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