MultiOptPy 1.20.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- multioptpy/Calculator/__init__.py +0 -0
- multioptpy/Calculator/ase_calculation_tools.py +424 -0
- multioptpy/Calculator/ase_tools/__init__.py +0 -0
- multioptpy/Calculator/ase_tools/fairchem.py +28 -0
- multioptpy/Calculator/ase_tools/gamess.py +19 -0
- multioptpy/Calculator/ase_tools/gaussian.py +165 -0
- multioptpy/Calculator/ase_tools/mace.py +28 -0
- multioptpy/Calculator/ase_tools/mopac.py +19 -0
- multioptpy/Calculator/ase_tools/nwchem.py +31 -0
- multioptpy/Calculator/ase_tools/orca.py +22 -0
- multioptpy/Calculator/ase_tools/pygfn0.py +37 -0
- multioptpy/Calculator/dxtb_calculation_tools.py +344 -0
- multioptpy/Calculator/emt_calculation_tools.py +458 -0
- multioptpy/Calculator/gpaw_calculation_tools.py +183 -0
- multioptpy/Calculator/lj_calculation_tools.py +314 -0
- multioptpy/Calculator/psi4_calculation_tools.py +334 -0
- multioptpy/Calculator/pwscf_calculation_tools.py +189 -0
- multioptpy/Calculator/pyscf_calculation_tools.py +327 -0
- multioptpy/Calculator/sqm1_calculation_tools.py +611 -0
- multioptpy/Calculator/sqm2_calculation_tools.py +376 -0
- multioptpy/Calculator/tblite_calculation_tools.py +352 -0
- multioptpy/Calculator/tersoff_calculation_tools.py +818 -0
- multioptpy/Constraint/__init__.py +0 -0
- multioptpy/Constraint/constraint_condition.py +834 -0
- multioptpy/Coordinate/__init__.py +0 -0
- multioptpy/Coordinate/polar_coordinate.py +199 -0
- multioptpy/Coordinate/redundant_coordinate.py +638 -0
- multioptpy/IRC/__init__.py +0 -0
- multioptpy/IRC/converge_criteria.py +28 -0
- multioptpy/IRC/dvv.py +544 -0
- multioptpy/IRC/euler.py +439 -0
- multioptpy/IRC/hpc.py +564 -0
- multioptpy/IRC/lqa.py +540 -0
- multioptpy/IRC/modekill.py +662 -0
- multioptpy/IRC/rk4.py +579 -0
- multioptpy/Interpolation/__init__.py +0 -0
- multioptpy/Interpolation/adaptive_interpolation.py +283 -0
- multioptpy/Interpolation/binomial_interpolation.py +179 -0
- multioptpy/Interpolation/geodesic_interpolation.py +785 -0
- multioptpy/Interpolation/interpolation.py +156 -0
- multioptpy/Interpolation/linear_interpolation.py +473 -0
- multioptpy/Interpolation/savitzky_golay_interpolation.py +252 -0
- multioptpy/Interpolation/spline_interpolation.py +353 -0
- multioptpy/MD/__init__.py +0 -0
- multioptpy/MD/thermostat.py +185 -0
- multioptpy/MEP/__init__.py +0 -0
- multioptpy/MEP/pathopt_bneb_force.py +443 -0
- multioptpy/MEP/pathopt_dmf_force.py +448 -0
- multioptpy/MEP/pathopt_dneb_force.py +130 -0
- multioptpy/MEP/pathopt_ewbneb_force.py +207 -0
- multioptpy/MEP/pathopt_gpneb_force.py +512 -0
- multioptpy/MEP/pathopt_lup_force.py +113 -0
- multioptpy/MEP/pathopt_neb_force.py +225 -0
- multioptpy/MEP/pathopt_nesb_force.py +205 -0
- multioptpy/MEP/pathopt_om_force.py +153 -0
- multioptpy/MEP/pathopt_qsm_force.py +174 -0
- multioptpy/MEP/pathopt_qsmv2_force.py +304 -0
- multioptpy/ModelFunction/__init__.py +7 -0
- multioptpy/ModelFunction/avoiding_model_function.py +29 -0
- multioptpy/ModelFunction/binary_image_ts_search_model_function.py +47 -0
- multioptpy/ModelFunction/conical_model_function.py +26 -0
- multioptpy/ModelFunction/opt_meci.py +50 -0
- multioptpy/ModelFunction/opt_mesx.py +47 -0
- multioptpy/ModelFunction/opt_mesx_2.py +49 -0
- multioptpy/ModelFunction/seam_model_function.py +27 -0
- multioptpy/ModelHessian/__init__.py +0 -0
- multioptpy/ModelHessian/approx_hessian.py +147 -0
- multioptpy/ModelHessian/calc_params.py +227 -0
- multioptpy/ModelHessian/fischer.py +236 -0
