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Prerelease mm_trj
edited logo edited Makefile's
This commit is contained in:
arcan1s
@ -45,7 +45,7 @@ PROJECT_BRIEF = "Program that creates PDB file with chosen aglomerate"
|
||||
# exceed 55 pixels and the maximum width should not exceed 200 pixels.
|
||||
# Doxygen will copy the logo to the output directory.
|
||||
|
||||
PROJECT_LOGO = /home/arcanis/Documents/github/moldyn/agl/logo.png
|
||||
PROJECT_LOGO = ./logo.png
|
||||
|
||||
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
|
||||
# base path where the generated documentation will be put.
|
||||
|
||||
@ -6,7 +6,7 @@ LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c messages.c print_struct.c read_agl.c select_mol.c set_center.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=agl
|
||||
EXECUTABLE=mm_agl
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
@ -17,5 +17,4 @@ $(EXECUTABLE): $(OBJECTS)
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||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
rm -f *.o test*
|
||||
|
||||
@ -45,7 +45,7 @@ PROJECT_BRIEF = "Program that searchs environment for chosen molecule b
|
||||
# exceed 55 pixels and the maximum width should not exceed 200 pixels.
|
||||
# Doxygen will copy the logo to the output directory.
|
||||
|
||||
PROJECT_LOGO = /home/arcanis/Documents/github/moldyn/envir/logo.png
|
||||
PROJECT_LOGO = ./logo.png
|
||||
|
||||
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
|
||||
# base path where the generated documentation will be put.
|
||||
|
||||
@ -6,7 +6,7 @@ LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c envir_search.c messages.c print_struct.c set_center.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=envir
|
||||
EXECUTABLE=mm_envir
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
@ -17,5 +17,4 @@ $(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
rm -f *.o test*
|
||||
|
||||
@ -38,15 +38,14 @@ PROJECT_NUMBER = V.1.0.1
|
||||
# for a project that appears at the top of each page and should give viewer
|
||||
# a quick idea about the purpose of the project. Keep the description short.
|
||||
|
||||
PROJECT_BRIEF = "radf - program that calculates radial distribution function RDF or radial-angles
|
||||
distribution function RADF"
|
||||
PROJECT_BRIEF = "Program that calculates radial distribution function RDF or radial-angles distribution function RADF"
|
||||
|
||||
# With the PROJECT_LOGO tag one can specify an logo or icon that is
|
||||
# included in the documentation. The maximum height of the logo should not
|
||||
# exceed 55 pixels and the maximum width should not exceed 200 pixels.
|
||||
# Doxygen will copy the logo to the output directory.
|
||||
|
||||
PROJECT_LOGO = /home/arcanis/Documents/github/moldyn/radf/logo.png
|
||||
PROJECT_LOGO = ./logo.png
|
||||
|
||||
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
|
||||
# base path where the generated documentation will be put.
|
||||
|
||||
@ -6,7 +6,7 @@ LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c messages.c radf.c radf_proc.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=radf
|
||||
EXECUTABLE=mm_radf
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
@ -17,5 +17,4 @@ $(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
rm -f *.o test*
|
||||
|
||||
@ -45,7 +45,7 @@ PROJECT_BRIEF = "Program that analyzes molecular dynamic trajectories u
