标题: 请教ORCA中的Cartesian coordinate(xyz)如何正确获取？ [打印本页] 作者Author: huangxc82 时间: 2018-12-20 20:16 标题: 请教ORCA中的Cartesian coordinate(xyz)如何正确获取？ 我是研究配合物的，想学习ORCA做些计算。现有的晶体结构数据用Mercury导出xyz文件得出来的结果往往跟别人的不一样，不知道正确应该是怎么弄的？
例如：文献Rechkemmer, Y.; Breitgo, F. D.; van der Meer, M.; Atanasov, M.; Hakl, M.; Orlita, M.; Neugebauer,
P.; Neese, F.; Sarkar, B.; van Slageren, J. A four-coordinate cobalt(II) single-ion magnet with coercivity and a very high energy barrier, Nat. Commun., 2016，7, 10467.
以下是由晶体数据cif文件导出的cartesian coordiante
Co 11.044075 1.049033 3.343833
S 8.778233 3.009365 4.338260
S 11.436216 3.021514 0.927285
S 10.911085 -2.028783 2.572360
S 13.086350 0.195189 5.607623
O 11.831675 -0.457679 5.965832
O 12.190188 3.072829 -0.307089
O 7.932628 3.087376 5.514618
O 10.078604 2.538577 0.821770
N 10.129890 -0.709778 2.995719
O 13.745286 0.856690 6.719380
O 10.274268 -2.765098 1.496671
O 10.002041 3.777012 4.382101
O 12.279513 -1.599559 2.301248
N 12.763688 1.147475 4.380638
N 9.203588 1.512595 3.968930
N 12.132218 2.149158 2.069879
C 6.102750 -0.600274 4.185849
H 5.209991 -0.543524 4.440812
C 13.461878 2.406053 2.476832
C 8.768876 -0.757896 3.381089
C 7.812799 3.620669 2.987123
H 6.989190 3.130059 2.933716
H 8.302930 3.513723 2.169194
H 7.622362 4.551214 3.125761
C 14.427920 3.121746 1.755657
H 14.215364 3.465765 0.918158
C 13.810062 1.853097 3.735184
C 11.003812 -3.088815 3.983562
H 11.425035 -2.620105 4.707846
H 11.518613 -3.868612 3.764082
H 10.118588 -3.352264 4.243280
C 11.350659 4.677504 1.548066
H 10.855060 4.685497 2.370384
H 10.910963 5.238612 0.903526
H 12.238071 5.006815 1.706457
C 15.091474 2.062514 4.237610
H 15.323718 1.705706 5.064501
C 15.701433 3.322690 2.280214
H 16.329986 3.809464 1.797907
C 6.915665 0.527698 4.273824
H 6.561405 1.326838 4.590790
C 14.178662 -1.054596 5.000852
H 13.766918 -1.507480 4.261570
H 14.363631 -1.684924 5.700993
H 14.999233 -0.649032 4.709675
C 8.260273 0.468710 3.888088
C 7.934815 -1.870202 3.306649
H 8.267686 -2.672859 2.973954
C 6.604548 -1.797786 3.725490
H 6.061916 -2.552964 3.694580
C 16.033210 2.800587 3.517167
H 16.882948 2.941424 3.868335
N 10.367481 0.401249 8.220075
C 8.952872 0.394534 7.706309
H 8.844953 1.109428 7.059940
H 8.345465 0.565904 8.442664
C 10.559013 -0.628570 9.296441
H 10.311821 -1.499487 8.947468
H 9.965460 -0.426826 10.035723
C 8.589011 -0.921433 7.057196
H 7.681911 -0.884026 6.743523
H 8.676027 -1.630572 7.700090
H 9.176730 -1.087048 6.317366
C 10.839382 2.775170 7.544442
H 11.110273 3.630421 7.886648
H 9.967891 2.851902 7.147732
H 11.467571 2.482626 6.880698
C 10.793930 1.770929 8.673850
H 11.672957 1.710502 9.079156
H 10.175707 2.086173 9.351677
C 11.982615 -0.689636 9.810573
H 12.047269 -1.360409 10.492973
