Unverified Commit e784afd6 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

use proper units (fmsec -> fs, psec -> ps and so on)

parent 293bfa04
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+2 −2
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@@ -552,9 +552,9 @@ when writing to XTC files. By default they are initialized for
whatever :doc:`units <units>` style is being used, to write out
coordinates in nanometers and time in picoseconds.  I.e. for *real*
units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the
Angstroms and fmsec used by *real* units are 0.1 nm and 0.001 psec
Angstroms and fs used by *real* units are 0.1 nm and 0.001 ps
respectively.  If you are using a units system with distance and time
units far from nm and psec, you may wish to write XTC files with
units far from nm and ps, you may wish to write XTC files with
different units, since the compression algorithm used in XTC files is
most effective when the typical magnitude of position data is between
10.0 and 0.1.
+10 −10
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@@ -154,8 +154,8 @@ specified in units of distance/time. This is effectively a "constant
engineering strain rate", where rate = V/L0 and L0 is the initial box
length.  The distance can be in lattice or box distance units.  See
the discussion of the units keyword below.  For example, if the
initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
after 10 psec, the box length will have doubled.  After 20 psec, it
initial box length is 100 Angstroms, and V is 10 Angstroms/ps, then
after 10 ps, the box length will have doubled.  After 20 ps, it
will have tripled.

The *erate* style changes a dimension of the box at a "constant
@@ -174,7 +174,7 @@ function of time will change as
where dt is the elapsed time (in time units).  Thus if *erate* R is
specified as 0.1 and time units are picoseconds, this means the box
length will increase by 10% of its original length every picosecond.
I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc.  R =
I.e. strain after 1 ps = 0.1, strain after 2 ps = 0.2, etc.  R =
-0.01 means the box length will shrink by 1% of its original length
every picosecond.  Note that for an "engineering" rate the change is
based on the original box length, so running with R = 1 for 10
@@ -201,7 +201,7 @@ The box length L as a function of time will change as
where dt is the elapsed time (in time units).  Thus if *trate* R is
specified as ln(1.1) and time units are picoseconds, this means the
box length will increase by 10% of its current (not original) length
every picosecond.  I.e. strain after 1 psec = 0.1, strain after 2 psec
every picosecond.  I.e. strain after 1 ps = 0.1, strain after 2 ps
= 0.21, etc.  R = ln(2) or ln(3) means the box length will double or
triple every picosecond.  R = ln(0.99) means the box length will
shrink by 1% of its current length every picosecond.  Note that for a
@@ -317,8 +317,8 @@ specified in units of distance/time. This is effectively an
initial box length perpendicular to the direction of shear.  The
distance can be in lattice or box distance units.  See the discussion
of the units keyword below.  For example, if the initial tilt factor
is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
is 5 Angstroms, and the V is 10 Angstroms/ps, then after 1 ps, the
tilt factor will be 15 Angstroms.  After 2 ps, it will be 25
Angstroms.

The *erate* style changes a tilt factor at a "constant engineering
@@ -342,9 +342,9 @@ box perpendicular to the shear direction (e.g. y box length for xy
deformation), and dt is the elapsed time (in time units).  Thus if
*erate* R is specified as 0.1 and time units are picoseconds, this
means the shear strain will increase by 0.1 every picosecond.  I.e. if
the xy shear strain was initially 0.0, then strain after 1 psec = 0.1,
strain after 2 psec = 0.2, etc.  Thus the tilt factor would be 0.0 at
time 0, 0.1\*ybox at 1 psec, 0.2\*ybox at 2 psec, etc, where ybox is the
the xy shear strain was initially 0.0, then strain after 1 ps = 0.1,
strain after 2 ps = 0.2, etc.  Thus the tilt factor would be 0.0 at
time 0, 0.1\*ybox at 1 ps, 0.2\*ybox at 2 ps, etc, where ybox is the
original y box length.  R = 1 or 2 means the tilt factor will increase
by 1 or 2 every picosecond.  R = -0.01 means a decrease in shear
strain by 0.01 every picosecond.
@@ -373,7 +373,7 @@ where T0 is the initial tilt factor and dt is the elapsed time (in
time units).  Thus if *trate* R is specified as ln(1.1) and time units
are picoseconds, this means the shear strain or tilt factor will
increase by 10% every picosecond.  I.e. if the xy shear strain was
initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec =
initially 0.1, then strain after 1 ps = 0.11, strain after 2 ps =
0.121, etc.  R = ln(2) or ln(3) means the tilt factor will double or
triple every picosecond.  R = ln(0.99) means the tilt factor will
shrink by 1% every picosecond.  Note that the change is continuous, so
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@@ -57,7 +57,7 @@ its current value(s) used to determine the flux.

If *eflux* is a numeric constant or equal-style variable which evaluates
to a scalar value, then *eflux* determines the change in aggregate energy
of the entire group of atoms per unit time, e.g. in eV/psec for
of the entire group of atoms per unit time, e.g. in eV/ps for
:doc:`metal units <units>`.  In this case it is an "extensive" quantity,
meaning its magnitude should be scaled with the number of atoms in the
group.  Note that since *eflux* also has per-time units (i.e. it is a
+1 −1
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@@ -188,7 +188,7 @@ particles.
*damp_com* is the characteristic time for reaching thermal equilibrium
of the centers of mass.  For example, a value of 100.0 means to relax
the temperature of the centers of mass in a timespan of (roughly) 100
time units (tau or fmsec or psec - see the :doc:`units <units>`
time units (tau or fs or ps - see the :doc:`units <units>`
command).  *damp_drude* is the characteristic time for reaching
thermal equilibrium of the dipoles. It is typically a few timesteps.

+1 −1
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@@ -196,7 +196,7 @@ The *units* keyword determines the meaning of the distance units used
to define the *linear* velocity and *wiggle* amplitude and *rotate*
origin.  This setting is ignored for the *variable* style.  A *box*
value selects standard units as defined by the :doc:`units <units>`
command, e.g. velocity in Angstroms/fmsec and amplitude and position
command, e.g. velocity in Angstroms/fs and amplitude and position
in Angstroms for units = real.  A *lattice* value means the velocity
units are in lattice spacings per time and the amplitude and position
are in lattice spacings.  The :doc:`lattice <lattice>` command must have
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