\(\renewcommand{\AA}{\text{Å}}\)

fix graphics/replica command

Syntax

fix ID group-ID graphics/replica Nevery type keyword args ...

  • ID, group-ID are documented in fix command

  • graphics/replica = style name of this fix command

  • Nevery = update graphics information every this many time steps

  • keyword = display or average

    display radius = radius for the atoms or -1 to use the radius dump image uses for the atom type
average radius = radius for the atoms or 0 to set the radius to that of the largest distance from the center

Examples

fix sf1 water graphics/replica 200 display 1.0 average 0

Description

Added in version TBD.

This fix allows to add spheres to images rendered with dump image using the fix keyword to represent atoms from all replicas of a multi-replica simulation.

The group-ID sets the group ID of the atoms selected to be represented. This may be a dynamic group.

The Nevery keyword determines how often the replica graphics data is updated. This should be the same value as the corresponding N parameter of the dump image command. LAMMPS will stop with an error message if the settings for this fix and the dump command are not compatible.

There are two keywords available that determine what is shown: display and average. With display all atoms in the fix group from all replica will be displayed. With average only the average position of the atoms with the same atom-ID across all replica will be shown.

The radius quantity determines the radius of the atoms. A value > 0 sets an explicit radius; a value < 0 will use the same radius used by dump image for local atoms of the same atom type. For the keyword average, a radius sets the atom radius to the largest distance of an atom to the average position across all replica.

Dump image info

Added in version TBD.

Fix graphics/replica is designed to be used with the fix keyword of dump image. The fix will add spheres based on the atoms in the fix group across all replica to dump image so that they are included in the rendered image.

The fflag1 setting of dump image fix are currently ignored.

and fflag2 setting of dump image fix is used as an adjustment to the radius of the rendered sphere. This can be used to grow or shrink the radius that is selected by dump image for the atom type.

Usage example

The following lines can be added to the peptide example input to run it in multi-partition mode with diverging trajectories and then visualize the atom positions from the different replica or the spread.

# reinitialize velocities differently on each partition
variable part uloop 16
velocity all create 275.0 $(12315235*v_part)

fix  sf1  peptide   graphics/replica 100 display 0.5
fix  sf2  peptide   graphics/replica 100 average 1.0

# must use dump image only on one partition
partition yes 1 dump viz peptide image 100 myimage-*.png element type size 600 600 zoom 1.77156 shiny 0.2  &
                 ssao yes 23184 0.4  fsaa yes bond atom type view 70 20 box no 0.0 axes yes 0.5 0.05 &
                 fix sf2 const 0 0 &
                 fix sf1 element 0 0 &

partition yes 1 dump_modify viz pad 6 backcolor black backcolor2 white &
             element C C O H N C C C O H H S O H &
             adiam 1*2 0.85 adiam 3 0.76 adiam 4 0.6 adiam 5 0.775 adiam 6*7 0.85 adiam 8 0.85 &
             adiam 9 0.76 adiam 10*11 0.6 adiam 12 0.9 adiam 13 0.76 adiam 14 0.6 &
             ftrans sf2 0.5 fcolor sf2 green

replica1 replica2

The following commands can be added to the neb.hop1 example to show the initial (left image below) and final (right image below) state of the minimized transition path between adjacent energy minima. Each yellow sphere represents the same atom in different replicas.

fix  sf1  nebatoms  graphics/replica 10 display 0.8
partition yes 1 dump viz all image 10 myimage-*.png type type size 600 600 zoom 1.5 &
                  shiny 0.2 fsaa yes box no 0.0 axes yes 0.5 0.05 fix sf1 const 0 0
partition yes 1 dump_modify viz pad 6 backcolor black backcolor2 white fcolor sf1 yellow

neb1 neb2

Restart, fix_modify, output, run start/stop, minimize info

No information about this fix is written to binary restart files.

None of the fix_modify options apply to this fix.

This fix is invoked during an energy minimization when using the minimize command and other commands the invoke minimizations like neb.

Restrictions

This fix is part of the GRAPHICS package. It is only only enabled if LAMMPS was built with that package. See the Build package page for more info.

Default

none