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get rid of (evil) tabs and trailing whitespace in bundled Pizza.py components

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This commit is contained in:
Axel Kohlmeyer
2019-09-19 07:34:27 -04:00
parent df3fad3b49
commit c26c8aca4f
6 changed files with 197 additions and 197 deletions
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70
tools/python/pizza/cfg.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# cfg tool
@ -11,14 +11,14 @@
oneline = "Convert LAMMPS snapshots to AtomEye CFG format"
docstr = """
c = cfg(d) d = object containing atom coords (dump, data)
c = cfg(d) d = object containing atom coords (dump, data)
c.one() write all snapshots to tmp.cfg
c.one("new") write all snapshots to new.cfg
c.many() write snapshots to tmp0000.cfg, tmp0001.cfg, etc
c.many("new") write snapshots to new0000.cfg, new0001.cfg, etc
c.single(N) write snapshot for timestep N to tmp.cfg
c.single(N,"file") write snapshot for timestep N to file.cfg
c.single(N) write snapshot for timestep N to tmp.cfg
c.single(N,"file") write snapshot for timestep N to file.cfg
"""
# History
@ -46,7 +46,7 @@ class cfg:
def __init__(self,data):
self.data = data
# --------------------------------------------------------------------
def one(self,*args):
@ -68,16 +68,16 @@ class cfg:
print >>f,"Number of particles = %d " % len(atoms)
print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
print >>f,"H0(1,1) = %20.10f A " % xlen
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(2,2) = %20.10f A " % ylen
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(3,3) = %20.10f A " % zlen
print >>f,"#"
for atom in atoms:
itype = int(atom[1])
xfrac = (atom[2]-box[0])/xlen
@ -85,14 +85,14 @@ class cfg:
zfrac = (atom[4]-box[2])/zlen
# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
print time,
sys.stdout.flush()
n += 1
f.close()
print "\nwrote %d snapshots to %s in CFG format" % (n,file)
# --------------------------------------------------------------------
def many(self,*args):
@ -104,7 +104,7 @@ class cfg:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
time,box,atoms,bonds,tris,lines = self.data.viz(which)
if n < 10:
file = root + "000" + str(n)
elif n < 100:
@ -112,7 +112,7 @@ class cfg:
elif n < 1000:
file = root + "0" + str(n)
else:
file = root + str(n)
file = root + str(n)
file += ".cfg"
f = open(file,"w")
@ -123,16 +123,16 @@ class cfg:
print >>f,"Number of particles = %d " % len(atoms)
print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
print >>f,"H0(1,1) = %20.10f A " % xlen
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(2,2) = %20.10f A " % ylen
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(3,3) = %20.10f A " % zlen
print >>f,"#"
for atom in atoms:
itype = int(atom[1])
xfrac = (atom[2]-box[0])/xlen
@ -140,14 +140,14 @@ class cfg:
zfrac = (atom[4]-box[2])/zlen
# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
print time,
sys.stdout.flush()
f.close()
n += 1
print "\nwrote %s snapshots in CFG format" % n
# --------------------------------------------------------------------
def single(self,time,*args):
@ -166,16 +166,16 @@ class cfg:
print >>f,"Number of particles = %d " % len(atoms)
print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time
print >>f,"H0(1,1) = %20.10f A " % xlen
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(1,2) = 0.0 A "
print >>f,"H0(1,3) = 0.0 A "
print >>f,"H0(2,1) = 0.0 A "
print >>f,"H0(2,2) = %20.10f A " % ylen
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(2,3) = 0.0 A "
print >>f,"H0(3,1) = 0.0 A "
print >>f,"H0(3,2) = 0.0 A "
print >>f,"H0(3,3) = %20.10f A " % zlen
print >>f,"#"
for atom in atoms:
itype = int(atom[1])
xfrac = (atom[2]-box[0])/xlen
@ -183,5 +183,5 @@ class cfg:
zfrac = (atom[4]-box[2])/zlen
# print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7])
print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac)
f.close()

160
tools/python/pizza/dump.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# dump tool
@ -12,15 +12,15 @@ oneline = "Read, write, manipulate dump files and particle attributes"
docstr = """
d = dump("dump.one") read in one or more dump files
d = dump("dump.1 dump.2.gz") can be gzipped
d = dump("dump.*") wildcard expands to multiple files
d = dump("dump.*",0) two args = store filenames, but don't read
d = dump("dump.1 dump.2.gz") can be gzipped
