Browse Source

Merge branch '1.0'

Peter Colberg 1 year ago
parent
commit
5e1113b90a

+ 1
- 5
examples/confined_dimer/tools/cluster.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 from matplotlib.patches import Circle
13 13
 from matplotlib.collections import PatchCollection
@@ -24,10 +24,6 @@ parser.add_argument("--figsize", type=float, nargs=2, default=(6.0, 6.0), help="
24 24
 parser.add_argument("--count", type=int, default=4, help="minimum number of spheres per cluster")
25 25
 args = parser.parse_args()
26 26
 
27
-mpl.rc("pgf", texsystem="lualatex", preamble=(r"\usepackage{amsmath,amssymb,bm,txfonts}",))
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-mpl.rc("font", family="serif", serif=(), size=10)
29
-mpl.rc("legend", fontsize=10, borderpad=0.2, borderaxespad=0.1, labelspacing=0.2, columnspacing=1.0, handletextpad=0.2, handlelength=1, numpoints=1)
30
-
31 27
 fig = plt.figure(figsize=args.figsize)
32 28
 ax = fig.add_subplot(1, 1, 1)
33 29
 

+ 1
- 5
examples/confined_dimer/tools/cluster_size.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py
@@ -20,10 +20,6 @@ parser.add_argument("--average", type=int, default=1, help="interval of moving a
20 20
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="lualatex", preamble=(r"\usepackage{amsmath,amssymb,bm,txfonts}",))
24
-mpl.rc("font", family="serif", serif=(), size=10)
25
-mpl.rc("legend", fontsize=10, borderpad=0.2, borderaxespad=0.1, labelspacing=0.2, columnspacing=1.0, handletextpad=0.2, handlelength=1, numpoints=1)
26
-
27 23
 fig = plt.figure(figsize=args.figsize)
28 24
 ax = fig.add_subplot(1, 1, 1)
29 25
 

+ 1
- 5
examples/confined_dimer/tools/dimer_mean_square_displacement.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", nargs="+", help="input filenames")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
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-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input[0], "r") as f:
27 23
   g = f["dynamics/dimer/mean_square_displacement"]
28 24
   time = g["time"][:]

+ 1
- 5
examples/confined_dimer/tools/dimer_orientation_autocorrelation.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="fi
20 20
 parser.add_argument("--block", type=int, default=2, help="block level")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
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-mpl.rc("font", family="serif", serif=(), size=11)
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-mpl.rc("legend", fontsize=11, numpoints=1)
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-
27 23
 with h5.File(args.input[0], "r") as f:
28 24
   g = f["dynamics/dimer/orientation_autocorrelation"]
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   time = g["time"][:]

+ 1
- 5
examples/confined_dimer/tools/dimer_velocity_autocorrelation.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="fi
20 20
 parser.add_argument("--block", type=int, default=2, help="block level")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
24
-mpl.rc("font", family="serif", serif=(), size=11)
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-mpl.rc("legend", fontsize=11, numpoints=1)
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-
27 23
 with h5.File(args.input[0], "r") as f:
28 24
   g = f["dynamics/dimer/velocity_autocorrelation"]
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   time = g["time"][:]

+ 1
- 5
examples/single_dimer/tools/cylindrical_density.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import matplotlib.patches as patches
13 13
 import numpy as np
@@ -24,10 +24,6 @@ parser.add_argument("--species", type=int, help="solvent species")
24 24
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 3.), help="figure size")
25 25
 args = parser.parse_args()
26 26
 
27
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
28
-mpl.rc("font", family="serif", serif=(), size=11)
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-mpl.rc("legend", fontsize=11, numpoints=1)
30
-
31 27
 with h5.File(args.input[0], "r") as f:
32 28
   g = f["structure/solvent/cylindrical_density"]
33 29
   radial = g["radial"][:]

+ 1
- 5
examples/single_dimer/tools/cylindrical_velocity.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import matplotlib.patches as patches
13 13
 import numpy as np
@@ -23,10 +23,6 @@ parser.add_argument("--samples", type=int, default=100, help="minimum number of
23 23
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.5), help="figure size")
24 24
 args = parser.parse_args()
25 25
 
26
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
27
-mpl.rc("font", family="serif", serif=(), size=11)
28
-mpl.rc("legend", fontsize=10, numpoints=1)
29
-
30 26
 with h5.File(args.input[0], "r") as f:
31 27
   g = f["fields/solvent/cylindrical_velocity"]
32 28
   radial = g["radial"][:]

+ 1
- 5
examples/single_dimer/tools/dimer_force.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", help="input filenames")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
23
-mpl.rc("font", family="serif", serif=[], size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
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 with h5.File(args.input, "r") as f:
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   g = f["particles/dimer"]
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   r = g["position"]["value"]

+ 1
- 5
examples/single_dimer/tools/dimer_force_distribution.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -21,10 +21,6 @@ parser.add_argument("--range", type=float, nargs=2, default=(-100., 100.), help=
21 21
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
22 22
 args = parser.parse_args()
23 23
 
24
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
25
-mpl.rc("font", family="serif", serif=[], size=11)
26
-mpl.rc("legend", fontsize=11, numpoints=1)
27
-
28 24
 count = 0
29 25
 hist = np.zeros([args.nbin])
30 26
 mean = 0.