- multioptpy/ModelHessian/fischerd3.py +360 -0
- multioptpy/ModelHessian/fischerd4.py +398 -0
- multioptpy/ModelHessian/gfn0xtb.py +633 -0
- multioptpy/ModelHessian/gfnff.py +709 -0
- multioptpy/ModelHessian/lindh.py +165 -0
- multioptpy/ModelHessian/lindh2007d2.py +707 -0
- multioptpy/ModelHessian/lindh2007d3.py +822 -0
- multioptpy/ModelHessian/lindh2007d4.py +1030 -0
- multioptpy/ModelHessian/morse.py +106 -0
- multioptpy/ModelHessian/schlegel.py +144 -0
- multioptpy/ModelHessian/schlegeld3.py +322 -0
- multioptpy/ModelHessian/schlegeld4.py +559 -0
- multioptpy/ModelHessian/shortrange.py +346 -0
- multioptpy/ModelHessian/swartd2.py +496 -0
- multioptpy/ModelHessian/swartd3.py +706 -0
- multioptpy/ModelHessian/swartd4.py +918 -0
- multioptpy/ModelHessian/tshess.py +40 -0
- multioptpy/Optimizer/QHAdam.py +61 -0
- multioptpy/Optimizer/__init__.py +0 -0
- multioptpy/Optimizer/abc_fire.py +83 -0
- multioptpy/Optimizer/adabelief.py +58 -0
- multioptpy/Optimizer/adabound.py +68 -0
- multioptpy/Optimizer/adadelta.py +65 -0
- multioptpy/Optimizer/adaderivative.py +56 -0
- multioptpy/Optimizer/adadiff.py +68 -0
- multioptpy/Optimizer/adafactor.py +70 -0
- multioptpy/Optimizer/adam.py +65 -0
- multioptpy/Optimizer/adamax.py +62 -0
- multioptpy/Optimizer/adamod.py +83 -0
- multioptpy/Optimizer/adamw.py +65 -0
- multioptpy/Optimizer/adiis.py +523 -0
- multioptpy/Optimizer/afire_neb.py +282 -0
- multioptpy/Optimizer/block_hessian_update.py +709 -0
- multioptpy/Optimizer/c2diis.py +491 -0
- multioptpy/Optimizer/component_wise_scaling.py +405 -0
- multioptpy/Optimizer/conjugate_gradient.py +82 -0
- multioptpy/Optimizer/conjugate_gradient_neb.py +345 -0
- multioptpy/Optimizer/coordinate_locking.py +405 -0
- multioptpy/Optimizer/dic_rsirfo.py +1015 -0
- multioptpy/Optimizer/ediis.py +417 -0
- multioptpy/Optimizer/eve.py +76 -0
- multioptpy/Optimizer/fastadabelief.py +61 -0
- multioptpy/Optimizer/fire.py +77 -0
- multioptpy/Optimizer/fire2.py +249 -0
- multioptpy/Optimizer/fire_neb.py +92 -0
- multioptpy/Optimizer/gan_step.py +486 -0
- multioptpy/Optimizer/gdiis.py +609 -0
- multioptpy/Optimizer/gediis.py +203 -0
- multioptpy/Optimizer/geodesic_step.py +433 -0
- multioptpy/Optimizer/gpmin.py +633 -0
- multioptpy/Optimizer/gpr_step.py +364 -0
- multioptpy/Optimizer/gradientdescent.py +78 -0
- multioptpy/Optimizer/gradientdescent_neb.py +52 -0
- multioptpy/Optimizer/hessian_update.py +433 -0
- multioptpy/Optimizer/hybrid_rfo.py +998 -0
- multioptpy/Optimizer/kdiis.py +625 -0
- multioptpy/Optimizer/lars.py +21 -0
- multioptpy/Optimizer/lbfgs.py +253 -0
- multioptpy/Optimizer/lbfgs_neb.py +355 -0
- multioptpy/Optimizer/linesearch.py +236 -0
- multioptpy/Optimizer/lookahead.py +40 -0
- multioptpy/Optimizer/nadam.py +64 -0
- multioptpy/Optimizer/newton.py +200 -0
- multioptpy/Optimizer/prodigy.py +70 -0
- multioptpy/Optimizer/purtubation.py +16 -0
- multioptpy/Optimizer/quickmin_neb.py +245 -0
- multioptpy/Optimizer/radam.py +75 -0
- multioptpy/Optimizer/rfo_neb.py +302 -0
- multioptpy/Optimizer/ric_rfo.py +842 -0
- multioptpy/Optimizer/rl_step.py +627 -0
- multioptpy/Optimizer/rmspropgrave.py +65 -0
- multioptpy/Optimizer/rsirfo.py +1647 -0
- multioptpy/Optimizer/rsprfo.py +1056 -0
- multioptpy/Optimizer/sadam.py +60 -0
- multioptpy/Optimizer/samsgrad.py +63 -0
- multioptpy/Optimizer/tr_lbfgs.py +678 -0
- multioptpy/Optimizer/trim.py +273 -0
- multioptpy/Optimizer/trust_radius.py +207 -0
- multioptpy/Optimizer/trust_radius_neb.py +121 -0
