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CTViz: A tool for the visualization of transport in nanocomposites
Accepted Manuscript Title: CTViz: A Tool for the Visualization of Transport in Nanocomposites Author: Benjamin Beach Joshua Brown Taylor Tarlton Pedro Derosa PII: DOI: Reference:
S1093-3263(16)30045-6 http://dx.doi.org/doi:10.1016/j.jmgm.2016.03.012 JMG 6679
To appear in:
Journal of Molecular Graphics and Modelling
Received date: Revised date: Accepted date:
12-6-2015 5-3-2016 24-3-2016
Please cite this article as: Benjamin Beach, Joshua Brown, Taylor Tarlton, Pedro Derosa, CTViz: A Tool for the Visualization of Transport in Nanocomposites, Journal of Molecular Graphics and Modelling http://dx.doi.org/10.1016/j.jmgm.2016.03.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
CTViz: A Tool for the Visualization of Transport in Nanocomposites
Benjamin Beach1, Joshua Brown1*, Taylor Tarlton1, Pedro Derosa1,2†
1
Louisiana Tech University, Institute for Micromanufacturing, Ruston LA 71272
2
Grambling State University, Department of Mathematics and Physics, Grambling, LA
71245
Keywords: Visualization, Nanocomposites, Transport Visualization
Graphical abstract CTViz, a visualization code for transport in hybrid material. CTViz can produce static and dynamic images from simulations of transport of point carriers in hybrid structures. Transparency and color shares are used to highlight relevant regions of the system, while others are dimmed or hidden. Publication and presentation quality images and animations can be produced.
Highlights CTViz is a visualization tool for charge transport in 3-D hybrid materials Produces publication and presentation quality visuals of relevant features Uses color and transparency to highlight important details hiding the rest It is easily adaptable for the visualization of particulate transport in general
CTViz: A Tool for the Visualization of Transport in Nanocomposites Benjamin Beach1, Joshua Brown1*, Taylor Tarlton1, Pedro Derosa1,2† 1
Louisiana Tech University
2
Grambling State University
Abstract A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths.
*Current affiliation: The University of Colorado †Corresponding Author, e-mail: [email protected]. Ph: (+1) 318-257-5139/Fax: (+1) 318-257-5104. Those interested in this GUI should contact the corresponding author.
Introduction The idea of embedding nanostructures in a continuous material has attracted a great deal of attention, as the resulting composites have interesting and potentially unprecedented properties.[1-12] The addition of fillers with mechanical, electrical, or thermal properties different from those of the matrix, such as hard fillers in soft matrices or conductive fillers in insulators, has been sought as a way to improve the properties of the matrix. Embedding good conductors into a non-conductive matrix results in larger conductivity than that of the bare matrix, as charges no longer have to bridge the full gap between contacts, but only between neighboring inserts.[13-18] Conduction arises when percolation paths are formed at sufficiently high nanoinsert concentrations.[13-15, 19-24] A hopping model was developed and implemented into a computer code where carriers are injected at one end of the sample and tracked as they travel through an arrangement of nanotubes (NTs), hopping from NT to NT through a non-conductive matrix [25]. The model does so in a 3-D array where thousands of NTs are distributed in a variety of configurations. As the code became more complex and the samples to model became larger, the task of making modifications to and finding errors in the code became increasingly challenging, thus triggering the creation of the visualization code that is the subject of this paper. CTViz was developed to produce visuals of the data output from a 3-D model of a nanocomposite, including the simulation box, stationary visualization of carriers’ paths, and animated carriers’ trajectories. An important feature of CTViz is the use of shades and transparency to highlight critical information. CTViz was designed for three main tasks: to help debug an existing simulation code, to help with data analysis of the transport processes in the sample, and to help communicate results with high quality visuals. Users have many options for tailoring the visualization capabilities in both stationary images and animations with high quality visuals and great flexibility on visualization modes.