|
||||
# exceed 55 pixels and the maximum width should not exceed 200 pixels.
|
||||
# Doxygen will copy the logo to the output directory.
|
||||
|
||||
PROJECT_LOGO = /home/arcanis/Documents/github/moldyn/statgen/logo.png
|
||||
PROJECT_LOGO = ./logo.png
|
||||
|
||||
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
|
||||
# base path where the generated documentation will be put.
|
||||
|
||||
@ -6,7 +6,7 @@ LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c coords.c graph.c messages.c stat_print.c stat_select.c stat_sort.c summary_stat.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=statgen
|
||||
EXECUTABLE=mm_statgen
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
@ -17,5 +17,4 @@ $(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
rm -f *.o test*
|
||||
|
||||
3
mm_trj/AUTHORS
Normal file
3
mm_trj/AUTHORS
Normal file
@ -0,0 +1,3 @@
|
||||
Current developers:
|
||||
|
||||
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>
|
||||
32
mm_trj/CMakeLists.txt
Normal file
32
mm_trj/CMakeLists.txt
Normal file
@ -0,0 +1,32 @@
|
||||
cmake_minimum_required (VERSION 2.8)
|
||||
|
||||
cmake_policy(SET CMP0003 OLD)
|
||||
cmake_policy(SET CMP0011 NEW)
|
||||
cmake_policy(SET CMP0015 NEW)
|
||||
|
||||
# set project name
|
||||
set (PROJECT mm_trj)
|
||||
# set additional cmake file
|
||||
include (${PROJECT}.cmake)
|
||||
|
||||
|
||||
# additional options
|
||||
OPTION (WITH_DEBUG_MODE "Build with debug mode" OFF)
|
||||
OPTION (ADD_INCLUDE "Add include files" OFF)
|
||||
|
||||
# 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
mm_trj/COPYING
Normal file
341
mm_trj/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
|
||||
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|
||||
want its recipients to know that what they have is not the original, so
|
||||
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|
||||
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|
||||
|
||||
Finally, any free program is threatened constantly by software
|
||||
patents. We wish to avoid the danger that redistributors of a free
|
||||
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|
||||
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
|
||||
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|
||||
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|
||||
Whether that is true depends on what the Program does.
|
||||
|
||||
1. You may copy and distribute verbatim copies of the Program's
|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
|
||||
You may charge a fee for the physical act of transferring a copy, and
|
||||
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|
||||
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||||
2. You may modify your copy or copies of the Program or any portion
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
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|
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|
||||
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|
||||
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|
||||
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||||
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||||
|
||||
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
|
||||
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|
||||
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|
||||
distribute the same sections as part of a whole which is a work based
|
||||
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|
||||
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|
||||
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||||
|
||||
Thus, it is not the intent of this section to claim rights or contest
|
||||
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|
||||
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||||
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||||
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||||
In addition, mere aggregation of another work not based on the Program
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|
||||
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|
||||
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|
||||
|
||||
3. You may copy and distribute the Program (or a work based on it,
|
||||
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||||
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||||
|
||||
a) Accompany it with the complete corresponding machine-readable
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||||
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||||
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||||
b) Accompany it with a written offer, valid for at least three
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years, to give any third party, for a charge no more than your
|
||||
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||||
machine-readable copy of the corresponding source code, to be
|
||||
distributed under the terms of Sections 1 and 2 above on a medium
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||||
customarily used for software interchange; or,
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||||
|
||||
c) Accompany it with the information you received as to the offer
|
||||
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||||
The source code for a work means the preferred form of the work for
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||||
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||||
If distribution of executable or object code is made by offering
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||||
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||||
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||||
4. You may not copy, modify, sublicense, or distribute the Program
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||||
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||||
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||||
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||||
However, parties who have received copies, or rights, from you under
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||||
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||||
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||||
5. You are not required to accept this License, since you have not
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||||
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all its terms and conditions for copying, distributing or modifying
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||||
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||||
6. Each time you redistribute the Program (or any work based on the
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||||
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||||
restrictions on the recipients' exercise of the rights granted herein.
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||||
You are not responsible for enforcing compliance by third parties to
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||||
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|
||||
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||||
7. If, as a consequence of a court judgment or allegation of patent
|
||||
infringement or for any other reason (not limited to patent issues),
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||||
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||||
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||||
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|
||||
distribute so as to satisfy simultaneously your obligations under this
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||||
License and any other pertinent obligations, then as a consequence you
|
||||
may not distribute the Program at all. For example, if a patent
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||||
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|
||||
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||||
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||||
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||||
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||||
If any portion of this section is held invalid or unenforceable under
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||||
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|
||||
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||||
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||||
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||||
It is not the purpose of this section to induce you to infringe any
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||||
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||||
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||||
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||||
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||||
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||||
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||||
This section is intended to make thoroughly clear what is believed to
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
the limitation as if written in the body of this License.
