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Re: [Question #293445]: Polyhedra Elements, Infinite Loop.

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: MikeZhao <question293445@xxxxxxxxxxxxxxxxxxxxx>
Date: Mon, 09 May 2016 07:57:37 -0000
Reply-to: question293445@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

MikeZhao gave more information on the question:
####Hi, I have tried to reproduce this bug, and the script is as
following:##############################

from libyade import yade
from yade import *


mat = PolyhedraMat()
mat.density = 2600 * 10e15 #kg/m^3 
mat.Ks = 1.5e8 
mat.Kn = 2E9   #Pa
mat.frictionAngle = 0.5 #rad
yade.O.materials.append(mat)
coords = dict()
coords[0] = [yade.Vector3(0.12506498908304559,0.004170586360067608,0.04718878419835185),
  yade.Vector3(0.07196917639353285,0.002130673955178613,0.04829019846239369),
  yade.Vector3(0.12452553414402667,0.05548698237982243,0.09674610334959563),
  yade.Vector3(0.10202107066713305,0.003501573781327025,0.09778836768091179)]
coords[1] = [yade.Vector3(0.14295032259085494,-0.006505603044225198,0.10466693700014766),
  yade.Vector3(0.11566808726849623,0.04373180022224347,0.10573503009510624),
  yade.Vector3(0.09295451012074624,-0.008001021823003239,0.10600124068861566),
  yade.Vector3(0.11621529452629992,-0.007042223507702154,0.05542740653091893)]
coords[2] = [yade.Vector3(0.2130315465641754,0.09686131087477995,0.053289505254753),
  yade.Vector3(0.164020561929353,0.04648070412681492,0.004219224080575502),
  yade.Vector3(0.1862772963099485,0.09652671335229797,0.00417259537268409),
  yade.Vector3(0.16288263942085443,0.09471008739327443,0.055098349410302505)]
coords[3] = [yade.Vector3(0.17228834709600793,0.10610590338541123,0.04456793567930975),
  yade.Vector3(0.17280626014182954,0.056807096563525575,-0.00527106604700384),
  yade.Vector3(0.19547690664041997,0.1064874328191193,-0.006528797650868522),
  yade.Vector3(0.1454828764592455,0.10501383881798207,-0.004532778418338768)]
coords[4] = [yade.Vector3(0.12518512144479108,0.004202482634043023,0.047282108263384234),
  yade.Vector3(0.07215900355266172,0.0022067170630582396,0.048405189227085095),
  yade.Vector3(0.09927440181878336,0.002841487802841776,-0.0020490482509290323),
  yade.Vector3(0.12194553936223902,0.053900337377603164,-0.003137962336613641)]
coords[5] = [yade.Vector3(0.1230094368221373,-0.01217837847454617,0.0385941766299165),
  yade.Vector3(0.09606163246660983,-0.009341849627069044,-0.010265958898953698),
  yade.Vector3(0.14605505129391785,-0.007892828978239817,-0.012758832943173034),
  yade.Vector3(0.1191666025858279,0.04146035772028468,-0.007885859751166355)]
coords[6] = [yade.Vector3(0.11631337631682945,-0.0072190647263523505,0.05526504476519887),
  yade.Vector3(0.11546679195549954,0.04339612477093768,0.10546948815801681),
  yade.Vector3(0.16283607913807063,0.09468384437456645,0.054801725781359986),
  yade.Vector3(0.1660494458383337,0.04445695707723045,0.10422688539183134)]
coords[7] = [yade.Vector3(0.12517826549319078,0.004210666781740674,0.04713033641567168),
  yade.Vector3(0.12503175035775993,0.05566147427541226,0.09662450106256898),
  yade.Vector3(0.1218967526875405,0.054092789281228446,-0.0033114695372207723),
  yade.Vector3(0.1723941910681486,0.10613783179410324,0.04465530410432424)]
coords[8] = [yade.Vector3(0.16282407041415756,0.0946878041824045,0.054807634434872056),
  yade.Vector3(0.1660391862703065,0.044454782962754805,0.10419776714643575),
  yade.Vector3(0.1641981030564517,0.04610198242630093,0.004203199959939556),
