Merge branch 'deepmodeling:develop' into develop

mohanchen · May 15, 2024 · 53b674e · 53b674e
2 parents 5d4b112 + 24a27b9
commit 53b674e
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -37,6 +37,7 @@ option(ENABLE_FFT_TWO_CENTER "Enable FFT-based two-center integral method." ON)
 option(ENABLE_GOOGLEBENCH "Enable GOOGLE-benchmark usage." OFF)
 option(ENABLE_RAPIDJSON "Enable rapid-json usage." OFF)
 option(ENABLE_CNPY "Enable cnpy usage." OFF)
+option(ENABLE_PEXSI "Enable support for PEXSI." OFF)
 
 # enable json support
 if(ENABLE_RAPIDJSON)
@@ -211,6 +212,14 @@ if(ENABLE_LCAO)
   if(ENABLE_FFT_TWO_CENTER)
     add_compile_definitions(USE_NEW_TWO_CENTER)
   endif()
+
+  if(ENABLE_PEXSI)
+    find_package(PEXSI REQUIRED)
+    target_link_libraries(${ABACUS_BIN_NAME} ${PEXSI_LIBRARY} ${SuperLU_DIST_LIBRARY} ${ParMETIS_LIBRARY} ${METIS_LIBRARY} pexsi)
+    include_directories(${PEXSI_INCLUDE_DIR} ${ParMETIS_INCLUDE_DIR})
+    add_compile_definitions(__PEXSI)
+    set(CMAKE_CXX_STANDARD 14)
+  endif()
 else()
   set(ENABLE_DEEPKS OFF)
   set(ENABLE_LIBRI OFF)

diff --git a/cmake/FindPEXSI.cmake b/cmake/FindPEXSI.cmake
@@ -0,0 +1,57 @@
+###############################################################################
+# - Find PEXSI
+# Find PEXSI and its dependencies.
+#
+#  PEXSI_FOUND          - True if pexsi is found.
+#  PEXSI_INCLUDE_DIR    - Where to find pexsi headers.
+#  PEXSI_LIBRARY        - pexsi library.
+#  ParMETIS_INCLUDE_DIR - Where to find pexsi headers.
+#  ParMETIS_LIBRARY     - parmetis library.
+#  METIS_LIBRARY        - metis library.
+#  SuperLU_DIST_LIBRARY - superlu_dist library.
+
+find_path(PEXSI_INCLUDE_DIR
+    NAMES c_pexsi_interface.h
+    HINTS ${PEXSI_DIR}
+    PATH_SUFFIXES "include"
+)
+
+find_library(PEXSI_LIBRARY
+    NAMES pexsi
+    HINTS ${PEXSI_DIR}
+    PATH_SUFFIXES "lib"
+)
+
+find_path(ParMETIS_INCLUDE_DIR
+    NAMES metis.h parmetis.h
+    HINTS ${ParMETIS_DIR}
+    PATH_SUFFIXES "include"
+)
+
+find_library(METIS_LIBRARY
+    NAMES metis
+    HINTS ${ParMETIS_DIR}
+    PATH_SUFFIXES "lib"
+)
+
+find_library(ParMETIS_LIBRARY
+    NAMES parmetis
+    HINTS ${ParMETIS_DIR}
+    PATH_SUFFIXES "lib"
+)
+
+find_library(SuperLU_DIST_LIBRARY
+    NAMES superlu_dist
+    HINTS ${SuperLU_DIST_DIR}
+    PATH_SUFFIXES "lib"
+)
+
+# Handle the QUIET and REQUIRED arguments and
+# set PEXSI_FOUND to TRUE if all variables are non-zero.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(PEXSI DEFAULT_MSG PEXSI_LIBRARY PEXSI_INCLUDE_DIR ParMETIS_LIBRARY METIS_LIBRARY SuperLU_DIST_LIBRARY)
+
+
+# Copy the results to the output variables and target.
+mark_as_advanced(PEXSI_LIBRARY PEXSI_INCLUDE_DIR ParMETIS_LIBRARY SuperLU_DIST_LIBRARY)
+
diff --git a/docs/advanced/input_files/input-main.md b/docs/advanced/input_files/input-main.md
@@ -377,6 +377,30 @@
     - [qo\_strategy](#qo_strategy)
     - [qo\_screening\_coeff](#qo_screening_coeff)
     - [qo\_thr](#qo_thr)
+  - [PEXSI](#pexsi)
+    - [pexsi\_npole](#pexsi_npole)
+    - [pexsi\_inertia](#pexsi_inertia)
+    - [pexsi\_nmax](#pexsi_nmax)
+    - [pexsi\_comm](#pexsi_comm)
+    - [pexsi\_storage](#pexsi_storage)
+    - [pexsi\_ordering](#pexsi_ordering)
+    - [pexsi\_row\_ordering](#pexsi_row_ordering)
+    - [pexsi\_nproc](#pexsi_nproc)
+    - [pexsi\_symm](#pexsi_symm)
+    - [pexsi\_trans](#pexsi_trans)
+    - [pexsi\_method](#pexsi_method)
+    - [pexsi\_nproc\_pole](#pexsi_nproc_pole)
+    - [pexsi\_temp](#pexsi_temp)
+    - [pexsi\_gap](#pexsi_gap)
+    - [pexsi\_delta\_e](#pexsi_delta_e)
+    - [pexsi\_mu\_lower](#pexsi_mu_lower)
+    - [pexsi\_mu\_upper](#pexsi_mu_upper)
+    - [pexsi\_mu](#pexsi_mu)
+    - [pexsi\_mu\_thr](#pexsi_mu_thr)
+    - [pexsi\_mu\_expand](#pexsi_mu_expand)
+    - [pexsi\_mu\_guard](#pexsi_mu_guard)
+    - [pexsi\_elec\_thr](#pexsi_elec_thr)
+    - [pexsi\_zero\_thr](#pexsi_zero_thr)
 
