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Merge remote-tracking branch 'github/develop' into collected-small-fixes

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Axel Kohlmeyer
2025-05-30 01:15:48 -04:00
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1
doc/src/Commands_fix.rst
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@ -29,6 +29,7 @@ OPT.
* :doc:`ave/grid <fix_ave_grid>`
* :doc:`ave/histo <fix_ave_histo>`
* :doc:`ave/histo/weight <fix_ave_histo>`
* :doc:`ave/moments <fix_ave_moments>`
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`

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doc/src/fix.rst
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@ -208,6 +208,7 @@ accelerated styles exist.
* :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/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:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing

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doc/src/fix_ave_moments.rst Normal file
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.. index:: fix ave/moments
fix ave/moments command
=======================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID ave/moments Nevery Nrepeat Nfreq value1 value2 ... moment1 moment2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* ave/moments = style name of this fix command
* Nevery = use input values every this many time steps
* Nrepeat = # of times to use input values for calculating averages
* Nfreq = calculate averages every this many time steps
* one or more input variables can be listed
* value = v_name
.. parsed-literal::
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
v_name = value calculated by an equal-style variable with name
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* one or more moments to compute can be listed
* moment = *mean* or *stddev* or *variance* or *skew* or *kurtosis*, see exact definitions below.
* zero or more keyword/arg pairs may be appended
* keyword = *start* or *history*
.. parsed-literal::
*start* args = Nstart
Nstart = invoke first after this time step
*history* args = Nrecent
Nrecent = keep a history of up to Nrecent outputs
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all ave/moments 1 1000 100 v_volume mean stddev
fix 1 all ave/moments 1 200 1000 v_volume variance kurtosis history 10
Description
"""""""""""
.. versionadded:: TBD
Using one or more values as input, calculate the moments of the underlying
(population) distributions based on samples collected every few time
steps over a time step window. The definitions of the moments calculated
are given below.
The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
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:`variable <variable>`. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity.
If you wish to spatial- or time-average or histogram per-atom
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
: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
reduce <compute_reduce>` command.
Many :doc:`computes <compute>` and :doc:`fixes <fix>` produce global
quantities. See their doc pages for details. :doc:`Variables <variable>`
of style *equal* and *vector* are the only ones that can be 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
appended, indicating the :math:`I^\text{th}` value of the vector is
used.
The result of this fix can be accessed as a vector, containing the
interleaved moments of each input in order. If M moments are requested,
then the moments of input 1 will be the first M values in the vector
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.
----------
For input values from a compute or fix or variable, the bracketed index
I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or "\*n"
or "m\*" or "m\*n". If :math:`N` is the size of the vector, then an
asterisk with no numeric values means all indices from 1 to :math:`N`.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to :math:`N` (inclusive). A
middle asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the vector
or cells of the array had been listed one by one. For examples, see the
description of this capability in :doc:`fix ave/time <fix_ave_time>`.
----------
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and
:math:`N_\text{freq}` arguments specify on what time steps the input
values will be used in order to contribute to the average. The final
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{repeat}` quantities, computed in the preceding portion of
the simulation once every :math:`N_\text{every}` time steps.
.. note::
Contrary to most fix ave/* commands, it is not required that Nevery *
Nrepeat <= Nfreq. This is to allow the user to choose the time
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`
(and :math:`N_\text{every}=1`), then on step 100 values from time steps
96, 97, 98, 99, and 100 will be used. The fix does not compute its
inputs on steps that are not required. If :math:`N_\text{freq}=5`,
:math:`N_\text{repeat}=8` and :math:`N_\text{every}=1`, then values
will first be calculated on step 5 from steps 1-5, on step 10 from 3-10,
on step 15 from 8-15 and so on, forming a rolling average over
timesteps that span a time window larger than Nfreq.
----------
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used. See the discussion above for how I
can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
Note that some fixes only produce their values on certain time steps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to
LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has been
previously defined in the input script. Only equal-style or vector-style
variables can be used, which both produce global values. Vector-style
variables require a bracketed term to specify the Ith element of the
vector calculated by the variable.
Note that variables of style *equal* and *vector* define a formula which
can reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of specifying quantities to
time average.
----------
The moments are output in the order requested in the arguments following
the last input. Any number and order of moments can be specified,
although it does not make much sense to specify the same moment multiple
times. All moments are computed using a correction of the sample estimators
used to obtain unbiased cumulants :math:`k_{1..4}` (see :ref:`(Cramer)
<Cramer1>`). The correction for variance is the standard Bessel
correction. For other moments, see :ref:`(Joanes)<Joanes1>`.
For *mean*, the arithmetic mean :math:`\bar{x} = \frac{1}{n}
\sum_{i=1}^{n} x_i` is calculated.
For *variance*, the Bessel-corrected sample variance :math:`var = k_2 =
\frac{1}{n - 1} \sum_{i=1}^{n} (x_i - \bar{x})^2` is calculated.
For *stddev*, the Bessel-corrected sample standard deviation
:math:`stddev = \sqrt{k_2}` is calculated.
For *skew*, the adjusted Fisher--Pearson standardized moment :math:`G_1
= \frac{k_3}{k_2^{3/2}} = \frac{k_3}{stddev^3}` is calculated.
For *kurtosis*, the adjusted Fisher--Pearson standardized moment
:math:`G_2 = \frac{k_4}{k_2^2}` is calculated.
----------
Fix invocation and output can be modified by optional keywords.
The *start* keyword specifies that the first computation should be no
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
time 0, so setting *start* to a larger value can avoid including a 0.0
in a longer series.
The *history* keyword stores the Nrecent most recent outputs on Nfreq
timesteps, so they can be accessed as global outputs of the fix. Nrecent
must be >= 1. The default is 1, meaning 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 store the outputs of the previous 10 Nfreq
time steps, i.e. a window of 10000 time steps:
.. code-block:: LAMMPS
fix 1 all ave/moments 1 200 1000 v_volume mean history 10
The previous results can be accessed as values in a global array output
by this fix. Each column of the array is the vector output of the N-th
preceding Nfreq timestep. For example, assuming a single moment is
calculated, the most recent result corresponding to the third input
value would be accessed as "f_name[3][1]", "f_name[3][4]" 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.
To illustrate the utility of keeping output history, consider using
this fix in conjunction with :doc:`fix halt <fix_halt>` to stop a run
automatically if a quantity is converged to within some desired tolerance:
.. code-block:: LAMMPS
variable target equal etot
fix aveg all ave/moments 1 200 1000 v_target mean stddev history 10
variable stopcond equal "abs(f_aveg[1]-f_aveg[1][10])<f_aveg[2]"
fix fhalt all halt 1000 v_stopcond == 1
In this example, every 1000 time steps, the average and standard
deviation of the total energy over the previous 200 time steps are
calculated. If the difference between the most recent and 10-th most
recent average is lower than the most recent standard deviation, the run
is stopped.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`.
This fix produces a global vector and global array which can be accessed
by various :doc:`output commands <Howto_output>`. The values can be
accessed on any time step, but may not be current.
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
definition. An array is produced having # of rows = length of vector
output (with an ordering which matches the vector) and # of columns =
value of *history*. There is always at least one column.
Each element of the global vector or array can be either "intensive" or
"extensive", depending on whether the values contributing to the element
are "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 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 :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This compute is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix ave/time <fix_ave_time>`,
Default
"""""""
The option defaults are history = 1, start = 0.
----------
.. _Cramer1:
**(Cramer)** Cramer, Mathematical Methods of Statistics, Princeton University Press (1946).
.. _Joanes1:
**(Joanes)** Joanes, Gill, The Statistician, 47, 183--189 (1998).

3
doc/utils/sphinx-config/false_positives.txt
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@ -631,6 +631,7 @@ cp
cpp
cpu
cradius
Cramer
createatoms
createAtoms
CreateIDs
@ -671,6 +672,7 @@ cuFFT
CuH
Cui
Cummins
cumulants
Cundall
cundall
Curk
@ -1772,6 +1774,7 @@ jik
JIK
jku
jN
Joanes
Joannopoulos
Jochim
Jonsson

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examples/PACKAGES/moments/in.converge Normal file
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@ -0,0 +1,35 @@
# Detect convergence in a simulation using the relative change in
# moments. This demonstrates the "history" option.
# ---------------------------------------------------------------------
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
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)
# compute mean and stddev over the preceding 5000 steps, every 20 steps
variable toteng equal "etotal"
fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
# Convergence criterion: stddev is smaller than threshold and was previously larger
# This avoids issues with system oscillations in the order of the averaging window
# that would otherwise lead to "nodes" in the stddev.
variable conv equal "(f_2[2] < 2.0) && (f_2[2][1] < f_2[2][5])"
fix 3 all halt 100 v_conv == 1
thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
thermo 100
run 10000

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examples/PACKAGES/moments/in.simple Normal file
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@ -0,0 +1,27 @@
# Perform a simple simulation and output the moments of the total energy
# ---------------------------------------------------------------------
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
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)
variable toteng equal "etotal"
fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
thermo_style custom step temp press etotal f_2[*]
thermo 100
run 10000

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examples/PACKAGES/moments/in.valtest Normal file
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@ -0,0 +1,28 @@
# Output raw and computed data. This can be used to perform the moment
# calculation in some external tool and validate our results
# ---------------------------------------------------------------------
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
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)
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

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examples/PACKAGES/moments/log.02May2025.converge.g++.1 Normal file
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@ -0,0 +1,171 @@
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 10 500 200 v_toteng mean stddev history 5
variable conv equal "(f_2[2] < 2) && (f_2[2][1] < f_2[2][5])"
fix 3 all halt 1000 v_conv == 1
thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
thermo 100
run 10000
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 Temp Press TotEng f_2[1][1] f_2[2][1] f_2[1][5] f_2[2][5] v_conv
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 512.04214 -124.66263 -2928.6 0 0 0 0 0
200 479.34328 -136.26635 -2931.3905 -2928.6251 2.1584834 0 0 0
300 480.05298 128.92946 -2933.9233 -2928.6251 2.1584834 0 0 0
400 471.83641 -29.253334 -2936.8631 -2931.3742 3.3668783 0 0 0
500 456.96309 -274.69336 -2939.9081 -2931.3742 3.3668783 0 0 0
600 450.32413 14.606227 -2942.973 -2934.277 5.0681849 0 0 0
700 431.71192 -45.641261 -2946.006 -2934.277 5.0681849 0 0 0
800 436.4217 589.91981 -2948.8885 -2937.2386 6.823233 0 0 0
900 407.84688 -3728.1499 -2951.6643 -2937.2386 6.823233 0 0 0
1000 401.69178 6695.3653 -2954.2959 -2940.1463 8.4728269 -2928.6251 2.1584834 0
1100 370.87469 -2294.843 -2956.9413 -2940.1463 8.4728269 -2928.6251 2.1584834 0
1200 375.15562 704.6568 -2959.3841 -2942.9613 10.001542 -2931.3742 3.3668783 0
1300 371.09077 -493.04016 -2961.6803 -2942.9613 10.001542 -2931.3742 3.3668783 0
1400 365.88512 490.98174 -2963.8365 -2945.6475 11.378724 -2934.277 5.0681849 0
1500 358.42655 -218.94911 -2965.8652 -2945.6475 11.378724 -2934.277 5.0681849 0
1600 329.08402 56.411923 -2967.7662 -2948.1844 12.597017 -2937.2386 6.823233 0
1700 317.74207 1192.918 -2969.557 -2948.1844 12.597017 -2937.2386 6.823233 0
1800 331.98966 -2205.7213 -2971.1465 -2950.559 13.653575 -2940.1463 8.4728269 0
1900 330.96814 1401.3066 -2972.6923 -2950.559 13.653575 -2940.1463 8.4728269 0
2000 315.41816 -909.41909 -2974.0785 -2952.7764 14.568194 -2942.9613 10.001542 0
2100 320.4269 1226.2006 -2975.3676 -2952.7764 14.568194 -2942.9613 10.001542 0
2200 302.88235 -1238.8052 -2976.5099 -2954.8327 15.341787 -2945.6475 11.378724 0
2300 300.4349 2667.202 -2977.5329 -2954.8327 15.341787 -2945.6475 11.378724 0
2400 292.94691 -5532.1854 -2978.3724 -2956.7266 15.978754 -2948.1844 12.597017 0
2500 286.12064 4647.3841 -2979.2217 -2956.7266 15.978754 -2948.1844 12.597017 0
2600 290.74305 -1950.526 -2979.9142 -2958.4592 16.485773 -2950.559 13.653575 0
2700 281.51347 937.60472 -2980.4808 -2958.4592 16.485773 -2950.559 13.653575 0
2800 279.71836 -801.62498 -2980.8899 -2960.032 16.869365 -2952.7764 14.568194 0
2900 277.41241 609.21495 -2981.1721 -2960.032 16.869365 -2952.7764 14.568194 0
3000 281.31161 -760.27203 -2981.3003 -2961.4399 17.128547 -2954.8327 15.341787 0
3100 284.72904 315.53038 -2981.297 -2961.4399 17.128547 -2954.8327 15.341787 0
3200 278.39445 516.25074 -2981.1224 -2962.6768 17.263037 -2956.7266 15.978754 0
3300 294.46998 -655.06212 -2980.8266 -2962.6768 17.263037 -2956.7266 15.978754 0
3400 290.04647 788.30424 -2980.3963 -2963.7417 17.280979 -2958.4592 16.485773 0
3500 283.218 -844.33188 -2979.8504 -2963.7417 17.280979 -2958.4592 16.485773 0
3600 288.76031 1339.2734 -2979.2382 -2964.6345 17.192698 -2960.032 16.869365 0
3700 289.44519 -3015.7161 -2978.5394 -2964.6345 17.192698 -2960.032 16.869365 0
3800 309.04206 5579.3265 -2977.8282 -2965.3649 17.01845 -2961.4399 17.128547 0
3900 309.34588 -4255.5213 -2977.1281 -2965.3649 17.01845 -2961.4399 17.128547 0
4000 305.79444 2358.1383 -2976.5251 -2965.9537 16.784519 -2962.6768 17.263037 0
4100 309.12957 -1401.6484 -2975.9173 -2965.9537 16.784519 -2962.6768 17.263037 0
4200 309.41928 1180.4111 -2975.3857 -2966.4277 16.516135 -2963.7417 17.280979 0
4300 299.88949 -1549.6591 -2974.927 -2966.4277 16.516135 -2963.7417 17.280979 0
4400 319.09918 1937.7006 -2974.5598 -2966.8138 16.232551 -2964.6345 17.192698 0
4500 326.48719 -1489.2073 -2974.311 -2966.8138 16.232551 -2964.6345 17.192698 0
4600 310.93392 37.586899 -2974.1959 -2967.1394 15.948448 -2965.3649 17.01845 0
4700 314.28994 317.12347 -2974.1763 -2967.1394 15.948448 -2965.3649 17.01845 0
4800 309.88756 -698.72705 -2974.2892 -2967.4334 15.675606 -2965.9537 16.784519 0
4900 309.53444 962.42921 -2974.5261 -2967.4334 15.675606 -2965.9537 16.784519 0
5000 316.06666 -1869.3275 -2974.8492 -2967.7182 15.421633 -2966.4277 16.516135 0
5100 304.82485 4042.6797 -2975.2715 -2967.7182 15.421633 -2966.4277 16.516135 0
5200 307.75342 -5058.4814 -2975.7195 -2969.5853 13.236776 -2966.8138 16.232551 0
5300 298.83511 3096.4566 -2976.3329 -2969.5853 13.236776 -2966.8138 16.232551 0
5400 296.85413 -1929.1654 -2976.8797 -2971.2747 11.121537 -2967.1394 15.948448 0
5500 295.88343 1449.3005 -2977.4488 -2971.2747 11.121537 -2967.1394 15.948448 0
5600 305.59328 -1504.0321 -2977.9573 -2972.77 9.1579616 -2967.4334 15.675606 0
5700 293.40683 2579.0134 -2978.4364 -2972.77 9.1579616 -2967.4334 15.675606 0
5800 297.93644 -2742.705 -2978.8276 -2974.0625 7.4101102 -2967.7182 15.421633 0
5900 290.39408 1189.4042 -2979.2224 -2974.0625 7.4101102 -2967.7182 15.421633 0
6000 293.73148 -232.54292 -2979.503 -2975.1594 5.8959922 -2969.5853 13.236776 0
6100 292.04933 -168.30971 -2979.6898 -2975.1594 5.8959922 -2969.5853 13.236776 0
6200 299.23747 839.17828 -2979.7883 -2976.0647 4.6378408 -2971.2747 11.121537 0
6300 294.92201 -1597.9426 -2979.7975 -2976.0647 4.6378408 -2971.2747 11.121537 0
6400 291.7185 3411.2916 -2979.6978 -2976.7848 3.643826 -2972.77 9.1579616 0
6500 285.34227 -4280.7968 -2979.4874 -2976.7848 3.643826 -2972.77 9.1579616 0
6600 295.53838 2138.7496 -2979.2799 -2977.3265 2.9178925 -2974.0625 7.4101102 0
6700 288.54718 -1818.7662 -2978.9379 -2977.3265 2.9178925 -2974.0625 7.4101102 0
6800 290.41342 2175.3559 -2978.543 -2977.7009 2.4532223 -2975.1594 5.8959922 0
6900 296.34456 -4782.08 -2978.0362 -2977.7009 2.4532223 -2975.1594 5.8959922 0
7000 303.74314 5905.219 -2977.577 -2977.9137 2.2279716 -2976.0647 4.6378408 0
7100 303.90284 -3291.7627 -2977.1308 -2977.9137 2.2279716 -2976.0647 4.6378408 0
7200 296.13966 2209.574 -2976.7001 -2977.9829 2.1708943 -2976.7848 3.643826 0
7300 295.79694 -1609.1898 -2976.2816 -2977.9829 2.1708943 -2976.7848 3.643826 0
