How to fix atomic coordinates when calculating lampps

LAMMPS LAMMPS Beginners
1

How can I fix the position of a given atom when calculating lammps?
The lammps.dat file is used as the atom data file.
Below is the content of the lammps.dat file.

# This file is created by Advance/NanoLabo.
214 atoms
3 atom types
0.00E+00 2.64E+01 xlo xhi
0.00E+00 5.30E+00 ylo yhi
0.00E+00 2.55E+01 zlo zhi
0.00E+00 1.04E+01 0.00E+00 xy xz yz
Atoms
1 1 5.44923 4.336078 12.72895
2 2 5.480979 0.8529571 12.60544
3 2 4.47004 4.438328 10.10232
4 1 4.715425 0.9020166 10.65572
5 1 3.782388 4.436574 8.308931
6 2 3.561453 2.674154 7.728994
7 1 2.880277 2.661494 5.949264
8 2 2.650179 4.419161 5.369706
9 1 1.972274 4.418965 3.612498
10 2 1.745081 0.8763467 3.046863
11 2 6.761083 3.481732 11.82477
12 2 5.888688 1.763382 9.477133
13 1 6.126233 3.510515 10.05495
14 1 5.209133 1.767458 7.712733
15 2 4.984787 0.0125489 7.129436
16 1 7.194354 1.769498 12.48009
17 1 4.307254 0.01036605 5.351234
18 2 4.069664 1.762653 4.748205
19 2 3.163006 3.531506 2.440124
20 1 3.401987 1.761837 2.966166
21 1 8.897061 2.47478 14.05845
22 2 8.989642 4.313187 13.68432
23 1 8.45336 4.390035 11.91956
24 2 8.202427 0.8210546 11.22633
25 1 7.553797 0.8518358 9.489166
26 2 7.314892 4.396541 8.893952
27 2 6.403837 2.655058 6.548186
28 1 6.64375 4.405482 7.13382
29 1 5.727207 2.66124 4.779319
30 2 5.492836 4.409269 4.155486
31 2 4.519524 0.8206398 1.702358
32 1 4.822255 4.395582 2.387464
33 1 10.53208 5.146276 13.3389
34 2 10.48895 1.645952 13.15956
35 1 9.874632 1.679597 11.30072
36 2 9.633009 3.455387 10.70933
37 1 8.982348 3.490425 8.934351
38 2 8.741019 1.745634 8.313684
39 1 8.067862 1.754392 6.553122
40 2 7.832875 5.294688 5.963197
41 1 7.158999 5.295709 4.193431
42 2 6.954295 1.766412 3.667879
43 1 12.12263 2.529189 12.93529
44 2 12.04339 4.322465 12.5961
45 1 11.29953 4.350069 10.74059
46 2 11.08201 0.8135684 10.11444
47 1 10.40337 0.8442305 8.337832
48 2 10.16546 4.393924 7.740179
49 1 9.495223 4.40276 5.969469
50 2 9.265843 2.649509 5.385347
51 1 8.59593 2.654039 3.621081
52 2 8.363623 4.407128 3.038408
53 2 13.39919 1.644189 11.9001
54 1 12.73152 1.695241 10.11995
55 2 12.49545 3.464876 9.534581
56 1 13.76143 5.195978 12.53449
57 1 11.82021 3.493877 7.754074
58 2 11.58869 1.745143 7.142265
59 1 10.91715 1.750078 5.370109
60 2 10.67945 5.29348 4.766743
61 2 9.784522 1.766489 2.444133
62 1 10.02191 5.291853 2.976204
63 1 15.5192 4.625174 14.20061
64 2 15.65218 2.775105 13.68188
65 1 15.02344 2.613742 11.94594
66 2 14.82735 4.325184 11.21333
67 1 14.1474 4.363583 9.488148
68 2 13.93285 0.837539 8.920682
69 2 13.00969 4.396013 6.565075
70 1 13.24934 0.8576509 7.150409
71 1 12.33257 4.396604 4.798481
72 2 12.10053 2.65235 4.178044
73 2 11.13121 4.351363 1.704163
74 1 11.44289 2.632621 2.399749
75 1 17.14783 1.904163 13.34583
76 2 17.09122 0.08549172 13.09466
77 1 16.43227 5.265326 11.24452
78 2 16.2617 1.731629 10.70251
79 1 15.58447 1.741734 8.909784
80 2 15.35219 3.493214 8.312538
81 1 14.6744 3.510614 6.552008
82 2 14.43833 1.760288 5.967013
83 1 13.76266 1.766041 4.208622
84 2 13.55473 0.004281571 3.686921
85 1 18.66716 4.4922 12.72908
86 2 18.69895 2.678207 12.60566
87 2 17.68782 4.390046 10.10262
88 1 17.93318 2.629225 10.656
89 1 17.00013 4.391805 8.309203
90 2 16.77919 0.857145 7.729258