d = dump("dump.*") wildcard expands to multiple files
d = dump("dump.*",0) two args = store filenames, but don't read
incomplete and duplicate snapshots are deleted
atoms will be unscaled if stored in files as scaled
self-describing column names assigned
self-describing column names assigned
time = d.next() read next snapshot from dump files
time = d.next() read next snapshot from dump files
used with 2-argument constructor to allow reading snapshots one-at-a-time
snapshot will be skipped only if another snapshot has same time stamp
@ -31,21 +31,21 @@ time = d.next() read next snapshot from dump files
d.map(1,"id",3,"x") assign names to columns (1-N)
not needed if dump file is self-describing
d.tselect.all() select all timesteps
d.tselect.one(N) select only timestep N
d.tselect.none() deselect all timesteps
d.tselect.skip(M) select every Mth step
d.tselect.all() select all timesteps
d.tselect.one(N) select only timestep N
d.tselect.none() deselect all timesteps
d.tselect.skip(M) select every Mth step
d.tselect.test("$t >= 100 and $t < 10000") select matching timesteps
d.delete() delete non-selected timesteps
d.delete() delete non-selected timesteps
selecting a timestep also selects all atoms in the timestep
skip() and test() only select from currently selected timesteps
test() uses a Python Boolean expression with $t for timestep value
Python comparison syntax: == != < > <= >= and or
d.aselect.all() select all atoms in all steps
d.aselect.all(N) select all atoms in one step
d.aselect.all() select all atoms in all steps
d.aselect.all(N) select all atoms in one step
d.aselect.test("$id > 100 and $type == 2") select match atoms in all steps
d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step
@ -56,24 +56,24 @@ d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step
Python comparison syntax: == != < > <= >= and or
$name must end with a space
d.write("file") write selected steps/atoms to dump file
d.write("file",head,app) write selected steps/atoms to dump file
d.scatter("tmp") write selected steps/atoms to multiple files
d.write("file") write selected steps/atoms to dump file
d.write("file",head,app) write selected steps/atoms to dump file
d.scatter("tmp") write selected steps/atoms to multiple files
write() can be specified with 2 additional flags
head = 0/1 for no/yes snapshot header, app = 0/1 for write vs append
scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc
d.scale() scale x,y,z to 0-1 for all timesteps
d.scale(100) scale atom coords for timestep N
d.unscale() unscale x,y,z to box size to all timesteps
d.unscale(1000) unscale atom coords for timestep N
d.wrap() wrap x,y,z into periodic box via ix,iy,iz
d.unwrap() unwrap x,y,z out of box via ix,iy,iz
d.owrap("other") wrap x,y,z to same image as another atom
d.sort() sort atoms by atom ID in all selected steps
d.sort("x") sort atoms by column value in all steps
d.sort(1000) sort atoms in timestep N
d.scale() scale x,y,z to 0-1 for all timesteps
d.scale(100) scale atom coords for timestep N
d.unscale() unscale x,y,z to box size to all timesteps
d.unscale(1000) unscale atom coords for timestep N
d.wrap() wrap x,y,z into periodic box via ix,iy,iz
d.unwrap() unwrap x,y,z out of box via ix,iy,iz
d.owrap("other") wrap x,y,z to same image as another atom
d.sort() sort atoms by atom ID in all selected steps
d.sort("x") sort atoms by column value in all steps
d.sort(1000) sort atoms in timestep N
scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms
wrap(), unwrap(), owrap() require ix,iy,iz be defined
@ -85,8 +85,8 @@ d.sort(1000) sort atoms in timestep N
m1,m2 = d.minmax("type") find min/max values for a column
d.set("$ke = $vx * $vx + $vy * $vy") set a column to a computed value
d.setv("type",vector) set a column to a vector of values
d.spread("ke",N,"color") 2nd col = N ints spread over 1st col
d.clone(1000,"color") clone timestep N values to other steps
d.spread("ke",N,"color") 2nd col = N ints spread over 1st col
d.clone(1000,"color") clone timestep N values to other steps
minmax() operates on selected timesteps and atoms
set() operates on selected timesteps and atoms
@ -107,17 +107,17 @@ d.clone(1000,"color") clone timestep N values to other steps
values at every timestep are set to value at timestep N for that atom ID
useful for propagating a color map
t = d.time() return vector of selected timestep values
t = d.time() return vector of selected timestep values
