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Release 1.0.3

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arcan1s
2013-08-30 19:18:24 +04:00
parent 176918b005
commit cdbaa00d06
69 changed files with 526 additions and 118 deletions
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3
mathmech/AUTHORS Normal file
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Current developers:
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>

9
mathmech/CMakeLists.txt
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@ -1,6 +1,6 @@
set ("PROJECT_VERSION_MAJOR" 1)
set ("PROJECT_VERSION_MINOR" 0)
set ("PROJECT_VERSION_PATCH" 2)
set ("PROJECT_VERSION_PATCH" 3)
set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
message (STATUS "Version ${PROJECT_VERSION}")
@ -15,10 +15,13 @@ set (COMPS mathmech
# install options
set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
if (CMAKE_COMPILER_IS_GNUCXX)
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")
set (QWT_LIBRARY_PATH "/usr/lib" CACHE STRING "Path to qwt library")
else ()
elseif (CMAKE_SYSTEM_NAME MATCHES Windows)
set (QWT_INCLUDE_PATH "C:/Qwt-6.1.0/include" CACHE STRING "Path to qwt include")
set (QWT_LIBRARY_PATH "C:/Qwt-6.1.0/lib" CACHE STRING "Path to qwt library")
endif()

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mathmech/COPYING Normal file
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@ -0,0 +1,341 @@
GNU GENERAL PUBLIC LICENSE
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Yoyodyne, Inc., hereby disclaims all copyright interest in the program
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This General Public License does not permit incorporating your program into
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19
mathmech/INSTALL Normal file
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CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components
-DQWT_INCLUDE_PATH - path to qwt includes
-DQWT_LIBRARY_PATH - path to qwt library
Install for Linux:
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
make
make install
Install for Windows:
create project file using 'cmake'
compile project
copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
You may also download compiled executable file for Win_x86.

4
mathmech/PKGBUILD
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@ -2,7 +2,7 @@
# Maintainer: Evgeniy "arcanis" Alexeev <esalexeev@gmail.com>
pkgname=mathmech
pkgver=1.0.2
pkgver=1.0.3
pkgrel=1
pkgdesc="Software package for analysis of molecular dynamics trajectories"
arch=(any)
@ -11,7 +11,7 @@ license=('GPL')
depends=('qt4' 'qwt')
makedepends=('unzip' 'cmake' 'automoc4')
source=(https://github.com/arcan1s/moldyn/releases/download/mm-${pkgver}/${pkgname}-${pkgver}-src.zip)
md5sums=('7c80789a74255108581583830258fe1c')
md5sums=('4eccb72efd4a8a531d7fda1aabc04f62')
_cmakekeys="-DCMAKE_INSTALL_PREFIX=/usr
-DQWT_INCLUDE_PATH=/usr/include/qwt
-DMM_PREFIX=mm_

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1
mathmech/mathmech/CMakeLists.txt
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@ -12,7 +12,6 @@ include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
# set libraries
set (LIBRARIES)

4
mathmech/mathmech/INSTALL
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@ -1,7 +1,8 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DQWT_INCLUDE_PATH - path to qwt includes
-DQWT_LIBRARY_PATH - path to qwt library
Install for Linux:
mkdir build && cd build
@ -11,4 +12,5 @@ Install for Linux:
Install for Windows:
create project file using 'cmake'
compile project
copy QtCore4.dll, QtGui4.dll, QtOpenGL4.dll, QtSvg4.dll, qwt.dll to directory with mathmech
You may also download compiled executable file for Win_x86.

2
mathmech/mathmech/README
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@ -1,3 +1,3 @@
Mathematical Molecular Mechanics is GUI for "mm" program pack
Version: 1.0.2
Version: 1.0.3
License: GPL

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IDI_ICON1 ICON DISCARDABLE "mathmech.ico"

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17
mathmech/mathmech/src/CMakeLists.txt
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@ -2,12 +2,15 @@
file (GLOB SOURCES *.cpp)
file (GLOB HEADERS *.h)
file (GLOB FORMS *.ui)
if (CMAKE_SYSTEM_NAME MATCHES Windows)
set (SOURCES ${SOURCES} ${PROJECT_RESOURCE_DIR}/res_icon.rc)
endif ()
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
set (LIBRARIES m qwt)
else ()
set (LIBRARIES qwt)
endif()
endif ()
set (LANGUAGES
eng
rus)
@ -61,7 +64,11 @@ target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRA
# install properties
install (TARGETS ${PROJECT} DESTINATION bin)
install (FILES ../mathmech.desktop
DESTINATION share/applications/)
install (FILES ../mathmech-logo.png
DESTINATION share/pixmaps/)
if (CMAKE_SYSTEM_NAME MATCHES Linux)
install (FILES ../mathmech.desktop
DESTINATION share/applications/)
install (FILES ../mathmech-logo.png
DESTINATION share/pixmaps/)
install (FILES ../mathmech.png
DESTINATION share/icons/hicolor/32x32/apps/)
endif ()

