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only sample neighboring windows

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Daniel Bauer
2018-06-17 11:54:25 +02:00
parent 0c2cd3fc0a
commit 025f397bc1
3 changed files with 81 additions and 46 deletions
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33
examples/example.py
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@@ -4,7 +4,9 @@ from copy import deepcopy
import matplotlib.pyplot as plt
import numpy as np
from adaptiveumbrella.runner import UmbrellaRunner
import sys
sys.path.append('..')
from adaptiveumbrella.runner import UmbrellaRunner
class WHAM2DRunner(UmbrellaRunner):
@@ -105,18 +107,25 @@ class MyUmbrellaRunner(WHAM2DRunner):
print("Writing new pmf to {}".format(filename))
pmf_to_plot = deepcopy(self.pmf.T)
pmf_to_plot[pmf_to_plot < 0] = None
plt.figure()
plt.imshow(pmf_to_plot, origin="bottom", cmap='jet')
ticks = [(x,x) for x in [-3, -2, -1, 0, 1, 2, 3]]
tick_positions = [ self._get_index_for_lambdas(x)[0] for x in ticks ]
tick_labels = [ str(x[0]) for x in ticks ]
plt.xticks(tick_positions, tick_labels)
plt.yticks(tick_positions, tick_labels)
frames_to_plot = deepcopy(self.sample_list.T)
frames_to_plot[frames_to_plot == 0] = None
cb = plt.colorbar(pad=0.1)
fig, (ax0, ax1) = plt.subplots(ncols=2, sharey=True)
im = ax0.imshow(pmf_to_plot, origin="bottom", cmap='jet')
cb = fig.colorbar(im, ax=ax0)
cb.set_label("kJ/mol")
im2 = ax1.imshow(frames_to_plot, origin="bottom")
cb2 = fig.colorbar(im2, ax=ax1, ticks=np.arange(0, self.max_iterations))
cb.set_label("cycle")
# ticks = [(x,x) for x in [-3, -2, -1, 0, 1, 2, 3]]
# tick_positions = [ self._get_index_for_lambdas(x)[0] for x in ticks ]
# tick_labels = [ str(x[0]) for x in ticks ]
# ax1.set_xticks(tick_positions, tick_labels)
# ax1.set_yticks(tick_positions, tick_labels)
# ax2.set_xticks(tick_positions, tick_labels)
# ax2.set_yticks(tick_positions, tick_labels)
plt.savefig(filename)
os.system("cp {} {}".format(filename, "tmp/pmf_current.pdf"))
@@ -146,6 +155,6 @@ runner.cvs_init = (1.4, -1.4)
runner.E_min = 10
runner.E_max = 100
runner.E_incr = 10
runner.max_iterations = 30
runner.max_iterations = 1
runner.run()