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-  no auto-download of user-pace src yet
-  lib/pace/*.cpp,*.h are provided explicitly yet.
- implement CMake integration in USER-PACE.cmake and in CMakeLists.txt
This commit is contained in:
Yury Lysogorskiy
2021-04-06 17:24:54 +02:00
parent 9da49d9c6f
commit 6a99f5b5c5
35 changed files with 11546 additions and 5 deletions
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6
cmake/CMakeLists.txt
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@ -119,7 +119,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF) USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -382,9 +382,9 @@ else()
endif() endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS) USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
if(PKG_${PKG_WITH_INCL}) if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL})
endif() endif()
endforeach() endforeach()

14
cmake/Modules/Packages/USER-PACE.cmake Normal file
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@ -0,0 +1,14 @@
set(PACE_EVALUATOR_PATH ${LAMMPS_LIB_SOURCE_DIR}/pace)
message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}")
set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH})
FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp)
set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH})
##### aceevaluator #####
add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES})
target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_compile_options(aceevaluator PRIVATE -O2)
set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE aceevaluator)

1
lib/pace/Install.py Normal file
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@ -0,0 +1 @@
# TODO

674
lib/pace/LICENSE Normal file
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@ -0,0 +1,674 @@
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HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

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[TODO/DONE] pair_pace.cpp and pair_pace.h will have to go into src/USER-PACE and thus also need to conform to our requirements.
[TODO] also src/USER-PACE would need to have an Install.sh file that integrates the settings from the lib folder into the conventional build process.
[TODO] there would have to be a lib/pace folder for building/interfacing to the library.
[TODO] how you organize your repo is up to you. a better way to describe what you would have to do is to point you to examples.
which of the examples is relevant depends on what build system you are using for your "PACE" external package.
If you are using CMake to build it, you can look at the KIM package
If you are using autoconf/automake, you can look at the USER-PLUMED package
If you are using neither (just a plain Makefile), you can look at the VORONOI or QUIP package
The following additional modifications are needed:
[TODO] lib/pace: needs one or more Makefile.lammps, a README and an Install.py file
[TODO] src/Makefile: needs support for the USER-PACE package and compiling via lib-pace. Also the package needs to be added to the PACKEXT and PACKLIB variables
[DONE] cmake/Modules/Packages/USER-PACE.cmake needs to be added
[DONE] cmake/CMakeLists.txt needs to include it in case the package is enabled.
[TODO] doc/src/Build_extra.rst needs to include the build instructions for CMake and traditional make
[TODO] doc/src/Package_user.rst and doc/src/Package_details.rst needs to contain relevant information and links
Because of the different build systems, there are different steps required, but each of the examples I've pointed out are tested and used regularly and thus should be working sufficiently well.
Mind you the QUIP package is set up in such a way, that no automatic download is possible and a manual download and compilation is required. So that is the least preferred and least convenient option.
We are happy to provide more details, but that requires that you first have something that already is following either of the suggested variants, so that we don't have to discuss in all generality.
I would also suggest to close this pull request here, leave all files in place, but then start a new branch from the current master and then move the few things over you need to retain,
add the build environment files and then start working on getting it to do what it should.

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Lysogorskiy Yury on 28.04.2020.
#include "ace_abstract_basis.h"
////embedding function
////case nemb = 1 only implementation
////F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) )
//// !! no prefactor wpre
void Fexp(DOUBLE_TYPE x, DOUBLE_TYPE m, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) {
DOUBLE_TYPE w = 1.e6;
DOUBLE_TYPE eps = 1e-10;
DOUBLE_TYPE lambda = pow(1.0 / w, m - 1.0);
if (abs(x) > eps) {
DOUBLE_TYPE g;
DOUBLE_TYPE a = abs(x);
DOUBLE_TYPE am = pow(a, m);
DOUBLE_TYPE w3x3 = pow(w * a, 3);
DOUBLE_TYPE sign_factor = (signbit(x) ? -1 : 1);
if (w3x3 > 30.0)
g = 0.0;
else
g = exp(-w3x3);
DOUBLE_TYPE omg = 1.0 - g;
F = sign_factor * (omg * am + lambda * g * a);
DOUBLE_TYPE dg = -3.0 * w * w * w * a * a * g;
DF = m * pow(a, m - 1.0) * omg - am * dg + lambda * dg * a + lambda * g;
} else {
F = lambda * x;
DF = lambda;
}
}
//Scaled-shifted embedding function
//F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) )
// !! no prefactor wpre
void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) {
DOUBLE_TYPE eps = 1e-10;
DOUBLE_TYPE a, xoff, yoff, nx, exprho;
if (abs(mexp - 1.0) < eps) {
F = rho;
DF = 1;
} else {
a = abs(rho);
exprho = exp(-a);
nx = 1. / mexp;
xoff = pow(nx, (nx / (1.0 - nx))) * exprho;
yoff = pow(nx, (1 / (1.0 - nx))) * exprho;
DOUBLE_TYPE sign_factor = (signbit(rho) ? -1 : 1);
F = sign_factor * (pow(xoff + a, mexp) - yoff);
DF = yoff + mexp * (-xoff + 1.0) * pow(xoff + a, mexp - 1.);
}
}
void ACEAbstractBasisSet::inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut,
DOUBLE_TYPE &fcut, DOUBLE_TYPE &dfcut) {
DOUBLE_TYPE rho_low = rho_cut - drho_cut;
if (rho_core >= rho_cut) {
fcut = 0;
dfcut = 0;
} else if (rho_core <= rho_low) {
fcut = 1;
dfcut = 0;
} else {
fcut = 0.5 * (1 + cos(M_PI * (rho_core - rho_low) / drho_cut));
dfcut = -0.5 * sin(M_PI * (rho_core - rho_low) / drho_cut) * M_PI / drho_cut;
}
}
void ACEAbstractBasisSet::FS_values_and_derivatives(Array1D<DOUBLE_TYPE> &rhos, DOUBLE_TYPE &value,
Array1D<DOUBLE_TYPE> &derivatives, DENSITY_TYPE ndensity) {
DOUBLE_TYPE F, DF = 0, wpre, mexp;
for (int p = 0; p < ndensity; p++) {
wpre = FS_parameters.at(p * ndensity + 0);
mexp = FS_parameters.at(p * ndensity + 1);
if (this->npoti == "FinnisSinclair")
Fexp(rhos(p), mexp, F, DF);
else if (this->npoti == "FinnisSinclairShiftedScaled")
FexpShiftedScaled(rhos(p), mexp, F, DF);
value += F * wpre; // * weight (wpre)
derivatives(p) = DF * wpre;// * weight (wpre)
}
}
void ACEAbstractBasisSet::_clean() {
delete[] elements_name;
elements_name = nullptr;
delete radial_functions;
radial_functions = nullptr;
}
ACEAbstractBasisSet::ACEAbstractBasisSet(const ACEAbstractBasisSet &other) {
ACEAbstractBasisSet::_copy_scalar_memory(other);
ACEAbstractBasisSet::_copy_dynamic_memory(other);
}
ACEAbstractBasisSet &ACEAbstractBasisSet::operator=(const ACEAbstractBasisSet &other) {
if (this != &other) {
// deallocate old memory
ACEAbstractBasisSet::_clean();
//copy scalar values
ACEAbstractBasisSet::_copy_scalar_memory(other);
//copy dynamic memory
ACEAbstractBasisSet::_copy_dynamic_memory(other);
}
return *this;
}
ACEAbstractBasisSet::~ACEAbstractBasisSet() {
ACEAbstractBasisSet::_clean();
}
void ACEAbstractBasisSet::_copy_scalar_memory(const ACEAbstractBasisSet &src) {
deltaSplineBins = src.deltaSplineBins;
FS_parameters = src.FS_parameters;
npoti = src.npoti;
nelements = src.nelements;
rankmax = src.rankmax;
ndensitymax = src.ndensitymax;
nradbase = src.nradbase;
lmax = src.lmax;
nradmax = src.nradmax;
cutoffmax = src.cutoffmax;
spherical_harmonics = src.spherical_harmonics;
rho_core_cutoffs = src.rho_core_cutoffs;
drho_core_cutoffs = src.drho_core_cutoffs;
E0vals = src.E0vals;
}
void ACEAbstractBasisSet::_copy_dynamic_memory(const ACEAbstractBasisSet &src) {//allocate new memory
if (src.elements_name == nullptr)
throw runtime_error("Could not copy ACEAbstractBasisSet::elements_name - array not initialized");
elements_name = new string[nelements];
//copy
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
elements_name[mu] = src.elements_name[mu];
}
radial_functions = src.radial_functions->clone();
}
SPECIES_TYPE ACEAbstractBasisSet::get_species_index_by_name(const string &elemname) {
for (SPECIES_TYPE t = 0; t < nelements; t++) {
if (this->elements_name[t] == elemname)
return t;
}
return -1;
}

