├── .github └── workflows │ ├── docs.yml │ ├── unittests_matrix.yml │ └── unittests_requirements.yml ├── LICENSE ├── README.md ├── arcann_training ├── __init__.py ├── __main__.py ├── assets │ ├── __init__.py │ ├── default_config.json │ ├── elements.json │ └── others │ │ ├── __init__.py │ │ ├── lammps_rerun.in │ │ ├── vmd_dcd_selection_index.tcl │ │ └── vmd_xyz_selection_index.tcl ├── common │ ├── __init__.py │ ├── check.py │ ├── filesystem.py │ ├── ipi.py │ ├── json.py │ ├── lammps.py │ ├── list.py │ ├── logging.py │ ├── machine.py │ ├── parsing_labeling.py │ ├── plumed.py │ ├── slurm.py │ ├── utils.py │ ├── xml.py │ └── xyz.py ├── exploration │ ├── __init__.py │ ├── check.py │ ├── clean.py │ ├── deviate.py │ ├── extract.py │ ├── launch.py │ ├── prepare.py │ └── utils.py ├── initialization │ ├── __init__.py │ ├── start.py │ └── utils.py ├── labeling │ ├── __init__.py │ ├── check.py │ ├── clean.py │ ├── extract.py │ ├── launch.py │ ├── prepare.py │ └── utils.py ├── test │ ├── __init__.py │ ├── check.py │ ├── clean.py │ ├── launch.py │ └── prepare.py ├── training │ ├── __init__.py │ ├── check.py │ ├── check_compress.py │ ├── check_freeze.py │ ├── clean.py │ ├── compress.py │ ├── freeze.py │ ├── increment.py │ ├── launch.py │ ├── prepare.py │ └── utils.py └── unittests │ ├── __init__.py │ ├── test_check.py │ ├── test_filesystem.py │ ├── test_ipi.py │ ├── test_json.py │ ├── test_lammps.py │ ├── test_list.py │ ├── test_machine.py │ ├── test_plumed.py │ ├── test_slurm.py │ ├── test_utils.py │ ├── test_utils_exploration.py │ ├── test_utils_initlialization.py │ ├── test_utils_training.py │ ├── test_xml.py │ └── test_xyz.py ├── docs ├── .pages ├── arcann_logo.svg ├── contributions │ ├── .pages │ ├── contributions.md │ └── unexpected_behavior.md ├── examples │ ├── .pages │ └── sn2.md ├── getting-started │ ├── .pages │ ├── hpc_configuration.md │ ├── installation.md │ └── requirements.md ├── index.md ├── project_details │ ├── .pages │ ├── acknowledgments.md │ ├── authors.md │ ├── funding.md │ └── license.md └── usage │ ├── .pages │ ├── exploration.md │ ├── initialization.md │ ├── iter_prerequisites.md │ ├── labeling.md │ ├── start.md │ ├── test.md │ └── training.md ├── examples ├── diels_alder_ethene_13butadiene │ ├── R │ │ ├── 000-training │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-exploration │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-labeling │ │ │ └── used_input.json │ │ ├── 001-training │ │ │ └── used_input.json │ │ ├── used_input.json │ │ └── user_files │ │ │ ├── 1_product_OPES1D20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_product_OPES1D50_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_product_OPES1D70_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_product_SMD_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_product_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_reactant_OPES1D20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_reactant_OPES1D50_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_reactant_OPES1D70_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_reactant_SMD_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_reactant_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_product_OPES1D20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_product_OPES1D50_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_product_OPES1D70_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_product_SMD_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_product_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_reactant_OPES1D20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_reactant_OPES1D50_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_reactant_OPES1D70_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_reactant_SMD_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_reactant_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── dptrain_2.1.json │ │ │ ├── job-array_CP2K_label_cpu_hpc1.sh │ │ │ ├── job-array_CP2K_label_cpu_hpc2.sh │ │ │ ├── job-array_lammps-deepmd_explore_gpu_hpc1.sh │ │ │ ├── job_CP2K_label_cpu_hpc1.sh │ │ │ ├── job_CP2K_label_cpu_hpc2.sh │ │ │ ├── job_deepmd_compress_gpu_hpc1.sh │ │ │ ├── job_deepmd_freeze_gpu_hpc1.sh │ │ │ ├── job_deepmd_test_gpu_hpc1.sh │ │ │ ├── job_deepmd_train_gpu_hpc1.sh │ │ │ ├── job_lammps-deepmd_explore_gpu_hpc1.sh │ │ │ ├── machine.json │ │ │ ├── plumed_atomdef_product_OPES1D20_300K.dat │ │ │ ├── plumed_atomdef_product_OPES1D50_300K.dat │ │ │ ├── plumed_atomdef_product_OPES1D70_300K.dat │ │ │ ├── plumed_atomdef_product_SMD_300K.dat │ │ │ ├── plumed_atomdef_product_free_300K.dat │ │ │ ├── plumed_atomdef_reactant_OPES1D20_300K.dat │ │ │ ├── plumed_atomdef_reactant_OPES1D50_300K.dat │ │ │ ├── plumed_atomdef_reactant_OPES1D70_300K.dat │ │ │ ├── plumed_atomdef_reactant_SMD_300K.dat │ │ │ ├── plumed_atomdef_reactant_free_300K.dat │ │ │ ├── plumed_colvars_product_OPES1D20_300K.dat │ │ │ ├── plumed_colvars_product_OPES1D50_300K.dat │ │ │ ├── plumed_colvars_product_OPES1D70_300K.dat │ │ │ ├── plumed_colvars_product_SMD_300K.dat │ │ │ ├── plumed_colvars_product_free_300K.dat │ │ │ ├── plumed_colvars_reactant_OPES1D20_300K.dat │ │ │ ├── plumed_colvars_reactant_OPES1D50_300K.dat │ │ │ ├── plumed_colvars_reactant_OPES1D70_300K.dat │ │ │ ├── plumed_colvars_reactant_SMD_300K.dat │ │ │ ├── plumed_colvars_reactant_free_300K.dat │ │ │ ├── plumed_product_OPES1D20_300K.dat │ │ │ ├── plumed_product_OPES1D50_300K.dat │ │ │ ├── plumed_product_OPES1D70_300K.dat │ │ │ ├── plumed_product_SMD_300K.dat │ │ │ ├── plumed_product_free_300K.dat │ │ │ ├── plumed_reactant_OPES1D20_300K.dat │ │ │ ├── plumed_reactant_OPES1D50_300K.dat │ │ │ ├── plumed_reactant_OPES1D70_300K.dat │ │ │ ├── plumed_reactant_SMD_300K.dat │ │ │ ├── plumed_reactant_free_300K.dat │ │ │ ├── plumed_walls_product_OPES1D20_300K.dat │ │ │ ├── plumed_walls_product_OPES1D50_300K.dat │ │ │ ├── plumed_walls_product_OPES1D70_300K.dat │ │ │ ├── plumed_walls_product_SMD_300K.dat │ │ │ ├── plumed_walls_product_free_300K.dat │ │ │ ├── plumed_walls_reactant_OPES1D20_300K.dat │ │ │ ├── plumed_walls_reactant_OPES1D50_300K.dat │ │ │ ├── plumed_walls_reactant_OPES1D70_300K.dat │ │ │ ├── plumed_walls_reactant_SMD_300K.dat │ │ │ ├── plumed_walls_reactant_free_300K.dat │ │ │ ├── product_OPES1D20_300K.in │ │ │ ├── product_OPES1D20_300K.lmp │ │ │ ├── product_OPES1D20_300K.pdb │ │ │ ├── product_OPES1D50_300K.in │ │ │ ├── product_OPES1D50_300K.lmp │ │ │ ├── product_OPES1D50_300K.pdb │ │ │ ├── product_OPES1D70_300K.in │ │ │ ├── product_OPES1D70_300K.lmp │ │ │ ├── product_OPES1D70_300K.pdb │ │ │ ├── product_SMD_300K.in │ │ │ ├── product_SMD_300K.lmp │ │ │ ├── product_SMD_300K.pdb │ │ │ ├── product_free_300K.in │ │ │ ├── product_free_300K.lmp │ │ │ ├── product_free_300K.pdb │ │ │ ├── properties.txt │ │ │ ├── reactant_OPES1D20_300K.in │ │ │ ├── reactant_OPES1D20_300K.lmp │ │ │ ├── reactant_OPES1D20_300K.pdb │ │ │ ├── reactant_OPES1D50_300K.in │ │ │ ├── reactant_OPES1D50_300K.lmp │ │ │ ├── reactant_OPES1D50_300K.pdb │ │ │ ├── reactant_OPES1D70_300K.in │ │ │ ├── reactant_OPES1D70_300K.lmp │ │ │ ├── reactant_OPES1D70_300K.pdb │ │ │ ├── reactant_SMD_300K.in │ │ │ ├── reactant_SMD_300K.lmp │ │ │ ├── reactant_SMD_300K.pdb │ │ │ ├── reactant_free_300K.in │ │ │ ├── reactant_free_300K.lmp │ │ │ └── reactant_free_300K.pdb │ └── initial_dataset │ │ ├── init_product │ │ ├── nopbc │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ ├── force.npy │ │ │ └── virial.npy │ │ └── type.raw │ │ ├── init_product_to_reactant │ │ ├── nopbc │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ ├── force.npy │ │ │ └── virial.npy │ │ └── type.raw │ │ ├── init_reactant_close │ │ ├── nopbc │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ ├── force.npy │ │ │ └── virial.npy │ │ └── type.raw │ │ └── init_reactant_to_product │ │ ├── nopbc │ │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ ├── force.npy │ │ └── virial.npy │ │ └── type.raw ├── inputs │ ├── exploration.json │ ├── initialization.json │ ├── labeling.json │ ├── test.json │ └── training.json ├── sn2_ch3cl_br │ ├── NR │ │ ├── 000-training │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-exploration │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-labeling │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-training │ │ │ └── used_input.json │ │ ├── 002-exploration │ │ │ └── used_input.json │ │ ├── 002-labeling │ │ │ └── used_input.json │ │ ├── 002-training │ │ │ └── used_input.json │ │ ├── 003-exploration │ │ │ └── used_input.json │ │ ├── 003-labeling │ │ │ └── used_input.json │ │ ├── 003-training │ │ │ └── used_input.json │ │ ├── 004-exploration │ │ │ └── used_input.json │ │ ├── 004-labeling │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 004-training │ │ │ └── used_input.json │ │ ├── 005-exploration │ │ │ └── used_input.json │ │ ├── 005-labeling │ │ │ └── used_input.json │ │ ├── 005-training │ │ │ └── used_input.json │ │ ├── 006-exploration │ │ │ └── used_input.json │ │ ├── 006-labeling │ │ │ └── used_input.json │ │ ├── 006-training │ │ │ └── used_input.json │ │ ├── 007-exploration │ │ │ └── used_input.json │ │ ├── 007-labeling │ │ │ └── used_input.json │ │ ├── used_input.json │ │ └── user_files │ │ │ ├── 1_ch3br_cl_close_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_close_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_free_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_smd_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_smd_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_close_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_close_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_free_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_smd_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_smd_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_close_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_close_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_free_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_smd_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_smd_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_close_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_close_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_free_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_free_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_smd_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_smd_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── ch3br_cl_close_300K.in │ │ │ ├── ch3br_cl_close_300K.lmp │ │ │ ├── ch3br_cl_free_300K.in │ │ │ ├── ch3br_cl_free_300K.lmp │ │ │ ├── ch3br_cl_smd_300K.in │ │ │ ├── ch3br_cl_smd_300K.lmp │ │ │ ├── ch3cl_br_close_300K.in │ │ │ ├── ch3cl_br_close_300K.lmp │ │ │ ├── ch3cl_br_free_300K.in │ │ │ ├── ch3cl_br_free_300K.lmp │ │ │ ├── ch3cl_br_smd_300K.in │ │ │ ├── ch3cl_br_smd_300K.lmp │ │ │ ├── dptrain_2.1.json │ │ │ ├── job-array_CP2K_label_cpu_hpc1.sh │ │ │ ├── job-array_CP2K_label_cpu_hpc2.sh │ │ │ ├── job-array_lammps-deepmd_explore_gpu_hpc1.sh │ │ │ ├── job_CP2K_label_cpu_hpc1.sh │ │ │ ├── job_CP2K_label_cpu_hpc2.sh │ │ │ ├── job_deepmd_compress_gpu_hpc1.sh │ │ │ ├── job_deepmd_freeze_gpu_hpc1.sh │ │ │ ├── job_deepmd_test_gpu_hpc1.sh │ │ │ ├── job_deepmd_train_gpu_hpc1.sh │ │ │ ├── job_lammps-deepmd_explore_gpu_hpc1.sh │ │ │ ├── machine.json │ │ │ ├── plumed_atomdef_ch3br_cl_close_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_free_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_smd_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_close_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_free_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_smd_300K.dat │ │ │ ├── plumed_ch3br_cl_close_300K.dat │ │ │ ├── plumed_ch3br_cl_free_300K.dat │ │ │ ├── plumed_ch3br_cl_smd_300K.dat │ │ │ ├── plumed_ch3cl_br_close_300K.dat │ │ │ ├── plumed_ch3cl_br_free_300K.dat │ │ │ ├── plumed_ch3cl_br_smd_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_close_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_free_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_smd_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_close_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_free_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_smd_300K.dat │ │ │ └── properties.txt │ ├── R │ │ ├── 000-training │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-exploration │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-labeling │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 001-training │ │ │ └── used_input.json │ │ ├── 002-exploration │ │ │ └── used_input.json │ │ ├── 002-labeling │ │ │ └── used_input.json │ │ ├── 002-training │ │ │ └── used_input.json │ │ ├── 003-exploration │ │ │ └── used_input.json │ │ ├── 003-labeling │ │ │ └── used_input.json │ │ ├── 003-training │ │ │ └── used_input.json │ │ ├── 004-exploration │ │ │ └── used_input.json │ │ ├── 004-labeling │ │ │ └── used_input.json │ │ ├── 004-training │ │ │ └── used_input.json │ │ ├── 005-exploration │ │ │ └── used_input.json │ │ ├── 005-labeling │ │ │ └── used_input.json │ │ ├── 005-training │ │ │ └── used_input.json │ │ ├── 006-exploration │ │ │ ├── input.json │ │ │ └── used_input.json │ │ ├── 006-labeling │ │ │ └── used_input.json │ │ └── user_files │ │ │ ├── 1_ch3br_cl_OPES1D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_OPES1D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_OPES1D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_OPES1D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_OPES1D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_OPES1D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_OPES2D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_OPES2D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_OPES2D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_OPES2D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3br_cl_OPES2D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3br_cl_OPES2D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_OPES1D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_OPES1D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_OPES1D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_OPES1D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_OPES1D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_OPES1D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_OPES2D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_OPES2D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_OPES2D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_OPES2D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 