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Updated utils to work with python3 #7

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6 changes: 3 additions & 3 deletions util/qbox_angle.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# qbox_angle.py
# extract angle defined by three atoms from Qbox output
# use: qbox_angle.py name1 name2 name3 file.r
Expand All @@ -7,7 +7,7 @@
import math

if len(sys.argv) != 5:
print "use: ",sys.argv[0]," name1 name2 name3 file.r"
print("use: ",sys.argv[0]," name1 name2 name3 file.r")
sys.exit()

name1 = ""
Expand Down Expand Up @@ -77,7 +77,7 @@ def endElement(self, name):
c = sp
c = max(-1.0,min(1.0,sp))
a = (180.0/math.pi)*math.acos(c)
print '%.4f' % a
print('%.4f' % a)
elif name == "position":
self.readPos1 = 0
self.readPos2 = 0
Expand Down
8 changes: 4 additions & 4 deletions util/qbox_distance.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# qbox_distance.py
# extract distance between two atoms from Qbox output
# use: qbox_distance.py name1 name2 file.r
Expand All @@ -7,7 +7,7 @@
import math

if len(sys.argv) != 4:
print "use: ",sys.argv[0]," name1 name2 file.r"
print("use: ",sys.argv[0]," name1 name2 file.r")
sys.exit()

name1 = ""
Expand Down Expand Up @@ -54,9 +54,9 @@ def endElement(self, name):
r2z = float(pos2[2])
#print "r1: ",self.r1x,self.r1y,self.r1z
#print "r2: ",self.r2x,self.r2y,self.r2z
print '%.4f' % math.sqrt((r1x-r2x)**2+
print('%.4f' % math.sqrt((r1x-r2x)**2+
(r1y-r2y)**2+
(r1z-r2z)**2)
(r1z-r2z)**2))
elif name == "position":
self.readPos1 = 0
self.readPos2 = 0
Expand Down
20 changes: 10 additions & 10 deletions util/qbox_dos.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# qbox_dos.py: extract electronic DOS from Qbox output
# generate DOS plot in gnuplot format
# use: qbox_dos.py [-last] [mu] emin emax [mu] width file.r
Expand All @@ -16,7 +16,7 @@

argc=len(sys.argv)
if (argc < 5) or (argc > 7) :
print "use: ",sys.argv[0]," [-last] [mu] emin emax width file.r"
print("use: ",sys.argv[0]," [-last] [mu] emin emax width file.r")
sys.exit()

# default chemical potential mu=0.0
Expand All @@ -29,15 +29,15 @@
lastonly = True
iarg += 1
if (argc < 6):
print "use: ",sys.argv[0]," [-last] [mu] emin emax width file.r"
print("use: ",sys.argv[0]," [-last] [mu] emin emax width file.r")
sys.exit()

# check for mu argument
if ((lastonly and (argc == 7)) or ((not lastonly) and (argc == 6))):
mu = float(sys.argv[iarg])
iarg += 1
if (argc < 6):
print "use: ",sys.argv[0]," [-last] [mu] emin emax width file.r"
print("use: ",sys.argv[0]," [-last] [mu] emin emax width file.r")
sys.exit()

emin = float(sys.argv[iarg])
Expand Down Expand Up @@ -108,17 +108,17 @@ def accumulate_dos(self):
self.dos_dn[j] += gauss(float(self.e[i])-self.mu-ej, width ) * self.weight

def print_dos(self):
print "# ",infile," mu=",self.mu," spin=0 width=",width
print("# ",infile," mu=",self.mu," spin=0 width=",width)
for j in range(ndos):
ej = emin + j * de
print ej, self.dos_up[j]
print(ej, self.dos_up[j])
if self.nspin == 2:
print
print
print "# ",infile," mu=",mu," spin=1 width=",width
print()
print()
print("# ",infile," mu=",mu," spin=1 width=",width)
for j in range(ndos):
ej = emin + j * de
print ej, self.dos_dn[j]
print(ej, self.dos_dn[j])

parser = xml.sax.make_parser()
handler = QboxOutputHandler()
Expand Down
12 changes: 6 additions & 6 deletions util/qbox_eig.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# qbox_eig.py: extract eigenvalues from Qbox output
# use: qbox_eig.py kpoint n ispin file.r
# extracts eigenvalue n at (ispin,kpoint)
Expand All @@ -10,8 +10,8 @@

