仓库源文站点原文


layout: post title: 三维空间随机旋转 categories:


生成分子初始构型的时候, 经常需要对分子进行随机旋转. 这并不是一个困难的工作, 因为早就有成熟的方法了. 在这里我展示几种不同的实现方法, 供参考.

下面是四种不同方法分别得到的球面上的随机点

Marsaglia方法

<figure><script>var Mol1=new ChemDoodle.TransformCanvas3D('Mol-1',642,396);Mol1.specs.shapes_color='#fff';Mol1.specs.backgroundColor='black';Mol1.specs.set3DRepresentation('Ball and Stick');Mol1.specs.projectionPerspective_3D=false;Mol1.specs.compass_display=true; /*//Mol1.specs.atoms_resolution_3D=15; //Mol1.specs.bonds_resolution_3D=15; //Mol1.specs.crystals_unitCellLineWidth=1.5;*/ Mol1.nextFrame=function(delta){var matrix=[];ChemDoodle.lib.mat4.identity(matrix);var change=delta*Math.PI/15000;ChemDoodle.lib.mat4.rotate(matrix,change,[1,0,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,1,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,0,1]);ChemDoodle.lib.mat4.multiply(this.rotationMatrix, matrix)}; Mol1.startAnimation=ChemDoodle._AnimatorCanvas.prototype.startAnimation;Mol1.stopAnimation=ChemDoodle._AnimatorCanvas.prototype.stopAnimation;Mol1.isRunning=ChemDoodle._AnimatorCanvas.prototype.isRunning;Mol1.dblclick=ChemDoodle.RotatorCanvas.prototype.dblclick;Mol1.timeout=5;Mol1.handle=null; var Fmol='1000\nRot. 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-1.608890\nH -0.293118 -3.160337 3.863463\nH -0.681419 -2.443330 -4.308805\nH 3.694539 2.715555 -1.994027\nH -3.778260 2.627827 -1.954296\nH 1.466902 -1.431002 -4.560749\nH 1.123690 1.891557 -4.489914\nH 4.375621 -0.666625 2.325844\nH -3.543796 1.673985 3.104720\nH 4.428153 -1.945230 1.267889\nH -1.377484 -3.425005 3.372222\nH 2.277456 1.561333 -4.168385\nH -1.438679 3.986639 2.652718\nH 0.543904 -3.252749 -3.758164\nH 1.606126 -1.618737 -4.449725\nH 1.716631 -4.586538 -1.008391\nH 4.423405 -0.057203 -2.330283\nH 0.867236 -1.940037 -4.525943\nH 4.762937 0.170261 -1.511769\nH 1.742883 4.672895 -0.355546\nH -2.689850 2.298029 3.533238\nH 0.085245 -4.888417 1.046955\nH -3.361781 0.552555 -3.659660\nH -4.390504 1.892907 1.463001\nH -3.194265 -2.749166 -2.690494\nH 2.694440 -3.543428 2.276864\nH 3.680167 1.424136 3.070539\nH 3.283753 1.632761 -3.398685\nH 3.900143 0.880367 -3.002306\nH -1.017126 3.619376 3.296297\nH -3.450405 -3.438915 -1.126308\nH 1.969910 4.590144 -0.223688\nH -3.963141 -2.694184 1.426494\nH -1.648708 -4.661836 -0.740976\nH -4.016274 -2.644010 -1.370676\nH -4.429879 -2.001843 -1.169955\nH -2.801171 -3.697362 1.866268\nH 0.578743 1.170902 -4.826390\nH -3.289595 -0.556401 3.724108\nH 2.109627 -1.839226 -4.143274\nH 4.992085 0.270494 0.076969\nH 4.463134 -0.005203 -2.253976\nH -4.713037 1.430145 -0.861372\nH 3.966628 2.724035 1.358489\nH 3.985601 2.310194 -1.943703\nH 2.563108 1.620736 3.975386\nH 3.935024 -0.554809 3.034432\nH 3.029493 -3.210152 2.348850\nH -3.188725 -2.853827 2.586060\nH 2.161166 -1.502824 -4.250986\nH 4.465117 -1.641860 1.538513\nH -0.882569 -2.632049 4.158532\nH 1.010737 -3.624194 3.292966\nH 3.786068 2.689919 1.852032\nH -2.494009 -2.974786 -3.151280\nH -1.688994 4.535149 -1.256868\nH 1.322456 4.640774 -1.309325\nH 1.743589 -4.620360 0.782410\nH -0.313964 -0.254712 4.983628\nH -0.180770 4.853833 1.186437\nH 2.941771 2.512003 -3.167937\nH 1.405856 2.556703 4.060399\nH 2.403939 -2.441433 3.641494\nH 4.934524 0.716344 -0.370570\nH 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-3.391285 -2.800416\nH -4.925403 0.770962 0.382132\nH -1.428581 0.028145 -4.791489\nH -1.831908 -2.781363 -3.729362\nH -4.044255 -0.826634 -2.821467\nH 0.468960 2.461344 -4.326876\nH -1.480276 -3.318271 3.434802\nH 1.508302 4.733230 0.567061\nH 3.242691 -3.733402 -0.739368\nH 0.300437 3.696898 -3.353012\nH -0.812267 1.834756 4.579726\nH -2.984183 3.698537 -1.554180\nH -4.496761 2.038510 -0.789695\nH 3.231711 2.221388 3.101851\nH -3.558272 2.727482 2.213491\nH -3.698813 2.674524 -2.041005\nH 0.313085 -4.519438 2.115812\nH 3.923677 3.098726 0.051520\nH 1.994252 -4.108331 -2.035823\nH 1.353244 -2.416827 4.162652\nH 0.858927 3.318996 -3.639575\nH 2.694772 3.106779 2.843612\nH 2.509926 2.528767 -3.507935\nH 2.001328 -4.281450 1.632137\nH 1.952761 4.327233 1.569005\nH 1.714596 -4.682423 -0.367530\nH -0.846501 4.564950 -1.855981\nH -1.764797 -4.641770 -0.582631\nH 4.632134 0.126356 -1.878130\nH -2.195671 -4.491328 -0.083667\nH -1.179270 4.847932 -0.326924\nH -0.007614 2.737857 -4.183788\nH 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1.873107\nH -0.701380 0.289344 4.942099\nH -1.296801 -3.192092 3.623376\nH -1.696904 1.704303 4.383591\nH 2.703106 1.036157 4.076714\nH 3.368096 0.179021 3.691054\nH -0.744035 4.588111 -1.842728\nH 1.646972 -4.054191 -2.418888\nH 0.014143 4.039158 2.947033\nH 0.800202 4.196883 -2.597278\nH 2.075168 -0.639302 -4.503884\nH -0.400980 4.848589 1.153429\nH 4.471191 1.873035 1.224823\nH -2.637607 3.432418 -2.502305\nH -0.696213 -3.907879 -3.040357\nH -3.621148 -1.474989 -3.116359\nH -2.562562 4.291149 -0.138982\nH -1.579986 -0.367483 4.729545\nH -2.373213 -4.390488 -0.302458\nH -0.199782 -2.890404 -4.075003\nH -2.449341 -2.931302 -3.226174\nH 1.031010 4.092502 -2.681128\nH -0.343113 -4.198036 -2.694210\nH 4.614871 1.919541 -0.135396\nH -0.058877 