Merge pull request #23 from ZLI-afk/devel

add gamma-line calculations for bcc and fcc

README.md

@@ -499,9 +499,8 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
 | **use_ele_temp** | int | 0 | Currently only support fp_style vasp. 0(default): no electron temperature. 1: eletron temperature as frame parameter. 2: electron temperature as atom parameter.
 | *#Data*
  | init_data_prefix | String | "/sharedext4/.../data/" | Prefix of initial data directories
- | ***init_data_sys*** | List of string|["CH4.POSCAR.01x01x01/.../deepmd"] |Directories of initial data. You may use either absolute or relative path here.
+ | ***init_data_sys*** | List of string|["CH4.POSCAR.01x01x01/.../deepmd"] |Directories of initial data. You may use either absolute or relative path here. Systems will be detected recursively in the directories.
  | ***sys_format*** | String | "vasp/poscar" | Format of initial data. It will be `vasp/poscar` if not set.
- | init_multi_systems | Boolean | false | If set to `true`, `init_data_sys` directories should contain sub-directories of various systems. DP-GEN will regard all of these sub-directories as inital data systems.
  | init_batch_size   | String of integer     | [8]                                                            | Each number is the batch_size of corresponding system  for training in `init_data_sys`. One recommended rule for setting the `sys_batch_size` and `init_batch_size` is that `batch_size` mutiply number of atoms ot the stucture should be larger than 32. If set to `auto`, batch size will be 32 divided by number of atoms. |
   | sys_configs_prefix | String | "/sharedext4/.../data/" | Prefix of `sys_configs`
  | **sys_configs**   | List of list of string         | [<br />["/sharedext4/.../POSCAR"], <br />["....../POSCAR"]<br />] | Containing directories of structures to be explored in iterations.Wildcard characters are supported here. |
@@ -571,7 +570,7 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
 | **user_fp_params** | Dict |  |Parameters for cp2k calculation. find detail in manual.cp2k.org. only the kind section must be set before use.  we assume that you have basic knowledge for cp2k input.
 | **external_input_path** | String |  | Conflict with key:user_fp_params, use the template input provided by user, some rules should be followed, read the following text in detail.
 | *fp_style == ABACUS*
-| **user_fp_params** | Dict |  |Parameters for ABACUS INPUT. find detail [Here](https://github.com/deepmodeling/abacus-develop/blob/develop/docs/input-main.md#out-descriptor). If `deepks_model` is set, the model file should be in the pseudopotential directory. 
+| **user_fp_params** | Dict |  |Parameters for ABACUS INPUT. find detail [Here](https://github.com/deepmodeling/abacus-develop/blob/develop/docs/input-main.md#out-descriptor). If `deepks_model` is set, the model file should be in the pseudopotential directory. You can also set `KPT` file by adding `k_points` that corresponds to a list of six integers in this dictionary.
 | **fp_orb_files** | List |  |List of atomic orbital files. The files should be in pseudopotential directory. 
 | **fp_dpks_descriptor** | String |  |DeePKS descriptor file name. The file should be in pseudopotential directory. 
 
