add dpnblist source code to dmff/dpnblist directory

dmff/dpnblist/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.15)
+# project(dpnblist LANGUAGES CUDA CXX)
+project(dpnblist LANGUAGES CXX)
+
+# Set C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Find CUDA
+find_package(CUDA QUIET)
+if (CUDA_FOUND)
+    message(STATUS "CUDA found, compiling CUDA version")
+    enable_language(CUDA)
+    set(CUDA_NVCC_FLAGS 61)
+    set(SOURCES
+        src/pywrap.cpp
+        src/nbList.cpp
+        src/box.cpp
+        src/nbSchAlg.cpp
+        src/SchAlg/hashSchAlgGPU.cu
+        src/SchAlg/hashSchAlgCPU.cpp
+        src/SchAlg/octreeSchAlgCPU.cpp 
+        src/SchAlg/octreeSchAlgGPU.cu 
+        src/SchAlg/cellSchAlgCPU.cpp
+        src/SchAlg/cellSchAlgGPU.cu
+    )
+else()
+    set(SOURCES
+        src/pywrap_CPU.cpp
+        src/nbList_CPU.cpp
+        src/box.cpp
+        src/nbSchAlg.cpp
+        src/SchAlg/hashSchAlgCPU.cpp
+        src/SchAlg/octreeSchAlgCPU.cpp 
+        src/SchAlg/cellSchAlgCPU.cpp
+    )
+endif()
+
+# Find pybind11
+find_package(pybind11 QUIET)
+if (NOT pybind11_FOUND)
+    add_subdirectory(${CMAKE_SOURCE_DIR}/external/pybind11-2.11.1)
+endif()
+
+# Add the pybind11 module
+pybind11_add_module(dpnblist SHARED)
+target_sources(dpnblist PRIVATE ${SOURCES})
+
+# Include directories
+target_include_directories(dpnblist PRIVATE
+    ${CMAKE_SOURCE_DIR}/src
+    ${CMAKE_SOURCE_DIR}/src/SchAlg
+)
+
+# Find and link OpenMP
+find_package(OpenMP REQUIRED)
+if(OpenMP_CXX_FOUND)
+    target_link_libraries(dpnblist PUBLIC OpenMP::OpenMP_CXX)
+endif()
+
+# Find and link Python3
+find_package(Python3 REQUIRED COMPONENTS Development)
+if (Python3_FOUND)
+    target_link_libraries(dpnblist PUBLIC Python3::Python)
+endif()
+
+# Add subdirectory for tests
+if(CMAKE_BUILD_TYPE MATCHES Debug)
+    add_library(dpnblist ${SOURCES})
+    target_include_directories(dpnblist PRIVATE
+        ${CMAKE_SOURCE_DIR}/src
+        ${CMAKE_SOURCE_DIR}/src/SchAlg
+    )
+    target_link_libraries(dpnblist PUBLIC OpenMP::OpenMP_CXX Python3::Python)
+    add_subdirectory(tests)
+endif()
+
+# Set position independent code
+set_target_properties(dpnblist PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+# Set compiler flags
+if (CUDA_FOUND)
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcompiler -fopenmp -O3 -arch=sm_${CUDA_NVCC_FLAGS}")
+endif()
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -O3")

dmff/dpnblist/LICENSE

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+MIT License
+
+Copyright (c) 2024 Zhu Benhao
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dmff/dpnblist/README.md