|
||||
|
||||
9. The Free Software Foundation may publish revised and/or new versions
|
||||
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|
||||
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|
||||
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||||
|
||||
Each version is given a distinguishing version number. If the Program
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
10. If you wish to incorporate parts of the Program into other free
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||||
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||||
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||||
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||||
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||||
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||||
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||||
|
||||
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
|
||||
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|
||||
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
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||||
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||||
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||||
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
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||||
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
mm_trj/INSTALL
Normal file
14
mm_trj/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.
|
||||
24
mm_trj/README
Normal file
24
mm_trj/README
Normal file
@ -0,0 +1,24 @@
|
||||
mm_trj - program that generates trajectory files
|
||||
Version : 1.0.1
|
||||
License : GPL
|
||||
|
||||
Usage:
|
||||
mm_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
mm_trj/logo.png
Executable file
BIN
mm_trj/logo.png
Executable file
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
32
mm_trj/mm_trj.cmake
Normal file
32
mm_trj/mm_trj.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 ()
|
||||
1889
mm_trj/mm_trj.doxygen
Normal file
1889
mm_trj/mm_trj.doxygen
Normal file
File diff suppressed because it is too large
Load Diff
29
mm_trj/src/CMakeLists.txt
Normal file
29
mm_trj/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
mm_trj/src/Makefile
Normal file
21
mm_trj/src/Makefile
Normal file
@ -0,0 +1,21 @@
|
||||
PROJECT=TRJ
|
||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
|
||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
|
||||
SOURCES=main.c add_main.c atom_types.c messages.c read_gmx.c read_puma.c print_trj.c
|
||||
OBJECTS=$(SOURCES:.c=.o)
|
||||
EXECUTABLE=mm_trj
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o test*
|
||||
|
||||
113
mm_trj/src/add_main.c
Normal file
113
mm_trj/src/add_main.c
Normal file
@ -0,0 +1,113 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "messages.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
||||
int error_checking (const char *input, const char *input_at, const char *output,
|
||||
const int step, const int type)
|
||||
/**
|
||||
* @brief function that checks errors in input variables
|
||||
* @code
|
||||
* error_checking (cell, from, input, num_needed_at, needed_at, output, to);
|
||||
* @endcode
|
||||
*
|
||||
* @param input input file name
|
||||
* @param input_at input file name with atom types
|
||||
* @param output output file name
|
||||
* @param step number of trajectory steps
|
||||
* @param type type of trajectory
|
||||
*
|
||||
* @return 11 - error in 'input_at'
|
||||
* @return 12 - error in 'input'
|
||||
* @return 13 - error in 'output'
|
||||
* @return 14 - error in 'step'
|
||||
* @return 15 - error in 'type'
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
if (input_at[0] == '#')
|
||||
return 11;
|
||||
if (input[0] == '#')
|
||||
return 12;
|
||||
if (output[0] == '#')
|
||||
return 13;
|
||||
if (step == 0)
|
||||
return 14;
|
||||
if (type == -1)
|
||||
return 15;
|
||||
|
||||
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 set_defaults
|
||||
*/
|
||||
