Merge branch 'publicGithubDevelop' of https://bitbucket.org/dftfedeve…

…lopers/dftfe into DOSbugFix

CMakeLists.txt

@@ -548,7 +548,7 @@ ENDIF()
 #
 # ELPA. Pass path to -DCMAKE_PREFIX_PATH
 #
-find_package(ELPA 2022 REQUIRED)
+find_package(ELPA 2024 REQUIRED)
 MESSAGE(STATUS "Will Link With ELPA")
 target_link_libraries(${TARGETLIB} PUBLIC ELPA::ELPA)
 

README.md

@@ -15,7 +15,7 @@ DFT-FE code builds on top of the deal.II library for everything that has to do w
 The steps to install the necessary dependencies and DFT-FE itself are described in the *Installation* section of the DFT-FE manual (compile doc/manual/manual.tex or download the development version manual [here](https://github.com/dftfeDevelopers/dftfe/blob/manual/manual-develop.pdf)). 
 
 We have created several shell based installation scripts for the development version of DFT-FE (`publicGithubDevelop` branch) on various machines:
- - [OLCF Frontier](https://github.com/dftfeDevelopers/install_DFTFE/tree/frontierScript)
+ - [OLCF Frontier](https://github.com/dftfeDevelopers/install_DFTFE/tree/frontierScriptROCM6)
  - [NERSC Perlmutter](https://github.com/dftfeDevelopers/install_DFTFE/tree/perlmutterScript)
  - [ALCF Polaris](https://github.com/dftfeDevelopers/install_DFTFE/tree/polarisScript)
  - [UMICH Greatlakes](https://github.com/dftfeDevelopers/install_DFTFE/tree/greatlakesScript)

cmake/FindELPA.cmake

@@ -18,7 +18,7 @@ find_package(PkgConfig)
 # elpa-2020.05.001.pc
 set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH TRUE)
 foreach(pkg elpa_openmp elpa) # prioritize elpa_openmp
- foreach(ver 2022.11.001)
+ foreach(ver 2024.03.001)
  pkg_search_module(PC_ELPA ${pkg})
  if(PC_ELPA_FOUND)
  break()

doc/manual/installation.tex

@@ -59,7 +59,7 @@ \subsubsection{Instructions for dependencies: ALGLIB, Libxc, spglib, Libxml2, Sc
 \item {\bf ScaLAPACK}: ScaLAPACK library is used by DFT-FE via ELPA for its parallel linear algebra routines involving dense matrices, as well being a dependency for ELPA. \textcolor{red}{\bf If Intel MKL math library is available, please skip this step, as the ScaLAPACK libraries therein can be used directly.} If Intel MKL math library is not available, Netlib ScaLAPACK \url{http://www.netlib.org/scalapack/} needs to be installed using the instructions below. Download the current release version (2.2.0) from \url{http://www.netlib.org/scalapack/#\_software}, and build a shared library (use \verb|BUILD_SHARED_LIBS=ON|, \verb|BUILD_STATIC_LIBS=OFF| and \verb|BUILD_TESTING=OFF|) installation of ScaLAPACK using cmake. We recommend using the ccmake gui interface for the installation. Further, use the appropriate compilers for \verb|CMAKE_C_COMPILER| and \verb|CMAKE_FORTRAN_COMPILER|, and also use \verb|-fPIC| flag for \verb|CMAKE_C_FLAGS| and \verb|-fPIC -fallow-argument-mismatch| for \verb|CMAKE_Fortran_FLAGS|. For best performance, ScaLAPACK must be linked to optimized BLAS-LAPACK libraries by using\\ \verb|USE_OPTIMIZED_LAPACK_BLAS=ON|, and providing external paths to BLAS-LAPACK libraries (MKL, OpenBlas, ESSL etc.) during the cmake configuration. 
 %Alternatively one can also use the python based installer~\url{http://www.netlib.org/scalapack/scalapack_installer.tgz} for Linux.
 
