pysisyphus - pysisyphus 1.0.0 release

Pysisyphus 1.0.0

Since the first commit on Wednesday July 5 2017 until today, pysisyphus came a long way. This release is a significant milestone for pysisyphus and adds many new features in the form of complex workflows that are seamlessly automated, numerous other additions, improvements, as well as various bugfixes.

The most notable features are outlined below: Pysisyphus now understands wavefunctions from various single-reference methods, can calculate different molecular integrals over Gaussian-type-orbitals and can calculate many useful molecular quantities in ground and excited states.

By shifting the focus on parsing the wavefunctions directly, many new exciting features become possible. Instead of wasting substantial time on implementing flags to carry out specific property calculations for each calculator and writing the associated parsing code, I put a focus on parsing the selected set of common wavefunction files. With the wavefunction and accompanying molecular integrals a great deal of interesting quantities can be calculated, e.g., overlap matrices, (transition) multipole moments, Coulomb tensors etc.

Nontheless, all good things come to an end. As an eager scientist working under the WissZeitVG your number one priority is not to congest the university and of course I complied. As I'm no more in acadima, I no longer have access to commerical/closed-source codes like Gaussian or Turbmole nor to the vast number of interesting papers, published by the scientifc community over the years.

As I'm not paid anymore, to work on pysisyphus I wont be able to keep up the support for it, as I did previously. So please consider this to be the final release of pysisyphus. Maybe, if I find some spare time I can fix an issue or add a new feature from a big backlog, that exists on my machine.

If you have a comment or a story to share, let me know at info@pysisyphus.org.

Release Highlights

Updated nix expressions for pysisyphus and associated projects from @sheepforce
Support for Wavefunctions and Molecular Integrals with focus on single reference methods (see wavefunction subdir)
- Parsing of many different wavefunction formats: .molden, .fchk, .aomix, ORCA .json/.bson/.molden, XTB .molden, TREXIO, Molcas HDF5 files
- Support for Cartesian and Spherical GTO basis functions
- Population and bond order analysis: Mulliken, IAO (10.1021/ct400687b), Mayer Bond Orders
- MO-localiatzion
  - Foster-Boys
  - Pipek-Mezey
  - Cholesky
- Molecular integration grids using Becke weighting
- Molecular integral backends with multiple backends
  - Python and Numba backends from sympleints, libcint
  - Overlap integrals
  - Kinetic integrals
  - Multipole integrals (Dipole, Quadrupole, Spherical Multipoles up to Quadrupole)
- Calculation of cube files via pysisyphus-addons
  - Detachment-attachment densities to visualized excited states (10.1021/j100039a012)
  - (Spin) Densities
(Grid) Distributed multipole analysis (10.1021/ct050190+)
- Uses code-generated integrals from sympleints; currently up to quadrupoles are implemented
- Uses code-generated multipole-shift operators
- See tests in tests/test_dma
Seamless property based Diabatization using unrelaxed densities from a single TDA/TD-DFT calculation to generate diabatic states and expectation values, e.g., diabatic couplings
- Boys diabatization using (transition) dipole moments
- Edmiston-Ruedenberg diabatization using Coulomb integrals via pysisyphus-addons (10.1021/jp101235a)
  - Implemented using fast density fitting integrals generated via sympleints
  - Cost-function maximization is carried out using gradients and Hessian matrices from automatic differentiation with JAX
  - Support for its $\varepsilon$ formulation that takes solvent parameters and temperature into account (see (10.1063/1.4766463)
- Simple interface is currently restricted to ORCA 5.0.4
- See tests in tests/test_diabatization and the documentation
1d Numerov's method for wavefunction calculation (10.1039/C6CP06698D, 10.1016/j.cplett.2019.04.016)
- Sparse formulation
- Support for periodic potentials
- See tests in tests/test_numerov
Automated calculation of hindered rotor partition functions using Gaussian Process Regression (see hindered_rotor subdir)
- Simple molecular fragmentation
- Automatic calculation of rotor moments of inertia (10.1063/1.473958)
- Automatic calculation of periodic potentials
- Nuclear wavefunctions and associated energy levels from periodic Numerov's method
- See tests in tests/test_hindered_rotor and the documentation TBD
Ab-initio calculation of Marcus dimension (10.1039/D3SC01402A)
- See tests in tests/test_marcusdim
- See documentation in TBD

