Messages

1

General Questions and Answers / Re: Job Manager is not opening in GUI

« on: April 19, 2020, 17:36 »

Hi My friend
I suffered the same problem, below is the reply from the customer support
This is an unfortunate issue. The solution is to close NanoLab, and remove the "Jobs_2019.12.hdf" file in the ".vnl" directory. On Windows, it is located in "C:\Users\USER\.vnl\Jobs_2019.12.hdf", and on Linux in "$HOME/.vnl/Jobs_2019.12.hdf". Then open NanoLab again, and the file will automatically be re-created and working.

enjoy it

best regards,

Jin-You Lu

2

General Questions and Answers / Li+ on graphene surface

« on: April 25, 2018, 09:05 »

Dear Quantumwise

Recently, I am interested in the Li+/ graphene interaction.
However,  I just found that in Quantumwise,  I can just change the charge number of the total system in the basis of "New Calculator".
To my understanding, If i want to have an ionic atom in the DFT simulation, I need to generate the ionic Pseudopotential of Li+ by myself.
Is there any ways to do that by using Quantumwise?
Thanks

Best
JinYou Lu

3

Scripts, Tutorials and Applications / Export QuantumEspresso input

« on: March 19, 2018, 08:31 »

Dear Sir

I have around 80 cif files, and I am wondering if it is possible to generate the quantumespresso input files efficiently by using script.

which may be similar to
BulkConfiguration=nlread("ZZZSSY01.cif")

Export???(("ZZZSSY01.in",BulkConfiguration)

Thank you so much

4

General Questions and Answers / Re: Calcite and Water

« on: December 5, 2016, 10:48 »

Dear Petr Khomyakov
Thanks a lot

5

General Questions and Answers / Re: Calcite and Water

« on: December 5, 2016, 07:36 »

Dear Jess Wellendorff

Thanks for the hightlights in the pseudopotentials use.
I follow procedure 1->2->3 to get adsorption energy (-1.14 eV) of one water molecule on calcite (10.4) surface. After considering BSSE, i get -1.04 eV (very close to -1 eV, shown in JPC paper). But is it necessary to do geometry optimization again for BSSE correction? (It takes time , the energy change during geometry optimization is around -0.03 eV )

for your comment 3, the author use quantumexpresso with PBE and ultrasoft  pseudopotentials to simulate this case. Quantumexpresso use Plane-Wave Self-Consistent Field. I think it is plane wave. Could you share some information on what the difference between  LCAO in ATK and plane wave method is ? Thanks a lot for your comments.

6

General Questions and Answers / Re: Calcite and Water

« on: November 30, 2016, 21:26 »

Thanks for your reply!
Yes, I am trying to get the absorption energy of water on calcite properly.
However, I got the value around of -2 eV different with -1 eV shown in the literature. (J. Phys. Chem. C 115, 10044 (2011) and J. Phys. Chem. C 118, 3078 (2014).

7

General Questions and Answers / Re: Calcite and Water

« on: November 28, 2016, 17:18 »

Dear Jess Wellendorff

a) I followed your instruction to study the adsorption energy of H2O on calcite.
Firstly, one water molecule is added to the relaxed calcite surface (bottom two layers fixed).
Then, a MD simulation with the NVT ensemble was done from 300k to 1k. (total time 200ps; time step 1ps). I consider the system achieve equilibrium.
The adsorption energy i got is -0.95eV similar to the result (-1 eV )published in Journal of Physical Chemistry C 118(6):3078-3087  (2014).
calcite+H2O= -40556.574 eV
calcite= -40088.730 eV
H2O=-466.867 eV
dE=-0.95eV.
b) However, if i further do the LBFGS geometry optimization for this equilibrium system.
i got calcite+H2O = -40557.62 eV, which means adsorption energy of -~2eV. I know this step is not suggested in the previous  discussion.
http://quantumwise.com/forum/index.php?topic=4148.msg19013#msg19013
But this way is similar to the tutorial of CO/Pd,
Could you help to advise why i get a different equilibrium state with a lower adsorption energy around -2.0 eV? ( which means more stable ? or something else).

c) In the beginning, i thought this is due to i didn't use proper boundary condition to remove dipole effect. So i use FFT2D with right-sided Dirichlet boundary and left-sided Neumann boundary to calculate the system again.

First, I calculate 4layers calcite again by using  LBFGS geometry optimization and fixing the bottom 2 layers. Same as previous case i did, but with a new boundary condition.
When i got surface relaxed calcite, i added one water  molecule to the surface of calcite.
Then, i directly use LBFGS geometry optimization to simulate the system and got a similar result of -2.4 eV.

The details of total energy for the system is as follows
calcite+H2O= -40551.210 eV
calcite= -40081.950 eV
H2O=-466.867 eV
dE=-2.393eV.

I attached script of case a and c for your reference.
log file it too big to attach it.
Thanks in advance.
 
 

8

General Questions and Answers / Re: Kawamura Three-body potential in MD simulation

« on: November 19, 2016, 16:03 »

Dear Julian Schneider

Do you have any update for that?
Thank you very much.

