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# Conflicts:
#	python/lammps/__init__.py
#	python/lammps/core.py
This commit is contained in:
Axel Kohlmeyer
2021-06-04 00:28:32 -04:00
parent 5599deae0a 2463c2dd71
commit 067fd48b57
35 changed files with 560 additions and 706 deletions
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8
doc/src/Python_install.rst
View File

@ -377,14 +377,6 @@ make MPI calls directly from Python in your script, if you desire.
We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
(aka mpi4py) and you will find installation instruction for it below.
.. note::
Older LAMMPS versions were also tested with `PyPar <https://github.com/daleroberts/pypar>`_
but we can no longer test it, since it does not work with the Python
(3.x) versions on our test servers. Since there have been no updates
to PyPar visible in its repository since November 2016 we have to assume
it is no longer maintained.
Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
follows:

2
doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
View File

@ -65,7 +65,7 @@
{% elif show_source and has_source and sourcename %}
<a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a>
{% endif %}
<a href="http://lammps.sandia.gov">Website</a>
<a href="https://www.lammps.org">Website</a>
<a href="Commands_all.html">Commands</a>
{% endif %}
</li>

9
doc/utils/sphinx-config/_themes/lammps_theme/layout.html
View File

@ -38,10 +38,11 @@
{% if favicon %}
<link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
{% endif %}
{# CANONICAL URL #}
{% if theme_canonical_url %}
<link rel="canonical" href="{{ theme_canonical_url }}{{ pagename }}.html"/>
{% endif %}
{#- CANONICAL URL #}
{%- if pageurl %}
<link rel="canonical" href="{{ pageurl|e }}" />
{%- endif -%}
{# JAVASCRIPTS #}
{%- block scripts %}

1
doc/utils/sphinx-config/_themes/lammps_theme/theme.conf
View File

@ -4,7 +4,6 @@ stylesheet = css/theme.css
pygments_style = default
[options]
canonical_url =
analytics_id =
collapse_navigation = False
sticky_navigation = False

5
doc/utils/sphinx-config/conf.py.in
View File

@ -15,6 +15,7 @@
import sys
import os
from datetime import date
has_enchant = False
try:
@ -76,7 +77,7 @@ master_doc = 'Manual'
# General information about the project.
project = 'LAMMPS'
copyright = '2003-2020 Sandia Corporation'
copyright = '2003-{} Sandia Corporation'.format(date.today().year)
def get_lammps_version():
import os
@ -255,6 +256,8 @@ htmlhelp_basename = 'LAMMPSdoc'
html_permalinks = True
html_baseurl = os.environ.get('LAMMPS_WEBSITE_BASEURL', '')
if 'epub' in sys.argv:
html_math_renderer = 'imgmath'
else:

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -2631,7 +2631,6 @@ PyLammps
pymbar
pymodule
pymol
pypar
pythonic
pytorch
pyy

21
examples/ELASTIC/compliance.py
View File

@ -8,6 +8,7 @@
# The units of Cij are whatever was used in log.lammps (usually GPa)
# The units of Sij are the inverse of that (usually 1/GPa)
from __future__ import print_function
from numpy import zeros
from numpy.linalg import inv
@ -44,9 +45,8 @@ cindices[20] = (4,5)
# open logfile
logfile = open("log.lammps",'r')
txt = logfile.read()
with open("log.lammps",'r') as logfile:
txt = logfile.read()
# search for 21 elastic constants
@ -56,7 +56,7 @@ s2 = 0
for ival in range(nvals):
s1 = txt.find(valstr,s2)
if (s1 == -1):
print "Failed to find elastic constants in log file"
print("Failed to find elastic constants in log file")
exit(1)
s1 += 1
s2 = txt.find("\n",s1)
@ -67,11 +67,11 @@ for ival in range(nvals):
c[i1,i2] = float(words[valpos])
c[i2,i1] = c[i1,i2]
print "C tensor [GPa]"
print("C tensor [GPa]")
for i in range(6):
for j in range(6):
print "%10.8g " % c[i][j],
print
print("%10.8g " % c[i][j], end="")
print()
# apply factor of 2 to columns of off-diagonal elements
@ -87,9 +87,8 @@ for i in range(6):
for j in range(3,6):
s[i][j] *= 0.5
print "S tensor [1/GPa]"
print("S tensor [1/GPa]")
for i in range(6):
for j in range(6):
print "%10.8g " % s[i][j],
print
print("%10.8g " % s[i][j], end="")
print()

