fix property/atom and set new floating point vector

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1

Hello,

I am trying to store the initial coordinates before I do some MC moves within a LAMMPS input script. I need to copy several atom coordinates at once for the kind of MC moves I am doing.

I am trying to use the fix property/atom

fix initial all property/atom d_x0 d_y0 d_z0
set atom * d_x0 x
set atom * d_y0 y
set atom * d_z0 z

This gives me the error “ERROR: Expected floating point parameter in input script or data file”

Are x, y and z floating point vectors?

My understanding was the “*” will allow you to set one vector to another?

http://lammps.sandia.gov/doc/set.html

Is it possible to do this?

Thanks

Josh

2

Hello,

I am trying to store the initial coordinates before I do some MC moves
within a LAMMPS input script. I need to copy several atom coordinates at
once for the kind of MC moves I am doing.

I am trying to use the fix property/atom

fix initial all property/atom d_x0 d_y0 d_z0
set atom * d_x0 x
set atom * d_y0 y
set atom * d_z0 z

This gives me the error "ERROR: Expected floating point parameter in input
script or data file"

Are x, y and z floating point vectors?

​only when you define an atom style variable.

anyway, fix property/atom seems like overkill for this. you can probably do
what you want to do simply with

fix pos0 all store/state 0 x y z​

and then access the fix later either directly or through an atom style
variable.

axel.

3

Thanks Axel for the quick reply.

I guess I am still struggling with the syntax.

I tried

fix pos0 all store/state 0 x y z
variable pos0x vector f_pos0[1]
variable pos0y vector f_pos0[2]
variable pos0z vector f_pos0[3]

set atom * x v_pos0x
set atom * x v_pos0y
set atom * x v_pos0z

This gives me “ERROR: Variable for set command is invalid style” for the “set atom * x v_pos0x” command.

When trying to just dump the first part I get a segmentation fault with

dump testdump all custom 1 dump.test f_pos0[1] f_pos0[2] f_pos0[3]

Thanks.

Josh

4

Thanks Axel for the quick reply.

I guess I am still struggling with the syntax.

I tried

fix pos0 all store/state 0 x y z
variable pos0x vector f_pos0[1]
variable pos0y vector f_pos0[2]
variable pos0z vector f_pos0[3]

​vector != atom​

set atom * x v_pos0x
set atom * x v_pos0y
set atom * x v_pos0z

This gives me "ERROR: Variable for set command is invalid style" for the
"set atom * x v_pos0x" command.

When trying to just dump the first part I get a segmentation fault with

dump testdump all custom 1 dump.test f_pos0[1] f_pos0[2] f_pos0[3]

​i have no problem at all with this modified version of the melt example:

units lj
atom_style atomic

lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0

velocity all create 3.0 87287

pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5

neighbor 0.3 bin
neigh_modify every 20 delay 0 check no

fix 1 all nve
fix 2 all store/state 0 x y z

variable x0 atom f_2[1]
variable y0 atom f_2[2]
variable z0 atom f_2[3]

dump id all custom 50 dump.melt f_2[*]

thermo 50
run 250

# restore positions and velocities and redo the same run
set atom * x v_x0
set atom * y v_y0
set atom * z v_z0
velocity all create 3.0 87287

run 250
​

5

Thanks Axel,

That works.

I didn’t see the “atom” style for the variable and was confusing it with vector. Your first message makes sense now to me.

Thanks again.

Josh