CREST 3.0 pre-release (crest-lab#250)

Long needed update of the main branch.

Signed-off-by: Philipp Pracht <pp555@cam.ac.uk>
Co-authored-by: Pit Steinbach <steinbach@pc.rwth-aachen.de>
Co-authored-by: GereonFeldmann <126183817+GereonFeldmann@users.noreply.github.com>
Co-authored-by: Christoph Bannwarth <bannwarth@pc.rwth-aachen.de>
Co-authored-by: Felix Zeller <95427480+zellerf@users.noreply.github.com>
Co-authored-by: Christoph Plett <82893466+cplett@users.noreply.github.com>

.github/workflows/build.yml

@@ -30,10 +30,10 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Setup Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.x
 
@@ -54,7 +54,14 @@ jobs:
         printenv >> $GITHUB_ENV
 
     - name: Install meson
-      run: pip3 install meson==0.60.1 ninja
+      run: pip3 install meson==0.63.3 ninja
+
+    - name: Git Sumbodules (including tblite patch)
+      run: |
+        git submodule update --init
+        cd subprojects/tblite
+        git apply ../packagefiles/tblite/tblite_patch.patch
+        cd ../../
 
     - name: Configure meson build
       run: meson setup ${{ env.BUILD_DIR }} --prefix=/

.github/workflows/stale.yml

@@ -0,0 +1,23 @@
+name: "Close stale issues and PRs"
+
+on:
+  schedule:
+    # Every day at 00:00
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/stale@v9.0.0
+        with:
+          stale-issue-message: 'This issue had no activity for **6 months**. It will be closed in **1 week** unless there is some new activity.'
+          stale-issue-label: 'stale'
+          exempt-issue-labels: 'bug,enhancement'
+          stale-pr-message: 'This pull request had no activity for **6 months**. It will be closed in **1 week** unless there is some new activity.'
+          stale-pr-label: 'stale'
+          days-before-stale: 180
+          days-before-close: 7
+          operations-per-run: 20

.gitignore

@@ -6,3 +6,4 @@ build_majestix
 build_commands
 _build*
 src/crest
+bin/

.gitmodules

@@ -0,0 +1,22 @@
+[submodule "subprojects/gfn0"]
+	path = subprojects/gfn0
+	url = https://github.com/pprcht/gfn0.git
+    branch = main
+[submodule "subprojects/toml-f"]
+	path = subprojects/toml-f
+	url = https://github.com/toml-f/toml-f.git
+    branch = main
+[submodule "subprojects/gfnff"]
+	path = subprojects/gfnff
+	url = https://github.com/pprcht/gfnff.git
+    branch = master 
+[submodule "subprojects/tblite"]
+	path = subprojects/tblite
+#	 url = https://github.com/tblite/tblite.git
+#    branch = main
+    url = https://github.com/pprcht/tblite.git
+    branch = ompleak
+[submodule "subprojects/lwoniom"]
+	path = subprojects/lwoniom
+	url = https://github.com/crest-lab/lwoniom
+    branch = main

CMakeLists.txt

@@ -16,25 +16,32 @@ cmake_minimum_required(VERSION 3.14)
 project(
   "crest"
   LANGUAGES "Fortran" "C"
-  VERSION "2.12.0"
+  VERSION "3.0"
 )
+set(SOVERSION "pre")
 
 # Follow GNU conventions for installing directories
 include(GNUInstallDirs)
 
 # General configuration information
-set(exe-deps)
+set(libs)
 add_subdirectory("config")
 
+
+#
+# Libraries
+#
+
 # OpenMP dependency
-if(NOT TARGET OpenMP::OpenMP_Fortran)
+if(NOT TARGET OpenMP::OpenMP_Fortran AND WITH_OpenMP)
   find_package(OpenMP REQUIRED)
   list(
-    APPEND exe-deps
+    APPEND libs
     OpenMP::OpenMP_Fortran
   )
 endif()
 
+# BLAS and LAPACK
 if(NOT TARGET BLAS::BLAS)
   find_package(BLAS REQUIRED)
   if(NOT TARGET BLAS::BLAS AND BLAS_FOUND)
@@ -52,32 +59,101 @@ if(NOT TARGET LAPACK::LAPACK)
   endif()
 endif()
 list(
-  APPEND exe-deps
+  APPEND libs
   LAPACK::LAPACK
   BLAS::BLAS
 )
 
-# General configuration information
+# tblite
+if(WITH_TBLITE)
+  find_package("tblite" REQUIRED)
+  add_definitions(-DWITH_TBLITE)
+  list(
+    APPEND libs
+    tblite::tblite
+  )
+endif()
+
+
+# toml-f
+if(WITH_TOMLF)
+  find_package("toml-f" REQUIRED)
+  add_definitions(-DWITH_TOMLF)
+  list(
+    APPEND libs
+    toml-f::toml-f
+  )
+endif()
+
+
+# GFN0-xTB
+if(WITH_GFN0)
+  find_package("gfn0" REQUIRED)
+  add_definitions(-DWITH_GFN0)
+  list(
+    APPEND libs
+    gfn0::gfn0
+  )
+endif()
+
+
+# GFN-FF
+if(WITH_GFNFF)
+  find_package("gfnff" REQUIRED)
+  add_definitions(-DWITH_GFNFF)
+  list(
+    APPEND libs
+    gfnff::gfnff
+  )
+endif()
+
+# XHCFF
+if(WITH_XHCFF)
+  find_package("xhcff" REQUIRED)
+  add_definitions(-DWITH_XHCFF)
+  list(
+    APPEND libs
+    xhcff::xhcff
+  )
+endif()
+
+
+
+
+#
+# CREST sources
+#
 set(prog)
 set(srcs)
 add_subdirectory("src")
 
