MultiOptPy 1.20.2__py3-none-any.whl

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Files changed (246) hide show
  1. multioptpy/Calculator/__init__.py +0 -0
  2. multioptpy/Calculator/ase_calculation_tools.py +424 -0
  3. multioptpy/Calculator/ase_tools/__init__.py +0 -0
  4. multioptpy/Calculator/ase_tools/fairchem.py +28 -0
  5. multioptpy/Calculator/ase_tools/gamess.py +19 -0
  6. multioptpy/Calculator/ase_tools/gaussian.py +165 -0
  7. multioptpy/Calculator/ase_tools/mace.py +28 -0
  8. multioptpy/Calculator/ase_tools/mopac.py +19 -0
  9. multioptpy/Calculator/ase_tools/nwchem.py +31 -0
  10. multioptpy/Calculator/ase_tools/orca.py +22 -0
  11. multioptpy/Calculator/ase_tools/pygfn0.py +37 -0
  12. multioptpy/Calculator/dxtb_calculation_tools.py +344 -0
  13. multioptpy/Calculator/emt_calculation_tools.py +458 -0
  14. multioptpy/Calculator/gpaw_calculation_tools.py +183 -0
  15. multioptpy/Calculator/lj_calculation_tools.py +314 -0
  16. multioptpy/Calculator/psi4_calculation_tools.py +334 -0
  17. multioptpy/Calculator/pwscf_calculation_tools.py +189 -0
  18. multioptpy/Calculator/pyscf_calculation_tools.py +327 -0
  19. multioptpy/Calculator/sqm1_calculation_tools.py +611 -0
  20. multioptpy/Calculator/sqm2_calculation_tools.py +376 -0
  21. multioptpy/Calculator/tblite_calculation_tools.py +352 -0
  22. multioptpy/Calculator/tersoff_calculation_tools.py +818 -0
  23. multioptpy/Constraint/__init__.py +0 -0
  24. multioptpy/Constraint/constraint_condition.py +834 -0
  25. multioptpy/Coordinate/__init__.py +0 -0
  26. multioptpy/Coordinate/polar_coordinate.py +199 -0
  27. multioptpy/Coordinate/redundant_coordinate.py +638 -0
  28. multioptpy/IRC/__init__.py +0 -0
  29. multioptpy/IRC/converge_criteria.py +28 -0
  30. multioptpy/IRC/dvv.py +544 -0
  31. multioptpy/IRC/euler.py +439 -0
  32. multioptpy/IRC/hpc.py +564 -0
  33. multioptpy/IRC/lqa.py +540 -0
  34. multioptpy/IRC/modekill.py +662 -0
  35. multioptpy/IRC/rk4.py +579 -0
  36. multioptpy/Interpolation/__init__.py +0 -0
  37. multioptpy/Interpolation/adaptive_interpolation.py +283 -0
  38. multioptpy/Interpolation/binomial_interpolation.py +179 -0
  39. multioptpy/Interpolation/geodesic_interpolation.py +785 -0
  40. multioptpy/Interpolation/interpolation.py +156 -0
  41. multioptpy/Interpolation/linear_interpolation.py +473 -0
  42. multioptpy/Interpolation/savitzky_golay_interpolation.py +252 -0
  43. multioptpy/Interpolation/spline_interpolation.py +353 -0
  44. multioptpy/MD/__init__.py +0 -0
  45. multioptpy/MD/thermostat.py +185 -0
  46. multioptpy/MEP/__init__.py +0 -0
  47. multioptpy/MEP/pathopt_bneb_force.py +443 -0
  48. multioptpy/MEP/pathopt_dmf_force.py +448 -0
  49. multioptpy/MEP/pathopt_dneb_force.py +130 -0
  50. multioptpy/MEP/pathopt_ewbneb_force.py +207 -0
  51. multioptpy/MEP/pathopt_gpneb_force.py +512 -0
  52. multioptpy/MEP/pathopt_lup_force.py +113 -0
  53. multioptpy/MEP/pathopt_neb_force.py +225 -0
  54. multioptpy/MEP/pathopt_nesb_force.py +205 -0
  55. multioptpy/MEP/pathopt_om_force.py +153 -0
  56. multioptpy/MEP/pathopt_qsm_force.py +174 -0
  57. multioptpy/MEP/pathopt_qsmv2_force.py +304 -0
  58. multioptpy/ModelFunction/__init__.py +7 -0
  59. multioptpy/ModelFunction/avoiding_model_function.py +29 -0
