Si demo (#114)

* update si example * update silicon.ipynb * update nrl * rename nrl notebook * update Sn soc example * chore: update Si_nrl.json * chore: rename Si_nrl.ipynb and Sn_soc.ipynb
deepmodeling · Apr 9, 2024 · 55b4d81 · 55b4d81
1 parent c4e8b49
commit 55b4d81
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Showing 40 changed files with 1,570 additions and 715 deletions.
diff --git a/dptb/tests/data/json_model/Si_nrl.json b/dptb/tests/data/json_model/Si_nrl.json
@@ -26,7 +26,10 @@
                 "rc": 6.6147151362875,
                 "w": 0.2645886054515
             },
-            "soc":{}
+            "soc": {},
+            "freeze": false,
+            "std": 0.01,
+            "push": false
         }
     },
     "model_params": {

diff --git a/dptb/utils/read_NRL_tojson.py b/dptb/utils/read_NRL_tojson.py
@@ -230,6 +230,7 @@ def nrl2dptb(input, NRL_data):
             "rc": Rcut * bohr2ang,
             "w": Lscreen * bohr2ang
         },
+        "soc":{},
         "freeze": freeze,
         "std": std,
         "push": push}
@@ -259,7 +260,11 @@ def nrl2dptb(input, NRL_data):
                 "method": f'NRL{overlap_type}',
                 "rc": Rcut * bohr2ang,
                 "w": Lscreen * bohr2ang
-            }
+            },
+            "soc":{},
+            "freeze": freeze,
+            "std": std,
+            "push": push
         }
     }
     model['model_params'] = nrl_tb

diff --git a/examples/NRL-TB/silicon/Si_nrl.ipynb b/examples/NRL-TB/silicon/Si_nrl.ipynb
diff --git a/examples/NRL-TB/silicon/input_n2j.json b/examples/NRL-TB/silicon/input_n2j.json
@@ -0,0 +1,15 @@
+{
+    "common_options": {
+        "basis": {
+            "Si": [
+                "3s",
+                "3p",
+                "d*"
+            ]
+        },
+        "device": "cpu",
+        "dtype": "float32",
+        "overlap": true,
+        "seed": 3982377700
+    }
+}
diff --git a/examples/NRL-TB/silicon/outv2spd/nrl_ckpt.json b/examples/NRL-TB/silicon/outv2spd/nrl_ckpt.json
@@ -25,7 +25,8 @@
                 "method": "NRL1",
                 "rc": 6.6147151362875,
                 "w": 0.2645886054515
-            }
+            },
+            "soc":{}
         }
     },
     "model_params": {

diff --git a/examples/NRL-TB/silicon/plot_v2.ipynb b/examples/NRL-TB/silicon/plot_v2.ipynb
diff --git a/examples/Sn_soc/Sn_soc.ipynb b/examples/Sn_soc/Sn_soc.ipynb
diff --git a/examples/Sn_soc/data/non_soc/BANDS_1.dat b/examples/Sn_soc/data/non_soc/BANDS_1.dat
diff --git a/examples/Sn_soc/data/non_soc/ref_eig_band.npy b/examples/Sn_soc/data/non_soc/ref_eig_band.npy
diff --git a/examples/Sn_soc/data/soc/BANDS_1.dat b/examples/Sn_soc/data/soc/BANDS_1.dat
diff --git a/examples/Sn_soc/data/soc/ref_eig_band.npy b/examples/Sn_soc/data/soc/ref_eig_band.npy
diff --git a/examples/Sn_soc/plot_v1json_nonsoc.ipynb b/examples/Sn_soc/plot_v1json_nonsoc.ipynb
diff --git a/examples/Sn_soc/plot_v1json_soc.ipynb b/examples/Sn_soc/plot_v1json_soc.ipynb
diff --git a/examples/Sn_soc/plot_v2_soc.ipynb b/examples/Sn_soc/plot_v2_soc.ipynb
diff --git a/examples/silicon/inputs/2-3_1_input.json b/examples/silicon/inputs/2-3_1_input.json
@@ -8,7 +8,7 @@
             "overlap": false
     },
     "train_options": {
-        "num_epoch": 1500,
+        "num_epoch": 50,
         "batch_size": 1,
         "ref_batch_size": 1,
         "optimizer": {
@@ -23,7 +23,7 @@
             "train": {"method": "eigvals"},
             "reference": {"method": "eigvals"}
         },
-        "save_freq": 500,
+        "save_freq": 50,
         "validation_freq": 10,
         "display_freq": 1
     },

