I'm trying to implement logistic regression in C++, but the predictions I'm getting are not even close to what I am expecting. I'm not sure if there is an error in my understanding of logistic regression or the code.
I have reviewed the algorithms and messed with the learning rate, but the results are very inconsistent.
double theta[4] = {0,0,0,0};
double x[2][3] = {
{1,1,1},
{9,9,9},
};
double y[2] = {0,1};
//prediction data
double test_x[1][3] = {
{9,9,9},
};
int test_m = sizeof(test_x) / sizeof(test_x[0]);
int m = sizeof(x) / sizeof(x[0]);
int n = sizeof(theta) / sizeof(theta[0]);
int xn = n - 1;
struct Logistic
{
double sigmoid(double total)
{
double e = 2.71828;
double sigmoid_x = 1 / (1 + pow(e, -total));
return sigmoid_x;
}
double h(int x_row)
{
double total = theta[0] * 1;
for(int c1 = 0; c1 < xn; ++c1)
{
total += theta[c1 + 1] * x[x_row][c1];
}
double final_total = sigmoid(total);
//cout << "final total: " << final_total;
return final_total;
}
double cost()
{
double hyp;
double temp_y;
double error;
for(int c1 = 0; c1 < m; ++c1)
{
//passes row of x to h to calculate sigmoid(xi * thetai)
hyp = h(c1);
temp_y = y[c1];
error += temp_y * log(hyp) + (1 - temp_y) * log(1 - hyp);
}// 1 / m
double final_error = -.5 * error;
return final_error;
}
void gradient_descent()
{
double alpha = .01;
for(int c1 = 0; c1 < n; ++c1)
{
double error = cost();
cout << "final error: " << error << "\n";
theta[c1] = theta[c1] - alpha * error;
cout << "theta: " << c1 << " " << theta[c1] << "\n";
}
}
void train()
{
for(int epoch = 0; epoch <= 10; ++epoch)
{
gradient_descent();
cout << "epoch: " << epoch << "\n";
}
}
vector<double> predict()
{
double temp_total;
double total;
vector<double> final_total;
//hypothesis equivalent function
temp_total = theta[0] * 1;
for(int c1 = 0; c1 < test_m; ++c1)
{
for(int c2 = 0; c2 < xn; ++c2)
{
temp_total += theta[c2 + 1] * test_x[c1][c2];
}
total = sigmoid(temp_total);
//cout << "final total: " << final_total;
final_total.push_back(total);
}
return final_total;
}
};
int main()
{
Logistic test;
test.train();
vector<double> prediction = test.predict();
for(int c1 = 0; c1 < test_m; ++c1)
{
cout << "prediction: " << prediction[c1] << "\n";
}
}
start with a very small learning rate wither larger iteration number at try. Haven`t tested ur code. But I guess the cost/error/energy jumps from hump to hump.
Somewhat unrelated to your question, but rather than computing e^-total using pow, use exp instead (it's a hell of a lot faster!). Also there is no need to make the sigmoid function a member func, make it static or just a normal C func (it doesn't require any member variable from your struct).
static double sigmoid(double total)
{
return 1.0 / (1.0 + exp(-total));
}
Related
This is going to be a long one. I am still very new to coding, started 3 months ago so I know my code is not perfect, any criticism beyond the question is more than welcome. I have specifically avoided using pointers because I do not fully understand them, I can use them but I dont trust that I will use them correctly in a program like this.
First things first, I have a version of this where there is only 1 hidden layer and the net works perfectly. I have started running into problems since I tried to expand the number of hidden layers.
Some info on the net:
-I am using softmax output activation as I have 3 output neurons.
-I am using tanh as my activation function on the rest of the net.
-The file being read for the input has a format of
"input: 0.56 0.76 0.23 0.67"
"output: 0.0 0.0 1.0" (this is the target)
-The weights for connecting layer 1 neuron to layer 2 neuron are stored in layer 1 one neuron.
-The bias's for each neuron are stored in that neuron.
-The target is 1.0 0.0 0.0 if the sum of the input numbers is below one, 0.0 1.0 0.0 if sum is between 1 and 2, 0.0 0.0 1.0 if sum is above 2.
-using L1 regularization.
Those problems specifically being:
The softmax output values do not move from an relatively equalised range ie:
(position 1 and 2 in the target vector have a roughly 50/50 occurance rate while position 3 less than 3% occurance rate. so by relatively equalised I mean the softmax output generally looks something like
"0.56.... 0.48.... 0.02..." even after 500 epochs.
