Releases: alec-glisman/Polyelectrolyte-Surface-Adsorption
Releases · alec-glisman/Polyelectrolyte-Surface-Adsorption
v0.4.0
Commits
- 7a275cd: Update input global directories and hardware configuration (Alec)
- 9826380: bug fix for non-vacuum system eqbm (Alec)
- 68215b3: Update plumed.dat file to remove WHOLEMOLECULES for N_CHAIN > 1 (Alec)
- 1356570: bug fix to 2 slab system mdp and added more production submission scripts (Alec)
- e7879ca: Add frozen groups to NVT production MDPs (Alec)
- f42d4d9: added files to concatenate trajectories (Alec)
- bf6b829: Remove unnecessary code and increase parallel jobs (Alec)
- b3705cc: updated concatenation scripts (Alec)
- fafea84: Add Polyelectrolyte to list of variables in .vscode/settings.json and add script for moving data from zeal to local directory (Alec)
- 980fa70: Add script for moving data from local to local directory (Alec)
- cc01d84: added HREMD input of T range explicitly (Alec)
- d02925d: started to write library files to mke crystalline sufaces (Alec)
- 91ca837: writing calcite (1 0 -1 4) symmetric is succeeding (Alec)
- ba314a3: generation code is functional but not yielding the expected results (Alec)
- e472c37: added files from Decai (Alec)
- 123171a: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption (Alec)
- 9c82b28: added 1000 ns run files and corrected NPT eqbm time (Alec)
- 7ad00c4: code working to construct unit cells (Alec)
- 5cae750: crystal replication stable (Alec)
- a6de61c: surfaces working with varying sizes respecting box dimensions (Alec)
- 8c29d2e: Update concatenation scripts to include new directories for archiving and dumping trajectories (Alec)
- 1525728: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption (Alec)
- 05cc6e8: added new surface structure files (Alec)
- 14a9971: duplicated z-thickness for aragonite 110 (Alec)
- 9f14a51: corrected offset (Alec)
- 165b786: bug fixes: two-slab system functional (Alec)
- ee91d59: updated structure files (Alec)
v0.3.1
Commits
- 1f5d5ce: Update debug message in 1eqbm_7.sh script (Alec)
- initialization stable for 1 slab vacuum systems, struggling to get 2 slab systems working #5 (Alec)
- a9648b3: 2slab creation stable, need to update topology (Alec) #5
- e30b425: using two "real" walls on all vacuum EM and first two EQBM (Alec) #5
- 98b5ca8: NPT equilibration and production no longer freeze crystal atoms (Alec) #5
- a7bb9ac: Add TwoSlabTopGenerator class to generate topology for a system with two slabs (Alec) #5
- need to adjust index making. Coordinates and topology stable #5 (Alec)
- appears 2-slab system is stable, but requires further testing #5 (Alec)
- 7bd6f25: all simulations in 7 with 2 slabs (Alec) #5
- 5d58024: added docs to twoslab_index.py and small bug fixes to scripts (Alec) #5
- 64078ca: Update hardware configuration in submission scripts (Alec) #5
- b12022c: Add second slab and update topology and index files (Alec) #5
- 06afc74: updated sampling workflow to check for more files and exit properly (Alec)
- 91d7c7d: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption (Alec)
- 4d6f9ab: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption into 4-slab-simulations (Alec) #5
v0.3.0
Commits
- 09d3fb3: increased all sigmas. Opes Explore running (Alec) #3
- 4bc1a21: added output to log of number of atoms in group (Alec) #3
- b621ba5: Added more logging output and shifted crystal in box to see solvation layers (Alec) #3
- c1159ac: increased barrier heights (Alec) #3
- cc58898: OneOPES Sampling running (Alec) #3
- 766a756: renamed directory for consistency (Alec) #3
- 1148fcc: updated walls to both me moveable and eqbm has shorter length (Alec) #3
- 4104418: updated submodule (Alec) #3
- 37578ff: closer walls and fixed gmx path on desktop (Alec) #3
- 8f02d67: shortened production time to 500 ns (Alec) #3
