complete region handling refactor
This commit is contained in:
Axel Kohlmeyer
144
src/variable.cpp
144
src/variable.cpp
@ -3043,18 +3043,18 @@ double Variable::eval_tree(Tree *tree, int i)
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}
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if (tree->type == GMASK) {
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if (atom->mask[i] & tree->ivalue1) return 1.0;
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if (atom->mask[i] & tree->ivalue) return 1.0;
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else return 0.0;
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}
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if (tree->type == RMASK) {
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if (domain->regions[tree->ivalue1]->match(atom->x[i][0], atom->x[i][1], atom->x[i][2])) return 1.0;
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if (tree->region->match(atom->x[i][0], atom->x[i][1], atom->x[i][2])) return 1.0;
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else return 0.0;
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}
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if (tree->type == GRMASK) {
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if ((atom->mask[i] & tree->ivalue1) &&
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(domain->regions[tree->ivalue2]->match(atom->x[i][0], atom->x[i][1], atom->x[i][2]))) return 1.0;
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if ((atom->mask[i] & tree->ivalue) &&
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(tree->region->match(atom->x[i][0], atom->x[i][1], atom->x[i][2]))) return 1.0;
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else return 0.0;
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}
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@ -3664,32 +3664,31 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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int igroup = group->find(args[0]);
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if (igroup == -1) {
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std::string mesg = "Group ID '";
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mesg += args[0];
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mesg += "' in variable formula does not exist";
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print_var_error(FLERR,mesg,ivar);
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const auto errmesg = fmt::format("Group {} in variable formula does not exist", args[0]);
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print_var_error(FLERR, errmesg, ivar);
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}
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// match word to group function
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double value = 0.0;
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const auto group_errmesg = fmt::format("Invalid {}() function in variable formula", word);
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if (strcmp(word,"count") == 0) {
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if (narg == 1) value = group->count(igroup);
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else if (narg == 2)
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value = group->count(igroup,region_function(args[1],ivar));
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"mass") == 0) {
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if (narg == 1) value = group->mass(igroup);
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else if (narg == 2) value = group->mass(igroup,region_function(args[1],ivar));
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"charge") == 0) {
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if (narg == 1) value = group->charge(igroup);
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else if (narg == 2)
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value = group->charge(igroup,region_function(args[1],ivar));
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"xcm") == 0) {
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atom->check_mass(FLERR);
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@ -3698,14 +3697,14 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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double masstotal = group->mass(igroup);
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group->xcm(igroup,masstotal,xcm);
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} else if (narg == 3) {
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int iregion = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->xcm(igroup,masstotal,xcm,iregion);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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auto region = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,region);
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group->xcm(igroup,masstotal,xcm,region);
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} else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"x") == 0) value = xcm[0];
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else if (strcmp(args[1],"y") == 0) value = xcm[1];
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else if (strcmp(args[1],"z") == 0) value = xcm[2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"vcm") == 0) {
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atom->check_mass(FLERR);
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@ -3714,38 +3713,38 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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double masstotal = group->mass(igroup);
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group->vcm(igroup,masstotal,vcm);
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} else if (narg == 3) {
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int iregion = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->vcm(igroup,masstotal,vcm,iregion);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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auto region = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,region);
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group->vcm(igroup,masstotal,vcm,region);
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} else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"x") == 0) value = vcm[0];
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else if (strcmp(args[1],"y") == 0) value = vcm[1];
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else if (strcmp(args[1],"z") == 0) value = vcm[2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"fcm") == 0) {
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double fcm[3];
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if (narg == 2) group->fcm(igroup,fcm);
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else if (narg == 3) group->fcm(igroup,fcm,region_function(args[2],ivar));
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"x") == 0) value = fcm[0];
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else if (strcmp(args[1],"y") == 0) value = fcm[1];
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else if (strcmp(args[1],"z") == 0) value = fcm[2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"bound") == 0) {
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double minmax[6];
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if (narg == 2) group->bounds(igroup,minmax);
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else if (narg == 3)
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group->bounds(igroup,minmax,region_function(args[2],ivar));
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"xmin") == 0) value = minmax[0];
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else if (strcmp(args[1],"xmax") == 0) value = minmax[1];
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else if (strcmp(args[1],"ymin") == 0) value = minmax[2];
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else if (strcmp(args[1],"ymax") == 0) value = minmax[3];
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else if (strcmp(args[1],"zmin") == 0) value = minmax[4];
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else if (strcmp(args[1],"zmax") == 0) value = minmax[5];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"gyration") == 0) {
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atom->check_mass(FLERR);
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@ -3755,16 +3754,16 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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group->xcm(igroup,masstotal,xcm);
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value = group->gyration(igroup,masstotal,xcm);
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} else if (narg == 2) {
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int iregion = region_function(args[1],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->xcm(igroup,masstotal,xcm,iregion);
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value = group->gyration(igroup,masstotal,xcm,iregion);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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auto region = region_function(args[1],ivar);
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double masstotal = group->mass(igroup,region);
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group->xcm(igroup,masstotal,xcm,region);
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value = group->gyration(igroup,masstotal,xcm,region);
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} else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"ke") == 0) {
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if (narg == 1) value = group->ke(igroup);
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else if (narg == 2) value = group->ke(igroup,region_function(args[1],ivar));
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"angmom") == 0) {
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atom->check_mass(FLERR);
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@ -3774,15 +3773,15 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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group->xcm(igroup,masstotal,xcm);
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group->angmom(igroup,xcm,lmom);
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} else if (narg == 3) {
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int iregion = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->xcm(igroup,masstotal,xcm,iregion);
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group->angmom(igroup,xcm,lmom,iregion);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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auto region = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,region);
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group->xcm(igroup,masstotal,xcm,region);
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group->angmom(igroup,xcm,lmom,region);
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} else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"x") == 0) value = lmom[0];
