ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
a210867025e19c1bd9243a863fdc3e66e62bc3c5
lammps/python/lammps.py
Richard Berger a210867025 Fixes lammps_create_atoms library function and its Python interface variant 
The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.
2017-03-15 22:13:06 -04:00

868 lines
27 KiB
Python
Raw Blame History

# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) 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
# the GNU General Public License.
#
# See the README file in the top-level LAMMPS directory.
# -------------------------------------------------------------------------
# Python wrappers on LAMMPS library via ctypes
# for python3 compatibility
from __future__ import print_function
# imports for simple LAMMPS python wrapper module "lammps"
import sys,traceback,types
from ctypes import *
from os.path import dirname,abspath,join
from inspect import getsourcefile
# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"
from collections import namedtuple
import os
import select
import re
class MPIAbortException(Exception):
def __init__(self, message):
self.message = message
def __str__(self):
return repr(self.message)
class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py_v2 = False
try:
from mpi4py import MPI
from mpi4py import __version__ as mpi4py_version
if mpi4py_version.split('.')[0] == '2':
has_mpi4py_v2 = True
except:
pass
# create instance of LAMMPS
def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
self.comm = comm
self.opened = 0
# determine module location
modpath = dirname(abspath(getsourcefile(lambda:0)))
self.lib = None
# if a pointer to a LAMMPS object is handed in,
# all symbols should already be available
try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL)
except:
self.lib = None
# load liblammps.so unless name is given
# if name = "g++", load liblammps_g++.so
# try loading the LAMMPS shared object from the location
# of lammps.py with an absolute path,
# so that LD_LIBRARY_PATH does not need to be set for regular install
# fall back to loading with a relative path,
# typically requires LD_LIBRARY_PATH to be set appropriately
if not self.lib:
try:
if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),
RTLD_GLOBAL)
except:
if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
# 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
# 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
# ptr is the desired instance of LAMMPS
# just convert it to ctypes ptr and store in self.lmp
if not ptr:
# with mpi4py v2, can pass MPI communicator to LAMMPS
# need to adjust for type of MPI communicator object
# allow for int (like MPICH) or void* (like OpenMPI)
if lammps.has_mpi4py_v2 and comm != None:
if lammps.MPI._sizeof(lammps.MPI.Comm) == sizeof(c_int):
MPI_Comm = c_int
else:
MPI_Comm = c_void_p
narg = 0
cargs = 0
if cmdargs:
cmdargs.insert(0,"lammps.py")
narg = len(cmdargs)
for i in range(narg):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*narg)(*cmdargs)
self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
MPI_Comm, c_void_p()]
else:
self.lib.lammps_open.argtypes = [c_int, c_int, \
MPI_Comm, c_void_p()]
self.lib.lammps_open.restype = None
self.opened = 1
self.lmp = c_void_p()
comm_ptr = lammps.MPI._addressof(comm)
comm_val = MPI_Comm.from_address(comm_ptr)
self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))
else:
self.opened = 1
if cmdargs:
cmdargs.insert(0,"lammps.py")
narg = len(cmdargs)
for i in range(narg):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*narg)(*cmdargs)
self.lmp = c_void_p()
self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
else:
self.lmp = c_void_p()
self.lib.lammps_open_no_mpi(0,None,byref(self.lmp))
# could use just this if LAMMPS lib interface supported it
# self.lmp = self.lib.lammps_open_no_mpi(0,None)
else:
# magic to convert ptr to ctypes ptr
pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
def __del__(self):
if self.lmp and self.opened:
self.lib.lammps_close(self.lmp)
self.opened = 0
def close(self):
if self.opened: self.lib.lammps_close(self.lmp)
self.lmp = None
self.opened = 0
def version(self):
return self.lib.lammps_version(self.lmp)
def file(self,file):
if file: file = file.encode()
self.lib.lammps_file(self.lmp,file)
# send a single command
def command(self,cmd):
if cmd: cmd = cmd.encode()
self.lib.lammps_command(self.lmp,cmd)
if self.uses_exceptions and self.lib.lammps_has_error(self.lmp):
sb = create_string_buffer(100)
error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
error_msg = sb.value.decode().strip()
if error_type == 2:
raise MPIAbortException(error_msg)
