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124
INSTALL.rst
124
INSTALL.rst
@ -2,9 +2,9 @@
|
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Installation
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============
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The |qp| can be downloaded on GitHub as an `archive
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<https://github.com/LCPQ/quantum_package/releases/latest>`_ or as a `git
|
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repository <https://github.com/LCPQ/quantum_package>`_.
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|qp| can be downloaded on GitHub as an `archive
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||||
<https://github.com/QuantumPackage/qp2/releases>`_ or as a `git
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repository <https://github.com/QuantumPackage/qp2>`_.
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.. code:: bash
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@ -19,16 +19,16 @@ Before anything, go into your :file:`quantum_package` directory and run
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This script will create the :file:`quantum_package.rc` bash script, which
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sets all the environment variables required for the normal operation of the
|
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*Quantum Package*. It will also initialize the git submodules that are
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sets all the environment variables required for the normal operation of
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|qp|. It will also initialize the git submodules that are
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required, and tell you which external dependencies are missing and need to be
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installed. The required dependencies are located in the
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`external/qp2-dependencies` directory, such that once QP is configured the
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`external/qp2-dependencies` directory, such that once |qp| is configured the
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internet connection is not needed any more.
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When all dependencies have been installed, (the :command:`configure` will
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inform you) source the :file:`quantum_package.rc` in order to load all
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environment variables and compile the |QP|.
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inform you what is missing) source the :file:`quantum_package.rc` in order to
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load all environment variables and compile |QP|.
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Now all the requirements are met, you can compile the programs using
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@ -37,6 +37,15 @@ Now all the requirements are met, you can compile the programs using
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make
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Installation of dependencies via a Conda environment
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====================================================
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.. code:: bash
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conda env create -f qp2.yml
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Requirements
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============
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@ -64,8 +73,8 @@ architecture. Modify it if needed, and run :command:`configure` with
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.. code:: bash
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cp ./config/gfortran.example config/gfortran.cfg
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./configure -c config/gfortran.cfg
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cp ./config/gfortran.example config/gfortran_avx.cfg
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./configure -c config/gfortran_avx.cfg
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.. note::
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@ -86,45 +95,33 @@ The command is to be used as follows:
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.. code:: bash
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./configure --install=<package>
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./configure -i <package>
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The following packages are supported by the :command:`configure` installer:
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* ninja
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* irpf90
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* zeromq
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* f77zmq
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* gmp
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* ocaml (:math:`\approx` 5 minutes)
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* ezfio
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* docopt
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* resultsFile
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* bats
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* zlib
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Example:
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.. code:: bash
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./configure -i ezfio
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./configure -i ninja
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.. note::
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When installing the ocaml package, you will be asked the location of where
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it should be installed. A safe option is to enter the path proposed by the
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|QP|:
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QP>> Please install it here: /your_quantum_package_directory/bin
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So just enter the proposition of the |QP| and press enter.
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If the :command:`configure` executable fails to install a specific dependency
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-----------------------------------------------------------------------------
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If the :command:`configure` executable does not succeed to install a specific
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dependency, there are some proposition of how to download and install the
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minimal dependencies to compile and use the |QP|.
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If the :command:`configure` executable does not succeed in installing a specific
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dependency, you should try to install the dependency on your system by yourself.
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Before doing anything below, try to install the packages with your package manager
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(:command:`apt`, :command:`yum`, etc).
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@ -149,11 +146,11 @@ IRPF90
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*IRPF90* is a Fortran code generator for programming using the Implicit Reference
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to Parameters (IRP) method.
