Refactor SOGKSpace to inherit from KSpace and integrate FFT functionality

- Changed inheritance of SOGKSpace from PPPM to KSpace.
- Updated includes to replace "pppm.h" with "kspace.h".
- Added new private methods for FFT operations: compute_finufft, compute_mesh_fft, ensure_fft_plan, and destroy_fft_plan.
- Introduced new member variables for FFT mesh configuration and data storage.
- Removed unused variables related to n_dl_user_specified and n_dl_from_model.

Author: Johnsonjz

deepmd/lib

@@ -0,0 +1 @@
+/home/zyjin/anaconda3/envs/base_env/lib/python3.13/site-packages/deepmd/lib

log.lammps

@@ -1,88 +1,146 @@
 LAMMPS (22 Jul 2025 - Update 4)
-units           metal
-plugin          load /data/zyjin/dp_pt/dp_devel/deepmd-kit-devel/build/sog_lmp_stable/lmp/plugin/libdeepmd_lmp.so
-Loading plugin: deepmd pair style v3.1.3-83-g3cba3c7a-dirty by Han Wang
-Loading plugin: deepspin pair style v3.1.3-83-g3cba3c7a-dirty by Duo Zhang
-Loading plugin: compute deeptensor/atom v3.1.3-83-g3cba3c7a-dirty by Han Wang
-Loading plugin: fix dplr v3.1.3-83-g3cba3c7a-dirty by Han Wang
-Loading plugin: kspace pppm/dplr v3.1.3-83-g3cba3c7a-dirty by Han Wang
-Loading plugin: kspace les v3.1.3-83-g3cba3c7a-dirty by DeepMD contributors
-Loading plugin: kspace sog v3.1.3-83-g3cba3c7a-dirty by DeepMD contributors
-atom_style      charge
-region          box block 0 10 0 10 0 10
-create_box      1 box
-Created orthogonal box = (0 0 0) to (10 10 10)
+units metal
+plugin load /data/zyjin/dp_pt/dp_devel/deepmd-kit-devel/build/sog_lmp_cxxdbg/lmp/plugin/libdeepmd_lmp.so
+Loading plugin: deepmd pair style v3.1.3-86-g12e2fc71-dirty by Han Wang
+Loading plugin: deepspin pair style v3.1.3-86-g12e2fc71-dirty by Duo Zhang
+Loading plugin: compute deeptensor/atom v3.1.3-86-g12e2fc71-dirty by Han Wang
+Loading plugin: fix dplr v3.1.3-86-g12e2fc71-dirty by Han Wang
+Loading plugin: kspace pppm/dplr v3.1.3-86-g12e2fc71-dirty by Han Wang
+Loading plugin: kspace les v3.1.3-86-g12e2fc71-dirty by DeepMD contributors
+Loading plugin: kspace sog v3.1.3-86-g12e2fc71-dirty by DeepMD contributors
+atom_style charge
+boundary p p p
+read_data /data/zyjin/dp_pt/dp_example/au-mgo/lmp/progress_report_20260601/results/lammps_md_20260602/stable.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (9.0474307 9.0474307 26.458861)
   1 by 1 by 1 MPI processor grid
-create_atoms    1 single 5.0 5.0 5.0
-Created 1 atoms
-  using lattice units in orthogonal box = (0 0 0) to (10 10 10)
-  create_atoms CPU = 0.000 seconds
-mass            1 1.0
-set             atom 1 charge 0.1
-Setting atom values ...
-  1 settings made for charge
+  reading atoms ...
+  110 atoms
+  read_data CPU = 0.001 seconds
+mass 1 24.305
+mass 2 15.999
+mass 3 26.9815385
+mass 4 196.96657
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+thermo 20
+thermo_style custom step temp press pe ke etotal
+thermo_modify flush yes
+timestep 0.0005
+velocity all create 300.0 20260602 mom yes rot yes dist gaussian
+pair_style deepmd /tmp/sog_model_frozen_try.pth sog_sr yes
+Summary of lammps deepmd module ...
+  >>> Info of deepmd-kit:
+  installed to:       /usr/local
+  source:             v3.1.3-86-g12e2fc71-dirty
+  source branch:      sog-lmp
+  source commit:      12e2fc71
+  source commit at:   2026-05-27 14:06:36 +0800
+  support model ver.: 1.1 
+  build variant:      cpu
+  build with pt lib:  torch;torch_library;/home/zyjin/anaconda3/envs/base_env/lib/python3.13/site-packages/torch/lib/libc10.so;/usr/local/cuda/lib64/libnvrtc.so;/home/zyjin/anaconda3/envs/base_env/lib/python3.13/site-packages/torch/lib/libc10_cuda.so
+  set tf intra_op_parallelism_threads: 16
+  set tf inter_op_parallelism_threads: 1
+  >>> Info of lammps module:
+  use deepmd-kit at:  /usr/local
+  source:             v3.1.3-86-g12e2fc71-dirty
+  source branch:      sog-lmp
+  source commit:      12e2fc71
+  source commit at:   2026-05-27 14:06:36 +0800
+  build with inc:     /home/zyjin/anaconda3/envs/base_env/lib/python3.13/site-packages/torch/include;/home/zyjin/anaconda3/envs/base_env/lib/python3.13/site-packages/torch/include/torch/csrc/api/include
+  build with lib:     /home/zyjin/anaconda3/envs/base_env/lib/python3.13/site-packages/torch/lib
+WARNING: pair_style deepmd sog_sr=yes enables latent_charge_to_q automatically (/data/zyjin/dp_pt/dp_devel/deepmd-kit-devel/source/lmp/pair_deepmd.cpp:919)
+pair_coeff * *
+include /data/zyjin/dp_pt/dp_example/au-mgo/lmp/progress_report_20260601/results/lammps_md_20260602/kspace_sog.inc
+# Auto-generated from sog_model.ckpt; do not edit manually.
+kspace_style sog 9.9999999999999995e-07 n_dl_from_model yes amp_from_model yes bandwidth_from_model yes b 1.6297670882677646 sigma 3.6337174090094129 m 16 remove_self_interaction yes
+run 0
 
