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Merge pull request #2447 from akohlmey/atom-style-template-fixes

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Fix bugs and update implementation of atom style template
This commit is contained in:
Axel Kohlmeyer
2020-10-27 13:03:05 -04:00
committed by GitHub
parent b8e84d0070 8976cf0230
commit 5872b05e2f
45 changed files with 27607 additions and 78 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
cmake/Modules/Tools.cmake
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@ -50,8 +50,8 @@ if(BUILD_LAMMPS_SHELL)
endif()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
install(DIRECTORY icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()

3
doc/src/atom_style.rst
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@ -42,6 +42,7 @@ Examples
atom_style hybrid charge body nparticle 2 5
atom_style spin
atom_style template myMols
atom_style hybrid template twomols charge
atom_style tdpd 2
Description
@ -239,6 +240,8 @@ can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
can be advantageous for large-scale coarse-grained systems.
The ``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::

2
doc/src/create_atoms.rst
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@ -28,7 +28,7 @@ Syntax
* zero or more keyword/value pairs may be appended
* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units*
.. code-block:: LAMMPS
.. parsed-literal::
*mol* value = template-ID seed
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command

10
doc/src/molecule.rst
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@ -79,9 +79,9 @@ make it easy to use the same molecule file in different molecule
templates or in different simulations. You can specify the same file
multiple times with different optional keywords.
The *offset*\ , *toff*\ , *aoff*\ , *doff*\ , *ioff* keywords add the
specified offset values to the atom types, bond types, angle types,
dihedral types, and/or improper types as they are read from the
The *offset*\ , *toff*\ , *boff*\ , *aoff*\ , *doff*\ , *ioff* keywords
add the specified offset values to the atom types, bond types, angle
types, dihedral types, and/or improper types as they are read from the
molecule file. E.g. if *toff* = 2, and the file uses atom types
1,2,3, then each created molecule will have atom types 3,4,5. For the
*offset* keyword, all five offset values must be specified, but
@ -484,9 +484,7 @@ of SHAKE clusters.
Restrictions
""""""""""""
This command must come after the simulation box is define by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.
None
Related commands
""""""""""""""""

8
doc/src/read_data.rst
View File

@ -618,7 +618,7 @@ of analysis.
* - tdpd
- atom-ID atom-type x y z cc1 cc2 ... ccNspecies
* - template
- atom-ID molecule-ID template-index template-atom atom-type x y z
- atom-ID atom-type molecule-ID template-index template-atom x y z
* - tri
- atom-ID molecule-ID atom-type triangleflag density x y z
* - wavepacket
@ -695,9 +695,9 @@ triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ ,
The *template-index* and *template-atom* are only defined used by
:doc:`atom_style template <atom_style>`. In this case the
:doc:`molecule <molecule>` command is used to define a molecule template
which contains one or more molecules. If an atom belongs to one of
those molecules, its *template-index* and *template-atom* are both set
to positive integers; if not the values are both 0. The
which contains one or more molecules (as separate files). If an atom
belongs to one of those molecules, its *template-index* and *template-atom*
are both set to positive integers; if not the values are both 0. The
*template-index* is which molecule (1 to Nmols) the atom belongs to.
The *template-atom* is which atom (1 to Natoms) within the molecule
the atom is.

15
doc/utils/sphinx-config/_themes/lammps_theme/layout.html
View File

@ -48,6 +48,15 @@
<!--[if lt IE 9]>
<script src="{{ pathto('_static/js/html5shiv.min.js', 1) }}"></script>
<![endif]-->
{# Keep modernizr in head - http://modernizr.com/docs/#installing #}
<script src="{{ pathto('_static/js/modernizr.min.js', 1) }}"></script>
{# for improved browser compatibility #}
<!--[if lte IE 11]>
<script src="{{ pathto('_static/polyfill.js', 1) }}"></script>
<![endif]-->
{%- if not embedded %}
{# XXX Sphinx 1.8.0 made this an external js-file, quick fix until we refactor the template to inherert more blocks directly from sphinx #}
{% if sphinx_version >= "1.8.0" %}
@ -103,12 +112,6 @@
{%- endif %}
{%- endblock %}
{%- block extrahead %} {% endblock %}
{# Keep modernizr in head - http://modernizr.com/docs/#installing #}
<script src="{{ pathto('_static/js/modernizr.min.js', 1) }}"></script>
{# for improved browser compatibility #}
<script src="{{ pathto('_static/polyfill.js', 1) }}"></script>
</head>
<body class="wy-body-for-nav">

1
examples/README
View File

@ -111,6 +111,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
streitz: Streitz-Mintmire potential for Al2O3
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
template: examples for using atom_style template and comparing to atom style molecular
threebody: regression test input for a variety of manybody potentials
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command

4
examples/gcmc/data.spce
View File

@ -28,8 +28,8 @@ LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.8 o
Masses
1 1.007940 # 1
2 15.999400 # 2
1 15.999400 # 1
2 1.007940 # 2
Atoms # full

63
examples/template/co2.mol Normal file
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@ -0,0 +1,63 @@
# CO2 molecule file. TraPPE model.
3 atoms
2 bonds
1 angles
Coords
1 0.0 0.0 0.0
2 -1.16 0.0 0.0
3 1.16 0.0 0.0
Types
1 1
2 2
3 2
Charges
1 0.7
2 -0.35
3 -0.35
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2
Shake Flags
1 0
2 0
3 0
Shake Atoms
1
2
3
Shake Bond Types
1
2
3

68
examples/template/cyclohexane.mol Normal file
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@ -0,0 +1,68 @@
LAMMPS molecule file. Cyclohexane(UA)
6 atoms
6 bonds
6 angles
6 dihedrals
Coords
1 0.000000 0.000000 0.000000
2 0.000000 0.000000 1.536000
3 1.431000 0.000000 2.094000
4 2.247000 1.176000 1.536000
5 2.247000 1.176000 0.000000
6 0.815000 1.176000 -0.557000
Types
1 1
2 1
3 1
4 1
5 1
6 1
Bonds
1 1 1 6
2 1 1 2
3 1 2 3
4 1 3 4
5 1 4 5
6 1 5 6
Angles
1 1 2 1 6
2 1 1 2 3
3 1 2 3 4
4 1 3 4 5
5 1 4 5 6
6 1 1 6 5
Dihedrals
1 1 2 1 6 5
2 1 6 1 2 3
3 1 1 2 3 4
4 1 2 3 4 5
5 1 3 4 5 6
6 1 4 5 6 1
Special Bond Counts
1 2 2 1
2 2 2 1
3 2 2 1
4 2 2 1
5 2 2 1
6 2 2 1
Special Bonds
1 2 6 3 5 4
2 3 1 4 6 5
3 4 2 5 1 6
4 5 3 6 2 1
5 6 4 1 3 2
6 1 5 2 4 3

