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phasediagram.py
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phasediagram.py
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from __future__ import print_function
import multiprocessing
try:
import cPickle as pickle
except:
import pickle
import os
import shutil
import subprocess
import time
import warnings
import numpy as np
from atatutils.clusterexpansion import ClusterExpansion as CE
def load_phase_diagram(filename):
f = open(filename, 'rb')
pd = pickle.load(f)
f.close()
return pd
def linear_interp(xp, yp):
def monomial_basis(x):
return np.interp(x, xp, yp)
return monomial_basis
class PhaseDiagram:
def __init__(self, cluster_expansion=None, pd_dir=None):
self.has_cluster_expansion = False
self.set_cluster_expansion(cluster_expansion)
if pd_dir is None:
self.pd_dir = 'phase_diagrams'
else:
self.pd_dir = pd_dir
if not os.path.exists(self.pd_dir):
os.mkdir(pd_dir)
self.level = 0
self.interpolate = []
self.ECI = None
self.prng_states = []
self.n_eci_written = 0
self.n_eci_run = multiprocessing.Value('i', 0)
self.n_ecis = 0
def set_cluster_expansion(self, cluster_expansion):
self.ce = cluster_expansion
if cluster_expansion is not None:
self.has_cluster_expansion = True
def generate_random_ECI(self, N=1):
if not self.has_cluster_expansion:
warnings.warn("Cluster Expansion must be set to generate ECI's")
return
ECI, prng_states = self.ce.sample_eci_with_state(N)
if self.ECI is not None:
self.ECI = np.vstack((self.ECI, ECI))
else:
self.ECI = ECI
self.prng_states += prng_states
self.n_ecis += N
def write_eci_to_file(self, N=1, which=None):
if which is None:
which = self.n_eci_written
if which + N > self.n_ecis:
self.generate_random_ECI(N=which + N - self.n_ecis)
for i in range(N):
idx = which + i
rank = self.prng_states[idx]
np.savetxt('reci_' + str(rank) + '.out', self.ECI[idx, :])
gsl, gsl_fold = self.ce.get_ground_state_line(ECI=self.ECI[idx, :])
gsl_file = open('gs_str_' + str(rank) + '.out', 'w')
for f in gsl_fold:
tmp = open(os.path.join(f, 'str.out'), 'r')
gsl_file.write(tmp.read())
gsl_file.write('end\n\n')
tmp.close()
self.n_eci_written += N
def _run_emc2(self, rank, start_phase, T0, T1, mu0, mu1, dT=15, dmu=0.04,
dx=1.e-2, er=50, k=8.617e-5, timeout=None):
ofile = os.path.join(self.pd_dir, "emc2" + str(start_phase) +
"_" + str(rank) + ".out")
process = subprocess.Popen(["emc2",
"-gs=" + str(start_phase),
"-T0=" + str(T0), "-T1=" + str(T1),
"-dT=" + str(dT),
"-mu0=" + str(mu0), "-mu1=" + str(mu1),
"-dmu=" + str(dmu),
"-dx=" + str(dx),
"-er=" + str(er), "-k=" + str(k),
"-o=" + ofile])
print("PID:", process.pid)
start = time.time()
if timeout is None:
timeout = 3600*24*10
while time.time() - start <= timeout:
if process.poll() is not None:
break
else:
time.sleep(600)
else:
print("timed out, killing process")
process.terminate()
self.n_eci_run.value += 1
def run_emc2(self, nproc, start_phase, T0, T1, mu0, mu1, dT=15, dmu=0.04,
dx=1.e-2, er=50, k=8.617e-5, timeout=None):
self.write_eci_to_file(nproc)
eci_run = self.n_eci_run.value
lock = multiprocessing.Lock()
for i in range(nproc):
shutil.copy('gs_str_{}.out'.format(self.prng_states[eci_run + i]),
'gs_str.out')
shutil.copy('reci_{}.out'.format(self.prng_states[eci_run + i]),
'eci.out')
p = [multiprocessing.Process(target=self._run_emc2,
args=(self.prng_states[eci_run + i],
start_phase, T0, T1, mu0, mu1,
dT, dmu, dx, er, k, timeout))
for i in range(nproc)]
for i in p:
i.start()
# self.wait_for_timeout(p, timeout)
for i in p:
i.join()
def _run_phb(self, rank, phase_1, phase_2, timeout=None,
T0=None, mu0=None, dT=15, dx=1.e-2,
er=50, k=8.617e-5, ltep=1):
ofile = os.path.join(self.pd_dir, "ph" + str(phase_1) + str(phase_2) +
"_" + str(self.level) + "_" + str(rank) + ".out")
if T0 is not None:
assert mu0 is not None
process = subprocess.Popen(["phb",
"-T=" + str(T0), "-mu=" + str(mu0),
"-gs1=" + str(phase_1),
"-gs2=" + str(phase_2),
"-dT=" + str(dT), "-dx=" + str(dx),
