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Added documentation for statgen
This commit is contained in:
arcan1s
3
agl/AUTHORS
Normal file
3
agl/AUTHORS
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
Current developers:
|
||||||
|
|
||||||
|
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>
|
||||||
31
agl/CMakeLists.txt
Normal file
31
agl/CMakeLists.txt
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@ -0,0 +1,31 @@
|
|||||||
|
cmake_minimum_required (VERSION 2.8)
|
||||||
|
|
||||||
|
cmake_policy(SET CMP0011 NEW)
|
||||||
|
cmake_policy(SET CMP0003 OLD)
|
||||||
|
|
||||||
|
# set project name
|
||||||
|
set (PROJECT 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)
|
||||||
|
|
||||||
|
# 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 (src)
|
||||||
341
agl/COPYING
Normal file
341
agl/COPYING
Normal file
@ -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. Our General Public Licenses are designed to make sure that you
|
||||||
|
have the freedom to distribute copies of free software (and charge for
|
||||||
|
this service if you wish), that you receive source code or can get it
|
||||||
|
if you want it, that you can change the software or use pieces of it
|
||||||
|
in new free programs; and that you know you can do these things.
|
||||||
|
|
||||||
|
To protect your rights, we need to make restrictions that forbid
|
||||||
|
anyone to deny you these rights or to ask you to surrender the rights.
|
||||||
|
These restrictions translate to certain responsibilities for you if you
|
||||||
|
distribute copies of the software, or if you modify it.
|
||||||
|
|
||||||
|
For example, if you distribute copies of such a program, whether
|
||||||
|
gratis or for a fee, you must give the recipients all the rights that
|
||||||
|
you have. You must make sure that they, too, receive or can get the
|
||||||
|
source code. And you must show them these terms so they know their
|
||||||
|
rights.
|
||||||
|
|
||||||
|
We protect your rights with two steps: (1) copyright the software, and
|
||||||
|
(2) offer you this license which gives you legal permission to copy,
|
||||||
|
distribute and/or modify the software.
|
||||||
|
|
||||||
|
Also, for each author's protection and ours, we want to make certain
|
||||||
|
that everyone understands that there is no warranty for this free
|
||||||
|
software. If the software is modified by someone else and passed on, we
|
||||||
|
want its recipients to know that what they have is not the original, so
|
||||||
|
that any problems introduced by others will not reflect on the original
|
||||||
|
authors' reputations.
|
||||||
|
|
||||||
|
Finally, any free program is threatened constantly by software
|
||||||
|
patents. We wish to avoid the danger that redistributors of a free
|
||||||
|
program will individually obtain patent licenses, in effect making the
|
||||||
|
program proprietary. To prevent this, we have made it clear that any
|
||||||
|
patent must be licensed for everyone's free use or not licensed at all.
|
||||||
|
|
||||||
|
The precise terms and conditions for copying, distribution and
|
||||||
|
modification follow.
|
||||||
|
|
||||||
|
GNU GENERAL PUBLIC LICENSE
|
||||||
|
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
|
||||||
|
|
||||||
|
0. This License applies to any program or other work which contains
|
||||||
|
a notice placed by the copyright holder saying it may be distributed
|
||||||
|
under the terms of this General Public License. The "Program", below,
|
||||||
|
refers to any such program or work, and a "work based on the Program"
|
||||||
|
means either the Program or any derivative work under copyright law:
|
||||||
|
that is to say, a work containing the Program or a portion of it,
|
||||||
|
either verbatim or with modifications and/or translated into another
|
||||||
|
language. (Hereinafter, translation is included without limitation in
|
||||||
|
the term "modification".) Each licensee is addressed as "you".
|
||||||
|
|
||||||
|
Activities other than copying, distribution and modification are not
|
||||||
|
covered by this License; they are outside its scope. The act of
|
||||||
|
running the Program is not restricted, and the output from the Program
|
||||||
|
is covered only if its contents constitute a work based on the
|
||||||
|
Program (independent of having been made by running the Program).
|
||||||
|
Whether that is true depends on what the Program does.
|
||||||
|
|
||||||
|
1. You may copy and distribute verbatim copies of the Program's
|
||||||
|
source code as you receive it, in any medium, provided that you
|
||||||
|
conspicuously and appropriately publish on each copy an appropriate
|
||||||
|
copyright notice and disclaimer of warranty; keep intact all the
|
||||||
|
notices that refer to this License and to the absence of any warranty;
|
||||||
|
and give any other recipients of the Program a copy of this License
|
||||||
|
along with the Program.
|
||||||
|
|
||||||
|
You may charge a fee for the physical act of transferring a copy, and
|
||||||
|
you may at your option offer warranty protection in exchange for a fee.
|
||||||
|
|
||||||
|
2. You may modify your copy or copies of the Program or any portion
|
||||||
|
of it, thus forming a work based on the Program, and copy and
|
||||||
|
distribute such modifications or work under the terms of Section 1
|
||||||
|
above, provided that you also meet all of these conditions:
|
||||||
|
|
||||||
|
a) You must cause the modified files to carry prominent notices
|
||||||
|
stating that you changed the files and the date of any change.
|
||||||
|
|
||||||
|
b) You must cause any work that you distribute or publish, that in
|
||||||
|
whole or in part contains or is derived from the Program or any
|
||||||
|
part thereof, to be licensed as a whole at no charge to all third
|
||||||
|
parties under the terms of this License.
|
||||||
|
|
||||||
|
c) If the modified program normally reads commands interactively
|
||||||
|
when run, you must cause it, when started running for such
|
||||||
|
interactive use in the most ordinary way, to print or display an
|
||||||
|
announcement including an appropriate copyright notice and a
|
||||||
|
notice that there is no warranty (or else, saying that you provide
|
||||||
|
a warranty) and that users may redistribute the program under
|
||||||
|
these conditions, and telling the user how to view a copy of this
|
||||||
|
License. (Exception: if the Program itself is interactive but
|
||||||
|
does not normally print such an announcement, your work based on
|
||||||
|
the Program is not required to print an announcement.)
|
||||||
|
|
||||||
|
These requirements apply to the modified work as a whole. If
|
||||||
|
identifiable sections of that work are not derived from the Program,
|
||||||
|
and can be reasonably considered independent and separate works in
|
||||||
|
themselves, then this License, and its terms, do not apply to those
|
||||||
|
sections when you distribute them as separate works. But when you
|
||||||
|
distribute the same sections as part of a whole which is a work based
|
||||||
|
on the Program, the distribution of the whole must be on the terms of
|
||||||
|
this License, whose permissions for other licensees extend to the
|
||||||
|
entire whole, and thus to each and every part regardless of who wrote it.
|
||||||
|
|
||||||
|
Thus, it is not the intent of this section to claim rights or contest
|
||||||
|
your rights to work written entirely by you; rather, the intent is to
|
||||||
|
exercise the right to control the distribution of derivative or
|
||||||
|
collective works based on the Program.
|
||||||
|
|
||||||
|
In addition, mere aggregation of another work not based on the Program
|
||||||
|
with the Program (or with a work based on the Program) on a volume of
|
||||||
|
a storage or distribution medium does not bring the other work under
|
||||||
|
the scope of this License.
|
||||||
|
|
||||||
|
3. You may copy and distribute the Program (or a work based on it,
|
||||||
|
under Section 2) in object code or executable form under the terms of
|
||||||
|
Sections 1 and 2 above provided that you also do one of the following:
|
||||||
|
|
||||||
|
a) Accompany it with the complete corresponding machine-readable
|
||||||
|
source code, which must be distributed under the terms of Sections
|
||||||
|
1 and 2 above on a medium customarily used for software interchange; or,
|
||||||
|
|
||||||
|
b) Accompany it with a written offer, valid for at least three
|
||||||
|
years, to give any third party, for a charge no more than your
|
||||||
|
cost of physically performing source distribution, a complete
|
||||||
|
machine-readable copy of the corresponding source code, to be
|
||||||
|
distributed under the terms of Sections 1 and 2 above on a medium
|
||||||
|
customarily used for software interchange; or,
|
||||||
|
|
||||||
|
c) Accompany it with the information you received as to the offer
|
||||||
|
to distribute corresponding source code. (This alternative is
|
||||||
|
allowed only for noncommercial distribution and only if you
|
||||||
|
received the program in object code or executable form with such
|
||||||
|
an offer, in accord with Subsection b above.)
|
||||||
|
|
||||||
|
The source code for a work means the preferred form of the work for
|
||||||
|
making modifications to it. For an executable work, complete source
|
||||||
|
code means all the source code for all modules it contains, plus any
|
||||||
|
associated interface definition files, plus the scripts used to
|
||||||
|
control compilation and installation of the executable. However, as a
|
||||||
|
special exception, the source code distributed need not include
|
||||||
|
anything that is normally distributed (in either source or binary
|
||||||
|
form) with the major components (compiler, kernel, and so on) of the
|
||||||
|
operating system on which the executable runs, unless that component
|
||||||
|
itself accompanies the executable.
|
||||||
|
|
||||||
|
If distribution of executable or object code is made by offering
|
||||||
|
access to copy from a designated place, then offering equivalent
|
||||||
|
access to copy the source code from the same place counts as
|
||||||
|
distribution of the source code, even though third parties are not
|
||||||
|
compelled to copy the source along with the object code.
|
||||||
|
|
||||||
|
4. You may not copy, modify, sublicense, or distribute the Program
|
||||||
|
except as expressly provided under this License. Any attempt
|
||||||
|
otherwise to copy, modify, sublicense or distribute the Program is
|
||||||
|
void, and will automatically terminate your rights under this License.
|
||||||
|
However, parties who have received copies, or rights, from you under
|
||||||
|
this License will not have their licenses terminated so long as such
|
||||||
|
parties remain in full compliance.
|
||||||
|
|
||||||
|
5. You are not required to accept this License, since you have not
|
||||||
|
signed it. However, nothing else grants you permission to modify or
|
||||||
|
distribute the Program or its derivative works. These actions are
|
||||||
|
prohibited by law if you do not accept this License. Therefore, by
|
||||||
|
modifying or distributing the Program (or any work based on the
|
||||||
|
Program), you indicate your acceptance of this License to do so, and
|
||||||
|
all its terms and conditions for copying, distributing or modifying
|
||||||
|
the Program or works based on it.
|
||||||
|
|
||||||
|
6. Each time you redistribute the Program (or any work based on the
|
||||||
|
Program), the recipient automatically receives a license from the
|
||||||
|
original licensor to copy, distribute or modify the Program subject to
|
||||||
|
these terms and conditions. You may not impose any further
|
||||||
|
restrictions on the recipients' exercise of the rights granted herein.
|
||||||
|
You are not responsible for enforcing compliance by third parties to
|
||||||
|
this License.
|
||||||
|
|
||||||
|
7. If, as a consequence of a court judgment or allegation of patent
|
||||||
|
infringement or for any other reason (not limited to patent issues),
|
||||||
|
conditions are imposed on you (whether by court order, agreement or
|
||||||
|
otherwise) that contradict the conditions of this License, they do not
|
||||||
|
excuse you from the conditions of this License. If you cannot
|
||||||
|
distribute so as to satisfy simultaneously your obligations under this
|
||||||
|
License and any other pertinent obligations, then as a consequence you
|
||||||
|
may not distribute the Program at all. For example, if a patent
|
||||||
|
license would not permit royalty-free redistribution of the Program by
|
||||||
|
all those who receive copies directly or indirectly through you, then
|
||||||
|
the only way you could satisfy both it and this License would be to
|
||||||
|
refrain entirely from distribution of the Program.
|
||||||
|
|
||||||
|
If any portion of this section is held invalid or unenforceable under
|
||||||
|
any particular circumstance, the balance of the section is intended to
|
||||||
|
apply and the section as a whole is intended to apply in other
|
||||||
|
circumstances.
|
||||||
|
|
||||||
|
It is not the purpose of this section to induce you to infringe any
|
||||||
|
patents or other property right claims or to contest validity of any
|
||||||
|
such claims; this section has the sole purpose of protecting the
|
||||||
|
integrity of the free software distribution system, which is
|
||||||
|
implemented by public license practices. Many people have made
|
||||||
|
generous contributions to the wide range of software distributed
|
||||||
|
through that system in reliance on consistent application of that
|
||||||
|
system; it is up to the author/donor to decide if he or she is willing
|
||||||
|
to distribute software through any other system and a licensee cannot
|
||||||
|
impose that choice.
|
||||||
|
|
||||||
|
This section is intended to make thoroughly clear what is believed to
|
||||||
|
be a consequence of the rest of this License.
|
||||||
|
|
||||||
|
8. If the distribution and/or use of the Program is restricted in
|
||||||
|
certain countries either by patents or by copyrighted interfaces, the
|
||||||
|
original copyright holder who places the Program under this License
|
||||||
|
may add an explicit geographical distribution limitation excluding
|
||||||
|
those countries, so that distribution is permitted only in or among
|
||||||
|
countries not thus excluded. In such case, this License incorporates
|
||||||
|
the limitation as if written in the body of this License.
|
||||||
|
|
||||||
|
9. The Free Software Foundation may publish revised and/or new versions
|
||||||
|
of the General Public License from time to time. Such new versions will
|
||||||
|
be similar in spirit to the present version, but may differ in detail to
|
||||||
|
address new problems or concerns.
|
||||||
|
|
||||||
|
Each version is given a distinguishing version number. If the Program
|
||||||
|
specifies a version number of this License which applies to it and "any
|
||||||
|
later version", you have the option of following the terms and conditions
|
||||||
|
either of that version or of any later version published by the Free
|
||||||
|
Software Foundation. If the Program does not specify a version number of
|
||||||
|
this License, you may choose any version ever published by the Free Software
|
||||||
|
Foundation.
|
||||||
|
|
||||||
|
10. If you wish to incorporate parts of the Program into other free
|
||||||
|
programs whose distribution conditions are different, write to the author
|
||||||
|
to ask for permission. For software which is copyrighted by the Free
|
||||||
|
Software Foundation, write to the Free Software Foundation; we sometimes
|
||||||
|
make exceptions for this. Our decision will be guided by the two goals
|
||||||
|
of preserving the free status of all derivatives of our free software and
|
||||||
|
of promoting the sharing and reuse of software generally.
|
||||||
|
|
||||||
|
NO WARRANTY
|
||||||
|
|
||||||
|
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
|
||||||
|
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
|
||||||
|
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
|
||||||
|
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
|
||||||
|
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||||
|
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
|
||||||
|
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
|
||||||
|
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
|
||||||
|
REPAIR OR CORRECTION.
|
||||||
|
|
||||||
|
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||||
|
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
|
||||||
|
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
|
||||||
|
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
|
||||||
|
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
|
||||||
|
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
|
||||||
|
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
|
||||||
|
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
|
||||||
|
POSSIBILITY OF SUCH DAMAGES.
|
||||||
|
|
||||||
|
END OF TERMS AND CONDITIONS
|
||||||
|
|
||||||
|
How to Apply These Terms to Your New Programs
|
||||||
|
|
||||||
|
If you develop a new program, and you want it to be of the greatest
|
||||||
|
possible use to the public, the best way to achieve this is to make it
|
||||||
|
free software which everyone can redistribute and change under these terms.
|
||||||
|
|
||||||
|
To do so, attach the following notices to the program. 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.
|
||||||
|
|
||||||
|
<one line to give the program's name and a brief idea of what it does.>
|
||||||
|
Copyright (C) 19yy <name of author>
|
||||||
|
|
||||||
|
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.
|
||||||
|
|
||||||
|
<signature of Ty Coon>, 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.
|
||||||
14
agl/INSTALL
Normal file
14
agl/INSTALL
Normal file
@ -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.
|
||||||
22
agl/agl.cmake
Normal file
22
agl/agl.cmake
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
# set directories
|
||||||
|
set (${PROJECT}_BINARY_DIR bin)
|
||||||
|
set (${PROJECT}_SOURCE_DIR src:include)
|
||||||
|
set (${PROJECT}_LIB_DIR lib)
|
||||||
|
|
||||||
|
set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
|
||||||
|
set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
|
||||||
|
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||||
|
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||||
|
|
||||||
|
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 ${ADD_CXX_FLAGS}")
|
||||||
|
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
|
||||||
|
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
|
||||||
|
else ()
|
||||||
|
message (STATUS "Flags not enabled")
|
||||||
|
endif ()
|
||||||
61
agl/src/CMakeLists.txt
Normal file
61
agl/src/CMakeLists.txt
Normal file
@ -0,0 +1,61 @@
|
|||||||
|
set ("${PROJECT}_VERSION_MAJOR" 1)
|
||||||
|
set ("${PROJECT}_VERSION_MINOR" 0)
|
||||||
|
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||||
|
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||||
|
|
||||||
|
message (STATUS ${${PROJECT}_VERSION})
|
||||||
|
|
||||||
|
## set files
|
||||||
|
# main files
|
||||||
|
set (MAIN_SOURCES main)
|
||||||
|
# not public srcs
|
||||||
|
set (PRIVATE_CLASSES)
|
||||||
|
# headers only files
|
||||||
|
SET (HEADERS_ONLY)
|
||||||
|
# public srcs
|
||||||
|
set (PUBLIC_CLASSES add_main
|
||||||
|
coords
|
||||||
|
envir_search
|
||||||
|
messages
|
||||||
|
print_struct
|
||||||
|
set_center)
|
||||||
|
# public headers
|
||||||
|
set (PUBLIC_HEADERS)
|
||||||
|
# shared libraries
|
||||||
|
if (CMAKE_COMPILER_IS_GNUCXX)
|
||||||
|
set (ADDITIONAL_LIB m)
|
||||||
|
else ()
|
||||||
|
set (ADDITIONAL_LIB)
|
||||||
|
endif()
|
||||||
|
set (SOURCES)
|
||||||
|
|
||||||
|
# append list
|
||||||
|
foreach (class ${PRIVATE_CLASSES})
|
||||||
|
LIST (APPEND SOURCES ${class}.c)
|
||||||
|
LIST (APPEND HEADERS ${class}.h)
|
||||||
|
endforeach ()
|
||||||
|
|
||||||
|
foreach (class ${HEADERS_ONLY})
|
||||||
|
LIST (APPEND HEADERS ${class}.h)
|
||||||
|
endforeach ()
|
||||||
|
|
||||||
|
foreach (class ${PUBLIC_CLASSES})
|
||||||
|
LIST (APPEND SOURCES ${class}.c)
|
||||||
|
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
|
||||||
|
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
|
||||||
|
endforeach ()
|
||||||
|
|
||||||
|
# message
|
||||||
|
message (STATUS "SOURCES: ${SOURCES}")
|
||||||
|
|
||||||
|
# link libraries and compile
|
||||||
|
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
|
||||||
|
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||||
|
|
||||||
|
# install properties
|
||||||
|
INSTALL (TARGETS ${PROJECT}
|
||||||
|
DESTINATION bin)
|
||||||
|
if (ADD_INCLUDE)
|
||||||
|
INSTALL (FILES ${PUBLIC_HEADERS}
|
||||||
|
DESTINATION include/${PROJECT})
|
||||||
|
endif ()
|
||||||
21
agl/src/Makefile
Normal file
21
agl/src/Makefile
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
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 set_center.c read_agl.c
|
||||||
|
OBJECTS=$(SOURCES:.c=.o)
|
||||||
|
EXECUTABLE=agl
|
||||||
|
|
||||||
|
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||||
|
|
||||||
|
$(EXECUTABLE): $(OBJECTS)
|
||||||
|
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||||
|
|
||||||
|
.c.o:
|
||||||
|
$(CC) $(CFLAGS) $< -o $@
|
||||||
|
|
||||||
|
clean:
|
||||||
|
rm -f *.o
|
||||||
|
|
||||||
53
agl/src/add_main.c
Normal file
53
agl/src/add_main.c
Normal file
@ -0,0 +1,53 @@
|
|||||||
|
/* Additional library for main.c (agl)
|
||||||
|
*/
|
||||||
|
|
||||||
|
#include <stdio.h>
|
||||||
|
|
||||||
|
// #include "messages.h"
|
||||||
|
|
||||||
|
|
||||||
|
int error_checking (const char *aglinp, const float *cell, const char *input,
|
||||||
|
const char *output)
|
||||||
|
{
|
||||||
|
if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
|
||||||
|
return 11;
|
||||||
|
if (input[0] == '#')
|
||||||
|
return 12;
|
||||||
|
if (output[0] == '#')
|
||||||
|
return 13;
|
||||||
|
if (aglinp[0] == '#')
|
||||||
|
return 14;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
|
||||||
|
const int mode, const char *str)
|
||||||
|
{
|
||||||
|
if ((quiet != 1) && (std_output != stderr))
|
||||||
|
message (0, mode, str, std_output);
|
||||||
|
if (log == 1)
|
||||||
|
message (1, mode, str, f_log);
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int set_defaults (char aglinp, float *cell, char *input, int *log, int *num_of_mol,
|
||||||
|
char *output, int *quiet, float *rad)
|
||||||
|
{
|
||||||
|
int i;
|
||||||
|
|
||||||
|
aglinp[0] = '#';
|
||||||
|
for (i=0; i<3; i++)
|
||||||
|
cell[i] = 0.0;
|
||||||
|
input[0] = '#';
|
||||||
|
*log = 0;
|
||||||
|
*num_of_mol = 1;
|
||||||
|
output[0] = '#';
|
||||||
|
*quiet = 0;
|
||||||
|
*rad = 6.0;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
338
agl/src/coords.c
Normal file
338
agl/src/coords.c
Normal file
@ -0,0 +1,338 @@
|
|||||||
|
/* Library for reading coordinates from input file
|
||||||
|
*
|
||||||
|
* Usage:
|
||||||
|
* reading_coords (mode, filename, type_interaction, labels,
|
||||||
|
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
|
||||||
|
* label_molecule, type_atoms, coords, char_type_atoms)
|
||||||
|
*/
|
||||||
|
|
||||||
|
#include <stdio.h>
|
||||||
|
#include <stdlib.h>
|
||||||
|
|
||||||
|
|
||||||
|
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)
|
||||||
|
/* filename - name of file with coordinates
|
||||||
|
* type_inter - type interaction (number of molecules for interaction)
|
||||||
|
* (number of molecules in aglomerate for agl)
|
||||||
|
* label_atom - types of atom for interaction
|
||||||
|
* (molecules in aglomerate for agl)
|
||||||
|
* cell - cell dimension
|
||||||
|
* num_mol - number of molecules for writing coordinates
|
||||||
|
* num_atoms - number of atoms for writing coordinates
|
||||||
|
* true_label_mol - massive of true numbers of molecule for atoms
|
||||||
|
* label_mol - massive of numbers of molecule for atoms
|
||||||
|
* type_atoms - massive of atom types for atoms
|
||||||
|
* coords - massive of coordinates
|
||||||
|
* ch_type_atoms - massive of char types for atoms
|
||||||
|
*/
|
||||||
|
{
|
||||||
|
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_*, at_symb - temp variables
|
||||||
|
* file_string - temp string variable
|
||||||
|
* atoms - total number of atoms in system
|
||||||
|
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
|
||||||
|
* ref_mol - number of molecule for reference
|
||||||
|
* not_tr_coords - not translated coordinates
|
||||||
|
* ref - coordinates of reference molecule
|
||||||
|
* inp - file with input data
|
||||||
|
*/
|
||||||
|
|
||||||
|
*num_atoms = 0;
|
||||||
|
*num_mol = 0;
|
||||||
|
|
||||||
|
// Reading file
|
||||||
|
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);
|
||||||
|
|
||||||
|
switch (mode)
|
||||||
|
{
|
||||||
|
case 0:
|
||||||
|
// for statgen
|
||||||
|
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:
|
||||||
|
// for envir and frad
|
||||||
|
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:
|
||||||
|
// for agl
|
||||||
|
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 1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
fclose (inp);
|
||||||
|
|
||||||
|
// Translation
|
||||||
|
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++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// free memory
|
||||||
|
free (not_tr_coords);
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
203
agl/src/main.c
Normal file
203
agl/src/main.c
Normal file
@ -0,0 +1,203 @@
|
|||||||
|
#include <math.h>
|
||||||
|
#include <stdio.h>
|
||||||
|
#include <stdlib.h>
|
||||||
|
#include <string.h>
|
||||||
|
|
||||||
|
// #include "add_main.h"
|
||||||
|
// #include "coords.h"
|
||||||
|
// #include "messages.h"
|
||||||
|
// #include "print_struct.h"
|
||||||
|
// #include "read_agl.h"
|
||||||
|
|
||||||
|
|
||||||
|
int main(int argc, char *argv[])
|
||||||
|
{
|
||||||
|
char tmp_str[2048];
|
||||||
|
int error, i, j, *tmp_int;
|
||||||
|
FILE *f_inp, *f_log;
|
||||||
|
|
||||||
|
char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
|
||||||
|
float cell[3], *coords;
|
||||||
|
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
|
||||||
|
*true_label_mol;
|
||||||
|
/* ch_type_atoms - massive of char types for atoms
|
||||||
|
* aglinp - input file with aglomerate name
|
||||||
|
* input - input file name
|
||||||
|
* logfile - log file name
|
||||||
|
* output - output file name
|
||||||
|
*
|
||||||
|
* cell - cell dimension
|
||||||
|
* coords - massive of coordinates
|
||||||
|
*
|
||||||
|
* label_mol - massive of numbers of molecule for atoms
|
||||||
|
* log - status of log-mode
|
||||||
|
* num_atoms - number of atoms for writing coordinates
|
||||||
|
* num_mol - number of molecules for writing coordinates
|
||||||
|
* num_needed_mol - number of needed molecules
|
||||||
|
* needed_mol - massive of needed molecules
|
||||||
|
* quiet - status of quiet-mode
|
||||||
|
* true_label_mol - massive of true numbers of molecule for atoms
|
||||||
|
*/
|
||||||
|
|
||||||
|
set_defaults (aglinp, cell, input, &log, &num_of_mol, output, &quiet, &rad);
|
||||||
|
|
||||||
|
for (i=1; i<argc; i++)
|
||||||
|
{
|
||||||
|
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
||||||
|
{
|
||||||
|
sprintf (tmp_str, " agl\n");
|
||||||
|
sprintf (tmp_str, "%sProgram for create PDB file with choosen aglomerate\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%sUsage:\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%sagl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]\n\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -a - input file with aglomerates (in format statgen)\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -o - output file with coordinates\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
|
||||||
|
sprintf (tmp_str, "%s -h - show this help and exit\n", tmp_str);
|
||||||
|
fputs (tmp_str, stdout);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
|
||||||
|
// input file
|
||||||
|
{
|
||||||
|
strcpy (aglinp, argv[i+1]);
|
||||||
|
i++;
|
||||||
|
}
|
||||||
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
|
||||||
|
// input file
|
||||||
|
{
|
||||||
|
strcpy (input, argv[i+1]);
|
||||||
|
i++;
|
||||||
|
}
|
||||||
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
|
||||||
|
// cell size
|
||||||
|
{
|
||||||
|
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
|
||||||
|
i++;
|
||||||
|
}
|
||||||
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
|
||||||
|
// output file
|
||||||
|
{
|
||||||
|
strcpy (output, argv[i+1]);
|
||||||
|
i++;
|
||||||
|
}
|
||||||
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
|
||||||
|
// log mode
|
||||||
|
{
|
||||||
|
log = 1;
|
||||||
|
strcpy (logfile, argv[i+1]);
|
||||||
|
i++;
|
||||||
|
}
|
||||||
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
|
||||||
|
// quiet mode
|
||||||
|
{
|
||||||
|
quiet = 1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (log == 1)
|
||||||
|
f_log = fopen (logfile, "w");
|
||||||
|
|
||||||
|
print_message (quiet, stdout, log, f_log, 0, argv[0]);
|
||||||
|
print_message (quiet, stdout, log, f_log, 1, argv[0]);
|
||||||
|
|
||||||
|
// error check
|
||||||
|
error = error_checking (aglinp, cell, input, output);
|
||||||
|
if (error != 0)
|
||||||
|
{
|
||||||
|
print_message (quiet, stderr, log, f_log, 17, argv[0]);
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
||||||
|
|
||||||
|
// processing
|
||||||
|
// initial variables
|
||||||
|
print_message (quiet, stdout, log, f_log, 3, input);
|
||||||
|
f_inp = fopen (input, "r");
|
||||||
|
if (f_inp == NULL)
|
||||||
|
{
|
||||||
|
print_message (quiet, stderr, log, f_log, 18, input);
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
fscanf (f_inp, "%i", &num_atoms);
|
||||||
|
fclose (f_inp);
|
||||||
|
ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
|
||||||
|
coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
|
||||||
|
label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
|
||||||
|
needed_mol = (int *) malloc (num_atoms * sizeof (int));
|
||||||
|
tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
|
||||||
|
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
|
||||||
|
// error checking
|
||||||
|
if ((ch_type_atoms == NULL) ||
|
||||||
|
(coords == NULL) ||
|
||||||
|
(label_mol == NULL) ||
|
||||||
|
(needed_mol == NULL) ||
|
||||||
|
(tmp_int == NULL) ||
|
||||||
|
(true_label_mol == NULL))
|
||||||
|
{
|
||||||
|
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||||
|
return 17;
|
||||||
|
}
|
||||||
|
sprintf (tmp_str, "%6cAglomerate file: '%s';\n%6cInput file: '%s';\n\
|
||||||
|
%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f\n",
|
||||||
|
' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], cell[1], cell[2]);
|
||||||
|
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||||
|
|
||||||
|
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||||
|
|
||||||
|
// reading aglomerate
|
||||||
|
print_message (quiet, stdout, log, f_log, 7, aglinp);
|
||||||
|
error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
|
||||||
|
|
||||||
|
if (error == 0)
|
||||||
|
{
|
||||||
|
sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", num_needed_mol);
|
||||||
|
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||||
|
// reading coordinates
|
||||||
|
print_message (quiet, stdout, log, f_log, 7, input);
|
||||||
|
error = reading_coords (1, input, num_needed_mol, needed_mol, cell, &num_mol,
|
||||||
|
&num_atoms, true_label_mol, label_mol, tmp_int, coords,
|
||||||
|
ch_type_atoms);
|
||||||
|
|
||||||
|
// analyze
|
||||||
|
if (error == 0)
|
||||||
|
{
|
||||||
|
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
|
||||||
|
' ', num_mol, ' ', num_atoms);
|
||||||
|
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||||
|
error =
|
||||||
|
if (error == 0)
|
||||||
|
{
|
||||||
|
print_message (quiet, stderr, log, f_log, 21, argv[0]);
|
||||||
|
error = print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
||||||
|
label_mol, ch_type_atoms, coords);
|
||||||
|
print_message (quiet, stderr, log, f_log, 12, output);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||||
|
|
||||||
|
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||||
|
// free memory
|
||||||
|
free (ch_type_atoms);
|
||||||
|
free (coords);
|
||||||
|
free (label_mol);
|
||||||
|
free (needed_mol);
|
||||||
|
free (tmp_int);
|
||||||
|
free (true_label_mol);
|
||||||
|
|
||||||
|
print_message (quiet, stdout, log, f_log, 16, argv[0]);
|
||||||
|
|
||||||
|
if (log == 1)
|
||||||
|
fclose (f_log);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
99
agl/src/messages.c
Normal file
99
agl/src/messages.c
Normal file
@ -0,0 +1,99 @@
|
|||||||
|
/* Library for printing messages at output
|
||||||
|
*
|
||||||
|
* Usage:
|
||||||
|
* message (log, mode, text, output)
|
||||||
|
*/
|
||||||
|
|
||||||
|
#include <stdio.h>
|
||||||
|
#include <time.h>
|
||||||
|
|
||||||
|
|
||||||
|
int message (const int log, const int mode, const char *text, FILE *output)
|
||||||
|
/* mode - number of message
|
||||||
|
* text - additional text
|
||||||
|
*/
|
||||||
|
{
|
||||||
|
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, "Starting 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:
|
||||||
|
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, "Printing summary statistic 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;
|
||||||
|
}
|
||||||
|
|
||||||
|
fputs (out, output);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
58
agl/src/print_struct.c
Normal file
58
agl/src/print_struct.c
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
/* Library for printing structure to pdb file
|
||||||
|
*
|
||||||
|
* Usage:
|
||||||
|
* print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
||||||
|
* label_mol, char_type_atoms, coords)
|
||||||
|
*/
|
||||||
|
|
||||||
|
#include <stdio.h>
|
||||||
|
|
||||||
|
|
||||||
|
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)
|
||||||
|
/* output - output file name
|
||||||
|
* num_needed_mol - number of needed molecules
|
||||||
|
* needed_mol - massive of needed molecules
|
||||||
|
* num_atoms - number of atoms
|
||||||
|
* label_mol - massive of numbers of molecule for atoms
|
||||||
|
* ch_type_atoms - massive of char types for atoms
|
||||||
|
* coords - massive of coordinates
|
||||||
|
*/
|
||||||
|
{
|
||||||
|
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
|
||||||
|
*/
|
||||||
|
|
||||||
|
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;
|
||||||
|
}
|
||||||
33
agl/src/read_agl.c
Normal file
33
agl/src/read_agl.c
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
/* Library for reading aglomerate from statgen-file
|
||||||
|
*
|
||||||
|
* Usage:
|
||||||
|
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol)
|
||||||
|
*/
|
||||||
|
|
||||||
|
#include <stdio.h>
|
||||||
|
|
||||||
|
|
||||||
|
int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
|
||||||
|
/* aglinp - input file with aglomerate
|
||||||
|
* num_needed_mol - number of needed molecules
|
||||||
|
* agl_class - aglomerate class
|
||||||
|
* needed_mol - massive of needed molecules
|
||||||
|
*/
|
||||||
|
{
|
||||||
|
char connect[256], tmp_str[256];
|
||||||
|
int i;
|
||||||
|
FILE *f_agl;
|
||||||
|
|
||||||
|
f_agl = fopen (aglinp, "r");
|
||||||
|
|
||||||
|
fgets (tmp_str, 256, f_agl);
|
||||||
|
sscanf (tmp_str, "AGL=%i=%s", num_needed_mol, agl_class);
|
||||||
|
for (i=0; i<*num_needed_mol; i++)
|
||||||
|
{
|
||||||
|
fgets (tmp_str, 256, f_agl);
|
||||||
|
sscanf (tmp_str, "%i=%s", &needed_mol[i], connect);
|
||||||
|
}
|
||||||
|
fclose (f_agl);
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
59
agl/src/select_mol.c
Normal file
59
agl/src/select_mol.c
Normal file
@ -0,0 +1,59 @@
|
|||||||
|
/* Library for select molecules in translations
|
||||||
|
*
|
||||||
|
* Usage:
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
|
#include <math.h>
|
||||||
|
|
||||||
|
|
||||||
|
int select_molecule (const int num_atoms, const int *label_mol, const int *true_label_mol, const float *coords, const int num_needed_mol, int *needed_mol)
|
||||||
|
{
|
||||||
|
float r, ref[3], rmin;
|
||||||
|
int i, j, k, *old_needed_mol;
|
||||||
|
|
||||||
|
old_needed_mol = (int *) malloc (num_needed_mol * sizeof (int));
|
||||||
|
if (old_needed_mol == NULL)
|
||||||
|
return 1;
|
||||||
|
|
||||||
|
// set first molecule
|
||||||
|
ref_mol = old_needed_mol[0];
|
||||||
|
needed_mol[0] = 0;
|
||||||
|
k = 1;
|
||||||
|
for (i=0; i<3; i++)
|
||||||
|
ref[i] = coords[3*0+i];
|
||||||
|
|
||||||
|
for (i=1; i<num_needed_mol; i++)
|
||||||
|
for (j=0; j<8*num_atoms; j++)
|
||||||
|
if (old_needed_mol[i] == true_label_mol[label_mol[j]])
|
||||||
|
{
|
||||||
|
if (j < num_atoms)
|
||||||
|
cur_mol = 0;
|
||||||
|
else
|
||||||
|
cur_mol = ((j - num_atoms) % 7) + 1;
|
||||||
|
// for (j=0; j<3; j++)
|
||||||
|
// centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
|
||||||
|
}
|
||||||
|
|
||||||
|
for (i=1; i<num_needed_mol; i++)
|
||||||
|
for (j=0; j<num_atoms; j++)
|
||||||
|
if (old_needed_mol[i] == true_label_mol[label_mol[j]])
|
||||||
|
{
|
||||||
|
if (ref_mol != true_label_mol[label_mol[j]])
|
||||||
|
{
|
||||||
|
ref_i = j;
|
||||||
|
rmin = sqrt (pow ((coords[3*j+0] - ref[0]), 2) + \
|
||||||
|
pow ((coords[3*j+1] - ref[1]), 2) + \
|
||||||
|
pow ((coords[3*j+2] - ref[2]), 2));
|
||||||
|
ref_mol = true_label_mol[label_mol[j]];
|
||||||
|
}
|
||||||
|
else
|
||||||
|
{
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
free (old_needed_mol);
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
@ -9,16 +9,16 @@ message (STATUS ${${PROJECT}_VERSION})
|
|||||||
# main files
|
# main files
|
||||||
set (MAIN_SOURCES main)
|
set (MAIN_SOURCES main)
|
||||||
# not public srcs
|
# not public srcs
|
||||||
set (PRIVATE_CLASSES)
|
set (PRIVATE_CLASSES add_main
|
||||||
|
coords
|
||||||
|
envir_search
|
||||||
|
messages
|
||||||
|
print_struct
|
||||||
|
set_center)
|
||||||
# headers only files
|
# headers only files
|
||||||
SET (HEADERS_ONLY)
|
SET (HEADERS_ONLY)
|
||||||
# public srcs
|
# public srcs
|
||||||
set (PUBLIC_CLASSES add_main
|
set (PUBLIC_CLASSES)
|
||||||
coords
|
|
||||||
envir_search
|
|
||||||
messages
|
|
||||||
print_struct
|
|
||||||
set_center)
|
|
||||||
# public headers
|
# public headers
|
||||||
set (PUBLIC_HEADERS)
|
set (PUBLIC_HEADERS)
|
||||||
# shared libraries
|
# shared libraries
|
||||||
|
|||||||
@ -3,7 +3,7 @@
|
|||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
// #include "messages.h"
|
#include "messages.h"
|
||||||
|
|
||||||
|
|
||||||
int error_checking (const float *cell, const char *input, const char *output)
|
int error_checking (const float *cell, const char *input, const char *output)
|
||||||
|
|||||||
@ -16,7 +16,9 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||||
/* filename - name of file with coordinates
|
/* filename - name of file with coordinates
|
||||||
* type_inter - type interaction (number of molecules for interaction)
|
* type_inter - type interaction (number of molecules for interaction)
|
||||||
|
* (number of molecules in aglomerate for agl)
|
||||||
* label_atom - types of atom for interaction
|
* label_atom - types of atom for interaction
|
||||||
|
* (molecules in aglomerate for agl)
|
||||||
* cell - cell dimension
|
* cell - cell dimension
|
||||||
* num_mol - number of molecules for writing coordinates
|
* num_mol - number of molecules for writing coordinates
|
||||||
* num_atoms - number of atoms for writing coordinates
|
* num_atoms - number of atoms for writing coordinates
|
||||||
@ -83,7 +85,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
break;
|
break;
|
||||||
case 1:
|
case 1:
|
||||||
// for envir
|
// for envir and frad
|
||||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
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+1] = cur_coords[1];
|
||||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||||
@ -101,6 +103,29 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
|
|
||||||
*num_atoms = *num_atoms + 1;
|
*num_atoms = *num_atoms + 1;
|
||||||
break;
|
break;
|
||||||
|
case 2:
|
||||||
|
// for agl
|
||||||
|
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 1;
|
default: return 1;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -22,6 +22,7 @@ int search_envir (const int num_of_mol, const int num_mol, const float *centr_co
|
|||||||
int i;
|
int i;
|
||||||
/* r - radius
|
/* r - radius
|
||||||
*/
|
*/
|
||||||
|
|
||||||
*num_needed_mol = 0;
|
*num_needed_mol = 0;
|
||||||
|
|
||||||
for (i=0; i<8*num_mol; i++)
|
for (i=0; i<8*num_mol; i++)
|
||||||
|
|||||||
@ -3,12 +3,12 @@
|
|||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
#include <string.h>
|
#include <string.h>
|
||||||
|
|
||||||
// #include "add_main.h"
|
#include "add_main.h"
|
||||||
// #include "coords.h"
|
#include "coords.h"
|
||||||
// #include "envir_search.h"
|
#include "envir_search.h"
|
||||||
// #include "messages.h"
|
#include "messages.h"
|
||||||
// #include "print_struct.h"
|
#include "print_struct.h"
|
||||||
// #include "set_center.h"
|
#include "set_center.h"
|
||||||
|
|
||||||
|
|
||||||
int main(int argc, char *argv[])
|
int main(int argc, char *argv[])
|
||||||
|
|||||||
@ -1,7 +1,8 @@
|
|||||||
cmake_minimum_required (VERSION 2.8)
|
cmake_minimum_required (VERSION 2.8)
|
||||||
|
|
||||||
cmake_policy(SET CMP0011 NEW)
|
|
||||||
cmake_policy(SET CMP0003 OLD)
|
cmake_policy(SET CMP0003 OLD)
|
||||||
|
cmake_policy(SET CMP0011 NEW)