Related Work Nanotechnology has pushed research interest towards the atomic scale and larger computer power has triggered an increase in popularity of bottom up approaches to
materials modeling. The size and complexity of molecular and coarse-grained systems that can be modeled has grown to the point that visual aids are an unavoidable requirement; as such, several tools have been produced for the purpose of molecular visualization. With no illusion of being fully inclusive, some examples of available visualization tools, which focus mainly on molecular and/or course-grained samples, are discussed below. Several visualization tools exist as a part of, or a complement to, quantum chemistry simulation software.
Example of molecular visualization tools include
EyeChem [26], Chimera [27], GaussView [32], Spartan [35], and Arguslab [36]. Ptuba [28], VMD [29], BioVEC [30] are or include visualization tools for biosystems. Materials Studio also falls within this category, although it provides a platform to a number of simulation tools [34]. Visualization tools are also important in the simulation of solids, crystalline and amorphous, as they allow the predictions form the simulations to be conveyed much more effectively. MaterialVis [37] and CrystalMaker [38] are just two examples. Other properties and processes involving large systems, such as fluid dynamics, heat transport, and mechanical performance, also benefit from graphical tools. Two of those tools that share some of the visualization capabilities of CTViz are VisFluid [39] and VisIt [40]. VisFluid was created to model the fluid flow, a continuous media, in porous materials and uses a simulation engine based on a dynamic percolation method. VisFluid can generate both images and animations of the 3D data and integrates the simulation with the visualization. Similar to CTViz, it makes use of both color and transparency to enhance the visualization of its information by making important regions of the system more visible. VisIt is an open-source general-purpose visualization, animation, and analysis tool that was originally developed to visualize and analyze the results of terascale simulations. VisIt is mostly based on finite elements, but also supports the visualization of scalar and vector field data for 2-D and 3-D structures. VisIt is highly parallelizable, capable of operating on massive systems with thousands of cores, or on a regular desktop workstation. It can produce and save presentation-quality visuals and animations of the simulation data. It was designed with a high degree of modularity featuring plugin architecture for custom readers, data operators, plots, and user interfaces.
Users can also develop their own additional plugins to meet their needs; however, as a general purpose tool, specific capabilities for particular applications, such as the one that motivated CTViz, are not immediately available. VisIt was developed at Lawrence Livermore National Lab where a many of other software for visualization or with great visual capabilities, were developed. The reader is directed to the national lab web page for a list and description of these software.[41]
Key Features of CTViz General Features The simulation box that CTViz visualizes consists of a distribution of cylinders originally intended to represent NTs. Each NT is a sequence of consecutive segments, each defined by a line connecting two points. The coordinates of each point is stored in the coordinate file and are used to generate a map of the NTs in the composite.
a)
b)
c)
d)
e)
f)
Figure 1: Sampling of the available visual options. (a) Default settings. (b) NT segments that spill outside the box are hidden. (c) Electrodes added on. (d-f) Cross-sectioning capabilities.
The NTs in the sample are plotted in a box and all segments outside the box (Figure 1a), if they exist, can be hidden for a cleaner view (Figure 1b). A pair of electrodes can then be drawn at each end of the sample by using a parallel view paradigm (Figure 1c). Additionally, the plot can be cross-sectioned in any of the three axial directions for a layered view of the sample (Figure 1d-f). The user can elect to see all NT segments that lie between two values of any of the three coordinates (Figure 1d-e), or to exclude all NT segments in that range (Figure 1f). This last feature, hiding a user-defined region, is not commonly available in existing software (although the difference is subtle, most codes do allow users to select what they want to see and hide the rest). Though it is possible in some software, like VMD, it normally requires custom scripts to execute, but in CTViz, it can be done with relative ease from the control panel. These options are available in all graphical modes, except the animation mode. One other motivation for this code was to obtain presentation and publication quality visuals. As such, this code was designed to give the user flexibility with the aesthetics. A list of these features is listed below. In all modes, the user can:
Choose between a black and white background color
Insert or hide electrodes and control their thickness and opacity
Draw or hide the bounds of the simulations box
Switch between parallel and perspective views
Add index labels, with adjustable font size, to individual NTs in the sample to assist with debugging or to pinpoint particular features
View the sample from any of the +x, +y, and +z directions, or the default viewing angle, with the click of a button
Dynamically rotate, zoom, and pan the sample
Control the visual diameter of the nanotubes as a factor of the diameter specified in the file (1 is the actual size and is the default value)
In certain modes, the user can:
Cross-section the sample in any combination of the three axial directions (does not work with the animation module)
Hide NT segments located outside the designated box (Works in all modes except the animation module)
Control the opacity range of NTs visited by carriers (works in modes where charge transport is visualized)
File I/O CTViz can use 6 different files to generate its plots and animations. Those are the same files that the in-house code that originated this tool either needs as input or produces as output. These files include two configuration files, the coordinates and the neighbor files, and four output files, percolation, trajectory, traps, and frequency files.
