Loading doc/src/fix_bond_react.txt +18 −16 Original line number Diff line number Diff line Loading @@ -24,11 +24,11 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization {group-ID} = user-assigned ID for all non-reacting atoms (group created internally) {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l react-group-ID = only atoms in this group are available for the reaction :l react-group-ID = only atoms in this group are considered for the reaction :l Nevery = attempt reaction every this many steps :l Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l Loading @@ -51,7 +51,7 @@ react = mandatory argument indicating new reaction specification :l molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre molecule mol1 pre_reacted_rxn1.txt molecule mol2 post_reacted_rxn1.txt Loading @@ -60,7 +60,7 @@ molecule mol4 post_reacted_rxn2.txt fix 5 all bond/react stabilization yes nvt_grp .03 & react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre [Description:] Loading Loading @@ -104,20 +104,22 @@ during the simulation. The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, fix bond/react command creates a "dynamic group"_group.html of this name that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is converted into a dynamic group, whose atoms are limited to those belonging to the original static group. In either case, this dynamic group-ID should then be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. By specifying an existing group, you may thermostat non-reacting parts of your system separately. as 'all'. If the group-ID is previously unused, the fix bond/react command creates a "dynamic group"_group.html that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is used as the parent group of new, internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group contains only non-reacting atoms at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this group, or a subset. should also be specified as this static group, or a subset. NOTE: If the group-ID is previously unused, the internally created group applies to all atoms in the system, i.e. you should generally Loading src/USER-MISC/fix_bond_react.cpp +19 −19 Original line number Diff line number Diff line Loading @@ -78,6 +78,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : fix1 = NULL; fix2 = NULL; fix3 = NULL; if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " "too few arguments"); Loading Loading @@ -433,11 +434,9 @@ FixBondReact::~FixBondReact() if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1); delete [] id_fix1; if (custom_exclude_flag == 0) { if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3); delete [] id_fix3; } } if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2); delete [] id_fix2; Loading Loading @@ -512,14 +511,14 @@ void FixBondReact::post_constructor() ifix = modify->find_fix(id_fix3); if (ifix == -1) { char **newarg = new char*[6]; newarg[0] = (char *) "bond_react_stabilization_internal"; newarg[0] = (char *) id_fix3; newarg[1] = (char *) "all"; // group ID is ignored newarg[2] = (char *) "property/atom"; newarg[3] = (char *) "i_statted_tags"; newarg[4] = (char *) "ghost"; newarg[5] = (char *) "yes"; modify->add_fix(6,newarg); fix2 = modify->fix[modify->nfix-1]; fix3 = modify->fix[modify->nfix-1]; delete [] newarg; } Loading @@ -527,17 +526,17 @@ void FixBondReact::post_constructor() statted_id = new char[len]; strcpy(statted_id,"statted_tags"); // if static group exists, duplicate it, use duplicate as parent group // original will be converted into dynamic per-atom property group if (igroup != -1) { char **newarg; newarg = new char*[3]; newarg[0] = (char *) "exclude_PARENT_group"; newarg[1] = (char *) "union"; newarg[2] = exclude_group; group->assign(3,newarg); delete [] newarg; } // if static group exists, use as parent group // also, rename dynamic exclude_group by appending '_REACT' char *exclude_PARENT_group; int n = strlen(exclude_group) + 1; exclude_PARENT_group = new char[n]; strcpy(exclude_PARENT_group,exclude_group); n += strlen("_REACT"); delete [] exclude_group; exclude_group = new char[n]; strcpy(exclude_group,exclude_PARENT_group); strcat(exclude_group,"_REACT"); group->find_or_create(exclude_group); char **newarg; Loading @@ -545,16 +544,17 @@ void FixBondReact::post_constructor() newarg[0] = exclude_group; newarg[1] = (char *) "dynamic"; if (igroup == -1) newarg[2] = (char *) "all"; else newarg[2] = (char *) "exclude_PARENT_group"; else newarg[2] = (char *) exclude_PARENT_group; newarg[3] = (char *) "property"; newarg[4] = (char *) "statted_tags"; group->assign(5,newarg); delete [] newarg; delete [] exclude_PARENT_group; // on to statted_tags (system-wide thermostat) // intialize per-atom statted_flags to 1 // (only if not already initialized by restart) if (fix2->restart_reset != 1) { if (fix3->restart_reset != 1) { int flag; int index = atom->find_custom("statted_tags",flag); int *i_statted_tags = atom->ivector[index]; Loading src/USER-MISC/fix_bond_react.h +3 −3 Original line number Diff line number Diff line Loading @@ -78,9 +78,9 @@ class FixBondReact : public Fix { class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template Fix *fix1; // nve/limit used to relax reaction sites Fix *fix2; // properties/atom used to indicate 1) indicate relaxing atoms // 2) system-wide thermostat // 3) to which 'react' atom belongs Fix *fix2; // properties/atom used to indicate 1) relaxing atoms // 2) to which 'react' atom belongs Fix *fix3; // property/atom used for system-wide thermostat class RanMars **random; class NeighList *list; Loading Loading
