Refactoring variable names for clarity.

CMakeLists.txt

@@ -1,6 +1,7 @@
 cmake_minimum_required(VERSION 3.1)
 project(TCC)
-message(STATUS "Is CMAKE INSTALL PREFIX deafult? :${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}")
+message(STATUS "CMAKE_INSTALL_PREFIX = ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "Is CMAKE_INSTALL_PREFIX set to its default value?: ${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}")
 message(STATUS "The source directory of CMAKE: ${CMAKE_SOURCE_DIR}")
 IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
     SET(CMAKE_INSTALL_PREFIX ${CMAKE_SOURCE_DIR}/bin)

inc/globals.h

@@ -20,8 +20,8 @@ extern int* cluster_list_width[]; // A list of pointers to the "m" storage width
 
 
 struct xyz_info {
-    int total_frames;
-    int data_width;
+    long total_frames;
+    long max_frames;
     long *num_particles;
     long *frame_offsets;
 };

inc/setup.h

@@ -15,7 +15,7 @@ void free_frame_variables();
 
 void analyse_cluster_dependencies();
 
-void setup_cluster_lists();
+void validate_cluster_lists();
 
 void print_version_number();
 

inc/version.h

@@ -3,6 +3,6 @@
 
 #define TCC_VERSION_MAJOR  1
 #define TCC_VERSION_MINOR  0
-#define TCC_VERSION_PATCH  3
+#define TCC_VERSION_PATCH  4
 
 #endif

src/input.c

@@ -8,7 +8,7 @@ void read_ini_file() {
 
     char errMsg[1000];
     dictionary  *   ini ;
-    const char *inputfilename = "inputparameters.ini";
+    const char *input_file_name = "inputparameters.ini";
 
     fXmolName = malloc(500 * sizeof(char)); 
     if (fXmolName==NULL) {
@@ -19,9 +19,9 @@ void read_ini_file() {
         Error_no_free("Initialise_Global_Variables(): fBoxSizeName[] malloc out of memory\n"); 
     }
 
-    ini = iniparser_load(inputfilename);
+    ini = iniparser_load(input_file_name);
     if (ini==NULL) {
-        sprintf(errMsg,"read_ini_file(): Error opening file %s", inputfilename);
+        sprintf(errMsg,"read_ini_file(): Error opening file %s", input_file_name);
         Error_no_free(errMsg);
     }
 
@@ -243,60 +243,59 @@ struct xyz_info parse_xyz_file() {
 
     char line[1000];
     char error_message[100];
-    int i;
-    int line_number;
+    int line_number = 0;
     int valid_long = 0;
-    FILE *xyzfile;
-    struct xyz_info input_xyz_info;
-
-    line_number = 0;
+    FILE *xyz_file;
+    struct xyz_info xyz_info;
 
-    initialize_xyz_info(&input_xyz_info);
+    initialize_xyz_info(&xyz_info);
 
-    xyzfile=fopen(fXmolName,"rb");    // open xmol trajecotry
-    if (xyzfile==NULL)  {
-        sprintf(error_message,"Error opening XYZ file %s",fXmolName);    // Always test file open
+    // Open the source XYZ file
+    xyz_file = fopen(fXmolName, "rb");
+    if (xyz_file == NULL) {
+        sprintf(error_message, "Error opening XYZ file %s", fXmolName);
         Error_no_free(error_message);
     }
 
