How to create for loop to add a value to each element in an array in Python

Question

I have an array as follows:

xyz = [[ 0.08778,  0.99666,  0.30648],
       [ 0.41688,  2.70076,  1.10135],
       [ 1.90494,  0.91685, -0.26984],
       [-0.44512,  1.73972, -1.24406],
       [-1.68572,  1.01617,  1.01221],
       [-0.1977 , -0.77177, -0.35553],
       [ 0.61588,  3.6995 ,  1.59813],
       [ 2.98863,  0.86173, -0.59616],
       [-0.78312,  2.20935, -2.22362],
       [-2.73208,  1.02071,  1.44702],
       [-0.36006, -1.82939, -0.72827]]

I want to add 0.005 to the first element (0.08778), and then save this array to a new file 'output0.xyz'. I then want to add 0.005 to the second element (0.99666) and keep the first element as its original value, and save this array to a new file 'output1.xyz', and so on. So I need to write 33 new files, each with just one of the numbers in xyz changed. Here is my code:

i = 30
number_atoms = 12
at_nums = [26.,  6.,  6.,  6.,  6.,  6.,  8.,  8.,  8.,  8.,  8.])

for atom in xyz:
    for coordinate in atom:
        coordinate += 0.005
       
        with open('output{}.xyz'.format(i), 'w') as f:
            f.write('{:.0f}\n\n'.format(number_atoms))
            for at_num_i, xyz_disp_i in zip(at_nums, xyz):
                f.write('{:.0f}\t{:.8f}\t{:.8f}\t{:.8f}\n'.format(at_num_i, *xyz_disp_i))

Currently this code is just saving the original array into a file called 'output30.xyz'. I've been stumped on this for a while now!

Maurice Meyer · Accepted Answer · 2020-12-02 12:30:32Z

1

You need copy xyz each iteration and change the values in the copy in order to keep track of original values:

number_atoms = 12
at_nums = [26., 6., 6., 6., 6., 6., 8., 8., 8., 8., 8.]

xyz = [
    [0.08778, 0.99666, 0.30648], [0.41688, 2.70076, 1.10135],
    [1.90494, 0.91685, -0.26984], [-0.44512, 1.73972, -1.24406],
    [-1.68572, 1.01617, 1.01221], [-0.1977, -0.77177, -0.35553],
    [0.61588, 3.6995, 1.59813], [2.98863, 0.86173, -0.59616],
    [-0.78312, 2.20935, -2.22362], [-2.73208, 1.02071, 1.44702],
    [-0.36006, -1.82939, -0.72827]
]

for i, atom in enumerate(xyz):
    for j, item in enumerate(atom):
        new_xyz = [row.copy() for row in xyz]
        new_xyz[i][j] += .005

        with open('/tmp/output{}.xyz'.format(i * 3 + j), 'w') as f:
            f.write('{:.0f}\n\n'.format(number_atoms))
            for at_num_i, xyz_disp_i in zip(at_nums, new_xyz):
                f.write(
                    '{:.0f}\t{:.8f}\t{:.8f}\t{:.8f}\n'.format(
                        at_num_i, *xyz_disp_i
                    )
                )

edited Dec 2, 2020 at 12:30

answered Dec 2, 2020 at 11:25

Maurice Meyer

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7 Comments

Dragmoogle Over a year ago

So this adds 0.005 to all three items [0.08778, 0.99666, 0.30648], and then all three [0.41688, 2.70076, 1.10135], ect.. And creates 11 new output files. I need it to add to each number individually, so that I will have 33 output files, one file for every number having 0.005 added to it.

Maurice Meyer Over a year ago

@Dragmoogle: But there are just 11 elements in xyz, can you clarify that in the question ?

Dragmoogle Over a year ago

So there are 11 elements in xyz. But there are 3 elements within each element. So I need it to create 33 new output files

Dragmoogle Over a year ago

I don't know how to clarify this question any more! My first output file needs to have 0.08778 + 0.005, with all other numbers the same. My 33rd output file needs to have -0.72827 + 0.005 with all other numbers the same.

Dragmoogle Over a year ago

Ah you are correct. I didn't notice that you have changed your original answer, Apologies for that, and thank you very much for your help. I will accept your answer now.

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