doc/src/fix_bond_react.txt +18 −16 Original line number Diff line number Diff line Loading @@ -24,11 +24,11 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization {group-ID} = user-assigned ID for all non-reacting atoms (group created internally) {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l react-group-ID = only atoms in this group are available for the reaction :l react-group-ID = only atoms in this group are considered for the reaction :l Nevery = attempt reaction every this many steps :l Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l Loading @@ -51,7 +51,7 @@ react = mandatory argument indicating new reaction specification :l molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre molecule mol1 pre_reacted_rxn1.txt molecule mol2 post_reacted_rxn1.txt Loading @@ -60,7 +60,7 @@ molecule mol4 post_reacted_rxn2.txt fix 5 all bond/react stabilization yes nvt_grp .03 & react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre [Description:] Loading Loading @@ -104,20 +104,22 @@ during the simulation. The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, fix bond/react command creates a "dynamic group"_group.html of this name that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is converted into a dynamic group, whose atoms are limited to those belonging to the original static group. In either case, this dynamic group-ID should then be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. By specifying an existing group, you may thermostat non-reacting parts of your system separately. as 'all'. If the group-ID is previously unused, the fix bond/react command creates a "dynamic group"_group.html that is initialized to include all atoms. If the group-ID is that of an existing static group, the group is used as the parent group of new, internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group contains only non-reacting atoms at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above. The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this group, or a subset. should also be specified as this static group, or a subset. NOTE: If the group-ID is previously unused, the internally created group applies to all atoms in the system, i.e. you should generally Loading
src/USER-MISC/fix_bond_react.cpp +19 −19 Original line number Diff line number Diff line Loading @@ -78,6 +78,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : fix1 = NULL; fix2 = NULL; fix3 = NULL; if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " "too few arguments"); Loading Loading @@ -433,11 +434,9 @@ FixBondReact::~FixBondReact() if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1); delete [] id_fix1; if (custom_exclude_flag == 0) { if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3); delete [] id_fix3; } } if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2); delete [] id_fix2; Loading Loading @@ -512,14 +511,14 @@ void FixBondReact::post_constructor() ifix = modify->find_fix(id_fix3); if (ifix == -1) { char **newarg = new char*[6]; newarg[0] = (char *) "bond_react_stabilization_internal"; newarg[0] = (char *) id_fix3; newarg[1] = (char *) "all"; // group ID is ignored newarg[2] = (char *) "property/atom"; newarg[3] = (char *) "i_statted_tags"; newarg[4] = (char *) "ghost"; newarg[5] = (char *) "yes"; modify->add_fix(6,newarg); fix2 = modify->fix[modify->nfix-1]; fix3 = modify->fix[modify->nfix-1]; delete [] newarg; } Loading @@ -527,17 +526,17 @@ void FixBondReact::post_constructor() statted_id = new char[len]; strcpy(statted_id,"statted_tags"); // if static group exists, duplicate it, use duplicate as parent group // original will be converted into dynamic per-atom property group if (igroup != -1) { char **newarg; newarg = new char*[3]; newarg[0] = (char *) "exclude_PARENT_group"; newarg[1] = (char *) "union"; newarg[2] = exclude_group; group->assign(3,newarg); delete [] newarg; } // if static group exists, use as parent group // also, rename dynamic exclude_group by appending '_REACT' char *exclude_PARENT_group; int n = strlen(exclude_group) + 1; exclude_PARENT_group = new char[n]; strcpy(exclude_PARENT_group,exclude_group); n += strlen("_REACT"); delete [] exclude_group; exclude_group = new char[n]; strcpy(exclude_group,exclude_PARENT_group); strcat(exclude_group,"_REACT"); group->find_or_create(exclude_group); char **newarg; Loading @@ -545,16 +544,17 @@ void FixBondReact::post_constructor() newarg[0] = exclude_group; newarg[1] = (char *) "dynamic"; if (igroup == -1) newarg[2] = (char *) "all"; else newarg[2] = (char *) "exclude_PARENT_group"; else newarg[2] = (char *) exclude_PARENT_group; newarg[3] = (char *) "property"; newarg[4] = (char *) "statted_tags"; group->assign(5,newarg); delete [] newarg; delete [] exclude_PARENT_group; // on to statted_tags (system-wide thermostat) // intialize per-atom statted_flags to 1 // (only if not already initialized by restart) if (fix2->restart_reset != 1) { if (fix3->restart_reset != 1) { int flag; int index = atom->find_custom("statted_tags",flag); int *i_statted_tags = atom->ivector[index]; Loading
src/USER-MISC/fix_bond_react.h +3 −3 Original line number Diff line number Diff line Loading @@ -78,9 +78,9 @@ class FixBondReact : public Fix { class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template Fix *fix1; // nve/limit used to relax reaction sites Fix *fix2; // properties/atom used to indicate 1) indicate relaxing atoms // 2) system-wide thermostat // 3) to which 'react' atom belongs Fix *fix2; // properties/atom used to indicate 1) relaxing atoms // 2) to which 'react' atom belongs Fix *fix3; // property/atom used for system-wide thermostat class RanMars **random; class NeighList *list; Loading