-\item {\bf ELPA}: ELPA library is used by DFT-FE for its parallel linear algebra routines involving dense matrices. ELPA requires the ScaLAPACK library (see above) as a dependency. Download the latest version elpa-2022.11.001 from \url{https://elpa.mpcdf.mpg.de/software/} and follow the installation instructions in there. Example of ELPA installation on UMICH Greatlakes supercomputer with GNU compiler, Open MPI library, and Intel MKL math library:
+\item {\bf ELPA}: ELPA library is used by DFT-FE for its parallel linear algebra routines involving dense matrices. ELPA requires the ScaLAPACK library (see above) as a dependency. Download the latest version elpa-2024.03.001 from \url{https://elpa.mpcdf.mpg.de/software/} and follow the installation instructions in there. Example of ELPA installation on UMICH Greatlakes supercomputer with GNU compiler, Open MPI library, and Intel MKL math library:
 \begin{verbatim}
 $ cd elpaDir
 $ mkdir build

include/dft.h

@@ -262,10 +262,10 @@ namespace dftfe
  double
  getFreeEnergy() const;
 
- distributedCPUVec<double>
+ const distributedCPUVec<double> &
  getRhoNodalOut() const;
 
- distributedCPUVec<double>
+ const distributedCPUVec<double> &
  getRhoNodalSplitOut() const;
 
  double
@@ -389,14 +389,28 @@ namespace dftfe
  * @brief Gets the current atom Locations in cartesian form
  * (origin at center of domain) from dftClass
  */
- std::vector<std::vector<double>>
+ const std::vector<std::vector<double>> &
  getAtomLocationsCart() const;
 
+
+ /**
+ * @brief Gets the current image atom Locations in cartesian form
+ * (origin at center of domain) from dftClass
+ */
+ const std::vector<std::vector<double>> &
+ getImageAtomLocationsCart() const;
+
+ /**
+ * @brief Gets the current image atom ids from dftClass
+ */
+ const std::vector<int> &
+ getImageAtomIDs() const;
+
  /**
  * @brief Gets the current atom Locations in fractional form
  * from dftClass (only applicable for periodic and semi-periodic BCs)
  */
- std::vector<std::vector<double>>
+ const std::vector<std::vector<double>> &
  getAtomLocationsFrac() const;
 
 
@@ -407,7 +421,7 @@ namespace dftfe
  * @return std::vector<std::vector<double>> 3 \times 3 matrix,lattice[i][j]
  * corresponds to jth component of ith lattice vector
  */
- std::vector<std::vector<double>>
+ const std::vector<std::vector<double>> &
  getCell() const;
 
  /**
@@ -420,19 +434,19 @@ namespace dftfe
  /**
  * @brief Gets the current atom types from dftClass
  */
- std::set<unsigned int>
+ const std::set<unsigned int> &
  getAtomTypes() const;
 
  /**
  * @brief Gets the current atomic forces from dftClass
  */
- std::vector<double>
+ const std::vector<double> &
  getForceonAtoms() const;
 
  /**
  * @brief Gets the current cell stress from dftClass
  */
- dealii::Tensor<2, 3, double>
+ const dealii::Tensor<2, 3, double> &
  getCellStress() const;
 
  /**

include/dftBase.h

@@ -88,10 +88,10 @@ namespace dftfe
  virtual double
  getFreeEnergy() const = 0;
 
- virtual distributedCPUVec<double>
+ virtual const distributedCPUVec<double> &
  getRhoNodalOut() const = 0;
 
- virtual distributedCPUVec<double>
+ virtual const distributedCPUVec<double> &
  getRhoNodalSplitOut() const = 0;
 
  virtual double
@@ -107,14 +107,28 @@ namespace dftfe
  * @brief Gets the current atom Locations in cartesian form
  * (origin at center of domain) from dftClass
  */
- virtual std::vector<std::vector<double>>
+ virtual const std::vector<std::vector<double>> &
  getAtomLocationsCart() const = 0;
 
+ /**
+ * @brief Gets the current image atom Locations in cartesian form
+ * (origin at center of domain) from dftClass
+ */
+ virtual const std::vector<std::vector<double>> &
+ getImageAtomLocationsCart() const = 0;
+
+ /**
+ * @brief Gets the current image atom ids from dftClass
+ */
+ virtual const std::vector<int> &
+ getImageAtomIDs() const = 0;
+
+
  /**
  * @brief Gets the current atom Locations in fractional form
  * from dftClass (only applicable for periodic and semi-periodic BCs)
  */
- virtual std::vector<std::vector<double>>
+ virtual const std::vector<std::vector<double>> &
  getAtomLocationsFrac() const = 0;
 