int set_defaults (char *input, char *input_at, int *log, char *output, int *step,
|
||||
int *total_types, int *type, int *quiet)
|
||||
/**
|
||||
* @brief function that sets default values of variables
|
||||
* @code
|
||||
* set_defaults (input, input_at, &log, output, &step, &type, &quiet);
|
||||
* @endcode
|
||||
*
|
||||
* @param input input file name
|
||||
* @param input_at input file name with atom types
|
||||
* @param log status of log-mode
|
||||
* @param output output file name
|
||||
* @param step number of trajectory steps
|
||||
* @param total_types number of different atom types
|
||||
* @param type type of trajectory
|
||||
* @param quiet status of quiet-mode
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
input[0] = '#';
|
||||
input_at[0] = '#';
|
||||
*log = 0;
|
||||
output[0] = '#';
|
||||
*step = 0;
|
||||
*total_types = 1024;
|
||||
*type = -1;
|
||||
*quiet = 0;
|
||||
|
||||
return 0;
|
||||
}
|
||||
22
mm_trj/src/add_main.h
Normal file
22
mm_trj/src/add_main.h
Normal file
@ -0,0 +1,22 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef ADD_MAIN_H
|
||||
#define ADD_MAIN_H
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
||||
/**
|
||||
* @fn print_message
|
||||
*/
|
||||
/**
|
||||
* @fn set_defaults
|
||||
*/
|
||||
|
||||
int error_checking (const char *, const char *, const char *, const int, const int);
|
||||
int print_message (const int, FILE *, const int, FILE *, const int, const char *);
|
||||
int set_defaults (char *, char *, int *, char *, int *, int *, int *, int *);
|
||||
|
||||
#endif /* ADD_MAIN_H */
|
||||
87
mm_trj/src/atom_types.c
Normal file
87
mm_trj/src/atom_types.c
Normal file
@ -0,0 +1,87 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn reading_atoms
|
||||
*/
|
||||
int reading_atoms (const char *input_at, int *num_types, int *num_mol, int *num_atoms,
|
||||
char *ch_atom_types, int *atom_types, const int total_types)
|
||||
/**
|
||||
* @brief function that reads atom types from input file
|
||||
* @code
|
||||
* reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types, atom_types,
|
||||
* total_types);
|
||||
* @endcode
|
||||
*
|
||||
* @param input_at input file name with atom types
|
||||
* @param num_types number of molecule types
|
||||
* @param num_mol massive of number of molecules of selected type
|
||||
* @param num_atoms massive of number of atoms of selected molecule
|
||||
* @param ch_atom_types massive of char atom types
|
||||
* @param atom_types massive of atom types
|
||||
* @param total_types number of different atom types
|
||||
*
|
||||
* @return 1 - error in opening file
|
||||
* @return 2 - error in file format
|
||||
* @return 3 - memory error
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char at_symb[2], tmp_str[256];
|
||||
int at_ndx, i, j, total_atoms;
|
||||
FILE *f_inp;
|
||||
|
||||
/* at_* temp variables
|
||||
* total_atoms total atom types
|
||||
* f_inp input file
|
||||
*/
|
||||
|
||||
f_inp = fopen (input_at, "r");
|
||||
if (f_inp == NULL)
|
||||
return 1;
|
||||
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "NUMTYPES=%i", num_types);
|
||||
if (*num_types == 0)
|
||||
return 2;
|
||||
else if (*num_types > total_types)
|
||||
return 3;
|
||||
|
||||
total_atoms = 0;
|
||||
for (i=0; i<*num_types; i++)
|
||||
{
|
||||
// read constants
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "NUMMOL=%i", &num_mol[i]);
|
||||
if (num_mol[i] == 0)
|
||||
return 2;
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "NUMAT=%i", &num_atoms[i]);
|
||||
if (num_atoms[i] == 0)
|
||||
return 2;
|
||||
else if ((total_atoms + num_atoms[i]) > total_types)
|
||||
return 2;
|
||||
|
||||
// read atoms
|
||||
for (j=0; j<num_atoms[i]; j++)
|
||||
{
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
at_ndx = -1;
|
||||
sscanf (tmp_str, "%2s=%i", at_symb, &at_ndx);
|
||||
if (at_ndx == -1)
|
||||
return 2;
|
||||
ch_atom_types[2*total_atoms+2*j+0] = at_symb[0];
|
||||
ch_atom_types[2*total_atoms+2*j+1] = at_symb[1];
|
||||
atom_types[total_atoms+j] = at_ndx;