- multioptpy/Optimizer/yogi.py +60 -0
- multioptpy/OtherMethod/__init__.py +0 -0
- multioptpy/OtherMethod/addf.py +1150 -0
- multioptpy/OtherMethod/dimer.py +895 -0
- multioptpy/OtherMethod/elastic_image_pair.py +629 -0
- multioptpy/OtherMethod/modelfunction.py +456 -0
- multioptpy/OtherMethod/newton_traj.py +454 -0
- multioptpy/OtherMethod/twopshs.py +1095 -0
- multioptpy/PESAnalyzer/__init__.py +0 -0
- multioptpy/PESAnalyzer/calc_irc_curvature.py +125 -0
- multioptpy/PESAnalyzer/cmds_analysis.py +152 -0
- multioptpy/PESAnalyzer/koopman_analysis.py +268 -0
- multioptpy/PESAnalyzer/pca_analysis.py +314 -0
- multioptpy/Parameters/__init__.py +0 -0
- multioptpy/Parameters/atomic_mass.py +20 -0
- multioptpy/Parameters/atomic_number.py +22 -0
- multioptpy/Parameters/covalent_radii.py +44 -0
- multioptpy/Parameters/d2.py +61 -0
- multioptpy/Parameters/d3.py +63 -0
- multioptpy/Parameters/d4.py +103 -0
- multioptpy/Parameters/dreiding.py +34 -0
- multioptpy/Parameters/gfn0xtb_param.py +137 -0
- multioptpy/Parameters/gfnff_param.py +315 -0
- multioptpy/Parameters/gnb.py +104 -0
- multioptpy/Parameters/parameter.py +22 -0
- multioptpy/Parameters/uff.py +72 -0
- multioptpy/Parameters/unit_values.py +20 -0
- multioptpy/Potential/AFIR_potential.py +55 -0
- multioptpy/Potential/LJ_repulsive_potential.py +345 -0
- multioptpy/Potential/__init__.py +0 -0
- multioptpy/Potential/anharmonic_keep_potential.py +28 -0
- multioptpy/Potential/asym_elllipsoidal_potential.py +718 -0
- multioptpy/Potential/electrostatic_potential.py +69 -0
- multioptpy/Potential/flux_potential.py +30 -0
- multioptpy/Potential/gaussian_potential.py +101 -0
- multioptpy/Potential/idpp.py +516 -0
- multioptpy/Potential/keep_angle_potential.py +146 -0
- multioptpy/Potential/keep_dihedral_angle_potential.py +105 -0
- multioptpy/Potential/keep_outofplain_angle_potential.py +70 -0
- multioptpy/Potential/keep_potential.py +99 -0
- multioptpy/Potential/mechano_force_potential.py +74 -0
- multioptpy/Potential/nanoreactor_potential.py +52 -0
- multioptpy/Potential/potential.py +896 -0
- multioptpy/Potential/spacer_model_potential.py +221 -0
- multioptpy/Potential/switching_potential.py +258 -0
- multioptpy/Potential/universal_potential.py +34 -0
- multioptpy/Potential/value_range_potential.py +36 -0
- multioptpy/Potential/void_point_potential.py +25 -0
- multioptpy/SQM/__init__.py +0 -0
- multioptpy/SQM/sqm1/__init__.py +0 -0
- multioptpy/SQM/sqm1/sqm1_core.py +1792 -0
- multioptpy/SQM/sqm2/__init__.py +0 -0
- multioptpy/SQM/sqm2/calc_tools.py +95 -0
- multioptpy/SQM/sqm2/sqm2_basis.py +850 -0
- multioptpy/SQM/sqm2/sqm2_bond.py +119 -0
- multioptpy/SQM/sqm2/sqm2_core.py +303 -0
- multioptpy/SQM/sqm2/sqm2_data.py +1229 -0
- multioptpy/SQM/sqm2/sqm2_disp.py +65 -0
- multioptpy/SQM/sqm2/sqm2_eeq.py +243 -0
- multioptpy/SQM/sqm2/sqm2_overlapint.py +704 -0
- multioptpy/SQM/sqm2/sqm2_qm.py +578 -0
- multioptpy/SQM/sqm2/sqm2_rep.py +66 -0
- multioptpy/SQM/sqm2/sqm2_srb.py +70 -0
- multioptpy/Thermo/__init__.py +0 -0
- multioptpy/Thermo/normal_mode_analyzer.py +865 -0
- multioptpy/Utils/__init__.py +0 -0
- multioptpy/Utils/bond_connectivity.py +264 -0
- multioptpy/Utils/calc_tools.py +884 -0
- multioptpy/Utils/oniom.py +96 -0
- multioptpy/Utils/pbc.py +48 -0
- multioptpy/Utils/riemann_curvature.py +208 -0
- multioptpy/Utils/symmetry_analyzer.py +482 -0
- multioptpy/Visualization/__init__.py +0 -0
- multioptpy/Visualization/visualization.py +156 -0
- multioptpy/WFAnalyzer/MO_analysis.py +104 -0
- multioptpy/WFAnalyzer/__init__.py +0 -0
