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This commit is contained in:
Axel Kohlmeyer
2022-03-06 05:24:29 -05:00
parent 72cbffee7d
commit 005f76a9e6
1 changed files with 109 additions and 122 deletions
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231
src/create_bonds.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -35,7 +34,7 @@
using namespace LAMMPS_NS;
enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER};
enum { MANY, SBOND, SANGLE, SDIHEDRAL, SIMPROPER };
/* ---------------------------------------------------------------------- */
@ -46,118 +45,122 @@ CreateBonds::CreateBonds(LAMMPS *lmp) : Command(lmp) {}
void CreateBonds::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Create_bonds command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use create_bonds unless atoms have IDs");
error->all(FLERR, "Create_bonds command before simulation box is defined");
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use create_bonds unless atoms have IDs");
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use create_bonds with non-molecular system");
error->all(FLERR, "Cannot use create_bonds with non-molecular system");
if (narg < 4) error->all(FLERR,"Illegal create_bonds command");
if (narg < 4) error->all(FLERR, "Illegal create_bonds command");
// parse args
int style;
int iarg = 0;
if (strcmp(arg[0],"many") == 0) {
if (strcmp(arg[0], "many") == 0) {
style = MANY;
if (narg != 6) error->all(FLERR,"Illegal create_bonds command");
if (narg != 6) error->all(FLERR, "Illegal create_bonds command");
igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Cannot find create_bonds group ID");
if (igroup == -1) error->all(FLERR, "Cannot find create_bonds group ID");
group1bit = group->bitmask[igroup];
igroup = group->find(arg[2]);
if (igroup == -1) error->all(FLERR,"Cannot find create_bonds group ID");
if (igroup == -1) error->all(FLERR, "Cannot find create_bonds group ID");
group2bit = group->bitmask[igroup];
btype = utils::inumeric(FLERR,arg[3],false,lmp);
rmin = utils::numeric(FLERR,arg[4],false,lmp);
rmax = utils::numeric(FLERR,arg[5],false,lmp);
if (rmin > rmax) error->all(FLERR,"Illegal create_bonds command");
btype = utils::inumeric(FLERR, arg[3], false, lmp);
rmin = utils::numeric(FLERR, arg[4], false, lmp);
rmax = utils::numeric(FLERR, arg[5], false, lmp);
if (rmin > rmax) error->all(FLERR, "Illegal create_bonds command");
iarg = 6;
} else if (strcmp(arg[0],"single/bond") == 0) {
} else if (strcmp(arg[0], "single/bond") == 0) {
style = SBOND;
if (narg < 4) error->all(FLERR,"Illegal create_bonds command");
btype = utils::inumeric(FLERR,arg[1],false,lmp);
batom1 = utils::tnumeric(FLERR,arg[2],false,lmp);
batom2 = utils::tnumeric(FLERR,arg[3],false,lmp);
if (batom1 == batom2)
error->all(FLERR,"Illegal create_bonds command");
if (narg < 4) error->all(FLERR, "Illegal create_bonds command");
btype = utils::inumeric(FLERR, arg[1], false, lmp);
batom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
batom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
if (batom1 == batom2) error->all(FLERR, "Illegal create_bonds command");
iarg = 4;
} else if (strcmp(arg[0],"single/angle") == 0) {
} else if (strcmp(arg[0], "single/angle") == 0) {
style = SANGLE;
if (narg < 5) error->all(FLERR,"Illegal create_bonds command");
atype = utils::inumeric(FLERR,arg[1],false,lmp);
aatom1 = utils::tnumeric(FLERR,arg[2],false,lmp);
aatom2 = utils::tnumeric(FLERR,arg[3],false,lmp);
aatom3 = utils::tnumeric(FLERR,arg[4],false,lmp);
if (narg < 5) error->all(FLERR, "Illegal create_bonds command");
atype = utils::inumeric(FLERR, arg[1], false, lmp);
aatom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
aatom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
aatom3 = utils::tnumeric(FLERR, arg[4], false, lmp);
if ((aatom1 == aatom2) || (aatom1 == aatom3) || (aatom2 == aatom3))
error->all(FLERR,"Illegal create_bonds command");
error->all(FLERR, "Illegal create_bonds command");
iarg = 5;
} else if (strcmp(arg[0],"single/dihedral") == 0) {
} else if (strcmp(arg[0], "single/dihedral") == 0) {
style = SDIHEDRAL;
if (narg < 6) error->all(FLERR,"Illegal create_bonds command");
dtype = utils::inumeric(FLERR,arg[1],false,lmp);
datom1 = utils::tnumeric(FLERR,arg[2],false,lmp);
datom2 = utils::tnumeric(FLERR,arg[3],false,lmp);
datom3 = utils::tnumeric(FLERR,arg[4],false,lmp);
datom4 = utils::tnumeric(FLERR,arg[5],false,lmp);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) ||
(datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4))
error->all(FLERR,"Illegal create_bonds command");
if (narg < 6) error->all(FLERR, "Illegal create_bonds command");
dtype = utils::inumeric(FLERR, arg[1], false, lmp);
datom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
datom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
datom3 = utils::tnumeric(FLERR, arg[4], false, lmp);
datom4 = utils::tnumeric(FLERR, arg[5], false, lmp);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || (datom2 == datom3) ||
(datom2 == datom4) || (datom3 == datom4))
error->all(FLERR, "Illegal create_bonds command");
iarg = 6;
} else if (strcmp(arg[0],"single/improper") == 0) {
} else if (strcmp(arg[0], "single/improper") == 0) {
style = SIMPROPER;
if (narg < 6) error->all(FLERR,"Illegal create_bonds command");
dtype = utils::inumeric(FLERR,arg[1],false,lmp);
datom1 = utils::tnumeric(FLERR,arg[2],false,lmp);
datom2 = utils::tnumeric(FLERR,arg[3],false,lmp);
datom3 = utils::tnumeric(FLERR,arg[4],false,lmp);
datom4 = utils::tnumeric(FLERR,arg[5],false,lmp);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) ||
(datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4))
error->all(FLERR,"Illegal create_bonds command");
if (narg < 6) error->all(FLERR, "Illegal create_bonds command");
dtype = utils::inumeric(FLERR, arg[1], false, lmp);
datom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
datom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
datom3 = utils::tnumeric(FLERR, arg[4], false, lmp);
datom4 = utils::tnumeric(FLERR, arg[5], false, lmp);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || (datom2 == datom3) ||
(datom2 == datom4) || (datom3 == datom4))
error->all(FLERR, "Illegal create_bonds command");
iarg = 6;
} else error->all(FLERR,"Illegal create_bonds command");
} else
error->all(FLERR, "Illegal create_bonds command");
// optional args
int specialflag = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"special") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_bonds command");
specialflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
if (strcmp(arg[iarg], "special") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal create_bonds command");
specialflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else error->all(FLERR,"Illegal create_bonds command");
} else
error->all(FLERR, "Illegal create_bonds command");
}
// error checks
if (style == MANY) {
if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in create_bonds command");
if (specialflag == 0)
error->all(FLERR,"Cannot use special no with create_bonds many");
error->all(FLERR, "Invalid bond type in create_bonds command");
if (specialflag == 0) error->all(FLERR, "Cannot use special no with create_bonds many");
} else if (style == SBOND) {
if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in create_bonds command");
error->all(FLERR, "Invalid bond type in create_bonds command");
} else if (style == SANGLE) {
if (atype <= 0 || atype > atom->nangletypes)
error->all(FLERR,"Invalid angle type in create_bonds command");
error->all(FLERR, "Invalid angle type in create_bonds command");
} else if (style == SDIHEDRAL) {
if (dtype <= 0 || dtype > atom->ndihedraltypes)
error->all(FLERR,"Invalid dihedral type in create_bonds command");
error->all(FLERR, "Invalid dihedral type in create_bonds command");
} else if (style == SIMPROPER) {
if (dtype <= 0 || dtype > atom->nimpropertypes)
error->all(FLERR,"Invalid improper type in create_bonds command");
error->all(FLERR, "Invalid improper type in create_bonds command");
}
// invoke creation method
if (style == MANY) many();
else if (style == SBOND) single_bond();
else if (style == SANGLE) single_angle();
else if (style == SDIHEDRAL) single_dihedral();
else if (style == SIMPROPER) single_improper();
if (style == MANY)
many();
else if (style == SBOND)
single_bond();
else if (style == SANGLE)
single_angle();
else if (style == SDIHEDRAL)
single_dihedral();
else if (style == SIMPROPER)
single_improper();
// trigger special list build
@ -171,8 +174,8 @@ void CreateBonds::command(int narg, char **arg)
void CreateBonds::many()
{
double rminsq = rmin*rmin;
double rmaxsq = rmax*rmax;
double rminsq = rmin * rmin;
double rmaxsq = rmax * rmax;
// store state before bond creation
@ -190,12 +193,11 @@ void CreateBonds::many()
// error check on cutoff
// if no pair style, neighbor list will be empty
if (force->pair == nullptr)
error->all(FLERR,"Create_bonds requires a pair style be defined");
if (force->pair == nullptr) error->all(FLERR, "Create_bonds requires a pair style be defined");
if (rmax > neighbor->cutneighmax)
error->all(FLERR,"Create_bonds max distance > neighbor cutoff");
error->all(FLERR, "Create_bonds max distance > neighbor cutoff");
if (rmax > neighbor->cutneighmin && comm->me == 0)
error->warning(FLERR,"Create_bonds max distance > minimum neighbor cutoff");
error->warning(FLERR, "Create_bonds max distance > minimum neighbor cutoff");
// require special_bonds 1-2 weights = 0.0 and KSpace = nullptr
// so that already bonded atom pairs do not appear in neighbor list
@ -204,11 +206,8 @@ void CreateBonds::many()
// note that with KSpace, pair with weight = 0 could still be in neigh list
if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0.0)
error->all(FLERR,"Create_bonds command requires "
"special_bonds 1-2 weights be 0.0");
if (force->kspace)
error->all(FLERR,"Create_bonds command requires "
"no kspace_style be defined");
error->all(FLERR, "Create_bonds command requires special_bonds 1-2 weights be 0.0");
if (force->kspace) error->all(FLERR, "Create_bonds command requires no kspace_style be defined");
// setup domain, communication and neighboring
// acquire ghosts and build standard neighbor lists
@ -220,13 +219,13 @@ void CreateBonds::many()
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost);
neighbor->build(1);
// build neighbor list this command needs based on earlier request
auto list = neighbor->find_list(this);
neighbor->build_one(list,1);
neighbor->build_one(list, 1);
// loop over all neighs of each atom
// compute distance between two atoms consistently on both procs
@ -242,9 +241,9 @@ void CreateBonds::many()
double newton_bond = force->newton_bond;
int nlocal = atom->nlocal;
int i,j,ii,jj,inum,jnum,flag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int i, j, ii, jj, inum, jnum, flag;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
inum = list->inum;
ilist = list->ilist;
@ -275,8 +274,9 @@ void CreateBonds::many()
delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp;
} else continue;
rsq = delx*delx + dely*dely + delz*delz;
} else
continue;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < rminsq || rsq > rmaxsq) continue;
// only consider bond creation if igroup and jgroup match I,J atoms
@ -291,8 +291,8 @@ void CreateBonds::many()
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom limit "
" of {} in create_bonds",atom->bond_per_atom);
error->one(FLERR, "New bond exceeded bonds per atom limit of {} in create_bonds",
atom->bond_per_atom);
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;
@ -305,7 +305,7 @@ void CreateBonds::many()
bigint nbonds = 0;
for (i = 0; i < nlocal; i++) nbonds += num_bond[i];
MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&nbonds, &atom->nbonds, 1, MPI_LMP_BIGINT, MPI_SUM, world);
if (!force->newton_bond) atom->nbonds /= 2;
// print new bond count
@ -313,8 +313,7 @@ void CreateBonds::many()
bigint nadd_bonds = atom->nbonds - nbonds_previous;
if (comm->me == 0)
utils::logmesg(lmp,"Added {} bonds, new total = {}\n",
nadd_bonds,atom->nbonds);
utils::logmesg(lmp, "Added {} bonds, new total = {}\n", nadd_bonds, atom->nbonds);
}
/* ---------------------------------------------------------------------- */
@ -334,9 +333,8 @@ void CreateBonds::single_bond()
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 2)
error->all(FLERR,"Create_bonds single/bond atoms do not exist");
