Welcome to pysisyphus documentation!
pysisyphus is a software-suite for the exploration of potential energy surfaces in ground- and excited states. It implements several methods to search for stationary points (minima and first order saddle points) and the calculation of minimum energy paths by means of IRC and Chain of States methods like Nudged Elastic Band and Growing String. Furthermore it provides tools to easily analyze & modify geometries (aligning, translating, interpolating, ...) and to visualize the calculation results/progress.
The required energies, gradients and hessians are calculated by calling external quantum chemistry codes. pysisyphus can also be used as a library to implement custom quantum chemistry workflows.
If any issues arise please open an issue and I'll see if it can be fixed and my time permits it. Contrubtions are welcome, so feel free to submit a PR.
This software is still work in progress. Use at your own risk. Also take a look at the license
Contents:
- 1. Overview of pysisyphus
- 2. Installation
- 3. Installation via Nix
- 4. Worked example
- 5. Coordinate Systems
- 5.1. Supported Coordinate Systems
- 5.2. Supported File Formats
- 5.3. YAML Input
- 5.4. Geometry & RedundantCoords
GeometryGeometry.__init__()Geometry.align_principal_axes()Geometry.all_energiesGeometry.approximate_radius()Geometry.as_ase_atoms()Geometry.as_g98_list()Geometry.as_xyz()Geometry.assert_cart_coords()Geometry.assert_compatibility()Geometry.atom_indices()Geometry.atom_typesGeometry.atom_xyz_iter()Geometry.atomic_numbersGeometry.bond_setsGeometry.calc_double_ao_overlap()Geometry.calc_energy_and_forces()Geometry.cart_coordsGeometry.cart_forcesGeometry.cart_gradientGeometry.cart_hessianGeometry.center()Geometry.center_of_massGeometry.center_of_mass_at()Geometry.centroidGeometry.clear()Geometry.commentGeometry.coord_typesGeometry.coordsGeometry.coords3dGeometry.coords_by_typeGeometry.copy()Geometry.copy_all()Geometry.covalent_radiiGeometry.del_atoms()Geometry.describe()Geometry.dump_xyz()Geometry.eckart_projection()Geometry.energyGeometry.fd_coords3d_gen()Geometry.forcesGeometry.get_energy_and_cart_forces_at()Geometry.get_energy_and_cart_hessian_at()Geometry.get_energy_and_forces_at()Geometry.get_energy_at()Geometry.get_energy_at_cart_coords()Geometry.get_fragments()Geometry.get_imag_frequencies()Geometry.get_normal_modes()Geometry.get_restart_info()Geometry.get_sphere_radius()Geometry.get_subgeom()Geometry.get_subgeom_without()Geometry.get_temporary_coords()Geometry.get_thermoanalysis()Geometry.get_trans_rot_projector()Geometry.gradientGeometry.hessianGeometry.inertia_tensorGeometry.is_analytical_2dGeometry.jmol()Geometry.layersGeometry.mass_weigh_hessian()Geometry.massesGeometry.masses_repGeometry.mm_invGeometry.mm_sqrt_invGeometry.modes3d()Geometry.moving_atomsGeometry.moving_atoms_jmol()Geometry.mw_coordsGeometry.mw_gradientGeometry.mw_hessianGeometry.principal_axes_are_aligned()Geometry.reparametrize()Geometry.reset_coords()Geometry.rmsd()Geometry.rotate()Geometry.set_calculator()Geometry.set_coord()Geometry.set_coords()Geometry.set_h5_hessian()Geometry.set_restart_info()Geometry.set_results()Geometry.standard_orientation()Geometry.sum_formulaGeometry.tmp_xyz_handle()Geometry.total_massGeometry.unweight_mw_hessian()Geometry.vdw_radiiGeometry.vdw_volume()Geometry.without_hydrogens()Geometry.zero_frozen_forces()
