DeePMD-kit API¶
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class
deepmd.Data.
DataSets
(sys_path, set_prefix, seed=None, shuffle_test=True)¶ -
check_batch_size
(batch_size)¶
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check_test_size
(test_size)¶
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get_batch
(batch_size)¶ returned property prefector [4] in order: energy, force, virial, atom_ener
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get_ener
()¶
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get_natoms
()¶
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get_natoms_2
(ntypes)¶
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get_natoms_vec
(ntypes)¶
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get_numb_set
()¶
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get_set
(data, idx=None)¶
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get_sys_numb_batch
(batch_size)¶
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get_test
()¶ returned property prefector [4] in order: energy, force, virial, atom_ener
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get_type_map
()¶
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load_batch_set
(set_name)¶
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load_data
(set_name, data_name, shape, is_necessary=True)¶
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load_energy
(set_name, nframes, nvalues, energy_file, atom_energy_file)¶ return : coeff_ener, ener, coeff_atom_ener, atom_ener
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load_set
(set_name, shuffle=True)¶
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load_test_set
(set_name, shuffle_test)¶
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load_type
(sys_path)¶
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load_type_map
(sys_path)¶
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numb_aparam
()¶
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numb_fparam
()¶
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reset_iter
()¶
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set_numb_batch
(batch_size)¶
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stats_energy
()¶
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class
deepmd.Data.
DeepmdData
(sys_path, set_prefix='set', shuffle_test=True, type_map=None, modifier=None)¶ -
add
(key, ndof, atomic=False, must=False, high_prec=False, type_sel=None, repeat=1)¶
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avg
(key)¶
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check_batch_size
(batch_size)¶
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check_test_size
(test_size)¶
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get_atom_type
()¶
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get_batch
(batch_size)¶
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get_data_dict
()¶
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get_natoms
()¶
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get_natoms_vec
(ntypes)¶
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get_ntypes
()¶
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get_numb_batch
(batch_size, set_idx)¶
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get_numb_set
()¶
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get_sys_numb_batch
(batch_size)¶
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get_test
(ntests=-1)¶
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get_type_map
()¶
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reduce
(key_out, key_in)¶
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reset_get_batch
()¶
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class
deepmd.DataModifier.
DipoleChargeModifier
(model_name, model_charge_map, sys_charge_map, ewald_h=1, ewald_beta=1)¶ -
build_fv_graph
()¶
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eval
(coord, box, atype, eval_fv=True)¶
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eval_fv
(coords, cells, atom_types, ext_f)¶
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modify_data
(data)¶
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class
deepmd.DataSystem.
DataSystem
(systems, set_prefix, batch_size, test_size, rcut, run_opt=None)¶ -
check_type_map_consistency
(type_map_list)¶
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compute_energy_shift
()¶
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format_name_length
(name, width)¶
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get_batch
(sys_idx=None, sys_weights=None, style='prob_sys_size')¶
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get_batch_size
()¶
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get_nbatches
()¶
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get_nsystems
()¶
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get_ntypes
()¶
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get_sys
(sys_idx)¶
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get_test
(sys_idx=None)¶
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get_type_map
()¶
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numb_fparam
()¶
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print_summary
(run_opt)¶
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process_sys_weights
(sys_weights)¶
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class
deepmd.DataSystem.
DeepmdDataSystem
(systems, batch_size, test_size, rcut, set_prefix='set', shuffle_test=True, type_map=None, modifier=None)¶ -
add
(key, ndof, atomic=False, must=False, high_prec=False, type_sel=None, repeat=1)¶
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add_dict
(adict)¶
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compute_energy_shift
(rcond=0.001, key='energy')¶
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get_batch
(sys_idx=None, sys_probs=None, auto_prob_style='prob_sys_size')¶ Get a batch of data from the data system
- sys_idx: int
- The index of system from which the batch is get. If sys_idx is not None, sys_probs and auto_prob_style are ignored If sys_idx is None, automatically determine the system according to sys_probs or auto_prob_style, see the following.
- sys_probs: list of float
- The probabilitis of systems to get the batch. Summation of positive elements of this list should be no greater than 1. Element of this list can be negative, the probability of the corresponding system is determined automatically by the number of batches in the system.
