From 747ed4244fcd6728e23172268e1b19b3567d704e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Wed, 28 May 2025 13:04:27 +0200 Subject: [PATCH] documentation updates based on review --- doc/src/Commands_fix.rst | 2 +- doc/src/fix.rst | 2 +- doc/src/fix_ave_moments.rst | 107 ++++++----- .../moments/log.02May2025.valtest.g++.1 | 178 ++++++++++++++++++ .../moments/log.02May2025.valtest.g++.4 | 178 ++++++++++++++++++ 5 files changed, 415 insertions(+), 52 deletions(-) create mode 100644 examples/PACKAGES/moments/log.02May2025.valtest.g++.1 create mode 100644 examples/PACKAGES/moments/log.02May2025.valtest.g++.4 diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index cdc7a4a89d..f8c0937e9f 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -26,10 +26,10 @@ OPT. * :doc:`ave/chunk ` * :doc:`ave/correlate ` * :doc:`ave/correlate/long ` - * :doc:`ave/moments ` * :doc:`ave/grid ` * :doc:`ave/histo ` * :doc:`ave/histo/weight ` + * :doc:`ave/moments ` * :doc:`ave/time ` * :doc:`aveforce ` * :doc:`balance ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 935cd842c9..d49850e7da 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -205,10 +205,10 @@ accelerated styles exist. * :doc:`ave/chunk ` - compute per-chunk time-averaged quantities * :doc:`ave/correlate ` - compute/output time correlations * :doc:`ave/correlate/long ` - alternative to :doc:`ave/correlate ` that allows efficient calculation over long time windows -* :doc:`ave/moments ` - compute moments of scalar quantities * :doc:`ave/grid ` - compute per-grid time-averaged quantities * :doc:`ave/histo ` - compute/output time-averaged histograms * :doc:`ave/histo/weight ` - weighted version of fix ave/histo +* :doc:`ave/moments ` - compute moments of scalar quantities * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom * :doc:`balance ` - perform dynamic load-balancing diff --git a/doc/src/fix_ave_moments.rst b/doc/src/fix_ave_moments.rst index c773069a0b..a89ebbca09 100644 --- a/doc/src/fix_ave_moments.rst +++ b/doc/src/fix_ave_moments.rst @@ -30,14 +30,14 @@ Syntax * 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 *delay* +* keyword = *start* or *history* .. parsed-literal:: *start* args = Nstart Nstart = invoke first after this time step - *history* args = Ndelay - Ndelay = keep a history of up to Ndelay invocations + *history* args = Nrecent + Nrecent = keep a history of up to Nrecent outputs Examples """""""" @@ -52,10 +52,10 @@ Description .. versionadded:: TBD -Using one or more variables as input every few time steps, calculate the -moments of the underlying distribution based on the samples collected -over a time step window. The definitions of the moments calculated are -given below. +Using one or more values as input, calculate the moments of the underlying +(population) distribution 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 @@ -64,30 +64,29 @@ fixes which store their own "group" definitions. Each listed value can be the result of a :doc:`compute ` or :doc:`fix ` or the evaluation of an equal-style or vector-style :doc:`variable `. In each case, the compute, fix, or variable -must produce a global quantity, quantity, not a per-atom or local -quantity. If you wish to spatial- or time-average or histogram per-atom +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 `, :doc:`fix ave/atom `, or :doc:`fix ave/histo ` commands. If you wish to sum a per-atom quantity into a single global quantity, see the :doc:`compute reduce ` command. -:doc:`Computes ` that produce global quantities are those which -do not have the word *atom* in their style name. Only a few :doc:`fixes -` produce global quantities. See the doc pages for individual -fixes for info on which ones produce such values. :doc:`Variables -` 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. +Many :doc:`computes ` and :doc:`fixes ` produce global +quantities. See their doc pages for details. :doc:`Variables ` +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. The first requested moment -of input 1 has index 1, the second index 2, the first of input 2 has -index 3 and so on. +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. ---------- @@ -112,21 +111,23 @@ values will be used in order to contribute to the average. The final statistics are generated on time steps that are a multiple of :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 every :math:`N_\text{every}` time steps. +the simulation once every :math:`N_\text{every}` time steps. .. note:: - Contrary to some fix ave/* commands, the values of this fix are not - restricted by any special relation: it is valid to have a window - larger than :math:`N_\text{freq}` as well as the other way around. + 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 values from time steps 96, 97, 98, -99, and 100 will be used. This means some intervening time steps do not -contribute to the result. If :math:`N_\text{freq}=5` and -:math:`N_\text{repeat}=10`, then values will first be calculated on step -5 from steps 1-5, on step 10 from 1-10, on step 15 from 5-15 and so on, -forming a rolling average. +(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. ---------- @@ -191,31 +192,36 @@ For *kurtosis*, the adjusted Fisher--Pearson standardized moment Fix invocation and output can be modified by optional keywords. -The *start* keyword specifies that the first invocation should be no +The *start* keyword specifies that the first computation should be no earlier than the step number given (but will still occur on a multiple 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* allows keeping a record of previous results. By default, -only the most recent invocation is accessible. +The *history* keyword stores the Nrecent most recent outputs on Nfreq +timesteps, so they can be accessed as global outputs of the fix. By +default, only the most recent output is accessible. For example, if +history 10 is specified and Nfreq = 1000, then on timestep 20000, the +Nfreq outputs from steps 20000, 19000, ... 11000 are available for +access. See below for details on how to access the history values. -For example, this will output values which are delayed by 10 -invocations, meaning 10000 time steps: +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 by additional rows on the fix output -array, containing the N-th last evaluation result. For example, the most recent -result of the first input value would be accessed as "f_name[1][1]", -"f_name[1][4]" is the 4th most recent and so on. Vector access is always the -same as the first array row, corresponding to the most recent result. +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, the most recent result of 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. -This fix can be used in conjunction with :doc:`fix halt ` to -stop a run automatically if a quantity is converged to within some -limit: +To illustrate the utility of keeping output history, consider using +this fix in conjunction with :doc:`fix halt ` to stop a run +automatically if a quantity is converged to within some desired tolerance: .. code-block:: LAMMPS @@ -244,15 +250,16 @@ accessed on any time step, but may not be current. A global vector is produced with the # of elements = number of moments * number of inputs. The moments are output in the order given in the fix -definition. An array is produced having # of rows = value of *history* -and # of columns = same as vector output, using the same ordering. +definition. An array is produced having # of rows = same as vector output, +using the same ordering and # of columns = value of *history*. There is +always at least one column. -Each element can be either "intensive" or "extensive", depending on whether -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. +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 ` command. This fix is not invoked during diff --git a/examples/PACKAGES/moments/log.02May2025.valtest.g++.1 b/examples/PACKAGES/moments/log.02May2025.valtest.g++.1 new file mode 100644 index 0000000000..86cbeee12b --- /dev/null +++ b/examples/PACKAGES/moments/log.02May2025.valtest.g++.1 @@ -0,0 +1,178 @@ +LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) + using 1 OpenMP thread(s) per MPI task +# create pure copper system +units metal +lattice fcc 3.75 +Lattice spacing in x,y,z = 3.75 3.75 3.75 +region box block 0 6 0 6 0 6 +create_box 2 box +Created orthogonal box = (0 0 0) to (22.5 22.5 22.5) + 1 by 1 by 1 MPI processor grid + +timestep 0.002 +create_atoms 1 box +Created 864 atoms + using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5) + create_atoms CPU = 0.001 seconds + +pair_style eam/alloy +pair_coeff * * AlCu.eam.alloy Cu Al + +# Initialize to a high temperature, then cool in npt ensemble +velocity all create 1000.0 