 [back to top](#full-list-of-input-keywords)
 
@@ -3530,4 +3554,146 @@ These variables are used to control the usage of QO analysis. QO further compres
 - **Description**: the convergence threshold determining the cutoff of generated orbital. Lower threshold will yield orbital with larger cutoff radius.
 - **Default**: 1.0e-6
 
+## PEXSI
+
+These variables are used to control the usage of PEXSI (Pole Expansion and Selected Inversion) method in calculations.
+
+### pexsi_npole
+
+- **Type**: Integer
+- **Description**: the number of poles used in the pole expansion method, should be a even number.
+- **Default**: 40
+
+### pexsi_inertia
+
+- **Type**: Boolean
+- **Description**: whether inertia counting is used at the very beginning.
+- **Default**: True
+
+### pexsi_nmax
+
+- **Type**: Integer
+- **Description**: maximum number of PEXSI iterations after each inertia counting procedure.
+- **Default**: 80
+
+### pexsi_comm
+
+- **Type**: Boolean
+- **Description**: whether to construct PSelInv communication pattern.
+- **Default**: True
+
+### pexsi_storage
+
+- **Type**: Boolean
+- **Description**: whether to use symmetric storage space used by the Selected Inversion algorithm for symmetric matrices.
+- **Default**: True
+
+### pexsi_ordering
+
+- **Type**: Integer
+- **Description**: ordering strategy for factorization and selected inversion. 0: Parallel ordering using ParMETIS, 1: Sequential ordering using METIS, 2: Multiple minimum degree ordering
+- **Default**: 0
+
+### pexsi_row_ordering
+
+- **Type**: Integer
+- **Description**: row permutation strategy for factorization and selected inversion, 0: No row permutation, 1: Make the diagonal entry of the matrix larger than the off-diagonal entries.
+- **Default**: 1
+
+### pexsi_nproc
+
+- **Type**: Integer
+- **Description**: number of processors for PARMETIS. Only used if pexsi_ordering == 0.
+- **Default**: 1
+
+### pexsi_symm
+
+- **Type**: Boolean
+- **Description**: whether the matrix is symmetric.
+- **Default**: True
+
+### pexsi_trans
+
+- **Type**: Boolean
+- **Description**: whether to factorize the transpose of the matrix.
+- **Default**: False
+
+### pexsi_method
+
+- **Type**: Integer
+- **Description**: the pole expansion method to be used. 1 for Cauchy Contour Integral method, 2 for Moussa optimized method.
+- **Default**: 1
+
+### pexsi_nproc_pole
+
+- **Type**: Integer
+- **Description**: the point parallelizaion of PEXSI. Recommend two points parallelization.
+- **Default**: 1
+
+### pexsi_temp
+
+- **Type**: Real
+- **Description**: temperature in Fermi-Dirac distribution, in Ry, should have the same effect as the smearing sigma when smearing method is set to Fermi-Dirac.
+- **Default**: 0.015
+
+### pexsi_gap
+
+- **Type**: Real
+- **Description**: spectral gap, this can be set to be 0 in most cases.
+- **Default**: 0
+
+### pexsi_delta_e
+
+- **Type**: Real
+- **Description**: an upper bound for the spectral radius of $S^{-1} H$.
+- **Default**: 20
+
+### pexsi_mu_lower
+
+- **Type**: Real
+- **Description**: initial guess of lower bound for mu.
+- **Default**: -10
+
+### pexsi_mu_upper
+
+- **Type**: Real
+- **Description**: initial guess of upper bound for mu.
+- **Default**: 10
+
+### pexsi_mu
+
+- **Type**: Real
+- **Description**: initial guess for mu (for the solver).
+- **Default**: 0
+
+### pexsi_mu_thr
+
+- **Type**: Real
+- **Description**: stopping criterion in terms of the chemical potential for the inertia counting procedure.
+- **Default**: 0.05
+
+### pexsi_mu_expand
+
+- **Type**: Real
+- **Description**: if the chemical potential is not in the initial interval, the interval is expanded by this value.
+- **Default**: 0.3
+
+### pexsi_mu_guard
+
+- **Type**: Real
+- **Description**: safe guard criterion in terms of the chemical potential to reinvoke the inertia counting procedure.
