forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10350 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
856f78e50a
commit
48510d047b
99
src/atom.cpp
99
src/atom.cpp
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@ -106,6 +106,13 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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improper_type = improper_atom1 = improper_atom2 = NULL;
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improper_atom3 = improper_atom4 = NULL;
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// custom atom arrays
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nivector = ndvector = 0;
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ivector = NULL;
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dvector = NULL;
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iname = dname = NULL;
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// initialize atom style and array existence flags
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// customize by adding new flag
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@ -223,6 +230,17 @@ Atom::~Atom()
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memory->destroy(improper_atom3);
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memory->destroy(improper_atom4);
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// delete custom atom arrays
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for (int i = 0; i < nivector; i++) {
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memory->destroy(ivector[i]);
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delete [] iname[i];
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}
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for (int i = 0; i < ndvector; i++) {
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memory->destroy(dvector[i]);
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delete [] dname[i];
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}
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// delete per-type arrays
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delete [] mass;
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@ -1439,6 +1457,87 @@ void Atom::update_callback(int ifix)
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if (extra_border[i] > ifix) extra_border[i]--;
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}
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/* ----------------------------------------------------------------------
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find custom per-atom vector with name
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return index if found, and flag = 0/1 for int/double
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return -1 if not found
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------------------------------------------------------------------------- */
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int Atom::find_custom(char *name, int &flag)
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{
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for (int i = 0; i < nivector; i++)
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if (iname[i] && strcmp(iname[i],name) == 0) {
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flag = 0;
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return i;
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}
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for (int i = 0; i < ndvector; i++)
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if (dname[i] && strcmp(dname[i],name) == 0) {
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flag = 1;
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return i;
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}
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return -1;
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}
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/* ----------------------------------------------------------------------
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add a custom variable with name of type flag = 0/1 for int/double
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assumes name does not already exist
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return index in ivector or dvector of its location
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------------------------------------------------------------------------- */
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int Atom::add_custom(char *name, int flag)
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{
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int index;
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if (flag == 0) {
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index = nivector;
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nivector++;
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iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
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"atom:iname");
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int n = strlen(name) + 1;
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iname[index] = new char[n];
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strcpy(iname[index],name);
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ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
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"atom:ivector");
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memory->create(ivector[index],nmax,"atom:ivector");
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} else {
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index = ndvector;
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ndvector++;
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dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
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"atom:dname");
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int n = strlen(name) + 1;
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dname[index] = new char[n];
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strcpy(dname[index],name);
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dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),
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"atom:dvector");
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memory->create(dvector[index],nmax,"atom:dvector");
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}
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return index;
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}
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/* ----------------------------------------------------------------------
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remove a custom variable of type flag = 0/1 for int/double at index
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free memory for vector and name and set ptrs to NULL
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ivector/dvector and iname/dname lists never shrink
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------------------------------------------------------------------------- */
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void Atom::remove_custom(int flag, int index)
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{
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if (flag == 0) {
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memory->destroy(ivector[index]);
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ivector[index] = NULL;
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delete [] iname[index];
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iname[index] = NULL;
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} else {
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memory->destroy(dvector[index]);
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dvector[index] = NULL;
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delete [] dname[index];
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dname[index] = NULL;
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}
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}
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/* ----------------------------------------------------------------------
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return a pointer to a named internal variable
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if don't recognize name, return NULL
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13
src/atom.h
13
src/atom.h
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@ -83,6 +83,15 @@ class Atom : protected Pointers {
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int **improper_type;
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int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
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// custom arrays used by fix property/atom
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int **ivector;
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double **dvector;
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char **iname,**dname;
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int nivector,ndvector;
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// used by USER-CUDA to flag used per-atom arrays
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unsigned int datamask;
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unsigned int datamask_ext;
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@ -176,6 +185,10 @@ class Atom : protected Pointers {
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void delete_callback(const char *, int);
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void update_callback(int);
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int find_custom(char *, int &);
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int add_custom(char *, int);
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void remove_custom(int, int);
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void *extract(char *);
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inline int* get_map_array() {return map_array;};
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@ -25,11 +25,6 @@ using namespace FixConst;
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enum{MOLECULE,INTEGER,DOUBLE};
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// NOTE: how to prevent atom style being changed after this fix defined?
