initial refactoring on AtomVec class
This commit is contained in:
Steve Plimpton
220
src/atom.cpp
220
src/atom.cpp
@ -44,9 +44,11 @@ using namespace LAMMPS_NS;
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using namespace MathConst;
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#define DELTA 1
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#define DELTA_MEMSTR 1024
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#define DELTA_PERATOM 64
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#define EPSILON 1.0e-6
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enum{DOUBLE,INT,BIGINT};
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/* ---------------------------------------------------------------------- */
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Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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@ -66,6 +68,11 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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binhead = NULL;
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next = permute = NULL;
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// data structure with info on per-atom vectors/arrays
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nperatom = maxperatom = 0;
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peratom = NULL;
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// initialize atom arrays
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// customize by adding new array
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@ -193,6 +200,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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pdscale = 1.0;
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// initialize peratom data structure
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peratom_create();
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// ntype-length arrays
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mass = NULL;
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@ -245,6 +256,12 @@ Atom::~Atom()
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memory->destroy(next);
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memory->destroy(permute);
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// delete peratom data struct
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for (int i = 0; i < nperatom; i++)
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delete [] peratom[i].name;
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memory->sfree(peratom);
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// delete atom arrays
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// customize by adding new array
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@ -403,6 +420,175 @@ void Atom::settings(Atom *old)
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}
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}
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/* ----------------------------------------------------------------------
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one-time creation of peratom data structure
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------------------------------------------------------------------------- */
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void Atom::peratom_create()
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{
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for (int i = 0; i < nperatom; i++)
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delete [] peratom[i].name;
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memory->sfree(peratom);
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peratom = NULL;
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nperatom = maxperatom = 0;
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// customize: add new peratom variables here, order does not matter
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// register tagint & imageint variables as INT or BIGINT
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int tagintsize = INT;
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if (sizeof(tagint) == 8) tagintsize = BIGINT;
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int imageintsize = INT;
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if (sizeof(imageint) == 8) imageintsize = BIGINT;
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add_peratom("id",&tag,tagintsize,0);
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add_peratom("type",&type,INT,0);
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add_peratom("mask",&mask,INT,0);
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add_peratom("image",&image,imageintsize,0);
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add_peratom("x",&x,DOUBLE,3);
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add_peratom("v",&v,DOUBLE,3);
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add_peratom("f",&f,DOUBLE,3,1); // set per-thread flag
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add_peratom("rmass",&rmass,DOUBLE,0);
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add_peratom("q",&q,DOUBLE,0);
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add_peratom("mu",&mu,DOUBLE,4);
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add_peratom("mu3",&mu,DOUBLE,3); // just first 3 values of mu[4]
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// finite size particles
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add_peratom("radius",&radius,DOUBLE,0);
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add_peratom("omega",&omega,DOUBLE,3);
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add_peratom("amgmom",&angmom,DOUBLE,3);
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add_peratom("torque",&torque,DOUBLE,3,1); // set per-thread flag
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add_peratom("ellipsoid",&ellipsoid,INT,0);
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add_peratom("line",&line,INT,0);
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add_peratom("tri",&tri,INT,0);
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add_peratom("body",&body,INT,0);
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// MOLECULE package
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add_peratom("molecule",&molecule,tagintsize,0);
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add_peratom("molindex",&molindex,INT,0);
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add_peratom("molatom",&molatom,INT,0);
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add_peratom("nspecial",&nspecial,INT,3);
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add_peratom_vary("special",&special,tagintsize,&maxspecial,&nspecial,3);
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add_peratom("num_bond",&num_bond,INT,0);
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add_peratom_vary("bond_type",&bond_type,INT,&bond_per_atom,&num_bond);
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add_peratom_vary("bond_atom",&bond_atom,tagintsize,&bond_per_atom,&num_bond);
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add_peratom("num_angle",&num_angle,INT,0);
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add_peratom_vary("angle_type",&angle_type,INT,&angle_per_atom,&num_angle);
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add_peratom_vary("angle_atom1",&angle_atom1,tagintsize,
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&angle_per_atom,&num_angle);
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add_peratom_vary("angle_atom2",&angle_atom2,tagintsize,
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&angle_per_atom,&num_angle);
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add_peratom_vary("angle_atom3",&angle_atom3,tagintsize,
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&angle_per_atom,&num_angle);
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add_peratom("num_dihedral",&num_dihedral,INT,0);
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add_peratom_vary("dihedral_type",&dihedral_type,INT,
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&dihedral_per_atom,&num_dihedral);
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add_peratom_vary("dihedral_atom1",&dihedral_atom1,tagintsize,
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&dihedral_per_atom,&num_dihedral);
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add_peratom_vary("dihedral_atom2",&dihedral_atom2,tagintsize,
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&dihedral_per_atom,&num_dihedral);
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add_peratom_vary("dihedral_atom3",&dihedral_atom3,tagintsize,
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&dihedral_per_atom,&num_dihedral);
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add_peratom_vary("dihedral_atom4",&dihedral_atom4,tagintsize,
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&dihedral_per_atom,&num_dihedral);
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add_peratom("num_improper",&num_improper,INT,0);
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add_peratom_vary("improper_type",&improper_type,INT,
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&improper_per_atom,&num_improper);
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add_peratom_vary("improper_atom1",&improper_atom1,tagintsize,
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&improper_per_atom,&num_improper);