 
@@ -125,7 +139,7 @@ namespace dftfe
  * @return std::vector<std::vector<double>> 3 \times 3 matrix,lattice[i][j]
  * corresponds to jth component of ith lattice vector
  */
- virtual std::vector<std::vector<double>>
+ virtual const std::vector<std::vector<double>> &
  getCell() const = 0;
 
  /**
@@ -138,20 +152,20 @@ namespace dftfe
  /**
  * @brief Gets the current atom types from dftClass
  */
- virtual std::set<unsigned int>
+ virtual const std::set<unsigned int> &
  getAtomTypes() const = 0;
 
  /**
  * @brief Gets the current atomic forces (configurational forces) from dftClass
  */
- virtual std::vector<double>
+ virtual const std::vector<double> &
  getForceonAtoms() const = 0;
 
 
  /**
  * @brief Gets the current cell stress from dftClass
  */
- virtual dealii::Tensor<2, 3, double>
+ virtual const dealii::Tensor<2, 3, double> &
  getCellStress() const = 0;
 
  /**

include/force.h

@@ -171,7 +171,7 @@ namespace dftfe
  * the three force components on each atom being the leading dimension.
  * Units- Hartree/Bohr
  */
- std::vector<double>
+ std::vector<double> &
  getAtomsForces();
 
  /** @brief prints the currently stored configurational forces on atoms and the Gaussian generator constant
@@ -244,7 +244,7 @@ namespace dftfe
  *
  * @return dealii::Tensor<2,3,double> second order stress Tensor in Hartree/Bohr^3
  */
- dealii::Tensor<2, 3, double>
+ dealii::Tensor<2, 3, double> &
  getStress();
 
  /** @brief get the value of Gaussian generator parameter (d_gaussianConstant).

pseudoConverters/pseudoPotentialToDftfeConverter.cc

@@ -606,14 +606,12 @@ namespace dftfe
  }
  void
  xmltoOrbitalFile(std::string file_path_in, std::string file_path_out)
- {
- // Extracting radial coordinates
+ { // Extracting radial coordinates
  std::vector<double> radial_coord;
  std::vector<std::string> radial_tag;
  radial_tag.push_back("PP_MESH");
  radial_tag.push_back("PP_R");
  radial_coord = XmlTagReaderMain(radial_tag, file_path_in);
-
  std::vector<std::string> pswfc_tag;
  pswfc_tag.push_back("PP_PSWFC");
  for (int i = 1; i <= xmlNodeChildCount(pswfc_tag, file_path_in); i++)
@@ -640,13 +638,32 @@ namespace dftfe
  {
  index = std::distance(attr_type.begin(), it);
  }
- std::string orbital_string = attr_value[index];
- for (auto &w : orbital_string)
+ std::string orbital_string_nl = attr_value[index];
+ for (auto &w : orbital_string_nl)
  {
  w = tolower(w);
  }
+ char n = orbital_string_nl[0];
+ char l;
+ if (orbital_string_nl[1] == 's')
+ {
+ l = '0';
+ }
+ if (orbital_string_nl[1] == 'p')
+ {
+ l = '1';
+ }
+ if (orbital_string_nl[1] == 'd')
+ {
+ l = '2';
+ }
+ if (orbital_string_nl[1] == 'f')
+ {
+ l = '3';
+ }
+ std::string orbital_string = "psi";
  std::fstream file;
- file.open(file_path_out + "/" + orbital_string + ".dat",
+ file.open(file_path_out + "/" + orbital_string + n + l + ".inp",
  std::ios::out);
  file << std::setprecision(12);
  if (file.is_open())

setupDevelopPetsc.sh

@@ -24,7 +24,7 @@ libxcDir="/home/vikramg/DFT-softwares-gcc/libxc/libxc-5.2.3/install_libxc5.2.3"
 spglibDir="/home/vikramg/DFT-softwares-gcc/spglib/install"
 xmlIncludeDir="/usr/include/libxml2"
 xmlLibDir="/usr/lib64"
-ELPA_PATH="/home/vikramg/DFT-softwares-gcc/elpa/install202211"
+ELPA_PATH="/home/vikramg/DFT-softwares-gcc/elpa/install2024"
 
 
 #Paths for optional external libraries