It's finally over! All files are python3 compatible (still need testing for debugging...) (f911ed1e) · Commits · Germain Clavier / pizza

src/matlab.py

+328 −303

Original line number	Diff line number	Diff line
		@@ -5,12 +5,29 @@
		# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		# certain rights in this software. This software is distributed under
		# the GNU General Public License.

		#
		# matlab tool
		#
		#
		#
		# History
		# 8/05, Matt Jones (BYU): original version
		#
		# ToDo list
		# allow choice of JPG or PNG or GIF when saving via "saveas" command
		# have vec/array import/export functions to pass variables between
		# Pizza.py and MatLab and have them named in MatLab

		oneline = "Create plots via MatLab numerical analysis program"
		# Variables
		# current = index of current figure (1-N)
		# figures = list of figure objects with each plot's attributes
		# so they aren't lost between replots
		# import command to yank MatLab variables back to Python
		# allow for alternate export command to name the variables from Python
		# in MatLab and vice versa

		docstr = """
		"""
		Create plots via MatLab numerical analysis program
		m = matlab() start up MatLab
		m.stop() shut down MatLab process

		@@ -75,37 +92,24 @@ m.curve(N,'b','-','v') set color, line style, symbol of curve N
		'<' = left triangle, 'p' = pentagram, 'h' = hexagram
		"""

		# History
		# 8/05, Matt Jones (BYU): original version

		# ToDo list
		# allow choice of JPG or PNG or GIF when saving via "saveas" command
		# have vec/array import/export functions to pass variables between
		# Pizza.py and MatLab and have them named in MatLab

		# Variables
		# current = index of current figure (1-N)
		# figures = list of figure objects with each plot's attributes
		# so they aren't lost between replots
		# import command to yank MatLab variables back to Python
		# allow for alternate export command to name the variables from Python
		# in MatLab and vice versa

		# Imports and external programs

		import types, os
		import os

		try: from DEFAULTS import PIZZA_MATLAB
		except: PIZZA_MATLAB = "matlab -nosplash -nodesktop -nojvm"
		try:
		from DEFAULTS import PIZZA_MATLAB
		except (ModuleNotFoundError, ImportError):
		PIZZA_MATLAB = "matlab -nosplash -nodesktop -nojvm"

		# Class definition


		class matlab:

		# --------------------------------------------------------------------

		def __init__(self):
		self.MATLAB = os.popen(PIZZA_MATLAB,'w')
		self.MATLAB = os.popen(PIZZA_MATLAB, "w")
		self.file = "tmp.matlab"
		self.figures = []
		self.select(1)
		@@ -119,15 +123,16 @@ class matlab:
		# --------------------------------------------------------------------

		def __call__(self, command):
		self.MATLAB.write(command + '\n')
		self.MATLAB.write(command + "\n")
		self.MATLAB.flush()

		# --------------------------------------------------------------------

		def enter(self):
		while 1:
		command = raw_input("matlab> ")
		if command == "quit" or command == "exit": return
		command = input("matlab> ")
		if command == "quit" or command == "exit":
		return
		self.__call__(command)

		# --------------------------------------------------------------------
		@@ -136,11 +141,12 @@ class matlab:
		def plot(self, *vectors):
		if len(vectors) == 1:
		file = self.file + ".%d.1" % self.current
		linear = range(len(vectors[0]))
		linear = list(range(len(vectors[0])))
		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:
		sys.exit("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])
		@@ -156,14 +162,20 @@ class matlab:
		for i in range(start, stop, skip):
		partial_vecs = []
		for vec in vectors:
		if i: partial_vecs.append(vec[:i])
		else: partial_vecs.append([0])
		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)
		else: newfile = file + str(n)
		if n < 10:
		newfile = file + "000" + str(n)
		elif n < 100:
		newfile = file + "00" + str(n)
		elif n < 1000:
		newfile = file + "0" + str(n)
		else:
		newfile = file + str(n)

		self.save(newfile)
		n += 1
		@@ -174,13 +186,14 @@ class matlab:
		def export(self, filename, *vectors):
		n = len(vectors[0])
		for vector in vectors:
		if len(vector) != n: raise StandardError,"vectors must be same length"
		f = open(filename,'w')
		if len(vector) != n:
		sys.exit("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):
		f.write("{}".format(vectors[j][i]))
		f.write('\n')
		f.close()

