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Re: [lammps-users] Buckingham Potential
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Re: [lammps-users] Buckingham Potential


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 21 May 2018 09:56:42 -0400



On Mon, May 21, 2018 at 1:40 AM, Afza Shahid <afza_shahid@...1250...6...> wrote:
Dear Dr. Axel Kohlmeyer
 
Thank you so much for your valuable feedback regarding my problem. Since I'm a beginner I face many trivial problems.  
Coming towards your comment on the problem, firstly the cutoff value of 2.5 was a typo. It was actually 20A. Sorry for that. Secondly, as you have mentioned about other interactions (Y-Y, Y-Zr, and Zr-Zr), the parameters for these interactions are not given anywhere in literature. I have no idea how to include the parameters of these interactions. 

​please refer to the publication where you took those parameters from. the authors must have given some form of explanation how they handled those interactions. beyond that, you should discuss with your adviser/supervisor/mentor. how to handle such a situation is a question about MD simulations and force fields in general and not a question about LAMMPS. that makes it off-topic for this list, but very much on-topic for your adviser/supervisor/mentor.

axel.​

 

Regards
Afza shahid


On Thursday, May 17, 2018 2:42 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:




On Thu, May 17, 2018 at 4:07 AM, Afza Shahid <afza_shahid@...16...> wrote:
Dear Steve 
I have run the simulation using arbitrary values for coefficients of buckingham potential and there is no error but when I give the actual values of coefficients of Buckingham potential there an error saying All pair coeff are not set. Input script is given below:

​that error message is self-explanatory! you are not providing pair_coeff entries for all pairs of atom types. where are the parameters for Y-Y, Y-Zr, and Zr-Zr interactions?
if you use pair_coeff * *, you implicitly assign parameters of all pairs of types.

also, your global non-bonded cutoff of 2.5 angstrom does not make any sense for a system with metal units. it *must* be wrong.

axel.

 

# ---------- Initialize Simulation --------------------- 
clear 
units metal 
dimension 3 
boundary p p p 
atom_style atomic 
atom_modify map array

# ---------- Create Atoms --------------------- 
read_data YzOO.in
#lattice fcc 4
#region box block 0 1 0 1 0 1 units lattice
#create_box 1 box

#lattice fcc 4 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1  
#create_atoms 1 box
mass 1 88.90
mass 2 91.22
mass 3 16.0
#replicate 1 1 1

# ---------- Define Interatomic Potential --------------------- 
pair_style buck 2.5
pair_coeff 1 3 2442.60 0.3054 17.51   #Y-O interaction
pair_coeff 2 3 1402.57 0.3312 5.10     #Zr-O interaction
pair_coeff 3 3 35686.18 0.2010 32.00  #O-O interaction
neighbor 2.0 bin 
neigh_modify every 1 delay 0 check yes
 
# ---------- Define Settings --------------------- 
compute eng all pe/atom 
compute eatoms all reduce sum c_eng 

# ---------- Run Minimization --------------------- 
reset_timestep 0 
fix 1 all box/relax iso 0.0 vmax 0.001
thermo 10 
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms 
min_style cg 
minimize 1e-25 1e-25 5000 10000 

variable natoms equal "count(all)" 
variable teng equal "c_eatoms"
variable length equal "lx"
variable ecoh equal "v_teng/v_natoms"

print "Total energy (eV) = ${teng};"
print "Number of atoms = ${natoms};"
print "Lattice constant (Angstoms) = ${length};"
print "Cohesive energy (eV) = ${ecoh};"

print "All done!" 


I have run the simulation with the pair coeff command given below (supposed values for coefficients) and it shows no error.
pair_style buck 2.5
pair_coeff * * 100.0 1.5 200.0 

Kindly help me where exactly the problem is.

Regards
Afza Shahid.



On Tuesday, May 15, 2018 7:16 PM, Steve Plimpton <sjplimp@...24...> wrote:


Please put the input script lines and the error message in your mail post.

Steve

On Tue, May 15, 2018 at 2:58 AM, Axel Kohlmeyer <akohlmey@...43...4...> wrote:


On Tue, May 15, 2018 at 4:17 AM, Afza Shahid via lammps-users <lammps-users@...396... sourceforge.net> wrote:
Dear LAMMPS users

I'm using this command:

pair_style buck 20
pair_coeff * * 2442.60 0.3054 17.51

cut off= 20A
A= 2442.60 A
rho= 0.3054 eV
C= 17.51 eV A^6

but there is an error saying that these parameters are out of bound. Can anybody help me with this problem. Whats wrong with this command.

​nothing. ​

 

Regards 
Afza Shahid

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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.

------------------------------ ------------------------------ ------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
______________________________ _________________
lammps-users mailing list
lammps-users@...396... sourceforge.net
https://lists.sourceforge.net/ lists/listinfo/lammps-users







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