fx,fy,... = d.atom(100,"fx","fy",...) return vector(s) for atom ID N
fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N
atom() returns vectors with one value for each selected timestep
vecs() returns vectors with one value for each selected atom in the timestep
index,time,flag = d.iterator(0/1) loop over dump snapshots
index,time,flag = d.iterator(0/1) loop over dump snapshots
time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects
d.atype = "color" set column returned as "type" by viz
d.extra(obj) extract bond/tri/line info from obj
d.atype = "color" set column returned as "type" by viz
d.extra(obj) extract bond/tri/line info from obj
iterator() loops over selected timesteps
iterator() called with arg = 0 first time, with arg = 1 on subsequent calls
@ -137,7 +137,7 @@ d.extra(obj) extract bond/tri/line info from obj
if extra() used to define lines, else NULL
atype is column name viz() will return as atom type (def = "type")
extra() extracts bonds/tris/lines from obj each time viz() is called
obj can be data object for bonds, cdata object for tris and lines,
obj can be data object for bonds, cdata object for tris and lines,
bdump object for bonds, tdump object for tris, ldump object for lines.
mdump object for tris
"""
@ -227,7 +227,7 @@ class dump:
for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1:
raise StandardError,"no dump file specified"
if len(list) == 1:
self.increment = 0
self.read_all()
@ -270,7 +270,7 @@ class dump:
self.tselect.all()
# print column assignments
if len(self.names):
print "assigned columns:",self.names2str()
else:
@ -304,15 +304,15 @@ class dump:
snap = self.read_snapshot(f)
if not snap:
self.nextfile += 1
if self.nextfile == len(self.flist): return -1
if self.nextfile == len(self.flist): return -1
f.close()
self.eof = 0
continue
self.eof = 0
continue
self.eof = f.tell()
f.close()
try:
self.findtime(snap.time)
continue
continue
except: break
# select the new snapshot with all its atoms
@ -334,7 +334,7 @@ class dump:
# assign column names (file must be self-describing)
# set scale_original to 0/1/-1 for unscaled/scaled/unknown
# convert xs,xu to x in names
def read_snapshot(self,f):
try:
snap = Snap()
@ -351,7 +351,7 @@ class dump:
else: snap.boxstr = words[1].strip()
if "xy" in snap.boxstr: snap.triclinic = 1
else: snap.triclinic = 0
words = f.readline().split()
if len(words) == 2:
snap.xlo,snap.xhi,snap.xy = float(words[0]),float(words[1]),0.0
@ -372,7 +372,7 @@ class dump:
else:
snap.zlo,snap.zhi,snap.yz = \
float(words[0]),float(words[1]),float(words[2])
item = f.readline()
if len(self.names) == 0:
self.scale_original = -1
@ -401,7 +401,7 @@ class dump:
else: self.names[words[i]] = i
if xflag == 0 and yflag == 0 and zflag == 0: self.scale_original = 0
if xflag == 1 and yflag == 1 and zflag == 1: self.scale_original = 1
if snap.natoms:
words = f.readline().split()
ncol = len(words)
@ -424,7 +424,7 @@ class dump:
# --------------------------------------------------------------------
# map atom column names
def map(self,*pairs):
if len(pairs) % 2 != 0:
raise StandardError, "dump map() requires pairs of mappings"
@ -509,7 +509,7 @@ class dump:
atoms[:,y] = (atoms[:,y] - snap.ylo)*h1inv + \
(atoms[:,z] - snap.zlo)*h3inv
atoms[:,z] = (atoms[:,z] - snap.zlo)*h2inv
# --------------------------------------------------------------------
# unscale coords from 0-1 to box size for all snapshots or just one
# use 6 params as h-matrix to treat orthogonal or triclinic boxes
@ -564,7 +564,7 @@ class dump:
atoms[:,x] = snap.xlo + atoms[:,x]*h0 + atoms[:,y]*h5 + atoms[:,z]*h4
atoms[:,y] = snap.ylo + atoms[:,y]*h1 + atoms[:,z]*h3
atoms[:,z] = snap.zlo + atoms[:,z]*h2
# --------------------------------------------------------------------
# wrap coords from outside box to inside
@ -577,7 +577,7 @@ class dump:
ix = self.names["ix"]
iy = self.names["iy"]
iz = self.names["iz"]
for snap in self.snaps:
xprd = snap.xhi - snap.xlo
yprd = snap.yhi - snap.ylo
@ -599,7 +599,7 @@ class dump:
ix = self.names["ix"]
iy = self.names["iy"]
iz = self.names["iz"]
for snap in self.snaps:
xprd = snap.xhi - snap.xlo
yprd = snap.yhi - snap.ylo
@ -612,10 +612,10 @@ class dump:
# --------------------------------------------------------------------
# wrap coords to same image as atom ID stored in "other" column
# if dynamic extra lines or triangles defined, owrap them as well
def owrap(self,other):
print "Wrapping to other ..."
id = self.names["id"]
x = self.names["x"]
y = self.names["y"]
@ -641,10 +641,10 @@ class dump:
# should bonds also be owrapped ?
if self.lineflag == 2 or self.triflag == 2:
self.objextra.owrap(snap.time,xprd,yprd,zprd,ids,atoms,iother,ix,iy,iz)
# --------------------------------------------------------------------
# convert column names assignment to a string, in column order
def names2str(self):
pairs = self.names.items()
values = self.names.values()
@ -697,7 +697,7 @@ class dump:
else: id = -1
if "type" in self.names: type = self.names["type"]
else: type = -1
for snap in self.snaps:
if not snap.tselect: continue
print snap.time,
@ -719,7 +719,7 @@ class dump:
print >>f,snap.ylo,snap.yhi
print >>f,snap.zlo,snap.zhi
print >>f,"ITEM: ATOMS",namestr
atoms = snap.atoms
nvalues = len(atoms[0])
for i in xrange(snap.natoms):
@ -743,7 +743,7 @@ class dump:
if not snap.tselect: continue
print snap.time,
sys.stdout.flush()
file = root + "." + str(snap.time)
f = open(file,"w")
print >>f,"ITEM: TIMESTEP"
@ -761,7 +761,7 @@ class dump:
print >>f,snap.ylo,snap.yhi
print >>f,snap.zlo,snap.zhi
print >>f,"ITEM: ATOMS",namestr
atoms = snap.atoms
nvalues = len(atoms[0])
for i in xrange(snap.natoms):
@ -803,7 +803,7 @@ class dump:
lhs = list[0][1:]
if not self.names.has_key(lhs):
self.newcolumn(lhs)
for item in list:
name = item[1:]
column = self.names[name]
@ -815,7 +815,7 @@ class dump:
if not snap.tselect: continue
for i in xrange(snap.natoms):
if snap.aselect[i]: exec ceq
# --------------------------------------------------------------------
# set a column value via an input vec for all selected snapshots/atoms
@ -835,7 +835,7 @@ class dump:
if snap.aselect[i]:
atoms[i][icol] = vec[m]
m += 1
# --------------------------------------------------------------------
# clone value in col across selected timesteps for atoms with same ID
@ -901,7 +901,7 @@ class dump:
columns.append(self.names[name])
values.append(self.nselect * [0])
ncol = len(columns)
id = self.names["id"]
m = 0
for snap in self.snaps:
@ -917,13 +917,13 @@ class dump:
if len(list) == 1: return values[0]
else: return values
# --------------------------------------------------------------------
# extract vector(s) of values for selected atoms at chosen timestep
def vecs(self,n,*list):
snap = self.snaps[self.findtime(n)]
if len(list) == 0:
raise StandardError, "no columns specified"
columns = []
@ -978,7 +978,7 @@ class dump:
del self.snaps[i]
else:
i += 1
# --------------------------------------------------------------------
# iterate over selected snapshots
@ -990,12 +990,12 @@ class dump:
self.iterate = i
return i,self.snaps[i].time,1
return 0,0,-1
# --------------------------------------------------------------------
# return list of atoms to viz for snapshot isnap
# if called with flag, then index is timestep, so convert to snapshot index
# augment with bonds, tris, lines if extra() was invoked
def viz(self,index,flag=0):
if not flag: isnap = index
else:
@ -1019,7 +1019,7 @@ class dump:
# create atom list needed by viz from id,type,x,y,z
# need Numeric/Numpy mode here
atoms = []
for i in xrange(snap.natoms):
if not snap.aselect[i]: continue
@ -1059,7 +1059,7 @@ class dump:
if self.triflag == 1: tris = self.trilist
elif self.triflag == 2:
tmp1,tmp2,tmp3,tmp4,tris,tmp5 = self.objextra.viz(time,1)
# create list of lines from static or dynamic tri list
# if dynamic, could eliminate lines for unselected atoms
@ -1070,7 +1070,7 @@ class dump:
tmp1,tmp2,tmp3,tmp4,tmp5,lines = self.objextra.viz(time,1)
return time,box,atoms,bonds,tris,lines
# --------------------------------------------------------------------
def findtime(self,n):
@ -1115,7 +1115,7 @@ class dump:
def extra(self,arg):
# data object, grab bonds statically
if type(arg) is types.InstanceType and ".data" in str(arg.__class__):
self.bondflag = 0
try:
@ -1132,7 +1132,7 @@ class dump:
raise StandardError,"could not extract bonds from data object"
# cdata object, grab tris and lines statically
elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__):
self.triflag = self.lineflag = 0
try:
@ -1147,32 +1147,32 @@ class dump:
raise StandardError,"could not extract tris/lines from cdata object"
# mdump object, grab tris dynamically
elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__):
self.triflag = 2
self.objextra = arg
# bdump object, grab bonds dynamically
elif type(arg) is types.InstanceType and ".bdump" in str(arg.__class__):
self.bondflag = 2
self.objextra = arg
# ldump object, grab lines dynamically
elif type(arg) is types.InstanceType and ".ldump" in str(arg.__class__):
self.lineflag = 2
self.objextra = arg
# tdump object, grab tris dynamically
elif type(arg) is types.InstanceType and ".tdump" in str(arg.__class__):
self.triflag = 2
self.objextra = arg
else:
raise StandardError,"unrecognized argument to dump.extra()"
# --------------------------------------------------------------------
def compare_atom(self,a,b):
@ -1181,7 +1181,7 @@ class dump:
elif a[0] > b[0]:
return 1
else:
return 0
return 0
# --------------------------------------------------------------------
# one snapshot
@ -1196,7 +1196,7 @@ class tselect:
def __init__(self,data):
self.data = data
# --------------------------------------------------------------------
def all(self):
@ -1243,7 +1243,7 @@ class tselect:
data.nselect -= 1
data.aselect.all()
print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
# --------------------------------------------------------------------
def test(self,teststr):
@ -1289,7 +1289,7 @@ class aselect:
data = self.data
# replace all $var with snap.atoms references and compile test string
pattern = "\$\w*"
list = re.findall(pattern,teststr)
for item in list:

66
tools/python/pizza/gnu.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# gnu tool
@ -11,12 +11,12 @@
oneline = "Create plots via GnuPlot plotting program"
docstr = """
g = gnu() start up GnuPlot
g.stop() shut down GnuPlot process
g = gnu() start up GnuPlot
g.stop() shut down GnuPlot process
g.plot(a) plot vector A against linear index
g.plot(a,b) plot B against A
g.plot(a,b,c,d,...) plot B against A, D against C, etc
g.plot(a,b) plot B against A
g.plot(a,b,c,d,...) plot B against A, D against C, etc
g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
each plot argument can be a tuple, list, or Numeric/NumPy vector
@ -29,21 +29,21 @@ g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot
g.enter() enter GnuPlot shell
g.enter() enter GnuPlot shell
gnuplot> plot sin(x) with lines type commands directly to GnuPlot
gnuplot> exit, quit exit GnuPlot shell
gnuplot> exit, quit exit GnuPlot shell
g.export("data",range(100),a,...) create file with columns of numbers
all vectors must be of equal length
could plot from file with GnuPlot command: plot 'data' using 1:2 with lines
g.select(N) figure N becomes the current plot
g.select(N) figure N becomes the current plot
subsequent commands apply to this plot
g.hide(N) delete window for figure N
g.save("file") save current plot as file.eps
g.hide(N) delete window for figure N
g.save("file") save current plot as file.eps
Set attributes for current plot:
@ -94,7 +94,7 @@ except: PIZZA_GNUTERM = "x11"
# Class definition
class gnu:
# --------------------------------------------------------------------
def __init__(self):
@ -102,7 +102,7 @@ class gnu:
self.file = "tmp.gnu"