+
+#
+# Executables
+#
 add_executable(
-  "${PROJECT_NAME}-exe"
+  ${PROJECT_NAME}-exe
   "${srcs}" "${prog}"
 )
 set_target_properties(
-  "${PROJECT_NAME}-exe"
+  ${PROJECT_NAME}-exe
   PROPERTIES
+  Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/include
+  RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}
   OUTPUT_NAME "${PROJECT_NAME}"
-  Fortran_MODULE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/include"
 )
 target_link_libraries(
-  "${PROJECT_NAME}-exe"
+  ${PROJECT_NAME}-exe
   PRIVATE
-  "${exe-deps}"
+  "${libs}"
 )
 
+get_target_property(OUT ${PROJECT_NAME}-exe LINK_LIBRARIES)
+message(STATUS ${OUT})
+
+#
+# Binary installing option
+#
 install(
   TARGETS
   "${PROJECT_NAME}-exe"

README.md

@@ -1,46 +1,81 @@
-# Conformer-Rotamer Ensemble Sampling Tool
+# CREST
 
 [![Latest Version](https://img.shields.io/github/v/release/crest-lab/crest)](https://github.com/crest-lab/crest/releases/latest)
 [![DOI](https://img.shields.io/badge/DOI-10.1039%2Fc9cp06869d%20-blue)](http://dx.doi.org/10.1039/c9cp06869d)
+![example workflow](https://github.com/crest-lab/crest/actions/workflows/build.yml/badge.svg)
+[![License: LGPL v3](https://img.shields.io/badge/License-LGPL_v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0)
+[![Github Downloads All Releases](https://img.shields.io/github/downloads/crest-lab/crest/total)](https://github.com/crest-lab/crest/releases)
 
-This is the offical repository of the CREST program developed by the Grimme group in Bonn.
-
-CREST is an extension to the [`xtb`](https://github.com/grimme-lab/xtb) program.
-It functions as an IO based OMP scheduler (*i.e.*, calculations are
-performed by the `xtb` program) and tool for the creation and analysation of
-structure ensembles.
+CREST (originally abbreviated from ***C***onformer-***R***otamer ***E***nsemble ***S***ampling ***T***ool) is a program for the automated exploration of the low-energy molecular chemical space.
+It functions as an OMP scheduler for calculations at with efficient force-field and semiempirical quantum mechanical methods such as xTB, and provides
+a variety capabilities for creation and analysis of structure ensembles.
 
 <div align="center">
-<img src="./assets/crest.png" alt="CREST" width="200">
+<img src="./assets/newtoc.png" alt="CREST" width="700">
 </div>
 
+---
+**NOTE: This is the 3.0 pre-release. Please report any bugs or issues ASAP. The program can be switched back to its previous behaviour via the `--legacy` option.**
+
+---
+
 
 ## Documentation
 
-The CREST documentation with installation instructions and application examples is hosted at         <https://crest-lab.github.io/crest-docs/>.
+The CREST documentation with installation instructions and application examples is hosted at <https://crest-lab.github.io/crest-docs/>.
 
 
 ## Installation quick guide
 
 For any installation make sure that you have correctly installed and sourced the [`xtb`](https://github.com/grimme-lab/xtb) program before attempting any calculations with CREST.
+**While `xtb` is technically not needed for the primary runtypes of CREST versions >3.0 thanks to an integration of [`tblite`](https://github.com/tblite/tblite), some functionalities, like QCG, still require it!**
 
 There are multiple possible ways of installing CREST. 
-For building the program from source we recommend the Intel `ifort` and `icc` compilers.
+For building the program from source we recommend the Intel `ifort` and `icc` compilers (tested with the 2021 version).
+
+Detailed build instructions can be found at <https://crest-lab.github.io/crest-docs/page/installation>.
 
