mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-06-28 14:51:41 +00:00
fixed envir and radf
This commit is contained in:
arcan1s
@ -4,6 +4,7 @@
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#include <stdio.h>
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#include "add_main.h"
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#include <mathmech/messages.h>
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#include <mathmech/var_types.h>
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@ -4,30 +4,18 @@
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#include <stdio.h>
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#include "add_main.h"
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#include <mathmech/messages.h>
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#include <mathmech/var_types.h>
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/**
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* @fn error_checking
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*/
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int error_checking (const float *cell, const char *input, const char *output)
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/**
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* @brief function that checks errors in input variables
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* @code
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* error_checking (cell, input, output);
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* @endcode
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*
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* @param cell massive of cell size
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* @param input input file name
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* @param output output file name
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*
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* @return 11 - error in 'cell'
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* @return 12 - error in 'input'
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* @return 13 - error in 'output'
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* @return 0 - exit without errors
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*/
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int error_checking (const system_info _system_info, const char *input,
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const char *output)
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{
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if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
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if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
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return 11;
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if (input[0] == '#')
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return 12;
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@ -43,21 +31,6 @@ int error_checking (const float *cell, const char *input, const char *output)
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*/
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int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
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const int mode, const char *str)
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/**
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* @brief function that prints message in log and stdout
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* @code
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* print_message (quiet, stdout, log, f_log, 0, str);
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* @endcode
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*
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* @param quiet status of quiet-mode
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* @param std_output stdout
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* @param log status of log-mode
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* @param f_log log file
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* @param mode number of message in "messages.c"
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* @param str additional text in message
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*
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* @return 0 - exit without errors
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*/
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{
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if ((quiet != 1) && (std_output != stderr))
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message (0, mode, str, std_output);
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@ -71,30 +44,13 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
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/**
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* @fn set_defaults
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*/
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int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output,
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int *quiet, float *rad)
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/**
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* @brief function that sets default values of variables
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* @code
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* set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
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* &type_inter, &quiet);
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* @endcode
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*
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* @param cell massive of cell size
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* @param input mask of trajectory files
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* @param log status of log-mode
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* @param num_of_mol number of molecule
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* @param output output file name
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* @param quiet status of quiet-mode
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* @param rad radius of environment sphere
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*
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* @return 0 - exit without errors
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*/
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int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol,
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char *output, int *quiet, float *rad)
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{
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int i;
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for (i=0; i<3; i++)
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cell[i] = 0.0;
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(*_system_info).cell[i] = 0.0;
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input[0] = '#';
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*log = 0;
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*num_of_mol = 1;
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@ -5,18 +5,75 @@
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#ifndef ADD_MAIN_H
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#define ADD_MAIN_H
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#include <mathmech/var_types.h>
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/**
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* @fn error_checking
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*/
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int error_checking (const system_info _system_info, const char *input,
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const char *output);
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/**
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* @brief function that checks errors in input variables
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* @code
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* error_checking (_system_info, input, output);
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* @endcode
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*
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* @param _system_info system information structure
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* @param input input file name
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* @param output output file name
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*
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* @return 11 - error in 'cell'
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* @return 12 - error in 'input'
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* @return 13 - error in 'output'
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* @return 0 - exit without errors
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*/
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/**
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* @fn print_message
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*/
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int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
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const int mode, const char *str);
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/**
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* @brief function that prints message in log and stdout
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* @code
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* print_message (quiet, stdout, log, f_log, 0, str);
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* @endcode
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*
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* @param quiet status of quiet-mode
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* @param std_output stdout
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* @param log status of log-mode
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* @param f_log log file
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* @param mode number of message in "messages.c"
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* @param str additional text in message
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*