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If you have *pip* for Python2, you can do
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If you have *pip* for Python2, you can do
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.. code:: bash
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python2 -m pip install --user irpf90
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python3 -m pip install --user irpf90
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Otherwise,
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@ -209,7 +206,7 @@ ZeroMQ and its Fortran binding
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.. code:: bash
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cp f77_zmq_free.h ${QP_ROOT}/src/ZMQ/f77_zmq.h
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cp f77_zmq_free.h ${QP_ROOT}/src/zmq/f77_zmq.h
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Zlib
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@ -262,53 +259,6 @@ With Debian or Ubuntu, you can use
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sudo apt install libgmp-dev
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libcap
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------
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Libcap is a library for getting and setting POSIX.1e draft 15 capabilities.
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* Download the latest version of libcap here:
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`<https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz>`_
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and move it in the :file:`${QP_ROOT}/external` directory
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* Extract the archive, go into the :file:`libcap-*/libcap` directory and run
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the following command
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.. code:: bash
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prefix=$QP_ROOT make install
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With Debian or Ubuntu, you can use
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.. code:: bash
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sudo apt install libcap-dev
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Bubblewrap
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----------
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Bubblewrap is an unprivileged sandboxing tool.
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* Download Bubblewrap here:
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`<https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz>`_
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and move it in the :file:`${QP_ROOT}/external` directory
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* Extract the archive, go into the :file:`bubblewrap-*` directory and run
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the following commands
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.. code:: bash
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./configure --prefix=$QP_ROOT && make -j 8
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make install-exec-am
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With Debian or Ubuntu, you can use
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.. code:: bash
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sudo apt install bubblewrap
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OCaml
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@ -327,7 +277,7 @@ OCaml
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`<https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh>`_
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and move it in the :file:`${QP_ROOT}/external` directory
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* If you use OCaml only with the |qp|, you can install the OPAM directory
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* If you use OCaml only with |qp|, you can install the OPAM directory
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containing the compiler and all the installed libraries in the
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:file:`${QP_ROOT}/external` directory as
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@ -352,14 +302,14 @@ OCaml
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.. code:: bash
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opam init --comp=4.07.1
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opam init --comp=4.11.1
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eval `${QP_ROOT}/bin/opam env`
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If the installation fails because of bwrap, you can initialize opam using:
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.. code:: bash
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opam init --disable-sandboxing --comp=4.07.1
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opam init --disable-sandboxing --comp=4.11.1
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eval `${QP_ROOT}/bin/opam env`
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* Install the required external OCaml libraries
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@ -369,17 +319,6 @@ OCaml
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opam install ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt
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EZFIO
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-----
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|
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*EZFIO* is the Easy Fortran Input/Output library generator.
|
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|
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* Download EZFIO here : `<https://gitlab.com/scemama/EZFIO/-/archive/master/EZFIO-master.tar.gz>`_ and move
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the downloaded archive in the :file:`${QP_ROOT}/external` directory
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* Extract the archive, and rename it as :file:`${QP_ROOT}/external/ezfio`
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Docopt
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------
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@ -406,7 +345,7 @@ resultsFile
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*resultsFile* is a Python package to extract data from output files of quantum chemistry
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codes.
