Wednesday, February 11, 2004

DMC of porphyrin


An all electron calculation of a large molecule (large by QMC standards, anyway):
Quantum Monte Carlo for electronic excitations of free-base porphyrin by Alan Aspuru-Guzik, Ouafae El Akramine, Jeffrey Grossman, and William Lester. The porphyrin they used has the formula C20 N4 H14, so 168 electrons.

Wednesday, February 04, 2004

Solid vs. Liquid, The Free Energy Battle


Determining the free energy difference between the solid and liquid states is essential for accurately mapping the phase diagram of a substance. Typically, one determines the free energies of the solid and liquid states through separate thermodynamic integrations, where each integration has one end point connected to a state with an analytically known free energy. In the solid state, the Einstein crystal (springs attaching particles to lattice sites) is often used as a starting point. In the liquid state, the low density gas can be used as an end point. Other more complicated scalings of the potential are also possible for the integration path.


A direct integration path between the solid and liquid states would be useful.
Gregory Grochola has published one such path in "Constrained fluid lambda-integration: Constructing a reversible thermodynamic path between the solid and liquid state"(JCP 120, 2122).


The basic path is to start with the liquid state and turn off the intermolecular potential. Then turn on a potential constraining particles to lattice sites (He used a Gaussian potential). The last step is to turn off the lattice potential while turning the intermolecular potential back on.


He mentions at the end that this method is not very computationally efficient. I would expect using Bennett's method for free energy differences would cut down on the number of intermediate states needed.


Questions


  1. Compare and contrast this path with the phase switching Monte Carlo technique (there's a reference in the article)
  2. Thermodynamic integration requires there be no phase transitions on the path. Is it immediately obvious that this path has no transitions? Under what conditions, if any, would a phase transition occur on the path?

Saturday, January 24, 2004

Hard Spheres on the Move


Cluster algorithms increase efficiency for systems on a lattice by flipping large numbers of connected spins at once. In "Cluster Monte Carlo algorithms", Werner Krauth summarizes work on how such algorithms can be used in a continuum hard sphere simulation.


The basic idea is to rotate particles by &pi around a randomly chosen axis. (The key observation is that this transformation is its own inverse). A practical algorithm (the pocket algorithm) chooses a collection of particles that can be rotated without any hard spheres overlapping. It starts with a single particle and rotates it. If it overlaps with any other particles, they are added to the collection. Then the new particles are tested in the same way, and the collection is built up of all the particles that need to be rotated to prevent any overlaps.


At high densities, this algorithm will fail because the pocket cluster will contain all (or most) of the particles in the system, and simply rotate the entire configuration. Despite this limitation, there are systems where these moves are useful (see the paper for some examples).


On another subject, suppose you wanted to keep the trial box size fixed, and see how the dynamics varied with density (which would be useful if one were studying the actual MC dynamics) At higher densities, the efficiency would get quite bad. Hirosi Watanabe, et al tackle this problem in A rejection-free Monte Carlo method for the hard-disk system. They use geometry rather than random sampling to determine the allowable move area (and acceptance probability). To actually choose a point, they use a rejection method (it's not clear why this method is called "rejection-free", then. Maybe because the rejections are not essential for maintaining detailed balance, and rejected moves don't need to be included in the average.). At the step of choosing a new point, the area they choose from is greatly reduced from the original trial area.

Friday, December 12, 2003

Reducing the Variance


Assaraf and Caffarel have published a couple of papers (JCP 119, 10536 and JCP 113, 4028) about reducing the variance for general estimators in QMC. The VMC energy has the well known zero variance property - the variance goes to zero as the trial wavefunction approaches an eigenstate. Through a "renormalization" , the authors show how to extend this property to quantities other than the energy.


The basic approach seems to be to add a term (with zero average) to the bare estimator. Then that added term can be optimized to reduce the variance. Their derivation starts with the Hellmann-Feynman theorem, but this seems confusing to me.


Why not start with the new estimator, O tilde = O + B. ("O tilde" and "O" are notations from the paper. "B" is my own notation for representing all the added terms) Then we demand < B > = 0, and use a Lagrange multiplier to enforce it while optimizing the variance (<(O+B)^2> - < O+B>^2)?