428
examples/template/h2o-co2.data Normal file
View File

@ -0,0 +1,428 @@
LAMMPS data file via write_data, version 22 Oct 2020, timestep = 0
384 atoms
4 atom types
2 bond types
2 angle types
-10.0 10.0 xlo xhi
-10.0 10.0 ylo yhi
-10.0 10.0 zlo zhi
Masses
1 15.9994
2 1
3 12.0107
4 15.9994
PairIJ Coeffs # lj/cut/coul/cut
1 1 0.15535 3.166 14
1 2 0 0 14
1 3 0.0912928 2.983 14
1 4 0.156159 3.108 14
2 2 0 0 14
2 3 0 1.4 14
2 4 0 1.525 14
3 3 0.053649 2.8 14
3 4 0.0917684 2.925 14
4 4 0.156973 3.05 14
Bond Coeffs # harmonic
1 1000 1
2 1000 1.16
Angle Coeffs # harmonic
1 100 109.47
2 100 180
Atoms # hybrid
1 1 -9.915603425183674 9.642074614047225 9.886373806057632 1 1 1 -0.8472 0 -1 -1
2 2 -9.955077256991814 9.952071397945474 -9.163725932085827 1 1 2 0.4236 0 -1 0
3 2 9.870680682175488 -9.594146011992699 9.277352126028195 1 1 3 0.4236 -1 0 -1
4 1 -5.377413308169694 -9.975845367284359 9.928445655374531 2 1 1 -0.8472 0 0 -1
5 2 -4.868089392205772 9.173804835517629 -9.939414010387674 2 1 2 0.4236 0 -1 0
6 2 -4.754497299624534 -9.19795946823327 -9.989031644986857 2 1 3 0.4236 0 0 0
7 1 0.2862645369165933 -9.834750023705109 9.802796207089045 3 1 1 -0.8472 0 0 -1
8 2 -0.20506315473823142 -9.416615546409432 -9.433183272761259 3 1 2 0.4236 0 0 0
9 2 -0.08120138217836187 9.25136557011454 9.630387065672213 3 1 3 0.4236 0 -1 -1
10 1 4.954244542709665 9.733846444128554 9.725750116636055 4 1 1 -0.8472 0 -1 -1
11 2 5.314186858355006 9.562011307112279 -9.357254293410282 4 1 2 0.4236 0 -1 0
12 2 4.731568598935329 -9.295857751240833 9.631504176774227 4 1 3 0.4236 0 0 -1
13 1 -9.885042196263848 -5.366646729833796 -9.977658232783796 5 1 1 -0.8472 0 0 0
14 2 -9.499988310087788 -4.607821917003056 -9.452410572081622 5 1 2 0.4236 0 0 0
15 2 9.385030506351637 -5.025531353163147 9.430068804865417 5 1 3 0.4236 -1 0 -1
16 1 -5.3381930384891545 -4.817187821023332 -9.98130637447481 6 1 1 -0.8472 0 0 0
17 2 -4.814226078866727 -5.143876565241305 -9.194731656774504 6 1 2 0.4236 0 0 0
18 2 -4.8475808826441185 -5.038935613735363 9.176038031249314 6 1 3 0.4236 0 0 -1
19 1 -0.17437585816420464 -5.00267209015634 -9.656881659301497 7 1 1 -0.8472 0 0 0
20 2 0.5142734508723548 -5.661488493390246 -9.959684850984493 7 1 2 0.4236 0 0 0
21 2 -0.3398975927081498 -4.335839416453415 9.61656651028599 7 1 3 0.4236 0 0 -1
22 1 5.027007160081784 -5.376778433628809 -9.926156239555816 8 1 1 -0.8472 0 0 0
23 2 5.040872603784614 -4.651165711374701 -9.238216835484566 8 1 2 0.4236 0 0 0
24 2 4.932120236133603 -4.97205585499649 9.164373075040384 8 1 3 0.4236 0 0 -1
25 1 -9.774983021942727 -0.11627625671956153 9.710187185567547 9 1 1 -0.8472 0 0 -1
26 2 -9.547719336441409 -0.18624762678535645 -9.31851372479864 9 1 2 0.4236 0 0 0
27 2 9.322702358384136 0.30252388350491777 9.608326539231093 9 1 3 0.4236 -1 0 -1
28 1 -4.839301125374413 -0.3224292196811998 9.864502598955395 10 1 1 -0.8472 0 0 -1
29 2 -4.437095111731628 0.2761002399087885 -9.442706303026958 10 1 2 0.4236 0 0 0
30 2 -5.723603762893959 0.04632897977241136 9.578203704071562 10 1 3 0.4236 0 0 -1
31 1 0.3575211513985558 0.13924369294039318 -9.96943701619651 11 1 1 -0.8472 0 0 0
32 2 -0.15738037709944985 -0.29662855771206287 -9.231291709389254 11 1 2 0.4236 0 0 0
33 2 -0.20014077429910587 0.1573848647716694 9.200728725585764 11 1 3 0.4236 0 0 -1
34 1 4.945607877161568 0.17822976107332558 -9.663221252242849 12 1 1 -0.8472 0 0 0
35 2 5.686261102802035 -0.4628832126235319 -9.864153208899683 12 1 2 0.4236 0 0 0
36 2 4.368131020036397 0.284653451550206 9.527374461142534 12 1 3 0.4236 0 0 -1
37 1 9.834131265901467 5.002816508870191 -9.652690475186276 13 1 1 -0.8472 -1 0 0
38 2 -9.523525531039581 4.309893511844079 -9.980134556788492 13 1 2 0.4236 0 0 0
39 2 9.689394265138116 5.68728997928573 9.63282503197477 13 1 3 0.4236 -1 0 -1
40 1 -4.896522832471423 4.844697230053857 -9.6633729049121 14 1 1 -0.8472 0 0 0
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43 1 0.08644475731548724 4.625177647828908 -9.986591646424854 15 1 1 -0.8472 0 0 0
44 2 0.483199632298402 5.33056133050579 -9.399236450405876 15 1 2 0.4236 0 0 0
45 2 -0.5696443896138887 5.044261021665302 9.38582809683073 15 1 3 0.4236 0 0 -1
46 1 5.279904505775219 4.8738580855036995 9.767866502301072 16 1 1 -0.8472 0 0 -1
47 2 5.051646557564443 5.834165665231483 9.928098703484146 16 1 2 0.4236 0 0 -1
48 2 4.6684489366603374 4.291976249264819 -9.695965205785217 16 1 3 0.4236 0 0 0
49 1 9.908445669769623 9.636632008310487 -4.912103567014368 17 1 1 -0.8472 -1 -1 0
50 2 -9.305514433129819 -9.862297561377305 -4.550114063115585 17 1 2 0.4236 0 0 0
51 2 9.397068763360195 -9.774334446933182 -5.537782369870047 17 1 3 0.4236 -1 0 0
52 1 -5.201907594124834 -9.68877920222961 -5.102563220356437 18 1 1 -0.8472 0 0 0
53 2 -4.940302726022812 9.565133612451614 -5.714840528272083 18 1 2 0.4236 0 -1 0
54 2 -4.857789679852353 -9.876354410222005 -4.182596251371481 18 1 3 0.4236 0 0 0
55 1 0.37327634941779875 -9.91440084751388 -4.961505484040201 19 1 1 -0.8472 0 0 0
56 2 -0.024482580199505652 9.563262486125167 -5.715772636834634 19 1 2 0.4236 0 -1 0
57 2 -0.34879376921829297 -9.648861638611287 -4.322721879125167 19 1 3 0.4236 0 0 0
58 1 5.099017423466195 9.70150361815792 -4.778099717040957 20 1 1 -0.8472 0 -1 0
59 2 5.136067712418359 9.715462771782358 -5.77729895393951 20 1 2 0.4236 0 -1 0
60 2 4.764914864115446 -9.416966389940278 -4.444601329019534 20 1 3 0.4236 0 0 0
61 1 9.67209962879851 -5.197853819118096 -5.0384641199861475 21 1 1 -0.8472 -1 0 0
62 2 9.738936599885 -4.205377815142725 -4.936039036490629 21 1 2 0.4236 -1 0 0
63 2 -9.41103622868351 -5.5967683657391785 -5.025496843523223 21 1 3 0.4236 0 0 0
64 1 -4.689795490189235 -5.165487837213749 -4.843375565356555 22 1 1 -0.8472 0 0 0
65 2 -4.832160266019467 -5.015491947934958 -5.82174165261749 22 1 2 0.4236 0 0 0
66 2 -5.478044243791298 -4.819020214851294 -4.334882782025955 22 1 3 0.4236 0 0 0
67 1 -0.0615634035841769 -4.677472055633765 -5.200823176306976 23 1 1 -0.8472 0 0 0
68 2 -0.6036354578743581 -5.514703146142694 -5.272716750031286 23 1 2 0.4236 0 0 0
69 2 0.6651988614585344 -4.807824798223541 -4.526460073661738 23 1 3 0.4236 0 0 0
70 1 4.802754604301762 -5.1046044449424395 -5.313522630242427 24 1 1 -0.8472 0 0 0
