Dear Dr. Plimpton and Dr. Kohlmeyer,
I would really appreciate it if you could look at my input file and give me some advice. I am trying to simulate NiTi nanoparticles, and noticed that in the output my temperature is varying more than I would like, and this concerns me. I think this has to do with my creating the sphere of atoms using LAMMPS rather than reading in a data file. When I do this, I am using the create_box command to create and fill the region with atoms, but also this is being used as my simulation box, which seems incorrect. How can I create the nanoparticle in LAMMPS and then enclose it in a much larger simulation box? Besides reading in the data file (which I could do), would create_region union work to create my sphere of particles and then enclose it in the simulation box, or is bounds only useful to join two things together (say an indenter and a surface)? This is my input file currently:
units metal
2 boundary s s s
3
4 atom_style atomic
5
6 lattice custom 3.015 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 &
7 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 origin 0 0 0
8
9 region mysphere sphere 0.0 0.0 0.0 20.0 units box side in
10
11 create_box 2 mysphere
12 create_atoms 2 region mysphere basis 1 1
13 mass 1 47.867
14 mass 2 58.6934
15
16 velocity all create 300.0 87287 rot yes dist gaussian
17
18 pair_style eam/fs
19 pair_coeff * * /home/ualacc/lammps/potentials/NiTi.eam.fs Ni Ti
20
21 neighbor 0.3 bin
22 neigh_modify delay 0 every 1 check yes
23
24 fix 1 all rigid single
25
26 thermo_style custom step temp etotal pxx pyy pzz pxy pxz pyz xlat ylat zlat vol
27
28 min_style cg
29 minimize 0.0 1.0e-6 1000 10000
30 min_modify line quadratic
31
32 unfix 1
33 fix 2 all nvt temp 300.0 300.0 0.01
34 compute 2 all temp
35 dump 2 all atom 100 2.equilibrate.lammpstrj
36
37 thermo 2
38 run 1000
39
40 min_style cg
41 minimize 0.0 1.0e-6 1000 10000
42 min_modify line quadratic
43
44 unfix 2
45 fix 3 all nvt temp 300.0 1400.0 0.01
46 compute 3 all temp
47 dump 3 all atom 100 2.heat.lammpstrj
48 thermo 3
49 run 1000
50
51 unfix 3
52 fix 4 all nvt temp 1400.0 300.0 0.01
53 compute 4 all temp
54 dump 4 all atom 100 10.quench.test.lammpstrj
55 thermo 4
56 run 1000
57
58 unfix 4
59 fix 5 all nvt temp 300.0 300.0 0.01
60 compute 5 all temp
61 dump 5 all atom 100 2.final.lammpstrj
62 thermo 5
63 run 1000
I am trying to do an equilibration, followed by a simulated annealing, a quench, and a final equilibration. I have tried shrink wrapped and periodic boundary conditions, performing the simulation with and without fix rigid, and no matter what I do during the equilibration step the temperature fluctuates like so:
Step Temp TotEng Pxx Pyy Pzz Pxy Pxz Pyz Xlat Ylat Zlat Volume
86 103 308.46816 6793.54 82605.203 82563.717 82582.053 3.2906202 -1.5518927 -12.834087 3.015 3.015 3.015 171179.22
87 104 308.17342 6807.5152 82818.677 82729.897 82740.354 -15.58442 -24.275952 15.903916 3.015 3.015 3.015 171179.22
88 106 306.95604 6819.1553 82939.5 82884.008 82908.484 15.001229 32.836523 42.006606 3.015 3.015 3.015 171179.22
89 108 304.96523 6830.698 83093.071 83107.244 83011.479 59.134381 85.931561 11.254073 3.015 3.015 3.015 171179.22
90 110 302.37388 6841.1119 83245.233 83210.682 83194.043 68.732741 93.870531 7.854265 3.015 3.015 3.015 171179.22
91 112 299.71715 6847.4228 83363.641 83281.043 83272.837 64.847115 108.96448 -12.743958 3.015 3.015 3.015 171179.22
92 114 297.44032 6858.0922 83422.659 83521.4 83376.583 80.269454 60.651908 48.860459 3.015 3.015 3.015 171179.22
93 116 296.05868 6862.2078 83514.037 83547.848 83437.046 112.72543 74.513247 55.398433 3.015 3.015 3.015 171179.22
94 118 296.04037 6861.9992 83144.626 83223.66 83156.905 128.71075 121.59985 84.856189 3.015 3.015 3.015 171853.45
95 120 297.45359 6864.7326 83127.084 83320.605 83162.062 100.00273 69.352123 124.5006 3.015 3.015 3.015 171853.45
96 122 300.40086 6864.1762 83105.487 83260.12 83172.553 121.82988 107.4153 129.19655 3.015 3.015 3.015 171853.45
97 124 304.88667 6864.5737 83075.774 83213.569 83242.948 122.1212 94.865785 133.47226 3.015 3.015 3.015 171853.45
98 126 310.73041 6864.5721 83073.972 83170.383 83246.372 129.32743 85.093727 84.76314 3.015 3.015 3.015 171853.45
99 128 317.71249 6860.9798 82964.802 83070.788 83271.155 152.60709 33.524504 52.807205 3.015 3.015 3.015 171853.45
100 130 325.67661 6857.0838 82910.343 83057.587 83143.281 157.7815 13.159352 54.646282 3.015 3.015 3.015 171853.45
101 132 334.951 6856.5559 82880.74 83050.106 83125.584 175.45759 9.2033273 33.49601 3.015 3.015 3.015 171853.45
102 134 346.00815 6855.3078 82209.026 82423.042 82577.483 180.94327 -6.4364659 84.434119 3.015 3.015 3.015 173059.6
Is there something I am missing? Any insight into this phenomena is greatly appreciated!
Best Regards,