Dear all,
I wish to study an MoS2/water system using LAMMPS. I have created the following input file using following parameters suggested by this paper and trying to learn the LAMMPS syntax: https://pubs.acs.org/doi/10.1021/acs.jpcc.7b00484 shown below.
Define initial structure
units real
atom_style full
Read positions data file
read_data data.lammps
Create bonds for the data file
Note that coefficients are as follows for atoms (from data.lammps)
1 H
2 0
3 Mo
4 S
create_bonds many 3 4 2.0 2.5 # Mo-S bonds
create_bonds many 1 2 1.0 1.2 # H-O bonds
Use this paper for force field parameterization (reaggregation section):
https://pubs.acs.org/doi/10.1021/acs.jpcc.7b00484
Cutoff distanec for both Lennard-Jones (L-J) and Coulombic interactions are set to 1.2 nm = 12 Å
pair_style lj/cut/coul/long 12.0
Particle-Particle-Particle-Mesh (PPPM) method
Calculate long-range electrostatic interactions between particles by dividing the calculation into a short range part handled by particle-particle summation and a large-range part solved using a grid-based Fourier transform method.
Specify this accuracy to be set to 10^-4, per paper
kspace_style pppm 1e-4
Define nonbonded L-J parameters for Mo-Mo and S-S interactions
Format is as follows: atom_coeff atom_coeff σ(Å) ε(kj/mol) q (e)
pair_coeff 3 3 4.43 0.485 0.5 # Mo-Mo
pair_coeff 4 4 3.34 2.085 -0.25 # S-S
Define bonded L-J parameters for Mo-S interaction
Format is as follows atom_coeff
bond_style harmonic
bond_coeff 1 430.4 2.41
Define the angle interactions in the LAMMPS script
angle_style harmonic
angle_coeff 1 1187.7 83.8 # S-Mo-S angle
angle_coeff 2 2050.0 83.8 # Mo-S-Mo angle
Lastly, we define the water ff parameters using the SPC/E model
LAMMPS provides example here: 8.4.6. SPC water model — LAMMPS documentation
pair_coeff 1 1 0.1553 3.166
pair_coeff 1 2 0.0 1.0
pair_coeff 2 2 0.0 1.0
Specify bond information for the water
bond_style zero
bond_coeff 1 1.0
Define the angle interactions for the water
angle_style zero
angle_coeff 1 109.47
This part of the code, specifies computation and running the calculation
We begin by performing a quick energy minimization of the system
Format is energytol forcetol maxiter maxeval
minimize 1.0e-4 1.0e-4 1000 1000
Define Nosé-Hoover barostat and thermostat, per paper
T = 300 K, P = 0.1 MPa
Format is as follows id atoms command(npt) temp tstart tstop tdamp(time units) isotropic(pressure setting) pstart pstop pdamp(time units)
fix NPT all npt temp 300.0 300.0 100.0 iso 0.1 0.1 1000.0
Lastly, we will equilibrate the system for 5 ns, per paper instructions
timestep 1.0
run 5000000
This is what my data.lammps file looks like (format attached below) - I simply converted it from POSCAR (vesta) format to lammps data format using ovito software. I am struggling to find out how to encode bond information. Is there any software which can help me with this? I tried to do it within the input script but LAMMPS throws the following error:
ERROR: Incorrect format in Atoms section of data file: 1 1 0 -2.150134844 -0.9737505046 -19.56606079 (…/atom.cpp:1066)
Last command: read_data data.lammps
Thank you for your help!
