# %%
import numpy as np
import matplotlib.pyplot as plt

import mdevaluate as md

DATA_DIR = "/data/skloth/python_packages/mdevaluate_examples/data"
path_to_sim = "/data/skloth/sim/IL_water/C4MIM_BF4_x50/T300_nvt"
trajectory = md.open(path_to_sim, topology="run.tpr", trajectory="out/traj_full.xtc")

oxygen_water = trajectory.subset(atom_name="OW", residue_name="SOL")
cation_indices = trajectory.subset(residue_name="amim").atom_subset.indices
cation_com = md.coordinates.center_of_masses(trajectory, atom_indices=cation_indices)
anion_com = trajectory.subset(atom_name="B", residue_name="BF4")


# %%
time, msd_oxygen_water = md.correlation.shifted_correlation(
    md.correlation.msd, oxygen_water.nojump, segments=100, skip=0.1, average=True
)
time, msd_cation_com = md.correlation.shifted_correlation(
    md.correlation.msd, cation_com.nojump, segments=100, skip=0.1, average=True
)
time, msd_anion_com = md.correlation.shifted_correlation(
    md.correlation.msd, anion_com.nojump, segments=100, skip=0.1, average=True
)

plt.figure()
plt.plot(time, msd_oxygen_water, ".", label="Water")
plt.plot(time, msd_cation_com, ".", label="Cation")
plt.plot(time, msd_anion_com, ".", label="Anion")
plt.legend()
plt.xscale("log")
plt.yscale("log")
plt.xlabel(r"$t$ in ps", fontsize=16)
plt.ylabel(r"$\langle r^2\rangle(t)$ in nm$^2$", fontsize=16)
plt.show()
plt.close()

# %%
import pandas as pd
msd_df = pd.DataFrame(
    {"t": time,
     "msd_water": msd_oxygen_water,
     "msd_cation": msd_cation_com,
     "msd_anion": msd_anion_com
     }
)
print(msd_df)
msd_df["cation"] = "C4mim"
msd_df["anion"] = "DCA"
msd_df["x_w"] = 50
msd_df["T"] = 300
print(msd_df)


# %%
def add_description(dataframe, cation, anion, x_w, T):
    dataframe["cation"] = cation
    dataframe["anion"] = anion
    dataframe["x_w"] = x_w
    dataframe["T"] = T
    return dataframe


msd_df = add_description(msd_df, "C4mim", "DCA", 50, 300)
print(msd_df)

#%%
msd_df.to_hdf(f"{DATA_DIR}/result.h5", key="msd")

msd_df = pd.read_hdf(f"{DATA_DIR}/result.h5", key="msd")

md.utils.cleanup_h5(f"{DATA_DIR}/result.h5")