@@ -1086,7 +1085,6 @@ Here is an example of `param.json` for QM7 dataset:
         },
         "_comment": "that's all"
     },
-    "use_clusters": true,
     "fp_style": "gaussian",
     "shuffle_poscar": false,
     "fp_task_max": 1000,
@@ -1109,7 +1107,7 @@ Here is an example of `param.json` for QM7 dataset:
 }
 ```
 
-Here `pick_data` is the data to simplify and currently only supports `MultiSystems` containing `System` with `deepmd/npy` format, and `use_clusters` should always be `true`. `init_pick_number` and `iter_pick_number` are the numbers of picked frames. `e_trust_lo`, `e_trust_hi` mean the range of the deviation of the frame energy, and `f_trust_lo` and `f_trust_hi` mean the range of the max deviation of atomic forces in a frame. `fp_style` can only be `gaussian` currently. Other parameters are as the same as those of generator.
+Here `pick_data` is the directory to data to simplify where the program recursively detects systems `System` with `deepmd/npy` format. `init_pick_number` and `iter_pick_number` are the numbers of picked frames. `e_trust_lo`, `e_trust_hi` mean the range of the deviation of the frame energy, and `f_trust_lo` and `f_trust_hi` mean the range of the max deviation of atomic forces in a frame. `fp_style` can only be `gaussian` currently. Other parameters are as the same as those of generator.
 
 
 ## Set up machine
@@ -1139,7 +1137,7 @@ an example of new dpgen's machine.json
 ```json
 {
   "api_version": "1.0",
-  "train": [
+  "train":
     {
       "command": "dp",
       "machine": {
@@ -1163,9 +1161,8 @@ an example of new dpgen's machine.json
         "para_deg": 3,
         "source_list": ["/home/user1234/deepmd.1.2.4.env"]
       }
-    }
-  ],
-  "model_devi":[
+    },
+  "model_devi":
     {
       "command": "lmp",
       "machine":{
@@ -1186,9 +1183,8 @@ an example of new dpgen's machine.json
         "group_size": 5,
         "source_list": ["/home/user1234/deepmd.1.2.4.env"]
       }
-    }
-  ],
-  "fp":[
+    },
+  "fp":
     {
       "command": "vasp_std",
       "machine":{
@@ -1210,7 +1206,6 @@ an example of new dpgen's machine.json
         "source_list": ["~/vasp.env"]
       }
     }
-  ]
 }
 ```
 note1: the key "local_root" in dpgen's machine.json is always `./`
@@ -1222,7 +1217,7 @@ When switching into a new machine, you may modifying the `MACHINE`, according to
 An example for `MACHINE` is:
 ```json
 {
-  "train": [
+  "train":
     {
       "machine": {
         "batch": "slurm",
@@ -1245,9 +1240,8 @@ An example for `MACHINE` is:
         "qos": "data"
       },
       "command": "USERPATH/dp"
-    }
-  ],
-  "model_devi": [
+    },
+  "model_devi":
     {
       "machine": {
         "batch": "slurm",
@@ -1271,9 +1265,8 @@ An example for `MACHINE` is:
       },
       "command": "lmp_serial",
       "group_size": 1
-    }
-  ],
-  "fp": [
+    },
+  "fp":
     {
       "machine": {
         "batch": "slurm",
@@ -1300,7 +1293,6 @@ An example for `MACHINE` is:
       "command": "vasp_gpu",
       "group_size": 1
     }
-  ]
 }
 ```
 Following table illustrates which key is needed for three types of machine: `train`,`model_devi`  and `fp`. Each of them is a list of dicts. Each dict can be considered as an independent environmnet for calculation.

doc/conf.py

@@ -40,10 +40,12 @@
 
 extensions = [
     'deepmodeling_sphinx',
+    'dargs.sphinx',
     "sphinx_rtd_theme",
     'myst_parser',
     'sphinx.ext.autosummary',
     'sphinx.ext.viewcode',
+    'sphinxarg.ext',
 ]
 
 

doc/index.rst

@@ -7,6 +7,8 @@ DPGEN's documentation
 .. toctree::
    :maxdepth: 2
    :caption: Overview
+
+   overview/cli
 
 
 .. _installation::
@@ -32,6 +34,9 @@ DPGEN's documentation
    :maxdepth: 2
    :caption: Init   
 
+   init/init-bulk-mdata
+   init/init-surf-mdata
+   init/init-reaction-mdata
 
 .. _autotest::
 
@@ -46,6 +51,8 @@ DPGEN's documentation
    :maxdepth: 2
    :caption: Simplify  
 
+   simplify/simplify-mdata
+
 
 .. _tutorial:
 

doc/init/init-bulk-mdata.rst

@@ -0,0 +1,6 @@
+dpgen init_bulk machine parameters
+==================================
+
+.. dargs::
+   :module: dpgen.data.arginfo
+   :func: init_bulk_mdata_arginfo

doc/init/init-reaction-mdata.rst

@@ -0,0 +1,6 @@
+dpgen init_reaction machine parameters
+======================================
+
+.. dargs::
+   :module: dpgen.data.arginfo
+   :func: init_reaction_mdata_arginfo

doc/init/init-surf-mdata.rst

@@ -0,0 +1,6 @@
+dpgen init_surf machine parameters
+==================================
+
+.. dargs::
+   :module: dpgen.data.arginfo
+   :func: init_surf_mdata_arginfo

doc/overview/cli.rst

@@ -0,0 +1,7 @@
+Command line interface
+======================
+
+.. argparse::
+   :module: dpgen.main
+   :func: main_parser
+   :prog: dpgen

doc/requirements.txt

@@ -2,6 +2,7 @@ sphinx>=4.0.2
 recommonmark
 sphinx_rtd_theme
 sphinx_markdown_tables
+sphinx-argparse
 myst-parser
 deepmodeling_sphinx
 .

doc/run/example-of-machine.md

@@ -20,7 +20,7 @@ In this section, we will show you how to perform train task at a local workstati
 In this example, we perform the `train` task on a local workstation.
 
 ```json
-"train": [
+"train":
     {
       "command": "dp",
       "machine": {
@@ -36,8 +36,7 @@ In this example, we perform the `train` task on a local workstation.
         "group_size": 1,
         "source_list": ["/home/user1234/deepmd.env"]
       }
-    }
-  ],
+    },
 ```
 
 The "command" for the train task in the DeePMD-kit is "dp".
@@ -51,7 +50,7 @@ In the resources parameter, "number_node", "cpu_per_node", and "gpu_per_node" sp
 In this example, we perform the model_devi task at a local Slurm workstation.
 
