Merge branch 'devel'

* ANN functionality is revised and extended, now fully-functional
* Eigen3 is removed from the codebase, build instructions are now set to use the external package
* Added the libint2 support, Libra is linked to the external libint2 libraries and can use them
* Added the MOLDEN-file procedures: constructing the molecular integrals using these files
* Added the CP2k workflow with libint2 support
* Added the xTB (in CP2k) workflow
* Pickling support for various Libra classes
* Simplified and generalized the multithreading calculations and made the workflows more user-friendly
* Added more efficient methods for SD overlap and time-overlap calculations
* Added user-friendly general NA-MD workflows, with a set of new recipes for common types of calculations
* Less memory-demanding saving in the files
* Fixed a memory leak in the NA-MD workflows

AUTHORS

@@ -1,6 +1,7 @@
 Alexey V. Akimov <alexeyak@buffalo.edu>
 Alexey V. Akimov <alexvakimov@gmail.com>
-Brendan Smith <bsmith24@buffalo.edu>
+Dr. Brendan Smith <bsmith24@buffalo.edu>
+Mr. Mohammad Shakiba <mshakiba.kerman.iran@gmail.com>
 Story Temen <storytem@buffalo.edu>
 Wei Li <liwei0099@gmail.com>
 Kosuke Sato <??>

CMakeLists.txt

@@ -1,17 +1,17 @@
-# Set the compiler as described here: https://cmake.org/Wiki/CMake_FAQ#How_do_I_use_a_different_compiler.3F
-#
-#  Verify that Cmake is up to date
-#
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
-#SET(CMAKE_LEGACY_CYGWIN_WIN32 0)
-
-
-#
-#  Project name
-#
-
-
-PROJECT("libra")
+# Set the compiler as described here: https://cmake.org/Wiki/CMake_FAQ#How_do_I_use_a_different_compiler.3F
+#
+#  Verify that Cmake is up to date
+#
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+#SET(CMAKE_LEGACY_CYGWIN_WIN32 0)
+
+
+#
+#  Project name
+#
+
+
+PROJECT("libra")
 
 #
 #  User-defined Find modules
@@ -28,7 +28,9 @@ MESSAGE("Advice: If this search fails, try setting cache variables: -DPYTHON_LIB
 MESSAGE("Hint to self: -DPYTHON_INCLUDE_DIR=/home/Alexey_2/Soft/Python-2.6.7/bin/include/python2.6 -DPYTHON_LIBRARY=/home/Alexey_2/Soft/Python-2.6.7/bin/bin")
 
 # For Linux and Cygwin
-FIND_PACKAGE(PythonLibs 3.7 REQUIRED)
+# Adapt it according to your system
+FIND_PACKAGE(PythonLibs 3.6 REQUIRED)
+#FIND_PACKAGE(PythonLibs 3.7 REQUIRED)
 
 IF(PYTHONLIBS_FOUND)
   MESSAGE("Success!")
@@ -50,19 +52,22 @@ MESSAGE(${PYTHON_INCLUDE_DIRS})
 #
 #  Boost library
 #
-
+
 MESSAGE("Looking for Boost libraries...")
 SET(Boost_NO_BOOST_CMAKE TRUE) # to fix the problem of finding python37 libs
 SET(Boost_USE_STATIC_LIBS=OFF)
 SET(Boost_USE_MULTITHREADED=OFF)
 SET(Boost_USE_STATIC_RUNTIME=OFF)
 
-
-FIND_PACKAGE(Boost REQUIRED)
+# Adapt it according to your system
+FIND_PACKAGE(Boost 1.73.0 REQUIRED)
+#FIND_PACKAGE(Boost REQUIRED)
 IF(Boost_FOUND)
   MESSAGE("Success!")
-  INCLUDE_DIRECTORIES("${Boost_INCLUDE_DIRS}")  
-  FIND_PACKAGE(Boost COMPONENTS python37 regex) # it seems that it is important to find sub-packages too!!!
+  INCLUDE_DIRECTORIES("${Boost_INCLUDE_DIRS}") 
+  # Adapt it based on your system
+  FIND_PACKAGE(Boost COMPONENTS python36 regex) # it seems that it is important to find sub-packages too!!!
+  #FIND_PACKAGE(Boost COMPONENTS python37 regex)
 ELSEIF(NOT Boost_FOUND)
   MESSAGE(FATAL_ERROR "Unable to find correct Boost version. Did you set BOOST_ROOT?")
 ENDIF()
@@ -73,6 +78,38 @@ MESSAGE("Found Boost include directory: ")
 MESSAGE("${Boost_INCLUDE_DIRS}")
 
 
+
+FIND_PACKAGE(Eigen3)
+IF(EIGEN3_FOUND)
+  INCLUDE_DIRECTORIES("${EIGEN3_INCLUDE_DIR}")   
+  MESSAGE("Found Eigen3 include directory: ")
+  MESSAGE("${EIGEN3_INCLUDE_DIR}")
+ELSEIF(NOT EIGEN3_FOUND)
+  MESSAGE(FATAL_ERROR "Unable to find Eigen3")
+ENDIF()
+
+
+SET(EIGEN3_INCLUDE_DIRS "${EIGEN3_INCLUDE_DIR}")
+
+# Remove CMakeCache.txt from the previous build, if you get an error finding libint2 due to problems 
+# in finding Eigen3
+
+# Libint2 2.7.0 CONFIG REQUIRED COMPONENTS shared gss e5 g5
+#FIND_PACKAGE(Libint2 MODULE 2.7.0)
+FIND_PACKAGE(Libint2 CONFIG 2.7.0 REQUIRED COMPONENTS shared gss e5 g5)
+IF(Libint2_FOUND)
+  INCLUDE_DIRECTORIES("${Libint2_INCLUDE_DIRS}")   
+  MESSAGE("Found Libint2 include directory: ")
+  MESSAGE("${Libint2_INCLUDE_DIRS}")
+  MESSAGE("Found Libint2_LIBRARIES: ")
+  MESSAGE("${Libint2_LIBRARIES}")
+  MESSAGE("Found Libint2_LIBRARY: ")
+  MESSAGE("${Libint2_LIBRARY}")
+ELSEIF(NOT Libint2_FOUND)
+  MESSAGE(FATAL_ERROR "Unable to find correct libint2")
+ENDIF()
+
+
 #
 # GNU compiler definitions
 #

README.md

@@ -10,7 +10,6 @@ The program website is [here](https://quantum-dynamics-hub.github.io/libra/index
 
 More:
 
-* [How to install](https://quantum-dynamics-hub.github.io/libra/installation.html)
 * [Training & Usage](https://github.com/compchem-cybertraining/Tutorials_Libra)
 * [Autogenerated Documentation](https://quantum-dynamics-hub.github.io/libra-code/)
 
@@ -27,6 +26,167 @@ for all users with the intent:
    knowledge and skills with others;
 
 
+## Installation (as of after 5/14/2021)
+
+### 1. Install miniconda (for Python 3.8) and activate Conda
+
+    mkdir Conda
+    cd Conda/
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh . 
+    sh ./Miniconda3-latest-Linux-x86_64.sh -b -u -p <install_dir>
+
+  Here, 
+
+  * the `-b` option will accept the license agreement and will skip all the prompts
+  * the `-u` option will tell the installer to do all the needed updates
+  * the `-p` option followed by the installation directory path (will be created), tells
+     the installed where to install the package.
+
+  To activate the installed base environment of Conda do:
+
+    eval "$(<path to bin/conda> shell.bash hook)"
+
+  For instance, 
+
+    eval "$(/projects/academic/cyberwksp21/Software/Conda/Miniconda3/bin/conda shell.bash hook)"
+
+
+  You will need to run this script every time you want to use a particular Conda and the 
+  corresponding environments, unless you include this command in your .bashrc or .bash_profile
+
+  Test it is working by doing:
+
+    which conda
+
+
+### 2. Download Libra 
+
+    mkdir libra
+    cd libra
+    git clone https://github.com/Quantum-Dynamics-Hub/libra-code.git .
+
+   and switch to the correct branch or tag - usually, it would be `devel` branch
+
+    git checkout devel
+
+
+### 3. Create the environment equipped with all Libra needs 
+
+#### 3.1. Simple way:
+
+Just execute the following script located in the root of Libra distribution:
+
+    sh ./libra_env_build.sh
+
+This script will create the environment called `libra` and will install all the
+needed stuff in it. You just need to activate it:
+
+    conda activate libra
+
+#### 3.2. Detailed instructions on what the script about does:
+
+It first creates and activates the `libra` environment:
+
+    conda create -n libra
+
+Update conda install if needed (e.g. if the output suggests it)
+
+    conda activate libra
+
+Thne, it installs all the dependencies and tools.
+
+Do this one by one, and in this order (should not matter too much, but who knows it)
+
+    > To automate the below procedures, you can use `-y` option to accept prompts (sometimes this will override)
+    > previous packages/conflicts, so be careful
+    > 
+    > You can also use `-q` to get rid of all the messages to the output, although i'd keep it to keep track of what's going on
+
+Basic stuff
+
+    conda install conda-build
+    conda install gcc_linux-64
+    conda install gxx_linux-64
+    conda install make
+    conda install boost
+    conda install cmake
+    conda install git
+    conda install -c anaconda h5py
+    conda install -c conda-forge/label/gcc7 eigen 
+    conda install -c psi4/label/dev libint2 
+    conda install -c anaconda gmp
+    conda install -c conda-forge/label/gcc7 mpfr 
+
+More, but still needed because some Python modules require those.
+We need to downgrade Python version here to 3.6 to enable Psi4 installation
+
+    conda install python=3.6
+    conda install -c psi4 psi4
+    conda install -c conda-forge matplotlib
+    conda install -c rmg py3dmol
+    conda install -c anaconda numpy
+    conda install -c anaconda scipy
+    conda install -c conda-forge llvm-openmp
+
+You can install Jupyter notebook using the following command. This will be useful and you can set up and access the Jupyter notebook 
+remotely from a cluster and load the tutorials
+
+    conda install -c conda-forge jupyterlab
+
+
+Used in some of the tutorials
+
+    conda install -c conda-forge/label/gcc7 imageio
+
+
+### 4. Adapt the CMakeLists.txt file according to your system
+
+   Because we had to downgrade Python to 3.6, we need to edit the CMakeLists.txt such that 
+   cmake is looking for the correct Python version
+
+    FIND_PACKAGE(PythonLibs 3.6 REQUIRED)
+
+   and also reflect it in the component of the Boost.Python to be found:
+
+    FIND_PACKAGE(Boost COMPONENTS python36 regex)
+
+   Same for Boost (see the error messages for what version of Boost the cmake can find). In my current
+   case, it suggest the version 1.73.0, so be it:
+
+    FIND_PACKAGE(Boost 1.73.0 REQUIRED)
+
+### 5. Create the build directory and make the Makefiles
+
+   Then in the libra directory, create the build directory:
+
+    cd libra
+    mkdir _build
+    cd _build
+    cmake ../
+
+### 6. Compile the package
+
+    make -j4
+
+### 7. Setup environmental variables
+
+   Add the following exports to your `.bash_profile` file
+
+    export PYTHONPATH=<path to the ppackage>/libra/_build/src:$PYTHONPATH
+    export LD_LIBRARY_PATH=<path to the ppackage>/libra/_build/src:$LD_LIBRARY_PATH
+
+### 8. Restart the terminal or source the bash profile and activate libra conda environment
+
+    source .bash_profile 
+    conda activate libra
+
+   And you should be ready to use Libra.
+
+
+* [Old instructions](https://quantum-dynamics-hub.github.io/libra/installation.html)
+
+
+
 ## Developers and Contributors
 
