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fix building

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arcan1s
2014-01-26 04:39:33 +04:00
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3
mathmech/mathmech/AUTHORS
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Current developers:
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>

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mathmech/mathmech/CMakeLists.txt
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# set project name
set (PROJECT mathmech)
set (SUBPROJECT mathmech)
# set additional cmake file
include (${PROJECT}.cmake)
include (${SUBPROJECT}.cmake)
# additional options
option (WITH_DEBUG_MODE "Build with debug mode" OFF)
# set libraries
set (LIBRARIES "")
foreach (LIBRARY ${LIBRARIES})
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
endforeach ()
# additional targets
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${PROJECT_SOURCE_DIR})
add_subdirectory (${SUBPROJECT_SOURCE_DIR})

341
mathmech/mathmech/COPYING
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GNU GENERAL PUBLIC LICENSE
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16
mathmech/mathmech/INSTALL
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CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DQWT_INCLUDE_PATH - path to qwt includes
-DQWT_LIBRARY_PATH - path to qwt library
Install for Linux:
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
make
make install
Install for Windows:
create project file using 'cmake'
compile project
copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
You may also download compiled executable file for Win_x86.

2
mathmech/mathmech/README
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Mathematical Molecular Mechanics is GUI for "mm" program pack
Version: 1.1.1
Version: 1.2.0
License: GPL

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mathmech/mathmech/mathmech.cmake
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# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_RESOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources)
set (PROJECT_TRANSLATION_DIR ${PROJECT_RESOURCE_DIR}/translations)
set (SUBPROJECT_BINARY_DIR bin)
set (SUBPROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (SUBPROJECT_RESOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources)
set (SUBPROJECT_TRANSLATION_DIR ${SUBPROJECT_RESOURCE_DIR}/translations)
# library path
link_directories (${PROJECT_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
set (EXECUTABLE_OUTPUT_PATH ${SUBPROJECT_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)

18
mathmech/mathmech/resources/translations/eng.ts
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@ -29,7 +29,7 @@ p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Liberation Serif&apos;; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Mathematical Molecular Mechanics&lt;/span&gt;&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Version:&lt;/span&gt; 1.1.1&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Version:&lt;/span&gt; 1.2.0&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;License:&lt;/span&gt; GPL&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Author:&lt;/span&gt; Evgeniy Alekseev&lt;/p&gt;
@ -604,7 +604,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
@ -633,7 +633,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
@ -732,7 +732,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is constructed. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, sphere volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
@ -759,7 +759,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is constructed. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, sphere volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
@ -924,7 +924,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
@ -953,7 +953,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
@ -1034,7 +1034,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is calculated. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step, A. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
@ -1061,7 +1061,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is calculated. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step, A. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;

