nClusters * nelements)
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int nproj; // number of elements in projection matrix (nComponents * Mdesc * nelements)
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int ncentroids; // number of centroids (nComponents * nClusters * nelements)
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int Njmax;
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int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters)
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int nCoeffAll; // number of coefficients for all elements = (nl1 + Mdesc*nClusters)*nelements
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int ncoeff; // number of coefficients in the input file
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int ns; // number of snapshots for radial basis functions
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int nd1, nd2, nd3, nd4, nd5, nd6, nd7, nd; // number of global descriptors
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int nl1, nl2, nl3, nl4, nl5, nl6, nl7, nl; // number of local descriptors
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int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions
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int nabf3, nabf4; // number of angular basis functions
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int P3, P4; // angular polynomial degrees
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int K3, K4, Q4; // number of monomials
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int *pn3, *pq3, *pc3; // arrays to compute 3-body angular basis functions
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int *pq4, *pa4, *pb4, *pc4; // arrays to compute 3-body angular basis functions
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int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters)
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int nCoeffAll; // number of coefficients for all elements = (nl1 + Mdesc*nClusters)*nelements
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int ncoeff; // number of coefficients in the input file
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int ns; // number of snapshots for radial basis functions
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int nd1, nd2, nd3, nd4, nd5, nd6, nd7, nd; // number of global descriptors
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int nl1, nl2, nl3, nl4, nl5, nl6, nl7, nl; // number of local descriptors
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int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions
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int nabf3, nabf4; // number of angular basis functions
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int P3, P4; // angular polynomial degrees
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int K3, K4, Q4; // number of monomials
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int *pn3, *pq3, *pc3; // arrays to compute 3-body angular basis functions
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int *pq4, *pa4, *pb4, *pc4; // arrays to compute 3-body angular basis functions
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int *tmpint;
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int nintmem; // number of integers in tmpint array
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int ndblmem; // number of doubles in tmpmem array
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int nintmem; // number of integers in tmpint array
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int ndblmem; // number of doubles in tmpmem array
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// four-body descriptors
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int *ind23, *ind32, nrbf23, nabf23, P23, n23, n32, nl23, nd23;
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@ -174,62 +176,64 @@ public:
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void mknewcoeff(double *c, int nc);
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void twobodydesc(double *d2, double *rbf, int *tj, int N);
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void twobodydescderiv(double *d2, double *dd2, double *rbf, double *rbfx,
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double *rbfy, double *rbfz, int *tj, int N);
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void twobody_forces(double *fij, double *cb2, double *rbfx, double *rbfy, double *rbfz, int *tj, int Nj);
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void twobodydescderiv(double *d2, double *dd2, double *rbf, double *rbfx, double *rbfy,
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double *rbfz, int *tj, int N);
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void twobody_forces(double *fij, double *cb2, double *rbfx, double *rbfy, double *rbfz, int *tj,
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int Nj);
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void threebodydesc(double *d3, double *sumU);
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void threebodydescderiv(double *dd3, double *sumU, double *Ux, double *Uy, double *Uz,
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int *atomtype, int N);
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int *atomtype, int N);