The weights at the hidden layer closer to inputlayer dont change much at all, which is what i think vanishing gradients are. I might be wrong on this. But the weights at hiddenlayer closest to output are ending up at between -50 & 50 (which i think is okay?)
Things I have tried:
I have tried using Relu, parametric Relu, exponential Relu, but with all of these the softmax output value for neuron 3 keeps rising, the other 2 neurons values keep falling. these values continue their trajectory until either 500 epochs have been reached or they just turn into nans. (I think this is to do with the structure of my code rather than the Relu function itself).
If I set the number of hidden layers above 3 while using relu, it immediately spits out nans, within the first epoch.
The backprop function is pretty long, but this is specifically because I have deconstructed it many times over to try and figure out where I might be mismatching values or something. I do have it in a condensed version but I feel I have a higher chance of being completely off the mark there than I do if I have it deconstructed.
I have included the Relu function code that I used, it is the first time I use it so I might be wrong on that aswell but I dont think so, I have double checked multiple times. The Relu in the code is specifically "Elu" or exponential relu.
here is the code for the net:
#include <iostream>
#include <fstream>
#include <cmath>
#include <vector>
#include <sstream>
#include <random>
#include <string>
#include <iomanip>
double randomt(double x, double y)
{
std::random_device rd;
std::mt19937 mt(rd());
std::uniform_real_distribution<double> dist(x, y);
return dist(mt);
}
class InputN
{
public:
double val{};
std::vector <double> weights{};
};
class HiddenN
{
public:
double preactval{};
double actval{};
double actvalPD{};
double preactvalpd{};
std::vector <double> weights{};
double bias{};
};
class OutputN
{
public:
double preactval{};
double actval{};
double preactvalpd{};
double bias{};
};
class Net
{
public:
std::vector <InputN> inneurons{};
std::vector <std::vector <HiddenN>> hiddenneurons{};
std::vector <OutputN> outputneurons{};
double lambda{ 0.015 };
double alpha{ 0.02 };
};
double tanhderiv(double val)
{
return 1 - tanh(val) * tanh(val);
}
double Relu(double val)
{
if (val < 0) return 0.01 *(exp(val) - 1);
else return val;
}
double Reluderiv(double val)
{
if (val < 0) return Relu(val) + 0.01;
else return 1;
}
double regularizer(double weight)
{
double absval{};
if (weight < 0) absval = weight - weight - weight;
else if (weight > 0 || weight == 0) absval = weight;
else;
if (absval > 0) return 1;
else if (absval < 0) return -1;
else if (absval == 0) return 0;
else return 2;
}
void feedforward(Net& net)
{
double sum{};
int prevlayer{};
for (size_t Hsize = 0; Hsize < net.hiddenneurons.size(); Hsize++)
{
//std::cout << "in first loop" << '\n';
prevlayer = Hsize - 1;
for (size_t Hel = 0; Hel < net.hiddenneurons[Hsize].size(); Hel++)
{
//std::cout << "in second loop" << '\n';
if (Hsize == 0)
{
//std::cout << "in first if" << '\n';
for (size_t Isize = 0; Isize < net.inneurons.size(); Isize++)
{
//std::cout << "in fourth loop" << '\n';
sum += (net.inneurons[Isize].val * net.inneurons[Isize].weights[Hel]);
}
net.hiddenneurons[Hsize][Hel].preactval = net.hiddenneurons[Hsize][Hel].bias + sum;
net.hiddenneurons[Hsize][Hel].actval = tanh(sum);
sum = 0;
//std::cout << "first if done" << '\n';
}
else
{
//std::cout << "in else" << '\n';
for (size_t prs = 0; prs < net.hiddenneurons[prevlayer].size(); prs++)
{
//std::cout << "in fourth loop" << '\n';
sum += net.hiddenneurons[prevlayer][prs].actval * net.hiddenneurons[prevlayer][prs].weights[Hel];
