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arcan1s
2013-07-28 04:03:28 +04:00
parent 1af86034e7
commit 7cab7c785f
48 changed files with 5349 additions and 297 deletions
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5
envir/CMakeLists.txt
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@ -1,7 +1,8 @@
cmake_minimum_required (VERSION 2.8)
cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0003 OLD)
cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT envir)
@ -28,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (src)
add_subdirectory (${${PROJECT}_SOURCE_DIR})

2
envir/README
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@ -1,4 +1,4 @@
envir - program for search environment for chosen molecule by geometric criterion
envir - program that searchs environment for chosen molecule by geometric criterion
Version: 1.0.1
License: GPL

65
envir/about.dox Normal file
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@ -0,0 +1,65 @@
/*!
* @mainpage envir
* @image latex ./logo.png
*
* @section intro_sec Introduction
*
* <b>About this program</b>:
* <ul>
* <li>Program that searchs environment for chosen molecule by geometric criterion
* </ul>
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
*</ul>
* <b>License</b>:
* <ul>
* <li>GPL
* </ul>
*
* @section How-To-Use How to use
* Usage:
* <pre>
* 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
* -c - cell size (float), A
* -o - output file with coordinates
* -n - number of molecule for search (integer). Default is 1
* -r - radius of environment (float). Default is 6.0
* -l - log enable
* -q - quiet enable
* -h - show this help and exit
* </pre>
*
* @page Install
*
* @section Requirements Requirements
* The application statgen requires the following external stuff:
* - cmake >= 2.8
* - gcc >= 4.8
*
* @section How-To How to install
*
* @subsection Linux Linux
* @code
* mkdir build && cd build
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
* make
* make install
* @endcode
*
* @subsection Windows Windows
* @code
* create project file using 'cmake'
* compile project
* @endcode
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* * initial release
*/

22
envir/envir.cmake
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@ -1,22 +1,32 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src:include)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
# 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 )
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 (STATUS "Flags not enabled")
message ("Unknown compiler")
endif ()

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48
envir/src/CMakeLists.txt
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@ -3,59 +3,27 @@ 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})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
## set files
# main files
set (MAIN_SOURCES main)
# not public srcs
set (PRIVATE_CLASSES add_main
coords
envir_search
messages
print_struct
set_center)
# headers only files
SET (HEADERS_ONLY)
# public srcs
set (PUBLIC_CLASSES)
# public headers
set (PUBLIC_HEADERS)
# shared libraries
# set files
aux_source_directory (. SOURCES)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
set (SOURCES)
# append list
foreach (class ${PRIVATE_CLASSES})
LIST (APPEND SOURCES ${class}.c)
LIST (APPEND HEADERS ${class}.h)
endforeach ()
foreach (class ${HEADERS_ONLY})
LIST (APPEND HEADERS ${class}.h)
endforeach ()
foreach (class ${PUBLIC_CLASSES})
LIST (APPEND SOURCES ${class}.c)
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
endforeach ()
# message
message (STATUS "SOURCES: ${SOURCES}")
# link libraries and compile
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
add_executable (${PROJECT} ${SOURCES})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT}
DESTINATION bin)
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS}
DESTINATION include/${PROJECT})
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()

59
envir/src/add_main.c
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@ -1,4 +1,5 @@
/* Additional library for main.c (envir)
/**
* @file
*/
#include <stdio.h>
@ -6,7 +7,25 @@
#include "messages.h"
/**
* @fn error_checking
*/
int error_checking (const float *cell, const char *input, const char *output)
/**
* @brief function that checks errors in input variables
* @code
* error_checking (cell, input, output);
* @endcode
*
* @param cell massive of cell size
* @param input first trajectory step
* @param output last trajectory step
*
* @return 11 - error in 'cell'
* @return 12 - error in 'input'
* @return 13 - error in 'output'
* @return 0 - exit without errors
*/
{
if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
return 11;
@ -19,8 +38,26 @@ int error_checking (const float *cell, const char *input, const char *output)
}
/**
* @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);
@ -31,8 +68,28 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
}
/**
* @fn set_defaults
*/
int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output,
int *quiet, float *rad)
/**
* @brief function for set default values of variables
* @code
* set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
* &type_inter, &quiet);
* @endcode
*
* @param cell massive of cell size
* @param input mask of trajectory files
* @param log status of log-mode
* @param num_of_mol number of molecule
* @param output output file name
* @param quiet status of quiet-mode
* @param rad radius of environment sphere
*
* @return 0 - exit without errors
*/
{
int i;

