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Description
Here is an example to compute the SNAP descriptor
Fe Cr Ni Co
1.000
8.6838020000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 11.6856200000000001 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.7084440000000001
Fe Cr Ni Co
24 24 24 24
Direct
0.7482575028771959 -0.0816076511130775 0.3883573700870691 Fe1
0.5343281663953185 0.0288952575900979 0.3132773685286716 Fe2
0.5622318426882603 0.2385316311843103 0.1511473701660075 Fe3
0.7481285271128937 0.7766134787884598 0.7153413794517141 Fe4
0.3321333213263039 -0.0855795413508226 0.7144947010665091 Fe5
0.5391762732498968 0.0335597084279653 0.4714349810840590 Fe6
0.3313652245871106 0.1336403203253229 0.5499914568241132 Fe7
0.1363354438528193 0.2537109712621153 0.3041714379858374 Fe8
0.1454385993600499 0.2468178838606766 0.4724108893280582 Fe9
0.5615259306925698 0.2338652121154034 0.3182250259796578 Fe10
0.3454569784064630 0.3612765090769681 0.3863215223608398 Fe11
-0.0802360532863370 0.5788670177534441 0.2252648320864880 Fe12
0.5579307312626428 0.4554880271650114 0.3094004727648391 Fe13
0.3435684047148934 0.5635533245133763 0.2321312028104120 Fe14
0.7354808412259976 0.1289208445936116 0.7146665831447087 Fe15
0.1303046753023618 0.2432605201949062 0.6314304586756014 Fe16
-0.0711457953555367 0.3532247326200921 0.7198230454906928 Fe17
0.3516052070279815 0.1294257386428790 0.7233498110952301 Fe18
0.3292382760454464 0.3580854075350731 0.7128777363308549 Fe19
-0.0755287833600996 0.5873817563809195 0.5544374732468729 Fe20
0.3316001447292327 0.5713980088347901 0.5521126089891525 Fe21
-0.0808023950799431 0.5789440354897729 0.3809066002972669 Fe22
0.1301457587356322 0.6830694477486005 0.3042682012298608 Fe23
0.1136251148978293 0.6809471812364257 0.4710231006966699 Fe24
-0.0629766777271062 0.7822109567143207 0.0620468838288503 Cr1
0.3420241502512379 -0.0818901350548794 0.0666151275072184 Cr2
-0.0589433061693484 0.7896928019223627 0.8762675666666920 Cr3
0.1481033307760817 0.0170644775373493 -0.0166913412938926 Cr4
-0.0802710609937905 0.1389228812848612 0.8747397259715858 Cr5
0.3324960656634041 -0.0846104015020170 0.8779354594255167 Cr6
0.5380719182680581 0.0240461353355663 -0.0110061824073727 Cr7
0.1242439659494770 0.0195702068011796 0.1633280801077433 Cr8
0.5622894211544667 0.0306807854439901 0.1504019112268535 Cr9
-0.0707330729097693 0.1248363373103010 0.0638242718374907 Cr10
0.1224302442639756 0.2551854330365013 -0.0231583726561332 Cr11
0.3326480728141890 0.1330096306400516 0.0601577088093512 Cr12
0.3252204506735644 0.3380650748526822 0.0563682182652846 Cr13
0.7349822117086502 0.3440185458709080 0.8717731686219208 Cr14
0.1206856167379220 0.4500865165904762 -0.0281405338428173 Cr15
0.7331811572857142 0.5612753110232919 0.8688066112722559 Cr16
0.3390323731471538 0.3499454885577317 0.8772988591358890 Cr17
0.5579123061534568 0.4578464814019282 -0.0166411135310410 Cr18
0.3436731975233889 0.5644698355756905 0.8742495437485724 Cr19
0.1127261998834151 0.4451248628656417 0.1599833821860396 Cr20
0.7480548266761495 0.5674718157872668 0.0624883024696781 Cr21
0.1228551733445788 0.6794889787619314 -0.0161173824727643 Cr22
0.3418433538673498 0.5537250056051798 0.0612010966840509 Cr23
0.5440416536443370 0.6905572832250236 -0.0073627279697467 Cr24
0.3350986123359331 0.1266787727138141 0.8795524241611709 Ni1
-0.0549199532647106 0.1238659138325566 0.2494416378859676 Ni2
0.3528212642342605 0.1327349340471451 0.2386697243851778 Ni3
0.1425205226927099 0.2378692786518816 0.1421649400793611 Ni4
-0.0715646211187220 0.3375533347824078 0.0606942991934784 Ni5
0.5312212323588216 0.2429669970442304 -0.0114670810170632 Ni6