2
mathmech/mathmech/src/mainwindow.cpp
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@ -19,7 +19,7 @@ MainWindow::MainWindow(QWidget *parent) :
ui(new Ui::MainWindow),
clear_items(new Clear_items(this)),
update_fields(new Update_fields(this))
{
{
ui->setupUi(this);
statgen_crit = new float[10];

8
mathmech/mathmech/src/mainwindow.ui
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@ -3715,14 +3715,6 @@
<addaction name="menuMenu"/>
<addaction name="menuHelp"/>
</widget>
<widget class="QToolBar" name="mainToolBar">
<attribute name="toolBarArea">
<enum>TopToolBarArea</enum>
</attribute>
<attribute name="toolBarBreak">
<bool>false</bool>
</attribute>
</widget>
<widget class="QStatusBar" name="statusBar"/>
<action name="actionExit">
<property name="text">

2
mathmech/mathmech/src/mathmech.pro.user
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@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE QtCreatorProject>
<!-- Written by QtCreator 2.8.1, 2013-08-30T03:38:54. -->
<!-- Written by QtCreator 2.8.1, 2013-08-30T19:09:45. -->
<qtcreator>
<data>
<variable>ProjectExplorer.Project.ActiveTarget</variable>

8
mathmech/mm_agl/CMakeLists.txt
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@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT ${MM_PREFIX}agl)
set (_PROJECT mm_agl)
# set additional cmake file
include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
include (${_PROJECT}.cmake)
# set libraries
set (LIBRARIES)

2
mathmech/mm_agl/INSTALL
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@ -1,7 +1,9 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
Install for Linux:
mkdir build && cd build

2
mathmech/mm_agl/README
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@ -1,5 +1,5 @@
mm_agl - program that creates PDB file with chosen agglomerate
Version: 1.0.2
Version: 1.0.3
License: GPL
Usage:

6
mathmech/mm_agl/mm_agl.cmake
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@ -1,8 +1,8 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}

2
mathmech/mm_agl/mm_agl.doxygen
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@ -32,7 +32,7 @@ PROJECT_NAME = mm_agl
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.2
PROJECT_NUMBER = V.1.0.3
# 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

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mathmech/mm_agl/src/CMakeLists.txt
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@ -19,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

12
mathmech/mm_agl/src/main.c
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@ -61,8 +61,14 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.2 (2013-07-27)
* * initial release
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* </ul>
*/
#include <math.h>
@ -128,7 +134,7 @@ 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 : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.3 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);

8
mathmech/mm_envir/CMakeLists.txt
View File

@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT ${MM_PREFIX}envir)
set (_PROJECT mm_envir)
# set additional cmake file
include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
include (${_PROJECT}.cmake)
# set libraries
set (LIBRARIES)

2
mathmech/mm_envir/INSTALL
View File

@ -1,7 +1,9 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
Install for Linux:
mkdir build && cd build

2
mathmech/mm_envir/README
View File

@ -1,5 +1,5 @@
mm_envir - program that searchs environment for chosen molecule by geometric criterion
Version: 1.0.2
Version: 1.0.3
License: GPL
Usage:

6
mathmech/mm_envir/mm_envir.cmake
View File

@ -1,8 +1,8 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}

2
mathmech/mm_envir/mm_envir.doxygen
View File

@ -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.1.0.2
PROJECT_NUMBER = V.1.0.3
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_envir/mm_envir.pdf
View File

Binary file not shown.

5
mathmech/mm_envir/src/CMakeLists.txt
View File

@ -19,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

12
mathmech/mm_envir/src/main.c
View File

@ -63,8 +63,14 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.2 (2013-07-27)
* * initial release
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* </ul>
*/
#include <math.h>
@ -130,7 +136,7 @@ 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 : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.3 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);

8
mathmech/mm_radf/CMakeLists.txt
View File

@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT ${MM_PREFIX}radf)
set (_PROJECT mm_radf)
# set additional cmake file
include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
include (${_PROJECT}.cmake)
# set libraries
set (LIBRARIES)

2
mathmech/mm_radf/INSTALL
View File

@ -1,7 +1,9 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
Install for Linux:
mkdir build && cd build

2
mathmech/mm_radf/README
View File

@ -1,6 +1,6 @@
mm_radf - program that calculates radial distribution function (RDF) or radial-angles
distribution function
Version : 1.0.2
Version : 1.0.3
License : GPL
Usage:

6
mathmech/mm_radf/mm_radf.cmake
View File

@ -1,8 +1,8 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}

2
mathmech/mm_radf/mm_radf.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_radf
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.2
PROJECT_NUMBER = V.1.0.3
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_radf/mm_radf.pdf
View File

Binary file not shown.

