add TBtrans Interface tbtrans_init.py and its test files (#50)

* add tbtrans_init and related files for Shell command * rename load_dptb_model as load_model * add or modify some docstring * add test files for tbtrans_init.py * modify test_tbtrans_init.py * add some comments * change test_hBN_struct to orthogonal unit cell * remove unnecessary sisl import * add warning for input structure file in vasp format. * add docstring to class * fix some small problems * rewrite orbitals_get function * hamil_get to hamil_get_write * add runtime error for .vasp and change R_vec assert * add comments to sort([2,1,0]) * add TODO for double leads and notes on Z-direction trans. * move set_nsc to hamiltonian_get * add notes on Hamil_sisl.set_nsc * add import properties in __init__ * remove unnecessary print * rewrite load_model in for * fix load_model docstring problem * delete load_model and merge its function to hamil_get_write * delete load_model * fix bugs in chemical_symbol determination * check _orbital_name_get
deepmodeling · Dec 11, 2023 · 287663d · 287663d
1 parent 2569acd
commit 287663d
Show file tree

Hide file tree

Showing 8 changed files with 1,070 additions and 1 deletion.
diff --git a/dptb/entrypoints/run.py b/dptb/entrypoints/run.py
@@ -23,6 +23,7 @@
 from dptb.postprocess.bandstructure.ifermi_api import ifermiapi, ifermi_installed, pymatgen_installed
 from dptb.postprocess.write_skparam import WriteNNSKParam
 from dptb.postprocess.NEGF import NEGF
+from dptb.postprocess.tbtrans_init import TBTransInputSet,sisl_installed
 
 __all__ = ["run"]
 
@@ -215,6 +216,14 @@ def run(
         negf.compute()
         log.info(msg='NEGF calculation successfully completed.')
 
+    if task == 'tbtrans_negf':
+        if not(sisl_installed):
+            log.error(msg="sisl is required to perform tbtrans calculation !")
+            raise RuntimeError
+
+        tbtrans_init = TBTransInputSet(apiHrk, run_opt, task_options)
+        tbtrans_init.hamil_get_write(write_nc=True)
+        log.info(msg='TBtrans input files are successfully generated.')
 
     if output:
         with open(os.path.join(output, "run_config.json"), "w") as fp:

diff --git a/dptb/postprocess/tbtrans_init.py b/dptb/postprocess/tbtrans_init.py
diff --git a/dptb/tests/data/test_negf/lead_R.nc b/dptb/tests/data/test_negf/lead_R.nc
diff --git a/dptb/tests/data/test_tbtrans/best_nnsk_b3.600_c3.600_w0.300.json b/dptb/tests/data/test_tbtrans/best_nnsk_b3.600_c3.600_w0.300.json
@@ -0,0 +1,122 @@
+{
+    "onsite": {
+        "N-N-2s-2s-0": [
+            0.02462027035653591,
+            0.007205560803413391
+        ],
+        "N-N-2s-2p-0": [
+            0.008309782482683659,
+            -0.007032226305454969
+        ],
+        "N-N-2p-2p-0": [
+            0.012606431730091572,
+            0.010783562436699867
+        ],
+        "N-N-2p-2p-1": [
+            0.0068643586710095406,
+            -0.011892829090356827
+        ],
+        "N-B-2s-2s-0": [
+            0.041020166128873825,
+            -0.007834071293473244
+        ],
+        "N-B-2s-2p-0": [
+            26.214815139770508,
+            -28.22139549255371
+        ],
+        "N-B-2p-2p-0": [
+            0.2541739046573639,
+            0.3701082468032837
+        ],
+        "N-B-2p-2p-1": [
+            -0.052932459861040115,
+            0.03325718641281128
+        ],
+        "B-N-2s-2s-0": [
+            -0.10863762348890305,
+            -0.10621777176856995
+        ],
+        "B-N-2s-2p-0": [
+            24.486974716186523,
+            26.85447883605957
+        ],
+        "B-N-2p-2p-0": [
+            0.13345032930374146,
+            -0.3127709925174713
+        ],
+        "B-N-2p-2p-1": [
+            -0.03844165802001953,
+            0.00011800970969488844
+        ],
+        "B-B-2s-2s-0": [
+            -0.007172069512307644,
+            0.007495054975152016
+        ],
+        "B-B-2s-2p-0": [
+            0.004442985635250807,
+            0.0030813836492598057
+        ],
+        "B-B-2p-2p-0": [
+            -0.0013882589992135763,
+            -6.591381679754704e-05
+        ],
+        "B-B-2p-2p-1": [
+            -0.009361814707517624,
+            -0.017272837460041046
+        ]
+    },
+    "hopping": {
+        "N-N-2s-2s-0": [
+            0.05967297405004501,
+            -0.21457917988300323
+        ],
+        "N-N-2s-2p-0": [
+            0.042178086936473846,
+            0.5767796635627747
+        ],
+        "N-N-2p-2p-0": [
+            0.1008036881685257,
+            0.5027011632919312
+        ],
+        "N-N-2p-2p-1": [
+            -0.005753065925091505,
+            -1.0040007829666138
+        ],
+        "N-B-2s-2s-0": [
+            0.06605493277311325,
+            2.485130786895752
+        ],
+        "N-B-2s-2p-0": [
+            -0.19711704552173615,
+            -1.884203314781189
+        ],
+        "N-B-2p-2s-0": [
+            -0.06678403168916702,
+            -2.8326284885406494
+        ],
+        "N-B-2p-2p-0": [
+            -0.2129121571779251,
+            3.601222276687622
+        ],
+        "N-B-2p-2p-1": [
+            0.034046269953250885,
+            -4.79115104675293
+        ],
+        "B-B-2s-2s-0": [
+            -0.061647042632102966,
+            -0.4071168601512909
+        ],
+        "B-B-2s-2p-0": [
+            0.048091448843479156,
+            0.8385105729103088
+        ],
+        "B-B-2p-2p-0": [
+            -0.11344866454601288,
+            0.5754562020301819
+        ],
+        "B-B-2p-2p-1": [
+            0.007624409161508083,
+            -0.7790966033935547
+        ]
+    }
+}
diff --git a/dptb/tests/data/test_tbtrans/negf_tbtrans.json b/dptb/tests/data/test_tbtrans/negf_tbtrans.json
@@ -0,0 +1,90 @@
+{
+    "common_options": {
+        "onsitemode": "strain",
+        "onsite_cutoff": 1.6,
+        "bond_cutoff": 3.6,
+        "env_cutoff": 3.5,
+        "atomtype": [
+            "N",
+            "B"
+        ],
+        "proj_atom_neles": {
+            "N": 5,
+            "B": 3
+        },
+        "proj_atom_anglr_m": {
+            "N": [
+                "2s",
+                "2p"
+            ],
+            "B": [
+                "2s",
+                "2p"
+            ]
+        }
+    },   
+    "model_options": {
+        "sknetwork": {
+            "sk_hop_nhidden": 1,
+            "sk_onsite_nhidden": 1
+        },
+        "skfunction": {
+            "sk_cutoff": 3.6,
+            "sk_decay_w": 0.3
+        }
+    },
+    "structure":"./test_hBN_zigzag_struct.xyz",
+	"task_options":
+        {
+            "task": "tbtrans_negf",
+            "scf": true,
+            "block_tridiagonal": false,