3.166111 -3.869402\nH 0.037682 -4.936811 0.791504\nH 0.471883 2.221437 -4.454497\nH -2.883361 3.783446 -1.540053\nH -2.809018 3.685593 -1.877717\nH -3.153463 3.584465 -1.485694\nH -2.973558 4.007867 0.308149\nH 1.902158 -3.810101 2.620100\nH -4.835412 0.469247 -1.182623\nH -1.310667 -0.858402 -4.748189\nH 1.216938 -4.410348 -2.016901\nH 4.940977 -0.424739 -0.637450\nH -4.531005 -1.023454 -1.850010\nH -1.481715 2.597825 -4.006972\nH -4.488745 -1.662551 -1.444678\nH 1.870132 -3.786549 -2.676687\nH 4.331122 2.230854 -1.124575\nH 4.238893 -0.456096 2.612233\nH 2.548574 3.976307 -1.641266\nH -2.262594 4.372812 -0.871310\nH 3.003222 -2.013139 -3.453683\nH -4.703013 -0.282377 -1.673897\nH -0.529976 -4.071999 2.852709\nH -2.091692 -1.621085 -4.242276\nH -1.689834 -3.453626 -3.196393\nH 0.502459 4.755628 1.459978\nH 0.960700 4.598126 -1.712978\nH 2.319395 -1.233061 -4.254406\nH 3.960916 -1.920862 2.370956\nH 3.911432 -2.615745 -1.690733\nH -1.749356 -4.425418 -1.534740\nH -1.656841 -2.931242 3.696309\nH 4.376520 2.056215 1.272026\nH -4.675767 1.202092 1.300838\nH 3.101380 3.355569 2.030173\nH -1.906570 -4.471375 -1.171237\nH -3.512801 -1.355757 3.289704\nH 1.345661 0.057223 4.815176\nH -0.339499 -4.225023 -2.652154\nH -0.166753 -4.894267 -1.009129\nH -2.993715 -3.334116 -2.218409\nH -1.379571 -4.805805 0.031941\nH -1.929206 1.947659 4.181482\nH 2.957975 2.881516 -2.819087\nH 2.692866 2.446178 -3.429969\nH 3.631832 -3.304397 0.943798\nH -0.982396 -4.737039 -1.263075\nH 1.544250 -4.359420 1.900197\nH -1.838816 4.553896 -0.938502\nH 3.600753 -2.299401 -2.597563\nH 0.520322 -0.130521 -4.971140\nH -1.060180 -4.777090 -1.027342\nH -3.586604 -2.800387 -2.072221\nH -1.833120 -4.202217 1.995256\nH -1.588563 2.344507 -4.120650\nH -3.577907 3.263491 -1.244270\nH 3.031461 3.962145 -0.334138\nH 1.432983 -4.481632 -1.691608\nH -0.011619 1.800174 4.664680\nH 0.697692 4.393768 2.282111\nH -0.472673 -4.955187 -0.471912\nH -3.071165 1.243115 -3.744678\nH 3.172501 2.330875 -3.082573\nH -2.045319 1.792031 4.195866\nH 3.667690 -1.323284 3.130011\nH -0.082528 1.580592 4.742881\nH 4.799404 1.380634 -0.244068\nH 4.368058 -0.231272 -2.422104\nH -1.935585 -4.058268 2.187230\nH -2.428737 -4.349540 -0.427481\nH 3.812723 -2.715055 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0.780497 -4.356487 2.326338\nH 2.750465 1.313700 3.963475\nH -1.011760 0.974754 -4.798562\nH -4.770384 0.866390 1.221805\nH 3.766999 -1.213399 -3.055713\nH -1.164476 -2.538103 -4.147533\nH -4.341670 2.466491 0.257535\nH -2.240410 -1.265336 -4.287131\nH 1.486989 4.590931 1.308517\nH 0.135118 4.971818 0.512608\nH 1.745693 4.520176 -1.233114\nH -2.965549 2.583005 3.087654\nH -3.774633 -3.032613 1.247159\nH -4.363068 -0.815623 2.301825\nH -1.121328 -4.870588 -0.141397\nH -0.894615 1.429711 -4.706972\nH 2.141341 -2.051960 -4.025434\nH -4.262038 -0.993019 -2.418459\nH -0.044248 4.977168 -0.475225\nH -3.987260 0.588450 2.958966\nH 4.612100 -1.836727 0.595794\nH 3.809963 2.118515 -2.448689\nH -0.416735 0.513667 4.956055\nH 1.679929 3.193249 3.461358\nH -0.989149 1.325956 4.718413\nH 4.719728 0.522674 1.565560\nH -2.222684 4.469975 -0.281061\nH -4.651128 -0.983341 -1.549209\nH -1.325749 3.579009 -3.230028\nH 2.212298 4.427428 0.709662\nH -2.470769 3.363574 2.753483\nH -3.936642 -0.545411 -3.034037\nH -2.180656 2.355318 3.833695\nH 2.676204 4.212713 -0.301632\nH -0.935074 -3.248969 -3.683726\nH -3.908905 -1.438340 -2.766159\nH -4.550876 1.665113 -1.231638\nH -0.664549 -0.228522 4.950369\nH 4.634746 -1.187338 -1.452364\nH 1.543326 -0.944582 -4.661106\nH 0.527477 -4.507064 -2.099558\nH -1.159769 4.783676 -0.878281\nH 1.505540 -0.936622 4.675050\nH 2.393779 -3.648220 -2.441375\nH 3.853746 3.169725 0.318566\nH 1.448594 -1.921070 -4.383043\nH -4.002663 -2.923079 -0.659009\nH 3.305459 3.742332 0.262475\nH 4.263958 2.610483 -0.063558\nH 1.015315 -4.871482 -0.487647\nH 1.057485 -0.105277 4.885759\nH 4.374704 -2.400636 0.314494\nH 4.612624 1.551834 -1.146958\nH -2.985555 3.207724 2.407690\nH 4.153620 -2.478167 1.267332\nH 2.884882 -0.898451 3.983747\nH -4.022449 1.015938 -2.790658\nH 0.853027 3.127824 3.806450\nH -4.387252 0.687265 2.297756\nH 2.180084 3.098087 -3.263294\nH 4.688512 0.710436 -1.585286\nH -0.927620 2.269302 -4.357727\nH -3.787604 -2.161688 -2.445642\nH -0.696996 2.039276 4.511712\nH 0.052653 -0.501226 4.974535\nH -0.307840 0.852294 4.917197\nH -3.620961 2.469813 -2.405964\nH -2.920770 2.139202 3.448611\nH 3.197435 -2.074474 -3.236197\nH 0.187388 -2.871036 4.089259\nH -3.704733 -3.350557 0.220729\nH -0.184317 0.090023 4.995791\nH 0.549766 -4.067568 2.855284\nH 2.771242 4.002482 1.140331\nH -4.951773 -0.473849 0.505387\nH -4.695198 -1.541735 0.760373\nH 1.599682 -4.686973 -0.687970\nH 2.688984 0.172577 -4.211838\nH 4.691218 -1.728474 -0.069643\nH -0.027042 1.699672 4.702168\nH -3.375368 2.702023 2.511168\nH -1.005328 -2.675709 4.102426\nH -0.181281 3.372780 -3.686664\nH -1.873360 2.538420 3.879040\nH 3.664832 3.349655 -0.590609\nH 4.501456 0.364612 -2.145682\nH -0.314450 4.262790 -2.594174\nH -0.162052 4.454705 -2.264806\nH -4.850576 -0.849993 -0.865691\nH -4.475822 -2.205814 