  yade.Vector3(0.11627599902436038,-0.007311015046615452,0.05527225087207195)]
coords[9] = [yade.Vector3(0.1255192872383347,0.004248839377251908,0.04705512287925926),
  yade.Vector3(0.12177640027256077,0.05401449241996102,-0.003310973765333125),
  yade.Vector3(0.17288309620166054,0.0567881426706257,-0.005251109507840107),
  yade.Vector3(0.17239800601486288,0.10615025111591658,0.04466410423643576)]
coords[10] = [yade.Vector3(0.16586255674847272,0.04442314808389014,0.10431426071039843),
  yade.Vector3(0.16306972984454005,0.09458742037006168,0.05488233416872211),
  yade.Vector3(0.13921142362682418,0.09338844867941465,0.1051850240520792),
  yade.Vector3(0.11532750614560142,0.043572756568788916,0.10524886894605867)]
coords[11] = [yade.Vector3(0.12553762857591796,0.05564020559697192,0.09672553666297364),
  yade.Vector3(0.12188774949220496,0.10432230228089284,0.04742164646483482),
  yade.Vector3(0.1723696031234631,0.10635275656158034,0.044620790102675174),
  yade.Vector3(0.14933095821244555,0.10569338022640279,0.09538317504306985)]
coords[12] = [yade.Vector3(0.2173311133734367,-0.00291435614061983,0.050878549630080615),
  yade.Vector3(0.2640348114070128,0.049396955137835985,0.0007687422103086969),
  yade.Vector3(0.23998126829150335,-0.0013654269667168015,0.0010097662543496304),
  yade.Vector3(0.26756518846385796,-0.0012810266002693128,0.0498993551659514)]
coords[13] = [yade.Vector3(0.21732797257016542,-0.002825738834439564,0.050857917624400034),
  yade.Vector3(0.2643104682138871,0.04965977725183429,0.0007946325029359932),
  yade.Vector3(0.21413337322661294,0.04673315137371154,0.002351451925924373),
  yade.Vector3(0.24055205822558823,-0.0012623876073627402,0.0011263572685819498)]
coords[14] = [yade.Vector3(0.11684058402337372,-0.009085754058001015,0.053739409517626374),
  yade.Vector3(0.11352951793316718,0.04177187066030047,0.004183023745490649),
  yade.Vector3(0.14217323386012334,-0.006452989526700384,0.0036098497893789668),
  yade.Vector3(0.1644013694517449,0.046503493854378464,0.004326814858653941)]
coords[15] = [yade.Vector3(0.2637084356089881,0.09876764976853986,0.05149223178153213),
  yade.Vector3(0.2396959807904555,0.09713654031739888,0.10229009831087897),
  yade.Vector3(0.2162816917857142,0.046327041778708195,0.10245497928163774),
  yade.Vector3(0.21311703372008567,0.09711576927222242,0.05302719647038486)]
coords[16] = [yade.Vector3(0.21285320791337656,0.09658584790099281,0.05320182231155868),
  yade.Vector3(0.21631826791890899,0.04629077883262786,0.10293727691506004),
  yade.Vector3(0.18921467064374317,0.09530049338079472,0.10395023930415494),
  yade.Vector3(0.23920000479363665,0.09726114269413852,0.1025765819700781)]
coords[17] = [yade.Vector3(0.34002725035910075,0.04510048314337398,0.055229611320042546),
  yade.Vector3(0.3537383479282825,0.0633432928241428,0.10015084407696109),
  yade.Vector3(0.39,0.049999999999999996,0.05000000000000001),
  yade.Vector3(0.3579867164836035,0.032435620079630995,0.10012409288993937)]
coords[18] = [yade.Vector3(0.33965202062041133,0.04388634694938733,0.056306530706325866),
  yade.Vector3(0.3181560969204755,0.04776502972123622,0.10129061767786542),
  yade.Vector3(0.35411889382007816,0.06274439181159348,0.1009636758226479),
  yade.Vector3(0.35835334390410967,0.03194857065409507,0.10128707730315725)]
coords[19] = [yade.Vector3(0.26765968163680837,-0.0013996803064605014,0.050006718727664934),
  yade.Vector3(0.2937720333371553,-0.0008968116225207979,0.09922004099051618),
  yade.Vector3(0.320377362490132,0.048645236636886295,0.09869326038971472),
  yade.Vector3(0.3206610508063692,0.0006884377120860586,0.04839969849996756)]
