Jacob Gissinger
36
.github/CODEOWNERS
vendored
36
.github/CODEOWNERS
vendored
@ -9,13 +9,37 @@ lib/kokkos/* @stanmoore1
|
||||
lib/molfile/* @akohlmey
|
||||
lib/qmmm/* @akohlmey
|
||||
lib/vtk/* @rbberger
|
||||
lib/kim/* @ellio167
|
||||
|
||||
# packages
|
||||
src/KOKKOS @stanmoore1
|
||||
src/USER-CGSDK @akohlmey
|
||||
src/USER-COLVARS @giacomofiorin
|
||||
src/USER-OMP @akohlmey
|
||||
src/USER-QMMM @akohlmey
|
||||
# whole packages
|
||||
src/COMPRESS/* @akohlmey
|
||||
src/GPU/* @ndtrung81
|
||||
src/KOKKOS/* @stanmoore1
|
||||
src/KIM/* @ellio167
|
||||
src/USER-CGDNA/* @ohenrich
|
||||
src/USER-CGSDK/* @akohlmey
|
||||
src/USER-COLVARS/* @giacomofiorin
|
||||
src/USER-DPD/* @timattox
|
||||
src/USER-INTEL/* @wmbrownintel
|
||||
src/USER-MANIFOLD/* @Pakketeretet2
|
||||
src/USER-MEAMC/* @martok
|
||||
src/USER-MOFFF/* @hheenen
|
||||
src/USER-MOLFILE/* @akohlmey
|
||||
src/USER-NETCDF/* @pastewka
|
||||
src/USER-PHONON/* @lingtikong
|
||||
src/USER-OMP/* @akohlmey
|
||||
src/USER-QMMM/* @akohlmey
|
||||
src/USER-REAXC/* @hasanmetin
|
||||
src/USER-TALLY/* @akohlmey
|
||||
src/USER-UEF/* @danicholson
|
||||
src/USER-VTK/* @rbberger
|
||||
|
||||
# individual files in packages
|
||||
src/GPU/pair_vashishta_gpu.* @andeplane
|
||||
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
|
||||
src/MANYBODY/pair_vashishta_table.* @andeplane
|
||||
src/USER-MISC/fix_bond_react.* @jrgissing
|
||||
src/USER-MISC/*_grem.* @dstelter92
|
||||
|
||||
# tools
|
||||
tools/msi2lmp/* @akohlmey
|
||||
|
||||
@ -101,7 +101,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
|
||||
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
|
||||
REAX REPLICA RIGID SHOCK SNAP SRD)
|
||||
set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
|
||||
USER-ATC USER-AWPMD USER-CGDNA USER-MESO
|
||||
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
|
||||
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
|
||||
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
|
||||
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
|
||||
@ -128,10 +128,6 @@ pkg_depends(USER-LB MPI)
|
||||
pkg_depends(USER-MISC MANYBODY)
|
||||
pkg_depends(USER-PHONON KSPACE)
|
||||
|
||||
if(ENABLE_BODY AND ENABLE_POEMS)
|
||||
message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
|
||||
endif()
|
||||
|
||||
######################################################
|
||||
# packages with special compiler needs or external libs
|
||||
######################################################
|
||||
|
||||
Binary file not shown.
BIN
doc/src/PDF/USER-CGDNA.pdf
Normal file
BIN
doc/src/PDF/USER-CGDNA.pdf
Normal file
Binary file not shown.
@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
|
||||
Package, Description, Doc page, Example, Library
|
||||
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
|
||||
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
|
||||
"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
|
||||
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
|
||||
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
|
||||
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
|
||||
@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
|
||||
|
||||
:line
|
||||
|
||||
USER-BOCS package :link(USER-BOCS),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
This package provides "fix bocs"_fix_bocs.html, a modified version
|
||||
of "fix npt"_fix_nh.html which includes the pressure correction to
|
||||
the barostat as outlined in:
|
||||
|
||||
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
|
||||
accurately describe the structure, pressure, and compressibility of
|
||||
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
|
||||
|
||||
[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
make yes-user-bocs
|
||||
make machine :pre
|
||||
|
||||
make no-user-bocs
|
||||
make machine :pre
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
|
||||
"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
|
||||
|
||||
See the following reference for information about the entire package:
|
||||
|
||||
Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
|
||||
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
|
||||
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
|
||||
|
||||
Example inputs are in the examples/USER/bocs folder.
|
||||
|
||||
:line
|
||||
|
||||
USER-CGDNA package :link(USER-CGDNA),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
A technical report with more information on the model, the structure of the input file,
|
||||
the setup tool and the performance of the LAMMPS-implementation of oxDNA
|
||||
can be found "here"_PDF/USER-CGDNA-overview.pdf.
|
||||
|
||||
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
|
||||
The article contains more information on the model, the structure of the input file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
|
||||
|
||||
:line
|
||||
|
||||
@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
:line
|
||||
|
||||
:link(Henrich2)
|
||||
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
:link(oxdna_fene)
|
||||
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
|
||||
@ -10,19 +10,29 @@ compute ackland/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID ackland/atom :pre
|
||||
compute ID group-ID ackland/atom keyword/value :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
ackland/atom = style name of this compute command :ul
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
ackland/atom = style name of this compute command :l
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {legacy} :l
|
||||
{legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all ackland/atom :pre
|
||||
compute 1 all ackland/atom
|
||||
compute 1 all ackland/atom legacy yes :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Defines a computation that calculates the local lattice structure
|
||||
according to the formulation given in "(Ackland)"_#Ackland.
|
||||
Historically, LAMMPS had two, slightly different implementations of
|
||||
the algorithm from the paper. With the {legacy} keyword, it is
|
||||
possible to switch between the pre-2015 ({legacy yes}) and post-2015
|
||||
implemention ({legacy no}). The post-2015 variant is the default.
|
||||
|
||||
In contrast to the "centro-symmetry
|
||||
parameter"_compute_centro_atom.html this method is stable against
|
||||
@ -66,7 +76,8 @@ integers defined above.
|
||||
|
||||
"compute centro/atom"_compute_centro_atom.html
|
||||
|
||||
[Default:] none
|
||||
[Default:]
|
||||
The keyword {legacy} defaults to {no}.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
112
doc/src/fix_bocs.txt
Normal file
112
doc/src/fix_bocs.txt
Normal file
@ -0,0 +1,112 @@
|
||||
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix bocs command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID bocs keyword values ... :pre
|
||||
|
||||
keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
|
||||
{temp} values = Tstart Tstop Tdamp
|
||||
{cgiso} values = Pstart Pstop Pdamp
|
||||
{basis set}
|
||||
{analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
|
||||
{linear_spline} values = input_filename
|
||||
{cubic_spline} values = input_filename :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
|
||||
|
||||
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
|
||||
|
||||
thermo_modify press 1_press :pre
|
||||
|
||||
|
||||
[Description:]
|
||||
|
||||
These commands incorporate a pressure correction as described by
|
||||
Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
|
||||
barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
|
||||
The first half of the command mimics a standard fix npt command:
|
||||
|
||||
fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
|
||||
|
||||
The two differences are replacing {npt} with {bocs}, and replacing
|
||||
{iso}/{aniso}/{etc} with {cgiso}.
|
||||
The rest of the command details what form you would like to use for
|
||||
the pressure correction equation. The choices are: {analytic}, {linear_spline},
|
||||
or {cubic_spline}.
|
||||
|
||||
With either spline method, the only argument that needs to follow it
|
||||
is the name of a file that contains the desired pressure correction
|
||||
as a function of volume. The file should be formatted so each line has:
|
||||
|
||||
Volume_i, PressureCorrection_i :pre
|
||||
|
||||
Note both the COMMA and the SPACE separating the volume's
|
||||
value and its corresponding pressure correction. The volumes in the file
|
||||
should be uniformly spaced. Both the volumes and the pressure corrections
|
||||
should be provided in the proper units, e.g. if you are using {units real},
|
||||
the volumes should all be in cubic angstroms, and the pressure corrections
|
||||
should all be in atomspheres. Furthermore, the table should start/end at a
|
||||
volume considerably smaller/larger than you expect your system to sample
|
||||
during the simulation. If the system ever reaches a volume outside of the
|
||||
range provided, the simulation will stop.
|
||||
|
||||
With the {analytic} option, the arguments are as follows:
|
||||
|
||||
... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
|
||||
|
||||
Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
|
||||
are using {units real}, {V_avg} should be in cubic angstroms, and the
|
||||
coefficients should all be in atmospheres * cubic angstroms.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
As this is computing a (modified) pressure, group-ID should be {all}.
|
||||
|
||||
The pressure correction has only been tested for use with an isotropic
|
||||
pressure coupling in 3 dimensions.
|
||||
|
||||
By default, LAMMPS will still report the normal value for the pressure
|
||||
if the pressure is printed via a {thermo} command, or if the pressures
|
||||
are written to a file every so often. In order to have LAMMPS report the
|
||||
modified pressure, you must include the {thermo_modify} command given in
|
||||
the examples. For the last argument in the command, you should put
|
||||
XXXX_press, where XXXX is the ID given to the fix bocs command (in the
|
||||
example, the ID of the fix bocs command is 1 ).
|
||||
|
||||
This fix is part of the USER-BOCS package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related:]
|
||||
|
||||
For more details about the pressure correction and the entire BOCS software
|
||||
package, visit the "BOCS package on github"_bocsgithub and read the release
|
||||
paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
|
||||
|
||||
|
||||
:link(bocsgithub,https://github.com/noid-group/BOCS)
|
||||
|
||||
:line
|
||||
|
||||
:link(bocs-Dunn1)
|
||||
[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
|
||||
|
||||
:link(bocs-Martyna)
|
||||
[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
|
||||
|
||||
:link(bocs-Dunn2)
|
||||
[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
|
||||
|
||||
|
||||
|
||||
@ -11,9 +11,9 @@ fix bond/react command :h3
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID bond/react common_keyword values ...
|
||||
react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||
react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||
react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||
... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
|
||||
@ -24,12 +24,13 @@ common_keyword = {stabilization}
|
||||
{stabilization} values = group-ID xmax
|
||||
group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all')
|
||||
{xmax} value = distance
|
||||
distance = xmax value that is used by an internally created "nve/limit"_nve_limit.html integrator
|
||||
distance = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator
|
||||
react = mandatory argument indicating new reaction specification
|
||||
react-ID = user-assigned name for the reaction
|
||||
react-group-ID = only atoms in this group are available for the reaction
|
||||
Nevery = attempt reaction every this many steps :l
|
||||
Rmin = bonding pair atoms separated by less than Rmin can initiate reaction (distance units) :l
|
||||
Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
|
||||
Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
|
||||
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
|
||||
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
|
||||
map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
|
||||
@ -46,15 +47,15 @@ react = mandatory argument indicating new reaction specification
|
||||
|
||||
molecule mol1 pre_reacted_topology.txt
|
||||
molecule mol2 post_reacted_topology.txt
|
||||
fix 5 all bond/react stabilization no react myrxn1 all 1 3.25 mol1 mol2 map_file.txt
|
||||
fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt
|
||||
|
||||
molecule mol1 pre_reacted_rxn1.txt
|
||||
molecule mol2 post_reacted_rxn1.txt
|
||||
molecule mol3 pre_reacted_rxn2.txt
|
||||
molecule mol4 post_reacted_rxn2.txt
|
||||
fix 5 all bond/react stabilization yes nvt_grp .03 &
|
||||
react myrxn1 all 1 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
|
||||
react myrxn2 all 1 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
|
||||
react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
|
||||
react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
|
||||
fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre
|
||||
|
||||
[Description:]
|
||||
@ -101,9 +102,14 @@ The group-ID set using the {stabilization} keyword should be a
|
||||
previously unused group-ID. The fix bond/react command creates a
|
||||
"dynamic group"_group.html of this name that excludes reacting atoms.
|
||||
This dynamic group-ID should then be used by a subsequent system-wide
|
||||
time integrator, as shown in the second example above. It is necessary
|
||||
to place the time integration command after the fix bond/react command
|
||||
due to the internal dynamic grouping performed by fix bond/react.
|
||||
time integrator, as shown in the second example above. It is currently
|
||||
necessary to place the time integration command after the fix
|
||||
bond/react command due to the internal dynamic grouping performed by
|
||||
fix bond/react.
|
||||
|
||||
NOTE: The internally created group currently applies to all atoms in
|
||||
the system, i.e. you should generally not have a separate thermostat
|
||||
which acts on the 'all' group.
|
||||
|
||||
The following comments pertain to each 'react' argument:
|
||||
|
||||
@ -118,21 +124,20 @@ modified to match the post-reaction template.
|
||||
|
||||
A bonding atom pair will be identified if several conditions are met.
|
||||
First, a pair of atoms within the specified react-group-ID of type
|
||||
typei and typej must be within a distance Rmin of each other. The atom
|
||||
types typei and typej are specified in the pre- and post-reaction
|
||||
templates. The distance calculation uses the pair neighbor list,
|
||||
therefore bonded neighbor exclusions may prevent a reaction between
|
||||
1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs
|
||||
are identified for an atom, the closest bonding atom partner is set as
|
||||
its "nearest" bonding partner. Then, if both an atomi and atomj have
|
||||
each other as their nearest bonding partners, these two atoms are
|
||||
identified as the bonding atom pair of the reaction site. Once this
|
||||
unique bonding atom pair is identified for each reaction, there could
|
||||
two or more reactions that involve a given atom on the same timestep.
|
||||
If this is the case, only one such reaction is permitted to occur.
|
||||
This reaction is chosen randomly from all potential reactions. This
|
||||
capability allows e.g. for different reaction pathways to proceed from
|
||||
identical reaction sites with user-specified probabilities.
|
||||
typei and typej must separated by a distance between Rmin and Rmax. It
|
||||
is possible that multiple bonding atom pairs are identified: if the
|
||||
bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4
|
||||
neighbors, the closest bonding atom partner is set as its bonding
|
||||
partner; otherwise, the farthest potential partner is chosen. Then, if
|
||||
both an atomi and atomj have each other as their nearest bonding
|
||||
partners, these two atoms are identified as the bonding atom pair of
|
||||
the reaction site. Once this unique bonding atom pair is identified
|
||||
for each reaction, there could two or more reactions that involve a
|
||||
given atom on the same timestep. If this is the case, only one such
|
||||
reaction is permitted to occur. This reaction is chosen randomly from
|
||||
all potential reactions. This capability allows e.g. for different
|
||||
reaction pathways to proceed from identical reaction sites with
|
||||
user-specified probabilities.
|
||||
|
||||
The pre-reacted molecule template is specified by a molecule command.
|
||||
This molecule template file contains a sample reaction site and its
|
||||
@ -262,9 +267,11 @@ angles, dihedrals or impropers are supported.
|
||||
A few capabilities to note: 1) You may specify as many 'react'
|
||||
arguments as desired. For example, you could break down a complicated
|
||||
reaction mechanism into several reaction steps, each defined by its
|
||||
own 'react' argument. 2) While typically a bond is formed between the
|
||||
bonding atom pairs specified in the pre-reacted molecule template,
|
||||
this is not required.
|
||||
own 'react' argument. 2) While typically a bond is formed or removed
|
||||
between the bonding atom pairs specified in the pre-reacted molecule
|
||||
template, this is not required. 3) By reversing the order of the pre-
|
||||
and post- reacted molecule templates in another 'react' argument, you
|
||||
can allow for the possibility of one or more reverse reactions.
|
||||
|
||||
The optional keywords deal with the probability of a given reaction
|
||||
occurring as well as the stable equilibration of each reaction site as
|
||||
@ -300,14 +307,14 @@ reaction:
|
||||
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
|
||||
|
||||
NOTE: This command must be added after the fix bond/react command, and
|
||||
will apply to all reaction steps.
|
||||
will apply to all reactions.
|
||||
|
||||
Computationally, each timestep this fix operates, it loops over
|
||||
neighbor lists and computes distances between pairs of atoms in the
|
||||
list. It also communicates between neighboring processors to
|
||||
coordinate which bonds are created. All of these operations increase
|
||||
the cost of a timestep. Thus you should be cautious about invoking
|
||||
this fix too frequently.
|
||||
neighbor lists (for bond-forming reactions) and computes distances
|
||||
between pairs of atoms in the list. It also communicates between
|
||||
neighboring processors to coordinate which bonds are created and/or
|
||||
removed. All of these operations increase the cost of a timestep. Thus
|
||||
you should be cautious about invoking this fix too frequently.
|
||||
|
||||
You can dump out snapshots of the current bond topology via the dump
|
||||
local command.
|
||||
|
||||
@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs
|
||||
should be chosen low enough, so as to mimic as closely as possible the
|
||||
self-consistent minimization. It must however be high enough, so that
|
||||
the dipoles can follow the local electric field exerted by the
|
||||
neighbouring atoms. The optimal value probably depends on the
|
||||
neighboring atoms. The optimal value probably depends on the
|
||||
temperature of the centers of mass and on the mass of the Drude
|
||||
particles.
|
||||
|
||||
|
||||
@ -14,14 +14,16 @@ fix_modify fix-ID keyword value ... :pre
|
||||
|
||||
fix-ID = ID of the fix to modify :ulb,l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
|
||||
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l
|
||||
{temp} value = compute ID that calculates a temperature
|
||||
{press} value = compute ID that calculates a pressure
|
||||
{energy} value = {yes} or {no}
|
||||
{virial} value = {yes} or {no}
|
||||
{respa} value = {1} to {max respa level} or {0} (for outermost level)
|
||||
{dynamic/dof} value = {yes} or {no}
|
||||
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
|
||||
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
|
||||
{bodyforces} value = {early} or {late}
|
||||
early/late = compute rigid-body forces/torques early or late in the timestep :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
@ -84,9 +86,8 @@ if you want virial contribution of the fix to be part of the
|
||||
relaxation criteria, although this seems unlikely.
|
||||
|
||||
NOTE: This option is only supported by fixes that explicitly say
|
||||
so. For some of these (e.g. the
|
||||
"fix shake"_fix_shake.html command) the default setting is
|
||||
{virial yes}, for others it is {virial no}.
|
||||
so. For some of these (e.g. the "fix shake"_fix_shake.html command)
|
||||
the default setting is {virial yes}, for others it is {virial no}.
|
||||
|
||||
For fixes that set or modify forces, it may be possible to select at
|
||||
which "r-RESPA"_run_style.html level the fix operates via the {respa}
|
||||
@ -120,6 +121,28 @@ compute to calculate temperature. See the "compute_modify
|
||||
dynamic/dof"_compute_modify.html command for a similar way to insure
|
||||
correct temperature normalization for those thermostats.
|
||||
|
||||
The {bodyforces} keyword determines whether the forces and torques
|
||||
acting on rigid bodies are computed {early} at the post-force stage of
|
||||
each timestep (right after per-atom forces have been computed and
|
||||
communicated among processors), or {late} at the final-integrate stage
|
||||
of each timestep (after any other fixes have finished their post-force
|
||||
tasks). Only the rigid-body integration fixes use this option, which
|
||||
includes "fix rigid"_fix_rigid.html and "fix
|
||||
rigid/small"_fix_rigid.html, and their variants, and also "fix
|
||||
poems"_fix_poems.html.
|
||||
|
||||
The default is {late}. If there are other fixes that add forces to
|
||||
individual atoms, then the rigid-body constraints will include these
|
||||
forces when time-integrating the rigid bodies. If {early} is
|
||||
specified, then new fixes can be written that use or modify the
|
||||
per-body force and torque, before time-integration of the rigid bodies
|
||||
occurs. Note however this has the side effect, that fixes such as
|
||||
"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
|
||||
"fix spring"_fix_spring.html, which add forces to individual atoms
|
||||
will have no effect on the motion of the rigid bodies if they are
|
||||
specified in the input script after the fix rigid command. LAMMPS
|
||||
will give a warning if that is the case.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
@ -130,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
|
||||
[Default:]
|
||||
|
||||
The option defaults are temp = ID defined by fix, press = ID defined
|
||||
by fix, energy = no, virial = different for each fix style, respa = 0.
|
||||
by fix, energy = no, virial = different for each fix style, respa = 0,
|
||||
bodyforce = late.
|
||||
|
||||
@ -106,12 +106,18 @@ off, and there is only a single fix poems defined.
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
|
||||
this fix style to set whether per-body forces and torques are computed
|
||||
early or late in a timestep, i.e. at the post-force stage or at the
|
||||
final-integrate stage, respectively.
|
||||
|
||||
No global or per-atom quantities are stored by this fix for access by
|
||||
various "output commands"_Section_howto.html#howto_15. No parameter
|
||||
of this fix can be used with the {start/stop} keywords of the
|
||||
"run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
|
||||
@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l
|
||||
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
theta0 = equilibrium angle theta (degrees)
|
||||
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
|
||||
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
|
||||
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
phi0 = equilibrium dihedral angle phi (degrees) :pre
|
||||
phi0 = equilibrium dihedral angle phi (degrees)
|
||||
keyword/value = optional keyword value pairs. supported keyword/value pairs:
|
||||
{mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
@ -155,11 +157,13 @@ associated with the restraint is
|
||||
with the following coefficients:
|
||||
|
||||
K (energy)
|
||||
n = 1
|
||||
n (multiplicity, >= 0)
|
||||
d (degrees) = phi0 + 180 :ul
|
||||
|
||||
K and phi0 are specified with the fix. Note that the value of n is
|
||||
hard-wired to 1. Also note that the energy will be a minimum when the
|
||||
K and phi0 are specified with the fix. Note that the value of the
|
||||
dihedral multiplicity {n} is set by default to 1. You can use the
|
||||
optional {mult} keyword to set it to a different positive integer.
|
||||
Also note that the energy will be a minimum when the
|
||||
current dihedral angle phi is equal to phi0.
|
||||
|
||||
:line
|
||||
|
||||
@ -223,10 +223,10 @@ via several options.
|
||||
|
||||
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
|
||||
specified as {molecule} or {custom}, you can define a system that has
|
||||
no rigid bodies initially. This is useful when you are using the {mol}
|
||||
keyword in conjunction with another fix that is adding rigid bodies
|
||||
on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
|
||||
"fix pour"_fix_pour.html.
|
||||
no rigid bodies initially. This is useful when you are using the
|
||||
{mol} keyword in conjunction with another fix that is adding rigid
|
||||
bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
|
||||
or "fix pour"_fix_pour.html.
|
||||
|
||||
For bodystyle {single} the entire fix group of atoms is treated as one
|
||||
rigid body. This option is only allowed for the {rigid} styles.
|
||||
@ -742,6 +742,11 @@ used to calculate the instantaneous pressure tensor. Note that the 2
|
||||
NVT rigid fixes do not use any external compute to compute
|
||||
instantaneous temperature.
|
||||
|
||||
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
|
||||
all rigid styles to set whether per-body forces and torques are
|
||||
computed early or late in a timestep, i.e. at the post-force stage or
|
||||
at the final-integrate stage or the timestep, respectively.
|
||||
|
||||
The 2 NVE rigid fixes compute a global scalar which can be accessed by
|
||||
various "output commands"_Section_howto.html#howto_15. The scalar
|
||||
value calculated by these fixes is "intensive". The scalar is the
|
||||
|
||||
@ -20,6 +20,7 @@ Fixes :h1
|
||||
fix_ave_time
|
||||
fix_aveforce
|
||||
fix_balance
|
||||
fix_bocs
|
||||
fix_bond_break
|
||||
fix_bond_create
|
||||
fix_bond_swap
|
||||
|
||||
@ -135,6 +135,7 @@ fix_ave_histo.html
|
||||
fix_ave_time.html
|
||||
fix_aveforce.html
|
||||
fix_balance.html
|
||||
fix_bocs.html
|
||||
fix_bond_break.html
|
||||
fix_bond_create.html
|
||||
fix_bond_react.html
|
||||
|
||||
@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above.
|
||||
This potential is intended for interactions between two layers of graphene.
|
||||
Therefore, to avoid interaction between layers in multi-layered materials,
|
||||
each layer should have a separate atom type and interactions should only
|
||||
be computed between atom types of neighbouring layers.
|
||||
be computed between atom types of neighboring layers.
|
||||
|
||||
The parameter file (e.g. CC.KC), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
|
||||
@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
A technical report with more information on the model, the structure of the input file,
|
||||
the setup tool and the performance of the LAMMPS-implementation of oxDNA
|
||||
can be found "here"_PDF/USER-CGDNA-overview.pdf.
|
||||
|
||||
Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
|
||||
The article contains more information on the model, the structure of the input file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
|
||||
|
||||
:line
|
||||
|
||||
@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
:line
|
||||
|
||||
:link(Henrich1)
|
||||
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
:link(Sulc1)
|
||||
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
|
||||
@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
A technical report with more information on the model, the structure of the input file,
|
||||
the setup tool and the performance of the LAMMPS-implementation of oxDNA
|
||||
can be found "here"_PDF/USER-CGDNA-overview.pdf.
|
||||
|
||||
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
|
||||
The article contains more information on the model, the structure of the input file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
|
||||
|
||||
:line
|
||||
|
||||
@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
:line
|
||||
|
||||
:link(Henrich)
|
||||
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
:link(Sulc2)
|
||||
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
|
||||
6
examples/USER/bocs/README
Normal file
6
examples/USER/bocs/README
Normal file
@ -0,0 +1,6 @@
|
||||
This folder contains the files to run a NPT simulation of 1 site CG methanol
|
||||
while employing a correction to the barostat.
|
||||
The pair force was computed via the Multi-Scale Coarse-Graining method.
|
||||
The resulting model was then iteratively pressure matched.
|
||||
The model accurately reproduces both structural (RDF) and thermodynamic
|
||||
(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.
|
||||
69
examples/USER/bocs/in.methanol
Normal file
69
examples/USER/bocs/in.methanol
Normal file
@ -0,0 +1,69 @@
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
|
||||
newton on
|
||||
timestep 1.0
|
||||
|
||||
read_data methanol.data
|
||||
|
||||
velocity all create 300.0 16802 dist gaussian
|
||||
|
||||
pair_style table spline 15000
|
||||
|
||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes one 10000
|
||||
neighbor 12.0 bin
|
||||
|
||||
thermo 500
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
|
||||
variable STEP equal step
|
||||
variable TEMP equal temp
|
||||
## volume from cubic angstroms to cubic nm
|
||||
variable VOL equal vol/1000.0
|
||||
## pressure from atm to bar
|
||||
variable PRESS equal press*1.01325
|
||||
variable PXX equal pxx*1.01325
|
||||
variable PYY equal pyy*1.01325
|
||||
variable PZZ equal pzz*1.01325
|
||||
variable PXY equal pxy*1.01325
|
||||
variable PXZ equal pxz*1.01325
|
||||
variable PYZ equal pyz*1.01325
|
||||
## energy from kcal/mol to kJ/mol
|
||||
variable KE equal ke*4.184
|
||||
variable PE equal pe*4.184
|
||||
variable UVDW equal evdwl*4.184
|
||||
|
||||
|
||||
##### SPECIAL COMMANDS FOR FIX_BOCS #####
|
||||
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
|
||||
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
|
||||
|
||||
# Report the modified pressure
|
||||
thermo_modify press 1_press
|
||||
|
||||
|
||||
|
||||
## Uncomment to save some data from simulation to files
|
||||
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
|
||||
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
|
||||
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
|
||||
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
|
||||
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
|
||||
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
|
||||
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
|
||||
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
|
||||
|
||||
## Prints a configuration to dump.txt every 500 steps
|
||||
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
|
||||
|
||||
# Write restart files to continue simulations
|
||||
#restart 10000 state1.restart state2.restart
|
||||
|
||||
## Run for this many steps
|
||||
run_style verlet
|
||||
run 10000
|
||||
|
||||
2505
examples/USER/bocs/lammps_nb_MET-MET.table
Normal file
2505
examples/USER/bocs/lammps_nb_MET-MET.table
Normal file
File diff suppressed because it is too large
Load Diff
143
examples/USER/bocs/log.20Apr18.methanol.g++.1
Normal file
143
examples/USER/bocs/log.20Apr18.methanol.g++.1
Normal file
@ -0,0 +1,143 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
|
||||
newton on
|
||||
timestep 1.0
|
||||
|
||||
read_data methanol.data
|
||||
orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
968 atoms
|
||||
|
||||
velocity all create 300.0 16802 dist gaussian
|
||||
|
||||
pair_style table spline 15000
|
||||
|
||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
|
||||
neigh_modify delay 0 every 1 check yes one 10000
|
||||
neighbor 12.0 bin
|
||||
|
||||
thermo 500
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
|
||||
variable STEP equal step
|
||||
variable TEMP equal temp
|
||||
## volume from cubic angstroms to cubic nm
|
||||
variable VOL equal vol/1000.0
|
||||
## pressure from atm to bar
|
||||
variable PRESS equal press*1.01325
|
||||
variable PXX equal pxx*1.01325
|
||||
variable PYY equal pyy*1.01325
|
||||
variable PZZ equal pzz*1.01325
|
||||
variable PXY equal pxy*1.01325
|
||||
variable PXZ equal pxz*1.01325
|
||||
variable PYZ equal pyz*1.01325
|
||||
## energy from kcal/mol to kJ/mol
|
||||
variable KE equal ke*4.184
|
||||
variable PE equal pe*4.184
|
||||
variable UVDW equal evdwl*4.184
|
||||
|
||||
|
||||
##### SPECIAL COMMANDS FOR FIX_BOCS #####
|
||||
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
|
||||
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
|
||||
|
||||
# Report the modified pressure
|
||||
thermo_modify press 1_press
|
||||
|
||||
|
||||
|
||||
## Uncomment to save some data from simulation to files
|
||||
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
|
||||
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
|
||||
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
|
||||
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
|
||||
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
|
||||
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
|
||||
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
|
||||
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
|
||||
|
||||
## Prints a configuration to dump.txt every 500 steps
|
||||
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
|
||||
|
||||
# Write restart files to continue simulations
|
||||
#restart 10000 state1.restart state2.restart
|
||||
|
||||
## Run for this many steps
|
||||
run_style verlet
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 24
|
||||
ghost atom cutoff = 24
|
||||
binsize = 12, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 300 1061.5961 1926.3291 107.006 66250.679
|
||||
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
|
||||
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
|
||||
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
|
||||
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
|
||||
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
|
||||
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
|
||||
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
|
||||
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
|
||||
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
|
||||
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
|
||||
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
|
||||
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
|
||||
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
|
||||
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
|
||||
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
|
||||
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
|
||||
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
|
||||
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
|
||||
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
|
||||
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
|
||||
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
|
||||
|
||||
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
|
||||
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
|
||||
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
|
||||
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
|
||||
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
|
||||
Other | | 0.1252 | | | 0.36
|
||||
|
||||
Nlocal: 968 ave 968 max 968 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9112 ave 9112 max 9112 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 404392 ave 404392 max 404392 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 404392
|
||||
Ave neighs/atom = 417.76
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:34
|
||||
143
examples/USER/bocs/log.20Apr18.methanol.g++.4
Normal file
143
examples/USER/bocs/log.20Apr18.methanol.g++.4
Normal file
@ -0,0 +1,143 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
|
||||
newton on
|
||||
timestep 1.0
|
||||
|
||||
read_data methanol.data
|
||||
orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
968 atoms
|
||||
|
||||
velocity all create 300.0 16802 dist gaussian
|
||||
|
||||
pair_style table spline 15000
|
||||
|
||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
|
||||
neigh_modify delay 0 every 1 check yes one 10000
|
||||
neighbor 12.0 bin
|
||||
|
||||
thermo 500
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
|
||||
variable STEP equal step
|
||||
variable TEMP equal temp
|
||||
## volume from cubic angstroms to cubic nm
|
||||
variable VOL equal vol/1000.0
|
||||
## pressure from atm to bar
|
||||
variable PRESS equal press*1.01325
|
||||
variable PXX equal pxx*1.01325
|
||||
variable PYY equal pyy*1.01325
|
||||
variable PZZ equal pzz*1.01325
|
||||
variable PXY equal pxy*1.01325
|
||||
variable PXZ equal pxz*1.01325
|
||||
variable PYZ equal pyz*1.01325
|
||||
## energy from kcal/mol to kJ/mol
|
||||
variable KE equal ke*4.184
|
||||
variable PE equal pe*4.184
|
||||
variable UVDW equal evdwl*4.184
|
||||
|
||||
|
||||
##### SPECIAL COMMANDS FOR FIX_BOCS #####
|
||||
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
|
||||
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
|
||||
|
||||
# Report the modified pressure
|
||||
thermo_modify press 1_press
|
||||
|
||||
|
||||
|
||||
## Uncomment to save some data from simulation to files
|
||||
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
|
||||
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
|
||||
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
|
||||
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
|
||||
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
|
||||
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
|
||||
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
|
||||
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
|
||||
|
||||
## Prints a configuration to dump.txt every 500 steps
|
||||
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
|
||||
|
||||
# Write restart files to continue simulations
|
||||
#restart 10000 state1.restart state2.restart
|
||||
|
||||
## Run for this many steps
|
||||
run_style verlet
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 24
|
||||
ghost atom cutoff = 24
|
||||
binsize = 12, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 300 1061.5961 1926.3291 107.006 66250.679
|
||||
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
|
||||
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
|
||||
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
|
||||
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
|
||||
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
|
||||
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
|
||||
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
|
||||
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
|
||||
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
|
||||
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
|
||||
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
|
||||
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
|
||||
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
|
||||
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
|
||||
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
|
||||
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
|
||||
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
|
||||
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
|
||||
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
|
||||
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
|
||||
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
|
||||
|
||||
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
|
||||
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
|
||||
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
|
||||
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
|
||||
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
|
||||
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
|
||||
Other | | 0.3112 | | | 1.08
|
||||
|
||||
Nlocal: 242 ave 244 max 239 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 5718.5 ave 5736 max 5702 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 100703 ave 108064 max 93454 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 402813
|
||||
Ave neighs/atom = 416.129
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:28
|
||||
991
examples/USER/bocs/methanol.data
Normal file
991
examples/USER/bocs/methanol.data
Normal file
@ -0,0 +1,991 @@
|
||||
LAMMPS Description
|
||||
|
||||
968 atoms
|
||||
0 bonds
|
||||
0 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
1 atom types
|
||||
0 bond types
|
||||
0 angle types
|
||||
0 dihedral types
|
||||
|
||||
0 40.4635 xlo xhi
|
||||
0 40.4635 ylo yhi
|
||||
0 40.4635 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 32.0424
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 36.39 8.05 27.55
|
||||
2 1 18.38 15.72 26.03
|
||||
3 1 3.52 1.77 23.57
|
||||
4 1 31.09 11.38 12.17
|
||||
5 1 13.3 34.8 2.89
|
||||
6 1 1.72 38.55 10.36
|
||||
7 1 38.6 23.16 6.19
|
||||
8 1 0.74 33.21 0.17
|
||||
9 1 26.97 9.53 11.24
|
||||
10 1 31.68 12.19 17.04
|
||||
11 1 15.19 9.06 0.2
|
||||
12 1 34.39 20.63 35.71
|
||||
13 1 21.79 4.93 6.49
|
||||
14 1 28.08 33.01 24.51
|
||||
15 1 37.03 20.52 32.9
|
||||
16 1 32.69 20 30.11
|
||||
17 1 23.77 38.59 18.79
|
||||
18 1 16.01 2.31 20.15
|
||||
19 1 5.65 15.5 28.5
|
||||
20 1 8.35 17.35 20.48
|
||||
21 1 31.24 24.68 27.4
|
||||
22 1 29.41 16.64 19.79
|
||||
23 1 37.42 31.93 26.68
|
||||
24 1 18.76 39.06 30.68
|
||||
25 1 22.97 35 20.81
|
||||
26 1 39.47 18.28 29.6
|
||||
27 1 34.37 19.4 0.17
|
||||
28 1 5.94 9.53 10.95
|
||||
29 1 11.45 38.44 14.64
|
||||
30 1 39.57 11.04 1.57
|
||||
31 1 25.91 20.97 12.79
|
||||
32 1 36.3 22.1 1.68
|
||||
33 1 21.87 22.49 3.43
|
||||
34 1 5.77 18.66 3.97
|
||||
35 1 7 7.59 18.42
|
||||
36 1 39.76 27.63 17.98
|
||||
37 1 10.26 23.18 5.11
|
||||
38 1 23.23 21.37 17.38
|
||||
39 1 7.47 37.37 5.57
|
||||
40 1 0.73 21.6 14.78
|
||||
41 1 2.27 30.22 14.93
|
||||
42 1 7.39 28.22 14.88
|
||||
43 1 27.48 1.11 25.02
|
||||
44 1 8.37 13.19 14.64
|
||||
45 1 7.11 33.57 0.65
|
||||
46 1 34.19 35.11 3.17
|
||||
47 1 7.52 3.2 20.33
|
||||
48 1 1.02 17.69 37.85
|
||||
49 1 8.59 6.21 10.26
|
||||
50 1 2.89 16.81 30.02
|
||||
51 1 27.05 9.07 32.8
|
||||
52 1 12.32 14.79 21.11
|
||||
53 1 26.63 22.69 16.75
|
||||
54 1 31.6 2.79 20.45
|
||||
55 1 35.11 0.74 12.16
|
||||
56 1 29.71 31.23 37.63
|
||||
57 1 38.22 19.02 18.12
|
||||
58 1 10.95 17.4 0.39
|
||||
59 1 1.65 19.87 6.67
|
||||
60 1 5.15 1.94 14.61
|
||||
61 1 8.2 31.43 15.72
|
||||
62 1 0.55 20.85 2.45
|
||||
63 1 15.27 31.74 0.33
|
||||
64 1 17.9 9.84 23.87
|
||||
65 1 1.46 8.39 19.24
|
||||
66 1 37.79 25.11 12.24
|
||||
67 1 14.11 27.19 30.7
|
||||
68 1 29.39 24.12 38.92
|
||||
69 1 39.15 20.32 39.86
|
||||
70 1 11.79 11.38 30.6
|
||||
71 1 29.87 30.18 32.5
|
||||
72 1 11.06 37.8 30.18
|
||||
73 1 20.11 4.59 35.57
|
||||
74 1 37.19 27.23 1.44
|
||||
75 1 18.83 26.13 35.26
|
||||
76 1 29.27 7.86 36.75
|
||||
77 1 34.83 29.59 37.82
|
||||
78 1 22.16 34.68 25.27
|
||||
79 1 5.95 14.65 25.55
|
||||
80 1 -0.04 3.48 29.91
|
||||
81 1 14.69 6.75 38.06
|
||||
82 1 16.8 23.69 3.14
|
||||
83 1 14.52 38.72 21.61
|
||||
84 1 37.36 15.13 27.98
|
||||
85 1 29.79 17.03 27.55
|
||||
86 1 21.01 0.39 0.9
|
||||
87 1 35.3 6.45 14.41
|
||||
88 1 13.74 34.69 10.01
|
||||
89 1 13.83 7.92 31.88
|
||||
90 1 26.88 37.81 22.36
|
||||
91 1 31.76 7.34 10.03
|
||||
92 1 11.98 37.49 19.61
|
||||
93 1 29.19 31.74 20.69
|
||||
94 1 39.15 10.97 21.06
|
||||
95 1 1.47 5 22.21
|
||||
96 1 -0.1 1.33 16.26
|
||||
97 1 34.74 34.78 30.66
|
||||
98 1 22.09 26.78 2.27
|
||||
99 1 36.58 34.8 16.19
|
||||
100 1 19.09 24.88 15.75
|
||||
101 1 2.21 31.42 38.32
|
||||
102 1 28.02 8.18 29.77
|
||||
103 1 15.99 16.78 17.61
|
||||
104 1 32.43 12.2 35.3
|
||||
105 1 26.54 38.8 30.88
|
||||
106 1 35.58 22.23 18.31
|
||||
107 1 28.3 30.81 2.96
|
||||
108 1 8.95 32.9 9.02
|
||||
109 1 28.51 30.02 29.39
|
||||
110 1 13 5.35 34.26
|
||||
111 1 37.9 36.79 1.37
|
||||
112 1 12.78 1.99 40.66
|
||||
113 1 21.19 34.55 17.45
|
||||
114 1 10.5 20 5.07
|
||||
115 1 16.19 21.64 18.49
|
||||
116 1 14.62 26.41 19.88
|
||||
117 1 27.97 2.89 28.03
|
||||
118 1 29.44 14.35 39.04
|
||||
119 1 2.29 24.16 33.8
|
||||
120 1 39.22 15.81 32.02
|
||||
121 1 7.31 19.66 18.18
|
||||
122 1 27.67 7.98 15.53
|
||||
123 1 31.23 4.04 33
|
||||
124 1 29.52 39.44 28.71
|
||||
125 1 30.86 20.28 15.84
|
||||
126 1 32.25 7.44 19.79
|
||||
127 1 34.68 15.68 1.18
|
||||
128 1 16.58 27.98 27.97
|
||||
129 1 32.27 24.24 15.82
|
||||
130 1 3.86 6.57 39.8
|
||||
131 1 9.1 2.88 13.12
|
||||
132 1 17.84 27.8 11.79
|
||||
133 1 4.77 10.88 6.75
|
||||
134 1 16.58 24.21 24.5
|
||||
135 1 10.17 19.31 38.32
|
||||
136 1 6.27 7.81 36.44
|
||||
137 1 34.76 37.89 29.76
|
||||
138 1 40.99 38.22 35.21
|
||||
139 1 25.04 21.79 36.88
|
||||
140 1 4.78 15.35 16.44
|
||||
141 1 19.24 5.77 40.18
|
||||
142 1 13.59 11.27 37.14
|
||||
143 1 1.61 23.83 39.61
|
||||
144 1 6.02 33.07 3.77
|
||||
145 1 0.85 7.4 35.42
|
||||
146 1 6.47 40.34 4.65
|
||||
147 1 16.45 36.52 15.44
|
||||
148 1 19.58 9.5 1.64
|
||||
149 1 1.36 1.72 35.53
|
||||
150 1 11.74 5.48 4.98
|
||||
151 1 25.45 40.36 15.44
|
||||
152 1 19.09 0.74 36.18
|
||||
153 1 31.78 37.98 1.84
|
||||
154 1 23.26 18.47 38.56
|
||||
155 1 7.29 22.87 25.86
|
||||
156 1 2.36 7.83 8.78
|
||||
157 1 39.61 25.94 21.12
|
||||
158 1 7.78 18.97 25.29
|
||||
159 1 36.56 19.61 26.7
|
||||
160 1 4.64 12.06 19.9
|
||||
161 1 21.05 33.08 0.87
|
||||
162 1 33.93 22.87 39.71
|
||||
163 1 33.62 29.48 20.83
|
||||
164 1 0.64 18.79 9.52
|
||||
165 1 27.53 16.7 22.51
|
||||
166 1 17.66 9.84 14.61
|
||||
167 1 31.23 22.44 24.98
|
||||
168 1 39.3 34.88 11.03
|
||||
169 1 24.01 10.56 0.09
|
||||
170 1 15.81 33.44 18.52
|
||||
171 1 19.92 30.61 19.25
|
||||
172 1 16.49 3.95 38.28
|
||||
173 1 18.6 38.87 24.98
|
||||
174 1 33.04 25.55 8.57
|
||||
175 1 16.9 35.09 22.94
|
||||
176 1 15.18 6.74 2.33
|
||||
177 1 40.54 12.58 31.65
|
||||
178 1 21.21 37.62 14.35
|
||||
179 1 33.52 38.19 14.89
|
||||
180 1 22.06 12.49 29.81
|
||||
181 1 19.49 29.03 2.52
|
||||
182 1 26.97 18.55 38.45
|
||||
183 1 24.1 11.86 17.22
|
||||
184 1 12.02 0.55 10.39
|
||||
185 1 3.8 35.94 19.94
|
||||
186 1 8.31 14.31 37.4
|
||||
187 1 29.03 8.28 22.92
|
||||
188 1 18.92 0.22 27.87
|
||||
189 1 26.79 24.9 24.62
|
||||
190 1 36.59 18.86 21.13
|
||||
191 1 33.06 13.58 30.17
|
||||
192 1 32.37 2.02 39.69
|
||||
193 1 22.65 25.97 32.59
|
||||
194 1 21.81 38.04 33.85
|
||||
195 1 36.82 37.68 19.22
|
||||
196 1 32.48 31.43 33.66
|
||||
197 1 8.75 36.66 20.34
