def main():
parser = argparse.ArgumentParser()
parser.add_argument('filename')
options = parser.parse_args()
results = collections.defaultdict(list)
with open(options.filename) as f:
for line in f:
for pattern in patterns:
m = pattern.search(line)
if m:
gd = m.groupdict()
iteration = gd['iter']
del gd['iter']
key, val = list(gd.items())[0]
results[key].append((float(iteration), float(val)))
fig, ax = util.make_figure()
for key, data in sorted(results.items()):
x, y = list(zip(*data))
ax.loglog(x, y, label=key)
util.save_columns(options.filename + '-' + key + '.tsv', x, y)
ax.set_xlabel('Conjugate Gradient Iteration')
ax.set_ylabel('Spinor Norms')
ax.set_title(options.filename)
util.save_figure(fig, options.filename)
def main():
options = _parse_args()
fig, ax = util.make_figure()
t, e = util.load_columns(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit//Runs/0106-bmw-rho011/shard-wflow.config-100.out.xml.e.tsv'
)
t, w = util.load_columns(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit//Runs/0106-bmw-rho011/shard-wflow.config-100.out.xml.w.tsv'
)
data = np.loadtxt('gradflow.000100', skiprows=1)
tm_traj = data[:, 0]
tm_t = data[:, 1]
tm_P = data[:, 2]
tm_Eplaq = data[:, 3]
tm_Esym = data[:, 4]
tm_tsqEplaq = data[:, 5]
tm_tsqEsym = data[:, 6]
tm_Wsym = data[:, 7]
for i, method in enumerate(
['gradient', 'chain-gradient', 'explicit-sym', 'explicit-asym']):
tm_my_w = wflow.derive_w(tm_t, tm_Esym, method=method)
ax.plot(tm_t + 0.1 * i, np.abs(tm_Wsym - tm_my_w), label=method)
ax.set_yscale('log')
ax.set_xlabel('$t/a^2$ (shifted)')
ax.set_ylabel(
r'$\left|(w/a)^\mathrm{tmLQCD} - (w/a)^\mathrm{Method}\right|$')
util.save_figure(fig, 'plot-wflow-norm')
x = np.linspace(0, 4, 1000)
y = np.sin(x)
z = x * (x**2 * np.cos(x) + 2 * x * np.sin(x))
fig, ax = util.make_figure()
for i, method in enumerate(
['gradient', 'chain-gradient', 'explicit-sym', 'explicit-asym']):
w = wflow.derive_w(x, y, method=method)
ax.plot(x + 0.1 * i, np.abs(z - w), label=method)
ax.set_xlabel('$x$ (shifted)')
ax.set_ylabel('absolute deviation from analytic $w(x)$')
ax.set_yscale('log')
util.save_figure(fig, 'plot-gradient-check')
def io_extract_mass(paths_in, path_out):
twopts_orig = correlators.loader.folded_list_loader(paths_in)
sample_count = 3 * len(twopts_orig)
b_twopts = bootstrap.Boot(
bootstrap.make_dist_draw(twopts_orig, sample_count))
b_corr_matrix = bootstrap.Boot([
correlators.corrfit.correlation_matrix(twopts)
for twopts in b_twopts.dist
])
omit_pre = 7
b_inv_corr_mat = bootstrap.Boot([
corr_matrix[omit_pre:, omit_pre:].getI()
for corr_matrix in b_corr_matrix.dist
])
time_extent = len(b_twopts.dist[0][0])
time = np.arange(time_extent)
fit_function = correlators.fit.cosh_fit_decorator(2 * (time_extent - 1))
b_fit_param = bootstrap.Boot([
perform_fits(time, bootstrap.average_arrays(twopts),
bootstrap.std_arrays(twopts), inv_corr_mat, fit_function,
(0.4, 1.0, 0.0), omit_pre)
for twopts, inv_corr_mat in zip(b_twopts.dist, b_inv_corr_mat.dist)
])
fig, ax = util.make_figure()
ax.errorbar(time, bootstrap.average_arrays(b_twopts.cen),
bootstrap.std_arrays(b_twopts.cen))
ax.plot(time, fit_function(time, *b_fit_param.cen))
ax.set_yscale('log')
util.save_figure(fig, 'test-corr.pdf')
print('cen', b_fit_param.cen[0])
print('val', b_fit_param.val[0])
print('err', b_fit_param.err[0])
print('len', len(twopts_orig), len(b_fit_param.dist))
np.savetxt(
path_out,
np.column_stack(
[b_fit_param.cen[0], b_fit_param.val[0], b_fit_param.err[0]]))
def plot_solver_data(path_in,
path_out,
ylabel,
title='Solver Data',
log_scale=False):
fig, ax = util.make_figure()
with open(path_in) as f:
data = json.load(f)
for solver, (x, y, yerr_down, yerr_up) in data.items():
x = np.array(x)
y = np.array(y)
yerr_down = np.array(yerr_down)
yerr_up = np.array(yerr_up)
label = solver
p = ax.plot(x, y, label=label)
ax.fill_between(x,
y - yerr_down,
y + yerr_up,
alpha=0.3,
color=p[0].get_color())
ax.set_title(title)
ax.set_xlabel('Update Number')
ax.set_ylabel(ylabel)
if log_scale:
ax.set_yscale('log')
util.dandify_axes(ax)
if log_scale:
start, end = ax.get_ylim()
print(start, end)
print(end / start)
if end / start < 15:
start = 10**int(np.log10(start) - 1)
end = 10**int(np.log10(end) + 1)
print('{:.10g} {:.10g}'.format(start, end))
ax.set_ylim(start, end)
util.dandify_figure(fig)
fig.savefig(path_out)
def main():
options = _parse_args()
pattern = re.compile(
r'0105-perf_nodes=(?P<A_nodes>\d+)_ntasks=(?P<B_ntasks>\d+)_cpus=(?P<C_cpus>\d+)_affinity=(?P<E_affinity>\w+?)/'
)
pattern_total_time = re.compile('HMC: total time = ([\d.]+) secs')
rows = []
for run in options.run:
print(run)
m = pattern.match(run)
if not m:
continue
cols1 = m.groupdict()
nodes = int(cols1['A_nodes'])
tasks = int(cols1['B_ntasks'])
cpus = int(cols1['C_cpus'])
cols1['D_SMT'] = tasks * cpus // 24
try:
cols2 = {
'QPhiX CG Perf':
np.loadtxt(
os.path.join(
run,
'extract-solver-QPhiX_Clover_CG-gflops_per_node.tsv'))
[1],
'QPhiX M-Shift Perf':
np.loadtxt(
os.path.join(
run,
'extract-solver-QPhiX_Clover_M-Shift_CG-gflops_per_node.tsv'
))[1],
}
except FileNotFoundError as e:
print(e)
continue
logfile = glob.glob(os.path.join(run, 'slurm-*.out'))[0]
with open(logfile) as f:
lines = f.readlines()
m = pattern_total_time.match(lines[-1])
if m:
cols2['minutes'] = float(m.group(1)) / 60
else:
cols2['minutes'] = 0
print(cols2.values())
rows.append((cols1, cols2))
print()
print()
for key in itertools.chain(sorted(cols1.keys()), sorted(cols2.keys())):
print('{:15s}'.format(str(key)[:13]), end='')
print()
for cols1, cols2 in rows:
for key, value in itertools.chain(sorted(cols1.items()),
sorted(cols2.items())):
print('{:15s}'.format(str(value)[:13]), end='')
print()
for x in cols1.keys():
for y in cols2.keys():
fig, ax = util.make_figure()
data = collections.defaultdict(list)
for c1, c2 in rows:
data[c1[x]].append(c2[y])
d = [value for key, value in sorted(data.items())]
l = [key for key, value in sorted(data.items())]
ax.boxplot(d, labels=l)
ax.set_xlabel(x)
ax.set_ylabel(y)
util.save_figure(fig, 'boxplot-{}-{}'.format(x, y))
def main():
options = _parse_args()
R = 300
# Read in the data from the paper.
a_inv_val = 1616
a_inv_err = 20
a_inv_dist = bootstrap.make_dist(a_inv_val, a_inv_err, n=R)
aml, ams, l, t, trajectories, ampi_val, ampi_err, amk_val, amk_err, f_k_f_pi_val, f_k_f_pi_err = util.load_columns(
'physical_point/gmor.txt')
ampi_dist = bootstrap.make_dist(ampi_val, ampi_err, n=R)
amk_dist = bootstrap.make_dist(amk_val, amk_err, n=R)
mpi_dist = [ampi * a_inv for ampi, a_inv in zip(ampi_dist, a_inv_dist)]
mk_dist = [amk * a_inv for amk, a_inv in zip(amk_dist, a_inv_dist)]
# Convert the data in lattice units into physical units.
mpi_dist = [a_inv * ampi for ampi, a_inv in zip(ampi_dist, a_inv_dist)]
mpi_val, mpi_avg, mpi_err = bootstrap.average_and_std_arrays(mpi_dist)
mpi_sq_dist = [mpi**2 for mpi in mpi_dist]
mpi_sq_val, mpi_sq_avg, mpi_sq_err = bootstrap.average_and_std_arrays(
mpi_sq_dist)
ampi_sq_dist = [ampi**2 for ampi in ampi_dist]
ampi_sq_val, ampi_sq_avg, ampi_sq_err = bootstrap.average_and_std_arrays(
ampi_sq_dist)
# Do a GMOR fit in order to extract `a B` and `a m_cr`.
popt_dist = [
op.curve_fit(gmor_pion, aml, ampi_sq)[0] for ampi_sq in ampi_sq_dist
]
aB_dist = [popt[0] for popt in popt_dist]
amcr_dist = [popt[1] for popt in popt_dist]
aB_val, aB_avg, aB_err = bootstrap.average_and_std_arrays(aB_dist)
amcr_val, amcr_avg, amcr_err = bootstrap.average_and_std_arrays(amcr_dist)
print('aB =', siunitx(aB_val, aB_err))
print('am_cr =', siunitx(amcr_val, amcr_err))
ams_paper = -0.057
ams_phys = ams_paper - amcr_val
ams_red = 0.9 * ams_phys
ams_bare_red = ams_red + amcr_val
print(ams_paper, ams_phys, ams_red, ams_bare_red)
print()
print('Mass preconditioning masses:')
amlq = aml - amcr_val
for i in range(3):
amprec = amlq * 10**i + amcr_val
kappa = 1 / (amprec * 2 + 8)
print('a m_prec:', amprec)
print('κ', kappa)
exit()
diff_dist = [
np.sqrt(2) * np.sqrt(mk**2 - 0.5 * mpi**2)
for mpi, mk in zip(mpi_dist, mk_dist)
]
diff_val, diff_avg, diff_err = bootstrap.average_and_std_arrays(diff_dist)
popt_dist = [
op.curve_fit(linear, mpi, diff)[0]
for mpi, diff in zip(mpi_dist, diff_dist)
]
fit_x = np.linspace(np.min(mpi_dist), np.max(mpi_dist), 100)
fit_y_dist = [linear(fit_x, *popt) for popt in popt_dist]
fit_y_val, fit_y_avg, fit_y_err = bootstrap.average_and_std_arrays(
fit_y_dist)