- multioptpy/Wrapper/__init__.py +0 -0
- multioptpy/Wrapper/autots.py +1239 -0
- multioptpy/Wrapper/ieip_wrapper.py +93 -0
- multioptpy/Wrapper/md_wrapper.py +92 -0
- multioptpy/Wrapper/neb_wrapper.py +94 -0
- multioptpy/Wrapper/optimize_wrapper.py +76 -0
- multioptpy/__init__.py +5 -0
- multioptpy/entrypoints.py +916 -0
- multioptpy/fileio.py +660 -0
- multioptpy/ieip.py +340 -0
- multioptpy/interface.py +1086 -0
- multioptpy/irc.py +529 -0
- multioptpy/moleculardynamics.py +432 -0
- multioptpy/neb.py +1267 -0
- multioptpy/optimization.py +1553 -0
- multioptpy/optimizer.py +709 -0
- multioptpy-1.20.2.dist-info/METADATA +438 -0
- multioptpy-1.20.2.dist-info/RECORD +246 -0
- multioptpy-1.20.2.dist-info/WHEEL +5 -0
- multioptpy-1.20.2.dist-info/entry_points.txt +9 -0
- multioptpy-1.20.2.dist-info/licenses/LICENSE +674 -0
- multioptpy-1.20.2.dist-info/top_level.txt +1 -0
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import numpy as np
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def cart2polar(point, reference_point=None):
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point = np.array(point, dtype=float)
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if reference_point is not None:
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point = point - reference_point
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n = len(point)
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polar_coords = np.zeros(n)
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r = np.linalg.norm(point)
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polar_coords[0] = r
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if r < 1e-9:
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return polar_coords
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for i in range(n-2):
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norm_partial = np.linalg.norm(point[i:])
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if norm_partial == 0:
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polar_coords[i+1] = 0
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else:
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polar_coords[i+1] = np.arccos(point[i] / norm_partial)
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if n > 1:
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last_angle = np.arctan2(point[-1], point[-2])
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if last_angle < 0:
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last_angle += 2 * np.pi
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polar_coords[-1] = last_angle
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return polar_coords
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def polar2cart(polar_coords, reference_point=None):
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r = polar_coords[0]
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n = len(polar_coords)
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if abs(r) < 1e-9:
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if reference_point is not None:
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return np.array(reference_point)
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return np.zeros(n)
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cartesian = np.zeros(n)
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cartesian[0] = r * np.cos(polar_coords[1]) if n > 1 else r
