refactoring

graph/graph.c

@@ -162,7 +162,14 @@ void main()
 	for (i=0; i<n; i++)
 		p[i] = 0;
 	iso();
-
+    
+    for (i=0; i<n; i++)
+      for (j=0; j<n; j++)
+        printf ("%lf\n", a[i][j]);
+      printf ("\n");
+    for (i=0; i<n; i++)
+      for (j=0; j<n; j++)
+        printf ("%lf\n", b[i][j]);
 
 	for (i=0; i<n; i++)
 		printf ("%i\t", p[i]);
@@ -176,5 +183,5 @@ void main()
 	else
 		printf ("\nGraphs aren't isomorthic.\n");
 	
-	getch();
+// 	getch();
 }

graph/graph.txt

@@ -0,0 +1,8 @@
+3
+0	1	0
+1	0	1
+0	1	0
+
+0	0	1
+0   0   1
+1	1   0

graph/new/graph.c

@@ -0,0 +1,152 @@
+/* Library for check isomorphic graph
+ * 
+ * Usage:
+ *                                           iso_check (number_of_vertex, graph)
+ */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "nrutil.h"
+
+
+int equat (const int num_mol_agl, float *c, const int rang, float *sol)
+{
+  int i, j, k, imax;
+  float max, res;
+  
+  for (i=0; i<num_mol_agl; i++)
+    if (i == rang)
+      c[i*num_mol_agl+num_mol_agl] = 1;
+    else
+      c[i*num_mol_agl+num_mol_agl] = 0;
+  
+  for (i=0; i<num_mol_agl; i++)
+  {
+    imax = 0;
+    max = c[imax*num_mol_agl+i];
+    for (j=i; j<num_mol_agl; j++)
+      if (fabs (c[j*num_mol_agl+i]) > max)
+      {
+        max = fabs (c[j*num_mol_agl+i]);
+        imax = j;
+      }
+    for (j=0; j<=num_mol_agl; j++)
+    {
+      res = c[i*num_mol_agl+j];
+      c[i*num_mol_agl+j] = c[imax*num_mol_agl+j];
+      c[imax*num_mol_agl+j] = res;
+    }
+    
+    for (j=0; j<num_mol_agl; j++)
+      if (j != i)
+      {
+        res = c[j*num_mol_agl+i] / c[i*num_mol_agl+i];
+        for(k=i; k<=num_mol_agl; k++)
+          c[j*num_mol_agl+k] = c[j*num_mol_agl+k] - (res * c[i*num_mol_agl+k]);
+      }
+  }
+  
+  for (i=0; i<num_mol_agl; i++)
+    sol[i] = c[i*num_mol_agl+num_mol_agl] / c[i*num_mol_agl+i];
+  
+  return 0;
+}
+
+
+int three_vertex (const int *matrix)
+{
+  int i, j;
+  int test_mtx[2][9] = {{0, 1, 0, 1, 0, 1, 0, 1, 0}, {0, 1, 1, 1, 0, 1, 1, 1, 0}};
+  
+  for (i=0; i<2; i++)
+    
+  
+  return 0;
+}
+
+
+int iso (const int N, const int *mtx, const int *ref_mtx)
+{
+  int i, j, k, *indx;
+  float *a, *b, *d, dmax, det, eps, **nr_mtx, *x;
+  
+//   initialization of variables
+  a = (float *) malloc (N * N * sizeof (float));
+  d = (float *) malloc (N * sizeof (float));
+  nr_mtx = matrix (1, N, 1, N);
+  indx = ivector (1, N);
+  x = vector (1, N);
+//   copy matrix
+  for (i=0; i<N; i++)
+    for (j=0; j<N; j++)
+      a[i*N+j] = mtx[i*N+j];
+//   create d-matrix
+  for (i=0; i<N; i++)
+  {
+    d[i] = 0;
+    for (j=0; j<N; j++)
+      if (j != i)
+        d[i] += a[i*N+j];
+  }
+  dmax = d[0];
+  for (i=0; i<N; i++)
+    if (d[i] > dmax)
+      dmax = d[i];
+  
+  for (i=0; i<N; i++)
+  {
+//     to nr object
+    for (j=1; j<=N; j++)
+      for (k=1; k<=N; k++)
+        nr_mtx[j][k] = a[(j-1)*N+(k-1)];
+    ludcmp (nr_mtx, N, indx, &det);
+    for(j=1; j<=N; j++) det *= nr_mtx[j][j];
+    
+//     define SLE
+    eps = sqrt (pow ((d + d[i]), 2) + 2 / n * (det + 2 + 2 / n)) - (d + d[i]);
+    for (j=0; j<N; j++)
+      for (k=0; k<N; k++)
+        if ((j == k) && (j == i))
+          a[j*N+k] = a[j*N+k] + eps;
+        else
+          a[j*N+k] = a[j*N+k];
+//     solution of SLE
+    for (j=1; j<=N; j++)
+    {
+      if (j == i)
+        x[j] = 1;
+      else
+        x[j] = 0;
+      for (k=1; k<=N; k++)
+        nr_mtx[j][k] = a[(j-1)*N+(k-1)];
+      ludcmp (nr_mtx, N, indx, &det);
+      lubksb (nr_mtx, N, indx, x);
+    }
+  }
+  
+  free_vector (i);
+  free_ivector (indx);
+  free_matrix (nr_mtx);
+  
+  return 0;
+}
+
+
+int iso_check (const int num_mol_agl, const int *matrix)
+{
+  int i, j, type;
+  
+  type = 0;
+  
+  switch (num_mol_agl)
+  {
+    case 2:
+      type = 1;
+      break;
+    case 3:
+      type = three_vertex (matrix);
+  }
+  
+  return type;
+}

graph/new/nr_lautil.c

@@ -0,0 +1,113 @@
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "nrutil.h"
+#define TINY 1.0e-20
+// #define N 2
+
+
+void ludcmp (float **a, int n, int *indx, float *d)
+{
+  int i, imax, j, k;
+  float big, dum, sum, temp;
+  float *vv;
+
+  vv = vector (1,n);
+  *d = 1.0;
+  for (i=1; i<=n; i++) 
+  {
+    big = 0.0;
+    for (j=1; j<=n; j++)
+      if ((temp = fabs(a[i][j])) > big) big = temp;
+    if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+    vv[i] = 1.0 / big;
+  }
+  
+  for (j=1; j<=n; j++) 
+  {
+    for (i=1; i<j; i++) 
+    {
+      sum = a[i][j];
+      for (k=1; k<i; k++) sum -= a[i][k] * a[k][j];
+      a[i][j] = sum;
+    }
+    big = 0.0;
+    for (i=j; i<=n; i++) 
+    {
+      sum = a[i][j];
+      for (k=1; k<j; k++)
+        sum -= a[i][k] * a[k][j];
+      a[i][j] = sum;
+      if ((dum = vv[i] * fabs(sum)) >= big) 
+      {
+        big = dum;
+        imax = i;
+      }
+    }
+    if (j != imax) 
+    {
+      for (k=1; k<=n; k++) 
+      {
+        dum = a[imax][k];
+        a[imax][k] = a[j][k];
+        a[j][k] = dum;
+      }
+      *d = -(*d);
+      vv[imax] = vv[j];
+    }
+    indx[j] = imax;
+    if (a[j][j] == 0.0) a[j][j] = TINY;
+    if (j != n) 
+    {
+      dum = 1.0 / a[j][j];
+      for (i=j+1; i<=n; i++) a[i][j] *= dum;
+    }
+  }
+  free_vector (vv, 1, n);
+}
+
+
+void lubksb (float **a, int n, int *indx, float b[])
+{
+  int i, ii=0, ip, j;
+  float sum;
+  
+  for (i=1; i<=n; i++)
+  {
+    ip = indx[i];
+    sum = b[ip];
+    b[ip] = b[i];
+    if (ii)
+      for (j=ii; j<=i-1; j++) sum -= a[i][j] * b[j];
+    else if (sum) ii = i;
+    b[i] = sum;
+  }
+  for (i=n; i>=1; i--) 
+  {
+    sum = b[i];
+    for (j=i+1; j<=n; j++) sum -= a[i][j] * b[j];
+    b[i] = sum / a[i][i];
+  }
+}
+
+
+// int main ()
+// {
+//   float **a, d;
+//   int i, j, *indx;
+//   
+//   float a_array[N][N] = {
+//     { 1.0, 2.0 },
+//     { 3.0, 4.0 }
+//   };
+//   a = matrix (1, N, 1, N);
+//   for (i=1; i<N+1; i++)
+//     for (j=1; j<N+1; j++)
+//       a[i][j] = a_array[i-1][j-1];
+//   indx = ivector (1, N);
+//   ludcmp (a, N, indx, &d);
+//   for(j=1; j<=N; j++) d *= a[j][j];
+//   printf ("%lf\n", d);
+// 
+//   return 0;
+// }