1
python/.gitignore vendored
View File

@ -1 +1,2 @@
/build
/*.egg-info

15
python/README
View File

@ -44,6 +44,7 @@ split.py parallel example
mc.py Monte Carlo energy relaxation wrapper on LAMMPS
gui.py GUI go/stop/temperature-slider to control LAMMPS
plot.py real-time temperature plot with GnuPlot via Pizza.py
matplotlib_plot.py real-time temperature plot with Matplotlib via Pizza.py
viz_tool.py real-time viz via some viz package
vizplotgui_tool.py combination of viz.py and plot.py and gui.py
@ -100,24 +101,24 @@ split.py in.simple # can run in parallel (see below)
gui.py in.gui 100
plot.py in.plot 10 1000 thermo_temp
matplotlib_plot.py in.plot 10 1000 thermo_temp
viz_tool.py in.viz 100 5000
vizplotgui_tool.py in.viz 100 thermo_temp
To run LAMMPS in parallel from Python, so something like this:
% mpirun -np 4 simple.py in.simple
% mpirun -np 4 python split.py in.simple
% mpirun -np P simple.py in.simple
% mpirun -np P python split.py in.simple
If you run simple.py as-is, this will invoke P instances of a
one-processor run, where both Python and LAMMPS will run on single
processors. Each running job will read the same input file, and write
to same log.lammps file, which isn't too useful.
However, if you have either the Pypar or mpi4py packages installed in
your Python, and uncomment the Pypar or mpi4py code in simple.py, then
the above commands will invoke 1 instance of a P-processor run. Both
Python and LAMMPS will run on P processors. The job will read the
input file and write a single log.lammps file.
However, if you have the mpi4py Python package installed and uncomment mpi4py
code in simple.py, then the above commands will invoke 1 instance of a
P-processor run. Both Python and LAMMPS will run on P processors. The job will
read the input file and write a single log.lammps file.
The split.py script can also be run in parallel. It uses mpi4py
version 2.0.0 (or later), which makes it possible to pass a

1
python/examples/.gitignore vendored Normal file
View File

@ -0,0 +1 @@
/tmp*

11
python/examples/gui.py
View File

@ -7,8 +7,7 @@
# in.lammps = LAMMPS input script
# Nfreq = query GUI every this many steps
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
# because I can't seem to do a MPI-style broadcast in Pypar
# IMPORTANT: this script cannot yet be run in parallel
from __future__ import print_function
import sys,time
@ -39,10 +38,6 @@ infile = sys.argv[1]
nfreq = int(sys.argv[2])
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from lammps import lammps
lmp = lammps()
@ -110,7 +105,3 @@ while 1:
if runflag: running = 1
else: running = 0
time.sleep(0.01)
# uncomment if running in parallel via Pypar
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

22
python/examples/matplotlib_plot.py
View File

@ -12,9 +12,6 @@
from __future__ import print_function
import sys
sys.path.append("./pizza")
import matplotlib
matplotlib.use('tkagg')
import matplotlib.pyplot as plt
# parse command line
@ -30,10 +27,10 @@ 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()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
@ -79,15 +76,16 @@ while ntimestep < nsteps:
ax = plt.gca()
ax.relim()
ax.autoscale_view(True, True, True)
fig.canvas.draw()
plt.pause(0.001)
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()
if sys.version_info[0] == 3:
if me == 0:
if sys.version_info[0] == 3:
input("Press Enter to exit...")
else:
else:
raw_input("Press Enter to exit...")

14
python/examples/pizza/dump.py
View File

@ -275,7 +275,7 @@ class dump:
print("no column assignments made")
elif len(self.names):
print("assigned columns:",self.names2str())
elif self.snaps[0].atoms == None:
elif self.snaps[0].atoms is None:
print("no column assignments made")
elif len(self.snaps[0].atoms[0]) == 5:
self.map(1,"id",2,"type",3,"x",4,"y",5,"z")
@ -969,12 +969,12 @@ class dump:
xhi = yhi = zhi = None
for snap in self.snaps:
if not snap.tselect: continue
if xlo == None or snap.xlo < xlo: xlo = snap.xlo
if xhi == None or snap.xhi > xhi: xhi = snap.xhi
if ylo == None or snap.ylo < ylo: ylo = snap.ylo
if yhi == None or snap.yhi > yhi: yhi = snap.yhi
if zlo == None or snap.zlo < zlo: zlo = snap.zlo
if zhi == None or snap.zhi > zhi: zhi = snap.zhi
if xlo is None or snap.xlo < xlo: xlo = snap.xlo
if xhi is None or snap.xhi > xhi: xhi = snap.xhi
if ylo is None or snap.ylo < ylo: ylo = snap.ylo
if yhi is None or snap.yhi > yhi: yhi = snap.yhi
if zlo is None or snap.zlo < zlo: zlo = snap.zlo
if zhi is None or snap.zhi > zhi: zhi = snap.zhi
return [xlo,ylo,zlo,xhi,yhi,zhi]
# --------------------------------------------------------------------