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for i in range(1, n-1):
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prod = r
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for j in range(1, i+1):
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prod *= np.sin(polar_coords[j])
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if i < n-1:
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cartesian[i] = prod * np.cos(polar_coords[i+1])
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else:
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cartesian[i] = prod
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prod = r
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prod *= np.sin(polar_coords[j])
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cartesian[-1] = prod * np.sin(polar_coords[-1])
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if reference_point is not None:
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cartesian += np.array(reference_point)
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return cartesian
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def compute_analytical_jacobian(p):
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"""
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Compute the Jacobian matrix analytically for the transformation
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from polar to Cartesian coordinates.
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Parameters:
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p (numpy.ndarray): Polar coordinates [r, θ₁, θ₂, ..., θₙ₋₁]
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numpy.ndarray: Jacobian matrix J where J[i,j] = ∂xᵢ/∂pⱼ
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"""
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p = np.asarray(p, dtype=float)
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n = len(p)
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r = p[0]
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J = np.zeros((n, n))
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# Handle the special case of zero radius
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if r < 1e-10:
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J[0, 0] = 1 # ∂x₁/∂r = 1 (all others zero)
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return J
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# Derivatives with respect to r (first column of Jacobian)
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# For all coordinates: ∂xᵢ/∂r = xᵢ/r
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x = cart2polar(p)
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J[i, 0] = x[i] / r
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return J # Only radius in 1D case
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# Derivatives with respect to θ₁ (second column)
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# ∂x₁/∂θ₁ = -r sin(θ₁)
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J[0, 1] = -r * np.sin(p[1])
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# For other coordinates, ∂xᵢ/∂θ₁ for i>1
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for i in range(1, n):
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# Replace sin(θ₁) with cos(θ₁) in the formula for xᵢ
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# Multiply by the remaining terms sin(θⱼ) and cos/sin terms
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deriv *= np.sin(p[j])
