Lammps input data for pcff based simulation

Hi! I generated a LAMMPS input data file of a CNT (10,10) unit cell for a PCFF forcefield. During minimization, I am getting the following error message: “Invalid atom ID in Angles section of data file.” The error appears only when I try to minimize the system which consists of a single unit cell. For multiple unit cell scenarios, it works fine. Here is my input file.

LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 / CGCMM for CNT_UC_1

 40 atoms
 60 bonds
120 angles
120 dihedrals
 40 impropers

1 atom types
1 bond types
1 angle types
1 dihedral types
1 improper types

-6.320800018    23.679199982 xlo xhi
-6.320800018    23.679199982 ylo yhi
-0.617199993     1.852200007 zlo zhi

Masses

1 12.011150 # cp

Pair Coeffs # lj/class2/coul/long

1 0.0640000000 4.0100000000 # cp

Bond Coeffs # class2

1 1.4170 470.8361 -627.6179 1327.6345 # cp-cp

Angle Coeffs # class2

1 118.9000 61.0226 -34.9931 0.0000 # cp-cp-cp

Dihedral Coeffs # class2

1 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000# cp-cp-cp-cp

Improper Coeffs # class2

1 7.1794 0.0000 # cp-cp-cp-cp

BondBond Coeffs

1 68.2856 1.4170 1.4170

BondAngle Coeffs

1 28.8708 28.8708 1.4170 1.4170

AngleAngle Coeffs

1 0.0000 0.0000 0.0000 118.9000 118.9000 118.9000

AngleAngleTorsion Coeffs

1 0.0000 118.9000 118.9000

EndBondTorsion Coeffs

1 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170

MiddleBondTorsion Coeffs

1 27.5989 -2.3120 0.0000 1.4170

BondBond13 Coeffs

1 53.0000 1.4170 1.4170

AngleTorsion Coeffs

1 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000

Atoms # full

  1      1   1  0.000000    15.318179499     8.250704498     0.000124440   0   0   0 # cp
  2      1   1  0.000000    15.260602409     9.651142501     0.000124603   0   0   0 # cp
  3      1   1  0.000000    15.125632420    10.323216849     1.234874639   0   0   0 # cp
  4      1   1  0.000000    14.638074400    11.637304181     1.234874891   0   0   0 # cp
  5      1   1  0.000000    14.302025147    12.234775398     0.000124939   0   0   0 # cp
  6      1   1  0.000000    13.432281414    13.333902335     0.000125127   0   0   0 # cp
  7      1   1  0.000000    12.928070237    13.798307424     1.234875166   0   0   0 # cp
  8      1   1  0.000000    11.761282434    14.574929150     1.234875320   0   0   0 # cp
  9      1   1  0.000000    11.138249090    14.860814374     0.000125329   0   0   0 # cp
 10      1   1  0.000000     9.788579001    15.238876205     0.000125349   0   0   0 # cp
 11      1   1  0.000000     9.107693852    15.318225224     1.234875360   0   0   0 # cp
 12      1   1  0.000000     7.707255579    15.260647878     1.234875382   0   0   0 # cp
 13      1   1  0.000000     7.035181653    15.125675536     0.000125373   0   0   0 # cp
 14      1   1  0.000000     5.721097266    14.638108972     0.000125356   0   0   0 # cp
 15      1   1  0.000000     5.123628815    14.302054827     1.234875336   0   0   0 # cp
 16      1   1  0.000000     4.024510226    13.432300497     1.234875190   0   0   0 # cp
 17      1   1  0.000000     3.560110217    12.928084660     0.000125179   0   0   0 # cp
 18      1   1  0.000000     2.783500119    11.761289166     0.000125148   0   0   0 # cp
 19      1   1  0.000000     2.497620238    11.138253356     1.234875139   0   0   0 # cp
 20      1   1  0.000000     2.119567205     9.788580952     1.234875136   0   0   0 # cp
 21      1   1  0.000000     2.040220449     9.107695539     0.000125152   0   0   0 # cp
 22      1   1  0.000000     2.097797967     7.707257563     0.000125168   0   0   0 # cp
 23      1   1  0.000000     2.232768013     7.035183225     1.234875166   0   0   0 # cp
 24      1   1  0.000000     2.720326050     5.721095930     1.234875140   0   0   0 # cp
 25      1   1  0.000000     3.056375064     5.123624585     0.000125137   0   0   0 # cp
 26      1   1  0.000000     3.926118267     4.024497226     0.000125180   0   0   0 # cp
 27      1   1  0.000000     4.430329331     3.560092013     1.234875182   0   0   0 # cp
 28      1   1  0.000000     5.597117298     2.783470477     1.234875145   0   0   0 # cp
 29      1   1  0.000000     6.220150757     2.497585475     0.000125121   0   0   0 # cp
 30      1   1  0.000000     7.569820992     2.119524168     0.000125049   0   0   0 # cp
 31      1   1  0.000000     8.250706152     2.040175266     1.234875018   0   0   0 # cp
 32      1   1  0.000000     9.651144417     2.097752470     1.234874900   0   0   0 # cp
 33      1   1  0.000000    10.323218365     2.232724593     0.000124873   0   0   0 # cp
 34      1   1  0.000000    11.637302950     2.720290592     0.000124712   0   0   0 # cp
 35      1   1  0.000000    12.234771438     3.056344678     1.234874669   0   0   0 # cp
 36      1   1  0.000000    13.333889858     3.926099251     1.234874525   0   0   0 # cp
 37      1   1  0.000000    13.798289619     4.430315290     0.000124505   0   0   0 # cp
 38      1   1  0.000000    14.574899310     5.597111010     0.000124424   0   0   0 # cp
 39      1   1  0.000000    14.860779157     6.220146832     1.234874401   0   0   0 # cp
 40      1   1  0.000000    15.238832588     7.569819105     1.234874420   0   0   0 # cp

