From 06d5443433e031b712e7f1312357cab7ac99dd9d Mon Sep 17 00:00:00 2001
From: AsymmetryChou <181240085@smail.nju.edu.cn>
Date: Wed, 28 Aug 2024 12:47:37 +0800
Subject: [PATCH] fix pbc bug to accomdate the removing of pbc in
 AtomicData_options

---
 dptb/negf/negf_hamiltonian_init.py                         | 7 +++++--
 .../tests/data/test_negf/test_negf_run/negf_chain_new.json | 3 +--
 .../data/test_negf/test_negf_run/negf_graphene_new.json    | 3 +--
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/dptb/negf/negf_hamiltonian_init.py b/dptb/negf/negf_hamiltonian_init.py
index 5c782b6a..756f8770 100644
--- 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
index 0ad717d3..d8140fbd 100644
--- 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"
 }
\ No newline at end of file
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
index 5ce5d1c2..269bdba1 100644
--- 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"
 }
\ No newline at end of file