Merge pull request #140 from deepmodeling/devel

Devel

Author: amcadmus

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "source/op/cuda/cub"]
+	path = source/op/cuda/cub
+	url = git://github.com/NVlabs/cub.git

README.md

@@ -32,6 +32,7 @@
 	    - [Include deepmd in the pair style](#include-deepmd-in-the-pair-style)
 	    - [Long-range interaction](#long-range-interaction)
 	- [Run path-integral MD with i-PI](#run-path-integral-md-with-i-pi)
+	- [Use deep potential with ASE](#use-deep-potential-with-ase)
 - [Troubleshooting](#troubleshooting)
 
 # About DeePMD-kit
@@ -150,7 +151,7 @@ One should remember to activate the virtual environment every time he/she uses d
 Clone the DeePMD-kit source code
 ```bash
 cd /some/workspace
-git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kit
+git clone --recursive https://github.com/deepmodeling/deepmd-kit.git deepmd-kit -b devel
 ```
 If one downloads the .zip file from the github, then the default folder of source code would be `deepmd-kit-master` rather than `deepmd-kit`. For convenience, you may want to record the location of source to a variable, saying `deepmd_source_dir` by
 ```bash
@@ -553,6 +554,30 @@ The option **`graph_file`** provides the file name of the frozen model.
 
 The `dp_ipi` gets the atom names from an [XYZ file](https://en.wikipedia.org/wiki/XYZ_file_format) provided by **`coord_file`** (meanwhile ignores all coordinates in it), and translates the names to atom types by rules provided by **`atom_type`**.
 
+## Use deep potential with ASE
+
+Deep potential can be set up as a calculator with ASE to obtain potential energies and forces.
+```python
+from ase import Atoms
+from deepmd.calculator import DP
+
+water = Atoms('H2O',
+              positions=[(0.7601, 1.9270, 1),
+                         (1.9575, 1, 1),
+                         (1., 1., 1.)],
+              cell=[100, 100, 100],
+              calculator=DP(model="frozen_model.pb"))
+print(water.get_potential_energy())
+print(water.get_forces())
+```
+
+Optimization is also available:
+```python
+from ase.optimize import BFGS
+dyn = BFGS(water)
+dyn.run(fmax=1e-6)
+print(water.get_positions())
+```
 
 # Troubleshooting
 In consequence of various differences of computers or systems, problems may occur. Some common circumstances are listed as follows. 

deepmd/__init__.py

@@ -3,6 +3,7 @@
 from .DeepPot    import DeepPot
 from .DeepDipole import DeepDipole
 from .DeepPolar  import DeepPolar
+from .DeepPolar  import DeepGlobalPolar
 from .DeepWFC    import DeepWFC
 
 set_mkl()

source/CMakeLists.txt

@@ -170,6 +170,11 @@ include_directories(${TensorFlow_INCLUDE_DIRS})
 if (BUILD_CPP_IF)
   set (LIB_DEEPMD		"deepmd")
   set (LIB_DEEPMD_OP		"deepmd_op")
+  if (USE_CUDA_TOOLKIT)
+    set (LIB_DEEPMD_OP_CUDA		"deepmd_op_cuda")
+  else()
+    set (LIB_DEEPMD_OP_CUDA		"")
+  endif()
   if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 4.9)
     set (LIB_DEEPMD_NATIVE	"deepmd_native_md")
     set (LIB_DEEPMD_IPI		"deepmd_ipi")

source/lib/include/NNPAtomMap.h

@@ -8,6 +8,7 @@ template <typename VALUETYPE>
 class NNPAtomMap 
 {
 public:
+  NNPAtomMap();
   NNPAtomMap(const vector<int >::const_iterator in_begin, 
 	     const vector<int >::const_iterator in_end);
   void forward (typename vector<VALUETYPE >::iterator out,

source/lib/include/NNPInter.h

@@ -5,10 +5,11 @@
 #include "tensorflow/core/framework/op.h"
 #include "tensorflow/core/framework/op_kernel.h"
 #include "tensorflow/core/framework/shape_inference.h"
-
+#include "NNPAtomMap.h"
 #include <vector>
 #include "version.h"
 
+typedef double compute_t;
 using namespace tensorflow;
 using namespace std;
 
@@ -53,6 +54,7 @@ class NNPInter
 {
 public:
   NNPInter () ;
+  ~NNPInter() ;
   NNPInter  (const string & model, const int & gpu_rank = 0);
   void init (const string & model, const int & gpu_rank = 0);