1_ch3cl_br_OPES2D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 1_ch3cl_br_OPES2D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_OPES1D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_OPES1D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_OPES1D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_OPES1D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_OPES1D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_OPES1D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_OPES2D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_OPES2D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_OPES2D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_OPES2D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3br_cl_OPES2D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3br_cl_OPES2D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_OPES1D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_OPES1D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_OPES1D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_OPES1D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_OPES1D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_OPES1D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_OPES2D_10_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_OPES2D_10_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_OPES2D_20_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_OPES2D_20_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── 2_ch3cl_br_OPES2D_5_300K_labeling_XXXXX_hpc1.inp │ │ │ ├── 2_ch3cl_br_OPES2D_5_300K_labeling_XXXXX_hpc2.inp │ │ │ ├── ch3br_cl_OPES1D_10_300K.in │ │ │ ├── ch3br_cl_OPES1D_10_300K.lmp │ │ │ ├── ch3br_cl_OPES1D_20_300K.in │ │ │ ├── ch3br_cl_OPES1D_20_300K.lmp │ │ │ ├── ch3br_cl_OPES1D_5_300K.in │ │ │ ├── ch3br_cl_OPES1D_5_300K.lmp │ │ │ ├── ch3br_cl_OPES2D_10_300K.in │ │ │ ├── ch3br_cl_OPES2D_10_300K.lmp │ │ │ ├── ch3br_cl_OPES2D_20_300K.in │ │ │ ├── ch3br_cl_OPES2D_20_300K.lmp │ │ │ ├── ch3br_cl_OPES2D_5_300K.in │ │ │ ├── ch3br_cl_OPES2D_5_300K.lmp │ │ │ ├── ch3cl_br_OPES1D_10_300K.in │ │ │ ├── ch3cl_br_OPES1D_10_300K.lmp │ │ │ ├── ch3cl_br_OPES1D_20_300K.in │ │ │ ├── ch3cl_br_OPES1D_20_300K.lmp │ │ │ ├── ch3cl_br_OPES1D_5_300K.in │ │ │ ├── ch3cl_br_OPES1D_5_300K.lmp │ │ │ ├── ch3cl_br_OPES2D_10_300K.in │ │ │ ├── ch3cl_br_OPES2D_10_300K.lmp │ │ │ ├── ch3cl_br_OPES2D_20_300K.in │ │ │ ├── ch3cl_br_OPES2D_20_300K.lmp │ │ │ ├── ch3cl_br_OPES2D_5_300K.in │ │ │ ├── ch3cl_br_OPES2D_5_300K.lmp │ │ │ ├── dptrain_2.1.json │ │ │ ├── job-array_CP2K_label_cpu_hpc1.sh │ │ │ ├── job-array_CP2K_label_cpu_hpc2.sh │ │ │ ├── job-array_lammps-deepmd_explore_gpu_hpc1.sh │ │ │ ├── job_CP2K_label_cpu_hpc1.sh │ │ │ ├── job_CP2K_label_cpu_hpc2.sh │ │ │ ├── job_deepmd_compress_gpu_hpc1.sh │ │ │ ├── job_deepmd_freeze_gpu_hpc1.sh │ │ │ ├── job_deepmd_test_gpu_hpc1.sh │ │ │ ├── job_deepmd_train_gpu_hpc1.sh │ │ │ ├── job_lammps-deepmd_explore_gpu_hpc1.sh │ │ │ ├── machine.json │ │ │ ├── plumed_atomdef_ch3br_cl_OPES1D_10_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_OPES1D_20_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_OPES1D_5_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_OPES2D_10_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_OPES2D_20_300K.dat │ │ │ ├── plumed_atomdef_ch3br_cl_OPES2D_5_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_OPES1D_10_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_OPES1D_20_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_OPES1D_5_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_OPES2D_10_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_OPES2D_20_300K.dat │ │ │ ├── plumed_atomdef_ch3cl_br_OPES2D_5_300K.dat │ │ │ ├── plumed_ch3br_cl_OPES1D_10_300K.dat │ │ │ ├── plumed_ch3br_cl_OPES1D_20_300K.dat │ │ │ ├── plumed_ch3br_cl_OPES1D_5_300K.dat │ │ │ ├── plumed_ch3br_cl_OPES2D_10_300K.dat │ │ │ ├── plumed_ch3br_cl_OPES2D_20_300K.dat │ │ │ ├── plumed_ch3br_cl_OPES2D_5_300K.dat │ │ │ ├── plumed_ch3cl_br_OPES1D_10_300K.dat │ │ │ ├── plumed_ch3cl_br_OPES1D_20_300K.dat │ │ │ ├── plumed_ch3cl_br_OPES1D_5_300K.dat │ │ │ ├── plumed_ch3cl_br_OPES2D_10_300K.dat │ │ │ ├── plumed_ch3cl_br_OPES2D_20_300K.dat │ │ │ ├── plumed_ch3cl_br_OPES2D_5_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_OPES1D_10_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_OPES1D_20_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_OPES1D_5_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_OPES2D_10_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_OPES2D_20_300K.dat │ │ │ ├── plumed_colvars_ch3br_cl_OPES2D_5_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_OPES1D_10_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_OPES1D_20_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_OPES1D_5_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_OPES2D_10_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_OPES2D_20_300K.dat │ │ │ ├── plumed_colvars_ch3cl_br_OPES2D_5_300K.dat │ │ │ └── properties.txt │ └── initial_dataset │ │ ├── init_ch3br_cl_xxxxx_1001_4001_60 │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ ├── force.npy │ │ │ └── virial.npy │ │ └── type.raw │ │ └── init_ch3cl_br_xxxxx_1001_4001_60 │ │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ ├── force.npy │ │ └── virial.npy │ │ └── type.raw └── user_files │ ├── exploration_lammps │ ├── SYSTEM1.in │ ├── SYSTEM2.in │ ├── plumed_SYSTEM2.dat │ ├── plumed_atomdef_SYSTEM2.dat │ └── plumed_colvars_SYSTEM2.dat │ ├── exploration_sander_emle │ ├── SYSTEM1.in │ ├── SYSTEM1.yaml │ ├── SYSTEM2.in │ ├── SYSTEM2.yaml │ ├── plumed_SYSTEM2.dat │ ├── plumed_atomdef_SYSTEM2.dat │ └── plumed_colvars_SYSTEM2.dat │ ├── job_exploration_ipi_slurm │ └── job_i-PI-deepmd_explore_gpu_myHPCkeyword1.sh │ ├── job_exploration_lammps_slurm │ ├── job-array_lammps-deepmd_explore_gpu_myHPCkeyword1.sh │ └── job_lammps-deepmd_explore_gpu_myHPCkeyword1.sh │ ├── job_exploration_sander_emle_slurm │ ├── job-array_sander_emle-deepmd_explore_gpu_myHPCkeyword1.sh │ └── job_sander_emle-deepmd_explore_gpu_myHPCkeyword1.sh │ ├── job_labeling_CP2K_slurm │ ├── job-array_CP2K_label_cpu_myHPCkeyword1.sh │ └── job_CP2K_label_cpu_myHPCkeyword1.sh │ ├── job_labeling_orca_slurm │ ├── job-array_ORCA_label_cpu_myHPCkeyword1.sh │ └── job_ORCA_label_cpu_myHPCkeyword1.sh │ ├── job_test_deepmd_slurm │ └── job_deepmd_test_gpu_myHPCkeyword1.sh │ ├── job_training_deepmd_slurm │ ├── job_deepmd_compress_gpu_myHPCkeyword1.sh │ ├── job_deepmd_freeze_gpu_myHPCkeyword1.sh │ └── job_deepmd_train_gpu_myHPCkeyword1.sh │ ├── labeling_cp2k │ ├── 1_SYSTEM1_labeling_XXXXX_myHPCkeyword1.inp │ ├── 1_SYSTEM2_labeling_XXXXX_myHPCkeyword1.inp │ ├── 2_SYSTEM1_labeling_XXXXX_myHPCkeyword1.inp │ └── 2_SYSTEM2_labeling_XXXXX_myHPCkeyword1.inp │ ├── labeling_orca │ ├── 1_SYSTEM1_labeling_XXXXX_myHPCkeyword1.inp │ └── 1_SYSTEM2_labeling_XXXXX_myHPCkeyword1.inp │ ├── machine.json │ └── training_deepmd │ ├── training_2.1.json │ └── training_2.2.json ├── mkdocs.yml ├── requirements.txt ├── setup.py └── tools ├── arcann_conda_linux-64_env.txt ├── arcann_conda_win-64_env.txt ├── download_arcann_environment.sh ├── force_explorations.sh └── skip_labeling.sh /.github/workflows/docs.yml: -------------------------------------------------------------------------------- 1 | name: Documentation Deployment 2 | on: [push, pull_request] 3 | 4 | permissions: 5 | contents: write 6 | jobs: 7 | deploy: 8 | runs-on: ubuntu-latest 9 | steps: 10 | - uses: actions/checkout@v4 11 | - name: Set up Python 3.x 12 | uses: actions/setup-python@v5 13 | with: 14 | python-version: 3.x 15 | - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 16 | - uses: actions/cache@v4 17 | with: 18 | key: mkdocs-${{ env.cache_id }} 19 | path: .cache 20 | restore-keys: | 21 | mkdocs- 22 | - run: pip install mkdocs mkdocs-awesome-pages-plugin mkdocs-markdownextradata-plugin 23 | - run: mkdocs gh-deploy --force --clean --verbose -------------------------------------------------------------------------------- /.github/workflows/unittests_requirements.yml: -------------------------------------------------------------------------------- 1 | name: Unit Tests Requirements 2 | 3 | on: [push, pull_request] 4 | 5 | jobs: 6 | test: 7 | runs-on: ubuntu-latest 8 | 9 | steps: 10 | - uses: actions/checkout@v4 11 | 12 | - name: Set up Python 3.10 13 | uses: actions/setup-python@v5 14 | with: 15 | python-version: "3.10" 16 | 17 | - name: Install dependencies 18 | run: | 19 | pip install -r requirements.txt 20 | 21 | - name: Run unit tests 22 | run: | 23 | python -m unittest discover arcann_training/unittests -------------------------------------------------------------------------------- /arcann_training/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/assets/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/assets/others/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/assets/others/lammps_rerun.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 2.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODELS_LIST_ out_freq 1 out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | dump dcd all dcd 1 _R_DCD_OUT_ 14 | 15 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 16 | thermo_modify flush yes 17 | thermo 1 18 | 19 | rerun _R_XYZ_IN_ dump x y z box no format xyz -------------------------------------------------------------------------------- /arcann_training/assets/others/vmd_dcd_selection_index.tcl: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------------------------------# 2 | # ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks # 3 | # Copyright 2022-2024 ArcaNN developers group # 4 | # # 5 | # SPDX-License-Identifier: AGPL-3.0-only # 6 | #----------------------------------------------------------------------------------------------------# 7 | # Created: 2022/01/01 8 | # Last modified: 2024/05/15 9 | 10 | # Load PDB file and clear all existing animations 11 | mol new _R_PDB_FILE_ 12 | animate delete all 13 | 14 | # Load XYZ file for trajectory and wait for it to finish loading 15 | mol addfile _R_DCD_FILE_ first 0 last -1 step 1 waitfor all 16 | 17 | # Open frame index file and iterate through each line 18 | set frame_index_file [open _R_FRAME_INDEX_FILE_ r] 19 | while {[gets $frame_index_file line] >=0 } { 20 | set frame [expr {round(double($line))}] 21 | set j [format "%05g" $frame] 22 | 23 | # Write out a single frame of the trajectory for the selected atoms 24 | animate write xyz _R_XYZ_OUT__$j.xyz beg $frame end $frame skip 0 waitfor all 25 | } 26 | 27 | # Close frame index file and exit VMD 28 | close $frame_index_file 29 | quit -------------------------------------------------------------------------------- /arcann_training/assets/others/vmd_xyz_selection_index.tcl: -------------------------------------------------------------------------------- 1 | #----------------------------------------------------------------------------------------------------# 2 | # ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks # 3 | # Copyright 2022-2024 ArcaNN developers group # 4 | # # 5 | # SPDX-License-Identifier: AGPL-3.0-only # 6 | #----------------------------------------------------------------------------------------------------# 7 | # Created: 2022/01/01 8 | # Last modified: 2024/05/15 9 | 10 | # Load PDB file and clear all existing animations 11 | mol new _R_PDB_FILE_ 12 | animate delete all 13 | 14 | # Load XYZ file for trajectory and wait for it to finish loading 15 | mol addfile _R_XYZ_FILE_ first 0 last -1 step 1 waitfor all 16 | 17 | # Open frame index file and iterate through each line 18 | set frame_index_file [open _R_FRAME_INDEX_FILE_ r] 19 | while {[gets $frame_index_file line] >=0 } { 20 | set frame [expr {round(double($line))}] 21 | set j [format "%05g" $frame] 22 | 23 | # Write out a single frame of the trajectory for the selected atoms 24 | animate write xyz _R_XYZ_OUT__$j.xyz beg $frame end $frame skip 0 waitfor all 25 | } 26 | 27 | # Close frame index file and exit VMD 28 | close $frame_index_file 29 | quit -------------------------------------------------------------------------------- /arcann_training/common/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/exploration/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/initialization/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/labeling/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/test/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/training/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/unittests/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /arcann_training/unittests/test_xyz.py: -------------------------------------------------------------------------------- 1 | """ 2 | #----------------------------------------------------------------------------------------------------# 3 | # ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks # 4 | # Copyright 2022-2024 ArcaNN developers group # 5 | # # 6 | # SPDX-License-Identifier: AGPL-3.0-only # 7 | #----------------------------------------------------------------------------------------------------# 8 | Created: 2022/01/01 9 | Last modified: 2024/07/14 10 | 11 | Test cases for the xyz module. 