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python 3 compatibility for examples/*.py files

Browse Source 
add from __future__ import
print statement -> print() function
xrange -> range
map() -> list(map())
range() -> list(range())
StandardError -> Exception
This commit is contained in:
danielque
2023-08-10 13:25:36 +02:00
parent 597e606bde
commit 539fd060c2
35 changed files with 106 additions and 88 deletions
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24
examples/group_energy.py
View File

@ -5,6 +5,8 @@
# return distance sq between 2 atoms with PBC
from __future__ import absolute_import
def distance(box,x1,y1,z1,x2,y2,z2):
delx = x2 - x1
@ -37,7 +39,7 @@ def distance(box,x1,y1,z1,x2,y2,z2):
# main script
if len(argv) < 3:
raise StandardError,"group_energy.py data.file dump.file1 dump.file2 ..."
raise Exception("group_energy.py data.file dump.file1 dump.file2 ...")
dt = data(argv[1]) # data file
q = dt.get("Atoms",4)
@ -75,32 +77,32 @@ while 1:
d.aselect.test("$id >= 1 and $id <= 7243 or $id >= 7274 and $id <= 14283",
time)
id2,type2,x2,y2,z2 = d.vecs(time,"id","type","x","y","z")
id1 = map(int,id1)
id2 = map(int,id2)
type1 = map(int,type1)
type2 = map(int,type2)
id1 = list(map(int,id1))
id2 = list(map(int,id2))
type1 = list(map(int,type1))
type2 = list(map(int,type2))
n1 = len(type1)
n2 = len(type2)
for i in xrange(n1):
for i in range(n1):
id1[i] -= 1
type1[i] -= 1
for i in xrange(n2):
for i in range(n2):
id2[i] -= 1
type2[i] -= 1
e_coul_sum = 0.0
e_vdwl_sum = 0.0
for i in xrange(n1):
for i in range(n1):
typei = type1[i]
qi = q[id1[i]]
for j in xrange(n2):
for j in range(n2):
rsq = distance(box,x1[i],y1[i],z1[i],x2[j],y2[j],z2[j])
if rsq < maxcut_sq:
eng_coul,eng_vdwl = p.single(rsq,typei,type2[j],qi,q[id2[j]])
e_coul_sum += eng_coul
e_vdwl_sum += eng_vdwl
print "eng_coul = %g at timestep %d" % (e_coul_sum,time)
print "eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time)
print("eng_coul = %g at timestep %d" % (e_coul_sum,time))
print("eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time))
d.tselect.none()
d.tselect.one(time)

6
examples/movie_flow.py
View File

@ -1,5 +1,7 @@
# movie of flow around obstacle
from __future__ import absolute_import
d = dump("dump.flow")
d.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"vx",7,"vy")
d.set("$ke = sqrt($vx*$vx + $vy*$vy)")
@ -7,8 +9,8 @@ d.spread("vx",100,"color")
d.atype = "color"
r = raster(d)
r.acol(range(100),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"])
r.arad(range(100),0.5)
r.acol(list(range(100)),["red","red","red","red","yellow","green","blue","purple","purple","purple","purple"])
r.arad(list(range(100)),0.5)
r.rotate(0,-90)
r.zoom(1.5)
r.file = "flow"

2
examples/movie_melt.py
View File

@ -1,6 +1,6 @@
# movie of melting LJ solid
a = dump("dump.melt")
a = dump("files/dump.melt")
a.tselect.test("$t == 0")
a.scale()
a.set("$ix = int($x * 4)")

6
examples/movie_micelle.py
View File

@ -1,10 +1,12 @@
# movie of self-assembling micelles
d = dump("dump.micelle")
from __future__ import absolute_import
d = dump("files/dump.micelle")
s = svg(d)
s.acol([1,2,3,4],["blue","red","cyan","yellow"])
s.arad(range(4),0.5)
s.arad(list(range(4)),0.5)
s.zoom(1.5)
s.file = "micelle"