 ```json
-"model_devi": [
+"model_devi":
     {
       "command": "lmp",
       "machine": {
@@ -70,7 +69,6 @@ In this example, we perform the model_devi task at a local Slurm workstation.
         "source_list": ["/home/user1234/lammps.env"]
       }
     }
-],
 ```
 
 The "command" for the model_devi task in the LAMMPS is "lmp".
@@ -84,7 +82,7 @@ In the resources parameter, we specify the name of the queue to which the task i
 In this example, we perform the fp task at a remote PBS cluster that can be accessed via SSH.
 
 ```json
-"fp": [
+"fp":
     {
       "command": "mpirun -n 32 vasp_std",
       "machine": {
@@ -106,7 +104,6 @@ In this example, we perform the fp task at a remote PBS cluster that can be acce
         "source_list": ["/home/user1234/vasp.env"]
       }
     }
-],
 ```
 
 VASP code is used for fp task and mpi is used for parallel computing, so "mpirun -n 32" is added to specify the number of parallel threads.

doc/simplify/simplify-mdata.rst

@@ -0,0 +1,6 @@
+dpgen simplify machine parameters
+=================================
+
+.. dargs::
+   :module: dpgen.simplify.arginfo
+   :func: simplify_mdata_arginfo

doc/toymodels/JiamengHuang_pr.md

@@ -0,0 +1,9 @@
+A new parameter "vol_abs" is added. If you want to use absolute volume to get EOS, you can add
+
+         "vol_abs":      true,
+
+in the "eos" part of property.json
+if it's not mentioned, "False" is set defaultly
+when you are using absolute volume, there will be a notation in the last line of output during "make" process, which is like
+
+treat vol_start and vol_end as absolute volume

dpgen/arginfo.py

@@ -0,0 +1,35 @@
+from typing import Tuple
+
+from dargs import Argument
+
+from dpgen.dispatcher.Dispatcher import mdata_arginfo
+
+
+def general_mdata_arginfo(name: str, tasks: Tuple[str]) -> Argument:
+    """Generate arginfo for general mdata.
+
+    Parameters
+    ----------
+    name : str
+        mdata name
+    tasks : tuple[str]
+        tuple of task keys, e.g. ("train", "model_devi", "fp")
+    
+    Returns
+    -------
+    Argument
+        arginfo
+    """
+
+    doc_api_version = "Please set to 1.0"
+    doc_run_mdata = "machine.json file"
+    arg_api_version = Argument("api_version", str, optional=False, doc=doc_api_version)
+
+    sub_fields = [arg_api_version]
+    doc_mdata = "Parameters of command, machine, and resources for %s"
+    for task in tasks:
+        sub_fields.append(Argument(
+            task, dict, optional=False, sub_fields=mdata_arginfo(),
+            doc=doc_mdata % task,
+        ))
+    return Argument(name, dict, sub_fields=sub_fields, doc=doc_run_mdata)

dpgen/auto_test/EOS.py

@@ -24,6 +24,8 @@ def __init__(self,
                 self.vol_start = parameter['vol_start']
                 self.vol_end = parameter['vol_end']
                 self.vol_step = parameter['vol_step']
+                parameter['vol_abs'] = parameter.get('vol_abs', False)
+                self.vol_abs = parameter['vol_abs']
             parameter['cal_type'] = parameter.get('cal_type', 'relaxation')
             self.cal_type = parameter['cal_type']
             default_cal_setting = {"relax_pos": True,
@@ -117,6 +119,10 @@ def make_confs(self,
 
             else:
                 print('gen eos from ' + str(self.vol_start) + ' to ' + str(self.vol_end) + ' by every ' + str(self.vol_step))
+                if self.vol_abs : 
+                    dlog.info('treat vol_start and vol_end as absolute volume')
+                else : 
+                    dlog.info('treat vol_start and vol_end as relative volume')
                 equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
                 if not os.path.exists(equi_contcar):
                     raise RuntimeError("please do relaxation first")
@@ -138,8 +144,13 @@ def make_confs(self,
                     task_list.append(output_task)
                     os.symlink(os.path.relpath(equi_contcar), 'POSCAR.orig')
                     # scale = (vol / vol_to_poscar) ** (1. / 3.)
-                    scale = vol ** (1. / 3.)
-                    eos_params = {'volume': vol * vol_to_poscar, 'scale': scale}
+
+                    if self.vol_abs :
+                        scale = (vol / vol_to_poscar) ** (1. / 3.)
+                        eos_params = {'volume': vol, 'scale': scale}
+                    else :
+                        scale = vol ** (1. / 3.)
+                        eos_params = {'volume': vol * vol_to_poscar, 'scale': scale}
                     dumpfn(eos_params, 'eos.json', indent=4)
                     self.parameter['scale2equi'].append(scale)  # 06/22
                     vasp.poscar_scale('POSCAR.orig', 'POSCAR', scale)