New Features

ES-overlaps for unrestricted calculations for TDA/TD-DFT like methods
Perturbative spin-orbit-couplings for TDDFT calculations using libcint 1-electron-spin-orbit integrals Support for pretabulated effective charges or Boettger factors (10.1021/jacsau.2c00659)
Geodesic interpolation via interface to geodesic-interpolate (10.1063/1.5090303, #310 from @cvsik)
Updated Geometry API
- Programmatic access (attributes/methods) to excited state related quantities and wavefunctions
- New attributes: Geometry.wavefunction, Geometry.allenergies, Geometry.td1tdms
- New method: Geometry.calcrelaxeddensity(root)
- Attributes and methods mentioned above are currently implemented for Gaussian16, ORCA 5.04, Turbomole 7.8 and PySCF calculators
Local force constants and decomposition of normal modes (10.1016/j.cplett.2020.137337). There is no simple to use interface yet. See tests at tests/test_local_force_constants
Calculation of Boltzmann weights from given energy levels and temperatures
Parallel COS calculations w/ dask from YAML input (#258, @Marclie)
Affine transformations in 3d
Calculation of charge-transfer numbers
RMSD external potential (See 10.1002/jcc.20110 and examples/opt/25uracildimerrmsdrestraint for an example)
Finite Difference Hessian
Switch from PyXTB to TBLite
3-image MEISC selection algorithm from 10.1063/5.0021923
Basic crest wrapper for conformer generation
Calculation of anharmonic partition functions. See tests at tests/test_partfuncs.
New optimizer: Cubic Newton (arxiv.org/abs/2112.02089)
Transition orbital projection approach for excited state tracking. See 10.1063/5.0081207. Use via ovlp_type: top.
Dedicated MoCoeffs class in calculators for dealing with MO-Coefficients in an efficient manner

Improvements

Refactored Optimizer code
- Energies and its derivatives are now calculated separately from Optimizer.get_step()
- Optimizer.run() main loop is now a generator
Refactored COS code
- More methods are now pure and can't initiate unintended calculations
- Lanczos-iterations are now enabled for NEBs to converge the tangent to the true transition vector
- Added approximate Hessian generation from COS as described in 10.1021/ct400319w, 123dd57f)
- ChainOfStates.propagate() to propagate root info along COS images, e.g., when doing ES-COS calculations
- Allow initializing GSM with more than 2 images
If available, the charge is also saved to HDF5 Hessians
Geometry.jmol() now accepts console commands
More robust Hessian projection when imposing Eckart conditions by enforcing standard orientation
Reworked run.run_calculations()
- More robust passing of chkfiles
- Support for calculations on different molecules
- Correct dumping of calculated Hessians
- Estimation of remaining calculation time
- Skipping of previously finished calculations for seamless restarting of failed calculations
hessianproj.gethessian_projector() now also supports a gradient vector in the construction of the projector
pysistrj
- Add --sample command to sample N geoms from given geometries
- Add --spline to select evenly distributed number of geometries from given geometries
Refactored initializer in LineSearch class
dynamics.wigner.getwignersampler() now accepts a seed for reproducibility
Calculation of excited state overlaps now also involves solving a min-cost-problem for improved state-pair assignment
Entangle OverlapCalculator.track_root() to make using the code easier
Improved thermochemistry report
Normal modes with imaginary eigenvalues are now reported in pysisthermo
Serpentine potential & test
Improved reaction rates report
LINEAR shortcut for creating linear bend & its complement when providing typed_prims input
Generation of interfragment bonds was reworked. Now much less interfragment bonds are created
Ability to converge to higher-order saddle points, e.g., of 2nd order
Converged quantities in geometry optimizations are now indicated by an *
Lanczos method implementation gives more output, uses a stricter approach (57b05493)
OpenMolcas calculator is now much more flexible and now supports CASPT2 gradients
Composite-calculator support more complex expressions (767434e)
Reworked relaxed scans
- Optimized geometries are now correctly dumped while scan is running
- Add visualization via pysisplot --scan

