Merge pull request #6 from david-c-miller/development

Development - Update to Version 0.2.0

.gitignore

@@ -29,3 +29,4 @@
 *.app
 
 bin/*
+test-output/*

Makefile

@@ -24,6 +24,14 @@
 
 include makefile.include
 
+#############################################
+#            VERSION (DO NOT EDIT)          #
+#############################################
+#                                           #
+FLAGS_BASE += -DVERSION='"0.2.0"'           #
+#                                           #
+#############################################
+
 #########################
 #   Local Directories   #
 #########################
@@ -45,14 +53,6 @@ BINC=$(CC)
 BINSUFFIX=$(CSUFFIX)
 BINFLAGS=$(CFLAGS)
 
-####################################
-#       VERSION (DO NOT EDIT)      #
-####################################
-#                                  #
-FLAGS_BASE += -DVERSION='"0.1.0"'  #
-#                                  #
-####################################
-
 OFLAG=$(OFLAG_DEBUG)
 #specific flags
 CFLAGS=$(CFLAGS_DEBUG)

README.md

@@ -11,13 +11,15 @@ Department of Physics and Astronomy
 ## Quick Install:
 
 Try the following:
+
 + change INSTALLDIR (typically a folder in PATH like /usr/local/bin)
   - this is defined in makefile.include or can be passed through make 
 + `make install`
   - this will run `make reset`, `make all`, and then install the binary files in
   the INSTALLDIR 
 
 Other options:
+
 + `make dir`
   - run this or manually make the necessary directories (./bin and ./obj) 
 + `make final`
@@ -31,8 +33,8 @@ Other options:
 + `make uninstall`
   - removes binary files from INSTALLDIR (whether linked or copied)
 
-You may need to run any of the above as root depending on 
-local folder privileges.
+You may need to run any of the above as root depending on local folder
+privileges.
 
 ## Information
 
@@ -157,7 +159,13 @@ delete all built files including the binary files.
 ### Git repository
 
 This code is available at:
-https://github.com/david-c-miller/cdw-unit-cell-generator.git
+[repository](https://github.com/david-c-miller/cdw-unit-cell-generator)
+
+For update to date releases see:
+[releases](https://github.com/david-c-miller/cdw-unit-cell-generator/releases)
+
+For other information go to:
+[cdw-unit-cell-generator](https://david-c-miller.github.io/cdw-unit-cell-generator/)
 
 ### Disclaimer
 

inc/header.h

@@ -53,36 +53,52 @@ static const double PI = 3.1415926535;
 static const double EPS = 10E-5;
 
 /* make sites */
-void make_m_site(Location atoms_m[], unsigned num, double orig_lattice[3],\
-	       int supercell[2][2], int randomize, int inversion, unsigned layers);
-void make_x_site(Location atomsX[], unsigned num, double orig_lattice[3],\
-	       int supercell[2][2], int inversion, unsigned layers);
+void make_m_site(Location atoms_m[], const unsigned num, double orig_lattice[3],\
+		 int supercell[2][2], const int randomize, const int inversion,\
+		 const unsigned layers);
+void make_x_site(Location atomsX[], const unsigned num, double orig_lattice[3],\
+		 int supercell[2][2], const int inversion, const unsigned layers);
 
 /* output */
-void print_vasp(Location loc_m[], Location loc_x[], unsigned n,\
-	       double lattice[3][3], char * name, char * elem_m, char * elem_x)\
-  __attribute((deprecated)); /* this function should not be used anymore */
-
 void print_vasp_to_file(Location loc_m[], Location loc_x[], unsigned n,\
 			double lattice[3][3], char * name, char * elem_m,\
 			char * elem_x, char * file_name);
 
-void print_xyz(Location loc_m[], Location loc_x[], unsigned n);
+void print_xyz_to_file(Location loc_m[], Location loc_x[], unsigned n,\
+		       char * filename) __attribute__((deprecated));
+
+/* these functions should not be used anymore */
+void print_vasp(Location loc_m[], Location loc_x[], unsigned n,\
+	       double lattice[3][3], char * name, char * elem_m, char * elem_x)\
+  __attribute__((deprecated)); 
+void print_xyz(Location loc_m[], Location loc_x[], unsigned n)\
+  __attribute__((deprecated));
+
 void print_help();
+void print_version();
+void print_test_start();
 
 /* fractional coordinate generation */
-void generate_frac_coord(double frac_loc[][3], unsigned num,\
-		       int supercell[2][2]);
+void generate_frac_coord(double frac_loc[][3], const unsigned num,\
+			 int supercell[2][2]);
 