7400 306.53289 988.50902 -2975.8992 -2977.931 2.1935882 -2977.3265 2.9178925 0
7500 303.89992 -631.22838 -2975.5597 -2977.931 2.1935882 -2977.3265 2.9178925 0
7600 303.83684 -348.48744 -2975.3074 -2977.7831 2.2226664 -2977.7009 2.4532223 0
7700 309.67313 1350.9414 -2975.1279 -2977.7831 2.2226664 -2977.7009 2.4532223 0
7800 309.74314 -1182.8905 -2975.0174 -2977.5683 2.2106484 -2977.9137 2.2279716 0
7900 309.42429 999.08033 -2975.0089 -2977.5683 2.2106484 -2977.9137 2.2279716 0
8000 315.51872 -1337.8894 -2975.0791 -2977.3233 2.1379295 -2977.9829 2.1708943 0
8100 314.80533 2392.3424 -2975.25 -2977.3233 2.1379295 -2977.9829 2.1708943 0
8200 303.80236 -3224.5976 -2975.4744 -2977.0851 2.0176342 -2977.931 2.1935882 0
8300 295.0505 3296.6912 -2975.8196 -2977.0851 2.0176342 -2977.931 2.1935882 0
8400 302.4154 -3314.5096 -2976.1586 -2976.8877 1.883051 -2977.7831 2.2226664 1
8500 300.95491 2971.1291 -2976.5859 -2976.8877 1.883051 -2977.7831 2.2226664 1
8600 301.68919 -2297.6673 -2976.9953 -2976.7596 1.785401 -2977.5683 2.2106484 1
8700 291.21002 1477.5703 -2977.4323 -2976.7596 1.785401 -2977.5683 2.2106484 1
8800 305.87126 -1085.459 -2977.8247 -2976.7169 1.7541517 -2977.3233 2.1379295 1
8900 296.17567 777.95805 -2978.2081 -2976.7169 1.7541517 -2977.3233 2.1379295 1
Fix halt condition for fix-id 3 met on step 9000 with value 1 (src/fix_halt.cpp:310)
9000 295.71917 -425.00708 -2978.5264 -2976.7595 1.7755885 -2977.0851 2.0176342 1
Loop time of 42.1758 on 1 procs for 9000 steps with 864 atoms
Performance: 36.874 ns/day, 0.651 hours/ns, 213.393 timesteps/s, 184.371 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 41.126 | 41.126 | 41.126 | 0.0 | 97.51
Neigh | 0.0078787 | 0.0078787 | 0.0078787 | 0.0 | 0.02
Comm | 0.26508 | 0.26508 | 0.26508 | 0.0 | 0.63
Output | 0.0096224 | 0.0096224 | 0.0096224 | 0.0 | 0.02
Modify | 0.65597 | 0.65597 | 0.65597 | 0.0 | 1.56
Other | | 0.1108 | | | 0.26
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: 0:00:42

171
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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 10 500 200 v_toteng mean stddev history 5
variable conv equal "(f_2[2] < 2) && (f_2[2][1] < f_2[2][5])"
fix 3 all halt 1000 v_conv == 1
thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
thermo 100
run 10000
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 Temp Press TotEng f_2[1][1] f_2[2][1] f_2[1][5] f_2[2][5] v_conv
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 492.38014 -134.33622 -2928.6874 0 0 0 0 0
200 484.82396 -214.26318 -2931.4603 -2928.6979 2.1805063 0 0 0
300 476.69743 15.78678 -2934.0022 -2928.6979 2.1805063 0 0 0
400 482.51415 141.67184 -2936.9347 -2931.4437 3.3715811 0 0 0
500 455.45411 2.4424602 -2939.9649 -2931.4437 3.3715811 0 0 0
600 455.20054 -6.8170934 -2943.0454 -2934.339 5.0598781 0 0 0
700 429.81168 -75.812923 -2946.0438 -2934.339 5.0598781 0 0 0
800 428.22097 604.18705 -2948.9285 -2937.2965 6.813037 0 0 0
900 399.10914 -3622.6904 -2951.7252 -2937.2965 6.813037 0 0 0
1000 394.62543 7905.9041 -2954.2925 -2940.2044 8.4668749 -2928.6979 2.1805063 0
1100 404.27007 -2565.5508 -2956.9736 -2940.2044 8.4668749 -2928.6979 2.1805063 0
1200 368.47178 741.43707 -2959.4264 -2943.0151 9.9914785 -2931.4437 3.3715811 0
1300 360.91266 -267.08372 -2961.69 -2943.0151 9.9914785 -2931.4437 3.3715811 0
1400 356.74405 158.09093 -2963.8501 -2945.696 11.36357 -2934.339 5.0598781 0
1500 335.45696 -71.007783 -2965.8817 -2945.696 11.36357 -2934.339 5.0598781 0
1600 331.01199 -454.90004 -2967.7708 -2948.2278 12.577884 -2937.2965 6.813037 0
1700 329.223 2428.4284 -2969.5452 -2948.2278 12.577884 -2937.2965 6.813037 0
1800 327.61481 -4757.648 -2971.1105 -2950.5985 13.632251 -2940.2044 8.4668749 0
1900 318.18741 2226.7765 -2972.6906 -2950.5985 13.632251 -2940.2044 8.4668749 0
2000 308.79313 -1089.8603 -2974.0899 -2952.8123 14.545164 -2943.0151 9.9914785 0
2100 303.32047 757.53534 -2975.3597 -2952.8123 14.545164 -2943.0151 9.9914785 0
2200 307.41102 -837.97246 -2976.4966 -2954.8654 15.317558 -2945.696 11.36357 0
2300 303.01088 1618.29 -2977.5454 -2954.8654 15.317558 -2945.696 11.36357 0
2400 297.59385 -3233.8282 -2978.4064 -2956.7565 15.953758 -2948.2278 12.577884 0
2500 288.72232 5209.2099 -2979.1999 -2956.7565 15.953758 -2948.2278 12.577884 0
2600 298.92201 -2193.618 -2979.8873 -2958.4845 16.457635 -2950.5985 13.632251 0
2700 282.61818 765.88178 -2980.4563 -2958.4845 16.457635 -2950.5985 13.632251 0
2800 273.63104 -389.49749 -2980.8636 -2960.0533 16.839029 -2952.8123 14.545164 0
2900 274.12166 -9.2552992 -2981.1421 -2960.0533 16.839029 -2952.8123 14.545164 0
3000 279.43592 212.25445 -2981.2716 -2961.4578 17.096628 -2954.8654 15.317558 0
3100 291.10071 -1139.205 -2981.2475 -2961.4578 17.096628 -2954.8654 15.317558 0
3200 281.53171 3124.6411 -2981.0818 -2962.6921 17.230604 -2956.7565 15.953758 0
3300 277.0223 -2795.9494 -2980.7825 -2962.6921 17.230604 -2956.7565 15.953758 0
3400 284.8443 1587.8876 -2980.3701 -2963.754 17.247489 -2958.4845 16.457635 0
3500 281.19 -1143.0785 -2979.8374 -2963.754 17.247489 -2958.4845 16.457635 0
3600 296.58287 1156.4706 -2979.2182 -2964.645 17.159411 -2960.0533 16.839029 0
3700 297.24517 -1888.4993 -2978.5352 -2964.645 17.159411 -2960.0533 16.839029 0
3800 290.81586 3843.3483 -2977.8509 -2965.3746 16.985916 -2961.4578 17.096628 0
3900 300.39456 -5584.8386 -2977.0837 -2965.3746 16.985916 -2961.4578 17.096628 0
4000 306.15811 3310.0105 -2976.5086 -2965.9619 16.752214 -2962.6921 17.230604 0
4100 295.907 -1475.0458 -2975.9096 -2965.9619 16.752214 -2962.6921 17.230604 0
4200 322.70162 933.76586 -2975.3867 -2966.4348 16.484219 -2963.754 17.247489 0
4300 306.69631 -512.7048 -2974.9324 -2966.4348 16.484219 -2963.754 17.247489 0
4400 309.23776 226.77219 -2974.5791 -2966.8208 16.201471 -2964.645 17.159411 0
4500 313.15783 508.29785 -2974.3263 -2966.8208 16.201471 -2964.645 17.159411 0
4600 316.26151 -2043.7571 -2974.1697 -2967.1463 15.918137 -2965.3746 16.985916 0
4700 312.27329 1831.682 -2974.1732 -2967.1463 15.918137 -2965.3746 16.985916 0
4800 307.61066 -1476.0019 -2974.2885 -2967.4397 15.645834 -2965.9619 16.752214 0
4900 305.73489 1303.4848 -2974.5506 -2967.4397 15.645834 -2965.9619 16.752214 0
5000 309.3774 -1574.6812 -2974.8687 -2967.7249 15.392787 -2966.4348 16.484219 0
5100 304.8602 2679.7476 -2975.3082 -2967.7249 15.392787 -2966.4348 16.484219 0
5200 297.54226 -5008.0905 -2975.7443 -2969.5904 13.211657 -2966.8208 16.201471 0
5300 306.18872 4840.4175 -2976.324 -2969.5904 13.211657 -2966.8208 16.201471 0
5400 299.57661 -2513.1706 -2976.8842 -2971.2774 11.099846 -2967.1463 15.918137 0
5500 302.30844 1301.3525 -2977.4539 -2971.2774 11.099846 -2967.1463 15.918137 0
5600 302.11038 -760.79712 -2977.9764 -2972.7712 9.1381778 -2967.4397 15.645834 0
5700 294.49825 718.67318 -2978.4584 -2972.7712 9.1381778 -2967.4397 15.645834 0
5800 305.97636 -478.64224 -2978.8638 -2974.0628 7.3929182 -2967.7249 15.392787 0
5900 291.93868 -419.74179 -2979.2292 -2974.0628 7.3929182 -2967.7249 15.392787 0
6000 289.50667 859.85085 -2979.5018 -2975.1575 5.8837236 -2969.5904 13.211657 0
6100 305.70118 -933.35917 -2979.6877 -2975.1575 5.8837236 -2969.5904 13.211657 0
6200 284.37805 1526.0707 -2979.806 -2976.062 4.6281363 -2971.2774 11.099846 0
6300 291.08863 -2156.6708 -2979.8064 -2976.062 4.6281363 -2971.2774 11.099846 0
6400 295.99073 2819.8245 -2979.7378 -2976.7827 3.6358684 -2972.7712 9.1381778 0
6500 298.06769 -3396.3504 -2979.5428 -2976.7827 3.6358684 -2972.7712 9.1381778 0
6600 301.78514 5496.6525 -2979.2768 -2977.3261 2.9112079 -2974.0628 7.3929182 0
6700 290.80665 -5229.4989 -2978.9177 -2977.3261 2.9112079 -2974.0628 7.3929182 0
6800 296.75761 2401.7807 -2978.5996 -2977.7014 2.4473856 -2975.1575 5.8837236 0
6900 295.77553 -1521.6269 -2978.1619 -2977.7014 2.4473856 -2975.1575 5.8837236 0
