Category Archives: Molecular Workbench

Happy New Year from Energy2D

In the year 2014, Energy2Dhas incorporated a radiation simulation engine and a particle simulation engine, expanding its modeling capacity and making it a truly multiphysics simulation package. To celebrate the New Year, I made some simulations that demonstrate these multiphysics features using objects shaped after the numbers of 2015.

These simulations feature the fluid dynamics engine, the heat conduction engine, the thermal radiation engine, and the particle dynamics engine. If you are curious enough, you can click this link to run the simulations.


These shapes were drawn using Energy2D's polygon and ring tools, which allow users to create a wide variety of arbitrary 2D shapes. Many users probably do not know how versatile the polygon tool actually is (the original triangle icon on the tool bar probably misleads some to think it is only good for drawing triangles -- so I changed it to look like a cross-section of an I-beam). The polygon tool allows one to easily draw a polygon with maximally 256 control points for adjusting its shape later. One can draw an approximate shape and then drag these control points to get it to the exact shape. To modify a shape even further, one can also insert a control point by double-clicking on an existing point. A new point will be added to the adjacent position, which you can then drag around. To delete a control point, just hold down the SHIFT key while double-clicking on it. In addition, a polygon can be rotated, twisted, compressed, or elongated using the corresponding fields in its property window (there is currently no graphical user interface for doing those things, however).

As for the New Year's resolutions, in 2015, the ring shape will be enhanced into a new tool called the shape subtractor, which allows users to subtract a shape from another to make a hollow one.

On the numerical simulation side, we will continue to improve the accuracy of the existing simulation engines by adding an explicit solver as an option for users to overcome some of the problems related to the implicit solvers.

On the multiphysics modeling side, we will try to support multiple fluids, which seems simple at first glance but has turned out to be a very difficult mathematical problem. With the capacity of multiple fluids, we will also be able to add an electromagnetism solver in order to model effects such as electrorheological fluids (fluids whose viscosity changes with respect to an applied electric field).

We wish all Energy2D users a very successful new year!

European scientists use Energy2D to simulate submarine eruptions

The November issue of the Remote Sensing of Environment published a research article "Magma emission rates from shallow submarine eruptions using airborne thermal imaging" by a team of Spanish scientists in collaboration with Italian and American scientists. The researchers used airborne infrared cameras to monitor the 2011–2012 submarine volcanic eruption at El Hierro, Canary Islands and used our Energy2D software to calculate the heat flux distribution from the sea floor to the sea surface. The two figures in the blog post are from their paper.

According to their paper, "volcanoes are widely spread out over the seabed of our planet, being concentrated mainly along mid-ocean ridges. Due to the depths where this volcanic activity occurs, monitoring submarine volcanic eruptions is a very difficult task." The use of thermal imaging in this research, unfortunately, can only detect temperature distribution on the sea surface. Energy2D simulations turn out to be a complementary tool for understanding the vertical body flow.

Their research was supported by the European Union and assisted by the Spanish Air Force.

Although Energy2D started out as an educational program, we are very pleased to witness that its power has grown to the point that even scientists find it useful in conducting serious scientific research. We are totally thrilled by the publication of the first scientific paper that documents the validity of Energy2D as a research tool and appreciate the efforts of the European scientists in adopting this piece of software in their work.

Beautiful Chemistry


It is hard for students to associate chemistry with beauty. The image of chemistry in schools is mostly linked to something dangerous, dirty, or smelly. Yet Dr. Yan Liang, a collaborator and a materials scientist with a Ph.D. degree from the University of Minnesota, is launching a campaign to change that image. The result of his work is now online at beautifulchemistry.net.

To bring the beauty of chemistry to the general public, Dr. Liang uses 4K UltraHD cameras and special lenses to capture chemical reactions in astonishing detail and advanced computer graphics to render stunning images of molecular structures.

Using the beauty of science to interest students has rarely been taken seriously by educators. The federal government has invested billions of dollars in instructional materials development. But from a layman's point of view, it is hard to imagine how children can be engaged in science if they do not fall in love with it. Beautiful Chemistry represents an attempt that could inspire a whole new genre of high-quality educational materials based on breathtaking scientific visualizations. How about Beautiful Physics and Beautiful Biology?

Our work is well aligned with this vision. Our interactive, visual Energy2D simulations bring a beautiful world of heat and mass flow to students like never seen before; our Energy3D software creates splendid 3D scenes based on scientific calculations; and our infrared visualization of the real world has uncovered a beautiful hidden universe through an IR lens. These materials demonstrate computational and experimental ways to marry science and beauty and have resulted in great enticements in science classrooms.