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|
||||
If you have *pip* for Python3, you can do
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||||
If you have *pip* for Python3, you can do
|
||||
|
||||
.. code:: bash
|
||||
|
||||
@ -414,3 +353,4 @@ If you have *pip* for Python3, you can do
|
||||
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||||
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||||
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||||
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@ -30,7 +30,8 @@
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- Fixed bug in DIIS
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- Fixed bug in molden (Au -> Angs)
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- Fixed bug with non-contiguous MOs in active space and deleter MOs
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- Network-free installation
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- Complete network-free installation
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- Fixed bug in selection when computing full PT2
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- Updated version of f77-zmq
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*** User interface
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@ -59,6 +60,7 @@
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symmetry in matrices
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- qp_export_as_tgz exports also plugin codes
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- Added a basis module containing basis set information
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- Added qp_run truncate_wf
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*** Code
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@ -195,48 +195,52 @@ def write_ezfio(res, filename):
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# P a r s i n g #
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# ~#~#~#~#~#~#~ #
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inucl = {}
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for i, a in enumerate(res.geometry):
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inucl[a.coord] = i
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nbasis = 0
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nucl_center = []
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nucl_index = []
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curr_center = -1
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nucl_shell_num = []
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ang_mom = []
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nshell = 0
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shell_prim_index = [1]
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nshell_tot = 0
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shell_index = []
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shell_prim_num = []
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for b in res.basis:
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s = b.sym
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if str.count(s, "y") + str.count(s, "x") == 0:
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c = b.center
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c = inucl[b.center]
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nshell += 1
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nshell_tot += 1
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if c != curr_center:
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curr_center = c
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nucl_center.append(nbasis+1)
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nucl_shell_num.append(nshell)
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nshell = 0
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nbasis += 1
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nucl_index.append(c+1)
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coefficient += b.coef[:len(b.prim)]
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exponent += [p.expo for p in b.prim]
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ang_mom.append(str.count(s, "z"))
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shell_prim_index.append(len(exponent)+1)
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shell_prim_num.append(len(b.prim))
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nucl_shell_num.append(nshell+1)
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nucl_shell_num = nucl_shell_num[1:]
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shell_index += [nshell_tot+1] * len(b.prim)
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|
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# ~#~#~#~#~ #
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# W r i t e #
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# ~#~#~#~#~ #
|
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ezfio.set_basis_basis("Read from ResultsFile")
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ezfio.set_basis_basis_nucleus_index(nucl_center)
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ezfio.set_basis_prim_num(len(coefficient))
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ezfio.set_basis_shell_num(len(ang_mom))
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ezfio.set_basis_basis_nucleus_index(nucl_index)
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ezfio.set_basis_prim_num(len(coefficient))
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ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
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||||
ezfio.set_basis_prim_coef(coefficient)
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ezfio.set_basis_prim_expo(exponent)
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ezfio.set_basis_shell_ang_mom(ang_mom)
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ezfio.set_basis_shell_prim_num(shell_prim_num)
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ezfio.set_basis_shell_prim_index(shell_prim_index)
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ezfio.set_basis_shell_index(shell_index)
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||||
|
||||
print("OK")
|
||||
|
||||
|
||||
@ -6,6 +6,7 @@ Usage:
|
||||
qp_plugins download <url> [-n <name>]
|
||||
qp_plugins install <name>...
|
||||
qp_plugins uninstall <name>
|
||||
qp_plugins remove <name>
|
||||
qp_plugins update [-r <repo>]
|
||||
qp_plugins create -n <name> [-r <repo>] [<needed_modules>...]
|
||||
|
||||
@ -24,6 +25,8 @@ Options:
|
||||
|
||||
uninstall Uninstall a plugin
|
||||
|
||||
remove Uninstall a plugin
|
||||
|
||||
update Update the repository
|
||||
|
||||
create
|
||||
@ -274,7 +277,7 @@ def main(arguments):
|
||||
subprocess.check_call(["qp_create_ninja", "update"])
|
||||
print("[ OK ]")
|
||||
|
||||
elif arguments["uninstall"]:
|
||||
elif arguments["uninstall"] or arguments["remove"]:
|
||||
|
||||
m_instance = ModuleHandler([QP_SRC])
|
||||
d_descendant = m_instance.dict_descendant
|
||||
|
||||
@ -7,12 +7,13 @@ setting all MOs as Active, except the n/2 first ones which are set as Core.
|
||||
If pseudo-potentials are used, all the MOs are set as Active.
