forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11797 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
207832a8b4
commit
bcd91423db
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@ -298,7 +298,7 @@ void FixBondBreak::post_integrate()
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}
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// remove J from special bond list for atom I
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// atom J will also do this
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// atom J will also do this, whatever proc it is on
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slist = special[i];
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n1 = nspecial[i][0];
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@ -330,7 +330,7 @@ void FixBondBreak::post_integrate()
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if (breakcount) next_reneighbor = update->ntimestep;
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if (!breakcount) return;
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// communicate final broken bond and 1-2 special neighbors
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// communicate final partner and 1-2 special neighbors
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// 1-2 neighs already reflect broken bonds
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commflag = 2;
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@ -370,8 +370,9 @@ void FixBondBreak::post_integrate()
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/* ----------------------------------------------------------------------
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insure all atoms 2 hops away from owned atoms are in ghost list
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this allows dihedral 1-2-3-4 to be properly deleted
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if I own atom 1, 2-3-4 are ghosts, and bond 3-4 is deleted
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since ghost 3 will store 4 as its finalpartner
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and special list of 1 to be properly updated
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if I own atom 1, but not 2,3,4, and bond 3-4 is deleted
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then 2,3 will be ghosts and 3 will store 4 as its finalpartner
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------------------------------------------------------------------------- */
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void FixBondBreak::check_ghosts()
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@ -484,6 +485,132 @@ void FixBondBreak::update_topology()
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}
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/* ----------------------------------------------------------------------
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break any angles owned by atom M that include atom IDs 1 and 2
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angle is broken if ID1-ID2 is one of 2 bonds in linear angle
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------------------------------------------------------------------------- */
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void FixBondBreak::break_angles(int m, tagint id1, tagint id2)
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{
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int j,found;
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int num_angle = atom->num_angle[m];
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int *angle_type = atom->angle_type[m];
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tagint *angle_atom1 = atom->angle_atom1[m];
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tagint *angle_atom2 = atom->angle_atom2[m];
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tagint *angle_atom3 = atom->angle_atom3[m];
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int i = 0;
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while (i < num_angle) {
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found = 0;
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if (angle_atom1[i] == id1 && angle_atom2[i] == id2) found = 1;
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else if (angle_atom2[i] == id1 && angle_atom3[i] == id2) found = 1;
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else if (angle_atom1[i] == id2 && angle_atom2[i] == id1) found = 1;
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else if (angle_atom2[i] == id2 && angle_atom3[i] == id1) found = 1;
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if (!found) i++;
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else {
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for (j = i; j < num_angle-1; j++) {
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angle_type[j] = angle_type[j+1];
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angle_atom1[j] = angle_atom1[j+1];
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angle_atom2[j] = angle_atom2[j+1];
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angle_atom3[j] = angle_atom3[j+1];
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}
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num_angle--;
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nangles++;
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}
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}
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atom->num_angle[m] = num_angle;
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}
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/* ----------------------------------------------------------------------
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break any dihedrals owned by atom M that include atom IDs 1,2,3
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dihedral is broken if ID1-ID2 is one of 3 bonds in linear dihedral
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------------------------------------------------------------------------- */
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void FixBondBreak::break_dihedrals(int m, tagint id1, tagint id2)
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{
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int j,found;
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int num_dihedral = atom->num_dihedral[m];
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int *dihedral_type = atom->dihedral_type[m];
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tagint *dihedral_atom1 = atom->dihedral_atom1[m];
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tagint *dihedral_atom2 = atom->dihedral_atom2[m];
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tagint *dihedral_atom3 = atom->dihedral_atom3[m];
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tagint *dihedral_atom4 = atom->dihedral_atom4[m];
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int i = 0;
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while (i < num_dihedral) {
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found = 0;
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if (dihedral_atom1[i] == id1 && dihedral_atom2[i] == id2) found = 1;
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else if (dihedral_atom2[i] == id1 && dihedral_atom3[i] == id2) found = 1;
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else if (dihedral_atom3[i] == id1 && dihedral_atom4[i] == id2) found = 1;
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else if (dihedral_atom1[i] == id2 && dihedral_atom2[i] == id1) found = 1;
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else if (dihedral_atom2[i] == id2 && dihedral_atom3[i] == id1) found = 1;
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else if (dihedral_atom3[i] == id2 && dihedral_atom4[i] == id1) found = 1;