-    while(feof(xyzfile) == 0) {
-        // Read in num particles
-        if(input_xyz_info.total_frames > 1000) {
-            Error_no_free("XYZ file has over 1000 frames, cannot process XYZ file");
+    while(feof(xyz_file) == 0) {
+        if(xyz_info.total_frames > xyz_info.max_frames) {
+            sprintf(error_message, "XYZ file has over %li frames, cannot process XYZ file", xyz_info.max_frames);
+            Error_no_free(error_message);
         }
+        // Read in num particles
         line[0] = '\n';
-        fgets(line, 1000, xyzfile);
+        fgets(line, 1000, xyz_file);
         if (line[0] != '\n') {
-            input_xyz_info.num_particles[input_xyz_info.total_frames] = get_long_from_string(line, &valid_long);
+            xyz_info.num_particles[xyz_info.total_frames] = get_long_from_string(line, &valid_long);
             if (valid_long != 1) {
-                sprintf(error_message, "Unable to read XYZ file. Expected number of particles on line: %d",
-                        line_number);
+                sprintf(error_message, "Unable to read XYZ file. Expected number of particles on line: %d", line_number);
                 Error_no_free(error_message);
             }
             line_number += 1;
-            input_xyz_info.frame_offsets[input_xyz_info.total_frames] = ftell(xyzfile);
-            for (i = 0; i < input_xyz_info.num_particles[input_xyz_info.total_frames]+1; i++) {
-                if(feof(xyzfile)) {
-                    sprintf(error_message, "Unexpected end of file at line %d. Some particles are missing.",
-                            line_number);
+            // Record where start of frame is
+            xyz_info.frame_offsets[xyz_info.total_frames] = ftell(xyz_file);
+            // Loop through particles checking that each line is valid
+            for (int i = 0; i < xyz_info.num_particles[xyz_info.total_frames] + 1; i++) {
+                if(feof(xyz_file)) {
+                    sprintf(error_message, "Unexpected end of file at line %d. Some particles are missing.", line_number);
                     Error_no_free(error_message);
                 }
-                try_read_line_from_file(xyzfile);
+                try_read_line_from_file(xyz_file);
                 line_number += 1;
 
             }
-            input_xyz_info.total_frames += 1;
+            xyz_info.total_frames += 1;
         }
     }
-    fclose(xyzfile);
-    return input_xyz_info;
+    fclose(xyz_file);
+    return xyz_info;
 }
 
 void initialize_xyz_info(struct xyz_info* input_xyz_info) {
     (*input_xyz_info).total_frames = 0;
-    (*input_xyz_info).data_width = 1000;
-    (*input_xyz_info).num_particles = malloc((*input_xyz_info).data_width * sizeof(long));
-    (*input_xyz_info).frame_offsets = malloc((*input_xyz_info).data_width * sizeof(long));
+    (*input_xyz_info).max_frames = 1000;
+    (*input_xyz_info).num_particles = malloc((*input_xyz_info).max_frames * sizeof(long));
+    (*input_xyz_info).frame_offsets = malloc((*input_xyz_info).max_frames * sizeof(long));
 }
 
 void free_xyz_info(struct xyz_info* input_xyz_info) {

src/main.c

@@ -75,7 +75,7 @@ int main(int argc, char **argv) {
     struct xyz_info input_xyz_info;
 
     print_version_number();
-    setup_cluster_lists();
+    validate_cluster_lists();
     read_ini_file();
     read_clusters_to_analyse();
     analyse_cluster_dependencies();

src/setup.c

@@ -291,15 +291,20 @@ void analyse_cluster_dependencies() {
     if(dosp4 == 1) dosp3 = 1;
 
 }
+//!  Check whether the cluster lists are valid.
+/*!
+*  Counts the number of clusters in the cluster_names at the beginning of
+*  the main function and then checks if the rest of the lists are this length.
+*/
+void validate_cluster_lists() {
 
-void setup_cluster_lists() {
     num_cluster_types = 0;
 
     while(strcmp(cluster_names[num_cluster_types], "-1") != 0) {
         if (strcmp(cluster_names[num_cluster_types], "11A") == 0) {
             eleven_A_number = num_cluster_types;
         }
-        else if (strcmp(cluster_names[num_cluster_types], "11A") == 0) {
+        else if (strcmp(cluster_names[num_cluster_types], "13A") == 0) {
             thirteen_A_number = num_cluster_types;
         }
         num_cluster_types += 1;
@@ -325,5 +330,6 @@ void setup_cluster_lists() {
 }
 
 void print_version_number() {
-    printf("The Topological Cluster Classification. Version %d.%d.%d.\n", TCC_VERSION_MAJOR, TCC_VERSION_MINOR, TCC_VERSION_PATCH);
+    printf("The Topological Cluster Classification. Version %d.%d.%d.\n",
+            TCC_VERSION_MAJOR, TCC_VERSION_MINOR, TCC_VERSION_PATCH);
 }

src/tools.c

@@ -54,7 +54,8 @@ double get_double_from_string(const char *buff, int *validDouble) {
 }
 
 int try_read_line_from_file(FILE *file_name) {
-    // Try to read a line from a file. If line successfuly read return 1 else return 0.
+    // Try to read a line from a file. If line successfully read return 1,
+    // else return 0.
     char line[1000];
     size_t line_length;