71 2 4.674742935683063 -5.484552334539641 -4.397433491136363 24 1 2 0.4236 0 0 0
72 2 5.522502460015175 -4.410843220517918 -5.28904387862121 24 1 3 0.4236 0 0 0
73 1 -9.83451039343324 -0.34326467353508094 -4.9458998177338245 25 1 1 -0.8472 0 0 0
74 2 -9.500257580872022 0.5235593797386398 -4.5759568290706625 25 1 2 0.4236 0 0 0
75 2 9.334767974305263 -0.18029470620355853 -5.478143353195513 25 1 3 0.4236 -1 0 0
76 1 -5.307686388170551 -0.09393136703842697 -4.788693917454198 26 1 1 -0.8472 0 0 0
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79 1 0.25915920502631956 0.1183661006970869 -5.258786105415057 27 1 1 -0.8472 0 0 0
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81 2 -0.6721579504645518 -0.17907891239614798 -5.46882334419513 27 1 3 0.4236 0 0 0
82 1 4.645093317547853 -0.032892978577141976 -5.145270693572841 28 1 1 -0.8472 0 0 0
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84 2 4.9703745308108305 0.7268752666532926 -4.58234515015024 28 1 3 0.4236 0 0 0
85 1 -9.935887941471492 4.620929536576184 -4.981574381668706 29 1 1 -0.8472 0 0 0
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98 2 9.902394946876838 9.380578255545881 -0.5571889055807204 33 1 2 0.4236 -1 -1 0
99 2 -9.930048429999529 -9.194004896790988 0.22167446122086756 33 1 3 0.4236 0 0 0
100 1 -5.055092848610487 9.62043108608943 -0.032194616393628146 34 1 1 -0.8472 0 -1 0
101 2 -4.242564100118214 -9.944998495531546 0.35627968294091067 34 1 2 0.4236 0 0 0
102 2 -5.702343051271298 -9.675432590557886 -0.3240850665472822 34 1 3 0.4236 0 0 0
103 1 -0.16422105747150104 -9.658585046539034 0.06790839076424156 35 1 1 -0.8472 0 0 0
104 2 0.24178705531724526 9.747651563696497 0.7625803609956086 35 1 2 0.4236 0 -1 0
105 2 -0.07756599784574403 9.910933482842538 -0.8304887517598495 35 1 3 0.4236 0 -1 0
106 1 5.252774480020046 -9.731538918744256 0.11035391158265477 36 1 1 -0.8472 0 0 0
107 2 4.897417222941987 -9.843232415673553 -0.8176614328409508 36 1 2 0.4236 0 0 0
108 2 4.849808297037967 9.57477133441781 0.7073075212582953 36 1 3 0.4236 0 -1 0
109 1 -9.974235357986496 -5.3824393899672485 -0.03493668449344743 37 1 1 -0.8472 0 0 0
110 2 -9.424638978370009 -4.718082489267676 -0.5414348828173003 37 1 2 0.4236 0 0 0
111 2 9.398874336356506 -4.8994781207650755 0.5763715673107472 37 1 3 0.4236 -1 0 0
112 1 -4.9279099757557 -5.3611565776237216 -0.11186255201619967 38 1 1 -0.8472 0 0 0
113 2 -4.312252322613385 -4.791643655121096 0.43273581570979314 38 1 2 0.4236 0 0 0
114 2 -5.759837701630914 -4.847199767255183 -0.3208732636935932 38 1 3 0.4236 0 0 0
115 1 -0.1760601646477313 -4.705054107276162 0.17364911312630318 39 1 1 -0.8472 0 0 0
116 2 -0.5420681618198102 -5.220988302880955 -0.6008292588839926 39 1 2 0.4236 0 0 0
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335 4 6.479552888446932 7.807048742079671 2.958267130078399 112 2 2 -0.35 0 0 0
336 4 8.520447111553068 7.192951257920329 2.041732869921601 112 2 3 -0.35 0 0 0
337 3 -7.5 -7.5 7.5 113 2 1 0.7 0 0 0
338 4 -7.6197834102650095 -6.871306065029082 8.46746879575316 113 2 2 -0.35 0 0 0
339 4 -7.3802165897349905 -8.128693934970917 6.53253120424684 113 2 3 -0.35 0 0 0
340 3 -2.5 -7.5 7.5 114 2 1 0.7 0 0 0
341 4 -3.6462582687736766 -7.5580642653980155 7.6682870237177 114 2 2 -0.35 0 0 0
342 4 -1.3537417312263231 -7.4419357346019845 7.3317129762823 114 2 3 -0.35 0 0 0
343 3 2.5 -7.5 7.5 115 2 1 0.7 0 0 0
344 4 1.3734554259918312 -7.525081897193473 7.224558134616524 115 2 2 -0.35 0 0 0
345 4 3.626544574008169 -7.474918102806527 7.775441865383476 115 2 3 -0.35 0 0 0
346 3 7.5 -7.5 7.5 116 2 1 0.7 0 0 0
347 4 8.414658305507071 -7.215850731078148 8.154415294089395 116 2 2 -0.35 0 0 0
348 4 6.585341694492928 -7.784149268921852 6.845584705910605 116 2 3 -0.35 0 0 0
349 3 -7.5 -2.5 7.5 117 2 1 0.7 0 0 0
350 4 -8.645413670915179 -2.6453055222059496 7.611865221123771 117 2 2 -0.35 0 0 0
351 4 -6.354586329084821 -2.3546944777940504 7.388134778876229 117 2 3 -0.35 0 0 0
352 3 -2.5 -2.5 7.5 118 2 1 0.7 0 0 0
353 4 -2.601509341816184 -1.9084001398846042 8.492625538174135 118 2 2 -0.35 0 0 0
354 4 -2.398490658183816 -3.091599860115396 6.507374461825866 118 2 3 -0.35 0 0 0
355 3 2.5 -2.5 7.5 119 2 1 0.7 0 0 0
356 4 2.2485924178438 -2.364925227008703 8.624343823452472 119 2 2 -0.35 0 0 0
357 4 2.7514075821562 -2.635074772991297 6.375656176547529 119 2 3 -0.35 0 0 0
358 3 7.5 -2.5 7.5 120 2 1 0.7 0 0 0
359 4 6.784038999809617 -1.8413110953985297 8.13176639128819 120 2 2 -0.35 0 0 0
360 4 8.215961000190383 -3.1586889046014703 6.86823360871181 120 2 3 -0.35 0 0 0
361 3 -7.5 2.5 7.5 121 2 1 0.7 0 0 0
362 4 -7.537548740040521 3.6593910439642627 7.49841908354891 121 2 2 -0.35 0 0 0
363 4 -7.462451259959479 1.340608956035737 7.50158091645109 121 2 3 -0.35 0 0 0
364 3 -2.5 2.5 7.5 122 2 1 0.7 0 0 0
365 4 -1.649121019955475 1.7301813803117607 7.3297523741731405 122 2 2 -0.35 0 0 0
366 4 -3.350878980044525 3.2698186196882393 7.6702476258268595 122 2 3 -0.35 0 0 0
367 3 2.5 2.5 7.5 123 2 1 0.7 0 0 0
368 4 3.2379752354871414 1.771831388509018 6.979651054534562 123 2 2 -0.35 0 0 0
369 4 1.7620247645128586 3.228168611490982 8.020348945465438 123 2 3 -0.35 0 0 0
370 3 7.5 2.5 7.5 124 2 1 0.7 0 0 0
371 4 7.334452984137467 1.3548227605993108 7.582239138478142 124 2 2 -0.35 0 0 0
372 4 7.665547015862533 3.645177239400689 7.417760861521858 124 2 3 -0.35 0 0 0
373 3 -7.5 7.5 7.5 125 2 1 0.7 0 0 0
374 4 -8.324913544328572 8.31456508779972 7.459982977108372 125 2 2 -0.35 0 0 0
375 4 -6.675086455671429 6.6854349122002805 7.540017022891628 125 2 3 -0.35 0 0 0
376 3 -2.5 7.5 7.5 126 2 1 0.7 0 0 0
377 4 -2.8359455597090397 6.421926623286971 7.76551530150699 126 2 2 -0.35 0 0 0
378 4 -2.1640544402909603 8.578073376713029 7.23448469849301 126 2 3 -0.35 0 0 0
379 3 2.5 7.5 7.5 127 2 1 0.7 0 0 0
380 4 1.4186788873677927 7.288670506833647 7.862883585594468 127 2 2 -0.35 0 0 0
381 4 3.5813211126322075 7.711329493166353 7.137116414405532 127 2 3 -0.35 0 0 0
382 3 7.5 7.5 7.5 128 2 1 0.7 0 0 0
383 4 6.9664096100856385 6.501410755376355 7.247609793547735 128 2 2 -0.35 0 0 0
384 4 8.03359038991436 8.498589244623645 7.752390206452265 128 2 3 -0.35 0 0 0

