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Fix merge conflicts, minor style fixes

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This commit is contained in:
Joel Thomas Clemmer
2021-11-01 18:13:06 -06:00
parent 69e600c404 b15c02e3cd
commit d7f7835069
1240 changed files with 46027 additions and 14730 deletions
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78
src/atom.cpp
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@ -35,7 +35,6 @@
#include "library.h"
#include <algorithm>
#include <cmath>
#include <cstring>
#ifdef LMP_INTEL
@ -44,6 +43,7 @@
#ifdef LMP_GPU
#include "fix_gpu.h"
#include <cmath>
#endif
using namespace LAMMPS_NS;
@ -261,6 +261,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
map_hash = nullptr;
unique_tags = nullptr;
reset_image_flag[0] = reset_image_flag[1] = reset_image_flag[2] = false;
atom_style = nullptr;
avec = nullptr;
@ -270,7 +271,7 @@ 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
}
@ -352,7 +353,7 @@ Atom::~Atom()
// delete mapping data structures
map_delete();
Atom::map_delete();
delete unique_tags;
}
@ -669,7 +670,7 @@ 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;
@ -693,11 +694,9 @@ 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:
@ -828,17 +827,13 @@ 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;
@ -1144,7 +1139,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
// remap atom into simulation box
// if atom is in my sub-domain, unpack its values
int flagx = 0, flagy = 0, flagz = 0;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
@ -1164,9 +1158,9 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
if ((domain->dimension == 2) && (imz != 0))
error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
if ((!domain->xperiodic) && (imx != 0)) { flagx = 1; imx = 0; }
if ((!domain->yperiodic) && (imy != 0)) { flagy = 1; imy = 0; }
if ((!domain->zperiodic) && (imz != 0)) { flagz = 1; imz = 0; }
if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; }
if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; }
if ((!domain->zperiodic) && (imz != 0)) { reset_image_flag[2] = true; imz = 0; }
}
imagedata = ((imageint) (imx + IMGMAX) & IMGMASK) |
(((imageint) (imy + IMGMAX) & IMGMASK) << IMGBITS) |
@ -1202,23 +1196,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
buf = next + 1;
}
// warn if reading data with non-zero image flags for non-periodic boundaries.
// we may want to turn this into an error at some point, since this essentially
// creates invalid position information that works by accident most of the time.
if (comm->me == 0) {
if (flagx)
error->warning(FLERR,"Non-zero imageflag(s) in x direction for "
"non-periodic boundary reset to zero");
if (flagy)
error->warning(FLERR,"Non-zero imageflag(s) in y direction for "
"non-periodic boundary reset to zero");
if (flagz)
error->warning(FLERR,"Non-zero imageflag(s) in z direction for "
"non-periodic boundary reset to zero");
}
delete [] values;
}
@ -1931,7 +1908,7 @@ void Atom::add_molecule(int narg, char **arg)
int ifile = 1;
int index = 1;
while (1) {
while (true) {
molecules = (Molecule **)
memory->srealloc(molecules,(nmolecule+1)*sizeof(Molecule *),
"atom::molecules");
@ -2475,7 +2452,7 @@ 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;
@ -2515,7 +2492,8 @@ 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;
}
@ -2536,27 +2514,27 @@ 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;
}
}
@ -2794,9 +2772,9 @@ 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];