How to insert equations into python script from txt file and generate another file? [duplicate]

Question

I'm asking this question again because I have not gathered a clear answer for my question.

I have a set of equations:

ref_energy = (K-(C/2)comp(a)) + C/2
form_E2 = relaxed_E_per_atom - ref_energy(comp_x)

I need to have a python script use these two equations using the values in the txt file to generate another x and y columns of values that will plot those values.

This is the first few lines of my txt file. the config is the name of the structure associated with four values

comp(a),form_E,comp_x,relaxed_E_per_atom
0,0,0,-8.15382173
1,0,0.33333333,-5.25358563
0.5,0.18614484,0.2,-6.33922213
0.5,-0.69658919,0.2,-6.69231575
0.5,-0.70549249,0.2,-6.69587707

Below is my script but I keep getting errors such as

Traceback (most recent call last):
  File "attempt_#2.py", line 80, in <module>
    x.append(float(row[0]))
ValueError: could not convert string to float: 'comp(a)'

I assume the x value isn't a numerical value in the configname, but not sure.

#!/bin/env/python
import numpy as np
import matplotlib.pyplot as plt 
import csv

Columns = 'configname,comp(a),form_E,comp_x,relaxed_E_per_atom'.split(',')
testdata ='''\
comp(a),form_E,comp_x,relaxed_E_per_atom
0,0,0,-8.15382173
1,0,0.33333333,-5.25358563
0.5,0.18614484,0.2,-6.33922213
0.5,-0.69658919,0.2,-6.69231575
0.5,-0.70549249,0.2,-6.69587707
'''

reader = csv.DictReader(StringIO(testdata))
desired_cols = (tuple(row[col] for col in columns) for row in reader)   
x=[]
y=[]
K=-2.69028905
C=-32.65176322
with open('values2.txt','r') as csvfile:
        points = csv.reader(csvfile,delimiter=',')
        for row in points:
            x.append(float(row[0]))
            y.append(float(row[1]))
allpoints=np.loadtxt('hmm.csv',delimiter=',')
ref_energy = (Kend-(Cend/2))*comp(a) + Cend/2
form_E = relaxed_E_per_atom-ref_energy(comp_x)
plt.scatter(x,y, label='Energy')
plt.xlabel('Composition KxC',fontsize=24)
plt.ylabel('Formation Energy per carbon (eV)',fontsize=18)
plt.title('Convex Hull Potassium Graphite')
plt.xticks(fontsize=20)
plt.yticks(fontsize=20)
plt.tight_layout()
plt.ylim(-0.08,0)
plt.xlim(0,1.01)
plt.show()

The problem is that you're treating the header line as a row of data. So it tries to turn headers like comp(a) into floats, which obviously won't work. The simplest answer is to add next(points) # skip header right about the for row in points:. — abarnert
– abarnert, Commented May 31, 2018 at 21:08
The attached dup is about editing a CSV file, rather than just reading it, but I think the answers explain nicely how to do what you want, why it's needed, and why it works. — abarnert
– abarnert, Commented May 31, 2018 at 21:10
Also, I notice that you're creating a DictReader for testdata. You can do the same thing for csvfile. That will not just skip the headers, but actually use them, to give you a dict with nicely named columns for each row, instead of just a list. (Which is explained better in the second answer on the dup question—or just in the csv docs.) — abarnert
– abarnert, Commented May 31, 2018 at 21:12
It worked but now it says, " x.append(float(row[0])) ValueError: could not convert string to float: 'form_E'" form_E is the second column — Jack Lee
– Jack Lee, Commented May 31, 2018 at 21:23
Do you have a blank line before the header line? That's usually not considered valid for a CSV file, but I've seen lots of people write Python code that generates files like that anyway, so… Anyway, if that's the problem, you just need to skip two lines at the start instead of one. — abarnert
– abarnert, Commented May 31, 2018 at 21:25

mad_ · Accepted Answer · 2018-05-31 21:09:15Z

1

Skip the first row

with open('values2.txt','r') as csvfile:
        points = csv.reader(csvfile,delimiter=',')
        next(points)
        for row in points:
            x.append(float(row[0]))
            y.append(float(row[1]))

answered May 31, 2018 at 21:09

mad_

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3 Comments

Jack Lee Over a year ago

It worked but now it says, " x.append(float(row[0])) ValueError: could not convert string to float: 'form_E'" form_E is the second column

mad_ Over a year ago

well next(points) should skip reading the first row.

Jack Lee Over a year ago

does the error have to do with my txt file containing five columns of data? or the error in x.append(float(row[0]))?

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