Loading doc/src/fix_bond_react.txt +12 −12 Original line number Diff line number Diff line Loading @@ -146,18 +146,18 @@ A bonding atom pair will be identified if several conditions are met. First, a pair of atoms I,J within the specified react-group-ID of type itype and jtype must be separated by a distance between {Rmin} and {Rmax}. It is possible that multiple bonding atom pairs are identified: if the bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as its bonding partner; otherwise, the farthest potential partner is chosen. Then, if both an atom I and atom J have each other as their nearest bonding partners, these two atoms are identified as the bonding atom pair of the reaction site. Once this unique bonding atom pair is identified for each reaction, there could two or more reactions that involve a given atom on the same timestep. If this is the case, only one such reaction is permitted to occur. This reaction is chosen randomly from all potential reactions. This capability allows e.g. for different reaction pathways to proceed from identical reaction sites with user-specified probabilities. identified: if the bonding atoms in the pre-reacted template are 1-2 neighbors, i.e. directly bonded, the farthest bonding atom partner is set as its bonding partner; otherwise, the closest potential partner is chosen. Then, if both an atom I and atom J have each other as their bonding partners, these two atoms are identified as the bonding atom pair of the reaction site. Once this unique bonding atom pair is identified for each reaction, there could two or more reactions that involve a given atom on the same timestep. If this is the case, only one such reaction is permitted to occur. This reaction is chosen randomly from all potential reactions. This capability allows e.g. for different reaction pathways to proceed from identical reaction sites with user-specified probabilities. The pre-reacted molecule template is specified by a molecule command. This molecule template file contains a sample reaction site and its Loading src/USER-MISC/fix_bond_react.cpp +21 −10 Original line number Diff line number Diff line Loading @@ -1022,6 +1022,7 @@ void FixBondReact::close_partner() rsq = delx*delx + dely*dely + delz*delz; if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue; if (closeneigh[rxnID] == 0) { if (rsq > distsq[i1][0]) { partner[i1] = tag[i2]; distsq[i1][0] = rsq; Loading @@ -1030,6 +1031,16 @@ void FixBondReact::close_partner() partner[i2] = tag[i1]; distsq[i2][0] = rsq; } } else { if (rsq < distsq[i1][1]) { partner[i1] = tag[i2]; distsq[i1][1] = rsq; } if (rsq < distsq[i2][1]) { partner[i2] = tag[i1]; distsq[i2][1] = rsq; } } } } } Loading Loading @@ -3027,7 +3038,7 @@ int FixBondReact::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) { buf[m++] = ubuf(partner[i]).d; if (closeneigh[rxnID] < 0) if (closeneigh[rxnID] != 0) buf[m++] = distsq[i][1]; else buf[m++] = distsq[i][0]; Loading @@ -3046,7 +3057,7 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) if (commflag != 1) { for (i = 0; i < n; i++) { j = list[i]; if (closeneigh[rxnID] < 0) if (closeneigh[rxnID] != 0) if (buf[m+1] < distsq[j][1]) { partner[j] = (tagint) ubuf(buf[m++]).i; distsq[j][1] = buf[m++]; Loading Loading
doc/src/fix_bond_react.txt +12 −12 Original line number Diff line number Diff line Loading @@ -146,18 +146,18 @@ A bonding atom pair will be identified if several conditions are met. First, a pair of atoms I,J within the specified react-group-ID of type itype and jtype must be separated by a distance between {Rmin} and {Rmax}. It is possible that multiple bonding atom pairs are identified: if the bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as its bonding partner; otherwise, the farthest potential partner is chosen. Then, if both an atom I and atom J have each other as their nearest bonding partners, these two atoms are identified as the bonding atom pair of the reaction site. Once this unique bonding atom pair is identified for each reaction, there could two or more reactions that involve a given atom on the same timestep. If this is the case, only one such reaction is permitted to occur. This reaction is chosen randomly from all potential reactions. This capability allows e.g. for different reaction pathways to proceed from identical reaction sites with user-specified probabilities. identified: if the bonding atoms in the pre-reacted template are 1-2 neighbors, i.e. directly bonded, the farthest bonding atom partner is set as its bonding partner; otherwise, the closest potential partner is chosen. Then, if both an atom I and atom J have each other as their bonding partners, these two atoms are identified as the bonding atom pair of the reaction site. Once this unique bonding atom pair is identified for each reaction, there could two or more reactions that involve a given atom on the same timestep. If this is the case, only one such reaction is permitted to occur. This reaction is chosen randomly from all potential reactions. This capability allows e.g. for different reaction pathways to proceed from identical reaction sites with user-specified probabilities. The pre-reacted molecule template is specified by a molecule command. This molecule template file contains a sample reaction site and its Loading
src/USER-MISC/fix_bond_react.cpp +21 −10 Original line number Diff line number Diff line Loading @@ -1022,6 +1022,7 @@ void FixBondReact::close_partner() rsq = delx*delx + dely*dely + delz*delz; if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue; if (closeneigh[rxnID] == 0) { if (rsq > distsq[i1][0]) { partner[i1] = tag[i2]; distsq[i1][0] = rsq; Loading @@ -1030,6 +1031,16 @@ void FixBondReact::close_partner() partner[i2] = tag[i1]; distsq[i2][0] = rsq; } } else { if (rsq < distsq[i1][1]) { partner[i1] = tag[i2]; distsq[i1][1] = rsq; } if (rsq < distsq[i2][1]) { partner[i2] = tag[i1]; distsq[i2][1] = rsq; } } } } } Loading Loading @@ -3027,7 +3038,7 @@ int FixBondReact::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) { buf[m++] = ubuf(partner[i]).d; if (closeneigh[rxnID] < 0) if (closeneigh[rxnID] != 0) buf[m++] = distsq[i][1]; else buf[m++] = distsq[i][0]; Loading @@ -3046,7 +3057,7 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) if (commflag != 1) { for (i = 0; i < n; i++) { j = list[i]; if (closeneigh[rxnID] < 0) if (closeneigh[rxnID] != 0) if (buf[m+1] < distsq[j][1]) { partner[j] = (tagint) ubuf(buf[m++]).i; distsq[j][1] = buf[m++]; Loading