graph/new/nrutil.c

@@ -0,0 +1,614 @@
+#if defined(__STDC__) || defined(ANSI) || defined(NRANSI) /* ANSI */
+
+#include <stdio.h>
+#include <stddef.h>
+#include <stdlib.h>
+#define NR_END 1
+#define FREE_ARG char*
+
+void nrerror(char error_text[])
+/* Numerical Recipes standard error handler */
+{
+    fprintf(stderr,"Numerical Recipes run-time error...\n");
+    fprintf(stderr,"%s\n",error_text);
+    fprintf(stderr,"...now exiting to system...\n");
+    exit(1);
+}
+
+float *vector(long nl, long nh)
+/* allocate a float vector with subscript range v[nl..nh] */
+{
+    float *v;
+
+    v=(float *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(float)));
+    if (!v) nrerror("allocation failure in vector()");
+    return v-nl+NR_END;
+}
+
+int *ivector(long nl, long nh)
+/* allocate an int vector with subscript range v[nl..nh] */
+{
+    int *v;
+
+    v=(int *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(int)));
+    if (!v) nrerror("allocation failure in ivector()");
+    return v-nl+NR_END;
+}
+
+unsigned char *cvector(long nl, long nh)
+/* allocate an unsigned char vector with subscript range v[nl..nh] */
+{
+    unsigned char *v;
+
+    v=(unsigned char *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(unsigned char)));
+    if (!v) nrerror("allocation failure in cvector()");
+    return v-nl+NR_END;
+}
+
+unsigned long *lvector(long nl, long nh)
+/* allocate an unsigned long vector with subscript range v[nl..nh] */
+{
+    unsigned long *v;
+
+    v=(unsigned long *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(long)));
+    if (!v) nrerror("allocation failure in lvector()");
+    return v-nl+NR_END;
+}
+
+double *dvector(long nl, long nh)
+/* allocate a double vector with subscript range v[nl..nh] */
+{
+    double *v;
+
+    v=(double *)malloc((size_t) ((nh-nl+1+NR_END)*sizeof(double)));
+    if (!v) nrerror("allocation failure in dvector()");
+    return v-nl+NR_END;
+}
+
+float **matrix(long nrl, long nrh, long ncl, long nch)
+/* allocate a float matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    float **m;
+
+    /* allocate pointers to rows */
+    m=(float **) malloc((size_t)((nrow+NR_END)*sizeof(float*)));
+    if (!m) nrerror("allocation failure 1 in matrix()");
+    m += NR_END;
+    m -= nrl;
+
+    /* allocate rows and set pointers to them */
+    m[nrl]=(float *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(float)));
+    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+    m[nrl] += NR_END;
+    m[nrl] -= ncl;
+
+    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+double **dmatrix(long nrl, long nrh, long ncl, long nch)
+/* allocate a double matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    double **m;
+
+    /* allocate pointers to rows */
+    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+    if (!m) nrerror("allocation failure 1 in matrix()");
+    m += NR_END;
+    m -= nrl;
+
+    /* allocate rows and set pointers to them */
+    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+    m[nrl] += NR_END;
+    m[nrl] -= ncl;
+
+    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+int **imatrix(long nrl, long nrh, long ncl, long nch)
+/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    int **m;
+
+    /* allocate pointers to rows */
+    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+    if (!m) nrerror("allocation failure 1 in matrix()");
+    m += NR_END;
+    m -= nrl;
+
+
+    /* allocate rows and set pointers to them */
+    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+    m[nrl] += NR_END;
+    m[nrl] -= ncl;
+
+    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+float **submatrix(float **a, long oldrl, long oldrh, long oldcl, long oldch,
+    long newrl, long newcl)
+/* point a submatrix [newrl..][newcl..] to a[oldrl..oldrh][oldcl..oldch] */
+{
+    long i,j,nrow=oldrh-oldrl+1,ncol=oldcl-newcl;
+    float **m;
+
+    /* allocate array of pointers to rows */
+    m=(float **) malloc((size_t) ((nrow+NR_END)*sizeof(float*)));
+    if (!m) nrerror("allocation failure in submatrix()");
+    m += NR_END;
+    m -= newrl;
+
+    /* set pointers to rows */
+    for(i=oldrl,j=newrl;i<=oldrh;i++,j++) m[j]=a[i]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+float **convert_matrix(float *a, long nrl, long nrh, long ncl, long nch)
+/* allocate a float matrix m[nrl..nrh][ncl..nch] that points to the matrix
+declared in the standard C manner as a[nrow][ncol], where nrow=nrh-nrl+1
+and ncol=nch-ncl+1. The routine should be called with the address
+&a[0][0] as the first argument. */
+{
+    long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    float **m;
+
+    /* allocate pointers to rows */
+    m=(float **) malloc((size_t) ((nrow+NR_END)*sizeof(float*)));
+    if (!m) nrerror("allocation failure in convert_matrix()");
+    m += NR_END;
+    m -= nrl;
+
+    /* set pointers to rows */
+    m[nrl]=a-ncl;
+    for(i=1,j=nrl+1;i<nrow;i++,j++) m[j]=m[j-1]+ncol;
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+float ***f3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh)
+/* allocate a float 3tensor with range t[nrl..nrh][ncl..nch][ndl..ndh] */
+{
+    long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1;
+    float ***t;
+
+    /* allocate pointers to pointers to rows */
+    t=(float ***) malloc((size_t)((nrow+NR_END)*sizeof(float**)));
+    if (!t) nrerror("allocation failure 1 in f3tensor()");
+    t += NR_END;
+    t -= nrl;
+
+    /* allocate pointers to rows and set pointers to them */
+    t[nrl]=(float **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(float*)));
+    if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
+    t[nrl] += NR_END;
+    t[nrl] -= ncl;
+
+    /* allocate rows and set pointers to them */
+    t[nrl][ncl]=(float *) malloc((size_t)((nrow*ncol*ndep+NR_END)*sizeof(float)));
+    if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
+    t[nrl][ncl] += NR_END;
+    t[nrl][ncl] -= ndl;
+
+    for(j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
+    for(i=nrl+1;i<=nrh;i++) {
+        t[i]=t[i-1]+ncol;
+        t[i][ncl]=t[i-1][ncl]+ncol*ndep;
+        for(j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
+    }
+
+    /* return pointer to array of pointers to rows */
+    return t;
+}
+
+void free_vector(float *v, long nl, long nh)
+/* free a float vector allocated with vector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_ivector(int *v, long nl, long nh)
+/* free an int vector allocated with ivector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_cvector(unsigned char *v, long nl, long nh)
+/* free an unsigned char vector allocated with cvector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_lvector(unsigned long *v, long nl, long nh)
+/* free an unsigned long vector allocated with lvector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_dvector(double *v, long nl, long nh)
+/* free a double vector allocated with dvector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_matrix(float **m, long nrl, long nrh, long ncl, long nch)
+/* free a float matrix allocated by matrix() */
+{
+    free((FREE_ARG) (m[nrl]+ncl-NR_END));
+    free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch)
+/* free a double matrix allocated by dmatrix() */
+{
+    free((FREE_ARG) (m[nrl]+ncl-NR_END));
+    free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void free_imatrix(int **m, long nrl, long nrh, long ncl, long nch)
+/* free an int matrix allocated by imatrix() */
+{
+    free((FREE_ARG) (m[nrl]+ncl-NR_END));
+    free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void free_submatrix(float **b, long nrl, long nrh, long ncl, long nch)
+/* free a submatrix allocated by submatrix() */
+{
+    free((FREE_ARG) (b+nrl-NR_END));
+}
+
+void free_convert_matrix(float **b, long nrl, long nrh, long ncl, long nch)
+/* free a matrix allocated by convert_matrix() */
+{
+    free((FREE_ARG) (b+nrl-NR_END));
+}
+
+void free_f3tensor(float ***t, long nrl, long nrh, long ncl, long nch,
+    long ndl, long ndh)
+/* free a float f3tensor allocated by f3tensor() */
+{
+    free((FREE_ARG) (t[nrl][ncl]+ndl-NR_END));
+    free((FREE_ARG) (t[nrl]+ncl-NR_END));
+    free((FREE_ARG) (t+nrl-NR_END));
+}
+
+#else /* ANSI */
+/* traditional - K&R */
+
+#include <stdio.h>
+#define NR_END 1
+#define FREE_ARG char*
+
+void nrerror(error_text)
+char error_text[];