"-er=" + str(er), "-k=" + str(k),
"-ltep=" + str(ltep),
"-ecifile=" + "reci_" + str(rank) +
".out",
"-o=" + ofile])
else:
assert mu0 is None
process = subprocess.Popen(["phb",
"-gs1=" + str(phase_1),
"-gs2=" + str(phase_2),
"-dT=" + str(dT), "-dx=" + str(dx),
"-er=" + str(er), "-k=" + str(k),
"-ltep=" + str(ltep),
"-ecifile=" + "reci_" + str(rank) +
".out",
"-o=" + ofile])
print("PID:", process.pid)
start = time.time()
if timeout is None:
timeout = 7200
while time.time() - start <= timeout:
if process.poll() is not None:
break
else:
time.sleep(600)
else:
print("timed out, killing process")
process.terminate()
self.n_eci_run.value += 1
def run_phb(self, phase_1, phase_2, nproc=1, timeout=7200,
T0=None, mu0=None, dT=25, dx=1.e-2, er=50, k=8.617e-5,
ltep=100):
self.write_eci_to_file(nproc)
eci_run = self.n_eci_run.value
lock = multiprocessing.Lock()
for i in range(nproc):
shutil.copy('gs_str_' +
str(self.prng_states[eci_run + i]) +
'.out', 'gs_str.out')
p = [multiprocessing.Process(target=self._run_phb,
args=(self.prng_states[eci_run + i],
phase_1, phase_2, timeout,
T0, mu0, dT, dx, er, k, ltep))
for i in range(nproc)]
for i in p:
i.start()
# self.wait_for_timeout(p, timeout)
for i in p:
i.join()
while True and (self.level < 4):
refine_run = []
for prng_id in self.prng_states[eci_run: eci_run + nproc]:
try:
pdd = np.loadtxt(os.path.join(self.pd_dir,
"ph" + str(phase_1) +
str(phase_2) +
"_" + str(self.level) + "_" +
str(prng_id) + ".out"))
except:
continue
# mus = (pdd[:, 2] + 1)/2
mus = pdd[:, 1]
refine = np.where(np.abs(mus[1:] - mus[:-1]) > 1e-6)[0]
if len(refine) > 0:
refine_from = refine[0]
refine_run.append((prng_id, pdd[refine_from, 0],
pdd[refine_from, 1]))
else:
refine_run.append((prng_id, pdd[-1, 0],
pdd[-1, 1]))
if len(refine_run) > 0:
self.level += 1
dT = dT/2
p = [multiprocessing.Process(target=self._run_phb,
args=(refine_run[i][0],
phase_1, phase_2, timeout,
refine_run[i][1],
refine_run[i][2],
dT, dx, er, k, ltep))
for i in range(len(refine_run))]
for i in p:
i.start()
# self.wait_for_timeout(p, timeout)
for i in p:
i.join()
else:
break
def wait_for_timeout(self, processes, timeout=7200): # 42300):
bool_list = [True]*len(processes)
start = time.time()
while time.time() - start <= timeout:
for i, p in enumerate(processes):
bool_list[i] = p.is_alive()
print(bool_list)
if np.any(bool_list):
time.sleep(10)
else:
break
else:
print("timed out, killing all processes")
for p in processes:
p.terminate()
def parse_current(self):
idir = os.getcwd()
os.chdir(self.pd_dir)
vnames = [i[:-4] for i in os.listdir('.') if
os.path.isfile(os.path.join('.', i)) and
i.startswith('ph') and i.endswith('.out')]
prng_ids = [i.split('_')[-1] for i in vnames]
prng_ids = list(set(prng_ids))
fnames = [i for i in os.listdir('.') if
os.path.isfile(os.path.join('.', i)) and
i.startswith('ph') and i.endswith('.out')]
fnames_id = []
for i in prng_ids:
fnames_id.append([])
for j, n in enumerate(vnames):
if n.split('_')[-1] == i:
fnames_id[-1].append(fnames[j])
self.vars = {}
with warnings.catch_warnings():
warnings.filterwarnings('error')
for i, f_id in enumerate(fnames_id):
f_id.sort(key=lambda x: x.split('_')[1])
d = []
for j, f in enumerate(f_id):
try:
farray = np.loadtxt(f)
d.append(farray)
if len(d[-1].shape) == 1:
d[-1] = d[-1].reshape(1, d[-1].shape[0])
except Warning:
print("Warning:", f, "empty")
continue
for idx in range(len(d)-1):
d[idx] = d[idx][d[idx][:, 0] < d[idx + 1][0, 0]]
self.vars[f_id[0][:-4]] = np.concatenate(d)
os.chdir(idir)
def save_pickled_state(self, filename=None):
if filename is None:
filename = 'phase_diagram.pkl'
f = open(filename, 'wb')
pickle.dump(self, f)
f.close()
@classmethod
def load_pickled_state(cls, filename):
f = open(filename, 'rb')
pd = pickle.load(f)
f.close()
return pd
def fit_phase_diagram(self, interp='spline', degree=3):
if interp == 'spline':
try:
from scipy.interpolate import interp1d
except:
print("WARNING: scipy not available. Using linear.")
