Merge branch 'devel' into devel

dpgen/auto_test/Gamma.py

@@ -22,9 +22,8 @@
 
 class Gamma(Property):
     """
-    Calculation of gamma line for bcc and fcc (v1.1 add half z judgement)
+    Calculation of common gamma lines for bcc and fcc
     """
-
     def __init__(self,
                  parameter):
         parameter['reproduce'] = parameter.get('reproduce', False)
@@ -34,9 +33,11 @@ def __init__(self,
                 self.miller_index = parameter['miller_index']
                 self.displace_direction = parameter['displace_direction']
                 self.lattice_type = parameter['lattice_type']
+
                 # parameter['min_slab_size'] = parameter.get('min_slab_size', 10)
                 # self.min_slab_size = parameter['min_slab_size']
                 parameter['min_supercell_size'] = parameter.get('min_supercell_size', (1,1,5))
+
                 self.min_supercell_size = parameter['min_supercell_size']
                 parameter['min_vacuum_size'] = parameter.get('min_vacuum_size', 20)
                 self.min_vacuum_size = parameter['min_vacuum_size']
@@ -45,10 +46,6 @@ def __init__(self,
                 parameter['n_steps'] = parameter.get('n_steps', 10)
                 self.n_steps = parameter['n_steps']
                 self.atom_num = None
-            #                parameter['pert_xz'] = parameter.get('pert_xz', 0.01)
-            #                self.pert_xz = parameter['pert_xz']
-            #                default_max_miller = 2
-            #                parameter['max_miller'] = parameter.get('max_miller', default_max_miller)
             parameter['cal_type'] = parameter.get('cal_type', 'relaxation')
             self.cal_type = parameter['cal_type']
             default_cal_setting = {"relax_pos": True,
@@ -276,8 +273,7 @@ def __displace_slab(self,
             all_slabs.append(slab.copy())
         return all_slabs
 
-    def __poscar_fix(self,
-                  poscar):
+    def __poscar_fix(self, poscar) -> None:
         # add position fix condition of x and y in POSCAR
         insert_pos = -self.atom_num
         fix_dict = {
@@ -297,8 +293,7 @@ def __poscar_fix(self,
             for ii in range(len(contents)):
                 fin2.write(contents[ii])
 
-    def __inLammpes_fix(self,
-                        inLammps):
+    def __inLammpes_fix(self, inLammps) -> None:
         # add position fix condition of x and y of in.lammps
         fix_dict = {
             'true': '0',
@@ -378,6 +373,7 @@ def _compute_lower(self,
                     str(miller_index) + '-' + structure_dir + ':', int(ii[-4:])/self.n_steps, sfe, epa, equi_epa)
                 res_data[int(ii[-4:])/self.n_steps] = [sfe, epa, equi_epa]
 
+
         else:
             if 'init_data_path' not in self.parameter:
                 raise RuntimeError("please provide the initial data path to reproduce")

tests/auto_test/confs/hp-Mo/POSCAR

@@ -0,0 +1,13 @@
+Mo2                                     
+   1.0000000000000000     
+     3.1623672675177916   -0.0000000000000000   -0.0000000000000000
+    -0.0000000000000000    3.1623672675177916   -0.0000000000000000
+     0.0000000000000000    0.0000000000000000    3.1623672675177916
+   Mo
+     2
+Direct
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
+  0.5000000000000000  0.5000000000000000  0.5000000000000000
+
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00

tests/auto_test/equi/vasp/CONTCAR_Mo_bcc

@@ -0,0 +1,10 @@
+Mo2 
+1.0
+3.1617699325125632e+00 0.0000000000000000e+00 0.0000000000000000e+00 
+-2.9607253805968378e-17 3.1617699325125632e+00 0.0000000000000000e+00 
+-6.1517551630255350e-18 -4.3742379676789617e-17 3.1617699325125632e+00 
+Mo 
+2 
+Cartesian
+   0.0000000000    0.0000000000    0.0000000000
+   1.5808849663    1.5808849663    1.5808849663

