Sphere Packing

This is an example using pyparm to generate a packing of spherocylinders, for the purpose of using them with ParView.


In [1]:
%load_ext autoreload
%autoreload 1

In [2]:
%aimport pyparm
%aimport pyparm.packmin
%aimport parview
import pyparm.d3 as sim
from pyparm.packmin import Minimizer

In [3]:
mn = Minimizer.randomized(80)
mn.itersteps = 100
locs = []
diams = []
names = names = [[str(round(d, 4)), str(n)] for n,d in enumerate(mn.diameters)]
for n, (P0, Fm) in enumerate(mn):
    if n % 10 == 0:
        print('{:4d} {:8.3g}, {:8.3g}. phi {:8.6f}'.format(n, P0, Fm, mn.phi))
    locs.append(mn.locs / mn.L % 1.0)
    diams.append(mn.diameters / mn.L)


   0   -0.997,  0.00158. phi 0.011555
  10   -0.993,  0.00067. phi 0.027166
  20    -0.99,  0.00049. phi 0.042718
  30   -0.983, 0.000554. phi 0.058211
  40   -0.981, 0.000424. phi 0.073610
  50   -0.971, 0.000365. phi 0.088906
  60   -0.955, 0.000567. phi 0.104050
  70   -0.955, 0.000461. phi 0.119029
  80   -0.948, 0.000396. phi 0.133944
  90   -0.941, 0.000333. phi 0.151008
 100   -0.918, 0.000287. phi 0.194879
 110   -0.871, 0.000226. phi 0.237006
 120    -0.82, 0.000233. phi 0.277011
 130   -0.821, 0.000249. phi 0.315880
 140   -0.643,  0.00124. phi 0.355829
 150   -0.597, 0.000867. phi 0.419531
 160   -0.424, 0.000511. phi 0.487084
 170    -0.16,  0.00104. phi 0.556929
 180 -0.00773, 0.000463. phi 0.608381
 190  0.00382, 0.000152. phi 0.619045
 200 0.000973, 7.12e-05. phi 0.625876
 210 0.000947, 3.66e-05. phi 0.627315
 220  0.00273, 7.27e-05. phi 0.628106
 230 9.95e-05, 9.24e-06. phi 0.628481
 240 3.13e-05, 4.92e-05. phi 0.628713
 250  -0.0033, 3.32e-05. phi 0.629705
 260 0.000274, 7.44e-06. phi 0.629851
 270 1.48e-09, 2.58e-11. phi 0.629855

In [4]:
locs = np.asarray(locs)
diams = np.asarray(diams)
s = parview.to_json(locs - 0.5, diams, names=names, L=1.0)
with open('packing_test.json', 'wt') as f:
    f.write(s)

In [7]:
s.encode()


