MaginnGroup/Cassandra issues and pull requests

#143 - Settings of GEMC-NVT simulation of water, hard to reach eqilibrium

Issue - State: open - Opened by qqlovekerry over 1 year ago

#142 - How to calculate the chemical potential of water at different temperatures?

Issue - State: open - Opened by qqlovekerry over 1 year ago - 2 comments

#141 - Add atompair overlap radii and energy table and ability to read XTC trajectory files.

Pull Request - State: open - Opened by rwsmith7531 over 1 year ago - 3 comments

#140 - Add atompair-specific overlap radii for use in Widom insertions

Issue - State: open - Opened by rwsmith7531 over 1 year ago

#139 - Use precalculated atom pair energy table to estimate CBMC energies

Issue - State: open - Opened by rwsmith7531 over 1 year ago

#138 - Add XTC trajectory file reading capablility to Cassandra

Issue - State: open - Opened by rwsmith7531 over 1 year ago

#137 - Running time of GCMC simulation does not scale with core numbers well, parrallel efficiency problem

Issue - State: closed - Opened by qqlovekerry almost 2 years ago - 2 comments

#136 - Insertion of a huge number of molecules in a GCMC simulation

Issue - State: closed - Opened by camjjr about 2 years ago - 5 comments

#135 - Update CI

Pull Request - State: closed - Opened by emarinri about 2 years ago

#134 - Fix CBMC dihedral selection

Pull Request - State: closed - Opened by rwsmith7531 about 2 years ago

#133 - High-energy CBMC dihedral trials incorrectly not flagged as overlap

Issue - State: closed - Opened by rwsmith7531 about 2 years ago

#132 - Error about dep.mk during compilation with make

Issue - State: open - Opened by qqlovekerry about 2 years ago

#131 - Add the size-weighted mixing rule

Pull Request - State: open - Opened by emarinri about 2 years ago

#130 - Validate log volume moves implementation

Issue - State: open - Opened by emarinri over 2 years ago

#129 - Fix GEMC examples and prevent log volume moves

Pull Request - State: closed - Opened by emarinri over 2 years ago

#128 - Inconsistent value of pressure in GCMC

Issue - State: closed - Opened by camjjr over 2 years ago - 6 comments

#127 - Address various floating-point exceptions

Pull Request - State: closed - Opened by emarinri over 2 years ago

#126 - Floating-point exceptions

Issue - State: closed - Opened by emarinri over 2 years ago

#125 - Add error for converting non-numeric strings to numbers.

Pull Request - State: closed - Opened by rwsmith7531 over 2 years ago

#124 - Chargeless Widom insertion species with ewald fix

Pull Request - State: closed - Opened by rwsmith7531 over 2 years ago

#123 - Functions for converting strings to numbers don't verify that the string is a valid number.

Issue - State: closed - Opened by rwsmith7531 over 2 years ago

#122 - Unreasonable Widom insertion results when inserting chargeless species in system with partial charges with ewald

Issue - State: closed - Opened by rwsmith7531 over 2 years ago

#121 - lammpstrj converter script argument type fix

Pull Request - State: closed - Opened by rwsmith7531 over 2 years ago

#120 - Wrong data type for lammpstrjconvert.py input argument nmols.

Issue - State: closed - Opened by rwsmith7531 over 2 years ago

#119 - No broken bonds in input XYZ

Pull Request - State: closed - Opened by emarinri over 2 years ago

#118 - No broken molecules in the input XYZ

Issue - State: closed - Opened by emarinri over 2 years ago
Labels: Type: Documentation

#117 - Include single point energies calculations from LAMMPS or other MD code as unit tests

Issue - State: open - Opened by emarinri over 2 years ago

#116 - Fix solids conect

Pull Request - State: closed - Opened by emarinri over 2 years ago

#115 - Create tests for mcfgen.py

Issue - State: open - Opened by emarinri over 2 years ago

#114 - Improve ring identification in mcfgen.py

Issue - State: open - Opened by emarinri over 2 years ago

#113 - Improve miscellaneous things regarding solid simulations

Pull Request - State: closed - Opened by emarinri over 2 years ago

#112 - Improve solids setup using mcfgen.py

Issue - State: closed - Opened by emarinri over 2 years ago
Labels: Type: Enhancement