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+# dpnblist
+ Resable and Modular Neighborlist Lib
+
+### Installation
+you can follow the below commands to build the project
+```
+cmake -B build
+cmake --build build
+```
+then a .so lib will be generated, which can be used in python.
+
+### Usage
+In our neighbor list library, we provide a full type of neighbor list and include three different types of algorithms: cell list, octree, and hash methods, and support CPU and GPU.  
+
+1. First, it is necessary to define a simulation system through the `box` class, mainly including two parameters, the `length` and `angle` of the simulation system, as shown in the table below:
+
+    |Box Parameter | Data Type |
+    |---|---|
+    |length  |  list |
+    |amgle   |   list |
+
+2. Then, specify different algorithms and platforms through the `NeighborList` class, with parameters as follows
+
+    |Parameter| Data Type |Value|
+    |---|---|---|
+    |mode|string|"Linked_Cell-CPU"  "Linked_Cell-GPU"  "Octree-CPU"  "Octree-GPU"  "Hash-CPU"  "Hash-GPU"|
+
+3. Finally, call the `build` method to generate the neighbor list, passing the `box`, `points`, and `cutoff` parameters. Then, use the `get_neighbor_pair` method to retrieve the neighbor list.
+
+Here's an example of usage:  
+```python
+import nblist
+import numpy as np
+
+nblist.set_num_threads(4)
+print(nblist.get_max_threads())
+num_particle = 30000
+shape = (num_particle, 3)
+points = np.random.random(shape) * domain_size
+domain_size = [50.0, 50.0, 50.0]
+angle = [90.0, 90.0, 90.0]
+cutoff = 6.0
+
+box = nblist.Box(domain_size, angle)
+nb = nblist.NeighborList("Linked_Cell-GPU")    # Linked_Cell-GPU  Linked_Cell-CPU  Octree-GPU  Octree-CPU  Hash-GPU  Hash-CPU
+nb.build(box, points, cutoff)
+pairs = nb.get_neighbor_pair()
+```

dmff/dpnblist/examples/nblist_test.py

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+import dpnblist
+import numpy as np
+import time
+import freud
+
+dpnblist.set_num_threads(4)
+print(dpnblist.get_max_threads())
+
+num_particle = 3000
+domain_size = [50.0, 50.0, 50.0]
+angle = [90.0, 90.0, 90.0]
+shape = (num_particle, 3)
+inputs = np.random.random(shape) * domain_size
+cutoff = 6.0
+
+box = dpnblist.Box(domain_size, angle)
+nb = dpnblist.NeighborList("Octree-CPU")    # Linked_Cell-GPU  Linked_Cell-CPU  Octree-GPU  Octree-CPU  Hash-GPU  Hash-CPU
+nb.build(box, inputs, cutoff)
+pairs = nb.get_neighbor_pair()
+lists = nb.get_neighbor_list()
+print(pairs[0:9])
+print(lists[0:3])

dmff/dpnblist/external/doctest-2.4.11/.clang-format

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+# https://clang.llvm.org/docs/ClangFormatStyleOptions.html
+
+DisableFormat: false
+Language: Cpp
+Standard: Cpp11
+IndentWidth: 4
+TabWidth: 4
+UseTab: Never
+ColumnLimit: 100
+ReflowComments: false
+SortIncludes: false
+
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
+AlignEscapedNewlinesLeft: false
+AlignOperands: true
+AlignTrailingComments: true
+AlignAfterOpenBracket: true
+DerivePointerAlignment: false
+PointerAlignment: Left
+IndentCaseLabels: true
+ContinuationIndentWidth: 8
+NamespaceIndentation: Inner
+CompactNamespaces: true
+FixNamespaceComments: true
+AccessModifierOffset: -4
+
+SpaceAfterControlStatementKeyword: false
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: Never
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Cpp11BracedListStyle: true
+
+KeepEmptyLinesAtTheStartOfBlocks: false
+MaxEmptyLinesToKeep: 1
+BinPackArguments: true
+BinPackParameters: true
+AlwaysBreakAfterReturnType: None
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakTemplateDeclarations: true
+BreakConstructorInitializersBeforeComma: true
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 8
+
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AllowShortBlocksOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortFunctionsOnASingleLine: All
+
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: false
+BreakStringLiterals: true
+BreakBeforeBraces: Custom
+BraceWrapping:
+    AfterClass: true
+    AfterEnum: true
+    AfterNamespace: false
+    AfterStruct: true
+    AfterUnion: true
+
+    BeforeCatch: false
+    BeforeElse: false
+    IndentBraces: false
+    AfterFunction: false
+    AfterControlStatement: false
+
+# penalties not thought of yet
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 60
+PenaltyBreakString: 1000
+PenaltyBreakFirstLessLess: 120
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 1000