14
envir/src/add_main.h
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@ -1,6 +1,20 @@
/**
* @file
*/
#ifndef ADD_MAIN_H
#define ADD_MAIN_H
/**
* @fn error_checking
*/
/**
* @fn print_message
*/
/**
* @fn set_defaults
*/
int error_checking (const float *, const char *, const char *);
int print_message (const int, FILE *, const int, FILE *, const int, const char *);
int set_defaults (float *, char *, int *, int *, char *, int *, float *);

114
envir/src/coords.c
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@ -1,52 +1,67 @@
/* Library for reading coordinates from input file
*
* Usage:
* reading_coords (mode, filename, type_interaction, labels,
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
* label_molecule, type_atoms, coords, char_type_atoms)
/**
* @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)
/* filename - name of file with coordinates
* type_inter - type interaction (number of molecules for interaction)
* (number of molecules in aglomerate for agl)
* label_atom - types of atom for interaction
* (molecules in aglomerate for agl)
* cell - cell dimension
* num_mol - number of molecules for writing coordinates
* num_atoms - number of atoms for writing coordinates
* true_label_mol - massive of true numbers of molecule for atoms
* label_mol - massive of numbers of molecule for atoms
* type_atoms - massive of atom types for atoms
* coords - massive of coordinates
* ch_type_atoms - massive of char types for atoms
/**
* @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_*, at_symb - temp variables
* file_string - temp string variable
* atoms - total number of atoms in system
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
* ref_mol - number of molecule for reference
* not_tr_coords - not translated coordinates
* ref - coordinates of reference molecule
* inp - file with input data
/* 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;
// Reading file
/// <pre> reading file </pre>
inp = fopen (filename, "r");
if (inp == NULL)
return 1;
@ -61,10 +76,11 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
// reading variables according to selected mode
switch (mode)
{
case 0:
// for statgen
// mode == 0 (selected atoms)
for (j=0; j<type_inter; j++)
if (cur_at_type == label_atom[j])
{
@ -85,7 +101,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
break;
case 1:
// for envir and frad
// 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];
@ -104,7 +120,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
break;
case 2:
// for agl
// mode == 2 (selected molecules)
for (j=0; j<type_inter; j++)
if (cur_mol == label_atom[j])
{
@ -126,18 +142,18 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
}
break;
default: return 1;
default: return 2;
}
}
fclose (inp);
// Translation
/// <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
// assign initial value to reference coordinates
ref_mol = label_mol[0];
for (i=0; i<3; i++)
ref[i] = coords[3*0+i];
@ -154,7 +170,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
for (x=0; x<3; x++)
{
if (ref[x] >= 0.0)
// if xyz >= 0.0 A
// if xyz >= 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
@ -167,7 +183,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
tr_num_atoms++;
}
else
// if xyz < 0.0 A
// if xyz < 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
@ -186,7 +202,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
for (y=x+1; y<3; y++)
{
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
// if xyz and xyz >= 0.0 A
// if xyz and xyz >= 0.0 A
{
for (j=0; j<3; j++)
if ((j == x) || (j == y))
@ -200,7 +216,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[x] < 0.0) && (ref[y] < 0.0))
// if xyz and xyz < 0.0 A
// if xyz and xyz < 0.0 A
{
for (j=0; j<3; j++)
if ((j == x) || (j == y))
@ -216,7 +232,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
for (y=0; y<3; y++)
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
// if xyz OR xyz >= 0.0
// if xyz OR xyz >= 0.0
{
for (j=0; j<3; j++)
{
@ -235,7 +251,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
// if x and y and z >= 0.0 A
// if x and y and z >= 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -247,7 +263,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
// if x and y >= 0.0 A and z < 0.0 A
// if x and y >= 0.0 A and z < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -259,7 +275,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
// if x and z >= 0.0 A and y < 0.0 A
// if x and z >= 0.0 A and y < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -271,7 +287,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
// if y and z >= 0.0 A and x < 0.0 A
// if y and z >= 0.0 A and x < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -283,7 +299,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
// if x and y < 0.0 A and z >= 0.0 A
// if x and y < 0.0 A and z >= 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -295,7 +311,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
// if x and z < 0.0 A and y >= 0.0 A
// if x and z < 0.0 A and y >= 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -307,7 +323,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
// if x >= 0.0 A and y and z < 0.0 A
// if x >= 0.0 A and y and z < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -319,7 +335,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
// if x and y and z < 0.0 A
// if x and y and z < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -331,7 +347,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
}
// free memory
/// <pre> free memory </pre>
free (not_tr_coords);
return 0;

