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Merge remote branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.txt
	doc/fix_tune_kspace.txt
	doc/group2ndx.txt
	src/DIPOLE/atom_vec_dipole.cpp
	src/DIPOLE/pair_lj_long_dipole_long.cpp
	src/MOLECULE/atom_vec_angle.cpp
	src/MOLECULE/atom_vec_bond.cpp
	src/MOLECULE/atom_vec_full.cpp
	src/MOLECULE/atom_vec_molecular.cpp
	src/PERI/atom_vec_peri.cpp
	src/USER-AWPMD/atom_vec_wavepacket.cpp
	src/USER-COLVARS/README
	src/USER-EFF/atom_vec_electron.cpp
	src/USER-SPH/atom_vec_meso.cpp
	src/atom.h
	src/atom_vec_atomic.cpp
	src/atom_vec_body.cpp
	src/atom_vec_charge.cpp
	src/atom_vec_ellipsoid.cpp
	src/atom_vec_line.cpp
	src/atom_vec_sphere.cpp
	src/atom_vec_tri.cpp
	src/fix_restrain.cpp
	src/force.cpp
	tools/restart2data.cpp
This commit is contained in:
Axel Kohlmeyer
2013-06-28 13:09:52 +02:00
parent f99231874b a92e8c271b
commit 2b1e3a30bd
70 changed files with 2219 additions and 820 deletions
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19
src/pair.cpp
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@ -71,6 +71,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
// pair_modify settings
compute_flag = 1;
manybody_flag = 0;
offset_flag = 0;
mix_flag = GEOMETRIC;
tail_flag = 0;
@ -172,11 +173,27 @@ void Pair::init()
if (tail_flag && domain->nonperiodic && comm->me == 0)
error->warning(FLERR,"Using pair tail corrections with nonperiodic system");
if (!allocated) error->all(FLERR,"All pair coeffs are not set");
// for manybody potentials
// check if bonded exclusions could invalidate the neighbor list
if (manybody_flag && atom->molecular) {
int flag = 0;
if (atom->nbonds > 0 && force->special_lj[1] == 0.0 &&
force->special_coul[1] == 0.0) flag = 1;
if (atom->nangles > 0 && force->special_lj[2] == 0.0 &&
force->special_coul[2] == 0.0) flag = 1;
if (atom->ndihedrals > 0 && force->special_lj[3] == 0.0 &&
force->special_coul[3] == 0.0) flag = 1;
if (flag && comm->me == 0)
error->warning(FLERR,"Using a manybody potential with "
"bonds/angles/dihedrals and special_bond exclusions");
}
// I,I coeffs must be set
// init_one() will check if I,J is set explicitly or inferred by mixing
if (!allocated) error->all(FLERR,"All pair coeffs are not set");
for (i = 1; i <= atom->ntypes; i++)
if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");