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 2) error->all(FLERR, "Create_bonds single/bond atoms do not exist");
// create bond once or 2x if newton_bond set
@ -346,7 +344,7 @@ void CreateBonds::single_bond()
if ((m = idx1) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
error->one(FLERR, "New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
bond_atom[m][num_bond[m]] = batom2;
num_bond[m]++;
@ -357,7 +355,7 @@ void CreateBonds::single_bond()
if ((m = idx2) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
error->one(FLERR, "New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
bond_atom[m][num_bond[m]] = batom1;
num_bond[m]++;
@ -383,9 +381,8 @@ void CreateBonds::single_angle()
if ((idx3 >= 0) && (idx3 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 3)
error->all(FLERR,"Create_bonds single/angle atoms do not exist");
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 3) error->all(FLERR, "Create_bonds single/angle atoms do not exist");
// create angle once or 3x if newton_bond set
@ -397,7 +394,7 @@ void CreateBonds::single_angle()
if ((m = idx2) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
error->one(FLERR, "New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
angle_atom1[m][num_angle[m]] = aatom1;
angle_atom2[m][num_angle[m]] = aatom2;
@ -410,7 +407,7 @@ void CreateBonds::single_angle()
if ((m = idx1) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
error->one(FLERR, "New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
angle_atom1[m][num_angle[m]] = aatom1;
angle_atom2[m][num_angle[m]] = aatom2;
@ -420,7 +417,7 @@ void CreateBonds::single_angle()
if ((m = idx3) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
error->one(FLERR, "New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
angle_atom1[m][num_angle[m]] = aatom1;
angle_atom2[m][num_angle[m]] = aatom2;
@ -450,9 +447,8 @@ void CreateBonds::single_dihedral()
if ((idx4 >= 0) && (idx4 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 4)
error->all(FLERR,"Create_bonds single/dihedral atoms do not exist");
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 4) error->all(FLERR, "Create_bonds single/dihedral atoms do not exist");
// create bond once or 4x if newton_bond set
@ -465,8 +461,7 @@ void CreateBonds::single_dihedral()
if ((m = idx2) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -480,8 +475,7 @@ void CreateBonds::single_dihedral()
if ((m = idx1) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -492,8 +486,7 @@ void CreateBonds::single_dihedral()
if ((m = idx3) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -504,8 +497,7 @@ void CreateBonds::single_dihedral()
if ((m = idx4) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -536,9 +528,8 @@ void CreateBonds::single_improper()
if ((idx4 >= 0) && (idx4 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (allcount != 4)
error->all(FLERR,"Create_bonds single/improper atoms do not exist");
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 4) error->all(FLERR, "Create_bonds single/improper atoms do not exist");
// create bond once or 4x if newton_bond set
@ -551,8 +542,7 @@ void CreateBonds::single_improper()
if ((m = idx2) >= 0) {
if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR,
"New improper exceeded impropers per atom in create_bonds");
error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2;
@ -566,8 +556,7 @@ void CreateBonds::single_improper()
if ((m = idx1) >= 0) {
if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR,
"New improper exceeded impropers per atom in create_bonds");
error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2;
@ -578,8 +567,7 @@ void CreateBonds::single_improper()
if ((m = idx3) >= 0) {
if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR,
"New improper exceeded impropers per atom in create_bonds");
error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2;
@ -590,8 +578,7 @@ void CreateBonds::single_improper()
if ((m = idx4) >= 0) {
if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR,
"New improper exceeded impropers per atom in create_bonds");
error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2;