apply some codeql recommendations
- remove unused imports - avoid overlaps of variable names with keywords - make some exception processing more explicit
This commit is contained in:
Axel Kohlmeyer
@ -18,9 +18,6 @@ from __future__ import print_function
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import os
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import sys
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import traceback
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import types
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import warnings
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from ctypes import *
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from os.path import dirname,abspath,join
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from inspect import getsourcefile
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@ -47,7 +44,7 @@ class ExceptionCheck:
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def __enter__(self):
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pass
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def __exit__(self, type, value, traceback):
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def __exit__(self, exc_type, exc_value, traceback):
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if self.lmp.has_exceptions and self.lmp.lib.lammps_has_error(self.lmp.lmp):
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raise self.lmp._lammps_exception
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@ -310,7 +307,7 @@ class lammps(object):
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# tested to work with mpi4py versions 2 and 3
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self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
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except:
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pass
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self.has_mpi4py = None
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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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@ -878,71 +875,71 @@ class lammps(object):
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# -------------------------------------------------------------------------
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def extract_compute(self,id,style,type):
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def extract_compute(self,cid,cstyle,ctype):
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"""Retrieve data from a LAMMPS compute
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This is a wrapper around the :cpp:func:`lammps_extract_compute`
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function of the C-library interface.
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This function returns ``None`` if either the compute id is not
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recognized, or an invalid combination of :ref:`style <py_style_constants>`
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and :ref:`type <py_type_constants>` constants is used. The
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recognized, or an invalid combination of :ref:`cstyle <py_style_constants>`
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and :ref:`ctype <py_type_constants>` constants is used. The
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names and functionality of the constants are the same as for
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the corresponding C-library function. For requests to return
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a scalar or a size, the value is returned, otherwise a pointer.
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:param id: compute ID
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:type id: string
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:param style: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
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:type style: int
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:param type: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
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:type type: int
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:param cid: compute ID
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:type cid: string
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:param cstyle: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
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:type cstyle: int
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:param ctype: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
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:type ctype: int
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:return: requested data as scalar, pointer to 1d or 2d double array, or None
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:rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType
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"""
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if id: id = id.encode()
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if cid: cid = cid.encode()
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else: return None
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if type == LMP_TYPE_SCALAR:
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if ctype == LMP_TYPE_SCALAR:
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if style == LMP_STYLE_GLOBAL:
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self.lib.lammps_extract_compute.restype = POINTER(c_double)
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with ExceptionCheck(self):
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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,cid,cstyle,ctype)
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return ptr[0]
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elif style == LMP_STYLE_ATOM:
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return None
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elif style == LMP_STYLE_LOCAL:
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self.lib.lammps_extract_compute.restype = POINTER(c_int)
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with ExceptionCheck(self):
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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,cid,cstyle,ctype)
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return ptr[0]
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elif type == LMP_TYPE_VECTOR:
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elif ctype == LMP_TYPE_VECTOR:
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self.lib.lammps_extract_compute.restype = POINTER(c_double)
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with ExceptionCheck(self):
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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,cid,cstyle,ctype)
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return ptr
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elif type == LMP_TYPE_ARRAY:
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elif ctype == LMP_TYPE_ARRAY:
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self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
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with ExceptionCheck(self):
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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,cid,cstyle,ctype)
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return ptr
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elif type == LMP_SIZE_COLS:
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if style == LMP_STYLE_GLOBAL \
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or style == LMP_STYLE_ATOM \
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or style == LMP_STYLE_LOCAL:
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elif ctype == LMP_SIZE_COLS:
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if cstyle == LMP_STYLE_GLOBAL \
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or cstyle == LMP_STYLE_ATOM \
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or cstyle == LMP_STYLE_LOCAL:
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self.lib.lammps_extract_compute.restype = POINTER(c_int)
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with ExceptionCheck(self):
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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,cid,cstyle,ctype)
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return ptr[0]
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elif type == LMP_SIZE_VECTOR or type == LMP_SIZE_ROWS:
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if style == LMP_STYLE_GLOBAL \
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or style == LMP_STYLE_LOCAL:
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elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS:
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if cstyle == LMP_STYLE_GLOBAL \
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or cstyle == LMP_STYLE_LOCAL:
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self.lib.lammps_extract_compute.restype = POINTER(c_int)
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with ExceptionCheck(self):
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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,cid,cstyle,ctype)
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return ptr[0]
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return None
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@ -952,25 +949,25 @@ class lammps(object):
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# in case of global data, 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,nrow=0,ncol=0):
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def extract_fix(self,fid,fstyle,ftype,nrow=0,ncol=0):
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"""Retrieve data from a LAMMPS fix
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This is a wrapper around the :cpp:func:`lammps_extract_fix`
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function of the C-library interface.