|
||||||
|
cmake_policy(SET CMP0015 NEW)
|
||||||
|
|
||||||
# set project name
|
# set project name
|
||||||
set (PROJECT statgen)
|
set (PROJECT statgen)
|
||||||
@ -28,4 +29,4 @@ set (LIBRARIES)
|
|||||||
set (TARGETS "")
|
set (TARGETS "")
|
||||||
set (HEADERS "")
|
set (HEADERS "")
|
||||||
|
|
||||||
add_subdirectory (src)
|
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||||
61
statgen/about.dox
Normal file
61
statgen/about.dox
Normal file
@ -0,0 +1,61 @@
|
|||||||
|
/*! @mainpage statgen
|
||||||
|
*
|
||||||
|
* @section intro_sec Introduction
|
||||||
|
*
|
||||||
|
* <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>
|
||||||
|
* 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
|
||||||
|
* </pre>
|
||||||
|
*
|
||||||
|
* @page Install
|
||||||
|
*
|
||||||
|
* @section Requirements Requirements
|
||||||
|
* The application statgen 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.1.0.1 (2013-07-27)
|
||||||
|
* * initial release
|
||||||
|
*/
|
||||||
BIN
statgen/logo.png
Executable file
BIN
statgen/logo.png
Executable file
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
@ -3,62 +3,27 @@ set ("${PROJECT}_VERSION_MINOR" 0)
|
|||||||
set ("${PROJECT}_VERSION_PATCH" 1)
|
set ("${PROJECT}_VERSION_PATCH" 1)
|
||||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
|
||||||
|
|
||||||
message (STATUS ${${PROJECT}_VERSION})
|
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
|
||||||
|
|
||||||
## set files
|
# set files
|
||||||
# main files
|
aux_source_directory (. SOURCES)
|
||||||
set (MAIN_SOURCES main)
|
|
||||||
# not public srcs
|
# set library
|
||||||
set (PRIVATE_CLASSES)
|
|
||||||
# headers only files
|
|
||||||
SET (HEADERS_ONLY)
|
|
||||||
# public srcs
|
|
||||||
set (PUBLIC_CLASSES add_main
|
|
||||||
coords
|
|
||||||
graph
|
|
||||||
int2char
|
|
||||||
messages
|
|
||||||
stat_print
|
|
||||||
stat_select
|
|
||||||
stat_sort
|
|
||||||
summary_stat)
|
|
||||||
# public headers
|
|
||||||
set (PUBLIC_HEADERS)
|
|
||||||
# shared libraries
|
|
||||||
if (CMAKE_COMPILER_IS_GNUCXX)
|
if (CMAKE_COMPILER_IS_GNUCXX)
|
||||||
set (ADDITIONAL_LIB m)
|
set (ADDITIONAL_LIB m)
|
||||||
else ()
|
else ()
|
||||||
set (ADDITIONAL_LIB)
|
set (ADDITIONAL_LIB)
|
||||||
endif()
|
endif()
|
||||||
set (SOURCES)
|
|
||||||
|
|
||||||
# append list
|
|
||||||
foreach (class ${PRIVATE_CLASSES})
|
|
||||||
LIST (APPEND SOURCES ${class}.c)
|
|
||||||
LIST (APPEND HEADERS ${class}.h)
|
|
||||||
endforeach ()
|
|
||||||
|
|
||||||
foreach (class ${HEADERS_ONLY})
|
|
||||||
LIST (APPEND HEADERS ${class}.h)
|
|
||||||
endforeach ()
|
|
||||||
|
|
||||||
foreach (class ${PUBLIC_CLASSES})
|
|
||||||
LIST (APPEND SOURCES ${class}.c)
|
|
||||||
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
|
|
||||||
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
|
|
||||||
endforeach ()
|
|
||||||
|
|
||||||
# message
|
# message
|
||||||
message (STATUS "SOURCES: ${SOURCES}")
|
message (STATUS "SOURCES: ${SOURCES}")
|
||||||
|
|
||||||
# link libraries and compile
|
# link libraries and compile
|
||||||
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
|
add_executable (${PROJECT} ${SOURCES})
|
||||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||||
|
|
||||||
# install properties
|
# install properties
|
||||||
INSTALL (TARGETS ${PROJECT}
|
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||||
DESTINATION bin)
|
|
||||||
if (ADD_INCLUDE)
|
if (ADD_INCLUDE)
|
||||||
INSTALL (FILES ${PUBLIC_HEADERS}
|
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||||
DESTINATION include/${PROJECT})
|
|
||||||
endif ()
|
endif ()
|
||||||
@ -1,14 +1,43 @@
|
|||||||
/* Additional library for main.c (statgen)
|
/**
|
||||||
|
* @file
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
// #include "messages.h"
|
#include "messages.h"
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn error_checking
|
||||||
|
*/
|
||||||
int error_checking (const float *cell, const int from, const char *input,
|
int error_checking (const float *cell, const int from, const char *input,
|
||||||
const int max_depth, const int num_of_inter, const char *output,
|
const int max_depth, const int num_of_inter, const char *output,
|
||||||
const int to, const int type_inter)
|
const int to, const int type_inter)
|
||||||
|
/**
|
||||||
|
* @brief function that checks errors in input variables
|
||||||
|
* @code
|
||||||
|
* error_checking (cell, from, input, max_depth, num_of_inter, output, to,
|
||||||
|
* type_inter);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param cell massive of cell size
|
||||||
|
* @param from first trajectory step
|
||||||
|
* @param input mask of trajectory files
|
||||||
|
* @param max_depth max depth for check cycles in graph analyze
|
||||||
|
* @param num_of_inter number of different interactions
|
||||||
|
* @param output output file name
|
||||||
|
* @param to last trajectory step
|
||||||
|
* @param type_inter number of atoms for interactions
|
||||||
|
*
|
||||||
|
* @return 11 - error in 'type_inter'
|
||||||
|
* @return 12 - error in 'cell'
|
||||||
|
* @return 13 - error in 'to' or 'from'
|
||||||
|
* @return 14 - error in 'num_of_inter'
|
||||||
|
* @return 15 - error in 'input'
|
||||||
|
* @return 16 - error in 'output'
|
||||||
|
* @return 19 - error in 'max_depth'
|
||||||
|
* @return 0 - exit without errors
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
if ((type_inter == 0) || (type_inter > 4))
|
if ((type_inter == 0) || (type_inter > 4))
|
||||||
return 11;
|
return 11;
|
||||||
@ -29,10 +58,35 @@ int error_checking (const float *cell, const int from, const char *input,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn printing_head
|
||||||
|
*/
|
||||||
int printing_head (const char *output, const int log, const int quiet,
|
int printing_head (const char *output, const int log, const int quiet,
|
||||||
const char *input, const int from, const int to, const float *cell,
|
const char *input, const int from, const int to, const float *cell,
|
||||||
const int type_inter, const int *label_atom,
|
const int type_inter, const int *label_atom,
|
||||||
const int num_of_inter, const float *crit, const int max_depth)
|
const int num_of_inter, const float *crit, const int max_depth)
|
||||||
|
/**
|
||||||
|
* @brief function that prints header in output file
|
||||||
|
* @code
|
||||||
|
* printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
|
||||||
|
* num_of_inter, crit, max_depth);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param output output file nams
|
||||||
|
* @param log status of log-mode
|
||||||
|
* @param quiet status of quiet-mode
|
||||||
|
* @param input mask of trajectory files
|
||||||
|
* @param from first trajectory step
|
||||||
|
* @param to last trajectory step
|
||||||
|
* @param cell massive of cell size
|
||||||
|
* @param type_inter number of atoms for interactions
|
||||||
|
* @param label_atom massive of atom types for interactions
|
||||||
|
* @param num_of_inter number of different interactions
|
||||||
|
* @param crit massive of criteria
|
||||||
|
* @param max_depth maximum depth for check cycles in graph analyze
|
||||||
|
*
|
||||||
|
* @return 0 - exit without errors
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
int i, j;
|
int i, j;
|
||||||
FILE *f_out;
|
FILE *f_out;
|
||||||
@ -65,9 +119,26 @@ int printing_head (const char *output, const int log, const int quiet,
|
|||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn print_message
|
||||||
|
*/
|
||||||
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
|
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
|
||||||
const int mode, const char *str)
|
const int mode, const char *str)
|
||||||
|
/**
|
||||||
|
* @brief function that prints message in log and stdout
|
||||||
|
* @code
|
||||||
|
* print_message (quiet, stdout, log, f_log, 0, str);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param quiet status of quiet-mode
|
||||||
|
* @param std_output stdout
|
||||||
|
* @param log status of log-mode
|
||||||
|
* @param f_log log file
|
||||||
|
* @param mode number of message in "messages.c"
|
||||||
|
* @param str additional text in message
|
||||||
|
*
|
||||||
|
* @return 0 - exit without errors
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
if ((quiet != 1) && (std_output != stderr))
|
if ((quiet != 1) && (std_output != stderr))
|
||||||
message (0, mode, str, std_output);
|
message (0, mode, str, std_output);
|
||||||
@ -78,8 +149,31 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn set_defaults
|
||||||
|
*/
|
||||||
int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth,
|
int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth,
|
||||||
int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
|
int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
|
||||||
|
/**
|
||||||
|
* @brief function for set default values of variables
|
||||||
|
* @code
|
||||||
|
* set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
|
||||||
|
* &type_inter, &quiet);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param cell massive of cell size
|
||||||
|
* @param from first trajectory step
|
||||||
|
* @param input mask of trajectory files
|
||||||
|
* @param log status of log-mode
|
||||||
|
* @param max_depth maximum depth for check cycles in graph analyze
|
||||||
|
* @param num_of_inter number of different interactions
|
||||||
|
* @param output output file name
|
||||||
|
* @param to last trajectory step
|
||||||
|
* @param type_inter number of atoms for interactions
|
||||||
|
* @param quiet status of quiet-mode
|
||||||
|
*
|
||||||
|
* @return 0 - exit without errors
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
int i;
|
int i;
|
||||||
|
|
||||||
|
|||||||
@ -1,6 +1,23 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef ADD_MAIN_H
|
#ifndef ADD_MAIN_H
|
||||||
#define ADD_MAIN_H
|
#define ADD_MAIN_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn error_checking
|
||||||
|
*/
|
||||||
|
/**
|
||||||
|
* @fn printing_head
|
||||||
|
*/
|
||||||
|
/**
|
||||||
|
* @fn print_message
|
||||||
|
*/
|
||||||
|
/**
|
||||||
|
* @fn set_defaults
|
||||||
|
*/
|
||||||
|
|
||||||
int error_checking (const float *, const int, const char *, const int, const int,
|
int error_checking (const float *, const int, const char *, const int, const int,
|
||||||
const char *, const int, const int);
|
const char *, const int, const int);
|
||||||
int printing_head (const char *, const int, const int, const char *, const int,
|
int printing_head (const char *, const int, const int, const char *, const int,
|
||||||
@ -1,50 +1,68 @@
|
|||||||
/* Library for reading coordinates from input file
|
/**
|
||||||
*
|
* @file
|
||||||
* Usage:
|
|
||||||
* reading_coords (mode, filename, type_interaction, labels,
|
|
||||||
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
|
|
||||||
* label_molecule, type_atoms, coords, char_type_atoms)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn reading_coords
|
||||||
|
*/
|
||||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||||
const int *label_atom, const float *cell, int *num_mol,
|
const int *label_atom, const float *cell, int *num_mol,
|
||||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||||
/* filename - name of file with coordinates
|
/**
|
||||||
* type_inter - type interaction (number of molecules for interaction)
|
* @brief function that reads coordinates from special file format
|
||||||
* label_atom - types of atom for interaction
|
* @code
|
||||||
* cell - cell dimension
|
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol,
|
||||||
* num_mol - number of molecules for writing coordinates
|
* &num_atoms, true_label_mol, label_mol, type_atoms,
|
||||||
* num_atoms - number of atoms for writing coordinates
|
* coords, ch_type_atoms);
|
||||||
* true_label_mol - massive of true numbers of molecule for atoms
|
* @endcode
|
||||||
* label_mol - massive of numbers of molecule for atoms
|
*
|
||||||
* type_atoms - massive of atom types for atoms
|
* @param mode mode of reading; '1' is statgen, '2' is envir or
|
||||||
* coords - massive of coordinates
|
* frad, '3' is agl
|
||||||
* ch_type_atoms - massive of char types for atoms
|
* @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];
|
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;
|
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];
|
float cur_coords[3], *not_tr_coords, ref[3];
|
||||||
FILE *inp;
|
FILE *inp;
|
||||||
/* cur_*, at_symb - temp variables
|
|
||||||
* file_string - temp string variable
|
/* cur_* temp variables
|
||||||
* atoms - total number of atoms in system
|
* at_symb temp variable
|
||||||
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
|
* file_string temp string variable
|
||||||
* ref_mol - number of molecule for reference
|
* atoms total number of atoms in system
|
||||||
* not_tr_coords - not translated coordinates
|
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
|
||||||
* ref - coordinates of reference molecule
|
* ref_mol number of molecule for reference in translation
|
||||||
* inp - file with input data
|
* 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_atoms = 0;
|
||||||
*num_mol = 0;
|
*num_mol = 0;
|
||||||
|
|
||||||
// Reading file
|
/// <pre> reading file </pre>
|
||||||
inp = fopen (filename, "r");
|
inp = fopen (filename, "r");
|
||||||
if (inp == NULL)
|
if (inp == NULL)
|
||||||
return 1;
|
return 1;
|
||||||
@ -59,10 +77,11 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
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);
|
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||||
|
|
||||||
|
// reading variables according to selected mode
|
||||||
switch (mode)
|
switch (mode)
|
||||||
{
|
{
|
||||||
case 0:
|
case 0:
|
||||||
// for statgen
|
// mode == 0 (selected atoms)
|
||||||
for (j=0; j<type_inter; j++)
|
for (j=0; j<type_inter; j++)
|
||||||
if (cur_at_type == label_atom[j])
|
if (cur_at_type == label_atom[j])
|
||||||
{
|
{
|
||||||
@ -83,7 +102,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
break;
|
break;
|
||||||
case 1:
|
case 1:
|
||||||
// for envir
|
// mode == 1 (all atoms)
|
||||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
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+1] = cur_coords[1];
|
||||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||||
@ -101,18 +120,41 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
|
|
||||||
*num_atoms = *num_atoms + 1;
|
*num_atoms = *num_atoms + 1;
|
||||||
break;
|
break;
|
||||||
default: return 1;
|
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);
|
fclose (inp);
|
||||||
|
|
||||||
// Translation
|
/// <pre> translation </pre>
|
||||||
tr_num_atoms = *num_atoms;
|
tr_num_atoms = *num_atoms;
|
||||||
for (i=0; i<*num_atoms; i++)
|
for (i=0; i<*num_atoms; i++)
|
||||||
for (j=0; j<3; j++)
|
for (j=0; j<3; j++)
|
||||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||||
|
|
||||||
// Assign initial value to reference coordinates
|
// assign initial value to reference coordinates
|
||||||
ref_mol = label_mol[0];
|
ref_mol = label_mol[0];
|
||||||
for (i=0; i<3; i++)
|
for (i=0; i<3; i++)
|
||||||
ref[i] = coords[3*0+i];
|
ref[i] = coords[3*0+i];
|
||||||
@ -129,7 +171,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
for (x=0; x<3; x++)
|
for (x=0; x<3; x++)
|
||||||
{
|
{
|
||||||
if (ref[x] >= 0.0)
|
if (ref[x] >= 0.0)
|
||||||
// if xyz >= 0.0 A
|
// if xyz >= 0.0 A
|
||||||
{
|
{
|
||||||
for (j=0; j<3; j++)
|
for (j=0; j<3; j++)
|
||||||
if (j == x)
|
if (j == x)
|
||||||
@ -142,7 +184,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
tr_num_atoms++;
|
tr_num_atoms++;
|
||||||
}
|
}
|
||||||
else
|
else
|
||||||
// if xyz < 0.0 A
|
// if xyz < 0.0 A
|
||||||
{
|
{
|
||||||
for (j=0; j<3; j++)
|
for (j=0; j<3; j++)
|
||||||
if (j == x)
|
if (j == x)
|
||||||
@ -161,7 +203,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
for (y=x+1; y<3; y++)
|
for (y=x+1; y<3; y++)
|
||||||
{
|
{
|
||||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||||
// if xyz and xyz >= 0.0 A
|
// if xyz and xyz >= 0.0 A
|
||||||
{
|
{
|
||||||
for (j=0; j<3; j++)
|
for (j=0; j<3; j++)
|
||||||
if ((j == x) || (j == y))
|
if ((j == x) || (j == y))
|
||||||
@ -175,7 +217,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||||
// if xyz and xyz < 0.0 A
|
// if xyz and xyz < 0.0 A
|
||||||
{
|
{
|
||||||
for (j=0; j<3; j++)
|
for (j=0; j<3; j++)
|
||||||
if ((j == x) || (j == y))
|
if ((j == x) || (j == y))
|
||||||
@ -191,7 +233,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
|
|
||||||
for (y=0; y<3; y++)
|
for (y=0; y<3; y++)
|
||||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||||
// if xyz OR xyz >= 0.0
|
// if xyz OR xyz >= 0.0
|
||||||
{
|
{
|
||||||
for (j=0; j<3; j++)
|
for (j=0; j<3; j++)
|
||||||
{
|
{
|
||||||
@ -210,7 +252,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||||
// if x and y and z >= 0.0 A
|
// 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+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+1] = not_tr_coords[3*i+1] - cell[1];
|
||||||
@ -222,7 +264,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
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
|
// 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+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+1] = not_tr_coords[3*i+1] - cell[1];
|
||||||
@ -234,7 +276,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
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
|
// 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+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+1] = not_tr_coords[3*i+1] + cell[1];
|
||||||
@ -246,7 +288,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
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
|
// 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+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+1] = not_tr_coords[3*i+1] - cell[1];
|
||||||
@ -258,7 +300,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
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
|
// 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+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+1] = not_tr_coords[3*i+1] + cell[1];
|
||||||
@ -270,7 +312,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
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
|
// 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+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+1] = not_tr_coords[3*i+1] - cell[1];
|
||||||
@ -282,7 +324,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
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
|
// 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+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+1] = not_tr_coords[3*i+1] + cell[1];
|
||||||
@ -294,7 +336,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
|
|
||||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||||
// if x and y and z < 0.0 A
|
// 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+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+1] = not_tr_coords[3*i+1] + cell[1];
|
||||||
@ -306,7 +348,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// free memory
|
/// <pre> free memory </pre>
|
||||||
free (not_tr_coords);
|
free (not_tr_coords);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
|
|||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef COORDS_H
|
#ifndef COORDS_H
|
||||||
#define COORDS_H
|
#define COORDS_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn reading_coords
|
||||||
|
*/
|
||||||
|
|
||||||
int reading_coords (const int, const char *, const int, const int *,
|
int reading_coords (const int, const char *, const int, const int *,
|
||||||
const float *, int *, int *, int *, int *, int *, float *,
|
const float *, int *, int *, int *, int *, int *, float *,
|
||||||
char *);
|
char *);
|
||||||
@ -1,46 +1,77 @@
|
|||||||
/* Library for graph structure analyze
|
/**
|
||||||
* Usage:
|
* @file
|
||||||
* graph_analyze (N, connect, max_depth, isomorphism_class)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <math.h>
|
#include <math.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn check_cycle
|
||||||
|
*/
|
||||||
int check_cycle (const int N, const int *pn)
|
int check_cycle (const int N, const int *pn)
|
||||||
// function to return number of cycles
|
/**
|
||||||
|
* @brief function that calculates number of cycles in graph
|
||||||
|
* @code
|
||||||
|
* cycle = check_cycle (N, pn);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param N number of vertexes
|
||||||
|
* @param pn massive of number of vertexes with weight equals to i
|
||||||
|
*
|
||||||
|
* @return number of cycles
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
int cycle, i;
|
int cycle, i;
|
||||||
/* cycle - number of cycle
|
/* cycle number of cycle
|
||||||
*/
|
*/
|
||||||
|
|
||||||
cycle = 0;
|
cycle = 0;
|
||||||
for (i=1; i<N; i++)
|
for (i=1; i<N; i++)
|
||||||
cycle += i*pn[i];
|
cycle += i*pn[i];
|
||||||
|
|
||||||
// for linear (0.5*cycle == N-1)
|
// for linear (0.5*cycle == N-1)
|
||||||
cycle = 0.5 * cycle - (N - 1);
|
cycle = 0.5 * cycle - (N - 1);
|
||||||
|
|
||||||
return cycle;
|
return cycle;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn check_cycle_size
|
||||||
|
*/
|
||||||
int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cycle)
|
int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cycle)
|
||||||
// function to return number of cycles of certain size
|
/**
|
||||||
|
* @brief function that returns number of cycles different size
|
||||||
|
* @code
|
||||||
|
* check_cycle_size (N, matrix, depth, n_cycle);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param N number of vertexes
|
||||||
|
* @param matrix connectivity matrix
|
||||||
|
* @param depth depth of search (maximum number of vertexes in cycle)
|
||||||
|
* @param n_cycle massive of number of cycle with number of vertexes
|
||||||
|
* equals to i
|
||||||
|
*
|
||||||
|
* @return 1 - memory error
|
||||||
|
* @return 0 - exit without errors
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
int cur_N, cycle, i, j, k, n, p, *vertex;
|
int cur_N, cycle, i, j, k, n, p, *vertex;
|
||||||
/* cur_N - current number of elements in submatrix
|
/* cur_N current number of elements in submatrix
|
||||||
* cycle - if (cycle == 1) that cycle exist
|
* cycle if (cycle == 1) that cycle exist
|
||||||
* n - number of samples
|
* n number of samples
|
||||||
* vertex - vertexes of subgraph
|
* vertex vertexes of subgraph
|
||||||
*/
|
*/
|
||||||
|
|
||||||
vertex = (int *) malloc (N * sizeof (int));
|
vertex = (int *) malloc (N * sizeof (int));
|
||||||
|
if (vertex == NULL)
|
||||||
|
return 1;
|
||||||
for (i=0; i<depth-2; i++)
|
for (i=0; i<depth-2; i++)
|
||||||
n_cycle[i] = 0;
|
n_cycle[i] = 0;
|
||||||
|
|
||||||
// matrix generation from
|
// matrix generation from
|
||||||
// http://wincode.org/acm-icpc/subsets-generation
|
// http://wincode.org/acm-icpc/subsets-generation
|
||||||
n = pow (2, N);
|
n = pow (2, N);
|
||||||
for (i=0; i<n; i++)
|
for (i=0; i<n; i++)
|
||||||
{
|
{
|
||||||
@ -54,7 +85,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
|
|||||||
|
|
||||||
if ((cur_N > 2) && (cur_N <= depth))
|
if ((cur_N > 2) && (cur_N <= depth))
|
||||||
{
|
{
|
||||||
// copy connectivity matrix
|
// copy connectivity matrix
|
||||||
cycle = 1;
|
cycle = 1;
|
||||||
for (j=0; j<cur_N; j++)
|
for (j=0; j<cur_N; j++)
|
||||||
{
|
{
|
||||||
@ -65,7 +96,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
|
|||||||
cycle = 0;
|
cycle = 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
// analyze subgraph
|
// analyze subgraph
|
||||||
if (cycle == 1)
|
if (cycle == 1)
|
||||||
n_cycle[cur_N-3]++;
|
n_cycle[cur_N-3]++;
|
||||||
}
|
}
|
||||||
@ -77,32 +108,56 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn check_tail
|
||||||
|
*/
|
||||||
int check_tail (const int *pn)
|
int check_tail (const int *pn)
|
||||||
// function to return number of tails
|
/**
|
||||||
|
* @brief function that calculates number of tails
|
||||||
|
* @code
|
||||||
|
* tails = check_tail (pn);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param pn massive of number of vertexes with weight equals to i
|
||||||
|
*
|
||||||
|
* @return number of tails
|
||||||
|
*/
|
||||||
{
|
{
|
||||||
return pn[1];
|
return pn[1];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn graph_analyze
|
||||||
|
*/
|
||||||
int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso)
|
int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso)
|
||||||
/* N - number of vertex in graph
|
/**
|
||||||
* matrix - connectivity matrix
|
* @brief function that analyzes graph isomorhic class
|
||||||
* max_depth - maximum depth for check_cycle_size
|
* @code
|
||||||
* iso - isomorphism class
|
* graph_analyze (N, matrix, max_depth, iso);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param N number of vertexes
|
||||||
|
* @param matrix connectivity matrix
|
||||||
|
* @param max_depth maximum depth of search for check_cycle_size
|
||||||
|
* @param iso isomorphism class
|
||||||
|
*
|
||||||
|
* @return 1 - memory error
|
||||||
|
* @return 0 - exit without errors
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
int depth, i, j, *n_cycle, p, *pn;
|
int depth, i, j, *n_cycle, p, *pn;
|
||||||
/* depth - depth for check_cycle_size
|
/* depth depth of search for check_cycle_size
|
||||||
* n_cycle - number of cycle
|
* n_cycle number of cycle
|
||||||
* p - current weight
|
* p current weight
|
||||||
* pn - total weight
|
* pn massive of number of vertexes with weight equals to i
|
||||||
*/
|
*/
|
||||||
|
|
||||||
if (max_depth > N)
|
if (max_depth > N)
|
||||||
depth = N;
|
depth = N;
|
||||||
else
|
else
|
||||||
depth = max_depth;
|
depth = max_depth;
|
||||||
// convert to matrix of weight
|
// convert to matrix of weight
|
||||||
pn = (int *) malloc (N * sizeof (int));
|
pn = (int *) malloc (N * sizeof (int));
|
||||||
n_cycle = (int *) malloc ((depth - 2) * sizeof (int));
|
n_cycle = (int *) malloc ((depth - 2) * sizeof (int));
|
||||||
if ((pn == NULL) ||
|
if ((pn == NULL) ||
|
||||||
@ -129,6 +184,7 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
|
|||||||
iso[i+2] = n_cycle[i];
|
iso[i+2] = n_cycle[i];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// free memory
|
||||||
free (n_cycle);
|
free (n_cycle);
|
||||||
free (pn);
|
free (pn);
|
||||||
|
|
||||||
|
|||||||
@ -1,6 +1,23 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef GRAPH_H
|
#ifndef GRAPH_H
|
||||||
#define GRAPH_H
|
#define GRAPH_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn graph_analyze
|
||||||
|
*/
|
||||||
|
/**
|
||||||
|
* @fn check_cycle
|
||||||
|
*/
|
||||||
|
/**
|
||||||
|
* @fn check_cycle_size
|
||||||
|
*/
|
||||||
|
/**
|
||||||
|
* @fn check_tail
|
||||||
|
*/
|
||||||
|
|
||||||
int graph_analyze (const int, const int *, const int, int *);
|
int graph_analyze (const int, const int *, const int, int *);
|
||||||
int check_cycle (const int, const int *);
|
int check_cycle (const int, const int *);
|
||||||
int check_cycle_size (const int, const int *, const int, int *);
|
int check_cycle_size (const int, const int *, const int, int *);
|
||||||
@ -1,12 +1,22 @@
|
|||||||
/* Library for converting integer to string
|
/**
|
||||||
* Usage
|
* @file
|
||||||
* char = conv (number, position)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn conv
|
||||||
|
*/
|
||||||
char conv (const int fnumb, const int dig_pos)
|
char conv (const int fnumb, const int dig_pos)
|
||||||
/* fnumb - integer
|
/**
|
||||||
* dig_pos - position
|
* @brief function that converts from integer to char
|
||||||
|
* @code
|
||||||
|
* char = conv (N, 0);
|
||||||
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param fnumb integer
|
||||||
|
* @param dig_pos position: ones=1, decimals=2, hundreds=3
|
||||||
|
*
|
||||||
|
* @return char
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
int d, h, o;
|
int d, h, o;
|
||||||
|
|||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef INT2CHAR_H
|
#ifndef INT2CHAR_H
|
||||||
#define INT2CHAR_H
|
#define INT2CHAR_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn conv
|
||||||
|
*/
|
||||||
|
|
||||||
char conv (const int, const int);
|
char conv (const int, const int);
|
||||||
|
|
||||||
#endif /* INT2CHAR_H */
|
#endif /* INT2CHAR_H */
|
||||||
@ -1,17 +1,21 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#include <math.h>
|
#include <math.h>
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
#include <string.h>
|
#include <string.h>
|
||||||
#include <time.h>
|
#include <time.h>
|
||||||
|
|
||||||
// #include "add_main.h"
|
#include "add_main.h"
|
||||||
// #include "coords.h"
|
#include "coords.h"
|
||||||
// #include "int2char.h"
|
#include "int2char.h"
|
||||||
// #include "messages.h"
|
#include "messages.h"
|
||||||
// #include "stat_print.h"
|
#include "stat_print.h"
|
||||||
// #include "stat_select.h"
|
#include "stat_select.h"
|
||||||
// #include "stat_sort.h"
|
#include "stat_sort.h"
|
||||||
// #include "summary_stat.h"
|
#include "summary_stat.h"
|
||||||
|
|
||||||
|
|
||||||
int main (int argc, char *argv[])
|
int main (int argc, char *argv[])
|
||||||
@ -26,40 +30,40 @@ int main (int argc, char *argv[])
|
|||||||
int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms,
|
int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms,
|
||||||
num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to,
|
num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to,
|
||||||
*true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
|
*true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
|
||||||
/* input - mask of input files
|
/* input mask of trajectory files
|
||||||
* logfile - log file name
|
* logfile log file name
|
||||||
* output - output file name
|
* output output file name
|
||||||
*
|
*
|
||||||
* cell - cell dimension
|
* cell massive of cell size
|
||||||
* coords - massive of coordinates
|
* coords massive of coordinates
|
||||||
* crit - massive of criteria
|
* crit massive of criteria
|
||||||
*
|
*
|
||||||
* agl - massive of aglomerates
|
* agl massive of aglomerates
|
||||||
* connect - connectivity graph for all molecules
|
* connect connectivity graph for all molecules
|
||||||
* from - start point
|
* from first trajectory step
|
||||||
* label_atom - types of atom for interaction
|
* label_atom massive of atom types for interactions
|
||||||
* label_mol - massive of numbers of molecule for atoms
|
* label_mol massive of numbers of molecule for atoms
|
||||||
* log - status of log-mode
|
* log status of log-mode
|
||||||
* max_depth - max depth for check cycles in graph analyze
|
* max_depth maximum depth for check cycles in graph analyze
|
||||||
* num_atoms - number of atoms for writing coordinates
|
* num_atoms number of atoms
|
||||||
* num_mol - number of molecules for writing coordinates
|
* num_mol number of molecules
|
||||||
* num_mol_agl - massive of numbers of molecule in aglomerates
|
* num_mol_agl massive of number of molecules in aglomerates
|
||||||
* num_of_inter - number of different interactions
|
* num_of_inter number of different interactions
|
||||||
* stat - massive of statistics
|
* stat massive of statistic
|
||||||
* stat_all - massive of summary statistics
|
* stat_all massive of summary statistic
|
||||||
* step - $(to - from + 1)
|
* step $(to - from + 1)
|
||||||
* to - finish point
|
* to last trajectory step
|
||||||
* true_label_mol - massive of true numbers of molecule for atoms
|
* true_label_mol massive of true numbers of molecule for atoms
|
||||||
* type_agl - massive of numbers of aglomerate types
|
* type_agl massive of number of aglomerate types
|
||||||
* type_atoms - massive of atom types for atoms
|
* type_atoms massive of atom types
|
||||||
* type_inter - type interaction (number of molecules for interaction)
|
* type_inter number of atoms for interactions
|
||||||
* quiet - status of quiet-mode
|
* quiet status of quiet-mode
|
||||||
*/
|
*/
|
||||||
|
|
||||||
set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
|
set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
|
||||||
&type_inter, &quiet);
|
&type_inter, &quiet);
|
||||||
|
|
||||||
// reading number of interactions
|
// reading number of interactions
|
||||||
for (i=1; i<argc; i++)
|
for (i=1; i<argc; i++)
|
||||||
if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
||||||
num_of_inter++;
|
num_of_inter++;
|
||||||
@ -71,7 +75,7 @@ int main (int argc, char *argv[])
|
|||||||
num_of_inter = 0;
|
num_of_inter = 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
// reading arguments
|
// reading arguments
|
||||||
for (i=1; i<argc; i++)
|
for (i=1; i<argc; i++)
|
||||||
{
|
{
|
||||||
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
||||||
@ -99,13 +103,13 @@ int main (int argc, char *argv[])
|
|||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
|
||||||
// mask of input files
|
// mask of input files
|
||||||
{
|
{
|
||||||
strcpy (input, argv[i+1]);
|
strcpy (input, argv[i+1]);
|
||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
|
||||||
// steps
|
// steps
|
||||||
{
|
{
|
||||||
sscanf (argv[i+1], "%i,%i", &from, &to);
|
sscanf (argv[i+1], "%i,%i", &from, &to);
|
||||||
if (from > to)
|
if (from > to)
|
||||||
@ -118,13 +122,13 @@ int main (int argc, char *argv[])
|
|||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
|
||||||
// cell size
|
// cell size
|
||||||
{
|
{
|
||||||
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
|
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
|
||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
|
||||||
// atom types
|
// atom types
|
||||||
{
|
{
|
||||||
type_inter = 1;
|
type_inter = 1;
|
||||||
for (j=0; j<strlen(argv[i+1]); j++)
|
for (j=0; j<strlen(argv[i+1]); j++)
|
||||||
@ -153,7 +157,7 @@ int main (int argc, char *argv[])
|
|||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
||||||
// criteria
|
// criteria
|
||||||
{
|
{
|
||||||
index = 0;
|
index = 0;
|
||||||
sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
|
sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
|
||||||
@ -172,26 +176,26 @@ int main (int argc, char *argv[])
|
|||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
|
||||||
// output file
|
// output file
|
||||||
{
|
{
|
||||||
strcpy (output, argv[i+1]);
|
strcpy (output, argv[i+1]);
|
||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'g'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'g'))
|
||||||
// graph isomorphism scan
|
// graph isomorphism scan
|
||||||
{
|
{
|
||||||
sscanf (argv[i+1], "%i", &max_depth);
|
sscanf (argv[i+1], "%i", &max_depth);
|
||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
|
||||||
// log mode
|
// log mode
|
||||||
{
|
{
|
||||||
log = 1;
|
log = 1;
|
||||||
strcpy (logfile, argv[i+1]);
|
strcpy (logfile, argv[i+1]);
|
||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
|
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
|
||||||
// quiet mode
|
// quiet mode
|
||||||
{
|
{
|
||||||
quiet = 1;
|
quiet = 1;
|
||||||
}
|
}
|
||||||
@ -203,7 +207,7 @@ int main (int argc, char *argv[])
|
|||||||
print_message (quiet, stdout, log, f_log, 0, argv[0]);
|
print_message (quiet, stdout, log, f_log, 0, argv[0]);
|
||||||
print_message (quiet, stdout, log, f_log, 1, argv[0]);
|
print_message (quiet, stdout, log, f_log, 1, argv[0]);
|
||||||
|
|
||||||
// error checking
|
// error checking
|
||||||
error = error_checking (cell, from, input, max_depth, num_of_inter, output, to,
|
error = error_checking (cell, from, input, max_depth, num_of_inter, output, to,
|
||||||
type_inter);
|
type_inter);
|
||||||
if (error != 0)
|
if (error != 0)
|
||||||
@ -214,8 +218,8 @@ int main (int argc, char *argv[])
|
|||||||
|
|
||||||
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
||||||
|
|
||||||
// processing
|
// processing
|
||||||
// initial variables
|
// initial variables
|
||||||
k = strlen (input);
|
k = strlen (input);
|
||||||
strcpy (filename, input);
|
strcpy (filename, input);
|
||||||
filename[k] = '.';
|
filename[k] = '.';
|
||||||
@ -237,13 +241,13 @@ int main (int argc, char *argv[])
|
|||||||
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
|
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
|
||||||
type_agl = (int *) malloc ((max_depth + 2) * sizeof (int));
|
type_agl = (int *) malloc ((max_depth + 2) * sizeof (int));
|
||||||
type_atoms = (int *) malloc (8 * num_atoms * sizeof (int));
|
type_atoms = (int *) malloc (8 * num_atoms * sizeof (int));
|
||||||
// temporary declaration of variables
|
// temporary declaration of variables
|
||||||
agl = (int *) malloc (2 * 2 * sizeof (int));
|
agl = (int *) malloc (2 * 2 * sizeof (int));
|
||||||
connect = (int *) malloc (2 * 2 * sizeof (int));
|
connect = (int *) malloc (2 * 2 * sizeof (int));
|
||||||
num_mol_agl = (int *) malloc (2 * sizeof (int));
|
num_mol_agl = (int *) malloc (2 * sizeof (int));
|
||||||
stat = (int *) malloc (2 * sizeof (int));
|
stat = (int *) malloc (2 * sizeof (int));
|
||||||
stat_all = (int *) malloc (2 * sizeof (int));
|
stat_all = (int *) malloc (2 * sizeof (int));
|
||||||
// error checking
|
// error checking
|
||||||
if ((coords == NULL) ||
|
if ((coords == NULL) ||
|
||||||
(label_mol == NULL) ||
|
(label_mol == NULL) ||
|
||||||
(true_label_mol == NULL) ||
|
(true_label_mol == NULL) ||
|
||||||
@ -258,7 +262,7 @@ int main (int argc, char *argv[])
|
|||||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||||
return 17;
|
return 17;
|
||||||
}
|
}
|
||||||
// set type_agl to zero
|
// set type_agl to zero
|
||||||
for (i=0; i<max_depth+2; i++)
|
for (i=0; i<max_depth+2; i++)
|
||||||
type_agl[i] = 0;
|
type_agl[i] = 0;
|
||||||
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n\
|
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n\
|
||||||
@ -280,15 +284,15 @@ int main (int argc, char *argv[])
|
|||||||
sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
|
sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
|
||||||
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||||
|
|
||||||
// head
|
// head
|
||||||
printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
|
printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
|
||||||
num_of_inter, crit, max_depth);
|
num_of_inter, crit, max_depth);
|
||||||
|
|
||||||
// main cycle
|
// main cycle
|
||||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||||
for (i=from; i<to+1; i++)
|
for (i=from; i<to+1; i++)
|
||||||
{
|
{
|
||||||
// reading coordinates
|
// reading coordinates
|
||||||
filename[k+1] = conv (i, 3);
|
filename[k+1] = conv (i, 3);
|
||||||
filename[k+2] = conv (i, 2);
|
filename[k+2] = conv (i, 2);
|
||||||
filename[k+3] = conv (i, 1);
|
filename[k+3] = conv (i, 1);
|
||||||
@ -304,7 +308,7 @@ int main (int argc, char *argv[])
|
|||||||
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||||
}
|
}
|
||||||
|
|
||||||
// resize dynamic arrays
|
// resize dynamic arrays
|
||||||
agl = (int *) realloc (agl, num_mol * num_mol * sizeof (int));
|
agl = (int *) realloc (agl, num_mol * num_mol * sizeof (int));
|
||||||
connect = (int *) realloc (connect, num_mol * num_mol * sizeof (int));
|
connect = (int *) realloc (connect, num_mol * num_mol * sizeof (int));
|
||||||
num_mol_agl = (int *) realloc (num_mol_agl, num_mol * sizeof (int));
|
num_mol_agl = (int *) realloc (num_mol_agl, num_mol * sizeof (int));
|
||||||
@ -315,7 +319,7 @@ int main (int argc, char *argv[])
|
|||||||
for (j=0; j<num_mol; j++)
|
for (j=0; j<num_mol; j++)
|
||||||
stat_all[j] = 0;
|
