DeePMD-kit’s documentation
DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning based model of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems.
Important
The project DeePMD-kit is licensed under GNU LGPLv3.0. If you use this code in any future publications, please cite this using Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. “DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics.” Computer Physics Communications 228 (2018): 178-184.
- 1. Installation
- 2. Data
- 3. Model
- 3.1. Overall
- 3.2. Descriptor
"se_e2_a"
- 3.3. Descriptor
"se_e2_r"
- 3.4. Descriptor
"se_e3"
- 3.5. Descriptor
"hybrid"
- 3.6. Determine
sel
- 3.7. Fit energy
- 3.8. Fit
tensor
likeDipole
andPolarizability
- 3.9. Type embedding approach
- 3.10. Deep potential long-range (DPLR)
- 3.11. Deep Potential - Range Correction (DPRc)
- 4. Training
- 5. Freeze and Compress
- 6. Test
- 7. Inference
- 8. Command line interface
- 9. Integrate with third-party packages
- 10. Use NVNMD
- 11. FAQs
- 11.1. How to tune Fitting/embedding-net size ?
- 11.2. How to control the number of nodes used by a job ?
- 11.3. Do we need to set rcut < half boxsize ?
- 11.4. How to set sel ?
- 11.5. Installation
- 11.6. The temperature undulates violently during early stages of MD
- 11.7. MD: cannot run LAMMPS after installing a new version of DeePMD-kit
- 11.8. Model compatibility
- Coding Conventions
- Create a model
- Atom Type Embedding
- Python API
- deepmd package
- Subpackages
- deepmd.cluster package
- deepmd.descriptor package
- deepmd.entrypoints package
- Submodules
- deepmd.entrypoints.compress module
- deepmd.entrypoints.config module
- deepmd.entrypoints.convert module
- deepmd.entrypoints.doc module
- deepmd.entrypoints.freeze module
- deepmd.entrypoints.main module
- deepmd.entrypoints.neighbor_stat module
- deepmd.entrypoints.test module
- deepmd.entrypoints.train module
- deepmd.entrypoints.transfer module
- deepmd.fit package
- deepmd.infer package
- deepmd.loggers package
- deepmd.loss package
- deepmd.model package
- deepmd.nvnmd package
- deepmd.op package
- deepmd.train package
- deepmd.utils package
- Submodules
- deepmd.utils.argcheck module
- deepmd.utils.batch_size module
- deepmd.utils.compat module
- deepmd.utils.convert module
- deepmd.utils.data module
- deepmd.utils.data_system module
- deepmd.utils.errors module
- deepmd.utils.graph module
- deepmd.utils.learning_rate module
- deepmd.utils.neighbor_stat module
- deepmd.utils.network module
- deepmd.utils.pair_tab module
- deepmd.utils.parallel_op module
- deepmd.utils.path module
- deepmd.utils.plugin module
- deepmd.utils.random module
- deepmd.utils.sess module
- deepmd.utils.tabulate module
- deepmd.utils.type_embed module
- deepmd.utils.weight_avg module
- Submodules
- deepmd.calculator module
- deepmd.common module
- deepmd.env module
- Subpackages
- deepmd package
- OP API
- C++ API
- Class Hierarchy
- File Hierarchy
- Full API
- Namespaces
- Classes and Structs
- Functions
- Function deepmd::check_status
- Function deepmd::convert_pbtxt_to_pb
- Function deepmd::get_env_nthreads
- Function deepmd::load_op_library
- Function deepmd::model_compatable
- Function deepmd::name_prefix
- Function deepmd::read_file_to_string
- Function deepmd::select_by_type
- Template Function deepmd::select_map(std::vector<VT>&, const std::vector<VT>&, const std::vector<int>&, const int&)
- Template Function deepmd::select_map(typename std::vector<VT>::iterator, const typename std::vector<VT>::const_iterator, const std::vector<int>&, const int&)
- Template Function deepmd::select_map_inv(std::vector<VT>&, const std::vector<VT>&, const std::vector<int>&, const int&)
- Template Function deepmd::select_map_inv(typename std::vector<VT>::iterator, const typename std::vector<VT>::const_iterator, const std::vector<int>&, const int&)
- Function deepmd::select_real_atoms
- Template Function deepmd::session_get_scalar
- Template Function deepmd::session_get_vector
- Function deepmd::session_input_tensors(std::vector<std::pair<std::string, tensorflow::Tensor>>&, const std::vector<VALUETYPE>&, const int&, const std::vector<int>&, const std::vector<VALUETYPE>&, const VALUETYPE&, const std::vector<VALUETYPE>&, const std::vector<VALUETYPE>&, const deepmd::AtomMap<VALUETYPE>&, const std::string)
