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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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684
tools/python/pizza/dump.py
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47
tools/python/pizza/gnu.py
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@ -6,17 +6,20 @@
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
from __future__ import print_function
# gnu tool
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 +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.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:
@ -84,12 +87,13 @@ g.curve(N,'r') set color of curve N
# Imports and external programs
import types, os
import os
import sys
try: from DEFAULTS import PIZZA_GNUPLOT
except: PIZZA_GNUPLOT = "gnuplot"
except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
try: from DEFAULTS import PIZZA_GNUTERM
except: PIZZA_GNUTERM = "x11"
except ImportError: PIZZA_GNUTERM = "x11"
# Class definition
@ -119,7 +123,10 @@ class gnu:
def enter(self):
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
self.__call__(command)
@ -133,7 +140,7 @@ class gnu:
self.export(file,linear,vectors[0])
self.figures[self.current-1].ncurves = 1
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):
file = self.file + ".%d.%d" % (self.current,i/2+1)
self.export(file,vectors[i],vectors[i+1])
@ -167,13 +174,13 @@ class gnu:
def export(self,filename,*vectors):
n = len(vectors[0])
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')
nvec = len(vectors)
for i in xrange(n):
for j in xrange(nvec):
print >>f,vectors[j][i],
print >>f
for i in range(n):
for j in range(nvec):
print(str(vectors[j][i])+" ",file=f,end='')
print ("",file=f)
f.close()
# --------------------------------------------------------------------
@ -350,7 +357,7 @@ class gnu:
self.__call__("set key off")
cmd = 'plot '
for i in range(fig.ncurves):
for i in range(int(fig.ncurves)):
file = self.file + ".%d.%d" % (self.current,i+1)
if len(fig.colors) > i and fig.colors[i]:
cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]

46
tools/python/pizza/pdbfile.py
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@ -6,6 +6,9 @@
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
from __future__ import print_function
# pdb tool
oneline = "Read, write PDB files in combo with LAMMPS snapshots"
@ -51,6 +54,7 @@ index,time,flag = p.iterator(1)
# History
# 8/05, Steve Plimpton (SNL): original version
# 3/17, Richard Berger (Temple U): improve Python 3 compatibility
# ToDo list
# 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
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
@ -74,7 +84,7 @@ class pdbfile:
def __init__(self,*args):
if len(args) == 1:
if type(args[0]) is types.StringType:
if type(args[0]) is string_types:
filestr = args[0]
self.data = None
else:
@ -83,7 +93,7 @@ class pdbfile:
elif len(args) == 2:
filestr = args[0]
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
# append .pdb if needed
@ -94,17 +104,17 @@ class pdbfile:
for file in list:
if '*' in file: flist += glob.glob(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 len(flist) == 0:
raise StandardError,"no PDB file specified"
raise Exception("no PDB file specified")
self.files = flist
else: self.files = []
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:
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
@ -112,7 +122,7 @@ class pdbfile:
try:
open(self.files[0],'r').close()
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]
urllib.urlretrieve(fetchstr,self.files[0])
@ -142,20 +152,20 @@ class pdbfile:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
self.convert(f,which)
print >>f,"END"
print time,
print("END",file=f)
print(time,end='')
sys.stdout.flush()
n += 1
else:
for file in self.files:
f.write(open(file,'r').read())
print >>f,"END"
print file,
print("END",file=f)
print(file,end='')
sys.stdout.flush()
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
@ -190,7 +200,7 @@ class pdbfile:
self.convert(f,which)
f.close()
print time,
print(time,end='')
sys.stdout.flush()
n += 1
@ -210,12 +220,12 @@ class pdbfile:
f = open(file,'w')
f.write(open(infile,'r').read())
f.close()
print file,
print(file,end='')
sys.stdout.flush()
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
@ -280,10 +290,10 @@ class pdbfile:
if self.atomlines.has_key(id):
(begin,end) = self.atomlines[id]
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:
for atom in atoms:
begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1])
middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4])
end = " 1.00 0.00 NONE"
print >>f,begin+middle+end
print(begin+middle+end,file=f)