+/* Numerical Recipes standard error handler */
+{
+    void exit();
+
+    fprintf(stderr,"Numerical Recipes run-time error...\n");
+    fprintf(stderr,"%s\n",error_text);
+    fprintf(stderr,"...now exiting to system...\n");
+    exit(1);
+}
+
+float *vector(nl,nh)
+long nh,nl;
+/* allocate a float vector with subscript range v[nl..nh] */
+{
+    float *v;
+
+    v=(float *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(float)));
+    if (!v) nrerror("allocation failure in vector()");
+    return v-nl+NR_END;
+}
+
+int *ivector(nl,nh)
+long nh,nl;
+/* allocate an int vector with subscript range v[nl..nh] */
+{
+    int *v;
+
+    v=(int *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(int)));
+    if (!v) nrerror("allocation failure in ivector()");
+    return v-nl+NR_END;
+}
+
+unsigned char *cvector(nl,nh)
+long nh,nl;
+/* allocate an unsigned char vector with subscript range v[nl..nh] */
+{
+    unsigned char *v;
+
+    v=(unsigned char *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(unsigned char)));
+    if (!v) nrerror("allocation failure in cvector()");
+    return v-nl+NR_END;
+}
+
+unsigned long *lvector(nl,nh)
+long nh,nl;
+/* allocate an unsigned long vector with subscript range v[nl..nh] */
+{
+    unsigned long *v;
+
+    v=(unsigned long *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(long)));
+    if (!v) nrerror("allocation failure in lvector()");
+    return v-nl+NR_END;
+}
+
+double *dvector(nl,nh)
+long nh,nl;
+/* allocate a double vector with subscript range v[nl..nh] */
+{
+    double *v;
+
+    v=(double *)malloc((unsigned int) ((nh-nl+1+NR_END)*sizeof(double)));
+    if (!v) nrerror("allocation failure in dvector()");
+    return v-nl+NR_END;
+}
+
+float **matrix(nrl,nrh,ncl,nch)
+long nch,ncl,nrh,nrl;
+/* allocate a float matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    float **m;
+
+    /* allocate pointers to rows */
+    m=(float **) malloc((unsigned int)((nrow+NR_END)*sizeof(float*)));
+    if (!m) nrerror("allocation failure 1 in matrix()");
+    m += NR_END;
+    m -= nrl;
+
+    /* allocate rows and set pointers to them */
+    m[nrl]=(float *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(float)));
+    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+    m[nrl] += NR_END;
+    m[nrl] -= ncl;
+
+    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+double **dmatrix(nrl,nrh,ncl,nch)
+long nch,ncl,nrh,nrl;
+/* allocate a double matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    double **m;
+
+    /* allocate pointers to rows */
+    m=(double **) malloc((unsigned int)((nrow+NR_END)*sizeof(double*)));
+    if (!m) nrerror("allocation failure 1 in matrix()");
+    m += NR_END;
+    m -= nrl;
+
+    /* allocate rows and set pointers to them */
+    m[nrl]=(double *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(double)));
+    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+    m[nrl] += NR_END;
+    m[nrl] -= ncl;
+
+    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+int **imatrix(nrl,nrh,ncl,nch)
+long nch,ncl,nrh,nrl;
+/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    int **m;
+
+    /* allocate pointers to rows */
+    m=(int **) malloc((unsigned int)((nrow+NR_END)*sizeof(int*)));
+    if (!m) nrerror("allocation failure 1 in matrix()");
+    m += NR_END;
+    m -= nrl;
+
+
+    /* allocate rows and set pointers to them */
+    m[nrl]=(int *) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(int)));
+    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+    m[nrl] += NR_END;
+    m[nrl] -= ncl;
+
+    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+float **submatrix(a,oldrl,oldrh,oldcl,oldch,newrl,newcl)
+float **a;
+long newcl,newrl,oldch,oldcl,oldrh,oldrl;
+/* point a submatrix [newrl..][newcl..] to a[oldrl..oldrh][oldcl..oldch] */
+{
+    long i,j,nrow=oldrh-oldrl+1,ncol=oldcl-newcl;
+    float **m;
+
+    /* allocate array of pointers to rows */
+    m=(float **) malloc((unsigned int) ((nrow+NR_END)*sizeof(float*)));
+    if (!m) nrerror("allocation failure in submatrix()");
+    m += NR_END;
+    m -= newrl;
+
+    /* set pointers to rows */
+    for(i=oldrl,j=newrl;i<=oldrh;i++,j++) m[j]=a[i]+ncol;
+
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+float **convert_matrix(a,nrl,nrh,ncl,nch)
+float *a;
+long nch,ncl,nrh,nrl;
+/* allocate a float matrix m[nrl..nrh][ncl..nch] that points to the matrix
+declared in the standard C manner as a[nrow][ncol], where nrow=nrh-nrl+1
+and ncol=nch-ncl+1. The routine should be called with the address
+&a[0][0] as the first argument. */
+{
+    long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1;
+    float **m;
+
+    /* allocate pointers to rows */
+    m=(float **) malloc((unsigned int) ((nrow+NR_END)*sizeof(float*)));
+    if (!m) nrerror("allocation failure in convert_matrix()");
+    m += NR_END;
+    m -= nrl;
+
+    /* set pointers to rows */
+    m[nrl]=a-ncl;
+    for(i=1,j=nrl+1;i<nrow;i++,j++) m[j]=m[j-1]+ncol;
+    /* return pointer to array of pointers to rows */
+    return m;
+}
+
+float ***f3tensor(nrl,nrh,ncl,nch,ndl,ndh)
+long nch,ncl,ndh,ndl,nrh,nrl;
+/* allocate a float 3tensor with range t[nrl..nrh][ncl..nch][ndl..ndh] */
+{
+    long i,j,nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1;
+    float ***t;
+
+    /* allocate pointers to pointers to rows */
+    t=(float ***) malloc((unsigned int)((nrow+NR_END)*sizeof(float**)));
+    if (!t) nrerror("allocation failure 1 in f3tensor()");
+    t += NR_END;
+    t -= nrl;
+
+    /* allocate pointers to rows and set pointers to them */
+    t[nrl]=(float **) malloc((unsigned int)((nrow*ncol+NR_END)*sizeof(float*)));
+    if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
+    t[nrl] += NR_END;
+    t[nrl] -= ncl;
+
+    /* allocate rows and set pointers to them */
+    t[nrl][ncl]=(float *) malloc((unsigned int)((nrow*ncol*ndep+NR_END)*sizeof(float)));
+    if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
+    t[nrl][ncl] += NR_END;
+    t[nrl][ncl] -= ndl;
+
+    for(j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
+    for(i=nrl+1;i<=nrh;i++) {
+        t[i]=t[i-1]+ncol;
+        t[i][ncl]=t[i-1][ncl]+ncol*ndep;
+        for(j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
+    }
+
+    /* return pointer to array of pointers to rows */
+    return t;
+}
+
+void free_vector(v,nl,nh)
+float *v;
+long nh,nl;
+/* free a float vector allocated with vector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_ivector(v,nl,nh)
+int *v;
+long nh,nl;
+/* free an int vector allocated with ivector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_cvector(v,nl,nh)
+long nh,nl;
+unsigned char *v;
+/* free an unsigned char vector allocated with cvector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_lvector(v,nl,nh)
+long nh,nl;
+unsigned long *v;
+/* free an unsigned long vector allocated with lvector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_dvector(v,nl,nh)
+double *v;
+long nh,nl;
+/* free a double vector allocated with dvector() */
+{
+    free((FREE_ARG) (v+nl-NR_END));
+}
+
+void free_matrix(m,nrl,nrh,ncl,nch)
+float **m;
+long nch,ncl,nrh,nrl;
+/* free a float matrix allocated by matrix() */
+{
+    free((FREE_ARG) (m[nrl]+ncl-NR_END));
+    free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void free_dmatrix(m,nrl,nrh,ncl,nch)
+double **m;
+long nch,ncl,nrh,nrl;
+/* free a double matrix allocated by dmatrix() */
+{
+    free((FREE_ARG) (m[nrl]+ncl-NR_END));
+    free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void free_imatrix(m,nrl,nrh,ncl,nch)
+int **m;
+long nch,ncl,nrh,nrl;
+/* free an int matrix allocated by imatrix() */
+{
+    free((FREE_ARG) (m[nrl]+ncl-NR_END));
+    free((FREE_ARG) (m+nrl-NR_END));
+}
+
+void free_submatrix(b,nrl,nrh,ncl,nch)
+float **b;
+long nch,ncl,nrh,nrl;
+/* free a submatrix allocated by submatrix() */
+{
+    free((FREE_ARG) (b+nrl-NR_END));
+}
+
+void free_convert_matrix(b,nrl,nrh,ncl,nch)
+float **b;
+long nch,ncl,nrh,nrl;
+/* free a matrix allocated by convert_matrix() */
+{
+    free((FREE_ARG) (b+nrl-NR_END));
+}
+
+void free_f3tensor(t,nrl,nrh,ncl,nch,ndl,ndh)
+float ***t;
+long nch,ncl,ndh,ndl,nrh,nrl;
+/* free a float f3tensor allocated by f3tensor() */
+{
+    free((FREE_ARG) (t[nrl][ncl]+ndl-NR_END));
+    free((FREE_ARG) (t[nrl]+ncl-NR_END));
+    free((FREE_ARG) (t+nrl-NR_END));
+}
+
+#endif /* ANSI */