dmff/dpnblist/external/doctest-2.4.11/.clang-tidy

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+Checks: '*,
+         -altera-id-dependent-backward-branch,
+         -altera-struct-pack-align,
+         -altera-unroll-loops,
+         -bugprone-easily-swappable-parameters,
+         -bugprone-macro-parentheses,
+         -bugprone-suspicious-include,
+         -cppcoreguidelines-avoid-magic-numbers,
+         -cppcoreguidelines-avoid-non-const-global-variables,
+         -cppcoreguidelines-macro-usage,
+         -cppcoreguidelines-non-private-member-variables-in-classes,
+         -cppcoreguidelines-owning-memory,
+         -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+         -cppcoreguidelines-pro-bounds-constant-array-index,
+         -cppcoreguidelines-pro-bounds-pointer-arithmetic,
+         -cppcoreguidelines-pro-type-member-init,
+         -cppcoreguidelines-pro-type-reinterpret-cast,
+         -cppcoreguidelines-pro-type-union-access,
+         -cppcoreguidelines-virtual-class-destructor,
+         -fuchsia-default-arguments-calls,
+         -fuchsia-default-arguments-declarations,
+         -fuchsia-overloaded-operator,
+         -google-build-using-namespace,
+         -google-explicit-constructor,
+         -google-readability-braces-around-statements,
+         -google-readability-function-size,
+         -google-readability-namespace-comments,
+         -google-readability-todo,
+         -google-runtime-int,
+         -google-runtime-references,
+         -hicpp-braces-around-statements,
+         -hicpp-explicit-conversions,
+         -hicpp-function-size,
+         -hicpp-member-init,
+         -hicpp-named-parameter,
+         -hicpp-no-array-decay,
+         -hicpp-no-assembler,
+         -hicpp-signed-bitwise,
+         -hicpp-uppercase-literal-suffix,
+         -llvm-header-guard,
+         -llvm-include-order,
+         -llvm-namespace-comment,
+         -llvmlibc-*,
+         -misc-no-recursion,
+         -misc-non-private-member-variables-in-classes,
+         -modernize-concat-nested-namespaces,
+         -modernize-use-default-member-init,
+         -modernize-use-nodiscard,
+         -modernize-use-trailing-return-type,
+         -readability-braces-around-statements,
+         -readability-function-cognitive-complexity,
+         -readability-function-size,
+         -readability-identifier-length,
+         -readability-implicit-bool-conversion,
+         -readability-magic-numbers,
+         -readability-named-parameter,
+         -readability-redundant-access-specifiers,
+         -readability-uppercase-literal-suffix'
+
+WarningsAsErrors: '*'
+
+HeaderFilterRegex: '.*h$'

dmff/dpnblist/external/doctest-2.4.11/.editorconfig

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+root = true
+
+[*]
+charset = utf-8
+trim_trailing_whitespace = true
+end_of_line = lf
+indent_style = space
+indent_size = 4
+insert_final_newline = true
+
+[*.yml]
+indent_size = 2

dmff/dpnblist/external/doctest-2.4.11/.gitattributes

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+* text=auto

dmff/dpnblist/external/doctest-2.4.11/.github/FUNDING.yml

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+github: onqtam
+patreon: onqtam
+custom: https://www.paypal.me/onqtam/10
+

dmff/dpnblist/external/doctest-2.4.11/.github/issue_template.md

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+## Description
+<!--
+If your issue is a bugreport, this means describing what you did,
+what did you want to happen and what actually did happen.
+
+If your issue is a feature request, describe the feature and why do you
+want it.
+-->
+
+
+### Steps to reproduce
+<!--
+This is only relevant for bug reports, but if you do have one,
+please provide a minimal set of steps to reproduce the problem.
+
+Usually this means providing a small and self-contained code using doctest
+and specifying compiler flags/tools used if relevant.
+-->
+
+
+### Extra information
+<!--
+Fill in any extra information that might be important for your issue.
+
+If your issue is a bugreport, definitely fill out at least the following.
+-->
+* doctest version: **v42.42.42**
+* Operating System: **Joe's discount operating system**
+* Compiler+version: **Hidden Dragon v1.2.3**