documentation updates based on review
This commit is contained in:
Sebastian Hütter
@ -26,10 +26,10 @@ OPT.
|
|||||||
* :doc:`ave/chunk <fix_ave_chunk>`
|
* :doc:`ave/chunk <fix_ave_chunk>`
|
||||||
* :doc:`ave/correlate <fix_ave_correlate>`
|
* :doc:`ave/correlate <fix_ave_correlate>`
|
||||||
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
|
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
|
||||||
* :doc:`ave/moments <fix_ave_moments>`
|
|
||||||
* :doc:`ave/grid <fix_ave_grid>`
|
* :doc:`ave/grid <fix_ave_grid>`
|
||||||
* :doc:`ave/histo <fix_ave_histo>`
|
* :doc:`ave/histo <fix_ave_histo>`
|
||||||
* :doc:`ave/histo/weight <fix_ave_histo>`
|
* :doc:`ave/histo/weight <fix_ave_histo>`
|
||||||
|
* :doc:`ave/moments <fix_ave_moments>`
|
||||||
* :doc:`ave/time <fix_ave_time>`
|
* :doc:`ave/time <fix_ave_time>`
|
||||||
* :doc:`aveforce <fix_aveforce>`
|
* :doc:`aveforce <fix_aveforce>`
|
||||||
* :doc:`balance <fix_balance>`
|
* :doc:`balance <fix_balance>`
|
||||||
|
|||||||
@ -205,10 +205,10 @@ accelerated styles exist.
|
|||||||
* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
|
* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
|
||||||
* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
|
* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
|
||||||
* :doc:`ave/correlate/long <fix_ave_correlate_long>` - alternative to :doc:`ave/correlate <fix_ave_correlate>` that allows efficient calculation over long time windows
|
* :doc:`ave/correlate/long <fix_ave_correlate_long>` - alternative to :doc:`ave/correlate <fix_ave_correlate>` that allows efficient calculation over long time windows
|
||||||
* :doc:`ave/moments <fix_ave_moments>` - compute moments of scalar quantities
|
|
||||||
* :doc:`ave/grid <fix_ave_grid>` - compute per-grid time-averaged quantities
|
* :doc:`ave/grid <fix_ave_grid>` - compute per-grid time-averaged quantities
|
||||||
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
|
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
|
||||||
* :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
|
* :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
|
||||||
|
* :doc:`ave/moments <fix_ave_moments>` - compute moments of scalar quantities
|
||||||
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
|
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
|
||||||
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
|
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
|
||||||
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
|
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
|
||||||
|
|||||||
@ -30,14 +30,14 @@ Syntax
|
|||||||
* one or more moments to compute can be listed
|
* one or more moments to compute can be listed
|
||||||
* moment = *mean* or *stddev* or *variance* or *skew* or *kurtosis*, see exact definitions below.
|
* moment = *mean* or *stddev* or *variance* or *skew* or *kurtosis*, see exact definitions below.
|
||||||
* zero or more keyword/arg pairs may be appended
|
* zero or more keyword/arg pairs may be appended
|
||||||
* keyword = *start* or *delay*
|
* keyword = *start* or *history*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
*start* args = Nstart
|
*start* args = Nstart
|
||||||
Nstart = invoke first after this time step
|
Nstart = invoke first after this time step
|
||||||
*history* args = Ndelay
|
*history* args = Nrecent
|
||||||
Ndelay = keep a history of up to Ndelay invocations
|
Nrecent = keep a history of up to Nrecent outputs
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -52,10 +52,10 @@ Description
|
|||||||
|
|
||||||
.. versionadded:: TBD
|
.. versionadded:: TBD
|
||||||
|
|
||||||
Using one or more variables as input every few time steps, calculate the
|
Using one or more values as input, calculate the moments of the underlying
|
||||||
moments of the underlying distribution based on the samples collected
|
(population) distribution based on samples collected every few time
|
||||||
over a time step window. The definitions of the moments calculated are
|
steps over a time step window. The definitions of the moments calculated
|
||||||
given below.