graph/new/nrutil.h

@@ -0,0 +1,101 @@
+#ifndef _NR_UTILS_H_
+#define _NR_UTILS_H_
+
+static float sqrarg;
+#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
+
+static double dsqrarg;
+#define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)
+
+static double dmaxarg1,dmaxarg2;
+#define DMAX(a,b) (dmaxarg1=(a),dmaxarg2=(b),(dmaxarg1) > (dmaxarg2) ?\
+        (dmaxarg1) : (dmaxarg2))
+
+static double dminarg1,dminarg2;
+#define DMIN(a,b) (dminarg1=(a),dminarg2=(b),(dminarg1) < (dminarg2) ?\
+        (dminarg1) : (dminarg2))
+
+static float maxarg1,maxarg2;
+#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?\
+        (maxarg1) : (maxarg2))
+
+static float minarg1,minarg2;
+#define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?\
+        (minarg1) : (minarg2))
+
+static long lmaxarg1,lmaxarg2;
+#define LMAX(a,b) (lmaxarg1=(a),lmaxarg2=(b),(lmaxarg1) > (lmaxarg2) ?\
+        (lmaxarg1) : (lmaxarg2))
+
+static long lminarg1,lminarg2;
+#define LMIN(a,b) (lminarg1=(a),lminarg2=(b),(lminarg1) < (lminarg2) ?\
+        (lminarg1) : (lminarg2))
+
+static int imaxarg1,imaxarg2;
+#define IMAX(a,b) (imaxarg1=(a),imaxarg2=(b),(imaxarg1) > (imaxarg2) ?\
+        (imaxarg1) : (imaxarg2))
+
+static int iminarg1,iminarg2;
+#define IMIN(a,b) (iminarg1=(a),iminarg2=(b),(iminarg1) < (iminarg2) ?\
+        (iminarg1) : (iminarg2))
+
+#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
+
+#if defined(__STDC__) || defined(ANSI) || defined(NRANSI) /* ANSI */
+
+void nrerror(char error_text[]);
+float *vector(long nl, long nh);
+int *ivector(long nl, long nh);
+unsigned char *cvector(long nl, long nh);
+unsigned long *lvector(long nl, long nh);
+double *dvector(long nl, long nh);
+float **matrix(long nrl, long nrh, long ncl, long nch);
+double **dmatrix(long nrl, long nrh, long ncl, long nch);
+int **imatrix(long nrl, long nrh, long ncl, long nch);
+float **submatrix(float **a, long oldrl, long oldrh, long oldcl, long oldch,
+    long newrl, long newcl);
+float **convert_matrix(float *a, long nrl, long nrh, long ncl, long nch);
+float ***f3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
+void free_vector(float *v, long nl, long nh);
+void free_ivector(int *v, long nl, long nh);
+void free_cvector(unsigned char *v, long nl, long nh);
+void free_lvector(unsigned long *v, long nl, long nh);
+void free_dvector(double *v, long nl, long nh);
+void free_matrix(float **m, long nrl, long nrh, long ncl, long nch);
+void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch);
+void free_imatrix(int **m, long nrl, long nrh, long ncl, long nch);
+void free_submatrix(float **b, long nrl, long nrh, long ncl, long nch);
+void free_convert_matrix(float **b, long nrl, long nrh, long ncl, long nch);
+void free_f3tensor(float ***t, long nrl, long nrh, long ncl, long nch,
+    long ndl, long ndh);
+
+#else /* ANSI */
+/* traditional - K&R */
+
+void nrerror();
+float *vector();
+float **matrix();
+float **submatrix();
+float **convert_matrix();
+float ***f3tensor();
+double *dvector();
+double **dmatrix();
+int *ivector();
+int **imatrix();
+unsigned char *cvector();
+unsigned long *lvector();
+void free_vector();
+void free_dvector();
+void free_ivector();
+void free_cvector();
+void free_lvector();
+void free_matrix();
+void free_submatrix();
+void free_convert_matrix();
+void free_dmatrix();
+void free_imatrix();
+void free_f3tensor();
+
+#endif /* ANSI */
+
+#endif /* _NR_UTILS_H_ */

stat_new/Makefile

@@ -1,20 +0,0 @@
-PROJECT=STATGEN
-
-CC=gcc
-CFLAGS=-c -Wall -fPIC
-LDFLAGS=-lm
-SOURCES=main.c coords.c int2str.c stat_print.c stat_select.c stat_sort.c summary_stat.c
-OBJECTS=$(SOURCES:.c=.o)
-EXECUTABLE=statgen
-
-$(PROJECT): $(SOURCES) $(EXECUTABLE)
-
-$(EXECUTABLE): $(OBJECTS)
-	$(CC) $(LDFLAGS) $(OBJECTS) -o $@
-
-.c.o:
-	$(CC) $(CFLAGS) $< -o $@
-
-clean:
-	rm -f *.o
-

