Merge pull request #474 from deepmodeling/master

update devel with master

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Create a bug report to help us eliminate issues and improve dpgen. If this
+  doesn’t look right, [choose a different type](https://github.com/deepmodeling/dpgen/issues/new/choose).
+title: "[BUG] _Replace With Suitable Title_"
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what the bug is.-->
+
+**DPGEN Version and Platform**
+
+<!--Please specify precisely which DPGEN version this issue was detected with ("import dpgen" in the python command line interface and type "print(dpgen.__version__)") and what platform (operating system and its version, hardware) you are running on.-->
+
+**Job submission and computing cluster configuration**
+
+<!--If the question is about job submission, Please specify your jobs submission system and your authority. If applicable, specify your computing system configurations as well.-->
+
+**Expected Behavior**
+
+<!--Describe the expected behavior.  Quote from the DPGEN manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual-->
+
+**Actual Behavior**
+
+<!--Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.  Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result".  Do not assume that the person reading this has any experience with or knowledge of your specific area of research.-->
+
+**Steps to Reproduce**
+
+<!--Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,21 @@
+---
+name: Feature request
+about: Suggest an idea for this project. If this doesn’t work right, [choose a different
+  type]( https://github.com/deepmodeling/dpgen/issues/new/choose).
+title: "[Feature Request] _Replace with Title_"
+labels: new feature
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a brief and concise description of the suggested feature or change-->
+
+**Detailed Description**
+
+<!--Please explain how you would like to see DPGEN enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/generic-issue.md

@@ -0,0 +1,25 @@
+---
+name: Generic issue
+about: For issues that do not fit any of the other categories. If this doesn’t work
+  right, [choose a different type]( https://github.com/deepmodeling/dpgen/issues/new/choose).
+title: _Replace With a Descriptive Title_
+labels: wontfix
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what the question is.-->
+
+**DPGEN Version and Platform**
+
+<!--Please specify precisely which DPGEN version this issue was detected with ("import dpgen" in the python command line interface and type "print(dpgen.__version__)") and what platform (operating system and its version, hardware) you are running on.-->
+
+**Job submission and computing cluster configuration**
+
+<!--If the question is about job submission, Please specify your jobs submission system and your authority. If applicable, specify your computing system configurations as well.-->
+
+**Details**
+
+<!--Please explain the issue in detail here-->

.github/ISSUE_TEMPLATE/parameters.md

@@ -0,0 +1,25 @@
+---
+name: Parameters
+about: Make a suggestion for a change of input parameters or a new output to dpgen.
+  If this doesn’t work right, [choose a different type]( https://github.com/deepmodeling/dpgen/issues/new/choose).
+title: "[Parameters] _Replace With Suitable Title_"
+labels: documentation, enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+<!--Please provide a clear and concise description of what your request is.-->
+
+**Summary**
+
+<!--Please provide a brief and concise description of the suggested feature or change-->
+
+**Detailed Description**
+
+<!--Please explain how you would like to see dpgen enhanced. Specify your material system, and exactly what behaviors or properties you are looking for, or what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation.-->
+
+**Further Information, Files, and Links**
+
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/request-for-help.md

@@ -0,0 +1,21 @@
+---
+name: Request for Help
+about: Don't post help requests here, go to [discussions](http://github.com/deepmodeling/dpgen/discussions)
+  instead. Or [choose a different type]( https://github.com/deepmodeling/dpgen/issues/new/choose).
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Before asking questions, you can
+
+search the previous issues or discussions
+check [Manual](https://github.com/deepmodeling/dpgen).
+
+Please **do not** post requests for help (e.g. with installing or using dpgen) here. 
+Instead go to [discussions](https://github.com/deepmodeling/dpgen/discussions).
+
+This issue tracker is for tracking dpgen development related issues only.
+
+Thanks for your cooperation.

README.md

@@ -21,7 +21,9 @@
 ## About DP-GEN
 
 [![GitHub release](https://img.shields.io/github/release/deepmodeling/dpgen.svg?maxAge=86400)](https://github.com/deepmodeling/dpgen/releases/)
-[![doi:10.1016/j.cpc.2020.107206](https://zenodo.org/badge/DOI/10.1016/j.cpc.2020.107206.svg)](https://doi.org/10.1016/j.cpc.2020.107206)
+[![doi:10.1016/j.cpc.2020.107206](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2020.107206-blue)](https://doi.org/10.1016/j.cpc.2020.107206)
+[![conda install](https://img.shields.io/conda/dn/conda-forge/dpgen?label=conda%20install)](https://anaconda.org/conda-forge/dpgen)
+[![pip install](https://img.shields.io/pypi/dm/dpgen?label=pip%20install)](https://pypi.org/project/dpgen)
 