Figure 2: Flowchart of the file inputs used by each module of CTViz.
In the in-house simulation code that CTViz serves, each nanotube is generated as a set of segments defined by the coordinate of the two end points. These coordinates are stored in the coordinate file with extension “.cor” and read by CTViz to generate a visual of the sample. When carriers progress through the nanocomposite, they do so by hopping from one NT to one of its closest neighbors. A separate file with “.nei” extension, the neighbor file, stores for each NT the list of neighboring NTs, the distances to them, and the coordinates of the points defining those distances. An example of these two files is provided as supplementary information. The frequency file, with extension “.freq”, contains for each NT the number of times that it has been visited by a carrier. A file where percolation paths are stored (with
extension .perc) contains only the NTs that are part of a completed percolation path. Further information is stored in the trajectory file (extension “.path”) where the trajectory of all carriers that reached the collection electrode, along with the distance of each hop and the amount of time required to make each hop, are stored. The same type of information is stored in the trap file (extension “.trap”) for those carriers that did not reach the opposite electrode (and are thus considered trapped). Not all these files have to be available, only those that are required for the current visualization. The program will even reproduce the information in the frequency file from the path and trap files if not present, although it requires the user to select manually carrier to account for, however having the frequency file available makes the visualization of most visited NTs more efficient. The file I/O scheme is summarized in Figure 2.
Charge Transport Trajectories: Shade and transparency are used to convey key information as individual trajectories of selected carriers are displayed. When only one trajectory is plotted, the color of each nanotube is determined by how early into the simulation, on average, the NT was visited by the carrier, scaling linearly from red (earlier) to blue (later). The transparency of each NT can be used to convey either the number of times a NT was visited, or the total amount of time, on average, carriers spent on the NT (determined by the hop rate at the junction, which is the limiting factor in this process), at the choice of the user. A large number of visits would show heavily transited areas or circular traps (carriers moving among NTs in a restricted area or geometrical traps). Carriers spending large amounts of time in a particular region will evidence the presence of energetic traps, where the energy needed to leave the region is high. The transparency of each NT is scaled linearly within a range that can be selected by the user. In order to provide a cleaner picture of the trajectories, CTViz only displays the NTs that have been visited by the selected carrier, while hiding the rest from the user’s view. A color scale can be added to the right side of the plot for additional clarity.
(a)
(b)
Figure 3: Sample trajectory plots. (a) Trajectory of a single charge. The transport direction is from right (red tubes) to left (blue tubes) As the figures come directly from the code, the legends are a little small when the figure are reduced to fit in this paper. The labels on the color scale of this figure say “Earliest” at the top and “Latests at the bottom”. (b) Trajectories of a number of charges combined in a single plot. Red areas are heavily visited; green areas are more visited than blue areas (see color scale on the right of the plot, The labels on the color scale of this figure say “776.0 Visits” at the top and “0.0 Visits” at the bottom”). This plot shows a bottleneck near the positive electrode.
CTViz can also simultaneously display the paths of a selection of carriers to more easily identify collective behaviors (figure 3b); in this case, the color is used to convey the frequency of visitation, while transparency helps identify the most relevant NTs in the transport process by dimming or hiding those NTs with low participation in the conduction. NT’s transparency is proportional to the frequency these NTs are visited by carriers. This sort of visualization method will make bottlenecks more obvious. A color scale can be added at the right side of the plot, as shown in Figure 3.
