@erh3cq Currently PyPrismatic can only run a full calculation and can't calculate individual steps, so you would be unable to perform a probe calculation in the same way that the GUI handles it. Without rewriting things, the easiest way to mimic the probe analyzer in pyprismatic would be to do the following:
1) Set the scan window around the part of the cell you want to run a probe through
2) Set the probe step in X and Y larger than the window, so only one probe is calculated
3) Run a full simulation in multislice and PRISM with your desired interpolation factor with 4D output turned on, and compare the results manually.
This will be slower than the probe analyzer on the GUI, since potential can't be reused, but should achieve the same effect. For similar reasons, the S-matrix can't be reused in pyprismatic, nor can it be saved and re-used in the command-line version. Whether or not it would be faster simulate the full image or two separate regions of interest depends largely on your specific simulation settings. I would recommend running a simulation on a small region of interest with a single frozen phonon and timing the two main steps in the PRISM calculation, PRISM02 (S-matrix) and PRISM03 (output). PRISM02 will take the same time no matter the size of your region of interest (depends on supercell size, interpolation factor, real space pixel size), while PRISM03 should be roughly linear in the number of probe positions you calculate.
@lerandc, I still haven't figured out the pyprismatic in GPU mode. Sorry to bother in a similar topic:
In file included from ./include/meta.h:20:0,
./include/defines.h:37:10: fatal error: cuComplex.h: No such file or directory
#include "cuComplex.h" ^~~~~~~~~~~~~ compilation terminated. error: command 'gcc' failed with exit status 1
It seems it is not able to find the cuComplex.h file.
I have checked that I have compiled my CMAKE in python_gpu mode:
Furthermore; the cuComplex.h is available in the Cuda-10.2 library.
Hi @lerandc ! It seems I found out the problem. The cuprismatic is not being compiled properly. When I use
cmake -DPRISMATIC_ENABLE_GPU=1 -DPRISMATIC_ENABLE_CLI=1 -DPRISMATIC_ENABLE_PYTHON_GPU=1 ../
Everything is compiled fine but the end I get:
CMake Warning: Manually-specified variables were not used by the project: PRISMATIC_ENABLE_PYTHON_GPU -- Build files have been written to: /home/tara/apps/prismatic/prismatic-1.2.1/build`
Thanks, @lerandc yeah that indeed solves the problem while cmake. Sorry I ran into another problem it seems while pip installing, there is some error generated. I think it is due to the fact that cuprismatic library is not found.
Can you say what I am doing wrong?
/home/tara/anaconda3/envs/4dsim/compiler_compat/ld: cannot find -lcuprismatic
Thanks a lot!!