+ 1
- 5
examples/single_dimer/tools/dimer_mean_square_displacement.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", nargs="+", help="input filenames")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input[0], "r") as f:
27 23
   g = f["dynamics/dimer/mean_square_displacement"]
28 24
   time = g["time"][:]

+ 1
- 5
examples/single_dimer/tools/dimer_orientation_autocorrelation.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="fi
20 20
 parser.add_argument("--block", type=int, default=2, help="block level")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
24
-mpl.rc("font", family="serif", serif=(), size=11)
25
-mpl.rc("legend", fontsize=11, numpoints=1)
26
-
27 23
 with h5.File(args.input[0], "r") as f:
28 24
   g = f["dynamics/dimer/orientation_autocorrelation"]
29 25
   time = g["time"][:]

+ 1
- 5
examples/single_dimer/tools/dimer_velocity.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("input", help="input filename")
20 20
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
24
-mpl.rc("font", family="serif", serif=(), size=11)
25
-mpl.rc("legend", fontsize=11, numpoints=1)
26
-
27 23
 with h5.File(args.input, "r") as f:
28 24
   g = f["particles/dimer"]
29 25
   r = g["position"]["value"]

+ 1
- 5
examples/single_dimer/tools/dimer_velocity_autocorrelation.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="fi
20 20
 parser.add_argument("--block", type=int, default=2, help="block level")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
24
-mpl.rc("font", family="serif", serif=(), size=11)
25
-mpl.rc("legend", fontsize=11, numpoints=1)
26
-
27 23
 with h5.File(args.input[0], "r") as f:
28 24
   g = f["dynamics/dimer/velocity_autocorrelation"]
29 25
   time = g["time"][:]

+ 1
- 5
examples/single_dimer/tools/dimer_velocity_distribution.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -22,10 +22,6 @@ parser.add_argument("--range", type=float, nargs=2, default=(-0.1, 0.1), help="r
22 22
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
23 23
 args = parser.parse_args()
24 24
 
25
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
26
-mpl.rc("font", family="serif", serif=[], size=11)
27
-mpl.rc("legend", fontsize=11, numpoints=1)
28
-
29 25
 count = 0
30 26
 hist = np.zeros([args.nbin])
31 27
 mean = 0.

+ 1
- 5
examples/single_dimer/tools/polar_density.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("--radius", type=float, required=True, help="radius")
20 20
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 6.), help="figure size")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
24
-mpl.rc("font", family="serif", serif=(), size=11)
25
-mpl.rc("legend", fontsize=11, numpoints=1)
26
-
27 23
 with h5.File(args.input[0], "r") as f:
28 24
   g = f["structure/solvent/polar_density"]
29 25
   polar = g["polar"][:]

+ 1
- 5
examples/single_dimer/tools/radial_density.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", nargs="+", help="input filenames")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 6.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", texsystem="xelatex", preamble=(r"\usepackage{amsmath,bm,txfonts}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input[0], "r") as f:
27 23
   g = f["structure/solvent/radial_density"]
28 24
   radial = g["radial"][:]

+ 1
- 5
tools/center_of_mass_velocity.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -20,10 +20,6 @@ parser.add_argument("input", help="input filename")
20 20
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
21 21
 args = parser.parse_args()
22 22
 
23
-mpl.rc("pgf", preamble=(r"\usepackage{amsmath,amssymb,bm}",))
24
-mpl.rc("font", family="serif", serif=(), size=11)
25
-mpl.rc("legend", fontsize=11, numpoints=1)
26
-
27 23
 with h5.File(args.input, "r") as f:
28 24
   g = f["observables/center_of_mass_velocity"]
29 25
   value = g["value"][:]

+ 1
- 5
tools/kinetic_energy.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", help="input filename")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", preamble=(r"\usepackage{amsmath,amssymb,bm}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input, "r") as f:
27 23
   g = f["observables/kinetic_energy"]
28 24
   value = g["value"][:]

+ 1
- 5
tools/potential_energy.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", help="input filename")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", preamble=(r"\usepackage{amsmath,amssymb,bm}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input, "r") as f:
27 23
   g = f["observables/potential_energy"]
28 24
   value = g["value"][:]

+ 1
- 5
tools/species.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", help="input filename")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", preamble=(r"\usepackage{amsmath,amssymb,bm}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input, "r") as f:
27 23
   g = f["observables/solvent/species"]
28 24
   value = g["value"][:]

+ 1
- 5
tools/temperature.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", help="input filename")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", preamble=(r"\usepackage{amsmath,amssymb,bm}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input, "r") as f:
27 23
   g = f["observables/temperature"]
28 24
   value = g["value"][:]

+ 1
- 5
tools/total_energy.py View File

@@ -7,7 +7,7 @@
7 7
 #
8 8
 
9 9
 import matplotlib as mpl
10
-mpl.use("pgf")
10
+mpl.use("agg")
11 11
 import matplotlib.pyplot as plt
12 12
 import numpy as np
13 13
 import h5py as h5
@@ -19,10 +19,6 @@ parser.add_argument("input", help="input filename")
19 19
 parser.add_argument("--figsize", type=float, nargs=2, default=(6., 4.), help="figure size")
20 20
 args = parser.parse_args()
21 21
 
22
-mpl.rc("pgf", preamble=(r"\usepackage{amsmath,amssymb,bm}",))
23
-mpl.rc("font", family="serif", serif=(), size=11)
24
-mpl.rc("legend", fontsize=11, numpoints=1)
25
-
26 22
 with h5.File(args.input, "r") as f:
27 23
   g = f["observables/total_energy"]
28 24
   value = g["value"][:]

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