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Arrays of nested structures - cannot allocate memory - HELP

Posted on 2004-11-10
Medium Priority
Last Modified: 2010-04-15
I am trying to build a molecular model of a material. Each material is composed of a user specified number of molecules and each molecule cis composed of a set number of atoms. I am trying to allocate memory to this structure as follows (please ignore the printf's as they are mainly for debugging purposes):

System *GenerateNewSystem () {
    int temp;
    int temp_check;
    int dummy;
    int temp_int[MAXBUF][MAXBUF];
    char temp_string[MAXBUF][MAXBUF];
    float temp_float[MAXBUF][MAXBUF];
    int mol_types;
    /* Variable Initialisation */
    System *material;
    /* Memory Allocation */
    material = xmalloc (sizeof material);
    /* material->temperature = GetFloat ("Specify material temperature (Kelvin): ", 0.0, INF);*/
    material->size = GetInt ("Specify the total number of molceules (Integer): ", 0, 9999999999);
    /* printf ("Please give this system a reference (Max 256 characters): ");
    scanf ("%s", &material->reference); */
    material->molecules = xmalloc (material->size * sizeof * material->molecules);
    mol_types = GetInt ("Specify the number of different molecule types: ",0 , material->size);
    temp_check = material->size; /* indicates how many molecules left to be allocated */

    dummy = 0; /* a running record of where in the array the molecules have been allocated up to */
    for (i=0; i<mol_types; i++) { /* allocate molecule & atomic details */
        printf ("\nYou currently have %d molecules left to allocate.", temp_check);
        printf ("Molecule %d:\n------------\n\n", (i+1));
        printf ("Specify label for this molecule: "); scanf ("%s", &temp_string[0]);
        temp_int[0][0] = GetInt ("Specify the number of atoms within this molecule: ",0 , 9999999999);

            printf ("mol: %d, i: %d, temp_int: %d", mol_types, i, temp_int[0][0]);
        for (k=0; k<temp_int[0][0]; k++) { /*Copy atom details into a temporary array */
              printf ("\nAtom %d Proton Number: ", (k+1));
              scanf ("%d", &temp_int[k][1]);
              printf ("Atom %d Neutron Number: ", (k+1));
              scanf ("%d", &temp_int[k][2]);
              printf ("Atom %d Charge: ", (k+1));
              scanf ("%f", &temp_float[k][1]);
              printf ("Atom %d Spin: ", (k+1));
              scanf ("%f", &temp_float[k][2]);
              printf ("Atom %d Symbol: ", (k+1));
              scanf ("%s", temp_string[k+1]);            

        printf ("\n\nSpecify the number of these molecules within the material (Less than %d): ", (temp_check - mol_types + 1));
        temp = GetInt ("", 0, temp_check);
        temp_check = temp_check - temp;        
        for (j=dummy; j<(dummy+temp); j++) {                  

            material->molecules[j] = xmalloc (sizeof material->molecules[j]);
                  printf ("-, ");
            material->molecules[j]->size = temp_int[0][0];
                  printf ("-, ");
            strncpy(material->molecules[j]->reference, temp_string[0], MAXBUF);
                  printf ("-, ");                  
            material->molecules[j]->atoms = xmalloc (material->molecules[j]->size * sizeof *material->molecules[j]->atoms); *IT FAILS ON THIS LINE*
                  printf ("-, ");
            material->molecules[j]->position.x = rand()/(RAND_MAX+1.0);
                  printf ("-, ");
            material->molecules[j]->position.y = rand()/(RAND_MAX+1.0);
                  printf ("-, ");
            material->molecules[j]->position.z = rand()/(RAND_MAX+1.0);
                  printf ("-\n");
            for (k=0; k<temp_int[0][0]; k++) {
      material->molecules[j]->atoms[k] = xmalloc (sizeof material->molecules[j]->atoms[k]); *OR FAILS ON THIS LINE*
                        printf ("*, ");
                material->molecules[j]->atoms[k]->p = temp_int[k][1];
                                                                printf ("*, ");
      material->molecules[j]->atoms[k]->n = temp_int[k][2];
                        printf ("*, ");
      material->molecules[j]->atoms[k]->charge = temp_float[k][1];
                                                                printf ("*, ");
      material->molecules[j]->atoms[k]->spin = temp_float[k][2];
                                                                printf ("*, ");
      strncpy (material->molecules[j]->atoms[k]->symbol, temp_string[k+1], 3);
                        printf ("*\n");
        dummy = j+1;
      return material;
'xmallox' is a wrapper for malloc where it will automatically check for available memory. 'getint' is a working integer checking input mask. My structures are as follows:

typedef struct tri_dimensional_floats {

    float x;
    float y;
    float z;
} Cartesian;

typedef struct atom_properties {
    int p;
    int n;
    char symbol[3];
    float spin;
    float charge;
    Cartesian position;
} Atom;

typedef struct molecule_properties {
    Atom **atoms;
    Cartesian position;
    char reference[MAXBUF];
    int size;
} Molecule;

typedef struct material_properties {
    Molecule **molecules;
    float temperature;
    char reference[MAXBUF];
    int size;
    struct material_properties *next;
} System;

Any help is appreciated as to why it fails on the two specified lines. It compiles fine but the error occurs at run-time.


Question by:Solaron
LVL 22

Assisted Solution

grg99 earned 150 total points
ID: 12545926
What is MAXBUF?

>   material = xmalloc (sizeof material);

This can never be correct.... You're asking for memory big enough to hold "material", which is just a pointer.

I think you mean:    material = xmalloc (sizeof (material *) );

or                       :    material = xmalloc ( sizeof ( System )  );
LVL 22

Expert Comment

ID: 12545959
The error above is probably causing the following lines that store values into  material-->field to wrreck the heap structure,
causing the later mallocs to fail.

Also have xmalloc print out the size of each allocation, and have it test the malloc() result for not NULL.

LVL 12

Expert Comment

ID: 12546037
Hi grg99,
> material = xmalloc (sizeof (*material) );


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Author Comment

ID: 12546568
I have tried both of those approaches to no success... it halts at exactly the same point. MAXBUF is an integer of 256. i use that just for test purposes. I understood that xmalloc (sizeof xxxxx) is allocating memory to a pointer where as xmalloc (sizeof *xxxxx) allocates pointer memory. Either way, they both cause the same error and i am pretty confident i do not need to bracket the 'sizeof'
LVL 22

Expert Comment

ID: 12546730
Ok, in your xmalloc, please print out the size.

  It had better be around  272, the apparent size of your "system" struct.

 If it's 4, you're taking the sizeof the wrong thing.

And you *do* need the parentheses in many cases, otherwise sizeof will be parsed incorrectly


Accepted Solution

van_dy earned 225 total points
ID: 12547916
>> material->molecules = xmalloc (material->size * sizeof * material->molecules);
replace with
  material->molecules = xmalloc (material->size * sizeof (* material->molecules));

>>material->molecules[j] = xmalloc (sizeof material->molecules[j]);
replace with
 material->molecules[j] = xmalloc (sizeof Moleule);

>>material->molecules[j]->atoms = xmalloc (material->molecules[j]->size * sizeof *material->molecules[j]->atoms); *IT FAILS ON THIS LINE*
replace with
material->molecules[j]->atoms = xmalloc (material->molecules[j]->size * sizeof (*material->molecules[j]->atoms)); *IT FAILS ON THIS LINE*

material->molecules[j]->atoms[k] = xmalloc (sizeof material->molecules[j]->atoms[k]); *OR FAILS ON THIS LINE*
replace with
material->molecules[j]->atoms[k] = xmalloc (sizeof Atom); *OR FAILS ON THIS LINE*

hope this helps,

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