Bonds

 1   1      1      2
 2   1      1     40
 3   1      1     40
 4   1      2      3
 5   1      2      3
 6   1      3      4
 7   1      4      5
 8   1      4      5
 9   1      5      6
10   1      6      7
11   1      6      7
12   1      7      8
13   1      8      9
14   1      8      9
15   1      9     10
16   1     10     11
17   1     10     11
18   1     11     12
19   1     12     13
20   1     12     13
21   1     13     14
22   1     14     15
23   1     14     15
24   1     15     16
25   1     16     17
26   1     16     17
27   1     17     18
28   1     18     19
29   1     18     19
30   1     19     20
31   1     20     21
32   1     20     21
33   1     21     22
34   1     22     23
35   1     22     23
36   1     23     24
37   1     24     25
38   1     24     25
39   1     25     26
40   1     26     27
41   1     26     27
42   1     27     28
43   1     28     29
44   1     28     29
45   1     29     30
46   1     30     31
47   1     30     31
48   1     31     32
49   1     32     33
50   1     32     33
51   1     33     34
52   1     34     35
53   1     34     35
54   1     35     36
55   1     36     37
56   1     36     37
57   1     37     38
58   1     38     39
59   1     38     39
60   1     39     40

Angles

 1   1      2      1     40
 2   1      2      1     40
 3   1     40      1     40
 4   1      1      2      3
 5   1      1      2      3
 6   1      3      2      3
 7   1      2      3      4
 8   1      2      3      2
 9   1      4      3      2
10   1      3      4      5
11   1      3      4      5
12   1      5      4      5
13   1      4      5      6
14   1      4      5      4
15   1      6      5      4
16   1      5      6      7
17   1      5      6      7
18   1      7      6      7
19   1      6      7      8
20   1      6      7      6
21   1      8      7      6
22   1      7      8      9
23   1      7      8      9
24   1      9      8      9
25   1      8      9     10
26   1      8      9      8
27   1     10      9      8
28   1      9     10     11
29   1      9     10     11
30   1     11     10     11
31   1     10     11     12
32   1     10     11     10
33   1     12     11     10
34   1     11     12     13
35   1     11     12     13
36   1     13     12     13
37   1     12     13     14
38   1     12     13     12
39   1     14     13     12
40   1     13     14     15
41   1     13     14     15
42   1     15     14     15
43   1     14     15     16
44   1     14     15     14
45   1     16     15     14
46   1     15     16     17
47   1     15     16     17
48   1     17     16     17
49   1     16     17     18
50   1     16     17     16
51   1     18     17     16
52   1     17     18     19
53   1     17     18     19
54   1     19     18     19
55   1     18     19     20
56   1     18     19     18
57   1     20     19     18
58   1     19     20     21
59   1     19     20     21
60   1     21     20     21
61   1     20     21     22
62   1     20     21     20
63   1     22     21     20
64   1     21     22     23
65   1     21     22     23
66   1     23     22     23
67   1     22     23     24
68   1     22     23     22
69   1     24     23     22
70   1     23     24     25
71   1     23     24     25
72   1     25     24     25
73   1     24     25     26
74   1     24     25     24
75   1     26     25     24
76   1     25     26     27
77   1     25     26     27
78   1     27     26     27
79   1     26     27     28
80   1     26     27     26
81   1     28     27     26
82   1     27     28     29
83   1     27     28     29
84   1     29     28     29
85   1     28     29     30
86   1     28     29     28
87   1     30     29     28
88   1     29     30     31
89   1     29     30     31
90   1     31     30     31
91   1     30     31     32
92   1     30     31     30
93   1     32     31     30
94   1     31     32     33