18
mathmech/mathmech/resources/translations/rus.ts
View File

@ -29,7 +29,7 @@ p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Liberation Serif&apos;; font-size:10pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p align=&quot;center&quot; style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Mathematical Molecular Mechanics&lt;/span&gt;&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Версия:&lt;/span&gt; 1.1.1&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Версия:&lt;/span&gt; 1.2.0&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Лицензия:&lt;/span&gt; GPL&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:600;&quot;&gt;Автор:&lt;/span&gt; Evgeniy Alekseev&lt;/p&gt;
@ -604,7 +604,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
@ -633,7 +633,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Использование&lt;/span&gt;&lt;br /&gt;mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Параметры&lt;/span&gt;&lt;br /&gt;-i МАСКА – маска снимков траектории&lt;br /&gt;-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории&lt;br /&gt;-c X,Y,Z – размер элементарной ячейки, А&lt;br /&gt;-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую&lt;br /&gt;-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &amp;quot;0-0:2.4,0-1:3.0&amp;quot; означает указание 0-0 взаимодействия &amp;lt;2.4 А и 0-1 &amp;lt;3.0 А.&lt;br /&gt;-o ФАЙЛ – генерируемый файл&lt;br /&gt;-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&amp;gt;= 3)&lt;br /&gt;-l ФАЙЛ – запись лога в указанный файл&lt;br /&gt;-q – не выводить сообщения в STDOUT&lt;br /&gt;-h – показать эту справку и выйти&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Форматы файлов&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Генерируемый файл (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;statgen ::: V.1.1.1&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;statgen ::: V.1.2.0&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Блок конфигурации &amp;quot;CONFIGURATION … END&amp;quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), маска файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), типы атомов (ATOMS=1,2,3,4), взаимодействия (INTERACTION=формат), максимальная глубина для проверки числа циклов (DEPTH=0, 0 – не проверять изоморфизм). Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Перечисление статистики по файлам.&lt;br /&gt;Имя файла (FILE=mask.001), блок статистики по файлу &amp;quot;STATISTIC … -----------------&amp;quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).&lt;br /&gt;Перечисление агломератов, найденных в данном файле. Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма). Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Общая статистика &amp;quot;.SUMMARY STATISTIC … ------------------------------------------------&amp;quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Пробел, размер агломерата (7 символов), пробел, общее число агломератов данной стехиометрии (7 символов), пробел, средняя концентрация агломератов данной стехиометрии (9 символов, 2 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии (9 символов, 5 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии, умноженная на число молекул в агломерате (10 символов, 5 десятичной части).&lt;/li&gt;
@ -732,7 +732,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is constructed. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, sphere volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
@ -759,7 +759,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Использование&lt;/span&gt;&lt;br /&gt;mm_radf -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -at ФОРМАТ -o ФАЙЛ [ -r ЧИСЛО,ЧИСЛО ] [ -rs ЧИСЛО ] [ -a ЧИСЛО,ЧИСЛО ] [ -as ЧИСЛО ] [ -m ] [ -l ФАЙЛ ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Параметры&lt;/span&gt;&lt;br /&gt;-i МАСКА – маска снимков траектории&lt;br /&gt;-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории&lt;br /&gt;-c X,Y,Z – размер элементарной ячейки, А&lt;br /&gt;-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат &amp;quot;1-2&amp;quot; или &amp;quot;1,2,3,-4,5,6&amp;quot; (автоматически включит расчет функции радиального распределения между центрами масс).&lt;br /&gt;-o ФАЙЛ – генерируемый файл&lt;br /&gt;-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0&lt;br /&gt;-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2&lt;br /&gt;-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0&lt;br /&gt;-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения&lt;br /&gt;-m – печать в виде матрицы&lt;br /&gt;-l ФАЙЛ – запись лога в указанный файл&lt;br /&gt;-q – не выводить сообщения в STDOUT&lt;br /&gt;-h – показать эту справку и выйти&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Форматы файлов&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Генерируемый файл (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;radf ::: V.1.1.1&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;radf ::: V.1.2.0&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Блок конфигурации &amp;quot;CONFIGURATION … END&amp;quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), матричный вывод (MATRIX=1), файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), тип расчета (MODE=0) (0 – для функции радиального распределения, 1 – для функции радиального распределения для центров масс, 2 – для функции радиально-углового распределения), радиальные критерии (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), угловые критерии для функции радиально-углового распределения (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), типы атомов (ATOM=1-2) или (ATOM=1,2,3-4,5,6). Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Блок результатов &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).&lt;br /&gt;Формат таблицы для функций радиального распределения (матричный вывод отключен)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, объем сферы (10 символов, 4 десятичной части), пробел, число молекул в данной сфере (9 символов), функция радиального распределения (9 символов, 6 десятичной части).&lt;br /&gt;Формат таблицы для функций радиального распределения (матричный вывод включен)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).&lt;br /&gt;Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, угол (9 символов, 2 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиально-углового распределения (9 символов, 6 десятичной части).&lt;br /&gt;Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)&lt;br /&gt; 0001.0000 04.000000 …&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Конец таблицы.&lt;/li&gt;&lt;/ul&gt;
