Can I add atoms of a new atom type after a read_restart?

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1

Hi,

I have crosslinked a polymer network in one simulation, then I want to add charges to the system and add in counterions in another simulation, but keeping the network geometry the same. Is this possible? I have tried looking at create_atoms, but I want to add atoms of type 4 which didn’t exist in the previous simulation.

Any ideas?

Yours

Sam

2

Hi,

I have crosslinked a polymer network in one simulation, then I want to add
charges to the system and add in counterions in another simulation, but
keeping the network geometry the same. Is this possible? I have tried
looking at create_atoms, but I want to add atoms of type 4 which didn't
exist in the previous simulation.

Any ideas?

no you can't do it as such.

but you can convert the restart to a data file, then increase
the number of atom types and take it from there.

the maximal number of atom types has to be defined at the
time when the box is created and cannot be changed later.

axel.

3

Okay. Thanks for that.

I have done that, but I had to add an extra line under Masses and Pair Coeffs but I still get an

ERROR: Incorrect atom format in data file (atom.cpp:533)

What am I doing wrong?

Sam

4

Okay. Thanks for that.

I have done that, but I had to add an extra line under Masses and Pair
Coeffs but I still get an

that is why i don't use those sections in the first place.

ERROR: Incorrect atom format in data file (atom.cpp:533)

What am I doing wrong?

no idea. probably some missing line or misformatted line.

impossible to tell without an example.
the data file format is not self-descriptive,
so it is difficult to assign errors in parsing.

axel.