1
General Questions and Answers / MPIDU_Complete_posted_with_error(1710)
« on: September 2, 2021, 10:20 »
During Raman calculation I am getting "MPIDU_Complete_posted_with_error(1710)" this error. How to overcome this?
Show Posts
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
2
General Questions and Answers / Magnitude of charge density using ATK
« on: June 13, 2021, 11:57 »
How to get the spatial coordinate (x, y, z coordinate) vs charge density in a text file.
3
General Questions and Answers / Re: Query regatding MD Simulation
« on: December 6, 2020, 18:48 »
Actually, I want to calculate the interaction energy from ab initio MD simulation? In ATK, potential energy and total energy is there however interaction is not there. But I have seen in a paper that they have calculated interaction energy using MD.
4
General Questions and Answers / Query regatding MD Simulation
« on: December 1, 2020, 17:01 »
Is it possible to perform MD simulation in acidic medium? If possible then how? How to calculate the interaction energy from MD simulation?
5
General Questions and Answers / Band Decomposed charge density of valence band and conduction band
« on: September 25, 2020, 15:55 »
I am interested to calculate the band decomposed charge density of valence band (VB) and conduction band (CB) as shown in the paper (J. Phys. Chem. C 2019, 123, 4567−4573). My system contains only carbon atoms with three different coordination and are represented by C1 (4 coordinated), C2 (3 coordinated) and C3 (two coordinated) and to check which atom is contributed in VB and CB. I have not found any direct analysis tool to perform this in ATK. However, I have performed Bloch state calculation as per the suggestion mentioned in the ATK forum. I have plotted the isosurface plot of Bloch state (BlochState.png) and observed that phase (radian) is plotted but I am interested in the electron density (Å^-3).
I have two queries in this regard,
(a) Could you please explain how I can plot charge density from the Bloch state or Eigen state?
(b) Could you please also explain what the physical interpretation of the BlochState plot is?
I am eagerly waiting for the response. Kindly note that I have communicated a paper and in the revision, reviewer asked to give the electron density plot of VB and CB.
I have two queries in this regard,
(a) Could you please explain how I can plot charge density from the Bloch state or Eigen state?
(b) Could you please also explain what the physical interpretation of the BlochState plot is?
I am eagerly waiting for the response. Kindly note that I have communicated a paper and in the revision, reviewer asked to give the electron density plot of VB and CB.
6
General Questions and Answers / Re: Phonon DOS
« on: September 4, 2020, 18:52 »
Sir As per your suggestion I have modified the script for my system and get the plot for phonon dos. Kindly noote that my system comsists of 26 C atoms with different coordination (2, 3 and 4) and I want to get the phonon dos for these three different coordination. Kindly suggest me how to modify the script. I have attached input and output for your reference. In my system the atom index 4, 5 is for 4 cordinated C atom, atom index 0, 1, 2, 3 is for 3 cordinated C atom, atom index 6-25 is for 2 cordinated C atom.
7
General Questions and Answers / MD Simulation
« on: September 4, 2020, 18:40 »
I was running a AIMD simulation using quantumATK for 10000 steps with a time step of 1fs using NooseHover thermostat. But unfortunately the calculation was terminated after 7000 steps. Kindly suggest me how to restart the calculation from there.
8
General Questions and Answers / Re: Phonon DOS
« on: September 2, 2020, 10:52 »
Thank you sir for your reply.
9
General Questions and Answers / Thermodynamic stability
« on: August 28, 2020, 22:05 »
Thank you very much sir for your kind reply.
I want to check thermodynamic stability of a 2D material at 300 K and 1000 K. I have run the simulation and obtained the required plot. But I am facing one problem, though I am perfoming the simulation using NVTNoseHoover thermostat but in the temperature vs time step plot it is observed that huge fluctuation in temperature is there w.r.t reserviour temperature. Could you please tell me how to overcome this? I have attached the input for your reference.
I want to check thermodynamic stability of a 2D material at 300 K and 1000 K. I have run the simulation and obtained the required plot. But I am facing one problem, though I am perfoming the simulation using NVTNoseHoover thermostat but in the temperature vs time step plot it is observed that huge fluctuation in temperature is there w.r.t reserviour temperature. Could you please tell me how to overcome this? I have attached the input for your reference.
10
General Questions and Answers / Phonon DOS
« on: August 26, 2020, 19:16 »
Could you please tell me how to get the projected phonondos using quantumATK? Actually I have a 2D carbon material in which three different coordination of Carbon atom is present and I want to investigate the contribution in the phonon dos for each type of carbon atom.
Thanking you in advance.
Thanking you in advance.
11
General Questions and Answers / Re: Query regarding thermoelectric calculation
« on: August 4, 2020, 15:40 »
Thank you sir for your response.
I am giving point by point answer of your comment.
Comment 1) In general you need to do a very careful optimization (relaxation) of the atomic structure when calculating phonons. In your case, the device seems to be a simple continuation of the electrodes, so it should be enough to do a fine relaxation of the electrode structure using OptimizeGeometry with a Force tolerance of 0.01 eV/Ang. At this point I would suggest to calculate the PhononBandstructure for the electrode to check that it looks reasonable. There shouldn't be phonon modes with negative energy.
From the relaxed electrode structure you make the device and calculate the DynamicalMatrix for the device.
Answer: Sir, I have optimized the electrodes with a force tolerance of 0.001 eV/Ang and calculate the phonon band structure in which no imaginary modes are present. After that I have repeat the electrodes and design a device followed by device optimization as mentioned in the study object. After that I runned the dynamical matrix and phonon transmission calculation. So sir should I think that my results are correct?
