Merge pull request #473 from amcadmus/master

merge devel into master

.github/workflows/mirror_gitee.yml

@@ -0,0 +1,19 @@
+name: Mirror to Gitee Repo
+
+on: [ push, delete, create ]
+
+# Ensures that only one mirror task will run at a time.
+concurrency:
+  group: git-mirror
+
+jobs:
+  git-mirror:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: wearerequired/git-mirror-action@v1
+        env:
+          ORGANIZATION: deepmodeling
+          SSH_PRIVATE_KEY: ${{ secrets.SYNC_GITEE_PRIVATE_KEY }}
+        with:
+          source-repo: "git@github.com:deepmodeling/dpgen.git"
+          destination-repo: "git@gitee.com:deepmodeling/dpgen.git"

.gitignore

@@ -39,3 +39,4 @@ dpgen.egg-info
 dbconfig.json
 .vscode/*
 .idea/*
+_build

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/README.md

@@ -0,0 +1,4 @@
+# How to contribute
+
+- If you want to add the documentation of a toy model, simply put your file in the directory doc/toymodels/ and push;
+- If you want to add a new directory for a new category of instructions, make a new directory and add it in doc/index.rst.

doc/conf.py

@@ -0,0 +1,80 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import subprocess
+# import sys
+import recommonmark
+from recommonmark.transform import AutoStructify
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'DPGEN'
+copyright = '2020, Deep Potential'
+author = 'Deep Potential'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+# extensions = [
+#     'recommonmark',
+#     "sphinx_rtd_theme",
+#     'myst_parser',
+#     'sphinx_markdown_tables',
+#     'sphinx.ext.autosummary'
+# ]
+
+extensions = [
+    "sphinx_rtd_theme",
+    'myst_parser',
+    'sphinx.ext.autosummary',
+]
+
+
+# Tell sphinx what the primary language being documented is.
+primary_domain = 'cpp'
+
+# Tell sphinx what the pygments highlight language should be.
+highlight_language = 'cpp'
+
+# 
+myst_heading_anchors = 4
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+# html_css_files = ['css/custom.css']
+
+autodoc_default_flags = ['members']
+autosummary_generate = True
+master_doc = 'index'

doc/index.rst

@@ -0,0 +1,28 @@
+==========================
+DPGEN's documentation
+==========================
+
+.. _tutorial:
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tutorial
+   :glob:  
+
+   toymodels/*
+
+
+.. _Contribution:
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contribution Guild
+
+   README.md
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. _feedback: 
+.. _affiliated packages: 

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/requirements.txt

@@ -0,0 +1,5 @@
+sphinx==3.2.1
+recommonmark==0.7.1
+sphinx_rtd_theme==0.5.2
+sphinx_markdown_tables==0.0.15
+myst-parser==0.13.7

doc/toymodels/black.md

@@ -0,0 +1 @@
+# This is a blank file to test sphinx-build

dpgen/__init__.py

@@ -36,15 +36,17 @@ def info():
     print('Date:    ' + __date__)
     print('Path:    ' + ROOT_PATH)
     print('')
-    # print('Dependency')
-    # print('------------')
-    # for modui in ['numpy', 'dpdata', 'pymatgen', 'monty', 'ase', 'paramiko', 'custodian' ]:
-    #     try:
-    #         mm = __import__(modui)
-    #         print('%10s %10s   %s' % (modui, mm.__version__, mm.__path__[0]))
-    #     except ImportError:
-    #         print('%10s %10s Not Found' % (modui, ''))
-    # print()
+    print('Dependency')
+    print('------------')
+    for modui in ['numpy', 'dpdata', 'pymatgen', 'monty', 'ase', 'paramiko', 'custodian' ]:
+        try:
+            mm = __import__(modui)
+            print('%10s %10s   %s' % (modui, mm.__version__, mm.__path__[0]))
+        except ImportError:
+            print('%10s %10s Not Found' % (modui, ''))
+        except AttributeError:
+            print('%10s %10s unknown version or path' %(modui, ''))
+    print()
 
     # reference
     print("""Reference

dpgen/auto_test/Surface.py

@@ -180,13 +180,13 @@ def _compute_lower(self,
             ptr_data += "Miller_Indices: \tSurf_E(J/m^2) EpA(eV) equi_EpA(eV)\n"
             for ii in all_tasks:
                 task_result = loadfn(os.path.join(ii, 'result_task.json'))
-                natoms = task_result['atom_numbs'][0]
-                epa = task_result['energies'][-1] / task_result['atom_numbs'][0]
+                natoms = np.sum(task_result['atom_numbs'])
+                epa = task_result['energies'][-1] / natoms
                 AA = np.linalg.norm(np.cross(task_result['cells'][0][0], task_result['cells'][0][1]))
 
                 equi_path = os.path.abspath(os.path.join(os.path.dirname(output_file), '../relaxation/relax_task'))
                 equi_result = loadfn(os.path.join(equi_path, 'result.json'))
-                equi_epa = equi_result['energies'][-1] / equi_result['atom_numbs'][0]
+                equi_epa = equi_result['energies'][-1] / np.sum(equi_result['atom_numbs'])
                 structure_dir = os.path.basename(ii)
 