0.318437\nH -2.694205 2.586055 -3.324692\nH 1.648458 -4.644068 0.845705\nH 1.963680 -3.367973 3.130610\nH 4.570587 0.964576 -1.783067\nH -1.098495 4.877771 0.025608\nH 3.373180 1.927227 -3.147611\nH 2.878991 -3.478566 2.147321\nH -2.129399 -0.413588 4.504953\nH -3.266877 3.408860 -1.645353\nH -0.914746 3.531343 3.419482\nH 2.573630 4.076729 1.325410\nH -3.059430 2.799546 -2.793283\nH -2.292741 -2.816558 3.436618\nH 1.051224 -1.139406 -4.753597\nH 2.520274 -2.981204 -3.124203\nH -3.774966 3.246150 0.460586\nH -2.138298 -3.597967 2.735382\nH 3.549202 -1.272001 3.284080\nH 0.432275 -4.953616 0.524244\nH 2.828516 -2.534625 -3.251949\nH -2.172365 -3.280776 -3.085019\nH 3.401710 -1.609141 -3.292269\nH -1.861038 2.787160 -3.710563\nH -4.933747 -0.219168 -0.781092\nH -3.510795 -3.257190 1.437021\nH 1.878884 0.420633 -4.614419\nH 1.986378 3.905877 2.407992\nH 0.791640 -2.122517 4.457379\nH 4.012967 2.024142 -2.190649\nH 1.797444 -1.272131 4.488973\nH -4.164560 -2.580834 -0.997866\nH -4.560926 1.660480 1.200318\nH 0.834993 1.154134 4.792782\nH -3.116028 -3.788030 0.970153\nH 4.395761 -0.962649 -2.179585\nH -3.797631 2.797261 -1.659316\nH 3.781780 -2.490371 2.120422\nH 1.739653 -1.447316 -4.458574\nH 4.142824 0.769746 -2.691560\nH -2.205519 4.346457 -1.115347\nH -0.090285 -0.230270 4.993879\nH -2.325752 2.047141 -3.924295\nH -0.011432 -1.075446 4.882959\nH 2.240034 -1.401754 4.244683\nH -0.195365 1.250831 4.837071\nH 2.619928 1.848982 3.836306\nH -1.251429 4.205861 -2.396801\nH 1.056272 0.691760 -4.837950\nH 0.598657 1.537521 -4.719919\nH 0.300166 -3.826166 3.204739\nH 1.048702 1.084888 -4.766890\nH 1.219331 -1.981305 4.425795\nH -4.770524 1.001564 -1.113091\nH -0.416613 -4.347948 2.433471\nH 2.723872 -3.173255 2.740616\nH -3.621963 2.332882 -2.537528\nH -1.450760 2.879281 3.821654\nH 0.095074 -4.338861 -2.482991\nH 4.746376 -1.521661 0.395553\nH 3.283610 -3.738424 -0.492026\nH -3.390970 -0.440175 -3.647954\nH -0.410355 2.840890 -4.094014\nH 2.131603 -1.172654 4.368198\nH 1.075533 -4.700925 1.320808\nH 1.827156 0.298220 4.644628\nH -3.914654 -1.588954 -2.674081\nH 2.499480 -4.030110 -1.584553\nH -2.091481 -4.493603 0.658205\nH 0.693667 1.848722 -4.593588\nH 3.499332 -3.398927 1.096345\nH -2.107777 -4.391047 1.129595\nH -4.118779 2.299274 -1.658011\nH -4.903370 -0.479211 0.852832\nH -2.177281 -2.417318 -3.796844\nH -4.767397 0.671825 1.349286\nH 3.253708 3.349440 1.787354\nH 0.655849 -3.823500 -3.154475\nH 3.481101 2.491255 2.583716\nH -4.637564 0.425726 1.819824\nH -3.749682 -1.054031 3.135108\nH 4.903869 -0.975474 0.022709\nH -1.705999 3.637597 2.976148\nH -4.947227 -0.401758 -0.602941\nH -2.831648 3.408036 2.316692\nH -0.751980 4.676924 -1.600285\nH 1.008208 4.752537 1.181909\nH -1.900585 1.987005 -4.176073\nH -1.275842 4.608730 -1.460079\nH 1.748735 -2.804306 3.752039\nH -1.137808 -4.709145 -1.236667\nH 2.609744 -2.898880 -3.128215\nH 2.032455 -4.249330 1.676999\nH 0.139939 2.420030 4.373085\nH -3.252889 -3.680362 -0.934690\nH -4.614881 0.370424 -1.888295\nH 2.952964 0.225252 4.028556\nH 1.083598 4.520928 1.840388\nH 3.118221 -1.541206 -3.591850\nH 2.807233 -1.116561 3.984060\nH 2.439907 -1.133917 -4.214390\nH -3.310704 -0.148096 -3.743969\nH 0.725537 -3.834539 3.125685\nH 0.789801 3.252949 3.714100\nH 3.199569 -2.520924 -2.899603\nH -4.919718 0.749774 -0.483954\nH 1.834007 0.910174 4.561579\nH 1.176699 -3.408503 3.463739\nH -3.888988 3.007580 0.911175\nH 2.504926 -3.306894 2.791020\nH -3.895388 3.076570 -0.600561\nH -0.909954 -0.711505 4.864745\nH -3.710428 -2.418367 -2.320395\nH 3.046359 1.556481 3.646514\nH 4.961977 0.388837 0.477064\nH 0.317755 3.386762 -3.664543\nH 1.211436 -0.581583 4.816034\nH -0.140351 -4.984594 -0.366223\nH 0.210059 -2.792384 4.142278\nH -4.753788 1.356595 0.749101\nH 1.611293 0.037162 -4.733112\nH -2.967934 3.879382 1.068532\n'; Mol1.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol1.startAnimation();Mol1.stopAnimation();function setProj1(yesPers){Mol1.specs.projectionPerspective_3D=yesPers;Mol1.setupScene();Mol1.repaint()}function setModel1(model){Mol1.specs.set3DRepresentation(model);Mol1.setupScene();Mol1.repaint()}function setSpeed1(){Mol1.timeout=500-document.getElementById('spd1').value;Mol1.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol1.startAnimation()}</script><br><span class='meta'>视图: <input type='radio' name='group2' onclick='setProj1(true)'>投影 <input type='radio' name='group2' onclick='setProj1(false)' checked=''>正交    速度: <input type='range' id='spd1' min='1' max='500' onchange='setSpeed1()'/><br>模型: <input type='radio' name='model' onclick='setModel1('Ball and Stick')' checked=''>球棍 <input type='radio' name='model' onclick='setModel1('van der Waals Spheres')'>范德华球 <input type='radio' name='model' onclick='setModel1('Stick')'>棍状 <input type='radio' name='model' onclick='setModel1('Wireframe')'>线框 <input type='radio' name='model' onclick='setModel1('Line')'>线型   <input type='checkbox' onclick='Mol1.specs.atoms_displayLabels_3D=this.checked;Mol1.repaint()'>名称<br>左键: 转动   滚轮: 缩放   双击: 自动旋转开关   Alt+左键: 移动</span><br><figurecaption>Fig.1</figurecaption></figure>

