make wall

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#1

Hi,

When I’m trying to make a wall with stripes, I find there are holes in the wall. i think the problem is about Y axis: 0.01 1 in stripe 1 and 1.01 1 in stripe2. And I also try to make different types of atoms the those stripes, as below. So my question is: how can I eliminate those holes in the wall?

region stripe1 block 0 30 0.01 1 6 6.5 units lattice
region stripe2 block 0 30 1.01 2 6 6.5 units lattice
region stripe3 block 0 30 2.01 3 6 6.5 units lattice
region stripe4 block 0 30 3.01 4 6 6.5 units lattice
region stripe5 block 0 30 4.01 5 6 6.5 units lattice
region stripe6 block 0 30 5.01 6 6 6.5 units lattice
region stripe7 block 0 30 6.01 7 6 6.5 units lattice
region stripe8 block 0 30 7.01 8 6 6.5 units lattice
region stripe9 block 0 30 8.01 9 6 6.5 units lattice
region stripe10 block 0 30 9.01 10 6 6.5 units lattice
region stripe11 block 0 30 10.01 11 6 6.5 units lattice
region stripe12 block 0 30 11.01 12 6 6.5 units lattice
region stripe13 block 0 30 12.01 13 6 6.5 units lattice
region stripe14 block 0 30 13.01 14 6 6.5 units lattice
region stripe15 block 0 30 14.01 15 6 6.5 units lattice
region stripe16 block 0 30 15.01 16 6 6.5 units lattice
region stripe17 block 0 30 16.01 17 6 6.5 units lattice
region stripe18 block 0 30 17.01 18 6 6.5 units lattice
region stripe19 block 0 30 18.01 19 6 6.5 units lattice
region stripe20 block 0 30 19.01 20 6 6.5 units lattice
region stripe21 block 0 30 20.01 21 6 6.5 units lattice
region stripe22 block 0 30 21.01 22 6 6.5 units lattice
region stripe23 block 0 30 22.01 23 6 6.5 units lattice
region stripe24 block 0 30 23.01 24 6 6.5 units lattice
region stripe25 block 0 30 24.01 25 6 6.5 units lattice
region stripe26 block 0 30 25.01 26 6 6.5 units lattice
region stripe27 block 0 30 26.01 27 6 6.5 units lattice
region stripe28 block 0 30 27.01 28 6 6.5 units lattice
region stripe29 block 0 30 28.01 29 6 6.5 units lattice
region stripe30 block 0 30 29.01 30 6 6.5 units lattice
region stripe31 block 0 30 30.01 31 6 6.5 units lattice
region stripe32 block 0 30 31.01 32 6 6.5 units lattice
region stripe33 block 0 30 32.01 33 6 6.5 units lattice
region stripe34 block 0 30 33.01 34 6 6.5 units lattice
region stripe35 block 0 30 34.01 35 6 6.5 units lattice
region stripe36 block 0 30 35.01 36 6 6.5 units lattice
region stripe37 block 0 30 36.01 37 6 6.5 units lattice
region stripe38 block 0 30 37.01 38 6 6.5 units lattice
region stripe39 block 0 30 38.01 39 6 6.5 units lattice
region stripe40 block 0 30 39.01 40 6 6.5 units lattice
region stripe41 block 0 30 40.01 41 6 6.5 units lattice
region stripe42 block 0 30 41.01 42 6 6.5 units lattice
region stripe43 block 0 30 42.01 43 6 6.5 units lattice
region stripe44 block 0 30 43.01 44 6 6.5 units lattice
region stripe45 block 0 30 44.01 45 6 6.5 units lattice
region stripe46 block 0 30 45.01 46 6 6.5 units lattice
region stripe47 block 0 30 46.01 47 6 6.5 units lattice
region stripe48 block 0 30 47.01 48 6 6.5 units lattice
region stripe49 block 0 30 48.01 49 6 6.5 units lattice
region stripe50 block 0 30 49.01 50 6 6.5 units lattice

create_atoms 2 region stripe1
create_atoms 2 region stripe3
create_atoms 2 region stripe5
create_atoms 2 region stripe7
create_atoms 2 region stripe9
create_atoms 2 region stripe11
create_atoms 2 region stripe13
create_atoms 2 region stripe15
create_atoms 2 region stripe17
create_atoms 2 region stripe19
create_atoms 2 region stripe21
create_atoms 2 region stripe23
create_atoms 2 region stripe25
create_atoms 2 region stripe27
create_atoms 2 region stripe29
create_atoms 2 region stripe31
create_atoms 2 region stripe33
create_atoms 2 region stripe35
create_atoms 2 region stripe37
create_atoms 2 region stripe39
create_atoms 2 region stripe41
create_atoms 2 region stripe43
create_atoms 2 region stripe45
create_atoms 2 region stripe47
create_atoms 2 region stripe49
create_atoms 3 region stripe2
create_atoms 3 region stripe4
create_atoms 3 region stripe6
create_atoms 3 region stripe8
create_atoms 3 region stripe10
create_atoms 3 region stripe12
create_atoms 3 region stripe14
create_atoms 3 region stripe16
create_atoms 3 region stripe18
create_atoms 3 region stripe20
create_atoms 3 region stripe22
create_atoms 3 region stripe24
create_atoms 3 region stripe26
create_atoms 3 region stripe28
create_atoms 3 region stripe30
create_atoms 3 region stripe32
create_atoms 3 region stripe34
create_atoms 3 region stripe36
create_atoms 3 region stripe38
create_atoms 3 region stripe40
create_atoms 3 region stripe42
create_atoms 3 region stripe44
create_atoms 3 region stripe46
create_atoms 3 region stripe48
create_atoms 3 region stripe50