|
||||
|
||||
Usage:
|
||||
qp_set_frozen_core [-q|--query] [(-l|-s|--large|--small)] EZFIO_DIR
|
||||
qp_set_frozen_core [-q|--query] [(-l|-s|-u|--large|--small|--unset)] EZFIO_DIR
|
||||
|
||||
Options:
|
||||
-q --query Prints in the standard output the number of frozen MOs
|
||||
-l --large Use a small core
|
||||
-s --small Use a large core
|
||||
-u --unset Unset frozen core
|
||||
|
||||
|
||||
Default numbers of frozen electrons:
|
||||
@ -88,7 +89,9 @@ def main(arguments):
|
||||
elif charge <= 54: n_frozen += 9
|
||||
elif charge <= 86: n_frozen += 18
|
||||
elif charge <= 118: n_frozen += 27
|
||||
elif arguments["--unset"]:
|
||||
|
||||
n_frozen = 0
|
||||
else: # default
|
||||
for charge in ezfio.nuclei_nucl_charge:
|
||||
if charge <= 4: pass
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
FC : gfortran -g -ffree-line-length-none -I . -fPIC
|
||||
LAPACK_LIB : -lblas -llapack
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 --assert
|
||||
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -35,14 +35,14 @@ OPENMP : 1 ; Append OpenMP flags
|
||||
# -ffast-math and the Fortran-specific
|
||||
# -fno-protect-parens and -fstack-arrays.
|
||||
[OPT]
|
||||
FCFLAGS : -Ofast
|
||||
FCFLAGS : -Ofast
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -Ofast
|
||||
FCFLAGS : -Ofast
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
@ -58,5 +58,5 @@ FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurpris
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -fopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
FC : gfortran -ffree-line-length-none -I . -mavx -g -fPIC
|
||||
LAPACK_LIB : -llapack -lblas
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32
|
||||
IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -42,7 +42,7 @@ FCFLAGS : -Ofast -mavx
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -Ofast
|
||||
FCFLAGS : -Ofast
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
@ -51,12 +51,12 @@ FCFLAGS : -Ofast
|
||||
# -g : Extra debugging information
|
||||
#
|
||||
[DEBUG]
|
||||
FCFLAGS : -fcheck=all -g
|
||||
FCFLAGS : -fcheck=all -g
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -fopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
FC : gfortran -g -ffree-line-length-none -I . -fPIC
|
||||
LAPACK_LIB : -lblas -llapack
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 --assert
|
||||
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -35,14 +35,14 @@ OPENMP : 1 ; Append OpenMP flags
|
||||
# -ffast-math and the Fortran-specific
|
||||
# -fno-protect-parens and -fstack-arrays.
|
||||
[OPT]
|
||||
FCFLAGS : -Ofast
|
||||
FCFLAGS : -Ofast
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -Ofast
|
||||
FCFLAGS : -Ofast
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
@ -59,5 +59,5 @@ FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurpris
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -fopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
FC : mpif90 -ffree-line-length-none -I . -g -fPIC
|
||||
LAPACK_LIB : -lblas -llapack
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -35,14 +35,14 @@ OPENMP : 1 ; Append OpenMP flags