91 1 16.09808 0.8697987 5.949489
92 2 15.86805 4.409206 5.36996
93 1 15.19023 4.409427 3.612726
94 2 14.96299 2.654959 3.04707
95 2 19.97909 0.0494463 11.82501
96 2 19.1065 1.767893 9.47745
97 1 19.34407 0.02074691 10.05523
98 1 18.42691 1.763814 7.713054
99 2 18.20259 3.518733 7.129756
100 1 20.41238 1.761676 12.48035
101 1 17.52513 3.520905 5.351537
102 2 17.28754 1.768628 4.748497
103 2 16.38099 5.296907 2.440387
104 1 16.61989 1.769477 2.966462
105 1 22.1152 1.056444 14.0587
106 2 22.20776 4.515147 13.68455
107 1 21.67142 4.438276 11.91979
108 2 21.42044 2.710141 11.22658
109 1 20.77166 2.679424 9.489464
110 2 20.53272 4.431818 8.89423
111 2 19.62166 0.8762367 6.548511
112 1 19.86157 4.422884 7.134102
113 1 18.94508 0.8700437 4.77964
114 2 18.71074 4.419113 4.155843
115 2 17.73741 2.710703 1.702684
116 1 18.04024 4.432825 2.3878
117 1 23.7502 3.682084 13.33904
118 2 23.70706 1.885308 13.15971
119 1 23.09268 1.851645 11.30088
120 2 22.85099 0.07585911 10.70948
121 1 22.20018 0.04084506 8.934556
122 2 21.95882 1.785628 8.313899
123 1 21.28568 1.776871 6.553357
124 2 21.05069 3.533669 5.963459
125 1 20.37686 3.532622 4.193691
126 2 20.1721 1.76484 3.668099
127 1 25.34076 1.00208 12.93537
128 2 25.26142 4.505917 12.59609
129 1 24.5175 4.478288 10.74063
130 2 24.29993 2.7177 10.11449
131 1 23.62116 2.687041 8.337959
132 2 23.38324 4.43445 7.740331
133 1 22.71299 4.425627 5.969641
134 2 22.48359 0.8817565 5.385506
135 1 21.8137 0.8771744 3.62123
136 2 21.58141 4.421179 3.038567
137 2 26.6171 1.887107 11.89996
138 1 25.94942 1.836038 10.11988
139 2 25.71331 0.0664223 9.53454
140 1 26.97937 3.632358 12.53436
141 1 25.03796 0.03742287 7.754118
142 2 24.80641 1.786145 7.142316
143 1 24.13486 1.7812 5.370188
144 2 23.89711 3.534872 4.766833
145 2 23.00221 1.764719 2.4442
146 1 23.23967 3.536435 2.976264
147 1 28.7368 4.203046 14.20051
148 2 28.8697 0.7561278 13.68189
149 1 28.24127 0.9174813 11.94578
150 2 28.0452 4.503166 11.21316
151 1 27.36526 4.464824 9.487978
152 2 27.15068 2.69376 8.92056
153 2 26.2274 4.43241 6.565057
154 1 26.46708 2.67365 7.150338
155 1 25.55023 4.431757 4.798497
156 2 25.31816 0.8788979 4.178019
157 2 24.34887 4.476877 1.704032
158 1 24.66055 0.8985357 2.399669
159 1 30.36541 1.62699 13.34575
160 2 30.30886 3.445692 13.09461
161 1 29.65009 3.563022 11.24432
162 2 29.47954 1.799628 10.70234
163 1 28.80231 1.789585 8.9096
164 2 28.57002 0.03810021 8.312354
165 1 27.89214 0.02068712 6.551861
166 2 27.65604 1.771018 5.966887
167 1 26.98031 1.765221 4.208519
168 2 26.77231 3.52699 3.686836
169 1 6.488817 3.711629 14.84714
170 1 9.046952 2.425713 17.83394
171 3 11.0734 0.3322053 15.52134
172 1 12.40777 3.908664 15.61751
173 3 14.31958 2.237516 15.36105
174 3 14.59489 3.477156 16.31174
175 1 15.09879 0.2779862 17.55622
176 1 19.0124 3.468103 16.56536
177 3 20.3162 3.156274 14.46716
178 1 22.37534 2.836408 16.68998
179 1 24.24591 4.605174 16.32194
180 3 25.95547 0.4597231 17.75354
181 1 26.28659 2.00982 16.11642
182 1 27.99557 4.082944 16.65506
183 3 30.60395 3.961983 15.5944
184 1 34.01027 1.762458 19.80479
185 3 9.845901 1.035065 19.34829
186 1 9.908449 0.1048922 17.46356
187 1 13.47995 4.889572 18.6668
188 3 13.99953 2.130165 18.18565
189 1 15.80012 3.010732 18.78903
190 1 19.04973 4.910858 19.43487
191 3 20.5526 0.8913329 18.59922
192 3 20.50001 3.422458 17.95627
