mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-06-28 06:41:42 +00:00
start moving to another architecture
This commit is contained in:
arcan1s
@ -1,28 +1,31 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy (SET CMP0003 OLD)
|
||||
cmake_policy (SET CMP0002 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" 1)
|
||||
set ("PROJECT_VERSION" ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
|
||||
set (PROJECT_LONG mathmech)
|
||||
set (PROJECT_VERSION_MAJOR 1)
|
||||
set (PROJECT_VERSION_MINOR 1)
|
||||
set (PROJECT_VERSION_PATCH 1)
|
||||
set (PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH})
|
||||
|
||||
message (STATUS "Version ${PROJECT_VERSION}")
|
||||
|
||||
set (COMPS mathmech
|
||||
mm_agl
|
||||
mm_envir
|
||||
mm_radf
|
||||
mm_statgen
|
||||
mm_trj
|
||||
mm_trj2pdb)
|
||||
mm
|
||||
agl
|
||||
envir
|
||||
radf
|
||||
statgen
|
||||
trj
|
||||
trj2pdb)
|
||||
|
||||
# install options
|
||||
set (MM_PREFIX "mm_" CACHE STRING "Prefix for mathmech tools")
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_DOCS "Add documentation" OFF)
|
||||
option (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
option (ADD_DOCS "Add documentation" OFF)
|
||||
if (CMAKE_SYSTEM_NAME MATCHES Linux)
|
||||
set (QWT_INCLUDE_PATH "/usr/include" CACHE STRING "Path to qwt include")
|
||||
set (QWT_LIBRARY_PATH "/usr/lib" CACHE STRING "Path to qwt library")
|
||||
|
||||
17
mathmech/agl/CMakeLists.txt
Normal file
17
mathmech/agl/CMakeLists.txt
Normal file
@ -0,0 +1,17 @@
|
||||
# set project name
|
||||
set (PROJECT agl)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES "")
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
add_subdirectory (../${LIBRARY} bin/${LIBRARY})
|
||||
include_directories (${CMAKE_CURRENT_SOURCE_DIR}/../${LIBRARY}/include/)
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -5,8 +5,9 @@ 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}/${PROJECT}
|
||||
include_directories (${PROJECT_INCLUDE_DIR}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
|
||||
# library path
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
@ -14,11 +14,8 @@ message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
|
||||
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
|
||||
|
||||
# link libraries and compile
|
||||
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
add_executable (${MM_PREFIX}${PROJECT} ${SOURCES} ${HEADERS})
|
||||
target_link_libraries (${MM_PREFIX}${PROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
install (TARGETS ${MM_PREFIX}${PROJECT} DESTINATION bin)
|
||||
@ -4,7 +4,7 @@
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "messages.h"
|
||||
#include <mathmech/messages.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -104,4 +104,4 @@ int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output
|
||||
*quiet = 0;
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -1,85 +1,6 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
/**
|
||||
* @mainpage mm_agl
|
||||
* @image latex ./logo.png
|
||||
*
|
||||
* @section intro_sec Introduction
|
||||
*
|
||||
* <b>About this program</b>:
|
||||
* <ul>
|
||||
* <li>Program that creates PDB file with chosen agglomerate
|
||||
* </ul>
|
||||
*
|
||||
* <b>Developer</b>:
|
||||
* <ul>
|
||||
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
|
||||
*</ul>
|
||||
* <b>License</b>:
|
||||
* <ul>
|
||||
* <li>GPL
|
||||
* </ul>
|
||||
*
|
||||
* @section How-To-Use How to use
|
||||
* Usage:
|
||||
* <pre>
|
||||
* mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
*
|
||||
* Parametrs:
|
||||
* -a - input file with agglomerates (in format statgen)
|
||||
* -i - input file with coordinates
|
||||
* -c - cell size (float), A
|
||||
* -o - output file name
|
||||
* -l - log enable
|
||||
* -q - quiet enable
|
||||
* -h - show this help and exit
|
||||
* </pre>
|
||||
*
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application mm_agl requires the following external stuff:
|
||||
* - cmake >= 2.8
|
||||
* - gcc >= 4.8
|
||||
*
|
||||
* @section How-To How to install
|
||||
*
|
||||
* @subsection Linux Linux
|
||||
* @code
|
||||
* mkdir build && cd build
|
||||
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
|
||||
* make
|
||||
* make install
|
||||
* @endcode
|
||||
*
|
||||
* @subsection Windows Windows
|
||||
* @code
|
||||
* create project file using 'cmake'
|
||||
* compile project
|
||||
* @endcode
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.1.1 (2013-09-03)
|
||||
* <ul>
|
||||
* <li>optimization
|
||||
* </ul>
|
||||
* V.1.1.0 (2013-09-02)
|
||||
* <ul>
|
||||
* <li>added help window
|
||||
* <li>added help docs
|
||||
* <li>small bug fixes
|
||||
* </ul>
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li>bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* <ul>
|
||||
* <li>initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
@ -87,12 +8,12 @@
|
||||
#include <string.h>
|
||||
|
||||
#include "add_main.h"
|
||||
#include "coords.h"
|
||||
#include "messages.h"
|
||||
#include "print_struct.h"
|
||||
#include "read_agl.h"
|
||||
#include "select_mol.h"
|
||||
#include "set_center.h"
|
||||
#include <mathmech/coords.h>
|
||||
#include <mathmech/messages.h>
|
||||
#include <mathmech/print_struct.h>
|
||||
#include <mathmech/read_agl.h>
|
||||
#include <mathmech/select_mol.h>
|
||||
#include <mathmech/set_center.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -318,4 +239,4 @@ int main(int argc, char *argv[])
|
||||
if (log == 1)
|
||||
fclose (f_log);
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -1,5 +1,3 @@
|
||||
set (PROJECT mathmech)
|
||||
# set directory
|
||||
set (PROJECT_DOCS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs)
|
||||
install (DIRECTORY ${PROJECT_DOCS_DIR}
|
||||
DESTINATION share/doc/${PROJECT})
|
||||
install (DIRECTORY ${PROJECT_DOCS_DIR} DESTINATION share/doc/${PROJECT_LONG})
|
||||
|
||||
17
mathmech/envir/CMakeLists.txt
Normal file
17
mathmech/envir/CMakeLists.txt
Normal file
@ -0,0 +1,17 @@
|
||||
# set project name
|
||||
set (PROJECT envir)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES "")
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
add_subdirectory (../${LIBRARY} bin/${LIBRARY})
|
||||
include_directories (${CMAKE_CURRENT_SOURCE_DIR}/../${LIBRARY}/include/)
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
@ -5,8 +5,9 @@ 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}/${PROJECT}
|
||||
include_directories (${PROJECT_INCLUDE_DIR}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
|
||||
# library path
|
||||
link_directories (${PROJECT_LIB_DIR})
|
||||
# executable path
|
||||
@ -14,11 +14,8 @@ message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
|
||||
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
|
||||
|
||||
# link libraries and compile
|
||||
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
add_executable (${MM_PREFIX}${PROJECT} ${SOURCES} ${HEADERS})
|
||||
target_link_libraries (${MM_PREFIX}${PROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
install (TARGETS ${MM_PREFIX}${PROJECT} DESTINATION bin)
|
||||
@ -4,7 +4,7 @@
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "messages.h"
|
||||
#include <mathmech/messages.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -103,4 +103,4 @@ int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *out
|
||||
*rad = 6.0;
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -1,87 +1,6 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
/**
|
||||
* @mainpage mm_envir
|
||||
* @image latex ./logo.png
|
||||
*
|
||||
* @section intro_sec Introduction
|
||||
*
|
||||
* <b>About this program</b>:
|
||||
* <ul>
|
||||
* <li>Program that searchs environment for chosen molecule by geometric criterion
|
||||
* </ul>
|
||||
*
|
||||
* <b>Developer</b>:
|
||||
* <ul>
|
||||
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
|
||||
*</ul>
|
||||
* <b>License</b>:
|
||||
* <ul>
|
||||
* <li>GPL
|
||||
* </ul>
|
||||
*
|
||||
* @section How-To-Use How to use
|
||||
* Usage:
|
||||
* <pre>
|
||||
* mm_envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]
|
||||
* [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
*
|
||||
* Parametrs:
|
||||
* -i - input file name
|
||||
* -c - cell size (float), A
|
||||
* -o - output file name
|
||||
* -n - number of molecule for search (integer). Default is 1
|
||||
* -r - radius of environment (float). Default is 6.0
|
||||
* -l - log enable
|
||||
* -q - quiet enable
|
||||
* -h - show this help and exit
|
||||
* </pre>
|
||||
*
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application mm_envir requires the following external stuff:
|
||||
* - cmake >= 2.8
|
||||
* - gcc >= 4.8
|
||||
*
|
||||
* @section How-To How to install
|
||||
*
|
||||
* @subsection Linux Linux
|
||||
* @code
|
||||
* mkdir build && cd build
|
||||
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
|
||||
* make
|
||||
* make install
|
||||
* @endcode
|
||||
*
|
||||
* @subsection Windows Windows
|
||||
* @code
|
||||
* create project file using 'cmake'
|
||||
* compile project
|
||||
* @endcode
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.1.1 (2013-09-03)
|
||||
* <ul>
|
||||
* <li>optimization
|
||||
* </ul>
|
||||
* V.1.1.0 (2013-09-02)
|
||||
* <ul>
|
||||
* <li>added help window
|
||||
* <li>added help docs
|
||||
* <li>small bug fixes
|
||||
* </ul>
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li>bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* <ul>
|
||||
* <li>initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
@ -89,11 +8,11 @@
|
||||
#include <string.h>
|
||||
|
||||
#include "add_main.h"
|
||||
#include "coords.h"
|
||||
#include "envir_search.h"
|
||||
#include "messages.h"
|
||||
#include "print_struct.h"
|
||||
#include "set_center.h"
|
||||
#include <mathmech/coords.h>
|
||||
#include <mathmech/envir_search.h>
|
||||
#include <mathmech/messages.h>
|
||||
#include <mathmech/print_struct.h>
|
||||
#include <mathmech/set_center.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -324,4 +243,4 @@ int main(int argc, char *argv[])
|
||||
if (log == 1)
|
||||
fclose (f_log);
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -1,9 +1,3 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy (SET CMP0003 OLD)
|
||||
cmake_policy (SET CMP0011 NEW)
|
||||
cmake_policy (SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mathmech)
|
||||
# set additional cmake file
|
||||
@ -11,18 +5,13 @@ include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
option (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
find_library ("${LIBRARY}_FOUND" ${LIBRARY})
|
||||
message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
|
||||
if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
|
||||
message (STATUS "Adding library sources")
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endif ()
|
||||
endforeach ()
|
||||
set (LIBRARIES "")
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
|
||||
@ -63,10 +63,7 @@ target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRA
|
||||
# install properties
|
||||
install (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (CMAKE_SYSTEM_NAME MATCHES Linux)
|
||||
install (FILES ../mathmech.desktop
|
||||
DESTINATION share/applications/)
|
||||
install (FILES ../mathmech-logo.png
|
||||
DESTINATION share/pixmaps/)
|
||||
install (FILES ../mathmech.png
|
||||
DESTINATION share/icons/hicolor/32x32/apps/)
|
||||
install (FILES ../mathmech.desktop DESTINATION share/applications/)
|
||||
install (FILES ../mathmech-logo.png DESTINATION share/pixmaps/)
|
||||
install (FILES ../mathmech.png DESTINATION share/icons/hicolor/32x32/apps/)
|
||||
endif ()
|
||||
|
||||
13
mathmech/mm/CMakeLists.txt
Normal file
13
mathmech/mm/CMakeLists.txt
Normal file
@ -0,0 +1,13 @@
|
||||
# set project name
|
||||
set (PROJECT mm)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
if (ADD_DOCS)
|
||||
include (doxygen.cmake)
|
||||
endif ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
13
mathmech/mm/doxygen.cmake
Normal file
13
mathmech/mm/doxygen.cmake
Normal file
@ -0,0 +1,13 @@
|
||||
# build docs
|
||||
find_package (Doxygen)
|
||||
if (DOXYGEN_FOUND)
|
||||
set (PROJECT_DOCS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs/html)
|
||||
set (DOXYGEN_INPUT ${CMAKE_CURRENT_SOURCE_DIR})
|
||||
configure_file (${CMAKE_CURRENT_SOURCE_DIR}/mm.doxygen ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
|
||||
add_custom_target (docs COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
|
||||
else (DOXYGEN_FOUND)
|
||||
message (STATUS "WARNING: Doxygen not found - Reference manual will not be created")
|
||||
endif ()
|
||||
|
||||
# instal properties
|
||||
# install (DIRECTORY ${PROJECT_DOCS_DIR} DESTINATION share/doc/${PROJECT_LONG})
|
||||
|
Before Width: | Height: | Size: 3.4 KiB After Width: | Height: | Size: 3.4 KiB |
26
mathmech/mm/mm.cmake
Normal file
26
mathmech/mm/mm.cmake
Normal file
@ -0,0 +1,26 @@
|
||||
# set directories
|
||||
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
|
||||
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
|
||||
|
||||
# include_path
|
||||
include_directories (${PROJECT_INCLUDE_DIR}
|
||||
${PROJECT_SOURCE_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
# flags
|
||||
if ( WITH_DEBUG_MODE )
|
||||
add_definitions ( -DDEBUG_MODE=1 )
|
||||
endif ()
|
||||
if ( CMAKE_COMPILER_IS_GNUCXX )
|
||||
set (ADD_CXX_FLAGS "-Wall")
|
||||
set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
|
||||
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
|
||||
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
|
||||
elseif ( MSVC )
|
||||
set (ADD_CXX_FLAGS "/W4")
|
||||
set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
|
||||
else ()
|
||||
message ("Unknown compiler")
|
||||
endif ()
|
||||
2314
mathmech/mm/mm.doxygen
Normal file
2314
mathmech/mm/mm.doxygen
Normal file
File diff suppressed because it is too large
Load Diff
@ -14,11 +14,8 @@ message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
|
||||
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
|
||||
|
||||
# link libraries and compile
|
||||
add_executable (${PROJECT} ${SOURCES} ${HEADERS})
|
||||
add_library (${PROJECT} SHARED ${SOURCES} ${HEADERS})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_DOCS)
|
||||
INSTALL (FILES ${PROJECT_SOURCE_DIR}/../${_PROJECT}.pdf DESTINATION share/doc/mathmech)
|
||||
endif ()
|
||||
install (TARGETS ${PROJECT} DESTINATION lib)
|
||||
103
mathmech/mm/src/main.c
Normal file
103
mathmech/mm/src/main.c
Normal file
@ -0,0 +1,103 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
/**
|
||||
* @mainpage libmm
|
||||
* @image latex ./logo.png
|
||||
*
|
||||
* @section intro_sec Introduction
|
||||
*
|
||||
* <b>About this program</b>:
|
||||
* <ul>
|
||||
* <li>Library for mathmech
|
||||
* </ul>
|
||||
*
|
||||
* <b>Developer</b>:
|
||||
* <ul>
|
||||
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
|
||||
*</ul>
|
||||
* <b>License</b>:
|
||||
* <ul>
|
||||
* <li>GPL
|
||||
* </ul>
|
||||
*
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application mmlib requires the following external stuff:
|
||||
* - cmake >= 2.8
|
||||
* - gcc >= 4.8
|
||||
*
|
||||
* @section How-To How to install
|
||||
*
|
||||
* @subsection Linux Linux
|
||||
* @code
|
||||
* mkdir build && cd build
|
||||
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
|
||||
* make
|
||||
* make install
|
||||
* @endcode
|
||||
*
|
||||
* @subsection Windows Windows
|
||||
* @code
|
||||
* create project file using 'cmake'
|
||||
* compile project
|
||||
* @endcode
|
||||
* You may also download compiled executable file for Win_x86.
|
||||
*
|
||||
* @page Changelog
|
||||
* V.1.1.1 (2013-09-03)
|
||||
* <ul>
|
||||
* <li>optimization
|
||||
* </ul>
|
||||
* V.1.1.0 (2013-09-02)
|
||||
* <ul>
|
||||
* <li>added help window
|
||||
* <li>added help docs
|
||||
* <li>small bug fixes
|
||||
* </ul>
|
||||
* V.1.0.3 (2013-08-30)
|
||||
* <ul>
|
||||
* <li>bug fixes
|
||||
* </ul>
|
||||
* V.1.0.1 (2013-07-27)
|
||||
* <ul>
|
||||
* <li>initial release
|
||||
* </ul>
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include <mathmech/atom_types.h>
|
||||
#include <mathmech/coords.h>
|
||||
#include <mathmech/envir_search.h>
|
||||
#include <mathmech/graph.h>
|
||||
#include <mathmech/messages.h>
|
||||
#include <mathmech/print_struct.h>
|
||||
#include <mathmech/print_trj.h>
|
||||
#include <mathmech/radf.h>
|
||||
#include <mathmech/radf_proc.h>
|
||||
#include <mathmech/read_agl.h>
|
||||
#include <mathmech/read_gmx.h>
|
||||
#include <mathmech/read_puma.h>
|
||||
#include <mathmech/select_mol.h>
|
||||
#include <mathmech/set_center.h>
|
||||
#include <mathmech/stat_print.h>
|
||||
#include <mathmech/stat_select.h>
|
||||
#include <mathmech/stat_sort.h>
|
||||
#include <mathmech/summary_stat.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn main
|
||||
*/
|
||||
int main(int argc, char *argv[])
|
||||
/**
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
@ -5,7 +5,7 @@
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
|
||||
#include "print_trj.h"
|
||||
#include <mathmech/print_trj.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -151,4 +151,4 @@ int rw_gmx (const char *input, const int step, const char *output, const int num
|
||||
fclose (f_inp);
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -4,7 +4,7 @@
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "print_trj.h"
|
||||
#include <mathmech/print_trj.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -91,4 +91,4 @@ int rw_puma (const char *input, const int step, const char *output, const int nu
|
||||
fclose (f_inp);
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -5,7 +5,7 @@
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
#include "graph.h"
|
||||
#include <mathmech/graph.h>
|
||||
|
||||
|
||||
/**
|
||||
@ -138,4 +138,4 @@ int printing_agl (const char *input, const char *output, const int *connect,
|
||||
free (iso);
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
@ -1,28 +0,0 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy (SET CMP0003 OLD)
|
||||
cmake_policy (SET CMP0011 NEW)
|
||||
cmake_policy (SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT ${MM_PREFIX}agl)
|
||||
set (_PROJECT mm_agl)
|
||||
# set additional cmake file
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
find_library ("${LIBRARY}_FOUND" ${LIBRARY})
|
||||
message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
|
||||
if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
|
||||
message (STATUS "Adding library sources")
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@ -1,20 +0,0 @@
|
||||
PROJECT=AGL
|
||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c messages.c print_struct.c read_agl.c select_mol.c set_center.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=mm_agl
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o test*
|
||||
@ -1,28 +0,0 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy (SET CMP0003 OLD)
|
||||
cmake_policy (SET CMP0011 NEW)
|
||||
cmake_policy (SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT ${MM_PREFIX}envir)
|
||||
set (_PROJECT mm_envir)
|
||||
# set additional cmake file
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
find_library ("${LIBRARY}_FOUND" ${LIBRARY})
|
||||
message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
|
||||
if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
|
||||
message (STATUS "Adding library sources")
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.4 KiB |
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@ -1,20 +0,0 @@
|
||||
PROJECT=ENVIR
|
||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c envir_search.c messages.c print_struct.c set_center.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=mm_envir
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o test*
|
||||
@ -1,354 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
const int *label_atom, const float *cell, int *num_mol,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/**
|
||||
* @brief function that reads coordinates from special file format
|
||||
* @code
|
||||
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms,
|
||||
* true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
|
||||
* @endcode
|
||||
*
|
||||
* @param mode mode of reading; '1' is statgen, '2' is envir or
|
||||
* frad, '3' is agl
|
||||
* @param filename input file name
|
||||
* @param type_inter number of needed atoms
|
||||
* (number of needed molecules)
|
||||
* @param label_atom massive of needed atom types
|
||||
* (massive of needed molecules)
|
||||
* @param cell massive of cell size
|
||||
* @param num_mol number of molecules
|
||||
* @param num_atoms number of atoms
|
||||
* @param true_label_mol massive of true numbers of molecule for atoms
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
* @param ch_type_atoms massive of char atom types
|
||||
*
|
||||
* @return 1 - file $filename does not exist
|
||||
* @return 2 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char at_symb[32], file_string[256];
|
||||
int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
|
||||
float cur_coords[3], *not_tr_coords, ref[3];
|
||||
FILE *inp;
|
||||
|
||||
/* cur_* temp variables
|
||||
* at_symb temp variable
|
||||
* file_string temp string variable
|
||||
* atoms total number of atoms in system
|
||||
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
|
||||
* ref_mol number of molecule for reference in translation
|
||||
* not_tr_coords massive of not translated coordinates
|
||||
* ref massive of coordinates of reference molecule
|
||||
* inp input file
|
||||
*/
|
||||
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
*num_atoms = 0;
|
||||
*num_mol = 0;
|
||||
|
||||
/// <pre> reading file </pre>
|
||||
inp = fopen (filename, "r");
|
||||
if (inp == NULL)
|
||||
return 1;
|
||||
|
||||
ref_mol = -1;
|
||||
fscanf (inp, "%i", &atoms);
|
||||
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
|
||||
fgets (file_string, 256, inp);
|
||||
for (i=0; i<atoms; i++)
|
||||
{
|
||||
fgets (file_string, 256, inp);
|
||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
||||
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||
|
||||
// reading variables according to selected mode
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
// mode == 0 (selected atoms)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_at_type == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// mode == 1 (all atoms)
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
case 2:
|
||||
// mode == 2 (selected molecules)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_mol == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
default: return 2;
|
||||
}
|
||||
}
|
||||
fclose (inp);
|
||||
|
||||
/// <pre> translation </pre>
|
||||
tr_num_atoms = *num_atoms;
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
for (j=0; j<3; j++)
|
||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||
|
||||
// assign initial value to reference coordinates
|
||||
ref_mol = label_mol[0];
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
{
|
||||
if (label_mol[i] != ref_mol)
|
||||
{
|
||||
ref_mol = label_mol[i];
|
||||
for (j=0; j<3; j++)
|
||||
ref[j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
if (ref[x] >= 0.0)
|
||||
// if xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
else
|
||||
// if xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
for (y=x+1; y<3; y++)
|
||||
{
|
||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz and xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||
// if xyz and xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (y=0; y<3; y++)
|
||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz OR xyz >= 0.0
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
{
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
if (j == y)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
if ((j != x) && (j != y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
/// <pre> free memory </pre>
|
||||
free (not_tr_coords);
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -1,16 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef COORDS_H
|
||||
#define COORDS_H
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
|
||||
int reading_coords (const int, const char *, const int, const int *,
|
||||
const float *, int *, int *, int *, int *, int *, float *,
|
||||
char *);
|
||||
|
||||
#endif /* COORDS_H */
|
||||
@ -1,119 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <time.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
int message (const int log, const int mode, const char *text, FILE *output)
|
||||
/**
|
||||
* @brief function that prints messages to output
|
||||
* @code
|
||||
* message (log, mode, text, output);
|
||||
* @endcode
|
||||
*
|
||||
* @param log equal to 1 if print to logfile
|
||||
* @param mode number of message
|
||||
* @param text additional text
|
||||
* @param output output file (may be stdout)
|
||||
*
|
||||
* @return 1 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char out[4096];
|
||||
|
||||
if (log == 1)
|
||||
{
|
||||
char time_str[256];
|
||||
|
||||
time_t t = time (NULL);
|
||||
struct tm* aTm = localtime (&t);
|
||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||
aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
|
||||
fputs (time_str, output);
|
||||
}
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
sprintf (out, "Start program: '%s'\n", text);
|
||||
break;
|
||||
case 1:
|
||||
sprintf (out, "Checking errors\n");
|
||||
break;
|
||||
case 2:
|
||||
sprintf (out, "Errors are not detected\n");
|
||||
break;
|
||||
case 3:
|
||||
sprintf (out, "Initialization of variables from file '%s'\n", text);
|
||||
break;
|
||||
case 4:
|
||||
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
|
||||
break;
|
||||
case 5:
|
||||
sprintf (out, "Initial parametrs: \n%s", text);
|
||||
break;
|
||||
case 6:
|
||||
sprintf (out, "Processing\n");
|
||||
break;
|
||||
case 7:
|
||||
sprintf (out, "Open file: '%s'\n", text);
|
||||
break;
|
||||
case 8:
|
||||
sprintf (out, "%s", text);
|
||||
break;
|
||||
case 9:
|
||||
sprintf (out, "%6cSize of variables was changed successfully\n", ' ');
|
||||
break;
|
||||
case 10:
|
||||
sprintf (out, "%6cConnectivity matrix was created successfully\n", ' ');
|
||||
break;
|
||||
case 11:
|
||||
sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' ');
|
||||
break;
|
||||
case 12:
|
||||
sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text);
|
||||
break;
|
||||
case 13:
|
||||
sprintf (out, "End of processing\n");
|
||||
break;
|
||||
case 14:
|
||||
sprintf (out, "Print result to file '%s'\n", text);
|
||||
break;
|
||||
case 15:
|
||||
sprintf (out, "Free memory\n");
|
||||
break;
|
||||
case 16:
|
||||
sprintf (out, "Exiting without errors\n");
|
||||
break;
|
||||
case 17:
|
||||
sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text);
|
||||
break;
|
||||
case 18:
|
||||
sprintf (out, "File '%s' not found\nError\n", text);
|
||||
break;
|
||||
case 19:
|
||||
sprintf (out, "Memory error\n");
|
||||
break;
|
||||
case 20:
|
||||
sprintf (out, "%6cCenter of molecules was set successfully\n", ' ');
|
||||
break;
|
||||
case 21:
|
||||
sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
|
||||
break;
|
||||
case 22:
|
||||
sprintf (out, "%6cRADF was appended successfully\n", ' ');
|
||||
break;
|
||||
default:
|
||||
return 1;
|
||||
break;
|
||||
}
|
||||
|
||||
fputs (out, output);
|
||||
return 0;
|
||||
}
|
||||
@ -1,14 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef MESSAGES_H
|
||||
#define MESSAGES_H
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
|
||||
int message (const int, const int, const char *, FILE *);
|
||||
|
||||
#endif /* MESSAGES_H */
|
||||
@ -1,69 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn print_structure
|
||||
*/
|
||||
int print_structure (const char *output, const int num_needed_mol, const int *needed_mol,
|
||||
const int num_atoms, const int *label_mol, const char *ch_type_atoms,
|
||||
const float *coords)
|
||||
/**
|
||||
* @brief function that prints structure to pdb file
|
||||
* @code
|
||||
* print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol,
|
||||
* char_type_atoms, coords);
|
||||
* @endcode
|
||||
*
|
||||
* @param output output file name
|
||||
* @param num_needed_mol number of needed molecules
|
||||
* @param needed_mol massive of number of needed molecules
|
||||
* @param num_atoms number of atoms
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param ch_type_atoms massive of char atom types
|
||||
* @param coords massive of coordinates
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int cur_atom, cur_atom_num, cur_mol, i, j;
|
||||
FILE *f_out;
|
||||
|
||||
/* cur_atom current atom
|
||||
* cur_atom_num true atom number
|
||||
* cur_mol current molecule
|
||||
* f_out output file
|
||||
*/
|
||||
|
||||
cur_atom = 1;
|
||||
f_out = fopen (output, "w");
|
||||
|
||||
for (i=0; i<num_needed_mol; i++)
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
{
|
||||
if (j < num_atoms)
|
||||
{
|
||||
cur_mol = 0;
|
||||
cur_atom_num = j;
|
||||
}
|
||||
else
|
||||
{
|
||||
cur_mol = ((j - num_atoms) % 7) + 1;
|
||||
cur_atom_num = (j - num_atoms) / 7;
|
||||
}
|
||||
if (needed_mol[i] == (8*label_mol[j]+cur_mol))
|
||||
{
|
||||
fprintf(f_out, "ATOM %5i %c%c MOL %4i %8.3f%8.3f%8.3f\n", cur_atom,
|
||||
ch_type_atoms[2*cur_atom_num+0], ch_type_atoms[2*cur_atom_num+1],
|
||||
i+1, coords[3*j+0], coords[3*j+1], coords[3*j+2]);
|
||||
cur_atom++;
|
||||
}
|
||||
}
|
||||
|
||||
fclose (f_out);
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -1,15 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef PRINT_STRUCTURE_H
|
||||
#define PRINT_STRUCTURE_H
|
||||
|
||||
/**
|
||||
* @fn print_structure
|
||||
*/
|
||||
|
||||
int print_structure (const char *, const int, const int *, const int, const int *,
|
||||
const char *, const float *);
|
||||
|
||||
#endif /* PRINT_STRUCTURE_H */
|
||||
@ -1,61 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
|
||||
/**
|
||||
* @fn set_center
|
||||
*/
|
||||
int set_center (const int num_atoms, const int num_mol, const int *label_mol,
|
||||
const float *coords, float *centr_coords)
|
||||
/**
|
||||
* @brief function that searchs center mass of molecules
|
||||
* @code
|
||||
* set_center (num_of_atoms, num_of_molecules, label_molecules, coords, centr_coords);
|
||||
* @endcode
|
||||
*
|
||||
* @param num_atoms number of atoms
|
||||
* @param num_mol number of molecules
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param coords massive of coordinates
|
||||
* @param centr_coords massive of centered coordinates
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int at_in_mol, cur_mol, i, j, k;
|
||||
|
||||
/* at_int_mol number of atoms in molecule
|
||||
* cur_mol current molecule
|
||||
*/
|
||||
|
||||
for (i=0; i<8*num_mol; i++)
|
||||
for (j=0; j<3; j++)
|
||||
centr_coords[i*3+j] = 0.0;
|
||||
|
||||
for (i=0; i<8*num_atoms; i++)
|
||||
{
|
||||
if (i < num_atoms)
|
||||
cur_mol = 0;
|
||||
else
|
||||
cur_mol = ((i - num_atoms) % 7) + 1;
|
||||
for (j=0; j<3; j++)
|
||||
centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
|
||||
}
|
||||
|
||||
at_in_mol = 0;
|
||||
cur_mol = 0;
|
||||
for (i=0; i<num_atoms; i++)
|
||||
if (cur_mol != label_mol[i])
|
||||
{
|
||||
for (j=0; j<8; j++)
|
||||
for (k=0; k<3; k++)
|
||||
centr_coords[3*(8*cur_mol+j)+k] = centr_coords[3*(8*cur_mol+j)+k] / at_in_mol;
|
||||
at_in_mol = 0;
|
||||
cur_mol = label_mol[i];
|
||||
}
|
||||
else
|
||||
at_in_mol++;
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -1,14 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef SET_CENTER_H
|
||||
#define SET_CENTER_H
|
||||
|
||||
/**
|
||||
* @fn set_center
|
||||
*/
|
||||
|
||||
int set_center (const int, const int, const int *, const float *, float *);
|
||||
|
||||
#endif /* SET_CENTER_H */
|
||||
@ -1,28 +0,0 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy (SET CMP0003 OLD)
|
||||
cmake_policy (SET CMP0011 NEW)
|
||||
cmake_policy (SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT ${MM_PREFIX}radf)
|
||||
set (_PROJECT mm_radf)
|
||||
# set additional cmake file
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
find_library ("${LIBRARY}_FOUND" ${LIBRARY})
|
||||
message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
|
||||
if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
|
||||
message (STATUS "Adding library sources")
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.4 KiB |
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@ -1,20 +0,0 @@
|
||||
PROJECT=RADF
|
||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c messages.c radf.c radf_proc.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=mm_radf
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o test*
|
||||
@ -1,354 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
const int *label_atom, const float *cell, int *num_mol,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/**
|
||||
* @brief function that reads coordinates from special file format
|
||||
* @code
|
||||
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms,
|
||||
* true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
|
||||
* @endcode
|
||||
*
|
||||
* @param mode mode of reading; '1' is statgen, '2' is envir or
|
||||
* frad, '3' is agl
|
||||
* @param filename input file name
|
||||
* @param type_inter number of needed atoms
|
||||
* (number of needed molecules)
|
||||
* @param label_atom massive of needed atom types
|
||||
* (massive of needed molecules)
|
||||
* @param cell massive of cell size
|
||||
* @param num_mol number of molecules
|
||||
* @param num_atoms number of atoms
|
||||
* @param true_label_mol massive of true numbers of molecule for atoms
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
* @param ch_type_atoms massive of char atom types
|
||||
*
|
||||
* @return 1 - file $filename does not exist
|
||||
* @return 2 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char at_symb[32], file_string[256];
|
||||
int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
|
||||
float cur_coords[3], *not_tr_coords, ref[3];
|
||||
FILE *inp;
|
||||
|
||||
/* cur_* temp variables
|
||||
* at_symb temp variable
|
||||
* file_string temp string variable
|
||||
* atoms total number of atoms in system
|
||||
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
|
||||
* ref_mol number of molecule for reference in translation
|
||||
* not_tr_coords massive of not translated coordinates
|
||||
* ref massive of coordinates of reference molecule
|
||||
* inp input file
|
||||
*/
|
||||
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
*num_atoms = 0;
|
||||
*num_mol = 0;
|
||||
|
||||
/// <pre> reading file </pre>
|
||||
inp = fopen (filename, "r");
|
||||
if (inp == NULL)
|
||||
return 1;
|
||||
|
||||
ref_mol = -1;
|
||||
fscanf (inp, "%i", &atoms);
|
||||
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
|
||||
fgets (file_string, 256, inp);
|
||||
for (i=0; i<atoms; i++)
|
||||
{
|
||||
fgets (file_string, 256, inp);
|
||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
||||
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||
|
||||
// reading variables according to selected mode
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
// mode == 0 (selected atoms)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_at_type == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// mode == 1 (all atoms)
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
case 2:
|
||||
// mode == 2 (selected molecules)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_mol == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
default: return 2;
|
||||
}
|
||||
}
|
||||
fclose (inp);
|
||||
|
||||
/// <pre> translation </pre>
|
||||
tr_num_atoms = *num_atoms;
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
for (j=0; j<3; j++)
|
||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||
|
||||
// assign initial value to reference coordinates
|
||||
ref_mol = label_mol[0];
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
{
|
||||
if (label_mol[i] != ref_mol)
|
||||
{
|
||||
ref_mol = label_mol[i];
|
||||
for (j=0; j<3; j++)
|
||||
ref[j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
if (ref[x] >= 0.0)
|
||||
// if xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
else
|
||||
// if xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