6
examples/movie_peptide.py
View File

@ -1,8 +1,8 @@
# movie of solvated peptide data
d = dump("dump.peptide")
d = dump("files/dump.peptide")
d.unwrap()
p = pdb("peptide",d)
r.file = "peptide"
p = pdbfile("files/peptide",d)
r = rasmol(p)
r.all()

2
examples/movie_tri.py
View File

@ -1,6 +1,6 @@
# movie of triangular particle data
d = dump("dump.tri")
d = dump("files/dump.tri")
d.set("$center = ((int($id)-1)/36+1)*36")
d.owrap("center")

2
examples/test_animate.py
View File

@ -11,4 +11,4 @@ a.next()
a.previous()
a.frame(1)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_bdump.py
View File

@ -9,4 +9,4 @@ dm.extra(b)
g = gl(dm)
v = vcr(g)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_cdata.py
View File

@ -31,4 +31,4 @@ c.select("A","B","C","linebox","organelle","nuchalf")
g = gl(c)
v = vcr(g)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_cfg.py
View File

@ -9,4 +9,4 @@ x.one()
x.many()
x.single(0,"tmp.single")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_chain.py
View File

@ -14,4 +14,4 @@ c.build(10,25)
c.write("tmp.data.chain")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

10
examples/test_clog.py
View File

@ -4,13 +4,13 @@
c = log("files/log.ccell")
print "# of vectors =",c.nvec
print "length of vectors =",c.nlen
print "names of vectors =",c.names
print("# of vectors =",c.nvec)
print("length of vectors =",c.nlen)
print("names of vectors =",c.names)
time,a,b = c.get("Step","prey","predator")
print a,b
print(a,b)
c.write("tmp.clog")
c.write("tmp.clog.two","Step","prey")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

10
examples/test_data.py
View File

@ -2,17 +2,19 @@
# requires files/data.micelle and dump.micelle
# creates tmp.data
from __future__ import absolute_import
d = data("files/data.micelle")
d.map(1,"id",3,"type",4,"x",5,"y",6,"z")
coeffs = d.get("Masses")
print "Masses",coeffs
print("Masses",coeffs)
x = d.get("Atoms",4)
print "X of 1st atom",x[0]
print("X of 1st atom",x[0])
d.title = "New LAMMPS data file"
natoms = d.headers["atoms"]
vec = range(1,natoms+1)
vec = list(range(1,natoms+1))
vec.reverse()
d.replace("Atoms",1,vec)
@ -27,4 +29,4 @@ while 1:
d.write("tmp.data")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

12
examples/test_dump.py
View File

@ -27,12 +27,12 @@ d.set("$xyz = $x + $y + $z")
d.spread("x",100,"color")
d.clone(0,"color")
print "Time",d.time()
print("Time",d.time())
color = d.atom(1,"color")
print "Color of atom 1",color
print("Color of atom 1",color)
d.aselect.test("$id <= 10")
color = d.vecs(1000,"color")
print "Color of 1st 10 atoms in step 1000",color
print("Color of 1st 10 atoms in step 1000",color)
d.atype = "color"
@ -42,13 +42,13 @@ while 1:
if flag == -1: break
time,box,atoms,bonds,tris,lines = d.viz(index)
colors = [atom[1] for atom in atoms]
print time,colors
print(time,colors)
d = dump("files/dump.peptide.*",0)
while 1:
time = d.next()
if time < 0: break
print "Incrementally read snaps =",d.nsnaps
print("Incrementally read snaps =",d.nsnaps)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

4
examples/test_ensight.py
View File

@ -1,4 +1,4 @@
# simple test of xyz tool
# simple test of ensight tool
# requires files/dump.micelle.*
# creates tmp*.case, etc
@ -8,4 +8,4 @@ e.one()
e.many()
e.single(0)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

