A problem of init_bulk

[Kangxuxin]

It's my param.json
{
"stages" : [1,2,3,4],
"cell_type": "hcp",
"latt": 4.479,
"super_cell": [2, 2, 2],
"elements": ["Mg", "Al"],
"potcars": ["./POTCAR_Mg","./POTCAR_Al"],
"relax_incar": "./INCAR_rlx",
"md_incar" : "./INCAR_md",
"scale": [1.00],
"skip_relax": false,
"pert_numb": 2,
"md_nstep" : 5,
"pert_box": 0.03,
"pert_atom": 0.01,
"coll_ndata": 5000,
"type_map" : [ "Mg", "Al"],
"_comment": "that's all"
}

Then error
Traceback (most recent call last):
File "/public/home/duanxiangmei/softwore/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/duanxiangmei/softwore/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/duanxiangmei/softwore/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 728, in gen_init_bulk
out_dir = out_dir_name(jdata)
File "/public/home/duanxiangmei/softwore/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 77, in out_dir_name
cell_type = jdata['cell_type']
KeyError: 'cell_type'

Thanks a lot

[AnguseZhang]

Your command is wrong. It should be dpgen init_bulk param.json machine.json, not dpgen init_bulk machine.json param.json.

[AnguseZhang]

Try execute manually cd /public/home/duanxiangmei/KXX/DPMD/LiSi/work/8fd83e9c14d87d8c1400c8a618a439e5a97390f8 && qsub d71295fa985da85306ba61212894f2b945a8a906.sub, and check what's wrong.

[Kangxuxin]

cat d71295fa985da85306ba61212894f2b945a8a906.sub
#!/bin/bash -l
#PBS -l select=1:ncpus=16:ngpus=0
#PBS -j oe
#PBS -q vasp

REMOTE_ROOT=/public/home/duanxiangmei/KXX/DPMD/LiSi/work/8fd83e9c14d87d8c1400c8a618a439e5a97390f8
echo 0 > $REMOTE_ROOT/d71295fa985da85306ba61212894f2b945a8a906_flag_if_job_task_fail
test $? -ne 0 && exit 1

{ source /public/software/profile.d/compiler_intel-compiler-2021.3.0.sh; }
{ source /public/software/profile.d/mpi_intelmpi-2021.3.0.sh; }

cd $REMOTE_ROOT
cd sys-0001-0001
test $? -ne 0 && exit 1
if [ ! -f d3d54e94b467ab16adbf3a342d0fe97550b1d9f1_task_tag_finished ] ;then
( mpirun -np 16 /public/software/apps/vasp5.4.4-neb/bin/vasp_std ) 1>>fp.log 2>>fp.log
if test $? -eq 0; then touch d3d54e94b467ab16adbf3a342d0fe97550b1d9f1_task_tag_finished; else echo 1 > $REMOTE_ROOT/d71295fa985da85306ba61212894f2b945a8a906_flag_if_job_task_fail;fi
fi &
wait

cd $REMOTE_ROOT
test $? -ne 0 && exit 1

wait
FLAG_IF_JOB_TASK_FAIL=$(cat d71295fa985da85306ba61212894f2b945a8a906_flag_if_job_task_fail)
if test $FLAG_IF_JOB_TASK_FAIL -eq 0; then touch d71295fa985da85306ba61212894f2b945a8a906_job_tag_finished; else exit 1;fi

[Kangxuxin]

Try execute manually cd /public/home/duanxiangmei/KXX/DPMD/LiSi/work/8fd83e9c14d87d8c1400c8a618a439e5a97390f8 && qsub d71295fa985da85306ba61212894f2b945a8a906.sub, and check what's wrong.

Can you find angthing wrong? teacher. I'm a beginner of dpgen, the question has been bothering me for days, help help me. Thanks.

[Kangxuxin]

Thanks, the problem has been solved by changing the batch_type from pbs to Shell

[luowh35]

I also meet the same problem, could u tell me how to change the batch_type from pbs to Shell?

[Kangxuxin]

Teacher, I have a new question.
There are four stages when generating the initial data, but mine only proceeds to two stage stops. AIMD will not carry out. And the temporary folder is empty.

[Kangxuxin]

font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; }         I change the batch_type from pbs to Shell in machine.json file, you can try. 康旭鑫 ***@***.***

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