From e9e0e82c4d7ec400a4797c3b30600d76a9c051ea Mon Sep 17 00:00:00 2001
From: arcan1s <esalexeev@gmail.com>
Date: Sat, 3 Aug 2013 02:09:24 +0400
Subject: [PATCH] Release radf-1.0.1 Edited shared library

---
 agl/src/main.c         | 20 +++++++++++++-------
 agl/src/messages.c     | 11 +++++++++--
 envir/src/main.c       | 22 ++++++++++++++--------
 envir/src/messages.c   | 11 +++++++++--
 radf/src/main.c        | 28 +++++++++++++++++-----------
 radf/src/radf_proc.c   |  5 ++---
 statgen/src/main.c     | 30 +++++++++++++++++++-----------
 statgen/src/messages.c | 11 +++++++++--
 8 files changed, 92 insertions(+), 46 deletions(-)

diff --git a/agl/src/main.c b/agl/src/main.c
index d119947..11831ca 100644
--- a/agl/src/main.c
+++ b/agl/src/main.c
@@ -87,6 +87,7 @@ int main(int argc, char *argv[])
  * @return 1              - error in error_checking
  * @return 2              - input file does not exist
  * @return 3              - memory error
+ * @return 4              - unknown flag
  * @return 0              - exit without errors
  */
 {
@@ -123,7 +124,7 @@ int main(int argc, char *argv[])
   
   for (i=1; i<argc; i++)
   {
-    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
+    if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
       sprintf (tmp_str, "                                        agl\n");
       sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str);
@@ -143,42 +144,47 @@ int main(int argc, char *argv[])
       fputs (tmp_str, stdout);
       return 0;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
 // input file
     {
       strcpy (aglinp, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
 // input file
     {
       strcpy (input, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
 // cell size
     {
       sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {
       strcpy (output, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
 // log mode
     {
       log = 1;
       strcpy (logfile, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
 // quiet mode
     {
       quiet = 1;
     }
+    else
+// unknown flag
+    {
+      return 4;
+    }
   }
   
   if (log == 1)
diff --git a/agl/src/messages.c b/agl/src/messages.c
index de13302..b7b4b3c 100644
--- a/agl/src/messages.c
+++ b/agl/src/messages.c
@@ -21,6 +21,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
  * @param text            additional text
  * @param output          output file (may be stdout)
  * 
+ * @return 1              - unknown mode
  * @return 0              - exit without errors
  */
 {
@@ -40,7 +41,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
   switch (mode)
   {
     case 0:
-      sprintf (out, "Starting program: '%s'\n", text);
+      sprintf (out, "Start program: '%s'\n", text);
       break;
     case 1:
       sprintf (out, "Checking errors\n");
@@ -82,7 +83,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
       sprintf (out, "End of processing\n");
       break;
     case 14:
-      sprintf (out, "Printing summary statistic to file '%s'\n", text);
+      sprintf (out, "Print result to file '%s'\n", text);
       break;
     case 15:
       sprintf (out, "Free memory\n");
@@ -105,6 +106,12 @@ int message (const int log, const int mode, const char *text, FILE *output)
     case 21:
       sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
       break;
+    case 22:
+      sprintf (out, "%6cRADF was appended successfully\n", ' ');
+      break;
+    default:
+      return 1;
+      break;
   }
   
   fputs (out, output);
diff --git a/envir/src/main.c b/envir/src/main.c
index 6fcf7bd..633cd17 100644
--- a/envir/src/main.c
+++ b/envir/src/main.c
@@ -88,6 +88,7 @@ int main(int argc, char *argv[])
  * @return 1              - error in error_checking
  * @return 2              - input file does not exist
  * @return 3              - memory error
+ * @return 4              - unknown flag
  * @return 0              - exit without errors
  */
 {
@@ -125,7 +126,7 @@ int main(int argc, char *argv[])
   
