water on graphene-coated copper

Dear Steve,

Dear All,

have you ever heard of people using minimization to remove excess
initial potential energy and running an equilibration before
accumulating results? i looks like you need to spend some more
"quality time" with an MD text book.

axel.

Thank you sir for the comment. I did incorporate the minimization along with a higher temp for velocity and seems like it is working and pretty stable…no errors, no warnings, no dangerous builds…

However when I wanted to used AtomEye to visualize it, it does not open (well actually a window quickly opens and closes…). I am ssh’ing to a remote server for MD simulations (I do ssh -Y … which takes care of visualization on a remote system). Would anyone know what is missing? I mean I have used XCrysDen to visualize DFT file and that worked pretty nicely. For LAMMPS I do need to use AtomEye since that is the only one available on the remote server!!

Regards,

Karim

Thank you sir for the comment. I did incorporate the minimization along with
a higher temp for velocity and seems like it is working and pretty
stable...no errors, no warnings, no dangerous builds...
However when I wanted to used AtomEye to visualize it, it does not open
(well actually a window quickly opens and closes...). I am ssh'ing to a
remote server for MD simulations (I do ssh -Y ... which takes care of
visualization on a remote system). Would anyone know what is missing? I mean

doing visualization on a remote machine via ssh is almost always
cumbersome. either transfer the data or use VNC.

I have used XCrysDen to visualize DFT file and that worked pretty nicely.
For LAMMPS I do need to use AtomEye since that is the only one available on
the remote server!!

again, just transfer the data and you can use whatever viz tool you prefer.

axel.

Excuse my confusion, what do you mean by transferring? If the files and scripts, I already have them on remote server…

Please advise.

Karim

Excuse my confusion, what do you mean by transferring? If the files and
scripts, I already have them on remote server...

excuse my rudeness, but i don't care. this is *not* a mailing list
devoted to teach people basic principles of visualizing simulation
data and the fact that you can also bring the data to the viz tool
instead of running whatever viz tool is available where the data is.
it most certainly is not a place for spoon feeding people.

please stick to questions about LAMMPS

thanks,
    axel.

Karim,

by "transferring" Dr. Kohlmeyer meant that you should copy your cfg files from the remote server to your local pc and make visualisation on it.

Oleg

11.12.2013, 11:12, "Behzad Jazizadeh" <[email protected]>:

Thank you Oleg,
Ok, it is clear now. However my own machine runs Windows…I use Virtual Box and XUbuntu to remotely access the server! So, I guess there is no other way unless I start using VNC, as Dr. Axel was suggesting…which then means I need to switch from Oracle Virtual Box to VNC…

Karim

Thank you Oleg,
Ok, it is clear now. However my own machine runs Windows...

so what? there are viz programs for windows, too. probably more than for linux.

I use Virtual Box
and XUbuntu to remotely access the server! So, I guess there is no other way

there are several X11 server software packages for windows.

unless I start using VNC, as Dr. Axel was suggesting...which then means I
need to switch from Oracle Virtual Box to VNC...

now this is *complete* nonsense. the way using VNC for remote
visualization works is to launch the VNC server on the remote side and
then use a viewer from remote (optionally with ssh tunnel). the viewer
you could run from your smartphone, if you feel like it.

axel

Thank you sir for the comment. I did incorporate the minimization along with
a higher temp for velocity and seems like it is working and pretty
stable...no errors, no warnings, no dangerous builds...
However when I wanted to used AtomEye to visualize it, it does not open
(well actually a window quickly opens and closes...). I am ssh'ing to a

Most of the time when AtomEye quickly opens and closes it indicates
that, excluding machine problems, you have an incorrect structure so
that coordination number is greater than 24.

Dear Ray, Thank you…
Could you be more specific? I am only using water model, the same as all (SPCE) models…what else is different? I am trying to see what is around each atom, used compute coord/atom as:

compute 1 all coord/atom 10.0 1*2

the system is still showing nothing, in the output and no visual…

I am justing pointing out that AtomEye terminates with an error if the
coordination number around any atom based on AtomEye's pre-defined
bond length cutoff exceeds 24, so it is a good idea to double check
your structure.

Please see this link
http://lammps.sandia.gov/doc/Section_howto.html#howto_15 for options
to output info from compute coord/atom.

