def __init__(self, filename, loadWork=True):
"""
Get data from header.
Parameters
----------
filename : string
Path to data file.
loadWork : bool or 'r'
Load dump arrays. (default: True)
NOTE: if loadWork=='r', force re-extract dumps from data file.
"""
if get_env(
'FORCE_DAT', default=False, vartype=bool
): # enforce choice of data structure with custom relations between parameters
_Dat.__init__(self, filename, loadWork=loadWork)
elif get_env(
'FORCE_DAT0', default=False, vartype=bool
): # enforce choice of data structure from simulation with general parameters
_Dat0.__init__(self, filename, loadWork=loadWork)
else: # guess data structure
try:
_Dat.__init__(
self, filename, loadWork=loadWork
) # simulation with custom relations between parameters
except ValueError:
_Dat0.__init__(
self, filename,
loadWork=loadWork) # simulation with general parameters
_N_cell = 100 # number of particles above which simulations should be launched with a cell list
_exec_dir = path.join(path.dirname(path.realpath(__file__)),
'build') # default executable directory
_exec_name = ['simulation0', 'simulation0_cell_list'
] # default executable name without and with a cell list
_out_dir = _exec_dir # default simulation output directory
# SCRIPT
if __name__ == '__main__':
# VARIABLE DEFINITIONS
# INPUT FILE PARAMETERS
inputFilename = get_env('INPUT_FILENAME', default='',
vartype=str) # input file from which to copy data
inputFrame = get_env('INPUT_FRAME', default=0,
vartype=int) # frame to copy as initial frame
if inputFilename == '':
# SYSTEM PARAMETERS
N = get_env('N', default=_N,
vartype=int) # number of particles in the system
Dr = get_env('DR', default=_Dr,
vartype=float) # rotational diffusivity
epsilon = get_env('EPSILON', default=Dr / 3.,
vartype=float) # coefficient parameter of potential
v0 = get_env('V0', default=_v0,
vartype=float) # self-propulsion velocity
D = get_env('D', default=epsilon,
_period = 1 # default period of dumping of positions and orientations in number of frames
_N_cell = 100 # number of particles above which simulations should be launched with a cell list
_exec_dir = path.join(path.dirname(path.realpath(__file__)), 'build') # default executable directory
_exec_name = ['simulation', 'simulation_cell_list'] # default executable name without and with a cell list
_out_dir = _exec_dir # default simulation output directory
# SCRIPT
if __name__ == '__main__':
# VARIABLE DEFINITIONS
# INPUT FILE PARAMETERS
inputFilename = get_env('INPUT_FILENAME', default='', vartype=str) # input file from which to copy data
inputFrame = get_env('INPUT_FRAME', default=0, vartype=int) # frame to copy as initial frame
if inputFilename == '':
# SYSTEM PARAMETERS
N = get_env('N', default=_N, vartype=int) # number of particles in the system
lp = get_env('LP', default=_lp, vartype=float) # dimensionless persistence length
phi = get_env('PHI', default=_phi, vartype=float) # packing fraction
g = get_env('TORQUE_PARAMETER', default=0, vartype=float) # torque parameter
else:
# SYSTEM PARAMETERS
with Dat(inputFilename, loadWork=False) as dat: # data object
N = dat.N # number of particles in the system
axn.add_artist(
plt.legend(loc='lower left',
ncol=1,
borderpad=0.025,
handletextpad=0.2,
handles=[
Line2D([0], [0],
color='black',
linestyle='--',
label=r'$\nu^{\rm RTP}_{\rm end}$'),
Line2D([0], [0],
color='black',
linestyle='-',
label=r'$\nu^{\rm RTP}_{\rm ave}$')
]))
fign.subplots_adjust(**adjust)
# show and save
if get_env('SAVE', default=False, vartype=bool):
def save(f, fname):
f.savefig(fname + '.eps')
f.savefig(fname + '.svg')
save(fig, 'exactPsiRTP')
save(fign, 'exactNuRTP')
if get_env('SHOW', default=True, vartype=bool):
plt.show()
_N_cell = 100 # number of particles above which simulations should be launched with a cell list
_exec_dir = path.join(path.dirname(path.realpath(__file__)), 'build') # default executable directory
_exec_name = ['simulation', 'simulation_cell_list'] # default executable name without and with a cell list
_slurm_path = path.join(path.dirname(path.realpath(__file__)), 'slurm.sh') # Slurm submitting script
_out_dir = _exec_dir # default simulation output directory
# SCRIPT
if __name__ == '__main__':
# VARIABLE DEFINITIONS
# CLONING PARAMETERS
nRuns = get_env('NRUNS', default=_nRuns, vartype=int) # number of different runs
initSim = get_env('INITSIM', default=_initSim, vartype=int) # number of initial number of iterations to "randomise" the systems