6
examples/test_gl.py
View File

@ -2,6 +2,8 @@
# requires files/dump.kinase
# creates tmp*.png
from __future__ import absolute_import
d = dump("files/dump.kinase")
g = gl(d)
@ -17,7 +19,7 @@ g.all()
from vizinfo import colors
g.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
g.arad(range(9),0.3)
g.arad(list(range(9)),0.3)
#g.label(0.2,0.4,'h',15,"red","test label #1")
#g.label(-0.2,-0.4,'h',15,"yellow","test label #2")
@ -25,4 +27,4 @@ g.show(0)
g.pan(60,130,1,60,30,0.5)
g.all(0,10,0)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

8
examples/test_gnu.py
View File

@ -1,17 +1,19 @@
# simple test of gnu tool
# creates tmp.eps
from __future__ import absolute_import
g = gnu()
g("plot sin(x) with lines")
a = range(10)
a = list(range(10))
b = [3,6,2,5,7,3,6,5,3,1]
g.plot(a)
g.plot(a,b)
g.plot(a,b,b,a)
g.mplot(0,10,2,"tmp",a,b)
g.mplot(2,10,2,"tmp",a,b)
g.export("tmp.gnu",a,b)
@ -30,4 +32,4 @@ g.ylog()
g.save("tmp")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_histo.py
View File

@ -10,4 +10,4 @@ g.ytitle("Particle Count")
g.title("Histogram of Particle Density")
g.plot(x,y)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

4
examples/test_image.py
View File

@ -4,6 +4,6 @@
i = image("files/bucky*.png")
i.convert("files/bucky*.png","tmp*.gif")
i.montage("","files/bucky*.png","tmp*.gif","tmpnew*.png")
i.view("")
i.view("*.png")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_ldump.py
View File

@ -12,4 +12,4 @@ g.lrad(1,5)
g.lcol(1,"green")
v = vcr(g)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

10
examples/test_log.py
View File

@ -4,13 +4,13 @@
lg = log("files/log.obstacle")
print "# of vectors =",lg.nvec
print "length of vectors =",lg.nlen
print "names of vectors =",lg.names
print("# of vectors =",lg.nvec)
print("length of vectors =",lg.nlen)
print("names of vectors =",lg.names)
time,temp,press = lg.get("Step","Temp","Press")
print temp,press
print(temp,press)
lg.write("tmp.log")
lg.write("tmp.log.two","Step","E_pair")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

6
examples/test_matlab.py
View File

@ -1,9 +1,11 @@
# simple test of matlab tool
# creates tmp.eps
from __future__ import absolute_import
m = matlab()
a = range(10)
a = list(range(10))
b = [3,6,2,5,7,3,6,5,3,1]
m.plot(a)
@ -30,4 +32,4 @@ m.ylog()
m.save("tmp")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

8
examples/test_mdump.py
View File

@ -12,7 +12,7 @@ m.tselect.all()
m.tselect.test("$t >= 100 and $t <= 200")
m.delete()
print "Time",m.time()
print("Time",m.time())
m.map(2,"spin")
m.etype = "spin"
@ -23,13 +23,13 @@ while 1:
if flag == -1: break
time,box,atoms,bonds,tris,lines = m.viz(index)
colors = [tri[1] for tri in tris]
print time,colors
print(time,colors)
m = dump("files/mesh.grain",0)
while 1:
time = m.next()
if time < 0: break
print "Incrementally read snaps =",m.nsnaps
print("Incrementally read snaps =",m.nsnaps)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

4
examples/test_pair.py
View File

@ -6,6 +6,6 @@ d = data("files/data.rhodo")
p.coeff(d)
p.init(8.0,10.0)
ev,ec = p.single(5.0,1,2,0.5,-0.5)
print "Energies",ev,ec
print("Energies",ev,ec)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_patch.py
View File

@ -7,4 +7,4 @@ p.build(100,"hex2",1,2,3)
p.build(50,"tri5",4,5)
p.write("tmp.data.patch")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

