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Merged
amcadmus merged 8 commits into from
Mar 7, 2021
Merged

New interface of neighbor list. Switching from descrpt_se_a to prod_env_mat #405

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cdf4664
changing neighbor list interface. add unittests for op prod_env_mat
Mar 5, 2021
08a14c1
CPU implementation of op prod_env_mat
Mar 5, 2021
2cd7684
shutdown the verbose debug information in test
Mar 5, 2021
b49add0
cleanup the code. switch to prod_env_mat_a in training
Mar 5, 2021
a3b1ca2
add old style nlist vars. Waiting for the update of gpu part
Mar 5, 2021
bb3ae4f
better impl. call prod_env_mat_a only once
Mar 5, 2021
9cb29e8
Merge remote-tracking branch 'upstream/api' into api
Mar 7, 2021
3c268cb
adjust the UT of prod_env_mat_r to new input nlist
Mar 7, 2021
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4 changes: 2 additions & 2 deletions deepmd/descriptor/se_a.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ def __init__ (self,
self.place_holders['natoms_vec'] = tf.placeholder(tf.int32, [self.ntypes+2], name=name_pfx+'t_natoms')
self.place_holders['default_mesh'] = tf.placeholder(tf.int32, [None], name=name_pfx+'t_mesh')
self.stat_descrpt, descrpt_deriv, rij, nlist \
= op_module.descrpt_se_a(self.place_holders['coord'],
= op_module.prod_env_mat_a(self.place_holders['coord'],
self.place_holders['type'],
self.place_holders['natoms_vec'],
self.place_holders['box'],
Expand Down Expand Up @@ -340,7 +340,7 @@ def build (self,
atype = tf.reshape (atype_, [-1, natoms[1]])

self.descrpt, self.descrpt_deriv, self.rij, self.nlist \
= op_module.descrpt_se_a (coord,
= op_module.prod_env_mat_a (coord,
atype,
natoms,
box,
Expand Down
9 changes: 7 additions & 2 deletions source/lib/include/neighbor_list.h
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Original file line number Diff line number Diff line change
Expand Up @@ -16,25 +16,30 @@ struct InputNlist
int * ilist;
int * numneigh;
int ** firstneigh;
InputNlist ()
: inum(0), ilist(NULL), numneigh(NULL), firstneigh(NULL)
{};
InputNlist (
int inum_,
int * ilist_,
int * numneigh_,
int ** firstneigh_
)
: inum(inum_), ilist(ilist_), numneigh(numneigh_), firstneigh(firstneigh_)
{}
{};
};

void convert_nlist(
InputNlist & to_nlist,
std::vector<std::vector<int> > & from_nlist
);

int max_numneigh(
const InputNlist & to_nlist
);

// build neighbor list.
// outputs

// nlist, max_list_size
// max_list_size is the maximal size of jlist.
// inputs
Expand Down
9 changes: 3 additions & 6 deletions source/lib/include/prod_env_mat.h
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
#pragma once
#include <vector>
#include "device.h"
#include "neighbor_list.h"

template<typename FPTYPE>
void prod_env_mat_a_cpu(
Expand All @@ -10,9 +11,7 @@ void prod_env_mat_a_cpu(
int * nlist,
const FPTYPE * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const FPTYPE * avg,
const FPTYPE * std,
Expand All @@ -30,9 +29,7 @@ void prod_env_mat_r_cpu(
int * nlist,
const FPTYPE * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const FPTYPE * avg,
const FPTYPE * std,
Expand Down
3 changes: 2 additions & 1 deletion source/lib/src/coord.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -33,10 +33,11 @@ copy_coord_cpu(
const FPTYPE * in_c,
const int * in_t,
const int & nloc,
const int & mem_nall,
const int & mem_nall_,
const float & rcut,
const Region<FPTYPE> & region)
{
const int mem_nall = mem_nall_;
std::vector<double> coord(nloc * 3);
std::vector<int> atype(nloc);
std::copy(in_c, in_c+nloc*3, coord.begin());
Expand Down
15 changes: 14 additions & 1 deletion source/lib/src/neighbor_list.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -757,6 +757,18 @@ convert_nlist(
}
}

int
max_numneigh(
const InputNlist & nlist
)
{
int max_num = 0;
for(int ii = 0; ii < nlist.inum; ++ii){
if(nlist.numneigh[ii] > max_num) max_num = nlist.numneigh[ii];
}
return max_num;
}

