Added on-the-fly MLFF

ChangeLog

@@ -3,6 +3,22 @@
 -Name
 -changes
 
+
+--------------
+August 11, 2024
+Name: Shashikant Kumar
+Changes: (mlff/, cyclix/, highT/, readfiles.c, initialization.c, md.c, tests/)
+1. Add on-the-fly MLFF MD feature
+2. Add SOAP descriptor
+3. Enable running MLFF-MD from a trained model, restart of on-the-fly MLFF model
+4. Enable MLFF for orthogonal, non-orthogonal unit cells
+5. Enable MLFF for all boundary conditions including cyclix
+6. Internal energy model based on linear regression
+7. Added MLFF manual
+8. Added MLFF tests
+9. Put tests for mlff, highT, and xc (mgga, exx, vdW) in separate folders in tests
+
+
 --------------
 June 24, 2024
 Name: Xin Jing

doc/.LaTeX/highT/Introduction.tex

@@ -35,7 +35,9 @@
 \begin{itemize}
     \item \url{https://doi.org/10.1016/j.cpc.2015.11.005},
      \url{https://doi.org/10.1016/j.cplett.2013.08.035},
-    \url{https://doi.org/10.1007/978-3-031-22340-2_12}
+    \url{https://doi.org/10.1007/978-3-031-22340-2_12},
+    \url{https://doi.org/10.1063/5.0204229},
+    \url{https://doi.org/10.48550/arXiv.2407.15290}
 %    \item Non-orthogonal systems: \url{https://doi.org/10.1016/j.cplett.2018.04.018}
 %    \item Linear solvers: \url{https://doi.org/10.1016/j.cpc.2018.07.007},    \url{https://doi.org/10.1016/j.jcp.2015.11.018}
 %    \item Stress tensor/pressure: \url{https://doi.org/10.1063/1.5057355}

doc/.LaTeX/mlff/Introduction.tex

@@ -0,0 +1,77 @@
+
+
+\begin{frame}[allowframebreaks]{\textbf{Contributors}} \label{Contributors}
+  %\begin{itemize}
+      %\item U.S. Department of Energy, Office of Science: DE-SC0019410
+      %\item U.S. National Science Foundation: 1333500 and 1553212
+  %\end{itemize}
+
+	\begin{itemize}
+	\item \textbf{Phanish Suryanarayana} (PI)
+	\begin{itemize}
+ 	    \item \textbf{Shashikant Kumar}: Code infrastructure, SOAP, Bayesian linear regression, UQ \\    
+ 	    \item \textbf{Abhiraj Sharma}: Boundary conditions, cyclix MLFF \\  
+ 	\end{itemize}
+  \item \textbf{Andrew J. Medford} (co-PI)
+  \item \textbf{John E. Pask} (co-PI)
+
+ 	\end{itemize}
+
+\end{frame}
+
+
+\begin{frame}[allowframebreaks]{\textbf{Citation}} \label{Citation}
+If you publish work using/regarding MLFF in SPARC, please cite some of the following articles, particularly those that are most relevant to your work:
+\begin{itemize}
+    \item \url{https://doi.org/10.1063/5.0180541}
+
+\end{itemize}
+\end{frame}
+
+
+\begin{frame}[allowframebreaks]{\textbf{Acknowledgements}} \label{Acknowledgements}
+\begin{itemize}
+    \item \textbf{U.S. Department of Energy, Office of Science: DE-SC0023445 
+        } \\
+\end{itemize}
+\end{frame}
+
+
+\begin{frame}[allowframebreaks]{\textbf{Comments}} \label{Introduction}
+The code will fail with the following options and the related input options are listed.
+\begin{itemize}
+  \item Relaxation algorithms specified using: \texttt{RELAX\_FLAG}
+\end{itemize}
+
+\end{frame}
+
+\begin{frame}[allowframebreaks]{\textbf{Input file options}} \label{Index}
+\vspace{-2mm}
+ \begin{block}{MLFF}
+\hyperlink{MLFF_FLAG}{\texttt{MLFF\_FLAG}} $\vert$
+%\hyperlink{MLFF_KERNEL_TYP}{\texttt{MLFF\_KERNEL\_TYP}} $\vert$ 
+%\hyperlink{MLFF_DESCRIPTOR_TYPE}{\texttt{MLFF\_DESCRIPTOR\_TYPE}} $\vert$
+\hyperlink{MLFF_RCUT_SOAP}{\texttt{MLFF\_RCUT\_SOAP}} $\vert$
+\hyperlink{MLFF_RADIAL_BASIS}{\texttt{MLFF\_RADIAL\_BASIS}} $\vert$ 
+%\hyperlink{MLFF_RADIAL_MIN}{\texttt{MLFF\_RADIAL\_MIN}} $\vert$
+%\hyperlink{MLFF_RADIAL_MAX}{\texttt{MLFF\_RADIAL\_MAX}} $\vert$
+\hyperlink{MLFF_ANGULAR_BASIS}{\texttt{MLFF\_ANGULAR\_BASIS}} $\vert$ 
+\hyperlink{MLFF_INITIAL_STEPS_TRAIN}{\texttt{MLFF\_INITIAL\_STEPS\_TRAIN}} $\vert$ 
+%\hyperlink{MLFF_hnl_FILE}{\texttt{MLFF\_hnl\_FILE}} $\vert$ 
+\hyperlink{MLFF_MODEL_FOLDER}{\texttt{MLFF\_MODEL\_FOLDER}} $\vert$ 
+\hyperlink{MLFF_IF_ATOM_DATA_AVAILABLE}{\texttt{MLFF\_IF\_ATOM\_DATA\_AVAILABLE}}  $\vert$ 
+\hyperlink{MLFF_REGUL_MIN}{\texttt{MLFF\_REGUL\_MIN}} $\vert$
+\hyperlink{MLFF_MAX_STR_STORE}{\texttt{MLFF\_MAX\_STR\_STORE}} $\vert$ 
+\hyperlink{MLFF_MAX_CONFIG_STORE}{\texttt{MLFF\_MAX\_CONFIG\_STORE}} $\vert$ 
+%\hyperlink{MLFF_WT_THREE_BODY_SOAP}{\texttt{MLFF\_WT\_THREE\_BODY\_SOAP}} $\vert$
+\hyperlink{MLFF_FACTOR_MULTIPLY_SIGMATOL}{\texttt{MLFF\_FACTOR\_MULTIPLY\_SIGMATOL}} $\vert$
+\hyperlink{MLFF_IF_SPARSIFY_BEFORE_TRAIN}{\texttt{MLFF\_IF\_SPARSIFY\_BEFORE\_TRAIN}} $\vert$
+\hyperlink{MLFF_EXPONENT_SOAP}{\texttt{MLFF\_EXPONENT\_SOAP}} $\vert$
+%\hyperlink{MLFF_TOL_FORCE}{\texttt{MLFF\_TOL\_FORCE}} $\vert$
+\hyperlink{MLFF_SCALE_FORCE}{\texttt{MLFF\_SCALE\_FORCE}} $\vert$
+\hyperlink{MLFF_SCALE_STRESS}{\texttt{MLFF\_SCALE\_STRESS}}
+\hyperlink{MLFF_PRINT_FLAG}{\texttt{MLFF\_PRINT\_FLAG}} $\vert$
+\hyperlink{MLFF_DFT_FQ}{\texttt{MLFF\_DFT\_FQ}} $\vert$ 
+\end{block}
+
+\end{frame}