 /* structure generation functions */
 int make_structure(double orig_lattice[3], int supercell[2][2],\
-		  int inversion, int randomize, unsigned layers,\
-		  AtomicSymbol elem_m, AtomicSymbol elem_x, int strained,\
-		  int strain_axis[3], int strain_min, int strain_max);
+		   const int inversion, const int randomize, const unsigned layers, \
+		   const AtomicSymbol elem_m, const AtomicSymbol elem_x,\
+		   const int strained, int strain_axis[3], const int strain_min, \
+		   const int strain_max);
 
+/* additional functions used throughout the code */
 double get_lattice_vector_angle(const int a, const int b);
 
 double dtor(double deg) __attribute__ ((const));
 int atob(char a) __attribute__ ((pure));
+
+/* test suite related functions */
+void test_print_vasp_monolayer();
+void test_print_vasp_bulk();
+void test_print_xyz_monolayer();
+void test_print_xyz_bulk();
 
 #endif

makefile.include

@@ -32,7 +32,8 @@ CC=gcc
 #debug flags are used by default
 #use make final to use the final flags
 FLAGS_BASE=-I$(IDIR) -I$(SDIR) -Wall -Wextra -pedantic\
-	-Werror -Wno-error=unused-parameter -Wno-error=unused-variable
+	-Werror -Wno-error=unused-parameter -Wno-error=unused-variable\
+	-Wno-error=pedantic
 #-ansi
 OFLAG_DEBUG=-O0 -g3 -pg $(WARN_FLAG)
 #-fpack-struct=4
@@ -98,7 +99,7 @@ _BIN = generateTMDSuperCell
 _DEPS = elements.h header.h
 
 #object (.o) files to be built
-_COBJ = tmd_functions.o printing.o fractional.o atomic_sites.o structure.o
+_COBJ = tmd_functions.o printing.o fractional.o atomic_sites.o structure.o testing.o
 
 #change to the local of desired installation (default is /usr/local/bin)
 INSTALLDIR:=/mnt/home/mill2723/local/bin

script-test-output.sh

@@ -1,8 +1,9 @@
 #!/bin/bash
 
 cd test-output
-../bin/generateTMDSuperCell 10 10 1 0 0 1 0 F F 1 2
-../bin/generateTMDSuperCell 10 10 1 0 0 1 1 F F 1 2
+../bin/generateTMDSuperCell -t
 
-../bin/generateTMDSuperCell 10 10 1 0 0 1 0 T F 1 2
-../bin/generateTMDSuperCell 10 10 1 0 0 1 1 T F 1 2
+# check with diff if the test files generated are the same
+# as the provided and verified files
+
+# need to make the verified files

src/atomic_sites.c

@@ -48,15 +48,16 @@
   which holds an x, y, and z coordinate along with the atomic symbol) size num
  */
 void make_m_site\
-(Location atoms_m[], unsigned num, double orig_lattice[3],\
- int supercell[2][2], int randomize, int inversion, unsigned layers)
+(Location atoms_m[], const unsigned num, double orig_lattice[3],\
+ int supercell[2][2], const int randomize, const int inversion,\
+ const unsigned layers)
 {
   /* used for randomization of coordinates */
   double r1 = 0, r2 = 0;
   /* scale of randomization (default is 3%) */
   double scale = orig_lattice[0] * 0.03;
 
-  unsigned n;
+  unsigned ii;
 
    /* fractional location of atom within supercell */
   double (*frac_loc)[3];
@@ -66,7 +67,7 @@ void make_m_site\
   generate_frac_coord(frac_loc, num, supercell);
 
   srand((unsigned)(time(NULL)));
-  for (n = 0; n < num; n++)
+  for (ii = 0; ii < num; ii++)
     {
       if (randomize)
 	{
@@ -86,50 +87,50 @@ void make_m_site\
       if (!(inversion) && !(layers == 1))
 	{
 	  /* itr 0 */
-	  atoms_m[n].x = (frac_loc[n][0] * orig_lattice[0])\
-	    - (frac_loc[n][1]*0.5*orig_lattice[0]) + r1;
+	  atoms_m[ii].x = (frac_loc[ii][0] * orig_lattice[0])\
+	    - (frac_loc[ii][1]*0.5*orig_lattice[0]) + r1;
 