|
||||
# -ffast-math and the Fortran-specific
|
||||
# -fno-protect-parens and -fstack-arrays.
|
||||
[OPT]
|
||||
FCFLAGS : -Ofast -msse4.2
|
||||
FCFLAGS : -Ofast -msse4.2
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -Ofast -msse4.2
|
||||
FCFLAGS : -Ofast -msse4.2
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
@ -51,7 +51,7 @@ FCFLAGS : -Ofast -msse4.2
|
||||
# -g : Extra debugging information
|
||||
#
|
||||
[DEBUG]
|
||||
FCFLAGS : -fcheck=all -g
|
||||
FCFLAGS : -fcheck=all -g
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
|
||||
63
config/ifort_2019_avx.cfg
Normal file
63
config/ifort_2019_avx.cfg
Normal file
@ -0,0 +1,63 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback
|
||||
FCFLAGS : -xAVX -O2 -ip -ftz -g
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
64
config/ifort_2019_avx_mpi.cfg
Normal file
64
config/ifort_2019_avx_mpi.cfg
Normal file
@ -0,0 +1,64 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : mpiifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g -traceback
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -march=corei7 -O2 -ip -ftz
|
||||
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
63
config/ifort_2019_mpi_rome.cfg
Normal file
63
config/ifort_2019_mpi_rome.cfg
Normal file
@ -0,0 +1,63 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : mpiifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback -shared-intel
|
||||
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
63
config/ifort_2019_rome.cfg
Normal file
63
config/ifort_2019_rome.cfg
Normal file
@ -0,0 +1,63 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback -shared-intel
|
||||
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
63
config/ifort_2019_sse4.cfg
Normal file
63
config/ifort_2019_sse4.cfg
Normal file
@ -0,0 +1,63 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
64
config/ifort_2019_sse4_mpi.cfg
Normal file
64
config/ifort_2019_sse4_mpi.cfg
Normal file
@ -0,0 +1,64 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : mpiifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FCFLAGS : -msse4.2 -O2 -ip -ftz -g -traceback
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -msse4.2 -O2 -ip -ftz
|
||||
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
63
config/ifort_2019_xHost.cfg
Normal file
63
config/ifort_2019_xHost.cfg
Normal file
@ -0,0 +1,63 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=64 -DINTEL -DSET_NESTED
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback
|
||||
FCFLAGS : -xHost -O2 -ip -ftz -g
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -9,7 +9,7 @@
|
||||
FC : mpiifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
63
config/ifort_2021_mpi_rome.cfg
Normal file
63
config/ifort_2021_mpi_rome.cfg
Normal file
@ -0,0 +1,63 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : mpiifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback -shared-intel
|
||||
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -xSSE2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -9,7 +9,7 @@
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
IRPF90_FLAGS : --ninja --align=32 -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -9,7 +9,7 @@
|
||||
FC : mpiifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL
|
||||
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -9,7 +9,7 @@
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=64 -DINTEL
|
||||
IRPF90_FLAGS : --ninja --align=64 -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
@ -1,66 +0,0 @@
|
||||
# Common flags
|
||||
##############
|
||||
#
|
||||
# -mkl=[parallel|sequential] : Use the MKL library
|
||||
# --ninja : Allow the utilisation of ninja. It is mandatory !
|
||||
# --align=32 : Align all provided arrays on a 32-byte boundary
|
||||
#
|
||||
[COMMON]
|
||||
FC : ifort -fpic
|
||||
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
|
||||
IRPF90 : irpf90
|
||||
IRPF90_FLAGS : --ninja --align=32 --assert -DINTEL
|
||||
|
||||
# Global options
|
||||
################
|
||||
#
|
||||
# 1 : Activate
|
||||
# 0 : Deactivate
|
||||
#
|
||||
[OPTION]
|
||||
MODE : DEBUG ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
|
||||
CACHE : 0 ; Enable cache_compile.py
|
||||
OPENMP : 1 ; Append OpenMP flags
|
||||
|
||||
# Optimization flags
|
||||
####################
|
||||
#
|
||||
# -xHost : Compile a binary optimized for the current architecture
|
||||
# -O2 : O3 not better than O2.
|
||||
# -ip : Inter-procedural optimizations
|
||||
# -ftz : Flushes denormal results to zero
|
||||
#
|
||||
[OPT]
|
||||
FC : -traceback
|
||||
FCFLAGS : -msse4.2 -O2 -ip -ftz -g
|
||||
|
||||
|
||||
# Profiling flags
|
||||
#################
|
||||
#
|
||||
[PROFILE]
