Add documentation (#79)

* fix bugs of import functions

* fix bug of context

* add example of new input

* new format of submit input. add dargs check.

* command line option for old-style compatibility

* fix s3 config of commands

* add showkey, fix minor issues

* add missing file

* fix bug

* add guidance for dpgen2 command and input scripts.

Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>

docs/alloy_configs.rst

@@ -0,0 +1,7 @@
+Alloy configs
+=============
+
+.. _alloy configs:
+.. dargs::
+   :module: dpgen2.utils.alloy_conf
+   :func: generate_alloy_conf_args

docs/cli.rst

@@ -1,6 +1,7 @@
 Command line interface
 ======================
 
+.. _fullcli:
 .. argparse::
    :module: dpgen2.entrypoint.main
    :func: main_parser

docs/index.rst

@@ -12,8 +12,13 @@ DPGEN2 is the 2nd generation of the Deep Potential GENerator.
    :maxdepth: 3
    :caption: User Guide
 
+   quickcli
    cli
+   input.md
+   submit_args
    op_configs
+   alloy_configs
+   step_configs
 
 .. _developer-guide:
 
@@ -31,4 +36,4 @@ DPGEN2 is the 2nd generation of the Deep Potential GENerator.
 * :ref:`search`
 
 .. _feedback: 
-.. _affiliated packages: 
+.. _affiliated packages: 

