def main():
parser = argparse.ArgumentParser()
parser.add_argument('-n', '--n_trajs', help='number of trajectories. Default=10', type=int, default=10)
parser.add_argument('-t', '--traj_length', help='trajectories length. Default=10000', type=int, default=10000)
args = parser.parse_args()
# these could be configured
kT = 15.0
dt = 0.1
mGamma = 1000.0
forcecalculator = muller.muller_force()
project = Project({'ConfFilename': os.path.join(mullermsm.__path__[0], 'conf.pdb'),
'NumTrajs': args.n_trajs,
'ProjectRootDir': '.',
'TrajFileBaseName': 'trj',
'TrajFilePath': 'Trajectories',
'TrajFileType': '.lh5',
'TrajLengths': [args.traj_length]*args.n_trajs})
if os.path.exists('ProjectInfo.h5'):
print >> sys.stderr, "The file ./ProjectInfo.h5 already exists. I don't want to overwrite anything, so i'm backing off"
sys.exit(1)
try:
os.mkdir('Trajectories')
except OSError:
print >> sys.stderr, "The directory ./Trajectores already exists. I don't want to overwrite anything, so i'm backing off"
sys.exit(1)
for i in range(args.n_trajs):
print 'simulating traj %s' % i
# select initial configs randomly from a 2D box
initial_x = [random.uniform(-1.5, 1.2), random.uniform(-0.2, 2)]
print 'starting conformation from randomly sampled points (%s, %s)' % (initial_x[0], initial_x[1])
print 'propagating for %s steps on the Muller potential with a Langevin integrator...' % args.traj_length
positions = muller.propagate(args.traj_length, initial_x, kT, dt, mGamma, forcecalculator)
# positions is N x 2, but we want to make it N x 1 x 3 where the additional
# column is just zeros. This way, being N x 1 x 3, it looks like a regular MD
# trajectory that would be N_frames x N_atoms x 3
positions3 = np.hstack((positions, np.zeros((len(positions),1)))).reshape((len(positions), 1, 3))
t = Trajectory.LoadTrajectoryFile(project['ConfFilename'])
t['XYZList'] = positions3
t.SaveToLHDF(project.GetTrajFilename(i))
print 'saving trajectory to %s' % project.GetTrajFilename(i)
project.SaveToHDF('ProjectInfo.h5')
print 'saved ProjectInfo.h5 file'
pickle.dump(metric.EuclideanMetric(), open('metric.pickl', 'w'))
print 'saved metric.pickl'
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-g', '--generators', default='Data/Gens.lh5', help='Path to Gens.lh5')
parser.add_argument('-p', '--project', default='ProjectInfo.h5', help='Path to ProjectInfo.h5')
parser.add_argument('-s', '--stride', default=5, type=int, help='Stride to plot the data at')
args = parser.parse_args()
gens = Trajectory.LoadTrajectoryFile(args.generators)
gens_x = gens['XYZList'][:,0,0]
gens_y = gens['XYZList'][:,0,1]
points = np.array([gens_x, gens_y]).transpose()
tri = Delaunay(points)
PL = []
for p in points:
PL.append(Voronoi.Site(x=p[0],y=p[1]))
v,eqn,edges,wtf = Voronoi.computeVoronoiDiagram(PL)
edge_points=[]
for (l,x1,x2) in edges:
if x1>=0 and x2>=0:
edge_points.append((v[x1],v[x2]))
lines = LineCollection(edge_points, linewidths=0.5, color='k')
fig = pp.figure()
ax = fig.add_subplot(111)
fig.gca().add_collection(lines)
maxx, minx= np.max(gens_x), np.min(gens_x)
maxy, miny = np.max(gens_y), np.min(gens_y)
# plot the background
plot_v(minx=minx, maxx=maxx, miny=miny, maxy=maxy, ax=ax)
pp.xlim(minx, maxx)
pp.ylim(miny, maxy)
# plot a single trajectory
p = Project.LoadFromHDF(args.project)
t = p.LoadTraj(0)
x = t['XYZList'][:,0,0][::args.stride]
y = t['XYZList'][:,0,1][::args.stride]
cm = pp.get_cmap('spectral')
n_points = len(x)
ax.set_color_cycle([cm(1.*i/(n_points-1)) for i in range(n_points-1)])
for i in range(n_points-1):
ax.plot(x[i:i+2],y[i:i+2])
pp.title('Voronoi Microstate Decomposition, with first trajectory')
pp.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-p', '--project', default='ProjectInfo.h5')
parser.add_argument(
'-t',
'--trajectories',
nargs='+',
help='''Supply either the path to a trajectory file (i.e. Data/Gens.lh5),
or an integer, which will be interepreted as a trajectory index
into the trajectories that accompany the project. default: plot all
of the trajectories''',
default=['-1'])
args = parser.parse_args()
p = Project.LoadFromHDF(args.project)
# record the bounding box of the points so that we know
# what to render for the background
maxx, minx, maxy, miny = 1.2, -1.5, 2, -0.2
# if -1 is included, add in ALL of the trajectories
if '-1' in args.trajectories:
args.trajectories.remove('-1')
args.trajectories.extend(range(p['NumTrajs']))
# remove duplicates
args.trajectories = set(args.trajectories)
for requested in args.trajectories:
if os.path.exists(str(requested)):
traj = Trajectory.LoadTrajectoryFile(str(requested))
print 'plotting %s' % requested
markersize = 50
else:
try:
i = int(requested)
traj = p.LoadTraj(i)
print 'plotting %s' % i
markersize = 5
except ValueError:
print >> sys.stderr, 'I couldnt figure out how to deal with the argument %s' % requested
continue
except IOError as e:
print >> sys.stderr, str(e)
continue
xyz = traj['XYZList']
x = xyz[:, 0, 0]
y = xyz[:, 0, 1]
maxx, maxy = max(np.max(x), maxx), max(np.max(y), maxy)
minx, miny = min(np.min(x), minx), min(np.min(y), miny)
pp.plot(x, y, '.', markersize=markersize, alpha=0.5)
plot_v(minx=minx, maxx=maxx, miny=miny, maxy=maxy)
pp.show()