- Function deepmd::session_input_tensors(std::vector<std::pair<std::string, tensorflow::Tensor>>&, const std::vector<VALUETYPE>&, const int&, const std::vector<int>&, const std::vector<VALUETYPE>&, InputNlist&, const std::vector<VALUETYPE>&, const std::vector<VALUETYPE>&, const deepmd::AtomMap<VALUETYPE>&, const int, const int, const std::string)
- Typedefs
- Core API
- Class Hierarchy
- File Hierarchy
- Full API
- Namespaces
- Classes and Structs
- Struct deepmd_exception
- Struct deepmd_exception_oom
- Template Struct EwaldParameters
- Struct InputNlist
- Template Struct Region
- Template Struct DescrptSeRGPUExecuteFunctor
- Template Struct GeluGPUExecuteFunctor
- Template Struct GeluGradGPUExecuteFunctor
- Template Struct GeluGradGradGPUExecuteFunctor
- Template Struct ProdForceSeAGPUExecuteFunctor
- Template Struct ProdForceSeRGPUExecuteFunctor
- Template Struct ProdVirialSeAGPUExecuteFunctor
- Template Struct ProdVirialSeRGPUExecuteFunctor
- Template Struct TabulateCheckerGPUExecuteFunctor
- Template Struct TabulateFusionGPUExecuteFunctor
- Template Struct TabulateFusionGradGPUExecuteFunctor
- Template Class SimulationRegion
- Functions
- Function build_nlist(std::vector<std::vector<int>>&, std::vector<std::vector<int>>&, const std::vector<double>&, const int&, const double&, const double&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const SimulationRegion<double>&, const std::vector<int>&)
- Function build_nlist(std::vector<std::vector<int>>&, std::vector<std::vector<int>>&, const std::vector<double>&, const double&, const double&, const std::vector<int>&, const SimulationRegion<double>&)
- Function build_nlist(std::vector<std::vector<int>>&, std::vector<std::vector<int>>&, const std::vector<double>&, const std::vector<int>&, const std::vector<int>&, const double&, const double&, const std::vector<int>&, const SimulationRegion<double>&)
- Function build_nlist(std::vector<std::vector<int>>&, std::vector<std::vector<int>>&, const std::vector<double>&, const double&, const double&, const SimulationRegion<double> *)
- Function compute_descriptor(std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<double>&, const int&, const std::vector<int>&, const SimulationRegion<double>&, const bool&, const int&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const int, const int, const int, const int)
- Function compute_descriptor(std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<double>&, const int&, const std::vector<int>&, const SimulationRegion<double>&, const bool&, const int&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const int, const int, const int, const int)
- Function compute_descriptor_se_a_ef_para
- Function compute_descriptor_se_a_ef_vert
- Function compute_descriptor_se_a_extf
- Function compute_dRdT
- Function compute_dRdT_1
- Function compute_dRdT_2
- Function copy_coord
- Template Function deepmd::build_nlist_cpu
- Template Function deepmd::build_nlist_gpu
- Template Function deepmd::compute_cell_info
- Function deepmd::convert_nlist
- Function deepmd::convert_nlist_gpu_device
- Template Function deepmd::convert_to_inter_cpu
- Template Function deepmd::convert_to_inter_gpu
- Template Function deepmd::convert_to_phys_cpu
- Template Function deepmd::convert_to_phys_gpu
- Template Function deepmd::copy_coord_cpu
- Template Function deepmd::copy_coord_gpu
- Function deepmd::cos_switch(const double&, const double&, const double&)
- Function deepmd::cos_switch(double&, double&, const double&, const double&, const double&)
- Template Function deepmd::cprod
- Function deepmd::cum_sum
- Template Function deepmd::delete_device_memory
- Template Function deepmd::dot1
- Template Function deepmd::dot2
- Template Function deepmd::dot3
- Template Function deepmd::dot4
- Template Function deepmd::dotmv3
- Function deepmd::DPGetDeviceCount
- Function deepmd::DPSetDevice
- Template Function deepmd::env_mat_a_cpu
- Template Function deepmd::env_mat_a_nvnmd_quantize_cpu
- Function deepmd::env_mat_nbor_update
- Template Function deepmd::env_mat_r_cpu
- Template Function deepmd::ewald_recp
- Template Function deepmd::format_nbor_list_gpu_cuda
- Template Function deepmd::format_nlist_cpu
- Function deepmd::free_nlist_gpu_device
- Template Function deepmd::gelu_cpu
- Template Function deepmd::gelu_gpu_cuda
- Template Function deepmd::gelu_grad_cpu
- Template Function deepmd::gelu_grad_gpu_cuda
- Template Function deepmd::gelu_grad_grad_cpu
- Template Function deepmd::gelu_grad_grad_gpu_cuda
- Template Function deepmd::init_region_cpu
- Template Function deepmd::invsqrt
- Specialized Template Function deepmd::invsqrt< double >