stat_new/coords.c

@@ -1,279 +0,0 @@
-/* Library for reading coordinates from input file
- * 
- * Usage:
- *                    reading_coords (filename, type_interaction, labels, cell, 
- *  &number_of_molecules, &number_of_atoms, true_label_molecule, label_molecule, 
- *                                                           type_atoms, coords)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-
-int reading_coords (char *filename, int type_inter, const int *label_atom, 
-                    const float *cell, int *num_mol, int *num_atoms, 
-                    int *true_label_mol, int *label_mol, 
-                    int *type_atoms, float *coords)
-/* filename         - name of file with coordinates
- * type_inter       - type interaction (number of molecules for interaction)
- * label_atom       - types of atom for interaction
- * cell             - cell dimension
- * num_mol          - number of molecules for writing coordinates
- * num_atoms        - number of atoms for writing coordinates
- * true_label_mol   - massive of true numbers of molecule for atoms
- * label_mol        - massive of numbers of molecule for atoms
- * type_atoms       - massive of atom types for atoms
- * coords           - massive of coordinates
- */
-{
-  char file_string[256];
-  int atoms, i, j, tr_num_atoms, ref_mol, x, y;
-  float not_tr_coords[750000], ref[3];
-  FILE *inp;
-/* file_string      - temp string variable
- * atoms            - total number of atoms in system
- * tr_num_atoms     - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
- * ref_mol          - number of molecule for reference
- * not_tr_coords    - not translated coordinates
- * ref              - coordinates of reference molecule
- * inp              - file with input data
- */
-  
-  *num_atoms = 0;
-  *num_mol = 0;
-  
-//   Reading file
-  inp = fopen (filename, "r");
-  if (inp == NULL)
-    return 1;
-  
-  ref_mol = -1;
-  fscanf (inp, "%i", &atoms);
-  for (i=0; i<atoms; i++)
-  {
-    fgets (file_string, 256, inp);
-    
-    for (j=0; j<type_inter; j++)
-      if (atoi (&file_string[47]) == label_atom[j])
-      {
-        not_tr_coords[3**num_atoms+0] = atof (&file_string[10]);
-        not_tr_coords[3**num_atoms+1] = atof (&file_string[23]);
-        not_tr_coords[3**num_atoms+2] = atof (&file_string[35]);
-        
-        if (ref_mol != atoi (&file_string[53]))
-        {
-          ref_mol = atoi (&file_string[53]);
-          true_label_mol[*num_mol] = ref_mol;
-          *num_mol = *num_mol + 1;
-        }
-        label_mol[*num_atoms] = *num_mol - 1;
-        type_atoms[*num_atoms] = j;
-        
-        *num_atoms = *num_atoms + 1;
-      }
-  }
-  fclose (inp);
-  
-//   Translation
-  tr_num_atoms = *num_atoms;
-  for (i=0; i<*num_atoms; i++)
-    for (j=0; j<3; j++)
-      coords[3*i+j] = not_tr_coords[3*i+j];
-  
-//   Assign initial value to reference coordinates
-  ref_mol = label_mol[0];
-  for (i=0; i<3; i++)
-    ref[i] = coords[i];
-  
-  for (i=0; i<*num_atoms; i++)
-  {
-    if (label_mol[i] != ref_mol)
-    {
-      ref_mol = label_mol[i];
-      for (j=0; j<3; j++)
-        ref[j] = not_tr_coords[3*i+j];
-    }
-    
-    for (x=0; x<3; x++)
-    {
-      if (ref[x] >= 0.0)
-//         if xyz >= 0.0 A
-     {
-        for (j=0; j<3; j++)
-          if (j == x)
-            coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
-          else
-            coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
-        
-        label_mol[tr_num_atoms] = label_mol[i];
-        type_atoms[tr_num_atoms] = type_atoms[i];
-        tr_num_atoms++;
-      }
-      else
-//         if xyz < 0.0 A
-      {
-        for (j=0; j<3; j++)
-          if (j == x)
-            coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
-          else
-            coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
-        
-        label_mol[tr_num_atoms] = label_mol[i];
-        type_atoms[tr_num_atoms] = type_atoms[i];
-        tr_num_atoms++;
-      }
-    }
-    
-    for (x=0; x<3; x++)
-    {
-      for (y=x+1; y<3; y++)
-      {
-        if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
-//         if xyz and xyz >= 0.0 A
-        {
-          for (j=0; j<3; j++)
-            if ((j == x) || (j == y))
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
-            else
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
-        
-          label_mol[tr_num_atoms] = label_mol[i];
-          type_atoms[tr_num_atoms] = type_atoms[i];
-          tr_num_atoms++;
-        }
-        
-        if ((ref[x] < 0.0) && (ref[y] < 0.0))
-//         if xyz and xyz < 0.0 A
-        {
-          for (j=0; j<3; j++)
-            if ((j == x) || (j == y))
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
-            else
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
-        
-          label_mol[tr_num_atoms] = label_mol[i];
-          type_atoms[tr_num_atoms] = type_atoms[i];
-          tr_num_atoms++;
-        }
-      }
-      
-      for (y=0; y<3; y++)
-        if ((ref[x] < 0.0) && (ref[y] >= 0.0))
-//           if xyz OR xyz >= 0.0
-        {
-          for (j=0; j<3; j++)
-          {
-            if (j == x)
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
-            if (j == y)
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
-            if ((j != x) && (j != y))
-              coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
-          }
-          
-          label_mol[tr_num_atoms] = label_mol[i];
-          type_atoms[tr_num_atoms] = type_atoms[i];
-          tr_num_atoms++;
-        }
-    }
-    
-    if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
-//       if x and y and z >= 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
-//       if x and y >= 0.0 A and z < 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
-//       if x and z >= 0.0 A and y < 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
-//       if y and z >= 0.0 A and x < 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
-//       if x and y < 0.0 A and z >= 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
-//       if x and z < 0.0 A and y >= 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
-//       if x >= 0.0 A and y and z < 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-    
-    if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
-//       if x and y and z < 0.0 A
-    {
-      coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
-      coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
-      coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
-      
-      label_mol[tr_num_atoms] = label_mol[i];
-      type_atoms[tr_num_atoms] = type_atoms[i];
-      tr_num_atoms++;
-    }
-  }
-  
-  return 0;
-}

stat_new/int2str.c

@@ -1,26 +0,0 @@
-/* Library for converting integer to string
- * Usage
- *                                                char = conv (number, position)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-
-
-char conv (int fnumb, int dig_pos)
-/* fnumb            - integer
- * dig_pos          - position
- */
-{
-  int d, h, o;
-  char const digit[] = "0123456789";
- 
-  h = fnumb / 100;
-  d = (fnumb % 100) / 10;
-  o = fnumb % 10;
-
-  if (dig_pos == 1) return digit[o];
-  if (dig_pos == 2) return digit[d];
-  if (dig_pos == 3) return digit[h];
-  else return digit[0];
-}

