Merge pull request #197 from xuqimen/master

ChangeLog

@@ -3,6 +3,17 @@
 -Name
 -changes
 
+--------------
+Sep 22, 2023
+Name: Qimen Xu, Ziao Tang, Yu Zhang
+Changes: (eigenSolver.c, electronicGroundState.c, initialization.c, occupation.c, orbitalElecDensInit.c, printing.c, readfiles.c, isddft.h, readfiles.h, utils/)
+1. Add band structure calculation feature.
+2. Add `readDens_cube` routine for reading input density file.
+3. Fix memory leak issues:
+(a) when ixc[2] is nonzero, countPotentialCalculate is not initialized,
+(b) EigenFilename is not initialized on processes with rank > 0.
+4. Add a python script in `utils/` for processing `.eigen` files and visualizing the band structure of a given system.
+
 --------------
 Sep 18, 2023
 Name: Xin Jing

doc/.LaTeX/BandStructure.tex

@@ -0,0 +1,153 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[allowframebreaks,c]{} \label{BandStructure}
+
+\begin{center}
+\Huge \textbf{Band structure}
+\end{center}
+
+\end{frame}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[allowframebreaks]{\texttt{BAND\_STRUCTURE}} \label{BAND_STRUCTURE}
+\vspace*{-12pt}
+\begin{columns}
+\column{0.4\linewidth}
+\begin{block}{Type}
+Integer
+\end{block}
+
+\begin{block}{Default}
+0
+\end{block}
+
+\column{0.4\linewidth}
+\begin{block}{Unit}
+No unit
+\end{block}
+
+\begin{block}{Example}
+\texttt{BAND\_STRUCTURE}: 1
+\end{block}
+\end{columns}
+
+\begin{block}{Description}
+Flag for calculation of the band structure.
+\end{block}
+
+%\begin{block}{Remark}
+%\end{block}
+
+\end{frame}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[allowframebreaks]{\texttt{KPT\_PATHS}} \label{KPT_PATHS}
+\vspace*{-12pt}
+\begin{columns}
+\column{0.4\linewidth}
+\begin{block}{Type}
+Double
+\end{block}
+
+\begin{block}{Default}
+None
+\end{block}
+
+\column{0.5\linewidth}
+\begin{block}{Unit}
+No unit
+\end{block}
+
+\begin{block}{Example}
+\texttt{KPT\_PATHS: 2\\}
+0.0 0.0 0.0 \# Gamma\\
+0.5 0.5 0.5 \# A\\
+0.5 0.5 0.5 \# A\\
+0.5 0.5 0.0 \# M
+\end{block}
+\end{columns}
+
+\begin{block}{Description}
+The k-point paths (high-symmetry lines) for band structure calculations.  It starts with the total number of high-symmetry lines, followed by fractional coordinates indicating the start and end points of each line.
+\end{block}
+
+\end{frame}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[allowframebreaks]{\texttt{KPT\_PER\_LINE}} \label{KPT_PER_LINE}
+\vspace*{-12pt}
+\begin{columns}
+\column{0.4\linewidth}
+\begin{block}{Type}
+Integer
+\end{block}
+
+\begin{block}{Default}
+10
+\end{block}
+
+\column{0.4\linewidth}
+\begin{block}{Unit}
+No unit
+\end{block}
+
+\begin{block}{Example}
+\texttt{KPT\_PER\_LINE}: 15
+\end{block}
+\end{columns}
+
+\begin{block}{Description}
+The number of k-points on each high-symmetry line.
+\end{block}
+
+\begin{block}{Remark}
+This value accounts for both endpoints of the high-symmetry line.
+\end{block}
+
+\end{frame}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[allowframebreaks]{\texttt{INPUT\_DENS\_FILE}} \label{INPUT_DENS_FILE}
+\vspace*{-12pt}
+\begin{columns}
+\column{0.4\linewidth}
+\begin{block}{Type}
+String
+\end{block}
+
+\begin{block}{Default}
+None
+\end{block}
+
+\column{0.4\linewidth}
+\begin{block}{Unit}
+No unit
+\end{block}
+
+\begin{block}{Example}
+\texttt{INPUT\_DENS\_FILE}: Si.dens Si.densUp Si.densDwn
+\end{block}
+\end{columns}
+
+\begin{block}{Description}
+The name of the input density file(s) in cube format. 
+\end{block}
+
+\begin{block}{Remark}
+For spin-unpolarized systems, only the total density file is required. For spin-polarized systems, three density files are required, which are the total electron density, spin-up density, and spin-down density, respectively.
+\end{block}
+
+\end{frame}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