95   1     31     32     33
96   1     33     32     33
97   1     32     33     34
98   1     32     33     32
99   1     34     33     32

100 1 33 34 35
101 1 33 34 35
102 1 35 34 35
103 1 34 35 36
104 1 34 35 34
105 1 36 35 34
106 1 35 36 37
107 1 35 36 37
108 1 37 36 37
109 1 36 37 38
110 1 36 37 36
111 1 38 37 36
112 1 37 38 39
113 1 37 38 39
114 1 39 38 39
115 1 38 39 40
116 1 38 39 38
117 1 40 39 38
118 1 1 40 39
119 1 1 40 1
120 1 39 40 1

Dihedrals

 1   1     40      1      2      3
 2   1     40      1      2      3
 3   1     40      1      2      3
 4   1     40      1      2      3
 5   1      2      1     40     39
 6   1      2      1     40     39
 7   1      1      2      3      4
 8   1      1      2      3      4
 9   1      2      3      4      5
10   1      2      3      4      5
11   1      2      3      4      5
12   1      2      3      4      5
13   1      3      4      5      6
14   1      3      4      5      6
15   1      4      5      6      7
16   1      4      5      6      7
17   1      4      5      6      7
18   1      4      5      6      7
19   1      5      6      7      8
20   1      5      6      7      8
21   1      6      7      8      9
22   1      6      7      8      9
23   1      6      7      8      9
24   1      6      7      8      9
25   1      7      8      9     10
26   1      7      8      9     10
27   1      8      9     10     11
28   1      8      9     10     11
29   1      8      9     10     11
30   1      8      9     10     11
31   1      9     10     11     12
32   1      9     10     11     12
33   1     10     11     12     13
34   1     10     11     12     13
35   1     10     11     12     13
36   1     10     11     12     13
37   1     11     12     13     14
38   1     11     12     13     14
39   1     12     13     14     15
40   1     12     13     14     15
41   1     12     13     14     15
42   1     12     13     14     15
43   1     13     14     15     16
44   1     13     14     15     16
45   1     14     15     16     17
46   1     14     15     16     17
47   1     14     15     16     17
48   1     14     15     16     17
49   1     15     16     17     18
50   1     15     16     17     18
51   1     16     17     18     19
52   1     16     17     18     19
53   1     16     17     18     19
54   1     16     17     18     19
55   1     17     18     19     20
56   1     17     18     19     20
57   1     18     19     20     21
58   1     18     19     20     21
59   1     18     19     20     21
60   1     18     19     20     21
61   1     19     20     21     22
62   1     19     20     21     22
63   1     20     21     22     23
64   1     20     21     22     23
65   1     20     21     22     23
66   1     20     21     22     23
67   1     21     22     23     24
68   1     21     22     23     24
69   1     22     23     24     25
70   1     22     23     24     25
71   1     22     23     24     25
72   1     22     23     24     25
73   1     23     24     25     26
74   1     23     24     25     26
75   1     24     25     26     27
76   1     24     25     26     27
77   1     24     25     26     27
78   1     24     25     26     27
79   1     25     26     27     28
80   1     25     26     27     28
81   1     26     27     28     29
82   1     26     27     28     29
83   1     26     27     28     29
84   1     26     27     28     29
85   1     27     28     29     30
86   1     27     28     29     30
87   1     28     29     30     31
88   1     28     29     30     31
89   1     28     29     30     31
90   1     28     29     30     31
91   1     29     30     31     32
92   1     29     30     31     32
93   1     30     31     32     33
94   1     30     31     32     33
95   1     30     31     32     33
96   1     30     31     32     33
97   1     31     32     33     34
98   1     31     32     33     34
99   1     32     33     34     35

