From e61bd701e143a6003b66417d3152f3567939cf47 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 14:32:29 +0800 Subject: [PATCH 01/15] fix bug of cmake script for finding tensorflow --- source/cmake/Findtensorflow.cmake | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/source/cmake/Findtensorflow.cmake b/source/cmake/Findtensorflow.cmake index 9281b67ac8..8901c698b9 100644 --- a/source/cmake/Findtensorflow.cmake +++ b/source/cmake/Findtensorflow.cmake @@ -29,7 +29,9 @@ if (BUILD_CPP_IF AND INSTALL_TENSORFLOW) ) endif () -string(REPLACE "lib64" "lib" TENSORFLOW_ROOT_NO64 ${TENSORFLOW_ROOT}) +if(DEFINED TENSORFLOW_ROOT) + string(REPLACE "lib64" "lib" TENSORFLOW_ROOT_NO64 ${TENSORFLOW_ROOT}) +endif(DEFINED TENSORFLOW_ROOT) # define the search path list(APPEND TensorFlow_search_PATHS ${TENSORFLOW_ROOT}) From 3ab5cbb0595c9479d3cbbdd6350cc06b7f1ce637 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 14:34:37 +0800 Subject: [PATCH 02/15] change pb files to test ProdEnvMat --- source/tests/infer/deepdipole.pbtxt | 12 +- source/tests/infer/deeppolar.pbtxt | 27 +- source/tests/infer/deeppot.pbtxt | 12 +- source/tests/infer/dipolecharge_d.pbtxt | 12819 +++ source/tests/infer/dipolecharge_e.pbtxt | 104104 +++++++++++++++++++++ source/tests/test_dipolecharge.py | 112 + 6 files changed, 117071 insertions(+), 15 deletions(-) create mode 100644 source/tests/infer/dipolecharge_d.pbtxt create mode 100644 source/tests/infer/dipolecharge_e.pbtxt create mode 100644 source/tests/test_dipolecharge.py diff --git a/source/tests/infer/deepdipole.pbtxt b/source/tests/infer/deepdipole.pbtxt index 354de0cb98..a8f09a3331 100644 --- a/source/tests/infer/deepdipole.pbtxt +++ b/source/tests/infer/deepdipole.pbtxt @@ -7382,8 +7382,8 @@ node { } } node { - name: "DescrptSeA" - op: "DescrptSeA" + name: "ProdEnvMatA" + op: "ProdEnvMatA" input: "Reshape" input: "Reshape_2" input: "t_natoms" @@ -7437,7 +7437,7 @@ node { node { name: "o_nlist" op: "Identity" - input: "DescrptSeA:3" + input: "ProdEnvMatA:3" attr { key: "T" value { @@ -7448,7 +7448,7 @@ node { node { name: "o_rij" op: "Identity" - input: "DescrptSeA:2" + input: "ProdEnvMatA:2" attr { key: "T" value { @@ -7459,7 +7459,7 @@ node { node { name: "o_rmat_deriv" op: "Identity" - input: "DescrptSeA:1" + input: "ProdEnvMatA:1" attr { key: "T" value { @@ -7470,7 +7470,7 @@ node { node { name: "Reshape_3" op: "Reshape" - input: "DescrptSeA" + input: "ProdEnvMatA" input: "Reshape_3/shape" attr { key: "T" diff --git a/source/tests/infer/deeppolar.pbtxt b/source/tests/infer/deeppolar.pbtxt index 64288c2e80..d7f29bdd87 100644 --- a/source/tests/infer/deeppolar.pbtxt +++ b/source/tests/infer/deeppolar.pbtxt @@ -6136,6 +6136,27 @@ node { } } } +node { + name: "model_attr/output_dim" + op: "Const" + attr { + key: "dtype" + value { + type: DT_INT32 + } + } + attr { + key: "value" + value { + tensor { + dtype: DT_INT32 + tensor_shape { + } + int_val: 9 + } + } + } +} node { name: "model_attr/model_type" op: "Const" @@ -7639,8 +7660,8 @@ node { } } node { - name: "DescrptSeA" - op: "DescrptSeA" + name: "ProdEnvMatA" + op: "ProdEnvMatA" input: "Reshape" input: "Reshape_2" input: "t_natoms" @@ -7694,7 +7715,7 @@ node { node { name: "Reshape_3" op: "Reshape" - input: "DescrptSeA" + input: "ProdEnvMatA" input: "Reshape_3/shape" attr { key: "T" diff --git a/source/tests/infer/deeppot.pbtxt b/source/tests/infer/deeppot.pbtxt index 5ca6c76d70..7a5ba00f78 100644 --- a/source/tests/infer/deeppot.pbtxt +++ b/source/tests/infer/deeppot.pbtxt @@ -10515,8 +10515,8 @@ node { } } node { - name: "DescrptSeA" - op: "DescrptSeA" + name: "ProdEnvMatA" + op: "ProdEnvMatA" input: "Reshape_2" input: "Reshape_4" input: "t_natoms" @@ -10570,7 +10570,7 @@ node { node { name: "o_nlist" op: "Identity" - input: "DescrptSeA:3" + input: "ProdEnvMatA:3" attr { key: "T" value { @@ -10581,7 +10581,7 @@ node { node { name: "o_rij" op: "Identity" - input: "DescrptSeA:2" + input: "ProdEnvMatA:2" 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"Neg" + op: "Neg" + input: "Reshape_14" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } +} +node { + name: "dipole_charge/o_nlist" + op: "Identity" + input: "dipole_charge/ProdEnvMatA:3" + attr { + key: "T" + value { + type: DT_INT32 + } + } +} +node { + name: "dipole_charge/o_rij" + op: "Identity" + input: "dipole_charge/ProdEnvMatA:2" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } +} +node { + name: "dipole_charge/o_rmat_deriv" + op: "Identity" + input: "dipole_charge/ProdEnvMatA:1" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } +} +node { + name: "ProdVirialSeA" + op: "ProdVirialSeA" + input: "Neg" + input: "dipole_charge/o_rmat_deriv" + input: "dipole_charge/o_rij" + input: "dipole_charge/o_nlist" + input: "dipole_charge/t_natoms" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } + attr { + key: "n_a_sel" + value { + i: 25 + } + } + attr { + key: "n_r_sel" + value { + i: 0 + } + } +} +node { + name: "o_dm_av" + op: "Identity" + input: "ProdVirialSeA:1" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } +} +node { + name: "o_dm_virial" + op: "Identity" + input: "ProdVirialSeA" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } +} +node { + name: "ProdForceSeA" + op: "ProdForceSeA" + input: "Neg" + input: "dipole_charge/o_rmat_deriv" + input: "dipole_charge/o_nlist" + input: "dipole_charge/t_natoms" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } + attr { + key: "n_a_sel" + value { + i: 25 + } + } + attr { + key: "n_r_sel" + value { + i: 0 + } + } +} +node { + name: "o_dm_force" + op: "Identity" + input: "ProdForceSeA" + attr { + key: "T" + value { + type: DT_DOUBLE + } + } +} +library { +} diff --git a/source/tests/test_dipolecharge.py b/source/tests/test_dipolecharge.py new file mode 100644 index 0000000000..94b94dffe2 --- /dev/null +++ b/source/tests/test_dipolecharge.py @@ -0,0 +1,112 @@ +import os,sys,platform,shutil,dpdata +import numpy as np +import unittest + +from infer.convert2pb import convert_pbtxt_to_pb +from deepmd.infer import DipoleChargeModifier +from common import tests_path + +from deepmd.run_options import GLOBAL_NP_FLOAT_PRECISION +if GLOBAL_NP_FLOAT_PRECISION == np.float32 : + default_places = 4 +else : + default_places = 10 + +class TestDipoleCharge(unittest.TestCase) : + def setUp(self): + convert_pbtxt_to_pb(str(tests_path / os.path.join("infer","dipolecharge_d.pbtxt")), "dipolecharge_d.pb") + self.dp = DipoleChargeModifier( + "dipolecharge_d.pb", + [-1.0, -3.0], + [1.0, 1.0, 1.0, 1.0, 1.0], + 4.0, + 0.2 + ) + self.coords = np.array([ + 4.6067455554, 8.8719311819, 6.3886531197, + 4.0044515745, 4.2449530507, 7.7902855220, + 2.6453069446, 0.8772647726, 1.2804446790, + 1.1445332290, 0.0067366438, 1.8606485070, + 7.1002867706, 5.0325506787, 3.1805888348, + 4.5352891138, 7.7389683929, 9.4260970128, + 2.1833238914, 9.0916071034, 7.2299906064, + 4.1040157820, 1.0496745045, 5.4748315591, + ], dtype = np.float64) + # 1.1445332290, 0.0067366438, 1.8606485070, + # 2.1833238914, 9.0916071034, 7.2299906064, + # 4.0044515745, 4.2449530507, 7.7902855220, + # 7.1002867706, 5.0325506787, 3.1805888348, + self.atype = np.array([0,3,2,1,3,4,1,4], dtype=int) + self.box = np.array([10., 0., 0., 0., 10., 0., 0., 0., 10.]) + self.expected_e = np.array([ + 3.671081837126222158e+00 + ]) + self.expected_f = np.array([ + 8.786854427753210128e-01,-1.590752486903602159e-01,-2.709225006303785932e-01,-4.449513960033193438e-01,-1.564291540964127813e-01,2.139031741772115178e-02,1.219699614140521193e+00,-5.580358618499958734e-02,-3.878662478349682585e-01,-1.286685244990778854e+00,1.886475802950296488e-01,3.904450515493615437e-01,1.605017382138404849e-02,2.138016869742287995e-01,-2.617514921203008965e-02,2.877081057057793712e-01,-3.846449683844421763e-01,3.048855616906603894e-02,-9.075632811311897807e-01,-6.509653472431625731e-03,2.302010972126376787e-01,2.370565856822822726e-01,3.600133435593881881e-01,1.243887532859055609e-02 + ]) + self.expected_v = np.array([ + 3.714071471995848417e-01,6.957130186032146613e-01,-1.158289779017217302e+00,6.957130186032139951e-01,-1.400130091653774933e+01,-3.631620234653316626e-01,-1.158289779017217302e+00,-3.631620234653316626e-01,3.805077486043773050e+00 + ]) + self.natoms = self.atype.size + self.coords = self.coords.reshape([-1, self.natoms, 3]) + + def tearDown(self): + os.remove("dipolecharge_d.pb") + + def test_attrs(self): + self.assertEqual(self.dp.get_ntypes(), 5) + self.assertAlmostEqual(self.dp.get_rcut(), 4.0, places = default_places) + self.assertEqual(self.dp.get_type_map(), ['A', 'B', 'C', 'D', 'E']) + + def test_1frame(self): + ee, ff, vv = self.dp.eval(self.coords, self.box, self.atype, eval_fv = True +) + # check shape of the returns + nframes = 1 + natoms = len(self.atype) + self.assertEqual(ee.shape, (nframes,)) + self.assertEqual(ff.shape, (nframes,natoms,3)) + self.assertEqual(vv.shape, (nframes,9)) + self.assertEqual(self.expected_e.shape, (nframes,)) + self.assertEqual(self.expected_f.shape, (nframes*natoms*3,)) + self.assertEqual(self.expected_v.shape, (nframes*9,)) + # np.savetxt('ee.out', ee.reshape([1, -1]), delimiter=',') + # np.savetxt('ff.out', ff.reshape([1, -1]), delimiter=',') + # np.savetxt('vv.out', vv.reshape([1, -1]), delimiter=',') + ee = ee.reshape([-1]) + ff = ff.reshape([-1]) + vv = vv.reshape([-1]) + for ii in range(ee.size): + self.assertAlmostEqual(ee[ii], self.expected_e[ii]) + for ii in range(ff.size): + self.assertAlmostEqual(ff[ii], self.expected_f[ii]) + for ii in range(vv.size): + self.assertAlmostEqual(vv[ii], self.expected_v[ii]) + + def test_2frame(self): + nframes = 2 + self.coords = np.tile(self.coords, [nframes, 1, 1]) + self.box = np.tile(self.box, [nframes, 1]) + ee, ff, vv = self.dp.eval(self.coords, self.box, self.atype, eval_fv = True +) + # check shape of the returns + natoms = len(self.atype) + self.assertEqual(ee.shape, (nframes,)) + self.assertEqual(ff.shape, (nframes,natoms,3)) + self.assertEqual(vv.shape, (nframes,9)) + self.expected_e = np.tile(self.expected_e, [nframes]) + self.expected_f = np.tile(self.expected_f, [nframes]) + self.expected_v = np.tile(self.expected_v, [nframes]) + self.assertEqual(self.expected_e.shape, (nframes,)) + self.assertEqual(self.expected_f.shape, (nframes*natoms*3,)) + self.assertEqual(self.expected_v.shape, (nframes*9,)) + ee = ee.reshape([-1]) + ff = ff.reshape([-1]) + vv = vv.reshape([-1]) + for ii in range(ee.size): + self.assertAlmostEqual(ee[ii], self.expected_e[ii]) + for ii in range(ff.size): + self.assertAlmostEqual(ff[ii], self.expected_f[ii]) + for ii in range(vv.size): + self.assertAlmostEqual(vv[ii], self.expected_v[ii]) + From 96679a93f496be86a8d60836b6adf92a552cc902 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 14:52:49 +0800 Subject: [PATCH 03/15] switched to new nlist interface. clean up c++ api. add unittests. --- source/api_cc/include/DataModifier.h | 10 +- source/api_cc/include/DeepTensor.h | 10 +- source/api_cc/include/NNPInter.h | 190 ++--- source/api_cc/include/common.h | 114 +-- source/api_cc/src/DataModifier.cc | 40 +- source/api_cc/src/DeepTensor.cc | 47 +- source/api_cc/src/NNPInter.cc | 904 +++++++++++------------ source/api_cc/src/common.cc | 737 +++++++++--------- source/api_cc/tests/CMakeLists.txt | 106 +++ source/api_cc/tests/test_deepdipole.cc | 106 +++ source/api_cc/tests/test_deeppolar.cc | 106 +++ source/api_cc/tests/test_deeppot.cc | 437 +++++++++++ source/api_cc/tests/test_dipolecharge.cc | 240 ++++++ source/api_cc/tests/test_utils.h | 50 ++ 14 files changed, 2070 insertions(+), 1027 deletions(-) create mode 100644 source/api_cc/tests/CMakeLists.txt create mode 100644 source/api_cc/tests/test_deepdipole.cc create mode 100644 source/api_cc/tests/test_deeppolar.cc create mode 100644 source/api_cc/tests/test_deeppot.cc create mode 100644 source/api_cc/tests/test_dipolecharge.cc create mode 100644 source/api_cc/tests/test_utils.h diff --git a/source/api_cc/include/DataModifier.h b/source/api_cc/include/DataModifier.h index 1bb3e26488..8d16d2ad6d 100644 --- a/source/api_cc/include/DataModifier.h +++ b/source/api_cc/include/DataModifier.h @@ -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 = ""); @@ -23,7 +23,7 @@ class DataModifier const std::vector> & pairs, const std::vector & 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 sel_types () const {assert(inited); return sel_type;}; diff --git a/source/api_cc/include/DeepTensor.h b/source/api_cc/include/DeepTensor.h index f73957137d..ec2c7de22b 100644 --- a/source/api_cc/include/DeepTensor.h +++ b/source/api_cc/include/DeepTensor.h @@ -17,14 +17,13 @@ class DeepTensor void compute (std::vector & value, const std::vector & coord, const std::vector & atype, - const std::vector & box, - const int nghost = 0); + const std::vector & box); void compute (std::vector & value, const std::vector & coord, const std::vector & atype, const std::vector & 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;}; @@ -51,13 +50,12 @@ class DeepTensor void compute_inner (std::vector & value, const std::vector & coord, const std::vector & atype, - const std::vector & box, - const int nghost = 0); + const std::vector & box); void compute_inner (std::vector & value, const std::vector & coord, const std::vector & atype, const std::vector & box, const int nghost, - const InternalNeighborList& lmp_list); + const InputNlist& inlist); }; diff --git a/source/api_cc/include/NNPInter.h b/source/api_cc/include/NNPInter.h index 11bfad9c27..da89cdc0cd 100644 --- a/source/api_cc/include/NNPInter.h +++ b/source/api_cc/include/NNPInter.h @@ -1,6 +1,7 @@ #pragma once #include "common.h" +#include "neighbor_list.h" typedef double compute_t; class NNPInter @@ -18,7 +19,6 @@ class NNPInter const std::vector & coord, const std::vector & atype, const std::vector & box, - const int nghost = 0, const std::vector& fparam = std::vector(), const std::vector& aparam = std::vector()); void compute (ENERGYTYPE & ener, @@ -28,7 +28,7 @@ class NNPInter const std::vector & atype, const std::vector & box, const int nghost, - const LammpsNeighborList & lmp_list, + const InputNlist & inlist, const int& ago, const std::vector& fparam = std::vector(), const std::vector& aparam = std::vector()); @@ -51,7 +51,7 @@ class NNPInter const std::vector & atype, const std::vector & box, const int nghost, - const LammpsNeighborList & lmp_list, + const InputNlist & lmp_list, const int& ago, const std::vector& fparam = std::vector(), const std::vector& aparam = std::vector()); @@ -91,7 +91,7 @@ class NNPInter bool init_nbor; std::vector sec_a; compute_t *array_double; - InternalNeighborList nlist; + NeighborListData nlist_data; NNPAtomMap nnpmap; int *ilist, *jrange, *jlist; int ilist_size, jrange_size, jlist_size; @@ -100,98 +100,98 @@ class NNPInter std::vector get_sel_a() const; }; -class NNPInterModelDevi -{ -public: - NNPInterModelDevi () ; - ~NNPInterModelDevi() ; - NNPInterModelDevi (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); - void init (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); -public: - void compute (ENERGYTYPE & ener, - std::vector & force, - std::vector & virial, - std::vector & model_devi, - const std::vector & coord, - const std::vector & atype, - const std::vector & box, - const std::vector & fparam = std::vector(), - const std::vector & aparam = std::vector()); - void compute (std::vector & all_ener, - std::vector > & all_force, - std::vector > & all_virial, - const std::vector & coord, - const std::vector & atype, - const std::vector & box, - const int nghost, - const LammpsNeighborList & lmp_list, - const int & ago, - const std::vector & fparam = std::vector(), - const std::vector & aparam = std::vector()); - void compute (std::vector & all_ener, - std::vector > & all_force, - std::vector > & all_virial, - std::vector > & all_atom_energy, - std::vector > & all_atom_virial, - const std::vector & coord, - const std::vector & atype, - const std::vector & box, - const int nghost, - const LammpsNeighborList & lmp_list, - const int & ago, - const std::vector & fparam = std::vector(), - const std::vector & aparam = std::vector()); - VALUETYPE cutoff () const {assert(inited); return rcut;}; - int numb_types () const {assert(inited); return ntypes;}; - int dim_fparam () const {assert(inited); return dfparam;}; - int dim_aparam () const {assert(inited); return daparam;}; -#ifndef HIGH_PREC - void compute_avg (ENERGYTYPE & dener, - const std::vector & all_energy); -#endif - void compute_avg (VALUETYPE & dener, - const std::vector & all_energy); - void compute_avg (std::vector & avg, - const std::vector > & xx); - void compute_std_e (std::vector & std, - const std::vector & avg, - const std::vector >& xx); - void compute_std_f (std::vector & std, - const std::vector & avg, - const std::vector >& xx); - void compute_relative_std_f (std::vector & std, - const std::vector & avg, - const VALUETYPE eps); -private: - unsigned numb_models; - std::vector sessions; - int num_intra_nthreads, num_inter_nthreads; - std::vector graph_defs; - bool inited; - template VT get_scalar(const std::string name) const; - // VALUETYPE get_rcut () const; - // int get_ntypes () const; - VALUETYPE rcut; - VALUETYPE cell_size; - int ntypes; - int dfparam; - int daparam; - void validate_fparam_aparam(const int & nloc, - const std::vector &fparam, - const std::vector &aparam)const ; +// class NNPInterModelDevi +// { +// public: +// NNPInterModelDevi () ; +// ~NNPInterModelDevi() ; +// NNPInterModelDevi (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); +// void init (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); +// public: +// void compute (ENERGYTYPE & ener, +// std::vector & force, +// std::vector & virial, +// std::vector & model_devi, +// const std::vector & coord, +// const std::vector & atype, +// const std::vector & box, +// const std::vector & fparam = std::vector(), +// const std::vector & aparam = std::vector()); +// void compute (std::vector & all_ener, +// std::vector > & all_force, +// std::vector > & all_virial, +// const std::vector & coord, +// const std::vector & atype, +// const std::vector & box, +// const int nghost, +// const LammpsNeighborList & lmp_list, +// const int & ago, +// const std::vector & fparam = std::vector(), +// const std::vector & aparam = std::vector()); +// void compute (std::vector & all_ener, +// std::vector > & all_force, +// std::vector > & all_virial, +// std::vector > & all_atom_energy, +// std::vector > & all_atom_virial, +// const std::vector & coord, +// const std::vector & atype, +// const std::vector & box, +// const int nghost, +// const LammpsNeighborList & lmp_list, +// const int & ago, +// const std::vector & fparam = std::vector(), +// const std::vector & aparam = std::vector()); +// VALUETYPE cutoff () const {assert(inited); return rcut;}; +// int numb_types () const {assert(inited); return ntypes;}; +// int dim_fparam () const {assert(inited); return dfparam;}; +// int dim_aparam () const {assert(inited); return daparam;}; +// #ifndef HIGH_PREC +// void compute_avg (ENERGYTYPE & dener, +// const std::vector & all_energy); +// #endif +// void compute_avg (VALUETYPE & dener, +// const std::vector & all_energy); +// void compute_avg (std::vector & avg, +// const std::vector > & xx); +// void compute_std_e (std::vector & std, +// const std::vector & avg, +// const std::vector >& xx); +// void compute_std_f (std::vector & std, +// const std::vector & avg, +// const std::vector >& xx); +// void compute_relative_std_f (std::vector & std, +// const std::vector & avg, +// const VALUETYPE eps); +// private: +// unsigned numb_models; +// std::vector sessions; +// int num_intra_nthreads, num_inter_nthreads; +// std::vector graph_defs; +// bool inited; +// template VT get_scalar(const std::string name) const; +// // VALUETYPE get_rcut () const; +// // int get_ntypes () const; +// VALUETYPE rcut; +// VALUETYPE cell_size; +// int ntypes; +// int dfparam; +// int daparam; +// void validate_fparam_aparam(const int & nloc, +// const std::vector &fparam, +// const std::vector &aparam)const ; - // copy neighbor list info from host - bool init_nbor; - compute_t *array_double; - std::vector > sec; - InternalNeighborList nlist; - NNPAtomMap nnpmap; - int *ilist, *jrange, *jlist; - int ilist_size, jrange_size, jlist_size; +// // copy neighbor list info from host +// bool init_nbor; +// compute_t *array_double; +// std::vector > sec; +// InternalNeighborList nlist; +// NNPAtomMap nnpmap; +// int *ilist, *jrange, *jlist; +// int ilist_size, jrange_size, jlist_size; - // function used for nborlist copy - std::vector > get_sel() const; - void cum_sum(const std::vector > n_sel); -}; +// // function used for nborlist copy +// std::vector > get_sel() const; +// void cum_sum(const std::vector > n_sel); +// }; diff --git a/source/api_cc/include/common.h b/source/api_cc/include/common.h index 4014b643b8..9e2110b03b 100644 --- a/source/api_cc/include/common.h +++ b/source/api_cc/include/common.h @@ -4,6 +4,7 @@ #include #include #include "version.h" +#include "neighbor_list.h" #include "NNPAtomMap.h" #include "tensorflow/core/platform/env.h" @@ -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 ilist; - std::vector jrange; - std::vector jlist; - void clear () {ilist.clear(); jrange.clear(); jlist.clear();} - void make_ptrs () { - pilist = &ilist[0]; pjrange = &jrange[0]; pjlist = &jlist[0]; - } + std::vector > jlist; + std::vector numneigh; + std::vector firstneigh; +public: + void copy_from_nlist(const InputNlist & inlist); + void shuffle(const std::vector & fwd_map); + void shuffle(const NNPAtomMap & map); + void shuffle_exclude_empty(const std::vector & 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 & fwd_map); - -void -shuffle_nlist (InternalNeighborList & list, - const NNPAtomMap & map); - -void -shuffle_nlist_exclude_empty (InternalNeighborList & list, - const std::vector & fwd_map); - - void select_by_type(std::vector & fwd_map, std::vector & bkw_map, @@ -125,8 +94,7 @@ session_input_tensors (std::vector> & input_tenso const std::vector & fparam_, const std::vector & aparam_, const NNPAtomMap& nnpmap, - const int nghost = 0, - const std::string scope = ""); + const std::string scope = ""); int session_input_tensors (std::vector> & input_tensors, @@ -134,40 +102,40 @@ session_input_tensors (std::vector> & input_tenso const int & ntypes, const std::vector & datype_, const std::vector & dbox, - InternalNeighborList & dlist, + InputNlist & dlist, const std::vector & fparam_, const std::vector & aparam_, const NNPAtomMap& nnpmap, const int nghost, const int ago, - const std::string scope = ""); - -int -session_input_tensors (std::vector> & input_tensors, - const std::vector & dcoord_, - const int & ntypes, - const std::vector & datype_, - const std::vector & dbox, - InternalNeighborList & dlist, - const std::vector & fparam_, - const std::vector & aparam_, - const NNPAtomMap& nnpmap, - const int nghost, - const std::string scope = ""); - -int -session_input_tensors (std::vector>& input_tensors, - const std::vector & dcoord_, - const int & ntypes, - const std::vector & atype_, - const std::vector & dbox, - const int * ilist, - const int * jrange, - const int * jlist, - const std::vector & fparam_, - const std::vector & aparam_, - const NNPAtomMap & nnpmap, - const int & nghost); + const std::string scope = ""); + +// int +// session_input_tensors (std::vector> & input_tensors, +// const std::vector & dcoord_, +// const int & ntypes, +// const std::vector & datype_, +// const std::vector & dbox, +// InputNlist & dlist, +// const std::vector & fparam_, +// const std::vector & aparam_, +// const NNPAtomMap& nnpmap, +// const int nghost, +// const std::string scope = ""); + +// int +// session_input_tensors (std::vector>& input_tensors, +// const std::vector & dcoord_, +// const int & ntypes, +// const std::vector & atype_, +// const std::vector & dbox, +// const int * ilist, +// const int * jrange, +// const int * jlist, +// const std::vector & fparam_, +// const std::vector & aparam_, +// const NNPAtomMap & nnpmap, +// const int & nghost); template diff --git a/source/api_cc/src/DataModifier.cc b/source/api_cc/src/DataModifier.cc index 8144451841..45ded50346 100644 --- a/source/api_cc/src/DataModifier.cc +++ b/source/api_cc/src/DataModifier.cc @@ -1,30 +1,33 @@ #include "DataModifier.h" -DataModifier:: -DataModifier() +DipoleChargeModifier:: +DipoleChargeModifier() : inited (false) { } -DataModifier:: -DataModifier(const std::string & model, +DipoleChargeModifier:: +DipoleChargeModifier(const std::string & model, const int & gpu_rank, const std::string &name_scope_) : inited (false), name_scope(name_scope_) { - get_env_nthreads(num_intra_nthreads, num_inter_nthreads); init(model, gpu_rank); } void -DataModifier:: +DipoleChargeModifier:: init (const std::string & model, const int & gpu_rank, const std::string &name_scope_) { - assert (!inited); + if (inited){ + std::cerr << "WARNING: deepmd-kit should not be initialized twice, do nothing at the second call of initializer" << std::endl; + return ; + } name_scope = name_scope_; SessionOptions options; + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); options.config.set_inter_op_parallelism_threads(num_inter_nthreads); options.config.set_intra_op_parallelism_threads(num_intra_nthreads); checkStatus(NewSession(options, &session)); @@ -45,7 +48,7 @@ init (const std::string & model, template VT -DataModifier:: +DipoleChargeModifier:: get_scalar (const std::string & name) const { return session_get_scalar(session, name, name_scope); @@ -53,14 +56,14 @@ get_scalar (const std::string & name) const template void -DataModifier:: +DipoleChargeModifier:: get_vector (std::vector & vec, const std::string & name) const { session_get_vector(vec, session, name, name_scope); } void -DataModifier:: +DipoleChargeModifier:: run_model (std::vector & dforce, std::vector & dvirial, Session * session, @@ -113,7 +116,7 @@ run_model (std::vector & dforce, void -DataModifier:: +DipoleChargeModifier:: compute (std::vector & dfcorr_, std::vector & dvcorr_, const std::vector & dcoord_, @@ -122,7 +125,7 @@ compute (std::vector & dfcorr_, const std::vector>& pairs, const std::vector & delef_, const int nghost, - const LammpsNeighborList & lmp_list) + const InputNlist & nlist) { // firstly do selection int nall = datype_.size(); @@ -151,20 +154,21 @@ compute (std::vector & dfcorr_, select_map(delef_real, delef_, real_fwd_map, 3); select_map(datype_real, datype_, real_fwd_map, 1); // internal nlist - InternalNeighborList nlist_; - convert_nlist_lmp_internal(nlist_, lmp_list); - shuffle_nlist_exclude_empty(nlist_, real_fwd_map); + NeighborListData nlist_data; + nlist_data.copy_from_nlist(nlist); + nlist_data.shuffle_exclude_empty(real_fwd_map); // sort atoms NNPAtomMap nnpmap (datype_real.begin(), datype_real.begin() + nloc_real); assert (nloc_real == nnpmap.get_type().size()); const std::vector & sort_fwd_map(nnpmap.get_fwd_map()); const std::vector & sort_bkw_map(nnpmap.get_bkw_map()); // shuffle nlist - InternalNeighborList nlist(nlist_); - shuffle_nlist (nlist, nnpmap); + nlist_data.shuffle(nnpmap); + InputNlist inlist; + nlist_data.make_inlist(inlist); // make input tensors std::vector> input_tensors; - int ret = session_input_tensors (input_tensors, dcoord_real, ntypes, datype_real, dbox, nlist, std::vector(), std::vector(), nnpmap, nghost_real, name_scope); + int ret = session_input_tensors (input_tensors, dcoord_real, ntypes, datype_real, dbox, inlist, std::vector(), std::vector(), nnpmap, nghost_real, 0, name_scope); assert (nloc_real == ret); // make bond idx map std::vector bd_idx(nall, -1); diff --git a/source/api_cc/src/DeepTensor.cc b/source/api_cc/src/DeepTensor.cc index 311cd1051d..a26729d8ef 100644 --- a/source/api_cc/src/DeepTensor.cc +++ b/source/api_cc/src/DeepTensor.cc @@ -12,7 +12,6 @@ DeepTensor(const std::string & model, const std::string &name_scope_) : inited (false), name_scope(name_scope_) { - get_env_nthreads(num_intra_nthreads, num_inter_nthreads); init(model, gpu_rank); } @@ -22,9 +21,13 @@ init (const std::string & model, const int & gpu_rank, const std::string &name_scope_) { - assert (!inited); + if (inited){ + std::cerr << "WARNING: deepmd-kit should not be initialized twice, do nothing at the second call of initializer" << std::endl; + return ; + } name_scope = name_scope_; SessionOptions options; + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); options.config.set_inter_op_parallelism_threads(num_inter_nthreads); options.config.set_intra_op_parallelism_threads(num_intra_nthreads); checkStatus (NewSession(options, &session)); @@ -96,20 +99,20 @@ DeepTensor:: compute (std::vector & dtensor_, const std::vector & dcoord_, const std::vector & datype_, - const std::vector & dbox, - const int nghost) + const std::vector & dbox) { std::vector dcoord; std::vector datype, fwd_map, bkw_map; int nghost_real; - select_real_atoms(fwd_map, bkw_map, nghost_real, dcoord_, datype_, nghost, ntypes); + select_real_atoms(fwd_map, bkw_map, nghost_real, dcoord_, datype_, 0, ntypes); + assert(nghost_real == 0); // resize to nall_real dcoord.resize(bkw_map.size() * 3); datype.resize(bkw_map.size()); // fwd map select_map(dcoord, dcoord_, fwd_map, 3); select_map(datype, datype_, fwd_map, 1); - compute_inner(dtensor_, dcoord, datype, dbox, nghost_real); + compute_inner(dtensor_, dcoord, datype, dbox); } void @@ -119,7 +122,7 @@ compute (std::vector & dtensor_, const std::vector & datype_, const std::vector & dbox, const int nghost, - const LammpsNeighborList & lmp_list) + const InputNlist & nlist) { std::vector dcoord; std::vector datype, fwd_map, bkw_map; @@ -132,10 +135,12 @@ compute (std::vector & dtensor_, select_map(dcoord, dcoord_, fwd_map, 3); select_map(datype, datype_, fwd_map, 1); // internal nlist - InternalNeighborList nlist; - convert_nlist_lmp_internal(nlist, lmp_list); - shuffle_nlist_exclude_empty(nlist, fwd_map); - compute_inner(dtensor_, dcoord, datype, dbox, nghost_real, nlist); + NeighborListData nlist_data; + nlist_data.copy_from_nlist(nlist); + nlist_data.shuffle_exclude_empty(fwd_map); + InputNlist inlist; + nlist_data.make_inlist(inlist); + compute_inner(dtensor_, dcoord, datype, dbox, nghost_real, inlist); } @@ -144,19 +149,18 @@ DeepTensor:: compute_inner (std::vector & dtensor_, const std::vector & dcoord_, const std::vector & datype_, - const std::vector & dbox, - const int nghost) + const std::vector & dbox) { int nall = dcoord_.size() / 3; - int nloc = nall - nghost; + int nloc = nall; NNPAtomMap nnpmap (datype_.begin(), datype_.begin() + nloc); assert (nloc == nnpmap.get_type().size()); std::vector> input_tensors; - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, std::vector(), std::vector(), nnpmap, nghost, name_scope); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, std::vector(), std::vector(), nnpmap, name_scope); assert (ret == nloc); - run_model (dtensor_, session, input_tensors, nnpmap, nghost); + run_model (dtensor_, session, input_tensors, nnpmap); } void @@ -166,18 +170,21 @@ compute_inner (std::vector & dtensor_, const std::vector & datype_, const std::vector & dbox, const int nghost, - const InternalNeighborList & nlist_) + const InputNlist & nlist) { int nall = dcoord_.size() / 3; int nloc = nall - nghost; NNPAtomMap nnpmap (datype_.begin(), datype_.begin() + nloc); assert (nloc == nnpmap.get_type().size()); - InternalNeighborList nlist(nlist_); - shuffle_nlist (nlist, nnpmap); + NeighborListData nlist_data; + nlist_data.copy_from_nlist(nlist); + nlist_data.shuffle(nnpmap); + InputNlist inlist; + nlist_data.make_inlist(inlist); std::vector> input_tensors; - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, std::vector(), std::vector(), nnpmap, nghost, name_scope); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, inlist, std::vector(), std::vector(), nnpmap, nghost, 0, name_scope); assert (nloc == ret); run_model (dtensor_, session, input_tensors, nnpmap, nghost); diff --git a/source/api_cc/src/NNPInter.cc b/source/api_cc/src/NNPInter.cc index 4ac454a324..cfb17a314c 100644 --- a/source/api_cc/src/NNPInter.cc +++ b/source/api_cc/src/NNPInter.cc @@ -173,14 +173,12 @@ NNPInter:: NNPInter () : inited (false), init_nbor (false) { - get_env_nthreads(num_intra_nthreads, num_inter_nthreads); } NNPInter:: NNPInter (const std::string & model, const int & gpu_rank, const std::string & file_content) : inited (false), init_nbor (false) { - get_env_nthreads(num_intra_nthreads, num_inter_nthreads); init(model, gpu_rank, file_content); } @@ -195,6 +193,7 @@ init (const std::string & model, const int & gpu_rank, const std::string & file_ return ; } SessionOptions options; + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); options.config.set_inter_op_parallelism_threads(num_inter_nthreads); options.config.set_intra_op_parallelism_threads(num_intra_nthreads); @@ -322,21 +321,20 @@ compute (ENERGYTYPE & dener, const std::vector & dcoord_, const std::vector & datype_, const std::vector & dbox, - const int nghost, const std::vector & fparam, const std::vector & aparam) { int nall = dcoord_.size() / 3; - int nloc = nall - nghost; + int nloc = nall; nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); assert (nloc == nnpmap.get_type().size()); validate_fparam_aparam(nloc, fparam, aparam); std::vector> input_tensors; - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, fparam, aparam, nnpmap, nghost); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, fparam, aparam, nnpmap); assert (ret == nloc); - run_model (dener, dforce_, dvirial, session, input_tensors, nnpmap, nghost); + run_model (dener, dforce_, dvirial, session, input_tensors, nnpmap); } void @@ -348,7 +346,7 @@ compute (ENERGYTYPE & dener, const std::vector & datype_, const std::vector & dbox, const int nghost, - const LammpsNeighborList & lmp_list, + const InputNlist & inlist, const int& ago, const std::vector & fparam, const std::vector & aparam_) @@ -370,11 +368,12 @@ compute (ENERGYTYPE & dener, } // internal nlist if (ago == 0){ - convert_nlist_lmp_internal(nlist, lmp_list); - shuffle_nlist_exclude_empty(nlist, fwd_map); + nlist_data.copy_from_nlist(inlist); + nlist_data.shuffle_exclude_empty(fwd_map); } compute_inner(dener, dforce, dvirial, dcoord, datype, dbox, nghost_real, ago, fparam, aparam); // bkw map + dforce_.resize(fwd_map.size() * 3); select_map(dforce_, dforce, bkw_map, 3); } @@ -399,13 +398,13 @@ compute_inner (ENERGYTYPE & dener, // agp == 0 means that the LAMMPS nbor list has been updated if (ago == 0) { - nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); - assert (nloc == nnpmap.get_type().size()); - - shuffle_nlist (nlist, nnpmap); + nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); + assert (nloc == nnpmap.get_type().size()); + nlist_data.shuffle(nnpmap); } - - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); + InputNlist inlist; + nlist_data.make_inlist(inlist); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, inlist, fparam, aparam, nnpmap, nghost, ago); assert (nloc == ret); run_model (dener, dforce_, dvirial, session, input_tensors, nnpmap, nghost); } @@ -446,7 +445,7 @@ compute (ENERGYTYPE & dener, const std::vector & datype_, const std::vector & dbox, const int nghost, - const LammpsNeighborList & lmp_list, + const InputNlist & nlist, const int & ago, const std::vector & fparam, const std::vector & aparam) @@ -459,13 +458,14 @@ compute (ENERGYTYPE & dener, if (ago == 0) { nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); assert (nloc == nnpmap.get_type().size()); - - // InternalNeighborList nlist; - convert_nlist_lmp_internal (nlist, lmp_list); - shuffle_nlist (nlist, nnpmap); + // make internal nlist data + nlist_data.copy_from_nlist(nlist); + nlist_data.shuffle(nnpmap); } - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); + InputNlist inlist; + nlist_data.make_inlist(inlist); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, inlist, fparam, aparam, nnpmap, nghost, ago); assert (nloc == ret); run_model (dener, dforce_, dvirial, datom_energy_, datom_virial_, session, input_tensors, nnpmap, nghost); } @@ -478,448 +478,448 @@ get_type_map(std::string & type_map){ -NNPInterModelDevi:: -NNPInterModelDevi () - : inited (false), - init_nbor (false), - numb_models (0) -{ - get_env_nthreads(num_intra_nthreads, num_inter_nthreads); -} - -NNPInterModelDevi:: -NNPInterModelDevi (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) - : inited (false), - init_nbor(false), - numb_models (0) -{ - get_env_nthreads(num_intra_nthreads, num_inter_nthreads); - init(models, gpu_rank, file_contents); -} - -NNPInterModelDevi::~NNPInterModelDevi() {} - -void -NNPInterModelDevi:: -init (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) -{ - if (inited){ - std::cerr << "WARNING: deepmd-kit should not be initialized twice, do nothing at the second call of initializer" << std::endl; - return ; - } - numb_models = models.size(); - sessions.resize(numb_models); - graph_defs.resize(numb_models); +// // NNPInterModelDevi:: +// // NNPInterModelDevi () +// // : inited (false), +// // init_nbor (false), +// // numb_models (0) +// // { +// // get_env_nthreads(num_intra_nthreads, num_inter_nthreads); +// // } + +// // NNPInterModelDevi:: +// // NNPInterModelDevi (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) +// // : inited (false), +// // init_nbor(false), +// // numb_models (0) +// // { +// // get_env_nthreads(num_intra_nthreads, num_inter_nthreads); +// // init(models, gpu_rank, file_contents); +// // } + +// // NNPInterModelDevi::~NNPInterModelDevi() {} + +// // void +// // NNPInterModelDevi:: +// // init (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) +// // { +// // if (inited){ +// // std::cerr << "WARNING: deepmd-kit should not be initialized twice, do nothing at the second call of initializer" << std::endl; +// // return ; +// // } +// // numb_models = models.size(); +// // sessions.resize(numb_models); +// // graph_defs.resize(numb_models); - int gpu_num = -1; - #if GOOGLE_CUDA - cudaGetDeviceCount(&gpu_num); - #endif // GOOGLE_CUDA - - SessionOptions options; - options.config.set_inter_op_parallelism_threads(num_inter_nthreads); - options.config.set_intra_op_parallelism_threads(num_intra_nthreads); - for (unsigned ii = 0; ii < numb_models; ++ii){ - if (file_contents.size() == 0) - checkStatus (ReadBinaryProto(Env::Default(), models[ii], &graph_defs[ii])); - else - graph_defs[ii].ParseFromString(file_contents[ii]); - } - #if GOOGLE_CUDA - if (gpu_num > 0) { - options.config.set_allow_soft_placement(true); - options.config.mutable_gpu_options()->set_per_process_gpu_memory_fraction(0.9); - options.config.mutable_gpu_options()->set_allow_growth(true); - cudaErrcheck(cudaSetDevice(gpu_rank % gpu_num)); - } - #endif // GOOGLE_CUDA - - for (unsigned ii = 0; ii < numb_models; ++ii) { - if (gpu_num > 0) { - std::string str = "/gpu:"; - str += std::to_string(gpu_rank % gpu_num); - graph::SetDefaultDevice(str, &graph_defs[ii]); - } - checkStatus (NewSession(options, &(sessions[ii]))); - checkStatus (sessions[ii]->Create(graph_defs[ii])); - } - rcut = get_scalar("descrpt_attr/rcut"); - cell_size = rcut; - ntypes = get_scalar("descrpt_attr/ntypes"); - dfparam = get_scalar("fitting_attr/dfparam"); - daparam = get_scalar("fitting_attr/daparam"); - if (dfparam < 0) dfparam = 0; - if (daparam < 0) daparam = 0; - // rcut = get_rcut(); - // cell_size = rcut; - // ntypes = get_ntypes(); - inited = true; +// // int gpu_num = -1; +// // #if GOOGLE_CUDA +// // cudaGetDeviceCount(&gpu_num); +// // #endif // GOOGLE_CUDA + +// // SessionOptions options; +// // options.config.set_inter_op_parallelism_threads(num_inter_nthreads); +// // options.config.set_intra_op_parallelism_threads(num_intra_nthreads); +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // if (file_contents.size() == 0) +// // checkStatus (ReadBinaryProto(Env::Default(), models[ii], &graph_defs[ii])); +// // else +// // graph_defs[ii].ParseFromString(file_contents[ii]); +// // } +// // #if GOOGLE_CUDA +// // if (gpu_num > 0) { +// // options.config.set_allow_soft_placement(true); +// // options.config.mutable_gpu_options()->set_per_process_gpu_memory_fraction(0.9); +// // options.config.mutable_gpu_options()->set_allow_growth(true); +// // cudaErrcheck(cudaSetDevice(gpu_rank % gpu_num)); +// // } +// // #endif // GOOGLE_CUDA + +// // for (unsigned ii = 0; ii < numb_models; ++ii) { +// // if (gpu_num > 0) { +// // std::string str = "/gpu:"; +// // str += std::to_string(gpu_rank % gpu_num); +// // graph::SetDefaultDevice(str, &graph_defs[ii]); +// // } +// // checkStatus (NewSession(options, &(sessions[ii]))); +// // checkStatus (sessions[ii]->Create(graph_defs[ii])); +// // } +// // rcut = get_scalar("descrpt_attr/rcut"); +// // cell_size = rcut; +// // ntypes = get_scalar("descrpt_attr/ntypes"); +// // dfparam = get_scalar("fitting_attr/dfparam"); +// // daparam = get_scalar("fitting_attr/daparam"); +// // if (dfparam < 0) dfparam = 0; +// // if (daparam < 0) daparam = 0; +// // // rcut = get_rcut(); +// // // cell_size = rcut; +// // // ntypes = get_ntypes(); +// // inited = true; - init_nbor = false; - ilist = NULL; jrange = NULL; jlist = NULL; - ilist_size = 0; jrange_size = 0; jlist_size = 0; -} - -template -VT -NNPInterModelDevi:: -get_scalar(const std::string name) const -{ - VT myrcut = 0; - for (unsigned ii = 0; ii < numb_models; ++ii){ - VT ret = session_get_scalar(sessions[ii], name); - if (ii == 0){ - myrcut = ret; - } - else { - assert (myrcut == ret); - } - } - return myrcut; -} - -// init the tmp array data -std::vector > -NNPInterModelDevi:: -get_sel () const -{ - std::vector > sec; - for (int ii = 0; ii < numb_models; ii++) { - std::vector sel; - std::istringstream is(graph_info(graph_defs[ii])); - std::string line = ""; - while(is >> line) { - if (line.find("sel") != line.npos) { - while (std::getline(is, line) && line != "}") { - if (line.find("i:") != line.npos) { - sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); - } - } break; - } - if (line.find("sel_a") != line.npos) { - while (std::getline(is, line) && line != "}") { - if (line.find("i:") != line.npos) { - sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); - } - } break; - } - } - sec.push_back(sel); - } - return sec; -} - -void -NNPInterModelDevi:: -cum_sum (const std::vector > n_sel) -{ - for (int ii = 0; ii < numb_models; ++ii) { - std::vector _sec; - _sec.resize (n_sel[ii].size() + 1); - _sec[0] = 0; - for (int jj = 1; jj < _sec.size(); ++jj) { - _sec[jj] = _sec[jj-1] + n_sel[ii][jj-1]; - } - sec.push_back(_sec); - } -} - -void -NNPInterModelDevi:: -validate_fparam_aparam(const int & nloc, - const std::vector &fparam, - const std::vector &aparam)const -{ - if (fparam.size() != dfparam) { - throw std::runtime_error("the dim of frame parameter provided is not consistent with what the model uses"); - } - if (aparam.size() != daparam * nloc) { - throw std::runtime_error("the dim of atom parameter provided is not consistent with what the model uses"); - } -} - -void -NNPInterModelDevi:: -compute (ENERGYTYPE & dener, - std::vector & dforce_, - std::vector & dvirial, - std::vector & model_devi, - const std::vector & dcoord_, - const std::vector & datype_, - const std::vector & dbox, - const std::vector & fparam, - const std::vector & aparam) -{ - if (numb_models == 0) return; - - nnpmap = NNPAtomMap (datype_.begin(), datype_.end()); - validate_fparam_aparam(nnpmap.get_type().size(), fparam, aparam); - - std::vector> input_tensors; - int nloc = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, fparam, aparam, nnpmap); - - std::vector all_energy (numb_models); - std::vector > all_force (numb_models); - std::vector > all_virial (numb_models); - - for (unsigned ii = 0; ii < numb_models; ++ii){ - run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap); - } - - dener = 0; - for (unsigned ii = 0; ii < numb_models; ++ii){ - dener += all_energy[ii]; - } - dener /= VALUETYPE(numb_models); - compute_avg (dvirial, all_virial); - compute_avg (dforce_, all_force); +// // init_nbor = false; +// // ilist = NULL; jrange = NULL; jlist = NULL; +// // ilist_size = 0; jrange_size = 0; jlist_size = 0; +// // } + +// // template +// // VT +// // NNPInterModelDevi:: +// // get_scalar(const std::string name) const +// // { +// // VT myrcut = 0; +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // VT ret = session_get_scalar(sessions[ii], name); +// // if (ii == 0){ +// // myrcut = ret; +// // } +// // else { +// // assert (myrcut == ret); +// // } +// // } +// // return myrcut; +// // } + +// // // init the tmp array data +// // std::vector > +// // NNPInterModelDevi:: +// // get_sel () const +// // { +// // std::vector > sec; +// // for (int ii = 0; ii < numb_models; ii++) { +// // std::vector sel; +// // std::istringstream is(graph_info(graph_defs[ii])); +// // std::string line = ""; +// // while(is >> line) { +// // if (line.find("sel") != line.npos) { +// // while (std::getline(is, line) && line != "}") { +// // if (line.find("i:") != line.npos) { +// // sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); +// // } +// // } break; +// // } +// // if (line.find("sel_a") != line.npos) { +// // while (std::getline(is, line) && line != "}") { +// // if (line.find("i:") != line.npos) { +// // sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); +// // } +// // } break; +// // } +// // } +// // sec.push_back(sel); +// // } +// // return sec; +// // } + +// // void +// // NNPInterModelDevi:: +// // cum_sum (const std::vector > n_sel) +// // { +// // for (int ii = 0; ii < numb_models; ++ii) { +// // std::vector _sec; +// // _sec.resize (n_sel[ii].size() + 1); +// // _sec[0] = 