Conduction Paths: As visualizing conduction paths is fundamental to understanding the process of charge transport, CTViz has the capability to display percolation paths independently from charge trajectories. In this case the color codes indicate the order in which NTs are visited by the carrier that travels the highlighted path (figure 4a). When several paths are shown simultaneously (figure 4b), the combination of color and transparency allows the user to clearly identify NTs that are associated with more conduction pathways. Those NTs may be visited by carriers following different paths.
(a)
(b)
Figure 4: Percolation paths plotting features. (a) Single conduction path (b) Overimposed conduction paths.
Electrode Neighbors: CTViz can selectively show only those NTs that are connected to the electrode, as shown in Figure 5. This helps identify low connectivity of the sample; if no NT’s are close enough to one of the electrodes, there will be no conductivity.
Figure 5: NTs neighboring the electrodes are displayed
Frequency File: CTViz can visualize data from a “.freq” file, which only contains the total number of visits to each NT. If the frequency file is selected to gather data for display, CTViz displays the total number of times each NT is visited throughout the simulation, using color and transparency as in the path plotting section. The results are the same as in figure 4b, but generating this plot from the frequency files allow for a quick summary of the most important NTs to charge transport without recalculating the frequencies each time the data is plotted.
Animation Capabilities There are several ways a user can customize the animation of carriers as they move through the sample:
Select which carrier to animate
Control the speed of the animation
Opt to leave behind a trace of the charge’s path with a thin white trace for a black background or a thin black trace for a white background (figure 6a)
Animate the paths of multiple carriers back-to-back
Display only every nth hop in the animation.
Select transparency range
Select the carrier’s radius
Save the animation as a .mp4 file
Select to plot only a specified section of the animation path
Pause and continue the animation
Dynamically display the “nearest neighbors” at each step of the carrier’s path, showing the options that the charge has for its next hop (figure 6b). The “nearest neighbors” are highlighted in blue and represent the set of NTs that the charge has the option to hop to next.
a)
b)
Figure 6: Animation feature. (a) Path tracing option. (b) Nearest neighbor option.
Implementation CTViz was written in Java, given the facility of Java for implementing GUIs and the very large number of Java libraries available online. The Eclipse IDE [42] was used to develop the tool. The 3-D graphical backend was implemented via Java3d [43] and the moviesaving feature was implemented via the Xuggler[44] library. The Zip4j [45] library was used to unzip the input files. In the current implementation, the version of the Xuggler library that was employed is distributed under the General Public License (GPL), which mandates that the tool must be open-source if the library is used. A view and description of the control panel is provided as supplementary information.
Imminent and Short Term Expansions Another planned feature is the creation of a network diagram for the NT network which would display connections between neighboring NTs along with the hop rates between these NTs (communicated via the transparency of the connections). Combined with the cross-sectioning feature of the tool, this could allow the user to obtain a far better grasp of the network structure of the sample, such as the locations of gaps that are prohibitive to charge transport or the location of highly conductive NT bundles. A module for creating 2D graphs containing certain sets of information, such as the distribution of times required for the charges to traverse the sample, is also in progress. The code’s user interface will be restructured to implement a more modular structure so that each graph can be controlled from within itself instead of all graphs being controlled from one central window. The interface will be modified to allow full control over the selection of which charge trajectories are plotted, as opposed to a range of consecutive carriers, and to make the color schemes for path plotting more customizable.
Conclusions CTViz has proven to be very useful in the development and optimization of a simulation code for carrier transport in nanocomposites. It has allowed to more readily discover the nature of various issues that emerged during the development process of such code. CTViz has grown to the point that it could be adapted for use in a variety of applications. Virtually any process where particulate transport is featured can be visualized by this code with the incorporation of the appropriate geometries into the visualization paradigm. Furthermore, the addition of a network diagram feature could make the code especially useful for the visualization of cross-linked polymers. By adding the option to hide NTs altogether, this code can potentially be adapted to visualize any particulate transport where the paths can be discretized; CTViz only needs the coordinates of the transported particles at each step. Certainly, most of the features of this code are more relevant to the visualization of transport in a network while the carrier is moving than just following carriers in an uniform media.