# BIASING PARAMETERS
gMin = get_env('GMIN', default=_gMin, vartype=float) # minimum value of the torque parameter
gMax = get_env('GMAX', default=_gMax, vartype=float) # maximum value of the torque parameter
gNum = get_env('GNUM', default=_gNum, vartype=int) # number of values of the torque parameter
gValues = np.linspace(gMin, gMax, gNum, endpoint=True) # array of values of the torque parameter
# RANDOM SEEDS
seed = get_env('SEED', default=_seed, vartype=int) # master random seed of master random seeds
random.seed(seed) # set seed
seeds = random.randint(1e7, size=(gNum, nRuns)) # master random seeds
# SLURM PARAMETERS
slurm = get_env('SLURM', default=False, vartype=bool) # use Slurm job scheduler (see active_work/slurm.sh)
}
} # biasing with respect to polarisation
_slurm_path = path.join(path.dirname(path.realpath(__file__)),
'slurm.sh') # Slurm submitting script
_out_dir = _exec_dir # default simulation output directory
# SCRIPT
if __name__ == '__main__':
# VARIABLE DEFINITIONS
# CLONING PARAMETERS
tmax = get_env('TMAX', default=_tmax,
vartype=float) # dimensionless time to simulate
nc = get_env('NC', default=_nc, vartype=int) # number of clones
nRuns = get_env('NRUNS', default=_nRuns,
vartype=int) # number of different runs
initSim = get_env(
'INITSIM', default=_initSim, vartype=int
) # number of initial elementary number of iterations to "randomise" the systems
# BIASING PARAMETERS
sMin = get_env('SMIN', default=_sMin,
vartype=float) # minimum value of the biasing parameter
sMax = get_env('SMAX', default=_sMax,
vartype=float) # maximum value of the biasing parameter
sNum = get_env('SNUM', default=_sNum,
vartype=int) # number of values of the biasing parameter
sValues = np.linspace(
1: ('cloningR_B1', 'cloningR_B1_C')
} # cloning bias `1' without and with control
_slurm_path = path.join(path.dirname(path.realpath(__file__)),
'slurm.sh') # Slurm submitting script
_out_dir = _exec_dir # default simulation output directory
# SCRIPT
if __name__ == '__main__':
# VARIABLE DEFINITIONS
# CLONING PARAMETERS
tmax = get_env('TMAX', default=_tmax,
vartype=float) # dimensionless time to simulate
nc = get_env('NC', default=_nc, vartype=int) # number of clones
nRuns = get_env('NRUNS', default=_nRuns,
vartype=int) # number of different runs
initSim = get_env(
'INITSIM', default=_initSim, vartype=int
) # number of initial elementary number of iterations to "randomise" the systems
bias = get_env('CLONING_BIAS', default=_bias, vartype=int) # cloning bias
# BIASING PARAMETERS
sMin = get_env('SMIN', default=_sMin,
vartype=float) # minimum value of the biasing parameter
sMax = get_env('SMAX', default=_sMax,
vartype=float) # maximum value of the biasing parameter
sNum = get_env('SNUM', default=_sNum,
vartype=int) # number of values of the biasing parameter
self.draw_circle(
particle,
color='black',
fill=False, # draw black circle
label=self.label)
# SCRIPT
if __name__ == '__main__': # executing as script
startTime = datetime.now()
# VARIABLE DEFINITIONS
mode = get_env('MODE', default='orientation') # plotting mode
if mode == 'orientation':
plotting_object = Orientation
elif mode == 'displacement':
plotting_object = Displacement
elif mode == 'velocity':
plotting_object = Velocity
elif mode == 'bare':
plotting_object = Bare
else:
raise ValueError('Mode %s is not known.' % mode) # mode is not known
dat_file = get_env('DAT_FILE', default=joinpath(getcwd(),
'out.dat')) # data file
dat = Dat(dat_file, loadWork=False) # data object
_period = 1 # default period of dumping of orientations in number of frames
_exec_dir = path.join(path.dirname(path.realpath(__file__)),
'build') # default executable directory
_exec_name = 'rotors' # default executable name
_out_dir = _exec_dir # default simulation output directory
# SCRIPT
if __name__ == '__main__':
# VARIABLE DEFINITIONS
# SYSTEM PARAMETERS
N = get_env('N', default=_N,
vartype=int) # number of particles in the system
Dr = get_env('DR', default=_Dr, vartype=float) # rotational diffusivity
g = get_env('G', default=-Dr / 2,
vartype=float) # aligning torque parameter
# SIMULATION PARAMETERS
seed = get_env('SEED', default=_seed, vartype=int) # random seed
dt = get_env('DT', default=_dt, vartype=float) # time step
Niter = get_env('NITER', default=_Niter,
vartype=int) # number of iterations
# NAMING PARAMETERS
launch = get_env('LAUNCH', default=_launch,
vartype=float) # launch identifier
# OUTPUT PARAMETERS