diff --git a/mathmech/CMakeLists.txt b/mathmech/CMakeLists.txt index 2e2da06..522ddf6 100644 --- a/mathmech/CMakeLists.txt +++ b/mathmech/CMakeLists.txt @@ -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 ${PROJECT_VERSION}") @@ -16,7 +22,6 @@ set (COMPS mathmech # install options set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools") OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF) -OPTION (ADD_INCLUDE "Add include files" OFF) OPTION (ADD_DOCS "Add documentation" OFF) if (CMAKE_SYSTEM_NAME MATCHES Linux) set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include") diff --git a/mathmech/PKGBUILD b/mathmech/PKGBUILD index 2b5106b..96099f3 100644 --- a/mathmech/PKGBUILD +++ b/mathmech/PKGBUILD @@ -2,7 +2,7 @@ # Maintainer: Evgeniy "arcanis" Alexeev pkgname=mathmech -pkgver=1.1.0 +pkgver=1.1.1 pkgrel=1 pkgdesc="Software package for analysis of molecular dynamics trajectories" arch=(any) @@ -11,13 +11,12 @@ license=('GPL') depends=('qt4' 'qwt') makedepends=('cmake' 'automoc4') source=(https://github.com/arcan1s/moldyn/releases/download/mm-${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 () diff --git a/mathmech/create_archive.sh b/mathmech/create_archive.sh new file mode 100755 index 0000000..6f918d2 --- /dev/null +++ b/mathmech/create_archive.sh @@ -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 diff --git a/mathmech/mathmech-1.1.0-src.zip b/mathmech/mathmech-1.1.0-src.zip deleted file mode 100644 index d1dd973..0000000 Binary files a/mathmech/mathmech-1.1.0-src.zip and /dev/null differ diff --git a/mathmech/mathmech-1.1.1-src.zip b/mathmech/mathmech-1.1.1-src.zip new file mode 100644 index 0000000..1e5799f Binary files /dev/null and b/mathmech/mathmech-1.1.1-src.zip differ diff --git a/mathmech/mathmech-1.1.1-win32.zip b/mathmech/mathmech-1.1.1-win32.zip new file mode 100755 index 0000000..4daa66b Binary files /dev/null and b/mathmech/mathmech-1.1.1-win32.zip differ diff --git a/mathmech/mathmech/README b/mathmech/mathmech/README index d89eb64..69d1415 100644 --- a/mathmech/mathmech/README +++ b/mathmech/mathmech/README @@ -1,3 +1,3 @@ Mathematical Molecular Mechanics is GUI for "mm" program pack -Version: 1.1.0 +Version: 1.1.1 License: GPL diff --git a/mathmech/mathmech/mathmech.cmake b/mathmech/mathmech/mathmech.cmake index 91f4335..6794343 100644 --- a/mathmech/mathmech/mathmech.cmake +++ b/mathmech/mathmech/mathmech.cmake @@ -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) diff --git a/mathmech/mathmech/resources/translations/eng.ts b/mathmech/mathmech/resources/translations/eng.ts index 02f1cbc..342e0e1 100644 --- a/mathmech/mathmech/resources/translations/eng.ts +++ b/mathmech/mathmech/resources/translations/eng.ts @@ -29,7 +29,7 @@ p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> <p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Mathematical Molecular Mechanics</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Version:</span> 1.1.0</p> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Version:</span> 1.1.1</p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">License:</span> GPL</p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Author:</span> Evgeniy Alekseev</p> @@ -604,7 +604,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -633,7 +633,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -732,7 +732,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />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 ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is constructed. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0<br />-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> @@ -759,7 +759,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />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 ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is constructed. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0<br />-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> @@ -924,7 +924,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -953,7 +953,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -1034,7 +1034,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />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 ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> @@ -1061,7 +1061,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />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 ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> diff --git a/mathmech/mathmech/resources/translations/rus.ts b/mathmech/mathmech/resources/translations/rus.ts index deb6e4f..3e4836f 100644 --- a/mathmech/mathmech/resources/translations/rus.ts +++ b/mathmech/mathmech/resources/translations/rus.ts @@ -29,7 +29,7 @@ p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Liberation Serif'; font-size:10pt; font-weight:400; font-style:normal;"> <p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Mathematical Molecular Mechanics</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Версия:</span> 1.1.0</p> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Версия:</span> 1.1.1</p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Лицензия:</span> GPL</p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Автор:</span> Evgeniy Alekseev</p> @@ -604,7 +604,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -633,7 +633,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую<br />-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &quot;0-0:2.4,0-1:3.0&quot; означает указание 0-0 взаимодействия &lt;2.4 А и 0-1 &lt;3.0 А.<br />-o ФАЙЛ – генерируемый файл<br />-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&gt;= 3)<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.0&quot;. Пустая строка.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.1&quot;. Пустая строка.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление статистики по файлам.<br />Имя файла (FILE=mask.001), блок статистики по файлу &quot;STATISTIC … -----------------&quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000001 <br />Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика &quot;.SUMMARY STATISTIC … ------------------------------------------------&quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -732,7 +732,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />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 ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is constructed. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria. Default is 0.0 and 90.0<br />-as NUMBER – angle change step. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> @@ -759,7 +759,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />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 ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат &quot;1-2&quot; или &quot;1,2,3,-4,5,6&quot; (автоматически включит расчет функции радиального распределения между центрами масс).<br />-o ФАЙЛ – генерируемый файл<br />-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0<br />-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2<br />-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0<br />-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения<br />-m – печать в виде матрицы<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.0&quot;. Пустая строка.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.1&quot;. Пустая строка.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок результатов &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).<br />Формат таблицы для функций радиального распределения (матричный вывод отключен)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />Формат таблицы для функций радиального распределения (матричный вывод включен)<br /> 0001.0000 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)<br /> 0001.0000 04.000000 …<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Конец таблицы.</li></ul> @@ -924,7 +924,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />mm_statgen -i MASK -s NUMBER,NUMBER -c X,Y,Z -a FORMAT -r FORMAT -o FILE [ -g NUMBER ] [ -l FILE ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-a FORMAT – numerical atom types. Maximum number of different atom types is 4. Types are comma separated<br />-r FORMAT – criteria, A. This flag can be used multiple times. Different interactions are comma separated. Type interaction, colon character, criterion. For example &quot;0-0:2.4,0-1:3.0&quot; means set 0-0 interaction as &lt;2.4 А and 0-1 interaction as &lt;3.0 A<br />-o FILE – output file<br />-g NUMBER – chech graph isomorphism. NUMBER is a maximum depth for search cycles (&gt;= 3)<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;statgen ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The enumeration of statistics on individual files.