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Merge pull request #6 from AnguseZhang/master
Update Readme and provide test case with methane.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| PREC=A | ||
| ENCUT=400.000000 | ||
| ISYM=0 | ||
| ALGO=fast | ||
| EDIFF=1E-6 | ||
| LREAL=F | ||
| NPAR=1 | ||
| KPAR=1 | ||
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| ISTART=0 | ||
| ICHARG=2 | ||
| ISIF=2 | ||
| ISMEAR=1 | ||
| SIGMA=0.200000 | ||
| IBRION=0 | ||
| MAXMIX=50 | ||
| NBLOCK=1 | ||
| KBLOCK=100 | ||
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| SMASS=0 | ||
| POTIM=2 | ||
| TEBEG=50 | ||
| TEEND=50 | ||
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| NSW=10 | ||
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| LWAVE=F | ||
| LCHARG=F | ||
| PSTRESS=0 | ||
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| KSPACING=2 | ||
| KGAMMA=F |
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| @@ -0,0 +1,23 @@ | ||
| PREC=A | ||
| ENCUT=400.000000 | ||
| # ISYM=0 | ||
| ALGO=fast | ||
| EDIFF=1.000000e-06 | ||
| LREAL=T | ||
| NPAR=1 | ||
| KPAR=1 | ||
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| NELMIN=4 | ||
| ISIF=2 | ||
| ISMEAR=0 | ||
| SIGMA=0.05 | ||
| IBRION=2 | ||
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| NSW=1000 | ||
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| LWAVE=F | ||
| LCHARG=F | ||
| PSTRESS=0 | ||
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| KSPACING=2 | ||
| KGAMMA=F |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,19 @@ | ||
| POSCAR file written by OVITO | ||
| 1.0000000000000000 | ||
| 10.0000000000000000 0.0000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 10.0000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 0.0000000000000000 10.0000000000000000 | ||
| H C | ||
| 4 1 | ||
| Direct | ||
| 0.5381543385532134 0.4068608007477559 0.3605730142093164 | ||
| 0.3945396557300829 0.4803205689390709 0.4384688400135213 | ||
| 0.5520924283424902 0.5654502852627673 0.4427087377775140 | ||
| 0.5281853047372259 0.4164147551778533 0.5391826568442692 | ||
| 0.5032505926369848 0.4672551598725561 0.4452323411553799 | ||
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| 0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
| 0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
| 0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
| 0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
| 0.00000000E+00 0.00000000E+00 0.00000000E+00 |
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| { | ||
| "cell_type": "diamond", | ||
| "super_cell": [1, 1, 1], | ||
| "elements": ["H","C"], | ||
| "from_poscar": true, | ||
| "from_poscar_path": "example/POSCAR", | ||
| "potcars": ["example/POTCAR" | ||
| ], | ||
| "relax_incar": "example/INCAR.rlx", | ||
| "md_incar" : "example/INCAR.md", | ||
| "scale": [1.00], | ||
| "skip_relax": false, | ||
| "pert_numb": 30, | ||
| "md_nstep" : 10, | ||
| "pert_box": 0.03, | ||
| "pert_atom": 0.01, | ||
| "deepgen_templ": "../generator/template/", | ||
| "coll_ndata": 5000, | ||
| "_comment": "that's all" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,81 @@ | ||
| #!/usr/bin/env python3 | ||
|
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||
| import os | ||
| import sys | ||
| from enum import Enum | ||
| from subprocess import Popen, PIPE | ||
|
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| class JobStatus (Enum) : | ||
| unsubmitted = 1 | ||
| waiting = 2 | ||
| running = 3 | ||
| terminated = 4 | ||
| finished = 5 | ||
| unknow = 100 | ||
|
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| class BatchJob (object): | ||
| """ | ||
| Abstract class of a batch job | ||
| It submit a job (leave the id in file tag_jobid) | ||
| It check the status of the job (return JobStatus) | ||
| NOTICE: I assume that when a job finishes, a tag file named tag_finished should be touched by the user. | ||
| TYPICAL USAGE: | ||
| job = DERIVED_BatchJob (dir, script) | ||
| job.submit () | ||
| stat = job.check_status () | ||
| """ | ||
| def __init__ (self, | ||
| job_dir = "", # dir of the job | ||
| job_script = "", # name of the job script | ||
| job_finish_tag = "tag_finished", # name of the tag for finished job | ||
| job_id_file = "tag_jobid") : # job id if making an existing job | ||
| self.job_dir = job_dir | ||
| self.job_script = job_script | ||
| self.job_id_file = job_dir + "/" + job_id_file | ||
| self.job_finish_tag = job_dir + "/" + job_finish_tag | ||
| self.cwd = os.getcwd() | ||
| self.submit_cmd = str(self.submit_command()) | ||
| def get_job_id (self) : | ||
| if True == os.path.exists (self.job_id_file) : | ||
| fp = open (self.job_id_file, 'r') | ||
| job_id = fp.read () | ||
| return str(job_id) | ||
| else : | ||
| return "" | ||
| def submit_command (self) : | ||
| """ | ||
| submission is | ||
| $ [command] [script] | ||
| """ | ||
| raise RuntimeError ("submit_command not implemented") | ||
| def check_status (self): | ||
| raise RuntimeError ("check_status not implemented") | ||
| def submit (self) : | ||
| if self.get_job_id () != "" : | ||
| stat = self.check_status() | ||
| if stat != JobStatus.terminated : | ||
| if stat == JobStatus.unknow : | ||
| raise RuntimeError ("unknown job status, terminate!") | ||
| print ("# job %s, dir %s already submitted (waiting, running or finished), would not submit again" % | ||
| (self.get_job_id(), self.job_dir)) | ||
| return self.get_job_id() | ||
| else : | ||
| print ("# find terminated job " + self.get_job_id() + ", submit again") | ||
| if (False == os.path.isdir (self.job_dir) ) : | ||
| raise RuntimeError ("cannot find job dir " + self.job_dir) | ||
| abs_job_script = self.job_dir + "/" + self.job_script | ||
| if False == os.path.exists (abs_job_script) : | ||
| raise RuntimeError ("cannot find job script " + abs_job_script) | ||
| cwd = os.getcwd() | ||
| os.chdir (self.job_dir) | ||
| ret = Popen([self.submit_cmd + " " + self.job_script], stdout=PIPE, stderr=PIPE, shell = True) | ||
| stdout, stderr = ret.communicate() | ||
| if str(stderr, encoding='ascii') != "": | ||
| raise RuntimeError (stderr) | ||
| job_id = str(stdout, encoding='ascii').replace('\n','').split()[-1] | ||
| print ("# job %s submitted, dir %s " % (job_id, self.job_dir)) | ||
| fp = open (self.job_id_file, 'w') | ||
| fp.write (job_id) | ||
| fp.close() | ||
| os.chdir (cwd) | ||
| return self.get_job_id() |
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