diff --git a/python/examples/matplotlib_plot.py b/python/examples/matplotlib_plot.py
new file mode 100755
index 0000000000000000000000000000000000000000..d4e304aa19f193e628369540b7ccc59cb5f86fba
--- /dev/null
+++ b/python/examples/matplotlib_plot.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python -i
+# preceding line should have path for Python on your machine
+
+# matplotlib_plot.py
+# Purpose: plot Temp of running LAMMPS simulation via matplotlib
+# Syntax: plot.py in.lammps Nfreq Nsteps compute-ID
+# in.lammps = LAMMPS input script
+# Nfreq = plot data point every this many steps
+# Nsteps = run for this many steps
+# compute-ID = ID of compute that calculates temperature
+# (or any other scalar quantity)
+
+from __future__ import print_function
+import sys
+sys.path.append("./pizza")
+import matplotlib
+matplotlib.use('tkagg')
+import matplotlib.pyplot as plt
+
+# parse command line
+
+argv = sys.argv
+if len(argv) != 5:
+ print("Syntax: plot.py in.lammps Nfreq Nsteps compute-ID")
+ sys.exit()
+
+infile = sys.argv[1]
+nfreq = int(sys.argv[2])
+nsteps = int(sys.argv[3])
+compute = sys.argv[4]
+
+me = 0
+# uncomment if running in parallel via Pypar
+#import pypar
+#me = pypar.rank()
+#nprocs = pypar.size()
+
+from lammps import lammps
+lmp = lammps()
+
+# run infile all at once
+# assumed to have no run command in it
+
+lmp.file(infile)
+lmp.command("thermo %d" % nfreq)
+
+# initial 0-step run to generate initial 1-point plot
+
+lmp.command("run 0 pre yes post no")
+value = lmp.extract_compute(compute,0,0)
+ntimestep = 0
+xaxis = [ntimestep]
+yaxis = [value]
+
+# create matplotlib plot
+# just proc 0 handles plotting
+
+if me == 0:
+ fig = plt.figure()
+ line, = plt.plot(xaxis, yaxis)
+ plt.xlim([0, nsteps])
+ plt.title(compute)
+ plt.xlabel("Timestep")
+ plt.ylabel("Temperature")
+ plt.show(block=False)
+
+# run nfreq steps at a time w/out pre/post, query compute, refresh plot
+import time
+
+while ntimestep < nsteps:
+ lmp.command("run %d pre no post no" % nfreq)
+ ntimestep += nfreq
+ value = lmp.extract_compute(compute,0,0)
+ xaxis.append(ntimestep)
+ yaxis.append(value)
+ if me == 0:
+ line.set_xdata(xaxis)
+ line.set_ydata(yaxis)
+ ax = plt.gca()
+ ax.relim()
+ ax.autoscale_view(True, True, True)
+ fig.canvas.draw()
+
+lmp.command("run 0 pre no post yes")
+
+# uncomment if running in parallel via Pypar
+#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
+#pypar.finalize()
+
+if sys.version_info[0] == 3:
+ input("Press Enter to exit...")
+else:
+ raw_input("Press Enter to exit...")
diff --git a/python/examples/pizza/dump.py b/python/examples/pizza/dump.py
index ec18cba62eefee12b189f1e7f4d2f64527dc5857..14645ac1f3ad13bb33b8b515d58b969238677f27 100644
--- a/python/examples/pizza/dump.py
+++ b/python/examples/pizza/dump.py
@@ -146,6 +146,8 @@ d.extra(data) extract bond/tri/line list from data
# History
# 8/05, Steve Plimpton (SNL): original version
# 12/09, David Hart (SNL): allow use of NumPy or Numeric
+# 03/17, Richard Berger (Temple U): improve Python 3 compatibility,
+# simplify read_snapshot by using reshape
# ToDo list
# try to optimize this line in read_snap: words += f.readline().split()
@@ -224,7 +226,7 @@ class dump:
self.flist = []
for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1:
- raise StandardError("no dump file specified")
+ raise Exception("no dump file specified")
if len(list) == 1:
self.increment = 0
@@ -299,7 +301,7 @@ class dump:
def next(self):
- if not self.increment: raise StandardError("cannot read incrementally")
+ if not self.increment: raise Exception("cannot read incrementally")
# read next snapshot in current file using eof as pointer
# if fail, try next file
@@ -344,13 +346,13 @@ class dump:
try:
snap = Snap()
item = f.readline()
- snap.time = int(f.readline().split()[0]) # just grab 1st field
+ snap.time = int(f.readline().decode().split()[0]) # just grab 1st field
item = f.readline()
- snap.natoms = int(f.readline())
+ snap.natoms = int(f.readline().decode())
snap.aselect = np.zeros(snap.natoms)
- item = f.readline()
+ item = f.readline().decode()
words = f.readline().split()
snap.xlo,snap.xhi = float(words[0]),float(words[1])
words = f.readline().split()
@@ -358,7 +360,7 @@ class dump:
words = f.readline().split()
snap.zlo,snap.zhi = float(words[0]),float(words[1])
- item = f.readline()
+ item = f.readline().decode()
if len(self.names) == 0:
words = item.split()[2:]
if len(words):
@@ -372,24 +374,22 @@ class dump:
else: self.names[words[i]] = i
if snap.natoms:
- words = f.readline().split()
+ words = f.readline().decode().split()
ncol = len(words)
for i in range(1,snap.natoms):
- words += f.readline().split()
+ words += f.readline().decode().split()
floats = map(float,words)
- if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
- else: atoms = np.zeros((snap.natoms,ncol),np.float)
- start = 0
- stop = ncol
- for i in range(snap.natoms):
- atoms[i] = floats[start:stop]
- start = stop
- stop += ncol
- else: atoms = None
- snap.atoms = atoms
+ if oldnumeric:
+ atom_data = np.array(list(floats),np.Float)
+ else:
+ atom_data = np.array(list(floats),np.float)
+
+ snap.atoms = atom_data.reshape((snap.natoms, ncol))
+ else:
+ snap.atoms = None
return snap
except:
- return 0
+ return None
# --------------------------------------------------------------------
# decide if snapshot i is scaled/unscaled from coords of first and last atom
@@ -417,7 +417,7 @@ class dump:
def map(self,*pairs):
if len(pairs) % 2 != 0:
- raise StandardError("dump map() requires pairs of mappings")
+ raise Exception("dump map() requires pairs of mappings")
for i in range(0,len(pairs),2):
j = i + 1
self.names[pairs[j]] = pairs[i]-1
@@ -734,7 +734,7 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
if snap.nselect != len(vec):
- raise StandardError("vec length does not match # of selected atoms")
+ raise Exception("vec length does not match # of selected atoms")
atoms = snap.atoms
m = 0
for i in range(snap.natoms):
@@ -800,7 +800,7 @@ class dump:
def atom(self,n,*list):
if len(list) == 0:
- raise StandardError("no columns specified")
+ raise Exception("no columns specified")
columns = []
values = []
for name in list:
@@ -816,7 +816,7 @@ class dump:
for i in range(snap.natoms):
if atoms[i][id] == n: break
if atoms[i][id] != n:
- raise StandardError("could not find atom ID in snapshot")
+ raise Exception("could not find atom ID in snapshot")
for j in range(ncol):
values[j][m] = atoms[i][columns[j]]
m += 1
@@ -831,7 +831,7 @@ class dump:
snap = self.snaps[self.findtime(n)]
if len(list) == 0:
- raise StandardError("no columns specified")
+ raise Exception("no columns specified")
columns = []
values = []
for name in list:
@@ -957,9 +957,9 @@ class dump:
# --------------------------------------------------------------------
def findtime(self,n):
- for i in range(self.nsnaps):
- if self.snaps[i].time == n: return i
- raise StandardError("no step %d exists" % n)
+ for i, snap in enumerate(self.snaps):
+ if snap.time == n: return i
+ raise Exception("no step %d exists" % n)
# --------------------------------------------------------------------
# return maximum box size across all selected snapshots
@@ -1008,7 +1008,7 @@ class dump:
nbonds = int(f.readline())
item = f.readline()
if not re.search("BONDS",item):
- raise StandardError("could not read bonds from dump file")
+ raise Exception("could not read bonds from dump file")
words = f.readline().split()
ncol = len(words)
@@ -1031,7 +1031,7 @@ class dump:
self.bondflag = 1
self.bondlist = bondlist
except:
- raise StandardError("could not read from bond dump file")
+ raise Exception("could not read from bond dump file")
# request bonds from data object
@@ -1047,7 +1047,7 @@ class dump:
self.bondflag = 1
self.bondlist = bondlist
except:
- raise StandardError("could not extract bonds from data object")
+ raise Exception("could not extract bonds from data object")
# request tris/lines from cdata object
@@ -1061,7 +1061,7 @@ class dump:
self.lineflag = 1
self.linelist = lines
except:
- raise StandardError("could not extract tris/lines from cdata object")
+ raise Exception("could not extract tris/lines from cdata object")
# request tris from mdump object
@@ -1070,10 +1070,10 @@ class dump:
self.triflag = 2
self.triobj = arg
except:
- raise StandardError("could not extract tris from mdump object")
+ raise Exception("could not extract tris from mdump object")
else:
- raise StandardError("unrecognized argument to dump.extra()")
+ raise Exception("unrecognized argument to dump.extra()")
# --------------------------------------------------------------------
diff --git a/python/examples/pizza/gl.py b/python/examples/pizza/gl.py