get_trans_rot_projector()get_trans_rot_vectors()inertia_tensor()HybridRedundantCoordsRedundantCoordsRedundantCoords.BRedundantCoords.B_invRedundantCoords.B_inv_primRedundantCoords.B_primRedundantCoords.Bt_invRedundantCoords.Bt_inv_primRedundantCoords.CRedundantCoords.PRedundantCoords.backtransform_hessian()RedundantCoords.bend_atom_indicesRedundantCoords.bend_indicesRedundantCoords.bond_atom_indicesRedundantCoords.bond_indicesRedundantCoords.bond_typed_primsRedundantCoords.cartesian_indicesRedundantCoords.clear()RedundantCoords.constrained_indicesRedundantCoords.coordsRedundantCoords.coords3dRedundantCoords.dihedral_atom_indicesRedundantCoords.dihedral_indicesRedundantCoords.eval()RedundantCoords.get_K_matrix()RedundantCoords.get_index_of_typed_prim()RedundantCoords.get_prim_internals_by_indices()RedundantCoords.inv_B()RedundantCoords.inv_Bt()RedundantCoords.linear_bend_indicesRedundantCoords.log()RedundantCoords.log_int_grad_msg()RedundantCoords.outofplane_indicesRedundantCoords.prim_coordsRedundantCoords.prim_indices_setRedundantCoords.prim_internalsRedundantCoords.primitivesRedundantCoords.print_typed_prims()RedundantCoords.project_hessian()RedundantCoords.project_vector()RedundantCoords.return_inds()RedundantCoords.rotation_indicesRedundantCoords.set_inds_from_typed_prims()RedundantCoords.set_primitive_indices()RedundantCoords.transform_forces()RedundantCoords.transform_hessian()RedundantCoords.transform_int_step()RedundantCoords.translation_indicesRedundantCoords.typed_prims
TMTRICTRIC
- 5.5. Related Literature
- 6. Calculators
- 6.1. YAML input
- 6.2. Calculator base classes
CalculatorCalculator.__init__()Calculator.apply_keep_kind()Calculator.apply_set_plans()Calculator.build_set_plans()Calculator.clean()Calculator.conf_keyCalculator.force_num_hessian()Calculator.geom_from_fn()Calculator.get_cmd()Calculator.get_energy()Calculator.get_forces()Calculator.get_hessian()Calculator.get_num_hessian()Calculator.get_restart_info()Calculator.keep()Calculator.log()Calculator.make_fn()Calculator.nameCalculator.popen()Calculator.prepare()Calculator.prepare_coords()Calculator.prepare_input()Calculator.prepare_path()Calculator.prepare_pattern()Calculator.prepare_turbo_coords()Calculator.prepare_xyz_string()Calculator.print_capabilities()Calculator.print_out_fn()Calculator.restore_org_hessian()Calculator.run()Calculator.run_after()Calculator.set_restart_info()Calculator.verify_chkfiles()
HessKindKeepKindSetPlan
- 6.3. OverlapCalculator base class
NTOsOverlapCalculatorOverlapCalculator.H5_MAPOverlapCalculator.OVLP_TYPE_VERBOSEOverlapCalculator.VALID_CDDSOverlapCalculator.VALID_KEYSOverlapCalculator.VALID_XYOverlapCalculator.calc_cdd_cube()OverlapCalculator.conf_threshOverlapCalculator.data_modelOverlapCalculator.dump_overlap_data()OverlapCalculator.from_overlap_data()OverlapCalculator.get_ci_coeffs_for()OverlapCalculator.get_h5_group()OverlapCalculator.get_indices()OverlapCalculator.get_mo_norms()OverlapCalculator.get_orbital_matrices()OverlapCalculator.get_ref_mos()OverlapCalculator.get_sao_from_mo_coeffs()OverlapCalculator.get_tden_overlaps()OverlapCalculator.get_top_differences()OverlapCalculator.prepare_overlap_data()OverlapCalculator.render_cdd_cube()OverlapCalculator.renorm_mos()OverlapCalculator.store_overlap_data()OverlapCalculator.stored_calculationsOverlapCalculator.track_root()
get_data_model()
- 6.4. Calculators with Excited state capabilities
- 6.5. Calculators with Ground state capabilities
- 6.6. Meta (wrapping) Calculators
- 6.7. Pure Python calculators
- 7. Minimization
- 7.1. YAML Example
- 7.2. Convergence Thresholds
- 7.3. Available Optimizers
ConvInfoOptimizerOptimizer.__init__()Optimizer.check_convergence()Optimizer.dump_restart_info()Optimizer.final_summary()Optimizer.fit_rigid()Optimizer.get_path_for_fn()Optimizer.get_restart_info()Optimizer.log()Optimizer.make_conv_dict()Optimizer.optimize()Optimizer.postprocess_opt()Optimizer.prepare_opt()Optimizer.print_opt_progress()Optimizer.procrustes()Optimizer.report_conv_thresholds()Optimizer.run()Optimizer.scale_by_max_step()Optimizer.set_restart_info()Optimizer.write_cycle_to_file()Optimizer.write_image_trjs()Optimizer.write_results()Optimizer.write_to_out_dir()
