ZGainsforth

import numpy as np
# from skimage.external.tifffile import imsave
from skimage.io import imsave
import os
import matplotlib.pyplot as plt

# The start and end cm-1 values of the stack as well as the number of images.  To know these look inside the ais file exported from the stack acquisition.
Startcm = 1300
Stopcm = 1372
Stepscm =13

ZGainsforth

#!/bin/zsh

source loadmyorca

orca Fe.inp | tee Fe.out

orca_mapspc Fe.out SOCABS -eV -x0700 -x1740 -n500 -w0.5

# streamlit run DrawSpec.py

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Convergence going the wrong way

• Check unit cell shape.
• Check bohr vs angstrom units.
• Are ecutwfc, ecutrho too low?
• Not enough kpoints?
• Reduce mixing beta.
• Try cg instead of david convergence algorithm.

XSPECTRA Pre-calculation checklist

• smearing in case excited state closes the band gap?

ZGainsforth

import h5py as h5
import glob2 as glob
from imageio import imsave
import numpy as np
import os
import plotly.express as px
import streamlit as st

def ExtractOnePtychoImage(FileName):
    d = h5.File(FileName, 'r')

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ZGainsforth

import numpy as np
from genfire.fileio import readMRC, writeMRC
from sklearn.cluster import KMeans

Els = ['Fe', 'Mg', 'S', 'O', 'Si']

Cubes = []
for El in Els:
    ThisCube = readMRC(El+'_reconstruction_cropped.mrc')
    # ThisCube -= np.min(ThisCube)

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Force pull

git fetch --all

git reset --hard origin/master

Remote settings

git remote -v # Verbose display of the remote.

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How to compile quantum espresso on mac or linux.

Disable anaconda during compilation.

On mac install macports version of gnu compilers: gcc-7 and gfortran-7
On linux install gnu compilers.

Install blas, fftw, mpich.

On OS X macports won't overwrite clang.  Stupid, but just put the macports compilers earlier in the path.

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ZGainsforth

import numpy as np
import matplotlib.pyplot as plt
from dask.distributed import Client, wait, as_completed

# We are going to use dask to produce a 2D output based on 3D input data that is relatively large and must be distributed in advance.

# For dask to work we need the "hard work" to be in a single function call.
def CalcOneElement(x, y, Full):
    print(f'{y} of {Full.shape[1]}, {x} of {Full.shape[2]}', end='\r')