Four elements system

Good morning,

I'm trying to calculate the enthalpy of an Al-Fe-Si-Ni system in a liquid state. I used a position's file for the initialization and then i applied a fix npt at 2000K and 0 bar. The thing is, after 2000 iterations, i keep getting "nan" as temperature, enthalpy, pressure and volume's values. I tried to visualize my system in Ovito and it doesn't seem to explode or implode. I also tried to do my fix npt at 1000K and i got the "nan" error after 9200 iterations. If you don't mind telling me what should i do to solve this problem. I'm attaching my data file, input file and output file.

####### DATA FILE ##############

LAMMPS Description

256 atoms

4 atom types

0.0 16.32 xlo xhi
0.0 16.32 ylo yhi
0.0 16.32 zlo zhi

Masses

1 26.9815
2 28.086
3 55.847
4 58.71

Atoms

1 1 0.00000 0.00000 0.00000
2 2 0.00000 2.03930 2.03930
3 3 2.03930 0.00000 2.03930
4 4 2.03930 0.00000 0.00000
5 1 0.00000 0.00000 4.07860
6 3 0.00000 2.03930 6.11790
7 2 2.03930 0.00000 6.11790
8 4 2.03930 2.03930 4.07860
9 1 0.00000 0.00000 8.15720
10 3 0.00000 2.03930 10.19650
11 2 2.03930 0.00000 10.19650
12 4 2.03930 2.03930 8.15720
13 1 0.00000 0.00000 12.23580
14 3 0.00000 2.03930 14.27510
15 2 2.03930 0.00000 14.27510
16 4 2.03930 2.03930 12.23580
17 1 0.00000 4.07860 0.00000
18 3 0.00000 6.11790 2.03930
19 2 2.03930 4.07860 2.03930
20 4 2.03930 6.11790 0.00000
21 1 0.00000 4.07860 4.07860
22 3 0.00000 6.11790 6.11790
23 2 2.03930 4.07860 6.11790
24 4 2.03930 6.11790 4.07860
25 1 0.00000 4.07860 8.15720
26 3 0.00000 6.11790 10.19650
27 2 2.03930 4.07860 10.19650
28 4 2.03930 6.11790 8.15720
29 1 0.00000 4.07860 12.23580
30 3 0.00000 6.11790 14.27510
31 2 2.03930 4.07860 14.27510
32 4 2.03930 6.11790 12.23580
33 1 0.00000 8.15720 0.00000
34 3 0.00000 10.19650 2.03930
35 2 2.03930 8.15720 2.03930
36 4 2.03930 10.19650 0.00000
37 1 0.00000 8.15720 4.07860
38 3 0.00000 10.19650 6.11790
39 2 2.03930 8.15720 6.11790
40 4 2.03930 10.19650 4.07860
41 1 0.00000 8.15720 8.15720
42 3 0.00000 10.19650 10.19650
43 2 2.03930 8.15720 10.19650
44 4 2.03930 10.19650 8.15720
45 1 0.00000 8.15720 12.23580
46 3 0.00000 10.19650 14.27510
47 2 2.03930 8.15720 14.27510
48 4 2.03930 10.19650 12.23580
49 1 0.00000 12.23580 0.00000
50 3 0.00000 14.27510 2.03930
51 2 2.03930 12.23580 2.03930
52 4 2.03930 14.27510 0.00000
53 1 0.00000 12.23580 4.07860
54 3 0.00000 14.27510 6.11790
55 2 2.03930 12.23580 6.11790
56 4 2.03930 14.27510 4.07860
57 1 0.00000 12.23580 8.15720
58 3 0.00000 14.27510 10.19650
59 2 2.03930 12.23580 10.19650
60 4 2.03930 14.27510 8.15720
61 1 0.00000 12.23580 12.23580
62 3 0.00000 14.27510 14.27510
63 2 2.03930 12.23580 14.27510
64 4 2.03930 14.27510 12.23580
65 1 4.07860 0.00000 0.00000
66 3 4.07860 2.03930 2.03930
67 2 6.11790 0.00000 2.03930
68 4 6.11790 2.03930 0.00000
69 1 4.07860 0.00000 4.07860
70 3 4.07860 2.03930 6.11790