<br />File name (FILE=mask.001), the statistic block for file &quot;STATISTIC ... -----------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000001 <br />Space, agglomerate size (7 characters), space, number of agglomerates of this size in the file (7 characters).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The summary statistic block &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. Table layout (2 rows) follows after specifying the block. The table format<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -953,7 +953,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />mm_statgen -i МАСКА -s ЧИСЛО,ЧИСЛО -c X,Y,Z -a ФОРМАТ -r ФОРМАТ -o ФАЙЛ [ -g ЧИСЛО ] [ -l ФАЙЛ ] [ -q ] [ -h ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-a ФОРМАТ – численные типы атомов. Максимальное число различных атомов 4. Типы атомов перечисляются через запятую<br />-r ФОРМАТ – критерии, А. Этот флаг может быть указан несколько раз. Различные взаимодействия перечисляются через запятую. Указывается тип взаимодействия, двоеточие, критерий. Например, &quot;0-0:2.4,0-1:3.0&quot; означает указание 0-0 взаимодействия &lt;2.4 А и 0-1 &lt;3.0 А.<br />-o ФАЙЛ – генерируемый файл<br />-g NUMBER – проверять изоморфизм графов. ЧИСЛО – максимальная глубина для проверки числа циклов (&gt;= 3)<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.0&quot;. Пустая строка.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;statgen ::: V.1.1.1&quot;. Пустая строка.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Перечисление статистики по файлам.<br />Имя файла (FILE=mask.001), блок статистики по файлу &quot;STATISTIC … -----------------&quot;. После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000001 <br />Пробел, размер агломерата (7 символов), пробел, число агломератов данной стехиометрии в файле (7 символов).<br />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).</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Общая статистика &quot;.SUMMARY STATISTIC … ------------------------------------------------&quot;..После указания блока следует разметка таблицы (2 строки). Формат таблицы<br /> 0000001 0000002 000003.00 004.00000 0005.00000<br />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).</li> @@ -1034,7 +1034,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Usage</span><br />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 ]<br /> <span style=" text-decoration: underline;">Parametrs</span><br />-i MASK – mask of trajectory files<br />-s NUMBER,NUMBER – first and last trajectory steps<br />-c X,Y,Z – cell size, A<br />-at FORMAT – numerical atom types between which the function is calculated. Format is &quot;1-2&quot; or &quot;1,2,3-4,5,6&quot; (automatically enable calculation of radial distribution function between centers of mass)<br />-o FILE – output file<br />-r NUMBER,NUMBER – radial criteria, A. Default is 2.0 and 15.0<br />-rs NUMBER – radius change step, A. Default is 0.2<br />-a NUMBER,NUMBER – angular criteria, deg. Default is 0.0 and 90.0<br />-as NUMBER – angle change step, deg. This option will enable calculation of radial-angles distribution function<br />-as – enable matrix output<br />-l FILE – print log to specified file<br />-q – do not print messages to STDOUT<br />-h – show this help and exit</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">File formats</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Output file (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.0&quot;. Blank line.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Program name and version are shown in the title. For example, &quot;radf ::: V.1.1.1&quot;. Blank line.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The configuration block &quot;CONFIGURATION ... END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The results block «SUMMARY STATISTIC … ------------------------------------------------». Table layout (2 rows) follows after specifying the block if matrix output disables.