Hi all,
I am using LAMMPS for MD simulations. There is a problem on my code because the simulation can not start, but I am really lost when I try to find it. I think the problem is in the pair_style command.
I want to model the melt of a Ag nanoparticle in LJ units. There’s another problem when I try to compute the radial distribution function, but I commented it.
I would appreciate if you could please help me to solve these problems.
Thanks all
Here is the code i am using:
Input for thermal relaxation
#------------------------INITIALIZATION----------------------------
units lj
boundary s s s
atom_style atomic
#-----------------------ATOM DEFINITION----------------------------
Generating a fcc structure
Ag atoms region
read_data nps201.data
Creating Ag atoms
group all type 1
mass 1 1.0
#------------------------FORCE FIELDS------------------------------
Interaction potential for silver atoms
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
#-------------------------SIMULATION PROCESS---------------------------------
Initial velocities at a given temperature
velocity all create 0.087 87287 mom yes rot yes dist uniform
Nose-Hoover thermostat (thermal relaxation at 200 K)
fix nvt1 all nvt temp 0.087 0.087 0.000004
fix 2 all momentum 10 linear 1 1 1 angular
fix 3 all recenter INIT INIT INIT units box
Timestep to make the integration of the motion equation
timestep 0.005
print “-----THERMAL RELAXATION------”
Parameters to print out on the screen and log.lammps file
thermo_style custom step temp pe etotal vol press enthalpy pxx pyy pzz cpu
thermo 1000
run 50000
unfix nvt1
Nose-Hoover thermostat (first annealing)
print “------FIRST ANNEALING----”
fix nvt2 all nvt temp 0.087 0.131 0.000004
run 50000
unfix nvt2
Nose-Hoover thermostat (second annealing)
print “-----SECOND ANNEALING-----”
fix nvt3 all nvt temp 0.131 0.654 0.000004
Saving atomic coordinates
dump 1 all xyz 5000 dump-melting.xyz
dump_modify 1 element Ag
dump mydump all custom 5000 dump.nano id type x y z mass
dump_modify mydump element Ag
Saving data to analyze
variable Temperature equal temp
variable TEnergy equal etotal/201.0
variable KEnergy equal ke/201.0
variable PEnergy equal pe/201.0
print “----- FIRST FIX AVE/TIME-----”
fix temp_out all ave/time 1000 10 10000 v_Temperature v_PEnergy v_KEnergy v_TEnergy ave window 2 file data.out mode scalar
#Radial Distribution Function
compute rdf1 all rdf 400
print “-----SECOND FIX AVE/TIME------”
fix rdf_out all ave/time 1000 10 10000 c_rdf1 ave window 2 file rdf.out mode scalar
Number of simulation steps
run 500000
#-----SIMULATION DONE-------
print “------SIMULATION COMPLETE------”
and the nps201.data file
Silver nanoparticle with 201 atoms
201 atoms
1 atom types
-0.41651 29.5835 xlo xhi
-0.639404 29.3606 ylo yhi
-1.03991 28.9601 zlo zhi
Atoms
1 1 8.46052 8.23763 13.9601
2 1 6.45298 12.3467 11.9462
3 1 8.35058 10.1425 11.7644
