在最后一行代码上出现段错误

Question

I'm hoping to implement a simple molecular dynamics program. My first step is to define the system as a series of atoms, each with a type, an id number, a 3 dimensional position vector, and a 3D velocity vector. Below is the program I've written to do so:

FILE *init;

static int randomVelocity(void)  
{  
     return rand()/RAND_MAX - 0.5;  
}  


int main(int argc, char *argv[])  
{  

    int iType;  
    int iID;  
    int i;  
    double* pdPosition;  
    double* pdVelocity;  
    char* line;  
    Atom* poAtoms;  
    int count = 0;  

    init = fopen("newdat.txt", "r+");  
    srand((unsigned)time(NULL));  
    line = malloc(81*sizeof(char));  
    while (fgets(line, 80, init) != NULL)    
    {  
         char* tok1;  
         char* tok2;  
         char* tok3;  
         char* tok4;  
         tok1 = strtok(line, " \t");  
         if ((tok1 == NULL) || (tok1[0] == '*'))   
         {  
              break;  
         }  
         tok2 = strtok(NULL, " \t");  
         tok3 = strtok(NULL, " \t");  
         tok4 = strtok(NULL, " \t");  
         iType = atoi(tok1);  
         iID = count;  
         pdPosition = (double*)malloc(3*sizeof(double));  
         pdVelocity = (double*)malloc(3*sizeof(double));     
         pdPosition[0] = atof(tok2);  
         pdPosition[1] = atof(tok3);  
         pdPosition[2] = atof(tok4);  
         pdVelocity[0] = randomVelocity();  
         pdVelocity[1] = randomVelocity();    
         pdVelocity[2] = randomVelocity();  
         poAtoms[count] = Atom_new(iType, iID, pdPosition, pdVelocity);  
         count++;  
    }  

    for (i = 0; i < count; i++)  
    {  
         Atom_print(poAtoms[i]);  
         Atom_free(poAtoms[i]);  
    }   

    free(line);  
    return 0;  
}

Here is the header file atom.h:

/**** atom.h ****/


typedef struct Atom_str *Atom;  

Atom Atom_new(int iType, int iID, double* adPosition, double* adVelocity);  

void Atom_free(Atom oAtom);  

void Atom_print(Atom oAtom);  

and the test input file:

1 5 7 9  
2 12 13 14  

The program compiles, but when I run it, I get the expected output followed by a seg fault. I'm using the GDB debugger, and the seg fault appears to happen on the very last line of code, after the return statement! Is it a memory management issue?

Answer 1

You've never malloc ed memory for poAtoms . Writing to wherever that uninitialized pointer points can easily cause a segfault.

Before you start reading the file, you should allocate some space,

unsigned expected_count = 2; // for the test input file, would be much larger in real runs
poAtoms = malloc(expected_count*sizeof(*poAtoms));

And then you have to check inside the read-loop that you're not writing past the allocated memory. Before

    poAtoms[count] = Atom_new(iType, iID, pdPosition, pdVelocity);

insert a check,

    if (expected_count <= count)
    {
        expected_count *= 2;   // double the space, could also be a smaller growth factor
        Atom *temp = realloc(poAtoms, expected_count*sizeof(*poAtoms));
        if (temp == NULL)
        {
            perror("Reallocation failed, exiting\n");
            exit(EXIT_FAILURE);
        }
        poAtoms = temp;
    }

if the allocated space for poAtoms is already used, try to get more with realloc , if that fails, abort unless you know how to fix it. If the reallocation succeeds, we can continue collecting new atoms.

Answer 2

What is tok1[0] doing in if condition ? Did you check a small code snippet for strtok that what is returned or checked when you try to print tok1[[0]?

Answer 3

Can you explain what does 1 5 7 9 represent in input file ? are thei type id and velocity . If so you can manipulate and differentiate them by hyphen and extract each value by strtok as NULL. Also check if fgets is appending NULL or may be * as you have tried to check in if condition probably for End of line . I have a gut felling that it can be the place where you are going wrong , Or if you can pleas explain your input file it would be helpful