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Lysogorskiy Yury on 28.04.2020.
#ifndef ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H
#define ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H
#include <vector>
#include <string>
#include "ace_c_basisfunction.h"
#include "ace_contigous_array.h"
#include "ace_radial.h"
#include "ace_spherical_cart.h"
#include "ace_types.h"
using namespace std;
/**
* Abstract basis set class
*/
class ACEAbstractBasisSet {
public:
SPECIES_TYPE nelements = 0; ///< number of elements in basis set
RANK_TYPE rankmax = 0; ///< maximum value of rank
DENSITY_TYPE ndensitymax = 0; ///< maximum number of densities \f$ \rho^{(p)} \f$
NS_TYPE nradbase = 0; ///< maximum number of radial \f$\textbf{basis}\f$ function \f$ g_{k}(r) \f$
LS_TYPE lmax = 0; ///< \f$ l_\textrm{max} \f$ - maximum value of orbital moment \f$ l \f$
NS_TYPE nradmax = 0; ///< maximum number \f$ n \f$ of radial function \f$ R_{nl}(r) \f$
DOUBLE_TYPE cutoffmax = 0; ///< maximum value of cutoff distance among all species in basis set
DOUBLE_TYPE deltaSplineBins = 0; ///< Spline interpolation density
string npoti = "FinnisSinclair"; ///< FS and embedding function combination
string *elements_name = nullptr; ///< Array of elements name for mapping from index (0..nelements-1) to element symbol (string)
AbstractRadialBasis *radial_functions = nullptr; ///< object to work with radial functions
ACECartesianSphericalHarmonics spherical_harmonics; ///< object to work with spherical harmonics in Cartesian representation
Array1D<DOUBLE_TYPE> rho_core_cutoffs; ///< energy-based inner cut-off
Array1D<DOUBLE_TYPE> drho_core_cutoffs; ///< decay of energy-based inner cut-off
vector<DOUBLE_TYPE> FS_parameters; ///< parameters for cluster functional, see Eq.(3) in implementation notes or Eq.(53) in <A HREF="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.99.014104"> PRB 99, 014104 (2019) </A>
// E0 values
Array1D<DOUBLE_TYPE> E0vals;
/**
* Default empty constructor
*/
ACEAbstractBasisSet() = default;
// copy constructor, operator= and destructor (see. Rule of Three)
/**
* Copy constructor (see. Rule of Three)
* @param other
*/
ACEAbstractBasisSet(const ACEAbstractBasisSet &other);
/**
* operator= (see. Rule of Three)
* @param other
* @return
*/
ACEAbstractBasisSet &operator=(const ACEAbstractBasisSet &other);
/**
* virtual destructor (see. Rule of Three)
*/
virtual ~ACEAbstractBasisSet();
/**
* Computing cluster functional \f$ F(\rho_i^{(1)}, \dots, \rho_i^{(P)}) \f$
* and its derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$
* @param rhos array with densities \f$ \rho^{(p)} \f$
* @param value (out) return value of cluster functional
* @param derivatives (out) array of derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$
* @param ndensity number \f$ P \f$ of densities to use
*/
void FS_values_and_derivatives(Array1D<DOUBLE_TYPE> &rhos, DOUBLE_TYPE &value, Array1D<DOUBLE_TYPE> &derivatives,
DENSITY_TYPE ndensity);
/**
* Computing hard core pairwise repulsive potential \f$ f_{cut}(\rho_i^{(\textrm{core})})\f$ and its derivative,
* see Eq.(29) of implementation notes
* @param rho_core value of \f$ \rho_i^{(\textrm{core})} \f$
* @param rho_cut \f$ \rho_{cut}^{\mu_i} \f$ value
* @param drho_cut \f$ \Delta_{cut}^{\mu_i} \f$ value
* @param fcut (out) return inner cutoff function
* @param dfcut (out) return derivative of inner cutoff function
*/
static void inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, DOUBLE_TYPE &fcut,
DOUBLE_TYPE &dfcut);
/**
* Virtual method to save potential to file
* @param filename file name
*/
virtual void save(const string &filename) = 0;
/**
* Virtual method to load potential from file
* @param filename file name
*/
virtual void load(const string filename) = 0;
/**
* Get the species index by its element name
* @param elemname element name
* @return species index
*/
SPECIES_TYPE get_species_index_by_name(const string &elemname);
// routines for copying and cleaning dynamic memory of the class (see. Rule of Three)
/**
* Routine for clean the dynamically allocated memory\n
* IMPORTANT! It must be idempotent for safety.
*/
virtual void _clean();
/**
* Copy dynamic memory from src. Must be override and extended in derived classes!
* @param src source object to copy from
*/
virtual void _copy_dynamic_memory(const ACEAbstractBasisSet &src);
/**
* Copy scalar values from src. Must be override and extended in derived classes!
* @param src source object to copy from
*/
virtual void _copy_scalar_memory(const ACEAbstractBasisSet &src);
};
void Fexp(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF);
void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF);
#endif //ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 11.01.20.
#ifndef ACE_ARRAY2DLM_H
#define ACE_ARRAY2DLM_H
#include <stdexcept>
#include <string>
#include "ace_arraynd.h"
#include "ace_contigous_array.h"
#include "ace_types.h"
using namespace std;
/**
* Contiguous array to organize values by \f$ (l,m) \f$ indiced (orbital moment and its projection).
* Only \f$ l_\textrm{max}\f$ should be provided, \f$ m = -l, \dots,l \f$
* for \f$ l = 0, \dots, l_\textrm{max}\f$
* @tparam T type of values to store
*/
template<typename T>
class Array2DLM : public ContiguousArrayND<T> {
using ContiguousArrayND<T>::array_name;
using ContiguousArrayND<T>::data;
using ContiguousArrayND<T>::size;
LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$
bool is_proxy = false; ///< flag to show, if object is owning the memory or just represent it (proxying)dimensions
public:
/**
* Default empty constructor
*/
Array2DLM() = default;
/**
* Parametrized constructor
* @param lmax maximum value of \f$ l \f$
* @param array_name name of the array
*/
explicit Array2DLM(LS_TYPE lmax, string array_name = "Array2DLM") {
init(lmax, array_name);
}
/**
* Constructor to create slices-proxy array, i.e. to provide access to the memory, but not to own it.
* @param lmax maximum value of \f$ l \f$
* @param data_ptr pointer to original data
* @param array_name name of the array
*/
Array2DLM(LS_TYPE lmax, T *data_ptr, string array_name = "Array2DLM") {
this->lmax = lmax;
this->size = (lmax + 1) * (lmax + 1);
this->data = data_ptr;
this->array_name = array_name;
is_proxy = true;
};
/**
* Destructor
*/
~Array2DLM() {
if (!is_proxy) {
if (data != nullptr) delete[] data;
}
data = nullptr;
}
/**
* Initialize array, allocate memory
* @param lmax maximum value of l
* @param array_name name of the array
*/
void init(LS_TYPE lmax, string array_name = "Array2DLM") {
if (is_proxy) {
char s[1024];
sprintf(s, "Could not re-initialize proxy-array %s\n", this->array_name.c_str());
throw logic_error(s);
}
this->lmax = lmax;
this->array_name = array_name;
//for m = -l .. l
if (size != (lmax + 1) * (lmax + 1)) {
size = (lmax + 1) * (lmax + 1);
if (data) delete[] data;
data = new T[size]{};
memset(data, 0.0, size * sizeof(T));
} else {
memset(data, 0, size * sizeof(T));
}
}
#ifdef MULTIARRAY_INDICES_CHECK
/**
* Check if indices (l,m) are within array
*/
void check_indices(LS_TYPE l, MS_TYPE m) const {
if ((l < 0) | (l > lmax)) {
fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax);
exit(EXIT_FAILURE);
}
if ((m < -l) | (m > l)) {
fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l);
exit(EXIT_FAILURE);
}
size_t ii = l * (l + 1) + m;
if (ii >= size) {
fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size);
exit(EXIT_FAILURE);
}
}
#endif
/**
* Accessing the array value by index (l,m) for reading
* @param l
* @param m
* @return array value
*/
inline const T &operator()(LS_TYPE l, MS_TYPE m) const {
#ifdef MULTIARRAY_INDICES_CHECK
check_indices(l, m);
#endif
//l^2 + l + m
return data[l * (l + 1) + m];
}
/**
* Accessing the array value by index (l,m) for writing
* @param l
* @param m
* @return array value
*/
inline T &operator()(LS_TYPE l, MS_TYPE m) {
#ifdef MULTIARRAY_INDICES_CHECK
check_indices(l, m);
#endif
//l^2 + l + m
return data[l * (l + 1) + m];
}
/**
* Convert array to STL vector<vector<T>> container
* @return vector<vector<T>> container
*/
vector<vector<T>> to_vector() const {
vector<vector<T>> res;
res.resize(lmax + 1);
for (int i = 0; i < lmax + 1; i++) {
res[i].resize(i + 1);
for (int j = 0; j < i + 1; j++) {
res[i][j] = operator()(i, j);
}
}
return res;
}
};
/**
* Contiguous array to organize values by \f$ (i_0, l , m) \f$ indices.
* Only \f$ d_{0}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$
* for \f$ l = 0, \dots, l_\textrm{max}\f$
* @tparam T type of values to store
*/
template<typename T>
class Array3DLM : public ContiguousArrayND<T> {
using ContiguousArrayND<T>::array_name;
using ContiguousArrayND<T>::data;
using ContiguousArrayND<T>::size;
LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$
size_t dim[1] = {0}; ///< linear dimension \f$ d_{0} \f$
size_t s[1] = {0}; ///< strides for linear dimensions
Array1D<Array2DLM<T> *> _proxy_slices; ///< slices representation
public:
/**
* Default empty constructor
*/
Array3DLM() = default;
/**
* Parametrized constructor
* @param array_name name of the array
*/
Array3DLM(string array_name) {
this->array_name = array_name;
};
/**
* Parametrized constructor
* @param d0 maximum value of \f$ i_0 \f$
* @param lmax maximum value of \f$ l \f$
* @param array_name name of the array
*/
explicit Array3DLM(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") {
init(d0, lmax, array_name);
}
/**
* Initialize array and its slices
* @param d0 maximum value of \f$ i_0 \f$
* @param lmax maximum value of \f$ l \f$
* @param array_name name of the array
*/
void init(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") {
this->array_name = array_name;
this->lmax = lmax;
dim[0] = d0;
s[0] = lmax * lmax;
if (size != s[0] * dim[0]) {
size = s[0] * dim[0];
if (data) delete[] data;
data = new T[size]{};
memset(data, 0, size * sizeof(T));
} else {
memset(data, 0, size * sizeof(T));
}
_proxy_slices.set_array_name(array_name + "_proxy");
//arrange proxy-slices
_clear_proxies();
_proxy_slices.resize(dim[0]);
for (size_t i0 = 0; i0 < dim[0]; ++i0) {
_proxy_slices(i0) = new Array2DLM<T>(this->lmax, &this->data[i0 * s[0]],
array_name + "_slice");
}
}
/**
* Release pointers to slices
*/
void _clear_proxies() {
for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) {
delete _proxy_slices(i0);
_proxy_slices(i0) = nullptr;
}
}
/**
* Destructor, clear proxies
*/
~Array3DLM() {
_clear_proxies();
}
/**
* Resize array to new dimensions
* @param d0
* @param lmax
*/
void resize(size_t d0, LS_TYPE lmax) {
_clear_proxies();
init(d0, lmax, this->array_name);
}
/**
* Get array dimensions
* @param d dimension index
* @return dimension along axis 'd'
*/
size_t get_dim(int d) const {
return dim[d];
}
#ifdef MULTIARRAY_INDICES_CHECK
/**
* Check if indices (i0, l,m) are within array
*/
void check_indices(size_t i0, LS_TYPE l, MS_TYPE m) const {
if ((l < 0) | (l > lmax)) {
fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax);
exit(EXIT_FAILURE);
}
if ((m < -l) | (m > l)) {
fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l);
exit(EXIT_FAILURE);
}
if ((i0 < 0) | (i0 >= dim[0])) {
fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1);
exit(EXIT_FAILURE);
}
size_t ii = i0 * s[0] + l * (l + 1) + m;
if (ii >= size) {
fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size);
exit(EXIT_FAILURE);
}
}
#endif
/**
* Accessing the array value by index (i0,l,m) for reading
* @param i0
* @param l
* @param m
* @return array value
*/
inline const T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) const {
#ifdef MULTIARRAY_INDICES_CHECK
check_indices(i0, l, m);
#endif
return data[i0 * s[0] + l * (l + 1) + m];
}
/**
* Accessing the array value by index (i0,l,m) for writing
* @param i0
* @param l
* @param m
* @return array value
*/
inline T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) {
#ifdef MULTIARRAY_INDICES_CHECK
check_indices(i0, l, m);
#endif
return data[i0 * s[0] + l * (l + 1) + m];
}
/**
* Return proxy Array2DLM pointing to i0, l=0, m=0 to read
* @param i0
* @return proxy Array2DLM pointing to i0, l=0, m=0
*/
inline const Array2DLM<T> &operator()(size_t i0) const {
return *_proxy_slices(i0);
}
/**
* Return proxy Array2DLM pointing to i0, l=0, m=0 to write
* @param i0
* @return proxy Array2DLM pointing to i0, l=0, m=0
*/
inline Array2DLM<T> &operator()(size_t i0) {
return *_proxy_slices(i0);
}
};
/**
* Contiguous array to organize values by \f$ (i_0, i_1, l , m) \f$ indices.
* Only \f$ d_{0}, d_{1}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$
* for \f$ l = 0, \dots, l_\textrm{max}\f$
* @tparam T type of values to store
*/
template<typename T>
class Array4DLM : public ContiguousArrayND<T> {
using ContiguousArrayND<T>::array_name;
using ContiguousArrayND<T>::data;
using ContiguousArrayND<T>::size;
LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$
size_t dim[2] = {0, 0}; ///< linear dimension \f$ d_{0}, d_{1} \f$
size_t s[2] = {0, 0}; ///< strides for linear dimensions
Array2D<Array2DLM<T> *> _proxy_slices; ///< slices representation
public:
/**
* Default empty constructor
*/
Array4DLM() = default;
/**
* Parametrized constructor
* @param array_name name of the array
*/
Array4DLM(string array_name) {
this->array_name = array_name;
};
/**
* Parametrized constructor
* @param d0 maximum value of \f$ i_0 \f$
* @param d1 maximum value of \f$ i_1 \f$
* @param lmax maximum value of \f$ l \f$
* @param array_name name of the array
*/
explicit Array4DLM(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") {
init(d0, d1, lmax, array_name);
}
/**
* Initialize array, reallocate memory and its slices
* @param d0 maximum value of \f$ i_0 \f$
* @param d1 maximum value of \f$ i_1 \f$
* @param lmax maximum value of \f$ l \f$
* @param array_name name of the array
*/
void init(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") {
this->array_name = array_name;
this->lmax = lmax;
dim[1] = d1;
dim[0] = d0;
s[1] = lmax * lmax;
s[0] = s[1] * dim[1];
if (size != s[0] * dim[0]) {
size = s[0] * dim[0];
if (data) delete[] data;
data = new T[size]{};
memset(data, 0, size * sizeof(T));
} else {
memset(data, 0, size * sizeof(T));
}
_proxy_slices.set_array_name(array_name + "_proxy");
//release old memory if there is any
_clear_proxies();
//arrange proxy-slices
_proxy_slices.resize(dim[0], dim[1]);
for (size_t i0 = 0; i0 < dim[0]; ++i0)
for (size_t i1 = 0; i1 < dim[1]; ++i1) {
_proxy_slices(i0, i1) = new Array2DLM<T>(this->lmax, &this->data[i0 * s[0] + i1 * s[1]],
array_name + "_slice");
}
}
/**
* Release pointers to slices
*/
void _clear_proxies() {
for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0)
for (size_t i1 = 0; i1 < _proxy_slices.get_dim(1); ++i1) {
delete _proxy_slices(i0, i1);
_proxy_slices(i0, i1) = nullptr;
}
}
/**
* Destructor, clear proxies
*/
~Array4DLM() {
_clear_proxies();
}
/**
* Deallocate memory, reallocate with the new dimensions
* @param d0
* @param lmax
*/
void resize(size_t d0, size_t d1, LS_TYPE lmax) {
_clear_proxies();
init(d0, d1, lmax, this->array_name);
}
/**
* Get array dimensions
* @param d dimension index
* @return dimension along axis 'd'
*/
size_t get_dim(int d) const {
return dim[d];
}
#ifdef MULTIARRAY_INDICES_CHECK
/**
* Check if indices (i0, l,m) are within array
*/
void check_indices(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const {
if ((l < 0) | (l > lmax)) {
fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax);
exit(EXIT_FAILURE);
}
if ((m < -l) | (m > l)) {
fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l);
exit(EXIT_FAILURE);
}
if ((i0 < 0) | (i0 >= dim[0])) {
fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1);
exit(EXIT_FAILURE);
}
if ((i1 < 0) | (i1 >= dim[1])) {
fprintf(stderr, "%s: index i1 = %ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1);
exit(EXIT_FAILURE);
}
size_t ii = i0 * s[0] + i1 * s[1] + l * (l + 1) + m;
if (ii >= size) {
fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size);
exit(EXIT_FAILURE);
}
}
#endif
/**
* Accessing the array value by index (i0,l,m) for reading
* @param i0
* @param i1
* @param l
* @param m
* @return array value
*/
inline const T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const {
#ifdef MULTIARRAY_INDICES_CHECK
check_indices(i0, i1, l, m);
#endif
return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m];
}
/**
* Accessing the array value by index (i0,l,m) for writing
* @param i0
* @param i1
* @param l
* @param m
* @return array value
*/
inline T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) {
#ifdef MULTIARRAY_INDICES_CHECK
check_indices(i0, i1, l, m);
#endif
return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m];
}
/**
* Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to read
* @param i0
* @param i1
* @return proxy Array2DLM pointing to i0, l=0, m=0
*/
inline const Array2DLM<T> &operator()(size_t i0, size_t i1) const {
return *_proxy_slices(i0, i1);
}
/**
* Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to write
* @param i0
* @param i1
* @return proxy Array2DLM pointing to i0, l=0, m=0
*/
inline Array2DLM<T> &operator()(size_t i0, size_t i1) {
return *_proxy_slices(i0, i1);
}
};
#endif //ACE_ARRAY2DLM_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 1.04.20.
#include "ace_c_basis.h"
#include "ships_radial.h"
using namespace std;
ACECTildeBasisSet::ACECTildeBasisSet(string filename) {
load(filename);
}
ACECTildeBasisSet::ACECTildeBasisSet(const ACECTildeBasisSet &other) {
ACECTildeBasisSet::_copy_scalar_memory(other);
ACECTildeBasisSet::_copy_dynamic_memory(other);
pack_flatten_basis();
}
ACECTildeBasisSet &ACECTildeBasisSet::operator=(const ACECTildeBasisSet &other) {
if (this != &other) {
_clean();
_copy_scalar_memory(other);
_copy_dynamic_memory(other);
pack_flatten_basis();
}
return *this;
}
ACECTildeBasisSet::~ACECTildeBasisSet() {
ACECTildeBasisSet::_clean();
}
void ACECTildeBasisSet::_clean() {
// call parent method
ACEFlattenBasisSet::_clean();
_clean_contiguous_arrays();
_clean_basis_arrays();
}
void ACECTildeBasisSet::_copy_scalar_memory(const ACECTildeBasisSet &src) {
ACEFlattenBasisSet::_copy_scalar_memory(src);
num_ctilde_max = src.num_ctilde_max;
}
void ACECTildeBasisSet::_copy_dynamic_memory(const ACECTildeBasisSet &src) {//allocate new memory
ACEFlattenBasisSet::_copy_dynamic_memory(src);
if (src.basis_rank1 == nullptr)
throw runtime_error("Could not copy ACECTildeBasisSet::basis_rank1 - array not initialized");
if (src.basis == nullptr) throw runtime_error("Could not copy ACECTildeBasisSet::basis - array not initialized");
basis_rank1 = new ACECTildeBasisFunction *[src.nelements];
basis = new ACECTildeBasisFunction *[src.nelements];
//copy basis arrays
for (SPECIES_TYPE mu = 0; mu < src.nelements; ++mu) {
basis_rank1[mu] = new ACECTildeBasisFunction[src.total_basis_size_rank1[mu]];
for (size_t i = 0; i < src.total_basis_size_rank1[mu]; i++) {
basis_rank1[mu][i] = src.basis_rank1[mu][i];
}
basis[mu] = new ACECTildeBasisFunction[src.total_basis_size[mu]];
for (size_t i = 0; i < src.total_basis_size[mu]; i++) {
basis[mu][i] = src.basis[mu][i];
}
}
//DON"T COPY CONTIGUOUS ARRAY, REBUILD THEM
}
void ACECTildeBasisSet::_clean_contiguous_arrays() {
ACEFlattenBasisSet::_clean_contiguous_arrays();
delete[] full_c_tildes_rank1;
full_c_tildes_rank1 = nullptr;
delete[] full_c_tildes;
full_c_tildes = nullptr;
}
//re-pack the constituent dynamic arrays of all basis functions in contiguous arrays
void ACECTildeBasisSet::pack_flatten_basis() {
compute_array_sizes(basis_rank1, basis);
//1. clean contiguous arrays
_clean_contiguous_arrays();
//2. allocate contiguous arrays
delete[] full_ns_rank1;
full_ns_rank1 = new NS_TYPE[rank_array_total_size_rank1];
delete[] full_ls_rank1;
full_ls_rank1 = new NS_TYPE[rank_array_total_size_rank1];
delete[] full_mus_rank1;
full_mus_rank1 = new SPECIES_TYPE[rank_array_total_size_rank1];
delete[] full_ms_rank1;
full_ms_rank1 = new MS_TYPE[rank_array_total_size_rank1];
delete[] full_c_tildes_rank1;
full_c_tildes_rank1 = new DOUBLE_TYPE[coeff_array_total_size_rank1];
delete[] full_ns;
full_ns = new NS_TYPE[rank_array_total_size];
delete[] full_ls;
full_ls = new LS_TYPE[rank_array_total_size];
delete[] full_mus;
full_mus = new SPECIES_TYPE[rank_array_total_size];
delete[] full_ms;
full_ms = new MS_TYPE[ms_array_total_size];
delete[] full_c_tildes;
full_c_tildes = new DOUBLE_TYPE[coeff_array_total_size];
//3. copy the values from private C_tilde_B_basis_function arrays to new contigous space
//4. clean private memory
//5. reassign private array pointers
//r = 0, rank = 1
size_t rank_array_ind_rank1 = 0;
size_t coeff_array_ind_rank1 = 0;
size_t ms_array_ind_rank1 = 0;
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
for (int func_ind_r1 = 0; func_ind_r1 < total_basis_size_rank1[mu]; ++func_ind_r1) {
ACECTildeBasisFunction &func = basis_rank1[mu][func_ind_r1];
//copy values ns from c_tilde_basis_function private memory to contigous memory part
full_ns_rank1[rank_array_ind_rank1] = func.ns[0];
//copy values ls from c_tilde_basis_function private memory to contigous memory part
full_ls_rank1[rank_array_ind_rank1] = func.ls[0];
//copy values mus from c_tilde_basis_function private memory to contigous memory part
full_mus_rank1[rank_array_ind_rank1] = func.mus[0];
//copy values ctildes from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_c_tildes_rank1[coeff_array_ind_rank1], func.ctildes,
func.ndensity * sizeof(DOUBLE_TYPE));
//copy values mus from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_ms_rank1[ms_array_ind_rank1], func.ms_combs,
func.num_ms_combs *
func.rank * sizeof(MS_TYPE));
//release memory of each ACECTildeBasisFunction if it is not proxy
func._clean();
func.mus = &full_mus_rank1[rank_array_ind_rank1];
func.ns = &full_ns_rank1[rank_array_ind_rank1];
func.ls = &full_ls_rank1[rank_array_ind_rank1];
func.ms_combs = &full_ms_rank1[ms_array_ind_rank1];
func.ctildes = &full_c_tildes_rank1[coeff_array_ind_rank1];
func.is_proxy = true;
rank_array_ind_rank1 += func.rank;
ms_array_ind_rank1 += func.rank *
func.num_ms_combs;
coeff_array_ind_rank1 += func.num_ms_combs * func.ndensity;
}
}
//rank>1, r>0
size_t rank_array_ind = 0;
size_t coeff_array_ind = 0;
size_t ms_array_ind = 0;
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) {
ACECTildeBasisFunction &func = basis[mu][func_ind];
//copy values mus from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_mus[rank_array_ind], func.mus,
func.rank * sizeof(SPECIES_TYPE));
//copy values ns from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_ns[rank_array_ind], func.ns,
func.rank * sizeof(NS_TYPE));
//copy values ls from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_ls[rank_array_ind], func.ls,
func.rank * sizeof(LS_TYPE));
//copy values mus from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_ms[ms_array_ind], func.ms_combs,
func.num_ms_combs *
func.rank * sizeof(MS_TYPE));
//copy values ctildes from c_tilde_basis_function private memory to contigous memory part
memcpy(&full_c_tildes[coeff_array_ind], func.ctildes,
func.num_ms_combs * func.ndensity * sizeof(DOUBLE_TYPE));
//release memory of each ACECTildeBasisFunction if it is not proxy
func._clean();
func.ns = &full_ns[rank_array_ind];
func.ls = &full_ls[rank_array_ind];
func.mus = &full_mus[rank_array_ind];
func.ctildes = &full_c_tildes[coeff_array_ind];
func.ms_combs = &full_ms[ms_array_ind];
func.is_proxy = true;
rank_array_ind += func.rank;
ms_array_ind += func.rank *
func.num_ms_combs;
coeff_array_ind += func.num_ms_combs * func.ndensity;
}
}
}
void fwrite_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) {
RANK_TYPE r;
fprintf(fptr, "ctilde_basis_func: ");
fprintf(fptr, "rank=%d ndens=%d mu0=%d ", func.rank, func.ndensity, func.mu0);
fprintf(fptr, "mu=(");
for (r = 0; r < func.rank; ++r)
fprintf(fptr, " %d ", func.mus[r]);
fprintf(fptr, ")\n");
fprintf(fptr, "n=(");
for (r = 0; r < func.rank; ++r)
fprintf(fptr, " %d ", func.ns[r]);
fprintf(fptr, ")\n");
fprintf(fptr, "l=(");
for (r = 0; r < func.rank; ++r)
fprintf(fptr, " %d ", func.ls[r]);
fprintf(fptr, ")\n");
fprintf(fptr, "num_ms=%d\n", func.num_ms_combs);
for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) {
fprintf(fptr, "<");
for (r = 0; r < func.rank; ++r)
fprintf(fptr, " %d ", func.ms_combs[m_ind * func.rank + r]);
fprintf(fptr, ">: ");
for (DENSITY_TYPE p = 0; p < func.ndensity; p++)
fprintf(fptr, " %.18f ", func.ctildes[m_ind * func.ndensity + p]);
fprintf(fptr, "\n");
}
}
void ACECTildeBasisSet::save(const string &filename) {
FILE *fptr;
fptr = fopen(filename.c_str(), "w");
fprintf(fptr, "nelements=%d\n", nelements);
//elements mapping
fprintf(fptr, "elements:");
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu)
fprintf(fptr, " %s", elements_name[mu].c_str());
fprintf(fptr, "\n\n");
fprintf(fptr, "lmax=%d\n\n", lmax);
fprintf(fptr, "embedding-function: %s\n", npoti.c_str());
fprintf(fptr, "%ld FS parameters: ", FS_parameters.size());
for (int i = 0; i < FS_parameters.size(); ++i) {
fprintf(fptr, " %f", FS_parameters.at(i));
}
fprintf(fptr, "\n");
//hard-core energy cutoff repulsion
fprintf(fptr, "core energy-cutoff parameters: ");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
fprintf(fptr, "%.18f %.18f\n", rho_core_cutoffs(mu_i), drho_core_cutoffs(mu_i));
// save E0 values
fprintf(fptr, "E0:");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
fprintf(fptr, " %.18f", E0vals(mu_i));
fprintf(fptr, "\n");
fprintf(fptr, "\n");
fprintf(fptr, "radbasename=%s\n", radial_functions->radbasename.c_str());
fprintf(fptr, "nradbase=%d\n", nradbase);
fprintf(fptr, "nradmax=%d\n", nradmax);
fprintf(fptr, "cutoffmax=%f\n", cutoffmax);
fprintf(fptr, "deltaSplineBins=%f\n", deltaSplineBins);
//hard-core repulsion
fprintf(fptr, "core repulsion parameters: ");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j)
fprintf(fptr, "%.18f %.18f\n", radial_functions->prehc(mu_i, mu_j), radial_functions->lambdahc(mu_j, mu_j));
//TODO: radial functions
//radparameter
fprintf(fptr, "radparameter=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j)
fprintf(fptr, " %.18f", radial_functions->lambda(mu_i, mu_j));
fprintf(fptr, "\n");
fprintf(fptr, "cutoff=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j)
fprintf(fptr, " %.18f", radial_functions->cut(mu_i, mu_j));
fprintf(fptr, "\n");
fprintf(fptr, "dcut=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j)
fprintf(fptr, " %.18f", radial_functions->dcut(mu_i, mu_j));
fprintf(fptr, "\n");
fprintf(fptr, "crad=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) {
for (NS_TYPE k = 0; k < nradbase; k++) {
for (NS_TYPE n = 0; n < nradmax; n++) {
for (LS_TYPE l = 0; l <= lmax; l++) {
fprintf(fptr, " %.18f", radial_functions->crad(mu_i, mu_j, n, l, k));
}
fprintf(fptr, "\n");
}
}
}
fprintf(fptr, "\n");
fprintf(fptr, "rankmax=%d\n", rankmax);
fprintf(fptr, "ndensitymax=%d\n", ndensitymax);
fprintf(fptr, "\n");
//num_c_tilde_max
fprintf(fptr, "num_c_tilde_max=%d\n", num_ctilde_max);
fprintf(fptr, "num_ms_combinations_max=%d\n", num_ms_combinations_max);
//write total_basis_size and total_basis_size_rank1
fprintf(fptr, "total_basis_size_rank1: ");
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
fprintf(fptr, "%d ", total_basis_size_rank1[mu]);
}
fprintf(fptr, "\n");
for (SPECIES_TYPE mu = 0; mu < nelements; mu++)
for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind)
fwrite_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]);
fprintf(fptr, "total_basis_size: ");
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
fprintf(fptr, "%d ", total_basis_size[mu]);
}
fprintf(fptr, "\n");
for (SPECIES_TYPE mu = 0; mu < nelements; mu++)
for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind)
fwrite_c_tilde_b_basis_func(fptr, basis[mu][func_ind]);
fclose(fptr);
}
void fread_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) {
RANK_TYPE r;
int res;
char buf[3][128];
res = fscanf(fptr, " ctilde_basis_func: ");
res = fscanf(fptr, "rank=%s ndens=%s mu0=%s ", buf[0], buf[1], buf[2]);
if (res != 3)
throw invalid_argument("Could not read C-tilde basis function");
func.rank = (RANK_TYPE) stol(buf[0]);
func.ndensity = (DENSITY_TYPE) stol(buf[1]);
func.mu0 = (SPECIES_TYPE) stol(buf[2]);
func.mus = new SPECIES_TYPE[func.rank];
func.ns = new NS_TYPE[func.rank];
func.ls = new LS_TYPE[func.rank];
res = fscanf(fptr, " mu=(");
for (r = 0; r < func.rank; ++r) {
res = fscanf(fptr, "%s", buf[0]);
if (res != 1)
throw invalid_argument("Could not read C-tilde basis function");
func.mus[r] = (SPECIES_TYPE) stol(buf[0]);
}
res = fscanf(fptr, " )"); // ")"
res = fscanf(fptr, " n=("); // "n="
for (r = 0; r < func.rank; ++r) {
res = fscanf(fptr, "%s", buf[0]);
if (res != 1)
throw invalid_argument("Could not read C-tilde basis function");
func.ns[r] = (NS_TYPE) stol(buf[0]);
}
res = fscanf(fptr, " )");
res = fscanf(fptr, " l=(");
for (r = 0; r < func.rank; ++r) {
res = fscanf(fptr, "%s", buf[0]);
if (res != 1)
throw invalid_argument("Could not read C-tilde basis function");
func.ls[r] = (NS_TYPE) stol(buf[0]);
}
res = fscanf(fptr, " )");
res = fscanf(fptr, " num_ms=%s\n", buf[0]);
if (res != 1)
throw invalid_argument("Could not read C-tilde basis function");
func.num_ms_combs = (SHORT_INT_TYPE) stoi(buf[0]);
func.ms_combs = new MS_TYPE[func.rank * func.num_ms_combs];
func.ctildes = new DOUBLE_TYPE[func.ndensity * func.num_ms_combs];
for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) {
res = fscanf(fptr, " <");
for (r = 0; r < func.rank; ++r) {
res = fscanf(fptr, "%s", buf[0]);
if (res != 1)
throw invalid_argument("Could not read C-tilde basis function");
func.ms_combs[m_ind * func.rank + r] = stoi(buf[0]);
}
res = fscanf(fptr, " >:");
for (DENSITY_TYPE p = 0; p < func.ndensity; p++) {
res = fscanf(fptr, "%s", buf[0]);
if (res != 1)
throw invalid_argument("Could not read C-tilde basis function");
func.ctildes[m_ind * func.ndensity + p] = stod(buf[0]);
}
}
}
string
format_error_message(const char *buffer, const string &filename, const string &var_name, const string &expected) {
string err_message = "File '" + filename + "': couldn't read '" + var_name + "'";
if (buffer)
err_message = err_message + ", read:'" + buffer + "'";
if (!expected.empty())
err_message = err_message + ". Expected format: '" + expected + "'";
return err_message;
}
void throw_error(const string &filename, const string &var_name, const string expected = "") {
throw invalid_argument(format_error_message(nullptr, filename, var_name, expected));
}
DOUBLE_TYPE stod_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") {
try {
return stod(buffer);
} catch (invalid_argument &exc) {
throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str());
}
}
int stoi_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") {
try {
return stoi(buffer);
} catch (invalid_argument &exc) {
throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str());
}
}
long int stol_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") {
try {
return stol(buffer);
} catch (invalid_argument &exc) {
throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str());
}
}
void ACECTildeBasisSet::load(const string filename) {
int res;
char buffer[1024], buffer2[1024];
string radbasename = "ChebExpCos";
FILE *fptr;
fptr = fopen(filename.c_str(), "r");
if (fptr == NULL)
throw invalid_argument("Could not open file " + filename);
//read number of elements
res = fscanf(fptr, " nelements=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "nelements", "nelements=[number]");
nelements = stoi_err(buffer, filename, "nelements", "nelements=[number]");
//elements mapping
elements_name = new string[nelements];
res = fscanf(fptr, " elements:");
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "elements", "elements: Ele1 Ele2 ...");
elements_name[mu] = buffer;
}
// load angular basis - only need spherical harmonics parameter
res = fscanf(fptr, " lmax=%s\n", buffer);
if (res != 1)
throw_error(filename, "lmax", "lmax=[number]");
lmax = stoi_err(buffer, filename, "lmax", "lmax=[number]");
spherical_harmonics.init(lmax);
// reading "embedding-function:"
bool is_embedding_function_specified = false;
res = fscanf(fptr, " embedding-function: %s", buffer);
if (res == 0) {
//throw_error(filename, "E0", " E0: E0-species1 E0-species2 ...");
this->npoti = "FinnisSinclair"; // default values
//printf("Warning! No embedding-function is specified, embedding-function: FinnisSinclair would be assumed\n");
is_embedding_function_specified = false;
} else {
this->npoti = buffer;
is_embedding_function_specified = true;
}
int parameters_size;
res = fscanf(fptr, "%s FS parameters:", buffer);
if (res != 1)
throw_error(filename, "FS parameters size", "[number] FS parameters: par1 par2 ...");
parameters_size = stoi_err(buffer, filename, "FS parameters size", "[number] FS parameters");
FS_parameters.resize(parameters_size);
for (int i = 0; i < FS_parameters.size(); ++i) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "FS parameter", "[number] FS parameters: [par1] [par2] ...");
FS_parameters[i] = stod_err(buffer, filename, "FS parameter", "[number] FS parameters: [par1] [par2] ...");
}
if (!is_embedding_function_specified) {
// assuming non-linear potential, and embedding function type is important
for (int j = 1; j < parameters_size; j += 2)
if (FS_parameters[j] != 1.0) { //if not ensure linearity of embedding function parameters
printf("ERROR! Your potential is non-linear\n");
printf("Please specify 'embedding-function: FinnisSinclair' or 'embedding-function: FinnisSinclairShiftedScaled' before 'FS parameters size' line\n");
throw_error(filename, "embedding-function", "FinnisSinclair or FinnisSinclairShiftedScaled");
}
printf("Notice! No embedding-function is specified, but potential has linear embedding, default embedding-function: FinnisSinclair would be assumed\n");
}
//hard-core energy cutoff repulsion
res = fscanf(fptr, " core energy-cutoff parameters:");
if (res != 0)
throw_error(filename, "core energy-cutoff parameters", "core energy-cutoff parameters: [par1] [par2]");
rho_core_cutoffs.init(nelements, "rho_core_cutoffs");
drho_core_cutoffs.init(nelements, "drho_core_cutoffs");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) {
res = fscanf(fptr, "%s %s", buffer, buffer2);
if (res != 2)
throw_error(filename, "core energy-cutoff parameters",
"core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ...");
rho_core_cutoffs(mu_i) = stod_err(buffer, filename, "rho core cutoff",
"core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ...");
drho_core_cutoffs(mu_i) = stod_err(buffer2, filename, "drho_core_cutoff",
"core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ...");
}
// atom energy shift E0 (energy of isolated atom)
E0vals.init(nelements);
// reading "E0:"
res = fscanf(fptr, " E0: %s", buffer);
if (res == 0) {
//throw_error(filename, "E0", " E0: E0-species1 E0-species2 ...");
E0vals.fill(0.0);
} else {
double E0 = atof(buffer);
E0vals(0) = E0;
for (SPECIES_TYPE mu_i = 1; mu_i < nelements; ++mu_i) {
res = fscanf(fptr, " %lf", &E0);
if (res != 1)
throw_error(filename, "E0", " couldn't read one of the E0 values");
E0vals(mu_i) = E0;
}
res = fscanf(fptr, "\n");
if (res != 0)
printf("file %s : format seems broken near E0; trying to continue...\n", filename.c_str());
}
// check which radial basis we need to load
res = fscanf(fptr, " radbasename=%s\n", buffer);
if (res != 1) {
throw_error(filename, "radbasename", "rabbasename=ChebExpCos|ChebPow|ACE.jl.Basic");
} else {
radbasename = buffer;
}
// printf("radbasename = `%s`\n", radbasename.c_str());
if (radbasename == "ChebExpCos" | radbasename == "ChebPow") {
_load_radial_ACERadial(fptr, filename, radbasename);
} else if (radbasename == "ACE.jl.Basic") {
_load_radial_SHIPsBasic(fptr, filename, radbasename);
} else {
throw invalid_argument(
("File '" + filename + "': I don't know how to read radbasename = " + radbasename).c_str());
}
res = fscanf(fptr, " rankmax=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "rankmax", "rankmax=[number]");
rankmax = stoi_err(buffer, filename, "rankmax", "rankmax=[number]");
res = fscanf(fptr, " ndensitymax=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "ndensitymax", "ndensitymax=[number]");
ndensitymax = stoi_err(buffer, filename, "ndensitymax", "ndensitymax=[number]");
// read the list of correlations to be put into the basis
//num_c_tilde_max
res = fscanf(fptr, " num_c_tilde_max=");
res = fscanf(fptr, "%s\n", buffer);
if (res != 1)
throw_error(filename, "num_c_tilde_max", "num_c_tilde_max=[number]");
num_ctilde_max = stol_err(buffer, filename, "num_c_tilde_max", "num_c_tilde_max=[number]");
res = fscanf(fptr, " num_ms_combinations_max=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]");
// throw invalid_argument(("File '" + filename + "': couldn't read num_ms_combinations_max").c_str());
num_ms_combinations_max = stol_err(buffer, filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]");
//read total_basis_size_rank1
total_basis_size_rank1 = new SHORT_INT_TYPE[nelements];
basis_rank1 = new ACECTildeBasisFunction *[nelements];
res = fscanf(fptr, " total_basis_size_rank1: ");
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "total_basis_size_rank1", "total_basis_size_rank1: [size_ele1] [size_ele2] ...");
// throw invalid_argument(("File '" + filename + "': couldn't read total_basis_size_rank1").c_str());
total_basis_size_rank1[mu] = stoi_err(buffer, filename, "total_basis_size_rank1",
"total_basis_size_rank1: [size_ele1] [size_ele2] ...");
basis_rank1[mu] = new ACECTildeBasisFunction[total_basis_size_rank1[mu]];
}
for (SPECIES_TYPE mu = 0; mu < nelements; mu++)
for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) {
fread_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]);
}
//read total_basis_size
res = fscanf(fptr, " total_basis_size: ");
total_basis_size = new SHORT_INT_TYPE[nelements];
basis = new ACECTildeBasisFunction *[nelements];
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "total_basis_size", "total_basis_size: [size_ele1] [size_ele2] ...");
total_basis_size[mu] = stoi_err(buffer, filename, "total_basis_size",
"total_basis_size: [size_ele1] [size_ele2] ...");
basis[mu] = new ACECTildeBasisFunction[total_basis_size[mu]];
}
for (SPECIES_TYPE mu = 0; mu < nelements; mu++)
for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) {
fread_c_tilde_b_basis_func(fptr, basis[mu][func_ind]);
}
fclose(fptr);
// radial_functions->radbasename = radbasename;
radial_functions->setuplookupRadspline();
pack_flatten_basis();
}
void ACECTildeBasisSet::compute_array_sizes(ACECTildeBasisFunction **basis_rank1, ACECTildeBasisFunction **basis) {
//compute arrays sizes
rank_array_total_size_rank1 = 0;
//ms_array_total_size_rank1 = rank_array_total_size_rank1;
coeff_array_total_size_rank1 = 0;
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
if (total_basis_size_rank1[mu] > 0) {
rank_array_total_size_rank1 += total_basis_size_rank1[mu];
ACEAbstractBasisFunction &func = basis_rank1[mu][0];//TODO: get total density instead of density from first function
coeff_array_total_size_rank1 += total_basis_size_rank1[mu] * func.ndensity;
}
}
rank_array_total_size = 0;
coeff_array_total_size = 0;
ms_array_total_size = 0;
max_dB_array_size = 0;
max_B_array_size = 0;
size_t cur_ms_size = 0;
size_t cur_ms_rank_size = 0;
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
cur_ms_size = 0;
cur_ms_rank_size = 0;
for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) {
auto &func = basis[mu][func_ind];
rank_array_total_size += func.rank;
ms_array_total_size += func.rank * func.num_ms_combs;
coeff_array_total_size += func.ndensity * func.num_ms_combs;
cur_ms_size += func.num_ms_combs;
cur_ms_rank_size += func.rank * func.num_ms_combs;
}
if (cur_ms_size > max_B_array_size)
max_B_array_size = cur_ms_size;
if (cur_ms_rank_size > max_dB_array_size)
max_dB_array_size = cur_ms_rank_size;
}
}
void ACECTildeBasisSet::_clean_basis_arrays() {
if (basis_rank1 != nullptr)
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
delete[] basis_rank1[mu];
basis_rank1[mu] = nullptr;
}
if (basis != nullptr)
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
delete[] basis[mu];
basis[mu] = nullptr;
}
delete[] basis;
basis = nullptr;
delete[] basis_rank1;
basis_rank1 = nullptr;
}
//pack into 1D array with all basis functions
void ACECTildeBasisSet::flatten_basis(C_tilde_full_basis_vector2d &mu0_ctilde_basis_vector) {
_clean_basis_arrays();
basis_rank1 = new ACECTildeBasisFunction *[nelements];
basis = new ACECTildeBasisFunction *[nelements];
delete[] total_basis_size_rank1;
delete[] total_basis_size;
total_basis_size_rank1 = new SHORT_INT_TYPE[nelements];
total_basis_size = new SHORT_INT_TYPE[nelements];
size_t tot_size_rank1 = 0;
size_t tot_size = 0;
for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) {
tot_size = 0;
tot_size_rank1 = 0;
for (auto &func: mu0_ctilde_basis_vector[mu]) {
if (func.rank == 1) tot_size_rank1 += 1;
else tot_size += 1;
}
total_basis_size_rank1[mu] = tot_size_rank1;
basis_rank1[mu] = new ACECTildeBasisFunction[tot_size_rank1];
total_basis_size[mu] = tot_size;
basis[mu] = new ACECTildeBasisFunction[tot_size];
}
for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) {
size_t ind_rank1 = 0;
size_t ind = 0;
for (auto &func: mu0_ctilde_basis_vector[mu]) {
if (func.rank == 1) { //r=0, rank=1
basis_rank1[mu][ind_rank1] = func;
ind_rank1 += 1;
} else { //r>0, rank>1
basis[mu][ind] = func;
ind += 1;
}
}
}
}
void ACECTildeBasisSet::_load_radial_ACERadial(FILE *fptr,
const string filename,
const string radbasename) {
int res;
char buffer[1024], buffer2[1024];
res = fscanf(fptr, " nradbase=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "nradbase", "nradbase=[number]");
// throw invalid_argument(("File '" + filename + "': couldn't read nradbase").c_str());
nradbase = stoi_err(buffer, filename, "nradbase", "nradbase=[number]");
res = fscanf(fptr, " nradmax=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "nradmax", "nradmax=[number]");
nradmax = stoi_err(buffer, filename, "nradmax", "nradmax=[number]");
res = fscanf(fptr, " cutoffmax=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "cutoffmax", "cutoffmax=[number]");
cutoffmax = stod_err(buffer, filename, "cutoffmax", "cutoffmax=[number]");
res = fscanf(fptr, " deltaSplineBins=");
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]");
// throw invalid_argument(("File '" + filename + "': couldn't read ntot").c_str());
deltaSplineBins = stod_err(buffer, filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]");
if (radial_functions == nullptr)
radial_functions = new ACERadialFunctions(nradbase, lmax, nradmax,
deltaSplineBins,
nelements,
cutoffmax, radbasename);
else
radial_functions->init(nradbase, lmax, nradmax,
deltaSplineBins,
nelements,
cutoffmax, radbasename);
//hard-core repulsion
res = fscanf(fptr, " core repulsion parameters:");
if (res != 0)
throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ...");
// throw invalid_argument(("File '" + filename + "': couldn't read core repulsion parameters").c_str());
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) {
res = fscanf(fptr, "%s %s", buffer, buffer2);
if (res != 2)
throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ...");
radial_functions->prehc(mu_i, mu_j) = stod_err(buffer, filename, "core repulsion parameters",
"core repulsion parameters: [prehc lambdahc] ...");
radial_functions->lambdahc(mu_i, mu_j) = stod_err(buffer2, filename, "core repulsion parameters",
"core repulsion parameters: [prehc lambdahc] ...");
}
//read radial functions parameter
res = fscanf(fptr, " radparameter=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "radparameter", "radparameter=[param_ele1] [param_ele2]");
radial_functions->lambda(mu_i, mu_j) = stod_err(buffer, filename, "radparameter",
"radparameter=[param_ele1] [param_ele2]");
}
res = fscanf(fptr, " cutoff=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "cutoff", "cutoff=[param_ele1] [param_ele2]");
radial_functions->cut(mu_i, mu_j) = stod_err(buffer, filename, "cutoff",
"cutoff=[param_ele1] [param_ele2]");
}
res = fscanf(fptr, " dcut=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) {
res = fscanf(fptr, " %s", buffer);
if (res != 1)
throw_error(filename, "dcut", "dcut=[param_ele1] [param_ele2]");
radial_functions->dcut(mu_i, mu_j) = stod_err(buffer, filename, "dcut", "dcut=[param_ele1] [param_ele2]");
}
res = fscanf(fptr, " crad=");
for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i)
for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j)
for (NS_TYPE k = 0; k < nradbase; k++)
for (NS_TYPE n = 0; n < nradmax; n++)
for (LS_TYPE l = 0; l <= lmax; l++) {
res = fscanf(fptr, "%s", buffer);
if (res != 1)
throw_error(filename, "crad", "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times");
radial_functions->crad(mu_i, mu_j, n, l, k) = stod_err(buffer, filename, "crad",
"crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times");
}
}
void ACECTildeBasisSet::_load_radial_SHIPsBasic(FILE *fptr,
const string filename,
const string radbasename) {
// create a radial basis object, and read it from the file pointer
SHIPsRadialFunctions *ships_radial_functions = new SHIPsRadialFunctions();
ships_radial_functions->fread(fptr);
//mimic ships_radial_functions to ACERadialFunctions
ships_radial_functions->nradial = ships_radial_functions->get_maxn();
ships_radial_functions->nradbase = ships_radial_functions->get_maxn();
nradbase = ships_radial_functions->get_maxn();
nradmax = ships_radial_functions->get_maxn();
cutoffmax = ships_radial_functions->get_rcut();
deltaSplineBins = 0.001;
ships_radial_functions->init(nradbase, lmax, nradmax,
deltaSplineBins,
nelements,
cutoffmax, radbasename);
if (radial_functions) delete radial_functions;
radial_functions = ships_radial_functions;
radial_functions->prehc.fill(0);
radial_functions->lambdahc.fill(1);
radial_functions->lambda.fill(0);
radial_functions->cut.fill(ships_radial_functions->get_rcut());
radial_functions->dcut.fill(0);
radial_functions->crad.fill(0);
}

