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
- df31894: Add exchange probability moving average plot (Alec) #3
- cd55d38: Add low barrier 5 script for OneOPES replica (Alec) #3
- aece836: removed todo (Alec) #3
- 003c5ec: updated initialization for monomers and no chain systems (Alec) #3
- 6b099f8: added eqbm script (Alec) #3
- 7896027: geometric temperature spacing (Alec) #3
- b17e029: upper left legend (Alec) #3
- d3660dc: updated tags (Alec) #3
- bf5abab: Add new OneOPES submission scripts (Alec) #3
- feb78b6: Add empty.dat file for plumed harmonic parameters (Alec) #3
- fb7ac51: corrected data copy command (Alec) #3
- 29c024d: removed call to mpirun on mdrun (Alec) #3
- b1495c2: Update job name and add index argument to batch script (Alec) #3
- 5dd7614: Update temperature settings for OneOPES replicas (Alec)
- 983ad13: Update first_dependency value in multiple_submission.sh (Alec)
- 8f989f3: Add data_archive/ to .gitignore and ignore .nfs* files (Alec)
- 3127747: added smaller calcite surfaces and new requirements (Alec)
- 3088478: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption (Alec)
- 6b961ef: added ability to reduce cutoff length (Alec)
- 5a9f898: bug fix: missing cpt file does not crash simulation. (Alec)
- 688d331: wang installation scripts (Alec)
- 1690912: Remove redundant code that replaces -nt with -ntomp in GMX_CPU_ARGS (Alec)
- 386d083: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption (Alec)
- e508a06: more test calculation files for Goddard (Alec)
- 0cf4a55: Fix issue with calculating average and standard deviation in exchange probabilities (Alec)
- 617444c: Merge branch 'main' of github.com:alec-glisman/Polyelectrolyte-Surface-Adsorption (Alec)
- dcc1d38: starting to archive old run files (Alec)
- ad2ed61: Update job configuration and batch script (Alec)
- da94c6d: Added production files for new DDPM model inputs (Alec)
- bfbefc4: moved files to archive (Alec)
- dfd5783: Update input_globals array in 2oneopes_6.sh (Alec)
- 128d327: starting production simulations (Alec)
- 49d6f73: Refactor code to improve performance and readability (Alec)
- 3c7cd45: Update time conversion and sort in probability_exchange.py, increase n_jobs in multiple_submission.sh (Alec)
- 8da714f: Add script to delete specific files (Alec)
- 4145576: Refactor file deletion logic to only consider files older than 48 hours (Alec)
- 93e9a26: Update data writing frequency for non-base replicas (Alec)
- 39ec4f6: Handle ValueError in ParseGmxLog (Alec)
- b9668e3: Add runtime information to equilibration script (Alec)
- bdb792d: Add logging statements to equilibration script (Alec)
- 038a1de: Update job parameters and batch script names (Alec)
- 9e207b2: Update n_jobs and batch_script variables (Alec)
- 62aaf85: Add script for archiving and moving data (Alec)
- e64fe33: added file down sampling (Alec)
- 8b0146e: Add downsample functionality and joblog option (Alec)
- 35971d6: Update file search to exclude files modified within the last 48 hours (Alec)
- 0e6abc8: Update data input directory in archive_data.sh script (Alec)
- e407d0d: Update data directories and add options for down-sampling and moving files (Alec)
- 3ef5f2c: small bug fix to control flow of moving files (Alec)
- f11c3d5: small updates to excluded patterns (Alec)
- 753ca89: slab simulations started (Alec)
- db87017: Update wall density in mdp files (Alec)
- 79f7bda: Update subproject commit hash (Alec)
- 7525b6d: Add vacuum layer and remove redundant code (Alec)
- a7610cc: Add debug statement for input global directories (Alec)