argc=len(sys.argv)
if ( not ( argc in [3,4,6,7] ) ):
print "use: ",sys.argv[0]," [ispin] [kx ky kz] n file.r"
print " ispin = 0..1, n = 1..neig"
print("use: ",sys.argv[0]," [ispin] [kx ky kz] n file.r")
print(" ispin = 0..1, n = 1..neig")
sys.exit()

if argc == 7:
Expand Down Expand Up @@ -46,7 +46,7 @@
n = int(sys.argv[1])
infile = sys.argv[2]

print "# ",infile," ispin=",ispin, " n=", n, " k=", kx, ky, kz
print("# ",infile," ispin=",ispin, " n=", n, " k=", kx, ky, kz)

# Qbox output handler to extract and process data
class QboxOutputHandler(xml.sax.handler.ContentHandler):
Expand Down Expand Up @@ -81,9 +81,9 @@ def endElement(self, name):
def print_eig(self):
self.e = self.buffer.split()
if n > int(self.n):
print "n>neig: neig=", self.n
print("n>neig: neig=", self.n)
else:
print self.e[n-1]
print(self.e[n-1])

parser = xml.sax.make_parser()
handler = QboxOutputHandler()
Expand Down
6 changes: 3 additions & 3 deletions util/qbox_force.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# qbox_force.py
# extract force of an atom from Qbox output
# use: qbox_force.py atom_name file.r
Expand All @@ -7,7 +7,7 @@
import math

if len(sys.argv) != 3:
print "use: ",sys.argv[0]," atom_name file.r"
print("use: ",sys.argv[0]," atom_name file.r")
sys.exit()

# Qbox output handler to extract and process <atomset>
Expand Down Expand Up @@ -36,7 +36,7 @@ def endElement(self, name):
fx = float(force[0])
fy = float(force[1])
fz = float(force[2])
print '%.8f'%fx,'%.8f'%fy,'%.8f'%fz
print('%.8f'%fx,'%.8f'%fy,'%.8f'%fz)
self.readForce = 0

atom_name = sys.argv[1]
Expand Down
35 changes: 21 additions & 14 deletions util/qbox_maxforce.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# Copyright 2016 The Regents of the University of California
# This file is part of Qbox
#
Expand All @@ -9,10 +9,11 @@
import os.path
import xml.sax
import sys
import urllib2
from urllib.error import HTTPError, URLError
from urllib.request import urlopen

def usage():
print "use: ",sys.argv[0]," {file|URL}"
print("use: ",sys.argv[0]," {file|URL}")
sys.exit()

argc=len(sys.argv)
Expand Down Expand Up @@ -76,9 +77,9 @@ def endElement(self, name):
if ( fz*fz > fzmax*fzmax ):
fzmax = fz
z_name = self.atomname[i]
print '%10.3e'%fxmax,'%-8s'%x_name,\
print('%10.3e'%fxmax,'%-8s'%x_name,\
'%10.3e'%fymax,'%-8s'%y_name,\
'%10.3e'%fzmax,'%-8s'%z_name
'%10.3e'%fzmax,'%-8s'%z_name)
self.inAtomset = 0

parser = xml.sax.make_parser()
Expand All @@ -96,14 +97,20 @@ def endElement(self, name):
else:
# attempt to open as a URL
try:
f = urllib2.urlopen(input_source)
s = f.read(8192)
while ( s !="" ):
parser.feed(s)
s = f.read(8192)
f.close()
except (ValueError,urllib2.HTTPError) as e:
print e
sys.exit()
with urlopen(input_source, timeout=10) as f:
s = f.read(8192)
while ( s !="" ):
parser.feed(s)
s = f.read(8192)
f.close()
except HTTPError as error:
print(error.status, error.reason)
sys.exit()
except URLError as error:
print(error.reason)
sys.exit()
except TimeoutError:
print("Request timed out")
sys.exit()

parser.reset()
43 changes: 25 additions & 18 deletions util/qbox_move_subsample.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# Copyright 2018 The Regents of the University of California
# This file is part of Qbox
#
Expand All @@ -10,10 +10,11 @@
import os.path
import xml.sax
import sys
import urllib2
from urllib.error import HTTPError, URLError
from urllib.request import urlopen