193 1 23.48471 0.120067 18.15881
194 3 25.0264 3.350832 18.1627
195 1 28.40405 1.951406 19.12891
196 1 28.74885 1.821156 16.4256
197 3 30.25368 3.271858 18.59352
198 1 32.29414 3.05019 17.34852
199 3 9.29077 3.054293 20.50207
200 1 11.28386 4.667903 20.2146
201 3 12.48107 1.607263 20.44427
202 3 12.70927 3.288112 19.58603
203 1 14.60216 1.999077 20.50682
204 1 17.28728 2.338991 20.49619
205 3 19.59746 2.482877 20.05659
206 1 21.38452 4.055708 20.44128
207 1 21.99267 0.8522979 20.34358
208 3 23.35001 2.829119 18.64906
209 1 25.60885 2.474075 20.22051
210 1 27.32411 2.136972 21.23912
211 3 29.60481 3.407786 20.36037
212 1 31.67431 0.7598267 20.60519
213 1 32.66035 3.5951 19.90818
214 2 29.47834 4.203046 16.01261
Velocities
1 0.00000000 0.00000000 0.00000000
2 0.00000000 0.00000000 0.00000000
3 0.00000000 0.00000000 0.00000000
4 0.00000000 0.00000000 0.00000000
5 0.00000000 0.00000000 0.00000000
6 0.00000000 0.00000000 0.00000000
7 0.00000000 0.00000000 0.00000000
8 0.00000000 0.00000000 0.00000000
9 0.00000000 0.00000000 0.00000000
10 0.00000000 0.00000000 0.00000000
11 0.00000000 0.00000000 0.00000000
12 0.00000000 0.00000000 0.00000000
13 0.00000000 0.00000000 0.00000000
14 0.00000000 0.00000000 0.00000000
15 0.00000000 0.00000000 0.00000000
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22 0.00000000 0.00000000 0.00000000
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24 0.00000000 0.00000000 0.00000000
25 0.00000000 0.00000000 0.00000000
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35 0.00000000 0.00000000 0.00000000
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55 0.00000000 0.00000000 0.00000000
56 0.00000000 0.00000000 0.00000000
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66 0.00000000 0.00000000 0.00000000
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70 0.00000000 0.00000000 0.00000000
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100 0.00000000 0.00000000 0.00000000
101 0.00000000 0.00000000 0.00000000
102 0.00000000 0.00000000 0.00000000
103 0.00000000 0.00000000 0.00000000
104 0.00000000 0.00000000 0.00000000
105 0.00000000 0.00000000 0.00000000
106 0.00000000 0.00000000 0.00000000
107 0.00000000 0.00000000 0.00000000
108 0.00000000 0.00000000 0.00000000
109 0.00000000 0.00000000 0.00000000
110 0.00000000 0.00000000 0.00000000
111 0.00000000 0.00000000 0.00000000
112 0.00000000 0.00000000 0.00000000
113 0.00000000 0.00000000 0.00000000
114 0.00000000 0.00000000 0.00000000
115 0.00000000 0.00000000 0.00000000
116 0.00000000 0.00000000 0.00000000
117 0.00000000 0.00000000 0.00000000
118 0.00000000 0.00000000 0.00000000
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120 0.00000000 0.00000000 0.00000000
121 0.00000000 0.00000000 0.00000000
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123 0.00000000 0.00000000 0.00000000
124 0.00000000 0.00000000 0.00000000
125 0.00000000 0.00000000 0.00000000
126 0.00000000 0.00000000 0.00000000
127 0.00000000 0.00000000 0.00000000
128 0.00000000 0.00000000 0.00000000
129 0.00000000 0.00000000 0.00000000
130 0.00000000 0.00000000 0.00000000
131 0.00000000 0.00000000 0.00000000
132 0.00000000 0.00000000 0.00000000
133 0.00000000 0.00000000 0.00000000
134 0.00000000 0.00000000 0.00000000
135 0.00000000 0.00000000 0.00000000
