Atoms in the liquid and solid phases get mixed up

LAMMPS
1

If you do the calculation with lammps, the atoms in the liquid and solid phases will be mixed. Please let me know how to resolve this.
The current in-file is as follows

Defining the system

units metal
boundary p p p
atom_style atomic
read_data lammps.dat
#group Si type 1
#group Cr type 3
#group C type 2
group kotei id 7 8 9 10 17 18 19 20 29 30 31 32 39 40 41 42 49 50 51 52 59 60 61 62 71 72 73 74 81 82 83 84 91 92 93 94 101 102 103 104 113 114 115 116 123 124 125 126 133 134 135 136 143 144 145 146 155 156 157 158 165 166 167 168
group sp id 1 2 3 4 5 6 11 12 13 14 15 16 21 22 23 24 25 26 27 28 33 34 35 36 37 38 43 44 45 46 47 48 53 54 55 56 57 58 63 64 65 66 67 68 69 70 75 76 77 78 79 80 85 86 87 88 89 90 95 96 97 98 99 105 106 107 108 109 110 111 112 117 118 119 120 121 122 127 128 129 130 131 132 137 138 139 140 141 142 147 148 149 150 151 152 153 154 159 160 161 162 163 164

pair_style nnp
pair_coeff * * ffield.sannp eatom zero Si Cr C

velocity all create 1873.0 15180

Statistical properties

#reset_timestep 0
compute RDF all rdf 60 1 1 1 3 1 2 3 1 3 3 3 2 2 1 2 3 2 2 cutoff 6.0
#fix rdfAve all ave/time 4135 1 4135 c_RDF[*] mode vector file lammps.rdf

ave/time N1 N2 N3

compute md1 Si msd
#fix msd1 all ave/time 4135 1 4135 c_md1[*] file Si.msd

compute md2 C msd
#fix msd2 all ave/time 4135 1 4135 c_md2[*] file C.msd

compute md1 C msd
#variable msdx equal c_md1[1]
#variable msdy equal c_md1[2]
#variable msdz equal c_md1[3]
#variable msd equal c_md1[4]
#variable istep equal step
#fix md1 all print 1 “{istep} {msdx} {msdy} {msdz} ${msd}” screen no file msd_C.dat

Setting for output

dump Dump all custom 1 tmpdir/lammps.dmp type x y z
thermo_style custom step time cpu pe ke etotal enthalpy temp press vol density cella cellb cellc cellalpha cellbeta cellgamma
thermo 1

Setting to run MD or minimization

>>> SCHEME-1

fix ensemble all nvt temp 1873.0 1873.0 0.001
fix kosou kotei setforce 0.0 0.0 0.0
fix ko sp spring/self 50
timestep 2.41837968e-03
run 4135
unfix ensemble

<<<

2

Here is the first step .

3

Hey @simongravelle, :wink:

Just a quick reminder that this post also contains resources on Common Markdown to format the posts, as well as do and don’t on how to post here. Please @iwasa, don’t hesitate to also give it a look.

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4

Just remove any time integrator fix, and your system will remain the same.

If that’s not sufficient, please explain why the mixing is a problem, what is the expected behaviour, and the scientific rationale. But before that, please follow the kind advice of @simongravelle and @Germain. You are embarrassing yourself with your posts and receiving zero help as the only possible outcome.

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