- 64a5db0: updated parameters (Alec) #3
- bd20eef: less slurm time cutoff (Alec) #3
- 93d33a5: added hremd eqbm (Alec) #3
- 256b121: added HREMD production sampling and fixed bugs on eqbm (Alec) #3
- 370e843: updated log file names (Alec) #3
- 4df7ff2: big fixes to global variable use (Alec) #3
- a8a7850: bug fixes for plumed restarts (Alec) #3
- b38d5e1: added metadynamics sampling (Alec) #3
- 8d507fc: added plumed FES utility (Alec) #3
- 265321e: updated help docs and input checking (Alec) #3
- 4e5468f: doc updates (Alec) #3
- 27cdbaf: even more information added to run.sh help flag (Alec) #3
- 1848976: corrected filename extension for HILLS.data (Alec) #3
- d53684d: scripts for new simulation files (Alec) #3
- 22eed5b: updated paths (Alec) #3
- 40fef86: corrected flags (Alec) #3
- 09f3014: added submit files (Alec) #3
- b60decd: added eqbm submission (Alec) #3
- 90467d7: added new monomer simulation experiments (Alec) #3
- 15e44ed: Merge branch 'alec-glisman/issue2' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption into alec-glisman/issue2 (Alec) #3
- 1b01b13: updated node paths (Alec) #3
- 2f2ebe5: started new runs and fixme (Alec) #3
- 9e0916f: updated no Ca CV to be crystalline Ca and corrected desktop node paths (Alec) #3
- 922040b: updated tags to be 1.x.x (Alec) #3
- 8511a00: updated single-monomer parameterization (Alec) #3
- a567d0a: added monomer eqbm and prod (Alec) #3
- 5f9e9c1: corrected input paths (Alec) #3
- 5911084: removed dangling calls to TAG_APPEND (Alec) #3
- 01cdec7: corrected opes tag (Alec) #3
- f9a2009: updated chain group addition (Alec) #3
- d9d580a: added opes explore production (Alec) #3
- 14f831d: reduced OPES barrier height from 50 to 30 (Alec) #3
- 93a4a3e: added more path and lib information to find correct files (Alec) #3
- cd97d42: bug fix: using crystal Ca data when no aqueous Ca (Alec) #3
- da45a73: submitted production runs (Alec) #3
- b728737: Merge branch 'alec-glisman/issue2' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption into alec-glisman/issue2 (Alec) #3
- 11bae24: bug fix: missing bond added to AN1 (Alec) #3
- bb3b70b: whitespace (Alec) #3
- 1d6366d: Update mdp files for production ensemble with (Alec) #3
- 0d75920: added submit files (Alec) #3
- bab7951: Update TAG_JOBID in 2-monomers scripts (Alec) #3
- be79ce8: updated parameter files for new convention (Alec) #3
- bc3f1a8: Merge branch 'alec-glisman/issue2' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption into alec-glisman/issue2 (Alec) #3
- 87d7ff9: next round of simulations (Alec) #3
- 68d5ec9: Merge branch 'alec-glisman/issue2' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption into alec-glisman/issue2 (Alec) #3
- f671c64: Update output control in energy minimization and (Alec) #3
- f9f0903: added further simulations (Alec) #3
- 6ef07de: fixed bugs to allow for eqbm restart (Alec) #3
- a0cd216: prepped simulations batch 3 (Alec) #3
- 18e1268: Add new submission scripts for OneOPES version (Alec) #3
- 0bb7063: added 1.4 runs (Alec) #3
- 84949fd: Update initialization and submission scripts (Alec) #3
- c007b29: harmonically restraining surface crystalline atoms (Alec) #3
- a34875e: Update BARRIER value to 5 in plumed files and added thermal CV sooner (Alec) #3
- b235701: bug fixes to write files (Alec) #3
- 15004c9: Add replica_lambda.py script for generating lambda (Alec) #3
- 0f0ba03: Update temperature maximum values in OPES (Alec) #3
- 8a39949: fixed CPU and GPU setting of parameters (Alec) #3
- 65662d0: Add initialization script and test system input (Alec) #3
- af82395: shellcheck fix (Alec) #3
- 8ae16d2: Add new keywords and launch configuration (Alec) #3
- 573bf67: Rewrote methods as class and updated for new simulations (Alec) #3
- 5325350: Update BARRIER values in plumed files (Alec) [#3](...