def main():
### get the folder structure
analysistype = "Energy_spectrum"
analysisdatabase = '/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/'
analysisdatabase += analysistype + '/'
datafolderbase = '/local/duman/SIMULATIONS/Cells_in_LAMMPS/density_0.8/'
savebase = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/PLOTS/"
savefolder = "Energy_spectrum"
### make the parameter choice
# motility
fp = [1.0, 5.0, 10.0]
eps = 1.0
areak = 10.0
param = fp
param_choice = 'fp'
# compressibility
# fp = 5.0
# eps = 5.0
# areak = [1.0, 10.0, 100.0]
# param = areak
# param_choice = 'areak'
# adhesion
# fp = 3.0
# areak = 10.0
# eps = [0.05, 1.0, 10.0]
# param = eps
# param_choice = 'eps'
data = {} # carries the data per parameter set
sims = {} # carries the simulation information per parameter set
for p in param:
if param_choice == 'areak':
datafolder, analysisfile = read_write.gen_folders(
eps, fp, p, savefolder, datafolderbase, analysisdatabase)
elif param_choice == 'eps':
datafolder, analysisfile = read_write.gen_folders(
p, fp, areak, savefolder, datafolderbase, analysisdatabase)
elif param_choice == 'fp':
datafolder, analysisfile = read_write.gen_folders(
eps, p, areak, savefolder, datafolderbase, analysisdatabase)
sims[p] = read_write.read_sim_info(datafolder)
x, y = read_write.read_2d_analysis_data(analysisfile)
data[p] = y
### plot the data as a function of the parameter
plot_data(x, data, param_choice, sims, savebase, savefolder)
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 collect_data(args, analysisdatabase, read_analysis_func):
""" collect analysis data per chosen parameter,
where the chosen param is an array and the rest are scalars"""
param = []
param_choice = ''
if args.eps == -1:
param_choice = 'eps'
param = [0.05, 1.0, 5.0, 20.0]
if args.fp == -1:
param_choice = 'fp'
param = [0.5, 1.0, 5.0]
if args.areak == -1:
param_choice = 'areak'
param = [1.0, 10.0, 100.0]
if args.kappa == -1:
param_choice = 'kappa'
param = [1.0, 10.0, 100.0, 1000.0]
data = {} # carries the data per parameter set
sims = {} # carries the simulation information per parameter set
for p in param:
if param_choice == 'areak':
datafolder, analysisfile = read_write.gen_folders(
args.eps, args.fp, p, args.kappa, args.savefolder, args.folder,
analysisdatabase)
elif param_choice == 'eps':
datafolder, analysisfile = read_write.gen_folders(
p, args.fp, args.areak, args.kappa, args.savefolder,
args.folder, analysisdatabase)
elif param_choice == 'fp':
datafolder, analysisfile = read_write.gen_folders(
args.eps, p, args.areak, args.kappa, args.savefolder,
args.folder, analysisdatabase)
elif param_choice == 'kappa':
datafolder, analysisfile = read_write.gen_folders(
args.eps, args.fp, args.areak, p, args.savefolder, args.folder,
analysisdatabase)
sims[p] = read_write.read_sim_info(datafolder, True)
out = read_analysis_func(analysisfile)
if type(out) == tuple:
if len(out) == 2:
x, y = out
else:
y = out
data[p] = y
if type(out) == tuple:
return x, data, param_choice, sims
else:
return param, data, param_choice, sims
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-e",
"--eps",
type=float,
help="Strength of LJ potential")
parser.add_argument("-f", "--fp", type=float, help="Propulsion force")
parser.add_argument("-a",
"--areak",
type=float,
help="Strength of area constraint potential")
parser.add_argument("-k", "--kappa", type=float, help="Bending rigidity")
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="Energy_spectrum", \
help="Specific folder for saving, as in Energy_spectrum")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### read general information from the folder
path1 = 'eps_' + str(args.eps) + '/fp_' + str(args.fp) + \
'/areak_' + str(args.areak) + '/kappa_' + str(args.kappa) + '/'
datafolder = args.folder + path1
sim = read_write.read_sim_info(datafolder)