+- **Default**: 0.2
+
+### pexsi_elec_thr
+
+- **Type**: Real
+- **Description**: stopping criterion of the PEXSI iteration in terms of the number of electrons compared to numElectronExact.
+- **Default**: 0.001
+
+### pexsi_zero_thr
+
+- **Type**: Real
+- **Description**: if the absolute value of CCS matrix element is less than this value, it will be considered as zero.
+- **Default**: 1e-10
+
 [back to top](#full-list-of-input-keywords)
diff --git a/docs/advanced/install.md b/docs/advanced/install.md
@@ -104,6 +104,18 @@ Currently supported math functions:
 cmake -B build -DUSE_ABACUS_LIBM=1
 ```
 
+## Build with PEXSI support
+
+ABACUS supports the PEXSI library for gamma only LCAO calculations. PEXSI version 2.0.0 is tested to work with ABACUS, please always use the latest version of PEXSI. 
+
+To build ABACUS with PEXSI support, you need to compile PEXSI (and its dependencies) first. Please refer to the [PEXSI Installation Guide](https://pexsi.readthedocs.io/en/latest/install.html) for more details. Note that PEXSI requires ParMETIS and SuperLU_DIST.
+
+After compiling PEXSI, you can set `ENABLE_PEXSI` to `ON`. If the libraries are not installed in standard paths, you can set `PEXSI_DIR`, `ParMETIS_DIR` and `SuperLU_DIST_DIR` to the corresponding directories.
+
+```bash
+cmake -B build -DENABLE_PEXSI=ON -DPEXSI_DIR=${path to PEXSI installation directory} -DParMETIS_DIR=${path to ParMETIS installation directory} -DSuperLU_DIST_DIR=${path to SuperLU_DIST installation directory}
+```
+
 ## Build ABACUS with make
 
 > Note: We suggest using CMake to configure and compile.

diff --git a/examples/pexsi/md_Si8/INPUT b/examples/pexsi/md_Si8/INPUT
@@ -0,0 +1,32 @@
+INPUT_PARAMETERS
+#Parameters (1.General)
+suffix                 Si_rescaling
+calculation            md
+nbands                 20
+symmetry               0
+pseudo_dir             ../../../tests/PP_ORB
+orbital_dir            ../../../tests/PP_ORB
+
+#Parameters (2.Iteration)
+ecutwfc                30
+scf_thr                1e-5
+scf_nmax               100
+
+#Parameters (3.Basis)
+basis_type             lcao
+ks_solver              pexsi
+gamma_only             1
+
+#Parameters (5.Mixing)
+mixing_type            broyden
+mixing_beta            0.3
+chg_extrap             second-order
+
+#Parameters (6.MD)
+md_type                nvt
+md_thermostat          rescaling
+md_tolerance           10
+md_nstep               10
+md_dt                  1
+md_tfirst              300
+md_tfreq               0.025
diff --git a/examples/pexsi/md_Si8/KPT b/examples/pexsi/md_Si8/KPT
@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+1 1 1 0 0 0
diff --git a/examples/pexsi/md_Si8/STRU b/examples/pexsi/md_Si8/STRU
@@ -0,0 +1,28 @@
+ATOMIC_SPECIES
+Si  28.085  Si_ONCV_PBE-1.0.upf
+
+NUMERICAL_ORBITAL
+Si_gga_8au_60Ry_2s2p1d.orb
+
+LATTICE_CONSTANT
+1.8897270    # 1 Angstrom = 1.8897270 bohr
+
+LATTICE_VECTORS
+5.43090      0.00000      0.00000
+0.00000      5.43090      0.00000
+0.00000      0.00000      5.43090
+
+ATOMIC_POSITIONS
+Direct 
+
+Si
+0.0
+8
+0.000	0.000	0.000	1	1	1
+0.000	0.500	0.500	1	1	1
+0.500	0.000	0.500	1	1	1
+0.500	0.500	0.000	1	1	1
+0.250	0.250	0.250	1	1	1
+0.250	0.750	0.750	1	1	1
+0.750	0.250	0.750	1	1	1
+0.750	0.750	0.250	1	1	1
diff --git a/examples/pexsi/scf_Si64/INPUT b/examples/pexsi/scf_Si64/INPUT
@@ -0,0 +1,20 @@
+INPUT_PARAMETERS
+suffix      test
+ntype       1
+nbands      200
+pseudo_dir          ../../../tests/PP_ORB
+orbital_dir         ../../../tests/PP_ORB
+
+calculation scf
+mixing_beta 0.4
+basis_type  lcao
+gamma_only  1
+symmetry    0
+
+ecutwfc     60
+lcao_dr         1e-3
+scf_nmax	      20
+
+ks_solver   pexsi
+
+pexsi_npole  40
diff --git a/examples/pexsi/scf_Si64/KPT b/examples/pexsi/scf_Si64/KPT
@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+1 1 1 0 0 0