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Add trans with higher k in tutorial2 #43

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cfd4a99
add self-enrgy for k20 in .gitignore
AsymmetryChou Sep 23, 2025
79aed84
add tutor2 in index.rst
AsymmetryChou Sep 23, 2025
0e56c4a
add hBN and MoS2
AsymmetryChou Sep 25, 2025
8494259
add MoS2
AsymmetryChou Sep 26, 2025
89051d8
add MoS2 model
AsymmetryChou Sep 26, 2025
4bab7f3
add hBN model
AsymmetryChou Sep 26, 2025
830bea6
add hBN TBT results
AsymmetryChou Sep 26, 2025
0ba2cfb
update tutor2
AsymmetryChou Sep 26, 2025
0691d17
add docs
AsymmetryChou Sep 26, 2025
ac3066e
Merge branch 'main' into update_tutor2
AsymmetryChou Sep 27, 2025
09c43f8
mv fig to _static
AsymmetryChou Sep 27, 2025
a737529
update formula
AsymmetryChou Sep 27, 2025
b09d496
rm unnecessary cell output
AsymmetryChou Sep 27, 2025
51b1ddd
add more docs
AsymmetryChou Sep 27, 2025
a085dc0
Merge branch 'main' into update_tutor2
AsymmetryChou Sep 27, 2025
6b54dda
update tutor2
AsymmetryChou Sep 30, 2025
db82209
Merge branch 'main' into update_tutor2
AsymmetryChou Sep 30, 2025
a08d054
fix structure name
AsymmetryChou Sep 30, 2025
3b57719
add time benchmark input for graphene and hBN
AsymmetryChou Sep 30, 2025
04c56ae
add negf.out.pth for hBN k70
AsymmetryChou Sep 30, 2025
ef4c47b
update MoS2 case
AsymmetryChou Sep 30, 2025
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,16 @@ dpnegf/tests/data/test_tbtrans/show.ipynb
# tutorial files
examples/graphene/negf_output_k20/self_energy/self_energy_leadL.h5
examples/graphene/negf_output_k20/self_energy/self_energy_leadR.h5

examples/hBN/negf_output_k20/self_energy/self_energy_leadL.h5
examples/hBN/negf_output_k20/self_energy/self_energy_leadR.h5
examples/hBN/negf_output_k50/self_energy/*
examples/hBN/negf_output_k100/self_energy/*
examples/hBN/negf_output_k70/self_energy/*




run_config.json
dpnegf/nnet/__pycache__/
dpnegf/sktb/__pycache__/
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175 changes: 144 additions & 31 deletions docs/hands_on/tutorial2_2d_mat.ipynb
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4 changes: 2 additions & 2 deletions examples/MoS2/negf.json
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@@ -1,5 +1,5 @@
{
"structure":"./struct_negf.xyz",
"structure":"./stru_negf.xyz",
"task_options":
{
"task": "negf",
Expand All @@ -11,7 +11,7 @@
"gamma_center": false,
"time_reversal_symmetry": true,
"nel_atom": {"Mo":6,"S":6},
"kmesh":[1,1,1],
"kmesh":[100,1,1],
"pbc":[true, false, false],
"device":{
"id":"24-48",
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Binary file added examples/MoS2/negf_output_k100/negf.out.pth
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2 changes: 1 addition & 1 deletion examples/graphene/negf.json
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@@ -1,5 +1,5 @@
{
"structure":"./struct_negf.xyz",
"structure":"./stru_negf.xyz",
"task_options":
{
"task": "negf",
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52 changes: 52 additions & 0 deletions examples/graphene/negf_time_bench.json
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@@ -0,0 +1,52 @@
{
"structure":"./stru_negf_time_bench.xyz",
"task_options":
{
"task": "negf",
"scf": false,
"block_tridiagonal": true,
"ele_T": 300,
"unit": "eV",
"stru_options":{
"gamma_center": false,
"time_reversal_symmetry": true,
"nel_atom": {"C": 4},
"kmesh":[1,1,1],
"pbc":[false, true, false],
"device":{
"id":"32-80",
"sort": true
},
"lead_L":{
"id":"0-32",
"voltage":0.0,
"kmesh_lead_Ef":[1,50,20],
"useBloch": false
},
"lead_R":{
"id":"80-112",
"voltage":0.0,
"kmesh_lead_Ef":[1,50,20],
"useBloch": false
}
},
"density_options": {
"method": "Fiori",
"integrate_way": "direct"
},
"poisson_options": {
"solver": "fmm",
"err": 1e-5
},
"sgf_solver": "Sancho-Rubio",
"espacing": 0.025,
"emin": -2.5,
"emax": 2.5,
"eta_lead":1e-5,
"eta_device":0.0,
"out_dos": false,
"out_tc": true,
"out_ldos": false,
"out_current_nscf": false
}
}
114 changes: 114 additions & 0 deletions examples/graphene/stru_negf_time_bench.xyz
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@@ -0,0 +1,114 @@
112
Lattice="30.0 0.0 0.0 0.0 5.0079999 0.0 0.0 0.0 104.0893232" Properties=species:S:1:pos:R:3 nsc="1 1 1" boundary_condition="PERIODIC PERIODIC PERIODIC PERIODIC PERIODIC PERIODIC" pbc="T T T"
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10 changes: 5 additions & 5 deletions examples/hBN/negf.json
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@@ -1,5 +1,5 @@
{
"structure":"./struct_negf.xyz",
"structure":"./stru_negf.xyz",
"task_options":
{
"task": "negf",
Expand All @@ -12,7 +12,7 @@
"time_reversal_symmetry": true,
"nel_atom": {"B": 3,
"N": 5},
"kmesh":[1,1,1],
"kmesh":[1,100,1],
"pbc":[false, true, false],
"device":{
"id":"32-64",
Expand Down Expand Up @@ -40,9 +40,9 @@
"err": 1e-5
},
"sgf_solver": "Sancho-Rubio",
"espacing": 0.05,
"emin": -10,
"emax": 10,
"espacing": 0.025,
"emin": -2.5,
"emax": 2.5,
"eta_lead":1e-5,
"eta_device":0.0,
"out_dos": true,
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53 changes: 53 additions & 0 deletions examples/hBN/negf_time_bench.json
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@@ -0,0 +1,53 @@
{
"structure":"./stru_negf_time_bench.xyz",
"task_options":
{
"task": "negf",
"scf": false,
"block_tridiagonal": true,
"ele_T": 300,
"unit": "eV",
"stru_options":{
"gamma_center": false,
"time_reversal_symmetry": true,
"nel_atom": {"B": 3,
"N": 5},
"kmesh":[1,1,1],
"pbc":[false, true, false],
"device":{
"id":"32-80",
"sort": true
},
"lead_L":{
"id":"0-32",
"voltage":0.0,
"kmesh_lead_Ef":[1,50,20],
"useBloch": false
},
"lead_R":{
"id":"80-112",
"voltage":0.0,
"kmesh_lead_Ef":[1,50,20],
"useBloch": false
}
},
"density_options": {
"method": "Fiori",
"integrate_way": "direct"
},
"poisson_options": {
"solver": "fmm",
"err": 1e-5
},
"sgf_solver": "Sancho-Rubio",
"espacing": 0.025,
"emin": -2,
"emax": 2,
"eta_lead":1e-5,
"eta_device":0.0,
"out_dos": false,
"out_tc": true,
"out_ldos": false,
"out_current_nscf": false
}
}
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