@ -924,7 +924,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated&lt;br /&gt;-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &amp;quot;0-0:2.4,0-1:3.0&amp;quot; means set 0-0 interaction as &amp;lt;2.4 А and 0-1 interaction as &amp;lt;3.0 A&lt;br /&gt;-o FILE – output file&lt;br /&gt;-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&amp;gt;= 3)&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;statgen ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), atom types (ATOMS=1,2,3,4), interactions (INTERACTION=format), maximum depth for check cycle number (DEPTH=0, 0 - do not check graph isomorphism). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The enumeration of statistics on individual files.&lt;br /&gt;File name (FILE=mask.001), the statistic block for file &amp;quot;STATISTIC ... -----------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).&lt;br /&gt;The enumeration of agglomerates in the file. Agglomerate title (AGL=2=1.3.4.) (1 – number of molecules in the agglomerate, 1.3.4. – agglomerate class, if verification of isomorphism is specified). The enumeration of molecules in the agglomerate. (0000001=2,3,4,5,) (1 – number of molecule (7 characters), equal sign, the enumeration of connected molecules separated by commas).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The summary statistic block &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. Table layout (2 rows) follows after specifying the block. The table format&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Space, agglomerate size (7 characters), space, total number of agglomerates of this size (7 characters), space, average concentration of agglomerates of this size (9 characters, 2 decimal part), space, probability of finding molecules in agglomerates of this size (9 characters, 5 decimal part), space, probability of finding molecules in agglomerates of this size multiplied by the size (10 characters, 5 decimal part).&lt;/li&gt;
@ -953,7 +953,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Использование&lt;/span&gt;&lt;br /&gt;mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Параметры&lt;/span&gt;&lt;br /&gt;-i МАСКА – маска снимков траектории&lt;br /&gt;-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории&lt;br /&gt;-c X,Y,Z – размер элементарной ячейки, А&lt;br /&gt;-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую&lt;br /&gt;-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &amp;quot;0-0:2.4,0-1:3.0&amp;quot; означает указание 0-0 взаимодействия &amp;lt;2.4 А и 0-1 &amp;lt;3.0 А.&lt;br /&gt;-o ФАЙЛ – генерируемый файл&lt;br /&gt;-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&amp;gt;= 3)&lt;br /&gt;-l ФАЙЛ – запись лога в указанный файл&lt;br /&gt;-q – не выводить сообщения в STDOUT&lt;br /&gt;-h – показать эту справку и выйти&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Форматы файлов&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Генерируемый файл (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;statgen ::: V.1.1.1&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;statgen ::: V.1.2.0&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Блок конфигурации &amp;quot;CONFIGURATION … END&amp;quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), маска файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), типы атомов (ATOMS=1,2,3,4), взаимодействия (INTERACTION=формат), максимальная глубина для проверки числа циклов (DEPTH=0, 0 – не проверять изоморфизм). Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Перечисление статистики по файлам.&lt;br /&gt;Имя файла (FILE=mask.001), блок статистики по файлу &amp;quot;STATISTIC … -----------------&amp;quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы&lt;br /&gt; 0000001 0000001 &lt;br /&gt;Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).&lt;br /&gt;Перечисление агломератов, найденных в данном файле. Заголовок агломерата (AGL=2=1.3.4.) (1 – число молекул в агломерате, 1.3.4. – класс агломерата, если указана проверка изоморфизма). Перечисление молекул в агломерате (0000001=2,3,4,5,) (1 – номер молекулы (7 символов), знак равенства, перечисление связанных молекул через запятую).&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Общая статистика &amp;quot;.SUMMARY STATISTIC … ------------------------------------------------&amp;quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы&lt;br /&gt; 0000001 0000002 000003.00 004.00000 0005.00000&lt;br /&gt;Пробел, размер агломерата (7 символов), пробел, общее число агломератов данной стехиометрии (7 символов), пробел, средняя концентрация агломератов данной стехиометрии (9 символов, 2 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии (9 символов, 5 десятичной части), пробел, вероятность нахождения молекулы в агломерате данной стехиометрии, умноженная на число молекул в агломерате (10 символов, 5 десятичной части).&lt;/li&gt;
@ -1034,7 +1034,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Usage&lt;/span&gt;&lt;br /&gt;mm_radf -i MASK -s NUMBER,NUMBER -c X,Y,Z -at FORMAT -o FILE [ -r NUMBER,NUMBER ] [ -rs NUMBER ] [ -a NUMBER,NUMBER ] [ -as NUMBER ] [ -m ] [ -l FILE ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Parametrs&lt;/span&gt;&lt;br /&gt;-i MASK – mask of trajectory files&lt;br /&gt;-s NUMBER,NUMBER – first and last trajectory steps&lt;br /&gt;-c X,Y,Z – cell size, A&lt;br /&gt;-at FORMAT – numerical atom types between which the function is calculated. Format is &amp;quot;1-2&amp;quot; or &amp;quot;1,2,3-4,5,6&amp;quot; (automatically enable calculation of radial distribution function between centers of mass)&lt;br /&gt;-o FILE – output file&lt;br /&gt;-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0&lt;br /&gt;-rs NUMBER – radius change step, A. Default is 0.2&lt;br /&gt;-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0&lt;br /&gt;-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function&lt;br /&gt;-as – enable matrix output&lt;br /&gt;-l FILE – print log to specified file&lt;br /&gt;-q – do not print messages to STDOUT&lt;br /&gt;-h – show this help and exit&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;File formats&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Output file (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.1.1&amp;quot;. Blank line.