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if (!found) i++;
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else {
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for (j = i; j < num_dihedral-1; j++) {
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dihedral_type[j] = dihedral_type[j+1];
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dihedral_atom1[j] = dihedral_atom1[j+1];
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dihedral_atom2[j] = dihedral_atom2[j+1];
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dihedral_atom3[j] = dihedral_atom3[j+1];
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dihedral_atom4[j] = dihedral_atom4[j+1];
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}
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num_dihedral--;
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ndihedrals++;
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}
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}
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atom->num_dihedral[m] = num_dihedral;
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}
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/* ----------------------------------------------------------------------
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break any impropers owned by atom M that include atom IDs 1,2,3
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improper is broken if ID1-ID2 is one of 3 bonds in improper (I-J,I-K,I-L)
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------------------------------------------------------------------------- */
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void FixBondBreak::break_impropers(int m, tagint id1, tagint id2)
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{
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int j,found;
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int num_improper = atom->num_improper[m];
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int *improper_type = atom->improper_type[m];
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tagint *improper_atom1 = atom->improper_atom1[m];
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tagint *improper_atom2 = atom->improper_atom2[m];
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tagint *improper_atom3 = atom->improper_atom3[m];
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tagint *improper_atom4 = atom->improper_atom4[m];
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int i = 0;
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while (i < num_improper) {
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found = 0;
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if (improper_atom1[i] == id1 && improper_atom2[i] == id2) found = 1;
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else if (improper_atom1[i] == id1 && improper_atom3[i] == id2) found = 1;
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else if (improper_atom1[i] == id1 && improper_atom4[i] == id2) found = 1;
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else if (improper_atom1[i] == id2 && improper_atom2[i] == id1) found = 1;
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else if (improper_atom1[i] == id2 && improper_atom3[i] == id1) found = 1;
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else if (improper_atom1[i] == id2 && improper_atom4[i] == id1) found = 1;
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if (!found) i++;
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else {
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for (j = i; j < num_improper-1; j++) {
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improper_type[j] = improper_type[j+1];
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improper_atom1[j] = improper_atom1[j+1];
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improper_atom2[j] = improper_atom2[j+1];
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improper_atom3[j] = improper_atom3[j+1];
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improper_atom4[j] = improper_atom4[j+1];
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}
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num_improper--;
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nimpropers++;
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}
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}
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atom->num_improper[m] = num_improper;
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}
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/* ----------------------------------------------------------------------
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re-build special list of atom M due to bond ID1-ID2 being formed
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does not affect 1-2 neighs (already include effects of new bond)
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may affect 1-3 and 1-4 bonds
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------------------------------------------------------------------------- */
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void FixBondBreak::rebuild_special(int m, tagint id1, tagint id2)
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@ -541,122 +668,6 @@ void FixBondBreak::rebuild_special(int m, tagint id1, tagint id2)
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memcpy(special[m],copy,cn3*sizeof(int));
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}
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/* ----------------------------------------------------------------------
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------------------------------------------------------------------------- */
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void FixBondBreak::break_angles(int m, tagint id1, tagint id2)
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{
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int j,found;
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int num_angle = atom->num_angle[m];
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int *angle_type = atom->angle_type[m];
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tagint *angle_atom1 = atom->angle_atom1[m];
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tagint *angle_atom2 = atom->angle_atom2[m];
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tagint *angle_atom3 = atom->angle_atom3[m];
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int i = 0;
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while (i < num_angle) {
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found = 0;
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if (angle_atom1[i] == id1 && angle_atom2[i] == id2) found = 1;
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else if (angle_atom2[i] == id1 && angle_atom3[i] == id2) found = 1;
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else if (angle_atom1[i] == id2 && angle_atom2[i] == id1) found = 1;
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else if (angle_atom2[i] == id2 && angle_atom3[i] == id1) found = 1;
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if (!found) i++;
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else {
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for (j = i; j < num_angle-1; j++) {
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angle_type[j] = angle_type[j+1];
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angle_atom1[j] = angle_atom1[j+1];
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angle_atom2[j] = angle_atom2[j+1];
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angle_atom3[j] = angle_atom3[j+1];
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}
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num_angle--;
