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DeePMD-kit  documentation - Home DeePMD-kit  documentation - Home

Getting Started

  • Getting Started
    • 1. Easy install
    • 2. DeePMD-kit Quick Start Tutorial

Advanced

  • 1. Backend
  • 2. Installation
    • 2.1. Easy install
    • 2.2. Install from source code
    • 2.3. Install from pre-compiled C library
    • 2.4. Install LAMMPS
    • 2.5. Install i-PI
    • 2.6. Building conda packages
    • 2.7. Install Node.js interface
    • 2.8. Easy install the latest development version
  • 3. Data
    • 3.1. System
    • 3.2. Formats of a system
    • 3.3. Prepare data with dpdata
  • 4. Model
    • 4.1. Overall
    • 4.2. Descriptor "se_e2_a"
    • 4.3. Descriptor "se_e2_r"
    • 4.4. Descriptor "se_e3"
    • 4.5. Descriptor "se_atten"
    • 4.6. Descriptor DPA-2
    • 4.7. Descriptor DPA3
    • 4.8. Descriptor DPA4
    • 4.9. Descriptor "hybrid"
    • 4.10. Determine sel
    • 4.11. Fit energy
    • 4.12. Fit spin energy
    • 4.13. Fit energy Hessian
    • 4.14. Fit tensor like Dipole and Polarizability
    • 4.15. Fit electronic density of states (DOS)
    • 4.16. Fit other properties
    • 4.17. Type embedding approach
    • 4.18. Descriptor "se_a_mask"
    • 4.19. Descriptor "se_e3_tebd"
    • 4.20. Deep potential long-range (DPLR)
    • 4.21. Deep Potential - Range Correction (DPRc)
    • 4.22. Linear model
    • 4.23. Interpolation or combination with a pairwise potential
    • 4.24. Change the model output bias for trained model
    • 4.25. Floating-point precision of the model
    • 4.26. Use dp show to show the model information
    • 4.27. Use dp pretrained to download built-in models
  • 5. Training
    • 5.1. Train a model
    • 5.2. Advanced options
    • 5.3. Learning rate
    • 5.4. Training Parameters
    • 5.5. Parallel training
    • 5.6. Multi-task training
    • 5.7. TensorBoard Usage
    • 5.8. Known limitations of using GPUs
    • 5.9. Finetune the pre-trained model
  • 6. Freeze and Compress
    • 6.1. Freeze a model
    • 6.2. Compress a model
  • 7. Test
    • 7.1. Test a model
    • 7.2. Calculate Model Deviation
  • 8. Inference
    • 8.1. Python interface
    • 8.2. C/C++ interface
    • 8.3. Node.js interface
  • 9. Command line interface
  • 10. Integrate with third-party packages
    • 10.1. Use deep potential with dpdata
    • 10.2. Use deep potential with ASE
    • 10.3. Run MD with LAMMPS
    • 10.4. Run path-integral MD with i-PI
    • 10.5. Running MD with GROMACS
    • 10.6. Interfaces out of DeePMD-kit
  • 11. Agent Skills
  • 12. Use NVNMD
  • 13. Runtime environment variables
  • 14. FAQs
    • 14.1. How to tune Fitting/embedding-net size ?
    • 14.2. How to control the parallelism of a job?
    • 14.3. Do we need to set rcut < half boxsize?
    • 14.4. How to set sel?
    • 14.5. Installation
    • 14.6. The temperature undulates violently during the early stages of MD
    • 14.7. MD: cannot run LAMMPS after installing a new version of DeePMD-kit
    • 14.8. Model compatibility
    • 14.9. Why does a model have low precision?

