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Merged
amcadmus merged 17 commits into from
Mar 11, 2021
Merged

Clean up C++ API. #409

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e61bd70
fix bug of cmake script for finding tensorflow
Mar 10, 2021
3ab5cbb
change pb files to test ProdEnvMat
Mar 10, 2021
96679a9
switched to new nlist interface. clean up c++ api. add unittests.
Mar 10, 2021
1623569
add destructor for InputNlist
Mar 10, 2021
0301688
freeze output_dim in tensor models
Mar 10, 2021
10116bf
DipoleChargeModifier determine number of atoms by input vector of ato…
Mar 10, 2021
ad2f64d
clean up outdated commented code
Mar 10, 2021
41a0501
add test CI for api_cc
njzjz Mar 10, 2021
94480b6
install tensorflow
njzjz Mar 10, 2021
296cafe
set INSTALL_PREFIX
njzjz Mar 10, 2021
1e0f71d
change the directory of version.h
njzjz Mar 10, 2021
e2f92c1
clean up model devi, add unittests
Mar 10, 2021
c3e950e
add UT for model devi in the atomic case
Mar 10, 2021
0fa68a1
fall back to some old name convention
Mar 10, 2021
9be17e3
Merge branch 'api-submit' into api
njzjz Mar 10, 2021
e30c7e5
cd api_cc/tests
njzjz Mar 10, 2021
5869d6f
Merge pull request #3 from njzjz/api
amcadmus Mar 11, 2021
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2 changes: 2 additions & 0 deletions deepmd/entrypoints/freeze.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,13 @@ def _make_node_names(model_type: str, modifier_type: Optional[str] = None) -> Li
nodes += [
"o_polar",
"model_attr/sel_type",
"model_attr/output_dim",
]
elif model_type == "global_polar":
nodes += [
"o_global_polar",
"model_attr/sel_type",
"model_attr/output_dim",
]
else:
raise RuntimeError(f"unknow model type {model_type}")
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4 changes: 3 additions & 1 deletion deepmd/infer/data_modifier.py
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Expand Up @@ -235,8 +235,10 @@ def eval(self,
tot_v
The virial modification
"""
atype = np.array(atype, dtype=int)
coord, atype, imap = self.sort_input(coord, atype)
natoms = coord.shape[1] // 3
# natoms = coord.shape[1] // 3
natoms = atype.size
nframes = coord.shape[0]
box = np.reshape(box, [nframes, 9])
atype = np.reshape(atype, [natoms])
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10 changes: 5 additions & 5 deletions source/api_cc/include/DataModifier.h
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,14 @@

#include "NNPInter.h"

class DataModifier
class DipoleChargeModifier
{
public:
DataModifier();
DataModifier(const std::string & model,
DipoleChargeModifier();
DipoleChargeModifier(const std::string & model,
const int & gpu_rank = 0,
const std::string & name_scope = "");
~DataModifier () {};
~DipoleChargeModifier () {};
void init (const std::string & model,
const int & gpu_rank = 0,
const std::string & name_scope = "");
Expand All @@ -23,7 +23,7 @@ class DataModifier
const std::vector<std::pair<int,int>> & pairs,
const std::vector<VALUETYPE> & delef_,
const int nghost,
const LammpsNeighborList & lmp_list);
const InputNlist & lmp_list);
VALUETYPE cutoff () const {assert(inited); return rcut;};
int numb_types () const {assert(inited); return ntypes;};
std::vector<int> sel_types () const {assert(inited); return sel_type;};
Expand Down
10 changes: 4 additions & 6 deletions source/api_cc/include/DeepTensor.h
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Original file line number Diff line number Diff line change
Expand Up @@ -17,14 +17,13 @@ class DeepTensor
void compute (std::vector<VALUETYPE> & value,
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost = 0);
const std::vector<VALUETYPE> & box);
void compute (std::vector<VALUETYPE> & value,
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost,
const LammpsNeighborList & lmp_list);
const InputNlist & inlist);
VALUETYPE cutoff () const {assert(inited); return rcut;};
int numb_types () const {assert(inited); return ntypes;};
int output_dim () const {assert(inited); return odim;};
Expand All @@ -51,13 +50,12 @@ class DeepTensor
void compute_inner (std::vector<VALUETYPE> & value,
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost = 0);
const std::vector<VALUETYPE> & box);
void compute_inner (std::vector<VALUETYPE> & value,
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost,
const InternalNeighborList& lmp_list);
const InputNlist& inlist);
};

29 changes: 9 additions & 20 deletions source/api_cc/include/NNPInter.h
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
#pragma once