                 Cf = 1.60217657e-16 / (1e-20 * 2) * 0.001

dpgen/auto_test/common_equi.py

@@ -1,6 +1,6 @@
 import glob
 import os
-
+import warnings
 from monty.serialization import dumpfn
 
 import dpgen.auto_test.lib.crys as crys
@@ -10,6 +10,8 @@
 from dpgen.auto_test.mpdb import get_structure
 from dpgen.dispatcher.Dispatcher import make_dispatcher
 from dpgen.remote.decide_machine import decide_fp_machine, decide_model_devi_machine
+from distutils.version import LooseVersion
+from dpgen.dispatcher.Dispatcher import make_submission
 
 lammps_task_type = ['deepmd', 'meam', 'eam_fs', 'eam_alloy']
 
@@ -149,23 +151,44 @@ def run_equi(confs,
     if len(run_tasks) == 0:
         return
     else:
+        # if LooseVersion()
         run_tasks = [os.path.basename(ii) for ii in all_task]
         machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
         print('%d tasks will be submited '%len(run_tasks))
         for ii in range(len(work_path_list)):
             work_path = work_path_list[ii]
             disp = make_dispatcher(machine, resources, work_path, [run_tasks[ii]], group_size)
             print("%s --> Runing... "%(work_path))
+
+        api_version = mdata.get('api_version', '0.9')
+        if LooseVersion(api_version) < LooseVersion('1.0'):
+            warnings.warn(f"the dpdispatcher will be updated to new version."
+                f"And the interface may be changed. Please check the documents for more details")
             disp.run_jobs(resources,
-                          command,
-                          work_path,
-                          [run_tasks[ii]],
-                          group_size,
-                          forward_common_files,
-                          forward_files,
-                          backward_files,
-                          outlog='outlog',
-                          errlog='errlog')
+                            command,
+                            work_path,
+                            [run_tasks[ii]],
+                            group_size,
+                            forward_common_files,
+                            forward_files,
+                            backward_files,
+                            outlog='outlog',
+                            errlog='errlog')
+        elif LooseVersion(api_version) >= LooseVersion('1.0'):
+            submission = make_submission(
+                mdata_machine=machine,
+                mdata_resource=resources,
+                commands=[command],
+                work_path=work_path,
+                run_tasks=run_tasks,
+                group_size=group_size,
+                forward_common_files=forward_common_files,
+                forward_files=forward_files,
+                backward_files=backward_files,
+                outlog = 'outlog',
+                errlog = 'errlog'
+            )
+            submission.run_submission()
 
 
 def post_equi(confs, inter_param):

dpgen/auto_test/common_prop.py

@@ -1,5 +1,7 @@
+from distutils.version import LooseVersion
 import glob
 import os
+import warnings
 from multiprocessing import Pool
 import dpgen.auto_test.lib.util as util
 from dpgen import dlog
@@ -12,6 +14,7 @@
 from dpgen.auto_test.calculator import make_calculator
 from dpgen.dispatcher.Dispatcher import make_dispatcher
 from dpgen.remote.decide_machine import decide_fp_machine, decide_model_devi_machine
+from dpgen.dispatcher.Dispatcher import make_submission
 
 lammps_task_type = ['deepmd', 'meam', 'eam_fs', 'eam_alloy']
 
@@ -196,7 +199,11 @@ def worker(work_path,
     run_tasks = [os.path.basename(ii) for ii in all_task]
     machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
     disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
-    disp.run_jobs(resources,
+    api_version = mdata.get('api_version', '0.9')
+    if LooseVersion(api_version) < LooseVersion('1.0'):
+        warnings.warn(f"the dpdispatcher will be updated to new version."
+            f"And the interface may be changed. Please check the documents for more details")
+        disp.run_jobs(resources,
                   command,
                   work_path,
                   run_tasks,
@@ -206,7 +213,21 @@ def worker(work_path,
                   backward_files,
                   outlog='outlog',
                   errlog='errlog')
-
+    elif LooseVersion(api_version) >= LooseVersion('1.0'):
+        submission = make_submission(
+                mdata_machine=machine,
+                mdata_resource=resources,
+                commands=[command],
+                work_path=work_path,
+                run_tasks=run_tasks,
+                group_size=group_size,
+                forward_common_files=forward_common_files,
+                forward_files=forward_files,
+                backward_files=backward_files,
+                outlog = 'outlog',
+                errlog = 'errlog'
+            )
+        submission.run_submission()
 
 def post_property(confs,
                   #                  inter_param,