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Re: [lammps-users] Inquiry on LAMMPS fix_deform and variable formula"
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Re: [lammps-users] Inquiry on LAMMPS fix_deform and variable formula"


From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Thu, 27 Jul 2017 12:31:00 -0700

Dear Dr. Axel Kohlmeyer,

Hello Dr. Kohlmeyer. Thank you for your e-mail.

I was curious if I could ask a question on an error that I obtained when I ran my LAMMPS simulation.

I used a "fix deform" command to change my simulation box such that the length of the box follows a triangular sinusoidal path using the following "variable" command. (L0 is the initial box length. Tp is the time period.)


However, I obtained an error statement: ERROR: Power by 0 in variable formula (../variable.cpp:1718)

Even when I looked at the LAMMPS error manual, I am not understanding this error since my variable formula does not have a zero powered to a number. I would greatly appreciate if you could inform me a clue in resolving this error. Thank you.

Sincerely,

Masato Koizumi

On Wed, Jul 19, 2017 at 9:53 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Wed, Jul 19, 2017 at 12:37 PM, MASATO KOIZUMI <mkoizumi@...5997...9...> wrote:
> Dear Dr. Axel Kohlmeyer,
>
> Hello Dr. Kohlmeyer. Thank you for your email.
>
> I created a LAMMPS input script that applies tensile and compressive stress
> on the simulation box that I created using "fix deform" command.
>
> I was curious if there is a way to perform cyclic loading without repeating
> the "fix deform" command. That is, I was curious if there is a way to
> perform cyclic loading (stretching and compressing) without changing the
> number of timesteps and the strain rate. Thank you.

please re-read the fix deform command documentation and pay special
attention to any mentioning of variables.

axel.

>
> Sincerely,
>
> Masato Koizumi
>
> On Thu, Jun 8, 2017 at 11:17 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>>
>>
>> On Thu, Jun 8, 2017 at 11:22 AM, MASATO KOIZUMI <mkoizumi@...3709...> wrote:
>>>
>>> Hello All,
>>>
>>> This is Masato Koizumi, and I am currently learning how to use LAMMPS.
>>>
>>> I was curious if I could ask a question on two commands in LAMMPS:
>>> special_bonds and pair_style hybrid/overlay.
>>>
>>> Observing the LAMMPS manual, I was curious if the command, "special_bonds
>>> lj/coul 0 1 1" means that there are two interactions acting between each
>>> pair of atoms: Lennard-Jones and Coloumb. Lennard-Jones is the pairwise
>>> interaction and Coulomb is the bond interaction. I was curious if the 0 1 1
>>> means that each pairs of atoms consist either one, two or three bonds. 0
>>> means that for one-bond pair, the LJ pair potential is turned off. Likewise,
>>> the 1's mean that for two-bond and three-bond pairs, the LJ pair potential
>>> is turned on.
>>
>>
>> this sounds a bit confused, but may be right. you may want to read up on
>> what is often called "exclusions" in your preferred MD textbook.
>> here is my way to describe it:
>>
>> if you have a system, where you have non-bonded interactions, e.g. via
>> pair style lj/cut/coul/cut, *and* bonded interactions e.g. via bond style
>> harmonic and angle style harmonic and dihedral style harmonic, then the
>> special_bonds scaling factors are applied to all 1-2, 1-3, and 1-4 pairs
>> connected by bonds. for the default setting (0/0/0), that means when two
>> atoms are connected with a bond (i.e. a 1-2 pair), the non-bonded
>> interaction is turned off, if there are two bonds to the same central atom
>> (a-b-c), then the 1-3 interaction (a-c) is scaled by the 1-3 factor. if
>> there is also a bond between a-c, then the 1-2 factor is applied. same rules
>> apply for 1-4 pairs and the 1-4 special bonds factor.
>>
>>>
>>>
>>>
>>> Lastly, for pair_style hybrid/overlay, I was curious if this command
>>> simply means that the potential energy between each pairs of atoms is the
>>> summation of the pair potentials. That is, pair_style hybrid/overlay lj/cut
>>> 2.5 coul/long 2.0 is defined as the summation of Lennard-Jones and Coulomb
>>> potential acting between each pairs of atoms.
>>
>>
>> yes, this would be the same as lj/cut/coul/long 2.5 2.0. please make a
>> test and see for yourself.
>>
>> axel.
>>
>>
>>>
>>>
>>> Thank you.
>>>
>>>
>>> Masato
>>>
>>>
>>>
>>>
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>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.