}
//std::cout << "fourth loop done" << '\n';
net.hiddenneurons[Hsize][Hel].preactval = net.hiddenneurons[Hsize][Hel].bias + sum;
net.hiddenneurons[Hsize][Hel].actval = tanh(sum);
//std::cout << "else done" << '\n';
sum = 0;
}
}
}
//std::cout << "first loop done " << '\n';
int lasthid = net.hiddenneurons.size() - 1;
for (size_t Osize = 0; Osize < net.outputneurons.size(); Osize++)
{
for (size_t Hsize = 0; Hsize < net.hiddenneurons[lasthid].size(); Hsize++)
{
sum += (net.hiddenneurons[lasthid][Hsize].actval * net.hiddenneurons[lasthid][Hsize].weights[Osize]);
}
net.outputneurons[Osize].preactval = net.outputneurons[Osize].bias + sum;
}
}
void softmax(Net& net)
{
double sum{};
for (size_t Osize = 0; Osize < net.outputneurons.size(); Osize++)
{
sum += exp(net.outputneurons[Osize].preactval);
}
for (size_t Osize = 0; Osize < net.outputneurons.size(); Osize++)
{
net.outputneurons[Osize].actval = exp(net.outputneurons[Osize].preactval) / sum;
}
}
void lossfunc(Net& net, std::vector <double> target)
{
int pos{ -1 };
double val{};
for (size_t t = 0; t < target.size(); t++)
{
pos += 1;
if (target[t] > 0)
{
break;
}
}
for (size_t s = 0; net.outputneurons.size(); s++)
{
val = -log(net.outputneurons[pos].actval);
}
}
void backprop(Net& net, std::vector<double>& target)
{
for (size_t outI = 0; outI < net.outputneurons.size(); outI++)
{
double PD = target[outI] - net.outputneurons[outI].actval;
net.outputneurons[outI].preactvalpd = PD * -1;
}
size_t lasthid = net.hiddenneurons.size() - 1;
for (size_t LH = 0; LH < net.hiddenneurons[lasthid].size(); LH++)
{
for (size_t LHW = 0; LHW < net.hiddenneurons[lasthid][LH].weights.size(); LHW++)
{
double weight = net.hiddenneurons[lasthid][LH].weights[LHW];
double PD = net.outputneurons[LHW].preactvalpd * net.hiddenneurons[lasthid][LH].actval;
PD = PD * -1;
double delta = PD - (net.lambda * regularizer(weight));
weight = weight + (net.alpha * delta);
net.hiddenneurons[lasthid][LH].weights[LHW] = weight;
}
}
for (size_t OB = 0; OB < net.outputneurons.size(); OB++)
{
double bias = net.outputneurons[OB].bias;
double BPD = net.outputneurons[OB].preactvalpd;
BPD = BPD * -1;
double Delta = BPD;
bias = bias + (net.alpha * Delta);
}
for (size_t HPD = 0; HPD < net.hiddenneurons[lasthid].size(); HPD++)
{
double PD{};
for (size_t HW = 0; HW < net.outputneurons.size(); HW++)
{
PD += net.hiddenneurons[lasthid][HPD].weights[HW] * net.outputneurons[HW].preactvalpd;
}
net.hiddenneurons[lasthid][HPD].actvalPD = PD;
PD = 0;
}
for (size_t HPD = 0; HPD < net.hiddenneurons[lasthid].size(); HPD++)
{
net.hiddenneurons[lasthid][HPD].preactvalpd = net.hiddenneurons[lasthid][HPD].actvalPD * tanhderiv(net.hiddenneurons[lasthid][HPD].preactval);
}
for (size_t AllHid = net.hiddenneurons.size() - 2; AllHid > -1; AllHid--)
{
size_t uplayer = AllHid + 1;
for (size_t cl = 0; cl < net.hiddenneurons[AllHid].size(); cl++)
{
for (size_t clw = 0; clw < net.hiddenneurons[AllHid][cl].weights.size(); clw++)
{
double weight = net.hiddenneurons[AllHid][cl].weights[clw];
double PD = net.hiddenneurons[uplayer][clw].preactvalpd * net.hiddenneurons[AllHid][cl].actval;
PD = PD * -1;
double delta = PD - (net.lambda * regularizer(weight));
weight = weight + (net.alpha * delta);
net.hiddenneurons[AllHid][cl].weights[clw] = weight;
}
}
for (size_t up = 0; up < net.hiddenneurons[uplayer].size(); up++)
{
double bias = net.hiddenneurons[uplayer][up].bias;
double PD = net.hiddenneurons[uplayer][up].preactvalpd;
PD = PD * -1;
double delta = PD;
bias = bias + (net.alpha * delta);
}
for (size_t APD = 0; APD < net.hiddenneurons[AllHid].size(); APD++)
{
double PD{};
for (size_t APDW = 0; APDW < net.hiddenneurons[AllHid][APD].weights.size(); APDW++)
