Cascella-Group-UiO/HyMD issues and pull requests

#228 - Changes in utils scripts

Pull Request - State: closed - Opened by hmcezar 2 months ago

#227 - Fix release action

Pull Request - State: closed - Opened by hmcezar about 1 year ago

#226 - Multi replica simulations

Pull Request - State: closed - Opened by hmcezar about 1 year ago - 1 comment

#225 - Fixes build

Pull Request - State: closed - Opened by hmcezar about 1 year ago

#224 - Fixes and new utils

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#223 - Fix dihedral parsing in topology and undefined dihedral angles

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#222 - Fixes some utils scripts

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#221 - Fix documentation for PLUMED interface

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#220 - PLUMED support

Pull Request - State: closed - Opened by hmcezar over 1 year ago - 1 comment

#219 - Update refs and docs

Pull Request - State: closed - Opened by samiransen23 over 1 year ago

#218 - Fix NPT simulations without electrostatics

Pull Request - State: closed - Opened by hmcezar over 1 year ago - 1 comment

#217 - Fix installation with newer numpy versions.

Pull Request - State: closed - Opened by hmcezar over 1 year ago - 1 comment

#216 - JOSS final paper version

Pull Request - State: closed - Opened by mortele over 1 year ago - 1 comment

#215 - Resolve rst links in documentation

Pull Request - State: closed - Opened by samiransen23 over 1 year ago

#214 - Community guidelines info

Pull Request - State: closed - Opened by samiransen23 over 1 year ago

#213 - Fix multiversion docs

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#212 - Version-controlled doc

Pull Request - State: closed - Opened by samiransen23 over 1 year ago - 1 comment

#211 - Fixes release action

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#210 - Fix CI tests

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#209 - Fixes error when running with PIC_Spectral_GPE

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#208 - Re add utils scripts

Pull Request - State: closed - Opened by hmcezar over 1 year ago

#207 - JOSS Review - Additional community guidelines suggestions

Issue - State: closed - Opened by blakeaw over 1 year ago - 3 comments

#206 - Release 2.0.0

Pull Request - State: closed - Opened by samiransen23 over 1 year ago

#205 - Unable to install

Issue - State: open - Opened by kiranvad almost 2 years ago

#204 - Update python CI testing version

Issue - State: open - Opened by mortele almost 2 years ago
Labels: testing

#203 - Remove non-UTF-8 characters in Fortran modules

Pull Request - State: closed - Opened by mortele almost 2 years ago - 1 comment

#202 - Numpy >=1.24 breaks install compilation of fortran codes due to non-UTF-8 characters

Issue - State: open - Opened by mortele almost 2 years ago
Labels: bug

#201 - HyMD profiling

Issue - State: open - Opened by hmcezar about 2 years ago
Labels: good first issue, optimization

#200 - Add documentation and scr barostat

Pull Request - State: closed - Opened by samiransen23 about 2 years ago - 1 comment

#199 - Broadcast root's PRNG to avoid comm in thermostat.

Pull Request - State: closed - Opened by hmcezar about 2 years ago - 1 comment

#198 - Fix electrostatic energy

Pull Request - State: closed - Opened by hmcezar about 2 years ago - 1 comment

#197 - Reduce communication in thermostat

Issue - State: closed - Opened by hmcezar about 2 years ago
Labels: optimization

#196 - Small fixes and enhancements

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

#194 - Warnings about memory leak

Pull Request - State: closed - Opened by hmcezar about 2 years ago - 1 comment

#193 - Add some unit tests

Pull Request - State: closed - Opened by hmcezar over 2 years ago - 3 comments

#192 - API reference documentation inaccurate

Issue - State: open - Opened by samiransen23 over 2 years ago - 1 comment
Labels: documentation

#191 - Add header and Logger unit testing

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

#190 - Add header to log file

Issue - State: closed - Opened by hmcezar over 2 years ago - 2 comments
Labels: enhancement

#189 - Add new utils scripts, including one to center a group in the box

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

#188 - Rewrite bonded forces routines in C

Pull Request - State: closed - Opened by Lun4m over 2 years ago

#187 - Center group of atoms in the box

Issue - State: closed - Opened by hmcezar over 2 years ago
Labels: enhancement

#186 - Memory usage

Issue - State: closed - Opened by hmcezar over 2 years ago - 13 comments
Labels: optimization

#185 - Fix domain_decomposition bug

Pull Request - State: closed - Opened by hmcezar over 2 years ago - 1 comment

#184 - pmesh ValueError when performing second domain_decomposition

Issue - State: closed - Opened by hmcezar over 2 years ago
Labels: bug

#183 - Fixes pytest warnings when passing None to pytest.warns().

