Figure 1 from Paper

import symd
import matplotlib.pyplot as plt
import matplotlib as mpl
import numpy as np
import pickle
import pandas as pd
import skunk
import svglib
import seaborn as sns

base_colors = [
    "f94144",
    "f3722c",
    "f8961e",
    "f9844a",
    "f9c74f",
    "90be6d",
    "43aa8b",
    "4d908e",
    "577590",
    "277da1",
]
colors = ["#" + c for c in base_colors]
sns.set_style("white")
sns.set_style("ticks")
sns.set(
    rc={
        "axes.facecolor": "#f5f4e9",
        "grid.color": "#AAAAAA",
        "axes.edgecolor": "#333333",
        "figure.facecolor": "#FFFFFF",
        "axes.grid": False,
        "axes.prop_cycle": plt.cycler("color", plt.cm.Dark2.colors),
        "font.family": "monospace",
    }
)
print(symd.__version__)

1.1.3

def run_sim(n, number_density, group, w=None, retries=5, pos_frames=0, steps=30000):
    for i in range(retries):
        try:
            np.random.seed(i)
            cell = symd.groups.get_cell(number_density, group, 3, n, w)
            md = symd.Symd(
                nparticles=n,
                cell=cell,
                ndims=3,
                images=2,
                force="lj",
                wyckoffs=w,
                group=group,
                steps=steps,
                exeDir="sim2d",
                start_temperature=0.5,
            )
            md.remove_overlap()
            if pos_frames > 0:
                md.log_positions(frames=pos_frames)
            md.log_output(period=int(1 / md.runParams["time_step"]))
            md.run()
            break
        except RuntimeError as e:
            print(e)
            md = None
    return md

np.random.seed(0)
md = run_sim(5, 0.2, 17, pos_frames=100)

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[4], line 2
      1 np.random.seed(0)
----> 2 md = run_sim(5, 0.2, 17, pos_frames=100)

Cell In[3], line 5, in run_sim(n, number_density, group, w, retries, pos_frames, steps)
      3 try:
      4     np.random.seed(i)
----> 5     cell = symd.groups.get_cell(number_density, group, 3, n, w)
      6     md = symd.Symd(
      7         nparticles=n,
      8         cell=cell,
   (...)
     16         start_temperature=0.5,
     17     )
     18     md.remove_overlap()

File /opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/symd/groups.py:653, in get_cell(number_density, group, dim, n, w)
    636 def get_cell(
    637     number_density: float,
    638     group: Union[int, Group],
   (...)
    641     w: Optional[List[int]] = None,
    642 ) -> List[float]:
    643     """
    644     Compute unit cell given number density, group, and number of particles in asymmetric unit.
    645 
   (...)
    651     :return: flattened unit cell (for use in symd MD engine)
    652     """
--> 653     import scipy.optimize as opt
    655     if w is None:
    656         w = []

ModuleNotFoundError: No module named 'scipy'

plt.plot(md.pe, label="potential")
plt.plot(md.ke, label="kinetic")
plt.plot(md.te, label="total")
plt.legend(loc="best")

All Sims

titles = [str(i) for i in range(1, 231, 14)]
df = pd.DataFrame()
retries = 3


def standardize(te):
    i = int(md.te.shape[0] * 0.2)
    te = md.te[i:]
    return te - np.mean(te)

for i, t in enumerate(titles):
    md = run_sim(4, 0.2, i + 1)
    df = df.assign(**{t: standardize(md.te)})

fig = plt.figure(figsize=(4, 5.7))
ax = plt.gca()
mx = df.shape[0] // 2
for i, n in enumerate(df.columns):
    color = colors[i % len(base_colors)]
    ax.plot(df[n] + i, color=color)
    offsetbox = mpl.offsetbox.TextArea(n)
    ab = mpl.offsetbox.AnnotationBbox(
        offsetbox,
        (mx, i),
        xybox=(mx, i),
        xycoords="data",
        boxcoords="data",
        arrowprops=None,
        bboxprops=dict(fc="#f5f4e9", lw=0),
    )
    ax.add_artist(ab)
ax.set_xlabel(r"Time [$\tau$]")
ax.set_facecolor("#f5f4e9")
ax.set_ylabel(r"$\Delta$ Energy [$\epsilon$]")
plt.savefig("energy3d.svg")