get_data_model()HessianOptimizerHessianOptimizer.__init__()HessianOptimizer.filter_small_eigvals()HessianOptimizer.get_alpha_step()HessianOptimizer.get_augmented_hessian()HessianOptimizer.get_newton_step()HessianOptimizer.get_newton_step_on_trust()HessianOptimizer.get_rs_step()HessianOptimizer.get_shifted_step_trans()HessianOptimizer.get_step_func()HessianOptimizer.housekeeping()HessianOptimizer.log_negative_eigenvalues()HessianOptimizer.prepare_opt()HessianOptimizer.prev_eigvec_maxHessianOptimizer.prev_eigvec_minHessianOptimizer.quadratic_model()HessianOptimizer.reset()HessianOptimizer.rfo_dictHessianOptimizer.rfo_model()HessianOptimizer.save_hessian()HessianOptimizer.set_new_trust_radius()HessianOptimizer.solve_rfo()HessianOptimizer.update_hessian()HessianOptimizer.update_trust_radius()
dummy_hessian_update()RFOptimizer
- 8. Minimization with Microiterations
- 9. Relaxed Scans
- 10. Excited State Optimization
- 11. Chain Of States Methods
- 11.1. String method
- 11.2. Nudged Elastic Band
- 11.3. General remarks
- 11.4. YAML example(s)
- 11.5. General advice for COS optimizations
- 11.6. Chain Of States base class
ChainOfStatesChainOfStates.as_xyz()ChainOfStates.atomsChainOfStates.calculate_forces()ChainOfStates.calculatorChainOfStates.cart_coordsChainOfStates.check_for_climbing_start()ChainOfStates.clear()ChainOfStates.concurrent_force_calcs()ChainOfStates.coordsChainOfStates.coords3dChainOfStates.describe()ChainOfStates.energyChainOfStates.forcesChainOfStates.get_climbing_forces()ChainOfStates.get_climbing_indices()ChainOfStates.get_dask_client()ChainOfStates.get_fixed_indices()ChainOfStates.get_hei_index()ChainOfStates.get_image_calc_counter_sum()ChainOfStates.get_perpendicular_forces()ChainOfStates.get_splined_hei()ChainOfStates.get_tangent()ChainOfStates.get_tangents()ChainOfStates.gradientChainOfStates.image_coordsChainOfStates.image_indsChainOfStates.last_indexChainOfStates.log()ChainOfStates.loggerChainOfStates.masses_repChainOfStates.max_image_numChainOfStates.moving_imagesChainOfStates.moving_indicesChainOfStates.par_image_calc()ChainOfStates.perpendicular_forcesChainOfStates.prepare_opt_cycle()ChainOfStates.resultsChainOfStates.rms()ChainOfStates.set_climbing_forces()ChainOfStates.set_coords_at()ChainOfStates.set_images()ChainOfStates.set_vector()ChainOfStates.set_zero_forces_for_fixed_images()ChainOfStates.valid_coord_typesChainOfStates.zero_fixed_vector()
- 11.7. Chain Of State Methods
- 11.8. Growing Chain Of States base class
- 11.9. Growing Chain Of State Methods
- 12. Transition State Optimization
- 13. Intrinsic Reaction Coordinate (IRC)
- 13.1. YAML example(s)
- 13.2. IRC base class
IRCIRC.__init__()IRC.coordsIRC.dump_data()IRC.dump_ends()IRC.energyIRC.get_conv_fact()IRC.get_endpoint_and_ts_geoms()IRC.get_full_irc_data()IRC.get_irc_data()IRC.get_path_for_fn()IRC.gradientIRC.initial_displacement()IRC.irc()IRC.log()IRC.m_sqrtIRC.mass_weigh_hessian()IRC.mw_coordsIRC.mw_gradientIRC.postprocess()IRC.prepare()IRC.report_bonds()IRC.report_conv_thresholds()IRC.run()IRC.set_data()IRC.unweight_vec()IRC.valid_displs
- 13.3. IRC Integrators
- 14. Diabatiziation
- 15. Plotting
- 16. Working with Geometries
- 17. pysisyphus
- 17.1. pysisyphus package
- 17.1.1. Subpackages
- 17.1.1.1. pysisyphus.benchmarks package
- 17.1.1.2. pysisyphus.calculators package
- 17.1.1.3. pysisyphus.cos package
- 17.1.1.4. pysisyphus.db package
- 17.1.1.5. pysisyphus.drivers package
- 17.1.1.6. pysisyphus.dynamics package
- 17.1.1.7. pysisyphus.intcoords package