<br />The table format for radial distribution function (matrix output disables)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial distribution function (matrix output enables)<br /> 0001.0000 04.000000<br />Space, sphere radius (9 characters, 4 decimal part), space, radial distribution function (9 characters, 6 decimal part).<br />The table format for radial-angles distribution function (matrix output disables)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />The table format for radial-angles distribution function (matrix output enables). Segment angle (9 characters, 2 decimal part) is shown in the title<br /> 0001.0000 04.000000 ...<br />Space, sphere radius (9 characters, 4 decimal part), space, radial-angles distribution function (9 characters, 6 decimal part) separated by spaces.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">End of the table</li></ul> @@ -1061,7 +1061,7 @@ p, li { white-space: pre-wrap; } <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Использование</span><br />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 ]<br /> <span style=" text-decoration: underline;">Параметры</span><br />-i МАСКА – маска снимков траектории<br />-s ЧИСЛО,ЧИСЛО – первый и последний шаги траектории<br />-c X,Y,Z – размер элементарной ячейки, А<br />-at ФОРМАТ – численные типы атомов между которыми строится функция. Формат &quot;1-2&quot; или &quot;1,2,3,-4,5,6&quot; (автоматически включит расчет функции радиального распределения между центрами масс).<br />-o ФАЙЛ – генерируемый файл<br />-r ЧИСЛО,ЧИСЛО – минимальный и максимальный радиус, А. По умолчанию 2.0 и 15.0<br />-rs ЧИСЛО – шаг изменения радиуса, А. По умолчанию 0.2<br />-a ЧИСЛО,ЧИСЛО – минимальный и максимальный угол, град. По умолчанию 0.0 и 90.0<br />-as ЧИСЛО – шаг изменения угла, град. Эта опция включит расчет функции радиально-углового распределения<br />-m – печать в виде матрицы<br />-l ФАЙЛ – запись лога в указанный файл<br />-q – не выводить сообщения в STDOUT<br />-h – показать эту справку и выйти</p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /> <span style=" text-decoration: underline;">Форматы файлов</span></p> <p align="justify" style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <span style=" font-style:italic;">Генерируемый файл (*.dat)</span></p> -<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.0&quot;. Пустая строка.</li> +<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li align="justify" style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">В заголовке указывается название программы и ее версия, например &quot;radf ::: V.1.1.1&quot;. Пустая строка.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок конфигурации &quot;CONFIGURATION … END&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.</li> <li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Блок результатов &quot;SUMMARY STATISTIC … ------------------------------------------------&quot;. После указания блока, если отключен матричный вывод, следует разметка таблицы (2 строки).<br />Формат таблицы для функций радиального распределения (матричный вывод отключен)<br /> 0001.0000 2.0000e-01 000000003 04.000000<br />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).<br />Формат таблицы для функций радиального распределения (матричный вывод включен)<br /> 0001.0000 04.000000<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиального распределения (9 символов, 6 десятичной части).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод отключен)<br /> 0001.0000 000005.00 2.0000e-01 000000003 04.000000<br />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).<br />Формат таблицы для функций радиально-углового распределения (матричный вывод включен). В заголовке указывается угол (9 символов, 2 десятичной части)<br /> 0001.0000 04.000000 …<br />Пробел, радиус сферы (9 символов, 4 десятичной части), пробел, функция радиально-углового распределения (9 символов, 6 десятичной части) через пробелы, соответствующие данному углу.</li> <li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Конец таблицы.