Merge dftbplus/main

pecchia · Jul 26, 2022 · 8396646 · 8396646
2 parents 23c99a2 + 44c4e6f
commit 8396646
Show file tree

Hide file tree

Showing 75 changed files with 5,436 additions and 1,888 deletions.
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -39,6 +39,8 @@ contributed to DFTB+ :
 
 * Sebastian Ehlert (University of Bonn, Germany)
 
+* Tammo van der Heide (University of Bremen, Germany)
+
 * Jan Hermann (Free University of Berlin, Germany)
 
 * Jacek Jakowski (Oak Ridge National Laboratory, USA)
@@ -52,8 +54,10 @@ contributed to DFTB+ :
 
 * Reinhard Maurer (University of Warwick, UK)
 
+* Tobias Melson (Max Planck Computing and Data Facility, Germany)
+
 * Izaac Mitchell (University of Newcastle, Australia)
-  
+
 * Thomas Niehaus (University of Lyon, France)
 
 * Alessandro Pecchia (University of Rome "Tor Vergata", Italy)
@@ -63,7 +67,7 @@ contributed to DFTB+ :
 
 * Jan Řezáč (Institute of Organic Chemistry and Biochemistry AS CR, Czech
   Republic)
-  
+
 * Cristián G. Sánchez (Universidad Nacional de Cuyo, Argentina)
 
 * Miguel Steiner (ETH Zurich, Switzerland)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,18 +8,27 @@ Notable project changes since release 1.3.1 (2017-02-22).
 Unreleased
 ==========
 
+
+Fixed
+-----
+
+- Onsite and +U potentials in real time-propagation, which was broken
+  in October 2019 by commit 11abba39b
+
+
+22.1 (2022-05-25)
+=================
+
 Added
 -----
 
 - Real time electronic dynamics for xTB Hamiltonian
 
-- Support for MPI-parallel GPU accelerated calculations via ELPA/ELSI library
-
 - Real time electronic dynamics for range separated DFTB
 
 - Support for MPI-parallel GPU accelerated calculations via ELPA/ELSI library
 
-- (Optionally) Rescale externally applied fields and dipole moments
+- (Optionally) rescale externally applied fields and dipole moments
   when implicit solvents are used
 
 - Enable lattice constraints in new geometry optimization driver
@@ -28,9 +37,17 @@ Added
 
 - API call for CM5 charges
 
+- Numerical Hessian calculation can be split over multiple runs
+
+
 Changed
 -------
 
+- PLUMED simulations may deliver due to an incompatible change in version 2.8.0
+  of the external PLUMED library slightly different results as before. See also
+  the `change log of PLUMED 2.8
+  <https://www.plumed.org/doc-v2.8/user-doc/html/_c_h_a_n_g_e_s-2-8.html>`_.
+
 - Allow electric fields in periodic systems even when interactions
   cross the sawtooth in the field
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -7,7 +7,7 @@ include(DftbPlusUtils)
 dftbp_ensure_out_of_source_build()
 dftbp_load_build_settings()
 
-set(DFTBPLUS_VERSION "21.2")
+set(DFTBPLUS_VERSION "22.1")
 
 project(dftbplus VERSION ${DFTBPLUS_VERSION} LANGUAGES Fortran C)
 
@@ -174,11 +174,14 @@ if(WITH_CHIMES)
   set(CMAKE_CXX_LINKER_PREFERENCE_PROPAGATES 0)
 endif()
 
+# If INCLUDE_INDIRECT_DEPS is non-empty, indirect dependencies must also be explicitely treated
+string(REGEX MATCH "(^|;)[Ss]ubmodule(^|;)" INCLUDE_INDIRECT_DEPS "${HYBRID_CONFIG_METHODS}")
+
 # Note: GIT_TAG hashes below must be updated with the utils/test/check_submodule_commits script!
 