 
 ### Precompiled binaries
 
 To use the statically linked binaries (Intel compilers)
 that can be found at the [release page](https://github.com/crest-lab/crest/releases),
 of this repository.
+The most recent program version is automatically build (`meson`/`ifort`) from the main branch and can be found at the [**continous release page**](https://github.com/crest-lab/crest/releases/tag/latest).
 Simply unpack the binary and add it to your *PATH* variable.
 ```bash
 unzip crest.zip
 ```
-The program should be directly executable in most cases.
+or
+```bash
+tar -xf crest-latest.tar.xz
+```
+The program should be directly executable.
+
+### Tested builds
+Working and tested builds of CREST (mostly on Ubuntu 20.04 LTS):
+
+| Build System | Compiler | Linear Algebra Backend | Build type     | Status     |
+|--------------|----------|------------------------|:--------------:|:----------:|
+| CMake | GNU (gcc 10.3.0)  | [OpenBLAS](https://github.com/xianyi/OpenBLAS) (with OpenMP) | dynamic | ✅ |
+| CMake | GNU (gcc 10.3.0)  |  [MKL shared (oneAPI 2023.1)](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html) | dynamic | ✅ |
+| Meson | [Intel (`ifort`/`icc` 2021.9.0)](https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html)   | [MKL static (oneAPI 2023.1)](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html) | static  | ✅ |
+| Meson | [Intel (`ifort` 2021.9.0/`icx` 2023.1.0)](https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html)   | [MKL static (oneAPI 2023.1)](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html) | static  | ✅ |
+
+
+
+Generally, subprojects should be initialized for the *default* build options, which can be done by 
+```bash
+git submodule init
+git submodule update
+```
+For more information about builds including subprojects see [here](./subprojects/README.md).
 
+Some basic build instructions can be found in the following dropdown tabs:
 
-### Meson
+<details open>
+<summary><h4><code>meson</code> build</h4></summary>
+<!-- blank line to recover markdown format-->
 
 For the setup an configuration of meson see also the [meson setup](https://github.com/grimme-lab/xtb/blob/master/meson/README.adoc) page hosted at the `xtb` repository.
 The chain of commands to build CREST with meson is:
@@ -51,35 +86,36 @@ meson setup _build --prefix=$PWD/_dist
 meson install -C _build
 ```
 
-When attempting to build with `gfortran` and `gcc`, add `-Dla_backend=mkl` to the meson setup        command. Tested with version 10.2 of the GNU compilers.
+The `meson` build of CREST is mainly focused on and tested with the Intel `ifort`/`icc` compilers.
+When using newer versions of Intel's oneAPI, replacing `icc` with `icx` should work. Please refrain from using `ifx` instead of `ifort`, however.
+When attempting to build with `gfortran` and `gcc`, add `-Dla_backend=mkl` to the meson setup command. Compatibility with the GNU compilers might be limited. We recommend the CMake build (see below) in this instance.
 
+By default the `meson` build will create a **statically** linked binary.
+</details>
 
-### Cmake
+<details>
+<summary><h4><code>CMake</code> build</h4></summary>
+<!-- blank line to recover markdown format-->
 
-For the setup of Cmake see also the [Cmake setup](https://github.com/grimme-lab/xtb/blob/master/cmake/README.adoc) page hosted at the `xtb` repository.
+For the setup of CMake see also the [CMake setup](https://github.com/grimme-lab/xtb/blob/master/cmake/README.adoc) page hosted at the `xtb` repository.
 Building CREST with CMake works with the following chain of commands:
-
 ```bash
-export FC=ifort CC=icc
+export FC=gfortran CC=gcc
 cmake -B _build -DCMAKE_BUILD_TYPE=Release
-make -C _build
 ```
-
-and to build the CREST binary
-
+and then to build the CREST binary
 ```bash
 make -C _build
 ```
 
-### Building via `make`
-
-In the `src` directory a `Makefile` can be found to build a statically linked binary. Modify the     makefile to your requirements and build the program via
-```bash
-make
-```
+The CMake build of CREST is focused on and tested with the GNU `gfortran`/`gcc` compilers. The Intel compilers could technically be used as well, but in our experience the respective build is more fragile than its static `meson` counterpart.
 
+By default the `CMake` build will create a **dynamically** linked binary.
+</details>
 
-### Conda
+<details>
+<summary><h4>Conda build</h4></summary>
+<!-- blank line to recover markdown format-->
 
 A [conda-forge](https://github.com/conda-forge) feedstock is maintained at <https://github.com/conda-forge/crest-feedstock>.
 
@@ -96,11 +132,13 @@ Once the `conda-forge` channel has been enabled, CREST can be installed with `co
 conda install crest
 ```
 
+The confa-forge distribution is based on a CMake/`gfortran` build. 
+</details>
 
 
 ---
 
-## Citations
+### Citations
 
 1. P. Pracht, F. Bohle, S. Grimme, *Phys. Chem. Chem. Phys.*, **2020**, 22, 7169-7192.
   DOI: [10.1039/C9CP06869D](https://dx.doi.org/10.1039/C9CP06869D)
@@ -117,7 +155,9 @@ conda install crest
 5. S. Spicher, C. Plett, P. Pracht, A. Hansen, S. Grimme,  *J. Chem. Theory Comput.*, **2022**,
   *18*, 3174-3189. DOI: [10.1021/acs.jctc.2c00239](https://dx.doi.org/10.1021/acs.jctc.2c00239)
 
-## License
+6. P. Pracht, C. Bannwarth, *J. Chem. Theory Comput.*, **2022**, *18 (10)*, 6370-6385. DOI: [10.1021/acs.jctc.2c00578](https://dx.doi.org/10.1021/acs.jctc.2c00578)
+
+### License
 
 CREST is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.