Downloading files in RiD-kit
The download command is executed through
rid download WORKFLOW_ID -p STEP-KEY -f FILE_NAME -a ITERATION_START -e ITERATION_END -o OUTPUT_DIR
ITERATION_START(default 1) specifies from which iteration to start download, ITERATION_END(default 100) specifies to which iteration to end download. OUTPUT_DIR(default “./”) is the output directories of the download.
The STEP-KEY in rid includes the following steps: prep-exploration, run-exploration, prep-select, run-select, prep-label, run-label, label-stats, collect-data, merge-data, train, model-devi.
The FILE_NAME in prep-exploration includes task_path. Which represents the input directory for Exploration MD simulation.
The FILE_NAME in run-exploration includes trajectory, conf_out,plm_out,md_log,bias_fig, model_devi_fig, dp_model_devi_fig (optional), dp_model_devi (optional), dp_selected_indices (optional), dp_selected_confs (optional), projected_fig (optional).
The trajectory represents the trajectories of each walker produced by the Exploration MD, conf_out represents the last frame in the trajectories and will be used in the next iteration, plm_out represents the CV output from PLUMED, md_log is the log file from the molecular dynamics simulation, bias_fig is the figure showing the biasing potential used in the simulation, model_devi_fig is the figure showing the deviation of the free energy model used in the simulation, dp_model_devi_fig (optional) is the figure showing the deviation of the Deep Potential (DP) model used in the simulation, dp_model_devi (optional) contains numerical data on the deviation of the Deep Potential model used in the simulation, dp_selected_indices (optional) contains the indices of configurations with high dp model deviation selected for further analysis or training, dp_selected_confs (optional) contains the actual configurations high dp model deviation, projected_fig (optional) is the figure showing some projection of the simulation trajectory, currently only support for projection on the path CV.
The FILE_NAME in prep-select includes cluster_fig, cluster_selection_index, cluster_selection_data.
The cluster_fig is the figure showing the distribution of the clusters on the trajectories, cluster_selection_index contains the indices of the configurations from each cluster, cluster_selection_data contains the actual configurations selected from each cluster.
The FILE_NAME in run-select includes selected_confs, selected_cv_init, model_devi, selected_indices,selected_conf_tags.
The selected_confs contains the configurations that have been selected for labeling MD in the next step, selected_cv_init contains the initial values of the collective variables (CVs) for the selected configurations, model_devi contains the deviation of the free energy model on the selected configurations from the last prep-select step, selected_indices contains the indices of the selected configurations, selected_conf_tags contains tags for the selected configurations.
The FILE_NAME in prep-label includes task_path. Which represents the input directory for Exploration MD simulation.
The FILE_NAME in run-label includes plm_out, cv_forces, mf_info, mf_fig,md_log.
The plm_out represents the CV output from PLUMED, cv_forces contains the collective variables (CVs) and the mean forces obtained from the simulation, mf_info contains information about the mean force (MF) calculated during the simulation, including the values and the standard deviation, mf_fig is the figure showing the running average of the mean force as a function of time, md_log is a log file from the MD simulation.
The FILE_NAME in label-stats includes mf_std_fig and cv_forces.
The mf_std_fig is a histogram showing the distribution of the standard deviation of the mean force, cv_forces is a filtered version of the same file in last run-label step, removing mean forces with high standard deviation.
The FILE_NAME in collect-data includes data_new. Which is the .npy file combining all the cv_forces files in the last step, represents the new training data.
The FILE_NAME in merge-data includes data_raw. Which is the .npy file containing all the training data in the previous iterations.
The FILE_NAME in train includes model, train_log, train_fig.
The model is the trained free energy model, train_log is the log of the training process. train_fig represents the training error during the training process.
The FILE_NAME in model_devi includes model_devi, model_devi_fig.
The model_devi is the model deviation on the trajectories of each walker using the newly trained free energy model, model_devi_fig is the figure of the model deviation.