self.figures = []
self.select(1)
# --------------------------------------------------------------------
def stop(self):
@ -114,7 +114,7 @@ class gnu:
def __call__(self,command):
self.GNUPLOT.write(command + '\n')
self.GNUPLOT.flush()
# --------------------------------------------------------------------
def enter(self):
@ -152,7 +152,7 @@ class gnu:
if i: partial_vecs.append(vec[:i])
else: partial_vecs.append([0])
self.plot(*partial_vecs)
if n < 10: newfile = file + "000" + str(n)
elif n < 100: newfile = file + "00" + str(n)
elif n < 1000: newfile = file + "0" + str(n)
@ -160,7 +160,7 @@ class gnu:
self.save(newfile)
n += 1
# --------------------------------------------------------------------
# write list of equal-length vectors to filename
@ -201,7 +201,7 @@ class gnu:
# do not continue until plot file is written out
# else script could go forward and change data file
# use tmp.done as semaphore to indicate plot is finished
def save(self,file):
self.__call__("set terminal postscript enhanced solid lw 2 color portrait")
cmd = "set output '%s.eps'" % file
@ -212,7 +212,7 @@ class gnu:
while not os.path.exists("tmp.done"): continue
self.__call__("set output")
self.select(self.current)
# --------------------------------------------------------------------
# restore default attributes by creating a new fig object
@ -221,7 +221,7 @@ class gnu:
fig.ncurves = self.figures[self.current-1].ncurves
self.figures[self.current-1] = fig
self.draw()
# --------------------------------------------------------------------
def aspect(self,value):
@ -245,12 +245,12 @@ class gnu:
else:
self.figures[self.current-1].ylimit = (values[0],values[1])
self.draw()
# --------------------------------------------------------------------
def label(self,x,y,text):
self.figures[self.current-1].labels.append((x,y,text))
self.figures[self.current-1].nlabels += 1
self.figures[self.current-1].nlabels += 1
self.draw()
# --------------------------------------------------------------------
@ -259,7 +259,7 @@ class gnu:
self.figures[self.current-1].nlabel = 0
self.figures[self.current-1].labels = []
self.draw()
# --------------------------------------------------------------------
def title(self,*strings):
@ -276,13 +276,13 @@ class gnu:
def xtitle(self,label):
self.figures[self.current-1].xtitle = label
self.draw()
# --------------------------------------------------------------------
def ytitle(self,label):
self.figures[self.current-1].ytitle = label
self.draw()
# --------------------------------------------------------------------
def xlog(self):
@ -291,7 +291,7 @@ class gnu:
else:
self.figures[self.current-1].xlog = 1
self.draw()
# --------------------------------------------------------------------
def ylog(self):
@ -300,7 +300,7 @@ class gnu:
else:
self.figures[self.current-1].ylog = 1
self.draw()
# --------------------------------------------------------------------
def curve(self,num,color):
@ -316,10 +316,10 @@ class gnu:
def draw(self):
fig = self.figures[self.current-1]
if not fig.ncurves: return
cmd = 'set size ratio ' + str(1.0/float(fig.aspect))
self.__call__(cmd)
cmd = 'set title ' + '"' + fig.title + '"'
self.__call__(cmd)
cmd = 'set xlabel ' + '"' + fig.xtitle + '"'
@ -331,11 +331,11 @@ class gnu:
else: self.__call__("unset logscale x")
if fig.ylog: self.__call__("set logscale y")
else: self.__call__("unset logscale y")
if fig.xlimit:
if fig.xlimit:
cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']'
self.__call__(cmd)
else: self.__call__("set xr [*:*]")
if fig.ylimit:
if fig.ylimit:
cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']'
self.__call__(cmd)
else: self.__call__("set yr [*:*]")