-pair_style      coul/long 6.0
-pair_coeff      * *
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- USER-DEEPMD package:
+
+@article{Wang_ComputPhysCommun_2018_v228_p178,
+  author = {Wang, Han and Zhang, Linfeng and Han, Jiequn and E, Weinan},
+  doi = {10.1016/j.cpc.2018.03.016},
+  url = {https://doi.org/10.1016/j.cpc.2018.03.016},
+  year = 2018,
+  month = {jul},
+  publisher = {Elsevier {BV}},
+  volume = 228,
+  journal = {Comput. Phys. Commun.},
+  title = {{DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics}},
+  pages = {178--184}
+}
+@article{Zeng_JChemPhys_2023_v159_p054801,
+  title  = {{DeePMD-kit v2: A software package for deep potential models}},
+  author =   {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and Zeyu Li
+         and Yixiao Chen and Mari{\'a}n Rynik and Li'ang Huang and Ziyao Li and 
+         Shaochen Shi and Yingze Wang and Haotian Ye and Ping Tuo and Jiabin
+         Yang and Ye Ding and Yifan Li and Davide Tisi and Qiyu Zeng and Han 
+         Bao and Yu Xia and Jiameng Huang and Koki Muraoka and Yibo Wang and 
+         Junhan Chang and Fengbo Yuan and Sigbj{\o}rn L{\o}land Bore and Chun
+         Cai and Yinnian Lin and Bo Wang and Jiayan Xu and Jia-Xin Zhu and 
+         Chenxing Luo and Yuzhi Zhang and Rhys E A Goodall and Wenshuo Liang
+         and Anurag Kumar Singh and Sikai Yao and Jingchao Zhang and Renata
+         Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and Darrin M
+         York and Weinan E and Roberto Car and Linfeng Zhang and Han Wang},
+  journal =  {J. Chem. Phys.},
+  volume =   159,
+  issue =    5,  
+  year =    2023,
+  pages  =   054801,
+  doi =      {10.1063/5.0155600},
+}
+@Article{Zeng_JChemTheoryComput_2025_v21_p4375,
+  author =   {Jinzhe Zeng and Duo Zhang and Anyang Peng and Xiangyu Zhang and Sensen
+             He and Yan Wang and Xinzijian Liu and Hangrui Bi and Yifan Li and Chun
+             Cai and Chengqian Zhang and Yiming Du and Jia-Xin Zhu and Pinghui Mo
+             and Zhengtao Huang and Qiyu Zeng and Shaochen Shi and Xuejian Qin and
+             Zhaoxi Yu and Chenxing Luo and Ye Ding and Yun-Pei Liu and Ruosong Shi
+             and Zhenyu Wang and Sigbj{\o}rn L{\o}land Bore and Junhan Chang and
+             Zhe Deng and Zhaohan Ding and Siyuan Han and Wanrun Jiang and Guolin
+             Ke and Zhaoqing Liu and Denghui Lu and Koki Muraoka and Hananeh Oliaei
+             and Anurag Kumar Singh and Haohui Que and Weihong Xu and Zhangmancang
+             Xu and Yong-Bin Zhuang and Jiayu Dai and Timothy J. Giese and Weile
+             Jia and Ben Xu and Darrin M. York and Linfeng Zhang and Han Wang},
+    title =    {{DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning
+             Potentials}},
+  journal =  {J. Chem. Theory Comput.},
+  year =     2025,
+  volume =   21,
+  number =   9,
+  pages =    {4375--4385},
+  doi =      {10.1021/acs.jctc.5c00340},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
-kspace_style    sog 1.0e-6 amp 0.1 bandwidth 0.5
-thermo_style    custom step pe
-thermo          1
-run             0
 WARNING: No fixes with time integration, atoms won't move
 For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
 PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 0.1
-For more information see https://docs.lammps.org/err0029 (src/kspace.cpp:335)
   using 12-bit tables for long-range coulomb
 WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:373)
   G vector (1/distance) = 1
-  grid = 30 30 30
+  grid = 20 20 54
   stencil order = 5
-  estimated absolute RMS force accuracy = 3.4929588e-07
-  estimated relative force accuracy = 2.4257256e-08
+  estimated absolute RMS force accuracy = 1.5438285e-06
+  estimated relative force accuracy = 1.0721295e-07
   using double precision KISS FFT
-  3d grid and FFT values/proc = 68921 27000
-Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+  3d grid and FFT values/proc = 44469 21600
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8
-  ghost atom cutoff = 8
-  binsize = 4, bins = 3 3 3
+  master list distance cutoff = 7
+  ghost atom cutoff = 7
+  binsize = 3.5, bins = 3 3 8
   1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
+  (1) pair deepmd, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 8.426 | 8.426 | 8.426 Mbytes
-   Step         PotEng    
-         0   0.001285803  
-Loop time of 1.302e-06 on 1 procs for 0 steps with 1 atoms
-
-153.6% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Kspace  | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.302e-06  |            |       |100.00
-
-Nlocal:              1 ave           1 max           1 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:             26 ave          26 max          26 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:              0 ave           0 max           0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 0
-Ave neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:00
+ERROR on proc 0: DeePMD-kit Error: DeePMD-kit PyTorch backend error: DeePMD-kit Error: charge tensor must have last dimension 1 to map to atom->q. (/data/zyjin/dp_pt/dp_devel/deepmd-kit-devel/source/lmp/pair_deepmd.cpp:382)

