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The d-SEAMS C++ core engine

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# d-SEAMS

**Deferred Structural Elucidation Analysis for Molecular Simulations**

[![Build Status](https://github.com/d-SEAMS/seams-core/actions/workflows/build_pkg.yml/badge.svg)](https://github.com/d-SEAMS/seams-core/actions/workflows/build_pkg.yml)

[![built with nix](https://builtwithnix.org/badge.svg)](https://builtwithnix.org)

- Check our build status [here](https://github.com/d-SEAMS/seams-core/actions/workflows/).
- The docs themselves are [here](https://docs.dseams.info) and development is
  ongoing [on GitHub](https://github.com/d-SEAMS/seams-core)
- We also have [a Zenodo community](https://zenodo.org/communities/d-seams/) for user-contributions like reviews, testimonials
  and tutorials
- Trajectories are hosted [on
  figshare](https://figshare.com/projects/d-SEAMS_Datasets/73545).
- Our [wiki is here](https://wiki.dseams.info)

\brief The C++ core of d-SEAMS, a molecular dynamics trajectory analysis engine.

\note The <a href="pages.html">related pages</a> describe the examples and how to obtain
the data-sets (trajectories) <a
href="https://figshare.com/projects/d-SEAMS_Datasets/73545">from figshare</a>.

\warning **If** you are unwilling to use the `nix` build system, then **please note** that you must manage the dependencies MANUALLY, including the compiler versions. Optionally, use the provided `conda` environment.

# Citation

- This has been published at the [Journal of Chemical Information and Modeling
  (JCIM)](https://doi.org/10.1021/acs.jcim.0c00031)

- You may also read [the preprint on arXiv](https://arxiv.org/abs/1909.09830)

If you use this software please cite the following:

Goswami, R., Goswami, A., & Singh, J. K. (2020). d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.0c00031

The corresponding `bibtex` entry is:

@Article{Goswami2020,
    author={Goswami, Rohit and Goswami, Amrita and Singh, Jayant Kumar},
    title={d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations},
    journal={Journal of Chemical Information and Modeling},
    year={2020},
    month={Mar},
    day={20},
    publisher={American Chemical Society},
    issn={1549-9596},
    doi={10.1021/acs.jcim.0c00031},
    url={https://doi.org/10.1021/acs.jcim.0c00031}
    }

# Compilation

We use a deterministic build system to generate both bug reports and uniform
usage statistics. This also handles the `lua` scripting engine.

\note The lua functions are documented on the [on the API Docs](https://docs.dseams.info/md_markdown_luafunctions)

We also provide a `conda` environment as a fallback, which is also recommended for MacOS users.

## Build

### Conda (working now)

Although we strongly suggest using `nix`, for MacOS systems, the following
instructions may be more suitable. We will assume the presence of [micromamba](https://mamba.readthedocs.io/en/latest/installation.html):

```bash
cd ~/seams-core
micromamba create -f environment.yml
micromamba activate dseams
luarocks install luafilesystem
```

Now the installation can proceed.

\note we do not install `lua-luafilesystem` within the `conda` environment because it is outdated on `osx`

```bash
mkdir build
cd build
export EIGEN3_INCLUDE_DIR=$CONDA_PREFIX/include/eigen3
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=YES -DCMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX ../
make -j$(nproc)
make install
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib $CONDA_PREFIX/bin/yodaStruct -c lua_inputs/config.yml
```

We have opted to install into the `conda` environment, if this is not the
intended behavior, use `/usr/local` instead.

### Spack (not working at the moment)

Manually this can be done in a painful way as follows:

```bash
spack install eigen@3.3.9 lua@5.2
spack install catch2 fmt yaml-cpp openblas boost cmake ninja meson
spack load catch2 fmt yaml-cpp openblas boost cmake ninja meson eigen@3.3.9 lua@5.2
luarocks install luafilesystem
```

Or better:

```bash
spack env activate $(pwd)
# After loading the packages
luarocks install luafilesystem
```

Now we can build and install as usual.

```bash
cmake -S . -B build -DCMAKE_BUILD_TYPE=RelWithDebInfo \
 -DCMAKE_EXPORT_COMPILE_COMMANDS=YES -GNinja \
 -DCMAKE_INSTALL_PREFIX=$HOME/.local \
 -DCMAKE_CXX_FLAGS="-pg -fsanitize=address " \
 -DCMAKE_EXE_LINKER_FLAGS=-pg -DCMAKE_SHARED_LINKER_FLAGS=-pg \
 -DBUILD_TESTING=NO
cmake --build build
```