### read the data
# path2 = 'eps_' + str(args.eps) + '_fp_' + str(args.fp) + \
# '_areak_' + str(args.areak) + '_kappa_' + str(args.kappa)
path2 = 'eps_' + str(args.eps) + '_fp_' + str(args.fp) + \
'_areak_' + str(args.areak)
analysisdatabase = '/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/'
analysisdatabase += args.savefolder + '/'
analysisdata = analysisdatabase + args.savefolder + '_' + path2 + '.txt'
x, y = read_write.read_2d_analysis_data(analysisdata)
### plot the data in the given time window
plot_data(x, y, sim, args.savebase, args.savefolder, args.save_eps)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-d", "--density", type=float, help="Density")
parser.add_argument("-ka", "--kappa", type=float, help="Bending rigidity")
parser.add_argument("-km",
"--km",
type=float,
help="Motor spring strength")
parser.add_argument("-p",
"--pa",
type=float,
help="Probability when filaments are antialigned")
parser.add_argument("-fl", "--folder", nargs="?", \
const='/local/duman/SIMULATIONS/Motor/Data/', \
help="Folder containing data, as in /local/duman/SIMULATIONS/Motor/Data/")
parser.add_argument("-sb", "--savebase", nargs="?", \
const = "/usr/users/iff_th2/duman/Motor/PLOTS/", \
help="Folder to save the data, as in /usr/users/iff_th2/duman/Motor/PLOTS/")
parser.add_argument("-sf", "--savefolder", nargs="?", const="Overlap_fnc", \
help="Specific folder for saving, as in Overlap_fnc")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### read general information from the folder
path1 = 'density_' + str(args.density) + '/kappa_' + str(args.kappa) + \
'/km_' + str(args.km) + '/panti_' + str(args.pa) + '/'
datafolder = args.folder + path1
sim = read_write.read_sim_info(datafolder)
### read the data
path2 = '_density_' + str(args.density) + '_kappa_' + str(args.kappa) + \
'_km_' + str(args.km) + '_panti_' + str(args.pa)
analysisdatabase = '/usr/users/iff_th2/duman/Motor/DATA/'
analysisdatabase += args.savefolder + '/'
analysisdata = analysisdatabase + args.savefolder + path2 + '.txt'
x, y = read_write.read_2d_analysis_data(analysisdata)
### plot the data in the given time window
plot_data(x, y, sim, args.savebase, args.savefolder, args.save_eps)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-a",
"--areak",
type=float,
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="Velocity_com", \
help="Specific folder for saving, as in Velocity_com")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### accummulate data as a function of areak -with a dictionary-
analysisdatabase = '/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/'
analysisdatabase += args.savefolder + '/'
eps = [0.05, 0.5, 1.0, 5.0, 10.0, 20.0]
fp = [0.0, 0.5, 1.0, 3.0, 5.0, 10.0]
#areak = [1.0, 10.0, 100.0]
alldata = {} # carries the data per parameter set
for e in eps:
for f in fp:
key = (e, f)
datafolder, analysisfile = read_write.gen_folders( \
e, f, args.areak, args.savefolder,
args.folder, analysisdatabase)
sim_info = read_write.read_sim_info(datafolder)
data_info = read_write.read_single_analysis_data(analysisfile)
alldata[key] = Data(e, f, data_info, sim_info)
### plot the data as a function of the parameter
plot_data(alldata, args.areak, args.savebase, args.savefolder,
args.save_eps)
return
def main():
### get the data folder
parser = argparse.ArgumentParser()
parser.add_argument("-e",
"--eps",
type=float,
help="Strength of LJ potential")
parser.add_argument("-f", "--fp", type=float, help="Propulsion force")
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="Static_struct", \
help="Specific folder for saving, as in Static_struct")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### accummulate data as a function of areak -with a dictionary-
analysisdatabase = '/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/'
analysisdatabase += args.savefolder + '/'
areak = [1.0, 10.0, 100.0]
