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Sync copies of pizza

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This commit is contained in:
Richard Berger
2021-06-02 13:09:52 -04:00
parent 3f1bbf7c71
commit 249a2a6783
6 changed files with 424 additions and 505 deletions
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76
python/examples/pizza/dump.py
View File

@ -3,7 +3,7 @@
# #
# Copyright (2005) Sandia Corporation. Under the terms of Contract # Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains # 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. # the GNU General Public License.
# for python3 compatibility # for python3 compatibility
@ -35,7 +35,7 @@ time = d.next() read next snapshot from dump files
d.map(1,"id",3,"x") assign names to atom columns (1-N) d.map(1,"id",3,"x") assign names to atom columns (1-N)
not needed if dump file is self-describing not needed if dump file is self-describing
d.tselect.all() select all timesteps d.tselect.all() select all timesteps
d.tselect.one(N) select only timestep N d.tselect.one(N) select only timestep N
d.tselect.none() deselect all timesteps d.tselect.none() deselect all timesteps
@ -227,7 +227,7 @@ class dump:
for word in words: self.flist += glob.glob(word) for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1: if len(self.flist) == 0 and len(list) == 1:
raise Exception("no dump file specified") raise Exception("no dump file specified")
if len(list) == 1: if len(list) == 1:
self.increment = 0 self.increment = 0
self.read_all() self.read_all()
@ -270,7 +270,7 @@ class dump:
self.tselect.all() self.tselect.all()
# set default names for atom columns if file wasn't self-describing # set default names for atom columns if file wasn't self-describing
if len(self.snaps) == 0: if len(self.snaps) == 0:
print("no column assignments made") print("no column assignments made")
elif len(self.names): elif len(self.names):
@ -341,7 +341,7 @@ class dump:
# return snapshot or 0 if failed # return snapshot or 0 if failed
# assign column names if not already done and file is self-describing # assign column names if not already done and file is self-describing
# convert xs,xu to x # convert xs,xu to x
def read_snapshot(self,f): def read_snapshot(self,f):
try: try:
snap = Snap() snap = Snap()
@ -414,7 +414,7 @@ class dump:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# map atom column names # map atom column names
def map(self,*pairs): def map(self,*pairs):
if len(pairs) % 2 != 0: if len(pairs) % 2 != 0:
raise Exception("dump map() requires pairs of mappings") raise Exception("dump map() requires pairs of mappings")
@ -492,7 +492,7 @@ class dump:
atoms[:,x] = snap.xlo + atoms[:,x]*xprd atoms[:,x] = snap.xlo + atoms[:,x]*xprd
atoms[:,y] = snap.ylo + atoms[:,y]*yprd atoms[:,y] = snap.ylo + atoms[:,y]*yprd
atoms[:,z] = snap.zlo + atoms[:,z]*zprd atoms[:,z] = snap.zlo + atoms[:,z]*zprd
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# wrap coords from outside box to inside # wrap coords from outside box to inside
@ -505,7 +505,7 @@ class dump:
ix = self.names["ix"] ix = self.names["ix"]
iy = self.names["iy"] iy = self.names["iy"]
iz = self.names["iz"] iz = self.names["iz"]
for snap in self.snaps: for snap in self.snaps:
xprd = snap.xhi - snap.xlo xprd = snap.xhi - snap.xlo
yprd = snap.yhi - snap.ylo yprd = snap.yhi - snap.ylo
@ -527,7 +527,7 @@ class dump:
ix = self.names["ix"] ix = self.names["ix"]
iy = self.names["iy"] iy = self.names["iy"]
iz = self.names["iz"] iz = self.names["iz"]
for snap in self.snaps: for snap in self.snaps:
xprd = snap.xhi - snap.xlo xprd = snap.xhi - snap.xlo
yprd = snap.yhi - snap.ylo yprd = snap.yhi - snap.ylo
@ -542,7 +542,7 @@ class dump:
def owrap(self,other): def owrap(self,other):
print("Wrapping to other ...") print("Wrapping to other ...")
id = self.names["id"] id = self.names["id"]
x = self.names["x"] x = self.names["x"]
y = self.names["y"] y = self.names["y"]
@ -551,7 +551,7 @@ class dump:
iy = self.names["iy"] iy = self.names["iy"]
iz = self.names["iz"] iz = self.names["iz"]
iother = self.names[other] iother = self.names[other]
for snap in self.snaps: for snap in self.snaps:
xprd = snap.xhi - snap.xlo xprd = snap.xhi - snap.xlo
yprd = snap.yhi - snap.ylo yprd = snap.yhi - snap.ylo
@ -568,7 +568,7 @@ class dump:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# convert column names assignment to a string, in column order # convert column names assignment to a string, in column order
def names2str(self): def names2str(self):
ncol = len(self.snaps[0].atoms[0]) ncol = len(self.snaps[0].atoms[0])
pairs = self.names.items() pairs = self.names.items()
@ -631,7 +631,7 @@ class dump:
print(snap.ylo,snap.yhi,file=f) print(snap.ylo,snap.yhi,file=f)
print(snap.zlo,snap.zhi,file=f) print(snap.zlo,snap.zhi,file=f)
print("ITEM: ATOMS",namestr,file=f) print("ITEM: ATOMS",namestr,file=f)
atoms = snap.atoms atoms = snap.atoms
nvalues = len(atoms[0]) nvalues = len(atoms[0])
for i in range(snap.natoms): for i in range(snap.natoms):
@ -655,7 +655,7 @@ class dump:
if not snap.tselect: continue if not snap.tselect: continue
print(snap.time,end='') print(snap.time,end='')
sys.stdout.flush() sys.stdout.flush()
file = root + "." + str(snap.time) file = root + "." + str(snap.time)
f = open(file,"w") f = open(file,"w")
print("ITEM: TIMESTEP",file=f) print("ITEM: TIMESTEP",file=f)
@ -667,7 +667,7 @@ class dump:
print(snap.ylo,snap.yhi,file=f) print(snap.ylo,snap.yhi,file=f)
print(snap.zlo,snap.zhi,file=f) print(snap.zlo,snap.zhi,file=f)
print("ITEM: ATOMS",namestr,file=f) print("ITEM: ATOMS",namestr,file=f)
atoms = snap.atoms atoms = snap.atoms
nvalues = len(atoms[0]) nvalues = len(atoms[0])
for i in range(snap.natoms): for i in range(snap.natoms):
@ -709,7 +709,7 @@ class dump:
lhs = list[0][1:] lhs = list[0][1:]
if not self.names.has_key(lhs): if not self.names.has_key(lhs):
self.newcolumn(lhs) self.newcolumn(lhs)
for item in list: for item in list:
name = item[1:] name = item[1:]
column = self.names[name] column = self.names[name]
@ -721,7 +721,7 @@ class dump:
if not snap.tselect: continue if not snap.tselect: continue
for i in range(snap.natoms): for i in range(snap.natoms):
if snap.aselect[i]: exec(ceq) if snap.aselect[i]: exec(ceq)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# set a column value via an input vec for all selected snapshots/atoms # set a column value via an input vec for all selected snapshots/atoms
@ -741,7 +741,7 @@ class dump:
if snap.aselect[i]: if snap.aselect[i]:
atoms[i][icol] = vec[m] atoms[i][icol] = vec[m]
m += 1 m += 1
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# clone value in col across selected timesteps for atoms with same ID # clone value in col across selected timesteps for atoms with same ID
@ -807,7 +807,7 @@ class dump:
columns.append(self.names[name]) columns.append(self.names[name])
values.append(self.nselect * [0]) values.append(self.nselect * [0])
ncol = len(columns) ncol = len(columns)
id = self.names["id"] id = self.names["id"]
m = 0 m = 0
for snap in self.snaps: for snap in self.snaps:
@ -823,13 +823,13 @@ class dump:
if len(list) == 1: return values[0] if len(list) == 1: return values[0]
else: return values else: return values
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# extract vector(s) of values for selected atoms at chosen timestep # extract vector(s) of values for selected atoms at chosen timestep
def vecs(self,n,*list): def vecs(self,n,*list):
snap = self.snaps[self.findtime(n)] snap = self.snaps[self.findtime(n)]
if len(list) == 0: if len(list) == 0:
raise Exception("no columns specified") raise Exception("no columns specified")
columns = [] columns = []
@ -884,7 +884,7 @@ class dump:
del self.snaps[i] del self.snaps[i]
else: else:
i += 1 i += 1
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# iterate over selected snapshots # iterate over selected snapshots
@ -896,11 +896,11 @@ class dump:
self.iterate = i self.iterate = i
return i,self.snaps[i].time,1 return i,self.snaps[i].time,1
return 0,0,-1 return 0,0,-1
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# return list of atoms to viz for snapshot isnap # return list of atoms to viz for snapshot isnap
# augment with bonds, tris, lines if extra() was invoked # augment with bonds, tris, lines if extra() was invoked
def viz(self,isnap): def viz(self,isnap):