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 1.04.20.
#ifndef ACE_C_BASIS_H
#define ACE_C_BASIS_H
#include "ace_flatten_basis.h"
typedef vector<vector<ACECTildeBasisFunction>> C_tilde_full_basis_vector2d;
/**
* ACE basis set of C-tilde basis functions
*/
class ACECTildeBasisSet : public ACEFlattenBasisSet {
public:
ACECTildeBasisFunction **basis_rank1 = nullptr; ///< two-dimensional array of first-rank basis function with indices: [species index][func index]
ACECTildeBasisFunction **basis = nullptr; ///< two-dimensional array of higher rank basis function with indices: [species index][func index]
DOUBLE_TYPE *full_c_tildes_rank1 = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size_rank1
DOUBLE_TYPE *full_c_tildes = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size
//TODO: remove?
SHORT_INT_TYPE num_ctilde_max = 0;
/**
* Default constructor
*/
ACECTildeBasisSet() = default;
/**
* Constructor from .ace file
*/
ACECTildeBasisSet(const string filename);
/**
* Copy constructor (see. Rule of Three)
* @param other
*/
ACECTildeBasisSet(const ACECTildeBasisSet &other);
/**
* operator= (see. Rule of Three)
* @param other
* @return
*/
ACECTildeBasisSet &operator=(const ACECTildeBasisSet &other);
/**
* Destructor (see. Rule of Three)
*/
~ACECTildeBasisSet() override;
/**
* Cleaning dynamic memory of the class (see. Rule of Three)
*/
void _clean() override;
/**
* Copying and cleaning dynamic memory of the class (see. Rule of Three)
* @param src
*/
void _copy_dynamic_memory(const ACECTildeBasisSet &src);
/**
* Copying scalar variables
* @param src
*/
void _copy_scalar_memory(const ACECTildeBasisSet &src);
/**
* Clean contiguous arrays (full_c_tildes_rank1, full_c_tildes) and those of base class
*/
void _clean_contiguous_arrays() override ;
/**
* Save potential to .ace file
* @param filename .ace file name
*/
void save(const string &filename) override;
/**
* Load potential from .ace
* @param filename .ace file name
*/
void load(const string filename) override;
/**
* Load the ACE type radial basis
*/
void _load_radial_ACERadial(FILE *fptr,
const string filename,
const string radbasename);
void _load_radial_SHIPsBasic(FILE * fptr,
const string filename,
const string radbasename );
/**
* Re-pack the constituent dynamic arrays of all basis functions in contiguous arrays
*/
void pack_flatten_basis() override;
/**
* Computes flatten array sizes
* @param basis_rank1 two-dimensional array of first-rank ACECTildeBasisFunctions
* @param basis two-dimensional array of higher-rank ACECTildeBasisFunctions
*/
void compute_array_sizes(ACECTildeBasisFunction** basis_rank1, ACECTildeBasisFunction** basis);
/**
* Clean basis arrays 'basis_rank1' and 'basis'
*/
void _clean_basis_arrays();
/**
* Pack two-dimensional vector of ACECTildeBasisFunction into 1D dynami array with all basis functions
* @param mu0_ctilde_basis_vector vector<vector<ACECTildeBasisFunction>>
*/
void flatten_basis(C_tilde_full_basis_vector2d& mu0_ctilde_basis_vector);
/**
* Empty stub implementation
*/
void flatten_basis() override{};
};
#endif //ACE_C_BASIS_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 26.02.20.
#ifndef ACE_C_BASISFUNCTION_H
#define ACE_C_BASISFUNCTION_H
#include <cstring>
#include <iomanip>
#include <iostream>
#include <sstream>
#include "ace_types.h"
//macros for copying the member-array from "other" object for C-tilde and B-basis
#define basis_mem_copy(other, array, size, type) if(other.array) { \
if(!is_proxy) delete[] array;\
array = new type[(size)];\
is_proxy = false;\
memcpy(array, other.array, (size) * sizeof(type));\
}
/**
* Abstract basis function, that stores general quantities
*/
struct ACEAbstractBasisFunction {
/**
* flattened array of computed combinations of (m1, m2, ..., m_rank)
* which have non-zero general Clebsch-Gordan coefficient:
* \f$ \mathbf{m}_1, \dots, \mathbf{m}_\mathrm{num ms combs}\f$ =
* \f$ (m_1, m_2, \dots, m_{rank})_1, \dots, (m_1, m_2, \dots, m_{rank})_{\mathrm{num ms combs}} \f$,
* size = num_ms_combs * rank,
* effective shape: [num_ms_combs][rank]
*/
MS_TYPE *ms_combs = nullptr;
/**
* species types of neighbours atoms \f$ \mathbf{\mu} = (\mu_1, \mu_2, \dots, \mu_{rank}) \f$,
* should be lexicographically sorted,
* size = rank,
* effective shape: [rank]
*/
SPECIES_TYPE *mus = nullptr;
/**
* indices for radial part \f$ \mathbf{n} = (n_1, n_2, \dots, n_{rank}) \f$,
* should be lexicographically sorted,
* size = rank,
* effective shape: [rank]
*/
NS_TYPE *ns = nullptr;
/**
* indices for radial part \f$ \mathbf{l} = (l_1, l_2, \dots, l_{rank}) \f$,
* should be lexicographically sorted,
* size = rank,
* effective shape: [rank]
*/
LS_TYPE *ls = nullptr;
SHORT_INT_TYPE num_ms_combs = 0; ///< number of different ms-combinations
RANK_TYPE rank = 0; ///< number of atomic base functions "A"s in basis function product B
DENSITY_TYPE ndensity = 0; ///< number of densities
SPECIES_TYPE mu0 = 0; ///< species type of central atom
/**
* whether ms array contains only "non-negative" ms-combinations.
* positive ms-combination is when the first non-zero m is positive (0 1 -1)
* negative ms-combination is when the first non-zero m is negative (0 -1 1)
*/
bool is_half_ms_basis = false;
/*
* flag, whether object is "owner" (i.e. responsible for memory cleaning) of
* the ms, ns, ls, mus and other dynamically allocated arrases or just a proxy for them
*/
bool is_proxy = false;
/**
* Copying static and dynamic memory variables from another ACEAbstractBasisFunction.
* Always copy the dynamic memory, even if the source is a proxy object
* @param other
*/
virtual void _copy_from(const ACEAbstractBasisFunction &other) {
rank = other.rank;
ndensity = other.ndensity;
mu0 = other.mu0;
num_ms_combs = other.num_ms_combs;
is_half_ms_basis = other.is_half_ms_basis;
is_proxy = false;
basis_mem_copy(other, mus, rank, SPECIES_TYPE)
basis_mem_copy(other, ns, rank, NS_TYPE)
basis_mem_copy(other, ls, rank, LS_TYPE)
basis_mem_copy(other, ms_combs, num_ms_combs * rank, MS_TYPE)
}
/**
* Clean the dynamically allocated memory if object is responsible for it
*/
virtual void _clean() {
//release memory if the structure is not proxy
if (!is_proxy) {
delete[] mus;
delete[] ns;
delete[] ls;
delete[] ms_combs;
}
mus = nullptr;
ns = nullptr;
ls = nullptr;
ms_combs = nullptr;
}
};
/**
* Representation of C-tilde basis function, i.e. the function that is summed up over a group of B-functions
* that differs only by intermediate coupling orbital moment \f$ L \f$ and coefficients.
*/
struct ACECTildeBasisFunction : public ACEAbstractBasisFunction {
/**
* c_tilde coefficients for all densities,
* size = num_ms_combs*ndensity,
* effective shape [num_ms_combs][ndensity]
*/
DOUBLE_TYPE *ctildes = nullptr;
/*
* Default constructor
*/
ACECTildeBasisFunction() = default;
// Because the ACECTildeBasisFunction contains dynamically allocated arrays, the Rule of Three should be
// fulfilled, i.e. copy constructor (copy the dynamic arrays), operator= (release previous arrays and
// copy the new dynamic arrays) and destructor (release all dynamically allocated memory)
/**
* Copy constructor, to fulfill the Rule of Three.
* Always copy the dynamic memory, even if the source is a proxy object.
*/
ACECTildeBasisFunction(const ACECTildeBasisFunction &other) {
_copy_from(other);
}
/*
* operator=, to fulfill the Rule of Three.
* Always copy the dynamic memory, even if the source is a proxy object
*/
ACECTildeBasisFunction &operator=(const ACECTildeBasisFunction &other) {
_clean();
_copy_from(other);
return *this;
}
/*
* Destructor
*/
~ACECTildeBasisFunction() {
_clean();
}
/**
* Copy from another object, always copy the memory, even if the source is a proxy object
* @param other
*/
void _copy_from(const ACECTildeBasisFunction &other) {
ACEAbstractBasisFunction::_copy_from(other);
is_proxy = false;
basis_mem_copy(other, ctildes, num_ms_combs * ndensity, DOUBLE_TYPE)
}
/**
* Clean the dynamically allocated memory if object is responsible for it
*/
void _clean() override {
ACEAbstractBasisFunction::_clean();
//release memory if the structure is not proxy
if (!is_proxy) {
delete[] ctildes;
}
ctildes = nullptr;
}
/**
* Print the information about basis function to cout, in order to ease the output redirection.
*/
void print() const {
using namespace std;
cout << "ACECTildeBasisFunction: ndensity= " << (int) this->ndensity << ", mu0 = " << (int) this->mu0 << " ";
cout << " mus=(";
for (RANK_TYPE r = 0; r < this->rank; r++)
cout << (int) this->mus[r] << " ";
cout << "), ns=(";
for (RANK_TYPE r = 0; r < this->rank; r++)
cout << this->ns[r] << " ";
cout << "), ls=(";
for (RANK_TYPE r = 0; r < this->rank; r++)
cout << this->ls[r] << " ";
cout << "), " << this->num_ms_combs << " m_s combinations: {" << endl;
for (int i = 0; i < this->num_ms_combs; i++) {
cout << "\t< ";
for (RANK_TYPE r = 0; r < this->rank; r++)
cout << this->ms_combs[i * this->rank + r] << " ";
cout << " >: c_tilde=";
for (DENSITY_TYPE p = 0; p < this->ndensity; ++p)
cout << " " << this->ctildes[i * this->ndensity + p] << " ";
cout << endl;
}
if (this->is_proxy)
cout << "proxy ";
if (this->is_half_ms_basis)
cout << "half_ms_basis";
cout << "}" << endl;
}
};
#endif //ACE_C_BASISFUNCTION_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 26.02.20.
#ifndef ACE_COMPLEX_H
#define ACE_COMPLEX_H
/**
A custom data structure for complex numbers and overloaded operations with them.
*/
struct ACEComplex {
public:
/**
Double, real part of the complex number
*/
DOUBLE_TYPE real;
/**
Double, imaginary part of the complex number
*/
DOUBLE_TYPE img;
ACEComplex &operator=(const ACEComplex &rhs) = default;
ACEComplex &operator=(const DOUBLE_TYPE &rhs) {
this->real = rhs;
this->img = 0.;
return *this;
}
/**
Overloading of arithmetical operator += ACEComplex
*/
ACEComplex &operator+=(const ACEComplex &rhs) {
this->real += rhs.real;
this->img += rhs.img;
return *this; // return the result by reference
}
/**
Overloading of arithmetical operator += DOUBLE_TYPE
*/
ACEComplex &operator+=(const DOUBLE_TYPE &rhs) {
this->real += rhs;
return *this; // return the result by reference
}
/**
Overloading of arithmetical operator *= DOUBLE_TYPE
*/
ACEComplex &operator*=(const DOUBLE_TYPE &rhs) {
this->real *= rhs;
this->img *= rhs;
return *this; // return the result by reference
}
/**
Overloading of arithmetical operator *= ACEComplex
*/
ACEComplex &operator*=(const ACEComplex &rhs) {
DOUBLE_TYPE old_real = this->real;
this->real = old_real * rhs.real - this->img * rhs.img;
this->img = old_real * rhs.img + this->img * rhs.real;
return *this; // return the result by reference
}
/**
Overloading of arithmetical operator * ACEComplex
*/
ACEComplex operator*(const ACEComplex &cm2) const {
ACEComplex res{real * cm2.real - img * cm2.img,
real * cm2.img + img * cm2.real};
return res;
}
/*
* Return complex conjugated copy of itself
*/
ACEComplex conjugated() const {
ACEComplex res{real, -img};
return res;
}
/*
* Complex conjugate itself inplace
*/
void conjugate() {
img = -img;
}
/*
* Multiplication by ACEComplex and return real-part only
*/
DOUBLE_TYPE real_part_product(const ACEComplex &cm2) const {
return real * cm2.real - img * cm2.img;
}
/*
* Multiplication by DOUBLE_TYPE and return real-part only
*/
DOUBLE_TYPE real_part_product(const DOUBLE_TYPE &cm2) const {
return real * cm2;
}
/*
* Overloading of arithmetical operator * by DOUBLE_TYPE
*/
ACEComplex operator*(const DOUBLE_TYPE &cm2) const {
ACEComplex res{real * cm2,
img * cm2};
return res;
}
/*
* Overloading of arithmetical operator + ACEComplex
*/
ACEComplex operator+(const ACEComplex &cm2) const {
ACEComplex res{real + cm2.real,
img + cm2.img};
return res;
}
/*
* Overloading of arithmetical operator + with DOUBLE_TYPE
*/
ACEComplex operator+(const DOUBLE_TYPE &cm2) const {
ACEComplex res{real + cm2, img};
return res;
}
/*
* Overloading of arithmetical operator == ACEComplex
*/
bool operator==(const ACEComplex &c2) const {
return (real == c2.real) && (img == c2.img);
}
/*
* Overloading of arithmetical operator == DOUBLE_TYPE
*/
bool operator==(const DOUBLE_TYPE &d2) const {
return (real == d2) && (img == 0.);
}
/*
* Overloading of arithmetical operator != ACEComplex
*/
bool operator!=(const ACEComplex &c2) const {
return (real != c2.real) || (img != c2.img);
}
/*
* Overloading of arithmetical operator != DOUBLE_TYPE
*/
bool operator!=(const DOUBLE_TYPE &d2) const {
return (real != d2) || (img != 0.);
}
};
/*
* double * complex for commutativity with complex * double
*/
inline ACEComplex operator*(const DOUBLE_TYPE &real, const ACEComplex &cm) {
return cm * real;
}
/*
* double + complex for commutativity with complex + double
*/
inline ACEComplex operator+(const DOUBLE_TYPE &real, const ACEComplex &cm) {
return cm + real;
}
/**
A structure to store the derivative of \f$ Y_{lm} \f$
*/
struct ACEDYcomponent {
public:
/**
complex, contains the three components of derivative of Ylm,
\f$ \frac{dY_{lm}}{dx}, \frac{dY_{lm}}{dy} and \frac{dY_{lm}}{dz}\f$
*/
ACEComplex a[3];
/*
* Overloading of arithmetical operator*= DOUBLE_TYPE
*/
ACEDYcomponent &operator*=(const DOUBLE_TYPE &rhs) {
this->a[0] *= rhs;
this->a[1] *= rhs;
this->a[2] *= rhs;
return *this;
}
/*
* Overloading of arithmetical operator * ACEComplex
*/
ACEDYcomponent operator*(const ACEComplex &rhs) const {
ACEDYcomponent res;
res.a[0] = this->a[0] * rhs;
res.a[1] = this->a[1] * rhs;
res.a[2] = this->a[2] * rhs;
return res;
}
/*
* Overloading of arithmetical operator * DOUBLE_TYPE
*/
ACEDYcomponent operator*(const DOUBLE_TYPE &rhs) const {
ACEDYcomponent res;
res.a[0] = this->a[0] * rhs;
res.a[1] = this->a[1] * rhs;
res.a[2] = this->a[2] * rhs;
return res;
}
/*
* Return conjugated copy of itself
*/
ACEDYcomponent conjugated() const {
ACEDYcomponent res;
res.a[0] = this->a[0].conjugated();
res.a[1] = this->a[1].conjugated();
res.a[2] = this->a[2].conjugated();
return res;
}
/*
* Conjugated itself in-place
*/
void conjugate() {
this->a[0].conjugate();
this->a[1].conjugate();
this->a[2].conjugate();
}
};
#endif //ACE_COMPLEX_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 11.01.20.
#ifndef ACE_CONTIGUOUSARRAYND_H
#define ACE_CONTIGUOUSARRAYND_H
#include <string>
#include "ace_types.h"
using namespace std;
/**
* Common predecessor class to represent multidimensional array of type T
* and store it in memory contiguous form
*
* @tparam T data type
*/
template<typename T>
class ContiguousArrayND {
protected:
T *data = nullptr; ///< pointer to contiguous data
size_t size = 0; ///< total array size
string array_name = "Array"; ///<array name
bool is_proxy_ = false; ///< array is proxy (wrapper) and not owner of the memory
public:
/**
* Default empty constructor
*/
ContiguousArrayND() = default;
/**
* Constructor with array name
* @param array_name name of array (for error logging)
*/
ContiguousArrayND(string array_name) : array_name(array_name) {};
/**
* Copy constructor
* @param other other ContiguousArrayND
*/
ContiguousArrayND(const ContiguousArrayND &other) : array_name(other.array_name), size(other.size), is_proxy_(other.is_proxy_) {
#ifdef MULTIARRAY_LIFE_CYCLE
cout<<array_name<<"::copy constructor"<<endl;
#endif
if(!is_proxy_) { //if not the proxy, then copy the values
if (size > 0) {
data = new T[size];
for (size_t ind = 0; ind < size; ind++)
data[ind] = other.data[ind];
}
} else { //is proxy, then copy the pointer
data = other.data;
}
}
/**
* Overload operator=
* @param other another ContiguousArrayND
* @return itself
*/
ContiguousArrayND &operator=(const ContiguousArrayND &other) {
#ifdef MULTIARRAY_LIFE_CYCLE
cout<<array_name<<"::operator="<<endl;
#endif
if (this != &other) {
array_name = other.array_name;
size = other.size;
is_proxy_ = other.is_proxy_;
if(!is_proxy_) { //if not the proxy, then copy the values
if (size > 0) {
if(data!=nullptr) delete[] data;
data = new T[size];
for (size_t ind = 0; ind < size; ind++)
data[ind] = other.data[ind];
}
} else { //is proxy, then copy the pointer
data = other.data;
}
}
return *this;
}
//TODO: make destructor virtual, check the destructors in inherited classes
/**
* Destructor
*/
~ContiguousArrayND() {
#ifdef MULTIARRAY_LIFE_CYCLE
cout<<array_name<<"::~destructor"<<endl;
#endif
if(! is_proxy_) {
delete[] data;
}
data = nullptr;
}
/**
* Set array name
* @param name array name
*/
void set_array_name(const string &name) {
this->array_name = name;
}
/**
* Get total number of elements in array (its size)
* @return array size
*/
size_t get_size() const {
return size;
}
/**
* Fill array with value
* @param value value to fill
*/
void fill(T value) {
for (size_t ind = 0; ind < size; ind++)
data[ind] = value;
}
/**
* Get array data at absolute index ind for reading
* @param ind absolute index
* @return array value
*/
inline const T &get_data(size_t ind) const {
#ifdef MULTIARRAY_INDICES_CHECK
if ((ind < 0) | (ind >= size)) {
printf("%s: get_data ind=%d out of range (0, %d)\n", array_name, ind, size);
exit(EXIT_FAILURE);
}
#endif
return data[ind];
}
/**
* Get array data at absolute index ind for writing
* @param ind absolute index
* @return array value
*/
inline T &get_data(size_t ind) {
#ifdef MULTIARRAY_INDICES_CHECK
if ((ind < 0) | (ind >= size)) {
printf("%s: get_data ind=%ld out of range (0, %ld)\n", array_name.c_str(), ind, size);
exit(EXIT_FAILURE);
}
#endif
return data[ind];
}
/**
* Get array data pointer
* @return data array pointer
*/
inline T* get_data() const {
return data;
}
/**
* Overload comparison operator==
* Compare the total size and array values elementwise.
*
* @param other another array
* @return
*/
bool operator==(const ContiguousArrayND &other) const {
if (this->size != other.size)
return false;
for (size_t i = 0; i < this->size; ++i)
if (this->data[i] != other.data[i])
return false;
return true;
}
/**
* Convert to flatten vector<T> container
* @return vector container
*/
vector<T> to_flatten_vector() const {
vector<T> res;
res.resize(size);
size_t vec_ind = 0;
for (int vec_ind = 0; vec_ind < size; vec_ind++)
res.at(vec_ind) = data[vec_ind];
return res;
} // end to_flatten_vector()
/**
* Set values from flatten vector<T> container
* @param vec container
*/
void set_flatten_vector(const vector<T> &vec) {
if (vec.size() != size)
throw std::invalid_argument("Flatten vector size is not consistent with expected size");
for (size_t i = 0; i < size; i++) {
data[i] = vec[i];
}
}
bool is_proxy(){
return is_proxy_;
}
};
#endif //ACE_CONTIGUOUSARRAYND_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 31.01.20.
#include "ace_evaluator.h"
#include "ace_abstract_basis.h"
#include "ace_types.h"
void ACEEvaluator::init(ACEAbstractBasisSet *basis_set) {
A.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, "A");
A_rank1.init(basis_set->nelements, basis_set->nradbase, "A_rank1");
rhos.init(basis_set->ndensitymax + 1, "rhos"); // +1 density for core repulsion
dF_drho.init(basis_set->ndensitymax + 1, "dF_drho"); // +1 density for core repulsion
}
void ACEEvaluator::init_timers() {
loop_over_neighbour_timer.init();
forces_calc_loop_timer.init();
forces_calc_neighbour_timer.init();
energy_calc_timer.init();
per_atom_calc_timer.init();
total_time_calc_timer.init();
}
//================================================================================================================
void ACECTildeEvaluator::set_basis(ACECTildeBasisSet &bas) {
basis_set = &bas;
init(basis_set);
}
void ACECTildeEvaluator::init(ACECTildeBasisSet *basis_set) {
ACEEvaluator::init(basis_set);
weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1,
"weights");
weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1");
DG_cache.init(1, basis_set->nradbase, "DG_cache");
DG_cache.fill(0);
R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache");
R_cache.fill(0);
DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache");
DR_cache.fill(0);
Y_cache.init(1, basis_set->lmax + 1, "Y_cache");
Y_cache.fill({0, 0});
DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache");
DY_cache.fill({0.});
//hard-core repulsion
DCR_cache.init(1, "DCR_cache");
DCR_cache.fill(0);
dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten");
}
void ACECTildeEvaluator::resize_neighbours_cache(int max_jnum) {
if(basis_set== nullptr) {
throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned");
}
if (R_cache.get_dim(0) < max_jnum) {
//TODO: implement grow
R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1);
R_cache.fill(0);
DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1);
DR_cache.fill(0);
DG_cache.resize(max_jnum, basis_set->nradbase);
DG_cache.fill(0);
Y_cache.resize(max_jnum, basis_set->lmax + 1);
Y_cache.fill({0, 0});
DY_cache.resize(max_jnum, basis_set->lmax + 1);
DY_cache.fill({0});
//hard-core repulsion
DCR_cache.init(max_jnum, "DCR_cache");
DCR_cache.fill(0);
}
}
// double** r - atomic coordinates of atom I
// int* types - atomic types if atom I
// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i];
// Usage: j = jlist_of_i[jj];
// jnum - number of J neighbors for each I atom. jnum = numneigh[i];
void
ACECTildeEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) {
if(basis_set== nullptr) {
throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned");
}
per_atom_calc_timer.start();
#ifdef PRINT_MAIN_STEPS
printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]);
#endif
DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0;
DOUBLE_TYPE r_norm;
DOUBLE_TYPE xn, yn, zn, r_xyz;
DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR;
DOUBLE_TYPE *r_hat;
SPECIES_TYPE mu_j;
RANK_TYPE r, rank, t;
NS_TYPE n;
LS_TYPE l;
MS_TYPE m, m_t;
SPECIES_TYPE *mus;
NS_TYPE *ns;
LS_TYPE *ls;
MS_TYPE *ms;
int j, jj, func_ind, ms_ind;
SHORT_INT_TYPE factor;
ACEComplex Y{0}, Y_DR{0.};
ACEComplex B{0.};
ACEComplex dB{0};
ACEComplex A_cache[basis_set->rankmax];
dB_flatten.fill({0.});
ACEDYcomponent grad_phi_nlm{0}, DY{0.};
//size is +1 of max to avoid out-of-boundary array access in double-triangular scheme
ACEComplex A_forward_prod[basis_set->rankmax + 1];
ACEComplex A_backward_prod[basis_set->rankmax + 1];
DOUBLE_TYPE inv_r_norm;
DOUBLE_TYPE r_norms[jnum];
DOUBLE_TYPE inv_r_norms[jnum];
DOUBLE_TYPE rhats[jnum][3];//normalized vector
SPECIES_TYPE elements[jnum];
const DOUBLE_TYPE xtmp = x[i][0];
const DOUBLE_TYPE ytmp = x[i][1];
const DOUBLE_TYPE ztmp = x[i][2];
DOUBLE_TYPE f_ji[3];
bool is_element_mapping = element_type_mapping.get_size() > 0;
SPECIES_TYPE mu_i;
if (is_element_mapping)
mu_i = element_type_mapping(type[i]);
else
mu_i = type[i];
const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i];
const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i];
ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i];
ACECTildeBasisFunction *basis = basis_set->basis[mu_i];
DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut;
DOUBLE_TYPE dF_drho_core;
//TODO: lmax -> lmaxi (get per-species type)
const LS_TYPE lmaxi = basis_set->lmax;
//TODO: nradmax -> nradiali (get per-species type)
const NS_TYPE nradiali = basis_set->nradmax;
//TODO: nradbase -> nradbasei (get per-species type)
const NS_TYPE nradbasei = basis_set->nradbase;
//TODO: get per-species type number of densities
const DENSITY_TYPE ndensity= basis_set->ndensitymax;
neighbours_forces.resize(jnum, 3);
neighbours_forces.fill(0);
//TODO: shift nullifications to place where arrays are used
weights.fill({0});
weights_rank1.fill(0);
A.fill({0});
A_rank1.fill(0);
rhos.fill(0);
dF_drho.fill(0);
#ifdef EXTRA_C_PROJECTIONS
basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1");
basis_projections.init(total_basis_size, ndensity, "c_projections");
#endif
//proxy references to spherical harmonics and radial functions arrays
const Array2DLM<ACEComplex> &ylm = basis_set->spherical_harmonics.ylm;
const Array2DLM<ACEDYcomponent> &dylm = basis_set->spherical_harmonics.dylm;
const Array2D<DOUBLE_TYPE> &fr = basis_set->radial_functions->fr;
const Array2D<DOUBLE_TYPE> &dfr = basis_set->radial_functions->dfr;
const Array1D<DOUBLE_TYPE> &gr = basis_set->radial_functions->gr;
const Array1D<DOUBLE_TYPE> &dgr = basis_set->radial_functions->dgr;
loop_over_neighbour_timer.start();
int jj_actual = 0;
SPECIES_TYPE type_j = 0;
int neighbour_index_mapping[jnum]; // jj_actual -> jj
//loop over neighbours, compute distance, consider only atoms within with r<cutoff(mu_i, mu_j)
for (jj = 0; jj < jnum; ++jj) {
j = jlist[jj];
xn = x[j][0] - xtmp;
yn = x[j][1] - ytmp;
zn = x[j][2] - ztmp;
type_j = type[j];
if (is_element_mapping)
mu_j = element_type_mapping(type_j);
else
mu_j = type_j;
DOUBLE_TYPE current_cutoff = basis_set->radial_functions->cut(mu_i, mu_j);
r_xyz = sqrt(xn * xn + yn * yn + zn * zn);
if (r_xyz >= current_cutoff)
continue;
inv_r_norm = 1 / r_xyz;
r_norms[jj_actual] = r_xyz;
inv_r_norms[jj_actual] = inv_r_norm;
rhats[jj_actual][0] = xn * inv_r_norm;
rhats[jj_actual][1] = yn * inv_r_norm;
rhats[jj_actual][2] = zn * inv_r_norm;
elements[jj_actual] = mu_j;
neighbour_index_mapping[jj_actual] = jj;
jj_actual++;
}
int jnum_actual = jj_actual;
//ALGORITHM 1: Atomic base A
for (jj = 0; jj < jnum_actual; ++jj) {
r_norm = r_norms[jj];
mu_j = elements[jj];
r_hat = rhats[jj];
//proxies
Array2DLM<ACEComplex> &Y_jj = Y_cache(jj);
Array2DLM<ACEDYcomponent> &DY_jj = DY_cache(jj);
basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j);
basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi);
//loop for computing A's
//rank = 1
for (n = 0; n < basis_set->nradbase; n++) {
GR = gr(n);
#ifdef DEBUG_ENERGY_CALCULATIONS
printf("-neigh atom %d\n", jj);
printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n));
printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n));
#endif
DG_cache(jj, n) = dgr(n);
A_rank1(mu_j, n) += GR * Y00;
}
//loop for computing A's
// for rank > 1
for (n = 0; n < nradiali; n++) {
auto &A_lm = A(mu_j, n);
for (l = 0; l <= lmaxi; l++) {
R = fr(n, l);
#ifdef DEBUG_ENERGY_CALCULATIONS
printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R);
#endif
DR_cache(jj, n, l) = dfr(n, l);
R_cache(jj, n, l) = R;
for (m = 0; m <= l; m++) {
Y = ylm(l, m);
#ifdef DEBUG_ENERGY_CALCULATIONS
printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img);
#endif
A_lm(l, m) += R * Y; //accumulation sum over neighbours
Y_jj(l, m) = Y;
DY_jj(l, m) = dylm(l, m);
}
}
}
//hard-core repulsion
rho_core += basis_set->radial_functions->cr;
DCR_cache(jj) = basis_set->radial_functions->dcr;
} //end loop over neighbours
//complex conjugate A's (for NEGATIVE (-m) terms)
// for rank > 1
for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) {
for (n = 0; n < nradiali; n++) {
auto &A_lm = A(mu_j, n);
for (l = 0; l <= lmaxi; l++) {
//fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm
for (m = 1; m <= l; m++) {
factor = m % 2 == 0 ? 1 : -1;
A_lm(l, -m) = A_lm(l, m).conjugated() * factor;
}
}
}
} //now A's are constructed
loop_over_neighbour_timer.stop();
// ==================== ENERGY ====================
energy_calc_timer.start();
#ifdef EXTRA_C_PROJECTIONS
basis_projections_rank1.fill(0);
basis_projections.fill(0);
#endif
//ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation
//rank=1
for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) {
ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind];
// ndensity = func->ndensity;
#ifdef PRINT_LOOPS_INDICES
printf("Num density = %d r = 0\n",(int) ndensity );
print_C_tilde_B_basis_function(*func);
#endif
double A_cur = A_rank1(func->mus[0], func->ns[0] - 1);
#ifdef DEBUG_ENERGY_CALCULATIONS
printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur);
printf(" coeff[0] = %f\n", func->ctildes[0]);
#endif
for (DENSITY_TYPE p = 0; p < ndensity; ++p) {
//for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1
rhos(p) += func->ctildes[p] * A_cur;
#ifdef EXTRA_C_PROJECTIONS
//aggregate C-projections separately
basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur;
#endif
}
} // end loop for rank=1
//rank>1
int func_ms_ind = 0;
int func_ms_t_ind = 0;// index for dB
for (func_ind = 0; func_ind < total_basis_size; ++func_ind) {
ACECTildeBasisFunction *func = &basis[func_ind];
//TODO: check if func->ctildes are zero, then skip
// ndensity = func->ndensity;
rank = func->rank;
r = rank - 1;
#ifdef PRINT_LOOPS_INDICES
printf("Num density = %d r = %d\n",(int) ndensity, (int)r );
print_C_tilde_B_basis_function(*func);
#endif
mus = func->mus;
ns = func->ns;
ls = func->ls;
//loop over {ms} combinations in sum
for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) {
ms = &func->ms_combs[ms_ind * rank]; // current ms-combination (of length = rank)
//loop over m, collect B = product of A with given ms
A_forward_prod[0] = 1;
A_backward_prod[r] = 1;
//fill forward A-product triangle
for (t = 0; t < rank; t++) {
//TODO: optimize ns[t]-1 -> ns[t] during functions construction
A_cache[t] = A(mus[t], ns[t] - 1, ls[t], ms[t]);
#ifdef DEBUG_ENERGY_CALCULATIONS
printf("A(x=%d, n=%d, l=%d, m=%d)=(%f,%f)\n", mus[t], ns[t], ls[t], ms[t], A_cache[t].real,
A_cache[t].img);
#endif
A_forward_prod[t + 1] = A_forward_prod[t] * A_cache[t];
}
B = A_forward_prod[t];
#ifdef DEBUG_FORCES_CALCULATIONS
printf("B = (%f, %f)\n", (B).real, (B).img);
#endif
//fill backward A-product triangle
for (t = r; t >= 1; t--) {
A_backward_prod[t - 1] =
A_backward_prod[t] * A_cache[t];
}
for (t = 0; t < rank; ++t, ++func_ms_t_ind) {
dB = A_forward_prod[t] * A_backward_prod[t]; //dB - product of all A's except t-th
dB_flatten(func_ms_t_ind) = dB;
#ifdef DEBUG_FORCES_CALCULATIONS
m_t = ms[t];
printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img);
#endif
}
for (DENSITY_TYPE p = 0; p < ndensity; ++p) {
//real-part only multiplication
rhos(p) += B.real_part_product(func->ctildes[ms_ind * ndensity + p]);
#ifdef EXTRA_C_PROJECTIONS
//aggregate C-projections separately
basis_projections(func_ind, p)+=B.real_part_product(func->ctildes[ms_ind * ndensity + p]);
#endif
#ifdef PRINT_INTERMEDIATE_VALUES
printf("rhos(%d) += %f\n", p, B.real_part_product(func->ctildes[ms_ind * ndensity + p]));
printf("Rho[i = %d][p = %d] = %f\n", i , p , rhos(p));
#endif
}
}//end of loop over {ms} combinations in sum
}// end loop for rank>1
#ifdef DEBUG_FORCES_CALCULATIONS
printf("rhos = ");
for(DENSITY_TYPE p =0; p<ndensity; ++p) printf(" %.20f ",rhos(p));
printf("\n");
#endif
// energy cutoff
rho_cut = basis_set->rho_core_cutoffs(mu_i);
drho_cut = basis_set->drho_core_cutoffs(mu_i);
basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut);
basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity);
dF_drho_core = evdwl * dfcut + 1;
for (DENSITY_TYPE p = 0; p < ndensity; ++p)
dF_drho(p) *= fcut;
evdwl_cut = evdwl * fcut + rho_core;
// E0 shift
evdwl_cut += basis_set->E0vals(mu_i);
#ifdef DEBUG_FORCES_CALCULATIONS
printf("dFrhos = ");
for(DENSITY_TYPE p =0; p<ndensity; ++p) printf(" %f ",dF_drho(p));
printf("\n");
#endif
//ALGORITHM 3: Weights and theta calculation
// rank = 1
for (int f_ind = 0; f_ind < total_basis_size_rank1; ++f_ind) {
ACECTildeBasisFunction *func = &basis_rank1[f_ind];
// ndensity = func->ndensity;
for (DENSITY_TYPE p = 0; p < ndensity; ++p) {
//for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1
weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p];
}
}
// rank>1
func_ms_ind = 0;
func_ms_t_ind = 0;// index for dB
DOUBLE_TYPE theta = 0;
for (func_ind = 0; func_ind < total_basis_size; ++func_ind) {
ACECTildeBasisFunction *func = &basis[func_ind];
// ndensity = func->ndensity;
rank = func->rank;
mus = func->mus;
ns = func->ns;
ls = func->ls;
for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) {
ms = &func->ms_combs[ms_ind * rank];
theta = 0;
for (DENSITY_TYPE p = 0; p < ndensity; ++p) {
theta += dF_drho(p) * func->ctildes[ms_ind * ndensity + p];
#ifdef DEBUG_FORCES_CALCULATIONS
printf("(p=%d) theta += dF_drho[p] * func.ctildes[ms_ind * ndensity + p] = %f * %f = %f\n",p, dF_drho(p), func->ctildes[ms_ind * ndensity + p],dF_drho(p)*func->ctildes[ms_ind * ndensity + p]);
printf("theta=%f\n",theta);
#endif
}
theta *= 0.5; // 0.5 factor due to possible double counting ???
for (t = 0; t < rank; ++t, ++func_ms_t_ind) {
m_t = ms[t];
factor = (m_t % 2 == 0 ? 1 : -1);
dB = dB_flatten(func_ms_t_ind);
weights(mus[t], ns[t] - 1, ls[t], m_t) += theta * dB; //Theta_array(func_ms_ind);
// update -m_t (that could also be positive), because the basis is half_basis
weights(mus[t], ns[t] - 1, ls[t], -m_t) +=
theta * (dB).conjugated() * factor;// Theta_array(func_ms_ind);
#ifdef DEBUG_FORCES_CALCULATIONS
printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img);
printf("theta = %f\n",theta);
printf("weights(n,l,m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], m_t, (theta * dB * 0.5).real,
(theta * dB * 0.5).img);
printf("weights(n,l,-m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], -m_t,
( theta * (dB).conjugated() * factor * 0.5).real,
( theta * (dB).conjugated() * factor * 0.5).img);
#endif
}
}
}
energy_calc_timer.stop();
// ==================== FORCES ====================
#ifdef PRINT_MAIN_STEPS
printf("\nFORCE CALCULATION\n");
printf("loop over neighbours\n");
#endif
forces_calc_loop_timer.start();
// loop over neighbour atoms for force calculations
for (jj = 0; jj < jnum_actual; ++jj) {
mu_j = elements[jj];
r_hat = rhats[jj];
inv_r_norm = inv_r_norms[jj];
Array2DLM<ACEComplex> &Y_cache_jj = Y_cache(jj);
Array2DLM<ACEDYcomponent> &DY_cache_jj = DY_cache(jj);
#ifdef PRINT_LOOPS_INDICES
printf("\nneighbour atom #%d\n", jj);
printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]);
#endif
forces_calc_neighbour_timer.start();
f_ji[0] = f_ji[1] = f_ji[2] = 0;
//for rank = 1
for (n = 0; n < nradbasei; ++n) {
if (weights_rank1(mu_j, n) == 0)
continue;
auto &DG = DG_cache(jj, n);
DGR = DG * Y00;
DGR *= weights_rank1(mu_j, n);
#ifdef DEBUG_FORCES_CALCULATIONS
printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1);
printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n));
printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n));
printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]);
#endif
f_ji[0] += DGR * r_hat[0];
f_ji[1] += DGR * r_hat[1];
f_ji[2] += DGR * r_hat[2];
}
//for rank > 1
for (n = 0; n < nradiali; n++) {
for (l = 0; l <= lmaxi; l++) {
R_over_r = R_cache(jj, n, l) * inv_r_norm;
DR = DR_cache(jj, n, l);
// for m>=0
for (m = 0; m <= l; m++) {
ACEComplex w = weights(mu_j, n, l, m);
if (w == 0)
continue;
//counting for -m cases if m>0
if (m > 0) w *= 2;
DY = DY_cache_jj(l, m);
Y_DR = Y_cache_jj(l, m) * DR;
grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r;
grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r;
grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r;
#ifdef DEBUG_FORCES_CALCULATIONS
printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m,
grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img,
grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img,
grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img);
printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m,w.real, w.img);
//if (m>0) w*=2;
printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m,
w.real_part_product(grad_phi_nlm.a[0]),
w.real_part_product(grad_phi_nlm.a[1]),
w.real_part_product(grad_phi_nlm.a[2])
);
#endif
// real-part multiplication only
f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]);
f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]);
f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]);
}
}
}
#ifdef PRINT_INTERMEDIATE_VALUES
printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i,
f_ji[0], f_ji[1], f_ji[2]
);
#endif
//hard-core repulsion
DCR = DCR_cache(jj);
#ifdef DEBUG_FORCES_CALCULATIONS
printf("DCR = %f\n",DCR);
#endif
f_ji[0] += dF_drho_core * DCR * r_hat[0];
f_ji[1] += dF_drho_core * DCR * r_hat[1];
f_ji[2] += dF_drho_core * DCR * r_hat[2];
#ifdef PRINT_INTERMEDIATE_VALUES
printf("with core-repulsion\n");
printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i,
f_ji[0], f_ji[1], f_ji[2]
);
printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]);
#endif
neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0];
neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1];
neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2];
forces_calc_neighbour_timer.stop();
}// end loop over neighbour atoms for forces
forces_calc_loop_timer.stop();
//now, energies and forces are ready
//energies(i) = evdwl + rho_core;
e_atom = evdwl_cut;
#ifdef PRINT_INTERMEDIATE_VALUES
printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl);
#endif
per_atom_calc_timer.stop();
}

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 31.01.20.
#ifndef ACE_EVALUATOR_H
#define ACE_EVALUATOR_H
#include "ace_abstract_basis.h"
#include "ace_arraynd.h"
#include "ace_array2dlm.h"
#include "ace_c_basis.h"
#include "ace_complex.h"
#include "ace_timing.h"
#include "ace_types.h"
/**
* Basic evaluator class, that should accept the basis set and implement the "compute_atom" method using given basis set.
*/
class ACEEvaluator {
protected:
Array2D<DOUBLE_TYPE> A_rank1 = Array2D<DOUBLE_TYPE>("A_rank1"); ///< 2D-array for storing A's for rank=1, shape: A(mu_j,n)
Array4DLM<ACEComplex> A = Array4DLM<ACEComplex>("A"); ///< 4D array with (l,m) last indices for storing A's for rank>1: A(mu_j, n, l, m)
Array1D<DOUBLE_TYPE> rhos = Array1D<DOUBLE_TYPE>("rhos"); ///< densities \f$ \rho^{(p)} \f$(ndensity), p = 0 .. ndensity-1
Array1D<DOUBLE_TYPE> dF_drho = Array1D<DOUBLE_TYPE>("dF_drho"); ///< derivatives of cluster functional wrt. densities, index = 0 .. ndensity-1
/**
* Initialize internal arrays according to basis set sizes
* @param basis_set
*/
void init(ACEAbstractBasisSet *basis_set);
public:
// set of timers for code profiling
ACETimer loop_over_neighbour_timer; ///< timer for loop over neighbours when constructing A's for single central atom
ACETimer per_atom_calc_timer; ///< timer for single compute_atom call
ACETimer forces_calc_loop_timer; ///< timer for forces calculations for single central atom
ACETimer forces_calc_neighbour_timer; ///< timer for loop over neighbour atoms for force calculations
ACETimer energy_calc_timer; ///< timer for energy calculation
ACETimer total_time_calc_timer; ///< timer for total calculations of all atoms within given atomic environment system
/**
* Initialize all timers
*/
void init_timers();
/**
* Mapping from external atoms types, i.e. LAMMPS, to internal SPECIES_TYPE, used in basis functions
*/
Array1D<int> element_type_mapping = Array1D<int>("element_type_mapping");
DOUBLE_TYPE e_atom = 0; ///< energy of current atom, including core-repulsion
/**
* temporary array for the pair forces between current atom_i and its neighbours atom_k
* neighbours_forces(k,3), k = 0..num_of_neighbours(atom_i)-1
*/
Array2D<DOUBLE_TYPE> neighbours_forces = Array2D<DOUBLE_TYPE>("neighbours_forces");
ACEEvaluator() = default;
virtual ~ACEEvaluator() = default;
/**
* The key method to compute energy and forces for atom 'i'.
* Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array
*
* @param i atom index
* @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3]
* @param type atomic types array of the real and ghost atoms, shape: [atom_ind]
* @param jnum number of neighbours of atom_i
* @param jlist array of neighbour indices, shape: [jnum]
*/
virtual void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) = 0;
/**
* Resize all caches over neighbours atoms
* @param max_jnum maximum number of neighbours
*/
virtual void resize_neighbours_cache(int max_jnum) = 0;
#ifdef EXTRA_C_PROJECTIONS
/**
* 2D array to store projections of basis function for rank = 1, shape: [func_ind][ndensity]
*/
Array2D<DOUBLE_TYPE> basis_projections_rank1 = Array2D<DOUBLE_TYPE>("basis_projections_rank1");
/**
* 2D array to store projections of basis function for rank > 1, shape: [func_ind][ndensity]
*/
Array2D<DOUBLE_TYPE> basis_projections = Array2D<DOUBLE_TYPE>("basis_projections");
#endif
};
//TODO: split into separate file
/**
* Evaluator for C-tilde basis set, that should accept the basis set and implement the "compute_atom" method using given basis set.
*/
class ACECTildeEvaluator : public ACEEvaluator {
/**
* Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes,
* 'i' is fixed for the current atom, shape: [nelements][nradbase]
*/
Array2D<DOUBLE_TYPE> weights_rank1 = Array2D<DOUBLE_TYPE>("weights_rank1");
/**
* Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes,
* 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m]
*/
Array4DLM<ACEComplex> weights = Array4DLM<ACEComplex>("weights");
/**
* cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m)
* shape:[max_jnum][nradbase]
*/
Array2D<DOUBLE_TYPE> DG_cache = Array2D<DOUBLE_TYPE>("DG_cache");
/**
* cache for \f$ R_{nl}(r)\f$
* shape:[max_jnum][nradbase][0..lmax]
*/
Array3D<DOUBLE_TYPE> R_cache = Array3D<DOUBLE_TYPE>("R_cache");
/**
* cache for derivatives of \f$ R_{nl}(r)\f$
* shape:[max_jnum][nradbase][0..lmax]
*/
Array3D<DOUBLE_TYPE> DR_cache = Array3D<DOUBLE_TYPE>("DR_cache");
/**
* cache for \f$ Y_{lm}(\hat{r})\f$
* shape:[max_jnum][0..lmax][m]
*/
Array3DLM<ACEComplex> Y_cache = Array3DLM<ACEComplex>("Y_cache");
/**
* cache for \f$ \nabla Y_{lm}(\hat{r})\f$
* shape:[max_jnum][0..lmax][m]
*/
Array3DLM<ACEDYcomponent> DY_cache = Array3DLM<ACEDYcomponent>("dY_dense_cache");
/**
* cache for derivatives of hard-core repulsion
* shape:[max_jnum]
*/
Array1D<DOUBLE_TYPE> DCR_cache = Array1D<DOUBLE_TYPE>("DCR_cache");
/**
* Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r],
* shape:[func_ms_r_ind]
*/
Array1D<ACEComplex> dB_flatten = Array1D<ACEComplex>("dB_flatten");
/**
* pointer to the ACEBasisSet object
*/
ACECTildeBasisSet *basis_set = nullptr;
/**
* Initialize internal arrays according to basis set sizes
* @param basis_set
*/
void init(ACECTildeBasisSet *basis_set);
public:
ACECTildeEvaluator() = default;
explicit ACECTildeEvaluator(ACECTildeBasisSet &bas) {
set_basis(bas);
}
/**
* set the basis function to the ACE evaluator
* @param bas
*/
void set_basis(ACECTildeBasisSet &bas);
/**
* The key method to compute energy and forces for atom 'i'.
* Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array
*
* @param i atom index
* @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3]
* @param type atomic types array of the real and ghost atoms, shape: [atom_ind]
* @param jnum number of neighbours of atom_i
* @param jlist array of neighbour indices, shape: [jnum]
*/
void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override;
/**
* Resize all caches over neighbours atoms
* @param max_jnum maximum number of neighbours
*/
void resize_neighbours_cache(int max_jnum) override;
};
#endif //ACE_EVALUATOR_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by yury on 28.04.2020.
#include "ace_flatten_basis.h"
ACEFlattenBasisSet::ACEFlattenBasisSet(const ACEFlattenBasisSet &other) {
_copy_scalar_memory(other);
_copy_dynamic_memory(other);
}
ACEFlattenBasisSet &ACEFlattenBasisSet::operator=(const ACEFlattenBasisSet &other) {
if (this != &other) {
_clean();
_copy_scalar_memory(other);
_copy_dynamic_memory(other);
}
return *this;
}
ACEFlattenBasisSet::~ACEFlattenBasisSet() {
ACEFlattenBasisSet::_clean();
}
void ACEFlattenBasisSet::_clean() {
//chained call of base class method
ACEAbstractBasisSet::_clean();
_clean_contiguous_arrays();
_clean_basissize_arrays();
}
void ACEFlattenBasisSet::_clean_basissize_arrays() {
delete[] total_basis_size;
total_basis_size = nullptr;
delete[] total_basis_size_rank1;
total_basis_size_rank1 = nullptr;
}
void ACEFlattenBasisSet::_clean_contiguous_arrays() {
delete[] full_ns_rank1;
full_ns_rank1 = nullptr;
delete[] full_ls_rank1;
full_ls_rank1 = nullptr;
delete[] full_mus_rank1;
full_mus_rank1 = nullptr;
delete[] full_ms_rank1;
full_ms_rank1 = nullptr;
//////
delete[] full_ns;
full_ns = nullptr;
delete[] full_ls;
full_ls = nullptr;
delete[] full_mus;
full_mus = nullptr;
delete[] full_ms;
full_ms = nullptr;
}
void ACEFlattenBasisSet::_copy_scalar_memory(const ACEFlattenBasisSet &src) {
ACEAbstractBasisSet::_copy_scalar_memory(src);
rank_array_total_size_rank1 = src.rank_array_total_size_rank1;
coeff_array_total_size_rank1 = src.coeff_array_total_size_rank1;
rank_array_total_size = src.rank_array_total_size;
ms_array_total_size = src.ms_array_total_size;
coeff_array_total_size = src.coeff_array_total_size;
max_B_array_size = src.max_B_array_size;
max_dB_array_size = src.max_dB_array_size;
num_ms_combinations_max = src.num_ms_combinations_max;
}
void ACEFlattenBasisSet::_copy_dynamic_memory(const ACEFlattenBasisSet &src) { //allocate new memory
ACEAbstractBasisSet::_copy_dynamic_memory(src);
if (src.total_basis_size_rank1 == nullptr)
throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size_rank1 - array not initialized");
if (src.total_basis_size == nullptr)
throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size - array not initialized");
delete[] total_basis_size_rank1;
total_basis_size_rank1 = new SHORT_INT_TYPE[nelements];
delete[] total_basis_size;
total_basis_size = new SHORT_INT_TYPE[nelements];
//copy
for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) {
total_basis_size_rank1[mu] = src.total_basis_size_rank1[mu];
total_basis_size[mu] = src.total_basis_size[mu];
}
}