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void threebody_forcecoeff(double *fb3, double *cb3, double *sumU);
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void fourbodydesc(double *d4, double *sumU);
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void fourbodydescderiv(double *d4, double *dd4, double *sumU, double *Ux, double *Uy, double *Uz,
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int *atomtype, int N);
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int *atomtype, int N);
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void fourbody_forcecoeff(double *fb4, double *cb4, double *sumU);
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void allbody_forces(double *fij, double *forcecoeff, double *rbf, double *rbfx, double *rbfy, double *rbfz,
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double *abf, double *abfx, double *abfy, double *abfz, int *tj, int Nj);
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void allbody_forces(double *fij, double *forcecoeff, double *Ux, double *Uy, double *Uz, int *tj, int Nj);
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void allbody_forces(double *fij, double *forcecoeff, double *rbf, double *rbfx, double *rbfy,
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double *rbfz, double *abf, double *abfx, double *abfy, double *abfz, int *tj,
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int Nj);
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void allbody_forces(double *fij, double *forcecoeff, double *Ux, double *Uy, double *Uz, int *tj,
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int Nj);
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void descriptors(double *gd, double *gdd, double *basedesc, double *probdesc, double *x, int *atomtype, int *alist,
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int *jlist, int *pairnumsum, int natom);
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void descriptors(double *gd, double *gdd, double *basedesc, double *probdesc, double *x,
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int *atomtype, int *alist, int *jlist, int *pairnumsum, int natom);
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void descriptors(double *gd, double *gdd, double *basedesc, double *x, int *atomtype, int *alist,
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int *jlist, int *pairnumsum, int natom);
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int *jlist, int *pairnumsum, int natom);
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void peratombase_descriptors(double *bd, double *bdd, double *rij, double *temp,
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int *tj, int Nj);
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void peratombase_descriptors(double *bd, double *bdd, double *rij, double *temp, int *tj, int Nj);
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double peratombase_coefficients(double *cb, double *bd, int *ti);
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double peratom_environment_descriptors(double *cb, double *bd, double *tm, int *ti);
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void peratomenvironment_descriptors(double *P, double *dP_dR, double *B, double *dB_dR, double *tmp, int elem, int nNeighbors);
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void peratomenvironment_descriptors(double *P, double *dP_dR, double *B, double *dB_dR,
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double *tmp, int elem, int nNeighbors);
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void base_descriptors(double *basedesc, double *x, int *atomtype, int *alist,
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int *jlist, int *pairnumsum, int natom);
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void base_descriptors(double *basedesc, double *x, int *atomtype, int *alist, int *jlist,
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int *pairnumsum, int natom);
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|
||||
void descriptors(double *basedesc, double *probdesc, double *x, int *atomtype, int *alist,
|
||||
int *jlist, int *pairnumsum, int natom);
|
||||
int *jlist, int *pairnumsum, int natom);
|
||||
|
||||
double peratomenergyforce(double *fij, double *rij, double *temp, int *ti, int *tj, int Nj);
|
||||
double peratomenergyforce2(double *fij, double *rij, double *temp, int *ti, int *tj, int Nj);
|
||||
|
||||
double energyforce(double *force, double *x, int *atomtype, int *alist,
|
||||
int *jlist, int *pairnumsum, int natom);
|
||||
double energyforce(double *force, double *x, int *atomtype, int *alist, int *jlist,
|
||||
int *pairnumsum, int natom);
|
||||
|
||||
void tallyforce(double *force, double *fij, int *ai, int *aj, int N);
|
||||
void tallyforce(double *force, double *fij, int *ai, int *aj, int N);
|
||||
|
||||
void fourbodydesc23(double* d23, double* d2, double *d3);
|
||||
void fourbodydescderiv23(double* dd23, double* d2, double *d3, double* dd2, double *dd3, int N);
|
||||
void fourbodydesc23(double *d23, double *d2, double *d3);
|
||||
void fourbodydescderiv23(double *dd23, double *d2, double *d3, double *dd2, double *dd3, int N);
|
||||
|
||||
void crossdesc(double *d12, double *d1, double *d2, int *ind1, int *ind2, int n12);
|
||||