Pull Request - State: closed - Opened by hmcezar over 2 years ago - 1 comment

#182 - pytest.warn(None) warnings

Issue - State: closed - Opened by hmcezar over 2 years ago
Labels: testing

#181 - Plumed support

Pull Request - State: closed - Opened by hmcezar over 2 years ago - 3 comments

#180 - Improve documentation of dihedrals

Issue - State: open - Opened by hmcezar over 2 years ago
Labels: documentation, enhancement

#179 - Add electric forces to output when appropriate.

Pull Request - State: closed - Opened by hmcezar over 2 years ago - 1 comment

#178 - Forces passed to store_data do not include elec_forces

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

#177 - Time is zero after first force computation

Issue - State: closed - Opened by hmcezar over 2 years ago - 1 comment
Labels: bug, enhancement

#176 - Changes unpacking of domain_decomposition and fixes time logging.

Pull Request - State: closed - Opened by hmcezar over 2 years ago - 1 comment

#175 - ValueError for prepare bonds

Issue - State: open - Opened by hmcezar over 2 years ago - 1 comment
Labels: bug

#174 - exec() cannot modify local variables

Issue - State: closed - Opened by hmcezar over 2 years ago - 3 comments
Labels: bug

#173 - Move protein backbone dipole declarations

Issue - State: open - Opened by Lun4m over 2 years ago
Labels: cleanup

#172 - Update docs and README, expand build instructions

Pull Request - State: closed - Opened by mortele over 2 years ago - 1 comment
Labels: documentation, cleanup

#171 - Fix dipole force redistribution

Pull Request - State: closed - Opened by Lun4m over 2 years ago - 1 comment

#170 - Change the way the Hamiltonian is specified

Issue - State: open - Opened by mortele over 2 years ago
Labels: enhancement, refactor, cleanup

#169 - Remove legacy scripts

Pull Request - State: closed - Opened by Lun4m over 2 years ago - 1 comment

#168 - Elec gpe pressure

Pull Request - State: closed - Opened by samiransen23 over 2 years ago

#165 - Fix sympy differentiation in Hamiltonian failing after sympy 1.10

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

#164 - Hamiltonian tests fail with sympy 1.10

Issue - State: closed - Opened by mortele over 2 years ago - 1 comment
Labels: bug

#163 - Adding contribution guidelines

Pull Request - State: closed - Opened by Lun4m over 2 years ago - 5 comments
Labels: JOSS-review

#162 - Add warning if total charge is not 0

Issue - State: closed - Opened by Lun4m over 2 years ago
Labels: bug, enhancement

#161 - Supplemental instructions to install MPI compiler

Issue - State: closed - Opened by blakeaw over 2 years ago - 4 comments
Labels: documentation, cleanup, JOSS-review

#160 - Error when running tests

Issue - State: closed - Opened by blakeaw over 2 years ago - 10 comments
Labels: bug, documentation, testing

#159 - Community guidelines

Issue - State: closed - Opened by yhtang over 2 years ago - 4 comments
Labels: documentation, JOSS-review

#158 - Documentation badge

Issue - State: closed - Opened by yhtang over 2 years ago - 2 comments
Labels: documentation, cleanup

#157 - Install non-Python dependencies with `dnf`

Issue - State: open - Opened by yhtang over 2 years ago - 5 comments
Labels: JOSS-review

#156 - Documentation for SquaredPhi Hamiltonian shows an incorrect expression

Issue - State: open - Opened by mortele almost 3 years ago
Labels: documentation, invalid

#155 - Add setting to disable PBC

Issue - State: closed - Opened by Lun4m almost 3 years ago - 2 comments
Labels: enhancement