6
python/examples/pizza/gl.py
View File

@ -851,7 +851,7 @@ class gl:
ncolor = self.vizinfo.ntcolor
for tri in self.tridraw:
itype = int(tri[1])
if itype > ncolor: raise StandardError("tri type too big")
if itype > ncolor: raise Exception("tri type too big")
red,green,blue = self.vizinfo.tcolor[itype]
glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,[red,green,blue,1.0]);
glMaterialf(GL_FRONT_AND_BACK,GL_SHININESS,self.shiny);
@ -909,7 +909,7 @@ class gl:
ymin >= ylo and ymax <= yhi and zmin >= zlo and zmax <= zhi:
if bond[10] > bound: continue
itype = int(bond[1])
if itype > ncolor: raise StandardError("bond type too big")
if itype > ncolor: raise Exception("bond type too big")
red,green,blue = self.vizinfo.bcolor[itype]
rad = self.vizinfo.brad[itype]
glPushMatrix()
@ -941,7 +941,7 @@ class gl:
ymin >= ylo and ymax <= yhi and \
zmin >= zlo and zmax <= zhi:
itype = int(tri[1])
if itype > ncolor: raise StandardError("tri type too big")
if itype > ncolor: raise Exception("tri type too big")
red,green,blue = self.vizinfo.tcolor[itype]
glMaterialfv(GL_FRONT_AND_BACK,GL_EMISSION,
[red,green,blue,1.0]);

14
python/examples/pizza/gnu.py
View File

@ -87,12 +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 -p"
except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
try: from DEFAULTS import PIZZA_GNUTERM
except: PIZZA_GNUTERM = "x11"
except ImportError: PIZZA_GNUTERM = "x11"
# Class definition
@ -122,6 +123,9 @@ class gnu:
def enter(self):
while 1:
if sys.version_info[0] == 3:
command = input("gnuplot> ")
else:
command = raw_input("gnuplot> ")
if command == "quit" or command == "exit": return
self.__call__(command)
@ -136,7 +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])
@ -170,7 +174,7 @@ 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 range(n):

12
python/examples/pizza/pdbfile.py
View File

@ -68,7 +68,7 @@ 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:
@ -93,7 +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
@ -104,17 +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

10
python/examples/pizza/vizinfo.py
View File

@ -79,7 +79,7 @@ class vizinfo:
# if list of types has a 0, increment each type value
if 0 in ids:
for i in xrange(len(ids)): ids[i] += 1
for i in range(len(ids)): ids[i] += 1
# extend storage list if necessary
# extend other arrays for same "which" so that gl::make_atom_calllist
@ -109,7 +109,7 @@ class vizinfo:
ntypes = len(ids)
nrgbs = len(rgbs)
for i in xrange(ntypes):
for i in range(ntypes):
id = ids[i]
if rgbs[0] == "loop":
@ -157,7 +157,7 @@ class vizinfo:
# if list of types has a 0, increment each type value
if 0 in ids:
for i in xrange(len(ids)): ids[i] += 1
for i in range(len(ids)): ids[i] += 1
# extend storage list if necessary
# extend other arrays for same "which" so that gl::make_atom_calllist
@ -220,7 +220,7 @@ class vizinfo:
# if list of types has a 0, increment each type value
if 0 in ids:
for i in xrange(len(ids)): ids[i] += 1
for i in range(len(ids)): ids[i] += 1
# extend storage list if necessary
# extend other arrays for same "which" so that gl::make_atom_calllist
@ -234,7 +234,7 @@ class vizinfo:
# if list lengths match, set directly, else set types to 1st fill value
if len(fills) == len(ids):
for i in xrange(len(ids)): self.tfill[ids[i]] = int(fills[i])
for i in range(len(ids)): self.tfill[ids[i]] = int(fills[i])
else:
for id in ids: self.tfill[id] = int(fills[0])