|
||||
198 1 14.88 15.11 28.76
|
||||
199 1 22.83 28.55 29.5
|
||||
200 1 2.98 12.06 2.88
|
||||
201 1 3.01 37 6.91
|
||||
202 1 14.79 16.69 3.66
|
||||
203 1 12.62 38.28 0.97
|
||||
204 1 40.07 21.27 25.25
|
||||
205 1 34.58 6.14 39.48
|
||||
206 1 11.51 30.52 33.53
|
||||
207 1 32.22 9.28 30.52
|
||||
208 1 0.7 4.01 38.87
|
||||
209 1 32.66 39.86 36.84
|
||||
210 1 27.34 34.57 21.76
|
||||
211 1 13.7 23.12 8.34
|
||||
212 1 28 9.71 6.29
|
||||
213 1 31.69 26.39 38.19
|
||||
214 1 2.04 20.93 36.95
|
||||
215 1 30.31 26.61 12.31
|
||||
216 1 25.37 20.63 9.4
|
||||
217 1 16.29 5.62 14.04
|
||||
218 1 1.36 1.95 4.97
|
||||
219 1 38.75 26.8 5.62
|
||||
220 1 40.28 29.89 12.27
|
||||
221 1 0.52 31.22 7.58
|
||||
222 1 15.64 21.64 14.71
|
||||
223 1 10.11 28.8 9.67
|
||||
224 1 19.03 37.3 38.87
|
||||
225 1 12.07 6.46 19.25
|
||||
226 1 36.22 21.11 15.02
|
||||
227 1 12.49 15.69 7.21
|
||||
228 1 25.2 30.8 19.71
|
||||
229 1 8.24 35.22 23.02
|
||||
230 1 9.94 4.1 1.86
|
||||
231 1 4.31 19.07 26.23
|
||||
232 1 22.03 19.99 14.19
|
||||
233 1 30.84 5.24 2.75
|
||||
234 1 35.51 30.52 32.3
|
||||
235 1 3.88 20.41 39.48
|
||||
236 1 30.86 0.39 31.56
|
||||
237 1 25.91 27.12 39.04
|
||||
238 1 33.39 5.37 4.51
|
||||
239 1 20.58 28.33 37.53
|
||||
240 1 11.83 21.81 39.11
|
||||
241 1 39.94 5.2 5.73
|
||||
242 1 29.89 33.21 15.44
|
||||
243 1 23.42 15.38 30.98
|
||||
244 1 28.66 11.56 16.13
|
||||
245 1 16.74 20.43 21.72
|
||||
246 1 9.31 0.26 22.42
|
||||
247 1 4.38 37.78 14.12
|
||||
248 1 13.86 4.65 16.99
|
||||
249 1 6.72 27.43 8.14
|
||||
250 1 33.45 18.74 19.98
|
||||
251 1 17.34 14.55 35.57
|
||||
252 1 14.21 37.39 28.76
|
||||
253 1 26.29 29.06 22.26
|
||||
254 1 36.52 26.18 15.62
|
||||
255 1 17.6 8.81 10.14
|
||||
256 1 21.95 25.19 17.69
|
||||
257 1 17.4 7.46 18.59
|
||||
258 1 6.15 29.7 35.99
|
||||
259 1 9.73 37.39 24.96
|
||||
260 1 28.58 28.21 36.19
|
||||
261 1 8.24 13.72 32.2
|
||||
262 1 13.25 34.6 22.71
|
||||
263 1 38.58 7.98 10.3
|
||||
264 1 18.29 29.75 23.51
|
||||
265 1 3.74 13.22 31.05
|
||||
266 1 30.78 0.7 24.57
|
||||
267 1 24.5 12.94 10.81
|
||||
268 1 33.88 26.44 1.96
|
||||
269 1 29.92 22.6 9.59
|
||||
270 1 15.87 21.94 33.44
|
||||
271 1 23.63 8.41 10.95
|
||||
272 1 26.53 0.01 7.58
|
||||
273 1 33.88 8.73 2.52
|
||||
274 1 39.74 31.46 36.87
|
||||
275 1 13.28 39.54 37
|
||||
276 1 24.74 35.41 32.14
|
||||
277 1 17.3 34.32 6.85
|
||||
278 1 24.43 13.36 5.63
|
||||
279 1 31.23 17.12 7.11
|
||||
280 1 15.58 37.85 34.06
|
||||
281 1 25.93 38.17 3.13
|
||||
282 1 31.84 34.34 39.67
|
||||
283 1 14.41 17.74 14.43
|
||||
284 1 9.4 1.78 29.53
|
||||
285 1 8.29 29.61 6.81
|
||||
286 1 7.13 17.36 -0.19
|
||||
287 1 38.04 19.52 11.25
|
||||
288 1 34.87 32.77 38.75
|
||||
289 1 27.18 22.49 5.69
|
||||
290 1 29.69 27.11 20.29
|
||||
291 1 25.23 2.22 39.75
|
||||
292 1 35.8 17.1 36.09
|
||||
293 1 20.53 17.67 35.47
|
||||
294 1 23.41 31.36 2.24
|
||||
295 1 25.17 20.09 29.2
|
||||
296 1 0.32 9.28 39.74
|
||||
297 1 22.49 18.77 29.89
|
||||
298 1 38.64 0.85 39.43
|
||||
299 1 18.55 5.87 9.15
|
||||
300 1 35.21 28.69 25.76
|
||||
301 1 39.24 15.68 6.36
|
||||
302 1 5.91 13.29 3.92
|
||||
303 1 0.5 21.25 21.62
|
||||
304 1 34.39 9.43 18.59
|
||||
305 1 22.7 1.03 8.79
|
||||
306 1 40.15 16.25 24.87
|
||||
307 1 16.52 13.69 10.25
|
||||
308 1 6.88 36.77 39.57
|
||||
309 1 11.95 37.1 7.59
|
||||
310 1 19.49 26.66 9.76
|
||||
311 1 36.34 29.89 29.31
|
||||
312 1 18.76 35.75 12.72
|
||||
313 1 23.15 38.68 4.96
|
||||
314 1 10.78 17.11 34.38
|
||||
315 1 13.58 14.89 0.34
|
||||
316 1 4.73 33.88 32.41
|
||||
317 1 12.68 29.51 17.07
|
||||
318 1 9.45 27 4.98
|
||||
319 1 29.02 19.27 6.45
|
||||
320 1 19.09 36.35 19.84
|
||||
321 1 23.13 6.75 19.78
|
||||
322 1 8.02 34.1 26.95
|
||||
323 1 26.03 14.18 1.57
|
||||
324 1 15.01 34.16 28.32
|
||||
325 1 28.71 36.53 15.08
|
||||
326 1 9.64 13.94 24.05
|
||||
327 1 1.24 36.96 30.41
|
||||
328 1 15.44 31.39 4.77
|
||||
329 1 25.72 14.42 38.01
|
||||
330 1 7.35 31.84 12.61
|
||||
331 1 32.33 16.79 3.07
|
||||
332 1 15.86 0.39 8.39
|
||||
333 1 27.69 7.32 25.74
|
||||
334 1 27.77 1.17 4.96
|
||||
335 1 29.38 26.68 23.48
|
||||
336 1 14.95 3.41 2.13
|
||||
337 1 2.45 38.8 17.54
|
||||
338 1 9.18 27.58 31.12
|
||||
339 1 36.62 15.23 23.66
|
||||
340 1 12.23 30.74 10.85
|
||||
341 1 12.87 0.23 24.05
|
||||
342 1 33.85 35.75 19.95
|
||||
343 1 36.36 30.35 13.94
|
||||
344 1 38.11 8.15 5.49
|
||||
345 1 15.58 1.29 29.89
|
||||
346 1 25.95 30.47 39.19
|
||||
347 1 27.69 15.5 13.37
|
||||
348 1 25.48 13.7 25.29
|
||||
349 1 0.72 39.53 4.41
|
||||
350 1 8.75 15.21 5.79
|
||||
351 1 10.49 26.46 27.25
|
||||
352 1 16.9 20.08 26.58
|
||||
353 1 3.95 4.33 20.25
|
||||
354 1 18.03 7.66 31.87
|
||||
355 1 21.35 2.88 17.26
|
||||
356 1 32.92 22.68 6.56
|
||||
357 1 21.72 4.62 12.02
|
||||
358 1 37.6 6.04 25.2
|
||||
359 1 22.22 23.78 7.36
|
||||
360 1 12.53 19.53 10.6
|
||||
361 1 17.87 26.05 19.32
|
||||
362 1 20.94 30.75 31.23
|
||||
363 1 22.33 11.87 35.79
|
||||
364 1 28.54 6.88 10.52
|
||||
365 1 29.58 26.13 8.56
|
||||
366 1 19.06 24.2 21.73
|
||||
367 1 25.05 38.41 26.91
|
||||
368 1 18.66 40.35 4.69
|
||||
369 1 11.87 6.75 12.72
|
||||
370 1 17.99 11.82 37.79
|
||||
371 1 8.97 24.7 0.61
|
||||
372 1 26.89 1.52 31.33
|
||||
373 1 6.88 22.51 14.06
|
||||
374 1 29.51 3.87 13.35
|
||||
375 1 0.95 14.53 10
|
||||
376 1 26.43 31.54 11.63
|
||||
377 1 6.1 35.16 11.28
|
||||
378 1 10.2 15.91 28.7
|
||||
379 1 13.24 25.67 24.3
|
||||
380 1 34.5 3.91 20.22
|
||||
381 1 22.48 2.17 5.2
|
||||
382 1 24.26 16.15 11.3
|
||||
383 1 20.63 32.57 27.3
|
||||
384 1 39.95 6.81 1.05
|
||||
385 1 24.38 34.78 38.27
|
||||
386 1 4.63 23.56 0.55
|
||||
387 1 33.5 8.38 36.97
|
||||
388 1 5.76 27.14 12.06
|
||||
389 1 37.45 26.58 32.25
|
||||
390 1 2.8 8.96 32.35
|
||||
391 1 5.29 39.84 30.1
|
||||
392 1 29.2 26.49 31.18
|
||||
393 1 33.91 27.39 12.89
|
||||
394 1 3.37 14.19 39.34
|
||||
395 1 30.68 28.7 27
|
||||
396 1 2.59 18.45 19.38
|
||||
397 1 13.55 0.75 27.35
|
||||
398 1 3.82 20.12 16.1
|
||||
399 1 37.72 0.72 34.29
|
||||
400 1 23.85 3.32 19.46
|
||||
401 1 4.78 0.67 38.23
|
||||
402 1 22.78 23.26 38.6
|
||||
403 1 11.56 39.29 4.23
|
||||
404 1 21.38 32.45 5.39
|
||||
405 1 8.32 19.42 9.52
|
||||
406 1 28.43 31.07 17.8
|
||||
407 1 11.02 5.75 39.84
|
||||
408 1 27.36 36.71 7.62
|
||||
409 1 34.22 16.74 27.88
|
||||
410 1 3.22 22.01 27.42
|
||||
411 1 29.2 15.76 32.33
|
||||
412 1 25.29 23.44 2.2
|
||||
413 1 10.8 32.43 39.96
|
||||
414 1 32.2 1.41 4.44
|
||||
415 1 32.94 15.59 37.21
|
||||
416 1 6.8 8.08 0.84
|
||||
417 1 10.42 9.91 37.73
|
||||
418 1 1.18 31.39 3.93
|
||||
419 1 10.1 36.38 38.57
|
||||
420 1 32.89 26.96 35.07
|
||||
421 1 28.12 11.93 25.96
|
||||
422 1 4.9 29.15 -0.25
|
||||
423 1 2.21 27.99 3.72
|
||||
424 1 11.33 3.94 25.55
|
||||
425 1 3.3 30.26 10.78
|
||||
426 1 11.57 27.26 19.31
|
||||
427 1 21.79 32.67 13.3
|
||||
428 1 4.96 26.53 33.78
|
||||
429 1 33.41 32.87 18.46
|
||||
430 1 13.92 30.37 20.3
|
||||
431 1 16.91 3.5 11.57
|
||||
432 1 -0.06 4.42 34.05
|
||||
433 1 7.04 24.33 16.85
|
||||
434 1 28.66 11.93 19.73
|
||||
435 1 30.21 1.75 36.36
|
||||
436 1 3.91 6.2 6.26
|
||||
437 1 7.01 25.6 27.34
|
||||
438 1 34 1.06 18.12
|
||||
439 1 29.14 8.5 3.09
|
||||
440 1 40.13 23.52 16.94
|
||||
441 1 21.69 22.38 26.78
|
||||
442 1 18.44 32.85 39.84
|
||||
443 1 38.87 1.99 27.63
|
||||
444 1 10.47 12.02 33.68
|
||||
445 1 9.65 19.94 21.88
|
||||
446 1 25.04 8.12 27.89
|
||||
447 1 12.18 16.78 31.09
|
||||
448 1 38.31 8.2 30.6
|
||||
449 1 0.11 5.21 18.12
|
||||
450 1 23.48 7.88 38.7
|
||||
451 1 7.9 11.99 7.04
|
||||
452 1 2.09 34.5 8.64
|
||||
453 1 19 18.3 0.42
|
||||
454 1 37.94 18.06 15.21
|
||||
455 1 25.05 33.33 29.55
|
||||
456 1 33.74 37.88 34.54
|
||||
457 1 36.07 29.5 17.47
|
||||
458 1 27.7 13.54 10.46
|
||||
459 1 27.18 23.18 21.06
|
||||
460 1 17.49 2.04 23.22
|
||||
461 1 23.84 26.31 36.76
|
||||
462 1 31.08 32.24 24.92
|
||||
463 1 17.7 28.73 16.66
|
||||
464 1 1.59 15.5 18.04
|
||||
465 1 33.49 18.99 8.75
|
||||
466 1 1.19 8.43 28.01
|
||||
467 1 5.43 20.26 22.25
|
||||
468 1 23.3 5.31 15.05
|
||||
469 1 27.09 4.47 21.96
|
||||
470 1 26.61 27.48 28.83
|
||||
471 1 13 3.18 13.4
|
||||
472 1 36.09 34.56 10.58
|
||||
473 1 19.09 15.33 7.48
|
||||
474 1 12.94 18.16 22.07
|
||||
475 1 38.8 16.16 36.73
|
||||
476 1 16.73 39.94 -0.46
|
||||
477 1 3.64 12.56 9.42
|
||||
478 1 27.64 3.31 18.29
|
||||
479 1 15.58 12.36 4.52
|
||||
480 1 15.37 11.18 18.19
|
||||
481 1 37.52 11.23 14.94
|
||||
482 1 37.16 2.3 10.01
|
||||
483 1 36.19 9.86 21.99
|
||||
484 1 36.38 21.09 4.76
|
||||
485 1 38.15 12.94 25.35
|
||||
486 1 15.1 29.65 24.64
|
||||
487 1 16.54 29.12 38.85
|
||||
488 1 33.86 11.39 14.4
|
||||
489 1 27.99 18.55 9.87
|
||||
490 1 0.66 1.26 8.28
|
||||
491 1 29.89 33.84 29.75
|
||||
492 1 6.64 33.3 6.74
|
||||
493 1 31.47 0.39 11.25
|
||||
494 1 8.76 15.96 10.74
|
||||
495 1 39.6 15.8 21.04
|
||||
496 1 22.38 28.55 19.85
|
||||
497 1 25.87 6.23 5.4
|
||||
498 1 36.24 26.67 38.61
|
||||
499 1 23.05 8.79 7.01
|
||||
500 1 32.05 4.16 8.87
|
||||
501 1 35.3 13.36 38.03
|
||||
502 1 39.91 25.91 36.45
|
||||
503 1 32.17 17.27 31.82
|
||||
504 1 29.99 21.54 20.57
|
||||
505 1 9.39 0.57 34.17
|
||||
506 1 22.12 17.22 13.03
|
||||
507 1 15.23 16.27 24.39
|
||||
508 1 26.32 25.89 13.26
|
||||
509 1 39.25 3.46 1.34
|
||||
510 1 32.56 10.28 7.96
|
||||
511 1 25.76 14.8 34.79
|
||||
512 1 32.12 5.38 36.94
|
||||
513 1 17.74 15.37 14.87
|
||||
514 1 21.93 3.26 25.26
|
||||
515 1 24.05 0.48 36.27
|
||||
516 1 8.2 19.02 33.92
|
||||
517 1 33.07 25.88 24.79
|
||||
518 1 12.54 0.52 32.8
|
||||
519 1 18.5 6.34 23.21
|
||||
520 1 35.93 10.26 34.79
|
||||
521 1 19.33 11.86 6.94
|
||||
522 1 1.63 5.31 25.43
|
||||
523 1 30.62 36.78 30.77
|
||||
524 1 12.25 26.79 13.74
|
||||
525 1 21 1.47 13.99
|
||||
526 1 22.24 29.36 34.11
|
||||
527 1 29.05 1.74 0.24
|
||||
528 1 19.34 25.14 39.77
|
||||
529 1 12.9 25.42 35.42
|
||||
530 1 4.1 20.69 33.31
|
||||
531 1 35.38 5.64 9.17
|
||||
532 1 5.01 34.03 23.36
|
||||
533 1 15.7 10.01 7.1
|
||||
534 1 25.95 19.48 24.73
|
||||
535 1 11.15 4.16 21.43
|
||||
536 1 1.47 3.23 13.72
|
||||
537 1 26.54 36.76 17.48
|
||||
538 1 7.65 30.6 27.73
|
||||
539 1 18.59 3.05 3.32
|
||||
540 1 6.92 36.14 15.67
|
||||
541 1 12.72 36.21 32.72
|
||||
542 1 16.33 26.24 14.35
|
||||
543 1 21.66 12.61 26.18
|
||||
544 1 15.72 32.37 10.71
|
||||
545 1 27.57 15.75 4.97
|
||||
546 1 20.18 39.13 18.44
|
||||
547 1 18.77 17.09 4.74
|
||||
548 1 12.75 14.08 17.89
|
||||
549 1 10.71 37.26 35.13
|
||||
550 1 20.88 32.12 9.94
|
||||
551 1 8.69 0.06 9.54
|
||||
552 1 1.58 12.61 26.42
|
||||
553 1 10.29 22.73 13.14
|
||||
554 1 23.31 25.7 4.97
|
||||
555 1 36.7 30.78 5.26
|
||||
556 1 5.6 28.71 23.76
|
||||
557 1 13.04 7.91 15.46
|
||||
558 1 40.24 33.53 34.5
|
||||
559 1 39.7 18.36 34.25
|
||||
560 1 23.52 22.84 21.14
|
||||
561 1 32.82 27.9 5.02
|
||||
562 1 1.52 33.77 27.04
|
||||
563 1 31.48 18.68 13.1
|
||||
564 1 34 24.07 34.55
|
||||
565 1 34.72 25.03 30.45
|
||||
566 1 18.92 5.7 16.54
|
||||
567 1 15.26 40.2 16.97
|
||||
568 1 24.55 16.8 26.26
|
||||
569 1 17.59 18.03 31.75
|
||||
570 1 12.08 27.38 38.42
|
||||
571 1 31.42 21.91 35.27
|
||||
572 1 9.68 6.93 36.96
|
||||
573 1 22.93 15.19 2.53
|
||||
574 1 11.83 24.38 2.24
|
||||
575 1 16.02 12.44 31.42
|
||||
576 1 20.24 10.7 20.15
|
||||
577 1 37.38 17.37 40.63
|
||||
578 1 3.74 17.41 22.49
|
||||
579 1 23.21 9.86 23.99
|
||||
580 1 2.49 36.56 38
|
||||
581 1 20.51 1.54 22.62
|
||||
582 1 8.23 33.44 33.15
|
||||
583 1 30.93 8.12 14.85
|
||||
584 1 36.35 3.92 37.65
|
||||
585 1 5.57 10.63 28.64
|
||||
586 1 30.24 22.84 4.6
|
||||
587 1 3.24 15.97 7.43
|
||||
588 1 22.64 0.7 27.09
|
||||
589 1 1.64 40.37 27.74
|
||||
590 1 30.53 35.28 3.5
|
||||
591 1 25.55 4.7 2.53
|
||||
592 1 22.04 29.56 12.29
|
||||
593 1 3.42 8.76 2.28
|
||||
594 1 16.37 37.65 7.87
|
||||
595 1 20.65 12.75 2.9
|
||||
596 1 8.07 20.49 2.6
|
||||
597 1 20.04 24.72 28.2
|
||||
598 1 29.75 0.33 16.1
|
||||
599 1 31.36 33.09 8.02
|
||||
600 1 8.6 10.56 2.65
|
||||
601 1 20.55 33.93 33.71
|
||||
602 1 23.11 -0.42 31.7
|
||||
603 1 27.07 6.69 18.5
|
||||
604 1 15.65 23.71 11.8
|
||||
605 1 23.88 24.17 30.1
|
||||
606 1 0.79 32.46 16.99
|
||||
607 1 25.96 20.19 2.43
|
||||
608 1 35.16 12.33 4.73
|
||||
609 1 16.53 17.12 10.45
|
||||
610 1 19.74 35.94 8.62
|
||||
611 1 -0.24 28.29 28.3
|
||||
612 1 33.15 4.39 12.64
|
||||
613 1 24.27 18.59 33.59
|
||||
614 1 0.3 9.61 23.54
|
||||
615 1 5.52 10.89 34.71
|
||||
616 1 9.85 26.26 34.42
|
||||
617 1 25.54 37.74 39.13
|
||||
618 1 4.11 29.65 5.81
|
||||
619 1 30.86 22.72 31.07
|
||||
620 1 39.54 34.54 23.24
|
||||
621 1 15.03 9.34 12.11
|
||||
622 1 21.93 38.49 9.53
|
||||
623 1 18.21 19.2 16.65
|
||||
624 1 38.71 32.83 14.49
|
||||
625 1 37.74 36.38 31.43
|
||||
626 1 7.57 2.2 1.07
|
||||
627 1 12.27 10.05 1.53
|
||||
628 1 18.32 19.55 12.51
|
||||
629 1 12.49 24.81 16.57
|
||||
630 1 35.07 31.62 22.85
|
||||
631 1 4.91 19.68 30.45
|
||||
632 1 11.36 2.92 36.19
|
||||
633 1 26.76 35.53 1.29
|
||||
634 1 1.13 14.55 14.77
|
||||
635 1 8.2 25.14 37.83
|
||||
636 1 -0.5 0.85 23.08
|
||||
637 1 17.95 18.01 37.61
|
||||
638 1 2.44 37.75 0.71
|
||||
639 1 3.77 23.41 17.91
|
||||
640 1 3.34 14.41 35.96
|
||||
641 1 14.89 31.42 31.76
|
||||
642 1 15.72 22.91 30.66
|
||||
643 1 37.42 3.13 5.51
|
||||
644 1 1.51 38.14 20.78
|
||||
645 1 12.55 18.16 25.81
|
||||
646 1 18.98 15.88 29.21
|
||||
647 1 17.33 32.04 27.87
|
||||
648 1 31.21 37.38 22.84
|
||||
649 1 11.88 32.4 31
|
||||
650 1 25.1 2.19 12.69
|
||||
651 1 38.85 39.1 27.87
|
||||
652 1 5.9 16.14 33.34
|
||||
653 1 6.3 17.5 36.46
|
||||
654 1 2.28 25.02 12.53
|
||||
655 1 19.33 25.49 6.78
|
||||
656 1 8.57 37.22 8.4
|
||||
657 1 22 38.61 24.14
|
||||
658 1 35.63 3.23 2.15
|
||||
659 1 37.35 22.64 9.99
|
||||
660 1 25.46 28.22 33.18
|
||||
661 1 13.99 4.21 9.07
|
||||
662 1 9.04 40.64 37.59
|
||||
663 1 17.46 6.49 27.93
|
||||
664 1 1.42 6.14 30.2
|
||||
665 1 25.82 28.28 10.33
|
||||
666 1 30.71 30.2 -0.02
|
||||
667 1 8.05 29.32 0.62
|
||||
668 1 6.49 3.17 6.65
|
||||
669 1 7.77 39.88 26.03
|
||||
670 1 28.53 12.14 30.96
|
||||
671 1 6.25 12.64 39.55
|
||||
672 1 3.78 7.96 25.83
|
||||
673 1 28.69 29.58 6.61
|
||||
674 1 5.32 18.55 8.6
|
||||
675 1 5.3 11.44 14.19
|
||||
676 1 39 12.03 36.99
|
||||
677 1 11.08 32.51 19.12
|
||||
678 1 38.48 1.03 20.34
|
||||
679 1 38.47 11.31 10.12
|
||||
680 1 3.65 20.3 11.99
|
||||
681 1 27.18 11.39 3.4
|
||||
682 1 29.61 20.72 38.86
|
||||
683 1 31.88 4.82 24.75
|
||||
684 1 14.52 36.61 25.66
|
||||
685 1 21.68 19.96 24.58
|
||||
686 1 1.2 13.59 23.16
|
||||
687 1 37.71 5.97 35.28
|
||||
688 1 19.81 22.04 37.54
|
||||
689 1 40.67 27.07 10.14
|
||||
690 1 38.57 13.96 13.75
|
||||
691 1 18.15 17.19 21.63
|
||||
692 1 3.76 27.51 30.32
|
||||
693 1 11.39 25.09 7.96
|
||||
694 1 28.95 22.02 13.33
|
||||
695 1 31.72 35.46 35.33
|
||||
696 1 15.17 6.03 23.94
|
||||
697 1 9.63 9.42 22.18
|
||||
698 1 27.76 4.1 38.61
|
||||
699 1 27.37 37.46 11.07
|
||||
700 1 35.69 15.24 6.39
|
||||
701 1 21.92 33.09 36.84
|
||||
702 1 4.79 15.51 13.28
|
||||
703 1 9.31 26.44 22.8
|
||||
704 1 30.14 38.31 6.98
|
||||
705 1 4.33 6.66 13.77
|
||||
706 1 3.66 27.15 37.83
|
||||
707 1 0.44 24.06 29.62
|
||||
708 1 35.4 9.59 9.8
|
||||
709 1 33.77 39.44 21.41
|
||||
710 1 29.2 18.74 24.38
|
||||
711 1 34.14 30 7.36
|
||||
712 1 16.02 4.37 6.43
|
||||
713 1 35.75 39.41 40.58
|
||||
714 1 15.32 11.84 23.24
|
||||
715 1 32.52 24.39 20.97
|
||||
716 1 11.45 2.9 7.16
|
||||
717 1 7.07 34.28 36.04
|
||||
718 1 11.41 8.83 7.57
|
||||
719 1 29.29 27.79 16.55
|
||||
720 1 2.41 9.16 16.14
|
||||
721 1 13.14 38.07 12.01
|
||||
722 1 37.45 14.26 18.3
|
||||
723 1 34.64 18.37 16.65
|
||||
724 1 29.26 34.28 33.46
|
||||
725 1 13.67 19.83 3.04
|
||||
726 1 19.64 2.6 32.95
|
||||
727 1 23.61 23.55 11.34
|
||||
728 1 6.87 22.5 36.5
|
||||
729 1 36.78 28.34 22.96
|
||||
730 1 11.3 13.98 9.84
|
||||
731 1 20.82 19.73 9.16
|
||||
732 1 12.65 12.61 6.16
|
||||
733 1 9.25 7.81 25.28
|
||||
734 1 25.4 29.36 5.84
|
||||
735 1 17.86 9.06 4.45
|
||||
736 1 35.84 40.51 26.06
|
||||
737 1 26.97 21.28 31.59
|
||||
738 1 39.94 38.14 24.86
|
||||
739 1 3.16 17.07 2.49
|
||||
740 1 14.08 15.4 36.99
|
||||
741 1 26.1 13.88 29.68
|
||||
742 1 26.36 20 20.56
|
||||
743 1 12.02 6.35 27.65
|
||||
744 1 11.21 19.14 15.27
|
||||
745 1 35.86 22.93 26.81
|
||||
746 1 32.26 12.62 2.68
|
||||
747 1 29.36 4.91 6.86
|
||||
748 1 20.14 7.97 29.32
|
||||
749 1 25.53 11.2 36.18
|
||||
750 1 30.36 14.25 24.79
|
||||
751 1 29.84 38.37 39.29
|
||||
752 1 15.79 36.4 4.26
|
||||
753 1 32.59 14.17 10.29
|
||||
754 1 13.89 34.54 15.42
|
||||
755 1 12.13 33.62 7.27
|
||||
756 1 25.86 23.81 33.97
|
||||
757 1 18.4 31.27 34.96
|
||||
758 1 6.58 40.49 17.57
|
||||
759 1 5.64 39.86 23.05
|
||||
760 1 25.32 33 16.24
|
||||
761 1 0.98 10.99 12.21
|
||||
762 1 32.86 23.75 12.41
|
||||
763 1 32.91 1.3 26.94
|
||||
764 1 9.46 8.66 31.47
|
||||
765 1 17.49 15.53 1.82
|
||||
766 1 8.17 18.16 15.3
|
||||
767 1 4.84 30.63 26.32
|
||||
768 1 6.75 37.1 30.8
|
||||
769 1 7.16 5.72 15.74
|
||||
770 1 20.09 17.82 19.18
|
||||
771 1 1.02 27.99 32.54
|
||||
772 1 21.44 1.28 38.4
|
||||
773 1 21.06 14.62 37.08
|
||||
774 1 27.82 18.99 15.96
|
||||
775 1 33.51 21.46 22.82
|
||||
776 1 8.29 2.79 17.09
|
||||
777 1 18.14 11.41 28.62
|
||||
778 1 17.94 28.54 32.73
|
||||
779 1 36.1 9.54 40.1
|
||||
780 1 36.55 2.62 22.97
|
||||
781 1 27.29 10.41 39.35
|
||||
782 1 22.04 37.76 2.02
|
||||
783 1 23.01 30.08 16.58
|
||||
784 1 6.34 15.31 21.61
|
||||
785 1 7.3 22.39 7.74
|
||||
786 1 38 5.77 21.04
|
||||
787 1 32.93 12.85 26.58
|
||||
788 1 22.43 15.36 16.72
|
||||
789 1 18.54 2.38 8.35
|
||||
790 1 0.62 31.88 23.84
|
||||
791 1 39.56 30.3 21.7
|
||||
792 1 7.56 11.78 25.2
|
||||
793 1 16.05 3.98 26.72
|
||||
794 1 24.33 36.16 13.16
|
||||
795 1 26.38 31.24 35.77
|
||||
796 1 14.94 26.46 -0.44
|
||||
797 1 3.53 28 19.79
|
||||
798 1 11.94 32.27 25.88
|
||||
799 1 34.59 15.06 19.23
|
||||
800 1 3.51 10.62 24.22
|
||||
801 1 13.18 21.59 35.52
|
||||
802 1 19.95 13.15 16.23
|
||||
803 1 24.48 9.63 19.58
|
||||
804 1 37.7 34.42 19.19
|
||||
805 1 22.84 19.59 5.52
|
||||
806 1 34.62 36.75 12.26
|
||||
807 1 10.33 21.85 25.15
|
||||
808 1 21.51 29.7 7.23
|
||||
809 1 34.05 3 30.58
|
||||
810 1 12.43 29.67 5.59
|
||||
811 1 18.94 21.82 29.31
|
||||
812 1 39.21 17.7 4
|
||||
813 1 7.04 2.97 37.09
|
||||
814 1 30.87 10.8 22.09
|
||||
815 1 33.54 7.16 23.15
|
||||
816 1 32.82 32.27 11.47
|
||||
817 1 21.8 14.54 21.61
|
||||
818 1 38.83 6.69 13.68
|
||||
819 1 30.37 39.05 18.66
|
||||
820 1 31.21 15.08 13.79
|
||||
821 1 1.07 11.97 35.04
|
||||
822 1 26.02 35.8 35.47
|
||||
823 1 27.64 33.32 8.04
|
||||
824 1 39.57 36.88 4.39
|
||||
825 1 14.48 30.97 36.87
|
||||
826 1 36.86 27.04 8.96
|
||||
827 1 34.73 26.27 19.55
|
||||
828 1 29.24 29.12 10.86
|
||||
829 1 8.35 39.9 13.92
|
||||
830 1 5.43 5.1 31.85
|
||||
831 1 18.36 22.31 5.89
|
||||
832 1 2.46 27.35 16.36
|
||||
833 1 21.76 37.05 27.45
|
||||
834 1 29.32 17.11 2.28
|
||||
835 1 3.58 21.98 3.09
|
||||
836 1 10.61 9.17 10.69
|
||||
837 1 25.15 17.54 6.05
|
||||
838 1 3.4 22.81 7.03
|
||||
839 1 16.12 23.66 38.29
|
||||
840 1 8.67 4.79 31.8
|
||||
841 1 27.82 0.02 20.45
|
||||
842 1 4.46 2.44 29.46
|
||||
843 1 39.11 22.69 36.33
|
||||
844 1 4.26 2.45 34.43
|
||||
845 1 13.47 3.5 30.9
|
||||
846 1 26.92 22.55 26.54
|
||||
847 1 5.66 30.07 30.65
|
||||
848 1 31.58 35.68 25.46
|
||||
849 1 31.23 5.65 27.78
|
||||
850 1 8.76 19.49 28.61
|
||||
851 1 24.13 8.02 2.3
|
||||
852 1 8.27 6.8 4.93
|
||||
853 1 15.31 34.36 37.63
|
||||
854 1 3.96 35.82 26.97
|
||||
855 1 24.95 4.01 29.96
|
||||
856 1 26.54 25.95 19.15
|
||||
857 1 17.76 29.23 5.35
|
||||
858 1 16.95 21.79 0.78
|
||||
859 1 17.52 39.02 13.01
|
||||
860 1 20.5 22.86 10.41
|
||||
861 1 27.67 27.07 2.78
|
||||
862 1 37.1 31.02 2.03
|
||||
863 1 37.17 2.24 16.34
|
||||
864 1 24.51 34.69 10.28
|
||||
865 1 17.38 13.41 21.4
|
||||
866 1 38 9.37 17.94
|
||||
867 1 35.67 25.27 5.3
|
||||
868 1 22.66 4.47 0.97
|
||||
869 1 20.06 28.17 27.42
|
||||
870 1 27.33 2.38 9.79
|
||||
871 1 36.4 10.73 31.42
|
||||
872 1 0.53 9.45 6.96
|
||||
873 1 12.89 9.03 25.13
|
||||
874 1 37.5 23.54 21.33
|
||||
875 1 7.19 28.87 19.11
|
||||
876 1 21.45 32.81 22.71
|
||||
877 1 8.76 8.3 13.51
|
||||
878 1 10.24 31.46 3.73
|
||||
879 1 15.93 9.7 35.82
|
||||
880 1 14.92 19.46 39.91
|
||||
881 1 13.02 22.03 27.3
|
||||
882 1 34.57 1.59 34.73
|
||||
883 1 0.5 21.04 30.77
|
||||
884 1 24.84 32.67 4.97
|
||||
885 1 30.96 4.24 17.34
|
||||
886 1 23.63 8.84 32.7
|
||||
887 1 6.84 3.83 26.13
|
||||
888 1 31.57 9.23 27.06
|
||||
889 1 14.99 35.15 0.07
|
||||
890 1 36.29 40.01 8.22
|
||||
891 1 18 36.86 35.66
|
||||
892 1 11.5 29.22 0.37
|
||||
893 1 35.18 36.03 24.88
|
||||
894 1 14.49 9.41 27.73
|
||||
895 1 10.12 12.91 0.99
|
||||
896 1 11.91 29.4 27.3
|
||||
897 1 25.51 28.68 14.56
|
||||
898 1 29.32 12.95 35.59
|
||||
899 1 2.96 0.59 0.53
|
||||
900 1 5.47 5.35 9.88
|
||||
901 1 8.93 39.33 1.78
|
||||
902 1 39.68 38.49 12.33
|
||||
903 1 3.78 1.24 11.85
|
||||
904 1 29.54 33.76 11.99
|
||||
905 1 7.48 6.16 28.8
|
||||
906 1 10.83 33.63 36.96
|
||||
907 1 22.03 19.06 21.39
|
||||
908 1 31.68 31 3.71
|
||||
909 1 35.32 0.3 30.88
|
||||
910 1 9.93 35.42 14.85
|
||||
911 1 21.01 10.66 12.97
|
||||
912 1 22.54 21.62 33.81
|
||||
913 1 12.48 12.46 25.15
|
||||
914 1 0.64 27.93 39.01
|
||||
915 1 13.88 27.29 3.8
|
||||
916 1 13.03 20.93 19.25
|
||||
917 1 5.7 37.48 34.09
|
||||
918 1 2.27 35.08 14.29
|
||||
919 1 21.75 26.44 13.48
|
||||
920 1 10.66 11.35 17.49
|
||||
921 1 36.67 34.72 27.69
|
||||
922 1 8.23 22.8 33.36
|
||||
923 1 4.79 4.05 3.48
|
||||
924 1 35.61 35 35.21
|
||||
925 1 31.38 37.67 10.06
|
||||
926 1 26.44 35.58 27.52
|
||||
927 1 25.53 4.47 8.03
|
||||
928 1 38.81 33.08 31.55
|
||||
929 1 29.62 39.68 34.32
|
||||
930 1 0.76 3.88 10.61
|
||||
931 1 24.06 30.13 24.84
|
||||
932 1 18.77 8.38 37.02
|
||||
933 1 2.81 24.14 24.45
|
||||
934 1 11.33 1.25 19.69
|
||||
935 1 1.61 26.53 6.48
|
||||
936 1 9.52 29.81 35.98
|
||||
937 1 7.83 31.75 20.77
|
||||
938 1 9.67 23.93 20.57
|
||||
939 1 33.96 16.95 24.79
|
||||
940 1 37.55 37.31 37.17
|
||||
941 1 6.2 24.19 31.13
|
||||
942 1 17.79 4.35 30.56
|
||||
943 1 13.51 20.25 30.45
|
||||
944 1 14.76 12.48 13.13
|
||||
945 1 32.56 27.52 30.41
|
||||
946 1 35.81 40.1 4.85
|
||||
947 1 39.01 25.43 27.07
|
||||
948 1 22.8 5.53 32.22
|
||||
949 1 2.35 39.55 32.5
|
||||
950 1 3.31 31.51 34.19
|
||||
951 1 40.63 37.01 15.9
|
||||
952 1 18.43 35.86 30.77
|
||||
953 1 37.01 39.18 15.57
|
||||
954 1 6.74 6.26 21.64
|
||||
955 1 5.22 24.94 22.53
|
||||
956 1 25.2 11.08 13.98
|
||||
957 1 14.66 -0.14 5
|
||||
958 1 14.96 8.38 20.32
|
||||
959 1 1.89 23.03 10.1
|
||||
960 1 33.01 11.23 39.32
|
||||
961 1 32.68 6.79 32.04
|
||||
962 1 6.25 25.81 3.82
|
||||
963 1 18.37 31.97 14.57
|
||||
964 1 9.74 30.21 22.71
|
||||
965 1 3.09 1.52 19.38
|
||||
966 1 33.98 37.34 5.63
|
||||
967 1 32.19 28.35 15.8
|
||||
968 1 24.4 15.49 19.39
|
||||
@ -32,8 +32,8 @@ thermo 50
|
||||
# dump 1 all xyz 100 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
|
||||
# stable at 800K
|
||||
fix 1 statted_grp nvt temp 800 800 100
|
||||
|
||||
@ -84,7 +84,9 @@ thermo 50
|
||||
|
||||
# dump 1 all xyz 100 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
@ -132,39 +134,42 @@ Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 800 3666.3948 0.80366765 0 0
|
||||
50 673.95238 -9670.9169 0.80366765 31 0
|
||||
100 693.69241 -4696.4359 0.80366765 57 22
|
||||
150 715.44689 -14740.892 0.80366765 77 50
|
||||
200 721.16898 -1411.95 0.80366765 84 66
|
||||
Loop time of 107.389 on 1 procs for 200 steps with 35200 atoms
|
||||
100 697.22819 -4624.0512 0.80366765 57 22
|
||||
150 723.60507 -17175.571 0.80366765 76 48
|
||||
200 736.71277 -12961.963 0.80366765 84 64
|
||||
Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
|
||||
|
||||
Performance: 0.161 ns/day, 149.151 hours/ns, 1.862 timesteps/s
|
||||
Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.191 | 27.191 | 27.191 | 0.0 | 25.32
|
||||
Bond | 11.46 | 11.46 | 11.46 | 0.0 | 10.67
|
||||
Kspace | 4.2507 | 4.2507 | 4.2507 | 0.0 | 3.96
|
||||
Neigh | 55.544 | 55.544 | 55.544 | 0.0 | 51.72
|
||||
Comm | 0.41715 | 0.41715 | 0.41715 | 0.0 | 0.39
|
||||
Output | 0.0011044 | 0.0011044 | 0.0011044 | 0.0 | 0.00
|
||||
Modify | 8.4756 | 8.4756 | 8.4756 | 0.0 | 7.89
|
||||
Other | | 0.04897 | | | 0.05
|
||||
Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
|
||||
Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
|
||||
Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
|
||||
Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
|
||||
Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
|
||||
Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
|
||||
Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
|
||||
Other | | 0.04545 | | | 0.04
|
||||
|
||||
Nlocal: 35200 ave 35200 max 35200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 38406 ave 38406 max 38406 min
|
||||
Nghost: 38403 ave 38403 max 38403 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6.92787e+06 ave 6.92787e+06 max 6.92787e+06 min
|
||||
Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 6927872
|
||||
Ave neighs/atom = 196.815
|
||||
Ave special neighs/atom = 9.83489
|
||||
Total # of neighbors = 6928101
|
||||
Ave neighs/atom = 196.821
|
||||
Ave special neighs/atom = 9.83727
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
Total wall time: 0:01:48
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:43
|
||||
|
||||
@ -84,7 +84,9 @@ thermo 50
|
||||
|
||||
# dump 1 all xyz 100 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
@ -132,39 +134,42 @@ Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 800 3666.3948 0.80366765 0 0
|
||||
50 673.95238 -9670.9169 0.80366765 31 0
|
||||
100 693.69241 -4696.4359 0.80366765 57 22
|
||||
150 715.43654 -14742.205 0.80366765 77 50
|
||||
200 721.1906 -1411.4303 0.80366765 84 66
|
||||
Loop time of 56.2311 on 4 procs for 200 steps with 35200 atoms
|
||||
100 697.22819 -4624.0512 0.80366765 57 22
|
||||
150 724.40407 -17166.729 0.80366765 76 49
|
||||
200 737.28582 -12968.224 0.80366765 84 65
|
||||
Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
|
||||
|
||||
Performance: 0.307 ns/day, 78.099 hours/ns, 3.557 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.86 | 14.034 | 14.406 | 5.8 | 24.96
|
||||
Bond | 5.5592 | 5.5952 | 5.6492 | 1.4 | 9.95
|
||||
Kspace | 2.3969 | 2.7523 | 2.9203 | 12.5 | 4.89
|
||||
Neigh | 27.265 | 27.268 | 27.271 | 0.0 | 48.49
|
||||
Comm | 0.75523 | 0.77355 | 0.79381 | 1.7 | 1.38
|
||||
Output | 0.00051904 | 0.0007363 | 0.0013669 | 0.0 | 0.00
|
||||
Modify | 5.7629 | 5.7634 | 5.7641 | 0.0 | 10.25
|
||||
Other | | 0.04441 | | | 0.08
|
||||
Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
|
||||
Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
|
||||
Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
|
||||
Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
|
||||
Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
|
||||
Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
|
||||
Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
|
||||
Other | | 0.03995 | | | 0.08
|
||||
|
||||
Nlocal: 8800 ave 8912 max 8666 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 18358.8 ave 18432 max 18189 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Neighs: 1.73197e+06 ave 1.77209e+06 max 1.68475e+06 min
|
||||
Nlocal: 8800 ave 8913 max 8652 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 18366 ave 18461 max 18190 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 6927873
|
||||
Ave neighs/atom = 196.815
|
||||
Ave special neighs/atom = 9.83489
|
||||
Total # of neighbors = 6928132
|
||||
Ave neighs/atom = 196.822
|
||||
Ave special neighs/atom = 9.83608
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
Total wall time: 0:00:57
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:52
|
||||
|
||||
@ -33,8 +33,8 @@ thermo 50
|
||||
# dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
|
||||
fix 1 statted_grp nvt temp 300 300 100
|
||||
|
||||
|
||||
@ -85,7 +85,9 @@ thermo 50
|
||||
|
||||
# dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
@ -131,235 +133,238 @@ Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 296.70408 -51.30066 0.0034851739 1 0
|
||||
100 275.26011 39.120329 0.0034851739 1 1
|
||||
150 438.68516 35.257539 0.0034851739 1 1
|
||||
200 394.48971 15.444537 0.0034851739 1 1
|
||||
250 356.00369 50.185792 0.0034851739 1 1
|
||||
300 301.25816 -26.891497 0.0034851739 1 1
|
||||
350 279.17264 12.694513 0.0034851739 1 1
|
||||
400 248.71641 10.684558 0.0034851739 1 1
|
||||
450 240.30602 12.963034 0.0034851739 1 1
|
||||
500 252.71279 0.91620356 0.0034851739 1 1
|
||||
550 300.56824 18.541436 0.0034851739 1 1
|
||||
600 306.46441 -1.9736081 0.0034851739 1 1
|
||||
650 336.4537 21.474831 0.0034851739 1 1
|
||||
700 323.46217 8.486376 0.0034851739 1 1
|
||||
750 271.87146 5.9615231 0.0034851739 1 1
|
||||
800 268.43041 36.676068 0.0034851739 1 1
|
||||
850 269.02683 7.6295416 0.0034851739 1 1
|
||||
900 282.03605 -1.4688833 0.0034851739 1 1
|
||||
950 243.69136 -22.771489 0.0034851739 1 1
|
||||
1000 285.01348 17.925748 0.0034851739 1 1
|
||||
1050 383.47985 0.70536985 0.0034851739 1 1
|
||||
1100 368.97167 -4.3046933 0.0034851739 1 1
|
||||
1150 373.64459 6.3491837 0.0034851739 1 1
|
||||
1200 332.90575 -36.501095 0.0034851739 1 1
|
||||
1250 314.04078 -13.382767 0.0034851739 1 1
|
||||
1300 305.84166 4.7713641 0.0034851739 1 1
|
||||
1350 286.22145 37.621803 0.0034851739 1 1
|
||||
1400 265.52855 23.621002 0.0034851739 1 1
|
||||
1450 281.807 -31.266828 0.0034851739 1 1
|
||||
1500 275.33855 33.495565 0.0034851739 1 1
|
||||
1550 273.04973 -22.913871 0.0034851739 1 1
|
||||
1600 308.18478 -17.98151 0.0034851739 1 1
|
||||
1650 333.27664 28.987529 0.0034851739 1 1
|
||||
1700 296.16091 -1.1440455 0.0034851739 1 1
|
||||
1750 365.75611 34.574845 0.0034851739 1 1
|
||||
1800 292.83503 -33.199654 0.0034851739 1 1
|
||||
1850 261.50282 42.608703 0.0034851739 1 1
|
||||
1900 315.14188 -31.058803 0.0034851739 1 1
|
||||
1950 335.12895 12.40597 0.0034851739 1 1
|
||||
2000 278.08586 -5.3178633 0.0034851739 1 1
|
||||
2050 283.23847 -3.3974302 0.0034851739 1 1
|
||||
2100 281.38904 0.70263324 0.0034851739 1 1
|
||||
2150 302.23197 23.372316 0.0034851739 1 1
|
||||
2200 337.49259 -4.8716803 0.0034851739 1 1
|
||||
2250 409.64134 -12.043721 0.0034851739 1 1
|
||||
2300 309.21764 -21.824645 0.0034851739 1 1
|
||||
2350 290.97879 18.690281 0.0034851739 1 1
|
||||
2400 341.816 -16.967741 0.0034851739 1 1
|
||||
2450 310.28034 27.375518 0.0034851739 1 1
|
||||
2500 248.89429 17.061192 0.0034851739 1 1
|
||||
2550 273.10927 0.10481657 0.0034851739 1 1
|
||||
2600 289.56101 -9.7239939 0.0034851739 1 1
|
||||
2650 298.99719 -33.140576 0.0034851739 1 1
|
||||
2700 326.05198 -24.509827 0.0034851739 1 1
|
||||
2750 319.20612 24.305526 0.0034851739 1 1
|
||||
2800 304.8715 -15.076941 0.0034851739 1 1
|
||||
2850 374.38923 2.0874883 0.0034851739 1 1
|
||||
2900 354.01554 -20.595102 0.0034851739 1 1
|
||||
2950 289.89296 48.39731 0.0034851739 1 1
|
||||
3000 312.10013 -8.5105997 0.0034851739 1 1
|
||||
3050 296.97004 -31.008446 0.0034851739 1 1
|
||||
3100 251.72228 35.710197 0.0034851739 1 1
|
||||
3150 315.35895 -43.331536 0.0034851739 1 1
|
||||
3200 334.67773 13.331058 0.0034851739 1 1
|
||||
3250 308.1669 37.236121 0.0034851739 1 1
|
||||
3300 329.47601 30.798598 0.0034851739 1 1
|
||||
3350 299.40055 2.0785585 0.0034851739 1 1
|
||||
3400 272.41031 32.744922 0.0034851739 1 1
|
||||
3450 279.34594 -26.181793 0.0034851739 1 1
|
||||
3500 288.89969 8.935052 0.0034851739 1 1
|
||||
3550 253.4967 9.7244709 0.0034851739 1 1
|
||||
3600 294.83266 19.33305 0.0034851739 1 1
|
||||
3650 290.23794 -5.4939069 0.0034851739 1 1
|
||||
3700 332.5222 -29.834229 0.0034851739 1 1
|
||||
3750 364.63024 20.706191 0.0034851739 1 1
|
||||
3800 295.3842 -6.9434004 0.0034851739 1 1
|
||||
3850 346.84424 37.796066 0.0034851739 1 1
|
||||
3900 265.67286 -0.31628068 0.0034851739 1 1
|
||||
3950 260.455 -2.2571902 0.0034851739 1 1
|
||||
4000 259.82636 -2.2286205 0.0034851739 1 1
|
||||
4050 257.79848 24.520293 0.0034851739 1 1
|
||||
4100 295.58626 -0.42318936 0.0034851739 1 1
|
||||
4150 265.81353 -49.092436 0.0034851739 1 1
|
||||
4200 302.10333 51.715259 0.0034851739 1 1
|
||||
4250 258.98448 -4.8516655 0.0034851739 1 1
|
||||
4300 327.83401 33.717282 0.0034851739 1 1
|
||||
4350 311.59571 23.580382 0.0034851739 1 1
|
||||
4400 300.64237 -31.866661 0.0034851739 1 1
|
||||
4450 294.15643 -0.11927421 0.0034851739 1 1
|
||||
4500 299.83605 -17.560873 0.0034851739 1 1
|
||||
4550 326.83265 32.818482 0.0034851739 1 1
|
||||
4600 260.39068 -8.0567902 0.0034851739 1 1
|
||||
4650 247.93553 19.462991 0.0034851739 1 1
|
||||
4700 214.22252 -34.118303 0.0034851739 1 1
|
||||
4750 203.15329 27.356205 0.0034851739 1 1
|
||||
4800 257.761 -10.407989 0.0034851739 1 1
|
||||
4850 307.1923 11.71101 0.0034851739 1 1
|
||||
4900 319.00942 4.7808306 0.0034851739 1 1
|
||||
4950 282.23989 24.996151 0.0034851739 1 1
|
||||
5000 311.53284 -3.0012665 0.0034851739 1 1
|
||||
5050 317.58212 32.567832 0.0034851739 1 1
|
||||
5100 267.51501 -47.695087 0.0034851739 1 1
|
||||
5150 260.19048 29.046388 0.0034851739 1 1
|
||||
5200 239.83552 -5.4890385 0.0034851739 1 1
|
||||
5250 234.8852 -18.172633 0.0034851739 1 1
|
||||
5300 236.43277 -39.06212 0.0034851739 1 1
|
||||
5350 280.90079 -2.6932923 0.0034851739 1 1
|
||||
5400 316.65266 23.071362 0.0034851739 1 1
|
||||
5450 345.63226 19.573323 0.0034851739 1 1
|
||||
5500 384.57334 41.507217 0.0034851739 1 1
|
||||
5550 317.14278 9.6992897 0.0034851739 1 1
|
||||
5600 279.93243 -12.076895 0.0034851739 1 1
|
||||
5650 268.06471 1.6196401 0.0034851739 1 1
|
||||
5700 271.85714 -40.378455 0.0034851739 1 1
|
||||
5750 313.88363 10.722639 0.0034851739 1 1
|
||||
5800 281.54495 31.914889 0.0034851739 1 1
|
||||
5850 293.34821 -8.3154922 0.0034851739 1 1
|
||||
5900 249.25216 -17.307353 0.0034851739 1 1
|
||||
5950 268.18639 -4.7222512 0.0034851739 1 1
|
||||
6000 302.99398 -52.615528 0.0034851739 1 1
|
||||
6050 314.57931 34.51318 0.0034851739 1 1
|
||||
6100 345.70348 30.334721 0.0034851739 1 1
|
||||
6150 316.59329 31.862519 0.0034851739 1 1
|
||||
6200 317.85346 -32.235221 0.0034851739 1 1
|
||||
6250 282.97676 0.2936745 0.0034851739 1 1
|
||||
6300 267.91814 19.265567 0.0034851739 1 1
|
||||
6350 226.20967 -13.093547 0.0034851739 1 1
|
||||
6400 307.73316 17.439598 0.0034851739 1 1
|
||||
6450 292.16253 -23.275163 0.0034851739 1 1
|
||||
6500 335.05939 26.936463 0.0034851739 1 1
|
||||
6550 380.73546 19.532416 0.0034851739 1 1
|
||||
6600 373.0103 30.879532 0.0034851739 1 1
|
||||
6650 335.37975 -2.1762828 0.0034851739 1 1
|
||||
6700 298.94272 -10.578587 0.0034851739 1 1
|
||||
6750 255.11531 -50.576215 0.0034851739 1 1
|
||||
6800 222.87459 3.0499548 0.0034851739 1 1
|
||||
6850 268.57213 -43.675945 0.0034851739 1 1
|
||||
6900 260.3024 4.7483005 0.0034851739 1 1
|
||||
6950 289.15855 31.62106 0.0034851739 1 1
|
||||
7000 289.11874 21.635533 0.0034851739 1 1
|
||||
7050 361.08776 22.445996 0.0034851739 1 1
|
||||
7100 368.95003 4.8383881 0.0034851739 1 1
|
||||
7150 331.47448 -36.200495 0.0034851739 1 1
|
||||
7200 304.7251 13.982693 0.0034851739 1 1
|
||||
7250 284.09747 0.53758275 0.0034851739 1 1
|
||||
7300 269.17023 -41.571482 0.0034851739 1 1
|
||||
7350 222.07071 25.564662 0.0034851739 1 1
|
||||
7400 304.09598 15.482955 0.0034851739 1 1
|
||||
7450 298.78752 -7.4335841 0.0034851739 1 1
|
||||
7500 328.78697 14.666097 0.0034851739 1 1
|
||||
7550 347.07038 -37.165295 0.0034851739 1 1
|
||||
7600 362.85673 20.52268 0.0034851739 1 1
|
||||
7650 347.15141 2.3383775 0.0034851739 1 1
|
||||
7700 262.10132 33.898374 0.0034851739 1 1
|
||||
7750 275.84724 -33.534813 0.0034851739 1 1
|
||||
7800 281.14075 -18.284372 0.0034851739 1 1
|
||||
7850 264.83337 -30.580199 0.0034851739 1 1
|
||||
7900 257.35275 -35.080567 0.0034851739 1 1
|
||||
7950 286.32446 26.594779 0.0034851739 1 1
|
||||
8000 248.36889 15.605894 0.0034851739 1 1
|
||||
8050 292.55015 28.811985 0.0034851739 1 1
|
||||
8100 312.47888 0.83990451 0.0034851739 1 1
|
||||
8150 285.58532 -15.258185 0.0034851739 1 1
|
||||
8200 292.22819 -38.233195 0.0034851739 1 1
|
||||
8250 321.6208 -19.052143 0.0034851739 1 1
|
||||
8300 319.41332 54.97437 0.0034851739 1 1
|
||||
8350 307.95647 32.009591 0.0034851739 1 1
|
||||
8400 345.58105 8.8535539 0.0034851739 1 1
|
||||
8450 357.75168 12.416896 0.0034851739 1 1
|
||||
8500 370.049 4.3288665 0.0034851739 1 1
|
||||
8550 360.62882 12.618614 0.0034851739 1 1
|
||||
8600 290.10834 -4.8081765 0.0034851739 1 1
|
||||
8650 297.7575 -5.1976816 0.0034851739 1 1
|
||||
8700 286.57505 -31.469549 0.0034851739 1 1
|
||||
8750 307.77059 19.338001 0.0034851739 1 1
|
||||
8800 231.68316 12.159459 0.0034851739 1 1
|
||||
8850 329.13623 -8.7262592 0.0034851739 1 1
|
||||
8900 286.40715 10.326025 0.0034851739 1 1
|
||||
8950 339.43101 2.7809618 0.0034851739 1 1
|
||||
9000 402.53799 19.481869 0.0034851739 1 1
|
||||
9050 349.56449 -4.8450179 0.0034851739 1 1
|
||||
9100 307.64739 16.889327 0.0034851739 1 1
|
||||
9150 276.54451 -34.808372 0.0034851739 1 1
|
||||
9200 233.18668 4.9409791 0.0034851739 1 1
|
||||
9250 266.48384 -19.850366 0.0034851739 1 1
|
||||
9300 289.14808 13.520201 0.0034851739 1 1
|
||||
9350 295.08335 17.156468 0.0034851739 1 1
|
||||
9400 338.08757 -31.112278 0.0034851739 1 1
|
||||
9450 336.64739 -25.697747 0.0034851739 1 1
|
||||
9500 338.10622 1.9241797 0.0034851739 1 1
|
||||
9550 294.82158 -12.043972 0.0034851739 1 1
|
||||
9600 268.9836 12.235553 0.0034851739 1 1
|
||||
9650 279.6269 28.710734 0.0034851739 1 1
|
||||
9700 279.88562 -10.865604 0.0034851739 1 1
|
||||
9750 287.56565 12.975819 0.0034851739 1 1
|
||||
9800 278.39949 4.2088595 0.0034851739 1 1
|
||||
9850 307.61259 9.341169 0.0034851739 1 1
|
||||
9900 317.53581 2.3948493 0.0034851739 1 1
|
||||
9950 332.52938 -14.809185 0.0034851739 1 1
|
||||
10000 401.93365 -7.637581 0.0034851739 1 1
|
||||
Loop time of 1.94139 on 1 procs for 10000 steps with 44 atoms
|
||||
100 274.25324 46.715512 0.0034851739 1 1
|
||||
150 471.61579 31.321598 0.0034851739 1 1
|
||||
200 362.87766 42.061118 0.0034851739 1 1
|
||||
250 367.58058 65.303109 0.0034851739 1 1
|
||||
300 372.38236 -52.421725 0.0034851739 1 1
|
||||
350 297.69957 17.869945 0.0034851739 1 1
|
||||
400 258.30433 49.19156 0.0034851739 1 1
|
||||
450 253.34384 -5.8162637 0.0034851739 1 1
|
||||
500 269.96465 -43.337517 0.0034851739 1 1
|
||||
550 303.23718 10.180246 0.0034851739 1 1
|
||||
600 329.59579 -48.97461 0.0034851739 1 1
|
||||
650 350.42568 50.983183 0.0034851739 1 1
|
||||
700 342.03272 35.43465 0.0034851739 1 1
|
||||
750 269.23405 -41.873166 0.0034851739 1 1
|
||||
800 245.15025 13.953092 0.0034851739 1 1
|
||||
850 257.85421 -3.1492141 0.0034851739 1 1
|
||||
900 316.15644 7.7798301 0.0034851739 1 1
|
||||
950 299.9124 -15.77014 0.0034851739 1 1
|
||||
1000 302.89968 -17.049693 0.0034851739 1 1
|
||||
1050 308.91651 71.84632 0.0034851739 1 1
|
||||
1100 348.43932 -18.742012 0.0034851739 1 1
|
||||
1150 309.03036 50.536311 0.0034851739 1 1
|
||||
1200 318.9761 -16.905746 0.0034851739 1 1
|
||||
1250 320.42806 -0.057975092 0.0034851739 1 1
|
||||
1300 289.7824 18.200772 0.0034851739 1 1
|
||||
1350 284.79836 -9.1978427 0.0034851739 1 1
|
||||
1400 325.43292 42.082833 0.0034851739 1 1
|
||||
1450 261.5041 -37.823325 0.0034851739 1 1
|
||||
1500 298.88723 -5.1647385 0.0034851739 1 1
|
||||
1550 291.37403 -7.7764201 0.0034851739 1 1
|
||||
1600 293.83475 22.2458 0.0034851739 1 1
|
||||
1650 293.80611 24.202512 0.0034851739 1 1
|
||||
1700 291.70205 -23.397884 0.0034851739 1 1
|
||||
1750 292.32437 -10.671214 0.0034851739 1 1
|
||||
1800 302.01367 -11.671025 0.0034851739 1 1
|
||||
1850 322.1651 24.438331 0.0034851739 1 1
|
||||
1900 310.45076 45.343592 0.0034851739 1 1
|
||||
1950 325.91745 -19.847809 0.0034851739 1 1
|
||||
2000 276.89662 63.387098 0.0034851739 1 1
|
||||
2050 311.33783 -24.683247 0.0034851739 1 1
|
||||
2100 346.2336 -27.526891 0.0034851739 1 1
|
||||
2150 345.30604 -15.722411 0.0034851739 1 1
|
||||
2200 346.7718 -17.857633 0.0034851739 1 1
|
||||
2250 304.28676 -1.9965581 0.0034851739 1 1
|
||||
2300 322.56372 -31.786868 0.0034851739 1 1
|
||||
2350 282.64326 6.1982735 0.0034851739 1 1
|
||||
2400 286.65759 -63.207781 0.0034851739 1 1
|
||||
2450 257.05528 32.931491 0.0034851739 1 1
|
||||
2500 283.64386 26.912373 0.0034851739 1 1
|
||||
2550 299.54005 27.277039 0.0034851739 1 1
|
||||
2600 283.92503 14.660972 0.0034851739 1 1
|
||||
2650 321.93453 -18.977358 0.0034851739 1 1
|
||||
2700 376.7189 31.826935 0.0034851739 1 1
|
||||
2750 372.20075 -32.821697 0.0034851739 1 1
|
||||
2800 361.40604 83.035183 0.0034851739 1 1
|
||||
2850 332.27269 -23.927452 0.0034851739 1 1
|
||||
2900 331.14638 -0.12328446 0.0034851739 1 1
|
||||
2950 303.67489 -24.078857 0.0034851739 1 1
|
||||
3000 311.40462 21.563537 0.0034851739 1 1
|
||||
3050 284.72849 -23.849667 0.0034851739 1 1
|
||||
3100 303.48477 39.347763 0.0034851739 1 1
|
||||
3150 264.2739 -0.22299879 0.0034851739 1 1
|
||||
3200 300.03351 31.545323 0.0034851739 1 1
|
||||
3250 288.56663 5.7225228 0.0034851739 1 1
|
||||
3300 200.13238 -31.239655 0.0034851739 1 1
|
||||
3350 231.32512 16.631728 0.0034851739 1 1
|
||||
3400 260.57402 2.1717992 0.0034851739 1 1
|
||||
3450 301.47128 -42.210623 0.0034851739 1 1
|
||||
3500 321.77414 40.074365 0.0034851739 1 1
|
||||
3550 353.21858 28.387783 0.0034851739 1 1
|
||||
3600 331.45989 -57.800858 0.0034851739 1 1
|
||||
3650 303.88123 44.86596 0.0034851739 1 1
|
||||
3700 329.73833 -0.80615652 0.0034851739 1 1
|
||||
3750 297.55588 -0.49626039 0.0034851739 1 1
|
||||
3800 286.38794 -10.010003 0.0034851739 1 1
|
||||
3850 290.17417 -43.51187 0.0034851739 1 1
|
||||
3900 247.88933 51.23735 0.0034851739 1 1
|
||||
3950 332.31324 -18.194985 0.0034851739 1 1
|
||||
4000 325.56802 18.402825 0.0034851739 1 1
|
||||
4050 338.37593 36.430977 0.0034851739 1 1
|
||||
4100 370.95478 39.290285 0.0034851739 1 1
|
||||
4150 348.47859 -7.0779678 0.0034851739 1 1
|
||||
4200 241.30632 -33.371788 0.0034851739 1 1
|
||||
4250 242.17258 -9.986197 0.0034851739 1 1
|
||||
4300 300.85311 -7.9244294 0.0034851739 1 1
|
||||
4350 273.15684 -21.257283 0.0034851739 1 1
|
||||
4400 305.77463 -5.8720722 0.0034851739 1 1
|
||||
4450 314.97697 45.0373 0.0034851739 1 1
|
||||
4500 310.77723 16.958773 0.0034851739 1 1
|
||||
4550 302.1742 12.156862 0.0034851739 1 1
|
||||
4600 319.74799 6.84889 0.0034851739 1 1
|
||||
4650 270.86805 -13.767905 0.0034851739 1 1
|
||||
4700 249.81731 -31.197487 0.0034851739 1 1
|
||||
4750 285.86481 -9.8916364 0.0034851739 1 1
|
||||
4800 233.98321 7.1338571 0.0034851739 1 1
|
||||
4850 302.60551 49.262889 0.0034851739 1 1
|
||||
4900 316.55056 34.663247 0.0034851739 1 1
|
||||
4950 357.32741 11.583006 0.0034851739 1 1
|
||||
5000 400.21045 -8.1781061 0.0034851739 1 1
|
||||
5050 390.01845 -20.490275 0.0034851739 1 1
|
||||
5100 378.84247 -41.328757 0.0034851739 1 1
|
||||
5150 324.02038 -15.023862 0.0034851739 1 1
|
||||
5200 262.08429 10.937354 0.0034851739 1 1
|
||||
5250 255.75508 16.381455 0.0034851739 1 1
|
||||
5300 277.84989 40.68232 0.0034851739 1 1
|
||||
5350 302.92832 9.1989494 0.0034851739 1 1
|
||||
5400 283.7196 -1.6584671 0.0034851739 1 1
|
||||
5450 300.71266 -4.7030295 0.0034851739 1 1
|
||||
5500 343.5499 -0.30550044 0.0034851739 1 1
|
||||
5550 369.51271 21.691649 0.0034851739 1 1
|
||||
5600 372.69789 -38.67994 0.0034851739 1 1
|
||||
5650 327.41266 11.352137 0.0034851739 1 1
|
||||
5700 278.98614 -23.827304 0.0034851739 1 1
|
||||
5750 308.30054 -20.756187 0.0034851739 1 1
|
||||
5800 341.45594 28.058441 0.0034851739 1 1
|
||||
5850 322.97844 -10.731921 0.0034851739 1 1
|
||||
5900 304.53591 32.825279 0.0034851739 1 1
|
||||
5950 287.1752 -36.780091 0.0034851739 1 1
|
||||
6000 296.52681 18.781896 0.0034851739 1 1
|
||||
6050 314.25442 15.992829 0.0034851739 1 1
|
||||
6100 313.86576 3.4342714 0.0034851739 1 1
|
||||
6150 325.64196 32.392039 0.0034851739 1 1
|
||||
6200 367.42931 -27.160706 0.0034851739 1 1
|
||||
6250 369.30798 39.020934 0.0034851739 1 1
|
||||
6300 328.92285 -23.175157 0.0034851739 1 1
|
||||
6350 305.63077 4.9024453 0.0034851739 1 1
|
||||
6400 241.70341 -13.676629 0.0034851739 1 1
|
||||
6450 265.66717 2.40612 0.0034851739 1 1
|
||||
6500 249.36037 13.420255 0.0034851739 1 1
|
||||
6550 294.53814 10.853462 0.0034851739 1 1
|
||||
6600 308.2025 18.995308 0.0034851739 1 1
|
||||
6650 305.43797 -49.56785 0.0034851739 1 1
|
||||
6700 320.27344 11.336281 0.0034851739 1 1
|
||||
6750 321.78666 -23.463899 0.0034851739 1 1
|
||||
6800 303.40388 7.6224553 0.0034851739 1 1
|
||||
6850 297.18966 51.52256 0.0034851739 1 1
|
||||
6900 284.18909 -8.4947203 0.0034851739 1 1
|
||||
6950 331.03663 13.233655 0.0034851739 1 1
|
||||
7000 311.37928 -43.265479 0.0034851739 1 1
|
||||
7050 286.81661 -14.174683 0.0034851739 1 1
|
||||
7100 302.84119 12.048954 0.0034851739 1 1
|
||||
7150 297.19357 -43.111968 0.0034851739 1 1
|
||||
7200 332.47359 26.048249 0.0034851739 1 1
|
||||
7250 262.70677 41.176242 0.0034851739 1 1
|
||||
7300 250.61405 -23.413982 0.0034851739 1 1
|
||||
7350 296.91117 35.88133 0.0034851739 1 1
|
||||
7400 245.09229 -13.447194 0.0034851739 1 1
|
||||
7450 272.28131 -23.322585 0.0034851739 1 1
|
||||
7500 209.04985 13.871239 0.0034851739 1 1
|
||||
7550 255.00955 4.9325621 0.0034851739 1 1
|
||||
7600 312.30937 -37.368274 0.0034851739 1 1
|
||||
7650 305.65903 55.245496 0.0034851739 1 1
|
||||
7700 325.09504 -18.347711 0.0034851739 1 1
|
||||
7750 363.28282 -22.479686 0.0034851739 1 1
|
||||
7800 350.17429 26.849547 0.0034851739 1 1
|
||||
7850 271.70853 -17.764575 0.0034851739 1 1
|
||||
7900 272.66484 -11.701967 0.0034851739 1 1
|
||||
7950 298.60202 -12.765675 0.0034851739 1 1
|
||||
8000 274.58852 49.641532 0.0034851739 1 1
|
||||
8050 304.72347 -0.55414183 0.0034851739 1 1
|
||||
8100 328.30757 -39.861301 0.0034851739 1 1
|
||||
8150 406.67601 2.8999409 0.0034851739 1 1
|
||||
8200 332.20083 -51.217399 0.0034851739 1 1
|
||||
8250 354.50609 53.128769 0.0034851739 1 1
|
||||
8300 337.2758 20.68562 0.0034851739 1 1
|
||||
8350 361.89708 -54.185869 0.0034851739 1 1
|
||||
8400 305.63496 24.058529 0.0034851739 1 1
|
||||
8450 303.27461 4.304683 0.0034851739 1 1
|
||||
8500 253.53694 -10.909021 0.0034851739 1 1
|
||||
8550 277.03017 23.241479 0.0034851739 1 1
|
||||
8600 291.41844 -22.240665 0.0034851739 1 1
|
||||
8650 307.85368 31.919587 0.0034851739 1 1
|
||||
8700 309.19724 0.53529642 0.0034851739 1 1
|
||||
8750 354.6583 11.565515 0.0034851739 1 1
|
||||
8800 329.78598 19.5996 0.0034851739 1 1
|
||||
8850 240.79198 21.803515 0.0034851739 1 1
|
||||
8900 318.40749 -59.816923 0.0034851739 1 1
|
||||
8950 308.47211 -57.808635 0.0034851739 1 1
|
||||
9000 271.51207 50.943482 0.0034851739 1 1
|
||||
9050 249.4005 6.7529187 0.0034851739 1 1
|
||||
9100 221.8772 47.196092 0.0034851739 1 1
|
||||
9150 297.9351 4.0058184 0.0034851739 1 1
|
||||
9200 274.85051 -24.774393 0.0034851739 1 1
|
||||
9250 336.04757 5.3799028 0.0034851739 1 1
|
||||
9300 380.44956 -22.389381 0.0034851739 1 1
|
||||
9350 336.9824 23.050616 0.0034851739 1 1
|
||||
9400 304.46425 32.530218 0.0034851739 1 1
|
||||
9450 317.55591 -22.265425 0.0034851739 1 1
|
||||
9500 323.70901 -7.0159787 0.0034851739 1 1
|
||||
9550 316.07308 28.062131 0.0034851739 1 1
|
||||
9600 262.74608 -0.78519192 0.0034851739 1 1
|
||||
9650 271.55045 -21.430123 0.0034851739 1 1
|
||||
