Unknown identifier in data file:

LAMMPS LAMMPS Beginners
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1

Good day,

I am trying to create a lammps input file for an octadene molecule using Avogadro software. how ever the lammps gives me an error when running it and says " Unknown identifier in data file. I am not sure where the problem is. Can someone assist me please? Kindly find the structure of my datafile below.

56

C 0.77180 -0.01970 0.00000
C -0.77180 0.01970 0.00000
C 1.32150 -1.46250 0.00000
C -1.32150 1.46250 -0.00000
C 2.86550 -1.50670 -0.00000
C -2.86550 1.50670 -0.00000
C 3.41540 -2.95090 0.00000
C -3.41540 2.95090 0.00000
C 4.96040 -2.99630 0.00000
C -4.96040 2.99630 0.00000
C 5.52250 -4.43690 -0.00000
C -5.52250 4.43690 -0.00000
C 7.06960 -4.47600 -0.00000
C -7.06960 4.47600 0.00000
C 7.64870 -5.91130 0.00000
C -7.64870 5.91130 0.00000
C 9.19080 -5.94750 0.00000
C -9.19080 5.94750 -0.00000
H 1.14340 0.50530 0.88480
H 1.14340 0.50530 -0.88480
H -1.14340 -0.50530 -0.88480
H -1.14340 -0.50530 0.88480
H 0.94870 -1.98690 0.88520
H 0.94870 -1.98690 -0.88520
H -0.94870 1.98690 -0.88520
H -0.94870 1.98690 0.88520
H 3.23650 -0.98080 -0.88480
H 3.23650 -0.98080 0.88480
H -3.23650 0.98080 -0.88480
H -3.23650 0.98080 0.88480
H 3.04150 -3.47420 -0.88450
H 3.04150 -3.47420 0.88450
H -3.04150 3.47420 0.88450
H -3.04150 3.47420 -0.88450
H 5.32910 -2.46820 -0.88440
H 5.32910 -2.46820 0.88440
H -5.32910 2.46820 0.88440
H -5.32910 2.46820 -0.88440
H 5.15110 -4.96230 -0.88430
H 5.15110 -4.96230 0.88430
H -5.15110 4.96230 -0.88430
H -5.15110 4.96230 0.88430
H 7.43610 -3.94700 -0.88470
H 7.43610 -3.94700 0.88470
H -7.43610 3.94700 -0.88470
H -7.43610 3.94700 0.88470
H 7.28930 -6.44510 -0.88380
H 7.28930 -6.44510 0.88380
H -7.28930 6.44510 0.88380
H -7.28930 6.44510 -0.88380
H 9.53900 -6.98090 -0.00000
H 9.58580 -5.45000 0.88780
H 9.58580 -5.45000 -0.88780
H -9.53900 6.98090 0.00000
H -9.58580 5.45000 -0.88780
H -9.58580 5.45000 0.88780

2

Quickest thing to do is to look at the LAMMPS’s example data files (such as https://github.com/lammps/lammps/tree/develop/examples/peptide ) and compare notes with yours. Then ask if you have further, more focused questions.

3

Thank you so much for your quick response, will have a look and come back if i have more focused questions as suggested thanks :slight_smile:

4

You are providing an .xyz format file, where a “LAMMPS data” file is required.
File formats matter and the read_data command does not know what to do with your file.
Moreover, a data file contains far more information than your .xyz file contains. To set up a simulation, it is not only required to know the positions of atoms, but also force field atom types (not elements!), connectivity information and the corresponding types and optionally the force field parameters need to be provided.

Classical MD does not work by just sticking a molecule into a simulation program and tell it to simulate it. There are many more steps needed, and they usually have to be done by the user.

I suggest you have a closer look at your text book describing classical MD and force fields for classical MD and think over what you have been doing and then discuss it with your adviser or tutor.

5

Thank you.

Nomsa.