coords[20] = [yade.Vector3(0.34036714726459744,-0.0006157988211561698,0.10171287876066418),
  yade.Vector3(0.31792097293982446,0.04735244221615521,0.1015664894544708),
  yade.Vector3(0.29052236039763824,-0.0018253296576239489,0.10279441934247124),
  yade.Vector3(0.31803466441498207,-0.0016869346711861043,0.05233186967437706)]
coords[21] = [yade.Vector3(0.3400645078465372,0.044654441938417444,0.055678191490572244),
  yade.Vector3(0.3582731453457583,-0.00020115906228151612,0.0679040496817514),
  yade.Vector3(0.39,0.05,0.05),
  yade.Vector3(0.35370638101308,-0.00047072650172147804,0.03742176358472203)]
coords[22] = [yade.Vector3(0.33891903942075335,0.043959993624221545,0.056271348929241814),
  yade.Vector3(0.3583800423588044,-0.0006776292816765301,0.0685709303240885),
  yade.Vector3(0.3532629620454773,-0.0011831930813333748,0.038011584213163245),
  yade.Vector3(0.31806518411358586,-0.0019153589786597477,0.05260708614676338)]
coords[23] = [yade.Vector3(0.3406269898265739,0.04657526158645474,0.053043034734462084),
  yade.Vector3(0.32052223811247904,0.0007491795858403753,0.04847150875387509),
  yade.Vector3(0.2675342454496866,-0.0013481437843854312,0.050047038102188246),
  yade.Vector3(0.32038131192820174,0.04866089379029212,0.09873867451138933)]
coords[24] = [yade.Vector3(0.33918270943891493,0.04393504824189187,0.05652576776216966),
  yade.Vector3(0.3179654906992738,0.04743828153760772,0.10164895600924545),
  yade.Vector3(0.34020232114985094,-0.0005759042896867211,0.101581650702399),
  yade.Vector3(0.3180049163583329,-0.0014344008598424912,0.052410777200650426)]
coords[25] = [yade.Vector3(0.33901541297196697,0.04469184827417817,0.056856826000989985),
  yade.Vector3(0.35403774480164457,0.06338011654963487,0.10089548378903998),
  yade.Vector3(0.3175693020287492,0.10011103678176002,0.051253166616434725),
  yade.Vector3(0.3580630462644306,0.09987706317939782,0.06771936175129514)]
coords[26] = [yade.Vector3(0.34053586096688865,0.04339847491990612,0.05666752641470075),
  yade.Vector3(0.3540083185549232,0.0630046649758691,0.10130130947233994),
  yade.Vector3(0.3180205197838511,0.04789034177813378,0.10107531114591663),
  yade.Vector3(0.318602256931087,0.09822556011100168,0.050476946523659465)]
coords[27] = [yade.Vector3(0.337384272433711,0.043418836853125836,0.056605547794034296),
  yade.Vector3(0.3172133683552361,-0.0025247347691041283,0.05356110766153559),
  yade.Vector3(0.3518314497979043,-0.0013486960823002637,0.03783554302438926),
  yade.Vector3(0.3474758292969533,0.034875862694859906,0.0011365542177931634)]
coords[28] = [yade.Vector3(0.33813221766393536,0.03990918021053585,0.0561296214491587),
  yade.Vector3(0.31688586538353886,-0.005554197143124332,0.05426599875436915),
  yade.Vector3(0.34763043594979237,0.030158530153556413,0.00038646968017986075),
  yade.Vector3(0.3120645123998747,0.04347001974912851,0.003035071297441013)]
coords[29] = [yade.Vector3(0.35404232027656607,-0.000670643504559202,0.03690447930206717),
  yade.Vector3(0.35261891512921917,0.03574021035919348,-0.0001513192883540876),
  yade.Vector3(0.31831949137691445,-0.0013133155476704253,0.050801057513527814),
  yade.Vector3(0.33900205841719544,-0.0013676463346582873,0.00037653426304356044)]
coords[30] = [yade.Vector3(0.3154773468107035,0.0478768025523955,-0.0003750241046195837),
  yade.Vector3(0.3190499767431456,-0.0031392067964503174,0.050152930972242084),
  yade.Vector3(0.3514640273227352,0.035501839689338385,-0.002201924690814242),
  yade.Vector3(0.33813832165789937,-0.0012890242076914991,-0.001809090413772028)]
coords[31] = [yade.Vector3(0.3580924270641726,0.10017025769423288,0.06777878908986454),
  yade.Vector3(0.33948671784631596,0.10034062934973582,0.10038417185863124),
  yade.Vector3(0.35366871277080814,0.06353542477163918,0.10046210591887281),
  yade.Vector3(0.3179499121703136,0.10056259321104632,0.05088722450776048)]
coords[32] = [yade.Vector3(0.3189082909278394,0.09837382421905506,0.050493268853504934),
  yade.Vector3(0.31826221342282685,0.047970601072941536,0.10107077276795723),
  yade.Vector3(0.33965803782789994,0.09946556907853178,0.10044412991767684),
  yade.Vector3(0.35416393420034176,0.06279833526006104,0.10144124757201503)]
coords[33] = [yade.Vector3(0.3397917115871815,0.04502675296269275,0.05533494881536639),
  yade.Vector3(0.3582025309008199,0.00014317880452878462,0.06773148040352515),
  yade.Vector3(0.3397896019539308,0.0002139526155162906,0.10041107475863192),
  yade.Vector3(0.3583821268454569,0.032529385549693764,0.10013384643749264)]
coords[34] = [yade.Vector3(0.33926138542192047,0.04404557863148736,0.05633113647108027),
  yade.Vector3(0.31801514769589545,0.0478091340063702,0.10141702834969835),
  yade.Vector3(0.35829000021093327,0.032050334524335075,0.10103805972439606),
  yade.Vector3(0.33997820637409987,-0.000405281742036457,0.10164263572831539)]
coords[35] = [yade.Vector3(0.33917696238715855,0.04395275291909157,0.056415897913316776),
  yade.Vector3(0.35817913519278016,-0.0006979958348646825,0.06862464815061284),
  yade.Vector3(0.31794736857556527,-0.0013834147240980362,0.05234229554410741),
  yade.Vector3(0.34014424662193654,-0.0007181946948149279,0.10158235261824326)]
coords[36] = [yade.Vector3(0.32626755857514134,0.19993023923781864,0.03751521632763393),
  yade.Vector3(0.3880185032688292,-0.047969499938545775,-0.07118306196681137),
  yade.Vector3(0.4506599953638908,-0.00244015316986685,0.04501276188915119),
  yade.Vector3(0.3985724364081437,0.032660022851117576,-0.0759416864150217)]
coords[37] = [yade.Vector3(0.3688475294737572,-0.031221969043579392,0.00904276630084963),
  yade.Vector3(0.3714685179171974,0.061797426598395266,0.09982968121832222),
  yade.Vector3(0.28151631529669574,0.09815357525595161,-0.0010489953610023708),
  yade.Vector3(0.32419954528516537,0.11014178251520193,-0.013023860246014464)]
coords[38] = [yade.Vector3(0.3305004669998695,0.046880195004764695,0.06035146013424279),
  yade.Vector3(0.3034576935181306,0.05277199053208914,0.007970200772785867),
  yade.Vector3(0.3397625368175628,0.10287529382148378,0.04286391449965104),
  yade.Vector3(0.30593906536383525,0.10035925497929359,0.05938913454615629)]
coords[39] = [yade.Vector3(0.3395956045436123,0.043303679750040666,0.05439412885607389),
  yade.Vector3(0.39,0.05000000000000002,0.049999999999999996),
  yade.Vector3(0.3601275064432374,0.06876674446712282,0.0016581609218861114),
  yade.Vector3(0.3561944415857906,0.03791445402708607,0.00010229252095118532)]
coords[40] = [yade.Vector3(0.34065675817181956,0.046757366236683,0.053183761179815395),
  yade.Vector3(0.3201379107535674,0.04853325851556118,0.09872487581553677),
  yade.Vector3(0.2672037719032582,0.0478384040243767,0.10061003735262794),
  yade.Vector3(0.31643426729685215,0.10115503479665185,0.0502757950712653)]
coords[41] = [yade.Vector3(0.3417478438562951,0.04545587536766879,0.05590543719633538),
  yade.Vector3(0.35471159596578805,0.10022084127887285,0.03690972865246111),
  yade.Vector3(0.35840081313672734,0.06704378441255258,0.00042536976878146046),
  yade.Vector3(0.39,0.075,0.025000000000000005)]
