ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'lammps:master' into type-labels

Browse Source
This commit is contained in:
Jacob Gissinger
2021-09-30 09:44:18 -04:00
committed by GitHub
parent f7bd07b3e6 4d84ceb822
commit 67ae6eb7b6
1396 changed files with 36153 additions and 25022 deletions
Download Patch File Download Diff File Expand all files Collapse all files

51
src/atom.cpp
View File

@ -36,7 +36,6 @@
#include "library.h"
#include <algorithm>
#include <cmath>
#include <cstring>
#ifdef LMP_INTEL
@ -45,6 +44,7 @@
#ifdef LMP_GPU
#include "fix_gpu.h"
#include <cmath>
#endif
using namespace LAMMPS_NS;
@ -275,7 +275,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
#define ATOM_CLASS
#define AtomStyle(key,Class) \
(*avec_map)[#key] = &avec_creator<Class>;
#include "style_atom.h"
#include "style_atom.h" // IWYU pragma: keep
#undef AtomStyle
#undef ATOM_CLASS
}
@ -362,7 +362,7 @@ Atom::~Atom()
// delete mapping data structures
map_delete();
Atom::map_delete();
delete unique_tags;
}
@ -677,7 +677,7 @@ void Atom::set_atomflag_defaults()
void Atom::create_avec(const std::string &style, int narg, char **arg, int trysuffix)
{
delete [] atom_style;
delete[] atom_style;
if (avec) delete avec;
atom_style = nullptr;
avec = nullptr;
@ -701,11 +701,9 @@ void Atom::create_avec(const std::string &style, int narg, char **arg, int trysu
std::string estyle = style + "/";
if (sflag == 1) estyle += lmp->suffix;
else estyle += lmp->suffix2;
atom_style = new char[estyle.size()+1];
strcpy(atom_style,estyle.c_str());
atom_style = utils::strdup(estyle);
} else {
atom_style = new char[style.size()+1];
strcpy(atom_style,style.c_str());
atom_style = utils::strdup(style);
}
// if molecular system:
@ -836,17 +834,13 @@ void Atom::modify_params(int narg, char **arg)
if (strcmp(arg[iarg],"id") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
if (domain->box_exist)
error->all(FLERR,
"Atom_modify id command after simulation box is defined");
if (strcmp(arg[iarg+1],"yes") == 0) tag_enable = 1;
else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 0;
else error->all(FLERR,"Illegal atom_modify command");
error->all(FLERR,"Atom_modify id command after simulation box is defined");
tag_enable = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"map") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
if (domain->box_exist)
error->all(FLERR,
"Atom_modify map command after simulation box is defined");
error->all(FLERR,"Atom_modify map command after simulation box is defined");
if (strcmp(arg[iarg+1],"array") == 0) map_user = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_user = 2;
else if (strcmp(arg[iarg+1],"yes") == 0) map_user = 3;
@ -2545,7 +2539,7 @@ This function is called, e.g. from :doc:`fix property/atom <fix_property_atom>`.
*/
int Atom::add_custom(const char *name, int flag, int cols)
{
int index;
int index = -1;
if ((flag == 0) && (cols == 0)) {
index = nivector;
@ -2585,7 +2579,8 @@ int Atom::add_custom(const char *name, int flag, int cols)
dcols = (int *) memory->srealloc(dcols,ndarray*sizeof(int),"atom:dcols");
dcols[index] = cols;
}
if (index < 0)
error->all(FLERR,"Invalid call to Atom::add_custom()");
return index;
}
@ -2606,27 +2601,27 @@ void Atom::remove_custom(int index, int flag, int cols)
{
if (flag == 0 && cols == 0) {
memory->destroy(ivector[index]);
ivector[index] = NULL;
ivector[index] = nullptr;
delete [] ivname[index];
ivname[index] = NULL;
ivname[index] = nullptr;
} else if (flag == 1 && cols == 0) {
memory->destroy(dvector[index]);
dvector[index] = NULL;
dvector[index] = nullptr;
delete [] dvname[index];
dvname[index] = NULL;
dvname[index] = nullptr;
} else if (flag == 0 && cols) {
memory->destroy(iarray[index]);
iarray[index] = NULL;
iarray[index] = nullptr;
delete [] ianame[index];
ianame[index] = NULL;
ianame[index] = nullptr;
} else if (flag == 1 && cols) {
memory->destroy(darray[index]);
darray[index] = NULL;
darray[index] = nullptr;
delete [] daname[index];
daname[index] = NULL;
daname[index] = nullptr;
}
}
@ -2859,9 +2854,9 @@ void *Atom::extract(const char *name)
if (!array) index = find_custom(&name[2],flag,cols);
else index = find_custom(&name[3],flag,cols);
if (index < 0) return NULL;
if (which != flag) return NULL;
if ((!array && cols) || (array && !cols)) return NULL;
if (index < 0) return nullptr;
if (which != flag) return nullptr;
if ((!array && cols) || (array && !cols)) return nullptr;
if (!which && !array) return (void *) ivector[index];
if (which && !array) return (void *) dvector[index];