9700 239.6022 14.483637 0.0034851739 1 1
|
||||
9750 338.1437 -0.72765302 0.0034851739 1 1
|
||||
9800 334.50189 19.495144 0.0034851739 1 1
|
||||
9850 354.87554 19.272719 0.0034851739 1 1
|
||||
9900 334.02141 -22.393457 0.0034851739 1 1
|
||||
9950 293.63651 19.178873 0.0034851739 1 1
|
||||
10000 319.81736 21.904414 0.0034851739 1 1
|
||||
Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
|
||||
|
||||
Performance: 445.042 ns/day, 0.054 hours/ns, 5150.945 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.26479 | 0.26479 | 0.26479 | 0.0 | 13.64
|
||||
Bond | 0.76875 | 0.76875 | 0.76875 | 0.0 | 39.60
|
||||
Kspace | 0.32111 | 0.32111 | 0.32111 | 0.0 | 16.54
|
||||
Neigh | 0.41333 | 0.41333 | 0.41333 | 0.0 | 21.29
|
||||
Comm | 0.025956 | 0.025956 | 0.025956 | 0.0 | 1.34
|
||||
Output | 0.0043445 | 0.0043445 | 0.0043445 | 0.0 | 0.22
|
||||
Modify | 0.12526 | 0.12526 | 0.12526 | 0.0 | 6.45
|
||||
Other | | 0.01786 | | | 0.92
|
||||
Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
|
||||
Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
|
||||
Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
|
||||
Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
|
||||
Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
|
||||
Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
|
||||
Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
|
||||
Other | | 0.01666 | | | 0.90
|
||||
|
||||
Nlocal: 44 ave 44 max 44 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 62 ave 62 max 62 min
|
||||
Nghost: 44 ave 44 max 44 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 812 ave 812 max 812 min
|
||||
Neighs: 823 ave 823 max 823 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 812
|
||||
Ave neighs/atom = 18.4545
|
||||
Total # of neighbors = 823
|
||||
Ave neighs/atom = 18.7045
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
|
||||
@ -85,7 +85,9 @@ thermo 50
|
||||
|
||||
# dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp defined
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
@ -131,235 +133,238 @@ Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
|
||||
Step Temp Press Density f_myrxns[1] f_myrxns[2]
|
||||
0 300 346.78165 0.0034851739 0 0
|
||||
50 296.70408 -51.30066 0.0034851739 1 0
|
||||
100 275.26011 39.120329 0.0034851739 1 1
|
||||
150 438.68516 35.257539 0.0034851739 1 1
|
||||
200 394.48971 15.444537 0.0034851739 1 1
|
||||
250 356.00369 50.185792 0.0034851739 1 1
|
||||
300 301.25816 -26.891497 0.0034851739 1 1
|
||||
350 279.17264 12.694513 0.0034851739 1 1
|
||||
400 248.71641 10.684558 0.0034851739 1 1
|
||||
450 240.30602 12.963034 0.0034851739 1 1
|
||||
500 252.71279 0.91620356 0.0034851739 1 1
|
||||
550 300.56824 18.541436 0.0034851739 1 1
|
||||
600 306.46441 -1.9736081 0.0034851739 1 1
|
||||
650 336.4537 21.474831 0.0034851739 1 1
|
||||
700 323.46217 8.486376 0.0034851739 1 1
|
||||
750 271.87146 5.9615231 0.0034851739 1 1
|
||||
800 268.43041 36.676068 0.0034851739 1 1
|
||||
850 269.02683 7.6295416 0.0034851739 1 1
|
||||
900 282.03605 -1.4688833 0.0034851739 1 1
|
||||
950 243.69136 -22.771489 0.0034851739 1 1
|
||||
1000 285.01348 17.925748 0.0034851739 1 1
|
||||
1050 383.47985 0.70536985 0.0034851739 1 1
|
||||
1100 368.97167 -4.3046933 0.0034851739 1 1
|
||||
1150 373.64459 6.3491837 0.0034851739 1 1
|
||||
1200 332.90575 -36.501095 0.0034851739 1 1
|
||||
1250 314.04078 -13.382767 0.0034851739 1 1
|
||||
1300 305.84166 4.7713641 0.0034851739 1 1
|
||||
1350 286.22145 37.621803 0.0034851739 1 1
|
||||
1400 265.52855 23.621002 0.0034851739 1 1
|
||||
1450 281.807 -31.266828 0.0034851739 1 1
|
||||
1500 275.33855 33.495565 0.0034851739 1 1
|
||||
1550 273.04973 -22.913871 0.0034851739 1 1
|
||||
1600 308.18478 -17.98151 0.0034851739 1 1
|
||||
1650 333.27664 28.987529 0.0034851739 1 1
|
||||
1700 296.16091 -1.1440455 0.0034851739 1 1
|
||||
1750 365.75611 34.574845 0.0034851739 1 1
|
||||
1800 292.83503 -33.199654 0.0034851739 1 1
|
||||
1850 261.50282 42.608703 0.0034851739 1 1
|
||||
1900 315.14188 -31.058803 0.0034851739 1 1
|
||||
1950 335.12895 12.40597 0.0034851739 1 1
|
||||
2000 278.08586 -5.3178633 0.0034851739 1 1
|
||||
2050 283.23847 -3.3974302 0.0034851739 1 1
|
||||
2100 281.38904 0.70263324 0.0034851739 1 1
|
||||
2150 302.23197 23.372316 0.0034851739 1 1
|
||||
2200 337.49259 -4.8716803 0.0034851739 1 1
|
||||
2250 409.64134 -12.043721 0.0034851739 1 1
|
||||
2300 309.21764 -21.824645 0.0034851739 1 1
|
||||
2350 290.97879 18.690281 0.0034851739 1 1
|
||||
2400 341.816 -16.967741 0.0034851739 1 1
|
||||
2450 310.28034 27.375518 0.0034851739 1 1
|
||||
2500 248.89429 17.061192 0.0034851739 1 1
|
||||
2550 273.10927 0.1048166 0.0034851739 1 1
|
||||
2600 289.56101 -9.7239939 0.0034851739 1 1
|
||||
2650 298.99719 -33.140576 0.0034851739 1 1
|
||||
2700 326.05198 -24.509827 0.0034851739 1 1
|
||||
2750 319.20612 24.305526 0.0034851739 1 1
|
||||
2800 304.8715 -15.076941 0.0034851739 1 1
|
||||
2850 374.38923 2.0874883 0.0034851739 1 1
|
||||
2900 354.01554 -20.595102 0.0034851739 1 1
|
||||
2950 289.89296 48.39731 0.0034851739 1 1
|
||||
3000 312.10013 -8.5105996 0.0034851739 1 1
|
||||
3050 296.97004 -31.008446 0.0034851739 1 1
|
||||
3100 251.72228 35.710197 0.0034851739 1 1
|
||||
3150 315.35895 -43.331536 0.0034851739 1 1
|
||||
3200 334.67773 13.331058 0.0034851739 1 1
|
||||
3250 308.1669 37.236121 0.0034851739 1 1
|
||||
3300 329.47601 30.798598 0.0034851739 1 1
|
||||
3350 299.40055 2.0785585 0.0034851739 1 1
|
||||
3400 272.41031 32.744921 0.0034851739 1 1
|
||||
3450 279.34594 -26.181793 0.0034851739 1 1
|
||||
3500 288.89969 8.935052 0.0034851739 1 1
|
||||
3550 253.4967 9.724471 0.0034851739 1 1
|
||||
3600 294.83266 19.33305 0.0034851739 1 1
|
||||
3650 290.23794 -5.493907 0.0034851739 1 1
|
||||
3700 332.5222 -29.83423 0.0034851739 1 1
|
||||
3750 364.63024 20.706191 0.0034851739 1 1
|
||||
3800 295.3842 -6.9434003 0.0034851739 1 1
|
||||
3850 346.84424 37.796066 0.0034851739 1 1
|
||||
3900 265.67286 -0.3162804 0.0034851739 1 1
|
||||
3950 260.455 -2.2571901 0.0034851739 1 1
|
||||
4000 259.82636 -2.2286207 0.0034851739 1 1
|
||||
4050 257.79848 24.520293 0.0034851739 1 1
|
||||
4100 295.58626 -0.42318895 0.0034851739 1 1
|
||||
4150 265.81352 -49.092436 0.0034851739 1 1
|
||||
4200 302.10333 51.715258 0.0034851739 1 1
|
||||
4250 258.98448 -4.8516657 0.0034851739 1 1
|
||||
4300 327.83401 33.717283 0.0034851739 1 1
|
||||
4350 311.59571 23.580382 0.0034851739 1 1
|
||||
4400 300.64237 -31.866661 0.0034851739 1 1
|
||||
4450 294.15642 -0.11927262 0.0034851739 1 1
|
||||
4500 299.83605 -17.560872 0.0034851739 1 1
|
||||
4550 326.83265 32.818481 0.0034851739 1 1
|
||||
4600 260.39068 -8.0567907 0.0034851739 1 1
|
||||
4650 247.93553 19.462991 0.0034851739 1 1
|
||||
4700 214.22252 -34.118304 0.0034851739 1 1
|
||||
4750 203.15329 27.356204 0.0034851739 1 1
|
||||
4800 257.761 -10.407986 0.0034851739 1 1
|
||||
4850 307.1923 11.711008 0.0034851739 1 1
|
||||
4900 319.00942 4.7808342 0.0034851739 1 1
|
||||
4950 282.2399 24.996151 0.0034851739 1 1
|
||||
5000 311.53284 -3.0012669 0.0034851739 1 1
|
||||
5050 317.58213 32.56782 0.0034851739 1 1
|
||||
5100 267.51502 -47.695103 0.0034851739 1 1
|
||||
5150 260.19047 29.046394 0.0034851739 1 1
|
||||
5200 239.8355 -5.4890372 0.0034851739 1 1
|
||||
5250 234.88522 -18.172649 0.0034851739 1 1
|
||||
5300 236.43278 -39.062111 0.0034851739 1 1
|
||||
5350 280.90083 -2.6932604 0.0034851739 1 1
|
||||
5400 316.65269 23.071363 0.0034851739 1 1
|
||||
5450 345.6322 19.573305 0.0034851739 1 1
|
||||
5500 384.57334 41.50729 0.0034851739 1 1
|
||||
5550 317.14286 9.6992981 0.0034851739 1 1
|
||||
5600 279.93246 -12.076859 0.0034851739 1 1
|
||||
5650 268.06471 1.6196502 0.0034851739 1 1
|
||||
5700 271.85714 -40.378489 0.0034851739 1 1
|
||||
5750 313.88361 10.722652 0.0034851739 1 1
|
||||
5800 281.54499 31.914883 0.0034851739 1 1
|
||||
5850 293.34819 -8.3155887 0.0034851739 1 1
|
||||
5900 249.25215 -17.307228 0.0034851739 1 1
|
||||
5950 268.18645 -4.7223601 0.0034851739 1 1
|
||||
6000 302.99402 -52.615432 0.0034851739 1 1
|
||||
6050 314.57946 34.513152 0.0034851739 1 1
|
||||
6100 345.70342 30.33474 0.0034851739 1 1
|
||||
6150 316.59329 31.862566 0.0034851739 1 1
|
||||
6200 317.85341 -32.23511 0.0034851739 1 1
|
||||
6250 282.97674 0.29367434 0.0034851739 1 1
|
||||
6300 267.91823 19.265617 0.0034851739 1 1
|
||||
6350 226.2098 -13.093573 0.0034851739 1 1
|
||||
6400 307.73307 17.439662 0.0034851739 1 1
|
||||
6450 292.16311 -23.275251 0.0034851739 1 1
|
||||
6500 335.05972 26.936588 0.0034851739 1 1
|
||||
6550 380.7351 19.532324 0.0034851739 1 1
|
||||
6600 373.01041 30.879146 0.0034851739 1 1
|
||||
6650 335.37897 -2.1766711 0.0034851739 1 1
|
||||
6700 298.94275 -10.578361 0.0034851739 1 1
|
||||
6750 255.11449 -50.575851 0.0034851739 1 1
|
||||
6800 222.87598 3.0488985 0.0034851739 1 1
|
||||
6850 268.57268 -43.676136 0.0034851739 1 1
|
||||
6900 260.30442 4.7484508 0.0034851739 1 1
|
||||
6950 289.15739 31.622589 0.0034851739 1 1
|
||||
7000 289.11733 21.636361 0.0034851739 1 1
|
||||
7050 361.08905 22.442487 0.0034851739 1 1
|
||||
7100 368.95006 4.8393179 0.0034851739 1 1
|
||||
7150 331.47878 -36.202032 0.0034851739 1 1
|
||||
7200 304.72518 13.982604 0.0034851739 1 1
|
||||
7250 284.0996 0.53900966 0.0034851739 1 1
|
||||
7300 269.17156 -41.572215 0.0034851739 1 1
|
||||
7350 222.06563 25.56579 0.0034851739 1 1
|
||||
7400 304.09479 15.48238 0.0034851739 1 1
|
||||
7450 298.79046 -7.4369454 0.0034851739 1 1
|
||||
7500 328.78217 14.672853 0.0034851739 1 1
|
||||
7550 347.06589 -37.168123 0.0034851739 1 1
|
||||
7600 362.84157 20.514912 0.0034851739 1 1
|
||||
7650 347.15916 2.3477485 0.0034851739 1 1
|
||||
7700 262.09822 33.901831 0.0034851739 1 1
|
||||
7750 275.85921 -33.536059 0.0034851739 1 1
|
||||
7800 281.16159 -18.288414 0.0034851739 1 1
|
||||
7850 264.83553 -30.566284 0.0034851739 1 1
|
||||
7900 257.35224 -35.087067 0.0034851739 1 1
|
||||
7950 286.30756 26.586163 0.0034851739 1 1
|
||||
8000 248.38175 15.601961 0.0034851739 1 1
|
||||
8050 292.59171 28.784541 0.0034851739 1 1
|
||||
8100 312.52852 0.87995053 0.0034851739 1 1
|
||||
8150 285.62346 -15.337252 0.0034851739 1 1
|
||||
8200 292.24175 -38.192576 0.0034851739 1 1
|
||||
8250 321.61618 -19.030398 0.0034851739 1 1
|
||||
8300 319.42189 55.078305 0.0034851739 1 1
|
||||
8350 308.00357 32.050518 0.0034851739 1 1
|
||||
8400 345.68186 8.7983733 0.0034851739 1 1
|
||||
8450 358.00849 12.434592 0.0034851739 1 1
|
||||
8500 370.14359 4.2184721 0.0034851739 1 1
|
||||
8550 360.6511 12.580836 0.0034851739 1 1
|
||||
8600 290.04938 -4.8422589 0.0034851739 1 1
|
||||
8650 297.95745 -5.3185591 0.0034851739 1 1
|
||||
8700 286.54284 -31.490479 0.0034851739 1 1
|
||||
8750 308.08791 19.24417 0.0034851739 1 1
|
||||
8800 231.72534 12.262217 0.0034851739 1 1
|
||||
8850 329.2349 -8.9133933 0.0034851739 1 1
|
||||
8900 287.64023 10.525164 0.0034851739 1 1
|
||||
8950 341.08296 2.80127 0.0034851739 1 1
|
||||
9000 403.71266 17.88418 0.0034851739 1 1
|
||||
9050 348.95132 -4.5813611 0.0034851739 1 1
|
||||
9100 307.98322 16.707575 0.0034851739 1 1
|
||||
9150 276.75719 -35.563923 0.0034851739 1 1
|
||||
9200 230.15547 3.8091656 0.0034851739 1 1
|
||||
9250 264.64479 -20.97438 0.0034851739 1 1
|
||||
9300 285.70467 13.881735 0.0034851739 1 1
|
||||
9350 297.515 13.599319 0.0034851739 1 1
|
||||
9400 341.45203 -28.494544 0.0034851739 1 1
|
||||
9450 319.29703 -27.907344 0.0034851739 1 1
|
||||
9500 332.50473 4.9891138 0.0034851739 1 1
|
||||
9550 293.10499 -8.3244772 0.0034851739 1 1
|
||||
9600 255.31174 2.2568315 0.0034851739 1 1
|
||||
9650 250.01932 5.7005159 0.0034851739 1 1
|
||||
9700 278.37409 -8.5970424 0.0034851739 1 1
|
||||
9750 294.86737 17.686447 0.0034851739 1 1
|
||||
9800 277.07345 -2.0856886 0.0034851739 1 1
|
||||
9850 295.54707 2.8365471 0.0034851739 1 1
|
||||
9900 311.51074 29.885116 0.0034851739 1 1
|
||||
9950 296.01363 12.206068 0.0034851739 1 1
|
||||
10000 341.35187 -3.0045464 0.0034851739 1 1
|
||||
Loop time of 3.64332 on 4 procs for 10000 steps with 44 atoms
|
||||
100 274.25324 46.715512 0.0034851739 1 1
|
||||
150 471.61579 31.321598 0.0034851739 1 1
|
||||
200 362.87766 42.061118 0.0034851739 1 1
|
||||
250 367.58058 65.303109 0.0034851739 1 1
|
||||
300 372.38236 -52.421725 0.0034851739 1 1
|
||||
350 297.69957 17.869945 0.0034851739 1 1
|
||||
400 258.30433 49.19156 0.0034851739 1 1
|
||||
450 253.34384 -5.8162637 0.0034851739 1 1
|
||||
500 269.96465 -43.337517 0.0034851739 1 1
|
||||
550 303.23718 10.180246 0.0034851739 1 1
|
||||
600 329.59579 -48.97461 0.0034851739 1 1
|
||||
650 350.42568 50.983183 0.0034851739 1 1
|
||||
700 342.03272 35.43465 0.0034851739 1 1
|
||||
750 269.23405 -41.873166 0.0034851739 1 1
|
||||
800 245.15025 13.953092 0.0034851739 1 1
|
||||
850 257.85421 -3.1492141 0.0034851739 1 1
|
||||
900 316.15644 7.7798301 0.0034851739 1 1
|
||||
950 299.9124 -15.77014 0.0034851739 1 1
|
||||
1000 302.89968 -17.049693 0.0034851739 1 1
|
||||
1050 308.91651 71.84632 0.0034851739 1 1
|
||||
1100 348.43932 -18.742012 0.0034851739 1 1
|
||||
1150 309.03036 50.536311 0.0034851739 1 1
|
||||
1200 318.9761 -16.905746 0.0034851739 1 1
|
||||
1250 320.42806 -0.057975092 0.0034851739 1 1
|
||||
1300 289.7824 18.200772 0.0034851739 1 1
|
||||
1350 284.79836 -9.1978427 0.0034851739 1 1
|
||||
1400 325.43292 42.082833 0.0034851739 1 1
|
||||
1450 261.5041 -37.823325 0.0034851739 1 1
|
||||
1500 298.88723 -5.1647385 0.0034851739 1 1
|
||||
1550 291.37403 -7.7764201 0.0034851739 1 1
|
||||
1600 293.83475 22.2458 0.0034851739 1 1
|
||||
1650 293.80611 24.202512 0.0034851739 1 1
|
||||
1700 291.70205 -23.397884 0.0034851739 1 1
|
||||
1750 292.32437 -10.671214 0.0034851739 1 1
|
||||
1800 302.01367 -11.671025 0.0034851739 1 1
|
||||
1850 322.1651 24.438331 0.0034851739 1 1
|
||||
1900 310.45076 45.343592 0.0034851739 1 1
|
||||
1950 325.91745 -19.847809 0.0034851739 1 1
|
||||
2000 276.89662 63.387098 0.0034851739 1 1
|
||||
2050 311.33783 -24.683247 0.0034851739 1 1
|
||||
2100 346.2336 -27.526891 0.0034851739 1 1
|
||||
2150 345.30604 -15.722411 0.0034851739 1 1
|
||||
2200 346.7718 -17.857633 0.0034851739 1 1
|
||||
2250 304.28676 -1.9965581 0.0034851739 1 1
|
||||
2300 322.56372 -31.786868 0.0034851739 1 1
|
||||
2350 282.64326 6.1982735 0.0034851739 1 1
|
||||
2400 286.65759 -63.207781 0.0034851739 1 1
|
||||
2450 257.05528 32.931491 0.0034851739 1 1
|
||||
2500 283.64386 26.912373 0.0034851739 1 1
|
||||
2550 299.54005 27.277039 0.0034851739 1 1
|
||||
2600 283.92503 14.660972 0.0034851739 1 1
|
||||
2650 321.93453 -18.977358 0.0034851739 1 1
|
||||
2700 376.7189 31.826935 0.0034851739 1 1
|
||||
2750 372.20075 -32.821697 0.0034851739 1 1
|
||||
2800 361.40604 83.035183 0.0034851739 1 1
|
||||
2850 332.27269 -23.927452 0.0034851739 1 1
|
||||
2900 331.14638 -0.12328446 0.0034851739 1 1
|
||||
2950 303.67489 -24.078857 0.0034851739 1 1
|
||||
3000 311.40462 21.563537 0.0034851739 1 1
|
||||
3050 284.72849 -23.849667 0.0034851739 1 1
|
||||
3100 303.48477 39.347763 0.0034851739 1 1
|
||||
3150 264.2739 -0.22299878 0.0034851739 1 1
|
||||
3200 300.03351 31.545323 0.0034851739 1 1
|
||||
3250 288.56663 5.7225229 0.0034851739 1 1
|
||||
3300 200.13238 -31.239655 0.0034851739 1 1
|
||||
3350 231.32512 16.631728 0.0034851739 1 1
|
||||
3400 260.57402 2.1717992 0.0034851739 1 1
|
||||
3450 301.47128 -42.210623 0.0034851739 1 1
|
||||
3500 321.77414 40.074365 0.0034851739 1 1
|
||||
3550 353.21858 28.387783 0.0034851739 1 1
|
||||
3600 331.45989 -57.800858 0.0034851739 1 1
|
||||
3650 303.88123 44.86596 0.0034851739 1 1
|
||||
3700 329.73833 -0.8061567 0.0034851739 1 1
|
||||
3750 297.55588 -0.49626022 0.0034851739 1 1
|
||||
3800 286.38794 -10.010003 0.0034851739 1 1
|
||||
3850 290.17417 -43.51187 0.0034851739 1 1
|
||||
3900 247.88933 51.23735 0.0034851739 1 1
|
||||
3950 332.31324 -18.194985 0.0034851739 1 1
|
||||
4000 325.56802 18.402825 0.0034851739 1 1
|
||||
4050 338.37594 36.430977 0.0034851739 1 1
|
||||
4100 370.95478 39.290285 0.0034851739 1 1
|
||||
4150 348.47859 -7.0779683 0.0034851739 1 1
|
||||
4200 241.30632 -33.371789 0.0034851739 1 1
|
||||
4250 242.17258 -9.9861962 0.0034851739 1 1
|
||||
4300 300.85311 -7.924429 0.0034851739 1 1
|
||||
4350 273.15684 -21.257282 0.0034851739 1 1
|
||||
4400 305.77464 -5.8720712 0.0034851739 1 1
|
||||
4450 314.97697 45.037299 0.0034851739 1 1
|
||||
4500 310.77723 16.958771 0.0034851739 1 1
|
||||
4550 302.17421 12.156862 0.0034851739 1 1
|
||||
4600 319.74799 6.8488914 0.0034851739 1 1
|
||||
4650 270.86805 -13.767907 0.0034851739 1 1
|
||||
4700 249.81731 -31.197484 0.0034851739 1 1
|
||||
4750 285.86481 -9.8916332 0.0034851739 1 1
|
||||
4800 233.98321 7.1338518 0.0034851739 1 1
|
||||
4850 302.60551 49.262886 0.0034851739 1 1
|
||||
4900 316.55055 34.663238 0.0034851739 1 1
|
||||
4950 357.32741 11.583013 0.0034851739 1 1
|
||||
5000 400.21044 -8.1780861 0.0034851739 1 1
|
||||
5050 390.01845 -20.490268 0.0034851739 1 1
|
||||
5100 378.84249 -41.328772 0.0034851739 1 1
|
||||
5150 324.02039 -15.023852 0.0034851739 1 1
|
||||
5200 262.08427 10.937367 0.0034851739 1 1
|
||||
5250 255.75506 16.381495 0.0034851739 1 1
|
||||
5300 277.84991 40.682283 0.0034851739 1 1
|
||||
5350 302.92834 9.1989644 0.0034851739 1 1
|
||||
5400 283.71964 -1.6583895 0.0034851739 1 1
|
||||
5450 300.71261 -4.703054 0.0034851739 1 1
|
||||
5500 343.54987 -0.30546396 0.0034851739 1 1
|
||||
5550 369.51272 21.691639 0.0034851739 1 1
|
||||
5600 372.69786 -38.679919 0.0034851739 1 1
|
||||
5650 327.41256 11.352201 0.0034851739 1 1
|
||||
5700 278.9861 -23.82728 0.0034851739 1 1
|
||||
5750 308.30037 -20.756238 0.0034851739 1 1
|
||||
5800 341.4559 28.058314 0.0034851739 1 1
|
||||
5850 322.9786 -10.731862 0.0034851739 1 1
|
||||
5900 304.53598 32.825105 0.0034851739 1 1
|
||||
5950 287.17515 -36.780057 0.0034851739 1 1
|
||||
6000 296.52688 18.782156 0.0034851739 1 1
|
||||
6050 314.25411 15.99272 0.0034851739 1 1
|
||||
6100 313.86572 3.4344108 0.0034851739 1 1
|
||||
6150 325.64197 32.39212 0.0034851739 1 1
|
||||
6200 367.4298 -27.161154 0.0034851739 1 1
|
||||
6250 369.30937 39.020881 0.0034851739 1 1
|
||||
6300 328.92245 -23.175612 0.0034851739 1 1
|
||||
6350 305.6293 4.9011587 0.0034851739 1 1
|
||||
6400 241.70456 -13.675247 0.0034851739 1 1
|
||||
6450 265.66574 2.4049735 0.0034851739 1 1
|
||||
6500 249.3592 13.420453 0.0034851739 1 1
|
||||
6550 294.5367 10.856753 0.0034851739 1 1
|
||||
6600 308.20246 18.992923 0.0034851739 1 1
|
||||
6650 305.43756 -49.57151 0.0034851739 1 1
|
||||
6700 320.27395 11.339101 0.0034851739 1 1
|
||||
6750 321.7875 -23.463361 0.0034851739 1 1
|
||||
6800 303.40316 7.6256997 0.0034851739 1 1
|
||||
6850 297.18652 51.52186 0.0034851739 1 1
|
||||
6900 284.19084 -8.496294 0.0034851739 1 1
|
||||
6950 331.04173 13.227745 0.0034851739 1 1
|
||||
7000 311.38027 -43.26105 0.0034851739 1 1
|
||||
7050 286.82046 -14.171194 0.0034851739 1 1
|
||||
7100 302.81691 12.058085 0.0034851739 1 1
|
||||
7150 297.18018 -43.110658 0.0034851739 1 1
|
||||
7200 332.46131 26.051496 0.0034851739 1 1
|
||||
7250 262.72288 41.161451 0.0034851739 1 1
|
||||
7300 250.62739 -23.440907 0.0034851739 1 1
|
||||
7350 296.92141 35.869216 0.0034851739 1 1
|
||||
7400 245.06807 -13.467896 0.0034851739 1 1
|
||||
7450 272.2659 -23.292836 0.0034851739 1 1
|
||||
7500 209.05776 13.888665 0.0034851739 1 1
|
||||
7550 255.03716 4.9662624 0.0034851739 1 1
|
||||
7600 312.26011 -37.350427 0.0034851739 1 1
|
||||
7650 305.5823 55.208039 0.0034851739 1 1
|
||||
7700 325.13382 -18.370791 0.0034851739 1 1
|
||||
7750 363.24898 -22.473126 0.0034851739 1 1
|
||||
7800 350.19254 26.792307 0.0034851739 1 1
|
||||
7850 271.76418 -17.843445 0.0034851739 1 1
|
||||
7900 272.70301 -11.709349 0.0034851739 1 1
|
||||
7950 298.5993 -12.736235 0.0034851739 1 1
|
||||
8000 274.52611 49.657345 0.0034851739 1 1
|
||||
8050 304.73711 -0.52485689 0.0034851739 1 1
|
||||
8100 328.29239 -39.901891 0.0034851739 1 1
|
||||
8150 406.52096 2.8669076 0.0034851739 1 1
|
||||
8200 332.17309 -51.168754 0.0034851739 1 1
|
||||
8250 354.68419 53.003157 0.0034851739 1 1
|
||||
8300 337.28934 20.766408 0.0034851739 1 1
|
||||
8350 361.81133 -54.159227 0.0034851739 1 1
|
||||
8400 305.59597 24.011667 0.0034851739 1 1
|
||||
8450 303.25823 4.423341 0.0034851739 1 1
|
||||
8500 253.50747 -11.026949 0.0034851739 1 1
|
||||
8550 277.13504 23.204625 0.0034851739 1 1
|
||||
8600 291.40211 -22.253861 0.0034851739 1 1
|
||||
8650 307.93765 32.14162 0.0034851739 1 1
|
||||
8700 309.1529 0.36279434 0.0034851739 1 1
|
||||
8750 355.10326 11.677219 0.0034851739 1 1
|
||||
8800 330.21328 19.235269 0.0034851739 1 1
|
||||
8850 241.29109 21.707386 0.0034851739 1 1
|
||||
8900 319.15363 -60.010115 0.0034851739 1 1
|
||||
8950 308.88552 -57.637014 0.0034851739 1 1
|
||||
9000 272.22373 51.15837 0.0034851739 1 1
|
||||
9050 248.84947 7.3390565 0.0034851739 1 1
|
||||
9100 221.91564 48.387079 0.0034851739 1 1
|
||||
9150 298.03506 2.9058639 0.0034851739 1 1
|
||||
9200 274.25114 -24.597819 0.0034851739 1 1
|
||||
9250 334.08373 5.1079577 0.0034851739 1 1
|
||||
9300 383.07285 -23.274763 0.0034851739 1 1
|
||||
9350 335.00581 20.94212 0.0034851739 1 1
|
||||
9400 309.23862 34.074744 0.0034851739 1 1
|
||||
9450 312.62262 -28.468057 0.0034851739 1 1
|
||||
9500 324.54274 2.851136 0.0034851739 1 1
|
||||
9550 313.32781 22.468182 0.0034851739 1 1
|
||||
9600 269.04372 4.064934 0.0034851739 1 1
|
||||
9650 270.98476 -21.520127 0.0034851739 1 1
|
||||
9700 236.8736 16.250728 0.0034851739 1 1
|
||||
9750 333.94686 1.6864148 0.0034851739 1 1
|
||||
9800 330.91875 12.150018 0.0034851739 1 1
|
||||
9850 343.8603 25.338853 0.0034851739 1 1
|
||||
9900 330.93364 -28.292992 0.0034851739 1 1
|
||||
9950 291.25518 25.795948 0.0034851739 1 1
|
||||
10000 319.25565 25.323846 0.0034851739 1 1
|
||||
Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
|
||||
|
||||
Performance: 237.146 ns/day, 0.101 hours/ns, 2744.751 timesteps/s
|
||||
94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
|
||||
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0029962 | 0.10426 | 0.34564 | 43.9 | 2.86
|
||||
Bond | 0.005929 | 0.29803 | 0.95305 | 71.2 | 8.18
|
||||
Kspace | 0.83969 | 1.5992 | 1.9344 | 35.6 | 43.89
|
||||
Neigh | 0.65468 | 0.66443 | 0.67431 | 0.9 | 18.24
|
||||
Comm | 0.1727 | 0.23754 | 0.2745 | 8.0 | 6.52
|
||||
Output | 0.0048738 | 0.010774 | 0.028434 | 9.8 | 0.30
|
||||
Modify | 0.62478 | 0.70376 | 0.779 | 6.5 | 19.32
|
||||
Other | | 0.02531 | | | 0.69
|
||||
Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
|
||||
Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
|
||||
Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
|
||||
Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
|
||||
Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
|
||||
Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
|
||||
Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
|
||||
Other | | 0.02359 | | | 0.66
|
||||
|
||||
Nlocal: 11 ave 40 max 0 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Nghost: 36 ave 47 max 7 min
|
||||
Nlocal: 11 ave 44 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 33 ave 44 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 203 ave 809 max 0 min
|
||||
Neighs: 205.75 ave 823 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 812
|
||||
Ave neighs/atom = 18.4545
|
||||
Total # of neighbors = 823
|
||||
Ave neighs/atom = 18.7045
|
||||
Ave special neighs/atom = 9.77273
|
||||
Neighbor list builds = 10000
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_restart restart_longrun
|
||||
# write_data restart_longrun.data
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
|
||||
83
examples/rigid/in.rigid.early
Normal file
83
examples/rigid/in.rigid.early
Normal file
@ -0,0 +1,83 @@
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
|
||||
clump6 clump7 clump8 clump9
|
||||
|
||||
fix_modify 1 bodyforces early
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
81
examples/rigid/in.rigid.nve
Normal file
81
examples/rigid/in.rigid.nve
Normal file
@ -0,0 +1,81 @@
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
|
||||
clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
83
examples/rigid/in.rigid.nve.early
Normal file
83
examples/rigid/in.rigid.nve.early
Normal file
@ -0,0 +1,83 @@
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
|
||||
clump6 clump7 clump8 clump9
|
||||
|
||||
fix_modify 1 bodyforces early
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
338
examples/rigid/log.20Apr18.rigid.atomfile.g++.1
Normal file
338
examples/rigid/log.20Apr18.rigid.atomfile.g++.1
Normal file
@ -0,0 +1,338 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
variable bodies atomfile bodies.txt
|
||||
fix 1 all rigid custom v_bodies
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 615179.112 tau/day, 71201.286 timesteps/s
|
||||
98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37
|
||||
Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06
|
||||
Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58
|
||||
Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70
|
||||
Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01
|
||||
Other | | 0.006017 | | | 4.28
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
338
examples/rigid/log.20Apr18.rigid.atomfile.g++.4
Normal file
338
examples/rigid/log.20Apr18.rigid.atomfile.g++.4
Normal file
@ -0,0 +1,338 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
variable bodies atomfile bodies.txt
|
||||
fix 1 all rigid custom v_bodies
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 451214.099 tau/day, 52223.854 timesteps/s
|
||||
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91
|
||||
Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27
|
||||
Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59
|
||||
Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38
|
||||
Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82
|
||||
Other | | 0.009611 | | | 5.02
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.1
Normal file
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.1
Normal file
@ -0,0 +1,338 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
|
||||
fix 1 all rigid custom v_bodies
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 621477.474 tau/day, 71930.263 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40
|
||||
Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59
|
||||
Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57
|
||||
Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73
|
||||
Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24
|
||||
Other | | 0.006207 | | | 4.46
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.4
Normal file
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.4
Normal file
@ -0,0 +1,338 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
|
||||
fix 1 all rigid custom v_bodies
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.202733 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 426175.966 tau/day, 49325.922 timesteps/s
|
||||
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0025222 | 0.0037088 | 0.0044038 | 1.2 | 1.83
|
||||
Neigh | 0.01135 | 0.012003 | 0.013654 | 0.9 | 5.92
|
||||
Comm | 0.088217 | 0.089948 | 0.091659 | 0.4 | 44.37
|
||||
Output | 0.0044014 | 0.0047023 | 0.0055132 | 0.7 | 2.32
|
||||
Modify | 0.080218 | 0.082638 | 0.084872 | 0.6 | 40.76
|
||||
Other | | 0.009733 | | | 4.80
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
337
examples/rigid/log.20Apr18.rigid.early.g++.1
Normal file
337
examples/rigid/log.20Apr18.rigid.early.g++.1
Normal file
@ -0,0 +1,337 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
fix_modify 1 bodyforces early
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.142284 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 607236.588 tau/day, 70282.013 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.010693 | 0.010693 | 0.010693 | 0.0 | 7.52
|
||||
Neigh | 0.037908 | 0.037908 | 0.037908 | 0.0 | 26.64
|
||||
Comm | 0.0087049 | 0.0087049 | 0.0087049 | 0.0 | 6.12
|
||||
Output | 0.0025849 | 0.0025849 | 0.0025849 | 0.0 | 1.82
|
||||
Modify | 0.076329 | 0.076329 | 0.076329 | 0.0 | 53.65
|
||||
Other | | 0.006064 | | | 4.26
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
337
examples/rigid/log.20Apr18.rigid.early.g++.4
Normal file
337
examples/rigid/log.20Apr18.rigid.early.g++.4
Normal file
@ -0,0 +1,337 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
fix_modify 1 bodyforces early
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.170899 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 505560.431 tau/day, 58513.939 timesteps/s
|
||||
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0024047 | 0.0038016 | 0.0044513 | 1.3 | 2.22
|
||||
Neigh | 0.011313 | 0.012043 | 0.013355 | 0.7 | 7.05
|
||||
Comm | 0.066761 | 0.069035 | 0.071617 | 0.7 | 40.40
|
||||
Output | 0.0038884 | 0.0041398 | 0.0048923 | 0.7 | 2.42
|
||||
Modify | 0.071143 | 0.072567 | 0.074478 | 0.4 | 42.46
|
||||
Other | | 0.009313 | | | 5.45
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
@ -8,7 +9,7 @@ pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
@ -91,13 +92,18 @@ timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 18 18 18
|
||||
Memory usage per processor = 3.62803 Mbytes
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
@ -151,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
|
||||
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
@ -173,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
@ -269,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
@ -290,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
|
||||
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589894 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550109 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620327 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
|
||||
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms
|
||||
Loop time of 0.155936 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 509796.561 tau/day, 59004.232 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 554075.151 tau/day, 64129.068 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88
|
||||
Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97
|
||||
Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68
|
||||
Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14
|
||||
Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64
|
||||
Other | | 0.006244 | | | 3.68
|
||||
Pair | 0.013007 | 0.013007 | 0.013007 | 0.0 | 8.34
|
||||
Neigh | 0.041885 | 0.041885 | 0.041885 | 0.0 | 26.86
|
||||
Comm | 0.0094752 | 0.0094752 | 0.0094752 | 0.0 | 6.08
|
||||
Output | 0.002636 | 0.002636 | 0.002636 | 0.0 | 1.69
|
||||
Modify | 0.082249 | 0.082249 | 0.082249 | 0.0 | 52.75
|
||||
Other | | 0.006683 | | | 4.29
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
@ -8,7 +9,7 @@ pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
@ -91,13 +92,18 @@ timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 18 18 18
|
||||
Memory usage per processor = 3.65531 Mbytes
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
@ -151,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
@ -160,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
@ -170,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
@ -268,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
@ -289,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.005315616 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814368 0 5269.5163 12.011415
|
||||
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589885 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550123 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
|
||||
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms
|
||||
Loop time of 0.194532 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 687503.421 tau/day, 79572.155 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 444142.918 tau/day, 51405.430 timesteps/s
|
||||
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76
|
||||
Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76
|
||||
Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89
|
||||
Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86
|
||||
Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41
|
||||
Other | | 0.004176 | | | 3.32
|
||||
Pair | 0.0025368 | 0.003831 | 0.0045376 | 1.2 | 1.97
|
||||
Neigh | 0.011299 | 0.012014 | 0.013005 | 0.6 | 6.18
|
||||
Comm | 0.081939 | 0.084112 | 0.087817 | 0.8 | 43.24
|
||||
Output | 0.0044608 | 0.0047221 | 0.0053811 | 0.6 | 2.43
|
||||
Modify | 0.078212 | 0.080219 | 0.082467 | 0.7 | 41.24
|
||||
Other | | 0.009634 | | | 4.95
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
337
examples/rigid/log.20Apr18.rigid.nve.early.g++.1
Normal file
337
examples/rigid/log.20Apr18.rigid.nve.early.g++.1
Normal file
@ -0,0 +1,337 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
fix_modify 1 bodyforces early
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.69 571.70921 0 5265.8153 32.005816
|
||||
100 16298.128 136.75661 0 5267.6488 16.449029
|
||||
150 16682.532 17.504156 0 5269.4124 14.901186
|
||||
200 16733.906 1.3755079 0 5269.4571 14.571305
|
||||
250 16738.861 -0.15272039 0 5269.4886 14.498342
|
||||
300 16738.608 -0.055216883 0 5269.5066 14.498
|
||||
350 16738.5 -0.017457072 0 5269.5104 14.498392
|
||||
400 16738.451 -0.0060161309 0 5269.5063 14.49851
|
||||
450 16738.435 -0.001271965 0 5269.5059 14.498571
|
||||
500 16738.443 -0.00081074175 0 5269.509 14.498598
|
||||
550 16738.452 -0.00083208965 0 5269.5118 14.498618
|
||||
600 16738.45 -0.00058358431 0 5269.5116 14.498617
|
||||
650 16738.443 -0.00047228525 0 5269.5093 14.4986
|
||||
700 16738.444 0 0 5269.5102 14.498612
|
||||
750 16738.461 0 0 5269.5157 14.498654
|
||||
800 16738.479 0 0 5269.521 14.498697
|
||||
850 16738.473 0 0 5269.5192 14.498683
|
||||
900 16738.449 0 0 5269.5116 14.498624
|
||||
950 16738.438 -0.0035324203 0 5269.5046 14.498537
|
||||
1000 16738.562 -0.051134242 0 5269.4963 14.498093
|
||||
1050 16737.343 0.32970192 0 5269.4934 14.527634
|
||||
1100 16737.878 0.16213235 0 5269.4941 14.533864
|
||||
1150 16738.682 -0.089236256 0 5269.4959 14.511765
|
||||
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
|
||||
1250 16738.45 0 0 5269.5119 14.512611
|
||||
1300 16738.475 0 0 5269.5199 14.512673
|
||||
1350 16738.484 0 0 5269.5228 14.512696
|
||||
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
|
||||
1450 16738.45 -0.0010933363 0 5269.511 14.512595
|
||||
1500 16738.445 -0.00057484239 0 5269.51 14.512591
|
||||
1550 16738.451 0 0 5269.5123 14.512615
|
||||
1600 16738.452 0 0 5269.5127 14.512618
|
||||
1650 16738.443 0 0 5269.5099 14.512596
|
||||
1700 16738.433 0 0 5269.5068 14.512572
|
||||
1750 16738.438 0 0 5269.5084 14.512584
|
||||
1800 16738.459 0 0 5269.5149 14.512635
|
||||
1850 16738.473 0 0 5269.5193 14.51267
|
||||
1900 16738.462 0 0 5269.5159 14.512644
|
||||
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
|
||||
2000 16738.463 -0.013425408 0 5269.5027 14.512382
|
||||
2050 16738.535 -0.036964311 0 5269.5017 14.512152
|
||||
2100 16738.621 -0.063490509 0 5269.5023 14.512108
|
||||
2150 16738.594 -0.056143934 0 5269.5012 14.512117
|
||||
2200 16738.536 -0.038486645 0 5269.5007 14.512277
|
||||
2250 16738.496 -0.023712406 0 5269.503 14.51242
|
||||
2300 16738.488 -0.013209094 0 5269.5109 14.51255
|
||||
2350 16738.486 -0.0045244524 0 5269.519 14.512693
|
||||
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
|
||||
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
|
||||
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
|
||||
2550 16738.552 -0.04420046 0 5269.4998 14.512177
|
||||
2600 16738.42 -0.004347531 0 5269.4982 14.512783
|
||||
2650 16734.241 1.3131302 0 5269.5 14.577195
|
||||
2700 16738.737 -0.10612056 0 5269.4961 14.503874
|
||||
2750 16732.705 1.7939719 0 5269.4974 14.629294
|
||||
2800 16738.558 -0.042867033 0 5269.5032 14.519893
|
||||
2850 16738.499 -0.01271227 0 5269.5146 14.518524
|
||||
2900 16738.486 -0.0032778045 0 5269.52 14.518712
|
||||
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
|
||||
3000 16738.647 -0.070862542 0 5269.5031 14.51803
|
||||
3050 16678.313 18.829038 0 5269.409 15.533426
|
||||
3100 16632.312 33.399217 0 5269.4975 14.588597
|
||||
3150 16739.318 -0.31388148 0 5269.4715 13.520782
|
||||
3200 16727.951 3.26736 0 5269.4741 12.288358
|
||||
3250 16686.364 16.353793 0 5269.4682 14.152517
|
||||
3300 16738.532 -0.031574462 0 5269.5064 13.310615
|
||||
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
|
||||
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
|
||||
3450 16738.489 -0.021623738 0 5269.5026 13.308001
|
||||
3500 16737.78 0.19719043 0 5269.4983 13.325999
|
||||
3550 16658.578 25.116206 0 5269.4834 13.778249
|
||||
3600 16738.51 -0.032864725 0 5269.4981 12.392389
|
||||
3650 16738.899 -0.15952703 0 5269.4938 12.383503
|
||||
3700 16738.879 -0.16025994 0 5269.487 12.382575
|
||||
3750 16738.878 -0.16608251 0 5269.4806 12.382765
|
||||
3800 16738.591 -0.078679341 0 5269.4776 12.383227
|
||||
3850 16738.429 -0.024729409 0 5269.4807 12.382942
|
||||
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
|
||||
3950 16738.428 -0.002521266 0 5269.5027 12.383324
|
||||
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
|
||||
4050 16738.488 0 0 5269.5241 12.383531
|
||||
4100 16738.468 0 0 5269.5178 12.383482
|
||||
4150 16738.422 0 0 5269.5033 12.383369
|
||||
4200 16738.387 0 0 5269.4921 12.383281
|
||||
4250 16738.383 0 0 5269.4908 12.38327
|
||||
4300 16738.4 0 0 5269.4964 12.383314
|
||||
4350 16738.423 0 0 5269.5036 12.38337
|
||||
4400 16738.441 0 0 5269.5092 12.383414
|
||||
4450 16738.45 0 0 5269.5121 12.383437
|
||||
4500 16738.45 0 0 5269.5122 12.383438
|
||||
4550 16738.442 0 0 5269.5095 12.383417
|
||||
4600 16738.425 0 0 5269.5042 12.383376
|
||||
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
|
||||
4700 16738.444 -0.024020551 0 5269.4862 12.382975
|
||||
4750 16738.49 -0.048521421 0 5269.4761 12.385777
|
||||
4800 16735.057 1.0347219 0 5269.4786 12.43543
|
||||
4850 16735.441 0.92650928 0 5269.4913 12.418653
|
||||
4900 16723.839 4.5908971 0 5269.5033 13.410103
|
||||
4950 16738.531 -0.021537669 0 5269.5159 13.089982
|
||||
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
|
||||
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
|
||||
5100 16738.404 0 0 5269.4976 13.090032
|
||||
5150 16738.421 0 0 5269.5029 13.090073
|
||||
5200 16738.44 0 0 5269.5087 13.090119
|
||||
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
|
||||
5300 16738.456 -0.0064376397 0 5269.5075 13.090026
|
||||
5350 16738.479 -0.020383842 0 5269.5007 13.089898
|
||||
5400 16735.845 0.79889481 0 5269.4909 13.136244
|
||||
5450 16735.558 0.87619898 0 5269.4778 12.324482
|
||||
5500 16711.494 8.47243 0 5269.4984 12.65658
|
||||
5550 16454.525 89.074845 0 5269.2031 16.996503
|
||||
5600 16713.084 7.9801091 0 5269.5065 13.774971
|
||||
5650 16738.676 -0.079987812 0 5269.5033 13.168292
|
||||
5700 16446.281 91.866085 0 5269.399 23.764658
|
||||
5750 16738.549 -0.039869082 0 5269.5034 13.378117
|
||||
5800 16738.487 -0.014994464 0 5269.5086 13.378394
|
||||
5850 16738.466 -0.0051267378 0 5269.512 13.378555
|
||||
5900 16738.462 -0.0043689966 0 5269.5113 13.378568
|
||||
5950 16738.528 -0.032727396 0 5269.5039 13.378192
|
||||
6000 16702.774 10.969422 0 5269.2502 13.788847
|
||||
6050 16682.271 17.483217 0 5269.3092 13.353098
|
||||
6100 16738.508 -0.028838289 0 5269.5016 12.521077
|
||||
6150 16738.425 -0.0067595568 0 5269.4974 12.521216
|
||||
6200 16738.401 -0.0011499904 0 5269.4955 12.521247
|
||||
6250 16738.455 0 0 5269.5136 12.521403
|
||||
6300 16738.523 0 0 5269.5352 12.521573
|
||||
6350 16738.503 0 0 5269.5287 12.521525
|
||||
6400 16738.427 0 0 5269.5047 12.521337
|
||||
6450 16738.399 0 0 5269.496 12.521268
|
||||
6500 16738.425 0 0 5269.5042 12.521331
|
||||
6550 16738.441 0 0 5269.5093 12.521372
|
||||
6600 16738.42 0 0 5269.5025 12.521319
|
||||
6650 16738.398 0 0 5269.4957 12.521266
|
||||
6700 16738.435 0 0 5269.5074 12.521355
|
||||
6750 16738.505 0 0 5269.5293 12.521527
|
||||
6800 16738.508 0 0 5269.5303 12.521536
|
||||
6850 16738.446 0 0 5269.5108 12.521384
|
||||
6900 16738.414 0 0 5269.5009 12.521306
|
||||
6950 16738.432 0 0 5269.5063 12.521348
|
||||
7000 16738.444 0 0 5269.5102 12.521378
|
||||
7050 16738.421 0 0 5269.5029 12.521322
|
||||
7100 16738.393 0 0 5269.4941 12.521253
|
||||
7150 16738.419 0 0 5269.5022 12.521315
|
||||
7200 16738.489 0 0 5269.5244 12.521489
|
||||
7250 16738.505 0 0 5269.5293 12.521528
|
||||
7300 16738.443 0 0 5269.5098 12.521376
|
||||
7350 16738.404 0 0 5269.4976 12.521281
|
||||
7400 16738.43 0 0 5269.5058 12.521343
|
||||
7450 16738.461 0 0 5269.5156 12.521421
|
||||
7500 16738.447 0 0 5269.5109 12.521385
|
||||
7550 16738.407 0 0 5269.4986 12.521288
|
||||
7600 16738.412 0 0 5269.5002 12.5213
|
||||
7650 16738.478 0 0 5269.5208 12.52146
|
||||
7700 16738.51 0 0 5269.5309 12.521541
|
||||
7750 16738.454 0 0 5269.5135 12.521405
|
||||
7800 16738.398 0 0 5269.4958 12.521267
|
||||
7850 16738.407 -0.0002118068 0 5269.4982 12.521283
|
||||
7900 16738.441 -0.00021679441 0 5269.509 12.521366
|
||||
7950 16738.446 -0.00023847865 0 5269.5107 12.52138
|
||||
8000 16738.423 0 0 5269.5035 12.521326
|
||||
8050 16738.423 0 0 5269.5034 12.521325
|
||||
8100 16738.478 -0.00069624411 0 5269.52 12.521447
|
||||
8150 16738.523 -0.0040058094 0 5269.531 12.521494
|
||||
8200 16738.486 -0.0092298399 0 5269.5142 12.521327
|
||||
8250 16738.458 -0.023189572 0 5269.4914 12.521008
|
||||
8300 16738.513 -0.045847775 0 5269.4861 12.520773
|
||||
8350 16723.734 4.5722877 0 5269.4516 12.849562
|
||||
8400 16738.466 -0.020202622 0 5269.497 12.835807
|
||||
8450 16738.437 -0.012822209 0 5269.4952 12.829975
|
||||
8500 16738.408 -0.001683355 0 5269.4972 12.8301
|
||||
8550 16738.464 -0.00097382251 0 5269.5155 12.830254
|
||||
8600 16738.669 -0.050581166 0 5269.5304 12.829973
|
||||
8650 15918.256 250.07455 0 5261.3774 24.539208
|
||||
8700 16738.446 0.00084613367 0 5269.5116 10.591358
|
||||
8750 16738.472 -0.010145611 0 5269.5089 10.590277
|
||||
8800 16738.468 0 0 5269.5176 10.590497
|
||||
8850 16738.508 0 0 5269.5303 10.590596
|
||||
8900 16738.509 0 0 5269.5306 10.590599
|
||||
8950 16738.496 0 0 5269.5266 10.590568
|
||||
9000 16738.477 0 0 5269.5204 10.59052
|
||||
9050 16738.455 0 0 5269.5135 10.590465
|
||||
9100 16738.477 0 0 5269.5205 10.590519
|
||||
9150 16738.512 0 0 5269.5315 10.590606
|
||||
9200 16738.502 0 0 5269.5285 10.590583
|
||||
9250 16738.493 0 0 5269.5254 10.590559
|
||||
9300 16738.482 0 0 5269.522 10.590532
|
||||
9350 16738.46 0 0 5269.5151 10.590478
|
||||
9400 16738.48 0 0 5269.5216 10.590528
|
||||
9450 16738.509 0 0 5269.5306 10.590599
|
||||
9500 16738.49 0 0 5269.5247 10.590554
|
||||
9550 16738.484 0 0 5269.5226 10.590536
|
||||
9600 16738.483 0 0 5269.5223 10.590534
|
||||
9650 16738.464 0 0 5269.5165 10.590489
|
||||
9700 16738.484 0 0 5269.5228 10.590537
|
||||
9750 16738.507 0 0 5269.53 10.590595
|
||||
9800 16738.482 0 0 5269.522 10.590532
|
||||
9850 16738.478 0 0 5269.5207 10.590521
|
||||
9900 16738.487 -0.00030979882 0 5269.5233 10.590538
|
||||
9950 16738.476 -0.00095967357 0 5269.5193 10.590496
|
||||
10000 16738.494 -0.00062714625 0 5269.5253 10.590548
|
||||
Loop time of 0.166298 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 519549.516 tau/day, 60133.046 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.011685 | 0.011685 | 0.011685 | 0.0 | 7.03
|
||||
Neigh | 0.038539 | 0.038539 | 0.038539 | 0.0 | 23.17
|
||||
Comm | 0.0086315 | 0.0086315 | 0.0086315 | 0.0 | 5.19
|
||||
Output | 0.0026531 | 0.0026531 | 0.0026531 | 0.0 | 1.60
|
||||
Modify | 0.098759 | 0.098759 | 0.098759 | 0.0 | 59.39
|
||||
Other | | 0.00603 | | | 3.63
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 49 ave 49 max 49 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3
|
||||
Ave neighs/atom = 0.037037
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
337
examples/rigid/log.20Apr18.rigid.nve.early.g++.4
Normal file
337
examples/rigid/log.20Apr18.rigid.nve.early.g++.4
Normal file
@ -0,0 +1,337 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
fix_modify 1 bodyforces early
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.69 571.70921 0 5265.8153 32.005816
|
||||
100 16298.128 136.75661 0 5267.6488 16.449029
|
||||
150 16682.532 17.504156 0 5269.4124 14.901186
|
||||
200 16733.906 1.3755079 0 5269.4571 14.571305
|
||||
250 16738.861 -0.15272039 0 5269.4886 14.498342
|
||||
300 16738.608 -0.055216883 0 5269.5066 14.498
|
||||
350 16738.5 -0.017457072 0 5269.5104 14.498392
|
||||
400 16738.451 -0.0060161309 0 5269.5063 14.49851
|
||||
450 16738.435 -0.001271965 0 5269.5059 14.498571
|
||||
500 16738.443 -0.00081074175 0 5269.509 14.498598
|
||||
550 16738.452 -0.00083208965 0 5269.5118 14.498618
|
||||
600 16738.45 -0.00058358431 0 5269.5116 14.498617
|
||||
650 16738.443 -0.00047228525 0 5269.5093 14.4986
|
||||
700 16738.444 0 0 5269.5102 14.498612
|
||||
750 16738.461 0 0 5269.5157 14.498654
|
||||
800 16738.479 0 0 5269.521 14.498697
|
||||
850 16738.473 0 0 5269.5192 14.498683
|
||||
900 16738.449 0 0 5269.5116 14.498624
|
||||
950 16738.438 -0.0035324203 0 5269.5046 14.498537
|
||||
1000 16738.562 -0.051134242 0 5269.4963 14.498093
|
||||
1050 16737.343 0.32970192 0 5269.4934 14.527634
|
||||
1100 16737.878 0.16213235 0 5269.4941 14.533864
|
||||
1150 16738.682 -0.089236256 0 5269.4959 14.511765
|
||||
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
|
||||
1250 16738.45 0 0 5269.5119 14.512611
|
||||
1300 16738.475 0 0 5269.5199 14.512673
|
||||
1350 16738.484 0 0 5269.5228 14.512696
|
||||
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
|
||||
1450 16738.45 -0.0010933363 0 5269.511 14.512595
|
||||
1500 16738.445 -0.00057484239 0 5269.51 14.512591
|
||||
1550 16738.451 0 0 5269.5123 14.512615
|
||||
1600 16738.452 0 0 5269.5127 14.512618
|
||||
1650 16738.443 0 0 5269.5099 14.512596
|
||||
1700 16738.433 0 0 5269.5068 14.512572
|
||||
1750 16738.438 0 0 5269.5084 14.512584
|
||||
1800 16738.459 0 0 5269.5149 14.512635
|
||||
1850 16738.473 0 0 5269.5193 14.51267
|
||||
1900 16738.462 0 0 5269.5159 14.512644
|
||||
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
|
||||
2000 16738.463 -0.013425408 0 5269.5027 14.512382
|
||||
2050 16738.535 -0.036964311 0 5269.5017 14.512152
|
||||
2100 16738.621 -0.063490509 0 5269.5023 14.512108
|
||||
2150 16738.594 -0.056143934 0 5269.5012 14.512117
|
||||
2200 16738.536 -0.038486645 0 5269.5007 14.512277
|
||||
2250 16738.496 -0.023712406 0 5269.503 14.51242
|
||||
2300 16738.488 -0.013209094 0 5269.5109 14.51255
|
||||
2350 16738.486 -0.0045244524 0 5269.519 14.512693
|
||||
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
|
||||
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
|
||||
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
|
||||
2550 16738.552 -0.04420046 0 5269.4998 14.512177
|
||||
2600 16738.42 -0.004347531 0 5269.4982 14.512783
|
||||
2650 16734.241 1.3131302 0 5269.5 14.577195
|
||||
2700 16738.737 -0.10612056 0 5269.4961 14.503874
|
||||
2750 16732.705 1.7939719 0 5269.4974 14.629294
|
||||
2800 16738.558 -0.042867033 0 5269.5032 14.519893
|
||||
2850 16738.499 -0.01271227 0 5269.5146 14.518524
|
||||
2900 16738.486 -0.0032778045 0 5269.52 14.518712
|
||||
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
|
||||
3000 16738.647 -0.070862542 0 5269.5031 14.51803
|
||||