0; +// // for (int jj = 1; jj < _sec.size(); ++jj) { +// // _sec[jj] = _sec[jj-1] + n_sel[ii][jj-1]; +// // } +// // sec.push_back(_sec); +// // } +// // } + +// // void +// // NNPInterModelDevi:: +// // validate_fparam_aparam(const int & nloc, +// // const std::vector &fparam, +// // const std::vector &aparam)const +// // { +// // if (fparam.size() != dfparam) { +// // throw std::runtime_error("the dim of frame parameter provided is not consistent with what the model uses"); +// // } +// // if (aparam.size() != daparam * nloc) { +// // throw std::runtime_error("the dim of atom parameter provided is not consistent with what the model uses"); +// // } +// // } + +// // void +// // NNPInterModelDevi:: +// // compute (ENERGYTYPE & dener, +// // std::vector & dforce_, +// // std::vector & dvirial, +// // std::vector & model_devi, +// // const std::vector & dcoord_, +// // const std::vector & datype_, +// // const std::vector & dbox, +// // const std::vector & fparam, +// // const std::vector & aparam) +// // { +// // if (numb_models == 0) return; + +// // nnpmap = NNPAtomMap (datype_.begin(), datype_.end()); +// // validate_fparam_aparam(nnpmap.get_type().size(), fparam, aparam); + +// // std::vector> input_tensors; +// // int nloc = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, fparam, aparam, nnpmap); + +// // std::vector all_energy (numb_models); +// // std::vector > all_force (numb_models); +// // std::vector > all_virial (numb_models); + +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap); +// // } + +// // dener = 0; +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // dener += all_energy[ii]; +// // } +// // dener /= VALUETYPE(numb_models); +// // compute_avg (dvirial, all_virial); +// // compute_avg (dforce_, all_force); - compute_std_f (model_devi, dforce_, all_force); +// // compute_std_f (model_devi, dforce_, all_force); - // for (unsigned ii = 0; ii < numb_models; ++ii){ - // cout << all_force[ii][573] << " " << all_force[ii][574] << " " << all_force[ii][575] << endl; - // } - // cout << dforce_[573] << " " - // << dforce_[574] << " " - // << dforce_[575] << " " - // << model_devi[191] << endl; -} - -void -NNPInterModelDevi:: -compute (std::vector & all_energy, - std::vector> & all_force, - std::vector> & all_virial, - const std::vector & dcoord_, - const std::vector & datype_, - const std::vector & dbox, - const int nghost, - const LammpsNeighborList & lmp_list, - const int & ago, - const std::vector & fparam, - const std::vector & aparam) -{ - if (numb_models == 0) return; - int nall = dcoord_.size() / 3; - int nloc = nall - nghost; - validate_fparam_aparam(nloc, fparam, aparam); - std::vector> input_tensors; - - // agp == 0 means that the LAMMPS nbor list has been updated - if (ago == 0) { - nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); - assert (nloc == nnpmap.get_type().size()); - - // InternalNeighborList nlist; - convert_nlist_lmp_internal (nlist, lmp_list); - shuffle_nlist (nlist, nnpmap); - } - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); - - all_energy.resize (numb_models); - all_force.resize (numb_models); - all_virial.resize (numb_models); - assert (nloc == ret); - for (unsigned ii = 0; ii < numb_models; ++ii) { - run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); - } -} - -void -NNPInterModelDevi:: -compute (std::vector & all_energy, - std::vector> & all_force, - std::vector> & all_virial, - std::vector> & all_atom_energy, - std::vector> & all_atom_virial, - const std::vector & dcoord_, - const std::vector & datype_, - const std::vector & dbox, - const int nghost, - const LammpsNeighborList & lmp_list, - const int & ago, - const std::vector & fparam, - const std::vector & aparam) -{ - if (numb_models == 0) return; - int nall = dcoord_.size() / 3; - int nloc = nall - nghost; - validate_fparam_aparam(nloc, fparam, aparam); - std::vector> input_tensors; - - // agp == 0 means that the LAMMPS nbor list has been updated - if (ago == 0) { - nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); - assert (nloc == nnpmap.get_type().size()); - - // InternalNeighborList nlist; - convert_nlist_lmp_internal (nlist, lmp_list); - shuffle_nlist (nlist, nnpmap); - } - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); - - all_energy.resize (numb_models); - all_force .resize (numb_models); - all_virial.resize (numb_models); - all_atom_energy.resize (numb_models); - all_atom_virial.resize (numb_models); - assert (nloc == ret); - for (unsigned ii = 0; ii < numb_models; ++ii) { - run_model (all_energy[ii], all_force[ii], all_virial[ii], all_atom_energy[ii], all_atom_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); - } -} - -void -NNPInterModelDevi:: -compute_avg (VALUETYPE & dener, - const std::vector & all_energy) -{ - assert (all_energy.size() == numb_models); - if (numb_models == 0) return; - - dener = 0; - for (unsigned ii = 0; ii < numb_models; ++ii){ - dener += all_energy[ii]; - } - dener /= (VALUETYPE)(numb_models); -} - -#ifndef HIGH_PREC -void -NNPInterModelDevi:: -compute_avg (ENERGYTYPE & dener, - const std::vector& all_energy) -{ - assert (all_energy.size() == numb_models); - if (numb_models == 0) return; - - dener = 0; - for (unsigned ii = 0; ii < numb_models; ++ii){ - dener += all_energy[ii]; - } - dener /= (ENERGYTYPE)(numb_models); -} -#endif - -void -NNPInterModelDevi:: -compute_avg (std::vector & avg, - const std::vector > & xx) -{ - assert (xx.size() == numb_models); - if (numb_models == 0) return; +// // // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // // cout << all_force[ii][573] << " " << all_force[ii][574] << " " << all_force[ii][575] << endl; +// // // } +// // // cout << dforce_[573] << " " +// // // << dforce_[574] << " " +// // // << dforce_[575] << " " +// // // << model_devi[191] << endl; +// // } + +// // void +// // NNPInterModelDevi:: +// // compute (std::vector & all_energy, +// // std::vector> & all_force, +// // std::vector> & all_virial, +// // const std::vector & dcoord_, +// // const std::vector & datype_, +// // const std::vector & dbox, +// // const int nghost, +// // const LammpsNeighborList & lmp_list, +// // const int & ago, +// // const std::vector & fparam, +// // const std::vector & aparam) +// // { +// // if (numb_models == 0) return; +// // int nall = dcoord_.size() / 3; +// // int nloc = nall - nghost; +// // validate_fparam_aparam(nloc, fparam, aparam); +// // std::vector> input_tensors; + +// // // agp == 0 means that the LAMMPS nbor list has been updated +// // if (ago == 0) { +// // nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); +// // assert (nloc == nnpmap.get_type().size()); + +// // // InternalNeighborList nlist; +// // convert_nlist_lmp_internal (nlist, lmp_list); +// // shuffle_nlist (nlist, nnpmap); +// // } +// // int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); + +// // all_energy.resize (numb_models); +// // all_force.resize (numb_models); +// // all_virial.resize (numb_models); +// // assert (nloc == ret); +// // for (unsigned ii = 0; ii < numb_models; ++ii) { +// // run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); +// // } +// // } + +// // void +// // NNPInterModelDevi:: +// // compute (std::vector & all_energy, +// // std::vector> & all_force, +// // std::vector> & all_virial, +// // std::vector> & all_atom_energy, +// // std::vector> & all_atom_virial, +// // const std::vector & dcoord_, +// // const std::vector & datype_, +// // const std::vector & dbox, +// // const int nghost, +// // const LammpsNeighborList & lmp_list, +// // const int & ago, +// // const std::vector & fparam, +// // const std::vector & aparam) +// // { +// // if (numb_models == 0) return; +// // int nall = dcoord_.size() / 3; +// // int nloc = nall - nghost; +// // validate_fparam_aparam(nloc, fparam, aparam); +// // std::vector> input_tensors; + +// // // agp == 0 means that the LAMMPS nbor list has been updated +// // if (ago == 0) { +// // nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); +// // assert (nloc == nnpmap.get_type().size()); + +// // // InternalNeighborList nlist; +// // convert_nlist_lmp_internal (nlist, lmp_list); +// // shuffle_nlist (nlist, nnpmap); +// // } +// // int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); + +// // all_energy.resize (numb_models); +// // all_force .resize (numb_models); +// // all_virial.resize (numb_models); +// // all_atom_energy.resize (numb_models); +// // all_atom_virial.resize (numb_models); +// // assert (nloc == ret); +// // for (unsigned ii = 0; ii < numb_models; ++ii) { +// // run_model (all_energy[ii], all_force[ii], all_virial[ii], all_atom_energy[ii], all_atom_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); +// // } +// // } + +// // void +// // NNPInterModelDevi:: +// // compute_avg (VALUETYPE & dener, +// // const std::vector & all_energy) +// // { +// // assert (all_energy.size() == numb_models); +// // if (numb_models == 0) return; + +// // dener = 0; +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // dener += all_energy[ii]; +// // } +// // dener /= (VALUETYPE)(numb_models); +// // } + +// // #ifndef HIGH_PREC +// // void +// // NNPInterModelDevi:: +// // compute_avg (ENERGYTYPE & dener, +// // const std::vector& all_energy) +// // { +// // assert (all_energy.size() == numb_models); +// // if (numb_models == 0) return; + +// // dener = 0; +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // dener += all_energy[ii]; +// // } +// // dener /= (ENERGYTYPE)(numb_models); +// // } +// // #endif + +// // void +// // NNPInterModelDevi:: +// // compute_avg (std::vector & avg, +// // const std::vector > & xx) +// // { +// // assert (xx.size() == numb_models); +// // if (numb_models == 0) return; - avg.resize(xx[0].size()); - fill (avg.begin(), avg.end(), VALUETYPE(0.)); +// // avg.resize(xx[0].size()); +// // fill (avg.begin(), avg.end(), VALUETYPE(0.)); - for (unsigned ii = 0; ii < numb_models; ++ii){ - for (unsigned jj = 0; jj < avg.size(); ++jj){ - avg[jj] += xx[ii][jj]; - } - } - - for (unsigned jj = 0; jj < avg.size(); ++jj){ - avg[jj] /= VALUETYPE(numb_models); - } -} +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // for (unsigned jj = 0; jj < avg.size(); ++jj){ +// // avg[jj] += xx[ii][jj]; +// // } +// // } + +// // for (unsigned jj = 0; jj < avg.size(); ++jj){ +// // avg[jj] /= VALUETYPE(numb_models); +// // } +// // } + + +// // // void +// // // NNPInterModelDevi:: +// // // compute_std (VALUETYPE & std, +// // // const VALUETYPE & avg, +// // // const vector& xx) +// // // { +// // // std = 0; +// // // assert(xx.size() == numb_models); +// // // for (unsigned jj = 0; jj < xx.size(); ++jj){ +// // // std += (xx[jj] - avg) * (xx[jj] - avg); +// // // } +// // // std = sqrt(std / VALUETYPE(numb_models)); +// // // // std = sqrt(std / VALUETYPE(numb_models-)); +// // // } + +// // void +// // NNPInterModelDevi:: +// // compute_std_e (std::vector & std, +// // const std::vector & avg, +// // const std::vector >&xx) +// // { +// // assert (xx.size() == numb_models); +// // if (numb_models == 0) return; + +// // unsigned ndof = avg.size(); +// // unsigned nloc = ndof; +// // assert (nloc == ndof); + +// // std.resize(nloc); +// // fill (std.begin(), std.end(), VALUETYPE(0.)); + +// // for (unsigned ii = 0; ii < numb_models; ++ii) { +// // for (unsigned jj = 0 ; jj < nloc; ++jj){ +// // const VALUETYPE * tmp_f = &(xx[ii][jj]); +// // const VALUETYPE * tmp_avg = &(avg[jj]); +// // VALUETYPE vdiff = xx[ii][jj] - avg[jj]; +// // std[jj] += vdiff * vdiff; +// // } +// // } + +// // for (unsigned jj = 0; jj < nloc; ++jj){ +// // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); +// // // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); +// // } +// // } + +// // void +// // NNPInterModelDevi:: +// // compute_std_f (std::vector & std, +// // const std::vector & avg, +// // const std::vector >&xx) +// // { +// // assert (xx.size() == numb_models); +// // if (numb_models == 0) return; + +// // unsigned ndof = avg.size(); +// // unsigned nloc = ndof / 3; +// // assert (nloc * 3 == ndof); + +// // std.resize(nloc); +// // fill (std.begin(), std.end(), VALUETYPE(0.)); + +// // for (unsigned ii = 0; ii < numb_models; ++ii) { +// for (unsigned jj = 0 ; jj < nloc; ++jj){ +// const VALUETYPE * tmp_f = &(xx[ii][jj*3]); +// const VALUETYPE * tmp_avg = &(avg[jj*3]); +// VALUETYPE vdiff[3]; +// vdiff[0] = tmp_f[0] - tmp_avg[0]; +// vdiff[1] = tmp_f[1] - tmp_avg[1]; +// vdiff[2] = tmp_f[2] - tmp_avg[2]; +// std[jj] += dot3(vdiff, vdiff); +// } +// } +// for (unsigned jj = 0; jj < nloc; ++jj){ +// std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); +// // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); +// } +// } // void // NNPInterModelDevi:: -// compute_std (VALUETYPE & std, -// const VALUETYPE & avg, -// const vector& xx) +// compute_relative_std_f (std::vector &std, +// const std::vector &avg, +// const VALUETYPE eps) // { -// std = 0; -// assert(xx.size() == numb_models); -// for (unsigned jj = 0; jj < xx.size(); ++jj){ -// std += (xx[jj] - avg) * (xx[jj] - avg); +// unsigned nloc = std.size(); +// for (unsigned ii = 0; ii < nloc; ++ii){ +// const VALUETYPE * tmp_avg = &(avg[ii*3]); +// VALUETYPE vdiff[3]; +// vdiff[0] = tmp_avg[0]; +// vdiff[1] = tmp_avg[1]; +// vdiff[2] = tmp_avg[2]; +// VALUETYPE f_norm = sqrt(dot3(vdiff, vdiff)); +// // relative std = std/(abs(f)+eps) +// std[ii] /= f_norm + eps; // } -// std = sqrt(std / VALUETYPE(numb_models)); -// // std = sqrt(std / VALUETYPE(numb_models-)); // } -void -NNPInterModelDevi:: -compute_std_e (std::vector & std, - const std::vector & avg, - const std::vector >&xx) -{ - assert (xx.size() == numb_models); - if (numb_models == 0) return; - - unsigned ndof = avg.size(); - unsigned nloc = ndof; - assert (nloc == ndof); - - std.resize(nloc); - fill (std.begin(), std.end(), VALUETYPE(0.)); - - for (unsigned ii = 0; ii < numb_models; ++ii) { - for (unsigned jj = 0 ; jj < nloc; ++jj){ - const VALUETYPE * tmp_f = &(xx[ii][jj]); - const VALUETYPE * tmp_avg = &(avg[jj]); - VALUETYPE vdiff = xx[ii][jj] - avg[jj]; - std[jj] += vdiff * vdiff; - } - } - - for (unsigned jj = 0; jj < nloc; ++jj){ - std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); - // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); - } -} - -void -NNPInterModelDevi:: -compute_std_f (std::vector & std, - const std::vector & avg, - const std::vector >&xx) -{ - assert (xx.size() == numb_models); - if (numb_models == 0) return; - - unsigned ndof = avg.size(); - unsigned nloc = ndof / 3; - assert (nloc * 3 == ndof); - - std.resize(nloc); - fill (std.begin(), std.end(), VALUETYPE(0.)); - - for (unsigned ii = 0; ii < numb_models; ++ii) { - for (unsigned jj = 0 ; jj < nloc; ++jj){ - const VALUETYPE * tmp_f = &(xx[ii][jj*3]); - const VALUETYPE * tmp_avg = &(avg[jj*3]); - VALUETYPE vdiff[3]; - vdiff[0] = tmp_f[0] - tmp_avg[0]; - vdiff[1] = tmp_f[1] - tmp_avg[1]; - vdiff[2] = tmp_f[2] - tmp_avg[2]; - std[jj] += dot3(vdiff, vdiff); - } - } - - for (unsigned jj = 0; jj < nloc; ++jj){ - std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); - // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); - } -} - -void -NNPInterModelDevi:: -compute_relative_std_f (std::vector &std, - const std::vector &avg, - const VALUETYPE eps) -{ - unsigned nloc = std.size(); - for (unsigned ii = 0; ii < nloc; ++ii){ - const VALUETYPE * tmp_avg = &(avg[ii*3]); - VALUETYPE vdiff[3]; - vdiff[0] = tmp_avg[0]; - vdiff[1] = tmp_avg[1]; - vdiff[2] = tmp_avg[2]; - VALUETYPE f_norm = sqrt(dot3(vdiff, vdiff)); - // relative std = std/(abs(f)+eps) - std[ii] /= f_norm + eps; - } -} - diff --git a/source/api_cc/src/common.cc b/source/api_cc/src/common.cc index 31981658ee..0bbce93120 100644 --- a/source/api_cc/src/common.cc +++ b/source/api_cc/src/common.cc @@ -60,92 +60,136 @@ select_real_atoms(std::vector & fwd_map, select_by_type(fwd_map, bkw_map, nghost_real, dcoord_, datype_, nghost, sel_type); } + void -convert_nlist_lmp_internal (InternalNeighborList & list, - const LammpsNeighborList & lmp_list) +NeighborListData:: +copy_from_nlist(const InputNlist & inlist) { - list.clear(); - int total_num_nei = 0; - int inum = lmp_list.inum; - for (int ii = 0; ii < inum; ++ii){ - total_num_nei += lmp_list.numneigh[ii]; - } - list.ilist.resize(inum); - list.jrange.resize(inum+1); - list.jlist.resize(total_num_nei); - memcpy(&list.ilist[0], lmp_list.ilist, inum*sizeof(int)); - list.jrange[0] = 0; - for (int ii = 0; ii < inum; ++ii){ - int jnum = lmp_list.numneigh[ii]; - list.jrange[ii+1] = list.jrange[ii] + jnum; - const int * jlist = lmp_list.firstneigh[ii]; - memcpy(&(list.jlist[list.jrange[ii]]), jlist, jnum*sizeof(int)); + int inum = inlist.inum; + ilist.resize(inum); + jlist.resize(inum); + memcpy(&ilist[0], inlist.ilist, inum*sizeof(int)); + for(int ii = 0; ii < inum; ++ii){ + int jnum = inlist.numneigh[ii]; + jlist[ii].resize(jnum); + memcpy(&jlist[ii][0], inlist.firstneigh[ii], jnum*sizeof(int)); } } + void -shuffle_nlist (InternalNeighborList & list, - const NNPAtomMap & map) +NeighborListData:: +shuffle(const NNPAtomMap & map) { const std::vector & fwd_map = map.get_fwd_map(); - shuffle_nlist(list, fwd_map); + shuffle(fwd_map); } void -shuffle_nlist (InternalNeighborList & list, - const std::vector & fwd_map) +NeighborListData:: +shuffle(const std::vector & fwd_map) { int nloc = fwd_map.size(); - for (unsigned ii = 0; ii < list.ilist.size(); ++ii){ - if (list.ilist[ii] < nloc) { - list.ilist[ii] = fwd_map[list.ilist[ii]]; + for(unsigned ii = 0; ii < ilist.size(); ++ii){ + if(ilist[ii] < nloc){ + ilist[ii] = fwd_map[ilist[ii]]; } } - for (unsigned ii = 0; ii < list.jlist.size(); ++ii){ - if (list.jlist[ii] < nloc) { - list.jlist[ii] = fwd_map[list.jlist[ii]]; + for(unsigned ii = 0; ii < jlist.size(); ++ii){ + for(unsigned jj = 0; jj < jlist[ii].size(); ++jj){ + if(jlist[ii][jj] < nloc){ + jlist[ii][jj] = fwd_map[jlist[ii][jj]]; + } } } } void -shuffle_nlist_exclude_empty (InternalNeighborList & list, - const std::vector & fwd_map) +NeighborListData:: +shuffle_exclude_empty (const std::vector & fwd_map) { - int old_nloc = fwd_map.size(); - shuffle_nlist(list, fwd_map); - std::vector new_ilist, new_jrange, new_jlist, new_icount; - new_ilist.reserve(list.ilist.size()); - new_icount.reserve(list.ilist.size()); - new_jrange.reserve(list.jrange.size()); - new_jlist.reserve(list.jlist.size()); - for(int ii = 0; ii < list.ilist.size(); ++ii){ - if(list.ilist[ii] >= 0){ - new_ilist.push_back(list.ilist[ii]); + shuffle(fwd_map); + std::vector new_ilist; + std::vector > new_jlist; + new_ilist.reserve(ilist.size()); + new_jlist.reserve(jlist.size()); + for(int ii = 0; ii < ilist.size(); ++ii){ + if(ilist[ii] >= 0){ + new_ilist.push_back(ilist[ii]); } } - new_jrange.resize(new_ilist.size()+1); - new_jrange[0] = 0; - int ci = 0; - for(int ii = 0; ii < list.ilist.size(); ++ii){ - if (list.ilist[ii] < 0) continue; - int js = list.jrange[ii]; - int je = list.jrange[ii+1]; - int cc = 0; - for (int jj = js; jj < je; ++jj){ - if (list.jlist[jj] >= 0) { - new_jlist.push_back(list.jlist[jj]); - cc++; - } + int new_inum = new_ilist.size(); + for(int ii = 0; ii < jlist.size(); ++ii){ + if(ilist[ii] >= 0){ + std::vector tmp_jlist; + tmp_jlist.reserve(jlist[ii].size()); + for(int jj = 0; jj < jlist[ii].size(); ++jj){ + if(jlist[ii][jj] >= 0){ + tmp_jlist.push_back(jlist[ii][jj]); + } + } + new_jlist.push_back(tmp_jlist); } - new_jrange[ci+1] = new_jrange[ci] + cc; - ci ++; } - list.ilist = new_ilist; - list.jrange = new_jrange; - list.jlist = new_jlist; + ilist = new_ilist; + jlist = new_jlist; +} + +void +NeighborListData:: +make_inlist(InputNlist & inlist) +{ + int nloc = ilist.size(); + numneigh.resize(nloc); + firstneigh.resize(nloc); + for(int ii = 0; ii < nloc; ++ii){ + numneigh[ii] = jlist[ii].size(); + firstneigh[ii] = &jlist[ii][0]; + } + inlist.inum = nloc; + inlist.ilist = &ilist[0]; + inlist.numneigh = &numneigh[0]; + inlist.firstneigh = &firstneigh[0]; } +// void +// shuffle_nlist_exclude_empty (InternalNeighborList & list, +// const std::vector & fwd_map) +// { +// int old_nloc = fwd_map.size(); +// shuffle_nlist(list, fwd_map); +// std::vector new_ilist, new_jrange, new_jlist, new_icount; +// new_ilist.reserve(list.ilist.size()); +// new_icount.reserve(list.ilist.size()); +// new_jrange.reserve(list.jrange.size()); +// new_jlist.reserve(list.jlist.size()); +// for(int ii = 0; ii < list.ilist.size(); ++ii){ +// if(list.ilist[ii] >= 0){ +// new_ilist.push_back(list.ilist[ii]); +// } +// } +// new_jrange.resize(new_ilist.size()+1); +// new_jrange[0] = 0; +// int ci = 0; +// for(int ii = 0; ii < list.ilist.size(); ++ii){ +// if (list.ilist[ii] < 0) continue; +// int js = list.jrange[ii]; +// int je = list.jrange[ii+1]; +// int cc = 0; +// for (int jj = js; jj < je; ++jj){ +// if (list.jlist[jj] >= 0) { +// new_jlist.push_back(list.jlist[jj]); +// cc++; +// } +// } +// new_jrange[ci+1] = new_jrange[ci] + cc; +// ci ++; +// } +// list.ilist = new_ilist; +// list.jrange = new_jrange; +// list.jlist = new_jlist; +// } + void checkStatus(const tensorflow::Status& status) { if (!status.ok()) { @@ -196,16 +240,13 @@ session_input_tensors (std::vector> & input_tenso const std::vector & fparam_, const std::vector & aparam_, const NNPAtomMap& nnpmap, - const int nghost, - const std::string scope) + const std::string scope) { - bool b_ghost = (nghost != 0); - - assert (dbox.size() == 9); + bool b_pbc = (dbox.size() == 9); int nframes = 1; int nall = dcoord_.size() / 3; - int nloc = nall - nghost; + int nloc = nall; assert (nall == datype_.size()); std::vector datype = nnpmap.get_type(); @@ -215,26 +256,6 @@ session_input_tensors (std::vector> & input_tenso } datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); - SimulationRegion region; - std::vector dbox_(9); - for (int dd = 0; dd < 9; ++dd) dbox_[dd] = dbox[dd]; - region.reinitBox (&dbox_[0]); - double box_l[3]; - region.toFaceDistance (box_l); - - std::vector ncell (3, 2); - for (int dd = 0; dd < 3; ++dd){ - ncell[dd] = box_l[dd] / cell_size; - if (ncell[dd] < 2) ncell[dd] = 2; - } - std::vector next(3, 0); - for (int dd = 0; dd < 3; ++dd){ - double cellh = box_l[dd] / ncell[dd]; - next[dd] = cellh / cell_size; - if (next[dd] * cellh < cell_size) next[dd]++; - assert (next[dd] * cellh >= cell_size); - } - TensorShape coord_shape ; coord_shape.AddDim (nframes); coord_shape.AddDim (nall * 3); @@ -245,11 +266,11 @@ session_input_tensors (std::vector> & input_tenso box_shape.AddDim (nframes); box_shape.AddDim (9); TensorShape mesh_shape ; - if (!b_ghost){ - mesh_shape.AddDim (6); + if (b_pbc){ + mesh_shape.AddDim(6); } else { - mesh_shape.AddDim (12); + mesh_shape.AddDim(0); } TensorShape natoms_shape ; natoms_shape.AddDim (2 + ntypes); @@ -290,8 +311,15 @@ session_input_tensors (std::vector> & input_tenso for (int jj = 0; jj < nall * 3; ++jj){ coord(ii, jj) = dcoord[jj]; } - for (int jj = 0; jj < 9; ++jj){ - box(ii, jj) = dbox[jj]; + if(b_pbc){ + for (int jj = 0; jj < 9; ++jj){ + box(ii, jj) = dbox[jj]; + } + } + else{ + for (int jj = 0; jj < 9; ++jj){ + box(ii, jj) = 0.; + } } for (int jj = 0; jj < nall; ++jj){ type(ii, jj) = datype[jj]; @@ -303,19 +331,13 @@ session_input_tensors (std::vector> & input_tenso aparam(ii, jj) = aparam_[jj]; } } - mesh (1-1) = 0; - mesh (2-1) = 0; - mesh (3-1) = 0; - mesh (4-1) = ncell[0]; - mesh (5-1) = ncell[1]; - mesh (6-1) = ncell[2]; - if (b_ghost){ - mesh(7-1) = -next[0]; - mesh(8-1) = -next[1]; - mesh(9-1) = -next[2]; - mesh(10-1) = ncell[0] + next[0]; - mesh(11-1) = ncell[1] + next[1]; - mesh(12-1) = ncell[2] + next[2]; + if (b_pbc){ + mesh (1-1) = 0; + mesh (2-1) = 0; + mesh (3-1) = 0; + mesh (4-1) = 0; + mesh (5-1) = 0; + mesh (6-1) = 0; } natoms (0) = nloc; natoms (1) = nall; @@ -347,7 +369,7 @@ session_input_tensors (std::vector> & input_tenso const int & ntypes, const std::vector & datype_, const std::vector & dbox, - InternalNeighborList & dlist, + InputNlist & dlist, const std::vector & fparam_, const std::vector & aparam_, const NNPAtomMap& nnpmap, @@ -439,13 +461,12 @@ session_input_tensors (std::vector> & input_tenso assert (stride * sizeof(int) == sizeof(int *)); assert (stride <= 4); mesh (0) = ago; - mesh (1) = dlist.ilist.size(); - mesh (2) = dlist.jrange.size(); - mesh (3) = dlist.jlist.size(); - dlist.make_ptrs(); - memcpy (&mesh(4), &(dlist.pilist), sizeof(int *)); - memcpy (&mesh(8), &(dlist.pjrange), sizeof(int *)); - memcpy (&mesh(12), &(dlist.pjlist), sizeof(int *)); + mesh (1) = dlist.inum; + mesh (2) = 0; + mesh (3) = 0; + memcpy (&mesh(4), &(dlist.ilist), sizeof(int *)); + memcpy (&mesh(8), &(dlist.numneigh), sizeof(int *)); + memcpy (&mesh(12), &(dlist.firstneigh), sizeof(int **)); natoms (0) = nloc; natoms (1) = nall; @@ -471,257 +492,257 @@ session_input_tensors (std::vector> & input_tenso return nloc; } -int -session_input_tensors (std::vector> & input_tensors, - const std::vector & dcoord_, - const int & ntypes, - const std::vector & datype_, - const std::vector & dbox, - InternalNeighborList & dlist, - const std::vector & fparam_, - const std::vector & aparam_, - const NNPAtomMap& nnpmap, - const int nghost, - const std::string scope) -{ - assert (dbox.size() == 9); - - int nframes = 1; - int nall = dcoord_.size() / 3; - int nloc = nall - nghost; - assert (nall == datype_.size()); - - std::vector datype = nnpmap.get_type(); - std::vector type_count (ntypes, 0); - for (unsigned ii = 0; ii < datype.size(); ++ii){ - type_count[datype[ii]] ++; - } - datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); - - TensorShape coord_shape ; - coord_shape.AddDim (nframes); - coord_shape.AddDim (nall * 3); - TensorShape type_shape ; - type_shape.AddDim (nframes); - type_shape.AddDim (nall); - TensorShape box_shape ; - box_shape.AddDim (nframes); - box_shape.AddDim (9); - TensorShape mesh_shape ; - mesh_shape.AddDim (16); - TensorShape natoms_shape ; - natoms_shape.AddDim (2 + ntypes); - TensorShape fparam_shape ; - fparam_shape.AddDim (nframes); - fparam_shape.AddDim (fparam_.size()); - TensorShape aparam_shape ; - aparam_shape.AddDim (nframes); - aparam_shape.AddDim (aparam_.size()); +// int +// session_input_tensors (std::vector> & input_tensors, +// const std::vector & dcoord_, +// const int & ntypes, +// const std::vector & datype_, +// const std::vector & dbox, +// InternalNeighborList & dlist, +// const std::vector & fparam_, +// const std::vector & aparam_, +// const NNPAtomMap& nnpmap, +// const int nghost, +// const std::string scope) +// { +// assert (dbox.size() == 9); + +// int nframes = 1; +// int nall = dcoord_.size() / 3; +// int nloc = nall - nghost; +// assert (nall == datype_.size()); + +// std::vector datype = nnpmap.get_type(); +// std::vector type_count (ntypes, 0); +// for (unsigned ii = 0; ii < datype.size(); ++ii){ +// type_count[datype[ii]] ++; +// } +// datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); + +// TensorShape coord_shape ; +// coord_shape.AddDim (nframes); +// coord_shape.AddDim (nall * 3); +// TensorShape type_shape ; +// type_shape.AddDim (nframes); +// type_shape.AddDim (nall); +// TensorShape box_shape ; +// box_shape.AddDim (nframes); +// box_shape.AddDim (9); +// TensorShape mesh_shape ; +// mesh_shape.AddDim (16); +// TensorShape natoms_shape ; +// natoms_shape.AddDim (2 + ntypes); +// TensorShape fparam_shape ; +// fparam_shape.AddDim (nframes); +// fparam_shape.AddDim (fparam_.size()); +// TensorShape aparam_shape ; +// aparam_shape.AddDim (nframes); +// aparam_shape.AddDim (aparam_.size()); -#ifdef HIGH_PREC - Tensor coord_tensor (DT_DOUBLE, coord_shape); - Tensor box_tensor (DT_DOUBLE, box_shape); - Tensor fparam_tensor (DT_DOUBLE, fparam_shape); - Tensor aparam_tensor (DT_DOUBLE, aparam_shape); -#else - Tensor coord_tensor (DT_FLOAT, coord_shape); - Tensor box_tensor (DT_FLOAT, box_shape); - Tensor fparam_tensor (DT_FLOAT, fparam_shape); - Tensor aparam_tensor (DT_FLOAT, aparam_shape); -#endif - Tensor type_tensor (DT_INT32, type_shape); - Tensor mesh_tensor (DT_INT32, mesh_shape); - Tensor natoms_tensor (DT_INT32, natoms_shape); - - auto coord = coord_tensor.matrix (); - auto type = type_tensor.matrix (); - auto box = box_tensor.matrix (); - auto mesh = mesh_tensor.flat (); - auto natoms = natoms_tensor.flat (); - auto fparam = fparam_tensor.matrix (); - auto aparam = aparam_tensor.matrix (); - - std::vector dcoord (dcoord_); - nnpmap.forward (dcoord.begin(), dcoord_.begin(), 3); +// #ifdef HIGH_PREC +// Tensor coord_tensor (DT_DOUBLE, coord_shape); +// Tensor box_tensor (DT_DOUBLE, box_shape); +// Tensor fparam_tensor (DT_DOUBLE, fparam_shape); +// Tensor aparam_tensor (DT_DOUBLE, aparam_shape); +// #else +// Tensor coord_tensor (DT_FLOAT, coord_shape); +// Tensor box_tensor (DT_FLOAT, box_shape); +// Tensor fparam_tensor (DT_FLOAT, fparam_shape); +// Tensor aparam_tensor (DT_FLOAT, aparam_shape); +// #endif +// Tensor type_tensor (DT_INT32, type_shape); +// Tensor mesh_tensor (DT_INT32, mesh_shape); +// Tensor natoms_tensor (DT_INT32, natoms_shape); + +// auto coord = coord_tensor.matrix (); +// auto type = type_tensor.matrix (); +// auto box = box_tensor.matrix (); +// auto mesh = mesh_tensor.flat (); +// auto natoms = natoms_tensor.flat (); +// auto fparam = fparam_tensor.matrix (); +// auto aparam = aparam_tensor.matrix (); + +// std::vector dcoord (dcoord_); +// nnpmap.forward (dcoord.begin(), dcoord_.begin(), 3); - for (int ii = 0; ii < nframes; ++ii){ - for (int jj = 0; jj < nall * 3; ++jj){ - coord(ii, jj) = dcoord[jj]; - } - for (int jj = 0; jj < 9; ++jj){ - box(ii, jj) = dbox[jj]; - } - for (int jj = 0; jj < nall; ++jj){ - type(ii, jj) = datype[jj]; - } - for (int jj = 0; jj < fparam_.size(); ++jj){ - fparam(ii, jj) = fparam_[jj]; - } - for (int jj = 0; jj < aparam_.size(); ++jj){ - aparam(ii, jj) = aparam_[jj]; - } - } +// for (int ii = 0; ii < nframes; ++ii){ +// for (int jj = 0; jj < nall * 3; ++jj){ +// coord(ii, jj) = dcoord[jj]; +// } +// for (int jj = 0; jj < 9; ++jj){ +// box(ii, jj) = dbox[jj]; +// } +// for (int jj = 0; jj < nall; ++jj){ +// type(ii, jj) = datype[jj]; +// } +// for (int jj = 0; jj < fparam_.size(); ++jj){ +// fparam(ii, jj) = fparam_[jj]; +// } +// for (int jj = 0; jj < aparam_.size(); ++jj){ +// aparam(ii, jj) = aparam_[jj]; +// } +// } - for (int ii = 0; ii < 16; ++ii) mesh(ii) = 0; +// for (int ii = 0; ii < 16; ++ii) mesh(ii) = 0; - mesh (0) = sizeof(int *) / sizeof(int); - assert (mesh(0) * sizeof(int) == sizeof(int *)); - const int & stride = mesh(0); - mesh (1) = dlist.ilist.size(); - assert (mesh(1) == nloc); - assert (stride <= 4); - dlist.make_ptrs(); - memcpy (&mesh(4), &(dlist.pilist), sizeof(int *)); - memcpy (&mesh(8), &(dlist.pjrange), sizeof(int *)); - memcpy (&mesh(12), &(dlist.pjlist), sizeof(int *)); - - natoms (0) = nloc; - natoms (1) = nall; - for (int ii = 0; ii < ntypes; ++ii) natoms(ii+2) = type_count[ii]; - - std::string prefix = ""; - if (scope != ""){ - prefix = scope + "/"; - } - input_tensors = { - {prefix+"t_coord", coord_tensor}, - {prefix+"t_type", type_tensor}, - {prefix+"t_box", box_tensor}, - {prefix+"t_mesh", mesh_tensor}, - {prefix+"t_natoms",natoms_tensor}, - }; - if (fparam_.size() > 0) { - input_tensors.push_back({prefix+"t_fparam", fparam_tensor}); - } - if (aparam_.size() > 0) { - input_tensors.push_back({prefix+"t_aparam", aparam_tensor}); - } - - return nloc; -} - -int -session_input_tensors ( - std::vector> & input_tensors, - const std::vector & dcoord_, - const int & ntypes, - const std::vector & datype_, - const std::vector & dbox, - const int * ilist, - const int * jrange, - const int * jlist, - const std::vector & fparam_, - const std::vector & aparam_, - const NNPAtomMap & nnpmap, - const int & nghost) -{ - assert (dbox.size() == 9); - - int nframes = 1; - int nall = dcoord_.size() / 3; - int nloc = nall - nghost; - assert (nall == datype_.size()); - - std::vector datype = nnpmap.get_type(); - std::vector type_count (ntypes, 0); - for (unsigned ii = 0; ii < datype.size(); ++ii) { - type_count[datype[ii]] ++; - } - datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); - - TensorShape coord_shape ; - coord_shape.AddDim (nframes); - coord_shape.AddDim (nall * 3); - TensorShape type_shape ; - type_shape.AddDim (nframes); - type_shape.AddDim (nall); - TensorShape box_shape ; - box_shape.AddDim (nframes); - box_shape.AddDim (9); - TensorShape mesh_shape; - mesh_shape.AddDim (16); - TensorShape natoms_shape; - natoms_shape.AddDim (2 + ntypes); - TensorShape fparam_shape; - fparam_shape.AddDim (nframes); - fparam_shape.AddDim (fparam_.size()); - TensorShape aparam_shape ; - aparam_shape.AddDim (nframes); - aparam_shape.AddDim (aparam_.size()); - - #ifdef HIGH_PREC - Tensor coord_tensor (DT_DOUBLE, coord_shape); - Tensor box_tensor (DT_DOUBLE, box_shape); - Tensor fparam_tensor(DT_DOUBLE, fparam_shape); - Tensor aparam_tensor(DT_DOUBLE, fparam_shape); - #else - Tensor coord_tensor (DT_FLOAT, coord_shape); - Tensor box_tensor (DT_FLOAT, box_shape); - Tensor fparam_tensor(DT_FLOAT, fparam_shape); - Tensor aparam_tensor(DT_FLOAT, fparam_shape); - #endif - Tensor type_tensor (DT_INT32, type_shape); - Tensor mesh_tensor (DT_INT32, mesh_shape); - Tensor natoms_tensor(DT_INT32, natoms_shape); - - auto coord = coord_tensor.matrix (); - auto type = type_tensor.matrix (); - auto box = box_tensor.matrix (); - auto mesh = mesh_tensor.flat (); - auto natoms = natoms_tensor.flat (); - auto fparam = fparam_tensor.matrix (); - auto aparam = aparam_tensor.matrix (); - - std::vector dcoord (dcoord_); - nnpmap.forward (dcoord.begin(), dcoord_.begin(), 3); - - for (int ii = 0; ii < nframes; ++ii) { - for (int jj = 0; jj < nall * 3; ++jj) { - coord(ii, jj) = dcoord[jj]; - } - for (int jj = 0; jj < 9; ++jj) { - box(ii, jj) = dbox[jj]; - } - for (int jj = 0; jj < nall; ++jj) { - type(ii, jj) = datype[jj]; - } - for (int jj = 0; jj < fparam_.size(); ++jj) { - fparam(ii, jj) = fparam_[jj]; - } - for (int jj = 0; jj < aparam_.size(); ++jj) { - aparam(ii, jj) = aparam_[jj]; - } - } +// mesh (0) = sizeof(int *) / sizeof(int); +// assert (mesh(0) * sizeof(int) == sizeof(int *)); +// const int & stride = mesh(0); +// mesh (1) = dlist.ilist.size(); +// assert (mesh(1) == nloc); +// assert (stride <= 4); +// dlist.make_ptrs(); +// memcpy (&mesh(4), &(dlist.pilist), sizeof(int *)); +// memcpy (&mesh(8), &(dlist.pjrange), sizeof(int *)); +// memcpy (&mesh(12), &(dlist.pjlist), sizeof(int *)); + +// natoms (0) = nloc; +// natoms (1) = nall; +// for (int ii = 0; ii < ntypes; ++ii) natoms(ii+2) = type_count[ii]; + +// std::string prefix = ""; +// if (scope != ""){ +// prefix = scope + "/"; +// } +// input_tensors = { +// {prefix+"t_coord", coord_tensor}, +// {prefix+"t_type", type_tensor}, +// {prefix+"t_box", box_tensor}, +// {prefix+"t_mesh", mesh_tensor}, +// {prefix+"t_natoms",natoms_tensor}, +// }; +// if (fparam_.size() > 0) { +// input_tensors.push_back({prefix+"t_fparam", fparam_tensor}); +// } +// if (aparam_.size() > 0) { +// input_tensors.push_back({prefix+"t_aparam", aparam_tensor}); +// } + +// return nloc; +// } + +// int +// session_input_tensors ( +// std::vector> & input_tensors, +// const std::vector & dcoord_, +// const int & ntypes, +// const std::vector & datype_, +// const std::vector & dbox, +// const int * ilist, +// const int * jrange, +// const int * jlist, +// const std::vector & fparam_, +// const std::vector & aparam_, +// const NNPAtomMap & nnpmap, +// const int & nghost) +// { +// assert (dbox.size() == 9); + +// int nframes = 1; +// int nall = dcoord_.size() / 3; +// int nloc = nall - nghost; +// assert (nall == datype_.size()); + +// std::vector datype = nnpmap.get_type(); +// std::vector type_count (ntypes, 0); +// for (unsigned ii = 0; ii < datype.size(); ++ii) { +// type_count[datype[ii]] ++; +// } +// datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); + +// TensorShape coord_shape ; +// coord_shape.AddDim (nframes); +// coord_shape.AddDim (nall * 3); +// TensorShape type_shape ; +// type_shape.AddDim (nframes); +// type_shape.AddDim (nall); +// TensorShape box_shape ; +// box_shape.AddDim (nframes); +// box_shape.AddDim (9); +// TensorShape mesh_shape; +// mesh_shape.AddDim (16); +// TensorShape natoms_shape; +// natoms_shape.AddDim (2 + ntypes); +// TensorShape fparam_shape; +// fparam_shape.AddDim (nframes); +// fparam_shape.AddDim (fparam_.size()); +// TensorShape aparam_shape ; +// aparam_shape.AddDim (nframes); +// aparam_shape.AddDim (aparam_.size()); + +// #ifdef HIGH_PREC +// Tensor coord_tensor (DT_DOUBLE, coord_shape); +// Tensor box_tensor (DT_DOUBLE, box_shape); +// Tensor fparam_tensor(DT_DOUBLE, fparam_shape); +// Tensor aparam_tensor(DT_DOUBLE, fparam_shape); +// #else +// Tensor coord_tensor (DT_FLOAT, coord_shape); +// Tensor box_tensor (DT_FLOAT, box_shape); +// Tensor fparam_tensor(DT_FLOAT, fparam_shape); +// Tensor aparam_tensor(DT_FLOAT, fparam_shape); +// #endif +// Tensor type_tensor (DT_INT32, type_shape); +// Tensor mesh_tensor (DT_INT32, mesh_shape); +// Tensor natoms_tensor(DT_INT32, natoms_shape); + +// auto coord = coord_tensor.matrix (); +// auto type = type_tensor.matrix (); +// auto box = box_tensor.matrix (); +// auto mesh = mesh_tensor.flat (); +// auto natoms = natoms_tensor.flat (); +// auto fparam = fparam_tensor.matrix (); +// auto aparam = aparam_tensor.matrix (); + +// std::vector dcoord (dcoord_); +// nnpmap.forward (dcoord.begin(), dcoord_.begin(), 3); + +// for (int ii = 0; ii < nframes; ++ii) { +// for (int jj = 0; jj < nall * 3; ++jj) { +// coord(ii, jj) = dcoord[jj]; +// } +// for (int jj = 0; jj < 9; ++jj) { +// box(ii, jj) = dbox[jj]; +// } +// for (int jj = 0; jj < nall; ++jj) { +// type(ii, jj) = datype[jj]; +// } +// for (int jj = 0; jj < fparam_.size(); ++jj) { +// fparam(ii, jj) = fparam_[jj]; +// } +// for (int jj = 0; jj < aparam_.size(); ++jj) { +// aparam(ii, jj) = aparam_[jj]; +// } +// } - for (int ii = 0; ii < 16; ++ii) mesh(ii) = 0; +// for (int ii = 0; ii < 16; ++ii) mesh(ii) = 0; - mesh (0) = sizeof(int *) / sizeof(int); - assert (mesh(0) * sizeof(int) == sizeof(int *)); - const int & stride = mesh(0); - // mesh (1) = dlist.ilist.size(); - mesh (1) = nloc; - assert (mesh(1) == nloc); - assert (stride <= 4); - memcpy (&mesh(4), &(ilist), sizeof(int *)); - memcpy (&mesh(8), &(jrange), sizeof(int *)); - memcpy (&mesh(12), &(jlist), sizeof(int *)); - - natoms (0) = nloc; - natoms (1) = nall; - for (int ii = 0; ii < ntypes; ++ii) natoms(ii+2) = type_count[ii]; +// mesh (0) = sizeof(int *) / sizeof(int); +// assert (mesh(0) * sizeof(int) == sizeof(int *)); +// const int & stride = mesh(0); +// // mesh (1) = dlist.ilist.size(); +// mesh (1) = nloc; +// assert (mesh(1) == nloc); +// assert (stride <= 4); +// memcpy (&mesh(4), &(ilist), sizeof(int *)); +// memcpy (&mesh(8), &(jrange), sizeof(int *)); +// memcpy (&mesh(12), &(jlist), sizeof(int *)); + +// natoms (0) = nloc; +// natoms (1) = nall; +// for (int ii = 0; ii < ntypes; ++ii) natoms(ii+2) = type_count[ii]; - input_tensors = { - {"t_coord", coord_tensor}, - {"t_type", type_tensor}, - {"t_box", box_tensor}, - {"t_mesh", mesh_tensor}, - {"t_natoms", natoms_tensor}, - }; - if (fparam_.size() > 0) { - input_tensors.push_back({"t_fparam", fparam_tensor}); - } - if (aparam_.size() > 0) { - input_tensors.push_back({"t_aparam", aparam_tensor}); - } - return nloc; -} \ No newline at end of file +// input_tensors = { +// {"t_coord", coord_tensor}, +// {"t_type", type_tensor}, +// {"t_box", box_tensor}, +// {"t_mesh", mesh_tensor}, +// {"t_natoms", natoms_tensor}, +// }; +// if (fparam_.size() > 0) { +// input_tensors.push_back({"t_fparam", fparam_tensor}); +// } +// if (aparam_.size() > 0) { +// input_tensors.push_back({"t_aparam", aparam_tensor}); +// } +// return nloc; +// } diff --git a/source/api_cc/tests/CMakeLists.txt b/source/api_cc/tests/CMakeLists.txt new file mode 100644 index 0000000000..4ffa71de3d --- /dev/null +++ b/source/api_cc/tests/CMakeLists.txt @@ -0,0 +1,106 @@ +cmake_minimum_required(VERSION 3.9) +project(deepmd_api_test) +set(CMAKE_LINK_WHAT_YOU_USE TRUE) + +if (NOT DEFINED BUILD_CPP_IF) + set(BUILD_CPP_IF TRUE) +endif (NOT DEFINED BUILD_CPP_IF) +add_definitions ("-DHIGH_PREC") + +enable_testing() + +set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + +message(${PROJECT_SOURCE_DIR}) +message(${CMAKE_SOURCE_DIR}) + +set(libname "deepmd") +set(LIB_BASE_DIR ${CMAKE_SOURCE_DIR}/../../lib) +include_directories(${LIB_BASE_DIR}/include) +file(GLOB LIB_SRC ${LIB_BASE_DIR}/src/*.cc ${LIB_BASE_DIR}/src/*.cpp) +add_library(${libname} SHARED ${LIB_SRC}) + +set(apiname "deepmd_api") +set(API_BASE_DIR ${CMAKE_SOURCE_DIR}/../) +include_directories(${API_BASE_DIR}/include) +include_directories(${CMAKE_SOURCE_DIR}) +file(GLOB API_SRC ${API_BASE_DIR}/src/*.cc ${API_BASE_DIR}/src/*.cpp) +add_library(${apiname} SHARED ${API_SRC}) +configure_file( + ${API_BASE_DIR}/include/version.h.in + version.h + @ONLY +) + +set(opname "deepmd_op") +set(OP_BASE_DIR ${CMAKE_SOURCE_DIR}/../../op) +# file(GLOB OP_SRC ${OP_BASE_DIR}/*.cc) +file(GLOB OP_SRC ${OP_BASE_DIR}/prod_force.cc ${OP_BASE_DIR}/prod_virial.cc ${OP_BASE_DIR}/descrpt.cc ${OP_BASE_DIR}/descrpt_se_a.cc ${OP_BASE_DIR}/descrpt_se_a_ef.cc ${OP_BASE_DIR}/descrpt_se_a_ef.cc ${OP_BASE_DIR}/descrpt_se_a_ef_para.cc ${OP_BASE_DIR}/descrpt_se_a_ef_vert.cc ${OP_BASE_DIR}/descrpt_se_r.cc ${OP_BASE_DIR}/pair_tab.cc ${OP_BASE_DIR}/prod_force_se_a.cc ${OP_BASE_DIR}/prod_virial_se_a.cc ${OP_BASE_DIR}/prod_force_se_r.cc ${OP_BASE_DIR}/prod_virial_se_r.cc ${OP_BASE_DIR}/soft_min.cc ${OP_BASE_DIR}/soft_min_force.cc ${OP_BASE_DIR}/soft_min_virial.cc ${OP_BASE_DIR}/ewald_recp.cc ${OP_BASE_DIR}/gelu_multi_device.cc ${OP_BASE_DIR}/map_aparam.cc ${OP_BASE_DIR}/neighbor_stat.cc ${OP_BASE_DIR}/unaggregated_grad.cc ${OP_BASE_DIR}/tabulate_multi_device.cc ${OP_BASE_DIR}/prod_env_mat_multi_device.cc) +add_library(${opname} SHARED ${OP_SRC}) + +list (APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/../../cmake/) +find_package(tensorflow REQUIRED) +include_directories(${TensorFlow_INCLUDE_DIRS}) + +find_package(Threads) +# find openmp +find_package(OpenMP) +if (OPENMP_FOUND) + set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") +endif() + +# define USE_CUDA_TOOLKIT +if (DEFINED USE_CUDA_TOOLKIT) + if (USE_CUDA_TOOLKIT) + find_package(CUDA REQUIRED) + else() + message(STATUS "Will not build nv GPU support") + endif() +else() + find_package(CUDA QUIET) + if (CUDA_FOUND) + set(USE_CUDA_TOOLKIT TRUE) + message(STATUS "Found CUDA in ${CUDA_TOOLKIT_ROOT_DIR}, build nv GPU support") + else() + set(USE_CUDA_TOOLKIT FALSE) + message(STATUS "No cuda support found, will not build nv GPU support") + endif() +endif() + +if (USE_CUDA_TOOLKIT) + add_definitions("-D GOOGLE_CUDA") + include_directories(${CUDA_INCLUDE_DIRS}) + add_subdirectory(${LIB_BASE_DIR}/src/cuda cuda_binary_dir) +endif() + +file(GLOB TEST_SRC test_*.cc) +add_executable( runUnitTests ${TEST_SRC} ) + +if (USE_CUDA_TOOLKIT) + target_link_libraries(runUnitTests gtest gtest_main ${libname} pthread deepmd_op_cuda) +else() + target_link_libraries(runUnitTests gtest gtest_main ${libname} ${apiname} ${opname} pthread ${TensorFlow_LIBRARY}) +endif() +add_test( runUnitTests runUnitTests ) + +find_package(GTest) +if(NOT GTEST_LIBRARY) + configure_file(CMakeLists.txt.in googletest-download/CMakeLists.txt) + execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" . + RESULT_VARIABLE result + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download ) + if(result) + message(FATAL_ERROR "CMake step for googletest failed: ${result}") + endif() + execute_process(COMMAND ${CMAKE_COMMAND} --build . + RESULT_VARIABLE result + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download ) + if(result) + message(FATAL_ERROR "Build step for googletest failed: ${result}") + endif() + set(gtest_force_shared_crt ON CACHE BOOL "" FORCE) + add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/googletest-src ${CMAKE_CURRENT_BINARY_DIR}/googletest-build EXCLUDE_FROM_ALL) +else () + include_directories(${GTEST_INCLUDE_DIRS}) +endif () diff --git a/source/api_cc/tests/test_deepdipole.cc b/source/api_cc/tests/test_deepdipole.cc new file mode 100644 index 0000000000..1c69e72cc6 --- /dev/null +++ b/source/api_cc/tests/test_deepdipole.cc @@ -0,0 +1,106 @@ +#include +#include +#include +#include +#include +#include "DeepTensor.h" +#include "SimulationRegion.h" +#include "neighbor_list.h" +#include "test_utils.h" + +#include "google/protobuf/text_format.h" +#include "google/protobuf/io/zero_copy_stream_impl.h" +#include +#include +#include + +class TestInferDeepDipole : public ::testing::Test +{ +protected: + std::vector coord = { + 12.83, 2.56, 2.18, + 12.09, 2.87, 2.74, + 00.25, 3.32, 1.68, + 3.36, 3.00, 1.81, + 3.51, 2.51, 2.60, + 4.27, 3.22, 1.56 + }; + std::vector atype = { + 0, 1, 1, 0, 1, 1 + }; + std::vector box = { + 13., 0., 0., 0., 13., 0., 0., 0., 13. + }; + std::vector expected_d = { + -9.274180565967479195e-01,2.698028341272042496e+00,2.521268387140979117e-01,2.927260638453461628e+00,-8.571926301526779923e-01,1.667785136187720063e+00 + }; + int natoms; + + DeepTensor dp; + + void SetUp() override { + std::string file_name = "../../tests/infer/deepdipole.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + std::fstream output("deepdipole.pb", std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + // check the string by the following commands + // string txt; + // protobuf::TextFormat::PrintToString(graph_def, &txt); + + dp.init("deepdipole.pb"); + + natoms = expected_d.size(); + }; + + void TearDown() override { + remove( "deepdipole.pb" ) ; + }; +}; + + +TEST_F(TestInferDeepDipole, cpu_build_nlist) +{ + EXPECT_EQ(dp.cutoff(), 4.); + EXPECT_EQ(dp.numb_types(), 2); + EXPECT_EQ(dp.output_dim(), 3); + std::vector sel_types = dp.sel_types(); + EXPECT_EQ(sel_types.size(), 1); + EXPECT_EQ(sel_types[0], 0); + + std::vector value; + dp.compute(value, coord, atype, box); + + EXPECT_EQ(value.size(), expected_d.size()); + for(int ii = 0; ii < expected_d.size(); ++ii){ + EXPECT_LT(fabs(value[ii] - expected_d[ii]), 1e-10); + } +} + +TEST_F(TestInferDeepDipole, cpu_lmp_nlist) +{ + float rc = dp.