Loading src/USER-REACTION/fix_bond_react.cpp +17 −35 Original line number Diff line number Diff line Loading @@ -41,6 +41,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "error.h" #include "input.h" #include "variable.h" #include "fmt/format.h" #include <algorithm> Loading Loading @@ -608,23 +609,16 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group void FixBondReact::post_constructor() { int len; // let's add the limit_tags per-atom property fix int len = strlen("bond_react_props_internal") + 1; id_fix2 = new char[len]; strcpy(id_fix2,"bond_react_props_internal"); std::string cmd = std::string("bond_react_props_internal"); id_fix2 = new char[cmd.size()+1]; strcpy(id_fix2,cmd.c_str()); int ifix = modify->find_fix(id_fix2); if (ifix == -1) { char **newarg = new char*[7]; newarg[0] = (char *) "bond_react_props_internal"; newarg[1] = (char *) "all"; // group ID is ignored newarg[2] = (char *) "property/atom"; newarg[3] = (char *) "i_limit_tags"; newarg[4] = (char *) "i_react_tags"; newarg[5] = (char *) "ghost"; newarg[6] = (char *) "yes"; modify->add_fix(7,newarg); delete [] newarg; cmd += std::string(" all property/atom i_limit_tags i_react_tags ghost yes"); modify->add_fix(cmd); } // create master_group if not already existing Loading @@ -645,22 +639,15 @@ void FixBondReact::post_constructor() // create exclude_group if not already existing, or use as parent group if static if (igroup == -1 || group->dynamic[igroup] == 0) { // create stabilization per-atom property len = strlen("bond_react_stabilization_internal") + 1; id_fix3 = new char[len]; strcpy(id_fix3,"bond_react_stabilization_internal"); cmd = std::string("bond_react_stabilization_internal"); id_fix3 = new char[cmd.size()+1]; strcpy(id_fix3,cmd.c_str()); ifix = modify->find_fix(id_fix3); if (ifix == -1) { char **newarg = new char*[6]; 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); cmd += std::string(" all property/atom i_statted_tags ghost yes"); modify->add_fix(cmd); fix3 = modify->fix[modify->nfix-1]; delete [] newarg; } len = strlen("statted_tags") + 1; Loading Loading @@ -737,21 +724,16 @@ void FixBondReact::post_constructor() // let's create a new nve/limit fix to limit newly reacted atoms len = strlen("bond_react_MASTER_nve_limit") + 1; id_fix1 = new char[len]; strcpy(id_fix1,"bond_react_MASTER_nve_limit"); cmd = std::string("bond_react_MASTER_nve_limit"); id_fix1 = new char[cmd.size()+1]; strcpy(id_fix1,cmd.c_str()); ifix = modify->find_fix(id_fix1); if (ifix == -1) { char **newarg = new char*[4]; newarg[0] = id_fix1; newarg[1] = master_group; newarg[2] = (char *) "nve/limit"; newarg[3] = nve_limit_xmax; modify->add_fix(4,newarg); cmd += fmt::format(" {} nve/limit {}",master_group,nve_limit_xmax); modify->add_fix(cmd); fix1 = modify->fix[modify->nfix-1]; delete [] newarg; } } } Loading Loading
src/USER-REACTION/fix_bond_react.cpp +17 −35 Original line number Diff line number Diff line Loading @@ -41,6 +41,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "error.h" #include "input.h" #include "variable.h" #include "fmt/format.h" #include <algorithm> Loading Loading @@ -608,23 +609,16 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group void FixBondReact::post_constructor() { int len; // let's add the limit_tags per-atom property fix int len = strlen("bond_react_props_internal") + 1; id_fix2 = new char[len]; strcpy(id_fix2,"bond_react_props_internal"); std::string cmd = std::string("bond_react_props_internal"); id_fix2 = new char[cmd.size()+1]; strcpy(id_fix2,cmd.c_str()); int ifix = modify->find_fix(id_fix2); if (ifix == -1) { char **newarg = new char*[7]; newarg[0] = (char *) "bond_react_props_internal"; newarg[1] = (char *) "all"; // group ID is ignored newarg[2] = (char *) "property/atom"; newarg[3] = (char *) "i_limit_tags"; newarg[4] = (char *) "i_react_tags"; newarg[5] = (char *) "ghost"; newarg[6] = (char *) "yes"; modify->add_fix(7,newarg); delete [] newarg; cmd += std::string(" all property/atom i_limit_tags i_react_tags ghost yes"); modify->add_fix(cmd); } // create master_group if not already existing Loading @@ -645,22 +639,15 @@ void FixBondReact::post_constructor() // create exclude_group if not already existing, or use as parent group if static if (igroup == -1 || group->dynamic[igroup] == 0) { // create stabilization per-atom property len = strlen("bond_react_stabilization_internal") + 1; id_fix3 = new char[len]; strcpy(id_fix3,"bond_react_stabilization_internal"); cmd = std::string("bond_react_stabilization_internal"); id_fix3 = new char[cmd.size()+1]; strcpy(id_fix3,cmd.c_str()); ifix = modify->find_fix(id_fix3); if (ifix == -1) { char **newarg = new char*[6]; 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); cmd += std::string(" all property/atom i_statted_tags ghost yes"); modify->add_fix(cmd); fix3 = modify->fix[modify->nfix-1]; delete [] newarg; } len = strlen("statted_tags") + 1; Loading Loading @@ -737,21 +724,16 @@ void FixBondReact::post_constructor() // let's create a new nve/limit fix to limit newly reacted atoms len = strlen("bond_react_MASTER_nve_limit") + 1; id_fix1 = new char[len]; strcpy(id_fix1,"bond_react_MASTER_nve_limit"); cmd = std::string("bond_react_MASTER_nve_limit"); id_fix1 = new char[cmd.size()+1]; strcpy(id_fix1,cmd.c_str()); ifix = modify->find_fix(id_fix1); if (ifix == -1) { char **newarg = new char*[4]; newarg[0] = id_fix1; newarg[1] = master_group; newarg[2] = (char *) "nve/limit"; newarg[3] = nve_limit_xmax; modify->add_fix(4,newarg); cmd += fmt::format(" {} nve/limit {}",master_group,nve_limit_xmax); modify->add_fix(cmd); fix1 = modify->fix[modify->nfix-1]; delete [] newarg; } } } Loading
