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This commit is contained in:
Axel Kohlmeyer
2024-06-25 20:07:34 -04:00
parent e3fb1f24bd
commit e5250a76ac
6 changed files with 191 additions and 185 deletions
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4
src/ML-POD/compute_pod_atom.h
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@ -32,8 +32,8 @@ class ComputePODAtom : public Compute {
void init_list(int, class NeighList *) override; void init_list(int, class NeighList *) override;
void compute_peratom() override; void compute_peratom() override;
double memory_usage() override; double memory_usage() override;
void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh, void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
double rcutsq, int i); int *numneigh, double rcutsq, int i);
void map_element2type(int narg, char **arg, int nelements); void map_element2type(int narg, char **arg, int nelements);
private: private:

4
src/ML-POD/compute_pod_global.h
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@ -32,8 +32,8 @@ class ComputePODGlobal : public Compute {
void init_list(int, class NeighList *) override; void init_list(int, class NeighList *) override;
void compute_array() override; void compute_array() override;
double memory_usage() override; double memory_usage() override;
void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh, void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
double rcutsq, int i); int *numneigh, double rcutsq, int i);
void map_element2type(int narg, char **arg, int nelements); void map_element2type(int narg, char **arg, int nelements);
private: private:

4
src/ML-POD/compute_pod_local.h
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@ -32,8 +32,8 @@ class ComputePODLocal : public Compute {
void init_list(int, class NeighList *) override; void init_list(int, class NeighList *) override;
void compute_array() override; void compute_array() override;
double memory_usage() override; double memory_usage() override;
void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh, void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
double rcutsq, int i); int *numneigh, double rcutsq, int i);
void map_element2type(int narg, char **arg, int nelements); void map_element2type(int narg, char **arg, int nelements);
private: private:

4
src/ML-POD/compute_podd_atom.h
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@ -32,8 +32,8 @@ class ComputePODDAtom : public Compute {
void init_list(int, class NeighList *) override; void init_list(int, class NeighList *) override;
void compute_peratom() override; void compute_peratom() override;
double memory_usage() override; double memory_usage() override;
void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype, int *numneigh, void lammpsNeighborList(double **x, int **firstneigh, tagint *atomid, int *atomtype,
double rcutsq, int i); int *numneigh, double rcutsq, int i);
void map_element2type(int narg, char **arg, int nelements); void map_element2type(int narg, char **arg, int nelements);
private: private:

72
src/ML-POD/eapod.h
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@ -41,10 +41,10 @@ namespace LAMMPS_NS {
class EAPOD : protected Pointers { class EAPOD : protected Pointers {
private: private:
int indexmap3(int *indx, int n1, int n2, int n3, int N1, int N2); int indexmap3(int *indx, int n1, int n2, int n3, int N1, int N2);
int crossindices(int *dabf1, int nabf1, int nrbf1, int nebf1, int crossindices(int *dabf1, int nabf1, int nrbf1, int nebf1, int *dabf2, int nabf2, int nrbf2,
int *dabf2, int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12); int nebf2, int dabf12, int nrbf12);
int crossindices(int *ind1, int *ind2, int *dabf1, int nabf1, int nrbf1, int nebf1, int crossindices(int *ind1, int *ind2, int *dabf1, int nabf1, int nrbf1, int nebf1, int *dabf2,
int *dabf2, int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12); int nabf2, int nrbf2, int nebf2, int dabf12, int nrbf12);
void init3bodyarray(int *np, int *pq, int *pc, int Pa3); void init3bodyarray(int *np, int *pq, int *pc, int Pa3);
@ -60,17 +60,19 @@ private:
void eigenvaluedecomposition(double *Phi, double *Lambda, int N); void eigenvaluedecomposition(double *Phi, double *Lambda, int N);
void myneighbors(double *rij, double *x, int *ai, int *aj, int *ti, int *tj, void myneighbors(double *rij, double *x, int *ai, int *aj, int *ti, int *tj, int *jlist,
int *jlist, int *pairnumsum, int *atomtype, int *alist, int i); int *pairnumsum, int *atomtype, int *alist, int i);
void radialbasis(double *rbf, double *rbfx, double *rbfy, double *rbfz, double *rij, double *besselparams, double rin, void radialbasis(double *rbf, double *rbfx, double *rbfy, double *rbfz, double *rij,
double rmax, int besseldegree, int inversedegree, int nbesselpars, int N); double *besselparams, double rin, double rmax, int besseldegree,
int inversedegree, int nbesselpars, int N);
void angularbasis(double *abf, double *abfx, double *abfy, double *abfz, double *rij, double *tm, int *pq, int N, int K); void angularbasis(double *abf, double *abfx, double *abfy, double *abfz, double *rij, double *tm,
int *pq, int N, int K);
void radialangularbasis(double *sumU, double *U, double *Ux, double *Uy, double *Uz, void radialangularbasis(double *sumU, double *U, double *Ux, double *Uy, double *Uz, double *rbf,
double *rbf, double *rbfx, double *rbfy, double *rbfz, double *abf, double *rbfx, double *rbfy, double *rbfz, double *abf, double *abfx,
double *abfx, double *abfy, double *abfz, int *atomtype, int N, int K, int M, int Ne); double *abfy, double *abfz, int *atomtype, int N, int K, int M, int Ne);
void MatMul(double *c, double *a, double *b, int r1, int c1, int c2); void MatMul(double *c, double *a, double *b, int r1, int c1, int c2);
@ -87,7 +89,6 @@ public:
double rcut; double rcut;
int true4BodyDesc; int true4BodyDesc;
int nelements; // number of elements int nelements; // number of elements
int pbc[3]; int pbc[3];
int *elemindex; int *elemindex;
@ -117,7 +118,8 @@ public:
double *bd; // base descriptors double *bd; // base descriptors
double *bdd; // derivatives of the base descriptors with respect to the atomic positions double *bdd; // derivatives of the base descriptors with respect to the atomic positions
double *pd; // multi-environment descriptors double *pd; // multi-environment descriptors
double *pdd; // derivative of the multi-environment descriptors with respect to the atomic positions double *
pdd; // derivative of the multi-environment descriptors with respect to the atomic positions
int nproj; // number of elements in projection matrix (nComponents * Mdesc * nelements) int nproj; // number of elements in projection matrix (nComponents * Mdesc * nelements)
int ncentroids; // number of centroids (nComponents * nClusters * nelements) int ncentroids; // number of centroids (nComponents * nClusters * nelements)
@ -174,9 +176,10 @@ public:
void mknewcoeff(double *c, int nc); void mknewcoeff(double *c, int nc);
void twobodydesc(double *d2, double *rbf, int *tj, int N); void twobodydesc(double *d2, double *rbf, int *tj, int N);
void twobodydescderiv(double *d2, double *dd2, double *rbf, double *rbfx, void twobodydescderiv(double *d2, double *dd2, double *rbf, double *rbfx, double *rbfy,
double *rbfy, double *rbfz, int *tj, int N); double *rbfz, int *tj, int N);
void twobody_forces(double *fij, double *cb2, double *rbfx, double *rbfy, double *rbfz, int *tj, int Nj); void twobody_forces(double *fij, double *cb2, double *rbfx, double *rbfy, double *rbfz, int *tj,
int Nj);
void threebodydesc(double *d3, double *sumU); void threebodydesc(double *d3, double *sumU);
void threebodydescderiv(double *dd3, double *sumU, double *Ux, double *Uy, double *Uz, void threebodydescderiv(double *dd3, double *sumU, double *Ux, double *Uy, double *Uz,
@ -188,25 +191,27 @@ public:
int *atomtype, int N); int *atomtype, int N);
void fourbody_forcecoeff(double *fb4, double *cb4, double *sumU); void fourbody_forcecoeff(double *fb4, double *cb4, double *sumU);
void allbody_forces(double *fij, double *forcecoeff, double *rbf, double *rbfx, double *rbfy, double *rbfz, void allbody_forces(double *fij, double *forcecoeff, double *rbf, double *rbfx, double *rbfy,
double *abf, double *abfx, double *abfy, double *abfz, int *tj, int Nj); double *rbfz, double *abf, double *abfx, double *abfy, double *abfz, int *tj,
void allbody_forces(double *fij, double *forcecoeff, double *Ux, double *Uy, double *Uz, int *tj, int Nj); int Nj);
void allbody_forces(double *fij, double *forcecoeff, double *Ux, double *Uy, double *Uz, int *tj,
int Nj);
void descriptors(double *gd, double *gdd, double *basedesc, double *probdesc, double *x, int *atomtype, int *alist, void descriptors(double *gd, double *gdd, double *basedesc, double *probdesc, double *x,
int *jlist, int *pairnumsum, int natom); int *atomtype, int *alist, int *jlist, int *pairnumsum, int natom);
void descriptors(double *gd, double *gdd, double *basedesc, double *x, int *atomtype, int *alist, void descriptors(double *gd, double *gdd, double *basedesc, double *x, int *atomtype, int *alist,
int *jlist, int *pairnumsum, int natom); int *jlist, int *pairnumsum, int natom);
void peratombase_descriptors(double *bd, double *bdd, double *rij, double *temp, void peratombase_descriptors(double *bd, double *bdd, double *rij, double *temp, int *tj, int Nj);
int *tj, int Nj);
double peratombase_coefficients(double *cb, double *bd, int *ti); double peratombase_coefficients(double *cb, double *bd, int *ti);
double peratom_environment_descriptors(double *cb, double *bd, double *tm, int *ti); double peratom_environment_descriptors(double *cb, double *bd, double *tm, int *ti);
void peratomenvironment_descriptors(double *P, double *dP_dR, double *B, double *dB_dR, double *tmp, int elem, int nNeighbors); void peratomenvironment_descriptors(double *P, double *dP_dR, double *B, double *dB_dR,
double *tmp, int elem, int nNeighbors);
void base_descriptors(double *basedesc, double *x, int *atomtype, int *alist, void base_descriptors(double *basedesc, double *x, int *atomtype, int *alist, int *jlist,
int *jlist, int *pairnumsum, int natom); int *pairnumsum, int natom);
void descriptors(double *basedesc, double *probdesc, double *x, int *atomtype, int *alist, void descriptors(double *basedesc, double *probdesc, double *x, int *atomtype, int *alist,
int *jlist, int *pairnumsum, int natom); int *jlist, int *pairnumsum, int natom);
@ -214,8 +219,8 @@ public:
double peratomenergyforce(double *fij, double *rij, double *temp, int *ti, int *tj, int Nj); 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 peratomenergyforce2(double *fij, double *rij, double *temp, int *ti, int *tj, int Nj);
double energyforce(double *force, double *x, int *atomtype, int *alist, double energyforce(double *force, double *x, int *atomtype, int *alist, int *jlist,
int *jlist, int *pairnumsum, int natom); 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);
@ -223,13 +228,12 @@ public:
void fourbodydescderiv23(double *dd23, double *d2, double *d3, double *dd2, double *dd3, int N); 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 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, void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1,
int *ind1, int *ind2, int n12, int N); int *ind2, int n12, int N);
void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, double *d2, int *ind1,
double *d2, int *ind1, int *ind2, int n12); int *ind2, int n12);
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS
#endif #endif