4 1 8.35058 12.1649 9.74198
5 1 6.53026 10.3295 13.9601
6 1 6.45298 12.3467 15.974
7 1 8.35058 10.1425 16.1558
8 1 8.49351 12.3216 13.9601
9 1 8.35058 12.1649 18.1782
10 1 8.46052 14.3606 7.83712
11 1 6.53026 14.3606 9.92897
12 1 6.45298 16.3745 11.9462
13 1 8.49351 14.3606 11.9211
14 1 8.35058 16.5563 9.74198
15 1 6.27497 14.3606 13.9601
16 1 6.45298 16.3745 15.974
17 1 8.49351 14.3606 15.9991
18 1 8.49351 16.3996 13.9601
19 1 6.53026 14.3606 17.9912
20 1 8.46052 14.3606 20.0831
21 1 8.35058 16.5563 18.1782
22 1 8.35058 18.5787 11.7644
23 1 6.53026 18.3917 13.9601
24 1 8.35058 18.5787 16.1558
25 1 8.46052 20.4836 13.9601
26 1 10.3654 8.12768 11.7644
27 1 12.5696 6.23009 11.9462
28 1 12.3878 8.12768 9.74198
29 1 10.5524 6.30737 13.9601
30 1 10.3654 8.12768 16.1558
31 1 12.5696 6.23009 15.974
32 1 12.5444 8.27062 13.9601
33 1 12.3878 8.12768 18.1782
34 1 10.3654 12.1649 7.72718
35 1 12.3878 10.1425 7.72718
36 1 12.5696 12.3467 5.82959
37 1 10.3927 10.1698 9.76933
38 1 10.4593 12.2697 11.8692
39 1 12.4926 10.2364 11.8692
40 1 12.4926 12.2697 9.83587
41 1 10.4583 10.2354 13.9601
42 1 10.4593 12.2697 16.051
43 1 12.4926 10.2364 16.051
44 1 12.512 12.2892 13.9601
45 1 10.3927 10.1698 18.1509
46 1 10.3654 12.1649 20.193
47 1 12.3878 10.1425 20.193
48 1 12.4926 12.2697 18.0843
49 1 12.5696 12.3467 22.0906
50 1 10.5524 14.3606 5.90687
51 1 10.3654 16.5563 7.72718
52 1 12.5444 14.3606 7.87012
53 1 12.5696 16.3745 5.82959
54 1 10.4583 14.3606 9.83492
55 1 10.4593 16.4515 11.8692
56 1 12.512 14.3606 11.8887
57 1 12.4926 16.4515 9.83587
58 1 10.5174 14.3606 13.9601
59 1 10.4593 16.4515 16.051
60 1 12.512 14.3606 16.0315
61 1 12.512 16.432 13.9601
62 1 10.4583 14.3606 18.0853
63 1 10.3654 16.5563 20.193
64 1 12.5444 14.3606 20.0501
65 1 12.4926 16.4515 18.0843
66 1 10.5524 14.3606 22.0133
67 1 12.5696 16.3745 22.0906
68 1 12.3878 18.5787 7.72718
69 1 10.3927 18.5514 9.76933
70 1 10.3654 20.5935 11.7644
71 1 12.4926 18.4848 11.8692
72 1 12.3878 20.5935 9.74198
73 1 10.4583 18.4858 13.9601
74 1 10.3654 20.5935 16.1558
75 1 12.4926 18.4848 16.051
76 1 12.5444 20.4506 13.9601
77 1 10.3927 18.5514 18.1509
78 1 12.3878 18.5787 20.193
79 1 12.3878 20.5935 18.1782
80 1 12.5696 22.4911 11.9462
81 1 10.5524 22.4138 13.9601
82 1 12.5696 22.4911 15.974
83 1 14.5835 8.23763 7.83712
84 1 14.5835 6.30737 9.92897
85 1 14.5835 8.27062 11.9211
86 1 16.5974 6.23009 11.9462
87 1 16.7792 8.12768 9.74198
88 1 14.5835 6.05207 13.9601
89 1 14.5835 8.27062 15.9991
90 1 16.5974 6.23009 15.974
91 1 16.6225 8.27062 13.9601
92 1 14.5835 6.30737 17.9912
93 1 14.5835 8.23763 20.0831
94 1 16.7792 8.12768 18.1782
95 1 14.5835 10.3295 5.90687
96 1 14.5835 12.3216 7.87012
97 1 16.7792 10.1425 7.72718
98 1 16.5974 12.3467 5.82959
99 1 14.5835 10.2354 9.83492
100 1 14.5835 12.2892 11.8887
101 1 16.6744 10.2364 11.8692
102 1 16.6744 12.2697 9.83587
103 1 14.5835 10.2945 13.9601
104 1 14.5835 12.2892 16.0315