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# Water molecule. SPC/E model.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 1
2 2
3 2
Charges
1 -0.8472
2 0.4236
3 0.4236
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2

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# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
units real
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
atom_style hybrid template twomols charge
boundary p p p
pair_style lj/cut/coul/long 12
pair_modify mix arithmetic tail yes
kspace_style pppm 0.0001
pair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
read_data h2o-co2.data
group h2o type 1 2
group co2 type 3 4
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300.0 34672
thermo 100
fix 1 all nve
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
run 2500

21
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# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data molecular-mix.data
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

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# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
read_restart molecular-mix.restart
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

42
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# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 &
extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
create_atoms 0 box mol cychex 734594
create_atoms 2 random 800 495437 box
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
#write_data molecular-mix.data
#write_restart molecular-mix.restart

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# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
create_atoms 0 box mol cychex 734594
create_atoms 2 random 800 495437 box
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
#write_data template-mix.data
#write_restart template-mix.restart

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# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data template-mix.data
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

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# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
read_restart template-mix.restart
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
units real
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
Read molecule template twomols:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Read molecule template twomols:
1 molecules
3 atoms with max type 4
2 bonds with max type 2
1 angles with max type 2
0 dihedrals with max type 0
0 impropers with max type 0
atom_style hybrid template twomols charge
boundary p p p
pair_style lj/cut/coul/long 12
pair_modify mix arithmetic tail yes
kspace_style pppm 0.0001
pair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
read_data h2o-co2.data
Reading data file ...
orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
256 template bonds
128 template angles
read_data CPU = 0.003 seconds
group h2o type 1 2
192 atoms in group h2o
group co2 type 3 4
192 atoms in group co2
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300.0 34672
thermo 100
fix 1 all nve
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
64 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
run 2500
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.21452218
grid = 8 8 8
stencil order = 5
estimated absolute RMS force accuracy = 0.0237525
estimated relative force accuracy = 7.1529949e-05
using double precision FFTW3
3d grid and FFT values/proc = 2197 512
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15
ghost atom cutoff = 15
binsize = 7.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
1 1.99995 1.29379e-05 192
1 328.411 6.25278e-13 64
Per MPI rank memory allocation (min/avg/max) = 5.625 | 5.625 | 5.625 Mbytes
Step Temp E_pair E_mol TotEng Press
0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
100 363.1919 -274.40147 44.351072 115.30094 -883.3694
200 427.79493 -329.78833 38.354106 115.34674 1523.3792
300 465.88637 -350.56147 22.604289 115.04411 385.4719
400 436.9596 -357.24661 57.161471 115.41032 2307.0158
SHAKE stats (type/ave/delta/count) on step 500
1 2.00000 4.02911e-07 192
1 328.410 5.78944e-05 64
500 480.93508 -378.08914 36.26854 115.49018 2822.245
600 457.38119 -381.9922 62.73272 115.65441 -387.65281
700 488.20843 -393.89334 45.144546 115.47805 3086.293
800 463.52123 -384.28537 59.827245 116.2942 3310.9672
900 500.42748 -424.29715 64.614956 116.16348 -612.56056
SHAKE stats (type/ave/delta/count) on step 1000
1 2.00000 8.23271e-07 192
1 328.410 5.98754e-05 64
1000 522.46734 -424.93564 44.24152 116.1088 3948.9908
1100 470.79532 -398.30875 66.721422 116.08177 2480.4521
1200 515.87076 -433.25982 58.802584 116.07313 1913.2295
1300 517.25521 -425.5203 49.308433 115.63494 3343.755
1400 515.28471 -427.75141 53.078285 115.29997 2755.9048
SHAKE stats (type/ave/delta/count) on step 1500
1 2.00000 8.95165e-07 192
1 328.410 7.19288e-05 64
1500 514.22181 -421.99736 48.624007 115.58906 2400.1515
1600 533.9392 -430.89564 38.263047 115.07866 4331.2167
1700 529.29154 -424.02106 35.673551 114.94439 2973.3181
1800 535.52166 -438.41572 43.952454 114.75272 1799.8588
1900 519.40791 -413.30717 34.399008 114.9856 4270.415
SHAKE stats (type/ave/delta/count) on step 2000
1 2.00000 8.04353e-07 192
1 328.410 7.97925e-05 64
2000 553.26572 -446.67936 35.423618 114.83268 1729.4708
2100 546.58793 -448.39367 43.475288 114.82028 1266.9778
2200 536.17021 -442.03485 46.968579 114.76641 2419.0965
2300 556.29724 -457.19766 43.217115 114.99049 1122.5796
2400 529.02178 -437.66639 49.530498 114.89949 1714.4747
SHAKE stats (type/ave/delta/count) on step 2500
1 2.00000 6.70601e-07 192
1 328.410 6.39002e-05 64
2500 500.56024 -423.00108 62.368402 115.33925 3750.7564
Loop time of 6.4485 on 1 procs for 2500 steps with 384 atoms
Performance: 33.496 ns/day, 0.717 hours/ns, 387.687 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 | 4.9332 | 4.9332 | 4.9332 | 0.0 | 76.50
Bond | 0.013685 | 0.013685 | 0.013685 | 0.0 | 0.21
Kspace | 0.33226 | 0.33226 | 0.33226 | 0.0 | 5.15
Neigh | 1.0663 | 1.0663 | 1.0663 | 0.0 | 16.54
Comm | 0.062471 | 0.062471 | 0.062471 | 0.0 | 0.97
Output | 0.00048861 | 0.00048861 | 0.00048861 | 0.0 | 0.01
Modify | 0.030447 | 0.030447 | 0.030447 | 0.0 | 0.47
Other | | 0.009605 | | | 0.15
Nlocal: 384.000 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5594.00 ave 5594 max 5594 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 129739.0 ave 129739 max 129739 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 129739
Ave neighs/atom = 337.86198
Ave special neighs/atom = 2.0000000
Neighbor list builds = 320
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
units real
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
Read molecule template twomols:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Read molecule template twomols:
1 molecules
3 atoms with max type 4
2 bonds with max type 2
1 angles with max type 2
0 dihedrals with max type 0
0 impropers with max type 0
atom_style hybrid template twomols charge
boundary p p p
pair_style lj/cut/coul/long 12
pair_modify mix arithmetic tail yes
kspace_style pppm 0.0001
pair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
read_data h2o-co2.data
Reading data file ...
orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
256 template bonds
128 template angles
read_data CPU = 0.002 seconds
group h2o type 1 2
192 atoms in group h2o
group co2 type 3 4
192 atoms in group co2
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
timestep 1.0
velocity all create 300.0 34672
thermo 100
fix 1 all nve
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
64 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
run 2500
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.21452218
grid = 8 8 8
stencil order = 5
estimated absolute RMS force accuracy = 0.0237525
estimated relative force accuracy = 7.1529949e-05
using double precision FFTW3
3d grid and FFT values/proc = 1053 128
Neighbor list info ...
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15
ghost atom cutoff = 15
binsize = 7.5, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
1 1.99995 1.29379e-05 192
1 328.411 6.25278e-13 64
Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes
Step Temp E_pair E_mol TotEng Press
