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start moving to another architecture
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arcan1s
21
mathmech/trj/src/CMakeLists.txt
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21
mathmech/trj/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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113
mathmech/trj/src/add_main.c
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113
mathmech/trj/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 *input, const char *input_at, const char *output,
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const int step, const int type)
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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, from, input, num_needed_at, needed_at, output, to);
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* @endcode
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*
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* @param input input file name
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* @param input_at input file name with atom types
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* @param output output file name
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* @param step number of trajectory steps
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* @param type type of trajectory
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*
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* @return 11 - error in 'input_at'
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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 'step'
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* @return 15 - error in 'type'
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* @return 0 - exit without errors
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*/
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{
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if (input_at[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 (step == 0)
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return 14;
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if (type == -1)
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return 15;
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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 *input, char *input_at, int *log, char *output, int *step,
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int *total_types, int *type, 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 (input, input_at, &log, output, &step, &type, &quiet);
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* @endcode
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*
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* @param input input file name
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* @param input_at input file name with atom types
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* @param log status of log-mode
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* @param output output file name
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* @param step number of trajectory steps
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* @param total_types number of different atom types
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* @param type type of trajectory
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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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input[0] = '#';
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input_at[0] = '#';
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*log = 0;
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output[0] = '#';
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*step = 0;
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*total_types = 1024;
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*type = -1;
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*quiet = 0;
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return 0;
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}
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22
mathmech/trj/src/add_main.h
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22
mathmech/trj/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 char *, const char *, const int, const int);
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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 *, char *, int *, char *, int *, int *, int *, int *);
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#endif /* ADD_MAIN_H */
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243
mathmech/trj/src/main.c
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243
mathmech/trj/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/atom_types.h>
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#include <mathmech/messages.h>
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#include <mathmech/print_trj.h>
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#include <mathmech/read_gmx.h>
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#include <mathmech/read_puma.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;
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FILE *f_inp, *f_log;
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char *ch_atom_types, input[256], input_at[256], logfile[256], output[256];
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float *coords;
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int *atom_types, log, *num_atoms, *num_mol, num_types, quiet, step, total_types, type;
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/* ch_atom_types massive of char atom types
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* input input file name
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* input_at input file name with atom types
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* logfile log file name
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* output mask of output files
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*
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* coords massive of coordinates
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*
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* atom_types massive of atom types
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* log status of log-mode
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* num_atoms massive of number of atoms of selected molecule
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* num_mol massive of number of molecule of selected type
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* num_types number of molecule types
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* quiet status of quiet-mode
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* step number of trajectory steps
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* total_types number of different atom types
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* type type of trajectory
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*/
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set_defaults (input, input_at, &log, output, &step, &total_types, &type, &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_trj\n");
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sprintf (tmp_str, "%sProgram that generates trajectory files\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_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]\n", tmp_str);
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sprintf (tmp_str, "%s [ -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 -i - input file name\n", tmp_str);
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sprintf (tmp_str, "%s -t - type of trajectory. Supported formats: gmx, puma\n", tmp_str);
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sprintf (tmp_str, "%s -s - number of trajectory steps (integer)\n", tmp_str);
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sprintf (tmp_str, "%s -a - input file with atom types. See file format in manual\n", tmp_str);
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sprintf (tmp_str, "%s -o - mask of output files\n", tmp_str);
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sprintf (tmp_str, "%s -tt - number of different atom types. Default is 1024\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] == '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] == 't') && (argv[i][2] == '\0'))
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// type
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{
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if ((argv[i+1][0] == 'g') && (argv[i+1][1] == 'm') && (argv[i+1][2] == 'x') &&
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(argv[i+1][3] == '\0'))
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// gromacs text file
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type = 0;
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else if ((argv[i+1][0] == 'p') && (argv[i+1][1] == 'u') && (argv[i+1][2] == 'm') &&
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(argv[i+1][3] == 'a') && (argv[i+1][4] == '\0'))
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// puma
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type = 1;
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i++;
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}
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else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
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// steps
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{
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sscanf (argv[i+1], "%i", &step);
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i++;
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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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// atom types
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{
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strcpy (input_at, argv[i+1]);
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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] == 't') && (argv[i][2] == 't') && (argv[i][3] == '\0'))
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// number of atom types
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{
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sscanf (argv[i+1], "%i", &total_types);
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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 (input, input_at, output, step, type);
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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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return 2;
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switch (type)
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{
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case 0:
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fgets (tmp_str, 256, f_inp);
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fgets (tmp_str, 256, f_inp);
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sscanf (tmp_str, " natoms=%i%s", &i, tmp_str);
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break;
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case 1:
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fgets (tmp_str, 256, f_inp);
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sscanf (tmp_str, "%s%s%i%s", tmp_str, tmp_str, &i, tmp_str);
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break;
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}
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fclose (f_inp);
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atom_types = (int *) malloc (total_types * sizeof (int));
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ch_atom_types = (char *) malloc (2 * total_types * sizeof (char));
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coords = (float *) malloc (3 * i * sizeof (float));
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num_atoms = (int *) malloc (total_types * sizeof (int));
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num_mol = (int *) malloc (total_types * sizeof (int));
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num_types = 0;
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if ((atom_types == NULL) ||
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(ch_atom_types == NULL) ||
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(coords == NULL) ||
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(num_atoms == NULL) ||
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(num_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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print_message (quiet, stdout, log, f_log, 6, argv[0]);
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// read atom types
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error = 1;
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error = reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types,
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atom_types, total_types);
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if (error == 0)
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{
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sprintf (tmp_str, "%6cLog: %i;\n%6cQuiet: %i;\n%6cInput file: %s;\n%6cTrajectory type: %i;\n\
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%6cNumber of trajectory step: %i;\n%6cInput file with atom types: %s;\n%6cMask of output file: %s;\n\
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%6cNumber of different atom types: %i;\n%6cNumber of different molecules: %i;\n%6cNumber of atoms in system: %i\n",
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' ', log, ' ', quiet, ' ', input, ' ', type, ' ', step, ' ', input_at, ' ', output,
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' ', total_types, ' ', num_types, ' ', i);
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print_message (quiet, stdout, log, f_log, 5, tmp_str);
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}
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else
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return 2;
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print_message (quiet, stdout, log, f_log, 6, argv[0]);
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// main cycle
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switch (type)
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{
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case 0:
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rw_gmx (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
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atom_types, coords);
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break;
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case 1:
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rw_puma (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
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atom_types, coords);
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break;
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}
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print_message (quiet, stdout, 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 (atom_types);
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free (ch_atom_types);
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free (coords);
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free (num_atoms);
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free (num_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);
|
||||
return 0;
|
||||
}
|
||||
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