fix pbc bug to accomdate the removing of pbc in AtomicData_options

deepmodeling · Aug 28, 2024 · 06d5443 · 06d5443
1 parent 482e7e1
commit 06d5443
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Showing 3 changed files with 7 additions and 6 deletions.
diff --git a/dptb/negf/negf_hamiltonian_init.py b/dptb/negf/negf_hamiltonian_init.py
@@ -172,11 +172,14 @@ def initialize(self, kpoints, block_tridiagnal=False,useBloch=False,bloch_factor
         # device_id[0] = n_proj_atom_pre
         # device_id[1] = n_proj_atom_pre + n_proj_atom_device
         # self.device_id = device_id
-    
+
         self.structase.set_pbc(self.pbc_negf)
+        self.structase.pbc[2] = True
         alldata = AtomicData.from_ase(self.structase, **self.AtomicData_options)
+        print('alldata[AtomicDataDict.PBC_KEY]',alldata[AtomicDataDict.PBC_KEY])
         alldata[AtomicDataDict.PBC_KEY][2] = True # force pbc in z-axis to get reasonable chemical environment in two ends
-
+        print('alldata[AtomicDataDict.PBC_KEY]',alldata[AtomicDataDict.PBC_KEY])
+
         alldata = AtomicData.to_AtomicDataDict(alldata.to(self.torch_device))
         self.alldata = self.model.idp(alldata)
         self.alldata[AtomicDataDict.KPOINT_KEY] = \

diff --git a/dptb/tests/data/test_negf/test_negf_run/negf_chain_new.json b/dptb/tests/data/test_negf/test_negf_run/negf_chain_new.json
@@ -52,8 +52,7 @@
         "out_current_nscf": true
 },    
 "AtomicData_options" :{
-    "r_max": 2.0,
-    "pbc": true
+    "r_max": 2.0
 },
 "structure":"./chain.vasp"
 }
diff --git a/dptb/tests/data/test_negf/test_negf_run/negf_graphene_new.json b/dptb/tests/data/test_negf/test_negf_run/negf_graphene_new.json
@@ -55,8 +55,7 @@
             "out_lcurrent": false
     },    
     "AtomicData_options" :{
-        "r_max": 2.0,
-        "pbc": true
+        "r_max": 2.0
     },
     "structure":"./graphene.xyz"
 }