   * Dr. Alexey Akimov (University at Buffalo, [link](https://akimovlab.github.io/index.html) )  
@@ -37,7 +197,7 @@ for all users with the intent:
       Libra/DFTB+, Libra/QE, Libra/ErgoSCF, Libra/CP2K, and Libra/Gaussian interfaces
 
   * Mr. Mohammad Shakiba (Shahid Bahonar University of Kerman, Iran)
-      Cube file processing scripts, Libra/CP2K and Libra/Gaussian interfaces
+      Cube file processing scripts, Libra/CP2K and Libra/Gaussian, Libra/Libint2 interfaces
 
   * Mrs. Story Temen (University at Buffalo)
       Implementation and testing of the HEOM codes
@@ -51,10 +211,10 @@ for all users with the intent:
   * Dr. Ekadashi Pradhan (York University) 
       Libra/QE interface, delta-SCF NA-M (Libra-X)
 
-  * Dr. Amber Jain (Indian Institute of Technology, Bombay)
+  * Dr. Amber Jain (Indian Institute of Technology Bombay, India)
       Implementation and testing of the HEOM codes
 
-  * Dr. Xiang Sun (Indian Institute of Technology, Bombay)
+  * Dr. Xiang Sun (NYU Shanghai, China)
       Implementation and testing of the FGR codes
 
 
@@ -64,9 +224,9 @@ This code is provided in the hope it will be useful.
 
   If you use the code in your research, please cite the following paper(s):
 
-  ### Parers that describe Libra and its features 
+  ### Papers that describe Libra or its features 
 
-  * [Initial Implementation](http://onlinelibrary.wiley.com/doi/10.1002/jcc.24367/full)
+  * [The initial implementation](http://onlinelibrary.wiley.com/doi/10.1002/jcc.24367/full)
   Akimov, A. V. "Libra: An open-Source 'methodology discovery' library for quantum and classical dynamics simulations" 
   *J. Comput. Chem.*  **2016**  37, 1626-1649
 

libra_env_build.sh

@@ -0,0 +1,23 @@
+conda create -n libra
+conda activate libra
+conda install -y conda-build
+conda install -y gcc_linux-64
+conda install -y gxx_linux-64
+conda install -y cmake
+conda install -y make
+conda install -y git
+conda install -y boost=1.73.0
+conda install -y -c anaconda h5py
+conda install -y -c conda-forge/label/gcc7 eigen
+conda install -y -c psi4/label/dev libint2
+conda install -y -c anaconda gmp
+conda install -y -c conda-forge/label/gcc7 mpfr 
+conda install -y python=3.6
+conda install -y -c psi4 psi4
+conda install -y -c conda-forge matplotlib
+conda install -y -c rmg py3dmol
+conda install -y -c anaconda numpy
+conda install -y -c anaconda scipy 
+conda install -y -c conda-forge/label/gcc7 imageio
+conda install -y -c conda-forge llvm-openmp
+