9

General Questions and Answers / Re: Kawamura Three-body potential in MD simulation

« on: November 14, 2016, 10:20 »

Dear Julian Schneider
For my current system H2O on calcite (CaCO3),
I need three body potential to describe, like H-O-H and C-O-C, and the parameters i can get from the supporting Information published in J. Phys. Chem. C, 2014, 118 (6), pp 3078–3087
http://pubs.acs.org/doi/suppl/10.1021/jp411151u/suppl_file/jp411151u_si_001.pdf

For other two-body potentials, i would try to use potential terms implemented in ATK-classical^^.
Thanks

10

General Questions and Answers / Kawamura Three-body potential in MD simulation

« on: November 13, 2016, 13:34 »

Hello~

I am trying to implement a three-body potential, as shown the equation below or in the attached file.
V_ijk3(r_ji,r_jk,θ)=-f{cos(2(θ_ijk-θ_o))-1}(k₁k₂)^1/2
k1=1/(exp[g_r(r_ij-r_m)]+1)
k2=1/(exp[g_r(r_jk-r_m)]+1)

https://www.researchgate.net/publication/29773387_Physical_Properties_of_Clay_Minerals_and_Water_By_means_Molecular_Dynamics_Simulations?enrichId=rgreq-dfafdda917aaf583a0706dddf4c0f460-XXX&enrichSource=Y292ZXJQYWdlOzI5NzczMzg3O0FTOjI2MDg1Nzk2NzkzNTQ4OEAxNDM5MjA0Nzk0NDM5&el=1_x_3

Is there internal potential which can be used to describe the equation?
Thanks

11

General Questions and Answers / Re: Use molecular dynamics to calculate the surface tension of argon liquid

« on: November 9, 2016, 09:01 »

I am back!
The normal direction of local pressure can be constant after averaging 3000 snaps. (100 time step snap once, and time step i set is 5 fs)
The lateral direction of local pressure is close to the literature.
The surface tension of Argon liquid vapor interface at 90k is 0.015 (which is close to 0.0145 N/m in the previous literature)

Thanks
Best
JY

12

Scripts, Tutorials and Applications / Re: How to make LAMMPS scripts in VNL Builder

« on: November 6, 2016, 14:54 »

After the calculation of Lammps, i can get a trajectory file.
The trajectory file can be imported into movie tool to visualize it.
(although there are difference between original ATK-generated trajectory file)
But can i save this file as a new trajectory file, which follows ATK format.

Thanks

13

General Questions and Answers / Re: Use molecular dynamics to calculate the surface tension of argon liquid

« on: October 26, 2016, 12:37 »

Dear  Julian Schneider
Thanks! I will check it and let you know my results.
Thanks again for your continuous help. i am very appreciated.

Best
JY

14

General Questions and Answers / Re: Use molecular dynamics to calculate the surface tension of argon liquid

« on: October 24, 2016, 12:23 »

It is simulation results with the same potential.  You can help to check these two references.

[1]  Molecular Physics 48(6):1357-1368 · April 1983
DOI: 10.1080/00268978300100971
I did similar simulation with the same potential in the ref. [1].
We can check the normal direction of pressure in a vapor/liquid equilibrium condition.
Figure 3 and 4 show normal and tangential direction of local pressure P(z), respectively.
The normal direction is almost constant for any z position. and for Pt, there is a transition between liquid and vapor.
https://www.researchgate.net/publication/239737668_The_Pressure_Tensor_at_the_Planar_Surface_of_a_Liquid

[2] International Journal of Chemical, Molecular, Nuclear, Materials and Metallurgical Engineering Vol:3, No:9, 2009
http://waset.org/publications/3746/molecular-dynamics-simulation-of-liquid-vapor-interface-on-the-solid-surface-using-the-gear-s-algorithm

The liquid and vapor density versus temperature can be found in ref. [2].
The calculated density of my simulation by using quantumwise agrees with the Fig .2.
But for surface tension, (Fig.3) the calculated value is very different. ( the surface tension value is also confirmed by appl 107, 143105 (2015), which show surface tension is 8.16 mJ/m^2 with the same order as ref. [2].

I attached figures for the reference.
Thanks for your help.

15

General Questions and Answers / Re: Use molecular dynamics to calculate the surface tension of argon liquid

« on: October 23, 2016, 09:56 »

Thanks for your reply.
Actually, i did several tests to extract the surface tension and local pressure with different number of argon and simulation box.
I always get a stable density aorund 1.2 (from MD_analyzer). But when i try to get local pressure and surface tension. The values are not comparable with the results in the literature.

One of examples is as follows:
Firstly, I place 2254 argon atoms at the center of a rectangular simulation box with 384x384x2500(A^3).
and I equilibrated the system at 100k by using Berendsen algorithm. This step can be found in the "Berendsen_thermostat.py" (my attached file).

Then, I wrap the atoms into the simulation box and used NVE verlet to extract surface tension and local pressure.
For P_zz(z) normal direction of local pressure, it should be constant for any z if the equilbrium between liquid and vapor is achieved.
But coomparing to the simulation result, it is not stable near and inside the argon liquid. (Figure 1)
For surface tension, it should be around 10*(10^-3)N/M.  But i got 23.3294240614 Ang*bar( 23*10^-5N/M).

Please help to check it. Thanks for your continuous help.