7000 303.59015 1530.7255 -2977.7097 -2977.9176 2.2219164 -2976.062 4.6281363 0
7100 297.51038 -3016.4426 -2977.2025 -2977.9176 2.2219164 -2976.062 4.6281363 0
7200 293.53789 2705.9808 -2976.7651 -2977.9894 2.1638143 -2976.7827 3.6358684 0
7300 301.78809 -1042.1076 -2976.3388 -2977.9894 2.1638143 -2976.7827 3.6358684 0
7400 307.50053 214.56923 -2975.9581 -2977.9394 2.1852009 -2977.3261 2.9112079 0
7500 301.98985 281.86495 -2975.6146 -2977.9394 2.1852009 -2977.3261 2.9112079 0
7600 318.37347 -1145.7795 -2975.3473 -2977.7949 2.2136707 -2977.7014 2.4473856 0
7700 314.94512 4536.9887 -2975.1351 -2977.7949 2.2136707 -2977.7014 2.4473856 0
7800 312.91485 -2980.6408 -2975.0156 -2977.5818 2.2038198 -2977.9176 2.2219164 0
7900 310.06854 2244.3877 -2975.0094 -2977.5818 2.2038198 -2977.9176 2.2219164 0
8000 308.55007 -2427.1464 -2975.0491 -2977.3378 2.1348358 -2977.9894 2.1638143 0
8100 323.02796 3187.4728 -2975.2081 -2977.3378 2.1348358 -2977.9894 2.1638143 0
8200 327.05029 -6447.7875 -2975.3162 -2977.0986 2.0196599 -2977.9394 2.1852009 0
8300 311.194 4273.1174 -2975.7217 -2977.0986 2.0196599 -2977.9394 2.1852009 0
8400 290.61931 -2301.019 -2976.0963 -2976.8989 1.8918948 -2977.7949 2.2136707 1
8500 314.00559 1966.1297 -2976.5206 -2976.8989 1.8918948 -2977.7949 2.2136707 1
8600 288.26541 -1608.4524 -2976.9304 -2976.7685 1.7971228 -2977.5818 2.2038198 1
8700 298.92083 1353.9988 -2977.355 -2976.7685 1.7971228 -2977.5818 2.2038198 1
8800 299.97274 -638.68301 -2977.766 -2976.722 1.7650747 -2977.3378 2.1348358 1
8900 300.66443 -279.62514 -2978.1476 -2976.722 1.7650747 -2977.3378 2.1348358 1
Fix halt condition for fix-id 3 met on step 9000 with value 1 (src/fix_halt.cpp:310)
9000 290.44715 489.06352 -2978.4892 -2976.7631 1.7846181 -2977.0986 2.0196599 1
Loop time of 14.7347 on 4 procs for 9000 steps with 864 atoms
Performance: 105.547 ns/day, 0.227 hours/ns, 610.804 timesteps/s, 527.735 katom-step/s
92.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.565 | 11.474 | 12.015 | 16.1 | 77.87
Neigh | 0.0020313 | 0.0020966 | 0.002163 | 0.1 | 0.01
Comm | 2.008 | 2.5374 | 3.4278 | 33.5 | 17.22
Output | 0.0030284 | 0.0036299 | 0.0051776 | 1.5 | 0.02
Modify | 0.42442 | 0.43307 | 0.44329 | 1.0 | 2.94
Other | | 0.2849 | | | 1.93
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: 0:00:14

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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 5 200 100 v_toteng mean stddev variance skew kurtosis
thermo_style custom step temp press etotal f_2[*]
thermo 100
run 10000
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 Temp Press TotEng f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 512.04214 -124.66263 -2928.6 -2927.1688 1.6797138 2.8214386 2.5218138 6.164012
200 479.34328 -136.26635 -2931.3905 -2928.6374 1.9791406 3.9169976 1.3377745 3.2426285
300 480.05298 128.92946 -2933.9233 -2929.9825 2.5401119 6.4521682 0.66415393 0.77130236
400 471.83641 -29.253334 -2936.8631 -2931.346 3.2640831 10.654239 0.29075579 -0.26904542
500 456.96309 -274.69336 -2939.9081 -2932.7721 4.1077082 16.873267 0.094954709 -0.72240572
600 450.32413 14.606227 -2942.973 -2934.2328 4.9928765 24.928816 0.0090731063 -0.93757177
700 431.71192 -45.641261 -2946.006 -2935.7111 5.8871117 34.658084 -0.024573652 -1.0540107
800 436.4217 589.91981 -2948.8885 -2937.1871 6.762411 45.730202 -0.028553126 -1.1275153
900 407.84688 -3728.1499 -2951.6643 -2938.652 7.6129868 57.957569 -0.020186137 -1.172618
1000 401.69178 6695.3653 -2954.2959 -2940.0921 8.423174 70.949861 -0.0018224075 -1.2051609
1100 370.87469 -2294.843 -2956.9413 -2942.9469 8.384346 70.297257 0.016964628 -1.2643199
1200 375.15562 704.6568 -2959.3841 -2945.7589 8.3201293 69.224551 0.070500644 -1.2400262
1300 371.09077 -493.04016 -2961.6803 -2948.5516 8.1425118 66.300499 0.11183042 -1.2099873
1400 365.88512 490.98174 -2963.8365 -2951.2897 7.8673969 61.895934 0.13639588 -1.198071
1500 358.42655 -218.94911 -2965.8652 -2953.9337 7.5491659 56.989906 0.15564307 -1.1896984
1600 329.08402 56.411923 -2967.7662 -2956.467 7.2016413 51.863637 0.17198437 -1.186472
1700 317.74207 1192.918 -2969.557 -2958.8765 6.8379658 46.757776 0.19041811 -1.1812241
1800 331.98966 -2205.7213 -2971.1465 -2961.1601 6.4614065 41.749774 0.20925197 -1.1714131
1900 330.96814 1401.3066 -2972.6923 -2963.3191 6.0867317 37.048302 0.22552163 -1.1523125
2000 315.41816 -909.41909 -2974.0785 -2965.3567 5.7020261 32.513101 0.2328316 -1.1454375
2100 320.4269 1226.2006 -2975.3676 -2967.2609 5.3260556 28.366869 0.24130517 -1.1432352
2200 302.88235 -1238.8052 -2976.5099 -2969.0355 4.9584282 24.58601 0.25200271 -1.141699
2300 300.4349 2667.202 -2977.5329 -2970.6815 4.5986371 21.147463 0.26764984 -1.1380521
2400 292.94691 -5532.1854 -2978.3724 -2972.201 4.2403749 17.980779 0.28797864 -1.1357902
2500 286.12064 4647.3841 -2979.2217 -2973.5946 3.8875889 15.113348 0.31556585 -1.1249025
2600 290.74305 -1950.526 -2979.9142 -2974.8686 3.5422986 12.547879 0.34719546 -1.0987558
2700 281.51347 937.60472 -2980.4808 -2976.0235 3.1955646 10.211633 0.38268676 -1.0664838
2800 279.71836 -801.62498 -2980.8899 -2977.0588 2.844105 8.0889331 0.41930147 -1.0460672
2900 277.41241 609.21495 -2981.1721 -2977.9673 2.4956133 6.2280855 0.47337432 -1.0140054
3000 281.31161 -760.27203 -2981.3003 -2978.7489 2.1466012 4.6078967 0.55325134 -0.95161956
3100 284.72904 315.53038 -2981.297 -2979.4023 1.7929581 3.2146986 0.66481771 -0.84726207
3200 278.39445 516.25074 -2981.1224 -2979.9226 1.4369984 2.0649644 0.82583409 -0.63830994
3300 294.46998 -655.06212 -2980.8266 -2980.3134 1.0905211 1.1892364 1.0357766 -0.22841943
3400 290.04647 788.30424 -2980.3963 -2980.5732 0.77030961 0.59337689 1.1867647 0.34447355
3500 283.218 -844.33188 -2979.8504 -2980.6995 0.54590076 0.29800764 0.78163948 -0.42619888
3600 288.76031 1339.2734 -2979.2382 -2980.6921 0.56032295 0.31396181 0.83603869 -0.30853278
3700 289.44519 -3015.7161 -2978.5394 -2980.5581 0.77708069 0.60385439 1.0796997 -0.022962365
3800 309.04206 5579.3265 -2977.8282 -2980.3052 1.0531468 1.1091181 0.890018 -0.56034495
3900 309.34588 -4255.5213 -2977.1281 -2979.9487 1.3153981 1.7302721 0.65242676 -0.95498589
4000 305.79444 2358.1383 -2976.5251 -2979.5068 1.5325477 2.3487025 0.44420123 -1.1839975
4100 309.12957 -1401.6484 -2975.9173 -2978.9985 1.6923829 2.86416 0.26850538 -1.3006942
4200 309.41928 1180.4111 -2975.3857 -2978.4446 1.7941259 3.2188877 0.11443933 -1.3365167
4300 299.88949 -1549.6591 -2974.927 -2977.8616 1.8268192 3.3372683 -0.018659059 -1.3293426
4400 319.09918 1937.7006 -2974.5598 -2977.273 1.7942266 3.219249 -0.13743367 -1.2958767
4500 326.48719 -1489.2073 -2974.311 -2976.7017 1.7042328 2.9044096 -0.25309558 -1.2385503
4600 310.93392 37.586899 -2974.1959 -2976.1697 1.5590672 2.4306905 -0.3757949 -1.1641151
4700 314.28994 317.12347 -2974.1763 -2975.6978 1.3661244 1.8662958 -0.51792367 -1.0609001
4800 309.88756 -698.72705 -2974.2892 -2975.3021 1.1422822 1.3048085 -0.69587053 -0.87319738
4900 309.53444 962.42921 -2974.5261 -2974.9944 0.89961859 0.80931361 -0.91892105 -0.49661907
5000 316.06666 -1869.3275 -2974.8492 -2974.7804 0.65817496 0.43319428 -1.0974595 0.048447651
5100 304.82485 4042.6797 -2975.2715 -2974.6661 0.47073268 0.22158926 -0.82059377 -0.31531887
5200 307.75342 -5058.4814 -2975.7195 -2974.6547 0.44733518 0.20010876 -0.68956594 -0.65171579
5300 298.83511 3096.4566 -2976.3329 -2974.7467 0.60599527 0.36723026 -1.0652601 0.032591262
5400 296.85413 -1929.1654 -2976.8797 -2974.9367 0.82832935 0.68612952 -0.91576774 -0.50322222
5500 295.88343 1449.3005 -2977.4488 -2975.215 1.044317 1.090598 -0.67574925 -0.92510515
5600 305.59328 -1504.0321 -2977.9573 -2975.5653 1.2243609 1.4990595 -0.46160433 -1.1708115
5700 293.40683 2579.0134 -2978.4364 -2975.97 1.3577316 1.843435 -0.27746111 -1.2993802
5800 297.93644 -2742.705 -2978.8276 -2976.411 1.4332742 2.054275 -0.11245859 -1.3584974
