Invalid bond type in Bonds section of molecule file

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1

Dear lammps users,

I am trying to import a molecule template in lammps (lammps-12dec2018) using molecule command.

Atom_style is set on “molecular”, bond, angle and dihedral style on “harmonic”.

My molecule file follow this format (described in ) :

Title line # skipped line

200 atoms
199 bonds
296 angles
196 dihedrals
0 impropers

Coords # atom_style is molecular

1 0.0 0.0 0.0
2 0.0 0.3 0.0
3 0.3 0.0 0.0

[skipped]

Types

1 1
2 2
3 1

[skipped diameters and masses section]

Bonds

1 1 1 2
2 1 3 4
3 1 5 6

[skipped]

Angles

1 1 1 3 5
2 1 3 5 7
3 1 5 7 9

[skipped]

Dihedrals

1 1 1 3 5 7
2 1 3 5 7 9
3 1 5 7 9 11

[skipped till EOF]

Lammps gives me this error message when I run my input script : Invalid bond type in Bonds section of molecule file (…/molecule.cpp:781)

When I remove Bonds section, I got an error message with Angles section and when Bonds, Angles and Dihedrals sections are removed, I got a message about the Types section, similar from the one cited above. Did I forget something before calling molecule command ? Regions and box are defined before I try to import my molecule. Same for units, boundary conditions and dimensions.

Thank you

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2

Molecule templates do not define bond types (or angle types, etc.). Each type must first be defined via a read_data or bond_coeff command, before it is referenced by a molecule command

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3

The number of available atom, bond and other types is locked in when the simulation box is created (either explicitly or implicitly). The corresponding commands have extra/xxx/types options to reserve additional entries.

When using a molecule file you have to make certain that you are not exceeding any limits. Please use the info command for displaying current settings.

Axel

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1 Like
4

Thank you for your reply.

I used info system command, that gives me :

[skipped]

Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Wed Feb 20 09:21:06 2019

System information:
Units = nano
Atom style = molecular
Atom map = (null)
Molecule type = standard
Atoms = 0, types = 1, style = none
Bonds = 0, types = 0, style = harmonic
Angles = 0, types = 0, style = harmonic
Dihedrals = 0, types = 0, style = multi/harmonic
Impropers = 0, types = 0, style = none
Special bond factors lj = 0 0 0
Special bond factors coul = 0 0 0
Kspace style = none

Dimensions = 3
Orthogonal box = 81.3 x 105.6 x 198
Boundaries = p,p p,p f,f
xlo, xhi = 0, 81.3
ylo, yhi = 0, 105.6
zlo, zhi = 0, 198

Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info

[skipped]

My molecule coordinates fit in the box.

Only one atom type does exist (I don’t understand which command created it … I used only units, boundary atom_style, bond_style, angle_style, dihedral_style, dimension, newton, variable, region, create_box commands before info command). Indeed there is no bond, angle and dihedral types. So I sought for create_bonds () or similar command but this one is creating bonds between two groups of atoms, which does not exist yet in my case.

So how can I create all missing atom, bond, angle and dihedral types before importing my molecule ?

Thank you

Charlotte

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5

Ok, sorry for the last message I sent it a bit too fast. I used bond/types, angle/types and dihedral/types keywords after create_box command, it seems to work now. I’ve understand that the create_box command also create a number of atom types that will be used in simulation box, I’ve change it.

Thank you

Charlotte

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