6567345 +fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt) +fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt) +fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111 + +variable toteng equal "etotal" +fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis + +thermo_style custom step etotal f_2[*] +thermo_modify format float %14.8f + +thermo 1 +run 100 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.6825 + ghost atom cutoff = 8.6825 + binsize = 4.34125, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.484 | 3.484 | 3.484 Mbytes + Step TotEng f_2[1] f_2[2] f_2[3] f_2[4] + 0 -2884.91592826 0.00000000 0.00000000 0.00000000 0.00000000 + 1 -2888.74461907 0.00000000 0.00000000 0.00000000 0.00000000 + 2 -2898.78491936 0.00000000 0.00000000 0.00000000 0.00000000 + 3 -2910.70619667 0.00000000 0.00000000 0.00000000 0.00000000 + 4 -2919.41734302 0.00000000 0.00000000 0.00000000 0.00000000 + 5 -2923.24980175 0.00000000 0.00000000 0.00000000 0.00000000 + 6 -2923.79800148 0.00000000 0.00000000 0.00000000 0.00000000 + 7 -2922.97580252 0.00000000 0.00000000 0.00000000 0.00000000 + 8 -2921.95601941 0.00000000 0.00000000 0.00000000 0.00000000 + 9 -2921.45319499 0.00000000 0.00000000 0.00000000 0.00000000 + 10 -2921.81460149 -2915.29004998 148.32538381 1.60272422 1.50844200 + 11 -2923.00059466 -2915.29004998 148.32538381 1.60272422 1.50844200 + 12 -2924.63075671 -2915.29004998 148.32538381 1.60272422 1.50844200 + 13 -2926.18037946 -2915.29004998 148.32538381 1.60272422 1.50844200 + 14 -2927.22356281 -2915.29004998 148.32538381 1.60272422 1.50844200 + 15 -2927.62053073 -2915.29004998 148.32538381 1.60272422 1.50844200 + 16 -2927.49949128 -2915.29004998 148.32538381 1.60272422 1.50844200 + 17 -2927.12292174 -2915.29004998 148.32538381 1.60272422 1.50844200 + 18 -2926.73637250 -2915.29004998 148.32538381 1.60272422 1.50844200 + 19 -2926.49482990 -2915.29004998 148.32538381 1.60272422 1.50844200 + 20 -2926.44714720 -2926.29565870 2.07215006 1.62317861 2.37019300 + 21 -2926.56102718 -2926.29565870 2.07215006 1.62317861 2.37019300 + 22 -2926.76734347 -2926.29565870 2.07215006 1.62317861 2.37019300 + 23 -2926.98403044 -2926.29565870 2.07215006 1.62317861 2.37019300 + 24 -2927.15193693 -2926.29565870 2.07215006 1.62317861 2.37019300 + 25 -2927.24498540 -2926.29565870 2.07215006 1.62317861 2.37019300 + 26 -2927.26914121 -2926.29565870 2.07215006 1.62317861 2.37019300 + 27 -2927.25021402 -2926.29565870 2.07215006 1.62317861 2.37019300 + 28 -2927.21637817 -2926.29565870 2.07215006 1.62317861 2.37019300 + 29 -2927.19085616 -2926.29565870 2.07215006 1.62317861 2.37019300 + 30 -2927.18360687 -2927.08195198 0.05722486 1.54894969 1.44984748 + 31 -2927.19243579 -2927.08195198 0.05722486 1.54894969 1.44984748 + 32 -2927.20805612 -2927.08195198 0.05722486 1.54894969 1.44984748 + 33 -2927.22285606 -2927.08195198 0.05722486 1.54894969 1.44984748 + 34 -2927.23274852 -2927.08195198 0.05722486 1.54894969 1.44984748 + 35 -2927.23953263 -2927.08195198 0.05722486 1.54894969 1.44984748 + 36 -2927.24805761 -2927.08195198 0.05722486 1.54894969 1.44984748 + 37 -2927.26215638 -2927.08195198 0.05722486 1.54894969 1.44984748 + 38 -2927.28298252 -2927.08195198 0.05722486 1.54894969 1.44984748 + 39 -2927.31025065 -2927.08195198 0.05722486 1.54894969 1.44984748 + 40 -2927.33874897 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 41 -2927.36224413 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 42 -2927.37729800 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 43 -2927.38671916 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 44 -2927.39115082 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 45 -2927.39614318 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 46 -2927.40444730 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 47 -2927.41888601 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 48 -2927.43954388 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 49 -2927.46210058 -2927.25378252 0.00209108 -0.65432756 -0.21113798 + 50 -2927.48270024 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 51 -2927.49822500 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 52 -2927.50765361 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 53 -2927.51223225 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 54 -2927.51510653 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 55 -2927.52035921 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 56 -2927.53170012 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 57 -2927.54910408 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 58 -2927.57357292 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 59 -2927.60356966 -2927.41212333 0.00148630 -0.72914987 -0.39161968 + 60 -2927.63344447 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 61 -2927.66186165 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 62 -2927.68810360 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 63 -2927.71163480 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 64 -2927.73036225 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 65 -2927.74726656 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 66 -2927.76525638 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 67 -2927.78432762 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 68 -2927.80305095 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 69 -2927.82406714 -2927.54449679 0.00204640 -1.06571776 0.04430271 + 70 -2927.84622122 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 71 -2927.86886493 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 72 -2927.89150302 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 73 -2927.91480122 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 74 -2927.93739399 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 75 -2927.96075707 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 76 -2927.98525702 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 77 -2928.00918972 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 78 -2928.03266453 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 79 -2928.05673430 -2927.75621522 0.00356092 0.06232090 -0.94076248 + 80 -2928.08120268 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 81 -2928.10618717 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 82 -2928.13191751 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 83 -2928.15675025 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 84 -2928.18178044 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 85 -2928.20538210 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 86 -2928.22991006 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 87 -2928.25238345 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 88 -2928.27490378 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 89 -2928.29697980 -2927.97383685 0.00511363 -0.03242365 -1.20956903 + 90 -2928.31902032 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 91 -2928.34079951 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 92 -2928.36448072 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 93 -2928.38918869 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 94 -2928.41578734 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 95 -2928.44466633 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 96 -2928.47414034 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 97 -2928.50507273 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 98 -2928.53751007 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 99 -2928.56947939 -2928.21552149 0.00511983 0.08421866 -1.19120544 + 100 -2928.60000318 -2928.46411283 0.00779929 -0.14908790 -1.24292534 +Loop time of 0.579661 on 1 procs for 100 steps with 864 atoms + +Performance: 29.811 ns/day, 0.805 hours/ns, 172.515 timesteps/s, 149.053 katom-step/s +96.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.54316 | 0.54316 | 0.54316 | 0.0 | 93.70 +Neigh | 0.0041212 | 0.0041212 | 0.0041212 | 0.0 | 0.71 +Comm | 0.0034702 | 0.0034702 | 0.0034702 | 0.0 | 0.60 +Output | 0.014085 | 0.014085 | 0.014085 | 0.0 | 2.43 +Modify | 0.01321 | 0.01321 | 0.01321 | 0.0 | 2.28 +Other | | 0.001612 | | | 0.28 + +Nlocal: 864 ave 864 max 864 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3767 ave 3767 max 3767 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 96746 ave 96746 max 96746 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 96746 +Ave neighs/atom = 111.97454 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/moments/log.02May2025.valtest.g++.4 b/examples/PACKAGES/moments/log.02May2025.valtest.g++.4 new file mode 100644 index 0000000000..f7321d2326 --- /dev/null +++ b/examples/PACKAGES/moments/log.02May2025.valtest.g++.4 @@ -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