fully restore steve's python formatting style
This commit is contained in:
Axel Kohlmeyer
110
python/lammps.py
110
python/lammps.py
@ -11,13 +11,18 @@
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# See the README file in the top-level LAMMPS directory.
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# -------------------------------------------------------------------------
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# Python wrapper on LAMMPS library via ctypes
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# Python wrappers on LAMMPS library via ctypes
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# for python3 compatibility
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from __future__ import print_function
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import sys, traceback, types
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# imports for simple LAMMPS python wrapper module "lammps"
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import sys,traceback,types
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from ctypes import *
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from os.path import dirname, abspath, join
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from os.path import dirname,abspath,join
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from inspect import getsourcefile
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# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"
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from collections import namedtuple
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import os
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import select
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@ -38,11 +43,11 @@ class lammps:
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# create instance of LAMMPS
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def __init__(self, name="", cmdargs=None, ptr=None, comm=None):
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def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
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# determine module location
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modpath = dirname(abspath(getsourcefile(lambda: 0)))
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modpath = dirname(abspath(getsourcefile(lambda:0)))
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# load liblammps.so unless name is given.
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# e.g. if name = "g++", load liblammps_g++.so
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@ -53,15 +58,11 @@ class lammps:
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# requires LD_LIBRARY_PATH to be set appropriately.
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try:
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if not name:
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self.lib = CDLL(join(modpath, "liblammps.so"), RTLD_GLOBAL)
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else:
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self.lib = CDLL(join(modpath, "liblammps_%s.so" % name), RTLD_GLOBAL)
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if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
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else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),RTLD_GLOBAL)
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except:
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if not name:
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self.lib = CDLL("liblammps.so", RTLD_GLOBAL)
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else:
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self.lib = CDLL("liblammps_%s.so" % name, RTLD_GLOBAL)
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if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
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else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
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# if no ptr provided, create an instance of LAMMPS
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# don't know how to pass an MPI communicator from PyPar
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@ -86,13 +87,13 @@ class lammps:
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narg = 0
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cargs = 0
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if cmdargs:
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cmdargs.insert(0, "lammps.py")
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cmdargs.insert(0,"lammps.py")
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narg = len(cmdargs)
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for i in range(narg):
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if type(cmdargs[i]) is str:
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cmdargs[i] = cmdargs[i].encode()
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cargs = (c_char_p * narg)(*cmdargs)
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self.lib.lammps_open.argtypes = [c_int, c_char_p * narg, \
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cargs = (c_char_p*narg)(*cmdargs)
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self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
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MPI_Comm, c_void_p()]
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else:
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self.lib.lammps_open.argtypes = [c_int, c_int, \
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@ -103,22 +104,22 @@ class lammps:
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self.lmp = c_void_p()
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comm_ptr = lammps.MPI._addressof(comm)
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comm_val = MPI_Comm.from_address(comm_ptr)
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self.lib.lammps_open(narg, cargs, comm_val, byref(self.lmp))
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self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))
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else:
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self.opened = 1
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if cmdargs:
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cmdargs.insert(0, "lammps.py")
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cmdargs.insert(0,"lammps.py")
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narg = len(cmdargs)
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for i in range(narg):
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if type(cmdargs[i]) is str:
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cmdargs[i] = cmdargs[i].encode()
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cargs = (c_char_p * narg)(*cmdargs)
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cargs = (c_char_p*narg)(*cmdargs)
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self.lmp = c_void_p()
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self.lib.lammps_open_no_mpi(narg, cargs, byref(self.lmp))
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self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
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else:
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self.lmp = c_void_p()
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self.lib.lammps_open_no_mpi(0, None, byref(self.lmp))
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self.lib.lammps_open_no_mpi(0,None,byref(self.lmp))
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# could use just this if LAMMPS lib interface supported it
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# self.lmp = self.lib.lammps_open_no_mpi(0,None)
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@ -139,26 +140,25 @@ class lammps:
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def version(self):
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return self.lib.lammps_version(self.lmp)
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def file(self, file):
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def file(self,file):
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file = file.encode()
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self.lib.lammps_file(self.lmp, file)
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self.lib.lammps_file(self.lmp,file)
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def command(self, cmd):
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def command(self,cmd):
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cmd = cmd.encode()
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self.lib.lammps_command(self.lmp, cmd)
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self.lib.lammps_command(self.lmp,cmd)
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def extract_global(self, name, type):
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def extract_global(self,name,type):
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name = name.encode()
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if type == 0:
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self.lib.lammps_extract_global.restype = POINTER(c_int)
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elif type == 1:
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self.lib.lammps_extract_global.restype = POINTER(c_double)
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else:
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return None
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ptr = self.lib.lammps_extract_global(self.lmp, name)
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else: return None
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ptr = self.lib.lammps_extract_global(self.lmp,name)
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return ptr[0]
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def extract_atom(self, name, type):
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def extract_atom(self,name,type):
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name = name.encode()
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if type == 0:
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self.lib.lammps_extract_atom.restype = POINTER(c_int)