Or more reasonably:

```bash
export INST_DIR=$HOME/.local
cd src
meson setup bbdir --prefix $INST_DIR
meson compile -C bbdir
meson install -C bbdir
# if not done
export PATH=$PATH:$INST_DIR/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$INST_DIR/lib
cd ../
yodaStruct -c lua_inputs/config.yml
```

### Nix (not working at the moment)

Since this project is built with `nix`, we can simply do the following from the
root directory (longer method):

```sh
# Make sure there are no artifacts
rm -rf build
# This will take a long time the first time as it builds the dependencies
nix-build . # Optional
# Install into your path
nix-env -if . # Required
# Run the command anywhere
yodaStruct -c lua_inputs/config.yml
```

A faster method of building the software is by using the [cachix binary cache](https://dseams.cachix.org/) as shown:

```bash
# Install cachix
nix-env -iA cachix -f https://cachix.org/api/v1/install
# Use the binary cache
cachix use dseams
# Faster with the cache than building from scratch
nix-build . # Optional
# Install into your path
nix-env -if . # Required
# Run the command anywhere
yodaStruct -c lua_inputs/config.yml
```

### Usage

Having installed the `yodaStruct` binary and library, we can now use it.

```bash
yodaStruct -c lua_inputs/config.yml
```

\note The paths in the `.yml` should be **relative to the folder from which the binary is called**.

If you're confused about how to handle the relative paths, run the command `yodaStruct -c lua_inputs/config.yml` in the top-level directory, and set the paths relative to the top-level directory. This is the convention used in the examples as well.

### Language Server Support

To generate a `compile_commands.json` file for working with a language server
like [ccls](https://github.com/MaskRay/ccls) use the following commands:

```sh
# Pure environment
nix-shell --pure
mkdir -p build && cd build
cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_EXPORT_COMPILE_COMMANDS=YES ../
cp compile_commands.json ../
```

Note that there is no need to actually compile the project if you simply need to
get the compiler database for the language server.

**Do Not** commit the `.json` file.

## Development

We can simply use the `nix` environment:

```sh
# From the project root
nix-shell --pure
```

# Running

This is built completely with nix:

```{bash}
# Install systemwide
nix-env -if .
```

To run the sample inputs, simply install the software, and ensure that `input/` is a child directory.

```{bash}
# Assuming you are in the src directory
# Check help with -h
yodaStruct -c lua_inputs/config.yml
```

## Tests

Apart from the [examples](https://docs.dseams.info/pages.html), the test-suite
can be run with the `yodaStruct_test` binary, which will drop into the
`nix` environment before building and executing `gdb`:

```{bash}
# Just run this
./testBuild.sh
# At this point the binary and library are copied into the root
# One might, in a foolhardy attempt, use gdb at this point
# Here be dragons :)
# USE NIX
# Anyway
gdb --args ./yodaStruct -c lua_inputs/config.yml
# quit gdb with quit
# Go run the test binary
cd shellBuild
./yodaStruct_test
```

Do note that the regular installation via `nix-env` runs the tests before the installation

# Developer Documentation

While developing, it is sometimes expedient to update the packages used. It is
then useful to note that we use [niv](https://github.com/nmattia/niv/) to handle our pinned packages (apart from
the ones built from Github). Thus, one might need, say:

```bash
niv update nixpkgs -b nixpkgs-unstable
```

Test the build with nix:

```bash
nix-build .
# Outputs are in ./result
# If you get a CMake error
rm -rf build
nix-store --delete /nix/store/$whatever # $whatever is the derivation complaining
nix-collect-garbage # then try again [worst case scenario]
```

## Leaks and performance

While testing for leaks, use `clang` (for
[AddressSanitizer](https://github.com/google/sanitizers/wiki/AddressSanitizer)
and
[LeakSanitizer](https://github.com/google/sanitizers/wiki/AddressSanitizerLeakSanitizer))
and the following:

```{bash}
# From the developer shell
export CXX=/usr/bin/clang++ && export CC=/usr/bin/clang
cmake .. -DCMAKE_CXX_FLAGS="-pg -fsanitize=address " -DCMAKE_EXE_LINKER_FLAGS=-pg -DCMAKE_SHARED_LINKER_FLAGS=-pg
```

# Overview

As of Mon Jan 20 15:57:18 2020, the lines of code calculated by
[cloc](http://cloc.sourceforge.net/) are as follows:

![Cloc Lines](https://raw.githubusercontent.com/d-SEAMS/seams-core/main/images/cloc-2020-01-20_15-56.png)

# Contributing

Please ensure that all contributions are formatted according to the
[clang-format](./clang-format) configuration file.

