From e3979f61439e1de397f861178b94c35dbaef4d40 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 4 Feb 2014 00:23:37 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11458 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_vacf.html | 8 +++++++- doc/compute_vacf.txt | 8 +++++++- doc/fix_ave_time.html | 17 +++++++++-------- doc/fix_ave_time.txt | 17 +++++++++-------- 4 files changed, 32 insertions(+), 18 deletions(-) diff --git a/doc/compute_vacf.html b/doc/compute_vacf.html index 0ddd758315..a46344aa7d 100644 --- a/doc/compute_vacf.html +++ b/doc/compute_vacf.html @@ -39,8 +39,14 @@ is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and averaged over atoms in the group.

The integral of the VACF versus time is proportional to the diffusion -coefficient of the diffusing atoms. +coefficient of the diffusing atoms. This can be computed in the +following manner, using the variable trap() function:

+
compute         2 all vacf
+fix             5 all vector 1 c_24
+variable        diff equal dt*trap(f_5)
+thermo_style    custom step v_diff 
+

IMPORTANT NOTE: If you want the quantities calculated by this compute to be continuous when running from a restart file, then you should use the same ID for this compute, as in the original diff --git a/doc/compute_vacf.txt b/doc/compute_vacf.txt index b397d9945b..bb1e157a2a 100644 --- a/doc/compute_vacf.txt +++ b/doc/compute_vacf.txt @@ -36,7 +36,13 @@ is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and averaged over atoms in the group. The integral of the VACF versus time is proportional to the diffusion -coefficient of the diffusing atoms. +coefficient of the diffusing atoms. This can be computed in the +following manner, using the "variable trap()"_variable.html function: + +compute 2 all vacf +fix 5 all vector 1 c_2[4] +variable diff equal dt*trap(f_5) +thermo_style custom step v_diff :pre IMPORTANT NOTE: If you want the quantities calculated by this compute to be continuous when running from a "restart file"_read_restart.html, diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index 1e987bf021..77c0fd34d8 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -304,13 +304,14 @@ of rows = length of the input vectors and # of columns = number of inputs.

If the fix prouduces a scalar or vector, then the scalar and each -element of the vector can be either "intensive" or "extensive". If -the fix produces an array, then all elements in the array must be the -same, either "intensive" or "extensive". If a compute or fix provides -the value being time averaged, then the compute or fix determines -whether the value is intensive or extensive; see the doc page for that -compute or fix for further info. Values produced by a variable are -treated as intensive. +element of the vector can be either "intensive" or "extensive", +depending on whether the values contributing to the scalar or vector +element are "intensive" or "extensive". If the fix produces an array, +then all elements in the array must be the same, either "intensive" or +"extensive". If a compute or fix provides the value being time +averaged, then the compute or fix determines whether the value is +intensive or extensive; see the doc page for that compute or fix for +further info. Values produced by a variable are treated as intensive.

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy @@ -324,7 +325,7 @@ minimization. ave/spatial, fix ave/histo, variable, fix ave/correlate,

-

Default: none +

Default:

The option defaults are mode = scalar, ave = one, start = 0, no file output, title 1,2,3 = strings as described above, and no off settings diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt index 79c46324fc..26fc0bc0b0 100644 --- a/doc/fix_ave_time.txt +++ b/doc/fix_ave_time.txt @@ -291,13 +291,14 @@ of rows = length of the input vectors and # of columns = number of inputs. If the fix prouduces a scalar or vector, then the scalar and each -element of the vector can be either "intensive" or "extensive". If -the fix produces an array, then all elements in the array must be the -same, either "intensive" or "extensive". If a compute or fix provides -the value being time averaged, then the compute or fix determines -whether the value is intensive or extensive; see the doc page for that -compute or fix for further info. Values produced by a variable are -treated as intensive. +element of the vector can be either "intensive" or "extensive", +depending on whether the values contributing to the scalar or vector +element are "intensive" or "extensive". If the fix produces an array, +then all elements in the array must be the same, either "intensive" or +"extensive". If a compute or fix provides the value being time +averaged, then the compute or fix determines whether the value is +intensive or extensive; see the doc page for that compute or fix for +further info. Values produced by a variable are treated as intensive. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy @@ -311,7 +312,7 @@ minimization"_minimize.html. ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html, "variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, -[Default:] none +[Default:] The option defaults are mode = scalar, ave = one, start = 0, no file output, title 1,2,3 = strings as described above, and no off settings