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@ -168,36 +168,35 @@ class lammps:
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self.lib.lammps_extract_atom.restype = POINTER(c_double)
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elif type == 3:
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self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
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else:
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return None
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ptr = self.lib.lammps_extract_atom(self.lmp, name)
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else: return None
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ptr = self.lib.lammps_extract_atom(self.lmp,name)
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return ptr
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def extract_compute(self, id, style, type):
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def extract_compute(self,id,style,type):
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id = id.encode()
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if type == 0:
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if style > 0: return None
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self.lib.lammps_extract_compute.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_compute(self.lmp, id, style, type)
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ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
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return ptr[0]
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if type == 1:
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self.lib.lammps_extract_compute.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_compute(self.lmp, id, style, type)
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ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
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return ptr
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if type == 2:
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self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
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ptr = self.lib.lammps_extract_compute(self.lmp, id, style, type)
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ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
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return ptr
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return None
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# in case of global datum, free memory for 1 double via lammps_free()
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# double was allocated by library interface function
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def extract_fix(self, id, style, type, i=0, j=0):
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def extract_fix(self,id,style,type,i=0,j=0):
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id = id.encode()
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if style == 0:
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self.lib.lammps_extract_fix.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_fix(self.lmp, id, style, type, i, j)
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ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
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result = ptr[0]
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self.lib.lammps_free(ptr)
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return result
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@ -208,7 +207,7 @@ class lammps:
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self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
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else:
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return None
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ptr = self.lib.lammps_extract_fix(self.lmp, id, style, type, i, j)
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ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
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return ptr
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else:
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return None
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@ -217,22 +216,22 @@ class lammps:
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# for vector, must copy nlocal returned values to local c_double vector
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# memory was allocated by library interface function
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def extract_variable(self, name, group, type):
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def extract_variable(self,name,group,type):
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name = name.encode()
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group = group.encode()
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if type == 0:
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self.lib.lammps_extract_variable.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_variable(self.lmp, name, group)
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ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
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result = ptr[0]
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self.lib.lammps_free(ptr)
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return result
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if type == 1:
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self.lib.lammps_extract_global.restype = POINTER(c_int)
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nlocalptr = self.lib.lammps_extract_global(self.lmp, "nlocal".encode())
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nlocalptr = self.lib.lammps_extract_global(self.lmp,"nlocal".encode())
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nlocal = nlocalptr[0]
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result = (c_double * nlocal)()
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result = (c_double*nlocal)()
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self.lib.lammps_extract_variable.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_variable(self.lmp, name, group)
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ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
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for i in range(nlocal): result[i] = ptr[i]
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self.lib.lammps_free(ptr)
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return result
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@ -242,10 +241,10 @@ class lammps:
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# value is converted to string
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# returns 0 for success, -1 if failed
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def set_variable(self, name, value):
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def set_variable(self,name,value):
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name = name.encode()
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value = str(value).encode()
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return self.lib.lammps_set_variable(self.lmp, name, str(value))
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return self.lib.lammps_set_variable(self.lmp,name,str(value))
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# return total number of atoms in system
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@ -254,25 +253,24 @@ class lammps:
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# return vector of atom properties gathered across procs, ordered by atom ID
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def gather_atoms(self, name, type, count):
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def gather_atoms(self,name,type,count):
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name = name.encode()
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natoms = self.lib.lammps_get_natoms(self.lmp)
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if type == 0:
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data = ((count * natoms) * c_int)()
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self.lib.lammps_gather_atoms(self.lmp, name, type, count, data)
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data = ((count*natoms)*c_int)()
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self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
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elif type == 1:
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data = ((count * natoms) * c_double)()
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self.lib.lammps_gather_atoms(self.lmp, name, type, count, data)
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else:
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return None
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data = ((count*natoms)*c_double)()
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self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
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else: return None
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return data
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# scatter vector of atom properties across procs, ordered by atom ID
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# assume vector is of correct type and length, as created by gather_atoms()
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def scatter_atoms(self, name, type, count, data):
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def scatter_atoms(self,name,type,count,data):
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name = name.encode()
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self.lib.lammps_scatter_atoms(self.lmp, name, type, count, data)
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self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
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####################################################################################
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