stat_new/main.c

@@ -1,362 +0,0 @@
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-
-// prototypes
-char conv (int, int);
-int create_matrix (int, int, const int *, const int *, const float *, int, 
-                   const float *, int *);
-int printing_agl (char *, char *, const int *, int, const int *, const int *, 
-                  const int *, const int *, int *);
-int proc_matrix (int, const int *, int *, int *, int *, int *);
-int reading_coords (char *, int, const int *, const float *, int *, int *, 
-                    int *, int *, int *, float *);
-int summary_statistic (char *, int, int, const int *, const int *);
-
-
-int error_checking (const float *cell, int from, const char *input, 
-                    int num_of_inter, const char *output, int to, int type_inter)
-{
-  if ((type_inter == 0) || (type_inter > 4))
-    return 11;
-  if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
-    return 12;
-  if ((to == -1) || (from == -1))
-    return 13;
-  if (num_of_inter == 0)
-    return 14;
-  if (input[0] == '#')
-    return 15;
-  if (output[0] == '#')
-    return 16;
-  
-  return 0;
-}
-
-
-int printing_head (const char *output, int log, int quiet, const char *input, 
-                   int from, int to, const float *cell, int type_inter, 
-                   const int *label_atom, int num_of_inter, const float *crit)
-{
-  int i;
-  FILE *f_out;
-  
-  f_out = fopen (output, "w");
-  fprintf (f_out, "statgen ::: V.1.0.0 ::: 2013-07-17\n\n");
-  fprintf (f_out, "CONFIGURATION\n");
-  
-  fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);
-  fprintf (f_out, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, from, to);
-  fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", cell[0], cell[1], cell[2]);
-  fprintf (f_out, "ATOMS=%i", label_atom[0]);
-  for (i=1; i<type_inter; i++)
-    fprintf (f_out, ",%i", label_atom[i]);
-  fprintf (f_out, "\n");
-  for (i=0; i<num_of_inter; i++)
-  {
-    fprintf (f_out, "INTERACTION=");
-    fprintf (f_out, "0-0:%4.2f,0-1:%4.2f,1-1:%4.2f,", crit[16*i+0], crit[16*i+1], 
-             crit[16*i+5]);
-    fprintf (f_out, "0-2:%4.2f,1-2:%4.2f,2-2:%4.2f,", crit[16*i+2], crit[16*i+6], 
-             crit[16*i+10]);
-    fprintf (f_out, "0-3:%4.2f,1-3:%4.2f,2-3:%4.2f,3-3:%4.2f\n", crit[16*i+3], 
-             crit[16*i+7], crit[16*i+11], crit[16*i+15]);
-  }
-    
-  fprintf (f_out, "END\n\n");
-  fclose (f_out);
-  
-  return 0;
-}
-
-
-int set_defaults (float *cell, int *from, char *input, int *log, int *num_of_inter, 
-                  char *output, int *to, int *type_agl, int *type_inter, int *quiet)
-{
-  int i;
-  
-  for (i=0; i<3; i++)
-    cell[i] = 0.0;
-  *from = -1;
-  input[0] = '#';
-  *log = 0;
-  *num_of_inter = 0;
-  output[0] = '#';
-  *to = -1;
-  type_agl[0] = 0;
-  type_agl[1] = 0;
-  *type_inter = 0;
-  *quiet = 0;
-  
-  return 0;
-}
-
-
-int main (int argc, char *argv[])
-{
-  char filename[256], tmp_str[256];
-  int error, i, index, j, k, label[2];
-  float label_fl;
-  FILE *f_inp;
-  
-  char input[256], logfile[256], output[256];
-  float cell[3], *coords, *crit;
-  int *agl, *connect, from, *label_atom, *label_mol, log, num_atoms, num_mol, 
-      *num_mol_agl, num_of_inter, *stat, *stat_all, step, to, *true_label_mol, 
-      type_agl[2], *type_atoms, type_inter, quiet;
-/* input            - mask of input files
- * logfile          - log file name
- * output           - output file name
- * 
- * cell             - cell dimension
- * coords           - massive of coordinates
- * crit             - massive of criteria
- * 
- * agl              - massive of aglomerates
- * connect          - connectivity graph for all molecules
- * from             - start point
- * label_atom       - types of atom for interaction
- * label_mol        - massive of numbers of molecule for atoms
- * log              - status of log-mode
- * num_atoms        - number of atoms for writing coordinates
- * num_mol          - number of molecules for writing coordinates
- * num_mol_agl      - massive of numbers of molecule in aglomerates
- * num_of_inter     - number of different interactions
- * stat             - massive of statistics
- * stat_all         - massive of summary statistics
- * step             - $(to - from + 1)
- * to               - finish point
- * true_label_mol   - massive of true numbers of molecule for atoms
- * type_agl         - massive of numbers of aglomerate types
- * type_atoms       - massive of atom types for atoms
- * type_inter       - type interaction (number of molecules for interaction)
- * quiet            - status of quiet-mode
- */
-  
-  set_defaults (cell, &from, input, &log, &num_of_inter, output, &to, type_agl, 
-                &type_inter, &quiet);
-  
-//   reading number of interactions
-  for (i=1; i<argc; i++)
-    if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
-      num_of_inter++;
-  if (num_of_inter > 0)
-  {
-    crit = (float *) malloc ( 16 * num_of_inter * sizeof (float));
-    for (i=0; i<16*num_of_inter; i++)
-      crit[i] = 0.0;
-    num_of_inter = 0;
-  }
-  
-//   reading arguments
-  for (i=1; i<argc; i++)
-  {
-    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
-    {
-      printf ("                                        statgen\n");
-      printf ("Program for analyze molecular dynamic trajectories\n");
-      printf ("Version : 1.0.0                                                    License : GPL\n");
-      printf ("                                                    Alekseev Evgeniy aka arcanis\n");
-      printf ("                                                    E-mail : esalexeev@gmail.com\n\n");
-      printf ("Usage:\n");
-      printf ("statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n");
-      printf ("Parametrs:\n");
-      printf ("  -i          - mask of input files\n");
-      printf ("  -s          - trajectory steps (integer)\n");
-      printf ("  -c          - cell size (float), A\n");
-      printf ("  -a          - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc\n");
-      printf ("  -r          - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction\n");
-      printf ("                (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times\n");
-      printf ("  -o          - output file name\n");
-      printf ("  -l          - log enable\n");
-      printf ("  -q          - quiet enable\n");
-      printf ("  -h          - show this help and exit\n");
-      return 0;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
-//       mask of input files
-    {
-      strcpy (input, argv[i+1]);
-      i++;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
-//       steps
-    {
-      sscanf (argv[i+1], "%i,%i", &from, &to);
-      if (from > to)
-      {
-        to += from;
-        from = to - from;
-        to -= from;
-      }
-      step = to - from + 1;
-      i++;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
-//       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'))
-//       atom types
-    {
-      type_inter = 1;
-      for (j=0; j<strlen(argv[i+1]); j++)
-        if (argv[i+1][j] == ',')
-          type_inter++;
-      
-      label_atom = (int *) malloc (type_inter * sizeof (int));
-      switch (type_inter)
-      {
-        case 1:
-          sscanf (argv[i+1], "%i", &label_atom[0]);
-          break;
-        case 2:
-          sscanf (argv[i+1], "%i,%i", &label_atom[0], &label_atom[1]);
-          break;
-        case 3:
-          sscanf (argv[i+1], "%i,%i,%i", &label_atom[0], &label_atom[1], &label_atom[2]);
-          break;
-        case 4:
-          sscanf (argv[i+1], "%i,%i,%i,%i", &label_atom[0], &label_atom[1], &label_atom[2], &label_atom[3]);
-          break;
-      }
-      
-      i++;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
-//       criteria
-    {
-      index = 0;
-      sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
-      crit[16*num_of_inter+4*label[0]+label[1]] = label_fl;
-      crit[16*num_of_inter+4*label[1]+label[0]] = label_fl;
-      for (j=index; j<strlen(argv[i+1]); j++)
-        if (argv[i+1][j] == ',')
-        {
-          index = j+1;
-          sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
-          crit[16*num_of_inter+4*label[0]+label[1]] = label_fl;
-          crit[16*num_of_inter+4*label[1]+label[0]] = label_fl;
-        }
-      
-      num_of_inter++;
-      i++;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
-//       output file
-    {
-      strcpy (output, argv[i+1]);
-      i++;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
-//       log mode
-    {
-      log = 1;
-      strcpy (logfile, argv[i+1]);
-      i++;
-    }
-    else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
-//       quiet mode
-    {
-      quiet = 1;
-    }
-  }
-  
-//   error checking
-  error = error_checking (cell, from, input, num_of_inter, output, to, type_inter);
-  if (error > 1)
-  {
-    printf ("Something wrong (error code: %i)!\nSee 'statgen -h' for more details\n", error);
-    return 1;
-  }
-  
-//   processing
-//   initial variables
-  k = strlen (input);
-  strcpy (filename, input);
-  filename[k] = '.';
-  filename[k+1] = conv (from, 3);
-  filename[k+2] = conv (from, 2);
-  filename[k+3] = conv (from, 1);
-  filename[k+4] = '\0';
-  f_inp = fopen (filename, "r");
-  if (f_inp == NULL)
-    return 1;
-  fscanf (f_inp, "%i", &num_atoms);
-  fclose (f_inp);
-  coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
-  label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
-  true_label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
-  type_atoms = (int *) malloc (8 * num_atoms * sizeof (int));
-  
-//   head
-  printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom, 
-                 num_of_inter, crit);
-  
-//   main cycle
-  for (i=from; i<to+1; i++)
-  {
-//     reading coordinates
-    filename[k+1] = conv (i, 3);
-    filename[k+2] = conv (i, 2);
-    filename[k+3] = conv (i, 1);
-    filename[k+4] = '\0';
-    error = reading_coords (filename, type_inter, label_atom, cell, &num_mol, 
-                            &num_atoms, true_label_mol, label_mol, type_atoms, coords);
-    
-//     initializate variables
-    if (i == from)
-    {
-      agl = (int *) malloc (num_mol * num_mol * sizeof (int));
-      connect = (int *) malloc (num_mol * num_mol * sizeof (int));
-      num_mol_agl = (int *) malloc (num_mol * sizeof (int));
-      stat = (int *) malloc (num_mol * sizeof (int));
-      stat_all = (int *) malloc (num_mol * sizeof (int));
-    }
-    
-    for (j=0; j<num_mol; j++)
-    {
-      num_mol_agl[j] = j;
-      printf ("%i - %i\n", j, num_mol_agl[j]);
-    }
-    
-//     analyze
-    error = 1;
-    error = create_matrix (num_mol, num_atoms, label_mol, type_atoms, coords, 
-                          num_of_inter, crit, connect);
-    if (error == 0)
-    {
-      error = 1;
-      error = proc_matrix (num_mol, connect, num_mol_agl, agl, stat, stat_all);
-      if (error == 0)
-        printing_agl (filename, output, connect, num_mol, true_label_mol, 
-                      num_mol_agl, agl, stat, type_agl);
-    }
-    
-  }
-  num_mol_agl[num_mol-1] = num_mol;
-  printf ("%i - %i\n", num_mol-1, num_mol_agl[num_mol]);
-
-//     tail
-  summary_statistic (output, step, num_mol, type_agl, stat_all);
-  printf ("%i - %i\n", num_mol-1, num_mol_agl[num_mol]);
-
-//   free memory
-  free (agl);
-  free (connect);
-  free (coords);
-  free (crit);
-  free (label_mol);
-//   memory crash here
-  free(num_mol_agl);
-//   free (stat);
-//   free (stat_all);
-  free (true_label_mol);
-  free (type_atoms);
-  
-  return 0;
-}