|
are given below.
|
||||||
|
|
||||||
The group specified with this command is ignored. However, note that
|
The group specified with this command is ignored. However, note that
|
||||||
specified values may represent calculations performed by computes and
|
specified values may represent calculations performed by computes and
|
||||||
@ -64,30 +64,29 @@ fixes which store their own "group" definitions.
|
|||||||
Each listed value can be the result of a :doc:`compute <compute>` or
|
Each listed value can be the result of a :doc:`compute <compute>` or
|
||||||
:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
|
:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
|
||||||
:doc:`variable <variable>`. In each case, the compute, fix, or variable
|
:doc:`variable <variable>`. In each case, the compute, fix, or variable
|
||||||
must produce a global quantity, quantity, not a per-atom or local
|
must produce a global quantity, not a per-atom or local quantity.
|
||||||
quantity. If you wish to spatial- or time-average or histogram per-atom
|
If you wish to spatial- or time-average or histogram per-atom
|
||||||
quantities from a compute, fix, or variable, then see the :doc:`fix
|
quantities from a compute, fix, or variable, then see the :doc:`fix
|
||||||
ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
|
ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
|
||||||
:doc:`fix ave/histo <fix_ave_histo>` commands. If you wish to sum a
|
:doc:`fix ave/histo <fix_ave_histo>` commands. If you wish to sum a
|
||||||
per-atom quantity into a single global quantity, see the :doc:`compute
|
per-atom quantity into a single global quantity, see the :doc:`compute
|
||||||
reduce <compute_reduce>` command.
|
reduce <compute_reduce>` command.
|
||||||
|
|
||||||
:doc:`Computes <compute>` that produce global quantities are those which
|
Many :doc:`computes <compute>` and :doc:`fixes <fix>` produce global
|
||||||
do not have the word *atom* in their style name. Only a few :doc:`fixes
|
quantities. See their doc pages for details. :doc:`Variables <variable>`
|
||||||
<fix>` produce global quantities. See the doc pages for individual
|
of style *equal* and *vector* are the only ones that can be used with
|
||||||
fixes for info on which ones produce such values. :doc:`Variables
|
this fix. Variables of style *atom* cannot be used, since they produce
|
||||||
<variable>` of style *equal* and *vector* are the only ones that can be
|
per-atom values.
|
||||||
used with this fix. Variables of style *atom* cannot be used, since
|
|
||||||
they produce per-atom values.
|
|
||||||
|
|
||||||
The input values must all be scalars or vectors with a bracketed term
|
The input values must all be scalars or vectors with a bracketed term
|
||||||
appended, indicating the :math:`I^\text{th}` value of the vector is
|
appended, indicating the :math:`I^\text{th}` value of the vector is
|
||||||
used.
|
used.
|
||||||
|
|
||||||
The result of this fix can be accessed as a vector, containing the
|
The result of this fix can be accessed as a vector, containing the
|
||||||
interleaved moments of each input in order. The first requested moment
|
interleaved moments of each input in order. If M moments are requested,
|
||||||
of input 1 has index 1, the second index 2, the first of input 2 has
|
then the moments of input 1 will be the first M values in the vector
|
||||||
index 3 and so on.
|
output by this fix. The moments of input 2 will the next M values, etc.
|
||||||
|
If there are N values, the vector length will be N*M.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -112,21 +111,23 @@ values will be used in order to contribute to the average. The final
|
|||||||
statistics are generated on time steps that are a multiple of
|
statistics are generated on time steps that are a multiple of
|
||||||
:math:`N_\text{freq}`\ . The average is over a window of up to
|
:math:`N_\text{freq}`\ . The average is over a window of up to
|
||||||
:math:`N_\text{repeat}` quantities, computed in the preceding portion of
|
:math:`N_\text{repeat}` quantities, computed in the preceding portion of
|
||||||
the simulation every :math:`N_\text{every}` time steps.
