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[lammps-users] Neb with reax
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[lammps-users] Neb with reax


From: Alexandra Davila <davila@...6924...>
Date: Mon, 14 Aug 2017 15:58:46 +0200

Dear Lammps-users,

I am trying to do a neb calculation with reax, my input file is attached (with coordinates files).

Probably I am doing a very "beginner" mistake, the error message is:
##
ERROR: Expected integer parameter in input script or data file (../neb.cpp:119)
Last command: neb 0.0001 0 1000 10 final coords.final
##

thanks for the help and patience,

# REAX potential for CHO system
# .....


units real

boundary p p f
atom_style charge
read_data coords.initial

pair_style reax/c NULL
pair_coeff * * ffield.reax.AuO Au
fix 1 all  qeq/reax 10 0.0 10.0 1e-6 reax/c

group freeze id 1:32
group unfrozen subtract all freeze


fix 2 freeze setforce 0.0 0.0 0.0

neighbor 2 bin
neigh_modify every 1 delay 0 check yes

#relax system
minimize	1.0e-6 1.0e-4 10000 100000
reset_timestep	0


# dump 
variable u equal part
dump unscaledDump all custom 1 dump.neb.$u id type x y z ix iy iz

timestep	0.01
thermo 100
#neb
min_style	quickmin
neb 0.0001 0 1000 10 final coords.final



1 1 1 0 0 0
2 1 1 2.93847 0 0
3 1 1 5.87695 0 0
4 1 1 8.81542 0 0
5 1 1 0 2.93847 0
6 1 1 2.93847 2.93847 0
7 1 1 5.87695 2.93847 0
8 1 1 8.81542 2.93847 0
9 1 1 0 5.87695 0
10 1 1 2.93847 5.87695 0
11 1 1 5.87695 5.87695 0
12 1 1 8.81542 5.87695 0
13 1 1 0 8.81542 0
14 1 1 2.93847 8.81542 0
15 1 1 5.87695 8.81542 0
16 1 1 8.81542 8.81542 0
17 1 1 1.46924 1.46924 2.07781
18 1 1 4.40771 1.46924 2.07781
19 1 1 7.34618 1.46924 2.07781
20 1 1 10.2847 1.46924 2.07781
21 1 1 1.46924 4.40771 2.07781
22 1 1 4.40771 4.40771 2.07781
23 1 1 7.34618 4.40771 2.07781
24 1 1 10.2847 4.40771 2.07781
25 1 1 1.46924 7.34618 2.07781
26 1 1 4.40771 7.34618 2.07781
27 1 1 7.34618 7.34618 2.07781
28 1 1 10.2847 7.34618 2.07781
29 1 1 1.46924 10.2847 2.07781
30 1 1 4.40771 10.2847 2.07781
31 1 1 7.34618 10.2847 2.07781
32 1 1 10.2847 10.2847 2.07781
33 1 1 11.7539 -0.00021138 4.16828
34 1 1 2.93872 -0.00024998 4.16825
35 1 1 5.87695 0.000138835 4.16876
36 1 1 8.81517 -0.00024998 4.16825
37 1 1 11.7539 2.93847 4.16789
38 1 1 2.93868 2.93847 4.16828
39 1 1 5.87695 2.93847 4.16885
40 1 1 8.81521 2.93847 4.16828
41 1 1 11.7539 5.87716 4.16828
42 1 1 2.93872 5.8772 4.16825
43 1 1 5.87695 5.87681 4.16876
44 1 1 8.81517 5.8772 4.16825
45 1 1 11.7539 8.81542 4.16885
46 1 1 2.93833 8.81542 4.16876
47 1 1 5.87695 8.81542 4.16862
48 1 1 8.81556 8.81542 4.16876
49 1 1 1.46991 1.46857 6.26383
50 1 1 4.40734 1.46939 6.26709
51 1 1 7.34655 1.46939 6.26709
52 1 1 10.284 1.46857 6.26383
53 1 1 1.46991 4.40838 6.26383
54 1 1 4.40734 4.40755 6.26709
55 1 1 7.34655 4.40755 6.26709
56 1 1 10.284 4.40838 6.26383
57 1 1 1.46908 7.34581 6.26709
58 1 1 4.40764 7.34611 6.2667
59 1 1 7.34626 7.34611 6.2667
60 1 1 10.2848 7.34581 6.26709
61 1 1 1.46908 10.285 6.26709
62 1 1 4.40764 10.2847 6.2667
63 1 1 7.34626 10.2847 6.2667
64 1 1 10.2848 10.285 6.26709
65 1 1 11.7539 2.93847 8.36507
#structure

