Method of information entropy for convergence assessment of molecular dynamics simulations
The lack of a reliable method to evaluate the convergence of molecular dynamics simulations has contributed to discrepancies in different areas of molecular dynamics. In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon i...
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description | The lack of a reliable method to evaluate the convergence of molecular dynamics simulations has contributed to discrepancies in different areas of molecular dynamics. In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated multidimensional fields such as the temperature field in a discrete spatial domain. It is demonstrated in this work that monitoring the information entropy of the atom position matrix provides a clear indicator of reaching steady state in radiation damage simulations, non-equilibrium molecular dynamics thermal conductivity computations, and simulations of Poiseuille and Couette flow in nanochannels. A main advantage of the present technique is that it is non-local and relies on fundamental quantities available in all molecular dynamics simulations. Unlike monitoring average temperature, the technique is applicable to simulations that conserve total energy such as reverse non-equilibrium molecular dynamics thermal conductivity computations and to simulations where energy dissipates through a boundary as in radiation damage simulations. The method is applied to simulations of iron using the Tersoff/ZBL splined potential, silicon using the Stillinger–Weber potential, and to Lennard–Jones fluid. Its applicability to both solids and fluids shows that the technique has potential for generalization to other areas in molecular dynamics. |
doi_str_mv | 10.1063/5.0019078 |
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In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated multidimensional fields such as the temperature field in a discrete spatial domain. It is demonstrated in this work that monitoring the information entropy of the atom position matrix provides a clear indicator of reaching steady state in radiation damage simulations, non-equilibrium molecular dynamics thermal conductivity computations, and simulations of Poiseuille and Couette flow in nanochannels. A main advantage of the present technique is that it is non-local and relies on fundamental quantities available in all molecular dynamics simulations. Unlike monitoring average temperature, the technique is applicable to simulations that conserve total energy such as reverse non-equilibrium molecular dynamics thermal conductivity computations and to simulations where energy dissipates through a boundary as in radiation damage simulations. The method is applied to simulations of iron using the Tersoff/ZBL splined potential, silicon using the Stillinger–Weber potential, and to Lennard–Jones fluid. 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In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated multidimensional fields such as the temperature field in a discrete spatial domain. It is demonstrated in this work that monitoring the information entropy of the atom position matrix provides a clear indicator of reaching steady state in radiation damage simulations, non-equilibrium molecular dynamics thermal conductivity computations, and simulations of Poiseuille and Couette flow in nanochannels. A main advantage of the present technique is that it is non-local and relies on fundamental quantities available in all molecular dynamics simulations. Unlike monitoring average temperature, the technique is applicable to simulations that conserve total energy such as reverse non-equilibrium molecular dynamics thermal conductivity computations and to simulations where energy dissipates through a boundary as in radiation damage simulations. The method is applied to simulations of iron using the Tersoff/ZBL splined potential, silicon using the Stillinger–Weber potential, and to Lennard–Jones fluid. Its applicability to both solids and fluids shows that the technique has potential for generalization to other areas in molecular dynamics.</description><subject>Applied physics</subject><subject>Computer simulation</subject><subject>Convergence</subject><subject>Couette flow</subject><subject>Domains</subject><subject>Energy conservation</subject><subject>Energy dissipation</subject><subject>Entropy</subject><subject>Entropy (Information theory)</subject><subject>Heat conductivity</subject><subject>Heat transfer</subject><subject>Molecular dynamics</subject><subject>Monitoring</subject><subject>Nanochannels</subject><subject>Position indicators</subject><subject>Radiation damage</subject><subject>Simulation</subject><subject>Steady state</subject><subject>Temperature distribution</subject><subject>Thermal conductivity</subject><issn>0021-8979</issn><issn>1089-7550</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNp90M9PwyAUB3BiNHFOD_4HjZ406YQWChzN4q9kxotevBDKHq7LChO6JfvvpXbRg4knkseH73s8hM4JnhBclTdsgjGRmIsDNCJYyJwzhg_RCOOC5EJyeYxOYlwmREQpR-j9GbqFn2feZo2zPrS6a7zLwHXBr3dZqmTGuy2ED3AGMh0jxNim6_5F61dgNisdsvnO6bYxMYtNmwp9RjxFR1avIpztzzF6u797nT7ms5eHp-ntLDcllV0OIJhghSBGcEG50NJYkKxmsuYUE8sIqXAtWMUBakOYrq0EyrUUUFFTy3KMLoZcH7tGRdN0YBZpaAemU6TimHKa0OWA1sF_biB2auk3waW5VEFp6lvwoldXgzLBxxjAqnVoWh12imDV71cxtd9vsteD7Tt-__gHb334hWo9t__hv8lfCoqJrg</recordid><startdate>20201007</startdate><enddate>20201007</enddate><creator>Talaat, Khaled</creator><creator>Cowen, Benjamin</creator><creator>Anderoglu, Osman</creator><general>American Institute of Physics</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>OTOTI</scope><orcidid>https://orcid.org/0000-0002-1797-6603</orcidid><orcidid>https://orcid.org/0000-0001-5529-6556</orcidid><orcidid>https://orcid.org/0000000155296556</orcidid><orcidid>https://orcid.org/0000000217976603</orcidid></search><sort><creationdate>20201007</creationdate><title>Method of information entropy for convergence assessment of molecular dynamics simulations</title><author>Talaat, Khaled ; Cowen, Benjamin ; Anderoglu, Osman</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c349t-ee8585281c878478a9cfe95b59b7401f51160b8567eebc15abf9e47a98e64cb93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Applied physics</topic><topic>Computer simulation</topic><topic>Convergence</topic><topic>Couette flow</topic><topic>Domains</topic><topic>Energy conservation</topic><topic>Energy dissipation</topic><topic>Entropy</topic><topic>Entropy (Information theory)</topic><topic>Heat conductivity</topic><topic>Heat transfer</topic><topic>Molecular dynamics</topic><topic>Monitoring</topic><topic>Nanochannels</topic><topic>Position indicators</topic><topic>Radiation damage</topic><topic>Simulation</topic><topic>Steady state</topic><topic>Temperature distribution</topic><topic>Thermal conductivity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Talaat, Khaled</creatorcontrib><creatorcontrib>Cowen, Benjamin</creatorcontrib><creatorcontrib>Anderoglu, Osman</creatorcontrib><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>OSTI.GOV</collection><jtitle>Journal of applied physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Talaat, Khaled</au><au>Cowen, Benjamin</au><au>Anderoglu, Osman</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Method of information entropy for convergence assessment of molecular dynamics simulations</atitle><jtitle>Journal of applied physics</jtitle><date>2020-10-07</date><risdate>2020</risdate><volume>128</volume><issue>13</issue><issn>0021-8979</issn><eissn>1089-7550</eissn><coden>JAPIAU</coden><abstract>The lack of a reliable method to evaluate the convergence of molecular dynamics simulations has contributed to discrepancies in different areas of molecular dynamics. In the present work, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated multidimensional fields such as the temperature field in a discrete spatial domain. It is demonstrated in this work that monitoring the information entropy of the atom position matrix provides a clear indicator of reaching steady state in radiation damage simulations, non-equilibrium molecular dynamics thermal conductivity computations, and simulations of Poiseuille and Couette flow in nanochannels. A main advantage of the present technique is that it is non-local and relies on fundamental quantities available in all molecular dynamics simulations. 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subjects | Applied physics Computer simulation Convergence Couette flow Domains Energy conservation Energy dissipation Entropy Entropy (Information theory) Heat conductivity Heat transfer Molecular dynamics Monitoring Nanochannels Position indicators Radiation damage Simulation Steady state Temperature distribution Thermal conductivity |
title | Method of information entropy for convergence assessment of molecular dynamics simulations |
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