#111 - Number of k-vectors is not consistent between orthogonal and cubic boxes

Issue - State: open - Opened by emarinri almost 3 years ago

#110 - Minimium image distance in a triclinic box

Issue - State: open - Opened by ryangmullen almost 3 years ago - 1 comment
Labels: Priority: High

#109 - Energy calculation in Cassandra

Issue - State: closed - Opened by ashomali about 3 years ago - 2 comments

#108 - Replace int64 seeds with int32 seeds in examples and tests

Pull Request - State: closed - Opened by rwsmith7531 about 3 years ago

#107 - Correct examples to only use seeds that can be stored as INT32

Issue - State: closed - Opened by rwsmith7531 over 3 years ago

#106 - Add trajectory reader and enhance Widom insertion support.

Pull Request - State: closed - Opened by rwsmith7531 over 3 years ago - 1 comment

#105 - Add counters for core overlap in Widom insertions.

Issue - State: closed - Opened by rwsmith7531 over 3 years ago

#104 - Update counters related to Widom insertions to INT64

Issue - State: closed - Opened by rwsmith7531 over 3 years ago

#103 - Add the ability to read and operate with pregenerated trajectories.

Issue - State: closed - Opened by rwsmith7531 over 3 years ago
Labels: Type: New feature

#102 - Update/azp

Pull Request - State: closed - Opened by rsdefever over 3 years ago

#101 - HMA

Pull Request - State: open - Opened by ajschult over 3 years ago - 3 comments

#100 - Implement GSD output file for Cassandra

Issue - State: open - Opened by rsdefever over 3 years ago - 10 comments
Labels: Type: Enhancement, Priority: Medium

#99 - Problem reading checkpoint

Issue - State: open - Opened by hmcezar over 3 years ago - 6 comments

#98 - Extend maximum number of MC steps by using INT64 for counters

Pull Request - State: closed - Opened by rsdefever over 3 years ago - 1 comment

#97 - Limits to integer size - long solubility runs

Issue - State: closed - Opened by bbefort over 3 years ago - 1 comment

#96 - Correct dimension labels in Apply_PBC_Anint.

Pull Request - State: closed - Opened by rwsmith7531 over 3 years ago - 8 comments

#95 - PBC box images based on wrong dimension

Issue - State: closed - Opened by rwsmith7531 over 3 years ago
Labels: Type: Bug

#94 - Implement HMA

Issue - State: open - Opened by ajschult almost 4 years ago - 12 comments

#93 - Add rtd documentation for Widom insertions.

Pull Request - State: closed - Opened by rwsmith7531 almost 4 years ago

#92 - move_rotate.f90 unused variables?

Issue - State: open - Opened by GarrettTow almost 4 years ago

#91 - Transform run_examples.py from Python 2 to Python 3

Issue - State: open - Opened by linhbngo almost 4 years ago - 1 comment

#90 - Allow dashes in file names

Pull Request - State: open - Opened by rwsmith7531 about 4 years ago

#89 - Update RTD property output section

Pull Request - State: closed - Opened by rsdefever about 4 years ago

#88 - Allow dashes in filenames?

Issue - State: open - Opened by rsdefever about 4 years ago - 2 comments

#87 - Checkpoint files with dashes result in error

Issue - State: closed - Opened by rmatsum836 about 4 years ago - 3 comments

#86 - Fix time counter for coordinate writing in simulations with lengths given in minutes

Issue - State: open - Opened by rwsmith7531 about 4 years ago
Labels: Type: Bug, Drivers

#85 - Add version info to auxillary scripts

Issue - State: open - Opened by rsdefever over 4 years ago

#84 - Hotfix/mcfgen

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#83 - MCF generated with mcfgen has doubled fragment connection.

