build surface by using ASE interface

README.md

@@ -199,7 +199,7 @@ Following is an example for `PARAM`, which generates data from a typical structu
     2,
     2
   ],
-  "z_min": 9,
+  "layer_numb": 3,
   "vacuum_max": 9,
   "vacuum_resol": [
     0.5,
@@ -251,7 +251,7 @@ The bold notation of key (such as **Elements**) means that it's a necessary key.
 | **Elements** | List of String | ["Mg"] | Atom types
 |  **cell_type** | String  | "hcp" | Specifying which typical structure to be generated. **Options** include fcc, hcp, bcc, sc, diamond.
 | **latt** | Float | 4.479 | Lattice constant for single cell.
-| **z_min** | Float | 9 | Thickness of slab (Angstrom).
+| **layer_numb** | Integer | 3 | Number of equavilent layers of slab.
 | **vacuum_max** | Float | 9 | Maximal thickness of vacuum (Angstrom).
 | **vacuum_resol** | List of float | [0.5, 1 ] | Interval of thichness of vacuum. If size of `vacuum_resol` is 1, the interval is fixed to its value. If size of `vacuum_resol` is 2, the interval is `vacuum_resol[0]` before `mid_point`, otherwise `vacuum_resol[1]` after `mid_point`.
 | **millers** | List of list of Integer | [[1,0,0]] | Miller indices. 

dpgen/data/surf.py

@@ -15,6 +15,11 @@
 from dpgen.remote.RemoteJob import SSHSession, JobStatus, SlurmJob, PBSJob, CloudMachineJob
 from pymatgen.core.surface import SlabGenerator,generate_all_slabs, Structure
 from pymatgen.io.vasp import Poscar
+#-----ASE-------
+from pymatgen.io.ase import AseAtomsAdaptor
+from ase.io import read
+from ase.build import general_surface
+
 
 def create_path (path) :
     path += '/'
@@ -195,10 +200,16 @@ def make_super_cell_pymatgen (jdata) :
     from_path = path_uc
     from_file = os.path.join(from_path, 'POSCAR.unit')
     ss = Structure.from_file(from_file)
+    # ase only support X type  element
+    for i in range(len(ss)):
+        ss[i]='X'
+    ss=AseAtomsAdaptor.get_atoms(ss)
+
 
     all_millers = jdata['millers']
     path_sc = os.path.join(out_dir, global_dirname_02)
-    z_min = jdata['z_min']
+    #z_min = jdata['z_min']
+    layer_numb = jdata['layer_numb']
     super_cell = jdata['super_cell']
 
     cwd = os.getcwd()    
@@ -211,11 +222,13 @@ def make_super_cell_pymatgen (jdata) :
             miller_str += str(ii)        
         path_cur_surf = create_path('surf-'+miller_str)
         os.chdir(path_cur_surf)
-        slabgen = SlabGenerator(ss, miller, z_min, 1e-3)
-        all_slabs = slabgen.get_slabs() 
+        #slabgen = SlabGenerator(ss, miller, z_min, 1e-3)
+        slab=general_surface.surface(ss,indices=miller,vacuum=1e-3,layers=layer_numb)
+        #all_slabs = slabgen.get_slabs() 
         dlog.info(os.getcwd())
-        dlog.info("Miller %s: The slab has %s termination, use the first one" %(str(miller), len(all_slabs)))
-        all_slabs[0].to('POSCAR', 'POSCAR')
+        #dlog.info("Miller %s: The slab has %s termination, use the first one" %(str(miller), len(all_slabs)))
+        #all_slabs[0].to('POSCAR', 'POSCAR')
+        slab.write('POSCAR',vasp5=True)
         if super_cell[0] > 1 or super_cell[1] > 1 :
             st=Structure.from_file('POSCAR')
             st.make_supercell([super_cell[0], super_cell[1], 1])
@@ -408,7 +421,7 @@ def pert_scaled(jdata) :
           tail_elongs = np.arange(mid_point, vacuum_max, vacuum_resol[1]).tolist()
           elongs = np.unique(head_elongs+tail_elongs).tolist()
        else:
-          raise RuntimeError("the length of vacuum_resol must equal 2")
+          raise RuntimeError("the length of vacuum_resol must equal 1 or 2")
 
     else:         
        vacuum_num = jdata['vacuum_numb']

dpgen/data/tools/bcc.py

@@ -9,7 +9,7 @@ def gen_box () :
 def poscar_unit (latt) :
     box = gen_box()
     ret  = ""
-    ret += "FCC : a = %f \n" % latt
+    ret += "BCC : a = %f \n" % latt
     ret += "%.16f\n" % (latt)
     ret += "%.16f %.16f %.16f\n" % (box[0][0], box[0][1], box[0][2])
     ret += "%.16f %.16f %.16f\n" % (box[1][0], box[1][1], box[1][2])

dpgen/main.py

@@ -105,8 +105,8 @@ def main():
         help="Collecting data from Deep Generator.")
     parser_db.add_argument('PATH', type=str,
                         help="root path for dpgen modeling")
-    parser_db.add_argument('CALCULATOR', type=str,
-                        help="calculator used for labeling: vasp/pwscf/gaussian")
+    parser_db.add_argument('ENGINE', type=str,
+                        help="engine used for labeling: vasp/pwscf/cp2k/gaussian/siesta")
     parser_db.add_argument('OUTPUT', type=str,
                         help="output filename : file.json/file.yaml")
     parser_db.add_argument("ID_PREFIX", type=str, default=None,

tests/data/surf-100.POSCAR

@@ -1,14 +1,20 @@
-Type6
-1.0
-2.899138 0.000000 0.000000
-0.000000 2.899138 0.000000
-0.000000 0.000000 16.400000
+ X 
+ 1.0000000000000000
+     4.0999999999999996    0.0000000000000000    0.0000000000000000
+     0.0000000000000000    4.0999999999999996    0.0000000000000000
+     0.0000000000000000    0.0000000000000000   10.2520000000000007
 Al 
-6 
-direct
-0.000000 0.000000 0.812500 Type0+
-0.000000 0.000000 0.312500 Type0+
-0.500000 0.500000 0.937500 Type0+
-0.000000 0.000000 0.562500 Type0+
-0.500000 0.500000 0.687500 Type0+
-0.500000 0.500000 0.437500 Type0+
+12 
+Cartesian
+  2.0499999999999998  2.0499999999999998  4.1010000000000000
+  0.0000000000000000  2.0499999999999998  6.1509999999999998
+  0.0000000000000000  0.0000000000000000  4.1010000000000000
+  0.0000000000000000  0.0000000000000000  8.2010000000000005
+  2.0499999999999998  2.0499999999999998  8.2010000000000005
+  2.0499999999999998  0.0000000000000000 10.2510000000000012
+  2.0499999999999998  0.0000000000000000  2.0510000000000002
+  0.0000000000000000  2.0499999999999998 10.2510000000000012
+  2.0499999999999998  0.0000000000000000  6.1509999999999998
+  2.0499999999999998  2.0499999999999998  0.0010000000000003
+  0.0000000000000000  2.0499999999999998  2.0510000000000002
+  0.0000000000000000  0.0000000000000000  0.0010000000000003

tests/data/surf.json

@@ -10,7 +10,7 @@
     1,
     1
   ],
-  "z_min": 9,
+  "layer_numb": 3,
   "vacuum_max": 9,
   "vacuum_resol": [
     0.5,