|
the simulation once every :math:`N_\text{every}` time steps.
|
||||||
|
|
||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
Contrary to some fix ave/* commands, the values of this fix are not
|
Contrary to most fix ave/* commands, it is not required that Nevery *
|
||||||
restricted by any special relation: it is valid to have a window
|
Nrepeat <= Nfreq. This is to allow the user to choose the time
|
||||||
larger than :math:`N_\text{freq}` as well as the other way around.
|
window and number of samples contributing to the output at each
|
||||||
|
Nfreq interval.
|
||||||
|
|
||||||
For example, if :math:`N_\text{freq}=100` and :math:`N_\text{repeat}=5`
|
For example, if :math:`N_\text{freq}=100` and :math:`N_\text{repeat}=5`
|
||||||
(and :math:`N_\text{every}=1`), then values from time steps 96, 97, 98,
|
(and :math:`N_\text{every}=1`), then on step 100 values from time steps
|
||||||
99, and 100 will be used. This means some intervening time steps do not
|
96, 97, 98, 99, and 100 will be used. The fix does not compute its
|
||||||
contribute to the result. If :math:`N_\text{freq}=5` and
|
inputs on steps that are not required. If :math:`N_\text{freq}=5`,
|
||||||
:math:`N_\text{repeat}=10`, then values will first be calculated on step
|
:math:`N_\text{repeat}=8` and :math:`N_\text{every}=1`, then values
|
||||||
5 from steps 1-5, on step 10 from 1-10, on step 15 from 5-15 and so on,
|
will first be calculated on step 5 from steps 1-5, on step 10 from 3-10,
|
||||||
forming a rolling average.
|
on step 15 from 8-15 and so on, forming a rolling average over
|
||||||
|
timesteps that span a time window larger than Nfreq.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -191,31 +192,36 @@ For *kurtosis*, the adjusted Fisher--Pearson standardized moment
|
|||||||
|
|
||||||
Fix invocation and output can be modified by optional keywords.
|
Fix invocation and output can be modified by optional keywords.
|
||||||
|
|
||||||
The *start* keyword specifies that the first invocation should be no
|
The *start* keyword specifies that the first computation should be no
|
||||||
earlier than the step number given (but will still occur on a multiple
|
earlier than the step number given (but will still occur on a multiple
|
||||||
of *Nfreq*). The default is step 0. Often input values can be 0.0 at
|
of *Nfreq*). The default is step 0. Often input values can be 0.0 at
|
||||||
time 0, so setting *start* to a larger value can avoid including a 0.0
|
time 0, so setting *start* to a larger value can avoid including a 0.0
|
||||||
in a longer series.
|
in a longer series.
|
||||||
|
|
||||||
The *history* allows keeping a record of previous results. By default,
|
The *history* keyword stores the Nrecent most recent outputs on Nfreq
|
||||||
only the most recent invocation is accessible.
|
timesteps, so they can be accessed as global outputs of the fix. By
|
||||||
|
default, only the most recent output is accessible. For example, if
|
||||||
|
history 10 is specified and Nfreq = 1000, then on timestep 20000, the
|
||||||
|
Nfreq outputs from steps 20000, 19000, ... 11000 are available for
|
||||||
|
access. See below for details on how to access the history values.
|
||||||
|
|
||||||
For example, this will output values which are delayed by 10
|
For example, this will store the outputs of the previous 10 Nfreq
|
||||||
invocations, meaning 10000 time steps:
|
time steps, i.e. a window of 10000 time steps:
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix 1 all ave/moments 1 200 1000 v_volume mean history 10
|
fix 1 all ave/moments 1 200 1000 v_volume mean history 10
|
||||||
|
|
||||||
The previous results can be accessed by additional rows on the fix output
|
The previous results can be accessed as values in a global array output
|
||||||
array, containing the N-th last evaluation result. For example, the most recent
|
by this fix. Each column of the array is the vector output of the N-th
|
||||||
result of the first input value would be accessed as "f_name[1][1]",
|
preceding Nfreq timestep. For example, the most recent result of the
|
||||||
"f_name[1][4]" is the 4th most recent and so on. Vector access is always the
|
third input value would be accessed as "f_name[3][1]", "f_name[3][4]"
|
||||||
same as the first array row, corresponding to the most recent result.