  60. multioptpy/ModelFunction/binary_image_ts_search_model_function.py +47 -0
  61. multioptpy/ModelFunction/conical_model_function.py +26 -0
  62. multioptpy/ModelFunction/opt_meci.py +50 -0
  63. multioptpy/ModelFunction/opt_mesx.py +47 -0
  64. multioptpy/ModelFunction/opt_mesx_2.py +49 -0
  65. multioptpy/ModelFunction/seam_model_function.py +27 -0
  66. multioptpy/ModelHessian/__init__.py +0 -0
  67. multioptpy/ModelHessian/approx_hessian.py +147 -0
  68. multioptpy/ModelHessian/calc_params.py +227 -0
  69. multioptpy/ModelHessian/fischer.py +236 -0
  70. multioptpy/ModelHessian/fischerd3.py +360 -0
  71. multioptpy/ModelHessian/fischerd4.py +398 -0
  72. multioptpy/ModelHessian/gfn0xtb.py +633 -0
  73. multioptpy/ModelHessian/gfnff.py +709 -0
  74. multioptpy/ModelHessian/lindh.py +165 -0
  75. multioptpy/ModelHessian/lindh2007d2.py +707 -0
  76. multioptpy/ModelHessian/lindh2007d3.py +822 -0
  77. multioptpy/ModelHessian/lindh2007d4.py +1030 -0
  78. multioptpy/ModelHessian/morse.py +106 -0
  79. multioptpy/ModelHessian/schlegel.py +144 -0
  80. multioptpy/ModelHessian/schlegeld3.py +322 -0
  81. multioptpy/ModelHessian/schlegeld4.py +559 -0
  82. multioptpy/ModelHessian/shortrange.py +346 -0
  83. multioptpy/ModelHessian/swartd2.py +496 -0
  84. multioptpy/ModelHessian/swartd3.py +706 -0
  85. multioptpy/ModelHessian/swartd4.py +918 -0
  86. multioptpy/ModelHessian/tshess.py +40 -0
  87. multioptpy/Optimizer/QHAdam.py +61 -0
  88. multioptpy/Optimizer/__init__.py +0 -0
  89. multioptpy/Optimizer/abc_fire.py +83 -0
  90. multioptpy/Optimizer/adabelief.py +58 -0
  91. multioptpy/Optimizer/adabound.py +68 -0
  92. multioptpy/Optimizer/adadelta.py +65 -0
  93. multioptpy/Optimizer/adaderivative.py +56 -0
  94. multioptpy/Optimizer/adadiff.py +68 -0
  95. multioptpy/Optimizer/adafactor.py +70 -0
  96. multioptpy/Optimizer/adam.py +65 -0
  97. multioptpy/Optimizer/adamax.py +62 -0
  98. multioptpy/Optimizer/adamod.py +83 -0
  99. multioptpy/Optimizer/adamw.py +65 -0
  100. multioptpy/Optimizer/adiis.py +523 -0
  101. multioptpy/Optimizer/afire_neb.py +282 -0
  102. multioptpy/Optimizer/block_hessian_update.py +709 -0
  103. multioptpy/Optimizer/c2diis.py +491 -0
  104. multioptpy/Optimizer/component_wise_scaling.py +405 -0
  105. multioptpy/Optimizer/conjugate_gradient.py +82 -0
  106. multioptpy/Optimizer/conjugate_gradient_neb.py +345 -0
  107. multioptpy/Optimizer/coordinate_locking.py +405 -0
  108. multioptpy/Optimizer/dic_rsirfo.py +1015 -0
  109. multioptpy/Optimizer/ediis.py +417 -0
  110. multioptpy/Optimizer/eve.py +76 -0
  111. multioptpy/Optimizer/fastadabelief.py +61 -0
  112. multioptpy/Optimizer/fire.py +77 -0
  113. multioptpy/Optimizer/fire2.py +249 -0
  114. multioptpy/Optimizer/fire_neb.py +92 -0
  115. multioptpy/Optimizer/gan_step.py +486 -0
  116. multioptpy/Optimizer/gdiis.py +609 -0
  117. multioptpy/Optimizer/gediis.py +203 -0
  118. multioptpy/Optimizer/geodesic_step.py +433 -0
  119. multioptpy/Optimizer/gpmin.py +633 -0
  120. multioptpy/Optimizer/gpr_step.py +364 -0
  121. multioptpy/Optimizer/gradientdescent.py +78 -0
  122. multioptpy/Optimizer/gradientdescent_neb.py +52 -0
  123. multioptpy/Optimizer/hessian_update.py +433 -0
  124. multioptpy/Optimizer/hybrid_rfo.py +998 -0
  125. multioptpy/Optimizer/kdiis.py +625 -0