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Lysogroskiy Yury on 28.04.2020.
#ifndef ACE_EVALUATOR_ACE_FLATTEN_BASIS_H
#define ACE_EVALUATOR_ACE_FLATTEN_BASIS_H
#include "ace_abstract_basis.h"
#include "ace_c_basisfunction.h"
#include "ace_radial.h"
#include "ace_spherical_cart.h"
#include "ace_types.h"
/**
* Basis set with basis function attributes, i.e. \f$ \mathbf{n}, \mathbf{l}, \mathbf{m}\f$, etc.
* packed into contiguous arrays for the cache-friendly memory layout.
*/
class ACEFlattenBasisSet : public ACEAbstractBasisSet {
public:
//arrays and its sizes for rank = 1 basis functions for packed basis
size_t rank_array_total_size_rank1 = 0; ///< size for full_ns_rank1, full_ls_rank1, full_Xs_rank1
size_t coeff_array_total_size_rank1 = 0; ///< size for full coefficients array (depends on B or C-Tilde basis)
NS_TYPE *full_ns_rank1 = nullptr; ///< ns contiguous package [rank_array_total_size_rank1]
LS_TYPE *full_ls_rank1 = nullptr; ///< ls contiguous package [rank_array_total_size_rank1]
SPECIES_TYPE *full_mus_rank1 = nullptr; ///< mus contiguous package [rank_array_total_size_rank1]
MS_TYPE *full_ms_rank1 = nullptr; ///< m_s contiguous package[rank_array_total_size_rank1]
//arrays and its sizes for rank > 1 basis functions for packed basis
size_t rank_array_total_size = 0; ///< size for full_ns, full_ls, full_Xs
size_t ms_array_total_size = 0; ///< size for full_ms array
size_t coeff_array_total_size = 0;///< size for full coefficients arrays (depends on B- or C- basis)
NS_TYPE *full_ns = nullptr; ///< ns contiguous package [rank_array_total_size]
LS_TYPE *full_ls = nullptr; ///< ls contiguous package [rank_array_total_size]
SPECIES_TYPE *full_mus = nullptr; ///< mus contiguous package [rank_array_total_size]
MS_TYPE *full_ms = nullptr; ///< //m_s contiguous package [ms_array_total_size]
/**
* Rearrange basis functions in contiguous memory to optimize cache access
*/
virtual void pack_flatten_basis() = 0;
virtual void flatten_basis() = 0;
//1D flat array basis representation: [mu]
SHORT_INT_TYPE *total_basis_size_rank1 = nullptr; ///< per-species type array of total_basis_rank1[mu] sizes
SHORT_INT_TYPE *total_basis_size = nullptr; ///< per-species type array of total_basis[mu] sizes
size_t max_B_array_size = 0; ///< maximum over elements array size for B[func_ind][ms_ind]
size_t max_dB_array_size = 0; ///< maximum over elements array size for dB[func_ind][ms_ind][r]
SHORT_INT_TYPE num_ms_combinations_max = 0; ///< maximum number of ms combinations among all basis functions
/**
* Default constructor
*/
ACEFlattenBasisSet() = default;
/**
* Copy constructor (see Rule of Three)
* @param other
*/
ACEFlattenBasisSet(const ACEFlattenBasisSet &other);
/**
* operator= (see Rule of Three)
* @param other
* @return
*/
ACEFlattenBasisSet &operator=(const ACEFlattenBasisSet &other);
/**
* Destructor (see Rule of Three)
*/
~ACEFlattenBasisSet() override;
// routines for copying and cleaning dynamic memory of the class (see Rule of Three)
/**
* Cleaning dynamic memory of the class (see. Rule of Three),
* must be idempotent for safety
*/
void _clean() override;
/**
* Copying scalar variables
* @param src
*/
void _copy_scalar_memory(const ACEFlattenBasisSet &src);
/**
* Copying and cleaning dynamic memory of the class (see. Rule of Three)
* @param src
*/
void _copy_dynamic_memory(const ACEFlattenBasisSet &src);
/**
* Clean contiguous arrays
*/
virtual void _clean_contiguous_arrays();
/**
* Release dynamic arrays with basis set sizes
*/
void _clean_basissize_arrays();
};
#endif //ACE_EVALUATOR_ACE_FLATTEN_BASIS_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <cmath>
#include <functional>
#include <stdexcept>
#include "ace_radial.h"
const DOUBLE_TYPE pi = 3.14159265358979323846264338327950288419; // pi
ACERadialFunctions::ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins,
SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff, string radbasename) {
init(nradb, lmax, nradial, deltaSplineBins, nelements, cutoff, radbasename);
}
void ACERadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins,
SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff, string radbasename) {
this->nradbase = nradb;
this->lmax = lmax;
this->nradial = nradial;
this->deltaSplineBins = deltaSplineBins;
this->nelements = nelements;
this->cutoff = cutoff;
this->radbasename = radbasename;
gr.init(nradbase, "gr");
dgr.init(nradbase, "dgr");
d2gr.init(nradbase, "d2gr");
fr.init(nradial, lmax + 1, "fr");
dfr.init(nradial, lmax + 1, "dfr");
d2fr.init(nradial, lmax + 1, "d2fr");
cheb.init(nradbase + 1, "cheb");
dcheb.init(nradbase + 1, "dcheb");
cheb2.init(nradbase + 1, "cheb2");
splines_gk.init(nelements, nelements, "splines_gk");
splines_rnl.init(nelements, nelements, "splines_rnl");
splines_hc.init(nelements, nelements, "splines_hc");
lambda.init(nelements, nelements, "lambda");
lambda.fill(1.);
cut.init(nelements, nelements, "cut");
cut.fill(1.);
dcut.init(nelements, nelements, "dcut");
dcut.fill(1.);
crad.init(nelements, nelements, nradial, (lmax + 1), nradbase, "crad");
crad.fill(0.);
//hard-core repulsion
prehc.init(nelements, nelements, "prehc");
prehc.fill(0.);
lambdahc.init(nelements, nelements, "lambdahc");
lambdahc.fill(1.);
}
/**
Function that computes Chebyshev polynomials of first and second kind
to setup the radial functions and the derivatives
@param n, x
@returns cheb1, dcheb1
*/
void ACERadialFunctions::calcCheb(NS_TYPE n, DOUBLE_TYPE x) {
if (n < 0) {
char s[1024];
sprintf(s, "The order n of the polynomials should be positive %d\n", n);
throw std::invalid_argument(s);
}
DOUBLE_TYPE twox = 2.0 * x;
cheb(0) = 1.;
dcheb(0) = 0.;
cheb2(0) = 1.;
if (nradbase > 1) {
cheb(1) = x;
cheb2(1) = twox;
}
for (NS_TYPE m = 1; m <= n - 1; m++) {
cheb(m + 1) = twox * cheb(m) - cheb(m - 1);
cheb2(m + 1) = twox * cheb2(m) - cheb2(m - 1);
}
for (NS_TYPE m = 1; m <= n; m++) {
dcheb(m) = m * cheb2(m - 1);
}
#ifdef DEBUG_RADIAL
for ( NS_TYPE m=0; m<=n; m++ ) {
printf(" m %d cheb %f dcheb %f \n", m, cheb(m), dcheb(m));
}
#endif
}
/**
Function that computes radial basis.
@param lam, nradbase, cut, dcut, r
@returns gr, dgr
*/
void ACERadialFunctions::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) {
/*lam is given by the formula (24), that contains cut */
if (r < cut) {
if (radbasename == "ChebExpCos") {
chebExpCos(lam, cut, dcut, r);
} else if (radbasename == "ChebPow") {
chebPow(lam, cut, dcut, r);
} else if (radbasename == "ChebLinear") {
chebLinear(lam, cut, dcut, r);
} else {
throw invalid_argument("Unknown radial basis function name: " + radbasename);
}
} else {
gr.fill(0);
dgr.fill(0);
}
}
/***
* Radial function: ChebExpCos, cheb exp scaling including cos envelope
* @param lam function parameter
* @param cut cutoff distance
* @param r function input argument
* @return fills in gr and dgr arrays
*/
void
ACERadialFunctions::chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) {
DOUBLE_TYPE y2, y1, x, dx;
DOUBLE_TYPE env, denv, fcut, dfcut;
/* scaled distance x and derivative*/
y1 = exp(-lam * r / cut);
y2 = exp(-lam);
x = 1.0 - 2.0 * ((y1 - y2) / (1 - y2));
dx = 2 * (lam / cut) * (y1 / (1 - y2));
/* calculation of Chebyshev polynomials from the recursion */
calcCheb(nradbase - 1, x);
gr(0) = cheb(0);
dgr(0) = dcheb(0) * dx;
for (NS_TYPE n = 2; n <= nradbase; n++) {
gr(n - 1) = 0.5 - 0.5 * cheb(n - 1);
dgr(n - 1) = -0.5 * dcheb(n - 1) * dx;
}
env = 0.5 * (1.0 + cos(M_PI * r / cut));
denv = -0.5 * sin(M_PI * r / cut) * M_PI / cut;
for (NS_TYPE n = 0; n < nradbase; n++) {
dgr(n) = gr(n) * denv + dgr(n) * env;
gr(n) = gr(n) * env;
}
// for radtype = 3 a smooth cut is already included in the basis function
dx = cut - dcut;
if (r > dx) {
fcut = 0.5 * (1.0 + cos(M_PI * (r - dx) / dcut));
dfcut = -0.5 * sin(M_PI * (r - dx) / dcut) * M_PI / dcut;
for (NS_TYPE n = 0; n < nradbase; n++) {
dgr(n) = gr(n) * dfcut + dgr(n) * fcut;
gr(n) = gr(n) * fcut;
}
}
}
/***
* Radial function: ChebPow, Radial function: ChebPow
* - argument of Chebyshev polynomials
* x = 2.0*( 1.0 - (1.0 - r/rcut)^lam ) - 1.0
* - radial function
* gr(n) = ( 1.0 - Cheb(n) )/2.0, n = 1,...,nradbase
* - the function fulfills:
* gr(n) = 0 at rcut
* dgr(n) = 0 at rcut for lam >= 1
* second derivative zero at rcut for lam >= 2
* -> the radial function does not require a separate cutoff function
* - corresponds to radial basis radtype=5 in Fortran code
*
* @param lam function parameter
* @param cut cutoff distance
* @param r function input argument
* @return fills in gr and dgr arrays
*/
void
ACERadialFunctions::chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) {
DOUBLE_TYPE y, dy, x, dx;
/* scaled distance x and derivative*/
y = (1.0 - r / cut);
dy = pow(y, (lam - 1.0));
y = dy * y;
dy = -lam / cut * dy;
x = 2.0 * (1.0 - y) - 1.0;
dx = -2.0 * dy;
calcCheb(nradbase, x);
for (NS_TYPE n = 1; n <= nradbase; n++) {
gr(n - 1) = 0.5 - 0.5 * cheb(n);
dgr(n - 1) = -0.5 * dcheb(n) * dx;
}
}
void
ACERadialFunctions::chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) {
DOUBLE_TYPE x, dx;
/* scaled distance x and derivative*/
x = (1.0 - r / cut);
dx = -1 / cut;
calcCheb(nradbase, x);
for (NS_TYPE n = 1; n <= nradbase; n++) {
gr(n - 1) = 0.5 - 0.5 * cheb(n);
dgr(n - 1) = -0.5 * dcheb(n) * dx;
}
}
/**
Function that computes radial functions.
@param nradbase, nelements, elei, elej
@returns fr, dfr
*/
void ACERadialFunctions::radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej) {
DOUBLE_TYPE frval, dfrval;
for (NS_TYPE n = 0; n < nradial; n++) {
for (LS_TYPE l = 0; l <= lmax; l++) {
frval = 0.0;
dfrval = 0.0;
for (NS_TYPE k = 0; k < nradbase; k++) {
frval += crad(elei, elej, n, l, k) * gr(k);
dfrval += crad(elei, elej, n, l, k) * dgr(k);
}
fr(n, l) = frval;
dfr(n, l) = dfrval;
}
}
}
void ACERadialFunctions::all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r) {
DOUBLE_TYPE lam = lambda(mu_i, mu_j);
DOUBLE_TYPE r_cut = cut(mu_i, mu_j);
DOUBLE_TYPE dr_cut = dcut(mu_i, mu_j);
// set up radial functions
radbase(lam, r_cut, dr_cut, r); //update gr, dgr
radfunc(mu_i, mu_j); // update fr(nr, l), dfr(nr, l)
}
void ACERadialFunctions::setuplookupRadspline() {
using namespace std::placeholders;
DOUBLE_TYPE lam, r_cut, dr_cut;
DOUBLE_TYPE cr_c, dcr_c, pre, lamhc;
// at r = rcut + eps the function and its derivatives is zero
for (SPECIES_TYPE elei = 0; elei < nelements; elei++) {
for (SPECIES_TYPE elej = 0; elej < nelements; elej++) {
lam = lambda(elei, elej);
r_cut = cut(elei, elej);
dr_cut = dcut(elei, elej);
splines_gk(elei, elej).setupSplines(gr.get_size(),
std::bind(&ACERadialFunctions::radbase, this, lam, r_cut, dr_cut,
_1),//update gr, dgr
gr.get_data(),
dgr.get_data(), deltaSplineBins, cutoff);
splines_rnl(elei, elej).setupSplines(fr.get_size(),
std::bind(&ACERadialFunctions::all_radfunc, this, elei, elej,
_1), // update fr(nr, l), dfr(nr, l)
fr.get_data(),
dfr.get_data(), deltaSplineBins, cutoff);
pre = prehc(elei, elej);
lamhc = lambdahc(elei, elej);
// radcore(r, pre, lamhc, cutoff, cr_c, dcr_c);
splines_hc(elei, elej).setupSplines(1,
std::bind(&ACERadialFunctions::radcore, _1, pre, lamhc, cutoff,
std::ref(cr_c), std::ref(dcr_c)),
&cr_c,
&dcr_c, deltaSplineBins, cutoff);
}
}
}
/**
Function that gets radial function from look-up table using splines.
@param r, nradbase_c, nradial_c, lmax, mu_i, mu_j
@returns fr, dfr, gr, dgr, cr, dcr
*/
void
ACERadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i,
SPECIES_TYPE mu_j, bool calc_second_derivatives) {
auto &spline_gk = splines_gk(mu_i, mu_j);
auto &spline_rnl = splines_rnl(mu_i, mu_j);
auto &spline_hc = splines_hc(mu_i, mu_j);
spline_gk.calcSplines(r, calc_second_derivatives); // populate splines_gk.values, splines_gk.derivatives;
for (NS_TYPE nr = 0; nr < nradbase_c; nr++) {
gr(nr) = spline_gk.values(nr);
dgr(nr) = spline_gk.derivatives(nr);
if (calc_second_derivatives)
d2gr(nr) = spline_gk.second_derivatives(nr);
}
spline_rnl.calcSplines(r, calc_second_derivatives);
for (size_t ind = 0; ind < fr.get_size(); ind++) {
fr.get_data(ind) = spline_rnl.values.get_data(ind);
dfr.get_data(ind) = spline_rnl.derivatives.get_data(ind);
if (calc_second_derivatives)
d2fr.get_data(ind) = spline_rnl.second_derivatives.get_data(ind);
}
spline_hc.calcSplines(r, calc_second_derivatives);
cr = spline_hc.values(0);
dcr = spline_hc.derivatives(0);
if (calc_second_derivatives)
d2cr = spline_hc.second_derivatives(0);
}
void
ACERadialFunctions::radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr,
DOUBLE_TYPE &dcr) {
/* pseudocode for hard core repulsion
in:
r: distance
pre: prefactor: read from input, depends on pair of atoms mu_i mu_j
lambda: exponent: read from input, depends on pair of atoms mu_i mu_j
cutoff: cutoff distance: read from input, depends on pair of atoms mu_i mu_j
out:
cr: hard core repulsion
dcr: derivative of hard core repulsion
function
\$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f
*/
DOUBLE_TYPE r2, lr2, y, x0, env, denv;
// repulsion strictly positive and decaying
pre = abs(pre);
lambda = abs(lambda);
r2 = r * r;
lr2 = lambda * r2;
if (lr2 < 50.0) {
y = exp(-lr2);
cr = pre * y / r;
dcr = -pre * y * (2.0 * lr2 + 1.0) / r2;
x0 = r / cutoff;
env = 0.5 * (1.0 + cos(pi * x0));
denv = -0.5 * sin(pi * x0) * pi / cutoff;
dcr = cr * denv + dcr * env;
cr = cr * env;
} else {
cr = 0.0;
dcr = 0.0;
}
}
void
ACERadialFunctions::evaluate_range(vector<DOUBLE_TYPE> r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i,
SPECIES_TYPE mu_j) {
if (nradbase_c > nradbase)
throw invalid_argument("nradbase_c couldn't be larger than nradbase");
if (nradial_c > nradial)
throw invalid_argument("nradial_c couldn't be larger than nradial");
if (mu_i > nelements)
throw invalid_argument("mu_i couldn't be larger than nelements");
if (mu_j > nelements)
throw invalid_argument("mu_j couldn't be larger than nelements");
gr_vec.resize(r_vec.size(), nradbase_c);
dgr_vec.resize(r_vec.size(), nradbase_c);
d2gr_vec.resize(r_vec.size(), nradbase_c);
fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1));
dfr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1));
d2fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1));
for (size_t i = 0; i < r_vec.size(); i++) {
DOUBLE_TYPE r = r_vec[i];
this->evaluate(r, nradbase_c, nradial_c, mu_i, mu_j, true);
for (NS_TYPE nr = 0; nr < nradbase_c; nr++) {
gr_vec(i, nr) = gr(nr);
dgr_vec(i, nr) = dgr(nr);
d2gr_vec(i, nr) = d2gr(nr);
}
for (NS_TYPE nr = 0; nr < nradial_c; nr++) {
for (LS_TYPE l = 0; l <= lmax; l++) {
fr_vec(i, nr, l) = fr(nr, l);
dfr_vec(i, nr, l) = dfr(nr, l);
d2fr_vec(i, nr, l) = d2fr(nr, l);
}
}
}
}
void SplineInterpolator::setupSplines(int num_of_functions, RadialFunctions func,
DOUBLE_TYPE *values,
DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff) {
this->deltaSplineBins = deltaSplineBins;
this->cutoff = cutoff;
this->ntot = static_cast<int>(cutoff / deltaSplineBins);
DOUBLE_TYPE r, c[4];
this->num_of_functions = num_of_functions;
this->values.resize(num_of_functions);
this->derivatives.resize(num_of_functions);
this->second_derivatives.resize(num_of_functions);
Array1D<DOUBLE_TYPE> f1g(num_of_functions);
Array1D<DOUBLE_TYPE> f1gd1(num_of_functions);
f1g.fill(0);
f1gd1.fill(0);
nlut = ntot;
DOUBLE_TYPE f0, f1, f0d1, f1d1;
int idx;
// cutoff is global cutoff
rscalelookup = (DOUBLE_TYPE) nlut / cutoff;
invrscalelookup = 1.0 / rscalelookup;
lookupTable.init(ntot + 1, num_of_functions, 4);
if (values == nullptr & num_of_functions > 0)
throw invalid_argument("SplineInterpolator::setupSplines: values could not be null");
if (dvalues == nullptr & num_of_functions > 0)
throw invalid_argument("SplineInterpolator::setupSplines: dvalues could not be null");
for (int n = nlut; n >= 1; n--) {
r = invrscalelookup * DOUBLE_TYPE(n);
func(r); //populate values and dvalues arrays
for (int func_id = 0; func_id < num_of_functions; func_id++) {
f0 = values[func_id];
f1 = f1g(func_id);
f0d1 = dvalues[func_id] * invrscalelookup;
f1d1 = f1gd1(func_id);
// evaluate coefficients
c[0] = f0;
c[1] = f0d1;
c[2] = 3.0 * (f1 - f0) - f1d1 - 2.0 * f0d1;
c[3] = -2.0 * (f1 - f0) + f1d1 + f0d1;
// store coefficients
for (idx = 0; idx <= 3; idx++)
lookupTable(n, func_id, idx) = c[idx];
// evaluate function values and derivatives at current position
f1g(func_id) = c[0];
f1gd1(func_id) = c[1];
}
}
}
void SplineInterpolator::calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives) {
DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2, w4l2;
DOUBLE_TYPE c[4];
int func_id, idx;
DOUBLE_TYPE x = r * rscalelookup;
int nl = static_cast<int>(floor(x));
if (nl <= 0)
throw std::invalid_argument("Encountered very small distance. Stopping.");
if (nl < nlut) {
wl = x - DOUBLE_TYPE(nl);
wl2 = wl * wl;
wl3 = wl2 * wl;
w2l1 = 2.0 * wl;
w3l2 = 3.0 * wl2;
w4l2 = 6.0 * wl;
for (func_id = 0; func_id < num_of_functions; func_id++) {
for (idx = 0; idx <= 3; idx++) {
c[idx] = lookupTable(nl, func_id, idx);
}
values(func_id) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3;
derivatives(func_id) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup;
if (calc_second_derivatives)
second_derivatives(func_id) = (c[2] + c[3] * w4l2) * rscalelookup * rscalelookup * 2;
}
} else { // fill with zeroes
values.fill(0);
derivatives.fill(0);
if (calc_second_derivatives)
second_derivatives.fill(0);
}
}
void SplineInterpolator::calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind) {
DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2;
DOUBLE_TYPE c[4];
int idx;
DOUBLE_TYPE x = r * rscalelookup;
int nl = static_cast<int>(floor(x));
if (nl <= 0)
throw std::invalid_argument("Encountered very small distance. Stopping.");
if (nl < nlut) {
wl = x - DOUBLE_TYPE(nl);
wl2 = wl * wl;
wl3 = wl2 * wl;
w2l1 = 2.0 * wl;
w3l2 = 3.0 * wl2;
for (idx = 0; idx <= 3; idx++) {
c[idx] = lookupTable(nl, func_ind, idx);
}
values(func_ind) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3;
derivatives(func_ind) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup;
} else { // fill with zeroes
values(func_ind) = 0;
derivatives(func_ind) = 0;
}
}