void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2,
|
||||
int *ind1, int *ind2, int n12, int N);
|
||||
void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1,
|
||||
double *d2, int *ind1, int *ind2, int n12);
|
||||
void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1,
|
||||
int *ind2, int n12, int N);
|
||||
void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, double *d2, int *ind1,
|
||||
int *ind2, int n12);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@ -25,7 +25,7 @@ PairStyle(pod,PairPOD);
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairPOD : public Pair {
|
||||
public:
|
||||
public:
|
||||
PairPOD(class LAMMPS *);
|
||||
~PairPOD() override;
|
||||
void compute(int, int) override;
|
||||
@ -36,14 +36,16 @@ public:
|
||||
double init_one(int, int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
void lammpsNeighborList(double *rij1, int *ai1, int *aj1, int *ti1, int *tj1, double **x, int **firstneigh, int *atomtype, int *map, int *numneigh,
|
||||
double rcutsq, int i);
|
||||
void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq, int i1);
|
||||
void NeighborList(double **x, int **firstneigh, int *atomtype, int *map, int *ilist, int *numneigh,
|
||||
double rcutsq, int i1);
|
||||
void lammpsNeighborList(double *rij1, int *ai1, int *aj1, int *ti1, int *tj1, double **x,
|
||||
int **firstneigh, int *atomtype, int *map, int *numneigh, double rcutsq,
|
||||
int i);
|
||||
void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq,
|
||||
int i1);
|
||||
void NeighborList(double **x, int **firstneigh, int *atomtype, int *map, int *ilist,
|
||||
int *numneigh, double rcutsq, int i1);
|
||||
void tallyenergy(double *ei, int istart, int Ni);
|
||||
void tallystress(double *fij, double *rij, int *ai, int *aj, int nlocal, int N);
|
||||
void tallyforce(double **force, double *fij, int *ai, int *aj, int N);
|
||||
void tallyforce(double **force, double *fij, int *ai, int *aj, int N);
|
||||
void divideInterval(int *intervals, int N, int M);
|
||||
int calculateNumberOfIntervals(int N, int intervalSize);
|
||||
int numberOfNeighbors();
|
||||
@ -63,13 +65,13 @@ public:
|
||||
void fourbodydesc(double *d4, int Ni);
|
||||
void fourbodydescderiv(double *dd4, int Nij);
|
||||
void crossdesc(double *d12, double *d1, double *d2, int *ind1, int *ind2, int n12, int Ni);
|
||||
void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2,
|
||||
int *ind1, int *ind2, int *idxi, int n12, int Ni, int Nij);
|
||||
void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1,
|
||||
int *ind2, int *idxi, int n12, int Ni, int Nij);
|
||||
void blockatombase_descriptors(double *bd1, double *bdd1, int Ni, int Nij);
|
||||
void blockatomenergyforce(double *ei, double *fij, int Ni, int Nij);
|
||||
|
||||
void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1,
|
||||
double *d2, int *ind1, int *ind2, int n12, int Ni);
|
||||
void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, double *d2, int *ind1,
|
||||
int *ind2, int n12, int Ni);
|
||||
void blockatom_base_descriptors(double *bd1, int Ni, int Nij);
|
||||
void blockatom_base_coefficients(double *ei, double *cb, double *B, int Ni);
|
||||
void blockatom_environment_descriptors(double *ei, double *cb, double *B, int Ni);
|
||||
@ -89,79 +91,79 @@ public:
|
||||
void saveintmatrix2binfile(std::string filename, int *A, int nrows, int ncols);
|
||||
void savedatafordebugging();
|
||||
|
||||
protected:
|
||||
protected:
|
||||
class EAPOD *fastpodptr;
|
||||
virtual void allocate();
|
||||
void grow_atoms(int Ni);
|
||||
void grow_pairs(int Nij);
|
||||
|
||||
int atomBlockSize; // size of each atom block
|
||||
int nAtomBlocks; // number of atoms blocks
|
||||
int atomBlocks[101]; // atom blocks
|
||||
int atomBlockSize; // size of each atom block
|
||||
int nAtomBlocks; // number of atoms blocks
|
||||
int atomBlocks[101]; // atom blocks
|
||||
|
||||
int ni; // total number of atoms i
|
||||
int nij; // total number of pairs (i,j)
|
||||
int nimax; // maximum number of atoms i
|
||||
int nijmax; // maximum number of pairs (i,j)
|
||||
int ni; // total number of atoms i
|
||||
int nij; // total number of pairs (i,j)
|
||||
int nimax; // maximum number of atoms i
|
||||
int nijmax; // maximum number of pairs (i,j)
|
||||
|
||||
int nelements; // number of elements
|
||||
int onebody; // one-body descriptors
|
||||
int besseldegree; // degree of Bessel functions
|
||||
int inversedegree; // degree of inverse functions
|
||||
int nbesselpars; // number of Bessel parameters
|
||||
int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters)
|
||||
int ns; // number of snapshots for radial basis functions
|
||||
int nl1, nl2, nl3, nl4, nl23, nl33, nl34, nl44, nl; // number of local descriptors
|
||||
int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions
|
||||
int nabf3, nabf4; // number of angular basis functions
|
||||
int K3, K4, Q4; // number of monomials
|
||||
int nelements; // number of elements
|
||||
int onebody; // one-body descriptors
|
||||
int besseldegree; // degree of Bessel functions
|
||||
int inversedegree; // degree of inverse functions
|
||||
int nbesselpars; // number of Bessel parameters
|
||||
int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters)
|
||||
int ns; // number of snapshots for radial basis functions
|
||||
