[lammps-users] Accessing astore through an input script

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1

Hello,
My group has written code in the past for calculating coupling constant based on two initial structures. We begin by finding our atomic structures in a different script and then saving the atom positions inside the Fix-> astore variable, using this method to set up the astore variable
char *newarg = new char[6];
newarg[0] = (char *) “TLS1”;
newarg[1] = (char *) “all”;
newarg[2] = (char *) “STORE”;
newarg[3] = (char *) “peratom”;
newarg[4] = (char *) “0”;
newarg[5] = (char *) “3”;

//Adds the Fix, and stores the pos1 array in the astore variable of the StoreFix command.
modify->add_fix(6,newarg);
int iTLS1 = modify->find_fix((char *) “TLS1”);
FixStore *TLS1 = (FixStore *) modify->fix[iTLS1];
lAtoms = TLS1->astore;

And then we copy values from atom->x into TLS1->astore.

When we want to calculate our coupling constant, we copy the atom positions back from TLS1->astore into atom->x. We do the same thing with our second structure as well.

I was wondering if it is possible to input values into astore through an input file, like in my attempt below

read_dump TLS.pos 0 x y z
fix TLS1 all all STORE peratom 0 3
run 0
fix TLSLat1 all STORELAT
read_dump TLS.pos 1 x y z
fix TLS2 all STORE peratom 0 3
fix TLSlat2 all STORELAT
run 0
couple_elastic 0.005 linear relax

This method does only seems initialize TLS1-> astore and TLS2-> astore, but not load any data into TLS1->astore and TLS2->astore. This makes sense to me given that it was written in a different forum post, https://lammps.sandia.gov/threads/msg83755.html, that it us up to the user to fill in astore. So, must I write a new script to do this, or is there is a method where I can use an input file?
Thank you

Thanks

2

You cannot expect an “internal” command to work from the LAMMPS command line and have its data accessible.
You can use fix store/state instead. https://docs.lammps.org/fix_store_state.html

axel.

3

I tried the fix store/state command, but it does not update the astore and I get a segmentation error.

what do you mean by that? remember that I cannot see from here what you have been doing. most likely it was not correct.

let me be a bit more specific (i expected that you would infer this from checking out the source code of fix store/state).

a) you define the store/state fix after reading the coordinates (and possible a run 0) and it should have the updated coordinates. you should be able to verify it with a write_dump command where you write out the current coordinates and what fix store/state has stored.
b) you have to access the contents of the fix store/state using the “normal” means to retrieve a per-atom property from a fix defined in an input.

  • pass the fix id as argument to the command/code trying to read it.
  • then look up the index of the fix instance in the array of fixes in Modify with modify->find_fix(ID)
  • get the pointer to the fix from the modify->fix array
  • check that this is the correct fix style and the data is present and has the desired dimensions
  • then you should be able to access the stored data from fix->array_atom

unlike the internal STORE fix, the fix store state data can be accessed from any LAMMPS command that allows access to per-atom data from fixes through f_ID references.

axel.

4

I tried the fix store/state command, but it does not update the astore and I get a segmentation error.

5

Okay, in that case our method of getting our structural data for calculating the coupling constant is not ideal?
I.E. we are copying atom positions over into fix->astore as opposed to using a premade fix?

6

it all depends on what you want to achieve. fix store/state has an interface to and can be controlled by LAMMPS scripting, fix STORE not.

there is no way to have script command access to internal data from C++ classes unless there is an interface. so the STORE fix data can only be accessed from C++ code.

axel.

7

Okay,
Thank you very much for the help