Published May 3, 2022
| Version 0.7.6
Software
Open
eljost/pysisyphus: ONIOM optimization, AFIR improvements, New coordinate systems
Description
Deprecations, Breaking Changes
- Updated handling of coordinate rebuilding. Previously, only the invalid coordinates (bends close to being linear, torsions with (nearly) collinear atoms) were dropped and no new coordinates were determined. Now a new set of coordinates is determined for the given coordinates and used in conjunction with the remaining valid coordinates.
- Support for nix flakes, provided by @sheepforce
- AFIR-Hessian
scripts/orca2cdd.py
for simple CDD-cube generation with Multiwfn from ORCA.cis
and.gbw
files- New coordinate systems:
hredund
andhdlc
that also contain the atomic Cartesian coordinates in addition to the regular set of internals. Alsocartesian
andmwcartesian
which will eventually supersedecart
. The former coordinate systems implement theCoordSys
protocol and should be more future-proof, e.g., with them Cartesian constraints using Lagrange multipliers could be implemented. See the commit message of c2a901b22828df20dbef1acc33fd1a78d0be7e61 for a more thorough discussion. - Flexible optimizer
LayerOpt
(type: layers
in YAML input), tailored to optimize multilayer-systems, e.g., in ONIOM calculations - Started to work on supporting rate calculations in pysisyphus, including simple tunnel corrections. See
get_rates_for_geoms()
andrender_rx_rates()
indrivers/rates.py
. - Extrapolation (before and after) a given set of geometries (see
pysistrj --help | grep extrapol
) --kcal
flag inpysisplot
to output energies inkcal mol⁻¹
instead ofkJ mol⁻¹
. Implemeting this was probably a bad idea and it may be removed again in future versions, because I really don't like cal :)- Support for
.mol2
inputs. Currently, the order"@<TRIPOS>MOLECULE
and@<TRIPOS>ATOM
is expected.
- Fixed energy/forces-mixing in EnergyMin calculator (see 10.1063/5.0021923)
climb_lanczos
is now supported by all subclasses ofChainOfStates
, e.g., NEB. Previously it was restricted toGrowingString
. By enabling it, the lowest curvature mode will be determined using the Lanczos algorithm on all climbing images. The lowest curvature will be used instead of the regular tangent.- Improved plot appearance in
pysisplot --cosforces
- Enabled
cartesian
coordinate system for COS optimizations - Take CG steps if possible, while growing a string. Previously only SD steps were taken while growing.
- Fixed many Sphinx-warnings while generating the documentation
- Convergence thresholds/targets are now reported in optimizations and IRC integrations. Fixes #196.
- Added two AFIR examples:
examples/opt/23_orca_afir
andexamples/opt/24_xtb_three_frag_afir
- Documented AFIR calculator
Files
eljost/pysisyphus-0.7.6.zip
Files
(11.9 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/eljost/pysisyphus/tree/0.7.6 (URL)