H 12.228349 0.163057 10.176556
H 12.574709 -0.911202 9.088301
H 10.831969 0.177445 7.586692
N 13.852476 -1.358970 0.104253
C 13.128643 -0.130606 -0.377506
H 13.058399 0.497165 0.358484
H 12.228349 -0.382065 -0.634663
C 15.184080 -1.015591 0.705994
H 15.085519 -0.233396 1.271155
H 15.804977 -0.791307 -0.003658
C 12.616758 -2.857817 -1.471430
H 12.732698 -3.552089 -2.123469
H 12.193105 -2.100560 -1.882041
H 12.066714 -3.182813 -0.753548
C 13.969874 -2.445538 -0.924925
H 14.402520 -3.217982 -0.526752
H 14.527696 -2.134131 -1.655245
C 13.788065 0.565265 -1.543676
H 13.273507 1.338028 -1.788762
H 13.836191 -0.036768 -2.289908
H 14.674748 0.837666 -1.294932
C 15.756121 -2.149478 1.524837
H 16.605859 -1.886348 1.885699
H 15.870603 -2.922241 0.965712
H 15.156006 -2.359534 2.244183
H 13.362223 -1.656150 0.759035
而作者却给出的却是
Co 0.0000000 0.0000000 0.0000000
N 0.9556520 -0.8790305 1.5376434
N 1.0136029 0.8784305 -1.4975479
N -0.9556520 0.8790305 1.5189305
N -0.8965462 -0.8790305 -1.5622846
S -2.2577131 1.7819194 1.3015361
S -2.3195970 -1.5875801 -1.4082010
S 2.2426337 -1.7951233 1.3541514
S 2.3732722 1.6643754 -1.2736513
O 2.5065965 1.8586759 0.1662548
O -2.4699800 -2.7754701 -2.2213390
O -2.2745853 2.9677662 2.1371723
O -2.5335315 -1.7586053 0.0103838
O 2.4899808 2.8875274 -2.0470264
O 2.2103488 -3.0125492 2.1425766
O -2.3599819 2.0053566 -0.1226941
O 2.3748354 -1.9952815 -0.0855500
C -0.4422016 0.5596021 5.2284705
C -0.4010278 -0.5044459 -2.8326449
C 0.5483924 -0.4385115 2.8195367
C -3.6507379 0.8061080 1.7901057
C -0.8363826 -0.9944828 -4.0718199
C 0.6473042 0.4497178 -2.7980847
C 3.6580148 -0.8587358 1.8476627
C -3.5217175 -0.4184504 -1.9766030
C 1.1950658 0.9001375 -3.9961328
C -0.2772935 -0.5258357 -5.2571860
C -1.0053742 0.9808735 4.0258478
C 3.6715994 0.5791823 -1.7834619
C -0.5158654 0.5035008 2.8040904
C 1.0941065 -0.8401278 4.0358364
C 0.6110868 -0.3280830 5.2420366
C 0.7307976 0.4204327 -5.2228785
H -0.7823189 0.8817583 6.0321362
H -3.6119220 0.6425760 2.7354138
H -3.6367969 -0.0299923 1.3196278
H -4.4601947 1.2772199 1.5799787
H -1.5058841 -1.6393264 -4.1020145
H 3.6990694 -0.0480991 1.3350834
H 4.4522205 -1.3754451 1.6942477
H 3.5900319 -0.6456482 2.7806297
H -3.4538736 0.3872528 -1.4588191
H -4.4022035 -0.7904769 -1.8765070
H -3.3621286 -0.2183963 -2.9015449
H 1.8798915 1.5291973 -3.9792717
H -0.5827774 -0.8494501 -6.0736901
H -1.7131532 1.5838150 4.0352717
H 3.6161211 -0.2406497 -1.2874178
H 4.5202674 0.9969240 -1.6195699
H 3.5824030 0.3914479 -2.7211873
H 1.7903133 -1.4573548 4.0458107
H 0.9985878 -0.5841031 6.0482582
H 1.0986480 0.7365482 -6.0165050
请问，这是坐标是怎么来的？ORCA manual 上也基本碰到金属原子基本就是 M 0.0000000 0.0000000 0.0000000
我是小白，还请各位专家赐教？也请原谅我问这么没有水平的问题。