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This function returns ``None`` if either the fix id is not
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recognized, or an invalid combination of :ref:`style <py_style_constants>`
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and :ref:`type <py_type_constants>` constants is used. The
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recognized, or an invalid combination of :ref:`fstyle <py_style_constants>`
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and :ref:`ftype <py_type_constants>` constants is used. The
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names and functionality of the constants are the same as for
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the corresponding C-library function. For requests to return
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a scalar or a size, the value is returned, also when accessing
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global vectors or arrays, otherwise a pointer.
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:param id: fix ID
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:type id: string
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:param style: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
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:type style: int
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:param type: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
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:type type: int
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:param fid: fix ID
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:type fid: string
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:param fstyle: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
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:type fstyle: int
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:param ftype: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
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:type ftype: int
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:param nrow: index of global vector element or row index of global array element
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:type nrow: int
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:param ncol: column index of global array element
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@ -979,53 +976,53 @@ class lammps(object):
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:rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType
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"""
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if id: id = id.encode()
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if fid: fid = fid.encode()
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else: return None
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if style == LMP_STYLE_GLOBAL:
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if type in (LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
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if fstyle == LMP_STYLE_GLOBAL:
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if ftype in (LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
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self.lib.lammps_extract_fix.restype = POINTER(c_double)
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with ExceptionCheck(self):
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ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,nrow,ncol)
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ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
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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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elif type in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
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elif ftype in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
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self.lib.lammps_extract_fix.restype = POINTER(c_int)
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with ExceptionCheck(self):
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ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,nrow,ncol)
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ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
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return ptr[0]
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else:
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return None
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elif style == LMP_STYLE_ATOM:
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if type == LMP_TYPE_VECTOR:
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elif fstyle == LMP_STYLE_ATOM:
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if ftype == LMP_TYPE_VECTOR:
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self.lib.lammps_extract_fix.restype = POINTER(c_double)
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elif type == LMP_TYPE_ARRAY:
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elif ftype == LMP_TYPE_ARRAY:
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self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
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elif type == LMP_SIZE_COLS:
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elif ftype == LMP_SIZE_COLS:
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self.lib.lammps_extract_fix.restype = POINTER(c_int)
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else:
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return None
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with ExceptionCheck(self):
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ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,nrow,ncol)
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if type == LMP_SIZE_COLS:
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ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
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if ftype == LMP_SIZE_COLS:
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return ptr[0]
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else:
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return ptr
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elif style == LMP_STYLE_LOCAL:
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if type == LMP_TYPE_VECTOR:
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elif fstyle == LMP_STYLE_LOCAL:
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if ftype == LMP_TYPE_VECTOR:
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self.lib.lammps_extract_fix.restype = POINTER(c_double)
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elif type == LMP_TYPE_ARRAY:
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elif ftype == LMP_TYPE_ARRAY:
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self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
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elif type in (LMP_TYPE_SCALAR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
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elif ftype in (LMP_TYPE_SCALAR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
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self.lib.lammps_extract_fix.restype = POINTER(c_int)
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else:
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return None
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with ExceptionCheck(self):
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ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,nrow,ncol)
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if type in (LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
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ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
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if ftype in (LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
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return ptr
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else:
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return ptr[0]
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