tadd = min(tges - t, tadd)
steps = int(tadd // (dt * measurement_stride))
# variables to cumulate data
traj = np.empty((steps, 3, N))
ts = np.empty(steps)
Es = np.empty(steps)
Epots = np.empty(steps)
Ekins = np.empty(steps)
Ts = np.empty(steps)
Ps = np.empty(steps)
# ==== CALCULATION ====
print "Simulating until tmax=%s..." % (t + tadd)
set_globals(L, N, rcut, shift)
rebuild_neighbor_lists(x, rcut + skin)
xup = x.copy()
f = compute_forces(x, fmax)
# calculate or load the data from the time before the current run will start
if os.path.exists(datafilename):
ts_old, Es_old, Epots_old, Ekins_old, Ts_old, Ps_old, traj_old = np.load(
datafilename)
else:
a, b, c = compute_energy(x, v)
d = compute_temperature(c)
e = compute_pressure(x, v)
ts_old = np.array([t])
Es_old = np.array([a])
Epots_old = np.array([b])
print "Usage: python %s FILE" % sys.argv[0]
datafilename = sys.argv[1]
else:
datafilename = "data/ljsim.dat"
# check whether data file exists
if not os.path.exists(datafilename):
print "ERROR: %s doesn't exist."
sys.exit(1)
print "Reading data from %s." % datafilename
datafile = open(datafilename, 'r')
ts, Es, Epots, Ekins, Ts, Ps, traj = pickle.load(datafile)
datafile.close()
set_globals(L, N, 42, 42)
"""==== Functions==== """
def compute_running_average(O,M):
length=np.shape(O)[0]
av=[]
for t in range(M-1,length):
summe = 0.0
for i in range(1,M+1):
summe+=O[t-M+i]
av.append(summe/M)
return np.array(av)
"""==== PLOTTING ===="""
# mean values
meanEs=np.mean(Es[:10])
print "Usage: python %s FILE" % sys.argv[0]
datafilename = sys.argv[1]
else:
datafilename = "data/ljsim.dat"
# check whether data file exists
if not os.path.exists(datafilename):
print "ERROR: %s doesn't exist."
sys.exit(1)
print "Reading data from %s." % datafilename
datafile = open(datafilename, 'r')
ts, Es, Epots, Ekins, Ts, Ps, traj = pickle.load(datafile)
datafile.close()
set_globals(L, N, 42, 42)
"""==== Functions==== """
def compute_running_average(O, M):
length = np.shape(O)[0]
av = []
for t in range(M - 1, length):
summe = 0.0
for i in range(1, M + 1):
summe += O[t - M + i]
av.append(summe / M)
return np.array(av)
"""==== PLOTTING ===="""
tadd = min(tges - t, tadd)
steps = int(tadd // (dt * measurement_stride))
# variables to cumulate data
traj = np.empty((steps, 3, N))
ts = np.empty(steps)
Es = np.empty(steps)
Epots = np.empty(steps)
Ekins = np.empty(steps)
Ts = np.empty(steps)
Ps = np.empty(steps)
# ==== CALCULATION ====
print "Simulating until tmax=%s..." % (t + tadd)
set_globals(L, N, rcut, shift)
rebuild_neighbor_lists(x, rcut + skin)
xup = x.copy()
f = compute_forces(x, fmax) + force_ld(v)
# calculate or load the data from the time before the current run will start
if os.path.exists(datafilename):
ts_old, Es_old, Epots_old, Ekins_old, Ts_old, Ps_old, traj_old = np.load(datafilename)
else:
a, b, c = compute_energy(x, v)
d = compute_temperature(c)
e = compute_pressure(x, v)
ts_old = np.array([t])
Es_old = np.array([a])
Epots_old = np.array([b])
Ekins_old = np.array([c])