BTW, Dr. Liang is the artist who designed the splash panes of Energy2D and Energy3D.

Simulating cool roofs with Energy3D

Fig. 1: Solar absorption of colors.
Cool roofs represent a simple solution that can save significant air-conditioning cost and help mitigate the urban heat island effect, especially in hot climates. Nobel Prize winner and former Secretary of Energy Steven Chu is a strong advocate of cool roofs. It was estimated that painting all the roofs and pavements around the world with reflective coatings would be "equivalent to getting 300 millions cars off the road!"

With Version 4.0 of Energy3D (BTW, this version supports 200+ worldwide locations -- with 150+ in the US), you can model cool roofs and evaluate how much energy you can save by switching from a dark-colored roof to a light-colored one. All you need to do is to set the colors of your roofs and other building blocks. Energy3D will automatically assign an albedo value to each building block according to the lightness of its color.

Figure 1 shows five rectangles in different gray colors (upper) and their thermal view (lower). In this thermal view, blue represents low energy absorption, red represents high energy absorption, and the colors in-between represents the energy absorption at the level in-between.

Now let's compare the thermal views of a black roof and a white roof of a cape code house, as shown in Figure 2. To produce Figure 2, the date was set to July 1st, the hottest time of the year in northern hemisphere, and the location was set to Boston.

Fig. 2: Compare dark and white roofs.
How much energy can we save if we switch from a perfectly black roof (100% absorption) to a perfectly white roof (0% absorption)? We can run the Annual Energy Analysis Tool of Energy3D to figure this out in a matter of seconds. The results are shown in Figure 3. Overall, the total yearly energy cost is cut from 6876 kWh to 6217 kWh for this small cape code house, about 10% of saving.

Figure 3 shows that the majority of savings comes from the reduction of AC cost. The reason that the color has no effect on heating in the winter is because the passive solar heat gains through the windows in this well-insulated house is enough to keep it warm during the sunshine hours. So the additional heat absorbed by the black roof in the same period doesn't offset the heating cost (it took me quite a while to figure out that this was not a bug in our code but actually the case in the simulation).

Fig. 3: Compare heating and AC costs (blue is white roof).
Of course, this result depends on other factors such as the U-value and thermal mass of the roof. In general, the better the roof is insulated, the less its color impacts the energy cost. With Energy3D, students can easily explore these design variables.

This new feature, along with others such as the heat flux visualization that we have introduced earlier, represents the increased capacity of Energy3D for performing function design using scientific simulations.

Here is a video that shows the heating effect on roofs of different colors.

Visualization of heat flux in Energy3D using vector fields

Fig. 1: Winter in Boston
One of the strengths of our Energy3D CAD software is its 3D visualizations of energy transfer. These visualizations not only allow students to see science concepts in action in engineering design, but also provide informative feedback for students to make their design choices based on scientific analyses of their design artifacts.

Fig. 2: Summer in Boston
A new feature has been added to Energy3D to visualize heat transfer across the building envelope using arrays of arrows. Each arrow represents the heat flux at a point on the surface of the building envelope. Its direction represents the direction of the heat flux and its length represents the magnitude of the heat flux, calculated by using Fourier's Law of Heat Conduction. Quantitatively, the length is proportional to the difference between the temperatures inside and outside the building, as well as the U-value of the material.

Fig. 3: Winter in Miami
The figures in this post show the heat flux visualizations of the same house in the winter and summer in Boston and Miami, respectively. Like the solar radiation heat map shown in the figures, the heat flux is the daily average. The U-value of the windows is greater than those of the walls and roof. Hence, you can see that the heat flux vectors in the winter sticking out of the windows are much longer than those sticking out of the walls or roof. In the summer, the heat flux vectors point into the house but they are much shorter, agreeing with the fact that Boston's summer is not very hot.

Fig. 4: Summer in Miami
Now move the same house to Miami. You can see that even in the winter, the daily average heat flux points inside the house, agreeing with the fact that Miami doesn't really have a winter. In the summer, however, the heat flux into the house becomes significantly large.

These visualizations give students clear ideas about where a house loses or gains energy the most. They can then adjust the insulation values of those weak points and run simulations to check if they have been fixed or not. Compared with just giving students some formulas or numbers to figure out what they actually mean to science and engineering practices, experiential learning like this should help students develop a true understanding of thermal conduction and insulation in the context of building science and technology.

Here is a YouTube video of the heat flux view.

