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some bugfixes

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Daniel Bauer
2018-06-17 13:56:50 +02:00
parent 025f397bc1
commit 3187ee7345
2 changed files with 48 additions and 33 deletions
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2
adaptiveumbrella/runner.py
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@@ -150,10 +150,10 @@ class UmbrellaRunner():
new_frames = self._get_new_frames(self.pmf, self.sample_list, root_frames)
self.num_iterations = 0
self.E = self.E_min
# outer main loop: increase E and calculate PMF until E > E_max
while True:
self.E = self.E_min
# stop if max iterations is reached
self.num_iterations += 1

67
examples/example.py
View File

@@ -55,10 +55,14 @@ class WHAM2DRunner(UmbrellaRunner):
periodicity_y = "pi"
tolerance = 0.1
frames_x, frames_y = 1002, 1002
min_x = self.cvs[0][0]
max_x = self.cvs[0][1]
min_y = self.cvs[1][0]
max_y = self.cvs[1][1]
# min_x = self.cvs[0][0]
# max_x = self.cvs[0][1]
# min_y = self.cvs[1][0]
# max_y = self.cvs[1][1]
min_x = -3
max_x = 3
min_y = -3
max_y = 3
cmd = "{exec} Px={px} {min_x} {max_x} {frames_x} Py={py} {min_y} {max_y} {frames_y} {tol} 298 0 {metafile} {outfile} 0".format(
exec=self.WHAM_EXEC,
@@ -102,31 +106,42 @@ class WHAM2DRunner(UmbrellaRunner):
class MyUmbrellaRunner(WHAM2DRunner):
cum_frames = [0]
def after_run_hook(self):
filename = "tmp/pmf_{}.pdf".format(self.num_iterations)
print("Writing new pmf to {}".format(filename))
pmf_to_plot = deepcopy(self.pmf.T)
pmf_to_plot = deepcopy(self.pmf)
pmf_to_plot[pmf_to_plot < 0] = None
frames_to_plot = deepcopy(self.sample_list.T)
frames_to_plot[frames_to_plot == 0] = None
pmf_to_plot[self.sample_list == 0] = None
pmf_to_plot = pmf_to_plot.T
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)
self.cum_frames.append(len(self.sample_list[self.sample_list > 0]))
fig, (ax0, ax1) = plt.subplots(ncols=2)
im = ax0.imshow(pmf_to_plot, origin='lower', cmap='jet')
cb = fig.colorbar(im, ax=ax0, orientation='horizontal', pad=0.15)
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)
ax1.plot(self.cum_frames, linewidth=0.5, marker="o", color='black')
ax1.set_xlabel("Cycles")
ax1.set_ylabel("Number of umbrella Windows")
plt.savefig(filename)
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 ]
ax0.set_yticks(tick_positions)
ax0.set_yticklabels(tick_labels)
ax0.set_xticks(tick_positions)
ax0.set_xticklabels(tick_labels)
ax0.set_ylabel("$\phi$")
ax0.set_xlabel("$\psi$")
fig.subplots_adjust(wspace=.5)
plt.savefig(filename, bbox_inches='tight', dpi=200)
os.system("cp {} {}".format(filename, "tmp/pmf_current.pdf"))
@@ -151,10 +166,10 @@ runner.cvs = np.array([
(-3, 3, 0.2),
(-3, 3, 0.2),
])
runner.cvs_init = (1.4, -1.4)
runner.E_min = 10
runner.E_max = 100
runner.E_incr = 10
runner.max_iterations = 1
runner.cvs_init = (-1.4, 1.4)
runner.E_min = 2
runner.E_max = 50
runner.E_incr = 5
runner.max_iterations = 30
runner.run()