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gswylq

木虫 (正式写手)

[求助] 沉积过程可视化

请教一下：
     沉积过程前后原子数不一致，因此用dump   1 all xyz 100 dump.xyz命令不能够可视化沉积的过程，只能看到全部沉积完的结果，不知道用什么命令可以可视化沉积的过程呢？
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1楼2013-09-06 20:57:13
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xieluxielu

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gswylq: 金币+10, ★★★★★最佳答案, 谢谢啊 2013-09-09 09:32:14
topo readvarxyz dump.xyz
赞一下 回复此楼
2楼2013-09-08 11:32:21
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gswylq

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引用回帖:
2楼: Originally posted by xieluxielu at 2013-09-08 11:32:21
topo readvarxyz dump.xyz

请教一下：在tkconsole输入topo readvarxyz dump.xy后报错，
can't read "a": no such variable
不知道如何解决啊？
dumpy.xyz文献如下：

126
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128
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1 8.9369 8.94175 10.755
2 2.6398 6.27879 24.5528
2 6.12478 4.72787 21.9765
2 5.21732 7.18691 24.503
2 4.64832 4.86577 23.1644
130
Atoms
1 10.8296 0.00719976 0.0625772
1 1.69874 1.7343 0.00243432
1 1.87438 0.0781248 1.74008
1 0.00362566 1.79157 1.82573
1 3.63569 0.0948195 0.00669278
1 5.3261 1.79142 0.0830821
1 5.50534 0.0884165 1.72875
1 3.56715 1.87511 1.92464
1 7.29915 10.8509 0.0325056
1 9.12295 1.85854 0.0736688
1 8.99319 0.0377599 1.74592
1 7.23238 1.79811 1.85654
1 0.041551 3.72517 0.0363237
1 1.8158 5.4222 0.064542
1 1.75911 3.68397 1.89005
1 0.0350754 5.43846 1.82299
1 3.63721 3.56647 0.0548272
1 5.37185 5.38646 0.0433533
1 5.42939 3.7091 1.74028
1 3.533 5.36282 1.88179
1 7.31402 3.52099 0.105034
1 9.08545 5.44869 0.0345939
1 8.97774 3.70895 1.795
1 7.29012 5.49005 1.91374
1 10.778 7.16235 0.010842
1 1.71449 9.09778 0.110151
1 1.71504 7.28232 1.8717
1 0.0476744 9.03005 1.87893
1 3.54886 7.17417 0.0197366
1 5.47853 9.10056 0.0283669
1 5.40406 7.31211 1.84686
1 3.62659 8.9973 1.77953
1 7.29773 7.11328 0.0685365
1 9.03862 8.94962 0.0151932
1 9.12266 7.29753 1.85996
1 7.29475 9.11867 1.72432
1 0.0381424 0.0611749 3.5349
1 1.87498 1.74423 3.64804
1 1.77867 0.0706868 5.47578
1 0.0367511 1.76426 5.38424
1 3.59912 10.781 3.50612
1 5.43555 1.88208 3.63111
1 5.52524 0.0138742 5.3394
1 3.69805 1.73628 5.40146
1 7.31815 10.7741 3.53804
1 8.97294 1.74934 3.55728
1 9.08155 10.7577 5.42362
1 7.25362 1.78733 5.45216
1 10.7925 3.66694 3.60109
1 1.89453 5.36189 3.56861
1 1.71114 3.67005 5.48031
1 0.0436088 5.439 5.34819
1 3.57905 3.60138 3.69205
1 5.45053 5.39381 3.69433
1 5.45607 3.60919 5.45401
1 3.55419 5.4273 5.39204
1 7.23144 3.59011 3.60724
1 9.06209 5.45111 3.66724
1 9.04187 3.6309 5.42732
1 7.20405 5.34429 5.507
1 10.8072 7.15695 3.72136
1 1.82827 9.12962 3.61122
1 1.82062 7.21964 5.49271
1 0.0268658 9.12017 5.4662
1 3.64951 7.32396 3.59363
1 5.3453 9.15343 3.64772
1 5.36545 7.20253 5.35037
1 3.56443 9.08605 5.3573
1 7.13706 7.35819 3.7071
1 9.14295 8.97027 3.6165
1 8.93702 7.1923 5.49666
1 7.13924 9.04276 5.50977
1 10.7718 0.0609509 7.26351
1 1.89314 1.81416 7.26994
1 1.90686 10.8073 9.02446
1 0.0136775 1.73579 8.94962
1 3.69785 0.014954 7.15756
1 5.38731 1.73153 7.1819
1 5.38868 0.0315716 9.1427
1 3.68341 1.80291 9.07957
1 7.15269 0.0656602 7.16578
1 9.03791 1.83991 7.14464
1 8.98415 10.7923 9.01902
1 7.33556 1.87214 9.0248
1 10.8012 3.65094 7.22811
1 1.91353 5.41905 7.27771
1 1.72948 3.63506 8.95026
1 0.0759363 5.52479 9.01379
1 3.58929 3.59823 7.25193
1 5.415 5.33871 7.32926
1 5.50213 3.54934 8.97906
1 3.66805 5.41412 9.1191
1 7.18763 3.52646 7.31132
1 9.07449 5.38224 7.27988
1 9.11522 3.62167 9.03432
1 7.21658 5.48477 9.07797
1 0.00357724 7.30192 7.25205
1 1.89852 9.04361 7.23989
1 1.81734 7.17761 9.08314
1 0.0379176 9.10869 8.95078
1 3.69883 7.16839 7.2993
1 5.41736 9.12336 7.27789
1 5.47524 7.15074 8.97958
1 3.63097 8.93989 8.99181
1 7.126 7.17729 7.22858
1 8.97355 9.11783 7.19907
1 8.94782 7.21503 9.04647
1 7.14213 8.94687 9.03035
1 0.0481143 10.7593 10.7514
1 1.72711 1.76632 10.7844
1 3.66427 10.7307 10.9492