  126. multioptpy/Optimizer/lars.py +21 -0
  127. multioptpy/Optimizer/lbfgs.py +253 -0
  128. multioptpy/Optimizer/lbfgs_neb.py +355 -0
  129. multioptpy/Optimizer/linesearch.py +236 -0
  130. multioptpy/Optimizer/lookahead.py +40 -0
  131. multioptpy/Optimizer/nadam.py +64 -0
  132. multioptpy/Optimizer/newton.py +200 -0
  133. multioptpy/Optimizer/prodigy.py +70 -0
  134. multioptpy/Optimizer/purtubation.py +16 -0
  135. multioptpy/Optimizer/quickmin_neb.py +245 -0
  136. multioptpy/Optimizer/radam.py +75 -0
  137. multioptpy/Optimizer/rfo_neb.py +302 -0
  138. multioptpy/Optimizer/ric_rfo.py +842 -0
  139. multioptpy/Optimizer/rl_step.py +627 -0
  140. multioptpy/Optimizer/rmspropgrave.py +65 -0
  141. multioptpy/Optimizer/rsirfo.py +1647 -0
  142. multioptpy/Optimizer/rsprfo.py +1056 -0
  143. multioptpy/Optimizer/sadam.py +60 -0
  144. multioptpy/Optimizer/samsgrad.py +63 -0
  145. multioptpy/Optimizer/tr_lbfgs.py +678 -0
  146. multioptpy/Optimizer/trim.py +273 -0
  147. multioptpy/Optimizer/trust_radius.py +207 -0
  148. multioptpy/Optimizer/trust_radius_neb.py +121 -0
  149. multioptpy/Optimizer/yogi.py +60 -0
  150. multioptpy/OtherMethod/__init__.py +0 -0
  151. multioptpy/OtherMethod/addf.py +1150 -0
  152. multioptpy/OtherMethod/dimer.py +895 -0
  153. multioptpy/OtherMethod/elastic_image_pair.py +629 -0
  154. multioptpy/OtherMethod/modelfunction.py +456 -0
  155. multioptpy/OtherMethod/newton_traj.py +454 -0
  156. multioptpy/OtherMethod/twopshs.py +1095 -0
  157. multioptpy/PESAnalyzer/__init__.py +0 -0
  158. multioptpy/PESAnalyzer/calc_irc_curvature.py +125 -0
  159. multioptpy/PESAnalyzer/cmds_analysis.py +152 -0
  160. multioptpy/PESAnalyzer/koopman_analysis.py +268 -0
  161. multioptpy/PESAnalyzer/pca_analysis.py +314 -0
  162. multioptpy/Parameters/__init__.py +0 -0
  163. multioptpy/Parameters/atomic_mass.py +20 -0
  164. multioptpy/Parameters/atomic_number.py +22 -0
  165. multioptpy/Parameters/covalent_radii.py +44 -0
  166. multioptpy/Parameters/d2.py +61 -0
  167. multioptpy/Parameters/d3.py +63 -0
  168. multioptpy/Parameters/d4.py +103 -0
  169. multioptpy/Parameters/dreiding.py +34 -0
  170. multioptpy/Parameters/gfn0xtb_param.py +137 -0
  171. multioptpy/Parameters/gfnff_param.py +315 -0
  172. multioptpy/Parameters/gnb.py +104 -0
  173. multioptpy/Parameters/parameter.py +22 -0
  174. multioptpy/Parameters/uff.py +72 -0
  175. multioptpy/Parameters/unit_values.py +20 -0
  176. multioptpy/Potential/AFIR_potential.py +55 -0
  177. multioptpy/Potential/LJ_repulsive_potential.py +345 -0
  178. multioptpy/Potential/__init__.py +0 -0
  179. multioptpy/Potential/anharmonic_keep_potential.py +28 -0
  180. multioptpy/Potential/asym_elllipsoidal_potential.py +718 -0
  181. multioptpy/Potential/electrostatic_potential.py +69 -0
  182. multioptpy/Potential/flux_potential.py +30 -0
  183. multioptpy/Potential/gaussian_potential.py +101 -0
  184. multioptpy/Potential/idpp.py +516 -0
  185. multioptpy/Potential/keep_angle_potential.py +146 -0
  186. multioptpy/Potential/keep_dihedral_angle_potential.py +105 -0
  187. multioptpy/Potential/keep_outofplain_angle_potential.py +70 -0
  188. multioptpy/Potential/keep_potential.py +99 -0
  189. multioptpy/Potential/mechano_force_potential.py +74 -0
  190. multioptpy/Potential/nanoreactor_potential.py +52 -0
