revert some things, my mental health is at an all time low
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SHA256:JiuxZNdA5bRWXPMUJChI0AQ75yC+cXY4xM0IaVwEVys
5 changed files with 108 additions and 93 deletions
5
Makefile
5
Makefile
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@ -6,7 +6,10 @@ ts := $(shell /usr/bin/date "+%d-%m__%H_%M_%S")
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.DEFAULT_GOAL = MD
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MD: $(SRC)/MD.cpp
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mtune=native -mavx -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mavx -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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MD-errors: $(SRC)/MD.cpp
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mtune=native -mavx -O2 -fopt-info-vec-all -ftree-vectorizer-verbose=2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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MDorig: $(SRC)/MD-original.cpp
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$(CC) $(CFLAGS) $(SRC)MD-original.cpp -lm -O2 -pg -o ./out/MD-original
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BIN
out/MD
BIN
out/MD
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BIN
out/MD-orig
Executable file
BIN
out/MD-orig
Executable file
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@ -540,7 +540,7 @@ void computeAccelerations() {
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}
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// returns sum of dv/dt*m/A (aka Pressure) from elastic collisions with walls
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double VelocityVerlet(double dt, int iter, double *PE, FILE *fp) {
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double VelocityVerlet(double dt, int iter, FILE *fp) {
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int i, j, k;
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double psum = 0.;
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194
src/MD.cpp
194
src/MD.cpp
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@ -32,6 +32,25 @@
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#include <stdlib.h>
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#include <string.h>
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// Readability
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typedef __m256d fourD;
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typedef __m128d twoD;
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#define load_4d(ptr) _mm256_load_pd(ptr)
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#define store_4d(ptr, val) _mm256_store_pd(ptr, val)
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#define store_lower_1d(ptr, val) _mm_store_pd(ptr, val)
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#define add_4d(a, b) _mm256_add_pd(a, b)
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#define add_2d(a, b) _mm_add_pd(a, b)
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#define hadd_4d(a, b) _mm256_hadd_pd(a, b)
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#define sub_4d(a, b) _mm256_sub_pd(a, b)
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#define mul_4d(a, b) _mm256_mul_pd(a, b)
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#define div_4d(a, b) _mm256_div_pd(a, b)
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#define create_4d(a) _mm256_set1_pd(a)
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#define get_lower_2d(a) _mm256_castpd256_pd128(a)
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#define get_upper_2d(a) _mm256_extractf128_pd(a, 1)
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#define ALIGNMENT 32
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// Number of particles
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int N;
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@ -55,11 +74,8 @@ double Tinit; // 2;
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const int MAXPART = 5001;
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// Position
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double r[MAXPART][3];
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// Velocity
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double v[MAXPART][3];
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// Acceleration
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double a[MAXPART][3];
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// Force
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double F[MAXPART][3];
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// atom type
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@ -394,6 +410,7 @@ void initialize() {
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int n, p, i, j, k;
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double pos;
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// Number of atoms in each direction
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n = int(ceil(pow(N, 1.0 / 3)));
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@ -489,96 +506,91 @@ void transposeMatrix2(double matT[MAXPART][3], double mat[3][MAXPART]) {
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}
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}
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double PotentialAndAccelerationSIMD(double dt) {
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memset(a, 0, sizeof(a));
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double Pot = 0.;
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for (int i = 0; i < N; i++) {
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__m256d riMinusRj[4];
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memset(riMinusRj, 0, sizeof(riMinusRj));
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double dist[4];
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memset(dist, 0, sizeof(dist));
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for (int j = i + 1; j < N; j += 4) {
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for (int k = 0; k < 4; k++) {
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double quot, rnorm, term1, term2;
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// CALCULATE POTENTIAL ENERGY
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// double dist = 0.;
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// double posItoJ[3]; // position of i relative to j
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// POT
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// double distTmp = r[i][k] - r[j][k];
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// dist += distTmp * distTmp;
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// ACCEL
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// posItoJ[k] = distTmp;
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// r[i]