doc/.LaTeX/Introduction.tex

@@ -361,6 +361,14 @@
   \hyperlink{FIRE_MAXMOV}{\texttt{FIRE\_MAXMOV}} $\vert$
   \hyperlink{RESTART_FLAG}{\texttt{RESTART\_FLAG}}
   \end{block}
+
+  \vspace{-2mm}
+  \begin{block}{Band structure}
+  \hyperlink{BAND_STRUCTURE}{\texttt{BAND\_STRUCTURE}} $\vert$
+  \hyperlink{KPT_PATHS}{\texttt{KPT\_PATHS}} $\vert$
+  \hyperlink{KPT_PER_LINE}{\texttt{KPT\_PER\_LINE}} $\vert$
+  \hyperlink{INPUT_DENS_FILE}{\texttt{INPUT\_DENS\_FILE}}
+  \end{block}
 
   \begin{block}{Print options}
   \hyperlink{PRINT_ATOMS}{\texttt{PRINT\_ATOMS}} $\vert$

doc/.LaTeX/Manual.tex

@@ -97,6 +97,7 @@
 \include{Stress}
 \include{MD}
 \include{Optimization}
+\include{BandStructure}
 \include{Print}
 \include{Paral}
 \include{SQ}

doc/.LaTeX/SCF.tex

@@ -86,7 +86,7 @@
 \end{block}
 
 \begin{block}{Default}
-4 or 6
+4, 6, or 10
 \end{block}
 
 \column{0.4\linewidth}
@@ -105,7 +105,7 @@
 
 \begin{block}{Remark}
 Values smaller than the default value of 4 can result in a significant increase in the number of SCF
-iterations. Larger values can sometimes reduce the number of SCF iterations. For non-collinear spin calculation, default is 6 otherwise 4.
+iterations. Larger values can sometimes reduce the number of SCF iterations. For non-collinear spin calculation, default is 6 otherwise 4. For band structure calculations, default is 10.
 \end{block}
 
 \end{frame}

src/eigenSolver.c

@@ -2385,4 +2385,4 @@ void Chol_orth(double *A, const int *descA, double *z, const int *descz, const i
     pdpotrf_("U", n, z, &ONE, &ONE, descz, &info);  
     pdtrsm_("R", "U", "N", "N", m, n, &alpha, z, &ONE, &ONE, descz, A, &ONE, &ONE, descA);
 #endif //(#ifdef USE_MKL)    
-}
+}

src/electronicGroundState.c

@@ -1267,7 +1267,7 @@ void Transfer_Veff_loc(SPARC_OBJ *pSPARC, double *Veff_phi_domain, double *Veff_
     if (rank == 0) printf("---Transfer Veff_loc: mpi_bcast (count = %d) to all bandcomms took %.3f ms\n",pSPARC->Nd_d_dmcomm,(t2-t1)*1e3);
 #endif
 
-    if ((pSPARC->countPotentialCalculate > 1) && (pSPARC->ixc[2]))
+    if ((pSPARC->ixc[2]) && (pSPARC->countPotentialCalculate > 1))
         Transfer_vxcMGGA3_phi_psi(pSPARC, pSPARC->vxcMGGA3, pSPARC->vxcMGGA3_loc_dmcomm); // only transfer the potential they are going to use
 }
 

src/include/isddft.h

@@ -29,7 +29,8 @@
 #define L_STRING 512
 #define L_ATMTYPE 8
 #define L_QMASS  60
-
+// max length of kpoint set
+#define L_kpoint 512
 