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deriv *= np.cos(p[i+1])
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else: # Last coordinate
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deriv *= np.sin(p[n-1])
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J[i, 1] = deriv
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# Derivatives with respect to other angles (remaining columns)
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for j in range(2, n): # For each angle θⱼ, j=2...n-1
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# xₖ doesn't depend on θⱼ for k < j-1
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J[k, j] = 0
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|
121
|
+
|
|
122
|
+
# For coordinates xₖ where k ≥ j-1
|
|
123
|
+
for k in range(j-1, n):
|
|
124
|
+
if k == j-1:
|
|
125
|
+
# ∂x_{j-1}/∂θⱼ = -r·sin(θ₁)·...·sin(θⱼ₋₁)·sin(θⱼ)
|
|
126
|
+
deriv = -r
|
|
127
|
+
for m in range(1, j):
|
|
128
|
+
deriv *= np.sin(p[m])
|
|
129
|
+
deriv *= np.sin(p[j])
|
|
130
|
+
J[k, j] = deriv
|
|
131
|
+
else: # k > j-1
|
|
132
|
+
# Start with radius
|
|
133
|
+
deriv = r
|
|
134
|
+
|
|
135
|
+
# Multiply by sin terms for angles θ₁...θⱼ₋₁
|
|
136
|
+
for m in range(1, j):
|
|
137
|
+
deriv *= np.sin(p[m])
|
|
138
|
+
|
|
139
|
+
# Replace sin(θⱼ) with cos(θⱼ) in the formula
|
|
140
|
+
deriv *= np.cos(p[j])
|
|
141
|
+
|
|
142
|
+
# Multiply by remaining sin terms for θⱼ₊₁...θₖ
|
|
143
|
+
for m in range(j+1, k+1):
|
|
144
|
+
deriv *= np.sin(p[m])
|
|
145
|
+
|
|
146
|
+
# For intermediate coordinates, multiply by cos(θₖ₊₁)
|
|
147
|
+
if k < n-1:
|
|
148
|
+
deriv *= np.cos(p[k+1])
|
|
149
|
+
else: # Last coordinate
|
|
150
|
+
deriv *= np.sin(p[n-1])
|
|
151
|
+
|
|
152
|
+
J[k, j] = deriv
|
|
153
|
+
|
|
154
|
+
# Special handling for the last angle θₙ₋₁
|
|
155
|
+
if n >= 3:
|
|
156
|
+
# Only the last two coordinates depend on the last angle
|
|
157
|
+
for i in range(0, n-2):
|
|
158
|
+
J[i, n-1] = 0
|
|
159
|
+
|
|
160
|
+
# Second-to-last coordinate: ∂x_{n-1}/∂θ_{n-1} = -r·sin(θ₁)·...·sin(θ_{n-2})·sin(θ_{n-1})
|
|
161
|
+
if n >= 3:
|
|
162
|
+
deriv = -r
|
|
163
|
+
for j in range(1, n-1):
|
|
164
|
+
deriv *= np.sin(p[j])
|
|
165
|
+
J[n-2, n-1] = deriv
|
|
166
|
+
|
|
167
|
+
# Last coordinate: ∂xₙ/∂θ_{n-1} = r·sin(θ₁)·...·sin(θ_{n-2})·cos(θ_{n-1})
|
|
168
|
+
deriv = r
|
|
169
|
+
for j in range(1, n-1):
|
|
170
|
+
deriv *= np.sin(p[j])
|
|
171
|
+
deriv *= np.cos(p[n-1])
|
|
172
|
+
J[n-1, n-1] = deriv
|
|
173
|
+
|
|
174
|
+
return J
|
|
175
|
+
|
|
176
|
+
def cart_grad_2_polar_grad(x, grad_x):
|
|
177
|
+
"""
|
|
178
|
+
Transform gradient from Cartesian to polar coordinates.
|
|
179
|
+
|
|
180
|
+
Parameters:
|
|
181
|
+
x (numpy.ndarray): Cartesian coordinates where gradient is evaluated
|
|
182
|
+
grad_x (numpy.ndarray): Gradient in Cartesian coordinates [∂f/∂x₁, ∂f/∂x₂, ..., ∂f/∂xₙ]
|
|
183
|
+
|
|
184
|
+
Returns:
|
|
185
|
+
numpy.ndarray: Gradient in polar coordinates [∂f/∂r, ∂f/∂θ₁, ..., ∂f/∂θₙ₋₁]
|
|
186
|
+
"""
|
|
187
|
+
x = np.asarray(x, dtype=float)
|
|
188
|
+
grad_x = np.asarray(grad_x, dtype=float)
|
|
189
|
+
|
|
190
|
+
# Convert to polar coordinates
|
|
191
|
+
p = cart2polar(x)
|
|
192
|
+
|
|
193
|
+
# Compute the Jacobian matrix analytically
|
|
194
|
+
J = compute_analytical_jacobian(p)
|
|
195
|
+
|
|
196
|
+
# Transform gradient: ∇ₚf = J^T · ∇ₓf
|
|
197
|
+
grad_p = np.dot(J.T, grad_x)
|
|
198
|
+
|
|
199
|
+
return grad_p
|