with open(filename, 'rb') as flow:
HoomdFlow = gsd.pygsd.GSDFile(flow)
hoomdTraj = gsd.hoomd.HOOMDTrajectory(HoomdFlow)
boxParams = (hoomdTraj.read_frame(0)).configuration.box
Lx = boxParams[0]
if boxParams[0] != boxParams[1] or boxParams[1] != boxParams[
2] or boxParams[0] != boxParams[2]:
print 'box dimensions are : ', boxParams[0]
print 'and are not supported (only isotropic systems supported)'
raise SystemExit
size_factor = (int(Lx / 9.3))
# size_factor = (int(Lx/(9.3/2))) ## debug only
Nframes = len(hoomdTraj)
print 'there are Nframes=', Nframes, 'in the file, but we only use trajDuration=', Nframes / every_forMemory, ' of them.'
Natoms = int(
float(module_filenamesHandler.filename_parser(filename[:-4], 'N')))
expectedDensity = 1.2
selectedAtoms, Nselected, expectedDensity = module_filenamesHandler.selectAtoms_function(
hoomdTraj[0].particles.typeid, kind, Lx, expectedDensity,
hoomdTraj[0].particles.position)
trajDuration = Nframes / every_forMemory
trajectory = np.zeros((trajDuration, Natoms, 3))
for time in range(0, trajDuration, 1):
## we only look 1 frame every "every_forMemory" frame, to save memory:
trajectory[time] = (hoomdTraj[time *
every_forMemory].particles.position
) # [selectedAtoms]
HoomdFlow.close()
print 'shape of your trajectory array:', np.shape(trajectory)
## "trajectory" is now the full array of all positions of all atoms (over time)
hoomdTraj = gsd.hoomd.HOOMDTrajectory(HoomdFlow);
dim = hoomdTraj.read_frame(0).configuration.dimensions
Nframes = hoomdTraj.file.nframes
boxParams = hoomdTraj.read_frame(0).configuration.box
Natoms = hoomdTraj[0].particles.N
atomIds = np.arange(Natoms, dtype=int).transpose() ## XXX to be added ?
atomTypes = np.array(hoomdTraj[0].particles.typeid, dtype=int).transpose()
Lx=boxParams[0]
if boxParams[0] != boxParams[1] or boxParams[1]!= boxParams[2] or boxParams[0]!= boxParams[2]:
print( 'box dimensions are : ', boxParams[0])
print( 'and are not supported (only isotropic systems supported)')
raise SystemExit
## TODO: use this time unit in the outputs ??
dt=0.00025
recPeriod = int(float(module_filenamesHandler.filename_parser(filename[:-4], 'rP')))
curStep = int(float(module_filenamesHandler.filename_parser(filename[:-4], 'cst')))
time_per_index = recPeriod*dt * frameSkipEvery # time_per_frame = recPeriod * dt
Nframes = len(hoomdTraj)/frameSkipEvery
Nframes_max = int(6e8/Natoms/3)
trajDuration = min(Nframes_max, Nframes)
## trajDuration should be related to the actual time observed in the simu,
## or at least the number of steps seen, indpeenent of number of atoms in the simulation...
print('there are Nframes=', Nframes, 'in the file, but we only use trajDuration=', trajDuration, ' of them.')
# print('TODO: if you need longer time sequences, you can split the atoms instead of splitting time, and do separate chuncks of the system using a mask, like selectedAtoms')
## for tests and/or RAM limitations:
selectedAtoms = np.arange(Natoms, dtype=int) #[:50]
additional_tag='-'
if slidingWindow:
plotting = 1
debug_or_choose_parameters = True
debug_or_choose_parameters = False
# above: from phop.py,may be useless.
## le read de decorated: issu de la partie plots de phop
## ensuite: issu de la partie eventsData de phop, analyse qui a sa place ici.
## ensuite:partie defintion med soft hard de construct, qui doit etre ici et non la bas.
################################################################################################################################################################
if "deco" in filename: # read the decorated file produced before #
if p_threshold_low == -1:
p_threshold_low = float(
module_filenamesHandler.filename_parser(filename[:-4], 'pLow'))
print('reading that the file has a p_threshold_low=', p_threshold_low,
' ...')
if p_threshold_low == 0.0:
p_threshold_low = 1e-7
print("correcting its threshold to :", p_threshold_low)
decoratedFlowRead = gsd.fl.GSDFile(
name=filename, mode='rb') # TODO : use with as instead of close()
atomTypes = decoratedFlowRead.read_chunk(frame=0, name='atomTypes')
boxParams = decoratedFlowRead.read_chunk(frame=0, name='configuration.box')
Lx = boxParams[0]
Ninitial = int(
float(module_filenamesHandler.filename_parser(filename[:-4], 'N')))
expectedDensity = float(
module_filenamesHandler.filename_parser(filename[:-4], 'rho'))
######
print('usage:')
print(
'run build_hyperwall.py [filename with "AVA=descriptors..."] [mode=1,2] '
)
filename = sys.argv[1]
rootname = module_filenamesHandler.get_rootname(filename)
suffix = module_filenamesHandler.get_suffix(filename)
mode = int(sys.argv[2])
cv_cross = 2
cv_cross = int(sys.argv[3])
Natoms = int(float(module_filenamesHandler.filename_parser(filename[:-4],
'N')))
seed = 4242
if "AVA=descriptors" in filename:
X_all_descriptors_array = np.loadtxt(filename)
else:
print(
"no way. Use correct file conttaing the ddescriptors (prodcued with B1)."
