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Added radf-1.0.1b
This commit is contained in:
arcan1s
@ -3,7 +3,7 @@ Version: 1.0.1
|
||||
License: GPL
|
||||
|
||||
Usage:
|
||||
agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]
|
||||
agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
|
||||
Parametrs:
|
||||
-a - input file with aglomerates (in format statgen)
|
||||
|
||||
@ -24,13 +24,13 @@
|
||||
* @section How-To-Use How to use
|
||||
* Usage:
|
||||
* <pre>
|
||||
* agl -a FILENAME -i FILENAME -c X,Y,Z -o FILEMANE [ -l LOGFILE] [ -q ] [ -h ]
|
||||
* agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
*
|
||||
* Parametrs:
|
||||
* -a - input file with aglomerates (in format statgen)
|
||||
* -i - input file with coordinates
|
||||
* -c - cell size (float), A
|
||||
* -o - output file with coordinates
|
||||
* -o - output file name
|
||||
* -l - log enable
|
||||
* -q - quiet enable
|
||||
* -h - show this help and exit
|
||||
@ -39,7 +39,7 @@
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application statgen requires the following external stuff:
|
||||
* The application agl requires the following external stuff:
|
||||
* - cmake >= 2.8
|
||||
* - gcc >= 4.8
|
||||
*
|
||||
@ -131,12 +131,12 @@ int main(int argc, char *argv[])
|
||||
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, "%sagl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -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 -o - output file name\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);
|
||||
|
||||
@ -3,7 +3,8 @@ Version: 1.0.1
|
||||
License: GPL
|
||||
|
||||
Usage:
|
||||
envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] [ -l LOGFILE] [ -q ] [ -h ]
|
||||
envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]
|
||||
[ -l LOGFILE ] [ -q ] [ -h ]
|
||||
|
||||
Parametrs:
|
||||
-i - input file with coordinates
|
||||
|
||||
@ -24,13 +24,13 @@
|
||||
* @section How-To-Use How to use
|
||||
* Usage:
|
||||
* <pre>
|
||||
* envir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]
|
||||
* [ -l LOGFILE] [ -q ] [ -h ]
|
||||
* envir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]
|
||||
* [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
*
|
||||
* Parametrs:
|
||||
* -i - input file with coordinates
|
||||
* -i - input file name
|
||||
* -c - cell size (float), A
|
||||
* -o - output file with coordinates
|
||||
* -o - output file name
|
||||
* -n - number of molecule for search (integer). Default is 1
|
||||
* -r - radius of environment (float). Default is 6.0
|
||||
* -l - log enable
|
||||
@ -41,7 +41,7 @@
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application statgen requires the following external stuff:
|
||||
* The application envir requires the following external stuff:
|
||||
* - cmake >= 2.8
|
||||
* - gcc >= 4.8
|
||||
*
|
||||
@ -133,11 +133,12 @@ int main(int argc, char *argv[])
|
||||
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, "%senvir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] [ -l LOGFILE] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%senvir -i INPUT -c X,Y,Z -o OUTPUT [ -n NUM_OF_MOLECULE ] [ -r RADIUS ]\n", tmp_str);
|
||||
sprintf (tmp_str, "%s [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -i - input file name\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 -o - output file name\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -n - number of molecule for search (integer). Default is 1\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -r - radius of environment (float). Default is 6.0\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
|
||||
|
||||
3
radf/AUTHORS
Normal file
3
radf/AUTHORS
Normal file
@ -0,0 +1,3 @@
|
||||
Current developers:
|
||||
|
||||
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>
|
||||
32
radf/CMakeLists.txt
Normal file
32
radf/CMakeLists.txt
Normal file
@ -0,0 +1,32 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy(SET CMP0003 OLD)
|
||||
cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT radf)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
|
||||
# set libraries
|
||||
set (LIBRARIES)
|
||||
foreach (LIBRARY ${LIBRARIES})
|
||||
find_library ("${LIBRARY}_FOUND" ${LIBRARY})
|
||||
message (STATUS "Check the ${LIBRARY} is installed: " ${${LIBRARY}_FOUND})
|
||||
if ("${${LIBRARY}_FOUND}" STREQUAL "${LIBRARY}_FOUND-NOTFOUND")
|
||||
message (STATUS "Adding library sources")
|
||||
add_subdirectory (../${LIBRARY} lib/${LIBRARY})
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
# additional targets
|
||||
set (TARGETS "")
|
||||
set (HEADERS "")
|
||||
|
||||
add_subdirectory (${${PROJECT}_SOURCE_DIR})
|
||||
341
radf/COPYING
Normal file
341
radf/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
radf/INSTALL
Normal file
14
radf/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.
|
||||
25
radf/README
Normal file
25
radf/README
Normal file
@ -0,0 +1,25 @@
|
||||
radf - program that calculates radial distribution function (RDF) or radial-angles
|
||||
distribution function
|
||||
Version : 1.0.1
|
||||
License : GPL
|
||||
|
||||
Usage:
|
||||
radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ]
|
||||
[ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -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-ATOM2' or 'A1,A2,A3-B1,B2,B3'
|
||||
(will enable RDF calculation for center mass automaticaly)
|
||||
-o - output file name
|
||||
-r - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
|
||||
-rs - radius step for analyze (float), A. Default is '0.2'
|
||||
-a - minimal and maximal angles for analyze (float), deg. Default is '0.0,90.0'
|
||||
-as - angle step for analyze (float), deg. This option will enable RADF
|
||||
calculation automaticaly
|
||||
-m - matrix output enable
|
||||
-l - log enable
|
||||
-q - quiet enable
|
||||
-h - show this help and exit
|
||||
BIN
radf/logo.png
Executable file
BIN
radf/logo.png
Executable file
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
32
radf/radf.cmake
Normal file
32
radf/radf.cmake
Normal file
@ -0,0 +1,32 @@
|
||||
# set directories
|
||||
set (${PROJECT}_BINARY_DIR bin)
|
||||
set (${PROJECT}_SOURCE_DIR src)
|
||||
set (${PROJECT}_INCLUDE_DIR include)
|
||||
set (${PROJECT}_LIB_DIR lib)
|
||||
|
||||
# include_path
|
||||
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
|
||||
${${PROJECT}_SOURCE_DIR})
|
||||
# library path
|
||||
link_directories (${${PROJECT}_LIB_DIR})
|
||||
# executable path
|
||||
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
|
||||
|
||||
# verbose
|
||||
set (CMAKE_VERBOSE_MAKEFILE ON)
|
||||
|
||||
# flags
|
||||
if ( WITH_DEBUG_MODE )
|
||||
add_definitions ( -DDEBUG_MODE=1 )
|
||||
endif ()
|
||||
if ( CMAKE_COMPILER_IS_GNUCXX )
|
||||
set (ADD_CXX_FLAGS "-Wall")
|
||||
set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
|
||||
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
|
||||
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
|
||||
elseif ( MSVC )
|
||||
set (ADD_CXX_FLAGS "/W4")
|
||||