</li></ul> diff --git a/mathmech/mathmech/src/CMakeLists.txt b/mathmech/mathmech/src/CMakeLists.txt index 7b98fe6..466c4b6 100644 --- a/mathmech/mathmech/src/CMakeLists.txt +++ b/mathmech/mathmech/src/CMakeLists.txt @@ -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 diff --git a/mathmech/mm_agl/README b/mathmech/mm_agl/README index 01a73c1..9d0c77a 100644 --- a/mathmech/mm_agl/README +++ b/mathmech/mm_agl/README @@ -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: diff --git a/mathmech/mm_agl/mm_agl.doxygen b/mathmech/mm_agl/mm_agl.doxygen index c72e767..5bc8dd1 100644 --- a/mathmech/mm_agl/mm_agl.doxygen +++ b/mathmech/mm_agl/mm_agl.doxygen @@ -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 diff --git a/mathmech/mm_agl/mm_agl.pdf b/mathmech/mm_agl/mm_agl.pdf index ed2a85f..082c214 100644 Binary files a/mathmech/mm_agl/mm_agl.pdf and b/mathmech/mm_agl/mm_agl.pdf differ diff --git a/mathmech/mm_agl/src/CMakeLists.txt b/mathmech/mm_agl/src/CMakeLists.txt index ba5b6dc..9a94e1b 100644 --- a/mathmech/mm_agl/src/CMakeLists.txt +++ b/mathmech/mm_agl/src/CMakeLists.txt @@ -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 () diff --git a/mathmech/mm_agl/src/main.c b/mathmech/mm_agl/src/main.c index 46f9ce6..b2305e9 100644 --- a/mathmech/mm_agl/src/main.c +++ b/mathmech/mm_agl/src/main.c @@ -61,13 +61,23 @@ * You may also download compiled executable file for Win_x86. * * @page Changelog + * V.1.1.1 (2013-09-03) + * + * V.1.1.0 (2013-09-02) + * * V.1.0.3 (2013-08-30) * * V.1.0.1 (2013-07-27) * */ @@ -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); diff --git a/mathmech/mm_envir/README b/mathmech/mm_envir/README index faed53e..97f9f71 100644 --- a/mathmech/mm_envir/README +++ b/mathmech/mm_envir/README @@ -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: diff --git a/mathmech/mm_envir/mm_envir.doxygen b/mathmech/mm_envir/mm_envir.doxygen index 032e61a..bf83981 100644 --- a/mathmech/mm_envir/mm_envir.doxygen +++ b/mathmech/mm_envir/mm_envir.doxygen @@ -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 diff --git a/mathmech/mm_envir/mm_envir.pdf b/mathmech/mm_envir/mm_envir.pdf index b979143..1e7cf35 100644 Binary files a/mathmech/mm_envir/mm_envir.pdf and b/mathmech/mm_envir/mm_envir.pdf differ diff --git a/mathmech/mm_envir/src/CMakeLists.txt b/mathmech/mm_envir/src/CMakeLists.txt index ba5b6dc..9a94e1b 100644 --- a/mathmech/mm_envir/src/CMakeLists.txt +++ b/mathmech/mm_envir/src/CMakeLists.txt @@ -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 () diff --git a/mathmech/mm_envir/src/main.c b/mathmech/mm_envir/src/main.c index 8e55b5b..8b8d250 100644 --- a/mathmech/mm_envir/src/main.c +++ b/mathmech/mm_envir/src/main.c @@ -63,13 +63,23 @@ * You may also download compiled executable file for Win_x86. * * @page Changelog + * V.1.1.1 (2013-09-03) + * + * V.1.1.0 (2013-09-02) + * * V.1.0.3 (2013-08-30) * * V.1.0.1 (2013-07-27) * */ @@ -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); diff --git a/mathmech/mm_radf/mm_radf.doxygen b/mathmech/mm_radf/mm_radf.doxygen index 5c96559..2ddc7ae 100644 --- a/mathmech/mm_radf/mm_radf.doxygen +++ b/mathmech/mm_radf/mm_radf.doxygen @@ -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 diff --git a/mathmech/mm_radf/mm_radf.pdf b/mathmech/mm_radf/mm_radf.pdf index 1d0a837..d24743b 100644 Binary files a/mathmech/mm_radf/mm_radf.pdf and b/mathmech/mm_radf/mm_radf.pdf differ diff --git a/mathmech/mm_radf/src/CMakeLists.txt b/mathmech/mm_radf/src/CMakeLists.txt index ba5b6dc..9a94e1b 100644 --- a/mathmech/mm_radf/src/CMakeLists.txt +++ b/mathmech/mm_radf/src/CMakeLists.txt @@ -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 () diff --git a/mathmech/mm_radf/src/add_main.c b/mathmech/mm_radf/src/add_main.c index bd68dd2..a88e68c 100644 --- a/mathmech/mm_radf/src/add_main.c +++ b/mathmech/mm_radf/src/add_main.c @@ -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); diff --git a/mathmech/mm_radf/src/main.c b/mathmech/mm_radf/src/main.c index 9b64a52..7b4f817 100644 --- a/mathmech/mm_radf/src/main.c +++ b/mathmech/mm_radf/src/main.c @@ -70,13 +70,23 @@ * You may also download compiled executable file for Win_x86. * * @page Changelog + * V.1.1.1 (2013-09-03) + * + * V.1.1.0 (2013-09-02) + * * V.1.0.3 (2013-08-30) * * V.1.0.1 (2013-07-27) * */ @@ -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); diff --git a/mathmech/mm_statgen/README b/mathmech/mm_statgen/README index 015569a..ce39282 100644 --- a/mathmech/mm_statgen/README +++ b/mathmech/mm_statgen/README @@ -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: diff --git a/mathmech/mm_statgen/mm_statgen.doxygen b/mathmech/mm_statgen/mm_statgen.doxygen index b44e3d1..2cf6dc0 100644 --- a/mathmech/mm_statgen/mm_statgen.doxygen +++ b/mathmech/mm_statgen/mm_statgen.doxygen @@ -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 diff --git a/mathmech/mm_statgen/mm_statgen.pdf b/mathmech/mm_statgen/mm_statgen.pdf index d610230..cd660db 100644 Binary files a/mathmech/mm_statgen/mm_statgen.pdf and b/mathmech/mm_statgen/mm_statgen.pdf differ diff --git a/mathmech/mm_statgen/src/CMakeLists.txt b/mathmech/mm_statgen/src/CMakeLists.txt index ba5b6dc..9a94e1b 100644 --- a/mathmech/mm_statgen/src/CMakeLists.txt +++ b/mathmech/mm_statgen/src/CMakeLists.txt @@ -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 () diff --git a/mathmech/mm_statgen/src/add_main.c b/mathmech/mm_statgen/src/add_main.c index 2e88247..f21b94a 100644 --- a/mathmech/mm_statgen/src/add_main.c +++ b/mathmech/mm_statgen/src/add_main.c @@ -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); diff --git a/mathmech/mm_statgen/src/main.c b/mathmech/mm_statgen/src/main.c index 447e12a..30a2bde 100644 --- a/mathmech/mm_statgen/src/main.c +++ b/mathmech/mm_statgen/src/main.c @@ -66,13 +66,23 @@ * You may also download compiled executable file for Win_x86. * * @page Changelog + * V.1.1.1 (2013-09-03) + * + * V.1.1.0 (2013-09-02) + * * V.1.0.3 (2013-08-30) * * V.1.0.1 (2013-07-27) * */ @@ -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); diff --git a/mathmech/mm_trj/mm_trj.doxygen b/mathmech/mm_trj/mm_trj.doxygen index ca0fcde..c15553b 100644 --- a/mathmech/mm_trj/mm_trj.doxygen +++ b/mathmech/mm_trj/mm_trj.doxygen @@ -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 diff --git a/mathmech/mm_trj/mm_trj.pdf b/mathmech/mm_trj/mm_trj.pdf index 8f306cc..014998d 100644 Binary files a/mathmech/mm_trj/mm_trj.pdf and b/mathmech/mm_trj/mm_trj.pdf differ diff --git a/mathmech/mm_trj/src/CMakeLists.txt b/mathmech/mm_trj/src/CMakeLists.txt index ba5b6dc..9a94e1b 100644 --- a/mathmech/mm_trj/src/CMakeLists.txt +++ b/mathmech/mm_trj/src/CMakeLists.txt @@ -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 () diff --git a/mathmech/mm_trj/src/main.c b/mathmech/mm_trj/src/main.c index ea180ec..702216e 100644 --- a/mathmech/mm_trj/src/main.c +++ b/mathmech/mm_trj/src/main.c @@ -63,13 +63,23 @@ * You may also download compiled executable file for Win_x86. * * @page Changelog + * V.1.1.1 (2013-09-03) + * + * V.1.1.0 (2013-09-02) + * * V.1.0.3 (2013-08-30) * * V.1.0.1 (2013-07-27) * */ @@ -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); diff --git a/mathmech/mm_trj2pdb/README b/mathmech/mm_trj2pdb/README index bd82ed9..8a55980 100644 --- a/mathmech/mm_trj2pdb/README +++ b/mathmech/mm_trj2pdb/README @@ -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: diff --git a/mathmech/mm_trj2pdb/mm_trj2pdb.doxygen b/mathmech/mm_trj2pdb/mm_trj2pdb.doxygen index 77d005b..be712fc 100644 --- a/mathmech/mm_trj2pdb/mm_trj2pdb.doxygen +++ b/mathmech/mm_trj2pdb/mm_trj2pdb.doxygen @@ -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 diff --git a/mathmech/mm_trj2pdb/mm_trj2pdb.pdf b/mathmech/mm_trj2pdb/mm_trj2pdb.pdf index 4ec958c..f7164c2 100644 Binary files a/mathmech/mm_trj2pdb/mm_trj2pdb.pdf and b/mathmech/mm_trj2pdb/mm_trj2pdb.pdf differ diff --git a/mathmech/mm_trj2pdb/src/CMakeLists.txt b/mathmech/mm_trj2pdb/src/CMakeLists.txt index ba5b6dc..9a94e1b 100644 --- a/mathmech/mm_trj2pdb/src/CMakeLists.txt +++ b/mathmech/mm_trj2pdb/src/CMakeLists.txt @@ -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 () diff --git a/mathmech/mm_trj2pdb/src/main.c b/mathmech/mm_trj2pdb/src/main.c index 3043eea..28b663d 100644 --- a/mathmech/mm_trj2pdb/src/main.c +++ b/mathmech/mm_trj2pdb/src/main.c @@ -59,13 +59,23 @@ * You may also download compiled executable file for Win_x86. * * @page Changelog + * V.1.1.1 (2013-09-03) + * + * V.1.1.0 (2013-09-02) + * * V.1.0.3 (2013-08-30) * * V.1.0.1 (2013-07-27) * */ @@ -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);