3050 16678.313 18.829038 0 5269.409 15.533426
|
||||
3100 16632.312 33.399217 0 5269.4975 14.588597
|
||||
3150 16739.318 -0.31388148 0 5269.4715 13.520782
|
||||
3200 16727.951 3.26736 0 5269.4741 12.288358
|
||||
3250 16686.364 16.353793 0 5269.4682 14.152517
|
||||
3300 16738.532 -0.031574462 0 5269.5064 13.310615
|
||||
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
|
||||
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
|
||||
3450 16738.489 -0.021623738 0 5269.5026 13.308001
|
||||
3500 16737.78 0.19719043 0 5269.4983 13.325999
|
||||
3550 16658.578 25.116206 0 5269.4834 13.778249
|
||||
3600 16738.51 -0.032864725 0 5269.4981 12.392389
|
||||
3650 16738.899 -0.15952703 0 5269.4938 12.383503
|
||||
3700 16738.879 -0.16025994 0 5269.487 12.382575
|
||||
3750 16738.878 -0.16608251 0 5269.4806 12.382765
|
||||
3800 16738.591 -0.078679341 0 5269.4776 12.383227
|
||||
3850 16738.429 -0.024729409 0 5269.4807 12.382942
|
||||
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
|
||||
3950 16738.428 -0.002521266 0 5269.5027 12.383324
|
||||
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
|
||||
4050 16738.488 0 0 5269.5241 12.383531
|
||||
4100 16738.468 0 0 5269.5178 12.383482
|
||||
4150 16738.422 0 0 5269.5033 12.383369
|
||||
4200 16738.387 0 0 5269.4921 12.383281
|
||||
4250 16738.383 0 0 5269.4908 12.38327
|
||||
4300 16738.4 0 0 5269.4964 12.383314
|
||||
4350 16738.423 0 0 5269.5036 12.38337
|
||||
4400 16738.441 0 0 5269.5092 12.383414
|
||||
4450 16738.45 0 0 5269.5121 12.383437
|
||||
4500 16738.45 0 0 5269.5122 12.383438
|
||||
4550 16738.442 0 0 5269.5095 12.383417
|
||||
4600 16738.425 0 0 5269.5042 12.383376
|
||||
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
|
||||
4700 16738.444 -0.024020551 0 5269.4862 12.382975
|
||||
4750 16738.49 -0.048521424 0 5269.4761 12.385777
|
||||
4800 16735.057 1.0347218 0 5269.4786 12.43543
|
||||
4850 16735.441 0.92650925 0 5269.4913 12.418653
|
||||
4900 16723.839 4.5908973 0 5269.5033 13.410103
|
||||
4950 16738.531 -0.021537669 0 5269.5159 13.089982
|
||||
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
|
||||
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
|
||||
5100 16738.404 0 0 5269.4976 13.090032
|
||||
5150 16738.421 0 0 5269.5029 13.090073
|
||||
5200 16738.44 0 0 5269.5087 13.090119
|
||||
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
|
||||
5300 16738.456 -0.0064376396 0 5269.5075 13.090026
|
||||
5350 16738.479 -0.020383843 0 5269.5007 13.089898
|
||||
5400 16735.845 0.79889489 0 5269.4909 13.136244
|
||||
5450 16735.558 0.87619907 0 5269.4778 12.324482
|
||||
5500 16711.494 8.4724273 0 5269.4984 12.656579
|
||||
5550 16454.525 89.074821 0 5269.2031 16.996502
|
||||
5600 16713.084 7.9801107 0 5269.5065 13.774972
|
||||
5650 16738.676 -0.079987805 0 5269.5033 13.168292
|
||||
5700 16446.281 91.866085 0 5269.399 23.764659
|
||||
5750 16738.549 -0.039869082 0 5269.5034 13.378118
|
||||
5800 16738.487 -0.014994465 0 5269.5086 13.378394
|
||||
5850 16738.466 -0.0051267396 0 5269.512 13.378555
|
||||
5900 16738.462 -0.004368998 0 5269.5113 13.378568
|
||||
5950 16738.528 -0.032727397 0 5269.5039 13.378192
|
||||
6000 16702.774 10.969422 0 5269.2502 13.788847
|
||||
6050 16682.271 17.483223 0 5269.3092 13.353098
|
||||
6100 16738.508 -0.028838294 0 5269.5016 12.521077
|
||||
6150 16738.425 -0.0067595586 0 5269.4974 12.521216
|
||||
6200 16738.401 -0.0011499906 0 5269.4955 12.521248
|
||||
6250 16738.455 0 0 5269.5136 12.521404
|
||||
6300 16738.523 0 0 5269.5352 12.521573
|
||||
6350 16738.503 0 0 5269.5287 12.521525
|
||||
6400 16738.427 0 0 5269.5047 12.521337
|
||||
6450 16738.399 0 0 5269.496 12.521268
|
||||
6500 16738.425 0 0 5269.5042 12.521331
|
||||
6550 16738.441 0 0 5269.5093 12.521372
|
||||
6600 16738.42 0 0 5269.5025 12.521319
|
||||
6650 16738.398 0 0 5269.4957 12.521266
|
||||
6700 16738.435 0 0 5269.5074 12.521355
|
||||
6750 16738.505 0 0 5269.5293 12.521527
|
||||
6800 16738.508 0 0 5269.5303 12.521536
|
||||
6850 16738.446 0 0 5269.5108 12.521384
|
||||
6900 16738.414 0 0 5269.5009 12.521306
|
||||
6950 16738.432 0 0 5269.5063 12.521348
|
||||
7000 16738.444 0 0 5269.5102 12.521379
|
||||
7050 16738.421 0 0 5269.5029 12.521322
|
||||
7100 16738.393 0 0 5269.4941 12.521253
|
||||
7150 16738.419 0 0 5269.5022 12.521315
|
||||
7200 16738.489 0 0 5269.5244 12.521489
|
||||
7250 16738.505 0 0 5269.5293 12.521528
|
||||
7300 16738.443 0 0 5269.5098 12.521377
|
||||
7350 16738.404 0 0 5269.4976 12.521281
|
||||
7400 16738.43 0 0 5269.5058 12.521344
|
||||
7450 16738.461 0 0 5269.5156 12.521421
|
||||
7500 16738.447 0 0 5269.5109 12.521385
|
||||
7550 16738.407 0 0 5269.4986 12.521288
|
||||
7600 16738.412 0 0 5269.5002 12.5213
|
||||
7650 16738.478 0 0 5269.5208 12.521461
|
||||
7700 16738.51 0 0 5269.5309 12.521541
|
||||
7750 16738.454 0 0 5269.5135 12.521406
|
||||
7800 16738.398 0 0 5269.4958 12.521267
|
||||
7850 16738.407 -0.00021180715 0 5269.4982 12.521283
|
||||
7900 16738.441 -0.0002167946 0 5269.509 12.521367
|
||||
7950 16738.446 -0.0002384787 0 5269.5107 12.52138
|
||||
8000 16738.423 0 0 5269.5035 12.521327
|
||||
8050 16738.423 0 0 5269.5034 12.521325
|
||||
8100 16738.478 -0.00069624484 0 5269.52 12.521448
|
||||
8150 16738.523 -0.0040058183 0 5269.531 12.521494
|
||||
8200 16738.486 -0.0092298512 0 5269.5142 12.521328
|
||||
8250 16738.458 -0.023189661 0 5269.4914 12.521008
|
||||
8300 16738.513 -0.045847765 0 5269.4861 12.520773
|
||||
8350 16723.735 4.5720344 0 5269.4516 12.849543
|
||||
8400 16738.466 -0.02019859 0 5269.497 12.835812
|
||||
8450 16738.437 -0.012822198 0 5269.4952 12.829979
|
||||
8500 16738.408 -0.0016833646 0 5269.4972 12.830104
|
||||
8550 16738.464 -0.00097382606 0 5269.5155 12.830258
|
||||
8600 16738.669 -0.050581176 0 5269.5304 12.829977
|
||||
8650 15918.073 250.131 0 5261.3761 24.542327
|
||||
8700 16738.446 0.00085039409 0 5269.5116 10.59114
|
||||
8750 16738.472 -0.010146632 0 5269.5089 10.590059
|
||||
8800 16738.468 0 0 5269.5176 10.590278
|
||||
8850 16738.508 0 0 5269.5303 10.590378
|
||||
8900 16738.509 0 0 5269.5306 10.590381
|
||||
8950 16738.496 0 0 5269.5266 10.590349
|
||||
9000 16738.477 0 0 5269.5204 10.590302
|
||||
9050 16738.455 0 0 5269.5135 10.590247
|
||||
9100 16738.477 0 0 5269.5205 10.590301
|
||||
9150 16738.512 0 0 5269.5315 10.590388
|
||||
9200 16738.502 0 0 5269.5285 10.590364
|
||||
9250 16738.493 0 0 5269.5254 10.59034
|
||||
9300 16738.482 0 0 5269.522 10.590314
|
||||
9350 16738.46 0 0 5269.5151 10.59026
|
||||
9400 16738.48 0 0 5269.5216 10.59031
|
||||
9450 16738.509 0 0 5269.5306 10.590381
|
||||
9500 16738.49 0 0 5269.5247 10.590335
|
||||
9550 16738.484 0 0 5269.5226 10.590318
|
||||
9600 16738.483 0 0 5269.5223 10.590316
|
||||
9650 16738.464 0 0 5269.5165 10.590271
|
||||
9700 16738.484 0 0 5269.5228 10.590319
|
||||
9750 16738.507 0 0 5269.53 10.590376
|
||||
9800 16738.482 0 0 5269.522 10.590314
|
||||
9850 16738.478 0 0 5269.5207 10.590303
|
||||
9900 16738.487 -0.00030979874 0 5269.5233 10.59032
|
||||
9950 16738.476 -0.00095967134 0 5269.5192 10.590278
|
||||
10000 16738.494 -0.00062714318 0 5269.5253 10.590329
|
||||
Loop time of 0.224811 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 384323.005 tau/day, 44481.829 timesteps/s
|
||||
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0032673 | 0.0039269 | 0.0048387 | 1.1 | 1.75
|
||||
Neigh | 0.010401 | 0.012159 | 0.015022 | 1.6 | 5.41
|
||||
Comm | 0.087584 | 0.08909 | 0.090645 | 0.4 | 39.63
|
||||
Output | 0.0042956 | 0.0045624 | 0.0052695 | 0.6 | 2.03
|
||||
Modify | 0.10208 | 0.10506 | 0.10697 | 0.6 | 46.73
|
||||
Other | | 0.01001 | | | 4.45
|
||||
|
||||
Nlocal: 20.25 ave 34 max 9 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 38.5 ave 43 max 26 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0.75 ave 2 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 3
|
||||
Ave neighs/atom = 0.037037
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
335
examples/rigid/log.20Apr18.rigid.nve.g++.1
Normal file
335
examples/rigid/log.20Apr18.rigid.nve.g++.1
Normal file
@ -0,0 +1,335 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.69 571.70921 0 5265.8153 32.005816
|
||||
100 16298.128 136.75661 0 5267.6488 16.449029
|
||||
150 16682.532 17.504156 0 5269.4124 14.901186
|
||||
200 16733.906 1.3755079 0 5269.4571 14.571305
|
||||
250 16738.861 -0.15272039 0 5269.4886 14.498342
|
||||
300 16738.608 -0.055216883 0 5269.5066 14.498
|
||||
350 16738.5 -0.017457072 0 5269.5104 14.498392
|
||||
400 16738.451 -0.0060161309 0 5269.5063 14.49851
|
||||
450 16738.435 -0.001271965 0 5269.5059 14.498571
|
||||
500 16738.443 -0.00081074175 0 5269.509 14.498598
|
||||
550 16738.452 -0.00083208965 0 5269.5118 14.498618
|
||||
600 16738.45 -0.00058358431 0 5269.5116 14.498617
|
||||
650 16738.443 -0.00047228525 0 5269.5093 14.4986
|
||||
700 16738.444 0 0 5269.5102 14.498612
|
||||
750 16738.461 0 0 5269.5157 14.498654
|
||||
800 16738.479 0 0 5269.521 14.498697
|
||||
850 16738.473 0 0 5269.5192 14.498683
|
||||
900 16738.449 0 0 5269.5116 14.498624
|
||||
950 16738.438 -0.0035324203 0 5269.5046 14.498537
|
||||
1000 16738.562 -0.051134242 0 5269.4963 14.498093
|
||||
1050 16737.343 0.32970192 0 5269.4934 14.527634
|
||||
1100 16737.878 0.16213235 0 5269.4941 14.533864
|
||||
1150 16738.682 -0.089236256 0 5269.4959 14.511765
|
||||
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
|
||||
1250 16738.45 0 0 5269.5119 14.512611
|
||||
1300 16738.475 0 0 5269.5199 14.512673
|
||||
1350 16738.484 0 0 5269.5228 14.512696
|
||||
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
|
||||
1450 16738.45 -0.0010933363 0 5269.511 14.512595
|
||||
1500 16738.445 -0.00057484239 0 5269.51 14.512591
|
||||
1550 16738.451 0 0 5269.5123 14.512615
|
||||
1600 16738.452 0 0 5269.5127 14.512618
|
||||
1650 16738.443 0 0 5269.5099 14.512596
|
||||
1700 16738.433 0 0 5269.5068 14.512572
|
||||
1750 16738.438 0 0 5269.5084 14.512584
|
||||
1800 16738.459 0 0 5269.5149 14.512635
|
||||
1850 16738.473 0 0 5269.5193 14.51267
|
||||
1900 16738.462 0 0 5269.5159 14.512644
|
||||
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
|
||||
2000 16738.463 -0.013425408 0 5269.5027 14.512382
|
||||
2050 16738.535 -0.036964311 0 5269.5017 14.512152
|
||||
2100 16738.621 -0.063490509 0 5269.5023 14.512108
|
||||
2150 16738.594 -0.056143934 0 5269.5012 14.512117
|
||||
2200 16738.536 -0.038486645 0 5269.5007 14.512277
|
||||
2250 16738.496 -0.023712406 0 5269.503 14.51242
|
||||
2300 16738.488 -0.013209094 0 5269.5109 14.51255
|
||||
2350 16738.486 -0.0045244524 0 5269.519 14.512693
|
||||
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
|
||||
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
|
||||
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
|
||||
2550 16738.552 -0.04420046 0 5269.4998 14.512177
|
||||
2600 16738.42 -0.004347531 0 5269.4982 14.512783
|
||||
2650 16734.241 1.3131302 0 5269.5 14.577195
|
||||
2700 16738.737 -0.10612056 0 5269.4961 14.503874
|
||||
2750 16732.705 1.7939719 0 5269.4974 14.629294
|
||||
2800 16738.558 -0.042867033 0 5269.5032 14.519893
|
||||
2850 16738.499 -0.01271227 0 5269.5146 14.518524
|
||||
2900 16738.486 -0.0032778045 0 5269.52 14.518712
|
||||
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
|
||||
3000 16738.647 -0.070862542 0 5269.5031 14.51803
|
||||
3050 16678.313 18.829038 0 5269.409 15.533426
|
||||
3100 16632.312 33.399217 0 5269.4975 14.588597
|
||||
3150 16739.318 -0.31388148 0 5269.4715 13.520782
|
||||
3200 16727.951 3.26736 0 5269.4741 12.288358
|
||||
3250 16686.364 16.353793 0 5269.4682 14.152517
|
||||
3300 16738.532 -0.031574462 0 5269.5064 13.310615
|
||||
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
|
||||
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
|
||||
3450 16738.489 -0.021623738 0 5269.5026 13.308001
|
||||
3500 16737.78 0.19719043 0 5269.4983 13.325999
|
||||
3550 16658.578 25.116206 0 5269.4834 13.778249
|
||||
3600 16738.51 -0.032864725 0 5269.4981 12.392389
|
||||
3650 16738.899 -0.15952703 0 5269.4938 12.383503
|
||||
3700 16738.879 -0.16025994 0 5269.487 12.382575
|
||||
3750 16738.878 -0.16608251 0 5269.4806 12.382765
|
||||
3800 16738.591 -0.078679341 0 5269.4776 12.383227
|
||||
3850 16738.429 -0.024729409 0 5269.4807 12.382942
|
||||
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
|
||||
3950 16738.428 -0.002521266 0 5269.5027 12.383324
|
||||
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
|
||||
4050 16738.488 0 0 5269.5241 12.383531
|
||||
4100 16738.468 0 0 5269.5178 12.383482
|
||||
4150 16738.422 0 0 5269.5033 12.383369
|
||||
4200 16738.387 0 0 5269.4921 12.383281
|
||||
4250 16738.383 0 0 5269.4908 12.38327
|
||||
4300 16738.4 0 0 5269.4964 12.383314
|
||||
4350 16738.423 0 0 5269.5036 12.38337
|
||||
4400 16738.441 0 0 5269.5092 12.383414
|
||||
4450 16738.45 0 0 5269.5121 12.383437
|
||||
4500 16738.45 0 0 5269.5122 12.383438
|
||||
4550 16738.442 0 0 5269.5095 12.383417
|
||||
4600 16738.425 0 0 5269.5042 12.383376
|
||||
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
|
||||
4700 16738.444 -0.024020551 0 5269.4862 12.382975
|
||||
4750 16738.49 -0.048521421 0 5269.4761 12.385777
|
||||
4800 16735.057 1.0347219 0 5269.4786 12.43543
|
||||
4850 16735.441 0.92650928 0 5269.4913 12.418653
|
||||
4900 16723.839 4.5908971 0 5269.5033 13.410103
|
||||
4950 16738.531 -0.021537669 0 5269.5159 13.089982
|
||||
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
|
||||
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
|
||||
5100 16738.404 0 0 5269.4976 13.090032
|
||||
5150 16738.421 0 0 5269.5029 13.090073
|
||||
5200 16738.44 0 0 5269.5087 13.090119
|
||||
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
|
||||
5300 16738.456 -0.0064376397 0 5269.5075 13.090026
|
||||
5350 16738.479 -0.020383842 0 5269.5007 13.089898
|
||||
5400 16735.845 0.79889481 0 5269.4909 13.136244
|
||||
5450 16735.558 0.87619898 0 5269.4778 12.324482
|
||||
5500 16711.494 8.47243 0 5269.4984 12.65658
|
||||
5550 16454.525 89.074845 0 5269.2031 16.996503
|
||||
5600 16713.084 7.9801091 0 5269.5065 13.774971
|
||||
5650 16738.676 -0.079987812 0 5269.5033 13.168292
|
||||
5700 16446.281 91.866085 0 5269.399 23.764658
|
||||
5750 16738.549 -0.039869082 0 5269.5034 13.378117
|
||||
5800 16738.487 -0.014994464 0 5269.5086 13.378394
|
||||
5850 16738.466 -0.0051267378 0 5269.512 13.378555
|
||||
5900 16738.462 -0.0043689966 0 5269.5113 13.378568
|
||||
5950 16738.528 -0.032727396 0 5269.5039 13.378192
|
||||
6000 16702.774 10.969422 0 5269.2502 13.788847
|
||||
6050 16682.271 17.483217 0 5269.3092 13.353098
|
||||
6100 16738.508 -0.028838289 0 5269.5016 12.521077
|
||||
6150 16738.425 -0.0067595568 0 5269.4974 12.521216
|
||||
6200 16738.401 -0.0011499904 0 5269.4955 12.521247
|
||||
6250 16738.455 0 0 5269.5136 12.521403
|
||||
6300 16738.523 0 0 5269.5352 12.521573
|
||||
6350 16738.503 0 0 5269.5287 12.521525
|
||||
6400 16738.427 0 0 5269.5047 12.521337
|
||||
6450 16738.399 0 0 5269.496 12.521268
|
||||
6500 16738.425 0 0 5269.5042 12.521331
|
||||
6550 16738.441 0 0 5269.5093 12.521372
|
||||
6600 16738.42 0 0 5269.5025 12.521319
|
||||
6650 16738.398 0 0 5269.4957 12.521266
|
||||
6700 16738.435 0 0 5269.5074 12.521355
|
||||
6750 16738.505 0 0 5269.5293 12.521527
|
||||
6800 16738.508 0 0 5269.5303 12.521536
|
||||
6850 16738.446 0 0 5269.5108 12.521384
|
||||
6900 16738.414 0 0 5269.5009 12.521306
|
||||
6950 16738.432 0 0 5269.5063 12.521348
|
||||
7000 16738.444 0 0 5269.5102 12.521378
|
||||
7050 16738.421 0 0 5269.5029 12.521322
|
||||
7100 16738.393 0 0 5269.4941 12.521253
|
||||
7150 16738.419 0 0 5269.5022 12.521315
|
||||
7200 16738.489 0 0 5269.5244 12.521489
|
||||
7250 16738.505 0 0 5269.5293 12.521528
|
||||
7300 16738.443 0 0 5269.5098 12.521376
|
||||
7350 16738.404 0 0 5269.4976 12.521281
|
||||
7400 16738.43 0 0 5269.5058 12.521343
|
||||
7450 16738.461 0 0 5269.5156 12.521421
|
||||
7500 16738.447 0 0 5269.5109 12.521385
|
||||
7550 16738.407 0 0 5269.4986 12.521288
|
||||
7600 16738.412 0 0 5269.5002 12.5213
|
||||
7650 16738.478 0 0 5269.5208 12.52146
|
||||
7700 16738.51 0 0 5269.5309 12.521541
|
||||
7750 16738.454 0 0 5269.5135 12.521405
|
||||
7800 16738.398 0 0 5269.4958 12.521267
|
||||
7850 16738.407 -0.0002118068 0 5269.4982 12.521283
|
||||
7900 16738.441 -0.00021679441 0 5269.509 12.521366
|
||||
7950 16738.446 -0.00023847865 0 5269.5107 12.52138
|
||||
8000 16738.423 0 0 5269.5035 12.521326
|
||||
8050 16738.423 0 0 5269.5034 12.521325
|
||||
8100 16738.478 -0.00069624411 0 5269.52 12.521447
|
||||
8150 16738.523 -0.0040058094 0 5269.531 12.521494
|
||||
8200 16738.486 -0.0092298399 0 5269.5142 12.521327
|
||||
8250 16738.458 -0.023189572 0 5269.4914 12.521008
|
||||
8300 16738.513 -0.045847775 0 5269.4861 12.520773
|
||||
8350 16723.734 4.5722877 0 5269.4516 12.849562
|
||||
8400 16738.466 -0.020202622 0 5269.497 12.835807
|
||||
8450 16738.437 -0.012822209 0 5269.4952 12.829975
|
||||
8500 16738.408 -0.001683355 0 5269.4972 12.8301
|
||||
8550 16738.464 -0.00097382251 0 5269.5155 12.830254
|
||||
8600 16738.669 -0.050581166 0 5269.5304 12.829973
|
||||
8650 15918.256 250.07455 0 5261.3774 24.539208
|
||||
8700 16738.446 0.00084613367 0 5269.5116 10.591358
|
||||
8750 16738.472 -0.010145611 0 5269.5089 10.590277
|
||||
8800 16738.468 0 0 5269.5176 10.590497
|
||||
8850 16738.508 0 0 5269.5303 10.590596
|
||||
8900 16738.509 0 0 5269.5306 10.590599
|
||||
8950 16738.496 0 0 5269.5266 10.590568
|
||||
9000 16738.477 0 0 5269.5204 10.59052
|
||||
9050 16738.455 0 0 5269.5135 10.590465
|
||||
9100 16738.477 0 0 5269.5205 10.590519
|
||||
9150 16738.512 0 0 5269.5315 10.590606
|
||||
9200 16738.502 0 0 5269.5285 10.590583
|
||||
9250 16738.493 0 0 5269.5254 10.590559
|
||||
9300 16738.482 0 0 5269.522 10.590532
|
||||
9350 16738.46 0 0 5269.5151 10.590478
|
||||
9400 16738.48 0 0 5269.5216 10.590528
|
||||
9450 16738.509 0 0 5269.5306 10.590599
|
||||
9500 16738.49 0 0 5269.5247 10.590554
|
||||
9550 16738.484 0 0 5269.5226 10.590536
|
||||
9600 16738.483 0 0 5269.5223 10.590534
|
||||
9650 16738.464 0 0 5269.5165 10.590489
|
||||
9700 16738.484 0 0 5269.5228 10.590537
|
||||
9750 16738.507 0 0 5269.53 10.590595
|
||||
9800 16738.482 0 0 5269.522 10.590532
|
||||
9850 16738.478 0 0 5269.5207 10.590521
|
||||
9900 16738.487 -0.00030979882 0 5269.5233 10.590538
|
||||
9950 16738.476 -0.00095967357 0 5269.5193 10.590496
|
||||
10000 16738.494 -0.00062714625 0 5269.5253 10.590548
|
||||
Loop time of 0.166547 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 518773.777 tau/day, 60043.261 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.011439 | 0.011439 | 0.011439 | 0.0 | 6.87
|
||||
Neigh | 0.038572 | 0.038572 | 0.038572 | 0.0 | 23.16
|
||||
Comm | 0.0085464 | 0.0085464 | 0.0085464 | 0.0 | 5.13
|
||||
Output | 0.0025046 | 0.0025046 | 0.0025046 | 0.0 | 1.50
|
||||
Modify | 0.099479 | 0.099479 | 0.099479 | 0.0 | 59.73
|
||||
Other | | 0.006005 | | | 3.61
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 49 ave 49 max 49 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3
|
||||
Ave neighs/atom = 0.037037
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
335
examples/rigid/log.20Apr18.rigid.nve.g++.4
Normal file
335
examples/rigid/log.20Apr18.rigid.nve.g++.4
Normal file
@ -0,0 +1,335 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.69 571.70921 0 5265.8153 32.005816
|
||||
100 16298.128 136.75661 0 5267.6488 16.449029
|
||||
150 16682.532 17.504156 0 5269.4124 14.901186
|
||||
200 16733.906 1.3755079 0 5269.4571 14.571305
|
||||
250 16738.861 -0.15272039 0 5269.4886 14.498342
|
||||
300 16738.608 -0.055216883 0 5269.5066 14.498
|
||||
350 16738.5 -0.017457072 0 5269.5104 14.498392
|
||||
400 16738.451 -0.0060161309 0 5269.5063 14.49851
|
||||
450 16738.435 -0.001271965 0 5269.5059 14.498571
|
||||
500 16738.443 -0.00081074175 0 5269.509 14.498598
|
||||
550 16738.452 -0.00083208965 0 5269.5118 14.498618
|
||||
600 16738.45 -0.00058358431 0 5269.5116 14.498617
|
||||
650 16738.443 -0.00047228525 0 5269.5093 14.4986
|
||||
700 16738.444 0 0 5269.5102 14.498612
|
||||
750 16738.461 0 0 5269.5157 14.498654
|
||||
800 16738.479 0 0 5269.521 14.498697
|
||||
850 16738.473 0 0 5269.5192 14.498683
|
||||
900 16738.449 0 0 5269.5116 14.498624
|
||||
950 16738.438 -0.0035324203 0 5269.5046 14.498537
|
||||
1000 16738.562 -0.051134242 0 5269.4963 14.498093
|
||||
1050 16737.343 0.32970192 0 5269.4934 14.527634
|
||||
1100 16737.878 0.16213235 0 5269.4941 14.533864
|
||||
1150 16738.682 -0.089236256 0 5269.4959 14.511765
|
||||
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
|
||||
1250 16738.45 0 0 5269.5119 14.512611
|
||||
1300 16738.475 0 0 5269.5199 14.512673
|
||||
1350 16738.484 0 0 5269.5228 14.512696
|
||||
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
|
||||
1450 16738.45 -0.0010933363 0 5269.511 14.512595
|
||||
1500 16738.445 -0.00057484239 0 5269.51 14.512591
|
||||
1550 16738.451 0 0 5269.5123 14.512615
|
||||
1600 16738.452 0 0 5269.5127 14.512618
|
||||
1650 16738.443 0 0 5269.5099 14.512596
|
||||
1700 16738.433 0 0 5269.5068 14.512572
|
||||
1750 16738.438 0 0 5269.5084 14.512584
|
||||
1800 16738.459 0 0 5269.5149 14.512635
|
||||
1850 16738.473 0 0 5269.5193 14.51267
|
||||
1900 16738.462 0 0 5269.5159 14.512644
|
||||
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
|
||||
2000 16738.463 -0.013425408 0 5269.5027 14.512382
|
||||
2050 16738.535 -0.036964311 0 5269.5017 14.512152
|
||||
2100 16738.621 -0.063490509 0 5269.5023 14.512108
|
||||
2150 16738.594 -0.056143934 0 5269.5012 14.512117
|
||||
2200 16738.536 -0.038486645 0 5269.5007 14.512277
|
||||
2250 16738.496 -0.023712406 0 5269.503 14.51242
|
||||
2300 16738.488 -0.013209094 0 5269.5109 14.51255
|
||||
2350 16738.486 -0.0045244524 0 5269.519 14.512693
|
||||
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
|
||||
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
|
||||
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
|
||||
2550 16738.552 -0.04420046 0 5269.4998 14.512177
|
||||
2600 16738.42 -0.004347531 0 5269.4982 14.512783
|
||||
2650 16734.241 1.3131302 0 5269.5 14.577195
|
||||
2700 16738.737 -0.10612056 0 5269.4961 14.503874
|
||||
2750 16732.705 1.7939719 0 5269.4974 14.629294
|
||||
2800 16738.558 -0.042867033 0 5269.5032 14.519893
|
||||
2850 16738.499 -0.01271227 0 5269.5146 14.518524
|
||||
2900 16738.486 -0.0032778045 0 5269.52 14.518712
|
||||
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
|
||||
3000 16738.647 -0.070862542 0 5269.5031 14.51803
|
||||
3050 16678.313 18.829038 0 5269.409 15.533426
|
||||
3100 16632.312 33.399217 0 5269.4975 14.588597
|
||||
3150 16739.318 -0.31388148 0 5269.4715 13.520782
|
||||
3200 16727.951 3.26736 0 5269.4741 12.288358
|
||||
3250 16686.364 16.353793 0 5269.4682 14.152517
|
||||
3300 16738.532 -0.031574462 0 5269.5064 13.310615
|
||||
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
|
||||
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
|
||||
3450 16738.489 -0.021623738 0 5269.5026 13.308001
|
||||
3500 16737.78 0.19719043 0 5269.4983 13.325999
|
||||
3550 16658.578 25.116206 0 5269.4834 13.778249
|
||||
3600 16738.51 -0.032864725 0 5269.4981 12.392389
|
||||
3650 16738.899 -0.15952703 0 5269.4938 12.383503
|
||||
3700 16738.879 -0.16025994 0 5269.487 12.382575
|
||||
3750 16738.878 -0.16608251 0 5269.4806 12.382765
|
||||
3800 16738.591 -0.078679341 0 5269.4776 12.383227
|
||||
3850 16738.429 -0.024729409 0 5269.4807 12.382942
|
||||
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
|
||||
3950 16738.428 -0.002521266 0 5269.5027 12.383324
|
||||
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
|
||||
4050 16738.488 0 0 5269.5241 12.383531
|
||||
4100 16738.468 0 0 5269.5178 12.383482
|
||||
4150 16738.422 0 0 5269.5033 12.383369
|
||||
4200 16738.387 0 0 5269.4921 12.383281
|
||||
4250 16738.383 0 0 5269.4908 12.38327
|
||||
4300 16738.4 0 0 5269.4964 12.383314
|
||||
4350 16738.423 0 0 5269.5036 12.38337
|
||||
4400 16738.441 0 0 5269.5092 12.383414
|
||||
4450 16738.45 0 0 5269.5121 12.383437
|
||||
4500 16738.45 0 0 5269.5122 12.383438
|
||||
4550 16738.442 0 0 5269.5095 12.383417
|
||||
4600 16738.425 0 0 5269.5042 12.383376
|
||||
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
|
||||
4700 16738.444 -0.024020551 0 5269.4862 12.382975
|
||||
4750 16738.49 -0.048521424 0 5269.4761 12.385777
|
||||
4800 16735.057 1.0347218 0 5269.4786 12.43543
|
||||
4850 16735.441 0.92650925 0 5269.4913 12.418653
|
||||
4900 16723.839 4.5908973 0 5269.5033 13.410103
|
||||
4950 16738.531 -0.021537669 0 5269.5159 13.089982
|
||||
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
|
||||
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
|
||||
5100 16738.404 0 0 5269.4976 13.090032
|
||||
5150 16738.421 0 0 5269.5029 13.090073
|
||||
5200 16738.44 0 0 5269.5087 13.090119
|
||||
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
|
||||
5300 16738.456 -0.0064376396 0 5269.5075 13.090026
|
||||
5350 16738.479 -0.020383843 0 5269.5007 13.089898
|
||||
5400 16735.845 0.79889489 0 5269.4909 13.136244
|
||||
5450 16735.558 0.87619907 0 5269.4778 12.324482
|
||||
5500 16711.494 8.4724273 0 5269.4984 12.656579
|
||||
5550 16454.525 89.074821 0 5269.2031 16.996502
|
||||
5600 16713.084 7.9801107 0 5269.5065 13.774972
|
||||
5650 16738.676 -0.079987805 0 5269.5033 13.168292
|
||||
5700 16446.281 91.866085 0 5269.399 23.764659
|
||||
5750 16738.549 -0.039869082 0 5269.5034 13.378118
|
||||
5800 16738.487 -0.014994465 0 5269.5086 13.378394
|
||||
5850 16738.466 -0.0051267396 0 5269.512 13.378555
|
||||
5900 16738.462 -0.004368998 0 5269.5113 13.378568
|
||||
5950 16738.528 -0.032727397 0 5269.5039 13.378192
|
||||
6000 16702.774 10.969422 0 5269.2502 13.788847
|
||||
6050 16682.271 17.483223 0 5269.3092 13.353098
|
||||
6100 16738.508 -0.028838294 0 5269.5016 12.521077
|
||||
6150 16738.425 -0.0067595586 0 5269.4974 12.521216
|
||||
6200 16738.401 -0.0011499906 0 5269.4955 12.521248
|
||||
6250 16738.455 0 0 5269.5136 12.521404
|
||||
6300 16738.523 0 0 5269.5352 12.521573
|
||||
6350 16738.503 0 0 5269.5287 12.521525
|
||||
6400 16738.427 0 0 5269.5047 12.521337
|
||||
6450 16738.399 0 0 5269.496 12.521268
|
||||
6500 16738.425 0 0 5269.5042 12.521331
|
||||
6550 16738.441 0 0 5269.5093 12.521372
|
||||
6600 16738.42 0 0 5269.5025 12.521319
|
||||
6650 16738.398 0 0 5269.4957 12.521266
|
||||
6700 16738.435 0 0 5269.5074 12.521355
|
||||
6750 16738.505 0 0 5269.5293 12.521527
|
||||
6800 16738.508 0 0 5269.5303 12.521536
|
||||
6850 16738.446 0 0 5269.5108 12.521384
|
||||
6900 16738.414 0 0 5269.5009 12.521306
|
||||
6950 16738.432 0 0 5269.5063 12.521348
|
||||
7000 16738.444 0 0 5269.5102 12.521379
|
||||
7050 16738.421 0 0 5269.5029 12.521322
|
||||
7100 16738.393 0 0 5269.4941 12.521253
|
||||
7150 16738.419 0 0 5269.5022 12.521315
|
||||
7200 16738.489 0 0 5269.5244 12.521489
|
||||
7250 16738.505 0 0 5269.5293 12.521528
|
||||
7300 16738.443 0 0 5269.5098 12.521377
|
||||
7350 16738.404 0 0 5269.4976 12.521281
|
||||
7400 16738.43 0 0 5269.5058 12.521344
|
||||
7450 16738.461 0 0 5269.5156 12.521421
|
||||
7500 16738.447 0 0 5269.5109 12.521385
|
||||
7550 16738.407 0 0 5269.4986 12.521288
|
||||
7600 16738.412 0 0 5269.5002 12.5213
|
||||
7650 16738.478 0 0 5269.5208 12.521461
|
||||
7700 16738.51 0 0 5269.5309 12.521541
|
||||
7750 16738.454 0 0 5269.5135 12.521406
|
||||
7800 16738.398 0 0 5269.4958 12.521267
|
||||
7850 16738.407 -0.00021180715 0 5269.4982 12.521283
|
||||
7900 16738.441 -0.0002167946 0 5269.509 12.521367
|
||||
7950 16738.446 -0.0002384787 0 5269.5107 12.52138
|
||||
8000 16738.423 0 0 5269.5035 12.521327
|
||||
8050 16738.423 0 0 5269.5034 12.521325
|
||||
8100 16738.478 -0.00069624484 0 5269.52 12.521448
|
||||
8150 16738.523 -0.0040058183 0 5269.531 12.521494
|
||||
8200 16738.486 -0.0092298512 0 5269.5142 12.521328
|
||||
8250 16738.458 -0.023189661 0 5269.4914 12.521008
|
||||
8300 16738.513 -0.045847765 0 5269.4861 12.520773
|
||||
8350 16723.735 4.5720344 0 5269.4516 12.849543
|
||||
8400 16738.466 -0.02019859 0 5269.497 12.835812
|
||||
8450 16738.437 -0.012822198 0 5269.4952 12.829979
|
||||
8500 16738.408 -0.0016833646 0 5269.4972 12.830104
|
||||
8550 16738.464 -0.00097382606 0 5269.5155 12.830258
|
||||
8600 16738.669 -0.050581176 0 5269.5304 12.829977
|
||||
8650 15918.073 250.131 0 5261.3761 24.542327
|
||||
8700 16738.446 0.00085039409 0 5269.5116 10.59114
|
||||
8750 16738.472 -0.010146632 0 5269.5089 10.590059
|
||||
8800 16738.468 0 0 5269.5176 10.590278
|
||||
8850 16738.508 0 0 5269.5303 10.590378
|
||||
8900 16738.509 0 0 5269.5306 10.590381
|
||||
8950 16738.496 0 0 5269.5266 10.590349
|
||||
9000 16738.477 0 0 5269.5204 10.590302
|
||||
9050 16738.455 0 0 5269.5135 10.590247
|
||||
9100 16738.477 0 0 5269.5205 10.590301
|
||||
9150 16738.512 0 0 5269.5315 10.590388
|
||||
9200 16738.502 0 0 5269.5285 10.590364
|
||||
9250 16738.493 0 0 5269.5254 10.59034
|
||||
9300 16738.482 0 0 5269.522 10.590314
|
||||
9350 16738.46 0 0 5269.5151 10.59026
|
||||
9400 16738.48 0 0 5269.5216 10.59031
|
||||
9450 16738.509 0 0 5269.5306 10.590381
|
||||
9500 16738.49 0 0 5269.5247 10.590335
|
||||
9550 16738.484 0 0 5269.5226 10.590318
|
||||
9600 16738.483 0 0 5269.5223 10.590316
|
||||
9650 16738.464 0 0 5269.5165 10.590271
|
||||
9700 16738.484 0 0 5269.5228 10.590319
|
||||
9750 16738.507 0 0 5269.53 10.590376
|
||||
9800 16738.482 0 0 5269.522 10.590314
|
||||
9850 16738.478 0 0 5269.5207 10.590303
|
||||
9900 16738.487 -0.00030979874 0 5269.5233 10.59032
|
||||
9950 16738.476 -0.00095967134 0 5269.5192 10.590278
|
||||
10000 16738.494 -0.00062714318 0 5269.5253 10.590329
|
||||
Loop time of 0.22441 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 385008.767 tau/day, 44561.200 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0032785 | 0.0039999 | 0.0052714 | 1.3 | 1.78
|
||||
Neigh | 0.010548 | 0.012524 | 0.016082 | 1.9 | 5.58
|
||||
Comm | 0.082771 | 0.087847 | 0.091037 | 1.1 | 39.15
|
||||
Output | 0.0042846 | 0.0045864 | 0.0054133 | 0.7 | 2.04
|
||||
Modify | 0.10401 | 0.10533 | 0.10736 | 0.4 | 46.94
|
||||
Other | | 0.01013 | | | 4.51
|
||||
|
||||
Nlocal: 20.25 ave 34 max 9 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 38.5 ave 43 max 26 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0.75 ave 2 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 3
|
||||
Ave neighs/atom = 0.037037
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
338
examples/rigid/log.20Apr18.rigid.poems.g++.1
Normal file
338
examples/rigid/log.20Apr18.rigid.poems.g++.1
Normal file
@ -0,0 +1,338 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384277
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184717
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.86699146
|
||||
1200 21815.003 45.317414 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064078
|
||||
1300 20780.781 217.36506 0 3680.8286 6.0538615
|
||||
1350 20558.971 254.36482 0 3680.8601 -3.6773954
|
||||
1400 21485.029 99.812918 0 3680.6511 -16.185473
|
||||
1450 21771.107 52.159607 0 3680.6775 -2.4756675
|
||||
1500 21520.948 93.503927 0 3680.3286 2.1023577
|
||||
1550 21351.418 121.68138 0 3680.2511 5.515995
|
||||
1600 20778.805 216.92177 0 3680.0559 15.089187
|
||||
1650 21477.638 100.21836 0 3679.8247 -1.1045739
|
||||
1700 18501.339 596.47922 0 3680.0357 -15.679682
|
||||
1750 18563.642 587.3479 0 3681.2882 33.532211
|
||||
1800 19110.186 494.82336 0 3679.8543 18.024046
|
||||
1850 21364.191 119.23543 0 3679.9339 2.5291075
|
||||
1900 20146.627 322.14849 0 3679.9197 5.7313175
|
||||
1950 20692.671 231.25345 0 3680.0319 4.297772
|
||||
2000 20943.905 189.11218 0 3679.7629 -22.64509
|
||||
2050 19668.055 401.83025 0 3679.8394 3.6251438
|
||||
2100 20280.434 299.76289 0 3679.8353 7.4807805
|
||||
2150 19181.835 483.52621 0 3680.4987 22.62081
|
||||
2200 21300.18 130.7021 0 3680.7322 4.710193
|
||||
2250 20486.914 266.64414 0 3681.1299 -8.6458025
|
||||
2300 18653.082 572.25481 0 3681.1017 -5.2636982
|
||||
2350 21513.563 95.608298 0 3681.2021 -9.3624751
|
||||
2400 21466.205 103.57569 0 3681.2765 -29.559707
|
||||
2450 20100.204 332.25468 0 3682.2886 35.739592
|
||||
2500 20764.513 221.64794 0 3682.4001 -12.46688
|
||||
2550 20436.771 276.13128 0 3682.2598 -22.419404
|
||||
2600 21466.252 104.57185 0 3682.2806 -10.080362
|
||||
2650 20817.269 212.81674 0 3682.3615 5.1374497
|
||||
2700 18565.157 588.46125 0 3682.6541 22.283866
|
||||
2750 20780.743 218.76366 0 3682.2208 -8.0046411
|
||||
2800 21032.22 176.82368 0 3682.1936 -7.078895
|
||||
2850 16817.729 879.49153 0 3682.4464 33.140849
|
||||
2900 19309.511 463.89319 0 3682.145 7.9225025
|
||||
2950 20544.978 257.86831 0 3682.0314 2.0523059
|
||||
3000 20616.438 246.0975 0 3682.1706 -0.2824889
|
||||
3050 18648.596 574.37266 0 3682.4721 -5.8677065
|
||||
3100 19147.135 490.76826 0 3681.9574 -1.9922835
|
||||
3150 18568.022 587.36965 0 3682.0399 14.694505
|
||||
3200 19720.841 395.38315 0 3682.1899 5.9162402
|
||||
3250 19008.557 514.50687 0 3682.5998 -3.4702895
|
||||
3300 21708.937 64.231264 0 3682.3874 -5.4808611
|
||||
3350 20548.477 257.62974 0 3682.3759 9.7818301
|
||||
3400 20508.84 264.0153 0 3682.1553 -12.578182
|
||||
3450 18736.579 559.11222 0 3681.8754 21.920437
|
||||
3500 21444.82 107.82706 0 3681.9638 0.093050651
|
||||
3550 20439.241 275.31015 0 3681.8503 -3.0785302
|
||||
3600 21547.1 90.778361 0 3681.9617 -5.9189729
|
||||
3650 15623.305 1079.996 0 3683.8802 36.064752
|
||||
3700 19912.452 363.09483 0 3681.8368 5.4802367
|
||||
3750 21289.7 133.2258 0 3681.5091 -10.884642
|
||||
3800 20214.875 312.09245 0 3681.2382 8.6419893
|
||||
3850 19853.031 372.13835 0 3680.9769 2.6229234
|
||||
3900 17863.409 703.8716 0 3681.1064 -1.4250404
|
||||
3950 19926.351 359.87227 0 3680.9307 -14.60997
|
||||
4000 17595.665 747.85423 0 3680.4651 24.228859
|
||||
4050 18408.194 611.80934 0 3679.8416 4.4236034
|
||||
4100 17506.503 762.1286 0 3679.8792 5.0526379
|
||||
4150 18479.134 600.76034 0 3680.6159 -6.6523095
|
||||
4200 18475.322 601.95797 0 3681.1783 1.3292995
|
||||
4250 18301.378 630.34119 0 3680.5709 2.5387332
|
||||
4300 19384.541 449.98455 0 3680.7414 5.8750989
|
||||
4350 18717.888 561.31715 0 3680.9651 3.7948584
|
||||
4400 18893.773 532.20993 0 3681.172 10.963539
|
||||
4450 20269.613 302.15984 0 3680.4286 -10.145642
|
||||
4500 19151.762 489.32407 0 3681.2845 21.695364
|
||||
4550 19914.708 361.54065 0 3680.6587 -4.2298372
|
||||
4600 21153.44 154.99598 0 3680.5693 2.3172078
|
||||
4650 21021.611 176.81454 0 3680.4164 1.9128023
|
||||
4700 21707.966 62.767734 0 3680.762 -5.2080189
|
||||
4750 16517.674 927.53839 0 3680.484 17.329608
|
||||
4800 21654.604 71.574174 0 3680.6749 -6.0650166
|
||||
4850 18135.978 657.28622 0 3679.9493 5.4803307
|
||||
4900 20389.048 282.49215 0 3680.6668 -2.8570431
|
||||
4950 17159.074 820.81472 0 3680.6604 31.273877
|
||||
5000 20788.159 215.88415 0 3680.5773 4.6345196
|
||||
5050 21366.767 119.68693 0 3680.8148 -9.9482889
|
||||
5100 20668.21 236.17655 0 3680.8782 3.8118334
|
||||
5150 20468.573 269.83696 0 3681.2657 -26.625943
|
||||
5200 19493.142 432.49135 0 3681.3483 -7.6677112
|
||||
5250 19626.594 410.09767 0 3681.1967 7.3622341
|
||||
5300 20771.914 219.12484 0 3681.1105 -7.0871793
|
||||
5350 21152.459 155.26401 0 3680.6738 5.9030557
|
||||
5400 21376.189 117.91075 0 3680.6088 -1.2004513
|
||||
5450 21455.06 105.15166 0 3680.995 -9.1675471
|
||||
5500 21227.896 143.35739 0 3681.3401 -6.646305
|
||||
5550 21149.831 156.61404 0 3681.5858 -12.953136
|
||||
5600 21364.198 120.94695 0 3681.6466 1.0372254
|
||||
5650 20219.777 311.34588 0 3681.3088 6.5026316
|
||||
5700 21163.024 154.3001 0 3681.4708 -0.47587262
|
||||
5750 19583.077 418.40745 0 3682.2535 24.609517
|
||||
5800 18801.324 548.79742 0 3682.3515 -12.082631
|
||||
5850 20875.4 203.07604 0 3682.3093 -8.1191161
|
||||
5900 20737.053 226.2734 0 3682.4489 -7.6845943
|
||||
5950 21260.028 139.21888 0 3682.5568 -2.2977046
|
||||
6000 19823.84 378.71803 0 3682.6914 -1.1163373
|
||||
6050 20487.214 268.03474 0 3682.5704 4.313979
|
||||
6100 17853.211 707.10918 0 3682.6443 16.762322
|
||||
6150 21322.705 129.06 0 3682.8441 2.7500936
|
||||
6200 21609.008 81.580972 0 3683.0823 0.37062555
|
||||
6250 20364.115 289.30707 0 3683.3262 13.176034
|
||||
6300 20201.9 316.16558 0 3683.149 -1.6318339
|
||||
6350 21151.879 157.75018 0 3683.0634 -23.337621
|
||||
6400 21453.129 107.45563 0 3682.9772 -0.60776225
|
||||
6450 21105.382 165.1926 0 3682.7562 4.244932
|
||||
6500 20746.748 224.6945 0 3682.4859 0.2929158
|
||||
6550 20913.725 197.29847 0 3682.9194 -15.792862
|
||||
6600 17956.374 690.52623 0 3683.2552 15.445255
|
||||
6650 20270.609 303.60078 0 3682.0357 -0.26503277
|
||||
6700 21442.931 109.08904 0 3682.9109 -2.8409166
|
||||
6750 20907.994 198.30695 0 3682.9726 0.91664072
|
||||
6800 20431.208 277.98326 0 3683.1845 -1.8537161
|
||||
6850 20312.052 297.88656 0 3683.2285 3.1028547
|
||||
6900 19458.401 439.97157 0 3683.0385 -4.1856293
|
||||
6950 20507.759 264.99217 0 3682.952 -1.4597973
|
||||
7000 20782.356 219.47456 0 3683.2006 -7.1967021
|
||||
7050 20560.324 256.07109 0 3682.7917 -10.720013
|
||||
7100 21652.145 74.086415 0 3682.7772 -0.61455054
|
||||
7150 20134.823 326.40272 0 3682.2065 11.689827
|
||||
7200 20778.071 219.16459 0 3682.1765 -1.796567
|
||||
7250 20153.065 323.13721 0 3681.9814 -0.1215538
|
||||
7300 19524.938 427.99711 0 3682.1534 -3.1139903
|
||||
7350 20554.595 256.63855 0 3682.4044 10.023083
|
||||
7400 18778.53 552.29852 0 3682.0534 -1.7145222
|
||||
7450 18972.509 520.15393 0 3682.2388 1.4489874
|
||||
7500 17680.668 736.20139 0 3682.9794 15.096954
|
||||
7550 19070.785 504.65403 0 3683.1182 2.2707533
|
||||
7600 20805.541 214.54957 0 3682.1398 -3.4306308
|
||||
7650 18473.262 604.25322 0 3683.1301 2.2083367
|
||||
7700 19294.016 466.99211 0 3682.6615 2.2666382
|
||||
7750 20995.664 183.47108 0 3682.7484 -13.935938
|
||||
7800 21042.433 175.06619 0 3682.1384 0.49855811
|
||||
7850 19343.054 459.21955 0 3683.0618 7.9049312
|
||||
7900 18382.898 619.01969 0 3682.8361 1.7996366
|
||||
7950 16092.435 1000.6563 0 3682.7287 29.993154
|
||||
8000 17551.635 757.47719 0 3682.7498 8.1753011
|
||||
8050 20309.875 298.25877 0 3683.2379 -1.9545317
|
||||
8100 21746.174 59.002125 0 3683.3645 -2.6980678
|
||||
8150 21478.427 103.44202 0 3683.1799 -10.930392
|
||||
8200 20986.729 185.46995 0 3683.2581 -14.298403
|
||||
8250 20744.064 225.47546 0 3682.8194 -6.4982356
|
||||
8300 19887.982 368.35069 0 3683.0143 1.5899179
|
||||
8350 21871.414 37.899202 0 3683.1348 -2.0554107
|
||||
8400 20002.858 348.98887 0 3682.7985 8.2963084
|
||||
8450 21553.861 90.985193 0 3683.2953 2.8575186
|
||||
8500 21605.143 82.347635 0 3683.2048 -4.711565
|
||||
8550 20151.76 324.4703 0 3683.097 -8.5109459
|
||||
8600 20564.158 255.77814 0 3683.1378 -1.3815408
|
||||
8650 19316.602 463.61706 0 3683.0507 -2.6895635
|
||||
8700 18157.859 656.69518 0 3683.0051 19.428927
|
||||
8750 18752.43 557.67555 0 3683.0805 1.9765973
|
||||
8800 20903.812 199.07408 0 3683.0428 1.9011523
|
||||
8850 20132.963 327.56826 0 3683.0621 3.0389961
|
||||
8900 21667.171 71.80023 0 3682.9954 -2.0042246
|
||||
8950 20346.973 292.00907 0 3683.1712 7.5582361
|
||||
9000 17889.448 695.59406 0 3677.1688 7.5315391
|
||||
9050 19446.144 441.90609 0 3682.9302 5.9819228
|
||||
9100 20384.34 285.05862 0 3682.4486 9.8610378
|
||||
9150 20023.515 344.98587 0 3682.2384 -0.40175043
|
||||
9200 17786.795 718.76166 0 3683.2275 10.984317
|
||||
9250 20843.023 208.42263 0 3682.2597 -7.4709344
|
||||
9300 21670.622 70.503925 0 3682.2742 -6.2303366
|
||||
9350 20642.313 241.21277 0 3681.5983 4.7423898
|
||||
9400 19228.566 476.44753 0 3681.2085 10.836639
|
||||
9450 21215.705 146.40003 0 3682.3509 -9.091421
|
||||
9500 21543.685 91.725901 0 3682.3401 -1.0608492
|
||||
9550 20143.22 324.98532 0 3682.1887 -5.995164
|
||||
9600 21234.294 142.96512 0 3682.0142 0.004838125
|
||||
9650 21025.207 177.8801 0 3682.0813 -5.4857701
|
||||
9700 20638.235 242.46577 0 3682.1716 -1.6014085
|
||||
9750 18374.191 620.54322 0 3682.9084 13.864712
|
||||
9800 19730.262 393.89083 0 3682.2679 5.7601754
|
||||
9850 21547.855 91.283379 0 3682.5926 2.1989329
|
||||
9900 20959.935 189.28821 0 3682.6108 2.1174676
|
||||
9950 21191.026 150.79441 0 3682.6321 8.3829825
|
||||
10000 20776.574 220.03769 0 3682.8 -1.8404787
|
||||
Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 28004.636 tau/day, 3241.277 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62
|
||||
Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55
|
||||
Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33
|
||||
Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10
|
||||
Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05
|
||||
Other | | 0.01105 | | | 0.36
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 82 ave 82 max 82 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 887 ave 887 max 887 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 887
|
||||
Ave neighs/atom = 10.9506
|
||||
Neighbor list builds = 992
|
||||
Dangerous builds = 939
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
338
examples/rigid/log.20Apr18.rigid.poems.g++.4
Normal file
338
examples/rigid/log.20Apr18.rigid.poems.g++.4
Normal file
@ -0,0 +1,338 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384277
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184717
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.86699147
|
||||
1200 21815.003 45.317414 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064078
|
||||
1300 20780.781 217.36506 0 3680.8286 6.0538614
|
||||
1350 20558.971 254.36483 0 3680.8601 -3.6773951
|
||||
1400 21485.029 99.812917 0 3680.6511 -16.185473
|
||||
1450 21771.107 52.15961 0 3680.6775 -2.4756673
|
||||
1500 21520.948 93.503926 0 3680.3286 2.1023576
|
||||
1550 21351.418 121.68137 0 3680.2511 5.5159947
|
||||
1600 20778.805 216.92177 0 3680.0559 15.089188
|
||||
1650 21477.638 100.21836 0 3679.8247 -1.1045741
|
||||
1700 18501.339 596.4792 0 3680.0357 -15.679682
|
||||
1750 18563.642 587.34785 0 3681.2882 33.53221
|
||||
1800 19110.185 494.82342 0 3679.8543 18.024046
|
||||
1850 21364.191 119.23548 0 3679.9339 2.5291079
|
||||
1900 20146.626 322.14873 0 3679.9197 5.7313282
|
||||
1950 20692.672 231.2533 0 3680.0319 4.2977759
|
||||
2000 20943.904 189.11231 0 3679.7629 -22.645089
|
||||
2050 19668.052 401.83077 0 3679.8394 3.6251598
|
||||
2100 20280.434 299.76292 0 3679.8353 7.4807838
|
||||
2150 19181.841 483.52513 0 3680.4987 22.620829
|
||||
2200 21300.185 130.70136 0 3680.7321 4.7101928
|
||||
2250 20486.897 266.64698 0 3681.1299 -8.6459184
|
||||
2300 18653.018 572.26538 0 3681.1017 -5.2635489
|
||||
2350 21513.576 95.606125 0 3681.202 -9.3627078
|
||||
2400 21466.185 103.579 0 3681.2764 -29.55912
|
||||
2450 20100.274 332.24291 0 3682.2886 35.736349
|
||||
2500 20764.562 221.63964 0 3682.4 -12.465656
|
||||
2550 20437.187 276.06174 0 3682.2596 -22.421308
|
||||
2600 21466.269 104.56898 0 3682.2805 -10.080867
|
||||
2650 20819.865 212.38395 0 3682.3615 5.1305357
|
||||
2700 18565.57 588.39438 0 3682.656 22.28768
|
||||
2750 20789.153 217.36229 0 3682.2211 -8.051962
|
||||
2800 21045.639 174.58656 0 3682.193 -7.0803377
|
||||
2850 16845.227 874.90505 0 3682.4429 32.992098
|
||||
2900 19319.232 462.27119 0 3682.1432 7.9276373
|
||||
2950 20558.495 255.61185 0 3682.0277 1.9151653
|
||||
3000 20615.868 246.18886 0 3682.1668 -0.016805532
|
||||
3050 18695.136 566.5914 0 3682.4474 -7.3528355
|
||||
3100 19381.554 451.57712 0 3681.8361 -2.0887636
|
||||
3150 19080.633 502.00742 0 3682.1129 5.2518182
|
||||
3200 20969.083 187.13559 0 3681.9828 12.156446
|
||||
3250 20474.81 269.6876 0 3682.156 1.4067779
|
||||
3300 18836.313 542.79266 0 3682.1781 -9.1497216
|
||||
3350 21397.694 116.27473 0 3682.557 -6.4412585
|
||||
3400 20886.812 201.52507 0 3682.6604 6.3038335
|
||||
3450 21604.639 81.93055 0 3682.7038 2.3769444
|
||||
3500 20847.621 207.85705 0 3682.4605 -2.758021
|
||||
3550 20627.979 244.69999 0 3682.6964 -0.33497747
|
||||
3600 19265.519 471.27582 0 3682.1956 2.3506222
|
||||
3650 20351.848 290.65727 0 3682.6319 3.5445062
|
||||
3700 18507.473 597.72931 0 3682.3082 -21.283074
|
||||
3750 20344.017 291.60622 0 3682.2757 6.5366987
|
||||
3800 20672.372 237.18966 0 3682.585 6.7310703
|
||||
3850 21366.943 122.07461 0 3683.2318 -3.5870721
|
||||
3900 20890.294 201.69901 0 3683.4147 -9.5644117
|
||||
3950 20684.181 235.91733 0 3683.2809 -4.8913079
|
||||
4000 21499.086 100.67563 0 3683.8566 1.1969651
|
||||
4050 18549.152 590.04529 0 3681.5707 -9.1914883
|
||||
4100 18436.457 604.2601 0 3677.003 3.6486137
|
||||
4150 19332.655 462.03124 0 3684.1404 -11.280758
|
||||
4200 21199.837 150.66602 0 3683.9722 0.14505208
|
||||
4250 19088.228 501.77395 0 3683.1453 1.6869973
|
||||
4300 16617.942 913.86736 0 3683.5244 9.1792322
|
||||
4350 19765.761 388.52744 0 3682.821 -4.1982973
|
||||
4400 20181.964 320.06096 0 3683.7216 5.3685715
|
||||
4450 20132.04 328.29106 0 3683.631 6.3340995
|
||||
4500 21026.359 179.13858 0 3683.5317 -15.365253
|
||||
4550 19273.765 471.36221 0 3683.6564 -0.71397595
|
||||
4600 20064.71 339.29348 0 3683.4117 -4.8121056
|
||||
4650 19821.01 380.27685 0 3683.7784 11.857115
|
||||
4700 18724.367 563.42963 0 3684.1575 13.250333
|
||||
4750 20467.467 273.2046 0 3684.449 -1.8076823
|
||||
4800 19630.315 412.48507 0 3684.2042 -9.0412254
|
||||
4850 19483.424 437.0206 0 3684.258 11.22465
|
||||
4900 18504.179 600.28485 0 3684.3146 -5.2345686
|
||||
4950 21436.13 111.62139 0 3684.3098 -5.8197915
|
||||
5000 18022.817 680.57727 0 3684.38 19.238942
|
||||
5050 20750.212 226.15635 0 3684.525 -0.73974419
|
||||
5100 20569.533 255.21358 0 3683.4691 -18.332775
|
||||
5150 21447.046 109.3048 0 3683.8124 -2.5745966
|
||||
5200 18985.753 519.77191 0 3684.0641 9.7821968
|
||||
5250 21334.568 128.16597 0 3683.9273 -0.61310451
|
||||
5300 18836.476 544.54018 0 3683.9528 -17.979429
|
||||
5350 18574.391 587.20088 0 3682.9327 40.990206
|
||||
5400 21003.047 183.40176 0 3683.9096 6.1115776
|
||||
5450 20693.875 234.62783 0 3683.607 5.4472209
|
||||
5500 17673.479 738.99306 0 3684.5729 -28.621738
|
||||
5550 19265.837 472.34663 0 3683.3195 -6.609151
|
||||
5600 20800.947 217.12409 0 3683.9486 2.6477049
|
||||
5650 21746.371 59.453265 0 3683.8485 1.5272163
|
||||
5700 20448.97 275.57425 0 3683.736 -7.9864104
|
||||
5750 19776.152 387.64417 0 3683.6695 -16.604848
|
||||
5800 15779.293 1055.4995 0 3685.3817 20.365883
|
||||
5850 21008.009 182.52093 0 3683.8557 -6.6727217
|
||||
5900 21566.123 89.588216 0 3683.9421 -7.8944316
|
||||
5950 21591.695 85.284975 0 3683.9009 -2.4895203
|
||||
6000 17737.17 726.79112 0 3682.9861 1.5643841
|
||||
6050 16648.524 907.73295 0 3682.487 3.0853478
|
||||
6100 19917.439 363.6324 0 3683.2056 4.358303
|
||||
6150 21767.004 56.152017 0 3683.986 -8.8722559
|
||||
6200 17654.098 742.15421 0 3684.5039 9.7673482
|
||||
6250 20125.754 329.65218 0 3683.9445 5.5050658
|
||||
6300 20160.047 323.44453 0 3683.4524 4.852504
|
||||
6350 20509.459 264.29515 0 3682.5383 2.5335834
|
||||
6400 17199.686 817.09171 0 3683.7061 8.3428304
|
||||
6450 18748.366 558.82243 0 3683.5501 0.23782614
|
||||
6500 19133.519 494.28383 0 3683.2037 8.1586096
|
||||
6550 20311.228 297.30741 0 3682.5122 -1.7015056
|
||||
6600 18879.49 536.62652 0 3683.2082 5.0874769
|
||||
6650 18189.35 651.42447 0 3682.9828 -15.223564
|
||||
6700 19925.861 361.90598 0 3682.8828 0.26811015
|
||||
6750 19420.312 445.30915 0 3682.0278 5.5725626
|
||||
6800 19925.024 361.87412 0 3682.7114 -3.9763013
|
||||
6850 16196.938 985.7242 0 3685.2138 2.8265047
|
||||