5
mathmech/mm_radf/src/CMakeLists.txt
View File

@ -19,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

12
mathmech/mm_radf/src/main.c
View File

@ -70,8 +70,14 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.2 (2013-07-27)
* * initial release
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* </ul>
*/
#include <math.h>
@ -147,7 +153,7 @@ 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 : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.3 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);

8
mathmech/mm_statgen/CMakeLists.txt
View File

@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT ${MM_PREFIX}statgen)
set (_PROJECT mm_statgen)
# set additional cmake file
include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
include (${_PROJECT}.cmake)
# set libraries
set (LIBRARIES)

2
mathmech/mm_statgen/INSTALL
View File

@ -1,7 +1,9 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
Install for Linux:
mkdir build && cd build

2
mathmech/mm_statgen/README
View File

@ -1,5 +1,5 @@
mm_statgen - program that analyzes molecular dynamic trajectories using topological analysis
Version: 1.0.2
Version: 1.0.3
License: GPL
Usage:

6
mathmech/mm_statgen/mm_statgen.cmake
View File

@ -1,8 +1,8 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}

2
mathmech/mm_statgen/mm_statgen.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_statgen
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.2
PROJECT_NUMBER = V.1.0.3
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_statgen/mm_statgen.pdf
View File

Binary file not shown.

5
mathmech/mm_statgen/src/CMakeLists.txt
View File

@ -19,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

12
mathmech/mm_statgen/src/main.c
View File

@ -66,8 +66,14 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.2 (2013-07-27)
* * initial release
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* </ul>
*/
#include <math.h>
@ -162,7 +168,7 @@ 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 : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.3 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);

8
mathmech/mm_trj/CMakeLists.txt
View File

@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT ${MM_PREFIX}trj)
set (_PROJECT mm_trj)
# set additional cmake file
include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
include (${_PROJECT}.cmake)
# set libraries
set (LIBRARIES)

2
mathmech/mm_trj/INSTALL
View File

@ -1,7 +1,9 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
Install for Linux:
mkdir build && cd build

2
mathmech/mm_trj/README
View File

@ -1,5 +1,5 @@
mm_trj - program that generates trajectory files
Version : 1.0.2
Version : 1.0.3
License : GPL
Usage:

6
mathmech/mm_trj/mm_trj.cmake
View File

@ -1,8 +1,8 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}

2
mathmech/mm_trj/mm_trj.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.2
PROJECT_NUMBER = V.1.0.3
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_trj/mm_trj.pdf
View File

Binary file not shown.

5
mathmech/mm_trj/src/CMakeLists.txt
View File

@ -19,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

12
mathmech/mm_trj/src/main.c
View File

@ -63,8 +63,14 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.2 (2013-07-27)
* * initial release
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* </ul>
*/
#include <math.h>
@ -127,7 +133,7 @@ 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 : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.3 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);

8
mathmech/mm_trj2pdb/CMakeLists.txt
View File

@ -6,13 +6,9 @@ cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT ${MM_PREFIX}trj2pdb)
set (_PROJECT mm_trj2pdb)
# set additional cmake file
include (${PROJECT}.cmake)
# additional options
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
OPTION (ADD_INCLUDE "Add include files" OFF)
include (${_PROJECT}.cmake)
# set libraries
set (LIBRARIES)

2
mathmech/mm_trj2pdb/INSTALL
View File

@ -1,7 +1,9 @@
CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
Install for Linux:
mkdir build && cd build

2
mathmech/mm_trj2pdb/README
View File

@ -1,5 +1,5 @@
mm_trj2pdb - program that creates PDB file from trajetory snapshot
Version: 1.0.2
Version: 1.0.3
License: GPL
Usage:

6
mathmech/mm_trj2pdb/mm_trj2pdb.cmake
View File

@ -1,8 +1,8 @@
# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR src)
set (PROJECT_INCLUDE_DIR include)
set (PROJECT_LIB_DIR lib)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}/${PROJECT}

2
mathmech/mm_trj2pdb/mm_trj2pdb.doxygen
View File

@ -32,7 +32,7 @@ PROJECT_NAME = mm_trj2pdb
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = V.1.0.2
PROJECT_NUMBER = V.1.0.3
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer

BIN
mathmech/mm_trj2pdb/mm_trj2pdb.pdf
View File

Binary file not shown.

5
mathmech/mm_trj2pdb/src/CMakeLists.txt
View File

@ -19,4 +19,7 @@ target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()
endif ()
if (ADD_DOCS)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
endif ()

12
mathmech/mm_trj2pdb/src/main.c
View File

@ -59,8 +59,14 @@
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.2 (2013-07-27)
* * initial release
* V.1.0.3 (2013-08-30)
* <ul>
* <li> Bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li> initial release
* </ul>
*/
#include <math.h>
@ -119,7 +125,7 @@ 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 : 1.0.2 License : GPL\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.3 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);

9
mathmech/update_ver.sh
View File

@ -38,11 +38,10 @@ fi
# work block
COMPONENTS=(mm_agl mm_envir mm_radf mm_statgen mm_trj mm_trj2pdb)
for COMPONENT in ${COMPONENTS[*]}; do
sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/src/main.c
sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/README
sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/$COMPONENT.doxygen
sed -i "s/Version : $OLDVER/Version : $NEWVER/g" $COMPONENT/src/main.c
sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README
sed -i "s/V.$OLDVER/V.$NEWVER/g" $COMPONENT/$COMPONENT.doxygen
done
COMPONENT=mathmech
sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/src/main.cpp
sed -i "s:$OLDVER:$NEWVER:g" $COMPONENT/README
sed -i "s/Version: $OLDVER/Version: $NEWVER/g" $COMPONENT/README