doc/.LaTeX/mlff/Manual_mlff.tex

@@ -0,0 +1,73 @@
+\documentclass[xcolor=dvipsnames,t]{beamer}
+%\usepackage[utf8]{inputenc}
+\usepackage{verbatim} % for comment
+\usetheme{Madrid}
+\usecolortheme{seahorse}
+\usepackage{beamerouterthemesplit}
+\usepackage[T1]{fontenc}
+
+\setbeamerfont{institute}{size=\normalsize}
+
+\title[] {SPARC - MLFF \\ {\normalsize Machine-learned force fields} \\ {\small User guide}}
+%\author{}
+%\author{Qimen Xu, Abhiraj Sharma, Phanish Suryanarayana, }
+
+\institute[]
+{
+Material Physics \& Mechanics Group \\
+PI: Phanish Suryanarayana \\
+%Main Developers: Shashikant Kumar, Abhiraj Sharma\\
+%Collaborators: J.E. Pask (LLNL)\\
+Georgia Institute of Technology \\
+\hyperlink{Contributors}{Contributors}\\
+\hyperlink{Citation}{Citation} \\
+\hyperlink{Acknowledgements}{Acknowledgements}
+}
+
+\date{}
+\setbeamertemplate{frametitle continuation}{}
+\setbeamertemplate{navigation symbols}{}
+\setbeamercolor{block title}{bg=Apricot!50,fg=black}
+%\addtobeamertemplate{block begin}{\vskip -\smallskipamount}{}
+%\addtobeamertemplate{block end}{}{\vskip -\smallskipamount}
+\addtobeamertemplate{block begin}{\vspace*{-0.6pt}}{}
+\addtobeamertemplate{block end}{}{\vspace*{-0.6pt}}
+\hypersetup{colorlinks,
+citecolor=violet,
+linkcolor=blue,
+menucolor=white, 
+anchorcolor=yellow
+filecolor=pink,  
+}
+
+
+\setbeamertemplate{footline}{
+    \hbox{%
+    \begin{beamercolorbox}[wd=\paperwidth,ht=1ex,dp=1.5ex,leftskip=2ex,rightskip=2ex]{page footer}%
+        \usebeamerfont{title in head/foot}%
+        \insertshorttitle \hfill
+            \insertsection \hfill
+        \insertframenumber{} / \inserttotalframenumber
+    \end{beamercolorbox}}%
+}
+
+\let\otp\titlepage
+\renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}}
+
+
+%\includeonly{Introduction,Stress,MD,Optimization,Print}
+%\includeonly{Introduction}
+
+\begin{document}
+
+%\frame{\titlepage}
+
+\begin{frame}[plain]
+ \titlepage
+\end{frame}
+
+\include{Introduction}
+\include{mlff}
+
+
+\end{document}