doc: update model_devi

doc/manual/model-deviation.md

@@ -13,26 +13,25 @@ TODO
 When you run multiple LAMMPS simulations with deepmd-kit, you may want to filter out the structures with model deviation for the next round. Consider the following example:
 
 * There are several LAMMPS jobs under path: `./workdir/lammps/*`
-* The trajectory of each job is stored in `./workdir/lammps/*/traj/*.lammpstrj`
+* The trajectory of each job is stored in `./workdir/lammps/*/dump.lammpstrj`
 * The model deviation of each job is stored in `./workdir/lammps/*/model_devi.out`
 * You want to filter out the structures whose max_devi_f is between 0.1 and 0.2
 
 Then you can use the following command to filter out the structures with model deviation:
 
 ```bash
-ai2-kit tool ase read "./workdir/lammps/*/traj/*.lammpstrj" --nat_sort \
-  - to_model_devi "./workdir/lammps/*/model_devi.out" \
+ai2-kit tool model_devi read "./workdir/lammps/*" --traj_file dump.lammpstrj --md_file model_devi.out \
   - grade --lo 0.1 --hi 0.2 --col max_devi_f \
   - dump_stats stats.tsv \
-  - to_ase --level bad \
-  - write bad.xyz
+  - write decent.xyz --level decent
 ```
 
 Explanation of the command:
-* The double quotes are required to prevent shell expansion of `*`. You must use double quotes with `ase read` and `to_model_devi` to avoid undetermined behavior.
-* The `--nat_sort` is used to sort the trajectory by the number of atoms in each frame. It's used to ensure the order of the trajectory is consistent with the model deviation file. 
-* The `to_model_devi` command is used to read the model deviation file. Note that the path of the model deviation file must be consistent with the trajectory file.
-* The `grade` command is used to grade the structures by the model deviation. The `--lo` and `--hi` are used to set the lower and upper bound of the model deviation. The structures whose  `max_devi_f` is below lo, between lo and hi, and above hi are graded as `good`, `bad`, and `ugly`, respectively.
-* The `dump_stats` command is used to dump the statistics of the grading to a file. The statistics include the number of structures in each grade.
- * The `to_ase` command is used to hand over selected structures back to `ase toolkit`. The `--level` is used to select the grade of the structures. The `bad` level is used to select the structures graded as `bad`.
-* The `write` command is used to write the selected structures to a file. The `bad.xyz` is the output file name.
+
+* `ai2-kit tool model_devi read "./workdir/lammps/*" --traj_file dump.lammpstrj --md_file model_devi.out`: read all LAMMPS trajectory and model deviation files
+
+* `- grade --lo 0.1 --hi 0.2 --col max_devi_f`: grade the structures by `max_devi_f` column, and grade the structures into 3 levels: `good`, `decent`, and `poor`. The structures with `max_devi_f` between 0.1 and 0.2 are graded as `decent`, and the structures with `max_devi_f` less than 0.1 are graded as `good`, and the structures with `max_devi_f` greater than 0.2 are graded as `poor`.
+
+* `- dump_stats stats.tsv`: dump the statistics of the grading process to `stats.tsv`
+
+* `- write decent.xyz --level decent`: write the structures with grade `decent` to `decent.xyz`