   for (i=1; i<argc; i++)
   {
-    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
+    if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
       sprintf (tmp_str, "                                        envir\n");
       sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
@@ -147,48 +148,53 @@ int main(int argc, char *argv[])
       fputs (tmp_str, stdout);
       return 0;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
 // input file
     {
       strcpy (input, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
 // cell size
     {
       sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {
       strcpy (output, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'n'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'n') && (argv[i][2] == '\0'))
 // number of molecule
     {
       sscanf (argv[i+1], "%i", &num_of_mol);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == '\0'))
 // radius of environment
     {
       sscanf (argv[i+1], "%f", &rad);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
 // log mode
     {
       log = 1;
       strcpy (logfile, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
 // quiet mode
     {
       quiet = 1;
     }
+    else
+// unknown flag
+    {
+      return 4;
+    }
   }
   
   if (log == 1)
diff --git a/envir/src/messages.c b/envir/src/messages.c
index de13302..b7b4b3c 100644
--- a/envir/src/messages.c
+++ b/envir/src/messages.c
@@ -21,6 +21,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
  * @param text            additional text
  * @param output          output file (may be stdout)
  * 
+ * @return 1              - unknown mode
  * @return 0              - exit without errors
  */
 {
@@ -40,7 +41,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
   switch (mode)
   {
     case 0:
-      sprintf (out, "Starting program: '%s'\n", text);
+      sprintf (out, "Start program: '%s'\n", text);
       break;
     case 1:
       sprintf (out, "Checking errors\n");
@@ -82,7 +83,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
       sprintf (out, "End of processing\n");
       break;
     case 14:
-      sprintf (out, "Printing summary statistic to file '%s'\n", text);
+      sprintf (out, "Print result to file '%s'\n", text);
       break;
     case 15:
       sprintf (out, "Free memory\n");
@@ -105,6 +106,12 @@ int message (const int log, const int mode, const char *text, FILE *output)
     case 21:
       sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
       break;
+    case 22:
+      sprintf (out, "%6cRADF was appended successfully\n", ' ');
+      break;
+    default:
+      return 1;
+      break;
   }
   
   fputs (out, output);
diff --git a/radf/src/main.c b/radf/src/main.c
index d85bca0..686dd93 100644
--- a/radf/src/main.c
+++ b/radf/src/main.c
@@ -94,6 +94,7 @@ int main(int argc, char *argv[])
  * @return 1              - error in error_checking
  * @return 2              - input file does not exist
  * @return 3              - memory error
+ * @return 4              - unknown flag
  * @return 0              - exit without errors
  */
 {
@@ -141,7 +142,7 @@ int main(int argc, char *argv[])
   
   for (i=1; i<argc; i++)
   {
-    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
+    if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
       sprintf (tmp_str, "                                        radf\n");
       sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
@@ -171,13 +172,13 @@ int main(int argc, char *argv[])
       fputs (tmp_str, stdout);
       return 0;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
 // input file
     {
       strcpy (input, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
 // steps
     {
       sscanf (argv[i+1], "%i,%i", &from, &to);
@@ -190,13 +191,13 @@ int main(int argc, char *argv[])
       step = to - from + 1;
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
 // cell size
     {
       sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 't'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 't') && (argv[i][3] == '\0'))
 // atom types
     {
       num_needed_at = 2;
@@ -210,7 +211,7 @@ int main(int argc, char *argv[])
                 &needed_at[3], &needed_at[4], &needed_at[5]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {
       strcpy (output, argv[i+1]);
@@ -228,7 +229,7 @@ int main(int argc, char *argv[])
       }
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == 's'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == 's') && (argv[i][3] == '\0'))
 // radius step
     {
       sscanf (argv[i+1], "%f", &r_step);
@@ -246,29 +247,34 @@ int main(int argc, char *argv[])
       }
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 's'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 's') && (argv[i][3] == '\0'))
 // angle step
     {
       sscanf (argv[i+1], "%f", &ang_step);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'm'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'm') && (argv[i][2] == '\0'))
 // matrix mode
     {
       matrix = 1;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
 // log mode
     {
       log = 1;
       strcpy (logfile, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
 // quiet mode
     {
       quiet = 1;
     }
+    else
+// unknown flag
+    {
+      return 4;
+    }
   }
   