  191. multioptpy/Potential/potential.py +896 -0
  192. multioptpy/Potential/spacer_model_potential.py +221 -0
  193. multioptpy/Potential/switching_potential.py +258 -0
  194. multioptpy/Potential/universal_potential.py +34 -0
  195. multioptpy/Potential/value_range_potential.py +36 -0
  196. multioptpy/Potential/void_point_potential.py +25 -0
  197. multioptpy/SQM/__init__.py +0 -0
  198. multioptpy/SQM/sqm1/__init__.py +0 -0
  199. multioptpy/SQM/sqm1/sqm1_core.py +1792 -0
  200. multioptpy/SQM/sqm2/__init__.py +0 -0
  201. multioptpy/SQM/sqm2/calc_tools.py +95 -0
  202. multioptpy/SQM/sqm2/sqm2_basis.py +850 -0
  203. multioptpy/SQM/sqm2/sqm2_bond.py +119 -0
  204. multioptpy/SQM/sqm2/sqm2_core.py +303 -0
  205. multioptpy/SQM/sqm2/sqm2_data.py +1229 -0
  206. multioptpy/SQM/sqm2/sqm2_disp.py +65 -0
  207. multioptpy/SQM/sqm2/sqm2_eeq.py +243 -0
  208. multioptpy/SQM/sqm2/sqm2_overlapint.py +704 -0
  209. multioptpy/SQM/sqm2/sqm2_qm.py +578 -0
  210. multioptpy/SQM/sqm2/sqm2_rep.py +66 -0
  211. multioptpy/SQM/sqm2/sqm2_srb.py +70 -0
  212. multioptpy/Thermo/__init__.py +0 -0
  213. multioptpy/Thermo/normal_mode_analyzer.py +865 -0
  214. multioptpy/Utils/__init__.py +0 -0
  215. multioptpy/Utils/bond_connectivity.py +264 -0
  216. multioptpy/Utils/calc_tools.py +884 -0
  217. multioptpy/Utils/oniom.py +96 -0
  218. multioptpy/Utils/pbc.py +48 -0
  219. multioptpy/Utils/riemann_curvature.py +208 -0
  220. multioptpy/Utils/symmetry_analyzer.py +482 -0
  221. multioptpy/Visualization/__init__.py +0 -0
  222. multioptpy/Visualization/visualization.py +156 -0
  223. multioptpy/WFAnalyzer/MO_analysis.py +104 -0
  224. multioptpy/WFAnalyzer/__init__.py +0 -0
  225. multioptpy/Wrapper/__init__.py +0 -0
  226. multioptpy/Wrapper/autots.py +1239 -0
  227. multioptpy/Wrapper/ieip_wrapper.py +93 -0
  228. multioptpy/Wrapper/md_wrapper.py +92 -0
  229. multioptpy/Wrapper/neb_wrapper.py +94 -0
  230. multioptpy/Wrapper/optimize_wrapper.py +76 -0
  231. multioptpy/__init__.py +5 -0
  232. multioptpy/entrypoints.py +916 -0
  233. multioptpy/fileio.py +660 -0
  234. multioptpy/ieip.py +340 -0
  235. multioptpy/interface.py +1086 -0
  236. multioptpy/irc.py +529 -0
  237. multioptpy/moleculardynamics.py +432 -0
  238. multioptpy/neb.py +1267 -0
  239. multioptpy/optimization.py +1553 -0
  240. multioptpy/optimizer.py +709 -0
  241. multioptpy-1.20.2.dist-info/METADATA +438 -0
  242. multioptpy-1.20.2.dist-info/RECORD +246 -0
  243. multioptpy-1.20.2.dist-info/WHEEL +5 -0
  244. multioptpy-1.20.2.dist-info/entry_points.txt +9 -0
  245. multioptpy-1.20.2.dist-info/licenses/LICENSE +674 -0
  246. multioptpy-1.20.2.dist-info/top_level.txt +1 -0
@@ -0,0 +1,62 @@
1
+ import numpy as np
2
+ import copy
3
+
4
+
5
+
6
+ class AdaMax:
7
+ def __init__(self, **config):
8
+ #arXiv:1412.6980v9
9
+ #not worked well
10
+ self.adam_count = 1
11
+ self.DELTA = 0.005
12
+ self.beta_m = 0.9
13
+ self.beta_v = 0.999
14
+ self.Epsilon = 1e-8
15
+ self.adamax_u = 1e-8
16
+ self.Initialization = True
17
+ self.config = config
18
+ self.hessian = None
19
+ self.bias_hessian = None
20
+ return
21
+
22
+ 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=[]):
23
+ print("AdaMax")
24
+ if self.Initialization:
25
+ self.adam_m = geom_num_list * 0.0
26