-	  atoms_m[n].y = (sqrt(3.0)*0.5*frac_loc[n][1] * orig_lattice[1]) +r2;
+	  atoms_m[ii].y = (sqrt(3.0)*0.5*frac_loc[ii][1] * orig_lattice[1]) +r2;
 
-	  atoms_m[n].z = 0.25 * orig_lattice[2];
+	  atoms_m[ii].z = 0.25 * orig_lattice[2];
 
 	  /* itr 1 */
-	  atoms_m[n+num].x = (frac_loc[n][0] * orig_lattice[0])\
-	    - (frac_loc[n][1]*0.5*orig_lattice[0]) + r1;
+	  atoms_m[ii+num].x = (frac_loc[ii][0] * orig_lattice[0])\
+	    - (frac_loc[ii][1]*0.5*orig_lattice[0]) + r1;
 
-	  atoms_m[n+num].y = (sqrt(3.0)*0.5*frac_loc[n][1] * orig_lattice[1]) +r2; 
+	  atoms_m[ii+num].y = (sqrt(3.0)*0.5*frac_loc[ii][1] * orig_lattice[1]) +r2; 
 
-	  atoms_m[n+num].z = 0.75 * orig_lattice[2];
+	  atoms_m[ii+num].z = 0.75 * orig_lattice[2];
 	}
       else
 	{
-	  atoms_m[n].x =  (frac_loc[n][0] * orig_lattice[0])\
-	    - (frac_loc[n][1]*0.5*orig_lattice[0]) + r1;
+	  atoms_m[ii].x =  (frac_loc[ii][0] * orig_lattice[0])\
+	    - (frac_loc[ii][1]*0.5*orig_lattice[0]) + r1;
 
-	  atoms_m[n].y = (sqrt(3.0)*0.5*frac_loc[n][1] * orig_lattice[1]) +r2;
+	  atoms_m[ii].y = (sqrt(3.0)*0.5*frac_loc[ii][1] * orig_lattice[1]) +r2;
 
-	  atoms_m[n].z = 0.5 * orig_lattice[2];
+	  atoms_m[ii].z = 0.5 * orig_lattice[2];
 	}
     }
 
   free (frac_loc);
 }/* end of makeMSite(...) */
 
 void make_x_site
-(Location atomsX[], unsigned num, double orig_lattice[3],\
- int supercell[2][2], int inversion, unsigned layers)
+(Location atomsX[], const unsigned num, double orig_lattice[3],\
+ int supercell[2][2], const int inversion, const unsigned layers)
 {
   /* correction vector for displacement of X atoms relative to M sites */
   double correction[2][2];
 
-  unsigned n;
+  unsigned ii;
   /* fractional location of atom within supercell */
   double (*frac_loc)[3];
 
   frac_loc = malloc(sizeof(double[3])*num);
   generate_frac_coord(frac_loc, num, supercell);
 
-  for (n = 0; n < num; n++)
+  for (ii = 0; ii < num; ii++)
     {
       /* generates the correction vectors for 1T and 2H phases */
       if (inversion)
@@ -150,54 +151,54 @@ void make_x_site
       if (!(inversion) && !(layers == 1))
 	{
 	  /* itr = 0 */
-	  atomsX[n].x =	((frac_loc[n][0] + correction[0][0]) * orig_lattice[0])\
-	    - ((frac_loc[n][1] + correction[0][1])*0.5*orig_lattice[0]);
+	  atomsX[ii].x =	((frac_loc[ii][0] + correction[0][0]) * orig_lattice[0])\
+	    - ((frac_loc[ii][1] + correction[0][1])*0.5*orig_lattice[0]);
 
-	  atomsX[n].y = (frac_loc[n][1] + correction[0][1])\
+	  atomsX[ii].y = (frac_loc[ii][1] + correction[0][1])\
 	    *sqrt(3)*0.5*orig_lattice[1];
 
-	  atomsX[n].z = 0.125 * orig_lattice[2];
+	  atomsX[ii].z = 0.125 * orig_lattice[2];
 
 	  /* itr = 1 */
-	  atomsX[n+num].x = ((frac_loc[n][0] + correction[1][0]) * orig_lattice[0]) \
-	    - ((frac_loc[n][1] + correction[1][1])*0.5*orig_lattice[0]);
+	  atomsX[ii+num].x = ((frac_loc[ii][0] + correction[1][0]) * orig_lattice[0]) \
+	    - ((frac_loc[ii][1] + correction[1][1])*0.5*orig_lattice[0]);
 