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + std::vector > nlist_data; + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + convert_nlist(inlist, nlist_data); + + std::vector value; + dp.compute(value, coord_cpy, atype_cpy, box, nall-nloc, inlist); + + EXPECT_EQ(value.size(), expected_d.size()); + for(int ii = 0; ii < expected_d.size(); ++ii){ + EXPECT_LT(fabs(value[ii] - expected_d[ii]), 1e-10); + } +} + diff --git a/source/api_cc/tests/test_deeppolar.cc b/source/api_cc/tests/test_deeppolar.cc new file mode 100644 index 0000000000..1d02ac5879 --- /dev/null +++ b/source/api_cc/tests/test_deeppolar.cc @@ -0,0 +1,106 @@ +#include +#include +#include +#include +#include +#include "DeepTensor.h" +#include "SimulationRegion.h" +#include "neighbor_list.h" +#include "test_utils.h" + +#include "google/protobuf/text_format.h" +#include "google/protobuf/io/zero_copy_stream_impl.h" +#include +#include +#include + +class TestInferDeepPolar : public ::testing::Test +{ +protected: + std::vector coord = { + 12.83, 2.56, 2.18, + 12.09, 2.87, 2.74, + 00.25, 3.32, 1.68, + 3.36, 3.00, 1.81, + 3.51, 2.51, 2.60, + 4.27, 3.22, 1.56 + }; + std::vector atype = { + 0, 1, 1, 0, 1, 1 + }; + std::vector box = { + 13., 0., 0., 0., 13., 0., 0., 0., 13. + }; + std::vector expected_d = { + 1.061407927405987051e-01,-3.569013342133873778e-01,-2.862108976089940138e-02,-3.569013342133875444e-01,1.304367268874677244e+00,1.037647501453442256e-01,-2.862108976089940138e-02,1.037647501453441284e-01,8.100521520762453409e-03,1.236797829492216616e+00,-3.717307430531632262e-01,7.371515676976750919e-01,-3.717307430531630041e-01,1.127222682121889058e-01,-2.239181552775717510e-01,7.371515676976746478e-01,-2.239181552775717787e-01,4.448255365635306879e-01 + }; + int natoms; + + DeepTensor dp; + + void SetUp() override { + std::string file_name = "../../tests/infer/deeppolar.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + std::fstream output("deeppolar.pb", std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + // check the string by the following commands + // string txt; + // protobuf::TextFormat::PrintToString(graph_def, &txt); + + dp.init("deeppolar.pb"); + + natoms = expected_d.size(); + }; + + void TearDown() override { + remove( "deeppolar.pb" ) ; + }; +}; + + +TEST_F(TestInferDeepPolar, cpu_build_nlist) +{ + EXPECT_EQ(dp.cutoff(), 6.); + EXPECT_EQ(dp.numb_types(), 2); + EXPECT_EQ(dp.output_dim(), 9); + std::vector sel_types = dp.sel_types(); + EXPECT_EQ(sel_types.size(), 1); + EXPECT_EQ(sel_types[0], 0); + + std::vector value; + dp.compute(value, coord, atype, box); + + EXPECT_EQ(value.size(), expected_d.size()); + for(int ii = 0; ii < expected_d.size(); ++ii){ + EXPECT_LT(fabs(value[ii] - expected_d[ii]), 1e-10); + } +} + +TEST_F(TestInferDeepPolar, cpu_lmp_nlist) +{ + float rc = dp.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + std::vector > nlist_data; + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + convert_nlist(inlist, nlist_data); + + std::vector value; + dp.compute(value, coord_cpy, atype_cpy, box, nall-nloc, inlist); + + EXPECT_EQ(value.size(), expected_d.size()); + for(int ii = 0; ii < expected_d.size(); ++ii){ + EXPECT_LT(fabs(value[ii] - expected_d[ii]), 1e-10); + } +} + diff --git a/source/api_cc/tests/test_deeppot.cc b/source/api_cc/tests/test_deeppot.cc new file mode 100644 index 0000000000..e59677dd66 --- /dev/null +++ b/source/api_cc/tests/test_deeppot.cc @@ -0,0 +1,437 @@ +#include +#include +#include +#include +#include +#include "NNPInter.h" +#include "SimulationRegion.h" +#include "neighbor_list.h" +#include "test_utils.h" + +#include "google/protobuf/text_format.h" +#include "google/protobuf/io/zero_copy_stream_impl.h" +#include +#include +#include + +class TestInferDeepPot : public ::testing::Test +{ +protected: + std::vector coord = { + 12.83, 2.56, 2.18, + 12.09, 2.87, 2.74, + 00.25, 3.32, 1.68, + 3.36, 3.00, 1.81, + 3.51, 2.51, 2.60, + 4.27, 3.22, 1.56 + }; + std::vector atype = { + 0, 1, 1, 0, 1, 1 + }; + std::vector box = { + 13., 0., 0., 0., 13., 0., 0., 0., 13. + }; + std::vector expected_e = { + -9.275780747115504710e+01,-1.863501786584258468e+02,-1.863392472863538103e+02,-9.279281325486221021e+01,-1.863671545232153903e+02,-1.863619822847602165e+02 + }; + std::vector expected_f = { + -3.034045420701179663e-01,8.405844663871177014e-01,7.696947487118485642e-02,7.662001266663505117e-01,-1.880601391333554251e-01,-6.183333871091722944e-01,-5.036172391059643427e-01,-6.529525836149027151e-01,5.432962643022043459e-01,6.382357912332115024e-01,-1.748518296794561167e-01,3.457363524891907125e-01,1.286482986991941552e-03,3.757251165286925043e-01,-5.972588700887541124e-01,-5.987006197104716154e-01,-2.004450304880958100e-01,2.495901655353461868e-01 + }; + std::vector expected_v = { + -2.912234126853306959e-01,-3.800610846612756388e-02,2.776624987489437202e-01,-5.053761003913598976e-02,-3.152373041953385746e-01,1.060894290092162379e-01,2.826389131596073745e-01,1.039129970665329250e-01,-2.584378792325942586e-01,-3.121722367954994914e-01,8.483275876786681990e-02,2.524662342344257682e-01,4.142176771106586414e-02,-3.820285230785245428e-02,-2.727311173065460545e-02,2.668859789777112135e-01,-6.448243569420382404e-02,-2.121731470426218846e-01,-8.624335220278558922e-02,-1.809695356746038597e-01,1.529875294531883312e-01,-1.283658185172031341e-01,-1.992682279795223999e-01,1.409924999632362341e-01,1.398322735274434292e-01,1.804318474574856390e-01,-1.470309318999652726e-01,-2.593983661598450730e-01,-4.236536279233147489e-02,3.386387920184946720e-02,-4.174017537818433543e-02,-1.003500282164128260e-01,1.525690815194478966e-01,3.398976109910181037e-02,1.522253908435125536e-01,-2.349125581341701963e-01,9.515545977581392825e-04,-1.643218849228543846e-02,1.993234765412972564e-02,6.027265332209678569e-04,-9.563256398907417355e-02,1.510815124001868293e-01,-7.738094816888557714e-03,1.502832772532304295e-01,-2.380965783745832010e-01,-2.309456719810296654e-01,-6.666961081213038098e-02,7.955566551234216632e-02,-8.099093777937517447e-02,-3.386641099800401927e-02,4.447884755740908608e-02,1.008593228579038742e-01,4.556718179228393811e-02,-6.078081273849572641e-02 + }; + int natoms; + double expected_tot_e; + std::vectorexpected_tot_v; + + NNPInter dp; + + void SetUp() override { + std::string file_name = "../../tests/infer/deeppot.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + std::fstream output("deeppot.pb", std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + // check the string by the following commands + // string txt; + // protobuf::TextFormat::PrintToString(graph_def, &txt); + + dp.init("deeppot.pb"); + + natoms = expected_e.size(); + EXPECT_EQ(natoms * 3, expected_f.size()); + EXPECT_EQ(natoms * 9, expected_v.size()); + expected_tot_e = 0.; + expected_tot_v.resize(9); + std::fill(expected_tot_v.begin(), expected_tot_v.end(), 0.); + for(int ii = 0; ii < natoms; ++ii){ + expected_tot_e += expected_e[ii]; + } + for(int ii = 0; ii < natoms; ++ii){ + for(int dd = 0; dd < 9; ++dd){ + expected_tot_v[dd] += expected_v[ii*9+dd]; + } + } + }; + + void TearDown() override { + remove( "deeppot.pb" ) ; + }; +}; + + +TEST_F(TestInferDeepPot, cpu_build_nlist) +{ + double ener; + std::vector force, virial; + dp.compute(ener, force, virial, coord, atype, box); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } +} + +TEST_F(TestInferDeepPot, cpu_build_nlist_atomic) +{ + double ener; + std::vector force, virial, atom_ener, atom_vir; + dp.compute(ener, force, virial, atom_ener, atom_vir, coord, atype, box); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + EXPECT_EQ(atom_ener.size(), natoms); + EXPECT_EQ(atom_vir.size(), natoms*9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } + for(int ii = 0; ii < natoms; ++ii){ + EXPECT_LT(fabs(atom_ener[ii] - expected_e[ii]), 1e-10); + } + for(int ii = 0; ii < natoms*9; ++ii){ + EXPECT_LT(fabs(atom_vir[ii] - expected_v[ii]), 1e-10); + } +} + + +TEST_F(TestInferDeepPot, cpu_lmp_nlist) +{ + float rc = dp.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + double ener; + std::vector force_, virial; + dp.compute(ener, force_, virial, coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + std::vector force; + _fold_back(force, force_, mapping, nloc, nall, 3); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } + + ener = 0.; + std::fill(force_.begin(), force_.end(), 0.0); + std::fill(virial.begin(), virial.end(), 0.0); + dp.compute(ener, force_, virial, coord_cpy, atype_cpy, box, nall-nloc, inlist, 1); + _fold_back(force, force_, mapping, nloc, nall, 3); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } +} + + +TEST_F(TestInferDeepPot, cpu_lmp_nlist_atomic) +{ + float rc = dp.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + double ener; + std::vector force_, atom_ener_, atom_vir_, virial; + std::vector force, atom_ener, atom_vir; + dp.compute(ener, force_, virial, atom_ener_, atom_vir_, coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + _fold_back(force, force_, mapping, nloc, nall, 3); + _fold_back(atom_ener, atom_ener_, mapping, nloc, nall, 1); + _fold_back(atom_vir, atom_vir_, mapping, nloc, nall, 9); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + EXPECT_EQ(atom_ener.size(), natoms); + EXPECT_EQ(atom_vir.size(), natoms*9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } + for(int ii = 0; ii < natoms; ++ii){ + EXPECT_LT(fabs(atom_ener[ii] - expected_e[ii]), 1e-10); + } + for(int ii = 0; ii < natoms*9; ++ii){ + EXPECT_LT(fabs(atom_vir[ii] - expected_v[ii]), 1e-10); + } + + ener = 0.; + std::fill(force_.begin(), force_.end(), 0.0); + std::fill(virial.begin(), virial.end(), 0.0); + std::fill(atom_ener_.begin(), atom_ener_.end(), 0.0); + std::fill(atom_vir_.begin(), atom_vir_.end(), 0.0); + dp.compute(ener, force_, virial, atom_ener_, atom_vir_, coord_cpy, atype_cpy, box, nall-nloc, inlist, 1); + _fold_back(force, force_, mapping, nloc, nall, 3); + _fold_back(atom_ener, atom_ener_, mapping, nloc, nall, 1); + _fold_back(atom_vir, atom_vir_, mapping, nloc, nall, 9); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + EXPECT_EQ(atom_ener.size(), natoms); + EXPECT_EQ(atom_vir.size(), natoms*9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } + for(int ii = 0; ii < natoms; ++ii){ + EXPECT_LT(fabs(atom_ener[ii] - expected_e[ii]), 1e-10); + } + for(int ii = 0; ii < natoms*9; ++ii){ + EXPECT_LT(fabs(atom_vir[ii] - expected_v[ii]), 1e-10); + } +} + + +TEST_F(TestInferDeepPot, cpu_lmp_nlist_2rc) +{ + float rc = dp.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc*2); + int nall = coord_cpy.size() / 3; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + double ener; + std::vector force_(nall*3, 0.0), virial(9, 0.0); + dp.compute(ener, force_, virial, coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + std::vector force; + _fold_back(force, force_, mapping, nloc, nall, 3); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } + + ener = 0.; + std::fill(force_.begin(), force_.end(), 0.0); + std::fill(virial.begin(), virial.end(), 0.0); + dp.compute(ener, force_, virial, coord_cpy, atype_cpy, box, nall-nloc, inlist, 1); + _fold_back(force, force_, mapping, nloc, nall, 3); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } +} + + +TEST_F(TestInferDeepPot, cpu_lmp_nlist_type_sel) +{ + float rc = dp.cutoff(); + + // add vir atoms + int nvir = 2; + std::vector coord_vir(nvir*3); + std::vector atype_vir(nvir, 2); + for(int ii = 0; ii < nvir; ++ii){ + coord_vir[ii] = coord[ii]; + } + coord.insert(coord.begin(), coord_vir.begin(), coord_vir.end()); + atype.insert(atype.begin(), atype_vir.begin(), atype_vir.end()); + natoms += nvir; + std::vector expected_f_vir(nvir*3, 0.0); + expected_f.insert(expected_f.begin(), expected_f_vir.begin(), expected_f_vir.end()); + + // build nlist + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + // dp compute + double ener; + std::vector force_(nall*3, 0.0), virial(9, 0.0); + dp.compute(ener, force_, virial, coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + // fold back + std::vector force; + _fold_back(force, force_, mapping, nloc, nall, 3); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } +} + + + +class TestInferDeepPotNoPbc : public ::testing::Test +{ +protected: + std::vector coord = { + 12.83, 2.56, 2.18, + 12.09, 2.87, 2.74, + 00.25, 3.32, 1.68, + 3.36, 3.00, 1.81, + 3.51, 2.51, 2.60, + 4.27, 3.22, 1.56 + }; + std::vector atype = { + 0, 1, 1, 0, 1, 1 + }; + std::vector box = {}; + std::vector expected_e = { + -9.255934839310273787e+01,-1.863253376736990106e+02,-1.857237299341402945e+02,-9.279308539717486326e+01,-1.863708105823244239e+02,-1.863635196514972563e+02 + }; + std::vector expected_f = { + -2.161037360255332107e+00,9.052994347015581589e-01,1.635379623977007979e+00,2.161037360255332107e+00,-9.052994347015581589e-01,-1.635379623977007979e+00,-1.167128117249453811e-02,1.371975700096064992e-03,-1.575265180249604477e-03,6.226508593971802341e-01,-1.816734122009256991e-01,3.561766019664774907e-01,-1.406075393906316626e-02,3.789140061530929526e-01,-6.018777878642909140e-01,-5.969188242856223736e-01,-1.986125696522633155e-01,2.472764510780630642e-01 + }; + std::vector expected_v = { + -7.042445481792056761e-01,2.950213647777754078e-01,5.329418202437231633e-01,2.950213647777752968e-01,-1.235900311906896754e-01,-2.232594111831812944e-01,5.329418202437232743e-01,-2.232594111831813499e-01,-4.033073234276823849e-01,-8.949230984097404917e-01,3.749002169013777030e-01,6.772391014992630298e-01,3.749002169013777586e-01,-1.570527935667933583e-01,-2.837082722496912512e-01,6.772391014992631408e-01,-2.837082722496912512e-01,-5.125052659994422388e-01,4.858210330291591605e-02,-6.902596153269104431e-03,6.682612642430500391e-03,-5.612247004554610057e-03,9.767795567660207592e-04,-9.773758942738038254e-04,5.638322117219018645e-03,-9.483806049779926932e-04,8.493873281881353637e-04,-2.941738570564985666e-01,-4.482529909499673171e-02,4.091569840186781021e-02,-4.509020615859140463e-02,-1.013919988807244071e-01,1.551440772665269030e-01,4.181857726606644232e-02,1.547200233064863484e-01,-2.398213304685777592e-01,-3.218625798524068354e-02,-1.012438450438508421e-02,1.271639330380921855e-02,3.072814938490859779e-03,-9.556241797915024372e-02,1.512251983492413077e-01,-8.277872384009607454e-03,1.505412040827929787e-01,-2.386150620881526407e-01,-2.312295470054945568e-01,-6.631490213524345034e-02,7.932427266386249398e-02,-8.053754366323923053e-02,-3.294595881137418747e-02,4.342495071150231922e-02,1.004599500126941436e-01,4.450400364869536163e-02,-5.951077548033092968e-02 + }; + int natoms; + double expected_tot_e; + std::vectorexpected_tot_v; + + NNPInter dp; + + void SetUp() override { + std::string file_name = "../../tests/infer/deeppot.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + std::fstream output("deeppot.pb", std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + + dp.init("deeppot.pb"); + + natoms = expected_e.size(); + EXPECT_EQ(natoms * 3, expected_f.size()); + EXPECT_EQ(natoms * 9, expected_v.size()); + expected_tot_e = 0.; + expected_tot_v.resize(9); + std::fill(expected_tot_v.begin(), expected_tot_v.end(), 0.); + for(int ii = 0; ii < natoms; ++ii){ + expected_tot_e += expected_e[ii]; + } + for(int ii = 0; ii < natoms; ++ii){ + for(int dd = 0; dd < 9; ++dd){ + expected_tot_v[dd] += expected_v[ii*9+dd]; + } + } + }; + + void TearDown() override { + remove( "deeppot.pb" ) ; + }; +}; + +TEST_F(TestInferDeepPotNoPbc, cpu_build_nlist) +{ + double ener; + std::vector force, virial; + dp.compute(ener, force, virial, coord, atype, box); + + EXPECT_EQ(force.size(), natoms*3); + EXPECT_EQ(virial.size(), 9); + + EXPECT_LT(fabs(ener - expected_tot_e), 1e-10); + for(int ii = 0; ii < natoms*3; ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-10); + } + for(int ii = 0; ii < 3*3; ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_tot_v[ii]), 1e-10); + } +} diff --git a/source/api_cc/tests/test_dipolecharge.cc b/source/api_cc/tests/test_dipolecharge.cc new file mode 100644 index 0000000000..8c517057f3 --- /dev/null +++ b/source/api_cc/tests/test_dipolecharge.cc @@ -0,0 +1,240 @@ +#include +#include +#include +#include +#include +#include "DeepTensor.h" +#include "DataModifier.h" +#include "SimulationRegion.h" +#include "Ewald.h" +#include "neighbor_list.h" +#include "test_utils.h" + +#include "google/protobuf/text_format.h" +#include "google/protobuf/io/zero_copy_stream_impl.h" +#include +#include +#include + +class TestDipoleCharge : public ::testing::Test +{ +protected: + std::vector coord = { + 4.6067455554, 8.8719311819, 6.3886531197, + 4.0044515745, 4.2449530507, 7.7902855220, + 2.6453069446, 0.8772647726, 1.2804446790, + 1.1445332290, 0.0067366438, 1.8606485070, + 7.1002867706, 5.0325506787, 3.1805888348, + 4.5352891138, 7.7389683929, 9.4260970128, + 2.1833238914, 9.0916071034, 7.2299906064, + 4.1040157820, 1.0496745045, 5.4748315591, + }; + std::vector atype = { + 0,3,2,1,3,4,1,4 + }; + std::vector box = { + 10., 0., 0., 0., 10., 0., 0., 0., 10. + }; + std::vector expected_e = { + 3.671081837126222158e+00 + }; + std::vector expected_f = { + 8.786854427753210128e-01,-1.590752486903602159e-01,-2.709225006303785932e-01,-4.449513960033193438e-01,-1.564291540964127813e-01,2.139031741772115178e-02,1.219699614140521193e+00,-5.580358618499958734e-02,-3.878662478349682585e-01,-1.286685244990778854e+00,1.886475802950296488e-01,3.904450515493615437e-01,1.605017382138404849e-02,2.138016869742287995e-01,-2.617514921203008965e-02,2.877081057057793712e-01,-3.846449683844421763e-01,3.048855616906603894e-02,-9.075632811311897807e-01,-6.509653472431625731e-03,2.302010972126376787e-01,2.370565856822822726e-01,3.600133435593881881e-01,1.243887532859055609e-02 + }; + std::vector expected_v = { + 3.714071471995848417e-01,6.957130186032146613e-01,-1.158289779017217302e+00,6.957130186032139951e-01,-1.400130091653774933e+01,-3.631620234653316626e-01,-1.158289779017217302e+00,-3.631620234653316626e-01,3.805077486043773050e+00 + }; + std::vector charge_map = { + 1., 1., 1., 1., 1., -1., -3. + }; + int natoms; + int ntypes; + std::vector type_asso; + double expected_tot_e; + std::vectorexpected_tot_v; + + DeepTensor dp; + DipoleChargeModifier dm; + + void SetUp() override { + std::string file_name = "../../tests/infer/dipolecharge_e.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + string model = "dipolecharge_e.pb"; + std::fstream output(model.c_str(), std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + // check the string by the following commands + // string txt; + // protobuf::TextFormat::PrintToString(graph_def, &txt); + + // dp.init("dipolecharge_d.pb"); + // dm.init("dipolecharge_d.pb"); + dp.init(model, 0, "dipole_charge"); + dm.init(model, 0, "dipole_charge"); + + natoms = atype.size(); + ntypes = 5; + type_asso.resize(ntypes, -1); + type_asso[1] = 5; + type_asso[3] = 6; + + EXPECT_EQ(natoms * 3, expected_f.size()); + EXPECT_EQ(9, expected_v.size()); + }; + + void TearDown() override { + remove( "dipolecharge_e.pb" ) ; + }; +}; + +static bool +_in_vec(const int & value, + const std::vector & vec) +{ + // naive impl. + for(int ii = 0; ii < vec.size(); ++ii){ + if(value == vec[ii]) return true; + } + return false; +} + +TEST_F(TestDipoleCharge, cpu_lmp_nlist) +{ + // build nlist + // float rc = dp.cutoff(); + float rc = 4.0; + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + int nghost = nall - nloc; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + // evaluate dipole + std::vector dipole, dipole_recd(nloc*3, 0.0); + dp.compute(dipole, coord_cpy, atype_cpy, box, nall-nloc, inlist); + + // add virtual atoms to the system + // // a lot of mappings + std::vector sel_types = dp.sel_types(); + std::vector sel_fwd, sel_bwd; + int sel_nghost; + select_by_type(sel_fwd, sel_bwd, sel_nghost, coord_cpy, atype_cpy, nghost, sel_types); + int sel_nall = sel_bwd.size(); + int sel_nloc = sel_nall - sel_nghost; + std::vector sel_atype(sel_bwd.size()); + select_map(sel_atype, atype, sel_fwd, 1); + NNPAtomMap nnp_map(sel_atype.begin(), sel_atype.begin() + sel_nloc); + const std::vector & sort_fwd_map(nnp_map.get_fwd_map()); + + // // add coords + std::vector add_coord; + std::vector add_atype; + std::vector> pairs; + for(int ii = 0; ii < nloc; ++ii){ + if(_in_vec(atype[ii], sel_types)){ + int res_idx = sort_fwd_map[sel_fwd[ii]]; + std::vector tmp_coord(3); + for(int dd = 0; dd < 3; ++dd){ + tmp_coord[dd] = coord[ii*3+dd] + dipole[res_idx*3+dd]; + dipole_recd[ii*3+dd] = dipole[res_idx*3+dd]; + } + pairs.push_back(std::pair(ii, add_atype.size()+atype.size())); + // std::cout << ii << " " + // << atype[ii] << " " + // << res_idx << " " + // << type_asso[atype[ii]] << " " + // << " pair " + // << pairs.back().first << " " << pairs.back().second << " " + // << std::endl; + add_coord.insert(add_coord.end(), tmp_coord.begin(), tmp_coord.end()); + add_atype.push_back(type_asso[atype[ii]]); + } + } + coord.insert(coord.end(), add_coord.begin(), add_coord.end()); + atype.insert(atype.end(), add_atype.begin(), add_atype.end()); + nloc = atype.size(); + EXPECT_EQ(atype.size()*3, coord.size()); + + // get charge value + std::vector charge(nloc); + for(int ii = 0; ii < nloc; ++ii){ + charge[ii] = charge_map[atype[ii]]; + } + + // compute the recp part of the ele interaction + double eener; + std::vector eforce, evirial; + SimulationRegion region; + region.reinitBox(&box[0]); + EwaldParameters eparam; + eparam.beta = 0.2; + eparam.spacing = 4; + EwaldReciprocal(eener, eforce, evirial, coord, charge, region, eparam); + + EXPECT_LT(fabs(eener - expected_e[0]), 1e-6); + EXPECT_EQ(eforce.size(), coord.size()); + EXPECT_EQ(evirial.size(), 9); + + // extend the system with virtual atoms, and build nlist + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + nall = coord_cpy.size() / 3; + nghost = nall - nloc; + ilist.resize(nloc); + numneigh.resize(nloc); + firstneigh.resize(nloc); + inlist.inum = nloc; + inlist.ilist = &ilist[0]; + inlist.numneigh = &numneigh[0]; + inlist.firstneigh = &firstneigh[0]; + convert_nlist(inlist, nlist_data); + + // compute force and virial + std::vector force_, force, virial; + dm.compute(force_, virial, coord_cpy, atype_cpy, box, pairs, eforce, nghost, inlist); + // for(int ii = 0; ii < force_.size(); ++ii){ + // std::cout << force_[ii] << " " ; + // } + // std::cout << std::endl; + _fold_back(force, force_, mapping, nloc, nall, 3); + + // compare force + EXPECT_EQ(force.size(), nloc*3); + // note nloc > expected_f.size(), because nloc contains virtual atoms. + for(int ii = 0; ii < expected_f.size(); ++ii){ + EXPECT_LT(fabs(force[ii] - expected_f[ii]), 1e-6); + } + + // add recp virial and viral corr to virial + // virial = virial_recp + virial_dipolecharge + virial_corr + for (int dd0 = 0; dd0 < 3; ++dd0){ + for (int dd1 = 0; dd1 < 3; ++dd1){ + virial[dd0*3+dd1] += evirial[dd0*3+dd1]; + } + } + for(int ii = 0; ii < pairs.size(); ++ii){ + int idx0 = pairs[ii].first; + int idx1 = pairs[ii].second; + for (int dd0 = 0; dd0 < 3; ++dd0){ + for (int dd1 = 0; dd1 < 3; ++dd1){ + virial[dd0*3+dd1] -= eforce[idx1*3+dd0] * dipole_recd[idx0*3+dd1]; + } + } + } + // compare virial + EXPECT_EQ(virial.size(), 3*3); + for(int ii = 0; ii < expected_v.size(); ++ii){ + EXPECT_LT(fabs(virial[ii] - expected_v[ii]), 1e-5); + } +} + diff --git a/source/api_cc/tests/test_utils.h b/source/api_cc/tests/test_utils.h new file mode 100644 index 0000000000..4135f46498 --- /dev/null +++ b/source/api_cc/tests/test_utils.h @@ -0,0 +1,50 @@ +#pragma once + +inline void +_fold_back( + std::vector &out, + const std::vector &in, + const std::vector &mapping, + const int nloc, + const int nall, + const int ndim) +{ + out.resize(nloc*ndim); + std::copy(in.begin(), in.begin() + nloc*ndim, out.begin()); + for(int ii = nloc; ii < nall; ++ii){ + int in_idx = ii; + int out_idx = mapping[in_idx]; + for(int dd = 0; dd < ndim; ++dd){ + out[out_idx * ndim + dd] += in[in_idx * ndim + dd]; + } + } +} + +inline void +_build_nlist( + std::vector> &nlist_data, + std::vector & coord_cpy, + std::vector & atype_cpy, + std::vector & mapping, + const std::vector & coord, + const std::vector & atype, + const std::vector & box, + const float & rc) +{ + SimulationRegion region; + region.reinitBox(&box[0]); + std::vector ncell, ngcell; + copy_coord(coord_cpy, atype_cpy, mapping, ncell, ngcell, coord, atype, rc, region); + std::vector nat_stt, ext_stt, ext_end; + nat_stt.resize(3); + ext_stt.resize(3); + ext_end.resize(3); + for (int dd = 0; dd < 3; ++dd){ + ext_stt[dd] = -ngcell[dd]; + ext_end[dd] = ncell[dd] + ngcell[dd]; + } + int nloc = coord.size() / 3; + int nall = coord_cpy.size() / 3; + std::vector> nlist_r_cpy; + build_nlist(nlist_data, nlist_r_cpy, coord_cpy, nloc, rc, rc, nat_stt, ncell, ext_stt, ext_end, region, ncell); +} From 1623569f784feb63f90ae6ac51909b4186cf92db Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 14:54:37 +0800 Subject: [PATCH 04/15] add destructor for InputNlist --- source/lib/include/neighbor_list.h | 1 + 1 file changed, 1 insertion(+) diff --git a/source/lib/include/neighbor_list.h b/source/lib/include/neighbor_list.h index 58d5f150ed..174fad1a9f 100644 --- a/source/lib/include/neighbor_list.h +++ b/source/lib/include/neighbor_list.h @@ -27,6 +27,7 @@ struct InputNlist ) : inum(inum_), ilist(ilist_), numneigh(numneigh_), firstneigh(firstneigh_) {}; + ~InputNlist(){}; }; void convert_nlist( From 03016888891e84fcc92005ac92889d6397437c1c Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 14:55:49 +0800 Subject: [PATCH 05/15] freeze output_dim in tensor models --- deepmd/entrypoints/freeze.