65  atoms
1  atom types

0.000000  11.75389275   xlo xhi
0.000000  11.75389275   ylo yhi
0.000000  30.00000000   zlo zhi


Masses

1   1

Atoms

1 1 1 0 0 0 0 0 0
2 1 1 2.93847 0 0 0 0 0
3 1 1 5.87695 0 0 0 0 0
4 1 1 8.81542 0 0 0 0 0
5 1 1 0 2.93847 0 0 0 0
6 1 1 2.93847 2.93847 0 0 0 0
7 1 1 5.87695 2.93847 0 0 0 0
8 1 1 8.81542 2.93847 0 0 0 0
9 1 1 0 5.87695 0 0 0 0
10 1 1 2.93847 5.87695 0 0 0 0
11 1 1 5.87695 5.87695 0 0 0 0
12 1 1 8.81542 5.87695 0 0 0 0
13 1 1 0 8.81542 0 0 0 0
14 1 1 2.93847 8.81542 0 0 0 0
15 1 1 5.87695 8.81542 0 0 0 0
16 1 1 8.81542 8.81542 0 0 0 0
17 1 1 1.46924 1.46924 2.07781 0 0 0
18 1 1 4.40771 1.46924 2.07781 0 0 0
19 1 1 7.34618 1.46924 2.07781 0 0 0
20 1 1 10.2847 1.46924 2.07781 0 0 0
21 1 1 1.46924 4.40771 2.07781 0 0 0
22 1 1 4.40771 4.40771 2.07781 0 0 0
23 1 1 7.34618 4.40771 2.07781 0 0 0
24 1 1 10.2847 4.40771 2.07781 0 0 0
25 1 1 1.46924 7.34618 2.07781 0 0 0
26 1 1 4.40771 7.34618 2.07781 0 0 0
27 1 1 7.34618 7.34618 2.07781 0 0 0
28 1 1 10.2847 7.34618 2.07781 0 0 0
29 1 1 1.46924 10.2847 2.07781 0 0 0
30 1 1 4.40771 10.2847 2.07781 0 0 0
31 1 1 7.34618 10.2847 2.07781 0 0 0
32 1 1 10.2847 10.2847 2.07781 0 0 0
33 1 1 11.7539 -2.49911e-08 4.16789 0 0 0
34 1 1 2.93868 -2.49916e-08 4.16828 0 0 0
35 1 1 5.87695 -2.49917e-08 4.16885 0 0 0
36 1 1 8.81521 -2.49911e-08 4.16828 0 0 0
37 1 1 11.7539 2.93868 4.16828 0 0 0
38 1 1 2.93872 2.93872 4.16825 0 0 0
39 1 1 5.87695 2.93833 4.16876 0 0 0
40 1 1 8.81517 2.93872 4.16825 0 0 0
41 1 1 11.7539 5.87695 4.16885 0 0 0
42 1 1 2.93833 5.87695 4.16876 0 0 0
43 1 1 5.87695 5.87695 4.16862 0 0 0
44 1 1 8.81556 5.87695 4.16876 0 0 0
45 1 1 11.7539 8.81521 4.16828 0 0 0
46 1 1 2.93872 8.81517 4.16825 0 0 0
47 1 1 5.87695 8.81556 4.16876 0 0 0
48 1 1 8.81517 8.81517 4.16825 0 0 0
49 1 1 1.46991 1.46991 6.26383 0 0 0
50 1 1 4.40734 1.46908 6.26709 0 0 0
51 1 1 7.34655 1.46908 6.26709 0 0 0
52 1 1 10.284 1.46991 6.26383 0 0 0
53 1 1 1.46908 4.40734 6.26709 0 0 0
54 1 1 4.40764 4.40764 6.2667 0 0 0
55 1 1 7.34626 4.40764 6.2667 0 0 0
56 1 1 10.2848 4.40734 6.26709 0 0 0
57 1 1 1.46908 7.34655 6.26709 0 0 0
58 1 1 4.40764 7.34626 6.2667 0 0 0
59 1 1 7.34626 7.34626 6.2667 0 0 0
60 1 1 10.2848 7.34655 6.26709 0 0 0
61 1 1 1.46991 10.284 6.26383 0 0 0
62 1 1 4.40734 10.2848 6.26709 0 0 0
63 1 1 7.34655 10.2848 6.26709 0 0 0
64 1 1 10.284 10.284 6.26383 0 0 0
65 1 1 11.7539 -2.49796e-08 8.36507 0 0 0