8
envir/src/coords.h
View File

@ -1,6 +1,14 @@
/**
* @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 *);

31
envir/src/envir_search.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for search environment
*
* Usage:
@ -8,19 +12,32 @@
#include <math.h>
/**
* @fn search_envir
*/
int search_envir (const int num_of_mol, const int num_mol, const float *centr_coords,
const double rad, int *needed_mol, int *num_needed_mol)
/* num_of_mol - number of molecule for search
* num_mol - number of molecules for writing coordinates
* centr_coords - massive of centered coordinates
* rad - criterion
* needed_mol - massive of needed molecules
* num_needed_mol - number of needed molecules
/**
* @brief function that searchs environment
* @code
* search_envir (number_of_molecule, num_mol, centr_coords, rad, needed_mol,
* &num_needed_mol);
* @endcode
*
* @param num_of_mol number of molecule
* @param num_mol number of molecules
* @param centr_coords massive of centered coordinates
* @param rad radius of environment sphere
* @param needed_mol massive of number of needed molecules
* @param num_needed_mol number of needed molecules
*
* @return 0 - exit without errors
*/
{
float r;
int i;
/* r - radius
/* r radius
*/
*num_needed_mol = 0;

8
envir/src/envir_search.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef ENVIR_SEARCH_H
#define ENVIR_SEARCH_H
/**
* @fn search_envir
*/
int search_envir (const int, const int, const float *, const double, int *, int *);
#endif /* ENVIR_SEARCH_H */

82
envir/src/main.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
@ -11,7 +15,16 @@
#include "set_center.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 tmp_str[2048];
int error, i, j, *tmp_int;
@ -21,25 +34,26 @@ int main(int argc, char *argv[])
float cell[3], *centr_coords, *coords, rad;
int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol,
*needed_mol, quiet, *true_label_mol;
/* ch_type_atoms - massive of char types for atoms
* input - input file name
* logfile - log file name
* output - output file name
/* ch_type_atoms massive of char atom types
* input input file name
* logfile log file name
* output output file name
*
* cell - cell dimension
* centr_coords - massive of coordinates of center molecules
* coords - massive of coordinates
* rad - criterion
* cell massive of cell size
* centr_coords massive of centered coordinates
* coords massive of coordinates
* rad radius of environment sphere
*
* label_mol - massive of numbers of molecule for atoms
* log - status of log-mode
* num_atoms - number of atoms for writing coordinates
* num_mol - number of molecules for writing coordinates
* num_needed_mol - number of needed molecules
* num_of_mol - number of molecule for search
* needed_mol - massive of needed molecules
* quiet - status of quiet-mode
* true_label_mol - massive of true numbers of molecule for atoms
* label_mol massive of numbers of molecule for atoms
* log status of log-mode
* num_atoms number of atoms
* num_mol number of molecules
* num_needed_mol number of needed molecules
* num_of_mol number of molecule
* needed_mol massive of number of needed molecules
* quiet status of quiet-mode
* true_label_mol massive of true numbers of molecule for atoms
*/
set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
@ -68,44 +82,44 @@ int main(int argc, char *argv[])
return 0;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
// input file
// input file
{
strcpy (input, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
// cell size
// cell size
{
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
// output file
// output file
{
strcpy (output, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'n'))
// number of molecule
// number of molecule
{
sscanf (argv[i+1], "%i", &num_of_mol);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
// radius of environment
// radius of environment
{
sscanf (argv[i+1], "%f", &rad);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
// log mode
// log mode
{
log = 1;
strcpy (logfile, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
// quiet mode
// quiet mode
{
quiet = 1;
}
@ -127,14 +141,14 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 2, argv[0]);
// processing
// initial variables
// processing
// initial variables
print_message (quiet, stdout, log, f_log, 3, input);
f_inp = fopen (input, "r");
if (f_inp == NULL)
{
print_message (quiet, stderr, log, f_log, 18, input);
return 1;
return 2;
}
fscanf (f_inp, "%i", &num_atoms);
fclose (f_inp);
@ -143,7 +157,7 @@ int main(int argc, char *argv[])
label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
// error checking
// error checking
if ((ch_type_atoms == NULL) ||
(coords == NULL) ||
(label_mol == NULL) ||
@ -151,7 +165,7 @@ int main(int argc, char *argv[])
(true_label_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 17;
return 3;
}
sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
@ -161,7 +175,7 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// reading coordinates
// reading coordinates
print_message (quiet, stdout, log, f_log, 7, input);
error = reading_coords (1, input, tmp_int, tmp_int, cell, &num_mol, &num_atoms,
true_label_mol, label_mol, tmp_int, coords, ch_type_atoms);
@ -173,15 +187,15 @@ int main(int argc, char *argv[])
' ', num_mol, ' ', num_atoms);
print_message (quiet, stdout, log, f_log, 8, tmp_str);
}
// error checking
// error checking
if ((centr_coords == NULL) ||
(needed_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 17;
return 3;
}
// analyze
// analyze
if (error == 0)
{
error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
@ -203,7 +217,7 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 13, argv[0]);
print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory
// free memory
free (ch_type_atoms);
free (centr_coords);
free (coords);

24
envir/src/messages.c
View File

@ -1,16 +1,27 @@
/* Library for printing messages at output
*
* Usage:
* message (log, mode, text, output)
/**
* @file
*/
#include <stdio.h>
#include <time.h>
/**
* @fn message
*/
int message (const int log, const int mode, const char *text, FILE *output)
/* mode - number of message
* text - additional text
/**
* @brief function that prints messages to output
* @code
* message (log, mode, text, output);
* @endcode
*
* @param log equal to 1 if print to logfile
* @param mode number of message
* @param text additional text
* @param output output file (may be stdout)
*
* @return 0 - exit without errors
*/
{
char out[4096];
@ -18,6 +29,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
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,

8
envir/src/messages.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef MESSAGES_H
#define MESSAGES_H
/**
* @fn message
*/
int message (const int, const int, const char *, FILE *);
#endif /* MESSAGES_H */

38
envir/src/print_struct.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for printing structure to pdb file
*
* Usage:
@ -8,23 +12,37 @@
#include <stdio.h>
/**
* @fn print_structure
*/
int print_structure (const char *output, const int num_needed_mol, const int *needed_mol,
const int num_atoms, const int *label_mol, const char *ch_type_atoms,
const float *coords)
/* output - output file name
* num_needed_mol - number of needed molecules
* needed_mol - massive of needed molecules
* num_atoms - number of atoms
* label_mol - massive of numbers of molecule for atoms
* ch_type_atoms - massive of char types for atoms
* coords - massive of coordinates
/**
* @brief function that prints structure to pdb file
* @code
* print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol,
* char_type_atoms, coords);
* @endcode
*
* @param output output file name
* @param num_needed_mol number of needed molecules
* @param needed_mol massive of number of needed molecules
* @param num_atoms number of atoms
* @param label_mol massive of numbers of molecule for atoms
* @param ch_type_atoms massive of char atom types
* @param coords massive of coordinates
*
* @return 0 - exit without errors
*/
{
int cur_atom, cur_atom_num, cur_mol, i, j;
FILE *f_out;
/* cur_atom - current atom
* cur_atom_num - true atom number
* cur_mol - current molecule
/* cur_atom current atom
* cur_atom_num true atom number
* cur_mol current molecule
* f_out output file
*/
cur_atom = 1;

8
envir/src/print_struct.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef PRINT_STRUCTURE_H
#define PRINT_STRUCTURE_H
/**
* @fn print_structure
*/
int print_structure (const char *, const int, const int *, const int, const int *,
const char *, const float *);

30
envir/src/set_center.c
View File

@ -1,3 +1,7 @@
/**
* @file
*/
/* Library for search center mass of molecules
*
* Usage:
@ -6,18 +10,30 @@
*/
/**
* @fn set_center
*/
int set_center (const int num_atoms, const int num_mol, const int *label_mol,
const float *coords, float *centr_coords)
/* num_atoms - number of atoms for writing coordinates
* num_mol - number of molecules for writing coordinates
* label_mol - massive of numbers of molecule for atoms
* coords - massive of coordinates
* coords - massive of coordinates of center molecules
/**
* @brief function that searchs center mass of molecules
* @code
* set_center (num_of_atoms, num_of_molecules, label_molecules, coords, centr_coords);
* @endcode
*
* @param num_atoms number of atoms
* @param num_mol number of molecules
* @param label_mol massive of numbers of molecule for atoms
* @param coords massive of coordinates
* @param centr_coords massive of centered coordinates
*
* @return 0 - exit without errors
*/
{
int at_in_mol, cur_mol, i, j, k;
/* at_int_mol - number of atoms in molecule
* cur_mol - current molecule
/* at_int_mol number of atoms in molecule
* cur_mol current molecule
*/
for (i=0; i<8*num_mol; i++)

8
envir/src/set_center.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef SET_CENTER_H
#define SET_CENTER_H
/**
* @fn set_center
*/
int set_center (const int, const int, const int *, const float *, float *);
#endif /* SET_CENTER_H */