def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-fl", "--folder", \
help="Folder containing data, as in /local/duman/SIMULATIONS/Cells_in_LAMMPS/.../")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/MOVIES/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Cells_in_LAMMPS/MOVIES/")
parser.add_argument("-ti","--init_time", nargs="?", const=10, type=int, \
help="First frame of the video (in terms of frame number), you can also leave it empty")
parser.add_argument("-tf","--fin_time", nargs="?", const=2000, type=int, \
help="Last frame of the video (in terms of frame number), you can also leave it empty")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### read the data and general information from the folder
sim, cells, beads = read_write.read_h5_file(args.folder)
beads.get_img_pos(sim.lx)
print "folder = ", args.folder
### plot the data in the given time window
plot_frames(beads, sim, args.init_time, args.fin_time, args.savebase,
args.save_eps)
return
def main():
### get the command line arguments
args = get_args()
### read the data and general information from the folder
beads, pols, sim = read_write.read_h5_file(args.folder)
print "folder = ", args.folder
print "Calculating image positions of beads"
beads.xi = misc_tools.get_img_pos(beads.xu, sim.lx)
if args.colorid == "orient":
print "Calculating bond orientations"
beads.calc_bond_orientations(beads.xu, \
sim.nsteps, sim.nbeads, sim.npols, sim.nbpp)
elif args.colorid == "id":
print "Generating polymer identities of beads"
beads.get_pol_ids(sim.nbeads, sim.nbpp)
### plot the data in the given time window
plot_frames(beads, sim, args.init_time, args.fin_time, \
args.savebase, args.colorid)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-fl", "--folder", \
help="Folder containing data, as in /local/duman/SIMULATIONS/Cells_in_LAMMPS/.../")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/")
parser.add_argument("-sf", "--savefolder", nargs="?", \
const='Overlap_fnc', \
help="Specific folder for saving, as in Overlap_fnc")
parser.add_argument("-b","--bending", action="store_true", help="Decide whether to include bending or not")
parser.add_argument("-s","--save_eps", action="store_true", help="Decide whether to save in eps or not")
args = parser.parse_args()
### read the data and general information from the folder
sim, cells, beads = read_write.read_h5_file(args.folder, args.bending)
print "folder = ", args.folder, " bending rigidity = ", sim.kappa
### calculate the 4 point susceptibility of displacements of the centre of mass of cells
threshold_amplitude = 7.0
delay, suscp = calc_4_pt_suscp(cells.xu, sim, threshold_amplitude)
### write the 4 point susceptibility data to the corresponding file
read_write.write_2d_analysis_data(delay, suscp, args.savebase, args.savefolder, sim, args.bending)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-fl", "--folder", \
help="Folder containing data, as in /local/duman/SIMULATIONS/Cells_in_LAMMPS/.../")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/PLOTS/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Cells_in_LAMMPS/PLOTS/")
parser.add_argument("-sf", "--savefolder", nargs="?", const="TRAJECTORY", \
help="Specific folder for saving, as in TRAJECTORY")
parser.add_argument("-ti","--init_time", nargs="?", const=10, type=int, \
help="First frame of the trajectory, you can also leave it empty")
parser.add_argument("-tf","--fin_time", nargs="?", const=2000, type=int, \
help="Last frame of the trajectory, you can also leave it empty")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### read the data and general information from the folder
sim, cells, beads = read_write.read_h5_file(args.folder)
print "folder = ", args.folder, "cells.xu = \n", cells.xu
### plot the data in the given time window
plot_traj(cells.xu, sim, args.init_time, args.fin_time, \
args.savebase, args.savefolder, args.save_eps)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-e", "--eps", type=float, nargs="?", const=-1, \
help="Strength of LJ potential")
parser.add_argument("-f", "--fp", type=float, nargs="?", const=-1, \
help="Propulsion force")
parser.add_argument("-a", "--areak", type=float, nargs="?", const=-1, \
help="Area constraint potential strength")
parser.add_argument("-fl", "--folder", nargs="?", \
const='/local/duman/SIMULATIONS/Cells_in_LAMMPS/density_0.8/', \
help="Folder containing data, as in /local/duman/SIMULATIONS/Cells_in_LAMMPS/density_0.8/")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/PLOTS/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Cells_in_LAMMPS/PLOTS/")
parser.add_argument("-sf", "--savefolder", nargs="?", const="Vorticity_field", \
help="Specific folder for saving, as in Vorticity_field")
parser.add_argument("-ti","--init_time", nargs="?", const=10, type=int, \
help="First frame of the video (in terms of frame number), you can also leave it empty")
parser.add_argument("-tf","--fin_time", nargs="?", const=1000, type=int, \
help="Last frame of the video (in terms of frame number), you can also leave it empty")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### read the data and general information from the folder
folder = args.folder + "eps_" + str(args.eps) + "/fp_" + str(args.fp) + \
"/areak_" + str(args.areak) + "/"
sim, cells, beads = read_write.read_h5_file(folder)
beads.get_img_pos(sim.lx)
cells.get_img_pos(sim.lx)
print "folder = ", args.folder
### read the vorticity data
analysisdatabase = '/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/'
analysisdatabase += args.savefolder + '/'
datafolder, analysisfile = read_write.gen_folders(args.eps, args.fp, args.areak, \
args.savefolder, args.folder, \
analysisdatabase)
sim = read_write.read_sim_info(datafolder)
data = read_write.read_multid_analysis_data(analysisfile)
### plot the data in the given time window
savebase = args.savebase + args.savefolder + "/"
os.system("mkdir -p " + savebase)
plot_vorticity(data, beads, cells, sim, args.init_time, args.fin_time,
savebase, args.save_eps)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-fl", "--folder", \
help="Folder containing data, as in /local/duman/SIMULATIONS/Cells_in_LAMMPS/.../")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/")
parser.add_argument("-sf", "--savefolder", nargs="?", \
const="MSD", \
help="Specific folder for saving, as in MSD")
parser.add_argument("-b",
"--bending",
action="store_true",
help="Decide whether to include bending or not")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### read the data and general information from the folder
sim, cells, beads = read_write.read_h5_file(args.folder, args.bending)
print "folder = ", args.folder, " bending rigidity = ", sim.kappa
### calculate MSD of the centre of mass of cells
delay, msd = calculate_drift_subtracted_MSD(cells.xu, sim)
print "folder = ", args.folder
### write the MSD data to the corresponding file
read_write.write_2d_analysis_data(delay, msd, args.savebase,
args.savefolder, sim, args.bending)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-fl", "--folder", \
help="Folder containing data, as in /local/duman/SIMULATIONS/Cells_in_LAMMPS/.../")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/")
parser.add_argument("-sf", "--savefolder", nargs="?", \
const="Empty_space", \
help="Specific folder for saving, as in Empty_space")
parser.add_argument("-b",
"--bending",
action="store_true",
help="Decide whether to include bending or not")
args = parser.parse_args()
### read the data and general information from the folder
sim, cells, beads = read_write.read_h5_file(args.folder, args.bending)
cells.get_img_pos(sim.lx)
beads.get_img_pos(sim.lx)
print "folder = ", args.folder
### calculate the empty spaces
empty_space_ratio = calc_empty_space_ratio(beads.xi, cells.xi, cells.nbpc,
sim)
print "folder = ", args.folder
### write the data to the corresponding file
read_write.write_single_analysis_data(empty_space_ratio, args.savebase,
args.savefolder, sim, args.bending)
return