12 | 13 | Classes: 14 | -------- 15 | """ 16 | 17 | # TODO : Add test cases for the xyz module 18 | 19 | # Standard library modules 20 | import unittest 21 | 22 | # Third-party modules 23 | 24 | 25 | if __name__ == "__main__": 26 | unittest.main() 27 | -------------------------------------------------------------------------------- /docs/.pages: -------------------------------------------------------------------------------- 1 | nav: 2 | - index.md 3 | - getting-started 4 | - usage 5 | - examples 6 | - contributions 7 | - project_details 8 | -------------------------------------------------------------------------------- /docs/contributions/.pages: -------------------------------------------------------------------------------- 1 | nav: 2 | - unexpected_behavior.md 3 | - contributions.md 4 | -------------------------------------------------------------------------------- /docs/contributions/contributions.md: -------------------------------------------------------------------------------- 1 | # Contributions 2 | 3 | We warmly welcome contributions to ArcaNN. If you have ideas, code contributions, or suggested optimizations, please feel free to submit them. 4 | -------------------------------------------------------------------------------- /docs/contributions/unexpected_behavior.md: -------------------------------------------------------------------------------- 1 | # Unexpected Behavior 2 | 3 | If you encounter any bugs or issues while working with ArcaNN, we encourage you to report them. 4 | Please don't hesitate to open an issue on our GitHub repository. 5 | To assist us in identifying the problem, you can use the -v 1 argument with ArcaNN to enable more verbose logging. 6 | -------------------------------------------------------------------------------- /docs/examples/.pages: -------------------------------------------------------------------------------- 1 | nav: 2 | - sn2.md -------------------------------------------------------------------------------- /docs/getting-started/.pages: -------------------------------------------------------------------------------- 1 | nav: 2 | - requirements.md 3 | - installation.md 4 | - hpc_configuration.md 5 | -------------------------------------------------------------------------------- /docs/getting-started/requirements.md: -------------------------------------------------------------------------------- 1 | # ArcaNN Requirements 2 | 3 | ## Installation Requirements ## 4 | 5 | To install and run the software, ensure the following dependencies are installed: 6 | 7 | - **Python**: `>= 3.10` 8 | - **Pip**: `>= 21.3` 9 | - **Setuptools**: `>= 60.0` 10 | - **Wheel**: `>= 0.37` 11 | - **NumPy**: `>= 1.22` 12 | 13 | ## External Programs for Trajectories/Structures Manipulation ## 14 | 15 | ArcaNN requires the following external programs for manipulating trajectories and structures: 16 | 17 | - **VMD**: `>= 1.9.3` 18 | - **Atomsk**: `>= b0.12.2` 19 | 20 | ## Supported Programs by Workflow Step ## 21 | 22 | Different steps in the workflow are supported by specific programs: 23 | 24 | - **DeePMD-kit**: `>= 2.0` (Used in **training** and **testing** steps) 25 | - **LAMMPS**: Must be compatible with DeePMD-kit (Used in **exploration**) 26 | - **i-PI**: Must be compatible with DeePMD-kit (Used in **exploration**) 27 | - **PLUMED**: Must be compatible with DeePMD-kit (Used in **exploration**) 28 | - **CP2K**: `>= 6.1` (Used in the **labeling** step) 29 | -------------------------------------------------------------------------------- /docs/project_details/.pages: -------------------------------------------------------------------------------- 1 | nav: 2 | - license.md 3 | - authors.md 4 | - funding.md 5 | - acknowledgments.md 6 | -------------------------------------------------------------------------------- /docs/project_details/authors.md: -------------------------------------------------------------------------------- 1 | To cite ArcaNN, please use: 2 | 3 | David, R.; de la Puente, M.; Gomez, A.; Anton, O.; Stirnemann, G.; Laage, D. ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials. Digital Discovery, 2024, DOI: [10.1039/D4DD00209A](https://doi.org/10.1039/D4DD00209A). 4 | -------------------------------------------------------------------------------- /docs/project_details/funding.md: -------------------------------------------------------------------------------- 1 | - Idex ANR-10-IDEX-0001-02PSL 2 | - ERC Grant Agreement No. 757111 3 | - GENCI Grant 2023-A0130707156 4 | -------------------------------------------------------------------------------- /docs/project_details/license.md: -------------------------------------------------------------------------------- 1 | [![GNU AGPL v3.0 License][license-shield]][license-url] 2 | 3 | Distributed under the GNU Affero General Public License v3.0. 4 | See `LICENSE` for more information. 5 | 6 | [license-shield]: https://img.shields.io/github/license/arcann-chem/arcann_training.svg?style=for-the-badge 7 | [license-url]: https://github.com/arcann-chem/arcann_training/blob/main/LICENSE 8 | -------------------------------------------------------------------------------- /docs/usage/.pages: -------------------------------------------------------------------------------- 1 | nav: 2 | - start.md 3 | - iter_prerequisites.md 4 | - initialization.md 5 | - training.md 6 | - exploration.md 7 | - labeling.md 8 | - test.md 9 | -------------------------------------------------------------------------------- /docs/usage/initialization.md: -------------------------------------------------------------------------------- 1 | # Initialization 2 | 3 | 4 | Now that you have decided the subsystems that you want to train your NNP on and prepared all the required files you can initialize the ArcaNN procedure by running (from the $WORK_DIR folder): 5 | 6 | ```bash 7 | python -m arcann_training initialization start 8 | ``` 9 | 10 | Now it should have generated your first `000-training` directory. In `$WORK_DIR` you will also find a `default_input.json` file that lools like this : 11 | 12 | ```JSON 13 | { 14 | "step_name": "initialization", 15 | "systems_auto": ["SYSNAME1", "SYSNAME2", "SYSNAME3"], 16 | "nnp_count": 3 17 | } 18 | ``` 19 | 20 | The `"systems_auto"` keyword contains the name of all the systems that were found in your `$WORK_DIR/user_files/` (i.e. all `LMP` files) directory and `"nnp_count"` is the number of NNP that is used by default in the committee. 21 | 22 | The initialization will create several folders. The most important one is the `control/` folder, in which essential data files will be stored throughout the iterative procedure. These files will be written in `.json` format and should NOT be modified. Right after initialization the only file in `control/` is `config.json`, which contains the essential information about your initialization choices (or defaults), such as your subsystem names and options. Finally the `000-training` empty folder should also have been created by the execution of the python script, where you will perform the first iteration of [training](../training). 23 | 24 | If at this point you want to modify the datasets used for the first training you simply have to create an `input.json` from the `default_input.json` file and remove or add the system names to the list. You could also change the number of NNP if you wish. Then you only have have to execute the command of the initialization phase again and your `000-training` directory will be updated. 25 | 26 | -------------------------------------------------------------------------------- /docs/usage/test.md: -------------------------------------------------------------------------------- 1 | # Test 2 | 3 | ## Test ## 4 | 5 | It is possible to perform tests at every iteration of the learning procedure (the code will create `XXX-test/` folders at every `increment` phase of a `training` step). However, doing this at every iteration is rather time consuming and is not really necessary (although you should obviously test your converged NNP thoroughly). Therefore, documentation on how to test at every iteration within the `arcann_training` procedure is still not ready, sorry! 6 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/000-training/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "a100_hpc1", 3 | "user_machine_keyword_freeze": "v100_hpc1", 4 | "user_machine_keyword_compress": "v100_hpc1" 5 | } 6 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/000-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "a100_hpc1", 3 | "user_machine_keyword_freeze": "v100_hpc1", 4 | "user_machine_keyword_compress": "v100_hpc1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 12.0, 10 | "mean_s_per_step": 0.108, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/001-exploration/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_nvs", 3 | "atomsk_path": "/lustre/fsn1/worksf/projects/rech/kro/commun/programs/atomsk/0.13.1/atomsk", 4 | "timestep_ps": 0.00025, 5 | "previous_start": false, 6 | "print_interval_mult": 0.0005, 7 | "ignore_first_x_ps": 0.1, 8 | "sigma_low": 0.15 9 | } 10 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/001-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_nvs", 3 | "job_email": "", 4 | "atomsk_path": "/home/rdavid/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/home/sw/target/generic/app/vmd/vmd-1.9.4a55/bin/vmd", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025, 0.00025], 10 | "previous_start": [false, false, false, false, false, false, false, false, false, false], 11 | "disturbed_start": [false, false, false, false, false, false, false, false, false, false], 12 | "print_interval_mult": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 13 | "job_walltime_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 14 | "exp_time_ps": [10.0, 10.0, 10.0, 10.0, 20.0, 10.0, 10.0, 10.0, 10.0, 20.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1], 21 | "disturbed_start_value": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 22 | "disturbed_start_indexes": [[], [], [], [], [], [], [], [], [], []], 23 | "disturbed_candidate_value": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], [], [], [], [], []] 25 | } -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/001-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_hpc1", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 6 | "walltime_second_job_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [10, 10, 10, 10, 10, 10, 10, 10, 10, 10], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/001-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "a100_hpc1", 3 | "user_machine_keyword_freeze": "v100_hpc1", 4 | "user_machine_keyword_compress": "v100_hpc1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 2.0, 10 | "mean_s_per_step": 0.018, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "systems_auto": ["product_free_300K", "product_OPES1D20_300K", "product_OPES1D50_300K", "product_OPES1D70_300K", "product_SMD_300K", "reactant_free_300K", "reactant_OPES1D20_300K", "reactant_OPES1D50_300K", "reactant_OPES1D70_300K", "reactant_SMD_300K"], 3 | "nnp_count": 3 4 | } -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_product_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_product_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_product_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_product_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_product_free_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_reactant_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_reactant_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_reactant_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_reactant_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_atomdef_reactant_free_300K.dat: -------------------------------------------------------------------------------- 1 | Ce1: GROUP ATOMS=1 2 | Ce2: GROUP ATOMS=4 3 | Cb1: GROUP ATOMS=7 4 | Cb2: GROUP ATOMS=10 5 | Cb3: GROUP ATOMS=12 6 | Cb4: GROUP ATOMS=14 7 | 8 | ethene: GROUP ATOMS=1-6 9 | 13butadiene: GROUP ATOMS=7-16 10 | e_com: COM ATOMS=ethene 11 | b_com: COM ATOMS=13butadiene 12 | 13 | a: FIXEDATOM AT=10,10,10 14 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_product_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_product_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_product_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_product_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_product_free_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_reactant_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_reactant_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_reactant_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_reactant_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_colvars_reactant_free_300K.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=a,e_com LABEL=CV_decom 2 | DISTANCE ATOMS=a,b_com LABEL=CV_dbcom 3 | 4 | DISTANCE ATOMS=Ce1,Cb1 LABEL=CV_d1 5 | DISTANCE ATOMS=Ce2,Cb4 LABEL=CV_d2 6 | SORT ARG=CV_d1,CV_d2 LABEL=CV_sort_d 7 | CUSTOM ARG=CV_d1,CV_d2 FUNC=(0.5*(x+y)) PERIODIC=NO LABEL=CV_dm 8 | 9 | TORSION ATOMS=Cb1,Cb2,Cb3,Cb4 LABEL=CV_dihed 10 | 11 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=colvars.txt FMT=%8.4f 12 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_product_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_product_OPES1D20_300K.dat 3 | INCLUDE FILE=plumed_colvars_product_OPES1D20_300K.dat 4 | INCLUDE FILE=plumed_walls_product_OPES1D20_300K.dat 5 | 6 | opes: OPES_METAD ... 7 | ARG=CV_dm 8 | SIGMA=0.05 9 | BARRIER=20 10 | PACE=500 11 | TEMP=300 12 | STATE_WFILE=state.data 13 | STATE_WSTRIDE=10000 14 | FILE=kernels.data 15 | ... 16 | 17 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 18 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 19 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 20 | 21 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d1,CV_d2,CV_dm,opes.bias FILE=opes.txt FMT=%8.4f 22 | FLUSH STRIDE=_R_PRINT_FREQ_ 23 | 24 | ENDPLUMED 25 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_product_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_product_OPES1D50_300K.dat 3 | INCLUDE FILE=plumed_colvars_product_OPES1D50_300K.dat 4 | INCLUDE FILE=plumed_walls_product_OPES1D50_300K.dat 5 | 6 | opes: OPES_METAD ... 7 | ARG=CV_dm 8 | SIGMA=0.05 9 | BARRIER=50 10 | PACE=500 11 | TEMP=300 12 | STATE_WFILE=state.data 13 | STATE_WSTRIDE=10000 14 | FILE=kernels.data 15 | ... 16 | 17 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 18 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 19 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 20 | 21 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d1,CV_d2,CV_dm,opes.bias FILE=opes.txt FMT=%8.4f 22 | FLUSH STRIDE=_R_PRINT_FREQ_ 23 | 24 | ENDPLUMED 25 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_product_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_product_OPES1D70_300K.dat 3 | INCLUDE FILE=plumed_colvars_product_OPES1D70_300K.dat 4 | INCLUDE FILE=plumed_walls_product_OPES1D70_300K.dat 5 | 6 | opes: OPES_METAD ... 