Best,
Chao

#2

Hi,

When I’m trying to make a wall with stripes, I find there are holes in the wall. i think the problem is about Y axis: 0.01 1 in stripe 1 and 1.01 1 in stripe2. And I also try to make different types of atoms the those stripes, as below. So my question is: how can I eliminate those holes in the wall?

image.png

#3

Hi,

When I'm trying to make a wall with stripes, I find there are holes in the
wall. i think the problem is about Y axis: 0.01 1 in stripe 1 and 1.01 1 in
stripe2. And I also try to make different types of atoms the those stripes,
as below. So my question is: how can I eliminate those holes in the wall?

define your regions so that they boundaries are
not exactly on any lattice point. if that happens,
then it is rather random, whether an atom is created
or not.

axel.

#4

@Chao,

May I Ask , the name of the visualiser program you are using to plot
the atoms ?

Thanks
Oscar G.

#5

@Chao,

May I Ask , the name of the visualiser program you are using to plot
the atoms ?

that has to be VMD. the three RGB colored arrows and the colors
of the atoms are a bit of a giveaway...

axel.

#6

I also tried “side out” in region command… and yes, there are no more holes but the E_pair is “inf”…So you said random, doea it mean there is no way out?

Step Temp E_pair E_mol TotEng Press
0 0 inf 0.5215306 inf nan
100 0.0023233581 inf 0.52120912 inf nan
200 0.0068223197 inf 0.5214045 inf nan
300 0.008407933 inf 0.52235954 inf nan
400 0.011545429 inf 0.52240857 inf nan
500 0.013517933 inf 0.52294769 inf nan
600 0.015880008 inf 0.52368303 inf nan
700 0.016442423 inf 0.52428146 inf nan
800 0.017763612 inf 0.52544998 inf nan
900 0.019153817 inf 0.52542355 inf nan
1000 0.01964162 inf 0.52547099 inf nan
1100 0.021621155 inf 0.52468586 inf nan
1200 0.02267136 inf 0.524683 inf nan
1300 0.020447654 inf 0.52519265 inf nan

#7

I also tried “side out” in region command… and yes, there are no more
holes but the E_pair is “inf”…So you said random, doea it mean there is
no way out?

random means that it is due to rounding.

that means that you have overlaps. just slightly shift the boundaries.
they don’t have to exactly match the lattice points.

let me try a little 1-d example (you need to look at
this in HTML mode or with a fixed width font to get it).

it looks like you set up your lattice like this:

and your regions like this:

however, if you define your lattice and regions like this:

there should be no more problem.
you have to watch for this in all 3 dimensions.

Step Temp E_pair E_mol TotEng Press
0 0 inf 0.5215306 inf nan

this has overlapping atoms. that is just as bad.

axel.

#8

@Oscar, I recognize it to be the highly-useful package called "VMD"
which stands for Visual Molecular Dynamics found at
http://www.ks.uiuc.edu/Research/vmd/

#9

@Axel Belive or not, I have never used VMD in my life.....

Right now i'm looking for a heavy atom plotter . I'm using atomeye to
visualise my data results, but im tempted to try VMD. Does someones
knows if i can visualise centrosymmetry parameter , CNA , and other
lammps Computes in VMD ? .

Thank you
Oscar G.

#10

@Axel Belive or not, I have never used VMD in my life.....

Right now i'm looking for a heavy atom plotter . I'm using atomeye to
visualise my data results, but im tempted to try VMD. Does someones

particularly when offloading the creation of images
to the embedded Tachyon raytracer in combination
with the ambient occlusion feature, one can do some
visually appealing pictures (it takes some creativity
in using VMD, too)
http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/

i have some examples of images and animations,
that i've worked on in the past posted here:

http://sites.google.com/site/akohlmey/images-and-movies

knows if i can visualise centrosymmetry parameter , CNA , and other
lammps Computes in VMD ? .

yes, but it is currently not very convenient.
also one have to keep in mind that VMD was
originally conceived for biomolecular simulations,
so there are some heuristics that won't work so
well for LAMMPS. the biggest problem is for
systems that don't have a constant number of atoms.
making VMD more applicable to non-bio problems
(e.g. quantum chemistry, or coarse grain modeling)
is on the TODO list, but since one major constraint
is to not impact the good performance for currently
well supported and more common applications,
progress is slow.

nevertheless, check out the bottom of this page
for some hints for tweaking how to read dump files.

http://sites.google.com/site/akohlmey/software/lammps-icms

you can then work around the issues with some Tcl scripting.
i've been recently making some tests with visualizing the
compute cna output (defined as compute 1). i start VMD with:

env LAMMPSREMAPFIELDS=vx=c_1 vmd-test eam_cna.lammpstrj

this stores the cna output in the x velocity per-atom data field.
the following little piece of Tcl script code will copy it to the
"user" field.

set sel [atomselect top all]
set nf [molinfo top get numframes]
for {set i 0} {$i < $nf} {incr i} {
   $sel frame $s
   $sel set user [$sel get vx]
}

and now you can color atoms by CNA
value or use atom selections of
user != 5 to only show those atoms
with a recognized coordination environment
and so on.

with this strategy you can read in up to
3 properties at a time and used them
either through vx, vy, vz or "velocity"
properties inside VMD or copy them
as shown to one of the 4 user fields.

axel.