Move writeTPL to be a method for Gaussian

@Decompose/initialize.m

@@ -3,7 +3,8 @@ function initialize(obj)
 % Calculation on the full molecule
 fullList = [obj.fragList{1}(:);obj.fragList{2}(:)];
 keywords = ['td ', obj.keywords];
-tempdir = writeTPL(obj,obj.fullIn.filename,fullList,keywords);
+name = obj.fullIn.filename;
+tempdir = obj.fullIn.writeTPL(name,fullList,keywords);
 obj.full = Gaussian(tempdir,obj.fullIn.filename,struct);
 obj.full.run();
 
@@ -19,7 +20,7 @@ function initialize(obj)
    obj.rlinks(2) * direction/norm(direction);
 for ifrag = 1:2
    name = [obj.fullIn.filename,'-',int2str(ifrag)];
-   tempdir = writeTPL(obj,name,obj.fragList{ifrag},obj.keywords,rLink{ifrag});
+   tempdir = obj.full.writeTPL(name,obj.fragList{ifrag},obj.keywords,rLink{ifrag});
    obj.frags{ifrag} =  Gaussian(tempdir,name,struct);
    obj.frags{ifrag}.run();
 end
@@ -44,38 +45,4 @@ function initialize(obj)
    ofull = obj.full.orb(:,:);
    obj.overlap{ifrag} = ofrag' * Stemp * ofull;
 end
-end
-
-
-function tempDir = writeTPL(obj,jobname,atoms,keywords,rLink)
-newline = char(10);
-syms{1} = 'H'; syms{6} = 'C'; syms{7} = 'N'; syms{8} = 'O';
-syms{15} = 'P'; syms{16} = 'S';
-tpl_file = [jobname,'.tpl'];
-tempDir = [tempname('C:\G09W\Scratch'), '\'];
-mkdir(tempDir);
-fid1 = fopen([tempDir,tpl_file],'w');
-
-fwrite(fid1,['%chk=temp.chk',newline]);
-fwrite(fid1,['# ',keywords,' NoSymmetry iop(3/33=4) pop=regular',newline]);
-fwrite(fid1,newline);
-fwrite(fid1,jobname);
-fwrite(fid1,newline);
-fwrite(fid1,newline);
-fwrite(fid1,'0 1');
-fwrite(fid1,newline);
-for iatom = atoms(:)'
-   fwrite(fid1,[' ',syms{obj.fullIn.Z(iatom)},' ']);
-   for ic = 1:3
-      fwrite(fid1,[num2str(obj.fullIn.rcart(ic,iatom)),' ']);
-   end
-   fwrite(fid1,newline);
-end
-if (nargin > 4)
-   fwrite(fid1,[' H ',num2str(rLink(:)'),newline]);
-end
-fwrite(fid1,newline);
-
-fclose(fid1);
-end
-
+end

@Gaussian/writeTPL.m

@@ -0,0 +1,35 @@
+function tempDir = writeTPL(obj,jobname,atoms,keywords,rLink)
+    if isempty(atoms)
+        atoms = 1:length(obj.Z);
+    end
+    newline = char(10);
+    syms{1} = 'H'; syms{6} = 'C'; syms{7} = 'N'; syms{8} = 'O';
+    syms{15} = 'P'; syms{16} = 'S';
+    tpl_file = [jobname,'.tpl'];
+    tempDir = [tempname('C:\G09W\Scratch'), '\'];
+    mkdir(tempDir);
+    fid1 = fopen([tempDir,tpl_file],'w');
+
+    fwrite(fid1,['%chk=temp.chk',newline]);
+    fwrite(fid1,['# ',keywords,' NoSymmetry iop(3/33=4) pop=regular',newline]);
+    fwrite(fid1,newline);
+    fwrite(fid1,jobname);
+    fwrite(fid1,newline);
+    fwrite(fid1,newline);
+    fwrite(fid1,sprintf('%d %d', obj.charge, obj.multiplicity));
+    fwrite(fid1,newline);
+    for iatom = atoms(:)'
+       fwrite(fid1,[' ',syms{obj.Z(iatom)},' ']);
+       for ic = 1:3
+          fwrite(fid1,[num2str(obj.rcart(ic,iatom)),' ']);
+       end
+       fwrite(fid1,newline);
+    end
+    if (nargin > 4)
+       fwrite(fid1,[' H ',num2str(rLink(:)'),newline]);
+    end
+    fwrite(fid1,newline);
+
+    fclose(fid1);
+end
+