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add bcc interstitial calculation and change some default parameters i…
…n lmp (#696) * metal testing for alloys and pair_coeff compatible with the latest lammps * add bcc self interstitial calculations * bcc interstitial optimization and change some default parameters in lmp * fix lmp default parameters * bcc interstitial optimization * add bcc interstitial unittest Co-authored-by: kevinwenminion <tongqi_wen@qq.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| V2 | ||
| 1.0000000000000000 | ||
| 2.9975462819866885 0.0000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 2.9975462819866885 0.0000000000000000 | ||
| 0.0000000000000000 0.0000000000000000 2.9975462819866885 | ||
| V | ||
| 2 | ||
| Direct | ||
| 0.0000000000000000 0.0000000000000000 0.0000000000000000 | ||
| 0.5000000000000000 0.5000000000000000 0.5000000000000000 | ||
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| 0.00000000E+00 0.00000000E+00 0.00000000E+00 | ||
| 0.00000000E+00 0.00000000E+00 0.00000000E+00 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| import os, sys, json, glob, shutil | ||
| import dpdata | ||
| import numpy as np | ||
| import unittest | ||
| import dpdata | ||
| from monty.serialization import loadfn, dumpfn | ||
| from pymatgen.core import Structure | ||
| from pymatgen.io.vasp import Incar | ||
| from pymatgen.symmetry.analyzer import SpacegroupAnalyzer | ||
| from pymatgen.analysis.defects.core import Interstitial as pmg_Interstitial | ||
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| sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) | ||
| __package__ = 'auto_test' | ||
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| from .context import make_kspacing_kpoints | ||
| from .context import setUpModule | ||
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| from dpgen.auto_test.Interstitial import Interstitial | ||
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| class TestInterstitial(unittest.TestCase): | ||
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| def setUp(self): | ||
| _jdata = { | ||
| "structures": ["confs/std-bcc"], | ||
| "interaction": { | ||
| "type": "vasp", | ||
| "incar": "vasp_input/INCAR.rlx", | ||
| "potcar_prefix": "vasp_input", | ||
| "potcars": {"V": "POTCAR"} | ||
| }, | ||
| "properties": [ | ||
| { | ||
| "type": "interstitial", | ||
| "supercell": [1, 1, 1], | ||
| "insert_ele": ["V"], | ||
| "bcc_self": True | ||
| } | ||
| ] | ||
| } | ||
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| self.equi_path = 'confs/std-bcc/relaxation/relax_task' | ||
| self.source_path = 'equi/vasp' | ||
| self.target_path = 'confs/std-bcc/interstitial_00' | ||
| if not os.path.exists(self.equi_path): | ||
| os.makedirs(self.equi_path) | ||
| if not os.path.exists(self.target_path): | ||
| os.makedirs(self.target_path) | ||
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| self.confs = _jdata["structures"] | ||
| self.inter_param = _jdata["interaction"] | ||
| self.prop_param = _jdata['properties'] | ||
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| self.interstitial = Interstitial(_jdata['properties'][0]) | ||
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| def tearDown(self): | ||
| if os.path.exists(self.equi_path): | ||
| shutil.rmtree(self.equi_path) | ||
| if os.path.exists(self.target_path): | ||
| shutil.rmtree(self.target_path) | ||
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| def test_task_type(self): | ||
| self.assertEqual('interstitial', self.interstitial.task_type()) | ||
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| def test_task_param(self): | ||
| self.assertEqual(self.prop_param[0], self.interstitial.task_param()) | ||
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| def test_make_confs_bcc(self): | ||
| if not os.path.exists(os.path.join(self.equi_path, 'CONTCAR')): | ||
| with self.assertRaises(RuntimeError): | ||
| self.interstitial.make_confs(self.target_path, self.equi_path) | ||
| shutil.copy(os.path.join(self.source_path, 'CONTCAR_V_bcc'), os.path.join(self.equi_path, 'CONTCAR')) | ||
| task_list = self.interstitial.make_confs(self.target_path, self.equi_path) | ||
| dfm_dirs = glob.glob(os.path.join(self.target_path, 'task.*')) | ||
| self.assertEqual(len(dfm_dirs), 7) | ||
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| incar0 = Incar.from_file(os.path.join('vasp_input', 'INCAR.rlx')) | ||
| incar0['ISIF'] = 3 | ||
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| self.assertEqual(os.path.realpath(os.path.join(self.equi_path, 'CONTCAR')), | ||
| os.path.realpath(os.path.join(self.target_path, 'POSCAR'))) | ||
| ref_st = Structure.from_file(os.path.join(self.target_path, 'POSCAR')) | ||
| dfm_dirs.sort() | ||
| for ii in dfm_dirs[:4]: | ||
| st_file = os.path.join(ii, 'POSCAR') | ||
| self.assertTrue(os.path.isfile(st_file)) | ||
| st0 = Structure.from_file(st_file) | ||
| inter_site = st0[-1] | ||
| inter = pmg_Interstitial(ref_st, inter_site, charge=0.0) | ||
| st1 = inter.generate_defect_structure(self.prop_param[0]['supercell']) | ||
| self.assertEqual(st0, st1) | ||
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| for ii in dfm_dirs[4:]: | ||
| st_file = os.path.join(ii, 'POSCAR') | ||
| self.assertTrue(os.path.isfile(st_file)) | ||
| st0 = Structure.from_file(st_file) | ||
| inter_site1 = st0.pop(-1) | ||
| inter_site2 = st0.pop(-1) | ||
| center = (inter_site1.coords + inter_site2.coords) / 2 | ||
| self.assertTrue((center[0] - center[1]) < 1e-4) | ||
| self.assertTrue((center[1] - center[2]) < 1e-4) |