Tutorial

  • Tutorials
  • Publications

Developer Guide

  • Find DeePMD-kit C/C++ library from CMake
  • Create a model in TensorFlow
  • Create a model in other backends
  • Atom Type Embedding
  • Coding Conventions
  • CI/CD
  • Python API
  • OP API
  • C++ API
    • Namespace tensorflow
    • Struct NeighborListData
    • Class AtomMap
    • Class DeepBaseModelBackend
    • Class DeepPot
    • Class DeepPotJAX
    • Class DeepPotPD
    • Class DeepPotTF
    • Class DeepSpinBackend
    • Class DeepSpinPT
    • Class DeepTensor
    • Class DeepTensorPT
    • Class DipoleChargeModifier
    • Class DipoleChargeModifierTF
    • Function deepmd::convert_pbtxt_to_pb
    • Function deepmd::get_backend
    • Function deepmd::load_op_library
    • Function deepmd::name_prefix
    • Function deepmd::read_file_to_string
    • Template Function deepmd::select_by_type
    • Template Function deepmd::select_map(typename std::vector<VT>::iterator, const typename std::vector<VT>::const_iterator, const std::vector<int>&, const int&, const int&, const 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&)
    • Template Function deepmd::select_real_atoms_coord
    • Template Function deepmd::session_get_scalar
    • Template 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 double&, const std::vector<VALUETYPE>&, const std::vector<VALUETYPE>&, const deepmd::AtomMap&, const std::string, const bool)
    • Template Function deepmd::session_input_tensors_mixed_type
    • Typedef deepmd::STRINGTYPE
  • C API
    • Namespace deepmd::hpp
    • Struct InputNlist
    • Struct DP_DeepBaseModelDevi
    • Struct DP_DeepPotModelDevi
    • Struct DP_DeepSpinModelDevi
    • Struct DP_DipoleChargeModifier
    • Class DeepBaseModel
    • Class DeepPot
    • Class DeepSpin
    • Class DeepTensor
    • Specialized Template Function _DP_DeepPotCompute< double >
    • Template Function _DP_DeepPotComputeMixedType
    • Specialized Template Function _DP_DeepPotComputeMixedType< float >
    • Specialized Template Function _DP_DeepPotComputeNList< double >
    • Template Function _DP_DeepPotModelDeviCompute
    • Specialized Template Function _DP_DeepPotModelDeviCompute< float >
    • Specialized Template Function _DP_DeepPotModelDeviComputeNList< double >
    • Template Function _DP_DeepSpinCompute
    • Specialized Template Function _DP_DeepSpinCompute< float >
    • Specialized Template Function _DP_DeepSpinComputeNList< double >
    • Template Function _DP_DeepSpinModelDeviCompute
    • Specialized Template Function _DP_DeepSpinModelDeviCompute< float >
    • Specialized Template Function _DP_DeepSpinModelDeviComputeNList< double >
    • Template Function _DP_DeepTensorCompute
    • Specialized Template Function _DP_DeepTensorCompute< float >
    • Specialized Template Function _DP_DeepTensorComputeNList< double >
    • Template Function _DP_DeepTensorComputeTensor
    • Specialized Template Function _DP_DeepTensorComputeTensor< float >
    • Specialized Template Function _DP_DeepTensorComputeTensorNList< double >
    • Template Function _DP_DipoleChargeModifierComputeNList
    • Specialized Template Function _DP_DipoleChargeModifierComputeNList< float >
    • Function _DP_Get_Energy_Pointer(double&, const int)
    • Function deepmd::hpp::convert_pbtxt_to_pb
    • Template Function deepmd::hpp::select_by_type
    • Template Function deepmd::hpp::validate_charge_spin
    • Function DP_DeepBaseModelCheckOK
    • Function DP_DeepBaseModelDeviGetCutoff
    • Function DP_DeepBaseModelDeviGetDimFParam
    • Function DP_DeepBaseModelDeviGetNumbTypesSpin
    • Function DP_DeepBaseModelDeviIsAParamNAll
    • Function DP_DeepBaseModelGetDimAParam
    • Function DP_DeepBaseModelGetNumbTypes
    • Function DP_DeepBaseModelGetTypeMap
    • Function DP_DeepBaseModelIsAParamNAll
    • Function DP_DeepPotCompute
    • Function DP_DeepPotCompute3
    • Function DP_DeepPotComputef2
    • Function DP_DeepPotComputeMixedType
    • Function DP_DeepPotComputeNList
    • Function DP_DeepPotComputeNList3
    • Function DP_DeepPotComputeNListf2
    • Function DP_DeepPotGetCutoff
    • Function DP_DeepPotGetDimChgSpin
