hello world
i obtain this code; ERROR on proc 0: Invalid Bonds section in molecule file (src/molecule.cpp:900)
when i use this file
WO3 molecule
4 atoms
6 bonds
4 angles
Coords
1 0.0 0.0 0.0 # Tungstène (W) at origin
2 1.0 0.0 0.0 # Oxygène (O) at x = 1.0
3 0.5 0.5 0.0 # Oxygène (O) at center of face
4 0.5 0.5 0.5 # Oxygène (O) at center of cube
Types
1 1 # Tungstène (W)
2 2 # Oxygène (O)
3 2
4 2
Bonds
1 1 1 2 # Bond between W and O1
2 1 1 3 # Bond between W and O2
3 1 1 4 # Bond between W and O3
4 2 2 3 # Bond between O1 and O2
5 2 2 4 # Bond between O1 and O3
6 2 3 4 # Bond between O2 and O3
Angles
1 1 2 3 # Angle between W-O1-O2
2 1 2 4 # Angle between W-O1-O3
3 2 3 4 # Angle between O1-O2-O3
4 1 2 3 # Angle between W-O3-O2
Special Bond Counts
1 3 3 0
2 3 2 0
3 2 2 0
4 2 1 0
Special Bonds
1 2 1
2 3 1
3 4 2
4 1 2
some one can help me to realise deposit WO3 on substract using lammps code?
There is lots of important information missing here:
- what is your LAMMPS version?
- what is your input file?
- what is the potential or force field you want to use for modeling WO3?
- what is your substrate?
What do you want to learn from this simulation?
Hello…I’m glad to read you…
I use the lammp 2020 version installed on windows 10
I would like to study the growth of WO3 on different substrates ( Ag, K, w…)…
Lennar Jones potential or MEAM potential,
As input file, I use a program ‘‘deposit.molecule’’…found in the lammp programs database…
That is four(!) years old, you should upgrade.
That is not a topic for a beginner. You should start with simulations of something simpler. You need to discuss with your adviser how to obtain the proper training. You (obviously) lacking a lot.
Neither of these have bonds, so you should not define bonds in your molecule file.
Otherwise you would also have to put bonded interactions into your input file. Most likely, the error message you see is because your input has an atom style (e.g. atomic) that does not support bonds.
There is no such file in the current LAMMPS distribution. So I cannot really say anything specific about what you are doing.
Please note that your posts contain many spelling errors. That is not a good sign. To be able to communicate well, you need to be precise in your descriptions.