|
is the 4th most recent and so on. The current vector output is always
|
||||||
|
the first column of the array, corresponding to the most recent result.
|
||||||
|
|
||||||
This fix can be used in conjunction with :doc:`fix halt <fix_halt>` to
|
To illustrate the utility of keeping output history, consider using
|
||||||
stop a run automatically if a quantity is converged to within some
|
this fix in conjunction with :doc:`fix halt <fix_halt>` to stop a run
|
||||||
limit:
|
automatically if a quantity is converged to within some desired tolerance:
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
@ -244,15 +250,16 @@ accessed on any time step, but may not be current.
|
|||||||
|
|
||||||
A global vector is produced with the # of elements = number of moments *
|
A global vector is produced with the # of elements = number of moments *
|
||||||
number of inputs. The moments are output in the order given in the fix
|
number of inputs. The moments are output in the order given in the fix
|
||||||
definition. An array is produced having # of rows = value of *history*
|
definition. An array is produced having # of rows = same as vector output,
|
||||||
and # of columns = same as vector output, using the same ordering.
|
using the same ordering and # of columns = value of *history*. There is
|
||||||
|
always at least one column.
|
||||||
|
|
||||||
Each element can be either "intensive" or "extensive", depending on whether
|
Each element of the global vector or array can be either "intensive" or
|
||||||
the values contributing to the element are "intensive" or "extensive". If a
|
"extensive", depending on whether the values contributing to the element
|
||||||
compute or fix provides the value being time averaged, then the compute or
|
are "intensive" or "extensive". If a compute or fix provides the value
|
||||||
fix determines whether the value is intensive or extensive; see the page
|
being time averaged, then the compute or fix determines whether the value
|
||||||
for that compute or fix for further info. Values produced by a variable
|
is intensive or extensive; see the page for that compute or fix for
|
||||||
are treated as intensive.
|
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
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
the :doc:`run <run>` command. This fix is not invoked during
|
the :doc:`run <run>` command. This fix is not invoked during
|
||||||
|
|||||||
178
examples/PACKAGES/moments/log.02May2025.valtest.g++.1
Normal file
178
examples/PACKAGES/moments/log.02May2025.valtest.g++.1
Normal file
@ -0,0 +1,178 @@
|
|||||||
|
LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# create pure copper system
|
||||||
|
units metal
|
||||||
|
lattice fcc 3.75
|
||||||
|
Lattice spacing in x,y,z = 3.75 3.75 3.75
|
||||||
|
region box block 0 6 0 6 0 6
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
|
||||||
|
timestep 0.002
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 864 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style eam/alloy
|
||||||
|
pair_coeff * * AlCu.eam.alloy Cu Al
|
||||||
|
|
||||||
|
# Initialize to a high temperature, then cool in npt ensemble
|
||||||
|
velocity all create 1000.0 6567345
|
||||||
|
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
|
||||||
|
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
|
||||||
|
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
|
||||||
|
|
||||||
|
variable toteng equal "etotal"
|
||||||
|
fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
|
||||||
|
|
||||||
|
thermo_style custom step etotal f_2[*]
|
||||||
|
thermo_modify format float %14.8f
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 8.6825
|
||||||
|
ghost atom cutoff = 8.6825
|
||||||
|
binsize = 4.34125, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eam/alloy, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.484 | 3.484 | 3.484 Mbytes
|
||||||
|
Step TotEng f_2[1] f_2[2] f_2[3] f_2[4]
|
||||||
|
0 -2884.91592826 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
1 -2888.74461907 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
2 -2898.78491936 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
3 -2910.70619667 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
4 -2919.41734302 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
5 -2923.24980175 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
6 -2923.79800148 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
7 -2922.97580252 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
8 -2921.95601941 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
9 -2921.45319499 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
10 -2921.81460149 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
11 -2923.00059466 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
12 -2924.63075671 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
13 -2926.18037946 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
14 -2927.22356281 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
15 -2927.62053073 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
16 -2927.49949128 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
17 -2927.12292174 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
18 -2926.73637250 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
19 -2926.49482990 -2915.29004998 148.32538381 1.60272422 1.50844200
|
||||||
|
20 -2926.44714720 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
21 -2926.56102718 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