 // TO PRINT IN COLOR
 #define RED   "\x1B[31m"
@@ -972,6 +973,18 @@ typedef struct _SPARC_OBJ{
 
     /* EigenValue problem*/
     int StandardEigenFlag;
+
+    /* Band structure plot*/
+    int n_kpt_line;
+    double kredx[L_kpoint],kredy[L_kpoint],kredz[L_kpoint];
+    double k1_inpt_kpt[L_kpoint],k2_inpt_kpt[L_kpoint],k3_inpt_kpt[L_kpoint];
+    int BandStructFlag;
+    int kpt_per_line;
+    char InDensTCubFilename[L_STRING];
+    char InDensUCubFilename[L_STRING];
+    char InDensDCubFilename[L_STRING]; 
+    int densfilecount;
+
 }SPARC_OBJ;
 
 
@@ -1229,6 +1242,16 @@ typedef struct _SPARC_INPUT_OBJ{
 
     char SPARCROOT[L_STRING]; // SPARC root directory
 
+
+    /* Band structure plot*/
+    int n_kpt_line;
+    double kredx[L_kpoint],kredy[L_kpoint],kredz[L_kpoint];
+    int BandStructFlag;
+    int kpt_per_line;
+    char InDensTCubFilename[L_STRING];
+    char InDensUCubFilename[L_STRING];
+    char InDensDCubFilename[L_STRING]; 
+    int densfilecount;
 }SPARC_INPUT_OBJ;
 
 

src/include/readfiles.h

@@ -52,6 +52,28 @@ void read_ion(SPARC_INPUT_OBJ *pSPARC_Input, SPARC_OBJ *pSPARC);
 void read_pseudopotential_PSP(SPARC_INPUT_OBJ *pSPARC_Input, SPARC_OBJ *pSPARC);
 
 
+/**
+ * @brief Read density in cube format.
+ * 
+ * @param filename Name of the density file in cube format.
+ * @param dens_gridsizes (OUTPUT) Grid sizes (in 3-dim) of the density read.
+ * @param dens_latvecs (OUTPUT) Lattice vectors (scaled) read.
+ * @return double* (OUTPUT) Density array.
+ */
+double* readDens_cube(char *filename, int dens_gridsizes[3], double dens_latvecs[9]);
+
+
+/**
+ * @brief Read data from cube file and check if the lattice vectors
+ * and the grid sizes match with the input lattice and grid.
+ * 
+ * @param pSPARC 
+ * @param filename File name of the cube file.
+ * @return double* Data from file, allocated within this function.
+ */
+double* read_vec_cube(SPARC_OBJ *pSPARC, char *filename);
+
+
 #endif // READFILES_H
 
 

src/include/tools.h

@@ -65,6 +65,31 @@ int strcmpi(const char *p1, const char *p2);
 void simplifyPath(char* path, char *newpath, size_t newlen);
 
 
+
+/**
+ * @brief Exact file path from a file name.
+ * 
+ * @param filename File name.
+ * @param path (OUTPUT) Path (relative or absolute) where the file is located.
+ * @param maxlen Maximum length of the path.
+ */
+void extract_path_from_file(const char *filename, char *path, int maxlen);
+
+
+/**
+ * @brief Combine a path and a file name and simplify the path.
+ *        
+ * If the file name is already provided in the absolute path form, then
+ * path is ignored. Otherwise, the new file name would be a simplified path
+ * equivalent to "path/fname".
+ * 
+ * @param path The path relative to which fname is given.
+ * @param fname The name provided relative to path.
+ * @param newfname (OUTPUT) The new file name.
+ */
+void combine_path_filename(const char *path, const char *fname, char *newfname, int maxlen);
+
+
 /**
  * @brief   The following code for factorizing an integer is copied from Rosetta Code
  *          https://rosettacode.org/wiki/Factors_of_an_integer#C . It is only used when