1 5.35957 1.8509 10.8847
1 7.25856 10.8302 10.7552
1 8.9599 1.72788 10.7502
1 0.00353992 3.61773 10.76
1 1.82951 5.52763 10.9004
1 3.5941 3.56406 10.8108
1 5.45598 5.37311 10.8178
1 7.13797 3.68895 10.7896
1 8.94895 5.38268 10.8745
1 10.7269 7.1902 10.8415
1 1.82661 8.96081 10.7951
1 3.58439 7.25349 10.7997
1 5.5155 9.01627 10.852
1 7.15465 7.23934 10.8161
1 8.92785 8.93312 10.7455
2 2.74302 6.30499 24.5284
2 6.67659 4.69275 21.5286
2 5.12727 7.12555 24.4664
2 4.08335 4.93604 23.6138
131
Atoms
1 10.8234 0.00410798 0.067463
1 1.69069 1.73513 0.00119801
1 1.87918 0.0815592 1.73712
1 0.00431169 1.79839 1.83031
1 3.6359 0.10073 0.00764218
1 5.32175 1.79457 0.0884863
1 5.50706 0.0923883 1.73001
1 3.56598 1.88433 1.93138
1 7.3064 0.0119254 0.0267803
1 9.13294 1.86494 0.0788682
1 8.9986 0.0364744 1.7424
1 7.23018 1.80135 1.8588
1 0.0452304 3.73247 0.0400543
1 1.8184 5.42364 0.0695175
1 1.75369 3.67684 1.89255
1 0.0344451 5.44312 1.8286
1 3.63214 3.5611 0.0598968
1 5.36857 5.38716 0.0486589
1 5.4318 3.71521 1.74282
1 3.53497 5.36473 1.88557
1 7.3174 3.5151 0.111716
1 9.08775 5.44947 0.0371319
1 8.97972 3.71473 1.80001
1 7.29193 5.50039 1.92526
1 10.7762 7.15847 0.0102738
1 1.70837 9.10098 0.118123
1 1.7102 7.28404 1.87903
1 0.0485966 9.0342 1.88512
1 3.54284 7.17031 0.0252269
1 5.48252 9.10404 0.0301575
1 5.40605 7.31512 1.84872
1 3.62647 8.99791 1.7705
1 7.3009 7.10352 0.0767122
1 9.04216 8.94251 0.0143095
1 9.12636 7.29904 1.86732
1 7.29756 9.11643 1.72321
1 0.0392743 0.0636215 3.52865
1 1.87708 1.74454 3.65376
1 1.77835 0.0739811 5.48197
1 0.0362451 1.76526 5.38022
1 3.60164 10.7826 3.49802
1 5.43784 1.8857 3.62924
1 5.52952 0.0164277 5.32727
1 3.70163 1.73276 5.3967
1 7.32383 10.7649 3.53732
1 8.97252 1.74845 3.55756
1 9.08137 10.7552 5.41723
1 7.25799 1.78781 5.44763
1 10.7871 3.66406 3.59972
1 1.89527 5.36704 3.57346
1 1.70553 3.66851 5.48435
1 0.0475265 5.4414 5.3518
1 3.5803 3.59794 3.70263
1 5.45095 5.39067 3.69621
1 5.45579 3.6078 5.46006
1 3.55311 5.42765 5.3921
1 7.2331 3.58994 3.6082
1 9.05626 5.45521 3.67187
1 9.0417 3.63094 5.42589
1 7.20311 5.33793 5.51511
1 10.8115 7.15585 3.73211
1 1.82445 9.13509 3.61266
1 1.82299 7.22082 5.4963
1 0.0333525 9.12322 5.46938
1 3.64686 7.32687 3.59153
1 5.3459 9.1635 3.64428
1 5.35727 7.20146 5.35351
1 3.56191 9.09024 5.35888
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1 9.14872 8.96829 3.62106
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1 5.38729 0.0344293 9.15004
1 3.6852 1.8016 9.0833
1 7.15066 0.0705433 7.17018
1 9.03911 1.84073 7.13839
1 8.97743 10.7868 9.01334
1 7.33933 1.87082 9.0227
1 10.8003 3.65267 7.22535
1 1.91933 5.42244 7.28052
1 1.72546 3.63637 8.9494
1 0.0776023 5.53166 9.01373
1 3.59144 3.59559 7.25181
1 5.41176 5.32905 7.33012
1 5.50143 3.54136 8.97798
1 3.6708 5.40763 9.128
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1 9.07494 5.38165 7.2835
1 9.12133 3.62469 9.0357
1 7.22083 5.48214 9.0771
1 0.0020459 7.30756 7.25169
1 1.90625 9.04439 7.23927
1 1.8173 7.17724 9.08255
1 0.0397409 9.10917 8.94394
1 3.70666 7.16415 7.29897
1 5.41324 9.12815 7.27921
1 5.47246 7.14808 8.98089
1 3.6369 8.93533 8.99141
1 7.11918 7.17338 7.22334
1 8.96495 9.118 7.20077
1 8.94465 7.21355 9.04036
1 7.13538 8.94533 9.02209
1 0.0497321 10.7502 10.742
1 1.72199 1.76211 10.7762
1 3.66706 10.719 10.9582
1 5.35751 1.85366 10.8902
1 7.25769 10.8286 10.7484
1 8.95934 1.72348 10.7439
1 0.00435098 3.61885 10.7506
1 1.83013 5.533 10.9068
1 3.5886 3.56134 10.8057
1 5.45355 5.37009 10.8179
1 7.13365 3.69065 10.7863
1 8.94228 5.37899 10.8766
1 10.7153 7.18838 10.8402
1 1.82603 8.95376 10.7905
1 3.58965 7.25605 10.7982
1 5.51933 9.01359 10.8537
1 7.14736 7.23556 10.8206
1 8.92081 8.92658 10.7375
2 2.81249 6.36069 24.5223
2 7.20398 4.65869 21.1036
2 5.0467 7.0694 24.4307
2 3.56871 4.96902 24.0244
2 9.17614 2.57577 23.1681
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3楼2013-09-09 10:39:51
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xieluxielu

