ghutchis

The 12 Steps of Grad School

by Geoff Hutchison (with thanks to Andrew Metz) http://hutchison.chem.pitt.edu/

1. Initial Optimism: (I will solve problem X and change the world!)
2. Pessimism: (Hmm, this problem is hard)
3. Apathy: (Meh, I’m getting okay results, but not great)
4. Delusion: (I’m not sure what’s going on - it’s complicated)
5. Cynicism: (Nobody can solve this..)
6. Procrastination: (Eh, it’s a multi-year project, one day won’t hurt)

ghutchis

element_symbols = [
  "Xx", "H", "He", "Li", "Be", "B", "C", "N", "O", "F",
  "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K",
  "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu",
  "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y",
  "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In",
  "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr",
  "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm",
  "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au",

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import os
import math

import pybel

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

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

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

ghutchis

include_directories(${CMAKE_CURRENT_BINARY_DIR})

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

ghutchis

#!/usr/bin/env python

from __future__ import print_function

import sys
import os

import pybel

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

include_directories(${CMAKE_CURRENT_BINARY_DIR})

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