{
PD += net.hiddenneurons[AllHid][APD].weights[APDW] * net.hiddenneurons[uplayer][APDW].preactvalpd;
}
net.hiddenneurons[AllHid][APD].actvalPD = PD;
PD = 0;
}
for (size_t PPD = 0; PPD < net.hiddenneurons[AllHid].size(); PPD++)
{
double PD = net.hiddenneurons[AllHid][PPD].actvalPD * tanhderiv(net.hiddenneurons[AllHid][PPD].preactval);
net.hiddenneurons[AllHid][PPD].preactvalpd = PD;
}
}
for (size_t IN = 0; IN < net.inneurons.size(); IN++)
{
for (size_t INW = 0; INW < net.inneurons[IN].weights.size(); INW++)
{
double weight = net.inneurons[IN].weights[INW];
double PD = net.hiddenneurons[0][INW].preactvalpd * net.inneurons[IN].val;
PD = PD * -1;
double delta = PD - (net.lambda * regularizer(weight));
weight = weight + (net.alpha * delta);
net.inneurons[IN].weights[INW] = weight;
}
}
for (size_t hidB = 0; hidB < net.hiddenneurons[0].size(); hidB++)
{
double bias = net.hiddenneurons[0][hidB].bias;
double PD = net.hiddenneurons[0][hidB].preactvalpd;
PD = PD * -1;
double delta = PD;
bias = bias + (net.alpha * delta);
net.hiddenneurons[0][hidB].bias = bias;
}
}
int main()
{
std::vector <double> invals{ };
std::vector <double> target{ };
Net net;
InputN Ineuron;
HiddenN Hneuron;
OutputN Oneuron;
int IN = 4;
int HIDLAYERS = 4;
int HID = 8;
int OUT = 3;
for (int i = 0; i < IN; i++)
{
net.inneurons.push_back(Ineuron);
for (int m = 0; m < HID; m++)
{
net.inneurons.back().weights.push_back(randomt(0.0, 0.5));
}
}
//std::cout << "first loop done" << '\n';
for (int s = 0; s < HIDLAYERS; s++)
{
net.hiddenneurons.push_back(std::vector <HiddenN>());
if (s == HIDLAYERS - 1)
{
for (int i = 0; i < HID; i++)
{
net.hiddenneurons[s].push_back(Hneuron);
for (int m = 0; m < OUT; m++)
{
net.hiddenneurons[s].back().weights.push_back(randomt(0.0, 0.5));
}
net.hiddenneurons[s].back().bias = 1.0;
}
}
else
{
for (int i = 0; i < HID; i++)
{
net.hiddenneurons[s].push_back(Hneuron);
for (int m = 0; m < HID; m++)
{
net.hiddenneurons[s].back().weights.push_back(randomt(0.0, 0.5));
}
net.hiddenneurons[s].back().bias = 1.0;
}
}
}
//std::cout << "second loop done" << '\n';
for (int i = 0; i < OUT; i++)
{
net.outputneurons.push_back(Oneuron);
net.outputneurons.back().bias = randomt(0.0, 0.5);
}
//std::cout << "third loop done" << '\n';
int count{};
std::ifstream fileread("N.txt");
for (int epoch = 0; epoch < 500; epoch++)
{
count = 0;
if (epoch == 100 || epoch == 100 * 2 || epoch == 100 * 3 || epoch == 100 * 4 || epoch == 499)
{
printvals("no", net);
}
fileread.clear(); fileread.seekg(0, std::ios::beg);
while (fileread.is_open())
{
std::cout << '\n' << "epoch: " << epoch << '\n';
std::string fileline{};
fileread >> fileline;
if (fileline == "in:")
{
std::string input{};
double nums{};
std::getline(fileread, input);
std::stringstream ss(input);
while (ss >> nums)
{
invals.push_back(nums);
}
}
if (fileline == "out:")
{
std::string output{};
double num{};
std::getline(fileread, output);
std::stringstream ss(output);
while (ss >> num)
{
target.push_back(num);
}
}
count += 1;
if (count == 2)
{
for (size_t inv = 0; inv < invals.size(); inv++)
{
net.inneurons[inv].val = invals[inv];
}
//std::cout << "calling feedforward" << '\n';
feedforward(net);
//std::cout << "ff done" << '\n';
softmax(net);
printvals("output", net);
std::cout << "target: " << '\n';
for (auto element : target) std::cout << element << " / ";
std::cout << '\n';
backprop(net, target);
invals.clear();
target.clear();
count = 0;
}
if (fileread.eof()) break;
}
}
//std::cout << "fourth loop done" << '\n';
return 1;
}
Much aprecciated to anyone who actually made it through all that! :)
Given a histogram, perform a bi-means gaussian fitting.