snap = self.snaps[isnap] snap = self.snaps[isnap]
@ -914,7 +914,7 @@ class dump:
# create atom list needed by viz from id,type,x,y,z # create atom list needed by viz from id,type,x,y,z
# need Numeric/Numpy mode here # need Numeric/Numpy mode here
atoms = [] atoms = []
for i in range(snap.natoms): for i in range(snap.natoms):
if not snap.aselect[i]: continue if not snap.aselect[i]: continue
@ -948,12 +948,12 @@ class dump:
elif self.triflag == 2: elif self.triflag == 2:
timetmp,boxtmp,atomstmp,bondstmp, \ timetmp,boxtmp,atomstmp,bondstmp, \
tris,linestmp = self.triobj.viz(time,1) tris,linestmp = self.triobj.viz(time,1)
lines = [] lines = []
if self.lineflag: lines = self.linelist if self.lineflag: lines = self.linelist
return time,box,atoms,bonds,tris,lines return time,box,atoms,bonds,tris,lines
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def findtime(self,n): def findtime(self,n):
@ -997,7 +997,7 @@ class dump:
def extra(self,arg): def extra(self,arg):
# read bonds from bond dump file # read bonds from bond dump file
if type(arg) is types.StringType: if type(arg) is types.StringType:
try: try:
f = open(arg,'r') f = open(arg,'r')
@ -1017,7 +1017,7 @@ class dump:
f.close() f.close()
# convert values to int and absolute value since can be negative types # convert values to int and absolute value since can be negative types
if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int) if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
else: bondlist = np.zeros((nbonds,4),np.int) else: bondlist = np.zeros((nbonds,4),np.int)
ints = [abs(int(value)) for value in words] ints = [abs(int(value)) for value in words]
@ -1032,9 +1032,9 @@ class dump:
self.bondlist = bondlist self.bondlist = bondlist
except: except:
raise Exception("could not read from bond dump file") raise Exception("could not read from bond dump file")
# request bonds from data object # request bonds from data object
elif type(arg) is types.InstanceType and ".data" in str(arg.__class__): elif type(arg) is types.InstanceType and ".data" in str(arg.__class__):
try: try:
bondlist = [] bondlist = []
@ -1050,7 +1050,7 @@ class dump:
raise Exception("could not extract bonds from data object") raise Exception("could not extract bonds from data object")
# request tris/lines from cdata object # request tris/lines from cdata object
elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__): elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__):
try: try:
tmp,tmp,tmp,tmp,tris,lines = arg.viz(0) tmp,tmp,tmp,tmp,tris,lines = arg.viz(0)
@ -1064,7 +1064,7 @@ class dump:
raise Exception("could not extract tris/lines from cdata object") raise Exception("could not extract tris/lines from cdata object")
# request tris from mdump object # request tris from mdump object
elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__): elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__):
try: try:
self.triflag = 2 self.triflag = 2
@ -1074,7 +1074,7 @@ class dump:
else: else:
raise Exception("unrecognized argument to dump.extra()") raise Exception("unrecognized argument to dump.extra()")
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def compare_atom(self,a,b): def compare_atom(self,a,b):
@ -1083,7 +1083,7 @@ class dump:
elif a[0] > b[0]: elif a[0] > b[0]:
return 1 return 1
else: else:
return 0 return 0
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# one snapshot # one snapshot
@ -1098,7 +1098,7 @@ class tselect:
def __init__(self,data): def __init__(self,data):
self.data = data self.data = data
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def all(self): def all(self):
@ -1145,7 +1145,7 @@ class tselect:
data.nselect -= 1 data.nselect -= 1
data.aselect.all() data.aselect.all()
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps)) print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def test(self,teststr): def test(self,teststr):
@ -1191,7 +1191,7 @@ class aselect:
data = self.data data = self.data
# replace all $var with snap.atoms references and compile test string # replace all $var with snap.atoms references and compile test string
pattern = "\$\w*" pattern = "\$\w*"
list = re.findall(pattern,teststr) list = re.findall(pattern,teststr)
for item in list: for item in list:

48
python/examples/pizza/gnu.py
View File

@ -3,7 +3,7 @@
# #
# Copyright (2005) Sandia Corporation. Under the terms of Contract # Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains # 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. # the GNU General Public License.