 if(WITH_MPI)
   set(MPIFX_GIT_REPOSITORY "https://github.com/dftbplus/mpifx.git")
-  set(MPIFX_GIT_TAG "0641eead6ff9bf04c7ca2ec676a281780e2029e2")  # do not change manually!
+  set(MPIFX_GIT_TAG "da51073aa87831a91ae756a9773e39ea000d1c3a")  # do not change manually!
   dftbp_config_hybrid_dependency(MpiFx MpiFx::MpiFx "${HYBRID_CONFIG_METHODS}" "QUIET"
     external/mpifx "${exclude}" "${MPIFX_GIT_REPOSITORY}" "${MPIFX_GIT_TAG}")
 
@@ -204,7 +207,7 @@ endif()
 
 if(WITH_TRANSPORT)
   set(LIBNEGF_GIT_REPOSITORY "https://github.com/libnegf/libnegf.git")
-  set(LIBNEGF_GIT_TAG "c8ed2caf9ed00fce1a7d9583a605bec211920d2b")  # do not change manually!
+  set(LIBNEGF_GIT_TAG "5b769f76406b12ec2faad30593cb061c5bec7d47")  # do not change manually!
   dftbp_config_hybrid_dependency(Negf Negf::Negf "${HYBRID_CONFIG_METHODS}" "QUIET"
     external/libnegf "${exclude}" "${LIBNEGF_GIT_REPOSITORY}" "${LIBNEGF_GIT_TAG}")
   #list(APPEND PKG_CONFIG_REQUIRES negf)
@@ -213,45 +216,54 @@ add_subdirectory(external/mudpack)
 
 if(WITH_TBLITE OR WITH_SDFTD3)
   set(MCTC_LIB_GIT_REPOSITORY "https://github.com/grimme-lab/mctc-lib.git")
-  set(MCTC_LIB_GIT_TAG "1f690009020fb5f196c1dc359056741738416db6")  # do not change manually!
+  set(MCTC_LIB_GIT_TAG "3d0e921085eb6ca535dfceec876bc99baf52f05d")  # do not change manually!
   dftbp_config_hybrid_dependency(mctc-lib mctc-lib::mctc-lib "${HYBRID_CONFIG_METHODS}" "QUIET"
     external/mctc-lib "${exclude}" "${MCTC_LIB_GIT_REPOSITORY}" "${MCTC_LIB_GIT_TAG}")
   #list(APPEND PKG_CONFIG_REQUIRES mctc-lib)
 
-  set(MSTORE_GIT_REPOSITORY "https://github.com/grimme-lab/mstore.git")
-  set(MSTORE_GIT_TAG "1f690009020fb5f196c1dc359056741738416db6")  # do not change manually!
-  dftbp_config_hybrid_dependency(mstore mstore::mstore "${HYBRID_CONFIG_METHODS}" "QUIET"
-    external/mstore "${exclude}" "${MSTORE_GIT_REPOSITORY}" "${MSTORE_GIT_TAG}")
-  #list(APPEND PKG_CONFIG_REQUIRES mstore)
+  if(INCLUDE_INDIRECT_DEPS)
+    set(MSTORE_GIT_REPOSITORY "https://github.com/grimme-lab/mstore.git")
+    set(MSTORE_GIT_TAG "90fc6fc4d8a6c3d72e5a910347a45edabf65343c")  # do not change manually!
+    dftbp_config_hybrid_dependency(mstore mstore::mstore "${HYBRID_CONFIG_METHODS}" "QUIET"
+      external/mstore "${exclude}" "${MSTORE_GIT_REPOSITORY}" "${MSTORE_GIT_TAG}")
+    #list(APPEND PKG_CONFIG_REQUIRES mstore)
+  endif()
 
-  set(TOML_F_GIT_REPOSITORY "https://github.com/toml-f/toml-f.git")
-  set(TOML_F_GIT_TAG "f066ec6e7fb96d8faf83ab6614ee664a26ad8d57")  # do not change manually!
-  dftbp_config_hybrid_dependency(toml-f toml-f::toml-f "${HYBRID_CONFIG_METHODS}" "QUIET"
-    external/toml-f "${exclude}" "${TOML_F_GIT_REPOSITORY}" "${TOML_F_GIT_TAG}")
-  #list(APPEND PKG_CONFIG_REQUIRES toml-f)
+  if(INCLUDE_INDIRECT_DEPS)
+    set(TOML_F_GIT_REPOSITORY "https://github.com/toml-f/toml-f.git")
+    set(TOML_F_GIT_TAG "f066ec6e7fb96d8faf83ab6614ee664a26ad8d57")  # do not change manually!
+    dftbp_config_hybrid_dependency(toml-f toml-f::toml-f "${HYBRID_CONFIG_METHODS}" "QUIET"
+      external/toml-f "${exclude}" "${TOML_F_GIT_REPOSITORY}" "${TOML_F_GIT_TAG}")
+    #list(APPEND PKG_CONFIG_REQUIRES toml-f)
+  endif()
 
