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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
# 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.
# 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)
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
@ -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 Exception("no dump file specified")
if len(list) == 1:
self.increment = 0
self.read_all()
@ -270,7 +270,7 @@ class dump:
self.tselect.all()
# set default names for atom columns if file wasn't self-describing
if len(self.snaps) == 0:
print("no column assignments made")
elif len(self.names):
@ -341,7 +341,7 @@ class dump:
# return snapshot or 0 if failed
# assign column names if not already done and file is self-describing
# convert xs,xu to x
def read_snapshot(self,f):
try:
snap = Snap()
@ -414,7 +414,7 @@ class dump:
# --------------------------------------------------------------------
# map atom column names
def map(self,*pairs):
if len(pairs) % 2 != 0:
raise Exception("dump map() requires pairs of mappings")
@ -492,7 +492,7 @@ class dump:
atoms[:,x] = snap.xlo + atoms[:,x]*xprd
atoms[:,y] = snap.ylo + atoms[:,y]*yprd
atoms[:,z] = snap.zlo + atoms[:,z]*zprd
# --------------------------------------------------------------------
# wrap coords from outside box to inside
@ -505,7 +505,7 @@ 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
@ -527,7 +527,7 @@ 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
@ -542,7 +542,7 @@ class dump:
def owrap(self,other):
print("Wrapping to other ...")
id = self.names["id"]
x = self.names["x"]
y = self.names["y"]
@ -551,7 +551,7 @@ class dump:
iy = self.names["iy"]
iz = self.names["iz"]
iother = self.names[other]
for snap in self.snaps:
xprd = snap.xhi - snap.xlo
yprd = snap.yhi - snap.ylo
@ -568,7 +568,7 @@ class dump:
# --------------------------------------------------------------------
# convert column names assignment to a string, in column order
def names2str(self):
ncol = len(self.snaps[0].atoms[0])
pairs = self.names.items()
@ -631,7 +631,7 @@ class dump:
print(snap.ylo,snap.yhi,file=f)
print(snap.zlo,snap.zhi,file=f)
print("ITEM: ATOMS",namestr,file=f)
atoms = snap.atoms
nvalues = len(atoms[0])
for i in range(snap.natoms):
@ -655,7 +655,7 @@ class dump:
if not snap.tselect: continue
print(snap.time,end='')
sys.stdout.flush()
file = root + "." + str(snap.time)
f = open(file,"w")
print("ITEM: TIMESTEP",file=f)
@ -667,7 +667,7 @@ class dump:
print(snap.ylo,snap.yhi,file=f)
print(snap.zlo,snap.zhi,file=f)
print("ITEM: ATOMS",namestr,file=f)
atoms = snap.atoms
nvalues = len(atoms[0])
for i in range(snap.natoms):
@ -709,7 +709,7 @@ 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]
@ -721,7 +721,7 @@ class dump:
if not snap.tselect: continue
for i in range(snap.natoms):
if snap.aselect[i]: exec(ceq)
# --------------------------------------------------------------------
# set a column value via an input vec for all selected snapshots/atoms
@ -741,7 +741,7 @@ 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
@ -807,7 +807,7 @@ 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:
@ -823,13 +823,13 @@ 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 Exception("no columns specified")
columns = []
@ -884,7 +884,7 @@ class dump:
del self.snaps[i]
else:
i += 1
# --------------------------------------------------------------------
# iterate over selected snapshots
@ -896,11 +896,11 @@ 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
# augment with bonds, tris, lines if extra() was invoked
def viz(self,isnap):
snap = self.snaps[isnap]
@ -914,7 +914,7 @@ class dump:
# create atom list needed by viz from id,type,x,y,z
# need Numeric/Numpy mode here
atoms = []
for i in range(snap.natoms):
if not snap.aselect[i]: continue
@ -948,12 +948,12 @@ class dump:
elif self.triflag == 2:
timetmp,boxtmp,atomstmp,bondstmp, \
tris,linestmp = self.triobj.viz(time,1)
lines = []
if self.lineflag: lines = self.linelist
return time,box,atoms,bonds,tris,lines
# --------------------------------------------------------------------
def findtime(self,n):
@ -997,7 +997,7 @@ class dump:
def extra(self,arg):
# read bonds from bond dump file
if type(arg) is types.StringType:
try:
f = open(arg,'r')
@ -1017,7 +1017,7 @@ class dump:
f.close()
# convert values to int and absolute value since can be negative types
if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
else: bondlist = np.zeros((nbonds,4),np.int)
ints = [abs(int(value)) for value in words]
@ -1032,9 +1032,9 @@ class dump:
self.bondlist = bondlist
except:
raise Exception("could not read from bond dump file")
# request bonds from data object
elif type(arg) is types.InstanceType and ".data" in str(arg.__class__):
try:
bondlist = []
@ -1050,7 +1050,7 @@ class dump:
raise Exception("could not extract bonds from data object")
# request tris/lines from cdata object
elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__):
try:
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")
# request tris from mdump object
elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__):
try:
self.triflag = 2
@ -1074,7 +1074,7 @@ class dump:
else:
raise Exception("unrecognized argument to dump.extra()")
# --------------------------------------------------------------------
def compare_atom(self,a,b):
@ -1083,7 +1083,7 @@ class dump:
elif a[0] > b[0]:
return 1
else:
return 0
return 0
# --------------------------------------------------------------------
# one snapshot
@ -1098,7 +1098,7 @@ class tselect:
def __init__(self,data):
self.data = data
# --------------------------------------------------------------------
def all(self):
@ -1145,7 +1145,7 @@ class tselect:
data.nselect -= 1
data.aselect.all()
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# --------------------------------------------------------------------
def test(self,teststr):
@ -1191,7 +1191,7 @@ 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:

48
python/examples/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.
# for python3 compatibility
@ -16,7 +16,7 @@ oneline = "Create plots via GnuPlot plotting program"
docstr = """
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
@ -35,14 +35,14 @@ g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot
g.enter() enter GnuPlot shell
gnuplot> plot sin(x) with lines type commands directly to GnuPlot
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
subsequent commands apply to this plot
g.hide(N) delete window for figure N
@ -98,7 +98,7 @@ except ImportError: PIZZA_GNUTERM = "x11"
# Class definition
class gnu:
# --------------------------------------------------------------------
def __init__(self):
@ -106,7 +106,7 @@ class gnu:
self.file = "tmp.gnu"
self.figures = []
self.select(1)
# --------------------------------------------------------------------
def stop(self):
@ -118,7 +118,7 @@ class gnu:
def __call__(self,command):
self.GNUPLOT.write(command + '\n')
self.GNUPLOT.flush()
# --------------------------------------------------------------------
def enter(self):
@ -159,7 +159,7 @@ 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)
@ -167,7 +167,7 @@ class gnu:
self.save(newfile)
n += 1
# --------------------------------------------------------------------
# write list of equal-length vectors to filename
@ -208,7 +208,7 @@ 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
@ -219,7 +219,7 @@ 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
@ -228,7 +228,7 @@ class gnu:
fig.ncurves = self.figures[self.current-1].ncurves
self.figures[self.current-1] = fig
self.draw()
# --------------------------------------------------------------------
def aspect(self,value):
@ -252,12 +252,12 @@ 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()
# --------------------------------------------------------------------
@ -266,7 +266,7 @@ class gnu:
self.figures[self.current-1].nlabel = 0
self.figures[self.current-1].labels = []
self.draw()
# --------------------------------------------------------------------
def title(self,*strings):
@ -283,13 +283,13 @@ 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):
@ -298,7 +298,7 @@ class gnu:
else:
self.figures[self.current-1].xlog = 1
self.draw()
# --------------------------------------------------------------------
def ylog(self):
@ -307,7 +307,7 @@ class gnu:
else:
self.figures[self.current-1].ylog = 1
self.draw()
# --------------------------------------------------------------------
def curve(self,num,color):
@ -323,10 +323,10 @@ 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 + '"'
@ -338,11 +338,11 @@ 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 [*:*]")
@ -372,7 +372,7 @@ class figure:
def __init__(self):
self.ncurves = 0
self.colors = []
self.colors = []
self.title = ""
self.xtitle = ""
self.ytitle = ""

28
python/examples/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.
# 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,
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, ...
@ -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
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)
@ -97,7 +97,7 @@ class pdbfile:
# flist = full list of all PDB input file names
# append .pdb if needed
if filestr:
list = filestr.split()
flist = []
@ -117,7 +117,7 @@ class pdbfile:
raise Exception("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()
@ -127,7 +127,7 @@ 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:
@ -145,7 +145,7 @@ class pdbfile:
f = open(file,'w')
# use template PDB file with each snapshot
if self.data:
n = flag = 0
while 1:
@ -163,7 +163,7 @@ class pdbfile:
print("END",file=f)
print(file,end='')
sys.stdout.flush()
f.close()
print("\nwrote %d datasets to %s in PDB format" % (n,file))
@ -199,7 +199,7 @@ class pdbfile:
f = open(file,'w')
self.convert(f,which)
f.close()
print(time,end='')
sys.stdout.flush()
n += 1
@ -216,13 +216,13 @@ class pdbfile:
else:
file = root + str(n)
file += ".pdb"
f = open(file,'w')
f.write(open(infile,'r').read())
f.close()
print(file,end='')
sys.stdout.flush()
n += 1
print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
@ -249,7 +249,7 @@ class pdbfile:
self.convert(f,which)
else:
f.write(open(self.files[time],'r').read())
f.close()
# --------------------------------------------------------------------
@ -268,8 +268,8 @@ 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: