From bb5727bb7b29e0ea051b34d50f44057c70a4e520 Mon Sep 17 00:00:00 2001 From: arcan1s Date: Mon, 22 Jul 2013 22:16:11 +0400 Subject: [PATCH] Release statgen-1.0.1 --- statgen/AUTHORS | 3 + statgen/CMakeLists.txt | 6 +- statgen/CMakeLists_bckp.txt | 23 --- statgen/COPYING | 341 +++++++++++++++++++++++++++++++++++ statgen/INSTALL | 14 ++ statgen/README | 21 +++ statgen/src/CMakeLists.txt | 29 ++- statgen/{ => src}/Makefile | 1 + statgen/statgen-1.0.1.tar.xz | Bin 0 -> 17096 bytes statgen/statgen.cmake | 7 +- 10 files changed, 399 insertions(+), 46 deletions(-) create mode 100644 statgen/AUTHORS delete mode 100644 statgen/CMakeLists_bckp.txt create mode 100644 statgen/COPYING create mode 100644 statgen/INSTALL create mode 100644 statgen/README rename statgen/{ => src}/Makefile (95%) create mode 100644 statgen/statgen-1.0.1.tar.xz diff --git a/statgen/AUTHORS b/statgen/AUTHORS new file mode 100644 index 0000000..2c0d60a --- /dev/null +++ b/statgen/AUTHORS @@ -0,0 +1,3 @@ +Current developers: + +Evgeniy Alekseev aka arcanis diff --git a/statgen/CMakeLists.txt b/statgen/CMakeLists.txt index 4386b69..f07a7c3 100644 --- a/statgen/CMakeLists.txt +++ b/statgen/CMakeLists.txt @@ -10,8 +10,8 @@ include (${PROJECT}.cmake) # additional options -OPTION (WITH_DEBUG_MODE "Build with debug mode" ON) -OPTION (ADD_INCLUDE "Add include files" ON) +OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF) +OPTION (ADD_INCLUDE "Add include files" OFF) # set libraries set (LIBRARIES) @@ -28,6 +28,4 @@ set (LIBRARIES) set (TARGETS "") set (HEADERS "") -message (STATUS "SOURCES: ${SOURCES}") - add_subdirectory (src) \ No newline at end of file diff --git a/statgen/CMakeLists_bckp.txt b/statgen/CMakeLists_bckp.txt deleted file mode 100644 index f8ff8e4..0000000 --- a/statgen/CMakeLists_bckp.txt +++ /dev/null @@ -1,23 +0,0 @@ -cmake_minimum_required(VERSION 2.8) - -project(statgen) - -set(MY_CXX_FLAGS "-Wall") -set(CMAKE_CXX_FLAGS "-O0 ${MY_CXX_FLAGS}") -set(CMAKE_SHARED_LINKER_FLAGS "-lm") - -set(SOURCE_EXE main.c) -set(SOURCE_LIB add_main.c - coords.c - graph.c - int2char.c - messages.c - stat_print.c - stat_select.c - stat_sort.c - summary_stat.c) - -add_library(stat SHARED ${SOURCE_LIB}) -add_executable(statgen ${SOURCE_EXE}) - -target_link_libraries(statgen stat) \ No newline at end of file diff --git a/statgen/COPYING b/statgen/COPYING new file mode 100644 index 0000000..eb47f5d --- /dev/null +++ b/statgen/COPYING @@ -0,0 +1,341 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Library General Public License instead.) You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) 19yy + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) 19yy name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Library General +Public License instead of this License. diff --git a/statgen/INSTALL b/statgen/INSTALL new file mode 100644 index 0000000..cbd6143 --- /dev/null +++ b/statgen/INSTALL @@ -0,0 +1,14 @@ +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) + +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 +You may also download compiled executable file for Win_x86. diff --git a/statgen/README b/statgen/README new file mode 100644 index 0000000..b05284d --- /dev/null +++ b/statgen/README @@ -0,0 +1,21 @@ +statgen - program for analyze molecular dynamic trajectories +Version: 1.0.1 +License: GPL + +Usage: + statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] [ -l LOGFILE ] [ -q ] [ -h ] + +Parametrs: + -i - mask of input files + -s - trajectory steps (integer) + -c - cell size (float), A + -a - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc + -r - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction + (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times + -o - output file name + -g - check graph isomorphism. DEPTH is max depth for check cycles (>= 3) + -l - log enable + -q - quiet enable + -h - show this help and exit + + diff --git a/statgen/src/CMakeLists.txt b/statgen/src/CMakeLists.txt index 59e4619..79f355e 100644 --- a/statgen/src/CMakeLists.txt +++ b/statgen/src/CMakeLists.txt @@ -13,7 +13,15 @@ set (PRIVATE_CLASSES) # headers only files SET (HEADERS_ONLY) # public srcs -set (PUBLIC_CLASSES) +set (PUBLIC_CLASSES add_main + coords + graph + int2char + messages + stat_print + stat_select + stat_sort + summary_stat) # public headers set (PUBLIC_HEADERS) # shared libraries @@ -23,17 +31,6 @@ else () set (ADDITIONAL_LIB) endif() set (SOURCES) -# for library -set (LIBRARY_NAME stat) -set (LIB_SOURCES add_main - coords - graph - int2char - messages - stat_print - stat_select - stat_sort - summary_stat) # append list foreach (class ${PRIVATE_CLASSES}) @@ -51,16 +48,16 @@ foreach (class ${PUBLIC_CLASSES}) LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h) endforeach () +# message +message (STATUS "SOURCES: ${SOURCES}") + # link libraries and compile -add_library (${LIBRARY_NAME} SHARED ${LIB_SOURCES}) add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES}) -target_link_libraries (${PROJECT} ${ADDITIONAL_LIB} ${LIBRARY_NAME}) +target_link_libraries (${PROJECT} ${ADDITIONAL_LIB}) # install properties INSTALL (TARGETS ${PROJECT} DESTINATION bin) -INSTALL (TARGETS ${LIBRARY_NAME} - DESTINATION lib${LIB_SUFFIX}) if (ADD_INCLUDE) INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT}) diff --git a/statgen/Makefile b/statgen/src/Makefile similarity index 95% rename from statgen/Makefile rename to statgen/src/Makefile index ff59737..fd42351 100644 --- a/statgen/Makefile +++ b/statgen/src/Makefile @@ -3,6 +3,7 @@ PROJECT=STATGEN CC=gcc CFLAGS=-c -Wall -fPIC LDFLAGS=-lm +SOURCES_DIR=src SOURCES=main.c add_main.c coords.c graph.c int2char.c messages.c stat_print.c stat_select.c stat_sort.c summary_stat.c OBJECTS=$(SOURCES:.c=.o) EXECUTABLE=statgen diff --git 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-v") + 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") else () - message ("Not enabled") + message (STATUS "Flags not enabled") endif () \ No newline at end of file