Add types for core.periodic_table/bonds/composition/ion/lattice/libxcfunc, new type MillerIndex and fix Lattice hash

[DanielYang59]

Summary

Add types annotations for:

• core.periodic_table
• core.bonds
• core.composition
• core.ion
• core.lattice
• core.libxcfunc

New custom type:

• New custom type MillerIndex = tuple[int, int, int]

Bug fixes:

1. Seem like a typo, I assume it should check if HO exists and replace them with OH. So the condition should be if (self.composition.get("H") and self.composition.get("O")) is not None:, fixed in b4a70ee:

   pymatgen/pymatgen/core/ion.py

   Lines 144 to 145 in 2e1c301

   	if self.composition.get("H") == self.composition.get("O") is not None:
   	formula = formula.replace("HO", "OH")

2. Magic number for hash of Lattice fixed in 88e4eda:

   pymatgen/pymatgen/core/lattice.py

   Lines 837 to 838 in 2e1c301

   	def __hash__(self) -> int:
   	return 7

Need confirmation:

1. In 710cb91, access to Lattice._pbc has been redirected to Lattice.pbc, with a setter method. Wondering if there is any reason for the previous implementation?
2. Is the following needed by anything?

   pymatgen/pymatgen/core/libxcfunc.py

   Lines 502 to 504 in 2e1c301

   	if __name__ == "__main__":
   	for xc in LibxcFunc:
   	print(xc)

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Walkthrough

The updates to pymatgen/core/periodic_table.py enhance functionality and consistency in the representation of chemical elements. Key changes include making certain properties non-optional, introducing methods for comparison and representation, and refining type annotations for more precise data handling. These modifications improve the robustness and usability of the module, facilitating easier manipulation and comparison of element properties in scientific computations.

Changes

File	Summary of Changes
.../periodic_table.py	- Non-optional properties for atomic radius and mass - Added comparison and representation methods - Updated type annotations for radii properties - New method to create elements from names - Modified validity check for symbols

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[DanielYang59]

@coderabbitai ignore

[DanielYang59]

@janosh Can you please review this at your convenience? Feel free to revert 24b1546 though (I personally don't like to have dunder methods scattered around the class randomly, but such change badly pollute Git Blame). Thanks!

[DanielYang59]

Please review this one as well @janosh. Appreciate your time!

[janosh]

thanks @DanielYang59, lgtm! 👍

[DanielYang59]

Thanks for reviewing @janosh!

Do you have any comments on the "Need Confirmation" section of the PR summary #3814 (comment)?

Regarding (1), I noticed multiple part of core.lattice access self._matrix instead of self.matrix where matrix is a property. I'm not sure if this is intended? Does it offer any benefit that I'm not aware of?

For example (not exhaustive):

pymatgen/pymatgen/core/lattice.py

Lines 111 to 112 in 578d29c

	def __str__(self) -> str:
	return "\n".join(" ".join([f"{i:.6f}" for i in row]) for row in self._matrix)

pymatgen/pymatgen/core/lattice.py

Lines 201 to 204 in 578d29c

	@property
	def metric_tensor(self) -> np.ndarray:
	"""The metric tensor of the lattice."""
	return np.dot(self._matrix, self._matrix.T)

Is it related to:

pymatgen/pymatgen/core/lattice.py

Line 44 in 578d29c

Properties lazily generated for efficiency.

[janosh]

using the attribute directly instead of the property method doesn't add to the call stack and so saves small amount of work.

but you can't lazy-load an attribute like you can a property. same with caching. that's probably what "Properties lazily generated for efficiency. " is referring to

In 710cb91, access to Lattice._pbc has been redirected to Lattice.pbc, with a setter method. Wondering if there is any reason for the previous implementation?

not that i'm aware. your way makes more sense imo

[janosh]

2. Is the following needed by anything?

pymatgen/pymatgen/core/libxcfunc.py

Lines 502 to 504 in 2e1c301

	if __name__ == "__main__":
	for xc in LibxcFunc:
	print(xc)

i think that's safe to remove

[DanielYang59]

Thanks for the input. It's very helpful. I would do them in a future PR.

