Python code to extract information from molecular dynamics simulation file

I have an output file from a molecular dynamics simulation. One part of the file is as follows:

     Entering Dynamics:    iteration =  3200
                           time      =   0.7740 pico-seconds


     Andersen thermostat:   22 collisions

ATOMIC_POSITIONS (angstrom)
O             1.2548684197        0.6424461240        0.7655878783    0   0   0
O            13.1348755441        1.7104775362        0.9831193322    0   0   0
Si            0.2961184815        3.9514997961        1.4334508031    0   0   0
Si            3.4858850598        6.3535750817       -0.0759632619    0   0   0
O             4.1551025227        5.0479390695        0.3635581483    0   0   0
Si            7.0355725487        6.6231051760        3.5097262837    0   0   0
O             6.2913557105        5.2296438029        3.7778484627    0   0   0
O             9.8141798579        5.2550557888        0.6738163980    0   0   0
Si            9.4725273964        6.6846863678        1.5204773455    0   0   0
Si            4.8006823796       11.3515927947        1.8133971611    0   0   0
O             5.9975449939        7.8470275094        3.2154093810    0   0   0
O             7.8754782756        9.8763121275        0.5722748194    0   0   0
O            -0.2959658746        0.0533054014        2.8651388320    0   0   0
Si            7.4183110714        1.6011961440        1.4468400910    0   0   0
O             5.0804368525       -0.3344709270        5.3555368062
Si           11.5338967914        1.7892923751        1.3908462020    0   0   0
O            12.0656978779        1.0046462656        4.0351985742
O             0.5207366786        4.4457166923        2.9846728696    0   0   0
Si            5.1841357277        4.0728488582        4.0746941885
O             5.1872386308        3.1106064770        2.7381557077    0   0   0
O             5.8056941280        3.0861498500        5.2873425714
O             8.4040054974        2.9471067707        1.1598483191    0   0   0
O             1.8608924768        6.1316507204        5.0920863017
O             3.7164141756        4.6241968448        4.3720160199
O            10.7430822384        6.8454765622        2.5612287404    0   0   0
Si            1.8961563104        7.4020010486        3.9672729592    0   0   0
O             3.4314681107        7.7675775631        3.6568414736    0   0   0
O             7.8525657574        7.1129666203        4.8139136918
Si            9.2285669588        9.1345382788        1.2296763780    0   0   0
O             8.0175722171        6.4483381802        2.2249489379    0   0   0
Si           -1.5864332607       10.6831540134        3.6182013263    0   0   0
O             4.6458025650        9.9775888757        2.7132759539    0   0   0
Si            4.9655131010       -0.8235046017        3.7462341115    0   0   0
O             8.7806776962       11.8629093332        4.0996484633
Si            9.8620383541       13.0065268916        4.4627978826
O            11.1203784142       11.3989385058        3.0725920949    0   0   0
Si            1.7370720581        0.4985632232        5.4133887769
O             7.8689631579       -0.8411424613        6.8001682976
O             1.8593021975        3.4289762669        5.3588309051
Si            8.2630864331        0.6006636472        6.0640224774
O             7.7797871380        2.0415566369        6.7014630911
O             1.7253534194        5.0053996874        7.1288337168
Si            2.8380624986        4.7709548130        5.7830629234
O             4.8238599095        6.1446392654        8.9217003102
O             6.1138021636        3.8559899537        7.9573682387
Si            5.4316507955        5.2744024202        7.6601085633
O             9.1685324914        4.4050300422        5.4453592810
Si            6.2413164651        2.6077699732        6.7965931056
Si           10.0301402752        5.4300848786        6.3239657737
O            13.7770558709        4.7605959661        6.6173171924
O             1.2583474444        8.5881843912        4.8423762424
Si            3.7672356322        7.4407292523        9.0018747173
O             4.4866104836        8.5787761710        7.9957768354
Si            7.7655911405        7.1471163307        6.4241215090
O             6.6577840429        6.1141075159        7.0251280749
O             9.3451435563        6.7756485511        6.9331690833
O            12.2125407892        9.8457335674        6.5913932616
Si            4.2384301635        9.6692959125        6.7673324052
O             5.0544710564       10.9211013065        7.3404829696
O             9.6907487259       10.2861855536        6.1779769547
C             3.7233324270        7.7989590137       10.8768331090
H             3.0282047684        7.0416044129       11.2795989504
H             4.6979392526        7.5564111614       11.2953932171
H             3.3833398135        8.7948495362       11.2347725215


     kinetic energy (Ekin) =           0.09821287 Ry
     temperature           =         279.39795411 K 
     Ekin + Etot (const)   =       -2637.60538954 Ry

     Writing config-only to output data dir ./SiO2.save/

It gives atomic positions like this for every iteration. I want to calculate the bond length that is the distance between highest z coordinate of the Si atom and the z coordinate of the C atom from the set of coordinates. The bond length should be calculated for every set of coordinates in the file and stored as an array or list. How to do it using a python script? I have tried a lot of methods but none of them giving me correct answer.

I tried this

import re

# Regular expression pattern to extract the Si atomic positions
pattern = r"Si\s+(-?\d+\.\d+)\s+(-?\d+\.\d+)\s+(-?\d+\.\d+)"

# List to store the highest z coordinate of Si atoms for each iteration
highest_z_coords = []

# Open the file containing the atomic positions and iterate over its lines
with open("cf3.txt", "r") as f:
    for line in f:
        # Check if the line contains the iteration number and atomic positions
        if "ATOMIC_POSITIONS (angstrom)\n" in line:
            # Initialize the highest z coordinate to a negative value
            highest_z = -float("inf")
            # Iterate over the next few lines to extract the atomic positions of Si atoms
            for i in range(6):
                next_line = next(f)
                # Use regular expression to extract the Si atomic positions
                match = re.search(pattern, next_line)
                if match:
                    # Extract the z coordinate of the Si atom and update the highest z coordinate
                    z_coord = float(match.group(3))
                    if z_coord > highest_z:
                        highest_z = z_coord
            # Add the highest z coordinate to the list for this iteration
            highest_z_coords.append(highest_z)

# Print the list of highest z coordinates for each iteration
print(highest_z_coords)

but it gives error.

source https://stackoverflow.com/questions/75963835/python-code-to-extract-information-from-molecular-dynamics-simulation-file