3.15. Deep Potential - Range Correction (DPRc)
Deep Potential - Range Correction (DPRc) is designed to combine with QM/MM method, and corrects energies from a low-level QM/MM method to a high-level QM/MM method:
See the JCTC paper for details.
3.15.1. Training data
Instead the normal ab initio data, one needs to provide the correction from a low-level QM/MM method to a high-level QM/MM method:
Two levels of data use the same MM method, so \(E_\text{MM}\) is eliminated.
3.15.2. Training the DPRc model
In a DPRc model, QM atoms and MM atoms have different atom types. Assuming we have 4 QM atom types (C, H, O, P) and 2 MM atom types (HW, OW):
"type_map": ["C", "H", "HW", "O", "OW", "P"]
As described in the paper, the DPRc model only corrects \(E_\text{QM}\) and \(E_\text{QM/MM}\) within the cutoff, so we use a hybrid descriptor to describe them separatedly:
"descriptor" :{
"type": "hybrid",
"list" : [
{
"type": "se_e2_a",
"sel": [6, 11, 0, 6, 0, 1],
"rcut_smth": 1.00,
"rcut": 9.00,
"neuron": [12, 25, 50],
"exclude_types": [[2, 2], [2, 4], [4, 4], [0, 2], [0, 4], [1, 2], [1, 4], [3, 2], [3, 4], [5, 2], [5, 4]],
"axis_neuron": 12,
"set_davg_zero": true,
"_comment": " QM/QM interaction"
},
{
"type": "se_e2_a",
"sel": [6, 11, 100, 6, 50, 1],
"rcut_smth": 0.50,
"rcut": 6.00,
"neuron": [12, 25, 50],
"exclude_types": [[0, 0], [0, 1], [0, 3], [0, 5], [1, 1], [1, 3], [1, 5], [3, 3], [3, 5], [5, 5], [2, 2], [2, 4], [4, 4]],
"axis_neuron": 12,
"set_davg_zero": true,
"_comment": " QM/MM interaction"
}
]
}
exclude_types can be generated by the following Python script:
from itertools import combinations_with_replacement, product
qm = (0, 1, 3, 5)
mm = (2, 4)
print("QM/QM:", list(map(list, list(combinations_with_replacement(mm, 2)) + list(product(qm, mm)))))
print("QM/MM:", list(map(list, list(combinations_with_replacement(qm, 2)) + list(combinations_with_replacement(mm, 2)))))
Also, DPRc assumes MM atom energies (atom_ener) are zero:
"fitting_net": {
"neuron": [240, 240, 240],
"resnet_dt": true,
"atom_ener": [null, null, 0.0, null, 0.0, null]
}
Note that atom_ener only works when descriptor/set_davg_zero is true.
3.15.3. Run MD simulations
The DPRc model has the best practices with the AMBER QM/MM module. An example is given by GitLab RutgersLBSR/AmberDPRc. In theory, DPRc is able to be used with any QM/MM package, as long as the DeePMD-kit package accepts QM atoms and MM atoms within the cutoff range and returns energies and forces.
3.15.4. Pairwise DPRc
If one wants to correct from a low-level method into a full DFT level, and the system is too large to do full DFT calculation, one may try the experimental pairwise DPRc model. In a pairwise DPRc model, the total energy is divided into QM internal energy and the sum of QM/MM energy for each MM residue \(l\):
In this way, the interaction between the QM region and each MM fragmentation can be computed and trained separately. Thus, the pairwise DPRc model is divided into two sub-DPRc models. qm_model is for the QM internal interaction and qmmm_model is for the QM/MM interaction. The configuration for these two models is similar to the non-pairwise DPRc model. It is noted that the se_atten descriptor should be used, as it is the only descriptor to support the mixed type.
{
"model": {
"type": "pairwise_dprc",
"type_map": [
"C",
"P",
"O",
"H",
"OW",
"HW"
],
"type_embedding": {
"neuron": [
8
],
"precision": "float32"
},
"qm_model": {
"descriptor": {
"type": "se_atten",
"stripped_type_embedding": true,
"sel": 24,
"rcut_smth": 0.50,
"rcut": 9.00,
"attn_layer": 0,
"neuron": [
25,
50,
100
],
"resnet_dt": false,
"axis_neuron": 12,
"precision": "float32",
"seed": 1
},
"fitting_net": {
"type": "ener",
"neuron": [
240,
240,
240
],
"resnet_dt": true,
"precision": "float32",
"atom_ener": [
null,
null,
null,
null,
0.0,
0.0
],
"seed": 1
}
},
"qmmm_model": {
"descriptor": {
"type": "se_atten",
"stripped_type_embedding": true,
"sel": 27,
"rcut_smth": 0.50,
"rcut": 6.00,
"attn_layer": 0,
"neuron": [
25,
50,
100
],
"resnet_dt": false,
"axis_neuron": 12,
"set_davg_zero": true,
"exclude_types": [
[
0,
0
],
[
0,
1
],
[
0,
2
],
[
0,
3
],
[
1,
1
],
[
1,
2
],
[
1,
3
],
[
2,
2
],
[
2,
3
],
[
3,
3
],
[
4,
4
],
[
4,
5
],
[
5,
5
]
],
"precision": "float32",
"seed": 1
},
"fitting_net": {
"type": "ener",
"neuron": [
240,
240,
240
],
"resnet_dt": true,
"seed": 1,
"precision": "float32",
"atom_ener": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
]
}
}
}
}
The pairwise model needs information for MM residues. The model uses aparam with the shape of nframes x natoms to get the residue index. The QM residue should always use 0 as the index. For example, 0 0 0 1 1 1 2 2 2 means these 9 atoms are grouped into one QM residue and two MM residues.