git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5792 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
149
src/atom.cpp
149
src/atom.cpp
@ -152,83 +152,83 @@ Atom::~Atom()
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delete avec;
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delete [] firstgroupname;
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memory->sfree(binhead);
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memory->sfree(next);
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memory->sfree(permute);
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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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// delete atom arrays
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// customize by adding new array
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memory->sfree(tag);
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memory->sfree(type);
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memory->sfree(mask);
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memory->sfree(image);
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memory->destroy_2d_double_array(x);
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memory->destroy_2d_double_array(v);
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memory->destroy_2d_double_array(f);
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memory->destroy(tag);
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memory->destroy(type);
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memory->destroy(mask);
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memory->destroy(image);
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memory->destroy(x);
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memory->destroy(v);
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memory->destroy(f);
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memory->sfree(q);
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memory->destroy_2d_double_array(mu);
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memory->destroy_2d_double_array(quat);
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memory->destroy_2d_double_array(omega);
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memory->destroy_2d_double_array(angmom);
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memory->destroy_2d_double_array(torque);
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memory->destroy(q);
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memory->destroy(mu);
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memory->destroy(quat);
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memory->destroy(omega);
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memory->destroy(angmom);
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memory->destroy(torque);
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memory->sfree(radius);
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memory->sfree(density);
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memory->sfree(rmass);
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memory->sfree(vfrac);
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memory->sfree(s0);
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memory->destroy_2d_double_array(x0);
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memory->destroy(radius);
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memory->destroy(density);
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memory->destroy(rmass);
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memory->destroy(vfrac);
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memory->destroy(s0);
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memory->destroy(x0);
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memory->sfree(spin);
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memory->sfree(eradius);
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memory->sfree(ervel);
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memory->sfree(erforce);
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memory->destroy(spin);
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memory->destroy(eradius);
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memory->destroy(ervel);
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memory->destroy(erforce);
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memory->sfree(molecule);
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memory->destroy(molecule);
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memory->destroy_2d_int_array(nspecial);
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memory->destroy_2d_int_array(special);
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memory->destroy(nspecial);
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memory->destroy(special);
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memory->sfree(num_bond);
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memory->destroy_2d_int_array(bond_type);
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memory->destroy_2d_int_array(bond_atom);
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memory->destroy(num_bond);
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memory->destroy(bond_type);
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memory->destroy(bond_atom);
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memory->sfree(num_angle);
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memory->destroy_2d_int_array(angle_type);
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memory->destroy_2d_int_array(angle_atom1);
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memory->destroy_2d_int_array(angle_atom2);
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memory->destroy_2d_int_array(angle_atom3);
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memory->destroy(num_angle);
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memory->destroy(angle_type);
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memory->destroy(angle_atom1);
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memory->destroy(angle_atom2);
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memory->destroy(angle_atom3);
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memory->sfree(num_dihedral);
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memory->destroy_2d_int_array(dihedral_type);
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memory->destroy_2d_int_array(dihedral_atom1);
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memory->destroy_2d_int_array(dihedral_atom2);
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memory->destroy_2d_int_array(dihedral_atom3);
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memory->destroy_2d_int_array(dihedral_atom4);
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memory->destroy(num_dihedral);
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memory->destroy(dihedral_type);
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memory->destroy(dihedral_atom1);
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memory->destroy(dihedral_atom2);
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memory->destroy(dihedral_atom3);
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memory->destroy(dihedral_atom4);
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memory->sfree(num_improper);
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memory->destroy_2d_int_array(improper_type);
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memory->destroy_2d_int_array(improper_atom1);
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memory->destroy_2d_int_array(improper_atom2);
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memory->destroy_2d_int_array(improper_atom3);
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memory->destroy_2d_int_array(improper_atom4);
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memory->destroy(num_improper);
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memory->destroy(improper_type);
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memory->destroy(improper_atom1);
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memory->destroy(improper_atom2);
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memory->destroy(improper_atom3);
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memory->destroy(improper_atom4);
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// delete per-type arrays
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delete [] mass;
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delete [] mass_setflag;
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memory->destroy_2d_double_array(shape);
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memory->destroy(shape);
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delete [] shape_setflag;
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delete [] dipole;
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delete [] dipole_setflag;
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// delete extra arrays
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memory->sfree(extra_grow);
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memory->sfree(extra_restart);
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memory->destroy_2d_double_array(extra);
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memory->destroy(extra_grow);
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memory->destroy(extra_restart);
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memory->destroy(extra);
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// delete mapping data structures
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@ -300,7 +300,7 @@ void Atom::init()
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// delete extra array since it doesn't persist past first run
