Periodic Boundary Conditions - Practical Implementation: Continuity and The Minimum Image Convention

Practical Implementation: Continuity and The Minimum Image Convention

To implement periodic boundary conditions in practice, at least two steps are needed.

The first is to make an object which leaves the simulation cell on one side enter back on the other. This is of course a simple operation, and could in code be e.g. (for the x dimension, assuming an orthogonal unit cell centered on the origin):

if (periodicx) then if (x < -xsize*0.5) x=x+xsize if (x >= xsize*0.5) x=x-xsize endif

The second is to make sure that every distance between atoms, or other vector calculated from one atom to another, has a length and direction which corresponds to the minimum image criterion. This can be achieved as follows to calculate e.g. the x direction distance component from atom i to atom j:

if (periodicx) then dx = x(j) - x(i) if (abs(dx) > xsize*0.5) dx = dx - sign(xsize,dx) endif

Naturally both operations should be repeated in all 3 dimensions.

These operations can be written in much more compact form for orthorhombic cells if the origin is shifted to a corner of the box. Then we have, in one dimension, for positions and distances respectively:

! After x(i) update without regard to PBC: x(i)=x(i)-floor(x(i)/xsize)*xsize !For a box with the origin at the lower left vertex ! Works for xs lying in any image. dx=x(j)-x(i) dx=dx-nint(dx/(0.5*xsize))*xsize

For non-orthorhombic cells the situation can be considerably more complicated.

In simulations of ionic systems considerably more complicated operations may be needed to handle the long-range Coulomb interactions.

Read more about this topic:  Periodic Boundary Conditions

Famous quotes containing the words practical, continuity, minimum, image and/or convention:

    “The three practical rules, then, which I have to offer, are,— 1. Never read any book that is not a year old. 2. Never read any but famed books. 3. Never read any but what you like.”
    —Ralph Waldo Emerson (1803–1882)

    “The dialectic between change and continuity is a painful but deeply instructive one, in personal life as in the life of a people. To “see the light” too often has meant rejecting the treasures found in darkness.”
    —Adrienne Rich (b. 1929)

    “After decades of unappreciated drudgery, American women just don’t do housework any more—that is, beyond the minimum that is required in order to clear a path from the bedroom to the front door so they can get off to work in the mourning.”
    —Barbara Ehrenreich (20th century)

    “As death, when we come to consider it closely, is the true goal of our existence, I have formed during the last few years such close relations with this best and truest friend of mankind, that his image is not only no longer terrifying to me, but is indeed very soothing and consoling! And I thank my God for graciously granting me the opportunity ... of learning that death is the key which unlocks the door to our true happiness.”
    —Wolfgang Amadeus Mozart (1756–1791)

    ““We’ll encounter opposition, won’t we, if we give women the same education that we give to men,” Socrates says to Galucon. “For then we’d have to let women ... exercise in the company of men. And we know how ridiculous that would seem.” ... Convention and habit are women’s enemies here, and reason their ally.”
    —Martha Nussbaum (b. 1947)