- Specialized Template Function deepmd::invsqrt< float >
- Template Function deepmd::malloc_device_memory(FPTYPE *&, const std::vector<FPTYPE>&)
- Template Function deepmd::malloc_device_memory(FPTYPE *&, const int)
- Template Function deepmd::malloc_device_memory(FPTYPE *&, std::vector<FPTYPE>&)
- Template Function deepmd::malloc_device_memory_sync(FPTYPE *&, const std::vector<FPTYPE>&)
- Template Function deepmd::malloc_device_memory_sync(FPTYPE *&, const FPTYPE *, const int)
- Template Function deepmd::malloc_device_memory_sync(FPTYPE *&, std::vector<FPTYPE>&)
- Template Function deepmd::map_aparam_cpu
- Function deepmd::max_numneigh
- Template Function deepmd::memcpy_device_to_host(const FPTYPE *, std::vector<FPTYPE>&)
- Template Function deepmd::memcpy_device_to_host(const FPTYPE *, FPTYPE *, const int)
- Template Function deepmd::memcpy_device_to_host(FPTYPE *, std::vector<FPTYPE>&)
- Template Function deepmd::memcpy_host_to_device(FPTYPE *, const std::vector<FPTYPE>&)
- Template Function deepmd::memcpy_host_to_device(FPTYPE *, const FPTYPE *, const int)
- Template Function deepmd::memcpy_host_to_device(FPTYPE *, std::vector<FPTYPE>&)
- Template Function deepmd::memset_device_memory
- Template Function deepmd::normalize_coord_cpu
- Template Function deepmd::normalize_coord_gpu
- Template Function deepmd::pair_tab_cpu
- Template Function deepmd::prod_env_mat_a_cpu
- Template Function deepmd::prod_env_mat_a_gpu_cuda
- Template Function deepmd::prod_env_mat_a_nvnmd_quantize_cpu
- Template Function deepmd::prod_env_mat_r_cpu
- Template Function deepmd::prod_env_mat_r_gpu_cuda
- Template Function deepmd::prod_force_a_cpu
- Template Function deepmd::prod_force_a_gpu_cuda
- Template Function deepmd::prod_force_grad_a_cpu
- Template Function deepmd::prod_force_grad_a_gpu_cuda
- Template Function deepmd::prod_force_grad_r_cpu
- Template Function deepmd::prod_force_grad_r_gpu_cuda
- Template Function deepmd::prod_force_r_cpu
- Template Function deepmd::prod_force_r_gpu_cuda
- Template Function deepmd::prod_virial_a_cpu
- Template Function deepmd::prod_virial_a_gpu_cuda
- Template Function deepmd::prod_virial_grad_a_cpu
- Template Function deepmd::prod_virial_grad_a_gpu_cuda
- Template Function deepmd::prod_virial_grad_r_cpu
- Template Function deepmd::prod_virial_grad_r_gpu_cuda
- Template Function deepmd::prod_virial_r_cpu
- Template Function deepmd::prod_virial_r_gpu_cuda
- Template Function deepmd::soft_min_switch_cpu
- Template Function deepmd::soft_min_switch_force_cpu
- Template Function deepmd::soft_min_switch_force_grad_cpu
- Template Function deepmd::soft_min_switch_virial_cpu
- Template Function deepmd::soft_min_switch_virial_grad_cpu
- Function deepmd::spline3_switch
- Template Function deepmd::spline5_switch
- Template Function deepmd::tabulate_fusion_se_a_cpu
- Template Function deepmd::tabulate_fusion_se_a_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_a_grad_cpu
- Template Function deepmd::tabulate_fusion_se_a_grad_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_a_grad_grad_cpu
- Template Function deepmd::tabulate_fusion_se_a_grad_grad_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_r_cpu
- Template Function deepmd::tabulate_fusion_se_r_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_r_grad_cpu
- Template Function deepmd::tabulate_fusion_se_r_grad_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_r_grad_grad_cpu
- Template Function deepmd::tabulate_fusion_se_r_grad_grad_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_t_cpu
- Template Function deepmd::tabulate_fusion_se_t_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_t_grad_cpu
- Template Function deepmd::tabulate_fusion_se_t_grad_gpu_cuda
- Template Function deepmd::tabulate_fusion_se_t_grad_grad_cpu
- Template Function deepmd::tabulate_fusion_se_t_grad_grad_gpu_cuda
- Template Function deepmd::test_encoding_decoding_nbor_info_gpu_cuda
- Function deepmd::use_nlist_map
- Template Function deepmd::volume_cpu
- Template Function deepmd::volume_gpu
- Function DPAssert(cudaError_t, const char *, int, bool)
- Function DPAssert(hipError_t, const char *, int, bool)
- Function env_mat_a
- Function env_mat_r
- Template Function format_nlist_i_cpu
- Function format_nlist_i_fill_a
- Function nborAssert(cudaError_t, const char *, int, bool)
- Function nborAssert(hipError_t, const char *, int, bool)
- Function omp_get_num_threads
- Function omp_get_thread_num
- Variables
- Defines
- Typedefs