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* @return 0 - exit without errors
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*/
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/**
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* @fn set_defaults
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*/
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int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol,
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char *output, int *quiet, float *rad);
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/**
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* @brief function that sets default values of variables
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* @code
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* set_defaults (&_system_info, &from, input, &log, &max_depth, &num_of_inter, output, &to,
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* &type_inter, &quiet);
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* @endcode
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*
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* @param _system_info system information structure
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* @param input mask of trajectory files
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* @param log status of log-mode
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* @param num_of_mol number of molecule
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* @param output output file name
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* @param quiet status of quiet-mode
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* @param rad radius of environment sphere
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*
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* @return 0 - exit without errors
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*/
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int error_checking (const float *, const char *, const char *);
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int print_message (const int, FILE *, const int, FILE *, const int, const char *);
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int set_defaults (float *, char *, int *, int *, char *, int *, float *);
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#endif /* ADD_MAIN_H */
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@ -14,6 +14,7 @@
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#include <mathmech/messages.h>
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#include <mathmech/print_struct.h>
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#include <mathmech/set_center.h>
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#include <mathmech/var_types.h>
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/**
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@ -32,33 +33,31 @@ int main(int argc, char *argv[])
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int error, i, *tmp_int;
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FILE *f_inp, *f_log;
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char *ch_type_atoms, input[256], logfile[256], output[256];
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float cell[3], *centr_coords, *coords, rad;
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int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol,
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*needed_mol, quiet, *true_label_mol;
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char input[256], logfile[256], output[256];
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float *centr_coords, rad;
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int log, num_needed_mol, num_of_mol, *needed_mol, quiet, *true_label_mol;
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atom_info *_atom_info;
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system_info _system_info;
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/* ch_type_atoms massive of char atom types
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* input input file name
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/* input input file name
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* logfile log file name
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* output output file name
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*
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* cell massive of cell size
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* centr_coords massive of centered coordinates
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* coords massive of coordinates
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* rad radius of environment sphere
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*
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* label_mol massive of numbers of molecule for atoms
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* log status of log-mode
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* num_atoms number of atoms
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* num_mol number of molecules
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* num_needed_mol number of needed molecules
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* num_of_mol number of molecule
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* needed_mol massive of number of needed molecules
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* quiet status of quiet-mode
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* true_label_mol massive of true numbers of molecule for atoms
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*
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* _atom_info atom information file
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* _system_info system information file
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*/
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set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
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set_defaults (&_system_info, input, &log, &num_of_mol, output, &quiet, &rad);
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for (i=1; i<argc; i++)
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{
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@ -93,7 +92,7 @@ int main(int argc, char *argv[])
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else if ((argv[i][0] == '-') && (argv[i][1] == 'c') && (argv[i][2] == '\0'))
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// cell size
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{
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sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
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sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1], &_system_info.cell[2]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
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@ -140,7 +139,7 @@ int main(int argc, char *argv[])
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print_message (quiet, stdout, log, f_log, 1, argv[0]);
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// error check
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error = error_checking (cell, input, output);
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error = error_checking (_system_info, input, output);
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if (error != 0)
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{
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print_message (quiet, stderr, log, f_log, 17, argv[0]);
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@ -158,17 +157,13 @@ int main(int argc, char *argv[])
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print_message (quiet, stderr, log, f_log, 18, input);
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return 2;
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}
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fscanf (f_inp, "%i", &num_atoms);
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fscanf (f_inp, "%i", &_system_info.num_atoms);
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fclose (f_inp);
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ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
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coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
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label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
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tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
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true_label_mol = (int *) malloc (num_atoms * sizeof (int));
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_atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
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tmp_int = (int *) malloc (8 * _system_info.num_atoms * sizeof (int));
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true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
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// error checking
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if ((ch_type_atoms == NULL) ||
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(coords == NULL) ||
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(label_mol == NULL) ||
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if ((_atom_info == NULL) ||
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(tmp_int == NULL) ||
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(true_label_mol == NULL))
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{
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@ -177,8 +172,9 @@ int main(int argc, char *argv[])
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}
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sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
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%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
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%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0],
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cell[1], cell[2], ' ' , num_of_mol, ' ', rad);
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%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ',
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_system_info.cell[0], _system_info.cell[1], _system_info.cell[2], ' ' , num_of_mol,
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' ', rad);
