From 6683976ce041a07824b7c7b1eb660057543921a1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Apr 2024 04:45:16 -0400 Subject: [PATCH 1/4] use explicit imports instead of wildcards --- python/lammps/core.py | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index 3498041454..626ece0770 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -18,12 +18,21 @@ from __future__ import print_function import os import sys -from ctypes import * # lgtm [py/polluting-import] -from os.path import dirname,abspath,join +from ctypes import CDLL, POINTER, RTLD_GLOBAL, CFUNCTYPE, py_object, byref, cast, sizeof, \ + create_string_buffer, c_int, c_int32, c_int64, c_double, c_void_p, c_char_p, pythonapi +from os.path import dirname, abspath, join from inspect import getsourcefile -from .constants import * # lgtm [py/polluting-import] -from .data import * # lgtm [py/polluting-import] +from .constants import LAMMPS_AUTODETECT, LAMMPS_STRING, \ + LAMMPS_INT, LAMMPS_INT_2D, LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, \ + LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, \ + LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, \ + LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS, \ + LMP_ERROR_WARNING, LMP_ERROR_ONE, LMP_ERROR_ALL, LMP_ERROR_WORLD, LMP_ERROR_UNIVERSE, \ + LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING, \ + get_ctypes_int + +from .data import NeighList # ------------------------------------------------------------------------- From ebd77afd58e387a458c9977be77e97e1fe7737ca Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Apr 2024 00:09:07 -0400 Subject: [PATCH 2/4] initialize in the constructor for the class that defines variable --- src/ML-IAP/mliap_descriptor.cpp | 1 + src/ML-IAP/mliap_descriptor_ace.cpp | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ML-IAP/mliap_descriptor.cpp b/src/ML-IAP/mliap_descriptor.cpp index 34f81c3902..b8acd6329e 100644 --- a/src/ML-IAP/mliap_descriptor.cpp +++ b/src/ML-IAP/mliap_descriptor.cpp @@ -28,6 +28,7 @@ MLIAPDescriptor::MLIAPDescriptor(LAMMPS *lmp) : cutghost(nullptr), radelem(nullptr), wjelem(nullptr) { cutmax = 0.0; + allocated_elements = 0; } /* ---------------------------------------------------------------------- */ diff --git a/src/ML-IAP/mliap_descriptor_ace.cpp b/src/ML-IAP/mliap_descriptor_ace.cpp index aa30ac3f81..d815fb744c 100644 --- a/src/ML-IAP/mliap_descriptor_ace.cpp +++ b/src/ML-IAP/mliap_descriptor_ace.cpp @@ -57,7 +57,6 @@ MLIAPDescriptorACE::MLIAPDescriptorACE(LAMMPS *_lmp, char *yacefilename) : { acemlimpl = new ACE_ML_impl; - allocated_elements = 0; //read in file with CG coefficients or c_tilde coefficients ctilde_file = yacefilename; delete acemlimpl->basis_set; From d16d3ee02b7726c634084d453eab97e5b76187bc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Apr 2024 00:19:42 -0400 Subject: [PATCH 3/4] replace wildcard imports with explicit ones --- python/lammps/numpy_wrapper.py | 8 ++++++-- python/lammps/pylammps.py | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py index 91042c43c8..4e33913a69 100644 --- a/python/lammps/numpy_wrapper.py +++ b/python/lammps/numpy_wrapper.py @@ -19,11 +19,15 @@ import warnings from ctypes import POINTER, c_void_p, c_char_p, c_double, c_int, c_int32, c_int64, cast +from .constants import LAMMPS_AUTODETECT, LAMMPS_INT, LAMMPS_INT_2D, \ + LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, \ + LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, \ + LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, \ + LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS, \ + LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING -from .constants import * # lgtm [py/polluting-import] from .data import NeighList - class numpy_wrapper: """lammps API NumPy Wrapper diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index 7dd3823bbf..4b740f35ff 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -28,7 +28,7 @@ import tempfile from collections import namedtuple from .core import lammps -from .constants import * # lgtm [py/polluting-import] +from .constants import LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING # ------------------------------------------------------------------------- From 38874c5aaaf52fccaa8760929416d12bcacbd954 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 Apr 2024 00:27:38 -0400 Subject: [PATCH 4/4] make more consistent --- python/lammps/core.py | 6 ++---- python/lammps/pylammps.py | 4 ++-- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/python/lammps/core.py b/python/lammps/core.py index 626ece0770..ae488dc241 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -23,16 +23,15 @@ from ctypes import CDLL, POINTER, RTLD_GLOBAL, CFUNCTYPE, py_object, byref, cast from os.path import dirname, abspath, join from inspect import getsourcefile -from .constants import LAMMPS_AUTODETECT, LAMMPS_STRING, \ +from lammps.constants import LAMMPS_AUTODETECT, LAMMPS_STRING, \ LAMMPS_INT, LAMMPS_INT_2D, LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, \ LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, \ LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, \ LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS, \ - LMP_ERROR_WARNING, LMP_ERROR_ONE, LMP_ERROR_ALL, LMP_ERROR_WORLD, LMP_ERROR_UNIVERSE, \ LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING, \ get_ctypes_int -from .data import NeighList +from lammps.data import NeighList # ------------------------------------------------------------------------- @@ -2081,7 +2080,6 @@ class lammps(object): :param caller: reference to some object passed to the callback function :type: object, optional """ - import numpy as np def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr): tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1) diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index 4b740f35ff..b5eabd6436 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -27,8 +27,8 @@ import sys import tempfile from collections import namedtuple -from .core import lammps -from .constants import LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING +from lammps.core import lammps +from lammps.constants import LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING # -------------------------------------------------------------------------