|
||||
}
|
||||
total_atoms += num_atoms[i];
|
||||
}
|
||||
|
||||
fclose (f_inp);
|
||||
|
||||
return 0;
|
||||
}
|
||||
14
mm_trj/src/atom_types.h
Normal file
14
mm_trj/src/atom_types.h
Normal file
@ -0,0 +1,14 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef ATOM_TYPES_H
|
||||
#define ATOM_TYPES_H
|
||||
|
||||
/**
|
||||
* @fn reading_atoms
|
||||
*/
|
||||
|
||||
int reading_atoms (const char *, int *, int *, int *, char *, int *, const int);
|
||||
|
||||
#endif /* ATOM_TYPES_H */
|
||||
313
mm_trj/src/main.c
Normal file
313
mm_trj/src/main.c
Normal file
@ -0,0 +1,313 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
/**
|
||||
* @mainpage mm_trj
|
||||
* @image latex ./logo.png
|
||||
*
|
||||
* @section intro_sec Introduction
|
||||
*
|
||||
* <b>About this program</b>:
|
||||
* <ul>
|
||||
* <li>Program that generates trajectory files
|
||||
* </ul>
|
||||
*
|
||||
* <b>Developer</b>:
|
||||
* <ul>
|
||||
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
|
||||
*</ul>
|
||||
* <b>License</b>:
|
||||
* <ul>
|
||||
* <li>GPL
|
||||
* </ul>
|
||||
*
|
||||
* @section How-To-Use How to use
|
||||
* Usage:
|
||||
* <pre>
|
||||
* mm_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 mm_trj 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 "atom_types.h"
|
||||
#include "messages.h"
|
||||
#include "print_trj.h"
|
||||
#include "read_gmx.h"
|
||||
#include "read_puma.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 4 - unknown flag
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char tmp_str[2048];
|
||||
int error, i;
|
||||
FILE *f_inp, *f_log;
|
||||
|
||||
char *ch_atom_types, input[256], input_at[256], logfile[256], output[256];
|
||||
float *coords;
|
||||
int *atom_types, log, *num_atoms, *num_mol, num_types, quiet, step, total_types, type;
|
||||
|
||||
/* ch_atom_types massive of char atom types
|
||||
* input input file name
|
||||
* input_at input file name with atom types
|
||||
* logfile log file name
|
||||
* output mask of output files
|
||||
*
|
||||
* coords massive of coordinates
|
||||
*
|
||||
* atom_types massive of atom types
|
||||
* log status of log-mode
|
||||
* num_atoms massive of number of atoms of selected molecule
|
||||
* num_mol massive of number of molecule of selected type
|
||||
* num_types number of molecule types
|
||||
* quiet status of quiet-mode
|
||||
* step number of trajectory steps
|
||||
* total_types number of different atom types
|
||||
* type type of trajectory
|
||||
*/
|
||||
|
||||
set_defaults (input, input_at, &log, output, &step, &total_types, &type, &quiet);
|
||||
|
||||
for (i=1; i<argc; i++)
|
||||
{
|
||||
if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
|
||||
{
|
||||
sprintf (tmp_str, " mm_trj\n");
|
||||
sprintf (tmp_str, "%sProgram that generates trajectory files\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, "%smm_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]\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 name\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -t - type of trajectory. Supported formats: gmx, puma\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -s - number of trajectory steps (integer)\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -a - input file with atom types. See file format in manual\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -o - mask of output files\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -tt - number of different atom types. Default is 1024\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') && (argv[i][2] == '\0'))
|
||||
// input file
|
||||
{
|
||||
strcpy (input, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 't') && (argv[i][2] == '\0'))
|
||||
// type
|
||||
{
|
||||
if ((argv[i+1][0] == 'g') && (argv[i+1][1] == 'm') && (argv[i+1][2] == 'x') &&
|
||||
(argv[i+1][3] == '\0'))
|
||||
// gromacs text file
|
||||
type = 0;
|
||||
else if ((argv[i+1][0] == 'p') && (argv[i+1][1] == 'u') && (argv[i+1][2] == 'm') &&
|
||||
(argv[i+1][3] == 'a') && (argv[i+1][4] == '\0'))