100 1 32 33 34 35
101 1 32 33 34 35
102 1 32 33 34 35
103 1 33 34 35 36
104 1 33 34 35 36
105 1 34 35 36 37
106 1 34 35 36 37
107 1 34 35 36 37
108 1 34 35 36 37
109 1 35 36 37 38
110 1 35 36 37 38
111 1 36 37 38 39
112 1 36 37 38 39
113 1 36 37 38 39
114 1 36 37 38 39
115 1 37 38 39 40
116 1 37 38 39 40
117 1 38 39 40 1
118 1 38 39 40 1
119 1 38 39 40 1
120 1 38 39 40 1

Impropers

 1   1      2      1     40     40 
 2   1      1      2      3      3 
 3   1      2      3      4      2 
 4   1      3      4      5      5 
 5   1      4      5      6      4 
 6   1      5      6      7      7 
 7   1      6      7      8      6 
 8   1      7      8      9      9 
 9   1      8      9     10      8 
10   1      9     10     11     11 
11   1     10     11     12     10 
12   1     11     12     13     13 
13   1     12     13     14     12 
14   1     13     14     15     15 
15   1     14     15     16     14 
16   1     15     16     17     17 
17   1     16     17     18     16 
18   1     17     18     19     19 
19   1     18     19     20     18 
20   1     19     20     21     21 
21   1     20     21     22     20 
22   1     21     22     23     23 
23   1     22     23     24     22 
24   1     23     24     25     25 
25   1     24     25     26     24 
26   1     25     26     27     27 
27   1     26     27     28     26 
28   1     27     28     29     29 
29   1     28     29     30     28 
30   1     29     30     31     31 
31   1     30     31     32     30 
32   1     31     32     33     33 
33   1     32     33     34     32 
34   1     33     34     35     35 
35   1     34     35     36     34 
36   1     35     36     37     37 
37   1     36     37     38     36 
38   1     37     38     39     39 
39   1     38     39     40     38 
40   1      1     40     39      1

I don’t see anything obviously wrong with your data file, but I have remarks :

  • your message is poorly formatted,
  • without the input, nobody can reproduce the error,
  • you seem to be using the 05Nov2018 version of LAMMPS, which is old,
  • the sentence “The error appears only when I try to minimize the system” is difficult to believe, because such error typically occurs when invoking the read_data command, and is not dependent or what your input does after that…

Simon

FYI, the date printed by msi2lmp reflects the last time it was updated, not the LAMMPS version used. msi2lmp has very few updates since nobody is actively developing it for many years.
A change log is in the README file in the tools/msi2lmp folder.

1 Like

I am using the LAMMPS (16 Mar 2018) version for my simulation. As you mentioned, the error flag occurs while reading the input data. I am unsure if the issue is with the format of my system data or if I should try using a different LAMMPS version. Interestingly, when my system consists of more than a single unit cell, I do not face any issues reading the data with the 16 Mar 2018 version.

My input script is

units real
boundary p p p

atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2

read_data CNT_UC_1.data

It probably won’t solve that particular issue, but I would update to a recent version if I were you.

Simon

I tried with lammps (2 Aug 2023) version. The issue is yet to be resolved.
“ERROR on proc 0: Invalid atom ID in Angles section of data file: 3 1 40 1 40 (… atom.cpp:1413)”

From what you copy-pasted, I can’t understand why you would get such an error message. All I can guess is that your data file is badly formatted (maybe there is a wrong number of blank line between some sections or something), but this cannot be detected from a copy-past, particularly because you did not properly format your message.

