def main(filename, outname, nframes=-1, natoms=-1):
"""
Perform analysis of dipoles in LAMMPS trajectory
:param lammpstrj: Filename of LAMMPS trajectory
:return: Number of frames in trajectory
"""
reader = FrameReader(filename)
if natoms < 0:
natoms = reader.total_atoms
else:
natoms = min(natoms, reader.total_atoms)
if nframes < 0:
nframes = reader.total_frames
else:
nframes = min(nframes, reader.total_frames)
frame = Frame(natoms)
with FrameWriter(outname) as writer:
for i in xrange(nframes):
# Read in frame from trajectory and process
progressBar(i, nframes)
reader.readFrame(i, frame)
frame.centreOnMolecule(1)
writer.writeFrame(i, frame)
return nframes
def main(filename, nframes=-1, natoms=-1):
"""
Perform analysis of dipoles in LAMMPS trajectory
:param lammpstrj: Filename of LAMMPS trajectory
:return: Number of frames in trajectory
"""
np.set_printoptions(precision=3, suppress=True)
reader = FrameReader(filename)
if natoms < 0:
natoms = reader.total_atoms
else:
natoms = min(natoms, reader.total_atoms)
if nframes < 0:
nframes = reader.total_frames
else:
nframes = min(nframes, reader.total_frames)
angle1 = np.zeros((nframes, 6))
angle2 = np.zeros((nframes, 6))
improper = np.zeros((nframes, 6))
angle3 = np.zeros((nframes, 6))
# center = []
center_ang = np.zeros((nframes, 6))
center_imp = np.zeros((nframes, 6))
frame = Frame(natoms)
print(nframes)
for i in xrange(nframes):
# Read in frame from trajectory and process
if i % 10 == 0:
progressBar(i, nframes)
reader.readFrame(i, frame)
frame.centreOnMolecule(1)
angle1_tmp = calcAnglesAll(frame)
angle2_tmp = calcAnglesAll(frame, 3)
angle3_tmp = calcAnglesPlane(frame)
improper_tmp = calcImpropersAll(frame)
center_ang_tmp, center_imp_tmp = calcConeCenters(frame)
# center.append([])
# center[i].append(calcConeCenters(frame))
# frame.show_atoms(0,6)
if not np.any(angle1_tmp):
print("AAAAAGH!!!!")
for j in xrange(6):
angle1[i, j] = angle1_tmp[j]
angle2[i, j] = angle2_tmp[j]
improper[i, j] = improper_tmp[j]
angle3[i, j] = angle3_tmp[j]
center_ang[i, j] = center_ang_tmp[j]
center_imp[i, j] = center_imp_tmp[j]
for j in xrange(6):
print("-" * 5)
print(boltzmannInvert(angle1[:, j]))
print(boltzmannInvert(angle2[:, j]))
print(boltzmannInvert(angle3[:, j]))
print(boltzmannInvert(improper[:, j]))
# plotHistogram(reduceArrays(improper[:, j]))
np.savetxt("arr1.dat", angle1)
np.savetxt("arr2.dat", angle2)
np.savetxt("arr3.dat", angle3)
np.savetxt("imp1.dat", improper)
np.savetxt("center_imp.dat", center_imp)
np.savetxt("center_ang.dat", center_ang)
# for i in range(nframes):
# print("Frame " + str(i+1) + ":")
# for j in range(5):
# print(" Bead " + str(j+1) + ":" + str(center[i][0][j]))
# analyseAngles(angle1)
# analyseAngles(angle2)
return nframes