71 2 6.11790 0.00000 6.11790
72 4 6.11790 2.03930 4.07860
73 1 4.07860 0.00000 8.15720
74 3 4.07860 2.03930 10.19650
75 2 6.11790 0.00000 10.19650
76 4 6.11790 2.03930 8.15720
77 1 4.07860 0.00000 12.23580
78 3 4.07860 2.03930 14.27510
79 2 6.11790 0.00000 14.27510
80 4 6.11790 2.03930 12.23580
81 1 4.07860 4.07860 0.00000
82 3 4.07860 6.11790 2.03930
83 2 6.11790 4.07860 2.03930
84 4 6.11790 6.11790 0.00000
85 1 4.07860 4.07860 4.07860
86 3 4.07860 6.11790 6.11790
87 2 6.11790 4.07860 6.11790
88 4 6.11790 6.11790 4.07860
89 1 4.07860 4.07860 8.15720
90 3 4.07860 6.11790 10.19650
91 2 6.11790 4.07860 10.19650
92 4 6.11790 6.11790 8.15720
93 1 4.07860 4.07860 12.23580
94 3 4.07860 6.11790 14.27510
95 2 6.11790 4.07860 14.27510
96 4 6.11790 6.11790 12.23580
97 1 4.07860 8.15720 0.00000
98 3 4.07860 10.19650 2.03930
99 2 6.11790 8.15720 2.03930
100 4 6.11790 10.19650 0.00000
101 1 4.07860 8.15720 4.07860
102 3 4.07860 10.19650 6.11790
103 2 6.11790 8.15720 6.11790
104 4 6.11790 10.19650 4.07860
105 1 4.07860 8.15720 8.15720
106 3 4.07860 10.19650 10.19650
107 2 6.11790 8.15720 10.19650
108 4 6.11790 10.19650 8.15720
109 1 4.07860 8.15720 12.23580
110 3 4.07860 10.19650 14.27510
111 2 6.11790 8.15720 14.27510
112 4 6.11790 10.19650 12.23580
113 1 4.07860 12.23580 0.00000
114 3 4.07860 14.27510 2.03930
115 2 6.11790 12.23580 2.03930
116 4 6.11790 14.27510 0.00000
117 1 4.07860 12.23580 4.07860
118 3 4.07860 14.27510 6.11790
119 2 6.11790 12.23580 6.11790
120 4 6.11790 14.27510 4.07860
121 1 4.07860 12.23580 8.15720
122 3 4.07860 14.27510 10.19650
123 2 6.11790 12.23580 10.19650
124 4 6.11790 14.27510 8.15720
125 1 4.07860 12.23580 12.23580
126 3 4.07860 14.27510 14.27510
127 2 6.11790 12.23580 14.27510
128 4 6.11790 14.27510 12.23580
129 1 8.15720 0.00000 0.00000
130 3 8.15720 2.03930 2.03930
131 2 10.19650 0.00000 2.03930
132 4 10.19650 2.03930 0.00000
133 1 8.15720 0.00000 4.07860
134 3 8.15720 2.03930 6.11790
135 2 10.19650 0.00000 6.11790
136 4 10.19650 2.03930 4.07860
137 1 8.15720 0.00000 8.15720
138 3 8.15720 2.03930 10.19650
139 2 10.19650 0.00000 10.19650
140 4 10.19650 2.03930 8.15720
141 1 8.15720 0.00000 12.23580
142 3 8.15720 2.03930 14.27510
143 2 10.19650 0.00000 14.27510
144 4 10.19650 2.03930 12.23580
145 1 8.15720 4.07860 0.00000
146 3 8.15720 6.11790 2.03930
147 2 10.19650 4.07860 2.03930
148 4 10.19650 6.11790 0.00000
149 1 8.15720 4.07860 4.07860
150 3 8.15720 6.11790 6.11790
151 2 10.19650 4.07860 6.11790
152 4 10.19650 6.11790 4.07860
153 1 8.15720 4.07860 8.15720
154 3 8.15720 6.11790 10.19650
155 2 10.19650 4.07860 10.19650
156 4 10.19650 6.11790 8.15720
157 1 8.15720 4.07860 12.23580
158 3 8.15720 6.11790 14.27510
159 2 10.19650 4.07860 14.27510
160 4 10.19650 6.11790 12.23580
161 1 8.15720 8.15720 0.00000
162 3 8.15720 10.19650 2.03930
163 2 10.19650 8.15720 2.03930
164 4 10.19650 10.19650 0.00000
165 1 8.15720 8.15720 4.07860