Their paper gives a particular form for B, that ensures the < B>=0 constraint is met (or at least that < B > vanishes as the trial wavefunction approaches the ground state).


Can this approach be used to reduce the variance in classical Monte Carlo as well? In principle, B could optimized in that case as well - the hard part is finding a special form as in Quantum Monte Carlo.


Added thoughts (12/14/2003): The primary application of this method is to forces, which are plagued by an infinite variance in QMC. This looks a like good way to improve computations of the force.


The paper looks at average values and variances as functions (or at least the polynomial order) of delta psi (the diference between the exact ground state and the trial wavefunction). For general (non-energy) estimators, the bias (or error) in the average value is linear in delta psi, and the variance is constant. Using their procedure, the error is quadratic and the variance is linear. It appears the added terms (B) cancel out the leading error terms in the estimator. The question is then, why stop at the leading order? Can a similar process by applied to cancel out the quadratic term in the average ??

Thursday, December 04, 2003

Free Energy Chronicles


Free energy calculations are annoyingly difficult. Computing averages with Metropolis is relatively easy,
but the free energy is hard to get. The usual method is thermodynamic integration over a path from a state of known free energy to the desired state. (Maybe it's the ensemble averages that are anomalously easy, making other quantities seem difficult by comparison) In addition, some other aspects about free energy calculations are bothering me as well.


The typical example for explaining Monte Carlo integration is to compute the area of an irregularly shaped field or pond by throwing rocks at it. But then computing the area (volume, free energy, whatever) is actually quite difficult in practice. Of course in this example, one has to compare the rocks falling in desired area to those falling in an enclosing area that can be computed analytically, so it's still computing the difference between two states.


Another issue that bothers my intuition is that if I were to wander around in a field I would have some idea how big the field is based on my wanderings. In other words, why can't we get the area from properties of the random walk. This could simply be pushing the analogy too far. A person wandering is not undergoing a truly random walk. They would likely walk in single direction until hitting an edge and then change direction. So imagine riding an out-of-control Segway around a field - would you still get a sense of the size of the field.


Additionally, a person is able to see the edges. So imagine being in a corn field (I am in central Illinois, after all - others can imagine a forest, with very soft trees) on an out-of-control Segway. Would it still be possible to get an idea of how big the field is based on the path taken and how often you bump into the edge?


So I'd like to look into some of the properties of random walks - how much information can be extracted. Are there theoretical limits? Can we change the random walk or come up with different estimators that would let us compute the area?


In order to investigate concrete but simple systems, I'm thinking of a series of systems to make the problem increasingly realistic for physical systems. The simplest and easiest to think about the area of an irregular region. More realistic, the area of the region is much less that the area of the enclosing square, and the region is long and snaky. Then go to higher dimensions, and eventually to a system of hard spheres. To be more generally applicable, the next step would be a general potential (think of a hilly field and we want to know the volume of soil is in the field)

Monday, November 10, 2003

Interesting notes


While searching for Monte Carlo information on the web, I ran across Jonathon Goodman's Monte-Carlo Course Materials. One interesting part was Alan Sokal's introductory notes near the bottom (see also this CiteSeer link). I liked these notes because they covered a practical method for computing the autocorrelation time.

Sunday, November 02, 2003

Optimization


Recently there were two papers in the Journal of Chemical Physics related to QMC optimization. The first, Geometry optimization in quantum Monte Carlo with solution mapping: Application to formaldehyde, is concerned with optimization of nuclear positions using only energy information, and not gradient (force) information, since it is noisier and harder to obtain. They use statistical experiment design techniques to pick coordinates at which to perform the energy computations, and fit that data to a quadratic form. The the geometry was then optimized using that fitted form.


The second paper is concerned with optimizing the one-body part of the wavefunction: Transcorrelated method for electronic systems coupled with variational Monte Carlo calculation. The authors use a transcorrelated Hamiltonian (some of the correlation has been moved into the Hamilitonian), and compute the SCF solution for the one-body orbitals. They use regular VMC to optimize the Jastrow factors. Note that the two calcuations are coupled, and to reach a solution the procedure is to alternately optimize the one-body and Jastrow factors.