LAMMPS data file written by OVITO Basic 3.11.1
900 atoms
4 atom types
0.0 15.96118927 xlo xhi
0.0 13.8227953824 ylo yhi
0.0 153.128326416 zlo zhi
-7.980594635 0.0 0.0 xy xz yz
Masses
1 1.00794 # H
2 15.9994 # O
3 95.94 # Mo
4 32.065 # S
Atoms # full
1 1 0 -2.150134844 -0.9737505046 -19.56606079
2 1 0 -3.33297641 -0.5618632624 -20.613867043
3 1 0 -3.761612615 2.818106807 -21.978468301
4 1 0 -3.860916074 4.278710752 -21.254979707
5 1 0 -1.649271307 1.339884436 -20.073121645
6 1 0 -0.9558494327 1.192024812 -21.544164869
7 1 0 3.459201684 2.943273541 -20.675701554
8 1 0 4.773925259 3.743896839 -21.220826484
9 1 0 -7.043327056 4.050425685 -21.826403785
10 1 0 -5.875959838 3.55559988 -20.797294306
11 1 0 6.87679331 -1.293857117 -20.888989891
12 1 0 5.663746802 -2.386775363 -20.915565598
13 1 0 -8.625420628 3.233712972 -20.340851422
14 1 0 6.316309771 2.67485338 -19.194099283
15 1 0 6.940017956 -3.378706057 -12.251903055
16 1 0 8.296584425 -3.625690688 -11.377034575
17 1 0 5.069556747 4.189717301 -10.3285894474
18 1 0 -10.080259456 5.503617027 -10.859629733
19 1 0 -1.228907738 1.605849588 -17.672261479
20 1 0 0.0442785651 2.1298486 -16.79414839
21 1 0 1.566082899 2.022815755 -10.6822099179
22 1 0 0.7236269754 3.417982179 -10.7843855052
23 1 0 3.277228617 -0.2262689947 -11.056558006
24 1 0 2.00545536 -0.5120646379 -12.0402134
25 1 0 -7.137339647 0.9139223282 -11.919340643
26 1 0 -6.509394017 2.348251596 -12.383074704
27 1 0 -3.12514731 0.8242672141 -9.7744849231
28 1 0 -3.835905295 0.7570547692 -11.243145116
29 1 0 -5.013675883 -2.149986428 -17.662570478
30 1 0 -3.990735331 -1.986506572 -18.924923519
31 1 0 -0.6438242821 1.934802716 -11.920492964
32 1 0 -1.27196943 0.6994204676 -12.784162823
33 1 0 -1.174669551 3.389344619 -6.473521979
34 1 0 -0.5356122062 1.918664033 -6.164712556
35 1 0 -1.771865391 -1.822074892 -13.103610455
36 1 0 -2.372385623 -0.6992837705 -14.126046628
37 1 0 0.9592677956 -0.9637816878 -2.913093237
38 1 0 1.728941781 -2.384059574 -2.6741963
39 1 0 -3.34759579 3.77956971 -7.631401339
40 1 0 -2.207156015 4.881284271 -8.021633003
41 1 0 -4.321563051 -2.205858094 -13.601343524
42 1 0 -4.51604176 -2.891378656 -12.132023371
43 1 0 4.442871887 -1.615980812 -5.517298354
44 1 0 6.03761609 -1.929776038 -5.675359882
45 1 0 -1.726999105 -6.3761968394 -11.67476238
46 1 0 -2.579903649 -6.8637871084 -12.979165329
47 1 0 1.968949147 1.650307328 -12.871481876
48 1 0 2.879349824 2.946109225 -13.269885185
49 1 0 -0.6757048392 1.627527773 -9.6945884775
50 1 0 -1.53711688 1.628049174 -8.307278258
51 1 0 2.286102819 -0.1849787409 -5.203001581
52 1 0 2.81165542 1.359926542 -5.141960464
53 1 0 4.197506927 -1.154546341 -19.937285478
54 1 0 3.061628334 -0.2907020083 -19.143425574
55 1 0 0.6539058995 -4.358454918 -4.501056771
56 1 0 1.628634882 -4.389923813 -3.191256199
57 1 0 -3.422806152 -1.81508617 -6.987197943
58 1 0 -2.395257586 -2.739825224 -6.117910908
59 1 0 -7.2385328687 5.6003903134 -18.78855219
60 1 0 -8.7441658505 5.0811076314 -19.1492093
61 1 0 -4.677449414 -2.034128648 -15.272958389
62 1 0 -4.407803402 -0.4435959494 -15.019651085
63 1 0 1.11568864 -2.490375062 -10.7742012919
64 1 0 0.001276855 -2.918966848 -9.6601749807
65 1 0 1.512860096 -1.996240257 -13.235795971