Accurate prediction of solar radiation using Energy3D: Part II

About a week ago, I reported our progress in modeling worldwide solar radiation with our Energy3D software. While our calculated insolation data for a horizontal surface agreed quite well with the data provided by the National Solar Radiation Data Base, those for a south-facing vertical surface did not work out as well. I suspected that the discrepancy was partly caused by missing the reflection of short-wave radiation: not all sunlight is absorbed by the Earth. A certain portion is reflected. The ability of a material to reflect sunlight is known as albedo. For example, fresh snow can reflect up to 90% of solar energy. People who live in the northern part of the country often experience strong reflection from snow or ice in the winter.

Figure 1. Calculated and measured insolation on a south-facing surface.
In the summer, the Sun is high in the sky. A south-facing plate doesn't get as much energy as in other seasons, especially near the Equator where the Sun is just above your head (such as Honolulu as included in the figures above). However, the ambient reflection can be significant. After incorporating this component into our equations following the convention in the ASHRAE solar radiation model, the agreement between the calculated and measured results significantly improves -- you can see this big improvement by comparing Figure 1 (new algorithm) with Figure 2 (old algorithm).

Figure 2. Results without considering reflected short-wave radiation.
This degree of accuracy is critically important to supporting meaningful engineering design projects on renewable energy sources that might be conducted by students across the country. We are working to refine our computational algorithms further based on 50 years' research on solar science. This work will lend Energy3D the scientific integrity needed for rational design, be it about sustainable architecture, urban planning, or solar parks.

Go to Part I and Part III.

Accurate prediction of solar radiation using Energy3D: Part I

Solar engineering and building design rely on accurate prediction of solar radiation at any given location. This is a core functionality of our Energy3D CAD software. We are proud to announce that, through continuous improvements of our mathematical model, Energy3D is now capable of modeling solar radiation with an impressive precision.

Figure 1. Comparison of measured and calculated solar radiation on a horizontal plate at 10 US locations.
Figure 1 shows that Energy3D's calculated results of solar energy density on a horizontal plate agree remarkably well with, the National Solar Radiation Database that houses 30 years of data measured by the National Renewable Energy Laboratory of the U.S. Department of Energy -- for 10 cities across the US. One striking success is the prediction of a dip of solar radiation in June for Miami, FL (see the second image of the first row). Overall, the predicted results are slightly smaller than the measured ones. 

Note that these results are theoretical calculations, not numerical fits (such as using an artificial neural network to predict based on previous data). It is pretty amazing if you think about this: Through some complex calculations the number for each month and each city come very close to the data measured for three decades at those weather stations scattered around the country! This is the holy grail of computer simulation. This success lays a solid foundation for our Energy3D software to be scientifically and engineeringly relevant.

Figure 2. Comparison of measured and calculated solar radiation on a south-facing plate at 10 US locations.
The National Renewable Energy Laboratory also measured the solar radiation on surfaces that tilt at different angles. The predicted trends for the solar energy density on an upright south-facing plate agree reasonably well (Figure 2) with the measured data. For example, both measured and calculated data show that solar radiation on a south-facing plate peaks in the spring and fall for most northern locations and in the winter for tropical locations. It is amazing that Energy3D also correctly predicts the exception --  Anchorage in Alaska, where the solar data peak only in the spring!

Quantitatively, Energy3D seems to underestimate the solar radiation more than in the horizontal case shown in Figure 1, especially for the summer months. We suspect that this is because a vertical plate has a larger contribution from the ambient radiation and reflection than a horizontal plate (which faces the sky). We are now working towards a better model to correct this problem.

For Energy3D to serve a global audience, we have collected geographical and climate data of more than 150 domestic and foreign locations and integrated them into the software (Version 3.2). If you live in the US, you are guaranteed to find at least one location in your state.

Go to Part II and Part III.

Multiphysics simulations of inelastic collisions with Energy2D

Figure 1. Mechano-thermal simulation of inelastic collision.
Many existing simulations of inelastic collisions show the changes of speeds and energy of the colliding objects without showing what happens to the lost energy, which is often converted into thermal energy that spreads out through heat transfer. With the new multiphysics modeling capabilities, the Energy2D software can show the complete picture of energy transfer from the mechanical form to the thermal form in a single simulation.

Figure 2. Thermal marks left by collisions.
Figure 1 shows the collisions of three identical balls (mass = 10 kg, speed = 1 m/s) with three fixed objects that have different elasticities (0, 0.5, and 1). The results show that, in the case of the completely inelastic collision, all the kinetic energy of the ball (5 J) is converted into thermal energy of the rectangular hit object (at this point, the particles in Energy2D do not hold thermal energy, but this will be changed in a future version), whereas in the case of completely elastic collision, the ball B1 does not lose any kinetic energy to the hit object. In the cases of inelastic collisions, you can see the thermal marks created by the collisions. The thermometers placed in the objects also register a rise of temperatures. This view resembles infrared images of floors taken immediately after being hit by tennis balls.