- auto_prob_style: float
Determine the probability of systems automatically. The method is assigned by this key and can be - “prob_uniform” : the probability all the systems are equal, namely 1.0/self.get_nsystems() - “prob_sys_size” : the probability of a system is proportional to the number of batches in the system - “prob_sys_size;stt_idx:end_idx:weight;stt_idx:end_idx:weight;…” :
the list of systems is devided into blocks. A block is specified by stt_idx:end_idx:weight, where stt_idx is the starting index of the system, end_idx is then ending (not including) index of the system, the probabilities of the systems in this block sums up to weight, and the relatively probabilities within this block is proportional to the number of batches in the system.
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get_batch_size
()¶
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get_data_dict
()¶
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get_nbatches
()¶
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get_nsystems
()¶
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get_ntypes
()¶
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get_sys
(idx)¶
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get_sys_ntest
(sys_idx=None)¶ Get number of tests for the currently selected system, or one defined by sys_idx.
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get_test
(sys_idx=None, n_test=-1)¶
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get_type_map
()¶
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print_summary
(run_opt, sys_probs=None, auto_prob_style='prob_sys_size')¶
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reduce
(key_out, key_in)¶
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class
deepmd.DeepDipole.
DeepDipole
(model_file, load_prefix='load', default_tf_graph=False)¶
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class
deepmd.DeepEval.
DeepEval
(model_file, load_prefix='load', default_tf_graph=False)¶ common methods for DeepPot, DeepWFC, DeepPolar, …
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make_natoms_vec
(atom_types)¶
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reverse_map
(vec, imap)¶
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sort_input
(coord, atom_type, sel_atoms=None)¶
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class
deepmd.DeepEval.
DeepTensor
(model_file, variable_name, variable_dof, load_prefix='load', default_tf_graph=False)¶ Evaluates a tensor model
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eval
(coords, cells, atom_types, atomic=True)¶
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get_ntypes
()¶
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get_rcut
()¶
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get_sel_type
()¶
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get_type_map
()¶
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class
deepmd.DeepPolar.
DeepGlobalPolar
(model_file, default_tf_graph=False)¶ -
eval
(coords, cells, atom_types)¶
-
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class
deepmd.DeepPolar.
DeepPolar
(model_file, default_tf_graph=False)¶
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class
deepmd.DeepPot.
DeepPot
(model_file, default_tf_graph=False)¶ -
eval
(coords, cells, atom_types, fparam=None, aparam=None, atomic=False)¶
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eval_inner
(coords, cells, atom_types, fparam=None, aparam=None, atomic=False)¶
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get_dim_aparam
()¶
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get_dim_fparam
()¶
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get_ntypes
()¶
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get_rcut
()¶
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get_type_map
()¶
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class
deepmd.DeepWFC.
DeepWFC
(model_file, default_tf_graph=False)¶
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class
deepmd.DescrptLocFrame.
DescrptLocFrame
(jdata)¶ -
build
(coord_, atype_, natoms, box_, mesh, suffix='', reuse=None)¶
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compute_input_stats
(data_coord, data_box, data_atype, natoms_vec, mesh)¶
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get_dim_out
()¶
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get_nlist
()¶
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get_ntypes
()¶
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get_rcut
()¶
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get_rot_mat
()¶
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prod_force_virial
(atom_ener, natoms)¶
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class
deepmd.DescrptSeA.
DescrptSeA
(jdata)¶ -
build
(coord_, atype_, natoms, box_, mesh, suffix='', reuse=None)¶
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compute_input_stats
(data_coord, data_box, data_atype, natoms_vec, mesh)¶
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get_dim_out
()¶
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get_dim_rot_mat_1
()¶
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get_nlist
()¶
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get_ntypes
()¶
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get_rcut
()¶
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get_rot_mat
()¶
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prod_force_virial
(atom_ener, natoms)¶
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class
deepmd.DescrptSeAR.
DescrptSeAR
(jdata)¶ -
build
(coord_, atype_, natoms, box, mesh, suffix='', reuse=None)¶
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compute_input_stats
(data_coord, data_box, data_atype, natoms_vec, mesh)¶
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get_dim_out
()¶
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get_nlist_a
()¶
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get_nlist_r
()¶
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get_ntypes
()¶
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get_rcut
()¶
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prod_force_virial
(atom_ener, natoms)¶
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class
deepmd.DescrptSeR.
DescrptSeR
(jdata)¶ -
build
(coord_, atype_, natoms, box_, mesh, suffix='', reuse=None)¶
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compute_input_stats
(data_coord, data_box, data_atype, natoms_vec, mesh)¶
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get_dim_out
()¶
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get_nlist
()¶
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get_ntypes
()¶
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get_rcut
()¶
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prod_force_virial
(atom_ener, natoms)¶
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class
deepmd.Fitting.