6900 19779.752 386.51634 0 3683.1416 16.798629
|
||||
6950 21043.144 176.83133 0 3684.0221 -4.193188
|
||||
7000 18555.362 589.47043 0 3682.0307 14.516315
|
||||
7050 21225.883 147.54974 0 3685.1969 -13.466586
|
||||
7100 21234.667 145.92615 0 3685.0373 -5.1951121
|
||||
7150 21483.472 104.62556 0 3685.2042 -5.6904048
|
||||
7200 21014.278 182.97687 0 3685.3566 1.044649
|
||||
7250 18588.789 587.96259 0 3686.094 22.707132
|
||||
7300 20202.932 318.14401 0 3685.2994 -10.795766
|
||||
7350 18304.22 634.7344 0 3685.4377 -1.6801482
|
||||
7400 20967.579 190.67822 0 3685.2747 -0.94800692
|
||||
7450 20991.588 186.07163 0 3684.6696 -1.411476
|
||||
7500 19056.583 507.18197 0 3683.2791 3.2026014
|
||||
7550 18542.455 594.92944 0 3685.3386 -27.908724
|
||||
7600 19895.73 367.08589 0 3683.0409 4.1334366
|
||||
7650 20384.942 285.88041 0 3683.3707 -7.515362
|
||||
7700 20683.189 235.46294 0 3682.6611 10.876437
|
||||
7750 20729.325 228.204 0 3683.0915 3.8844308
|
||||
7800 21667.475 71.752748 0 3682.9985 -15.457992
|
||||
7850 19043.652 508.96807 0 3682.9101 -5.8335792
|
||||
7900 21079.827 169.61123 0 3682.9158 -1.3216223
|
||||
7950 20713.266 230.43917 0 3682.6502 -0.20026535
|
||||
8000 20606.41 248.06357 0 3682.4652 4.2844844
|
||||
8050 20284.503 302.0469 0 3682.7973 6.3402329
|
||||
8100 21859.537 39.514865 0 3682.7711 -13.302141
|
||||
8150 18495.181 600.26329 0 3682.7934 9.9318242
|
||||
8200 21458.549 105.63828 0 3682.0631 -7.7419285
|
||||
8250 18704.511 564.30958 0 3681.728 14.680489
|
||||
8300 20689.366 233.57049 0 3681.7982 2.3067527
|
||||
8350 20692.974 232.67005 0 3681.499 4.2743386
|
||||
8400 20240.086 307.5395 0 3680.8872 1.9694217
|
||||
8450 19075.969 501.34689 0 3680.6751 11.056078
|
||||
8500 21456.727 103.36067 0 3679.4818 -3.4512371
|
||||
8550 20393.16 279.84781 0 3678.7078 6.3282998
|
||||
8600 20898.88 195.43751 0 3678.5842 -14.393947
|
||||
8650 20297.482 295.3169 0 3678.2306 -0.96829147
|
||||
8700 21079.56 164.72934 0 3677.9893 -8.339122
|
||||
8750 21142.519 154.18527 0 3677.9384 -4.6169442
|
||||
8800 20143.871 320.23161 0 3677.5435 6.5710426
|
||||
8850 21030.065 172.88831 0 3677.8992 1.3973883
|
||||
8900 19814.648 375.22097 0 3677.6624 2.6996208
|
||||
8950 17392.382 778.87517 0 3677.6055 11.963975
|
||||
9000 19209.163 476.44659 0 3677.9738 8.7050034
|
||||
9050 20143.824 320.17051 0 3677.4745 -5.8044332
|
||||
9100 21400.78 110.99404 0 3677.7908 -3.0027429
|
||||
9150 21834.471 38.970732 0 3678.0493 -2.5838117
|
||||
9200 21344.715 120.55831 0 3678.0108 4.8187829
|
||||
9250 20998.277 178.31959 0 3678.0324 -1.2009012
|
||||
9300 21141.788 154.4658 0 3678.0971 -21.693564
|
||||
9350 21439.398 105.00432 0 3678.2374 -16.113694
|
||||
9400 21296.282 128.83877 0 3678.2191 -2.9990284
|
||||
9450 19050.623 503.10319 0 3678.207 15.622525
|
||||
9500 20845.847 203.77117 0 3678.079 -1.7504827
|
||||
9550 18808.956 543.38757 0 3678.2135 -2.6611868
|
||||
9600 20612.559 242.57373 0 3678.0002 -0.1650541
|
||||
9650 20522.637 257.28926 0 3677.7288 6.8876074
|
||||
9700 20970.074 182.75754 0 3677.7699 -4.5350279
|
||||
9750 18297.505 625.06808 0 3674.6522 32.429153
|
||||
9800 21042.472 170.78969 0 3677.8684 5.4901963
|
||||
9850 20444.092 270.84839 0 3678.197 6.9444494
|
||||
9900 21597.787 78.901871 0 3678.533 2.3445932
|
||||
9950 18376.854 616.35469 0 3679.1636 -8.55063
|
||||
10000 21490.054 97.234379 0 3678.9101 -0.36115606
|
||||
Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 25554.943 tau/day, 2957.748 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29
|
||||
Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86
|
||||
Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44
|
||||
Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21
|
||||
Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24
|
||||
Other | | 0.03255 | | | 0.96
|
||||
|
||||
Nlocal: 20.25 ave 81 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 45.5 ave 82 max 12 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 218.75 ave 875 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 875
|
||||
Ave neighs/atom = 10.8025
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 945
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
342
examples/rigid/log.20Apr18.rigid.poems2.g++.1
Normal file
342
examples/rigid/log.20Apr18.rigid.poems2.g++.1
Normal file
@ -0,0 +1,342 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:363)
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:363)
|
||||
WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12167.633 1505.5478 0 3758.8133 35.125973
|
||||
100 17556.978 512.66277 0 3763.9549 11.137534
|
||||
150 19579.586 138.04942 0 3763.8987 -29.953971
|
||||
200 19757.51 105.30542 0 3764.1036 -0.030645317
|
||||
250 18218.374 390.10747 0 3763.8804 13.711001
|
||||
300 19383.039 174.40688 0 3763.8586 5.7240693
|
||||
350 20125.986 36.972611 0 3764.0071 1.9559205
|
||||
400 18888.816 266.10975 0 3764.0386 9.6362168
|
||||
450 19307.656 188.2511 0 3763.743 1.9326206
|
||||
500 16331.197 738.56392 0 3762.8597 9.1715579
|
||||
550 19318.722 186.16172 0 3763.7027 3.0115336
|
||||
600 19455.268 161.20621 0 3764.0336 0.55208034
|
||||
650 18487.011 340.03216 0 3763.5528 -8.0359122
|
||||
700 17321.201 556.32471 0 3763.9545 -13.631751
|
||||
750 18979.187 249.04389 0 3763.7082 -2.6072455
|
||||
800 19342.456 181.85552 0 3763.7918 8.1918726
|
||||
850 19070.641 232.19342 0 3763.7936 7.3148472
|
||||
900 19478.873 156.65987 0 3763.8586 2.4284987
|
||||
950 19912.415 76.437437 0 3763.9216 -1.4667227
|
||||
1000 16003.749 802.39753 0 3766.0548 46.642188
|
||||
1050 19859.583 86.64176 0 3764.3424 -2.1961943
|
||||
1100 19229.575 203.61488 0 3764.6473 -10.632365
|
||||
1150 18821.6 279.15861 0 3764.64 -0.89495035
|
||||
1200 19392.695 173.59744 0 3764.8373 1.8508753
|
||||
1250 16459.624 717.32104 0 3765.3995 33.478127
|
||||
1300 19343.863 182.59043 0 3764.7874 0.75890736
|
||||
1350 20019.643 57.503573 0 3764.8448 0.31444671
|
||||
1400 18549.582 329.31436 0 3764.4221 10.738303
|
||||
1450 15163.926 957.47585 0 3765.6103 -17.92346
|
||||
1500 19223.688 204.15177 0 3764.0939 -1.6134528
|
||||
1550 18147.996 404.12677 0 3764.8668 8.4194783
|
||||
1600 18615.043 317.42469 0 3764.6548 -2.3288917
|
||||
1650 20120.654 38.887903 0 3764.935 -8.7620301
|
||||
1700 19450.907 162.98262 0 3765.0025 2.3254748
|
||||
1750 19374.631 177.37975 0 3765.2744 8.9328771
|
||||
1800 19424.404 167.93963 0 3765.0514 0.081227378
|
||||
1850 17936.203 442.85082 0 3764.3699 6.6011902
|
||||
1900 19982.595 64.406292 0 3764.8868 -2.95296
|
||||
1950 16215.781 761.92636 0 3764.8487 13.995056
|
||||
2000 18584.444 322.1163 0 3763.6801 7.1653369
|
||||
2050 20107.965 41.025841 0 3764.723 -0.31088772
|
||||
2100 20002.324 60.594786 0 3764.7288 -6.7919989
|
||||
2150 16949.875 626.57523 0 3765.4409 3.50855
|
||||
2200 20010.954 58.808121 0 3764.5403 -10.862112
|
||||
2250 18982.734 247.00818 0 3762.3293 -0.53817452
|
||||
2300 18401.254 354.88774 0 3762.5274 1.0921595
|
||||
2350 19390.545 172.93755 0 3763.7793 -3.3523777
|
||||
2400 16080.137 786.51156 0 3764.3147 -16.202632
|
||||
2450 18870.17 268.79443 0 3763.2704 11.201845
|
||||
2500 19688.736 117.49945 0 3763.5616 4.3786781
|
||||
2550 18869.811 268.97474 0 3763.3842 -5.6659314
|
||||
2600 17021.088 611.38597 0 3763.4393 6.3051835
|
||||
2650 18743.998 292.7827 0 3763.8934 2.4233167
|
||||
2700 19745.629 106.63088 0 3763.2289 -0.34816161
|
||||
2750 19527.584 147.21131 0 3763.4306 -1.6219417
|
||||
2800 18195.354 392.99533 0 3762.5053 24.376674
|
||||
2850 18550.094 327.77867 0 3762.9812 4.2654596
|
||||
2900 20174.105 27.269108 0 3763.2144 1.7109311
|
||||
2950 17744.679 476.70478 0 3762.7564 0.46336417
|
||||
3000 19161.715 214.56545 0 3763.0311 2.3774967
|
||||
3050 18357.87 363.54089 0 3763.1465 7.5885138
|
||||
3100 18851.02 272.19735 0 3763.1269 8.0560784
|
||||
3150 19586.208 136.32381 0 3763.3995 -10.118566
|
||||
3200 19300.444 189.2076 0 3763.3639 -12.590066
|
||||
3250 18680.955 303.88073 0 3763.3168 -1.0138975
|
||||
3300 18444.612 347.49752 0 3763.1664 8.9271155
|
||||
3350 19006.554 243.54359 0 3763.2757 4.7398999
|
||||
3400 17842.797 459.11352 0 3763.3351 28.63048
|
||||
3450 19801.317 96.103613 0 3763.0141 4.0933253
|
||||
3500 18599.338 318.61343 0 3762.9353 6.3657111
|
||||
3550 19737.266 107.84071 0 3762.89 1.3861757
|
||||
3600 19002.648 244.0525 0 3763.0613 8.7615304
|
||||
3650 19154.418 215.94396 0 3763.0584 -2.6243193
|
||||
3700 19036.117 237.84014 0 3763.047 -5.6841944
|
||||
3750 20045.863 50.759281 0 3762.9562 -2.1930939
|
||||
3800 19331.877 182.69303 0 3762.6703 0.57474959
|
||||
3850 18193.947 393.70074 0 3762.9502 -4.1144639
|
||||
3900 19675.638 119.2295 0 3762.8663 0.46172332
|
||||
3950 19506.743 150.36614 0 3762.7259 5.8020668
|
||||
4000 17985.008 431.80897 0 3762.366 10.755615
|
||||
4050 19947.208 68.962683 0 3762.8902 -2.0041629
|
||||
4100 19936.06 70.997196 0 3762.8602 -6.6295574
|
||||
4150 19011.006 242.10402 0 3762.6608 -12.682711
|
||||
4200 18108.183 409.44214 0 3762.8094 -0.42654932
|
||||
4250 18734.162 293.70086 0 3762.9901 8.8549986
|
||||
4300 16619.218 686.30953 0 3763.9426 43.405681
|
||||
4350 18818.184 277.95188 0 3762.8007 20.953883
|
||||
4400 18649.616 307.93211 0 3761.5647 -3.6011031
|
||||
4450 18626.995 313.23564 0 3762.6792 -2.5430627
|
||||
4500 18133.284 405.27778 0 3763.2934 3.057056
|
||||
4550 19985.929 61.792735 0 3762.8908 1.9540846
|
||||
4600 18664.305 306.02805 0 3762.3809 1.2395242
|
||||
4650 19822.408 92.030223 0 3762.8466 -1.0496216
|
||||
4700 19218.014 203.93895 0 3762.8305 0.74203538
|
||||
4750 19425.781 165.36374 0 3762.7306 4.0113982
|
||||
4800 18604.891 317.55244 0 3762.9026 16.671366
|
||||
4850 19648.156 124.29963 0 3762.8471 4.1073
|
||||
4900 18928.508 257.76023 0 3763.0394 -4.3547566
|
||||
4950 19795.841 97.135231 0 3763.0317 -10.401888
|
||||
5000 20150.671 31.452661 0 3763.0584 -3.352706
|
||||
5050 18694.789 300.8954 0 3762.8933 11.690808
|
||||
5100 16936.745 627.00902 0 3763.4434 -0.56880353
|
||||
5150 18446.99 346.49004 0 3762.5992 8.409244
|
||||
5200 18532.691 330.61677 0 3762.5966 10.358529
|
||||
5250 18342.743 366.3264 0 3763.1306 -9.5622676
|
||||
5300 20038.203 52.234825 0 3763.0131 -3.6974868
|
||||
5350 19337.092 182.06755 0 3763.0106 -0.045248915
|
||||
5400 19561.005 140.5518 0 3762.9602 1.3850963
|
||||
5450 19415.557 167.29181 0 3762.7654 2.6966013
|
||||
5500 18646.823 309.81657 0 3762.9319 7.4858844
|
||||
5550 19165.312 214.07271 0 3763.2046 1.4335924
|
||||
5600 18879.507 266.90953 0 3763.1146 7.8746695
|
||||
5650 19824.482 91.786842 0 3762.9872 -2.4395467
|
||||
5700 19699.85 114.8239 0 3762.9442 4.2779932
|
||||
5750 19535.697 145.24886 0 3762.9706 5.9452722
|
||||
5800 18275.446 378.66191 0 3763.0038 11.965062
|
||||
5850 19931.992 71.873259 0 3762.9828 -2.3097575
|
||||
5900 18528.705 331.64793 0 3762.8897 -18.312104
|
||||
5950 16535.446 701.02536 0 3763.1451 -14.797902
|
||||
6000 18678.807 303.76763 0 3762.806 -3.2732626
|
||||
6050 16661.525 677.73561 0 3763.2031 17.862761
|
||||
6100 18100.317 410.39139 0 3762.3019 -4.9765779
|
||||
6150 16487.861 707.08907 0 3760.3967 32.53899
|
||||
6200 16823.279 647.56578 0 3762.9878 -9.8237219
|
||||
6250 18418.096 351.89624 0 3762.6548 -2.0149855
|
||||
6300 18822.067 277.01314 0 3762.5811 5.3782716
|
||||
6350 19300.198 188.57243 0 3762.6832 -1.9316023
|
||||
6400 18425.789 350.70367 0 3762.8868 2.6884393
|
||||
6450 18708.506 297.50643 0 3762.0447 -13.808707
|
||||
6500 19528.099 146.10805 0 3762.4226 -1.5991505
|
||||
6550 19701.841 114.01327 0 3762.5023 4.4322487
|
||||
6600 18892.934 262.83827 0 3761.5297 10.689265
|
||||
6650 19041.669 235.52692 0 3761.7619 -1.1425512
|
||||
6700 19352.162 178.40501 0 3762.1388 -0.55130997
|
||||
6750 16177.653 765.61942 0 3761.481 4.6526477
|
||||
6800 19007.323 242.63753 0 3762.5122 3.6202242
|
||||
6850 14255.206 1125.4974 0 3765.3503 -31.10433
|
||||
6900 18481.408 340.4703 0 3762.9532 0.53246054
|
||||
6950 19227.569 202.33363 0 3762.9946 -0.94126626
|
||||
7000 18771.85 286.70279 0 3762.9714 3.151759
|
||||
7050 18689.51 301.95602 0 3762.9765 8.0511724
|
||||
7100 18599.258 318.83229 0 3763.1394 -0.86222116
|
||||
7150 17739.189 478.35458 0 3763.3896 11.976827
|
||||
7200 19492.829 153.62536 0 3763.4084 -8.6815909
|
||||
7250 18797.718 282.17319 0 3763.232 -19.897633
|
||||
7300 18353.871 364.09362 0 3762.9585 5.4538454
|
||||
7350 19040.053 237.34144 0 3763.2772 6.5600248
|
||||
7400 19452.586 160.98629 0 3763.317 -9.0542585
|
||||
7450 19033.845 238.45033 0 3763.2365 3.2654681
|
||||
7500 18137.358 404.80969 0 3763.5796 -7.2639486
|
||||
7550 16863.391 642.47654 0 3765.3267 31.248679
|
||||
7600 16374.538 731.74039 0 3764.0622 29.566291
|
||||
7650 19837.917 89.823014 0 3763.5114 -2.6605403
|
||||
7700 15593.154 876.08807 0 3763.7093 -9.7668717
|
||||
7750 16609.929 687.32679 0 3763.2396 1.0775966
|
||||
7800 17513.384 519.87756 0 3763.0968 3.4979836
|
||||
7850 20022.015 56.036771 0 3763.8173 -4.316185
|
||||
7900 17681.324 489.71547 0 3764.0347 5.1978443
|
||||
7950 18320.382 371.17872 0 3763.8421 6.1860655
|
||||
8000 20014.059 57.688322 0 3763.9956 -9.0623854
|
||||
8050 16203.013 762.61545 0 3763.1735 31.662714
|
||||
8100 18749.745 291.57889 0 3763.7538 -14.015057
|
||||
8150 19411.326 169.05845 0 3763.7485 -4.3392799
|
||||
8200 17994.991 431.56932 0 3763.9751 6.8158642
|
||||
8250 19325.923 185.1137 0 3763.9883 9.4923883
|
||||
8300 17354.302 550.33316 0 3764.0927 6.1636399
|
||||
8350 19900.895 78.431831 0 3763.7828 -4.5224196
|
||||
8400 17775.757 471.62915 0 3763.4361 12.949899
|
||||
8450 19909.324 76.935162 0 3763.8471 -2.950115
|
||||
8500 18601.933 318.79405 0 3763.5965 6.0173542
|
||||
8550 18685.758 303.59497 0 3763.9205 2.7277487
|
||||
8600 19297.521 190.12606 0 3763.741 4.8998933
|
||||
8650 17396.37 542.14326 0 3763.6932 39.937715
|
||||
8700 17134.714 590.99465 0 3764.0898 10.37328
|
||||
8750 14348.104 1106.7544 0 3763.8106 -3.8604659
|
||||
8800 19830.924 90.929138 0 3763.3225 0.26603444
|
||||
8850 18551.537 326.53747 0 3762.0072 -1.5369982
|
||||
8900 20040.322 52.066026 0 3763.2367 -12.667979
|
||||
8950 19314.585 186.54793 0 3763.3228 -0.64755555
|
||||
9000 19117.66 222.84553 0 3763.153 5.2990011
|
||||
9050 19072.016 231.26038 0 3763.1152 -1.6513695
|
||||
9100 19284.933 191.73976 0 3763.0237 -3.932358
|
||||
9150 17356.576 548.61808 0 3762.7988 1.3659056
|
||||
9200 18939.549 255.43703 0 3762.761 3.3037106
|
||||
9250 19621.961 129.5012 0 3763.1976 1.667
|
||||
9300 16898.033 633.79921 0 3763.0647 7.5941845
|
||||
9350 19662.75 122.10836 0 3763.3584 -3.3144828
|
||||
9400 16118.338 778.70243 0 3763.5799 9.8684537
|
||||
9450 17362.374 548.18847 0 3763.443 6.8117548
|
||||
9500 17873.057 453.37389 0 3763.1993 9.5651746
|
||||
9550 19282.305 192.593 0 3763.3901 -4.987757
|
||||
9600 18236.48 386.36263 0 3763.4886 8.8658343
|
||||
9650 17695.571 486.6517 0 3763.6093 12.471421
|
||||
9700 19044.003 237.04652 0 3763.7138 0.84430497
|
||||
9750 17937.299 442.4372 0 3764.1592 3.981475
|
||||
9800 18179.761 396.86987 0 3763.4923 -11.397273
|
||||
9850 19157.292 215.8937 0 3763.5404 -7.7648682
|
||||
9900 19719.066 111.98124 0 3763.6602 5.5378968
|
||||
9950 18103.235 410.65473 0 3763.1056 28.201374
|
||||
10000 18479.903 341.32548 0 3763.5297 -5.0581298
|
||||
Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 27486.104 tau/day, 3181.262 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88
|
||||
Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46
|
||||
Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39
|
||||
Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10
|
||||
Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80
|
||||
Other | | 0.01151 | | | 0.37
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 67 ave 67 max 67 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 599 ave 599 max 599 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 599
|
||||
Ave neighs/atom = 7.39506
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 945
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
342
examples/rigid/log.20Apr18.rigid.poems2.g++.4
Normal file
342
examples/rigid/log.20Apr18.rigid.poems2.g++.4
Normal file
@ -0,0 +1,342 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:363)
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:363)
|
||||
WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12167.633 1505.5478 0 3758.8133 35.125973
|
||||
100 17556.978 512.66277 0 3763.9549 11.137534
|
||||
150 19579.586 138.04942 0 3763.8987 -29.953971
|
||||
200 19757.51 105.30542 0 3764.1036 -0.030645317
|
||||
250 18218.374 390.10747 0 3763.8804 13.711001
|
||||
300 19383.039 174.40688 0 3763.8586 5.7240693
|
||||
350 20125.986 36.972611 0 3764.0071 1.9559205
|
||||
400 18888.816 266.10975 0 3764.0386 9.6362168
|
||||
450 19307.656 188.2511 0 3763.743 1.9326206
|
||||
500 16331.197 738.56392 0 3762.8597 9.1715579
|
||||
550 19318.722 186.16172 0 3763.7027 3.0115336
|
||||
600 19455.268 161.20621 0 3764.0336 0.55208034
|
||||
650 18487.011 340.03216 0 3763.5528 -8.0359122
|
||||
700 17321.201 556.32471 0 3763.9545 -13.631751
|
||||
750 18979.187 249.04389 0 3763.7082 -2.6072455
|
||||
800 19342.456 181.85552 0 3763.7918 8.1918726
|
||||
850 19070.641 232.19342 0 3763.7936 7.3148472
|
||||
900 19478.873 156.65987 0 3763.8586 2.4284987
|
||||
950 19912.415 76.437437 0 3763.9216 -1.4667227
|
||||
1000 16003.749 802.39753 0 3766.0548 46.642188
|
||||
1050 19859.583 86.64176 0 3764.3424 -2.1961943
|
||||
1100 19229.575 203.61488 0 3764.6473 -10.632365
|
||||
1150 18821.6 279.15861 0 3764.64 -0.89495035
|
||||
1200 19392.695 173.59744 0 3764.8373 1.8508753
|
||||
1250 16459.624 717.32104 0 3765.3995 33.478127
|
||||
1300 19343.863 182.59043 0 3764.7874 0.75890736
|
||||
1350 20019.643 57.503573 0 3764.8448 0.31444671
|
||||
1400 18549.582 329.31436 0 3764.4221 10.738303
|
||||
1450 15163.926 957.47584 0 3765.6103 -17.923459
|
||||
1500 19223.688 204.15172 0 3764.0939 -1.6134536
|
||||
1550 18147.996 404.12676 0 3764.8668 8.4194774
|
||||
1600 18615.043 317.42466 0 3764.6548 -2.3288957
|
||||
1650 20120.654 38.887927 0 3764.935 -8.7620244
|
||||
1700 19450.906 162.98284 0 3765.0025 2.3254707
|
||||
1750 19374.632 177.37954 0 3765.2744 8.9328778
|
||||
1800 19424.403 167.93971 0 3765.0514 0.081234023
|
||||
1850 17936.311 442.83087 0 3764.3699 6.600894
|
||||
1900 19982.596 64.40607 0 3764.8868 -2.9530102
|
||||
1950 16215.95 761.89459 0 3764.8482 13.994238
|
||||
2000 18584.39 322.12621 0 3763.68 7.1654863
|
||||
2050 20107.966 41.025634 0 3764.723 -0.31093298
|
||||
2100 20002.346 60.590652 0 3764.7288 -6.7919499
|
||||
2150 16949.612 626.62391 0 3765.441 3.5094585
|
||||
2200 20010.952 58.808492 0 3764.5403 -10.862255
|
||||
2250 18982.727 247.00941 0 3762.3292 -0.53796622
|
||||
2300 18401.351 354.86992 0 3762.5275 1.0919209
|
||||
2350 19390.5 172.94589 0 3763.7793 -3.3526281
|
||||
2400 16081.648 786.23133 0 3764.3143 -16.197875
|
||||
2450 18870.722 268.69249 0 3763.2707 11.192419
|
||||
2500 19687.71 117.6898 0 3763.562 4.387789
|
||||
2550 18872.129 268.54506 0 3763.3838 -5.6577428
|
||||
2600 17017.179 612.11028 0 3763.4397 6.3187623
|
||||
2650 18766.343 288.63699 0 3763.8856 2.3968008
|
||||
2700 19737.998 108.02069 0 3763.2054 -0.30752024
|
||||
2750 19508.797 150.69812 0 3763.4384 -1.6171126
|
||||
2800 18394.822 355.73011 0 3762.1787 21.193311
|
||||
2850 18561.108 325.76417 0 3763.0065 3.9331499
|
||||
2900 20124.042 36.554163 0 3763.2286 0.54133121
|
||||
2950 15727.607 849.90471 0 3762.4245 13.885323
|
||||
3000 17991.206 431.32693 0 3763.0317 9.9953567
|
||||
3050 18834.86 275.34241 0 3763.2795 9.1519305
|
||||
3100 18986.272 247.38123 0 3763.3575 -1.8754521
|
||||
3150 19979.145 63.575968 0 3763.4177 -11.800026
|
||||
3200 19953.846 68.376593 0 3763.5332 -6.7719573
|
||||
3250 15646.02 867.19502 0 3764.6062 16.433911
|
||||
3300 16946.252 625.14854 0 3763.3433 4.3975456
|
||||
3350 19006.567 243.97026 0 3763.7048 5.3392405
|
||||
3400 18082.133 414.87059 0 3763.4138 15.143954
|
||||
3450 18273.719 379.36162 0 3763.3836 5.4465204
|
||||
3500 19783.17 100.06678 0 3763.6167 1.9588505
|
||||
3550 19794.99 97.904519 0 3763.6435 -3.0349395
|
||||
3600 18357.708 363.98291 0 3763.5585 -2.1229788
|
||||
3650 19647.179 125.48949 0 3763.8559 1.2967845
|
||||
3700 18806.632 281.78709 0 3764.4967 5.125718
|
||||
3750 18982.747 248.97053 0 3764.294 -0.72036085
|
||||
3800 19597.926 135.04805 0 3764.2935 -3.2129291
|
||||
3850 18914.042 261.7133 0 3764.3136 -12.163282
|
||||
3900 18646.326 311.16482 0 3764.1881 5.1808943
|
||||
3950 18589.554 321.36256 0 3763.8726 4.9554103
|
||||
4000 17877.615 453.02456 0 3763.694 9.8457113
|
||||
4050 19440.059 164.15739 0 3764.1684 -5.4054486
|
||||
4100 18505.545 337.36023 0 3764.313 4.8468985
|
||||
4150 19220.307 204.85944 0 3764.1755 -6.5040818
|
||||
4200 19058.915 234.79578 0 3764.2245 3.1852011
|
||||
4250 19867.025 85.136186 0 3764.2149 5.6156236
|
||||
4300 16989.857 616.86564 0 3763.1355 -3.4041875
|
||||
4350 19782.09 100.85847 0 3764.2085 3.2531098
|
||||
4400 19879.56 82.559198 0 3763.9593 1.6340828
|
||||
4450 19409.95 169.46676 0 3763.9019 -1.824265
|
||||
4500 19742.977 107.72786 0 3763.8347 -0.72711698
|
||||
4550 17166.529 585.04113 0 3764.028 -0.38806102
|
||||
4600 19604.596 133.61426 0 3764.0949 -5.2712214
|
||||
4650 18865.608 270.23956 0 3763.8707 1.5751363
|
||||
4700 20190.139 25.270932 0 3764.1855 -10.159924
|
||||
4750 20043.487 52.56327 0 3764.3201 -4.713579
|
||||
4800 19361.931 178.70311 0 3764.246 4.2460799
|
||||
4850 19460.365 160.29083 0 3764.0621 3.5079181
|
||||
4900 18252.89 384.16194 0 3764.3268 4.1870604
|
||||
4950 19516.947 150.07365 0 3764.3231 4.0238527
|
||||
5000 19041.145 238.27335 0 3764.4113 8.2280019
|
||||
5050 19519.408 149.66793 0 3764.3731 -0.088904966
|
||||
5100 18087.848 415.34004 0 3764.9416 8.9482852
|
||||
5150 19392.463 173.43121 0 3764.628 -6.6722716
|
||||
5200 19683.968 119.46663 0 3764.6458 -2.0330852
|
||||
5250 19675.404 121.09497 0 3764.6884 3.0627309
|
||||
5300 18627.53 314.96107 0 3764.5038 5.2692141
|
||||
5350 20022.616 56.725346 0 3764.6172 -7.7034469
|
||||
5400 19353.4 180.6482 0 3764.6112 -2.3897589
|
||||
5450 16966.649 622.29693 0 3764.2689 6.3601638
|
||||
5500 17584.292 508.42495 0 3764.7753 5.949219
|
||||
5550 19169.69 214.76864 0 3764.7113 3.3778997
|
||||
5600 19491.814 155.19149 0 3764.7866 -0.20031164
|
||||
5650 19079.585 231.70394 0 3764.9605 7.3017226
|
||||
5700 19686.564 119.34 0 3765 0.98980357
|
||||
5750 19639.909 127.89886 0 3764.919 2.3982612
|
||||
5800 19474.109 158.55418 0 3764.8706 3.4940447
|
||||
5850 16957.663 624.72623 0 3765.0342 10.739819
|
||||
5900 19950.579 70.027987 0 3764.5796 4.6925057
|
||||
5950 19759.601 105.38621 0 3764.5716 3.0958319
|
||||
6000 19129.749 221.96406 0 3764.5102 -1.0612997
|
||||
6050 16087.951 785.36134 0 3764.6115 -15.255986
|
||||
6100 18851.976 272.98306 0 3764.0896 4.9341766
|
||||
6150 19532.23 147.4113 0 3764.4909 1.3206073
|
||||
6200 18051.604 421.79367 0 3764.6833 2.587863
|
||||
6250 18922.77 259.81211 0 3764.0287 10.363589
|
||||
6300 18402.504 356.81518 0 3764.6864 8.3589218
|
||||
6350 19315.369 187.64457 0 3764.5647 1.0716382
|
||||
6400 19700.59 116.50438 0 3764.7618 2.165408
|
||||
6450 19596.362 135.79675 0 3764.7527 1.6466783
|
||||
6500 20217.677 20.884953 0 3764.8993 -3.5893732
|
||||
6550 18278.991 379.95981 0 3764.9582 7.0433091
|
||||
6600 20142.999 34.761283 0 3764.9462 1.7083655
|
||||
6650 20185.488 26.899017 0 3764.9524 -0.65741058
|
||||
6700 17942.962 441.72909 0 3764.4999 -3.691039
|
||||
6750 16435.681 720.9581 0 3764.6028 -9.4583249
|
||||
6800 17825.95 463.58979 0 3764.6916 6.1557503
|
||||
6850 19440.75 164.52796 0 3764.6669 -11.921703
|
||||
6900 18824.905 278.4897 0 3764.5832 -1.4668322
|
||||
6950 19069.14 233.25502 0 3764.5772 6.8149838
|
||||
7000 18983.209 249.29193 0 3764.701 15.140158
|
||||
7050 15623.103 872.33684 0 3765.5041 7.3268767
|
||||
7100 20090.283 44.006184 0 3764.429 2.6959947
|
||||
7150 15535.27 888.39683 0 3765.2987 -4.1285644
|
||||
7200 19425.575 167.19079 0 3764.5195 4.9190857
|
||||
7250 18684.497 304.24754 0 3764.3396 7.3927682
|
||||
7300 17632.518 498.82765 0 3764.1087 5.1101854
|
||||
7350 18969.793 251.66375 0 3764.5884 -3.7865508
|
||||
7400 17700.626 486.89931 0 3764.7931 -8.8531288
|
||||
7450 17897.361 450.31562 0 3764.6417 -3.6095062
|
||||
7500 18795.228 284.03842 0 3764.6361 8.3567203
|
||||
7550 18658.285 309.34015 0 3764.5781 0.4306691
|
||||
7600 19230.039 203.5385 0 3764.6567 0.80253549
|
||||
7650 19513.551 150.86999 0 3764.4906 0.32848159
|
||||
7700 19494.849 154.28788 0 3764.4452 -4.2498631
|
||||
7750 20011.058 58.832118 0 3764.5835 0.54896615
|
||||
7800 19241.055 201.57548 0 3764.7338 -0.26200786
|
||||
7850 19512.742 151.11436 0 3764.5851 2.7308876
|
||||
7900 19688.007 118.68023 0 3764.6075 0.80454178
|
||||
7950 16891.645 636.56823 0 3764.6507 -25.839253
|
||||
8000 19425.572 167.33746 0 3764.6657 -2.8744687
|
||||
8050 19444.916 163.57779 0 3764.4882 8.5388183
|
||||
8100 19540.338 145.77731 0 3764.3585 5.5606379
|
||||
8150 17997.991 429.85951 0 3762.8208 20.179487
|
||||
8200 19463.886 159.50302 0 3763.9264 0.19577123
|
||||
8250 19517.733 149.53457 0 3763.9295 2.3294314
|
||||
8300 19236.221 201.66041 0 3763.9236 5.8204747
|
||||
8350 18662.608 308.25544 0 3764.2939 5.4422482
|
||||
8400 19030.046 239.38211 0 3763.4647 3.7940188
|
||||
8450 18058.148 419.70672 0 3763.8081 4.4010713
|
||||
8500 16866.001 641.00564 0 3764.3392 -19.894815
|
||||
8550 19484.364 155.35821 0 3763.5737 4.2635496
|
||||
8600 18562.912 326.16323 0 3763.7395 11.288271
|
||||
8650 19256.188 197.67578 0 3763.6365 -4.1872666
|
||||
8700 19653.945 124.27148 0 3763.8909 -7.4888761
|
||||
8750 19590.834 136.12748 0 3764.0596 1.0605539
|
||||
8800 19065.424 233.46882 0 3764.1029 1.8432113
|
||||
8850 18961.297 252.69734 0 3764.0486 6.7414134
|
||||
8900 19879.711 82.777822 0 3764.2058 0.12631864
|
||||
8950 18689.712 302.80546 0 3763.8632 5.1584036
|
||||
9000 19114.403 224.23511 0 3763.9393 -4.5856366
|
||||
9050 17626.3 500.49518 0 3764.6248 -3.9436947
|
||||
9100 18552.501 328.86032 0 3764.5087 -0.32810034
|
||||
9150 15039.846 979.12961 0 3764.2862 16.571104
|
||||
9200 19146.923 218.64681 0 3764.3733 -4.6264398
|
||||
9250 17606.161 503.14852 0 3763.5487 13.13675
|
||||
9300 18002.328 430.47362 0 3764.2381 4.9326117
|
||||
9350 19980.452 64.168644 0 3764.2524 -5.6111349
|
||||
9400 18953.798 254.44926 0 3764.4118 2.3662302
|
||||
9450 17151.075 588.59472 0 3764.7197 4.3116983
|
||||
9500 19128.858 221.38199 0 3763.763 3.6641306
|
||||
9550 18217.322 390.53199 0 3764.1101 1.8537154
|
||||
9600 19094.478 227.98925 0 3764.0038 3.972665
|
||||
9650 19577.649 138.55507 0 3764.0456 4.0408247
|
||||
9700 19331.361 184.31942 0 3764.2011 -4.7996733
|
||||
9750 18999.798 245.87295 0 3764.3541 -0.26741334
|
||||
9800 18987.181 248.37105 0 3764.5157 6.1717595
|
||||
9850 20094.73 43.013036 0 3764.2593 -8.9770288
|
||||
9900 18988.815 247.63984 0 3764.087 -6.3990966
|
||||
9950 18290.808 377.34967 0 3764.5363 7.7453525
|
||||
10000 19558.326 142.47047 0 3764.3828 3.4110829
|
||||
Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 24418.438 tau/day, 2826.208 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00
|
||||
Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63
|
||||
Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05
|
||||
Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19
|
||||
Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14
|
||||
Other | | 0.0352 | | | 0.99
|
||||
|
||||
Nlocal: 20.25 ave 36 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 17.5 ave 37 max 1 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 154.25 ave 393 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 617
|
||||
Ave neighs/atom = 7.61728
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 948
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
340
examples/rigid/log.20Apr18.rigid.property.g++.1
Normal file
340
examples/rigid/log.20Apr18.rigid.property.g++.1
Normal file
@ -0,0 +1,340 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
fix 0 all property/atom i_bodies
|
||||
|
||||
read_data data.rigid-property fix 0 NULL Bodies
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
# assemble bodies from per-atom custom integer property bodies
|
||||
fix 1 all rigid custom i_bodies
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.140719 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 613990.898 tau/day, 71063.761 timesteps/s
|
||||
97.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.010882 | 0.010882 | 0.010882 | 0.0 | 7.73
|
||||
Neigh | 0.037245 | 0.037245 | 0.037245 | 0.0 | 26.47
|
||||
Comm | 0.0092154 | 0.0092154 | 0.0092154 | 0.0 | 6.55
|
||||
Output | 0.0024879 | 0.0024879 | 0.0024879 | 0.0 | 1.77
|
||||
Modify | 0.074702 | 0.074702 | 0.074702 | 0.0 | 53.09
|
||||
Other | | 0.006187 | | | 4.40
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
340
examples/rigid/log.20Apr18.rigid.property.g++.4
Normal file
340
examples/rigid/log.20Apr18.rigid.property.g++.4
Normal file
@ -0,0 +1,340 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
fix 0 all property/atom i_bodies
|
||||
|
||||
read_data data.rigid-property fix 0 NULL Bodies
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
# assemble bodies from per-atom custom integer property bodies
|
||||
fix 1 all rigid custom i_bodies
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.206235 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 418940.303 tau/day, 48488.461 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0026572 | 0.004187 | 0.0050838 | 1.5 | 2.03
|
||||
Neigh | 0.012115 | 0.012789 | 0.013634 | 0.5 | 6.20
|
||||
Comm | 0.084275 | 0.089969 | 0.095318 | 1.5 | 43.62
|
||||
Output | 0.0048559 | 0.0051559 | 0.0059836 | 0.7 | 2.50
|
||||
Modify | 0.077074 | 0.083586 | 0.088022 | 1.5 | 40.53
|
||||
Other | | 0.01055 | | | 5.11
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:00
|
||||
458
examples/rigid/log.20Apr18.rigid.tnr.g++.1
Normal file
458
examples/rigid/log.20Apr18.rigid.tnr.g++.1
Normal file
@ -0,0 +1,458 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Tethered nanorods
|
||||
|
||||
atom_style molecular
|
||||
|
||||
read_data data.rigid.tnr
|
||||
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5600 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
1600 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify bond parameters
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify initial velocities
|
||||
|
||||
velocity all create 1.4 109345
|
||||
|
||||
# Specify rigid components
|
||||
|
||||
group rods type 2
|
||||
4000 atoms in group rods
|
||||
group tethers subtract all rods
|
||||
1600 atoms in group tethers
|
||||
|
||||
neigh_modify exclude molecule/intra rods delay 0 every 1
|
||||
|
||||
# Specify the pair potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
pair_coeff * * 1.0 1.0 1.122
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
|
||||
# Specify output
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
|
||||
thermo_modify flush yes lost warn
|
||||
|
||||
timestep 0.005
|
||||
|
||||
fix 1 rods rigid molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
fix 2 tethers nve
|
||||
fix 3 all langevin 1.4 1.4 1.0 437624
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 45 45 45
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
|
||||
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
|
||||
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
|
||||
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
|
||||
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
|
||||
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
|
||||
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
|
||||
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
|
||||
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
|
||||
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
|
||||
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
|
||||
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
|
||||
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
|
||||
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
|
||||
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
|
||||
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
|
||||
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
|
||||
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
|
||||
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
|
||||
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
|
||||
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
|
||||
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
|
||||
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216998 -0.0032636911
|
||||
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
|
||||
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738261 0.0090537939 0.013165402
|
||||
2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678
|
||||
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
|
||||
2700 1.4138077 5.9369067 7.047377 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379
|
||||
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106
|
||||
2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134
|
||||
3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861
|
||||
3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037
|
||||
3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321
|
||||
3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736
|
||||
3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532
|
||||
3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716
|
||||
3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599
|
||||
3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767
|
||||
3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832
|
||||
3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184
|
||||
4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721
|
||||
4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459
|
||||
4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681
|
||||
4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067
|
||||
4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185
|
||||
4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378
|
||||
4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102
|
||||
4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176
|
||||
4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431
|
||||
4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736
|
||||
5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324
|
||||
Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms
|
||||
|
||||
Performance: 320596.735 tau/day, 742.122 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81
|
||||
Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95
|
||||
Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64
|
||||
Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38
|
||||
Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06
|
||||
Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58
|
||||
Other | | 0.1735 | | | 2.57
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1352 ave 1352 max 1352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5257 ave 5257 max 5257 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5257
|
||||
Ave neighs/atom = 0.93875
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 766
|
||||
Dangerous builds = 0
|
||||
|
||||
# Replace fix rigid and fix langevin with new ones
|
||||
|
||||
unfix 1
|
||||
unfix 3
|
||||
|
||||
fix 3 tethers langevin 1.4 1.4 1.0 198450
|
||||
|
||||
# Test different integrators for rods
|
||||
|
||||
fix 1 rods rigid/nve molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nve"
|
||||
rigid/nve
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
5000 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554
|
||||
5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085
|
||||
5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108
|
||||
5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935
|
||||
5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084
|
||||
5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628
|
||||
5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843
|
||||
5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286
|
||||
5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054
|
||||
5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358
|
||||
6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488
|
||||
Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 306205.780 tau/day, 708.810 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.149 | 0.149 | 0.149 | 0.0 | 10.56
|
||||
Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82
|
||||
Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19
|
||||
Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30
|
||||
Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06
|
||||
Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60
|
||||
Other | | 0.03491 | | | 2.47
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1347 ave 1347 max 1347 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5592 ave 5592 max 5592 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5592
|
||||
Ave neighs/atom = 0.998571
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 153
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nvt"
|
||||
rigid/nvt
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
6000 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429
|
||||
6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278
|
||||
6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897
|
||||
6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564
|
||||
6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155
|
||||
6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487
|
||||
6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719
|
||||
6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031
|
||||
6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821
|
||||
6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742
|
||||
7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771
|
||||
Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 299769.942 tau/day, 693.912 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36
|
||||
Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71
|
||||
Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94
|
||||
Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29
|
||||
Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06
|
||||
Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20
|
||||
Other | | 0.03506 | | | 2.43
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1351 ave 1351 max 1351 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5541 ave 5541 max 5541 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5541
|
||||
Ave neighs/atom = 0.989464
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 153
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
compute myTemp all temp
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt iso"
|
||||
rigid/npt iso
|
||||
fix_modify 1 temp myTemp
|
||||
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
7000 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521
|
||||
7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973
|
||||
7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938
|
||||
7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059
|
||||
7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524
|
||||
7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326
|
||||
7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195
|
||||
7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457
|
||||
7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129
|
||||
7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936
|
||||
8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995
|
||||
Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 139749.554 tau/day, 323.494 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40
|
||||
Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56
|
||||
Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35
|
||||
Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35
|
||||
Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03
|
||||
Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92
|
||||
Other | | 0.04324 | | | 1.40
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2922 ave 2922 max 2922 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 24639 ave 24639 max 24639 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 24639
|
||||
Ave neighs/atom = 4.39982
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 335
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt x"
|
||||
rigid/npt x
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368
|
||||
8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024
|
||||
8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975
|
||||
8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871
|
||||
8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782
|
||||
8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368
|
||||
8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773
|
||||
8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679
|
||||
8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819
|
||||
8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357
|
||||
9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504
|
||||
Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 141361.930 tau/day, 327.227 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76
|
||||
Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63
|
||||
Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25
|
||||
Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87
|
||||
Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03
|
||||
Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20
|
||||
Other | | 0.03837 | | | 1.26
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3326 ave 3326 max 3326 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 31301 ave 31301 max 31301 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 31301
|
||||
Ave neighs/atom = 5.58946
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 168
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph iso"
|
||||
rigid/nph iso
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.787 | 7.787 | 7.787 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579
|
||||
9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042
|
||||
9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329
|
||||
9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893
|
||||
9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244
|
||||
9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087
|
||||
9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896
|
||||
9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362
|
||||
9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545
|
||||
9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207
|
||||
10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467
|
||||
Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 133348.758 tau/day, 308.678 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00
|
||||
Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48
|
||||
Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10
|
||||
Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90
|
||||
Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02
|
||||
Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30
|
||||
Other | | 0.03849 | | | 1.19
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3617 ave 3617 max 3617 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 35834 ave 35834 max 35834 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 35834
|
||||
Ave neighs/atom = 6.39893
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph xy couple"
|
||||
rigid/nph xy couple
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.793 | 7.793 | 7.793 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513
|
||||
10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871
|
||||
10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525
|
||||
10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543
|
||||
10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677
|
||||
10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067
|
||||
10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719
|
||||
10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951
|
||||
10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606
|
||||
10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411
|
||||
11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472
|
||||
Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 126326.531 tau/day, 292.423 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96
|
||||
Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36
|
||||
Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57
|
||||
Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88
|
||||
Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02
|
||||
Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07
|
||||
Other | | 0.03903 | | | 1.14
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3805 ave 3805 max 3805 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 40038 ave 40038 max 40038 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 40038
|
||||
Ave neighs/atom = 7.14964
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:22
|
||||
458
examples/rigid/log.20Apr18.rigid.tnr.g++.4
Normal file
458
examples/rigid/log.20Apr18.rigid.tnr.g++.4
Normal file
@ -0,0 +1,458 @@
|
||||
LAMMPS (20 Apr 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Tethered nanorods
|
||||
|
||||
atom_style molecular
|
||||
|
||||
read_data data.rigid.tnr
|
||||
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
5600 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
1600 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify bond parameters
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify initial velocities
|
||||
|
||||
velocity all create 1.4 109345
|
||||
|
||||
# Specify rigid components
|
||||
|
||||
group rods type 2
|
||||
4000 atoms in group rods
|
||||
group tethers subtract all rods
|
||||
1600 atoms in group tethers
|
||||
|
||||
neigh_modify exclude molecule/intra rods delay 0 every 1
|
||||
|
||||
# Specify the pair potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
pair_coeff * * 1.0 1.0 1.122
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
|
||||
# Specify output
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
|
||||
thermo_modify flush yes lost warn
|
||||
|
||||
timestep 0.005
|
||||
|
||||
fix 1 rods rigid molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
fix 2 tethers nve
|
||||
fix 3 all langevin 1.4 1.4 1.0 437624
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 45 45 45
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
|
||||
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
|
||||
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
|
||||
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
|
||||
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
|
||||
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
|
||||
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
|
||||
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