set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
|
||||
else ()
|
||||
message ("Unknown compiler")
|
||||
endif ()
|
||||
1890
radf/radf.doxygen
Normal file
1890
radf/radf.doxygen
Normal file
File diff suppressed because it is too large
Load Diff
29
radf/src/CMakeLists.txt
Normal file
29
radf/src/CMakeLists.txt
Normal file
@ -0,0 +1,29 @@
|
||||
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 ${${PROJECT}_VERSION}")
|
||||
|
||||
# set files
|
||||
aux_source_directory (. SOURCES)
|
||||
|
||||
# set library
|
||||
if (CMAKE_COMPILER_IS_GNUCXX)
|
||||
set (ADDITIONAL_LIB m)
|
||||
else ()
|
||||
set (ADDITIONAL_LIB)
|
||||
endif()
|
||||
|
||||
# message
|
||||
message (STATUS "SOURCES: ${SOURCES}")
|
||||
|
||||
# link libraries and compile
|
||||
add_executable (${PROJECT} ${SOURCES})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
21
radf/src/Makefile
Normal file
21
radf/src/Makefile
Normal file
@ -0,0 +1,21 @@
|
||||
PROJECT=RADF
|
||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c messages.c radf.c radf_proc.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=radf
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
211
radf/src/add_main.c
Normal file
211
radf/src/add_main.c
Normal file
@ -0,0 +1,211 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "messages.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
||||
int error_checking (const float *cell, const int from, const char *input,
|
||||
const int num_needed_at, const int *needed_at,
|
||||
const char *output, const int to)
|
||||
/**
|
||||
* @brief function that checks errors in input variables
|
||||
* @code
|
||||
* error_checking (cell, from, input, num_needed_at, needed_at, output, to);
|
||||
* @endcode
|
||||
*
|
||||
* @param cell massive of cell size
|
||||
* @param from first trajectory step
|
||||
* @param input input file name
|
||||
* @param num_needed_at number of needed atom types
|
||||
* @param needed_at massive of number of needed atom types
|
||||
* @param output output file name
|
||||
* @param to last trajectory step
|
||||
*
|
||||
* @return 11 - error in 'cell'
|
||||
* @return 12 - error in 'input'
|
||||
* @return 13 - error in 'output'
|
||||
* @return 14 - error in 'from' or 'to'
|
||||
* @return 15 - error in 'num_needed_at'
|
||||
* @return 16 - error in 'needed_at'
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
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 ((from == -1) || (to == -1))
|
||||
return 14;
|
||||
if ((num_needed_at != 2) && (num_needed_at != 6))
|
||||
return 15;
|
||||
if (num_needed_at == 6)
|
||||
if ((needed_at[0] == needed_at[1]) ||
|
||||
(needed_at[0] == needed_at[2]) ||
|
||||
(needed_at[1] == needed_at[2]) ||
|
||||
(needed_at[3] == needed_at[4]) ||
|
||||
(needed_at[3] == needed_at[5]) ||
|
||||
(needed_at[4] == needed_at[5]))
|
||||
return 16;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn print_message
|
||||
*/
|
||||
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
|
||||
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))
|
||||
message (0, mode, str, std_output);
|
||||
if (log == 1)
|
||||
message (1, mode, str, f_log);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn printing_head
|
||||
*/
|
||||
int printing_head (const char *output, const int log, const int quiet, const int matrix,
|
||||
const char *input, const int from, const int to, const float *cell,
|
||||
const int mode, const double r_min, const double r_max,
|
||||
const double r_step, const double ang_min, const double ang_max,
|
||||
const double ang_step, const int *needed_at)
|
||||
/**
|
||||
* @brief function that prints header in output file
|
||||
* @code
|
||||
* printing_head (output, log, quiet, matrix, input, from, to, cell, mode, r_min,
|
||||
* r_max, r_step, ang_min, ang_max, ang_step, needed_at);
|
||||
* @endcode
|
||||
*
|
||||
* @param output output file nams
|
||||
* @param log status of log-mode
|
||||
* @param quiet status of quiet-mode
|
||||
* @param matrix status of matrix-mode
|
||||
* @param input mask of trajectory files
|
||||
* @param from first trajectory step
|
||||
* @param to last trajectory step
|
||||
* @param cell massive of cell size
|
||||
* @param mode 0 - if RDF, 1 - if RDF for center mass, 2 - if RADF
|
||||
* @param r_max maximal radius
|
||||
* @param r_min minimal radius
|
||||
* @param r_step radius step
|
||||
* @param ang_max maximal angle for RADF
|
||||
* @param ang_min minimal angle for RADF
|
||||
* @param ang_step anlge step for RADF
|
||||
* @param needed_at massive of number of needed atom types
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
FILE *f_out;
|
||||
|
||||
f_out = fopen (output, "w");
|
||||
fprintf (f_out, "radf ::: V.1.0.1 ::: 2013-07-23\n\n");
|
||||
fprintf (f_out, "CONFIGURATION\n");
|
||||
|
||||
fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix);
|
||||
fprintf (f_out, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, from, to);
|
||||
fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", cell[0], cell[1], cell[2]);
|
||||
fprintf (f_out, "MODE=%i\n", mode);
|
||||
fprintf (f_out, "R_MIN=%.3f\nR_MAX=%.3f\nR_STEP=%.3f", r_min, r_max, r_step);
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
fprintf (f_out, "ATOM=%i-%i\n", needed_at[0], needed_at[1]);
|
||||
break;
|
||||
case 1:
|
||||
fprintf (f_out, "ATOM=%i,%i,%i-%i,%i,%i\n", needed_at[0], needed_at[1],
|
||||
needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
|
||||
break;
|
||||
case 2:
|
||||
fprintf (f_out, "ANG_MIN=%.2f\nANG_MAX=%.2f\nANG_STEP=%.2f\n\
|
||||
ATOM=%i,%i,%i-%i,%i,%i\n",ang_min, ang_max, ang_step, needed_at[0], needed_at[1],
|
||||
needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
|
||||
break;
|
||||
}
|
||||
|
||||
fprintf (f_out, "END\n\n");
|
||||
fclose (f_out);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn set_defaults
|
||||
*/
|
||||
int set_defaults (float *ang_max, float *ang_min, float *ang_step, float *cell,
|
||||
int *from, char *input, int *log, int *matrix, float *r_max,
|
||||
float *r_min, float *r_step, char *output, int *to, int *quiet)
|
||||
/**
|
||||
* @brief function that sets default values of variables
|
||||
* @code
|
||||
* set_defaults (&ang_max, &ang_min, &ang_step, cell, &from, input, &log, &r_max,
|
||||
* &r_min, &r_step, output, &to, &quiet);
|
||||
* @endcode
|
||||
*
|
||||
* @param ang_max maximal angle for RADF
|
||||
* @param ang_min minimal angle for RADF
|
||||
* @param ang_step angle step
|
||||
* @param cell massive of cell size
|
||||
* @param from first trajectory step
|
||||
* @param input mask of trajectory files
|
||||
* @param log status of log-mode
|
||||
* @param matrix status of matrix-mode
|
||||
* @param r_max maximal radius
|
||||
* @param r_min minimal radius
|
||||
* @param r_step radius step
|
||||
* @param output output file name
|
||||
* @param to last trajectory step
|
||||
* @param quiet status of quiet-mode
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int i;
|
||||
|
||||
*ang_max = 90.0;
|
||||
*ang_min = 0.0;
|
||||