20
src/ML-POD/pair_pod.h
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@ -36,11 +36,13 @@ public:
double init_one(int, int) override; double init_one(int, int) override;
double memory_usage() 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, void lammpsNeighborList(double *rij1, int *ai1, int *aj1, int *ti1, int *tj1, double **x,
double rcutsq, int i); int **firstneigh, int *atomtype, int *map, int *numneigh, double rcutsq,
void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq, int i1); int i);
void NeighborList(double **x, int **firstneigh, int *atomtype, int *map, int *ilist, int *numneigh, void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq,
double rcutsq, int i1); 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 tallyenergy(double *ei, int istart, int Ni);
void tallystress(double *fij, double *rij, int *ai, int *aj, int nlocal, int N); 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);
@ -63,13 +65,13 @@ public:
void fourbodydesc(double *d4, int Ni); void fourbodydesc(double *d4, int Ni);
void fourbodydescderiv(double *dd4, int Nij); void fourbodydescderiv(double *dd4, int Nij);
void crossdesc(double *d12, double *d1, double *d2, int *ind1, int *ind2, int n12, int Ni); 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, void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1,
int *ind1, int *ind2, int *idxi, int n12, int Ni, int Nij); int *ind2, int *idxi, int n12, int Ni, int Nij);
void blockatombase_descriptors(double *bd1, double *bdd1, 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 blockatomenergyforce(double *ei, double *fij, int Ni, int Nij);
void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, void crossdesc_reduction(double *cb1, double *cb2, double *c12, double *d1, double *d2, int *ind1,
double *d2, int *ind1, int *ind2, int n12, int Ni); int *ind2, int n12, int Ni);
void blockatom_base_descriptors(double *bd1, int Ni, int Nij); void blockatom_base_descriptors(double *bd1, int Ni, int Nij);
void blockatom_base_coefficients(double *ei, double *cb, double *B, int Ni); void blockatom_base_coefficients(double *ei, double *cb, double *B, int Ni);
void blockatom_environment_descriptors(double *ei, double *cb, double *B, int Ni); void blockatom_environment_descriptors(double *ei, double *cb, double *B, int Ni);