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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11507 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-02-07 21:17:22 +00:00
parent e62361cbf7
commit 784d229527
4 changed files with 46 additions and 28 deletions
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11
src/MC/fix_bond_break.cpp
View File

@ -128,13 +128,14 @@ int FixBondBreak::setmask()
void FixBondBreak::init()
{
// require special bonds = 0,1,1
// require special bonds = *,1,1
// [0] can be anything b/c I,J are removed from each other's special list
// [1],[2] must be 1.0 b/c only special lists of I,J are updated when
// bond I-J is broken, not special lists of neighbors of I,J,etc
int flag = 0;
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0) flag = 1;
if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
force->special_coul[3] != 1.0) flag = 1;
if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) flag = 1;
if (force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0) flag = 1;
if (flag) error->all(FLERR,"Fix bond/break requires special_bonds = 0,1,1");
// warn if angles, dihedrals, impropers are being used

36
src/MC/fix_bond_create.cpp
View File

@ -180,16 +180,17 @@ void FixBondCreate::init()
if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
// require special bonds = 0,1,1
// require special bonds = *,1,1
// [0] can be anything b/c duplicate bond is checked for
// [1],[2] must be 1 b/c only special lists of I,J are updated when
// bond I-J is created, not special lists of neighbors of I,J,etc
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0)
error->all(FLERR,"Fix bond/create requires special_bonds lj = 0,1,1");
if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
error->all(FLERR,"Fix bond/create requires special_bonds lj = *,1,1");
if (atom->q_flag)
if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
force->special_coul[3] != 1.0)
error->all(FLERR,"Fix bond/create requires special_bonds coul = 0,1,1");
if (force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
error->all(FLERR,"Fix bond/create requires special_bonds coul = *,1,1");
// warn if angles, dihedrals, impropers are being used
@ -267,7 +268,7 @@ void FixBondCreate::setup(int vflag)
void FixBondCreate::post_integrate()
{
int i,j,m,ii,jj,inum,jnum,itype,jtype,n1,n3,possible;
int i,j,k,m,ii,jj,inum,jnum,itype,jtype,n1,n3,possible;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
tagint *slist;
@ -309,6 +310,8 @@ void FixBondCreate::post_integrate()
double **x = atom->x;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int *mask = atom->mask;
int *type = atom->type;
@ -345,6 +348,16 @@ void FixBondCreate::post_integrate()
}
if (!possible) continue;
// do not allow a duplicate bond to be created
// check existing bonds of both I and J
for (k = 0; k < num_bond[i]; k++)
if (bond_atom[i][k] == tag[j]) possible = 0;
if (j < nlocal)
for (k = 0; k < num_bond[j]; k++)
if (bond_atom[j][k] == tag[i]) possible = 0;
if (!possible) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@ -386,8 +399,6 @@ void FixBondCreate::post_integrate()
// and probability constraint is satisfied
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int newton_bond = force->newton_bond;
@ -437,11 +448,10 @@ void FixBondCreate::post_integrate()
// increment bondcount, convert atom to new type if limit reached
bondcount[i]++;
if (type[i] == iatomtype) {
if (type[i] == iatomtype)
if (bondcount[i] == imaxbond) type[i] = inewtype;
} else {
else
if (bondcount[i] == jmaxbond) type[i] = jnewtype;
}
// count the created bond once

4
src/fix.h
View File

@ -196,6 +196,10 @@ class Fix : protected Pointers {
void v_setup(int);
void v_tally(int, int *, double, double *);
inline int sbmask(int j) {
return j >> SBBITS & 3;
}
// union data struct for packing 32-bit and 64-bit ints into double bufs
// see atom_vec.h for documentation

23
src/read_data.cpp
View File

@ -139,10 +139,9 @@ 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;
@ -180,7 +179,6 @@ void ReadData::command(int narg, char **arg)
atom->allocate_type_arrays();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
@ -428,16 +426,19 @@ 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);
@ -445,7 +446,8 @@ 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);
@ -455,7 +457,8 @@ 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);
@ -465,7 +468,7 @@ 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);
}