Simon

It’s not obvious to me how to define the angle spanned by atom 40, atom 1 and atom 40 (again).

LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 / CGCMM for CNT_UC_1

     40 atoms
     60 bonds
    120 angles
    120 dihedrals
     40 impropers

   1 atom types
   1 bond types
   1 angle types
   1 dihedral types
   1 improper types

    -6.320800018    23.679199982 xlo xhi
    -6.320800018    23.679199982 ylo yhi
    -0.617199993     1.852200007 zlo zhi

Masses

   1  12.011150 # cp

Pair Coeffs # lj/class2/coul/long

   1   0.0640000000   4.0100000000 # cp

Bond Coeffs # class2

   1     1.4170   470.8361  -627.6179  1327.6345 # cp-cp

Angle Coeffs # class2

   1   118.9000    61.0226   -34.9931     0.0000 # cp-cp-cp

Dihedral Coeffs # class2

   1     8.3667     0.0000     1.1932     0.0000     0.0000     0.0000# cp-cp-cp-cp

Improper Coeffs # class2

  1     7.1794     0.0000 # cp-cp-cp-cp

BondBond Coeffs

  1    68.2856     1.4170     1.4170 

BondAngle Coeffs

  1    28.8708    28.8708     1.4170     1.4170 

AngleAngle Coeffs

  1     0.0000     0.0000     0.0000   118.9000   118.9000   118.9000 

AngleAngleTorsion Coeffs

  1     0.0000   118.9000   118.9000 

EndBondTorsion Coeffs

1    -0.1185     6.3204     0.0000    -0.1185     6.3204     0.0000     1.4170     1.4170 

MiddleBondTorsion Coeffs

  1    27.5989    -2.3120     0.0000     1.4170 

BondBond13 Coeffs

  1    53.0000     1.4170     1.4170 

AngleTorsion Coeffs

  1     1.9767     1.0239     0.0000     1.9767     1.0239     0.0000   118.9000   118.9000 

Atoms # full

      1      1   1  0.000000    15.318179499     8.250704498     0.000124440   0   0   0 # cp
      2      1   1  0.000000    15.260602409     9.651142501     0.000124603   0   0   0 # cp
      3      1   1  0.000000    15.125632420    10.323216849     1.234874639   0   0   0 # cp
      4      1   1  0.000000    14.638074400    11.637304181     1.234874891   0   0   0 # cp
      5      1   1  0.000000    14.302025147    12.234775398     0.000124939   0   0   0 # cp
      6      1   1  0.000000    13.432281414    13.333902335     0.000125127   0   0   0 # cp
      7      1   1  0.000000    12.928070237    13.798307424     1.234875166   0   0   0 # cp
      8      1   1  0.000000    11.761282434    14.574929150     1.234875320   0   0   0 # cp
      9      1   1  0.000000    11.138249090    14.860814374     0.000125329   0   0   0 # cp
     10      1   1  0.000000     9.788579001    15.238876205     0.000125349   0   0   0 # cp
     11      1   1  0.000000     9.107693852    15.318225224     1.234875360   0   0   0 # cp
     12      1   1  0.000000     7.707255579    15.260647878     1.234875382   0   0   0 # cp
     13      1   1  0.000000     7.035181653    15.125675536     0.000125373   0   0   0 # cp
     14      1   1  0.000000     5.721097266    14.638108972     0.000125356   0   0   0 # cp
     15      1   1  0.000000     5.123628815    14.302054827     1.234875336   0   0   0 # cp
     16      1   1  0.000000     4.024510226    13.432300497     1.234875190   0   0   0 # cp
     17      1   1  0.000000     3.560110217    12.928084660     0.000125179   0   0   0 # cp
     18      1   1  0.000000     2.783500119    11.761289166     0.000125148   0   0   0 # cp
     19      1   1  0.000000     2.497620238    11.138253356     1.234875139   0   0   0 # cp
     20      1   1  0.000000     2.119567205     9.788580952     1.234875136   0   0   0 # cp
     21      1   1  0.000000     2.040220449     9.107695539     0.000125152   0   0   0 # cp
     22      1   1  0.000000     2.097797967     7.707257563     0.000125168   0   0   0 # cp
     23      1   1  0.000000     2.232768013     7.035183225     1.234875166   0   0   0 # cp
     24      1   1  0.000000     2.720326050     5.721095930     1.234875140   0   0   0 # cp
     25      1   1  0.000000     3.056375064     5.123624585     0.000125137   0   0   0 # cp
     26      1   1  0.000000     3.926118267     4.024497226     0.000125180   0   0   0 # cp
     27      1   1  0.000000     4.430329331     3.560092013     1.234875182   0   0   0 # cp
     28      1   1  0.000000     5.597117298     2.783470477     1.234875145   0   0   0 # cp
     29      1   1  0.000000     6.220150757     2.497585475     0.000125121   0   0   0 # cp
     30      1   1  0.000000     7.569820992     2.119524168     0.000125049   0   0   0 # cp
     31      1   1  0.000000     8.250706152     2.040175266     1.234875018   0   0   0 # cp
     32      1   1  0.000000     9.651144417     2.097752470     1.234874900   0   0   0 # cp
     33      1   1  0.000000    10.323218365     2.232724593     0.000124873   0   0   0 # cp
     34      1   1  0.000000    11.637302950     2.720290592     0.000124712   0   0   0 # cp
     35      1   1  0.000000    12.234771438     3.056344678     1.234874669   0   0   0 # cp
     36      1   1  0.000000    13.333889858     3.926099251     1.234874525   0   0   0 # cp
     37      1   1  0.000000    13.798289619     4.430315290     0.000124505   0   0   0 # cp
     38      1   1  0.000000    14.574899310     5.597111010     0.000124424   0   0   0 # cp
     39      1   1  0.000000    14.860779157     6.220146832     1.234874401   0   0   0 # cp
     40      1   1  0.000000    15.238832588     7.569819105     1.234874420   0   0   0 # cp