template <typename FPTYPE>
int
build_nlist_cpu(
Expand All @@ -765,9 +777,10 @@ build_nlist_cpu(
const FPTYPE * c_cpy,
const int & nloc,
const int & nall,
const int & mem_size,
const int & mem_size_,
const float & rcut)
{
const int mem_size = mem_size_;
*max_list_size = 0;
nlist.inum = nloc;
FPTYPE rcut2 = rcut * rcut;
Expand Down
42 changes: 16 additions & 26 deletions source/lib/src/prod_env_mat.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,7 @@ void prod_env_mat_a_cpu(
int * nlist,
const FPTYPE * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const FPTYPE * avg,
const FPTYPE * std,
Expand Down Expand Up @@ -45,13 +43,14 @@ void prod_env_mat_a_cpu(
// build nlist
std::vector<std::vector<int > > d_nlist_a(nloc);

assert(nloc == inlist.inum);
for (unsigned ii = 0; ii < nloc; ++ii) {
d_nlist_a.reserve (jrange[nloc] / nloc + 10);
d_nlist_a[ii].reserve(max_nbor_size);
}
for (unsigned ii = 0; ii < nloc; ++ii) {
int i_idx = ilist[ii];
for (unsigned jj = jrange[ii]; jj < jrange[ii+1]; ++jj) {
int j_idx = jlist[jj];
int i_idx = inlist.ilist[ii];
for(unsigned jj = 0; jj < inlist.numneigh[ii]; ++jj){
int j_idx = inlist.firstneigh[ii][jj];
d_nlist_a[i_idx].push_back (j_idx);
}
}
Expand Down Expand Up @@ -96,9 +95,7 @@ void prod_env_mat_r_cpu(
int * nlist,
const FPTYPE * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const FPTYPE * avg,
const FPTYPE * std,
Expand Down Expand Up @@ -128,13 +125,14 @@ void prod_env_mat_r_cpu(
// build nlist
std::vector<std::vector<int > > d_nlist_a(nloc);

assert(nloc == inlist.inum);
for (unsigned ii = 0; ii < nloc; ++ii) {
d_nlist_a.reserve (jrange[nloc] / nloc + 10);
d_nlist_a[ii].reserve(max_nbor_size);
}
for (unsigned ii = 0; ii < nloc; ++ii) {
int i_idx = ilist[ii];
for (unsigned jj = jrange[ii]; jj < jrange[ii+1]; ++jj) {
int j_idx = jlist[jj];
int i_idx = inlist.ilist[ii];
for(unsigned jj = 0; jj < inlist.numneigh[ii]; ++jj){
int j_idx = inlist.firstneigh[ii][jj];
d_nlist_a[i_idx].push_back (j_idx);
}
}
Expand Down Expand Up @@ -180,9 +178,7 @@ void prod_env_mat_a_cpu<double>(
int * nlist,
const double * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const double * avg,
const double * std,
Expand All @@ -200,9 +196,7 @@ void prod_env_mat_a_cpu<float>(
int * nlist,
const float * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const float * avg,
const float * std,
Expand All @@ -220,9 +214,7 @@ void prod_env_mat_r_cpu<double>(
int * nlist,
const double * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const double * avg,
const double * std,
Expand All @@ -240,9 +232,7 @@ void prod_env_mat_r_cpu<float>(
int * nlist,
const float * coord,
const int * type,
const int * ilist,
const int * jrange,
const int * jlist,
const InputNlist & inlist,
const int max_nbor_size,
const float * avg,
const float * std,
Expand Down
35 changes: 11 additions & 24 deletions source/lib/tests/test_env_mat_a.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -397,15 +397,11 @@ TEST_F(TestEnvMatA, prod_cpu)
max_nbor_size = nlist_a_cpy[ii].size();
}
}
std::vector<int> ilist(nloc), jlist(tot_nnei), jrange(nloc+1, 0);
for (int ii = 0; ii < nloc; ++ii){
ilist[ii] = ii;
jrange[ii+1] = jrange[ii] + nlist_a_cpy[ii].size();
int jj, cc;
for (jj = jrange[ii], cc = 0; jj < jrange[ii+1]; ++jj, ++cc){
jlist[jj] = nlist_a_cpy[ii][cc];
}
}
std::vector<int> ilist(nloc), numneigh(nloc);
std::vector<int*> firstneigh(nloc);
InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]);
convert_nlist(inlist, nlist_a_cpy);