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print_message (quiet, stdout, log, f_log, 5, tmp_str);
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print_message (quiet, stdout, log, f_log, 6, argv[0]);
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@ -186,14 +182,14 @@ int main(int argc, char *argv[])
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// reading coordinates
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print_message (quiet, stdout, log, f_log, 7, input);
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error = 1;
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error = reading_coords (1, input, tmp_int[0], tmp_int, cell, &num_mol, &num_atoms,
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true_label_mol, label_mol, tmp_int, coords, ch_type_atoms);
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centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
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needed_mol = (int *) malloc (num_mol * sizeof (int));
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error = reading_coords (0, input, tmp_int[0], tmp_int, &_system_info, true_label_mol,
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_atom_info);
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centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
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needed_mol = (int *) malloc (_system_info.num_mol * sizeof (int));
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if (error == 0)
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{
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sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
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' ', num_mol, ' ', num_atoms);
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' ', _system_info.num_mol, ' ', _system_info.num_atoms);
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print_message (quiet, stdout, log, f_log, 8, tmp_str);
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}
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// error checking
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@ -208,21 +204,21 @@ int main(int argc, char *argv[])
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if (error == 0)
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{
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error = 1;
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error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
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error = set_center (_system_info, _atom_info, centr_coords);
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}
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if (error == 0)
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{
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print_message (quiet, stderr, log, f_log, 20, argv[0]);
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error = 1;
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error = search_envir (num_of_mol, num_mol, centr_coords, rad, needed_mol,
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error = search_envir (num_of_mol, _system_info, centr_coords, rad, needed_mol,
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&num_needed_mol);
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}
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if (error == 0)
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{
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print_message (quiet, stderr, log, f_log, 21, argv[0]);
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error = 1;
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error = print_structure (output, num_needed_mol, needed_mol, num_atoms,
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label_mol, ch_type_atoms, coords);
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error = print_structure (output, num_needed_mol, needed_mol, _system_info,
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_atom_info);
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}
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if (error == 0)
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print_message (quiet, stderr, log, f_log, 12, output);
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@ -231,10 +227,8 @@ int main(int argc, char *argv[])
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print_message (quiet, stdout, log, f_log, 15, argv[0]);
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// free memory
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free (ch_type_atoms);
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free (_atom_info);
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free (centr_coords);
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free (coords);
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free (label_mol);
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free (needed_mol);
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free (tmp_int);
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free (true_label_mol);
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@ -53,16 +53,16 @@ typedef struct
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*/
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typedef struct
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{
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int first;
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int last;
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int from;
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int to;
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float cell[3];
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int num_atoms;
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int num_mol;
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} system_info;
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/**
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* @brief system information structure
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* @var first last trajectory step
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* @var last first trajectory step
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* @var from last trajectory step
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* @var to first trajectory step
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* @var cell cell size
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* @var num_atoms number of atoms
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* @var num_mol number of molecules
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@ -49,7 +49,7 @@ int print_result (const char *output, const int matrix, const int mode,
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r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step;
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dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step;
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ro = _system_info.num_atoms / (2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
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norm = radf[i] / (dv * ro * _system_info.num_atoms * (_system_info.last - _system_info.first + 1));
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norm = radf[i] / (dv * ro * _system_info.num_atoms * (_system_info.to - _system_info.from + 1));
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if (matrix == 0)
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fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
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else
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@ -66,7 +66,7 @@ int print_result (const char *output, const int matrix, const int mode,
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r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step;
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dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step;
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ro = _system_info.num_atoms / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
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norm = radf[i] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.last - _system_info.first + 1));
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norm = radf[i] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.to - _system_info.from + 1));
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if (matrix == 0)
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fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
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else
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@ -96,7 +96,7 @@ int print_result (const char *output, const int matrix, const int mode,
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ang = _radf_info.ang_min + (0.5 + j) * _radf_info.ang_step;
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dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * _radf_info.r_step * (M_PI * _radf_info.ang_step / 180);
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ro = _system_info.num_atoms / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
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norm = radf[n*i+j] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.last - _system_info.first + 1));
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norm = radf[n*i+j] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.to - _system_info.from + 1));
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if (matrix == 0)
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fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[n*i+j] / 2, norm);
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else
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@ -4,46 +4,25 @@
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|
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#include <stdio.h>
|
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|
||||
#include "add_main.h"
|
||||
#include <version.h>
|
||||
#include <mathmech/messages.h>
|
||||
#include <mathmech/var_types.h>
|
||||
|
||||
|
||||
/**
|
||||
* @fn error_checking
|
||||
*/
|
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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;
|
||||
|
||||
@ -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 */
|
||||
@ -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]);
|
||||
|
||||
Reference in New Issue
Block a user