coords[42] = [yade.Vector3(0.3332553478726043,0.1103111348872082,-0.0003136328083456299),
  yade.Vector3(0.3153917343169667,0.058460055456408005,-0.011186365118382382),
  yade.Vector3(0.3516163770831925,0.10170877452128037,0.03524635480284278),
  yade.Vector3(0.3540869592044894,0.07857076579771193,-0.010499902915645143)]
coords[43] = [yade.Vector3(0.3274940510809254,0.10776125144117334,-0.0025979864743322888),
  yade.Vector3(0.3085078227069035,0.05712746553725052,-0.0028690543080733266),
  yade.Vector3(0.310075651775672,0.10483282362269161,0.04978514301785493),
  yade.Vector3(0.3449888056890983,0.10731753619717507,0.03294166663079286)]
coords[44] = [yade.Vector3(0.3394570666922459,0.04521007510462394,0.05761767553780922),
  yade.Vector3(0.3180154801176482,0.1002207730904212,0.05142867739475787),
  yade.Vector3(0.35412043517865244,0.09964440763636444,0.03762578193660765),
  yade.Vector3(0.3584500389747902,0.10036310263242866,0.06820207334998866)]
coords[45] = [yade.Vector3(0.34141247866615343,0.04445271430229274,0.05511767527479387),
  yade.Vector3(0.3546458974331371,0.036193159505438596,-0.00044090088417408566),
  yade.Vector3(0.3564335635811485,-0.0003517053876518142,0.03687878717856112),
  yade.Vector3(0.39,0.025,0.025)]
coords[46] = [yade.Vector3(0.05017839882110636,0.04477824410745488,0.04498935656219054),
  yade.Vector3(0.03515419676529324,0.06310211844755091,0.00009608932388172411),
  yade.Vector3(0.04921093901242242,0.09990731156112101,-0.0003070484653836282),
  yade.Vector3(0.033732806543292713,0.09965194064520293,0.03492406248747011)]
coords[47] = [yade.Vector3(0.049696240452831615,0.04693953247805987,0.04404401057309133),
  yade.Vector3(0.04642974946011187,0.10201041614970373,-0.0008504226393848263),
  yade.Vector3(0.06792028301008651,0.10252059859662326,0.0494392254971401),
  yade.Vector3(0.031571915167676275,0.10126490833734197,0.034870461389054565)]
coords[48] = [yade.Vector3(0.3434751552224152,0.10529395374488333,-0.002508391278708763),
  yade.Vector3(0.3563463665376061,0.10339146156874146,0.035758154690780364),
  yade.Vector3(0.39,0.1,-8.673617379884035e-18),
  yade.Vector3(0.35987993159250903,0.0706985152579884,-0.0017507853318611856)]
coords[49] = [yade.Vector3(0.340200875430057,0.04629627319033907,0.05303066398373089),
  yade.Vector3(0.31615048561082176,0.051130632003293125,-0.0011608946308054521),
  yade.Vector3(0.26721234363134605,-0.0014217803383828435,0.05000726835901002),
  yade.Vector3(0.3200918660393349,0.0006058525328950133,0.04847417030786972)]
coords[50] = [yade.Vector3(0.05000942105609215,0.04643868525677235,0.04356336509456606),
  yade.Vector3(0.03339896917522457,0.06381047293651679,-0.0011554607377499016),
  yade.Vector3(0.06979576574945677,0.05204063359005626,-0.0022670134585104414),
  yade.Vector3(0.04610258269263751,0.10116891705797729,-0.0016609154487266884)]
coords[51] = [yade.Vector3(0.0496294351533465,0.045189308005676436,0.0446863473595121),
  yade.Vector3(0.030053815415883103,0.10006160316423646,0.06870766397837277),
  yade.Vector3(0,0.05,0.05),
  yade.Vector3(0.03383875550213479,0.09995518255646706,0.03487398936369969)]
coords[52] = [yade.Vector3(0.04957445069636635,0.046942847092024745,0.0439884329959704),
  yade.Vector3(0.028815159335200864,0.10094236589010112,0.06871835405236817),
  yade.Vector3(0.031592504903322695,0.101414091803428,0.034826400865550805),
  yade.Vector3(0.06800291914441199,0.10248938070951155,0.049530629472430976)]
coords[53] = [yade.Vector3(0.34076805465555476,0.04455410425253957,0.05523108045052036),
  yade.Vector3(0.39,0.049999999999999996,0.05),
  yade.Vector3(0.35433100318670296,0.03637856332726638,-0.000050973327122560974),
  yade.Vector3(0.39,0.024999999999999994,0.02499999999999999)]
coords[54] = [yade.Vector3(0.3389012636970622,0.0013423407249780039,-0.00365088549986288),
  yade.Vector3(0.31672545125398055,0.051295009774042305,-0.0005488706559895855),
  yade.Vector3(0.31959206444695065,-0.0013374035037279613,0.047403320349323624),
  yade.Vector3(0.28893838079763884,0.00044022730488731295,-0.001671509988844324)]
coords[55] = [yade.Vector3(0.3552495586085922,0.03714209333486319,0.00012142895818941998),
  yade.Vector3(0.39,0.05,0.05),
  yade.Vector3(0.3591108670291623,0.06756414768330807,0.00003237248766895656),
  yade.Vector3(0.39,0.075,0.025)]
coords[56] = [yade.Vector3(0.3326969494787476,0.044904686993537515,0.05563976325691751),
  yade.Vector3(0.3091453064715574,0.050855419984827566,0.0012789518833821803),
  yade.Vector3(0.3123134193948781,0.10078824078763467,0.05105376195821165),
  yade.Vector3(0.2599282954001859,0.10235713170824758,0.05282180779001569)]
coords[57] = [yade.Vector3(0.2843422420655907,0.09923764072670029,0.0017509703149992707),
  yade.Vector3(0.3149247182477903,0.10014113962941198,0.051054925324999154),
  yade.Vector3(0.3134544472122879,0.05000051401426121,0.0013937881371087618),
  yade.Vector3(0.2620584814051718,0.0994895512265356,0.052400041855008926)]
coords[58] = [yade.Vector3(0.3400311370155243,0.0458587415791786,0.05324962895171098),
  yade.Vector3(0.26333601397832596,0.09861467525304587,0.0513735302773009),
  yade.Vector3(0.2631673435631067,0.04921171541657626,0.0006390913014940845),
  yade.Vector3(0.3160569810192673,0.05102121717520493,-0.0009803624421689978)]
coords[59] = [yade.Vector3(0.04971633366050463,0.045265229435627705,0.044746977864694684),
  yade.Vector3(0.03143401096746476,0.032710177008707944,-0.00023309350765968184),
  yade.Vector3(0.03533989204823962,0.06334209273733228,-0.0002131586944926385),
  yade.Vector3(2.0816681711721685e-17,0.05,0.04999999999999999)]
coords[60] = [yade.Vector3(0.04946742922439447,0.046672343917341604,0.043558321263417035),
  yade.Vector3(0.03073285869944652,0.03278077152481386,-0.0011015352733618946),
  yade.Vector3(0.06992477921834403,0.05194778743585704,-0.0020119141816365566),
  yade.Vector3(0.03353053832780498,0.0638050457047234,-0.0014337628830923873)]
coords[61] = [yade.Vector3(0.32770567530773703,0.11137604522482,-0.009973300831847935),
  yade.Vector3(0.3107704672525277,0.10556108641082654,0.04287299911769453),
  yade.Vector3(0.3083995426255764,0.060695768678551185,-0.01299915951015336),
  yade.Vector3(0.27796555009534213,0.10914547705638583,-0.005236757296721847)]
coords[62] = [yade.Vector3(0.3405460089465247,0.04672468468677354,0.05333597083639236),
  yade.Vector3(0.31629274905985166,0.10103305863870843,0.050497572132385544),
  yade.Vector3(0.2672794399688527,0.04787325322725318,0.10046405156744936),
  yade.Vector3(0.26343072387940986,0.09904888480352328,0.05176079103379818)]
coords[63] = [yade.Vector3(0.2630518843461558,0.04915182849052646,0.0006470299953058589),
  yade.Vector3(0.31570518510315126,0.05083373765541963,-0.0011216060744026809),
  yade.Vector3(0.2631568596582025,0.09880120273577873,0.05144073777689125),
  yade.Vector3(0.285404552399122,0.09995331255219878,0.0006259655653348042)]
coords[64] = [yade.Vector3(0.39,0.075,0.02500000000000001),
  yade.Vector3(0.39,0.1,-1.734723475976807e-18),
  yade.Vector3(0.3544290330189974,0.10051854106317909,0.03645821795191911),
  yade.Vector3(0.3587173035913949,0.0680326865512382,-0.00030850231174175957)]