Fixes

yaml constructor for angstrom was faulty
since scipy 1.11 (-1)!! is 0 and not -1 anymore ...
Add warning when thermoanalysis package is missing and fixed failing import
Dont't crash in pysis merge when OBabel FF opt fails
Cubic displacement from TS when initializing IRCs was faulty
ursina is now listed as optional dependency in setup.cfg
augmentbond returned wrong geometry in runopt driver
max linesearch was broken in TSHessianOptimizer
DLC constraints didn't really work
FakseASE was incompatible w/ ase >= 3.23.0
IRC Rx. coordinate was inaccurate
Filter out eigenvectors w/ vanishing gradient in RFOptimizer
Don't add hydrogen_bonds that are already bonds. Sped up their detection.
g-factor for link atoms in ONIOM calculations is now chosen based on the atom pair identities
MOPAC calculator method was always PM7 and user input was ignored
Interpolator classes now return interpolated geometries with the original coord_type (c1b14bf7)

Deprecations & Deletions

Removed MicroOptimizer and associated code
Finally removed deprecated/* and tests_staging/* directories

- Python
Published by eljost 11 months ago

Bugfixes & Improvements

More robust handling of internal coordinate rebuilding

- Python
Published by eljost about 4 years ago

pysisyphus - Bugifx release

Addition

Internal coordinates of model layer can now be rebuilt on-the-fly in LayerOpt optimizations.

Bugfixes & Improvements

AFIR-HDF5 dump is now closed between calculations, allowing pysisplot --afir while the calculation is still running
Loading initial Hessians with coordiante type cart was faulty.

- Python
Published by eljost about 4 years ago

pysisyphus - ONIOM optimization, AFIR improvements, New coordinate systems

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.

Addition

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 and hdlc that also contain the atomic Cartesian coordinates in addition to the regular set of internals. Also cartesian and mwcartesian which will eventually supersede cart. The former coordinate systems implement the CoordSys 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() and render_rx_rates() indrivers/rates.py.
Extrapolation (before and after) a given set of geometries (see pysistrj --help | grep extrapol)
--kcal flag in pysisplot to output energies in kcal mol⁻¹ instead of kJ 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.

Bugfixes & Improvements

Fixed energy/forces-mixing in EnergyMin calculator (see 10.1063/5.0021923)
climb_lanczos is now supported by all subclasses of ChainOfStates, e.g., NEB. Previously it was restricted to GrowingString. 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.

Miscellaneous

Added two AFIR examples: examples/opt/23_orca_afir and examples/opt/24_xtb_three_frag_afir
Documented AFIR calculator

- Python
Published by eljost about 4 years ago

pysisyphus - Updates for nix-CI

Small post release containing several fixes for the nix-CI running on gitlab. This release includes no functional changes.

- Python
Published by eljost over 4 years ago

pysisyphus - Bugfixes, improved thermochemistry, Nix improvements, pKa calculation

Deprecations and Breaking Changes

Entries for Gaussian-related utilities (formchk, unfchk, rwfdump) in .pysisyphusrc must be updated. Please see the documentation. For the above mentioned commands the trailing _cmd has been dropped (fchk_cmd=[path to fchk] is now only fchk=[path to fchk]). Alternatively, if the binaries are available on $PATH they should be found automatically by pysisyphus and their addition to .pysisyphusrc is not required. Whether the binaries are found is easily checked by executing pysisrc on the command line.

Addition

Ability to dump calculations results to JSON (provide dump: true to calculator in YAML input)
Remote calculator to execute calculations on external machines using Fabric
pysisreplace entry point to substitute atoms in existing geometries with new residues, e.g, OEt, OMe or Ph. Idea from 10.1002/wcms.1510
pysisrc entry point to check available software and to generate a proper .pysisyphusrc
An additional block can be given in barrier block for calculation of solvated energies (see examples/complex/08_trispericyclic)
scripts/aciddrain.py for batch calculation of pKa-values using luigi and LFER fitting (linear free energy relationship)
EnergyMin calculator to optimize to allow, e.g., different multiplicities along a COS, see 10.1063/5.0021923
Methods to center and randomly rotate geometries (Geometry.center() and Geometry.rotate())
Formed/broken bonds are now reported along an IRC integration

Bugfixes & Improvements

TDEN overlaps are much faster
Fixed several deprecation warnings
Update Github action workflows
Improved integration with thermoanalysis and fixed calculation of wavenumbers of normal modes
Amound of requested memory is now checked and adjusted if too much was requested
endopt can now be requested without previous IRC run
Gathered more global configuration values in config.py, e.g., default temperature and pressure, default sub-directory to store external QC program logs
Disabled long running tests in CI to save time in the test suite
@sheepforce updated nix-related files
Parsing of TURBOMOLE Hessians for bigger systems was faulty (fixes #173)

