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## Errata in An Introduction to Computer Simulation Methods

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Sign error - Nov 23, 2009 at 9:29AM
Larry Engelhardt
17 Posts

In the right-hand side of equation (9.56) on page 341, the term "u(x + Delta x, t)" appears twice.  One of these should be replaced with "u(x - Delta x, t)".

Missing minus signs on page 329 - Nov 9, 2009 at 5:14PM
Larry Engelhardt
17 Posts

On page 329 (equations 9.34 - 9.37) the lower limits of the integrals and the summations are each missing a minus sign.

Error in IdealDemon - Feb 21, 2009 at 2:26PM
Larry Engelhardt
17 Posts

This is not actually an "error", as I initially thought that it was.  Currently the variables systemEnergyAccumulator and demonEnergyAccumulator are being updated every time that a change is proposed, rather than being updated once per MCS.  Unless the number of MCS is large, these two methods of averaging will yield different results.  The code below shows the changes that will result in data only being accumulated once per MCS.

Alternate method for IdealDemon.java:

public void doOneMCStep() {
for(int j = 0;j LESSTHAN N;++j) {
int particleIndex = (int) (Math.random()*N); // choose particle at random
double dv = (2.0*Math.random()-1.0)*delta;   // random change in velocity
double trialVelocity = v[particleIndex]+dv;
double dE = 0.5*(trialVelocity*trialVelocity-v[particleIndex]*v[particleIndex]);
if(dE LESSTHANOREQUALTO demonEnergy) {
v[particleIndex] = trialVelocity;
acceptedMoves++;
systemEnergy += dE;
demonEnergy -= dE;
}
}
systemEnergyAccumulator += systemEnergy;
demonEnergyAccumulator += demonEnergy;
mcs++;
}

Alternate code for IdealDemonApp.java:

control.println("Mean Ed = "+idealGas.demonEnergyAccumulator/idealGas.mcs);
control.println("Mean E = "+idealGas.systemEnergyAccumulator/idealGas.mcs);

Post edited February 21, 2009 at 2:53 PM EST.

Current Replies - View all
Re: Error in IdealDemon   (Jan Tobochnik - Feb 23, 2009 at 10:18AM)
Sign in Problem 8.4 - Jan 21, 2009 at 2:50PM
Larry Engelhardt
17 Posts

In the code that is listed in Problem 8.4(a), the line

y[i] = (i - 0.5) *Ly/N;

should contain a + sign rather than a - sign,

y[i] = (i + 0.5) *Ly/N;

otherwise the bottom molecule will begin outside of the box.

PBCs in setRandomPositions() - Jan 17, 2009 at 12:21PM
Larry Engelhardt
17 Posts

In the setRandomPositions() method in the file LJParticles.java, the periodic boundary conditions are not taken into account when determining whether or not two molecules are overlapping, often causing the simulation to get stuck when using these initial conditions.  Listing 8.4 in the CSM texbook correctly incorporates the PBCs in the lines:

double dx = pbcSeparation(state[4*i]-state[4*j], Lx);
double dy = pbcSeparation(state[4*i+2]-state[4*j+2], Ly);

Exercise 8.2 - Jan 15, 2009 at 7:13PM
Larry Engelhardt
17 Posts

In part (b) of Exercise 8.2, the line of code that is listed contains extra slashes (\).

The line should read:

return x<0 ? x%L + L:  x%L;

Missing "?" in problem 8.10 - Dec 13, 2008 at 9:27AM
Larry Engelhardt
17 Posts

On page 278, the first sentence of problem 8.10(a) ends with a period which should be a question mark.

Typo in subscripts in Eq. 6.66(c) - Nov 24, 2008 at 6:54PM
Larry Engelhardt
17 Posts

In equation 6.66(c) on page 188, the subscripts are incorrect.  In order to correctly represent the reactions, Eq. 6.66(c) should read

dC/dt = k_5*B - k_6*C

rather than

dC/dt = k_4*B - k_5*C

BifurcateApp.java plotting too few data points - Nov 19, 2008 at 3:36PM
Larry Engelhardt
17 Posts

The file BifurcateApp.java (from Ch. 6 of CSM) shows the bifurcation that occurs for the logistic map as a function of the parameter r.  The application receives the number of data points to be plotted (per r value) as input (from the user) through the control window, which is written into the variable "nplot".  However, the application only plots 0.75*nplot data points, because the command i++ appears twice in the loop for dataset 1.  It appears both as the iterator for the for loop,

for(int i = nplot/2+1; i lessthan nplot; i++)

and it appears as the last statement within the body of the for loop,

i++;

Post edited December 13, 2008 at 9:31 AM EST.

Post edited December 13, 2008 at 9:33 AM EST.

Error in Lorenz.java - Nov 18, 2008 at 8:27PM
Larry Engelhardt
17 Posts

The file Lorenz.java is meant to simulate the model represented by Eqs. 6.33 (a)-(c) on page 167 of CSM.  However, there is an error in the getRate method.

The line,

rate[2] = (state[0]*state[1]-state[2])*b;

should be modified to read

rate[2] = state[0]*state[1] - b*state[2];

in order to correctly represent Eq. 6.33c.

Axis labels in GraphicalSolutionApp.java in Ch. 6 - Nov 12, 2008 at 10:06AM
Larry Engelhardt
17 Posts

The file GraphicalSolutionApp.java (listing 6.3 in the CSM textbook) is used to graphically show how the logistic map is iterated.  The quantity on the horizontal axis should be "x" (the current value of x_n), and the quantity on the vertical axis should be "f(x)" (the next value of x_n).  These axis are mislabeled as "iterations" for the horizontal-axis label and "x" for the vertical-axis label.

Sign error in Ch. 9 dealing with Huygen's wavelets - Nov 1, 2008 at 2:17PM
Larry Engelhardt
17 Posts

In the CSM textbook, there is an error in Eq. 9.62 of on page 347.  Specifically, the "-" sign should be a "+" sign.  This equation reads:

E(r,t) = Re(E)*cos(omega*t) - Im(E)*sin(omega*t)

and it should read:

E(r,t) = Re(E)*cos(omega*t) + Im(E)*sin(omega*t)

In the related code (HuygensApp.java), the calculation includes three minus signs:

E(r,t) = Re(E)*cos(-omega*t) - Im(E)*sin(-omega*t)

which is equivalent to the second equation above.  In other words, E(r,t) can be simplified slightly in HuygensApp.java by writing it without minus signs as:

E(r,t) = Re(E)*cos(omega*t) + Im(E)*sin(omega*t)

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