diff --git a/examples/silicon/inputs/2-3_2_input.json b/examples/silicon/inputs/2-3_2_input.json
@@ -8,7 +8,7 @@
             "overlap": false
     },
     "train_options": {
-        "num_epoch": 1500,
+        "num_epoch": 50,
         "batch_size": 1,
         "ref_batch_size": 1,
         "optimizer": {
@@ -23,7 +23,7 @@
             "train": {"method": "eigvals"},
             "reference": {"method": "eigvals"}
         },
-        "save_freq": 500,
+        "save_freq": 50,
         "validation_freq": 10,
         "display_freq": 1
     },

diff --git a/examples/silicon/inputs/2-4_input.json b/examples/silicon/inputs/2-4_input.json
@@ -8,7 +8,7 @@
             "overlap": false
     },
     "train_options": {
-        "num_epoch": 1500,
+        "num_epoch": 50,
         "batch_size": 1,
         "optimizer": {
             "lr": 0.001,
@@ -22,7 +22,7 @@
             "train": {"method": "eigvals"},
             "reference": {"method": "eigvals"}
         },
-        "save_freq": 500,
+        "save_freq": 50,
         "validation_freq": 10,
         "display_freq": 1
     },

diff --git a/examples/silicon/ref_ckpts/dptb/checkpoint/mix.ep1461.pth b/examples/silicon/ref_ckpts/dptb/checkpoint/mix.ep1461.pth
diff --git a/examples/silicon/ref_ckpts/dptb/checkpoint/mix.ep50.pth b/examples/silicon/ref_ckpts/dptb/checkpoint/mix.ep50.pth
diff --git a/examples/silicon/ref_ckpts/dptb/checkpoint/mix.iter1000.pth b/examples/silicon/ref_ckpts/dptb/checkpoint/mix.iter1000.pth
diff --git a/examples/silicon/ref_ckpts/dptb/checkpoint/mix.iter1500.pth b/examples/silicon/ref_ckpts/dptb/checkpoint/mix.iter1500.pth
diff --git a/examples/silicon/ref_ckpts/dptb/checkpoint/mix.iter500.pth b/examples/silicon/ref_ckpts/dptb/checkpoint/mix.iter500.pth
diff --git a/examples/silicon/ref_ckpts/dptb/train_config.json b/examples/silicon/ref_ckpts/dptb/train_config.json
@@ -13,7 +13,7 @@
         "seed": 3982377700
     },
     "train_options": {
-        "num_epoch": 1500,
+        "num_epoch": 50,
         "batch_size": 1,
         "optimizer": {
             "lr": 0.001,
@@ -36,11 +36,17 @@
                 "diff_on": false,
                 "eout_weight": 0.01,
                 "diff_weight": 0.01
+            },
+            "reference": {
+                "method": "eigvals",
+                "diff_on": false,
+                "eout_weight": 0.01,
+                "diff_weight": 0.01
             }
         },
-        "save_freq": 500,
+        "save_freq": 50,
         "validation_freq": 10,
-        "display_freq": 100,
+        "display_freq": 1,
         "ref_batch_size": 1,
         "val_batch_size": 1,
         "max_ckpt": 4
@@ -83,12 +89,23 @@
                 "w": 0.1
             },
             "freeze": true,
+            "soc": {},
             "std": 0.01,
-            "push": false
+            "push": null
         }
     },
     "data_options": {
         "train": {
+            "root": "./data/",
+            "prefix": "kpathmd100",
+            "get_eigenvalues": true,
+            "type": "DefaultDataset",
+            "separator": ".",
+            "get_Hamiltonian": false,
+            "get_overlap": false,
+            "get_DM": false
+        },
+        "reference": {
             "root": "./data/",
             "prefix": "kpath_spk",
             "get_eigenvalues": true,

diff --git a/examples/silicon/ref_ckpts/nnsk/checkpoint/nnsk.ep495.pth b/examples/silicon/ref_ckpts/nnsk/checkpoint/nnsk.ep495.pth
diff --git a/examples/silicon/ref_ckpts/nnsk/checkpoint/nnsk.iter500.pth b/examples/silicon/ref_ckpts/nnsk/checkpoint/nnsk.iter500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_2/checkpoint/nnsk.ep500.pth b/examples/silicon/ref_ckpts/nnsk_2/checkpoint/nnsk.ep500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_2/checkpoint/nnsk.iter500.pth b/examples/silicon/ref_ckpts/nnsk_2/checkpoint/nnsk.iter500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_3/checkpoint/nnsk.iter1500.pth b/examples/silicon/ref_ckpts/nnsk_3/checkpoint/nnsk.iter1500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_3/checkpoint/nnsk.iter_rs4.832_w0.300.pth b/examples/silicon/ref_ckpts/nnsk_3/checkpoint/nnsk.iter_rs4.832_w0.300.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_4/checkpoint/nnsk.iter1500.pth b/examples/silicon/ref_ckpts/nnsk_4/checkpoint/nnsk.iter1500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_4/checkpoint/nnsk.iter_rs5.000_w0.097.pth b/examples/silicon/ref_ckpts/nnsk_4/checkpoint/nnsk.iter_rs5.000_w0.097.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_md100/checkpoint/nnsk.ep50.pth b/examples/silicon/ref_ckpts/nnsk_md100/checkpoint/nnsk.ep50.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_md100/checkpoint/nnsk.ep500.pth b/examples/silicon/ref_ckpts/nnsk_md100/checkpoint/nnsk.ep500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_md100/checkpoint/nnsk.iter500.pth b/examples/silicon/ref_ckpts/nnsk_md100/checkpoint/nnsk.iter500.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_md25/checkpoint/nnsk.ep499.pth b/examples/silicon/ref_ckpts/nnsk_md25/checkpoint/nnsk.ep499.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_md25/checkpoint/nnsk.ep50.pth b/examples/silicon/ref_ckpts/nnsk_md25/checkpoint/nnsk.ep50.pth
diff --git a/examples/silicon/ref_ckpts/nnsk_md25/checkpoint/nnsk.iter500.pth b/examples/silicon/ref_ckpts/nnsk_md25/checkpoint/nnsk.iter500.pth
diff --git a/examples/silicon/run/band.json b/examples/silicon/run/band.json
@@ -12,13 +12,16 @@
                 [0.5000000000,   0.0000000000,   0.5000000000,   1 ]
                 ],
         "klabels":["G","X","X/U","K","G","L","W","X"],
-        "E_fermi":-9.307,
+        "nel_atom":{"Si":4},
+        "E_fermi":-4.722,
         "emin":-15,
         "emax":10,
         "ref_band": "./data/kpath.0/eigenvalues.npy"
     },
     "AtomicData_options": {
         "r_max": 5.0,
+        "er_max":5.0, 
+        "oer_max":2.5,
         "pbc": true
     }
 }
diff --git a/examples/silicon/run/band_2.json b/examples/silicon/run/band_2.json
@@ -15,9 +15,16 @@
                 [0.5000000000, -0.500000000, 0.0000000000, 1]
                 ],
         "klabels":["G","X","Y","G","Z","R_2","G","T_2","U_2","G","V_2"],
+        "nel_atom":{"Si":4},
         "E_fermi":-9.702,
         "emin":-14,
         "emax":12,
         "ref_band": "./data/kpathmd100.0/eigenvalues_ref.npy"
+    },
+    "AtomicData_options": {
+        "r_max": 5.0,
+        "er_max":5.0, 
+        "oer_max":2.5,
+        "pbc": true
     }
 }
diff --git a/examples/silicon/silicon.ipynb b/examples/silicon/silicon.ipynb