22 -2926.76734347 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
23 -2926.98403044 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
24 -2927.15193693 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
25 -2927.24498540 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
26 -2927.26914121 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
27 -2927.25021402 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
28 -2927.21637817 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
29 -2927.19085616 -2926.29565870 2.07215006 1.62317861 2.37019300
|
||||||
|
30 -2927.18360687 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
31 -2927.19243579 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
32 -2927.20805612 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
33 -2927.22285606 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
34 -2927.23274852 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
35 -2927.23953263 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
36 -2927.24805761 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
37 -2927.26215638 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
38 -2927.28298252 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
39 -2927.31025065 -2927.08195198 0.05722486 1.54894969 1.44984748
|
||||||
|
40 -2927.33874897 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
41 -2927.36224413 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
42 -2927.37729800 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
43 -2927.38671916 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
44 -2927.39115082 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
45 -2927.39614318 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
46 -2927.40444730 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
47 -2927.41888601 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
48 -2927.43954388 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
49 -2927.46210058 -2927.25378252 0.00209108 -0.65432756 -0.21113798
|
||||||
|
50 -2927.48270024 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
51 -2927.49822500 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
52 -2927.50765361 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
53 -2927.51223225 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
54 -2927.51510653 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
55 -2927.52035921 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
56 -2927.53170012 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
57 -2927.54910408 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
58 -2927.57357292 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
59 -2927.60356966 -2927.41212333 0.00148630 -0.72914987 -0.39161968
|
||||||
|
60 -2927.63344447 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
61 -2927.66186165 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
62 -2927.68810360 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
63 -2927.71163480 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
64 -2927.73036225 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
65 -2927.74726656 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
66 -2927.76525638 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
67 -2927.78432762 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
68 -2927.80305095 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
69 -2927.82406714 -2927.54449679 0.00204640 -1.06571776 0.04430271
|
||||||
|
70 -2927.84622122 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
71 -2927.86886493 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
72 -2927.89150302 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
73 -2927.91480122 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
74 -2927.93739399 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
75 -2927.96075707 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
76 -2927.98525702 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
77 -2928.00918972 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
78 -2928.03266453 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
79 -2928.05673430 -2927.75621522 0.00356092 0.06232090 -0.94076248
|
||||||
|
80 -2928.08120268 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
81 -2928.10618717 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
82 -2928.13191751 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
83 -2928.15675025 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
84 -2928.18178044 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
85 -2928.20538210 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
86 -2928.22991006 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
87 -2928.25238345 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
88 -2928.27490378 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
89 -2928.29697980 -2927.97383685 0.00511363 -0.03242365 -1.20956903
|
||||||
|
90 -2928.31902032 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
91 -2928.34079951 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
92 -2928.36448072 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
93 -2928.38918869 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
94 -2928.41578734 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
95 -2928.44466633 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
96 -2928.47414034 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
97 -2928.50507273 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