0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
100 363.1919 -274.40147 44.351072 115.30094 -883.3694
200 427.79493 -329.78833 38.354106 115.34674 1523.3792
300 465.88637 -350.56147 22.60429 115.0441 385.47189
400 436.9596 -357.24661 57.161471 115.41032 2307.0158
SHAKE stats (type/ave/delta/count) on step 500
1 2.00000 4.02911e-07 192
1 328.410 5.78945e-05 64
500 480.93505 -378.08914 36.268541 115.49016 2822.245
600 457.38144 -381.99241 62.732739 115.65446 -387.65505
700 488.20801 -393.89265 45.144482 115.47829 3086.2987
800 463.5234 -384.28682 59.826927 116.2945 3310.9691
900 500.48024 -424.35693 64.621298 116.16022 -612.4406
SHAKE stats (type/ave/delta/count) on step 1000
1 2.00000 8.21157e-07 192
1 328.410 5.79572e-05 64
1000 522.3905 -424.85292 44.232122 116.10905 3948.1535
1100 466.7856 -395.03916 67.204265 116.02145 2555.2069
1200 505.58079 -424.30563 59.681049 116.12127 1919.2701
1300 510.78441 -418.28838 48.398524 115.804 3476.7443
1400 494.39282 -407.60176 52.9665 115.47219 2343.5129
SHAKE stats (type/ave/delta/count) on step 1500
1 2.00000 7.21617e-07 192
1 328.410 8.01168e-05 64
1500 533.48096 -444.9571 53.263393 115.58182 1055.8053
1600 548.84084 -449.81134 43.134527 115.20409 3084.0678
1700 522.65205 -419.10648 37.279839 115.1519 1813.2589
1800 497.72839 -403.88156 45.774501 115.17212 1822.8113
1900 535.04509 -434.52042 40.685094 114.9275 4216.4353
SHAKE stats (type/ave/delta/count) on step 2000
1 2.00000 1.03652e-06 192
1 328.410 5.49305e-05 64
2000 540.42903 -436.41996 37.284032 114.74637 1422.0078
2100 534.80707 -439.51681 46.068646 115.08833 1460.2864
2200 507.8413 -419.62464 51.912776 115.18345 3790.8003
2300 553.37305 -456.23124 45.592723 115.55197 515.72888
2400 538.60716 -447.65657 51.130476 115.62382 2087.6217
SHAKE stats (type/ave/delta/count) on step 2500
1 2.00000 6.38759e-07 192
1 328.410 5.54712e-05 64
2500 507.38323 -436.58125 69.949293 115.8278 3313.9095
Loop time of 2.62759 on 4 procs for 2500 steps with 384 atoms
Performance: 82.205 ns/day, 0.292 hours/ns, 951.443 timesteps/s
93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1769 | 1.3595 | 1.5961 | 13.1 | 51.74
Bond | 0.0040634 | 0.0042451 | 0.0044163 | 0.2 | 0.16
Kspace | 0.37643 | 0.62177 | 0.8124 | 20.0 | 23.66
Neigh | 0.35517 | 0.35603 | 0.35688 | 0.1 | 13.55
Comm | 0.15521 | 0.16781 | 0.18101 | 2.8 | 6.39
Output | 0.00039921 | 0.00083364 | 0.0018058 | 0.0 | 0.03
Modify | 0.081231 | 0.095032 | 0.10957 | 3.5 | 3.62
Other | | 0.02238 | | | 0.85
Nlocal: 96.0000 ave 105 max 84 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 3764.00 ave 3776 max 3755 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 32527.2 ave 34260 max 29030 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 130109
Ave neighs/atom = 338.82552
Ave special neighs/atom = 2.0000000
Neighbor list builds = 321
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data molecular-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
scanning dihedrals ...
2 = max dihedrals/atom
reading bonds ...
3072 bonds
reading angles ...
3072 angles
reading dihedrals ...
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 10.74 | 10.74 | 10.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.6807 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.020 ns/day, 2.178 hours/ns, 127.545 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 | 14.196 | 14.196 | 14.196 | 0.0 | 90.53
Bond | 0.58712 | 0.58712 | 0.58712 | 0.0 | 3.74
Neigh | 0.6978 | 0.6978 | 0.6978 | 0.0 | 4.45
Comm | 0.082724 | 0.082724 | 0.082724 | 0.0 | 0.53
Output | 0.00052338 | 0.00052338 | 0.00052338 | 0.0 | 0.00
Modify | 0.078892 | 0.078892 | 0.078892 | 0.0 | 0.50
Other | | 0.0374 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data molecular-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
scanning dihedrals ...
2 = max dihedrals/atom
reading bonds ...
3072 bonds
reading angles ...
3072 angles
reading dihedrals ...
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.039 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 8.101 | 8.197 | 8.483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 4.33662 on 4 procs for 2000 steps with 3872 atoms
Performance: 39.847 ns/day, 0.602 hours/ns, 461.188 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6239 | 3.6669 | 3.7143 | 1.8 | 84.56
Bond | 0.14954 | 0.15355 | 0.15614 | 0.7 | 3.54
Neigh | 0.17931 | 0.17933 | 0.17934 | 0.0 | 4.14
Comm | 0.23604 | 0.28181 | 0.32663 | 6.5 | 6.50
Output | 0.00034802 | 0.00069388 | 0.0017292 | 0.0 | 0.02
Modify | 0.029915 | 0.036141 | 0.039601 | 1.9 | 0.83
Other | | 0.01821 | | | 0.42
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
restoring atom style molecular from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.008 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 10.74 | 10.74 | 10.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.5879 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.086 ns/day, 2.165 hours/ns, 128.305 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 | 14.116 | 14.116 | 14.116 | 0.0 | 90.56
Bond | 0.58742 | 0.58742 | 0.58742 | 0.0 | 3.77
Neigh | 0.68543 | 0.68543 | 0.68543 | 0.0 | 4.40
Comm | 0.082574 | 0.082574 | 0.082574 | 0.0 | 0.53
Output | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.00
Modify | 0.078446 | 0.078446 | 0.078446 | 0.0 | 0.50
Other | | 0.03761 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:697)
restoring atom style molecular from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_restart CPU = 0.031 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 8.101 | 8.197 | 8.483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 5.2142 on 4 procs for 2000 steps with 3872 atoms
Performance: 33.140 ns/day, 0.724 hours/ns, 383.568 timesteps/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5706 | 3.6724 | 3.7809 | 4.9 | 70.43
Bond | 0.14654 | 0.1524 | 0.15708 | 1.2 | 2.92
Neigh | 0.18217 | 0.1822 | 0.18221 | 0.0 | 3.49
Comm | 0.74346 | 0.8715 | 0.9808 | 10.9 | 16.71
Output | 0.00034776 | 0.00084716 | 0.0023413 | 0.0 | 0.02
Modify | 0.12457 | 0.18985 | 0.31013 | 17.4 | 3.64
Other | | 0.145 | | | 2.78
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.003 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 12.28 | 12.28 | 12.28 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
100 0 -4351.8383 516.49891 -3835.3394 11635.037
190 0 -6191.8175 457.61209 -5734.2054 4365.373
Loop time of 3.46057 on 1 procs for 190 steps with 3872 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
43897850768892.8 -5729.17187196146 -5734.20542785978
Force two-norm initial, final = 1.1080994e+15 72.746805
Force max component initial, final = 4.6607099e+14 17.394645
Final line search alpha, max atom move = 0.0041634525 0.072421779
Iterations, force evaluations = 190 297
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0573 | 3.0573 | 3.0573 | 0.0 | 88.35
Bond | 0.10271 | 0.10271 | 0.10271 | 0.0 | 2.97
Neigh | 0.26654 | 0.26654 | 0.26654 | 0.0 | 7.70
Comm | 0.013532 | 0.013532 | 0.013532 | 0.0 | 0.39
Output | 3.3796e-05 | 3.3796e-05 | 3.3796e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02041 | | | 0.59
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12122.0 ave 12122 max 12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774375.0 ave 774375 max 774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6191.8175 457.61209 -4580.3339 4842.3161
100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
Loop time of 18.6761 on 1 procs for 2500 steps with 3872 atoms
Performance: 11.566 ns/day, 2.075 hours/ns, 133.861 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 | 17.06 | 17.06 | 17.06 | 0.0 | 91.35
Bond | 0.73068 | 0.73068 | 0.73068 | 0.0 | 3.91
Neigh | 0.63671 | 0.63671 | 0.63671 | 0.0 | 3.41
Comm | 0.10272 | 0.10272 | 0.10272 | 0.0 | 0.55
Output | 0.00064976 | 0.00064976 | 0.00064976 | 0.0 | 0.00
Modify | 0.098028 | 0.098028 | 0.098028 | 0.0 | 0.52
Other | | 0.04742 | | | 0.25
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11793.0 ave 11793 max 11793 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770411.0 ave 770411 max 770411 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770411
Ave neighs/atom = 198.96978
Ave special neighs/atom = 3.9669421
Neighbor list builds = 33
Dangerous builds = 0
write_data molecular-mix.data
System init for write_data ...
Total wall time: 0:00:22

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.011 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 9.623 | 9.719 | 10.01 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
100 0 -3410.6986 572.28283 -2838.4158 14603.831
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
204 0 -6137.0238 483.14639 -5653.8774 4952.4081
Loop time of 1.10481 on 4 procs for 204 steps with 3872 atoms
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.54300441078755e+16 -5648.75822692028 -5653.87742448419
Force two-norm initial, final = 8.7430661e+18 74.636845
Force max component initial, final = 4.1468626e+18 8.6800755
Final line search alpha, max atom move = 0.0032186736 0.02793833
Iterations, force evaluations = 204 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.89902 | 0.90561 | 0.90821 | 0.4 | 81.97
Bond | 0.029749 | 0.030411 | 0.031345 | 0.4 | 2.75
Neigh | 0.088655 | 0.088662 | 0.088666 | 0.0 | 8.03
Comm | 0.063187 | 0.068096 | 0.070678 | 1.1 | 6.16
Output | 4.8304e-05 | 0.00011426 | 0.00031124 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01191 | | | 1.08
Nlocal: 968.000 ave 980 max 954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 6630.00 ave 6644 max 6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 193550.0 ave 195957 max 191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6137.0238 483.14639 -4500.0059 5429.3513
100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
Loop time of 5.954 on 4 procs for 2500 steps with 3872 atoms
Performance: 36.278 ns/day, 0.662 hours/ns, 419.886 timesteps/s
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4642 | 4.6298 | 4.8946 | 7.5 | 77.76
Bond | 0.18992 | 0.19849 | 0.20566 | 1.3 | 3.33
Neigh | 0.18926 | 0.18928 | 0.18929 | 0.0 | 3.18
Comm | 0.56456 | 0.82727 | 1.0096 | 17.9 | 13.89
Output | 0.00044023 | 0.00092791 | 0.0020343 | 0.0 | 0.02
Modify | 0.077974 | 0.080378 | 0.082874 | 0.8 | 1.35
Other | | 0.02782 | | | 0.47
Nlocal: 968.000 ave 989 max 944 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 6381.50 ave 6416 max 6351 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 192557.0 ave 197456 max 188754 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 770229
Ave neighs/atom = 198.92278
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
write_data molecular-mix.data
System init for write_data ...
Total wall time: 0:00:07

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.001 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 8.050 | 8.050 | 8.050 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
100 0 -4351.8383 516.49891 -3835.3394 11635.037
190 0 -6191.8175 457.61209 -5734.2054 4365.373
Loop time of 3.4619 on 1 procs for 190 steps with 3872 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
43897850768892.8 -5729.17187196146 -5734.20542785978
Force two-norm initial, final = 1.1080994e+15 72.746805
Force max component initial, final = 4.6607099e+14 17.394645
Final line search alpha, max atom move = 0.0041634525 0.072421779
Iterations, force evaluations = 190 297
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0549 | 3.0549 | 3.0549 | 0.0 | 88.24
Bond | 0.10344 | 0.10344 | 0.10344 | 0.0 | 2.99
Neigh | 0.2695 | 0.2695 | 0.2695 | 0.0 | 7.78
Comm | 0.013772 | 0.013772 | 0.013772 | 0.0 | 0.40
Output | 3.3707e-05 | 3.3707e-05 | 3.3707e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02027 | | | 0.59
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12122.0 ave 12122 max 12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774375.0 ave 774375 max 774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6191.8175 457.61209 -4580.3339 4842.3161
100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
Loop time of 18.7845 on 1 procs for 2500 steps with 3872 atoms
Performance: 11.499 ns/day, 2.087 hours/ns, 133.089 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 | 17.14 | 17.14 | 17.14 | 0.0 | 91.25
Bond | 0.74217 | 0.74217 | 0.74217 | 0.0 | 3.95
Neigh | 0.65005 | 0.65005 | 0.65005 | 0.0 | 3.46
Comm | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.55
Output | 0.0006739 | 0.0006739 | 0.0006739 | 0.0 | 0.00
Modify | 0.099647 | 0.099647 | 0.099647 | 0.0 | 0.53
Other | | 0.04816 | | | 0.26
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11793.0 ave 11793 max 11793 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770411.0 ave 770411 max 770411 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770411
Ave neighs/atom = 198.96978
Ave special neighs/atom = 3.9669421
Neighbor list builds = 33
Dangerous builds = 0
write_data template-mix.data
System init for write_data ...
Total wall time: 0:00:22

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
create_atoms CPU = 0.001 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 5.345 | 5.441 | 5.728 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
100 0 -3410.6986 572.28283 -2838.4158 14603.831
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
204 0 -6137.0238 483.14639 -5653.8774 4952.4081
Loop time of 1.08919 on 4 procs for 204 steps with 3872 atoms
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.54300441078755e+16 -5648.75822692028 -5653.87742448419
Force two-norm initial, final = 8.7430661e+18 74.636845
Force max component initial, final = 4.1468626e+18 8.6800755
Final line search alpha, max atom move = 0.0032186736 0.02793833
Iterations, force evaluations = 204 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.8748 | 0.88765 | 0.9004 | 1.2 | 81.50
Bond | 0.029354 | 0.029865 | 0.030434 | 0.2 | 2.74
Neigh | 0.07699 | 0.077483 | 0.077966 | 0.2 | 7.11
Comm | 0.072926 | 0.084481 | 0.097433 | 3.8 | 7.76
Output | 4.7316e-05 | 0.00010999 | 0.00029778 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009602 | | | 0.88
Nlocal: 968.000 ave 980 max 954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 6630.00 ave 6644 max 6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 193550.0 ave 195957 max 191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 4.220 | 4.507 | 4.603 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6137.0238 483.14639 -4500.0059 5429.3513
100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
Loop time of 5.70106 on 4 procs for 2500 steps with 3872 atoms
Performance: 37.888 ns/day, 0.633 hours/ns, 438.515 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4476 | 4.5874 | 4.9593 | 10.1 | 80.47
Bond | 0.18485 | 0.19038 | 0.19543 | 0.9 | 3.34
Neigh | 0.18057 | 0.18059 | 0.18062 | 0.0 | 3.17
Comm | 0.30256 | 0.67081 | 0.81456 | 26.1 | 11.77
Output | 0.00042399 | 0.00053327 | 0.00085633 | 0.0 | 0.01
Modify | 0.035251 | 0.043755 | 0.052209 | 4.0 | 0.77
Other | | 0.02758 | | | 0.48
Nlocal: 968.000 ave 989 max 944 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 6381.50 ave 6416 max 6351 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 192557.0 ave 197456 max 188754 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 770229
Ave neighs/atom = 198.92278
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
write_data template-mix.data
System init for write_data ...
Total wall time: 0:00:06

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data template-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
3072 template bonds
3072 template angles
3072 template dihedrals
read_data CPU = 0.016 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 6.879 | 6.879 | 6.879 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.3795 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.236 ns/day, 2.136 hours/ns, 130.043 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 | 13.905 | 13.905 | 13.905 | 0.0 | 90.41
Bond | 0.58069 | 0.58069 | 0.58069 | 0.0 | 3.78
Neigh | 0.69766 | 0.69766 | 0.69766 | 0.0 | 4.54
Comm | 0.08196 | 0.08196 | 0.08196 | 0.0 | 0.53
Output | 0.00052444 | 0.00052444 | 0.00052444 | 0.0 | 0.00
Modify | 0.077644 | 0.077644 | 0.077644 | 0.0 | 0.50
Other | | 0.03568 | | | 0.23
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 2: continuing from data file
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data template-mix.data
Reading data file ...
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
3872 atoms
reading velocities ...
3872 velocities
3072 template bonds
3072 template angles
3072 template dihedrals
read_data CPU = 0.022 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 4.193 | 4.289 | 4.575 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 4.67813 on 4 procs for 2000 steps with 3872 atoms
Performance: 36.938 ns/day, 0.650 hours/ns, 427.522 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5547 | 3.689 | 3.8706 | 5.9 | 78.86
Bond | 0.14554 | 0.15424 | 0.1658 | 2.0 | 3.30
Neigh | 0.19598 | 0.19599 | 0.19599 | 0.0 | 4.19
Comm | 0.39992 | 0.57068 | 0.7172 | 14.9 | 12.20
Output | 0.00034507 | 0.00063055 | 0.0014842 | 0.0 | 0.01
Modify | 0.036995 | 0.043513 | 0.048096 | 2.0 | 0.93
Other | | 0.02411 | | | 0.52
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697)
restoring atom style template from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.002 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 6.879 | 6.879 | 6.879 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
2600 303.69861 -4872.1658 1620.5986 252.72467 8824.1501
2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748
2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133
2900 302.323 -4949.4247 1661.0637 200.05824 10788.039
3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027
3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096
3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25
3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758
3400 308.43113 -5035.583 1732.7837 256.09989 11520.651
3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351
3600 294.00064 -5011.409 1768.0298 149.01058 11257.53
3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281
3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396
3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891
4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067
4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757
4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093
4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023
4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256
4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338
Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 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 | 13.88 | 13.88 | 13.88 | 0.0 | 90.40
Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78
Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53
Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54
Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00
Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51
Other | | 0.03687 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11670.0 ave 11670 max 11670 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770032.0 ave 770032 max 770032 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770032
Ave neighs/atom = 198.87190
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
restoring atom style template from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.006 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
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) = 4.193 | 4.289 | 4.575 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501
2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482
2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261
2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69
3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074
3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502
3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923
3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992
3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101
3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685
3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938
3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666
3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208
3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557
4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379
4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056
4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605
4300 300.50984 -5082.4128 1742.354 127.43881 11003.298
4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004
4500 302.62639 -5033.3284 1753.488 212.07956 11150.514
Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms
Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 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 | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50
Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49
Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04
Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57
Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02
Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96
Other | | 0.01937 | | | 0.44
Nlocal: 968.000 ave 977 max 956 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 6322.75 ave 6345 max 6308 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 192555.0 ave 195249 max 188636 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 770221
Ave neighs/atom = 198.92071
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
Total wall time: 0:00:04

17011
examples/template/molecular-mix.data Normal file
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1
src/MISC/fix_deposit.cpp
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@ -718,7 +718,6 @@ void FixDeposit::options(int narg, char **arg)
error->all(FLERR,"Illegal fix deposit command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
int n = strlen(arg[iarg+1]) + 1;

37
src/MOLECULE/atom_vec_template.cpp
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@ -44,7 +44,7 @@ AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
fields_restart = (char *) "molecule molindex molatom";
fields_create = (char *) "molecule molindex molatom";
fields_data_atom = (char *) "id molecule molindex molatom type x";
fields_data_vel = (char *) "";
fields_data_vel = (char *) "id v";
setup_fields();
}
@ -64,12 +64,6 @@ void AtomVecTemplate::process_args(int narg, char **arg)
onemols = &atom->molecules[imol];
nset = atom->molecules[imol]->nset;
// error check on molecule template fields
for (int i = 0; i < nset; i++)
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Atom style template molecule must have atom types");
// set bonds_allow,angles_allow,etc based on the molecules in template set
// similar to how atom_style bond,angle,full set it
@ -112,6 +106,27 @@ void AtomVecTemplate::create_atom_post(int ilocal)
molatom[ilocal] = -1;
}
/* ----------------------------------------------------------------------
modify values for AtomVec::pack_data() to pack
------------------------------------------------------------------------- */
void AtomVecTemplate::pack_data_pre(int ilocal)
{
molindex[ilocal]++;
molatom[ilocal]++;
}
/* ----------------------------------------------------------------------
unmodify values packed by AtomVec::pack_data()
------------------------------------------------------------------------- */
void AtomVecTemplate::pack_data_post(int ilocal)
{
molindex[ilocal]--;
molatom[ilocal]--;
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
@ -119,11 +134,11 @@ void AtomVecTemplate::create_atom_post(int ilocal)
void AtomVecTemplate::data_atom_post(int ilocal)
{
int molindex_one = molindex[ilocal];
int molatom_one = molatom[ilocal];
int molindex_one = --molindex[ilocal];
int molatom_one = --molatom[ilocal];
if (molindex_one < 0 || molindex_one >= nset)
if ((molindex_one < -1) || (molindex_one >= nset))
error->one(FLERR,"Invalid template index in Atoms section of data file");
if (molatom_one < 0 || molatom_one >= onemols[molindex_one]->natoms)
if ((molatom_one < -1) || ((molindex_one >= 0) && (molatom_one >= onemols[molindex_one]->natoms)))
error->one(FLERR,"Invalid template atom in Atoms section of data file");
}

2
src/MOLECULE/atom_vec_template.h
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@ -31,6 +31,8 @@ class AtomVecTemplate : public AtomVec {
void grow_pointers();
void process_args(int, char **);
void create_atom_post(int);
void pack_data_pre(int);
void pack_data_post(int);
void data_atom_post(int);
private:

4
src/RIGID/fix_shake.cpp
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@ -2536,13 +2536,13 @@ void FixShake::stats()
auto mesg = fmt::format("SHAKE stats (type/ave/delta/count) on step {}\n",
update->ntimestep);
for (i = 1; i < nb; i++) {
const auto bcnt = b_count_all[i];
const auto bcnt = b_count_all[i]/2;
if (bcnt)
mesg += fmt::format("{:>6d} {:<9.6} {:<11.6} {:>8d}\n",i,
b_ave_all[i]/bcnt,b_max_all[i]-b_min_all[i],bcnt);
}
for (i = 1; i < na; i++) {
const auto acnt = a_count_all[i];
const auto acnt = a_count_all[i]/3;
if (acnt)
mesg += fmt::format("{:>6d} {:<9.6} {:<11.6} {:>8d}\n",i,
a_ave_all[i]/acnt,a_max_all[i]-a_min_all[i],acnt);