docs/input.md

@@ -0,0 +1,178 @@
+(inputscript)=
+# Guide on writing input scripts for dpgen2 commands
+
+## Preliminaries
+
+The reader of this doc is assumed to be familiar with the concurrent learning algorithm that the dpgen2 implements. If not, one may check [this paper](https://doi.org/10.1016/j.cpc.2020.107206).
+
+## The input script for all dpgen2 commands
+
+For all the dpgen2 commands, one need to provide `dflow2` global configurations. For example,
+```json
+    "dflow_config" : {
+	"host" : "http://address.of.the.host:port"
+    },
+    "dflow_s3_config" : {
+	"s3_endpoint" : "address.of.the.s3.sever:port"
+    },
+```
+The `dpgen` simply pass all keys of `"dflow_config"` to `dflow.config` and all keys of `"dflow_s3_config"` to `dflow.s3_config`. 
+
+
+## The input script for `submit` and `resubmit`
+
+The full documentation of the `submit` and `resubmit` script can be [found here](submitargs). This documentation provides a fast guide on how to write the input script.
+
+In the input script of `dpgen2 submit` and `dpgen2 resubmit`, one needs to provide the definition of the workflow and how they are executed in the input script. One may find an example input script in the [dpgen2 Al-Mg alloy example](../examples/almg/input.json).
+
+The definition of the workflow can be provided by the following sections:
+
+### Inputs
+
+This section provides the inputs to start a dpgen2 workflow. An example for the Al-Mg alloy 
+```json
+"inputs": {
+	"type_map":		["Al", "Mg"],
+	"mass_map":		[27, 24],
+	"init_data_sys":	[
+		"path/to/init/data/system/0",
+		"path/to/init/data/system/1"
+	],
+}
+```
+The key `"init_data_sys"` provides the initial training data to kick-off the training of deep potential (DP) models.
+
+
+### Training
+
+This section defines how a model is trained. 
+```json
+"train" : {
+	"type" : "dp",
+	"numb_models" : 4,
+	"config" : {},
+	"template_script" : {
+		"_comment" : "omitted content of tempalte script"
+	},
+	"_comment" : "all"
+}
+```
+The `"type" : "dp"` tell the traning method is `"dp"`, i.e. calling [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit) to train DP models. 
+The `"config"` key defines the training configs, see [the full documentation](rundptrainargs). 
+The `"template_script"` provides the template training script in `json` format. 
+
+
+### Exploration
+
+This section defines how the configuration space is explored. 
+```json
+"explore" : {
+	"type" : "lmp",
+	"config" : {
+		"command": "lmp -var restart 0"
+	},
+	"max_numb_iter" :	5,
+	"conv_accuracy" :	0.9,
+	"fatal_at_max" :	false,
+	"f_trust_lo":		0.05,
+	"f_trust_hi":		0.50,
+	"configurations":	[
+		{
+		"lattice" : ["fcc", 4.57],
+		"replicate" : [2, 2, 2],
+		"numb_confs" : 30,
+		"concentration" : [[1.0, 0.0], [0.5, 0.5], [0.0, 1.0]]
+		}
+		{
+		"lattice" : ["fcc", 4.57],
+		"replicate" : [3, 3, 3],
+		"numb_confs" : 30,
+		"concentration" : [[1.0, 0.0], [0.5, 0.5], [0.0, 1.0]]
+		}
+	],
+	"stages":	[
+		{ "_idx": 0, "ensemble": "nvt", "nsteps": 20, "press": null, "conf_idx": [0], "temps": [50,100], "trj_freq": 10, "n_sample" : 3 },
+		{ "_idx": 1, "ensemble": "nvt", "nsteps": 20, "press": null, "conf_idx": [1], "temps": [50,100], "trj_freq": 10, "n_sample" : 3 }
+	],
+}
+```
+The `"type" : "lmp"` means that configurations are explored by LAMMPS DPMD runs. 
+The `"config"` key defines the lmp configs, see [the full documentation](runlmpargs). 
+The `"configurations"` provides the initial configurations (coordinates of atoms and the simulation cell) of the DPMD simulations. It is a list. The elements of the list can be 
+
+- `list[str]`: The strings provides the path to the configuration files.
+- `dict`: Automatic alloy configuration generator. See [the detailed doc](alloy_configs) of the allowed keys.
+
+The `"stages"` defines the exploration stages. It is a list of `dict`s, with each `dict` defining a stage. The `"ensemble"`, `"nsteps"`, `"press"`, `"temps"`, `"traj_freq"` keys are self-explanatory. `"conf_idx"` pickes initial configurations of DPMD simulations from the `"configurations"` list, it provides the index of the element in the `"configurations"` list. `"n_sample"` tells the number of confgiruations randomly sampled from the set picked by `"conf_idx"` for each thermodynamic state. All configurations picked by `"conf_idx"` has the same possibility to be sampled. The default value of `"n_sample"` is `null`, in this case all picked configurations are sampled. In the example, each stage have 3 samples and 2 thermodynamic states (NVT, T=50 and 100K), then each iteration run 3x2=6 NVT DPMD simulatins.
+
+
+### FP
+
+This section defines the first-principle (FP) calculation . 
+
+```json
+"fp" : {
+	"type" :	"vasp",
+	"config" : {
+		"command": "source /opt/intel/oneapi/setvars.sh && mpirun -n 16 vasp_std"
+	},
+	"task_max":	2,
+	"pp_files":	{"Al" : "vasp/POTCAR.Al", "Mg" : "vasp/POTCAR.Mg"},
+	"incar":         "vasp/INCAR",
+	"_comment" : "all"
+}
+```
+The `"type" : "vasp"` means that first-principles are VASP calculations. 
+The `"config"` key defines the vasp configs, see [the full documentation](runvaspargs). 
+The `"task_max"` key defines the maximal number of vasp calculations in each dpgen2 iteration.
+The `"pp_files"` and `"incar"` keys provides the pseudopotential files and the template incar file.
+
+
+### Configuration of dflow step
+
+The execution units of the dpgen2 are the dflow `Step`s. How each step is executed is defined by the `"step_configs"`.
+```json
+"step_configs":{
+	"prep_train_config" : {
+		"_comment" : "content omitted"
+	},
+	"run_train_config" : {
+		"_comment" : "content omitted"
+	},
+	"prep_explore_config" : {
+		"_comment" : "content omitted"
+	},
+	"run_explore_config" : {
+		"_comment" : "content omitted"
+	},
+	"prep_fp_config" : {
+		"_comment" : "content omitted"
+	},
+	"run_fp_config" : {
+		"_comment" : "content omitted"
+	},
+	"select_confs_config" : {
+		"_comment" : "content omitted"
+	},
+	"collect_data_config" : {
+		"_comment" : "content omitted"
+	},
+	"cl_step_config" : {
+		"_comment" : "content omitted"
+	},
+	"_comment" : "all"
+},
+```
+The configs for prepare training, run training, prepare exploration, run exploration, prepare fp, run fp, select configurations, collect data and concurrent learning steps are given correspondingly.
+
+The readers are refered to [this page](stepconfigargs) for a full documentation of the step configs.
+
+Any of the config in the `step_configs` can be ommitted. If so, the configs of the step is set to the default step configs, which is provided by the following section, for example,
+```json
+"default_step_config" : {
+	"template_config" : {
+	    "image" : "dpgen2:x.x.x"
+	}
+},
+```
+The way of writing the `default_step_config` is the same as any step config in the `step_configs`. One may refer to [this page](stepconfigargs) for full documentation.

docs/op_configs.rst

@@ -3,18 +3,21 @@ OP Configs
 
 RunDPTrain
 ----------
+.. _rundptrainargs:
 .. dargs::
    :module: dpgen2.op.run_dp_train
    :func: config_args
 
 RunLmp
 ------
+.. _runlmpargs:
 .. dargs::
    :module: dpgen2.op.run_lmp
    :func: config_args
 
 RunVasp
 -------
+.. _runvaspargs:
 .. dargs::
    :module: dpgen2.op.run_vasp
    :func: config_args