Ray

Hello again,

For the water on graphene system I have merged the two data files into one (ice.dat + graphene.dat). I reformatted my graphene data file to start from the end of the water atom ids but since my second column on water model specifies molecule number, and for graphene there are no molecules, i just have a different set of values after my water atoms are read…

.
.
.
956 319 1 0.42379999 35.938000 42.413139 3.8468986
957 319 1 0.42379999 35.938000 41.538593 5.0829678
958 320 2 -0.84759998 35.938000 41.497326 11.462218
959 320 1 0.42379999 35.938000 42.413139 11.182723
960 320 1 0.42379999 35.938000 41.538593 12.418793

#graphene data begins from here:

961 3 0 0 0
962 3 1.42 0 0
963 3 2.13 1.22972 0
964 3 3.55 1.22972 0
.
.
.

You can not have different atom styles in a same data file. Merging
data files is not a bad idea, but just make water "atomic" or graphene
"full".

Ray

Dear Ray, Thanks.
But the data files do not read “atomic or full”, do they?
In the scrip i define the atom_style to be full…so do you mean that i need to eliminate the molecule IID column from my data file for water? since the first is the number of atoms, second one for water is the number of molecules while for graphene is the atom type.
I appreciate any help. Thanks.

Dear Ray, Thanks.
But the data files do not read "atomic or full", do they?

http://lammps.sandia.gov/doc/read_data.html. Atomic and full are
explained here.

In the scrip i define the atom_style to be full...so do you mean that i need
to eliminate the molecule IID column from my data file for water? since the

Make all three consistent - as simple as that.

Ray

No, the data file does not contain the words full or atomic. However, in your input script you do specify one or the other.

In the small data file excerpt you sent:

960 320 1 0.42379999 35.938000 41.538593 12.418793

#graphene data begins from here:

961 3 0 0 0

note that the water data has 7 columns of information and the graphene has only 5. This is because your are specifying your atoms using two separate data styles.

You need to choose one data style and use it to describe both graphene and water.

Michael

Thanks Michael,

True. the 2nd column is Molecule ID and the 4th one is charge…So I tried to match my graphene data to that, so that starting from graphene i have just one more molecule ID (i.e. if there are 320 molecules right before reaching graphene, then the 321st one is graphene all the way to the end) and used the charge = 0 on column 4. But LAMMPS is giving me error right at the beginning that: #LAMMPS data file written by crystalmaker2lammps.f90

1360 atoms
640 bonds
320 angles
0 dihedrals
0 impropers
3 atom types
1 bond types
1 angle types
0 dihedral types
0 improper types

-0.75694412 44.165558 xlo xhi
0.38127473 47.066074 ylo yhi
0.17900842 44.193867 zlo zhi

Masses

1 1.0079401
2 15.9994
3 12.01

Atoms

.
.
.
949 317 2 -0.84759998 35.938 33.716557 33.469646
950 317 1 0.42379999 35.938 34.632324 33.190151
951 317 1 0.42379999 35.938 33.757778 34.42622
952 318 2 -0.84759998 35.938 33.716557 40.805428
953 318 1 0.42379999 35.938 34.632324 40.525932
954 318 1 0.42379999 35.938 33.757778 41.762047
955 319 2 -0.84759998 35.938 41.497326 4.1263928
956 319 1 0.42379999 35.938 42.413139 3.8468986
957 319 1 0.42379999 35.938 41.538593 5.0829678
958 320 2 -0.84759998 35.938 41.497326 11.462218
959 320 1 0.42379999 35.938 42.413139 11.182723
960 320 1 0.42379999 35.938 41.538593 12.418793
961 321 3 0 0 0 0
962 321 3 0 1.42 0 0
963 321 3 0 2.13 1.22972 0
964 321 3 0 3.55 1.22972 0
965 321 3 0 4.26 0 0
966 321 3 0 5.68 0 0
967 321 3 0 6.39 1.22972 0
968 321 3 0 7.81 1.22972 0
969 321 3 0 8.52 0 0
970 321 3 0 9.94 0 0
.
.
.
i should emphasize that none of these methods work!! and really they should not…fundamentally different styles of data files. However there has to be a way around it…am I correct? But all over the web whatever data file I see for water is very similar to the above style and graphene is just very simple: no molecule ID and no charge.

I would really appreciate any help.

Thanks,
Karim.

the situation is very simple and can be easily resolved. all you have
to do is simply follow the documentation and create a single data file
in a single consistent format. several people already pointed it out
to you. why is it so difficult to understand, that you can use *any*
atom style for as long as it is a superset of the the minimum required
style. countless people have managed to do this. but they didn't do it
by guessing or cutting and pasting. complaining that "it doesn't work"
is not helpful at all. all it means is that you didn't pay close
enough attention and were not careful enough.

axel.