Couldn't locate cfg file

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1

Dear all,

Though the below mentioned code works well, I couldn’t locate cfg file of the output. Kindly help me with same.

MOLECULE FILE:

16 atoms
16 bonds
31 angles
10 impropers

16 atom types
16 bond types
31 angle types
10 improper types

-1.874300 48.125700 xlo xhi
-0.959350 49.040650 ylo yhi
-0.959590 49.040410 zlo zhi

Masses

1 12.011
2 12.011
3 12.011
4 12.011
5 12.011
6 15.999
7 1.008
8 1.008
9 1.008
10 1.008
11 1.008
12 1.008
13 1.008
14 1.008
15 1.008
16 1.008

Pair Coeffs

1 0.066 3.5000000
2 0.066 3.5000000
3 0.066 3.5000000
4 0.066 3.5000000
5 0.066 3.5000000
6 0.170 3.1200000
7 0.030 2.5000000
8 0.030 2.5000000
9 0.030 2.5000000
10 0.030 2.5000000
11 0.030 2.5000000
12 0.030 2.5000000
13 0.030 2.5000000
14 0.030 2.5000000
15 0.030 2.5000000
16 0.000 0.0000000

Bond Coeffs

1 268.0000 1.5290
2 268.0000 1.5290
3 268.0000 1.5290
4 268.0000 1.5290
5 320.0000 1.4100
6 340.0000 1.0900
7 340.0000 1.0900
8 340.0000 1.0900
9 340.0000 1.0900
10 340.0000 1.0900
11 340.0000 1.0900
12 340.0000 1.0900
13 340.0000 1.0900
14 340.0000 1.0900
15 553.0000 0.9450
16 268.0000 1.5290

Angle Coeffs

1 58.350 112.700
2 58.350 112.700
3 58.350 112.700
4 50.000 109.500
5 37.500 110.700
6 37.500 110.700
7 37.500 110.700
8 37.500 110.700
9 37.500 110.700
10 37.500 110.700
11 37.500 110.700
12 37.500 110.700
13 37.500 110.700
14 55.000 108.500
15 50.000 109.500
16 37.500 110.700
17 37.500 110.700
18 33.000 107.800
19 33.000 107.800
20 37.500 110.700
21 37.500 110.700
22 58.350 112.700
23 33.000 107.800
24 37.500 110.700
25 37.500 110.700
26 35.000 109.500
27 37.500 110.700
28 37.500 110.700
29 33.000 107.800
30 58.350 112.700
31 37.500 110.700

Improper Coeffs

1 0.000 -1 2
2 0.000 -1 2
3 0.000 -1 2
4 0.000 -1 2
5 0.000 -1 2
6 0.000 -1 2
7 0.000 -1 2
8 0.000 -1 2
9 0.000 -1 2
10 0.000 -1 2

Atoms

1 1 1 -0.18760000 1.000 1.00000 0.00000
2 1 2 -0.18470000 -0.520 1.00000 0.00000
3 1 3 -0.22290000 -0.854 1.00000 1.48150
4 1 4 0.06970000 0.187 0.06764 2.09766
5 1 5 -0.22880000 1.374 0.05277 1.13652
6 1 6 -0.58160000 0.571 0.52195 3.38495
7 1 7 0.09400000 1.374 2.00753 0.21804
8 1 8 0.09400000 1.417 0.68136 -0.95959
9 1 9 0.09760000 -0.900 0.09000 -0.47832
10 1 10 0.09760000 -0.936 1.86690 -0.52121
11 1 11 0.10210000 -1.874 0.65069 1.66998
12 1 12 0.10210000 -0.773 2.01259 1.89493
13 1 13 0.13280000 -0.218 -0.94432 2.20535
14 1 14 0.10450000 1.499 -0.95935 0.73371
15 1 15 0.10450000 2.318 0.34418 1.60840
16 1 16 0.40690000 0.966 1.40503 3.28568

Bonds

1 1 2 1
2 2 3 2
3 3 4 3
4 4 5 1
5 5 6 4
6 6 7 1
7 7 8 1
8 8 9 2
9 9 10 2
10 10 11 3
11 11 12 3
12 12 13 4
13 13 14 5
14 14 15 5
15 15 16 6
16 16 5 4

Angles

1 1 1 2 3
2 2 2 3 4
3 3 2 1 5
4 4 3 4 6
5 5 2 1 7
6 6 2 1 8
7 7 1 2 9
8 8 1 2 10
9 9 2 3 11
10 10 2 3 12
11 11 3 4 13
12 12 1 5 14
13 13 1 5 15
14 14 4 6 16
15 15 5 4 6
16 16 4 3 11
17 17 5 1 8
18 18 9 2 10
19 19 11 3 12
20 20 5 1 7
21 21 4 5 15
22 22 1 5 4
23 23 14 5 15
24 24 5 4 13
25 25 3 2 9
26 26 6 4 13
27 27 4 5 14
28 28 4 3 12
29 29 7 1 8
30 30 3 4 5
31 31 3 2 10

Impropers

1 1 4 3 5 6
2 2 1 2 5 7
3 3 1 2 5 8
4 4 2 9 3 1
5 5 2 1 10 3
6 6 3 2 11 4
7 7 3 4 2 12
8 8 4 5 3 13
9 9 5 1 4 14
10 10 5 1 4 15

SOURCE CODE:

#-----INITIALIZATION-----
units real
dimension 3
boundary p p p
atom_style full
#-----Force Fields-----
pair_style lj/cut/coul/long 15.0 15.0
pair_modify tail yes
bond_style harmonic
angle_style harmonic
improper_style cvff
kspace_style pppm 1.0e-4
read_data cyclopentanol.txt
replicate 5 5 4
compute eng all pe/atom
compute eatoms all reduce sum c_eng
#-----Equilibriation-----
group cyclopentanol type 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
neighbor 2.0 bin
neigh_modify delay 1 every 1 check no
velocity cyclopentanol create 300 13431343 dist uniform
timestep 1
fix mynpt cyclopentanol npt temp 300.0 300.0 100 iso 1.0 1.0 100 mtk yes tloop 10 ploop 10
min_style cg
minimize 1e-25 1e-25 2000000 2000000
thermo 1
thermo_style custom step temp pe ke etotal press
#-----Output-----
dump mf1 all cfg 100 dump.equi_*.cfg mass type xs ys zs c_eng fx fy fz
dump_modify mf1 element C1 C2 C3 C4 C5 O6 H7 H8 H9 H10 H11 H12 H13 H14 H15 H16
run 1000
print “System is equilibiriated”

Thanks,
Deep

2

there should not be one file, but 10 files, and they should be in the same folder where your data file is.

axel.

3

Yes sir, it should be a bunch of 10. But I could locate a single in any corner of my operating system.
Kindly help me with the same.

4

Yes sir, it should be a bunch of 10. But I could locate a single in any corner of my operating system.
Kindly help me with the same.

do you have proof, that your calculation actually completed? and that you have sufficient storage space/quote to write out those files?

axel.

5

Yes. Actually, the output screen of console has “The system is equilibriated” written on it, which is the last command of our code. So, apparently the calculation must have been completed. Moreover, the console screen also possess output data of pressure vs Temperature vs Energy at different time steps.
And regarding the issue of space availability, I even tried to run the code in another desktop but the same issue persists.

Thanks & Regards,
Deep