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Add atomSize keyword to the ppafm-plot-results.py #390

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Add atomSize keyword to the ppafm-plot-results.py #390

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495ffd4
add input_plot.xyz to demostrate how to plot with atoms overlayed
huangchieh May 12, 2026
c9dd9d2
add a line to demostrate how to plot with atoms overlayed
huangchieh May 12, 2026
4189502
add a line to demostrate how to plot with atoms overlayed
huangchieh May 12, 2026
35ad149
add atomSize keyword to fix issue #389
huangchieh May 12, 2026
9bf5730
set default size to 0.15
huangchieh May 12, 2026
dc4cdcf
formating
huangchieh May 12, 2026
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1 change: 1 addition & 0 deletions examples/PTCDA_single/example_ptcda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def example_ptcda_single():
generate_elff_point_charges(["--input", "PTCDA.xyz", "--tip", "s"])
relaxed_scan(["--klat", "0.5", "--charge", "-0.10"])
plot_results(["--klat", "0.5", "--charge", "-0.10", "--arange", "0.5", "2.0", "2", "--df"])
plot_results(["--klat", "0.5", "--charge", "-0.10", "--arange", "0.5", "2.0", "2", "--df", "--atoms", "--atomSize", "0.15"])
Comment on lines 18 to +20


if __name__ == "__main__":
Expand Down
40 changes: 40 additions & 0 deletions examples/PTCDA_single/input_plot.xyz
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
38
Same as PTCDA.xyz for demonstration. You may also select a subset of atoms, such as the top layer in a multilayer structure.
1 7.045637 6.005613 9.947120 +0.15
1 9.897932 2.612194 9.943020 +0.15
1 8.275515 4.509521 9.942140 +0.15
1 12.336543 10.425948 9.938079 +0.15
1 10.715512 12.324056 9.934680 +0.15
1 5.466648 7.962514 9.914780 +0.15
1 13.565891 8.930334 9.897579 +0.15
1 15.144142 6.972851 9.869899 +0.15
6 8.460736 9.700870 9.961119 0.0
6 11.676272 3.889107 9.958080 0.0
6 9.391591 8.577521 9.956319 0.0
6 12.150413 5.235732 9.956060 0.0
6 8.879125 7.226835 9.953480 0.0
6 9.803928 6.100850 9.951800 0.0
6 11.219312 6.358704 9.945880 0.0
6 8.935446 11.048403 9.945498 0.0
6 10.806843 8.835349 9.945320 0.0
6 12.627057 2.771961 9.945019 0.0
6 11.731363 7.709653 9.932579 0.0
6 14.500405 4.381420 9.928359 0.0
6 10.264659 3.653138 9.924319 0.0
6 7.056579 9.446457 9.921079 0.0
6 7.456229 7.025884 9.919660 0.0
6 10.348140 11.283277 9.917400 0.0
6 7.986501 12.165751 9.914699 0.0
6 9.355124 4.729154 9.914160 0.0
6 6.111767 10.553017 9.908559 0.0
6 11.256785 10.206996 9.908120 0.0
6 13.555310 5.488973 9.906280 0.0
6 6.563246 8.112073 9.905699 0.0
6 13.153859 7.910466 9.873319 0.0
6 14.047411 6.822740 9.865199 0.0
8 14.000075 3.084865 10.031318 -0.2
8 6.611246 11.853327 9.959440 -0.2
8 15.736978 4.488921 9.837521 -0.2
8 12.372576 1.563458 9.825279 -0.2
8 4.874570 10.445600 9.820059 -0.2
8 8.241626 13.369424 9.801439 -0.2
3 changes: 3 additions & 0 deletions examples/PTCDA_single/run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,3 +9,6 @@ ppafm-relaxed-scan -k 0.5 -q -0.10

# ======= STEP 3 : Plot the results
ppafm-plot-results -k 0.5 -q -0.10 --arange 0.5 2.0 2 --df

# ======= STEP 4 : Plot the results with atoms overlayed
ppafm-plot-results -k 0.5 -q -0.10 --arange 0.5 2.0 2 --df --atoms --atomSize 0.15
Comment on lines 11 to +14
24 changes: 11 additions & 13 deletions ppafm/cli/plot_results.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,6 @@
# this makes it run without Xserver (e.g. on supercomputer) # see http://stackoverflow.com/questions/4931376/generating-matplotlib-graphs-without-a-running-x-server


atom_size = 0.15


def main(argv=None):
# fmt: off
parser = common.CLIParser( description="Plot results for a scan with a specified charge, amplitude, and spring constant.Images are saved in folder Q{charge}K{klat}/Amp{Amplitude}." )
Expand All @@ -34,6 +31,7 @@ def main(argv=None):
parser.add_argument( "--Fz", action="store_true", help="Plot images for z-component of the (short-range) force acting on the tip in eV/Angstrom")
parser.add_argument( "--pos", action="store_true", help="Save probe particle positions" )
parser.add_argument( "--atoms", action="store_true", help="Plot atoms to images")
parser.add_argument( "--atomSize", action="store", type=float, default=0.15, help="Size of atoms in images")
parser.add_argument( "--bonds", action="store_true", help="Plot bonds to images")
parser.add_argument( "--cbar", action="store_true", help="Plot colorbars to images")
parser.add_argument( "--WSxM", action="store_true", help="Save frequency shift into WsXM *.dat files" )
Expand Down Expand Up @@ -146,7 +144,7 @@ def main(argv=None):
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
markersize=2.0,
cbar=opt_dict["cbar"],
)
Expand All @@ -167,7 +165,7 @@ def main(argv=None):
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
)

Expand All @@ -178,7 +176,7 @@ def main(argv=None):
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
)

Expand All @@ -189,7 +187,7 @@ def main(argv=None):
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
)

Expand All @@ -203,7 +201,7 @@ def main(argv=None):
extent=extent,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
)

Expand Down Expand Up @@ -329,7 +327,7 @@ def main(argv=None):
cmap=parameters.colorscale,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
cbar_label="df [Hz]",
)
Expand All @@ -354,7 +352,7 @@ def main(argv=None):
cmap=parameters.colorscale,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
)

Expand Down Expand Up @@ -386,7 +384,7 @@ def main(argv=None):
cmap=parameters.colorscale_kpfm,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
symmetric_map=True,
V0=args.V0,
Expand All @@ -401,7 +399,7 @@ def main(argv=None):
cmap=parameters.colorscale_kpfm,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
symmetric_map=False,
cbar_label="V_LCPD [V]",
Expand Down Expand Up @@ -436,7 +434,7 @@ def main(argv=None):
cmap=parameters.colorscale,
atoms=atoms,
bonds=bonds,
atomSize=atom_size,
atomSize=args.atomSize,
cbar=opt_dict["cbar"],
cbar_label="Fz [eV/Angstrom]",
)
Expand Down
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