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else if (strcmp(args[1],"y") == 0) value = lmom[1];
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else if (strcmp(args[1],"z") == 0) value = lmom[2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"torque") == 0) {
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atom->check_mass(FLERR);
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@ -3792,15 +3791,15 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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group->xcm(igroup,masstotal,xcm);
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group->torque(igroup,xcm,tq);
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} else if (narg == 3) {
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int iregion = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->xcm(igroup,masstotal,xcm,iregion);
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group->torque(igroup,xcm,tq,iregion);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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auto region = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,region);
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group->xcm(igroup,masstotal,xcm,region);
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group->torque(igroup,xcm,tq,region);
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} else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"x") == 0) value = tq[0];
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else if (strcmp(args[1],"y") == 0) value = tq[1];
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else if (strcmp(args[1],"z") == 0) value = tq[2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"inertia") == 0) {
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atom->check_mass(FLERR);
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@ -3810,18 +3809,18 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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group->xcm(igroup,masstotal,xcm);
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group->inertia(igroup,xcm,inertia);
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} else if (narg == 3) {
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int iregion = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->xcm(igroup,masstotal,xcm,iregion);
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group->inertia(igroup,xcm,inertia,iregion);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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auto region = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,region);
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group->xcm(igroup,masstotal,xcm,region);
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group->inertia(igroup,xcm,inertia,region);
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} else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"xx") == 0) value = inertia[0][0];
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else if (strcmp(args[1],"yy") == 0) value = inertia[1][1];
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else if (strcmp(args[1],"zz") == 0) value = inertia[2][2];
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else if (strcmp(args[1],"xy") == 0) value = inertia[0][1];
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else if (strcmp(args[1],"yz") == 0) value = inertia[1][2];
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else if (strcmp(args[1],"xz") == 0) value = inertia[0][2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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} else if (strcmp(word,"omega") == 0) {
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atom->check_mass(FLERR);
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@ -3833,17 +3832,17 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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group->inertia(igroup,xcm,inertia);
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group->omega(angmom,inertia,omega);
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} else if (narg == 3) {
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int iregion = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,iregion);
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group->xcm(igroup,masstotal,xcm,iregion);
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group->angmom(igroup,xcm,angmom,iregion);
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group->inertia(igroup,xcm,inertia,iregion);
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auto region = region_function(args[2],ivar);
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double masstotal = group->mass(igroup,region);
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group->xcm(igroup,masstotal,xcm,region);
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group->angmom(igroup,xcm,angmom,region);
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group->inertia(igroup,xcm,inertia,region);
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group->omega(angmom,inertia,omega);
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} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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} else print_var_error(FLERR,group_errmesg,ivar);
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if (strcmp(args[1],"x") == 0) value = omega[0];
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else if (strcmp(args[1],"y") == 0) value = omega[1];
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else if (strcmp(args[1],"z") == 0) value = omega[2];
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else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
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else print_var_error(FLERR,group_errmesg,ivar);
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}
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// delete stored args
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@ -3864,21 +3863,16 @@ int Variable::group_function(char *word, char *contents, Tree **tree, Tree **tre
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/* ---------------------------------------------------------------------- */
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int Variable::region_function(char *id, int ivar)
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Region *Variable::region_function(char *id, int ivar)
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{
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int iregion = domain->find_region(id);
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if (iregion == -1) {
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std::string mesg = "Region ID '";
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mesg += id;
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mesg += "' in variable formula does not exist";
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print_var_error(FLERR,mesg,ivar);
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}
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auto region = domain->get_region_by_id(id);
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if (!region)
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print_var_error(FLERR, fmt::format("Region {} in variable formula does not exist", id), ivar);
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// init region in case sub-regions have been deleted
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domain->regions[iregion]->init();
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return iregion;
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region->init();
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return region;
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}
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/* ----------------------------------------------------------------------
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@ -4149,7 +4143,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
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auto newtree = new Tree();
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newtree->type = GMASK;
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newtree->ivalue1 = group->bitmask[igroup];
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newtree->ivalue = group->bitmask[igroup];
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treestack[ntreestack++] = newtree;
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} else if (strcmp(word,"rmask") == 0) {
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@ -4158,12 +4152,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
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if (narg != 1)
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print_var_error(FLERR,"Invalid special function in variable formula",ivar);
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int iregion = region_function(args[0],ivar);
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domain->regions[iregion]->prematch();
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auto region = region_function(args[0],ivar);
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region->prematch();
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auto newtree = new Tree();
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newtree->type = RMASK;
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newtree->ivalue1 = iregion;
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newtree->region = region;
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treestack[ntreestack++] = newtree;
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} else if (strcmp(word,"grmask") == 0) {
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@ -4175,13 +4169,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
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int igroup = group->find(args[0]);
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if (igroup == -1)
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print_var_error(FLERR,"Group ID in variable formula does not exist",ivar);
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int iregion = region_function(args[1],ivar);
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domain->regions[iregion]->prematch();
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auto region = region_function(args[1],ivar);
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region->prematch();
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auto newtree = new Tree();
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newtree->type = GRMASK;
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newtree->ivalue1 = group->bitmask[igroup];
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newtree->ivalue2 = iregion;
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newtree->ivalue = group->bitmask[igroup];
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newtree->region = region;
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treestack[ntreestack++] = newtree;
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// special function for file-style or atomfile-style variables
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