This project fits two Gaussian curves to one histogram with an initial threshold value, and uses the curves to determine the ideal threshold value. At each iteration, the histogram is divided into 2 parts, a Gaussian is called for each part of the histogram.
My calculations must be wrong considering my resultant curve is nonsensical. Can anyone spot what's going on here? I've included my functions for calculating the biMeans Gaussian curve, the fitGauss (computes Gaussian Curve), the mean, the variance, and the Gaussian value.
int biMeanGauss (int thrVal){
double sum1, sum2, total = 0.0;
int bestThr = thrVal;
double minDiff = 99999999.0;
for (int i = thrVal; i < (maxVal-offSet); i++) {
set1DZero(GaussAry);
sum1 = fitGauss(0, i);
cout << "Sum1: " <<sum1 << endl;
sum2 = fitGauss(i, maxVal);
cout << "Sum2: " << sum2 << endl;
total = sum1 + sum2;
cout << "Total: " << total << endl;
if (total < minDiff) {
minDiff = total;
bestThr = i;
cout << "Total < MinDiff, so BestThr: " <<bestThr << endl;
}
else;
}
return bestThr;
}
double fitGauss(int leftIndex, int rightIndex){
double mean, var, sum = 0.0;
double Gval;
mean = computeMean(leftIndex, rightIndex, maxCount);
var = computeVar (leftIndex, rightIndex, mean);
for (int index = leftIndex; index <= rightIndex; index ++){
Gval = computeGaussian(histAry[index], mean, var);
sum += abs(Gval - histAry[index]);
GaussAry[index] = (int)Gval;
GaussImg[index][(int)Gval]= 1;
}
return sum;
};
double computeMean(int leftIndex, int rightIndex, int maxCount) {
int mean, n, sum = 0;
for (int i = leftIndex; i <= rightIndex; i++){
sum += (i*histAry[i]);
n++;
if (histAry[i] > maxCount){
maxCount = histAry[i];
}
}
mean = (sum / (double) n);
return mean;
}
double computeVar(int leftIndex, int rightIndex, int mean) {
double var = 0;
double sum = 0;
double n = 0;
for (int i = leftIndex; i <= rightIndex; i++) {
sum += histAry[i]*(i - mean) * (i - mean);
n++;
}
var = (sum / n);
return var;
}
double computeGaussian(int index, double mean, double var) {
double Gval = 0;
Gval = maxCount * exp(-(((index - mean)*(index - mean)) / (2 * var)));
return Gval;
}
I am used to write C++ project in CodeBlocks, but for some stupid reasons I have to show it to my teacher in VisualStudio. I tried to make a console app or an empty project, and copied my main file there, but with the first one I get bunch of erorrs and the second one I get 'The system cannot find the way specified'. What is different in VisualStudio? I don't understand at all what is wrong.