@ -365,7 +365,7 @@ class figure:
def __init__(self):
self.ncurves = 0
self.colors = []
self.colors = []
self.title = ""
self.xtitle = ""
self.ytitle = ""

46
tools/python/pizza/log.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# log tool
@ -28,7 +28,7 @@ nvec = l.nvec # of vectors of thermo info
nlen = l.nlen length of each vectors
names = l.names list of vector names
t,pe,... = l.get("Time","KE",...) return one or more vectors of values
l.write("file.txt") write all vectors to a file
l.write("file.txt") write all vectors to a file
l.write("file.txt","Time","PE",...) write listed vectors to a file
get and write allow abbreviated (uniquely) vector names
@ -89,7 +89,7 @@ class log:
# --------------------------------------------------------------------
# read all thermo from all files
def read_all(self):
self.read_header(self.flist[0])
if self.nvec == 0: raise StandardError,"log file has no values"
@ -100,7 +100,7 @@ class log:
print
# sort entries by timestep, cull duplicates
self.data.sort(self.compare)
self.cull()
self.nlen = len(self.data)
@ -133,9 +133,9 @@ class log:
else:
count = 0
for i in range(self.nvec):
if self.names[i].find(key) == 0:
count += 1
index = i
if self.names[i].find(key) == 0:
count += 1
index = i
if count == 1:
map.append(index)
else:
@ -161,9 +161,9 @@ class log:
else:
count = 0
for i in range(self.nvec):
if self.names[i].find(key) == 0:
count += 1
index = i
if self.names[i].find(key) == 0:
count += 1
index = i
if count == 1:
map.append(index)
else:
@ -226,7 +226,7 @@ class log:
keywords.insert(0,"Step")
i = 0
for keyword in keywords:
self.names.append(keyword)
self.names.append(keyword)
self.ptr[keyword] = i
i += 1
@ -236,7 +236,7 @@ class log:
line = txt[s1:s2]
words = line.split()
for i in range(len(words)):
self.names.append(words[i])
self.names.append(words[i])
self.ptr[words[i]] = i
self.nvec = len(self.names)
@ -275,43 +275,43 @@ class log:
if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2
if self.style == 2:
s1 = txt.find("\n",s1) + 1
s1 = txt.find("\n",s1) + 1
elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1
s1 = 0
elif s1 == -1 and s2 >= 0: # found s2, but no s1
last = 1
last = 1
s1 = 0
elif s1 >= 0 and s2 == -1: # found s1, but no s2
last = 1
if self.style == 1:
s2 = txt.rfind("\n--",s1) + 1
else:
s1 = txt.find("\n",s1) + 1
s1 = txt.find("\n",s1) + 1
s2 = txt.rfind("\n",s1) + 1
eof -= len(txt) - s2
eof -= len(txt) - s2
elif s1 == -1 and s2 == -1: # found neither
# could be end-of-file section
# or entire read was one chunk
# or entire read was one chunk
if txt.find("Loop time of",start) == start: # end of file, so exit
eof -= len(txt) - start # reset eof to "Loop"
break
eof -= len(txt) - start # reset eof to "Loop"
break
last = 1 # entire read is a chunk
last = 1 # entire read is a chunk
s1 = 0
if self.style == 1:
s2 = txt.rfind("\n--",s1) + 1
else:
s2 = txt.rfind("\n",s1) + 1
eof -= len(txt) - s2
if s1 == s2: break
eof -= len(txt) - s2
if s1 == s2: break
chunk = txt[s1:s2-1]
start = s2
# split chunk into entries
# parse each entry for numeric fields, append to data
if self.style == 1:
sections = chunk.split("\n--")
pat1 = re.compile("Step\s*(\S*)\s")

28
tools/python/pizza/pdbfile.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# pdb tool
@ -22,7 +22,7 @@ p = pdbfile("3CRO",d) read in single PDB file with snapshot data
if only one 4-char file specified and it is not found,
it will be downloaded from http://www.rcsb.org as 3CRO.pdb
d arg is object with atom coordinates (dump, data)
p.one() write all output as one big PDB file to tmp.pdb
p.one("mine") write to mine.pdb
p.many() write one PDB file per snapshot: tmp0000.pdb, ...
