Added mirror mode.

AIM plots for mirror mode are still buggy.

irc_mirror_mode_replace_atoms.m

@@ -0,0 +1,13 @@
+function ms0 = irc_mirror_mode_replace_atoms(ms0,replacelist)
+
+    for aind=1:numel(replacelist.A)
+        buf = [ ms0.x(replacelist.A(aind)) ms0.y(replacelist.A(aind)) ms0.z(replacelist.A(aind))];
+        ms0.x(replacelist.A(aind)) = ms0.x(replacelist.B(aind));
+        ms0.y(replacelist.A(aind)) = ms0.y(replacelist.B(aind));
+        ms0.z(replacelist.A(aind)) = ms0.z(replacelist.B(aind));
+        ms0.x(replacelist.B(aind)) = buf(1);
+        ms0.y(replacelist.B(aind)) = buf(2);
+        ms0.z(replacelist.B(aind)) = buf(3);
+    end
+
+end

irc_save_gjf_file.m

@@ -0,0 +1,9 @@
+function irc_save_gjf_file(ms0, odir, gjf_odir, fullgtemplname)
+    order=1:ms0.atomnum;
+    if exist([odir filesep gjf_odir filesep ms0.desc '.gjf'],'file')~=2 %create input Gaussian file
+        if exist([odir filesep gjf_odir],'dir')~=7
+            mkdir(odir,gjf_odir);
+        end
+        savemolgs([odir filesep gjf_odir],ms0,3,order,fullgtemplname); %Gaussian with XYZ
+    end
+end