Merge branch 'develop' of github.com:deepmodeling/abacus-develop into develop

Author: dyzheng

Dockerfile

@@ -1,5 +1,10 @@
 # To build this Dockerfile, run `docker build -t abacus - < Dockerfile`.
-# Pull image with `docker pull ghcr.io/deepmodeling/abacus:latest`.
+# Alternatively, pull the image with `docker pull ghcr.io/deepmodeling/abacus:latest`.
+# Also available at `docker pull registry.dp.tech/deepmodeling/abacus:latest`.
+
+# Docker images are aimed for evaluating ABACUS.
+# For production use, please compile ABACUS from source code and run in bare-metal for a better performace.
+
 FROM ubuntu:22.04
 RUN apt update && apt install -y --no-install-recommends \
     libopenblas-dev liblapack-dev libscalapack-mpi-dev libelpa-dev libfftw3-dev libcereal-dev libxc-dev \
@@ -17,10 +22,11 @@ RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
 # If you have trouble cloning repo, replace "github.com" with "gitee.com".
 CMD mpirun --use-hwthread-cpus abacus
 
-# To run ABACUS built by this image with all available threads, execute `docker run -v <host>:<wd> -w <wd/input> abacus`.
+# To run ABACUS built by this image with all available threads, execute `docker run -v <host>:<wd> -w <wd/input> abacus:latest`.
 # Replace '<host>' with the path to all files(including pseudopotential files), '<wd>' with a path to working directory, and '<wd/input>' with the path to input folder(containing 'INPUT', 'STRU', etc.).
-# e.g. after clone the repo to `$HOME` and pulled this image, execute `docker run -v ~/abacus-develop/tests/integrate:/workspace -w /workspace/101_PW_15_f_pseudopots abacus`.
-# To run ABACUS with a given MPI process number, execute `docker run -v <host>:<wd> -w <wd/input> -it --entrypoint mpirun abacus -np <processes> abacus`. Note: the first "abacus" is the name of the image, the second "abacus" is the name of the executable file. Do not use '--cpus' flag of 'docker run' to specify the number of processes.
+# e.g. after cloning the repo to `$HOME` and pulling image, execute `docker run -v ~/abacus-develop/tests/integrate:/workspace -w /workspace/101_PW_15_f_pseudopots abacus:latest`.
+# To run ABACUS with a given MPI process number, execute `docker run -v <host>:<wd> -w <wd/input> -it --entrypoint mpirun abacus:latest -np <processes> abacus`.
+# Note: It would be better using all available CPUs. Docker uses CFS to share the CPU resources, which will result in bad CPU affinity.
 
 # To use this image as developing environment, execute `docker run -it --entrypoint /bin/bash abacus`.
 # Please refer to https://docs.docker.com/engine/reference/commandline/run/ for more details.

Dockerfile.gnu

@@ -16,3 +16,10 @@ RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-wit
     unzip -q libtorch.zip && rm libtorch.zip && \
     cd libtorch && cp -r . /usr/local && \
     cd .. && rm -r libtorch
+
+RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+    cd abacus-develop && \
+    cmake -B build -DENABLE_DEEPKS=ON && \
+    cmake --build build -j`nproc` && \
+    cmake --install build && \
+    cd .. && rm -rf abacus-develop

Dockerfile.intel

@@ -47,3 +47,16 @@ RUN source /opt/intel/oneapi/setvars.sh \
 	&& make PREFIX=/usr/local install \
 	&& ln -s /usr/local/include/elpa-2021.05.002/elpa /usr/local/include/ \
 	&& cd /tmp && rm -rf elpa-2021.05.002
+
+RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.9.1%2Bcpu.zip \
+        --no-check-certificate --quiet -O libtorch.zip && \
+    unzip -q libtorch.zip && rm libtorch.zip && \
+    cd libtorch && cp -r . /usr/local && \
+    cd .. && rm -r libtorch
+
+RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+    cd abacus-develop && \
+    cmake -B build -DENABLE_DEEPKS=ON && \
+    cmake --build build -j`nproc` && \
+    cmake --install build && \
+    cd .. && rm -rf abacus-develop

docs/examples/dpgen.md

@@ -163,6 +163,7 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide
     "fp_pp_path": "./",
     "fp_pp_files": ["Al_ONCV_PBE-1.0.upf"],   # the pseudopotential file
     "fp_orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"],  # the orbital file (use only in LCAO calculation)
+    "k_points":[2, 2, 2, 0, 0, 0],  # k-mesh setting
     "user_fp_params":{  # All the ABACUS input paramters are defined here
     "ntype": 1,         # defining input parameters from INPUT files is not supported yet.
     "ecutwfc": 80,      
@@ -175,7 +176,6 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide
     "smearing_sigma": 0.002,
     "scf_thr":1e-8,
     "cal_force":1,        # calculate force must be set to 1 in dpgen calculation
-    "k_points":[2, 2, 2, 0, 0, 0],  # k-mesh setting
     "kspacing": 0.01  # when KSPACING is set, the above k_points setting becomes invalid.
     }
 }
@@ -186,4 +186,4 @@ Notes:
 - The ABACUS-DPGEN interface can be used in both pw and lcao basis.
 
