10. Excited State Optimization

pysisyphus offers excited state (ES) tracking, to follow diadiabatic states along an optimization. ES tracking is enabled by putting track: True in the calc section of your YAML input. In ES optimizations pysisyphus may use additional programs (wfoverlap, Multiwfn, jmol) if requested. Please see the installation instructions for information on how to set them up.

Please consider reading the relevant sections (2 and 3; 4 discusses examples) of the pysisyphus paper. Additionally the user should think about the relevance between equilibrium/non-equilibrium solvation when calculating ES-gradients with implicit solvation. Serveral programs, e.g., Gaussian use equilibrium solvation when doing ES-optimization. It is in the responsibility of the user to add the relevant keywords when using pysisyphus, e.g., EqSolv for Gaussian.

10.1. YAML Example

A bare-bone input for the S1 optimization of the 1H-amino-keto tautomer of cytosin at the TD-DFT/PBE0/def2-SVP level of theory using ORCA is shown below. The full example is found here.

 type: orca
 keywords: pbe0 def2-svp rijcosx def2/J def2-svp/C
 # Calculate 2 ES by TD-DFT, follow the first one
 blocks: "%tddft nroots 2 iroot 1 tda false end"
 charge: 0
 mult: 1
 pal: 4
 mem: 2000
 # ES-tracking related keywords follow from here
 # Enable ES-tracking, this is important.
 track: True
 # Track ES by transition density overlaps
 ovlp_type: tden
 type: redund
 fn: cytosin.xyz

Additional keywords are possible in the calc section. The default values are shown below.

 # Controls calculation of charge-density-differences cubes and rendering
 # Cubes are calcualted by Multiwfn, rendering is handled by jmol.
 # Possible values are: (None, calc, render).
 #  None: No cube calculation/rendering
 #  calc: Cube calculation by Multiwfn.
 #  render: Same as 'calc' and cubes are then rendered by jmol.
 cdds: None
 # Overlap type. Using 'wf' requires the external wfoverlap binary. The remaining
 # options are implemented directly in pysisyphus.
 # Possible values are (wf, tden, nto, nto_org).
 #  wf: Wavefunction overlaps using the external wfoverlap program.
 #  tden: Transition density matrix overlaps.
 #  nto: Natural transition orbital overlaps.
 #  nto_org: Natural transition orbital overlaps as described by García.
 #  top: Transition orbital projection
 ovlp_type: wf
 # Controls the reference cycle that is used in the overlap calculation. The default
 # 'adapt' is recommended.
 # Possible values are (first, previous, adapt)
 #  first: Keep first calculation as reference cycle. Reliable when only minor
 #         geometrical changes are expected.
 #  previous: Use previous cycle as reference.
 #  adapat: Use adaptive algorithm. Please see the pysisyphus paper for a discussion
 #          at the end of section 3.
 ovlp_with: adapt
 # Thresholds controlling the update of the reference cycle.
 # The first number specifies the minimum overlap that must be exceeded, for an update
 # of the reference cycle. Assuming a value of 0.5 (50 %), the reference cycle update
 # is skipped, if the overlaps between the current states and the reference state don't
 # exceed 50 %.
 # The last two numbers define an interval for the ratio between the second highest
 # overlap, and the highest overlap. If the ratio is small, e.g., below 0.3, then both
 # states are sufficiently different, and no reference cycle update is needed. If the ratio
 # is bigger (> 0.6), then the states are quite similar, and an update is currently not
 # advised.
 # Possible values [three positive floats between 0. and 1.]
 adapt_args: [0.5, 0.3, 0.6]
 # Explicitly calculate the AO-overlap matrix in a double molecule calculation. Only
 # supported by Turbomole and Gaussian calculators. If False, the approximate AO
 # overlap matrix is reconstructed from inverting the MO-coefficient matrix.
 # Possible values: (True, False)
 double_mol: False
 # Absolute CI-coefficients below this threshold are ignored in the overlap calculation.
 # Possible values: positive float
 conf_thresh: 0.0001
 # nto/natural transition orbital specific
 # Number of NTOs to consider in the overlap calculation. Only relevant for 'nto'
 # and 'nto_org' ovlp_types.
 # Possible values: positive integer
 use_ntos: 4
 # Dynamically decide on number of NTOs according to their participation ratio. Only
 # relevant for 'nto_org'
 # Possible values: boolean
 pr_nto: False
 # wfoverlap/wavefunction overlaps specific
 # Number of core orbitals to neglect in a wfoverlap calculation. Only relevant
 # for the 'wf' ovlp_type. Must be >= 0.
 # Possible values: positive integer
 ncore: 0
 # tden/transition density matrix specific
 # Controls which set of MO coefficients (at current cycle, or the reference cycle)
 # is used to recover the AO overlap matrix.
 # Possible values: (ref, cur)
 mos_ref: cur
 # Controls whether the set of MO coefficents that was NOT used for recovering the AO
 # overlap matrix is re-normalized, using the recovered AO overlap matrix. If set to
 # True and mos_ref = cur, then the MO coefficients at the reference cycle will be re-
 # normalized, and vice versa.
 # Possible values: (True, False)
 mos_renorm: True

By brief reasoning it would seem that mos_ref: ref and mos_renorm: True are more sensible choices, which is possibly true. Right now the present defaults are kept for legacy reasons, and I'll update them after testing out the alternatives.

Please also see Example - Excited State Tracking for possible visualizations when optimizing ES.

10.2. Optimization of Conical Intersections

pysisyphus implements the projected gradient method using an updated branching plane, as developed by Maede, Ohno and Morokuma. Currently, CI-optimization is not enabled for YAML input. An illustrative example is found in tests/test_conic_intersect.