source/lmp/pair_deepmd.cpp

@@ -2,14 +2,10 @@
 #include <string.h>
 
 #include <cassert>
-#include <cctype>
-#include <cmath>
-#include <cstdlib>
 #include <iomanip>
 #include <iostream>
 #include <limits>
 #include <map>
-#include <regex>
 #include <sstream>
 
 #include "atom.h"
@@ -39,21 +35,6 @@
 using namespace LAMMPS_NS;
 using namespace std;
 
-namespace {
-
-bool has_json_suffix(const std::string& path) {
-  if (path.size() < 5) {
-    return false;
-  }
-  std::string suffix = path.substr(path.size() - 5);
-  for (char& c : suffix) {
-    c = static_cast<char>(std::tolower(static_cast<unsigned char>(c)));
-  }
-  return suffix == ".json";
-}
-
-}  // namespace
-
 static const char cite_user_deepmd_package[] =
     "USER-DEEPMD package:\n\n"
     "@article{Wang_ComputPhysCommun_2018_v228_p178,\n"
@@ -140,90 +121,12 @@ PairDeepMD::PairDeepMD(LAMMPS* lmp)
     : PairDeepBaseModel(
           lmp, cite_user_deepmd_package, deep_pot, deep_pot_model_devi) {
   latent_charge_to_q = false;
-  model_n_dl = 0.0;
-  has_model_n_dl = 0;
 }
 