Also worth north is the regen_libxcfunc.py dev script seems to depend on the comments to work properly. This feels so weird and might be good to improve this as well.

pymatgen/dev_scripts/regen_libxcfunc.py

Lines 107 to 111 in 578d29c

	# [1] insert new enum values in list
	start = lines.index("#begin_include_dont_touch\n")
	stop = lines.index("#end_include_dont_touch\n")
	lines.insert(stop, enum_list)
	del lines[start + 1 : stop]

pymatgen/pymatgen/core/libxcfunc.py

Lines 34 to 408 in 578d29c

	@unique
	class LibxcFunc(Enum):
	"""Enumerator with the identifiers. This object is used by Xcfunc
	declared in xcfunc.py to create an internal representation of the XC functional.
	This is a low level object, client code should not interact with LibxcFunc directly
	but use the API provided by Xcfunc.
	"""
	# Warning: the following header is required by `regen_libxcfunc.py`
	# begin_include_dont_touch
	LDA_C_1D_CSC = 18
	LDA_C_1D_LOOS = 26
	LDA_C_2D_AMGB = 15
	LDA_C_2D_PRM = 16
	LDA_C_GOMBAS = 24
	LDA_C_HL = 4
	LDA_C_GL = 5
	LDA_C_vBH = 17
	LDA_C_ML1 = 22
	LDA_C_ML2 = 23
	LDA_C_PW = 12
	LDA_C_PW_MOD = 13
	LDA_C_OB_PW = 14
	LDA_C_PW_RPA = 25
	LDA_C_PZ = 9
	LDA_C_PZ_MOD = 10
	LDA_C_OB_PZ = 11
	LDA_C_RC04 = 27
	LDA_C_RPA = 3
	LDA_C_VWN = 7
	LDA_C_VWN_1 = 28
	LDA_C_VWN_2 = 29
	LDA_C_VWN_3 = 30
	LDA_C_VWN_4 = 31
	LDA_C_VWN_RPA = 8
	LDA_C_WIGNER = 2
	LDA_K_TF = 50
	LDA_K_LP = 51
	LDA_X = 1
	LDA_C_XALPHA = 6
	LDA_X_1D = 21
	LDA_X_2D = 19
	LDA_XC_KSDT = 259
	LDA_XC_TETER93 = 20
	LDA_XC_ZLP = 43
	GGA_C_AM05 = 135
	GGA_C_FT97 = 88
	GGA_C_LM = 137
	GGA_C_LYP = 131
	GGA_C_OP_B88 = 87
	GGA_C_OP_PBE = 86
	GGA_C_OP_G96 = 85
	GGA_C_OP_PW91 = 262
	GGA_C_OP_XALPHA = 84
	GGA_C_OPTC = 200
	GGA_C_P86 = 132
	GGA_C_PBE = 130
	GGA_C_PBE_SOL = 133
	GGA_C_XPBE = 136
	GGA_C_PBE_JRGX = 138
	GGA_C_RGE2 = 143
	GGA_C_APBE = 186
	GGA_C_SPBE = 89
	GGA_C_REGTPSS = 83
	GGA_C_ZPBESOL = 63
	GGA_C_PBEINT = 62
	GGA_C_ZPBEINT = 61
	GGA_C_PBELOC = 246
	GGA_C_BGCP = 39
	GGA_C_PBEFE = 258
	GGA_C_PW91 = 134
	GGA_C_Q2D = 47
	GGA_C_SOGGA11 = 152
	GGA_C_SOGGA11_X = 159
	GGA_C_TCA = 100
	GGA_C_REVTCA = 99