Figure 3. Collisions in Energy2D.
Energy2D supports particle collisions with all the 2D shapes that it provides: rectangles, ellipses, polygons, and blobs. Figure 2 shows the thermal marks on two blobs created by a few bouncing particles. And Figure 3 shows another simulation of collision dynamics with a lot of particles bouncing off complex shapes (boy, it took me quite a while in this July 4 weekend to hunt down most of the bugs in the collision code).

The multiphysics functionality of Energy2D is an exciting new feature as it allows more realistic modeling of natural phenomena. Even in science classrooms, realism of simulations is not just something that is nice to have. If computer simulations are to rival real experiments, it must produce not only the expected effects but also the unexpected side effects. Capable of achieving just that, a multiphysics simulation can create a deep and wide learning space just like real experiments. For engineering design, this depth and breadth are not options -- there is no open-endedness without this depth and breadth and there is no engineering without open-endedness.

Simulating thermal radiation with Energy2D

Figure 1: Stefan's Law in action.
The original ray-tracing radiation solver in our Energy2D software suffers from performance problems as well as inaccuracies (no, light particles do not travel that slowly as shown in it). After some sleepless nights, I finally implemented a real radiation solver, coupled it with the heat and fluid solvers, and supported both the convex and concave shapes (see this short paper for the mathematics and the algorithms). At last, Energy2D is capable of simulating all three heat transfer mechanisms in a decent way.

Figure 2: Radiation in a box.
Able to simulate heat, fluid, radiation, particles, and any combination of them, Energy2D is now one step closer towards a full multiphysics capacity. Despite the fact that all these complex calculations are done in real time on a single computer, the software still runs at a pretty amazing speed on an average Windows tablet (such as the Surface Pro). I guess this is why our industry friends love it (although Energy2D is mostly designed for K-12 students, to my surprise, quite a number of engineers are using it to do conceptual product design). Who doesn't like a CFD tool for dummies that can save time from the long preprocessor-solver-postprocessor cycle?

Figure 1 shows a simulation that illustrates radiation heat transfer. As you can see, energy can "jump" from a high-temperature object (a radiator) to a low-temperature one without heating the medium between them (unlike the cases of conduction and convection). Users
Figure 3. Radiation in a circle.
can adjust the temperature of the radiator on the left and investigate how the radiation heat transfer increases with respect to the temperature, as per Stefan-Boltzmann's Law. The image also shows the view factor field used in the computation. The simulation provides many subtleties. For example, if you observe carefully, you can find that the radiation barrier used to separate the left compartment from the right one increases the heating on the right side of the upper left object and the left side of the upper right object -- because it reflects the radiation from the two radiators at the lower part of the box to the two sides!

Figures 2 and 3 show radiation among different shapes in an enclosed space. They show how accurate the radiation solver may be. The radiation heating on the side walls seems to make sense. In Figure 2, the upper one gets the most radiation energy because it is the closest to the radiator. The right one gets the least because part of it is blocked from the radiator by the other object in a box. A further test case using a symmetric setup shows its accuracy.

Global pattern of insolation predicted by Energy3D

Figure 1. Global insolation pattern from Pole to Pole
The Sun's power drives the climate of the Earth. Accurately modeling the incident solar radiation, namely, insolation, at a given location is important to the design of high-performance buildings. As I have blogged last week, the insolation calculation in our Energy3D software considers the incident angle of the Sun to the surface, the duration of the day, and the air mass. And we have recently incorporated the effect of altitude and the ambient inputs.

Figure 2. Real data for the three locations (source)
In Energy3D, we can easily investigate the global pattern of insolation by horizontally placing a sensor module on the ground and then collecting the sensor data throughout the year. We can easily change the latitude and collect a new set of data. Figure 1 shows the global insolation pattern from the North Pole to the South Pole. The time integral of each curve represents the total solar energy a location at the corresponding latitude receives. There is an interesting observation from Figure 1: The Equator doesn't actually have the highest peak value and its peak values are not in the summer but in the spring and fall. However, because the insolation does not differ very much from season to season in the Equator, its time integral is much larger, which is the Equator is hot all year round.
Figure 3. Energy3D's prediction


How accurate are the predictions of Energy3D? Let's pick three locations that someone has collected real data, as shown in Figure 2. More insolation data can be found on this website. (Surprisingly, the peak solar energy at the South Pole is higher than the peak solar energy at the Equator.)

Figure 3 shows that the insolation values predicted by Energy3D. As you can see, the predicted trend agrees reasonably well with the trend in the real data. Overall, Energy3D tends to underestimate the insolation by about 50% (after unit conversion), however.