Bonds

     1   1      1      2
     2   1      1     40
     3   1      1     40
     4   1      2      3
     5   1      2      3
     6   1      3      4
     7   1      4      5
     8   1      4      5
     9   1      5      6
    10   1      6      7
    11   1      6      7
    12   1      7      8
    13   1      8      9
    14   1      8      9
    15   1      9     10
    16   1     10     11
    17   1     10     11
    18   1     11     12
    19   1     12     13
    20   1     12     13
    21   1     13     14
    22   1     14     15
    23   1     14     15
    24   1     15     16
    25   1     16     17
    26   1     16     17
    27   1     17     18
    28   1     18     19
    29   1     18     19
    30   1     19     20
    31   1     20     21
    32   1     20     21
    33   1     21     22
    34   1     22     23
    35   1     22     23
    36   1     23     24
    37   1     24     25
    38   1     24     25
    39   1     25     26
    40   1     26     27
    41   1     26     27
    42   1     27     28
    43   1     28     29
    44   1     28     29
    45   1     29     30
    46   1     30     31
    47   1     30     31
    48   1     31     32
    49   1     32     33
    50   1     32     33
    51   1     33     34
    52   1     34     35
    53   1     34     35
    54   1     35     36
    55   1     36     37
    56   1     36     37
    57   1     37     38
    58   1     38     39
    59   1     38     39
    60   1     39     40