   set(S_DFTD3_GIT_REPOSITORY "https://github.com/awvwgk/simple-dftd3.git")
-  set(S_DFTD3_GIT_TAG "6623834fe0be9f6ed22f9c0cb1c61ea121753c28")  # do not change manually!
+  set(S_DFTD3_GIT_TAG "02dead293e59408100eb382e97be56e2a03fb317")  # do not change manually!
   dftbp_config_hybrid_dependency(s-dftd3 s-dftd3::s-dftd3 "${HYBRID_CONFIG_METHODS}" "QUIET"
     external/s-dftd3 "${exclude}" "${S_DFTD3_GIT_REPOSITORY}" "${S_DFTD3_GIT_TAG}")
   #list(APPEND PKG_CONFIG_REQUIRES s-dftd3)
 endif()
 
 if(WITH_TBLITE)
-  set(MULTICHARGE_GIT_REPOSITORY "https://github.com/grimme-lab/multicharge.git")
-  set(MULTICHARGE_GIT_TAG "46ea4e370b1a59e01cc022d1f65c64bae8dbf968")  # do not change manually!
-  dftbp_config_hybrid_dependency(multicharge multicharge::multicharge "${HYBRID_CONFIG_METHODS}" "QUIET"
-    external/multicharge "${exclude}" "${MULTICHARGE_GIT_REPOSITORY}" "${MULTICHARGE_GIT_TAG}")
-  #list(APPEND PKG_CONFIG_REQUIRES multicharge)
-
-  set(DFTD4_GIT_REPOSITORY "https://github.com/dftd4/dftd4.git")
-  set(DFTD4_GIT_TAG "b1faf68231d8b0fd44cf0701e9f27c8092bd7926")  # do not change manually!
-  dftbp_config_hybrid_dependency(dftd4 dftd4::dftd4 "${HYBRID_CONFIG_METHODS}" "QUIET"
-    external/dftd4 "${exclude}" "${DFTD4_GIT_REPOSITORY}" "${DFTD4_GIT_TAG}")
-  #list(APPEND PKG_CONFIG_REQUIRES dftd4)
+  if(INCLUDE_INDIRECT_DEPS)
+    set(MULTICHARGE_GIT_REPOSITORY "https://github.com/grimme-lab/multicharge.git")
+    set(MULTICHARGE_GIT_TAG "46ea4e370b1a59e01cc022d1f65c64bae8dbf968")  # do not change manually!
+    dftbp_config_hybrid_dependency(multicharge multicharge::multicharge "${HYBRID_CONFIG_METHODS}"
+      "QUIET" external/multicharge "${exclude}" "${MULTICHARGE_GIT_REPOSITORY}"
+      "${MULTICHARGE_GIT_TAG}")
+    #list(APPEND PKG_CONFIG_REQUIRES multicharge)
+  endif()
+
+  if(INCLUDE_INDIRECT_DEPS)
+    set(DFTD4_GIT_REPOSITORY "https://github.com/dftd4/dftd4.git")
+    set(DFTD4_GIT_TAG "f572723f5a5cb8243ea88b0253e182088311c6f3")  # do not change manually!
+    dftbp_config_hybrid_dependency(dftd4 dftd4::dftd4 "${HYBRID_CONFIG_METHODS}" "QUIET"
+      external/dftd4 "${exclude}" "${DFTD4_GIT_REPOSITORY}" "${DFTD4_GIT_TAG}")
+    #list(APPEND PKG_CONFIG_REQUIRES dftd4)
+  endif()
 