木虫 (著名写手)

天天
引用回帖:
3楼: Originally posted by gswylq at 2013-09-09 03:39:51
请教一下：在tkconsole输入topo readvarxyz dump.xy后报错，
can't read "a": no such variable
不知道如何解决啊？
dumpy.xyz文献如下：

126
Atoms
1 0 0 0
1 1.8075 1.8075 0
1 1.807 ...

我试了一下，没问题
估计你把文件名输错了
你写的是“dumpy.xyz”

topo readvarxyz dump.xyz
其中dump.xyz 是你的文件名
在这里强调一点，必须是xyz格式的才能用这个命令
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4楼2013-09-11 20:51:37
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gswylq

木虫 (正式写手)
引用回帖:
4楼: Originally posted by xieluxielu at 2013-09-11 20:51:37
我试了一下，没问题
估计你把文件名输错了
你写的是“dumpy.xyz”

topo readvarxyz dump.xyz
其中dump.xyz 是你的文件名
在这里强调一点，必须是xyz格式的才能用这个命令...

我的vmd版本不行，换了一个，可以了。谢谢哈
有时间烦帮我看看这个帖子哈
http://muchong.com/bbs/viewthread.php?tid=5693318&authorid=659377
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5楼2013-09-13 15:08:03
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xieluxielu

木虫 (著名写手)

天天
这种类似的问题以前尝试过，没搞定
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6楼2013-09-13 21:01:55
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于相江1124

新虫 (初入文坛)
你好，我是lammps初学者，也是模拟沉积过程，在建模上遇到了问题，能否看一下你In文件中的建模语句。  谢谢~
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7楼2018-07-12 09:12:32
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于相江1124

新虫 (初入文坛)
引用回帖:
2楼: Originally posted by xieluxielu at 2013-09-08 11:32:21
topo readvarxyz dump.xyz

您好，我想请教您一下，用lammps模拟沉积原子时，如何对入射角度进行控制，我看了fix deposit命令仍没弄明白这个问题。谢谢指教
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8楼2018-10-18 17:27:55
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于相江1124

新虫 (初入文坛)
楼主您好，我想请教您一下，用lammps模拟沉积原子时，如何对入射角度进行控制，我看了fix deposit命令仍没弄明白这个问题。谢谢指教
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9楼2018-10-18 17:29:39
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