#include "common.h"
#include "neighbor_list.h"
typedef double compute_t;

class NNPInter
Expand All @@ -18,7 +19,6 @@ class NNPInter
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost = 0,
const std::vector<VALUETYPE>& fparam = std::vector<VALUETYPE>(),
const std::vector<VALUETYPE>& aparam = std::vector<VALUETYPE>());
void compute (ENERGYTYPE & ener,
Expand All @@ -28,7 +28,7 @@ class NNPInter
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost,
const LammpsNeighborList & lmp_list,
const InputNlist & inlist,
const int& ago,
const std::vector<VALUETYPE>& fparam = std::vector<VALUETYPE>(),
const std::vector<VALUETYPE>& aparam = std::vector<VALUETYPE>());
Expand All @@ -51,7 +51,7 @@ class NNPInter
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost,
const LammpsNeighborList & lmp_list,
const InputNlist & lmp_list,
const int& ago,
const std::vector<VALUETYPE>& fparam = std::vector<VALUETYPE>(),
const std::vector<VALUETYPE>& aparam = std::vector<VALUETYPE>());
Expand Down Expand Up @@ -91,10 +91,9 @@ class NNPInter
bool init_nbor;
std::vector<int> sec_a;
compute_t *array_double;
InternalNeighborList nlist;
NeighborListData nlist_data;
InputNlist nlist;
NNPAtomMap<VALUETYPE> nnpmap;
int *ilist, *jrange, *jlist;
int ilist_size, jrange_size, jlist_size;

// function used for neighbor list copy
std::vector<int> get_sel_a() const;
Expand All @@ -108,23 +107,14 @@ class NNPInterModelDevi
NNPInterModelDevi (const std::vector<std::string> & models, const int & gpu_rank = 0, const std::vector<std::string> & file_contents = std::vector<std::string>());
void init (const std::vector<std::string> & models, const int & gpu_rank = 0, const std::vector<std::string> & file_contents = std::vector<std::string>());
public:
void compute (ENERGYTYPE & ener,
std::vector<VALUETYPE> & force,
std::vector<VALUETYPE> & virial,
std::vector<VALUETYPE> & model_devi,
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const std::vector<VALUETYPE> & fparam = std::vector<VALUETYPE>(),
const std::vector<VALUETYPE> & aparam = std::vector<VALUETYPE>());
void compute (std::vector<ENERGYTYPE> & all_ener,
std::vector<std::vector<VALUETYPE> > & all_force,
std::vector<std::vector<VALUETYPE> > & all_virial,
const std::vector<VALUETYPE> & coord,
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost,
const LammpsNeighborList & lmp_list,
const InputNlist & lmp_list,
const int & ago,
const std::vector<VALUETYPE> & fparam = std::vector<VALUETYPE>(),
const std::vector<VALUETYPE> & aparam = std::vector<VALUETYPE>());
Expand All @@ -137,7 +127,7 @@ class NNPInterModelDevi
const std::vector<int> & atype,
const std::vector<VALUETYPE> & box,
const int nghost,
const LammpsNeighborList & lmp_list,
const InputNlist & lmp_list,
const int & ago,
const std::vector<VALUETYPE> & fparam = std::vector<VALUETYPE>(),
const std::vector<VALUETYPE> & aparam = std::vector<VALUETYPE>());
Expand Down Expand Up @@ -184,10 +174,9 @@ class NNPInterModelDevi
bool init_nbor;
compute_t *array_double;
std::vector<std::vector<int> > sec;
InternalNeighborList nlist;
NNPAtomMap<VALUETYPE> nnpmap;
int *ilist, *jrange, *jlist;
int ilist_size, jrange_size, jlist_size;
NeighborListData nlist_data;
InputNlist nlist;

// function used for nborlist copy
std::vector<std::vector<int> > get_sel() const;
Expand Down
114 changes: 41 additions & 73 deletions source/api_cc/include/common.h
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
#include <string>
#include <iostream>
#include "version.h"
#include "neighbor_list.h"
#include "NNPAtomMap.h"