std::vector<double > em(nloc * ndescrpt), em_deriv(nloc * ndescrpt * 3), rij(nloc * nnei * 3);
std::vector<int> nlist(nloc * nnei);
std::vector<double > avg(ntypes * ndescrpt, 0);
Expand All @@ -417,9 +413,7 @@ TEST_F(TestEnvMatA, prod_cpu)
&nlist[0],
&posi_cpy[0],
&atype_cpy[0],
&ilist[0],
&jrange[0],
&jlist[0],
inlist,
max_nbor_size,
&avg[0],
&std[0],
Expand Down Expand Up @@ -452,15 +446,10 @@ TEST_F(TestEnvMatA, prod_cpu_equal_cpu)
max_nbor_size = nlist_a_cpy[ii].size();
}
}
std::vector<int> ilist(nloc), jlist(tot_nnei), jrange(nloc+1, 0);
for (int ii = 0; ii < nloc; ++ii){
ilist[ii] = ii;
jrange[ii+1] = jrange[ii] + nlist_a_cpy[ii].size();
int jj, cc;
for (jj = jrange[ii], cc = 0; jj < jrange[ii+1]; ++jj, ++cc){
jlist[jj] = nlist_a_cpy[ii][cc];
}
}
std::vector<int> ilist(nloc), numneigh(nloc);
std::vector<int*> firstneigh(nloc);
InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]);
convert_nlist(inlist, nlist_a_cpy);
std::vector<double > em(nloc * ndescrpt), em_deriv(nloc * ndescrpt * 3), rij(nloc * nnei * 3);
std::vector<int> nlist(nloc * nnei);
std::vector<double > avg(ntypes * ndescrpt, 0);
Expand All @@ -472,9 +461,7 @@ TEST_F(TestEnvMatA, prod_cpu_equal_cpu)
&nlist[0],
&posi_cpy[0],
&atype_cpy[0],
&ilist[0],
&jrange[0],
&jlist[0],
inlist,
max_nbor_size,
&avg[0],
&std[0],
Expand Down
35 changes: 11 additions & 24 deletions source/lib/tests/test_env_mat_r.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -249,15 +249,11 @@ TEST_F(TestEnvMatR, prod_cpu)
max_nbor_size = nlist_a_cpy[ii].size();
}
}
std::vector<int> ilist(nloc), jlist(tot_nnei), jrange(nloc+1, 0);
for (int ii = 0; ii < nloc; ++ii){
ilist[ii] = ii;
jrange[ii+1] = jrange[ii] + nlist_a_cpy[ii].size();
int jj, cc;
for (jj = jrange[ii], cc = 0; jj < jrange[ii+1]; ++jj, ++cc){
jlist[jj] = nlist_a_cpy[ii][cc];
}
}
std::vector<int> ilist(nloc), numneigh(nloc);
std::vector<int*> firstneigh(nloc);
InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]);
convert_nlist(inlist, nlist_a_cpy);

std::vector<double > em(nloc * ndescrpt), em_deriv(nloc * ndescrpt * 3), rij(nloc * nnei * 3);
std::vector<int> nlist(nloc * nnei);
std::vector<double > avg(ntypes * ndescrpt, 0);
Expand All @@ -269,9 +265,7 @@ TEST_F(TestEnvMatR, prod_cpu)
&nlist[0],
&posi_cpy[0],
&atype_cpy[0],
&ilist[0],
&jrange[0],
&jlist[0],
inlist,
max_nbor_size,
&avg[0],
&std[0],
Expand Down Expand Up @@ -304,15 +298,10 @@ TEST_F(TestEnvMatR, prod_cpu_equal_cpu)
max_nbor_size = nlist_a_cpy[ii].size();
}
}
std::vector<int> ilist(nloc), jlist(tot_nnei), jrange(nloc+1, 0);
for (int ii = 0; ii < nloc; ++ii){
ilist[ii] = ii;
jrange[ii+1] = jrange[ii] + nlist_a_cpy[ii].size();
int jj, cc;
for (jj = jrange[ii], cc = 0; jj < jrange[ii+1]; ++jj, ++cc){
jlist[jj] = nlist_a_cpy[ii][cc];
}
}
std::vector<int> ilist(nloc), numneigh(nloc);
std::vector<int*> firstneigh(nloc);
InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]);
convert_nlist(inlist, nlist_a_cpy);
std::vector<double > em(nloc * ndescrpt), em_deriv(nloc * ndescrpt * 3), rij(nloc * nnei * 3);
std::vector<int> nlist(nloc * nnei);
std::vector<double > avg(ntypes * ndescrpt, 0);
Expand All @@ -324,9 +313,7 @@ TEST_F(TestEnvMatR, prod_cpu_equal_cpu)
&nlist[0],
&posi_cpy[0],
&atype_cpy[0],
&ilist[0],
&jrange[0],
&jlist[0],
inlist,
max_nbor_size,
&avg[0],
&std[0],
Expand Down
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