0.1226594065594771 0.0317491070221349 0.6413047657680162 Ni7
0.3187129324229180 0.1414302364786806 0.3880607143521026 Ni8
-0.0787332553183502 0.3481098991752256 0.2333814857792408 Ni9
0.3374696935743123 0.3441537547857966 0.2199963280895294 Ni10
0.5406456757074839 0.4580210549376071 0.1386298986710587 Ni11
0.1275282416618896 0.6776679371740653 0.1449710741560399 Ni12
0.5407285886988210 0.6823206642009582 0.1449869891632806 Ni13
0.1202618392266429 0.0341061064795877 0.7945153574727071 Ni14
0.5436996375550709 0.0126254319411379 0.8078075715201327 Ni15
0.1509776478091048 0.2482375774670064 0.8035359835767311 Ni16
0.5267992061541708 0.2384725842531248 0.8045545440401353 Ni17
0.5358804818442429 0.4561777637814682 0.4772477783286492 Ni18
0.5275350589522885 0.4516953315271248 0.6431700046166252 Ni19
0.1212637045386341 0.4564430470954901 0.7983158612017842 Ni20
0.1092871532538397 0.6684395008566084 0.6430044885413221 Ni21
0.1359070600642438 0.6692148127356530 0.7985004752857763 Ni22
0.5260668080640255 0.6670934019761040 0.6326291770209704 Ni23
0.5278229512833205 0.6699576060149141 0.7988888014624491 Ni24
0.3247598229439133 -0.0728384116546662 0.3938123979688886 Co1
-0.0781391607040326 -0.0817373832111604 0.2259218035853838 Co2
0.1363861129030809 0.0293432440897445 0.3136771535105578 Co3
0.3365184973125827 -0.0862230673254821 0.2320147049574102 Co4
0.7477300841267455 -0.0729075564668370 0.5596633250244263 Co5
0.1181878628738886 0.0220193708164394 0.4799889791757860 Co6
0.7315355647215356 0.1390041777843195 0.5585295399085995 Co7
0.3088589537163560 0.7846370154086818 0.5560423425770242 Co8
0.5596154771838419 0.0103439098652874 0.6362635280744547 Co9
-0.0614055916981986 0.1478654962252752 0.4016209371214616 Co10
-0.0847649451242670 0.3488980473436583 0.4066067905898254 Co11
0.5360244280097588 0.2380635344979556 0.4683290082709656 Co12
0.1154908875167812 0.4579286336540124 0.3099473124136292 Co13
0.5321563066500133 0.2357846652552454 0.6340901746856659 Co14
0.7427449405225960 0.3583626713858571 0.5621632543617942 Co15
0.1180116727672971 0.4500728245484621 0.4755410529521575 Co16
0.1249867281635394 0.4639642569243224 0.6349432190737669 Co17
0.3241045799984845 0.3533736335769946 0.5600631100063125 Co18
0.3350226087605406 0.5706817438869312 0.3891830406627162 Co19
0.5259942591966054 0.6907395585343353 0.3089058343397984 Co20
0.5117700749049783 0.6953999873348612 0.4733320499471494 Co21
0.5257627937624557 0.4601527347286665 0.8000856100069491 Co22
0.7353564717389918 0.5652793775597701 0.7147175111678788 Co23
0.3195558811681796 0.5677105707698864 0.7078931560630702 Co24
from pyxtal_ff.descriptors.SNAP import SO4_Bispectrum
from ase.io import read
import time
test = read('POSCAR', format='vasp')
print(test)
lmax, rcut = 3, 5.0
weights = {'Co': 0.6,
'Cr': 0.4,
'Fe': 0.7,
'Ni': 0.5}
f = SO4_Bispectrum(weights,
lmax = lmax,
rcut = rcut,
derivative = True, #dxdr
stress = True, #rdxdr
)
x = f.calculate(test)
for key, item in x.items():
if type(item) == list:
print(key, type(item), len(item))
else:
print(key, type(item), item.shape)Executing the above script should give you the following output
Atoms(symbols='Co24Cr24Fe24Ni24', pbc=True, cell=[8.683802, 11.68562, 15.708444])
x <class 'numpy.ndarray'> (96, 30)
dxdr <class 'numpy.ndarray'> (3026, 30, 3)
elements <class 'list'> 96
seq <class 'numpy.ndarray'> (3026, 2)
rdxdr <class 'numpy.ndarray'> (3026, 30, 3, 3)
list of output:
x: N_atoms * N_descriptorsdxdr: [N_distance_pairs, N_descriptors, 3]elements: [N_atoms]seq: [N_distance_pairs, 2]rdxdr: [N_distance_pairs, N_descriptors, 3, 3]
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