*ang_step = 0.0;
|
||||
for (i=0; i<3; i++)
|
||||
cell[i] = 0.0;
|
||||
*from = -1;
|
||||
input[0] = '#';
|
||||
*log = 0;
|
||||
*matrix = 0;
|
||||
*r_max = 15.0;
|
||||
*r_min = 2.0;
|
||||
*r_step = 0.2;
|
||||
output[0] = '#';
|
||||
*to = -1;
|
||||
*quiet = 0;
|
||||
|
||||
return 0;
|
||||
}
|
||||
31
radf/src/add_main.h
Normal file
31
radf/src/add_main.h
Normal file
@ -0,0 +1,31 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef ADD_MAIN_H
|
||||
#define ADD_MAIN_H
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
||||
/**
|
||||
* @fn print_message
|
||||
*/
|
||||
/**
|
||||
* @fn printing_head
|
||||
*/
|
||||
/**
|
||||
* @fn set_defaults
|
||||
*/
|
||||
|
||||
int error_checking (const float *, const int, const char *, const int, const int *,
|
||||
const char *, const int);
|
||||
int print_message (const int, FILE *, const int, FILE *, const int, const char *);
|
||||
int printing_head (const char *, const int, const int, const int, const char *,
|
||||
const int, const int, const float *, const int, const double,
|
||||
const double, const double, const double, const double, const double,
|
||||
const int *);
|
||||
int set_defaults (float *, float *, float *, float *, int *, char *, int *, int *,
|
||||
float *, float *, float *, char *, int *, int *);
|
||||
|
||||
#endif /* ADD_MAIN_H */
|
||||
354
radf/src/coords.c
Normal file
354
radf/src/coords.c
Normal file
@ -0,0 +1,354 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
const int *label_atom, const float *cell, int *num_mol,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/**
|
||||
* @brief function that reads coordinates from special file format
|
||||
* @code
|
||||
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms,
|
||||
* true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
|
||||
* @endcode
|
||||
*
|
||||
* @param mode mode of reading; '1' is statgen, '2' is envir or
|
||||
* frad, '3' is agl
|
||||
* @param filename input file name
|
||||
* @param type_inter number of needed atoms
|
||||
* (number of needed molecules)
|
||||
* @param label_atom massive of needed atom types
|
||||
* (massive of needed molecules)
|
||||
* @param cell massive of cell size
|
||||
* @param num_mol number of molecules
|
||||
* @param num_atoms number of atoms
|
||||
* @param true_label_mol massive of true numbers of molecule for atoms
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
* @param ch_type_atoms massive of char atom types
|
||||
*
|
||||
* @return 1 - file $filename does not exist
|
||||
* @return 2 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char at_symb[32], file_string[256];
|
||||
int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
|
||||
float cur_coords[3], *not_tr_coords, ref[3];
|
||||
FILE *inp;
|
||||
|
||||
/* cur_* temp variables
|
||||
* at_symb temp variable
|
||||
* file_string temp string variable
|
||||
* atoms total number of atoms in system
|
||||
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
|
||||
* ref_mol number of molecule for reference in translation
|
||||
* not_tr_coords massive of not translated coordinates
|
||||
* ref massive of coordinates of reference molecule
|
||||
* inp input file
|
||||
*/
|
||||
|
||||
/// <b>Work blocks</b>
|
||||
|
||||
*num_atoms = 0;
|
||||
*num_mol = 0;
|
||||
|
||||
/// <pre> reading file </pre>
|
||||
inp = fopen (filename, "r");
|
||||
if (inp == NULL)
|
||||
return 1;
|
||||
|
||||
ref_mol = -1;
|
||||
fscanf (inp, "%i", &atoms);
|
||||
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
|
||||
fgets (file_string, 256, inp);
|
||||
for (i=0; i<atoms; i++)
|
||||
{
|
||||
fgets (file_string, 256, inp);
|
||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
||||
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||
|
||||
// reading variables according to selected mode
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
// mode == 0 (selected atoms)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_at_type == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// mode == 1 (all atoms)
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
case 2:
|
||||
// mode == 2 (selected molecules)
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_mol == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
default: return 2;
|
||||
}
|
||||
}
|
||||
fclose (inp);
|
||||
|
||||
/// <pre> translation </pre>
|
||||
tr_num_atoms = *num_atoms;
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
for (j=0; j<3; j++)
|
||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||
|
||||
// assign initial value to reference coordinates
|
||||
ref_mol = label_mol[0];
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
{
|
||||
if (label_mol[i] != ref_mol)
|
||||
{
|
||||
ref_mol = label_mol[i];
|
||||
for (j=0; j<3; j++)
|
||||
ref[j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
if (ref[x] >= 0.0)
|
||||
// if xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
else
|
||||
// if xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
for (y=x+1; y<3; y++)
|
||||
{
|
||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz and xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||
// if xyz and xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (y=0; y<3; y++)
|
||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz OR xyz >= 0.0
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
{
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
if (j == y)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
if ((j != x) && (j != y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
/// <pre> free memory </pre>
|
||||
free (not_tr_coords);
|
||||
|
||||
return 0;
|
||||
}
|
||||
16
radf/src/coords.h
Normal file
16
radf/src/coords.h
Normal file
@ -0,0 +1,16 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef COORDS_H
|
||||
#define COORDS_H
|
||||
|
||||
/**
|
||||
* @fn reading_coords
|
||||
*/
|
||||
|
||||
int reading_coords (const int, const char *, const int, const int *,
|
||||
const float *, int *, int *, int *, int *, int *, float *,
|
||||
char *);
|
||||
|
||||
#endif /* COORDS_H */
|
||||
414
radf/src/main.c
Normal file
414
radf/src/main.c
Normal file
@ -0,0 +1,414 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
/**
|
||||
* @mainpage radf
|
||||
* @image latex ./logo.png
|
||||
*
|
||||
* @section intro_sec Introduction
|
||||
*
|
||||
* <b>About this program</b>:
|
||||
* <ul>
|
||||
* <li>Program that calculates radial distribution function (RDF) or radial-angles
|
||||
* distribution function
|
||||
* </ul>
|
||||
*
|
||||
* <b>Developer</b>:
|
||||
* <ul>
|
||||
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
|
||||
*</ul>
|
||||
* <b>License</b>:
|
||||
* <ul>
|
||||
* <li>GPL
|
||||
* </ul>
|
||||
*
|
||||
* @section How-To-Use How to use
|
||||
* Usage:
|
||||
* <pre>
|
||||
* radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ]
|
||||
* [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -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-ATOM2' or 'A1,A2,A3-B1,B2,B3'
|
||||
* (will enable RDF calculation for center mass automaticaly)
|
||||
* -o - output file name
|
||||
* -r - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
|
||||
* -rs - radius step for analyze (float), A. Default is '0.2'
|
||||
* -a - minimal and maximal angles for analyze (float), deg. Default is '0.0,90.0'
|
||||
* -as - angle step for analyze (float), deg. This option will enable RADF
|
||||
* calculation automaticaly
|
||||
* -m - matrix output enable
|
||||
* -l - log enable
|
||||
* -q - quiet enable
|
||||
* -h - show this help and exit
|
||||
* </pre>
|
||||
*
|
||||
* @page Install
|
||||
*
|
||||
* @section Requirements Requirements
|
||||
* The application radf 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
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "add_main.h"
|
||||
#include "coords.h"
|
||||
#include "messages.h"
|
||||
#include "radf.h"
|
||||
#include "radf_proc.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn main
|
||||
*/
|
||||
int main(int argc, char *argv[])
|
||||
/**
|
||||
* @return 1 - error in error_checking
|
||||
* @return 2 - input file does not exist
|
||||
* @return 3 - memory error
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char filename[256], tmp_str[2048];
|
||||
int error, i, j;
|
||||
FILE *f_inp, *f_log;
|
||||
|
||||
char input[256], logfile[256], output[256];
|
||||
float ang_max, ang_min, ang_step, cell[3], *coords, r_max, r_min, r_step;
|
||||
int from, *label_mol, log, matrix, mode, num_atoms, num_mol, num_needed_at,
|
||||
needed_at[6], quiet, *radf, step, to, *true_label_mol, *type_atoms;
|
||||
|
||||
/* input input file name
|
||||
* logfile log file name
|
||||
* output output file name
|
||||
*
|
||||
* ang_max maximal angle for RADF
|
||||
* ang_min minimal angle for RADF
|
||||
* ang_step anlge step for RADF
|
||||
* cell massive of cell size
|
||||
* coords massive of coordinates
|
||||
* r_max maximal radius
|
||||
* r_min minimal radius
|
||||
* r_step radius step
|
||||
*
|
||||
* from first trajectory step
|
||||
* label_mol massive of numbers of molecule for atoms
|
||||
* log status of log-mode
|
||||
* matrix status of matrix-mode
|
||||
* mode 0 - if RDF, 1 - if RDF for center mass, 2 - if RADF
|
||||
* num_atoms number of atoms
|
||||
* num_mol number of molecules
|
||||
* num_needed_at number of needed atom types
|
||||
* needed_at massive of number of needed atom types
|
||||
* quiet status of quiet-mode
|
||||
* radf not normed RADF
|
||||
* step $(to - from + 1)
|
||||
* to last trajectory step
|
||||
* true_label_mol massive of true numbers of molecule for atoms
|
||||
* type_atoms massive of atom types
|
||||
*/
|
||||
|
||||
set_defaults (&ang_max, &ang_min, &ang_step, cell, &from, input, &log, &matrix,
|
||||
&r_max, &r_min, &r_step, output, &to, &quiet);
|
||||
|
||||
for (i=1; i<argc; i++)
|
||||
{
|
||||
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
||||
{
|
||||
sprintf (tmp_str, " radf\n");
|
||||
sprintf (tmp_str, "%sProgram that calculates radial distribution function (RDF) or radial-angles\n", tmp_str);
|
||||
sprintf (tmp_str, "%sdistribution function\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 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, "%sradf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ]\n", tmp_str);
|
||||
sprintf (tmp_str, "%s [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -i - mask of input files\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -s - trajectory steps (integer)\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -at - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3'\n", tmp_str);
|
||||
sprintf (tmp_str, "%s (will enable RDF calculation for center mass automaticaly)\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -r - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -rs - radius step for analyze (float), A. Default is '0.2'\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -a - minimal and maximal angles for analyze (float), deg. Default is '0.0,90.0'\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -as - angle step for analyze (float), deg. This option will enable RADF\n", tmp_str);
|
||||
sprintf (tmp_str, "%s calculation automaticaly\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -m - matrix output enable\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] == 'i'))
|
||||
// input file
|
||||
{
|
||||
strcpy (input, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
|
||||
// steps
|
||||
{
|
||||
sscanf (argv[i+1], "%i,%i", &from, &to);
|
||||
if (from > to)
|
||||
{
|
||||
to += from;
|
||||
from = to - from;
|
||||
to -= from;
|
||||
}
|
||||
step = to - from + 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] == 'a') && (argv[i][2] == 't'))
|
||||
// atom types
|
||||
{
|
||||
num_needed_at = 2;
|
||||
for (j=0; j<strlen(argv[i+1]); j++)
|
||||
if (argv[i+1][j] == ',')
|
||||
num_needed_at++;
|
||||
if (num_needed_at == 2)
|
||||
sscanf (argv[i+1], "%i-%i", &needed_at[0], &needed_at[1]);
|
||||
else if (num_needed_at == 6)
|
||||
sscanf (argv[i+1], "%i,%i,%i-%i,%i,%i", &needed_at[0], &needed_at[1], &needed_at[2],
|
||||
&needed_at[3], &needed_at[4], &needed_at[5]);
|
||||
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] == 'r') && (argv[i][2] == '\0'))
|
||||
// radii
|
||||
{
|
||||
sscanf (argv[i+1], "%f,%f", &r_min, &r_max);
|
||||
if (r_min > r_max)
|
||||
{
|
||||
r_min += r_max;
|
||||
r_max = r_min - r_max;
|
||||
r_min -= r_max;
|
||||
}
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == 's'))
|
||||
// radius step
|
||||
{
|
||||
sscanf (argv[i+1], "%f", &r_step);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
|
||||
// angles
|
||||
{
|
||||
sscanf (argv[i+1], "%f,%f", &ang_min, &ang_max);
|
||||
if (ang_min > ang_max)
|
||||
{
|
||||
ang_min += ang_max;
|
||||
ang_max = ang_min - ang_max;
|
||||
ang_min -= ang_max;
|
||||
}
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 's'))
|
||||
// angle step
|
||||
{
|
||||
sscanf (argv[i+1], "%f", &ang_step);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'm'))
|
||||
// matrix mode
|
||||
{
|
||||
matrix = 1;
|
||||
}
|
||||
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 (cell, from, input, num_needed_at, needed_at, output, to);
|
||||
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
|
||||
// set mode
|
||||
if ((num_needed_at == 6) && (ang_step != 0.0))
|
||||
mode = 2;
|
||||
else if (num_needed_at == 6)
|
||||
mode = 1;
|
||||
else if (num_needed_at == 2)
|
||||
mode = 0;
|
||||
|
||||
sprintf (filename, "%s.%03i", input, from);
|
||||
print_message (quiet, stdout, log, f_log, 3, filename);
|
||||
f_inp = fopen (filename, "r");
|
||||
if (f_inp == NULL)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 18, filename);
|
||||
return 2;
|
||||
}
|
||||
fscanf (f_inp, "%i", &num_atoms);
|
||||
fclose (f_inp);
|
||||
coords = (float *) malloc (2 * 3 * 8 * num_atoms * sizeof (float));
|
||||
label_mol = (int *) malloc (2 * 8 * num_atoms * sizeof (int));
|
||||
if (mode == 2)
|
||||
{
|
||||
i = (r_max - r_min) / r_step;
|
||||
j = (ang_max - ang_min) / ang_step;
|
||||
i *= j;
|
||||
}
|
||||
else
|
||||
i = (r_max - r_min) / r_step;
|
||||
radf = (int *) malloc (i * sizeof (int));
|
||||
for (j=0; j<i; j++)
|
||||
radf[j] = 0;
|
||||
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
|
||||
type_atoms = (int *) malloc (2 * 8 * num_atoms * sizeof (int));
|
||||
// error checking
|
||||
if ((coords == NULL) ||
|
||||
(label_mol == NULL) ||
|
||||
(radf == NULL) ||
|
||||
(true_label_mol == NULL) ||
|
||||
(type_atoms == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 3;
|
||||
}
|
||||
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cMatrix mode: %i;\n\
|
||||
%6cMask: %s;\n%6cFirst step: %i;\n%6cLast step: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cMode: %i;\n\
|
||||
%6cR_MIN: %6.3f; R_MAX: %6.3f; R_STEP: %6.3f;\n", ' ', output, ' ', log, ' ', quiet, ' ', matrix,
|
||||
' ', input, ' ', from, ' ', to, ' ', cell[0], cell[1], cell[2], ' ', mode, ' ', r_min, r_max, r_step);
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
sprintf (tmp_str, "%s%6cATOM TYPES: %i-%i\n", tmp_str, ' ', needed_at[0], needed_at[1]);
|
||||
break;
|
||||
case 1:
|
||||
sprintf (tmp_str, "%s%6cATOM TYPES: %i,%i,%i-%i,%i,%i\n", tmp_str, ' ', needed_at[0], needed_at[1],
|
||||
needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
|
||||
break;
|
||||
case 2:
|
||||
sprintf (tmp_str, "%s%6cANG_MIN: %6.2f; ANG_MAX: %6.2f; ANG_STEP: %6.2f;\n\
|
||||
%6cATOM TYPES: %i,%i,%i-%i,%i,%i\n", tmp_str, ' ', ang_min, ang_max, ang_step, ' ', needed_at[0],
|
||||
needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
|
||||
break;
|
||||
}
|
||||
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||
|
||||
// head
|
||||
printing_head (output, log, quiet, matrix, input, from, to, cell, mode, r_min,
|
||||
r_max, r_step, ang_min, ang_max, ang_step, needed_at);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||
// main cycle
|
||||
for (i=from; i<to+1; i++)
|
||||
{
|
||||
sprintf (filename, "%s.%03i", input, i);
|
||||
print_message (quiet, stdout, log, f_log, 7, filename);
|
||||
error = reading_coords (0, filename, num_needed_at, needed_at, cell, &num_mol,
|
||||
&num_atoms, true_label_mol, label_mol, type_atoms,
|
||||
coords, tmp_str);
|
||||
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 = 1;
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
error = search_rdf (num_atoms, type_atoms, label_mol, coords, r_min,
|
||||
r_max, r_step, radf);
|
||||
break;
|
||||
case 1:
|
||||
error = search_rdf_centr (num_atoms, type_atoms, label_mol, coords, r_min,
|
||||
r_max, r_step, radf);
|
||||
if (error == 0)
|
||||
case 2:
|
||||
error = search_radf (num_atoms, type_atoms, label_mol, coords, r_min, r_max,
|
||||
r_step, ang_min, ang_max, ang_step, radf);
|
||||
break;
|
||||
}
|
||||
if (error == 0)
|
||||
print_message (quiet, stdout, log, f_log, 22, argv[0]);
|
||||
}
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||
print_message (quiet, stdout, log, f_log, 14, output);
|
||||
// tail
|
||||
print_result (output, matrix, mode, step, num_atoms, r_min, r_max, r_step, ang_min,
|
||||
ang_max, ang_step, cell, radf);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||
// free memory
|
||||
free (coords);
|
||||
free (label_mol);
|
||||
free (radf);
|
||||
free (type_atoms);
|
||||
free (true_label_mol);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 16, argv[0]);
|
||||
|
||||
if (log == 1)
|
||||
fclose (f_log);
|
||||
return 0;
|
||||
}
|
||||
119
radf/src/messages.c
Normal file
119
radf/src/messages.c
Normal file
@ -0,0 +1,119 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <time.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
int message (const int log, const int mode, const char *text, FILE *output)
|
||||
/**
|
||||
* @brief function that prints messages to output
|
||||
* @code
|
||||
* message (log, mode, text, output);
|
||||
* @endcode
|
||||
*
|
||||
* @param log equal to 1 if print to logfile
|
||||
* @param mode number of message
|
||||
* @param text additional text
|
||||
* @param output output file (may be stdout)
|
||||
*
|
||||
* @return 1 - unknown mode
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char out[4096];
|
||||
|
||||
if (log == 1)
|
||||
{
|
||||
char time_str[256];
|
||||
|
||||
time_t t = time (NULL);
|
||||
struct tm* aTm = localtime (&t);
|
||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||
aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
|
||||
fputs (time_str, output);
|
||||
}
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
sprintf (out, "Start program: '%s'\n", text);
|
||||
break;
|
||||
case 1:
|
||||
sprintf (out, "Checking errors\n");
|
||||
break;
|
||||
case 2:
|
||||
sprintf (out, "Errors are not detected\n");
|
||||
break;
|
||||
case 3:
|
||||
sprintf (out, "Initialization of variables from file '%s'\n", text);
|
||||
break;
|
||||
case 4:
|
||||
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
|
||||
break;
|
||||
case 5:
|
||||
sprintf (out, "Initial parametrs: \n%s", text);
|
||||
break;
|
||||
case 6:
|
||||
sprintf (out, "Processing\n");
|
||||
break;
|
||||
case 7:
|
||||
sprintf (out, "Open file: '%s'\n", text);
|
||||
break;
|
||||
case 8:
|
||||
sprintf (out, "%s", text);
|
||||
break;
|
||||
case 9:
|
||||
sprintf (out, "%6cSize of variables was changed successfully\n", ' ');
|
||||
break;
|
||||
case 10:
|
||||
sprintf (out, "%6cConnectivity matrix was created successfully\n", ' ');
|
||||
break;
|
||||
case 11:
|
||||
sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' ');
|
||||
break;
|
||||
case 12:
|
||||
sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text);
|
||||
break;
|
||||
case 13:
|
||||
sprintf (out, "End of processing\n");
|
||||
break;
|
||||
case 14:
|
||||
sprintf (out, "Print result to file '%s'\n", text);
|
||||
break;
|
||||
case 15:
|
||||
sprintf (out, "Free memory\n");
|
||||
break;
|
||||
case 16:
|
||||
sprintf (out, "Exiting without errors\n");
|
||||
break;
|
||||
case 17:
|
||||
sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text);
|
||||
break;
|
||||
case 18:
|
||||
sprintf (out, "File '%s' not found\nError\n", text);
|
||||
break;
|
||||
case 19:
|
||||
sprintf (out, "Memory error\n");
|
||||
break;
|
||||
case 20:
|
||||
sprintf (out, "%6cCenter of molecules was set successfully\n", ' ');
|
||||
break;
|
||||
case 21:
|
||||
sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
|
||||
break;
|
||||
case 22:
|
||||
sprintf (out, "%6cRADF was appended successfully\n", ' ');
|
||||
break;
|
||||
default:
|
||||
return 1;
|
||||
break;
|
||||
}
|
||||
|
||||
fputs (out, output);
|
||||
return 0;
|
||||
}
|
||||
14
radf/src/messages.h
Normal file
14
radf/src/messages.h
Normal file
@ -0,0 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef MESSAGES_H
|
||||
#define MESSAGES_H
|
||||
|
||||
/**
|
||||
* @fn message
|
||||
*/
|
||||
|
||||
int message (const int, const int, const char *, FILE *);
|
||||
|
||||
#endif /* MESSAGES_H */
|
||||
302
radf/src/radf.c
Normal file
302