stat_all[j] = 0;
|
||||||
}
|
}
|
||||||
// error checking
|
// error checking
|
||||||
if ((agl == NULL) ||
|
if ((agl == NULL) ||
|
||||||
(connect == NULL) ||
|
(connect == NULL) ||
|
||||||
(num_mol_agl == NULL) ||
|
(num_mol_agl == NULL) ||
|
||||||
@ -327,7 +331,7 @@ int main (int argc, char *argv[])
|
|||||||
}
|
}
|
||||||
print_message (quiet, stdout, log, f_log, 9, argv[0]);
|
print_message (quiet, stdout, log, f_log, 9, argv[0]);
|
||||||
|
|
||||||
// analyze
|
// analyze
|
||||||
if (error == 0)
|
if (error == 0)
|
||||||
{
|
{
|
||||||
error = 1;
|
error = 1;
|
||||||
@ -352,11 +356,11 @@ int main (int argc, char *argv[])
|
|||||||
|
|
||||||
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||||
print_message (quiet, stdout, log, f_log, 14, output);
|
print_message (quiet, stdout, log, f_log, 14, output);
|
||||||
// tail
|
// tail
|
||||||
summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
|
summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
|
||||||
|
|
||||||
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||||
// free memory
|
// free memory
|
||||||
free (agl);
|
free (agl);
|
||||||
free (connect);
|
free (connect);
|
||||||
free (coords);
|
free (coords);
|
||||||
|
|||||||
@ -1,16 +1,27 @@
|
|||||||
/* Library for printing messages at output
|
/**
|
||||||
*
|
* @file
|
||||||
* Usage:
|
|
||||||
* message (log, mode, text, output)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include <time.h>
|
#include <time.h>
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn message
|
||||||
|
*/
|
||||||
int message (const int log, const int mode, const char *text, FILE *output)
|
int message (const int log, const int mode, const char *text, FILE *output)
|
||||||
/* mode - number of message
|
/**
|
||||||
* text - additional text
|
* @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 0 - exit without errors
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
char out[4096];
|
char out[4096];
|
||||||
@ -18,6 +29,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
|
|||||||
if (log == 1)
|
if (log == 1)
|
||||||
{
|
{
|
||||||
char time_str[256];
|
char time_str[256];
|
||||||
|
|
||||||
time_t t = time (NULL);
|
time_t t = time (NULL);
|
||||||
struct tm* aTm = localtime (&t);
|
struct tm* aTm = localtime (&t);
|
||||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||||
|
|||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef MESSAGES_H
|
#ifndef MESSAGES_H
|
||||||
#define MESSAGES_H
|
#define MESSAGES_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn message
|
||||||
|
*/
|
||||||
|
|
||||||
int message (const int, const int, const char *, FILE *);
|
int message (const int, const int, const char *, FILE *);
|
||||||
|
|
||||||
#endif /* MESSAGES_H */
|
#endif /* MESSAGES_H */
|
||||||
@ -1,57 +1,69 @@
|
|||||||
/* Library for printing aglomerates
|
/**
|
||||||
*
|
* @file
|
||||||
* Usage:
|
|
||||||
* printing_agl (input_file, output_file, number_of_molecules,
|
|
||||||
* true_label_molecules, num_of_molecules_in_aglomerates, aglomerates,
|
|
||||||
* statistic, max_depth, type_of_aglomerate)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
|
|
||||||
// #include "graph.h"
|
#include "graph.h"
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn printing_agl
|
||||||
|
*/
|
||||||
int printing_agl (const char *input, const char *output, const int *connect,
|
int printing_agl (const char *input, const char *output, const int *connect,
|
||||||
const int num_mol, const int *true_label_mol, const int *num_mol_agl,
|
const int num_mol, const int *true_label_mol, const int *num_mol_agl,
|
||||||
const int *agl, const int *stat, const int max_depth, int *type_agl)
|
const int *agl, const int *stat, const int max_depth, int *type_agl)
|
||||||
/* input - name of file with coordinates
|
/**
|
||||||
* output - name of output file
|
* @brief function that prints aglomerates to output file
|
||||||
* connect - connectivity graph for all molecules
|
* @code
|
||||||
* num_mol - number of molecules
|
* printing_agl (input_file, output_file, number_of_molecules,
|
||||||
* true_label_mol - massive of true numbers of molecule for atoms
|
* true_label_molecules, num_of_molecules_in_aglomerates, aglomerates,
|
||||||
* num_mol_agl - massive of numbers of molecule in aglomerates
|
* statistic, max_depth, type_of_aglomerate);
|
||||||
* agl - massive of aglomerates
|
* @endcode
|
||||||
* stat - massive of statistics
|
*
|
||||||
* max_depth - max depth for check cycles in graph analyze
|
* @param input input file name
|
||||||
* type_agl - massive of numbers of aglomerate types
|
* @param output output file name
|
||||||
|
* @param connect connectivity graph for all molecules
|
||||||
|
* @param num_mol number of molecules
|
||||||
|
* @param true_label_mol massive of true numbers of molecule for atoms
|
||||||
|
* @param num_mol_agl massive of number of molecules in aglomerates
|
||||||
|
* @param agl massive of aglomerates
|
||||||
|
* @param stat massive of statistic
|
||||||
|
* @param max_depth maximum depth for check cycles in graph analyze
|
||||||
|
* @param type_agl massive of number of aglomerate types
|
||||||
|
*
|
||||||
|
* @return 1 - memory error
|
||||||
|
* @return 0 - exit without errors
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
int error, i, *iso, j, k, *label_matrix, *matrix;
|
int error, i, *iso, j, k, *label_matrix, *matrix;
|
||||||
FILE *f_out;
|
FILE *f_out;
|
||||||
/* iso - isomorphic graph in database
|
/* iso isomorphic graph in database
|
||||||
* label_matrix - massive of indexes of molecule
|
* label_matrix massive of indexes of molecule
|
||||||
* matrix - connectivity graph
|
* matrix connectivity graph
|
||||||
* f_out - output file
|
* f_out output file
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
/// <b>Work blocks</b>
|
||||||
|
|
||||||
iso = (int *) malloc (max_depth * sizeof (int));
|
iso = (int *) malloc (max_depth * sizeof (int));
|
||||||
if (iso == NULL)
|
if (iso == NULL)
|
||||||
return 1;
|
return 1;
|
||||||
f_out = fopen (output, "a");
|
f_out = fopen (output, "a");
|
||||||
|
|
||||||
// head
|
/// <pre> print header </pre>
|
||||||
fprintf (f_out, "FILE=%s\nSTATISTIC\n| n | N |\n-----------------\n", input);
|
fprintf (f_out, "FILE=%s\nSTATISTIC\n| n | N |\n-----------------\n", input);
|
||||||
for (i=0; i<num_mol; i++)
|
for (i=0; i<num_mol; i++)
|
||||||
if (stat[i] != 0)
|
if (stat[i] != 0)
|
||||||
fprintf (f_out, " %7i %7i \n", i+1, stat[i]);
|
fprintf (f_out, " %7i %7i \n", i+1, stat[i]);
|
||||||
fprintf (f_out, "-----------------\n");
|
fprintf (f_out, "-----------------\n");
|
||||||
|
|
||||||
// body
|
/// <pre> print body </pre>
|
||||||
for (i=0; i<num_mol; i++)
|
for (i=0; i<num_mol; i++)
|
||||||
if (num_mol_agl[i] > 0)
|
if (num_mol_agl[i] > 0)
|
||||||
{
|
{
|
||||||
// creating connectivity graph
|
/// <pre> creating connectivity graph </pre>
|
||||||
label_matrix = (int *) malloc (num_mol * sizeof (int));
|
label_matrix = (int *) malloc (num_mol * sizeof (int));
|
||||||
matrix = (int *) malloc (num_mol_agl[i] * num_mol_agl[i] * sizeof (int));
|
matrix = (int *) malloc (num_mol_agl[i] * num_mol_agl[i] * sizeof (int));
|
||||||
if ((matrix == NULL) ||
|
if ((matrix == NULL) ||
|
||||||
@ -71,34 +83,34 @@ int printing_agl (const char *input, const char *output, const int *connect,
|
|||||||
matrix[label_matrix[agl[num_mol*i+k]]*num_mol_agl[i]+label_matrix[agl[num_mol*i+j]]] = 1;
|
matrix[label_matrix[agl[num_mol*i+k]]*num_mol_agl[i]+label_matrix[agl[num_mol*i+j]]] = 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// graph topology analyze
|
/// <pre> graph topology analyze </pre>
|
||||||
if (max_depth > 0)
|
if (max_depth > 0)
|
||||||
error = graph_analyze (num_mol_agl[i], matrix, max_depth, iso);
|
error = graph_analyze (num_mol_agl[i], matrix, max_depth, iso);
|
||||||
if (error > 0)
|
if (error > 0)
|
||||||
return 1;
|
return 1;
|
||||||
|
|
||||||
// printing class of aglomerate
|
// print class of aglomerate
|
||||||
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
|
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
|
||||||
for (j=0; j<max_depth; j++)
|
for (j=0; j<max_depth; j++)
|
||||||
{
|
{
|
||||||
// number of tails
|
// number of tails
|
||||||
if (j == 0)
|
if (j == 0)
|
||||||
if (iso[j] > 2)
|
if (iso[j] > 2)
|
||||||
// branched
|
// branched
|
||||||
type_agl[3]++;
|
type_agl[3]++;
|
||||||
else
|
else
|
||||||
// not branched
|
// not branched
|
||||||
type_agl[2]++;
|
type_agl[2]++;
|
||||||
// number of cycles
|
// number of cycles
|
||||||
else if (j == 1)
|
else if (j == 1)
|
||||||
if (iso[j] > 0)
|
if (iso[j] > 0)
|
||||||
// cycle
|
// cycle
|
||||||
type_agl[1]++;
|
type_agl[1]++;
|
||||||
else
|
else
|
||||||
// linear
|
// linear
|
||||||
type_agl[0]++;
|
type_agl[0]++;
|
||||||
else if (j > 1)
|
else if (j > 1)
|
||||||
// number of n_cycles
|
// number of n_cycles
|
||||||
type_agl[j+2] += iso[j];
|
type_agl[j+2] += iso[j];
|
||||||
|
|
||||||
fprintf (f_out, "%i.", iso[j]);
|
fprintf (f_out, "%i.", iso[j]);
|
||||||
@ -108,20 +120,21 @@ int printing_agl (const char *input, const char *output, const int *connect,
|
|||||||
{
|
{
|
||||||
fprintf (f_out, "%7i=", true_label_mol[agl[num_mol*i+j]]);
|
fprintf (f_out, "%7i=", true_label_mol[agl[num_mol*i+j]]);
|
||||||
for (k=0; k<num_mol_agl[i]; k++)
|
for (k=0; k<num_mol_agl[i]; k++)
|
||||||
{
|
|
||||||
if (matrix[j*num_mol_agl[i]+k] == 1)
|
if (matrix[j*num_mol_agl[i]+k] == 1)
|
||||||
fprintf (f_out, "%i,", true_label_mol[agl[num_mol*i+k]]);
|
fprintf (f_out, "%i,", true_label_mol[agl[num_mol*i+k]]);
|
||||||
}
|
|
||||||
fprintf (f_out, "\n");
|
fprintf (f_out, "\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
// free memory
|
/// <pre> free memory </pre>
|
||||||
free (matrix);
|
free (matrix);
|
||||||
free (label_matrix);
|
free (label_matrix);
|
||||||
}
|
}
|
||||||
|
|
||||||
fprintf (f_out, "---------------------------------------------------\n");
|
fprintf (f_out, "---------------------------------------------------\n");
|
||||||
fclose (f_out);
|
fclose (f_out);
|
||||||
|
|
||||||
|
/// <pre> free memory </pre>
|
||||||
free (iso);
|
free (iso);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef STAT_PRINT_H
|
#ifndef STAT_PRINT_H
|
||||||
#define STAT_PRINT_H
|
#define STAT_PRINT_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn printing_agl
|
||||||
|
*/
|
||||||
|
|
||||||
int printing_agl (const char *, const char *, const int *, const int, const int *,
|
int printing_agl (const char *, const char *, const int *, const int, const int *,
|
||||||
const int *, const int *, const int *, const int,int *);
|
const int *, const int *, const int *, const int,int *);
|
||||||
|
|
||||||
@ -1,35 +1,47 @@
|
|||||||
/* Library for creating connectivity matrix
|
/**
|
||||||
*
|
* @file
|
||||||
* Usage:
|
|
||||||
* create_matrix (number_of_molecules, number_of_atoms, label_molecule,
|
|
||||||
* type_atoms, coords, number_of_interactions, criteria, connect_matrix)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <math.h>
|
#include <math.h>
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn create_matrix
|
||||||
|
*/
|
||||||
int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
||||||
const int *type_atoms, const float *coords, const int num_of_inter,
|
const int *type_atoms, const float *coords, const int num_of_inter,
|
||||||
const float *crit, int *connect)
|
const float *crit, int *connect)
|
||||||
/* num_mol - number of molecules
|
/**
|
||||||
* num_atoms - number of atoms
|
* @brief function that creates connectivity matrix
|
||||||
* label_mol - massive of numbers of molecule for atoms
|
* @code
|
||||||
* type_atoms - massive of atom types for atoms
|
* create_matrix (number_of_molecules, number_of_atoms, label_molecule,
|
||||||
* coords - massive of coordinates
|
* type_atoms, coords, number_of_interactions, criteria, connect_matrix);
|
||||||
* num_of_inter - number of different interactions
|
* @endcode
|
||||||
* crit - massive of criteria
|
*
|
||||||
* connect - connectivity graph for all molecules
|
* @param num_mol number of molecules
|
||||||
|
* @param num_atoms number of atoms
|
||||||
|
* @param label_mol massive of numbers of molecule for atoms
|
||||||
|
* @param type_atoms massive of atom types
|
||||||
|
* @param coords massive of coordinates
|
||||||
|
* @param num_of_inter number of different interactions
|
||||||
|
* @param crit massive of criteria
|
||||||
|
* @param connect connectivity graph for all molecules
|
||||||
|
*
|
||||||
|
* @return 1 - memory error
|
||||||
|
* @return 0 - exit without errors
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
float r;
|
float r;
|
||||||
int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
|
int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
|
||||||
/* r - radius
|
/* r radius
|
||||||
* cur_num_inter - current number of true interactions
|
* cur_num_inter current number of true interactions
|
||||||
* num_inter - needed number of true interactions
|
* num_inter needed number of true interactions
|
||||||
* label_inter - temporary massive of true interactions
|
* label_inter temporary massive of true interactions
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
/// <b>Work blocks</b>
|
||||||
|
|
||||||
label_inter = (int ***) malloc (num_mol * sizeof (int **));
|
label_inter = (int ***) malloc (num_mol * sizeof (int **));
|
||||||
for (i=0; i<num_mol; i++)
|
for (i=0; i<num_mol; i++)
|
||||||
{
|
{
|
||||||
@ -44,10 +56,10 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
|||||||
if (label_inter == NULL)
|
if (label_inter == NULL)
|
||||||
return 1;
|
return 1;
|
||||||
|
|
||||||
// creating initial connectivity matrix
|
/// <pre> creating initial connectivity matrix </pre>
|
||||||
for (i=0; i<num_atoms*8; i++)
|
for (i=0; i<num_atoms*8; i++)
|
||||||
for (j=i+1; j<num_atoms*8; j++)
|
for (j=i+1; j<num_atoms*8; j++)
|
||||||
// if atoms from different molecules
|
// if atoms from different molecules
|
||||||
if (label_mol[i] != label_mol[j])
|
if (label_mol[i] != label_mol[j])
|
||||||
{
|
{
|
||||||
r = sqrt (pow ((coords[3*i+0]-coords[3*j+0]), 2) +
|
r = sqrt (pow ((coords[3*i+0]-coords[3*j+0]), 2) +
|
||||||
@ -68,10 +80,10 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
|||||||
for (j=0; j<num_mol; j++)
|
for (j=0; j<num_mol; j++)
|
||||||
connect[i*num_mol+j] = 0;
|
connect[i*num_mol+j] = 0;
|
||||||
|
|
||||||
// processing of initial connectivity matrix
|
/// <pre> processing of initial connectivity matrix </pre>
|
||||||
for (k=0; k<num_of_inter; k++)
|
for (k=0; k<num_of_inter; k++)
|
||||||
{
|
{
|
||||||
// determination of the number of interactions
|
// determination of the number of interactions
|
||||||
num_inter = 0;
|
num_inter = 0;
|
||||||
for (l=0; l<16; l++)
|
for (l=0; l<16; l++)
|
||||||
if (crit[16*k+l] != 0.0)
|
if (crit[16*k+l] != 0.0)
|
||||||
@ -92,7 +104,7 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// free memory
|
/// <pre> free memory</pre>
|
||||||
for (i=0; i<num_mol; i++)
|
for (i=0; i<num_mol; i++)
|
||||||
{
|
{
|
||||||
for (j=0; j<num_mol; j++)
|
for (j=0; j<num_mol; j++)
|
||||||
|
|||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef STAT_SELECT_H
|
#ifndef STAT_SELECT_H
|
||||||
#define STAT_SELECT_H
|
#define STAT_SELECT_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn create_matrix
|
||||||
|
*/
|
||||||
|
|
||||||
int create_matrix (const int, const int, const int *, const int *, const float *,
|
int create_matrix (const int, const int, const int *, const int *, const float *,
|
||||||
const int, const float *, int *);
|
const int, const float *, int *);
|
||||||
|
|
||||||
@ -1,29 +1,41 @@
|
|||||||
/* Library for processing connectivity matrix
|
/**
|
||||||
*
|
* @file
|
||||||
* Usage:
|
|
||||||
* proc_matrix (number_of_molecules, connect_matrix,
|
|
||||||
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn proc_matrix
|
||||||
|
*/
|
||||||
int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *agl,
|
int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *agl,
|
||||||
int *stat, int *stat_all)
|
int *stat, int *stat_all)
|
||||||
/* num_mol - number of molecules
|
/**
|
||||||
* connect - connectivity graph for all molecules
|
* @brief function that processes connectivity matrix
|
||||||
* num_mol_agl - massive of numbers of molecule in aglomerates
|
* @code
|
||||||
* agl - massive of aglomerates
|
* proc_matrix (number_of_molecules, connect_matrix,
|
||||||
* stat - massive of statistics
|
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic);
|
||||||
* stat_all - massive of summary statistics
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param num_mol number of molecules
|
||||||
|
* @param connect connectivity graph for all molecules
|
||||||
|
* @param num_mol_agl massive of number of molecules in aglomerates
|
||||||
|
* @param agl massive of aglomerates
|
||||||
|
* @param stat massive of statistic
|
||||||
|
* @param stat_all massive of summary statistic
|
||||||
|
*
|
||||||
|
* @return 1 - memory error
|
||||||
|
* @return 0 - exit without errors
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
int i, j, k, p, *bin;
|
int i, j, k, p, *bin;
|
||||||
/* p - weight / graph index
|
/* p weight / graph index
|
||||||
* bin - binary massive of labels
|
* bin binary massive of labels
|
||||||
*/
|
*/
|
||||||
|
|
||||||
// definition and zeroing
|
/// <b>Work blocks</b>
|
||||||
|
|
||||||
|
// definition and zeroing
|
||||||
bin = (int *) malloc (num_mol * sizeof (int));
|
bin = (int *) malloc (num_mol * sizeof (int));
|
||||||
if (bin == NULL)
|
if (bin == NULL)
|
||||||
return 1;
|
return 1;
|
||||||
@ -36,7 +48,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
|||||||
agl[num_mol*i+j] = 0;
|
agl[num_mol*i+j] = 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
// select non-bonded molecules
|
/// <pre> select non-bonded molecules </pre>
|
||||||
for (i=0; i<num_mol; i++)
|
for (i=0; i<num_mol; i++)
|
||||||
{
|
{
|
||||||
p = 0;
|
p = 0;
|
||||||
@ -50,7 +62,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// unwraping of connectivity matrix
|
/// <pre> unwraping of connectivity matrix </pre>
|
||||||
p = 0;
|
p = 0;
|
||||||
for (i=0; i<num_mol; i++)
|
for (i=0; i<num_mol; i++)
|
||||||
if (bin[i] == 1)
|
if (bin[i] == 1)
|
||||||
@ -71,7 +83,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
|||||||
p++;
|
p++;
|
||||||
}
|
}
|
||||||
|
|
||||||
// filling statistic array
|
/// <pre> filling statistic array </pre>
|
||||||
i = 0;
|
i = 0;
|
||||||
while (num_mol_agl[i] > 0)
|
while (num_mol_agl[i] > 0)
|
||||||
{
|
{
|
||||||
@ -80,6 +92,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
|
|||||||
i++;
|
i++;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/// <pre> free memory </pre>
|
||||||
free (bin);
|
free (bin);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
|
|||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef STAT_SORT_H
|
#ifndef STAT_SORT_H
|
||||||
#define STAT_SORT_H
|
#define STAT_SORT_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn proc_matrix
|
||||||
|
*/
|
||||||
|
|
||||||
int proc_matrix (const int, const int *, int *, int *, int *, int *);
|
int proc_matrix (const int, const int *, int *, int *, int *, int *);
|
||||||
|
|
||||||
#endif /* STAT_SORT_H */
|
#endif /* STAT_SORT_H */
|
||||||
@ -1,29 +1,39 @@
|
|||||||
/* Library for summary statistic
|
/**
|
||||||
* Usage:
|
* @file
|
||||||
* summary_statistic (filename, number_of_step, number_of_molecules,
|
|
||||||
* max_depth, type_of_aglomerate, summary_statistic)
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn summary_statistic
|
||||||
|
*/
|
||||||
int summary_statistic (const char *filename, const int step, const int num_mol,
|
int summary_statistic (const char *filename, const int step, const int num_mol,
|
||||||
const int max_depth, const int *type_agl, const int *stat_all)
|
const int max_depth, const int *type_agl, const int *stat_all)
|
||||||
/* filename - name of output file
|
/**
|
||||||
* step - number of steps
|
* @brief function that prints summary statistic
|
||||||
* num_mol - number of molecules
|
* @code
|
||||||
* max_depth - max depth for check cycles in graph analyze
|
* summary_statistic (filename, number_of_step, number_of_molecules, max_depth,
|
||||||
* type_agl - massive of numbers of aglomerate types
|
* type_of_aglomerate, summary_statistic);
|
||||||
* stat_all - massive of summary statistics
|
* @endcode
|
||||||
|
*
|
||||||
|
* @param filename output file name
|
||||||
|
* @param step number of steps
|
||||||
|
* @param num_mol number of molecules
|
||||||
|
* @param max_depth maximum depth for check cycles in graph analyze
|
||||||
|
* @param type_agl massive of number of aglomerate types
|
||||||
|
* @param stat_all massive of summary statistic
|
||||||
|
*
|
||||||
|
* @return 0 - exit without errors
|
||||||
*/
|
*/
|
||||||
{
|
{
|
||||||
float conc, p, pn, type[2], x, y;
|
float conc, p, pn, type[2], x, y;
|
||||||
int i, index;
|
int i, index;
|
||||||
FILE *f_out;
|
FILE *f_out;
|
||||||
/* conc - concentrate of aglomerates
|
/* conc concentrate of aglomerates
|
||||||
* p - probability of aglomerates
|
* p probability of aglomerates
|
||||||
* pn - weight probability of aglomerates
|
* pn weight probability of aglomerates
|
||||||
* f_out - output file
|
* f_out output file
|
||||||
*/
|
*/
|
||||||
|
|
||||||
index = 0;
|
index = 0;
|
||||||
@ -31,19 +41,19 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
|
|||||||
if (stat_all[i] != 0)
|
if (stat_all[i] != 0)
|
||||||
index = i;
|
index = i;
|
||||||
|
|
||||||
// head
|
// head
|
||||||
f_out = fopen (filename, "a");
|
f_out = fopen (filename, "a");
|
||||||
fprintf (f_out, "SUMMARY STATISTIC\n");
|
fprintf (f_out, "SUMMARY STATISTIC\n");
|
||||||
fprintf (f_out, "| n | N | C | p | pn |\n------------------------------------------------\n");
|
fprintf (f_out, "| n | N | C | p | pn |\n------------------------------------------------\n");
|
||||||
|
|
||||||
for (i=0; i<index+1; i++)
|
for (i=0; i<index+1; i++)
|
||||||
{
|
{
|
||||||
// calculating concentrates
|
// calculating concentrates
|
||||||
x = stat_all[i];
|
x = stat_all[i];
|
||||||
y = step;
|
y = step;
|
||||||
conc = x / y;
|
conc = x / y;
|
||||||
|
|
||||||
// calculating probabilityes
|
// calculating probabilityes
|
||||||
x = (i + 1) * stat_all[i];
|
x = (i + 1) * stat_all[i];
|
||||||
y = step * num_mol;
|
y = step * num_mol;
|
||||||
p = x / y;
|
p = x / y;
|
||||||
@ -54,18 +64,18 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
|
|||||||
|
|
||||||
if (max_depth > 0)
|
if (max_depth > 0)
|
||||||
{
|
{
|
||||||
// types of aglomerates
|
// types of aglomerates
|
||||||
fprintf (f_out, "------------------------------------------------\n");
|
fprintf (f_out, "------------------------------------------------\n");
|
||||||
// linear and cycle
|
// linear and cycle
|
||||||
x = type_agl[0] + type_agl[1];
|
x = type_agl[0] + type_agl[1];
|
||||||
type[0] = type_agl[0];
|
type[0] = type_agl[0];
|
||||||
type[1] = type_agl[1];
|
type[1] = type_agl[1];
|
||||||
fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
|
fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
|
||||||
// branched
|
// branched
|
||||||
type[0] = type_agl[2];
|
type[0] = type_agl[2];
|
||||||
type[1] = type_agl[3];
|
type[1] = type_agl[3];
|
||||||
fprintf (f_out, "NOT BRANCHED=%7.5f\nBRANCHED=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
|
fprintf (f_out, "NOT BRANCHED=%7.5f\nBRANCHED=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
|
||||||
// n_cycle
|
// n_cycle
|
||||||
x = 0;
|
x = 0;
|
||||||
for (i=4; i<max_depth+2; i++)
|
for (i=4; i<max_depth+2; i++)
|
||||||
x += type_agl[i];
|
x += type_agl[i];
|
||||||
|
|||||||
@ -1,6 +1,14 @@
|
|||||||
|
/**
|
||||||
|
* @file
|
||||||
|
*/
|
||||||
|
|
||||||
#ifndef SUMMARY_STAT_H
|
#ifndef SUMMARY_STAT_H
|
||||||
#define SUMMARY_STAT_H
|
#define SUMMARY_STAT_H
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @fn summary_statistic
|
||||||
|
*/
|
||||||
|
|
||||||
int summary_statistic (const char *, const int, const int, const int, const int *,
|
int summary_statistic (const char *, const int, const int, const int, const int *,
|
||||||
const int *);
|
const int *);
|
||||||
|
|
||||||
@ -1,22 +1,32 @@
|
|||||||
# set directories
|
# set directories
|
||||||
set (${PROJECT}_BINARY_DIR bin)
|
set (${PROJECT}_BINARY_DIR bin)
|
||||||
set (${PROJECT}_SOURCE_DIR src:include)
|
set (${PROJECT}_SOURCE_DIR src)
|
||||||
|
set (${PROJECT}_INCLUDE_DIR include)
|
||||||
set (${PROJECT}_LIB_DIR lib)
|
set (${PROJECT}_LIB_DIR lib)
|
||||||
|
|
||||||
set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
|
# include_path
|
||||||
set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
|
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||||
|
${${PROJECT}_SOURCE_DIR})
|
||||||
|
# library path
|
||||||
|
link_directories (${${PROJECT}_LIB_DIR})
|
||||||
|
# executable path
|
||||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||||
|
|
||||||
|
# verbose
|
||||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||||
|
|
||||||
|
# flags
|
||||||
if ( WITH_DEBUG_MODE )
|
if ( WITH_DEBUG_MODE )
|
||||||
ADD_DEFINITIONS ( -DDEBUG_MODE=1 )
|
add_definitions ( -DDEBUG_MODE=1 )
|
||||||
endif ()
|
endif ()
|
||||||
|
|
||||||
if ( CMAKE_COMPILER_IS_GNUCXX )
|
if ( CMAKE_COMPILER_IS_GNUCXX )
|
||||||
set (ADD_CXX_FLAGS "-Wall")
|
set (ADD_CXX_FLAGS "-Wall")
|
||||||
set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
|
set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
|
||||||
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
|
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
|
||||||
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
|
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
|
||||||
|
elseif ( MSVC )
|
||||||
|
set (ADD_CXX_FLAGS "/W4")
|
||||||
|
set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
|
||||||
else ()
|
else ()
|
||||||
message (STATUS "Flags not enabled")
|
message ("Unknown compiler")
|
||||||
endif ()
|
endif ()
|
||||||
1890
statgen/statgen.doxygen
Normal file
1890
statgen/statgen.doxygen
Normal file
File diff suppressed because it is too large
Load Diff
BIN
statgen/statgen.pdf
Normal file
BIN
statgen/statgen.pdf
Normal file
Binary file not shown.
Reference in New Issue
Block a user