105 1 16.6744 10.2364 16.051
106 1 16.6549 12.2892 13.9601
107 1 14.5835 10.2354 18.0853
108 1 14.5835 12.3216 20.0501
109 1 16.7792 10.1425 20.193
110 1 16.6744 12.2697 18.0843
111 1 14.5835 10.3295 22.0133
112 1 16.5974 12.3467 22.0906
113 1 14.5835 14.3606 5.65157
114 1 14.5835 16.3996 7.87012
115 1 16.6225 14.3606 7.87012
116 1 16.5974 16.3745 5.82959
117 1 14.5835 14.3606 9.89405
118 1 14.5835 16.432 11.8887
119 1 16.6549 14.3606 11.8887
120 1 16.6744 16.4515 9.83587
121 1 14.5835 14.3606 13.9601
122 1 14.5835 16.432 16.0315
123 1 16.6549 14.3606 16.0315
124 1 16.6549 16.432 13.9601
125 1 14.5835 14.3606 18.0261
126 1 14.5835 16.3996 20.0501
127 1 16.6225 14.3606 20.0501
128 1 16.6744 16.4515 18.0843
129 1 14.5835 14.3606 22.2686
130 1 16.5974 16.3745 22.0906
131 1 14.5835 18.3917 5.90687
132 1 14.5835 20.4836 7.83712
133 1 16.7792 18.5787 7.72718
134 1 14.5835 18.4858 9.83492
135 1 14.5835 20.4506 11.9211
136 1 16.6744 18.4848 11.8692
137 1 16.7792 20.5935 9.74198
138 1 14.5835 18.4266 13.9601
139 1 14.5835 20.4506 15.9991
140 1 16.6744 18.4848 16.051
141 1 16.6225 20.4506 13.9601
142 1 14.5835 18.4858 18.0853
143 1 14.5835 20.4836 20.0831
144 1 16.7792 18.5787 20.193
145 1 16.7792 20.5935 18.1782
146 1 14.5835 18.3917 22.0133
147 1 14.5835 22.4138 9.92897
148 1 16.5974 22.4911 11.9462
149 1 14.5835 22.6691 13.9601
150 1 16.5974 22.4911 15.974
151 1 14.5835 22.4138 17.9912
152 1 18.8016 8.12768 11.7644
153 1 18.6146 6.30737 13.9601
154 1 18.8016 8.12768 16.1558
155 1 20.7065 8.23763 13.9601
156 1 18.8016 12.1649 7.72718
157 1 18.7743 10.1698 9.76933
158 1 18.7077 12.2697 11.8692
159 1 20.8164 10.1425 11.7644
160 1 20.8164 12.1649 9.74198
161 1 18.7087 10.2354 13.9601
162 1 18.7077 12.2697 16.051
163 1 20.8164 10.1425 16.1558
164 1 20.6735 12.3216 13.9601
165 1 18.7743 10.1698 18.1509
166 1 18.8016 12.1649 20.193
167 1 20.8164 12.1649 18.1782
168 1 18.6146 14.3606 5.90687
169 1 18.8016 16.5563 7.72718
170 1 20.7065 14.3606 7.83712
171 1 18.7087 14.3606 9.83492
172 1 18.7077 16.4515 11.8692
173 1 20.6735 14.3606 11.9211
174 1 20.8164 16.5563 9.74198
175 1 18.6495 14.3606 13.9601
176 1 18.7077 16.4515 16.051
177 1 20.6735 14.3606 15.9991
178 1 20.6735 16.3996 13.9601
179 1 18.7087 14.3606 18.0853
180 1 18.8016 16.5563 20.193
181 1 20.7065 14.3606 20.0831
182 1 20.8164 16.5563 18.1782
183 1 18.6146 14.3606 22.0133
184 1 18.7743 18.5514 9.76933
185 1 18.8016 20.5935 11.7644
186 1 20.8164 18.5787 11.7644
187 1 18.7087 18.4858 13.9601
188 1 18.8016 20.5935 16.1558
189 1 20.8164 18.5787 16.1558
190 1 20.7065 20.4836 13.9601
191 1 18.7743 18.5514 18.1509
192 1 18.6146 22.4138 13.9601
193 1 22.714 12.3467 11.9462
194 1 22.6367 10.3295 13.9601
195 1 22.714 12.3467 15.974
196 1 22.6367 14.3606 9.92897
197 1 22.714 16.3745 11.9462
198 1 22.892 14.3606 13.9601
199 1 22.714 16.3745 15.974
200 1 22.6367 14.3606 17.9912
201 1 22.6367 18.3917 13.9601