Note: Those interested in this software should contact the corresponding author Dr. Pedro Derosa at [email protected]
Acknowledgements This project is supported by AF contract FA8650-13-C-5800 from the AFRL Materials & Manufacturing Directorate, WPAFB. Dr. Asheley Blackford, Program Manager.
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S1093-3263(16)30045-6 http://dx.doi.org/doi:10.1016/j.jmgm.2016.03.012 JMG 6679
To appear in:
Journal of Molecular Graphics and Modelling
Received date: Revised date: Accepted date:
12-6-2015 5-3-2016 24-3-2016
Please cite this article as: Benjamin Beach, Joshua Brown, Taylor Tarlton, Pedro Derosa, CTViz: A Tool for the Visualization of Transport in Nanocomposites, Journal of Molecular Graphics and Modelling http://dx.doi.org/10.1016/j.jmgm.2016.03.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
CTViz: A Tool for the Visualization of Transport in Nanocomposites
Benjamin Beach1, Joshua Brown1*, Taylor Tarlton1, Pedro Derosa1,2†
1
Louisiana Tech University, Institute for Micromanufacturing, Ruston LA 71272
2
Grambling State University, Department of Mathematics and Physics, Grambling, LA
71245
Keywords: Visualization, Nanocomposites, Transport Visualization
Graphical abstract CTViz, a visualization code for transport in hybrid material. CTViz can produce static and dynamic images from simulations of transport of point carriers in hybrid structures. Transparency and color shares are used to highlight relevant regions of the system, while others are dimmed or hidden. Publication and presentation quality images and animations can be produced.
Highlights CTViz is a visualization tool for charge transport in 3-D hybrid materials Produces publication and presentation quality visuals of relevant features Uses color and transparency to highlight important details hiding the rest It is easily adaptable for the visualization of particulate transport in general
CTViz: A Tool for the Visualization of Transport in Nanocomposites Benjamin Beach1, Joshua Brown1*, Taylor Tarlton1, Pedro Derosa1,2† 1
Louisiana Tech University
2
Grambling State University
Abstract A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths.
*Current affiliation: The University of Colorado †Corresponding Author, e-mail: [email protected]. Ph: (+1) 318-257-5139/Fax: (+1) 318-257-5104. Those interested in this GUI should contact the corresponding author.
Introduction The idea of embedding nanostructures in a continuous material has attracted a great deal of attention, as the resulting composites have interesting and potentially unprecedented properties.[1-12] The addition of fillers with mechanical, electrical, or thermal properties different from those of the matrix, such as hard fillers in soft matrices or conductive fillers in insulators, has been sought as a way to improve the properties of the matrix. Embedding good conductors into a non-conductive matrix results in larger conductivity than that of the bare matrix, as charges no longer have to bridge the full gap between contacts, but only between neighboring inserts.[13-18] Conduction arises when percolation paths are formed at sufficiently high nanoinsert concentrations.[13-15, 19-24] A hopping model was developed and implemented into a computer code where carriers are injected at one end of the sample and tracked as they travel through an arrangement of nanotubes (NTs), hopping from NT to NT through a non-conductive matrix [25]. The model does so in a 3-D array where thousands of NTs are distributed in a variety of configurations. As the code became more complex and the samples to model became larger, the task of making modifications to and finding errors in the code became increasingly challenging, thus triggering the creation of the visualization code that is the subject of this paper. CTViz was developed to produce visuals of the data output from a 3-D model of a nanocomposite, including the simulation box, stationary visualization of carriers’ paths, and animated carriers’ trajectories. An important feature of CTViz is the use of shades and transparency to highlight critical information. CTViz was designed for three main tasks: to help debug an existing simulation code, to help with data analysis of the transport processes in the sample, and to help communicate results with high quality visuals. Users have many options for tailoring the visualization capabilities in both stationary images and animations with high quality visuals and great flexibility on visualization modes.
Related Work Nanotechnology has pushed research interest towards the atomic scale and larger computer power has triggered an increase in popularity of bottom up approaches to
materials modeling. The size and complexity of molecular and coarse-grained systems that can be modeled has grown to the point that visual aids are an unavoidable requirement; as such, several tools have been produced for the purpose of molecular visualization. With no illusion of being fully inclusive, some examples of available visualization tools, which focus mainly on molecular and/or course-grained samples, are discussed below. Several visualization tools exist as a part of, or a complement to, quantum chemistry simulation software.