7 | ARG=CV_dm 8 | SIGMA=0.05 9 | BARRIER=70 10 | PACE=500 11 | TEMP=300 12 | STATE_WFILE=state.data 13 | STATE_WSTRIDE=10000 14 | FILE=kernels.data 15 | ... 16 | 17 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 18 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 19 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 20 | 21 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d1,CV_d2,CV_dm,opes.bias FILE=opes.txt FMT=%8.4f 22 | FLUSH STRIDE=_R_PRINT_FREQ_ 23 | 24 | ENDPLUMED 25 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_product_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_product_SMD_300K.dat 3 | INCLUDE FILE=plumed_colvars_product_SMD_300K.dat 4 | INCLUDE FILE=plumed_walls_product_SMD_300K.dat 5 | 6 | smd: MOVINGRESTRAINT ... 7 | ARG=CV_d1,CV_d2 8 | STEP0=0 AT0=1.5,1.5 KAPPA0=0.0,0.0 9 | STEP1=20000 AT1=1.5,1.5 KAPPA1=100,100.0 10 | STEP2=60000 AT2=3.5,3.5 KAPPA2=100,100.0 11 | STEP3=80000 AT3=3.5,3.5 KAPPA3=0.0,0.0 12 | ... 13 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 14 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 15 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 16 | 17 | FLUSH STRIDE=_R_PRINT_FREQ_ 18 | 19 | ENDPLUMED 20 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_product_free_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_product_free_300K.dat 3 | INCLUDE FILE=plumed_colvars_product_free_300K.dat 4 | INCLUDE FILE=plumed_walls_product_free_300K.dat 5 | 6 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 7 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 8 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 9 | 10 | FLUSH STRIDE=_R_PRINT_FREQ_ 11 | 12 | ENDPLUMED 13 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_reactant_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_reactant_OPES1D20_300K.dat 3 | INCLUDE FILE=plumed_colvars_reactant_OPES1D20_300K.dat 4 | INCLUDE FILE=plumed_walls_reactant_OPES1D20_300K.dat 5 | 6 | opes: OPES_METAD ... 7 | ARG=CV_dm 8 | SIGMA=0.05 9 | BARRIER=20 10 | PACE=500 11 | TEMP=300 12 | STATE_WFILE=state.data 13 | STATE_WSTRIDE=10000 14 | FILE=kernels.data 15 | ... 16 | 17 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 18 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 19 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 20 | 21 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d1,CV_d2,CV_dm,opes.bias FILE=opes.txt FMT=%8.4f 22 | FLUSH STRIDE=_R_PRINT_FREQ_ 23 | 24 | ENDPLUMED 25 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_reactant_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_reactant_OPES1D50_300K.dat 3 | INCLUDE FILE=plumed_colvars_reactant_OPES1D50_300K.dat 4 | INCLUDE FILE=plumed_walls_reactant_OPES1D50_300K.dat 5 | 6 | opes: OPES_METAD ... 7 | ARG=CV_dm 8 | SIGMA=0.05 9 | BARRIER=50 10 | PACE=500 11 | TEMP=300 12 | STATE_WFILE=state.data 13 | STATE_WSTRIDE=10000 14 | FILE=kernels.data 15 | ... 16 | 17 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 18 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 19 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 20 | 21 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d1,CV_d2,CV_dm,opes.bias FILE=opes.txt FMT=%8.4f 22 | FLUSH STRIDE=_R_PRINT_FREQ_ 23 | 24 | ENDPLUMED 25 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_reactant_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_reactant_OPES1D70_300K.dat 3 | INCLUDE FILE=plumed_colvars_reactant_OPES1D70_300K.dat 4 | INCLUDE FILE=plumed_walls_reactant_OPES1D70_300K.dat 5 | 6 | opes: OPES_METAD ... 7 | ARG=CV_dm 8 | SIGMA=0.05 9 | BARRIER=70 10 | PACE=500 11 | TEMP=300 12 | STATE_WFILE=state.data 13 | STATE_WSTRIDE=10000 14 | FILE=kernels.data 15 | ... 16 | 17 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 18 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 19 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 20 | 21 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d1,CV_d2,CV_dm,opes.bias FILE=opes.txt FMT=%8.4f 22 | FLUSH STRIDE=_R_PRINT_FREQ_ 23 | 24 | ENDPLUMED 25 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_reactant_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_reactant_SMD_300K.dat 3 | INCLUDE FILE=plumed_colvars_reactant_SMD_300K.dat 4 | INCLUDE FILE=plumed_walls_reactant_SMD_300K.dat 5 | 6 | smd: MOVINGRESTRAINT ... 7 | ARG=CV_d1,CV_d2 8 | STEP0=0 AT0=3.5,3.5 KAPPA0=0.0,0.0 9 | STEP1=20000 AT1=3.5,3.5 KAPPA1=100,100.0 10 | STEP2=60000 AT2=1.5,1.5 KAPPA2=100,100.0 11 | STEP3=80000 AT3=1.5,1.5 KAPPA3=0.0,0.0 12 | ... 13 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 14 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 15 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 16 | 17 | FLUSH STRIDE=_R_PRINT_FREQ_ 18 | 19 | ENDPLUMED 20 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_reactant_free_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | INCLUDE FILE=plumed_atomdef_reactant_free_300K.dat 3 | INCLUDE FILE=plumed_colvars_reactant_free_300K.dat 4 | INCLUDE FILE=plumed_walls_reactant_free_300K.dat 5 | 6 | UPPER_WALLS ARG=CV_d1 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d1 7 | UPPER_WALLS ARG=CV_d2 AT=4.0 KAPPA=100.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_d2 8 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=uwall_d1.*,uwall_d2.* FILE=walls_extra.txt FMT=%8.4f 9 | 10 | FLUSH STRIDE=_R_PRINT_FREQ_ 11 | 12 | ENDPLUMED 13 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_product_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_product_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_product_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_product_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_product_free_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_reactant_OPES1D20_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_reactant_OPES1D50_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_reactant_OPES1D70_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_reactant_SMD_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/plumed_walls_reactant_free_300K.dat: -------------------------------------------------------------------------------- 1 | UPPER_WALLS ARG=CV_decom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_decom 2 | UPPER_WALLS ARG=CV_dbcom AT=5.0 KAPPA=50.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_dbcom 3 | 4 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*) FILE=walls_com.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_OPES1D20_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_OPES1D20_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:28 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.672423000000 9.643799000000 9.585367000000 18 | 2 2 7.920487000000 8.999847000000 9.003841000000 19 | 3 2 8.163383000000 10.607055000000 9.821354000000 20 | 4 1 9.822374000000 10.072773000000 8.630744000000 21 | 5 2 9.480360000000 10.584936000000 7.710755000000 22 | 6 2 10.428313000000 9.219909000000 8.296670000000 23 | 7 1 9.242449000000 8.863813000000 10.775004000000 24 | 8 2 9.616731000000 7.877082000000 10.446360000000 25 | 9 2 8.458161000000 8.740817000000 11.578832000000 26 | 10 1 10.381330000000 9.599596000000 11.427342000000 27 | 11 2 10.699511000000 9.277832000000 12.457583000000 28 | 12 1 10.956055000000 10.709654000000 10.864376000000 29 | 13 2 11.851407000000 11.132137000000 11.417493000000 30 | 14 1 10.806159000000 11.097155000000 9.404295000000 31 | 15 2 11.870573000000 10.980072000000 9.010580000000 32 | 16 2 10.637380000000 12.168723000000 9.238313000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_OPES1D50_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_OPES1D50_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:28 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.672423000000 9.643799000000 9.585367000000 18 | 2 2 7.920487000000 8.999847000000 9.003841000000 19 | 3 2 8.163383000000 10.607055000000 9.821354000000 20 | 4 1 9.822374000000 10.072773000000 8.630744000000 21 | 5 2 9.480360000000 10.584936000000 7.710755000000 22 | 6 2 10.428313000000 9.219909000000 8.296670000000 23 | 7 1 9.242449000000 8.863813000000 10.775004000000 24 | 8 2 9.616731000000 7.877082000000 10.446360000000 25 | 9 2 8.458161000000 8.740817000000 11.578832000000 26 | 10 1 10.381330000000 9.599596000000 11.427342000000 27 | 11 2 10.699511000000 9.277832000000 12.457583000000 28 | 12 1 10.956055000000 10.709654000000 10.864376000000 29 | 13 2 11.851407000000 11.132137000000 11.417493000000 30 | 14 1 10.806159000000 11.097155000000 9.404295000000 31 | 15 2 11.870573000000 10.980072000000 9.010580000000 32 | 16 2 10.637380000000 12.168723000000 9.238313000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_OPES1D70_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_OPES1D70_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:28 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.672423000000 9.643799000000 9.585367000000 18 | 2 2 7.920487000000 8.999847000000 9.003841000000 19 | 3 2 8.163383000000 10.607055000000 9.821354000000 20 | 4 1 9.822374000000 10.072773000000 8.630744000000 21 | 5 2 9.480360000000 10.584936000000 7.710755000000 22 | 6 2 10.428313000000 9.219909000000 8.296670000000 23 | 7 1 9.242449000000 8.863813000000 10.775004000000 24 | 8 2 9.616731000000 7.877082000000 10.446360000000 25 | 9 2 8.458161000000 8.740817000000 11.578832000000 26 | 10 1 10.381330000000 9.599596000000 11.427342000000 27 | 11 2 10.699511000000 9.277832000000 12.457583000000 28 | 12 1 10.956055000000 10.709654000000 10.864376000000 29 | 13 2 11.851407000000 11.132137000000 11.417493000000 30 | 14 1 10.806159000000 11.097155000000 9.404295000000 31 | 15 2 11.870573000000 10.980072000000 9.010580000000 32 | 16 2 10.637380000000 12.168723000000 9.238313000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_SMD_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_SMD_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:28 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.672423000000 9.643799000000 9.585367000000 18 | 2 2 7.920487000000 8.999847000000 9.003841000000 19 | 3 2 8.163383000000 10.607055000000 9.821354000000 20 | 4 1 9.822374000000 10.072773000000 8.630744000000 21 | 5 2 9.480360000000 10.584936000000 7.710755000000 22 | 6 2 10.428313000000 9.219909000000 8.296670000000 23 | 7 1 9.242449000000 8.863813000000 10.775004000000 24 | 8 2 9.616731000000 7.877082000000 10.446360000000 25 | 9 2 8.458161000000 8.740817000000 11.578832000000 26 | 10 1 10.381330000000 9.599596000000 11.427342000000 27 | 11 2 10.699511000000 9.277832000000 12.457583000000 28 | 12 1 10.956055000000 10.709654000000 10.864376000000 29 | 13 2 11.851407000000 11.132137000000 11.417493000000 30 | 14 1 10.806159000000 11.097155000000 9.404295000000 31 | 15 2 11.870573000000 10.980072000000 9.010580000000 32 | 16 2 10.637380000000 12.168723000000 9.238313000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_free_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/product_free_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:28 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.672423000000 9.643799000000 9.585367000000 18 | 2 2 7.920487000000 8.999847000000 9.003841000000 19 | 3 2 8.163383000000 10.607055000000 9.821354000000 20 | 4 1 9.822374000000 10.072773000000 8.630744000000 21 | 5 2 9.480360000000 10.584936000000 7.710755000000 22 | 6 2 10.428313000000 9.219909000000 8.296670000000 23 | 7 1 9.242449000000 8.863813000000 10.775004000000 24 | 8 2 9.616731000000 7.877082000000 10.446360000000 25 | 9 2 8.458161000000 8.740817000000 11.578832000000 26 | 10 1 10.381330000000 9.599596000000 11.427342000000 27 | 11 2 10.699511000000 9.277832000000 12.457583000000 28 | 12 1 10.956055000000 10.709654000000 10.864376000000 29 | 13 2 11.851407000000 11.132137000000 11.417493000000 30 | 14 1 10.806159000000 11.097155000000 9.404295000000 31 | 15 2 11.870573000000 10.980072000000 9.010580000000 32 | 16 2 10.637380000000 12.168723000000 9.238313000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/properties.txt: -------------------------------------------------------------------------------- 1 | type 2 | C 1 3 | H 2 4 | 5 | masses 6 | C 12.01100000 7 | H 1.00800000 8 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_OPES1D20_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_OPES1D20_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:35 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.116278000000 11.406504000000 10.655949000000 18 | 2 2 9.119088000000 11.243899000000 11.105393000000 19 | 3 2 7.627528000000 12.339127000000 10.883857000000 20 | 4 1 7.515775000000 10.414935000000 9.883732000000 21 | 5 2 6.536716000000 10.554333000000 9.411366000000 22 | 6 2 8.041814000000 9.476833000000 9.683805000000 23 | 7 1 10.711524000000 10.918441000000 8.221564000000 24 | 8 2 10.764661000000 11.969725000000 7.845369000000 25 | 9 2 9.986976000000 10.142392000000 7.780867000000 26 | 10 1 11.423501000000 10.632094000000 9.364009000000 27 | 11 2 12.074656000000 11.441806000000 9.693735000000 28 | 12 1 11.471154000000 9.322998000000 10.091292000000 29 | 13 2 12.433719000000 9.084624000000 10.684061000000 30 | 14 1 10.494183000000 8.341340000000 9.881631000000 31 | 15 2 10.561650000000 7.300425000000 10.293477000000 32 | 16 2 9.636644000000 8.549760000000 9.207471000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_OPES1D50_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_OPES1D50_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:35 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.116278000000 11.406504000000 10.655949000000 18 | 2 2 9.119088000000 11.243899000000 11.105393000000 19 | 3 2 7.627528000000 12.339127000000 10.883857000000 20 | 4 1 7.515775000000 10.414935000000 9.883732000000 21 | 5 2 6.536716000000 10.554333000000 9.411366000000 22 | 6 2 8.041814000000 9.476833000000 9.683805000000 23 | 7 1 10.711524000000 10.918441000000 8.221564000000 24 | 8 2 10.764661000000 11.969725000000 7.845369000000 25 | 9 2 9.986976000000 10.142392000000 7.780867000000 26 | 10 1 11.423501000000 10.632094000000 9.364009000000 27 | 11 2 12.074656000000 11.441806000000 9.693735000000 