		# --------------------------------------------------------------------
		@@ -207,11 +220,13 @@ class matlab:
		# use tmp.done as semaphore to indicate plot is finished

		def save(self, file):
		if os.path.exists("tmp.done"): os.remove("tmp.done")
		if os.path.exists("tmp.done"):
		os.remove("tmp.done")
		cmd = "saveas(gcf,'%s.eps','psc2')" % file
		self.__call__(cmd)
		self.__call__("!touch tmp.done")
		while not os.path.exists("tmp.done"): continue
		while not os.path.exists("tmp.done"):
		continue

		# --------------------------------------------------------------------
		# restore default attributes by creating a new fig object
		@@ -305,10 +320,13 @@ class matlab:

		def curve(self, num, *settings):
		fig = self.figures[self.current - 1]
		while len(fig.curves) < num: fig.curves.append('')
		while len(fig.curves) < num:
		fig.curves.append("")
		value = settings[0]
		if len(settings) >= 2: value += settings[1]
		if len(settings) >= 3: value += settings[2]
		if len(settings) >= 2:
		value += settings[1]
		if len(settings) >= 3:
		value += settings[2]
		fig.curves[num - 1] = value
		self.draw()

		@@ -318,15 +336,20 @@ class matlab:

		def draw(self):
		fig = self.figures[self.current - 1]
		if not fig.ncurves: return
		if not fig.ncurves:
		return
		self.__call__("figure(%d)" % self.current)

		if not fig.xlog and not fig.ylog: cmd = "plot"
		elif fig.xlog and not fig.ylog: cmd = "semilogx"
		elif not fig.xlog and fig.ylog: cmd = "semilogy"
		elif fig.xlog and fig.ylog: cmd = "loglog"
		if not fig.xlog and not fig.ylog:
		cmd = "plot"
		elif fig.xlog and not fig.ylog:
		cmd = "semilogx"
		elif not fig.xlog and fig.ylog:
		cmd = "semilogy"
		elif fig.xlog and fig.ylog:
		cmd = "loglog"

		cmd += '('
		cmd += "("
		for i in range(fig.ncurves):
		file = self.file + ".%d.%d" % (self.current, i + 1)
		readcmd = "pizza%d = importdata('%s');" % (i + 1, file)
		@@ -347,7 +370,8 @@ class matlab:
		self.__call__("xlabel('%s','FontSize',16)" % fig.xtitle)
		self.__call__("ylabel('%s','FontSize',16)" % fig.ytitle)

		if fig.xlimit == 0 or fig.ylimit == 0: self.__call__("axis auto")
		if fig.xlimit == 0 or fig.ylimit == 0:
		self.__call__("axis auto")
		if fig.xlimit:
		self.__call__("xlim([%g,%g])" % (fig.xlimit[0], fig.xlimit[1]))
		if fig.ylimit:
		@@ -359,11 +383,12 @@ class matlab:
		text = fig.labels[i][2] # kludge to set label font size
		self.__call__("text(%g,%g,'%s','FontSize',16)" % (x, y, text))


		# --------------------------------------------------------------------
		# class to store settings for a single plot

		class figure:

		class figure:
		def __init__(self):
		self.ncurves = 0
		self.curves = []

src/raster.py

+797 −541

File changed.

Preview size limit exceeded, changes collapsed.

src/sdata.py

+1643 −1404

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src/svg.py

+752 −627

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src/tdump.py

+344 −323

Original line number	Diff line number	Diff line
		@@ -5,12 +5,31 @@
		# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		# certain rights in this software. This software is distributed under
		# the GNU General Public License.

		#
		# tdump tool
		#
		#
		#
		# History
		# 4/11, Steve Plimpton (SNL): original version
		#
		# Variables
		# flist = list of dump file names
		# increment = 1 if reading snapshots one-at-a-time
		# nextfile = which file to read from via next()
		# eof = ptr into current file for where to read via next()
		# nsnaps = # of snapshots
		# snaps = list of snapshots
		# names = dictionary of column names:
		# key = "id", value = column # (0 to M-1)
		# Snap = one snapshot
		# time = time stamp
		# natoms = # of atoms
		# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float)
		# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1

		oneline = "Read dump files with triangle info"

		docstr = """
		"""
		Read dump files with triangle info
		t = tdump("dump.one") read in one or more dump files
		t = tdump("dump.1 dump.2.gz") can be gzipped
		t = tdump("dump.*") wildcard expands to multiple files
		@@ -36,7 +55,7 @@ time,box,atoms,bonds,tris,lines = t.viz(index) return list of viz objects
		viz() returns line info for specified timestep index
		can also call as viz(time,1) and will find index of preceding snapshot
		time = timestep value
		box = \[xlo,ylo,zlo,xhi,yhi,zhi\]
		box = [xlo,ylo,zlo,xhi,yhi,zhi]
		atoms = NULL
		bonds = NULL
		tris = id,type,x1,y1,z1,x2,y2,z2,x3,y3,z3 for each tri as 2d array
		@@ -49,60 +68,44 @@ t.owrap(...) wrap tris to same image as their atoms
		useful for wrapping all molecule's atoms/tris the same so it is contiguous
		"""

