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manifold_thylakoid.h
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Mon, Oct 14, 19:55

manifold_thylakoid.h
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#ifndef LMP_MANIFOLD_THYLAKOID_H
#define LMP_MANIFOLD_THYLAKOID_H
#include "manifold.h"
#include <cassert>
#include <vector>
#include "manifold_thylakoid_shared.h"
namespace LAMMPS_NS {
namespace user_manifold {
class manifold_thylakoid : public manifold {
public:
enum { NPARAMS = 3 };
manifold_thylakoid( LAMMPS *lmp, int, char ** );
virtual ~manifold_thylakoid();
virtual double g( const double *x );
virtual void n( const double *x, double *n );
static const char* type(){ return "thylakoid"; }
virtual const char *id(){ return type(); }
static int expected_argc(){ return NPARAMS; }
virtual int nparams(){ return NPARAMS; }
virtual void post_param_init();
virtual void checkup(); // Some diagnostics...
private:
void init_domains();
thyla_part *get_thyla_part( const double *x, int *err_flag, std::size_t *idx = NULL );
int is_in_domain( thyla_part *p, const double *x );
void check_overlap();
std::vector<thyla_part*> parts;
thyla_part *make_plane_part (double a, double b, double c,
const std::vector<double> &pt);
thyla_part *make_cyl_part (double a, double b, double c,
const std::vector<double> &pt, double R);
thyla_part *make_sphere_part(const std::vector<double> &pt, double R);
thyla_part *make_cyl_to_plane_part(double X0, double R0, double R, double s,
const std::vector<double> &pt );
void set_domain( thyla_part *p, const std::vector<double> &lo,
const std::vector<double> &hi );
void add_part( thyla_part *part, double x0, double y0,
double z0, double x1, double y1, double z1 )
{
int me = -1;
MPI_Comm_rank(world, &me);
std::vector<double> lo(3), hi(3);
lo[0] = x0; lo[1] = y0; lo[2] = z0;
hi[0] = x1; hi[1] = y1; hi[2] = z1;
set_domain(part, lo, hi);
parts.push_back( part );
fprintf(my_screen,"This is proc %d: Added part %p of type %d, "
"size is now %lu.\n", me, part, part->type, parts.size());
fflush(my_screen);
}
void print_part_data( FILE *fp_doms, FILE *fp_coms );
void assert_part_ok( const thyla_part *part ){
if( !part ) error->one(FLERR,"Error! Part was NULL!");
}
// Coefficients for the thylakoid model. At the moment it is just
// a cylinder, we slowly expand it.
double pad; // Padding to make sure periodic images are mapped back properly.
FILE *my_screen;
double LB, lT, lB, wB, LT;
// Domain size:
double x0, y0, z0;
double x1, y1, z1;
double Lx, Ly, Lz;
};
} // namespace LAMMPS_NS
}
#endif // LMP_MANIFOLD_THYLAKOID_H

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