def get_unique_atomtypes(fit_dir):
"""
given a list of xyz-files, determine the atomic numbers that are present
in any file. For each atom combination a repulsive potential is fitted.
"""
xyz_filenames = glob.glob("%s/FIT_PATHS/*.xyz" % fit_dir)
unique_atomtypes = []
for f in xyz_filenames:
for atomlist in XYZ.read_xyz_it(f):
# atomic numbers in first frame
for Zi, posi in atomlist:
if not Zi in unique_atomtypes:
unique_atomtypes.append(Zi)
unique_atomtypes = np.sort(unique_atomtypes)
print("")
print("Atom Types:")
print("-----------")
for Zi in unique_atomtypes:
print(" %s" % AtomicData.atom_names[Zi - 1])
print("")
return unique_atomtypes
def pyrene_dimer_analysis(xyz_traj_file, out_file, qmmm_partitioning=None):
"""
This function analyses the relative displacement between two pyrene units in a dimer.
'xyz_traj_file' is a xyz-file that contains the geometries for each time step.
The horizontal (Rx,Ry) and vertical (Rz) displacements are written to a table in 'out_file'.
If the file contains additional molecules (e.g. MM molecules), the atom indeces belonging
to the dimer should be specified as a list in qmmm_partioning.
"""
fh = open(out_file, "w")
print("# TSTEP R_X / Angstrom R_Y / Angstrom R_Z / Angstrom",
file=fh)
# process one geometry after the other
for i, atomlist in enumerate(XYZ.read_xyz_it(xyz_traj_file)):
if qmmm_partitioning != None:
# select the atoms belonging to the dimer pair
atomlist = [atomlist[j] for j in qmmm_partitioning]
nat = len(atomlist)
assert nat == 52, "Pyrene dimer should contain 52 atoms!"
#
monomer1 = atomlist[:nat / 2]
monomer2 = atomlist[nat / 2:]
# compute the enclosing box for each pyrene unit
box1 = MoleculeBox(monomer1)
box2 = MoleculeBox(monomer2)
# distance between the centers of the enclosing boxes
vec = box2.center - box1.center
# decompose distance between centers into a part that is perpendicular to the
# plane of the 1st monomer and another one that is horizontal to it by projecting
# onto the z-axis of the box belonging to the 1st monomer
vec_vertical = np.dot(box1.axes[2], vec) * box1.axes[2]
## The x-axis is parallel to the vector passing through atoms C12 and C10
#xaxis = np.array(atomlist[9][1]) - np.array(atomlist[11][1])
# In the geometries with periodic boundary conditions the x-axis passes
# through atoms C3 and C23
xaxis = np.array(atomlist[2][1]) - np.array(atomlist[22][1])
# remove z-component from x-axis
xaxis -= np.dot(box1.axes[2], xaxis) * box1.axes[2]
xaxis /= la.norm(xaxis)
## The y-axis is parallel to the vector passing through atoms C11 and C13
#yaxis = np.array(atomlist[10][1]) - np.array(atomlist[12][1])
# In the geometries with periodic boundary conditions the y-axis passes
# through atoms C14 and C4
yaxis = np.array(atomlist[13][1]) - np.array(atomlist[3][1])
yaxis -= np.dot(box1.axes[2], yaxis) * box1.axes[2]
yaxis /= la.norm(yaxis)
vec_horizontal = vec - vec_vertical
Rx = np.dot(xaxis, vec_horizontal) * AtomicData.bohr_to_angs
Ry = np.dot(yaxis, vec_horizontal) * AtomicData.bohr_to_angs
Rz = la.norm(vec_vertical) * AtomicData.bohr_to_angs
print("%d %8.6f %8.6f %8.6f" % (i, Rx, Ry, Rz), file=fh)
fh.close()
for arg in args:
try:
atom_ids = [int(i)-1 for i in arg.split()]
coord_specs.append(atom_ids)
except ValueError:
# probably this argument is an xyz-file
assert ".xyz" in arg, "%s does not have .xyz suffix nor is it a list of integer" % arg
xyz_files.append(arg)
if len(xyz_files) < 1:
print("At least one xyz-file should be specified!")
exit(-1)
coords_trajs = []
for f in xyz_files:
coords_timeseries = []
for geom in XYZ.read_xyz_it(f):
coords = []
for atom_ids in coord_specs:
coords.append( get_coord(geom, atom_ids) )
coords_timeseries.append(coords)
coords_trajs.append( np.array(coords_timeseries) )
ntrajs = len(xyz_files)
nsteps = min(list(map(len, coords_trajs))) # find length of shorted trajectories
ncoords = len(coord_specs)
#
coords_data = np.zeros((ntrajs,nsteps,ncoords), dtype=float)
for i in range(0, ntrajs):
coords_data[i,:,:] = coords_trajs[i][:nsteps,:]
# average over trajectories
coords_avg = np.sum(coords_data, axis=0) / float(ntrajs)
show a plot of the calculated bond indeces
"""
from matplotlib.pyplot import plot, xlabel, ylabel, legend, show, savefig
from numpy import loadtxt
b = loadtxt(out_file)
(ntraj, ndist) = b.shape
xlabel("MD steps")
ylabel("bond index $b_i = \\sum_j r_{ij}$")
for n in range(0, ndist):
at = AtomicData.atom_names[atomlist[n][0] - 1]
plot(b[:, n], label="%s%d" % (at, n))
legend()
savefig(out_file + ".png")
show()
if __name__ == "__main__":
if len(sys.argv) < 3:
print "Usage: %s <xyz-file with list of nuclear geometries> <output file with bond indeces>" % sys.argv[
0]
exit(-1)
xyz_file = sys.argv[1]
out_file = sys.argv[2]
fh = open(out_file, 'w')
for atomlist in XYZ.read_xyz_it(xyz_file):
for bi in bond_indeces(atomlist):
print >> fh, "%.7f " % bi,
print >> fh, ""
fh.close()
plot_bond_indeces(atomlist, out_file)
# all isomers should have different connectivities
n = len(isomers)
for i in range(0, n):
for j in range(i + 1, n):
if np.sum(
(isomer_connectivities[i] - isomer_connectivities[j])**2) == 0:
print "WARNING: Isomer %d and %d in file '%s' have the same adjacency matrices!" % (
i + 1, j + 1, isomer_file)
fh = open(opts.out_file, "w")
print >> fh, "# isomer indeces refer to the geometries in '%s'" % isomer_file
print >> fh, "# GEOMETRY ISOMER(S)"
print "classify geometries by comparison with isomers"
for i_step, atomlist in enumerate(XYZ.read_xyz_it(dynamics_file)):
if i_step % opts.step != 0:
continue
# Each fragment has to be analyzed separately separately
fragments = MolecularGraph.disconnected_fragments(atomlist,
hydrogen_bonds=True)
# The geometry is assigned the index of the isomer which it resembles.
# If the molecule consists of several fragments each fragment is assigned
# separately.
if len(fragments) == 1:
# disconnected_fragments sometimes messes up, ;(. If there is only one fragment,
# it is better to use the original ordering of the atoms.