166 3 8.15720 10.19650 6.11790
167 2 10.19650 8.15720 6.11790
168 4 10.19650 10.19650 4.07860
169 1 8.15720 8.15720 8.15720
170 3 8.15720 10.19650 10.19650
171 2 10.19650 8.15720 10.19650
172 4 10.19650 10.19650 8.15720
173 1 8.15720 8.15720 12.23580
174 3 8.15720 10.19650 14.27510
175 2 10.19650 8.15720 14.27510
176 4 10.19650 10.19650 12.23580
177 1 8.15720 12.23580 0.00000
178 3 8.15720 14.27510 2.03930
179 2 10.19650 12.23580 2.03930
180 4 10.19650 14.27510 0.00000
181 1 8.15720 12.23580 4.07860
182 3 8.15720 14.27510 6.11790
183 2 10.19650 12.23580 6.11790
184 4 10.19650 14.27510 4.07860
185 1 8.15720 12.23580 8.15720
186 3 8.15720 14.27510 10.19650
187 2 10.19650 12.23580 10.19650
188 4 10.19650 14.27510 8.15720
189 1 8.15720 12.23580 12.23580
190 3 8.15720 14.27510 14.27510
191 2 10.19650 12.23580 14.27510
192 4 10.19650 14.27510 12.23580
193 1 12.23580 0.00000 0.00000
194 3 12.23580 2.03930 2.03930
195 2 14.27510 0.00000 2.03930
196 4 14.27510 2.03930 0.00000
197 1 12.23580 0.00000 4.07860
198 3 12.23580 2.03930 6.11790
199 2 14.27510 0.00000 6.11790
200 4 14.27510 2.03930 4.07860
201 1 12.23580 0.00000 8.15720
202 3 12.23580 2.03930 10.19650
203 2 14.27510 0.00000 10.19650
204 4 14.27510 2.03930 8.15720
205 1 12.23580 0.00000 12.23580
206 3 12.23580 2.03930 14.27510
207 2 14.27510 0.00000 14.27510
208 4 14.27510 2.03930 12.23580
209 1 12.23580 4.07860 0.00000
210 3 12.23580 6.11790 2.03930
211 2 14.27510 4.07860 2.03930
212 4 14.27510 6.11790 0.00000
213 1 12.23580 4.07860 4.07860
214 3 12.23580 6.11790 6.11790
215 2 14.27510 4.07860 6.11790
216 4 14.27510 6.11790 4.07860
217 1 12.23580 4.07860 8.15720
218 3 12.23580 6.11790 10.19650
219 2 14.27510 4.07860 10.19650
220 4 14.27510 6.11790 8.15720
221 1 12.23580 4.07860 12.23580
222 3 12.23580 6.11790 14.27510
223 2 14.27510 4.07860 14.27510
224 4 14.27510 6.11790 12.23580
225 1 12.23580 8.15720 0.00000
226 3 12.23580 10.19650 2.03930
227 2 14.27510 8.15720 2.03930
228 4 14.27510 10.19650 0.00000
229 1 12.23580 8.15720 4.07860
230 3 12.23580 10.19650 6.11790
231 2 14.27510 8.15720 6.11790
232 4 14.27510 10.19650 4.07860
233 1 12.23580 8.15720 8.15720
234 3 12.23580 10.19650 10.19650
235 2 14.27510 8.15720 10.19650
236 4 14.27510 10.19650 8.15720
237 1 12.23580 8.15720 12.23580
238 3 12.23580 10.19650 14.27510
239 2 14.27510 8.15720 14.27510
240 4 14.27510 10.19650 12.23580
241 1 12.23580 12.23580 0.00000
242 3 12.23580 14.27510 2.03930
243 2 14.27510 12.23580 2.03930
244 4 14.27510 14.27510 0.00000
245 1 12.23580 12.23580 4.07860
246 3 12.23580 14.27510 6.11790
247 2 14.27510 12.23580 6.11790
248 4 14.27510 14.27510 4.07860
249 1 12.23580 12.23580 8.15720
250 3 12.23580 14.27510 10.19650
251 2 14.27510 12.23580 10.19650
252 4 14.27510 14.27510 8.15720
253 1 12.23580 12.23580 12.23580
254 3 12.23580 14.27510 14.27510
255 2 14.27510 12.23580 14.27510
256 4 14.27510 14.27510 12.23580