Issue - State: closed - Opened by hmcezar over 4 years ago - 5 comments

#82 - Example PR

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#81 - Complete documentation conversion to RTD

Issue - State: open - Opened by rsdefever over 4 years ago - 1 comment
Labels: Type: Documentation

#80 - Add unit testing

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: Type: Tests

#79 - Overhaul mcfgen.py and library_setup.py

Issue - State: open - Opened by rsdefever over 4 years ago

#78 - Fixed mcfgen error when there were no connected atoms in pdb.

Pull Request - State: closed - Opened by hmcezar over 4 years ago - 9 comments

#77 - MCFGen exits with keyError when the molecule has no fragments (pdb without CONECT)

Issue - State: closed - Opened by hmcezar over 4 years ago

#76 - Doc additions: restricted insertions, RTD link in README

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#75 - Fix broken code-blocks

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#74 - Rtd migration part 1

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#73 - Bugfix for gfortran multiring atoms

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#72 - Update README to GitHub releases and conda installation

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#71 - Add docs for shift-force option

Pull Request - State: closed - Opened by rsdefever over 4 years ago
Labels: Type: Documentation

#70 - Add bump2version configuration file

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#69 - Add up to 23 character atom name support for custom mixing rules

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#68 - Make config structures unreasonable with low Rcutoff_Low

Issue - State: open - Opened by rsdefever over 4 years ago

#67 - Fix/ring fragments

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#66 - Change deletion move acceptance criteria for restricted insertions

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#65 - SPC/E water NPT example README is incorrect

Issue - State: open - Opened by rwsmith7531 over 4 years ago
Labels: Examples

#64 - Add Widom insertion module

Pull Request - State: closed - Opened by rwsmith7531 over 4 years ago - 6 comments
Labels: Type: New feature

#63 - Expand maximum line length and number of items per line

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#62 - Fragment generation fails for fused rings/ring systems

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment
Labels: Type: Enhancement

#61 - Write tolerance to MCF for fixed bonds

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#60 - Cassandra does not write bond tolerances to MCF file

Issue - State: closed - Opened by rsdefever over 4 years ago
Labels: Type: Bug

#59 - Cassandra fragment generation error for cage structure

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment

#58 - Initialize identity_switch trial counter to zero

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#57 - ntrials for identity switch moves is not initialized to zero

Issue - State: closed - Opened by rsdefever over 4 years ago
Labels: Type: Bug, Priority: Medium

#56 - library setup fails with space in file path

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: Type: Bug, Priority: High

#55 - ignore text after ! when parsing the input file

Pull Request - State: closed - Opened by ryangmullen over 4 years ago - 1 comment

#54 - Add support for shifted-force LJ potential

Pull Request - State: closed - Opened by rsdefever over 4 years ago
Labels: Energy evaluation

#53 - Clarify error message for invalid VDW type in MCF file

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#52 - mcfgen.py does not throw error if no charges are listed

Issue - State: open - Opened by rsdefever over 4 years ago
Labels: Type: Bug

#51 - Support for NpT GEMC with single box volume fluctuations

Issue - State: closed - Opened by rsdefever over 4 years ago - 1 comment
Labels: Type: Enhancement, Priority: Medium

#50 - Update version info for release

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#49 - Update docs

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#48 - Add Makefile for conda installation

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#47 - Edit README: Azure badge, contributing path, bash export example

Pull Request - State: closed - Opened by rsdefever over 4 years ago

#36 - Slow cloning of Cassandra

Issue - State: closed - Opened by jshahOSU over 4 years ago - 1 comment

#18 - Add installation instructions to documentation

Issue - State: closed - Opened by emarinri over 5 years ago
Labels: Type: Documentation, Priority: Medium

#12 - Improvement on custom mixing rules

Issue - State: open - Opened by emarinri almost 6 years ago
Labels: Type: Enhancement, Energy evaluation

GitHub / MaginnGroup/Cassandra issues and pull requests