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__m256d ri = _mm256_loadu_pd(r[i]);
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// r[j]
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__m256d rj = _mm256_loadu_pd(r[j + k]);
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// r[i] - r[j]
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__m256d rij = _mm256_sub_pd(ri, rj);
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riMinusRj[k] = rij;
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// riMinusRj * riMinusRj
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__m256d distTmp = _mm256_mul_pd(rij, rij);
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dist[k] = distTmp[0] + distTmp[1] + distTmp[2];
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}
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__m256d dists = _mm256_loadu_pd(dist);
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__m256d quot = _mm256_div_pd(_mm256_set1_pd(sigma * sigma), dists);
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__m256d term2 = _mm256_mul_pd(quot, _mm256_mul_pd(quot, quot));
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__m256d Pots =
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_mm256_mul_pd(_mm256_set1_pd(epsilon_8),
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_mm256_mul_pd(term2, _mm256_sub_pd(term2, _mm256_set1_pd(1.))));
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Pot += Pots[0] + Pots[1] + Pots[2] + Pots[3];
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// quot = sigma * sigma / dist;
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// term2 = quot * quot * quot;
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// Pot += epsilon_8 * term2 * (term2 - 1.);
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__m256d distSqd = _mm256_mul_pd(dists, _mm256_mul_pd(dists, dists));
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__m256d rSqd_inv7 = _mm256_mul_pd(distSqd, _mm256_mul_pd(distSqd, dists));
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__m256d f8 = _mm256_div_pd(
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_mm256_sub_pd(_mm256_set1_pd(48.), _mm256_mul_pd(_mm256_set1_pd(24.), distSqd)),
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rSqd_inv7);
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// // From derivative of Lennard-Jones with sigma and epsilon
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// // set equal to 1 in natural units!
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// double distSqd = dist * dist * dist;
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// double rSqd_inv7 = distSqd * distSqd * dist;
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// double f = (48. - (24. * distSqd)) / rSqd_inv7;
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// Go back to the original loop
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for (int k = 0; k < 4; k++) {
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__m256d tmp = _mm256_mul_pd(riMinusRj[k], _mm256_set1_pd(f8[k]));
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__m256d aI = _mm256_loadu_pd(a[i]);
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__m256d aJ = _mm256_loadu_pd(a[i]);
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_mm256_storeu_pd(a[i], _mm256_add_pd(aI, tmp));
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_mm256_storeu_pd(a[j], _mm256_sub_pd(aJ, tmp));
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// // from F = ma, where m = 1 in natural units!
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// for (int k = 0; k < 3; k++) {
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// double tmp = posItoJ[k] * f;
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// a[i][k] += tmp;
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// a[j][k] -= tmp;
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// }
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//
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// }
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// for (int j = 0; j < 3; j++) {
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// v[i][j] += 0.5 * a[i][j] * dt;
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// }
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}
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}
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}
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//}
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return Pot;
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}
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// double PotentialAndAccelerationSIMD(double dt) {
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// for (int i = 0; i < N; i++) {
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// for (int j = 0; j < 3; j++)
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// a[i][j] = 0.;
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// }
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// double Pot = 0.;
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//
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// for (int i = 0; i < N; i++) {
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//
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// fourD rij4[4];
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// memset(rij4, 0, sizeof(rij4));
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// double *dist = (double *)_mm_malloc(4 * sizeof(double), ALIGNMENT);
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// memset(dist, 0, sizeof(double) * 4);
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// //__m256i mask =
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// //_mm256_setr_epi64x(0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF, 0);
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//
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// for (int j = i + 1; j < N; j += 4) {
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// fourD ri = load_4d(r[i]);
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// int numParts = fmin(4, N - j);
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// for (int k = 0; k < numParts; k++) {
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// if (j + k >= N) {
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// break;
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// }
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// double quot, rnorm, term1, term2;
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//
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// fourD rj = load_4d(r[j + k]);
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// fourD rij = sub_4d(ri, rj);
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// fourD distTmp = mul_4d(rij, rij);
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// rij4[k] = rij;
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//