@ -36,7 +36,7 @@ p.single(N,"new") write as new.pdb
if one file in str arg and d: one new PDB file per snapshot
using input PDB file as template
multiple input PDB files with a d is not allowed
index,time,flag = p.iterator(0)
index,time,flag = p.iterator(1)
@ -87,7 +87,7 @@ class pdbfile:
# flist = full list of all PDB input file names
# append .pdb if needed
if filestr:
list = filestr.split()
flist = []
@ -107,7 +107,7 @@ class pdbfile:
raise StandardError, "no input PDB file(s)"
# grab PDB file from http://rcsb.org if not a local file
if len(self.files) == 1 and len(self.files[0]) == 8:
try:
open(self.files[0],'r').close()
@ -117,7 +117,7 @@ class pdbfile:
urllib.urlretrieve(fetchstr,self.files[0])
if self.data and len(self.files): self.read_template(self.files[0])
# --------------------------------------------------------------------
# write a single large PDB file for concatenating all input data or files
# if data exists:
@ -135,7 +135,7 @@ class pdbfile:
f = open(file,'w')
# use template PDB file with each snapshot
if self.data:
n = flag = 0
while 1:
@ -153,7 +153,7 @@ class pdbfile:
print >>f,"END"
print file,
sys.stdout.flush()
f.close()
print "\nwrote %d datasets to %s in PDB format" % (n,file)
@ -189,7 +189,7 @@ class pdbfile:
f = open(file,'w')
self.convert(f,which)
f.close()
print time,
sys.stdout.flush()
n += 1
@ -206,13 +206,13 @@ class pdbfile:
else:
file = root + str(n)
file += ".pdb"
f = open(file,'w')
f.write(open(infile,'r').read())
f.close()
print file,
sys.stdout.flush()
n += 1
print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)
@ -239,7 +239,7 @@ class pdbfile:
self.convert(f,which)
else:
f.write(open(self.files[time],'r').read())
f.close()
# --------------------------------------------------------------------
@ -258,8 +258,8 @@ class pdbfile:
# --------------------------------------------------------------------
# read a PDB file and store ATOM lines
def read_template(self,file):
def read_template(self,file):
lines = open(file,'r').readlines()
self.atomlines = {}
for line in lines:

24
tools/python/pizza/xyz.py
View File

@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# xyz tool
@ -11,14 +11,14 @@
oneline = "Convert LAMMPS snapshots to XYZ format"
docstr = """
x = xyz(d) d = object containing atom coords (dump, data)
x = xyz(d) d = object containing atom coords (dump, data)
x.one() write all snapshots to tmp.xyz
x.one("new") write all snapshots to new.xyz
x.many() write snapshots to tmp0000.xyz, tmp0001.xyz, etc
x.many("new") write snapshots to new0000.xyz, new0001.xyz, etc
x.single(N) write snapshot for timestep N to tmp.xyz
x.single(N,"file") write snapshot for timestep N to file.xyz
x.single(N) write snapshot for timestep N to tmp.xyz
x.single(N,"file") write snapshot for timestep N to file.xyz
"""
# History
@ -41,7 +41,7 @@ class xyz:
def __init__(self,data):
self.data = data
# --------------------------------------------------------------------
def one(self,*args):
@ -61,14 +61,14 @@ class xyz:
for atom in atoms:
itype = int(atom[1])
print >>f,itype,atom[2],atom[3],atom[4]
print time,
sys.stdout.flush()
n += 1
f.close()
print "\nwrote %d snapshots to %s in XYZ format" % (n,file)
# --------------------------------------------------------------------
def many(self,*args):
@ -80,7 +80,7 @@ class xyz:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
time,box,atoms,bonds,tris,lines = self.data.viz(which)
if n < 10:
file = root + "000" + str(n)
elif n < 100:
@ -88,7 +88,7 @@ class xyz:
elif n < 1000:
file = root + "0" + str(n)
else:
file = root + str(n)
file = root + str(n)
file += ".xyz"
f = open(file,"w")
print >>f,len(atoms)
@ -100,9 +100,9 @@ class xyz:
sys.stdout.flush()
f.close()
n += 1
print "\nwrote %s snapshots in XYZ format" % n
# --------------------------------------------------------------------
def single(self,time,*args):