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fixed envir and radf

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arcan1s
2014-01-28 04:44:30 +04:00
parent 0714cb6541
commit 30630ca541
9 changed files with 280 additions and 300 deletions
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1
mathmech/agl/src/add_main.c
View File

@ -4,6 +4,7 @@
#include <stdio.h> #include <stdio.h>
#include "add_main.h"
#include <mathmech/messages.h> #include <mathmech/messages.h>
#include <mathmech/var_types.h> #include <mathmech/var_types.h>

60
mathmech/envir/src/add_main.c
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@ -4,30 +4,18 @@
#include <stdio.h> #include <stdio.h>
#include "add_main.h"
#include <mathmech/messages.h> #include <mathmech/messages.h>
#include <mathmech/var_types.h>
/** /**
* @fn error_checking * @fn error_checking
*/ */
int error_checking (const float *cell, const char *input, const char *output) int error_checking (const system_info _system_info, 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 input file name
* @param output output file name
*
* @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)) if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
return 11; return 11;
if (input[0] == '#') if (input[0] == '#')
return 12; return 12;
@ -43,21 +31,6 @@ int error_checking (const float *cell, const char *input, const char *output)
*/ */
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
const int mode, const char *str) const int mode, const char *str)
/**
* @brief function that prints message in log and stdout
* @code
* print_message (quiet, stdout, log, f_log, 0, str);
* @endcode
*
* @param quiet status of quiet-mode
* @param std_output stdout
* @param log status of log-mode
* @param f_log log file
* @param mode number of message in "messages.c"
* @param str additional text in message
*
* @return 0 - exit without errors
*/
{ {
if ((quiet != 1) && (std_output != stderr)) if ((quiet != 1) && (std_output != stderr))
message (0, mode, str, std_output); message (0, mode, str, std_output);
@ -71,30 +44,13 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
/** /**
* @fn set_defaults * @fn set_defaults
*/ */
int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output, int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol,
int *quiet, float *rad) char *output, int *quiet, float *rad)
/**
* @brief function that sets 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; int i;
for (i=0; i<3; i++) for (i=0; i<3; i++)
cell[i] = 0.0; (*_system_info).cell[i] = 0.0;
input[0] = '#'; input[0] = '#';
*log = 0; *log = 0;
*num_of_mol = 1; *num_of_mol = 1;

65
mathmech/envir/src/add_main.h
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@ -5,18 +5,75 @@
#ifndef ADD_MAIN_H #ifndef ADD_MAIN_H
#define ADD_MAIN_H #define ADD_MAIN_H
#include <mathmech/var_types.h>
/** /**
* @fn error_checking * @fn error_checking
*/ */
int error_checking (const system_info _system_info, const char *input,
const char *output);
/**
* @brief function that checks errors in input variables
* @code
* error_checking (_system_info, input, output);
* @endcode
*
* @param _system_info system information structure
* @param input input file name
* @param output output file name
*
* @return 11 - error in 'cell'
* @return 12 - error in 'input'
* @return 13 - error in 'output'
* @return 0 - exit without errors
*/
/** /**
* @fn print_message * @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
*/
/** /**
* @fn set_defaults * @fn set_defaults
*/ */
int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol,
char *output, int *quiet, float *rad);
/**
* @brief function that sets default values of variables
* @code
* set_defaults (&_system_info, &from, input, &log, &max_depth, &num_of_inter, output, &to,
* &type_inter, &quiet);
* @endcode
*
* @param _system_info system information structure
* @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 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 *);
#endif /* ADD_MAIN_H */ #endif /* ADD_MAIN_H */

68
mathmech/envir/src/main.c
View File

@ -14,6 +14,7 @@
#include <mathmech/messages.h> #include <mathmech/messages.h>
#include <mathmech/print_struct.h> #include <mathmech/print_struct.h>
#include <mathmech/set_center.h> #include <mathmech/set_center.h>
#include <mathmech/var_types.h>
/** /**
@ -32,33 +33,31 @@ int main(int argc, char *argv[])
int error, i, *tmp_int; int error, i, *tmp_int;
FILE *f_inp, *f_log; FILE *f_inp, *f_log;
char *ch_type_atoms, input[256], logfile[256], output[256]; char input[256], logfile[256], output[256];
float cell[3], *centr_coords, *coords, rad; float *centr_coords, rad;
int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol, int log, num_needed_mol, num_of_mol, *needed_mol, quiet, *true_label_mol;
*needed_mol, quiet, *true_label_mol; atom_info *_atom_info;
system_info _system_info;
/* ch_type_atoms massive of char atom types /* input input file name
* input input file name
* logfile log file name * logfile log file name
* output output file name * output output file name
* *
* cell massive of cell size
* centr_coords massive of centered coordinates * centr_coords massive of centered coordinates
* coords massive of coordinates
* rad radius of environment sphere * rad radius of environment sphere
* *
* label_mol massive of numbers of molecule for atoms
* log status of log-mode * log status of log-mode
* num_atoms number of atoms
* num_mol number of molecules
* num_needed_mol number of needed molecules * num_needed_mol number of needed molecules
* num_of_mol number of molecule * num_of_mol number of molecule
* needed_mol massive of number of needed molecules * needed_mol massive of number of needed molecules
* quiet status of quiet-mode * quiet status of quiet-mode
* true_label_mol massive of true numbers of molecule for atoms * true_label_mol massive of true numbers of molecule for atoms
*
* _atom_info atom information file
* _system_info system information file
*/ */
set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad); set_defaults (&_system_info, input, &log, &num_of_mol, output, &quiet, &rad);
for (i=1; i<argc; i++) for (i=1; i<argc; i++)
{ {
@ -93,7 +92,7 @@ int main(int argc, char *argv[])
else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
// cell size // cell size
{ {
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]); sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
@ -140,7 +139,7 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 1, argv[0]); print_message (quiet, stdout, log, f_log, 1, argv[0]);
// error check // error check
error = error_checking (cell, input, output); error = error_checking (_system_info, input, output);
if (error != 0) if (error != 0)
{ {
print_message (quiet, stderr, log, f_log, 17, argv[0]); print_message (quiet, stderr, log, f_log, 17, argv[0]);
@ -158,17 +157,13 @@ int main(int argc, char *argv[])
print_message (quiet, stderr, log, f_log, 18, input); print_message (quiet, stderr, log, f_log, 18, input);
return 2; return 2;
} }
fscanf (f_inp, "%i", &num_atoms); fscanf (f_inp, "%i", &_system_info.num_atoms);
fclose (f_inp); fclose (f_inp);
ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char)); _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float)); tmp_int = (int *) malloc (8 * _system_info.num_atoms * sizeof (int));
label_mol = (int *) malloc (8 * num_atoms * sizeof (int)); true_label_mol = (int *) malloc (_system_info.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) || if ((_atom_info == NULL) ||
(coords == NULL) ||
(label_mol == NULL) ||
(tmp_int == NULL) || (tmp_int == NULL) ||
(true_label_mol == NULL)) (true_label_mol == NULL))
{ {
@ -177,8 +172,9 @@ int main(int argc, char *argv[])
} }
sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\ 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\ %6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], %6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ',
cell[1], cell[2], ' ' , num_of_mol, ' ', rad); _system_info.cell[0], _system_info.cell[1], _system_info.cell[2], ' ' , num_of_mol,
' ', rad);
print_message (quiet, stdout, log, f_log, 5, tmp_str); print_message (quiet, stdout, log, f_log, 5, tmp_str);
print_message (quiet, stdout, log, f_log, 6, argv[0]); print_message (quiet, stdout, log, f_log, 6, argv[0]);
@ -186,14 +182,14 @@ int main(int argc, char *argv[])
// reading coordinates // reading coordinates
print_message (quiet, stdout, log, f_log, 7, input); print_message (quiet, stdout, log, f_log, 7, input);
error = 1; error = 1;
error = reading_coords (1, input, tmp_int[0], tmp_int, cell, &num_mol, &num_atoms, error = reading_coords (0, input, tmp_int[0], tmp_int, &_system_info, true_label_mol,
true_label_mol, label_mol, tmp_int, coords, ch_type_atoms); _atom_info);
centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float)); centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
needed_mol = (int *) malloc (num_mol * sizeof (int)); needed_mol = (int *) malloc (_system_info.num_mol * sizeof (int));
if (error == 0) if (error == 0)
{ {
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n", sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
' ', num_mol, ' ', num_atoms); ' ', _system_info.num_mol, ' ', _system_info.num_atoms);
print_message (quiet, stdout, log, f_log, 8, tmp_str); print_message (quiet, stdout, log, f_log, 8, tmp_str);
} }
// error checking // error checking
@ -208,21 +204,21 @@ int main(int argc, char *argv[])
if (error == 0) if (error == 0)
{ {
error = 1; error = 1;
error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords); error = set_center (_system_info, _atom_info, centr_coords);
} }
if (error == 0) if (error == 0)
{ {
print_message (quiet, stderr, log, f_log, 20, argv[0]); print_message (quiet, stderr, log, f_log, 20, argv[0]);
error = 1; error = 1;
error = search_envir (num_of_mol, num_mol, centr_coords, rad, needed_mol, error = search_envir (num_of_mol, _system_info, centr_coords, rad, needed_mol,
&num_needed_mol); &num_needed_mol);
} }
if (error == 0) if (error == 0)
{ {
print_message (quiet, stderr, log, f_log, 21, argv[0]); print_message (quiet, stderr, log, f_log, 21, argv[0]);
error = 1; error = 1;
error = print_structure (output, num_needed_mol, needed_mol, num_atoms, error = print_structure (output, num_needed_mol, needed_mol, _system_info,
label_mol, ch_type_atoms, coords); _atom_info);
} }
if (error == 0) if (error == 0)
print_message (quiet, stderr, log, f_log, 12, output); print_message (quiet, stderr, log, f_log, 12, output);
@ -231,10 +227,8 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 15, argv[0]); print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory // free memory
free (ch_type_atoms); free (_atom_info);
free (centr_coords); free (centr_coords);
free (coords);
free (label_mol);
free (needed_mol); free (needed_mol);
free (tmp_int); free (tmp_int);
free (true_label_mol); free (true_label_mol);

8
mathmech/mm/include/mathmech/var_types.h
View File

@ -53,16 +53,16 @@ typedef struct
*/ */
typedef struct typedef struct
{ {
int first; int from;
int last; int to;
float cell[3]; float cell[3];
int num_atoms; int num_atoms;
int num_mol; int num_mol;
} system_info; } system_info;
/** /**
* @brief system information structure * @brief system information structure
* @var first last trajectory step * @var from last trajectory step
* @var last first trajectory step * @var to first trajectory step
* @var cell cell size * @var cell cell size
* @var num_atoms number of atoms * @var num_atoms number of atoms
* @var num_mol number of molecules * @var num_mol number of molecules

6
mathmech/mm/src/radf_proc.c
View File

@ -49,7 +49,7 @@ int print_result (const char *output, const int matrix, const int mode,
r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step; r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step;
dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step; dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step;
ro = _system_info.num_atoms / (2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]); ro = _system_info.num_atoms / (2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
norm = radf[i] / (dv * ro * _system_info.num_atoms * (_system_info.last - _system_info.first + 1)); norm = radf[i] / (dv * ro * _system_info.num_atoms * (_system_info.to - _system_info.from + 1));
if (matrix == 0) if (matrix == 0)
fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm); fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
else else
@ -66,7 +66,7 @@ int print_result (const char *output, const int matrix, const int mode,
r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step; r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step;
dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step; dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step;
ro = _system_info.num_atoms / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]); ro = _system_info.num_atoms / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
norm = radf[i] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.last - _system_info.first + 1)); norm = radf[i] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.to - _system_info.from + 1));
if (matrix == 0) if (matrix == 0)
fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm); fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
else else
@ -96,7 +96,7 @@ int print_result (const char *output, const int matrix, const int mode,
ang = _radf_info.ang_min + (0.5 + j) * _radf_info.ang_step; ang = _radf_info.ang_min + (0.5 + j) * _radf_info.ang_step;
dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * _radf_info.r_step * (M_PI * _radf_info.ang_step / 180); dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * _radf_info.r_step * (M_PI * _radf_info.ang_step / 180);
ro = _system_info.num_atoms / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]); ro = _system_info.num_atoms / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
norm = radf[n*i+j] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.last - _system_info.first + 1)); norm = radf[n*i+j] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.to - _system_info.from + 1));
if (matrix == 0) if (matrix == 0)
fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[n*i+j] / 2, norm); fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[n*i+j] / 2, norm);
else else

142
mathmech/radf/src/add_main.c
View File

@ -4,46 +4,25 @@
#include <stdio.h> #include <stdio.h>
#include "add_main.h"
#include <version.h> #include <version.h>
#include <mathmech/messages.h> #include <mathmech/messages.h>
#include <mathmech/var_types.h>
/** /**
* @fn error_checking * @fn error_checking
*/ */
int error_checking (const float *cell, const int from, const char *input, int error_checking (const char *input, const int num_needed_at, const int *needed_at,
const int num_needed_at, const int *needed_at, const char *output, const system_info _system_info)
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)) if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
return 11; return 11;
if (input[0] == '#') if (input[0] == '#')
return 12; return 12;
if (output[0] == '#') if (output[0] == '#')
return 13; return 13;
if ((from == -1) || (to == -1)) if ((_system_info.from == -1) || (_system_info.to == -1))
return 14; return 14;
if ((num_needed_at != 2) && (num_needed_at != 6)) if ((num_needed_at != 2) && (num_needed_at != 6))
return 15; return 15;
@ -65,21 +44,6 @@ int error_checking (const float *cell, const int from, const char *input,
*/ */
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log, int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
const int mode, const char *str) const int mode, const char *str)
/**
* @brief function that prints message in log and stdout
* @code
* print_message (quiet, stdout, log, f_log, 0, str);
* @endcode
*
* @param quiet status of quiet-mode
* @param std_output stdout
* @param log status of log-mode
* @param f_log log file
* @param mode number of message in "messages.c"
* @param str additional text in message
*
* @return 0 - exit without errors
*/
{ {
if ((quiet != 1) && (std_output != stderr)) if ((quiet != 1) && (std_output != stderr))
message (0, mode, str, std_output); message (0, mode, str, std_output);
@ -94,36 +58,8 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
* @fn printing_head * @fn printing_head
*/ */
int printing_head (const char *output, const int log, const int quiet, const int matrix, 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 char *input, const system_info _system_info, const int mode,
const int mode, const double r_min, const double r_max, const radf_info _radf_info, const int *needed_at)
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; FILE *f_out;
@ -132,10 +68,13 @@ int printing_head (const char *output, const int log, const int quiet, const int
fprintf (f_out, "CONFIGURATION\n"); fprintf (f_out, "CONFIGURATION\n");
fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix); 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, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, _system_info.from,
fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", cell[0], cell[1], cell[2]); _system_info.to);
fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", _system_info.cell[0], _system_info.cell[1],
_system_info.cell[2]);
fprintf (f_out, "MODE=%i\n", mode); 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); fprintf (f_out, "R_MIN=%.3f\nR_MAX=%.3f\nR_STEP=%.3f\n", _radf_info.r_min,
_radf_info.r_max, _radf_info.r_step);
switch (mode) switch (mode)
{ {
case 0: case 0:
@ -143,12 +82,12 @@ int printing_head (const char *output, const int log, const int quiet, const int
break; break;
case 1: case 1:
fprintf (f_out, "ATOM=%i,%i,%i-%i,%i,%i\n", needed_at[0], needed_at[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]); needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
break; break;
case 2: case 2:
fprintf (f_out, "ANG_MIN=%.2f\nANG_MAX=%.2f\nANG_STEP=%.2f\n\ 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], ATOM=%i,%i,%i-%i,%i,%i\n", _radf_info.ang_min, _radf_info.ang_max, _radf_info.ang_step,
needed_at[2], needed_at[3], needed_at[4], needed_at[5]); needed_at[0], needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
break; break;
} }
@ -162,50 +101,25 @@ needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
/** /**
* @fn set_defaults * @fn set_defaults
*/ */
int set_defaults (float *ang_max, float *ang_min, float *ang_step, float *cell, int set_defaults (system_info *_system_info, radf_info *_radf_info, char *input,
int *from, char *input, int *log, int *matrix, float *r_max, int *log, int *matrix, char *output, int *quiet)
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; int i;
*ang_max = 90.0; (*_radf_info).ang_max = 90.0;
*ang_min = 0.0; (*_radf_info).ang_min = 0.0;
*ang_step = 0.0; (*_radf_info).ang_step = 0.0;
for (i=0; i<3; i++) for (i=0; i<3; i++)
cell[i] = 0.0; (*_system_info).cell[i] = 0.0;
*from = -1; (*_system_info).from = -1;
input[0] = '#'; input[0] = '#';
*log = 0; *log = 0;
*matrix = 0; *matrix = 0;
*r_max = 15.0; (*_radf_info).r_max = 15.0;
*r_min = 2.0; (*_radf_info).r_min = 2.0;
*r_step = 0.2; (*_radf_info).r_step = 0.2;
output[0] = '#'; output[0] = '#';
*to = -1; (*_system_info).to = -1;
*quiet = 0; *quiet = 0;
return 0; return 0;

98
mathmech/radf/src/add_main.h
View File

@ -5,27 +5,105 @@
#ifndef ADD_MAIN_H #ifndef ADD_MAIN_H
#define ADD_MAIN_H #define ADD_MAIN_H
#include <mathmech/var_types.h>
/** /**
* @fn error_checking * @fn error_checking
*/ */
int error_checking (const char *input, const int num_needed_at, const int *needed_at,
const char *output, const system_info _system_info);
/**
* @brief function that checks errors in input variables
* @code
* error_checking (input, num_needed_at, needed_at, output, _system_info);
* @endcode
*
* @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 _system_info system information structure
*
* @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
*/
/** /**
* @fn print_message * @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
*/
/** /**
* @fn printing_head * @fn printing_head
*/ */
int printing_head (const char *output, const int log, const int quiet, const int matrix,
const char *input, const system_info _system_info, const int mode,
const radf_info _radf_info, const int *needed_at);
/**
* @brief function that prints header in output file
* @code
* printing_head (output, log, quiet, matrix, input, _system_info, mode, _radf_info,
* 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 _system_info system information structure
* @param mode 0 - if RDF, 1 - if RDF for center mass, 2 - if RADF
* @param _radf_info radf information structure
* @param needed_at massive of number of needed atom types
*
* @return 0 - exit without errors
*/
/** /**
* @fn set_defaults * @fn set_defaults
*/ */
int set_defaults (system_info *_system_info, radf_info *_radf_info, char *input,
int *log, int *matrix, char *output, int *quiet);
/**
* @brief function that sets default values of variables
* @code
* set_defaults (&_system_info, &_radf_info, input, &log, &matrix, output, &quiet);
* @endcode
*
* @param _system_info system information structure
* @param _radf_info radf information structure
* @param input mask of trajectory files
* @param log status of log-mode
* @param output output file name
* @param quiet status of quiet-mode
*
* @return 0 - exit without errors
*/
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 */ #endif /* ADD_MAIN_H */

132
mathmech/radf/src/main.c
View File

@ -13,6 +13,7 @@
#include <mathmech/messages.h> #include <mathmech/messages.h>
#include <mathmech/radf.h> #include <mathmech/radf.h>
#include <mathmech/radf_proc.h> #include <mathmech/radf_proc.h>
#include <mathmech/var_types.h>
/** /**
@ -32,42 +33,30 @@ int main(int argc, char *argv[])
FILE *f_inp, *f_log; FILE *f_inp, *f_log;
char input[256], logfile[256], output[256]; char input[256], logfile[256], output[256];
float ang_max, ang_min, ang_step, cell[3], *coords, r_max, r_min, r_step; int log, matrix, mode, num_needed_at, needed_at[6], quiet, *radf, *true_label_mol;
int from, *label_mol, log, matrix, mode, num_atoms, num_mol, num_needed_at, atom_info *_atom_info;
needed_at[6], quiet, *radf, step, to, *true_label_mol, *type_atoms; radf_info _radf_info;
system_info _system_info;
/* input input file name /* input input file name
* logfile log file name * logfile log file name
* output output 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 * log status of log-mode
* matrix status of matrix-mode * matrix status of matrix-mode
* mode 0 - if RDF, 1 - if RDF for center mass, 2 - if RADF * 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 * num_needed_at number of needed atom types
* needed_at massive of number of needed atom types * needed_at massive of number of needed atom types
* quiet status of quiet-mode * quiet status of quiet-mode
* radf not normed RADF * radf not normed RADF
* step $(to - from + 1)
* to last trajectory step
* true_label_mol massive of true numbers of molecule for atoms * true_label_mol massive of true numbers of molecule for atoms
* type_atoms massive of atom types *
* _atom_info atom information structure
* _radf_info radf information structure
* _system_info system information structure
*/ */
set_defaults (&ang_max, &ang_min, &ang_step, cell, &from, input, &log, &matrix, set_defaults (&_system_info, &_radf_info, input, &log, &matrix, output, &quiet);
&r_max, &r_min, &r_step, output, &to, &quiet);
for (i=1; i<argc; i++) for (i=1; i<argc; i++)
{ {
@ -110,20 +99,19 @@ int main(int argc, char *argv[])
else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
// steps // steps
{ {
sscanf (argv[i+1], "%i,%i", &from, &to); sscanf (argv[i+1], "%i,%i", &_system_info.from, &_system_info.to);
if (from > to) if (_system_info.from > _system_info.to)
{ {
to += from; _system_info.to += _system_info.from;
from = to - from; _system_info.from = _system_info.to - _system_info.from;
to -= from; _system_info.to -= _system_info.from;
} }
step = to - from + 1;
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
// cell size // cell size
{ {
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]); sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 't') && (argv[i][3] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 't') && (argv[i][3] == '\0'))
@ -149,37 +137,37 @@ int main(int argc, char *argv[])
else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == '\0'))
// radii // radii
{ {
sscanf (argv[i+1], "%f,%f", &r_min, &r_max); sscanf (argv[i+1], "%f,%f", &_radf_info.r_min, &_radf_info.r_max);
if (r_min > r_max) if (_radf_info.r_min > _radf_info.r_max)
{ {
r_min += r_max; _radf_info.r_min += _radf_info.r_max;
r_max = r_min - r_max; _radf_info.r_max = _radf_info.r_min - _radf_info.r_max;
r_min -= r_max; _radf_info.r_min -= _radf_info.r_max;
} }
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == 's') && (argv[i][3] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == 's') && (argv[i][3] == '\0'))
// radius step // radius step
{ {
sscanf (argv[i+1], "%f", &r_step); sscanf (argv[i+1], "%f", &_radf_info.r_step);
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
// angles // angles
{ {
sscanf (argv[i+1], "%f,%f", &ang_min, &ang_max); sscanf (argv[i+1], "%f,%f", &_radf_info.ang_min, &_radf_info.ang_max);
if (ang_min > ang_max) if (_radf_info.ang_min > _radf_info.ang_max)
{ {
ang_min += ang_max; _radf_info.ang_min += _radf_info.ang_max;
ang_max = ang_min - ang_max; _radf_info.ang_max = _radf_info.ang_min - _radf_info.ang_max;
ang_min -= ang_max; _radf_info.ang_min -= _radf_info.ang_max;
} }
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 's') && (argv[i][3] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 's') && (argv[i][3] == '\0'))
// angle step // angle step
{ {
sscanf (argv[i+1], "%f", &ang_step); sscanf (argv[i+1], "%f", &_radf_info.ang_step);
i++; i++;
} }
else if ((argv[i][0] == '-') && (argv[i][1] == 'm') && (argv[i][2] == '\0')) else if ((argv[i][0] == '-') && (argv[i][1] == 'm') && (argv[i][2] == '\0'))
@ -213,7 +201,7 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 1, argv[0]); print_message (quiet, stdout, log, f_log, 1, argv[0]);
// error check // error check
error = error_checking (cell, from, input, num_needed_at, needed_at, output, to); error = error_checking (input, num_needed_at, needed_at, output, _system_info);
if (error != 0) if (error != 0)
{ {
print_message (quiet, stderr, log, f_log, 17, argv[0]); print_message (quiet, stderr, log, f_log, 17, argv[0]);
@ -225,14 +213,14 @@ int main(int argc, char *argv[])
// processing // processing
// initial variables // initial variables
// set mode // set mode
if ((num_needed_at == 6) && (ang_step != 0.0)) if ((num_needed_at == 6) && (_radf_info.ang_step != 0.0))
mode = 2; mode = 2;
else if (num_needed_at == 6) else if (num_needed_at == 6)
mode = 1; mode = 1;
else if (num_needed_at == 2) else if (num_needed_at == 2)
mode = 0; mode = 0;
sprintf (filename, "%s.%03i", input, from); sprintf (filename, "%s.%03i", input, _system_info.from);
print_message (quiet, stdout, log, f_log, 3, filename); print_message (quiet, stdout, log, f_log, 3, filename);
f_inp = fopen (filename, "r"); f_inp = fopen (filename, "r");
if (f_inp == NULL) if (f_inp == NULL)
@ -240,29 +228,25 @@ int main(int argc, char *argv[])
print_message (quiet, stderr, log, f_log, 18, filename); print_message (quiet, stderr, log, f_log, 18, filename);
return 2; return 2;
} }
fscanf (f_inp, "%i", &num_atoms); fscanf (f_inp, "%i", &_system_info.num_atoms);
fclose (f_inp); fclose (f_inp);
coords = (float *) malloc (2 * 3 * 8 * num_atoms * sizeof (float)); _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
label_mol = (int *) malloc (2 * 8 * num_atoms * sizeof (int));
if (mode == 2) if (mode == 2)
{ {
i = (r_max - r_min) / r_step; i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
j = (ang_max - ang_min) / ang_step; j = (_radf_info.ang_max - _radf_info.ang_min) / _radf_info.ang_step;
i *= j; i *= j;
} }
else else
i = (r_max - r_min) / r_step; i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
radf = (int *) malloc (i * sizeof (int)); radf = (int *) malloc (i * sizeof (int));
for (j=0; j<i; j++) for (j=0; j<i; j++)
radf[j] = 0; radf[j] = 0;
true_label_mol = (int *) malloc (num_atoms * sizeof (int)); true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
type_atoms = (int *) malloc (2 * 8 * num_atoms * sizeof (int));
// error checking // error checking
if ((coords == NULL) || if ((_atom_info == NULL) ||
(label_mol == NULL) ||
(radf == NULL) || (radf == NULL) ||
(true_label_mol == NULL) || (true_label_mol == NULL))
(type_atoms == NULL))
{ {
print_message (quiet, stderr, log, f_log, 19, argv[0]); print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 3; return 3;
@ -270,7 +254,9 @@ int main(int argc, char *argv[])
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cMatrix mode: %i;\n\ 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\ %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, %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); ' ', input, ' ', _system_info.from, ' ', _system_info.to, ' ', _system_info.cell[0],
_system_info.cell[1], _system_info.cell[2], ' ', mode, ' ', _radf_info.r_min,
_radf_info.r_max, _radf_info.r_step);
switch (mode) switch (mode)
{ {
case 0: case 0:
@ -282,44 +268,41 @@ needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
break; break;
case 2: case 2:
sprintf (tmp_str, "%s%6cANG_MIN: %6.2f; ANG_MAX: %6.2f; ANG_STEP: %6.2f;\n\ 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], %6cATOM TYPES: %i,%i,%i-%i,%i,%i\n", tmp_str, ' ', _radf_info.ang_min, _radf_info.ang_max,
needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]); _radf_info.ang_step, ' ', needed_at[0], needed_at[1], needed_at[2], needed_at[3],
needed_at[4], needed_at[5]);
break; break;
} }
print_message (quiet, stdout, log, f_log, 5, tmp_str); print_message (quiet, stdout, log, f_log, 5, tmp_str);
// head // head
printing_head (output, log, quiet, matrix, input, from, to, cell, mode, r_min, printing_head (output, log, quiet, matrix, input, _system_info, mode, _radf_info,
r_max, r_step, ang_min, ang_max, ang_step, needed_at); needed_at);
print_message (quiet, stdout, log, f_log, 6, argv[0]); print_message (quiet, stdout, log, f_log, 6, argv[0]);
// main cycle // main cycle
for (i=from; i<to+1; i++) for (i=_system_info.from; i<_system_info.to+1; i++)
{ {
sprintf (filename, "%s.%03i", input, i); sprintf (filename, "%s.%03i", input, i);
print_message (quiet, stdout, log, f_log, 7, filename); print_message (quiet, stdout, log, f_log, 7, filename);
error = reading_coords (0, filename, num_needed_at, needed_at, cell, &num_mol, error = reading_coords (0, filename, num_needed_at, needed_at, &_system_info,
&num_atoms, true_label_mol, label_mol, type_atoms, true_label_mol, _atom_info);
coords, tmp_str);
if (error == 0) if (error == 0)
{ {
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n", sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
' ', num_mol, ' ', num_atoms); ' ', _system_info.num_mol, ' ', _system_info.num_atoms);
print_message (quiet, stdout, log, f_log, 8, tmp_str); print_message (quiet, stdout, log, f_log, 8, tmp_str);
error = 1; error = 1;
switch (mode) switch (mode)
{ {
case 0: case 0:
error = search_rdf (num_atoms, type_atoms, label_mol, coords, r_min, error = search_rdf (_system_info, _atom_info, _radf_info, radf);
r_max, r_step, radf);
break; break;
case 1: case 1:
error = search_rdf_centr (num_atoms, type_atoms, label_mol, coords, r_min, error = search_rdf_centr (_system_info, _atom_info, _radf_info, radf);
r_max, r_step, radf);
if (error == 0) if (error == 0)
case 2: case 2:
error = search_radf (num_atoms, type_atoms, label_mol, coords, r_min, r_max, error = search_radf (_system_info, _atom_info, _radf_info, radf);
r_step, ang_min, ang_max, ang_step, radf);
break; break;
} }
} }
@ -330,15 +313,12 @@ needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
print_message (quiet, stdout, log, f_log, 13, argv[0]); print_message (quiet, stdout, log, f_log, 13, argv[0]);
print_message (quiet, stdout, log, f_log, 14, output); print_message (quiet, stdout, log, f_log, 14, output);
// tail // tail
print_result (output, matrix, mode, step, num_atoms, r_min, r_max, r_step, ang_min, print_result (output, matrix, mode, _system_info, _radf_info, radf);
ang_max, ang_step, cell, radf);
print_message (quiet, stdout, log, f_log, 15, argv[0]); print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory // free memory
free (coords); free (_atom_info);
free (label_mol);
free (radf); free (radf);
free (type_atoms);
free (true_label_mol); free (true_label_mol);
print_message (quiet, stdout, log, f_log, 16, argv[0]); print_message (quiet, stdout, log, f_log, 16, argv[0]);