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/deepmd/entrypoints/freeze.py b/deepmd/entrypoints/freeze.py index c42ae2f968..d47dffaf87 100755 --- a/deepmd/entrypoints/freeze.py +++ b/deepmd/entrypoints/freeze.py @@ -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}") From 10116bfdba429d5d252b77af90eaab7887e1017d Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 14:56:18 +0800 Subject: [PATCH 06/15] DipoleChargeModifier determine number of atoms by input vector of atom types --- deepmd/infer/data_modifier.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/deepmd/infer/data_modifier.py b/deepmd/infer/data_modifier.py index 1cf4446f7d..0db33c2b02 100644 --- a/deepmd/infer/data_modifier.py +++ b/deepmd/infer/data_modifier.py @@ -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]) From ad2f64d58f61eedf340a950e8504d4b3375e56df Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 15:07:42 +0800 Subject: [PATCH 07/15] clean up outdated commented code --- source/api_cc/src/common.cc | 292 ------------------------------------ 1 file changed, 292 deletions(-) diff --git a/source/api_cc/src/common.cc b/source/api_cc/src/common.cc index 0bbce93120..4603c82492 100644 --- a/source/api_cc/src/common.cc +++ b/source/api_cc/src/common.cc @@ -152,44 +152,6 @@ make_inlist(InputNlist & inlist) inlist.firstneigh = &firstneigh[0]; } -// void -// shuffle_nlist_exclude_empty (InternalNeighborList & list, -// const std::vector & fwd_map) -// { -// int old_nloc = fwd_map.size(); -// shuffle_nlist(list, fwd_map); -// std::vector new_ilist, new_jrange, new_jlist, new_icount; -// new_ilist.reserve(list.ilist.size()); -// new_icount.reserve(list.ilist.size()); -// new_jrange.reserve(list.jrange.size()); -// new_jlist.reserve(list.jlist.size()); -// for(int ii = 0; ii < list.ilist.size(); ++ii){ -// if(list.ilist[ii] >= 0){ -// new_ilist.push_back(list.ilist[ii]); -// } -// } -// new_jrange.resize(new_ilist.size()+1); -// new_jrange[0] = 0; -// int ci = 0; -// for(int ii = 0; ii < list.ilist.size(); ++ii){ -// if (list.ilist[ii] < 0) continue; -// int js = list.jrange[ii]; -// int je = list.jrange[ii+1]; -// int cc = 0; -// for (int jj = js; jj < je; ++jj){ -// if (list.jlist[jj] >= 0) { -// new_jlist.push_back(list.jlist[jj]); -// cc++; -// } -// } -// new_jrange[ci+1] = new_jrange[ci] + cc; -// ci ++; -// } -// list.ilist = new_ilist; -// list.jrange = new_jrange; -// list.jlist = new_jlist; -// } - void checkStatus(const tensorflow::Status& status) { if (!status.ok()) { @@ -492,257 +454,3 @@ session_input_tensors (std::vector> & input_tenso return nloc; } -// int -// session_input_tensors (std::vector> & input_tensors, -// const std::vector & dcoord_, -// const int & ntypes, -// const std::vector & datype_, -// const std::vector & dbox, -// InternalNeighborList & dlist, -// const std::vector & fparam_, -// const std::vector & aparam_, -// const NNPAtomMap& nnpmap, -// const int nghost, -// const std::string scope) -// { -// assert (dbox.size() == 9); - -// int nframes = 1; -// int nall = dcoord_.size() / 3; -// int nloc = nall - nghost; -// assert (nall == datype_.size()); - -// std::vector datype = nnpmap.get_type(); -// std::vector type_count (ntypes, 0); -// for (unsigned ii = 0; ii < datype.size(); ++ii){ -// type_count[datype[ii]] ++; -// } -// datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); - -// TensorShape coord_shape ; -// coord_shape.AddDim (nframes); -// coord_shape.AddDim (nall * 3); -// TensorShape type_shape ; -// type_shape.AddDim (nframes); -// type_shape.AddDim (nall); -// TensorShape box_shape ; -// box_shape.AddDim (nframes); -// box_shape.AddDim (9); -// TensorShape mesh_shape ; -// mesh_shape.AddDim (16); -// TensorShape natoms_shape ; -// natoms_shape.AddDim (2 + ntypes); -// TensorShape fparam_shape ; -// fparam_shape.AddDim (nframes); -// fparam_shape.AddDim (fparam_.size()); -// TensorShape aparam_shape ; -// aparam_shape.AddDim (nframes); -// aparam_shape.AddDim (aparam_.size()); - -// #ifdef HIGH_PREC -// Tensor coord_tensor (DT_DOUBLE, coord_shape); -// Tensor box_tensor (DT_DOUBLE, box_shape); -// Tensor fparam_tensor (DT_DOUBLE, fparam_shape); -// Tensor aparam_tensor (DT_DOUBLE, aparam_shape); -// #else -// Tensor coord_tensor (DT_FLOAT, coord_shape); -// Tensor box_tensor (DT_FLOAT, box_shape); -// Tensor fparam_tensor (DT_FLOAT, fparam_shape); -// Tensor aparam_tensor (DT_FLOAT, aparam_shape); -// #endif -// Tensor type_tensor (DT_INT32, type_shape); -// Tensor mesh_tensor (DT_INT32, mesh_shape); -// Tensor natoms_tensor (DT_INT32, natoms_shape); - -// auto coord = coord_tensor.matrix (); -// auto type = type_tensor.matrix (); -// auto box = box_tensor.matrix (); -// auto mesh = mesh_tensor.flat (); -// auto natoms = natoms_tensor.flat (); -// auto fparam = fparam_tensor.matrix (); -// auto aparam = aparam_tensor.matrix (); - -// std::vector dcoord (dcoord_); -// nnpmap.forward (dcoord.begin(), dcoord_.begin(), 3); - -// for (int ii = 0; ii < nframes; ++ii){ -// for (int jj = 0; jj < nall * 3; ++jj){ -// coord(ii, jj) = dcoord[jj]; -// } -// for (int jj = 0; jj < 9; ++jj){ -// box(ii, jj) = dbox[jj]; -// } -// for (int jj = 0; jj < nall; ++jj){ -// type(ii, jj) = datype[jj]; -// } -// for (int jj = 0; jj < fparam_.size(); ++jj){ -// fparam(ii, jj) = fparam_[jj]; -// } -// for (int jj = 0; jj < aparam_.size(); ++jj){ -// aparam(ii, jj) = aparam_[jj]; -// } -// } - -// for (int ii = 0; ii < 16; ++ii) mesh(ii) = 0; - -// mesh (0) = sizeof(int *) / sizeof(int); -// assert (mesh(0) * sizeof(int) == sizeof(int *)); -// const int & stride = mesh(0); -// mesh (1) = dlist.ilist.size(); -// assert (mesh(1) == nloc); -// assert (stride <= 4); -// dlist.make_ptrs(); -// memcpy (&mesh(4), &(dlist.pilist), sizeof(int *)); -// memcpy (&mesh(8), &(dlist.pjrange), sizeof(int *)); -// memcpy (&mesh(12), &(dlist.pjlist), sizeof(int *)); - -// natoms (0) = nloc; -// natoms (1) = nall; -// for (int ii = 0; ii < ntypes; ++ii) natoms(ii+2) = type_count[ii]; - -// std::string prefix = ""; -// if (scope != ""){ -// prefix = scope + "/"; -// } -// input_tensors = { -// {prefix+"t_coord", coord_tensor}, -// {prefix+"t_type", type_tensor}, -// {prefix+"t_box", box_tensor}, -// {prefix+"t_mesh", mesh_tensor}, -// {prefix+"t_natoms",natoms_tensor}, -// }; -// if (fparam_.size() > 0) { -// input_tensors.push_back({prefix+"t_fparam", fparam_tensor}); -// } -// if (aparam_.size() > 0) { -// input_tensors.push_back({prefix+"t_aparam", aparam_tensor}); -// } - -// return nloc; -// } - -// int -// session_input_tensors ( -// std::vector> & input_tensors, -// const std::vector & dcoord_, -// const int & ntypes, -// const std::vector & datype_, -// const std::vector & dbox, -// const int * ilist, -// const int * jrange, -// const int * jlist, -// const std::vector & fparam_, -// const std::vector & aparam_, -// const NNPAtomMap & nnpmap, -// const int & nghost) -// { -// assert (dbox.size() == 9); - -// int nframes = 1; -// int nall = dcoord_.size() / 3; -// int nloc = nall - nghost; -// assert (nall == datype_.size()); - -// std::vector datype = nnpmap.get_type(); -// std::vector type_count (ntypes, 0); -// for (unsigned ii = 0; ii < datype.size(); ++ii) { -// type_count[datype[ii]] ++; -// } -// datype.insert (datype.end(), datype_.begin() + nloc, datype_.end()); - -// TensorShape coord_shape ; -// coord_shape.AddDim (nframes); -// coord_shape.AddDim (nall * 3); -// TensorShape type_shape ; -// type_shape.AddDim (nframes); -// type_shape.AddDim (nall); -// TensorShape box_shape ; -// box_shape.AddDim (nframes); -// box_shape.AddDim (9); -// TensorShape mesh_shape; -// mesh_shape.AddDim (16); -// TensorShape natoms_shape; -// natoms_shape.AddDim (2 + ntypes); -// TensorShape fparam_shape; -// fparam_shape.AddDim (nframes); -// fparam_shape.AddDim (fparam_.size()); -// TensorShape aparam_shape ; -// aparam_shape.AddDim (nframes); -// aparam_shape.AddDim (aparam_.size()); - -// #ifdef HIGH_PREC -// Tensor coord_tensor (DT_DOUBLE, coord_shape); -// Tensor box_tensor (DT_DOUBLE, box_shape); -// Tensor fparam_tensor(DT_DOUBLE, fparam_shape); -// Tensor aparam_tensor(DT_DOUBLE, fparam_shape); -// #else -// Tensor coord_tensor (DT_FLOAT, coord_shape); -// Tensor box_tensor (DT_FLOAT, box_shape); -// Tensor fparam_tensor(DT_FLOAT, fparam_shape); -// Tensor aparam_tensor(DT_FLOAT, fparam_shape); -// #endif -// Tensor type_tensor (DT_INT32, type_shape); -// Tensor mesh_tensor (DT_INT32, mesh_shape); -// Tensor natoms_tensor(DT_INT32, natoms_shape); - -// auto coord = coord_tensor.matrix (); -// auto type = type_tensor.matrix (); -// auto box = box_tensor.matrix (); -// auto mesh = mesh_tensor.flat (); -// auto natoms = natoms_tensor.flat (); -// auto fparam = fparam_tensor.matrix (); -// auto aparam = aparam_tensor.matrix (); - -// std::vector dcoord (dcoord_); -// nnpmap.forward (dcoord.begin(), dcoord_.begin(), 3); - -// for (int ii = 0; ii < nframes; ++ii) { -// for (int jj = 0; jj < nall * 3; ++jj) { -// coord(ii, jj) = dcoord[jj]; -// } -// for (int jj = 0; jj < 9; ++jj) { -// box(ii, jj) = dbox[jj]; -// } -// for (int jj = 0; jj < nall; ++jj) { -// type(ii, jj) = datype[jj]; -// } -// for (int jj = 0; jj < fparam_.size(); ++jj) { -// fparam(ii, jj) = fparam_[jj]; -// } -// for (int jj = 0; jj < aparam_.size(); ++jj) { -// aparam(ii, jj) = aparam_[jj]; -// } -// } - -// for (int ii = 0; ii < 16; ++ii) mesh(ii) = 0; - -// mesh (0) = sizeof(int *) / sizeof(int); -// assert (mesh(0) * sizeof(int) == sizeof(int *)); -// const int & stride = mesh(0); -// // mesh (1) = dlist.ilist.size(); -// mesh (1) = nloc; -// assert (mesh(1) == nloc); -// assert (stride <= 4); -// memcpy (&mesh(4), &(ilist), sizeof(int *)); -// memcpy (&mesh(8), &(jrange), sizeof(int *)); -// memcpy (&mesh(12), &(jlist), sizeof(int *)); - -// natoms (0) = nloc; -// natoms (1) = nall; -// for (int ii = 0; ii < ntypes; ++ii) natoms(ii+2) = type_count[ii]; - -// input_tensors = { -// {"t_coord", coord_tensor}, -// {"t_type", type_tensor}, -// {"t_box", box_tensor}, -// {"t_mesh", mesh_tensor}, -// {"t_natoms", natoms_tensor}, -// }; -// if (fparam_.size() > 0) { -// input_tensors.push_back({"t_fparam", fparam_tensor}); -// } -// if (aparam_.size() > 0) { -// input_tensors.push_back({"t_aparam", aparam_tensor}); -// } -// return nloc; -// } From 41a05014812b50a0b029d7cf089fc558244e818b Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 10 Mar 2021 02:41:20 -0500 Subject: [PATCH 08/15] add test CI for api_cc --- source/api_cc/tests/CMakeLists.txt | 2 +- .../CMakeLists.txt.in => cmake/googletest.cmake.in} | 0 source/install/test_cc.sh | 12 ++++++++++++ source/lib/tests/CMakeLists.txt | 2 +- 4 files changed, 14 insertions(+), 2 deletions(-) rename source/{lib/tests/CMakeLists.txt.in => cmake/googletest.cmake.in} (100%) diff --git a/source/api_cc/tests/CMakeLists.txt b/source/api_cc/tests/CMakeLists.txt index 4ffa71de3d..6015c00166 100644 --- a/source/api_cc/tests/CMakeLists.txt +++ b/source/api_cc/tests/CMakeLists.txt @@ -86,7 +86,7 @@ add_test( runUnitTests runUnitTests ) find_package(GTest) if(NOT GTEST_LIBRARY) - configure_file(CMakeLists.txt.in googletest-download/CMakeLists.txt) + configure_file(../../cmake/googletest.cmake.in googletest-download/CMakeLists.txt) execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" . RESULT_VARIABLE result WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download ) diff --git a/source/lib/tests/CMakeLists.txt.in b/source/cmake/googletest.cmake.in similarity index 100% rename from source/lib/tests/CMakeLists.txt.in rename to source/cmake/googletest.cmake.in diff --git a/source/install/test_cc.sh b/source/install/test_cc.sh index 6464a9a904..ecab79ab24 100755 --- a/source/install/test_cc.sh +++ b/source/install/test_cc.sh @@ -16,3 +16,15 @@ make -j${NPROC} #------------------ ${BUILD_TMP_DIR}/runUnitTests + +#------------------ + +BUILD_TMP_DIR=${SCRIPT_PATH}/../build_cc_tests +mkdir -p ${BUILD_TMP_DIR} +cd ${BUILD_TMP_DIR} +cmake ../api_cc/tests +make -j${NPROC} + +#------------------ +${BUILD_TMP_DIR}/runUnitTests + diff --git a/source/lib/tests/CMakeLists.txt b/source/lib/tests/CMakeLists.txt index c3b54f2a09..874f9768a2 100644 --- a/source/lib/tests/CMakeLists.txt +++ b/source/lib/tests/CMakeLists.txt @@ -59,7 +59,7 @@ add_test( runUnitTests runUnitTests ) find_package(GTest) if(NOT GTEST_LIBRARY) - configure_file(CMakeLists.txt.in googletest-download/CMakeLists.txt) + configure_file(../../cmake/googletest.cmake.in googletest-download/CMakeLists.txt) execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" . RESULT_VARIABLE result WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download ) From 94480b62311c87531a1addd05c133fb30ec47931 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 10 Mar 2021 02:58:36 -0500 Subject: [PATCH 09/15] install tensorflow --- source/install/test_cc.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/install/test_cc.sh b/source/install/test_cc.sh index ecab79ab24..23426e4b4e 100755 --- a/source/install/test_cc.sh +++ b/source/install/test_cc.sh @@ -22,7 +22,7 @@ ${BUILD_TMP_DIR}/runUnitTests BUILD_TMP_DIR=${SCRIPT_PATH}/../build_cc_tests mkdir -p ${BUILD_TMP_DIR} cd ${BUILD_TMP_DIR} -cmake ../api_cc/tests +cmake -DINSTALL_TENSORFLOW=TRUE ../api_cc/tests make -j${NPROC} #------------------ From 296cafe5cbf6bca820d4e7dd2425d6f26e0e1373 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 10 Mar 2021 03:11:29 -0500 Subject: [PATCH 10/15] set INSTALL_PREFIX --- source/install/test_cc.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/source/install/test_cc.sh b/source/install/test_cc.sh index 23426e4b4e..0c5333f41c 100755 --- a/source/install/test_cc.sh +++ b/source/install/test_cc.sh @@ -20,9 +20,11 @@ ${BUILD_TMP_DIR}/runUnitTests #------------------ BUILD_TMP_DIR=${SCRIPT_PATH}/../build_cc_tests +INSTALL_PREFIX=${SCRIPT_PATH}/../../dp mkdir -p ${BUILD_TMP_DIR} +mkdir -p ${INSTALL_PREFIX} cd ${BUILD_TMP_DIR} -cmake -DINSTALL_TENSORFLOW=TRUE ../api_cc/tests +cmake -DINSTALL_TENSORFLOW=TRUE -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} ../api_cc/tests make -j${NPROC} #------------------ From 1e0f71db172b9a525b4330bae7675fccc0a157e9 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 10 Mar 2021 06:04:46 -0500 Subject: [PATCH 11/15] change the directory of version.h --- source/api_cc/tests/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/api_cc/tests/CMakeLists.txt b/source/api_cc/tests/CMakeLists.txt index 6015c00166..aedb5b0f20 100644 --- a/source/api_cc/tests/CMakeLists.txt +++ b/source/api_cc/tests/CMakeLists.txt @@ -28,7 +28,7 @@ file(GLOB API_SRC ${API_BASE_DIR}/src/*.cc ${API_BASE_DIR}/src/*.cpp) add_library(${apiname} SHARED ${API_SRC}) configure_file( ${API_BASE_DIR}/include/version.h.in - version.h + ${CMAKE_SOURCE_DIR}/version.h @ONLY ) From e2f92c11eff368f17e315ebeede3b7dbefd2c077 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 22:45:11 +0800 Subject: [PATCH 12/15] clean up model devi, add unittests --- source/api_cc/include/NNPInter.h | 175 ++-- source/api_cc/src/NNPInter.cc | 884 +++++++++--------- .../api_cc/tests/test_deeppot_model_devi.cc | 160 ++++ source/lmp/fix_dplr.cpp | 4 +- source/lmp/fix_dplr.h | 2 +- source/lmp/pair_nnp.cpp | 6 +- source/tests/infer/deeppot-1.pbtxt | 12 +- 7 files changed, 694 insertions(+), 549 deletions(-) create mode 100644 source/api_cc/tests/test_deeppot_model_devi.cc diff --git a/source/api_cc/include/NNPInter.h b/source/api_cc/include/NNPInter.h index da89cdc0cd..2586bfd89e 100644 --- a/source/api_cc/include/NNPInter.h +++ b/source/api_cc/include/NNPInter.h @@ -92,106 +92,95 @@ class NNPInter std::vector sec_a; compute_t *array_double; NeighborListData nlist_data; + InputNlist nlist; NNPAtomMap nnpmap; - int *ilist, *jrange, *jlist; - int ilist_size, jrange_size, jlist_size; // function used for neighbor list copy std::vector get_sel_a() const; }; -// class NNPInterModelDevi -// { -// public: -// NNPInterModelDevi () ; -// ~NNPInterModelDevi() ; -// NNPInterModelDevi (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); -// void init (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); -// public: -// void compute (ENERGYTYPE & ener, -// std::vector & force, -// std::vector & virial, -// std::vector & model_devi, -// const std::vector & coord, -// const std::vector & atype, -// const std::vector & box, -// const std::vector & fparam = std::vector(), -// const std::vector & aparam = std::vector()); -// void compute (std::vector & all_ener, -// std::vector > & all_force, -// std::vector > & all_virial, -// const std::vector & coord, -// const std::vector & atype, -// const std::vector & box, -// const int nghost, -// const LammpsNeighborList & lmp_list, -// const int & ago, -// const std::vector & fparam = std::vector(), -// const std::vector & aparam = std::vector()); -// void compute (std::vector & all_ener, -// std::vector > & all_force, -// std::vector > & all_virial, -// std::vector > & all_atom_energy, -// std::vector > & all_atom_virial, -// const std::vector & coord, -// const std::vector & atype, -// const std::vector & box, -// const int nghost, -// const LammpsNeighborList & lmp_list, -// const int & ago, -// const std::vector & fparam = std::vector(), -// const std::vector & aparam = std::vector()); -// VALUETYPE cutoff () const {assert(inited); return rcut;}; -// int numb_types () const {assert(inited); return ntypes;}; -// int dim_fparam () const {assert(inited); return dfparam;}; -// int dim_aparam () const {assert(inited); return daparam;}; -// #ifndef HIGH_PREC -// void compute_avg (ENERGYTYPE & dener, -// const std::vector & all_energy); -// #endif -// void compute_avg (VALUETYPE & dener, -// const std::vector & all_energy); -// void compute_avg (std::vector & avg, -// const std::vector > & xx); -// void compute_std_e (std::vector & std, -// const std::vector & avg, -// const std::vector >& xx); -// void compute_std_f (std::vector & std, -// const std::vector & avg, -// const std::vector >& xx); -// void compute_relative_std_f (std::vector & std, -// const std::vector & avg, -// const VALUETYPE eps); -// private: -// unsigned numb_models; -// std::vector sessions; -// int num_intra_nthreads, num_inter_nthreads; -// std::vector graph_defs; -// bool inited; -// template VT get_scalar(const std::string name) const; -// // VALUETYPE get_rcut () const; -// // int get_ntypes () const; -// VALUETYPE rcut; -// VALUETYPE cell_size; -// int ntypes; -// int dfparam; -// int daparam; -// void validate_fparam_aparam(const int & nloc, -// const std::vector &fparam, -// const std::vector &aparam)const ; +class NNPInterModelDevi +{ +public: + NNPInterModelDevi () ; + ~NNPInterModelDevi() ; + NNPInterModelDevi (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); + void init (const std::vector & models, const int & gpu_rank = 0, const std::vector & file_contents = std::vector()); +public: + void compute (std::vector & all_ener, + std::vector > & all_force, + std::vector > & all_virial, + const std::vector & coord, + const std::vector & atype, + const std::vector & box, + const int nghost, + const InputNlist & lmp_list, + const int & ago, + const std::vector & fparam = std::vector(), + const std::vector & aparam = std::vector()); + void compute (std::vector & all_ener, + std::vector > & all_force, + std::vector > & all_virial, + std::vector > & all_atom_energy, + std::vector > & all_atom_virial, + const std::vector & coord, + const std::vector & atype, + const std::vector & box, + const int nghost, + const InputNlist & lmp_list, + const int & ago, + const std::vector & fparam = std::vector(), + const std::vector & aparam = std::vector()); + VALUETYPE cutoff () const {assert(inited); return rcut;}; + int numb_types () const {assert(inited); return ntypes;}; + int dim_fparam () const {assert(inited); return dfparam;}; + int dim_aparam () const {assert(inited); return daparam;}; +#ifndef HIGH_PREC + void compute_avg (ENERGYTYPE & dener, + const std::vector & all_energy); +#endif + void compute_avg (VALUETYPE & dener, + const std::vector & all_energy); + void compute_avg (std::vector & avg, + const std::vector > & xx); + void compute_std_e (std::vector & std, + const std::vector & avg, + const std::vector >& xx); + void compute_std_f (std::vector & std, + const std::vector & avg, + const std::vector >& xx); + void compute_relative_std_f (std::vector & std, + const std::vector & avg, + const VALUETYPE eps); +private: + unsigned numb_models; + std::vector sessions; + int num_intra_nthreads, num_inter_nthreads; + std::vector graph_defs; + bool inited; + template VT get_scalar(const std::string name) const; + // VALUETYPE get_rcut () const; + // int get_ntypes () const; + VALUETYPE rcut; + VALUETYPE cell_size; + int ntypes; + int dfparam; + int daparam; + void validate_fparam_aparam(const int & nloc, + const std::vector &fparam, + const std::vector &aparam)const ; -// // copy neighbor list info from host -// bool init_nbor; -// compute_t *array_double; -// std::vector > sec; -// InternalNeighborList nlist; -// NNPAtomMap nnpmap; -// int *ilist, *jrange, *jlist; -// int ilist_size, jrange_size, jlist_size; + // copy neighbor list info from host + bool init_nbor; + compute_t *array_double; + std::vector > sec; + NNPAtomMap nnpmap; + NeighborListData nlist_data; + InputNlist nlist; -// // function used for nborlist copy -// std::vector > get_sel() const; -// void cum_sum(const std::vector > n_sel); -// }; + // function used for nborlist copy + std::vector > get_sel() const; + void cum_sum(const std::vector > n_sel); +}; diff --git a/source/api_cc/src/NNPInter.cc b/source/api_cc/src/NNPInter.cc index cfb17a314c..55686bde81 100644 --- a/source/api_cc/src/NNPInter.cc +++ b/source/api_cc/src/NNPInter.cc @@ -173,12 +173,14 @@ NNPInter:: NNPInter () : inited (false), init_nbor (false) { + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); } NNPInter:: NNPInter (const std::string & model, const int & gpu_rank, const std::string & file_content) : inited (false), init_nbor (false) { + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); init(model, gpu_rank, file_content); } @@ -226,8 +228,6 @@ init (const std::string & model, const int & gpu_rank, const std::string & file_ inited = true; init_nbor = false; - ilist = NULL; jrange = NULL; jlist = NULL; - ilist_size = 0; jrange_size = 0; jlist_size = 0; } void @@ -346,7 +346,7 @@ compute (ENERGYTYPE & dener, const std::vector & datype_, const std::vector & dbox, const int nghost, - const InputNlist & inlist, + const InputNlist & lmp_list, const int& ago, const std::vector & fparam, const std::vector & aparam_) @@ -368,7 +368,7 @@ compute (ENERGYTYPE & dener, } // internal nlist if (ago == 0){ - nlist_data.copy_from_nlist(inlist); + nlist_data.copy_from_nlist(lmp_list); nlist_data.shuffle_exclude_empty(fwd_map); } compute_inner(dener, dforce, dvirial, dcoord, datype, dbox, nghost_real, ago, fparam, aparam); @@ -401,10 +401,9 @@ compute_inner (ENERGYTYPE & dener, nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); assert (nloc == nnpmap.get_type().size()); nlist_data.shuffle(nnpmap); + nlist_data.make_inlist(nlist); } - InputNlist inlist; - nlist_data.make_inlist(inlist); - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, inlist, fparam, aparam, nnpmap, nghost, ago); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); assert (nloc == ret); run_model (dener, dforce_, dvirial, session, input_tensors, nnpmap, nghost); } @@ -445,7 +444,7 @@ compute (ENERGYTYPE & dener, const std::vector & datype_, const std::vector & dbox, const int nghost, - const InputNlist & nlist, + const InputNlist & lmp_list, const int & ago, const std::vector & fparam, const std::vector & aparam) @@ -458,14 +457,13 @@ compute (ENERGYTYPE & dener, if (ago == 0) { nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); assert (nloc == nnpmap.get_type().size()); - // make internal nlist data - nlist_data.copy_from_nlist(nlist); + + nlist_data.copy_from_nlist(lmp_list); nlist_data.shuffle(nnpmap); + nlist_data.make_inlist(nlist); } - InputNlist inlist; - nlist_data.make_inlist(inlist); - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, inlist, fparam, aparam, nnpmap, nghost, ago); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); assert (nloc == ret); run_model (dener, dforce_, dvirial, datom_energy_, datom_virial_, session, input_tensors, nnpmap, nghost); } @@ -478,448 +476,446 @@ get_type_map(std::string & type_map){ -// // NNPInterModelDevi:: -// // NNPInterModelDevi () -// // : inited (false), -// // init_nbor (false), -// // numb_models (0) -// // { -// // get_env_nthreads(num_intra_nthreads, num_inter_nthreads); -// // } - -// // NNPInterModelDevi:: -// // NNPInterModelDevi (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) -// // : inited (false), -// // init_nbor(false), -// // numb_models (0) -// // { -// // get_env_nthreads(num_intra_nthreads, num_inter_nthreads); -// // init(models, gpu_rank, file_contents); -// // } - -// // NNPInterModelDevi::~NNPInterModelDevi() {} - -// // void -// // NNPInterModelDevi:: -// // init (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) -// // { -// // if (inited){ -// // std::cerr << "WARNING: deepmd-kit should not be initialized twice, do nothing at the second call of initializer" << std::endl; -// // return ; -// // } -// // numb_models = models.size(); -// // sessions.resize(numb_models); -// // graph_defs.resize(numb_models); - -// // int gpu_num = -1; -// // #if GOOGLE_CUDA -// // cudaGetDeviceCount(&gpu_num); -// // #endif // GOOGLE_CUDA - -// // SessionOptions options; -// // options.config.set_inter_op_parallelism_threads(num_inter_nthreads); -// // options.config.set_intra_op_parallelism_threads(num_intra_nthreads); -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // if (file_contents.size() == 0) -// // checkStatus (ReadBinaryProto(Env::Default(), models[ii], &graph_defs[ii])); -// // else -// // graph_defs[ii].ParseFromString(file_contents[ii]); -// // } -// // #if GOOGLE_CUDA -// // if (gpu_num > 0) { -// // options.config.set_allow_soft_placement(true); -// // options.config.mutable_gpu_options()->set_per_process_gpu_memory_fraction(0.9); -// // options.config.mutable_gpu_options()->set_allow_growth(true); -// // cudaErrcheck(cudaSetDevice(gpu_rank % gpu_num)); -// // } -// // #endif // GOOGLE_CUDA - -// // for (unsigned ii = 0; ii < numb_models; ++ii) { -// // if (gpu_num > 0) { -// // std::string str = "/gpu:"; -// // str += std::to_string(gpu_rank % gpu_num); -// // graph::SetDefaultDevice(str, &graph_defs[ii]); -// // } -// // checkStatus (NewSession(options, &(sessions[ii]))); -// // checkStatus (sessions[ii]->Create(graph_defs[ii])); -// // } -// // rcut = get_scalar("descrpt_attr/rcut"); -// // cell_size = rcut; -// // ntypes = get_scalar("descrpt_attr/ntypes"); -// // dfparam = get_scalar("fitting_attr/dfparam"); -// // daparam = get_scalar("fitting_attr/daparam"); -// // if (dfparam < 0) dfparam = 0; -// // if (daparam < 0) daparam = 0; -// // // rcut = get_rcut(); -// // // cell_size = rcut; -// // // ntypes = get_ntypes(); -// // inited = true; - -// // init_nbor = false; -// // ilist = NULL; jrange = NULL; jlist = NULL; -// // ilist_size = 0; jrange_size = 0; jlist_size = 0; -// // } - -// // template -// // VT -// // NNPInterModelDevi:: -// // get_scalar(const std::string name) const -// // { -// // VT myrcut = 0; -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // VT ret = session_get_scalar(sessions[ii], name); -// // if (ii == 0){ -// // myrcut = ret; -// // } -// // else { -// // assert (myrcut == ret); -// // } -// // } -// // return myrcut; -// // } - -// // // init the tmp array data -// // std::vector > -// // NNPInterModelDevi:: -// // get_sel () const -// // { -// // std::vector > sec; -// // for (int ii = 0; ii < numb_models; ii++) { -// // std::vector sel; -// // std::istringstream is(graph_info(graph_defs[ii])); -// // std::string line = ""; -// // while(is >> line) { -// // if (line.find("sel") != line.npos) { -// // while (std::getline(is, line) && line != "}") { -// // if (line.find("i:") != line.npos) { -// // sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); -// // } -// // } break; -// // } -// // if (line.find("sel_a") != line.npos) { -// // while (std::getline(is, line) && line != "}") { -// // if (line.find("i:") != line.npos) { -// // sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); -// // } -// // } break; -// // } -// // } -// // sec.push_back(sel); -// // } -// // return sec; -// // } - -// // void -// // NNPInterModelDevi:: -// // cum_sum (const std::vector > n_sel) -// // { -// // for (int ii = 0; ii < numb_models; ++ii) { -// // std::vector _sec; -// // _sec.resize (n_sel[ii].size() + 1); -// // _sec[0] = 0; -// // for (int jj = 1; jj < _sec.size(); ++jj) { -// // _sec[jj] = _sec[jj-1] + n_sel[ii][jj-1]; -// // } -// // sec.push_back(_sec); -// // } -// // } - -// // void -// // NNPInterModelDevi:: -// // validate_fparam_aparam(const int & nloc, -// // const std::vector &fparam, -// // const std::vector &aparam)const -// // { -// // if (fparam.size() != dfparam) { -// // throw std::runtime_error("the dim of frame parameter provided is not consistent with what the model uses"); -// // } -// // if (aparam.size() != daparam * nloc) { -// // throw std::runtime_error("the dim of atom parameter provided is not consistent with what the model uses"); -// // } -// // } - -// // void -// // NNPInterModelDevi:: -// // compute (ENERGYTYPE & dener, -// // std::vector & dforce_, -// // std::vector & dvirial, -// // std::vector & model_devi, -// // const std::vector & dcoord_, -// // const std::vector & datype_, -// // const std::vector & dbox, -// // const std::vector & fparam, -// // const std::vector & aparam) -// // { -// // if (numb_models == 0) return; - -// // nnpmap = NNPAtomMap (datype_.begin(), datype_.end()); -// // validate_fparam_aparam(nnpmap.get_type().size(), fparam, aparam); - -// // std::vector> input_tensors; -// // int nloc = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, fparam, aparam, nnpmap); - -// // std::vector all_energy (numb_models); -// // std::vector > all_force (numb_models); -// // std::vector > all_virial (numb_models); - -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap); -// // } - -// // dener = 0; -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // dener += all_energy[ii]; -// // } -// // dener /= VALUETYPE(numb_models); -// // compute_avg (dvirial, all_virial); -// // compute_avg (dforce_, all_force); - -// // compute_std_f (model_devi, dforce_, all_force); - -// // // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // // cout << all_force[ii][573] << " " << all_force[ii][574] << " " << all_force[ii][575] << endl; -// // // } -// // // cout << dforce_[573] << " " -// // // << dforce_[574] << " " -// // // << dforce_[575] << " " -// // // << model_devi[191] << endl; -// // } - -// // void -// // NNPInterModelDevi:: -// // compute (std::vector & all_energy, -// // std::vector> & all_force, -// // std::vector> & all_virial, -// // const std::vector & dcoord_, -// // const std::vector & datype_, -// // const std::vector & dbox, -// // const int nghost, -// // const LammpsNeighborList & lmp_list, -// // const int & ago, -// // const std::vector & fparam, -// // const std::vector & aparam) -// // { -// // if (numb_models == 0) return; -// // int nall = dcoord_.size() / 3; -// // int nloc = nall - nghost; -// // validate_fparam_aparam(nloc, fparam, aparam); -// // std::vector> input_tensors; - -// // // agp == 0 means that the LAMMPS nbor list has been updated -// // if (ago == 0) { -// // nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); -// // assert (nloc == nnpmap.get_type().size()); - -// // // InternalNeighborList nlist; -// // convert_nlist_lmp_internal (nlist, lmp_list); -// // shuffle_nlist (nlist, nnpmap); -// // } -// // int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); - -// // all_energy.resize (numb_models); -// // all_force.resize (numb_models); -// // all_virial.resize (numb_models); -// // assert (nloc == ret); -// // for (unsigned ii = 0; ii < numb_models; ++ii) { -// // run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); -// // } -// // } - -// // void -// // NNPInterModelDevi:: -// // compute (std::vector & all_energy, -// // std::vector> & all_force, -// // std::vector> & all_virial, -// // std::vector> & all_atom_energy, -// // std::vector> & all_atom_virial, -// // const std::vector & dcoord_, -// // const std::vector & datype_, -// // const std::vector & dbox, -// // const int nghost, -// // const LammpsNeighborList & lmp_list, -// // const int & ago, -// // const std::vector & fparam, -// // const std::vector & aparam) -// // { -// // if (numb_models == 0) return; -// // int nall = dcoord_.size() / 3; -// // int nloc = nall - nghost; -// // validate_fparam_aparam(nloc, fparam, aparam); -// // std::vector> input_tensors; - -// // // agp == 0 means that the LAMMPS nbor list has been updated -// // if (ago == 0) { -// // nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); -// // assert (nloc == nnpmap.get_type().size()); - -// // // InternalNeighborList nlist; -// // convert_nlist_lmp_internal (nlist, lmp_list); -// // shuffle_nlist (nlist, nnpmap); -// // } -// // int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); - -// // all_energy.resize (numb_models); -// // all_force .resize (numb_models); -// // all_virial.resize (numb_models); -// // all_atom_energy.resize (numb_models); -// // all_atom_virial.resize (numb_models); -// // assert (nloc == ret); -// // for (unsigned ii = 0; ii < numb_models; ++ii) { -// // run_model (all_energy[ii], all_force[ii], all_virial[ii], all_atom_energy[ii], all_atom_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); -// // } -// // } - -// // void -// // NNPInterModelDevi:: -// // compute_avg (VALUETYPE & dener, -// // const std::vector & all_energy) -// // { -// // assert (all_energy.size() == numb_models); -// // if (numb_models == 0) return; - -// // dener = 0; -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // dener += all_energy[ii]; -// // } -// // dener /= (VALUETYPE)(numb_models); -// // } - -// // #ifndef HIGH_PREC -// // void -// // NNPInterModelDevi:: -// // compute_avg (ENERGYTYPE & dener, -// // const std::vector& all_energy) -// // { -// // assert (all_energy.size() == numb_models); -// // if (numb_models == 0) return; - -// // dener = 0; -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // dener += all_energy[ii]; -// // } -// // dener /= (ENERGYTYPE)(numb_models); -// // } -// // #endif - -// // void -// // NNPInterModelDevi:: -// // compute_avg (std::vector & avg, -// // const std::vector > & xx) -// // { -// // assert (xx.size() == numb_models); -// // if (numb_models == 0) return; +NNPInterModelDevi:: +NNPInterModelDevi () + : inited (false), + init_nbor (false), + numb_models (0) +{ + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); +} + +NNPInterModelDevi:: +NNPInterModelDevi (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) + : inited (false), + init_nbor(false), + numb_models (0) +{ + get_env_nthreads(num_intra_nthreads, num_inter_nthreads); + init(models, gpu_rank, file_contents); +} + +NNPInterModelDevi::~NNPInterModelDevi() {} + +void +NNPInterModelDevi:: +init (const std::vector & models, const int & gpu_rank, const std::vector & file_contents) +{ + if (inited){ + std::cerr << "WARNING: deepmd-kit should not be initialized twice, do nothing at the second call of initializer" << std::endl; + return ; + } + numb_models = models.size(); + sessions.resize(numb_models); + graph_defs.resize(numb_models); -// // avg.resize(xx[0].size()); -// // fill (avg.begin(), avg.end(), VALUETYPE(0.)); + int gpu_num = -1; + #if GOOGLE_CUDA + cudaGetDeviceCount(&gpu_num); + #endif // GOOGLE_CUDA + + SessionOptions options; + options.config.set_inter_op_parallelism_threads(num_inter_nthreads); + options.config.set_intra_op_parallelism_threads(num_intra_nthreads); + for (unsigned ii = 0; ii < numb_models; ++ii){ + if (file_contents.size() == 0) + checkStatus (ReadBinaryProto(Env::Default(), models[ii], &graph_defs[ii])); + else + graph_defs[ii].ParseFromString(file_contents[ii]); + } + #if GOOGLE_CUDA + if (gpu_num > 0) { + options.config.set_allow_soft_placement(true); + options.config.mutable_gpu_options()->set_per_process_gpu_memory_fraction(0.9); + options.config.mutable_gpu_options()->set_allow_growth(true); + cudaErrcheck(cudaSetDevice(gpu_rank % gpu_num)); + } + #endif // GOOGLE_CUDA + + for (unsigned ii = 0; ii < numb_models; ++ii) { + if (gpu_num > 0) { + std::string str = "/gpu:"; + str += std::to_string(gpu_rank % gpu_num); + graph::SetDefaultDevice(str, &graph_defs[ii]); + } + checkStatus (NewSession(options, &(sessions[ii]))); + checkStatus (sessions[ii]->Create(graph_defs[ii])); + } + rcut = get_scalar("descrpt_attr/rcut"); + cell_size = rcut; + ntypes = get_scalar("descrpt_attr/ntypes"); + dfparam = get_scalar("fitting_attr/dfparam"); + daparam = get_scalar("fitting_attr/daparam"); + if (dfparam < 0) dfparam = 0; + if (daparam < 0) daparam = 0; + // rcut = get_rcut(); + // cell_size = rcut; + // ntypes = get_ntypes(); + inited = true; -// // for (unsigned ii = 0; ii < numb_models; ++ii){ -// // for (unsigned jj = 0; jj < avg.size(); ++jj){ -// // avg[jj] += xx[ii][jj]; -// // } -// // } - -// // for (unsigned jj = 0; jj < avg.size(); ++jj){ -// // avg[jj] /= VALUETYPE(numb_models); -// // } -// // } - - -// // // void -// // // NNPInterModelDevi:: -// // // compute_std (VALUETYPE & std, -// // // const VALUETYPE & avg, -// // // const vector& xx) -// // // { -// // // std = 0; -// // // assert(xx.size() == numb_models); -// // // for (unsigned jj = 0; jj < xx.size(); ++jj){ -// // // std += (xx[jj] - avg) * (xx[jj] - avg); -// // // } -// // // std = sqrt(std / VALUETYPE(numb_models)); -// // // // std = sqrt(std / VALUETYPE(numb_models-)); -// // // } - -// // void -// // NNPInterModelDevi:: -// // compute_std_e (std::vector & std, -// // const std::vector & avg, -// // const std::vector >&xx) -// // { -// // assert (xx.size() == numb_models); -// // if (numb_models == 0) return; - -// // unsigned ndof = avg.size(); -// // unsigned nloc = ndof; -// // assert (nloc == ndof); + init_nbor = false; +} + +template +VT +NNPInterModelDevi:: +get_scalar(const std::string name) const +{ + VT myrcut = 0; + for (unsigned ii = 0; ii < numb_models; ++ii){ + VT ret = session_get_scalar(sessions[ii], name); + if (ii == 0){ + myrcut = ret; + } + else { + assert (myrcut == ret); + } + } + return myrcut; +} + +// init the tmp array data +std::vector > +NNPInterModelDevi:: +get_sel () const +{ + std::vector > sec; + for (int ii = 0; ii < numb_models; ii++) { + std::vector sel; + std::istringstream is(graph_info(graph_defs[ii])); + std::string line = ""; + while(is >> line) { + if (line.find("sel") != line.npos) { + while (std::getline(is, line) && line != "}") { + if (line.find("i:") != line.npos) { + sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); + } + } break; + } + if (line.find("sel_a") != line.npos) { + while (std::getline(is, line) && line != "}") { + if (line.find("i:") != line.npos) { + sel.push_back(atoi((line.substr(line.find("i:") + 2)).c_str())); + } + } break; + } + } + sec.push_back(sel); + } + return sec; +} + +void +NNPInterModelDevi:: +cum_sum (const std::vector > n_sel) +{ + for (int ii = 0; ii < numb_models; ++ii) { + std::vector _sec; + _sec.resize (n_sel[ii].size() + 1); + _sec[0] = 0; + for (int jj = 1; jj < _sec.size(); ++jj) { + _sec[jj] = _sec[jj-1] + n_sel[ii][jj-1]; + } + sec.push_back(_sec); + } +} + +void +NNPInterModelDevi:: +validate_fparam_aparam(const int & nloc, + const std::vector &fparam, + const std::vector &aparam)const +{ + if (fparam.size() != dfparam) { + throw std::runtime_error("the dim of frame parameter provided is not consistent with what the model uses"); + } + if (aparam.size() != daparam * nloc) { + throw std::runtime_error("the dim of atom parameter provided is not consistent with what the model uses"); + } +} + +// void +// NNPInterModelDevi:: +// compute (ENERGYTYPE & dener, +// std::vector & dforce_, +// std::vector & dvirial, +// std::vector & model_devi, +// const std::vector & dcoord_, +// const std::vector & datype_, +// const std::vector & dbox, +// const std::vector & fparam, +// const std::vector & aparam) +// { +// if (numb_models == 0) return; + +// nnpmap = NNPAtomMap (datype_.begin(), datype_.end()); +// validate_fparam_aparam(nnpmap.get_type().size(), fparam, aparam); + +// std::vector> input_tensors; +// int nloc = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, cell_size, fparam, aparam, nnpmap); + +// std::vector all_energy (numb_models); +// std::vector > all_force (numb_models); +// std::vector > all_virial (numb_models); + +// for (unsigned ii = 0; ii < numb_models; ++ii){ +// run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap); +// } + +// dener = 0; +// for (unsigned ii = 0; ii < numb_models; ++ii){ +// dener += all_energy[ii]; +// } +// dener /= VALUETYPE(numb_models); +// compute_avg (dvirial, all_virial); +// compute_avg (dforce_, all_force); -// // std.resize(nloc); -// // fill (std.begin(), std.end(), VALUETYPE(0.)); +// compute_std_f (model_devi, dforce_, all_force); -// // for (unsigned ii = 0; ii < numb_models; ++ii) { -// // for (unsigned jj = 0 ; jj < nloc; ++jj){ -// // const VALUETYPE * tmp_f = &(xx[ii][jj]); -// // const VALUETYPE * tmp_avg = &(avg[jj]); -// // VALUETYPE vdiff = xx[ii][jj] - avg[jj]; -// // std[jj] += vdiff * vdiff; -// // } -// // } - -// // for (unsigned jj = 0; jj < nloc; ++jj){ -// // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); -// // // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); -// // } -// // } - -// // void -// // NNPInterModelDevi:: -// // compute_std_f (std::vector & std, -// // const std::vector & avg, -// // const std::vector >&xx) -// // { -// // assert (xx.size() == numb_models); -// // if (numb_models == 0) return; - -// // unsigned ndof = avg.size(); -// // unsigned nloc = ndof / 3; -// // assert (nloc * 3 == ndof); +// // for (unsigned ii = 0; ii < numb_models; ++ii){ +// // cout << all_force[ii][573] << " " << all_force[ii][574] << " " << all_force[ii][575] << endl; +// // } +// // cout << dforce_[573] << " " +// // << dforce_[574] << " " +// // << dforce_[575] << " " +// // << model_devi[191] << endl; +// } + +void +NNPInterModelDevi:: +compute (std::vector & all_energy, + std::vector> & all_force, + std::vector> & all_virial, + const std::vector & dcoord_, + const std::vector & datype_, + const std::vector & dbox, + const int nghost, + const InputNlist & lmp_list, + const int & ago, + const std::vector & fparam, + const std::vector & aparam) +{ + if (numb_models == 0) return; + int nall = dcoord_.size() / 3; + int nloc = nall - nghost; + validate_fparam_aparam(nloc, fparam, aparam); + std::vector> input_tensors; + + // agp == 0 means that the LAMMPS nbor list has been updated + if (ago == 0) { + nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); + assert (nloc == nnpmap.get_type().size()); + + nlist_data.copy_from_nlist(lmp_list); + nlist_data.shuffle(nnpmap); + nlist_data.make_inlist(nlist); + } + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); + + all_energy.resize (numb_models); + all_force.resize (numb_models); + all_virial.resize (numb_models); + assert (nloc == ret); + for (unsigned ii = 0; ii < numb_models; ++ii) { + run_model (all_energy[ii], all_force[ii], all_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); + } +} + +void +NNPInterModelDevi:: +compute (std::vector & all_energy, + std::vector> & all_force, + std::vector> & all_virial, + std::vector> & all_atom_energy, + std::vector> & all_atom_virial, + const std::vector & dcoord_, + const std::vector & datype_, + const std::vector & dbox, + const int nghost, + const InputNlist & lmp_list, + const int & ago, + const std::vector & fparam, + const std::vector & aparam) +{ + if (numb_models == 0) return; + int nall = dcoord_.size() / 3; + int nloc = nall - nghost; + validate_fparam_aparam(nloc, fparam, aparam); + std::vector> input_tensors; + + // agp == 0 means that the LAMMPS nbor list has been updated + if (ago == 0) { + nnpmap = NNPAtomMap (datype_.begin(), datype_.begin() + nloc); + assert (nloc == nnpmap.get_type().size()); + + nlist_data.copy_from_nlist(lmp_list); + nlist_data.shuffle(nnpmap); + nlist_data.make_inlist(nlist); + } + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, fparam, aparam, nnpmap, nghost, ago); + + all_energy.resize (numb_models); + all_force .resize (numb_models); + all_virial.resize (numb_models); + all_atom_energy.resize (numb_models); + all_atom_virial.resize (numb_models); + assert (nloc == ret); + for (unsigned ii = 0; ii < numb_models; ++ii) { + run_model (all_energy[ii], all_force[ii], all_virial[ii], all_atom_energy[ii], all_atom_virial[ii], sessions[ii], input_tensors, nnpmap, nghost); + } +} + +void +NNPInterModelDevi:: +compute_avg (VALUETYPE & dener, + const std::vector & all_energy) +{ + assert (all_energy.size() == numb_models); + if (numb_models == 0) return; + + dener = 0; + for (unsigned ii = 0; ii < numb_models; ++ii){ + dener += all_energy[ii]; + } + dener /= (VALUETYPE)(numb_models); +} + +#ifndef HIGH_PREC +void +NNPInterModelDevi:: +compute_avg (ENERGYTYPE & dener, + const std::vector& all_energy) +{ + assert (all_energy.size() == numb_models); + if (numb_models == 0) return; + + dener = 0; + for (unsigned ii = 0; ii < numb_models; ++ii){ + dener += all_energy[ii]; + } + dener /= (ENERGYTYPE)(numb_models); +} +#endif + +void +NNPInterModelDevi:: +compute_avg (std::vector & avg, + const std::vector > & xx) +{ + assert (xx.size() == numb_models); + if (numb_models == 0) return; -// // std.resize(nloc); -// // fill (std.begin(), std.end(), VALUETYPE(0.)); + avg.resize(xx[0].size()); + fill (avg.begin(), avg.end(), VALUETYPE(0.)); -// // for (unsigned ii = 0; ii < numb_models; ++ii) { -// for (unsigned jj = 0 ; jj < nloc; ++jj){ -// const VALUETYPE * tmp_f = &(xx[ii][jj*3]); -// const VALUETYPE * tmp_avg = &(avg[jj*3]); -// VALUETYPE vdiff[3]; -// vdiff[0] = tmp_f[0] - tmp_avg[0]; -// vdiff[1] = tmp_f[1] - tmp_avg[1]; -// vdiff[2] = tmp_f[2] - tmp_avg[2]; -// std[jj] += dot3(vdiff, vdiff); -// } -// } + for (unsigned ii = 0; ii < numb_models; ++ii){ + for (unsigned jj = 0; jj < avg.size(); ++jj){ + avg[jj] += xx[ii][jj]; + } + } + + for (unsigned jj = 0; jj < avg.size(); ++jj){ + avg[jj] /= VALUETYPE(numb_models); + } +} -// for (unsigned jj = 0; jj < nloc; ++jj){ -// std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); -// // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); -// } -// } // void // NNPInterModelDevi:: -// compute_relative_std_f (std::vector &std, -// const std::vector &avg, -// const VALUETYPE eps) +// compute_std (VALUETYPE & std, +// const VALUETYPE & avg, +// const vector& xx) // { -// unsigned nloc = std.size(); -// for (unsigned ii = 0; ii < nloc; ++ii){ -// const VALUETYPE * tmp_avg = &(avg[ii*3]); -// VALUETYPE vdiff[3]; -// vdiff[0] = tmp_avg[0]; -// vdiff[1] = tmp_avg[1]; -// vdiff[2] = tmp_avg[2]; -// VALUETYPE f_norm = sqrt(dot3(vdiff, vdiff)); -// // relative std = std/(abs(f)+eps) -// std[ii] /= f_norm + eps; +// std = 0; +// assert(xx.size() == numb_models); +// for (unsigned jj = 0; jj < xx.size(); ++jj){ +// std += (xx[jj] - avg) * (xx[jj] - avg); // } +// std = sqrt(std / VALUETYPE(numb_models)); +// // std = sqrt(std / VALUETYPE(numb_models-)); // } +void +NNPInterModelDevi:: +compute_std_e (std::vector & std, + const std::vector & avg, + const std::vector >&xx) +{ + assert (xx.size() == numb_models); + if (numb_models == 0) return; + + unsigned ndof = avg.size(); + unsigned nloc = ndof; + assert (nloc == ndof); + + std.resize(nloc); + fill (std.begin(), std.end(), VALUETYPE(0.)); + + for (unsigned ii = 0; ii < numb_models; ++ii) { + for (unsigned jj = 0 ; jj < nloc; ++jj){ + const VALUETYPE * tmp_f = &(xx[ii][jj]); + const VALUETYPE * tmp_avg = &(avg[jj]); + VALUETYPE vdiff = xx[ii][jj] - avg[jj]; + std[jj] += vdiff * vdiff; + } + } + + for (unsigned jj = 0; jj < nloc; ++jj){ + std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); + // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); + } +} + +void +NNPInterModelDevi:: +compute_std_f (std::vector & std, + const std::vector & avg, + const std::vector >&xx) +{ + assert (xx.size() == numb_models); + if (numb_models == 0) return; + + unsigned ndof = avg.size(); + unsigned nloc = ndof / 3; + assert (nloc * 3 == ndof); + + std.resize(nloc); + fill (std.begin(), std.end(), VALUETYPE(0.)); + + for (unsigned ii = 0; ii < numb_models; ++ii) { + for (unsigned jj = 0 ; jj < nloc; ++jj){ + const VALUETYPE * tmp_f = &(xx[ii][jj*3]); + const VALUETYPE * tmp_avg = &(avg[jj*3]); + VALUETYPE vdiff[3]; + vdiff[0] = tmp_f[0] - tmp_avg[0]; + vdiff[1] = tmp_f[1] - tmp_avg[1]; + vdiff[2] = tmp_f[2] - tmp_avg[2]; + std[jj] += dot3(vdiff, vdiff); + } + } + + for (unsigned jj = 0; jj < nloc; ++jj){ + std[jj] = sqrt(std[jj] / VALUETYPE(numb_models)); + // std[jj] = sqrt(std[jj] / VALUETYPE(numb_models-1)); + } +} + +void +NNPInterModelDevi:: +compute_relative_std_f (std::vector &std, + const std::vector &avg, + const VALUETYPE eps) +{ + unsigned nloc = std.size(); + for (unsigned ii = 0; ii < nloc; ++ii){ + const VALUETYPE * tmp_avg = &(avg[ii*3]); + VALUETYPE vdiff[3]; + vdiff[0] = tmp_avg[0]; + vdiff[1] = tmp_avg[1]; + vdiff[2] = tmp_avg[2]; + VALUETYPE f_norm = sqrt(dot3(vdiff, vdiff)); + // relative std = std/(abs(f)+eps) + std[ii] /= f_norm + eps; + } +} + diff --git a/source/api_cc/tests/test_deeppot_model_devi.cc b/source/api_cc/tests/test_deeppot_model_devi.cc new file mode 100644 index 0000000000..a911bcd4d8 --- /dev/null +++ b/source/api_cc/tests/test_deeppot_model_devi.cc @@ -0,0 +1,160 @@ +#include +#include +#include +#include +#include +#include "NNPInter.h" +#include "SimulationRegion.h" +#include "neighbor_list.h" +#include "test_utils.h" + +#include "google/protobuf/text_format.h" +#include "google/protobuf/io/zero_copy_stream_impl.h" +#include +#include +#include + +class TestInferDeepPotModeDevi : public ::testing::Test +{ +protected: + std::vector coord = { + 12.83, 2.56, 2.18, + 12.09, 2.87, 2.74, + 00.25, 3.32, 1.68, + 3.36, 3.00, 1.81, + 3.51, 2.51, 2.60, + 4.27, 3.22, 1.56 + }; + std::vector atype = { + 0, 1, 1, 0, 1, 1 + }; + std::vector box = { + 13., 0., 0., 0., 13., 0., 0., 0., 13. + }; + int natoms; + + NNPInter dp0; + NNPInter dp1; + NNPInterModelDevi dp_md; + + void SetUp() override { + { + std::string file_name = "../../tests/infer/deeppot.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + std::fstream output("deeppot.pb", std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + dp0.init("deeppot.pb"); + } + { + std::string file_name = "../../tests/infer/deeppot-1.pbtxt"; + int fd = open(file_name.c_str(), O_RDONLY); + protobuf::io::ZeroCopyInputStream* input = new protobuf::io::FileInputStream(fd); + GraphDef graph_def; + protobuf::TextFormat::Parse(input, &graph_def); + delete input; + std::fstream output("deeppot-1.pb", std::ios::out | std::ios::trunc | std::ios::binary); + graph_def.SerializeToOstream(&output); + dp1.init("deeppot-1.pb"); + } + dp_md.init(std::vector({"deeppot.pb", "deeppot-1.pb"})); + }; + + void TearDown() override { + remove( "deeppot.pb" ) ; + //remove( "deeppot-1.pb" ) ; + }; +}; + +TEST_F(TestInferDeepPotModeDevi, attrs) +{ + EXPECT_EQ(dp0.cutoff(), dp_md.cutoff()); + EXPECT_EQ(dp0.numb_types(), dp_md.numb_types()); + EXPECT_EQ(dp0.dim_fparam(), dp_md.dim_fparam()); + EXPECT_EQ(dp0.dim_aparam(), dp_md.dim_aparam()); + EXPECT_EQ(dp1.cutoff(), dp_md.cutoff()); + EXPECT_EQ(dp1.numb_types(), dp_md.numb_types()); + EXPECT_EQ(dp1.dim_fparam(), dp_md.dim_fparam()); + EXPECT_EQ(dp1.dim_aparam(), dp_md.dim_aparam()); +} + + +TEST_F(TestInferDeepPotModeDevi, cpu_lmp_list) +{ + float rc = dp_md.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + int nmodel = 2; + std::vector edir(nmodel), emd; + std::vector > fdir_(nmodel), fdir(nmodel), vdir(nmodel), fmd_, fmd(nmodel), vmd; + dp0.compute(edir[0], fdir_[0], vdir[0], coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + dp1.compute(edir[1], fdir_[1], vdir[1], coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + dp_md.compute(emd, fmd_, vmd, coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + for(int kk = 0; kk < nmodel; ++kk){ + _fold_back(fdir[kk], fdir_[kk], mapping, nloc, nall, 3); + _fold_back(fmd[kk], fmd_[kk], mapping, nloc, nall, 3); + } + + + EXPECT_EQ(edir.size(), emd.size()); + EXPECT_EQ(fdir.size(), fmd.size()); + EXPECT_EQ(vdir.size(), vmd.size()); + for(int kk = 0; kk < nmodel; ++kk){ + EXPECT_EQ(fdir[kk].size(), fmd[kk].size()); + EXPECT_EQ(vdir[kk].size(), vmd[kk].size()); + } + for(int kk = 0; kk < nmodel; ++kk){ + EXPECT_LT(fabs(edir[kk] - emd[kk]), 1e-10); + for(int ii = 0; ii < fdir[0].size(); ++ii){ + EXPECT_LT(fabs(fdir[kk][ii] - fmd[kk][ii]), 1e-10); + } + for(int ii = 0; ii < vdir[0].size(); ++ii){ + EXPECT_LT(fabs(vdir[kk][ii] - vmd[kk][ii]), 1e-10); + } + } + + std::vector avg_f, std_f; + dp_md.compute_avg(avg_f, fmd); + dp_md.compute_std_f(std_f, avg_f, fmd); + + // manual compute std f + std::vector manual_std_f(nloc); + EXPECT_EQ(fmd[0].size(), nloc * 3); + for(int ii = 0; ii < nloc; ++ii){ + std::vector avg_f(3, 0.0); + for(int dd = 0; dd < 3; ++dd){ + for(int kk = 0; kk < nmodel; ++kk){ + avg_f[dd] += fmd[kk][ii*3+dd]; + } + avg_f[dd] /= (nmodel) * 1.0; + } + double std = 0.; + for(int kk = 0; kk < nmodel; ++kk){ + for(int dd = 0; dd < 3; ++dd){ + double tmp = fmd[kk][ii*3+dd] - avg_f[dd]; + std += tmp * tmp; + } + } + std /= nmodel * 1.0; + manual_std_f[ii] = sqrt(std); + } + + EXPECT_EQ(manual_std_f.size(), std_f.size()); + for(int ii = 0; ii < std_f.size(); ++ii){ + EXPECT_LT(fabs(manual_std_f[ii] - std_f[ii]), 1e-10); + } +} + diff --git a/source/lmp/fix_dplr.cpp b/source/lmp/fix_dplr.cpp index 03fef55420..637f36bda9 100644 --- a/source/lmp/fix_dplr.cpp +++ b/source/lmp/fix_dplr.cpp @@ -263,7 +263,7 @@ void FixDPLR::pre_force(int vflag) } // get lammps nlist NeighList * list = pair_nnp->list; - LammpsNeighborList lmp_list (list->inum, list->ilist, list->numneigh, list->firstneigh); + InputNlist lmp_list (list->inum, list->ilist, list->numneigh, list->firstneigh); // declear output vector tensor; // compute @@ -417,7 +417,7 @@ void FixDPLR::post_force(int vflag) } // lmp nlist NeighList * list = pair_nnp->list; - LammpsNeighborList lmp_list (list->inum, list->ilist, list->numneigh, list->firstneigh); + InputNlist lmp_list (list->inum, list->ilist, list->numneigh, list->firstneigh); // bonded pairs vector > valid_pairs; get_valid_pairs(valid_pairs); diff --git a/source/lmp/fix_dplr.h b/source/lmp/fix_dplr.h index e52215151c..a1bb7e1d60 100644 --- a/source/lmp/fix_dplr.h +++ b/source/lmp/fix_dplr.h @@ -37,7 +37,7 @@ namespace LAMMPS_NS { private: PairNNP * pair_nnp; DeepTensor dpt; - DataModifier dtm; + DipoleChargeModifier dtm; std::string model; int ntypes; std::vector sel_type; diff --git a/source/lmp/pair_nnp.cpp b/source/lmp/pair_nnp.cpp index fd2adb2729..401506df9f 100644 --- a/source/lmp/pair_nnp.cpp +++ b/source/lmp/pair_nnp.cpp @@ -360,7 +360,7 @@ void PairNNP::compute(int eflag, int vflag) multi_models_no_mod_devi = (numb_models > 1 && (out_freq == 0 || update->ntimestep % out_freq != 0)); multi_models_mod_devi = (numb_models > 1 && (out_freq > 0 && update->ntimestep % out_freq == 0)); if (do_ghost) { - LammpsNeighborList lmp_list (list->inum, list->ilist, list->numneigh, list->firstneigh); + InputNlist lmp_list (list->inum, list->ilist, list->numneigh, list->firstneigh); if (single_model || multi_models_no_mod_devi) { if ( ! (eflag_atom || vflag_atom) ) { #ifdef HIGH_PREC @@ -583,7 +583,7 @@ void PairNNP::compute(int eflag, int vflag) else { if (numb_models == 1) { #ifdef HIGH_PREC - nnp_inter.compute (dener, dforce, dvirial, dcoord, dtype, dbox, nghost); + nnp_inter.compute (dener, dforce, dvirial, dcoord, dtype, dbox); #else vector dcoord_(dcoord.size()); vector dbox_(dbox.size()); @@ -592,7 +592,7 @@ void PairNNP::compute(int eflag, int vflag) vector dforce_(dforce.size(), 0); vector dvirial_(dvirial.size(), 0); double dener_ = 0; - nnp_inter.compute (dener_, dforce_, dvirial_, dcoord_, dtype, dbox_, nghost); + nnp_inter.compute (dener_, dforce_, dvirial_, dcoord_, dtype, dbox_); for (unsigned dd = 0; dd < dforce.size(); ++dd) dforce[dd] = dforce_[dd]; for (unsigned dd = 0; dd < dvirial.size(); ++dd) dvirial[dd] = dvirial_[dd]; dener = dener_; diff --git a/source/tests/infer/deeppot-1.pbtxt b/source/tests/infer/deeppot-1.pbtxt index 4ad2deb6ff..3f8034de55 100644 --- a/source/tests/infer/deeppot-1.pbtxt +++ b/source/tests/infer/deeppot-1.pbtxt @@ -10515,8 +10515,8 @@ node { } } node { - name: "DescrptSeA" - op: "DescrptSeA" + name: "ProdEnvMatA" + op: "ProdEnvMatA" input: "Reshape_2" input: "Reshape_4" input: "t_natoms" @@ -10570,7 +10570,7 @@ node { node { name: "o_nlist" op: "Identity" - input: "DescrptSeA:3" + input: "ProdEnvMatA:3" attr { key: "T" value { @@ -10581,7 +10581,7 @@ node { node { name: "o_rij" op: "Identity" - input: "DescrptSeA:2" + input: "ProdEnvMatA:2" attr { key: "T" value { @@ -10592,7 +10592,7 @@ node { node { name: "o_rmat_deriv" op: "Identity" - input: "DescrptSeA:1" + input: "ProdEnvMatA:1" attr { key: "T" value { @@ -10603,7 +10603,7 @@ node { node { name: "Reshape_5" op: "Reshape" - input: "DescrptSeA" + input: "ProdEnvMatA" input: "Reshape_5/shape" attr { key: "T" From c3e950e80eb2a6e60fc78af846e1f1a4f0f1af9f Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 22:50:39 +0800 Subject: [PATCH 13/15] add UT for model devi in the atomic case --- .../api_cc/tests/test_deeppot_model_devi.cc | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/source/api_cc/tests/test_deeppot_model_devi.cc b/source/api_cc/tests/test_deeppot_model_devi.cc index a911bcd4d8..0c3d3103fe 100644 --- a/source/api_cc/tests/test_deeppot_model_devi.cc +++ b/source/api_cc/tests/test_deeppot_model_devi.cc @@ -158,3 +158,60 @@ TEST_F(TestInferDeepPotModeDevi, cpu_lmp_list) } } + +TEST_F(TestInferDeepPotModeDevi, cpu_lmp_list_atomic) +{ + float rc = dp_md.cutoff(); + int nloc = coord.size() / 3; + std::vector coord_cpy; + std::vector atype_cpy, mapping; + std::vector > nlist_data; + _build_nlist(nlist_data, coord_cpy, atype_cpy, mapping, + coord, atype, box, rc); + int nall = coord_cpy.size() / 3; + std::vector ilist(nloc), numneigh(nloc); + std::vector firstneigh(nloc); + InputNlist inlist(nloc, &ilist[0], &numneigh[0], &firstneigh[0]); + convert_nlist(inlist, nlist_data); + + int nmodel = 2; + std::vector edir(nmodel), emd; + std::vector > fdir_(nmodel), fdir(nmodel), vdir(nmodel), fmd_, fmd(nmodel), vmd, aedir(nmodel), aemd, avdir(nmodel), avdir_(nmodel), avmd(nmodel), avmd_; + dp0.compute(edir[0], fdir_[0], vdir[0], aedir[0], avdir_[0], coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + dp1.compute(edir[1], fdir_[1], vdir[1], aedir[1], avdir_[1], coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + dp_md.compute(emd, fmd_, vmd, aemd, avmd_, coord_cpy, atype_cpy, box, nall-nloc, inlist, 0); + for(int kk = 0; kk < nmodel; ++kk){ + _fold_back(fdir[kk], fdir_[kk], mapping, nloc, nall, 3); + _fold_back(fmd[kk], fmd_[kk], mapping, nloc, nall, 3); + _fold_back(avdir[kk], avdir_[kk], mapping, nloc, nall, 9); + _fold_back(avmd[kk], avmd_[kk], mapping, nloc, nall, 9); + } + + EXPECT_EQ(edir.size(), emd.size()); + EXPECT_EQ(fdir.size(), fmd.size()); + EXPECT_EQ(vdir.size(), vmd.size()); + EXPECT_EQ(aedir.size(), aemd.size()); + EXPECT_EQ(avdir.size(), avmd.size()); + for(int kk = 0; kk < nmodel; ++kk){ + EXPECT_EQ(fdir[kk].size(), fmd[kk].size()); + EXPECT_EQ(vdir[kk].size(), vmd[kk].size()); + EXPECT_EQ(aedir[kk].size(), aemd[kk].size()); + EXPECT_EQ(avdir[kk].size(), avmd[kk].size()); + } + for(int kk = 0; kk < nmodel; ++kk){ + EXPECT_LT(fabs(edir[kk] - emd[kk]), 1e-10); + for(int ii = 0; ii < fdir[0].size(); ++ii){ + EXPECT_LT(fabs(fdir[kk][ii] - fmd[kk][ii]), 1e-10); + } + for(int ii = 0; ii < vdir[0].size(); ++ii){ + EXPECT_LT(fabs(vdir[kk][ii] - vmd[kk][ii]), 1e-10); + } + for(int ii = 0; ii < aedir[0].size(); ++ii){ + EXPECT_LT(fabs(aedir[kk][ii] - aemd[kk][ii]), 1e-10); + } + for(int ii = 0; ii < avdir[0].size(); ++ii){ + EXPECT_LT(fabs(avdir[kk][ii] - avmd[kk][ii]), 1e-10); + } + } +} + From 0fa68a163c977186405ba575156d8d68946f8973 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 10 Mar 2021 22:59:45 +0800 Subject: [PATCH 14/15] fall back to some old name convention --- source/api_cc/src/DataModifier.cc | 10 +++++----- source/api_cc/src/DeepTensor.cc | 20 +++++++++---------- .../api_cc/tests/test_deeppot_model_devi.cc | 2 +- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/source/api_cc/src/DataModifier.cc b/source/api_cc/src/DataModifier.cc index 45ded50346..49e62be76c 100644 --- a/source/api_cc/src/DataModifier.cc +++ b/source/api_cc/src/DataModifier.cc @@ -125,7 +125,7 @@ compute (std::vector & dfcorr_, const std::vector>& pairs, const std::vector & delef_, const int nghost, - const InputNlist & nlist) + const InputNlist & lmp_list) { // firstly do selection int nall = datype_.size(); @@ -155,7 +155,7 @@ compute (std::vector & dfcorr_, select_map(datype_real, datype_, real_fwd_map, 1); // internal nlist NeighborListData nlist_data; - nlist_data.copy_from_nlist(nlist); + nlist_data.copy_from_nlist(lmp_list); nlist_data.shuffle_exclude_empty(real_fwd_map); // sort atoms NNPAtomMap nnpmap (datype_real.begin(), datype_real.begin() + nloc_real); @@ -164,11 +164,11 @@ compute (std::vector & dfcorr_, const std::vector & sort_bkw_map(nnpmap.get_bkw_map()); // shuffle nlist nlist_data.shuffle(nnpmap); - InputNlist inlist; - nlist_data.make_inlist(inlist); + InputNlist nlist; + nlist_data.make_inlist(nlist); // make input tensors std::vector> input_tensors; - int ret = session_input_tensors (input_tensors, dcoord_real, ntypes, datype_real, dbox, inlist, std::vector(), std::vector(), nnpmap, nghost_real, 0, name_scope); + int ret = session_input_tensors (input_tensors, dcoord_real, ntypes, datype_real, dbox, nlist, std::vector(), std::vector(), nnpmap, nghost_real, 0, name_scope); assert (nloc_real == ret); // make bond idx map std::vector bd_idx(nall, -1); diff --git a/source/api_cc/src/DeepTensor.cc b/source/api_cc/src/DeepTensor.cc index a26729d8ef..5a26b85a68 100644 --- a/source/api_cc/src/DeepTensor.cc +++ b/source/api_cc/src/DeepTensor.cc @@ -122,7 +122,7 @@ compute (std::vector & dtensor_, const std::vector & datype_, const std::vector & dbox, const int nghost, - const InputNlist & nlist) + const InputNlist & lmp_list) { std::vector dcoord; std::vector datype, fwd_map, bkw_map; @@ -136,11 +136,11 @@ compute (std::vector & dtensor_, select_map(datype, datype_, fwd_map, 1); // internal nlist NeighborListData nlist_data; - nlist_data.copy_from_nlist(nlist); + nlist_data.copy_from_nlist(lmp_list); nlist_data.shuffle_exclude_empty(fwd_map); - InputNlist inlist; - nlist_data.make_inlist(inlist); - compute_inner(dtensor_, dcoord, datype, dbox, nghost_real, inlist); + InputNlist nlist; + nlist_data.make_inlist(nlist); + compute_inner(dtensor_, dcoord, datype, dbox, nghost_real, nlist); } @@ -170,7 +170,7 @@ compute_inner (std::vector & dtensor_, const std::vector & datype_, const std::vector & dbox, const int nghost, - const InputNlist & nlist) + const InputNlist & nlist_) { int nall = dcoord_.size() / 3; int nloc = nall - nghost; @@ -178,13 +178,13 @@ compute_inner (std::vector & dtensor_, assert (nloc == nnpmap.get_type().size()); NeighborListData nlist_data; - nlist_data.copy_from_nlist(nlist); + nlist_data.copy_from_nlist(nlist_); nlist_data.shuffle(nnpmap); - InputNlist inlist; - nlist_data.make_inlist(inlist); + InputNlist nlist; + nlist_data.make_inlist(nlist); std::vector> input_tensors; - int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, inlist, std::vector(), std::vector(), nnpmap, nghost, 0, name_scope); + int ret = session_input_tensors (input_tensors, dcoord_, ntypes, datype_, dbox, nlist, std::vector(), std::vector(), nnpmap, nghost, 0, name_scope); assert (nloc == ret); run_model (dtensor_, session, input_tensors, nnpmap, nghost); diff --git a/source/api_cc/tests/test_deeppot_model_devi.cc b/source/api_cc/tests/test_deeppot_model_devi.cc index 0c3d3103fe..fced03d4eb 100644 --- a/source/api_cc/tests/test_deeppot_model_devi.cc +++ b/source/api_cc/tests/test_deeppot_model_devi.cc @@ -65,7 +65,7 @@ class TestInferDeepPotModeDevi : public ::testing::Test void TearDown() override { remove( "deeppot.pb" ) ; - //remove( "deeppot-1.pb" ) ; + remove( "deeppot-1.pb" ) ; }; }; From e30c7e5bc54f62f7fa2fbfcf4efcdfc0261f2106 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 10 Mar 2021 14:04:38 -0500 Subject: [PATCH 15/15] cd api_cc/tests --- source/install/test_cc.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/source/install/test_cc.sh b/source/install/test_cc.sh index 0c5333f41c..f28bff9e7b 100755 --- a/source/install/test_cc.sh +++ b/source/install/test_cc.sh @@ -28,5 +28,6 @@ cmake -DINSTALL_TENSORFLOW=TRUE -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} ../api_ make -j${NPROC} #------------------ +cd ${SCRIPT_PATH}/../api_cc/tests ${BUILD_TMP_DIR}/runUnitTests