	GGA_C_WI0 = 153
	GGA_C_WI = 148
	GGA_C_WL = 147
	GGA_K_DK = 516
	GGA_K_PERDEW = 517
	GGA_K_VSK = 518
	GGA_K_VJKS = 519
	GGA_K_ERNZERHOF = 520
	GGA_K_MEYER = 57
	GGA_K_OL1 = 512
	GGA_X_OL2 = 183
	GGA_K_OL2 = 513
	GGA_K_PEARSON = 511
	GGA_K_TFVW = 52
	GGA_K_VW = 500
	GGA_K_GE2 = 501
	GGA_K_GOLDEN = 502
	GGA_K_YT65 = 503
	GGA_K_BALTIN = 504
	GGA_K_LIEB = 505
	GGA_K_ABSP1 = 506
	GGA_K_ABSP2 = 507
	GGA_K_GR = 508
	GGA_K_LUDENA = 509
	GGA_K_GP85 = 510
	GGA_X_2D_B86 = 128
	GGA_X_2D_B86_MGC = 124
	GGA_X_2D_B88 = 127
	GGA_X_2D_PBE = 129
	GGA_X_AIRY = 192
	GGA_X_LAG = 193
	GGA_X_AK13 = 56
	GGA_X_AM05 = 120
	GGA_X_B86 = 103
	GGA_X_B86_MGC = 105
	GGA_X_B86_R = 41
	GGA_X_B88 = 106
	GGA_X_OPTB88_VDW = 139
	GGA_X_MB88 = 149
	GGA_K_LLP = 522
	GGA_K_FR_B88 = 514
	GGA_K_THAKKAR = 523
	GGA_X_BAYESIAN = 125
	GGA_X_BPCCAC = 98
	GGA_X_C09X = 158
	GGA_X_CAP = 270
	GGA_X_DK87_R1 = 111
	GGA_X_DK87_R2 = 112
	GGA_X_EV93 = 35
	GGA_X_FT97_A = 114
	GGA_X_FT97_B = 115
	GGA_X_G96 = 107
	GGA_X_HCTH_A = 34
	GGA_X_HERMAN = 104
	GGA_X_HJS_PBE = 525
	GGA_X_HJS_PBE_SOL = 526
	GGA_X_HJS_B88 = 527
	GGA_X_HJS_B97X = 528
	GGA_X_HJS_B88_V2 = 46
	GGA_X_HTBS = 191
	GGA_X_ITYH = 529
	GGA_X_KT1 = 145
	GGA_XC_KT2 = 146
	GGA_X_LB = 160
	GGA_X_LBM = 182
	GGA_X_LG93 = 113
	GGA_X_LV_RPW86 = 58
	GGA_X_MPBE = 122
	GGA_X_N12 = 82
	GGA_X_GAM = 32
	GGA_X_OPTX = 110
	GGA_X_PBE = 101
	GGA_X_PBE_R = 102
	GGA_X_PBE_SOL = 116
	GGA_X_XPBE = 123
	GGA_X_PBE_JSJR = 126
	GGA_X_PBEK1_VDW = 140
	GGA_X_RGE2 = 142
	GGA_X_APBE = 184
	GGA_X_PBEINT = 60
	GGA_X_PBE_TCA = 59
	GGA_X_LAMBDA_LO_N = 45
	GGA_X_LAMBDA_CH_N = 44
	GGA_X_LAMBDA_OC2_N = 40
	GGA_X_PBE_MOL = 49
	GGA_X_BGCP = 38
	GGA_X_PBEFE = 265
	GGA_K_APBE = 185
	GGA_K_REVAPBE = 55
	GGA_K_TW1 = 187
	GGA_K_TW2 = 188
	GGA_K_TW3 = 189
	GGA_K_TW4 = 190
	GGA_K_APBEINT = 54
	GGA_K_REVAPBEINT = 53
	GGA_X_PBEA = 121
	GGA_X_PW86 = 108
	GGA_X_RPW86 = 144
	GGA_K_FR_PW86 = 515
	GGA_X_PW91 = 109
	GGA_X_MPW91 = 119
	GGA_K_LC94 = 521
	GGA_X_Q2D = 48
	GGA_X_RPBE = 117
	GGA_X_SFAT = 530
	GGA_X_SOGGA11 = 151
	GGA_X_SSB_SW = 90
	GGA_X_SSB = 91
	GGA_X_SSB_D = 92
	GGA_X_VMT_PBE = 71
	GGA_X_VMT_GE = 70
