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

programming style and format updates

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-04-12 22:52:07 -04:00
parent 467cae9436
commit ef4e41d2a2
28 changed files with 580 additions and 787 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
src/fix_update_special_bonds.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -16,15 +15,12 @@
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "pair.h"
#include <cstring>
#include <vector>
#include <utility>
using namespace LAMMPS_NS;
@ -33,15 +29,9 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixUpdateSpecialBonds::FixUpdateSpecialBonds(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal fix update/special/bonds command");
}
/* ---------------------------------------------------------------------- */
FixUpdateSpecialBonds::~FixUpdateSpecialBonds()
Fix(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR, "Illegal fix update/special/bonds command");
}
/* ---------------------------------------------------------------------- */
@ -59,21 +49,18 @@ int FixUpdateSpecialBonds::setmask()
void FixUpdateSpecialBonds::setup(int /*vflag*/)
{
// Require atoms know about all of their bonds and if they break
if (force->newton_bond)
error->all(FLERR,"Fix update/special/bonds requires Newton bond off");
if (force->newton_bond) error->all(FLERR, "Fix update/special/bonds requires Newton bond off");
if (!atom->avec->bonds_allow)
error->all(FLERR,"Fix update/special/bonds requires atom bonds");
if (!atom->avec->bonds_allow) error->all(FLERR, "Fix update/special/bonds requires atom bonds");
// special lj must be 0 1 1 to censor pair forces between bonded particles
// special coulomb must be 1 1 1 to ensure all pairs are included in the
// neighbor list and 1-3 and 1-4 special bond lists are skipped
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0)
error->all(FLERR,"Fix update/special/bonds requires special LJ weights = 0,1,1");
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
error->all(FLERR, "Fix update/special/bonds requires special LJ weights = 0,1,1");
if (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
force->special_coul[3] != 1.0)
error->all(FLERR,"Fix update/special/bonds requires special Coulomb weights = 1,1,1");
error->all(FLERR, "Fix update/special/bonds requires special Coulomb weights = 1,1,1");
new_broken_pairs.clear();
broken_pairs.clear();
@ -107,7 +94,7 @@ void FixUpdateSpecialBonds::pre_exchange()
for (m = 0; m < n1; m++)
if (slist[m] == tagj) break;
n3 = nspecial[i][2];
for (; m < n3-1; m++) slist[m] = slist[m+1];
for (; m < n3 - 1; m++) slist[m] = slist[m + 1];
nspecial[i][0]--;
nspecial[i][1]--;
nspecial[i][2]--;
@ -119,7 +106,7 @@ void FixUpdateSpecialBonds::pre_exchange()
for (m = 0; m < n1; m++)
if (slist[m] == tagi) break;
n3 = nspecial[j][2];
for (; m < n3-1; m++) slist[m] = slist[m+1];
for (; m < n3 - 1; m++) slist[m] = slist[m + 1];
nspecial[j][0]--;
nspecial[j][1]--;
nspecial[j][2]--;
@ -135,14 +122,14 @@ void FixUpdateSpecialBonds::pre_exchange()
void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
{
int i1,i2,j,jj,jnum;
int *jlist,*numneigh,**firstneigh;
int i1, i2, j, jj, jnum;
int *jlist, *numneigh, **firstneigh;
tagint tag1, tag2;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
NeighList *list = force->pair->list; // may need to be generalized to work with pair hybrid*
NeighList *list = force->pair->list; // may need to be generalized to work with pair hybrid*
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -161,9 +148,8 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
jnum = numneigh[i1];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= SPECIALMASK; // Clear special bond bits
if (tag[j] == tag2)
jlist[jj] = j;
j &= SPECIALMASK; // Clear special bond bits
if (tag[j] == tag2) jlist[jj] = j;
}
}
@ -172,13 +158,11 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
jnum = numneigh[i2];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= SPECIALMASK; // Clear special bond bits
if (tag[j] == tag1)
jlist[jj] = j;
j &= SPECIALMASK; // Clear special bond bits
if (tag[j] == tag1) jlist[jj] = j;
}
}
}
new_broken_pairs.clear();
}
@ -186,9 +170,7 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
void FixUpdateSpecialBonds::add_broken_bond(int i, int j)
{
tagint *tag = atom->tag;
std::pair <tagint, tagint> tag_pair = std::make_pair(tag[i],tag[j]);
auto tag_pair = std::make_pair(atom->tag[i], atom->tag[j]);
new_broken_pairs.push_back(tag_pair);
broken_pairs.push_back(tag_pair);
}