radf/src/radf.c
Normal file
@ -0,0 +1,302 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
|
||||
// pi
|
||||
#if !defined __USE_BSD && !defined __USE_XOPEN
|
||||
#ifndef M_PI
|
||||
#define M_PI 3.14159265358979323846
|
||||
#endif /* __USE_BSD && __USE_XOPEN */
|
||||
#endif /* M_PI */
|
||||
|
||||
|
||||
/**
|
||||
* @fn search_rdf
|
||||
*/
|
||||
int search_rdf (const int num_atoms, const int *type_atoms, const int *label_mol,
|
||||
const float *coords, const double r_min, const double r_max,
|
||||
const double r_step, int *radf)
|
||||
/**
|
||||
* @brief function that searchs molecule for rdf massive
|
||||
* @code
|
||||
* search_rdf (num_atoms, type_atoms, label_mol, coords, r_min, r_max, r_step, radf);
|
||||
* @endcode
|
||||
*
|
||||
* @param num_atoms number of atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param coords massive of coordinates
|
||||
* @param r_min minimal radius
|
||||
* @param r_max maximal radius
|
||||
* @param r_step radius step
|
||||
* @param radf not normed RDF
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
float r;
|
||||
int i, j, k;
|
||||
|
||||
/* r radius
|
||||
*/
|
||||
|
||||
for (i=0; i<num_atoms; i++)
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
if (((type_atoms[i] == 0) && (type_atoms[j] == 1)) ||
|
||||
((type_atoms[i] == 1) && (type_atoms[j] == 0)))
|
||||
{
|
||||
r = sqrt (pow ((coords[3*i+0] - coords[3*j+0]), 2) +
|
||||
pow ((coords[3*i+1] - coords[3*j+1]), 2) +
|
||||
pow ((coords[3*i+2] - coords[3*j+2]), 2));
|
||||
|
||||
if ((r >= r_min) && (r <= r_max))
|
||||
{
|
||||
k = (r - r_min) / r_step;
|
||||
radf[k]++;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn search_rdf_centr
|
||||
*/
|
||||
int search_rdf_centr (const int num_atoms, const int *type_atoms, const int *label_mol,
|
||||
const float *coords, const double r_min, const double r_max,
|
||||
const double r_step, int *radf)
|
||||
/**
|
||||
* @brief function that searchs molecule for rdf massive by centered coordinates
|
||||
* @code
|
||||
* search_rdf_centr (num_atoms, type_atoms, label_mol, coords, r_min, r_max, r_step,
|
||||
* radf);
|
||||
* @endcode
|
||||
*
|
||||
* @param num_atoms number of atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param coords massive of coordinates
|
||||
* @param r_min minimal radius
|
||||
* @param r_max maximal radius
|
||||
* @param r_step radius step
|
||||
* @param radf not normed RDF
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
* @return 1 - error in set center (missing atoms)
|
||||
*/
|
||||
{
|
||||
float r, cur_coords[2][3];
|
||||
int coef, cur_at, i, j, k, l;
|
||||
|
||||
/* cur_coords centered coordinates
|
||||
* r radius
|
||||
* coef ==1 if j<num_atoms, ==7 if j>=num_atoms
|
||||
* cur_at number of founded atoms
|
||||
*/
|
||||
|
||||
for (i=0; i<num_atoms; i++)
|
||||
if ((type_atoms[i] == 0) || (type_atoms[i] == 3))
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
if (((type_atoms[i] == 0) && (type_atoms[j] == 3)) ||
|
||||
((type_atoms[i] == 3) && (type_atoms[j] == 0)))
|
||||
{
|
||||
// set center for i-molecule
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[0][l] = coords[3*i+l];
|
||||
cur_at = 1;
|
||||
for (k=1; k<6; k++)
|
||||
if (label_mol[i+k] == label_mol[i])
|
||||
if ((type_atoms[i+k] == type_atoms[i] + 1) ||
|
||||
(type_atoms[i+k] == type_atoms[i] + 2))
|
||||
{
|
||||
cur_at++;
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[0][l] += coords[3*(i+k)+l];
|
||||
}
|
||||
if (cur_at == 3)
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[0][l] = cur_coords[0][l] / cur_at;
|
||||
else
|
||||
return 1;
|
||||
// set center for j-molecule
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[1][l] = coords[3*j+l];
|
||||
cur_at = 1;
|
||||
if (j < num_atoms)
|
||||
coef = 1;
|
||||
else
|
||||
coef = 7;
|
||||
for (k=1; k<6; k++)
|
||||
if (label_mol[j+coef*k] == label_mol[j])
|
||||
if ((type_atoms[j+coef*k] == type_atoms[j] + 1) ||
|
||||
(type_atoms[j+coef*k] == type_atoms[j] + 2))
|
||||
{
|
||||
cur_at++;
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[1][l] += coords[3*(j+coef*k)+l];
|
||||
}
|
||||
if (cur_at == 3)
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[1][l] = cur_coords[1][l] / cur_at;
|
||||
else
|
||||
return 1;
|
||||
|
||||
r = sqrt (pow ((cur_coords[0][0] - cur_coords[1][0]), 2) +
|
||||
pow ((cur_coords[0][1] - cur_coords[1][1]), 2) +
|
||||
pow ((cur_coords[0][2] - cur_coords[1][2]), 2));
|
||||
|
||||
if ((r >= r_min) && (r <= r_max))
|
||||
{
|
||||
k = (r - r_min) / r_step;
|
||||
radf[k]++;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @fn search_radf
|
||||
*/
|
||||
int search_radf (const int num_atoms, const int *type_atoms, const int *label_mol,
|
||||
const float *coords, const double r_min, const double r_max,
|
||||
const double r_step, const double ang_min, const double ang_max,
|
||||
const double ang_step, int *radf)
|
||||
/**
|
||||
* @brief function that searchs molecule for radf massive
|
||||
* @code
|
||||
* search_radf (num_atoms, type_atoms, label_mol, coords, r_min, r_max, r_step,
|
||||
* ang_min, ang_max, ang_step, radf);
|
||||
* @endcode
|
||||
*
|
||||
* @param num_atoms number of atoms
|
||||
* @param type_atoms massive of atom types
|
||||
* @param label_mol massive of numbers of molecule for atoms
|
||||
* @param coords massive of coordinates
|
||||
* @param r_min minimal radius
|
||||
* @param r_max maximal radius
|
||||
* @param r_step radius step
|
||||
* @param ang_min minimal angle
|
||||
* @param ang_max maximal angle
|
||||
* @param ang_step anlge step
|
||||
* @param radf not normed RADF
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
* @return 1 - error in set center (missing atoms)
|
||||
*/
|
||||
{
|
||||
float ang, cos_ang, cur_coords[2][3], normal[2][3], r;
|
||||
int coef, cur_at, i, j, k, l, n, n_max, plane_index[6];
|
||||
|
||||
/* ang angle
|
||||
* cur_coords centered coordinates
|
||||
* normal normal to planes
|
||||
* r radius
|
||||
* coef ==1 if j<num_atoms, ==7 if j>=num_atoms
|
||||
* cur_at number of founded atoms
|
||||
* n_max range of angles
|
||||
* plane_index atoms forming plane
|
||||
*/
|
||||
|
||||
for (i=0; i<num_atoms; i++)
|
||||
if ((type_atoms[i] == 0) || (type_atoms[i] == 3))
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
if (((type_atoms[i] == 0) && (type_atoms[j] == 3)) ||
|
||||
((type_atoms[i] == 3) && (type_atoms[j] == 0)))
|
||||
{
|
||||
// set center for i-molecule
|
||||
plane_index[type_atoms[i]] = i;
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[0][l] = coords[3*i+l];
|
||||
cur_at = 1;
|
||||
for (k=1; k<6; k++)
|
||||
if (label_mol[i+k] == label_mol[i])
|
||||
if ((type_atoms[i+k] == type_atoms[i] + 1) ||
|
||||
(type_atoms[i+k] == type_atoms[i] + 2))
|
||||
{
|
||||
cur_at++;
|
||||
plane_index[type_atoms[i+k]] = i + k;
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[0][l] += coords[3*(i+k)+l];
|
||||
}
|
||||
if (cur_at == 3)
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[0][l] = cur_coords[0][l] / cur_at;
|
||||
else
|
||||
return 1;
|
||||
// set center for j-molecule
|
||||
plane_index[type_atoms[j]] = j;
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[1][l] = coords[3*j+l];
|
||||
cur_at = 1;
|
||||
if (j < num_atoms)
|
||||
coef = 1;
|
||||
else
|
||||
coef = 7;
|
||||
for (k=1; k<6; k++)
|
||||
if (label_mol[j+coef*k] == label_mol[j])
|
||||
if ((type_atoms[j+coef*k] == type_atoms[j] + 1) ||
|
||||
(type_atoms[j+coef*k] == type_atoms[j] + 2))
|
||||
{
|
||||
cur_at++;
|
||||
plane_index[type_atoms[j+coef*k]] = j + coef * k;
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[1][l] += coords[3*(j+coef*k)+l];
|
||||
}
|
||||
if (cur_at == 3)
|
||||
for (l=0; l<3; l++)
|
||||
cur_coords[1][l] = cur_coords[1][l] / cur_at;
|
||||
else
|
||||
return 1;
|
||||
|
||||
r = sqrt (pow ((cur_coords[0][0] - cur_coords[1][0]), 2) +
|
||||
pow ((cur_coords[0][1] - cur_coords[1][1]), 2) +
|
||||
pow ((cur_coords[0][2] - cur_coords[1][2]), 2));
|
||||
// define planes
|
||||
normal[0][0] = (coords[3*plane_index[1]+1] - coords[3*plane_index[0]+1]) *
|
||||
(coords[3*plane_index[2]+2] - coords[3*plane_index[0]+2]) -
|
||||
(coords[3*plane_index[1]+2] - coords[3*plane_index[0]+2]) *
|
||||
(coords[3*plane_index[2]+1] - coords[3*plane_index[0]+1]);
|
||||
normal[0][1] = (coords[3*plane_index[1]+2] - coords[3*plane_index[0]+2]) *
|
||||
(coords[3*plane_index[2]+0] - coords[3*plane_index[0]+0]) -
|
||||
(coords[3*plane_index[1]+0] - coords[3*plane_index[0]+0]) *
|
||||
(coords[3*plane_index[2]+2] - coords[3*plane_index[0]+2]);
|
||||
normal[0][2] = (coords[3*plane_index[1]+0] - coords[3*plane_index[0]+0]) *
|
||||
(coords[3*plane_index[2]+1] - coords[3*plane_index[0]+1]) -
|
||||
(coords[3*plane_index[1]+1] - coords[3*plane_index[0]+1]) *
|
||||
(coords[3*plane_index[2]+0] - coords[3*plane_index[0]+0]);
|
||||
normal[1][0] = (coords[3*plane_index[4]+1] - coords[3*plane_index[3]+1]) *
|
||||
(coords[3*plane_index[5]+2] - coords[3*plane_index[3]+2]) -
|
||||
(coords[3*plane_index[4]+2] - coords[3*plane_index[3]+2]) *
|
||||
(coords[3*plane_index[5]+1] - coords[3*plane_index[3]+1]);
|
||||
normal[1][1] = (coords[3*plane_index[4]+2] - coords[3*plane_index[3]+2]) *
|
||||
(coords[3*plane_index[5]+0] - coords[3*plane_index[3]+0]) -
|
||||
(coords[3*plane_index[4]+0] - coords[3*plane_index[3]+0]) *
|
||||
(coords[3*plane_index[5]+2] - coords[3*plane_index[3]+2]);
|
||||
normal[1][2] = (coords[3*plane_index[4]+0] - coords[3*plane_index[3]+0]) *
|
||||
(coords[3*plane_index[5]+1] - coords[3*plane_index[3]+1]) -
|
||||
(coords[3*plane_index[4]+1] - coords[3*plane_index[3]+1]) *
|
||||
(coords[3*plane_index[5]+0] - coords[3*plane_index[3]+0]);
|
||||
cos_ang = (normal[0][0] * normal[1][0] + normal[0][1] * normal[1][1] + normal[0][2] * normal[1][2]) /
|
||||
(sqrt (pow ((normal[0][0]), 2) + pow ((normal[0][1]), 2) + pow ((normal[0][2]), 2)) *
|
||||
sqrt (pow ((normal[1][0]), 2) + pow ((normal[1][1]), 2) + pow ((normal[1][2]), 2)));
|
||||
ang = 180 / M_PI * acos (cos_ang);
|
||||
if (ang > 90)
|
||||
ang = 180 - ang;
|
||||
|
||||
n_max = (ang_max - ang_min) / ang_step;
|
||||
if ((r >= r_min) && (r <= r_max))
|
||||
if ((ang >= ang_min) && (ang <= ang_max))
|
||||
{
|
||||
k = (r - r_min) / r_step;
|
||||
n = (ang - ang_min) / ang_step;
|
||||
radf[n_max*k+n]++;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
26
radf/src/radf.h
Normal file
26
radf/src/radf.h
Normal file
@ -0,0 +1,26 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef RADF_H
|
||||
#define RADF_H
|
||||
|
||||
/**
|
||||
* @fn search_rdf
|
||||
*/
|
||||
/**
|
||||
* @fn search_rdf_centr
|
||||
*/
|
||||
/**
|
||||
* @fn search_radf
|
||||
*/
|
||||
|
||||
int search_rdf (const int, const int *, const int *, const float *, const double,
|
||||
const double, const double, int *);
|
||||
int search_rdf_centr (const int, const int *, const int *, const float *, const double,
|
||||
const double, const double, int *);
|
||||
int search_radf (const int, const int *, const int *, const float *, const double,
|
||||
const double, const double, const double, const double, const double,
|
||||
int *);
|
||||
|
||||
#endif /* RADF_H */
|
||||
138
radf/src/radf_proc.c
Normal file
138
radf/src/radf_proc.c
Normal file
@ -0,0 +1,138 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
|
||||
// pi
|
||||
#if !defined __USE_BSD && !defined __USE_XOPEN
|
||||
#ifndef M_PI
|
||||
#define M_PI 3.14159265358979323846
|
||||
#endif /* __USE_BSD && __USE_XOPEN */
|
||||
#endif /* M_PI */
|
||||
|
||||
|
||||
/**
|
||||
* @fn print_result
|
||||
*/
|
||||
int print_result (const char *output, const int matrix, const int mode,
|
||||
const int step, const int num_atoms, const double r_min,
|
||||
const double r_max, const double r_step, const double ang_min,
|
||||
const double ang_max, const double ang_step, const float *cell,
|
||||
const int *radf)
|
||||
/**
|
||||
* @brief function that print result to output file
|
||||
* @code
|
||||
* print_result (output, matrix, mode, step, num_atoms, r_min, r_max, r_step, ang_min,
|
||||
* ang_max, ang_step, cell, radf);
|
||||
* @endcode
|
||||
*
|
||||
* @param output output file name
|
||||
* @param matrix status of matrix-mode
|
||||
* @param mode 1 - if RDF, 2 - if RDF for center mass, 3 - if RADF
|
||||
* @param step $(to - from + 1)
|
||||
* @param num_atoms number of atoms
|
||||
* @param r_min minimal radius
|
||||
* @param r_max maximal radius
|
||||
* @param r_step radius step
|
||||
* @param ang_min minimal angle
|
||||
* @param ang_max maximal angle
|
||||
* @param ang_step angle step
|
||||
* @param cell cell size
|
||||
* @param radf not normed RADF
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
float ang, dv, norm, r, ro;
|
||||
int i, j, k, n;
|
||||
FILE *f_out;
|
||||
|
||||
/* ang angle
|
||||
* dv volume
|
||||
* norm normed RDF
|
||||
* r radius
|
||||
* ro density
|
||||
* f_out output file
|
||||
*/
|
||||
|
||||
f_out = fopen (output, "a");
|
||||
fprintf (f_out, "SUMMARY STATISTIC\n");
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
if (matrix == 0)
|
||||
fprintf (f_out, "| r | dV | RDF | RDFnorm |\n------------------------------------------\n");
|
||||
k = (r_max - r_min) / r_step;
|
||||
for (i=0; i<k; i++)
|
||||
{
|
||||
r = r_min + (0.5 + i) * r_step;
|
||||
dv = 4 * M_PI * pow (r, 2) * r_step;
|
||||
ro = num_atoms / (2 * cell[0] * cell[1] * cell[2]);
|
||||
norm = radf[i] / (dv * ro * num_atoms * step);
|
||||
if (matrix == 0)
|
||||
fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
|
||||
else
|
||||
fprintf (f_out, " %9.4f %9.6f\n", r, norm);
|
||||
}
|
||||
fprintf (f_out, "------------------------------------------\n");
|
||||
break;
|
||||
case 1:
|
||||
if (matrix == 0)
|
||||
fprintf (f_out, "| r | dV | RDF | RDFnorm |\n------------------------------------------\n");
|
||||
k = (r_max - r_min) / r_step;
|
||||
for (i=0; i<k; i++)
|
||||
{
|
||||
r = r_min + (0.5 + i) * r_step;
|
||||
dv = 4 * M_PI * pow (r, 2) * r_step;
|
||||
ro = num_atoms / (3 * 2 * cell[0] * cell[1] * cell[2]);