28 | 12 1 11.471154000000 9.322998000000 10.091292000000 29 | 13 2 12.433719000000 9.084624000000 10.684061000000 30 | 14 1 10.494183000000 8.341340000000 9.881631000000 31 | 15 2 10.561650000000 7.300425000000 10.293477000000 32 | 16 2 9.636644000000 8.549760000000 9.207471000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_OPES1D70_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_OPES1D70_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:35 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.116278000000 11.406504000000 10.655949000000 18 | 2 2 9.119088000000 11.243899000000 11.105393000000 19 | 3 2 7.627528000000 12.339127000000 10.883857000000 20 | 4 1 7.515775000000 10.414935000000 9.883732000000 21 | 5 2 6.536716000000 10.554333000000 9.411366000000 22 | 6 2 8.041814000000 9.476833000000 9.683805000000 23 | 7 1 10.711524000000 10.918441000000 8.221564000000 24 | 8 2 10.764661000000 11.969725000000 7.845369000000 25 | 9 2 9.986976000000 10.142392000000 7.780867000000 26 | 10 1 11.423501000000 10.632094000000 9.364009000000 27 | 11 2 12.074656000000 11.441806000000 9.693735000000 28 | 12 1 11.471154000000 9.322998000000 10.091292000000 29 | 13 2 12.433719000000 9.084624000000 10.684061000000 30 | 14 1 10.494183000000 8.341340000000 9.881631000000 31 | 15 2 10.561650000000 7.300425000000 10.293477000000 32 | 16 2 9.636644000000 8.549760000000 9.207471000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_SMD_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_SMD_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:35 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.116278000000 11.406504000000 10.655949000000 18 | 2 2 9.119088000000 11.243899000000 11.105393000000 19 | 3 2 7.627528000000 12.339127000000 10.883857000000 20 | 4 1 7.515775000000 10.414935000000 9.883732000000 21 | 5 2 6.536716000000 10.554333000000 9.411366000000 22 | 6 2 8.041814000000 9.476833000000 9.683805000000 23 | 7 1 10.711524000000 10.918441000000 8.221564000000 24 | 8 2 10.764661000000 11.969725000000 7.845369000000 25 | 9 2 9.986976000000 10.142392000000 7.780867000000 26 | 10 1 11.423501000000 10.632094000000 9.364009000000 27 | 11 2 12.074656000000 11.441806000000 9.693735000000 28 | 12 1 11.471154000000 9.322998000000 10.091292000000 29 | 13 2 12.433719000000 9.084624000000 10.684061000000 30 | 14 1 10.494183000000 8.341340000000 9.881631000000 31 | 15 2 10.561650000000 7.300425000000 10.293477000000 32 | 16 2 9.636644000000 8.549760000000 9.207471000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_free_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary f f f 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/R/user_files/reactant_free_300K.lmp: -------------------------------------------------------------------------------- 1 | # File generated with Atomsk by rdavid on 2024-08-26 16:56:35 2 | 3 | 16 atoms 4 | 2 atom types 5 | 6 | 0.000000000000 20.000000000000 xlo xhi 7 | 0.000000000000 20.000000000000 ylo yhi 8 | 0.000000000000 20.000000000000 zlo zhi 9 | 10 | Masses 11 | 12 | 1 12.01100000 # C 13 | 2 1.00800000 # H 14 | 15 | Atoms # atomic 16 | 17 | 1 1 8.116278000000 11.406504000000 10.655949000000 18 | 2 2 9.119088000000 11.243899000000 11.105393000000 19 | 3 2 7.627528000000 12.339127000000 10.883857000000 20 | 4 1 7.515775000000 10.414935000000 9.883732000000 21 | 5 2 6.536716000000 10.554333000000 9.411366000000 22 | 6 2 8.041814000000 9.476833000000 9.683805000000 23 | 7 1 10.711524000000 10.918441000000 8.221564000000 24 | 8 2 10.764661000000 11.969725000000 7.845369000000 25 | 9 2 9.986976000000 10.142392000000 7.780867000000 26 | 10 1 11.423501000000 10.632094000000 9.364009000000 27 | 11 2 12.074656000000 11.441806000000 9.693735000000 28 | 12 1 11.471154000000 9.322998000000 10.091292000000 29 | 13 2 12.433719000000 9.084624000000 10.684061000000 30 | 14 1 10.494183000000 8.341340000000 9.881631000000 31 | 15 2 10.561650000000 7.300425000000 10.293477000000 32 | 16 2 9.636644000000 8.549760000000 9.207471000000 33 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/initial_dataset/init_product/nopbc: -------------------------------------------------------------------------------- 1 | True 2 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/initial_dataset/init_product/set.000/box.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arcann-chem/arcann_training/f224ee0216674e8345ab212b3c55a310fa17c6ee/examples/diels_alder_ethene_13butadiene/initial_dataset/init_product/set.000/box.npy -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/initial_dataset/init_product/set.000/coord.npy: -------------------------------------------------------------------------------- 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/examples/diels_alder_ethene_13butadiene/initial_dataset/init_product_to_reactant/nopbc: -------------------------------------------------------------------------------- 1 | True 2 | -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/initial_dataset/init_product_to_reactant/set.000/box.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arcann-chem/arcann_training/f224ee0216674e8345ab212b3c55a310fa17c6ee/examples/diels_alder_ethene_13butadiene/initial_dataset/init_product_to_reactant/set.000/box.npy -------------------------------------------------------------------------------- /examples/diels_alder_ethene_13butadiene/initial_dataset/init_product_to_reactant/set.000/coord.npy: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /examples/inputs/initialization.json: -------------------------------------------------------------------------------- 1 | { 2 | "step_name": "initialization", 3 | "systems_auto": { "value": null, "_comment": "list of str", "_default": "auto-populated by taking each *.lmp file in the user_files directory"}, 4 | "nnp_count": { "value": null, "_comment": "int", "_default": 3} 5 | } -------------------------------------------------------------------------------- /examples/inputs/labeling.json: -------------------------------------------------------------------------------- 1 | { 2 | "step_name": "labeling", 3 | "user_machine_keyword_label": { "value": null, "_comment": "null (use machine.json default), str (shortcut used in machine.json (ex: v100), list of str (project,allocation,arch, ex [myproject,myalloc,v100]) ", "_default": null}, 4 | "job_email": { "value": null, "_comment": "str", "_default": ""}, 5 | "labeling_program": { "value": null, "_comment": "str", "_default": "cp2k"}, 6 | "walltime_first_job_h" : { "value": null, "_comment": "float or list of float", "_default": [0.5]}, 7 | "walltime_second_job_h" : { "value": null, "_comment": "float or list of float", "_default": [1.0]}, 8 | "nb_nodes" : { "value": null, "_comment": "int or list of int", "_default": [1]}, 9 | "nb_mpi_per_node" : { "value": null, "_comment": "int or list of int", "_default": [10]}, 10 | "nb_threads_per_mpi" : { "value": null, "_comment": "int or list of int", "_default": [1]} 11 | } -------------------------------------------------------------------------------- /examples/inputs/test.json: -------------------------------------------------------------------------------- 1 | { 2 | "step_name": "test", 3 | "user_machine_keyword_test": { "value": null, "_comment": "null (use machine.json default), str (shortcut used in machine.json (ex: v100), list of str (project,allocation,arch, ex [myproject,myalloc,v100]) ", "_default": null}, 4 | "job_email": { "value": null, "_comment": "str", "_default": ""}, 5 | "job_walltime_h" : { "value": null, "_comment": "float or list of float", "_default": 2.0}, 6 | "is_compressed" : { "value": null, "_comment": "bool", "_default": true}, 7 | "deepmd_model_version": { "value": null, "_comment": "float, values: 2.0 or 2.1 or 2.2, -1 will take the highest dptrain_VERSION.json in the user_files folder", "_default": -1} 8 | } -------------------------------------------------------------------------------- /examples/inputs/training.json: -------------------------------------------------------------------------------- 1 | { 2 | "step_name": "training", 3 | "user_machine_keyword_train": { "value": null, "_comment": "null (use machine.json default), str (shortcut used in machine.json (ex: a100), list of str (project,allocation,arch, ex [myproject,myalloc,a100]) ", "_default": null}, 4 | "user_machine_keyword_freeze": { "value": null, "_comment": "null (use machine.json default), str (shortcut used in machine.json (ex: v100), list of str (project,allocation,arch, ex [myproject,myalloc,v100]) ", "_default": null}, 5 | "user_machine_keyword_compress": { "value": null, "_comment": "null (use machine.json default), str (shortcut used in machine.json (ex: v100), list of str (project,allocation,arch, ex [myproject,myalloc,v100]) ", "_default": null}, 6 | "job_email": { "value": null, "_comment": "str", "_default": ""}, 7 | "use_initial_datasets": { "value": null, "_comment": "boolean", "_default": true}, 8 | "use_extra_datasets": { "value": null, "_comment": "boolean", "_default": false}, 9 | "deepmd_model_version": { "value": null, "_comment": "float, values: 2.0 or 2.1 or 2.2, -1 will take the highest dptrain_VERSION.json in the user_files folder", "_default": -1}, 10 | "job_walltime_train_h":{ "value": null, "_comment": "float or int, -1 means auto,", "_default": -1}, 11 | "mean_s_per_step": { "value": null, "_comment": "float", "_default": 0.10}, 12 | "start_lr": { "value": null, "_comment": "float", "_default": 0.001}, 13 | "stop_lr": { "value": null, "_comment": "float", "_default": 1e-06}, 14 | "decay_rate": { "value": null, "_comment": "float", "_default": 0.90}, 15 | "decay_steps": { "value": null, "_comment": "int", "_default": 5000}, 16 | "decay_steps_fixed": { "value": null, "_comment": "boolean", "_default": false}, 17 | "numb_steps": { "value": null, "_comment": "int", "_default": 400000}, 18 | "numb_test": { "value": null, "_comment": "int", "_default": 0} 19 | } -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/000-training/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "job_walltime_train_h": 12.0 4 | } 5 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/000-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 12.0, 10 | "mean_s_per_step": 0.108, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/001-exploration/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "sigma_low": 0.15 3 | } 4 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/001-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 14 | "exp_time_ps": [10.0, 10.0, 41.0, 10.0, 10.0, 41.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/001-labeling/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "nb_mpi_per_node": 16 4 | } 5 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/001-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 6 | "walltime_second_job_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [16, 16, 16, 16, 16, 16], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/001-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 5.204166666666667, 10 | "mean_s_per_step": 0.0468375, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/002-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 14 | "exp_time_ps": [20.0, 40.0, 41.0, 40.0, 20.0, 41.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/002-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.7780846428571428, 0.7788836111111112, 0.5, 0.7691795833333332, 0.8215420833333333, 0.7813870833333333], 6 | "walltime_second_job_h": [0.5404636742424243, 0.5916468333333333, 0.6537405555555555, 0.5667988257575758, 0.5581629761904763, 0.5584038020833333], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [16, 16, 16, 16, 16, 16], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/002-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 6.106944444444444, 10 | "mean_s_per_step": 0.0549625, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/003-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [1.0, 1.5, 0.5, 1.0, 0.5, 0.5], 14 | "exp_time_ps": [80.0, 160.0, 41.0, 80.0, 40.0, 41.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/003-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.7780846428571428, 0.8731616666666666, 0.7534175000000001, 0.80905125, 0.7984392499999999, 0.8496004166666666], 6 | "walltime_second_job_h": [0.5404636742424243, 0.6125835833333334, 0.5451851666666666, 0.5206186111111113, 0.5305069166666667, 0.5317459375000001], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [16, 16, 16, 16, 16, 16], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/003-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 5.878333333333333, 10 | "mean_s_per_step": 0.052905, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/004-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [1.5, 2.5, 0.5, 1.5, 1.5, 0.5], 14 | "exp_time_ps": [160.0, 320.0, 41.0, 160.0, 160.0, 41.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/004-labeling/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_myproject1", 3 | "nb_mpi_per_node": 10 4 | } 5 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/004-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_myproject1", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.8494185119047619, 0.8731616666666666, 0.9070224999999998, 0.9075345833333334, 0.8722140000000002, 0.8680127083333333], 6 | "walltime_second_job_h": [0.5637818452380952, 0.6125835833333334, 0.5676958333333333, 0.5875071527777778, 0.5637670000000001, 0.5599991666666667], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [10, 10, 10, 10, 10, 10], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/004-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 7.0, 10 | "mean_s_per_step": 0.063, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/005-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [3.0, 3.0, 0.5, 3.0, 3.0, 0.5], 14 | "exp_time_ps": [400.0, 400.0, 41.0, 400.0, 400.0, 41.