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[lammps-users] Inquiry on Results Using Compute Bond/Local
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[lammps-users] Inquiry on Results Using Compute Bond/Local


From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Mon, 16 Apr 2018 04:53:05 -0700

Dear Dr. Steve Plimpton and LAMMPS Users,

Thank you, Dr. Plimpton for your advice.


I was curious if I could ask a question regarding the compute bond/local command.

I am currently studying the force-displacement response of a polymer strand in a freely jointed chain where I define polymer strand as the polymer chain segment flanked by two crosslinks. 

I have created a simple polymer matrix consisting 4 chains each comprised of 10 beads. There are 5 crosslink bonds that link these different chains. The bonds that connect to form a chain and the crosslink bonds are governed by FENE potential and non-connected beads interact with LJ potential. 

I have applied uniaxial deformation such that the simulation box elongates to twice its original box length (stretch = 2.0) at strain rate of 0.00001 in LJ units.

However, I have plotted (and attached) the average bond lengths for the 4 chains with respect to stretch, and I am observing a random fluctuation without any signs of upward trend. I am expecting that the average bond length of the 4 chains should increase with respect to increasing stretch. 

Furthermore, I have plotted (and attached) the tension experienced by polymer strand at maximum elongation (stretch = 2.0) and the strand tension varies randomly with respect to r/L (strand end-to-end distance/strand contour length). 

In both of these plots, I should see an upward trend, and I should not see data points in the negative region of the force plot since this would imply bonds being compressed when in fact the simulation box is elongating. 

I tried with larger stretch but I am continuing to see random pattern in these plots.

Following the documentation, I understand that compute bond/local calculates the bond length, bond potential and bond force between every atom, but I was curious if I am interpreting and using the compute bond incorrectly. Simulating a larger polymer matrix, I am obtaining reasonable stress strain curve, but I am still seeing random fluctuation in bond length and force as well as in strand tension.

According to the documentation and from physical interpretation, I should see an upward trend in both of the attached plots. I would greatly appreciate if I could request for any comments or advice.

I also attached my LAMMPS script and the external data file if needed. Thank you so much for your time.

Sincerely,

Masato Koizumi



On Thu, Apr 12, 2018 at 8:55 AM, Steve Plimpton <sjplimp@...24...> wrote:
The error is likely due to the original data file (or read_data) command not
allowing for extra space for more future atoms types (2,3).  See
the read_data command for how to do this.

Steve

On Thu, Apr 12, 2018 at 4:31 AM, MASATO KOIZUMI <mkoizumi@...3709...> wrote:
Dear LAMMPS Users,

Thank you for your advice, Wahab.

I am currently writing script that deposits water molecules into a simulation box filled with molecules. My input script reads a data file (via read_data command) that consists of 1 atom type and 1 bond type. A portion of my data file is displayed as follows:

1250 atoms
1225 bonds

1 atom types
1 bond types

-5.6859149999999996e+000 5.6859149999999996e+000 xlo xhi
-5.6859149999999996e+000 5.6859149999999996e+000 ylo yhi
-5.6859149999999996e+000 5.6859149999999996e+000 zlo zhi

Masses
1 1

Pair Coeffs
1 1 1

Bond Coeffs
1 30 1.5 1 1

Atoms # bond

1021 21 1 0 -4.1502851628629784e+00 -5.0205756757887103e+00 5.5686512384180418e+00 0 1 -1
1124 23 1 0 -2.2865743827773772e+00 -5.5953483083714382e+00 -4.6511594383680359e+00 1 0 0
1123 23 1 0 -1.9036279292246638e+00 -4.8641269372881135e+00 -5.2194964650898221e+00 1 0 0


Meanwhile, using fix deposit command, the molecule command reads the data file that consists of 2 atom types labeled as type 2 and type 3 as follows

# dimer molecule

2 atoms
1 bonds

Coords
1 0 0 0
2 1 0 0

Types
1 2
2 3

Bonds
1 1 1 2

Special Bond Counts
1 1 0 0
2 1 0 0

Special Bonds
1 2
2 1

My fix deposit command are specified as:

fix    7 addatoms deposit 100 0 100 12345 region slab near 0.0 mol dimer vx -1.0 -1.0 vy -1.0 -1.0 vz -1.0 -1.0

                
               
However, I am obtaining an error that states "Invalid atom type in fix deposit mol command (../fix_deposit.cpp:115)"

Reading the documentation, I am coming to the conclusion that I need to specify "0" for the type argument in fix deposit, since my atom type in my original read_data file is 1 and my atoms in molecule file has type 2 and type 3. Therefore, the dump file will consist of atoms that will contain type 1, 2 and 3 atoms.

I was curious if I could request for any advice on this error. Thank you.

Sincerely,

Masato Koizumi

On Thu, Apr 12, 2018 at 2:56 AM, Wahab Mirco <Mirco.Wahab@...7554...g.de> wrote:
On 12.04.2018 11:32, MASATO KOIZUMI wrote:

> Hello. Just following up, I was curious if LAMMPS could perform a
> mu-P-T, i.e. constant chemical potential, constant pressure and constant
> temperature. I am planning to create a dynamic simulation where
> molecules are inserted into the simulation box under isobaric and
> isothermal conditions. I would like to have the volume of the simulation
> box change.

A µ-P-T ensemble isn't a real thermodynamical ensemble. You can figure
that out if you consider the relation of µ and P in an ideal gas.
(https://en.wikipedia.org/wiki/Gibbs%E2%80%93Duhem_equation)

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Attachment: Stress_Strain.in
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Attachment: Tension Plot.png
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Attachment: Bond Plot.png
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