deepmd.tf.nvnmd.entrypoints
Submodules
Package Contents
Classes
Generate the mapping table describing the relastionship of | |
Generate the binary model file (model.pb). |
Functions
| Save the dictionary of weight to a npy file. |
- deepmd.tf.nvnmd.entrypoints.save_weight(sess, file_name: str = 'nvnmd/weight.npy')[source]
Save the dictionary of weight to a npy file.
- class deepmd.tf.nvnmd.entrypoints.MapTable(config_file: str, weight_file: str, map_file: str)[source]
Generate the mapping table describing the relastionship of atomic distance, cutoff function, and embedding matrix.
three mapping table will be built:
\(r^2_{ji} \rightarrow s_{ji}\)\(r^2_{ji} \rightarrow h_{ji}\)\(r^2_{ji} \rightarrow \mathcal{G}_{ji}\)where \(s_{ji}\) is cut-off function, \(h_{ji} = \frac{s(r_{ji})}{r_{ji}}\), and \(\mathcal{G}_{ji}\) is embedding matrix.
The mapping funciton can be define as:
\(y = f(x) = y_{k} + (x - x_{k}) * dy_{k}\)\(y_{k} = f(x_{k})\)\(dy_{k} = \frac{f(x_{k+1}) - f(x_{k})}{dx}\)\(x_{k} \leq x < x_{k+1}\)\(x_{k} = k * dx\)where \(dx\) is interpolation interval.
- Parameters:
- config_file
input file name an .npy file containing the configuration information of NVNMD model
- weight_file
input file name an .npy file containing the weights of NVNMD model
- map_file
output file name an .npy file containing the mapping tables of NVNMD model
References
DOI: 10.1038/s41524-022-00773-z
- build_map_coef(cfgs, x, ys, grads, grad_grads, Nr, Nc)[source]
Build mapping table coefficient cfgs: cfg list cfg = x0, x1, dx.
coef4: a x^3 + b x^2 + c x + d = y: / d = y0 | c = y0’ | b = (3 y1 - dx dy’ - 2dx y0’ - 3y0) / dx^2 a = (dx y1’ - 2 y1 + dx y0’ + 2 y0) / dx^3
- cal_coef4(cfgs, x, y, dy)[source]
Build mapping table coefficient for one line coef4: a x^3 + b x^2 + c x + d = y: / d = y0 | c = y0’ | b = (3 y1 - dx dy’ - 2dx y0’ - 3y0) / dx^2 a = (dx y1’ - 2 y1 + dx y0’ + 2 y0) / dx^3.
- class deepmd.tf.nvnmd.entrypoints.Wrap(config_file: str, weight_file: str, map_file: str, model_file: str)[source]
Generate the binary model file (model.pb).
the model file can be use to run the NVNMD with lammps the pair style need set as:
pair_style nvnmd model.pb pair_coeff * *
- Parameters:
- config_file
input file name an .npy file containing the configuration information of NVNMD model
- weight_file
input file name an .npy file containing the weights of NVNMD model
- map_file
input file name an .npy file containing the mapping tables of NVNMD model
- model_file
output file name an .pb file containing the model using in the NVNMD
References
DOI: 10.1038/s41524-022-00773-z
- wrap_head(nhs, nws)[source]
Wrap the head information.
version nhead nheight nwidth rcut cut-off radius ntype number of atomic species nnei number of neighbors atom_ener atom bias energy
- wrap_dscp()[source]
Wrap the configuration of descriptor.
version 0: [NBIT_IDX_S2G-1:0] SHIFT_IDX_S2G
[NBIT_NEIB*NTYPE-1:0] SELs [NBIT_FIXD*M1*NTYPE*NTYPE-1:0] GSs [NBIT_FLTE-1:0] NEXPO_DIV_NI
version 1:
[NBIT_FLTE-1:0] NEXPO_DIV_NI