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/005-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_myproject1", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.8494185119047619, 0.9211195833333332, 1.1386053125000002, 0.9075345833333334, 1.1415554166666668, 1.1635191666666667], 6 | "walltime_second_job_h": [0.5637818452380952, 0.5955537500000001, 0.7364276041666666, 0.5875071527777778, 0.7275935416666667, 0.7919179166666667], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [10, 10, 10, 10, 10, 10], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/005-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 8.0, 10 | "mean_s_per_step": 0.072, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/006-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [3.0, 3.0, 3.0, 3.0, 3.0, 3.0], 14 | "exp_time_ps": [400.0, 400.0, 410.0, 400.0, 400.0, 410.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/006-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_myproject1", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.8494185119047619, 1.3205066666666667, 1.1563591666666668, 0.9075345833333334, 1.1415554166666668, 1.1635191666666667], 6 | "walltime_second_job_h": [0.5637818452380952, 0.8250083333333333, 0.8024708333333334, 0.5875071527777778, 0.7275935416666667, 0.7919179166666667], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [10, 10, 10, 10, 10, 10], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/006-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 8.0, 10 | "mean_s_per_step": 0.072, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/007-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [3.0, 3.0, 3.0, 3.0, 3.0, 3.0], 14 | "exp_time_ps": [400.0, 400.0, 410.0, 400.0, 400.0, 410.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.15, 0.15, 0.15, 0.15, 0.15, 0.15], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/007-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_myproject1", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.9335972916666666, 1.1555845052083331, 1.1739045512820514, 0.9075345833333334, 1.143174583333333, 1.142574375], 6 | "walltime_second_job_h": [0.6347164583333333, 0.7910226822916667, 0.7841560897435896, 0.5875071527777778, 0.7637216666666666, 0.76276375], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [10, 10, 10, 10, 10, 10], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "systems_auto": ["ch3br_cl_close_300K", "ch3br_cl_free_300K", "ch3br_cl_smd_300K", "ch3cl_br_close_300K", "ch3cl_br_free_300K", "ch3cl_br_smd_300K"], 3 | "nnp_count": 3 4 | } -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/ch3br_cl_close_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/ch3br_cl_free_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/ch3br_cl_smd_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/ch3cl_br_close_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/ch3cl_br_free_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/ch3cl_br_smd_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/dptrain_2.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "model": { 3 | "type_map": ["C", "H", "Cl", "Br", "N"], 4 | "descriptor": { 5 | "seed": 2082608865, 6 | "type": "se_e2_a", 7 | "sel": [40, 65, 1, 1, 25], 8 | "rcut": 6.0, 9 | "rcut_smth": 0.5, 10 | "neuron": [20, 40, 80], 11 | "axis_neuron": 16, 12 | "resnet_dt": false 13 | }, 14 | "fitting_net": { 15 | "seed": 2082608865, 16 | "neuron": [240, 240, 240], 17 | "resnet_dt": true 18 | } 19 | }, 20 | "learning_rate": { 21 | "type": "exp", 22 | "decay_steps": 5000, 23 | "start_lr": 0.002, 24 | "stop_lr": 7.010533249765748e-08 25 | }, 26 | "loss": { 27 | "start_pref_e": 0.01, 28 | "limit_pref_e": 1, 29 | "start_pref_f": 1000, 30 | "limit_pref_f": 1, 31 | "start_pref_v": 0.0, 32 | "limit_pref_v": 0.0 33 | }, 34 | "training": { 35 | "seed": 2082608865, 36 | "disp_file": "lcurve.out", 37 | "disp_freq": 1000, 38 | "numb_test": 0, 39 | "save_freq": 1000, 40 | "save_ckpt": "model.ckpt", 41 | "disp_training": true, 42 | "time_training": true, 43 | "profiling": false, 44 | "training_data": { 45 | "systems": ["../data.init/init_system.0_reactant", "../data.init/init_system.0_product"], 46 | "set_prefix": "set", 47 | "batch_size": 1 48 | } 49 | } 50 | } 51 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_atomdef_ch3br_cl_close_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_atomdef_ch3br_cl_free_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_atomdef_ch3br_cl_smd_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_atomdef_ch3cl_br_close_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_atomdef_ch3cl_br_free_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_atomdef_ch3cl_br_smd_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_ch3br_cl_close_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_close_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_close_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=11.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | # This for close one X 16 | UPPER_WALLS ARG=CV_d_CMeCl AT=3.0 KAPPA=5.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_CV_d_CMeCl 17 | 18 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 19 | 20 | FLUSH STRIDE=_R_PRINT_FREQ_ 21 | 22 | ENDPLUMED 23 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_ch3br_cl_free_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_free_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_free_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=11.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 16 | 17 | FLUSH STRIDE=_R_PRINT_FREQ_ 18 | 19 | ENDPLUMED 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_ch3br_cl_smd_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_smd_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_smd_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=11.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 16 | 17 | smd: MOVINGRESTRAINT ... 18 | ARG=CV_d_CMeCl 19 | STEP0=0 AT0=2.5 KAPPA0=1.0 20 | STEP1=2000 AT1=2.5 KAPPA1=1.0 21 | STEP2=220000 AT2=10.0 KAPPA2=1.0 22 | STEP3=420000 AT3=2.5 KAPPA3=1.0 23 | STEP4=620000 AT4=10.0 KAPPA4=1.0 24 | STEP5=820000 AT5=2.5 KAPPA5=1.0 25 | ... 26 | 27 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,smd.* FILE=SMD.txt FMT=%8.4f 28 | 29 | FLUSH STRIDE=_R_PRINT_FREQ_ 30 | 31 | ENDPLUMED 32 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_ch3cl_br_close_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_close_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_close_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=11.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | # This for close one X 16 | UPPER_WALLS ARG=CV_d_CMeBr AT=3.0 KAPPA=5.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_CV_d_CMeBr 17 | 18 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 19 | 20 | FLUSH STRIDE=_R_PRINT_FREQ_ 21 | 22 | ENDPLUMED 23 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_ch3cl_br_free_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_free_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_free_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=11.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 16 | 17 | FLUSH STRIDE=_R_PRINT_FREQ_ 18 | 19 | ENDPLUMED 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_ch3cl_br_smd_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_smd_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_smd_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=11.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 16 | 17 | smd: MOVINGRESTRAINT ... 18 | ARG=CV_d_CMeBr 19 | STEP0=0 AT0=2.5 KAPPA0=1.0 20 | STEP1=2000 AT1=2.5 KAPPA1=1.0 21 | STEP2=220000 AT2=10.0 KAPPA2=1.0 22 | STEP3=420000 AT3=2.5 KAPPA3=1.0 23 | STEP4=620000 AT4=10.0 KAPPA4=1.0 24 | STEP5=820000 AT5=2.5 KAPPA5=1.0 25 | ... 26 | 27 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeBr,smd.* FILE=SMD.txt FMT=%8.4f 28 | 29 | FLUSH STRIDE=_R_PRINT_FREQ_ 30 | 31 | ENDPLUMED 32 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_colvars_ch3br_cl_close_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_colvars_ch3br_cl_free_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_colvars_ch3br_cl_smd_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_colvars_ch3cl_br_close_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_colvars_ch3cl_br_free_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/plumed_colvars_ch3cl_br_smd_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/NR/user_files/properties.txt: -------------------------------------------------------------------------------- 1 | type 2 | C 1 3 | H 2 4 | Cl 3 5 | Br 4 6 | N 5 7 | 8 | masses 9 | C 12.01100000 10 | H 1.00800000 11 | Cl 35.45000000 12 | Br 79.90400000 13 | N 14.00700000 14 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/000-training/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1" 3 | } 4 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/000-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 12.0, 10 | "mean_s_per_step": 0.108, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/001-exploration/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "previous_start": false, 3 | "print_interval_mult": 0.001 4 | } 5 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/001-labeling/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "nb_mpi_per_node": 32 3 | } 4 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/001-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 6 | "walltime_second_job_h": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/001-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 8.0, 10 | "mean_s_per_step": 0.072, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/002-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [false, false, false, false, false, false, false, false, false, false, false, false], 11 | "disturbed_start": [false, false, false, false, false, false, false, false, false, false, false, false], 12 | "print_interval_mult": [0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001], 13 | "job_walltime_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 14 | "exp_time_ps": [40.0, 40.0, 10.0, 40.0, 20.0, 10.0, 40.0, 10.0, 10.0, 40.0, 40.0, 10.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400, 400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], [], [], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], [], [], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/002-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5184864814814815, 0.5223677908805032, 0.5241222955974841, 0.5, 0.5415369791666667, 0.5806607945736434, 0.5209083333333333, 0.5349042059748426, 0.5313470512820514, 0.5376801041666668, 0.5435324537037036, 0.5550287934027778], 6 | "walltime_second_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/002-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 7.0, 10 | "mean_s_per_step": 0.063, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/003-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [false, false, false, false, false, false, false, false, false, false, false, false], 11 | "disturbed_start": [false, false, false, false, false, false, false, false, false, false, false, false], 12 | "print_interval_mult": [0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001], 13 | "job_walltime_h": [1.5, 0.5, 0.5, 1.5, 1.0, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 14 | "exp_time_ps": [160.0, 40.0, 40.0, 160.0, 80.0, 40.0, 40.0, 20.0, 40.0, 40.0, 40.0, 20.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400, 400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], [], [], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], [], [], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/003-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5088067857142856, 0.5421542916666667, 0.5395768229166668, 0.5, 0.5155238611111111, 0.5721574387254902, 0.5088936111111111, 0.5228968055555556, 0.5335622641509434, 0.5123036174242426, 0.5121724999999999, 0.527094496855346], 6 | "walltime_second_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/003-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 8.0, 10 | "mean_s_per_step": 0.072, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/004-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [false, false, false, false, false, false, false, false, false, false, false, false], 11 | "disturbed_start": [false, false, false, false, false, false, false, false, false, false, false, false], 12 | "print_interval_mult": [0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001], 13 | "job_walltime_h": [3.0, 1.5, 1.5, 1.5, 2.5, 1.0, 1.5, 1.0, 1.5, 1.5, 1.5, 1.0], 14 | "exp_time_ps": [400.0, 160.0, 160.0, 160.0, 320.0, 80.0, 160.0, 80.0, 160.0, 160.0, 160.0, 80.0], 15 | "max_exp_time_ps": [400, 400, 400, 400, 400, 400, 400, 400, 400, 400, 400, 400], 16 | "max_candidates": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], [], [], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], [], [], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/004-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5399155, 0.5106159722222222, 0.5220752818627451, 0.5029445833333335, 0.5485616666666666, 0.5506797596153845, 0.537925, 0.5147291666666667, 0.5271977298850575, 0.5257898611111111, 0.5121724999999999, 0.5435653459119497], 6 | "walltime_second_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/004-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 8.0, 10 | "mean_s_per_step": 0.072, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/005-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5, 0.5841352083333333, 0.5, 0.5029445833333335, 0.5534332638888888, 0.5486247916666667, 0.5, 0.5147291666666667, 0.5, 0.5257898611111111, 0.5121724999999999, 0.5510231712962962], 6 | "walltime_second_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/005-training/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_train": "v100_myproject1", 3 | "user_machine_keyword_freeze": "v100_myproject1", 4 | "user_machine_keyword_compress": "v100_myproject1", 5 | "job_email": "", 6 | "use_initial_datasets": true, 7 | "use_extra_datasets": false, 8 | "deepmd_model_version": 2.1, 9 | "job_walltime_train_h": 8.0, 10 | "mean_s_per_step": 0.072, 11 | "start_lr": 0.001, 12 | "stop_lr": 1e-06, 13 | "decay_rate": 0.9172759353897796, 14 | "decay_steps": 5000, 15 | "decay_steps_fixed": false, 16 | "numb_steps": 400000, 17 | "numb_test": 0 18 | } 19 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/006-exploration/input.json: -------------------------------------------------------------------------------- 1 | { 2 | "previous_start": true, 3 | "print_interval_mult": 0.01, 4 | "max_exp_time_ps": 1000 5 | } 6 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/006-exploration/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_exp": "v100_myproject1", 3 | "job_email": "", 4 | "atomsk_path": "/programs/apps/atomsk/0.13.1/atomsk", 5 | "vmd_path": "/prod/vmd/1.9.4a43/bin/vmd_LINUXAMD64", 6 | "exploration_type": ["lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps", "lammps"], 7 | "traj_count": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], 8 | "temperature_K": [300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0, 300.0], 9 | "timestep_ps": [0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005], 10 | "previous_start": [true, true, true, true, true, true, true, true, true, true, true, true], 11 | "disturbed_start": [false, false, false, false, false, false, false, false, false, false, false, false], 12 | "print_interval_mult": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01], 13 | "job_walltime_h": [6.0, 7.5, 6.0, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 5.0], 14 | "exp_time_ps": [800.0, 1000.0, 800.