Merge pull request #218 from shashikant193/master

ChangeLog

@@ -3,6 +3,13 @@
 -Name
 -changes
 
+--------------
+September 05, 2024
+Name: Shashikant Kumar
+Changes: (doc/, tests/, cyclix/mlff, highT/mlff)
+1. Renamed the cyclix_test, mlff_tests, xc_test, highT_tests folder names to cyclix, mlff, xc, highT
+2. Renamed the Manual for cyclix, highT and mlff and also updated the citations within the manuals
+3. Fixed some python version related bugs in SPARC_testing_script.py
 
 --------------
 September 05, 2024

doc/.LaTeX/Introduction.tex

@@ -12,6 +12,7 @@
     \item Symmetry-adaption for cyclic and/or helical symmetries.
     \item Linear-scaling Spectral Quadrature (SQ) method.
     \item Soft and transferable table of SPMS pseudopotentials.
+    \item On-the-fly machine-learned force field (MLFF) molecular dynamics (MD) simulations.
   \end{itemize}
   % Additional details regarding the formulation and implementation of SPARC can be found in the accompanying paper. Please direct any questions and report any bugs to Prof.~Phanish Suryanarayana.
 
@@ -30,7 +31,7 @@
         \item \textbf{Xin Jing}: Code infrastructure, Hybrid functionals, SOC \\  
  	    \item \textbf{Abhiraj Sharma}: Code infrastructure, k-points, PBE, Stress, Non-orthogonal, Relaxation, NLCC \\   
  	    \item \textbf{Boqin Zhang}: vdW-DF, DFT-D3, meta-GGA (SCAN) \\  
- 	    \item \textbf{Shashikant Kumar}: Testing framework, NLCC \\  
+ 	    \item \textbf{Shashikant Kumar}: Testing framework, NLCC, MLFF \\  
             \item \textbf{Mostafa Faghih Shojaei}: SPMS table of pseudopotentials \\ 
             \item \textbf{Swarnava Ghosh}: Preliminary development \\
             \item \textbf{Deepa Phanish}: Initial development
@@ -54,20 +55,23 @@
 \begin{frame}[allowframebreaks]{\textbf{Citation}} \label{Citation}
 If you publish work using/regarding SPARC, please cite some of the following articles, particularly those that are most relevant to your work:
 \begin{itemize}
-    \item General: \url{https://doi.org/10.1016/j.softx.2021.100709}, \url{https://doi.org/10.1016/j.cpc.2016.09.020}, \url{https://doi.org/10.1016/j.cpc.2017.02.019}
+    \item General: \url{https://doi.org/10.1016/j.simpa.2024.100649} (v2), \url{https://doi.org/10.1016/j.softx.2021.100709} (v1), \url{https://doi.org/10.1016/j.cpc.2016.09.020} (initial developments, isolated systems), \url{https://doi.org/10.1016/j.cpc.2017.02.019} (initial developments, extended systems)
     \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 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}
-    \item Atomic forces: \url{https://doi.org/10.1016/j.cpc.2016.09.020}, \url{https://doi.org/10.1016/j.cpc.2017.02.019}
-    \item Mixing: \url{https://doi.org/10.1016/j.cplett.2016.01.033}, \url{https://doi.org/10.1016/j.cplett.2015.06.029}, \url{https://doi.org/10.1016/j.cplett.2019.136983}
+    \item Atomic forces: \url{https://doi.org/10.1016/j.cpc.2016.09.020} (isolated systems), \url{https://doi.org/10.1016/j.cpc.2017.02.019} (extended systems)
+    \item Mixing: \url{https://doi.org/10.1016/j.cplett.2016.01.033}, \url{https://doi.org/10.1016/j.cplett.2015.06.029} (restarting), \url{https://doi.org/10.1016/j.cplett.2019.136983} (preconditioning)
     \item SPMS pseudopotentials: \url{https://doi.org/10.1016/j.cpc.2022.108594}
     \item Cyclic and/or helical symmetry:
     \url{https://doi.org/10.1103/PhysRevB.103.035101},
-    \url{https://doi.org/10.1103/PhysRevB.100.125143}
+    \url{https://doi.org/10.1103/PhysRevB.100.125143} (initial developments, extended systems),
+    \url{https://doi.org/10.1016/j.jmps.2016.08.007} (initial developments, isolated systems)
     \item O(N) Spectral Quadrature method:
-    \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/10.1016/j.cpc.2015.11.005} (initial implementation),
+    \url{https://doi.org/10.1016/j.cplett.2013.08.035} (formulation),
+    \url{https://doi.org/10.1007/978-3-031-22340-2_12} (detailed mathematical formulation)
+    \item On-the-fly MLFF:
+    \url{https://doi.org/10.1063/5.0180541}, \url{https://doi.org/10.1063/5.0204229} (SQ), \url{https://doi.org/10.48550/arXiv.2408.07554} (Cyclix), \url{https://doi.org/10.48550/arXiv.2407.15290} (internal energy)
 \end{itemize}
 \end{frame}
 