	GGA_X_VMT84_PBE = 69
	GGA_X_VMT84_GE = 68
	GGA_X_WC = 118
	GGA_X_WPBEH = 524
	GGA_XC_XLYP = 166
	GGA_XC_PBE1W = 173
	GGA_XC_MPWLYP1W = 174
	GGA_XC_PBELYP1W = 175
	GGA_XC_B97_D = 170
	GGA_XC_HCTH_93 = 161
	GGA_XC_HCTH_120 = 162
	GGA_XC_HCTH_147 = 163
	GGA_XC_HCTH_407 = 164
	GGA_C_HCTH_A = 97
	GGA_XC_B97_GGA1 = 96
	GGA_XC_HCTH_P14 = 95
	GGA_XC_HCTH_P76 = 94
	GGA_XC_HCTH_407P = 93
	GGA_C_N12 = 80
	GGA_C_N12_SX = 79
	GGA_C_GAM = 33
	GGA_XC_EDF1 = 165
	GGA_X_OPTPBE_VDW = 141
	GGA_XC_MOHLYP = 194
	GGA_XC_MOHLYP2 = 195
	GGA_X_SOGGA = 150
	GGA_XC_OBLYP_D = 67
	GGA_XC_OPWLYP_D = 66
	GGA_XC_OPBE_D = 65
	GGA_XC_TH_FL = 196
	GGA_XC_TH_FC = 197
	GGA_XC_TH_FCFO = 198
	GGA_XC_TH_FCO = 199
	GGA_XC_TH1 = 154
	GGA_XC_TH2 = 155
	GGA_XC_TH3 = 156
	GGA_XC_TH4 = 157
	GGA_XC_VV10 = 255
	HYB_GGA_XC_CAP0 = 477
	HYB_GGA_X_N12_SX = 81
	HYB_GGA_X_SOGGA11_X = 426
	HYB_GGA_XC_B97 = 407
	HYB_GGA_XC_B97_1 = 408
	HYB_GGA_XC_B97_2 = 410
	HYB_GGA_XC_B97_K = 413
	HYB_GGA_XC_B97_3 = 414
	HYB_GGA_XC_SB98_1a = 420
	HYB_GGA_XC_SB98_1b = 421
	HYB_GGA_XC_SB98_1c = 422
	HYB_GGA_XC_SB98_2a = 423
	HYB_GGA_XC_SB98_2b = 424
	HYB_GGA_XC_SB98_2c = 425
	HYB_GGA_XC_WB97 = 463
	HYB_GGA_XC_WB97X = 464
	HYB_GGA_XC_WB97X_V = 466
	HYB_GGA_XC_WB97X_D = 471
	HYB_GGA_XC_B97_1p = 266
	HYB_GGA_XC_LC_VV10 = 469
	HYB_GGA_XC_B1WC = 412
	HYB_GGA_XC_B1LYP = 416
	HYB_GGA_XC_B1PW91 = 417
	HYB_GGA_XC_mPW1PW = 418
	HYB_GGA_XC_mPW1K = 405
	HYB_GGA_XC_BHANDH = 435
	HYB_GGA_XC_BHANDHLYP = 436
	HYB_GGA_XC_MPWLYP1M = 453
	HYB_GGA_XC_B3PW91 = 401
	HYB_GGA_XC_B3LYP = 402
	HYB_GGA_XC_B3LYP5 = 475
	HYB_GGA_XC_B3P86 = 403
	HYB_GGA_XC_MPW3PW = 415
	HYB_GGA_XC_MPW3LYP = 419
	HYB_GGA_XC_MB3LYP_RC04 = 437
	HYB_GGA_XC_REVB3LYP = 454
	HYB_GGA_XC_B3LYPs = 459
	HYB_GGA_XC_CAM_B3LYP = 433
	HYB_GGA_XC_TUNED_CAM_B3LYP = 434
	HYB_GGA_XC_CAMY_B3LYP = 470
	HYB_GGA_XC_CAMY_BLYP = 455
	HYB_GGA_XC_EDF2 = 476
	HYB_GGA_XC_HSE03 = 427
	HYB_GGA_XC_HSE06 = 428
	HYB_GGA_XC_LRC_WPBEH = 465
	HYB_GGA_XC_LRC_WPBE = 473
	HYB_GGA_XC_HJS_PBE = 429
	HYB_GGA_XC_HJS_PBE_SOL = 430
	HYB_GGA_XC_HJS_B88 = 431
	HYB_GGA_XC_HJS_B97X = 432
	HYB_GGA_XC_LCY_BLYP = 468
	HYB_GGA_XC_LCY_PBE = 467