|
||||
norm = radf[i] / (dv * ro * num_atoms / 3 * step);
|
||||
if (matrix == 0)
|
||||
fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
|
||||
else
|
||||
fprintf (f_out, " %9.4f %9.6f\n", r, norm);
|
||||
}
|
||||
fprintf (f_out, "------------------------------------------\n");
|
||||
break;
|
||||
case 2:
|
||||
if (matrix == 0)
|
||||
fprintf (f_out, "| r | ang | dV | RDF | RDFnorm |\n----------------------------------------------------\n");
|
||||
k = (r_max - r_min) / r_step;
|
||||
n = (ang_max - ang_min) / ang_step;
|
||||
if (matrix == 1)
|
||||
{
|
||||
fprintf (f_out, " r\\ang ");
|
||||
for (j=0; j<n; j++)
|
||||
fprintf (f_out, " %9.2f", ang_min+(0.5+j)*ang_step);
|
||||
fprintf (f_out, "\n");
|
||||
}
|
||||
for (i=0; i<k; i++)
|
||||
{
|
||||
if (matrix == 1)
|
||||
fprintf (f_out, " %9.4f", r);
|
||||
for (j=0; j<n; j++)
|
||||
{
|
||||
r = r_min + (0.5 + i) * r_step;
|
||||
ang = ang_min + (0.5 + j) * ang_step;
|
||||
dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * r_step * (M_PI * ang_step / 180);
|
||||
// dv = 4;
|
||||
ro = num_atoms / (3 * 2 * cell[0] * cell[1] * cell[2]);
|
||||
norm = radf[i] / (dv * ro * num_atoms / 3 * step);
|
||||
if (matrix == 0)
|
||||
fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[i] / 2, norm);
|
||||
else
|
||||
fprintf (f_out, " %9.6f", norm);
|
||||
}
|
||||
if (matrix == 1)
|
||||
fprintf (f_out, "\n");
|
||||
}
|
||||
fprintf (f_out, "----------------------------------------------------\n");
|
||||
break;
|
||||
}
|
||||
|
||||
fclose (f_out);
|
||||
|
||||
return 0;
|
||||
}
|
||||
16
radf/src/radf_proc.h
Normal file
16
radf/src/radf_proc.h
Normal file
@ -0,0 +1,16 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef RADF_PROC_H
|
||||
#define RADF_PROC_H
|
||||
|
||||
/**
|
||||
* @fn print_result
|
||||
*/
|
||||
|
||||
int print_result (const char *, const int, const int, const int, const int, const double,
|
||||
const double, const double, const double, const double, const double,
|
||||
const float *, const int *);
|
||||
|
||||
#endif /* RADF_PROC_H */
|
||||
@ -3,7 +3,8 @@ Version: 1.0.1
|
||||
License: GPL
|
||||
|
||||
Usage:
|
||||
statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
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
|
||||
|
||||
@ -4,7 +4,7 @@ CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c graph.c int2char.c messages.c stat_print.c stat_select.c stat_sort.c summary_stat.c
|
||||
SOURCES=main.c add_main.c coords.c graph.c messages.c stat_print.c stat_select.c stat_sort.c summary_stat.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=statgen
|
||||
|
||||
|
||||
@ -1,33 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
|
||||
/**
|
||||
* @fn conv
|
||||
*/
|
||||
char conv (const int fnumb, const int dig_pos)
|
||||
/**
|
||||
* @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;
|
||||
char const digit[] = "0123456789";
|
||||
|
||||
h = fnumb / 100;
|
||||
d = (fnumb % 100) / 10;
|
||||
o = fnumb % 10;
|
||||
|
||||
if (dig_pos == 1) return digit[o];
|
||||
if (dig_pos == 2) return digit[d];
|
||||
if (dig_pos == 3) return digit[h];
|
||||
else return digit[0];
|
||||
}
|
||||
@ -1,14 +0,0 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef INT2CHAR_H
|
||||
#define INT2CHAR_H
|
||||
|
||||
/**
|
||||
* @fn conv
|
||||
*/
|
||||
|
||||
char conv (const int, const int);
|
||||
|
||||
#endif /* INT2CHAR_H */
|
||||
@ -25,7 +25,7 @@
|
||||
* Usage:
|
||||
* <pre>
|
||||
* statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]
|
||||
* [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
* [ -l LOGFILE ] [ -q ] [ -h ]
|
||||
*
|
||||
* Parametrs:
|
||||
* -i - mask of input files
|
||||
@ -78,7 +78,6 @@
|
||||
|
||||
#include "add_main.h"
|
||||
#include "coords.h"
|
||||
#include "int2char.h"
|
||||
#include "messages.h"
|
||||
#include "stat_print.h"
|
||||
#include "stat_select.h"
|
||||
@ -98,7 +97,7 @@ int main (int argc, char *argv[])
|
||||
*/
|
||||
{
|
||||
char filename[256], tmp_str[2048];
|
||||
int error, i, index, j, k, label[2];
|
||||
int error, i, index, j, label[2];
|
||||
float label_fl;
|
||||
FILE *f_inp, *f_log;
|
||||
|
||||
@ -164,7 +163,8 @@ int main (int argc, char *argv[])
|
||||
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, "%sstatgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sstatgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]\n", tmp_str);
|
||||
sprintf (tmp_str, "%s [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -i - mask of input files\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -s - trajectory steps (integer)\n", tmp_str);
|
||||
@ -298,13 +298,7 @@ int main (int argc, char *argv[])
|
||||
|
||||
// processing
|
||||
// initial variables
|
||||
k = strlen (input);
|
||||
strcpy (filename, input);
|
||||
filename[k] = '.';
|
||||
filename[k+1] = conv (from, 3);
|
||||
filename[k+2] = conv (from, 2);
|
||||
filename[k+3] = conv (from, 1);
|
||||
filename[k+4] = '\0';
|
||||
sprintf (filename, "%s.%03i", input, from);
|
||||
print_message (quiet, stdout, log, f_log, 3, filename);
|
||||
f_inp = fopen (filename, "r");
|
||||
if (f_inp == NULL)
|
||||
@ -327,15 +321,15 @@ int main (int argc, char *argv[])
|
||||
stat_all = (int *) malloc (2 * sizeof (int));
|
||||
// error checking
|
||||
if ((coords == NULL) ||
|
||||
(label_mol == NULL) ||
|
||||
(true_label_mol == NULL) ||
|
||||
(type_agl == NULL) ||
|
||||
(type_atoms == NULL) ||
|
||||
(agl == NULL) ||
|
||||
(connect == NULL) ||
|
||||
(num_mol_agl == NULL) ||
|
||||
(stat == NULL) ||
|
||||
(stat_all == NULL))
|
||||
(label_mol == NULL) ||
|
||||
(true_label_mol == NULL) ||
|
||||
(type_agl == NULL) ||
|
||||
(type_atoms == NULL) ||
|
||||
(agl == NULL) ||
|
||||
(connect == NULL) ||
|
||||
(num_mol_agl == NULL) ||
|
||||
(stat == NULL) ||
|
||||
(stat_all == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 3;
|
||||
@ -371,15 +365,12 @@ int main (int argc, char *argv[])
|
||||
for (i=from; i<to+1; i++)
|
||||
{
|
||||
// reading coordinates
|
||||
filename[k+1] = conv (i, 3);
|
||||
filename[k+2] = conv (i, 2);
|
||||
filename[k+3] = conv (i, 1);
|
||||
filename[k+4] = '\0';
|
||||
sprintf (filename, "%s.%03i", input, i);
|
||||
print_message (quiet, stdout, log, f_log, 7, filename);
|
||||
error = reading_coords (0, filename, type_inter, label_atom, cell, &num_mol,
|
||||
&num_atoms, true_label_mol, label_mol, type_atoms,
|
||||
coords, tmp_str);
|
||||
if (error != 1)
|
||||
if (error == 0)
|
||||
{
|
||||
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
|
||||
' ', num_mol, ' ', num_atoms);
|
||||
@ -399,10 +390,10 @@ int main (int argc, char *argv[])
|
||||
}
|
||||
// error checking
|
||||
if ((agl == NULL) ||
|
||||
(connect == NULL) ||
|
||||
(num_mol_agl == NULL) ||
|
||||
(stat == NULL) ||
|
||||
(stat_all == NULL))
|
||||
(connect == NULL) ||
|
||||
(num_mol_agl == NULL) ||
|
||||
(stat == NULL) ||
|
||||
(stat_all == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 3;
|
||||
|
||||
Reference in New Issue
Block a user