Loading doc/fix_msd.html +31 −11 Original line number Diff line number Diff line Loading @@ -13,26 +13,40 @@ </H3> <P><B>Syntax:</B> </P> <PRE>fix ID group-ID msd N file <PRE>fix ID group-ID msd N file keyword value ... </PRE> <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <LI>msd = style name of this fix command <LI>N = compute mean-squared displacement every this many timesteps <LI>file = filename to write mean-squared displacement info to <LI>zero or more keyword/value pairs may be appended <LI>keyword = <I>com</I> <PRE> <I>com</I> value = <I>yes</I> or <I>no</I> </PRE> </UL> <P><B>Examples:</B> </P> <PRE>fix 1 all msd 100 diff.out fix 1 all msd 1000 diff.out com yes </PRE> <P><B>Description:</B> </P> <P>Compute the mean-squared displacement (MSD) of the group of atoms every N steps, including all effects due to atoms passing thru periodic boundaries. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. The "origin" of the displacement for each atom is its position at the time the fix command was issued. Write the results to the specified file. periodic boundaries. The MSD is the square of the displacement of each atom, averaged over all the atoms in the group. The displacement of an atom is from its original position at the time the fix command was issued. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. </P> <P>The MSD values versus time are written to the specified file. </P> <P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix rigid</A> command), it's periodic image flags are altered, Loading @@ -42,6 +56,10 @@ MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the atoms in the bodies. </P> <P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated. </P> <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> </P> <P>This fix writes the original coordinates of diffusing atoms to <A HREF = "restart.html">binary Loading @@ -64,6 +82,8 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A> </P> <P><A HREF = "fix_coord_original.html">fix coord/original</A> </P> <P><B>Default:</B> none <P><B>Default:</B> </P> <P>The option default is com = no. </P> </HTML> doc/fix_msd.txt +25 −12 Original line number Diff line number Diff line Loading @@ -10,26 +10,33 @@ fix msd command :h3 [Syntax:] fix ID group-ID msd N file :pre fix ID group-ID msd N file keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command msd = style name of this fix command N = compute mean-squared displacement every this many timesteps file = filename to write mean-squared displacement info to :ul ID, group-ID are documented in "fix"_fix.html command :ulb,l msd = style name of this fix command :l N = compute mean-squared displacement every this many timesteps :l file = filename to write mean-squared displacement info to :l zero or more keyword/value pairs may be appended :l keyword = {com} :l {com} value = {yes} or {no} :pre :ule [Examples:] fix 1 all msd 100 diff.out :pre fix 1 all msd 100 diff.out fix 1 all msd 1000 diff.out com yes :pre [Description:] Compute the mean-squared displacement (MSD) of the group of atoms every N steps, including all effects due to atoms passing thru periodic boundaries. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. The "origin" of the displacement for each atom is its position at the time the fix command was issued. Write the results to the specified file. periodic boundaries. The MSD is the square of the displacement of each atom, averaged over all the atoms in the group. The displacement of an atom is from its original position at the time the fix command was issued. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. The MSD values versus time are written to the specified file. IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix rigid"_fix_rigid.html command), it's periodic image flags are altered, Loading @@ -39,6 +46,10 @@ MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a "dump file"_dump.html containing coordinates of the atoms in the bodies. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated. [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the original coordinates of diffusing atoms to "binary Loading @@ -61,4 +72,6 @@ This fix is not invoked during "energy minimization"_minimize.html. "fix coord/original"_fix_coord_original.html [Default:] none [Default:] The option default is com = no. Loading
doc/fix_msd.html +31 −11 Original line number Diff line number Diff line Loading @@ -13,26 +13,40 @@ </H3> <P><B>Syntax:</B> </P> <PRE>fix ID group-ID msd N file <PRE>fix ID group-ID msd N file keyword value ... </PRE> <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <LI>msd = style name of this fix command <LI>N = compute mean-squared displacement every this many timesteps <LI>file = filename to write mean-squared displacement info to <LI>zero or more keyword/value pairs may be appended <LI>keyword = <I>com</I> <PRE> <I>com</I> value = <I>yes</I> or <I>no</I> </PRE> </UL> <P><B>Examples:</B> </P> <PRE>fix 1 all msd 100 diff.out fix 1 all msd 1000 diff.out com yes </PRE> <P><B>Description:</B> </P> <P>Compute the mean-squared displacement (MSD) of the group of atoms every N steps, including all effects due to atoms passing thru periodic boundaries. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. The "origin" of the displacement for each atom is its position at the time the fix command was issued. Write the results to the specified file. periodic boundaries. The MSD is the square of the displacement of each atom, averaged over all the atoms in the group. The displacement of an atom is from its original position at the time the fix command was issued. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. </P> <P>The MSD values versus time are written to the specified file. </P> <P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix rigid</A> command), it's periodic image flags are altered, Loading @@ -42,6 +56,10 @@ MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the atoms in the bodies. </P> <P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated. </P> <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> </P> <P>This fix writes the original coordinates of diffusing atoms to <A HREF = "restart.html">binary Loading @@ -64,6 +82,8 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A> </P> <P><A HREF = "fix_coord_original.html">fix coord/original</A> </P> <P><B>Default:</B> none <P><B>Default:</B> </P> <P>The option default is com = no. </P> </HTML>
doc/fix_msd.txt +25 −12 Original line number Diff line number Diff line Loading @@ -10,26 +10,33 @@ fix msd command :h3 [Syntax:] fix ID group-ID msd N file :pre fix ID group-ID msd N file keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command msd = style name of this fix command N = compute mean-squared displacement every this many timesteps file = filename to write mean-squared displacement info to :ul ID, group-ID are documented in "fix"_fix.html command :ulb,l msd = style name of this fix command :l N = compute mean-squared displacement every this many timesteps :l file = filename to write mean-squared displacement info to :l zero or more keyword/value pairs may be appended :l keyword = {com} :l {com} value = {yes} or {no} :pre :ule [Examples:] fix 1 all msd 100 diff.out :pre fix 1 all msd 100 diff.out fix 1 all msd 1000 diff.out com yes :pre [Description:] Compute the mean-squared displacement (MSD) of the group of atoms every N steps, including all effects due to atoms passing thru periodic boundaries. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. The "origin" of the displacement for each atom is its position at the time the fix command was issued. Write the results to the specified file. periodic boundaries. The MSD is the square of the displacement of each atom, averaged over all the atoms in the group. The displacement of an atom is from its original position at the time the fix command was issued. The slope of the mean-squared displacement versus time is proportional to the diffusion coefficient of the diffusing atoms. The MSD values versus time are written to the specified file. IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix rigid"_fix_rigid.html command), it's periodic image flags are altered, Loading @@ -39,6 +46,10 @@ MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a "dump file"_dump.html containing coordinates of the atoms in the bodies. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated. [Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the original coordinates of diffusing atoms to "binary Loading @@ -61,4 +72,6 @@ This fix is not invoked during "energy minimization"_minimize.html. "fix coord/original"_fix_coord_original.html [Default:] none [Default:] The option default is com = no.