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Program name and version are shown in the title. For example, &amp;quot;radf ::: V.1.2.0&amp;quot;. Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The configuration block &amp;quot;CONFIGURATION ... END&amp;quot;. Print log (LOG=1), do not print messages to STDOUT (QUIET=1), matrix output (MATRIX=1), mask of trajectory files (MASK=mask), first (FIRST=1) and last (LAST=1) trajectory steps, sell size (CELL=1.0000,2.0000,3.0000), mode (MODE=0) (0 – radial distribution function, 1 – radial distribution function between centers of mass, 2 – radial-angles distribution function), radial criteria (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), angular criteria for radial-angles distribution function (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), atom types (ATOM=1-2) or (ATOM=1,2,3-4,5,6). Blank line.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.&lt;br /&gt;The table format for radial distribution function (matrix output disables)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment volume (10 characters, 4 decimal part), space, number of molecules in this radius (9 characters), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial distribution function (matrix output enables)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output disables)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, segment angle (9 characters, 2 decimal part), segment volume (10 characters, 4 decimal part), space, number of molecules in this segment (9 characters), space, radial-angles distribution function (9 characters, 6 decimal part).&lt;br /&gt;The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title&lt;br /&gt; 0001.0000 04.000000 ...&lt;br /&gt;Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;End of the table&lt;/li&gt;&lt;/ul&gt;
@ -1061,7 +1061,7 @@ p, li { white-space: pre-wrap; }
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Использование&lt;/span&gt;&lt;br /&gt;mm_radf -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -at ФОРМАТ -o ФАЙЛ [ -r ЧИСЛО,ЧИСЛО ] [ -rs ЧИСЛО ] [ -a ЧИСЛО,ЧИСЛО ] [ -as ЧИСЛО ] [ -m ] [ -l ФАЙЛ ] [ -q ] [ -h ]&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Параметры&lt;/span&gt;&lt;br /&gt;-i МАСКА – маска снимков траектории&lt;br /&gt;-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории&lt;br /&gt;-c X,Y,Z – размер элементарной ячейки, А&lt;br /&gt;-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат &amp;quot;1-2&amp;quot; или &amp;quot;1,2,3,-4,5,6&amp;quot; (автоматически включит расчет функции радиального распределения между центрами масс).&lt;br /&gt;-o ФАЙЛ – генерируемый файл&lt;br /&gt;-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0&lt;br /&gt;-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2&lt;br /&gt;-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0&lt;br /&gt;-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения&lt;br /&gt;-m – печать в виде матрицы&lt;br /&gt;-l ФАЙЛ – запись лога в указанный файл&lt;br /&gt;-q – не выводить сообщения в STDOUT&lt;br /&gt;-h – показать эту справку и выйти&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt; &lt;span style=&quot; text-decoration: underline;&quot;&gt;Форматы файлов&lt;/span&gt;&lt;/p&gt;
&lt;p align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;span style=&quot; font-style:italic;&quot;&gt;Генерируемый файл (*.dat)&lt;/span&gt;&lt;/p&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;radf ::: V.1.1.1&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;ul style=&quot;margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;&quot;&gt;&lt;li align=&quot;justify&quot; style=&quot; margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;В заголовке указывается название программы и ее версия, например &amp;quot;radf ::: V.1.2.0&amp;quot;. Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Блок конфигурации &amp;quot;CONFIGURATION … END&amp;quot;. Печать лога (LOG=1), не выводить сообщения в STDOUT (QUIET=1), матричный вывод (MATRIX=1), файлов (MASK=mask), первый (FIRST=1) и последний (LAST=1) шаги траектории, размер ячейки (CELL=1.0000,2.0000,3.0000), тип расчета (MODE=0) (0 – для функции радиального распределения, 1 – для функции радиального распределения для центров масс, 2 – для функции радиально-углового распределения), радиальные критерии (R_MIN=0.100) (R_MAX=0.100) (R_STEP=0.100), угловые критерии для функции радиально-углового распределения (ANG_MIN=0.10) (ANG_MAX=0.10) (ANG_STEP=0.10), типы атомов (ATOM=1-2) или (ATOM=1,2,3-4,5,6). Пустая строка.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Блок результатов &amp;quot;SUMMARY STATISTIC … ------------------------------------------------&amp;quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).&lt;br /&gt;Формат таблицы для функций радиального распределения (матричный вывод отключен)&lt;br /&gt; 0001.0000 2.0000e-01 000000003 04.000000&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиального распределения (9 символов, 6 десятичной части).&lt;br /&gt;Формат таблицы для функций радиального распределения (матричный вывод включен)&lt;br /&gt; 0001.0000 04.000000&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).&lt;br /&gt;Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)&lt;br /&gt; 0001.0000 000005.00 2.0000e-01 000000003 04.000000&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, угол (9 символов, 2 десятичной части), пробел, объем сегмента (10 символов, 4 десятичной части), пробел, число молекул в данном сегменте (9 символов), функция радиально-углового распределения (9 символов, 6 десятичной части).&lt;br /&gt;Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)&lt;br /&gt; 0001.0000 04.000000 …&lt;br /&gt;Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.&lt;/li&gt;
&lt;li style=&quot; margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Конец таблицы.&lt;/li&gt;&lt;/ul&gt;