doc/.LaTeX/cyclix/Introduction.tex

@@ -49,8 +49,8 @@
 \begin{frame}[allowframebreaks]{\textbf{Citation}} \label{Citation}
 If you publish work using/regarding SPARC-cyclix, please cite the following article, in addition to SPARC citations:
 \begin{itemize}
-    \item \url{https://doi.org/10.1103/PhysRevB.103.035101}
-    \item Additional references for initial developments: \url{https://doi.org/10.1016/j.jmps.2016.08.007}, \url{https://doi.org/10.1103/PhysRevB.100.125143}
+    \item \url{https://doi.org/10.1103/PhysRevB.103.035101}, \url{https://doi.org/10.1103/PhysRevB.100.125143} (initial developments, extended systems), \url{https://doi.org/10.1016/j.jmps.2016.08.007} (initial developments, isolated systems)
+%    \item Additional references for initial developments: \url{https://doi.org/10.1016/j.jmps.2016.08.007}, \url{https://doi.org/10.1103/PhysRevB.100.125143}
 %    \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/highT/Introduction.tex

@@ -33,11 +33,11 @@
 \begin{frame}[allowframebreaks]{\textbf{Citation}} \label{Citation}
 If you publish work using/regarding SPARC-SQ, please cite the following articles, in addition to SPARC citations:
 \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/10.1063/5.0204229},
-    \url{https://doi.org/10.48550/arXiv.2407.15290}
+    \item \url{https://doi.org/10.1016/j.cpc.2015.11.005} (initial implementation),
+     \url{https://doi.org/10.1016/j.cplett.2013.08.035} (formulation),
+    \url{https://doi.org/10.1007/978-3-031-22340-2_12} (detailed mathematical formulation),
+%    \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

@@ -23,7 +23,7 @@
 \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}, \url{https://doi.org/10.48550/arXiv.2408.07554} (Cyclix-DFT)
+    \item \url{https://doi.org/10.1063/5.0180541}, \url{https://doi.org/10.1063/5.0204229} (SQ), \url{https://doi.org/10.48550/arXiv.2408.07554} (Cyclix), \url{https://doi.org/10.48550/arXiv.2407.15290} (internal energy)
 
 \end{itemize}
 \end{frame}

src/makefile

@@ -33,7 +33,7 @@ ENABLE_SIMD_COMPLEX = 1
 # BLASROOT = /usr/lib64
 # LDFLAGS += -L$(BLASROOT)
 
-CPPFLAGS = -Iinclude/ -Ixc/exx/include -Ixc/vdW/d3/include -Ixc/vdW/vdWDF/include -Ixc/mgga/include -IhighT/include -Icyclix/include -Icyclix/cyclix_mlff -IhighT/mlff_highT -Imlff/
+CPPFLAGS = -Iinclude/ -Ixc/exx/include -Ixc/vdW/d3/include -Ixc/vdW/vdWDF/include -Ixc/mgga/include -IhighT/include -Icyclix/include -Icyclix/mlff -IhighT/mlff -Imlff/
 LDLIBS   = -lrt
 
 ifeq ($(USE_MKL), 1)
@@ -102,7 +102,7 @@ OBJSC = main.o initialization.o readfiles.o atomdata.o parallelization.o relax.o
         cyclix/cyclix_stress.o \
         mlff/covariance_matrix.o mlff/regression.o mlff/spherical_harmonics.o mlff/soap_descriptor.o mlff/sparc_mlff_interface.o \
         mlff/bessel_NR.o mlff/nrutils.o mlff/sparsification.o mlff/tools_mlff.o mlff/mlff_read_write.o \
-        mlff/descriptor.o mlff/ddbp_tools.o highT/mlff_highT/internal_energy_model.o cyclix/cyclix_mlff/cyclix_mlff_tools.o \
+        mlff/descriptor.o mlff/ddbp_tools.o highT/mlff/internal_energy_model.o cyclix/mlff/cyclix_mlff_tools.o \
         mlff/hnl_soap.o
 
 LIBBASE = ../lib/sparc