docs/quickcli.md

@@ -0,0 +1,86 @@
+# Guide on dpgen2 commands
+
+One may use dpgen2 through command line interface. A full documentation of the cli is found [here](fullcli)
+
+## Submit a workflow 
+The dpgen2 workflow can be submitted via the `submit` command
+```bash
+dpgen2 submit input.json
+```
+where `input.json` is the input script. A guide of writing the script is found [here](inputscript).
+When a workflow is submitted, a ID (WFID) of the workflow will be printed for later reference.
+
+## Check the convergence of a workflow
+The convergence of stages of the workflow can be checked by the `status` command. It prints the indexes of the finished stages, iterations, and the accurate, candidate and failed ratio of explored configurations of each iteration. 
+```bash
+$ dpgen2 status input.json WFID
+#   stage  id_stg.    iter.      accu.      cand.      fail.
+# Stage    0  --------------------
+        0        0        0     0.8333     0.1667     0.0000
+        0        1        1     0.7593     0.2407     0.0000
+        0        2        2     0.7778     0.2222     0.0000
+        0        3        3     1.0000     0.0000     0.0000
+# Stage    0  converged YES  reached max numb iterations NO 
+# All stages converged
+```
+
+## Watch the progress of a workflow
+The progress of a workflow can be watched on-the-fly
+```bash
+$ dpgen2 watch input.json WFID
+INFO:root:steps iter-000000--prep-run-train----------------------- finished
+INFO:root:steps iter-000000--prep-run-lmp------------------------- finished
+INFO:root:steps iter-000000--prep-run-fp-------------------------- finished
+INFO:root:steps iter-000000--collect-data------------------------- finished
+INFO:root:steps iter-000001--prep-run-train----------------------- finished
+INFO:root:steps iter-000001--prep-run-lmp------------------------- finished
+...
+```
+The artifacts can be downloaded on-the-fly with `-d` flag.
+
+
+## Show the keys of steps
+
+Each dpgen2 step is assigned a unique key. The keys of the finished steps can be checked with `showkey` command
+```bash                                                                                                                                                                              $ dpgen2 watch input.json WFID
+                   0 : init--scheduler
+                   1 : init--id
+                   2 : iter-000000--prep-train
+              3 -> 6 : iter-000000--run-train-0000 -> iter-000000--run-train-0003
+                   7 : iter-000000--prep-run-train
+                   8 : iter-000000--prep-lmp
+             9 -> 17 : iter-000000--run-lmp-000000 -> iter-000000--run-lmp-000008
+                  18 : iter-000000--prep-run-lmp
+                  19 : iter-000000--select-confs
+                  20 : iter-000000--prep-fp
+            21 -> 24 : iter-000000--run-fp-000000 -> iter-000000--run-fp-000003
+                  25 : iter-000000--prep-run-fp
+                  26 : iter-000000--collect-data
+                  27 : iter-000000--block
+                  28 : iter-000000--scheduler
+                  29 : iter-000000--id
+                  30 : iter-000001--prep-train
+            31 -> 34 : iter-000001--run-train-0000 -> iter-000001--run-train-0003
+                  35 : iter-000001--prep-run-train
+                  36 : iter-000001--prep-lmp
+            37 -> 45 : iter-000001--run-lmp-000000 -> iter-000001--run-lmp-000008
+                  46 : iter-000001--prep-run-lmp
+                  47 : iter-000001--select-confs
+                  48 : iter-000001--prep-fp
+            49 -> 52 : iter-000001--run-fp-000000 -> iter-000001--run-fp-000003
+                  53 : iter-000001--prep-run-fp
+                  54 : iter-000001--collect-data
+                  55 : iter-000001--block
+                  56 : iter-000001--scheduler
+                  57 : iter-000001--id
+```
+
+
+## Resubmit a workflow
+
+If a workflow stopped abnormally, one may submit a new workflow with some steps of the old workflow reused. 
+```bash
+dpgen2 resubmit input.json WFID --reuse 0-49
+```
+The steps of workflow WDID 0-49 will be reused in the new workflow. The indexes of the steps are printed by `dpgen2 showkey`. In the example, all the steps before the `iter-000001--run-fp-000000` will be used in the new workflow.
+

docs/step_configs.rst

@@ -0,0 +1,9 @@
+Step Configs
+============
+
+.. _stepconfigargs:
+Configurations for dflow steps
+------------------------------
+.. dargs::
+   :module: dpgen2.utils.step_config
+   :func: step_conf_args

docs/submit_args.rst

@@ -0,0 +1,7 @@
+Arguments of the submit script
+==============================
+
+.. _submitargs:
+.. dargs::
+   :module: dpgen2.entrypoint.submit_args
+   :func: submit_args

dpgen2/entrypoint/main.py

@@ -21,6 +21,9 @@
 from .status import (
     status,
 )
+from .showkey import (
+    showkey,
+)
 from .download import (
     download,
 )
@@ -93,6 +96,21 @@ def main_parser() -> argparse.ArgumentParser:
         "-o", "--old-compatible", action='store_true', help="compatible with old-style input script used in dpgen2 < 0.0.6."
     )
 
+    ##########################################
+    # show key
+    parser_showkey = subparsers.add_parser(
+        "showkey",
+        help="Print the keys of the successful DPGEN2 steps",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser_showkey.add_argument(
+        "CONFIG", help="the config file in json format."
+    )
+    parser_showkey.add_argument(
+        "ID", help="the ID of the existing workflow."
+    )
+
+
     ##########################################
     # status
     parser_status = subparsers.add_parser(
@@ -213,6 +231,13 @@ def main():
         status(
             wfid, config,
         )        
+    elif args.command == "showkey":
+        with open(args.CONFIG) as fp:
+            config = json.load(fp)
+        wfid = args.ID
+        showkey(
+            wfid, config,
+        )        
     elif args.command == "download":
         with open(args.CONFIG) as fp:
             config = json.load(fp)