|
||||
// puma
|
||||
type = 1;
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
|
||||
// steps
|
||||
{
|
||||
sscanf (argv[i+1], "%i", &step);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
|
||||
// atom types
|
||||
{
|
||||
strcpy (input_at, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
|
||||
// output file
|
||||
{
|
||||
strcpy (output, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 't') && (argv[i][1] == 't') && (argv[i][2] == '\0'))
|
||||
// number of atom types
|
||||
{
|
||||
sscanf (argv[i+1], "%i", &total_types);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
|
||||
// log mode
|
||||
{
|
||||
log = 1;
|
||||
strcpy (logfile, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
|
||||
// quiet mode
|
||||
{
|
||||
quiet = 1;
|
||||
}
|
||||
else
|
||||
// unknown flag
|
||||
{
|
||||
return 4;
|
||||
}
|
||||
}
|
||||
|
||||
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 (input, input_at, output, step, type);
|
||||
if (error != 0)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 17, argv[0]);
|
||||
return 1;
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
||||
|
||||
// processing
|
||||
// initial variables
|
||||
print_message (quiet, stdout, log, f_log, 3, input);
|
||||
f_inp = fopen (input, "r");
|
||||
if (f_inp == NULL)
|
||||
return 2;
|
||||
switch (type)
|
||||
{
|
||||
case 0:
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, " natoms=%i%s", &i, tmp_str);
|
||||
break;
|
||||
case 1:
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "%s%s%i%s", tmp_str, tmp_str, &i, tmp_str);
|
||||
break;
|
||||
}
|
||||
fclose (f_inp);
|
||||
atom_types = (int *) malloc (total_types * sizeof (int));
|
||||
ch_atom_types = (char *) malloc (2 * total_types * sizeof (char));
|
||||
coords = (float *) malloc (3 * i * sizeof (float));
|
||||
num_atoms = (int *) malloc (total_types * sizeof (int));
|
||||
num_mol = (int *) malloc (total_types * sizeof (int));
|
||||
num_types = 0;
|
||||
if ((atom_types == NULL) ||
|
||||
(ch_atom_types == NULL) ||
|
||||
(coords == NULL) ||
|
||||
(num_atoms == NULL) ||
|
||||
(num_mol == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 3;
|
||||
}
|
||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||
// read atom types
|
||||
error = 1;
|
||||
error = reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types,
|
||||
atom_types, total_types);
|
||||
if (error == 0)
|
||||
{
|
||||
sprintf (tmp_str, "%6cLog: %i;\n%6cQuiet: %i;\n%6cInput file: %s;\n%6cTrajectory type: %i;\n\
|
||||
%6cNumber of trajectory step: %i;\n%6cInput file with atom types: %s;\n%6cMask of output file: %s;\n\
|
||||
%6cNumber of different atom types: %i;\n%6cNumber of different molecules: %i;\n%6cNumber of atoms in system: %i\n",
|
||||
' ', log, ' ', quiet, ' ', input, ' ', type, ' ', step, ' ', input_at, ' ', output,
|
||||
' ', total_types, ' ', num_types, ' ', i);
|
||||
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||
}
|
||||
else
|
||||
return 2;
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||
// main cycle
|
||||
switch (type)
|
||||
{
|
||||
case 0:
|
||||
rw_gmx (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
|
||||
atom_types, coords);
|
||||
break;
|
||||
case 1:
|
||||
rw_puma (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
|
||||
atom_types, coords);
|
||||
break;
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||
// free memory
|
||||
free (atom_types);
|
||||
free (ch_atom_types);
|
||||
free (coords);
|
||||
free (num_atoms);
|
||||
free (num_mol);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 16, argv[0]);
|
||||
|
||||
if (log == 1)
|
||||
fclose (f_log);
|
||||
return 0;
|
||||
}
|
||||
119
mm_trj/src/messages.c
Normal file
119
mm_trj/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
mm_trj/src/messages.h
Normal file
14
mm_trj/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 */
|
||||
BIN
mm_trj/src/mm_trj
Executable file
BIN
mm_trj/src/mm_trj
Executable file
Binary file not shown.