	HYB_GGA_XC_O3LYP = 404
	HYB_GGA_XC_X3LYP = 411
	HYB_GGA_XC_PBEH = 406
	HYB_GGA_XC_PBE0_13 = 456
	HYB_GGA_XC_HPBEINT = 472
	MGGA_XC_TPSSLYP1W = 242
	MGGA_C_BC95 = 240
	MGGA_C_CC06 = 229
	MGGA_C_CS = 72
	MGGA_C_M08_HX = 78
	MGGA_C_M08_SO = 77
	MGGA_C_M11 = 76
	MGGA_C_M11_L = 75
	MGGA_C_MN12_L = 74
	MGGA_C_MN12_SX = 73
	MGGA_C_MN15_L = 261
	MGGA_C_MN15 = 269
	MGGA_C_PKZB = 239
	MGGA_C_TPSS = 231
	MGGA_C_REVTPSS = 241
	MGGA_C_TPSSLOC = 247
	MGGA_C_SCAN = 267
	MGGA_C_M05 = 237
	MGGA_C_M05_2X = 238
	MGGA_C_VSXC = 232
	MGGA_C_M06_L = 233
	MGGA_C_M06_HF = 234
	MGGA_C_M06 = 235
	MGGA_C_M06_2X = 236
	MGGA_C_DLDF = 37
	MGGA_X_2D_PRHG07 = 210
	MGGA_X_2D_PRHG07_PRP10 = 211
	MGGA_X_BR89 = 206
	MGGA_X_BJ06 = 207
	MGGA_X_TB09 = 208
	MGGA_X_RPP09 = 209
	MGGA_X_GVT4 = 204
	MGGA_X_LTA = 201
	MGGA_X_M05 = 214
	MGGA_X_M05_2X = 215
	MGGA_X_M06_2X = 218
	MGGA_X_M06_L = 203
	MGGA_X_M06_HF = 216
	MGGA_X_M06 = 217
	MGGA_X_M08_HX = 219
	MGGA_X_M08_SO = 220
	MGGA_X_M11 = 225
	MGGA_X_M11_L = 226
	MGGA_X_MBEEF = 249
	MGGA_X_MBEEFVDW = 250
	MGGA_X_MK00 = 230
	MGGA_X_MK00B = 243
	MGGA_X_MN12_L = 227
	MGGA_X_MN15_L = 260
	MGGA_X_MS0 = 221
	MGGA_X_MS1 = 222
	MGGA_X_MS2 = 223
	MGGA_X_MVS = 257
	MGGA_X_PKZB = 213
	MGGA_X_SCAN = 263
	MGGA_X_TAU_HCTH = 205
	MGGA_X_TPSS = 202
	MGGA_X_MODTPSS = 245
	MGGA_X_REVTPSS = 212
	MGGA_X_BLOC = 244
	MGGA_XC_B97M_V = 254
	MGGA_XC_OTPSS_D = 64
	MGGA_XC_ZLP = 42
	HYB_MGGA_X_MVSH = 474
	HYB_MGGA_XC_M05 = 438
	HYB_MGGA_XC_M05_2X = 439
	HYB_MGGA_XC_B88B95 = 440
	HYB_MGGA_XC_B86B95 = 441
	HYB_MGGA_XC_PW86B95 = 442
	HYB_MGGA_XC_BB1K = 443
	HYB_MGGA_XC_MPW1B95 = 445
	HYB_MGGA_XC_MPWB1K = 446
	HYB_MGGA_XC_X1B95 = 447
	HYB_MGGA_XC_XB1K = 448
	HYB_MGGA_XC_M06_HF = 444
	HYB_MGGA_XC_M06 = 449
	HYB_MGGA_XC_M06_2X = 450
	HYB_MGGA_XC_PW6B95 = 451
	HYB_MGGA_XC_PWB6K = 452
	HYB_MGGA_XC_TPSSH = 457
	HYB_MGGA_XC_REVTPSSH = 458
	HYB_MGGA_X_DLDF = 36
	HYB_MGGA_XC_M08_HX = 460
	HYB_MGGA_XC_M08_SO = 461
	HYB_MGGA_XC_M11 = 462
	HYB_MGGA_X_MN12_SX = 248
	HYB_MGGA_X_MN15 = 268
	HYB_MGGA_X_MS2H = 224
	HYB_MGGA_X_SCAN0 = 264
	HYB_MGGA_XC_WB97M_V = 531
	# end_include_dont_touch