Merge pull request #2 from BaozCWJ/master

Fix

README.md

@@ -1,2 +1,42 @@
-# dpgen
+<span style="font-size:larger;">dpgen Manual</span>
+========
+
+# Table of contents
+- [About dpgen](#About-dpgen)
+- [genenrator](#generator)
+- [auto_test](#auto_test)
+  - [How to write `param.json`](##How-to-write-`param.json`)
+  - [How to write `machine.json`](##How-to-write-`machine.json`)
+- [Troubleshooting](#Troubleshooting)
+# About dpgen
 The deep potential generator
+# generator
+# auto_test
+At this step, we assume that you have prepared some graph files like `graph.*.pb` and the particular pseudopotential `POTCAR`.
+Then you only need one command to achieve automatic testing of physical properties.
+```
+python run.py param.json machine.json
+```
+## How to write `param.json`
+We take Cu as an example to show the parameter settings of `param.json`.
+
+The first part is the fundamental setting for particular alloy system. 
+```
+    "_comment": "models",
+    "potcar_map" : {
+	"Cu" : "/somewhere/POTCAR",
+        "Zr" : "/elsewhere/POTCAR"
+    },
+    "conf_dir":"the folder of configuration",
+    "task_type":"deepmd",
+    "task":"eos",
+```
+You need to add the specified paths of necessary `POTCAR` files in "potcar_map". The different `POTCAR` paths are separated by commas.
+Then you also need to add the folder path of particular configuration, which contains `POSCAR` file. For your convenience, we recommend that you use `gen_confs.py` to generate configurations by the following command.
+```
+python gen_confs.py Cu
+```
+It will store the various configurations of the given element or alloy in **confs** folder.
+## How to write `machine.json`
+
+# Troubleshooting

auto_test/lib/ovito_file_convert.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env ovitos
+'''
+This Script is adapted from Alexander Stukowski, the author of OVITO.
+See: http://forum.ovito.org/index.php?topic=131.0 for details.
+'''
+import os
+import sys
+import argparse
+import numpy as np
+
+from ovito.io import *
+
+supp_ofmt = ['lammps_dump', 'lammps_data', 'vasp']
+supp_exts = ['dump', 'lmp', 'poscar/POSCAR']
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-m", "--ofmt", type=str, 
+                    help="the output format, supported: " + str(supp_ofmt))
+parser.add_argument("INPUT", type=str, 
+                    help="the input file")
+parser.add_argument("OUTPUT", type=str, 
+                    help="the output file, supported ext: " + str(supp_exts))
+args = parser.parse_args()
+
+fin = args.INPUT
+fout = args.OUTPUT
+if args.ofmt is not None :
+    ofmt = args.ofmt
+else :
+    ext = fout.split('.')[-1]
+    if ext == 'dump' :
+        ofmt = 'lammps_dump'
+    elif ext == 'lmp' :
+        ofmt = 'lammps_data'
+    elif ext == 'poscar' or ext == 'POSCAR' :
+        ofmt = 'vasp'
+if not ofmt in supp_ofmt :
+    raise RuntimeError ("output format " + ofmt + " is not supported. use one of " + str(supp_ofmt))
+
+columns = None
+if ofmt == "lammps_dump" :
+    columns=["Particle Identifier", "Particle Type", "Position.X", "Position.Y", "Position.Z"]
+
+node = import_file(fin)
+if columns is not None :
+    export_file(node, fout, ofmt, columns = columns)
+else :
+    export_file(node, fout, ofmt)

auto_test/machine.json

@@ -5,7 +5,7 @@
 	"hostname" :	"localhost",
 	"port" :	22,
 	"username":	"username",
-    "password":     "password",
+    	"password":     "password",
 	"work_path" :	"the path of workplace",
 	"_comment" :	"that's all"
     },
@@ -28,7 +28,7 @@
 	"hostname" :	"localhost",
 	"port" :	22,
 	"username":	"username",
-    "password":     "password",
+    	"password":     "password",
 	"work_path" :	"the path of workplace",
 	"_comment" :	"that's all"
     },

auto_test/param.json

@@ -4,8 +4,8 @@
 	"Cu" : "/somewhere/POTCAR" 
     },
     "conf_dir":"the folder of configuration",
-    "task_type":1,
-    "task":2,
+    "task_type":"deepmd",
+    "task":"eos",
 
     "vasp_params":	{
 	"ecut":		520,