raise Exception(error_msg)
# send a list of commands
def commands_list(self,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
def extract_global(self,name,type):
if name: name = name.encode()
if type == 0:
self.lib.lammps_extract_global.restype = POINTER(c_int)
elif type == 1:
self.lib.lammps_extract_global.restype = POINTER(c_double)
else: return None
ptr = self.lib.lammps_extract_global(self.lmp,name)
return ptr[0]
# extract per-atom info
def extract_atom(self,name,type):
if name: name = name.encode()
if type == 0:
self.lib.lammps_extract_atom.restype = POINTER(c_int)
elif type == 1:
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int))
elif type == 2:
self.lib.lammps_extract_atom.restype = POINTER(c_double)
elif type == 3:
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
else: return None
ptr = self.lib.lammps_extract_atom(self.lmp,name)
return ptr
# extract compute info
def extract_compute(self,id,style,type):
if id: id = id.encode()
if type == 0:
if style > 0: return None
self.lib.lammps_extract_compute.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr[0]
if type == 1:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr
if type == 2:
self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr
return None
# extract fix info
# in case of global datum, free memory for 1 double via lammps_free()
# double was allocated by library interface function
def extract_fix(self,id,style,type,i=0,j=0):
if id: id = id.encode()
if style == 0:
self.lib.lammps_extract_fix.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
result = ptr[0]
self.lib.lammps_free(ptr)
return result
elif (style == 1) or (style == 2):
if type == 1:
self.lib.lammps_extract_fix.restype = POINTER(c_double)
elif type == 2:
self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
else:
return None
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr
else:
return None
# extract variable info
# free memory for 1 double or 1 vector of doubles via lammps_free()
# for vector, must copy nlocal returned values to local c_double vector
# memory was allocated by library interface function
def extract_variable(self,name,group,type):
if name: name = name.encode()
if group: group = group.encode()
if type == 0:
self.lib.lammps_extract_variable.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
result = ptr[0]
self.lib.lammps_free(ptr)
return result
if type == 1:
self.lib.lammps_extract_global.restype = POINTER(c_int)
nlocalptr = self.lib.lammps_extract_global(self.lmp,"nlocal".encode())
nlocal = nlocalptr[0]
result = (c_double*nlocal)()
self.lib.lammps_extract_variable.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
for i in range(nlocal): result[i] = ptr[i]
self.lib.lammps_free(ptr)
return result
return None
# set variable value
# value is converted to string
# returns 0 for success, -1 if failed
def set_variable(self,name,value):
if name: name = name.encode()
if value: value = str(value).encode()
return self.lib.lammps_set_variable(self.lmp,name,str(value))
# return current value of thermo keyword
def get_thermo(self,name):
if name: name = name.encode()
self.lib.lammps_get_thermo.restype = c_double
return self.lib.lammps_get_thermo(self.lmp,name)
# return total number of atoms in system
def get_natoms(self):
return self.lib.lammps_get_natoms(self.lmp)
# return vector of atom properties gathered across procs, ordered by atom ID
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: how could we insure are converting to correct Python type
# e.g. for Python list or NumPy, etc
# ditto for extact_atom() above
def gather_atoms(self,name,type,count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
elif type == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
else: return None
return data
# scatter vector of atom properties across procs, ordered by atom ID
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: how could we insure are passing correct type to LAMMPS
# e.g. for Python list or NumPy, etc
def scatter_atoms(self,name,type,count,data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
# create N atoms on all procs
# N = global number of atoms
# id = ID of each atom (optional, can be None)
# type = type of each atom (1 to Ntypes) (required)
# x = coords of each atom as (N,3) array (required)
# v = velocity of each atom as (N,3) array (optional, can be None)
# NOTE: how could we insure are passing correct type to LAMMPS
# e.g. for Python list or NumPy, etc
# ditto for gather_atoms() above
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
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,image_lmp,shrinkexceed)