球坐标分布方法: 生成正确分布的球坐标

<figure><script>var Mol2=new ChemDoodle.TransformCanvas3D('Mol-2',642,396);Mol2.specs.shapes_color='#fff';Mol2.specs.backgroundColor='black';Mol2.specs.set3DRepresentation('Ball and Stick');Mol2.specs.projectionPerspective_3D=false;Mol2.specs.compass_display=true; /*//Mol2.specs.atoms_resolution_3D=15; //Mol2.specs.bonds_resolution_3D=15; //Mol2.specs.crystals_unitCellLineWidth=1.5;*/ Mol2.nextFrame=function(delta){var matrix=[];ChemDoodle.lib.mat4.identity(matrix);var change=delta*Math.PI/15000;ChemDoodle.lib.mat4.rotate(matrix,change,[1,0,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,1,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,0,1]);ChemDoodle.lib.mat4.multiply(this.rotationMatrix, matrix)}; Mol2.startAnimation=ChemDoodle._AnimatorCanvas.prototype.startAnimation;Mol2.stopAnimation=ChemDoodle._AnimatorCanvas.prototype.stopAnimation;Mol2.isRunning=ChemDoodle._AnimatorCanvas.prototype.isRunning;Mol2.dblclick=ChemDoodle.RotatorCanvas.prototype.dblclick;Mol2.timeout=5;Mol2.handle=null; var Fmol='1000\nRot. Method: 2\nH -2.201301 -1.474038 4.240458\nH -4.054429 -2.193922 -1.936056\nH 1.008412 -4.268102 2.401335\nH -2.448898 4.312543 -0.636297\nH 3.343791 2.457979 2.788799\nH 2.094499 -3.533522 2.850841\nH -4.262153 0.105089 2.612089\nH 4.661351 -1.651850 -0.737022\nH -0.968710 -3.702158 3.218016\nH 2.661547 2.491581 -3.421723\nH 1.936840 -2.112929 4.096850\nH -1.374779 -4.780428 -0.507438\nH -3.001042 -3.871365 -1.003136\nH -1.427015 4.372143 1.961632\nH 4.733385 -1.324702 0.916639\nH 1.054227 -3.475182 -3.436818\nH -3.234653 -1.011517 -3.676119\nH 0.550806 -1.114158 4.843063\nH 4.817009 -1.096942 -0.770154\nH 1.869551 3.586947 2.939148\nH 4.513908 -2.037419 0.688158\nH 4.007105 0.503797 -2.947762\nH -0.537422 -3.538155 3.491795\nH 1.385183 4.052118 2.581009\nH -3.965107 1.760191 2.485891\nH 0.984809 -4.890412 -0.337675\nH 3.846612 2.664291 -1.762138\nH 3.160818 -0.447646 3.848226\nH 2.598739 4.097486 1.207132\nH 4.951701 -0.325584 -0.612086\nH -0.963455 0.196926 4.902344\nH -1.748394 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3.718913 1.247127 -3.100703\nH 3.210401 3.763674 0.726696\nH -4.741615 1.571271 0.219533\nH -4.536575 1.682324 1.260665\nH 0.235889 4.316685 -2.512088\nH 3.098067 -3.810279 0.940084\nH -0.472255 3.345971 -3.685302\nH 2.793066 -0.982660 -4.029040\nH -1.159710 0.940105 4.771926\nH -4.734634 -0.688456 -1.452331\nH -0.005134 3.688560 -3.375574\nH 1.785756 0.693442 -4.618465\nH -0.815898 -1.213053 4.781508\nH 2.283766 -4.012543 1.919351\nH 3.190200 -1.537937 -3.529500\nH 2.330425 -3.709452 -2.410204\nH -3.948323 3.066695 0.078293\nH -1.029921 1.941713 4.490993\nH 2.136283 0.391822 -4.503640\nH 0.432836 -3.729059 3.302541\nH -1.708769 -2.610156 -3.907325\nH -3.796563 -0.813021 -3.150414\nH -0.016131 3.752860 3.303904\nH 2.189949 4.465441 0.513767\nH 1.255188 -4.808271 0.552299\nH 2.896294 -0.589944 -4.032797\nH -1.187993 -3.079999 -3.755300\nH 1.274569 0.385433 -4.819431\nH 1.488555 4.580886 -1.341522\nH -1.619386 3.212671 3.472223\nH -1.875019 1.707257 -4.309243\nH -4.826135 -0.427031 1.235340\nH -0.362750 -2.720426 -4.179437\nH 4.858305 -0.157808 1.171311\nH -2.530024 -1.479180 4.051050\nH 4.123116 0.963667 2.659184\nH -3.755710 -2.201626 2.459163\nH 0.212513 -2.796559 4.139335\nH 0.114319 4.994907 -0.194523\nH 3.879985 0.765088 3.059470\nH -0.984677 4.500195 1.943878\nH 4.214478 -2.175469 1.582879\nH 0.109943 2.830471 -4.120236\nH -2.250879 -1.557148 -4.184356\nH -0.589041 0.267431 -4.957975\nH 0.163487 2.368562 4.400362\nH -0.098586 3.363557 3.698211\nH 2.721829 1.492287 3.919786\nH -4.146667 2.267467 -1.632098\nH 3.802124 0.767823 -3.155044\nH 3.171886 3.861367 -0.170239\nH 4.305348 -2.474538 0.583648\nH 3.142857 3.098038 -2.350449\nH 3.177236 -3.575622 1.456056\nH -4.100038 -2.311694 -1.686937\nH 0.373280 -4.867336 -1.081529\nH -0.288761 -2.395481 4.379302\nH -2.260993 -3.373858 2.916332\nH 0.229915 -3.813079 3.226076\nH 3.104858 -3.900743 -0.379545\nH 1.411958 1.274855 -4.623972\nH -3.258935 -0.111507 3.790371\nH -4.079462 2.738353 0.927048\nH -2.127582 2.361318 3.859737\nH -0.276772 1.692310 4.696753\nH 3.845192 -3.161532 0.468206\nH 4.861759 0.369985 1.107434\nH 0.619395 4.244715 2.568802\nH 1.388160 -4.752244 0.699421\nH 2.457859 4.058466 1.577270\nH 4.570552 -1.870015 0.783004\nH 3.926369 1.349154 2.786289\nH 0.579455 4.854750 -1.046726\nH 3.330406 -3.320105 1.698616\nH -2.202678 -2.456574 3.756788\nH -0.015250 2.031984 -4.568458\nH 1.355292 -4.546610 -1.578456\nH -4.293345 -2.561374 0.080953\nH 1.305697 4.669665 1.220404\nH -4.135327 -1.318135 -2.482255\nH 0.994987 -3.288485 -3.632612\nH -3.843001 1.713609 -2.700906\nH 4.467139 2.201684 -0.444138\nH 4.504091 2.089932 -0.587660\nH 1.256631 -4.341526 2.138230\nH 1.630770 2.852688 3.768655\nH -1.469776 -0.762265 4.717914\nH -2.570013 -1.339359 4.074451\nH 0.534220 4.890941 -0.890678\nH 0.369779 4.866990 1.084282\nH -4.971550 -0.095089 0.524066\nH -2.542629 -2.583669 3.443790\nH 3.257835 -1.802183 3.337462\nH -3.303687 -1.044583 -3.604788\nH 3.297648 3.265069 -1.861408\nH 1.337437 -1.457342 4.592104\nH -0.666649 -4.877453 -0.875233\nH 0.566748 4.575411 -1.935047\nH -4.278188 -0.367268 2.561683\nH -4.722817 -1.371612 0.902044\nH -2.413273 -4.377734 -0.107520\nH -1.252458 -4.107604 2.561042\nH -1.437832 4.759268 0.531038\nH -0.827715 2.730392 4.106074\nH 3.101059 2.550375 -2.979769\nH -2.043895 4.556168 -0.252650\nH 2.423581 -2.265661 -3.740727\nH 1.440076 0.829209 4.715781\nH -2.590694 -4.084032 1.268459\nH -0.054889 2.141449 -4.517874\nH 1.069146 -4.692985 -1.353815\nH -2.242153 2.461927 -3.729834\nH 0.013585 -3.535039 -3.536003\nH 4.331684 -2.385110 0.740114\nH 0.729333 -1.211887 -4.795769\nH 2.811111 2.014483 3.611027\nH 4.385469 -1.167397 -2.098774\nH -2.228241 2.517067 3.701259\nH -3.169441 3.638575 1.309740\nH 4.295840 0.237305 2.547439\nH 2.337289 -4.408404 -0.321016\nH -0.509412 -1.299263 -4.801293\nH 1.300063 -3.362493 3.464603\nH 1.460505 -1.646382 -4.489583\nH 3.421391 -3.246669 1.659284\nH -4.252957 1.387086 2.233461\nH -1.074505 1.987137 -4.460575\nH -2.427228 0.718800 -4.311831\nH -0.322911 -4.246766 -2.619294\nH 0.721640 -4.372623 -2.315038\nH 2.573970 -4.259624 -0.479876\nH -0.399330 -1.097113 4.861777\nH 1.577522 -4.187675 2.230427\nH 3.308316 -3.172334 1.997834\nH -3.499821 -2.376908 -2.664876\nH 4.973889 -0.489282 -0.145023\nH 0.826427 -4.849559 -0.893752\nH 2.531258 -0.320296 4.300017\nH 0.728669 -2.483212 4.278166\nH 3.763442 -3.249327 -0.527617\nH -0.042113 -2.064053 4.553890\nH -2.518388 4.117889 1.304114\nH 1.183841 -0.292113 -4.849040\nH -4.351093 -2.423737 0.439877\nH -3.857416 -0.326557 -3.164444\nH 0.140308 4.977192 0.455930\nH -4.336927 -2.020172 1.452573\n'; Mol2.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol2.startAnimation();Mol2.stopAnimation();function setProj2(yesPers){Mol2.specs.projectionPerspective_3D=yesPers;Mol2.setupScene();Mol2.repaint()}function setModel2(model){Mol2.specs.set3DRepresentation(model);Mol2.setupScene();Mol2.repaint()}function setSpeed2(){Mol2.timeout=500-document.getElementById('spd2').value;Mol2.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol2.startAnimation()}</script><br><span class='meta'>视图: <input type='radio' name='group2' onclick='setProj2(true)'>投影 <input type='radio' name='group2' onclick='setProj2(false)' checked=''>正交    速度: <input type='range' id='spd2' min='1' max='500' onchange='setSpeed2()'/><br>模型: <input type='radio' name='model' onclick='setModel2('Ball and Stick')' checked=''>球棍 <input type='radio' name='model' onclick='setModel2('van der Waals Spheres')'>范德华球 <input type='radio' name='model' onclick='setModel2('Stick')'>棍状 <input type='radio' name='model' onclick='setModel2('Wireframe')'>线框 <input type='radio' name='model' onclick='setModel2('Line')'>线型   <input type='checkbox' onclick='Mol2.specs.atoms_displayLabels_3D=this.checked;Mol2.repaint()'>名称<br>左键: 转动   滚轮: 缩放   双击: 自动旋转开关   Alt+左键: 移动</span><br><figurecaption>Fig.2</figurecaption></figure>