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// e.g. what if replicate happens, will it wipe out molecule_flag
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// will it copy ivectors in atom.h ??
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// maybe setting of atom->mol_flag should happen in fix init
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/* ---------------------------------------------------------------------- */
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FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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@ -42,6 +37,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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int iarg = 3;
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nvalue = narg-iarg;
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style = new int[nvalue];
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index = new int[nvalue];
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molecule_flag = 0;
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@ -58,9 +54,19 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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nvalue++;
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} else if (strstr(arg[iarg],"i_") == arg[iarg]) {
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style[nvalue] = INTEGER;
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int tmp;
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index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
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if (index[nvalue] >= 0)
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error->all(FLERR,"Fix property/atom vector name already exists");
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index[nvalue] = atom->add_custom(&arg[iarg][2],0);
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nvalue++;
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} else if (strstr(arg[iarg],"d_") == arg[iarg]) {
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style[nvalue] = DOUBLE;
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int tmp;
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index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
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if (index[nvalue] >= 0)
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error->all(FLERR,"Fix property/atom vector name already exists");
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index[nvalue] = atom->add_custom(&arg[iarg][2],1);
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nvalue++;
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} else break;
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@ -111,11 +117,14 @@ FixPropertyAtom::~FixPropertyAtom()
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memory->destroy(atom->molecule);
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atom->molecule = NULL;
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} else if (style[m] == INTEGER) {
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atom->remove_custom(0,index[m]);
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} else if (style[m] == DOUBLE) {
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atom->remove_custom(1,index[m]);
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}
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}
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delete [] style;
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delete [] index;
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}
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/* ---------------------------------------------------------------------- */
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@ -187,8 +196,10 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
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if ((m = atom->map(tagdata)) >= 0) {
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for (j = 0; j < nvalue; j++) {
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if (style[j] == MOLECULE) atom->molecule[m] = atoi(values[j+1]);
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else if (style[j] == INTEGER) atom->molecule[m] = atoi(values[j+1]);
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else if (style[j] == DOUBLE) atom->molecule[m] = atof(values[j+1]);
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else if (style[j] == INTEGER)
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atom->ivector[index[j]][m] = atoi(values[j+1]);
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else if (style[j] == DOUBLE)
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atom->dvector[index[j]][m] = atof(values[j+1]);
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}
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}
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@ -235,13 +246,13 @@ void FixPropertyAtom::grow_arrays(int nmax)
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size_t nbytes = (nmax-nmax_old) * sizeof(int);
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memset(&atom->molecule[nmax_old],0,nbytes);
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} else if (style[m] == INTEGER) {
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memory->grow(atom->molecule,nmax,"atom:molecule");
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memory->grow(atom->ivector[index[m]],nmax,"atom:ivector");
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size_t nbytes = (nmax-nmax_old) * sizeof(int);
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memset(&atom->molecule[nmax_old],0,nbytes);
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memset(&atom->ivector[index[m]][nmax_old],0,nbytes);
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} else if (style[m] == DOUBLE) {
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memory->grow(atom->molecule,nmax,"atom:molecule");
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memory->grow(atom->dvector[index[m]],nmax,"atom:dvector");
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size_t nbytes = (nmax-nmax_old) * sizeof(double);
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memset(&atom->molecule[nmax_old],0,nbytes);
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memset(&atom->dvector[index[m]][nmax_old],0,nbytes);
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}
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}
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@ -258,9 +269,9 @@ void FixPropertyAtom::copy_arrays(int i, int j, int delflag)
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if (style[m] == MOLECULE)
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atom->molecule[j] = atom->molecule[i];
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else if (style[m] == INTEGER)
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atom->molecule[j] = atom->molecule[i];
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atom->ivector[index[m]][j] = atom->ivector[index[m]][i];
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else if (style[m] == DOUBLE)
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atom->molecule[j] = atom->molecule[i];
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atom->dvector[index[m]][j] = atom->dvector[index[m]][i];
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}
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}