5900 290.39408 1189.4042 -2979.2224 -2976.8733 1.4576633 2.1247823 0.030209056 -1.3466833
6000 293.73148 -232.54292 -2979.503 -2977.3408 1.4300816 2.0451335 0.15663025 -1.2965878
6100 292.04933 -168.30971 -2979.6898 -2977.7936 1.3523929 1.8289665 0.28027258 -1.2214523
6200 299.23747 839.17828 -2979.7883 -2978.2154 1.2284868 1.5091798 0.40149929 -1.1382373
6300 294.92201 -1597.9426 -2979.7975 -2978.589 1.072002 1.1491883 0.53769821 -1.0262094
6400 291.7185 3411.2916 -2979.6978 -2978.9013 0.89165749 0.79505308 0.70748196 -0.83601078
6500 285.34227 -4280.7968 -2979.4874 -2979.1407 0.69727552 0.48619315 0.91500724 -0.4890805
6600 295.53838 2138.7496 -2979.2799 -2979.3084 0.50938648 0.25947459 1.0827149 -0.0043801382
6700 288.54718 -1818.7662 -2978.9379 -2979.3979 0.3658125 0.13381879 0.85573626 -0.20104653
6800 290.41342 2175.3559 -2978.543 -2979.4085 0.34439248 0.11860618 0.70989241 -0.55138716
6900 296.34456 -4782.08 -2978.0362 -2979.3362 0.47081063 0.22166265 1.1051059 0.16381282
7000 303.74314 5905.219 -2977.577 -2979.182 0.65635739 0.43080502 0.97456755 -0.34269231
7100 303.90284 -3291.7627 -2977.1308 -2978.9595 0.83412944 0.69577192 0.71973637 -0.85687335
7200 296.13966 2209.574 -2976.7001 -2978.6767 0.98885368 0.97783159 0.50554418 -1.124705
7300 295.79694 -1609.1898 -2976.2816 -2978.3446 1.1093729 1.2307082 0.32952142 -1.2657581
7400 306.53289 988.50902 -2975.8992 -2977.977 1.1910167 1.4185209 0.17936365 -1.331845
7500 303.89992 -631.22838 -2975.5597 -2977.5901 1.2352698 1.5258915 0.033110856 -1.3362459
7600 303.83684 -348.48744 -2975.3074 -2977.1915 1.2312686 1.5160224 -0.094817417 -1.3063491
7700 309.67313 1350.9414 -2975.1279 -2976.7984 1.1829266 1.3993154 -0.21343083 -1.2573517
7800 309.74314 -1182.8905 -2975.0174 -2976.4294 1.0913021 1.1909402 -0.3401118 -1.198459
7900 309.42429 999.08033 -2975.0089 -2976.0995 0.96393318 0.92916717 -0.48456322 -1.1149956
8000 315.51872 -1337.8894 -2975.0791 -2975.822 0.81535467 0.66480324 -0.67906685 -0.90499956
8100 314.80533 2392.3424 -2975.25 -2975.6019 0.64582022 0.41708376 -0.90521871 -0.5328796
8200 303.80236 -3224.5976 -2975.4744 -2975.4481 0.47449379 0.22514436 -1.0884377 -0.00018150871
8300 295.0505 3296.6912 -2975.8196 -2975.3667 0.34164698 0.11672266 -0.83269043 -0.31809119
8400 302.4154 -3314.5096 -2976.1586 -2975.3606 0.32904826 0.10827276 -0.73500255 -0.57861735
8500 300.95491 2971.1291 -2976.5859 -2975.4288 0.44584452 0.19877734 -1.0760301 0.014924509
8600 301.68919 -2297.6673 -2976.9953 -2975.5682 0.60852433 0.37030186 -0.91802963 -0.5143582
8700 291.21002 1477.5703 -2977.4323 -2975.7733 0.76843347 0.59048999 -0.68059043 -0.92051715
8800 305.87126 -1085.459 -2977.8247 -2976.0327 0.90672273 0.82214612 -0.47413162 -1.1492716
8900 296.17567 777.95805 -2978.2081 -2976.3349 1.0129061 1.0259789 -0.29734681 -1.271416
9000 295.71917 -425.00708 -2978.5264 -2976.6672 1.0786137 1.1634075 -0.14055755 -1.3302079
9100 296.85578 -533.46289 -2978.8197 -2977.0152 1.1000855 1.2101882 0.0045950751 -1.3434868
9200 293.949 605.27065 -2979.0349 -2977.3702 1.0854405 1.1781811 0.123965 -1.3093197
9300 289.11704 -896.44753 -2979.1981 -2977.7166 1.0353526 1.071955 0.23898813 -1.2558296
9400 285.34521 1181.7542 -2979.2879 -2978.0404 0.95298596 0.90818224 0.36461645 -1.1736585
9500 296.17714 -2503.9848 -2979.2668 -2978.3301 0.8407037 0.70678272 0.50841734 -1.0540275
9600 296.43744 4912.6395 -2979.1829 -2978.5736 0.70352404 0.49494608 0.68312042 -0.86335848
9700 288.63317 -3935.8902 -2979.0381 -2978.7635 0.55322477 0.30605764 0.88509388 -0.54108379
9800 296.27133 1365.4106 -2978.8723 -2978.8969 0.40665162 0.16536554 1.0460992 -0.092552905
9900 299.37628 -1267.2668 -2978.5934 -2978.9673 0.29467695 0.086834506 0.80391757 -0.38307943
10000 296.60645 1950.1018 -2978.2725 -2978.9739 0.28169006 0.079349287 0.70171659 -0.62026504
Loop time of 47.4814 on 1 procs for 10000 steps with 864 atoms
Performance: 36.393 ns/day, 0.659 hours/ns, 210.609 timesteps/s, 181.966 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 46.299 | 46.299 | 46.299 | 0.0 | 97.51
Neigh | 0.010908 | 0.010908 | 0.010908 | 0.0 | 0.02
Comm | 0.29643 | 0.29643 | 0.29643 | 0.0 | 0.62
Output | 0.0090682 | 0.0090682 | 0.0090682 | 0.0 | 0.02
Modify | 0.7406 | 0.7406 | 0.7406 | 0.0 | 1.56
Other | | 0.1254 | | | 0.26
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: 0:00:47

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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 = 0.010 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 5 200 100 v_toteng mean stddev variance skew kurtosis
thermo_style custom step temp press etotal f_2[*]
thermo 100
run 10000
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 Temp Press TotEng f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 492.38014 -134.33622 -2928.6874 -2927.2291 1.7092959 2.9216925 2.5081594 6.099781
200 484.82396 -214.26318 -2931.4603 -2928.71 2.0003214 4.0012857 1.3645049 3.3103886
300 476.69743 15.78678 -2934.0022 -2930.0515 2.5470901 6.4876682 0.6954232 0.86102766
400 482.51415 141.67184 -2936.9347 -2931.4152 3.2681043 10.680505 0.30641098 -0.22337036
500 455.45411 2.4424602 -2939.9649 -2932.8397 4.1076295 16.87262 0.10483325 -0.6997127
600 455.20054 -6.8170934 -2943.0454 -2934.2947 4.9842257 24.842506 0.018003661 -0.92490336
700 429.81168 -75.812923 -2946.0438 -2935.7704 5.8766819 34.53539 -0.019539731 -1.0444564
800 428.22097 604.18705 -2948.9285 -2937.2449 6.7522047 45.592268 -0.026384526 -1.1194924
900 399.10914 -3622.6904 -2951.7252 -2938.7094 7.6043904 57.826753 -0.019997758 -1.1658244
1000 394.62543 7905.9041 -2954.2925 -2940.15 8.4168551 70.84345 -0.0026187371 -1.2004009
1100 404.27007 -2565.5508 -2956.9736 -2943.0009 8.3722389 70.094384 0.015852037 -1.2665587
1200 368.47178 741.43707 -2959.4264 -2945.8091 8.3127243 69.101386 0.069744698 -1.2412651
1300 360.91266 -267.08372 -2961.69 -2948.5981 8.1334656 66.153263 0.1116445 -1.2129213
1400 356.74405 158.09093 -2963.8501 -2951.3302 7.8574973 61.740264 0.13825232 -1.1999727
1500 335.45696 -71.007783 -2965.8817 -2953.9689 7.5384846 56.82875 0.15915227 -1.1877331
1600 331.01199 -454.90004 -2967.7708 -2956.5 7.1862592 51.642321 0.17403957 -1.1840985
1700 329.223 2428.4284 -2969.5452 -2958.9073 6.8228029 46.55064 0.19027454 -1.1778276
1800 327.61481 -4757.648 -2971.1105 -2961.1863 6.4445074 41.531675 0.20819854 -1.1712539
1900 318.18741 2226.7765 -2972.6906 -2963.3396 6.0703365 36.848986 0.22378928 -1.1556732
2000 308.79313 -1089.8603 -2974.0899 -2965.3712 5.6913723 32.391718 0.23279863 -1.1445916
2100 303.32047 757.53534 -2975.3597 -2967.2741 5.3153102 28.252523 0.23857925 -1.1465858
2200 307.41102 -837.97246 -2976.4966 -2969.0433 4.9515105 24.517456 0.25216298 -1.1426077
2300 303.01088 1618.29 -2977.5454 -2970.6862 4.593227 21.097734 0.26914071 -1.1356519
2400 297.59385 -3233.8282 -2978.4064 -2972.2049 4.235209 17.936995 0.28804295 -1.1332908
2500 288.72232 5209.2099 -2979.1999 -2973.5963 3.8804647 15.058006 0.31533205 -1.1258312
2600 298.92201 -2193.618 -2979.8873 -2974.8649 3.5301507 12.461964 0.34927897 -1.1048024
2700 282.61818 765.88178 -2980.4563 -2976.0148 3.1852407 10.145758 0.3879755 -1.0655899
2800 273.63104 -389.49749 -2980.8636 -2977.0468 2.8322558 8.021673 0.4259426 -1.0370247
2900 274.12166 -9.2552992 -2981.1421 -2977.9525 2.4816703 6.1586877 0.47721359 -1.0061337
3000 279.43592 212.25445 -2981.2716 -2978.7309 2.1328425 4.5490171 0.5532015 -0.94983292
3100 291.10071 -1139.205 -2981.2475 -2979.3812 1.7828537 3.1785674 0.66452451 -0.83906914
3200 281.53171 3124.6411 -2981.0818 -2979.9003 1.4287164 2.0412304 0.81952022 -0.6386061
3300 277.0223 -2795.9494 -2980.7825 -2980.287 1.0830229 1.1729385 1.0186688 -0.26502454
3400 284.8443 1587.8876 -2980.3701 -2980.5435 0.76893619 0.59126286 1.1646672 0.27529682