- 17.1.1.8. pysisyphus.interpolate package
- 17.1.1.9. pysisyphus.io package
- 17.1.1.10. pysisyphus.irc package
- 17.1.1.11. pysisyphus.line_searches package
- 17.1.1.12. pysisyphus.modefollow package
- 17.1.1.13. pysisyphus.optimizers package
- 17.1.1.14. pysisyphus.plotters package
- 17.1.1.15. pysisyphus.stocastic package
- 17.1.1.16. pysisyphus.tests package
- 17.1.1.17. pysisyphus.tsoptimizers package
- 17.1.1.18. pysisyphus.wrapper package
- 17.1.2. Submodules
- 17.1.3. pysisyphus.Geometry module
- 17.1.4. pysisyphus.TableFormatter module
- 17.1.5. pysisyphus.TablePrinter module
- 17.1.6. pysisyphus.color module
- 17.1.7. pysisyphus.config module
- 17.1.8. pysisyphus.constants module
- 17.1.9. pysisyphus.elem_data module
- 17.1.10. pysisyphus.exceptions module
- 17.1.11. pysisyphus.filtertrj module
- 17.1.12. pysisyphus.helpers module
FinalHessianResultalign_coords()align_geoms()check_for_end_sign()complete_fragments()confirm_input()do_final_hessian()fit_rigid()geom_from_xyz_file()geom_loader()geoms_from_trj()get_coords_diffs()get_geom_getter()get_tangent_trj_str()imag_modes_from_geom()index_array_from_overlaps()match_geoms()norm_max_rms()np_print()pick_image_inds()print_barrier()procrustes()shake_coords()simple_peaks()slugify_worker()
- 17.1.13. pysisyphus.helpers_pure module
OrderedEnumapprox_float()cache_arrays()check_mem()chunks()describe()eigval_to_wavenumber()estimate()expand()file_or_str()filter_fixture_store()find_closest_sequence()full_expand()get_box()get_clock()get_cubic_crystal()get_input()get_molecular_radius()get_random_path()get_ratio()hash_args()hash_arr()highlight_text()increment_fn()interpolate_colors()json_to_results()kill_dir()log()merge_sets()molecular_volume()recursive_update()remove_duplicates()report_frozen_atoms()report_isotopes()results_to_json()rms()sort_by_central()standard_state_corr()timed()to_sets()to_subscript_num()touch()
- 17.1.14. pysisyphus.init_logging module
- 17.1.15. pysisyphus.linalg module
cross3()eigvec_grad()finite_difference_hessian()get_rot_mat()get_rot_mat_for_coords()gram_schmidt()make_unit_vec()matrix_power()multi_component_sym_mat()norm3()orthogonalize_against()perp_comp()pivoted_cholesky()pivoted_cholesky2()quaternion_to_rot_mat()rmsd_grad()rot_quaternion()svd_inv()sym_mat_from_tril()sym_mat_from_triu()
- 17.1.16. pysisyphus.pack module
- 17.1.17. pysisyphus.peakdetect module
- 17.1.18. pysisyphus.plot module
CDD_PNG_FNSanim_cos()get_en_conv()get_force_unit()list_h5_groups()load_h5()parse_args()plot_afir()plot_all_energies()plot_cos_energies()plot_cos_forces()plot_cycle()plot_gau()plot_irc()plot_irc_h5()plot_md()plot_opt()plot_overlaps()plot_scan()plot_trj_energies()render_cdds()run()spline_plot_cycles()
- 17.1.19. pysisyphus.run module
RunResultcheck_asserts()copy_yaml_and_geometries()do_clean()do_rmsds()get_calc_closure()get_defaults()get_last_calc_cycle()load_run_dict()main()parse_args()print_bibtex()print_header()run()run_calculations()run_endopt()run_from_dict()run_irc()run_md()run_mdp()run_preopt()run_scan()run_stocastic()run_tsopt_from_cos()setup_run_dict()
- 17.1.20. pysisyphus.socket_helper module
- 17.1.21. pysisyphus.testing module
- 17.1.22. pysisyphus.thermo module
- 17.1.23. pysisyphus.trj module
GotNoGeometryExceptionalign()append()center()centerm()dump_geoms()every()frag_sort()get()get_geoms()get_interactively()hardsphere_merge()match()origin()parse_args()print_internal_vals()print_internals()read_geoms()run()shake()spline_redistribute()standard_orientation()standardize_geoms()translate()
- 17.1.24. pysisyphus.version module
- 17.1.25. pysisyphus.xyzloader module
- 17.1.26. pysisyphus.yaml_mods module
- 17.1.27. Module contents
- 17.1.1. Subpackages
- 17.1. pysisyphus package