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@ -281,11 +292,20 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
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buf[m++] = molecule[j];
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}
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} else if (style[j] == INTEGER) {
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int *ivector = atom->ivector[index[k]];
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = ivector[j];
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}
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} else if (style[j] == DOUBLE) {
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double *dvector = atom->dvector[index[k]];
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = dvector[j];
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}
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}
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}
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printf("PBORDER %ld %d\n",update->ntimestep,m);
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return m;
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}
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@ -304,9 +324,17 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
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last = first + n;
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for (i = first; i < last; i++)
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molecule[i] = static_cast<int> (buf[m++]);
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} else if (style[k] == INTEGER) {
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} else if (style[k] == DOUBLE) {
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}
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} else if (style[k] == INTEGER) {
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int *ivector = atom->ivector[index[k]];
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last = first + n;
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for (i = first; i < last; i++)
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ivector[i] = static_cast<int> (buf[m++]);
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} else if (style[k] == DOUBLE) {
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double *dvector = atom->dvector[index[k]];
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last = first + n;
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for (i = first; i < last; i++)
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dvector[i] = buf[m++];
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}
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}
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return m;
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@ -320,8 +348,8 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
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{
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for (int m = 0; m < nvalue; m++) {
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if (style[m] == MOLECULE) buf[m] = atom->molecule[i];
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else if (style[m] == INTEGER) buf[m] = atom->molecule[i];
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else if (style[m] == DOUBLE) buf[m] = atom->molecule[i];
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else if (style[m] == INTEGER) buf[m] = atom->ivector[index[m]][i];
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else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
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}
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return nvalue;
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}
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@ -336,9 +364,9 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
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if (style[m] == MOLECULE)
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atom->molecule[nlocal] = static_cast<int> (buf[m]);
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else if (style[m] == INTEGER)
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atom->molecule[nlocal] = static_cast<int> (buf[m]);
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atom->ivector[index[m]][nlocal] = static_cast<int> (buf[m]);
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else if (style[m] == DOUBLE)
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atom->molecule[nlocal] = buf[m];
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atom->dvector[index[m]][nlocal] = buf[m];
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}
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return nvalue;
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}
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@ -352,8 +380,8 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
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buf[0] = nvalue+1;
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for (int m = 1; m <= nvalue; m++) {
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if (style[m] == MOLECULE) buf[m] = atom->molecule[i];
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else if (style[m] == INTEGER) buf[m] = atom->molecule[i];
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else if (style[m] == DOUBLE) buf[m] = atom->molecule[i];
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else if (style[m] == INTEGER) buf[m] = atom->ivector[index[m]][i];
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else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
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}
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return nvalue+1;
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}
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@ -376,9 +404,9 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
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if (style[i] == MOLECULE)
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atom->molecule[nlocal] = static_cast<int> (extra[nlocal][m++]);
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else if (style[m] == INTEGER)
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atom->molecule[nlocal] = static_cast<int> (extra[nlocal][m++]);
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atom->ivector[index[m]][nlocal] = static_cast<int> (extra[nlocal][m++]);
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else if (style[m] == DOUBLE)
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atom->molecule[nlocal] = extra[nlocal][m++];
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atom->dvector[index[m]][nlocal] = extra[nlocal][m++];
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}
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}
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@ -48,7 +48,7 @@ class FixPropertyAtom : public Fix {
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private:
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int nvalue,border,molecule_flag;
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int *style;
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int *style,*index;
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int nmax_old; // length of peratom arrays the last time they grew
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};
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