def merge_files():
path = argv[2]
fmt = argv[3]
wins = [int(argv[4]), int(argv[5])]
lipids = int(argv[6])
num_resamples = int(argv[7])
hs_files = []
for i in range(0, wins[0]):
hs_files.append([])
for j in range(0, wins[1]):
filename = fmt % ((i + j * wins[0]), lipids)
filename = os.path.join(path, filename)
if os.path.exists(filename):
hs_files[i].append(filename)
result = None
for r in range(0, num_resamples):
h = HistogramND(2)
fs = resample(hs_files)
h.read(fs[0])
for i in range(1, len(fs)):
th = HistogramND(2)
th.read(fs[i])
h.merge(th)
h = h.norm_dos()
if result == None:
result = np.copy(
np.append(np.reshape(h[:, 0], (h.shape[0], 1)), np.reshape(h[:, 2], (h.shape[0], 1)), axis=1)
)
else:
result = np.append(result, np.reshape(h[:, 2], (result.shape[0], 1)), axis=1)
opath = "."
final = np.reshape(result[:, 0], (result.shape[0], 1))
final = np.append(final, np.reshape(np.mean(result[:, 1:], axis=1), (result.shape[0], 1)), axis=1)
final = np.append(final, np.reshape(np.std(result[:, 1:], axis=1), (result.shape[0], 1)), axis=1)
np.savetxt(os.path.join(opath, "Lipid%d.dos_deriv.dat" % lipids), MyMath.derivatives(final[:, 0:2]))
array_lipid = np.ones((final.shape[0], 1)) * lipids
final = np.append(final, np.reshape(array_lipid, ((final.shape[0], 1))), axis=1)
np.savetxt(os.path.join(opath, "Lipid%d.ave_dos.dat" % lipids), final, fmt="%.2f %.2f %.2f %d")
dT = 0.01
kb = 1
num_files = 1
num_points = 1000
num_atoms = 1000
result = result[67:,]
thermo_result = DOS.thermo(result, dT, num_points, 1000)
np.savetxt(os.path.join(opath, "Lipid%d.thermo_dos.dat" % lipids), thermo_result)
def split_files():
path = argv[2]
fmt = argv[3]
index = [int(argv[4]), int(argv[5])]
num = index[1] - index[0] + 1
print "# Number of file %d" % num
for i in range(index[0], index[1] + 1):
h = HistogramND(2)
filename = os.path.join(path, fmt % i)
print " -> %s" % filename
h.read(filename)
h = h.split()
for one in h:
fn = "P%07d_%d.dat" % (i, one.min_each_dim[1])
fn = os.path.join(path, fn)
one.write(fn)
def split_files():
path = argv[2]
fmt = argv[3]
index = [int(argv[4]), int(argv[5])]
num = index[1] - index[0] + 1
print "# Number of file %d" % num
for i in range(index[0], index[1] + 1):
h = HistogramND(2)
filename = os.path.join(path, fmt % i)
print " -> %s" % filename
h.read(filename)
h = h.split()
for one in h:
fn = "P%07d_%d.dat" % (i, one.min_each_dim[1])
fn = os.path.join(path, fn)
one.write(fn)
def merge_files():
path = argv[2]
fmt = argv[3]
wins = [int(argv[4]), int(argv[5])]
lipids = int(argv[6])
num_resamples = int(argv[7])
hs_files = []
for i in range(0, wins[0]):
hs_files.append([])
for j in range(0, wins[1]):
filename = fmt % ((i + j * wins[0]), lipids)
filename = os.path.join(path, filename)
if os.path.exists(filename):
hs_files[i].append(filename)
result = None
for r in range(0, num_resamples):
h = HistogramND(2)
fs = resample(hs_files)
h.read(fs[0])
for i in range(1, len(fs)):
th = HistogramND(2)
th.read(fs[i])
h.merge(th)
h = h.norm_dos()
if result == None:
result = np.copy(
np.append(np.reshape(h[:, 0], (h.shape[0], 1)),
np.reshape(h[:, 2], (h.shape[0], 1)),
axis=1))
else:
result = np.append(result,
np.reshape(h[:, 2], (result.shape[0], 1)),
axis=1)
opath = "."
final = np.reshape(result[:, 0], (result.shape[0], 1))
final = np.append(final,
np.reshape(np.mean(result[:, 1:], axis=1),
(result.shape[0], 1)),
axis=1)
final = np.append(final,
np.reshape(np.std(result[:, 1:], axis=1),
(result.shape[0], 1)),
axis=1)
np.savetxt(os.path.join(opath, "Lipid%d.dos_deriv.dat" % lipids),
MyMath.derivatives(final[:, 0:2]))
array_lipid = np.ones((final.shape[0], 1)) * lipids
final = np.append(final,
np.reshape(array_lipid, ((final.shape[0], 1))),
axis=1)
np.savetxt(os.path.join(opath, "Lipid%d.ave_dos.dat" % lipids),
final,
fmt="%.2f %.2f %.2f %d")
dT = 0.01
kb = 1
num_files = 1
num_points = 1000
num_atoms = 1000
thermo_result = DOS.thermo(result, dT, num_points, 1000)
np.savetxt(os.path.join(opath, "Lipid%d.thermo_dos.dat" % lipids),
thermo_result)