coords[65] = [yade.Vector3(0.04956668563287012,0.04556918682487886,0.044674075276778136),
  yade.Vector3(0.030607360570378623,0.032186597746470695,0.09988440605724103),
  yade.Vector3(1.0408340855860843e-17,0.04999999999999998,0.05000000000000002),
  yade.Vector3(0.033990437462080345,0.06530761153821317,0.09980253600663341)]
coords[66] = [yade.Vector3(0.04941503772746345,0.046353730626855036,0.044366249177514916),
  yade.Vector3(0.0310501060039661,0.032547843484774755,0.09952756532768975),
  yade.Vector3(0.03410054603531969,0.06576964704109514,0.09948369348590935),
  yade.Vector3(0.07039490804709367,0.05112498941899609,0.09875097610502102)]
coords[67] = [yade.Vector3(0.3400446573651375,0.045377620113847425,0.05570088101969649),
  yade.Vector3(0.3582989301538421,0.10020341652202924,0.06791365862061104),
  yade.Vector3(0.3540580906481444,0.10026578968121491,0.03737796575626966),
  yade.Vector3(0.39000000000000007,0.04999999999999999,0.05)]
coords[68] = [yade.Vector3(0.3402396204211532,0.04430770782031176,0.05557158319392032),
  yade.Vector3(0.39,0.05,0.05),
  yade.Vector3(0.39,0.025,0.024999999999999998),
  yade.Vector3(0.3547509647721951,-0.00039522822398567817,0.03697219640524982)]
coords[69] = [yade.Vector3(0.39,3.469446951953614e-18,3.469446951953614e-18),
  yade.Vector3(0.35431485762538717,0.036556261035973744,-0.00009225369413471546),
  yade.Vector3(0.39,0.025,0.025),
  yade.Vector3(0.3541899401444528,-0.00023392859647868545,0.03652979646927742)]
coords[70] = [yade.Vector3(0.04984279152693431,0.04547745108625738,0.044759271633182385),
  yade.Vector3(0.029736500804246415,0.10026948547939302,0.06868510676472478),
  yade.Vector3(0.0342532871439357,0.06530114536183888,0.09973333755625383),
  yade.Vector3(4.163336342344337e-17,0.07499999999999998,0.07499999999999998)]
coords[71] = [yade.Vector3(0.04908882895418844,0.046595140311610835,0.044113020365703526),
  yade.Vector3(0.028835291899109446,0.1007764857624299,0.068652326113262),
  yade.Vector3(0.06808354167594313,0.10212157216756822,0.049375835122775276),
  yade.Vector3(0.03465178645361693,0.06549742300039849,0.09957616709619158)]
coords[72] = [yade.Vector3(0.3392198194364152,-0.0010461937886508347,0.0006587026913589446),
  yade.Vector3(0.35441939118207477,-0.000375431479610883,0.03719749055893131),
  yade.Vector3(0.3530284904108212,0.03585200816496293,0.0003300769402833272),
  yade.Vector3(0.39,1.734723475976807e-18,1.734723475976807e-18)]

O.dt = 0.0001
for i in range(73):
    b = yade.utils.tetraPoly(coords[i], dynamic=None, fixed=True, wire=True, color=None, highlight=False, noBound=False, material=mat, mask=1, chain=-1)
    O.bodies.append(b)

# basic YADE engines fo tetrahedra contact
O.engines = [
	ForceResetter(),
	InsertionSortCollider([Bo1_Polyhedra_Aabb()]),
	InteractionLoop(
		[Ig2_Polyhedra_Polyhedra_PolyhedraGeom()],
		[Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
		[Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]
	),
	NewtonIntegrator(damping=0),
]


#################################################################################

After calling O.step() for several times, this bug will occur.
By the way, 
in Polyhedra_support.cpp, I have modified 
#define DISTANCE_LIMIT 1E-8 ##(Default value is 2E-11)
#define MERGE_PLANES_LIMIT 1E-8 ##(Default value is 1E-18)

I have visualized those polyhedra, noticing that there are several large
polyhedra on the top, it seems those large polyhedra have enormous
contact with others, and there might be some extreme situations among
them.

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