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add_peratom_vary("improper_atom2",&improper_atom2,tagintsize,
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&improper_per_atom,&num_improper);
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add_peratom_vary("improper_atom3",&improper_atom3,tagintsize,
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&improper_per_atom,&num_improper);
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add_peratom_vary("improper_atom4",&improper_atom4,tagintsize,
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&improper_per_atom,&num_improper);
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// PERI package
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add_peratom("vfrac",&vfrac,DOUBLE,0);
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add_peratom("s0",&s0,DOUBLE,0);
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add_peratom("x0",&x0,DOUBLE,3);
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// SPIN package
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add_peratom("sp",&sp,DOUBLE,4);
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add_peratom("fm",&fm,DOUBLE,3,1);
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add_peratom("fm_long",&fm_long,DOUBLE,3,1);
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}
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/* ----------------------------------------------------------------------
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add info for a single per-atom vector/array to PerAtom data struct
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cols = 0: per-atom vector
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cols = N: static per-atom array with N columns
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use add_peratom_vary() when column count varies per atom
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------------------------------------------------------------------------- */
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void Atom::add_peratom(const char *name, void *address,
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int datatype, int cols, int threadflag)
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{
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if (nperatom == maxperatom) {
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maxperatom += DELTA_PERATOM;
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peratom = (PerAtom *)
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memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
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}
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int n = strlen(name) + 1;
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peratom[nperatom].name = new char[n];
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strcpy(peratom[nperatom].name,name);
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peratom[nperatom].address = address;
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peratom[nperatom].datatype = datatype;
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peratom[nperatom].cols = cols;
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peratom[nperatom].threadflag = threadflag;
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peratom[nperatom].address_length = NULL;
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nperatom++;
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}
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/* ----------------------------------------------------------------------
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add info for a single per-atom array to PerAtom data struct
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cols = address of int variable with max columns per atom
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for collength = 0:
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length = address of peratom vector with column count per atom
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e.g. num_bond
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for collength = N:
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length = address of peratom array with column count per atom
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collength = index of column (1 to N) in peratom array with count
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e.g. nspecial
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------------------------------------------------------------------------- */
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void Atom::add_peratom_vary(const char *name, void *address,
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int datatype, int *cols, void *length, int collength)
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{
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if (nperatom == maxperatom) {
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maxperatom += DELTA_PERATOM;
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peratom = (PerAtom *)
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memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
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}
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int n = strlen(name) + 1;
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peratom[nperatom].name = new char[n];
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strcpy(peratom[nperatom].name,name);
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peratom[nperatom].address = address;
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peratom[nperatom].datatype = datatype;
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peratom[nperatom].cols = -1;
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peratom[nperatom].threadflag = 0;
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peratom[nperatom].address_maxcols = cols;
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peratom[nperatom].address_length = length;
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peratom[nperatom].collength = collength;
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nperatom++;
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}
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/* ----------------------------------------------------------------------
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create an AtomVec style
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called from lammps.cpp, input script, restart file, replicate
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@ -2296,11 +2482,7 @@ void *Atom::extract(char *name)
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bigint Atom::memory_usage()
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{
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memlength = DELTA_MEMSTR;
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memory->create(memstr,memlength,"atom:memstr");
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memstr[0] = '\0';
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bigint bytes = avec->memory_usage();
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memory->destroy(memstr);
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bytes += max_same*sizeof(int);
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if (map_style == 1)
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@ -2316,31 +2498,3 @@ bigint Atom::memory_usage()
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return bytes;
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}
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/* ----------------------------------------------------------------------
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accumulate per-atom vec names in memstr, padded by spaces
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return 1 if padded str is not already in memlist, else 0
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------------------------------------------------------------------------- */
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int Atom::memcheck(const char *str)
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{
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int n = strlen(str) + 3;
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char *padded = new char[n];
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strcpy(padded," ");
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strcat(padded,str);
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strcat(padded," ");
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if (strstr(memstr,padded)) {
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delete [] padded;
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return 0;
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}
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if ((int)strlen(memstr) + n >= memlength) {
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memlength += DELTA_MEMSTR;
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memory->grow(memstr,memlength,"atom:memstr");
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}
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strcat(memstr,padded);
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delete [] padded;
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return 1;
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}
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