-	  atomsX[n+num].y = (frac_loc[n][1] + correction[1][1])\
+	  atomsX[ii+num].y = (frac_loc[ii][1] + correction[1][1])\
 	    *sqrt(3)*0.5*orig_lattice[1];
 
-	  atomsX[n+num].z = 0.375 * orig_lattice[2];
+	  atomsX[ii+num].z = 0.375 * orig_lattice[2];
 
 	  /* itr = 2 */
-	  atomsX[n+2*num].x = ((frac_loc[n][0] - correction[0][0]) * orig_lattice[0])\
-	    - ((frac_loc[n][1] - correction[0][1])*0.5*orig_lattice[0]);
+	  atomsX[ii+2*num].x = ((frac_loc[ii][0] - correction[0][0]) * orig_lattice[0])\
+	    - ((frac_loc[ii][1] - correction[0][1])*0.5*orig_lattice[0]);
 
-	  atomsX[n+2*num].y = (frac_loc[n][1] - correction[0][1])\
+	  atomsX[ii+2*num].y = (frac_loc[ii][1] - correction[0][1])\
 	    *sqrt(3)*0.5*orig_lattice[1];
 
-	  atomsX[n+2*num].z = 0.625 * orig_lattice[2];
+	  atomsX[ii+2*num].z = 0.625 * orig_lattice[2];
 
 	  /* itr = 3 */
-	  atomsX[n+3*num].x  = ((frac_loc[n][0] - correction[1][0]) * orig_lattice[0])\
-	    - ((frac_loc[n][1] - correction[1][1])*0.5*orig_lattice[0]);
+	  atomsX[ii+3*num].x  = ((frac_loc[ii][0] - correction[1][0]) * orig_lattice[0])\
+	    - ((frac_loc[ii][1] - correction[1][1])*0.5*orig_lattice[0]);
 
-	  atomsX[n+3*num].y = (frac_loc[n][1] - correction[1][1])\
+	  atomsX[ii+3*num].y = (frac_loc[ii][1] - correction[1][1])\
 	    *sqrt(3)*0.5*orig_lattice[1];
 
-	  atomsX[n+3*num].z = 0.875 * orig_lattice[2];
+	  atomsX[ii+3*num].z = 0.875 * orig_lattice[2];
 	}
       else
 	{
 	  /* itr = 0 */
-	  atomsX[n].x = ((frac_loc[n][0] + correction[0][0]) * orig_lattice[0])\
-	    - ((frac_loc[n][1] + correction[0][1])*0.5*orig_lattice[0]);
-	  atomsX[n].y = (frac_loc[n][1] + correction[0][1]) * sqrt(3)*0.5*orig_lattice[1];
-	  atomsX[n].z = 0.75 * orig_lattice[2];
+	  atomsX[ii].x = ((frac_loc[ii][0] + correction[0][0]) * orig_lattice[0])\
+	    - ((frac_loc[ii][1] + correction[0][1])*0.5*orig_lattice[0]);
+	  atomsX[ii].y = (frac_loc[ii][1] + correction[0][1]) * sqrt(3)*0.5*orig_lattice[1];
+	  atomsX[ii].z = 0.75 * orig_lattice[2];
 
 	  /* itr = 1 */
-	  atomsX[n+num].x = ((frac_loc[n][0] + correction[1][0]) * orig_lattice[0]) \
-	    - ((frac_loc[n][1] + correction[1][1])*0.5*orig_lattice[0]);
-	  atomsX[n+num].y = (frac_loc[n][1] + correction[1][1]) * sqrt(3)*0.5*orig_lattice[1];
-	  atomsX[n+num].z = 0.25 * orig_lattice[2];
+	  atomsX[ii+num].x = ((frac_loc[ii][0] + correction[1][0]) * orig_lattice[0]) \
+	    - ((frac_loc[ii][1] + correction[1][1])*0.5*orig_lattice[0]);
+	  atomsX[ii+num].y = (frac_loc[ii][1] + correction[1][1]) * sqrt(3)*0.5*orig_lattice[1];
+	  atomsX[ii+num].z = 0.25 * orig_lattice[2];
 	}
 
     }

src/fractional.c

@@ -43,7 +43,7 @@
  */
 
 void generate_frac_coord\
-(double frac_loc[][3], unsigned num, int supercell[2][2])
+(double frac_loc[][3], const unsigned num, int supercell[2][2])
 {
   unsigned xmax = 0, ymax = 0, count = 0, ix, jy, kk;
   double min_angle;