# document this?
@property
def uses_exceptions(self):
try:
if self.lib.lammps_has_error:
return True
except(AttributeError):
return False
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
################################################################################
# Alternative Python Wrapper
# Written by Richard Berger <richard.berger@temple.edu>
################################################################################
class OutputCapture(object):
""" Utility class to capture LAMMPS library output """
def __init__(self):
self.stdout_pipe_read, self.stdout_pipe_write = os.pipe()
self.stdout_fd = 1
def __enter__(self):
self.stdout = os.dup(self.stdout_fd)
os.dup2(self.stdout_pipe_write, self.stdout_fd)
return self
def __exit__(self, type, value, tracebac):
os.dup2(self.stdout, self.stdout_fd)
os.close(self.stdout)
os.close(self.stdout_pipe_read)
os.close(self.stdout_pipe_write)
# check if we have more to read from the pipe
def more_data(self, pipe):
r, _, _ = select.select([pipe], [], [], 0)
return bool(r)
# read the whole pipe
def read_pipe(self, pipe):
out = ""
while self.more_data(pipe):
out += os.read(pipe, 1024).decode()
return out
@property
def output(self):
return self.read_pipe(self.stdout_pipe_read)
class Variable(object):
def __init__(self, lammps_wrapper_instance, name, style, definition):
self.wrapper = lammps_wrapper_instance
self.name = name
self.style = style
self.definition = definition.split()
@property
def value(self):
if self.style == 'atom':
return list(self.wrapper.lmp.extract_variable(self.name, "all", 1))
else:
value = self.wrapper.lmp_print('"${%s}"' % self.name).strip()
try:
return float(value)
except ValueError:
return value
class AtomList(object):
def __init__(self, lammps_wrapper_instance):
self.lmp = lammps_wrapper_instance
self.natoms = self.lmp.system.natoms
self.dimensions = self.lmp.system.dimensions
def __getitem__(self, index):
if self.dimensions == 2:
return Atom2D(self.lmp, index + 1)
return Atom(self.lmp, index + 1)
class Atom(object):
def __init__(self, lammps_wrapper_instance, index):
self.lmp = lammps_wrapper_instance
self.index = index
@property
def id(self):
return int(self.lmp.eval("id[%d]" % self.index))
@property
def type(self):
return int(self.lmp.eval("type[%d]" % self.index))
@property
def mol(self):
return self.lmp.eval("mol[%d]" % self.index)
@property
def mass(self):
return self.lmp.eval("mass[%d]" % self.index)
@property
def position(self):
return (self.lmp.eval("x[%d]" % self.index),
self.lmp.eval("y[%d]" % self.index),
self.lmp.eval("z[%d]" % self.index))
@position.setter
def position(self, value):
self.lmp.set("atom", self.index, "x", value[0])
self.lmp.set("atom", self.index, "y", value[1])
self.lmp.set("atom", self.index, "z", value[2])
@property
def velocity(self):
return (self.lmp.eval("vx[%d]" % self.index),
self.lmp.eval("vy[%d]" % self.index),
self.lmp.eval("vz[%d]" % self.index))
@property
def force(self):
return (self.lmp.eval("fx[%d]" % self.index),
self.lmp.eval("fy[%d]" % self.index),
self.lmp.eval("fz[%d]" % self.index))
@property
def charge(self):
return self.lmp.eval("q[%d]" % self.index)
class Atom2D(Atom):
def __init__(self, lammps_wrapper_instance, index):
super(Atom2D, self).__init__(lammps_wrapper_instance, index)
@property
def position(self):
return (self.lmp.eval("x[%d]" % self.index),
self.lmp.eval("y[%d]" % self.index))
@position.setter
def position(self, value):
self.lmp.set("atom", self.index, "x", value[0])
self.lmp.set("atom", self.index, "y", value[1])
@property
def velocity(self):
return (self.lmp.eval("vx[%d]" % self.index),
self.lmp.eval("vy[%d]" % self.index))
@property
def force(self):
return (self.lmp.eval("fx[%d]" % self.index),
self.lmp.eval("fy[%d]" % self.index))
def get_thermo_data(output):
""" traverse output of runs and extract thermo data columns """
if isinstance(output, str):
lines = output.splitlines()
else:
lines = output
runs = []
columns = []
in_run = False
for line in lines:
if line.startswith("Memory usage per processor"):
in_run = True
elif in_run and len(columns) == 0:
# first line after memory usage are column names
columns = line.split()
current_run = {}