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ACE_RADIAL_FUNCTIONS_H
#define ACE_RADIAL_FUNCTIONS_H
#include "ace_arraynd.h"
#include "ace_types.h"
#include <functional>
using namespace std;
//typedef void (*RadialFunctions)(DOUBLE_TYPE x);
typedef std::function<void(DOUBLE_TYPE)> RadialFunctions;
/**
* Class that implement spline interpolation and caching for radial functions
*/
class SplineInterpolator {
public:
DOUBLE_TYPE cutoff = 0; ///< cutoff
DOUBLE_TYPE deltaSplineBins = 0.001;
int ntot = 10000; ///< Number of bins for look-up tables.
int nlut = 10000; ///< number of nodes in look-up table
DOUBLE_TYPE invrscalelookup = 1; ///< inverse of conversion coefficient from distance to lookup table within cutoff range
DOUBLE_TYPE rscalelookup = 1; ///< conversion coefficient from distance to lookup table within cutoff range
int num_of_functions = 0;///< number of functions to spline-interpolation
Array1D<DOUBLE_TYPE> values;// = Array1D<DOUBLE_TYPE>("values"); ///< shape: [func_ind]
Array1D<DOUBLE_TYPE> derivatives;// = Array1D<DOUBLE_TYPE>("derivatives");///< shape: [func_ind]
Array1D<DOUBLE_TYPE> second_derivatives;// = Array1D<DOUBLE_TYPE>("second_derivatives");///< shape: [func_ind]
Array3D<DOUBLE_TYPE> lookupTable = Array3D<DOUBLE_TYPE>("lookupTable");///< shape: [ntot+1][func_ind][4]
/**
* Setup splines
*
* @param num_of_functions number of functions
* @param func subroutine, that update `values` and `dvalues` arrays
* @param values values
* @param dvalues derivatives
*/
void setupSplines(int num_of_functions, RadialFunctions func,
DOUBLE_TYPE *values,
DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff);
/**
* Populate `values` and `derivatives` arrays with a spline-interpolation for
* all functions
*
* @param r
*
* @return: populate 'values' and 'derivatives'
*/
void calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives = false);
/**
* Populate `values` and `derivatives` arrays with a spline-interpolation for
* all functions
*
* @param r
*
* @return: populate 'values' and 'derivatives'
*/
void calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind);
};
/**
* Interface class for radial basis functions with rank=1 (g_k), R_nl (rank>1) and hard-core repulsion radial functions
*/
class AbstractRadialBasis {
public:
SPECIES_TYPE nelements = 0; ///< number of elements
Array2D<DOUBLE_TYPE> cut = Array2D<DOUBLE_TYPE>("cut"); ///< cutoffs, shape: [nelements][nelements]
Array2D<DOUBLE_TYPE> dcut = Array2D<DOUBLE_TYPE>("dcut"); ///< decay of cutoff, shape: [nelements][nelements]
DOUBLE_TYPE cutoff = 0; ///< cutoff
// int ntot = 10000; ///< Number of bins for look-up tables.
DOUBLE_TYPE deltaSplineBins;
LS_TYPE lmax = 0; ///< maximum value of `l`
NS_TYPE nradial = 0; ///< maximum number `n` of radial functions \f$ R_{nl}(r) \f$
NS_TYPE nradbase = 0; ///< number of radial basis functions \f$ g_k(r) \f$
// Arrays for look-up tables.
Array2D<SplineInterpolator> splines_gk; ///< array of spline interpolator to store g_k, shape: [nelements][nelements]
Array2D<SplineInterpolator> splines_rnl; ///< array of spline interpolator to store R_nl, shape: [nelements][nelements]
Array2D<SplineInterpolator> splines_hc; ///< array of spline interpolator to store R_nl shape: [nelements][nelements]
//--------------------------------------------------------------------------
string radbasename = "ChebExpCos"; ///< type of radial basis functions \f$ g_{k}(r) \f$ (default="ChebExpCos")
/**
Arrays to store radial functions.
*/
Array1D<DOUBLE_TYPE> gr = Array1D<DOUBLE_TYPE>("gr"); ///< g_k(r) functions, shape: [nradbase]
Array1D<DOUBLE_TYPE> dgr = Array1D<DOUBLE_TYPE>("dgr"); ///< derivatives of g_k(r) functions, shape: [nradbase]
Array1D<DOUBLE_TYPE> d2gr = Array1D<DOUBLE_TYPE>("d2gr"); ///< derivatives of g_k(r) functions, shape: [nradbase]
Array2D<DOUBLE_TYPE> fr = Array2D<DOUBLE_TYPE>("fr"); ///< R_nl(r) functions, shape: [nradial][lmax+1]
Array2D<DOUBLE_TYPE> dfr = Array2D<DOUBLE_TYPE>(
"dfr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1]
Array2D<DOUBLE_TYPE> d2fr = Array2D<DOUBLE_TYPE>(
"d2fr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1]
DOUBLE_TYPE cr; ///< hard-core repulsion
DOUBLE_TYPE dcr; ///< derivative of hard-core repulsion
DOUBLE_TYPE d2cr; ///< derivative of hard-core repulsion
Array5D<DOUBLE_TYPE> crad = Array5D<DOUBLE_TYPE>(
"crad"); ///< expansion coefficients of radial functions into radial basis function, see Eq. (27) of PRB, shape: [nelements][nelements][lmax + 1][nradial][nradbase]
Array2D<DOUBLE_TYPE> lambda = Array2D<DOUBLE_TYPE>(
"lambda"); ///< distance scaling parameter Eq.(24) of PRB, shape: [nelements][nelements]
Array2D<DOUBLE_TYPE> prehc = Array2D<DOUBLE_TYPE>(
"prehc"); ///< hard-core repulsion coefficients (prefactor), shape: [nelements][nelements]
Array2D<DOUBLE_TYPE> lambdahc = Array2D<DOUBLE_TYPE>(
"lambdahc");; ///< hard-core repulsion coefficients (lambdahc), shape: [nelements][nelements]
virtual void
evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j,
bool calc_second_derivatives = false) = 0;
virtual void
init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff,
string radbasename = "ChebExpCos") = 0;
/**
* Function that sets up the look-up tables for spline-representation of radial functions.
*/
virtual void setuplookupRadspline() = 0;
virtual AbstractRadialBasis *clone() const = 0;
virtual ~AbstractRadialBasis() = default;
};
/**
Class to store radial functions and their associated functions. \n
*/
class ACERadialFunctions final : public AbstractRadialBasis {
public:
//--------------------------------------------------------------------------
/**
Arrays to store Chebyshev polynomials.
*/
Array1D<DOUBLE_TYPE> cheb = Array1D<DOUBLE_TYPE>(
"cheb"); ///< Chebyshev polynomials of the first kind, shape: [nradbase+1]
Array1D<DOUBLE_TYPE> dcheb = Array1D<DOUBLE_TYPE>(
"dcheb"); ///< derivatives Chebyshev polynomials of the first kind, shape: [nradbase+1]
Array1D<DOUBLE_TYPE> cheb2 = Array1D<DOUBLE_TYPE>(
"cheb2"); ///< Chebyshev polynomials of the second kind, shape: [nradbase+1]
//--------------------------------------------------------------------------
Array2D<DOUBLE_TYPE> gr_vec;
Array2D<DOUBLE_TYPE> dgr_vec;
Array2D<DOUBLE_TYPE> d2gr_vec;
Array3D<DOUBLE_TYPE> fr_vec;
Array3D<DOUBLE_TYPE> dfr_vec;
Array3D<DOUBLE_TYPE> d2fr_vec;
//------------------------------------------------------------------------
/**
* Default constructor
*/
ACERadialFunctions() = default;
/**
* Parametrized constructor
*
* @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase
* @param lmax maximum orbital moment - lmax
* @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial
* @param ntot Number of bins for spline look-up tables.
* @param nelements numer of elements
* @param cutoff cutoff
* @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos")
*/
ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins,
SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff, string radbasename = "ChebExpCos");
/**
* Initialize arrays for given parameters
*
* @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase
* @param lmax maximum orbital moment - lmax
* @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial
* @param ntot Number of bins for spline look-up tables.
* @param nelements numer of elements
* @param cutoff cutoff
* @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos")
*/
void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff,
string radbasename = "ChebExpCos") final;
/**
* Destructor
*/
~ACERadialFunctions() final = default;
/**
* Function that computes Chebyshev polynomials of first and second kind
* to setup the radial functions and the derivatives
*
* @param n maximum polynom order
* @param x
*
* @returns fills cheb, dcheb and cheb2 arrays
*/
void calcCheb(NS_TYPE n, DOUBLE_TYPE x);
/**
* Function that computes radial basis functions \$f g_k(r) \$f, see Eq.(21) of PRB paper
* @param lam \$f \lambda \$f parameter, see eq. (24) of PRB paper
* @param cut cutoff
* @param dcut cutoff decay
* @param r distance
*
* @return function fills gr and dgr arrays
*/
void radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r);
/**
* Function that computes radial core repulsion \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f,
* and its derivative, see Eq.(27) of implementation notes.
*
* @param r distance
* @param pre prefactor: read from input, depends on pair of atoms mu_i mu_j
* @param lambda exponent: read from input, depends on pair of atoms mu_i mu_j
* @param cutoff cutoff distance: read from input, depends on pair of atoms mu_i mu_j
* @param cr (out) hard core repulsion
* @param dcr (out) derivative of hard core repulsion
*/
static void radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr,
DOUBLE_TYPE &dcr);
/**
* Function that sets up the look-up tables for spline-representation of radial functions.
*/
void setuplookupRadspline() final;
/**
* Function that computes radial functions \f$ R_{nl}(r)\f$ (see Eq. 27 from PRB paper)
* and its derivatives for all range of n,l,
* ONLY if radial basis functions (gr and dgr) are computed.
* @param elei first species type
* @param elej second species type
*
* @return fills in fr, dfr arrays
*/
void radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej);
/**
* Compute all radial functions R_nl(r), radial basis functions g_k(r) and hard-core repulsion function hc(r)
*
* @param r distance
* @param nradbase_c
* @param nradial_c
* @param mu_i
* @param mu_j
*
* @return update gr(k), dgr(k), fr(n,l), dfr(n,l), cr, dcr
*/
void evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j,
bool calc_second_derivatives = false) final;
void
evaluate_range(vector<DOUBLE_TYPE> r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i,
SPECIES_TYPE mu_j);
void chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r);
void chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r);
void chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r);
/**
* Setup all radial functions for element pair mu_i-mu_j and distance r
* @param mu_i first specie type
* @param mu_j second specie type
* @param r distance
* @return update fr(nr, l), dfr(nr, l)
*/
void all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r);
ACERadialFunctions *clone() const override {
return new ACERadialFunctions(*this);
};
};
#endif