#include "tensorflow/core/platform/env.h"
Expand All @@ -27,52 +28,20 @@ typedef float VALUETYPE;
typedef double ENERGYTYPE;
#endif

struct LammpsNeighborList
struct NeighborListData
{
int inum;
const int * ilist;
const int * numneigh;
const int *const* firstneigh;
LammpsNeighborList (int inum_,
const int * ilist_,
const int * numneigh_,
const int *const* firstneigh_)
: inum(inum_), ilist(ilist_), numneigh(numneigh_), firstneigh(firstneigh_)
{
}
};

struct InternalNeighborList
{
int * pilist;
int * pjrange;
int * pjlist;
std::vector<int > ilist;
std::vector<int > jrange;
std::vector<int > jlist;
void clear () {ilist.clear(); jrange.clear(); jlist.clear();}
void make_ptrs () {
pilist = &ilist[0]; pjrange = &jrange[0]; pjlist = &jlist[0];
}
std::vector<std::vector<int> > jlist;
std::vector<int > numneigh;
std::vector<int* > firstneigh;
public:
void copy_from_nlist(const InputNlist & inlist);
void shuffle(const std::vector<int> & fwd_map);
void shuffle(const NNPAtomMap<VALUETYPE> & map);
void shuffle_exclude_empty(const std::vector<int> & fwd_map);
void make_inlist(InputNlist & inlist);
};

void
convert_nlist_lmp_internal (InternalNeighborList & list,
const LammpsNeighborList & lmp_list);

void
shuffle_nlist (InternalNeighborList & list,
const std::vector<int> & fwd_map);

void
shuffle_nlist (InternalNeighborList & list,
const NNPAtomMap<VALUETYPE> & map);

void
shuffle_nlist_exclude_empty (InternalNeighborList & list,
const std::vector<int> & fwd_map);


void
select_by_type(std::vector<int> & fwd_map,
std::vector<int> & bkw_map,
Expand Down Expand Up @@ -125,49 +94,48 @@ session_input_tensors (std::vector<std::pair<std::string, Tensor>> & input_tenso
const std::vector<VALUETYPE> & fparam_,
const std::vector<VALUETYPE> & aparam_,
const NNPAtomMap<VALUETYPE>& nnpmap,
const int nghost = 0,
const std::string scope = "");
const std::string scope = "");

int
session_input_tensors (std::vector<std::pair<std::string, Tensor>> & input_tensors,
const std::vector<VALUETYPE> & dcoord_,
const int & ntypes,
const std::vector<int> & datype_,
const std::vector<VALUETYPE> & dbox,
InternalNeighborList & dlist,
InputNlist & dlist,
const std::vector<VALUETYPE> & fparam_,
const std::vector<VALUETYPE> & aparam_,
const NNPAtomMap<VALUETYPE>& nnpmap,
const int nghost,
const int ago,
const std::string scope = "");

int
session_input_tensors (std::vector<std::pair<std::string, Tensor>> & input_tensors,
const std::vector<VALUETYPE> & dcoord_,
const int & ntypes,
const std::vector<int> & datype_,
const std::vector<VALUETYPE> & dbox,
InternalNeighborList & dlist,
const std::vector<VALUETYPE> & fparam_,
const std::vector<VALUETYPE> & aparam_,
const NNPAtomMap<VALUETYPE>& nnpmap,
const int nghost,
const std::string scope = "");

int
session_input_tensors (std::vector<std::pair<std::string, Tensor>>& input_tensors,
const std::vector<VALUETYPE> & dcoord_,
const int & ntypes,
const std::vector<int> & atype_,
const std::vector<VALUETYPE> & dbox,
const int * ilist,
const int * jrange,
const int * jlist,
const std::vector<VALUETYPE> & fparam_,
const std::vector<VALUETYPE> & aparam_,
const NNPAtomMap<VALUETYPE> & nnpmap,
const int & nghost);
const std::string scope = "");

// int
// session_input_tensors (std::vector<std::pair<std::string, Tensor>> & input_tensors,
// const std::vector<VALUETYPE> & dcoord_,
// const int & ntypes,
// const std::vector<int> & datype_,
// const std::vector<VALUETYPE> & dbox,
// InputNlist & dlist,
// const std::vector<VALUETYPE> & fparam_,
// const std::vector<VALUETYPE> & aparam_,
// const NNPAtomMap<VALUETYPE>& nnpmap,
// const int nghost,
// const std::string scope = "");

// int
// session_input_tensors (std::vector<std::pair<std::string, Tensor>>& input_tensors,
// const std::vector<VALUETYPE> & dcoord_,
// const int & ntypes,
// const std::vector<int> & atype_,
// const std::vector<VALUETYPE> & dbox,
// const int * ilist,
// const int * jrange,
// const int * jlist,
// const std::vector<VALUETYPE> & fparam_,
// const std::vector<VALUETYPE> & aparam_,
// const NNPAtomMap<VALUETYPE> & nnpmap,
// const int & nghost);


template<typename VT>
Expand Down
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