Miscellaneous

QC-logfiles etc. are now dumped to qm_calcs subdirectory
Christmas themed logo for next christmas season ;)
Tighted default overachieve_factor to 5
Switched from setup.py to setup.cfg and pyproject.toml

- Python
Published by eljost over 4 years ago

pysisyphus - First beta of 0.7.5

Deprecations and Breaking Changes

Entries for Gaussian-related utilities (formchk, unfchk, rwfdump) in .pysisyphusrc must be updated. Please see the documentation. For the above mentioned commands the trailing _cmd has been dropped (fchk_cmd=[path to fchk] is now only fchk=[path to fchk]). Alternatively, if the binaries are available on $PATH they should be found automatically by pysisyphus and their addition to .pysisyphusrc is not required. Whether the binaries are found is easily checked by executing pysisrc on the command line.

- Python
Published by eljost over 4 years ago

pysisyphus - Conical intersection optimization, Normal Mode visualization, Improved Bends and Torsions

Addition

Calculator for Conical intersection optimization (type: conical), implementing the updated branching plane algorithm. See examples/opt/17_orca_conical_intersection.
Simple ursina-based script that can read and visualize pysisyphus HDF5 Hessians to animate imaginary modes (scripts/modes3d.py)
Dipole moment calculation in OpenMM calculator
New internal coordinates: BondedFragment and DummyTorsion; suitable for optimization of water interaction energies, as needed for parametrizing CGENFF.
Alternative implementations of bends and torsions, using atan2 instead of acos, that are numerically more stable. 2nd derivatives of Torsions are now calculated using the code-generated derivatives, starting from the atan2 expression.
Support for exit sign to cleanly shutdown calculations
perf driver to benchmark calculation-speedups with varying pal
Implemented Bofills TS-Hessian update hessian_update: ts_bofill
Support for ALPB solvent in XTB calculator
Frozen atoms can now be excluded from the internal coordinate setup algorithm (please see the documentation)

Bugfixes

pr_nto argument to OverlapCalculator was ignored
Don't try to call thermoanalysis, when it is not installed
IRC classes now respect out_dir argument
Requesting 2nd derivative of Rotations w.r.t. Cartesian coordinates led to a crash

Miscellaneous

Version string is now dumped to RUN.yaml
Improved Growing-Newton-Trajectory class
Improved printing of internal coordinates in pysistrj --internals
Relaxed scans are more robust
Speeded up some internal coordinates by avoiding calls to numpy methods
MO-coefficients can now be set in .gbw files
Initial dimer calculation can now be read from a HDF5 Hessian imaginary mode
Energy change is now reported in the first column of an optimization
Switched from plain down-scaling to shifted-Newton-step when proposed RFO-step is too big
Interpolation in internal coordinates is now more robust

- Python
Published by eljost over 4 years ago

pysisyphus - 0.7.4 first pre-release

- Python
Published by eljost over 4 years ago

pysisyphus - Bugfixes, Refactoring for more consistency

Addition

Added ability to retry/rerun crashed calculations (retry_calc: 1). For now only supported by ORCA.
Support for fragments: total in endopt: section. This allows optimizing the system as whole as well as optimizing the separate fragments
Single geometries from multi-geometry input files can now be accessed via pythons index-notation: fn: multi_geoms.trj[1] would only load the second geometry from multi_geoms.trj
Very basic support for preconditioning of position and rotation. precontr: in YAML input; runs before preopt. Still very slow for sizable systems.
pr_nto keyword support for OverlapCalculator to dynamically select the number of NTO pairs in overlap calculations

Bugfixes

Hessian was unnecessarily recalculated in TS optimizations after COS runs
Fixed Eckart projection to remove translation and rotation. Adapted from geomeTRIC
Eckart projection in calculation of initial displacement from TS in IRC runs was never carried out
Made parsing & storing of MO and CI coefficients in store_overlap_data() much more consistent