		# History
		# 4/11, Steve Plimpton (SNL): original version

		# Variables
		# flist = list of dump file names
		# increment = 1 if reading snapshots one-at-a-time
		# nextfile = which file to read from via next()
		# eof = ptr into current file for where to read via next()
		# nsnaps = # of snapshots
		# snaps = list of snapshots
		# names = dictionary of column names:
		# key = "id", value = column # (0 to M-1)
		# Snap = one snapshot
		# time = time stamp
		# natoms = # of atoms
		# xlo,xhi,ylo,yhi,zlo,zhi = box bounds (float)
		# atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1

		# Imports and external programs

		import sys, commands, re, glob, types
		import sys
		import subprocess
		import re
		import glob
		import types
		from math import sqrt
		from os import popen

		try:
		import numpy as np
		oldnumeric = False
		except:
		import Numeric as np
		oldnumeric = True

		try: from DEFAULTS import PIZZA_GUNZIP
		except: PIZZA_GUNZIP = "gunzip"
		try:
		from DEFAULTS import PIZZA_GUNZIP
		except (ModuleNotFoundError, ImportError):
		PIZZA_GUNZIP = "gunzip"

		# Class definition


		class tdump:

		# --------------------------------------------------------------------

		def __init__(self,*list):
		def __init__(self, *args):
		self.snaps = []
		self.nsnaps = 0
		self.names = {}

		# flist = list of all dump file names

		words = list[0].split()
		words = args[0].split()
		self.flist = []
		for word in words: self.flist += glob.glob(word)
		if len(self.flist) == 0 and len(list) == 1:
		raise StandardError,"no ldump file specified"
		for word in words:
		self.flist += glob.glob(word)
		if len(self.flist) == 0 and len(args) == 1:
		sys.exit("no ldump file specified")

		if len(list) == 1:
		if len(args) == 1:
		self.increment = 0
		self.read_all()
		else:
		@@ -119,44 +122,47 @@ class tdump:

		for file in self.flist:
		if file[-3:] == ".gz":
		f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r')
		else: f = open(file)
		f = popen("%s -c %s" % (PIZZA_GUNZIP, file), "r")
		else:
		f = open(file)

		snap = self.read_snapshot(f)
		while snap:
		self.snaps.append(snap)
		print snap.time,
		print(snap.time)
		sys.stdout.flush()
		snap = self.read_snapshot(f)

		f.close()
		print
		print("\n")

		# sort entries by timestep, cull duplicates

		self.snaps.sort(self.compare_time)
		self.cull()
		self.nsnaps = len(self.snaps)
		print "read %d snapshots" % self.nsnaps
		print("read %d snapshots" % self.nsnaps)

		# --------------------------------------------------------------------
		# read next snapshot from list of files

		def next(self):

		if not self.increment: raise StandardError,"cannot read incrementally"
		if not self.increment:
		sys.exit("cannot read incrementally")

		# read next snapshot in current file using eof as pointer
		# if fail, try next file
		# if new snapshot time stamp already exists, read next snapshot

		while 1:
		f = open(self.flist[self.nextfile],'rb')
		f = open(self.flist[self.nextfile], "rb")
		f.seek(self.eof)
		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
		@@ -165,7 +171,8 @@ class tdump:
		try:
		self.findtime(snap.time)
		continue
		except: break
		except Exception:
		break

		self.snaps.append(snap)
		snap = self.snaps[self.nsnaps]
		@@ -198,21 +205,21 @@ class tdump:
		if snap.natoms:
		words = f.readline().split()
		ncol = len(words)
		for i in xrange(1,snap.natoms):
		for i in range(1, snap.natoms):
		words += f.readline().split()
		floats = map(float,words)
		if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
		else: atoms = np.zeros((snap.natoms,ncol),np.float)
		values = list(map(float, words))
		atoms = np.zeros((snap.natoms, ncol), dtype=np.float)
		start = 0
		stop = ncol
		for i in xrange(snap.natoms):
		atoms[i] = floats[start:stop]
		for i in range(snap.natoms):
		atoms[i] = values[start:stop]
		start = stop
		stop += ncol
		else: atoms = None
		else:
		atoms = None
		snap.atoms = atoms
		return snap
		except:
		except Exception:
		return 0

		# --------------------------------------------------------------------
		@@ -220,7 +227,7 @@ class tdump:

		def map(self, *pairs):
		if len(pairs) % 2 != 0:
		raise StandardError, "tdump map() requires pairs of mappings"
		sys.exit("tdump map() requires pairs of mappings")
		for i in range(0, len(pairs), 2):
		j = i + 1
		self.names[pairs[j]] = pairs[i] - 1
		@@ -250,9 +257,10 @@ class tdump:
		# --------------------------------------------------------------------

		def findtime(self, n):
		for i in xrange(self.nsnaps):
		if self.snaps[i].time == n: return i
		raise StandardError, "no step %d exists" % n
		for i in range(self.nsnaps):
		if self.snaps[i].time == n:
		return i
		sys.exit("no step %d exists" % n)

		# --------------------------------------------------------------------
		# delete successive snapshots with duplicate time stamp
		@@ -270,21 +278,23 @@ class tdump:
		# if called with flag, then index is timestep, so convert to snapshot index

		def viz(self, index, flag=0):
		if not flag: isnap = index
		if not flag:
		isnap = index
		else:
		times = self.time()
		n = len(times)
		i = 0
		while i < n:
		if times[i] > index: break
		if times[i] > index:
		break
		i += 1
		isnap = i - 1
		snap = self.snaps[isnap]

		time = snap.time
		box = [snap.xlo, snap.ylo, snap.zlo, snap.xhi, snap.yhi, snap.zhi]
		id = self.names["id"]
		type = self.names["type"]
		atid = self.names["id"]
		attype = self.names["type"]
		corner1x = self.names["corner1x"]
		corner1y = self.names["corner1y"]
		corner1z = self.names["corner1z"]
		@@ -299,15 +309,22 @@ class tdump:
		# don't add tri if all 4 values are 0 since not a line

		tris = []
		for i in xrange(snap.natoms):
		for i in range(snap.natoms):
		atom = snap.atoms[i]
		c1 = [atom[corner1x], atom[corner1y], atom[corner1z]]
		c2 = [atom[corner2x], atom[corner2y], atom[corner2z]]
		c3 = [atom[corner3x], atom[corner3y], atom[corner3z]]
		n = normal(c1, c2, c3)
		if c1[0] == 0.0 and c1[1] == 0.0 and c1[2] == 0.0 and \
		c2[0] == 0.0 and c2[1] == 0.0 and c2[2] == 0.0: continue
		tris.append([atom[id],atom[type]] + c1 + c2 + c3 + n)
		if (
		c1[0] == 0.0
		and c1[1] == 0.0
		and c1[2] == 0.0
		and c2[0] == 0.0
		and c2[1] == 0.0
		and c2[2] == 0.0
		):
		continue
		tris.append([atom[atid], atom[attype]] + c1 + c2 + c3 + n)

		return time, box, None, None, tris, None

		@@ -316,7 +333,7 @@ class tdump:
		# invoked by dump() when it does an owrap() on its atoms

		def owrap(self, time, xprd, yprd, zprd, idsdump, atomsdump, iother, ix, iy, iz):
		id = self.names["id"]
		atid = self.names["id"]
		corner1x = self.names["corner1x"]
		corner1y = self.names["corner1y"]
		corner1z = self.names["corner1z"]
		@@ -335,8 +352,8 @@ class tdump:
		# jdump = atom J in dump's atoms that atom I was owrapped on
		# delx,dely = offset applied to atom I and thus to line I

		for i in xrange(snap.natoms):
		tag = atoms[i][id]
		for i in range(snap.natoms):
		tag = atoms[i][atid]
		idump = idsdump[tag]
		jdump = idsdump[atomsdump[idump][iother]]
		delx = (atomsdump[idump][ix] - atomsdump[jdump][ix]) * xprd
		@@ -352,15 +369,19 @@ class tdump:
		atoms[i][corner3y] += dely
		atoms[i][corner3z] += delz


		# --------------------------------------------------------------------
		# one snapshot


		class Snap:
		pass


		# --------------------------------------------------------------------
		# compute normal for a triangle with 3 vertices


		def normal(x, y, z):
		v1 = 3 * [0]
		v1[0] = y[0] - x[0]