3500 281.19 -1143.0785 -2979.8374 -2980.6693 0.54860209 0.30096426 0.79069857 -0.36626891
3600 296.58287 1156.4706 -2979.2182 -2980.6646 0.55745952 0.31076112 0.81914175 -0.31895116
3700 297.24517 -1888.4993 -2978.5352 -2980.5318 0.77195451 0.59591377 1.0713124 -0.027796216
3800 290.81586 3843.3483 -2977.8509 -2980.2819 1.0444771 1.0909324 0.88270245 -0.57339499
3900 300.39456 -5584.8386 -2977.0837 -2979.9273 1.3073719 1.7092212 0.65444496 -0.94023014
4000 306.15811 3310.0105 -2976.5086 -2979.4859 1.5269967 2.3317191 0.45120199 -1.1665402
4100 295.907 -1475.0458 -2975.9096 -2978.9779 1.6878413 2.8488082 0.27738537 -1.2909517
4200 322.70162 933.76586 -2975.3867 -2978.425 1.7872637 3.1943116 0.12322364 -1.3421568
4300 306.69631 -512.7048 -2974.9324 -2977.8465 1.8221493 3.3202281 -0.016769435 -1.3380921
4400 309.23776 226.77219 -2974.5791 -2977.2621 1.788532 3.1988469 -0.14279249 -1.3044784
4500 313.15783 508.29785 -2974.3263 -2976.6947 1.6959722 2.8763217 -0.26351575 -1.2425552
4600 316.26151 -2043.7571 -2974.1697 -2976.1635 1.5525328 2.4103582 -0.38443906 -1.156175
4700 312.27329 1831.682 -2974.1732 -2975.6917 1.3614048 1.8534231 -0.52504872 -1.0383081
4800 307.61066 -1476.0019 -2974.2885 -2975.296 1.1354139 1.2891647 -0.69734331 -0.84719677
4900 305.73489 1303.4848 -2974.5506 -2974.9905 0.8913743 0.79454814 -0.90609876 -0.50216921
5000 309.3774 -1574.6812 -2974.8687 -2974.7812 0.65272109 0.42604482 -1.0613188 0.00291608
5100 304.8602 2679.7476 -2975.3082 -2974.6718 0.4727141 0.22345862 -0.75321909 -0.42028824
5200 297.54226 -5008.0905 -2975.7443 -2974.6646 0.45797515 0.20974124 -0.66557441 -0.64583954
5300 306.18872 4840.4175 -2976.324 -2974.7575 0.61348896 0.3763687 -1.0084709 -0.10258503
5400 299.57661 -2513.1706 -2976.8842 -2974.9472 0.83376011 0.69515592 -0.88189118 -0.55222188
5500 302.30844 1301.3525 -2977.4539 -2975.2244 1.0486412 1.0996484 -0.65075151 -0.94687541
5600 302.11038 -760.79712 -2977.9764 -2975.5765 1.2259535 1.502962 -0.44510538 -1.1709493
5700 294.49825 718.67318 -2978.4584 -2975.9844 1.357155 1.8418697 -0.27309672 -1.2848748
5800 305.97636 -478.64224 -2978.8638 -2976.429 1.4331646 2.0539608 -0.1197893 -1.3417863
5900 291.93868 -419.74179 -2979.2292 -2976.8905 1.4535887 2.1129201 0.024018983 -1.349863
6000 289.50667 859.85085 -2979.5018 -2977.3557 1.4249736 2.0305497 0.15271261 -1.3095465
6100 305.70118 -933.35917 -2979.6877 -2977.8064 1.3480601 1.8172659 0.27785119 -1.2402584
6200 284.37805 1526.0707 -2979.806 -2978.2265 1.2296781 1.5121082 0.40681415 -1.1355005
6300 291.08863 -2156.6708 -2979.8064 -2978.6017 1.0733214 1.1520189 0.54137333 -1.0156432
6400 295.99073 2819.8245 -2979.7378 -2978.9165 0.8941904 0.79957647 0.7073501 -0.82385123
6500 298.06769 -3396.3504 -2979.5428 -2979.1626 0.70228297 0.49320137 0.91043588 -0.48653641
6600 301.78514 5496.6525 -2979.2768 -2979.3329 0.51276653 0.26292952 1.0681056 -0.036293782
6700 290.80665 -5229.4989 -2978.9177 -2979.4217 0.36990055 0.13682642 0.81466085 -0.37332419
6800 296.75761 2401.7807 -2978.5996 -2979.4338 0.34589164 0.11964103 0.65253856 -0.7737558
6900 295.77553 -1521.6269 -2978.1619 -2979.3685 0.46007271 0.21166689 1.0427138 -0.013014477
7000 303.59015 1530.7255 -2977.7097 -2979.225 0.63320287 0.40094588 0.93012255 -0.45527217
7100 297.51038 -3016.4426 -2977.2025 -2979.0103 0.81101521 0.65774567 0.7114444 -0.84465178
7200 293.53789 2705.9808 -2976.7651 -2978.7294 0.97512025 0.95085951 0.52979295 -1.0479526
7300 301.78809 -1042.1076 -2976.3388 -2978.3998 1.1024575 1.2154126 0.35564664 -1.2137023
7400 307.50053 214.56923 -2975.9581 -2978.0341 1.188001 1.4113463 0.20025025 -1.3077784
7500 301.98985 281.86495 -2975.6146 -2977.6451 1.2301918 1.5133718 0.063886193 -1.3465506
7600 318.37347 -1145.7795 -2975.3473 -2977.2486 1.2295055 1.5116837 -0.066939137 -1.3475567
7700 314.94512 4536.9887 -2975.1351 -2976.8564 1.1948121 1.427576 -0.19450637 -1.2864658
7800 312.91485 -2980.6408 -2975.0156 -2976.4828 1.1134406 1.2397499 -0.32749726 -1.207718
7900 310.06854 2244.3877 -2975.0094 -2976.1462 0.99080702 0.98169854 -0.48336959 -1.0840695
8000 308.55007 -2427.1464 -2975.0491 -2975.8566 0.83800849 0.70225823 -0.65822117 -0.89212512
8100 323.02796 3187.4728 -2975.2081 -2975.6251 0.66510054 0.44235872 -0.84857729 -0.62984027
8200 327.05029 -6447.7875 -2975.3162 -2975.4608 0.49730291 0.24731018 -1.0534735 -0.14095413
8300 311.194 4273.1174 -2975.7217 -2975.3642 0.35491458 0.12596436 -0.95967595 -0.04445204
8400 290.61931 -2301.019 -2976.0963 -2975.3446 0.31530296 0.09941596 -0.69056625 -0.72257435
8500 314.00559 1966.1297 -2976.5206 -2975.3995 0.41659574 0.17355201 -1.1134124 0.18107632
8600 288.26541 -1608.4524 -2976.9304 -2975.526 0.57968749 0.33603759 -1.0014591 -0.34698354
8700 298.92083 1353.9988 -2977.355 -2975.7203 0.74176087 0.55020919 -0.74109062 -0.86227705
8800 299.97274 -638.68301 -2977.766 -2975.9682 0.87950613 0.77353104 -0.50839929 -1.1555064
8900 300.66443 -279.62514 -2978.1476 -2976.262 0.99526406 0.99055054 -0.33059914 -1.261881
9000 290.44715 489.06352 -2978.4892 -2976.5918 1.0763797 1.1585932 -0.17871557 -1.3082755
9100 289.06733 -1063.4482 -2978.784 -2976.943 1.1174524 1.2486999 -0.037767225 -1.3120851
9200 297.63931 2664.6535 -2979.0202 -2977.3033 1.1127042 1.2381106 0.090936095 -1.2913777
9300 297.9983 -4684.428 -2979.1316 -2977.6563 1.0596342 1.1228247 0.20756305 -1.2867214
9400 285.14009 2779.1548 -2979.2804 -2977.9868 0.98034602 0.96107833 0.33668495 -1.2294268
9500 284.11569 -2437.5003 -2979.2918 -2978.2852 0.87286876 0.76189987 0.48407552 -1.1274969
9600 291.97193 2772.1396 -2979.2473 -2978.5402 0.74294711 0.55197041 0.67450455 -0.91152584
9700 292.59563 -3615.4496 -2979.0801 -2978.7442 0.59448857 0.35341666 0.91630006 -0.47180257
9800 296.1785 4869.2744 -2978.8849 -2978.891 0.43463281 0.18890568 1.1020846 0.093881572
9900 298.44745 -3587.7391 -2978.5978 -2978.9712 0.30680426 0.094128854 0.8532075 -0.19634913
10000 297.99863 1312.5643 -2978.3205 -2978.9854 0.27829395 0.077447522 0.60818263 -0.79004935
Loop time of 15.3108 on 4 procs for 10000 steps with 864 atoms
Performance: 112.862 ns/day, 0.213 hours/ns, 653.136 timesteps/s, 564.309 katom-step/s
92.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.428 | 12.158 | 12.621 | 13.0 | 79.41
Neigh | 0.0019158 | 0.0020708 | 0.002163 | 0.2 | 0.01
Comm | 1.936 | 2.3948 | 3.0967 | 28.3 | 15.64
Output | 0.0026067 | 0.0037308 | 0.0066123 | 2.7 | 0.02
Modify | 0.44688 | 0.45929 | 0.47131 | 1.6 | 3.00
Other | | 0.2928 | | | 1.91
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: 0:00:15

178
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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
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@ -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

635
src/EXTRA-FIX/fix_ave_moments.cpp Normal file
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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Sebastian Huetter (OvGU)
------------------------------------------------------------------------- */
#include "fix_ave_moments.h"
#include "arg_info.h"
#include "compute.h"
#include "error.h"
#include "input.h"
#include "math_special.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
#include "variable.h"
#include <algorithm>
using namespace LAMMPS_NS;
using namespace FixConst;
using MathSpecial::square;
using MathSpecial::cube;
enum { MEAN, STDDEV, VARIANCE, SKEW, KURTOSIS };
/* ---------------------------------------------------------------------- */
FixAveMoments::FixAveMoments(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), nvalues(0), result_list(nullptr), window_list(nullptr)
{
// this fix's data is always accessible (but might be meaningless)
global_freq = 1;
dynamic_group_allow = 1;
time_depend = 1;
// EXAMPLE:
// fix ID group-ID ave/moments Nevery Nrepeat Nfreq value1 ... valueN moment1 ... momentM keyword value ...