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// fourD temp = hadd_4d(distTmp, distTmp);
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// twoD lo = get_lower_2d(temp);
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// twoD hi = get_upper_2d(temp);
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// twoD sum = add_2d(lo, hi);
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//
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// // Convert the scalar result to a double
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// double finalSum;
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// store_lower_1d(&dist[k], sum);
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// }
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// fourD dists = load_4d(dist);
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// fourD quot = div_4d(create_4d(sigma * sigma), dists);
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// fourD term2 = mul_4d(quot, mul_4d(quot, quot));
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// fourD Pots = mul_4d(create_4d(epsilon_8), mul_4d(term2, sub_4d(term2, create_4d(1.))));
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// // Perform horizontal addition and store the result in a scalar
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// fourD temp = hadd_4d(Pots, Pots);
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// twoD lo = get_lower_2d(temp);
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// twoD hi = get_upper_2d(temp);
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// twoD sum = add_2d(lo, hi);
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//
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// // Convert the scalar result to a double
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// double finalSum;
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// store_lower_1d(&finalSum, sum);
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// Pot += finalSum;
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//
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// fourD distSqd = mul_4d(dists, mul_4d(dists, dists));
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// fourD rSqd_inv7 = mul_4d(distSqd, mul_4d(distSqd, dists));
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// fourD f8 = div_4d(sub_4d(create_4d(48.), mul_4d(create_4d(24.), distSqd)), rSqd_inv7);
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//
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// // Go back to the original loop
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// for (int k = 0; k < numParts; k++) {
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// if (j + k >= N) {
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// break;
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// }
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// fourD tmp = mul_4d(rij4[k], create_4d(f8[k]));
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// fourD aI = load_4d(a[i]);
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// fourD aJ = load_4d(a[j + k]);
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// fourD sum = add_4d(aI, tmp);
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// fourD sub = sub_4d(aJ, tmp);
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// store_4d(a[i], sum);
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// store_4d(a[j + k], sub);
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// }
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// }
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// }
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// //}
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//
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// return Pot;
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// }
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double PotentialAndAcceleration(double dt) {
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memset(a, 0, sizeof(a));
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double Pot = 0.;
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for (int i = 0; i < N; i++) {
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for (int i = 0; i < N-1; i++) {
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double ri[3] = {r[i][0], r[i][1], r[i][2]};
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for (int j = i + 1; j < N; j++) {
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double quot, rnorm, term1, term2;
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// CALCULATE POTENTIAL ENERGY
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@ -587,7 +599,7 @@ double PotentialAndAcceleration(double dt) {
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for (int k = 0; k < 3; k++) {
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// POT
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double distTmp = r[i][k] - r[j][k];
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double distTmp = ri[k] - r[j][k];
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dist += distTmp * distTmp;
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// ACCEL
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posItoJ[k] = distTmp;
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@ -597,7 +609,7 @@ double PotentialAndAcceleration(double dt) {
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double distSqd = dist * dist * dist;
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double rSqd_inv7 = distSqd * distSqd * dist;
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double f = (48. - (24. * distSqd)) / rSqd_inv7;
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// from F = ma, where m = 1 in natural units!
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// from F = ma, where m = 1 in natural units!
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for (int k = 0; k < 3; k++) {
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double tmp = posItoJ[k] * f;
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a[i][k] += tmp;
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@ -646,8 +658,8 @@ void computeAccelerations() {
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int i, j, k;
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double f, rSqd, tmp = 0.;
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double rij[3]; // position of i relative to j
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memset(a, 0, sizeof(a));
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memset(a, 0, sizeof(a));
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for (i = 0; i < N - 1; i++) { // loop over all distinct pairs i,j
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for (j = i + 1; j < N; j++) {
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// initialize r^2 to zero
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