data = {} # carries the data per parameter set
sims = {} # carries the simulation information per parameter set
for a in areak:
datafolder, analysisfile = read_write.gen_folders(
args.eps, args.fp, a, args.savefolder, args.folder,
analysisdatabase)
sims[a] = read_write.read_sim_info(datafolder)
x, y = read_write.read_2d_analysis_data(analysisfile)
data[a] = y
### plot the data as a function of the parameter
plot_data(x, data, sims, args.savebase, args.savefolder, args.save_eps)
return
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-e", "--eps", type=float, \
help="Strength of LJ potential")
parser.add_argument("-f", "--fp", type=float, \
help="Propulsion force")
parser.add_argument("-a", "--areak", type=float, \
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/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="Corr_length", \
help="Specific folder for saving, as in Corr_length")
parser.add_argument("-s", "--save", action="store_true",
help="Save for the phase diagram or not")
args = parser.parse_args()
### read the data and general information from the folder
print "Calculating enstrophy for the following parameters : ", \
args.eps, ", ", args.fp, ", ", args.areak
### get the simulation data
folder = args.folder + "eps_" + str(args.eps) + \
"/fp_" + str(args.fp) + "/areak_" + str(args.areak) + "/"
sim = read_write.read_sim_info(folder)
### calculate correlation length
ens_folder = "/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/"
aname = "Enstrophy"
ens_folder += aname
ens_file = ens_folder + "/" + aname + "_eps_" + str(args.eps) + \
"_fp_" + str(args.fp) + "_areak_" + str(args.areak) + ".txt"
ens = read_write.read_single_analysis_data(ens_file)
### write the data
savebase = args.savebase + args.savefolder + "/"
os.system("mkdir -p " + savebase)
savefile = savebase + args.savefolder + "_eps_" + str(args.eps) + \
"_fp_" + str(args.fp) + "_areak_" + str(args.areak) + ".txt"
read_write.write_single_analysis_data(ens, savefile)
### collect the data for a phase diagram
if args.save:
aname = "PHASE_DIAGRAM"
savebase = args.savebase + aname + "/"
os.system("mkdir -p " + savebase)
savefile = savebase + aname + ".txt"
fl = open(savefile, "a")
fl.write(str(sim.eps) + "\t" + str(sim.fp) + "\t" + str(sim.areak) \
+ "\t" + str(ens) + "\n")
fl.close()
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="Vel_corr_length", \
help="Specific folder for saving, as in Vel_corr_length")
parser.add_argument("-s",
"--save_eps",
action="store_true",
help="Decide whether to save in eps or not")
args = parser.parse_args()
### accummulate data as a function of areak -with a dictionary-
analysisdatabase = '/usr/users/iff_th2/duman/Cells_in_LAMMPS/DATA/'
analysisdatabase += args.savefolder + '/'
### detect the parameter choice
param = []
param_choice = ''
if args.eps == -1:
param_choice = 'eps'
param = [0.05, 0.5, 1.0, 5.0, 10.0, 20.0]
if args.fp == -1:
param_choice = 'fp'
param = [0.0, 0.5, 1.0, 3.0, 5.0, 10.0]
if args.areak == -1:
param_choice = 'areak'
param = [1.0, 10.0, 100.0]
data = {} # carries the data per parameter set
sims = {} # carries the simulation information per parameter set
for p in param:
if param_choice == 'areak':
datafolder, analysisfile = read_write.gen_folders(
args.eps, args.fp, p, args.savefolder, args.folder,
analysisdatabase)
elif param_choice == 'eps':
datafolder, analysisfile = read_write.gen_folders(
p, args.fp, args.areak, args.savefolder, args.folder,
analysisdatabase)
elif param_choice == 'fp':
datafolder, analysisfile = read_write.gen_folders(
args.eps, p, args.areak, args.savefolder, args.folder,
analysisdatabase)
sims[p] = read_write.read_sim_info(datafolder)
x, y = read_write.read_2d_analysis_data(analysisfile)
data[p] = y
### plot the data as a function of the parameter
plot_data(x, data, param_choice, sims, args.savebase, args.savefolder,
args.save_eps)
return