66 1 0 0.0309115386 -1.474832798 -12.790123247
67 1 0 5.183217492 -3.263309853 -17.609736084
68 1 0 4.020270641 -2.148990445 -17.87900448
69 1 0 -9.372338324 4.276324491 -17.160657181
70 1 0 5.055937384 3.774762504 -17.416136525
71 1 0 10.136951002 -4.031695823 -15.838275147
72 1 0 9.114366465 -2.760992812 -15.758936236
73 1 0 -2.150134844 -0.9737505046 0.09549427
74 1 0 -3.33297641 -0.5618632624 -0.952311983
75 1 0 -3.761612615 2.818106807 -2.316913241
76 1 0 -3.860916074 4.278710752 -1.593424647
77 1 0 7.327414674 -1.81916643 -19.19366388
78 1 0 -7.578424758 -0.6501467288 -18.762046393
79 1 0 1.800423915 4.694429522 -7.585210169
80 1 0 1.257932584 3.536876659 -6.569121715
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82 1 0 5.79621491 -1.375553233 -10.6652511544
83 1 0 -1.649271307 1.339884436 -0.411566585
84 1 0 -0.9558494327 1.192024812 -1.882609809
85 1 0 1.676260959 4.364696525 -14.596437148
86 1 0 3.070439189 5.196863607 -14.422015964
87 1 0 4.037184907 2.489621152 -10.4196850367
88 1 0 4.74482978 2.27727486 -11.875989478
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213 1 0 4.812992687 -4.370904561 -9.0116535684
214 1 0 6.022101096 -5.468313141 -8.9913553159
215 1 0 9.623188693 -5.5325771634 -1.014586874
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246 1 0 6.236700113 -4.55966967 -2.545317595
247 1 0 6.940017956 -3.378706057 7.409652005
248 1 0 8.296584425 -3.625690688 8.284520485
249 1 0 5.069556747 4.189717301 9.3329656126
250 1 0 -10.080259456 5.503617027 8.801925327
251 1 0 -1.228907738 1.605849588 1.989293581
252 1 0 0.0442785651 2.1298486 2.86740667
253 1 0 1.566082899 2.022815755 8.9793451421
254 1 0 0.7236269754 3.417982179 8.8771695548
255 1 0 3.277228617 -0.2262689947 8.604997054
256 1 0 2.00545536 -0.5120646379 7.62134166
257 1 0 -7.137339647 0.9139223282 7.742214417
258 1 0 -6.509394017 2.348251596 7.278480356
259 1 0 -3.12514731 0.8242672141 9.8870701369
260 1 0 -3.835905295 0.7570547692 8.418409944
261 1 0 -5.013675883 -2.149986428 1.998984582
262 1 0 -3.990735331 -1.986506572 0.736631541
263 1 0 -0.6438242821 1.934802716 7.741062096
264 1 0 -1.27196943 0.6994204676 6.877392237
265 1 0 -1.174669551 3.389344619 13.188033081
266 1 0 -0.5356122062 1.918664033 13.496842504
267 1 0 -1.771865391 -1.822074892 6.557944605
268 1 0 -2.372385623 -0.6992837705 5.535508432
269 1 0 0.9592677956 -0.9637816878 16.748461823
270 1 0 1.728941781 -2.384059574 16.98735876
271 1 0 -3.34759579 3.77956971 12.030153721
272 1 0 -2.207156015 4.881284271 11.639922057
273 1 0 -4.321563051 -2.205858094 6.060211536
274 1 0 -4.51604176 -2.891378656 7.529531689
275 1 0 4.442871887 -1.615980812 14.144256706
276 1 0 6.03761609 -1.929776038 13.986195178
277 1 0 -1.726999105 -6.3761968394 7.98679268
278 1 0 -2.579903649 -6.8637871084 6.682389731
279 1 0 1.968949147 1.650307328 6.790073184
280 1 0 2.879349824 2.946109225 6.391669875
281 1 0 -0.6757048392 1.627527773 9.9669665825
282 1 0 -1.53711688 1.628049174 11.354276802
283 1 0 2.286102819 -0.1849787409 14.458553479
284 1 0 2.81165542 1.359926542 14.519594596
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286 1 0 3.061628334 -0.2907020083 0.518129486
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…