+ self.adam_v = geom_num_list * 0.0
27
+ self.Initialization = False
28
+
29
+ adam_count = self.adam_count
30
+ adam_m = self.adam_m
31
+ adam_v = self.adam_v
32
+ new_adam_m = adam_m*0.0
33
+ new_adam_v = adam_v*0.0
34
+
35
+
36
+ for i in range(len(geom_num_list)):
37
+ new_adam_m[i] = copy.copy(self.beta_m*adam_m[i] + (1.0-self.beta_m)*(B_g[i]))
38
+ new_adamax_u = max(self.beta_v*self.adamax_u, np.linalg.norm(B_g))
39
+
40
+ move_vector = []
41
+
42
+ for i in range(len(geom_num_list)):
43
+ move_vector.append((self.DELTA / (self.beta_m ** adam_count + self.Epsilon)) * (adam_m[i] / (new_adamax_u + self.Epsilon)))
44
+
45
+ self.adam_m = new_adam_m
46
+ self.adam_v = new_adam_v
47
+ self.adam_count += 1
48
+
49
+ return move_vector#Bohr
50
+ def set_hessian(self, hessian):
51
+ self.hessian = hessian
52
+ return
53
+
54
+ def set_bias_hessian(self, bias_hessian):
55
+ self.bias_hessian = bias_hessian
56
+ return
57
+
58
+ def get_hessian(self):
59
+ return self.hessian
60
+
61
+ def get_bias_hessian(self):
62
+ return self.bias_hessian
@@ -0,0 +1,83 @@
1
+ import numpy as np
2
+ import copy
3
+
4
+
5
+
6
+
7
+ class Adamod:
8
+ def __init__(self, **config):
9
+ #AdaDiff
10
+ #ref. https://iopscience.iop.org/article/10.1088/1742-6596/2010/1/012027/pdf Dian Huang et al 2021 J. Phys.: Conf. Ser. 2010 012027
11
+ self.adam_count = 1
12
+ self.DELTA = 10.0
13
+ self.beta_m = 0.9
14
+ self.beta_v = 0.999
15
+ self.beta_s = 0.999
16
+ self.Epsilon = 1e-8
17
+ self.Initialization = True
18
+ self.config = config
19
+ self.hessian = None
20
+ self.bias_hessian = None
21
+ return
22
+
23
+ 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=[]):
24
+ print("Adamod")
25
+ if self.Initialization:
26
+ self.adam_m = geom_num_list * 0.0
27
+ self.adam_v = geom_num_list * 0.0
28
+ self.adam_r = geom_num_list * 0.0
29
+ self.adam_s = geom_num_list * 0.0
30
+ self.Initialization = False
31
+
32
+ adam_count = self.adam_count
33
+
34
+ new_adam_m = self.adam_m*0.0
35
+ new_adam_v = self.adam_v*0.0
36
+ new_adam_r = self.adam_r*0.0
37
+ new_adam_s = self.adam_s*0.0
38
+ new_adam_m_hat = self.adam_m*0.0
39
+ new_adam_v_hat = self.adam_v*0.0
40
+ new_adam_r_hat = self.adam_r*0.0
41
+
42
+ for i in range(len(geom_num_list)):
43
+ new_adam_m[i] = copy.copy(self.beta_m*self.adam_m[i] + (1.0-self.beta_m)*(B_g[i]))
44
+ new_adam_v[i] = copy.copy(self.beta_v*self.adam_v[i] + (1.0-self.beta_v)*(B_g[i])**2)
45
+
46
+
47
+
48
+ for i in range(len(geom_num_list)):
49
+ new_adam_m_hat[i] = copy.copy(new_adam_m[i]/(1 - self.beta_m**adam_count))
50
+ new_adam_v_hat[i] = copy.copy((new_adam_v[i] + self.Epsilon)/(1 - self.beta_v**adam_count))
51
+ new_adam_s[i] = self.DELTA / (np.sqrt(self.beta_v) + self.Epsilon)
52
+ new_adam_r[i] = self.beta_s * self.adam_r[i] + (1 - self.beta_s) * new_adam_s[i]
53
+
54
+ for i in range(len(geom_num_list)):
55
+ for j in range(len(new_adam_r_hat[i])):
56
+ new_adam_r_hat[i][j] = min(new_adam_r[i][j], new_adam_s[i][j])
57
+
58
+ move_vector = []
59
+
60
+ for i in range(len(geom_num_list)):
61
+ move_vector.append(new_adam_r_hat[i]*new_adam_m_hat[i])
62
+
63
+ self.adam_m = new_adam_m
64
+ self.adam_v = new_adam_v
65
+ self.adam_r = new_adam_r
66
+ self.adam_s = new_adam_s
67
+ self.adam_count += 1
68
+
69
+ return move_vector#Bohr.