// the first six arguments are fixed & need at least one input and moment
const int nfixedargs = 6;
if (narg < nfixedargs + 2) utils::missing_cmd_args(FLERR, "fix ave/moments", error);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
// scan values to count them
nvalues = 0;
// first input name is position after the fixed args
int iarg = nfixedargs;
while (iarg < narg) {
if (utils::strmatch(arg[iarg],"^[cfv]_")) {
nvalues++;
iarg++;
} else break;
}
if (nvalues == 0)
error->all(FLERR, nfixedargs,
"No values from computes, fixes, or variables used in fix ave/moments command");
// next, the moments
iarg = consume_moments(iarg, narg, arg);
if (moments.empty())
error->all(FLERR, nfixedargs,
"No values from computes, fixes, or variables used in fix ave/moments command");
// parse optional keywords which must follow the data
options(iarg,narg,arg);
// expand args if any have wildcard character "*"
// this can reset nvalues
int expand = 0;
char **earg;
int *amap = nullptr;
nvalues = utils::expand_args(FLERR, nvalues, &arg[nfixedargs], /* mode=scalar */ 0, earg, lmp, &amap);
if (earg != &arg[nfixedargs]) expand = 1;
arg = earg;
// parse values
values.clear();
for (int i = 0; i < nvalues; i++) {
ArgInfo argi(arg[i]);
value_t val;
val.keyword = arg[i];
val.which = argi.get_type();
val.argindex = argi.get_index1();
val.iarg = (expand ? amap[i] : i) + nfixedargs;
val.varlen = 0;
val.id = argi.get_name();
val.val.c = nullptr;
if ((val.which == ArgInfo::NONE) || (val.which == ArgInfo::UNKNOWN) || (argi.get_dim() > 1))
error->all(FLERR, val.iarg, "Invalid fix ave/moments argument: {}", arg[i]);
values.push_back(val);
}
if (nvalues != (int)values.size())
error->all(FLERR, Error::NOPOINTER,
"Could not parse value data consistently for fix ave/moments");
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0) error->all(FLERR, 3, "Illegal fix ave/moments nevery value: {}", nevery);
if (nrepeat <= 0) error->all(FLERR, 4, "Illegal fix ave/moments nrepeat value: {}", nrepeat);
if (nfreq <= 0) error->all(FLERR, 5, "Illegal fix ave/moments nfreq value: {}", nfreq);
for (auto &val : values) {
switch (val.which) {
case ArgInfo::COMPUTE:
val.val.c = modify->get_compute_by_id(val.id);
if (!val.val.c)
error->all(FLERR, val.iarg, "Compute ID {} for fix ave/moments does not exist", val.id);
if (val.argindex == 0 && (val.val.c->scalar_flag == 0))
error->all(FLERR, val.iarg, "Fix ave/moments compute {} does not calculate a scalar", val.id);
if (val.argindex && (val.val.c->vector_flag == 0))
error->all(FLERR, val.iarg, "Fix ave/moments compute {} does not calculate a vector", val.id);
if (val.argindex && (val.argindex > val.val.c->size_vector) &&
(val.val.c->size_vector_variable == 0))
error->all(FLERR, val.iarg, "Fix ave/moments compute {} vector is accessed out-of-range{}",
val.id, utils::errorurl(20));
if (val.argindex && val.val.c->size_vector_variable) val.varlen = 1;
break;
case ArgInfo::FIX:
val.val.f = modify->get_fix_by_id(val.id);
if (!val.val.f) error->all(FLERR,"Fix ID {} for fix ave/moments does not exist", val.id);
if ((val.argindex == 0) && (val.val.f->scalar_flag == 0))
error->all(FLERR, val.iarg, "Fix ave/moments fix {} does not calculate a scalar", val.id);
if (val.argindex && (val.val.f->vector_flag == 0))
error->all(FLERR, val.iarg, "Fix ave/moments fix {} does not calculate a vector", val.id);
if (val.argindex && (val.val.f->size_vector_variable))
error->all(FLERR, val.iarg, "Fix ave/moments fix {} vector cannot be variable length", val.id);
if (val.argindex && (val.argindex > val.val.f->size_vector))
error->all(FLERR, val.iarg, "Fix ave/moments fix {} vector is accessed out-of-range{}",
val.id, utils::errorurl(20));
if (nevery % val.val.f->global_freq)
error->all(FLERR, val.iarg, "Fix {} for fix ave/moments not computed at compatible time{}",
val.id, utils::errorurl(7));
break;
case ArgInfo::VARIABLE:
int ivariable = input->variable->find(val.id.c_str());
if (ivariable < 0)
error->all(FLERR, val.iarg, "Variable name {} for fix ave/moments does not exist", val.id);
if ((val.argindex == 0) && (input->variable->equalstyle(ivariable) == 0))
error->all(FLERR, val.iarg, "Fix ave/moments variable {} is not equal-style variable", val.id);
if ((val.argindex) && (input->variable->vectorstyle(ivariable) == 0))
error->all(FLERR, val.iarg, "Fix ave/moments variable {} is not vector-style variable",
val.id);
break;
}
}
// if wildcard expansion occurred, free earg memory from expand_args()
// wait to do this until after file comment lines are printed
if (expand) {
for (int i = 0; i < nvalues; i++) delete[] earg[i];
memory->sfree(earg);
memory->sfree(amap);
}
// allocate memory for averaging
window_list = nullptr;
result_list = nullptr;
// one window of nvalues columns and nrepeat rows (=all scalars of one value are consecutive)
memory->create(window_list, nvalues, nrepeat, "ave/moments:window_list");
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < nrepeat; j++)
window_list[i][j] = 0.0;
// this fix produces a global vector and array
vector_flag = 1;
size_vector = nvalues * moments.size();
array_flag = 1;
size_array_rows = size_vector;
size_array_cols = nhistory;
// produce nmoments outputs per value with nhistory depth
memory->create(result_list, nhistory, size_vector, "ave/moments:result_list");
for (int i = 0; i < nhistory; i++)
for (int j = 0; j < size_vector; j++)
result_list[i][j] = 0.0;
// intensive/extensive flags set by compute,fix,variable that produces value
extvector = -1;
extarray = -2;
extlist = new int[size_vector];
int extvalue = 0;
int i = 0;
for (auto &val : values) {
switch (val.which) {
case ArgInfo::COMPUTE:
if (val.argindex == 0) extvalue = val.val.c->extscalar;
else if (val.val.f->extvector >= 0) extvalue = val.val.c->extvector;
else extvalue = val.val.c->extlist[val.argindex-1];
break;
case ArgInfo::FIX:
if (val.argindex == 0) extvalue = val.val.f->extscalar;
else if (val.val.f->extvector >= 0) extvalue = val.val.f->extvector;
else extvalue = val.val.f->extlist[val.argindex-1];
break;
case ArgInfo::VARIABLE:
extvalue = 0;
break;
}
if (extvalue == -1)
error->all(FLERR, Error::NOLASTLINE, "Fix ave/moments cannot set output array "
"intensive/extensive from these inputs");
if (extarray < -1) extarray = extvalue;
else if (extvalue != extarray)
error->all(FLERR, Error::NOLASTLINE, "Fix ave/moments cannot set output array "
"intensive/extensive from these inputs");
for (int j=0; j < (int)moments.size(); j++)
extlist[i + j] = extvalue;
i += moments.size();
}
// initializations
iwindow = window_filled = 0;
iresult = 0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid_comp_next = -1;
nvalid = -1;
setnextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveMoments::~FixAveMoments()
{
values.clear();
moments.clear();
delete[] extlist;
memory->destroy(window_list);
memory->destroy(result_list);
}
/* ---------------------------------------------------------------------- */
int FixAveMoments::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveMoments::init()
{
// update indices/pointers for all computes,fixes,variables
for (auto &val : values) {
switch (val.which) {
case ArgInfo::COMPUTE:
val.val.c = modify->get_compute_by_id(val.id);
if (!val.val.c)
error->all(FLERR, Error::NOLASTLINE, "Compute ID {} for fix ave/moments does not exist",
val.id);
break;
case ArgInfo::FIX:
val.val.f = modify->get_fix_by_id(val.id);
if (!val.val.f)
error->all(FLERR, Error::NOLASTLINE, "Fix ID {} for fix ave/moments does not exist", val.id);
break;
case ArgInfo::VARIABLE:
val.val.v = input->variable->find(val.id.c_str());
if (val.val.v < 0)
error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix ave/moments does not exist",
val.id);
break;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
setnextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveMoments::setup(int /*vflag*/)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveMoments::end_of_step()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
// always take new values
append_values();
// if window boundary reached, do a compute, otherwise just schedule next take
if (ntimestep == nvalid_comp_next) {
update_results();
setnextvalid();
} else {
nvalid += nevery;
}
modify->addstep_compute(nvalid);
}
/* ----------------------------------------------------------------------
return scalar value
------------------------------------------------------------------------- */
double FixAveMoments::compute_scalar()
{
return 0.0;
