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start moving to another architecture
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21
mathmech/agl/src/CMakeLists.txt
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21
mathmech/agl/src/CMakeLists.txt
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@ -0,0 +1,21 @@
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# set files
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file (GLOB SOURCES *.c)
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file (GLOB HEADERS *.h)
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# set library
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if (CMAKE_COMPILER_IS_GNUCXX)
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set (ADDITIONAL_LIB m)
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else ()
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set (ADDITIONAL_LIB)
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endif ()
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# message
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message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
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message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
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# link libraries and compile
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add_executable (${MM_PREFIX}${PROJECT} ${SOURCES} ${HEADERS})
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target_link_libraries (${MM_PREFIX}${PROJECT} ${ADDITIONAL_LIB} ${LIBRARIES})
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# install properties
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install (TARGETS ${MM_PREFIX}${PROJECT} DESTINATION bin)
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107
mathmech/agl/src/add_main.c
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107
mathmech/agl/src/add_main.c
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/**
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* @file
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*/
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#include <stdio.h>
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#include <mathmech/messages.h>
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/**
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* @fn error_checking
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*/
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int error_checking (const char *aglinp, const float *cell, 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 (aglinp, cell, input, output);
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* @endcode
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*
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* @param aglinp agglomerate file name
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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 14 - error in 'aglinp'
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* @return 0 - exit without errors
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*/
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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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return 11;
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if (input[0] == '#')
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return 12;
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if (output[0] == '#')
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return 13;
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if (aglinp[0] == '#')
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return 14;
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return 0;
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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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if ((quiet != 1) && (std_output != stderr))
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message (0, mode, str, std_output);
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if (log == 1)
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message (1, mode, str, f_log);
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return 0;
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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 (char *aglinp, float *cell, char *input, int *log, char *output, int *quiet)
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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 (aglinp, cell, input, &log, output, &quiet);
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* @endcode
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*
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* @param aglinp agglomerate file name
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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 output output file name
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* @param quiet status of quiet-mode
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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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int i;
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aglinp[0] = '#';
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for (i=0; i<3; i++)
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cell[i] = 0.0;
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input[0] = '#';
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*log = 0;
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output[0] = '#';
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*quiet = 0;
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return 0;
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}
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22
mathmech/agl/src/add_main.h
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22
mathmech/agl/src/add_main.h
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/**
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* @file
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*/
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#ifndef ADD_MAIN_H
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#define ADD_MAIN_H
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/**
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* @fn error_checking
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*/
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/**
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* @fn print_message
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*/
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/**
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* @fn set_defaults
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*/
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int error_checking (const char *, 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 (char *, float *, char *, int *, char *, int *);
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#endif /* ADD_MAIN_H */
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242
mathmech/agl/src/main.c
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242
mathmech/agl/src/main.c
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/**
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* @file
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*/
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "add_main.h"
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#include <mathmech/coords.h>
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#include <mathmech/messages.h>
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#include <mathmech/print_struct.h>
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#include <mathmech/read_agl.h>
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#include <mathmech/select_mol.h>
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#include <mathmech/set_center.h>
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/**
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* @fn main
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*/
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int main(int argc, char *argv[])
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/**
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* @return 1 - error in error_checking
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* @return 2 - input file does not exist
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* @return 3 - memory error
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* @return 4 - unknown flag
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* @return 0 - exit without errors
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*/
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{
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char tmp_str[2048];
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int error, i, *tmp_int;
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FILE *f_inp, *f_log;
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char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
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float cell[3], *centr_coords, *coords;
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int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
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*true_label_mol;
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/* aglinp agglomerate file name
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* ch_type_atoms massive of char atom types
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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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*
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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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* 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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set_defaults (aglinp, cell, input, &log, output, &quiet);
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for (i=1; i<argc; i++)
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{
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if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
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{
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sprintf (tmp_str, " mm_agl\n");
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sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str);
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sprintf (tmp_str, "%sVersion : 1.1.1 License : GPL\n", tmp_str);
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sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
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sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
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sprintf (tmp_str, "%sUsage:\n", tmp_str);
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sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
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sprintf (tmp_str, "%sParametrs:\n", tmp_str);
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sprintf (tmp_str, "%s -a - input file with agglomerates (in format statgen)\n", tmp_str);
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sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
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sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
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sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
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sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
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sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
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sprintf (tmp_str, "%s -h - show this help and exit\n", tmp_str);
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fputs (tmp_str, stdout);
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return 0;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
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// input file
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{
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strcpy (aglinp, argv[i+1]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'i') && (argv[i][2] == '\0'))
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// input file
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{
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strcpy (input, argv[i+1]);
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i++;
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}
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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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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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// output file
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{
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strcpy (output, argv[i+1]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
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// log mode
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{
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log = 1;
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strcpy (logfile, argv[i+1]);
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
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// quiet mode
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{
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quiet = 1;
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}
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else
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// unknown flag
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{
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return 4;
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}
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}
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if (log == 1)
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f_log = fopen (logfile, "w");
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print_message (quiet, stdout, log, f_log, 0, argv[0]);
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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 (aglinp, cell, 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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return 1;
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}
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print_message (quiet, stdout, log, f_log, 2, argv[0]);
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// processing
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// initial variables
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print_message (quiet, stdout, log, f_log, 3, input);
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f_inp = fopen (input, "r");
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if (f_inp == NULL)
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{
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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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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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needed_mol = (int *) malloc (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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// 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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(needed_mol == NULL) ||
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(tmp_int == NULL) ||
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(true_label_mol == NULL))
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{
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print_message (quiet, stderr, log, f_log, 19, argv[0]);
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return 3;
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}
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sprintf (tmp_str, "%6cAglomerate file: '%s';\n%6cInput file: '%s';\n\
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%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f\n",
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' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], cell[1], cell[2]);
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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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// reading agglomerate
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print_message (quiet, stdout, log, f_log, 7, aglinp);
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error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
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if (error == 0)
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{
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sprintf (tmp_str, "%6cNumber of molecules in agglomerate: %i\n", ' ', num_needed_mol);
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print_message (quiet, stdout, log, f_log, 8, tmp_str);
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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 (2, input, num_needed_mol, needed_mol, cell, &num_mol,
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&num_atoms, true_label_mol, label_mol, tmp_int, coords,
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ch_type_atoms);
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centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
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if (centr_coords == NULL)
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{
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print_message (quiet, stderr, log, f_log, 19, argv[0]);
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return 3;
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}
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}
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// analyze
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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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print_message (quiet, stdout, log, f_log, 8, tmp_str);
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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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}
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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 = select_molecule (centr_coords, num_needed_mol, 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, 4, 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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}
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if (error == 0)
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print_message (quiet, stderr, log, f_log, 12, output);
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print_message (quiet, stderr, log, f_log, 13, argv[0]);
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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 (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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print_message (quiet, stdout, log, f_log, 16, argv[0]);
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|
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if (log == 1)
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fclose (f_log);
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||||
return 0;
|
||||
}
|
||||
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