here is my code
#include <iostream>
#include <fstream>
#include <math.h>
using namespace std;
const int kroku = 1000;
const double aa = 0; //pocatecni bod intervalu
const double bb = 1; //konečný bod intervalu
double a; //parametr
const double h = (bb - aa) / kroku; //krok
double p(double t) { //(py')' - qy = f
return exp(a*pow(t, 2));
}
double q(double t) {
return -exp(a*pow(t, 2))*pow(a, 2)*pow(t, 2);
}
double dp(double t) {
return 2 * t*a*exp(a*pow(t, 2));
}
double y[kroku + 1]; //řešení původní rce
double dydx[kroku + 1];
double z[kroku + 1]; //řešení dílčí rce
double dzdx[kroku + 1];
double x[kroku + 1]; //rozdělení intervalu (aa, bb) po krocích h
void generateX() { //generuje hodnoty x
for (int k = 0; k <= kroku; k++) {
x[k] = aa + k*h;
}
}
double partial(double pp1, double pp2, double w[kroku + 1], double dwdx[kroku + 1], double v)//řešení rce (pw')' - qw = g s pp
{
w[v] = pp1; //inicializace - počáteční podmínka
dwdx[v] = pp2; //inicialzace - počáteční podmínka
for (int i = 0; i <= kroku; i++) { //substituce dwdx proměnná -> dwdx = (w_(n+1) - w_n)/h) && dwdx =
w[i + 1] = h*dwdx[i] + w[i];
dwdx[i + 1] = (h / p(aa + h*i))*(q(aa + h*i)*w[i] - dp(aa + h*i)*dwdx[i]) + dwdx[i];
}
return 0;
}
double omega1, omega2; //nové počáteční podmínky omega1 = y(x0), omega2 = y'(x0)
void print(double N[kroku + 1])
{
fstream file;
file.open("data.dat", ios::out | ios::in | ios::trunc);//otevření/vytvoření(trunc) souboru
if (file.is_open()) //zápis do souboru
{
cout << "Writing";
file << "#" << "X" << " " << "Y" << endl;
for (int j = 0; j <= kroku; j++) {
file << x[j] << " " << N[j] << endl;
}
file << "#end";
}
else
{
cout << "Somethinq went wrong!";
}
file.close();
}
int main()
{
double alpha; //pocatecni podminka y(aa) = alpha
double beta; //y(bb) = beta
cout << "Assign the value of beta " << endl;
cin >> beta;
cout << "Assign the value of alpha " << endl;
cin >> alpha;
cout << "Assign the value of parameter a" << endl;
cin >> a;
double alpha1 = 0; //alpha1*p(aa)*y'(aa) - beta1*y(aa) = gamma1
//double alpha2 = 0; //alpha2*p(bb)*y'(bb) + beta2*y(bb) = gamma2
double beta1 = -1;
double beta2 = 1;
double gamma1 = alpha;
double gamma2 = beta;
generateX();
partial(alpha1, beta1 / p(aa), z, dzdx, aa); //(pz')'-qz = 0
omega1 = gamma2 / beta2;
omega2 = 1 / (z[kroku] * p(bb))*(gamma1 + dzdx[kroku] * p(bb));
partial(omega1, omega2, y, dydx, aa);//(py')' - qy = f = 0
print(y);
return 0;
strong text}
when I add
#include "stdafx.h"
I get four errors
2x 'Expression must have integral or unscoped enum type'
2x 'subscript is not of integral type'
for these lines
w[v] = pp1;
dwdx[v] = pp2;
Could anyone please help me? Thank you a lot
array subscript v in your line
w[v]
can not be double. It must be of interger type.
I am trying to calculate distances between particles in a box. If the distance calculated is greater than a preset cut-off distance, then the potential energy is 0. Otherwise, it is 1.
There are some rounding issues I think and I am not familiar with variable types and passing variables through functions to know what to do next.
The error
When I calculate d0 by hand I get d0 = 0.070 - this is not what the computer gets! The computer gets a number on the order of e-310.
All of the calculated distances (dij) are no shorter than 1/14, which is much larger than e-310. According to my if statement, if dij>d0, then U=0, so I should get a total energy of 0, but this is what I get:
d0 is 6.95322e-310
i is 0 j is 1 dij is 0.0714286 d0 is 6.95322e-310 Uij is 1
.....
Energy of the system is 24976
Please let me know if I could provide any more information. I did not include the entirety of my code, but the other portion involves no manipulation of d0.
I copied the relevant pieces of code below
Part 1: relevant box data
class Vector {
public:
double x;
double y;
Vector() {
}
Vector (double x_, double y_) {
x = x_;
y = y_;
}
double len() {
return sqrt(x*x + y*y);
}
double lenSqr() {
return x*x + y*y;
}
};
class Atom
{
public:
Vector pos;
Vector vel;
Vector force;
Atom (double x_, double y_) {
pos = Vector(x_, y_);
}
};
class BoxData
{
public:
const double Len = 1.;
const double LenHalf = 0.5 * Len;
long double d = 1. / 14; // d is the distance between each atom
in the initial trigonal lattice
int nu = 7; // auxillary parameter - will be varied
long double d0 = d * (1 - 2^(nu - 8)); // cutoff distance
double alpha = d - d0; // maximum allowed displacement
};
int main() {
// Initialize box
LoadBox();
// Institute a for loop here
SystemEnergy();
MonteCarloMove();
return 0;
}
//Putting atoms into box
void LoadBox()
{
ofstream myfile("init.dat", ios::out);
//Load atoms in box in triangular offset lattice
const double x_shift = 1. / 14;
const double y_shift = 1. / 16;
double x = 0;
double y = 0;
double x_offset = 0;
for (y = 0; y <= 1. - y_shift; y += y_shift) {
for (x = x_offset; x < 0.99; x += x_shift) {
// create atom in position (x, y)
// and store it in array of atoms
atoms.push_back(Atom(x, y));
}
// every new row flip offset 0 -> 1/28 -> 0 -> 1/28...