|
||||
FC : -p -g
|
||||
FCFLAGS : -msse4.2 -O2 -ip -ftz
|
||||
|
||||
|
||||
# Debugging flags
|
||||
#################
|
||||
#
|
||||
# -traceback : Activate backtrace on runtime
|
||||
# -fpe0 : All floating point exaceptions
|
||||
# -C : Checks uninitialized variables, array subscripts, etc...
|
||||
# -g : Extra debugging information
|
||||
# -msse4.2 : Valgrind needs a very simple x86 executable
|
||||
#
|
||||
[DEBUG]
|
||||
FC : -g -traceback
|
||||
FCFLAGS : -msse4.2 -check all -debug all -fpe-all=0 -implicitnone
|
||||
|
||||
|
||||
# OpenMP flags
|
||||
#################
|
||||
#
|
||||
[OPENMP]
|
||||
FC : -qopenmp
|
||||
IRPF90_FLAGS : --openmp
|
||||
|
||||
@ -204,6 +204,9 @@ _qp_Complete()
|
||||
uninstall)
|
||||
COMPREPLY=( $(compgen -W "$(qp_plugins list -i)" -- $cur ) )
|
||||
return 0;;
|
||||
remove)
|
||||
COMPREPLY=( $(compgen -W "$(qp_plugins list -i)" -- $cur ) )
|
||||
return 0;;
|
||||
create)
|
||||
COMPREPLY=( $(compgen -W "-n " -- $cur ) )
|
||||
return 0;;
|
||||
|
||||
@ -91,7 +91,7 @@ let run ?o b au c d m p cart xyz_file =
|
||||
| Element e -> Element.to_string e
|
||||
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
|
||||
in
|
||||
Hashtbl.find basis_table key
|
||||
Hashtbl.find basis_table key
|
||||
in
|
||||
|
||||
let temp_filename =
|
||||
@ -132,7 +132,7 @@ let run ?o b au c d m p cart xyz_file =
|
||||
Element.to_string elem.Atom.element
|
||||
in
|
||||
Hashtbl.add basis_table key new_channel
|
||||
) nuclei
|
||||
) nuclei
|
||||
end
|
||||
| Some (key, basis) -> (*Aux basis *)
|
||||
begin
|
||||
@ -277,6 +277,16 @@ let run ?o b au c d m p cart xyz_file =
|
||||
) nuclei
|
||||
in
|
||||
|
||||
let z_core =
|
||||
List.map (fun x ->
|
||||
Positive_int.to_int x.Pseudo.n_elec
|
||||
|> float_of_int
|
||||
) pseudo
|
||||
in
|
||||
let nucl_num = (List.length z_core) in
|
||||
Ezfio.set_pseudo_nucl_charge_remove (Ezfio.ezfio_array_of_list
|
||||
~rank:1 ~dim:[| nucl_num |] ~data:z_core);
|
||||
|
||||
let molecule =
|
||||
let n_elec_to_remove =
|
||||
List.fold_left (fun accu x ->
|
||||
@ -293,13 +303,13 @@ let run ?o b au c d m p cart xyz_file =
|
||||
Molecule.nuclei =
|
||||
let charges =
|
||||
list_map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|
||||
|> Float.of_int) pseudo
|
||||
|> Float.of_int) pseudo
|
||||
|> Array.of_list
|
||||
in
|
||||
List.mapi (fun i x ->
|
||||
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|
||||
|> Charge.of_float }
|
||||
) molecule.Molecule.nuclei
|
||||
) molecule.Molecule.nuclei
|
||||
}
|
||||
in
|
||||
let nuclei =
|
||||
@ -356,11 +366,11 @@ let run ?o b au c d m p cart xyz_file =
|
||||
in
|
||||
if (x > accu) then x
|
||||
else accu
|
||||
) 0 x.Pseudo.non_local
|
||||
) 0 x.Pseudo.non_local
|
||||
in
|
||||
if (x > accu) then x
|
||||
else accu
|
||||
) 0 pseudo
|
||||
) 0 pseudo
|
||||
in
|
||||
|
||||
let kmax =
|
||||
@ -368,10 +378,10 @@ let run ?o b au c d m p cart xyz_file =
|
||||
list_map (fun x ->
|
||||
List.filter (fun (y,_) ->
|
||||
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
|
||||
x.Pseudo.non_local
|
||||
|> List.length ) pseudo
|
||||
x.Pseudo.non_local
|
||||
|> List.length ) pseudo
|
||||
|> List.fold_left (fun accu x ->
|
||||
if accu > x then accu else x) 0
|
||||
if accu > x then accu else x) 0
|
||||
)
|
||||
|> Array.fold_left (fun accu i ->
|
||||
if i > accu then i else accu) 0
|
||||
@ -396,11 +406,11 @@ let run ?o b au c d m p cart xyz_file =
|
||||
in
|
||||
tmp_array_dz_k.(i).(j) <- y;
|
||||
tmp_array_n_k.(i).(j) <- z;
|
||||
) x.Pseudo.local
|
||||
) x.Pseudo.local
|
||||
) pseudo ;
|
||||
let concat_2d tmp_array =
|
||||
let data =
|
||||
Array.map Array.to_list tmp_array
|
||||
Array.map Array.to_list tmp_array
|
||||
|> Array.to_list
|
||||
|> List.concat
|
||||
in
|
||||
@ -438,14 +448,14 @@ let run ?o b au c d m p cart xyz_file =
|
||||
tmp_array_dz_kl.(k).(i).(j) <- y;
|
||||
tmp_array_n_kl.(k).(i).(j) <- z;
|
||||
last_idx.(k) <- i+1;
|
||||
) x.Pseudo.non_local
|
||||
) x.Pseudo.non_local
|
||||
) pseudo ;
|
||||
let concat_3d tmp_array =
|
||||
let data =
|
||||
Array.map (fun x ->
|
||||
Array.map Array.to_list x
|
||||
|> Array.to_list
|
||||
|> List.concat) tmp_array
|
||||
|> List.concat) tmp_array
|
||||
|> Array.to_list
|
||||
|> List.concat
|
||||
in
|
||||
@ -513,8 +523,8 @@ let run ?o b au c d m p cart xyz_file =
|
||||
Ezfio.set_ao_basis_ao_num ao_num;
|
||||
Ezfio.set_ao_basis_ao_basis b;
|
||||
Ezfio.set_basis_basis b;
|
||||
let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
|
||||
and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
|
||||
let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
|
||||
and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
|
||||
and ao_power=
|
||||
let l = list_map (fun (x,_,_) -> x) long_basis in
|
||||
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
|
||||
@ -526,7 +536,7 @@ let run ?o b au c d m p cart xyz_file =
|
||||
else s) 0 ao_prim_num
|
||||
in
|
||||
let gtos =
|
||||
list_map (fun (_,x,_) -> x) long_basis
|
||||
list_map (fun (_,x,_) -> x) long_basis
|
||||
in
|
||||
|
||||
let create_expo_coef ec =
|
||||
@ -534,10 +544,10 @@ let run ?o b au c d m p cart xyz_file =
|
||||
begin match ec with
|
||||
| `Coefs -> list_map (fun x->
|
||||
list_map (fun (_,coef) ->
|
||||
AO_coef.to_float coef) x.Gto.lc) gtos
|
||||
AO_coef.to_float coef) x.Gto.lc) gtos
|
||||
| `Expos -> list_map (fun x->
|
||||
list_map (fun (prim,_) -> AO_expo.to_float
|
||||
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
|
||||
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
|
||||
end
|
||||
in
|
||||
let rec get_n n accu = function
|
||||
@ -567,7 +577,7 @@ let run ?o b au c d m p cart xyz_file =
|
||||
list_map ( fun (g,_) -> g.Gto.lc ) basis
|
||||
in
|
||||
let ang_mom =
|
||||
list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
|
||||
list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
|
||||
let x, _ = List.hd l in
|
||||
Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
|
||||
) lc
|
||||
@ -577,7 +587,7 @@ let run ?o b au c d m p cart xyz_file =
|
||||
|> List.concat
|
||||
in
|
||||
let coef =
|
||||
list_map (fun l ->
|
||||
list_map (fun l ->
|
||||
list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
|
||||
) lc
|
||||
|> List.concat