    • Function DP_DeepPotGetNumbTypes
    • Function DP_DeepPotGetTypeMap
    • Function DP_DeepPotIsAParamNAll
    • Function DP_DeepPotModelDeviCompute
    • Function DP_DeepPotModelDeviCompute3
    • Function DP_DeepPotModelDeviComputef2
    • Function DP_DeepPotModelDeviComputeNList
    • Function DP_DeepPotModelDeviComputeNList3
    • Function DP_DeepPotModelDeviComputeNListf2
    • Function DP_DeepPotModelDeviGetCutoff
    • Function DP_DeepPotModelDeviGetDimChgSpin
    • Function DP_DeepPotModelDeviGetNumbTypes
    • Function DP_DeepPotModelDeviHasDefaultFParam
    • Function DP_DeepSpinCheckOK
    • Function DP_DeepSpinComputef2
    • Function DP_DeepSpinComputeNListf2
    • Function DP_DeepSpinGetDimAParam
    • Function DP_DeepSpinGetNumbTypes
    • Function DP_DeepSpinGetTypeMap
    • Function DP_DeepSpinIsAParamNAll
    • Function DP_DeepSpinModelDeviCompute2
    • Function DP_DeepSpinModelDeviComputeNList2
    • Function DP_DeepSpinModelDeviGetCutoff
    • Function DP_DeepSpinModelDeviGetDimFParam
    • Function DP_DeepSpinModelDeviGetNumbTypesSpin
    • Function DP_DeepSpinModelDeviIsAParamNAll
    • Function DP_DeepTensorCompute
    • Function DP_DeepTensorComputeNList
    • Function DP_DeepTensorComputeTensor
    • Function DP_DeepTensorComputeTensorNList
    • Function DP_DeepTensorGetCutoff
    • Function DP_DeepTensorGetNumbTypes
    • Function DP_DeepTensorGetSelTypes
    • Function DP_DeleteChar
    • Function DP_DeleteDeepBaseModelDevi
    • Function DP_DeleteDeepPotModelDevi
    • Function DP_DeleteDeepSpinModelDevi
    • Function DP_DeleteDipoleChargeModifier
    • Function DP_DipoleChargeModifierCheckOK
    • Function DP_DipoleChargeModifierComputeNListf
    • Function DP_DipoleChargeModifierGetNumbSelTypes
    • Function DP_DipoleChargeModifierGetSelTypes
    • Function DP_NewDeepPotModelDevi
    • Function DP_NewDeepPotWithParam
    • Function DP_NewDeepSpin
    • Function DP_NewDeepSpinModelDeviWithParam
    • Function DP_NewDeepTensor
    • Function DP_NewDipoleChargeModifier
    • Function DP_NewNlist
    • Function DP_NlistCheckOK
    • Function DP_NlistSetMask
    • Function DP_ReadFileToChar
    • Function DP_SelectByType
    • Define DP_CHECK_OK
    • Define DP_REQUIRES_OK
    • Typedef DP_DeepBaseModelDevi
    • Typedef DP_DeepPotModelDevi
    • Typedef DP_DeepSpinModelDevi
    • Typedef DP_DipoleChargeModifier
  • Core API
    • Namespace std
    • Struct deepmd_exception_oom
    • Struct InputNlist
    • Template Struct DescrptSeRGPUExecuteFunctor
    • Template Struct GeluGradGPUExecuteFunctor
    • Template Struct ProdForceSeAGPUExecuteFunctor
    • Template Struct ProdVirialSeAGPUExecuteFunctor
    • Template Struct TabulateCheckerGPUExecuteFunctor
    • Template Struct TabulateFusionGradGPUExecuteFunctor
    • 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 std::vector<int>&, const std::vector<int>&, const double&, const double&, const std::vector<int>&, 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_se_a_ef_para
    • Function compute_descriptor_se_a_extf
    • Function compute_dRdT_1
    • Function copy_coord
    • Template Function deepmd::build_nlist_gpu
    • Function deepmd::convert_nlist
    • Template Function deepmd::convert_to_inter_cpu
    • Template Function deepmd::convert_to_phys_cpu
    • Template Function deepmd::copy_coord_cpu
    • Function deepmd::cos_switch(const double&, const double&, const double&)
    • Template Function deepmd::cprod
    • Template Function deepmd::delete_device_memory
    • Template Function deepmd::dot2
    • Template Function deepmd::dot4
    • Function deepmd::DPGetDeviceCount
    • Function deepmd::DPSetDevice
    • Template Function deepmd::env_mat_a_nvnmd_quantize_cpu
    • Template Function deepmd::env_mat_r_cpu
    • Function deepmd::filter_ftype_gpu
    • Template Function deepmd::format_nlist_cpu
    • Template Function deepmd::gelu_cpu
    • Template Function deepmd::gelu_grad_cpu
    • Template Function deepmd::gelu_grad_grad_cpu
    • Function deepmd::group_atoms_cpu
    • Template Function deepmd::invsqrt
    • Specialized Template Function deepmd::invsqrt< float >
    • Template Function deepmd::malloc_device_memory(FPTYPE *&, const int)
    • Template Function deepmd::malloc_device_memory_sync(FPTYPE *&, const std::vector<FPTYPE>&)
    • Template Function deepmd::malloc_device_memory_sync(FPTYPE *&, std::vector<FPTYPE>&)
    • Function deepmd::max_numneigh
    • Template Function deepmd::memcpy_device_to_host(const FPTYPE *, FPTYPE *, const int)
    • Template Function deepmd::memcpy_host_to_device(FPTYPE *, const FPTYPE *, const int)
    • Template Function deepmd::memset_device_memory
    • Template Function deepmd::normalize_coord_cpu
    • Template Function deepmd::pair_tab_cpu
    • Template Function deepmd::prod_env_mat_a_gpu
    • Template Function deepmd::prod_env_mat_r_cpu
    • Template Function deepmd::prod_force_a_cpu(FPTYPE *, const FPTYPE *, const FPTYPE *, const int *, const int, const int, const int, const int)
    • Template Function deepmd::prod_force_a_gpu
    • Template Function deepmd::prod_force_grad_a_gpu
    • Template Function deepmd::prod_force_grad_r_gpu
    • Template Function deepmd::prod_force_r_gpu
    • Template Function deepmd::prod_virial_a_gpu
    • Template Function deepmd::prod_virial_grad_a_gpu
    • Template Function deepmd::prod_virial_grad_r_gpu
    • Template Function deepmd::prod_virial_r_gpu
    • Template Function deepmd::soft_min_switch_force_cpu
    • Template Function deepmd::soft_min_switch_virial_cpu
    • Function deepmd::spline3_switch
    • Template Function deepmd::tabulate_fusion_se_a_cpu
    • Template Function deepmd::tabulate_fusion_se_a_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_a_grad_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_r_cpu
    • Template Function deepmd::tabulate_fusion_se_r_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_r_grad_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_t_cpu
    • Template Function deepmd::tabulate_fusion_se_t_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_t_grad_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_t_tebd_cpu
    • Template Function deepmd::tabulate_fusion_se_t_tebd_grad_cpu
    • Template Function deepmd::tabulate_fusion_se_t_tebd_grad_grad_cpu
    • Template Function deepmd::test_encoding_decoding_nbor_info_gpu
    • Function deepmd::use_nei_info_gpu
    • Template Function deepmd::volume_cpu
    • Template Function dotmul_flt_nvnmd
    • Function DPAssert(hipError_t, const char *, int, bool)
    • Function env_mat_r
    • Template Function find_max_expo(int64_t&, T *, int64_t, int64_t)
    • Function format_nlist_i_fill_a
    • Function nborAssert(cudaError_t, const char *, int, bool)
    • Function omp_get_num_threads
    • Template Function split_flt
    • Define DPErrcheck
    • Define GPU_MAX_NBOR_SIZE
    • Define gpuDeviceSynchronize
    • Define gpuGetLastError
    • Define gpuMemcpy
    • Define gpuMemcpyDeviceToDevice
    • Define gpuMemcpyDeviceToHost
    • Define gpuMemcpyHostToDevice
    • Define gpuMemset
    • Define MOASPNDIM
    • Define NBIT_FLTF
    • Define nborErrcheck
    • Define TPB
    • Typedef uint_64

Project Details

  • License
  • Authors and Credits
  • Logo
  • .rst

FAQs

14. FAQs#

As a consequence of differences in computers or systems, problems may occur. Some common circumstances are listed as follows. In addition, some frequently asked questions are listed as follows. If other unexpected problems occur, you’re welcome to contact us for help.

Troubleshooting

  • 14.1. How to tune Fitting/embedding-net size ?
  • 14.2. How to control the parallelism of a job?
  • 14.3. Do we need to set rcut < half boxsize?
  • 14.4. How to set sel?
  • 14.5. Installation
  • 14.6. The temperature undulates violently during the early stages of MD
  • 14.7. MD: cannot run LAMMPS after installing a new version of DeePMD-kit
  • 14.8. Model compatibility
  • 14.9. Why does a model have low precision?

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13. Runtime environment variables

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14.1. How to tune Fitting/embedding-net size ?

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