2
src/atom.cpp
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@ -1910,7 +1910,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
}
if (molecular != 1) return;
if (molecular != Atom::MOLECULAR) return;
// add bond topology info
// for molecular atom styles, but not atom style template

4
src/info.cpp
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@ -109,7 +109,7 @@ static const char *varstyles[] = {
"index", "loop", "world", "universe", "uloop", "string", "getenv",
"file", "atomfile", "format", "equal", "atom", "vector", "python", "internal", "(unknown)"};
static const char *mapstyles[] = { "none", "array", "hash" };
static const char *mapstyles[] = { "none", "array", "hash", "yes" };
static const char *commstyles[] = { "brick", "tiled" };
static const char *commlayout[] = { "uniform", "nonuniform", "irregular" };
@ -348,6 +348,7 @@ void Info::command(int narg, char **arg)
commstyles[comm->style], commlayout[comm->layout],
comm->ghost_velocity ? "yes" : "no");
if (domain->box_exist) {
if (comm->mode == 0)
fmt::print(out,"Communication mode = single\n"
"Communication cutoff = {}\n",
@ -362,6 +363,7 @@ void Info::command(int narg, char **arg)
fmt::print(out,"Communication cutoff for type {} = {:.8}\n", i, cut);
}
}
}
fmt::print(out,"Nprocs = {}, Nthreads = {}\n",comm->nprocs,comm->nthreads);
if (domain->box_exist)
fmt::print(out,"Processor grid = {} x {} x {}\n",comm->procgrid[0],

29
src/molecule.cpp
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@ -55,9 +55,6 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (index >= narg) error->all(FLERR,"Illegal molecule command");
if (domain->box_exist == 0)
error->all(FLERR,"Molecule command before simulation box is defined");
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
@ -728,7 +725,7 @@ void Molecule::types(char *line)
}
for (int i = 0; i < natoms; i++)
if (type[i] <= 0 || type[i] > atom->ntypes)
if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes)))
error->all(FLERR,"Invalid atom type in molecule file");
for (int i = 0; i < natoms; i++)
@ -912,7 +909,7 @@ void Molecule::bonds(int flag, char *line)
if ((atom1 <= 0) || (atom1 > natoms) ||
(atom2 <= 0) || (atom2 > natoms) || (atom1 == atom2))
error->one(FLERR,"Invalid atom ID in Bonds section of molecule file");
if (itype <= 0 || itype > atom->nbondtypes)
if ((itype <= 0) || (domain->box_exist && (itype > atom->nbondtypes)))
error->one(FLERR,"Invalid bond type in Bonds section of molecule file");
if (flag) {
@ -983,7 +980,7 @@ void Molecule::angles(int flag, char *line)
(atom3 <= 0) || (atom3 > natoms) ||
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->one(FLERR,"Invalid atom ID in Angles section of molecule file");
if (itype <= 0 || itype > atom->nangletypes)
if ((itype <= 0) || (domain->box_exist && (itype > atom->nangletypes)))
error->one(FLERR,"Invalid angle type in Angles section of molecule file");
if (flag) {
@ -1071,9 +1068,8 @@ void Molecule::dihedrals(int flag, char *line)
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,
"Invalid atom ID in dihedrals section of molecule file");
if (itype <= 0 || itype > atom->ndihedraltypes)
error->one(FLERR,
"Invalid dihedral type in dihedrals section of molecule file");
if ((itype <= 0) || (domain->box_exist && (itype > atom->ndihedraltypes)))
error->one(FLERR,"Invalid dihedral type in Dihedrals section of molecule file");
if (flag) {
m = atom2-1;
@ -1171,9 +1167,8 @@ void Molecule::impropers(int flag, char *line)
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,
"Invalid atom ID in impropers section of molecule file");
if (itype <= 0 || itype > atom->nimpropertypes)
error->one(FLERR,
"Invalid improper type in impropers section of molecule file");
if ((itype <= 0) || (domain->box_exist && (itype > atom->nimpropertypes)))
error->one(FLERR,"Invalid improper type in Impropers section of molecule file");
if (flag) {
m = atom2-1;
@ -1476,6 +1471,11 @@ void Molecule::shakeatom_read(char *line)
nwant = 5;
break;
case 0:
values.next_int();
nwant = 1;
break;
default:
error->one(FLERR,"Invalid shake atom in molecule file");
}
@ -1542,6 +1542,11 @@ void Molecule::shaketype_read(char *line)
nwant = 4;
break;
case 0:
values.next_int();
nwant = 1;
break;
default:
error->one(FLERR,"Invalid shake type data in molecule file");
}

2
src/read_data.cpp
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@ -796,11 +796,13 @@ void ReadData::command(int narg, char **arg)
for (int i = 0; i < nlocal; i++) {
imol = molindex[i];
iatom = molatom[i];
if (imol >=0) {
nbonds += onemols[imol]->num_bond[iatom];
nangles += onemols[imol]->num_angle[iatom];
ndihedrals += onemols[imol]->num_dihedral[iatom];
nimpropers += onemols[imol]->num_improper[iatom];
}
}
MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&nangles,&atom->nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);

38
src/read_restart.cpp
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@ -472,19 +472,33 @@ void ReadRestart::command(int narg, char **arg)
if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all restart atoms correctly");
if (me == 0) {
if (atom->nbonds) {
utils::logmesg(lmp,fmt::format(" {} bonds\n",atom->nbonds));
}
if (atom->nangles) {
utils::logmesg(lmp,fmt::format(" {} angles\n",atom->nangles));
}
if (atom->ndihedrals) {
utils::logmesg(lmp,fmt::format(" {} dihedrals\n",atom->ndihedrals));
}
if (atom->nimpropers) {
utils::logmesg(lmp,fmt::format(" {} impropers\n",atom->nimpropers));
if ((atom->molecular == Atom::TEMPLATE) && (me == 0)) {
std::string mesg;
if (atom->nbonds)
mesg += fmt::format(" {} template bonds\n",atom->nbonds);
if (atom->nangles)
mesg += fmt::format(" {} template angles\n",atom->nangles);
if (atom->ndihedrals)
mesg += fmt::format(" {} template dihedrals\n",atom->ndihedrals);
if (atom->nimpropers)
mesg += fmt::format(" {} template impropers\n",atom->nimpropers);
utils::logmesg(lmp,mesg);
}
if ((atom->molecular == Atom::MOLECULAR) && (me == 0)) {
std::string mesg;
if (atom->nbonds)
mesg += fmt::format(" {} bonds\n",atom->nbonds);
if (atom->nangles)
mesg += fmt::format(" {} angles\n",atom->nangles);
if (atom->ndihedrals)
mesg += fmt::format(" {} dihedrals\n",atom->ndihedrals);
if (atom->nimpropers)
mesg += fmt::format(" {} impropers\n",atom->nimpropers);
utils::logmesg(lmp,mesg);
}
// check that atom IDs are valid

9
src/write_data.cpp
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@ -233,7 +233,7 @@ void WriteData::header()
fmt::print(fp,"{} atoms\n{} atom types\n",atom->natoms,atom->ntypes);
// do not write molecular topology info for atom_style template
// only write out number of types for atom style template
if (atom->molecular == Atom::MOLECULAR) {
if (atom->nbonds || atom->nbondtypes)
@ -250,6 +250,13 @@ void WriteData::header()
nimpropers,atom->nimpropertypes);
}
if (atom->molecular == Atom::TEMPLATE) {
if (atom->nbondtypes) fmt::print(fp,"{} bond types\n",atom->nbondtypes);
if (atom->nangletypes) fmt::print(fp,"{} angle types\n",atom->nangletypes);
if (atom->ndihedraltypes) fmt::print(fp,"{} dihedral types\n",atom->ndihedraltypes);
if (atom->nimpropertypes) fmt::print(fp,"{} improper types\n",atom->nimpropertypes);
}
// bonus info
if (atom->ellipsoid_flag) fmt::print(fp,"{} ellipsoids\n",atom->nellipsoids);