########## INPUT FILE #####################

#Calcul de l'enthalpie de formation à pression constante pour un système AlFeSiNi 25/25/25/25
#Walid

#-------------------- Initialisation -------------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic

#------------------- Création d'atomes -------------------

read_data Position_file2.xyz

#------------------- Potentiel interatomique --------------
pair_style meam
pair_coeff * * library.meam AlS SiS FeS Ni NULL AlS SiS FeS Ni
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
delete_atoms overlap 0.35 all all

#------------------------- Run ------------------------
velocity all create 2000 492390
min_style cg
minimize 1e-25 1e-25 5000 5000

timestep 0.001
fix 1 all npt temp 2000 2000 0.1 iso 0 0 0.1

thermo 100
thermo_style custom step temp enthalpy press vol
thermo_modify flush yes

dump 1 all cfg 500 dump.AlFeSiNi_*.cfg mass type xs ys zs

compute myRDF all rdf 50
fix 2 all ave/time 5000 1 5000 c_myRDF[*] file tmpAlFeSiNi.rdf mode vector

run 10000

variable natoms equal "count(all)"

print "Number of atoms = ${natoms};"

print "All done!"

################## OUTPUT FILE ###########################

LAMMPS (8 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
   using 1 OpenMP thread(s) per MPI task
#Calcul de l'enthalpie de formation à pression constante pour un système AlFeSiNi 25/25/25/25
#Walid

#-------------------- Initialisation -------------------
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
   using 1 OpenMP thread(s) per MPI task
units metal
dimension 3
boundary p p p
atom_style atomic

#------------------- Création d'atomes -------------------

read_data Position_file2.xyz
   orthogonal box = (0 0 0) to (16.32 16.32 16.32)
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   256 atoms

#------------------- Potentiel interatomique --------------
pair_style meam
pair_coeff * * library.meam AlS SiS FeS Ni NULL AlS SiS FeS Ni
Reading potential file library.meam with DATE: 2012-06-29
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
delete_atoms overlap 0.35 all all
Neighbor list info ...
   update every 1 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 6
   ghost atom cutoff = 6
   binsize = 3, bins = 6 6 6
   3 neighbor lists, perpetual/occasional/extra = 2 1 0
   (1) command delete_atoms, occasional, copy from (2)
       attributes: full, newton on
       pair build: copy
       stencil: none
       bin: none
   (2) pair meam, perpetual
       attributes: full, newton on
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
   (3) pair meam, perpetual, half/full from (2)
       attributes: half, newton on
       pair build: halffull/newton
       stencil: none
       bin: none
Deleted 0 atoms, new total = 256

#------------------------- Run ------------------------
velocity all create 2000 492390
min_style cg
minimize 1e-25 1e-25 5000 5000
Neighbor list info ...
   update every 1 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 6
   ghost atom cutoff = 6
   binsize = 3, bins = 6 6 6
   2 neighbor lists, perpetual/occasional/extra = 2 0 0
   (1) pair meam, perpetual
       attributes: full, newton on
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
   (2) pair meam, perpetual, half/full from (1)
       attributes: half, newton on
       pair build: halffull/newton
       stencil: none
       bin: none
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes
Step Temp E_pair E_mol TotEng Press
        0 2000 -905.35792 0 -839.43524 -194572.08
      504 2000 -969.12191 0 -903.19924 -176682
Loop time of 3.87511 on 1 procs for 504 steps with 256 atoms

98.4% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
   Stopping criterion = energy tolerance
   Energy initial, next-to-last, final =
         -905.357916084 -969.12191125 -969.12191125
   Force two-norm initial, final = 50.1119 1.63319
   Force max component initial, final = 34.0049 0.558963
   Final line search alpha, max atom move = 0.00559071 0.003125
   Iterations, force evaluations = 504 1961

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

Good morning,

I’m trying to calculate the enthalpy of an Al-Fe-Si-Ni system in a
liquid state. I used a position’s file for the initialization and then
i applied a fix npt at 2000K and 0 bar. The thing is, after 2000
iterations, i keep getting “nan” as temperature, enthalpy, pressure
and volume’s values. I tried to visualize my system in Ovito and it
doesn’t seem to explode or implode. I also tried to do my fix npt at
1000K and i got the “nan” error after 9200 iterations. If you don’t
mind telling me what should i do to solve this problem. I’m attaching
my data file, input file and output file.

try changing the time constant for the barostat. 0.1ps is pretty short and may not result in a stable propagation of the underlying thermostat DOFs. try 1ps or 10ps.

axel.