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Christoph Ortner on 20.12.2020
#ifndef ACE_RECURSIVE_H
#define ACE_RECURSIVE_H
#include "ace_abstract_basis.h"
#include "ace_arraynd.h"
#include "ace_array2dlm.h"
#include "ace_c_basis.h"
#include "ace_complex.h"
#include "ace_timing.h"
#include "ace_types.h"
#include "ace_evaluator.h"
#include <list>
#include <utility>
#include <algorithm>
#include <map>
#include <vector>
using namespace std;
typedef pair<vector<int>, vector<int> > TPARTITION;
typedef list<TPARTITION> TPARTITIONS;
typedef map<vector<int>, int> TDAGMAP;
class ACEDAG {
TPARTITIONS find_2partitions(vector<int> v);
void insert_node(TDAGMAP &dagmap,
vector<int> node,
vector<DOUBLE_TYPE> c);
// the following fields are used only for *construction*, not evaluation
int dag_idx; // current index of dag node
Array2D<int> nodes_pre; //TODO: YL: better to use vector<>
Array2D<DOUBLE_TYPE> coeffs_pre; //TODO: YL: better to use vector<>
Array1D<bool> haschild; //TODO: YL: better to use vector<>
/* which heuristic to choose for DAG construction?
* 0 : the simple original heuristic
* 1 : prioritize 2-correlation nodes and build the rest from those
*/
int heuristic = 0;
public:
ACEDAG() = default;
void init(Array2D<int> Aspec, Array2D<int> AAspec,
Array1D<int> orders, Array2D<DOUBLE_TYPE> coeffs,
int heuristic );
Array1D<ACEComplex> AAbuf;
Array1D<ACEComplex> w;
Array2D<int> Aspec;
// nodes in the graph
Array2D<int> nodes;
Array2D<DOUBLE_TYPE> coeffs;
// total number of nodes in the dag
int num_nodes;
// number of interior nodes (with children)
int num2_int;
// number of leaf nodes (nc = no child)
int num2_leaf;
// number of 1-particle basis functions
// (these will be stored in the first num1 entries of AAbuf)
int get_num1() { return Aspec.get_dim(0); };
// total number of n-correlation basis functions n > 1.
int get_num2() { return num_nodes - get_num1(); };
int get_num2_int() { return num2_int; }; // with children
int get_num2_leaf() { return num2_leaf; }; // without children
// debugging tool
void print();
};
/**
* Recursive Variant of the ACETildeEvaluator; should be 100% compatible
*/
class ACERecursiveEvaluator : public ACEEvaluator {
/**
* Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes,
* 'i' is fixed for the current atom, shape: [nelements][nradbase]
*/
Array2D<DOUBLE_TYPE> weights_rank1 = Array2D<DOUBLE_TYPE>("weights_rank1");
/**
* Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes,
* 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m]
*/
Array4DLM<ACEComplex> weights = Array4DLM<ACEComplex>("weights");
/**
* cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m)
* shape:[max_jnum][nradbase]
*/
Array2D<DOUBLE_TYPE> DG_cache = Array2D<DOUBLE_TYPE>("DG_cache");
/**
* cache for \f$ R_{nl}(r)\f$
* shape:[max_jnum][nradbase][0..lmax]
*/
Array3D<DOUBLE_TYPE> R_cache = Array3D<DOUBLE_TYPE>("R_cache");
/**
* cache for derivatives of \f$ R_{nl}(r)\f$
* shape:[max_jnum][nradbase][0..lmax]
*/
Array3D<DOUBLE_TYPE> DR_cache = Array3D<DOUBLE_TYPE>("DR_cache");
/**
* cache for \f$ Y_{lm}(\hat{r})\f$
* shape:[max_jnum][0..lmax][m]
*/
Array3DLM<ACEComplex> Y_cache = Array3DLM<ACEComplex>("Y_cache");
/**
* cache for \f$ \nabla Y_{lm}(\hat{r})\f$
* shape:[max_jnum][0..lmax][m]
*/
Array3DLM<ACEDYcomponent> DY_cache = Array3DLM<ACEDYcomponent>("dY_dense_cache");
/**
* cache for derivatives of hard-core repulsion
* shape:[max_jnum]
*/
Array1D<DOUBLE_TYPE> DCR_cache = Array1D<DOUBLE_TYPE>("DCR_cache");
/**
* Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r],
* shape:[func_ms_r_ind]
*/
Array1D<ACEComplex> dB_flatten = Array1D<ACEComplex>("dB_flatten");
/**
* pointer to the ACEBasisSet object
*/
ACECTildeBasisSet *basis_set = nullptr;
/**
* Initialize internal arrays according to basis set sizes
* @param basis_set
*/
void init(ACECTildeBasisSet *basis_set, int heuristic);
/* convert the PACE to the ACE.jl format to prepare for DAG construction*/
Array2D<int> jl_Aspec;
Array2D<int> jl_AAspec;
Array1D<int> jl_AAspec_flat;
Array1D<int> jl_orders;
Array2D<DOUBLE_TYPE> jl_coeffs;
void acejlformat();
/* the main event : the computational graph */
ACEDAG dag;
bool recursive = true;
public:
ACERecursiveEvaluator() = default;
explicit ACERecursiveEvaluator(ACECTildeBasisSet &bas,
bool recursive = true) {
set_recursive(recursive);
set_basis(bas);
}
/**
* set the basis function to the ACE evaluator
* @param bas
*/
void set_basis(ACECTildeBasisSet &bas, int heuristic = 0);
/**
* The key method to compute energy and forces for atom 'i'.
* Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array
*
* @param i atom index
* @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3]
* @param type atomic types array of the real and ghost atoms, shape: [atom_ind]
* @param jnum number of neighbours of atom_i
* @param jlist array of neighbour indices, shape: [jnum]
*/
void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override;
/**
* Resize all caches over neighbours atoms
* @param max_jnum maximum number of neighbours
*/
void resize_neighbours_cache(int max_jnum) override;
/******* public functions related to recursive evaluator ********/
// print out the DAG for visual inspection
void print_dag() {dag.print();}
// print out the jl format for visual inspection
// should be converted into a proper test
void test_acejlformat();
void set_recursive(bool tf) { recursive = tf; }
/********************************/
};
#endif //ACE_RECURSIVE_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Ralf Drautz, Yury Lysogorskiy
#include <cmath>
#include "ace_spherical_cart.h"
ACECartesianSphericalHarmonics::ACECartesianSphericalHarmonics(LS_TYPE lm) {
init(lm);
}
void ACECartesianSphericalHarmonics::init(LS_TYPE lm) {
lmax = lm;
alm.init(lmax, "alm");
blm.init(lmax, "blm");
cl.init(lmax + 1);
dl.init(lmax + 1);
plm.init(lmax, "plm");
dplm.init(lmax, "dplm");
ylm.init(lmax, "ylm");
dylm.init(lmax, "dylm");
pre_compute();
}
/**
Destructor for ACECartesianSphericalHarmonics.
@param None
@returns None
*/
ACECartesianSphericalHarmonics::~ACECartesianSphericalHarmonics() {}
void ACECartesianSphericalHarmonics::pre_compute() {
DOUBLE_TYPE a, b;
DOUBLE_TYPE lsq, ld, l1, l2;
DOUBLE_TYPE msq;
for (LS_TYPE l = 1; l <= lmax; l++) {
lsq = l * l;
ld = 2 * l;
l1 = (4 * lsq - 1);
l2 = lsq - ld + 1;
for (MS_TYPE m = 0; m < l - 1; m++) {
msq = m * m;
a = sqrt((DOUBLE_TYPE(l1)) / (DOUBLE_TYPE(lsq - msq)));
b = -sqrt((DOUBLE_TYPE(l2 - msq)) / (DOUBLE_TYPE(4 * l2 - 1)));
alm(l, m) = a;
blm(l, m) = b;
}
}
for (LS_TYPE l = 1; l <= lmax; l++) {
cl(l) = -sqrt(1.0 + 0.5 / (DOUBLE_TYPE(l)));
dl(l) = sqrt(DOUBLE_TYPE(2 * (l - 1) + 3));
}
}
void ACECartesianSphericalHarmonics::compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi) {
// requires -1 <= rz <= 1 , NO CHECKING IS PERFORMED !!!!!!!!!
// prefactors include 1/sqrt(2) factor compared to reference
DOUBLE_TYPE t;
// l=0, m=0
//plm(0, 0) = Y00/sq1o4pi; //= sq1o4pi;
plm(0, 0) = Y00; //= 1;
dplm(0, 0) = 0.0;
if (lmaxi > 0) {
// l=1, m=0
plm(1, 0) = Y00 * sq3 * rz;
dplm(1, 0) = Y00 * sq3;
// l=1, m=1
plm(1, 1) = -sq3o2 * Y00;
dplm(1, 1) = 0.0;
// loop l = 2, lmax
for (LS_TYPE l = 2; l <= lmaxi; l++) {
for (MS_TYPE m = 0; m < l - 1; m++) {
plm(l, m) = alm(l, m) * (rz * plm(l - 1, m) + blm(l, m) * plm(l - 2, m));
dplm(l, m) = alm(l, m) * (plm(l - 1, m) + rz * dplm(l - 1, m) + blm(l, m) * dplm(l - 2, m));
}
t = dl(l) * plm(l - 1, l - 1);
plm(l, l - 1) = t * rz;
dplm(l, l - 1) = t;
plm(l, l) = cl(l) * plm(l - 1, l - 1);
dplm(l, l) = 0.0;
}
}
} //end compute_barplm
void ACECartesianSphericalHarmonics::compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi) {
// requires rx^2 + ry^2 + rz^2 = 1 , NO CHECKING IS PERFORMED !!!!!!!!!
DOUBLE_TYPE real;
DOUBLE_TYPE img;
MS_TYPE m;
ACEComplex phase;
ACEComplex phasem, mphasem1;
ACEComplex dyx, dyy, dyz;
ACEComplex rdy;
phase.real = rx;
phase.img = ry;
//compute barplm
compute_barplm(rz, lmaxi);
//m = 0
m = 0;
for (LS_TYPE l = 0; l <= lmaxi; l++) {
ylm(l, m).real = plm(l, m);
ylm(l, m).img = 0.0;
dyz.real = dplm(l, m);
rdy.real = dyz.real * rz;
dylm(l, m).a[0].real = -rdy.real * rx;
dylm(l, m).a[0].img = 0.0;
dylm(l, m).a[1].real = -rdy.real * ry;
dylm(l, m).a[1].img = 0.0;
dylm(l, m).a[2].real = dyz.real - rdy.real * rz;
dylm(l, m).a[2].img = 0;
}
//m = 0
m = 1;
for (LS_TYPE l = 1; l <= lmaxi; l++) {
ylm(l, m) = phase * plm(l, m);
// std::cout << "Re ylm(" << l << "," << m <<")= " << ylm(l, m).real << std::endl;
// std::cout << "Im ylm(" << l << "," << m <<")= " << ylm(l, m).img << std::endl;
dyx.real = plm(l, m);
dyx.img = 0.0;
dyy.real = 0.0;
dyy.img = plm(l, m);
dyz.real = phase.real * dplm(l, m);
dyz.img = phase.img * dplm(l, m);
rdy.real = rx * dyx.real + +rz * dyz.real;
rdy.img = ry * dyy.img + rz * dyz.img;
dylm(l, m).a[0].real = dyx.real - rdy.real * rx;
dylm(l, m).a[0].img = -rdy.img * rx;
dylm(l, m).a[1].real = -rdy.real * ry;
dylm(l, m).a[1].img = dyy.img - rdy.img * ry;
dylm(l, m).a[2].real = dyz.real - rdy.real * rz;
dylm(l, m).a[2].img = dyz.img - rdy.img * rz;
}
// m > 1
phasem = phase;
for (MS_TYPE m = 2; m <= lmaxi; m++) {
mphasem1.real = phasem.real * DOUBLE_TYPE(m);
mphasem1.img = phasem.img * DOUBLE_TYPE(m);
phasem = phasem * phase;
for (LS_TYPE l = m; l <= lmaxi; l++) {
ylm(l, m).real = phasem.real * plm(l, m);
ylm(l, m).img = phasem.img * plm(l, m);
dyx = mphasem1 * plm(l, m);
dyy.real = -dyx.img;
dyy.img = dyx.real;
dyz = phasem * dplm(l, m);
rdy.real = rx * dyx.real + ry * dyy.real + rz * dyz.real;
rdy.img = rx * dyx.img + ry * dyy.img + rz * dyz.img;
dylm(l, m).a[0].real = dyx.real - rdy.real * rx;
dylm(l, m).a[0].img = dyx.img - rdy.img * rx;
dylm(l, m).a[1].real = dyy.real - rdy.real * ry;
dylm(l, m).a[1].img = dyy.img - rdy.img * ry;
dylm(l, m).a[2].real = dyz.real - rdy.real * rz;
dylm(l, m).a[2].img = dyz.img - rdy.img * rz;
}
}
}

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Ralf Drautz, Yury Lysogorskiy
#ifndef ACE_SPHERICAL_CART_H
#define ACE_SPHERICAL_CART_H
#include <cmath>
#include "ace_arraynd.h"
#include "ace_array2dlm.h"
#include "ace_complex.h"
#include "ace_types.h"
using namespace std;
const DOUBLE_TYPE sq1o4pi = 0.28209479177387814347; // sqrt(1/(4*pi))
const DOUBLE_TYPE sq4pi = 3.54490770181103176384; // sqrt(4*pi)
const DOUBLE_TYPE sq3 = 1.73205080756887719318;//sqrt(3), numpy
const DOUBLE_TYPE sq3o2 = 1.22474487139158894067;//sqrt(3/2), numpy
//definition of common factor for spherical harmonics = Y00
//const DOUBLE_TYPE Y00 = sq1o4pi;
const DOUBLE_TYPE Y00 = 1;
/**
Class to store spherical harmonics and their associated functions. \n
All the associated members such as \f$ P_{lm}, Y_{lm}\f$ etc are one dimensional arrays of length (L+1)*(L+2)/2. \n
The value that corresponds to a particular l, m configuration can be accessed through a \code ylm(l,m) \endcode \n
*/
class ACECartesianSphericalHarmonics {
public:
/**
int, the number of spherical harmonics to be found
*/
LS_TYPE lmax;
/**
* Default constructor
*/
ACECartesianSphericalHarmonics() = default;
/**
* Parametrized constructor. Dynamically initialises all the arrays.
* @param lmax maximum orbital moment
*/
explicit ACECartesianSphericalHarmonics(LS_TYPE lmax);
/**
* Initialize internal arrays and precompute necessary coefficients
* @param lm maximum orbital moment
*/
void init(LS_TYPE lm);
/**
* Destructor
*/
~ACECartesianSphericalHarmonics();
/**
* Precompute necessaary helper arrays Precomputes the value of \f$ a_{lm}, b_{lm}, c_l, d_l \f$
*/
void pre_compute();
/**
Function that computes \f$ \bar{P}_{lm} \f$ for the corresponding lmax value
Input is \f$ \hat{r}_z \f$ which is the $z$-component of the bond direction.
For each \f$ \hat{r}_z \f$, this computes the whole range of \f$ \bar{P}_{lm} \f$ values
and its derivatives upto the lmax specified, which is a member of the class.
@param rz, DOUBLE_TYPE
@returns None
*/
void compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi);
/**
Function that computes \f$ Y_{lm} \f$ for the corresponding lmax value
Input is the bond-directon vector \f$ \hat{r}_x, \hat{r}_y, \hat{r}_z \f$
Each \f$ Y_{lm} \f$ value is a ACEComplex object with real and imaginary parts. This function also
finds the derivatives, which are stored in the Dycomponent class, with each component being a
ACEComplex object.
@param rx, DOUBLE_TYPE
@param ry, DOUBLE_TYPE
@param rz, DOUBLE_TYPE
@param lmaxi, int
*/
void compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi);
Array2DLM<DOUBLE_TYPE> alm;
Array2DLM<DOUBLE_TYPE> blm;
Array1D<DOUBLE_TYPE> cl;
Array1D<DOUBLE_TYPE> dl;
Array2DLM<DOUBLE_TYPE> plm;
Array2DLM<DOUBLE_TYPE> dplm;
Array2DLM<ACEComplex> ylm; ///< Values of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call
Array2DLM<ACEDYcomponent> dylm;///< Values of gradients of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call
};
#endif

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 19.02.20.
#ifndef ACE_TIMING_H
#define ACE_TIMING_H
#include <chrono>
using namespace std::chrono;
using Clock = std::chrono::high_resolution_clock;
using TimePoint = std::chrono::time_point<Clock>;
using Duration = Clock::duration;
//////////////////////////////////////////
#ifdef FINE_TIMING
/**
* Helper class for timing the code.
* The timer should be initialized to reset measured time and
* then call "start" and "stop" before and after measured code.
* The measured time is stored in "duration" variable
*/
struct ACETimer {
Duration duration; ///< measured duration
TimePoint start_moment; ///< start moment of current measurement
ACETimer() { init(); };
/**
* Reset timer
*/
void init() { duration = std::chrono::nanoseconds(0); }
/**
* Start timer
*/
void start() { start_moment = Clock::now(); }
/**
* Stop timer, update measured "duration"
*/
void stop() { duration += Clock::now() - start_moment; }
/**
* Get duration in microseconds
*/
long as_microseconds() { return std::chrono::duration_cast<std::chrono::microseconds>(duration).count(); }
/**
* Get duration in nanoseconds
*/
long as_nanoseconds() { return std::chrono::duration_cast<std::chrono::nanoseconds>(duration).count(); }
};
#else // EMPTY Definitions
/**
* Helper class for timing the code.
* The timer should be initialized to reset measured time and
* then call "start" and "stop" before and after measured code.
* The measured time is stored in "duration" variable
*/
struct ACETimer {
Duration duration; ///< measured duration
TimePoint start_moment; ///< start moment of current measurement
ACETimer() {};
/**
* Reset timer
*/
void init() {}
/**
* Start timer
*/
void start() {}
/**
* Stop timer, update measured "duration"
*/
void stop() {}
/**
* Get duration in microseconds
*/
long as_microseconds() {return 0; }
/**
* Get duration in nanoseconds
*/
long as_nanoseconds() {return 0; }
};
#endif
//////////////////////////////////////////
#endif //ACE_TIMING_H

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Yury Lysogorskiy on 20.01.20.
#ifndef ACE_TYPES_H
#define ACE_TYPES_H
typedef char RANK_TYPE;
typedef int SPECIES_TYPE;
typedef short int NS_TYPE;
typedef short int LS_TYPE;
typedef short int DENSITY_TYPE;
typedef short int MS_TYPE;
typedef short int SHORT_INT_TYPE;
typedef double DOUBLE_TYPE;
#endif

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Lysogorskiy Yury on 07.04.2020.
#ifndef ACE_VERSION_H
#define ACE_VERSION_H
#define VERSION_YEAR 2021
#define VERSION_MONTH 2
#define VERSION_DAY 3
#endif //ACE_VERSION_Hls