71
mm_trj/src/print_trj.c
Normal file
71
mm_trj/src/print_trj.c
Normal file
@ -0,0 +1,71 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn printing_trj
|
||||
*/
|
||||
int printing_trj (const char *filename, const int atoms, const int num_types, const int *num_mol,
|
||||
const int *num_atoms, const char *ch_atom_types, const int *atom_types,
|
||||
const float *coords)
|
||||
/**
|
||||
* @brief function that prints trajectory snapshots
|
||||
* @code
|
||||
* printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types,
|
||||
* atom_types, coords);
|
||||
* @endcode
|
||||
*
|
||||
* @param filename output file name
|
||||
* @param atoms number of atoms in system
|
||||
* @param num_types number of molecule types
|
||||
* @param num_mol massive of number of molecule of selected type
|
||||
* @param num_atoms massive of number of atoms of selected molecule
|
||||
* @param ch_atom_types massive of char atom types
|
||||
* @param atom_types massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
*
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
int cur_mol, cur_type[2], i, j, k, l;
|
||||
FILE *f_out;
|
||||
|
||||
/* cur_mol number of current molecule
|
||||
* cur_type number of current atom type
|
||||
* f_out output file
|
||||
*/
|
||||
|
||||
cur_mol = 1;
|
||||
f_out = fopen (filename, "w");
|
||||
fprintf (f_out, " %6i\n", atoms);
|
||||
|
||||
i = 0;
|
||||
while (i < atoms)
|
||||
{
|
||||
cur_type[0] = 0;
|
||||
for (j=0; j<num_types; j++)
|
||||
{
|
||||
for (k=0; k<num_mol[j]; k++)
|
||||
{
|
||||
cur_type[1] = cur_type[0];
|
||||
for (l=0; l<num_atoms[j]; l++)
|
||||
{
|
||||
fprintf (f_out, "%5i %c%c %12.6f%12.6f%12.6f %2i %4i\n", i+1,
|
||||
ch_atom_types[2*cur_type[1]+0], ch_atom_types[2*cur_type[1]+1], coords[3*i+0],
|
||||
coords[3*i+1], coords[3*i+2], atom_types[cur_type[1]], cur_mol);
|
||||
cur_type[1]++;
|
||||
i++;
|
||||
}
|
||||
cur_mol++;
|
||||
}
|
||||
cur_type[0] += num_atoms[j];
|
||||
}
|
||||
}
|
||||
|
||||
fclose (f_out);
|
||||
|
||||
return 0;
|
||||
}
|
||||
15
mm_trj/src/print_trj.h
Normal file
15
mm_trj/src/print_trj.h
Normal file
@ -0,0 +1,15 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef PRINT_TRJ_H
|
||||
#define PRINT_TRJ_H
|
||||
|
||||
/**
|
||||
* @fn printing_trj
|
||||
*/
|
||||
|
||||
int printing_trj (const char *, const int, const int, const int *, const int *,
|
||||
const char *, const int *, const float *);
|
||||
|
||||
#endif /* PRINT_TRJ_H */
|
||||
38
mm_trj/src/read_gmx.c
Normal file
38
mm_trj/src/read_gmx.c
Normal file
@ -0,0 +1,38 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "print_trj.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn rw_gmx
|
||||
*/
|
||||
int rw_gmx (const char *input, const int step, const char *output, const int num_types,
|
||||
const int *num_mol, const int *num_atoms, const char *ch_atom_types,
|
||||
const int *atom_types, float *coords)
|
||||
/**
|
||||
* @brief function that read GROMACS trajectory file and write to output
|
||||
* @code
|
||||
* rw_gmx (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
|
||||
* atom_types, coords);
|
||||
* @endcode
|
||||
*
|
||||
* @param input input file name
|
||||
* @param step number of trajectory steps
|
||||
* @param output mask of output files
|
||||
* @param num_types number of molecule types
|
||||
* @param num_mol massive of number of molecule of selected type
|
||||
* @param num_atoms massive of number of atoms of selected molecule
|
||||
* @param ch_atom_types massive of char atom types
|
||||
* @param atom_types massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
*
|
||||
* @return 1 - file does not exist
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
15
mm_trj/src/read_gmx.h
Normal file
15
mm_trj/src/read_gmx.h
Normal file
