DMA, Local force constants, Marcus dimension#265

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eljost wants to merge 398 commits intomasterfrom dev

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Commits on Oct 2, 2024

mod: implemented get_all_energies for PySCF and added a test
Johannes Steinmetzer
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mod: implemented get_all_energies for Gaussian16 and added a test

eljost
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add: get_all_energies() for DFTB+ calculator
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add: Solve min-cost-problem for better ES overlaps
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mod: keep integration grid in dedicated dataclass
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add: simple MolGrid construction from Wavefunction
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add: GDMA (DMA w/ numerical integration)
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add: Grids similar to the original GDMA grids

eljost
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mod: update dma.py to use pysisyphus-addons
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add: wavefunction attribute Geometry
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fix: add missing control paths
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add: Gaussian16.get_wavefunction()

eljost
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mod: remove densities-key check in parse_orca_densities
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add: functions to construct relaxed ES density from Turbomole calculations
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add: calculation of relaxed ES density for ORCA and Turbomole
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added reference and deleted two unused imports
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fix: add missing control_path directory
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add: Gaussian.get_relaxed_density() for ESs

eljost
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mod: enable wavefunction_dump by default for turbomole
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add: Geometry.td_1tdm attribute holding transition-densities
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add: CI-coeff parsing from Gaussian log files

eljost
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add: mpmath-based higher precision Cart2Sph coefficients
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add: numba-accelerated integrals
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fix: add warning when thermoanalysis package is missing
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fix: dont't crash in pysis merge when OBabel FF opt fails
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add: radial grid as described in Stone's GDMA paper
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mod: made dma.run_dma() more robust
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add: Orient input generator from DMA calculations
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fix: Turbomle gradient files w/ multiple cycles
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mod: also report imaginary wavenums in pysisthermo
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mod: lift restriction to spherical bfs for FCHK wavefuncs
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add: parsing of singlet-triplet excitations from Gaussian
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add: singlet-triplet SOC as done in PySOC
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mod: (hopefully) greatly improved TablePrinter
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mod: enable use of Boettger factors for perturbative SOCs
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mod: added some comments & references for SOC
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fix: eval_density() after update to numba 0.59
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mod: update GHA and requirements to Python 3.12
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add: plotting of CT numbers and spectra
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add: ORCA wrapper for spectrum_ctnum in 'scripts/orca_ctnums.py'
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fix: skip wavefunction sanity-check w/o Shells
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mod: allow kwargs when creating PySCFShells from Pyscf-mol
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fix: use abs of change to determine JacobiSweeps convergence
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add: edmiston-ruedenberg diabatization using Jacobi-sweeps
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mod: updated comments and integer dtypes in Shells.as_arrays()
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mod: updates to Jacobi-Sweep driver
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mod: report basis function type when printing Wavefunction
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add: docstrings & typing for diabatization.py
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add: derivation of expressions for edmiston-ruedenberg jac.sweeps
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fix: finally a working ER-localizer w/ Jacobi Sweeps
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fix: MO-coefficient-reordereding w/ shells.ordering="pysis"
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fix: update pysisyphus-addons module path for GDMA
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add: detachment and attachment densities in the MO basis
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add: tests for excited state density matrix builds
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fix: report negative of maximum detachment density eigenvalue
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fix: PySCF basis function ordering was wrong
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add: parsing of Turbomole coord files
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fix: scipy import was missing
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fix: PySCF-permutation matrices
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mod: update actions in nix CI
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add: ability to delete bondsn in orca_ctnums.py

eljost
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mod: factored out Gaussian16.parse_all_energies

eljost
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fix: add missing io.coord module
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add: soc-driver script
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add: ability to dump DiabatizationResult to .npz
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fix: singlet-triplet optimizations are now possible for ORCA
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add: ConicalIntersection calculator results are also dumped
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mod: improved reporting when cutting clusters from PDB/PSF files
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fix: typo in docstring
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fix: assert in ct-number calculation was too restrictive
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fix: orca_ctnums.py also looks for *.log now

eljost
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add: get_box_grid
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fix: ensure that ES energy is set when root is set for ORCA
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mod: started to entangle OverlapCalculator.track_root()
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add: ChainOfStates.propagate() to propagate root info along COS
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mod: improve reporting in COS optimization
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mod: also store MO-energies in WF objects
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black
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mod: set/get chkfiles for OpenMolcas
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mod: set MO ens when creating wavefunction from PySCF kernel
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add: convert Shells to ris-Shells for TDDFT-ris
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fix: parsing of ORCA energies
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mod: make Composite-calculator support more complex expressions
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add: helper functions that returns boosting composite calcs
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add/fix: updated PyXTB to use TBLite project
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fix: plotting of MD runs
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mod: deleted unused/wrong? constant
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mod: formatted & commented EGO calculator
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mod: support grid kwargs in spectra-broadening
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mod: loosened threshold in trans&rot vector construction
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add: AU2FS conversion constant
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mod: use dataclass in dynamics driver instead of namedtuple
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add: serpentine potential & test
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del: ORCA.parse_orca_gbw and ORCA.ORCA.parse_cis
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mod: enabled tden-overlaps for unrestricted calculations
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fix: majke f-string backwards compatible
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add: creation of MOCoeffs objects from parsed FCHK data
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add: ES tracking w/ Gaussian and unrestricted calculations
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fix: cyclical import; moved MOCoeffs to root dir
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fix: parse_turbo_mos now also handles alpha/beta files
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mod: do lazy PySCF import in Composite calculator
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mod: make PySCF imports lazy for wrapping calculators
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add: enable unrestricted Overlaps for Turbomole
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add: Tracking of unrestricted ES-calcs w/ PySCF
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fix: sometimes iroot wasn't inserted properly
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add: test for ORCA singlet-triplet ES opt w/ tracking
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add: singlet-triplet ES w/ PySCF & test for it
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add: missing keys cist_a/trip_a for Turbomole for S->T ES
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fix: energy parsing w/ PySCF
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fix: shape bug when resorting MO energies
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fix: updated baseline image after change to annotate
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fix: re-enable wf-overlap ES-tracking
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add: re-enable NTO-ES-tracking for unrestricted calculations
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fix: respect pal choice in PySCF
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mod: don't delete forces in Xtb energy calculations
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mod: refactor fit_rigid/procrustes calls out of Optimizer.optimize()
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mod: renamed Optimizer.optimize() to Optimizer.get_step()
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mod: Warning TBLite calc, as it uses all threads by default
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mod: calculate energy and derivatives outside of Optimizers.get_step
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fix: various failing tests after Optimizer refactoring
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mod: report frame in title when animating COS opt w/ AnaPot calc
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add: Geometry.calc_energy to explicitly calculate energy
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mod: massive refactoring of COS classes
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fix: safe fixes from ruff
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del: removed MicroOptimizer and associated code
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fix: AdaptiveNeb & failing tests related to COS-refactor
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mod: disentangled COS forces calculation
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fix: typo that prevented creation of calculator2
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fix: added missing f-prefixes in some f-strings
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mod: 3-image MEISC selection algorithm from 10.1063/5.0021923
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add: test for MEISC image selection
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mod: report calculation times in COS opt WF propagation
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add: atom picking in modes3.py and quitting w/ ESC or q
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add: basic crest wrapper
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add: reading & writing of TREXIO files to/from wavefunction
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add: wf export to trexio
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fix: mol2 parser didn't stay in a line when parsing atoms
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add: determine ECP electrons from ORCA json
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mod: fix coordinate width in XYZ renderer
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add: allow level of theory selection in crest wrapper
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add: rotation matrix for rotation around given vector
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add: support for different cart_coords in Geometry.get_subgeom()
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mod: update logging of EnergyMin calculator
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mod: also store number of ECP electrons in trexio
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mod: updated default wavelength bounds for spectrum plotting
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add: helper for ensemble spectra
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improved plot appearance for cubic displacement
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fix: cubic displacement from TS was faulty
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add: taylor_closure for cubic displacement
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add computed_zorder arg for 3d plots of AnaPots
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update logo
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formatting changes
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fix: spectrum_ctnum test was failing
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mod: allow atomic numbers in XYZ strings
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updated examples/complex/07_diels_alder
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add: ability to select number of geometries in pysistrj --spline
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add: ursina is now listed as optional dependency in setup.cfg
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fix: augment_bond returned wrong geometry in run_opt driver
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fix: added some missing attributes to GrowingNT.py
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fix: max linesearch was broken in TSHessianOptimizer
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add: allow initializing GSM with more than 2 images
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make run.run_tsopt_from_cos easier to use
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fix: DLC constraints didn't really work
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mod: consistent internals when typed_prims are given
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mod: consinder user-defined bonds at earlier stage
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mod: updated limits in FourWellAnaPot plots
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mod: improved thermochemistry report
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fix: skip chkfile propagation in run_calcs when atoms differ
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imporved rxrates report
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fix: FakseASE was incompatible w/ ase >= 3.23.0
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add: script to generate a Hessian file for a single atom
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fix: updated tests for XTB 6.7.0
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add: enabled caspt2 block for OpenMolcas
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mod: formatting in thermoanalysis & c´oordinate printing
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fix: enable standard orientation in Hess-projector construction
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fix: hessian_projection was still faulty
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fix: various tests
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fix: davidson seesm to fail w/ std. orient in Hessian projector
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mod: IRC summaries; rx. coordinate is now correct
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fix: NEb test was lacking images