   set(TBLITE_GIT_REPOSITORY "https://github.com/tblite/tblite.git")
-  set(TBLITE_GIT_TAG "7bde301ead9b71e08f0ecc19390128f7209644d2")  # do not change manually!
+  set(TBLITE_GIT_TAG "0542ce7ae0e323941156949a0620ca260bc0ce7f")  # do not change manually!
   dftbp_config_hybrid_dependency(tblite tblite::tblite "${HYBRID_CONFIG_METHODS}" "QUIET"
     external/tblite "${exclude}" "${TBLITE_GIT_REPOSITORY}" "${TBLITE_GIT_TAG}")
   #list(APPEND PKG_CONFIG_REQUIRES tblite)
@@ -262,7 +274,8 @@ endif()
 if(WITH_CHIMES)
   set(CHIMES_GIT_REPOSITORY "https://github.com/dftbplus/chimes_calculator.git")
   set(CHIMES_GIT_TAG "98e365365d3b3e4b11b363b4a50dd2ad6cc825d4")  # do not change manually!
-  dftbp_config_hybrid_dependency(ChimesCalc ChimesCalc::ChimesCalc_Fortran "${HYBRID_CONFIG_METHODS}" "QUIET"
+  dftbp_config_hybrid_dependency(ChimesCalc ChimesCalc::ChimesCalc_Fortran
+    "${HYBRID_CONFIG_METHODS}" "QUIET"
   external/chimes "${exclude}" "${CHIMES_GIT_REPOSITORY}" "${CHIMES_GIT_TAG}")
 endif()
 

diff --git a/INSTALL.rst b/INSTALL.rst
@@ -12,11 +12,11 @@ Requirements
 
 In order to compile DFTB+, you need the following software components:
 
-* Fortran 2003 compliant compiler
+* Fortran compiler supporting Fortran 2008 and OpenMP 4.0
 
 * C compiler
 
-* C++ compiler (built with ELSI/PEXSI or ChIMES support)
+* C++ compiler (when built with ELSI/PEXSI or ChIMES support)
 
 * CMake (version 3.16 or newer)
 
@@ -27,6 +27,34 @@ In order to compile DFTB+, you need the following software components:
 * Python (version >= 3.2) for the source preprocessor
 
 
+Fortran compiler
+----------------
+
+The following Fortran compilers are known to build DFTB+ correctly:
+
+* GNU >= 9
+
+* Intel >= 19 or >= 2020 (when built to include the tblite library, as tblite is
+  known to produce incorrect results with Intel 19)
+
+* NAG >= 7.1 (when built without OpenMP support)
+
+
+The following Fortran compilers are known to fail to build DFTB+:
+
+* NAG (when built with OpenMP support, unsupported OpenMP 4.0 constructs, last
+  tested version: 7.1)
+
+* NVIDIA (internal compiler error & unsupported OpenMP 4.0 constructs, last
+  tested version: 22.3)
+
+
+Older versions of the compilers above are likely to fail due to missing Fortran
+features and/or compiler bugs. Compilers by other vendors may work, but have not
+been tested extensively (see also `Tested build environments
+<#tested-build-environments>`_ and `Testing DFTB+ <#testing-dftb>`_).
+
+
 Optional extra dependencies
 ---------------------------
 
@@ -87,7 +115,7 @@ following architectures:
 +---------------+----------------------+-------------+------------------+-----+
 | Architecture  | Compiler             | MPI         | Ext. libraries   |Notes|
 +===============+======================+=============+==================+=====+
-| x86_64 /      | GNU Fortran/C 8.4    | OpenMPI 3.1 | OpenBlas 0.3.7,  |     |
+| x86_64 /      | GNU Fortran/C 9.2    | OpenMPI 4.0 | OpenBlas 0.3.7,  |     |
 | Linux         |                      |             | ScaLAPACK 2.1    |     |
 |               |                      |             | ELSI 2.6.1       |     |
 +---------------+----------------------+-------------+------------------+-----+
@@ -98,20 +126,16 @@ following architectures:
 | x86_64 /      | Intel Fortran/C 19.0 | MPICH 3.3   | MKL 19.0         |     |
 | Linux         |                      |             | ELSI 2.6.1       |     |
 +---------------+----------------------+-------------+------------------+-----+
-| x86_64 /      | NAG Fortran 7.0      | MPICH 3.3   | OpenBlas 0.3.7   | [1] |
+| x86_64 /      | NAG Fortran 7.1      | MPICH 3.4   | OpenBlas 0.3.18  | [1] |
 | Linux         | GNU C 9.2            |             | ScaLAPACK 2.1    |     |
-|               |                      |             | ELSI 2.5.0       |     |
 +---------------+----------------------+-------------+------------------+-----+
-| x86_64 /      | GNU Fortran/C 9.4    | --          | OpenBlas 0.3.18  | [2] |
+| x86_64 /      | GNU Fortran/C 9.4    | --          | OpenBlas 0.3.20  | [2] |
 | OS X          |                      |             |                  |     |
 +---------------+----------------------+-------------+------------------+-----+
 
