Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
Abstract
:1. Introduction
2. Molecular Model/Systems Studied
3. Simulator-Descriptor Suite
3.1. Simulator
3.2. Descriptor
4. Simu-D: Applications
4.1. Packing Efficiency of Semi-Flexible Athermal Polymers (3-D)
4.2. Entropy-Driven Crystallization of Semi-Flexible Athermal Polymers
4.3. Phase Behavior of Athermal Blends (Polymers and Monomers)
4.4. Energy-Driven Cluster and Crystal Formation of Attractive Chains
4.5. Polymers under Confinement
4.6. Polymer Nanocomposites
4.7. Comparison with Independent Algorithms
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Name | Type | Description |
---|---|---|
D | Categorical | Number of dimensions |
dconf | Categorical | Number of confined dimensions |
Nch | Categorical | Number of chains |
Nat | Numerical | Total number of atoms |
Nhigh | Numerical | Maximum number of monomers per chain |
Nlow | Numerical | Minimum number of monomers per chain |
N | Categorical | Average number of monomers per chain |
Nmon | Numerical | Number of single monomers |
Ntrials | Numerical | Number of trials per move in configurational bias scheme |
Opttrials | Flag | Flag to select the density-dependence of Ntrials |
ccbcut | Numerical | Maximum number of monomers moved in a CCB move |
disp | Numerical | Maximum displacement of monomer moves |
φ | Numerical | Packing density |
dl | Numerical | Bond gap for chains |
Nanocomp | Flag | Inclusion of nanoparticles |
Ncyl | Numerical | Number of nanocylinders |
Nsph | Numerical | Number of nanospheres |
dcyl | Numerical | Diameter of nanocylinders |
dsph | Numerical | Diameter of nanospheres |
dircyl | Array | Direction of nanocylinders |
Numerical | Diameter designation | |
Numerical | Collision diameter for Square-Well/shoulder model | |
Numerical | Range of interaction for Square-Well/shoulder model | |
Numerical | Intensity of interaction for Square-Well/shoulder model | |
OptSW | Flag | Creation of a second cell grid to improve SW performance. |
Numerical | Intensity of interaction for Square-Well/shoulder of Walls | |
Numerical | Range of interaction for Square-Well/shoulder model of Walls | |
Numerical | Intensity of interaction for Square-Well/shoulder of Nanoparticles | |
Numerical | Range of interaction for Square-Well/shoulder model of Nanoparticles | |
θeq | Numerical | Supplement of the equilibrium bending angle in radians |
kbend | Numerical | Energy constant for bending angle potential |
NPT | Flag | True: Enables NPT ensemble. False: Enables NVT ensemble |
T | Numerical | Temperature |
P | Numerical | Pressure |
Shrink | Flag | True: Runs shrinkage production until a target density. False: Runs normal simulation |
flucvol | Numerical | Maximum box length reduction when attempting shrinkage |
Numerical | Target density for the shrinkage production | |
Isotropic | Flag | True: Volume changes are equal in all direction. False: Volume change is anisotropic |
Cluster | Flag | Flag to enable cluster moves when there are more than one |
rclust | Numerical | Radius to detect clusters |
Vec | Flag | Storage of vectors for crystallographic elements |
Kiss | Numerical | Coordination number of reference crystal |
Geom | Flag | Check polymer geometry |
Neighs | Numerical | Maximum number of Voronoi neighbors |
HCP | Flag | CCE analysis for HCP crystal |
FCC | Flag | CCE analysis for FCC crystal |
BCC | Flag | CCE analysis for BCC crystal |
HEX | Flag | CCE analysis for HEX crystal |
FIV | Flag | CCE analysis for FIV symmetry |
HON | Flag | CCE analysis for HON crystal |
SQU | Flag | CCE analysis for SQU crystal |
TRI | Flag | CCE analysis for TRI crystal |
PEN | Flag | CCE analysis for PEN symmetry |
Thres | Numerical | CCE threshold of similarity |
Step | Numerical | Step of the mesh discretization (azimuthal and polar angles) |
Fast | Flag | No full optimization if norm less than threshold |
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Herranz, M.; Martínez-Fernández, D.; Ramos, P.M.; Foteinopoulou, K.; Karayiannis, N.C.; Laso, M. Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions. Int. J. Mol. Sci. 2021, 22, 12464. https://doi.org/10.3390/ijms222212464
Herranz M, Martínez-Fernández D, Ramos PM, Foteinopoulou K, Karayiannis NC, Laso M. Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions. International Journal of Molecular Sciences. 2021; 22(22):12464. https://doi.org/10.3390/ijms222212464
Chicago/Turabian StyleHerranz, Miguel, Daniel Martínez-Fernández, Pablo Miguel Ramos, Katerina Foteinopoulou, Nikos Ch. Karayiannis, and Manuel Laso. 2021. "Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions" International Journal of Molecular Sciences 22, no. 22: 12464. https://doi.org/10.3390/ijms222212464