Atomic order in POSCAR and the data file about dynaphopy HOT 4 CLOSED

I see, I think the issue is related to the fact that in the unit cell that you define in phonolammps probably the atoms of the same element type are not correlative. Am I right?. The standard in POSCAR format is that, in your case, first you write all Si atoms and then all O atoms. If not then it generates this unconventional POSCAR file that probably Dynaphopy cannot read correctly.

from dynaphopy.

I see, I think the issue is related to the fact that in the unit cell that you define in phonolammps probably the atoms of the same element type are not correlative. Am I right?. The standard in POSCAR format is that, in your case, first you write all Si atoms and then all O atoms. If not then it generates this unconventional POSCAR file that probably Dynaphopy cannot read correctly.

Sorry for the late reply. Inspired by you, I think I have found a solution. I can modify the atomic order in POSCAR and Force Constants output by phonolammps through post-processing, so that dynaphopy can recognize it normally.

Besides, I have two other questions to ask.

1. Can dybnaphopy be calculated in parallel? It takes a long time to read the atomic trajectory when calculating the line width and the renormalized force constant. When I calculated the amorphous sio2 with 624 atoms, the atomic trajectories were output in the last 40W steps, once every 10 steps, that is, 4W atomic trajectories were output, which needed to run for 15h. I'm running on a supercomputer with a single core, and I don't know if dynaphopy can run on multiple cores.

2. I'm also a little uncertain about the setting of the time step. I use the' -ts' command to set the time step. The time step set in the process of track output is 0.0005 ps, which is output once every 10 steps. A total of 40W steps are run and 4W tracks are output. According to the instructions of dynaphopy, I set "-ts 0.0005". I'm not sure if my settings are correct, because I see "Using 40000 steps" in Dynappy's output log. Will Dynappy automatically consider that I output every ten steps (I use lammps to output only the velocity of atoms， Is there anything else I need to pay attention to)?

I really appreciate your help.

from dynaphopy.

1. Yes, but depends on the algorithm. Using psm you can choose the algorithm to compute the power spectra. https://abelcarreras.github.io/DynaPhoPy/description.html

• ME method is implemented in parallel (OpenMP).
• Usual FFT method uses Numpy (usually not parallel but I think that it is possible to compile numpy with MKL to get some parallelization).
• FFTW via pyfftw (which is parallel).
• You can use GPU using CUDA version (this requires: https://github.com/abelcarreras/cuda_functions and a NVIDIA GPU)

2. Dynaphopy reads the information in ITEM: TIMESTEP to know the dumping ratio. The number in -ts should be the "real" time step you set in the LAMMPS input.

from dynaphopy.

1. Yes, but depends on the algorithm. Using psm you can choose the algorithm to compute the power spectra. https://abelcarreras.github.io/DynaPhoPy/description.html

• ME method is implemented in parallel (OpenMP).
• Usual FFT method uses Numpy (usually not parallel but I think that it is possible to compile numpy with MKL to get some parallelization).
• FFTW via pyfftw (which is parallel).
• You can use GPU using CUDA version (this requires: https://github.com/abelcarreras/cuda_functions and a NVIDIA GPU)

2. Dynaphopy reads the information in ITEM: TIMESTEP to know the dumping ratio. The number in -ts should be the "real" time step you set in the LAMMPS input.

Thank you very much for your patient help. I have made it clear. Now I can run in parallel. Thank you again.

from dynaphopy.