stat_new/stat_print.c

@@ -1,107 +0,0 @@
-/* Library for printing aglomerates
- * 
- * Usage:
- *                  printing_agl (input_file, output_file, number_of_molecules, 
- *          true_label_molecules, num_of_molecules_in_aglomerates, aglomerates, 
- *                                                statistic, type_of_aglomerate)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-
-
-int printing_agl (char *input, char *output, const int *connect, int num_mol, 
-                  const int *true_label_mol, const int *num_mol_agl, 
-                  const int *agl, const int *stat, int *type_agl)
-/* input            - name of file with coordinates
- * output           - name of output file
- * connect          - connectivity graph for all molecules
- * num_mol          - number of molecules
- * true_label_mol   - massive of true numbers of molecule for atoms
- * num_mol_agl      - massive of numbers of molecule in aglomerates
- * agl              - massive of aglomerates
- * stat             - massive of statistics
- * type_agl         - massive of numbers of aglomerate types
- */
-{
-  int i, iso, j, k, p, type, *label_matrix, **matrix;
-  FILE *f_out;
-/* iso              - isomorphic graph in database
- * type             - number of cycle in aglomerates
- * label_matrix     - massive of indexes of molecule
- * matrix           - connectivity graph
- * f_out            - output file
- */
-  
-  f_out = fopen (output, "a");
-  
-//   head
-  fprintf (f_out, "FILE=%s\nSTATISTIC:\n|   n   |   N   |\n-----------------\n", input);
-  for (i=0; i<num_mol; i++)
-    if (stat[i] != 0)
-      fprintf (f_out, " %7i %7i \n", i+1, stat[i]);
-  fprintf (f_out, "-----------------\n");
-  
-//   body
-  for (i=0; i<num_mol; i++)
-    if (num_mol_agl[i] > 0)
-    {
-//       creating connectivity graph
-      matrix = (int **) malloc (num_mol_agl[i] * sizeof (int *));
-      for (j=0; j<num_mol_agl[i]; j++)
-      {
-        matrix[j] = (int *) malloc (num_mol_agl[i] * sizeof (int));
-        for (k=0; k<num_mol_agl[i]; k++)
-          matrix[j][k] = 0;
-      }
-      label_matrix = (int *) malloc (num_mol * sizeof (int));
-      for (j=0; j<num_mol_agl[i]; j++)
-        label_matrix[agl[num_mol*i+j]] = j;
-      for (j=0; j<num_mol_agl[i]; j++)
-        for (k=j+1; k<num_mol_agl[i]; k++)
-          if (connect[num_mol*agl[num_mol*i+j]+agl[num_mol*i+k]] == 1)
-          {
-            matrix[label_matrix[agl[num_mol*i+j]]][label_matrix[agl[num_mol*i+k]]] = 1;
-            matrix[label_matrix[agl[num_mol*i+k]]][label_matrix[agl[num_mol*i+j]]] = 1;
-          }
-//       TODO: analyze of topology
-      iso = 0;
-      p = 0;
-      for (j=0; j<num_mol_agl[i]; j++)
-        for (k=0; k<num_mol_agl[i]; k++)
-          p += matrix[j][k];
-      if (p == (2*num_mol_agl[i]-2))
-      {
-        type = 0;
-        type_agl[0]++;
-      }
-      else
-      {
-        type = (p - (2*num_mol_agl[i]-2)) / 2;
-        type_agl[1]++;
-      }
-      
-//       printing class of aglomerate
-      fprintf (f_out, "AGL=%i=%i=%i\n", num_mol_agl[i], type, iso);
-      for (j=0; j<num_mol_agl[i]; j++)
-      {
-        fprintf (f_out, "%7i=", true_label_mol[agl[num_mol*i+j]]);
-        for (k=0; k<num_mol_agl[i]; k++)
-        {
-          if (matrix[j][k] == 1)
-            fprintf (f_out, "%i,", true_label_mol[agl[num_mol*i+k]]);
-        }
-        fprintf (f_out, "\n");
-      }
-      
-//       free memory
-      for (j=0; j<num_mol_agl[i]; j++)
-        free (matrix[j]);
-      free (matrix);
-      free (label_matrix);
-    }
-  
-  fprintf (f_out, "---------------------------------------------------\n");
-  fclose (f_out);
-  return 0;
-}

stat_new/stat_select.c

@@ -1,104 +0,0 @@
-/* Library for creating connectivity matrix
- * 
- * Usage:
- *          create_matrix (number_of_molecules, number_of_atoms, label_molecule,
- *         type_atoms, coords, number_of_interactions, criteria, connect_matrix)
- */
-
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-
-int create_matrix (int num_mol, int num_atoms, const int *label_mol, 
-                   const int *type_atoms, const float *coords, int num_of_inter, 
-                   const float *crit, int *connect)
-/* num_mol          - number of molecules
- * num_atoms        - number of atoms
- * label_mol        - massive of numbers of molecule for atoms
- * type_atoms       - massive of atom types for atoms
- * coords           - massive of coordinates
- * num_of_inter     - number of different interactions
- * crit             - massive of criteria
- * connect          - connectivity graph for all molecules
- */
-{
-  float r;
-  int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
-/* r                - radius
- * cur_num_inter    - current number of true interactions
- * num_inter        - needed number of true interactions
- * label_inter      - temporary massive of true interactions
- */
-  
-  label_inter = (int ***) malloc (num_mol * sizeof (int **));
-  for (i=0; i<num_mol; i++)
-  {
-    label_inter[i] = (int **) malloc (num_mol * sizeof (int *));
-    for (j=0; j<num_mol; j++)
-    {
-      label_inter[i][j] = (int *) malloc (16 * sizeof (int));
-      for (k=0; k<16; k++)
-        label_inter[i][j][k] = 0;
-    }
-  }
-  
-//   creating initial connectivity matrix
-  for (i=0; i<num_atoms*8; i++)
-    for (j=i+1; j<num_atoms*8; j++)
-//       if atoms from different molecules
-      if (label_mol[i] != label_mol[j])
-      {
-        r = sqrt (pow ((coords[3*i+0]-coords[3*j+0]), 2) + 
-          pow ((coords[3*i+1]-coords[3*j+1]), 2) + 
-          pow ((coords[3*i+2]-coords[3*j+2]), 2));
-        for (k=0; k<num_of_inter; k++)
-          if (crit[16*k+4*type_atoms[i]+type_atoms[j]] != 0.0)
-            if (r < crit[16*k+4*type_atoms[i]+type_atoms[j]])
-            {
-              label_inter[label_mol[i]][label_mol[j]][4*type_atoms[i]+type_atoms[j]] = 1;
-              label_inter[label_mol[i]][label_mol[j]][4*type_atoms[j]+type_atoms[i]] = 1;
-              label_inter[label_mol[j]][label_mol[i]][4*type_atoms[i]+type_atoms[j]] = 1;
-              label_inter[label_mol[j]][label_mol[i]][4*type_atoms[j]+type_atoms[i]] = 1;
-            }
-      }
-  
-  for (i=0; i<num_mol; i++)
-    for (j=0; j<num_mol; j++)
-      connect[i*num_mol+j] = 0;
-  
-//   processing of initial connectivity matrix
-  for (k=0; k<num_of_inter; k++)
-  {
-//     determination of the number of interactions
-    num_inter = 0;
-    for (l=0; l<16; l++)
-      if (crit[16*k+l] != 0.0)
-        num_inter++;
-    
-    for (i=0; i<num_mol; i++)
-      for (j=i+1; j<num_mol; j++)
-      {
-        cur_num_inter = 0;
-        for (l=0; l<16; l++)
-          cur_num_inter += label_inter[i][j][l];
-        
-        if (cur_num_inter == num_inter)
-        {
-          connect[i*num_mol+j] = 1;
-          connect[j*num_mol+i] = 1;
-        }
-      }
-  }
-  
-//   free memory
-  for (i=0; i<num_mol; i++)
-  {
-    for (j=0; j<num_mol; j++)
-      free (label_inter[i][j]);
-    free (label_inter[i]);
-  }
-  free (label_inter);
-  
-  return 0;
-}

stat_new/stat_sort.c

@@ -1,83 +0,0 @@
-/* Library for processing connectivity matrix
- * 
- * Usage:
- *                             proc_matrix (number_of_molecules, connect_matrix, 
- *   num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-
-
-int proc_matrix (int num_mol, const int *connect, int *num_mol_agl, int *agl, 
-                 int *stat, int *stat_all)
-/* num_mol          - number of molecules
- * connect          - connectivity graph for all molecules
- * num_mol_agl      - massive of numbers of molecule in aglomerates
- * agl              - massive of aglomerates
- * stat             - massive of statistics
- * stat_all         - massive of summary statistics
- */
-{
-  int i, j, k, p, *bin;
-  /* p              - weight / graph index
-   * bin            - binary massive of labels
-   */
-  
-//   definition and zeroing
-  bin = (int *) malloc (num_mol * sizeof (int));
-  for (i=0; i<num_mol; i++)
-  {
-    bin[i] = 1;
-    stat[i] = 0;
-    num_mol_agl[i] = 0;
-    for (j=0; j<num_mol; j++)
-      agl[num_mol*i+j] = 0;
-  }
-  
-//   select non-bonded molecules
-  for (i=0; i<num_mol; i++)
-  {
-    p = 0;
-    for (j=0; j<num_mol; j++)
-      p += connect[i*num_mol+j];
-    if (p == 0)
-    {
-      bin[i] = 0;
-      stat[0]++;
-      stat_all[0]++;
-    }
-  }
-  
-//   unwraping of connectivity matrix
-  p = 0;
-  for (i=0; i<num_mol; i++)
-    if (bin[i] == 1)
-    {
-      agl[num_mol*p+num_mol_agl[p]] = i;
-      num_mol_agl[p]++;
-      bin[i] = 0;
-      
-      for (j=0; j<num_mol_agl[p]; j++)
-        for (k=0; k<num_mol; k++)
-          if ((connect[agl[num_mol*p+j]*num_mol+k] == 1) && (bin[k] == 1))
-          {
-            agl[num_mol*p+num_mol_agl[p]] = k;
-            num_mol_agl[p]++;
-            bin[k] = 0;
-          }
-      
-      p++;
-    }
-  
-//   filling statistic array
-  for (i=0; i<num_mol; i++)
-  {
-    stat[num_mol_agl[i]-1]++;
-    stat_all[num_mol_agl[i]-1]++;
-  }
-  
-  free (bin);
-  
-  return 0;
-}