# for python3 compatibility # for python3 compatibility
@ -16,7 +16,7 @@ oneline = "Create plots via GnuPlot plotting program"
docstr = """ docstr = """
g = gnu() start up GnuPlot g = gnu() start up GnuPlot
g.stop() shut down GnuPlot process g.stop() shut down GnuPlot process
g.plot(a) plot vector A against linear index g.plot(a) plot vector A against linear index
g.plot(a,b) plot B against A 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,c,d,...) plot B against A, D against C, etc
@ -35,14 +35,14 @@ 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> 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 g.export("data",range(100),a,...) create file with columns of numbers
all vectors must be of equal length all vectors must be of equal length
could plot from file with GnuPlot command: plot 'data' using 1:2 with lines 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 subsequent commands apply to this plot
g.hide(N) delete window for figure N g.hide(N) delete window for figure N
@ -98,7 +98,7 @@ except ImportError: PIZZA_GNUTERM = "x11"
# Class definition # Class definition
class gnu: class gnu:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def __init__(self): def __init__(self):
@ -106,7 +106,7 @@ class gnu:
self.file = "tmp.gnu" self.file = "tmp.gnu"
self.figures = [] self.figures = []
self.select(1) self.select(1)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def stop(self): def stop(self):
@ -118,7 +118,7 @@ class gnu:
def __call__(self,command): def __call__(self,command):
self.GNUPLOT.write(command + '\n') self.GNUPLOT.write(command + '\n')
self.GNUPLOT.flush() self.GNUPLOT.flush()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def enter(self): def enter(self):
@ -159,7 +159,7 @@ class gnu:
if i: partial_vecs.append(vec[:i]) if i: partial_vecs.append(vec[:i])
else: partial_vecs.append([0]) else: partial_vecs.append([0])
self.plot(*partial_vecs) self.plot(*partial_vecs)
if n < 10: newfile = file + "000" + str(n) if n < 10: newfile = file + "000" + str(n)
elif n < 100: newfile = file + "00" + str(n) elif n < 100: newfile = file + "00" + str(n)
elif n < 1000: newfile = file + "0" + str(n) elif n < 1000: newfile = file + "0" + str(n)
@ -167,7 +167,7 @@ class gnu:
self.save(newfile) self.save(newfile)
n += 1 n += 1
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# write list of equal-length vectors to filename # write list of equal-length vectors to filename
@ -208,7 +208,7 @@ class gnu:
# do not continue until plot file is written out # do not continue until plot file is written out
# else script could go forward and change data file # else script could go forward and change data file
# use tmp.done as semaphore to indicate plot is finished # use tmp.done as semaphore to indicate plot is finished
def save(self,file): def save(self,file):
self.__call__("set terminal postscript enhanced solid lw 2 color portrait") self.__call__("set terminal postscript enhanced solid lw 2 color portrait")
cmd = "set output '%s.eps'" % file cmd = "set output '%s.eps'" % file
@ -219,7 +219,7 @@ class gnu:
while not os.path.exists("tmp.done"): continue while not os.path.exists("tmp.done"): continue
self.__call__("set output") self.__call__("set output")
self.select(self.current) self.select(self.current)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# restore default attributes by creating a new fig object # restore default attributes by creating a new fig object
@ -228,7 +228,7 @@ class gnu:
fig.ncurves = self.figures[self.current-1].ncurves fig.ncurves = self.figures[self.current-1].ncurves
self.figures[self.current-1] = fig self.figures[self.current-1] = fig
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def aspect(self,value): def aspect(self,value):
@ -252,12 +252,12 @@ class gnu:
else: else:
self.figures[self.current-1].ylimit = (values[0],values[1]) self.figures[self.current-1].ylimit = (values[0],values[1])
