Merge branch 'merzlab:master' into QUICK_Constrained_Optimization

.github/workflows/mpi.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Install deps
         run: sudo apt-get -y install gfortran openmpi-bin openmpi-common libopenmpi-dev
       - name: Configure mpi
-        run: ./configure --mpi --prefix $PWD/install gnu
+        run: ./configure --mpi --enablef --prefix $PWD/install gnu
       - name: Build mpi
         run: make
       - name: Install mpi
@@ -44,12 +44,14 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Install deps
-        run: sudo apt-get -y install gfortran cmake openmpi-bin openmpi-common libopenmpi-dev
+        run: |
+             sudo apt-get update
+             sudo apt-get -y install gfortran cmake openmpi-bin openmpi-common libopenmpi-dev
       - name: Configure MPI
         run: |
              mkdir build
              cd build
-             cmake .. -DCOMPILER=GNU -DMPI=TRUE -DCMAKE_INSTALL_PREFIX=$(pwd)/../install
+             cmake .. -DCOMPILER=GNU -DMPI=TRUE -DENABLEF=TRUE -DCMAKE_INSTALL_PREFIX=$(pwd)/../install
       - name: Build MPI
         run: |
              cd build

.github/workflows/serial.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Install deps
         run: sudo apt-get -y install gfortran
       - name: Configure serial
-        run: ./configure --serial --prefix $PWD/install gnu
+        run: ./configure --serial --enablef --prefix $PWD/install gnu
       - name: Build serial
         run: make
       - name: Install serial
@@ -42,12 +42,14 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Install deps
-        run: sudo apt-get -y install gfortran cmake
+        run: |
+             sudo apt-get update
+             sudo apt-get -y install gfortran cmake
       - name: Configure serial
         run: |
              mkdir build
              cd build
-             cmake .. -DCOMPILER=GNU -DCMAKE_INSTALL_PREFIX=$(pwd)/../install
+             cmake .. -DCOMPILER=GNU -DENABLEF=TRUE -DCMAKE_INSTALL_PREFIX=$(pwd)/../install
       - name: Build serial
         run: |
              cd build

CMake-Options.md

@@ -26,5 +26,5 @@ These options allow you do adjust this behavior.
 By default QUICK will only build the serial version.  This can be changed with these options:
 - `-DMPI=TRUE`: Also build MPI versions of all programs.
 - `-DCUDA=TRUE`: Also build CUDA versions of all programs.  If both MPI and CUDA are active at the same time, CUDA MPI versions will additionally be built.
-- `-DQUICK_USER_ARCH=<kepler|maxwell|pascal|volta|turing|ampere>`: Build CUDA code only for the given architecture.  If not provided, quick will compile for all supported architectures in your CUDA version.
+- `-DQUICK_USER_ARCH=<kepler|maxwell|pascal|volta|turing|ampere|adalovelace>`: Build CUDA code only for the given architecture.  If not provided, quick will compile for all supported architectures in your CUDA version.
 - `-DQUICK_VERBOSE_PTXAS=TRUE`: Pass -v flag to ptxas to dump details about compiled functions in CUDA code.

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.9.0) # version 3.9.0 needed for FindMPI and FindOpenMP versions which provide imported targets
 
-project(quick LANGUAGES NONE VERSION 22.03)
+project(quick LANGUAGES NONE VERSION 24.03)
 
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/quick-cmake)
 
@@ -36,7 +36,7 @@ if(NOT INSIDE_AMBER)
 
 endif()
 
-option(ENABLEF "Enables the compilation of QUICK's time consuming f functions in the ERI code of cuda version." FALSE)
+option(ENABLEF "Enables the support for f functions in the ERI code." FALSE)
 
 # Compiler flags
 # These should really go into cmake/CompilerFlags.cmake but with the
@@ -236,6 +236,11 @@ if(INSIDE_AMBER)
   add_definitions(-DCEW)
 endif()
 