70
+
71
+ def set_hessian(self, hessian):
72
+ self.hessian = hessian
73
+ return
74
+
75
+ def set_bias_hessian(self, bias_hessian):
76
+ self.bias_hessian = bias_hessian
77
+ return
78
+
79
+ def get_hessian(self):
80
+ return self.hessian
81
+
82
+ def get_bias_hessian(self):
83
+ return self.bias_hessian
@@ -0,0 +1,65 @@
1
+ import numpy as np
2
+ import copy
3
+
4
+
5
+
6
+ class AdamW:
7
+ def __init__(self, **config):
8
+ #AdamW
9
+ #arXiv:2302.06675v4
10
+ self.adam_count = 1
11
+ self.beta_m = 0.9
12
+ self.beta_v = 0.999
13
+ self.DELTA = 0.06
14
+ self.AdamW_lambda = 0.001
15
+ self.Epsilon = 1e-12
16
+ self.Initialization = True
17
+ self.config = config
18
+ self.hessian = None
19
+ self.bias_hessian = None
20
+
21
+ 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=[]):
22
+ print("AdamW")
23
+ if self.Initialization:
24
+ self.adam_m = geom_num_list * 0.0
25
+ self.adam_v = geom_num_list * 0.0
26
+
27
+ self.Initialization = False
28
+
29
+ new_adam_m = self.adam_m*0.0
30
+ new_adam_v = self.adam_v*0.0
31
+ new_adam_m_hat = self.adam_m*0.0
32
+ new_adam_v_hat = self.adam_v*0.0
33
+ for i in range(len(geom_num_list)):
34
+ new_adam_m[i] = copy.copy(self.beta_m*self.adam_m[i] + (1.0-self.beta_m)*(B_g[i]))
35
+ new_adam_v[i] = copy.copy(self.beta_v*self.adam_v[i] + (1.0-self.beta_v)*(B_g[i])**2)
36
+
37
+
38
+ move_vector = []
39
+ for i in range(len(geom_num_list)):
40
+ new_adam_m_hat[i] = copy.copy(new_adam_m[i]/(1 - self.beta_m**self.adam_count))
41
+ new_adam_v_hat[i] = copy.copy((new_adam_v[i] + self.Epsilon)/(1 - self.beta_v**self.adam_count))
42
+
43
+
44
+ for i in range(len(geom_num_list)):
45
+ move_vector.append(self.DELTA*new_adam_m_hat[i]/np.sqrt(new_adam_v_hat[i]+self.Epsilon) + self.AdamW_lambda * geom_num_list[i])
46
+
47
+ self.adam_m = new_adam_m
48
+ self.adam_v = new_adam_v
49
+ self.adam_count += 1
50
+
51
+ return move_vector#Bohr
52
+
53
+ def set_hessian(self, hessian):
54
+ self.hessian = hessian
55
+ return
56
+
57
+ def set_bias_hessian(self, bias_hessian):
58
+ self.bias_hessian = bias_hessian
59
+ return
60
+
61
+ def get_hessian(self):
62
+ return self.hessian
63
+
64
+ def get_bias_hessian(self):
65
+ return self.bias_hessian