|
||||
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
|
||||
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
|
||||
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
|
||||
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
|
||||
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
|
||||
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
|
||||
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
|
||||
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431
|
||||
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
|
||||
1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
|
||||
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
|
||||
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
|
||||
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901
|
||||
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
|
||||
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
|
||||
2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
|
||||
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028
|
||||
2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539
|
||||
2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112
|
||||
2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357
|
||||
2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412
|
||||
2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892
|
||||
3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658
|
||||
3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485
|
||||
3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783
|
||||
3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048
|
||||
3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724
|
||||
3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433
|
||||
3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225
|
||||
3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455
|
||||
3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624
|
||||
3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689
|
||||
4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626
|
||||
4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172
|
||||
4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746
|
||||
4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924
|
||||
4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638
|
||||
4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334
|
||||
4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263
|
||||
4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225
|
||||
4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449
|
||||
4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056
|
||||
5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771
|
||||
Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms
|
||||
|
||||
Performance: 624133.913 tau/day, 1444.754 timesteps/s
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85
|
||||
Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91
|
||||
Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76
|
||||
Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58
|
||||
Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10
|
||||
Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02
|
||||
Other | | 0.2 | | | 5.78
|
||||
|
||||
Nlocal: 1400 ave 1844 max 907 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 642 ave 714 max 581 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 1307.25 ave 1883 max 682 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 5229
|
||||
Ave neighs/atom = 0.93375
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 762
|
||||
Dangerous builds = 0
|
||||
|
||||
# Replace fix rigid and fix langevin with new ones
|
||||
|
||||
unfix 1
|
||||
unfix 3
|
||||
|
||||
fix 3 tethers langevin 1.4 1.4 1.0 198450
|
||||
|
||||
# Test different integrators for rods
|
||||
|
||||
fix 1 rods rigid/nve molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nve"
|
||||
rigid/nve
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215
|
||||
5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298
|
||||
5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911
|
||||
5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068
|
||||
5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373
|
||||
5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707
|
||||
5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387
|
||||
5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341
|
||||
5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223
|
||||
5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198
|
||||
6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689
|
||||
Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 544612.641 tau/day, 1260.677 timesteps/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55
|
||||
Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66
|
||||
Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30
|
||||
Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11
|
||||
Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09
|
||||
Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66
|
||||
Other | | 0.04459 | | | 5.62
|
||||
|
||||
Nlocal: 1400 ave 1844 max 884 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 713.5 ave 818 max 656 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Neighs: 1315 ave 1956 max 573 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 5260
|
||||
Ave neighs/atom = 0.939286
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 156
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nvt"
|
||||
rigid/nvt
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779
|
||||
6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027
|
||||
6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881
|
||||
6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499
|
||||
6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801
|
||||
6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659
|
||||
6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155
|
||||
6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075
|
||||
6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066
|
||||
6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381
|
||||
7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375
|
||||
Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 531376.713 tau/day, 1230.039 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74
|
||||
Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62
|
||||
Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33
|
||||
Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10
|
||||
Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09
|
||||
Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04
|
||||
Other | | 0.04134 | | | 5.09
|
||||
|
||||
Nlocal: 1400 ave 1861 max 953 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 732.5 ave 799 max 634 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 1478.5 ave 2087 max 852 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 5914
|
||||
Ave neighs/atom = 1.05607
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 154
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
compute myTemp all temp
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt iso"
|
||||
rigid/npt iso
|
||||
fix_modify 1 temp myTemp
|
||||
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619
|
||||
7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475
|
||||
7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823
|
||||
7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808
|
||||
7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154
|
||||
7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934
|
||||
7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266
|
||||
7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104
|
||||
7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242
|
||||
7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921
|
||||
8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435
|
||||
Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 292430.022 tau/day, 676.921 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82
|
||||
Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35
|
||||
Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30
|
||||
Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68
|
||||
Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03
|
||||
Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73
|
||||
Other | | 0.04563 | | | 3.09
|
||||
|
||||
Nlocal: 1400 ave 1711 max 1074 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 1617 ave 1748 max 1514 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 6221.75 ave 8875 max 3829 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 24887
|
||||
Ave neighs/atom = 4.44411
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 340
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt x"
|
||||
rigid/npt x
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531
|
||||
8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895
|
||||
8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249
|
||||
8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714
|
||||
8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747
|
||||
8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867
|
||||
8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873
|
||||
8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702
|
||||
8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987
|
||||
8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801
|
||||
9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686
|
||||
Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 304989.819 tau/day, 705.995 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25
|
||||
Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42
|
||||
Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36
|
||||
Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21
|
||||
Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04
|
||||
Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92
|
||||
Other | | 0.03963 | | | 2.80
|
||||
|
||||
Nlocal: 1400 ave 1641 max 1120 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 1593.5 ave 1674 max 1480 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 7766.25 ave 10004 max 5618 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 31065
|
||||
Ave neighs/atom = 5.54732
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 168
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph iso"
|
||||
rigid/nph iso
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595
|
||||
9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716
|
||||
9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967
|
||||
9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325
|
||||
9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319
|
||||
9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422
|
||||
9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125
|
||||
9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226
|
||||
9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283
|
||||
9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026
|
||||
10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892
|
||||
Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 293069.938 tau/day, 678.403 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07
|
||||
Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37
|
||||
Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66
|
||||
Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03
|
||||
Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04
|
||||
Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18
|
||||
Other | | 0.0391 | | | 2.65
|
||||
|
||||
Nlocal: 1400 ave 1629 max 1159 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 1760.25 ave 1871 max 1635 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Neighs: 9467.75 ave 11967 max 6712 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 37871
|
||||
Ave neighs/atom = 6.76268
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 163
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph xy couple"
|
||||
rigid/nph xy couple
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506
|
||||
10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812
|
||||
10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461
|
||||
10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255
|
||||
10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884
|
||||
10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428
|
||||
10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401
|
||||
10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703
|
||||
10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507
|
||||
10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896
|
||||
11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759
|
||||
Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 287222.965 tau/day, 664.868 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15
|
||||
Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36
|
||||
Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36
|
||||
Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19
|
||||
Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03
|
||||
Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41
|
||||
Other | | 0.0375 | | | 2.49
|
||||
|
||||
Nlocal: 1400 ave 1605 max 1229 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 1859 ave 1964 max 1718 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 10208.2 ave 13091 max 7670 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 40833
|
||||
Ave neighs/atom = 7.29161
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 160
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:10
|
||||
@ -1,332 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 18 18 18
|
||||
Memory usage per processor = 2.96781 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384277
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184717
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.86699149
|
||||
1200 21815.003 45.317414 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064078
|
||||
1300 20780.781 217.36506 0 3680.8286 6.0538616
|
||||
1350 20558.971 254.36482 0 3680.8601 -3.6773952
|
||||
1400 21485.029 99.812921 0 3680.6511 -16.185473
|
||||
1450 21771.107 52.15961 0 3680.6775 -2.4756673
|
||||
1500 21520.948 93.503927 0 3680.3286 2.1023576
|
||||
1550 21351.418 121.68137 0 3680.2511 5.5159947
|
||||
1600 20778.805 216.92177 0 3680.0559 15.089188
|
||||
1650 21477.638 100.21836 0 3679.8247 -1.1045746
|
||||
1700 18501.339 596.47914 0 3680.0357 -15.679679
|
||||
1750 18563.642 587.34785 0 3681.2882 33.532209
|
||||
1800 19110.185 494.8234 0 3679.8543 18.024046
|
||||
1850 21364.191 119.23545 0 3679.9339 2.5291103
|
||||
1900 20146.626 322.14867 0 3679.9197 5.7313218
|
||||
1950 20692.672 231.25325 0 3680.0319 4.2977763
|
||||
2000 20943.904 189.11235 0 3679.7629 -22.645121
|
||||
2050 19668.057 401.82994 0 3679.8394 3.6251916
|
||||
2100 20280.442 299.76155 0 3679.8353 7.4807949
|
||||
2150 19181.86 483.522 0 3680.4987 22.620507
|
||||
2200 21300.161 130.70534 0 3680.7322 4.7102665
|
||||
2250 20486.943 266.63931 0 3681.1299 -8.6456512
|
||||
2300 18653.122 572.24819 0 3681.1018 -5.2637122
|
||||
2350 21513.523 95.614901 0 3681.2021 -9.3621767
|
||||
2400 21466.272 103.56446 0 3681.2765 -29.561368
|
||||
2450 20100.105 332.27123 0 3682.2887 35.744287
|
||||
2500 20764.395 221.6677 0 3682.4001 -12.468906
|
||||
2550 20435.699 276.31055 0 3682.2603 -22.413697
|
||||
2600 21466.467 104.53618 0 3682.2807 -10.078508
|
||||
2650 20814.737 213.23892 0 3682.3617 5.1390411
|
||||
2700 18565.761 588.3578 0 3682.6513 22.27664
|
||||
2750 20772.36 220.1607 0 3682.2206 -7.9448198
|
||||
2800 21018.563 179.10058 0 3682.1945 -7.0717829
|
||||
2850 16789.412 884.21472 0 3682.4501 33.279015
|
||||
2900 19304.363 464.75282 0 3682.1466 7.947554
|
||||
2950 20513.758 263.07578 0 3682.0355 2.2361434
|
||||
3000 20617.309 245.95251 0 3682.1706 -0.75213689
|
||||
3050 18567.52 587.90473 0 3682.4914 -4.0112006
|
||||
3100 18696.577 566.20617 0 3682.3023 -1.4814167
|
||||
3150 19864.606 371.56078 0 3682.3284 8.9362836
|
||||
3200 18902.643 532.04614 0 3682.4867 0.76630303
|
||||
3250 21110.454 163.86212 0 3682.271 -1.6253894
|
||||
3300 19369.939 454.05833 0 3682.3816 4.9066544
|
||||
3350 19082.603 501.69905 0 3682.133 3.5982292
|
||||
3400 19527.779 426.918 0 3681.5478 6.9612143
|
||||
3450 19892.953 366.19989 0 3681.6921 3.0050426
|
||||
3500 19708.981 396.84552 0 3681.6756 7.0757635
|
||||
3550 20256.096 306.23937 0 3682.2554 -1.752138
|
||||
3600 21289.889 133.93823 0 3682.253 -3.7462615
|
||||
3650 18333.877 627.18028 0 3682.8264 -15.276791
|
||||
3700 19829.133 377.33753 0 3682.1931 -6.269648
|
||||
3750 20771.635 220.07171 0 3682.0109 -28.479036
|
||||
3800 18373.813 619.79253 0 3682.0947 29.594781
|
||||
3850 19320.99 461.92786 0 3682.0928 -5.3212101
|
||||
3900 16119.825 995.68064 0 3682.3182 -8.4683118
|
||||
3950 15556.948 1091.3655 0 3684.1902 20.98273
|
||||
4000 20000.464 348.24891 0 3681.6596 7.1589745
|
||||
4050 18870.219 536.59924 0 3681.6358 -3.7997025
|
||||
4100 19889.518 367.49253 0 3682.4122 -14.091266
|
||||
4150 15789.623 1051.3399 0 3682.9438 -4.4152389
|
||||
4200 20548.889 256.83493 0 3681.6498 0.92234153
|
||||
4250 20681.925 235.46113 0 3682.4487 -11.515773
|
||||
4300 19330.404 460.80975 0 3682.5437 -22.351775
|
||||
4350 19369.443 453.35405 0 3681.5945 29.418242
|
||||
4400 20762.165 222.24133 0 3682.6021 2.6627047
|
||||
4450 19984.657 350.71294 0 3681.4891 28.88731
|
||||
4500 21167.58 154.25344 0 3682.1834 -3.0784322
|
||||
4550 18133.576 660.73671 0 3682.9995 2.5305835
|
||||
4600 19935.069 360.36826 0 3682.8798 2.4575034
|
||||
4650 21413.76 113.86464 0 3682.8246 -5.1271547
|
||||
4700 21716.333 63.609419 0 3682.9982 -2.4708049
|
||||
4750 21352.947 124.36961 0 3683.1941 -0.29026265
|
||||
4800 19043.788 508.8617 0 3682.8264 14.797006
|
||||
4850 20516.121 263.78758 0 3683.1411 7.1348281
|
||||
4900 20624.5 245.81827 0 3683.235 0.34708051
|
||||
4950 20317.197 296.68937 0 3682.8889 -0.55065946
|
||||
5000 18346.865 625.37246 0 3683.1832 7.3371413
|
||||
5050 18867.53 538.49153 0 3683.0799 1.9249866
|
||||
5100 18790.276 551.17224 0 3682.885 2.2333017
|
||||
5150 20241.365 311.84683 0 3685.4076 -3.998004
|
||||
5200 17685.058 739.76418 0 3687.2739 3.2835025
|
||||
5250 18496.626 604.58166 0 3687.3526 -10.185776
|
||||
5300 18420.042 617.82026 0 3687.8273 -16.392458
|
||||
5350 18767.338 559.0349 0 3686.9246 4.5320767
|
||||
5400 20423.245 284.90517 0 3688.7794 -8.6356656
|
||||
5450 21080.398 176.18494 0 3689.5846 -16.450038
|
||||
5500 16684.424 909.12643 0 3689.8637 49.94555
|
||||
5550 20132.31 335.03663 0 3690.4216 -16.018038
|
||||
5600 20430.923 285.17562 0 3690.3295 -5.0773675
|
||||
5650 20479.943 276.55962 0 3689.8834 5.4334564
|
||||
5700 20061.532 345.95553 0 3689.5441 -16.230658
|
||||
5750 20523.759 268.92217 0 3689.5487 -4.4128812
|
||||
5800 18900.356 537.65462 0 3687.7139 13.605549
|
||||
5850 20280.502 310.27193 0 3690.3556 -4.7884959
|
||||
5900 19050.26 515.66087 0 3690.7042 7.8864722
|
||||
5950 19566.917 430.2997 0 3691.4525 31.715268
|
||||
6000 18878.118 544.75449 0 3691.1076 -4.2415329
|
||||
6050 19308.682 471.70734 0 3689.821 -10.561614
|
||||
6100 18776.194 560.04764 0 3689.4133 -7.7286747
|
||||
6150 21475.064 110.1508 0 3689.3281 -3.6506391
|
||||
6200 19975 360.82675 0 3689.9934 10.282021
|
||||
6250 21396.341 123.5341 0 3689.5909 -5.7215163
|
||||
6300 18533.423 600.87422 0 3689.778 15.408027
|
||||
6350 20653.152 247.19253 0 3689.3846 8.5607784
|
||||
6400 19716.537 403.41487 0 3689.5044 13.165575
|
||||
6450 21120.66 168.79838 0 3688.9084 -0.50382728
|
||||
6500 19700.345 404.7155 0 3688.1064 13.941375
|
||||
6550 10818.393 1892.037 0 3695.1025 38.423155
|
||||
6600 18684.478 574.84755 0 3688.9273 5.9176985
|
||||
6650 19219.732 486.04269 0 3689.3314 18.287659
|
||||
6700 20058.587 344.88255 0 3687.9804 6.5372086
|
||||
6750 21279.318 142.77333 0 3689.3264 2.498188
|
||||
6800 20671.545 244.25024 0 3689.5078 -4.1356416
|
||||
6850 21203.598 155.82001 0 3689.753 -0.0083061182
|
||||
6900 21699.344 73.301497 0 3689.8588 -8.0309898
|
||||
6950 20951.212 197.19403 0 3689.0627 0.76668303
|
||||
7000 20166.275 329.02869 0 3690.0746 2.0083318
|
||||
7050 21554.944 97.465792 0 3689.9564 -3.2420086
|
||||
7100 20817.494 220.25476 0 3689.8372 0.17206182
|
||||
7150 21481.11 109.84029 0 3690.0253 -3.6814741
|
||||
7200 21266.824 145.53099 0 3690.0016 -2.060543
|
||||
7250 19434.684 450.81331 0 3689.9273 9.4822765
|
||||
7300 21246.525 148.96573 0 3690.0532 3.3208839
|
||||
7350 19749.269 398.60049 0 3690.1454 1.0929662
|
||||
7400 20354.792 297.70261 0 3690.168 1.547159
|
||||
7450 19996.859 357.16723 0 3689.977 -0.68412025
|
||||
7500 20179.628 326.53243 0 3689.8038 -2.4805507
|
||||
7550 18765.184 561.65039 0 3689.1811 -1.7976428
|
||||
7600 19457.496 447.04428 0 3689.9603 -1.9055522
|
||||
7650 18206.823 655.57276 0 3690.0433 1.2797964
|
||||
7700 19152.344 497.77422 0 3689.8315 18.145069
|
||||
7750 21387.484 125.48654 0 3690.0673 -2.9915772
|
||||
7800 18127.052 668.61425 0 3689.7896 9.044869
|
||||
7850 21419.557 120.08889 0 3690.015 6.2651717
|
||||
7900 21817.182 53.739819 0 3689.9368 -4.2387416
|
||||
7950 18215.195 654.15494 0 3690.0208 -54.628049
|
||||
8000 21523.503 102.58018 0 3689.8307 -4.84236
|
||||
8050 20720.799 236.28689 0 3689.7535 -9.3725225
|
||||
8100 21196.483 157.3232 0 3690.0704 -7.7222497
|
||||
8150 20869.667 211.65308 0 3689.9309 -6.8438295
|
||||
8200 17790.052 725.72497 0 3690.7336 -25.697688
|
||||
8250 19634.94 417.71929 0 3690.2094 8.861604
|
||||
8300 19135.784 500.92443 0 3690.2218 -3.1245167
|
||||
8350 20191.718 324.93312 0 3690.2195 6.5736107
|
||||
8400 20695.239 241.02378 0 3690.2302 -14.592221
|
||||
8450 21793.857 57.609525 0 3689.9191 -11.509747
|
||||
8500 21271.088 144.43102 0 3689.6124 -0.091587085
|
||||
8550 20064.337 345.21754 0 3689.2737 9.5058471
|
||||
8600 20282.86 308.2307 0 3688.7074 2.265529
|
||||
8650 21223.055 151.24306 0 3688.419 1.7296834
|
||||
8700 18875.342 542.42055 0 3688.3108 6.367148
|
||||
8750 20922.65 201.55122 0 3688.6595 3.4208578
|
||||
8800 21406.54 120.8539 0 3688.6106 1.8253729
|
||||
8850 19868.524 377.05623 0 3688.477 16.327796
|
||||
8900 20025.322 348.94892 0 3686.5025 17.063406
|
||||
8950 21224.374 151.3567 0 3688.7524 -0.11028753
|
||||
9000 21318.309 135.862 0 3688.9135 -0.50826819
|
||||
9050 17538.618 768.00136 0 3691.1043 37.978645
|
||||
9100 21247.861 147.84641 0 3689.1566 -6.7773259
|
||||
9150 18455.677 613.08767 0 3689.0339 -3.4844751
|
||||
9200 19486.859 441.03829 0 3688.8482 -18.602827
|
||||
9250 21774.926 59.710446 0 3688.8648 -13.379919
|
||||
9300 17628.877 750.72321 0 3688.8694 27.797974
|
||||
9350 19827.334 383.85708 0 3688.4128 6.5459021
|
||||
9400 20020.126 351.61742 0 3688.3051 -14.332562
|
||||
9450 21596.338 88.904175 0 3688.2939 1.5779716
|
||||
9500 18981.418 524.60141 0 3688.1711 5.4352409
|
||||
9550 18652.616 579.05144 0 3687.8208 25.600729
|
||||
9600 21198.037 155.23097 0 3688.2371 -3.3586596
|
||||
9650 19958.317 361.32544 0 3687.7115 4.2910178
|
||||
9700 19129.101 499.5993 0 3687.7828 13.267102
|
||||
9750 21913.967 35.689587 0 3688.0174 -7.3222905
|
||||
9800 21314.694 135.43794 0 3687.8869 -9.5613518
|
||||
9850 20899.743 204.82802 0 3688.1185 -2.6321428
|
||||
9900 20288.244 306.5013 0 3687.8753 3.6196618
|
||||
9950 19271.015 475.88527 0 3687.7211 -1.8196764
|
||||
10000 21122.24 167.82714 0 3688.2005 -3.8464842
|
||||
Loop time of 3.6648 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 23575.670 tau/day, 2728.665 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.15599 | 0.15599 | 0.15599 | 0.0 | 4.26
|
||||
Neigh | 0.099093 | 0.099093 | 0.099093 | 0.0 | 2.70
|
||||
Comm | 0.0088665 | 0.0088665 | 0.0088665 | 0.0 | 0.24
|
||||
Output | 0.0016377 | 0.0016377 | 0.0016377 | 0.0 | 0.04
|
||||
Modify | 3.392 | 3.392 | 3.392 | 0.0 | 92.56
|
||||
Other | | 0.007194 | | | 0.20
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 95 ave 95 max 95 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 744 ave 744 max 744 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 744
|
||||
Ave neighs/atom = 9.18519
|
||||
Neighbor list builds = 992
|
||||
Dangerous builds = 941
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -1,332 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 18 18 18
|
||||
Memory usage per processor = 2.94053 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384276
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184718
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.8669916
|
||||
1200 21815.003 45.317417 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064076
|
||||
1300 20780.781 217.36504 0 3680.8286 6.0538619
|
||||
1350 20558.972 254.3648 0 3680.8601 -3.6773987
|
||||
1400 21485.029 99.812949 0 3680.6511 -16.185471
|
||||
1450 21771.108 52.15959 0 3680.6775 -2.4756681
|
||||
1500 21520.948 93.503949 0 3680.3286 2.1023578
|
||||
1550 21351.418 121.6814 0 3680.2511 5.5159978
|
||||
1600 20778.805 216.92171 0 3680.0559 15.089182
|
||||
1650 21477.639 100.2182 0 3679.8247 -1.1045944
|
||||
1700 18501.343 596.47853 0 3680.0357 -15.67963
|
||||
1750 18563.643 587.34767 0 3681.2882 33.532167
|
||||
1800 19110.19 494.82264 0 3679.8543 18.024034
|
||||
1850 21364.196 119.23454 0 3679.9339 2.5291491
|
||||
1900 20146.643 322.14595 0 3679.9197 5.731152
|
||||
1950 20692.67 231.25357 0 3680.0319 4.2977641
|
||||
2000 20943.904 189.11223 0 3679.763 -22.645645
|
||||
2050 19668.152 401.81407 0 3679.8394 3.6255896
|
||||
2100 20280.572 299.73976 0 3679.8351 7.4809355
|
||||
2150 19182.121 483.47905 0 3680.4992 22.615309
|
||||
2200 21299.76 130.77281 0 3680.7327 4.7114154
|
||||
2250 20487.784 266.4995 0 3681.1302 -8.6406776
|
||||
2300 18655.125 571.91487 0 3681.1023 -5.2671669
|
||||
2350 21512.614 95.766913 0 3681.2025 -9.3523428
|
||||
2400 21467.773 103.31519 0 3681.2773 -29.600307
|
||||
2450 20096.937 332.80159 0 3682.2911 35.890912
|
||||
2500 20761.446 222.16118 0 3682.4022 -12.528127
|
||||
2550 20409.6 280.67234 0 3682.2723 -22.277373
|
||||
2600 21469.964 103.95529 0 3682.2826 -10.038267
|
||||
2650 20708.138 231.00516 0 3682.3615 5.3659502
|
||||
2700 18584.743 585.07862 0 3682.5357 21.785261
|
||||
2750 20503.019 264.91491 0 3682.0847 -4.5583917
|
||||
2800 20584.075 251.44664 0 3682.1258 -6.5084595
|
||||
2850 17277.076 802.33356 0 3681.8462 15.519513
|
||||
2900 19392.956 449.92915 0 3682.0885 -4.3829957
|
||||
2950 18371.786 620.29835 0 3682.2626 7.2117592
|
||||
3000 20412.015 280.25302 0 3682.2555 0.32492606
|
||||
3050 20858.248 205.65269 0 3682.0273 4.5055715
|
||||
3100 21561.094 88.438447 0 3681.9541 -3.7523733
|
||||
3150 15471.278 1103.4497 0 3681.9961 -14.576367
|
||||
3200 15386.973 1117.8815 0 3682.377 15.051163
|
||||
3250 19741.037 392.04755 0 3682.2204 -2.6610995
|
||||
3300 20870.191 203.58229 0 3681.9475 -4.7795545
|
||||
3350 16648.228 907.66571 0 3682.3704 -8.9242511
|
||||
3400 20104.016 331.58603 0 3682.2554 6.4783858
|
||||
3450 21421.316 112.28228 0 3682.5015 -8.3484987
|
||||
3500 19284.533 467.80739 0 3681.8962 -12.835452
|
||||
3550 20160.125 322.4476 0 3682.4684 1.6574827
|
||||
3600 16682.415 902.73752 0 3683.14 22.383296
|
||||
3650 16762.19 890.14636 0 3683.8446 16.119412
|
||||
3700 17858.568 707.37212 0 3683.8 -1.6582504
|
||||
3750 20029.881 345.15986 0 3683.4733 -3.1415889
|
||||
3800 20734 227.99158 0 3683.6582 -7.9580418
|
||||
3850 20741.089 226.39408 0 3683.2423 8.3055765
|
||||
3900 18671.251 571.42296 0 3683.2981 -3.7468858
|
||||
3950 19547.209 423.14256 0 3681.0108 5.8312279
|
||||
4000 19739.799 393.58799 0 3683.5544 18.604884
|
||||
4050 20014.121 347.8176 0 3683.5044 9.93387
|
||||
4100 20503.654 266.08691 0 3683.3626 8.1304118
|
||||
4150 18309.702 632.29807 0 3683.9151 -0.0021480359
|
||||
4200 20509.423 265.60353 0 3683.8408 -2.1658857
|
||||
4250 21805.541 50.325935 0 3684.5828 1.082842
|
||||
4300 21420.551 114.90431 0 3684.9962 -1.7985998
|
||||
4350 20256.928 308.74187 0 3684.8966 -11.669472
|
||||
4400 21633.488 79.629274 0 3685.2106 -0.96131785
|
||||
4450 20793.327 219.66955 0 3685.2241 1.3752349
|
||||
4500 18719.484 564.86754 0 3684.7816 2.6308699
|
||||
4550 20966.335 190.68308 0 3685.0722 -18.587627
|
||||
4600 19428.962 446.59618 0 3684.7565 -4.4051672
|
||||
4650 18408.956 616.85009 0 3685.0095 2.777272
|
||||
4700 19215.779 482.57562 0 3685.2054 19.441016
|
||||
4750 20155.927 326.13401 0 3685.4553 6.1734993
|
||||
4800 20918.085 199.31832 0 3685.6659 3.4407437
|
||||
4850 20236.958 312.07276 0 3684.899 3.2612893
|
||||
4900 21419.89 115.36879 0 3685.3505 -4.675951
|
||||
4950 19707.901 401.14828 0 3685.7985 -10.730734
|
||||
5000 19407.201 450.64394 0 3685.1775 17.518981
|
||||
5050 21527.598 97.655186 0 3685.5882 -9.2294707
|
||||
5100 21581.933 88.595517 0 3685.5843 -20.669485
|
||||
5150 21161.214 158.48503 0 3685.3541 -2.7587502
|
||||
5200 21166.679 157.24762 0 3685.0275 -18.180044
|
||||
5250 20909.576 200.23507 0 3685.1644 -16.617303
|
||||
5300 21911.746 33.236563 0 3685.1942 -5.8313967
|
||||
5350 20857.303 208.87453 0 3685.0916 12.176312
|
||||
5400 20958.96 191.96694 0 3685.1269 3.6116429
|
||||
5450 20433.179 279.61178 0 3685.1415 13.324529
|
||||
5500 19604.675 416.88499 0 3684.3308 21.536484
|
||||
5550 18171.145 655.92915 0 3684.4534 -9.2269804
|
||||
5600 19799.907 385.12116 0 3685.1056 22.202165
|
||||
5650 19711.882 399.30581 0 3684.6194 15.93063
|
||||
5700 17908.833 699.52405 0 3684.3295 0.35530356
|
||||
5750 18606.518 583.538 0 3684.6243 -4.4540843
|
||||
5800 21814.053 48.974627 0 3684.6501 -1.5206358
|
||||
5850 18029.107 679.9357 0 3684.7868 12.137677
|
||||
5900 21090.739 169.64502 0 3684.7682 -1.5051545
|
||||
5950 21086.26 170.29075 0 3684.6674 -2.8164474
|
||||
6000 21285.771 136.95608 0 3684.5846 -26.582739
|
||||
6050 21203.994 150.87822 0 3684.8772 -2.6617226
|
||||
6100 21481.553 104.57796 0 3684.8368 -16.524974
|
||||
6150 20354.4 292.57675 0 3684.9767 2.7960207
|
||||
6200 21326.591 130.75243 0 3685.1843 -1.5929194
|
||||
6250 21505.087 101.07817 0 3685.2593 -3.7821931
|
||||
6300 21296.273 135.6593 0 3685.0382 -0.55635908
|
||||
6350 21295.389 135.86485 0 3685.0964 5.6614093
|
||||
6400 16552.242 926.02655 0 3684.7336 14.177218
|
||||
6450 20148.951 327.1151 0 3685.2736 7.4561085
|
||||
6500 20962.151 191.79415 0 3685.486 -4.5436711
|
||||
6550 21710.328 67.433972 0 3685.8219 -5.7678572
|
||||
6600 20698.571 234.79099 0 3684.5528 -2.1984068
|
||||
6650 17892.287 704.05484 0 3686.1026 11.525836
|
||||
6700 21272.999 141.26589 0 3686.7657 0.44088069
|
||||
6750 19558.993 426.46448 0 3686.2966 -16.907401
|
||||
6800 20350.247 295.23951 0 3686.9474 1.1284348
|
||||
6850 18665.05 573.5326 0 3684.3742 17.088712
|
||||
6900 19769.199 392.1551 0 3687.0216 6.7562425
|
||||
6950 19439.159 446.99138 0 3686.8512 -6.0105763
|
||||
7000 19379.907 456.53471 0 3686.5192 -9.0505095
|
||||
7050 19983.754 356.02523 0 3686.651 -5.6274314
|
||||
7100 19867.737 375.47627 0 3686.7658 17.315482
|
||||
7150 19258.794 477.47344 0 3687.2724 14.316676
|
||||
7200 21282.428 139.96051 0 3687.0318 -0.77043459
|
||||
7250 19828.603 381.98919 0 3686.7564 6.5142869
|
||||
7300 20574.582 257.8245 0 3686.9215 -3.6547118
|
||||
7350 21613.467 84.771568 0 3687.0161 -7.5188826
|
||||
7400 21817.009 50.844944 0 3687.0131 -14.888864
|
||||
7450 14937.538 1197.4257 0 3687.0154 1.7540499
|
||||
7500 18326.914 632.40374 0 3686.8894 8.3397357
|
||||
7550 13611.007 1418.4727 0 3686.9739 -19.379482
|
||||
7600 19173.985 491.9482 0 3687.6123 17.229001
|
||||
7650 16911.504 867.33649 0 3685.9204 -21.042834
|
||||
7700 21752.116 61.143705 0 3686.4963 -10.344487
|
||||
7750 20208.337 318.26355 0 3686.3197 13.385814
|
||||
7800 21649.909 77.950987 0 3686.2692 -1.7911084
|
||||
7850 20139.64 329.50319 0 3686.1098 -5.5805093
|
||||
7900 21355.026 126.7642 0 3685.9352 -7.7062172
|
||||
7950 21336.178 129.88925 0 3685.9188 -2.059298
|
||||
8000 21047.596 177.71546 0 3685.6482 0.37963466
|
||||
8050 19217.351 482.62331 0 3685.5152 6.5582595
|
||||
8100 20499.057 268.7173 0 3685.2268 -1.1959737
|
||||
8150 21494.301 102.83829 0 3685.2219 -1.6427647
|
||||
8200 20074.928 339.19817 0 3685.0195 6.285123
|
||||
8250 17335.157 793.47566 0 3682.6685 22.877381
|
||||
8300 17340.544 794.62619 0 3684.7168 3.9147755
|
||||
8350 20529.345 262.51162 0 3684.0691 4.031768
|
||||
8400 18884.747 537.47827 0 3684.9361 22.853404
|
||||
8450 20341.86 293.10484 0 3683.4148 0.33856656
|
||||
8500 19300.282 467.58127 0 3684.2949 12.35507
|
||||
8550 21631.936 78.254534 0 3683.5772 -10.992959
|
||||
8600 20204.913 316.83233 0 3684.3178 20.74228
|
||||
8650 21018.189 181.32054 0 3684.352 1.8412068
|
||||
8700 20161.304 323.97907 0 3684.1964 -2.646629
|
||||
8750 19081.79 504.00155 0 3684.2998 -10.088053
|
||||
8800 20834.489 211.76247 0 3684.1773 14.896336
|
||||
8850 20929.355 196.18335 0 3684.4092 -1.2602398
|
||||
8900 21491.074 102.47788 0 3684.3235 -1.4696758
|
||||
8950 20474.735 271.69461 0 3684.1504 -6.9489258
|
||||
9000 21128.641 162.40732 0 3683.8474 -7.7928168
|
||||
9050 18421.801 614.46442 0 3684.7646 24.40313
|
||||
9100 19301.292 466.98873 0 3683.8707 4.4687046
|
||||
9150 21575.705 88.213763 0 3684.1646 -0.94696984
|
||||
9200 20004.776 350.05448 0 3684.1838 -7.3466605
|
||||
9250 21384.079 120.14472 0 3684.1578 -8.3773844
|
||||
9300 21980.599 20.702393 0 3684.1356 -12.666293
|
||||
9350 21686.606 69.517984 0 3683.9524 -8.8366533
|
||||
9400 20732.704 228.46247 0 3683.9131 -6.4080307
|
||||
9450 19798.859 384.34696 0 3684.1568 7.6198484
|
||||
9500 20270.695 305.22664 0 3683.6758 1.5862486
|
||||
9550 16496.156 935.28481 0 3684.6441 15.001468
|
||||
9600 20642.429 241.08853 0 3681.4934 -9.2159382
|
||||
9650 21292.587 135.4474 0 3684.2119 -0.54770976
|
||||
9700 18888.158 536.60518 0 3684.6315 5.3236926
|
||||
9750 18750.018 559.35922 0 3684.3623 -9.9424949
|
||||
9800 20544.772 259.71076 0 3683.8394 8.732202
|
||||
9850 16698.125 901.90076 0 3684.9216 9.9553329
|
||||
9900 21450.963 109.58687 0 3684.7474 -4.8001999
|
||||
9950 20664.461 240.66995 0 3684.7468 -3.4840781
|
||||
10000 18951.367 526.45428 0 3685.0155 21.512727
|
||||
Loop time of 3.89095 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 22205.346 tau/day, 2570.063 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.012426 | 0.039516 | 0.089301 | 15.3 | 1.02
|
||||
Neigh | 0.012618 | 0.027118 | 0.055113 | 10.4 | 0.70
|
||||
Comm | 0.16629 | 0.21469 | 0.26329 | 8.2 | 5.52
|
||||
Output | 0.0051188 | 0.0053029 | 0.0055087 | 0.2 | 0.14
|
||||
Modify | 3.5241 | 3.5783 | 3.6729 | 3.0 | 91.96
|
||||
Other | | 0.02605 | | | 0.67
|
||||
|
||||
Nlocal: 20.25 ave 81 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 46.25 ave 95 max 14 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 249.25 ave 997 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 997
|
||||
Ave neighs/atom = 12.3086
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 943
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -1,336 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:352)
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:352)
|
||||
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 18 18 18
|
||||
Memory usage per processor = 3.53031 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12167.633 1505.5478 0 3758.8133 35.125973
|
||||
100 17556.978 512.66277 0 3763.9549 11.137534
|
||||
150 19579.586 138.04942 0 3763.8987 -29.953971
|
||||
200 19757.51 105.30542 0 3764.1036 -0.030645317
|
||||
250 18218.374 390.10747 0 3763.8804 13.711001
|
||||
300 19383.039 174.40688 0 3763.8586 5.7240693
|
||||
350 20125.986 36.972611 0 3764.0071 1.9559205
|
||||
400 18888.816 266.10975 0 3764.0386 9.6362168
|
||||
450 19307.656 188.2511 0 3763.743 1.9326206
|
||||
500 16331.197 738.56392 0 3762.8597 9.1715579
|
||||
550 19318.722 186.16172 0 3763.7027 3.0115336
|
||||
600 19455.268 161.20621 0 3764.0336 0.55208034
|
||||
650 18487.011 340.03216 0 3763.5528 -8.0359122
|
||||
700 17321.201 556.32471 0 3763.9545 -13.631751
|
||||
750 18979.187 249.04389 0 3763.7082 -2.6072455
|
||||
800 19342.456 181.85552 0 3763.7918 8.1918726
|
||||
850 19070.641 232.19342 0 3763.7936 7.3148472
|
||||
900 19478.873 156.65987 0 3763.8586 2.4284987
|
||||
950 19912.415 76.437437 0 3763.9216 -1.4667227
|
||||
1000 16003.749 802.39753 0 3766.0548 46.642188
|
||||
1050 19859.583 86.64176 0 3764.3424 -2.1961943
|
||||
1100 19229.575 203.61488 0 3764.6473 -10.632365
|
||||
1150 18821.6 279.15861 0 3764.64 -0.89495035
|
||||
1200 19392.695 173.59744 0 3764.8373 1.8508753
|
||||
1250 16459.624 717.32104 0 3765.3995 33.478127
|
||||
1300 19343.863 182.59043 0 3764.7874 0.75890736
|
||||
1350 20019.643 57.503573 0 3764.8448 0.31444671
|
||||
1400 18549.582 329.31436 0 3764.4221 10.738303
|
||||
1450 15163.926 957.47585 0 3765.6103 -17.923459
|
||||
1500 19223.688 204.15175 0 3764.0939 -1.6134531
|
||||
1550 18147.996 404.12677 0 3764.8668 8.4194779
|
||||
1600 18615.043 317.42467 0 3764.6548 -2.3288934
|
||||
1650 20120.654 38.887913 0 3764.935 -8.7620277
|
||||
1700 19450.907 162.98272 0 3765.0025 2.3254731
|
||||
1750 19374.632 177.37966 0 3765.2744 8.9328774
|
||||
1800 19424.404 167.93966 0 3765.0514 0.081230261
|
||||
1850 17936.249 442.84231 0 3764.3699 6.6010636
|
||||
1900 19982.595 64.406198 0 3764.8868 -2.9529813
|
||||
1950 16215.852 761.91287 0 3764.8485 13.994708
|
||||
2000 18584.422 322.12049 0 3763.68 7.1654003
|
||||
2050 20107.965 41.025754 0 3764.723 -0.3109069
|
||||
2100 20002.333 60.593017 0 3764.7288 -6.7919784
|
||||
2150 16949.762 626.59623 0 3765.441 3.508941
|
||||
2200 20010.953 58.808279 0 3764.5403 -10.862172
|
||||
2250 18982.73 247.00892 0 3762.3292 -0.53807815
|
||||
2300 18401.298 354.87973 0 3762.5274 1.0920554
|
||||
2350 19390.524 172.9415 0 3763.7793 -3.3524932
|
||||
2400 16080.801 786.38838 0 3764.3146 -16.200514
|
||||
2450 18870.412 268.74976 0 3763.2705 11.197736
|
||||
2500 19688.29 117.58223 0 3763.5618 4.382644
|
||||
2550 18870.825 268.78678 0 3763.384 -5.6623656
|
||||
2600 17019.35 611.70808 0 3763.4395 6.3109641
|
||||
2650 18753.285 291.0596 0 3763.8902 2.4120296
|
||||
2700 19742.456 107.20901 0 3763.2193 -0.33061303
|
||||
2750 19522.438 148.16759 0 3763.4339 -1.6254851
|
||||
2800 18304.801 372.55152 0 3762.3295 22.6368
|
||||
2850 18465.36 343.48495 0 3762.9961 4.4169272
|
||||
2900 20151.999 31.372926 0 3763.2245 1.2013699
|
||||
2950 15498.143 892.80071 0 3762.8272 13.263724
|
||||
3000 18728.301 294.65113 0 3762.855 8.1897838
|
||||
3050 18538.466 330.25223 0 3763.3015 8.5865739
|
||||
3100 19081.409 229.5907 0 3763.1849 -4.8573813
|
||||
3150 18498.802 337.11548 0 3762.8195 1.0555321
|
||||
3200 19925.897 73.358029 0 3763.339 -7.7325108
|
||||
3250 19780.108 100.23785 0 3763.2209 -5.5974972
|
||||
3300 19221.043 203.82387 0 3763.2763 4.2703251
|
||||
3350 19025.292 240.11329 0 3763.3156 5.7708328
|
||||
3400 18153.696 401.52086 0 3763.3164 21.076943
|
||||
3450 18611.375 316.50396 0 3763.0548 -3.5484945
|
||||
3500 19931.319 71.969274 0 3762.9543 1.8764978
|
||||
3550 19747.562 106.05439 0 3763.0103 -2.5506186
|
||||
3600 18491.39 338.4134 0 3762.7449 -4.0527808
|
||||
3650 19757.998 104.19207 0 3763.0806 1.4865598
|
||||
3700 20108.003 39.345514 0 3763.0498 0.062827129
|
||||
3750 19222.505 203.28065 0 3763.0039 0.33719277
|
||||
3800 19286.383 191.08831 0 3762.6406 -0.1826802
|
||||
3850 19450.083 161.09138 0 3762.9587 -0.2708263
|
||||
3900 18002.304 429.25655 0 3763.0166 -4.6832439
|
||||
3950 17186.829 582.26502 0 3765.0111 55.816834
|
||||
4000 16826.434 645.84974 0 3761.856 19.675962
|
||||
4050 19227.526 202.18151 0 3762.8344 -0.2596098
|
||||
4100 19908.792 76.084531 0 3762.8978 -2.796813
|
||||
4150 17821.329 462.63065 0 3762.8768 13.069155
|
||||
4200 19917.133 74.574998 0 3762.9329 -6.4181155
|
||||
4250 19012.618 241.96787 0 3762.823 4.0847974
|
||||
4300 19077.34 229.98133 0 3762.8221 4.324323
|
||||
4350 19361.128 177.47406 0 3762.8681 -7.377974
|
||||
4400 18565.044 324.95107 0 3762.9223 2.5229032
|
||||
4450 19352.406 178.98756 0 3762.7665 0.10862717
|
||||
4500 18482.218 340.15496 0 3762.788 12.518301
|
||||
4550 18359.732 362.83749 0 3762.7879 3.7500902
|
||||
4600 19623.618 128.71624 0 3762.7196 -1.1328521
|
||||
4650 17565.707 509.99904 0 3762.9078 1.7135935
|
||||
4700 19876.052 81.892814 0 3762.6431 0.32476108
|
||||
4750 19022.676 239.92262 0 3762.6403 -0.24613022
|
||||
4800 18862.685 269.24248 0 3762.3324 6.2733979
|
||||
4850 19899.174 77.426145 0 3762.4584 0.42535238
|
||||
4900 18250.865 382.72867 0 3762.5185 23.308462
|
||||
4950 18895.847 263.22651 0 3762.4575 8.0634675
|
||||
5000 19096.705 225.69358 0 3762.1204 3.6816481
|
||||
5050 16546.294 698.91312 0 3763.0416 17.453618
|
||||
5100 19501.208 151.20999 0 3762.5449 -1.1231291
|
||||
5150 19479.879 155.00669 0 3762.3917 -3.983378
|
||||
5200 17397.818 541.23039 0 3763.0485 6.1109992
|
||||
5250 18564.869 324.10557 0 3762.0442 9.2244762
|
||||
5300 16271.663 747.52374 0 3760.7947 -6.5256602
|
||||
5350 19831.418 89.851887 0 3762.3367 -2.3453958
|
||||
5400 18723.697 294.67435 0 3762.0256 4.6822081
|
||||
5450 19547.28 142.21934 0 3762.086 -5.5243408
|
||||
5500 19415.447 166.68729 0 3762.1404 -9.5658991
|
||||
5550 18492.721 337.54773 0 3762.1256 6.5184903
|
||||
5600 19391.389 171.14375 0 3762.1416 -0.53835361
|
||||
5650 18503.465 334.62751 0 3761.1951 4.6580363
|
||||
5700 18153.344 399.91064 0 3761.6409 12.851587
|
||||
5750 18342.297 365.14769 0 3761.8694 2.7148176
|
||||
5800 19583.241 135.64969 0 3762.1758 -1.089608
|
||||
5850 15967.283 804.18382 0 3761.088 11.278762
|
||||
5900 19040.271 235.35509 0 3761.3312 5.1352158
|
||||
5950 17920.962 443.17951 0 3761.8762 4.9621366
|
||||
6000 19100.92 224.3946 0 3761.602 -9.537589
|
||||
6050 17982.119 432.3251 0 3762.3472 -2.851617
|
||||
6100 16233.096 755.46191 0 3761.5908 25.113316
|
||||
6150 18316.543 370.01118 0 3761.9635 -1.7445703
|
||||
6200 18483.464 339.13282 0 3761.9966 -2.0857447
|
||||
6250 18609.406 315.56032 0 3761.7467 -12.289208
|
||||
6300 17167.919 582.68212 0 3761.9264 -3.8263397
|
||||
6350 17870.329 452.58116 0 3761.9013 -3.3843134
|
||||
6400 19309.717 186.11786 0 3761.9913 -4.9462739
|
||||
6450 17964.073 435.39924 0 3762.0794 12.272972
|
||||
6500 18772.847 285.61959 0 3762.0727 6.7928648
|
||||
6550 18915.116 259.41365 0 3762.213 -4.1449761
|
||||
6600 19446.628 161.18763 0 3762.415 -2.1906581
|
||||
6650 16348.787 734.99282 0 3762.546 -9.9624546
|
||||
6700 19066.684 231.43863 0 3762.3061 -5.362833
|
||||
6750 14890.323 1004.547 0 3762.0143 37.373013
|
||||
6800 18235.19 385.253 0 3762.1401 0.21012662
|
||||
6850 16447.997 716.11276 0 3762.0382 -9.2095411
|
||||
6900 18343.362 364.81902 0 3761.7379 10.417932
|
||||
6950 16014.084 797.13348 0 3762.7046 6.7906777
|
||||
7000 19120.393 221.29236 0 3762.1059 -1.3461375
|
||||
7050 18055.409 418.30136 0 3761.8957 1.5772317
|
||||
7100 18407.231 353.41868 0 3762.1652 0.61071769
|
||||
7150 18728.136 293.64021 0 3761.8136 5.1649654
|
||||
7200 17706.628 483.07628 0 3762.0815 18.000708
|
||||
7250 19349.505 178.89673 0 3762.1385 2.540201
|
||||
7300 20016.293 55.389159 0 3762.1101 -1.5793163
|
||||
7350 19398.573 169.86661 0 3762.1949 -5.060123
|
||||
7400 19466.526 157.37407 0 3762.2862 1.7158273
|
||||
7450 18440.348 347.09196 0 3761.9712 12.781963
|
||||
7500 19989.907 60.555934 0 3762.3906 -1.5033319
|
||||
7550 19667.28 120.27403 0 3762.363 -3.3502366
|
||||
7600 18497.707 336.15863 0 3761.66 1.7887539
|
||||
7650 17901.957 447.17282 0 3762.3501 0.016725252
|
||||
7700 19758.725 103.3129 0 3762.3361 -23.534448
|
||||
7750 19443.957 161.6532 0 3762.386 -10.323924
|
||||
7800 19776.178 100.1773 0 3762.4324 6.0854422
|
||||
7850 19242.512 198.86705 0 3762.2952 5.2823659
|
||||
7900 19499.929 151.30366 0 3762.4017 12.299911
|
||||
7950 19630.317 127.19541 0 3762.4393 8.0799632
|
||||
8000 19872.384 82.421129 0 3762.4923 2.2126691
|
||||
8050 17747.038 476.27982 0 3762.7683 -7.7042786
|
||||
8100 18832.654 274.78106 0 3762.3095 13.882157
|
||||
8150 19949.814 68.09711 0 3762.5072 -0.54410896
|
||||
8200 17555.866 511.02517 0 3762.1115 6.2471175
|
||||
8250 17800.1 465.9992 0 3762.314 13.583485
|
||||
8300 19755.224 103.89732 0 3762.2721 -1.487243
|
||||
8350 17583.61 506.17539 0 3762.3995 -9.7819128
|
||||
8400 18529.003 330.75623 0 3762.0532 14.731228
|
||||
8450 20155.902 29.797078 0 3762.3716 -8.5711085
|
||||
8500 18047.548 420.54645 0 3762.685 7.3875118
|
||||
8550 19790.794 97.493375 0 3762.4553 -3.3427911
|
||||
8600 19997.902 59.172074 0 3762.4874 3.3479688
|
||||
8650 19987.319 61.148363 0 3762.5037 -1.889232
|
||||
8700 19363.91 176.41833 0 3762.3276 -9.4291288
|
||||
8750 18712.689 296.3979 0 3761.7107 5.9221369
|
||||
8800 19783.17 98.860518 0 3762.4105 -3.5262066
|
||||
8850 18796.049 281.60057 0 3762.3504 -8.2913002
|
||||
8900 16738.277 662.62261 0 3762.3035 8.5838631
|
||||
8950 17869.613 452.25006 0 3761.4377 11.561101
|
||||
9000 18682.512 302.27997 0 3762.0043 3.8878724
|
||||
9050 17513.759 518.50265 0 3761.7914 23.05778
|
||||
9100 17500.686 521.57944 0 3762.4473 -2.8435751
|
||||
9150 19645.683 124.43597 0 3762.5254 -3.0193092
|
||||
9200 18898.897 262.76552 0 3762.5612 3.5891701
|
||||
9250 20114.279 37.614866 0 3762.4813 -0.58120871
|
||||
9300 19562.613 139.54073 0 3762.2468 -3.2630158
|
||||
9350 19679.811 118.05865 0 3762.468 -3.4644363
|
||||
9400 19297.384 188.84527 0 3762.4349 0.40498037
|
||||
9450 18267.029 379.52581 0 3762.309 -0.13762867
|
||||
9500 19951.072 67.63844 0 3762.2814 -7.575539
|
||||
9550 19134.562 218.46835 0 3761.9057 -1.9626244
|
||||
9600 19089.093 227.29178 0 3762.3089 -1.94158
|
||||
9650 16964.603 620.71289 0 3762.3061 16.987042
|
||||
9700 18846.881 271.3129 0 3761.4761 3.4458802
|
||||
9750 19309.225 186.0142 0 3761.7966 9.4048627
|
||||
9800 16359.704 733.51007 0 3763.0849 15.870164
|
||||
9850 19958.532 66.203725 0 3762.2282 6.0043645
|
||||
9900 19864.564 83.502384 0 3762.1253 -0.65360617
|
||||
9950 18996.789 244.25101 0 3762.1749 -2.4961826
|
||||
10000 17933.494 441.33587 0 3762.3532 -6.0731708
|
||||
Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 22733.175 tau/day, 2631.155 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97
|
||||
Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00
|
||||
Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29
|
||||
Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04
|
||||
Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51
|
||||
Other | | 0.007383 | | | 0.19
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 71 ave 71 max 71 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 612 ave 612 max 612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 612
|
||||
Ave neighs/atom = 7.55556
|
||||
Neighbor list builds = 989
|
||||
Dangerous builds = 906
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -1,336 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:352)
|
||||
WARNING: More than one fix poems (../fix_poems.cpp:352)
|
||||
WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 18 18 18
|
||||
Memory usage per processor = 3.50303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12167.633 1505.5478 0 3758.8133 35.125973
|
||||
100 17556.978 512.66277 0 3763.9549 11.137534
|
||||
150 19579.586 138.04942 0 3763.8987 -29.953971
|
||||