4
examples/test_pdbfile.py
View File

@ -15,6 +15,6 @@ while 1:
p.single(time,"tmp.single")
n += 1
print "Incrementally processed %d PDB files" % n
print("Incrementally processed %d PDB files" % n)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_plotview.py
View File

@ -15,4 +15,4 @@ p.no(2)
p.file("tmp.plotview")
p.save()
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

6
examples/test_rasmol.py
View File

@ -8,14 +8,14 @@ p = pdbfile("files/peptide",d)
r = rasmol(p)
r.file = "tmp"
print "kill image window when ready to contine ..."
print("kill image window when ready to contine ...")
r.show(0)
r.all()
# change RasMol settings, run all() with those settings
print "change RasMol settings as desired, then type 'quit' ..."
print("change RasMol settings as desired, then type 'quit' ...")
r.run(0)
r.all("tmp.rasmol")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

10
examples/test_raster.py
View File

@ -2,6 +2,8 @@
# requires files/dump.kinase
# creates tmp*.png
from __future__ import absolute_import
d = dump("files/dump.kinase")
r = raster(d)
@ -10,7 +12,7 @@ r.rotate(60,130)
r.box(1)
r.file = "tmp"
print "kill image window when ready to contine ..."
print("kill image window when ready to contine ...")
r.show(0)
r.all()
a1 = animate("tmp0*png")
@ -18,14 +20,14 @@ a1 = animate("tmp0*png")
from vizinfo import colors
r.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
r.arad(range(9),0.3)
r.arad(list(range(9)),0.3)
r.label(0.2,0.4,'h',15,"red","test label #1")
r.label(-0.2,-0.4,'h',15,"yellow","test label #2")
print "kill image window when ready to contine ..."
print("kill image window when ready to contine ...")
r.show(0)
r.pan(60,130,1,60,30,0.5)
r.all(0,10,0)
a2 = animate("tmp0*png")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

10
examples/test_svg.py
View File

@ -2,6 +2,8 @@
# requires files/dump.kinase
# creates tmp*.png
from __future__ import absolute_import
d = dump("files/dump.kinase")
s = svg(d)
@ -10,20 +12,20 @@ s.rotate(60,130)
s.box(1)
s.file = "tmp"
print "kill image window when ready to contine ..."
print("kill image window when ready to contine ...")
s.show(0)
s.all()
from vizinfo import colors
s.acol([1,4,6,8,9],["gray","red","blue","green","yellow"])
s.arad(range(9),0.3)
s.arad(list(range(9)),0.3)
s.label(0.2,0.4,'h',15,"red","test label #1")
s.label(-0.2,-0.4,'h',15,"yellow","test label #2")
print "kill image window when ready to contine ..."
print("kill image window when ready to contine ...")
s.show(0)
s.pan(60,130,1,60,30,0.5)
s.all(0,10,0)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_vcr.py
View File

@ -13,4 +13,4 @@ v.clipxlo(0.2)
v.clipxhi(0.5)
v.play()
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

10
examples/test_vec.py
View File

@ -4,13 +4,13 @@
v = vec("files/vec.txt")
print "# of vectors =",v.nvec
print "length of vectors =",v.nlen
print "names of vectors =",v.names
print("# of vectors =",v.nvec)
print("length of vectors =",v.nlen)
print("names of vectors =",v.names)
time,temp,press = v.get(1,"col2",6)
print temp,press
print(temp,press)
v.write("tmp.vec")
v.write("tmp.vec.two","col1",3)
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_vmd.py
View File

@ -8,4 +8,4 @@ v.rep('VDW')
v.new('files/peptide.pdb','pdb')
v.flush()
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_vtk.py
View File

@ -8,4 +8,4 @@ v.one()
v.many()
v.single(0,"tmp.single")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")

2
examples/test_xyz.py
View File

@ -8,4 +8,4 @@ x.one()
x.many()
x.single(0,"tmp.single")
print "all done ... type CTRL-D to exit Pizza.py"
print("all done ... type CTRL-D to exit Pizza.py")