for col in columns:
current_run[col] = []
elif line.startswith("Loop time of "):
in_run = False
columns = None
thermo_data = namedtuple('ThermoData', list(current_run.keys()))(*list(current_run.values()))
r = {'thermo' : thermo_data }
runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
elif in_run and len(columns) > 0:
values = [float(x) for x in line.split()]
for i, col in enumerate(columns):
current_run[col].append(values[i])
return runs
class PyLammps(object):
"""
More Python-like wrapper for LAMMPS (e.g., for iPython)
See examples/ipython for usage
"""
def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
if ptr:
if isinstance(ptr,PyLammps):
self.lmp = ptr.lmp
elif isinstance(ptr,lammps):
self.lmp = ptr
else:
self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=ptr,comm=comm)
else:
self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=None,comm=comm)
print("LAMMPS output is captured by PyLammps wrapper")
self._cmd_history = []
self.runs = []
def __del__(self):
if self.lmp: self.lmp.close()
self.lmp = None
def close(self):
if self.lmp: self.lmp.close()
self.lmp = None
def version(self):
return self.lmp.version()
def file(self,file):
self.lmp.file(file)
def write_script(self,filename):
""" Write LAMMPS script file containing all commands executed up until now """
with open(filename, "w") as f:
for cmd in self._cmd_history:
f.write("%s\n" % cmd)
def command(self,cmd):
self.lmp.command(cmd)
self._cmd_history.append(cmd)
def run(self, *args, **kwargs):
output = self.__getattr__('run')(*args, **kwargs)
self.runs += get_thermo_data(output)
return output
@property
def last_run(self):
if len(self.runs) > 0:
return self.runs[-1]
return None
@property
def atoms(self):
return AtomList(self)
@property
def system(self):
output = self.info("system")
d = self._parse_info_system(output)
return namedtuple('System', d.keys())(*d.values())
@property
def communication(self):
output = self.info("communication")
d = self._parse_info_communication(output)
return namedtuple('Communication', d.keys())(*d.values())
@property
def computes(self):
output = self.info("computes")
return self._parse_element_list(output)
@property
def dumps(self):
output = self.info("dumps")
return self._parse_element_list(output)
@property
def fixes(self):
output = self.info("fixes")
return self._parse_element_list(output)
@property
def groups(self):
output = self.info("groups")
return self._parse_groups(output)
@property
def variables(self):
output = self.info("variables")
vars = {}
for v in self._parse_element_list(output):
vars[v['name']] = Variable(self, v['name'], v['style'], v['def'])
return vars
def eval(self, expr):
value = self.lmp_print('"$(%s)"' % expr).strip()
try:
return float(value)
except ValueError:
return value
def _split_values(self, line):
return [x.strip() for x in line.split(',')]
def _get_pair(self, value):
return [x.strip() for x in value.split('=')]
def _parse_info_system(self, output):
lines = output[6:-2]
system = {}
for line in lines:
if line.startswith("Units"):
system['units'] = self._get_pair(line)[1]
elif line.startswith("Atom style"):
system['atom_style'] = self._get_pair(line)[1]
elif line.startswith("Atom map"):
system['atom_map'] = self._get_pair(line)[1]
elif line.startswith("Atoms"):
parts = self._split_values(line)
system['natoms'] = int(self._get_pair(parts[0])[1])
system['ntypes'] = int(self._get_pair(parts[1])[1])
system['style'] = self._get_pair(parts[2])[1]
elif line.startswith("Kspace style"):
system['kspace_style'] = self._get_pair(line)[1]
elif line.startswith("Dimensions"):
system['dimensions'] = int(self._get_pair(line)[1])
elif line.startswith("Orthogonal box"):
system['orthogonal_box'] = [float(x) for x in self._get_pair(line)[1].split('x')]
elif line.startswith("Boundaries"):
system['boundaries'] = self._get_pair(line)[1]
elif line.startswith("xlo"):
keys, values = [self._split_values(x) for x in self._get_pair(line)]
for key, value in zip(keys, values):
system[key] = float(value)
elif line.startswith("ylo"):
keys, values = [self._split_values(x) for x in self._get_pair(line)]
for key, value in zip(keys, values):
system[key] = float(value)
elif line.startswith("zlo"):