四元数方法: 生成随机的单位四元数

<figure><script>var Mol3=new ChemDoodle.TransformCanvas3D('Mol-3',642,396);Mol3.specs.shapes_color='#fff';Mol3.specs.backgroundColor='black';Mol3.specs.set3DRepresentation('Ball and Stick');Mol3.specs.projectionPerspective_3D=false;Mol3.specs.compass_display=true; /*//Mol3.specs.atoms_resolution_3D=15; //Mol3.specs.bonds_resolution_3D=15; //Mol3.specs.crystals_unitCellLineWidth=1.5;*/ Mol3.nextFrame=function(delta){var matrix=[];ChemDoodle.lib.mat4.identity(matrix);var change=delta*Math.PI/15000;ChemDoodle.lib.mat4.rotate(matrix,change,[1,0,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,1,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,0,1]);ChemDoodle.lib.mat4.multiply(this.rotationMatrix, matrix)}; Mol3.startAnimation=ChemDoodle._AnimatorCanvas.prototype.startAnimation;Mol3.stopAnimation=ChemDoodle._AnimatorCanvas.prototype.stopAnimation;Mol3.isRunning=ChemDoodle._AnimatorCanvas.prototype.isRunning;Mol3.dblclick=ChemDoodle.RotatorCanvas.prototype.dblclick;Mol3.timeout=5;Mol3.handle=null; var Fmol='1000\nRot. Method: 3\nH -2.224344 4.246457 -1.421230\nH 2.168126 -0.405250 -4.487204\nH 3.292293 -2.551659 -2.765835\nH -1.490713 -2.568612 -4.022438\nH -0.469493 0.297664 4.969001\nH 3.231164 -1.867654 -3.327378\nH 2.784692 4.124846 0.480763\nH -3.978348 -0.632513 2.961870\nH 0.133999 4.817598 -1.331463\nH -0.524888 4.497387 2.120850\nH -2.151130 -4.374187 1.113162\nH -3.512321 -1.310338 3.308567\nH -3.908976 -0.870088 2.993802\nH -1.984864 3.271394 3.218431\nH 1.414715 0.648749 4.751600\nH 3.901034 -1.291734 2.848395\nH -1.983560 -1.776295 4.232052\nH -2.848584 1.363073 3.876545\nH 4.050619 1.020216 2.748025\nH -0.182675 -3.488617 3.577175\nH -4.892145 -0.477277 -0.916039\nH -4.143254 -0.930474 2.639634\nH -2.246620 1.932615 4.027120\nH -0.009129 1.614960 4.732000\nH 0.557732 -4.902164 0.811003\nH 4.633489 0.958360 -1.616270\nH 1.232010 4.758467 -0.916047\nH 0.975281 4.898421 -0.233014\nH -0.964263 -4.132787 -2.643912\nH -0.064613 4.439233 -2.299790\nH 4.244456 2.150515 -1.536188\nH -0.444816 4.261063 2.577884\nH -3.880258 3.009796 0.940599\nH 1.041092 -3.328403 3.582996\nH -1.144894 -0.485585 -4.842874\nH 4.826739 -1.299593 0.116826\nH -2.589580 4.254961 -0.435180\nH 2.037474 -2.005225 4.102167\nH 0.276891 1.213483 4.842602\nH -1.634210 2.371053 4.087477\nH -2.844165 -3.991732 0.988332\nH 0.272677 -1.368384 4.801372\nH 2.474975 3.375537 2.735004\nH -3.606039 1.465613 3.138226\nH -1.124455 -4.332126 -2.228966\nH -4.507111 1.886297 1.061998\nH -1.873098 4.311461 -1.703763\nH -0.219134 -2.494463 4.327775\nH -1.689012 1.894261 4.308017\nH 2.681547 -3.325600 2.598016\nH 1.910951 -0.255522 -4.613347\nH 0.043383 4.865033 1.153071\nH 2.680753 1.953663 -3.741225\nH -4.914306 0.684534 -0.617260\nH -4.785134 0.990781 1.058702\nH 0.452013 4.715084 1.601146\nH -1.882239 2.611042 3.826178\nH -3.712964 3.344661 -0.164740\nH -1.562385 4.609371 -1.145711\nH 2.587154 2.134963 -3.707907\nH -1.025518 4.269457 2.391663\nH 4.430859 2.165934 0.822326\nH 3.505659 2.283319 -2.738031\nH 1.123907 -1.161654 4.731532\nH 1.300239 -4.541526 1.638269\nH -3.617252 3.059831 1.597788\nH -2.583989 4.230990 -0.649404\nH 0.637453 0.491039 -4.934829\nH -2.498054 1.359448 4.112375\nH 0.580964 4.965659 0.068609\nH -0.625955 4.917593 0.652272\nH 3.034149 -0.121102 3.972313\nH -2.890217 -0.354654 4.064587\nH -4.269185 -0.209741 2.594237\nH 2.013395 3.579065 2.852460\nH 0.737845 -2.695023 4.146376\nH -1.517832 4.620009 1.162629\nH -0.424554 -3.422728 3.620039\nH 4.792503 0.442354 -1.355078\nH -4.137030 2.807453 0.056483\nH 0.447302 4.978594 -0.116273\nH 3.050996 2.891963 2.707024\nH 4.235056 -0.000417 -2.657875\nH -3.629233 -0.177167 -3.434717\nH -1.628498 3.805093 -2.805221\nH -4.168132 -2.595981 -0.942100\nH 0.349016 -3.511766 -3.541990\nH 3.050338 -1.567255 -3.638564\nH 2.791811 3.360489 -2.431646\nH 3.324485 -1.457992 -3.438322\nH -1.535740 1.381243 4.553424\nH 4.722354 1.101742 1.218826\nH -2.022208 2.263512 -3.973310\nH 4.518746 2.057450 0.589772\nH -0.125220 -3.050064 -3.959978\nH -1.234286 1.414930 4.634060\nH 4.512219 0.152751 2.148615\nH -0.238819 4.908525 0.921602\nH -4.355696 -1.041523 -2.223318\nH 3.934252 -0.429111 3.055737\nH 4.701173 0.477835 -1.634212\nH 1.369604 -4.782582 0.501093\nH -0.156283 -4.984749 -0.357572\nH -3.509250 -3.084751 1.780304\nH 2.033060 -0.492381 -4.541391\nH -4.841400 0.421416 1.176117\nH 1.051463 0.251504 4.881718\nH -4.420331 0.648369 2.245060\nH 4.794703 -0.394140 1.362157\nH 3.088540 3.775450 -1.098588\nH 3.760388 -0.481679 -3.259979\nH 4.398591 2.139106 1.037604\nH 2.929528 3.169132 -2.524771\nH 1.342597 -4.637757 1.299477\nH 3.204517 3.078146 -2.292615\nH -2.206794 3.917372 2.187293\nH 3.290773 -2.760885 -2.558970\nH -3.189598 -1.620638 3.492850\nH 2.700892 -1.935045 -3.736413\nH 0.471598 -1.841590 4.624515\nH 3.058770 -2.220472 -3.273137\nH -2.759889 4.047200 1.001590\nH 1.987712 0.345993 4.574854\nH -3.203650 -0.627179 -3.787251\nH -1.582668 4.628080 -1.037323\nH -2.679824 -1.041434 -4.090716\nH -3.203659 -3.037920 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2.559676 -0.445584 4.271945\nH 2.441335 -1.219700 -4.189536\nH -2.192035 3.988634 -2.070212\nH 2.546874 4.137295 -1.181621\nH 4.101842 -2.325445 1.663488\nH 3.199126 0.058036 -3.842164\nH -0.491765 -2.835792 4.088576\nH 0.076619 4.225272 2.672303\nH 4.385662 2.388861 0.243529\nH 3.303999 -3.122107 -2.082316\nH 4.426087 2.133985 0.925127\nH 0.168164 -3.309412 3.744264\nH -0.592895 0.707713 -4.914023\nH 0.076368 3.031869 -3.975165\nH 2.019675 1.843134 -4.186141\nH 2.427703 4.369836 0.103902\nH -4.215905 0.504538 -2.640377\nH -1.823059 1.517707 4.401479\nH -3.254102 -3.327798 1.826629\nH -4.873137 0.093260 1.115274\nH 2.667920 -4.200199 0.490435\nH 4.059751 -2.138354 1.986419\nH 4.213528 -2.321241 -1.363092\nH 2.874357 -3.646322 -1.855373\nH -1.729847 -4.018003 -2.421422\nH 2.162209 0.012693 4.508291\nH -0.679747 -0.514579 -4.926779\nH 4.616464 0.230329 1.906622\nH -1.118496 4.853811 0.435299\nH 0.567099 4.142377 2.742100\nH 2.994290 1.963797 3.489660\nH 2.629947 3.141710 -2.865840\nH 3.580910 2.823425 2.050697\nH 2.285236 3.864438 2.200867\nH 4.188679 2.045301 -1.808788\nH -0.435149 -0.058623 4.980684\nH 4.522312 -1.057684 1.852027\nH -3.631450 1.579146 -3.052683\nH -3.235478 2.574126 -2.811682\nH -3.290990 -3.733806 -0.477573\nH -0.920858 2.064489 4.459810\nH -2.124023 -1.782281 -4.160769\nH -0.942939 4.624529 1.650635\nH 1.635091 3.483964 3.191939\nH 3.939780 3.076025 0.127301\nH -4.600072 1.927438 0.352592\nH -0.668819 -3.088647 -3.874654\nH 1.370417 -3.164966 -3.620076\nH 2.432174 0.860189 4.283060\nH 2.231144 -4.059805 -1.881483\nH 0.905494 -4.870941 0.673807\nH -2.117427 -4.501065 0.506871\nH -4.982859 -0.240225 0.336760\nH -1.817947 4.193587 -2.027041\nH 1.569342 -3.063925 -3.626228\nH -2.790962 0.589873 4.106407\nH 0.773507 4.844007 -0.968135\nH 0.336402 -0.523452 -4.961132\nH 0.990751 -4.808357 -0.947690\nH 4.818290 0.239804 1.313994\nH 4.149972 2.143630 -1.783980\nH 2.588916 4.080440 1.283559\nH -1.251370 -2.162243 -4.331141\nH 1.043932 0.098171 4.888821\nH -4.326415 -0.378197 -2.477721\nH 3.991103 -3.009516 -0.117915\nH 0.690751 -4.527382 2.006409\nH 1.720618 -1.691791 -4.379191\nH 0.050000 -0.135805 4.997905\nH 3.910258 -0.089821 -3.114773\nH 1.397189 -3.578774 -3.200037\nH 2.060134 -1.216835 -4.390348\nH -1.582984 -4.657436 -0.895798\nH -2.561676 3.653816 2.255536\nH 2.296278 -0.578207 -4.403724\nH -1.127850 1.235915 4.711737\nH 1.653148 -4.159713 -2.227979\nH -4.061410 -2.050434 -2.073805\nH -3.639964 -2.499409 2.345979\nH -0.666559 4.950605 0.217270\nH 4.845739 1.229752 -0.080755\nH -4.702562 -0.920125 1.428034\nH 4.839846 -0.438882 -1.176126\n'; Mol3.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol3.startAnimation();Mol3.stopAnimation();function setProj3(yesPers){Mol3.specs.projectionPerspective_3D=yesPers;Mol3.setupScene();Mol3.repaint()}function setModel3(model){Mol3.specs.set3DRepresentation(model);Mol3.setupScene();Mol3.repaint()}function setSpeed3(){Mol3.timeout=500-document.getElementById('spd3').value;Mol3.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol3.startAnimation()}</script><br><span class='meta'>视图: <input type='radio' name='group2' onclick='setProj3(true)'>投影 <input type='radio' name='group2' onclick='setProj3(false)' checked=''>正交    速度: <input type='range' id='spd3' min='1' max='500' onchange='setSpeed3()'/><br>模型: <input type='radio' name='model' onclick='setModel3('Ball and Stick')' checked=''>球棍 <input type='radio' name='model' onclick='setModel3('van der Waals Spheres')'>范德华球 <input type='radio' name='model' onclick='setModel3('Stick')'>棍状 <input type='radio' name='model' onclick='setModel3('Wireframe')'>线框 <input type='radio' name='model' onclick='setModel3('Line')'>线型   <input type='checkbox' onclick='Mol3.specs.atoms_displayLabels_3D=this.checked;Mol3.repaint()'>名称<br>左键: 转动   滚轮: 缩放   双击: 自动旋转开关   Alt+左键: 移动</span><br><figurecaption>Fig.3</figurecaption></figure>