Angles

     1   1      2      1     40
     2   1      2      1     40
     3   1     40      1     40
     4   1      1      2      3
     5   1      1      2      3
     6   1      3      2      3
     7   1      2      3      4
     8   1      2      3      2
     9   1      4      3      2
    10   1      3      4      5
    11   1      3      4      5
    12   1      5      4      5
    13   1      4      5      6
    14   1      4      5      4
    15   1      6      5      4
    16   1      5      6      7
    17   1      5      6      7
    18   1      7      6      7
    19   1      6      7      8
    20   1      6      7      6
    21   1      8      7      6
    22   1      7      8      9
    23   1      7      8      9
    24   1      9      8      9
    25   1      8      9     10
    26   1      8      9      8
    27   1     10      9      8
    28   1      9     10     11
    29   1      9     10     11
    30   1     11     10     11
    31   1     10     11     12
    32   1     10     11     10
    33   1     12     11     10
    34   1     11     12     13
    35   1     11     12     13
    36   1     13     12     13
    37   1     12     13     14
    38   1     12     13     12
    39   1     14     13     12
    40   1     13     14     15
    41   1     13     14     15
    42   1     15     14     15
    43   1     14     15     16
    44   1     14     15     14
    45   1     16     15     14
    46   1     15     16     17
    47   1     15     16     17
    48   1     17     16     17
    49   1     16     17     18
    50   1     16     17     16
    51   1     18     17     16
    52   1     17     18     19
    53   1     17     18     19
    54   1     19     18     19
    55   1     18     19     20
    56   1     18     19     18
    57   1     20     19     18
    58   1     19     20     21
    59   1     19     20     21
    60   1     21     20     21
    61   1     20     21     22
    62   1     20     21     20
    63   1     22     21     20
    64   1     21     22     23
    65   1     21     22     23
    66   1     23     22     23
    67   1     22     23     24
    68   1     22     23     22
    69   1     24     23     22
    70   1     23     24     25
    71   1     23     24     25
    72   1     25     24     25
    73   1     24     25     26
    74   1     24     25     24
    75   1     26     25     24
    76   1     25     26     27
    77   1     25     26     27
    78   1     27     26     27
    79   1     26     27     28
    80   1     26     27     26
    81   1     28     27     26
    82   1     27     28     29
    83   1     27     28     29
    84   1     29     28     29
    85   1     28     29     30
    86   1     28     29     28
    87   1     30     29     28
    88   1     29     30     31
    89   1     29     30     31
    90   1     31     30     31
    91   1     30     31     32
    92   1     30     31     30
    93   1     32     31     30
    94   1     31     32     33
    95   1     31     32     33
    96   1     33     32     33
    97   1     32     33     34
    98   1     32     33     32
    99   1     34     33     32
   100   1     33     34     35
   101   1     33     34     35
   102   1     35     34     35
   103   1     34     35     36
   104   1     34     35     34
   105   1     36     35     34
   106   1     35     36     37
   107   1     35     36     37
   108   1     37     36     37
   109   1     36     37     38
   110   1     36     37     36
   111   1     38     37     36
   112   1     37     38     39
   113   1     37     38     39
   114   1     39     38     39
   115   1     38     39     40
   116   1     38     39     38
   117   1     40     39     38
   118   1      1     40     39
   119   1      1     40      1
   120   1     39     40      1