26
mathmech/mathmech/src/CMakeLists.txt
View File

@ -3,7 +3,7 @@ file (GLOB SOURCES *.cpp)
file (GLOB HEADERS *.h)
file (GLOB FORMS *.ui)
if (CMAKE_SYSTEM_NAME MATCHES Windows)
set (SOURCES ${SOURCES} ${PROJECT_RESOURCE_DIR}/res_icon.rc)
set (SOURCES ${SOURCES} ${SUBPROJECT_RESOURCE_DIR}/res_icon.rc)
endif ()
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -14,18 +14,18 @@ endif ()
set (LANGUAGES
eng
rus)
set (RESOURCES ${PROJECT_RESOURCE_DIR}/resources.qrc)
set (RESOURCES ${SUBPROJECT_RESOURCE_DIR}/resources.qrc)
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
message (STATUS "${PROJECT} FORMS: ${FORMS}")
message (STATUS "${SUBPROJECT} SOURCES: ${SOURCES}")
message (STATUS "${SUBPROJECT} HEADERS: ${HEADERS}")
message (STATUS "${SUBPROJECT} FORMS: ${FORMS}")
# compile
project (${PROJECT})
project (${SUBPROJECT})
# include_path
link_directories (${QWT_LIBRARY_PATH})
include_directories (${PROJECT_SOURCE_DIR}
include_directories (${SUBPROJECT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
${QWT_INCLUDE_PATH})
@ -35,8 +35,8 @@ qt4_add_resources (QRC_SOURCES ${RESOURCES})
qt4_wrap_cpp (MOC_SOURCES ${HEADERS})
qt4_wrap_ui (UI_HEADERS ${FORMS})
foreach (LANGUAGE ${LANGUAGES})
set (TS ${PROJECT_TRANSLATION_DIR}/${LANGUAGE}.ts)
set (QM ${PROJECT_TRANSLATION_DIR}/${LANGUAGE}.qm)
set (TS ${SUBPROJECT_TRANSLATION_DIR}/${LANGUAGE}.ts)
set (QM ${SUBPROJECT_TRANSLATION_DIR}/${LANGUAGE}.qm)
set (TRANSLATIONS ${TRANSLATIONS} ${TS})
set (TRANSLATIONS_BINARY ${TRANSLATIONS_BINARY} ${QM})
add_custom_command (
@ -50,18 +50,18 @@ add_custom_target (
add_custom_command (
TARGET translations
COMMAND ${QT_LRELEASE_EXECUTABLE} ${TRANSLATIONS})
message (STATUS "${PROJECT} TRANSLATIONS: ${TRANSLATIONS_BINARY}")
message (STATUS "${SUBPROJECT} TRANSLATIONS: ${TRANSLATIONS_BINARY}")
source_group ("Header Files" FILES ${HEADERS})
source_group ("Source Files" FILES ${SOURCES})
source_group ("Generated Files" FILES ${MOC_SOURCES})
source_group ("Resource Files" FILES ${QRC_SOURCES})
add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURCES} ${QRC_SOURCES} ${TRANSLATIONS})
target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
add_executable (${SUBPROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURCES} ${QRC_SOURCES} ${TRANSLATIONS})
target_link_libraries (${SUBPROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY})
# install properties
install (TARGETS ${PROJECT} DESTINATION bin)
install (TARGETS ${SUBPROJECT} DESTINATION bin)
if (CMAKE_SYSTEM_NAME MATCHES Linux)
install (FILES ../mathmech.desktop DESTINATION share/applications/)
install (FILES ../mathmech-logo.png DESTINATION share/pixmaps/)