   if (log == 1)
diff --git a/radf/src/radf_proc.c b/radf/src/radf_proc.c
index 64c23dd..9c32a3f 100644
--- a/radf/src/radf_proc.c
+++ b/radf/src/radf_proc.c
@@ -117,11 +117,10 @@ int print_result (const char *output, const int matrix, const int mode,
           r = r_min + (0.5 + i) * r_step;
           ang = ang_min + (0.5 + j) * ang_step;
           dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * r_step * (M_PI * ang_step / 180);
-//           dv = 4;
           ro = num_atoms  / (3 * 2 * cell[0] * cell[1] * cell[2]);
-          norm = radf[i] / (dv * ro * num_atoms / 3 * step);
+          norm = radf[n*i+j] / (dv * ro * num_atoms / 3 * step);
           if (matrix == 0)
-            fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[i] / 2, norm);
+            fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[n*i+j] / 2, norm);
           else
             fprintf (f_out, " %9.6f", norm);
         }
diff --git a/statgen/src/main.c b/statgen/src/main.c
index 9bbd6cc..a9f35b5 100644
--- a/statgen/src/main.c
+++ b/statgen/src/main.c
@@ -93,6 +93,7 @@ int main (int argc, char *argv[])
  * @return 1              - error in error_checking
  * @return 2              - input file does not exist
  * @return 3              - memory error
+ * @return 4              - unknown flag
  * @return 0              - exit without errors
  */
 {
@@ -142,11 +143,13 @@ int main (int argc, char *argv[])
   
 // reading number of interactions
   for (i=1; i<argc; i++)
-    if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
+    if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == '\0'))
       num_of_inter++;
   if (num_of_inter > 0)
   {
     crit = (float *) malloc ( 16 * num_of_inter * sizeof (float));
+    if (crit == NULL)
+      return 3;
     for (i=0; i<16*num_of_inter; i++)
       crit[i] = 0.0;
     num_of_inter = 0;
@@ -155,7 +158,7 @@ int main (int argc, char *argv[])
 // reading arguments
   for (i=1; i<argc; i++)
   {
-    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
+    if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
     {
       sprintf (tmp_str, "                                        statgen\n");
       sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
@@ -180,13 +183,13 @@ int main (int argc, char *argv[])
       fputs (tmp_str, stdout);
       return 0;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
 // mask of input files
     {
       strcpy (input, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
 // steps
     {
       sscanf (argv[i+1], "%i,%i", &from, &to);
@@ -199,13 +202,13 @@ int main (int argc, char *argv[])
       step = to - from + 1;
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
 // cell size
     {
       sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
 // atom types
     {
       type_inter = 1;
@@ -234,7 +237,7 @@ int main (int argc, char *argv[])
       
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == '\0'))
 // criteria
     {
       index = 0;
@@ -253,30 +256,35 @@ int main (int argc, char *argv[])
       num_of_inter++;
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
 // output file
     {
       strcpy (output, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'g'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'g') && (argv[i][2] == '\0'))
 // graph isomorphism scan
     {
       sscanf (argv[i+1], "%i", &max_depth);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
 // log mode
     {
       log = 1;
       strcpy (logfile, argv[i+1]);
       i++;
     }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
 // quiet mode
     {
       quiet = 1;
     }
+    else
+// unknown flag
+    {
+      return 4;
+    }
   }
   
   if (log == 1)
diff --git a/statgen/src/messages.c b/statgen/src/messages.c
index de13302..b7b4b3c 100644
--- a/statgen/src/messages.c
+++ b/statgen/src/messages.c
@@ -21,6 +21,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
  * @param text            additional text
  * @param output          output file (may be stdout)
  * 
+ * @return 1              - unknown mode
  * @return 0              - exit without errors
  */
 {
@@ -40,7 +41,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
   switch (mode)
   {
     case 0:
-      sprintf (out, "Starting program: '%s'\n", text);
+      sprintf (out, "Start program: '%s'\n", text);
       break;
     case 1:
       sprintf (out, "Checking errors\n");
@@ -82,7 +83,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
       sprintf (out, "End of processing\n");
       break;
     case 14:
-      sprintf (out, "Printing summary statistic to file '%s'\n", text);
+      sprintf (out, "Print result to file '%s'\n", text);
       break;
     case 15:
       sprintf (out, "Free memory\n");
@@ -105,6 +106,12 @@ int message (const int log, const int mode, const char *text, FILE *output)
     case 21:
       sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
       break;
+    case 22:
+      sprintf (out, "%6cRADF was appended successfully\n", ' ');
+      break;
+    default:
+      return 1;
+      break;
   }
   
   fputs (out, output);