#154 - Set default verbose to 1

Pull Request - State: closed - Opened by Lun4m almost 3 years ago - 1 comment

#153 - Default verbose should be 1

Issue - State: closed - Opened by Lun4m almost 3 years ago

#151 - Calculate test coverage for open pull requests, only push to Codecov for accepted ones

Issue - State: closed - Opened by mortele almost 3 years ago - 1 comment
Labels: refactor, cleanup

#150 - Fix crash caused by missing thermostat specification

Pull Request - State: closed - Opened by mortele almost 3 years ago - 1 comment

#149 - Fix error in torque computation in store_data

Pull Request - State: closed - Opened by mortele almost 3 years ago - 3 comments
Labels: bug, documentation, enhancement, cleanup

#148 - Build docs for open pull requests, only publish for accepted ones

Issue - State: closed - Opened by mortele almost 3 years ago - 1 comment
Labels: documentation

#147 - Remove attempted printing of dipole_forces

Pull Request - State: closed - Opened by mortele almost 3 years ago - 1 comment

#146 - Dipole forces are being incorrectly being attempted written to file

Issue - State: closed - Opened by mortele almost 3 years ago - 1 comment
Labels: bug, cleanup

#145 - compute_field_and_kinetic_energy accepts a bunch of unused paramters

Issue - State: open - Opened by mortele almost 3 years ago
Labels: cleanup

#144 - Electrostatic force/energy functions are using hard-coded Gaussian filters

Issue - State: closed - Opened by mortele almost 3 years ago
Labels: bug, refactor, cleanup

#143 - Errors when running HyMD

Issue - State: closed - Opened by Lun4m almost 3 years ago - 5 comments
Labels: bug, cleanup

#142 - Docs setup

Pull Request - State: closed - Opened by mortele almost 3 years ago - 1 comment

#141 - Utils folder is messy

Issue - State: closed - Opened by Lun4m almost 3 years ago - 2 comments
Labels: documentation, cleanup

#140 - Remove unused files

Pull Request - State: closed - Opened by Lun4m almost 3 years ago - 3 comments

#138 - Only print the non-zero energy types to log

Issue - State: closed - Opened by mortele almost 3 years ago
Labels: enhancement, cleanup

#137 - Index based connectivity

Pull Request - State: closed - Opened by Lun4m almost 3 years ago

#136 - Hot fix bonds_4 tests

Pull Request - State: closed - Opened by Lun4m almost 3 years ago - 1 comment

#135 - Electrostatic and dihedrals

Pull Request - State: closed - Opened by Lun4m almost 3 years ago - 1 comment

#132 - Copying arrays in update field

Issue - State: open - Opened by Lun4m almost 3 years ago
Labels: refactor, optimization, cleanup

#128 - no termostat in config.toml

Issue - State: closed - Opened by lasse-steinnes about 3 years ago - 1 comment
Labels: bug

#126 - Replace type based connectivity with index based connectivity

Issue - State: open - Opened by Lun4m about 3 years ago - 1 comment
Labels: enhancement, refactor

#122 - Shift lines from main.py to input_parser.py

Issue - State: closed - Opened by samiransen23 about 3 years ago
Labels: enhancement

#110 - Numpy seed not set correctly

Issue - State: closed - Opened by samiransen23 over 3 years ago - 2 comments
Labels: refactor

#109 - VMD plugin labelling problem

Issue - State: closed - Opened by samiransen23 over 3 years ago - 4 comments

#108 - Random lipids misplaced in specific frames

Issue - State: closed - Opened by samiransen23 over 3 years ago - 6 comments

#104 - VMD crashes if bonds are specified in the H5MD file

Issue - State: closed - Opened by Lun4m over 3 years ago - 10 comments
Labels: bug

#100 - h5py and -disable-mpiio

Issue - State: closed - Opened by sigbjobo over 3 years ago - 3 comments
Labels: bug

#99 - Use the official H5MD specification for unit systems

Issue - State: closed - Opened by mortele over 3 years ago - 1 comment
Labels: enhancement

#76 - Make the time_step input determine the inner rRESPA step, not the outer

Issue - State: closed - Opened by mortele over 3 years ago
Labels: documentation, enhancement, refactor

GitHub / Cascella-Group-UiO/HyMD issues and pull requests