Miscellaneous

coord_type in optimizations and wavenumber of imaginary mode in IRC runs is now reported
Added separate ORCA5 calculator (type: orca5) so ORCA4 and ORCA5 can be setup in parallel
Refactored geometry loading via get_geoms and read_geoms in trj.py to support arbitrary kwargs
All preopt/tsopt/endopt sections can now contain a geom section, e.g., to control the coord_type
Requested and actual energy lowering is now reported in IRC runs
Wavenumber/frequencies are now also reported when thermoanalysis is printed

- Python
Published by eljost almost 5 years ago

pysisyphus - Bugfixes & expanded documentation

Bugfixes

Added missing files for worked example of trispericyclic reaction in examples/complex/08_trispericyclic/
Initial displacement from TS using 3rd derivatives of the energy (displ: energy_cubic) should now be more reliable. The resulting HDF5 dump can be reused via the displ_third_h5: [path to hdf5] option (see the IRC documentation)

Miscellaneous

Improved calculator documentation for ORCA, XTB, Turbomole and Calculators in general
Added Citation.cff
Updated Turbomole tests and added Turbomole Growing String examples using the native pysisyphus calculator as well as the QCEngine wrapper

- Python
Published by eljost almost 5 years ago

pysisyphus - Translation-Rotation internal coordinates, OpenMM calculator, Relaxed scans

Addition

Geometry loading from pubchem via pubchem:[name], e.g., pubchem:thymine or pubchem:methane
Growing Newton Trajectory (experimental) as described in 10.1063/1.1885467
Enabled TRIC for improved optimizations of solvated and/or non-covalently bound systems (see 10.1063/1.4952956, coord_type: tric)
Calculators for preconditioning of translation and rotation described here 10.1002/jcc.26495, useful for docking and preparing input geometries for COS methods.
Driver for 1d relaxed scans in internal coordinates (keyword scan). See 8. Relaxed Scans in the documentation
Basic support for reading & writing CHARMM coordinate card files
OpenMM calculator using ParmEd

Bugfixes

Improved parsing & writing of PDB files
Post-HF Psi4 calculations returned only HF energy

Miscellaneous

Refactored RedundantCoords and updated pysistrj --internals
ONIOM calculator now uses sparse matrices for calculations involving the Jacobian

- Python
Published by eljost almost 5 years ago

pysisyphus - MicroOptimizer

Addition

MicroOptimizer; allows implementing microcycles for multi-level calculations

- Python
Published by eljost about 5 years ago

pysisyphus - ONIOM improvments, Batch calculations, Thermochemistry

Addition

scripts/frag.py for easy fragmentation to generate indices for ONIOM calculations
Experimental ONIOM2-optimizer (type: oniom) supporting microiterations
Freezing atoms, see the documentation
Partial linesearch for LBFGS-optimizer (line_search=True, disabled by default) -Composite calculator to support composite methods ;)
Matrix/Batch calculations using MultiCalc
Improved IPIServer; now supports coordinate update
pysis -cp [new dest] [add files] now supports copying additional files [add files] to [new dest]
Thermochemical analysis when thermoanalysis package is installed
Improved reporting of barriers after endopt
IRC trajectories are now dumped while running
Initial displacement from TS using 3rd derivatives along transition vector
Electronic embedding with charge redistribution in ONIOM calculator

Bugfixes

Interpolation in internal coordinates is now more robust, when some primitives become ill defined
Numerous fixes & fixed DeprecationWarnings

Miscellaneous

IRC now supports out_dir argument
Simplified functions for geometry loading, now geom_loader should always be used
EulerPC now supports looser cycles that aid in the beginning of tricky IRC integrations
IRCs now respect stop/converged signs
Updated versioneer to 0.19

- Python
Published by eljost about 5 years ago

pysisyphus - ONIOM improvments, Batch calculations, Thermochemistry

Addition

scripts/frag.py for easy fragmentation to generate indices for ONIOM calculations
Experimental ONIOM2-optimizer (type: oniom) supporting microiterations
Freezing atoms, see the documentation
Partial linesearch for LBFGS-optimizer (line_search=True, disabled by default) -Composite calculator to support composite methods ;)
Matrix/Batch calculations using MultiCalc
Improved IPIServer; now supports coordinate update
pysis -cp [new dest] [add files] now supports copying additional files [add files] to [new dest]
Thermochemical analysis when thermoanalysis package is installed
Improved reporting of barriers after endopt
IRC trajectories are now dumped while running
Initial displacement from TS using 3rd derivatives along transition vector
Electronic embedding with charge redistribution in ONIOM calculator

Bugfixes

Interpolation in internal coordinates is now more robust, when some primitives become ill defined
Numerous fixes & fixed DeprecationWarnings

Miscellaneous

IRC now supports out_dir argument
Simplified functions for geometry loading, now geom_loader should always be used
EulerPC now supports looser cycles that aid in the beginning of tricky IRC integrations
IRCs now respect stop/converged signs
Updated versioneer to 0.19

- Python
Published by eljost about 5 years ago

pysisyphus - Constraints, new internal coordinates, OpenBabel forcefields, MD improvments

Addition

Support for constraints with coord_type: redund, see the documentation
Several new (internal, more or less...) coordinates
- CartesianX, CartesianY, CartesianZ
- TranslationX, TranslationY, TranslationZ and beginnings of rotational coordinates as in geomeTRIC (see 10.1063/1.4952956 and geomeTRIC)
New method to obtain TS-guess based on 10.1002/jcc.23910 that makes use of the new constraints support. See tests/testbirkholzinterpolation for an unit test.
xtb-python calculator (PyXTB)
OpenBabel force field calculator, using the python interface
Ability to specify different isotope masses, e.g., to constrain atoms in IRC runs (see examples/complex/08hcndeuteriumtsoptirc)
Many improvements for the internal (still experimental) MD module
- Very experimental metadynamics support
- Colvar (CV) gradients from automatic differentiation or explicit implementation
- Added Bond, Bend and Dihedral CVs (periodicity of dihedrals is not yet implemented)
- Plotting of free energy curve/surface for 1 and 2 CVs using pysisplot --gau [gau1] [gau2]
- MD can now be started from YAML input
- Plotting with pysisplot --md (total energy, conserved quantity, temperature, including running average)
- Fixed CSVR thermostat
- Added Berendsen thermostat
- Dumping to HDF5
- Added wrapper script to validate pysisyphus MD runs with physical-validation (see 10.1371/journal.pone.0202764)
Internal, small (solvent) molecule DB, preoptimized at different levels of theory, that can also be accessed from the Packmol wrapper pysispack
Easy access and usage of benchmark/test sets (Baker, Baker-TS, S22, Birkholz, ...) via benchmarks-subpackage
Added test set for COS calculations, intended for GFN2-XTB optimizations
Parser for [Geometries]-section in .molden-files
rx_mode argument for TSHessianOptimizers. Allows for easy specification of complicated approximate eigenvectors, used for selecting an initial eigenvector for uphill following.
rot_disable_pos_curv and trans_force_f_perp arguments for the Dimer calculator. The first one fixes the initial Dimer orientation until the curvature becomes negative. The latter argument controls whether always perpendicular and parallel force components are returned.
I-PI-Server calculator that supports the I-PI socket protocol. The present implementation works, e.g., with DFTB+ as client. See examples/opt/10h2oxtbipiserver for an example.

Bugfixes

PrimType could not be specified in YAML input when additional primitive internals were requested
Velocity is now properly rescaled after removal of v_com
Dropped assert that prevented runs with multiple geoms
Wrong final energy for Baker-TS case 15

Miscellaneous

Printing of additional platform information
PySCF verbosity can no be controlled with the verbosity argument
First PR from outside of our group, thanks to @bapride11, who improved the Dimer calculator (added rotation_remove_trans)
Optimization thresholds are now also plotted in pysisplot --opt
Simplified implementation of the using()-decorator that declares test dependencies
LinearBends/LinearAngles aren't propagated to the TS guess in run_tsopt_from_cos, as this is usually a bad idea. Now only the bonding skeleton is propagated to the TS guess.

- Python
Published by eljost over 5 years ago

pysisyphus - DFTB+ calculator, Davidson algorithm, Preconditioner improvements, faster Nix installation

Addition

DFTB+ calculator that supports ES tracking
Davidson algorithm to converge normal modes after TS optimization. Allows verifying the nature/order of the saddle point, without explicit Hessian calculation (do_davidson: True). See examples/tsopt/04dielsalderxtbtsopt_davidson for an example.
New, faster algorithms to detect bonds and bends in large(r) systems. Dihedral detection is yet to be updated and still slow for big systems.
More finegrained control over preconditioner construction, selectable via kind: full|full_fast|bonds_bends|bonds
- full/full_fast: Use bonds, bends, dihedrals
- bonds_bends: Use bonds and bends
- bonds: Only bonds.
Preconditioner construction was vastly accelerated.
Backtracking line search that also uses gradient information. Useful for XTB calculations, as the gradient is always available with the energy
Support for (re)using GFN-FF topology files in the XTB calculator
Nix installation using cached binaries, thanks to Cachix and @sheepforce. See the documentation on how to set up binary caching.

Bugfixes

Updated code to work with recently released h5py 3.0.0
pysisplot -o crash when no rendered CDDs were available
Handling of TS-optimization after COS optimization when HEI is first or last image
Line search now checks for very small alphas and aborts if necessary

Miscellaneous

Added scikit-learn dependency, as the new bond detection uses a KD-Tree
Updated GS2 IRC integrator

- Python
Published by eljost over 5 years ago

pysisyphus - Robustness fixes

Addition

Linesearch in min and max subspaces for RSPRFO (disabled be default). Use min_line_search: True, max_line_search: True to enable it
AFIR enhancments:
- Support for arbitrary number of fragments
- Different rhos (push/pull) and gammas can now be specified for every fragment pair
- Hydrogens are ignored by default. Use ignore_hydrogen: False to enable AFIR forces on hydrogens
pysistrj [input] --topdb converts geometries to PDB with automated fragment detection
quiet mode for XTB calculator (prevents creation of log files etc.)
Enabled minimum dynamic path from YAML input (still undocumented, see `examples/mdp/01_trispericyclic)
run_tsopt_from_cos now supports coord_type: cart|dlc (default dlc)
Basic test suite that ships with a pysisyphus installation (execut with pytest --pyargs pysisyphus.tests -v)
Enabled QCEngine calculator from YAML input
On-the-fly internal coordinate rebuilding for GrowingString
After endopt not only RMSDs are compared, but also bond matrices, making it easier to judge if a COS/TSOpt/IRC/EndOpt run was successful
Basic Dalton calculator using daltonproject (energies & gradient)
MO re-normalization for TDEN overlaps when AO overlaps are reconstructed from MO coefficients (disabled by default, use mo_renorm: True)
Ability to select which set of MO coefficients (reference/current) is used to recover AO overlaps (default cur, use mos_ref: cur|ref)

Bugfixes

Nix build of wfoverlap failed
Disabled Eckart projection in hessian saving of analytical potentials
Orthogonal direction for LinearBend and LinearDisplacement is now kept throughout the lifetime of the coordinate
Allow pysis [yaml] --cp [dest] to be run outside the dir [yaml] resides in
Dihedral generation in situations with 4 collinear atoms
Generation of 3N-6 DLCs is now enforced
More reasonable threshold for inverting WIlson B-matrix (1e-7 for eigenvalues of G matrix, corresponding to 3.16e-4 for singular values)

Miscellaneous

No more "hand-coded" constants, now the scipy.constants package is used
Double damping is now enabled by default in StringOptimizer (double_damp: true)

- Python
Published by eljost over 5 years ago

pysisyphus - Nix support and many robustness fixes

Addition

Installation of pysisyphus & dependencies like QC codes using Nix thanks to @sheepforce
DLC coordinate weighting
On-the-fly primitive coordinate rebuilding if the current set becomes invalid/ill-defined
Arbitrary precision calculation of internal derivatives using mpmath
Revamped RFOptimizer
Added second type for linear bends (LinearDisplacement) and OutOfPlane coordinate (both are not used yet)
RMSDs and barrier heights are now reported after "endopt" runs if possible

Bugfixes

Generated derivatives for dihedrals fail at 0° and 180° ... disabled them for now
pinv is now used with proper rcond value ...

