pablopiaggi Goto Github PK

chiral-symmetry-breaking

Analysis scripts and input files to reproduce simulations of manuscript "Critical behavior in a chiral molecular model" by Piaggi, Car, Stillinger, and Debenedetti. Output files are available at https://doi.org/10.34770/aby7-r955

conda

Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)

crystallization-of-iceih

Input files and results of paper: Phase equilibrium of liquid water and hexagonal from ice enhanced sampling molecular dynamics simulations

crystallization-of-silicon

Tutorial: Crystallization of silicon using enhanced sampling simulations

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

environmentfinder

Tool for finding atomic environments in crystal structures

histogramwitherrorbars

Construct histograms with error bars given by a confidence interval calculated from bootstrapped samples.

icenucleationseeding-scan-ml

Data of paper: Piaggi et al., "Homogeneous ice nucleation in an ab initio machine learning model of water", PNAS, 119, e2207294119, (2022) https://www.pnas.org/doi/full/10.1073/pnas.2207294119 or arXiv preprint arXiv:2203.01376 (2022) https://arxiv.org/abs/2203.01376

jcp-2017-localpairentropy

Data of paper: Piaggi and Parrinello, J. Chem. Phys. 147, 114112 (2017); https://doi.org/10.1063/1.4998408

jcp-2019

Input files and results of paper: Calculation of phase diagrams in the multithermal-multibaric ensemble, Pablo Piaggi and Michele Parrinello, J. Chem. Phys. 150, 244119 (2019); https://doi.org/10.1063/1.5102104

lammps

Public/backup repository of the LAMMPS MD software package

lammps_chiraltetramer

LAMMPS 1Feb2014 with chiral tetramer model \\ Initial code by Jonathan Zimmerman, significant modifications by Nikolai Petsev, and further improvements by Pablo Piaggi \\ See also https://github.com/npetsev/LAMMPS-tetramer

masterclass-2022

masterclass-22-12

Data for PLUMED Masterclass 22.12 - Liquid-solid chemical potential differences with the environment similarity CV

mishima-melting-lines-2023

Analysis and input files to reproduce simulations of manuscript "Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point" by Piaggi, Gartner, Car, and Debenedetti

phaseequilibriumwatericescan

Input files to reproduce the results of the paper: Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional

phonolammps

LAMMPS interface for phonon calculations using phonopy

plumed-nest

Draft nest

plumed2

Development version of plumed 2

pnas-2018-polymorphism

Input files to reproduce the paper "Predicting polymorphism in molecular crystals using orientational entropy" by Piaggi and Parrinello

prl-2017-pairentropy

Input files to reproduce the results of the paper: Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

prl-2019

Input files and results of paper: Multithermal-multibaric molecular simulations from a variational principle, Pablo Piaggi and Michele Parrinello, Phys. Rev. Lett. 122, 050601 (2019) ; https://doi.org/10.1103/PhysRevLett.122.050601

running_gromacs

tip4p-ice-phase-diagram