13
python/examples/pizza/vmd.py
View File

@ -45,17 +45,16 @@ v.debug([True|False]) display generated VMD script commands?
# Imports and external programs
import types, os
import numpy
import os
try: from DEFAULTS import PIZZA_VMDNAME
except: PIZZA_VMDNAME = "vmd"
except ImportError: PIZZA_VMDNAME = "vmd"
try: from DEFAULTS import PIZZA_VMDDIR
except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
except ImportError: PIZZA_VMDDIR = "/usr/local/lib/vmd"
try: from DEFAULTS import PIZZA_VMDDEV
except: PIZZA_VMDDEV = "win"
except ImportError: PIZZA_VMDDEV = "win"
try: from DEFAULTS import PIZZA_VMDARCH
except: PIZZA_VMDARCH = "LINUXAMD64"
except ImportError: PIZZA_VMDARCH = "LINUXAMD64"
# try these settings for a Mac
#PIZZA_VMDNAME = "vmd"
@ -64,7 +63,7 @@ except: PIZZA_VMDARCH = "LINUXAMD64"
#PIZZA_VMDARCH = "MACOSXX86"
try: import pexpect
except:
except ImportError:
print("pexpect from http://pypi.python.org/pypi/pexpect", \
"is required for vmd tool")
raise

13
python/examples/plot.py
View File

@ -28,10 +28,10 @@ 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()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
@ -57,7 +57,7 @@ if me == 0:
gn = gnu()
gn.plot(xaxis,yaxis)
gn.xrange(0,nsteps)
gn.title(compute,"Timestep","Temperature")
gn.title(compute.replace('_', ' '),"Timestep","Temperature")
# run nfreq steps at a time w/out pre/post, query compute, refresh plot
@ -71,6 +71,5 @@ while ntimestep < nsteps:
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

10
python/examples/simple.py
View File

@ -9,7 +9,7 @@
# Parallel syntax: mpirun -np 4 simple.py in.lammps
# in.lammps = LAMMPS input script
# also need to uncomment either Pypar or mpi4py sections below
# also need to uncomment mpi4py sections below
from __future__ import print_function
import sys
@ -27,11 +27,6 @@ infile = sys.argv[1]
me = 0
# uncomment this if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
@ -133,8 +128,5 @@ lmp.reset_box([0,0,0],[10,10,8],0,0,0)
boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()
if me == 0: print("Box info",boxlo,boxhi,xy,yz,xz,periodicity,box_change)
# uncomment if running in parallel via Pypar
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)

11
python/examples/viz_atomeye.py
View File

@ -28,10 +28,10 @@ nfreq = int(sys.argv[2])
nsteps = int(sys.argv[3])
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
@ -68,6 +68,5 @@ while ntimestep < nsteps:
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

11
python/examples/viz_gl.py
View File

@ -24,10 +24,10 @@ nfreq = int(sys.argv[2])
nsteps = int(sys.argv[3])
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
@ -83,6 +83,5 @@ while ntimestep < nsteps:
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

11
python/examples/viz_pymol.py
View File

@ -24,10 +24,10 @@ nfreq = int(sys.argv[2])
nsteps = int(sys.argv[3])
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
@ -78,6 +78,5 @@ while ntimestep < nsteps:
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

11
python/examples/viz_vmd.py
View File

@ -24,10 +24,10 @@ nfreq = int(sys.argv[2])
nsteps = int(sys.argv[3])
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
@ -87,6 +87,5 @@ if me == 0:
#v.enter()
#v.stop()
# uncomment if running in parallel via Pypar
# uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

11
python/examples/vizplotgui_atomeye.py
View File

@ -9,9 +9,6 @@
# compute-ID = ID of compute that calculates temperature
# (or any other scalar quantity)
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
# because I can't seem to do a MPI-style broadcast in Pypar
from __future__ import print_function
import sys,os,time
sys.path.append("./pizza")
@ -59,10 +56,6 @@ nfreq = int(sys.argv[2])
compute = sys.argv[3]
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from lammps import lammps
lmp = lammps()
@ -163,7 +156,3 @@ while 1:
time.sleep(0.01)
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()

11
python/examples/vizplotgui_gl.py
View File

@ -9,9 +9,6 @@
# compute-ID = ID of compute that calculates temperature
# (or any other scalar quantity)
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
# because I can't seem to do a MPI-style broadcast in Pypar
from __future__ import print_function
import sys,time
sys.path.append("./pizza")
@ -55,10 +52,6 @@ nfreq = int(sys.argv[2])
compute = sys.argv[3]
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from lammps import lammps
lmp = lammps()
@ -176,7 +169,3 @@ while 1:
time.sleep(0.01)
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()

11
python/examples/vizplotgui_pymol.py
View File

@ -9,9 +9,6 @@
# compute-ID = ID of compute that calculates temperature
# (or any other scalar quantity)
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
# because I can't seem to do a MPI-style broadcast in Pypar
from __future__ import print_function
import sys,time
sys.path.append("./pizza")
@ -57,10 +54,6 @@ nfreq = int(sys.argv[2])
compute = sys.argv[3]
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from lammps import lammps
lmp = lammps()
@ -172,7 +165,3 @@ while 1:
time.sleep(0.01)
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()