keys, values = [self._split_values(x) for x in self._get_pair(line)]
for key, value in zip(keys, values):
system[key] = float(value)
elif line.startswith("Molecule type"):
system['molecule_type'] = self._get_pair(line)[1]
elif line.startswith("Bonds"):
parts = self._split_values(line)
system['nbonds'] = int(self._get_pair(parts[0])[1])
system['nbondtypes'] = int(self._get_pair(parts[1])[1])
system['bond_style'] = self._get_pair(parts[2])[1]
elif line.startswith("Angles"):
parts = self._split_values(line)
system['nangles'] = int(self._get_pair(parts[0])[1])
system['nangletypes'] = int(self._get_pair(parts[1])[1])
system['angle_style'] = self._get_pair(parts[2])[1]
elif line.startswith("Dihedrals"):
parts = self._split_values(line)
system['ndihedrals'] = int(self._get_pair(parts[0])[1])
system['nangletypes'] = int(self._get_pair(parts[1])[1])
system['dihedral_style'] = self._get_pair(parts[2])[1]
elif line.startswith("Impropers"):
parts = self._split_values(line)
system['nimpropers'] = int(self._get_pair(parts[0])[1])
system['nimpropertypes'] = int(self._get_pair(parts[1])[1])
system['improper_style'] = self._get_pair(parts[2])[1]
return system
def _parse_info_communication(self, output):
lines = output[6:-3]
comm = {}
for line in lines:
if line.startswith("MPI library"):
comm['mpi_version'] = line.split(':')[1].strip()
elif line.startswith("Comm style"):
parts = self._split_values(line)
comm['comm_style'] = self._get_pair(parts[0])[1]
comm['comm_layout'] = self._get_pair(parts[1])[1]
elif line.startswith("Processor grid"):
comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
elif line.startswith("Communicate velocities for ghost atoms"):
comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
elif line.startswith("Nprocs"):
parts = self._split_values(line)
comm['nprocs'] = int(self._get_pair(parts[0])[1])
comm['nthreads'] = int(self._get_pair(parts[1])[1])
return comm
def _parse_element_list(self, output):
lines = output[6:-3]
elements = []
for line in lines:
element_info = self._split_values(line.split(':')[1].strip())
element = {'name': element_info[0]}
for key, value in [self._get_pair(x) for x in element_info[1:]]:
element[key] = value
elements.append(element)
return elements
def _parse_groups(self, output):
lines = output[6:-3]
groups = []
group_pattern = re.compile(r"(?P<name>.+) \((?P<type>.+)\)")
for line in lines:
m = group_pattern.match(line.split(':')[1].strip())
group = {'name': m.group('name'), 'type': m.group('type')}
groups.append(group)
return groups
def lmp_print(self, s):
""" needed for Python2 compatibility, since print is a reserved keyword """
return self.__getattr__("print")(s)
def __getattr__(self, name):
def handler(*args, **kwargs):
cmd_args = [name] + [str(x) for x in args]
with OutputCapture() as capture:
self.command(' '.join(cmd_args))
output = capture.output
if 'verbose' in kwargs and kwargs['verbose']:
print(output)
lines = output.splitlines()
if len(lines) > 1:
return lines
elif len(lines) == 1:
return lines[0]
return None
return handler
class IPyLammps(PyLammps):
"""
iPython wrapper for LAMMPS which adds embedded graphics capabilities
"""
def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
super(IPyLammps, self).__init__(name=name,cmdargs=cmdargs,ptr=ptr,comm=comm)
def image(self, filename="snapshot.png", group="all", color="type", diameter="type",
size=None, view=None, center=None, up=None, zoom=1.0):
cmd_args = [group, "image", filename, color, diameter]
if size:
width = size[0]
height = size[1]
cmd_args += ["size", width, height]
if view:
theta = view[0]
phi = view[1]
cmd_args += ["view", theta, phi]
if center:
flag = center[0]
Cx = center[1]
Cy = center[2]
Cz = center[3]
cmd_args += ["center", flag, Cx, Cy, Cz]
if up:
Ux = up[0]
Uy = up[1]
Uz = up[2]
cmd_args += ["up", Ux, Uy, Uz]
if zoom:
cmd_args += ["zoom", zoom]
cmd_args.append("modify backcolor white")
self.write_dump(*cmd_args)
from IPython.core.display import Image
return Image('snapshot.png')
def video(self, filename):
from IPython.display import HTML
return HTML("<video controls><source src=\"" + filename + "\"></video>")
Reference in New Issue View Git Blame Copy Permalink