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def label(self,x,y,text): def label(self,x,y,text):
self.figures[self.current-1].labels.append((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() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
@ -266,7 +266,7 @@ class gnu:
self.figures[self.current-1].nlabel = 0 self.figures[self.current-1].nlabel = 0
self.figures[self.current-1].labels = [] self.figures[self.current-1].labels = []
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def title(self,*strings): def title(self,*strings):
@ -283,13 +283,13 @@ class gnu:
def xtitle(self,label): def xtitle(self,label):
self.figures[self.current-1].xtitle = label self.figures[self.current-1].xtitle = label
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def ytitle(self,label): def ytitle(self,label):
self.figures[self.current-1].ytitle = label self.figures[self.current-1].ytitle = label
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def xlog(self): def xlog(self):
@ -298,7 +298,7 @@ class gnu:
else: else:
self.figures[self.current-1].xlog = 1 self.figures[self.current-1].xlog = 1
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def ylog(self): def ylog(self):
@ -307,7 +307,7 @@ class gnu:
else: else:
self.figures[self.current-1].ylog = 1 self.figures[self.current-1].ylog = 1
self.draw() self.draw()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def curve(self,num,color): def curve(self,num,color):
@ -323,10 +323,10 @@ class gnu:
def draw(self): def draw(self):
fig = self.figures[self.current-1] fig = self.figures[self.current-1]
if not fig.ncurves: return if not fig.ncurves: return
cmd = 'set size ratio ' + str(1.0/float(fig.aspect)) cmd = 'set size ratio ' + str(1.0/float(fig.aspect))
self.__call__(cmd) self.__call__(cmd)
cmd = 'set title ' + '"' + fig.title + '"' cmd = 'set title ' + '"' + fig.title + '"'
self.__call__(cmd) self.__call__(cmd)
cmd = 'set xlabel ' + '"' + fig.xtitle + '"' cmd = 'set xlabel ' + '"' + fig.xtitle + '"'
@ -338,11 +338,11 @@ class gnu:
else: self.__call__("unset logscale x") else: self.__call__("unset logscale x")
if fig.ylog: self.__call__("set logscale y") if fig.ylog: self.__call__("set logscale y")
else: self.__call__("unset 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]) + ']' cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']'
self.__call__(cmd) self.__call__(cmd)
else: self.__call__("set xr [*:*]") else: self.__call__("set xr [*:*]")
if fig.ylimit: if fig.ylimit:
cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']' cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']'
self.__call__(cmd) self.__call__(cmd)
else: self.__call__("set yr [*:*]") else: self.__call__("set yr [*:*]")
@ -372,7 +372,7 @@ class figure:
def __init__(self): def __init__(self):
self.ncurves = 0 self.ncurves = 0
self.colors = [] self.colors = []
self.title = "" self.title = ""
self.xtitle = "" self.xtitle = ""
self.ytitle = "" self.ytitle = ""

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

@ -3,7 +3,7 @@
# #
# Copyright (2005) Sandia Corporation. Under the terms of Contract # Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains # 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. # the GNU General Public License.
# for python3 compatibility # for python3 compatibility
@ -25,7 +25,7 @@ p = pdbfile("3CRO",d) read in single PDB file with snapshot data
if only one 4-char file specified and it is not found, if only one 4-char file specified and it is not found,
it will be downloaded from http://www.rcsb.org as 3CRO.pdb it will be downloaded from http://www.rcsb.org as 3CRO.pdb
d arg is object with atom coordinates (dump, data) d arg is object with atom coordinates (dump, data)
p.one() write all output as one big PDB file to tmp.pdb p.one() write all output as one big PDB file to tmp.pdb
p.one("mine") write to mine.pdb p.one("mine") write to mine.pdb
p.many() write one PDB file per snapshot: tmp0000.pdb, ... p.many() write one PDB file per snapshot: tmp0000.pdb, ...
