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example

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Daniel Bauer
2018-06-17 22:39:35 +02:00
parent f905853d29
commit 510cc6f04b
4 changed files with 54 additions and 38 deletions
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2
examples/data/sim.sh
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@@ -18,6 +18,6 @@ sed -i -e "s/LAMBDA2/${lambda2}/g" $FOLDER/plumed.dat
cd $FOLDER
source /usr/local/gromacs/bin/GMXRC
gmx --quiet mdrun -deffnm topol -plumed plumed.dat -nsteps 100000 2>&1
gmx --quiet mdrun -deffnm topol -plumed plumed.dat -nsteps 250000 2>&1
cd ../..

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31
examples/example.py Normal file → Executable file
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@@ -1,3 +1,4 @@
#!/usr/bin/env python3
import os
from copy import deepcopy
@@ -110,7 +111,7 @@ class MyUmbrellaRunner(WHAM2DRunner):
cum_frames = [0]
def after_run_hook(self):
filename = "tmp/pmf_{}.pdf".format(self.num_iterations)
filename = "tmp/pmf_{}.pdf".format("%02d" % self.num_iterations)
print("Writing new pmf to {}".format(filename))
pmf_to_plot = deepcopy(self.pmf)
pmf_to_plot[pmf_to_plot < 0] = None
@@ -128,13 +129,13 @@ class MyUmbrellaRunner(WHAM2DRunner):
ax1.set_xlabel("Cycles")
ax1.set_ylabel("Number of umbrella Windows")
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)
# 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("$\psi$")
@@ -163,13 +164,13 @@ class MyUmbrellaRunner(WHAM2DRunner):
runner = MyUmbrellaRunner()
runner.WHAM_EXEC = "/opt/wham/wham-2d/wham-2d"
runner.cvs = np.array([
(-3, 3, 0.2),
(-3, 3, 0.2),
(-3, 3, 0.3),
(-3, 3, 0.3),
])
runner.cvs_init = (-1.4, 1.4)
runner.E_min = 2
runner.E_max = 50
runner.E_incr = 5
runner.max_iterations = 30
runner.cvs_init = (-1.8, 1.8)
runner.E_min = 5
runner.E_max = 100
runner.E_incr = 10
runner.max_iterations = 100
runner.run()