@ -0,0 +1,15 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef READ_GMX_H
|
||||
#define READ_GMX_H
|
||||
|
||||
/**
|
||||
* @fn rw_gmx
|
||||
*/
|
||||
|
||||
int rw_gmx (const char *, const int, const char *, const int, const int *,
|
||||
const int *, const char *, const int *, float *);
|
||||
|
||||
#endif /* READ_GMX_H */
|
||||
87
mm_trj/src/read_puma.c
Normal file
87
mm_trj/src/read_puma.c
Normal file
@ -0,0 +1,87 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
#include "print_trj.h"
|
||||
|
||||
|
||||
/**
|
||||
* @fn rw_puma
|
||||
*/
|
||||
int rw_puma (const char *input, const int step, const char *output, const int num_types,
|
||||
const int *num_mol, const int *num_atoms, const char *ch_atom_types,
|
||||
const int *atom_types, float *coords)
|
||||
/**
|
||||
* @brief function that read PUMA trajectory file and write to output
|
||||
* @code
|
||||
* rw_puma (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
|
||||
* atom_types, coords);
|
||||
* @endcode
|
||||
*
|
||||
* @param input input file name
|
||||
* @param step number of trajectory steps
|
||||
* @param output mask of output files
|
||||
* @param num_types number of molecule types
|
||||
* @param num_mol massive of number of molecule of selected type
|
||||
* @param num_atoms massive of number of atoms of selected molecule
|
||||
* @param ch_atom_types massive of char atom types
|
||||
* @param atom_types massive of atom types
|
||||
* @param coords massive of coordinates
|
||||
*
|
||||
* @return 1 - file does not exist
|
||||
* @return 0 - exit without errors
|
||||
*/
|
||||
{
|
||||
char filename[256], tmp_str[256];
|
||||
float cell[3];
|
||||
int atoms, i, j, k, l, m, n;
|
||||
FILE *f_inp;
|
||||
|
||||
f_inp = fopen (input, "r");
|
||||
if (f_inp == NULL)
|
||||
return 1;
|
||||
|
||||
for (i=0; i<step; i++)
|
||||
{
|
||||
// initial variables
|
||||
sprintf (filename, "%s.%03i", output, i+1);
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "%s%s%i%s", tmp_str, tmp_str, &atoms, tmp_str);
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "%f%f%f", &cell[0], &cell[1], &cell[2]);
|
||||
|
||||
for (j=0; j<atoms; j++)
|
||||
{
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
sscanf (tmp_str, "%f%f%f", &coords[3*j+0], &coords[3*j+1], &coords[3*j+2]);
|
||||
}
|
||||
fgets (tmp_str, 256, f_inp);
|
||||
|
||||
// processing coordinates
|
||||
j = 0;
|
||||
while (j < atoms)
|
||||
for (k=0; k<num_types; k++)
|
||||
for (l=0; l<num_mol[k]; l++)
|
||||
{
|
||||
for (m=0; m<3; m++)
|
||||
{
|
||||
while (coords[3*j+m] > cell[m]/2)
|
||||
for (n=j; n<j+num_atoms[k]; n++)
|
||||
coords[3*n+m] -= cell[m];
|
||||
while (coords[3*j+m] < -cell[m]/2)
|
||||
for (n=j; n<j+num_atoms[k]; n++)
|
||||
coords[3*n+m] += cell[m];
|
||||
}
|
||||
j += num_atoms[k];
|
||||
}
|
||||
// write to output
|
||||
printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types,
|
||||
atom_types, coords);
|
||||
}
|
||||
|
||||
fclose (f_inp);
|
||||
|
||||
return 0;
|
||||
}
|
||||
15
mm_trj/src/read_puma.h
Normal file
15
mm_trj/src/read_puma.h
Normal file
@ -0,0 +1,15 @@
|
||||
/**
|
||||
* @file
|
||||
*/
|
||||
|
||||
#ifndef READ_PUMA_H
|
||||
#define READ_PUMA_H
|
||||
|
||||
/**
|
||||
* @fn rw_puma
|
||||
*/
|
||||
|
||||
int rw_puma (const char *, const int, const char *, const int, const int *,
|
||||
const int *, const char *, const int *, float *);
|
||||
|
||||
#endif /* READ_PUMA_H */
|
||||
32
mm_trj/src/types
Normal file
32
mm_trj/src/types
Normal file
@ -0,0 +1,32 @@
|
||||
NUMTYPES=2
|
||||
NUMMOL=3
|
||||
NUMAT=12
|
||||
CL=5
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
NUMMOL=97
|
||||
NUMAT=15
|
||||
CL=1
|
||||
CT=4
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
CA=2
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
HC=3
|
||||
Reference in New Issue
Block a user