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 640.0], 15 | "max_exp_time_ps": [1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000], 16 | "max_candidates": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50], 17 | "sigma_low": [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2], 18 | "sigma_high": [0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7], 19 | "sigma_high_limit": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 20 | "ignore_first_x_ps": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 21 | "disturbed_start_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 22 | "disturbed_start_indexes": [[], [], [], [], [], [], [], [], [], [], [], []], 23 | "disturbed_candidate_value": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 24 | "disturbed_candidate_indexes": [[], [], [], [], [], [], [], [], [], [], [], []] 25 | } 26 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/006-labeling/used_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "user_machine_keyword_label": "cpu_rome", 3 | "job_email": "", 4 | "labeling_program": "cp2k", 5 | "walltime_first_job_h": [0.5, 0.5215830284552845, 0.5, 0.5029445833333335, 0.5534332638888888, 0.5357512499999999, 0.5, 0.5147291666666667, 0.537637361111111, 0.5257898611111111, 0.5121724999999999, 0.5510231712962962], 6 | "walltime_second_job_h": [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5], 7 | "nb_nodes": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 8 | "nb_mpi_per_node": [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32], 9 | "nb_threads_per_mpi": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 | } 11 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3br_cl_OPES1D_10_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3br_cl_OPES1D_20_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3br_cl_OPES1D_5_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3br_cl_OPES2D_10_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3br_cl_OPES2D_20_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3br_cl_OPES2D_5_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3cl_br_OPES1D_10_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3cl_br_OPES1D_20_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3cl_br_OPES1D_5_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3cl_br_OPES2D_10_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3cl_br_OPES2D_20_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/ch3cl_br_OPES2D_5_300K.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/dptrain_2.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "model": { 3 | "type_map": ["C", "H", "Cl", "Br", "N"], 4 | "descriptor": { 5 | "seed": 2082608865, 6 | "type": "se_e2_a", 7 | "sel": [40, 65, 1, 1, 25], 8 | "rcut": 6.0, 9 | "rcut_smth": 0.5, 10 | "neuron": [20, 40, 80], 11 | "axis_neuron": 16, 12 | "resnet_dt": false 13 | }, 14 | "fitting_net": { 15 | "seed": 2082608865, 16 | "neuron": [240, 240, 240], 17 | "resnet_dt": true 18 | } 19 | }, 20 | "learning_rate": { 21 | "type": "exp", 22 | "decay_steps": 5000, 23 | "start_lr": 0.002, 24 | "stop_lr": 7.010533249765748e-08 25 | }, 26 | "loss": { 27 | "start_pref_e": 0.01, 28 | "limit_pref_e": 1, 29 | "start_pref_f": 1000, 30 | "limit_pref_f": 1, 31 | "start_pref_v": 0.0, 32 | "limit_pref_v": 0.0 33 | }, 34 | "training": { 35 | "seed": 2082608865, 36 | "disp_file": "lcurve.out", 37 | "disp_freq": 1000, 38 | "numb_test": 0, 39 | "save_freq": 1000, 40 | "save_ckpt": "model.ckpt", 41 | "disp_training": true, 42 | "time_training": true, 43 | "profiling": false, 44 | "training_data": { 45 | "systems": ["../data.init/init_system.0_reactant", "../data.init/init_system.0_product"], 46 | "set_prefix": "set", 47 | "batch_size": 1 48 | } 49 | } 50 | } 51 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3br_cl_OPES1D_10_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3br_cl_OPES1D_20_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3br_cl_OPES1D_5_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3br_cl_OPES2D_10_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3br_cl_OPES2D_20_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3br_cl_OPES2D_5_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3cl_br_OPES1D_10_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3cl_br_OPES1D_20_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3cl_br_OPES1D_5_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3cl_br_OPES2D_10_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3cl_br_OPES2D_20_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_atomdef_ch3cl_br_OPES2D_5_300K.dat: -------------------------------------------------------------------------------- 1 | Cl: GROUP ATOMS=5 2 | Br: GROUP ATOMS=6 3 | CMe: GROUP ATOMS=1 4 | H1: GROUP ATOMS=2 5 | H2: GROUP ATOMS=3 6 | H3: GROUP ATOMS=4 7 | HMe: GROUP ATOMS=H1,H2,H3 8 | ANCMe: GROUP ATOMS=7-234:6 9 | ANCN: GROUP ATOMS=11-234:6 10 | ANNC: GROUP ATOMS=12-234:6 11 | ANHMe: GROUP ATOMS=7-234 REMOVE=ANCMe,ANCN,ANNC -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3br_cl_OPES1D_10_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_OPES1D_10_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_OPES1D_10_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_Dd 17 | SIGMA=0.05 18 | BARRIER=10 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_Dd,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3br_cl_OPES1D_20_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_OPES1D_20_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_OPES1D_20_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_Dd 17 | SIGMA=0.05 18 | BARRIER=20 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_Dd,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3br_cl_OPES1D_5_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_OPES1D_5_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_OPES1D_5_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_Dd 17 | SIGMA=0.05 18 | BARRIER=5 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_Dd,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3br_cl_OPES2D_10_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_OPES2D_10_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_OPES2D_10_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_d_CMeCl,CV_d_CMeBr 17 | SIGMA=0.05,0.05 18 | BARRIER=10 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,CV_d_CMeBr,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3br_cl_OPES2D_20_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_OPES2D_20_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_OPES2D_20_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_d_CMeCl,CV_d_CMeBr 17 | SIGMA=0.05,0.05 18 | BARRIER=20 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,CV_d_CMeBr,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3br_cl_OPES2D_5_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3br_cl_OPES2D_5_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3br_cl_OPES2D_5_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_d_CMeCl,CV_d_CMeBr 17 | SIGMA=0.05,0.05 18 | BARRIER=5 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,CV_d_CMeBr,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3cl_br_OPES1D_10_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_OPES1D_10_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_OPES1D_10_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_Dd 17 | SIGMA=0.05 18 | BARRIER=10 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_Dd,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3cl_br_OPES1D_20_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_OPES1D_20_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_OPES1D_20_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_Dd 17 | SIGMA=0.05 18 | BARRIER=20 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_Dd,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3cl_br_OPES1D_5_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_OPES1D_5_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_OPES1D_5_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_Dd 17 | SIGMA=0.05 18 | BARRIER=5 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_Dd,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3cl_br_OPES2D_10_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_OPES2D_10_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_OPES2D_10_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_d_CMeCl,CV_d_CMeBr 17 | SIGMA=0.05,0.05 18 | BARRIER=10 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,CV_d_CMeBr,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3cl_br_OPES2D_20_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_OPES2D_20_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_OPES2D_20_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_d_CMeCl,CV_d_CMeBr 17 | SIGMA=0.05,0.05 18 | BARRIER=20 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,CV_d_CMeBr,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_ch3cl_br_OPES2D_5_300K.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef_ch3cl_br_OPES2D_5_300K.dat 4 | INCLUDE FILE=plumed_colvars_ch3cl_br_OPES2D_5_300K.dat 5 | 6 | # Walls on C-H distances 7 | UWALLS DATA=CV_ds_CMeHMe AT=1.4 KAPPA=200 LABEL=uwall_CMeHMe 8 | LWALLS DATA=CV_ds_CMeHMe AT=0.8 KAPPA=200 LABEL=lwall_CMeHMe 9 | LWALLS DATA=CV_ds_ANCNANHMe AT=1.8 KAPPA=200 LABEL=lwall_ANCNANHMe 10 | 11 | # Walls on CMe-X distances (not too far, no dissociation, whatever CH3-X is) 12 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.lowest AT=3.0 KAPPA=200 LABEL=uwall_ds_lowest_CMeClCMeBr 13 | UPPER_WALLS ARG=CV_ds_CMeClCMeBr.highest AT=5.0 KAPPA=200 LABEL=uwall_ds_highest_CMeClCMeBr 14 | 15 | opes: OPES_METAD ... 16 | ARG=CV_d_CMeCl,CV_d_CMeBr 17 | SIGMA=0.05,0.05 18 | BARRIER=5 19 | PACE=2000 20 | TEMP=300 21 | FILE=kernels_000.data 22 | ... 23 | 24 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=CV_d_CMeCl,CV_d_CMeBr,opes.bias FILE=OPES.txt FMT=%8.4f 25 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(CV_.*) FILE=COLVAR.txt FMT=%8.4f 26 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=(uwall_.*),(lwall_.*) FILE=WALLS.txt FMT=%8.4f 27 | 28 | FLUSH STRIDE=_R_PRINT_FREQ_ 29 | 30 | ENDPLUMED 31 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3br_cl_OPES1D_10_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3br_cl_OPES1D_20_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3br_cl_OPES1D_5_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3br_cl_OPES2D_10_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3br_cl_OPES2D_20_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3br_cl_OPES2D_5_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3cl_br_OPES1D_10_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3cl_br_OPES1D_20_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3cl_br_OPES1D_5_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3cl_br_OPES2D_10_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3cl_br_OPES2D_20_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/plumed_colvars_ch3cl_br_OPES2D_5_300K.dat: -------------------------------------------------------------------------------- 1 | # Distances CMe-X 2 | DISTANCE ATOMS=CMe,Cl LABEL=CV_d_CMeCl 3 | DISTANCE ATOMS=CMe,Br LABEL=CV_d_CMeBr 4 | COMBINE ARG=CV_d_CMeCl,CV_d_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_Dd 5 | DISTANCES ATOMS1=CMe,Cl ATOMS2=CMe,Br LOWEST HIGHEST LABEL=CV_ds_CMeClCMeBr 6 | 7 | # Coordinations CMe-X 8 | COORDINATION GROUPA=CMe GROUPB=Cl NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeCl 9 | COORDINATION GROUPA=CMe GROUPB=Br NN=8 MM=16 D_0=0 R_0=2.5 LABEL=CV_CN_CMeBr 10 | COMBINE ARG=CV_CN_CMeCl,CV_CN_CMeBr PERIODIC=NO COEFFICIENTS=1,-1 LABEL=CV_DCN 11 | 12 | # Distances C-H 13 | DISTANCES GROUPA=CMe GROUPB=HMe LOWEST HIGHEST LABEL=CV_ds_CMeHMe 14 | DISTANCES LOWMEM GROUPA=ANCN GROUPB=ANHMe LOWEST HIGHEST LABEL=CV_ds_ANCNANHMe 15 | 16 | # Angle 17 | ANGLE ATOMS=Cl,CMe,Br LABEL=CV_a_ClCMeBr 18 | TORSION ATOMS=H1,H2,H3,CMe LABEL=CV_t_H1H2H3CMe 19 | 20 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/R/user_files/properties.txt: -------------------------------------------------------------------------------- 1 | type 2 | C 1 3 | H 2 4 | Cl 3 5 | Br 4 6 | N 5 7 | 8 | masses 9 | C 12.01100000 10 | H 1.00800000 11 | Cl 35.45000000 12 | Br 79.90400000 13 | N 14.00700000 14 | -------------------------------------------------------------------------------- /examples/sn2_ch3cl_br/initial_dataset/init_ch3br_cl_xxxxx_1001_4001_60/set.000/box.npy: -------------------------------------------------------------------------------- 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/examples/user_files/exploration_lammps/SYSTEM1.