Example of molecular visualization tools include
EyeChem [26], Chimera [27], GaussView [32], Spartan [35], and Arguslab [36]. Ptuba [28], VMD [29], BioVEC [30] are or include visualization tools for biosystems. Materials Studio also falls within this category, although it provides a platform to a number of simulation tools [34]. Visualization tools are also important in the simulation of solids, crystalline and amorphous, as they allow the predictions form the simulations to be conveyed much more effectively. MaterialVis [37] and CrystalMaker [38] are just two examples. Other properties and processes involving large systems, such as fluid dynamics, heat transport, and mechanical performance, also benefit from graphical tools. Two of those tools that share some of the visualization capabilities of CTViz are VisFluid [39] and VisIt [40]. VisFluid was created to model the fluid flow, a continuous media, in porous materials and uses a simulation engine based on a dynamic percolation method. VisFluid can generate both images and animations of the 3D data and integrates the simulation with the visualization. Similar to CTViz, it makes use of both color and transparency to enhance the visualization of its information by making important regions of the system more visible. VisIt is an open-source general-purpose visualization, animation, and analysis tool that was originally developed to visualize and analyze the results of terascale simulations. VisIt is mostly based on finite elements, but also supports the visualization of scalar and vector field data for 2-D and 3-D structures. VisIt is highly parallelizable, capable of operating on massive systems with thousands of cores, or on a regular desktop workstation. It can produce and save presentation-quality visuals and animations of the simulation data. It was designed with a high degree of modularity featuring plugin architecture for custom readers, data operators, plots, and user interfaces.
Users can also develop their own additional plugins to meet their needs; however, as a general purpose tool, specific capabilities for particular applications, such as the one that motivated CTViz, are not immediately available. VisIt was developed at Lawrence Livermore National Lab where a many of other software for visualization or with great visual capabilities, were developed. The reader is directed to the national lab web page for a list and description of these software.[41]
Key Features of CTViz General Features The simulation box that CTViz visualizes consists of a distribution of cylinders originally intended to represent NTs. Each NT is a sequence of consecutive segments, each defined by a line connecting two points. The coordinates of each point is stored in the coordinate file and are used to generate a map of the NTs in the composite.
a)
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Figure 1: Sampling of the available visual options. (a) Default settings. (b) NT segments that spill outside the box are hidden. (c) Electrodes added on. (d-f) Cross-sectioning capabilities.
The NTs in the sample are plotted in a box and all segments outside the box (Figure 1a), if they exist, can be hidden for a cleaner view (Figure 1b). A pair of electrodes can then be drawn at each end of the sample by using a parallel view paradigm (Figure 1c). Additionally, the plot can be cross-sectioned in any of the three axial directions for a layered view of the sample (Figure 1d-f). The user can elect to see all NT segments that lie between two values of any of the three coordinates (Figure 1d-e), or to exclude all NT segments in that range (Figure 1f). This last feature, hiding a user-defined region, is not commonly available in existing software (although the difference is subtle, most codes do allow users to select what they want to see and hide the rest). Though it is possible in some software, like VMD, it normally requires custom scripts to execute, but in CTViz, it can be done with relative ease from the control panel. These options are available in all graphical modes, except the animation mode. One other motivation for this code was to obtain presentation and publication quality visuals. As such, this code was designed to give the user flexibility with the aesthetics. A list of these features is listed below. In all modes, the user can:
Choose between a black and white background color
Insert or hide electrodes and control their thickness and opacity
Draw or hide the bounds of the simulations box
Switch between parallel and perspective views
Add index labels, with adjustable font size, to individual NTs in the sample to assist with debugging or to pinpoint particular features
View the sample from any of the +x, +y, and +z directions, or the default viewing angle, with the click of a button
Dynamically rotate, zoom, and pan the sample
Control the visual diameter of the nanotubes as a factor of the diameter specified in the file (1 is the actual size and is the default value)
In certain modes, the user can:
Cross-section the sample in any combination of the three axial directions (does not work with the animation module)
Hide NT segments located outside the designated box (Works in all modes except the animation module)
Control the opacity range of NTs visited by carriers (works in modes where charge transport is visualized)
File I/O CTViz can use 6 different files to generate its plots and animations. Those are the same files that the in-house code that originated this tool either needs as input or produces as output. These files include two configuration files, the coordinates and the neighbor files, and four output files, percolation, trajectory, traps, and frequency files.