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if (nextra_store) {
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memory->destroy_2d_double_array(extra);
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memory->destroy(extra);
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extra = NULL;
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nextra_store = 0;
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}
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@ -420,8 +420,7 @@ void Atom::map_init()
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MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
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if (map_style == 1) {
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map_array = (int *)
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memory->smalloc((map_tag_max+1)*sizeof(int),"atom:map_array");
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memory->create(map_array,map_tag_max+1,"atom:map_array");
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for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
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} else {
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@ -605,7 +604,7 @@ void Atom::map_one(int global, int local)
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void Atom::map_delete()
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{
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if (map_style == 1) {
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if (map_tag_max) memory->sfree(map_array);
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if (map_tag_max) memory->destroy(map_array);
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} else {
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if (map_nhash) {
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delete [] map_bucket;
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@ -696,20 +695,21 @@ int Atom::tag_consecutive()
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int Atom::count_words(const char *line)
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{
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int n = strlen(line) + 1;
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char *copy = (char *) memory->smalloc(n*sizeof(char),"copy");
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char *copy;
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memory->create(copy,n,"atom:copy");
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strcpy(copy,line);
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char *ptr;
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if (ptr = strchr(copy,'#')) *ptr = '\0';
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if (strtok(copy," \t\n\r\f") == NULL) {
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memory->sfree(copy);
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memory->destroy(copy);
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return 0;
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}
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n = 1;
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while (strtok(NULL," \t\n\r\f")) n++;
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memory->sfree(copy);
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memory->destroy(copy);
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return n;
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}
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@ -1066,7 +1066,7 @@ void Atom::allocate_type_arrays()
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for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
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}
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if (avec->shape_type) {
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shape = memory->create_2d_double_array(ntypes+1,3,"atom:shape");
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memory->create(shape,ntypes+1,3,"atom:shape");
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shape_setflag = new int[ntypes+1];
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for (int itype = 1; itype <= ntypes; itype++) shape_setflag[itype] = 0;
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}
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@ -1365,11 +1365,11 @@ void Atom::sort()
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// reallocate per-atom vectors if needed
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if (nlocal > maxnext) {
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memory->sfree(next);
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memory->sfree(permute);
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memory->destroy(next);
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memory->destroy(permute);
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maxnext = atom->nmax;
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next = (int *) memory->smalloc(maxnext*sizeof(int),"atom:next");
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permute = (int *) memory->smalloc(maxnext*sizeof(int),"atom:permute");
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memory->create(next,maxnext,"atom:next");
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memory->create(permute,maxnext,"atom:permute");
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}
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// insure there is one extra atom location at end of arrays for swaps
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@ -1497,9 +1497,9 @@ void Atom::setup_sort_bins()
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// reallocate per-bin memory if needed
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if (nbins > maxbin) {
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memory->sfree(binhead);
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memory->destroy(binhead);
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maxbin = nbins;
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binhead = (int *) memory->smalloc(maxbin*sizeof(int),"atom:binhead");
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memory->create(binhead,maxbin,"atom:binhead");
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}
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}
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@ -1528,18 +1528,14 @@ void Atom::add_callback(int flag)
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if (flag == 0) {
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if (nextra_grow == nextra_grow_max) {
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nextra_grow_max += DELTA;
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extra_grow = (int *)
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memory->srealloc(extra_grow,nextra_grow_max*sizeof(int),
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"atom:extra_grow");
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memory->grow(extra_grow,nextra_grow_max,"atom:extra_grow");
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}
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extra_grow[nextra_grow] = ifix;
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nextra_grow++;
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} else if (flag == 1) {
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if (nextra_restart == nextra_restart_max) {
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nextra_restart_max += DELTA;
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extra_restart = (int *)
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memory->srealloc(extra_restart,nextra_restart_max*sizeof(int),
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"atom:extra_restart");
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memory->grow(extra_restart,nextra_restart_max,"atom:extra_restart");
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}
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extra_restart[nextra_restart] = ifix;
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nextra_restart++;
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@ -1619,7 +1615,7 @@ void *Atom::extract(char *name)
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double Atom::memory_usage()
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{
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memlength = DELTA_MEMSTR;
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memstr = (char *) memory->smalloc(memlength*sizeof(char),"atom:memstr");
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memory->create(memstr,memlength,"atom:memstr");
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memstr[0] = '\0';
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double bytes = avec->memory_usage();
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@ -1630,7 +1626,7 @@ double Atom::memory_usage()
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bytes += map_nhash*sizeof(HashElem);
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}
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memory->sfree(memstr);
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memory->destroy(memstr);
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return bytes;
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}
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@ -1654,8 +1650,7 @@ int Atom::memcheck(const char *str)
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if (strlen(memstr) + n >= memlength) {
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memlength += DELTA_MEMSTR;
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memstr = (char *) memory->srealloc(memstr,memlength*sizeof(char),
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"atom: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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