d-SEAMS

The C++ core of d-SEAMS, a molecular dynamics trajectory analysis engine. Deferred Structural Elucidation Analysis for Molecular Simulations

Note
The related pages describe the examples and how to obtain the data-sets (trajectories) from figshare.
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

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

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

## Build

### Conda

Although we strongly suggest using nix, for MacOS systems, the following instructions may be more suitable. We will assume the presence of micromamba:

micromamba create -f environment.yml
micromamba activate dseams

Now the installation can proceed.

Note
we do not install a new version of cmake within the conda environment because of conflicts with lua
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=YES -DCMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX ../ make -j$(nproc)
make install

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

### Nix

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

# 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 as shown:

# 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.

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 use the following commands:

# 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:

# From the project root
nix-shell --pure

# Running

This is built completely with nix:

# Install systemwide
nix-env -if .

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

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

## Tests

Apart from the examples, the test-suite can be run with the yodaStruct_test binary, which will drop into the nix environment before building and executing gdb:

# Just run this
./testBuild.sh
# 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 to handle our pinned packages (apart from the ones built from Github). Thus, one might need, say:

niv update nixpkgs -b nixpkgs-unstable

Test the build with nix:

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 and LeakSanitizer) and the following:

# From the developer shell
export CXX=/usr/bin/clang++ && export CC=/usr/bin/clang

# Overview

As of Mon Jan 20 15:57:18 2020, the lines of code calculated by cloc are as follows:

# Contributing

Please ensure that all contributions are formatted according to the clang-format configuration file.

Specifically, consider using the following:

Where some of the above suggestions are derived from this depreciated githook.

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:

./scripts/git-pre-commit-format install

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

# Acknowledgements

The following tools are used in this project:

## Third Party Libraries

The libraries used are: