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2014-01-26 03:49:43 +04:00
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mathmech/radf/AUTHORS Normal file
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Current developers:
Evgeniy Alekseev aka arcanis <esalexeev (at) gmail (dot) com>

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mathmech/radf/CMakeLists.txt Normal file
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# set project name
set (PROJECT radf)
# set additional cmake file
include (${PROJECT}.cmake)
# set libraries
set (LIBRARIES "")
foreach (LIBRARY ${LIBRARIES})
add_subdirectory (../${LIBRARY} bin/${LIBRARY})
include_directories (${CMAKE_CURRENT_SOURCE_DIR}/../${LIBRARY}/include/)
endforeach ()
# additional targets
set (TARGETS "")
set (HEADERS "")
add_subdirectory (${PROJECT_SOURCE_DIR})

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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
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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
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When we speak of free software, we are referring to freedom, not
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0. This License applies to any program or other work which contains
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END OF TERMS AND CONDITIONS
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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
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(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
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You should have received a copy of the GNU General Public License
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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.

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CMakeFlags:
-DCMAKE_INSTALL_PREFIX= - install prefix (default is '/usr/local')
-DADD_INCLUDE=1 - install include files (default is disable)
-DADD_DOCS=1 - install documentation (default is disable)
-DWITH_DEBUG_MODE=1 - compile with flag '-g' (default is disable)
-DMM_PREFIX - prefix for mm components (test flag)
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.

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mm_radf - program that calculates radial distribution function (RDF) or radial-angles
distribution function (RADF)
Version : 1.1.1
License : GPL
Usage:
mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -at ... -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
-a5 - 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

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# set directories
set (PROJECT_BINARY_DIR bin)
set (PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
set (PROJECT_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
set (PROJECT_LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR}/lib)
# include_path
include_directories (${PROJECT_INCLUDE_DIR}
${PROJECT_SOURCE_DIR})
# library path
link_directories (${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 ()

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# set files
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif ()
# message
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_executable (${MM_PREFIX}${PROJECT} ${SOURCES} ${HEADERS})
target_link_libraries (${MM_PREFIX}${PROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
# install properties
install (TARGETS ${MM_PREFIX}${PROJECT} DESTINATION bin)

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mathmech/radf/src/add_main.c Normal file
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/**
* @file
*/
#include <stdio.h>
#include <mathmech/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.1.1.1\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\n", 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;
}

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/**
* @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 */

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/**
* @file
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "add_main.h"
#include <mathmech/coords.h>
#include <mathmech/messages.h>
#include <mathmech/radf.h>
#include <mathmech/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 4 - unknown flag
* @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') && (argv[i][2] == '\0'))
{
sprintf (tmp_str, " mm_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 : 1.1.1 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_radf -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') && (argv[i][2] == '\0'))
// input file
{
strcpy (input, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
// 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') && (argv[i][2] == '\0'))
// 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') && (argv[i][3] == '\0'))
// 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') && (argv[i][2] == '\0'))
// 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') && (argv[i][3] == '\0'))
// 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') && (argv[i][3] == '\0'))
// angle step
{
sscanf (argv[i+1], "%f", &ang_step);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'm') && (argv[i][2] == '\0'))
// matrix mode
{
matrix = 1;
}
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 (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;
}