Dihedrals

     1   1     40      1      2      3
     2   1     40      1      2      3
     3   1     40      1      2      3
     4   1     40      1      2      3
     5   1      2      1     40     39
     6   1      2      1     40     39
     7   1      1      2      3      4
     8   1      1      2      3      4
     9   1      2      3      4      5
    10   1      2      3      4      5
    11   1      2      3      4      5
    12   1      2      3      4      5
    13   1      3      4      5      6
    14   1      3      4      5      6
    15   1      4      5      6      7
    16   1      4      5      6      7
    17   1      4      5      6      7
    18   1      4      5      6      7
    19   1      5      6      7      8
    20   1      5      6      7      8
    21   1      6      7      8      9
    22   1      6      7      8      9
    23   1      6      7      8      9
    24   1      6      7      8      9
    25   1      7      8      9     10
    26   1      7      8      9     10
    27   1      8      9     10     11
    28   1      8      9     10     11
    29   1      8      9     10     11
    30   1      8      9     10     11
    31   1      9     10     11     12
    32   1      9     10     11     12
    33   1     10     11     12     13
    34   1     10     11     12     13
    35   1     10     11     12     13
    36   1     10     11     12     13
    37   1     11     12     13     14
    38   1     11     12     13     14
    39   1     12     13     14     15
    40   1     12     13     14     15
    41   1     12     13     14     15
    42   1     12     13     14     15
    43   1     13     14     15     16
    44   1     13     14     15     16
    45   1     14     15     16     17
    46   1     14     15     16     17
    47   1     14     15     16     17
    48   1     14     15     16     17
    49   1     15     16     17     18
    50   1     15     16     17     18
    51   1     16     17     18     19
    52   1     16     17     18     19
    53   1     16     17     18     19
    54   1     16     17     18     19
    55   1     17     18     19     20
    56   1     17     18     19     20
    57   1     18     19     20     21
    58   1     18     19     20     21
    59   1     18     19     20     21
    60   1     18     19     20     21
    61   1     19     20     21     22
    62   1     19     20     21     22
    63   1     20     21     22     23
    64   1     20     21     22     23
    65   1     20     21     22     23
    66   1     20     21     22     23
    67   1     21     22     23     24
    68   1     21     22     23     24
    69   1     22     23     24     25
    70   1     22     23     24     25
    71   1     22     23     24     25
    72   1     22     23     24     25
    73   1     23     24     25     26
    74   1     23     24     25     26
    75   1     24     25     26     27
    76   1     24     25     26     27
    77   1     24     25     26     27
    78   1     24     25     26     27
    79   1     25     26     27     28
    80   1     25     26     27     28
    81   1     26     27     28     29
    82   1     26     27     28     29
    83   1     26     27     28     29
    84   1     26     27     28     29
    85   1     27     28     29     30
    86   1     27     28     29     30
    87   1     28     29     30     31
    88   1     28     29     30     31
    89   1     28     29     30     31
    90   1     28     29     30     31
    91   1     29     30     31     32
    92   1     29     30     31     32
    93   1     30     31     32     33
    94   1     30     31     32     33
    95   1     30     31     32     33
    96   1     30     31     32     33
    97   1     31     32     33     34
    98   1     31     32     33     34
    99   1     32     33     34     35
   100   1     32     33     34     35
   101   1     32     33     34     35
   102   1     32     33     34     35
   103   1     33     34     35     36
   104   1     33     34     35     36
   105   1     34     35     36     37
   106   1     34     35     36     37
   107   1     34     35     36     37
   108   1     34     35     36     37
   109   1     35     36     37     38
   110   1     35     36     37     38
   111   1     36     37     38     39
   112   1     36     37     38     39
   113   1     36     37     38     39
   114   1     36     37     38     39
   115   1     37     38     39     40
   116   1     37     38     39     40
   117   1     38     39     40      1
   118   1     38     39     40      1
   119   1     38     39     40      1
   120   1     38     39     40      1

Impropers

     1   1      2      1     40     40 
     2   1      1      2      3      3 
     3   1      2      3      4      2 
     4   1      3      4      5      5 
     5   1      4      5      6      4 
     6   1      5      6      7      7 
     7   1      6      7      8      6 
     8   1      7      8      9      9 
     9   1      8      9     10      8 
    10   1      9     10     11     11 
    11   1     10     11     12     10 
    12   1     11     12     13     13 
    13   1     12     13     14     12 
    14   1     13     14     15     15 
    15   1     14     15     16     14 
    16   1     15     16     17     17 
    17   1     16     17     18     16 
    18   1     17     18     19     19 
    19   1     18     19     20     18 
    20   1     19     20     21     21 
    21   1     20     21     22     20 
    22   1     21     22     23     23 
    23   1     22     23     24     22 
    24   1     23     24     25     25 
    25   1     24     25     26     24 
    26   1     25     26     27     27 
    27   1     26     27     28     26 
    28   1     27     28     29     29 
    29   1     28     29     30     28 
    30   1     29     30     31     31 
    31   1     30     31     32     30 
    32   1     31     32     33     33 
    33   1     32     33     34     32 
    34   1     33     34     35     35 
    35   1     34     35     36     34 
    36   1     35     36     37     37 
    37   1     36     37     38     36 
    38   1     37     38     39     39 
    39   1     38     39     40     38 
    40   1      1     40     39      1 

Is there an alternative method to define angles across periodic images? or Is it a limitation of the LAMMPS framework with the PCFF force field when simulating a system with a single unit cell?

If your input geometry is this small, then it is impossible to get any meaningful results from it due to massive finite size effects. Since you are doing classical MD with fast to compute potentials, you should just create a supercell based on multiple unit cells and forget about the rest. Trying to make the simulation work for such a tiny system is not a smart choice.

My objective is to determine the phonon dispersion from harmonic interatomic force constants using the PCFF forcefield. I planned to use the phonolammps package, which requires a unit cell to generate the supercell. Further the generated band structure can be analyzed with phononpy package. Since this method isn’t working, I need to pursue an alternative approach.