螺线方法: 近似均匀分布的球面点

<figure><script>var Mol4=new ChemDoodle.TransformCanvas3D('Mol-4',642,396);Mol4.specs.shapes_color='#fff';Mol4.specs.backgroundColor='black';Mol4.specs.set3DRepresentation('Ball and Stick');Mol4.specs.projectionPerspective_3D=false;Mol4.specs.compass_display=true; /*//Mol4.specs.atoms_resolution_3D=15; //Mol4.specs.bonds_resolution_3D=15; //Mol4.specs.crystals_unitCellLineWidth=1.5;*/ Mol4.nextFrame=function(delta){var matrix=[];ChemDoodle.lib.mat4.identity(matrix);var change=delta*Math.PI/15000;ChemDoodle.lib.mat4.rotate(matrix,change,[1,0,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,1,0]);ChemDoodle.lib.mat4.rotate(matrix,change,[0,0,1]);ChemDoodle.lib.mat4.multiply(this.rotationMatrix, matrix)}; Mol4.startAnimation=ChemDoodle._AnimatorCanvas.prototype.startAnimation;Mol4.stopAnimation=ChemDoodle._AnimatorCanvas.prototype.stopAnimation;Mol4.isRunning=ChemDoodle._AnimatorCanvas.prototype.isRunning;Mol4.dblclick=ChemDoodle.RotatorCanvas.prototype.dblclick;Mol4.timeout=5;Mol4.handle=null; var Fmol='1000\nRot. Method: 4\nH 0.223551 -0.000000 -4.995000\nH -0.285367 -0.261420 -4.985000\nH 0.043658 0.497463 -4.975000\nH 0.359327 -0.468678 -4.965000\nH -0.659078 0.116582 -4.955000\nH 0.624023 0.396952 -4.945000\nH -0.208618 -0.776050 -4.935000\nH -0.397658 0.765665 -4.925000\nH 0.862323 -0.314919 -4.915000\nH -0.896651 -0.370124 -4.905000\nH 0.432027 0.923216 -4.895000\nH 0.319095 -1.017326 -4.885000\nH -0.961271 0.557076 -4.875000\nH 1.127109 0.247792 -4.865000\nH -0.687508 -0.977910 -4.855000\nH -0.158750 1.225061 -4.845000\nH 0.974072 -0.820949 -4.835000\nH -1.310130 -0.054178 -4.825000\nH 0.955153 0.950504 -4.815000\nH -0.063871 -1.381266 -4.805000\nH -0.907904 1.087973 -4.795000\nH 1.437486 -0.193412 -4.785000\nH -1.217357 -0.847005 -4.775000\nH 0.332482 1.477914 -4.765000\nH 0.768619 -1.341343 -4.755000\nH -1.501806 0.479117 -4.745000\nH 1.458065 0.673663 -4.735000\nH -0.631346 -1.508568 -4.725000\nH -0.563172 1.565762 -4.715000\nH 1.497770 -0.787186 -4.705000\nH -1.662788 -0.438306 -4.695000\nH 0.944652 1.469152 -4.685000\nH 0.300344 -1.747618 -4.675000\nH -1.422633 1.101767 -4.665000\nH 1.818864 0.150689 -4.655000\nH -1.256567 -1.358313 -4.645000\nH 0.009148 1.875284 -4.635000\nH 1.276471 -1.407123 -4.625000\nH -1.915789 0.177555 -4.615000\nH 1.551549 1.177570 -4.605000\nH -0.352828 -1.939455 -4.595000\nH -1.062248 1.688018 -4.585000\nH 1.945529 -0.533189 -4.575000\nH -1.814780 -0.931315 -4.565000\nH 0.716797 1.933437 -4.555000\nH 0.785750 -1.930174 -4.545000\nH -1.902786 0.901766 -4.535000\nH 2.032644 0.626686 -4.525000\nH -1.086179 -1.853372 -4.515000\nH -0.455407 2.120750 -4.505000\nH 1.785182 -1.268109 -4.495000\nH -2.193186 -0.273333 -4.485000\nH 1.445632 1.698388 -4.475000\nH 0.082008 -2.248789 -4.465000\nH -1.593356 1.616847 -4.455000\nH 2.286549 -0.116913 -4.445000\nH -1.779890 -1.470634 -4.435000\nH 0.321677 2.305623 -4.425000\nH 1.330956 -1.932959 -4.415000\nH -2.305340 0.530453 -4.405000\nH 2.074322 1.175228 -4.395000\nH -0.741346 -2.285209 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4.435000\nH -2.033985 1.051134 4.445000\nH 2.190988 0.593758 4.455000\nH -1.203931 -1.901138 4.465000\nH -0.392944 2.195443 4.475000\nH 1.756707 -1.341177 4.485000\nH -2.180965 -0.195871 4.495000\nH 1.461951 1.602397 4.505000\nH 0.004364 -2.148198 4.515000\nH -1.439990 1.565504 4.525000\nH 2.097960 -0.179827 4.535000\nH -1.651269 -1.271332 4.545000\nH 0.355043 2.031236 4.555000\nH 1.098311 -1.718863 4.565000\nH -1.949167 0.519733 4.575000\nH 1.768088 0.922843 4.585000\nH -0.672465 -1.853042 4.595000\nH -0.746856 1.798939 4.605000\nH 1.744285 -0.811938 4.615000\nH -1.811596 -0.572271 4.625000\nH 0.936995 1.624443 4.635000\nH 0.400987 -1.806429 4.645000\nH -1.495172 1.046631 4.655000\nH 1.783988 0.234864 4.665000\nH -1.140002 -1.358224 4.675000\nH -0.075713 1.745005 4.685000\nH 1.215435 -1.216426 4.695000\nH -1.690382 0.074724 4.705000\nH 1.275396 1.068710 4.715000\nH -0.214776 -1.621187 4.725000\nH -0.920010 1.316570 4.735000\nH 1.538643 -0.342861 4.745000\nH -1.339778 -0.771342 4.755000\nH 0.457484 1.444120 4.765000\nH 0.624749 -1.345014 4.775000\nH -1.339126 0.557239 4.785000\nH 1.332425 0.482305 4.795000\nH -0.640806 -1.225293 4.805000\nH -0.346112 1.302298 4.815000\nH 1.104366 -0.706931 4.825000\nH -1.255035 -0.218315 4.835000\nH 0.754395 0.978194 4.845000\nH 0.101118 -1.191113 4.855000\nH -0.848720 0.781952 4.865000\nH 1.111020 -0.003163 4.875000\nH -0.788227 -0.717964 4.885000\nH 0.092004 1.015141 4.895000\nH 0.588015 -0.771501 4.905000\nH -0.903535 0.162477 4.915000\nH 0.729284 0.460999 4.925000\nH -0.210827 -0.775453 4.935000\nH -0.339007 0.657305 4.945000\nH 0.628040 -0.231388 4.955000\nH -0.546532 -0.223781 4.965000\nH 0.212945 0.451696 4.975000\nH 0.114773 -0.369597 4.985000\nH -0.193099 0.112640 4.995000\n'; Mol4.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol4.startAnimation();Mol4.stopAnimation();function setProj4(yesPers){Mol4.specs.projectionPerspective_3D=yesPers;Mol4.setupScene();Mol4.repaint()}function setModel4(model){Mol4.specs.set3DRepresentation(model);Mol4.setupScene();Mol4.repaint()}function setSpeed4(){Mol4.timeout=500-document.getElementById('spd4').value;Mol4.loadMolecule(ChemDoodle.readXYZ(Fmol));Mol4.startAnimation()}</script><br><span class='meta'>视图: <input type='radio' name='group2' onclick='setProj4(true)'>投影 <input type='radio' name='group2' onclick='setProj4(false)' checked=''>正交    速度: <input type='range' id='spd4' min='1' max='500' onchange='setSpeed4()'/><br>模型: <input type='radio' name='model' onclick='setModel4('Ball and Stick')' checked=''>球棍 <input type='radio' name='model' onclick='setModel4('van der Waals Spheres')'>范德华球 <input type='radio' name='model' onclick='setModel4('Stick')'>棍状 <input type='radio' name='model' onclick='setModel4('Wireframe')'>线框 <input type='radio' name='model' onclick='setModel4('Line')'>线型   <input type='checkbox' onclick='Mol4.specs.atoms_displayLabels_3D=this.checked;Mol4.repaint()'>名称<br>左键: 转动   滚轮: 缩放   双击: 自动旋转开关   Alt+左键: 移动</span><br><figurecaption>Fig.4</figurecaption></figure>

前面三种是通常所谓的随机点, 最后的这种点可用于一些特殊的情况. 这种点涉及到的知识很多, 这里就不多说了. 如果需要请参考后面的资料.

代码

<table class="highlighttable"><th colspan="2" style="text-align:left">bash</th><tr><td><div class="linenodiv" style="background-color: #f0f0f0; padding-right: 10px"><pre style="line-height:125%"> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100</pre></div></td><td class="code"><div class="highlight"><pre style="line-height:125%"><span></span><span style="color: #AA22FF">echo</span> <span style="color: #BB4444">"1</span> <span style="color: #BB4444">mol</span> <span style="color: #BB4444">H 0 0 5"</span> | awk <span style="color: #BB4444">'</span> BEGIN<span style="color: #666666">{</span> <span style="color: #B8860B">Pi</span><span style="color: #666666">=</span>4*atan2<span style="color: #666666">(</span>1,1<span style="color: #666666">)</span>; <span style="color: #B8860B">TwoPi</span><span style="color: #666666">=</span>2*Pi <span style="color: #B8860B">method</span><span style="color: #666666">=</span>3; <span style="color: #B8860B">Nmax</span><span style="color: #666666">=</span>1000 <span style="color: #666666">}</span> <span style="color: #666666">{</span> <span style="color: #B8860B">Natm</span><span style="color: #666666">=</span><span style="color: #B8860B">$1</span>; getline <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">i</span><span style="color: #666666">=</span>1; i<<span style="color: #666666">=</span>Natm; i++<span style="color: #666666">)</span> <span style="color: #666666">{</span> getline; Satm<span style="color: #666666">[</span>i<span style="color: #666666">]=</span><span style="color: #B8860B">$1</span>; Xatm<span style="color: #666666">[</span>i<span style="color: #666666">]=</span><span style="color: #B8860B">$2</span>; Yatm<span style="color: #666666">[</span>i<span style="color: #666666">]=</span><span style="color: #B8860B">$3</span>; Zatm<span style="color: #666666">[</span>i<span style="color: #666666">]=</span><span style="color: #B8860B">$4</span> <span style="color: #666666">}</span> print Nmax*Natm<span style="color: #BB4444">"\nRot. Method: "</span>method <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">n</span><span style="color: #666666">=</span>1; n<<span style="color: #666666">=</span>Nmax; n++<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #B8860B">isang</span><span style="color: #666666">=</span>getAxi<span style="color: #666666">(</span>method, axi, n, Nmax<span style="color: #666666">)</span> <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>isang<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #B8860B">tht</span><span style="color: #666666">=</span>Pi <span style="color: #B8860B">x</span><span style="color: #666666">=</span>.5*axi<span style="color: #666666">[</span>1<span style="color: #666666">]</span> <span style="color: #B8860B">y</span><span style="color: #666666">=</span>.5*axi<span style="color: #666666">[</span>2<span style="color: #666666">]</span> <span style="color: #B8860B">z</span><span style="color: #666666">=</span>.5*<span style="color: #666666">(</span>axi<span style="color: #666666">[</span>3<span style="color: #666666">]</span>+1<span style="color: #666666">)</span> <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #666666">{</span> <span style="color: #B8860B">tht</span><span style="color: #666666">=</span>axi<span style="color: #666666">[</span>0<span style="color: #666666">]</span> <span style="color: #B8860B">x</span><span style="color: #666666">=</span>axi<span style="color: #666666">[</span>1<span style="color: #666666">]</span> <span style="color: #B8860B">y</span><span style="color: #666666">=</span>axi<span style="color: #666666">[</span>2<span style="color: #666666">]</span> <span style="color: #B8860B">z</span><span style="color: #666666">=</span>axi<span style="color: #666666">[</span>3<span style="color: #666666">]</span> <span style="color: #666666">}</span> AxiRotMat<span style="color: #666666">(</span>isang, tht, x, y, z<span style="color: #666666">)</span> <span style="color: #AA22FF; font-weight: bold">for</span><span style="color: #666666">(</span><span style="color: #B8860B">i</span><span style="color: #666666">=</span>1; i<<span style="color: #666666">=</span>Natm; i++<span style="color: #666666">)</span> <span style="color: #666666">{</span> V<span style="color: #666666">[</span>1<span style="color: #666666">]=</span>Xatm<span style="color: #666666">[</span>i<span style="color: #666666">]</span>; V<span style="color: #666666">[</span>2<span style="color: #666666">]=</span>Yatm<span style="color: #666666">[</span>i<span style="color: #666666">]</span>; V<span style="color: #666666">[</span>3<span style="color: #666666">]=</span>Zatm<span style="color: #666666">[</span>i<span style="color: #666666">]</span> RotVect<span style="color: #666666">(</span>RotMat, V<span style="color: #666666">)</span> <span style="color: #AA22FF">printf</span> <span style="color: #BB4444">"%s %9.6f %9.6f %9.6f\n"</span>, Satm<span style="color: #666666">[</span>i<span style="color: #666666">]</span>, V<span style="color: #666666">[</span>1<span style="color: #666666">]</span>, V<span style="color: #666666">[</span>2<span style="color: #666666">]</span>, V<span style="color: #666666">[</span>3<span style="color: #666666">]</span> <span style="color: #666666">}</span> <span style="color: #666666">}</span> <span style="color: #AA22FF">exit</span> <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">function</span> acos<span style="color: #666666">(</span>x<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #AA22FF; font-weight: bold">return</span> atan2<span style="color: #666666">(</span>sqrt<span style="color: #666666">(</span>1-x*x<span style="color: #666666">)</span>,x<span style="color: #666666">)</span> <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">function</span> getAxi<span style="color: #666666">(</span>method, axi, Ipnt, Npnt, i,r1,r2,tht1,tht2<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #B8860B">isang</span><span style="color: #666666">=</span>1; ;axi<span style="color: #666666">[</span>0<span style="color: #666666">]=</span>0 <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span><span style="color: #B8860B">method</span><span style="color: #666666">==</span>1<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># Marsaglia Method</span> <span style="color: #AA22FF; font-weight: bold">while</span><span style="color: #666666">(</span>1<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #B8860B">r1</span><span style="color: #666666">=</span>2*rand<span style="color: #666666">()</span>-1 <span style="color: #B8860B">r2</span><span style="color: #666666">=</span>2*rand<span style="color: #666666">()</span>-1 <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>r1*r1+r2*r2<1<span style="color: #666666">)</span> <span style="color: #AA22FF">break</span> <span style="color: #666666">}</span> <span style="color: #B8860B">tht1</span><span style="color: #666666">=</span>r1*r1+r2*r2 axi<span style="color: #666666">[</span>1<span style="color: #666666">]=</span>2*r1*sqrt<span style="color: #666666">(</span>1-tht1<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>2<span style="color: #666666">]=</span>2*r2*sqrt<span style="color: #666666">(</span>1-tht1<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>3<span style="color: #666666">]=</span>1-2*tht1 <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span><span style="color: #B8860B">method</span><span style="color: #666666">==</span>2<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># theta distributuion Method</span> <span style="color: #B8860B">tht1</span><span style="color: #666666">=</span>acos<span style="color: #666666">(</span>2*rand<span style="color: #666666">()</span>-1<span style="color: #666666">)</span> <span style="color: #008800; font-style: italic"># tht1=rand()*Pi # can NOT use</span> <span style="color: #B8860B">tht2</span><span style="color: #666666">=</span>rand<span style="color: #666666">()</span>*TwoPi axi<span style="color: #666666">[</span>1<span style="color: #666666">]=</span>sin<span style="color: #666666">(</span>tht1<span style="color: #666666">)</span>*cos<span style="color: #666666">(</span>tht2<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>2<span style="color: #666666">]=</span>sin<span style="color: #666666">(</span>tht1<span style="color: #666666">)</span>*sin<span style="color: #666666">(</span>tht2<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>3<span style="color: #666666">]=</span>cos<span style="color: #666666">(</span>tht1<span style="color: #666666">)</span> <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span><span style="color: #B8860B">method</span><span style="color: #666666">==</span>3<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #B8860B">isang</span><span style="color: #666666">=0</span> <span style="color: #008800; font-style: italic"># 四元数方法</span> <span style="color: #B8860B">tht1</span><span style="color: #666666">=</span>rand<span style="color: #666666">()</span>*TwoPi <span style="color: #B8860B">tht2</span><span style="color: #666666">=</span>rand<span style="color: #666666">()</span>*TwoPi <span style="color: #B8860B">r1</span><span style="color: #666666">=</span>sqrt<span style="color: #666666">(</span>1-rand<span style="color: #666666">())</span> <span style="color: #B8860B">r2</span><span style="color: #666666">=</span>sqrt<span style="color: #666666">(</span>1-r1*r1<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>0<span style="color: #666666">]=</span>sin<span style="color: #666666">(</span>tht1<span style="color: #666666">)</span>*r1 axi<span style="color: #666666">[</span>1<span style="color: #666666">]=</span>cos<span style="color: #666666">(</span>tht1<span style="color: #666666">)</span>*r1 axi<span style="color: #666666">[</span>2<span style="color: #666666">]=</span>sin<span style="color: #666666">(</span>tht2<span style="color: #666666">)</span>*r2 axi<span style="color: #666666">[</span>3<span style="color: #666666">]=</span>cos<span style="color: #666666">(</span>tht2<span style="color: #666666">)</span>*r2 <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span><span style="color: #B8860B">method</span><span style="color: #666666">==</span>4<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># Sprial Method, for regular equidistributed</span> Ipnt-- <span style="color: #B8860B">r1</span> <span style="color: #666666">=</span> -1+2*<span style="color: #666666">(</span>Ipnt+0.5<span style="color: #666666">)</span>/Npnt <span style="color: #008800; font-style: italic"># +0.5 表示在厚度的中点处取点</span> <span style="color: #B8860B">tht2</span> <span style="color: #666666">=</span> Pi*<span style="color: #666666">(</span>sqrt<span style="color: #666666">(</span>5<span style="color: #666666">)</span>-1<span style="color: #666666">)</span>*Ipnt <span style="color: #B8860B">r2</span> <span style="color: #666666">=</span> sqrt<span style="color: #666666">(</span>1-r1*r1<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>1<span style="color: #666666">]</span> <span style="color: #666666">=</span> r2*cos<span style="color: #666666">(</span>tht2<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>2<span style="color: #666666">]</span> <span style="color: #666666">=</span> r2*sin<span style="color: #666666">(</span>tht2<span style="color: #666666">)</span> axi<span style="color: #666666">[</span>3<span style="color: #666666">]</span> <span style="color: #666666">=</span> r1 <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">return</span> isang <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">function</span> RotVect<span style="color: #666666">(</span>RotMat, V<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># 按照矩阵RotMat旋转矢量V</span> <span style="color: #B8860B">Vx</span> <span style="color: #666666">=</span> V<span style="color: #666666">[</span>1<span style="color: #666666">]</span>; <span style="color: #B8860B">Vy</span> <span style="color: #666666">=</span> V<span style="color: #666666">[</span>2<span style="color: #666666">]</span>; <span style="color: #B8860B">Vz</span> <span style="color: #666666">=</span> V<span style="color: #666666">[</span>3<span style="color: #666666">]</span> V<span style="color: #666666">[</span>1<span style="color: #666666">]=</span> RotMat<span style="color: #666666">[</span>1,1<span style="color: #666666">]</span>*Vx + RotMat<span style="color: #666666">[</span>1,2<span style="color: #666666">]</span>*Vy + RotMat<span style="color: #666666">[</span>1,3<span style="color: #666666">]</span>*Vz V<span style="color: #666666">[</span>2<span style="color: #666666">]=</span> RotMat<span style="color: #666666">[</span>2,1<span style="color: #666666">]</span>*Vx + RotMat<span style="color: #666666">[</span>2,2<span style="color: #666666">]</span>*Vy + RotMat<span style="color: #666666">[</span>2,3<span style="color: #666666">]</span>*Vz V<span style="color: #666666">[</span>3<span style="color: #666666">]=</span> RotMat<span style="color: #666666">[</span>3,1<span style="color: #666666">]</span>*Vx + RotMat<span style="color: #666666">[</span>3,2<span style="color: #666666">]</span>*Vy + RotMat<span style="color: #666666">[</span>3,3<span style="color: #666666">]</span>*Vz <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">function</span> AxiRotMat<span style="color: #666666">(</span>isang, tht, x, y, z, w,rsq<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># 绕矢量(x,y,z)旋转tht弧度,四元数方法</span> <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>isang<span style="color: #666666">)</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># w 为角度, 使用 轴-角 计算旋转矩阵</span> <span style="color: #B8860B">w</span><span style="color: #666666">=</span>cos<span style="color: #666666">(</span>tht/2<span style="color: #666666">)</span> <span style="color: #B8860B">rsq</span><span style="color: #666666">=</span>sqrt<span style="color: #666666">(</span>x*x+y*y+z*z<span style="color: #666666">)</span>; <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>rsq>0<span style="color: #666666">)</span> <span style="color: #B8860B">rsq</span> <span style="color: #666666">=</span> sin<span style="color: #666666">(</span>tht/2<span style="color: #666666">)</span>/rsq x *<span style="color: #666666">=</span> rsq; y *<span style="color: #666666">=</span> rsq; z *<span style="color: #666666">=</span> rsq <span style="color: #666666">}</span> <span style="color: #AA22FF; font-weight: bold">else</span> <span style="color: #666666">{</span> <span style="color: #008800; font-style: italic"># 否则直接使用传入的四元数构建</span> <span style="color: #B8860B">w</span><span style="color: #666666">=</span>tht <span style="color: #B8860B">rsq</span><span style="color: #666666">=</span>sqrt<span style="color: #666666">(</span>x*x+y*y+z*z+w*w<span style="color: #666666">)</span>; <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>rsq>0<span style="color: #666666">)</span> <span style="color: #B8860B">rsq</span> <span style="color: #666666">=</span> 1/rsq x *<span style="color: #666666">=</span> rsq; y *<span style="color: #666666">=</span> rsq; z *<span style="color: #666666">=</span> rsq; w *<span style="color: #666666">=</span> rsq <span style="color: #666666">}</span> RotMat<span style="color: #666666">[</span>1,1<span style="color: #666666">]=</span> 1-2*<span style="color: #666666">(</span>y*y+z*z<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>1,2<span style="color: #666666">]=</span> 2*<span style="color: #666666">(</span>x*y-w*z<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>1,3<span style="color: #666666">]=</span> 2*<span style="color: #666666">(</span>x*z+w*y<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>2,1<span style="color: #666666">]=</span> 2*<span style="color: #666666">(</span>x*y+w*z<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>2,2<span style="color: #666666">]=</span> 1-2*<span style="color: #666666">(</span>x*x+z*z<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>2,3<span style="color: #666666">]=</span> 2*<span style="color: #666666">(</span>y*z-w*x<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>3,1<span style="color: #666666">]=</span> 2*<span style="color: #666666">(</span>x*z-w*y<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>3,2<span style="color: #666666">]=</span> 2*<span style="color: #666666">(</span>y*z+w*x<span style="color: #666666">)</span>; RotMat<span style="color: #666666">[</span>3,3<span style="color: #666666">]=</span> 1-2*<span style="color: #666666">(</span>x*x+y*y<span style="color: #666666">)</span>; <span style="color: #AA22FF; font-weight: bold">if</span><span style="color: #666666">(</span>x*x+y*y+z*z+w*w<span style="color: #666666">==</span>0<span style="color: #666666">)</span> <span style="color: #666666">{</span> RotMat<span style="color: #666666">[</span>1,1<span style="color: #666666">]=</span>-1; RotMat<span style="color: #666666">[</span>2,2<span style="color: #666666">]=</span>-1; RotMat<span style="color: #666666">[</span>3,3<span style="color: #666666">]=</span>-1 <span style="color: #666666">}</span> <span style="color: #666666">}</span> <span style="color: #BB4444">'</span></pre></div> </td></tr></table>

参考资料