def usage():
print "use: ",sys.argv[0]," interval cmd {file|URL}"
print("use: ",sys.argv[0]," interval cmd {file|URL}")
sys.exit()

argc=len(sys.argv)
Expand Down Expand Up @@ -62,17 +63,17 @@ def endElement(self, name):
elif name == "atomset":
self.step += 1
if ( self.step % interval == 0 ):
print "#",input_source,"iteration",self.step
print("#",input_source,"iteration",self.step)
avec = self.cell_a.split()
bvec = self.cell_b.split()
cvec = self.cell_c.split()
print "set cell ",avec[0],avec[1],avec[2],\
print("set cell ",avec[0],avec[1],avec[2],\
bvec[0],bvec[1],bvec[2],\
cvec[0],cvec[1],cvec[2]
cvec[0],cvec[1],cvec[2])
for i in range(len(self.tau)):
print "move ",self.atomname[i]," to ",\
self.tau[i][0],self.tau[i][1],self.tau[i][2]
print cmd
print("move ",self.atomname[i]," to ",\
self.tau[i][0],self.tau[i][1],self.tau[i][2])
print(cmd)
self.inAtomset = 0

parser = xml.sax.make_parser()
Expand All @@ -90,14 +91,20 @@ def endElement(self, name):
else:
# attempt to open as a URL
try:
f = urllib2.urlopen(input_source)
s = f.read(8192)
while ( s !="" ):
parser.feed(s)
s = f.read(8192)
f.close()
except (ValueError,urllib2.HTTPError) as e:
print e
sys.exit()
with urlopen(input_source, timeout=10) as f:
s = f.read(8192)
while ( s !="" ):
parser.feed(s)
s = f.read(8192)
f.close()
except HTTPError as error:
print(error.status, error.reason)
sys.exit()
except URLError as error:
print(error.reason)
sys.exit()
except TimeoutError:
print("Request timed out")
sys.exit()

parser.reset()
43 changes: 25 additions & 18 deletions util/qbox_move_to.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
# Copyright 2018 The Regents of the University of California
# This file is part of Qbox
#
Expand All @@ -9,10 +9,11 @@
import os.path
import xml.sax
import sys
import urllib2
from urllib.error import HTTPError, URLError
from urllib.request import urlopen

def usage():
print "use: ",sys.argv[0]," [-iter i] {file|URL}"
print("use: ",sys.argv[0]," [-iter i] {file|URL}")
sys.exit()

argc=len(sys.argv)
Expand Down Expand Up @@ -72,18 +73,18 @@ def endElement(self, name):
self.step += 1
if ( self.step == iter ):
if ( iter_option ):
print "#",input_source,"iteration",iter
print("#",input_source,"iteration",iter)
else:
print "#",input_source
print("#",input_source)
avec = self.cell_a.split()
bvec = self.cell_b.split()
cvec = self.cell_c.split()
print "set cell ",avec[0],avec[1],avec[2],\
print("set cell ",avec[0],avec[1],avec[2],\
bvec[0],bvec[1],bvec[2],\
cvec[0],cvec[1],cvec[2]
cvec[0],cvec[1],cvec[2])
for i in range(len(self.tau)):
print "move ",self.atomname[i]," to ",\
self.tau[i][0],self.tau[i][1],self.tau[i][2]
print("move ",self.atomname[i]," to ",\
self.tau[i][0],self.tau[i][1],self.tau[i][2])
self.inAtomset = 0
self.done = ( self.step >= iter )

Expand All @@ -102,14 +103,20 @@ def endElement(self, name):
else:
# attempt to open as a URL
try:
f = urllib2.urlopen(input_source)
s = f.read(8192)
while ( s !="" and not handler.done ):
parser.feed(s)
s = f.read(8192)
f.close()
except (ValueError,urllib2.HTTPError) as e:
print e
sys.exit()
with urlopen(input_source, timeout=10) as f:
s = f.read(8192)
while ( s !="" and not handler.done ):
parser.feed(s)
s = f.read(8192)
f.close()
except HTTPError as error:
print(error.status, error.reason)
sys.exit()
except URLError as error:
print(error.reason)
sys.exit()
except TimeoutError:
print("Request timed out")
sys.exit()

parser.reset()
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