"stringify" and "vectorize" per-atom data handling in Atom class
This commit is contained in:
Axel Kohlmeyer
76
src/atom.cpp
76
src/atom.cpp
@ -47,7 +47,6 @@ using namespace LAMMPS_NS;
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using namespace MathConst;
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#define DELTA 1
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#define DELTA_PERATOM 64
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#define EPSILON 1.0e-6
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/* ----------------------------------------------------------------------
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@ -105,11 +104,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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binhead = nullptr;
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next = permute = nullptr;
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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 = nullptr;
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// --------------------------------------------------------------------
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// 1st customization section: customize by adding new per-atom variables
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@ -285,11 +279,11 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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Atom::~Atom()
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{
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delete [] atom_style;
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delete[] atom_style;
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delete avec;
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delete avec_map;
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delete [] firstgroupname;
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delete[] firstgroupname;
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memory->destroy(binhead);
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memory->destroy(next);
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memory->destroy(permute);
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@ -302,12 +296,6 @@ Atom::~Atom()
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memory->destroy(v);
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memory->destroy(f);
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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 custom atom arrays
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for (int i = 0; i < nivector; i++) {
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@ -384,12 +372,7 @@ void Atom::settings(Atom *old)
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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 = nullptr;
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nperatom = maxperatom = 0;
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peratom.clear();
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// --------------------------------------------------------------------
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// 2nd customization section: add peratom variables here, order does not matter
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@ -566,23 +549,11 @@ void Atom::peratom_create()
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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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void Atom::add_peratom(const std::string &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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peratom[nperatom].name = utils::strdup(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 = nullptr;
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nperatom++;
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PerAtom item = {name, address, nullptr, nullptr, datatype, cols, 0, threadflag};
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peratom.push_back(item);
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}
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/* ----------------------------------------------------------------------
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@ -591,15 +562,13 @@ void Atom::add_peratom(const char *name, void *address,
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see atom_style tdpd as an example
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------------------------------------------------------------------------- */
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void Atom::add_peratom_change_columns(const char *name, int cols)
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void Atom::add_peratom_change_columns(const std::string &name, int cols)
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{
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for (int i = 0; i < nperatom; i++) {
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if (strcmp(name,peratom[i].name) == 0) {
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peratom[i].cols = cols;
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return;
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}
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}
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error->all(FLERR,"Could not find name of peratom array for column change");
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auto match = std::find_if(peratom.begin(), peratom.end(),
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[&n = name] (const PerAtom &p) { return p.name == n; });
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if (match != peratom.end()) (*match).cols = cols;
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else error->all(FLERR,"Could not find per-atom array name {} for column change", name);
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}
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/* ----------------------------------------------------------------------
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@ -614,25 +583,11 @@ void Atom::add_peratom_change_columns(const char *name, int cols)
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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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void Atom::add_peratom_vary(const std::string &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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peratom[nperatom].name = utils::strdup(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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PerAtom item = {name, address, length, cols, datatype, -1, collength, 0};
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peratom.push_back(item);
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}
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/* ----------------------------------------------------------------------
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@ -2894,4 +2849,3 @@ double Atom::memory_usage()
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return bytes;
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}
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11
src/atom.h
11
src/atom.h
@ -208,7 +208,7 @@ class Atom : protected Pointers {
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// per-atom data struct describing all per-atom vectors/arrays
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struct PerAtom {
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char *name;
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std::string name;
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void *address;
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void *address_length;
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int *address_maxcols;
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@ -218,8 +218,7 @@ class Atom : protected Pointers {
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int threadflag;
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};
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PerAtom *peratom;
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int nperatom, maxperatom;
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std::vector<PerAtom> peratom;
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// custom vectors and arrays used by fix property/atom
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@ -288,9 +287,9 @@ class Atom : protected Pointers {
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void settings(class Atom *);
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void peratom_create();
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void add_peratom(const char *, void *, int, int, int threadflag = 0);
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void add_peratom_change_columns(const char *, int);
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void add_peratom_vary(const char *, void *, int, int *, void *, int collength = 0);
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void add_peratom(const std::string &, void *, int, int, int threadflag = 0);
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void add_peratom_change_columns(const std::string &, int);
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void add_peratom_vary(const std::string &, void *, int, int *, void *, int collength = 0);
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void create_avec(const std::string &, int, char **, int);
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virtual AtomVec *new_avec(const std::string &, int, int &);
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@ -2280,7 +2280,7 @@ void AtomVec::setup_fields()
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error->all(FLERR, "Atom style fields_data_vel must have 'id' and 'v' as first two fields");
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// process field strings
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// return # of fields and matching index into atom->peratom (in Method struct)
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// return # of fields and matching index into atom.peratom (in Method struct)
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ngrow = process_fields(fields_grow, default_grow, &mgrow);
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ncopy = process_fields(fields_copy, default_copy, &mcopy);
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@ -2317,8 +2317,8 @@ void AtomVec::setup_fields()
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else
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threads = nullptr;
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for (int i = 0; i < ngrow; i++) {
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Atom::PerAtom *field = &atom->peratom[mgrow.index[i]];
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threads[i] = field->threadflag == 1;
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const auto &field = atom->peratom[mgrow.index[i]];
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threads[i] = field.threadflag == 1;
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}
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// set style-specific sizes
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@ -2373,7 +2373,7 @@ void AtomVec::setup_fields()
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size_data_atom = 0;
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for (n = 0; n < ndata_atom; n++) {
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cols = mdata_atom.cols[n];
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if (strcmp(atom->peratom[mdata_atom.index[n]].name, "x") == 0) xcol_data = size_data_atom + 1;
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if (atom->peratom[mdata_atom.index[n]].name == "x") xcol_data = size_data_atom + 1;
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if (cols == 0)
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size_data_atom++;
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else
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@ -2402,8 +2402,8 @@ int AtomVec::process_fields(const std::vector<std::string> &words,
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// process fields one by one, add to index vector
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Atom::PerAtom *peratom = atom->peratom;
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int nperatom = atom->nperatom;
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const auto &peratom = atom->peratom;
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const int nperatom = peratom.size();
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// allocate memory in method
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method->resize(nfield);
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@ -2442,14 +2442,14 @@ int AtomVec::process_fields(const std::vector<std::string> &words,
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void AtomVec::init_method(int nfield, Method *method)
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{
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for (int i = 0; i < nfield; i++) {
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Atom::PerAtom *field = &atom->peratom[method->index[i]];
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method->pdata[i] = (void *) field->address;
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method->datatype[i] = field->datatype;
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method->cols[i] = field->cols;
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const auto &field = atom->peratom[method->index[i]];
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method->pdata[i] = (void *) field.address;
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method->datatype[i] = field.datatype;
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method->cols[i] = field.cols;
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if (method->cols[i] < 0) {
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method->maxcols[i] = field->address_maxcols;
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method->collength[i] = field->collength;
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method->plength[i] = field->address_length;
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method->maxcols[i] = field.address_maxcols;
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method->collength[i] = field.collength;
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method->plength[i] = field.address_length;
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}
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}
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}
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