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix 1 all nve 24 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 25 | fix 3 all momentum 1 linear 1 1 1 26 | 27 | run _R_NUMBER_OF_STEPS_ 28 | 29 | write_restart _R_RESTART_OUT_ -------------------------------------------------------------------------------- /examples/user_files/exploration_lammps/SYSTEM2.in: -------------------------------------------------------------------------------- 1 | units metal 2 | boundary p p p 3 | atom_style atomic 4 | 5 | neighbor 1.0 bin 6 | neigh_modify every 10 delay 0 check no 7 | 8 | read_data _R_DATA_FILE_ 9 | 10 | pair_style deepmd _R_MODEL_FILES_ out_freq _R_PRINT_FREQ_ out_file _R_DEVI_OUT_ 11 | pair_coeff * * 12 | 13 | timestep _R_TIMESTEP_ 14 | 15 | dump dcd all dcd _R_PRINT_FREQ_ _R_DCD_OUT_ 16 | 17 | thermo_style custom step time etotal ke pe temp press vol density cella cellb cellc cpuremain 18 | thermo_modify flush yes 19 | thermo _R_PRINT_FREQ_ 20 | 21 | velocity all create _R_TEMPERATURE_ _R_SEED_VEL_ dist gaussian 22 | 23 | fix pl all plumed plumedfile _R_PLUMED_IN_ outfile _R_PLUMED_OUT_ 24 | fix 1 all nve 25 | fix 2 all temp/csvr _R_TEMPERATURE_ _R_TEMPERATURE_ $(100.0*dt) _R_SEED_THER_ 26 | fix 3 all momentum 1 linear 1 1 1 27 | 28 | run _R_NUMBER_OF_STEPS_ 29 | 30 | write_restart _R_RESTART_OUT_ -------------------------------------------------------------------------------- /examples/user_files/exploration_lammps/plumed_SYSTEM2.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef__R_SYSTEM_.dat 4 | INCLUDE FILE=plumed_colvars__R_SYSTEM_.dat 5 | 6 | metad: METAD ARG=d1 SIGMA=0.05 HEIGHT=1.0 PACE=1000 7 | 8 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=d1,metad.bias FILE=metad.txt FMT=%8.4f 9 | 10 | FLUSH STRIDE=_R_PRINT_FREQ_ 11 | 12 | ENDPLUMED -------------------------------------------------------------------------------- /examples/user_files/exploration_lammps/plumed_atomdef_SYSTEM2.dat: -------------------------------------------------------------------------------- 1 | ATOM1: GROUP ATOMS=1 2 | ATOM2: GROUP ATOMS=2 -------------------------------------------------------------------------------- /examples/user_files/exploration_lammps/plumed_colvars_SYSTEM2.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=ATOM1,ATOM2 LABEL=d1 2 | 3 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=d1 FILE=COLVAR.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/SYSTEM1.in: -------------------------------------------------------------------------------- 1 | Production 2 | &cntrl 3 | imin=0, 4 | ntx=1, 5 | irest=0, 6 | nstlim=_R_NUMBER_OF_STEPS_, 7 | dt=_R_TIMESTEP_, 8 | ntf=1, 9 | ntc=1, 10 | tempi=_R_TEMPERATURE_, 11 | temp0=_R_TEMPERATURE_, 12 | ntpr=_R_PRINT_FREQ_, 13 | ntwx=_R_PRINT_FREQ_, 14 | cut=10.0, 15 | ntb=1, 16 | ntp=0, 17 | ntt=3, 18 | gamma_ln=2.0, 19 | nmropt=0, 20 | ifqnt=1, 21 | ig=_R_SEED_VEL_, 22 | iwrap=1 23 | / 24 | &qmmm 25 | qmmask=':CHO', 26 | qmcharge=-2, 27 | qm_theory='EXTERN', 28 | qmcut=12, 29 | qm_ewald=0 30 | / 31 | &orc 32 | method='BLYP', 33 | basis='6-31G*', 34 | num_threads=1 35 | / 36 | &wt type='END' / 37 | -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/SYSTEM1.yaml: -------------------------------------------------------------------------------- 1 | backend: deepmd 2 | deepmd_model: 3 | - model1.pb 4 | - model2.pb 5 | - model3.pb 6 | deepmd_deviation: deviation.dat 7 | device: null 8 | energy_file: emle_energy.txt 9 | energy_frequency: 0 10 | external_backend: null 11 | interpolate_steps: null 12 | lambda_interpolate: null 13 | log_file: emle_log.txt 14 | log_level: ERROR 15 | method: electrostatic 16 | mm_charges: null 17 | model: model.mat 18 | orca_path: null 19 | orca_template: null 20 | parm7: null 21 | plugin_path: null 22 | qm_indices: null 23 | rascal_model: null 24 | restart: false 25 | sqm_theory: null 26 | qm_xyz_file: null 27 | qm_xyz_frequency: null 28 | -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/SYSTEM2.in: -------------------------------------------------------------------------------- 1 | Production 2 | &cntrl 3 | imin=0, 4 | ntx=1, 5 | irest=0, 6 | nstlim=_R_NUMBER_OF_STEPS_, 7 | dt=_R_TIMESTEP_, 8 | ntf=1, 9 | ntc=1, 10 | tempi=_R_TEMPERATURE_, 11 | temp0=_R_TEMPERATURE_, 12 | ntpr=_R_PRINT_FREQ_, 13 | ntwx=_R_PRINT_FREQ_, 14 | cut=10.0, 15 | ntb=1, 16 | ntp=0, 17 | ntt=3, 18 | gamma_ln=2.0, 19 | nmropt=0, 20 | ifqnt=1, 21 | ig=_R_SEED_VEL_, 22 | iwrap=1, 23 | plumed=1, 24 | plumedfile='_R_PLUMED_IN_' 25 | / 26 | &qmmm 27 | qmmask=':CHO', 28 | qmcharge=-2, 29 | qm_theory='EXTERN', 30 | qmcut=12, 31 | qm_ewald=0 32 | / 33 | &orc 34 | method='BLYP', 35 | basis='6-31G*', 36 | num_threads=1 37 | / 38 | &wt type='END' / 39 | -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/SYSTEM2.yaml: -------------------------------------------------------------------------------- 1 | backend: deepmd 2 | deepmd_model: 3 | - model1.pb 4 | - model2.pb 5 | - model3.pb 6 | deepmd_deviation: deviation.dat 7 | device: null 8 | energy_file: emle_energy.txt 9 | energy_frequency: 0 10 | external_backend: null 11 | interpolate_steps: null 12 | lambda_interpolate: null 13 | log_file: emle_log.txt 14 | log_level: ERROR 15 | method: electrostatic 16 | mm_charges: null 17 | model: model.mat 18 | orca_path: null 19 | orca_template: null 20 | parm7: null 21 | plugin_path: null 22 | qm_indices: null 23 | rascal_model: null 24 | restart: false 25 | sqm_theory: null 26 | qm_xyz_file: null 27 | qm_xyz_frequency: null 28 | -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/plumed_SYSTEM2.dat: -------------------------------------------------------------------------------- 1 | UNITS LENGTH=A ENERGY=kcal/mol 2 | 3 | INCLUDE FILE=plumed_atomdef__R_SYSTEM_.dat 4 | INCLUDE FILE=plumed_colvars__R_SYSTEM_.dat 5 | 6 | metad: METAD ARG=d1 SIGMA=0.05 HEIGHT=1.0 PACE=1000 7 | 8 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=d1,metad.bias FILE=metad.txt FMT=%8.4f 9 | 10 | FLUSH STRIDE=_R_PRINT_FREQ_ 11 | 12 | ENDPLUMED -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/plumed_atomdef_SYSTEM2.dat: -------------------------------------------------------------------------------- 1 | ATOM1: GROUP ATOMS=1 2 | ATOM2: GROUP ATOMS=2 -------------------------------------------------------------------------------- /examples/user_files/exploration_sander_emle/plumed_colvars_SYSTEM2.dat: -------------------------------------------------------------------------------- 1 | DISTANCE ATOMS=ATOM1,ATOM2 LABEL=d1 2 | 3 | PRINT STRIDE=_R_PRINT_FREQ_ ARG=d1 FILE=COLVAR.txt FMT=%8.4f -------------------------------------------------------------------------------- /examples/user_files/labeling_orca/1_SYSTEM1_labeling_XXXXX_myHPCkeyword1.inp: -------------------------------------------------------------------------------- 1 | ! B3LYP D3BJ 6-31G* TightSCF NoFrozenCore KeepDens Engrad 2 | 3 | %MaxCore 1024 4 | 5 | %pal nprocs _R_NB_MPI_ end 6 | 7 | %elprop Polar 1 end 8 | 9 | *xyzfile -2 1 labeling_XXXXX.xyz 10 | -------------------------------------------------------------------------------- /examples/user_files/labeling_orca/1_SYSTEM2_labeling_XXXXX_myHPCkeyword1.inp: -------------------------------------------------------------------------------- 1 | ! B3LYP D3BJ 6-31G* TightSCF NoFrozenCore KeepDens Engrad 2 | 3 | %MaxCore 1024 4 | 5 | %pal nprocs _R_NB_MPI_ end 6 | 7 | %elprop Polar 1 end 8 | 9 | *xyzfile -2 1 labeling_XXXXX.xyz 10 | -------------------------------------------------------------------------------- /examples/user_files/training_deepmd/training_2.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "model": { 3 | "type_map": ["O", "H"], 4 | "descriptor": { 5 | "type": "se_e2_a", 6 | "sel": [46, 92], 7 | "rcut_smth": 0.50, 8 | "rcut": 6.00, 9 | "neuron": [25, 50, 100], 10 | "resnet_dt": false, 11 | "axis_neuron": 16, 12 | "type_one_side": true, 13 | "precision": "float64", 14 | "seed": 1 15 | }, 16 | "fitting_net": { 17 | "neuron": [240, 240, 240], 18 | "resnet_dt": true, 19 | "precision": "float64", 20 | "seed": 1 21 | } 22 | }, 23 | "learning_rate": { 24 | "type": "exp", 25 | "decay_steps": 5000, 26 | "start_lr": 0.001, 27 | "stop_lr": 1.0e-6 28 | }, 29 | "loss": { 30 | "type": "ener", 31 | "start_pref_e": 0.02, 32 | "limit_pref_e": 2.0, 33 | "start_pref_f": 1000.0, 34 | "limit_pref_f": 1.0, 35 | "start_pref_v": 0.0, 36 | "limit_pref_v": 0.0 37 | }, 38 | "training": { 39 | "seed": 10, 40 | "numb_steps": 1000000, 41 | "disp_file": "lcurve.out", 42 | "disp_freq": 1000, 43 | "numb_test": 0, 44 | "save_freq": 1000, 45 | "save_ckpt": "model.ckpt", 46 | "disp_training": true, 47 | "time_training": true, 48 | "profiling": false, 49 | "training_data": { 50 | "systems": ["../data/"], 51 | "batch_size": 1, 52 | "set_prefix": "set" 53 | } 54 | } 55 | } -------------------------------------------------------------------------------- /examples/user_files/training_deepmd/training_2.2.json: -------------------------------------------------------------------------------- 1 | { 2 | "model": { 3 | "type_map": ["O", "H"], 4 | "descriptor": { 5 | "type": "se_e2_a", 6 | "sel": [46, 92], 7 | "rcut_smth": 0.50, 8 | "rcut": 6.00, 9 | "neuron": [25, 50, 100], 10 | "resnet_dt": false, 11 | "axis_neuron": 16, 12 | "type_one_side": true, 13 | "precision": "float64", 14 | "seed": 1 15 | }, 16 | "fitting_net": { 17 | "neuron": [240, 240, 240], 18 | "resnet_dt": true, 19 | "precision": "float64", 20 | "seed": 1 21 | } 22 | }, 23 | "learning_rate": { 24 | "type": "exp", 25 | "decay_steps": 5000, 26 | "start_lr": 0.001, 27 | "stop_lr": 1.0e-6 28 | }, 29 | "loss": { 30 | "type": "ener", 31 | "start_pref_e": 0.02, 32 | "limit_pref_e": 2.0, 33 | "start_pref_f": 1000.0, 34 | "limit_pref_f": 1.0, 35 | "start_pref_v": 0.0, 36 | "limit_pref_v": 0.0 37 | }, 38 | "training": { 39 | "seed": 10, 40 | "numb_steps": 1000000, 41 | "disp_file": "lcurve.out", 42 | "disp_freq": 1000, 43 | "numb_test": 0, 44 | "save_freq": 1000, 45 | "save_ckpt": "model.ckpt", 46 | "disp_training": true, 47 | "time_training": true, 48 | "profiling": false, 49 | "training_data": { 50 | "systems": ["../data/"], 51 | "batch_size": 1, 52 | "set_prefix": "set" 53 | } 54 | } 55 | } -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- 1 | site_name: ArcanNN - Training 2 | Home: index.md 3 | plugins: 4 | - search 5 | - awesome-pages 6 | - markdownextradata 7 | theme: readthedocs 8 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | pip>=21.3 2 | setuptools>=58.5 3 | wheel>=0.38 4 | numpy>=1.22 5 | pyyaml>=6.0 -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | 3 | setup( 4 | name="arcann_training", 5 | version="1.0.0", 6 | author="Rolf David", 7 | author_email="", 8 | description="", 9 | url="https://github.com/arcann-chem/arcann", 10 | license="GNU Affero General Public License v3", 11 | packages=find_packages(), 12 | package_data={ 13 | "arcann_training.assets": ["*.json"], 14 | "arcann_training.assets.others": ["*.in", "*.tcl"], 15 | }, 16 | classifiers=[ 17 | "Development Status :: 4 - Beta", 18 | "License :: OSI Approved :: GNU Affero General Public License v3", 19 | "Intended Audience :: Science/Research", 20 | "Programming Language :: Python :: 3", 21 | "Programming Language :: Python :: 3.7", 22 | "Programming Language :: Python :: 3.8", 23 | "Programming Language :: Python :: 3.9", 24 | "Programming Language :: Python :: 3.10", 25 | "Programming Language :: Python :: 3.11", 26 | ], 27 | python_requires=">=3.7", 28 | install_requires=["numpy>=1.15", "pyyaml>=3.13"], 29 | ) 30 | -------------------------------------------------------------------------------- /tools/force_explorations.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #----------------------------------------------------------------------------------------------------# 3 | # ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks # 4 | # Copyright 2022-2024 ArcaNN developers group # 5 | # # 6 | # SPDX-License-Identifier: AGPL-3.0-only # 7 | #----------------------------------------------------------------------------------------------------# 8 | # Created: 2024/05/26 9 | # Last modified: 2024/06/27 10 | #----------------------------------------------------------------------------------------------------# 11 | 12 | # Check if the input file exists 13 | input_file="failed_explorations.txt" 14 | if [[ ! -f "$input_file" ]]; then 15 | echo "Error: File '$input_file' not found!" 16 | exit 1 17 | fi 18 | 19 | # Read the input file line by line 20 | while IFS= read -r directory; do 21 | # Trim leading and trailing whitespaces 22 | directory=$(echo "$directory" | xargs) 23 | 24 | # Check if the directory is not empty 25 | if [[ -n "$directory" ]]; then 26 | # Create the "force" file in the directory 27 | touch "$directory/force" && echo "Created force file in: $directory" 28 | else 29 | echo "Warning: Empty line encountered in the input file." 30 | fi 31 | done < "$input_file" 32 | 33 | echo "Script execution completed." -------------------------------------------------------------------------------- /tools/skip_labeling.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #----------------------------------------------------------------------------------------------------# 3 | # ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks # 4 | # Copyright 2022-2024 ArcaNN developers group # 5 | # # 6 | # SPDX-License-Identifier: AGPL-3.0-only # 7 | #----------------------------------------------------------------------------------------------------# 8 | # Created: 2024/05/26 9 | # Last modified: 2024/06/27 10 | #----------------------------------------------------------------------------------------------------# 11 | 12 | # Check if the input file is provided as an argument 13 | if [[ -z "$1" ]]; then 14 | echo "Error: No input file specified!" 15 | echo "Usage: $0 " 16 | exit 1 17 | fi 18 | 19 | # Check if the input file exists 20 | input_file="$1" 21 | if [[ ! -f "$input_file" ]]; then 22 | echo "Error: File '$input_file' not found!" 23 | exit 1 24 | fi 25 | 26 | # Read the input file line by line 27 | while IFS= read -r line; do 28 | # Trim leading and trailing whitespaces 29 | line=$(echo "$line" | xargs) 30 | directory=$(dirname "$line") 31 | 32 | # Check if the directory is not empty 33 | if [[ -n "$directory" ]]; then 34 | # Create the "skip" file in the directory 35 | touch "$directory/skip" && echo "Created skip file in: $directory" 36 | else 37 | echo "Warning: Empty line encountered in the input file." 38 | fi 39 | done < "$input_file" 40 | 41 | echo "Script execution completed." --------------------------------------------------------------------------------