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

@ -4,46 +4,25 @@
#include <stdio.h>
#include "add_main.h"
#include <version.h>
#include <mathmech/messages.h>
#include <mathmech/var_types.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
*/
int error_checking (const char *input, const int num_needed_at, const int *needed_at,
const char *output, const system_info _system_info)
{
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;
if (input[0] == '#')
return 12;
if (output[0] == '#')
return 13;
if ((from == -1) || (to == -1))
if ((_system_info.from == -1) || (_system_info.to == -1))
return 14;
if ((num_needed_at != 2) && (num_needed_at != 6))
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,
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);
@ -94,36 +58,8 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
* @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
*/
const char *input, const system_info _system_info, const int mode,
const radf_info _radf_info, const int *needed_at)
{
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, "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, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, _system_info.from,
_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, "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)
{
case 0:
@ -143,12 +82,12 @@ int printing_head (const char *output, const int log, const int quiet, const int
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]);
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]);
ATOM=%i,%i,%i-%i,%i,%i\n", _radf_info.ang_min, _radf_info.ang_max, _radf_info.ang_step,
needed_at[0], needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
break;
}
@ -162,50 +101,25 @@ needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
/**
* @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 set_defaults (system_info *_system_info, radf_info *_radf_info, char *input,
int *log, int *matrix, char *output, int *quiet)
{
int i;
*ang_max = 90.0;
*ang_min = 0.0;
*ang_step = 0.0;
(*_radf_info).ang_max = 90.0;
(*_radf_info).ang_min = 0.0;
(*_radf_info).ang_step = 0.0;
for (i=0; i<3; i++)
cell[i] = 0.0;
*from = -1;
(*_system_info).cell[i] = 0.0;
(*_system_info).from = -1;
input[0] = '#';
*log = 0;
*matrix = 0;
*r_max = 15.0;
*r_min = 2.0;
*r_step = 0.2;
(*_radf_info).r_max = 15.0;
(*_radf_info).r_min = 2.0;
(*_radf_info).r_step = 0.2;
output[0] = '#';
*to = -1;
(*_system_info).to = -1;
*quiet = 0;
return 0;

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

@ -5,27 +5,105 @@
#ifndef ADD_MAIN_H
#define ADD_MAIN_H
#include <mathmech/var_types.h>
/**
* @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
*/
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
*/
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
*/
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/radf.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;
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;
int log, matrix, mode, num_needed_at, needed_at[6], quiet, *radf, *true_label_mol;
atom_info *_atom_info;
radf_info _radf_info;
system_info _system_info;
/* 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
*
* _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,
&r_max, &r_min, &r_step, output, &to, &quiet);
set_defaults (&_system_info, &_radf_info, input, &log, &matrix, output, &quiet);
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'))
// steps
{
sscanf (argv[i+1], "%i,%i", &from, &to);
if (from > to)
sscanf (argv[i+1], "%i,%i", &_system_info.from, &_system_info.to);
if (_system_info.from > _system_info.to)
{
to += from;
from = to - from;
to -= from;
_system_info.to += _system_info.from;
_system_info.from = _system_info.to - _system_info.from;
_system_info.to -= _system_info.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]);
sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
i++;
}
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'))
// radii
{
sscanf (argv[i+1], "%f,%f", &r_min, &r_max);
if (r_min > r_max)
sscanf (argv[i+1], "%f,%f", &_radf_info.r_min, &_radf_info.r_max);
if (_radf_info.r_min > _radf_info.r_max)
{
r_min += r_max;
r_max = r_min - r_max;
r_min -= r_max;
_radf_info.r_min += _radf_info.r_max;
_radf_info.r_max = _radf_info.r_min - _radf_info.r_max;
_radf_info.r_min -= _radf_info.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);
sscanf (argv[i+1], "%f", &_radf_info.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)
sscanf (argv[i+1], "%f,%f", &_radf_info.ang_min, &_radf_info.ang_max);
if (_radf_info.ang_min > _radf_info.ang_max)
{
ang_min += ang_max;
ang_max = ang_min - ang_max;
ang_min -= ang_max;
_radf_info.ang_min += _radf_info.ang_max;
_radf_info.ang_max = _radf_info.ang_min - _radf_info.ang_max;
_radf_info.ang_min -= _radf_info.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);
sscanf (argv[i+1], "%f", &_radf_info.ang_step);
i++;
}
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]);
// 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)
{
print_message (quiet, stderr, log, f_log, 17, argv[0]);
@ -225,14 +213,14 @@ int main(int argc, char *argv[])
// processing
// initial variables
// set mode
if ((num_needed_at == 6) && (ang_step != 0.0))
if ((num_needed_at == 6) && (_radf_info.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);
sprintf (filename, "%s.%03i", input, _system_info.from);
print_message (quiet, stdout, log, f_log, 3, filename);
f_inp = fopen (filename, "r");
if (f_inp == NULL)
@ -240,29 +228,25 @@ int main(int argc, char *argv[])
print_message (quiet, stderr, log, f_log, 18, filename);
return 2;
}
fscanf (f_inp, "%i", &num_atoms);
fscanf (f_inp, "%i", &_system_info.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));
_atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
if (mode == 2)
{
i = (r_max - r_min) / r_step;
j = (ang_max - ang_min) / ang_step;
i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
j = (_radf_info.ang_max - _radf_info.ang_min) / _radf_info.ang_step;
i *= j;
}
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));
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));
true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
// error checking
if ((coords == NULL) ||
(label_mol == NULL) ||
if ((_atom_info == NULL) ||
(radf == NULL) ||
(true_label_mol == NULL) ||
(type_atoms == NULL))
(true_label_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
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\
%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);
' ', 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)
{
case 0:
@ -282,44 +268,41 @@ 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]);
%6cATOM TYPES: %i,%i,%i-%i,%i,%i\n", tmp_str, ' ', _radf_info.ang_min, _radf_info.ang_max,
_radf_info.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);
printing_head (output, log, quiet, matrix, input, _system_info, mode, _radf_info,
needed_at);
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// 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);
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);
error = reading_coords (0, filename, num_needed_at, needed_at, &_system_info,
true_label_mol, _atom_info);
if (error == 0)
{
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);
error = 1;
switch (mode)
{
case 0:
error = search_rdf (num_atoms, type_atoms, label_mol, coords, r_min,
r_max, r_step, radf);
error = search_rdf (_system_info, _atom_info, _radf_info, radf);
break;
case 1:
error = search_rdf_centr (num_atoms, type_atoms, label_mol, coords, r_min,
r_max, r_step, radf);
error = search_rdf_centr (_system_info, _atom_info, _radf_info, 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);
error = search_radf (_system_info, _atom_info, _radf_info, radf);
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, 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_result (output, matrix, mode, _system_info, _radf_info, radf);
print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory
free (coords);
free (label_mol);
free (_atom_info);
free (radf);
free (type_atoms);
free (true_label_mol);
print_message (quiet, stdout, log, f_log, 16, argv[0]);