   void print_summary(const string &pre) const;
@@ -74,6 +76,7 @@ class NNPInter
 		const vector<VALUETYPE> &	box, 
 		const int			nghost,
 		const LammpsNeighborList &	lmp_list,
+		const int				&   ago,
 		const vector<VALUETYPE>	&	fparam = vector<VALUETYPE>(),
 		const vector<VALUETYPE>	&	aparam = vector<VALUETYPE>());
   void compute (ENERGYTYPE &			ener,
@@ -96,6 +99,7 @@ class NNPInter
 		const vector<VALUETYPE> &	box, 
 		const int			nghost, 
 		const LammpsNeighborList &	lmp_list,
+		const int 				&   ago,
 		const vector<VALUETYPE>	&	fparam = vector<VALUETYPE>(),
 		const vector<VALUETYPE>	&	aparam = vector<VALUETYPE>());
   VALUETYPE cutoff () const {assert(inited); return rcut;};
@@ -118,12 +122,30 @@ class NNPInter
   void validate_fparam_aparam(const int & nloc,
 			      const vector<VALUETYPE> &fparam,
 			      const vector<VALUETYPE> &aparam)const ;
+
+  // copy neighbor list info from host
+  bool init_nbor;
+  std::vector<int> sec_a;
+  compute_t *array_double;
+  InternalNeighborList nlist;
+  NNPAtomMap<VALUETYPE> nnpmap;
+  unsigned long long *array_longlong;
+  int *ilist, *jrange, *jlist, *array_int;
+  int ilist_size, jrange_size, jlist_size;
+  int arr_int_size, arr_ll_size, arr_dou_size;
+
+  // function used for neighbor list copy
+  vector<int> get_sel_a() const;
+#ifdef USE_CUDA_TOOLKIT
+  void update_nbor(const InternalNeighborList & nlist, const int nloc);
+#endif
 };
 
 class NNPInterModelDevi
 {
 public:
   NNPInterModelDevi () ;
+  ~NNPInterModelDevi() ;
   NNPInterModelDevi  (const vector<string> & models, const int & gpu_rank = 0);
   void init (const vector<string> & models, const int & gpu_rank = 0);
 public:
@@ -144,6 +166,7 @@ class NNPInterModelDevi
 		const vector<VALUETYPE> &	box,
 		const int			nghost,
 		const LammpsNeighborList &	lmp_list,
+		const int 				&   ago,
 		const vector<VALUETYPE>	&	fparam = vector<VALUETYPE>(),
 		const vector<VALUETYPE>	&	aparam = vector<VALUETYPE>());
   void compute (vector<ENERGYTYPE> &		all_ener,
@@ -156,6 +179,7 @@ class NNPInterModelDevi
 		const vector<VALUETYPE> &	box,
 		const int			nghost,
 		const LammpsNeighborList &	lmp_list,
+		const int 				&   ago,
 		const vector<VALUETYPE>	&	fparam = vector<VALUETYPE>(),
 		const vector<VALUETYPE>	&	aparam = vector<VALUETYPE>());
   VALUETYPE cutoff () const {assert(inited); return rcut;};
@@ -176,6 +200,9 @@ class NNPInterModelDevi
   void compute_std_f (vector<VALUETYPE> &		std,
 		      const vector<VALUETYPE> &		avg,
 		      const vector<vector<VALUETYPE> >& xx);
+  void compute_relative_std_f (vector<VALUETYPE> &		std,
+		      const vector<VALUETYPE> &		avg,
+		      const VALUETYPE eps);
 private:
   unsigned numb_models;
   vector<Session*> sessions;
@@ -193,6 +220,25 @@ class NNPInterModelDevi
   void validate_fparam_aparam(const int & nloc,
 			      const vector<VALUETYPE> &fparam,
 			      const vector<VALUETYPE> &aparam)const ;
+
+  // copy neighbor list info from host
+  bool init_nbor;
+  compute_t *array_double;
+  vector<vector<int> > sec;
+  InternalNeighborList nlist;
+  NNPAtomMap<VALUETYPE> nnpmap;
+  unsigned long long *array_longlong;
+  int max_sec_size = 0, max_sec_back = 0;
+  int *ilist, *jrange, *jlist, *array_int;
+  int ilist_size, jrange_size, jlist_size, arr_int_size, arr_ll_size, arr_dou_size;
+
+  // function used for nborlist copy
+  void get_max_sec();
+  vector<vector<int> > get_sel() const;
+  void cum_sum(const std::vector<std::vector<int32> > n_sel);
+#ifdef USE_CUDA_TOOLKIT
+  void update_nbor(const InternalNeighborList & nlist, const int nloc);
+#endif
 };
 
 

source/lib/src/NNPAtomMap.cc

@@ -3,6 +3,10 @@
 #include <algorithm>
 #include <cassert>
 
+template <typename VALUETYPE>
+NNPAtomMap<VALUETYPE>::
+NNPAtomMap() {}
+
 template <typename VALUETYPE>
 NNPAtomMap<VALUETYPE>::
 NNPAtomMap(const vector<int >::const_iterator in_begin,