wfnTools

Tools to parse and combine CP2K's .wfn wavefunction files

Consider:

• a sistem with two fragments, we want to compute the interaction
• the wave function / basis set of the fragmentA, a
• the wave function / basis set of the fragmentB, b
• the geometry of the fragmentA, A
• the geometry of the fragmentB, B
• by convention, A is the framework (or surface, bigger molecule) and B is the adsorbate
• Aa and Aab, means the wfn of fragmentA with the basis set of A (a), or both A and B (ab)
• the non-counterpoise-corrected interaction energy is: E=E(ABab)-E(Aa)-E(Bb)
• the counterpoise-corrected interaction energy is: E=E(ABab)-E(Aab)-E(Bab)
• E=E(Aab)-E(Aa) is the difference in the energy due to a better minimization of the wave function of the fragment A when the basis set of B is added. This value should be negative.
• Different atom types can be specified for the same element: use the convention "type = elementX" with X being a scalar. For example, in an antiferromagnetic calculation one can use Cu1 and Cu2 to specify atoms with opposite spin. It is possible to use any number (e.g., Cu10, Cu3333), but NOT letters or symbols (e.g., Cu_1, CuUP, CuSpin1, ..., are not read correctly)

Installation

git clone https://github.com/danieleongari/cp2k_wfntools.git
cd cp2k_wfntools
pip install .

In the latter, append --user for a local installation.

Examples:

1) Print the formatted wavefunction:

wfntools parse -a fragment.wfn -o outputname

Prints the file outputname.fwfn

2) Combine two wavefunctions:

wfntools combine -a fragmentA.wfn -b fragmentB.wfn -o outputname

Prints the combined outputname.wfn of the two fragments

3) Combine two wavefunctions and geometries:

wfntools combine -a fragmentA.wfn -b fragmentB.wfn -A fragmentA.xyz -B fragmentB.xyz -o outputname

• Prints the combined outputname.wfn of the two fragments.
• Prints the combined outputname_nolabel.xyz of the two fragments, for visualization.
• Prints the combined outputname_label.xyz of the two fragments, to be used for CP2K with "A" and "B" labels for the atoms.
• Prints the combined outputname.kind h the CP2K's &KIND section. Use -bs and -pot options to specify the basis set and the pseudopotential choice Advanced options:
• Use -kindA and -kindB to specify the kind atom to read, and then use -bs read and -pot read to print the read values

TODO: use the -check keyword to check if the number of atoms are consistent in the geometry and wfn files.

4) Prepare the inputs for a Counterpoise Corrected calculation (recycling the wavefunctions)

wfntools cp -ab bothfragments.wfn -AB bothfragments_label.xyz -o outputname

• Prints outputname_A.xyz (no label), outputname_Aab.wfn and outputname_Aab.kind
• Prints outputname_B.xyz (no label), outputname_Bab.wfn and outputname_Bab.kind and, if -sbs option is used:
• Prints outputname_Aa.wfn and outputname_Aa.kind
• Prints outputname_Bb.wfn and outputname_Bb.kind

NB: if the ab.wfn was not computed with labelled geometry, the method does not work, because the atomic &KIND are mixed!

Advanced options:

• -qA and -qB to specify the charge of the fragments (default: 0)
• multA and multB to specify the multiplicity of the fragments (default: 1)
• -kindAB to specify the kind atom to read, and then use -bs read and -pot read to print the read values

Utilities:

5) Insert the fragment B in a pore of fragment A:

wfntools makeAB -A fragment1.xyz -B fragment2.xyz -cell unitcell1.cell -o outputname -nout 10

This is an usefull utility to generate a number of -nout starting configurations of combined geometries, possibly to later adjust in Avogadro. Fragment B is inserted in a random not-overlapping position, conisdering the atoms as rigid spheres with a defined radius (from UFF) possibly scaled by a factor -srad. Prints outputname_AB_1.xyz outputname_B_1.xyz outputname_AB_2.xyz outputname_B_2.xyz ... outputname_AB_nout.xyz outputname_B_nout.xyz ... Note: to avoid infinite loops in case of narrow pores, after ``-maxfail` (default: 100) overlapping insertions, the algorithm is stopped.

6) Label A and B in the AB geometry file:

wfntools labelAB -AB both_fragments.xyz -nA 156 -o outputname

or

wfntools labelAB -AB both_fragments.xyz -nB 3 -o outputname

Print a new outputname_label.xyz file where A and B are labelled according to the number of -nA atoms in A (or specifying -nB). Use the -swapAB option to read first B and then A in the .xyz file.

7) Swap A and B labels in the AB geometry file:

wfntools swaplAB -AB both_fragments.xyz -o outputname

Print a new outputname_label.xyz file where A and B are labels are swapped.

Development

Set up automatic code formatting:

pip install -e .[pre-commit]
pre-commit install