Miscellaneous

Removed redund_v2. LinearBends are now used by default if necessary
Primitive internal setup & update was moved outside the RedundantCoord class into separate function, which should facilitate reuse
Generated code for primitives is now verified against finite differences

- Python
Published by eljost almost 6 years ago

pysisyphus - Revamped Growing String Method

Addition

Added parsers for cjson (as produced by Avogadro) and Z-Matrix
(L)-BFGS with double damping
rmsforceonly argument for Optimizers to use only rms(forces) for checking convergence
Reworked GSM implementation
- Enabled Climbing Image
- GSM reparametrization is much more robust
- Added L-BFGS to StringOptimizer (with double damping)
- DLC recreation can now be toggled
- Energy-weighted parametrization for increased density around the Highest Energy Image
- Upwinding tangents are used throughout, except for the frontier nodes
- Per-Image coordinate scaling can be used in StringOptimizer
Added new geom: block to the YAML input
Optimization convergence can now be signalled by the operator by creating a converged file
Added more safeguards to runtsoptfrom_cos w.r.t. selecting the initial root to follow
Added mem argument to XTB calculator. Enabled GFN-FF

Bugfixes

HDF5 files in optimizations are now opened/closed in every cycle, instead of keeping them open all the time.
Present comment was ignored in Geometry.as_xyz()
String has to be fully grown to indicate convergence
HEI splining was faulty
Present Hessian at optimized TS was not carried over to IRC calculation but it was recalculated (costly)

Miscellaneous

Improved logging in L-BFGS optimizations

- Python
Published by eljost almost 6 years ago

pysisyphus - Multiwfn logging

Multiwfn calls are now logged
Default commands are used when checking for the availability of software (Multiwfn, Jmol, ...)
Added TD-DFT optimization example using ORCA

- Python
Published by eljost almost 6 years ago

pysisyphus - Robustness fixes

Addition

TIP3P water calculator
Restricted Step Algorithm (RSA) for geometry optimizations
Reference to pysisyphus-paper; corresponding BibTex entry is display by pysis --bibtex
HDF5 Hessian dump after "do_hess: True"

Bugfixes

Made OverlapCalculator (hopefully) more robust
- Multiwfn (MWFN) crashes shouldn't crash pysisyphus anymore
- After MWFN crash subsequent MWFN calls are avoided/disabled
- Proper fallbacks for the "cdds" argument are used when MWFN and/or Jmol are not available

Miscellaneous

Started to add basic MD functionality (constraints via RATTLE, thermostating via CSVR) but this won't be ready anytime soon

- Python
Published by eljost almost 6 years ago

pysisyphus -

Added "pcm" and "solvent" keywords to Psi4 calculator
- Allowed more complex basis set input for Psi4 calculator

- Python
Published by eljost almost 6 years ago

pysisyphus -

Deprecated

"opt_ends" option in "irc" section. This is now handled in the "endopt" section.

Addition

Analytical Rastrigin function with many local minima
Updated stocastic search code & added tests
Very simple and barebones PDB parser & writer
Ability to omit Link atoms in ONIOM
ONIOM Hessian
ONIOM gradient & Hessian are now calculated using a Jacobian, which simplifies the code
Enabled ONIOM for YAML input
Added support for fragments and simple selection by regular expressions to Geometry
Optimizer data is not dumped to YAML anymore, but written to separate HDF5 groups, which is way way faster
Calculated Hessians from optimizations/IRCs are now dumped into a more useful HDF5 file with additional information. The file can easily be used as input for the "thermoanalysis" software to calculate thermochemical corrections (G, H, S, etc.)
Imaginary frequencies (< -10 cm⁻¹) after final hessian calculation are now written to .trj for easy inspection
Location of .pysisyphusrc can now be read from PYSISRC environment variable
Added thin packmol wrapper (pysispack) for easy creation of initial MD configurations
MD related functionality now operates in sane units
Initial GFN1-XTB hessian for (TS)-optimizations using different calculators
Simple intial Hessians for cartesian geometries through back-transformation of internal coordinate model Hessians
NumFreq can now be requested for ORCA calculator
Added "endopt" section (simlar to "preopt") to configure optimizations started from IRC endpoints
Josephine

Bugfixes

overachieve_factor is now also respected with "baker" thresh
Definition of dihedrals in rings
Multistep jobs (preopt, opt, tsopt) lead to overwritten yaml dumps. This is now fixed.
Simplified/unified plotting of COS methods (cosens/cosforces)
Unit conversion for inline xyz coordinates
Sometimes the last IRC points were not dumped to HDF5

Miscellaneous

Unified Hessian attributes in IRC integrators that use Hessians
Deprecated old code
Dropped dependencies: attrs, pandas, pytest-harvest
Updated plotting documentation