200 19757.51 105.30542 0 3764.1036 -0.030645317
|
||||
250 18218.374 390.10747 0 3763.8804 13.711001
|
||||
300 19383.039 174.40688 0 3763.8586 5.7240693
|
||||
350 20125.986 36.972611 0 3764.0071 1.9559205
|
||||
400 18888.816 266.10975 0 3764.0386 9.6362168
|
||||
450 19307.656 188.2511 0 3763.743 1.9326206
|
||||
500 16331.197 738.56392 0 3762.8597 9.1715579
|
||||
550 19318.722 186.16172 0 3763.7027 3.0115336
|
||||
600 19455.268 161.20621 0 3764.0336 0.55208034
|
||||
650 18487.011 340.03216 0 3763.5528 -8.0359122
|
||||
700 17321.201 556.32471 0 3763.9545 -13.631751
|
||||
750 18979.187 249.04389 0 3763.7082 -2.6072455
|
||||
800 19342.456 181.85552 0 3763.7918 8.1918726
|
||||
850 19070.641 232.19342 0 3763.7936 7.3148472
|
||||
900 19478.873 156.65987 0 3763.8586 2.4284987
|
||||
950 19912.415 76.437437 0 3763.9216 -1.4667227
|
||||
1000 16003.749 802.39753 0 3766.0548 46.642188
|
||||
1050 19859.583 86.64176 0 3764.3424 -2.1961943
|
||||
1100 19229.575 203.61488 0 3764.6473 -10.632365
|
||||
1150 18821.6 279.15861 0 3764.64 -0.89495035
|
||||
1200 19392.695 173.59744 0 3764.8373 1.8508753
|
||||
1250 16459.624 717.32104 0 3765.3995 33.478127
|
||||
1300 19343.863 182.59043 0 3764.7874 0.75890736
|
||||
1350 20019.643 57.503573 0 3764.8448 0.31444671
|
||||
1400 18549.582 329.31436 0 3764.4221 10.738303
|
||||
1450 15163.926 957.47585 0 3765.6103 -17.923459
|
||||
1500 19223.688 204.15176 0 3764.0939 -1.6134529
|
||||
1550 18147.996 404.12677 0 3764.8668 8.4194781
|
||||
1600 18615.043 317.42468 0 3764.6548 -2.3288926
|
||||
1650 20120.654 38.887908 0 3764.935 -8.7620288
|
||||
1700 19450.907 162.98267 0 3765.0025 2.3254739
|
||||
1750 19374.631 177.3797 0 3765.2744 8.9328773
|
||||
1800 19424.404 167.93965 0 3765.0514 0.081228843
|
||||
1850 17936.227 442.84645 0 3764.3699 6.6011251
|
||||
1900 19982.595 64.406244 0 3764.8868 -2.952971
|
||||
1950 16215.818 761.91942 0 3764.8486 13.994877
|
||||
2000 18584.433 322.11846 0 3763.6801 7.1653695
|
||||
2050 20107.965 41.025796 0 3764.723 -0.31089763
|
||||
2100 20002.329 60.593879 0 3764.7288 -6.7919882
|
||||
2150 16949.817 626.58598 0 3765.4409 3.5087505
|
||||
2200 20010.954 58.8082 0 3764.5403 -10.862143
|
||||
2250 18982.732 247.00854 0 3762.3293 -0.53812607
|
||||
2300 18401.276 354.88369 0 3762.5274 1.0921058
|
||||
2350 19390.535 172.93951 0 3763.7793 -3.3524354
|
||||
2400 16080.475 786.44896 0 3764.3146 -16.201558
|
||||
2450 18870.293 268.77171 0 3763.2704 11.199749
|
||||
2500 19688.508 117.54164 0 3763.5617 4.3806994
|
||||
2550 18870.328 268.87896 0 3763.3841 -5.6641099
|
||||
2600 17020.211 611.54841 0 3763.4394 6.3081434
|
||||
2650 18748.838 291.88478 0 3763.8917 2.4175163
|
||||
2700 19743.991 106.92945 0 3763.224 -0.33916964
|
||||
2750 19525.446 147.60906 0 3763.4324 -1.6251174
|
||||
2800 18257.411 381.40184 0 3762.4038 23.39495
|
||||
2850 18496.796 337.65425 0 3762.9868 4.3657735
|
||||
2900 20163.418 29.253902 0 3763.2203 1.4431917
|
||||
2950 16823.317 646.69817 0 3762.1273 4.9041552
|
||||
3000 19223.007 203.2529 0 3763.069 4.0414458
|
||||
3050 17391.02 542.93746 0 3763.4968 15.139863
|
||||
3100 19205.6 206.57791 0 3763.1705 4.8519241
|
||||
3150 19835.659 90.247763 0 3763.5179 -14.900053
|
||||
3200 18962.776 251.5838 0 3763.2089 -13.706561
|
||||
3250 19418.837 167.29058 0 3763.3716 -2.0866468
|
||||
3300 18628.291 313.69067 0 3763.3742 5.9919715
|
||||
3350 17465.974 529.14439 0 3763.5841 14.122593
|
||||
3400 18488.661 339.6186 0 3763.4448 21.526798
|
||||
3450 19163.152 214.26098 0 3762.9928 4.1888096
|
||||
3500 18000.27 429.81789 0 3763.2011 5.4734485
|
||||
3550 19582.423 136.71887 0 3763.0935 -2.5335675
|
||||
3600 19634.325 127.2219 0 3763.208 -1.9728322
|
||||
3650 19428.114 165.40707 0 3763.2059 -2.3318779
|
||||
3700 19861.116 85.356944 0 3763.3414 -3.9097609
|
||||
3750 19337.239 182.43992 0 3763.4102 -3.3559651
|
||||
3800 19493.146 153.40349 0 3763.2453 -0.71089657
|
||||
3850 18607.616 317.74889 0 3763.6037 3.475832
|
||||
3900 19719.59 111.5553 0 3763.3313 0.58876668
|
||||
3950 19756.661 104.5522 0 3763.1931 3.7526698
|
||||
4000 17904.708 447.1673 0 3762.854 12.270654
|
||||
4050 19588.087 135.80435 0 3763.2279 0.94578945
|
||||
4100 19065.901 232.38235 0 3763.1048 -2.7495195
|
||||
4150 18775.075 286.2257 0 3763.0915 -3.7039858
|
||||
4200 18800.725 281.46601 0 3763.0817 0.15619543
|
||||
4250 19732.687 108.90618 0 3763.1075 3.0865861
|
||||
4300 18278.151 377.63653 0 3762.4794 1.5768601
|
||||
4350 17915.757 445.4804 0 3763.2133 -3.7040484
|
||||
4400 15987.794 802.41575 0 3763.1183 22.252078
|
||||
4450 19302.37 188.69495 0 3763.2079 0.91081327
|
||||
4500 20039.32 52.304099 0 3763.2893 -2.0828905
|
||||
4550 19535.953 145.4374 0 3763.2064 -3.3804255
|
||||
4600 19700.723 114.79823 0 3763.0803 -1.1761163
|
||||
4650 17804.641 465.85788 0 3763.0136 7.5947192
|
||||
4700 19913.881 75.240289 0 3762.996 -2.1100557
|
||||
4750 19982.484 62.535995 0 3762.996 -4.5821237
|
||||
4800 17400.76 540.21707 0 3762.58 -5.8418778
|
||||
4850 19199.88 206.90989 0 3762.4433 3.4536341
|
||||
4900 19173.92 212.11327 0 3762.8392 5.0387071
|
||||
4950 19236.635 200.57537 0 3762.9152 -1.4932783
|
||||
5000 19077.616 230.04967 0 3762.9415 4.3742655
|
||||
5050 19893.763 78.909747 0 3762.94 -1.5796711
|
||||
5100 18884.746 265.68301 0 3762.8583 2.2767949
|
||||
5150 17417.096 537.54036 0 3762.9286 -2.8632555
|
||||
5200 18247.844 383.60092 0 3762.8312 10.384179
|
||||
5250 19494.107 152.60532 0 3762.6251 -4.7617287
|
||||
5300 18739.781 292.46206 0 3762.7919 23.210048
|
||||
5350 19310.938 186.62363 0 3762.7232 14.895327
|
||||
5400 19540.39 144.14287 0 3762.7336 6.094624
|
||||
5450 20074.459 45.247888 0 3762.7403 -2.0871835
|
||||
5500 19986.377 61.668045 0 3762.849 -2.4551918
|
||||
5550 19038.904 237.07578 0 3762.7987 5.4250813
|
||||
5600 19439.124 163.1438 0 3762.9816 4.1291468
|
||||
5650 19480.321 155.58325 0 3763.0501 -3.5308058
|
||||
5700 19869.291 83.651379 0 3763.1497 -7.8661592
|
||||
5750 19991.447 61.068554 0 3763.1884 -6.8473586
|
||||
5800 19454.072 160.36805 0 3762.9739 1.527662
|
||||
5850 17994.409 430.95597 0 3763.2539 -5.6078082
|
||||
5900 19209.794 205.74997 0 3763.1193 8.4113055
|
||||
5950 19046.427 236.06321 0 3763.1793 10.463356
|
||||
6000 19409.899 168.95271 0 3763.3785 2.542067
|
||||
6050 18068.174 417.35443 0 3763.3125 10.498199
|
||||
6100 19549.253 143.21885 0 3763.4509 2.3075797
|
||||
6150 18464.719 344.0303 0 3763.4228 0.46469762
|
||||
6200 19811.205 94.62725 0 3763.3689 1.2382763
|
||||
6250 18715.36 297.26445 0 3763.0718 -3.4541762
|
||||
6300 17115.664 594.09913 0 3763.6666 4.2065564
|
||||
6350 18155.927 400.71764 0 3762.9264 1.1521258
|
||||
6400 19873.093 83.169067 0 3763.3716 0.16383592
|
||||
6450 19991.88 61.13218 0 3763.3321 -1.3008128
|
||||
6500 19434.416 164.40698 0 3763.3728 -13.593422
|
||||
6550 19855.253 86.645329 0 3763.544 -0.85704037
|
||||
6600 19251.141 198.41152 0 3763.4376 4.3027745
|
||||
6650 19741.815 107.69047 0 3763.582 4.994835
|
||||
6700 19633.466 127.69333 0 3763.5203 6.3677145
|
||||
6750 16231.353 757.83705 0 3763.6431 -1.5978692
|
||||
6800 18863.396 270.1114 0 3763.3329 -11.915909
|
||||
6850 19644.779 125.29421 0 3763.2163 -1.151217
|
||||
6900 18883.642 266.06889 0 3763.0397 -4.3950749
|
||||
6950 19042.364 236.54144 0 3762.9052 5.5718878
|
||||
7000 18351.868 364.38028 0 3762.8743 7.8958273
|
||||
7050 19981.031 62.840667 0 3763.0316 -5.8572298
|
||||
7100 19796.372 97.073665 0 3763.0685 -3.5178361
|
||||
7150 19805.385 95.235221 0 3762.899 -2.5481726
|
||||
7200 18722.055 295.86113 0 3762.9084 13.826356
|
||||
7250 19537.304 144.54234 0 3762.5616 1.2288666
|
||||
7300 18787.328 283.49504 0 3762.6299 9.0044469
|
||||
7350 18886.005 265.52121 0 3762.9295 6.6791881
|
||||
7400 19891.864 79.239278 0 3762.9178 -2.3882842
|
||||
7450 18164.752 399.07065 0 3762.9137 3.9400481
|
||||
7500 18702.612 299.582 0 3763.0286 4.7987316
|
||||
7550 19884.986 80.231665 0 3762.6365 -0.75016515
|
||||
7600 19549.059 142.16243 0 3762.3586 -2.1035756
|
||||
7650 18223.668 387.9047 0 3762.658 -17.064339
|
||||
7700 19428.4 164.79531 0 3762.6473 -2.8342541
|
||||
7750 19239.584 199.93029 0 3762.8163 3.1746033
|
||||
7800 19458.005 159.46176 0 3762.7961 1.714515
|
||||
7850 18320.308 369.77051 0 3762.4202 2.1422976
|
||||
7900 18817.415 278.04812 0 3762.7546 0.94492621
|
||||
7950 19892.761 79.115928 0 3762.9606 1.4948501
|
||||
8000 19592.344 134.7639 0 3762.9758 -1.8520224
|
||||
8050 19316.109 185.70579 0 3762.7631 -4.8061205
|
||||
8100 19867.017 83.850395 0 3762.9277 -3.496391
|
||||
8150 19129.936 220.29802 0 3762.8789 -2.8357376
|
||||
8200 18449.554 346.30415 0 3762.8883 1.4417837
|
||||
8250 18405.197 354.49049 0 3762.8602 6.7020283
|
||||
8300 18310.437 372.25376 0 3763.0755 3.9043508
|
||||
8350 18842.702 273.55075 0 3762.94 -10.987272
|
||||
8400 18574.308 323.33378 0 3763.0204 12.008785
|
||||
8450 15368.628 918.21692 0 3764.2591 34.80292
|
||||
8500 18432.887 349.54013 0 3763.0378 0.00064258465
|
||||
8550 15777.73 841.79263 0 3763.5945 15.473699
|
||||
8600 17205.381 576.4515 0 3762.6331 2.3985544
|
||||
8650 19773.742 101.48276 0 3763.2869 2.3978892
|
||||
8700 19059.824 232.99716 0 3762.5941 5.2611349
|
||||
8750 19006.086 243.41125 0 3763.0568 4.7880403
|
||||
8800 19492.691 153.0188 0 3762.7763 1.9118755
|
||||
8850 19625.883 128.44474 0 3762.8675 3.4157389
|
||||
8900 19916.97 74.635094 0 3762.9629 -10.157254
|
||||
8950 16012.956 798.16801 0 3763.5302 16.904998
|
||||
9000 19364.051 177.00354 0 3762.9389 -13.373346
|
||||
9050 19133.929 219.61882 0 3762.9389 -7.3824392
|
||||
9100 18657.168 307.85939 0 3762.8905 9.3071421
|
||||
9150 17975.904 434.21548 0 3763.0867 6.9609506
|
||||
9200 19075.282 230.41699 0 3762.8767 7.0961232
|
||||
9250 20115.276 37.578674 0 3762.6298 1.8678552
|
||||
9300 18195.486 393.20682 0 3762.7413 13.272552
|
||||
9350 19617.155 129.85893 0 3762.6653 -2.0849447
|
||||
9400 19276.325 193.03425 0 3762.724 -2.8963555
|
||||
9450 18642.803 310.4759 0 3762.8467 3.407984
|
||||
9500 19175.951 211.72785 0 3762.8298 -0.39025564
|
||||
9550 17669.191 490.85942 0 3762.9319 5.3867954
|
||||
9600 18481.199 340.29485 0 3762.7391 8.9004886
|
||||
9650 20091.442 42.504743 0 3763.1422 -1.3206133
|
||||
9700 19651.405 124.04835 0 3763.1975 1.4000525
|
||||
9750 19138.245 219.03637 0 3763.1558 5.8352794
|
||||
9800 19189.146 209.67958 0 3763.2251 6.214691
|
||||
9850 19899.376 78.096337 0 3763.166 -0.75102404
|
||||
9900 19447.247 161.27279 0 3762.6149 -6.4166376
|
||||
9950 19807.083 95.152663 0 3763.1309 -0.88933698
|
||||
10000 18972.157 249.56342 0 3762.9258 1.9189241
|
||||
Loop time of 3.99472 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 21628.565 tau/day, 2503.306 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74
|
||||
Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53
|
||||
Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46
|
||||
Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12
|
||||
Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58
|
||||
Other | | 0.02291 | | | 0.57
|
||||
|
||||
Nlocal: 20.25 ave 37 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 17.75 ave 33 max 4 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 144.75 ave 356 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 579
|
||||
Ave neighs/atom = 7.14815
|
||||
Neighbor list builds = 994
|
||||
Dangerous builds = 958
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -1,452 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Tethered nanorods
|
||||
|
||||
atom_style molecular
|
||||
|
||||
read_data data.rigid.tnr
|
||||
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5600 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
1600 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify bond parameters
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify initial velocities
|
||||
|
||||
velocity all create 1.4 109345
|
||||
|
||||
# Specify rigid components
|
||||
|
||||
group rods type 2
|
||||
4000 atoms in group rods
|
||||
group tethers subtract all rods
|
||||
1600 atoms in group tethers
|
||||
|
||||
neigh_modify exclude molecule rods delay 0 every 1
|
||||
|
||||
# Specify the pair potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
pair_coeff * * 1.0 1.0 1.122
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
|
||||
# Specify output
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
|
||||
thermo_modify flush yes lost warn
|
||||
|
||||
timestep 0.005
|
||||
|
||||
fix 1 rods rigid molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
fix 2 tethers nve
|
||||
fix 3 all langevin 1.4 1.4 1.0 437624
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 45 45 45
|
||||
Memory usage per processor = 7.32042 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
|
||||
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
|
||||
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
|
||||
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
|
||||
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
|
||||
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
|
||||
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
|
||||
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
|
||||
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
|
||||
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
|
||||
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
|
||||
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
|
||||
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
|
||||
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
|
||||
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
|
||||
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
|
||||
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
|
||||
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
|
||||
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
|
||||
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
|
||||
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
|
||||
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
|
||||
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
|
||||
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
|
||||
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
|
||||
2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
|
||||
2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
|
||||
2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
|
||||
2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
|
||||
2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
|
||||
3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
|
||||
3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
|
||||
3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
|
||||
3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
|
||||
3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
|
||||
3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
|
||||
3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
|
||||
3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
|
||||
3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
|
||||
3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
|
||||
4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
|
||||
4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
|
||||
4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
|
||||
4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
|
||||
4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
|
||||
4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
|
||||
4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
|
||||
4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
|
||||
4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
|
||||
4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
|
||||
5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
|
||||
Loop time of 6.51777 on 1 procs for 5000 steps with 5600 atoms
|
||||
|
||||
Performance: 331401.531 tau/day, 767.133 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96
|
||||
Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70
|
||||
Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80
|
||||
Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54
|
||||
Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05
|
||||
Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23
|
||||
Other | | 0.1774 | | | 2.72
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1351 ave 1351 max 1351 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5254 ave 5254 max 5254 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5254
|
||||
Ave neighs/atom = 0.938214
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 766
|
||||
Dangerous builds = 0
|
||||
|
||||
# Replace fix rigid and fix langevin with new ones
|
||||
|
||||
unfix 1
|
||||
unfix 3
|
||||
|
||||
fix 3 tethers langevin 1.4 1.4 1.0 198450
|
||||
|
||||
# Test different integrators for rods
|
||||
|
||||
fix 1 rods rigid/nve molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nve"
|
||||
rigid/nve
|
||||
run 1000
|
||||
Memory usage per processor = 7.32042 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
|
||||
5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
|
||||
5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
|
||||
5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
|
||||
5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
|
||||
5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
|
||||
5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
|
||||
5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
|
||||
5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
|
||||
5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
|
||||
6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
|
||||
Loop time of 1.37139 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 315008.398 tau/day, 729.186 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52
|
||||
Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59
|
||||
Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58
|
||||
Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46
|
||||
Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05
|
||||
Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21
|
||||
Other | | 0.03562 | | | 2.60
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1347 ave 1347 max 1347 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5399 ave 5399 max 5399 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5399
|
||||
Ave neighs/atom = 0.964107
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 153
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nvt"
|
||||
rigid/nvt
|
||||
run 1000
|
||||
Memory usage per processor = 7.32042 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
|
||||
6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
|
||||
6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
|
||||
6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
|
||||
6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
|
||||
6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
|
||||
6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
|
||||
6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
|
||||
6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
|
||||
6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
|
||||
7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
|
||||
Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 311550.061 tau/day, 721.181 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48
|
||||
Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53
|
||||
Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04
|
||||
Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42
|
||||
Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05
|
||||
Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92
|
||||
Other | | 0.03559 | | | 2.57
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1284 ave 1284 max 1284 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5677 ave 5677 max 5677 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5677
|
||||
Ave neighs/atom = 1.01375
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 151
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
compute myTemp all temp
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt iso"
|
||||
rigid/npt iso
|
||||
fix_modify 1 temp myTemp
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 7.32042 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
|
||||
7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
|
||||
7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
|
||||
7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
|
||||
7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
|
||||
7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
|
||||
7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
|
||||
7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
|
||||
7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
|
||||
7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
|
||||
8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
|
||||
Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 141281.224 tau/day, 327.040 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18
|
||||
Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34
|
||||
Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68
|
||||
Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35
|
||||
Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02
|
||||
Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82
|
||||
Other | | 0.04962 | | | 1.62
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2963 ave 2963 max 2963 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 25797 ave 25797 max 25797 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 25797
|
||||
Ave neighs/atom = 4.60661
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 334
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt x"
|
||||
rigid/npt x
|
||||
run 1000
|
||||
Memory usage per processor = 7.32428 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
|
||||
8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
|
||||
8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
|
||||
8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
|
||||
8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
|
||||
8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
|
||||
8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
|
||||
8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
|
||||
8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
|
||||
8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
|
||||
9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
|
||||
Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 146727.069 tau/day, 339.646 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63
|
||||
Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47
|
||||
Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57
|
||||
Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79
|
||||
Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02
|
||||
Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20
|
||||
Other | | 0.03878 | | | 1.32
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3244 ave 3244 max 3244 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 30929 ave 30929 max 30929 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 30929
|
||||
Ave neighs/atom = 5.52304
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 165
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph iso"
|
||||
rigid/nph iso
|
||||
run 1000
|
||||
Memory usage per processor = 7.32428 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
|
||||
9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
|
||||
9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
|
||||
9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
|
||||
9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
|
||||
9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
|
||||
9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
|
||||
9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
|
||||
9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
|
||||
9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
|
||||
10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
|
||||
Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 137864.384 tau/day, 319.131 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70
|
||||
Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34
|
||||
Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58
|
||||
Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82
|
||||
Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02
|
||||
Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29
|
||||
Other | | 0.03924 | | | 1.25
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3635 ave 3635 max 3635 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 38235 ave 38235 max 38235 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 38235
|
||||
Ave neighs/atom = 6.82768
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 165
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph xy couple"
|
||||
rigid/nph xy couple
|
||||
run 1000
|
||||
Memory usage per processor = 7.32811 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
|
||||
10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
|
||||
10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
|
||||
10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
|
||||
10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
|
||||
10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
|
||||
10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
|
||||
10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
|
||||
10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
|
||||
10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
|
||||
11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
|
||||
Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 134004.591 tau/day, 310.196 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25
|
||||
Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28
|
||||
Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58
|
||||
Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78
|
||||
Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02
|
||||
Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87
|
||||
Other | | 0.03903 | | | 1.21
|
||||
|
||||
Nlocal: 5600 ave 5600 max 5600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3799 ave 3799 max 3799 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 39646 ave 39646 max 39646 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 39646
|
||||
Ave neighs/atom = 7.07964
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 158
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:21
|
||||
@ -1,452 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# Tethered nanorods
|
||||
|
||||
atom_style molecular
|
||||
|
||||
read_data data.rigid.tnr
|
||||
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
5600 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
1600 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify bond parameters
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
# Specify initial velocities
|
||||
|
||||
velocity all create 1.4 109345
|
||||
|
||||
# Specify rigid components
|
||||
|
||||
group rods type 2
|
||||
4000 atoms in group rods
|
||||
group tethers subtract all rods
|
||||
1600 atoms in group tethers
|
||||
|
||||
neigh_modify exclude molecule rods delay 0 every 1
|
||||
|
||||
# Specify the pair potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
pair_coeff * * 1.0 1.0 1.122
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
|
||||
# Specify output
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
|
||||
thermo_modify flush yes lost warn
|
||||
|
||||
timestep 0.005
|
||||
|
||||
fix 1 rods rigid molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
fix 2 tethers nve
|
||||
fix 3 all langevin 1.4 1.4 1.0 437624
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 45 45 45
|
||||
Memory usage per processor = 6.96454 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
|
||||
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
|
||||
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
|
||||
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
|
||||
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
|
||||
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
|
||||
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
|
||||
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
|
||||
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
|
||||
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
|
||||
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
|
||||
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
|
||||
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
|
||||
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
|
||||
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
|
||||
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
|
||||
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
|
||||
1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
|
||||
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
|
||||
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
|
||||
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
|
||||
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
|
||||
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
|
||||
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
|
||||
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
|
||||
2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
|
||||
2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
|
||||
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
|
||||
2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
|
||||
2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
|
||||
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
|
||||
3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
|
||||
3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
|
||||
3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
|
||||
3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
|
||||
3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
|
||||
3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
|
||||
3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
|
||||
3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
|
||||
3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
|
||||
4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
|
||||
4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
|
||||
4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
|
||||
4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
|
||||
4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
|
||||
4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
|
||||
4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
|
||||
4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
|
||||
4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
|
||||
4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
|
||||
5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
|
||||
Loop time of 3.14543 on 4 procs for 5000 steps with 5600 atoms
|
||||
|
||||
Performance: 686709.553 tau/day, 1589.605 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05
|
||||
Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82
|
||||
Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94
|
||||
Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51
|
||||
Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09
|
||||
Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32
|
||||
Other | | 0.1658 | | | 5.27
|
||||
|
||||
Nlocal: 1400 ave 1868 max 905 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 648.25 ave 688 max 598 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 1202.5 ave 1821 max 698 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 4810
|
||||
Ave neighs/atom = 0.858929
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 759
|
||||
Dangerous builds = 0
|
||||
|
||||
# Replace fix rigid and fix langevin with new ones
|
||||
|
||||
unfix 1
|
||||
unfix 3
|
||||
|
||||
fix 3 tethers langevin 1.4 1.4 1.0 198450
|
||||
|
||||
# Test different integrators for rods
|
||||
|
||||
fix 1 rods rigid/nve molecule
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nve"
|
||||
rigid/nve
|
||||
run 1000
|
||||
Memory usage per processor = 6.98553 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
|
||||
5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
|
||||
5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
|
||||
5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
|
||||
5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
|
||||
5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
|
||||
5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
|
||||
5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
|
||||
5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
|
||||
5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
|
||||
6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
|
||||
Loop time of 0.74555 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 579437.739 tau/day, 1341.291 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48
|
||||
Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54
|
||||
Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13
|
||||
Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51
|
||||
Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07
|
||||
Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08
|
||||
Other | | 0.03125 | | | 4.19
|
||||
|
||||
Nlocal: 1400 ave 1868 max 935 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 633.75 ave 695 max 541 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 1263 ave 1799 max 710 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 5052
|
||||
Ave neighs/atom = 0.902143
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 153
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nvt"
|
||||
rigid/nvt
|
||||
run 1000
|
||||
Memory usage per processor = 6.98553 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
|
||||
6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
|
||||
6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
|
||||
6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
|
||||
6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
|
||||
6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
|
||||
6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
|
||||
6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
|
||||
6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
|
||||
6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
|
||||
7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
|
||||
Loop time of 0.761012 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 567665.504 tau/day, 1314.041 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58
|
||||
Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52
|
||||
Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41
|
||||
Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25
|
||||
Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07
|
||||
Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58
|
||||
Other | | 0.02726 | | | 3.58
|
||||
|
||||
Nlocal: 1400 ave 1832 max 970 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 652.5 ave 749 max 561 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1407.5 ave 2071 max 748 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 5630
|
||||
Ave neighs/atom = 1.00536
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 149
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
compute myTemp all temp
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt iso"
|
||||
rigid/npt iso
|
||||
fix_modify 1 temp myTemp
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 6.98553 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
|
||||
7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
|
||||
7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
|
||||
7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
|
||||
7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
|
||||
7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
|
||||
7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
|
||||
7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
|
||||
7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
|
||||
7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
|
||||
8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
|
||||
Loop time of 1.40621 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 307209.818 tau/day, 711.134 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72
|
||||
Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23
|
||||
Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07
|
||||
Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56
|
||||
Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03
|
||||
Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12
|
||||
Other | | 0.04594 | | | 3.27
|
||||
|
||||
Nlocal: 1400 ave 1820 max 1010 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 1576 ave 1694 max 1470 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 6543 ave 9989 max 3497 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 26172
|
||||
Ave neighs/atom = 4.67357
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 337
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/npt x"
|
||||
rigid/npt x
|
||||
run 1000
|
||||
Memory usage per processor = 7.00192 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
|
||||
8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
|
||||
8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
|
||||
8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
|
||||
8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
|
||||
8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
|
||||
8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
|
||||
8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
|
||||
8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
|
||||
8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
|
||||
9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
|
||||
Loop time of 1.3981 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 308990.110 tau/day, 715.255 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77
|
||||
Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27
|
||||
Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80
|
||||
Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50
|
||||
Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03
|
||||
Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58
|
||||
Other | | 0.04265 | | | 3.05
|
||||
|
||||
Nlocal: 1400 ave 1770 max 1095 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 1578.5 ave 1693 max 1493 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 7868 ave 12041 max 4579 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 31472
|
||||
Ave neighs/atom = 5.62
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 167
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph iso"
|
||||
rigid/nph iso
|
||||
run 1000
|
||||
Memory usage per processor = 7.00192 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
|
||||
9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
|
||||
9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
|
||||
9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
|
||||
9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
|
||||
9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
|
||||
9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
|
||||
9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
|
||||
9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
|
||||
9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
|
||||
10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
|
||||
Loop time of 1.38185 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 312625.215 tau/day, 723.669 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51
|
||||
Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28
|
||||
Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29
|
||||
Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07
|
||||
Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03
|
||||
Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25
|
||||
Other | | 0.03557 | | | 2.57
|
||||
|
||||
Nlocal: 1400 ave 1669 max 1139 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 1761.5 ave 1898 max 1632 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 9311.75 ave 12525 max 5959 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 37247
|
||||
Ave neighs/atom = 6.65125
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 165
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
|
||||
800 rigid bodies with 4000 atoms
|
||||
print "rigid/nph xy couple"
|
||||
rigid/nph xy couple
|
||||
run 1000
|
||||
Memory usage per processor = 7.00192 Mbytes
|
||||
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
||||
10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
|
||||
10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
|
||||
10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
|
||||
10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
|
||||
10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
|
||||
10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
|
||||
10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
|
||||
10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
|
||||
10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
|
||||
10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
|
||||
11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
|
||||
Loop time of 1.36647 on 4 procs for 1000 steps with 5600 atoms
|
||||
|
||||
Performance: 316143.197 tau/day, 731.813 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17
|
||||
Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31
|
||||
Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56
|
||||
Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48
|
||||
Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03
|
||||
Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05
|
||||
Other | | 0.03282 | | | 2.40
|
||||
|
||||
Nlocal: 1400 ave 1607 max 1199 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 1819.25 ave 1940 max 1712 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 9882 ave 12628 max 7201 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 39528
|
||||
Ave neighs/atom = 7.05857
|
||||
Ave special neighs/atom = 0.571429
|
||||
Neighbor list builds = 156
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:10
|
||||
@ -1,9 +1,9 @@
|
||||
|
||||
$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
|
||||
colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \
|
||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
||||
colvarparse.h colvaratoms.h colvardeps.h
|
||||
$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
|
||||
colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \
|
||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
|
||||
colvarparse.h colvardeps.h lepton/include/Lepton.h \
|
||||
lepton/include/lepton/CompiledExpression.h \
|
||||
lepton/include/lepton/ExpressionTreeNode.h \
|
||||
@ -29,7 +29,7 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
|
||||
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
|
||||
colvarbias_alb.h
|
||||
$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
|
||||
colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \
|
||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \
|
||||
colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
|
||||
lepton/include/lepton/CompiledExpression.h \
|
||||
lepton/include/lepton/ExpressionTreeNode.h \
|
||||
@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
|
||||
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
|
||||
colvargrid.h
|
||||
$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
|
||||
colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \
|
||||
colvartypes.h colvar.h colvarparse.h colvardeps.h \
|
||||
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
||||
colvarvalue.h colvar.h colvarparse.h colvardeps.h \
|
||||
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
|
||||
lepton/include/lepton/ExpressionTreeNode.h \
|
||||
lepton/include/lepton/windowsIncludes.h \
|
||||
@ -55,7 +55,7 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
|
||||
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
|
||||
colvarbias_histogram.h colvarbias.h colvargrid.h
|
||||
$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
|
||||
colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \
|
||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
|
||||
colvarparse.h colvardeps.h lepton/include/Lepton.h \
|
||||
lepton/include/lepton/CompiledExpression.h \
|
||||
lepton/include/lepton/ExpressionTreeNode.h \
|
||||
@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
|
||||
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
|
||||
colvarbias_meta.h colvarbias.h colvargrid.h
|
||||
$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
|
||||
colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \
|
||||
colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
|
||||
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
||||
colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
|
||||
colvardeps.h lepton/include/Lepton.h \
|
||||
lepton/include/lepton/CompiledExpression.h \
|
||||
lepton/include/lepton/ExpressionTreeNode.h \
|
||||
@ -171,7 +171,7 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
|
||||
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
|
||||
colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h
|
||||
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
|
||||
colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \
|
||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
|
||||
colvarparse.h
|
||||
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
|
||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \
|
||||
@ -204,7 +204,7 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
|
||||
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
|
||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h
|
||||
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
|
||||
colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \
|
||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
||||
colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \
|
||||
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
|
||||
lepton/include/lepton/ExpressionTreeNode.h \
|
||||
|
||||
@ -77,6 +77,8 @@ int colvar::cvc::init(std::string const &conf)
|
||||
|
||||
if (cvm::debug())
|
||||
cvm::log("Done initializing cvc base object.\n");
|
||||
|
||||
return error_code;
|
||||
}
|
||||
|
||||
|
||||
|
||||
2
lib/latte/.gitignore
vendored
2
lib/latte/.gitignore
vendored
@ -2,4 +2,4 @@
|
||||
/filelink
|
||||
/liblink
|
||||
/includelink
|
||||
/LATTE-master
|
||||
/LATTE-*
|
||||
|
||||
8
lib/vtk/Makefile.lammps.fedora28_vtk7
Normal file
8
lib/vtk/Makefile.lammps.fedora28_vtk7
Normal file
@ -0,0 +1,8 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
# settings for VTK 7.1.1 on Fedora 28. This seems to work with Fedora versions going back to at least 23 and VTK version 6.x.
