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‎LICENSE‎

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‎README‎

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// _____________________________________ _____ |
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// ___/ __ \__/ __ \_/ __ \__/ __ \__/ /________/ / |
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// __/ /_/ /_/ /_/ // / / /_/ /_/ /_/ __ \/ _ \/ __/ |
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// _/ ____/_/ _, _// /_/ /_/ ____/_/ / / / __/ /_ |
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// /_/ /_/ |_| \____/ /_/ /_/ /_/\___/\__/ |
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//---------------------------------------------------------
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This file is part of the PROPhet code, which was written
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by Brian Kolb and Levi Lentz in the group of Alexie
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Kolpak at MIT.
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See the documentation in doc/PROPhet_documentation.pdf for
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a full description of PROPhet.
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Please see the LICENSE file for license information
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***********************************************************
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Compilation instructions
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--------------------------------------------------------
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Compilation follows the standard linux paradigm:
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./configure [options]
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make
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make install
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If you want to use PROPhet potentials in the LAMMPS MD code,
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you should execute:
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./configure [options] --enable-lammps=LAMMPS_DIR
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make
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make install
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where LAMMPS_DIR is the directory with the LAMMPS source.
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This will make the lammps library of PROPhet, and attempt
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to insert it into the LAMMPS package system. The LAMMPS
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code must be relinked after completion to link in the
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PROPhet library. If automatic instalation fails, the
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library can be inserted into LAMMPS by following the
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instructions given in the documentation.
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Usage instructions can be found in the documentation,
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and by looking in the examples directory. A fully
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annotated input_file is also included in the
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examples directory.
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Description of classes in this package. The descriptions
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apply to the *.h and associated *.cpp files
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--------------------------------------------------------
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Analysis : A class to provide statistical analysis of a
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fit during a "-validate" run
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Art : Some logos, etc.
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Atom : A class for holding name and atomic number of
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atoms.
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Common : A single wrapper class to include headers for
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common classes. Also defined here are random
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number generators.
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DFT_IO : An interface class for interacting with DFT
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codes.
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Error : A class defining an Error and Warning routine
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which provide useful information at runtime.
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FHIAIMS : An interface to the FHI-Aims DFT code
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Functional : A high-level class to perform machine learning
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fits to properties of interest other than
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structure, which is handled by the Potential
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class
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Functional_params : General parameters for a run
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Grid_data : Data in grid format. This is mainly used for
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charge density.
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Network : Abstract interface class for a machine learning
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method.
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Network_node : Abstract interface class for a node in a neural
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network.
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NN : A class to implement a nueral network
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NN_node : A class to implement a node in a neural
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network
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Optimizer : This class performs the optimization of a
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network.
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pair_nn : A class which can be linked into the LAMMPS code
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to use a PROPhet potential in LAMMPS.
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Parallel : A wrapper to MPI functions
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Potential : A high-level class to perform fits based on
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structure.
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QE : An interface to the Quantum Espresso DFT code.
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Setup : This class handles user input and run setup.
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Structure : This class holds structural information and
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performs operations allowing structure fits.
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System_data : A container class to hold training properties.
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System : A wrapper for
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Tables : This class implements expensive functions via
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look-up-tables with spline interpolation.
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VASP : An interface to the VASP DFT-code
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xml_reader : A wrapper for the pugixml xml parser.
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In addition, two files are provided for the
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pugixml xml parser (see http://pugixml.org/)
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-----------------------------------------------------
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pugiconfig.hpp
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pugixml.hpp
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‎README.md‎

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```
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// _____________________________________ _____ |
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// ___/ __ \__/ __ \_/ __ \__/ __ \__/ /________/ / |
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// __/ /_/ /_/ /_/ // / / /_/ /_/ /_/ __ \/ _ \/ __/ |
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// _/ ____/_/ _, _// /_/ /_/ ____/_/ / / / __/ /_ |
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// /_/ /_/ |_| \____/ /_/ /_/ /_/\___/\__/ |
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//---------------------------------------------------------
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```
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PROPhet was ceated by
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Brian Kolb and Levi Lentz
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in the [group of Alexie Kolpak](http://kolpak.mit.edu/) at [![MIT](https://github.com/biklooost/PROPhet/blob/gh-pages/images/MIT-logo-red-gray-54x28.png)](http://web.mit.edu/)
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See the [documentation](http://biklooost.github.io/PROPhet/doc/PROPhet_documentation.pdf) for
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a full description of PROPhet.
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Please see the [LICENSE](https://github.com/biklooost/PROPhet/blob/master/LICENSE) file for license information
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---
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### [Description of PROPhet](https://biklooost.github.io/PROPhet/)
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---
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PROPhet (short for PROPerty Prophet) couples neural networks with first-principles physics and chemistry codes to
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allow sophisticated prediction of material properties. In general, PROPhet is used to
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find mappings between a set of material or system properties and other properties. Some
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specific uses of PROPhet are to:
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* Find a mapping between atomic configuration and other properties, including the total energy, creating an analytical potential, which can be used for molecular dynamics with the [LAMMPS](http://lammps.sandia.gov/) code
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* Construct density functionals for exchange-correlation energy, kinetic energy, or just about
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anything else
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* Find a mapping between a set of descriptors (an arbitrary combination of material properties) and other properties
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See the [PROPhet project page](https://biklooost.github.io/PROPhet/) for more details.
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### Interfaces with other codes
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---
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At the moment, PROPhet can couple automatically to the first-principles codes
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- [VASP](https://www.vasp.at/)
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- [Quantum Espresso](http://www.quantum-espresso.org/)
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- [FHI-Aims](https://aimsclub.fhi-berlin.mpg.de/)
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meaning it can extract many common properties directly from the output files of these codes, without user interaction. Interfaces to other codes can be easily added.
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In addition, potentials created in PROPhet can be used for molecular dynamics runs with the freely-available [LAMMPS](http://lammps.sandia.gov/) MD code. See the [documentation](http://biklooost.github.io/PROPhet/doc/PROPhet_documentation.pdf#page=16) for more details.
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### Compiling Information
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---
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Compilation follows the standard linux paradigm:
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```
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./configure [options]
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make
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make install
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```
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If you want to use PROPhet potentials in the [LAMMPS](http://lammps.sandia.gov/) MD code,
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you should execute:
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```
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./configure [options] --enable-lammps=LAMMPS_DIR
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make
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make install
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```
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where LAMMPS_DIR is the directory with the LAMMPS source.
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This will make the lammps library of PROPhet, and attempt
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to insert it into the LAMMPS package system. The LAMMPS
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code must be relinked after completion to link in the
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PROPhet library. If automatic instalation fails, the
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library can be inserted into LAMMPS by following the
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instructions given in the [documentation](http:/biklooost.github.io/PROPhet/doc/PROPhet_documentation.pdf#page=6).
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### Usage Instructions
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---
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Usage instructions including a tutorial can be found in the [documentation](http://biklooost.github.io/PROPhet/doc/PROPhet_documentation.pdf#page=8),
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and by looking in the [doc/tutorial](https://github.com/biklooost/PROPhet/tree/master/doc/tutorial) directory. A fully
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annotated input_file is also included in the
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[doc](https://github.com/biklooost/PROPhet/tree/master/doc) directory.
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‎bin/.git_ignore‎

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‎doc/PROPhet_documentation.pdf‎

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