@ -39,7 +39,7 @@ p.single(N,"new") write as new.pdb
if one file in str arg and d: one new PDB file per snapshot if one file in str arg and d: one new PDB file per snapshot
using input PDB file as template using input PDB file as template
multiple input PDB files with a d is not allowed multiple input PDB files with a d is not allowed
index,time,flag = p.iterator(0) index,time,flag = p.iterator(0)
index,time,flag = p.iterator(1) index,time,flag = p.iterator(1)
@ -97,7 +97,7 @@ class pdbfile:
# flist = full list of all PDB input file names # flist = full list of all PDB input file names
# append .pdb if needed # append .pdb if needed
if filestr: if filestr:
list = filestr.split() list = filestr.split()
flist = [] flist = []
@ -117,7 +117,7 @@ class pdbfile:
raise Exception("no input PDB file(s)") raise Exception("no input PDB file(s)")
# grab PDB file from http://rcsb.org if not a local file # grab PDB file from http://rcsb.org if not a local file
if len(self.files) == 1 and len(self.files[0]) == 8: if len(self.files) == 1 and len(self.files[0]) == 8:
try: try:
open(self.files[0],'r').close() open(self.files[0],'r').close()
@ -127,7 +127,7 @@ class pdbfile:
urllib.urlretrieve(fetchstr,self.files[0]) urllib.urlretrieve(fetchstr,self.files[0])
if self.data and len(self.files): self.read_template(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 # write a single large PDB file for concatenating all input data or files
# if data exists: # if data exists:
@ -145,7 +145,7 @@ class pdbfile:
f = open(file,'w') f = open(file,'w')
# use template PDB file with each snapshot # use template PDB file with each snapshot
if self.data: if self.data:
n = flag = 0 n = flag = 0
while 1: while 1:
@ -163,7 +163,7 @@ class pdbfile:
print("END",file=f) print("END",file=f)
print(file,end='') print(file,end='')
sys.stdout.flush() sys.stdout.flush()
f.close() f.close()
print("\nwrote %d datasets to %s in PDB format" % (n,file)) print("\nwrote %d datasets to %s in PDB format" % (n,file))
@ -199,7 +199,7 @@ class pdbfile:
f = open(file,'w') f = open(file,'w')
self.convert(f,which) self.convert(f,which)
f.close() f.close()
print(time,end='') print(time,end='')
sys.stdout.flush() sys.stdout.flush()
n += 1 n += 1
@ -216,13 +216,13 @@ class pdbfile:
else: else:
file = root + str(n) file = root + str(n)
file += ".pdb" file += ".pdb"
f = open(file,'w') f = open(file,'w')
f.write(open(infile,'r').read()) f.write(open(infile,'r').read())
f.close() f.close()
print(file,end='') print(file,end='')
sys.stdout.flush() sys.stdout.flush()
n += 1 n += 1
print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root)) print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
@ -249,7 +249,7 @@ class pdbfile:
self.convert(f,which) self.convert(f,which)
else: else:
f.write(open(self.files[time],'r').read()) f.write(open(self.files[time],'r').read())
f.close() f.close()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
@ -268,8 +268,8 @@ class pdbfile:
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# read a PDB file and store ATOM lines # read a PDB file and store ATOM lines
def read_template(self,file): def read_template(self,file):
lines = open(file,'r').readlines() lines = open(file,'r').readlines()
self.atomlines = {} self.atomlines = {}
for line in lines: for line in lines:

684
tools/python/pizza/dump.py
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File diff suppressed because it is too large Load Diff

47
tools/python/pizza/gnu.py
View File

@ -6,17 +6,20 @@
# 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. # the GNU General Public License.
# for python3 compatibility
from __future__ import print_function
# gnu tool # gnu tool
oneline = "Create plots via GnuPlot plotting program" oneline = "Create plots via GnuPlot plotting program"
docstr = """ docstr = """
g = gnu() start up GnuPlot g = gnu() start up GnuPlot
g.stop() shut down GnuPlot process g.stop() shut down GnuPlot process
g.plot(a) plot vector A against linear index g.plot(a) plot vector A against linear index
g.plot(a,b) plot B against A 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,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 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 each plot argument can be a tuple, list, or Numeric/NumPy vector
@ -29,21 +32,21 @@ 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("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> 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 g.export("data",range(100),a,...) create file with columns of numbers
all vectors must be of equal length all vectors must be of equal length
could plot from file with GnuPlot command: plot 'data' using 1:2 with lines 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 subsequent commands apply to this plot
g.hide(N) delete window for figure N g.hide(N) delete window for figure N
g.save("file") save current plot as file.eps g.save("file") save current plot as file.eps
Set attributes for current plot: Set attributes for current plot:
@ -84,12 +87,13 @@ g.curve(N,'r') set color of curve N
# Imports and external programs # Imports and external programs
import types, os import os
import sys
try: from DEFAULTS import PIZZA_GNUPLOT try: from DEFAULTS import PIZZA_GNUPLOT
except: PIZZA_GNUPLOT = "gnuplot" except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
try: from DEFAULTS import PIZZA_GNUTERM try: from DEFAULTS import PIZZA_GNUTERM
except: PIZZA_GNUTERM = "x11" except ImportError: PIZZA_GNUTERM = "x11"
# Class definition # Class definition
@ -119,7 +123,10 @@ class gnu:
def enter(self): def enter(self):
while 1: while 1:
command = raw_input("gnuplot> ") if sys.version_info[0] == 3:
command = input("gnuplot> ")
else:
command = raw_input("gnuplot> ")
if command == "quit" or command == "exit": return if command == "quit" or command == "exit": return
self.__call__(command) self.__call__(command)
@ -133,7 +140,7 @@ class gnu:
self.export(file,linear,vectors[0]) self.export(file,linear,vectors[0])
self.figures[self.current-1].ncurves = 1 self.figures[self.current-1].ncurves = 1
else: else:
if len(vectors) % 2: raise StandardError,"vectors must come in pairs" if len(vectors) % 2: raise Exception("vectors must come in pairs")
for i in range(0,len(vectors),2): for i in range(0,len(vectors),2):
file = self.file + ".%d.%d" % (self.current,i/2+1) file = self.file + ".%d.%d" % (self.current,i/2+1)
self.export(file,vectors[i],vectors[i+1]) self.export(file,vectors[i],vectors[i+1])
@ -167,13 +174,13 @@ class gnu:
def export(self,filename,*vectors): def export(self,filename,*vectors):
n = len(vectors[0]) n = len(vectors[0])
for vector in vectors: for vector in vectors:
if len(vector) != n: raise StandardError,"vectors must be same length" if len(vector) != n: raise Exception("vectors must be same length")
f = open(filename,'w') f = open(filename,'w')
nvec = len(vectors) nvec = len(vectors)
for i in xrange(n): for i in range(n):
for j in xrange(nvec): for j in range(nvec):
print >>f,vectors[j][i], print(str(vectors[j][i])+" ",file=f,end='')
print >>f print ("",file=f)
f.close() f.close()
# -------------------------------------------------------------------- # --------------------------------------------------------------------
@ -350,7 +357,7 @@ class gnu:
self.__call__("set key off") self.__call__("set key off")
cmd = 'plot ' cmd = 'plot '
for i in range(fig.ncurves): for i in range(int(fig.ncurves)):
file = self.file + ".%d.%d" % (self.current,i+1) file = self.file + ".%d.%d" % (self.current,i+1)
if len(fig.colors) > i and fig.colors[i]: if len(fig.colors) > i and fig.colors[i]:
cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i] cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]

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

@ -6,6 +6,9 @@
# 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. # the GNU General Public License.
# for python3 compatibility
from __future__ import print_function
# pdb tool # pdb tool
oneline = "Read, write PDB files in combo with LAMMPS snapshots" oneline = "Read, write PDB files in combo with LAMMPS snapshots"
@ -51,6 +54,7 @@ index,time,flag = p.iterator(1)
# History # History
# 8/05, Steve Plimpton (SNL): original version # 8/05, Steve Plimpton (SNL): original version
# 3/17, Richard Berger (Temple U): improve Python 3 compatibility
# ToDo list # ToDo list
# for generic PDB file (no template) from a LJ unit system, # for generic PDB file (no template) from a LJ unit system,
@ -64,7 +68,13 @@ index,time,flag = p.iterator(1)
# Imports and external programs # Imports and external programs
import sys, types, glob, urllib import sys, glob, urllib
PY3 = sys.version_info[0] == 3
if PY3:
string_types = str,
else:
string_types = basestring
# Class definition # Class definition
@ -74,7 +84,7 @@ class pdbfile:
def __init__(self,*args): def __init__(self,*args):
if len(args) == 1: if len(args) == 1:
if type(args[0]) is types.StringType: if type(args[0]) is string_types:
filestr = args[0] filestr = args[0]
self.data = None self.data = None
else: else:
@ -83,7 +93,7 @@ class pdbfile:
elif len(args) == 2: elif len(args) == 2:
filestr = args[0] filestr = args[0]
self.data = args[1] self.data = args[1]
else: raise StandardError, "invalid args for pdb()" else: raise Exception("invalid args for pdb()")
# flist = full list of all PDB input file names # flist = full list of all PDB input file names
# append .pdb if needed # append .pdb if needed
@ -94,17 +104,17 @@ class pdbfile:
for file in list: for file in list:
if '*' in file: flist += glob.glob(file) if '*' in file: flist += glob.glob(file)
else: flist.append(file) else: flist.append(file)
for i in xrange(len(flist)): for i in range(len(flist)):
if flist[i][-4:] != ".pdb": flist[i] += ".pdb" if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
if len(flist) == 0: if len(flist) == 0:
raise StandardError,"no PDB file specified" raise Exception("no PDB file specified")
self.files = flist self.files = flist
else: self.files = [] else: self.files = []
if len(self.files) > 1 and self.data: if len(self.files) > 1 and self.data:
raise StandardError, "cannot use multiple PDB files with data object" raise Exception("cannot use multiple PDB files with data object")
if len(self.files) == 0 and not self.data: if len(self.files) == 0 and not self.data:
raise StandardError, "no input PDB file(s)" raise Exception("no input PDB file(s)")
# grab PDB file from http://rcsb.org if not a local file # grab PDB file from http://rcsb.org if not a local file
@ -112,7 +122,7 @@ class pdbfile:
try: try:
open(self.files[0],'r').close() open(self.files[0],'r').close()
except: except:
print "downloading %s from http://rcsb.org" % self.files[0] print("downloading %s from http://rcsb.org" % self.files[0])
fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0] fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0]
urllib.urlretrieve(fetchstr,self.files[0]) urllib.urlretrieve(fetchstr,self.files[0])
@ -142,20 +152,20 @@ class pdbfile:
which,time,flag = self.data.iterator(flag) which,time,flag = self.data.iterator(flag)
if flag == -1: break if flag == -1: break
self.convert(f,which) self.convert(f,which)
print >>f,"END" print("END",file=f)
print time, print(time,end='')
sys.stdout.flush() sys.stdout.flush()
n += 1 n += 1
else: else:
for file in self.files: for file in self.files:
f.write(open(file,'r').read()) f.write(open(file,'r').read())
print >>f,"END" print("END",file=f)
print file, print(file,end='')
sys.stdout.flush() sys.stdout.flush()
f.close() f.close()
print "\nwrote %d datasets to %s in PDB format" % (n,file) print("\nwrote %d datasets to %s in PDB format" % (n,file))
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# write series of numbered PDB files # write series of numbered PDB files
@ -190,7 +200,7 @@ class pdbfile:
self.convert(f,which) self.convert(f,which)
f.close() f.close()
print time, print(time,end='')
sys.stdout.flush() sys.stdout.flush()
n += 1 n += 1
@ -210,12 +220,12 @@ class pdbfile:
f = open(file,'w') f = open(file,'w')
f.write(open(infile,'r').read()) f.write(open(infile,'r').read())
f.close() f.close()
print file, print(file,end='')
sys.stdout.flush() sys.stdout.flush()
n += 1 n += 1
print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root) print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# write a single PDB file # write a single PDB file
@ -280,10 +290,10 @@ class pdbfile:
if self.atomlines.has_key(id): if self.atomlines.has_key(id):
(begin,end) = self.atomlines[id] (begin,end) = self.atomlines[id]
line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end) line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
print >>f,line, print(line,file=f,end='')
else: else:
for atom in atoms: for atom in atoms:
begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1]) begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1])
middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4]) middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4])
end = " 1.00 0.00 NONE" end = " 1.00 0.00 NONE"
print >>f,begin+middle+end print(begin+middle+end,file=f)