Loading doc/compute_rdf.html +6 −5 Original line number Diff line number Diff line Loading @@ -79,10 +79,11 @@ a specific histogram if the following criteria are met: if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the molecular topology, their pairwise interaction may be turned off, and thus they will not appear in the neighbor list, and will not contribute to g(r). More specifically, this is true of pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are contribute to g(r). More specifically, this is true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions is set by the <A HREF = "special_bonds.html">special_bonds</A> command. interactions are set by the <A HREF = "special_bonds.html">special_bonds</A> command. </P> <P>It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the <I>itypeN</I> and <I>jtypeN</I> Loading @@ -92,8 +93,8 @@ arguments are specified. scaling it by the idealized number of how many counts there would be if atoms of type <I>jtypeN</I> were uniformly distributed. Thus it involves the count of <I>itypeN</I> atoms, the count of <I>jtypeN</I> atoms, the volume of the entire simulation box, and the volume of the thin bin shell in 3d (or the area of the thin bin ring in 2d). volume of the entire simulation box, and the volume of the bin's thin shell in 3d (or the area of the bin's thin ring in 2d). </P> <P>A coordination number coord(r) is also calculated, which is the sum of g(r) values for all bins up to and including the current bin. Loading doc/compute_rdf.txt +6 −5 Original line number Diff line number Diff line Loading @@ -76,10 +76,11 @@ The last point is relevant for molecular systems with bonds, because if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the molecular topology, their pairwise interaction may be turned off, and thus they will not appear in the neighbor list, and will not contribute to g(r). More specifically, this is true of pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are contribute to g(r). More specifically, this is true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions is set by the "special_bonds"_special_bonds.html command. interactions are set by the "special_bonds"_special_bonds.html command. It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the {itypeN} and {jtypeN} Loading @@ -89,8 +90,8 @@ The g(r) value for a bin is calculated from the histogram count by scaling it by the idealized number of how many counts there would be if atoms of type {jtypeN} were uniformly distributed. Thus it involves the count of {itypeN} atoms, the count of {jtypeN} atoms, the volume of the entire simulation box, and the volume of the thin bin shell in 3d (or the area of the thin bin ring in 2d). volume of the entire simulation box, and the volume of the bin's thin shell in 3d (or the area of the bin's thin ring in 2d). A coordination number coord(r) is also calculated, which is the sum of g(r) values for all bins up to and including the current bin. Loading Loading
doc/compute_rdf.html +6 −5 Original line number Diff line number Diff line Loading @@ -79,10 +79,11 @@ a specific histogram if the following criteria are met: if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the molecular topology, their pairwise interaction may be turned off, and thus they will not appear in the neighbor list, and will not contribute to g(r). More specifically, this is true of pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are contribute to g(r). More specifically, this is true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions is set by the <A HREF = "special_bonds.html">special_bonds</A> command. interactions are set by the <A HREF = "special_bonds.html">special_bonds</A> command. </P> <P>It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the <I>itypeN</I> and <I>jtypeN</I> Loading @@ -92,8 +93,8 @@ arguments are specified. scaling it by the idealized number of how many counts there would be if atoms of type <I>jtypeN</I> were uniformly distributed. Thus it involves the count of <I>itypeN</I> atoms, the count of <I>jtypeN</I> atoms, the volume of the entire simulation box, and the volume of the thin bin shell in 3d (or the area of the thin bin ring in 2d). volume of the entire simulation box, and the volume of the bin's thin shell in 3d (or the area of the bin's thin ring in 2d). </P> <P>A coordination number coord(r) is also calculated, which is the sum of g(r) values for all bins up to and including the current bin. Loading
doc/compute_rdf.txt +6 −5 Original line number Diff line number Diff line Loading @@ -76,10 +76,11 @@ The last point is relevant for molecular systems with bonds, because if two atoms I,J are involved in 1-2, 1-3, 1-4 interactions within the molecular topology, their pairwise interaction may be turned off, and thus they will not appear in the neighbor list, and will not contribute to g(r). More specifically, this is true of pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are contribute to g(r). More specifically, this is true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions is set by the "special_bonds"_special_bonds.html command. interactions are set by the "special_bonds"_special_bonds.html command. It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the {itypeN} and {jtypeN} Loading @@ -89,8 +90,8 @@ The g(r) value for a bin is calculated from the histogram count by scaling it by the idealized number of how many counts there would be if atoms of type {jtypeN} were uniformly distributed. Thus it involves the count of {itypeN} atoms, the count of {jtypeN} atoms, the volume of the entire simulation box, and the volume of the thin bin shell in 3d (or the area of the thin bin ring in 2d). volume of the entire simulation box, and the volume of the bin's thin shell in 3d (or the area of the bin's thin ring in 2d). A coordination number coord(r) is also calculated, which is the sum of g(r) values for all bins up to and including the current bin. Loading