int nl1, nl2, nl3, nl4, nl23, nl33, nl34, nl44, nl; // number of local descriptors
|
||||
int nrbf2, nrbf3, nrbf4, nrbfmax; // number of radial basis functions
|
||||
int nabf3, nabf4; // number of angular basis functions
|
||||
int K3, K4, Q4; // number of monomials
|
||||
|
||||
// environmental variables
|
||||
int nClusters; // number of environment clusters
|
||||
int nComponents; // number of principal components
|
||||
int Mdesc; // number of base descriptors
|
||||
int nClusters; // number of environment clusters
|
||||
int nComponents; // number of principal components
|
||||
int Mdesc; // number of base descriptors
|
||||
|
||||
double rin; // inner cut-off radius
|
||||
double rcut; // outer cut-off radius
|
||||
double rmax; // rcut - rin
|
||||
double rin; // inner cut-off radius
|
||||
double rcut; // outer cut-off radius
|
||||
double rmax; // rcut - rin
|
||||
|
||||
double *rij; // (xj - xi) for all pairs (I, J)
|
||||
double *fij; // force for all pairs (I, J)
|
||||
double *ei; // energy for each atom I
|
||||
int *typeai; // types of atoms I only
|
||||
int *numij; // number of pairs (I, J) for each atom I
|
||||
int *idxi; // storing linear indices of atom I for all pairs (I, J)
|
||||
int *ai; // IDs of atoms I for all pairs (I, J)
|
||||
int *aj; // IDs of atoms J 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)
|
||||
double *rij; // (xj - xi) for all pairs (I, J)
|
||||
double *fij; // force for all pairs (I, J)
|
||||
double *ei; // energy for each atom I
|
||||
int *typeai; // types of atoms I only
|
||||
int *numij; // number of pairs (I, J) for each atom I
|
||||
int *idxi; // storing linear indices of atom I for all pairs (I, J)
|
||||
int *ai; // IDs of atoms I for all pairs (I, J)
|
||||
int *aj; // IDs of atoms J 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)
|
||||
|
||||
double besselparams[3];
|
||||
double *Phi ; // eigenvectors matrix ns x ns
|
||||
double *rbf; // radial basis functions nij x nrbfmax
|
||||
double *rbfx; // x-derivatives of radial basis functions nij x nrbfmax
|
||||
double *rbfy; // y-derivatives of radial basis functions nij x nrbfmax
|
||||
double *rbfz; // z-derivatives of radial basis functions nij x nrbfmax
|
||||
double *abf; // angular basis functions nij x K3
|
||||
double *abfx; // x-derivatives of angular basis functions nij x K3
|
||||
double *abfy; // y-derivatives of angular basis functions nij x K3
|
||||
double *abfz; // z-derivatives of angular basis functions nij x K3
|
||||
double *abftm ; // angular basis functions 4 x K3
|
||||
double *sumU; // sum of radial basis functions ni x K3 x nrbfmax x nelements
|
||||
double *forcecoeff; // force coefficients ni x K3 x nrbfmax x nelements
|
||||
double *Proj; // PCA Projection matrix
|
||||
double *Centroids; // centroids of the clusters
|
||||
double *bd; // base descriptors ni x Mdesc
|
||||
double *cb; // force coefficients for base descriptors ni x Mdesc
|
||||
double *pd; // environment probability descriptors ni x nClusters
|
||||
double *bdd; // base descriptors derivatives 3 x nij x Mdesc
|
||||
double *pdd; // environment probability descriptors derivatives 3 x nij x nClusters
|
||||
double *coefficients; // coefficients nCoeffPerElement x nelements
|
||||
int *pq3, *pn3, *pc3; // arrays to compute 3-body angular basis functions
|
||||
int *pa4, *pb4, *pc4; // arrays to compute 4-body angular basis functions
|
||||
int *ind33l, *ind33r; // nl33
|
||||
int *ind34l, *ind34r; // nl34
|
||||
int *ind44l, *ind44r; // nl44
|
||||
double *Phi; // eigenvectors matrix ns x ns
|
||||
double *rbf; // radial basis functions nij x nrbfmax
|
||||
double *rbfx; // x-derivatives of radial basis functions nij x nrbfmax
|
||||
double *rbfy; // y-derivatives of radial basis functions nij x nrbfmax
|
||||
double *rbfz; // z-derivatives of radial basis functions nij x nrbfmax
|
||||
double *abf; // angular basis functions nij x K3
|
||||
double *abfx; // x-derivatives of angular basis functions nij x K3
|
||||
double *abfy; // y-derivatives of angular basis functions nij x K3
|
||||
double *abfz; // z-derivatives of angular basis functions nij x K3
|
||||
double *abftm; // angular basis functions 4 x K3
|
||||
double *sumU; // sum of radial basis functions ni x K3 x nrbfmax x nelements
|
||||
double *forcecoeff; // force coefficients ni x K3 x nrbfmax x nelements
|
||||
double *Proj; // PCA Projection matrix
|
||||
double *Centroids; // centroids of the clusters
|
||||
double *bd; // base descriptors ni x Mdesc
|
||||
double *cb; // force coefficients for base descriptors ni x Mdesc
|
||||
double *pd; // environment probability descriptors ni x nClusters
|
||||
double *bdd; // base descriptors derivatives 3 x nij x Mdesc
|
||||
double *pdd; // environment probability descriptors derivatives 3 x nij x nClusters
|
||||
double *coefficients; // coefficients nCoeffPerElement x nelements
|
||||
int *pq3, *pn3, *pc3; // arrays to compute 3-body angular basis functions
|
||||
int *pa4, *pb4, *pc4; // arrays to compute 4-body angular basis functions
|
||||
int *ind33l, *ind33r; // nl33
|
||||
int *ind34l, *ind34r; // nl34
|
||||
int *ind44l, *ind44r; // nl44
|
||||
int *elemindex;
|
||||
|
||||
bool peratom_warn; // print warning about missing per-atom energies or stresses
|
||||
|
||||
Reference in New Issue
Block a user