eljost
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add: numba_multipole backend
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mod: drop joblib/caching in shells
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mod: use numba multipole backend by default
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fix: failed tests
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fix: flake8 fixes; removed unused code

eljost
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fix: passed exc_ens instead of all_ens in orca_ctnums.py
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mod: 'kind' field for DiabatizationResult
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mod: refactor out recovering of S mat from C mat
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add: ability to sort DiabatizationResult and improved report
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add: new driver for running calculations
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add: basic hash of calcs in run_calculations
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add: support for stable calcs in ORCA.run_calculation()
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add: Geometry.dump_trj() for easy dumping of trajectories
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add: charge is now dumped in orca2pysis.py Hessian converter
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mod: improve column widths in tableprinter
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add: 1d sparse Numerov method as in 10.1039/C6CP06698D
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add: calculation of anharmonic partition functions
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add: support for periodic potentials in 1d Numerov
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mod: reworked relaxed scans
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add deuterium mass to Numerov test
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fix: failing import when thermoanalysis is not installed
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Commits on Oct 3, 2024

fix: faulty timing.render() duration function
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Commits on Oct 18, 2024

fix: test for periodic numerov
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Commits on Oct 21, 2024

add: rotor moment of inertias
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Commits on Oct 22, 2024

add: rotor examples for numerov
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Commits on Oct 25, 2024

add: calculation of hindered rotor partition functions
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Commits on Oct 28, 2024

add: enabled hindered_rotor calculation via YAML input
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fix: failing test after update in run_calculations
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fix: add missing file
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Commits on Oct 29, 2024

fix: re-creatign a symlink to a json results file failed
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fix: spectrum_ct_num failed when graphiv was available
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fix: test_ts_hessian_update
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fix: add left/right_images to growing string test
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fix: added more files to .gitgnore
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fix: rotation code was wrong
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re-enabled alignment in hindered_rotor
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add reporting of single-point calc. timings in hindered_rotor
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add report after hindered_rotor calculation
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Commits on Oct 30, 2024

add: manually halt hindered_rotor calc by touching 'converged_hr'
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mod: updated convergence check in hindered_rotor
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Commits on Nov 4, 2024

fix: typed_prims contain normal use normal int indices again
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mod/fix: always work on a copy of opt_kwargs in run_opt
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fix: fragmentation for hr with > 2 initial fragments
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Commits on Nov 5, 2024

add: 'pysistrj --calcs' to plot results from plain calculations
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fix: (hopefully) allow plotting of old IRC HDF5 files
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fix: test fixes after xtb update to 6.7.1
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mod: filter out eigenvectors w/ vanishing gradient
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mod: exclude integrals from flake8
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mod: run pytest w/ --color=yes in github actions
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Commits on Nov 6, 2024

fix: further round of test fixes
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fix: don't add hydrogen_bonds that are already bonds
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Commits on Nov 7, 2024

add: RotorInfo class for more control about rotor atoms
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mod: include trans-rot-projector in inverse of Wilson-B mat
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mod: keep constraints when rebuilding coordinates
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fix: enabling project_tr was a bad idea
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Commits on Nov 8, 2024

fix: remove type hint from optional addon
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fix: use capitalized atoms when converting to ASE
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Commits on Nov 12, 2024

add: "LINEAR" shortcut for creating linear bend & its complement
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add: new diabatization driver
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Commits on Nov 14, 2024

mod: refactored diabatization
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fix: make diabatization.driver importable w/o pysisyphus_addons
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Commits on Nov 15, 2024

mod: switch to HDF5 file for diabatization
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Commits on Nov 16, 2024

mod: dump more datasets to HDF5 file
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Commits on Nov 19, 2024

mod: hdf5 data models now require a dtype
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mod: also write diabatization kinds to HDF5
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Commits on Nov 22, 2024

add: also consider spin-densities in chimerabatch
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add: method to io.cube.Cube to createa new cube from ref. cube and vol_data
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Commits on Nov 25, 2024

fix: added missing h5_fn in dia driver test
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Commits on Nov 27, 2024

mod: report fragments in orca_ctnums.py
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fix: mention files explicitly in .gitignore
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