|
||||
@ -585,12 +595,16 @@ let run ?o b au c d m p cart xyz_file =
|
||||
let shell_prim_num =
|
||||
list_map List.length lc
|
||||
in
|
||||
let shell_prim_idx =
|
||||
let shell_idx =
|
||||
let rec make_list n accu = function
|
||||
| 0 -> accu
|
||||
| i -> make_list n (n :: accu) (i-1)
|
||||
in
|
||||
let rec aux count accu = function
|
||||
| [] -> List.rev accu
|
||||
| l::rest ->
|
||||
let newcount = count+(List.length l) in
|
||||
aux newcount (count::accu) rest
|
||||
let new_l = make_list count accu (List.length l) in
|
||||
aux (count+1) new_l rest
|
||||
in
|
||||
aux 1 [] lc
|
||||
in
|
||||
@ -602,26 +616,18 @@ let run ?o b au c d m p cart xyz_file =
|
||||
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
|
||||
Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
|
||||
~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
|
||||
Ezfio.set_basis_shell_prim_index (Ezfio.ezfio_array_of_list
|
||||
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_idx) ;
|
||||
Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
|
||||
~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
|
||||
Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
|
||||
~rank:1 ~dim:[| nucl_num |]
|
||||
~data:(
|
||||
list_map (fun (_,n) -> Nucl_number.to_int n) basis
|
||||
|> List.fold_left (fun accu i ->
|
||||
match accu with
|
||||
| [] -> []
|
||||
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((h+1,i)::(h+1,j)::rest)
|
||||
) [(0,0)]
|
||||
|> List.rev
|
||||
|> List.map fst
|
||||
)) ;
|
||||
~rank:1 ~dim:[| shell_num |]
|
||||
~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
|
||||
) ;
|
||||
Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
|
||||
~rank:1 ~dim:[| nucl_num |]
|
||||
~data:(
|
||||
list_map (fun (_,n) -> Nucl_number.to_int n) basis
|
||||
|> List.fold_left (fun accu i ->
|
||||
match accu with
|
||||
|> List.fold_left (fun accu i ->
|
||||
match accu with
|
||||
| [] -> [(1,i)]
|
||||
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest)
|
||||
) []
|
||||
@ -717,7 +723,7 @@ If a file with the same name as the basis set exists, this file will be read. O
|
||||
|
||||
anonymous "FILE" Mandatory "Input file in xyz format or z-matrix.";
|
||||
]
|
||||
|> set_specs
|
||||
|> set_specs
|
||||
end;
|
||||
|
||||
|
||||
@ -741,7 +747,7 @@ If a file with the same name as the basis set exists, this file will be read. O
|
||||
| None -> 0
|
||||
| Some x -> ( if x.[0] = 'm' then
|
||||
~- (int_of_string (String.sub x 1 (String.length x - 1)))
|
||||
else
|
||||
else
|
||||
int_of_string x )
|
||||
in
|
||||
|
||||
|
||||
27
scripts/cipsi_save.sh
Normal file
27
scripts/cipsi_save.sh
Normal file
@ -0,0 +1,27 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
# This script runs a CIPSI calculation as a sequence of single CIPSI iterations.
|
||||
# After each iteration, the EZFIO directory is saved.
|
||||
#
|
||||
# Usage: cipsi_save [EZFIO_FILE] [NDET]
|
||||
#
|
||||
# Example: cipsi_save file.ezfio 10000
|
||||
|
||||
EZ=$1
|
||||
NDETMAX=$2
|
||||
|
||||
qp set_file ${EZ}
|
||||
qp reset -d
|
||||
qp set determinants read_wf true
|
||||
declare -i NDET
|
||||