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

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
	src/MC/fix_bond_create.cpp
	src/read_data.cpp
This commit is contained in:
Axel Kohlmeyer
2014-02-08 10:31:25 -05:00
parent 5e1ba08d23 63c9df46a9
commit f2cc64ee8b
10 changed files with 63 additions and 77 deletions
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26
src/read_data.cpp
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@ -184,10 +184,9 @@ void ReadData::command(int narg, char **arg)
} else error->all(FLERR,"Illegal read_data command");
}
// perform 1-pass read if no molecular topoogy in file
// perform 2-pass read if molecular topology
// 1st pass calculates max topology/atom
// perform 2-pass read if molecular topology,
// first pass calculates max topology/atom
int atomflag,topoflag;
int bondflag,angleflag,dihedralflag,improperflag;
@ -226,10 +225,6 @@ void ReadData::command(int narg, char **arg)
atom->allocate_type_arrays();
atom->avec->grow(n);
// initialize here, in case there are no bonds in the data file yet.
atom->bond_per_atom = atom->extra_bond_per_atom;
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
@ -497,16 +492,19 @@ void ReadData::command(int narg, char **arg)
if (!topoflag) break;
firstpass = 0;
// reallocate bond,angle,diehdral,improper arrays via grow(),
// using new bond,angle,dihedral,improper per-atom values from 1st pass
// reallocate bond,angle,diehdral,improper arrays via grow()
// use new bond,angle,dihedral,improper per-atom values from 1st pass
// should leave other atom arrays unchanged, since already nmax in length
// if bonds/etc not in data file, initialize per-atom size
// with extra settings before grow() of these topology arrays
if (bondflag) {
memory->destroy(atom->bond_type);
memory->destroy(atom->bond_atom);
atom->bond_type = NULL;
atom->bond_atom = NULL;
}
} else atom->bond_per_atom = atom->extra_bond_per_atom;
if (angleflag) {
memory->destroy(atom->angle_type);
memory->destroy(atom->angle_atom1);
@ -514,7 +512,8 @@ void ReadData::command(int narg, char **arg)
memory->destroy(atom->angle_atom3);
atom->angle_type = NULL;
atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
}
} else atom->angle_per_atom = atom->extra_angle_per_atom;
if (dihedralflag) {
memory->destroy(atom->dihedral_type);
memory->destroy(atom->dihedral_atom1);
@ -524,7 +523,8 @@ void ReadData::command(int narg, char **arg)
atom->dihedral_type = NULL;
atom->dihedral_atom1 = atom->dihedral_atom2 =
atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
}
} else atom->dihedral_per_atom = atom->extra_dihedral_per_atom;
if (improperflag) {
memory->destroy(atom->improper_type);
memory->destroy(atom->improper_atom1);
@ -534,7 +534,7 @@ void ReadData::command(int narg, char **arg)
atom->improper_type = NULL;
atom->improper_atom1 = atom->improper_atom2 =
atom->improper_atom3 = atom->improper_atom4 = NULL;
}
} else atom->improper_per_atom = atom->extra_improper_per_atom;
atom->avec->grow(atom->nmax);
}