98 -2928.53751007 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
99 -2928.56947939 -2928.21552149 0.00511983 0.08421866 -1.19120544
|
||||||
|
100 -2928.60000318 -2928.46411283 0.00779929 -0.14908790 -1.24292534
|
||||||
|
Loop time of 0.579661 on 1 procs for 100 steps with 864 atoms
|
||||||
|
|
||||||
|
Performance: 29.811 ns/day, 0.805 hours/ns, 172.515 timesteps/s, 149.053 katom-step/s
|
||||||
|
96.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.54316 | 0.54316 | 0.54316 | 0.0 | 93.70
|
||||||
|
Neigh | 0.0041212 | 0.0041212 | 0.0041212 | 0.0 | 0.71
|
||||||
|
Comm | 0.0034702 | 0.0034702 | 0.0034702 | 0.0 | 0.60
|
||||||
|
Output | 0.014085 | 0.014085 | 0.014085 | 0.0 | 2.43
|
||||||
|
Modify | 0.01321 | 0.01321 | 0.01321 | 0.0 | 2.28
|
||||||
|
Other | | 0.001612 | | | 0.28
|
||||||
|
|
||||||
|
Nlocal: 864 ave 864 max 864 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3767 ave 3767 max 3767 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 96746 ave 96746 max 96746 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 96746
|
||||||
|
Ave neighs/atom = 111.97454
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
178
examples/PACKAGES/moments/log.02May2025.valtest.g++.4
Normal file
178
examples/PACKAGES/moments/log.02May2025.valtest.g++.4
Normal file
@ -0,0 +1,178 @@
|
|||||||
|
LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# create pure copper system
|
||||||
|
units metal
|
||||||
|
lattice fcc 3.75
|
||||||
|
Lattice spacing in x,y,z = 3.75 3.75 3.75
|
||||||
|
region box block 0 6 0 6 0 6
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
|
||||||
|
timestep 0.002
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 864 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style eam/alloy
|
||||||
|
pair_coeff * * AlCu.eam.alloy Cu Al
|
||||||
|
|
||||||
|
# Initialize to a high temperature, then cool in npt ensemble
|
||||||
|
velocity all create 1000.0 6567345
|
||||||
|
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
|
||||||
|
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
|
||||||
|
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
|
||||||
|
|
||||||
|
variable toteng equal "etotal"
|
||||||
|
fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
|
||||||
|
|
||||||
|
thermo_style custom step etotal f_2[*]
|
||||||
|
thermo_modify format float %14.8f
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 8.6825
|
||||||
|
ghost atom cutoff = 8.6825
|
||||||
|
binsize = 4.34125, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eam/alloy, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.42 | 3.42 | 3.42 Mbytes
|
||||||
|
Step TotEng f_2[1] f_2[2] f_2[3] f_2[4]
|
||||||
|
0 -2884.91592826 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
1 -2888.74473521 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
2 -2898.78463435 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
3 -2910.70366466 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
4 -2919.40999553 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
5 -2923.23570887 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
6 -2923.77707961 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
7 -2922.94386730 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
8 -2921.92251474 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
9 -2921.42476103 0.00000000 0.00000000 0.00000000 0.00000000
|
||||||
|
10 -2921.79501042 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
11 -2922.99498349 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
12 -2924.64023395 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
13 -2926.19980790 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
14 -2927.25022454 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
15 -2927.64953875 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
16 -2927.52804735 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
17 -2927.14916045 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
18 -2926.76078244 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
19 -2926.51878380 -2915.27419717 148.08574615 1.60354430 1.51194865
|
||||||
|
20 -2926.47129883 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
21 -2926.59030835 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
22 -2926.80121221 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
23 -2927.02526150 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
24 -2927.20079704 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
25 -2927.30192483 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
26 -2927.33194351 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
27 -2927.31647527 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
28 -2927.28391864 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
29 -2927.25821953 -2926.31628615 2.10313655 1.62594474 2.38000930
|
||||||
|
30 -2927.25085808 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
31 -2927.25723201 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
32 -2927.27197789 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
33 -2927.28667044 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
34 -2927.29879455 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
35 -2927.30701891 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
36 -2927.31785921 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
37 -2927.33272014 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
38 -2927.35282056 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