However my transmission spectra significantly deviates from FF method. Can you please explain me what may be probable reason?
2) The thermoelectric properties are changing with doping concentration. So you should either plot the properties vs. doping (or vs. Fermi level) or pick a relevant one.
Answer: Sir can you please explain me the procedure for incoporation of doping concentration in the calculation.
I am giving point by point answer of your comment.
Comment 1) In general you need to do a very careful optimization (relaxation) of the atomic structure when calculating phonons. In your case, the device seems to be a simple continuation of the electrodes, so it should be enough to do a fine relaxation of the electrode structure using OptimizeGeometry with a Force tolerance of 0.01 eV/Ang. At this point I would suggest to calculate the PhononBandstructure for the electrode to check that it looks reasonable. There shouldn't be phonon modes with negative energy.
From the relaxed electrode structure you make the device and calculate the DynamicalMatrix for the device.
Answer: Sir, I have optimized the electrodes with a force tolerance of 0.001 eV/Ang and calculate the phonon band structure in which no imaginary modes are present. After that I have repeat the electrodes and design a device followed by device optimization as mentioned in the study object. After that I runned the dynamical matrix and phonon transmission calculation. So sir should I think that my results are correct?
However my transmission spectra significantly deviates from FF method. Can you please explain me what may be probable reason?
2) The thermoelectric properties are changing with doping concentration. So you should either plot the properties vs. doping (or vs. Fermi level) or pick a relevant one.
Answer: Sir can you please explain me the procedure for incoporation of doping concentration in the calculation.
12
General Questions and Answers / Query regarding thermoelectric calculation
« on: July 22, 2020, 19:08 »
The error that I have encountered and mentioned in the previous mail has now been sorted out. Actually, I have run again the dynamical matrix but I have kept the name of .hdf5 file same as that of the previous calculation and also run phonon transmission calculation in a single run and now the calculation finished normally. However, I have several queries related to thermoelectric properties.
1. The electron transmission spectra and phonon transmission spectra using force field (FF) and DFT methods differ significantly, which is quite obvious. However, the nature of the transmission spectra using FF and mentioned in other papers is showing a step function with integer values while the same spectra obtained using DFT functional is not obeying the above condition. Kindly suggest me whether my calculation is correct or I have done something wrong. Actually, I am doing first time this type of calculation without confirming the results it is very difficult for me to proceed further.
2. Can you please suggest to me how to evaluate the thermoelectric properties for n-type and p-type doping as mentioned in the papers attached below?
3. Can you please tell me which peak I should take for evaluating the thermoelectric properties? Is it the highest peak in the given energy range or the first peak around the Fermi level?
1. The electron transmission spectra and phonon transmission spectra using force field (FF) and DFT methods differ significantly, which is quite obvious. However, the nature of the transmission spectra using FF and mentioned in other papers is showing a step function with integer values while the same spectra obtained using DFT functional is not obeying the above condition. Kindly suggest me whether my calculation is correct or I have done something wrong. Actually, I am doing first time this type of calculation without confirming the results it is very difficult for me to proceed further.
2. Can you please suggest to me how to evaluate the thermoelectric properties for n-type and p-type doping as mentioned in the papers attached below?
3. Can you please tell me which peak I should take for evaluating the thermoelectric properties? Is it the highest peak in the given energy range or the first peak around the Fermi level?
13
General Questions and Answers / Re: Regarding phonon transmission calculation using quantumATK
« on: July 10, 2020, 17:54 »
As per the suggestion I have run the first dynamical matrix in parallel mode then run the phonon transmission calculation in serial mode but unfortunately an error occurred during the simulation. I am attaching here the input and output files.
14
General Questions and Answers / Re: Regarding phonon transmission calculation using quantumATK
« on: July 3, 2020, 16:24 »
Whether it poosible to finish the caluclation using serial mode.
Actually I have planned to calculate thermoelectric properties of graphdiyne system using GGA functional. There are 36 atoms in the unit cells and I will repeat this unit cell atleast 3 to 4 times to prepare device configuration. i.e. roughly 144 atoms in the device model.
Now my questions is whether it is possible to finish the job using GGA functional for 144 atoms using serial mode.
Another point is that after preparing the device whether device optimization is required. What should be the minimum K-point along Z-direction to get the correct thermoelectric results.
Actually I have planned to calculate thermoelectric properties of graphdiyne system using GGA functional. There are 36 atoms in the unit cells and I will repeat this unit cell atleast 3 to 4 times to prepare device configuration. i.e. roughly 144 atoms in the device model.
Now my questions is whether it is possible to finish the job using GGA functional for 144 atoms using serial mode.
Another point is that after preparing the device whether device optimization is required. What should be the minimum K-point along Z-direction to get the correct thermoelectric results.
15
General Questions and Answers / Regarding phonon transmission calculation using quantumATK
« on: June 30, 2020, 09:57 »
I have optimized a unit cell of pentagraphene and then design a device configuration by repating it along z direction for calculating its thermoelectric properties. After optimizing the device I have runned for phonon transmission calculation using semiemperical theory. But after generating the dynamical matrix from displaced forces within a few minutes the phonon transmission calculation has started but after around roughly 3 days I have observed no progress in the output. I am not understanding why semi emperical calculation is taking so much time. I have attached the relevant files. Kindly suggest me what should I do to get the correct phonon transmission spectra?