There is this linear system given by the following 2d array:
1.0 0.0 -1.0 -4.9 -5.9 -6.9 -7.9
0.0 1.0 2.0 4.4 5.4 6.4 7.4
0.0 0.0 0.0 5.7 5.7 -3.3 -3.3
0.0 0.0 0.0 2.9 2.9 2.9 2.9
0.0 0.0 0.0 7.0 -1.0 -3.0 -3.0
0.0 0.0 -20.0 -65.9 -89.9 -100.9 128.9
Whenever I get a 0 in my main diagonal (when row equals column), I want to change the order of the rows, so there's no zeroes on my main diagonal.
In this case, the row 2(counting from 0) should be traded with row 5 (also counting from 0) because with this, there is no 0s on the main diagonal.
I'm already doing that, but I'm "deleting" the first line and appending it on the end of the linear system. How should I make this logic to know where to exactly trade the rows?
The code is as follows:
void change_order(double linear[6][7], unsigned int qty) {
double aux[100];
// dynamically create an array of pointers of size `m`
double **matrix = (double **)malloc((qty + 1) * sizeof(double *));
// dynamically allocate memory of size `n` for each row
for (int r = 0; r < qty+ 1; r++) {
matrix[r] = (double *)malloc((qty + 1) * sizeof(double));
}
for (int i = 0; i < qty; i++) {
for (int j = 0; j < qty+ 1; j++) {
if (i == 0)
aux[j] = linear[i][j];
}
}
for (int i = 0; i < qty; i++) {
for (int j = 0; j < qty+ 1; j++) {
matrix[i][j] = linear[i][j];
}
}
remove_line(matrix, 0, qty);
for (int i = 0; i < qty; i++) {
for (int j = 0; j < qty+ 1; j++) {
linear[i][j] = matrix[i][j];
}
}
for (int i = 0; i < qty; i++) {
for (int j = 0; j < qty+ 1; j++) {
if (i == qty- 1) {
linear[i][j] = aux[j];
}
}
}
}
void remove_line(double ** linear, int row, unsigned int qty) {
qty--;
free(linear[row]);
while (row < qty) {
linear[row] = linear[row + 1];
row++;
}
}
int main() {
double matrix[][7] = {
{1.0, 0.0, -1.0, -4.9, -5.9, -6.9, -7.9},
{0.0, 1.0, 2.0, 4.4, 5.4, 6.4, 7.4},
{0.0 , 0.0, 0.0, 5.7, 5.7, -3.3, -3.3},
{0.0 , 0.0, 0.0, 2.9, 2.9, 2.9, 2.9},
{0.0 , 0.0, 0.0, 7.0, -1.0, -3.0, -3.0},
{0.0 , 0.0, -20.0, -65.9, -89.9, -100.9, 128.9}
};
change_order(matrix, 6);
}
Example input:
0 3 2 28
4 0 2 24
2 3 0 16
4 2 1 0
Can be exchanged for:
4 0 2 24
2 3 0 16
4 2 1 0
0 3 2 28
If I'm understanding your requirements correctly, would you please try the following:
#include <stdio.h>
#include <stdlib.h>
#define ROWS 6
#define COLS 7
/*
* search for a trade line to be swapped below the n'th row
*/
int search_trade(double matrix[][COLS], int qty, int n)
{
for (int i = n + 1; i < qty; i++) {
if (matrix[i][n] != 0.0) {
return i; // i'th row is a nice trade
}
}
return -1; // not found
}
/*
* swap m'th row and n'th row
*/
void swap(double matrix[][COLS], int qty, int m, int n)
{
int j;
double tmp;
for (j = 0; j < qty + 1; j++) {
tmp = matrix[m][j];
matrix[m][j] = matrix[n][j];
matrix[n][j] = tmp;
}
}
void change_order(double linear[][COLS], int qty) {
for (int i = 0; i < qty; i++) {
if (linear[i][i] == 0.0) { // found 0 in the diagonal
int k = search_trade(linear, qty, i); // search for the trade row
if (k < 0) { // no applicable trade
fprintf(stderr, "cannot find the row to swap. abort.\n");
exit(1);
} else {
swap(linear, qty, i, k); // swap i'th row and k'th row
}
}
}
}
/*
* print the elements of the matrix
*/
void matprint(double matrix[][COLS], int qty)
{
for (int i = 0; i < qty; i++) {
for (int j = 0; j < qty + 1; j++) {
printf("%.2f%s", matrix[i][j], j == qty ? "\n" : " ");
}
}
printf("\n");
}
int main() {
double matrix[][COLS] = {
{1.0, 0.0, -1.0, -4.9, -5.9, -6.9, -7.9},
{0.0, 1.0, 2.0, 4.4, 5.4, 6.4, 7.4},
{0.0 , 0.0, 0.0, 5.7, 5.7, -3.3, -3.3},
{0.0 , 0.0, 0.0, 2.9, 2.9, 2.9, 2.9},
{0.0 , 0.0, 0.0, 7.0, -1.0, -3.0, -3.0},
{0.0 , 0.0, -20.0, -65.9, -89.9, -100.9, 128.9}
};
matprint(matrix, ROWS);
change_order(matrix, ROWS);
matprint(matrix, ROWS);
}
Output:
0.00 1.00 2.00 4.40 5.40 6.40 7.40
0.00 0.00 0.00 5.70 5.70 -3.30 -3.30
0.00 0.00 0.00 2.90 2.90 2.90 2.90
0.00 0.00 0.00 7.00 -1.00 -3.00 -3.00
0.00 0.00 -20.00 -65.90 -89.90 -100.90 128.90
1.00 0.00 -1.00 -4.90 -5.90 -6.90 -7.90
0.00 1.00 2.00 4.40 5.40 6.40 7.40
0.00 0.00 -20.00 -65.90 -89.90 -100.90 128.90
0.00 0.00 0.00 2.90 2.90 2.90 2.90
0.00 0.00 0.00 7.00 -1.00 -3.00 -3.00
0.00 0.00 0.00 5.70 5.70 -3.30 -3.30
You'll see the 2nd row and the 5th row are swapped.
