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Import plot module in not refactored plotting scripts
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All plotting scripts that have not been refactored, yet, need to import
the plotting module `mdtools.plot` now, because it is not loaded
together with mdtools anymore.

The plotting scripts that have not been refactored, yet, are:

  * All `scripts/dynamics/plot_renewal_envents_*.py` scripts.

  * `scripts/structure/plot_topological_map.py`.
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@andthum
andthum committed Sep 3, 2021
1 parent 412d5e5 commit a4089ce
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Showing 17 changed files with 800 additions and 565 deletions.
38 changes: 23 additions & 15 deletions scripts/dynamics/plot_renewal_events_displ_hist.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
#!/usr/bin/env python3


# This file is part of MDTools.
# Copyright (C) 2020 Andreas Thum
# Copyright (C) 2021 The MDTools Development Team and all contributors
# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
Expand All @@ -18,6 +18,9 @@
# along with MDTools. If not, see <http://www.gnu.org/licenses/>.


__author__ = "Andreas Thum"


import sys
import os
from datetime import datetime
Expand All @@ -28,6 +31,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
import mdtools.plot as mdtplt # TODO: Replace deprecated functions
plt.style.use("default") # TODO: Use MDTools plotting style


if __name__ == '__main__':
Expand Down Expand Up @@ -227,18 +232,20 @@
frameon=False,
clear=True,
tight_layout=True)
mdt.plot.hist(ax=axis,
x=data,
xmin=args.XMIN,
xmax=args.XMAX,
ymin=args.YMIN,
ymax=args.YMAX,
xlabel=r'$' + xlabel[i] + r'$ / ' + args.LUNIT,
ylabel=r'$p(' + xlabel[i] + r')$',
bins=bins[i],
range=(args.START, args.STOP),
density=True)
mdt.plot.plot(
mdtplt.hist(
ax=axis,
x=data,
xmin=args.XMIN,
xmax=args.XMAX,
ymin=args.YMIN,
ymax=args.YMAX,
xlabel=r'$' + xlabel[i] + r'$ / ' + args.LUNIT,
ylabel=r'$p(' + xlabel[i] + r')$',
bins=bins[i],
range=(args.START, args.STOP),
density=True,
)
mdtplt.plot(
ax=axis,
x=x[i],
y=mdt.stats.gaussian(x=x[i],
Expand All @@ -251,7 +258,8 @@
xlabel=r'$' + xlabel[i] + r'$ / ' + args.LUNIT,
ylabel=r'$p(' + xlabel[i] + r')$',
label="Fit",
color='black')
color='black',
)
plt.tight_layout()
pdf.savefig()
plt.close()
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71 changes: 42 additions & 29 deletions scripts/dynamics/plot_renewal_events_displ_vs_post0.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
#!/usr/bin/env python3


# This file is part of MDTools.
# Copyright (C) 2020 Andreas Thum
# Copyright (C) 2021 The MDTools Development Team and all contributors
# listed in the file AUTHORS.rst
#
# MDTools is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
Expand All @@ -18,6 +18,9 @@
# along with MDTools. If not, see <http://www.gnu.org/licenses/>.


__author__ = "Andreas Thum"


import sys
import os
from datetime import datetime
Expand All @@ -27,6 +30,8 @@
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import mdtools as mdt
import mdtools.plot as mdtplt # TODO: Replace deprecated functions
plt.style.use("default") # TODO: Use MDTools plotting style


if __name__ == '__main__':
Expand Down Expand Up @@ -319,7 +324,7 @@
axis = axes[1]

axis.axhline(y=0, color='black')
img = mdt.plot.scatter(
img = mdtplt.scatter(
ax=axis,
x=pos_t0,
y=displ.T[i],
Expand All @@ -331,7 +336,8 @@
xlabel=r'${}(t_0)$ / {}'.format(args.DIRECTION, args.LUNIT),
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
marker='x',
cmap='plasma')
cmap='plasma',
)
cbar = plt.colorbar(img, ax=axis)
cbar.set_label(label=r'$\tau_{renew}$ / ' + args.TUNIT,
fontsize=fontsize_labels)
Expand All @@ -346,18 +352,20 @@
length=0.5 * tick_length,
labelsize=0.8 * fontsize_ticks)

mdt.plot.vlines(ax=axis,
x=bins,
start=axis.get_ylim()[0],
stop=axis.get_ylim()[1],
xmin=args.XMIN,
xmax=args.XMAX,
ymin=args.YMIN,
ymax=args.YMAX,
color='black',
linestyle='dotted')

mdt.plot.plot(
mdtplt.vlines(
ax=axis,
x=bins,
start=axis.get_ylim()[0],
stop=axis.get_ylim()[1],
xmin=args.XMIN,
xmax=args.XMAX,
ymin=args.YMIN,
ymax=args.YMAX,
color='black',
linestyle='dotted',
)

mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=displ_means.T[i][1:],
Expand All @@ -369,9 +377,10 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r' \rangle$',
color='red',
marker='o')
marker='o',
)

mdt.plot.plot(
mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=msd_means.T[i][1:],
Expand All @@ -383,9 +392,10 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r'^2 \rangle$',
color='blue',
marker='^')
marker='^',
)

mdt.plot.plot(
mdtplt.plot(
ax=axis,
x=bins[1:] - np.diff(bins) / 2,
y=displ_vars.T[i][1:],
Expand All @@ -397,22 +407,25 @@
ylabel=r'$\Delta ' + ylabel[i] + r'(\tau_{renew})$ / ' + args.LUNIT,
label=r'$\langle \Delta ' + ylabel[i] + r'^2 \rangle - \langle \Delta ' + ylabel[i] + r' \rangle ^2$',
color='green',
marker='s')
marker='s',
)

axis.legend(loc='lower left',
numpoints=1,
frameon=True,
fontsize=fontsize_legend)

if args.INFILE2 is not None:
mdt.plot.plot(ax=axes[0],
x=data[:, 0],
y=data[:, 1],
xmin=args.XMIN,
xmax=args.XMAX,
ymin=np.min(data[:, 1]),
ymax=np.max(data[:, 1]),
color='black')
mdtplt.plot(
ax=axes[0],
x=data[:, 0],
y=data[:, 1],
xmin=args.XMIN,
xmax=args.XMAX,
ymin=np.min(data[:, 1]),
ymax=np.max(data[:, 1]),
color='black',
)
axes[0].xaxis.set_visible(False)
axes[0].yaxis.set_visible(False)
axes[0].spines['bottom'].set_visible(False)
Expand Down

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