 
-[back to top](#abacus-wannier90-interface)
+[back to top](#abacus-wannier90-interface)

source/input.cpp

@@ -1851,9 +1851,21 @@ bool Input::Read(const std::string &fn)
         }
     }
 
-    if (basis_type == "pw") // pengfei Li add 2015-1-31
+    if (basis_type == "pw" && gamma_only !=0) // pengfei Li add 2015-1-31
     {
         gamma_only = 0;
+        GlobalV::ofs_running << " WARNING : gamma_only has not been implemented for pw yet" << std::endl;
+        GlobalV::ofs_running << " the INPUT parameter gamma_only has been reset to 0" << std::endl;
+        GlobalV::ofs_running << " and a new KPT is generated with gamma point as the only k point" << std::endl;
+
+		GlobalV::ofs_warning << " Auto generating k-points file: " << GlobalV::global_kpoint_card << std::endl;
+		std::ofstream ofs(GlobalV::global_kpoint_card.c_str());
+		ofs << "K_POINTS" << std::endl;
+		ofs << "0" << std::endl;
+		ofs << "Gamma" << std::endl;
+		ofs << "1 1 1 0 0 0" << std::endl;
+		ofs.close();
+
         // std::cout << "gamma_only =" << gamma_only << std::endl;
     }
     else if ((basis_type == "lcao" || basis_type == "lcao_in_pw") && (gamma_only == 1))

source/input_conv.cpp

@@ -4,6 +4,7 @@
 #include "module_base/global_function.h"
 #include "module_base/global_variable.h"
 #include "module_cell/unitcell.h"
+#include "module_surchem/surchem.h"
 #include "module_symmetry/symmetry.h"
 #include "src_io/berryphase.h"
 #include "src_io/chi0_hilbert.h"
@@ -14,7 +15,6 @@
 #include "src_ions/ions_move_basic.h"
 #include "src_pw/global.h"
 #include "src_pw/occupy.h"
-#include "module_surchem/surchem.h"
 #ifdef __EXX
 #include "src_ri/exx_abfs-jle.h"
 #endif
@@ -27,10 +27,9 @@
 #include "src_lcao/local_orbital_charge.h"
 #endif
 #include "module_base/timer.h"
-#include "module_surchem/efield.h"
-
 #include "module_elecstate/elecstate_lcao.h"
 #include "module_hsolver/hsolver_lcao.h"
+#include "module_surchem/efield.h"
 
 void Input_Conv::Convert(void)
 {
@@ -97,6 +96,7 @@ void Input_Conv::Convert(void)
     Ions_Move_Basic::relax_bfgs_rmin = INPUT.relax_bfgs_rmin;
     Ions_Move_Basic::relax_bfgs_init = INPUT.relax_bfgs_init;
     Ions_Move_Basic::out_stru = INPUT.out_stru; // mohan add 2012-03-23
+    Lattice_Change_Basic::out_stru = INPUT.out_stru;
 
     GlobalV::CAL_STRESS = INPUT.cal_stress;
 
@@ -203,15 +203,15 @@ void Input_Conv::Convert(void)
         GlobalV::NPOL = 1;
     }
 
-//----------------------------------------------------------
-// Yu Liu add 2022-05-18
-//----------------------------------------------------------
+    //----------------------------------------------------------
+    // Yu Liu add 2022-05-18
+    //----------------------------------------------------------
     GlobalV::EFIELD_FLAG = INPUT.efield_flag;
     GlobalV::DIP_COR_FLAG = INPUT.dip_cor_flag;
     Efield::efield_dir = INPUT.efield_dir;
     Efield::efield_pos_max = INPUT.efield_pos_max;
     Efield::efield_pos_dec = INPUT.efield_pos_dec;
-    Efield::efield_amp  = INPUT.efield_amp ;
+    Efield::efield_amp = INPUT.efield_amp;
 
 //----------------------------------------------------------
 // Fuxiang He add 2016-10-26
@@ -308,7 +308,7 @@ void Input_Conv::Convert(void)
         if (GlobalV::MY_RANK == 0)
             system(command0.c_str());
         if (INPUT.dft_functional == "hf" || INPUT.dft_functional == "pbe0" || INPUT.dft_functional == "hse"
-            || INPUT.dft_functional == "opt_orb" || INPUT.dft_functional == "scan0" )
+            || INPUT.dft_functional == "opt_orb" || INPUT.dft_functional == "scan0")
         {
             GlobalC::restart.info_save.save_charge = true;
             GlobalC::restart.info_save.save_H = true;
@@ -449,7 +449,7 @@ void Input_Conv::Convert(void)
     hsolver::HSolverLCAO::out_mat_hs = INPUT.out_mat_hs;
     hsolver::HSolverLCAO::out_mat_hsR = INPUT.out_mat_hs2; // LiuXh add 2019-07-16
     elecstate::ElecStateLCAO::out_wfc_lcao = INPUT.out_wfc_lcao;
-    if(INPUT.calculation == "nscf" && !INPUT.towannier90 && !INPUT.berry_phase)
+    if (INPUT.calculation == "nscf" && !INPUT.towannier90 && !INPUT.berry_phase)
     {
         elecstate::ElecStateLCAO::need_psi_grid = false;
     }