The main concept is:
Seek the diagonal elements for value 0.
If 0 is found, search for a trade row which has a non-zero value in the same column.
If no trade rows are found, the program prints an error message and aborts.
If a trade row is found, swap the rows.
[Edit]
Answering your comment, the code assumes the count of cols == count of rows + 1.
As your provided example has 4x4 matrix, let me add an extra column as:
double matrix[][COLS] = {
{0, 3, 2, 28, -1},
{4, 0, 2, 24, -1},
{2, 3, 0, 16, -1},
{4, 2, 1, 0, -1}
};
(Please note the value -1 is a dummy value and meaningless so far.)
And modify the #define lines as:
#define ROWS 4
#define COLS 5
Then the program will output:
0.00 3.00 2.00 28.00 -1.00
4.00 0.00 2.00 24.00 -1.00
2.00 3.00 0.00 16.00 -1.00
4.00 2.00 1.00 0.00 -1.00
4.00 0.00 2.00 24.00 -1.00
0.00 3.00 2.00 28.00 -1.00
4.00 2.00 1.00 0.00 -1.00
2.00 3.00 0.00 16.00 -1.00
which shows the rows are properly rearranged having no 0 values in the diagonal.
(BTW your expected result breaks having 0 in the diagonal in the last row.)
**You can make a main function like as follows:
//after passing the linear function
int i,j, temp; // declare i and j as global variables**
for(i=0,i<qty+1,i++)
{
for (j=0;j<qty+1;j++)
{
if(i==j & matrix[i][j]==0)
{
remove_line;
temp = i;
break;
}
}
} // here we are looking for a zero in the diagonal.
for (;i<qty+1;i++)
{
if(matrix[i][j]!=0)
{
matrix[temp][j] = linear[i][j]
}
}
// **here we are increasing the rows till we get a non zero element and then
interchanging the values.**
Related
Below I have a sample table stored in a text file - random.dat.
0.00 0.01 2.30 300
2.00 0.015 1.45 102
4.00 0.03 6.08 174
6.00 5.95 0.05 225
Now I want to read the contents of the table and store into an array. I have the following code that almost does the job.
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
int main()
{
int i,j;
int M = 3, N = 3;
FILE *fp;
double value1[M][N];
fp = fopen("random.dat","r");
if (fp == NULL)
{
exit(1);
}
for (i = 0; i < M; i++)
{
for (j = 0; j < N; j++)
{
fscanf(fp, "%lf", &value1[i][j]);
if (feof(fp))
{
break;
}
}
}
\*Just to check that my code has stored the arrays properly, I put the following printf statements*/
printf("%lf\n", value1[0][0]);
printf("%lf\n", value1[0][1]);
printf("%lf\n", value1[0][2]);
printf("%lf\n", value1[0][3]);
printf("%lf\n", value1[1][0]);
printf("%lf\n", value1[1][1]);
printf("%lf\n", value1[1][2]);
printf("%lf\n", value1[1][3]);
}
The values that I want and thought the program would give me:
value1[0][0] = 0.00 value1[0][1] = 0.01 value1[0][2] = 2.30 value1[0][3] = 300
value1[1][0] = 2.00 value1[1][1] = 0.015 value1[1][2] = 1.45 value1[1][3] = 102
Instead, it gives me,
value1[0][0] = 0.00 value1[0][1] = 0.01 value1[0][2] = 2.30 value1[0][3] = 300.0
value1[1][0] = 300.0 value1[1][1] = 2.00 value1[1][2] = 0.015 value1[1][3] = 1.45
I couldn't figure out a solution for this. Can someone point where I have made an error?
Thank you
If M and N are 3, value1 [0] [3] is out of bounds. Change N to 4.
I need to store the results of two array's divisions in another array using pointers. But it displayed: arr3 = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
How should I use a pointer to calculating that division part?
#include <stdio.h>
int main()
{
double arr1[10] = {10.0, 9.0, 8.0, 7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0};
double arr2[10] = {1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,};
double arr3[10];
double *ptr=arr3;
int i=0;
for(i=0;i<10;i++)
{
*ptr = arr1[i]/arr2[i];
ptr++;
}
printf("arr3= ");
for(i=0;i<10;i++)
{
printf("%.2f ",*ptr);
ptr++;
}
return 0;
}
Just run at them as pointers as well. Also you needed to reset ptr to the head of the array after the first iteration.
double *ptr=arr3;
double *ptr1=arr1;
double *ptr2=arr2;
for(int i=0;i<10;i++)
{
*ptr = (*ptr1)/(*ptr2);
ptr++;ptr1++;ptr2++;
}
ptr=arr3;
for(i=0;i<10;i++)
{
printf("%.2f ",*ptr);
ptr++;
}
you need to reset your ptr to ptr=arr3; before your second loop, since what you are doing now is filling values untill 9 and displaying from 10 to 19 (adresses relative to arr3)
I am trying to write a simple program in C to calculate pairwise interaction (Coulomb force) between two chain of beads.Both chains contain 10 beads but one chain is positively charged and the other one is negatively charged. I am reading the x,y,z coordinates and the charge information from two files (Charge from 7th column of atom.psf and coordinates from 6th 7th and 8th columns of beads.pdb).
Here are the contents of the files:
atom.psf
20 !NATOM
1 A 1 CHN A A 1.000000 0.0000 0
2 A 1 CHN A A 1.000000 0.0000 0
3 A 1 CHN A A 1.000000 0.0000 0
4 A 1 CHN A A 1.000000 0.0000 0
5 A 1 CHN A A 1.000000 0.0000 0
6 A 1 CHN A A 1.000000 0.0000 0
7 A 1 CHN A A 1.000000 0.0000 0
8 A 1 CHN A A 1.000000 0.0000 0
9 A 1 CHN A A 1.000000 0.0000 0
10 A 1 CHN A A 1.000000 0.0000 0
11 A 2 CHN A A -1.000000 0.0000 0
12 A 2 CHN A A -1.000000 0.0000 0
13 A 2 CHN A A -1.000000 0.0000 0
14 A 2 CHN A A -1.000000 0.0000 0
15 A 2 CHN A A -1.000000 0.0000 0
16 A 2 CHN A A -1.000000 0.0000 0
17 A 2 CHN A A -1.000000 0.0000 0
18 A 2 CHN A A -1.000000 0.0000 0
19 A 2 CHN A A -1.000000 0.0000 0
20 A 2 CHN A A -1.000000 0.0000 0
18 !NBOND: bonds
1 2 2 3 3 4 4 5
5 6 6 7 7 8 8 9
9 10 11 12 12 13 13 14
14 15 15 16 16 17 17 18
18 19 19 20
beads.pdb
ATOM 1 A CHN 1 1.000 0.000 0.000 1.00 0.00 A
ATOM 2 A CHN 1 2.000 0.000 0.000 1.00 0.00 A
ATOM 3 A CHN 1 3.000 0.000 0.000 1.00 0.00 A
ATOM 4 A CHN 1 4.000 0.000 0.000 1.00 0.00 A
ATOM 5 A CHN 1 5.000 0.000 0.000 1.00 0.00 A
ATOM 6 A CHN 1 6.000 0.000 0.000 1.00 0.00 A
ATOM 7 A CHN 1 7.000 0.000 0.000 1.00 0.00 A
ATOM 8 A CHN 1 8.000 0.000 0.000 1.00 0.00 A
ATOM 9 A CHN 1 9.000 0.000 0.000 1.00 0.00 A
ATOM 10 A CHN 1 10.000 0.000 0.000 1.00 0.00 A
ATOM 11 A CHN 2 1.000 80.000 0.000 1.00 0.00 A
ATOM 12 A CHN 2 2.000 80.000 0.000 1.00 0.00 A
ATOM 13 A CHN 2 3.000 80.000 0.000 1.00 0.00 A
ATOM 14 A CHN 2 4.000 80.000 0.000 1.00 0.00 A
ATOM 15 A CHN 2 5.000 80.000 0.000 1.00 0.00 A
ATOM 16 A CHN 2 6.000 80.000 0.000 1.00 0.00 A
ATOM 17 A CHN 2 7.000 80.000 0.000 1.00 0.00 A
ATOM 18 A CHN 2 8.000 80.000 0.000 1.00 0.00 A
ATOM 19 A CHN 2 9.000 80.000 0.000 1.00 0.00 A
ATOM 20 A CHN 2 10.000 80.000 0.000 1.00 0.00 A
I am having trouble with my final output. At every timestep (t=0 to 100), I need to write the coordinates of 20 atoms. My trial code is given below.
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#define Epsilon0 8.85e-12 // Permittivity of free space (C^2/(N m^2))
#define Constant (1/(4*M_PI*Epsilon0)) // Useful constant
#define gamma 100.0
#define ROW 20
int row, col, j, t;
float x[20], y[20], z[20], q[20], dx, dy, dz, R, Fx, Fy, Fz, F, v, shift;
int main()
{
FILE *psf=fopen("atom.psf", "r");
FILE *pdb=fopen("beads.pdb", "r");
FILE *fout=fopen("out.txt", "a");
FILE *fout2=fopen("coord.dump", "a");
fprintf(fout2, "ITEM: TIMESTEP\n 100\n");
fprintf(fout2, "ITEM: NUMBER OF ATOMS\n 20\n");
fprintf(fout2, "ITEM: ATOMS id type x y z\n");
char buffer[1024];
fgets(buffer, 1024, psf);
int i = 0;
for(i=0 ; (i<ROW) && (psf != NULL); i++)
{
fscanf (psf,"%*8d%*4s%*4d%*6s%*5s%*6s%11f%*14f%*12d", &q[i]);
fscanf (pdb,"%*4s%*7d%*5s%*4s%*6d%12f%8f%8f%*6f%*6f%*9s", &x[i], &y[i], &z[i]);
}
for (t=0; t<100; t++)
{
//F = 0.0;
v = F/gamma;
shift = v*t;
x[i] = x[i] + shift;
y[i] = y[i] + shift;
z[i] = z[i] + shift;
for(i=0; i<ROW; i++)
{
Fx = Fy = Fz = F = 0.0;
// Loop over other charges to compute force on this charge
for (j=0 ; j<ROW ; j++)
{
//simply skip this itearation
if(i == j)
continue;
// Compute the components of vector distance between two charges
dx = x[i] - x[j];
dy = y[i] - y[j];
dz = z[i] - z[j];
R = sqrt(dx*dx + dy*dy + dz*dz);
// Compute the x and y components of the force between
// these two charges using Coulomb's law
Fx += Constant*q[i]*q[j]*dx/(R*R*R);
Fy += Constant*q[i]*q[j]*dy/(R*R*R);
Fz += Constant*q[i]*q[j]*dz/(R*R*R);
}
F = sqrt(Fx*Fx + Fy*Fy + Fz*Fz);
fprintf(fout, "%d %3.3g %3.3g %3.3g %3.3g\n", i+1, Fx, Fy, Fz, F);
//fprintf(fout2, "%d %3.3g %3.3g %3.3g\n", i+1, x[i], y[i], z[i]);
}
fprintf(fout2, "%d %3.3g %3.3g %3.3g\n", i, x[i], y[i], z[i]);
}
}
This is probably a situation where instead of attempting to keep track of numerous separate arrays containing various information, life can be made a lot easier if you simply create a struct that captures the needed information for each bead and then create a single array of struct. For example, you want to capture the x,y,z position, charge, and component forces acting on each bead. (I included the total force as well, but that is optional). Your struct for each bead (I called it beads) could be as simple as:
typedef struct {
float x, y, z, chrg, fx, fy, fz, f;
} beads;
In your code, you simply create an array of beads (one for each bead you need information on). For example, creating an array of beads with 20 elements, you could do something like the following:
#define Eo 8.85e-12F
#define KEair (1/(4*M_PI*Eo))
enum { NATM = 20, MAXL = 128 }; /* constants for number of beads/line len */
...
beads atoms[NATM] = {{ .x = 0.0 }};
Now we have an array of struct called atoms to store information in. You can read information from each of your files and store the x, y, z positions for each bead as well as the charge. Then you can compute the force acting on each bead by computing the force due to every other bead and summing the information in the remaining force component and total members of each struct. You may do something like:
for (i = 0; i < NATM; i++) { /* for each bead */
for (size_t j = 0; j < NATM; j++) { /* compute force from every other */
if (i == j) continue; /* excluding itself */
float dx = atoms[j].x - atoms[i].x, /* calculate component distances */
dy = atoms[j].y - atoms[i].y,
dz = atoms[j].z - atoms[i].z,
d = sqrt (dx * dx + dy * dy + dz * dz); /* total distance */
/* compute component and total forces acting on each bead (sum) */
atoms[i].fx += (KEair * atoms[i].chrg *atoms[j].chrg * dx)/(d * d * d);
atoms[i].fy += (KEair * atoms[i].chrg *atoms[j].chrg * dy)/(d * d * d);
atoms[i].fz += (KEair * atoms[i].chrg *atoms[j].chrg * dz)/(d * d * d);
atoms[i].f += (KEair * atoms[i].chrg *atoms[j].chrg)/(d * d);
}
}
(you can confirm the approach to the sum at System of discrete charges)
Putting it altogether, you could do something like the following:
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#define Eo 8.85e-12F
#define KEair (1/(4*M_PI*Eo))
enum { NATM = 20, MAXL = 128 };
typedef struct {
float x, y, z, chrg, fx, fy, fz, f;
} beads;
FILE *xfopen (const char *fn, const char *mode);
float sqrt_fisr (float x);
int main (int argc, char **argv) {
beads atoms[NATM] = {{ .x = 0.0 }};
size_t i;
char buf[MAXL] = ""; /* open/read atom.psf */
FILE *fp = xfopen (argc > 1 ? argv[1] : "dat/atom.psf", "r");
fgets (buf, MAXL, fp); /* read/discard 1st line */
for (i = 0; i < NATM && fgets (buf, MAXL, fp); i++) { /* read/parse data */
if (sscanf (buf, "%*s %*s %*s %*s %*s %*s %f", &atoms[i].chrg) != 1) {
fprintf (stderr, "error: read of charge failed, atom[%zu].\n", i);
return 1;
}
}
fclose (fp);
if (i != NATM) { /* validate NATM lines read */
fprintf (stderr, "error: only '%zu' charge values read.\n", i);
return 1;
}
/* open/read beads.pdb */
fp = xfopen (argc > 2 ? argv[2] : "dat/beads.pdb", "r");
for (i = 0; i < NATM && fgets (buf, MAXL, fp); i++) { /* read/parse data */
if (sscanf (buf, "%*s %*s %*s %*s %*s %f %f %f", &atoms[i].x,
&atoms[i].y, &atoms[i].z) != 3) {
fprintf (stderr, "error: read of position failed, atom[%zu].\n", i);
return 1;
}
}
fclose (fp);
if (i != NATM) { /* validate NATM lines read */
fprintf (stderr, "error: only '%zu' position values read.\n", i);
return 1;
}
for (i = 0; i < NATM; i++) { /* for each bead */
for (size_t j = 0; j < NATM; j++) { /* compute force from every other */
if (i == j) continue; /* excluding itself */
float dx = atoms[j].x - atoms[i].x, /* calculate component distances */
dy = atoms[j].y - atoms[i].y,
dz = atoms[j].z - atoms[i].z,
d = sqrt (dx * dx + dy * dy + dz * dz); /* total distance */
/* compute component and total forces acting on each bead (sum) */
atoms[i].fx += (KEair * atoms[i].chrg *atoms[j].chrg * dx)/(d * d * d);
atoms[i].fy += (KEair * atoms[i].chrg *atoms[j].chrg * dy)/(d * d * d);
atoms[i].fz += (KEair * atoms[i].chrg *atoms[j].chrg * dz)/(d * d * d);
atoms[i].f += (KEair * atoms[i].chrg *atoms[j].chrg)/(d * d);
}
}
for (i = 0; i < NATM; i++) /* output forces on each bead (component and total) */
printf (" atom[%2zu] %5.2f %5.2f %5.2f %+.2f %15.2f %15.2f %5.2f %15.2f\n",
i, atoms[i].x, atoms[i].y, atoms[i].z, atoms[i].chrg,
atoms[i].fx, atoms[i].fy, atoms[i].fz, atoms[i].f);
return 0;
}
/** simple fopen with error check */
FILE *xfopen (const char *fn, const char *mode)
{
FILE *fp = fopen (fn, mode);
if (!fp) {
fprintf (stderr, "xfopen() error: file open failed '%s'.\n", fn);
exit (EXIT_FAILURE);
}
return fp;
}
Example Use/Output
$ ./bin/coulomb
atom[ 0] 1.00 0.00 0.00 +1.00 13844509696.00 -13956823.00 0.00 13831302144.00
atom[ 1] 2.00 0.00 0.00 +1.00 4741866496.00 -13982750.00 0.00 22712082432.00
atom[ 2] 3.00 0.00 0.00 +1.00 2353591552.00 -14002249.00 0.00 24819521536.00
atom[ 3] 4.00 0.00 0.00 +1.00 1171170304.00 -14015272.00 0.00 25635096576.00
atom[ 4] 5.00 0.00 0.00 +1.00 359584800.00 -14021791.00 0.00 25947308032.00
atom[ 5] 6.00 0.00 0.00 +1.00 -359584608.00 -14021791.00 0.00 25947308032.00
atom[ 6] 7.00 0.00 0.00 +1.00 -1171170944.00 -14015272.00 0.00 25635096576.00
atom[ 7] 8.00 0.00 0.00 +1.00 -2353592320.00 -14002249.00 0.00 24819521536.00
atom[ 8] 9.00 0.00 0.00 +1.00 -4741866496.00 -13982751.00 0.00 22712082432.00
atom[ 9] 10.00 0.00 0.00 +1.00 -13844510720.00 -13956824.00 0.00 13831303168.00
atom[10] 1.00 80.00 0.00 -1.00 13844507648.00 13956823.00 0.00 13831302144.00
atom[11] 2.00 80.00 0.00 -1.00 4741867008.00 13982750.00 0.00 22712080384.00
atom[12] 3.00 80.00 0.00 -1.00 2353592064.00 14002249.00 0.00 24819521536.00
atom[13] 4.00 80.00 0.00 -1.00 1171170944.00 14015272.00 0.00 25635096576.00
atom[14] 5.00 80.00 0.00 -1.00 359585056.00 14021791.00 0.00 25947308032.00
atom[15] 6.00 80.00 0.00 -1.00 -359584864.00 14021791.00 0.00 25947308032.00
atom[16] 7.00 80.00 0.00 -1.00 -1171170560.00 14015272.00 0.00 25635096576.00
atom[17] 8.00 80.00 0.00 -1.00 -2353591808.00 14002249.00 0.00 24819521536.00
atom[18] 9.00 80.00 0.00 -1.00 -4741867008.00 13982751.00 0.00 22712080384.00
atom[19] 10.00 80.00 0.00 -1.00 -13844509696.00 13956824.00 0.00 13831304192.00
Looking at the output graphically, the forces increase from the end to a maximum in the center of each string or beads -- that checks, and the forces acting upon the beads in the X-direction is the greatest at each end and reverses direction at midpoint -- also a check. For example:
Total Force Acting on Each Bead
Forces acting in the X direction on Each Bead
Look things over and let me know if you have any questions.
Here's what I would change in your code:
Epsilon and Constant should be declared as constants:
"#define Epsilon0 8.85e-12"
"#define Constant (1/(4*pi*Epsilon0))""
Move the "i != j" inside the loop. That would prevent the loop from stopping if you hit that condition. You would just be skipping that iteration instead of stopping completely.
You don't really need the xi, yi , zij, Fx, Fy, Fz, Rij arrays. You can use simple variables as placeholders instead.
During each iteration of the inner loop, you would be calculating the partial force du to bead j. You need to add that force to the cumulative force.
In order to do that you can declare Fx, Fy and Fz outside of the loops, initialize the 3 variable to 0 inside the first loop and then add partial forces inside the inner loop.
Move the fprintf outside of the inner loop (but keep it inside the external loop)
UPDATE
This code does not handle I/O errors
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#define Epsilon0 8.85e-12 // Permittivity of free space (C^2/(N m^2))
#define Constant (1/(4*M_PI*Epsilon0)) // Useful constant
#define ROW 20
int row, col, j;
float x[20], y[20], z[20], q[20], dx, dy, dz, R, Fx, Fy, Fz, F;
int main()
{
FILE *psf=fopen("atom.psf", "r");
FILE *pdb=fopen("beads.pdb", "r");
FILE *fout=fopen("out.txt", "w");
char buffer[1024];
fgets(buffer, 1024, psf);
int i = 0;
for( ; (i<ROW) && (psf != NULL); i++)
{
fscanf (psf,"%*8d%*4s%*4d%*6s%*5s%*6s%11f%*14f%*12d", &q[i]);
fscanf (pdb,"%*4s%*7d%*5s%*4s%*6d%12f%8f%8f%*6f%*6f%*9s", &x[i], &y[i], &z[i]);
}
for(i=0; i<ROW; i++)
{
Fx = Fy = Fz = F = 0.0;
// Loop over other charges to compute force on this charge
for (j=0 ; j<ROW ; j++)
{
//simply skip this itearation
if(i == j)
continue;
// Compute the components of vector distance between two charges
dx = x[i] - x[j];
dy = y[i] - y[j];
dz = z[i] - z[j];
R = sqrt(dx*dx + dy*dy + dz*dz);
// Compute the x and y components of the force between
// these two charges using Coulomb's law
Fx += Constant*q[i]*q[j]*dx/(R*R*R);
Fy += Constant*q[i]*q[j]*dy/(R*R*R);
Fz += Constant*q[i]*q[j]*dz/(R*R*R);
}
F = sqrt(Fx*Fx + Fy*Fy + Fz*Fz);
fprintf(fout, "%d %g %g %g, %g\n", i+1, Fx, Fy, Fz, F);
}
}
Something that may help
The for loop,
`for (j = 0; j<ROW && i != j; j++)`
Will exit when i == j as the loop condition is false. For example when i is 1 will only iterate through the loop once, when j is 0.
Use if statement inside the for loop to skip the current charge, i.e when i == j
for (j = 0; j<ROW ; j++)
{
if (i != j)
{
DO CALCULATION... `
Also, think that Fx[i] will only ever have store the force due to an single j charge as it is assignment for each iteration rather than a sum.
Consider changing to accumlate for each interation, i.e. Fx[i] += then calculate F[i] when this for loop has completed
I am testing the functions of Intel MKL in a C test-program and I found that I just can't make the spareblas: mkl_scsrmm function CSR one-based indexing work. I am using CSR with the val, columns, pntrb and pntre variation. The original examples where placed in:
"...mkl\examples\examples_core_c\spblasc\source\cspblas_scsr.c"
This is the first code for zero-based indexing:
Example #1
#include <stdio.h>
#include "mkl_types.h"
#include "mkl_spblas.h"
int main() {
#define M 2
#define NNZ 4
MKL_INT m = M, nnz = NNZ;
float values[NNZ] = {2.0,4.0,4.0,2.0};
MKL_INT columns[NNZ] = {1,2,1,2};
MKL_INT rowIndex[M+1] = {1,3,5};
#define N 2
MKL_INT n = N;
float b[M][N] = {2.0, 1.0, 5.0, 2.0};
float c[M][N] = {0.0, 0.0, 0.0, 0.0};
float alpha = 1.0, beta = 0.0;
char transa, uplo, nonunit;
char matdescra[6];
MKL_INT i, j, is;
transa = 'N';
matdescra[0] = 'S';
matdescra[1] = 'L';
matdescra[2] = 'N';
matdescra[3] = 'F';
mkl_scsrmm(&transa, &m, &n, &m, &alpha, matdescra, values, columns, rowIndex, &(rowIndex[1]), &(b[0][0]), &n, &beta, &(c[0][0]), &n);
printf(" \n");
printf(" OUTPUT DATA FOR MKL_SCSRMM\n");
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
printf("%7.1f", c[i][j]);
};
printf("\n");
};
return 0;
}
The results I get are this:
Zero-based indexing(the right one):
24.0 10.0
18.0 8.0
One-based indexing:
8.0 10.0
18.0 24.0
Though it seems like it only changes the diagonal elements position, with 3x3 matrix the solution its completly different from the right one. I suspected that it might be something with the input format of the matrix b. I think that there's lack of clarity on the description of array b for the function mkl_scsrmm placed in the MKL reference manual. Thus I changed b format, in this example and it worked (I placed elements position in this order: `{2.0, 5.0, 1.0, 2.0}) But I did the same for another 3x3 example I coded and it didn't work so I think it may be just a coincidence. I don't really know what to do with this problem, I would like to understand what happens here.
References:
CSR format
https://software.intel.com/en-us/node/471374
Spare Blas mkl_scsrmm function
https://software.intel.com/sites/products/documentation/doclib/iss/2013/mkl/mklman/hh_goto.htm#GUID-78C55D9B-86FF-4A9F-B5D5-D2F61B9314FC.htm
Spare Blas Interface Considerations
https://software.intel.com/sites/products/documentation/doclib/iss/2013/mkl/mklman/hh_goto.htm#GUID-34C8DB79-0139-46E0-8B53-99F3BEE7B2D4.htm
And here is another example, the 3x3 one:
Example #2
// matrix A
//
// 2 4 3
// 4 2 1
// 3 1 6
//
// matrix B
//
// 2 1 3
// 4 5 6
// 7 8 9
//
// ZERO-BASED INDEXING
//
// a = {2 4 3 4 2 1 3 1 6}
// columns= {0 1 2 0 1 2 0 1 2}
// idexRow = {0 3 6 9}
//
// b = {2 1 3 4 5 6 7 8 9} (row order array)
//
// We print the array in row-major order
//
// ONE-BASED INDEXING
//
// a = {2 4 3 4 2 1 3 1 6}
// columns={1 2 3 1 2 3 1 2 3}
// indexRow = {0 3 6 9}
//
// b = {2 4 7 1 5 8 3 6 9} (column order array)
//
// We print the array in column-major order (because the resoult is in column major order, ie transposed)
//
//
//
#include <stdio.h>
#include "mkl_types.h"
#include "mkl_spblas.h"
int main()
{
#define M 3
#define NNZ 9
#define N 3
MKL_INT m = M, nnz = NNZ, n=N;
float a[NNZ] = {2.0,4.0,3.0,4.0,2.0,1.0,3.0,1.0,6.0};
MKL_INT columns[NNZ] = {0,1,2,0,1,2,0,1,2};
MKL_INT rowIndex[M+1] = {0,3,6,9};
float b[M][N] = {2.0, 1.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0};
float c[M][N] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
float alpha = 1.0, beta = 0.0;
MKL_INT i, j;
char transa;
char matdescra[6];
float a1[NNZ] = {2.0,4.0,3.0,4.0,2.0,1.0,3.0,1.0,6.0};
MKL_INT columns1[NNZ] = {1,2,3,1,2,3,1,2,3};
MKL_INT rowIndex1[M+1] = {1,4,7,10};
float b1[M][N] = {2.0, 4.0, 7.0, 1.0, 5.0, 8.0, 3.0, 6.0, 9.0};
float c1[M][N] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
//********************************
//ZERO-BASED INDEXING
//********************************
transa = 'n';
matdescra[0] = 's';
matdescra[1] = 'l';
matdescra[2] = 'n';
matdescra[3] = 'c';
mkl_scsrmm(&transa, &m, &n, &m, &alpha, matdescra, a, columns, rowIndex, &(rowIndex[1]), &(b[0][0]), &n, &beta, &(c[0][0]), &n);
printf(" \n");
printf(" Right Solution: ZERO-BASED: C \n");
for (i = 0; i < m; i++)
{
for (j = 0; j < n; j++) {
printf("%7.1f", c[i][j]);
};
printf("\n");
};
printf(" \n");
printf(" ZERO-BASED: C' \n");
for (i = 0; i < m; i++)
{
for (j = 0; j < n; j++)
{
printf("%7.1f", c[j][i]);
};
printf("\n");
};
//********************************
//ONE-BASED INDEXING
//********************************
matdescra[3] = 'f';
mkl_scsrmm(&transa, &m, &n, &m, &alpha, matdescra, a1, columns1, rowIndex1, &(rowIndex1[1]), &(b1[0][0]), &n, &beta, &(c1[0][0]), &n);
printf(" \n");
printf(" ONE-BASED: C \n");
for (i = 0; i < m; i++)
{
for (j = 0; j < n; j++)
{
printf("%7.1f", c1[i][j]);
};
printf("\n");
};
printf(" \n");
printf(" ONE-BASED: C' \n");
for (i = 0; i < m; i++)
{
for (j = 0; j < n; j++)
{
printf("%7.1f", c1[j][i]);
};
printf("\n");
};
return 0;
}
I asked the same question at Intel's forum and I got some help there and get to the solution of the problem. The deal was that when calling the routine from C interface with zero-based indexing you can send the matrix stored in an array following row-major order (native C array storage), and when you call the routine with one-based indexing you have to store the matrix in column-major order. This changes the way the matrix B and C need to be stored, and the way the result will be stored. For the matrix A it only changes the indexing (from 0 to 1). From Intel's documentation you may think that the C interface accepts always the row-major ordering for both types of indexing.
Notice that it that in general, column-major ordering is not the same as storing the transposed matrix in row-major ordering (it is the same if matrices are square).
I have a little problem, I would like to convert a matrix 10*10 in a CSR or COO sparse matrix/format. The matrix is:
1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
-0.45 0.10 -0.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 -0.45 0.10 -0.45 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 -0.45 0.10 -0.45 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 -0.45 0.10 -0.45 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 -0.45 0.10 -0.45 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 -0.45 0.10 -0.45 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 -0.45 0.10 -0.45 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.45 0.10 -0.45
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
I am using the "CUSP" functions but it did not work, once tha matrix A I would like just to convert in other format. Can you help me?
Well I would like also to use this matrix to solve the system Ax=b, using bicgstab:
b=
0.00000
0.34202
0.64279
0.86603
0.98481
0.98481
0.86603
0.64279
0.34202
0.00000
My code for this is:
int n = 10, r;
cusp::coo_matrix<int,float,cusp::device_memory> A(n, n, 3*n - 4);
cusp::array1d<float, cusp::device_memory> x(A.num_rows, 0);
cusp::array1d<float, cusp::device_memory> b(A.num_rows, 1);
b[0]=0.00000;
b[1]=0.34202;
b[2]=0.64279;
b[3]=0.86603;
b[4]=0.98481;
b[5]=0.98481;
b[6]=0.86603;
b[7]=0.64279;
b[8]=0.34202;
b[9]=0.00000;
i=0;
// row 0
A.row_indices[i] = 0.0;
A.column_indices[i] = 0.0;
A.values[i] = 1.00;
++i;
// rows 1 through n - 2
for (r = 1; r != n - 1; ++r) {
A.row_indices[i] = r;
A.column_indices[i] = r - 1;
A.values[i] = -0.45;
++i;
A.row_indices[i] = r;
A.column_indices[i] = r;
A.values[i] = 0.10;
++i;
A.row_indices[i] = r;
A.column_indices[i] = r + 1;
A.values[i] = -0.45;
++i;
}
// row n - 1
A.row_indices[i] = n - 1;
A.column_indices[i] = n - 1;
A.values[i] = 1.00;
++i;
// set stopping criteria:
// iteration_limit = 100
// relative_tolerance = 1e-3
cusp::verbose_monitor<ValueType> monitor(b, 100, 1e-3);
// set preconditioner (identity)
cusp::identity_operator<ValueType, MemorySpace> M(A.num_rows, A.num_rows);
// solve the linear system A x = b
cusp::krylov::bicgstab(A, x, b, monitor, M);
cusp::print(x);
The result using Octave should be something similar to:
0.00000
0.32441
0.60970
0.82144
0.93411
0.93411
0.82144
0.60970
0.32441
0.00000
But is also with negative numbers, so WRONG.
For COO, you have to set three array elements for each entry: the row and column indices as well as the value. You can create a matrix like the one you describe using code like this for COO:
int n = 10, i = 0, r;
cusp::csr_matrix<int,float,cusp::host_memory> A(n, n, 3*n - 4);
// row 0
A.row_indices[i] = 0;
A.column_indices[i] = 0;
A.values[i] = 1.00;
++i;
// rows 1 through n - 2
for (r = 1; r != n - 1; ++r) {
A.row_indices[i] = r;
A.column_indices[i] = r - 1;
A.values[i] = -0.45;
++i;
A.row_indices[i] = r;
A.column_indices[i] = r;
A.values[i] = 0.10;
++i;
A.row_indices[i] = r;
A.column_indices[i] = r + 1;
A.values[i] = -0.45;
++i;
}
// row n - 1
A.row_indices[i] = n - 1;
A.column_indices[i] = n - 1;
A.values[i] = 1.00;
++i;
For CSR you have to specify a column and a value for every entry, and also the index of the first entry for every row including a one-past-the-end index for the one-past-the-end row. A similar piece of code for CSR:
int n = 10, i = 0, r = 0;
cusp::csr_matrix<int,float,cusp::host_memory> A(n, n, 3*n - 4);
// row 0
A.row_offsets[r] = i;
A.column_indices[i] = 0;
A.values[i] = 1.00;
++i;
// rows 1 through n - 2
for (++r; r != n - 1; ++r) {
A.row_offsets[r] = i;
A.column_indices[i] = r - 1;
A.values[i] = -0.45;
++i;
A.column_indices[i] = r;
A.values[i] = 0.10;
++i;
A.column_indices[i] = r + 1;
A.values[i] = -0.45;
++i;
}
// row n - 1
A.row_offsets[r] = i;
A.column_indices[i] = r;
A.values[i] = 1.00;
++i;
++r;
A.row_offsets[r] = i;
To “convert” the matrix from some other format, you have to let us know in what form your original data is stored. Conversion from a cusp::array2d should work by simply passing that array to the constructor. In general, creating the matrix in sparse format in the first place like the code above does will provide better scalability.
Also note that your example matrix is arranged in diagonal bands, so cusp::dia_matrix would be better suited, both in terms of easy encoding and in terms of better performance. To create such a tridiagonal matrix, you can use the following code:
int n = 10, r = 0;
cusp::dia_matrix<int,float,cusp::host_memory> A(n, n, 3*n - 4, 3);
A.diagonal_offsets[0] = -1;
A.diagonal_offsets[1] = 0;
A.diagonal_offsets[2] = 1;
// row 0
A.values(r,0) = A.values(r,2) = 0.00;
A.values(r,1) = 1.00;
// rows 1 through n - 2
for (++r; r != n - 1; ++r) {
A.values(r,0) = A.values(r,2) = -0.45;
A.values(r,1) = 0.10;
}
// row n - 1
A.values(r,0) = A.values(r,2) = 0.00;
A.values(r,1) = 1.00;
About this linear equation you try to solve: could it be that octave is operating on a different matrix than the one you pasted into your question? Because with sage I get negative numbers in the result as well:
n = 10
d = dict()
d[(0,0)] = d[(n-1, n-1)] = 1
for r in range(1, n-1):
d[(r, r-1)] = d[(r, r+1)] = -45/100
d[(r,r)] = 1/10
A = matrix(RDF, n, n, d)
b = vector(RDF, [
0.00000,
0.34202,
0.64279,
0.86603,
0.98481,
0.98481,
0.86603,
0.64279,
0.34202,
0.00000,
])
for i in A.solve_right(b):
print('{:+.5f}'.format(float(i)))
gives the following vector x:
+0.00000
-0.45865
-0.86197
-1.16132
-1.32062
-1.32062
-1.16132
-0.86197
-0.45865
+0.00000