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixAveMoments::compute_vector(int i)
{
return compute_array(i, 0);
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveMoments::compute_array(int i, int j)
{
if (i >= size_vector) return 0.0;
if (j >= nhistory) return 0.0;
// locate the j'th previous result in the ring buffer, relative to the
// row before iresult (the current insert cursor)
int row = (iresult - 1 - j + nhistory) % nhistory;
return result_list[row][i];
}
/* ----------------------------------------------------------------------
parse moment names
------------------------------------------------------------------------- */
int FixAveMoments::consume_moments(int iarg, int narg, char **arg)
{
moments.clear();
while (iarg < narg) {
if (strcmp(arg[iarg],"mean") == 0)
moments.push_back(MEAN);
else if (strcmp(arg[iarg],"stddev") == 0)
moments.push_back(STDDEV);
else if (strcmp(arg[iarg],"variance") == 0)
moments.push_back(VARIANCE);
else if (strcmp(arg[iarg],"skew") == 0)
moments.push_back(SKEW);
else if (strcmp(arg[iarg],"kurtosis") == 0)
moments.push_back(KURTOSIS);
else
break;
iarg++;
}
return iarg;
}
/* ----------------------------------------------------------------------
parse optional args
------------------------------------------------------------------------- */
void FixAveMoments::options(int iarg, int narg, char **arg)
{
// option defaults
nhistory = 1;
startstep = 0;
// optional args
while (iarg < narg) {
if (strcmp(arg[iarg],"history") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/moments history", error);
nhistory = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nhistory <= 0)
error->all(FLERR, iarg+2, "Illegal ave/moments history argument {}; must be > 0",
nhistory);
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/moments start", error);
startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Unknown fix ave/moments keyword {}", arg[iarg]);
}
}
/* ----------------------------------------------------------------------
return next timestep no earlier than `after`, rounded to next
multiple of freq
------------------------------------------------------------------------- */
bigint next_after(const bigint ts, const bigint after, const int freq)
{
if (ts >= after) return ts;
return ts + ((after - ts) / freq + 1) * freq;
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
this is either a step to take data
or a step to take and compute the values (nfreq multiple)
startstep is lower bound on nfreq multiple
------------------------------------------------------------------------- */
void FixAveMoments::setnextvalid()
{
bigint ntimestep = update->ntimestep;
if (nvalid_comp_next > ntimestep) {
// next window end boundary is still in the future, just increment
nvalid = ntimestep + nevery;
return;
}
// get next window end first
bigint next_comp = (ntimestep/nfreq)*nfreq + nfreq;
nvalid_comp_next = next_after(next_comp, startstep, nfreq);
// from there, calculate the first time we have to take a value
bigint ntake = nvalid_comp_next - static_cast<bigint>(nrepeat-1)*nevery;
nvalid = next_after(ntake, ntimestep, nevery);
}
/* ---------------------------------------------------------------------- */
void FixAveMoments::get_values(std::vector<double>& scalars)
{
// accumulate results of computes,fixes,variables to local copy
int i = 0;
double scalar = 0.0;
for (auto &val : values) {
switch (val.which) {
case ArgInfo::COMPUTE:
// invoke compute if not previously invoked
// ensure no out-of-range access to variable-length compute vector
if (val.argindex == 0) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) {
val.val.c->compute_scalar();
val.val.c->invoked_flag |= Compute::INVOKED_SCALAR;
}
scalar = val.val.c->scalar;
} else {
if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) {
val.val.c->compute_vector();
val.val.c->invoked_flag |= Compute::INVOKED_VECTOR;
}
if (val.varlen && (val.val.c->size_vector < val.argindex)) scalar = 0.0;
else scalar = val.val.c->vector[val.argindex-1];
}
break;
case ArgInfo::FIX:
// access fix fields, guaranteed to be ready
if (val.argindex == 0)
scalar = val.val.f->compute_scalar();
else
scalar = val.val.f->compute_vector(val.argindex-1);
break;
case ArgInfo::VARIABLE:
// evaluate equal-style or vector-style variable
// if index exceeds vector length, use a zero value
// this can be useful if vector length is not known a priori
if (val.argindex == 0)
scalar = input->variable->compute_equal(val.val.v);
else {
double *varvec;
int nvec = input->variable->compute_vector(val.val.v,&varvec);
if (val.argindex > nvec) scalar = 0.0;
else scalar = varvec[val.argindex-1];
}
break;
}
scalars[i] = scalar;
++i;
}
}
/* ---------------------------------------------------------------------- */
void FixAveMoments::append_values()
{
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
std::vector<double> scalars(nvalues);
get_values(scalars);
// transpose for faster access later
for (int i=0; i<nvalues; i++) {
window_list[i][iwindow] = scalars[i];
}
if (++iwindow >= nrepeat) {
window_filled = 1;
iwindow = 0;
}
}
void FixAveMoments::update_results()
{
const int count = window_filled ? nrepeat : iwindow;
// Delay until we can safely do all moments. Avoids branching in the hot loop.
if (count<3) return;
double *result = result_list[iresult];
// zero out previous values
for (int i = 0; i < size_vector; i++)
result[i] = 0.0;
const double inv_n = 1.0 / count;
const double fk2 = (double)count / (count - 1);
const double fk3 = square((double)count) / ((count - 1) * (count - 2));
const double np1_nm3 = (count+1.0)/(count-3.0);
const double _3_nm1_nm3 = 3.0 * (count-1.0)/(count-3.0);
// Each value is a series that can be processed individually
for (int i = 0; i < nvalues; i++) {
const double* series = window_list[i];
// first pass: mean
double mean = 0.0;
for (int j = 0; j<count; j++)
mean += series[j] * inv_n;
// second pass: calculate biased sample moments
double m2 = 0.0;
double m3 = 0.0;
double m4 = 0.0;
for (int j = 0; j<count; j++) {
const double dx = series[j] - mean;
double y = square(dx) * inv_n;
m2 += y;
y *= dx;
m3 += y;
y *= dx;
m4 += y;
}
// obtain unbiased cumulants as defined by Cramér and
// reported i.e. in https://doi.org/10.1111/1467-9884.00122
const double k2 = fk2 * m2;
const double k3 = fk3 * m3;
const double k4 = fk3 * (np1_nm3 * m4 - _3_nm1_nm3 * square(m2));
// corrected sample standard deviation
const double stddev = sqrt(k2);
// adjusted Fisher-Pearson standardized moment coefficient G1
const double G1 = k3 / cube(stddev);
// adjusted Fisher-Pearson standardized moment coefficient G2 (from unbiased cumulant)
const double G2 = k4 / square(k2);
// map to result array, starting at value interleave offset
double* rfirst = &result[i * moments.size()];
for (int j = 0; j < (int)moments.size(); j++) {
switch(moments[j]) {
case MEAN:
rfirst[j] = mean;
break;
case STDDEV:
rfirst[j] = stddev;
break;
case VARIANCE:
rfirst[j] = k2;
break;
case SKEW:
rfirst[j] = G1;
break;
case KURTOSIS:
rfirst[j] = G2;
break;
}
}
}
if (++iresult >= nhistory)
iresult = 0;
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
// clang-format off
FixStyle(ave/moments,FixAveMoments);
// clang-format on
#else
#ifndef LMP_FIX_AVE_MOMENTS_H
#define LMP_FIX_AVE_MOMENTS_H
#include "fix.h"
namespace LAMMPS_NS {
class FixAveMoments : public Fix {
public:
FixAveMoments(class LAMMPS *, int, char **);
~FixAveMoments() override;
int setmask() override;
void init() override;
void setup(int) override;
void end_of_step() override;
double compute_scalar() override;
double compute_vector(int) override;
double compute_array(int, int) override;
private:
struct value_t {
int which; // type of data: COMPUTE, FIX, VARIABLE
int argindex; // 1-based index if data is vector, else 0
int iarg; // argument index in original argument list
int varlen; // 1 if value is from variable-length compute
std::string id; // compute/fix/variable ID
std::string keyword; // column keyword in output
union {
class Compute *c;
class Fix *f;
int v;
} val;
};
std::vector<value_t> values;
std::vector<int> moments;
int nrepeat, nfreq;
int nvalues;
bigint nvalid, nvalid_comp_next;
int startstep;
int nhistory, iresult;
double **result_list;
int iwindow, window_filled;
double **window_list;
int consume_moments(int iarg, int narg, char **arg);
void options(int, int, char **);
void setnextvalid();
void get_values(std::vector<double>& scalars);
void append_values();
void update_results();
};
} // namespace LAMMPS_NS
#endif
#endif