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I have a ReaxFF species data file that I am trying to plot via python. I am able to get the data separated but can't figure out how to maintain a time dependence. The data is formatted in a .csv like below:

Timestep No_Moles No_Specs C29H24O32N45 C C2O4N8 C2 N2 CO4N8

2800 12 6 1 2 3 2 3 1

Timestep No_Moles No_Specs C34H24O40N59 C C2O4N8 C2 N2

2900 10 5 1 2 2 1 4

Timestep No_Moles No_Specs C38H24O44N67 C N2 C2O4N8

3000 8 4 1 2 4 1

I am trying to plot a timestep dependent concentration of each species and can, for example, separate "C" and maintain its concentration dependence with the code below:

with open('species.out') as f:
    lines = f.read()
    rows = lines.split()
    
    lines = lines.split('\n')
    rows = np.asarray(rows)
   
    header = []
    numbers = []
    arange = np.arange(len(rows))
 # arrange arrays so that headers have same index as numbers
    for i in arange :
        numcheck = rows[i].isnumeric() 
        if numcheck == True :
            numbers = np.append(numbers, rows[i])
            
        if numcheck == False :
            header = np.append(header, rows[i])
    
    brange = np.arange(len(header))
    temp=[]
    for j in brange:
        if header[j] != "#" :
            temp = np.append(temp, header[j])
            
    header = temp

crange = np.arange(len(header))
C_species= []
Time = []
for L in crange:
    if header[L] == "Timestep":
        Time = np.append(Time, numbers[L])
    if header[L] == 'C':
        C_species = np.append(C_species, numbers[L])

I just don't know how to do this for all species and have "zeros" for species that haven't been formed yet.

I have tried using pandas csv_reader and itertools islice but I can't quite figure out how to accomplish what I need to.

Gabe Bjerke
  • 1

0 Answers0