interp = 'linear'
degree = 1
self.parse_current()
for k in self.vars.keys():
T = self.vars[k][:, 0]
xl = self.vars[k][:, 2]/2 + 0.5
xr = self.vars[k][:, 3]/2 + 0.5
x = np.concatenate((xl, xr))
y = np.concatenate((T, T))
p = x.argsort()
x = x[p]
y = y[p]
if (interp == 'spline' or interp == 'polynomial') and degree > 1:
x = x[3:-3]
y = y[3:-3]
if interp == 'spline':
self.interpolate.append(interp1d(x, y, kind=3))
if interp == 'polynomial':
z = np.polyfit(x, y, deg=degree)
self.interpolate.append(np.poly1d(z))
elif interp == 'linear' or degree == 1:
self.interpolate.append(linear_interp(x, y))
def plot(self, interp='spline', degree=3):
import matplotlib.pyplot as plt
if interp == 'spline':
try:
from scipy.interpolate import interp1d
except:
print("WARNING: scipy not available. Using linear.")
interp = 'linear'
degree = 1
self.parse_current()
all_y = np.empty((len(self.vars.keys()), 200))
for i, k in enumerate(self.vars.keys()):
is_atat = False
T = self.vars[k][:, 0]
xl = self.vars[k][:, 2]/2 + 0.5
xr = self.vars[k][:, 3]/2 + 0.5
x = np.concatenate((xl, xr))
y = np.concatenate((T, T))
p = x.argsort()
x = x[p]
y = y[p]
if k.split('_')[1] == 'atat':
is_atat = True
c = 'k'
else:
c = '0.75'
if (interp == 'spline' or interp == 'polynomial') and degree > 1:
x = x[3:-3]
y = y[3:-3]
if interp == 'spline':
interpolate = interp1d(x, y, kind=3)
if interp == 'polynomial':
z = np.polyfit(x, y, deg=degree)
interpolate = np.poly1d(z)
xi = np.linspace(np.min(x), np.max(x), 200)
yi = interpolate(xi)
all_y[i, :] = yi
lw = 1
s = 30
if is_atat:
lw = 2
s = 60
plt.scatter(x, y, s=s, c=c, marker='o')
plt.plot(xi, yi, color=c, lw=lw)
elif interp == 'linear' or degree == 1:
plt.plot(x, y, 'o-', color=c)
interpolate = linear_interp(x, y)
xi = np.linspace(np.min(x), np.max(x), 200)
yi = interpolate(xi)
all_y[i, :] = yi
# if (interp == 'spline' or interp == 'polynomial') and degree > 1:
y = np.percentile(all_y, [2.5, 50, 97.5], axis=0)
plt.plot(xi, y[1, :], color='r', lw=2)
plt.fill_between(xi, y[0, :], y[2, :], facecolor='red', alpha=0.2)
plt.grid()
plt.xlim([0, 1])
plt.ylim(ymin=0)
plt.xlabel("%" + "Ge" + " in " + "SiGe", fontsize=34)
plt.ylabel("Temperature [K]", fontsize=34)
plt.tick_params(axis='both', labelsize=30)
plt.show(block=False)
if __name__ == "__main__":
pd = PhaseDiagram()
pd.plot()
cluster_diameters = [9.0, 0.0, 0.0, 0.0, 0.0]
ce = CE(diameters=cluster_diameters)
ce.fit()
pd.set_cluster_expansion(ce)
pd.run_phb(0, 1)