)
raise SystemExit
Nsamples = len(X_all_descriptors_array[:, 0]) / 2
print("found ", Nsamples, " samples (hard, soft)")
#hard_descriptors = X_all_descriptors_array[0:Nsamples,:]
#soft_descriptors = X_all_descriptors_array[Nsamples: ,:]
y_correct_labels = np.zeros(2 * Nsamples) - 1
y_correct_labels[Nsamples:] += 2
plt.rcParams['text.latex.unicode']=True
plt.rcParams.update(module_importPlotParams.fparams())
plt.ion() ## optional
######
print('usage:')
print('run '+sys.argv[0]+' [filename] [kind]')
filename = sys.argv[1]
kind = sys.argv[2]
# kind = module_filenamesHandler.filename_parser(filename[:-4], 'kind')
if "softness-R" in filename : # read the decorated file produced before #
p_threshold_low = float(module_filenamesHandler.filename_parser(filename[:-4], 'pLow'))
# print('reading that the file has a p_threshold_low=', p_threshold_low, ' ...')
# if p_threshold_low ==0 :
# p_threshold_low= 1e-7
# print("correcting its threshold to :",p_threshold_low)
# Natoms = int(float(module_filenamesHandler.filename_parser(filename[:-4], 'N')) )
# selectedAtoms = np.arange(Natoms, dtype=int)
# if 'tagBonusNum' in filename :
# Natoms = int(module_filenamesHandler.filename_parser(filename[:-4], 'tagBonusNum'))
# selectedAtoms = selectedAtoms[:Natoms]
decoratedFlowRead = gsd.fl.GSDFile(name=filename, mode='rb') # TODO : use with as instead of close()
atomTypes = decoratedFlowRead.read_chunk(frame=0, name='atomTypes')
print('run ' + sys.argv[0] + ' [rootname_AVA] [Nexamples] ')
verbose = True
verbose = False
rootname_AVA = sys.argv[1]
Nexamples = int(sys.argv[2])
throwBoundaries_steps = 10
soft_delay = 2 ## time frames, which is not a well controlled unit
### parameters to define hard and soft instants ###
#hard_factor = 2
Natoms = int(
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'N')))
p_threshold_low = max(
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'pl')),
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'pLow')))
p_threshold_high = float(
module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'ph'))
slowWindow = int(
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'sW')))
fastWindow = int(
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'fW')))
kind = module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'kind')
curStep = int(
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'cst')) /
1e6)
recPeriod = int(
float(module_filenamesHandler.filename_parser(rootname_AVA[:-4], 'rP')))
import sys
import module_filenamesHandler
import module_descriptors
import module_dist_compute
print('usage:')
print('run '+sys.argv[0]+' [deco-traj.gsd] [hyperplane_name.dat??] ')
# run B3-assign-softness.py KA_rho=12e-1_N=1e3_T=43e-2_type=FIRE-traj-deco_cst=91e6_rP=1000_LL=60000_SLID_pLow=0.002_rec=100.gsd KA_rho=12e-1_N=1e3_T=43e-2_type=FIRE-traj-deco_cst=91e6_rP=1000_LL=60000_SLID_pLow=0.002_rec=100_kind=A_pl=0.002_ph=0.08_sW=500_fW=2_AVA=descriptors_fam=1_Nex=10000_hyperplane.dat
filename = sys.argv[1]
hyperplane_name = sys.argv[2]
outputName_softness_R=filename[:-4]+"_SOFT=softness-R.gsd"
Natoms = int(float(module_filenamesHandler.filename_parser(filename[:-4], 'N')))
kind = module_filenamesHandler.filename_parser(hyperplane_name[:-4], 'kind')
descriptor_family_parameters = np.loadtxt("B0_fam=1_type=radial.dat")
descriptor_family_name=1
# hyperplane_name = filename[:-4]+"_hyperplane.dat"
hyperplane = np.loadtxt(hyperplane_name)
descriptor_averages = hyperplane[:,0]
descriptor_stdDevs = hyperplane[:,1]
a_hyperplane = hyperplane[:,2]
with open(hyperplane_name, 'r') as flow:
flow.readline()
b_intercept = float((flow.readline()).split()[-1])
analyzer_period = 4e3
if len(sys.argv) > 7:
analyzer_period = int(float(sys.argv[7]))
tauT = 1 # float(sys.argv[2])
if len(sys.argv) > 8:
tauT = float(sys.argv[8])
rootname = module_filenamesHandler.get_rootname(filename)
dt = 0.0025
if len(sys.argv) > 9:
dt = float(sys.argv[9])
if dt != 0.0025:
if 'dt=' not in filename:
rootname += "_dt=" + str(dt)
else:
dt = float(
module_filenamesHandler.filename_parser(filename[:-4], 'dt'))
#rootname+="_dt="+str(dt)
#print "accepting, for once, the incoming"
module_filenamesHandler.log_action(rootname, '\n\n' + str(sys.argv) + '\n')
TemperatureGoal = float(
module_filenamesHandler.filename_parser(filename[:-4], 'T'))
#TemperatureGoal = 0.23 #45
notice_level = 1
thermostat = 'NVT'
if len(sys.argv) > 10:
thermostat = str(sys.argv[10])
if thermostat == 'MB':
notice_level = 0
interactionType = "LJ"
if len(sys.argv) > 11:
interactionType = sys.argv[11]