|
||||
# You need to install vtk-devel and all its dependencies using "dnf install vtk-devel"
|
||||
vtk_SYSINC = -I/usr/include/vtk
|
||||
vtk_SYSLIB = -lvtkCommonCore -lvtkIOCore -lvtkCommonDataModel -lvtkIOXML -lvtkIOLegacy -lvtkIOParallelXML
|
||||
vtk_SYSPATH = -L/usr/lib64/vtk
|
||||
|
||||
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -734,6 +734,8 @@
|
||||
/pair_hbond_dreiding_morse.h
|
||||
/pair_ilp_graphene_hbn.cpp
|
||||
/pair_ilp_graphene_hbn.h
|
||||
/pair_kim.cpp
|
||||
/pair_kim.h
|
||||
/pair_kolmogorov_crespi_full.cpp
|
||||
/pair_kolmogorov_crespi_full.h
|
||||
/pair_kolmogorov_crespi_z.cpp
|
||||
|
||||
@ -134,6 +134,7 @@ fi
|
||||
if (test $1 = "USER-MISC") then
|
||||
depend GPU
|
||||
depend USER-OMP
|
||||
depend USER-INTEL
|
||||
fi
|
||||
|
||||
if (test $1 = "USER-REAXC") then
|
||||
|
||||
@ -61,13 +61,13 @@ namespace GPU_EXTRA {
|
||||
else
|
||||
error->all(FLERR,"Unknown error in GPU library");
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) {
|
||||
int ifix = modify->find_fix("package_gpu");
|
||||
if (ifix < 0)
|
||||
error->all(FLERR,"The package gpu command is required for gpu styles");
|
||||
};
|
||||
}
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@ -1264,15 +1264,15 @@ void *PairKIM::extract(const char *str, int &dim)
|
||||
int ier;
|
||||
int dummyint;
|
||||
int isIndexed = 0;
|
||||
int maxLine = 1024;
|
||||
const int MAXLINE = 1024;
|
||||
int rank;
|
||||
int validParam = 0;
|
||||
int numParams;
|
||||
int *speciesIndex = new int[maxLine];
|
||||
char *paramStr = new char[maxLine];
|
||||
int *speciesIndex = new int[MAXLINE];
|
||||
char *paramStr = new char[MAXLINE];
|
||||
char *paramName;
|
||||
char *indexStr;
|
||||
char message[maxLine];
|
||||
char message[MAXLINE];
|
||||
int offset;
|
||||
double* paramPtr;
|
||||
|
||||
@ -1354,7 +1354,7 @@ void *PairKIM::extract(const char *str, int &dim)
|
||||
}
|
||||
kim_error(__LINE__,"get_rank",kimerror);
|
||||
|
||||
int *shape = new int[maxLine];
|
||||
int *shape = new int[MAXLINE];
|
||||
dummyint = (*pkim).get_shape(paramName, shape, &kimerror);
|
||||
if (kimerror == KIM_STATUS_FAIL)
|
||||
{
|
||||
|
||||
@ -2261,7 +2261,7 @@ void MSM::restriction(int n)
|
||||
double ***qgrid2 = qgrid[n+1];
|
||||
|
||||
int k = 0;
|
||||
int index[p+2];
|
||||
int *index = new int[p+2];
|
||||
for (int nu=-p; nu<=p; nu++) {
|
||||
if (nu%2 == 0 && nu != 0) continue;
|
||||
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
|
||||
@ -2317,7 +2317,7 @@ void MSM::restriction(int n)
|
||||
}
|
||||
qgrid2[kp][jp][ip] += q2sum;
|
||||
}
|
||||
|
||||
delete[] index;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -2348,7 +2348,7 @@ void MSM::prolongation(int n)
|
||||
double ***v5grid2 = v5grid[n+1];
|
||||
|
||||
int k = 0;
|
||||
int index[p+2];
|
||||
int *index = new int[p+2];
|
||||
for (int nu=-p; nu<=p; nu++) {
|
||||
if (nu%2 == 0 && nu != 0) continue;
|
||||
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
|
||||
@ -2420,7 +2420,7 @@ void MSM::prolongation(int n)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
delete[] index;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -310,10 +310,10 @@ double PairComb3::init_one(int i, int j)
|
||||
|
||||
void PairComb3::read_lib()
|
||||
{
|
||||
unsigned int maxlib = 1024;
|
||||
const unsigned int MAXLIB = 1024;
|
||||
int i,j,k,l,nwords,m;
|
||||
int ii,jj,kk,ll,mm,iii;
|
||||
char s[maxlib];
|
||||
char s[MAXLIB];
|
||||
char **words = new char*[80];
|
||||
|
||||
// open libraray file on proc 0
|
||||
@ -327,8 +327,8 @@ void PairComb3::read_lib()
|
||||
}
|
||||
|
||||
// read and store at the same time
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -339,7 +339,7 @@ void PairComb3::read_lib()
|
||||
ccutoff[4] = atof(words[4]);
|
||||
ccutoff[5] = atof(words[5]);
|
||||
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -351,7 +351,7 @@ void PairComb3::read_lib()
|
||||
ch_a[5] = atof(words[5]);
|
||||
ch_a[6] = atof(words[6]);
|
||||
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -359,7 +359,7 @@ void PairComb3::read_lib()
|
||||
nsplrad = atoi(words[1]);
|
||||
nspltor = atoi(words[2]);
|
||||
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -367,7 +367,7 @@ void PairComb3::read_lib()
|
||||
maxy = atoi(words[1]);
|
||||
maxz = atoi(words[2]);
|
||||
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -376,7 +376,7 @@ void PairComb3::read_lib()
|
||||
maxconj = atoi(words[2]);
|
||||
|
||||
for (l=0; l<nsplpcn; l++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -385,14 +385,14 @@ void PairComb3::read_lib()
|
||||
dvmaxxcn[l] = atof(words[3]);
|
||||
}
|
||||
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
ntab = atoi(words[0]);
|
||||
|
||||
for (i=0; i<ntab+1; i++){
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -405,7 +405,7 @@ void PairComb3::read_lib()
|
||||
for (i=0; i<maxx+1; i++)
|
||||
for (j=0; j<maxy+1; j++)
|
||||
for (k=0; k<maxz+1; k++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -423,7 +423,7 @@ void PairComb3::read_lib()
|
||||
for (i=0; i<maxx; i++)
|
||||
for (j=0; j<maxy; j++)
|
||||
for (k=0; k<maxz; k++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -432,7 +432,7 @@ void PairComb3::read_lib()
|
||||
jj = atoi(words[2]);
|
||||
kk = atoi(words[3]);
|
||||
for(iii=0; iii<2; iii++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -447,7 +447,7 @@ void PairComb3::read_lib()
|
||||
for (i=0; i<maxxc+1; i++)
|
||||
for (j=0; j<maxyc+1; j++)
|
||||
for (k=0; k<maxconj; k++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -465,7 +465,7 @@ void PairComb3::read_lib()
|
||||
for (i=0; i<maxxc; i++)
|
||||
for (j=0; j<maxyc; j++)
|
||||
for (k=0; k<maxconj-1; k++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -474,7 +474,7 @@ void PairComb3::read_lib()
|
||||
jj = atoi(words[2]);
|
||||
kk = atoi(words[3])-1;
|
||||
for (iii=0; iii<2; iii++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -489,7 +489,7 @@ void PairComb3::read_lib()
|
||||
for (i=0; i<maxxc+1; i++)
|
||||
for (j=0; j<maxyc+1; j++)
|
||||
for (k=0; k<maxconj; k++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -507,7 +507,7 @@ void PairComb3::read_lib()
|
||||
for (i=0; i<maxxc; i++)
|
||||
for (j=0; j<maxyc; j++)
|
||||
for (k=0; k<maxconj-1; k++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
@ -516,7 +516,7 @@ void PairComb3::read_lib()
|
||||
jj = atoi(words[2]);
|
||||
kk = atoi(words[3])-1;
|
||||
for(iii=0; iii<2; iii++) {
|
||||
fgets(s,maxlib,fp);
|
||||
fgets(s,MAXLIB,fp);
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(s," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
|
||||
|
||||
@ -1349,7 +1349,7 @@ void FixGCMC::attempt_molecule_insertion()
|
||||
MathExtra::quat_to_mat(quat,rotmat);
|
||||
|
||||
double insertion_energy = 0.0;
|
||||
bool procflag[natoms_per_molecule];
|
||||
bool *procflag = new bool[natoms_per_molecule];
|
||||
|
||||
for (int i = 0; i < natoms_per_molecule; i++) {
|
||||
MathExtra::matvec(rotmat,onemols[imol]->x[i],molcoords[i]);
|
||||
@ -1472,6 +1472,7 @@ void FixGCMC::attempt_molecule_insertion()
|
||||
update_gas_atoms_list();
|
||||
ninsertion_successes += 1.0;
|
||||
}
|
||||
delete[] procflag;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1934,7 +1935,7 @@ void FixGCMC::attempt_molecule_deletion_full()
|
||||
grow_molecule_arrays(nmolq);
|
||||
|
||||
int m = 0;
|
||||
int tmpmask[atom->nlocal];
|
||||
int *tmpmask = new int[atom->nlocal];
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
if (atom->molecule[i] == deletion_molecule) {
|
||||
tmpmask[i] = atom->mask[i];
|
||||
@ -1982,6 +1983,7 @@ void FixGCMC::attempt_molecule_deletion_full()
|
||||
if (force->kspace) force->kspace->qsum_qsq();
|
||||
}
|
||||
update_gas_atoms_list();
|
||||
delete[] tmpmask;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -2426,9 +2428,9 @@ void FixGCMC::update_gas_atoms_list()
|
||||
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);
|
||||
tagint maxmol_all;
|
||||
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
|
||||
double comx[maxmol_all];
|
||||
double comy[maxmol_all];
|
||||
double comz[maxmol_all];
|
||||
double *comx = new double[maxmol_all];
|
||||
double *comy = new double[maxmol_all];
|
||||
double *comz = new double[maxmol_all];
|
||||
for (int imolecule = 0; imolecule < maxmol_all; imolecule++) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (molecule[i] == imolecule) {
|
||||
@ -2458,7 +2460,9 @@ void FixGCMC::update_gas_atoms_list()
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
delete[] comx;
|
||||
delete[] comy;
|
||||
delete[] comz;
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
|
||||
@ -21,6 +21,7 @@
|
||||
#include "fix_mscg.h"
|
||||
#include "mscg.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
@ -284,11 +285,9 @@ void FixMSCG::end_of_step()
|
||||
if (domain->triclinic == 1)
|
||||
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
|
||||
|
||||
int natoms = atom->natoms;
|
||||
int nlocal = atom->nlocal;
|
||||
tagint *tag = atom->tag;
|
||||
double **x = atom->x;
|
||||
double *prd_half = domain->prd_half;
|
||||
int i,ii,j;
|
||||
|
||||
// trajectory information
|
||||
|
||||
@ -57,10 +57,10 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
|
||||
molecule mpiio mscg opt peri poems \
|
||||
python qeq reax replica rigid shock snap srd voronoi
|
||||
|
||||
PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
|
||||
PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
|
||||
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
|
||||
user-intel user-lb user-manifold user-meamc user-meso \
|
||||
user-mgpt user-misc user-molfile \
|
||||
user-mgpt user-misc user-mofff user-molfile \
|
||||
user-netcdf user-omp user-phonon user-qmmm user-qtb \
|
||||
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
|
||||
user-uef user-vtk
|
||||
@ -267,7 +267,7 @@ package:
|
||||
@echo 'make yes-all install all pgks in src dir'
|
||||
@echo 'make no-all remove all pkgs from src dir'
|
||||
@echo 'make yes-standard (yes-std) install all standard pkgs'
|
||||
@echo 'make no-standard (no-srd) remove all standard pkgs'
|
||||
@echo 'make no-standard (no-std) remove all standard pkgs'
|
||||
@echo 'make yes-user install all user pkgs'
|
||||
@echo 'make no-user remove all user pkgs'
|
||||
@echo 'make yes-lib install all pkgs with libs (included or ext)'
|
||||
|
||||
@ -267,6 +267,10 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
poems = new Workspace;
|
||||
|
||||
// compute per body forces and torques inside final_integrate() by default
|
||||
|
||||
earlyflag = 0;
|
||||
|
||||
// print statistics
|
||||
|
||||
int nsum = 0;
|
||||
@ -351,12 +355,26 @@ void FixPOEMS::init()
|
||||
int i,ibody;
|
||||
|
||||
// warn if more than one POEMS fix
|
||||
// if earlyflag, warn if any post-force fixes come after POEMS fix
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
|
||||
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems");
|
||||
|
||||
if (earlyflag) {
|
||||
int pflag = 0;
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1;
|
||||
if (pflag && (modify->fmask[i] & POST_FORCE) &&
|
||||
!modify->fix[i]->rigid_flag) {
|
||||
char str[128];
|
||||
sprintf(str,"Fix %d alters forces after fix poems",modify->fix[i]->id);
|
||||
error->warning(FLERR,str);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// error if npt,nph fix comes before rigid fix
|
||||
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
@ -696,7 +714,8 @@ void FixPOEMS::setup(int vflag)
|
||||
|
||||
// use post_force() to compute initial fcm & torque
|
||||
|
||||
post_force(vflag);
|
||||
compute_forces_and_torques();
|
||||
//post_force(vflag);
|
||||
|
||||
// setup for POEMS
|
||||
|
||||
@ -727,12 +746,29 @@ void FixPOEMS::initial_integrate(int vflag)
|
||||
set_xv();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPOEMS::post_force(int vflag)
|
||||
{
|
||||
if (earlyflag) compute_forces_and_torques();
|
||||
|
||||
/*
|
||||
for (int ibody = 0; ibody < nbody; ibody++) {
|
||||
if (ibody == 0) {
|
||||
printf("PFF %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
|
||||
printf("PFT %d %g %g %g\n",ibody,
|
||||
torque[ibody][0],torque[ibody][1],torque[ibody][2]);
|
||||
}
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute fcm,torque on each rigid body
|
||||
only count joint atoms in 1st body
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixPOEMS::post_force(int vflag)
|
||||
void FixPOEMS::compute_forces_and_torques()
|
||||
{
|
||||
int i,ibody;
|
||||
int xbox,ybox,zbox;
|
||||
@ -790,6 +826,18 @@ void FixPOEMS::post_force(int vflag)
|
||||
|
||||
void FixPOEMS::final_integrate()
|
||||
{
|
||||
if (!earlyflag) compute_forces_and_torques();
|
||||
|
||||
/*
|
||||
for (int ibody = 0; ibody < nbody; ibody++) {
|
||||
if (ibody == 0) {
|
||||
printf("FI %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
|
||||
printf("TQ %d %g %g %g\n",ibody,
|
||||
torque[ibody][0],torque[ibody][1],torque[ibody][2]);
|
||||
}
|
||||
}
|
||||
*/
|
||||
|
||||
// perform POEMS integration
|
||||
|
||||
poems->LobattoTwo(vcm,omega,torque,fcm);
|
||||
@ -1615,6 +1663,21 @@ int FixPOEMS::unpack_exchange(int nlocal, double *buf)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPOEMS::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"bodyforces") == 0) {
|
||||
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
|
||||
if (strcmp(arg[1],"early") == 0) earlyflag = 1;
|
||||
else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
|
||||
else error->all(FLERR,"Illegal fix_modify command");
|
||||
return 2;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPOEMS::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
|
||||
@ -47,6 +47,7 @@ class FixPOEMS : public Fix {
|
||||
void pre_neighbor();
|
||||
int dof(int);
|
||||
void deform(int);
|
||||
int modify_param(int, char **);
|
||||
void reset_dt();
|
||||
|
||||
private:
|
||||
@ -55,6 +56,7 @@ class FixPOEMS : public Fix {
|
||||
double *step_respa;
|
||||
int nlevels_respa;
|
||||
double total_ke;
|
||||
int earlyflag; // 1 if forces and torques are computed at post_force()
|
||||
|
||||
// atom assignment to rigid bodies
|
||||
// double count joint atoms as being in multiple bodies
|
||||
@ -96,6 +98,7 @@ class FixPOEMS : public Fix {
|
||||
|
||||
// internal class functions
|
||||
|
||||
void compute_forces_and_torques();
|
||||
void readfile(char *);
|
||||
int readline(FILE *, char **, int *);
|
||||
void jointbuild();
|
||||
|
||||
@ -47,7 +47,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
|
||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
||||
|
||||
// add current directory to PYTHONPATH
|
||||
PyObject * py_path = PySys_GetObject("path");
|
||||
PyObject * py_path = PySys_GetObject((char *)"path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
|
||||
|
||||
@ -136,7 +136,7 @@ void FixPythonMove::init()
|
||||
{
|
||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
||||
PyObject *py_move_obj = (PyObject *) py_move;
|
||||
PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init");
|
||||
PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init");
|
||||
if (!py_init) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
|
||||
@ -303,7 +303,7 @@ void NEB::run()
|
||||
update->minimize->setup();
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (uscreen)
|
||||
if (uscreen) {
|
||||
if (verbose) {
|
||||
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
@ -317,7 +317,8 @@ void NEB::run()
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
}
|
||||
if (ulogfile)
|
||||
}
|
||||
if (ulogfile) {
|
||||
if (verbose) {
|
||||
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
@ -331,6 +332,7 @@ void NEB::run()
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
print_status();
|
||||
|
||||
@ -588,7 +590,7 @@ void NEB::print_status()
|
||||
MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);
|
||||
}
|
||||
|
||||
double one[numall];
|
||||
double one[7];
|
||||
one[0] = fneb->veng;
|
||||
one[1] = fneb->plen;
|
||||
one[2] = fneb->nlen;
|
||||
|
||||
@ -174,7 +174,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
||||
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
|
||||
molecule = new tagint[nlocal];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1);
|
||||
if (mask[i] & groupbit)
|
||||
molecule[i] = (tagint)((tagint)value[i] - minval + 1);
|
||||
delete[] value;
|
||||
} else error->all(FLERR,"Unsupported fix rigid custom property");
|
||||
} else {
|
||||
@ -624,6 +625,10 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
setupflag = 0;
|
||||
|
||||
// compute per body forces and torques at final_integrate() by default
|
||||
|
||||
earlyflag = 0;
|
||||
|
||||
// print statistics
|
||||
|
||||
int nsum = 0;
|
||||
@ -711,12 +716,26 @@ void FixRigid::init()
|
||||
avec_tri = (AtomVecTri *) atom->style_match("tri");
|
||||
|
||||
// warn if more than one rigid fix
|
||||
// if earlyflag, warn if any post-force fixes come after POEMS fix
|
||||
|
||||
int count = 0;
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
|
||||
if (modify->fix[i]->rigid_flag) count++;
|
||||
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
|
||||
|
||||
if (earlyflag) {
|
||||
int rflag = 0;
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (modify->fix[i]->rigid_flag) rflag = 1;
|
||||
if (rflag && (modify->fmask[i] & POST_FORCE) &&
|
||||
!modify->fix[i]->rigid_flag) {
|
||||
char str[128];
|
||||
sprintf(str,"Fix %d alters forces after fix rigid",modify->fix[i]->id);
|
||||
error->warning(FLERR,str);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// error if npt,nph fix comes before rigid fix
|
||||
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
@ -944,7 +963,7 @@ void FixRigid::initial_integrate(int vflag)
|
||||
which are added in when final_integrate() calculates a new fcm/torque
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigid::post_force(int vflag)
|
||||
void FixRigid::apply_langevin_thermostat()
|
||||
{
|
||||
if (me == 0) {
|
||||
double gamma1,gamma2;
|
||||
@ -1008,7 +1027,7 @@ void FixRigid::enforce2d()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigid::final_integrate()
|
||||
void FixRigid::compute_forces_and_torques()
|
||||
{
|
||||
int i,ibody;
|
||||
double dtfm;
|
||||
@ -1062,9 +1081,7 @@ void FixRigid::final_integrate()
|
||||
|
||||
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// update vcm and angmom
|
||||
// include Langevin thermostat forces
|
||||
// fflag,tflag = 0 for some dimensions in 2d
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
|
||||
@ -1073,6 +1090,31 @@ void FixRigid::final_integrate()
|
||||
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
|
||||
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
|
||||
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigid::post_force(int vflag)
|
||||
{
|
||||
if (langflag) apply_langevin_thermostat();
|
||||
if (earlyflag) compute_forces_and_torques();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigid::final_integrate()
|
||||
{
|
||||
int ibody;
|
||||
double dtfm;
|
||||
|
||||
if (!earlyflag) compute_forces_and_torques();
|
||||
|
||||
// update vcm and angmom
|
||||
// fflag,tflag = 0 for some dimensions in 2d
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
|
||||
// update vcm by 1/2 step
|
||||
|
||||
@ -2342,7 +2384,7 @@ void FixRigid::write_restart_file(char *file)
|
||||
sprintf(outfile,"%s.rigid",file);
|
||||
FILE *fp = fopen(outfile,"w");
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
char str[192];
|
||||
sprintf(str,"Cannot open fix rigid restart file %s",outfile);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
@ -2587,6 +2629,32 @@ void FixRigid::zero_rotation()
|
||||
set_v();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixRigid::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"bodyforces") == 0) {
|
||||
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
|
||||
if (strcmp(arg[1],"early") == 0) earlyflag = 1;
|
||||
else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
|
||||
else error->all(FLERR,"Illegal fix_modify command");
|
||||
|
||||
// reset fix mask
|
||||
// must do here and not in init,
|
||||
// since modify.cpp::init() uses fix masks before calling fix::init()
|
||||
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->id,id) == 0) {
|
||||
if (earlyflag) modify->fmask[i] |= POST_FORCE;
|
||||
else if (!langflag) modify->fmask[i] &= ~POST_FORCE;
|
||||
break;
|
||||
}
|
||||
return 2;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return temperature of collection of rigid bodies
|
||||
non-active DOF are removed by fflag/tflag and in tfactor
|
||||
|
||||
@ -38,7 +38,6 @@ class FixRigid : public Fix {
|
||||
void final_integrate_respa(int, int);
|
||||
void write_restart_file(char *);
|
||||
virtual double compute_scalar();
|
||||
virtual int modify_param(int, char **) {return 0;}
|
||||
|
||||
double memory_usage();
|
||||
void grow_arrays(int);
|
||||
@ -55,6 +54,7 @@ class FixRigid : public Fix {
|
||||
void reset_dt();
|
||||
void zero_momentum();
|
||||
void zero_rotation();
|
||||
virtual int modify_param(int, char **);
|
||||
virtual void *extract(const char*, int &);
|
||||
double extract_ke();
|
||||
double extract_erotational();
|
||||
@ -70,6 +70,7 @@ class FixRigid : public Fix {
|
||||
char *infile; // file to read rigid body attributes from
|
||||
int rstyle; // SINGLE,MOLECULE,GROUP
|
||||
int setupflag; // 1 if body properties are setup, else 0
|
||||
int earlyflag; // 1 if forces/torques computed at post_force()
|
||||
|
||||
int dimension; // # of dimensions
|
||||
int nbody; // # of rigid bodies
|
||||
@ -144,6 +145,8 @@ class FixRigid : public Fix {
|
||||
void set_v();
|
||||
void setup_bodies_static();
|
||||
void setup_bodies_dynamic();
|
||||
void apply_langevin_thermostat();
|
||||
void compute_forces_and_torques();
|
||||
void readfile(int, double *, double **, double **, double **,
|
||||
imageint *, int *);
|
||||
};
|
||||
|
||||
@ -620,87 +620,14 @@ void FixRigidNH::final_integrate()
|
||||
akin_t = akin_r = 0.0;
|
||||
}
|
||||
|
||||
// sum over atoms to get force and torque on rigid body
|
||||
// late calculation of forces and torques (if requested)
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
if (triclinic) {
|
||||
xy = domain->xy;
|
||||
xz = domain->xz;
|
||||
yz = domain->yz;
|
||||
}
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
|
||||
for (ibody = 0; ibody < nbody; ibody++)
|
||||
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (body[i] < 0) continue;
|
||||
ibody = body[i];
|
||||
|
||||
sum[ibody][0] += f[i][0];
|
||||
sum[ibody][1] += f[i][1];
|
||||
sum[ibody][2] += f[i][2];
|
||||
|
||||
xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
|
||||
|
||||
if (triclinic == 0) {
|
||||
xunwrap = x[i][0] + xbox*xprd;
|
||||
yunwrap = x[i][1] + ybox*yprd;
|
||||
zunwrap = x[i][2] + zbox*zprd;
|
||||
} else {
|
||||
xunwrap = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
|
||||
yunwrap = x[i][1] + ybox*yprd + zbox*yz;
|
||||
zunwrap = x[i][2] + zbox*zprd;
|
||||
}
|
||||
|
||||
dx = xunwrap - xcm[ibody][0];
|
||||
dy = yunwrap - xcm[ibody][1];
|
||||
dz = zunwrap - xcm[ibody][2];
|
||||
|
||||
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
|
||||
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
|
||||
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
|
||||
}
|
||||
|
||||
// extended particles add their torque to torque of body
|
||||
|
||||
if (extended) {
|
||||
double **torque_one = atom->torque;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (body[i] < 0) continue;
|
||||
ibody = body[i];
|
||||
|
||||
if (eflags[i] & TORQUE) {
|
||||
sum[ibody][3] += torque_one[i][0];
|
||||
sum[ibody][4] += torque_one[i][1];
|
||||
sum[ibody][5] += torque_one[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
|
||||
if (!earlyflag) compute_forces_and_torques();
|
||||
|
||||
// update vcm and angmom
|
||||
// include Langevin thermostat forces
|
||||
// fflag,tflag = 0 for some dimensions in 2d
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
|
||||
fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
|
||||
fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
|
||||
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
|
||||
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
|
||||
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
|
||||
|
||||
// update vcm by 1/2 step
|
||||
|
||||
@ -1324,7 +1251,7 @@ int FixRigidNH::modify_param(int narg, char **arg)
|
||||
return 2;
|
||||
}
|
||||
|
||||
return 0;
|
||||
return FixRigid::modify_param(narg,arg);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -643,80 +643,9 @@ void FixRigidNHSmall::final_integrate()
|
||||
scale_r *= exp(-dtq * (pdim * mtk_term2));
|
||||
}
|
||||
|
||||
// sum over atoms to get force and torque on rigid body
|
||||
// late calculation of forces and torques (if requested)
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double dx,dy,dz;
|
||||
double unwrap[3];
|
||||
double *xcm,*fcm,*tcm;
|
||||
|
||||
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
|
||||
fcm = body[ibody].fcm;
|
||||
fcm[0] = fcm[1] = fcm[2] = 0.0;
|
||||
tcm = body[ibody].torque;
|
||||
tcm[0] = tcm[1] = tcm[2] = 0.0;
|
||||
}
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (atom2body[i] < 0) continue;
|
||||
Body *b = &body[atom2body[i]];
|
||||
|
||||
fcm = b->fcm;
|
||||
fcm[0] += f[i][0];
|
||||
fcm[1] += f[i][1];
|
||||
fcm[2] += f[i][2];
|
||||
|
||||
domain->unmap(x[i],xcmimage[i],unwrap);
|
||||
xcm = b->xcm;
|
||||
dx = unwrap[0] - xcm[0];
|
||||
dy = unwrap[1] - xcm[1];
|
||||
dz = unwrap[2] - xcm[2];
|
||||
|
||||
tcm = b->torque;
|
||||
tcm[0] += dy*f[i][2] - dz*f[i][1];
|
||||
tcm[1] += dz*f[i][0] - dx*f[i][2];
|
||||
tcm[2] += dx*f[i][1] - dy*f[i][0];
|
||||
}
|
||||
|
||||
// extended particles add their torque to torque of body
|
||||
|
||||
if (extended) {
|
||||
double **torque = atom->torque;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (atom2body[i] < 0) continue;
|
||||
|
||||
if (eflags[i] & TORQUE) {
|
||||
tcm = body[atom2body[i]].torque;
|
||||
tcm[0] += torque[i][0];
|
||||
tcm[1] += torque[i][1];
|
||||
tcm[2] += torque[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// reverse communicate fcm, torque of all bodies
|
||||
|
||||
commflag = FORCE_TORQUE;
|
||||
comm->reverse_comm_fix(this,6);
|
||||
|
||||
// include Langevin thermostat forces and torques
|
||||
|
||||
if (langflag) {
|
||||
for (int ibody = 0; ibody < nlocal_body; ibody++) {
|
||||
fcm = body[ibody].fcm;
|
||||
fcm[0] += langextra[ibody][0];
|
||||
fcm[1] += langextra[ibody][1];
|
||||
fcm[2] += langextra[ibody][2];
|
||||
tcm = body[ibody].torque;
|
||||
tcm[0] += langextra[ibody][3];
|
||||
tcm[1] += langextra[ibody][4];
|
||||
tcm[2] += langextra[ibody][5];
|
||||
}
|
||||
}
|
||||
if (!earlyflag) compute_forces_and_torques();
|
||||
|
||||
// update vcm and angmom
|
||||
// include Langevin thermostat forces
|
||||
@ -1440,7 +1369,7 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
|
||||
return 2;
|
||||
}
|
||||
|
||||
return 0;
|
||||
return FixRigidSmall::modify_param(narg,arg);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -457,6 +457,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
|
||||
avec_line = (AtomVecLine *) atom->style_match("line");
|
||||
avec_tri = (AtomVecTri *) atom->style_match("tri");
|
||||
|
||||
// compute per body forces and torques inside final_integrate() by default
|
||||
|
||||
earlyflag = 0;
|
||||
|
||||
// print statistics
|
||||
|
||||
int one = 0;
|
||||
@ -555,9 +559,22 @@ void FixRigidSmall::init()
|
||||
|
||||
int count = 0;
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
|
||||
if (modify->fix[i]->rigid_flag) count++;
|
||||
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
|
||||
|
||||
if (earlyflag) {
|
||||
int rflag = 0;
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (modify->fix[i]->rigid_flag) rflag = 1;
|
||||
if (rflag && (modify->fmask[i] & POST_FORCE) &&
|
||||
!modify->fix[i]->rigid_flag) {
|
||||
char str[128];
|
||||
sprintf(str,"Fix %d alters forces after fix rigid",modify->fix[i]->id);
|
||||
error->warning(FLERR,str);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// error if npt,nph fix comes before rigid fix
|
||||
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
@ -770,10 +787,10 @@ void FixRigidSmall::initial_integrate(int vflag)
|
||||
/* ----------------------------------------------------------------------
|
||||
apply Langevin thermostat to all 6 DOF of rigid bodies I own
|
||||
unlike fix langevin, this stores extra force in extra arrays,
|
||||
which are added in when final_integrate() calculates a new fcm/torque
|
||||
which are added in when a new fcm/torque are calculated
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidSmall::post_force(int vflag)
|
||||
void FixRigidSmall::apply_langevin_thermostat()
|
||||
{
|
||||
double gamma1,gamma2;
|
||||
|
||||
@ -850,10 +867,18 @@ void FixRigidSmall::enforce2d()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidSmall::final_integrate()
|
||||
void FixRigidSmall::post_force(int vflag)
|
||||
{
|
||||
if (langflag) apply_langevin_thermostat();
|
||||
if (earlyflag) compute_forces_and_torques();
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidSmall::compute_forces_and_torques()
|
||||
{
|
||||
int i,ibody;
|
||||
double dtfm;
|
||||
|
||||
//check(3);
|
||||
|
||||
@ -931,6 +956,18 @@ void FixRigidSmall::final_integrate()
|
||||
tcm[2] += langextra[ibody][5];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidSmall::final_integrate()
|
||||
{
|
||||
double dtfm;
|
||||
|
||||
//check(3);
|
||||
|
||||
if (!earlyflag) compute_forces_and_torques();
|
||||
|
||||
// update vcm and angmom, recompute omega
|
||||
|
||||
@ -3384,6 +3421,33 @@ void FixRigidSmall::zero_rotation()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixRigidSmall::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"bodyforces") == 0) {
|
||||
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
|
||||
if (strcmp(arg[1],"early") == 0) earlyflag = 1;
|
||||
else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
|
||||
else error->all(FLERR,"Illegal fix_modify command");
|
||||
|
||||
// reset fix mask
|
||||
// must do here and not in init,
|
||||
// since modify.cpp::init() uses fix masks before calling fix::init()
|
||||
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->id,id) == 0) {
|
||||
if (earlyflag) modify->fmask[i] |= POST_FORCE;
|
||||
else if (!langflag) modify->fmask[i] &= ~POST_FORCE;
|
||||
break;
|
||||
}
|
||||
|
||||
return 2;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *FixRigidSmall::extract(const char *str, int &dim)
|
||||
{
|
||||
if (strcmp(str,"body") == 0) {
|
||||
|
||||
@ -63,6 +63,7 @@ class FixRigidSmall : public Fix {
|
||||
void reset_dt();
|
||||
void zero_momentum();
|
||||
void zero_rotation();
|
||||
int modify_param(int, char **);
|
||||
void *extract(const char*, int &);
|
||||
double extract_ke();
|
||||
double extract_erotational();
|
||||
@ -78,6 +79,7 @@ class FixRigidSmall : public Fix {
|
||||
|
||||
char *infile; // file to read rigid body attributes from
|
||||
int setupflag; // 1 if body properties are setup, else 0
|
||||
int earlyflag; // 1 if forces/torques are computed at post_force()
|
||||
int commflag; // various modes of forward/reverse comm
|
||||
int customflag; // 1 if custom property/variable define bodies
|
||||
int nbody; // total # of rigid bodies
|
||||
@ -191,6 +193,8 @@ class FixRigidSmall : public Fix {
|
||||
void create_bodies(tagint *);
|
||||
void setup_bodies_static();
|
||||
void setup_bodies_dynamic();
|
||||
void apply_langevin_thermostat();
|
||||
void compute_forces_and_torques();
|
||||
void readfile(int, double **, int *);
|
||||
void grow_body();
|
||||
void reset_atom2body();
|
||||
|
||||
19
src/USER-BOCS/README
Normal file
19
src/USER-BOCS/README
Normal file
@ -0,0 +1,19 @@
|
||||
This user package implements the pressure correction to the barostat as
|
||||
outlined in:
|
||||
|
||||
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
|
||||
accurately describe the structure, pressure, and compressibility of
|
||||
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
|
||||
|
||||
doi: 10.1063/1.4937383
|
||||
|
||||
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
|
||||
https://github.com/noid-group/BOCS
|
||||
|
||||
See the following reference for information about the entire package:
|
||||
|
||||
Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
|
||||
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
|
||||
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
|
||||
|
||||
Example inputs are in the examples/USER/bocs folder.
|
||||
444
src/USER-BOCS/compute_pressure_bocs.cpp
Normal file
444
src/USER-BOCS/compute_pressure_bocs.cpp
Normal file
@ -0,0 +1,444 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
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.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include <cstring>
|
||||
#include <cstdlib>
|
||||
#include "compute_pressure_bocs.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "bond.h"
|
||||
#include "angle.h"
|
||||
#include "dihedral.h"
|
||||
#include "improper.h"
|
||||
#include "kspace.h"
|
||||
#include "error.h"
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg),
|
||||
vptr(NULL), id_temp(NULL)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal compute pressure/bocs command");
|
||||
if (igroup) error->all(FLERR,"Compute pressure/bocs must use group all");
|
||||
|
||||
scalar_flag = vector_flag = 1;
|
||||
size_vector = 6;
|
||||
extscalar = 0;
|
||||
extvector = 0;
|
||||
pressflag = 1;
|
||||
timeflag = 1;
|
||||
|
||||
p_match_flag = 0;
|
||||
phi_coeff = NULL;
|
||||
|
||||
// store temperature ID used by pressure computation
|
||||
// insure it is valid for temperature computation
|
||||
|
||||
if (strcmp(arg[3],"NULL") == 0) id_temp = NULL;
|
||||
else {
|
||||
int n = strlen(arg[3]) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,arg[3]);
|
||||
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
|
||||
if (modify->compute[icompute]->tempflag == 0)
|
||||
error->all(FLERR,"Compute pressure/bocs temperature ID does not "
|
||||
"compute temperature");
|
||||
}
|
||||
|
||||
// process optional args
|
||||
|
||||
if (narg == 4) {
|
||||
keflag = 1;
|
||||
pairflag = 1;
|
||||
bondflag = angleflag = dihedralflag = improperflag = 1;
|
||||
kspaceflag = fixflag = 1;
|
||||
} else {
|
||||
keflag = 0;
|
||||
pairflag = 0;
|
||||
bondflag = angleflag = dihedralflag = improperflag = 0;
|
||||
kspaceflag = fixflag = 0;
|
||||
int iarg = 4;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
|
||||
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
|
||||
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
|
||||
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
|
||||
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
|
||||
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
|
||||
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
|
||||
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
|
||||
else if (strcmp(arg[iarg],"virial") == 0) {
|
||||
pairflag = 1;
|
||||
bondflag = angleflag = dihedralflag = improperflag = 1;
|
||||
kspaceflag = fixflag = 1;
|
||||
} else error->all(FLERR,"Illegal compute pressure/bocs command");
|
||||
iarg++;
|
||||
}
|
||||
}
|
||||
|
||||
// error check
|
||||
|
||||
if (keflag && id_temp == NULL)
|
||||
error->all(FLERR,"Compute pressure/bocs requires temperature ID "
|
||||
"to include kinetic energy");
|
||||
|
||||
vector = new double[6];
|
||||
nvirial = 0;
|
||||
vptr = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputePressureBocs::~ComputePressureBocs()
|
||||
{
|
||||
delete [] id_temp;
|
||||
delete [] vector;
|
||||
delete [] vptr;
|
||||
if (phi_coeff) free(phi_coeff);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePressureBocs::init()
|
||||
{
|
||||
boltz = force->boltz;
|
||||
nktv2p = force->nktv2p;
|
||||
dimension = domain->dimension;
|
||||
|
||||
// set temperature compute, must be done in init()
|
||||
// fixes could have changed or compute_modify could have changed it
|
||||
|
||||
if (keflag) {
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
|
||||
temperature = modify->compute[icompute];
|
||||
}
|
||||
|
||||
// detect contributions to virial
|
||||
// vptr points to all virial[6] contributions
|
||||
|
||||
delete [] vptr;
|
||||
nvirial = 0;
|
||||
vptr = NULL;
|
||||
|
||||
if (pairflag && force->pair) nvirial++;
|
||||
if (bondflag && atom->molecular && force->bond) nvirial++;
|
||||
if (angleflag && atom->molecular && force->angle) nvirial++;
|
||||
if (dihedralflag && atom->molecular && force->dihedral) nvirial++;
|
||||
if (improperflag && atom->molecular && force->improper) nvirial++;
|
||||
if (fixflag)
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->virial_flag) nvirial++;
|
||||
|
||||
if (nvirial) {
|
||||
vptr = new double*[nvirial];
|
||||
nvirial = 0;
|
||||
if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
|
||||
if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;
|
||||
if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial;
|
||||
if (dihedralflag && force->dihedral)
|
||||
vptr[nvirial++] = force->dihedral->virial;
|
||||
if (improperflag && force->improper)
|
||||
vptr[nvirial++] = force->improper->virial;
|
||||
if (fixflag)
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->virial_flag)
|
||||
vptr[nvirial++] = modify->fix[i]->virial;
|
||||
}
|
||||
|
||||
// flag Kspace contribution separately, since not summed across procs
|
||||
|
||||
if (kspaceflag && force->kspace) kspace_virial = force->kspace->virial;
|
||||
else kspace_virial = NULL;
|
||||
}
|
||||
|
||||
/* Extra functions added for BOCS */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the pressure correction for the analytical basis set
|
||||
------------------------------------------------------------------------- */
|
||||
double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff,
|
||||
int N_mol, double vavg, double vCG)
|
||||
{
|
||||
double correction = 0.0;
|
||||
for (int i = 1; i <= N_basis; ++i)
|
||||
{
|
||||
correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) *
|
||||
pow( ( 1 / vavg ) * ( vCG - vavg ),i-1);
|
||||
}
|
||||
return correction;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Find the relevant index position if using a spline basis set
|
||||
------------------------------------------------------------------------- */
|
||||
double ComputePressureBocs::find_index(double * grid, double value)
|
||||
{
|
||||
int i;
|
||||
double spacing = fabs(grid[1]-grid[0]);
|
||||
int gridsize = spline_length;
|
||||
for (i = 0; i < (gridsize-1); ++i)
|
||||
{
|
||||
if (value >= grid[i] && value <= grid[i+1]) { return i; }
|
||||
}
|
||||
|
||||
if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; }
|
||||
|
||||
for (int i = 0; i < gridsize; ++i)
|
||||
{
|
||||
fprintf(stderr, "grid %d: %f\n",i,grid[i]);
|
||||
}
|
||||
char * errmsg = (char *) calloc(100,sizeof(char));
|
||||
sprintf(errmsg,"Value %f does not fall within spline grid.\n",value);
|
||||
error->all(FLERR,errmsg);
|
||||
|
||||
exit(1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the pressure correction for a spline basis set
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
|
||||
double vCG)
|
||||
{
|
||||
int i = find_index(grid[0],vCG);
|
||||
double correction, deltax = vCG - grid[0][i];
|
||||
|
||||
if (basis_type == 1)
|
||||
{
|
||||
correction = grid[1][i] + (deltax) *
|
||||
( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
|
||||
}
|
||||
else if (basis_type == 2)
|
||||
{
|
||||
correction = grid[1][i] + (grid[2][i] * deltax) +
|
||||
(grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
|
||||
}
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
|
||||
}
|
||||
return correction;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
send cg info from fix_bocs to compute_pressure_bocs for the analytical
|
||||
basis set
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
|
||||
double *sent_phi_coeff, int sent_N_mol, double sent_vavg)
|
||||
{
|
||||
if (basis_type == 0) { p_basis_type = 0; }
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
|
||||
}
|
||||
|
||||
p_match_flag = 1;
|
||||
|
||||
N_basis = sent_N_basis;
|
||||
if (phi_coeff) free(phi_coeff);
|
||||
phi_coeff = ((double *) calloc(N_basis, sizeof(double)) );
|
||||
for (int i=0; i<N_basis; i++) { phi_coeff[i] = sent_phi_coeff[i]; }
|
||||
|
||||
N_mol = sent_N_mol;
|
||||
vavg = sent_vavg;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
send cg info from fix_bocs to compute_pressure_bocs for a spline basis
|
||||
set
|
||||
------------------------------------------------------------------------- */
|
||||
void ComputePressureBocs::send_cg_info(int basis_type,
|
||||
double ** in_splines, int gridsize)
|
||||
{
|
||||
if (basis_type == 1) { p_basis_type = 1; }
|
||||
else if (basis_type == 2) { p_basis_type = 2; }
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
|
||||
}
|
||||
splines = in_splines;
|
||||
spline_length = gridsize;
|
||||
p_match_flag = 1;
|
||||
}
|
||||
|
||||
/* End of new functions for BOCS */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute total pressure, averaged over Pxx, Pyy, Pzz
|
||||
------------------------------------------------------------------------- */
|
||||
double ComputePressureBocs::compute_scalar()
|
||||
{
|
||||
invoked_scalar = update->ntimestep;
|
||||
if (update->vflag_global != invoked_scalar)
|
||||
error->all(FLERR,"Virial was not tallied on needed timestep");
|
||||
|
||||
// invoke temperature if it hasn't been already
|
||||
|
||||
double t;
|
||||
double volume, correction = 0;
|
||||
if (keflag) {
|
||||
if (temperature->invoked_scalar != update->ntimestep)
|
||||
t = temperature->compute_scalar();
|
||||
else t = temperature->scalar;
|
||||
}
|
||||
|
||||
if (dimension == 3) {
|
||||
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
|
||||
volume = (domain->xprd * domain->yprd * domain->zprd);
|
||||
|
||||
/* MRD NJD if block */
|
||||
if ( p_basis_type == 0 )
|
||||
{
|
||||
correction = get_cg_p_corr(N_basis,phi_coeff,N_mol,vavg,volume);
|
||||
}
|
||||
else if ( p_basis_type == 1 || p_basis_type == 2 )
|
||||
{
|
||||
correction = get_cg_p_corr(splines, p_basis_type, volume);
|
||||
}
|
||||
|
||||
virial_compute(3,3);
|
||||
if (keflag)
|
||||
scalar = (temperature->dof * boltz * t +
|
||||
virial[0] + virial[1] + virial[2]) / 3.0 *
|
||||
inv_volume * nktv2p + (correction);
|
||||
else
|
||||
scalar = (virial[0] + virial[1] + virial[2]) / 3.0 *
|
||||
inv_volume * nktv2p + (correction);
|
||||
} else {
|
||||
if (p_match_flag)
|
||||
{
|
||||
error->all(FLERR,"Pressure matching not implemented in 2-d.\n");
|
||||
exit(1);
|
||||
} // The rest of this can probably be deleted.
|
||||
inv_volume = 1.0 / (domain->xprd * domain->yprd);
|
||||
virial_compute(2,2);
|
||||
if (keflag)
|
||||
scalar = (temperature->dof * boltz * t +
|
||||
virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
|
||||
else
|
||||
scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
|
||||
}
|
||||
|
||||
return scalar;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute pressure tensor
|
||||
assume KE tensor has already been computed
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputePressureBocs::compute_vector()
|
||||
{
|
||||
invoked_vector = update->ntimestep;
|
||||
if (update->vflag_global != invoked_vector)
|
||||
error->all(FLERR,"Virial was not tallied on needed timestep");
|
||||
|
||||
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
|
||||
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
|
||||
"tensor components with kspace_style msm");
|
||||
|
||||
// invoke temperature if it hasn't been already
|
||||
|
||||
double *ke_tensor;
|
||||
if (keflag) {
|
||||
if (temperature->invoked_vector != update->ntimestep)
|
||||
temperature->compute_vector();
|
||||
ke_tensor = temperature->vector;
|
||||
}
|
||||
|
||||
if (dimension == 3) {
|
||||
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
|
||||
virial_compute(6,3);
|
||||
if (keflag) {
|
||||
for (int i = 0; i < 6; i++)
|
||||
vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
|
||||
} else
|
||||
for (int i = 0; i < 6; i++)
|
||||
vector[i] = virial[i] * inv_volume * nktv2p;
|
||||
} else {
|
||||
inv_volume = 1.0 / (domain->xprd * domain->yprd);
|
||||
virial_compute(4,2);
|
||||
if (keflag) {
|
||||
vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
|
||||
vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
|
||||
vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
|
||||
vector[2] = vector[4] = vector[5] = 0.0;
|
||||
} else {
|
||||
vector[0] = virial[0] * inv_volume * nktv2p;
|
||||
vector[1] = virial[1] * inv_volume * nktv2p;
|
||||
vector[3] = virial[3] * inv_volume * nktv2p;
|
||||
vector[2] = vector[4] = vector[5] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePressureBocs::virial_compute(int n, int ndiag)
|
||||
{
|
||||
int i,j;
|
||||
double v[6],*vcomponent;
|
||||
|
||||
for (i = 0; i < n; i++) v[i] = 0.0;
|
||||
|
||||
// sum contributions to virial from forces and fixes
|
||||
|
||||
for (j = 0; j < nvirial; j++) {
|
||||
vcomponent = vptr[j];
|
||||
for (i = 0; i < n; i++) v[i] += vcomponent[i];
|
||||
}
|
||||
|
||||
// sum virial across procs
|
||||
|
||||
MPI_Allreduce(v,virial,n,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// KSpace virial contribution is already summed across procs
|
||||
|
||||
if (kspace_virial)
|
||||
for (i = 0; i < n; i++) virial[i] += kspace_virial[i];
|
||||
|
||||
// LJ long-range tail correction, only if pair contributions are included
|
||||
|
||||
if (force->pair && pairflag && force->pair->tail_flag)
|
||||
for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePressureBocs::reset_extra_compute_fix(const char *id_new)
|
||||
{
|
||||
delete [] id_temp;
|
||||
int n = strlen(id_new) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id_new);
|
||||
}
|
||||
114
src/USER-BOCS/compute_pressure_bocs.h
Normal file
114
src/USER-BOCS/compute_pressure_bocs.h
Normal file
@ -0,0 +1,114 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
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.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(PRESSURE/BOCS,ComputePressureBocs)
|
||||
|
||||
#else
|
||||
|
||||
|
||||
#ifndef LMP_COMPUTE_PRESSURE_BOCS_H
|
||||
#define LMP_COMPUTE_PRESSURE_BOCS_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// ComputePressure -> ComputePressureBocs MRD NJD
|
||||
class ComputePressureBocs : public Compute {
|
||||
public:
|
||||
ComputePressureBocs(class LAMMPS *, int, char **);
|
||||
virtual ~ComputePressureBocs();
|
||||
virtual void init();
|
||||
virtual double compute_scalar();
|
||||
virtual void compute_vector();
|
||||
void reset_extra_compute_fix(const char *);
|
||||
|
||||
double compute_cg_scalar();
|
||||
double get_cg_p_corr(int, double *, int, double, double);
|
||||
double get_cg_fluct(double, double);
|
||||
void send_cg_info(int, int, double*, int, double);
|
||||
void send_cg_info(int, double **, int);
|
||||
double get_cg_p_corr(double **, int, double);
|
||||
double find_index(double* , double);
|
||||
|
||||
protected:
|
||||
double boltz,nktv2p,inv_volume;
|
||||
int nvirial,dimension;
|
||||
double **vptr;
|
||||
double *kspace_virial;
|
||||
Compute *temperature;
|
||||
char *id_temp;
|
||||
double virial[6];
|
||||
int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
|
||||
int fixflag,kspaceflag;
|
||||
|
||||
// NJD MRD
|
||||
int p_basis_type;
|
||||
int p_match_flag;
|
||||
double vavg;
|
||||
int N_mol;
|
||||
int N_basis;
|
||||
double *phi_coeff;
|
||||
double ** splines;
|
||||
int spline_length;
|
||||
|
||||
void virial_compute(int, int);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Compute pressure must use group all
|
||||
|
||||
Virial contributions computed by potentials (pair, bond, etc) are
|
||||
computed on all atoms.
|
||||
|
||||
E: Could not find compute pressure temperature ID
|
||||
|
||||
The compute ID for calculating temperature does not exist.
|
||||
|
||||
E: Compute pressure temperature ID does not compute temperature
|
||||
|
||||
The compute ID assigned to a pressure computation must compute
|
||||
temperature.
|
||||
|
||||
E: Compute pressure requires temperature ID to include kinetic energy
|
||||
|
||||
The keflag cannot be used unless a temperature compute is provided.
|
||||
|
||||
E: Virial was not tallied on needed timestep
|
||||
|
||||
You are using a thermo keyword that requires potentials to
|
||||
have tallied the virial, but they didn't on this timestep. See the
|
||||
variable doc page for ideas on how to make this work.
|
||||
|
||||
E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm
|
||||
|
||||
Otherwise MSM will compute only a scalar pressure. See the kspace_modify
|
||||
command for details on this setting.
|
||||
|
||||
*/
|
||||
2431
src/USER-BOCS/fix_bocs.cpp
Normal file
2431
src/USER-BOCS/fix_bocs.cpp
Normal file
File diff suppressed because it is too large
Load Diff
302
src/USER-BOCS/fix_bocs.h
Normal file
302
src/USER-BOCS/fix_bocs.h
Normal file
@ -0,0 +1,302 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
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.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(bocs,FixBocs)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_BOCS_H
|
||||
#define LMP_FIX_BOCS_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixBocs : public Fix {
|
||||
public:
|
||||
FixBocs(class LAMMPS *, int, char **); // MRD NJD
|
||||
virtual ~FixBocs(); // MRD NJD
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void setup(int);
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void initial_integrate_respa(int, int, int);
|
||||
void final_integrate_respa(int, int);
|
||||
virtual void pre_exchange();
|
||||
double compute_scalar();
|
||||
virtual double compute_vector(int);
|
||||
void write_restart(FILE *);
|
||||
virtual int pack_restart_data(double *); // pack restart data
|
||||
virtual void restart(char *);
|
||||
int modify_param(int, char **);
|
||||
void reset_target(double);
|
||||
void reset_dt();
|
||||
virtual void *extract(const char*,int &);
|
||||
double memory_usage();
|
||||
|
||||
|
||||
protected:
|
||||
int dimension,which;
|
||||
double dtv,dtf,dthalf,dt4,dt8,dto;
|
||||
double boltz,nktv2p,tdof;
|
||||
double vol0; // reference volume
|
||||
double t0; // reference temperature
|
||||
// used for barostat mass
|
||||
double t_start,t_stop;
|
||||
double t_current,t_target,ke_target;
|
||||
double t_freq;
|
||||
|
||||
int tstat_flag; // 1 if control T
|
||||
int pstat_flag; // 1 if control P
|
||||
|
||||
int pstyle,pcouple,allremap;
|
||||
int p_flag[6]; // 1 if control P on this dim, 0 if not
|
||||
double p_start[6],p_stop[6];
|
||||
double p_freq[6],p_target[6];
|
||||
double omega[6],omega_dot[6];
|
||||
double omega_mass[6];
|
||||
double p_current[6];
|
||||
double drag,tdrag_factor; // drag factor on particle thermostat
|
||||
double pdrag_factor; // drag factor on barostat
|
||||
int kspace_flag; // 1 if KSpace invoked, 0 if not
|
||||
int nrigid; // number of rigid fixes
|
||||
int dilate_group_bit; // mask for dilation group
|
||||
int *rfix; // indices of rigid fixes
|
||||
char *id_dilate; // group name to dilate
|
||||
class Irregular *irregular; // for migrating atoms after box flips
|
||||
|
||||
// MRD NJD
|
||||
int p_basis_type;
|
||||
int p_match_flag;
|
||||
double vavg;
|
||||
int N_mol;
|
||||
int N_p_match;
|
||||
double *p_match_coeffs;
|
||||
double ** splines;
|
||||
int spline_length;
|
||||
|
||||
|
||||
int nlevels_respa;
|
||||
double *step_respa;
|
||||
|
||||
char *id_temp,*id_press;
|
||||
class Compute *temperature,*pressure;
|
||||
int tcomputeflag,pcomputeflag; // 1 = compute was created by fix
|
||||
// 0 = created externally
|
||||
|
||||
double *eta,*eta_dot; // chain thermostat for particles
|
||||
double *eta_dotdot;
|
||||
double *eta_mass;
|
||||
int mtchain; // length of chain
|
||||
int mtchain_default_flag; // 1 = mtchain is default
|
||||
|
||||
double *etap; // chain thermostat for barostat
|
||||
double *etap_dot;
|
||||
double *etap_dotdot;
|
||||
double *etap_mass;
|
||||
int mpchain; // length of chain
|
||||
|
||||
int mtk_flag; // 0 if using Hoover barostat
|
||||
int pdim; // number of barostatted dims
|
||||
double p_freq_max; // maximum barostat frequency
|
||||
|
||||
double p_hydro; // hydrostatic target pressure
|
||||
|
||||
int nc_tchain,nc_pchain;
|
||||
double factor_eta;
|
||||
double sigma[6]; // scaled target stress
|
||||
double fdev[6]; // deviatoric force on barostat
|
||||
int deviatoric_flag; // 0 if target stress tensor is hydrostatic
|
||||
double h0_inv[6]; // h_inv of reference (zero strain) box
|
||||
int nreset_h0; // interval for resetting h0
|
||||
|
||||
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
|
||||
|
||||
int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
|
||||
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
|
||||
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
|
||||
int dipole_flag; // 1 if dipole is updated, 0 if not.
|
||||
int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
|
||||
|
||||
int scaleyz; // 1 if yz scaled with lz
|
||||
int scalexz; // 1 if xz scaled with lz
|
||||
int scalexy; // 1 if xy scaled with ly
|
||||
int flipflag; // 1 if box flips are invoked as needed
|
||||
|
||||
int pre_exchange_flag; // set if pre_exchange needed for box flips
|
||||
|
||||
double fixedpoint[3]; // location of dilation fixed-point
|
||||
|
||||
void couple();
|
||||
virtual void remap();
|
||||
void nhc_temp_integrate();
|
||||
void nhc_press_integrate();
|
||||
|
||||
int read_F_table(char *, int);
|
||||
void build_cubic_splines(double **);
|
||||
|
||||
virtual void nve_x(); // may be overwritten by child classes
|
||||
virtual void nve_v();
|
||||
virtual void nh_v_press();
|
||||
virtual void nh_v_temp();
|
||||
virtual void compute_temp_target();
|
||||
virtual int size_restart_global();
|
||||
|
||||
void compute_sigma();
|
||||
void compute_deviatoric();
|
||||
double compute_strain_energy();
|
||||
void compute_press_target();
|
||||
void nh_omega_dot();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Target temperature for fix bocs cannot be 0.0
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Invalid fix bocs command for a 2d simulation
|
||||
|
||||
Cannot control z dimension in a 2d model.
|
||||
|
||||
E: Fix bocs dilate group ID does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Invalid fix bocs command pressure settings
|
||||
|
||||
If multiple dimensions are coupled, those dimensions must be
|
||||
specified.
|
||||
|
||||
E: Cannot use fix bocs on a non-periodic dimension
|
||||
|
||||
When specifying a diagonal pressure component, the dimension must be
|
||||
periodic.
|
||||
|
||||
E: Cannot use fix bocs on a 2nd non-periodic dimension
|
||||
|
||||
When specifying an off-diagonal pressure component, the 2nd of the two
|
||||
dimensions must be periodic. E.g. if the xy component is specified,
|
||||
then the y dimension must be periodic.
|
||||
|
||||
E: Cannot use fix bocs with yz scaling when z is non-periodic dimension
|
||||
|
||||
The 2nd dimension in the barostatted tilt factor must be periodic.
|
||||
|
||||
E: Cannot use fix bocs with xz scaling when z is non-periodic dimension
|
||||
|
||||
The 2nd dimension in the barostatted tilt factor must be periodic.
|
||||
|
||||
E: Cannot use fix bocs with xy scaling when y is non-periodic dimension
|
||||
|
||||
The 2nd dimension in the barostatted tilt factor must be periodic.
|
||||
|
||||
E: Cannot use fix bocs with both yz dynamics and yz scaling
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use fix bocs with both xz dynamics and xz scaling
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use fix bocs with both xy dynamics and xy scaling
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Can not specify Pxy/Pxz/Pyz in fix bocs with non-triclinic box
|
||||
|
||||
Only triclinic boxes can be used with off-diagonal pressure components.
|
||||
See the region prism command for details.
|
||||
|
||||
E: Invalid fix bocs pressure settings
|
||||
|
||||
Settings for coupled dimensions must be the same.
|
||||
|
||||
E: Using update dipole flag requires atom style sphere
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Using update dipole flag requires atom attribute mu
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: The dlm flag must be used with update dipole
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix bocs damping parameters must be > 0.0
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use fix npt and fix deform on same component of stress tensor
|
||||
|
||||
This would be changing the same box dimension twice.
|
||||
|
||||
E: Temperature ID for fix bocs does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pressure ID for fix bocs does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix bocs has tilted box too far in one step - periodic cell is too far from equilibrium state
|
||||
|
||||
Self-explanatory. The change in the box tilt is too extreme
|
||||
on a short timescale.
|
||||
|
||||
E: Could not find fix_modify temperature ID
|
||||
|
||||
The compute ID for computing temperature does not exist.
|
||||
|
||||
E: Fix_modify temperature ID does not compute temperature
|
||||
|
||||
The compute ID assigned to the fix must compute temperature.
|
||||
|
||||
W: Temperature for fix modify is not for group all
|
||||
|
||||
The temperature compute is being used with a pressure calculation
|
||||
which does operate on group all, so this may be inconsistent.
|
||||
|
||||
E: Pressure ID for fix modify does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Could not find fix_modify pressure ID
|
||||
|
||||
The compute ID for computing pressure does not exist.
|
||||
|
||||
E: Fix_modify pressure ID does not compute pressure
|
||||
|
||||
The compute ID assigned to the fix must compute pressure.
|
||||
|
||||
*/
|
||||
@ -2,22 +2,29 @@ This package contains a LAMMPS implementation of coarse-grained
|
||||
models of DNA, which can be used to model sequence-specific
|
||||
DNA strands.
|
||||
|
||||
See the doc pages and [1,2,3] for the individual bond and pair styles.
|
||||
The packages contains also a new Langevin-type rigid-body integrator,
|
||||
which has also its own doc page and is explained in [4].
|
||||
Please cite [1] and the relevant oxDNA articles in any publication
|
||||
that uses this package.
|
||||
|
||||
[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
|
||||
See the doc pages and [2,3,4] for the individual bond and pair styles.
|
||||
The packages contains also a new Langevin-type rigid-body integrator,
|
||||
which has also its own doc page and is explained in [5].
|
||||
|
||||
[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
|
||||
"Coarse-grained simulation of DNA using LAMMPS",
|
||||
Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
|
||||
and thermodynamic properties of a coarse-grained DNA model",
|
||||
J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
|
||||
[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
|
||||
self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
|
||||
[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
|
||||
Improved Structural Properties and Salt Dependence into a Coarse-Grained
|
||||
Model of DNA, J. Chem. Phys. 142, 234901 (2015).
|
||||
|
||||
[4] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
|
||||
[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
|
||||
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
|
||||
144114 (2015).
|
||||
|
||||
@ -28,7 +35,7 @@ well as DNA duplexes or arrays of duplexes can be found in
|
||||
/examples/USER/cgdna/util/. A technical report with more information
|
||||
on the models, the structure of the input and data file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA can be found
|
||||
in /doc/src/PDF/USER-CGDNA-overview.pdf.
|
||||
in /doc/src/PDF/USER-CGDNA.pdf.
|
||||
|
||||
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
|
||||
with the MOLECULE and ASPHERE packages. These should be included in
|
||||
@ -40,9 +47,8 @@ The creator of this package is:
|
||||
|
||||
Dr Oliver Henrich
|
||||
University of Strathclyde, Glasgow, UK
|
||||
oliver.henrich at strath.ac.uk
|
||||
University of Edinburgh, UK
|
||||
ohenrich at staffmail.ed.ac.uk
|
||||
oliver d o t henrich a t strath d o t ac d o t uk
|
||||
|
||||
|
||||
--------------------------------------------------------------------------
|
||||
|
||||
|
||||
@ -242,7 +242,7 @@ void BondOxdnaFene::coeff(int narg, char **arg)
|
||||
void BondOxdnaFene::init_style()
|
||||
{
|
||||
/* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude
|
||||
the ss excluded volume interaction between nearest neighbours */
|
||||
the ss excluded volume interaction between nearest neighbors */
|
||||
|
||||
force->special_lj[1] = 0.0;
|
||||
force->special_lj[2] = 1.0;
|
||||
|
||||
@ -157,7 +157,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over pair interaction neighbours of my atoms
|
||||
// loop over pair interaction neighbors of my atoms
|
||||
|
||||
for (ia = 0; ia < anum; ia++) {
|
||||
|
||||
@ -183,7 +183,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
|
||||
for (ib = 0; ib < bnum; ib++) {
|
||||
|
||||
b = blist[ib];
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
|
||||
b &= NEIGHMASK;
|
||||
|
||||
btype = type[b];
|
||||
|
||||
@ -122,7 +122,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over pair interaction neighbours of my atoms
|
||||
// loop over pair interaction neighbors of my atoms
|
||||
|
||||
for (ia = 0; ia < anum; ia++) {
|
||||
|
||||
@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
|
||||
for (ib = 0; ib < bnum; ib++) {
|
||||
|
||||
b = blist[ib];
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
|
||||
b &= NEIGHMASK;
|
||||
btype = type[b];
|
||||
|
||||
@ -186,7 +186,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
|
||||
|
||||
}
|
||||
|
||||
// knock out nearest-neighbour interaction between adjacent backbone sites
|
||||
// knock out nearest-neighbor interaction between adjacent backbone sites
|
||||
fpair *= factor_lj;
|
||||
evdwl *= factor_lj;
|
||||
|
||||
|
||||
@ -163,7 +163,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over pair interaction neighbours of my atoms
|
||||
// loop over pair interaction neighbors of my atoms
|
||||
|
||||
for (ia = 0; ia < anum; ia++) {
|
||||
|
||||
@ -189,7 +189,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
|
||||
for (ib = 0; ib < bnum; ib++) {
|
||||
|
||||
b = blist[ib];
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
|
||||
b &= NEIGHMASK;
|
||||
|
||||
btype = type[b];
|
||||
|
||||
@ -152,7 +152,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over pair interaction neighbours of my atoms
|
||||
// loop over pair interaction neighbors of my atoms
|
||||
|
||||
for (ia = 0; ia < anum; ia++) {
|
||||
|
||||
@ -179,7 +179,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
|
||||
for (ib = 0; ib < bnum; ib++) {
|
||||
|
||||
b = blist[ib];
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
|
||||
b &= NEIGHMASK;
|
||||
|
||||
btype = type[b];
|
||||
@ -222,7 +222,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
|
||||
evdwl = F3(rsq_ss,cutsq_ss_ast[atype][btype],cut_ss_c[atype][btype],lj1_ss[atype][btype],
|
||||
lj2_ss[atype][btype],epsilon_ss[atype][btype],b_ss[atype][btype],fpair);
|
||||
|
||||
// knock out nearest-neighbour interaction between ss
|
||||
// knock out nearest-neighbor interaction between ss
|
||||
fpair *= factor_lj;
|
||||
evdwl *= factor_lj;
|
||||
|
||||
|
||||
@ -168,7 +168,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over pair interaction neighbours of my atoms
|
||||
// loop over pair interaction neighbors of my atoms
|
||||
|
||||
for (ia = 0; ia < anum; ia++) {
|
||||
|
||||
@ -188,7 +188,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
|
||||
for (ib = 0; ib < bnum; ib++) {
|
||||
|
||||
b = blist[ib];
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
|
||||
b &= NEIGHMASK;
|
||||
|
||||
btype = type[b];
|
||||
|
||||
@ -160,7 +160,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over pair interaction neighbours of my atoms
|
||||
// loop over pair interaction neighbors of my atoms
|
||||
|
||||
for (ia = 0; ia < anum; ia++) {
|
||||
|
||||
@ -180,7 +180,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
|
||||
for (ib = 0; ib < bnum; ib++) {
|
||||
|
||||
b = blist[ib];
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
|
||||
factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
|
||||
b &= NEIGHMASK;
|
||||
|
||||
btype = type[b];
|
||||
|
||||
@ -260,6 +260,7 @@ void FixRX::post_constructor()
|
||||
error->all(FLERR,"fix rx cannot be combined with fix property/atom");
|
||||
|
||||
char **tmpspecies = new char*[maxspecies];
|
||||
int tmpmaxstrlen = 0;
|
||||
for(int jj=0; jj < maxspecies; jj++)
|
||||
tmpspecies[jj] = NULL;
|
||||
|
||||
@ -320,6 +321,7 @@ void FixRX::post_constructor()
|
||||
error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx.");
|
||||
tmpspecies[nUniqueSpecies] = new char[strlen(word)+1];
|
||||
strcpy(tmpspecies[nUniqueSpecies],word);
|
||||
tmpmaxstrlen = MAX(tmpmaxstrlen,strlen(word));
|
||||
nUniqueSpecies++;
|
||||
}
|
||||
word = strtok(NULL, " \t\n\r\f");
|
||||
@ -354,9 +356,9 @@ void FixRX::post_constructor()
|
||||
newarg2[0] = id_fix_species_old;
|
||||
newarg2[1] = group->names[igroup];
|
||||
newarg2[2] = (char *) "property/atom";
|
||||
char *str1 = new char[tmpmaxstrlen+3];
|
||||
char *str2 = new char[tmpmaxstrlen+6];
|
||||
for(int ii=0; ii<nspecies; ii++){
|
||||
char str1[2+strlen(tmpspecies[ii])+1];
|
||||
char str2[2+strlen(tmpspecies[ii])+4];
|
||||
strcpy(str1,"d_");
|
||||
strcpy(str2,"d_");
|
||||
strncat(str1,tmpspecies[ii],strlen(tmpspecies[ii]));
|
||||
@ -367,6 +369,8 @@ void FixRX::post_constructor()
|
||||
strcpy(newarg[ii+3],str1);
|
||||
strcpy(newarg2[ii+3],str2);
|
||||
}
|
||||
delete[] str1;
|
||||
delete[] str2;
|
||||
newarg[nspecies+3] = (char *) "ghost";
|
||||
newarg[nspecies+4] = (char *) "yes";
|
||||
newarg2[nspecies+3] = (char *) "ghost";
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user