+            "ele_T": 500,
+            "unit": "Hartree",
+            "scf_options":{
+                "mode": "PDIIS",
+                "mixing_period": 3,
+                "step_size": 0.05,
+                "n_history": 6,
+                "abs_err": 1e-6,
+                "rel_err": 1e-4,
+                "max_iter": 100
+            },
+            "stru_options":{
+                "pbc":[false, true, false],
+                "kmesh":[1,1,1],
+                "device":{
+                    "id":"8-12",
+                    "sort": true
+                },
+                "lead_L":{
+                    "id":"0-8",
+                    "voltage":0.0
+                },
+                "lead_R":{
+                    "id":"12-20",
+                    "voltage":0.0
+                }
+            },
+            "poisson_options": {
+                "solver": "fmm",
+                "err": 1e-5
+            },
+            "sgf_solver": "Sancho-Rubio",
+            "espacing": 0.1,
+            "emin": -2,
+            "emax": 2,
+            "e_fermi": -9.874357223510742,
+            "density_options":{
+                "method": "Ozaki"
+            },
+            "eta_lead":1e-5,
+            "eta_device":0.0,
+            "out_dos": true,
+            "out_tc": true,
+            "out_ldos": true,
+            "out_current_nscf": true,
+            "out_density": true,
+            "out_lcurrent": true
+    }
+}
diff --git a/dptb/tests/data/test_tbtrans/test_hBN_zigzag_struct.xyz b/dptb/tests/data/test_tbtrans/test_hBN_zigzag_struct.xyz
@@ -0,0 +1,22 @@
+20
+Lattice="30.0 0.0 0.0 0.0 4.337055133 0.0 0.0 0.0 12.519999742500001" Properties=species:S:1:pos:R:3 pbc="T T T"
+N       15.00000000       3.97563387       0.62599999
+B       15.00000000       2.52994883       0.62599999
+N       15.00000000       1.80710631       1.87799996
+B       15.00000000       0.36142126       1.87799996
+N       15.00000000       3.97563387       3.12999994
+B       15.00000000       2.52994883       3.12999994
+N       15.00000000       1.80710631       4.38199991
+B       15.00000000       0.36142126       4.38199991
+N       15.00000000       3.97563387       5.63399988
+B       15.00000000       2.52994883       5.63399988
+N       15.00000000       1.80710631       6.88599986
+B       15.00000000       0.36142126       6.88599986
+N       15.00000000       3.97563387       8.13799983
+B       15.00000000       2.52994883       8.13799983
+N       15.00000000       1.80710631       9.38999981
+B       15.00000000       0.36142126       9.38999981
+N       15.00000000       3.97563387      10.64199978
+B       15.00000000       2.52994883      10.64199978
+N       15.00000000       1.80710631      11.89399976
+B       15.00000000       0.36142126      11.89399976
diff --git a/dptb/tests/test_tbtrans_init.py b/dptb/tests/test_tbtrans_init.py
@@ -0,0 +1,106 @@
+import pytest
+from dptb.nnops.apihost import NNSKHost
+from dptb.plugins.init_nnsk import InitSKModel
+from dptb.nnops.NN2HRK import NN2HRK
+from dptb.postprocess.tbtrans_init import TBTransInputSet
+from dptb.utils.tools import j_loader
+import numpy as np
+
+@pytest.fixture(scope='session', autouse=True)
+def root_directory(request):
+    return str(request.config.rootdir)
+
+
+def test_tbtrans_init(root_directory):
+
+    # check whether sisl is installed: if not, skip this test
+    try:
+        import sisl
+    except:
+        pytest.skip('sisl is not installed which is necessary for TBtrans Input Generation. Therefore, skipping test_tbtrans_init.')
+
+    model_ckpt = f'{root_directory}/dptb/tests/data/test_tbtrans/best_nnsk_b3.600_c3.600_w0.300.json'
+    config = f'{root_directory}/dptb/tests/data/test_tbtrans/negf_tbtrans.json'
+    apihost = NNSKHost(checkpoint=model_ckpt, config=config)
+    apihost.register_plugin(InitSKModel())
+    apihost.build()
+    apiHrk = NN2HRK(apihost=apihost, mode='nnsk')
+
+    run_opt = {
+            "run_sk": True,
+            "init_model":model_ckpt,
+            "results_path":f'{root_directory}/dptb/tests/data/test_tbtrans/',
+            "structure":f'{root_directory}/dptb/tests/data/test_tbtrans/test_hBN_zigzag_struct.xyz',
+            "log_path": '/data/DeepTB/dptb_Zjj/DeePTB/dptb/tests/data/test_tbtrans/output',
+            "log_level": 5,
+            "use_correction":False
+        }
+
+    jdata = j_loader(config)
+    jdata = jdata['task_options']
+    tbtrans_hBN = TBTransInputSet(apiHrk=apiHrk,run_opt=run_opt, jdata=jdata)
+
+    # check _orbitals_name_get