for (y=x+1; y<3; y++)
|
||||
{
|
||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz and xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||
// if xyz and xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (y=0; y<3; y++)
|
||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz OR xyz >= 0.0
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
{
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
if (j == y)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
if ((j != x) && (j != y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
/// <pre> free memory </pre>
|
||||
free (not_tr_coords);
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -1,16 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef COORDS_H
|
||||
#define COORDS_H
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
|
||||
int reading_coords (const int, const char *, const int, const int *,
|
||||
const float *, int *, int *, int *, int *, int *, float *,
|
||||
char *);
|
||||
|
||||
#endif /* COORDS_H */
|
||||
@ -1,119 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <time.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
int message (const int log, const int mode, const char *text, FILE *output)
|
||||
/**
|
||||
* @brief function that prints messages to output
|
||||
* @code
|
||||
* message (log, mode, text, output);
|
||||
* @endcode
|
||||
*
|
||||
* @param log equal to 1 if print to logfile
|
||||
* @param mode number of message
|
||||
* @param text additional text
|
||||
* @param output output file (may be stdout)
|
||||
*
|
||||
* @return 1 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char out[4096];
|
||||
|
||||
if (log == 1)
|
||||
{
|
||||
char time_str[256];
|
||||
|
||||
time_t t = time (NULL);
|
||||
struct tm* aTm = localtime (&t);
|
||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||
aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
|
||||
fputs (time_str, output);
|
||||
}
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
sprintf (out, "Start program: '%s'\n", text);
|
||||
break;
|
||||
case 1:
|
||||
sprintf (out, "Checking errors\n");
|
||||
break;
|
||||
case 2:
|
||||
sprintf (out, "Errors are not detected\n");
|
||||
break;
|
||||
case 3:
|
||||
sprintf (out, "Initialization of variables from file '%s'\n", text);
|
||||
break;
|
||||
case 4:
|
||||
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
|
||||
break;
|
||||
case 5:
|
||||
sprintf (out, "Initial parametrs: \n%s", text);
|
||||
break;
|
||||
case 6:
|
||||
sprintf (out, "Processing\n");
|
||||
break;
|
||||
case 7:
|
||||
sprintf (out, "Open file: '%s'\n", text);
|
||||
break;
|
||||
case 8:
|
||||
sprintf (out, "%s", text);
|
||||
break;
|
||||
case 9:
|
||||
sprintf (out, "%6cSize of variables was changed successfully\n", ' ');
|
||||
break;
|
||||
case 10:
|
||||
sprintf (out, "%6cConnectivity matrix was created successfully\n", ' ');
|
||||
break;
|
||||
case 11:
|
||||
sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' ');
|
||||
break;
|
||||
case 12:
|
||||
sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text);
|
||||
break;
|
||||
case 13:
|
||||
sprintf (out, "End of processing\n");
|
||||
break;
|
||||
case 14:
|
||||
sprintf (out, "Print result to file '%s'\n", text);
|
||||
break;
|
||||
case 15:
|
||||
sprintf (out, "Free memory\n");
|
||||
break;
|
||||
case 16:
|
||||
sprintf (out, "Exiting without errors\n");
|
||||
break;
|
||||
case 17:
|
||||
sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text);
|
||||
break;
|
||||
case 18:
|
||||
sprintf (out, "File '%s' not found\nError\n", text);
|
||||
break;
|
||||
case 19:
|
||||
sprintf (out, "Memory error\n");
|
||||
break;
|
||||
case 20:
|
||||
sprintf (out, "%6cCenter of molecules was set successfully\n", ' ');
|
||||
break;
|
||||
case 21:
|
||||
sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
|
||||
break;
|
||||
case 22:
|
||||
sprintf (out, "%6cRADF was appended successfully\n", ' ');
|
||||
break;
|
||||
default:
|
||||
return 1;
|
||||
break;
|
||||
}
|
||||
|
||||
fputs (out, output);
|
||||
return 0;
|
||||
}
|
||||
@ -1,14 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef MESSAGES_H
|
||||
#define MESSAGES_H
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
|
||||
int message (const int, const int, const char *, FILE *);
|
||||
|
||||
#endif /* MESSAGES_H */
|
||||
@ -1,28 +0,0 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy (SET CMP0003 OLD)
|
||||
cmake_policy (SET CMP0011 NEW)
|
||||
cmake_policy (SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT ${MM_PREFIX}statgen)
|
||||
set (_PROJECT mm_statgen)
|
||||
# set additional cmake file
|
||||
include (${_PROJECT}.cmake)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
find_library ("${LIBRARY}_FOUND" ${LIBRARY})
|
||||
message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
|
||||
if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
|
||||
message (STATUS "Adding library sources")
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${PROJECT_SOURCE_DIR})
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.4 KiB |
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Reference in New Issue
Block a user