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nangles++;
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}
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}
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atom->num_angle[m] = num_angle;
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}
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/* ----------------------------------------------------------------------
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------------------------------------------------------------------------- */
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void FixBondBreak::break_dihedrals(int m, tagint id1, tagint id2)
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{
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int j,found;
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int num_dihedral = atom->num_dihedral[m];
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int *dihedral_type = atom->dihedral_type[m];
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tagint *dihedral_atom1 = atom->dihedral_atom1[m];
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tagint *dihedral_atom2 = atom->dihedral_atom2[m];
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tagint *dihedral_atom3 = atom->dihedral_atom3[m];
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tagint *dihedral_atom4 = atom->dihedral_atom4[m];
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int i = 0;
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while (i < num_dihedral) {
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found = 0;
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if (dihedral_atom1[i] == id1 && dihedral_atom2[i] == id2) found = 1;
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else if (dihedral_atom2[i] == id1 && dihedral_atom3[i] == id2) found = 1;
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else if (dihedral_atom3[i] == id1 && dihedral_atom4[i] == id2) found = 1;
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else if (dihedral_atom1[i] == id2 && dihedral_atom2[i] == id1) found = 1;
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else if (dihedral_atom2[i] == id2 && dihedral_atom3[i] == id1) found = 1;
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else if (dihedral_atom3[i] == id2 && dihedral_atom4[i] == id1) found = 1;
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if (!found) i++;
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else {
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for (j = i; j < num_dihedral-1; j++) {
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dihedral_type[j] = dihedral_type[j+1];
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dihedral_atom1[j] = dihedral_atom1[j+1];
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dihedral_atom2[j] = dihedral_atom2[j+1];
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dihedral_atom3[j] = dihedral_atom3[j+1];
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dihedral_atom4[j] = dihedral_atom4[j+1];
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}
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num_dihedral--;
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ndihedrals++;
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}
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}
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atom->num_dihedral[m] = num_dihedral;
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}
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/* ----------------------------------------------------------------------
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------------------------------------------------------------------------- */
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void FixBondBreak::break_impropers(int m, tagint id1, tagint id2)
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{
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int j,found;
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int num_improper = atom->num_improper[m];
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int *improper_type = atom->improper_type[m];
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tagint *improper_atom1 = atom->improper_atom1[m];
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tagint *improper_atom2 = atom->improper_atom2[m];
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tagint *improper_atom3 = atom->improper_atom3[m];
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tagint *improper_atom4 = atom->improper_atom4[m];
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int i = 0;
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while (i < num_improper) {
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found = 0;
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if (improper_atom1[i] == id1 && improper_atom2[i] == id2) found = 1;
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else if (improper_atom1[i] == id1 && improper_atom3[i] == id2) found = 1;
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else if (improper_atom1[i] == id1 && improper_atom4[i] == id2) found = 1;
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else if (improper_atom1[i] == id2 && improper_atom2[i] == id1) found = 1;
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else if (improper_atom1[i] == id2 && improper_atom3[i] == id1) found = 1;
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else if (improper_atom1[i] == id2 && improper_atom4[i] == id1) found = 1;
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if (!found) i++;
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else {
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for (j = i; j < num_improper-1; j++) {
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improper_type[j] = improper_type[j+1];
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improper_atom1[j] = improper_atom1[j+1];
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improper_atom2[j] = improper_atom2[j+1];
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improper_atom3[j] = improper_atom3[j+1];
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improper_atom4[j] = improper_atom4[j+1];
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}
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num_improper--;
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nimpropers++;
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}
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}
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atom->num_improper[m] = num_improper;
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}
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/* ----------------------------------------------------------------------
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remove all ID duplicates in copy from Nstart:Nstop-1
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compare to all previous values in copy
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@ -67,10 +67,10 @@ class FixBondBreak : public Fix {
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void check_ghosts();
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void update_topology();
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void rebuild_special(int, tagint, tagint);
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void break_angles(int, tagint, tagint);
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void break_dihedrals(int, tagint, tagint);
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void break_impropers(int, tagint, tagint);
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void rebuild_special(int, tagint, tagint);
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int dedup(int, int, tagint *);
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// DEBUG
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