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simplify and reformat

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This commit is contained in:
Axel Kohlmeyer
2021-05-26 15:40:15 -04:00
parent 4794b4cd38
commit 769183c94f
2 changed files with 76 additions and 90 deletions
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78
src/USER-RANN/rann_fingerprint.cpp
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@ -1,4 +1,4 @@
/* -*- c++ -*- ---------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
@ -43,74 +43,36 @@ Fingerprint::Fingerprint(PairRANN *_pair)
pair = _pair; pair = _pair;
} }
Fingerprint::~Fingerprint() { // Smooth cutoff, goes from 1 to zero over the interval rc-dr to rc.
// Same as MEAM uses. Used by generateradialtable and generatexpcuttable.
} double Fingerprint::cutofffunction(double r, double rc, double dr)
{
bool Fingerprint::parse_values(std::string line,std::vector<std::string> line1) {
return false;
}
void Fingerprint::init(int *i,int id) {
}
void Fingerprint::allocate() {
}
void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) {
}
void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) {
}
void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) {
}
void Fingerprint::compute_fingerprint(double *features,double *dfeaturesx,double *dfeaturesy,double * dfeaturesz,double *sx, double *sy, double *sz, double *Sik, double *dSikx, double*dSiky, double *dSikz, double *dSijkx, double *dSijky, double *dSijkz, bool *Bij, int ii,int sid,double *xn,double *yn,double*zn,int *tn,int jnum,int *jl) {
}
void Fingerprint::write_values(FILE *fid) {
}
int Fingerprint::get_length() {
return 0;
}
//Smooth cutoff, goes from 1 to zero over the interval rc-dr to rc. Same as MEAM uses. Used by generateradialtable and generatexpcuttable.
double Fingerprint::cutofffunction(double r,double rc, double dr) {
double out; double out;
if (r < (rc -dr))out=1; if (r < (rc - dr))
else if (r>rc)out=0; out = 1;
else if (r > rc)
out = 0;
else { else {
out = 1-(rc-r)/dr; out = 1 - (rc - r) / dr;
out *= out; out *= out;
out *= out; out *= out;
out = 1-out; out = 1 - out;
out *= out; out *= out;
} }
return out; return out;
} }
void Fingerprint::generate_rinvssqrttable() { void Fingerprint::generate_rinvssqrttable()
{
int buf = 5; int buf = 5;
int m; int m;
double r1; double r1;
double cutmax = pair->cutmax; double cutmax = pair->cutmax;
int res = pair->res; int res = pair->res;
rinvsqrttable = new double[res+buf]; rinvsqrttable = new double[res + buf];
for (m=0;m<(res+buf);m++) { for (m = 0; m < (res + buf); m++) {
r1 = cutmax*cutmax*(double)(m)/(double)(res); r1 = cutmax * cutmax * (double) (m) / (double) (res);
rinvsqrttable[m] = 1/sqrt(r1); rinvsqrttable[m] = 1 / sqrt(r1);
} }
} }

88
src/USER-RANN/rann_fingerprint.h
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@ -35,38 +35,62 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
#include "pair_rann.h" #include "pair_rann.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {
namespace RANN { namespace RANN {
class Fingerprint { class Fingerprint {
public: public:
Fingerprint(PairRANN *); Fingerprint(PairRANN *);
virtual ~Fingerprint(); virtual ~Fingerprint() {}
virtual bool parse_values(std::string,std::vector<std::string>);
virtual void write_values(FILE *);
virtual void init(int*,int);
virtual void allocate();
void init_screen(int);
virtual void compute_fingerprint(double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//no screen,no spin
virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//screen
virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,int,int,double*,double*,double*,int*,int,int*);//spin
virtual void compute_fingerprint(double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int*,int,int*);//spin,screen
virtual int get_length();
virtual double cutofffunction(double,double, double);
virtual void generate_rinvssqrttable();
bool spin;
bool screen;
int n_body_type;//i-j vs. i-j-k vs. i-j-k-l, etc.
bool empty;
bool fullydefined;
int startingneuron;
int id;//based on ordering of fingerprints listed for i-j in potential file
const char *style;
int* atomtypes;
double *rinvsqrttable;
double rc;
PairRANN *pair;
};
}
}
virtual bool parse_values(std::string, std::vector<std::string>) { return false; }
virtual void write_values(FILE *) {}
virtual void init(int *, int) {}
virtual void allocate() {}
void init_screen(int);
//no screen,no spin
virtual void compute_fingerprint(double *, double *, double *, double *, int, int, double *,
double *, double *, int *, int, int *)
{
}
//screen
virtual void compute_fingerprint(double *, double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *, bool *, int,
int, double *, double *, double *, int *, int, int *)
{
}
//spin
virtual void compute_fingerprint(double *, double *, double *, double *, double *, double *,
double *, int, int, double *, double *, double *, int *, int,
int *)
{
}
//spin,screen
virtual void compute_fingerprint(double *, double *, double *, double *, double *, double *,
double *, double *, double *, double *, double *, double *,
double *, double *, bool *, int, int, double *, double *,
double *, int *, int, int *)
{
}
virtual int get_length(){return 0};
virtual double cutofffunction(double, double, double);
virtual void generate_rinvssqrttable();
bool spin;
bool screen;
int n_body_type; //i-j vs. i-j-k vs. i-j-k-l, etc.
bool empty;
bool fullydefined;
int startingneuron;
int id; //based on ordering of fingerprints listed for i-j in potential file
const char *style;
int *atomtypes;
double *rinvsqrttable;
double rc;
PairRANN *pair;
};
} // namespace RANN
} // namespace LAMMPS_NS
#endif /* RANN_FINGERPRINT_H_ */ #endif /* RANN_FINGERPRINT_H_ */