tests/auto_test/test_gamma.py

@@ -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.structure import Structure
+from pymatgen.core.surface import SlabGenerator
+from pymatgen.io.vasp import Incar
+from pymatgen.io.ase import AseAtomsAdaptor
+from ase.lattice.cubic import BodyCenteredCubic as bcc
+from ase.lattice.cubic import FaceCenteredCubic as fcc
+from ase.lattice.hexagonal import HexagonalClosedPacked as hcp
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+__package__ = 'auto_test'
+
+from .context import make_kspacing_kpoints
+from .context import setUpModule
+
+from dpgen.auto_test.Gamma import Gamma
+
+class TestGamma(unittest.TestCase):
+
+    def setUp(self):
+        _jdata = {
+            "structures":    ["confs/hp-Mo"],
+            "interaction": {
+                "type":          "vasp",
+                "incar":         "vasp_input/INCAR_Mo",
+                "potcar_prefix": "vasp_input",
+                "potcars":      {"Mo": "POTCAR_Mo"}
+            },
+            "properties": [
+                {
+                    "type": "gamma",
+                    "lattice_type": "bcc",
+                    "miller_index": [1, 1, 0],
+                    "displace_direction": [1, 1, 1],
+                    "min_supercell_size": [1, 1, 10],
+                    "min_vacuum_size": 10,
+                    "add_fix": ["true", "true", "false"],
+                    "n_steps": 20
+                }
+            ]
+        }
+
+        self.equi_path = 'confs/hp-Mo/relaxation/relax_task'
+        self.source_path = 'equi/vasp'
+        self.target_path = 'confs/hp-Mo/gamma_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)
+
+        self.confs = _jdata["structures"]
+        self.inter_param = _jdata["interaction"]
+        self.prop_param = _jdata['properties']
+
+        self.gamma = Gamma(_jdata['properties'][0])
+
+    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)
+
+    def test_task_type(self):
+        self.assertEqual('gamma', self.gamma.task_type())
+
+    def test_task_param(self):
+        self.assertEqual(self.prop_param[0], self.gamma.task_param())
+
+    def test_make_confs_bcc(self):
+        if not os.path.exists(os.path.join(self.equi_path, 'CONTCAR')):
+            with self.assertRaises(RuntimeError):
+                self.gamma.make_confs(self.target_path, self.equi_path)
+        shutil.copy(os.path.join(self.source_path, 'CONTCAR_Mo_bcc'), os.path.join(self.equi_path, 'CONTCAR'))
+        task_list = self.gamma.make_confs(self.target_path, self.equi_path)
+        dfm_dirs = glob.glob(os.path.join(self.target_path, 'task.*'))
+        self.assertEqual(len(dfm_dirs), self.gamma.n_steps+1)
+
+        incar0 = Incar.from_file(os.path.join('vasp_input', 'INCAR.rlx'))
+        incar0['ISIF'] = 4
+
+        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:
+            st_file = os.path.join(ii, 'POSCAR')
+            self.assertTrue(os.path.isfile(st_file))
+            st0 = Structure.from_file(st_file)
+            st1_file = os.path.join(ii, 'POSCAR.tmp')
+            self.assertTrue(os.path.isfile(st1_file))
+            st1 = Structure.from_file(st1_file)
+            with open(st1_file, mode='r') as f:
+                z_coord_str = f.readlines()[-1].split()[-2]
+                z_coord = float(z_coord_str)
+            self.assertTrue(z_coord <= 1)

tests/auto_test/vasp_input/INCAR_Mo

@@ -0,0 +1,33 @@
+#Parameters
+SYSTEM  =  Mo_hcp
+PREC    =  Accurate
+ISTART   =  0
+ICHARG  =   2
+#Electronic Relaxation 
+ENCUT   =  800     # test
+NELM    =  100
+NELMIN  =  6
+NELMDL  =  -5
+EDIFF   =  1e-06   # test
+LREAL   =  False
+ALGO    =   Normal  # or normal
+#Ionic relaxation
+IBRION  =   2
+#POTIM   =  0.3
+ISIF    =   3
+EDIFFG  =  -0.01   # test
+#ISYM    =   0
+NSW     =   100
+ISMEAR  =  1
+SIGMA   =  0.1    # test
+# Write flags
+LWAVE    =  False
+LCHARG   =  False
+#parallel related
+#KPAR   = 16
+NPAR    =  4
+#KPAR = 1
+KSPACING = 0.1    # test
+KGAMMA  = False
+
+PSTRESS = 0.0