39 -2927.37849130 -2927.13609190 0.06387000 1.52055179 1.31247839
|
||||||
|
40 -2927.40448350 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
41 -2927.42423249 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
42 -2927.43769919 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
43 -2927.44493813 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
44 -2927.44923137 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
45 -2927.45439729 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
46 -2927.46365674 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
47 -2927.48173952 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
48 -2927.50371663 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
49 -2927.52750629 -2927.32080685 0.00219675 -0.52051260 -0.50322958
|
||||||
|
50 -2927.54872274 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
51 -2927.56277664 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
52 -2927.57050508 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
53 -2927.57241043 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
54 -2927.57517748 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
55 -2927.58161786 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
56 -2927.59393740 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
57 -2927.61367876 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
58 -2927.64096296 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
59 -2927.67356621 -2927.47358404 0.00168128 -0.79883601 -0.48497973
|
||||||
|
60 -2927.70625176 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
61 -2927.73673853 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
62 -2927.76292153 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
63 -2927.78541405 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
64 -2927.80292853 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
65 -2927.81988675 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
66 -2927.83680256 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
67 -2927.85379296 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
68 -2927.87418119 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
69 -2927.89451588 -2927.60908846 0.00241645 -1.10903745 0.07175615
|
||||||
|
70 -2927.91602570 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
71 -2927.93874793 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
72 -2927.96195498 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
73 -2927.98521535 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
74 -2928.01060565 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
75 -2928.03584561 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
76 -2928.06090892 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
77 -2928.08509438 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
78 -2928.11095399 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
79 -2928.13711339 -2927.82832077 0.00334657 0.04700770 -0.91589129
|
||||||
|
80 -2928.16413424 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
81 -2928.19005959 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
82 -2928.21654649 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
83 -2928.24249986 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
84 -2928.26861892 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
85 -2928.29480718 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
86 -2928.32144325 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
87 -2928.34727619 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
88 -2928.37131285 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
89 -2928.39531126 -2928.04905744 0.00575008 -0.05409710 -1.19501222
|
||||||
|
90 -2928.41739503 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
91 -2928.43978811 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
92 -2928.46316822 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
93 -2928.48654219 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
94 -2928.51132482 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
95 -2928.53938009 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
96 -2928.56852408 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
97 -2928.59814410 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
98 -2928.62787940 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
99 -2928.65853178 -2928.30652706 0.00595440 0.06693205 -1.24851322
|
||||||
|
100 -2928.68735978 -2928.55806426 0.00711607 -0.13829819 -1.25519738
|
||||||
|
Loop time of 0.327437 on 4 procs for 100 steps with 864 atoms
|
||||||
|
|
||||||
|
Performance: 52.774 ns/day, 0.455 hours/ns, 305.402 timesteps/s, 263.868 katom-step/s
|
||||||
|
91.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.27213 | 0.27259 | 0.27312 | 0.1 | 83.25
|
||||||
|
Neigh | 0.00096945 | 0.0015991 | 0.0022533 | 1.5 | 0.49
|
||||||
|
Comm | 0.026726 | 0.027088 | 0.027516 | 0.2 | 8.27
|
||||||
|
Output | 0.0029839 | 0.0048706 | 0.0097487 | 4.0 | 1.49
|
||||||
|
Modify | 0.012374 | 0.016834 | 0.018623 | 2.0 | 5.14
|
||||||
|
Other | | 0.004455 | | | 1.36
|
||||||
|
|
||||||
|
Nlocal: 216 ave 224 max 204 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||||
|
Nghost: 2147 ave 2159 max 2139 min
|
||||||
|
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||||
|
Neighs: 24185.8 ave 26045 max 21309 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 96743
|
||||||
|
Ave neighs/atom = 111.97106
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user