if (x_offset < x_shift / 4) {
x_offset = x_shift / 2;
} else {
x_offset = 0.0;
}
}
const int numAtoms = atoms.size();
//print the position of each atom in the file init.dat
for (int i = 0; i < numAtoms; i++) {
myfile << "x is " << atoms[i].pos.x << " y is " << atoms[i].pos.y << endl;
}
myfile.close();
}
Part 2 : Energy calculation
vector<Atom> atoms;
BoxData box_;
void SystemEnergy()
{
ofstream myfile("energy.dat", ios::out);
double box_Len, box_LenHalf, box_d0;
double dij; // distance between two atoms
double Uij; // energy between two particles
double UTotal = 0;
double pbcx, pbcy; // pbc -> periodic boundary condition
double dx, dy;
myfile << "d0 is " << box_d0 << endl;
// define the number of atoms as the size of the array of atoms
const int numAtoms = atoms.size();
//pick atoms
for (int i=0; i<numAtoms-1; i++) { // pick one atom -> "Atom a"
Atom &a = atoms[i];
for (int j=i+1; j<numAtoms; j++) { // pick another atom -> "Atom b"
Atom &b = atoms[j];
dx = a.pos.x - b.pos.x;
dy = a.pos.y - b.pos.y;
pbcx = 0.0;
pbcy = 0.0;
// enforce periodic boundary conditions
if(dx > box_LenHalf) pbcx =- box_Len;
if(dx < -box_LenHalf) pbcx =+ box_Len;
if(dy > box_LenHalf) pbcy =- box_Len;
if(dy < -box_LenHalf) pbcy =+ box_Len;
dx += pbcx;
dy += pbcy;
// calculate distance between atoms
dij = sqrt(dx*dx + dy*dy);
// compare dij to the cutoff distance to determine energy
if (dij > box_d0) {
Uij = 0;
} else {
Uij = 1;
}
myfile << "i is " << i << " j is " << j << " dij is " << dij << " d0 is " << box_d0 << " Uij is " << Uij << endl;
UTotal += Uij; // sum the energies
}
}
myfile << "Energy of the system is " << UTotal << endl;
myfile.close();
}
Sorry for the formatting issues - getting the hang of copy/pasting to the forum.
I am writing a harmonic oscillator program , but it does an exponential decay instead and I am not sure why. I have the code below. I use F= -k x and F = m a
I assume m = 1 and k = 1, so a = -x
So my equations to find velocity and position are
v(t) = v(t-dt) - x(t-dt) * dt
x(t) = x(t-dt) + v(t-dt) * dt
I am not sure what I am doing wrong
The code associated with this is
#include <iostream>
#include <fstream>
using namespace std;
double updateX(double intialV, double intialX, double step);
double updateV(double intialV, double intialX, double step);
int main()
{
long double position[2];long double velocity[2];
position[0] = 0.0; velocity[0] = 1.0; double time = 0.0; double step = .1;
ofstream outputFile;
outputFile.open("velo1.dat");
outputFile << time << " " << position[0] << " " << velocity[0] << "\n";
for(int i = 1; i < 50; i++)
{
time = i * step;
velocity[1] = updateV(velocity[0], position[0], step);
position[1] = updateX(velocity[0], position[0], step);
outputFile << time << " " << position[1] << " " << velocity[1] << "\n";
velocity[0] = velocity[1];
position[0] = velocity[1];
}
return 0;
outputFile.close();
}
double updateX(double intialV, double intialX, double step)
{
double stuff =(intialX + intialV * step);
return stuff;
}
double updateV(double intialV, double intialX, double step)
{
double stuff = (intialV - intialX * step) ;
return stuff;
}