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Release 1.1.1

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* optimization
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arcan1s
2013-09-03 18:09:26 +04:00
parent 6b0a2a47db
commit 473d195ea9
41 changed files with 172 additions and 100 deletions
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9
mathmech/CMakeLists.txt
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@ -1,6 +1,12 @@
cmake_minimum_required (VERSION 2.8)
cmake_policy (SET CMP0003 OLD)
cmake_policy (SET CMP0011 NEW)
cmake_policy (SET CMP0015 NEW)
set ("PROJECT_VERSION_MAJOR" 1)
set ("PROJECT_VERSION_MINOR" 1)
set ("PROJECT_VERSION_PATCH" 0)
set ("PROJECT_VERSION_PATCH" 1)
set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
message (STATUS "Version ${PROJECT_VERSION}")
@ -16,7 +22,6 @@ set (COMPS mathmech
# install options
set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
OPTION (ADD_DOCS "Add documentation" OFF)
if (CMAKE_SYSTEM_NAME MATCHES Linux)
set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include")

7
mathmech/PKGBUILD
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@ -2,7 +2,7 @@
# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
pkgname=mathmech
pkgver=1.1.0
pkgver=1.1.1
pkgrel=1
pkgdesc="Software package for analysis of molecular dynamics trajectories"
arch=(any)
@ -11,13 +11,12 @@ license=('GPL')
depends=('qt4' 'qwt')
makedepends=('cmake' 'automoc4')
source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
md5sums=('80420d6aa723d0944891113a510f06fe')
md5sums=('6a7f3dd17ae4ad0498110aaaadea5a2b')
_cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
-DQWT_INCLUDE_PATH=/usr/include/qwt
-DQWT_LIBRARY_PATH=/usr/lib
-DMM_PREFIX=mm_
-DADD_INCLUDE=0
-DADD_DOCS=0
-DADD_DOCS:BOOL=0
-DCMAKE_BUILD_TYPE=Release"
build ()

18
mathmech/create_archive.sh Executable file
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@ -0,0 +1,18 @@
#!/bin/bash
FILES="docs mathmech mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb AUTHORS CMakeLists.txt COPYING docs.cmake INSTALL"
ARCHIVE="mathmech"
VERSION=`grep -m1 PROJECT_VERSION_MAJOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
`grep -m1 PROJECT_VERSION_MINOR CMakeLists.txt | awk '{print $3}' | cut -c 1`.\
`grep -m1 PROJECT_VERSION_PATCH CMakeLists.txt | awk '{print $3}' | cut -c 1`
# create archive
if [ -e ${ARCHIVE}-${VERSION}-src.zip ]; then
rm -f ${ARCHIVE}-${VERSION}-src.zip
fi
zip -9 -y -r -q ${ARCHIVE}-${VERSION}-src.zip ${FILES}
# update md5sum
MD5SUMS=`md5sum ${ARCHIVE}-${VERSION}-src.zip | awk '{print $1}'`
sed -i "/md5sums=('[0-9A-Fa-f]*/s/[^'][^)]*/md5sums=('${MD5SUMS}'/" PKGBUILD
sed -i "s/pkgver=[0-9.]*/pkgver=${VERSION}/" PKGBUILD

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mathmech/mathmech-1.1.0-src.zip
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mathmech/mathmech-1.1.1-src.zip Normal file
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mathmech/mathmech-1.1.1-win32.zip Executable file
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mathmech/mathmech/README
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@ -1,3 +1,3 @@
Mathematical Molecular Mechanics is GUI for "mm" program pack
Version: 1.1.0
Version: 1.1.1
License: GPL

2
mathmech/mathmech/mathmech.cmake
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@ -1,8 +1,6 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
set (PROJECT_RESOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/resources)
set (PROJECT_TRANSLATION_DIR ${PROJECT_RESOURCE_DIR}/translations)

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; 1.1.0&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;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;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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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
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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;Версия:&lt;/span&gt; 1.1.0&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;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;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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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.1.1.0&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.1.1.1&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;

12
mathmech/mathmech/src/CMakeLists.txt
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@ -16,17 +16,16 @@ set (LANGUAGES
rus)
set (RESOURCES ${PROJECT_RESOURCE_DIR}/resources.qrc)
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "HEADERS: ${HEADERS}")
message (STATUS "FORMS: ${FORMS}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
message (STATUS "${PROJECT} FORMS: ${FORMS}")
# compile
project (${PROJECT})
# include_path
link_directories (${QWT_LIBRARY_PATH})
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}
${PROJECT_SOURCE_DIR}
include_directories (${PROJECT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
${QWT_INCLUDE_PATH})
@ -51,7 +50,7 @@ add_custom_target (
add_custom_command (
TARGET translations
COMMAND ${QT_LRELEASE_EXECUTABLE} ${TRANSLATIONS})
message (STATUS "TRANSLATIONS: ${TRANSLATIONS_BINARY}")
message (STATUS "${PROJECT} TRANSLATIONS: ${TRANSLATIONS_BINARY}")
source_group ("Header Files" FILES ${HEADERS})
source_group ("Source Files" FILES ${SOURCES})
@ -59,7 +58,6 @@ 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})
# install properties

2
mathmech/mm_agl/README
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@ -1,5 +1,5 @@
mm_agl - program that creates PDB file with chosen agglomerate
Version: 1.1.0
Version: 1.1.1
License: GPL
Usage:

2
mathmech/mm_agl/mm_agl.doxygen
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@ -32,7 +32,7 @@ PROJECT_NAME = mm_agl
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.1.0
PROJECT_NUMBER = V.1.1.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_agl/mm_agl.pdf
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11
mathmech/mm_agl/src/CMakeLists.txt
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@ -1,5 +1,6 @@
# set files
aux_source_directory (. SOURCES)
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -9,17 +10,15 @@ else ()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${PROJECT} ${SOURCES})
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

16
mathmech/mm_agl/src/main.c
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@ -61,13 +61,23 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* <li>initial release
* </ul>
*/
@ -134,7 +144,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_agl\n");
sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_envir/README
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@ -1,5 +1,5 @@
mm_envir - program that searchs environment for chosen molecule by geometric criterion
Version: 1.1.0
Version: 1.1.1
License: GPL
Usage:

2
mathmech/mm_envir/mm_envir.doxygen
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@ -32,7 +32,7 @@ PROJECT_NAME = mm_envir
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.1.0
PROJECT_NUMBER = V.1.1.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
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11
mathmech/mm_envir/src/CMakeLists.txt
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@ -1,5 +1,6 @@
# set files
aux_source_directory (. SOURCES)
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -9,17 +10,15 @@ else ()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${PROJECT} ${SOURCES})
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

16
mathmech/mm_envir/src/main.c
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@ -63,13 +63,23 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* <li>initial release
* </ul>
*/
@ -136,7 +146,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_envir\n");
sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_radf/mm_radf.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_radf
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.1.0
PROJECT_NUMBER = V.1.1.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_radf/mm_radf.pdf
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Binary file not shown.

11
mathmech/mm_radf/src/CMakeLists.txt
View File

@ -1,5 +1,6 @@
# set files
aux_source_directory (. SOURCES)
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -9,17 +10,15 @@ else ()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${PROJECT} ${SOURCES})
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

2
mathmech/mm_radf/src/add_main.c
View File

@ -127,7 +127,7 @@ int printing_head (const char *output, const int log, const int quiet, const int
FILE *f_out;
f_out = fopen (output, "w");
fprintf (f_out, "radf ::: V.1.1.0\n\n");
fprintf (f_out, "radf ::: V.1.1.1\n\n");
fprintf (f_out, "CONFIGURATION\n");
fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix);

16
mathmech/mm_radf/src/main.c
View File

@ -70,13 +70,23 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* <li>initial release
* </ul>
*/
@ -153,7 +163,7 @@ int main(int argc, char *argv[])
sprintf (tmp_str, " mm_radf\n");
sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
sprintf (tmp_str, "%sdistribution function\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_statgen/README
View File

@ -1,5 +1,5 @@
mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
Version: 1.1.0
Version: 1.1.1
License: GPL
Usage:

2
mathmech/mm_statgen/mm_statgen.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_statgen
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.1.0
PROJECT_NUMBER = V.1.1.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_statgen/mm_statgen.pdf
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Binary file not shown.

11
mathmech/mm_statgen/src/CMakeLists.txt
View File

@ -1,5 +1,6 @@
# set files
aux_source_directory (. SOURCES)
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -9,17 +10,15 @@ else ()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${PROJECT} ${SOURCES})
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

2
mathmech/mm_statgen/src/add_main.c
View File

@ -92,7 +92,7 @@ int printing_head (const char *output, const int log, const int quiet,
FILE *f_out;
f_out = fopen (output, "w");
fprintf (f_out, "statgen ::: V.1.1.0\n\n");
fprintf (f_out, "statgen ::: V.1.1.1\n\n");
fprintf (f_out, "CONFIGURATION\n");
fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);

16
mathmech/mm_statgen/src/main.c
View File

@ -66,13 +66,23 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* <li>initial release
* </ul>
*/
@ -168,7 +178,7 @@ int main (int argc, char *argv[])
{
sprintf (tmp_str, " mm_statgen\n");
sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_trj/mm_trj.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.1.0
PROJECT_NUMBER = V.1.1.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_trj/mm_trj.pdf
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Binary file not shown.

11
mathmech/mm_trj/src/CMakeLists.txt
View File

@ -1,5 +1,6 @@
# set files
aux_source_directory (. SOURCES)
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -9,17 +10,15 @@ else ()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${PROJECT} ${SOURCES})
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

16
mathmech/mm_trj/src/main.c
View File

@ -63,13 +63,23 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* <li>initial release
* </ul>
*/
@ -133,7 +143,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_trj\n");
sprintf (tmp_str, "%sProgram that generates trajectory files\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);

2
mathmech/mm_trj2pdb/README
View File

@ -1,5 +1,5 @@
mm_trj2pdb - program that creates PDB file from trajetory snapshot
Version: 1.1.0
Version: 1.1.1
License: GPL
Usage:

2
mathmech/mm_trj2pdb/mm_trj2pdb.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj2pdb
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.1.0
PROJECT_NUMBER = V.1.1.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_trj2pdb/mm_trj2pdb.pdf
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Binary file not shown.

11
mathmech/mm_trj2pdb/src/CMakeLists.txt
View File

@ -1,5 +1,6 @@
# set files
aux_source_directory (. SOURCES)
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
@ -9,17 +10,15 @@ else ()
endif ()
# message
message (STATUS "SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${PROJECT} ${SOURCES})
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

16
mathmech/mm_trj2pdb/src/main.c
View File

@ -59,13 +59,23 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* <li>initial release
* </ul>
*/
@ -125,7 +135,7 @@ int main(int argc, char *argv[])
{
sprintf (tmp_str, " mm_trj2pdb\n");
sprintf (tmp_str, "%sProgram for create PDB file from trajectory snapshot\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);