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/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Christoph Ortner on 03.06.2020
#include "ships_radial.h"
#include <functional>
#include <cmath>
#include <string>
using namespace std;
void SHIPsRadPolyBasis::_init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut,
DOUBLE_TYPE xl, DOUBLE_TYPE xr,
int pl, int pr, size_t maxn) {
this->p = p;
this->r0 = r0;
this->rcut = rcut;
this->xl = xl;
this->xr = xr;
this->pl = pl;
this->pr = pr;
this->maxn = maxn;
this->A.resize(maxn);
this->B.resize(maxn);
this->C.resize(maxn);
this->P.resize(maxn);
this->dP_dr.resize(maxn);
}
void SHIPsRadPolyBasis::fread(FILE *fptr)
{
int res; //for fscanf result
int maxn, p, pl, pr, ntests;
double r0, xl, xr, a, b, c, rcut;
// transform parameters
res = fscanf(fptr, "transform parameters: p=%d r0=%lf\n", &p, &r0);
if (res != 2)
throw invalid_argument("Couldn't read line: transform parameters: p=%d r0=%lf");
// cutoff parameters
res = fscanf(fptr, "cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d\n",
&rcut, &xl, &xr, &pl, &pr);
if (res != 5)
throw invalid_argument("Couldn't read cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d");
// basis size
res = fscanf(fptr, "recursion coefficients: maxn = %d\n", &maxn);
if (res != 1)
throw invalid_argument("Couldn't read recursion coefficients: maxn = %d");
// initialize and allocate
this->_init(r0, p, rcut, xl, xr, pl, pr, maxn);
// read basis coefficients
for (int i = 0; i < maxn; i++) {
res = fscanf(fptr, " %lf %lf %lf\n", &a, &b, &c);
if (res != 3)
throw invalid_argument("Couldn't read line: A_n B_n C_n");
this->A(i) = DOUBLE_TYPE(a);
this->B(i) = DOUBLE_TYPE(b);
this->C(i) = DOUBLE_TYPE(c);
}
// // check there are no consistency tests (I don't have time to fix this now)
// res = fscanf(fptr, "tests: ntests = %d\n", &ntests);
// if (res != 1)
// throw invalid_argument("Couldn't read line: tests: ntests = %d");
// if (ntests != 0)
// throw invalid_argument("must have ntests = 0!");
// ---------------------------------------------------------------------
// run the consistency test this could be moved into a separate function
double r, Pn, dPn;
double err = 0.0;
res = fscanf(fptr, "tests: ntests = %d\n", &ntests);
if (res != 1)
throw invalid_argument("Couldn't read line: tests: ntests = %d");
for (size_t itest = 0; itest < ntests; itest++) {
// read an r argument
res = fscanf(fptr, " r=%lf\n", &r);
// printf("r = %lf \n", r);
if (res != 1)
throw invalid_argument("Couldn't read line: r=%lf");
// printf("test %d, r=%f, maxn=%d \n", itest, r, maxn);
// evaluate the basis
this->calcP(r, maxn, SPECIES_TYPE(0), SPECIES_TYPE(0));
// compare against the stored values
for (size_t n = 0; n < maxn; n++) {
res = fscanf(fptr, " %lf %lf\n", &Pn, &dPn);
if (res != 2)
throw invalid_argument("Couldn't read test value line: %lf %lf");
err = max(err, abs(Pn - this->P(n)) + abs(dPn - this->dP_dr(n)));
// printf(" %d %e %e \n", int(n),
// abs(Pn - this->P(n)),
// abs(dPn - this->dP_dr(n)));
}
}
if (ntests > 0)
printf("Maximum Test error = %e\n", err);
// ---------------------------------------------------------------------
}
size_t SHIPsRadPolyBasis::get_maxn()
{
return this->maxn;
}
// Julia code: ((1+r0)/(1+r))^p
void SHIPsRadPolyBasis::transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const {
x_out = pow((1 + r0) / (1 + r), p); // ==pow( (1 + r) / (1 + r0), -p );
dx_out = -p * pow((1 + r) / (1 + r0), -p - 1) / (1 + r0);
}
void SHIPsRadPolyBasis::fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const {
if ( ((x < xl) && (pl > 0)) || ((x > xr) && (pr > 0)) ) {
f_out = 0.0;
df_out = 0.0;
} else {
f_out = pow(x - xl, pl) * pow(x - xr, pr);
df_out = pl * pow(x - xl, pl - 1) * pow(x - xr, pr) + pow(x - xl, pl) * pr * pow(x - xr, pr - 1);
}
}
/* ------------------------------------------------------------------------
Julia Code
P[1] = J.A[1] * _fcut_(J.pl, J.tl, J.pr, J.tr, t)
if length(J) == 1; return P; end
P[2] = (J.A[2] * t + J.B[2]) * P[1]
@inbounds for n = 3:length(J)
P[n] = (J.A[n] * t + J.B[n]) * P[n-1] + J.C[n] * P[n-2]
end
return P
------------------------------------------------------------------------ */
void SHIPsRadPolyBasis::calcP(DOUBLE_TYPE r, size_t maxn,
SPECIES_TYPE z1, SPECIES_TYPE z2) {
if (maxn > this->maxn)
throw invalid_argument("Given maxn couldn't be larger than global maxn");
if (maxn > P.get_size())
throw invalid_argument("Given maxn couldn't be larger than global length of P");
DOUBLE_TYPE x, dx_dr; // dx -> dx/dr
transform(r, x, dx_dr);
// printf("r = %f, x = %f, fcut = %f \n", r, x, fcut(x));
DOUBLE_TYPE f, df_dx;
fcut(x, f, df_dx); // df -> df/dx
//fill with zeros
P.fill(0);
dP_dr.fill(0);
P(0) = A(0) * f;
dP_dr(0) = A(0) * df_dx * dx_dr; // dP/dr; chain rule: df_cut/dr = df_cut/dx * dx/dr
if (maxn > 0) {
P(1) = (A(1) * x + B(1)) * P(0);
dP_dr(1) = A(1) * dx_dr * P(0) + (A(1) * x + B(1)) * dP_dr(0);
}
for (size_t n = 2; n < maxn; n++) {
P(n) = (A(n) * x + B(n)) * P(n - 1) + C(n) * P(n - 2);
dP_dr(n) = A(n) * dx_dr * P(n - 1) + (A(n) * x + B(n)) * dP_dr(n - 1) + C(n) * dP_dr(n - 2);
}
}
// ====================================================================
bool SHIPsRadialFunctions::has_pair() {
return this->haspair;
}
void SHIPsRadialFunctions::load(string fname) {
FILE * fptr = fopen(fname.data(), "r");
size_t res = fscanf(fptr, "radbasename=ACE.jl.Basic\n");
if (res != 0)
throw("SHIPsRadialFunctions::load : couldnt read radbasename=ACE.jl.Basic");
this->fread(fptr);
fclose(fptr);
}
void SHIPsRadialFunctions::fread(FILE *fptr){
int res;
size_t maxn;
char hasE0, haspair;
DOUBLE_TYPE c;
// check whether we have a pair potential
res = fscanf(fptr, "haspair: %c\n", &haspair);
if (res != 1)
throw("SHIPsRadialFunctions::load : couldn't read haspair");
// read the radial basis
this->radbasis.fread(fptr);
// read the pair potential
if (haspair == 't') {
this->haspair=true;
fscanf(fptr, "begin repulsive potential\n");
fscanf(fptr, "begin polypairpot\n");
// read the basis parameters
pairbasis.fread(fptr);
maxn = pairbasis.get_maxn();
// read the coefficients
fscanf(fptr, "coefficients\n");
paircoeffs.resize(maxn);
for (size_t n = 0; n < maxn; n++) {
fscanf(fptr, "%lf\n", &c);
paircoeffs(n) = c;
}
fscanf(fptr, "end polypairpot\n");
// read the spline parameters
fscanf(fptr, "spline parameters\n");
fscanf(fptr, " e_0 + B exp(-A*(r/ri-1)) * (ri/r)\n");
fscanf(fptr, "ri=%lf\n", &(this->ri));
fscanf(fptr, "e0=%lf\n", &(this->e0));
fscanf(fptr, "A=%lf\n", &(this->A));
fscanf(fptr, "B=%lf\n", &(this->B));
fscanf(fptr, "end repulsive potential\n");
}
}
size_t SHIPsRadialFunctions::get_maxn()
{
return this->radbasis.get_maxn();
}
DOUBLE_TYPE SHIPsRadialFunctions::get_rcut()
{
return max(radbasis.rcut, pairbasis.rcut);
}
void SHIPsRadialFunctions::fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) {
radbasis.calcP(r, maxn, z1, z2);
for (NS_TYPE n = 0; n < maxn; n++) {
gr(n) = radbasis.P(n);
dgr(n) = radbasis.dP_dr(n);
}
}
void SHIPsRadialFunctions::fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) {
radbasis.calcP(r, maxn, z1, z2);
for (NS_TYPE n = 0; n < maxn; n++) {
for (LS_TYPE l = 0; l <= lmax; l++) {
fr(n, l) = radbasis.P(n);
dfr(n, l) = radbasis.dP_dr(n);
}
}
}
void SHIPsRadialFunctions::setuplookupRadspline() {
}
void SHIPsRadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins,
SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff, string radbasename) {
//mimic ACERadialFunctions::init
this->nradbase = nradb;
this->lmax = lmax;
this->nradial = nradial;
this->deltaSplineBins = deltaSplineBins;
this->nelements = nelements;
this->cutoff = cutoff;
this->radbasename = radbasename;
gr.init(nradbase, "gr");
dgr.init(nradbase, "dgr");
fr.init(nradial, lmax + 1, "fr");
dfr.init(nradial, lmax + 1, "dfr");
splines_gk.init(nelements, nelements, "splines_gk");
splines_rnl.init(nelements, nelements, "splines_rnl");
splines_hc.init(nelements, nelements, "splines_hc");
lambda.init(nelements, nelements, "lambda");
lambda.fill(1.);
cut.init(nelements, nelements, "cut");
cut.fill(1.);
dcut.init(nelements, nelements, "dcut");
dcut.fill(1.);
crad.init(nelements, nelements, (lmax + 1), nradial, nradbase, "crad");
crad.fill(0.);
//hard-core repulsion
prehc.init(nelements, nelements, "prehc");
prehc.fill(0.);
lambdahc.init(nelements, nelements, "lambdahc");
lambdahc.fill(1.);
}
void SHIPsRadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i,
SPECIES_TYPE mu_j, bool calc_second_derivatives) {
if (calc_second_derivatives)
throw invalid_argument("SHIPsRadialFunctions has not `calc_second_derivatives` option");
radbasis.calcP(r, nradbase_c, mu_i, mu_j);
for (NS_TYPE nr = 0; nr < nradbase_c; nr++) {
gr(nr) = radbasis.P(nr);
dgr(nr) = radbasis.dP_dr(nr);
}
for (NS_TYPE nr = 0; nr < nradial_c; nr++) {
for (LS_TYPE l = 0; l <= this->lmax; l++) {
fr(nr, l) = radbasis.P(nr);
dfr(nr, l) = radbasis.dP_dr(nr);
}
}
if (this->has_pair())
this->evaluate_pair(r, mu_i, mu_j);
else {
cr = 0;
dcr = 0;
}
}
void SHIPsRadialFunctions::evaluate_pair(DOUBLE_TYPE r,
SPECIES_TYPE mu_i,
SPECIES_TYPE mu_j,
bool calc_second_derivatives) {
// spline_hc.calcSplines(r);
// cr = spline_hc.values(0);
// dcr = spline_hc.derivatives(0);
// the outer polynomial potential
if (r > ri) {
pairbasis.calcP(r, pairbasis.get_maxn(), mu_i, mu_j);
cr = 0;
dcr = 0;
for (size_t n = 0; n < pairbasis.get_maxn(); n++) {
cr += paircoeffs(n) * pairbasis.P(n);
dcr += paircoeffs(n) * pairbasis.dP_dr(n);
}
}
else { // the repulsive core part
cr = e0 + B * exp(-A * (r/ri - 1)) * (ri/r);
dcr = B * exp( - A * (r/ri-1) ) * ri * ( - A / ri / r - 1/(r*r) );
}
// fix double-counting
cr *= 0.5;
dcr *= 0.5;
}

158
lib/pace/ships_radial.h Normal file
View File

@ -0,0 +1,158 @@
/*
* Performant implementation of atomic cluster expansion and interface to LAMMPS
*
* Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
* Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
* Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
*
* ^1: Ruhr-University Bochum, Bochum, Germany
* ^2: University of Cambridge, Cambridge, United Kingdom
* ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
* ^4: University of British Columbia, Vancouver, BC, Canada
*
*
* See the LICENSE file.
* This FILENAME is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
// Created by Christoph Ortner on 03.06.2020
#ifndef SHIPs_RADIAL_FUNCTIONS_H
#define SHIPs_RADIAL_FUNCTIONS_H
#include "ace_arraynd.h"
#include "ace_types.h"
#include "ace_radial.h"
class SHIPsRadPolyBasis {
public:
// transform parameters
int p = 0;
DOUBLE_TYPE r0 = 0.0;
// cutoff parameters
DOUBLE_TYPE rcut = 0.0;
DOUBLE_TYPE xl = 0.0;
DOUBLE_TYPE xr = 0.0;
int pl = 0;
int pr = 0;
// basis size
size_t maxn = 0;
// recursion parameters
Array1D<DOUBLE_TYPE> A = Array1D<DOUBLE_TYPE>("SHIPs radial basis: A");
Array1D<DOUBLE_TYPE> B = Array1D<DOUBLE_TYPE>("SHIPs radial basis: B");
Array1D<DOUBLE_TYPE> C = Array1D<DOUBLE_TYPE>("SHIPs radial basis: C");
// temporary storage for evaluating the basis
Array1D<DOUBLE_TYPE> P = Array1D<DOUBLE_TYPE>("SHIPs radial basis: P");
Array1D<DOUBLE_TYPE> dP_dr = Array1D<DOUBLE_TYPE>("SHIPs radial basis: dP");
//////////////////////////////////
SHIPsRadPolyBasis() = default;
~SHIPsRadPolyBasis() = default;
// distance transform
void transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const;
// cutoff function
void fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const;
void fread(FILE *fptr);
void _init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut,
DOUBLE_TYPE xl, DOUBLE_TYPE xr,
int pl, int pr, size_t maxn);
void calcP(DOUBLE_TYPE r, size_t maxn, SPECIES_TYPE z1, SPECIES_TYPE z2);
size_t get_maxn();
};
class SHIPsRadialFunctions : public AbstractRadialBasis {
public:
// radial basis
SHIPsRadPolyBasis radbasis;
// pair potential basis
bool haspair = false;
SHIPsRadPolyBasis pairbasis;
// pair potential coefficients
Array1D<DOUBLE_TYPE> paircoeffs = Array1D<DOUBLE_TYPE>("SHIPs pairpot coeffs: paircoeffs");
// spline parameters for repulsive core
DOUBLE_TYPE ri = 0.0;
DOUBLE_TYPE e0 = 0.0;
DOUBLE_TYPE A = 0.0;
DOUBLE_TYPE B = 0.0;
//////////////////////////////////
SHIPsRadialFunctions() = default;
~SHIPsRadialFunctions() override = default;
void fread(FILE *fptr);
void load(string fname);
size_t get_maxn();
DOUBLE_TYPE get_rcut();
bool has_pair();
void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements,
DOUBLE_TYPE cutoff,
string radbasename) override;
void
evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j,
bool calc_second_derivatives = false) override;
void
evaluate_pair(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j,
bool calc_second_derivatives = false);
void setuplookupRadspline() override;
SHIPsRadialFunctions *clone() const override {
return new SHIPsRadialFunctions(*this);
};
/**
* Helper method, that populate `fr` and `dfr` 2D-arrays (n,l) with P(n), dP_dr for given coordinate r
* @param r
* @param maxn
* @param z1
* @param z2
*/
void fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2);
void fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2);
};
#endif

4
src/Makefile
View File

@ -63,7 +63,7 @@ PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \
python voronoi \ python voronoi \
user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-plumed user-qmmm user-quip user-scafacos \ user-netcdf user-plumed user-qmmm user-quip user-scafacos \
user-smd user-vtk user-mesont user-smd user-vtk user-mesont user-pace
PACKSYS = compress mpiio python user-lb PACKSYS = compress mpiio python user-lb
@ -71,7 +71,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont
PACKEXT = kim latte mscg voronoi \ PACKEXT = kim latte mscg voronoi \
user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \
user-smd user-vtk user-smd user-vtk user-pace
PACKALL = $(PACKAGE) $(PACKUSER) PACKALL = $(PACKAGE) $(PACKUSER)

68
src/USER-PACE/Install.sh Normal file
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@ -0,0 +1,68 @@
# Install.sh file that integrates the settings from the lib folder into the conventional build process (make build?)
# COPIED FROM src/KIM/Install.sh:
# # Install/unInstall package files in LAMMPS
# # mode = 0/1/2 for uninstall/install/update
# mode=$1
# # enforce using portable C locale
# LC_ALL=C
# export LC_ALL
# # arg1 = file, arg2 = file it depends on
# action () {
# if (test $mode = 0) then
# rm -f ../$1
# elif (! cmp -s $1 ../$1) then
# if (test -z "$2" || test -e ../$2) then
# cp $1 ..
# if (test $mode = 2) then
# echo " updating src/$1"
# fi
# fi
# elif (test -n "$2") then
# if (test ! -e ../$2) then
# rm -f ../$1
# fi
# fi
# }
# # all package files with no dependencies
# for file in *.cpp *.h; do
# test -f ${file} && action $file
# done
# # edit 2 Makefile.package files to include/exclude package info
# if (test $1 = 1) then
# if (test -e ../Makefile.package) then
# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package
# sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kim_SYSINC) |' ../Makefile.package
# sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kim_SYSLIB) |' ../Makefile.package
# sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kim_SYSPATH) |' ../Makefile.package
# fi
# if (test -e ../Makefile.package.settings) then
# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings
# # multiline form needed for BSD sed on Macs
# sed -i -e '4 i \
# include ..\/..\/lib\/kim\/Makefile.lammps
# ' ../Makefile.package.settings
# fi
# elif (test $1 = 0) then
# if (test -e ../Makefile.package) then
# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package
# fi
# if (test -e ../Makefile.package.settings) then
# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings
# fi
# fi

674
src/USER-PACE/LICENSE Normal file
View File

@ -0,0 +1,674 @@
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458
src/USER-PACE/pair_pace.cpp Normal file
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/*
Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
^1: Ruhr-University Bochum, Bochum, Germany
^2: University of Cambridge, Cambridge, United Kingdom
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
^4: University of British Columbia, Vancouver, BC, Canada
This FILENAME is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
//
// Created by Lysogorskiy Yury on 27.02.20.
//
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_pace.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
#include "ace_version.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
//added YL
//keywords for ACE evaluator style
#define RECURSIVE_KEYWORD "recursive"
#define PRODUCT_KEYWORD "product"
int elements_num_pace = 104;
char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na",
"Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn",
"Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr",
"Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb",
"Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd",
"Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir",
"Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th",
"Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr"
};
int AtomicNumberByName_pace(char *elname) {
for (int i = 1; i < elements_num_pace; i++)
if (strcmp(elname, elements_pace[i]) == 0)
return i;
return -1;
}
/* ---------------------------------------------------------------------- */
PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) {
//single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
nelements = 0;
ace = NULL;
potential_file_name = NULL;
elements = NULL;
map = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairPACE::~PairPACE() {
if (copymode) return;
if (elements)
for (int i = 0; i < nelements; i++) delete[] elements[i];
delete[] elements;
delete[] potential_file_name;
delete basis_set;
delete ace;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(map);
memory->destroy(scale);
}
}
/* ---------------------------------------------------------------------- */
void PairPACE::compute(int eflag, int vflag) {
int i, j, ii, jj, inum, jnum;
double delx, dely, delz, evdwl;
double fij[3];
int *ilist, *jlist, *numneigh, **firstneigh;
ev_init(eflag, vflag);
// downwards modified by YL
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *type = atom->type;
// number of atoms in cell
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// number of atoms including ghost atoms
int nall = nlocal + atom->nghost;
// inum: length of the neighborlists list
inum = list->inum;
// ilist: list of "i" atoms for which neighbor lists exist
ilist = list->ilist;
//numneigh: the length of each these neigbor list
numneigh = list->numneigh;
// the pointer to the list of neighbors of "i"
firstneigh = list->firstneigh;
if (inum != nlocal) {
char str[128];
snprintf(str,128,"inum: %d nlocal: %d are different",inum, nlocal);
error->all(FLERR,str);
}
// Aidan Thompson told RD (26 July 2019) that practically always holds:
// inum = nlocal
// i = ilist(ii) < inum
// j = jlist(jj) < nall
// neighborlist contains neighbor atoms plus skin atoms,
// skin atoms can be removed by setting skin to zero but here
// they are disregarded anyway
//determine the maximum number of neighbours
int max_jnum = -1;
int nei = 0;
for (ii = 0; ii < list->inum; ii++) {
i = ilist[ii];
jnum = numneigh[i];
nei = nei + jnum;
if (jnum > max_jnum)
max_jnum = jnum;
}
ace->resize_neighbours_cache(max_jnum);
//loop over atoms
for (ii = 0; ii < list->inum; ii++) {
i = list->ilist[ii];
const int itype = type[i];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// checking if neighbours are actually within cutoff range is done inside compute_atom
// mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom
// by using 'ace->element_type_mapping' array
// x: [r0 ,r1, r2, ..., r100]
// i = 0 ,1
// jnum(0) = 50
// jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total]
try {
ace->compute_atom(i, x, type, jnum, jlist);
} catch (exception &e) {
error->all(FLERR, e.what());
exit(EXIT_FAILURE);
}
// 'compute_atom' will update the `ace->e_atom` and `ace->neighbours_forces(jj, alpha)` arrays
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
const int jtype = type[j];
j &= NEIGHMASK;
delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp;
fij[0] = scale[itype][jtype]*ace->neighbours_forces(jj, 0);
fij[1] = scale[itype][jtype]*ace->neighbours_forces(jj, 1);
fij[2] = scale[itype][jtype]*ace->neighbours_forces(jj, 2);
f[i][0] += fij[0];
f[i][1] += fij[1];
f[i][2] += fij[2];
f[j][0] -= fij[0];
f[j][1] -= fij[1];
f[j][2] -= fij[2];
// tally per-atom virial contribution
if (vflag)
ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0,
fij[0], fij[1], fij[2],
-delx, -dely, -delz);
}
// tally energy contribution
if (eflag) {
// evdwl = energy of atom I
evdwl = scale[1][1]*ace->e_atom;
ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0);
}
}
if (vflag_fdotr) virial_fdotr_compute();
// end modifications YL
}
/* ---------------------------------------------------------------------- */
void PairPACE::allocate() {
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n + 1, n + 1, "pair:setflag");
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
memory->create(map, n + 1, "pair:map");
memory->create(scale, n + 1, n + 1,"pair:scale");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPACE::settings(int narg, char **arg) {
if (narg > 1) {
error->all(FLERR,
"Illegal pair_style command. Correct form:\n\tpair_style pace\nor\n\tpair_style pace ");
error->all(FLERR, RECURSIVE_KEYWORD);
error->all(FLERR, "or\n\tpair_style pace ");
error->all(FLERR, PRODUCT_KEYWORD);
}
recursive = true; // default evaluator style: RECURSIVE
if (narg > 0) {
if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0)
recursive = true;
else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) {
recursive = false;
} else {
error->all(FLERR,
"Illegal pair_style command: pair_style pace ");
error->all(FLERR, arg[0]);
error->all(FLERR, "\nCorrect form:\n\tpair_style pace\nor\n\tpair_style pace recursive");
}
}
if (comm->me == 0) {
if (screen) fprintf(screen, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY);
if (logfile) fprintf(logfile, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY);
if (recursive) {
if (screen) fprintf(screen, "Recursive evaluator is used\n");
if (logfile) fprintf(logfile, "Recursive evaluator is used\n");
} else {
if (screen) fprintf(screen, "Product evaluator is used\n");
if (logfile) fprintf(logfile, "Product evaluator is used\n");
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPACE::coeff(int narg, char **arg) {
if (narg < 4)
error->all(FLERR,
"Incorrect args for pair coefficients. Correct form:\npair_coeff * * <potential.ace> elem1 elem2 ...");
if (!allocated) allocate();
//number of provided elements in pair_coeff line
int ntypes_coeff = narg - 3;
if (ntypes_coeff != atom->ntypes) {
char error_message[1024];
snprintf(error_message, 1024,
"Incorrect args for pair coefficients. You provided %d elements in pair_coeff, but structure has %d atom types",
ntypes_coeff, atom->ntypes);
error->all(FLERR, error_message);
}
char *type1 = arg[0];
char *type2 = arg[1];
char *potential_file_name = arg[2];
char **elemtypes = &arg[3];
// insure I,J args are * *
if (strcmp(type1, "*") != 0 || strcmp(type2, "*") != 0)
error->all(FLERR, "Incorrect args for pair coefficients");
//load potential file
basis_set = new ACECTildeBasisSet();
if (comm->me == 0) {
if (screen) fprintf(screen, "Loading %s\n", potential_file_name);
if (logfile) fprintf(logfile, "Loading %s\n", potential_file_name);
}
basis_set->load(potential_file_name);
if (comm->me == 0) {
if (screen) fprintf(screen, "Total number of basis functions\n");
if (logfile) fprintf(logfile, "Total number of basis functions\n");
for (SPECIES_TYPE mu = 0; mu < basis_set->nelements; mu++) {
int n_r1 = basis_set->total_basis_size_rank1[mu];
int n = basis_set->total_basis_size[mu];
if (screen) fprintf(screen, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n);
if (logfile) fprintf(logfile, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n);
}
}
// read args that map atom types to pACE elements
// map[i] = which element the Ith atom type is, -1 if not mapped
// map[0] is not used
ace = new ACERecursiveEvaluator();
ace->set_recursive(recursive);
ace->element_type_mapping.init(atom->ntypes + 1);
for (int i = 1; i <= atom->ntypes; i++) {
char *elemname = elemtypes[i - 1];
int atomic_number = AtomicNumberByName_pace(elemname);
if (atomic_number == -1) {
char error_msg[1024];
snprintf(error_msg, 1024, "String '%s' is not a valid element\n", elemname);
error->all(FLERR, error_msg);
}
SPECIES_TYPE mu = basis_set->get_species_index_by_name(elemname);
if (mu != -1) {
if (comm->me == 0) {
if (screen)
fprintf(screen, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu);
if (logfile)
fprintf(logfile, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu);
}
map[i] = mu;
ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator
} else {
char error_msg[1024];
snprintf(error_msg, 1024, "Element %s is not supported by ACE-potential from file %s", elemname,
potential_file_name);
error->all(FLERR, error_msg);
}
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
setflag[i][j] = 1;
scale[i][j] = 1.0;
}
}
// set setflag i,j for type pairs where both are mapped to elements
int count = 1;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
ace->set_basis(*basis_set, 1);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPACE::init_style() {
if (atom->tag_enable == 0)
error->all(FLERR, "Pair style pACE requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR, "Pair style pACE requires newton pair on");
// request a full neighbor list
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPACE::init_one(int i, int j) {
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
//cutoff from the basis set's radial functions settings
scale[j][i] = scale[i][j];
return basis_set->radial_functions->cut(map[i], map[j]);
}
/* ----------------------------------------------------------------------
extract method for extracting value of scale variable
---------------------------------------------------------------------- */
void *PairPACE::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"scale") == 0) return (void *) scale;
return NULL;
}

97
src/USER-PACE/pair_pace.h Normal file
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@ -0,0 +1,97 @@
/*
Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
^1: Ruhr-University Bochum, Bochum, Germany
^2: University of Cambridge, Cambridge, United Kingdom
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
^4: University of British Columbia, Vancouver, BC, Canada
This FILENAME is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
//
// Created by Lysogorskiy Yury on 27.02.20.
//
#ifdef PAIR_CLASS
PairStyle(pace,PairPACE)
#else
#ifndef LMP_PAIR_PACE_H
#define LMP_PAIR_PACE_H
#include "pair.h"
#include "ace_evaluator.h"
#include "ace_recursive.h"
#include "ace_c_basis.h"
namespace LAMMPS_NS {
class PairPACE : public Pair {
public:
PairPACE(class LAMMPS *);
virtual ~PairPACE();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
double init_one(int, int);
void *extract(const char *, int &);
// virtual double memory_usage();
protected:
ACECTildeBasisSet *basis_set = nullptr;
ACERecursiveEvaluator *ace = nullptr;
char *potential_file_name;
virtual void allocate();
void read_files(char *, char *);
inline int equal(double *x, double *y);
double rcutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
int *map; // mapping from atom types to elements
int *jlist_local;
int *type_local;
double **scale;
bool recursive = false; // "recursive" option for ACERecursiveEvaluator
};
}
#endif
#endif