-All builds are also tested with the optional ARPACK-NG 3.7 and PLUMED 2.5
-libraries.
-
 Notes:
 
-[1] Only Debug build is tested regulary with OpenMP turned off.
+[1] Only Debug build is tested regulary with OpenMP turned off and without ELSI.
 [2] Only partial testing of the serial version.
 
 
@@ -148,6 +172,13 @@ include the Slater-Koster (slako) data for testing the compiled code.
 For more information see the detailed help for this tool by issuing
 ``./utils/get_opt_externals -h``.
 
+Slater-Koster file locations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The DFTB+ code checks the shell variable `DFTBPLUS_PARAM_DIR` when
+setting the path to check the Prefix keyword for finding data. If
+unset, it assumes the local directory as the starting path.
+
 
 Building
 ========

diff --git a/README.rst b/README.rst
@@ -28,12 +28,28 @@ management framework using `Miniconda
 ``conda-forge`` channel in order to be able to access DFTB+. (Please consult the
 conda documentation for how to set-up your conda environment.)
 
-We provide several build variants (mpi, non-mpi), choose the one suiting your
-needs. For example, by issuing ::
+We recommend the use of the `mamba installer <https://mamba.readthedocs.io/>`_,
+as we have experienced dependency resolution problems with the original conda
+installer in the past::
 
-  conda install 'dftbplus=*=nompi_*'
+  conda install -n base mamba
 
-you obtain the latest stable non-MPI version of DFTB+.
+We provide several build variants, choose the one suiting your needs. For
+example, by issuing ::
+
+  mamba install 'dftbplus=*=nompi_*'
+
+or ::
+
+  mamba install 'dftbplus=*=mpi_mpich_*'
+
+or ::
+
+  mamba install 'dftbplus=*=mpi_openmpi_*'
+
+to get the last stable release of DFTB+ with, respectively,
+serial (OpenMP-threaded) build or with MPI-parallelized build using either the
+MPICH or the Open MPI framework.
 
 
 Downloading the binary

diff --git a/app/misc/units/printunits.F90 b/app/misc/units/printunits.F90
@@ -17,18 +17,24 @@
 
 !> Printing out the conversion factors for the different units
 program printunits
-  use dftbp_common_unitconversion
-  use dftbp_common_constants
+  use dftbp_common_unitconversion, only : lengthUnits, inverseLengthUnits, energyUnits, forceUnits,&
+      & timeUnits, freqUnits, volumeUnits, chargeUnits, eFieldUnits, bFieldUnits, pressureUnits,&
+      & velocityUnits, dipoleUnits, massUnits, angularUnits, massDensityUnits, TUnit
   implicit none
 
+  type(TUnit) :: localUnit
   integer :: ii
 
   write(*,*)"Convert from unit to a.u. by multiplying with"
   #:for names, units in CONVERSIONS
     write(*,*)
-    write(*,"(A)")"${names}$:"
+    write(*,"(a)")"${names}$:"
     do ii = 1, size(${units}$)
-      write(*,"(1X,A20,E24.15)") ${units}$(ii)%name, ${units}$(ii)%convertValue
+      ! Workaround: nag 7.1
+      ! Can not print derived type, if part of an array
+      ! write(*,"(1x,dt)") ${units}$(ii)
+      localUnit = ${units}$(ii)
+      write(*,"(1x,dt)") localUnit
     end do
   #:endfor