+    element_orbital_name = tbtrans_hBN._orbitals_name_get(['2s', '2p']) 
+    assert element_orbital_name == ['2s', '2py', '2pz', '2px']
+    element_orbital_name = tbtrans_hBN._orbitals_name_get(['3s', '3p', 'd*']) 
+    assert element_orbital_name == ['3s', '3py', '3pz', '3px', 'dxy*', 'dyz*', 'dz2*', 'dxz*', 'dx2-y2*']
+
+
+
+    tbtrans_hBN.hamil_get_write(write_nc=False)
+    assert (tbtrans_hBN.allbonds_all[0].detach().numpy()-np.array([5, 0, 5, 0, 0, 0, 0])).max()<1e-5
+    assert (tbtrans_hBN.allbonds_all[50].detach().numpy()-np.array([ 5,  2,  5, 18,  0,  0, -1])).max()<1e-5
+    assert (tbtrans_hBN.hamil_block_all[0].detach().numpy()-   np.array([[-0.73303634,  0.        ,  0.        ,  0.        ],
+                                                                        [ 0.        ,  0.04233637,  0.        ,  0.        ],
+                                                                        [ 0.        ,  0.        ,  0.04233636,  0.        ],
+                                                                        [ 0.        ,  0.        ,  0.        , -0.27156556]])).max()<1e-5
+    assert (tbtrans_hBN.hamil_block_all[50].detach().numpy()-np.array([[-0.03164609, -0.        ,  0.02028139, -0.        ],
+                                                                        [ 0.        ,  0.00330366,  0.        ,  0.        ],
+                                                                        [-0.02028139,  0.        , -0.05393751,  0.        ],
+                                                                        [ 0.        ,  0.        ,  0.        ,  0.00330366]])).max()<1e-5
+    assert (tbtrans_hBN.allbonds_lead_L[0].detach().numpy()-np.array([5, 0, 5, 0, 0, 0, 0])).max()<1e-5
+    assert (tbtrans_hBN.allbonds_lead_L[50].detach().numpy()-np.array([5, 4, 7, 7, 0, 0, 0])).max()<1e-5
+    assert (tbtrans_hBN.hamil_block_lead_L[0].detach().numpy()-np.array([[-0.73303634,  0.        ,  0.        ,  0.        ],
+                                                                        [ 0.        ,  0.04233637,  0.        ,  0.        ],
+                                                                        [ 0.        ,  0.        ,  0.04233636,  0.        ],
+                                                                        [ 0.        ,  0.        ,  0.        , -0.27156556]])).max()<1e-5
+    assert (tbtrans_hBN.hamil_block_lead_L[50].detach().numpy()-np.array([[ 0.1145315 , -0.06116847,  0.10594689,  0.        ],
+                                                                            [ 0.15539739, -0.04634972,  0.22751862,  0.        ],
+                                                                            [-0.26915616,  0.22751862, -0.30906558,  0.        ],
+                                                                            [-0.        ,  0.        ,  0.        ,  0.08500822]])).max()<1e-5
+
+
+    # tbtrans_hBN.hamil_write()
+    # check the hamiltonian through Hk at Gamma and M 
+    H_lead = tbtrans_hBN.H_lead_L
+    G_eigs = sisl.BandStructure(H_lead, [[0., 0.,0.]], 1, ["G"])
+    M_eigs = sisl.BandStructure(H_lead, [[0, 0.5 ,0 ]], 1, ["M"])
+    Ef = -9.874358177185059
+    G_eigs = G_eigs.apply.array.eigh() -Ef
+    M_eigs = M_eigs.apply.array.eigh() -Ef
+
+    G_eigs_right = np.array([[-19.95362763, -17.10774579, -17.10774579, -16.9118761 ,
+            -11.20609829, -10.01050689, -10.01050689,  -8.11443067,
+            -8.11443067,  -7.60442045,  -6.6550603 ,  -3.79211664,
+            -3.79211663,  -3.22863532,  -3.22863532,  -3.17535758,
+            3.18703263,   3.24031037,   3.24031037,   6.45306332,
+            7.70583557,   7.91107113,  10.91058699,  10.91058699,
+            23.64785516,  23.64785516,  28.30755414,  28.30755428,
+            28.65719263,  30.78452851,  33.25399887,  33.25399887]])
+
+    M_eigs_right = np.array([[-18.69653568, -18.69653568, -16.91187582, -16.91187582,
+            -11.20609828, -11.20609828,  -7.44726991,  -7.44726991,
+            -6.65506047,  -6.65506047,  -5.79252308,  -5.79252308,
+            -5.2193769 ,  -5.2193769 ,  -3.17535758,  -3.17535758,
+            3.18703263,   3.18703263,   5.84906816,   5.84906816,
+            7.74726616,   7.74726616,   7.91107121,   7.91107121,
+            28.12912079,  28.12912079,  28.65719227,  28.65719227,
+            29.54182975,  29.54182975,  30.78452877,  30.78452877]])
+
+    assert (G_eigs[0]-G_eigs_right[0]).max()<1e-5
+    assert (M_eigs[0]-M_eigs_right[0]).max()<1e-5
+
+
+
+