stat_new/summary_stat.c

@@ -1,64 +0,0 @@
-/* Library for summary statistic
- * Usage:
- *            summary_statistic (filename, number_of_step, number_of_molecules, 
- *                                        type_of_aglomerate, summary_statistic)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-
-
-int summary_statistic (char *filename, int step, int num_mol, const int *type_agl, const int *stat_all)
-/* filename         - name of output file
- * step             - number of steps
- * num_mol          - number of molecules
- * type_agl         - massive of numbers of aglomerate types
- * stat_all         - massive of summary statistics
- */
-{
-  float conc, p, pn, type[2], x, y;
-  int i, index;
-  FILE *f_out;
-/* conc             - concentrate of aglomerates
- * p                - probability of aglomerates
- * pn               - weight probability of aglomerates
- * f_out            - output file
- */
-  
-  index = 0;
-  for (i=0; i<num_mol; i++)
-    if (stat_all[i] != 0)
-      index = i;
-  
-//   head
-  f_out = fopen (filename, "a");
-  fprintf (f_out, "SUMMARY STATISTIC:\n");
-  fprintf (f_out, "|   n   |   N   |    C    |    p    |    pn    |\n------------------------------------------------\n");
-  
-  for (i=0; i<index+1; i++)
-  {
-//     calculating concentrates
-    x = stat_all[i];
-    y = step;
-    conc = x / y;
-    
-//     calculating probabilityes
-    x = (i + 1) * stat_all[i];
-    y = step * num_mol;
-    p = x / y;
-    pn = (i + 1) * p;
-    
-    fprintf (f_out, " %7i %7i %9.2f %9.5f %10.5f\n", i+1, stat_all[i], conc, p, pn);
-  }
-  
-//   types of aglomerates
-  x = type_agl[0] + type_agl[1];
-  type[0] = type_agl[0];
-  type[1] = type_agl[1];
-  fprintf (f_out, "------------------------------------------------\n");
-  fprintf (f_out, "LINEAR=%.5f\nCYCLE=%.5f\n", type[0]/x, type[1]/x);
-  
-  fclose (f_out);
-  
-  return 0;
-}

statgen/CMakeLists.txt

@@ -1,23 +1,33 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required (VERSION 2.8)
 
-project(statgen)
+cmake_policy(SET CMP0011 NEW)
+cmake_policy(SET CMP0003 OLD)
 
-set(MY_CXX_FLAGS  "-Wall")
-set(CMAKE_CXX_FLAGS "-O0 ${MY_CXX_FLAGS}")
-set(CMAKE_SHARED_LINKER_FLAGS "-lm")
+# set project name
+set (PROJECT statgen)
+# set additional cmake file
+include (${PROJECT}.cmake)
 
-set(SOURCE_EXE main.c)
-set(SOURCE_LIB add_main.c 
-               coords.c 
-               graph.c 
-               int2char.c 
-               messages.c 
-               stat_print.c
-               stat_select.c
-               stat_sort.c
-               summary_stat.c)
 
-add_library(stat SHARED ${SOURCE_LIB})
-add_executable(statgen ${SOURCE_EXE})
+# additional options
+OPTION (WITH_DEBUG_MODE "Build with debug mode" ON)
+OPTION (ADD_INCLUDE "Add include files" ON)
 
-target_link_libraries(statgen stat)
+# set libraries
+set (LIBRARIES)
+  foreach (LIBRARY ${LIBRARIES})
+    find_library ("${LIBRARY}_FOUND" ${LIBRARY})
+      message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
+      if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
+        message (STATUS "Adding library sources")
+        add_subdirectory (../${LIBRARY} lib/${LIBRARY})
+      endif ()
+  endforeach ()
+
+# additional targets
+set (TARGETS "")
+set (HEADERS "")
+
+message (STATUS "SOURCES: ${SOURCES}")
+
+add_subdirectory (src)

statgen/CMakeLists_bckp.txt

@@ -0,0 +1,23 @@
+cmake_minimum_required(VERSION 2.8)
+
+project(statgen)
+
+set(MY_CXX_FLAGS  "-Wall")
+set(CMAKE_CXX_FLAGS "-O0 ${MY_CXX_FLAGS}")
+set(CMAKE_SHARED_LINKER_FLAGS "-lm")
+
+set(SOURCE_EXE main.c)
+set(SOURCE_LIB add_main.c 
+               coords.c 
+               graph.c 
+               int2char.c 
+               messages.c 
+               stat_print.c
+               stat_select.c
+               stat_sort.c
+               summary_stat.c)
+
+add_library(stat SHARED ${SOURCE_LIB})
+add_executable(statgen ${SOURCE_EXE})
+
+target_link_libraries(statgen stat)

statgen/src/CMakeLists.txt

@@ -0,0 +1,61 @@
+set ("${PROJECT}_VERSION_MAJOR" 1)
+set ("${PROJECT}_VERSION_MINOR" 0)
+set ("${PROJECT}_VERSION_PATCH" 1)
+set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
+
+message (STATUS ${${PROJECT}_VERSION})
+
+## set files
+# main files
+set (MAIN_SOURCES main)
+# not public srcs
+set (PRIVATE_CLASSES)
+# headers only files
+SET (HEADERS_ONLY)
+# public srcs
+set (PUBLIC_CLASSES add_main 
+                    coords 
+                    graph 
+                    int2char 
+                    messages 
+                    stat_print 
+                    stat_select 
+                    stat_sort 
+                    summary_stat)
+# public headers
+set (PUBLIC_HEADERS)
+# shared libraries
+if (CMAKE_COMPILER_IS_GNUCXX)
+  set (ADDITIONAL_LIB m)
+else ()
+  set (ADDITIONAL_LIB)
+endif()
+set (SOURCES)
+
+# append list
+foreach (class ${PRIVATE_CLASSES})
+  LIST (APPEND SOURCES ${class}.c)
+  LIST (APPEND HEADERS ${class}.h)
+endforeach ()
+
+foreach (class ${HEADERS_ONLY})
+  LIST (APPEND HEADERS ${class}.h)
+endforeach ()
+
+foreach (class ${PUBLIC_CLASSES})
+  LIST (APPEND SOURCES ${class}.c)
+  LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
+  LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
+endforeach ()
+
+# link libraries and compile
+add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
+target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
+
+# install properties
+INSTALL (TARGETS ${PROJECT} 
+         DESTINATION bin)
+if (ADD_INCLUDE)
+  INSTALL (FILES ${PUBLIC_HEADERS} 
+           DESTINATION include/${PROJECT})
+endif ()

statgen/src/main.c

@@ -4,14 +4,14 @@
 #include <string.h>
 #include <time.h>
 
-#include "add_main.h"
-#include "coords.h"
-#include "int2char.h"
-#include "messages.h"
-#include "stat_print.h"
-#include "stat_select.h"
-#include "stat_sort.h"
-#include "summary_stat.h"
+// #include "add_main.h"
+// #include "coords.h"
+// #include "int2char.h"
+// #include "messages.h"
+// #include "stat_print.h"
+// #include "stat_select.h"
+// #include "stat_sort.h"
+// #include "summary_stat.h"
 
 
 int main (int argc, char *argv[])

statgen/src/stat_print.c

@@ -9,7 +9,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "graph.h"
+// #include "graph.h"
 
 
 int printing_agl (const char *input, const char *output, const int *connect, 

statgen/statgen.cmake

@@ -0,0 +1,22 @@
+# set directories
+set ("${PROJECT}_BINARY_DIR"  bin)
+set ("${PROJECT}_SOURCE_DIR" src:include)
+set ("${PROJECT}_LIB_DIR" lib)
+
+set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
+set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
+set (EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/${${PROJECT}_BINARY_DIR})
+set (CMAKE_VERBOSE_MAKEFILE ON)
+set (CMAKE_BUILD_TYPE Debug)
+
+if ( WITH_DEBUG_MODE )
+  ADD_DEFINITIONS ( -DDEBUG_MODE=1 )
+endif ()
+
+if ( CMAKE_COMPILER_IS_GNUCXX )
+  set (ADD_CXX_FLAGS  "-Wall -v")
+  set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
+  set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
+else ()
+  message ("not yet")
+endif ()