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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import copy
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class SAdam:
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def __init__(self, **config):
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#arXiv:1908.00700v2
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self.adam_count = 1
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self.DELTA = 10.0
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self.beta_m = 0.9
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self.beta_v = 0.999
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self.Epsilon = 1e-8
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self.Initialization = True
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self.config = config
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self.hessian = None
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self.bias_hessian = None
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return
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def run(self, geom_num_list, B_g, pre_B_g=[], pre_geom=[], B_e=0.0, pre_B_e=0.0, pre_move_vector=[], initial_geom_num_list=[], g=[], pre_g=[]):
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print("SAdam")
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if self.Initialization:
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self.adam_m = geom_num_list * 0.0
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self.adam_v = geom_num_list * 0.0
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self.Initialization = False
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adam_count = self.adam_count
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adam_m = self.adam_m
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adam_v = self.adam_v
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new_adam_m = adam_m*0.0
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new_adam_v = adam_v*0.0
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for i in range(len(geom_num_list)):
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new_adam_m[i] = copy.copy(self.beta_m*adam_m[i] + (1.0-self.beta_m)*(B_g[i]))
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new_adam_v[i] = copy.copy(self.beta_v*adam_v[i] + (1.0-self.beta_v)*(B_g[i])**2)
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move_vector = []
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for i in range(len(geom_num_list)):
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move_vector.append(self.DELTA*new_adam_m[i]/(np.log(1.0 + np.exp(np.sqrt(new_adam_v[i])))+self.Epsilon))
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self.adam_m = new_adam_m
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return move_vector#Bohr.
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def set_hessian(self, hessian):
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self.hessian = hessian
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return
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return self.bias_hessian
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class SAMSGrad:
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def run(self, geom_num_list, B_g, pre_B_g=[], pre_geom=[], B_e=0.0, pre_B_e=0.0, pre_move_vector=[], initial_geom_num_list=[], g=[], pre_g=[]):
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adam_v = self.adam_v
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new_adam_m[i] = copy.copy(self.beta_m*adam_m[i] + (1.0-self.beta_m)*(B_g[i]))
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new_adam_v[i] = copy.copy(self.beta_v*adam_v[i] + (1.0-self.beta_v)*(B_g[i])**2)
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for j in range(len(new_adam_v[i])):
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new_adam_v[i][j] = max(new_adam_v[i][j], adam_v[i][j])
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move_vector = []
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move_vector.append(self.DELTA*new_adam_m[i]/(np.log(1.0 + np.exp(np.sqrt(new_adam_v[i])))+self.Epsilon))
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self.adam_m = new_adam_m
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self.adam_count += 1
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return move_vector#Bohr
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self.hessian = hessian
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return
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54
|
+
|
|
55
|
+
def set_bias_hessian(self, bias_hessian):
|
|
56
|
+
self.bias_hessian = bias_hessian
|
|
57
|
+
return
|
|
58
|
+
|
|
59
|
+
def get_hessian(self):
|
|
60
|
+
return self.hessian
|
|
61
|
+
|
|
62
|
+
def get_bias_hessian(self):
|
|
63
|
+
return self.bias_hessian
|