 PairDeepMD::~PairDeepMD() {
   // Ensure base class destructor is called
 }
 
-bool PairDeepMD::parse_model_n_dl_from_json(const std::string& model_path,
-                                            double& n_dl_out) const {
-  if (!has_json_suffix(model_path)) {
-    return false;
-  }
-
-  std::string content;
-  try {
-    deepmd_compat::read_file_to_string(model_path, content);
-  } catch (...) {
-    return false;
-  }
-
-  static const std::regex n_dl_pattern(
-      R"("n_dl"\s*:\s*([-+]?(?:\d+\.?\d*|\.\d+)(?:[eE][-+]?\d+)?))");
-
-  std::smatch match;
-  if (!std::regex_search(content, match, n_dl_pattern)) {
-    return false;
-  }
-
-  const double candidate = std::strtod(match[1].str().c_str(), nullptr);
-  if (!(std::isfinite(candidate) && candidate > 0.0)) {
-    return false;
-  }
-
-  n_dl_out = candidate;
-  return true;
-}
-
-void PairDeepMD::detect_model_n_dl(const std::vector<std::string>& models) {
-  has_model_n_dl = 0;
-  model_n_dl = 0.0;
-
-  double first_n_dl = 0.0;
-  bool found = false;
-
-  for (const auto& model_path : models) {
-    double parsed = 0.0;
-    if (!parse_model_n_dl_from_json(model_path, parsed)) {
-      continue;
-    }
-    if (!found) {
-      first_n_dl = parsed;
-      found = true;
-      continue;
-    }
-    if (std::fabs(parsed - first_n_dl) > 1e-12 && comm->me == 0) {
-      error->warning(
-          FLERR,
-          "pair_style deepmd found inconsistent n_dl across model JSON files; "
-          "using the first model value");
-    }
-  }
-
-  if (found) {
-    has_model_n_dl = 1;
-    model_n_dl = first_n_dl;
-  }
-}
-
-void* PairDeepMD::extract(const char* str, int& dim) {
-  if (strcmp(str, "deepmd_model_n_dl") == 0) {
-    dim = 0;
-    if (has_model_n_dl) {
-      return (void*)&model_n_dl;
-    }
-    return nullptr;
-  }
-  if (strcmp(str, "deepmd_model_n_dl_available") == 0) {
-    dim = 0;
-    return (void*)&has_model_n_dl;
-  }
-  return PairDeepBaseModel::extract(str, dim);
-}
-
 void PairDeepMD::compute(int eflag, int vflag) {
   if (numb_models == 0) {
     return;
@@ -712,7 +615,6 @@ void PairDeepMD::settings(int narg, char** arg) {
   for (int ii = 0; ii < iarg; ++ii) {
     models.push_back(arg[ii]);
   }
-  detect_model_n_dl(models);
   numb_models = models.size();
   if (numb_models == 1) {
     try {

source/lmp/pair_deepmd.h

@@ -44,7 +44,6 @@ class PairDeepMD : public PairDeepBaseModel {
  public:
   PairDeepMD(class LAMMPS*);
   ~PairDeepMD() override;
-  void* extract(const char*, int&) override;
   void settings(int, char**) override;
   void coeff(int, char**) override;
   void compute(int, int) override;
@@ -56,14 +55,8 @@ class PairDeepMD : public PairDeepBaseModel {
   deepmd_compat::DeepPotModelDevi deep_pot_model_devi;
 
  private:
-  bool parse_model_n_dl_from_json(const std::string& model_path,
-                                  double& n_dl_out) const;
-  void detect_model_n_dl(const std::vector<std::string>& models);
-
   CommBrickDeepMD* commdata_;
   bool latent_charge_to_q;
-  double model_n_dl;
-  int has_model_n_dl;
 };
 
 }  // namespace LAMMPS_NS