ghutchis

Are you a student? Know a student?

Want to get paid to write open source chemistry code this summer?

Following up on a successful 2016 and 2017, the Open Chemistry "umbrella" group of open source chemistry projects is looking for student proposals for Google Summer of Code (https://summerofcode.withgoogle.com/how-it-works/)

Applications and proposals are due from March 12th until March 27th. Students who are selected are paid between $US 2400 and $US 6600 for completing their work (https://developers.google.com/open-source/gsoc/help/student-stipends#amounts).

Students can submit their own ideas or work on suggested projects (Avogadro, cclib, RDKit, 3Dmol.js, MSDK, NWChem, Open Babel, DeepChem, etc.) Ideas range from easy-to-use web repositories for computational chemistry, OpenMM and GPU enabled molecular mechanics, volumetric rendering, to advanced analytical methods for quantum chemistry. http://wiki.openchemistry.org/GSoC_Ideas_2018

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import logging
import numpy as np
from cclib.io import ccopen
from nms import nmsgenerator
from masses import element_masses

ghutchis

include_directories(${CMAKE_CURRENT_BINARY_DIR})

avogadro_plugin(ResetView
  "Manipulate the view camera."
  ExtensionPlugin
  resetview.h
  ResetView
  "resetview.cpp"
  ""
)

ghutchis

The largest complaints about Avogadro v1.x were about crashes and slow performance on large systems. To solve this, we needed to rewrite the code essentially from the ground up. Marcus Hanwell and others at Kitware contributed significantly to this effort.

The new architecture also makes it much easier to extend, whether for your own specific needs, or to connect with a wide variety of chemistry software.

Major Features in Avogadro 2

• Improved stability using a new code architecture
• Dramatically improved rendering performance, up to millions of atoms

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import os

import pybel

ghutchis

include_directories(${CMAKE_CURRENT_BINARY_DIR})

avogadro_plugin(ResetView
  "Manipulate the view camera."
  ExtensionPlugin
  resetview.h
  ResetView
  "resetview.cpp"
  ""
)

ghutchis

2018 Avogadro Community Survey

Quick Summary (tldr)

• Many users find Avogadro from a friend, peer or instructor (~45%)
• By far, most download binaries (>80%)
  • Many use package managers (42%)
• Responses were heavily from Linux (71%) and Mac (60%) users, despite most SourceForge downloads from Windows users (66%)
• Heavily educated, with >90% of responses with at least a graduate degree
• Many can code: >40% report Python knowledge, >10% report C/C++ knowledge

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Code style / quality

• Updated header comments
• clazy
• clang-tidy
• Replacing jsoncpp

Plugin Ecosystem

• Guides and examples for plugins
• Website directory needs

• Register GitHub repo

ghutchis

Avogadro

• get / modify selection (e.g., enlarge by x Å)
• create enantiomer
• “Random alloy” - Replace x% atom X -> atom Y

Scikit-nano https://docs.scikit-nano.org

• MWNT
• Graphene or TMDC multilayers?

Pymatgen https://github.com/materialsproject/pymatgen

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import os
import math

import pybel