# Physical meson masses from FLAG paper.
mpi_phys_dist = bootstrap.make_dist(134.8, 0.3, R)
mk_phys_dist = bootstrap.make_dist(494.2, 0.3, R)
mpi_phys_val, mpi_phys_avg, mpi_phys_err = bootstrap.average_and_std_arrays(
mpi_phys_dist)
ampi_phys_dist = [
mpi_phys / a_inv for a_inv, mpi_phys in zip(a_inv_dist, mpi_phys_dist)
]
amk_phys_dist = [
mk_phys / a_inv for a_inv, mk_phys in zip(a_inv_dist, mk_phys_dist)
]
ampi_phys_val, ampi_phys_avg, ampi_phys_err = bootstrap.average_and_std_arrays(
ampi_phys_dist)
amk_phys_val, amk_phys_avg, amk_phys_err = bootstrap.average_and_std_arrays(
amk_phys_dist)
print('aM_pi phys =', siunitx(ampi_phys_val, ampi_phys_err))
print('aM_k phys =', siunitx(amk_phys_val, amk_phys_err))
new_b_dist = [
np.sqrt(mk_phys**2 - 0.5 * mpi_phys**2) - popt[0] * mpi_phys for
mpi_phys, mk_phys, popt in zip(mpi_phys_dist, mk_phys_dist, popt_dist)
]
diff_sqrt_phys_dist = [
np.sqrt(mk_phys**2 - 0.5 * mpi_phys**2)
for mpi_phys, mk_phys in zip(mpi_phys_dist, mk_phys_dist)
]
diff_sqrt_phys_val, diff_sqrt_phys_avg, diff_sqrt_phys_err = bootstrap.average_and_std_arrays(
diff_sqrt_phys_dist)
ex_x = np.linspace(120, 700, 100)
ex_y_dist = [
linear(ex_x, popt[0], b) for popt, b in zip(popt_dist, new_b_dist)
]
ex_y_val, ex_y_avg, ex_y_err = bootstrap.average_and_std_arrays(ex_y_dist)
ams_art_dist = [
linear(mpi, popt[0], b)**2 / a_inv**2 / aB - amcr
for mpi, popt, b, a_inv, aB, amcr in zip(
mpi_dist, popt_dist, new_b_dist, a_inv_dist, aB_dist, amcr_dist)
]
ams_art_val, ams_art_avg, ams_art_err = bootstrap.average_and_std_arrays(
ams_art_dist)
print('a m_s with artifacts', siunitx(ams_art_val, ams_art_err))
fig, ax = util.make_figure()
ax.fill_between(fit_x,
fit_y_val + fit_y_err,
fit_y_val - fit_y_err,
color='red',
alpha=0.2)
ax.plot(fit_x, fit_y_val, label='Fit', color='red')
ax.fill_between(ex_x,
ex_y_val + ex_y_err,
ex_y_val - ex_y_err,
color='orange',
alpha=0.2)
ax.plot(ex_x, ex_y_val, label='Extrapolation', color='orange')
ax.errorbar(mpi_val,
diff_val,
xerr=mpi_err,
yerr=diff_err,
linestyle='none',
label='Data (Dürr 2010)')
ax.errorbar([mpi_phys_val], [diff_sqrt_phys_val],
xerr=[mpi_phys_err],
yerr=[diff_sqrt_phys_err],
label='Physical Point (Aoki)')
util.save_figure(fig, 'test')
np.savetxt('artifact-bmw-data.tsv',
np.column_stack([mpi_val, diff_val, mpi_err, diff_err]))
np.savetxt('artifact-bmw-fit.tsv', np.column_stack([fit_x, fit_y_val]))
np.savetxt('artifact-bmw-band.tsv',
bootstrap.pgfplots_error_band(fit_x, fit_y_val, fit_y_err))
np.savetxt(
'artifact-phys-data.tsv',
np.column_stack([[mpi_phys_val], [diff_sqrt_phys_val], [mpi_phys_err],
[diff_sqrt_phys_err]]))
np.savetxt('artifact-phys-fit.tsv', np.column_stack([ex_x, ex_y_val]))
np.savetxt('artifact-phys-band.tsv',
bootstrap.pgfplots_error_band(ex_x, ex_y_val, ex_y_err))
np.savetxt('artifact-ms.tsv',
np.column_stack([mpi_val, ams_art_val, mpi_err, ams_art_err]))
# Compute the strange quark mass that is needed to obtain a physical meson
# mass difference, ignoring lattice artifacts.
ams_phys_dist = [(amk_phys**2 - 0.5 * ampi_phys**2) / aB - amcr
for ampi_phys, amk_phys, aB, amcr in zip(
ampi_phys_dist, amk_phys_dist, aB_dist, amcr_dist)]
ams_phys_cen, ams_phys_val, ams_phys_err = bootstrap.average_and_std_arrays(
ams_phys_dist)
print('M_K = {} MeV <== am_s ='.format(siunitx(494.2, 0.3)),
siunitx(ams_phys_cen, ams_phys_err))
aml_phys_dist = [
op.newton(lambda aml: gmor_pion(aml, *popt) - ampi_phys**2,
np.min(aml))
for popt, ampi_phys in zip(popt_dist, ampi_phys_dist)
]
fit_x = np.linspace(np.min(aml_phys_dist), np.max(aml), 100)
fit_y_dist = [
np.sqrt(gmor_pion(fit_x, *popt)) * a_inv
for popt, a_inv in zip(popt_dist, a_inv_dist)
]
fit_y_cen, fit_y_val, fit_y_err = bootstrap.average_and_std_arrays(
fit_y_dist)
np.savetxt('physical_point/mpi-vs-aml-data.tsv',
np.column_stack([aml, mpi_val, mpi_err]))
np.savetxt('physical_point/mpi-vs-aml-fit.tsv',
np.column_stack([fit_x, fit_y_cen]))
np.savetxt('physical_point/mpi-vs-aml-band.tsv',
bootstrap.pgfplots_error_band(fit_x, fit_y_cen, fit_y_err))
aml_phys_val, aml_phys_avg, aml_phys_err = bootstrap.average_and_std_arrays(
aml_phys_dist)
mpi_cen, mpi_val, mpi_err = bootstrap.average_and_std_arrays(mpi_dist)
#aml_240_val, aml_240_avg, aml_240_err = bootstrap.average_and_std_arrays(aml_240_dist)
print('M_pi = {} MeV <== am_l ='.format(siunitx(134.8, 0.3)),
siunitx(aml_phys_val, aml_phys_err))
#print('M_pi = 240 MeV <== am_l =', siunitx(aml_240_val, aml_240_err))
fig = pl.figure()
ax = fig.add_subplot(2, 1, 1)
ax.fill_between(fit_x,
fit_y_val - fit_y_err,
fit_y_val + fit_y_err,
color='0.8')
ax.plot(fit_x, fit_y_val, color='black', label='GMOR Fit')
ax.errorbar(aml,
mpi_val,
yerr=mpi_err,
color='blue',
marker='+',
linestyle='none',
label='Data')
ax.errorbar([aml_phys_val], [135],
xerr=[aml_phys_err],
marker='+',
color='red',
label='Extrapolation')
#ax.errorbar([aml_240_val], [240], xerr=[aml_240_err], marker='+', color='red')
ax.set_title('Extrapolation to the Physical Point')
ax.set_xlabel(r'$a m_\mathrm{ud}$')
ax.set_ylabel(r'$M_\pi / \mathrm{MeV}$')
util.dandify_axes(ax)
ax = fig.add_subplot(2, 1, 2)
ax.hist(aml_phys_dist - aml_phys_val, bins=50)
ax.locator_params(nbins=6)
ax.set_title('Bootstrap Bias')
ax.set_xlabel(
r'$(a m_\mathrm{ud}^\mathrm{phys})^* - a m_\mathrm{ud}^\mathrm{phys}$')
util.dandify_axes(ax)
util.dandify_figure(fig)
fig.savefig('physical_point/GMOR.pdf')
np.savetxt('physical_point/ampi-sq-vs-aml.tsv',
np.column_stack([aml, ampi_sq_val, ampi_sq_err]))
np.savetxt('physical_point/mpi-sq-vs-aml.tsv',
np.column_stack([aml, mpi_sq_val, mpi_sq_err]))
def load_average_corr(paths):
t = util.load_columns(paths[0])[0]
reals = [util.load_columns(path)[1] for path in paths]
a = np.row_stack(reals)
return t, np.mean(a, axis=0), np.std(a, axis=0) / np.sqrt(len(reals))
source_0 = load_average_corr(
glob.glob(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit/Runs/0120-Mpi270-L24-T96/corr/T=0/extract/corr/*.tsv'
))
source_20 = load_average_corr(
glob.glob(
'/home/mu/Dokumente/Studium/Master_Science_Physik/Masterarbeit/Runs/0120-Mpi270-L24-T96/corr/extract/corr/*.tsv'
))
fig, ax = util.make_figure()
print([x.shape for x in source_0])
ax.errorbar(source_0[0], source_0[1], source_0[2], label='T = 0')
ax.errorbar(source_20[0], source_20[1], source_20[2], label='T = 20')
ax.set_title('Different Source time with Chroma')
ax.set_xlabel(r'$t$')
ax.set_ylabel(r'$C(t)$')
ax.set_yscale('log')
util.save_figure(fig, 'chroma-source_t20')