Specifically, consider using the following:

- [Sublime Plugin](https://github.com/rosshemsley/SublimeClangFormat) for users
  of Sublime Text

- [format-all](https://github.com/lassik/emacs-format-all-the-code) for Emacs
- [vim-clang-format](https://github.com/rhysd/vim-clang-format) for Vim
- Visual Studio: http://llvm.org/builds/, or use the [integrated support in Visual Studio 2017](https://blogs.msdn.microsoft.com/vcblog/2018/03/13/clangformat-support-in-visual-studio-2017-15-7-preview-1/)
- Xcode: https://github.com/travisjeffery/ClangFormat-Xcode

Where some of the above suggestions are derived from [this depreciated githook](https://github.com/andrewseidl/githook-clang-format).

Also, do note that we have a `CONTRIBUTING` file you **need to read** to
contribute, for certain reasons, like, common sense.

## Commit Hook
Note that we expect compliance with the `clang-format` as mentioned above, and this may be enforced by using the provided scripts for a pre-commit hook:
```bash
./scripts/git-pre-commit-format install
```

This will ensure that new commits are in accordance to the `clang-format` file.

## Development Builds

The general idea is to drop into an interactive shell with the dependencies and then use `cmake` as usual.

```bash
nix-shell --pure --run bash --show-trace --verbose
cd build
cmake .. -DCMAKE_BUILD_TYPE=Debug -DNO_WARN=TRUE \
 -DFIND_EIGEN=TRUE \
 -DCMAKE_EXPORT_COMPILE_COMMANDS=1 \
 -G "Ninja"
ninja
# Test
cd ../
yodaStruct -c lua_inputs/config.yml
# Debug
gdb --args yodaStruct -c lua_inputs/config.yml
```
To load debugging symbols from the shared library, when you are inside `gdb` (from the top-level directory, for instance), use the following command:

```bash
add-symbol-file build/libyodaLib.so
```
Then you can set breakpoints in the C++ code; for instance:

```bash
b seams_input.cpp:408
```

# Acknowledgements

The following tools are used in this project:

- [CMake](https://cmake.org/) for compilation ([cmake-init](https://github.com/cginternals/cmake-init) was used as a reference)
- [Clang](https://clang.llvm.org/) because it is more descriptive with better tools
- [Doxygen](https://www.doxygen.org) for the developer API
- [clang-format](https://clang.llvm.org/docs/ClangFormat.html) for code formatting
  - [clang-format-hooks](https://github.com/barisione/clang-format-hooks) for `git` hooks to enforce formatting
- [lua](https://www.lua.org) for the scripting engine
- [yaml](http://yaml.org/) for the configuration

## Third Party Libraries

The libraries used are:

- [backward-cpp](https://github.com/bombela/backward-cpp) for better stacktraces without `gdb`
- [cxxopts](https://github.com/jarro2783/cxxopts) for parsing command line options
- [rang](https://github.com/agauniyal/rang) for terminal styles (ANSI)
- [sol2](https://github.com/ThePhD/sol2) for interfacing with lua
- [yaml-cpp](https://github.com/jbeder/yaml-cpp) for working with `yaml`
- [fmt](https://github.com/fmtlib/fmt) for safe and fast formatting
- [Linear Algebra PACKage (LAPACK)](http://www.netlib.org/lapack/)
- [Basic Linear Algebra Subprograms (BLAS)](http://www.netlib.org/blas/)
- [Spectra](https://github.com/yixuan/spectra/)
- [Boost Geometry](https://www.boost.org/doc/libs/1_68_0/libs/geometry/doc/html/index.html) for working with different coordinates
- [Boost Math](https://www.boost.org/doc/libs/?view=category_math) for spherical harmonics
- [Blaze](https://bitbucket.org/blaze-lib/blaze/) for very fast modern linear algebra
- [nanoflann](https://github.com/jlblancoc/nanoflann) to calculate nearest neighbors
- [icecream-cpp](https://github.com/renatoGarcia/icecream-cpp) for pretty-printing and debugging

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