index 765653c9836d7be4cde8e3fdc9c5a76f685b1e69..908db67052e1db71ef0f4fbfcfea2c8f2cc9a955 100644
--- a/python/examples/pizza/gl.py
+++ b/python/examples/pizza/gl.py
@@ -638,7 +638,7 @@ class gl:
fraction*(self.scale_stop - self.scale_start)
self.viewupright()
- if n == nstart or self.panflag: self.center = compute_center(box)
+ if n == nstart or self.panflag: self.center = compute_center(box)
if bonds: self.bonds_augment(bonds)
diff --git a/python/examples/pizza/pdbfile.py b/python/examples/pizza/pdbfile.py
index 2ca85b64da81ec4afcf183cfeabc91490cdcc3bc..51c88604249491dae6f5772be1be949f71e801fe 100644
--- a/python/examples/pizza/pdbfile.py
+++ b/python/examples/pizza/pdbfile.py
@@ -54,6 +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,
@@ -68,6 +69,12 @@ index,time,flag = p.iterator(1)
# Imports and external programs
import sys, types, glob, urllib
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+ string_types = str,
+else:
+ string_types = basestring
# Class definition
@@ -77,7 +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:
diff --git a/python/examples/viz_atomeye.py b/python/examples/viz_atomeye.py
index d9cf4dcef274f3675d8891d6f64608893d0165a4..d7f83f274dfd57f985322d8f3c05db7d9506f779 100755
--- a/python/examples/viz_atomeye.py
+++ b/python/examples/viz_atomeye.py
@@ -42,7 +42,7 @@ lmp = lammps()
lmp.file(infile)
lmp.command("thermo %d" % nfreq)
-lmp.command("dump python all cfg %d tmp.cfg.* id type xs ys zs" % nfreq)
+lmp.command("dump python all cfg %d tmp.cfg.* mass type xs ys zs id" % nfreq)
# initial 0-step run to generate dump file and image
diff --git a/python/examples/vizplotgui_atomeye.py b/python/examples/vizplotgui_atomeye.py
index 02f119b7260c0411316f13270c65d53aa642b306..8f5f4e3dfff638264cf8dd17ce5f07edad185528 100755
--- a/python/examples/vizplotgui_atomeye.py
+++ b/python/examples/vizplotgui_atomeye.py
@@ -73,7 +73,7 @@ lmp = lammps()
lmp.file(infile)
lmp.command("thermo %d" % nfreq)
-lmp.command("dump python all cfg %d tmp.cfg.* id type xs ys zs" % nfreq)
+lmp.command("dump python all cfg %d tmp.cfg.* mass type xs ys zs id" % nfreq)
# initial 0-step run to generate initial 1-point plot, dump file, and image
diff --git a/python/lammps.py b/python/lammps.py
index 7344a16be30fb8ab47e3ffc1f6cd939dae95b4fe..a36abb87e8fd408f953f58f0f5b14b2cb9f38e55 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -190,12 +190,15 @@ class lammps(object):
# send a list of commands
def commands_list(self,cmdlist):
- args = (c_char_p * len(cmdlist))(*cmdlist)
+ cmds = [x.encode() for x in cmdlist if type(x) is str]
+ args = (c_char_p * len(cmdlist))(*cmds)
self.lib.lammps_commands_list(self.lmp,len(cmdlist),args)
# send a string of commands
def commands_string(self,multicmd):
+ if type(multicmd) is str:
+ multicmd = multicmd.encode()
self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))
# extract global info
@@ -359,19 +362,27 @@ class lammps(object):
# e.g. for Python list or NumPy, etc
# ditto for gather_atoms() above
- def create_atoms(self,n,id,type,x,v):
+ def create_atoms(self,n,id,type,x,v,image=None,shrinkexceed=False):
if id:
id_lmp = (c_int * n)()
id_lmp[:] = id
- else: id_lmp = id
+ else:
+ id_lmp = id
+
+ if image:
+ image_lmp = (c_int * n)()
+ image_lmp[:] = image
+ else:
+ image_lmp = image
+
type_lmp = (c_int * n)()
type_lmp[:] = type
- self.lib.lammps_create_atoms(self.lmp,n,id_lmp,type_lmp,x,v)
+ self.lib.lammps_create_atoms(self.lmp,n,id_lmp,type_lmp,x,v,image_lmp,shrinkexceed)
+
- # document this?
-
@property
def uses_exceptions(self):
+ """ Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """
try:
if self.lib.lammps_has_error:
return True
diff --git a/src/library.cpp b/src/library.cpp
index 5980b135eb1bd8ee00f417b662e63339a9f9b0c2..da491f71528a319a69a2e28f822ac72e6ad14399 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -971,11 +971,9 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
xdata[0] = x[3*i];
xdata[1] = x[3*i+1];
xdata[2] = x[3*i+2];
- if (image) {
- if (!domain->ownatom(id[i],xdata,&image[i],shrinkexceed)) continue;
- } else {
- if (!domain->ownatom(id[i],xdata,NULL,shrinkexceed)) continue;
- }
+ imageint * img = image ? &image[i] : NULL;
+ tagint tag = id ? id[i] : -1;
+ if (!domain->ownatom(tag, xdata, img, shrinkexceed)) continue;
atom->avec->create_atom(type[i],xdata);
if (id) atom->tag[nlocal] = id[i];