DipoleFittingSeA
(jdata, descrpt)¶ -
build
(input_d, rot_mat, natoms, reuse=None, suffix='')¶
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get_out_size
()¶
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get_sel_type
()¶
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class
deepmd.Fitting.
EnerFitting
(jdata, descrpt)¶ -
build
(inputs, input_dict, natoms, reuse=None, suffix='')¶
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compute_input_stats
(all_stat, protection)¶
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compute_output_stats
(all_stat)¶
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get_numb_aparam
()¶
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get_numb_fparam
()¶
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class
deepmd.Fitting.
GlobalPolarFittingSeA
(jdata, descrpt)¶ -
build
(input_d, rot_mat, natoms, reuse=None, suffix='')¶
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get_out_size
()¶
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get_sel_type
()¶
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class
deepmd.Fitting.
PolarFittingLocFrame
(jdata, descrpt)¶ -
build
(input_d, rot_mat, natoms, reuse=None, suffix='')¶
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get_out_size
()¶
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get_sel_type
()¶
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class
deepmd.Fitting.
PolarFittingSeA
(jdata, descrpt)¶ -
build
(input_d, rot_mat, natoms, reuse=None, suffix='')¶
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compute_input_stats
(all_stat, protection=0.01)¶
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get_out_size
()¶
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get_sel_type
()¶
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class
deepmd.Fitting.
WFCFitting
(jdata, descrpt)¶ -
build
(input_d, rot_mat, natoms, reuse=None, suffix='')¶
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get_out_size
()¶
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get_sel_type
()¶
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get_wfc_numb
()¶
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class
deepmd.LearningRate.
LearningRateExp
(jdata)¶ -
build
(global_step, stop_batch=None)¶
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start_lr
()¶
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value
(batch)¶
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class
deepmd.Loss.
EnerDipoleLoss
(jdata, **kwarg)¶ -
build
(learning_rate, natoms, model_dict, label_dict, suffix)¶
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print_header
()¶
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print_on_training
(sess, natoms, feed_dict_test, feed_dict_batch)¶
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class
deepmd.Loss.
EnerStdLoss
(jdata, **kwarg)¶ -
build
(learning_rate, natoms, model_dict, label_dict, suffix)¶
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print_header
()¶
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print_on_training
(sess, natoms, feed_dict_test, feed_dict_batch)¶
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class
deepmd.Loss.
TensorLoss
(jdata, **kwarg)¶ -
build
(learning_rate, natoms, model_dict, label_dict, suffix)¶
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print_header
()¶
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print_on_training
(sess, natoms, feed_dict_test, feed_dict_batch)¶
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class
deepmd.Model.
DipoleModel
(jdata, descrpt, fitting)¶
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class
deepmd.Model.
GlobalPolarModel
(jdata, descrpt, fitting)¶
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class
deepmd.Model.
Model
(jdata, descrpt, fitting)¶ -
build
(coord_, atype_, natoms, box, mesh, input_dict, suffix='', reuse=None)¶
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data_stat
(data)¶
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get_ntypes
()¶
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get_rcut
()¶
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get_type_map
()¶
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model_type
= 'ener'¶
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class
deepmd.Model.
PolarModel
(jdata, descrpt, fitting)¶
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class
deepmd.Model.
TensorModel
(jdata, descrpt, fitting, var_name)¶ -
build
(coord_, atype_, natoms, box, mesh, input_dict, suffix='', reuse=None)¶
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data_stat
(data)¶
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get_ntypes
()¶
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get_out_size
()¶
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get_rcut
()¶
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get_sel_type
()¶
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get_type_map
()¶
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class
deepmd.Model.
WFCModel
(jdata, descrpt, fitting)¶
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deepmd.Model.
make_all_stat
(data, nbatches, merge_sys=True)¶ pack data for statistics Parameters ———- data:
The data- merge_sys: bool (True)
- Merge system data
- all_stat:
A dictionary of list of list storing data for stat. if merge_sys == False data can be accessed by
all_stat[key][sys_idx][batch_idx][frame_idx]- else merge_sys == True can be accessed by
- all_stat[key][batch_idx][frame_idx]
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deepmd.Model.
merge_sys_stat
(all_stat)¶
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deepmd.Network.
one_layer
(inputs, outputs_size, activation_fn=<function tanh>, precision=tf.float64, stddev=1.0, bavg=0.0, name='linear', reuse=None, seed=None, use_timestep=False, trainable=True, useBN=False)¶