Out[7]:
b'[{"spheres": [{"diameter": 0.052818640460908214, "loc": [0.16439099372541366, 0.1796084219151588, -0.39124502256232885], "names": ["1.0", "0"]}, {"diameter": 0.052818640460908214, "loc": [-0.40230337702310937, -0.4428610904555445, 0.14639428761303497], "names": ["1.0", "1"]}, {"diameter": 0.052818640460908214, "loc": [-0.29289372653327517, 0.007474957537074833, 0.015613305388615384], "names": ["1.0", "2"]}, {"diameter": 0.052818640460908214, "loc": [-0.43952426672131073, -0.40662570351498656, -0.15049761308916182], "names": ["1.0", "3"]}, {"diameter": 0.052818640460908214, "loc": [-0.27139184848915704, 0.26779732809220613, -0.015917100919745575], "names": ["1.0", "4"]}, {"diameter": 0.052818640460908214, "loc": [0.1824241849350402, -0.292735486537074, -0.04668956694321108], "names": ["1.0", "5"]}, {"diameter": 0.052818640460908214, "loc": [0.39555090516879154, -0.34595927446971914, -0.38402591046413415], "names": ["1.0", "6"]}, {"diameter": 0.052818640460908214, "loc": [-0.22229578688772123, 0.48094617788576566, 0.010794509414975617], "names": ["1.0", "7"]}, {"diameter": 0.052818640460908214, "loc": [0.09645201851832796, 0.4641393740283303, 0.35907777034461286], "names": ["1.0", "8"]}, {"diameter": 0.052818640460908214, "loc": [-0.4680160144951799, 0.16257680748074432, -0.08123482987626224], "names": ["1.0", "9"]}, {"diameter": 0.052818640460908214, "loc": [-0.2856352096669988, 0.3415740943598886, -0.2857478582511248], "names": ["1.0", "10"]}, {"diameter": 0.052818640460908214, "loc": [-0.22046897607428817, -0.3897126629543167, -0.028755677765474996], "names": ["1.0", "11"]}, {"diameter": 0.052818640460908214, "loc": [-0.43552828755563266, 0.20482104746788388, -0.26096853398165815], "names": ["1.0", "12"]}, {"diameter": 0.052818640460908214, "loc": [-0.3689929487253671, -0.0394584524719771, 0.11426132610576922], "names": ["1.0", "13"]}, {"diameter": 0.052818640460908214, "loc": [-0.27045874454119667, 0.4329041464892487, -0.453503916770864], "names": ["1.0", "14"]}, {"diameter": 0.052818640460908214, "loc": [0.13121352515193396, -0.10856987360595194, 0.28326697501591225], "names": ["1.0", "15"]}, {"diameter": 0.052818640460908214, "loc": [0.14757939086785532, -0.38526931758574334, -0.1637637097424403], "names": ["1.0", "16"]}, {"diameter": 0.052818640460908214, "loc": [-0.4691350671934864, 0.21305084694686827, 0.26923302035354146], "names": ["1.0", "17"]}, {"diameter": 0.052818640460908214, "loc": [-0.23487693733638754, 0.036067340794813996, 0.2596314093347226], "names": ["1.0", "18"]}, {"diameter": 0.052818640460908214, "loc": [0.1973078081902132, 0.21734740951005915, 0.008361200829130944], "names": ["1.0", "19"]}, {"diameter": 0.052818640460908214, "loc": [-0.47517202389252977, 0.26444914728988567, 0.27949360704306636], "names": ["1.0", "20"]}, {"diameter": 0.052818640460908214, "loc": [-0.10608269493655764, 0.14450752900433594, -0.1422365100929423], "names": ["1.0", "21"]}, {"diameter": 0.052818640460908214, "loc": [0.4592853794933347, -0.13810438714268614, -0.33952882228757963], "names": ["1.0", "22"]}, {"diameter": 0.052818640460908214, "loc": [0.32478367291805943, -0.004096790954666751, -0.0701543213085683], "names": ["1.0", "23"]}, {"diameter": 0.052818640460908214, "loc": [0.08312246295340187, -0.047659555220363636, 0.02057422688255972], "names": ["1.0", "24"]}, {"diameter": 0.052818640460908214, "loc": [-0.4002657303834255, 0.31407545671766435, -0.36094643016424355], "names": ["1.0", "25"]}, {"diameter": 0.052818640460908214, "loc": [-0.30472113607046125, -0.023386208204661363, -0.22101425029727656], "names": ["1.0", "26"]}, {"diameter": 0.052818640460908214, "loc": [0.2774836413068529, -0.07079040674369164, 0.22830579562606856], "names": ["1.0", "27"]}, {"diameter": 0.052818640460908214, "loc": [0.2398806281613437, 0.21522819888512013, 0.42878606262334196], "names": ["1.0", "28"]}, {"diameter": 0.052818640460908214, "loc": [-0.39121643215526347, 0.27593645316541016, 0.302120835344993], "names": ["1.0", "29"]}, {"diameter": 0.052818640460908214, "loc": [0.46807650306848614, 0.4391317974333856, -0.11185980373992971], "names": ["1.0", "30"]}, {"diameter": 0.052818640460908214, "loc": [0.4544260904690075, 0.2917490262003246, 0.3387245696329464], "names": ["1.0", "31"]}, {"diameter": 0.052818640460908214, "loc": [-0.19560873474489093, 0.3778872290342141, 0.39762260656029125], "names": ["1.0", "32"]}, {"diameter": 0.052818640460908214, "loc": [-0.13230247182415994, 0.43172076422874184, 0.3814082564540663], "names": ["1.0", "33"]}, {"diameter": 0.052818640460908214, "loc": [0.3417974698516312, -0.036875317035911126, 0.26783834449088184], "names": ["1.0", "34"]}, {"diameter": 0.052818640460908214, "loc": [0.25184974432214713, -0.2231269117869783, -0.3841989460045532], "names": ["1.0", "35"]}, {"diameter": 0.052818640460908214, "loc": [-0.4799488029832419, 0.17697348601486762, -0.17890162944213833], "names": ["1.0", "36"]}, {"diameter": 0.052818640460908214, "loc": 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In [9]:
import gzip
with gzip.open('packing_test.json.gz', 'wb') as f:
    f.write(s.encode())

In [ ]: