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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
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@ -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: