Avoiding integer overflow in Nim - performance

I started learning Nim yesterday and decided to code a little test to make a performance comparison with Rust. The code was fairly easy to write and works for values up to 10^9. However, I need to test it with at least 10^12, which gives incorrect values because of an overflow, even while using uint.
I've been trying different conversions for most variables but I can't seem to avoid the overflow. Of course, any suggestions to make the code easier to read are more than welcome!
import math
import sequtils
import unsigned
proc sum_min_pfactor(N : uint) : uint =
proc f(n : uint) : uint =
return n*(n+1) div 2 - 1
var
v = int(math.sqrt(float(N)))
used = newSeqWith(v+1,false)
s_sum,s_cnt,l_cnt,l_sum = newSeq[uint](v+1)
ret = 0.uint
for i in -1..v-1:
s_cnt[i+1] = i.uint
for i in 0..v:
s_sum[i] = f(i.uint)
for i in 1..v:
l_cnt[i] = N div i.uint - 1
l_sum[i] = f(N div i.uint)
for p in 2..v:
if s_cnt[p] == s_cnt[p-1]:
continue
var p_cnt = s_cnt[p - 1]
var p_sum = s_sum[p - 1]
var q = p * p
ret += p.uint * (l_cnt[p] - p_cnt)
l_cnt[1] -= l_cnt[p] - p_cnt
l_sum[1] -= (l_sum[p] - p_sum) * p.uint
var interval = (p and 1) + 1
var finish = min(v,N.int div q)
for i in countup(p+interval,finish,interval):
if used[i]:
continue
var d = i * p
if d <= v:
l_cnt[i] -= l_cnt[d] - p_cnt
l_sum[i] -= (l_sum[d] - p_sum) * p.uint
else:
var t = N.int div d
l_cnt[i] -= s_cnt[t] - p_cnt
l_sum[i] -= (s_sum[t] - p_sum) * p.uint
if q <= v:
for i in countup(q,finish-1,p*interval):
used[i] = true
for i in countdown(v,q-1):
var t = i div p
s_cnt[i] -= s_cnt[t] - p_cnt
s_sum[i] -= (s_sum[t] - p_sum) * p.uint
return l_sum[1] + ret
echo(sum_min_pfactor(uint(math.pow(10,2))))

How do you solve it in Rust? Rust's ints should also be 64bit at most. In your f function it gets a bit difficult when n is 10000000000. You have a few choices:
You could use floats instead, but have lower precision
You could use int128, but with lower performance: https://bitbucket.org/nimcontrib/NimLongInt/src
Or you could use bigints:
https://github.com/FedeOmoto/nim-gmp (high performance, depends on GMP)
https://github.com/def-/nim-bigints (low performance, written in Nim, not tested much)
Some stylistic changes:
import math
proc sum_min_pfactor(N: int): int =
proc f(n: int): int =
n*(n+1) div 2 - 1
var
v = math.sqrt(N.float).int
s_cnt, s_sum, l_cnt, l_sum = newSeq[int](v+1)
used = newSeq[bool](v+1)
for i in 0..v: s_cnt[i] = i-1
for i in 1..v: s_sum[i] = f(i)
for i in 1..v: l_cnt[i] = N div i - 1
for i in 1..v: l_sum[i] = f(N div i)
for p in 2..v:
if s_cnt[p] == s_cnt[p-1]:
continue
let
p_cnt = s_cnt[p - 1]
p_sum = s_sum[p - 1]
q = p * p
result += p * (l_cnt[p] - p_cnt)
l_cnt[1] -= l_cnt[p] - p_cnt
l_sum[1] -= (l_sum[p] - p_sum) * p
let interval = (p and 1) + 1
let finish = min(v,N div q)
for i in countup(p+interval,finish,interval):
if used[i]:
continue
let d = i * p
if d <= v:
l_cnt[i] -= l_cnt[d] - p_cnt
l_sum[i] -= (l_sum[d] - p_sum) * p
else:
let t = N div d
l_cnt[i] -= s_cnt[t] - p_cnt
l_sum[i] -= (s_sum[t] - p_sum) * p
if q <= v:
for i in countup(q,finish-1,p*interval):
used[i] = true
for i in countdown(v,q-1):
let t = i div p
s_cnt[i] -= s_cnt[t] - p_cnt
s_sum[i] -= (s_sum[t] - p_sum) * p
result += l_sum[1]
for i in 2..12:
echo sum_min_pfactor(int(math.pow(10,i.float)))

Please also take a look at the bignum package: https://github.com/FedeOmoto/bignum
It's a higher level wrapper around nim-gmp so you don't have to deal with low level stuff like the different programming models (GMP uses long C type extensively, so it's a bit troublesome when targeting Win64 - LLP64).

Related

Reverse the isometric projection algorithm

I've got this code:
const a = 2; // always > 0 and known in advance
const b = 3; // always > 0 and known in advance
const c = 4; // always > 0 and known in advance
for (let x = 0; x <= a; x++) {
for (let y = 0; y <= b; y++) {
for (let z = 0; z <= c; z++) {
for (let p = 0; p <= 1; p++) {
for (let q = 0; q <= 2; q++) {
let u = b + x - y + p;
let v = a + b + 2 * c - x - y - 2 * z + q;
let w = c + x + y - z;
}
}
}
}
}
The code generates (a+1)*(b+1)*(c+1)*2*3 triplets of (u,v,w), each of them is unique. And because of that fact, I think it should be possible to write reversed version of this algorithm that will calculate x,y,z,p,q based on u,v,w. I understand that there are only 3 equations and 5 variables to get, but known boundaries for x,y,z,p,q and the fact that all variables are integers should probably help.
for (let u = ?; u <= ?; u++) {
for (let v = ?; v <= ?; v++) {
for (let w = ?; w <= ?; w++) {
x = ?;
y = ?;
z = ?;
p = ?;
q = ?;
}
}
}
I even managed to produce the first line: for (let u = 0; u <= a + b + 1; u++) by taking the equation for u and finding min and max but I'm struggling with moving forward. I understand that min and max values for v are depending on u, but can't figure out the formulas.
Examples are in JS, but I will be thankful for any help in any programming language or even plain math formulas.
If anyone is interested in what this code is actually about - it projects voxel 3d model to triangles on a plain. u,v are resulting 2d coordinates and w is distance from the camera. Reversed algorithm will be actually a kind of raytracing.
UPDATE: Using line equations from 2 points I managed to create minmax conditions for v and code now looks like this:
for (let u = 0; u <= a + b + 1; u++) {
let minv = u <= a ? a - u : -a + u - 1;
let maxv = u <= b ? a + 2 * c + u + 2 : a + 2 * b + 2 * c - u + 3;
for (let v = minv; v <= maxv; v++) {
...
}
}
I think I know what to do with x, y, z, p, q on the last step so the problem left is minw and maxw. As far as I understand those values should depend both on u and v and I must use plane equations?
If the triplets are really unique (didn't check that) and if p and q always go up to 1 and 2 (respectively), then you can "group" triplets together and go up the loop chain.
We'll first find the 3 triplets that where made in the same "q loop" : the triplets make with the same x,y,z,p. As only q change, the only difference will be v, and it will be 3 consecutive numbers.
For that, let's group triplets such that, in a group, all triplets have the same u and same w. Then we sort triplets in groups by their v parameters, and we group them 3 by 3. Inside each group it's easy to assign the correct q variable to each triplet.
Then reduce the groups of 3 into the first triplet (the one with q == 0). We start over to assign the p variable : Group all triplets such that they have same v and w inside a group. Then sort them by the u value, and group them 2 by 2. This let's us find their p value. Remember that each triplet in the group of 3 (before reducing) has that same p value.
Then, for each triplet, we have found p and q. We solve the 3 equation for x,y,z :
z = -1 * ((v + w) - a - b - 3c -q)/3
y = (w - u + z + b - c - p)/2
x = u + y - b - p
After spending some time with articles on geometry and with the huge help from Wolfram Alpha, I managed to write needed equations myself. And yes, I had to use plane equations.
const a = 2; // always > 0 and known in advance
const b = 3; // always > 0 and known in advance
const c = 4; // always > 0 and known in advance
const minu = 0;
const maxu = a + b + 1;
let minv, maxv, minw, maxw;
let x, y, z, p, q;
for (let u = minu; u <= maxu; u++) {
if (u <= a) {
minv = a - u;
} else {
minv = -a + u - 1;
}
if (u <= b) {
maxv = a + 2 * c + u + 2;
} else {
maxv = a + 2 * b + 2 * c - u + 3;
}
for (let v = minv; v <= maxv; v++) {
if (u <= b && v >= a + u + 1) {
minw = (-a + 2 * b - 3 * u + v - 2) / 2;
} else if (u > b && v >= a + 2 * b - u + 2) {
minw = (-a - 4 * b + 3 * u + v - 5) / 2;
} else {
minw = a + b - v;
}
if (u <= a && v <= a + 2 * c - u + 1) {
maxw = (-a + 2 * b + 3 * u + v - 1) / 2;
} else if (u > a && v <= -a + 2 * c + u) {
maxw = (5 * a + 2 * b - 3 * u + v + 2) / 2;
} else {
maxw = a + b + 3 * c - v + 2;
}
minw = Math.round(minw);
maxw = Math.round(maxw);
for (let w = minw; w <= maxw; w++) {
z = (a + b + 3 * c - v - w + 2) / 3;
q = Math.round(2 - (z % 1) * 3);
z = Math.floor(z);
y = (a + 4 * b + q - 3 * u - v + 2 * w + 3) / 6;
p = 1 - (y % 1) * 2;
y = Math.floor(y);
x = (a - 2 * b - 3 * p + q + 3 * u - v + 2 * w) / 6;
x = Math.round(x);
}
}
}
This code passes my tests, but if someone can create better solution, I would be very interested.

Solving Project Euler #12 with Matlab

I am trying to solve Problem #12 of Project Euler with Matlab and this is what I came up with to find the number of divisors of a given number:
function [Divisors] = ND(n)
p = primes(n); %returns a row vector containing all the prime numbers less than or equal to n
i = 1;
count = 0;
Divisors = 1;
while n ~= 1
while rem(n, p(i)) == 0 %rem(a, b) returns the remainder after division of a by b
count = count + 1;
n = n / p(i);
end
Divisors = Divisors * (count + 1);
i = i + 1;
count = 0;
end
end
After this, I created a function to evaluate the number of divisors of the product n * (n + 1) / 2 and when this product achieves a specific limit:
function [solution] = Solution(limit)
n = 1;
product = 0;
while(product < limit)
if rem(n, 2) == 0
product = ND(n / 2) * ND(n + 1);
else
product = ND(n) * ND((n + 1) / 2);
end
n = n + 1;
end
solution = n * (n + 1) / 2;
end
I already know the answer and it's not what comes back from the function Solution. Could someone help me find what's wrong with the coding.
When I run Solution(500) (500 is the limit specified in the problem), I get 76588876, but the correct answer should be:
76576500.
The trick is quite simple while it also bothering me for a while: The iteration in you while loop is misplaced, which would cause the solution a little bigger than the true answer.
function [solution] = Solution(limit)
n = 1;
product = 0;
while(product < limit)
n = n + 1; %%%But Here
if rem(n, 2) == 0
product = ND(n / 2) * ND(n + 1);
else
product = ND(n) * ND((n + 1) / 2);
end
%n = n + 1; %%%Not Here
end
solution = n * (n + 1) / 2;
end
The output of Matlab 2015b:
>> Solution(500)
ans =
76576500

Understanding Spark correlation algorithm

I was reading Spark correlation algorithm source code and while going through the code, I coulddn't understand this particular peace of code.
This is from the file : org/apache/spark/mllib/linalg/BLAS.scala
def spr(alpha: Double, v: Vector, U: Array[Double]): Unit = {
val n = v.size
v match {
case DenseVector(values) =>
NativeBLAS.dspr("U", n, alpha, values, 1, U)
case SparseVector(size, indices, values) =>
val nnz = indices.length
var colStartIdx = 0
var prevCol = 0
var col = 0
var j = 0
var i = 0
var av = 0.0
while (j < nnz) {
col = indices(j)
// Skip empty columns.
colStartIdx += (col - prevCol) * (col + prevCol + 1) / 2
av = alpha * values(j)
i = 0
while (i <= j) {
U(colStartIdx + indices(i)) += av * values(i)
i += 1
}
j += 1
prevCol = col
}
}
}
I do not know Scala and that could be the reason I could not understand it. Can someone explain what is happening here.
It is being called from Rowmatrix.scala
def computeGramianMatrix(): Matrix = {
val n = numCols().toInt
checkNumColumns(n)
// Computes n*(n+1)/2, avoiding overflow in the multiplication.
// This succeeds when n <= 65535, which is checked above
val nt = if (n % 2 == 0) ((n / 2) * (n + 1)) else (n * ((n + 1) / 2))
// Compute the upper triangular part of the gram matrix.
val GU = rows.treeAggregate(new BDV[Double](nt))(
seqOp = (U, v) => {
BLAS.spr(1.0, v, U.data)
U
}, combOp = (U1, U2) => U1 += U2)
RowMatrix.triuToFull(n, GU.data)
}
The correlation is defined here:
https://en.wikipedia.org/wiki/Pearson_correlation_coefficient
The final goal is to understand the Spark correlation algorithm.
Update 1: Relevent paper https://stanford.edu/~rezab/papers/linalg.pdf

How to find ith item in zigzag ordering?

A question last week defined the zig zag ordering on an n by m matrix and asked how to list the elements in that order.
My question is how to quickly find the ith item in the zigzag ordering? That is, without traversing the matrix (for large n and m that's much too slow).
For example with n=m=8 as in the picture and (x, y) describing (row, column)
f(0) = (0, 0)
f(1) = (0, 1)
f(2) = (1, 0)
f(3) = (2, 0)
f(4) = (1, 1)
...
f(63) = (7, 7)
Specific question: what is the ten billionth (1e10) item in the zigzag ordering of a million by million matrix?
Let's assume that the desired element is located in the upper half of the matrix. The length of the diagonals are 1, 2, 3 ..., n.
Let's find the desired diagonal. It satisfies the following property:
sum(1, 2 ..., k) >= pos but sum(1, 2, ..., k - 1) < pos. The sum of 1, 2, ..., k is k * (k + 1) / 2. So we just need to find the smallest integer k such that k * (k + 1) / 2 >= pos. We can either use a binary search or solve this quadratic inequality explicitly.
When we know the k, we just need to find the pos - (k - 1) * k / 2 element of this diagonal. We know where it starts and where we should move(up or down, depending on the parity of k), so we can find the desired cell using a simple formula.
This solution has an O(1) or an O(log n) time complexity(it depends on whether we use a binary search or solve the inequation explicitly in step 2).
If the desired element is located in the lower half of the matrix, we can solve this problem for a pos' = n * n - pos + 1 and then use symmetry to get the solution to the original problem.
I used 1-based indexing in this solution, using 0-based indexing might require adding +1 or -1 somewhere, but the idea of the solution is the same.
If the matrix is rectangular, not square, we need to consider the fact the length of diagonals look this way: 1, 2, 3, ..., m, m, m, .., m, m - 1, ..., 1(if m <= n) when we search for the k, so the sum becomes something like k * (k + 1) / 2 if k <= m and k * (k + 1) / 2 + m * (k - m) otherwise.
import math, random
def naive(n, m, ord, swap = False):
dx = 1
dy = -1
if swap:
dx, dy = dy, dx
cur = [0, 0]
for i in range(ord):
cur[0] += dy
cur[1] += dx
if cur[0] < 0 or cur[1] < 0 or cur[0] >= n or cur[1] >= m:
dx, dy = dy, dx
if cur[0] >= n:
cur[0] = n - 1
cur[1] += 2
if cur[1] >= m:
cur[1] = m - 1
cur[0] += 2
if cur[0] < 0: cur[0] = 0
if cur[1] < 0: cur[1] = 0
return cur
def fast(n, m, ord, swap = False):
if n < m:
x, y = fast(m, n, ord, not swap)
return [y, x]
alt = n * m - ord - 1
if alt < ord:
x, y = fast(n, m, alt, swap if (n + m) % 2 == 0 else not swap)
return [n - x - 1, m - y - 1]
if ord < (m * (m + 1) / 2):
diag = int((-1 + math.sqrt(1 + 8 * ord)) / 2)
parity = (diag + (0 if swap else 1)) % 2
within = ord - (diag * (diag + 1) / 2)
if parity: return [diag - within, within]
else: return [within, diag - within]
else:
ord -= (m * (m + 1) / 2)
diag = int(ord / m)
within = ord - diag * m
diag += m
parity = (diag + (0 if swap else 1)) % 2
if not parity:
within = m - within - 1
return [diag - within, within]
if __name__ == "__main__":
for i in range(1000):
n = random.randint(3, 100)
m = random.randint(3, 100)
ord = random.randint(0, n * m - 1)
swap = random.randint(0, 99) < 50
na = naive(n, m, ord, swap)
fa = fast(n, m, ord, swap)
assert na == fa, "(%d, %d, %d, %s) ==> (%s), (%s)" % (n, m, ord, swap, na, fa)
print fast(1000000, 1000000, 9999999999, False)
print fast(1000000, 1000000, 10000000000, False)
So the 10-billionth element (the one with ordinal 9999999999), and the 10-billion-first element (the one with ordinal 10^10) are:
[20331, 121089]
[20330, 121090]
An analytical solution
In the general case, your matrix will be divided in 3 areas:
an initial triangle t1
a skewed part mid where diagonals have a constant length
a final triangle t2
Let's call p the index of your diagonal run.
We want to define two functions x(p) and y(p) that give you the column and row of the pth cell.
Initial triangle
Let's look at the initial triangular part t1, where each new diagonal is one unit longer than the preceding.
Now let's call d the index of the diagonal that holds the cell, and
Sp = sum(di) for i in [0..p-1]
We have p = Sp + k, with 0 <=k <= d and
Sp = d(d+1)/2
if we solve for d, it brings
d²+d-2p = 0, a quadratic equation where we retain only the positive root:
d = (-1+sqrt(1+8*p))/2
Now we want the highest integer value closest to d, which is floor(d).
In the end, we have
p = d + k with d = floor((-1+sqrt(1+8*p))/2) and k = p - d(d+1)/2
Let's call
o(d) the function that equals 1 if d is odd and 0 otherwise, and
e(d) the function that equals 1 if d is even and 0 otherwise.
We can compute x(p) and y(p) like so:
d = floor((-1+sqrt(1+8*p))/2)
k = p - d(d+1)/2
o = d % 2
e = 1 - o
x = e*d + (o-e)*k
y = o*d + (e-o)*k
even and odd functions are used to try to salvage some clarity, but you can replace
e(p) with 1 - o(p) and have slightly more efficient but less symetric formulaes for x and y.
Middle part
let's consider the smallest matrix dimension s, i.e. s = min (m,n).
The previous formulaes hold until x or y (whichever comes first) reaches the value s.
The upper bound of p such as x(i) <= s and y(i) <= s for all i in [0..p]
(i.e. the cell indexed by p is inside the initial triangle t1) is given by
pt1 = s(s+1)/2.
For p >= pt1, diagonal length remains equal to s until we reach the second triangle t2.
when inside mid, we have:
p = s(s+1)/2 + ds + k with k in [0..s[.
which yields:
d = floor ((p - s(s+1)/2)/s)
k = p - ds
We can then use the same even/odd trick to compute x(p) and y(p):
p -= s(s+1)/2
d = floor (p / s)
k = p - d*s
o = (d+s) % 2
e = 1 - o
x = o*s + (e-o)*k
y = e*s + (o-e)*k
if (n > m)
x += d+e
y -= e
else
y += d+o
x -= o
Final triangle
Using symetry, we can calculate pt2 = m*n - s(s+1)/2
We now face nearly the same problem as for t1, except that the diagonal may run in the same direction as for t1 or in the reverse direction (if n+m is odd).
Using symetry tricks, we can compute x(p) and y(p) like so:
p = n*m -1 - p
d = floor((-1+sqrt(1+8*p))/2)
k = p - d*(d+1)/2
o = (d+m+n) % 2
e = 1 - $o;
x = n-1 - (o*d + (e-o)*k)
y = m-1 - (e*d + (o-e)*k)
Putting all together
Here is a sample c++ implementation.
I used 64 bits integers out of sheer lazyness. Most could be replaced by 32 bits values.
The computations could be made more effective by precomputing a few more coefficients.
A good part of the code could be factorized, but I doubt it is worth the effort.
Since this is just a quick and dirty proof of concept, I did not optimize it.
#include <cstdio> // printf
#include <algorithm> // min
using namespace std;
typedef long long tCoord;
void panic(const char * msg)
{
printf("PANIC: %s\n", msg);
exit(-1);
}
struct tPoint {
tCoord x, y;
tPoint(tCoord x = 0, tCoord y = 0) : x(x), y(y) {}
tPoint operator+(const tPoint & p) const { return{ x + p.x, y + p.y }; }
bool operator!=(const tPoint & p) const { return x != p.x || y != p.y; }
};
class tMatrix {
tCoord n, m; // dimensions
tCoord s; // smallest dimension
tCoord pt1, pt2; // t1 / mid / t2 limits for p
public:
tMatrix(tCoord n, tCoord m) : n(n), m(m)
{
s = min(n, m);
pt1 = (s*(s + 1)) / 2;
pt2 = n*m - pt1;
}
tPoint diagonal_cell(tCoord p)
{
tCoord x, y;
if (p < pt1) // inside t1
{
tCoord d = (tCoord)floor((-1 + sqrt(1 + 8 * p)) / 2);
tCoord k = p - (d*(d + 1)) / 2;
tCoord o = d % 2;
tCoord e = 1 - o;
x = o*d + (e - o)*k;
y = e*d + (o - e)*k;
}
else if (p < pt2) // inside mid
{
p -= pt1;
tCoord d = (tCoord)floor(p / s);
tCoord k = p - d*s;
tCoord o = (d + s) % 2;
tCoord e = 1 - o;
x = o*s + (e - o)*k;
y = e*s + (o - e)*k;
if (m > n) // vertical matrix
{
x -= o;
y += d + o;
}
else // horizontal matrix
{
x += d + e;
y -= e;
}
}
else // inside t2
{
p = n * m - 1 - p;
tCoord d = (tCoord)floor((-1 + sqrt(1 + 8 * p)) / 2);
tCoord k = p - (d*(d + 1)) / 2;
tCoord o = (d + m + n) % 2;
tCoord e = 1 - o;
x = n - 1 - (o*d + (e - o)*k);
y = m - 1 - (e*d + (o - e)*k);
}
return{ x, y };
}
void check(void)
{
tPoint move[4] = { { 1, 0 }, { -1, 1 }, { 1, -1 }, { 0, 1 } };
tPoint pos;
tCoord dir = 0;
for (tCoord p = 0; p != n * m ; p++)
{
tPoint dc = diagonal_cell(p);
if (pos != dc) panic("zot!");
pos = pos + move[dir];
if (dir == 0)
{
if (pos.y == m - 1) dir = 2;
else dir = 1;
}
else if (dir == 3)
{
if (pos.x == n - 1) dir = 1;
else dir = 2;
}
else if (dir == 1)
{
if (pos.y == m - 1) dir = 0;
else if (pos.x == 0) dir = 3;
}
else
{
if (pos.x == n - 1) dir = 3;
else if (pos.y == 0) dir = 0;
}
}
}
};
void main(void)
{
const tPoint dim[] = { { 10, 10 }, { 11, 11 }, { 10, 30 }, { 30, 10 }, { 10, 31 }, { 31, 10 }, { 11, 31 }, { 31, 11 } };
for (tPoint d : dim)
{
printf("Checking a %lldx%lld matrix...", d.x, d.y);
tMatrix(d.x, d.y).check();
printf("done\n");
}
tCoord p = 10000000000;
tMatrix matrix(1000000, 1000000);
tPoint cell = matrix.diagonal_cell(p);
printf("Coordinates of %lldth cell: (%lld,%lld)\n", p, cell.x, cell.y);
}
Results are checked against "manual" sweep of the matrix.
This "manual" sweep is a ugly hack that won't work for a one-row or one-column matrix, though diagonal_cell() does work on any matrix (the "diagonal" sweep becomes linear in that case).
The coordinates found for the 10.000.000.000th cell of a 1.000.000x1.000.000 matrix seem consistent, since the diagonal d on which the cell stands is about sqrt(2*1e10), approx. 141421, and the sum of cell coordinates is about equal to d (121090+20330 = 141420). Besides, it is also what the two other posters report.
I would say there is a good chance this lump of obfuscated code actually produces an O(1) solution to your problem.

MATLAB code running slow on MacBookPro, triple while loop

I have been running a MATLAB program for almost six hours now, and it is still not complete. It is cycling through three while loops (the outer two loops are n=855, the inner loop is n=500). Is this a surprise that it is taking this long? Is there anything I can do to increase the speed? I am including the code below, as well as the variable data types underneath that.
while i < (numAtoms + 1)
pointAccessible = ones(numPoints,1);
j = 1;
while j <(numAtoms + 1)
if (i ~= j)
k=1;
while k < (numPoints + 1)
if (pointAccessible(k) == 1)
sphereCoord = [cell2mat(atomX(i)) + p + sphereX(k), cell2mat(atomY(i)) + p + sphereY(k), cell2mat(atomZ(i)) + p + sphereZ(k)];
neighborCoord = [cell2mat(atomX(j)), cell2mat(atomY(j)), cell2mat(atomZ(j))];
coords(1,:) = [sphereCoord];
coords(2,:) = [neighborCoord];
if (pdist(coords) < (atomRadius(j) + p))
pointAccessible(k)=0;
end
end
k = k + 1;
end
end
j = j+1;
end
remainingPoints(i) = sum(pointAccessible);
i = i +1;
end
Variable Data Types:
numAtoms = 855
numPoints = 500
p = 1.4
atomRadius = <855 * 1 double>
pointAccessible = <500 * 1 double>
atomX, atomY, atomZ = <1 * 855 cell>
sphereX, sphereY, sphereZ = <500 * 1 double>
remainingPoints = <855 * 1 double>

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