Figure 2: Flowchart of the file inputs used by each module of CTViz.
In the in-house simulation code that CTViz serves, each nanotube is generated as a set of segments defined by the coordinate of the two end points. These coordinates are stored in the coordinate file with extension “.cor” and read by CTViz to generate a visual of the sample. When carriers progress through the nanocomposite, they do so by hopping from one NT to one of its closest neighbors. A separate file with “.nei” extension, the neighbor file, stores for each NT the list of neighboring NTs, the distances to them, and the coordinates of the points defining those distances. An example of these two files is provided as supplementary information. The frequency file, with extension “.freq”, contains for each NT the number of times that it has been visited by a carrier. A file where percolation paths are stored (with
extension .perc) contains only the NTs that are part of a completed percolation path. Further information is stored in the trajectory file (extension “.path”) where the trajectory of all carriers that reached the collection electrode, along with the distance of each hop and the amount of time required to make each hop, are stored. The same type of information is stored in the trap file (extension “.trap”) for those carriers that did not reach the opposite electrode (and are thus considered trapped). Not all these files have to be available, only those that are required for the current visualization. The program will even reproduce the information in the frequency file from the path and trap files if not present, although it requires the user to select manually carrier to account for, however having the frequency file available makes the visualization of most visited NTs more efficient. The file I/O scheme is summarized in Figure 2.
Charge Transport Trajectories: Shade and transparency are used to convey key information as individual trajectories of selected carriers are displayed. When only one trajectory is plotted, the color of each nanotube is determined by how early into the simulation, on average, the NT was visited by the carrier, scaling linearly from red (earlier) to blue (later). The transparency of each NT can be used to convey either the number of times a NT was visited, or the total amount of time, on average, carriers spent on the NT (determined by the hop rate at the junction, which is the limiting factor in this process), at the choice of the user. A large number of visits would show heavily transited areas or circular traps (carriers moving among NTs in a restricted area or geometrical traps). Carriers spending large amounts of time in a particular region will evidence the presence of energetic traps, where the energy needed to leave the region is high. The transparency of each NT is scaled linearly within a range that can be selected by the user. In order to provide a cleaner picture of the trajectories, CTViz only displays the NTs that have been visited by the selected carrier, while hiding the rest from the user’s view. A color scale can be added to the right side of the plot for additional clarity.
(a)
(b)
Figure 3: Sample trajectory plots. (a) Trajectory of a single charge. The transport direction is from right (red tubes) to left (blue tubes) As the figures come directly from the code, the legends are a little small when the figure are reduced to fit in this paper. The labels on the color scale of this figure say “Earliest” at the top and “Latests at the bottom”. (b) Trajectories of a number of charges combined in a single plot. Red areas are heavily visited; green areas are more visited than blue areas (see color scale on the right of the plot, The labels on the color scale of this figure say “776.0 Visits” at the top and “0.0 Visits” at the bottom”). This plot shows a bottleneck near the positive electrode.
CTViz can also simultaneously display the paths of a selection of carriers to more easily identify collective behaviors (figure 3b); in this case, the color is used to convey the frequency of visitation, while transparency helps identify the most relevant NTs in the transport process by dimming or hiding those NTs with low participation in the conduction. NT’s transparency is proportional to the frequency these NTs are visited by carriers. This sort of visualization method will make bottlenecks more obvious. A color scale can be added at the right side of the plot, as shown in Figure 3.
Conduction Paths: As visualizing conduction paths is fundamental to understanding the process of charge transport, CTViz has the capability to display percolation paths independently from charge trajectories. In this case the color codes indicate the order in which NTs are visited by the carrier that travels the highlighted path (figure 4a). When several paths are shown simultaneously (figure 4b), the combination of color and transparency allows the user to clearly identify NTs that are associated with more conduction pathways. Those NTs may be visited by carriers following different paths.
(a)
(b)
Figure 4: Percolation paths plotting features. (a) Single conduction path (b) Overimposed conduction paths.
Electrode Neighbors: CTViz can selectively show only those NTs that are connected to the electrode, as shown in Figure 5. This helps identify low connectivity of the sample; if no NT’s are close enough to one of the electrodes, there will be no conductivity.
Figure 5: NTs neighboring the electrodes are displayed
Frequency File: CTViz can visualize data from a “.freq” file, which only contains the total number of visits to each NT. If the frequency file is selected to gather data for display, CTViz displays the total number of times each NT is visited throughout the simulation, using color and transparency as in the path plotting section. The results are the same as in figure 4b, but generating this plot from the frequency files allow for a quick summary of the most important NTs to charge transport without recalculating the frequencies each time the data is plotted.
Animation Capabilities There are several ways a user can customize the animation of carriers as they move through the sample:
Select which carrier to animate
Control the speed of the animation
Opt to leave behind a trace of the charge’s path with a thin white trace for a black background or a thin black trace for a white background (figure 6a)
Animate the paths of multiple carriers back-to-back
Display only every nth hop in the animation.
Select transparency range
Select the carrier’s radius
Save the animation as a .mp4 file
Select to plot only a specified section of the animation path
Pause and continue the animation
Dynamically display the “nearest neighbors” at each step of the carrier’s path, showing the options that the charge has for its next hop (figure 6b). The “nearest neighbors” are highlighted in blue and represent the set of NTs that the charge has the option to hop to next.
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Figure 6: Animation feature. (a) Path tracing option. (b) Nearest neighbor option.
Implementation CTViz was written in Java, given the facility of Java for implementing GUIs and the very large number of Java libraries available online. The Eclipse IDE [42] was used to develop the tool. The 3-D graphical backend was implemented via Java3d [43] and the moviesaving feature was implemented via the Xuggler[44] library. The Zip4j [45] library was used to unzip the input files. In the current implementation, the version of the Xuggler library that was employed is distributed under the General Public License (GPL), which mandates that the tool must be open-source if the library is used. A view and description of the control panel is provided as supplementary information.
Imminent and Short Term Expansions Another planned feature is the creation of a network diagram for the NT network which would display connections between neighboring NTs along with the hop rates between these NTs (communicated via the transparency of the connections). Combined with the cross-sectioning feature of the tool, this could allow the user to obtain a far better grasp of the network structure of the sample, such as the locations of gaps that are prohibitive to charge transport or the location of highly conductive NT bundles. A module for creating 2D graphs containing certain sets of information, such as the distribution of times required for the charges to traverse the sample, is also in progress. The code’s user interface will be restructured to implement a more modular structure so that each graph can be controlled from within itself instead of all graphs being controlled from one central window. The interface will be modified to allow full control over the selection of which charge trajectories are plotted, as opposed to a range of consecutive carriers, and to make the color schemes for path plotting more customizable.
Conclusions CTViz has proven to be very useful in the development and optimization of a simulation code for carrier transport in nanocomposites. It has allowed to more readily discover the nature of various issues that emerged during the development process of such code. CTViz has grown to the point that it could be adapted for use in a variety of applications. Virtually any process where particulate transport is featured can be visualized by this code with the incorporation of the appropriate geometries into the visualization paradigm. Furthermore, the addition of a network diagram feature could make the code especially useful for the visualization of cross-linked polymers. By adding the option to hide NTs altogether, this code can potentially be adapted to visualize any particulate transport where the paths can be discretized; CTViz only needs the coordinates of the transported particles at each step. Certainly, most of the features of this code are more relevant to the visualization of transport in a network while the carrier is moving than just following carriers in an uniform media.
Note: Those interested in this software should contact the corresponding author Dr. Pedro Derosa at [email protected]
Acknowledgements This project is supported by AF contract FA8650-13-C-5800 from the AFRL Materials & Manufacturing Directorate, WPAFB. Dr. Asheley Blackford, Program Manager.
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