+# set general preprocessor flag for enabling F functions
+if(ENABLEF)
+  add_definitions(-DENABLEF)
+endif()
+
 # CUDA compiler flags
 # --------------------------------------------------------------------
 include(QUICKCudaConfig)
@@ -284,6 +289,9 @@ if(INSIDE_AMBER)
 	# install tests dir
 	install(DIRECTORY test USE_SOURCE_PERMISSIONS DESTINATION AmberTools/src/quick COMPONENT Tests ${TESTS_EXCLUDE_OPTION})
 
+        # install runtest script
+        install(PROGRAMS tools/runtest DESTINATION AmberTools/src/quick COMPONENT Tests)
+
 else()
 	# Standalone install
 

README.md

@@ -24,20 +24,21 @@ Features
 * Supports QM/MM calculations with Amber22 and later
 * Fortran API to use QUICK as QM energy and force engine
 * MPI parallelization for CPU platforms
-* Massively parallel GPU implementation via CUDA/HIP for Nvidia/AMD GPUs
+* Massively parallel GPU implementation via CUDA/HIP for Nvidia/AMD GPUs (HIP available in QUICK-23.08, currently disabled)
 * Multi-GPU support via MPI + CUDA/HIP, also across multiple compute nodes
 
 Limitations
 -----------
-* Supports energy/gradient calculations with basis functions up to d
+* Supports energy/gradient calculations with basis functions up to f
 * Supports only Cartesian basis functions (no spherical harmonics)
 * Effective core potentials (ECPs) are not supported
 * DFT calculations are performed exclusively using the SG1 grid system 
 * No meta-GGA functionals, no range-separated hybrid functionals
+* HIP (AMD GPU support) is currently disabled (available in QUICK-23.08 but not QUICK-24.03)
 
 Installation
 ------------
-Supported platforms: Linux (x86 and ARM), macOS (only Intel x86 tested)
+Supported platforms: Linux (x86 and ARM), macOS (x86 and ARM)
 
 * [Installation Guide](https://quick-docs.readthedocs.io/en/23.8.0/installation-guide.html#installation-guide)
    1. [Compatible Compilers and Hardware](https://quick-docs.readthedocs.io/en/23.8.0/installation-guide.html#compatible-compilers-and-hardware)
@@ -56,10 +57,12 @@ A list of installation and runtime issues can be found [here](https://quick-docs
 
 Citation
 --------
-Please cite QUICK-23.08 as follows.
+Please cite QUICK-24.03 as follows.
 
 Manathunga, M.; Shajan, A.; Smith, J.; Miao, Y.; He, X.; Ayers, K;
-Brothers, E.; Götz, A. W.; Merz, K. M. QUICK-23.08 University of California San Diego, CA and Michigan State University, East Lansing, MI, 2023.
+Brothers, E.; Götz, A. W.; Merz, K. M. QUICK-24.03 
+University of California San Diego, CA and
+Michigan State University, East Lansing, MI, 2024.
 
 If you perform density functional theory calculations please also cite:
 
@@ -99,9 +102,16 @@ Cruzeiro, V. W. D.; Manathunga, M.; Merz, K. M.; Götz, A. W.
 Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK.
 [*J. Chem. Inf. Model.* 61, 2109–2115 (2021)](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00169).
 
-If you perform geometry optimization calculations using the DL-FIND optimizer please also cite:
+If you perform geometry optimizations please cite:
 
-Kästner, J.; Carr, J. M.; Keal, T. W.; Thiel, W.; Wander, A.; Sherwood, P. DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations. 
+Shajan, A.; Manathunga, M.; Götz, A.W.; Merz, K.M.
+Geometry optimization: A comparison of different open-source geometry optimizers.
+[*J. Chem. Theory Comput.* 19, 7533-7541 (2023)](https://doi.org/10.1021/acs.jctc.3c00188).
+
+If you use the DL-FIND for the geometry optimizations please also cite:
+
+Kästner, J.; Carr, J. M.; Keal, T. W.; Thiel, W.; Wander, A.; Sherwood, P.
+DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations. 
 [*J. Phys. Chem. A* 113, 11856-11865 (2009)](https://pubs.acs.org/doi/10.1021/jp9028968).
 
 License