Geometry: Modify

See examples in Modify.mw

Notations

• A::list geometry to modify
• tA::list transformed geometry
• Co::list:=[] conectivity

Procedures

• TransformAtoms(A,R,/t,J,$)::tA transforms atoms as R.A+t,
  • R::{Matrix,numeric,list} transformation matrix or scalar, a list is considered as the matrix diagonal;
  • t::Vector:=<0,0,0> translation, if Tvs are present in A then t is transformed to Cartesians by those Tvs;
  • J::list:=[0] list of atoms to transform.
  Note that R is applied to Tvs whereas t is not.

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• ChangeDihedral(A,lsi,val,/Co,{opt4CA,frags},$)::tA change dihedral or improper, where
  • lsi::[posint,posint,posint,posint] defines the dihedral;
  • val::numeric value of the dihedral to set;
  • Co::Vector:=`if`(nops(A[1])>3,map2(op,4,A),ConnectAtoms(A,op(opt4CA))) connectivity;
  • opt4CA::list:=[] options for generating Co;
  • frags::[list(posint),list(posint)]:=[[],[]] explicitly provide fragments (e.g. if dihedral is locked), set Co=[] to speed up.
  The dihedral is assumed to be defined across the bond whose removal divide the molecules in two diconnected fragments at least. The same connectivity rule applies to impropers.

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• JoinMol(mols,joints,/dets,rcov,{output,printout},$) join molecules, where
  • mols::list(list) list of list of atoms;
  • joints::list([m1,[i1,j1,k1],[i2,j2,k2],d,b]) list of joints, where
    • m1::integer index of molecule to which the current molecule m2 is to be attached (negative values are counted from m2),
    • i1::integer index of atom from molecule m1 to which the attachment is to be made,
    • j1::integer additional atom from molecule m1 to define the connecting dihedral,
    • k1::integer terminal atom from molecule m1 to be removed,
    • i2,j2,k2::integer the same for molecule m2,
    • d::numeric value of the dihedral (j1,i1,i2,j2) to set,
    • b::numeric bond length (i1,i2) to set (if omitted then covalent bond length is used);
  • dets::list({1,-1}):=[1$nops(molecules)] if -1 then the corresponding molecule is inverted;
  • rcov::list(string=numeric):=[] supersedes tb_rcov for overlapping entries;
  • output::string:="a" "a" for transformed atoms, "j" for the formed joints.
  Only tree-like growth is allowed (no loops).

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• AttachPoints(P,b,n,{a34},$)::newpoints attach n=1..3 new points to the first point of P::list(Vector(3)) at the bond length b in such a way as to maximize distance between points in the first coordination shell. Minimum 2 points are required in P. If the coordination shell is complete (e.g. 4 atoms in tetrahedron or 6 atoms in octahedron), the new atom is added at the location of the first point. Here a34::realcons:=0 is the angle between 3rd and 4th points if different from the perfect tetrahedron.

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• AliphaticDihedrals(A,/T,{atoms14,printout,printxyz,overwrite},$)::list([posint$4]) determine all aliphatic dihedrals, where
  • T::list:=["CC2H2"] which atoms types are allowed for the two central atoms of the dihedral, see ClassifyAtoms command;
  • atoms14::list:=["C"] which elements are allowed for the two terminal atoms of the dihedral;
  • printxyz::string:="" aliphatic chains will be saved to this file.
  If multiple definitions of the same dihedral are found an error is raised.
• Alkane(n,{CC:=1.527,CCC:=113.46,CH:=1.099,HCH:=105.98,CCH:=111.55},$)::Atoms generate linear alkane of n carbons. Default values of geometrical parameters correspond to CAM-B3LYPp2p.
• SortAlkane(A,i0,/convention,Co,{printout},$)::permutation sort alkane atoms using A[i0] as the root hydrogen. Three conventions are supported convention::{"line","loop","zigzag"}:="loop", see examples.