 DP-GEN (Deep Generator)  is a software written in Python, delicately designed to generate a deep learning based model of interatomic potential energy and force field. DP-GEN is depedent on DeepMD-kit (https://github.com/deepmodeling/deepmd-kit/blob/master/README.md). With highly scalable interface with common softwares for molecular simulation, DP-GEN is capable to  automatically prepare scripts and maintain job queues on HPC machines (High Performance Cluster) and analyze results.
 

dpgen/auto_test/Lammps.py

@@ -17,7 +17,7 @@ def __init__(self,
         self.inter_type = inter_parameter['type']
         self.type_map = inter_parameter['type_map']
         self.in_lammps = inter_parameter.get('in_lammps', 'auto')
-        if self.type_map == 'meam':
+        if self.inter_type == 'meam':
             self.model = list(map(os.path.abspath, inter_parameter['model']))
         else:
             self.model = os.path.abspath(inter_parameter['model'])

dpgen/dispatcher/PBS.py

@@ -16,7 +16,7 @@ def check_status(self) :
             = self.context.block_call ("qstat " + job_id)
         err_str = stderr.read().decode('utf-8')
         if (ret != 0) :
-            if str("qstat: Unknown Job Id") in err_str :
+            if str("qstat: Unknown Job Id") in err_str or str("Job has finished") in err_str:
                 if self.check_finish_tag() :
                     return JobStatus.finished
                 else :

dpgen/generator/run.py

@@ -2307,7 +2307,7 @@ def post_fp_vasp (iter_index,
     dlog.info("failed frame: %6d in %6d  %6.2f %% " % (icount, tcount, rfail * 100.))
 
     if rfail>ratio_failed:
-       raise RuntimeError("find too many unsuccessfully terminated jobs")
+       raise RuntimeError("find too many unsuccessfully terminated jobs. Too many FP tasks are not converged. Please check your input parameters (e.g. INCAR) or configuration (e.g. POSCAR) in directories \'iter.*.*/02.fp/task.*.*/.\'")
 
 
 def post_fp_pwscf (iter_index,

examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json

@@ -0,0 +1,79 @@
+{
+  "_comment" : "This is an example of DP-GEN on Local device running with 4 GPUs",
+  "_comment" : "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU",
+  "train": [
+    {
+      "_comment" : "Specify the installed path of DeePMD-kit",
+      "_comment" : "The version of DeePMD-kit should be 1.*",
+      "command": "/home/user/anaconda3/bin/dp",
+      "_comment" : "Specify machine settings",
+      "machine": {
+        "_comment" : "Supported batches include slurm, pbs, shell, lsf.",
+        "batch": "shell",
+        "work_path": "/tmp/dpwork",
+        "_comment": "that's all"
+      },
+      "resources":{
+        "_comment" : "The number of nodes.",
+        "numb_node":     1,
+        "_comment" : "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.",
+        "numb_gpu":      0,
+        "_comment" : "The number of CPUs.",
+        "task_per_node": 4,
+        "_comment" : "The number of GPUs that can be used for each task.",
+        "manual_cuda_devices": 4,
+        "_comment" : "The number of tasks that can be run in each GPU.",
+        "manual_cuda_multiplicity":1,
+        "_comment" : "Allow the multi-GPU task running.",
+        "cuda_multi_task": true,
+        "module_list":   [],
+        "_comment" : "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ",
+        "source_list":   ["/opt/intel/parallel_studio_xe_2020/psxevars.sh"]
+      },
+      "_comment" : "DP-GEN will put 4 tasks together in one submitting script.",
+      "group_size": 4
+    }
+  ],
+
+  "model_devi": [
+    {
+      "machine": {
+        "batch":     "shell",
+        "work_path": "/tmp/dpwork"
+      },
+      "resources": {
+        "numb_node":     1,
+        "numb_gpu":      0,
+        "task_per_node": 4,
+        "manual_cuda_devices": 4,
+        "manual_cuda_multiplicity":1,
+        "cuda_multi_task": true,
+        "source_list":   [],
+        "module_list":   []
+      },
+      "command":    "/home/user/Soft/Deepmd/lammps-stable_29Oct2020/src/lmp_mpi",
+      "group_size": 4
+    }
+  ],
+
+  "fp": [
+    {
+      "machine": {
+        "batch":     "shell",
+        "work_path": "/tmp/dpwork"
+      },
+      "resources": {
+        "allow_failure": true,
+        "ratio_failue":  0.05,
+        "task_per_node": 16,
+        "with_mpi":      true,
+        "_comment" : "Load the intel compiler.",
+        "source_list":   ["/opt/intel/parallel_studio_xe_2020/psxevars.sh"],
+        "envs":          {"PATH" : "/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH"},
+        "_comment" : "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;"
+      },
+      "command":    "vasp_std",
+      "group_size": 1
+    }
+  ]
+}