136 0.00000000 0.00000000 0.00000000
137 0.00000000 0.00000000 0.00000000
138 0.00000000 0.00000000 0.00000000
139 0.00000000 0.00000000 0.00000000
140 0.00000000 0.00000000 0.00000000
141 0.00000000 0.00000000 0.00000000
142 0.00000000 0.00000000 0.00000000
143 0.00000000 0.00000000 0.00000000
144 0.00000000 0.00000000 0.00000000
145 0.00000000 0.00000000 0.00000000
146 0.00000000 0.00000000 0.00000000
147 0.00000000 0.00000000 0.00000000
148 0.00000000 0.00000000 0.00000000
149 0.00000000 0.00000000 0.00000000
150 0.00000000 0.00000000 0.00000000
151 0.00000000 0.00000000 0.00000000
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154 0.00000000 0.00000000 0.00000000
155 0.00000000 0.00000000 0.00000000
156 0.00000000 0.00000000 0.00000000
157 0.00000000 0.00000000 0.00000000
158 0.00000000 0.00000000 0.00000000
159 0.00000000 0.00000000 0.00000000
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168 0.00000000 0.00000000 0.00000000
169 0.00000000 0.00000000 0.00000000
170 0.00000000 0.00000000 0.00000000
171 0.00000000 0.00000000 0.00000000
172 0.00000000 0.00000000 0.00000000
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174 0.00000000 0.00000000 0.00000000
175 0.00000000 0.00000000 0.00000000
176 0.00000000 0.00000000 0.00000000
177 0.00000000 0.00000000 0.00000000
178 0.00000000 0.00000000 0.00000000
179 0.00000000 0.00000000 0.00000000
180 0.00000000 0.00000000 0.00000000
181 0.00000000 0.00000000 0.00000000
182 0.00000000 0.00000000 0.00000000
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184 0.00000000 0.00000000 0.00000000
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186 0.00000000 0.00000000 0.00000000
187 0.00000000 0.00000000 0.00000000
188 0.00000000 0.00000000 0.00000000
189 0.00000000 0.00000000 0.00000000
190 0.00000000 0.00000000 0.00000000
191 0.00000000 0.00000000 0.00000000
192 0.00000000 0.00000000 0.00000000
193 0.00000000 0.00000000 0.00000000
194 0.00000000 0.00000000 0.00000000
195 0.00000000 0.00000000 0.00000000
196 0.00000000 0.00000000 0.00000000
197 0.00000000 0.00000000 0.00000000
198 0.00000000 0.00000000 0.00000000
199 0.00000000 0.00000000 0.00000000
200 0.00000000 0.00000000 0.00000000
201 0.00000000 0.00000000 0.00000000
202 0.00000000 0.00000000 0.00000000
203 0.00000000 0.00000000 0.00000000
204 0.00000000 0.00000000 0.00000000
205 0.00000000 0.00000000 0.00000000
206 0.00000000 0.00000000 0.00000000
207 0.00000000 0.00000000 0.00000000
208 0.00000000 0.00000000 0.00000000
209 0.00000000 0.00000000 0.00000000
210 0.00000000 0.00000000 0.00000000
211 0.00000000 0.00000000 0.00000000
212 0.00000000 0.00000000 0.00000000
213 0.00000000 0.00000000 0.00000000
214 0.00000000 0.00000000 0.00000000
Masses
1 2.81E+01 # Si
2 1.20E+01 # C
3 5.20E+01 # Cr
2

Have a look on the fix setforce command (fix setforce command — LAMMPS documentation). I think it can help you. PS: if you use setforce, make sure you also set the velocity to 0 either manually in the LAMMPS data file (seems to be the case of all atoms in the file you show, so it’s fine) or using the velocity command (velocity command — LAMMPS documentation)

3

This wont be helpful here.

What about fix spring/self ? Another solution is to simply exclude the atom from any fix integrating the equation of motion.

Simon

edit: @ceciliaalvares’ solution works too