Merge pull request #333 from OrderN/drb-update-manual
Updates to fix RTD and add information on restarting
This commit is contained in:
David Bowler
GitHub
commit
a0acfc97aa
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@ -5,6 +5,11 @@
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# Required
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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.12"
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# Build documentation in the docs/ directory with Sphinx
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#sphinx:
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# configuration: docs/CONQUEST-manual/conf.py
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@ -14,6 +19,5 @@ formats: all
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# Optionally set the version of Python and requirements required to build your docs
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python:
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version: 3.7
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install:
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- requirements: docs/requirements.txt
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@ -295,7 +295,31 @@ find the energy.
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Go to :ref:`top <groundstate>`.
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.. _ gs_scf_adv:
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.. _gs_scf_restart:
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Restarting SCF
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~~~~~~~~~~~~~~
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The SCF cycle can be restarted from a previous density matrix or
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charge density, which may significantly speed up convergence.
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The density matrix is automatically written out in the files ``Kmatrix2.*`` or
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``Lmatrix2.*`` (depending on whether diagonalisation or linear scaling
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is being used). These files are read in, and the initial
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charge density made from them by setting the flags:
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::
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General.LoadDM T
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SC.MakeInitialChargeFromK T
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The charge density is not written out by default; this can be changed by
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setting ``IO.DumpChargeDensity T`` which results in the files ``chden.nnn``
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being created. To read these in as the initial charge density, the flag
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``General.LoadRho T`` should be set.
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Go to :ref:`top <groundstate>`.
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.. _gs_scf_adv:
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Advanced options
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~~~~~~~~~~~~~~~~
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@ -119,8 +119,9 @@ General.NewRun (*boolean*)
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*default*: T
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General.LoadL (*boolean*)
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Specifies whether to load a previous L matrix from files
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General.LoadDM (*boolean*)
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Specifies whether to load a previous density matrix (K or L depending on
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whether diagonalisation or linear scaling are selected) from files
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*default*: F
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@ -532,6 +533,11 @@ SC.MetricFactor (*real*)
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*default*: 0.1
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SC.MakeInitialChargeFromK (*boolean*)
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Flag determining whether initial charge is made from the density matrix
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*default*: T
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Go to :ref:`top <input_tags>`.
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.. _input_dm:
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@ -7,32 +7,6 @@ Installation
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You will need to download and compile the code before you can use it;
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we do not supply binaries.
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.. _install_spack:
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Installing with Spack
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-----------
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CONQUEST and all of its dependencies can be installed with `Spack<https://spack.io/>`_.
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The CONQUEST package requires Spack v0.21 or later. If Spack isn't available or up to date on your
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system, it is relatively straightforward to install it with user permissions following the
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`install instructions<https://spack.readthedocs.io/en/latest/getting_started.html#installation>`_.
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When setting up Spack on a new system, it is recommended to configure it to use available
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`system compilers<https://spack.readthedocs.io/en/latest/getting_started.html#compiler-configuration>`_
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and `system packages<https://spack.readthedocs.io/en/latest/getting_started.html#system-packages>`_.
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Once spack is installed and set up, install CONQUEST with:
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``spack install conquest``
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and load the ``Conquest`` executable to ``PATH`` with
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``spack load conquest``
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The build can be customized by adding options to the
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`Spack spec<https://spack.readthedocs.io/en/latest/basic_usage.html#specs-dependencies>`_ ``conquest``.
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The CONQUEST package includes variants for OpenMP support and different matrix multiplication kernels,
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please see the `Spack package<https://spack.readthedocs.io/en/latest/package_list.html#conquest>`_ for
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more details.
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.. _install_down:
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Downloading
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@ -50,6 +24,8 @@ unpacked:
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`<https://github.com/OrderN/CONQUEST-release/archive/master.zip>`_
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Go to :ref:`top <install>`
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.. _install_compile:
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Compiling
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@ -99,6 +75,8 @@ Once these are set, you should make the executable using ``make``.
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The ion file generation code is compiled using the same options
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required for the main code.
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Go to :ref:`top <install>`
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Multi-threading
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~~~~~~~~~~~~~~~
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@ -107,3 +85,32 @@ CONQUEST can use OpenMP for multi-threading; some multi-threading is available t
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Compiler flags to enable OpenMP are dependent on the vendor, but should be specified via ``COMPFLAGS`` and ``LINKFLAGS`` in the ``system.make`` file. If compiling with OpenMP then you should also change the variable ``OMP_DUMMY`` in the same file to be blank to enable the number of threads to be included in the output.
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On some systems, the default stack size for OpenMP is set to be rather small, and this can cause a segmentation fault when running with multiple threads. We recommend testing the effect of the environment variable ``OMP_STACKSIZE`` (and suggest setting it to 50M or larger as a first test).
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Go to :ref:`top <install>`
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.. _install_spack:
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Installing with Spack
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-----------
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CONQUEST and all of its dependencies can be installed with `Spack <https://spack.io/>`_.
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The CONQUEST package requires Spack v0.21 or later. If Spack isn't available or up to date on your
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system, it is relatively straightforward to install it with user permissions following the
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`install instructions <https://spack.readthedocs.io/en/latest/getting_started.html#installation>`_.
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When setting up Spack on a new system, it is recommended to configure it to use available
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`system compilers <https://spack.readthedocs.io/en/latest/getting_started.html#compiler-configuration>`_
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and `system packages <https://spack.readthedocs.io/en/latest/getting_started.html#system-packages>`_.
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Once spack is installed and set up, install CONQUEST with:
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``spack install conquest``
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and load the ``Conquest`` executable to ``PATH`` with
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``spack load conquest``
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The build can be customized by adding options to the
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`Spack spec <https://spack.readthedocs.io/en/latest/basic_usage.html#specs-dependencies>`_ ``conquest``.
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The CONQUEST package includes variants for OpenMP support and different matrix multiplication kernels; more details can be found in the `Spack CONQUEST package <https://spack.readthedocs.io/en/latest/package_list.html#conquest>`_.
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Go to :ref:`top <install>`
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