11
python/examples/vizplotgui_vmd.py
View File

@ -9,9 +9,6 @@
# compute-ID = ID of compute that calculates temperature
# (or any other scalar quantity)
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
# because I can't seem to do a MPI-style broadcast in Pypar
from __future__ import print_function
import sys,time
sys.path.append("./pizza")
@ -56,10 +53,6 @@ nfreq = int(sys.argv[2])
compute = sys.argv[3]
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from lammps import lammps
lmp = lammps()
@ -171,7 +164,3 @@ while 1:
time.sleep(0.01)
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()

8
python/lammps/__init__.py
View File

@ -25,18 +25,18 @@ def get_version_number():
vstring = None
if version_info.major == 3 and version_info.minor >= 8:
from importlib.metadata import version
from importlib.metadata import version, PackageNotFoundError
try:
vstring = version('lammps')
except: # lgtm [py/catch-base-exception]
except PackageNotFoundError:
# nothing to do, ignore
pass
else:
from pkg_resources import get_distribution
from pkg_resources import get_distribution, DistributionNotFound
try:
vstring = get_distribution('lammps').version
except: # lgtm [py/catch-base-exception]
except DistributionNotFound:
# nothing to do, ignore
pass

3
python/lammps/constants.py
View File

@ -11,8 +11,6 @@
# See the README file in the top-level LAMMPS directory.
# -------------------------------------------------------------------------
from ctypes import c_int, c_int32, c_int64
# various symbolic constants to be used
# in certain calls to select data formats
LAMMPS_AUTODETECT = None
@ -42,6 +40,7 @@ LMP_VAR_ATOM = 1
# -------------------------------------------------------------------------
def get_ctypes_int(size):
from ctypes import c_int, c_int32, c_int64
if size == 4:
return c_int32
elif size == 8:

15
python/lammps/core.py
View File

@ -100,7 +100,7 @@ class lammps(object):
try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL)
except: # lgtm [py/catch-base-exception]
except OSError:
self.lib = None
# load liblammps.so unless name is given
@ -307,13 +307,12 @@ class lammps(object):
from mpi4py import __version__ as mpi4py_version
# tested to work with mpi4py versions 2 and 3
self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
except: # lgtm [py/catch-base-exception]
except ImportError:
# ignore failing import
pass
# if no ptr provided, create an instance of LAMMPS
# don't know how to pass an MPI communicator from PyPar
# but we can pass an MPI communicator from mpi4py v2.0.0 and later
# we can pass an MPI communicator from mpi4py v2.0.0 and later
# no_mpi call lets LAMMPS use MPI_COMM_WORLD
# cargs = array of C strings from args
# if ptr, then are embedding Python in LAMMPS input script
@ -1134,10 +1133,10 @@ class lammps(object):
with ExceptionCheck(self):
if dtype == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
self.lib.lammps_gather_atoms(self.lmp,name,dtype,count,data)
elif dtype == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
self.lib.lammps_gather_atoms(self.lmp,name,dtype,count,data)
else:
return None
return data
@ -1150,10 +1149,10 @@ class lammps(object):
with ExceptionCheck(self):
if dtype == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
self.lib.lammps_gather_atoms_concat(self.lmp,name,dtype,count,data)
elif dtype == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
self.lib.lammps_gather_atoms_concat(self.lmp,name,dtype,count,data)
else:
return None
return data

8
python/setup.py
View File

@ -8,8 +8,14 @@ LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
if not os.path.exists(LAMMPS_SOURCE_DIR):
# allows installing and building wheel from current directory
LAMMPS_DIR = os.path.realpath(os.path.join(os.environ['PWD'], '..'))
LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
def get_lammps_version():
with open(os.path.join(LAMMPS_SOURCE_DIR, 'version.h'), 'r') as f:
version_h_file = os.path.join(LAMMPS_SOURCE_DIR, 'version.h')
with open(version_h_file, 'r') as f:
line = f.readline()
start_pos = line.find('"')+1
end_pos = line.find('"', start_pos)

588
tools/python/pizza/dump.py
View File

File diff suppressed because it is too large Load Diff

27
tools/python/pizza/gnu.py
View File

@ -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
# gnu tool
oneline = "Create plots via GnuPlot plotting program"
@ -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
@ -119,6 +123,9 @@ class gnu:
def enter(self):
while 1:
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
View File

@ -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)